THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A commercial antibody supplier and knockout mice producer.
The set of ontologies used within the Monarch Initiative. MONARCH members are free to add new imports.
Sarah Cannon Research Institute; Tennessee; USA
A global cancer institute of the Hospital Corporation of America which offers integrated cancer services with access to current therapies.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 10,2024. A commercial antibody supplier and provider of various services., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Neuroshare - Open data specifications and software for neurophysiology
Neuroshare aims to develop a standard for accessing neurophysiological data from any vendor's acquisition device or software. An API is defined, and vendors and communities are encouraged to provide implementations of a library of functions that can read data files collected with that vendor's instrument or software. The neuroshare.org website is a collaborative, vendor-neutral area dedicated to public domain standards and software for neurophysiology.This website is part of an SBIR program funded by the National Institute for Neural Disorders and Stroke and it is currently being administered by Bionic Technologies, LLC. The goals of the SBIR program are to (Phase I) create open library and format standards for neurophysiological experiment data and (Phase II) create a set of free, open-source software tools for low-level handling and processing of neurophysiological data. Upon completion of Phase I and II, neuroshare.org will be maintained by a yet to be determined consortium of government, academic and industry partners. The SBIR was awarded in the fall of 2001 and Phase I officially began in Dec, 2001. The detailed goals of the program are summarized below:Phase I goals :(1) Establish a working group to develop and define the API library of functions.(2) A vendor-neutral web site to facilitate the development of the standards and software and publish the completed products. This site has been dubbed Neuroshare. The home page can be found at neuroshare.sourceforge.net.(3) An open, standardized API library definition for accessing neurophysiology data files. This will allow developers to produce analysis programs that can access a variety of proprietary data formats through libraries supplied by the data format owners. The manner of support will be completely determined by the research groups and vendors that supply the libraries. The Phase I standard was created by a working group consisting of international members from industry and academia. Draft standards were published for public review and comment on the neuroshare web site and revised by the working group.The grant has been awarded as a fast-track program so that Phase II begins immediately upon completion of the Phase I milestones in June 2002. Phase II will produce :(1) A set of neuroshare-compliant API libraries for existing data formats developed in collaboration with individual equipment vendors and research groups.(2) A utility for analyzing compliant API libraries for integrity and specification conformance, as well as for error checking imported data files.(3) A set of template programs in C that are meant to be used as an example on how to create a Neuroshare API compliant library and how to call it from an application,(4) An open, standardized file format for neurophysiological experiment data. This format will provide research groups and vendors with a file format for exchanging and/or publishing neural data. The format will also be powerful enough for use as a native format for researchers or vendors that wish to support it in data acquisition hardware/software.(5) Import filters that interface neuroshare-compliant API libraries to Visual Basic, MATLAB, and LabVIEW, NeuroExplorer, and Stranger analysis environments.(6) A utility program for quick header information viewing and searching to aid the organization and management of data files in the standard and proprietary formats.(7) A data file editing program for reviewing, editing, annotating, and splicing neural data files through the neuroshare API libraries and/or standard file formats. The suite will be developed in C, optimized for speed, and will run within 32-bit Windows operating systems. The availability of source code will enable eventual ports to Unix/Linux if desired(8) An add-on for the editing program that will allow review and real-time playback of multi-modal data accessible through the API and/or standard file format. These modes will include neurophysiological signals such as spikes, local field potentials and EEG, as well as experimental signals such as kinematics, stimulation, audio, video, and imaging data.(9) C and MATLAB framework programs for detection and classification of extracellular spikes in the standard data files based on classical and user-supplied algorithms.(10) A complete MATLAB application for reading data from the standard format and performing reverse correlation analysis. This program will serve as a tutorial and modifiable template for users performing analysis in MATLAB.(11) A set of export filters for creating neurophysiological data files with the neural simulation environments NEURON, NEOSIM, GENESIS, and NSL.(12) A comprehensive documentation, and help file set for all of the developed applications.Phase II will require two years of development work and software products will be made available as they are completed. As stated above, the Phase II software products will be made available as free, open-source tools. We have not decided on a license model yet, but are currently leaning towards the GNU General Public License. Revisions and bug-fixes will be maintained through the neuroshare.org website. The mission of neuroshare.org is very focused, but the specific goal list of Phase II may evolve somewhat as software is released and user feedback is received. We very interested in public suggestions about how to improve this development effort and web site. Please direct your feedback to commentsneuroshare.org or refer to our contacts page for other addresses.BackgroundThis endeavor grew out of a meeting held at the Society for Neuroscience 2000 Annual Conference in New Orleans (agenda posted here) to discuss the development of standard data formats for neuroscience. From this meeting, it was clear that although everyone supported the idea of better data portability, many vendors present wanted a standardized API (Application Program Interface) library rather than a universal data format. Based on this meeting, we submitted an SBIR application (with letters of support from key attendants of the SFN meeting) to fund the development of a standardized API definition, data format, and a suite of open source data handling and review tools.
A young state university located in the southern part of Portugal.
Commercial antibody supplier that provides research materials for projects such as: protein purification, protein analysis, protein estimation assays, DNA purification, plasmid DNA isolation and transformation, protein quantification assays, and coupled assays for methylation. This supplier also provides buffers, reagents, education programs, and training programs.
University at Albany SUNY Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31, 2025. Facility that conducts wide variety of research programs ranging from cell biology to community-based participatory research. Research is conducted through four academic departments including: the Cancer Research Center, the Prevention Research Center, the Public Health Preparedness Center, the Cardiac Quality improvement initiative and the Center for Health Workforce Studies. This facility also hosts research projects and faculty scholarships to aid Master's and Doctoral students in course work, laboratory rotations and internships.
ncdfFlow: A package that provides ncdf based storage for flow cytometry data
Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data.
Annotated index for computational neurobiology, focusing on compartmental modeling and realistic simulations of biological neural systems. Has resources to find modeling software and software for computational morphology, phase plane and spike train analysis, and web based neuroinformatics. Provides links to major laboratories, researchers, conferences, education and funding for theoretical neurobiology.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Microscope that enables bright field and fluorescence imaging options.
Offline spike sorting software. This software tool for viewing and classifying action potential waveforms (spikes) previously collected from single electrodes, stereotrodes and tetrodes accepts file types from many data acquisition companies and software programs.
Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements.
University of Pittsburgh Conte Center for the Neuroscience of Mental Disorders
Conte Center for the Neuroscience of Mental Disorders
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Conte Center for the Neuroscience of Mental Disorders (CCNMD) at the University of Pittsburgh offers a highly interactive scientific environment for the study of the neurobiology of schizophrenia. Integrates the laboratory and clinical research activities of investigators from the University of Pittsburgh Schools of Medicine and Arts and Sciences and the adjacent Carnegie Mellon University.
Software application for viewing and editing sequence trace files.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach.
Tablet - Next Generation Sequence Assembly Visualization
A lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.
An organization that specifically operates in Kansas and the the western half of Missouri, and provides help with connecting the community to organ and tissue procurement, as well as generates general public awareness. This organization is a federally certified non-profit Organ Procurement Organization (OPO) that is meant to help in several facets of transplant and procurement services.
Steve Silberman's personal blog highlighting science, culture, politics and neurodiversity. Steve is an investigative reporter for Wired and other national magazines.
Ludwig Boltzmann Cluster Translationale Onkologie
Ludwig Boltzmann Cluster Translational Oncology
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. The projected cluster includes the LBIs for Applied Cancer Research, Clinical Oncology and Photodynamic Therapy, Gynecology and Gynecologic Oncology, Stem Cell Transplantation and Surgical Oncology. The aim of the projected cluster Translational Oncology is the cooperative investigation of genetic and molecular biological characteristics of the tumor cells involved in minimal residual disease (MRD) in vitro and translation of the experimental and diagnostic results into the clinical practice involving therapeutic modalities with the newest generation of antitumoral drugs. Minimal residual disease is the designation for the occurrence of a low number of tumor cells remaining clinically undetected following curative therapy that give rise to tumor relapses. MRD is a central question in cancer therapy, since a major subpopulation of patients which underwent curative resection and therapy ultimately relapse and would have received more aggressive adjuvant therapy, provided that residual disease had been clearly proven. Otherwise low-risk patients would have not been treated aggressively in an adjuvant setting. MRD can be detected by methods in bone marrow or by extremely sensitive PCR (polymerase-chain-reaction)-based methods in peripheral blood. PCR-based methods allow for the characterization of tumor-specific gene expression in circulating tumor cells and thereby provide additional information in regard to malignity of cells and prognosis. The different participating institutions have extensive experience in patient care, organization of clinical studies and laboratory investigation. In particular, expert knowledge in stem cell transplantation and histological detection of MRD, multicentric clinical testing of new anticancer drugs, specialized treatment of various selected tumor entities such as neuroendocrine tumors, gene expression analysis of circulating tumor cells and tumor signatures, and in vitro characterization of chemosensitivity as well as tumor cell biology have been acquired at the individual LBIs in the past and are complementary to each other to be combined in a larger cluster structure. The detection of circulating tumor cells will be supported by ongoing EU (OVCAD OVarian CAncer Diagnosis) and GenAU projects aiming at identification of ovarian cancer cells in the blood. The assessment of methylated DNA sequences (suppressor genes) in peripheral blood as an indicator of MRD can be performed with the help of OncoLab Diagnostics GmbH. Cooperative action in this cluster, using a common tumor bank/clinical data collection and the combined clinical and experimental efforts are the base for the execution of the presented MRD project.
Montreal Neurological Institute Podcasts
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Collection of podcasts which features experts of the Montreal Neurological Institute and Hospital talking about their research, along with important issues and current events regarding it.
PAMGO - Plant-Associated Microbe Gene Ontology
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 10, 2016. A consortium that created universal descriptors to describe functionally similar gene products and their attributes across all organisms. In 2004, the PAMGO interest group joined the GO consortium to extend the GO to include terms describing various processes related to microbe-host interactions. The organization uses a controlled vocabulary to set a process in place to describe plant associated microbes and their interactions with their plant-hosts. These higher order terms can describe gene products of all types of symbionts (e.g. parasites, commensals, and mutualists), including prokaryotes and eukaryotes that associate with plant or animal hosts. This initiative is a multi-institutional collaborative effort to pool information and research in: the bacteria Dickeya dadantii, Pseudomonas syringae pv tomato and Agrobacterium tumefaciens, the fungus Magnaporthe grisea, the oomycetes Phytophthora sojae and Phytophthora ramorum, and the nematode Meloidogyne hapla.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.
Cleveland Clinic Lerner Research Institute Labs and Facilities
Cleveland Clinic Lerner Research Institute Labs & Facilities
Cleveland Clinic LRI Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023.Offers services in peptide synthesis, peptide modification, purification and quality analysis, N-terminal protein sequencing by Edman degradation, biomolecular interaction analysis and equilibrium and kinetic measurements.
GenomicRanges - Representation and manipulation of genomic intervals
Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.
The Epilepsy Foundation of America is the national voluntary agency dedicated solely to the welfare of the almost 3 million people with epilepsy in the U.S. and their families. The organization works to ensure that people with seizures are able to participate in all life experiences; to improve how people with epilepsy are perceived, accepted and valued in society; and to promote research for a cure. :Typical of the Foundations national programs are its Jeanne A. Carpenter Epilepsy Legal Defense Fund, the H.O.P.E. (Helping Other People with Epilepsy) Mentoring Program, a Public Policy Institute, Seniors and Womens Health Initiatives, the Kids Speak Up advocacy program, a school personnel training program, outreach to youth and to the Hispanic community, employment programs and a research grants program. Services commonly provided in local communities are information and referral, counseling, patient and family advocacy, school and community education, support groups and camps for children. Its Web site offers the most comprehensive, medically approved consumer information about epilepsy and seizures on the Internet and is the trusted source for millions of people who seek reliable information about epilepsy. : Each year the Foundation also invites research investigators to apply for grants and fellowships to test new ideas and follow new research leads. The applications, more than a hundred in an average year, are ranked according to merit by a blue ribbon panel of research scientists, and funded according to available resources. Additionally, the Epilepsy Foundation offers a series of training fellowships in basic, clinical and behavioral science to scientists at the start of their careers. These fellowships, awarded to young people at the nation's leading research institutes, have in many cases been the first steps on a lifetime commitment to solving the medical and scientific puzzle of why epilepsy develops and how it can be treated or prevented. Specifically, the Gowers Fellowship is awarded annually to a physician/scientist who is embarking on a career in academic clinical medicine and who wishes to undertake a specific project in epilepsy research. Sponsors: The Epilepsy Foundation is funded primarily through individual donations from the general public and receives restricted grant support from the federal government, foundations and private industry.
Portal that aims to inspire connections, clinical advances and accelerate progress toward multiple sclerosis cures. MSDF updates its site with news and information about topics relevant to multiple sclerosis and hosts discussions about controversial subjects with the goal of spreading information and enabling collaboration between researchers. MSDF provides access to drug development pipelines, tissue repositories, the MS gene, animal models, and clinical trials.
A support vector machine for calling variants from next-gen sequencing data. It takes as input a BAM-formatted alignment of sequencing reads, and emits a VCF formatted file describing where all the SNPs (single nucleotide polymorphisms) are.
Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data.
A software package that provides functions to read raw RT-qPCR data of different platforms.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.
BlackOPs: RNA-Seq Variant Blacklist Tool
Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls.
Mouse Single Nucleotide Polymorphism Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This website contains a database of the mouse SNP. DNA sequencing was performed along with genotyping. There is information on genotyping, mouse strain, and haplotype map.
Multi-channel data acquisition software. Multi-channel stimulation/acquisition software with programmable experiment control and automation, software Lock-in amplifier and Photometry/Imaging extension. PATCHMASTER supports all HEKA amplifiers and data acquisition hardware.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Information Portal to Biological Macromolecular Structures provides variety of software tools made available through the RCSB. These tools include: data extraction and deposition preparation tools, data format conversion and validation tools, data parsing tools, dictionary and data management tools, visualization tools that support PDBx/mmCIF, and other PDBx/mmCIF software library tools.
Manuals for R created on Debian Linux that can be downloaded as PDF files, EPUB files (for R-devel and R-patched), or directly browsed as HTML. They may differ from the manuals for Mac or Windows on platform-specific pages, but most parts will be identical for all platforms.
TADS - Treatment for Adolescents with Depression Study
Treatment for Adolescents with Depression Study
Treatment for Adolescents with Depression Study (TADS)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression.
University of Tennessee Genome Science and Technology Graduate Program
Graduate School of Genome Science and Technology
University of Tennessee Genome Science & Technology
University of Tennessee Genome Science Technology
UT-ORNL Graduate School of Genome Science and Technology
Graduate School of Genome Science and Technology (GST) is a Life Science graduate program founded on two premises. First, whole-genome sequences and related large-scale datasets have transformed how we perform biological research, a trend that is gathering momentum and is anticipated to frame the way the biology research is accomplished for many years to come. Second, advances in technology, whether at the level of instrumentation, computation, or wet lab reagents, have long been a powerful driving force in biology. The GST program is home to faculty mentors from many walks of life. The virulence factors of pathogenic fungi and the engineering of photosynthetic reaction complexes for bioenergy harvesting are just two examples from the cornucopia of research projects being pursued in GST.
Institute for Magnetic Resonance Safety, Education and Research
The Institute for Magnetic Resonance Safety, Education, and Research (IMRSER) was formed in response to the growing need for information and research on matters pertaining to magnetic resonance (MR) safety. The IMRSER is the first independent, multidisciplinary, professional organization devoted to promoting awareness, understanding, and communication of MR safety issues through education and research. Mission Statement To promote awareness and understanding of MR safety, To disseminate information regarding current and emerging MR safety issues, To develop and provide materials and resources to facilitate MR safety-related education and training, To respond to critical MR safety issues with a sense of urgency, and To advance the field of MR safety through support of scientific research. Functions and activities of the IMRSER include development of up-to-date MR safety materials and dissemination of this information to the MR community. This is accomplished predominantly through the efforts of the Advisory Boards. Members of the Advisory Boards of the Institute for Magnetic Resonance Safety, Education, and Research (IMRSER) are charged with creating recommendations, guidelines, position papers, and educational materials pertaining to existing or emerging MR safety issues. This is achieved by utilizing the pertinent peer-reviewed literature and by relying on each members extensive clinical, research, or other appropriate experience. Notably, documents developed by the IMRSER incorporate MR safety guidelines and recommendations created by the International Society for Magnetic Resonance in Medicine (ISMRM), the American College of Radiology (ACR), the Food and Drug Administration (FDA), the National Electrical Manufacturers Association (NEMA), the Medical Devices Agency (MDA), the International Electrotechnical Commission (IEC), and other similar organizations. The IMRSERs rigorous development and review process for MR safety documents ensures that authoritative and relevant information is produced in a timely manner for rapid dissemination to the MR community. The MR safety information is provided to MR healthcare professionals and others as hard copy and electronic publications. Additionally, this information is posted on the IMRSER web site as well as on www.MRIsafety.com (currently with over 92,000 registered users). The Institute for Magnetic Resonance Safety, Education, and Research permits all members of the MR community to use the MRI Safety Guidelines posted on this web site. Please be sure to read and understand our disclaimer.
Graphical User-friendly Analysis of Relaxation Dispersion Data
MATLAB software designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data.
MTOPS Prostate Samples Analysis Consortium
MTOPS Prostate Samples Analysis (MPSA) Consortium
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Cross-disciplinary, multi-institutional network with wide range of experts to analyze serum and tissue samples collected in the Medical Therapy of Prostatic Symptoms (MTOPS) trial. Consortium aims to discover and validate biomarkers for the detection, risk assessment, and disease progression assessment of benign prostatic hyperplasia (BPH).
A software tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data.
Software visualization tool based on the VTK library. Its main feature is to measure and display surface-to-surface distance between two triangle meshes using user-specified uniform sampling. Offers all the basic tools to visualize meshes such as color, opacity, smoothing, down sampling or type of representation.
Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs.
Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq.
flowCL - Semantic labelling of flow cytometric cell populations
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.
A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly.
Basic Alignment Tool for MAny Nucleotides
A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.
Software for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing.
A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.
flowBin - Combining multitube flow cytometry data by binning
A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers.
eSLDB - eukaryotic Subcellular Localization database
eukaryotic Subcellular Localization database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.
CorMut - Detect the correlated mutations based on selection pressure
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.
Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.
Fast and Accurate Classification of Sequences
Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.
Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 25,2022. Project (2001-2004) to build and deploy a prototype infrastructure for making scholarly claims about the significance of research documents. "Claims" are made by making connections between ideas. Any claim is open to counterarguments. The connections are grounded in a discourse/argumentation ontology, which makes possible innovative services for navigating, visualizing and analyzing the network as it grows. They have evolved a suite of prototype tools for modelling conceptual networks of ideas and arguments, publishing them for reuse and argumentation, and navigating, searching and filtering this repository as it grows. Some of these are freely available to play with, but WARNING! they are no longer able to support them. The system they have built is called ClaiMaker. Others include ClaimSpotter, ClaiMapper, ClaimFinder, ClaimBlogger and ClaiMaker Microsoft Word plug-in. Additionally, the ScholOnto RDF Schema is available, http://projects.kmi.open.ac.uk/scholonto/resources/Scholonto2.rdfs User Communities: They envisage such a tool as having potential not only in scholarly publishing, but for corporate knowledge analysis, and in education. Complementary work: ScholOnto's focus on net-centric representations of research is complemented by work on augmenting more conventional textual documents, with threaded commentary and debate. An open source web publishing tool is available called D3E (Digital Document Discourse Environment). Many applications are illustrated on the site, including the award-winning Journal of Interactive Media in Education.We are no longer able to support tools, so are not able to assist if you have problems or lose data.
DIScovery of Structural Events Containing Transcripts
Dissect: DIScovery of Structural Events Containing Transcripts
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data.
Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.
Geometric Analysis of Structural Variants
Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions.
ghostm: GPU-based HOmology Search Tool for Metagenomics
GPU-based HOmology Search Tool for Metagenomics
Software homology search tool for huge short reads generated by next-generation sequencers.Can detect remote homologs like BLAST and is about 40 times more efficient than BLAST by using a GPU-computing technique.
Colorado College Department of Psychology
A department within Colorado College that is dedicated to providing academic programs for undergraduate education. Students are educated in a variety of research techniques, statistics and design experiments.
Cross Collaboration Initiatives at the NIH
National Institutes of Health Division of Program Coordination Planning and Strategic Initiatives
NIH Division of Program Coordination Planning and Strategic Initiatives
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. NIH Division of Program Coordination Planning and Strategic Initiatives.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan, analysis program MPView and several software utilities.
nFuse: Discovery of Complex Genomic Rearrangements in Cancer
Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).
Software image processing toolkit. Provides collection of libraries and command-line tools to assist in processing and analyzing imaging data. Used for adult and neonatal brain MR image registration, including rigid, affine, and non-rigid transformations, as well as reconstruction of cortical surface meshes.
PD5: A Software Library for the Development of Primer Design Applications
An open-source C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications.
An antibody supplier for the purposes of life science and biomedical research. This company has a wide variety of immunological reagents that focus on areas of research such as cancer, cell biology, epigenetics, immunology and infectious diseases.
A supplier of cancer and infectious disease diagnostic reagents. The company also provides services such as tissue-based and molecular diagnostics to their partners to accelerate their in vitro diagnostic device (IVD) product development and commercialization.
National Laboratory for Scientific Computing; Rio de Janeiro; Brazil
Laboratorio Nacional de Computacao Cientifica
Laboratório Nacional de Computação Científica
National Laboratory for Scientific Computing
Brazilian laboratory dedicated to conducting research, developing and training of human resources for scientific computing with special emphasis on construction and application of mathematical and computational models for solving scientific and technological problems.
Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.
Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.
VariantAnnotation - Annotation of Genetic Variants
Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A free bioinformatics software tool to help identify fusion transcripts from paired-end transcriptome sequencing data. The source codes of SnowShoes-FTD are provided in two formats: one configured to run on the Sun Grid Engine for parallelization with shorter run time, and the other formatted to run on a single LINUX node.
timecourse - Statistical Analysis for Developmental Microarray Time Course Data
Software functions for data analysis and graphical displays for developmental microarray time course data.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Social networking site for academic researchers that allows researchers to share papers, find people working in a field and see analytics on papers etc
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. XML vocabulary and schema for strategic plans, designed to create a world wide web of intentions, stakeholders and results.
Software tool for MRI intensity standardization by aligning histograms of higher dimensions. The methods defined in http://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2006/Jaeger06-ANM.pdf are implemented as and ITK filter.
Scalable particle fluid simulation code for Lagrangian particle-based fluid simulation. This adaptive sampling strategy allows using smaller (and thus more) particles in geometrically complex regions, while less particles are used for thick flat fluid volumes. Additionally, a novel distance-based particle surface definition is implemented which hides the particle granularity and allows dynamic resampling near the fluid-air interface. The code is implemented in C++ and should compile on Linux.
Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression.
RNA STRAND-The RNA secondary STRucture and statistical ANalysis Database
RNA secondary STRucture and statistical ANalysis Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A scientific community-crowdsourced database containing the RNA secondary structures of known types and organisms. It is meant to provide a simple and powerful way to analyze, search and update a shared repository of information.
A system of databases which stores information on the influence of mutations in regulatory gene regions . This tool helps recognize protein binding sites that are being altered by mutation. It has four cross-linked sub databases that focus on specific aspects including: (1) the effect of single nucleotide mutations in regulatory gene regions and their interaction with nuclear proteins; (2) references to original publications on the subject; (3) the experimental details of these publications; and (4) the protocols of these experiments. This resource is aimed at providing information to further research on the influence of specific sequence alterations on disease susceptibility, drug resistance and healthcare.
Generalized Ontological Algorithmic Logical Invariants Extractor
Generalized Ontological Algorithmic Logical Invariants Extractor (GOALIE)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Generalized Ontological Algorithmic Logical Invariants Extractor (GOALIE) is a tool for the construction of time-course dependent enrichments. Requires an ODBC connection to an instance of the GO database. Platform: Windows compatible, Mac OS X compatible, Linux compatible
Danish Multiple Sclerosis Center Genetics in MS
Danish Multiple Sclerosis Center: Genetics in MS
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. We have collected DNA for more than 15 years, and today we have DNA from more than 1,800 Danish MS patients and 1,200 controls, all kept in the Danish Multiple Sclerosis Biobank in DMSC. In order to increase the sample size for genetic testing, we have participated in the Nordic MS Genetic Network since 1994, and today the Nordic material consists of more than 6,000 MS cases and 6,000 controls. The research in DMSC is focused on the candidate gene approaches and the genetic influence on the differences in treatment response. We are part of the IMSGC (International Multiple Sclerosis Genetic Consortium) and the Wellcome Trust Case Control Consortium (WTCCC), where 23 research groups from 15 countries are performing the largest set of MS genome-wide association study (GWAS), genotyping 11,000 cases and 11,000 controls using 500,000 SNP chip. Primary results have elucidated associations to more than 100 gene variations (SNPs). Following this collaboration we are joining the Immunochip Consortium, where 1,000 Danish cases and 1,000 Danish controls participate in a large scale genetic analysis, investigating best genes/regions/SNPs in MS together with other international MS research groups and 9 other autoimmune diseases research groups, looking for shared autoimmune genes. The risk of MS has been increasing over the last 50 years, especially among women older than 40 years. On this background we have initiated a project looking at aspects of gender differences, including different treatment responses. Furthermore, we have initiated a large-scale vitamin D project, investigating gene variations within the vitamin D pathway, and the importance of vitamin D in clinical and immunological disease activity. In addition, we have collected more than 800 questionnaires from MS patients dealing in detail with lifestyle and environmental exposure for a project studying gene-environmental interactions.
Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).
Signaling Networks Analysis and Visualization
Desktop application for analysis and visualization of large-scale cell signaling networks.
Software that combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download.
EPIGEN: An international consortium dedicated to tackling epilepsy through genetics
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Repository of neuron types characterized by machine-readable part-relation-value triple-based neuron properties. A Curator Interface facilitates the direct knowledge transfer of information from the participating neuroscientist for entry into the Neuron Registry.
Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK).
An open-source JAVA program that is surprisingly efficient at predicting active siRNAs.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Server to rapidly design primers for real-time PCR measurement of eukaryotic expression.
THIS RESOURCE IS NO LONGER IN SERVICE, documented October 28, 2015. Interactive, informative and educational community platform dedicated to cognitive science or the multidisciplinary exploration of the mind. This online platform, will help gather and link information providing a thorough and reliable source of information for students and professionals in the field, as well as help bridge the gap between academia and the society. Due to the multidisciplinary nature of cognitive science, the work is becoming increasingly specialized. Therefore to keep an eye on the bigger picture, it seems necessary to bring the discoveries of various disciplines together in one place, look at their similarities and differences and discuss them for future directions.
Biomedical Simulations Resource Workshops
Forum for the dissemination of leading-edge methodologies for modeling and simulation in biomedicine, they serve to foster substantive interactions among Workshop attendees.
Biomedical Simulations Resource Short Courses
Short courses to train the broader biomedical research community in the modeling and simulation methodologies developed by Resource Scientists and others.
RmiR.Hs.miRNA: Various databases of microRNA Targets
Software package for various databases of microRNA Targets.
Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.
TERC: Tissue Engineering Resource Center
Biomedical technology research center designed to advance basis and clinical aspects of tissue engineering, to provide training for investigators and dissemination of scientific findings and new techniques. Expertise and facilities are focused on research, problem solving and training for biomedical community through integrated systems approach to challenges in tissue engineering. Mission for TERC is to engineer human tissues for medical impact. Includes Functional human tissue grafts: human tissues for application in regenerative medicine;Human disease models in vitro: in vitro models of human disease to provide new experimental tools to understand progression of disease, effects and mechanisms of drug action; Biological materials research: bioengineering tools for cell biology studies in context of tissue development, regeneration and disease.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Society helps people affected by Multiple Sclerosis by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward.
University of California at San Diego Cognitive Science Graduate Student Fellowship Opportunities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. This resource is a frequently updated listing of graduate student in cognitive science fellowship opportunities. For current opportunities, please see the PDF document.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Biomedical technology research center that develops basic scientific understanding and new techniques required for advancing clinical applications of lasers and spectroscopy. LBRC merges optical spectroscopy, imaging, scattering, and interferometry techniques to study biophysics and biochemistry of healthy and diseased biological structures from subcellular to entire-organ scale.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function.
The Brain Trauma Foundation (BTF) is a national non-profit organization dedicated to improving the outcome of traumatic brain injury (TBI) patients worldwide by developing best practices guidelines, quality improvement programs, conducting clinical research, and educating medical professionals and consumers. Our efforts also focus on public education aimed at increasing awareness and understanding of the symptoms of a concussion. Our goal is to better educate coaches, nurses, athletes, parents and all citizens about the importance of recognizing concussions and taking the appropriate steps to ensure people receive appropriate care. Also by educating healthcare professionals on the immediate care for coma patients, we estimate that thousands of lives could be saved each year in the U.S., millions worldwide, and more would be spared life-long disabilities. Research has proven that all brain damage does not occur at the moment of impact but rather evolves over the ensuing hours and days after the initial injury, due to brain swelling and inadequate oxygen and blood flow to the injured brain. In most cases, this secondary damage can be controlled by applying scientific, evidence-based diagnostic and treatment Guidelines, which BTF has developed with medical organizations and physicians with expertise in TBI. BTF offers updated continuing education activities for all levels of health care professionals caring for TBI patients. The online activities include recorded presentations, live web-based lectures, and interactive learning modules based on the latest scientific-evidence. Also available on the BTF Learning Portal is an online version of the EMS course developed in coordination with National Highway Traffic Safety Administration. The Brain Trauma Foundation leads the way in cutting-edge clinical research on Traumatic Brain Injury (TBI). Improving diagnosis and treatment of TBI requires a focus on clinical research. Our mission is to improve the outcome of TBI patients worldwide. BTF's research spans the spectrum from concussion to coma. BTF is conducting innovative research into the cause diagnosis of concussion. Also, BTF develops Best TBI Practice Guidelines, which when followed can significantly improve a patient's outcome. The Foundation is currently conducting studies and leading consortiums of investigators from multiple universities and disciplines in many TBI research areas that will have immediate impact on patient outcomes.
Treephyler: fast taxonomic profiling of metagenomes
A software tool for fast taxonomic profiling of metagenomes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Gene Ontology dedicated to the functions of mobile genetic elements. The terms defined are used to annotate phage and plasmid protein families in ACLAME. Note: The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up.
A database of organized information related to human medical genetics, such as attributes of conditions with a genetic contribution.
A free online service to easily create and share webpages.
Blog about brain technology and science news that covers topics such as high-resolution brain imaging, brain maps API and whole-brain atlases.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software package for knowledge management of neuroscientific literature. Used for creating knowledge models that answer specific questions with direct links to the literature.
A fully extendable software framework, for property-based design of synthetic DNA sequences.
Open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer 2.0 is developed for the Windows 7, 64-bit operating system and requires a minimum of 4 GB of RAM. This version does not run on 32-bit computers, Mac or Linux OS.
A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.
Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment.
Software to access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis.
Body Mass Index (BMI) for adults can be calculated using only height and weight. Body mass index (BMI) is a measure of body fat based on height and weight that applies to adult men and women.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software)
Faceted Search Based Ontology Visualizer
Software that allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy.
BWH Partners Tissue and Blood Repository
Brigham and Women's Hospital Partners Tissue and Blood Repository
Brigham and Women's Hospital PartnersTissue and Blood Repository Core
Partners Tissue and Blood Repository Core
A repository which provides specimen acquisition, processing and storage services, and access to archived frozen tissue specimens to the BWH/MGH/DFCI research community.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor.
Symptom Score for Benign Prostatic Hyperplasia
American Urological Association's Symptom Score for Benign Prostatic Hyperplasia
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Adapted from the American Urology Association Symptom Score for Benign Prostatic Hyperplasia, this chart will assist physicians, researchers, and patients in assessing the severity of the problem.
An algorithm used to predict and analyse binding modes of docking molecules. Users can search ligand databases for compounds that inhibit enzymatic activity and bind to particular molecules and nucleic acid targets. Molecular docking is used to predict a predominant binding mode(s) of a ligand in three-dimensional structure. This method can be used for molecular biology and computer-assisted drug design.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease.
The World-Wide Web Virtual Library:Neurosciences
World-Wide Web Virtual Library:Neuroscience
World-Wide Web Virtual Library:Neuroscience (Biosciences)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A website that provides links to many neuroscience resources on the web as well as links to university neuroscience and neurobiology program home-pages.
Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology.
Genetics of Kidneys in Diabetes (GoKinD) Study
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Collect, store, and distribute genetic samples from cases and controls of type 1 diabetes and diabetic nephropathy for investigator-driven research into the genetic basis of diabetic nephropathy. As the risk of kidney complications in type 1 diabetes appears to have a considerable genetic component, this study assembled a large data resource for researchers attempting to identify causative genetic variants. The types of data collected allowed traditional case-control testing, a rapid and often powerful approach, and family-based analysis, a robust approach that is not influenced by population substructure.
An ontology covering the anatomy of Porifera (sponges).
International Union of Basic and Clinical Pharmacology
Voluntary, non-governmental, non-profit pharmacologist association promoting international cooperation, sponsoring international and regional activities, encouraging free exchange of scientists and ideas, developing public awareness, establishing advisory committees. Has official relations with the World Health Organization (WHO). Helps pharmacologists to participate with other branches of science in international activities, either directly or under ICSU, WHO and UNESCO. Member of the International Council for Science (ICSU) and participates in the work of its scientific committees. Has its own publishing program. Pharmacology International, is published every June and December. Member Directory is maintained continually, as an online resource. Provides IUPHAR Receptor Database, major on-line repository of characterization data for receptors and drugs, and the IUPHAR Ion Channels Database. Official Reports from The IUPHAR Committee on Receptor Nomenclature and Drug Classification are published in Pharmacological Reviews. IUPHAR World Congresses of Pharmacology are held every few years.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Project Halo is a staged, long-range research effort by Vulcan Inc. towards the development of a Digital Aristotlea reasoning system capable of answering novel questions and solving advanced problems in a broad range of scientific disciplines and related human affairs. The project focuses on creating two primary functions: a tutor capable of instructing and assessing students in those subjects, and a research assistant with broad, interdisciplinary skills to help scientists and others in their work. Vulcan began work towards this ambitious vision in 2003 with the Halo Pilot a six-month effort to investigate the feasibility of creating a scientific knowledge base capable of answering novel questions from the AP (1st year college level) chemistry test. Three teams SRI International, Cycorp, and Ontoprise developed knowledge bases, for a limited section of an AP-chemistry syllabus, that were able to correctly answer 40 to 50 percent of the associated questions from the AP test. Since 2004, Project Halo has worked to improve these systems, with an emphasis on enabling knowledge entry by domain experts, instead of specialists in artificial intelligence software. In 2004, Vulcan began the development of Automated User-Centered Reasoning and Acquisition System (AURA), by SRI, that enables domain experts (graduate students in Biology, Chemistry, and Physics) to enter knowledge from introductory science textbooks. In 2006, an evaluation of AURA showed that students could create AURA knowledge bases that correctly answered 40 percent of the questions on a limited AP exam. In 2008, the next evaluation demonstrated an improvement of that score to 70 percent correct. In parallel, Project Halo has sponsored Ontoprise to develop semantic extensions to MediaWiki, the software that Wikipedia runs on. Ontoprise has developed a set of Semantic MediaWiki (SMW)+ extensions to MediaWiki that provide a community-based environment for authoring ontologies and creating semantically enhanced wikis. SMW+ has been widely used and is being applied in project management, enterprise collaboration and knowledge management, business intelligence, and the management of large terminology sets. In 2007, Vulcan began a new effort, Halo Advanced Research (HalAR), to address the difficult knowledge representation and reasoning (KR) challenges that prevent the realization of Digital Aristotle. This effort has produced a new semantic rule language and reasoning system, Semantic Inferencing on Large Knowledge (SILK), which includes major advances, including for default and higher-order reasoning over the web.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An enzyme developer and provider of biochemical and consultancy services. Its consultancy services include organizing proof of concepts and planning startup companies, laboratories, and analytical methods. The company also offers writing and editing services for scientific and grant proposals, as well as technology assessments. The company is located in central Israel; however, all of their services are offered worldwide.
A commercial organization that supplies researchers with life science instruments, reagents and consumables, and lab services.
Sage Bionetworks, Mount Sinai School of Medicine (MSSM), University of Pennsylvania (Penn), the National Institute of Mental Health (NIMH), and Takeda Pharmaceuticals Company Limited (TAKEDA) have launched a Public-Private Pre-Competitive Consortium, the CommonMind Consortium, to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. This collaboration brings together disease area expertise, large scale and well curated brain sample collections, and data management and analysis expertise from the respective institutions. As many as 450 million people worldwide are believed to be living with a mental or behavioral disorder: schizophrenia and bipolar disorder are two of the top six leading causes of years lived with disability according to the World Health Organization. The burden on the individual as well as on society is significant with estimates for the health care costs for these individuals as high as four percent GNP. This highlights a grave need for new therapies to alleviate this suffering. Researchers from MSSM including Dr. Pamela Sklar, Dr. Joseph Buxbaum and Dr. Eric Schadt will join with Dr. Raquel Gur and Dr. Chang-Gyu Hahn from Penn to combine their extensive brain bank collections for the generation of whole genome scale RNA and DNA sequence data. Dr.Pamela Sklar, Professor of Psychiatry and Neuroscience at MSSM commented this is an exciting opportunity for us to use the newest genomic methods to really expand our understanding of the molecular underpinnings of neuropsychiatric disease, while Dr Raquel Gur, Professor of Psychiatry from Penn observed this will be a great complement to some of the large-scale genetic analyses that have been carried out to date because it will give a more complete mechanistic picture. The CommonMind Consortium is committed to generating an open resource for the community and invites others with common goals to contact us at info (at) CommonMind.org.
A genomics and proteomics company that offers customizable oligonucleotide and peptide microarray products for nucleic acid and protein-profiling, biomarker-screening, drug screening, and development of diagnostic-devices.
Software that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
Java-based software platform designed for the implementation, distribution and application of classifiers and methods for regression analyses for all kinds of data. Unfortunately, technical issues and some pecularities of fMRI data prevented the import and classification of neuroimaging data in this software. A tool for the integration of fMRI data in WEKA is presented, and thereby provide a way to access a broad collection of recent analysis tools for data classification.
University of Maryland Labs and Facilities
University of Maryland Labs & Facilities
A collection of laboratories hosted through the University of Maryland. These laboratories include: the BioAnalytical Service Laboratory, Biotechnology Research and Education Program, and the Sequencing Core.
University of Texas Medical Branch at Galveston
A division of the University of Texas that is dedicated to medical education.
Public research university in Gainesville, Florida, United States. Member of state university system of Florida with undergraduate and graduate programs in arts and sciences.
GEOquery - Get data from NCBI Gene Expression Omnibus (GEO)
Software that establishes a bridge between GEO and BioConductor.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG.
Database and integrated tools to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data.
University of Washington Department of Biochemistry
A department within the University of Washington which focuses on both undergraduate and postgraduate education in biochemistry.
Louisiana State University Health Sciences Center New Orleans; Louisiana; USA
Louisiana State University Health Sciences Center - New Orleans
Louisiana State University Health Sciences Center New Orleans
LSU Health Sciences Center - New Orleans
A Louisiana-based university with programs in dentistry, medicine, public health, patient care and allied health professions. This university Includes a graduate program in fields including neuroscience, pharmacology, and genetics.
Software to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, they improve the estimation of background rates for each category.
University of Florida College of Medicine; Florida; USA
University of Florida College of Medicine
A medical school which offers degrees in medicine, in addition to medical science, biomedical engineering, physician assistant studies and an interdisciplinary program in biomedical sciences.
University of Stuttgart; Stuttgart; Germany
A public research university with 10 programs in disciplines of science, social science and humanities. The institution has technical programs in civil, mechanical, industrial and electrical engineering.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.
Morphometry BIRN Multi-site Multi-session Structural MRI Data
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th,2023. Calibration data set of spoiled gradient-recalled echo magnetic resonance imaging data from five healthy volunteers (four males and one female) scanned twice at four sites having 1.5T systems from different vendors (Siemens, GE, Marconi Medical Systems) pooled by the Morphometry Testbed's (MBIRN). Some subjects were also scanned a single time at another site. One subject was only scanned twice at three sites (subject 73213384) and once at another site. For each subject, four Fast Low-Angle Shot (FLASH) scans with flip angles of 3, 5, 20, and 30 degrees were obtained in a single scan session, from which tissue proton density and T1 maps can be derived. These data were acquired to investigate various metrics of within-site and across-site reproducibility. The images have been defaced so that no facial features can be reconstructed from these data. The Morphometry Testbed (MBIRN) of the Biomedical Informatics Research Network (BIRN) focused on pooling and analyzing of neuroimaging data acquired at multiple sites. Specific applications include potential relationships between anatomical differences and specific memory dysfunctions, such as Alzheimer's disease. With the completion of the initial BIRN testbed phase, each of the original BIRN testbeds have now been retired in order to focus on new users in other biomedical domains.
A comprehensive software toolkit for post-processing, visualization and advanced analysis of GWAS results.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Ontology-based knowledgebase for synaptic genes. These genes encode components of the synapse including neurotransmitters and their receptors, adhesion / cytoskeletal proteins, scaffold proteins, transporters, and others. It integrates various and complex data sources for synaptic genes and proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017. Repository for sharing of neuroscience data, text, images, sounds, movies, models and simulations.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Organization which focuses on the promotion of health and increased quality of life for South Africans through research, development and technology. This organization conducts basic laboratory investigations, clinical research and public health studies, and its research focuses around the study of TB, HIV, chronic diseases, alcohol and drug abuse, and women's health.
High-field extension of the Colin27 single-subject atlas with additional high-resolution, quantitative, averaged scans at both 3T and 7T.
Covariance estimation library used in Improved Estimation and Interpretation of Correlations in Neural Circuits.
A PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed.
A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets.
Genome-wide Microsatellite Analyzing Tool
Genome-wide Microsatellite Analyzing Tool (GMATo)
A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A measure of receptive vocabulary that is administered in a computerized adaptive format. The respondent is presented with an audio recording of a word and four photographic images on the computer screen and is asked to select the picture that most closely matches the meaning of the word. This test takes approximately 4 minutes to administer and is recommended for ages 3-85.
A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface.
An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.
ERIN: Educational Resources In Neuroscience
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A database that lists, reviews, and rates resources for teaching neuroscience at the graduate and undergraduate level.
Mind Hacks: Neuroscience and psychology tricks to find out what's going on inside your brain. Mind Hacks is also a book by Tom Stafford and Matt Webb.
A sequence of fully automated voxel-wise rigid registration that utilizes stable structures of reference for assessment of craniofacial changes overtime.The major strengths of this method are that registration does not depend on the precision of the 3D surface models and that a stable structure of reference can be used without the simple best fit of all surfaces.
A software tool for the quantitative analysis of various n-dimensional (n-D) image registration techniques. The series of 'C' subroutines which comprise the WAIR library can be easily incorporated into the user's site specific programs and adapted to their particular needs. Wavelet-space triangle analysis is applicable for studying a family of warps on single or multiple n-D data sets. For each data set the WAIR routine assigns a positive real number to every warp alignment in the family, and the best warp for the given data will be the one with the smallest value. It uses the original data prior to warping and the target of the warp in determining warp ranking in reduced wavelet space. Cluster group classification (CGC) is applicable for analyzing the overall performance of a family of warps of a group of data sets. A single number is assigned to each registration alignment, based on its group-clustering characteristics. Spread group classification (SGC) gives preference to registration techniques that spread apart baseline versus activation functional signal for group data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Assessment test that measures how much difficulty a person might have hearing in a noisy environment. A recorded voice instructs the participant to listen to and then repeat words. The task becomes increasingly difficult as the background noise gets louder. This test was developed to measure a person's ability to recognize single words presented amid varying levels of background noise. Recommended for participants ages 6-85 and takes approximately six minutes to administer.
Assessment scale that is a 28 question self test used to screen patients for dissociative identity disorder (formerly called Multiple Personality Disorder). The 28 questions ask the patient about their experiences and their daily life and how often certain events happen.
University of Vermont Labs and Facilities; Center of Biomedical Research Excellence (COBRE) in Neuroscience
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A university-based lab facility for research in biomedicine and neuroscience. The center was created to expand neuroscience research and training, develop shared core facilities and provide funding for research by neuroscience faculty. There is an emphasis on interdisciplinary neuroscience research and dialogue between basic and clinical neuroscientists.
A 29 item aggression assessment where participants rank certain statements along a 5 point continuum from "extremely uncharacteristic of me"to "extremely characteristic of me". The scores are normalized on a scale of 0 to 1, with 1 being the highest level of aggression. The questionnaire returns scores for 4 dimensions of aggression: Physical Aggression, Verbal Aggression, Anger, Hostility.
Illuminate - Analytics toolkit for Illumina sequencer metrics
Python module and utilities to parse the metrics binaries output by Illumina sequencers, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, it allows you to print sequencing run metrics to the command line as well as work with the data programmatically.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website.
University of Washington Nath Research Group
University of Washington Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. University of Washington - affiliated research lab focused on understanding the roles of protein dynamics in health and human disease. They focus on developing methods to characterize and control protein dynamics through utilizing methods like single-molecule fluorescence, computational modeling, and protein engineering. There is an emphasis on proteins involved in degenerative disorders such as Alzheimer's disease, stress responses and drug metabolism.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Web services to access UNAVCO data collection. Adding /gps, /met, /pore, /tilt, and /strain gives the sensor JSON description.
Community ontology for the concise, controlled description of environmental features and habitats. It provides a structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A contract research organization that provides genomics services such as sequencing, bioinformatics, NGS data analysis and whole exome sequencing. EdgeBio is a CLIA-approved service provider.
MIMOSA - Mixture Models for Single-Cell Assays
MIMOSA: Mixture Models For Single Cell Assays
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.
A collection of user interfaces packaged into TexMol that allows a user to interactively submit protein-protein docking jobs to a remote computing cluster, monitor the status of the jobs and retrieve and visually display/compare the results.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software with two main applications: predicting the binding mode of three-dimensional proteins and virtual high-throughput screening (vHTS) which allows screening of compounds at rapid speeds.
Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures.
Google Tech Talks is a grass-roots program at Google for sharing information of interest to the technical community. At its best, it's part of an ongoing discussion about our world featuring top experts in diverse fields. Presentations range from the broadest of perspective overviews to the most technical of deep dives, on topics well-established to wildly speculative.
An integrated platform for predicting protein-ligand interactions, the visualization of new ideas and analyzing protein targets.
A complete drug designing software suite with an accessible web-server for targeted directed lead molecule discovery.
Acquisition and Analysis for Electron Tomography
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software platform for low dose electron tomography (ET) for all processing steps: acquisition, alignment, reconstruction, and analysis. Requires: Matlab R2008a and Image Processing Toolbox (V6.1)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems.
HEM - Heterogeneous error model for identification of differentially expressed genes under multiple conditions
Software package that fits heterogeneous error models for analysis of microarray data
Forum for collaborative projects in the field of brain science. Everyone is invited to submit projects, either existing ones that you want to see featured or new ones that you want launch and work on in a collaborative, open way.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software program that screens large libraries of compounds including ligands, and their docking.
Cascleave 2.0 - Caspase substrate cleavage site prediction
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A novel tool developed using Java program for the high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates.
A note taking software that synchronizes information such as notes, web clips, audio files, photos and video collected across multiple devices. It allows for easy sharing and collaboration on projects.
MetaDE: Microarray meta-analysis for differentially expressed gene detection
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A database of resources on cancer processes such as cell death. It is a subset of a larger database on cancer proteomics that focuses on anti-cancer drugs and cancer types in addition to cancer processes. It utilizes scientific articles from PubMed, UniProt and other resources along with information such as author information, sample types and useful hyperlinks.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A standard next-generation paper (NGP) digital format for reading and digitally archiving scientific research papers to offer better imaging, data sharing and an improved reading experience. The NGP format is designed to retain traditional elements (i.e. Abstract, Introduction, etc.). Papers are viewed using any web browser running on any computing platform, including mobile devices. A button menu system provides navigation between pages. The format provides a more streamlined reading experience by providing as much information to the reader inline as possible, without requiring the user to skip between pages. To accomplish this, pop-up figure and reference details provide additional information without disrupting the flow of the paper. Clicking on standard figure data reveals full-resolution images, and live web links can be optionally followed from pop-up citations or inline links for additional information. Multimedia, such as hi-definition video or audio clips, is easily embedded within the new NGP format. The reader may also customize their reading experience by selecting alternative text and background color themes. The NGP format was created using non-proprietary open-source software including HTML and Javascript, and can be packaged to run offline independent of a live Internet connection. Data are fully captured and communicated utilizing the latest technologies available. The SCORE Imaging (Petzold et al.) paper was submitted to the publisher using this format to take advantage of its superior technical capabilities (http://zfishbook.org/NGP/).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software package for the prediction of calpain cleavage sites.
Type 1 Diabetes - Rapid Access to Intervention Development
Type 1 Diabetes - Rapid Access to Intervention Development (T1D-RAID)
NOTE: The T1D-RAID program is not currently accepting applications. Cooperative program that makes available, on a competitive basis, NCI resources for the pre-clinical development of drugs, natural products, and biologics to facilitate translation to the clinic of novel, scientifically meritorious therapeutic interventions for type 1 diabetes and its complications. A partial listing of those services includes: high-throughput screening, studies in animal models, formulation, pharmacology and toxicology studies, and bulk substances acquisition. Requests to T1D-RAID are brief (20 pages or less), and should clearly outline the resources required to ready the proposed therapeutic agent for clinical trials. T1D-RAID should enable entry into the clinic of promising molecules that are not otherwise likely to receive an adequate and timely clinical test. T1D-RAID is designed to accomplish the tasks that are rate-limiting in bringing discoveries from the laboratory to the clinic. Once a project has been approved, NIDDKstaff interact directly with the Principal Investigator (PI). NCI contractors perform the T1D-RAID-approved tasks under the direction of NIDDKand NCI staff. The required tasks will vary from project to project. In some cases T1D-RAID will support only one or two key missing steps necessary to bring a compound to the clinic; in other cases it may be necessary to supply the entire portfolio of development requirements needed to file an IND. Examples of tasks that can be supported by T1D-RAID include, but are not limited to: * Definition or optimization of dose and schedule for in vivo activity * Development of pharmacology assays * Conduct of pharmacology studies with a pre-determined assay * Acquisition of bulk substance (GMP and non-GMP) * Scale-up production from lab-scale to clinical-trials lot scale * Development of suitable formulations * Development of analytical methods for bulk substances * Production of dosage forms * Stability assurance of dosage forms * Range-finding initial toxicology * IND-directed toxicology, with correlative pharmacology and histopathology * Planning of clinical trials * Regulatory affairs, so that FDA requirements are likely to be satisfied by participating investigators seeking to test new molecular entities in the clinic * IND filing advice The output of T1D-RAID activities will be both products and information that will be made fully available to the originating investigator for support of an IND application and clinical trials. T1D-RAID does not sponsor clinical trials.
An online collaborative editor for academics that use citations and/or formulas. The editor focuses on the content rather than the layout, so that with the same text, it can be published in multiple ways: On a website, as a printed book, or as an ebook.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software tool for predicting granzyme B and caspase cleavage sites.
Coalition For Accelerating Standards and Therapies
Coalition For Accelerating Standards and Therapies (CFAST)
Consortium establishing data standards, tools and methods for conducting research in therapeutic areas important to public health including Alzheimer's disease, Parkinson's disease, multiple sclerosis, polycystic kidney disease, and tuberculosis.CDISC and C-Path have agreed to discontinue using separate CFAST brand, but they both remain committed to this mission and continue to partner to develop and publish therapeutic area data standards.
Research foundation that funds research to develop new treatments for multiple myeloma, an incurable blood cancer.
Queensland Cyber Infrastructure Foundation Ltd
Queensland Parallel Supercomputing Foundation
the Queensland Cyber Infrastructure Foundation
Provides digital infrastructure capabilities for research and innovation across Queensland and Australia. Provides services, infrastructure and support for computation and data driven collaborative research and its application in industry. Members are six Queensland universities – The University of Queensland, Queensland University of Technology, Griffith University, James Cook University, CQUniversity, and the University of Southern Queensland. The University of the Sunshine Coast is an associate member. Member employees provide support and development services.
Organization and funder of polycystic kidney disease research to find treatments. The organization also raises awareness for the disease through education, advocacy and support.
Washington University School of Medicine Knight Alzheimers Disease Research Center
Charles F. and Joanne Knight Alzheimer's Disease Research Center
Knight Alzheimer's Disease Research Center
Knight Alzheimers Disease Research Center
Washington University School of Medicine in St. Louis Knight ADRC
The Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC) supports researchers and our surrounding community in their pursuit of answers that will lead to improved diagnosis and care for persons with Alzheimer disease (AD). The Center is committed to the long-term goal of finding a way to effectively treat and prevent AD. The Knight ADRC facilitates advanced research on the clinical, genetic, neuropathological, neuroanatomical, biomedical, psychosocial, and neuropsychological aspects of Alzheimer disease, as well as other related brain disorders.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Drosophila neurobiology with 3D images, enhancer traps, Golgi impregnations and protocols. This data contains a schematic view onto the brain of an adult fly is a clickable imagemap. The set of links overlaps with those of the 3D-clickable version, but is not identical.
Software package that allows inferring gene regulatory networks with direct physical interactions from microarray expression data using C3NET.
ANU Centre for Advanced Microscopy Core Facility
Australian National University Centre for Advanced Microscopy
Centre for Advanced Microscopy provides open access, state-of-the art microscopy and microanalysis equipment and expertise to national and international researchers, students and industry partners in the materials and life sciences. Offers services to support experimental design, data acquisition and analysis, train users in the use of instruments and help with sample preparation, provide research collaboration.
Council for Scientific and Industrial Research; Gauteng; South Africa
Council for Scientific and Industrial Research
A leading scientific and technology research, development and implementation organization in Africa that undertakes directed research and development for socio-economic growth and improving the quality of life of South African citizens.
An antibody supplier based out of the Silicon Valley which has a focus on products used for proteomic research. The company supplies products such as ELISA based antibody arrays, DNA and protein microarray substrates and imaging system calibration and validation tools.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software that infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles.
An algorithm for the inference of gene regulatory networks from expression data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for learning parsimonious regulatory networks from systems biology data sets de novo. Software that utilizes inference algorithm to model genetic regulatory networks.Inferelator 2.0 is scalable framework for reconstruction of dynamic regulatory network models., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Clinical Data Interchange Standards Consortium
A global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. Its mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website.
MODENT - A Tool For Reconstructing Gene Regulatory Networks
A computational tool that reconstructs gene regulatory networks from high throughput experimental data.
Portal for placebo controlled trial of the effects of 48-hour infusion of corticosteroids on death and on neurological disability, among adults with head injury and some impairment of consciousness. The outcomes will be measured by rates of death and neurological disability. Patients are recruited (or entered by their doctors when informed consent is not obtainable due to impaired cognitive functioning) on a case-by-case basis as head injured patients come through emergency departments. Randomization is done via a 24-hour telephone line that will denote which pack of medication (either the corticosteroids or saline solution as control) to give.
Miller Lab at the Penn State Center for Comparative Genomics and Bioinformatics
A portal for the Miller Lab at Penn State that does research in comparative genomics and bioinformatics. The website has resources such as web-based applications for genetic databases, software for genomic analysis and publications from the lab.
AusBiotech: Australia's Biotechnology Organization
A portal to Australia's biotechnology industry organization and national network that represents members from sectors including but not limited to human health, agriculture and the environment. The organization provides representation and support to their member companies.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A public research university with twelve main academic disciplines that include science, engineering, agriculture and medicine. The university has campuses across China in locations such as Yuquan, Zhijiang and Zhoushan. It has studies available in undergraduate, graduate and post-doctorate degrees.
A software-based network that provides efficient multicast and reduction communications for parallel and distributed tools and systems. Some key features of this resource include scalable data aggregation, multiple concurrent data channels and high-bandwidth communication.
An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight.
MSU Subzero Science and Engineering Research Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A suite of laboratories that study the effect of the cold on projects across several scientific disciplines. These facilities have the ability to simulate other environmental conditions such as solar radiation and humidity in addition to subzero temperatures.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: MRI examination of sedated non-human primate subjects. The magnetic resonance imaging (MRI) core provides ONPRC investigators with equipment and assistance to perform MRI exams of sedated NHP subjects.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available.
Brigham and Women's Hospital Labs and Facilities
Brigham and Womens Hospital Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A service-providing lab facility based in the Brigham and Women's Hospital. Services include imaging and access to a specimen bank.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Plug-in tool to filter out duplicate reads that is specifically well-suited to handle those coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers.
Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Provides accessible location for storing and efficiently retrieving tools which aid simulations of neuronal and network compartmental models. Simulation tools can be coded in any language for any environment. Simulation tools code can be viewed before downloading or auto-launching.
Queen Mary University of London Labs and Facilities
Queen Mary University of London Labs & Facilities
A collection of laboratory and research facilities in London that cover several domains including but not limited to: biological and chemical sciences, cancer research, condensed matter and material physics, computational research and clinical trials.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A database to store the curated epigenetic data from studies of prostate cancer retrieved by literature mining. The Prostate Epigenetic Database (PEpiD) is meant as a resource for finding previous studies of prostate cancer in humans, mice and rats. Searches can be targeted through the categories of DNA methylation, histone modification, and microRNA.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Blog by Bethany Brookshire on all that is good, bad, and weird in physiology and neuroscience. Scicurious is the pen name of Bethany Brookshire who has a PhD in Physiology from the Wake Forest University School of Medicine. She has a Bachelor of Arts in Philosophy and a Bachelor of Science in Biology from the College of William and Mary. She is currently finishing up a post-doc in psychiatry at the University of Pennsylvania. Her professional interests are in neurophysiology, specifically the interactions of neurotransmitter systems. Having obtained her PhD, she wishes to further her career in science writing, education, and research. You can also find her writing at SciAm blogs.
TAPIR: target prediction for plant microRNAs
Web server designed for prediction of plant microRNA targets.
Brain Architecture Management System Nested Regions
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7th, 2019. BAMS is an online resource for information about neural circuitry. The BAMS Nested Regions view focuses on the major brain regions and their relationships.
A genomics data analysis platform which generates decision models for healthcare organizations and medical research. This service is meant to utilize data through machine learning methods.
A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes.
Software using a Hidden Markov Model for SNP (single nucleotide polymorphism) and indel identification with AB-SOLiD color-space as well as regular letter-space reads.
Web based integrative platform for transcriptional regulation studies.
PSGInfer: Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs
Software for inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.
Pharmaceuticals and Medical Devices Agency
Japanese Pharmaceuticals and Medical Devices Agency
Pharmaceuticals and Medical Devices Agency - Japan
Pharmaceuticals and Medical Devices Agency Japan
A Japanese regulatory government agency which regulates the safety, efficacy and quality of pharmaceuticals and medical devices in order to protect the public health of the people. The agency plays three main roles: drug and medical device testing, post-marketing drug safety, and victim compensation for those affected by adverse drug reactions from pharmaceuticals or other biological products. It is an incorporated administrative agency with non-civil service status.
Philipps-University Marburg; Marburg; Germany
A public university in Germany which has a heavy emphasis on research. The institution has programs in a wide range of fields, most notably life sciences, nano sciences, material sciences and medicine.
Paris; Universite Pierre et Marie Curie
Sorbonne Université; Pierre and Marie Curie University
A public research university in France that emphasizes medical and scientific research centered on four themes: life and health, the living earth and environment, matter and new materials and modeling and engineering. It is a member of the Sorbonne Universities alliance.
Pohang University of Science and Technology; Pohang; South Korea
Pohang University of Science and Technology
A private university in Pohang, South Korea which has an emphasis on the education and research at both the undergraduate and graduate levels. This institution is home to four government-funded research centers in basic sciences such as the National Institute for Nanomaterials Technology. They have the highest educational investment and the most per-student scholarship support in Korea.
Polish Academy of Sciences Poznan; Poznan; Poland
An academy of sciences that is based in Poland. The academy is an important institution for the development of science research in Poland, in addition to being part of a larger network of research institutes.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 26, 2016. A data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Polish Academy of Sciences Warsaw; Warsaw; Poland
Polish state sponsored institution of higher learning. Headquartered in Warsaw, it is responsible for spearheading development of science across country by society of distinguished scholars and network of research institutes. Polish research institution comprised of smaller institutes with goal to support development of science and establishing standards of research quality and ethics.
Polish Ministry of Science and Higher Education
Ministry of Science and Higher Education (Poland)
Ministry of Science and Higher Education - Republic of Poland
Polish Ministry of Science Higher Education
Polish governmental agency that administers governmental activities in science and higher education. Funding is provided by the state for scientific research.
Polytechnic University of Catalonia; Barcelona; Spain
Universitat Politecnica de Catalunya BarcelonaTech
Universitat Politècnica de Catalunya BarcelonaTech
A public research university in Spain which specializes in the fields of architecture, engineering and technology at the undergraduate, graduate and postdoctoral level. UPC focuses heavily on internationalization, this is demonstrated through their large population of international PhD and master's degree students. They are a member of the Top Industrial Managers for Europe network and several university federations, including the Conference of European Schools for Advanced Engineering Education and Research (CESAER).
Polytechnic University of Madrid; Madrid; Spain
A public technical university in Madrid with progams at the undergraduate, graduate and postdoctorate level in fields such as architecture and mining in addition to engineering in areas including forestry, agriculture, computer science and aeronautics.
Polytechnic University of Milan; Milan; Italy
A technical university in Italy that offers programs in engineering, architecture and design at the undergraduate, graduate and postdoctoral level. The university has two main campuses in the city of Milan where teaching and research occur; there are several satellite campuses scattered across five different cities.
Polytechnic University of Valencia; Valencia; Spain
A technical university in Spain which offers degree programs in 14 different faculties, including business administration, computer science and industrial engineering at the undergraduate, graduate and postdoctoral level. The school has five different campuses.
Pompeu Fabra University; Barcelona; Spain
Public university in Spain that offers programs in social sciences and humanities, health and life sciences, international training in communication and communication sciences. Has colleges based on topics such as law, translation and interpretation, and engineering. Research is organized into economics and business, experimental sciences and health, law.
Ponce School of Medicine and Health Sciences; Puerto Rico; USA
Ponce School of Medicine & Health Sciences
Ponce School of Medicine and Health Sciences
A private university in Puerto Rico which offers graduate degrees in medicine, clinical psychology, biomedical sciences, medical sciences and public health. The Ponce Research Institute, housed at the university, does research in basic, behavioral, public health and clinical sciences, focusing on areas such as non-communicable diseases, health disparities, and community health and outreach.
Pondicherry University; Puducherry; India
A public university in India that has several schools focused on different areas of study, including but not limited to: management, technology, physical and chemical sciences, social sciences and international studies. The university houses a Central Instrumentation Facility that provides three services: the Mechanical Shop, the Glass blowing Shop and the Electrical Shop, all of which provide support in the repair and servicing of scientific equipment as well as the fabrication of components for experimental setups.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis.
University of Wollongong Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Molecular Horizons members are supported by laboratories and facilities. These include Laser Chemistry Laboratory, NMR Facility, Mass Spectrometry Facility, X-Ray Laboratory, Spectroscopy facilities. Other Major Equipment and facilities are available at Illawarra Health and Medical Research Institute.
College of the Holy and Undivided Trinity of Queen Elizabeth near Dublin
Trinity College Dublin - University of Dublin
A public university, which is a part of the University of Dublin, and contains three main academic disciplines: Arts, Humanities and Social Sciences; Engineering, Mathematics and Sciences; and Health Sciences. The institution offers degrees at the undergraduate and graduate level.
Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data.
Software that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs.
Pontifical Catholic University of Argentina School of Medical Sciences; Buenos Aires; Argentina
Pontifical Catholic University of Argentina School of Medical Sciences
Pontificia Universidad Cat�lica Argentina Facultad de Ciencias M�dicas
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. Private medical school in Buenos Aires that offers degree programs in the medical sciences. Resource is in Spanish.
MicroArray Classification BEnchmarking Tool on Host server
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. Web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset.
Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers.
A software tool for the proteomics community that may help improving analysis of proteomic experimental data.
Simulation Experiment Description Markup Language
An XML-based format for encoding simulation experiments. SED-ML allows to define the models to use, the experimental tasks to run and which results to produce.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An online atlas of neural function, maintained by Cambridge University and the MRC Cognition and Brain Sciences Unit (CBSU).
A software tool to generate simulated single-end or paired-end RNA-Seq reads. # It allows users to randomly assign expression levels of transcripts and generate simulated single-end or paired-end RNA-Seq reads. # It is able to generate RNA-Seq reads that have a specified positional bias profile. # It is able to simulate random read errors from sequencing platforms. # The simulator consists of a few simple Python scripts. All scripts are command line driven, allowing users to invoke and design more functions.
An R software package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines.
Software implementing a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets.
A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.
Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.
A non-profit patient organization dedicated to educate, support and advocate for home dialysis. Their main focus is advocating and supporting those on home hemodialysis and peritoneal dialysis modalities. Membership is free and inclusive of dialyzors, care partners, nurses, nephrologists, renal professionals and others.
Progress and Health Foundation; Seville; Spain
Fundacion Publica Andaluza Progreso y Salud
An organization that supports the public health system in Andalusia, Spain through three main activities: research and innovation in health, technologies line information and communication, and training and evaluation of professional skills. It also provides management support to the Health Quality Agency of Andalusia, which is the driving entity of the Andalusian Quality Model. Resource is in Spanish.
Pusan National University; Busan; South Korea
A national public university in Busan, South Korea which offers degree programs in a wide variety of disciplines such as nursing, education, nano technologies and the creative arts at both the undergraduate and graduate level.
Public university in Ontario, Canada that offers degree programs in the social sciences and engineering at both the undergraduate, graduate, postdoctorate and professional level. The university operates six research centers that focus on disciplines such as neuroscience, computing, human mobility and Southern African research.
Queens University Belfast; Ireland; United Kingdom
A public research university in Belfast, Ireland that offers degree programs in a wide variety of disciplines at the undergraduate, graduate and postgraduate level.
University of Illinois College of Pharmacy
A public pharmacy school, part of the University of Illinois. It offers a four-year professional degree program that leads to the PharmD, the highest level of professional education in pharmacy. The college also offers programs leading to six master's degrees and four doctorate degrees, covering a spectrum of research areas within the pharmaceutical sciences.
CNTools - Convert segment data into a region by sample matrix to allow for other high level computational analyses
Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.
THIS RESOURCE HAS BEEN DISCONTINUED, documented April 15, 2016. New GEArray Expression Analysis Suite 2.0 was released at Dec 21, 2006, please read Release Notices for details. SABiosciences' GEArray Analysis Suite uses advanced Java functionality. In order to experience full functionality of this Portal, the following free programs and upgrades for PC and Macs should be properly installed. PC Environment Downloads Browser compatibility is not an issue on Windows systems, so all operating systems running Windows 98 and above and either Internet explorer or Netscape should be fine. Java 1.4.1 or above is required--this should download automatically upon the first entry into the Portal. If this does not happen, Java 1.5 is available for download from the following URL: Java 1.5 Mac Environment Downloads Browser compatibility is an issue, and Mac Operating Systems prior to Panther are not able to fully take advantage of this Portal's functionality. These programs need to be downloaded and installed in a specific order as follows: Panther 10.3.5 (Operating System), Safari 1.2 (Compatible Internet Browser) and Java 1.4.2 (Java environment). Abstract. INTRODUCTION: Toll-like receptors (TLR) comprehend an emerging family of receptors that recognize pathogen-associated molecular patterns and promote the activation of leukocytes. Surgical trauma and ischemia-reperfusion injury are likely to provide exposure to endogenous ligands for TLR in virtually all kidney transplant recipients. METHODS: Macroarray (GEArray OHS-018.2 Series-Superarray) analyses of 128 genes involved in TLR signaling pathway were performed in nephrectomy samples of patients with chronic allograft nephropathy (CAN) and acute rejection (AR, vascular and non vascular). The analysis of each membrane was performed by GEArray Expression Analysis Suite 2.0. RESULTS: Macroarray profile identified a gene expression signature that could discriminate CAN and AR. Three genes were significantly expressed between CAN and vascular AR: Pellino 2; IL 8 and UBE2V1. In relation to vascular and non-vascular AR, there were only two genes with statistical significance: IL-6 and IRAK-3. CONCLUSION: Vascular and non-vascular AR and CAN showed different expression of a few genes in TLR pathway. The analysis of nephrectomy showed that activation of TLR pathway is present in AR and CAN. Sponsor. This work was supported by the inconditional grant from Fundao de Amparo a Pesquisa do Estado de So Paulo (FAPESP, 04/08311-6), from Conselho Nacional de Pesquisa e Desenvolvimento (CNPq) and from Fundao Osvaldo Ramos.
SeqMan Pro - Software for Contig Assembly and Analysis Including SNP Discovery Coverage Evaluation and Project Annotation
Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen.
National University of Singapore, Computational Bioengineering Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Computational Bioengineering Laboratory in the Division of Bioengineering at the National University of Singapore has expertise in mathematical modeling, software and algorithm development, numerical techniques such as finite element analysis, computer simulation and visualization, signal and image processing plus an understanding of the biological systems that drive our efforts. The following are the main themes underlying the Computational Bioengineering Laboratory projects: - Computational Biology - Computational Physiology - Biosignal & Bioimage Processing - Integrated Physiology & the Physiome Project
Proteomics and Human Proteome: From Bench to Bedside
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. This website contains lecture videos from the events and discussions of the SEProt congress meeting, the theme of which is Human proteome. From Bench to Bedside. Sponsors: These videos are supported by the University of Navarra.
Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results.
An open-source stand-alone computer program for visually comparing 2D gel images.
cn.farms - factor analysis for copy number estimation
Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff.
Laboratory information management system for proteomics. The software works with 2DPAGE-based proteomics workflow.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software suite for the assembly and analysis of Sanger sequencing data within the SeqMan Pro application. The software's functions include: assembling reads into groups based on sequence names, trimming vector and poor quality data, restoration of sequence ends and designing of sequence primers.
Software package for clonality testing providing statistical tests for clonality versus independence of tumors from the same patient based on their loss of heterozygosity (LOH) or genomewide copy number profiles.
Platform-independent array copy number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes.
Software for DNA Copy Number and loss of heterozygosity (LOH) analysis designed with high-throughput diagnostic laboratories in mind.
Dataset of the spike and laser timestamps from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings." The code will analyze spike trains around laser pulses to determine if a cell is significantly activated by the laser, and therefore expresses an excitatory opsin, such as channelrhodopsin-2. It returns an excel sheet that simply identifies the activated cells.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for a Lab Information Management System (LIMS) for high-throughput screening of small molecule and RNAi biological assays.
Zebrafish Neuroscience Research Consortium
Zebrafish Neuroscience Research Consortium (ZNRC)
A group of scientists who collaborate and promote zebrafish neuroscience research. The consortium has opportunities for networking, scholarly publications and zebrafish-related symposia and conferences. The consortium is a supporter of the Zebrafish Neurophenome Project (ZNP), an initiative for a database of zebrafish behavioral and physiological data in an online, open source format.
A basic fastq compressor, designed primarily for high performance.
Penn Cell and Developmental Biology Zebrafish Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Core facility that provides the following services: Maintenance of transgenic or mutant zebrafish lines, Zebrafish research training, Zebrafish embryo supply service. The CDB Zebrafish Core facility provides services and training to Penn faculty interested in using the zebrafish model system as part of their research program.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Core facility that provides the following services: Clinical data management, Project operations and compliance support, Custom database application development, Research technology support, Proposal development service. The Clinical Research Computing Unit (CRCU) is a designated core research facility within Penn Medicine, specializing in clinical research informatics (CRI) collaboration and research IT services with a growing number of clinical and translational research investigators at Penn. The CRCU currently supports 58 funded projects, valued at more than $336 M (total costs, all years) to Penn. Although situated within the Center for Clinical Epidemiology and Biostatistics (CCEB), the CRCU supports an increasing volume of its research portfolio led by PIs external to the CCEB. This year the total value of these research programs was $ 243 M, so that the proportion attributable to PIs external to CCEB exceeded 70% ($243 M / $336 M = 72%). Established originally on April 1, 1997, within the Biostatistics Unit of the Center for Clinical Epidemiology and Biostatistics (CCEB) at the University of Pennsylvania School of Medicine, the primary foci were to develop a research computing base for the new program in Biostatistics, as well as to create the capacity and resources to compete successfully for data coordinating centers (DCCs) of federally funded, large-scale, multi center clinical trials, and epidemiological studies. These technology resources also permitted CCEB faculty and staff to provide essential collaborative CRI support for Penn investigators throughout the wide array of basic science and clinical departments, centers, and institutes, thus enhancing their likelihood of funding success. On July 1, 2002, the CRCU restructured its operations and expanded its focus in response to the overall research project growth within the CCEB and the University. The CRCU, as an organizational unit, moved from within the Biostatistics Unit of the CCEB to a CCEB-wide organizational service center for both the Biostatistics and Clinical Epidemiology units. With this restructuring, the CRCU now has two faculty co-directors; one representing each of the CCEB units. The faculty directors ensure that the overall strategy and goals of the service center are aligned with the overall goals of the CCEB, as well as Penn Medicine. In 2005, the leadership model was expanded with the appointment of four (4) Directors of Operations, each of whom report directly to the faculty directors and manage a specialty sub-unit of staff to more effectively coordinate the evolving complexities of the more than 58 sponsored project teams. The original two (2) Senior Directors now focus their leadership efforts on technology infrastructure, new methodologies, special projects and fostering strategic collaborations with other Penn departments, commercial vendors, and other institutions. The University of Pennsylvania aspires to excellence in all domains. The CRCU embraces these ideals, as it partners with faculty and staff to conduct biomedical, behavioral, clinical and translational biomedical research at the highest levels of excellence. Advances in healthcare and improvements in quality of life through research depend on thoughtful science and uncompromising integrity in the collection and handling of information. The CRCU excels in the support of biomedical and clinical research by providing expertise in all facets of research information management, and by understanding the regulatory and cultural environments in which research is conducted. The CRCU fosters collaborative relationships with investigators in the CCEB, other Centers and Institutes throughout the School of Medicine, and across the University, to take an active partnership role in meeting their research goals. The CRCU is committed to continuous improvement in the expertise offered and the services provided, through an emphasis on education and training for staff and through the use of leading technologies and creative solutions.
A developer tool to provide batch processing capability for pipelines. Users input data into a input table and run analysis with it. It is used to power CamBA and Brainwaver User interfaces.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software which converts DICOM images to NIfTI format.
Penn Community Outreach Using Health System Informatics Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Informatics core for the purpose of promoting clinical research by collecting data from the Penn Health System.
A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.
A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.
A collection of both commercial and noncommercial software products which includes: Mascot Distiller, Mascot Parser, and Mascot Server. Mascot Distiller is commercial and provides a single interface to process raw data into de-isotoped peak lists. This tool can also be used for the easy distribution of search and quantitative results to colleagues. The non-commercial Mascot Parser software provides an API (Application Programmer Interface) that makes it easier to access search results written in C++, Java, Python and Perl. Mascot Server is non-commercial, and is a collection of peptide mass fingerprints as well as a MS/MS database. A selection of popular sequence databases are available online and include SwissProt, NCBInr, and the EST divisions of EMBL. This server is best used for evaluating and searching for smaller data sets.
Research Network and Patient Registry Inventory Ontology
Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries
An ontology for DICOM as used in the SeDI project.
Ontology for representing events, time, and their relationships.
An ontology for standardized, systematic description of effects, consequences and mechanisms of variations.
Open source software that integrates various forms of microarray data from diverse annotation and primary data sources. This software provides a programmatic framework (API set) that will be used for collaborative development and deploys an easy to maintain client-server architecture.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An anatomy ontology covering the vertebrate skeletal system that integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system.
Commercial antibody vendor that provides products that utilize in-vitro cloning technology to create rabbit clonal and monospecific clonal antibodies. This company produces antibodies which correspond strictly to the conserved linear epitope of the antigen molecule.
An open source graphic viewer. Some features include batch conversion, paint options, basic editing and several supported file formats. It is compatible with Windows 9x, ME, NT, 2000, XP, 2003 , 2008, Vista, Windows 7, Windows 8, and Windows 10.
A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Software for pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets. It has the ability to quickly analyze sequence data for DNA methylation. This software integrates customized scripting and existing utilities tools that work on both paired end and single end data.
A data analysis pipeline for the Methyl-MAPS method.
annotare: a tool for annotating high-throughput biomedical investigations and resulting data
A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations.
Software R package to test association between methylation at CpG sites across genome and phenotype of interest, adjusting for any relevant covariates. Can perform standard analyses of large datasets without need to manually input data. Can handle mixed effects models with chip or batch entering model as random intercept. Includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.
A fully automatic array image analysis software which can process single or multiple array images. Koadarray automatically finds the spot locations within each image and quantifies the spot intensity data. It can be used in conjunction with radioactive applications, macroarray applications, fluorescent microarray image analysis and fluorescent microplate images.
Alternative Splicing Annotation Project II Database
Alternative Splicing Annotation Project II
THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. An expanded version of the Alternative Splicing Annotation Project (ASAP) database with a new interface and integration of comparative features using UCSC BLASTZ multiple alignments. It supports 9 vertebrate species, 4 insects, and nematodes, and provides with extensive alternative splicing analysis and their splicing variants. As for human alternative splicing data, newly added EST libraries were classified and included into previous tissue and cancer classification, and lists of tissue and cancer (normal) specific alternatively spliced genes are re-calculated and updated. They have created a novel orthologous exon and intron databases and their splice variants based on multiple alignment among several species. These orthologous exon and intron database can give more comprehensive homologous gene information than protein similarity based method. Furthermore, splice junction and exon identity among species can be valuable resources to elucidate species-specific genes. ASAP II database can be easily integrated with pygr (unpublished, the Python Graph Database Framework for Bioinformatics) and its powerful features such as graph query, multi-genome alignment query and etc. ASAP II can be searched by several different criteria such as gene symbol, gene name and ID (UniGene, GenBank etc.). The web interface provides 7 different kinds of views: (I) user query, UniGene annotation, orthologous genes and genome browsers; (II) genome alignment; (III) exons and orthologous exons; (IV) introns and orthologous introns; (V) alternative splicing; (IV) isoform and protein sequences; (VII) tissue and cancer vs. normal specificity. ASAP II shows genome alignments of isoforms, exons, and introns in UCSC-like genome browser. All alternative splicing relationships with supporting evidence information, types of alternative splicing patterns, and inclusion rate for skipped exons are listed in separate tables. Users can also search human data for tissue- and cancer-specific splice forms at the bottom of the gene summary page. The p-values for tissue-specificity as log-odds (LOD) scores, and highlight the results for LOD >= 3 and at least 3 EST sequences are all also reported.
Social Phobia/Social Anxiety Association
This resource provides information on: -- a definition of social anxiety disorder (social phobia) -- practical examples of what life is like for people with social phobia, -- an invitation to join a free moderated mailing list edited specifically for people with social phobia (social anxiety disorder)
Software tools for processing RAD Sequencing Illumina reads. Version 1.0 is a pipeline for transforming Illumina reads into candidate genetic markers.
Igor Pro - Technical graphing and data analysis
Software used for visualizing and graphing data, image processing, and programming. It is designed for use by scientists and engineers and supports large data sets, evenly spaced data, and various data import formats. The software includes a suite of image processing operations for image filtering, manipulation, and quantification and is completely programmable.
A medical technology company whose research and products revolve around peripheral nerve repair.
Georgia Institute of Technology Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. University affiliated laboratory which is composed of two main departments, the Center for Organic Photonics and Electronics (COPE) and the Magnetic Resonance Laboratory. COPE creates flexible organic photonic and electronic materials and devices. The Magnetic Resonance Laboratory performs MRI and magnetic bore.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 9, 2017.
A stem cell bank in Malaysia which provides and carries out long-term human stem cells and tissue cryopreservation and research. The general public can use their biobanking services for personal use.
Defense Advanced Research Projects Agency
A military affiliated research institute which focuses on funding and approving new and ongoing programs while ensuring a balanced investment portfolio. This organization is mainly concerned with making investments in technologies that can be used for national security.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016.
Dutch Ministry of Education Culture and Science
Dutch Ministry responsible for education, culture, science, research, gender equality and communications.This organization also strives to make a good work environment for teachers, artists and researchers.
A federal grant-making agency supporting research, preservation, public programs, and education in the humanities.
Center for Computational Biology at UCLA
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Center focused on the development of computational biological atlases of different populations, subjects, modalities, and spatio-temporal scales with 3 types of resources: (1) Stand-alone computational software tools (image and volume processing, analysis, visualization, graphical workflow environments). (2) Infrastructure Resources (Databases, computational Grid, services). (3) Web-services (web-accessible resources for processing, validation and exploration of multimodal/multichannel data including clinical data, imaging data, genetics data and phenotypic data). The CCB develops novel mathematical, computational, and engineering approaches to map biological form and function in health and disease. CCB computational tools integrate neuroimaging, genetic, clinical, and other relevant data to enable the detailed exploration of distinct spatial and temporal biological characteristics. Generalizable mathematical approaches are developed and deployed using Grid computing to create practical biological atlases that describe spatiotemporal change in biological systems. The efforts of CCB make possible discovery-oriented science and the accumulation of new biological knowledge. The Center has been divided into cores organized as follows: - Core 1 is focused on mathematical and computational research. Core 2 is involved in the development of tools to be used by Core 3. Core 3 is composed of the driving biological projects; Mapping Genomic Function, Mapping Biological Structure, and Mapping Brain Phenotype. - Cores 4 - 7 provide the infrastructure for joint structure within the Center as well as the development of new approaches and procedures to augment the research and development of Cores 1-3. These cores are: (4)Infrastructure and Resources, (5) Education and Training, (6) Dissemination, and (7) Administration and Management. The main focus of the CCB is on the brain, and specifically on neuroimaging. This area has a long tradition of sophisticated mathematical and computational techniques. Nevertheless, new developments in related areas of mathematics and computational science have emerged in recent years, some from related application areas such as Computer Graphics, Computer Vision, and Image Processing, as well as from Computational Mathematics and the Computational Sciences. We are confident that many of these ideas can be applied beneficially to neuroimaging.
National Health Research Institutes; Taipei; Taiwan
Nonprofit, government-funded research organization dedicated to the enhancement of medical research and the improvement of health care in Taiwan. Research interests include both aspects of basic biomedical sciences and specific diseases such as cancer, mental disorders and infectious diseases. The institute is meant to provide direction to national science and technology development in health and medical care, educate young scientists and physicians, establish an objective and fair system for research, and promoting domestic and international cooperation.
National Institute for Basic Biology; Okazaki; Japan
An organization which promotes studies in biology by conducting research itself as well as in cooperation with other research institutions. This organization covers a wide variety of biological fields, such as cell biology, developmental biology, neurobiology, evolutionary biology and theoretical biology. NIBB also offers graduate education programs through the Graduate University for Advanced Studies (SOKENDAI). This program provides five-year Doctoral courses for university graduates and a three-year senior Doctoral course for those with a Master's degree already.
Reference-free ddRADseq analysis software tools. The pipeline script generates reference-sorted, indexed BAM from uniqued reads from radtag sequencing lanes.
Photo-editing software including editing features, fast brushes, creative tools and color selection that will help turn snapshots into beautiful, gallery-worthy images.
University of Utah School of Medicine; Utah; USA
An university in Utah which provides opportunities in teaching, research and clinical experience for developing physicians. This organization provides MD degrees, physician training, residency, fellowship specialty training and degrees in public health or research.
An academic organization in Burlington, Vermont. This university provides undergraduate, graduate and medical degrees.
An undergraduate and postgraduate university which is located in Zaragoza, Spain.
University of Zurich; Zurich; Switzerland
University located in Zürich, Switzerland was founded in 1833. Has faculties in Philosophy, Human Medicine, Economic Sciences, Law, Mathematics and Natural Sciences, Theology and Veterinary Medicine. Offers the widest range of subjects and courses of any Swiss higher education institution. As of October 2018, 23 Nobel laureates and 1 Turing Award winner have been affiliated with University of Zurich as alumni, faculty or researchers.
Washington University in St. Louis; Missouri; USA
Private research university in Greater St. Louis with its main campus mostly in unincorporated St. Louis County, Missouri and Clayton, Missouri.
An university in China which offers undergraduate, master's, and doctorate degrees. This organization has a total of 20 different programs.
A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks.
A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants.
A multi-platform NMR processing application.
A collection of cloud-scale DNA sequence analysis tools.
2-D chemical structure drawing software program.
A time efficient read alignment tool built on the top of BWA.
ARACHNE: a whole-genome shotgun assembler
A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.
Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com.
HudsonAlpha Institute for Biotechnology Genomics Services Lab
A lab that offers genetic research tools such as RNA sequencing and a variety of arrays.
A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.
Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance.
A bioinformatic tool for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays.
Software using a realignment-based SNP calling method for 454 and Ion Torrent sequencing data.
Software package to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.
pvac: PCA-based gene filtering for Affymetrix arrays
Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).
Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.
Mississippi State University; Mississippi; USA
Public university in Mississippi with land, sea and space grants that offers degree programs in areas such as agriculture and applied sciences at the undergraduate and graduate levels.
A public university in Ohio with land, sea and space grants that offers degree programs and research at the undergraduate and graduate level.
A public research university in Poland. The school offers degree programs in business, humanities, chemistry, global studies and more at the undergraduate, graduate and doctoral level.
University of Puerto Rico Medical Mycology Lab
A lab facility associated with the University of Puerto Rico. The lab provides services like air quality analysis as well as instruments like microscopes and spore traps.
A lab facility at Vanderbilt University Medical Center that provides histological sample preparation.
An antibody supplier that also provides diagnostic components, assay reagents and contract biologic RandD and manufacturing services. The company focuses on providing services to help clients develop, manufacture and commercialize their products.
A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.
A private liberal arts college that offers degrees in social sciences, humanities and natural sciences at the undergraduate level.
London School of Economics and Political Science; London; United Kingdom
London School of Economics and Political Science
A public research university in London with an emphasis in social science degree programs such as law, mathematics, public affairs and international history. The university offers degrees at the undergraduate, graduate and doctoral level.
A public university in Israel with degree programs in areas such as arts, engineering, humanities, the law and medicine at the undergraduate and graduate level. The university has affiliated but independent schools that focus on specific areas such as music, environmental studies, dentistry, social work, education and neuroscience.
A national university in China with degree programs that include engineering, economics, humanities, law and art at the undergraduate, graduate and doctoral level.
A private, historically black university that offers degree programs at the undergraduate, graduate, doctoral and professional levels. The university has programs that include veterinarian studies, allied health, nursing, education
University of Southern Queensland; Queensland; Australia
A public university in Australia that offers degree programs in business, law and education as well as health, engineering and the sciences at the undergraduate level. The university also does research at three research institutes and seven research centers which focus on a wide range of business, agricultural, scientific, environmental, and technological issues.
University of Texas at Dallas; Texas; USA
A public research university in Texas that offers degree programs in engineering, business, political science and the natural sciences at the undergraduate and graduate levels. The university also houses research that focuses on space science, bioengineering, cybersecurity, nanotechnology, and behavioral and brain sciences.
A data compressor for files. This software is freely available, patent free, and is organized as a library with a programming interface.
A supplier of various biochemical products for research in pharmacy and biotechnology as well as the specialty ingredients market. Examples of products include active pharmaceutical ingredients, stem cell therapies, drinking water sanitizers and agriculture services and products.
Software for detecting copy number variations from next generation sequencing data. Used to identify regions of discrete copy number changes while simultaneously accounting for effects of multiple confounders.
University of Massachusetts; Massachusetts; USA
A five-campus public university system in Massachusetts. The system includes four universities, a medical school, and a satellite campus.
A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.
A public research university in Sydney, Australia that offers a wide range of degree programs at the undergraduate and graduate level.
An antibody supplier that provides a range of human antigens, serum and plasma, and cell culture reagents.
The Environmental Determinants of Diabetes in the Young
International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes.
Trans-Institute Angiogenesis Research Program
Trans-Institute Angiogenesis Research Program (TARP)
Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests.
LiGraph - Convert a sugar graph to ASCII IUPAC sugar nomenclature or as a graph
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Web service that generates schematic drawings of oligosaccharides which are often used to display glycan structure.
Search for carbohydrate containing PDB entries by criteria like species or the compound / classification terms. You can choose predefined, frequent terms from the pull-down-menus or enter your own queries manually.
is-rSNP: in silico regulatory SNP detection
Software tool that predicts whether a single nucleotide polymorphism (SNP) is a regulatory SNP (rSNP). For a given SNP, and using a statistical framework, it can successfully predict the set of transcription factors (TFs) for which binding is affected. The algorithm provides the statistical power to scan large numbers of SNPs, making it suitable to use to screen all associated SNPs output by a typical genome-wide association studies (GWAS).
Illuminus: the genotype calling algorithm
A fast and accurate algorithm for assigning single nucleotide polymorphism (SNP) genotypes to microarray data from the Illumina BeadArray technology.
QUALIFIER - Quality Control of Gated Flow Cytometry Experiments
Software that provides quality control and quality assessment tools for gated flow cytometry data.
Web accessible database of data extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in Protein Data Bank . Website supports query types including searches by chemical structure, substructure and similarity, protein sequence, ligand and protein names, affinity ranges and molecular weight . Data sets generated by BindingDB queries can be downloaded in form of annotated SDfiles for further analysis, or used as basis for virtual screening of compound database uploaded by user. Data are linked to structural data in PDB via PDB IDs and chemical and sequence searches, and to literature in PubMed via PubMed IDs .
World Health Organization: The Global Health Library
The Global Health Library assembles health data, readable in many languages. The GHL aims to: * point to reliable information collections and systems, in which different users and user groups (ministries of health, policy makers, health workers, information providers, patients and their families, general public) can focus on the knowledge that best meets their health information needs; * act as a facilitator enabling access to information contents produced by numerous key providers - be they commercial companies, government institutions, civil society, not-for-profit organizations, and regional or international bodies; and * strive for universality, with focus on developing countries, and will act as a resource locator for print materials essential to areas that do not have access to electronic content.
Wiley Interdisciplinary Reviews series combines features of encyclopedic reference works and review journals in innovative online format. They are designed to promote cross-disciplinary research ethos while maintaining the highest scientific and presentational standards, but should be viewed first and foremost as evolving online databases of cutting-edge reviews.
FunctSNP - Linking SNPs to functional knowledge
An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge.
Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Comprehensive database of Protein-Protein and Protein-Small molecules interaction, consisting of more than 320,000 interactions captured from more than 1500 abstracts, approximately 1600 published journals and more than 60,000 references. The strength of NetPro lies in the complete manual curation of literature. It covers several entities other than proteins as interacting partners, like RNA, DNA, processes, etc. with well defined, exhaustive interaction terms. NetPro has received several accolades for the quality and quantity of data it contains. It has become an important resource for target identification, validation and pathway research and has subscribers from all over the globe including 3 of the top 5 pharmas.
Projection of Protein Networks across Species
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2022. System to annotate human genes based on gene interactions in model organisms. Data are transferred from amenable species like yeast, fly, and worm through homology, and functional gene annotation is facilitated through framework of large database. Used to perform interolog analysis by projection of model organism interaction data onto homologous human proteins, and thus serves as an accelerator for analysis of uncharacterized human proteins.
Protein-Protein Interactions Table for Human herpesvirus 1
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The scope of the project includes molecular information pertaining to oral pathogens, bacterial and viral. The website contains a table of protein-protein interactions for human herpesvirus 1. It is operated for the U.S. Department of Energy's National Nuclear Security Administration.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2,2022. It is a repository of interactions found by Entangle and compiled into various tables for use by the RNA community. This data does not have a user interface, but data can be accessed in tables. It contains raw Excel/Access Databases and data processed into useful Figures for people who don't want to wade through the primary data. At present it contains informations from 42 PDBs.
flowStats - Statistical methods for the analysis of flow cytometry data
Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.
dbSTS: database of Sequence Tagged Sites
NCBI dbSTS: database of Sequence Tagged Sites
THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences.
BD Biosciences | FACSCalibur Flow Cytometry System
Automated benchtop flow cytometry system. It allows measuring four fluorochrome-conjugates, forward and side scatter., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Portal as data resource, map repository, and GIS service provider for federally-funded scientists conducting research in the Arctic and Antarctic. The PGC holds an extensive collection of satellite imagery and aerial photography at varying resolutions.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Database of processed seismic reflection / refraction data providing access to metadata, SEG-Y files, navigation files, seismic profile images, processing histories and more. The main features of the web site include a geographic search engine using Google Plugins, a metadata search engine, and metadata pages for the various seismic programs. Metadata are uploaded into mySQL, a public-domain SQL server, and then PHP scripts query the metadata and directories, creating web pages, displaying images, and providing ftp links.
Blog about random findings from data written by Leon French.
Software which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed.
Input either normalized MNI coordinates from a 3D image, or input real world XYZ matrix coordinates, and this code will convert coordinates of one type to the other.
Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.
rTANDEM - Interfaces the tandem protein identification algorithm in R
An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.
flowFlowJo - Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm
A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.
Discussion forum on licensing issues in software and data. All are invited to participate or join the project and contribute. A listing of software licenses are available.
Local Binary Pattern Analysis Tools for MR Brain Images
The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology.
OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images.
R software package for transcription factor (TF) target gene prediction based on ChIP-seq data. Version 0.4 contains code to compute FDR-corrected q-values via permutations of the peak-to-gene assignments (ClosestGene only).
Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories.
NICHD Developmental Neuroethology - Laboratory of Comparative Ethology
Developmental Neuroethology - Laboratory of Comparative Ethology
NICHD Laboratory of Comparative Ethology
Understanding the mechanisms underlying the expression and perception of auditory communication in nonhuman primates provides important insights for understanding the neural systems that mediate nonverbal auditory communication in humans. Our research is devoted to understanding the changes in vocal behavior that are associated with maturation and social experience under normative conditions, and to investigating neural systems to define their roles in auditory communication. The anterior cingulate gyrus, in the frontal cerebral cortex, is an essential neural system for the expression of the primate isolation call, a structural and functional equivalent of the cry sounds of humans. Bilateral removal of this structure in adult squirrel monkeys resulted in a long-lasting inability to emit isolation calls. Partial recovery, often over many weeks, initially took the form of production of short, faint and uninflected versions of the typical isolation call. Humans suffering infarct damage to this region likewise show an initial recovery in the form of short, faint, monosyllabic sounds, suggesting that the anterior cingulate gyrus of nonhuman primates is the evolutionary precursor of a neural structure involved in human affective expression and speech. Our working model of isolation call production is that the anterior cingulate gyrus is the site where the command to produce this vocalization is initiated. Since the anterior cingulate region also has reciprocal connections with temporal lobe auditory cortex, a presumptive feedback pathway exists for registering commands to initiate vocalization with the temporal lobe cortex, which plays a major role in perceiving and decoding the acoustic details of species-specific vocalizations. At present, we do not know the role of the anterior cingulate gyrus in the production of infant vocalizations. However, we have found that neonatal removal of the amygdala, an important forebrain component of the limbic system, or portions of the inferotemporal gyrus, which sends projections to the amygdala, result in significant changes in the vocal behavior of infant rhesus macaques. Vocal development is a dynamic process, and a pattern shared by several nonhuman primates has emerged regarding the nature of this process. Infants are highly vocal during periods of brief separation from their caregiver, and we take advantage of this to document the range of vocalizations produced by infants of different ages. In the neonatal period, infants of 3 species of nonhuman primate (rhesus macaque, squirrel monkey and common marmoset) all produce sounds that vary widely in their acoustic structure. Many of these bear a striking similarity to sounds used in a variety of social settings by adults, suggesting that neural systems responsible for generating adult vocalizations are already in place during early infancy. As infants mature, their vocal behavior during brief periods of social separation becomes much more stereotyped. It isn't until much later in development, as individuals engage in a variety of social interactions with peers and adults, that the sounds expressed in early infancy begin to re-appear in adult contexts. The role of individual experience during development is currently being explored to determine the mechanisms leading to the acquisition of adult vocal skills.
PSCBS: Analysis of Parent-Specific DNA Copy Numbers
Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
A resource for online accredited courses in a wide variety of areas, including accounting, animal care, beauty, building and construction, business, education, design and writing. This resource is based in Australia.
This project is meant for planning the NITRC Grantee meetings. A website for organizing meetings for the Neuroimaging Informatics Tools and Resources Clearinghouse, to facilitate participants meeting one another, and promote discussion of common interests and collaboration.
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.
Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS.
Software for detecting artifacts and performing individual region-of-interest based statistical analysis of fMRI data and enables users of fMRI technology to produce more detailed, consistent and reliable results.
Scribe encodes papers to populate the BrainMap Database
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results.
Software toolbox for counting the frequency of K-tuple from sequencing datasets and calculate the dissimilarity.
Vervet (Chlorocebus aethiops sabaeus) probabilistic atlas that defines an anatomical space (template) with associated tissue and regional prior probability maps. The atlas was produced from whole head MRI of 10 normal adult animal subjects. The package consists of two atlases. The Biased directory contains the average template and probabilistic atlases for selected tissue classes constructed by registering the training population to one subject. The Unbiased directory contains the atlas constructed using unbiased estimation. The atlas is suitable for use in any segmentation tool using a probabilistic atlas, for example those in Slicer.
Free bookmarklet for Chrome, Firefox and Safari that allows you to instantly get article level metrics for any recent paper. Simply drag the button below to your bookmarks bar, navigate to a journal article page, and hit Altmetric it!
Service to monitor, search and measure conversations about your publications and those of your competitors captured by Altmetric including tweets, blog posts, news stories and other content that mention scholarly articles. Use the Explorer to deliver insights, track mentions and measure levels of attention over time.
Database platform that aggregates post-publication peer reviews and ratings. It also includes a large-scale bibliographic database and features free reference management tools.
Non-profit organization working towards developing an open platform for the collaborative evaluation of knowledge. It will combine sentence-level critique with community peer-review to provide commentary, references, and insight on top of news, blogs, scientific articles, books, terms of service, ballot initiatives, legislation and regulations, software code and more.
Protein complex Expansion using Protein-Protein intERaction networks
Protein complex Expansion using Protein-Protein intERactions
A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...).
Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).
Disorder Index: National Institute of Neurological Disorders and Stroke (NINDS)
Disorders index from the National Institute of Neurological Disorders and Stroke (NINDS)
National Institute of Neurological Disorders and Stroke Disorder Index
Reference disease data set of neurological diseases along with their definitions, etiology, treatment, prognosis, ongoing research, clinical trials information and publications. The Disorder Index includes synonyms and research topics. Navigation is by letter of the alphabet., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Resource that discusses MNI brain, and the difference between the MNI brain and the brain in the Talairach atlas. Approaches to converting MNI coordinates to Talairach coordinates and a few other methods for locating your activation are also presented.Matlab function that transforms MNI coordinates to Talaraich coordinates. The inverse function, tal2mni is also available.
OLINgui - Graphical user interface for OLIN
Software package providing a graphical user interface for the OLIN package.
Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures.
A job search resource for careers in neuroscience. The website connects members with employment opportunities, professional development resources and educational materials about career paths.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2022. A database of molecular imaging probes for various diseases, such as Parkinson's disease, dopamine disorder and prion disorders.
PsychoGenics, a leader in preclinical neurobiology and in the provision of CNS drug discovery solutions, works with pharmaceutical companies and not-for-profit organizations to validate targets and select compounds to advance into clinical trials. PsychoGenics transforms drug discovery by combining expertise in behavioral neurobiology with the power of bioinformatics in conjunction with proprietary, high-throughput behavioral testing platforms that rapidly screen compound libraries for CNS activity.
Matlab code for preprocessing gas chromatography mass spectrometry data.
Video tracking software that tracks and analyzes the behavior, movement, and activity of any animal.
ALS Association - Fighting Lou Gehrig's Disease
Amyotrophic Lateral Sclerosis Association
Established in 1985, The ALS Association is the only national non-profit organization fighting Lou Gehrig's Disease on every front. By leading the way in global research, providing assistance for people with ALS through a nationwide network of chapters, coordinating multidisciplinary care through certified clinical care centers, and fostering government partnerships, The Association builds hope and enhances quality of life while aggressively searching for new treatments and a cure. As the preeminent ALS organization, The Association leads the way in research, care services, public education, and public policy giving help and hope to those facing the disease. The Association's nationwide network of chapters provides comprehensive patient services and support to the ALS community. The mission of The ALS Association is to lead the fight to treat and cure ALS through global research and nationwide advocacy, while also empowering people with Lou Gehrig's Disease and their families to live fuller lives by providing them with compassionate care and support. The ALS Association has committed more than $58 million to find effective treatments and a cure for Lou Gehrig's Disease. Our global research effort has helped increase the number of scientists working on ALS, advanced new discoveries and treatments, and has shed light on the complex genetic and environmental factors involved in ALS. Diversity exemplifies The ALS Association's research philosophy. The Association spearheads investigator-initiated projects that originate from the minds of scientists. It also has ALS Association-initiated projects in which research ideas come from a small, blue ribbon committee of scientists who reach out with specific projects for designated scientists in the field. The ALS Association offers multi-year grants to established investigators, as well as one-year starter research awards. The Association is proud to administer The Milton Safenowitz Post-Doctoral Fellowship for ALS Research, which is the only post-doctoral fellowship for ALS research. In addition, The ALS Association's Sheila Essey Award, the premier ALS award, recognizes achievement in research. The ALS Association holds workshops each year that bring together scientists researching ALS and other neurodegenerative diseases to generate new research suggestions and fresh insight. In addition, our TREAT ALS (Transitional Research Advancing Therapy for ALS) initiative combines efficient new drug discovery with priorities set for existing drug candidates to accelerate clinical testing of compounds with promise for the disease. Our Clinical Management Research Program focuses on managing the care of people with ALS in such areas as nutrition, respiration, mobility and psychosocial needs. Since 1998, The Association has funded 21 clinical management research projects representing a total commitment of $750,000. The Association produces a series of manuals and videos as well as a DVD, called Living with ALS, that educate patients about all aspects of the disease.
OntoMorph is a tab plugin for Protege-OWL 3 that allows a user to mark-up portions of a Neurolucida neuron morphology with OWL instances. A user loads a Neurolucida morphology file, either from their hard drive or from an arbitrary URL, into an interface that allows them to zoom, rotate, and translate the morphology. The interface allows them to select points on the morphology to indicate points, segments, or subtrees of the morphology they wish to assign to an OWL instance. After this selection has been made, OntoMorph saves the selection to the currently active OWL instance in the ontology that is currently loaded into Protege. No modifications are made to the Neurolucida file itself. As a result, an association is created between that portion of the morphology and the OWL instance, such that selecting the OWL instance allows retrieval of the portion. Upon retrieval, the morphology portion can be highlighted, so the user can keep track of what pieces each instance refer to.
Algorithm for testing significance of clustering in RNA-seq data.
International Consortium for Brain Mapping
ICBM - International Consortium for Brain Mapping
International Consortium for Brain Mapping (ICBM)
Probabilistic reference system for human brain, including tools to establish this reference system for structural and functional anatomy on both macroscopic (in vivo) and microscopic (post mortem) levels. Project has expanded neuroinformatics tools for data sharing and created Conforming Site System that allows laboratories worldwide to contribute data to evolving atlas. Through implementation of ICBM data sharing policy space, they are fostering data exchange while still providing for scientific credit assignment and subject confidentiality.ICBM atlas collection consists of ICBM Template, tool developed to provide reference that includes both set of coordinates and associated anatomical labels; the ICBM 452 T1 atlas, average of T1-weighted MRIs of normal young adult brains, ICBM probabilistic atlases, and Cytoarchitectonic Atlas. ICBM Subject Database is web-based database infrastructure that simplifies image dataset collection, organization and dissemination. Authorized users may view representations of data and form collections of datasets that can be downloaded or fed directly into Pipeline environment for distributed processing and analysis.
Private, non-profit institution dedicated to utilizing knowledge in science, engineering, technology and health to improve government decision making and public policy as well as increase public education and understanding. The council collects, analyzes and shares information and knowledge through activities such as consensus studies, meetings and workshops, and program and research management.
National Spasmodic Dysphonia Association
The mission of the National Spasmodic Dysphonia Association is to advance medical research into the causes of and treatments for spasmodic dysphonia, promote physician and public awareness of the disorder, and provide support to those affected by spasmodic dysphonia.
Software automated coordinate based system to retrieve brain labels from the 1988 Talairach Atlas. Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach Atlas.
Software to plot primary analysis quality control metrics to assess potential SMRTcell loading problems.
Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard.
A web system, which could search and display to current CAGE library information in CAGE Database.
Data analysis service that predicts tyrosine sulfation sites in protein sequences.
Rdisop - Decomposition of Isotopic Patterns
Rdisop: Decomposition of Isotopic Patterns
Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.
Software Python library for reading and writing PacBio data files.
GeneExpressionSignature - Gene Expression Signature based Similarity Metric
An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.
RegenBase - repairing the injured nervous system
Information framework and knowledge base to facilitate research about nervous system regeneration. It includes minimal information standards, an ontology that is linked to other ontologies, and a knowledge base built with a triple store and a relational database.
sybil - Efficient Constrained Based Modelling in R
sybil: sybil - Efficient Constrained Based Modelling in R
A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.
A software package for creating, merging, and querying multi-string BWTs.
A series of programs for determining the free metal concentration in the presence of chelators or total metal given a desired free concentration.
Laboratory modules designed for high school students covering sea urchin embryology including fertilization and development.
A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization
Genome BioInformatics Research Lab - gff2ps
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.
Reprever: resolving low-copy duplicated sequences using template drive
Software that identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon for any genomic regions that are increased in copy number.
A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.
Search engine for Life scientists that ranks reagents by the amount of data available, such as publications, reviews, characterization images and tested applications. It displays reagents such as antibodies, proteins, ELISA kits and biomolecules. Its proprietary search algorithm is unique and rapidly analyzes the end-user's search query against its large database, while powerful filters allow the user to enhance search results. As iSpyBio syncs with supplier and other public databases, it is always up-to-date - allowing iSpyBio to exclude out of stock items, whilst also showing the most recent testing results and peer-reviewed publications.
ANSI-accredited standards developing organization providing a comprehensive framework and related standards for the exchange, integration, sharing, and retrieval of electronic health information that supports clinical practice and the management, delivery and evaluation of health services. HL7's 2,300+ members include approximately 500 corporate members who represent more than 90% of the information systems vendors serving healthcare. HL7 provides standards for interoperability that improve care delivery, optimize workflow, reduce ambiguity and enhance knowledge transfer among all of their stakeholders, including healthcare providers, government agencies, the vendor community, fellow SDOs and patients.
Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)).
Non-Human Genome Segmental Duplication Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It contains information about segmental duplications in the genomes of chimpanzee, mouse, and rat. The criteria used to identify regions of segmental duplication are: * Sequence identity of at least 90% * Sequence length of at least 5 kb * Not be entirely composed of repetitive elements. BACKGROUND: The high quality of the mouse genome draft sequence and its associated annotations are an invaluable biological resource. Identifying recent duplications in the mouse genome, especially in regions containing genes, may highlight important events in recent murine evolution. In addition, detecting recent sequence duplications can reveal potentially problematic regions of the genome assembly. We use BLAST-based computational heuristics to identify large (>/= 5 kb) and recent (>/= 90% sequence identity) segmental duplications in the mouse genome sequence. Here we present a database of recently duplicated regions of the mouse genome found in the mouse genome sequencing consortium (MGSC) February 2002 and February 2003 assemblies. RESULTS: We determined that 33.6 Mb of 2,695 Mb (1.2%) of sequence from the February 2003 mouse genome sequence assembly is involved in recent segmental duplications, which is less than that observed in the human genome (around 3.5-5%). From this dataset, 8.9 Mb (26%) of the duplication content consisted of "unmapped" chromosome sequence. Moreover, we suspect that an additional 18.5 Mb of sequence is involved in duplication artifacts arising from sequence misassignment errors in this genome assembly. By searching for genes that are located within these regions, we identified 675 genes that mapped to duplicated regions of the mouse genome. Sixteen of these genes appear to have been duplicated independently in the human genome. From our dataset we further characterized a 42 kb recent segmental duplication of Mater, a maternal-effect gene essential for embryogenesis in mice. CONCLUSION: Our results provide an initial analysis of the recently duplicated sequence and gene content of the mouse genome. Many of these duplicated loci, as well as regions identified to be involved in potential sequence misassignment errors, will require further mapping and sequencing to achieve accuracy. A Genome Browser database was set up to display the identified duplication content presented in this work. This data will also be relevant to the growing number of investigators who use the draft genome sequence for experimental design and analysis. The segmental duplication data and summary statistics are available for download and can also be visualized in a genome browser in the GBrowse section. Selected annotation tracks (except the segmental duplication track) have also been obtained from UCSC and loaded into the genome browser. Detailed information (e.g. overlapping genes, overlapping clones, detailed alignment) can be obtained by clicking on a duplication cluster in GBrowse. Both keyword search and BLAT search are available. Analyses based on previous genome assemblies can be found in the Previous Analyses section. Recent Developments The Non-Human Genome Segmental Duplication Database is continually updated including the archived copies of the analysis of all previous genome assemblies and will include all new species as they become available. Acknowledgments We thank The Centre for Applied Genomics at the Hospital for Sick Children (HSC) as well as collaborators worldwide. Supported by Genome Canada the Howard Hughes Medical Institute International Scholar Program (to S.W.S.) and the HSC Foundation.
A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available.
Denver University Department of Psychology
University of Denver Department of Psychology
The department of psychology at Denver University that offers degrees at the undergraduate, graduate and doctoral level. The doctoral programs have specializations such as Affect/Social, Child Clinical, Cognitive, and Developmental.
Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.
Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases.
An ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. Please note: The ontology metrics displayed by BioPortal do not distinguish IAO-developed terms from terms imported from other ontologies.
Neurosciences on the Internet http://www.neuroguide.com/
Neurosciences on the Internet Neuroguide.com
A searchable and browsable index of neuroscience resources available on the internet including neurobiology, neurology, neurosurgery, psychiatry, psychology, cognitive science sites and information on human neurological diseases. Two categories exist: Best Bets and Cutaneous Fields of Peripheral Nerves.
National Center for Biotechnology Information (NCBI) Organismal Classification
National Center for Biotechnology Information Organismal Classification
Ontology that is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl.
miRprimer - Automatic design of primers for miR-specific RT-qPCR
Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70).
iBMQ - integrated Bayesian Modeling of eQTL data
Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently.
NIMBL: Numerical Identification of Methylation Biomarker Lists
Numerical Identification of Methylation Biomarker Lists
MATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays.
Gene Bridges - The Recombineering Company
A biotech company that commercializes its patented Red/ET recombination worldwide as licenses and supplies several products for the pharmaceutical and biotech industry as well as academia. It operates from the Technologie Park in Heidelberg and provides customized in-house DNA modification of any kind. Recombineering with Red/ET allows cloning, subcloning and modification of DNA at any chosen position. It permits precise engineering of DNA molecules of any size, including very large ones such as BACs or the E.coli chromosome.
Sampling protocols produced by the BrainNet Europe Consortium generally with five types of dissection and brain processing procedures defined in all disease related protocols. * Fresh brain dissection * Fresh brain processing * Dissection of formalin-fixed brain * Histology and immunohistochemistry * Processing fresh brain
A nonprofit health organization that works to improve the quality of life of Canadians affected by Alzheimer's disease and other dementias. This organization also supports research on the cause and potential cures for the disease through education and funding.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8, 2025. R function for computing predictions and simulating data from both Mlxtran and PharmML models that is based on MlxCompute, the model simulation engine developed by Lixoft. MlxCompute combines the Mlxtran language interpreter with the equation solvers to compute efficiently complex systems of ordinary differential equations (ODEs) and delayed differential equations (DDEs). Simulx takes advantage of the modularity of hierarchical models for simulating different components of a model: models for population parameters, individual covariates, individual parameters and longitudinal data, including continuous, count, categorical, and time-to-event data. It is also extremely flexible for defining complex dose regimens. Simulx will be the core of the next version of the DDMoRe Clinical Trial Simulator.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Standard for encoding of models, associated tasks and their annotation as used in pharmacometrics.
Italian pharmaceutical company involved in research, manufacture and marketing of drugs. sigma-tau is present today in the most advanced research sectors, maintaining constant relations with scientific institutions with a world-wide reputation in the development of joint projects and in the implementation of original and innovative research programs.
A contract research organization (CRO) specializing in preclinical oncology services. As a pioneer in the field of patient derived tumor xenografts (PDX), they provide tailored solutions to the problems faced by preclinical oncology researchers. They assist with the identification of the best drug candidates and the validation of their targets and deliver in-depth bioinformatics analyses, laying the groundwork for the successful planning of clinical trials. Their diverse tumor model collection enables them to recommend the right assays and models to answer their customers' questions. Their AAALAC accredited facilities with IVC system, separate model development unit, large cage capacity of over 14,500 mice and proprietary electronic measurement system with an integrated database and by continuously maintaining important PDX models in mice, they are able to provide the highest standard of testing within a reasonable timeframe.
Bio-derived Feedstocks for Sustainable UK-Based Manufacture of Chemicals and Pharmaceutical Intermediates
Project aiming to establish a range of new technologies to enable the synthesis of a range of chemicals from sugar beet pulp (SBP) in a cost-effective and sustainable manner. The chemical and pharmaceutical industries are currently reliant on petrochemical derived intermediates for the synthesis of a wide range of valuable products. Decreasing petrochemical reserves and concerns over costs and greenhouse gas emissions are driving the search for renewable sources of organic synthons. The UK is self-sufficient in the production of SBP which is a by-product of sugar beet production (8 million tonnes grown per year) and processing. The ability to convert SBP into chemicals and pharmaceutical intermediates will therefore have significant economic and environmental benefits. SBP is rich in carbohydrate (nearly 80% by weight) which is made up of roughly equal proportions of 2 biological polymers; cellulose and pectin. To be cost-effective it will be necessary to find uses for each of these substances. The consortium will develop a biorefinery approach for the selective breakdown of both polymers, purification of the breakdown compounds and their use to synthesize a range of added value products such as speciality chemicals, pharmaceuticals and biodegradable polymers. It is already known that cellulose can be broken down into hexose sugars and fermented to ethanol for use in biofuels. The focus is on the release of galacturonic acid and arabinose (from pectin) and their conversion, by chemical or enzymatic means, into added value products. Synthetic Biology methods will also be explored to test the feasibility of metabolically engineering microbial cells to simultaneously breakdown the polymeric feed material and synthesize a desired product, such as aromatic compounds, in a single integrated process. In conducting this research the consortium will adopt a holistic, systems-led, approach to biorefinery design and operation. Computer-based modelling tools will be used to assess the efficiency of raw material, water and energy utilization. Economic and Life Cycle Analysis (LCA) approaches will then be employed to identify the most cost-effective and environmentally benign product and process combinations. The project is supported by a range of industrial partners from raw material producer to intermediate technology providers and end-user chemical and pharmaceutical companies. This is crucial in providing business and socio-economic insights regarding the adoption of renewable resources into their current product portfolios. The company partners will also provide the material and equipment resources for the large-scale verification of project outcomes and their ultimate transition into commercial manufacture. The Intellectual Property (IP) expected to be generated by the consortium will most likely be related to new biocatalysts, synthetic routes, USD devices and modelling software. The data is accessible programmatically using one of three application programming interfaces GtR, GtR-2 and CERIF.
UC San Diego Library Digital Asset Management System
A digital repository designed to store and manage digital assets of UC San Diego. The flexible architecture can accept a variety of data formats, schemas and web services when ingesting digital assets. It stores digital content files and allows for the creation, indexing and searching of associated metadata to locate and retrieve the content files. Content can be composed of files in any format, including text, sound, video, and images. The DAMS is also designed to facilitate the transfer and submission of the Library's digital assets to Chronopolis and the California Digital Library's Merritt, and can easily be extended to serve other purposes. Additionally, the DAMS is able to export data in many formats, including METS, HTML, OAI, RSS, CSV. Future plans include linking data sets with other universities and organizations. For more information about the DAMS, including the data model and technical diagram, see Github, https://github.com/ucsdlib: * DAMS Manual, https://github.com/ucsdlib/dams/wiki/DAMS-Manual * DAMS Hydra Head, https://github.com/ucsdlib/damspas * DAMS REST API, https://github.com/ucsdlib/dams/wiki/REST-API * DAMS Ontology, https://github.com/ucsdlib/dams/tree/master/ontology Additional information on Hydra is available at Project Hydra and Duraspace.
AlzProtect - Therapeutic Solutions for Neurodegeneration
Commercial organization that develops drug candidates in the field of neurodegenerative diseases and particularly Alzheimer's. Their main objective is the development of a drug against Alzheimer's disease from molecules patented by Inserm and the University of Lille II.
A drug and diagnostic discovery company.
The UK's professional body for chemical scientists, supporting and representing members and bringing together chemical scientists from all over the world. This not-for-profit organisation has an international publishing business and their activities span education, conferences, science policy and the promotion of chemistry to the public. They have offices in Europe, Asia, North America and South America.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 5,2025. A not-for-profit membership organization, supporting the Open PHACTS Discovery Platform: A sustainable, open, and interoperable information infrastructure for applied life science research and development. The foundation is the successor organization of the Open PHACTS project, and aims to ensure the sustainability of the Open PHACTS Discovery Platform infrastructure. OPF also acts as a hub for scientific research and development relevant to the life sciences, and serves as a forum for the scientific community, allowing idea exchange between the pharmaceutical industry, academia and SMEs. OPF is a UK-based not-for-profit membership organization, but operates in an international commercial environment.
Portal devoted to aging relevant scientific data and resources.
Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms.
TDARACNE - Network reverse engineering from time course data
Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.
A drug discovery company focused on small-molecule drugs targeting G-protein-coupled receptors (GPCRs), the largest family of druggable targets. Heptares creates new medicines targeting previously undruggable or challenging GPCRs, a superfamily of receptors linked to many diseases. They are pioneering a structure-based drug design approach to GPCRs, leveraging proprietary technologies for protein stabilization, structure determination, and fragment-based discovery. Their partners include Cubist, MorphoSys, AstraZeneca, MedImmune and Takeda. Their objective is to build a broad pipeline of novel medicines to transform the treatment of serious diseases, including Alzheimer's disease, schizophrenia, diabetes, ADHD and chronic migraine.
Brain Systems Connections Associations and Network Relationships
A database of neuroscience-related concepts that utilizes visualization tools for the purpose of research, education and knowledge discovery. The data comes from PubMed abstracts and an algorithm that assumes related terms will appear together. The topics can include computational modeling, behavioral functions and neurological degeneration.
European College of Neuropsychopharmacology
A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity.
A hosting site for the distributed version control systems (DVCS) Git and Mercurial. The service offering includes an issue tracker and wiki, as well as integration with a number of popular services such as Basecamp, Flowdock, and Twitter.
A list of Wordpress plugins that are useful for authoring scientific papers. Listed plugins include BibTeX Importer, Link to Link, Broken Link Checker, and Contact Info Options, among many others.
A blog featuring articles on the brain, consciousness, cognitive science, psychology and neurology. This resource is in Russian.
Institute for Transcriptional Informatics-Molecular Informatics Resource for the Analysis of Gene Expression
A resource for information pertaining to methodologies, tools and technologies of gene expression. The website offers resources for sequence analysis, database services, and other technologies of gene expression and regulation.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Flu Wikie is a topical portal on the flu. Major categories include health, Flu Symptoms, Avian Influenza, Swine Flu, Cold, Vaccination, Pandemic, Vitamin D, and Immune System. Many articles on topic are included.
International private stem cell storage bank to collect, assess and cryogenically store living tooth cells from deciduous baby teeth. Tooth cell banking is a safe, natural and completely noninvasive method of collecting and preserving valuable stem cells which could hold the key to your child's health. Simply enroll, send us your child's tooth when it falls out, and they'll do the rest. Stem cell treatment to repair or replace damaged tissues or organs is the cornerstone of future medical science. Children's milk teeth, (baby teeth) have been identified as a rich source of these stem cells and have the potential to treat some of the worst illnesses and diseases facing people today. Stem cells from teeth (mesenchymal stem cells) are different from those found in cord blood (hematopoietic stem cells). Cord blood cells can be used to treat blood disorders such as leukemia, but stem cells from teeth are different. Stem cells from teeth can be used to grow a range of tissues including bone, nerve, fat, muscle and cartilage and may one day be used to grow entire organs. It is widely believed that stem cells will be used to treat a wide variety of diseases and injuries within the next decade. Their UK facility is regulated by the Human Tissue Authority (HTA), and they hold a full license. They are also registered with the Food and Drug Administration (FDA) in the US. BioEDEN, Ltd is ISO 9001:2008 accredited by the British Assessment Bureau. When you enroll for the BioEDEN service, you will be offered the opportunity to consent to donate any excess cells. BioEDEN will provide these cells to leading academic and clinical research centers to help further the progression of this technology to useful clinical applications. BioEDEN will only provide cells to researchers that have full ethical approval for their research and will be guided by our Advisory team as to the most appropriate research to support. The cells will be donated in accordance with strict regulatory guidelines and anonymity of the donor will be strictly assured at all times. Donation of cells is an entirely opt in service. If you choose not to give consent to donate, BioEDEN will simply store the cells for your child.
Center for patient care, education and research on cancer. The institute focuses its research on prevention methods, early detection, treatment and finding cures.
Windber Research Institute Tissue Banking
Under the direction of Stella Somiari, Ph.D., the tissue bank at Windber Research Institute acquires and banks large numbers of high quality and well annotated normal and diseased tissue specimens. These specimens are obtained from fully informed and consented donors using Institutional Review Board (IRB) approved protocols and are accompanied by detailed clinical, family history and demographic information. The tissue bank has established Standard Operating Procedures (SOPs) for tissue acquisition, handling, processing, packaging and shipping. All collaborators at participating clinics/medical centers utilize these procedures to ensure that the integrity of the specimen is maintained. Tissue types in our collection include plasma, serum, tissue embedded in optimum cutting temperature (OCT), formalin fixed paraffin embedded, and flash frozen. We also isolate and bank tissue derived products such as DNA, RNA and protein for research. Very stringent SOPs are in place for the process of extraction of these tissue-derived products and for quality control/quality assurance (QA/QC). The WRI tissue bank currently has 5 isothermal freezers each with the capacity to store 36,000 specimens. For all specimens obtained from surgical procedures, routine histology is performed to obtain representative Hematoxylin and Eosin (H & E) stained sections for imaging/archiving. All H & E sections are imaged on the Trestle SL-50 imaging system and these images are available online to designated collaborative sites. A certified pathologist verifies all tissue specimens and WRI has telepathology capabilities, which can also be utilized for pathology verification when a second pathologist opinion is required to confirm specimen diagnosis. Other uses of the telepathology capabilities include the verification of Laser Capture Microdissection (LCM) sections (by pathologist) to ensure the correct areas are captured for research. The telepathology system at WRI is the Trestle Corporation's Medmicro system, which permits the pathologist to remotely view, navigate and share images at sub-micron resolution over standard internet connections in real-time.
Software that implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data).
BAIT - Software to help analyse Strand-Seq data
Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 9, 2022. A consumer health database that provides up-to-date information on diseases, conditions, injuries, drugs, supplements, treatment options, and healthy living, with a special focus on comparative effectiveness research from institutions around the world. PubMed Health includes * consumer guides summarizing comparative effectiveness research * fact sheets on diseases and conditions * information on drugs and supplements * encyclopedic overviews of health topics * links to external Web sites PubMed Health has a special focus on comparative effectiveness research, in particular that research which evaluates the available evidence of the benefits and harms of different treatment options for different groups of people. In Comparative Effectiveness Research, experts often synthesize the evidence from dozens, or even hundreds, of individual studies.
Boston University Alzheimer's Disease Center Neuropathology Core Facility
Boston University Alzheimer's Disease Center - Neuropathology
Boston University Alzheimer's Disease Center - Neuropathology Core
BU Alzheimer's Disease Center - Neuropathology
The Neuropathology Core leads neuropathological analyses of brains donated by research registry participants of the Boston University Alzheimer's Disease Center. The Core works with the Clinical Core to carry out the Brain Tissue Donation Program, which provides brain tissue for analyses that will help to understand the underlying pathology of AD. The Core also works closely with the Data Management and Statistics Core to maintain a comprehensive computerized database of information resulting from neuropathological analyses. The Boston University Brain Bank of the Neuropathology Core documents neuropathological findings of Center research registry participants, but also of brain donors from important related BUSM studies such as the Framingham Heart Study and the Centenarian Study.
AVEXIS Receptor Network with Integrated Expression
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.
Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations.
A suite of software programs for analyzing and visualizing 4C-seq data.
Two University College London (UCL) biobanks, one based at the Royal Free Hospital (RFH) Campus and the other based at Bloomsbury supporting Pathology and the Cancer Institute, will act as physical repositories for collections of biological samples and data from patients consented at UCLH, Partners Hospitals and external sources. This will incorporate collections of existing stored samples and new collections. UCL-RFH BioBank, the physical repository at the Royal Free, presents a unique opportunity to advance medical research through making access to research tissue easier, faster and much more efficient. The BioBank is both a physical repository, with capacity for up to 1 million cryogenically stored samples and a virtual repository for all tissue, cell, plasma, serum, DNA and RNA samples stored throughout UCLP. In particular, samples considered "relevant material", such as tissues and cells, that are licensed by the Human Tissue Authority, can be stored long term. Existing holdings of tissues and cells where appropriate can be transferred to the Physical BioBank at the Royal Free. UCL - Royal Free BioBank provides a flexible approach to banking, allowing the Depositor to pick and choose services that are tailored to fit their requirements. Collaborations arising from publicizing of the existence of the holdings are entirely at the discretion of the depositor, as the facility ensures that access to the deposits remains at the decision of the Depositor/User. UCL Biobank for studying Health and Disease (based at Pathology-Rockefeller building and the UCL-Cancer Institute will support projects principally involved in the study of human disease. The aim is to support primarily, research in the Pathology Department, UCLH and the UCL-Cancer Institute but it will also support other UCLH partners. The biobank will store normal and pathological specimens, surplus to diagnostic requirements, from relevant tissues and bodily fluids. Stored tissues will include; snap-frozen or cryopreserved tissue, formalin-fixed tissue, paraffin-embedded tissues, and slides prepared for histological examination. Tissues will include resection specimens obtained surgically or by needle core biopsy. Bodily fluids will include; whole blood, serum, plasma, urine, cerebrospinal fluid, milk, saliva and buccal smears and cytological specimens such as sputum and cervical smears. Fine needle aspirates obtained from tissues and bodily cavities (e.g. pleura and peritoneum) will also be collected. Where appropriate the biobank will also store separated cells, protein, DNA and RNA isolated from collected tissues and bodily fluids described above. Some of the tissue and aspirated samples will be stored in the diagnostic archive.
A non-profit tissue bank that facilitates the distribution of non-transplantable tissue to the medical and research community. It provides snap frozen low post mortem interval (PMI) tissue, normal and diseased tissue, plastinated specimens, anatomical specimens, and specialty specimens. The foundation also works to increase public awareness of research tissue donation for medical research.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 13, 2016. A dataset about transcriptional regulation in eukaryotic cells, including data such as transcription factors and their binding sites and profiles. Resource is in Chinese.
Portal serves as resource to understand the current state of medical data quality and the factors that affect it. The information is gathered from anecdotal and empirical examples from peer-reviewed journals, popular media and author contributions. Issues of importance include understanding and measuring medical data quality, contributing factors, best practices, and the effects of data quality on secondary uses of medical data.
WikiMD is a free wiki based medical encyclopedia and medical wiki community that any registered user can edit. This medical encyclopedia with articles, links, images and information on everything related to medicine and health, has great potential to provide patients with reliable health information as wikiMD is edited by users with close supervision by medical professionals. WikiMD is a sister project of Residentscafe.com - a place for medical students, residency applicants, residents, fellows and attending physicians. Major categories of WikiMD: *Video of the day *Did you know? *Gray's Anatomy *USMLE (United States Medical Licensing Examination) Wiki *Disease Index *Medical Resources *Health Encyclopedia Use the info at your own risk!
A portal for developing a community of librarians that teach and support the practice of evidence-based medicine (EBM). The site offers a forum for sharing teaching materials, discussing issues and asking for advice from colleagues.
Mfuzz - Soft clustering of time series gene expression data
Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Children's Cancer and Leukaemia Group Tissue Bank
Children's Cancer and Leukemia Group Tissue Bank
Tissue bank that provides access to tissue samples and an anonymized version of the tissue bank database.Bank has large collection of tumour, DNA and other tissue samples from childhood cancer patients.
Center for Academic Research & Training in Anthropogeny
Center for Academic Research and Training in Anthropogeny
A virtual organization that promotes transdisciplinary research into anthropogeny, or the study of human origins. The research interests are broad and include finding the structural and molecular differences between humans and apes, identifying and explaining external mechanisms, and defining the evolutionary origins of humans. The center hosts symposia as well as visiting professors for the anthropogeny graduate program.
NERC Environmental Bioinformatics Centre
NERC Environmental Bioinformatics Center
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Data sharing platform based on the ISA software suite - including an annotation tool and a database - that holds environmental omic data in standards-compliant format. It uses various approaches to provide new discovery, interoperability and integration opportunities for environmental scientists, including the development of tools, databases, standard and ontologies. The main tool for collecting environmental omics data from researchers is the EnvBase data catalogue. The NEBC Toolbox contains a range of tools developed by NEBC to support environmental researchers. The data include next generation sequencing, microarray and ABI sequencing technologies. ISAconfigurator and ISAcreator ensure that the extensive information relating to environmental sampling is consistently collected by the NERC experimentalists, according to the appropriate MIBBI checklist(s), and then reported centrally to NEBC. A local instance of the BII runs as an internal prototype database that will soon provide public and private access to NERC research projects outputs, as appropriate. In accordance with the NERC Data Policy, and when data sets are declared ready for public release, the NEBC team will use the ISAconverter to perform (combined) submissions to the appropriate public repositories (ENA, or SRA, ArrayExpress and PRIDE) to ensure long term stewardship.
ADA Genetics of non-insulin dependent diabetes mellitus Study
ADA The GENNID Study: Genetics of Non-Insulin Dependent Diabetes
American Diabetes Association GENNID Study
The purpose of the American Diabetes Association (ADA), GENNID Study (Genetics of non-insulin dependent diabetes mellitus, NIDDM) is to establish a national database and cell repository consisting of information and genetic material from families with well-documented NIDDM. The GENNID Study will provide investigators with the information and samples necessary to conduct genetic linkage studies and locate the genes for NIDDM. Non-Hispanic white, Hispanic, African-American, and Japanese-American multiplex NIDDM families, with a minimum of one affected sib-pair, are being collected by the eight Harold Rifkin Family Acquisition Centers. Detailed family and medical histories are obtained from all participants. Family members with diabetes have fasting blood samples drawn, while nondiabetic family members have an oral glucose tolerance test and, when possible, insulin sensitivity and insulin secretion measurements by frequently sampled intravenous glucose tolerance testing or euglycemic insulin clamp. Lymphoblastoid cell lines are established for all participants. DNA samples and extensive phenotypic data are available from the American Diabetes Association's GENNID study (Genetics of NIDDM). GENNID has collected detailed family histories and a broad array of data on 170 large pedigrees, all of which contain at least one affected sib pair, with a total of 650 affected individuals and approximately 1,200 total subjects. Included are approximately 65 Caucasian, 60 Hispanic, 25 African American, and 20 Japanese American pedigrees. In addition, GENNID also contains DNA and data on 1,000 additional affected sib pairs in each of three groups, African American, Caucasian, and Hispanic. DNA and phenotypic data, including race, gender and age, are available for all members of the pedigrees. The data set includes multiple metabolic factors, including carbohydrate metabolism, lipid metabolism, and body size measures, as well as lifestyle variables obtained by questionnaire (e.g., employment, exercise, etc.). The GENNID resource is ideally suited for genetic linkage and association studies as well as SNP discovery and typing. Investigators interested in obtaining the DNA samples and/or data will need to submit a proposal to the Association that addresses the genetics of type 2 diabetes.
MaryGold - Variation analysis of metagenomic samples
Software package that enables detection of sequence variation between metagenomic samples.
OSU Comprehensive Cancer Center Leukemia Tissue Bank Shared Resource
OSUCCC Leukemia Tissue Bank Shared Resource
The OSU Comprehensive Cancer Center Leukemia Tissue Bank Shared Resource (LTBSR) facilitates the successful translation of basic leukemia research to the clinical setting via an extensive repository of tissue samples and accompanying pathologic, cytogenetic and clinical data for ready correlation of clinical and biological results. The LTBSR, which is an NCI-sponsored biorepository, has more than 40,000 vials of cryopreserved viable cells and 13,000 vials of matched frozen plasma and/or serum samples from more than 4,000 patients treated for leukemia and other malignancies. Committed to furthering translational research efforts for OSUCCC - James members and the cancer research community, the LTBSR provides investigators with training and technical support as well as procurement, processing, storage, retrieval and distribution of clinical research materials. In many cases, the LTBSR serves as the central processing lab for multi-site trials in which the principal investigator is an OSUCCC - James member. The LTBSR's goals are to: * Provide a central collection, processing and a state-of-the-art repository for samples collected from leukemia patients treated on OSUCCC - James protocols, and * Provide materials to investigators involved in collaborative studies with OSU, who examine relevant cellular and molecular properties of leukemia and correlate these properties with clinical or population-based outcomes.
"Neuroscience Videos" Neuroscience Articles
Neuroscience News provides "Neuroscience Videos" and corresponding articles.
Nonprofit alliance of national organizations and state teams dedicated to increasing organ, eye and tissue donation. Donate Life America manages and promotes the national brand for donation, Donate Life, and assists Donate Life State Teams and national partners in facilitating high-performing donor registries; developing and executing effective multi-media donor education programs; and motivating the American public to registeras organ, eye and tissue donors.
Database of controlled vocabulary to describe each trait as a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant (or individual). Some examples include: plant height, disease resistance, and photosensitivity.
The OpenMS Proteomics Pipeline Assistant
A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Hybrid binning tool that achieves high binning efficiency by utilizing both "compositional" and "similarity" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Feinstein Institute for Medical Research Biorepository
The Biorepository was designed to collect, process, and distribute large numbers of high quality research specimens quickly and efficiently. The data that is collected is primarily human DNA from whole blood along with other human specimen types. The data are collected, processed, stored and later distributed to support a large number of research studies. Biobanking of other specimen types include cells, RNA, serum, plasma and tissue. The Biorepository serves as a storage facility for tracking specimen inventory using bar code technologies. The Biorepository also conducts most operations using modern laboratory automation and robotics, an efficient way to avoid processing errors inherent in the handling of larger numbers of specimens.
A resource and online book on neurology and neurosurgery. The book covers topics such as neurological symptoms, consciousness and unconsciousness, trauma, seizure disorders and dementia.
A podcast hosted by Kristin Sanford and Justin Jackson to explain recent scientific research and developments in a wide range of scientific phenomenon.
A program for designing primer pairs that amplify multiple target sequences using DNA thermodynamics and one class support vector machines. Written in Python.
IMPACT: International Mission for Prognosis and Analysis of Clinical Trials in TBI
International Mission for Prognosis and Analysis of Clinical Trials in TBI
Project focused on advancing knowledge of prognosis, trial design and treatment in Traumatic Brain Injury. IMPACT has developed and validated prognostic models for classification and characterization of TBI series, and participated in development of standardization of data collection in TBI studies.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Data analysis service for accurate phylogenetic classification of variable-length DNA fragments.
Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide.
University of Michigan Human Breast Cancer Cell Lines
University of Michigan Human Breast Cancer Cell Lines (SUM-LINES)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Asterand, Inc., the Detroit-based supplier of human tissue products and services, announces the distribution of eleven breast cancer cell lines, derived at the University of Michigan. The University has agreed to license the marketing of the breast cancer cell lines, known as the SUM lines, through Asterand in an effort to provide an exceptional tool to a broad base of researchers studying the disease. There are an estimated 1.2 million new diagnoses worldwide of breast cancer each year. The cell lines can be used to study all aspects of breast cancer biology, from new drug target identification to cell signaling to effects of novel drugs on cellular proliferation.
A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java.
Sequence Search and Alignment by Hashing Algorithm
A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported.
A weekly podcast hosted by Steve Mirsky on topics relating to developments in science and technology through interviews with leading scientists and journalists. This podcast is affiliated with Scientific American.
An archived portal of clinical studies, both ongoing and completed, that have been conducted and supported by the National Eye Institute (NEI) since 1970. The portal covers corneal diseases, glaucoma, epidemiology, lens and cataract, retinal diseases, strabismus, amblyopia and visual processing.
Indiana University-Bloomington Neuroscience Program
Indiana University Bloomington Neuroscience
Indiana University Bloomington Neuroscience Program
A neuroscience PhD program based at Indiana University that focuses on technical skills and the conceptual framework needed to puruse a career of research and/or teaching in neuroscience. Faculty of the neuroscience department fall into one of four areas of research: Molecular and Cellular Neuroscience, Behavioral Neuroscience, Cognitive and Computational Neuroscience and Clinical and Translational Neuroscience.
A nonprofit organ procurement agency based in Iowa. The organization facilitates both organ and tissue recovery in cooperation with local hospitals. The network also works to support public education, hospital development and family support services.
American Tissue Services Foundation - ATSF
A non-profit organization that facilitates the donation of tissues. It supports healthcare agencies, coroners, medical examiners and funeral professionals through donations and training, as well as partnering with organizations that utilize tissue in medical care and research.
NDRI is a Not-For-Profit (501c3) Corporation dedicated to providing the highest quality human biomaterials for research. NDRI makes it easy for researchers to get the human tissues and organs they need, prepared, preserved and shipped precisely according to their specific scientific protocols, as quickly as possible, and in the largest available quantities. NDRI provides researchers with protocol specific human neurological tissues such as brain stem, spinal cord, and basal ganglia, among others. In addition to control specimens, NDRI recovers tissues from donors with a variety of diseases, including Down syndrome, Parkinsons disease, Alzheimers disease, schizophrenia, and dementia. Through the NDRI 24/7 referral and procurement system, research consented biospecimens can be provided from low post mortem interval donors preserved at 4ºC, frozen or snap frozen, fixed, paraffin embedded, or as unstained slides.
Emory ADRC Tissue and Biospecimen Banking Facility
Emory ADRC Tissue & Biospecimen Banking Facility
Emory Tissue & Biospecimen Banking Facility
Emory Tissue and Biospecimen Banking Facilities
The Alzheimer's Disease Research Center at Emery University maintains an active brain bank to facilitate the acquisition, storage, handling and distribution of well-characterized autopsy brain tissue and other materials to investigators. It contains frozen tissue and brain specimens, formalin fixed tissue, paraformaldehyde fixed tissue, and cryopreserved tissue. The ADRC also has access to tissues and samples related to other neurodegenerative diseases. It contains plasma samples, serum samples, lymphoblast cell lines, and cerebrospinal fluid.
Estimating Species Richness Using 16S rRNA Pyrosequences
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. Software tool for estimating Species Richness Using 16S rRNA Pyrosequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
DySC: Software for Greedy Clustering of 16S rRNA Reads
Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy.
Interactive demonstrations of sensory perception phenomena from Dale Purves' website. You may read the empirical explanations and download high resolution images.
Fast Phylogenetic Scaffolding of Ancient Contigs
Fast Phylogenetic Scaffolding of Ancient Contigs (FPSAC) and application to the medieval Black Death agent
FPSAC: fast phylogenetic scaffolding of ancient contigs
Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome.
SNPiR: Reliable Identification of Genomic Variants Using RNA-seq Data
Software for reliable Identification of Genomic Variants Using RNA-seq Data.
Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores.
Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Brain Architecture Management System Connectivity Data
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. Database of information about brain region circuitry, it collates data from the literature on tract tracing studies and provides tools for analysis and visualization of connectivity between brain regions., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.
Genomic Evolutionary Rate Profiling: GERP
Software that identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element. GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using "shuffled" alignments in which the order of columns is randomized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.
Lady Scientist chronicles the author's journey through grad school and navigating the so-called Two Body Problem. The author, Amanda (at) Lady Scientist, is a recent Ph.D. graduate in biochemistry and molecular biology.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. System that retrieves relevant UniProt IDs from BioThesaurus entries using a soft string matching algorithm.
VariantMaster - Extract causative variants for monogenic and sporadic genetic diseases
Software program that extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, it integrates phenotypes and genotypes, and employs Annovar to produce additional information as allelic frequencies in general population and damaging scores.
Microbial Genetics Program - Exploration of Microbial Diversity
Mission: Dynamically evolve sequencing, finishing, annotation and analysis processes, exploit new technologies, and develop expertise to deliver high quality and high throughput sequence-based microbial science by listening to and responding to DOE Users and scientific community needs. GOALS 1. Expand product catalog and increase sample throughput while maintaining highest quality The MGP has been expanding its product catalog beyond a finished microbial genome and has projected to significantly up ramp throughput for the majority of its current products namely Draft Genomes, Single Cell Genomes, Quick Draft Genomes, Resequencing projects and RNAseq Project. This projected increase in microbial genomes is going hand-in-hand with and has been stimulated by new high throughput technologies and capabilities (de novo microbial Illumina assemblies, single cell genomics, Genologic sample tracking). The increased throughput will support the user community as well as JGI scientists by enabling DOE-relevant science at a grander scale. As the Program aims to generate hundreds of microbial genomes per year, our goal is to scale our production efficiency and maintain our trademark quality to best support our science mission. 2. Expand sequence space One of the ongoing missions of the MGP is to expand the coverage of the phylogenomic sequence space by generating reference genome datasets from highly diverse braches in bacterial and archaeal tree of life. The value of such effort includes the generation of phylogenetic anchors for metagenomic datasets, the improvement of annotation, an increased insight into phylogenetic distribution of functions, the discovery of novel genes, protein families, pathways and a better understanding on evolutionary diversication. 3. Make Single Cell Genomes a robust User product As the vast majority of microbes are uncultured to date, single cell genomics will be a crucial component of the MGP over the next several years to drive not only JGI science but also User community proposed single cell research. Going hand-in-hand are R&D efforts in selective single cell isolations, testing the effects of fixation of single cell sequencing, as well as single cell transcriptomics. 4. Sequence Pangenomes Combining similar genomes together creating pangenomes will allow more compact genome sequence storage and visualization and expedite analysis and annotation. Moreover, the pangenome as a representation of the whole group of organisms may be more representative of a given species within the environment. The MGP thus thrives to enable the sequencing and analysis of pangenomes. Current technology allows the sequencing of one organism strain at a time. Assuming that for most cases, several dozen strains may need to be sequenced in order to generate a more accurate pangenome for every microbial species, it becomes evident that the cost for doing so may be prohibitively high. Our goal here will be to explore new approaches and technologies for generating these pangenomes at a very low cost and analogous to what is the cost today for a single strain. 5. Expand and improve microbial annotation using transcriptomic data To improve annotation of gene structure, establish accurate transcription level and timing, provide information on gene regulation and generate information for expanding understanding of systems biology, the MGP thieves to generate transcriptomics data for larger sets of Bacteria and/or Archaea. This will enable the identification of novel regulator RNAs, as well as facilitate the understanding of uncharacterized protein families. 6. Maintain and evolve a top quality data management system To enable state of the art and world class comparative analysis of internal and external scientific projects, the JGI data integration and visualization management system for comparative analysis of microbial genomes, namely IMG, needs to be maintained and continuously evolved. The system needs to be able to support and integrate all data generated by JGI (WGS, reseq, RNAseq, -other omics data), as well as by the user community, enabling annotation and manual curation of the annotation, comparative analysis, gene-centric and pathway centric analyzes. The system should also facilitate the interation of associated metadata, enable data sharing and distribution, as well as automated data GenBank submissions. Lastly, the system needs to have the ability to scale enabling the annotation of thousands of genomes per year. 7. Drive Flagship projects To stay at the forefront of microbial genomic research, be recognized as such and enable the development new methods and tools, the MGP aims to drive DOE mission relevant flagship projects. Novel tools and methods developed will ultimately serve the user community if proven useful and implemented as part of a larger pipeline. MGP flagship projects are the GEBA and GEBA uncultured projects, as well as the GEBA-RNB, the proposed Microbial Earth and the Microbial Dark Matter Projects.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Beta software used to align and browse a genome.
GeneWays: A System for Extracting Analyzing Visualizing and Integrating Molecular Pathway Data
GeneWays: A System for Extracting Analyzing Visualizing Integrating Molecular Pathway Data
System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. A web crawler that can intelligently acquire social media content on the Internet to meet the specific online data source acquisition needs of cancer researchers.
Software application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms.
flowQ: Quality control for flow cytometry
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data.
Preprocessed versions of the ADHD-200 Global Competition data including both preprocessed versions of structural and functional datasets previously made available by the ADHD-200 consortium, as well as initial standard subject-level analyses. The ADHD-200 Sample is pleased to announce the unrestricted public release of 776 resting-state fMRI and anatomical datasets aggregated across 8 independent imaging sites, 491 of which were obtained from typically developing individuals and 285 in children and adolescents with ADHD (ages: 7-21 years old). Accompanying phenotypic information includes: diagnostic status, dimensional ADHD symptom measures, age, sex, intelligence quotient (IQ) and lifetime medication status. Preliminary quality control assessments (usable vs. questionable) based upon visual timeseries inspection are included for all resting state fMRI scans. In accordance with HIPAA guidelines and 1000 Functional Connectomes Project protocols, all datasets are anonymous, with no protected health information included. They hope this release will open collaborative possibilities and contributions from researchers not traditionally addressing brain data so for those whose specialties lay outside of MRI and fMRI data processing, the competition is now one step easier to join. The preprocessed data is being made freely available through efforts of The Neuro Bureau as well as the ADHD-200 consortium. They ask that you acknowledge both of these organizations in any publications (conference, journal, etc.) that make use of this data. None of the preprocessing would be possible without the freely available imaging analysis packages, so please also acknowledge the relevant packages and resources as well as any other specific release related acknowledgements. You must be logged into NITRC to download the ADHD-200 datasets, http://www.nitrc.org/projects/neurobureau
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 3,2023. Collection of miRNA target interactions. Manually curated collection of experimentally supported microRNA targets in several animal species of central scientific interest, plants and viruses. Database is functionally linked to several other relevant and useful databases such as Ensembl, Hugo, UCSC and SwissProt., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Inner Ear Proteins in Health and Disease
THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. The fully federated database provides information on proteins identified in inner ear structures and fluids in health and disease. in addition, protein maps derived from 2d electrophoresis/mass spectrometry are displayed.
Jefferson Hospital for Neuroscience Alzheimers Disease and Dementia Center
Jefferson Hospital for Neuroscience Alzheimer's Disease and Dementia Center
Jefferson Hospital for Neuroscience Alzheimer's Disease Dementia Center
Jefferson Hospital for Neuroscience Alzheimers Disease Dementia Center
Jefferson Alzheimer's Disease and Dementia Center
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. If you or someone you love has been diagnosed with dementia caused by Alzheimer's disease, you'll be in good hands at Jefferson. Our neurologists and psychiatrists are dedicated to: Compassionate care for individuals with Alzheimer's disease; Supporting families; Advancing care through research into the epidemiology and treatment of neurodegenerative diseases. We interact with patients very early in the disease progression, when impairment is typically mild; deliver state-of-the-art care; provide information; build care-giving skills; and help caregivers connect with community support and plan for the future.
Medical University of South Carolina Health News
MUSC's Health News RSS Feeds includes topic of a interest you can subscribe to by copying the corresponding URL into your preferred RSS software. You will automatically receive this feed each time it's published. Topics include: Brain Waves, Diabetes Health, Kids Health, Heart Care, Men's Health, Women's Health, and Community Blog.
Database Enabled Code for Ideal Probe Hybridization Employing R
A software toolset that can be used for deciphering and managing DNA sequences efficiently using the R statistical programming language., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. The blog of the Whole Brain Catalog.
NGSmethPipe - A tool to generate high-quality methylation maps
A software tool which generates high-quality methylation maps.
A software module for cleaning 454 pyrosequencing reads using filters such as read duplication, length, complexity, base-pair quality and number of undetermined bases. The software also uses flowgram files of paired-end sequences to validate paired-ends files of another file.
Distributed short read Error Correction on GPUs
Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models.
drFAST: di-base read Fast Alignment Search Tool
A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.
MPscan: index free mapping of multiple short reads on a genome
Web tool for index free mapping of multiple short reads on a genome.
Tool for Alignment of Pyrosequencing Reads
An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies.
A large-scale English terminological database that contains over 2.2.M lexical entries (3.3M semantic relations), terminological variants and rich linguistic information (subcategorization frames) which supports text mining systems. It is primarily intended to support text mining and information retrieval in the biomedical domain. The BioLexicon provides specific information to help determine the relevant facts to be extracted. BioLexicon is available in a relational database format (MySQL dump format) and it adheres to the EAGLES/ISO standards for lexical resources.
LORIS - Longitudinal Online Research and Imaging System
Longitudinal Online Research and Imaging System
Longitudinal Online Research Imaging System
A modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included.
neurodudes - at the intersection of neuroscience and AI
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Neurodudes is intended to be an open forum at the intersection of neuroscience and ai. regular readers are encouraged to post appropriate material. make sure to put your name somewhere in the post. The ultimate neurodudes RSS feed combines neuro/ai/cogsci-related RSS feeds from many sources, sometimes filtering along the way so as to minimize offtopic posts.
Brain Evolution in the News pulls in blogs from a variety of resources on topic.
Simple Web-service Offering Repository Deposit
A software that is used for the management of data and to deposit content between different locations. A request from an authenticated user is sent to implement for the "service document", which returns details of the collection that user is allowed to deposit within the repository. At this point, the user can deposit their file into a collection, which can then be accessed at a different location.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool for identifying coding region variants which disrupt pre-mRNA splicing and the underlying mechanism.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.
A collection of cook-book like manuals for various microarray designs. MAGMA is a collaboration between the Norwegian Microarray Consortium NMC and MolMine AS
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy.
Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A repository of sequence specificity models and condition-specific regulatory activities for a large number of DNA- and RNA-binding proteins in Saccharomyces cerevisiae. Accurate and comprehensive information about the nucleotide sequence specificity of trans-acting factors (TFs) is essential for computational and experimental analyses of gene regulatory networks. The sequence specificities in TransfactomeDB, represented as position-specific affinity matrices (PSAMs), are directly estimated from genomewide measurements of TF-binding using our previously published MatrixREDUCE algorithm, which is based on a biophysical model. For each mRNA expression profile in the NCBI Gene Expression Omnibus, we used sequence-based regression analysis to estimate the post-translational regulatory activity of each TF for which a PSAM is available. The trans-factor activity profiles across multiple experiments available in TransfactomeDB allow the user to explore potential regulatory roles of hundreds of TFs in any of thousands of microarray experiments.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Many Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on a certain microarray is a very laborious process requiring a high level of expertise. Onto-Design database is able to assist the designers of custom microarrays by providing the means to select genes based on their experiment. Design custom microarrays based on GO terms of interest. User account required. Platform: Online tool
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released
Boston University School of Medicine Cardiovascular Proteomics Center
The Cardiovascular Proteomics Center is a research center funded by the NIH/NHLBI to analyze and identify proteins that may be modified or created by oxidative stress. The CPC is developing and applying new proteomics methodology and instrumentation to the analysis of known proteins and those yet to be discovered.
Baylor College of Medicine - Shaw Laboratory
The mission of the Baylor College of Medicine - Shaw Laboratory is to apply methods of statistics and bioinformatics to the analysis of large scale genomic data. Our vision is data integration to reveal the underlying connections between genes and processes in order to cure disease and improve healthcare.
USP Molecular Genetics and Bioinformatics Laboratory
University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory
University of Sao Paulo Molecular Genetics and Bioinformatics Laboratory
USP Laboratorio de Genetica Molecular e Bioinformatica
USP Molecular Genetics and Bioinformatic Laboratory
USP Molecular Genetics Bioinformatics Laboratory
Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory.
Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.
The primary objective of this study is to establish a biobank of blood samples from amphetamine dependent patients in order to study genetic risk factors for this disease. This may ultimately shed new light on the pathophysiology of substance dependence and its relation to other psychiatric disorders, and suggest new approaches to prevention and treatment. Types of samples * EDTA whole blood * DNA Number of sample donors: 104 (June 2010)
Model: Hebbian Mirror Neuron System (H-MNS) (Keysers - Perrett)
A conceptual model of how Hebbian learning between the areas STS, PF, F5 allows recognition of the actions of others by associating them with self-produced actions.
Blog by Craig Mod: Thinking about the future of books and publishing and story telling.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Aims to investigate the relation between specific genetic variations, personality factors and pain experience in healthy subjects.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Annotator is an open-source JavaScript library and tool that can be added to any webpage to make it annotatable. Annotations can have comments, tags, users and more. Moreover, the Annotator is designed for easy extensibility so its a cinch to add a new feature or behavior. Adding annotation to your webpage using the Annotator is easy. Full instructions are in the Getting Started section of the docs, but it is just two short steps. First, you need to download the Annotator library (or link to the hosted version), include it on your page along with jQuery. Then add the following line to initialize the annotator. $("#content").annotator(); Plug-ins can be included for adding functionality such as user accounts, tags, filtering and formatting. You'll need to store your data somewhere, luckily we've made this very simple to do using AnnotateIt, a hosted web service for storing annotations. Alternatively if you'd like to integrate the annotator with your own storage system check out the Docs for more information on the annotation format and store plugin. The bookmarklet is a simple tool that allows you to add the annotator to any webpage and save your annotations to AnnotateIt. Check it out at http://annotateit.org/.
John D. and Catherine T. MacArthur Foundation
The John D. and Catherine T. MacArthur Foundation supports creative people and effective institutions committed to building a more just, verdant, and peaceful world. In addition to selecting the MacArthur Fellows, the Foundation works to defend human rights, advance global conservation and security, make cities better places, and understand how technology is affecting children and society. MacArthur is one of the nation's largest independent foundations. Through the support it provides, the Foundation fosters the development of knowledge, nurtures individual creativity, strengthens institutions, helps improve public policy, and provides information to the public, primarily through support for public interest media. The Foundation makes grants and loans through four programs. * International Programs focus on international issues, including human rights and international justice, peace and security, conservation and sustainable development, higher education in Nigeria and Russia, migration, and population and reproductive health. MacArthur grantees work in about 60 countries; the Foundation has offices in India, Mexico, Nigeria, and Russia. * U.S. Programs address issues in the United States, including community and economic development; housing, with a focus on the preservation of affordable rental housing; juvenile justice reform; education, with an emerging interest in digital media and learning; and policy research and analysis. * Media, Culture, and Special Initiatives support public interest media, including public radio, documentary programming, and work to explore the use of digital technologies to reach and engage the public. Grants are also made to arts and cultural institutions in the Chicago area and for special initiatives. * The MacArthur Fellows Program awards five-year, unrestricted fellowships to individuals across all ages and fields who show exceptional merit and promise of continued creative work. It is limited to U.S. citizens and residents. John D. MacArthur (1897-1978) developed and owned Bankers Life and Casualty Company and other businesses, as well as considerable property in Florida and New York. His wife Catherine (1909-1981) held positions in many of these companies and served as a director of the Foundation.
MedIC Automated Pipeline Scheduler Medical Image Processing Analysis and Visualization
The exploratory development tree of Java Image Science Toolkit (JIST), an extension to the MIPAV (Medical Image Processing, Analysis, and Visualization) plug-in framework that allows the user to design and execute pipelines, which are multi-stage processing tasks.. New features and designs are tested here before general release into the JIST project. JIST was formerly known as the MedIC Automated Pipeline Scheduler (MAPS).
Contains comprehensive data on HIV genetic sequences and immunological epitopes. This collection of databases contains tools to visualize and analyze HIV-related data.
PRACSIS - Prognosis and Risk in Acute Coronary Syndromes In Sweden
PRACSIS - Prognosis Risk in Acute Coronary Syndromes In Sweden
Prognosis and Risk in Acute Coronary Syndromes In Sweden
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. PRACSIS (Prognosis and Risk in Acute Coronary Syndromes In Sweden) aims to study prognosis and its predictors in a consecutive series of patients with acute coronary syndrome (ACS). The study is comprised of patients between 18 and 80 years diagnosed at the coronary care unit at the Sahlgrenska University Hospital with unstable angina, non-ST-elevation MI or ST-elevation MI. Extensive information on medical history and blood samples for analyses of biochemical markers and genetic factors have been collected.
Commissariat a l''Energie Atomique et aux Energies Alternatives
Commissariat �� l''��nergie atomique et aux ��nergies alternatives
French Alternative Energies and Atomic Energy Commission
A French government-funded technological research organization and ensures that the nuclear deterrent remains effective in the future. A prominent player in the European Research Area, it is involved in setting up collaborative projects with many partners around the world. The CEA is active in four main areas: low-carbon energies, defense and security, information technologies and health technologies. In each of these fields, the CEA maintains a cross-disciplinary culture of engineers and researchers, building on the synergies between fundamental and technological research.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. The system enables automatic and manual curation of evidence supporting each association, as well as user-enabled entry of their own annotations. Phenotypes are recorded using controlled vocabularies such as the Disease Ontology to facilitate computational inference and linking to external data sources. The gene-to-phenotype associations are filtered by stringent criteria to focus on the annotations most likely to be relevant. Neurocarta is constantly growing and currently holds more than 30,000 lines of evidence linking over 6,800 genes to 1,800 different phenotypes. Neurocarta is a one-stop shop for researchers looking for candidate genes for any disorder of interest. In Neurocarta, they can review the evidence linking genes to phenotypes and filter out the evidence they're not interested in. In addition, researchers can enter their own annotations from their experiments and analyze them in the context of existing public annotations. Neurocarta's in-depth annotation of neurodevelopmental disorders makes it a unique resource for neuroscientists working on brain development.
Gatsby is a Foundation set up by David Sainsbury to realize his charitable objectives. Gatsby works in areas that David Sainsbury and the Trustees are particularly passionate about and where they believe charitable funding can make a real difference. Gatsby is currently active in six tightly-focused areas: * Plant science research * Neuroscience research * Science and engineering education * Economic development in Africa * Public policy research and advice * The Arts We have also supported significant programs in mental health - in particular through the founding of the Centre for Mental Health - although we are no longer focusing on this area. Across all areas, we aim to be more than a funder. We act as an enabler for projects, designing, developing, overseeing and, in some cases, delivering activities. We are proactive in putting together projects to achieve our aims. Rather than wait for third-party proposals, we identify areas of need, commission research and design interventions in partnership with sector and industry experts. We take a long-term view as we do not think much can be achieved by short, one-off projects. We build long relationships with the organizations we support, allowing both them and us to learn from successes and failures and to develop sustainable change. We are particularly enthusiastic about supporting innovation. David Sainsbury has long believed that private foundations have an important role to play in testing imaginative models and new ideas that governments may see as too risky for public funding, even when they have significant potential to benefit the public if they succeed. Gatsby can incubate such models, giving them the support they need to prove themselves and build the track-records that will encourage others to scale them up. We will continue to support and undertake both large- and small-scale work, employing different methods and models depending on the different challenges, but always ultimately looking to deliver long-term, sustainable change. Registered Charity No. 251988
ProQuest Dissertations and Theses Global
ProQuest Dissertations & Theses Database
ProQuest Dissertations and Theses Full text is a comprehensive collection of dissertations and theses, as well as the official digital dissertations archive for the Library of Congress and the database of record for graduate research. PQDT Full Text includes nearly 3 million searchable citations to dissertations and theses available for download in PDF format. The database offers full text for most of the dissertations added since 1997 and strong retrospective full-text coverage for older graduate works. Full-text dissertations are archived as submitted by the degree-granting institution. Each dissertation published since July 1980 includes a 350-word abstract written by the author. Masters theses published since 1988 include 150-word abstracts. Simple bibliographic citations are available for dissertations dating from 1637. ProQuest Dissertations and Theses Full Text also offers researchers unlimited access to digital copies from their own institutions as well as affordable copies from others.
The Mission of the Sarah Jane Brain Project is to create a model system of care for children and young adults suffering from all Pediatric Acquired Brain Injuries in order to advance our knowledge of the brain fifty years over the next five years! As a father of a child suffering from a Pediatric Acquired Brain Injury (PABI), I have spent countless hours searching the internet and speaking with Sarah Jane's development team (doctors, therapists and other professionals) trying to improve the development of my daughter. What I found was that while there are a countless number of wonderful and informative prevention sites for Shaken Baby Syndrome and advocacy sites for brain injuries, there is no one centralized resource for research and rehabilitation for PABI. Furthermore, many of the issues families and children face are the same whether the brain injury was caused by a car crash, a sports-related concussion, an assault or by a tumor. No one person or organization has all the answers to the questions that parents of children suffering from PABI face. Yet through my own experience, I learned that the coordination and dissemination of Sarah Jane's medical and therapy records and data in an orderly manner greatly helps her development team better help her. These wonderful individuals are constantly looking for additional ways to improve Sarah Jane's progress by speaking with their colleagues, reading literature on brain injury, and collaborating with other parents. But they all admit there is a considerable amount that still needs to be learned about the human brain, particularly the developing brain. The field of neuroscience today is similar to the computer science field of the 1950s and 1960s: you have a diverse group of very smart people working independently of one another throughout the United States and the world, yet few know what the others are doing behind closed doors. Fast- forward 50 years and many of the breakthroughs in the computer industry have been made utilizing the principles of open source a research method that promotes free and open access to the design and production of goods and knowledge. Its use was made well-known through the creation of the Linux computer operating system, in which professionals share knowledge to make corrections and fix problems. Open source is commonly used by millions of people today through the Wikipedia online free encyclopedia, a collection of public entries on established subjects that allows anyone to make additions or corrections. The National Institute of Mental Health launched The Human Brain Project in 1993 to develop and support the new science of neuro-informatics. From this initiative, it became obvious what needed to be done. That's why we created the Sarah Jane Brain Virtual Center of Excellence an ecosystem for professionals and families dealing with PABI around the world and a vehicle to help implement the PABI Plan by establishing a model system for PABI.
Bayesian estimation of bacterial communities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities.
ProGlycProt - A Repository of Experimentally Characterized GlycoProteins of Prokaryotes
Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time.
The e-mouse.org is an online resource that aims to bring together and provide users with all information related to the laboratory mouse and its use as a model organism. Users can find direct links to MRB, a resource management project that provides a dynamic and interactive view of most world wide available mouse resources, as well as the CreZOO, MMdb and Fleming Databases, three more specialized mouse repositories, all developed and hosted at the B.S.R.C. Alexander Fleming Institute. Additionally e-mouse.org provides links to major European and international mouse resources like the Mouse Genome Informatics (MGI), European Mouse Mutant Archive (EMMA), International Mouse Strain Resource (IMSR) and Ensembl. Users interested in retrieving information regarding the use of mouse models are encouraged to visit MRB which provides an index of publicly available mouse resources intended for both bench scientists and bioinformaticians. * Mouse Resource Browser (MRB) is a resource management project that provides a dynamic and interactive view of most world wide available mouse resources, classified in 22 categories. * CreZOO is the European virtual repository of Cre and other targeted conditional driver strains. Its aim is to capture and disseminate extant and new information on all Cre driver strains. * MUGEN Mouse Database (MMdb) is a virtual and fully searchable repository of murine models of immune processes and immunological diseases. * Fleming Database is a fully searchable resource developed to host all mouse strains developed and/or housed in BSRC Al. Fleming's animal house. * MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. * EMMA is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. * IMSR is a searchable online database of mouse strains and stocks available worldwide, including inbred, mutant, and genetically engineered mice. The goal of the IMSR is to assist the international scientific community in locating and obtaining mouse resources for research. * Ensembl is a project that produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
Neuroamer is a researcher-oriented blog about neuroscience, psychiatry, and psychology. It is an attempt to fill the space between journal articles and pop science journalism.
flipflop - Fast lasso-based isoform prediction as a flow problem
Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.
PREDiction of Subcellular Location from the N-terminal Sequence
Web tool using an algorithm that exploits neural networks, Markov Chains, and HMMs for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence and aims to classify proteins into five groups: Chloroplast, Thylakoid, Mitochondrion, Secreted proteins, and Other. As input PredSL requires the protein's sequence in fasta format.
Incorporated Research Institutions for Seismology Data Management Center Web Services
Incorporated Research Institutions for Seismology DMC Web Services
IRIS Data Management Center Web Services
Web services provided by the Incorporated Research Institutions for Seismology (IRIS) Data Management Center (DMC) to acquire data and metadata.
CAST - Compositional Bias Detection Algorithm
A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity.
A meta-list that is a compilation of other biology related wikipedia pages. These listings include the wiki name, description, year of inception, pages, new pages, users, active users, new edits, and wiki logo. The table can also be downloaded in a csv formatted table.
A blog by a Romanian clinical psychologist and psychotherapist Lucia Grosaru. Major categories include: General, lifestyle, news, pensees, psychologists, psychotherapy, self-help and video. Lucia Grosaru is the President and a Founding Member of the Romanian Institute Sic Cogito, Founding Member for The Romanian Center of Psychology and a Founding Editor of The Romanian Journal of Psychology, Psychotherapy and Neuroscience. Lucia is an integrative psychotherapist, clinical psychologist and a Certified Rorschach Inkblot Test Specialist (Method: Scuola Romana Rorschach, Italy). She has graduated the Psychology and Educational Science Faculty at the University of Bucharest in 2008 and the Cognitive Psychodiagnosis and Counseling Master's Programme in 2010.
A blog covering psychology, neuroscience, philosophy, quantum physics, and anything else worth writing about, by William Lu. William Lu is currently a postdoctoral fellow specializing in neuropsychology and rehabilitation psychology
Database of mutations associated with all major known forms of oculocutaneous and ocular albinism. The Albinism Database is part of the Locus Specific Mutation Databases of the Human Genome Variation Society and accepts the submission of new mutations. A link is provided for submission of new mutations. Columns in the database include: type of albinism, human locus, omim link, link to table of mutations and polymorphisms, and map of mutation locations.
PANDA: Phosphor Antibody Array Data Analysis
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies.
A Python package for representing electrophysiology data, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data (such as OpenElectrophy, NeuroTools, G-node, Helmholtz, PyNN) by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.
Pathline: A Tool For Comparative Genomics
Software visualization tool for comparative functional genomics that supports analysis of three types of biological data at once: functional data such as gene activity measurements; pathway data that presents a series of reactions within a cellular process; and phylogenetic data describing ancestral relationships between species. The design of Pathline includes two new visual encoding techniques. The first is an encoding of a linearized metabolic pathway representation that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is a curvemap, a matrix layout of temporal expression data for enhanced perception of trends in gene and cell activity levels across multiple species.
National Addiction and HIV Data Archive Program (NAHDAP)
National Addiction & HIV DATA Archive Program
National Addiction & HIV DATA Archive Program (NAHDAP)
National Addiction and HIV DATA Archive Program
National Addiction HIV Data Archive Program
Archive that acquires, preserves and disseminates data relevant to drug addiction and HIV research. Collection of data on drug addiction and HIV infection in United States. Most of datasets are raw data from surveys, interviews, and administrative records. They were originally gathered in research projects and for administrative purposes. Some datasets have been used in published studies. Bibliographies of these studies are available . Provides access to research data and technical assistance for data depositors. Provides e-workshops on data preparation and data systems.
FEED: Feeding Experiments End-User Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of physiologic data and associated metadata related to feeding behavior for a number of mammalian species, including human. The data contain information on muscle activity, bone and muscle strain, jaw and oropharyngeal apparatus motion, and intra-oral pressure and were generated using several techniques (e.g., electromyography, cineradiography, sonomicrometry). The data are searchable and can be downloaded into csv format.
Africa Centre for Health and Population Studies Biobank
THIS RESOURCE IS NO LONGER IN SERVICE, documented November 30, 2015. Extensive collection of biological specimens of various kinds that are mostly collected from the population around the Africa Centre in northern KwaZulu-Natal, but there are also specimens collected from populations in and around Durban and elsewhere in KwaZulu-Natal. The results of tests carried out on these specimens are generally stored in the main databases of the various studies involved, and are linkable back to the demographic and other data collected from the individuals concerned. The Biobank is curated by staff of the Africa Centre's Virology Laboratory in Durban, where all the specimens are currently stored, mostly in -80C freezers. A particular strength of its holdings are the dried blood spot (DBS), specimens five drops of blood on a filter-paper card, obtained via a finger-prick - of which there are now nearly 115,000. The following is a list of its holdings (May 2011): * 67,700 DBS specimens collected since late 2002 primarily for HIV prevalence estimation of the population covered by the Africa Centre Demographic Surveillance population. All have at least been tested for HIV, and just over 21% give a Positive result. Specimens are collected annually, so for some individuals we might have a sequence of 8-10 specimens covering 2002-2011. * 36,601 DBS specimens collected by the Vertical Transmission Study (VTS) between Sep 2001 and Dec 2006. This study focussed on mother-child pairs and investigated the vertical transmission of HIV from mother to child. DBS specimens were collected from both the mothers (at initial screening, and then from their children at Birth, 6, 10, 14, 18, 22 weeks, and 7, 8, 9, 12, 15, 18, 21 and 24 months. * 6,585 DBS specimens collected as part of the KZN IMPACT study of PMTCT effectiveness in six districts of kwaZulu-Natal. The specimens were collected during 2004-2006 from infants aged 4-8 weeks when mothers brought them to clinics for immunisation. These DBS specimens are stored at room temperature, not in freezers. * 3,524 DBS specimens collected as part of the Kesho Bora study from Sep 2007 . They were collected from mothers at enrollment, and from the infants at delivery, 2 weeks, and at 4, 5, 7, 8 and 15 months. * 50,068 Plasma specimens * 28,775 breastmilk specimens * 11,277 breastmilk products (Pellets and lactoserum). These have all been extracted from the BM specimens in prev. item? * 11,188 RNA and DNA products extracted from DBS and plasma specimens from all our major studies. * 5,735 Serum specimens * 3,505 cell pellets * 1,778 whole blood specimens * 1,284 Peripheral Blood Mononuclear Cells from the Kesho Bora study mothers (665) and their children (619) * 179 skin tissue specimens from the KST study (Kaposi's Sarcoma) * 176 foreskins
University of Neurosurgery Webinar Series
Congress of Neurological Surgeons Webinar Series
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. A series of of webinars offered directly to users' computers. The webinars are offered in a variety of subjects, including neurotrauma, spine, tumor and vascular. Each webinars costs $35 US and offers CME credit.
A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.
University of California Curation Center Merritt
Data repository service from the University of California Curation Center (UC3) that lets the UC community manage, archive, and share its valuable digital content. Merritt provides long-term preservation of digital assets, allows researchers to share data with others, or meet the data sharing and preservation requirements of a grant-funded project.
Forward-in-time simulation of Recombination
Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits.
Software integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Platform has collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible,
A research center whose primary functions are research, training, and outreach using nonhuman primates to study six of the ten major causes of death in the United States. Educational training includes programs designed to teach both pre- and postdoctoral veterinarians how to conduct biomedical research. Scientific outreach extends to investigators at Wake Forest School of Medicine and across the nation who require expertise, infrastructure, and monkeys to be used in studies that advance human health and well-being.
Gmcloser - Closing the gaps in scaffolds with preassembled contigs
Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.
UCSF Brain Tumor Research Center Tissue Bank
UCSF Brain Tumor Research Center Tissue Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Brain Tumor Research Center Tissue Bank began collecting tissue in 1978 and has established an organized repository of characterized tissues--frozen, paraffin-embedded, blood and cultures--that are maintained in a manner useful for a wide range of studies. Samples are collected only from patients who have agreed to have their tissues banked and used for future research. Consent documents are maintained in a secure area and associated clinical data are held in a double-password protected computer database. Each sample received into the Tissue Bank is non-identifying number. No protected health information (PHI) is released. To obtain samples, investigators submit a request form to the Manager. The request form requires an explanation of the tissue requested (type, number of samples, justification), description of the study, CHR approval (see new policy regarding human vs. non-human research) and Project Leader authorization. The Manager reviews each request for feasibility before presentation to the Scientific Core Committee. The UCSF Neurosurgery Tissue Bank makes its inventory of stock cell lines available to all investigators. Requested cells are grown in T-25 flasks and shipped FedEx Priority Overnight at the receipient's expense. However, if you prefer, we can ship the frozen cells, packed in dry ice. (Note: some countries restrict dry ice shipments.)
The open access F1000 Reports journals add an extra dimension to F1000, providing unique, peer-reviewed reports on emerging themes in biology and medicine. F1000 Section Heads ensure coverage of the latest advances by selecting topics and nominating experts to provide context for the evaluated literature. These open access journals are freely available to all users without barriers or the need for a subscription, and are currently indexed and/or abstracted by PubMed, PubMed Central, Scopus, Embase, Global Health and CAB Abstracts.
Wired Science covers what's new on the front lines of science, from deep space to DNA sequencing.
An independent, privately-held online and print publisher based in New York that serves the global community of scientists, technology professionals, and executives who use and develop the latest advanced tools in molecular biology research and molecular diagnostics. GenomeWeb's editorial mission is to serve readers with exclusive, in-depth coverage of the technology, institutions, and scientists that make up the worldwide research enterprise of molecular biology. We operate the largest online news organization focused on advanced research tools in genomics, proteomics, and bioinformatics. Our expert editors report and write with precision and clarity. GenomeWeb users can be found in major scientific organizations around the world, including biopharmaceutical companies, important research universities, biomedical institutes, and government laboratories. Our advertisers include leading suppliers of research tools, analytical instruments, and information technology. Getting started is easy - just register, and use your workplace e-mail address to maximize your access to content. Once you're logged in, you'll have complete free access to GenomeWeb Daily News, The Daily Scan, all of Genome Technology magazine, every GenomeWeb blog, and much more. GenomeWeb Free Content * GenomeWeb Daily News offers breaking news as well as feature articles on genomics, proteomics, bioinformatics, and more. Daily News covers not only the science and business news, but also regulatory and policy updates. Published online and twice daily by e-mail bulletin. * The Daily Scan is a roundup of the most interesting mainstream media articles, blog posts, and peer-reviewed literature relevant to genomic and proteomic scientists. Published daily online and by e-mail bulletin. * Genome Technology: GenomeWeb's magazine covers news, trends, people, and technologies in the systems biology field. It also includes Tech Guides, which feature expert troubleshooting advice on specific lab challenges, and Research Trend Digests. Published 10 times per year. Subscriptions to the print edition are free to active researchers in the US and $29 per year for non-scientists or anyone outside the US. Non-US researchers are eligible for a free subscription to the digital edition of Genome Technology. We may contact subscribers from time to time to requalify for the magazine, in compliance with our third-party readership audit. * Careers: Our Careers page includes content to help scientists in their jobs, with links to relevant external blog posts, profiles of alternative job paths, and more. Careers also includes our Job Listings board, where anyone can post job ads for free. * Cancer Minute: Updated daily and published by e-mail bulletin weekly, Cancer Minute rounds up the latest oncology peer-reviewed literature as well as news and blog posts. * Informatics Iron: This blog covers high-performance computing and the hardware side of bioinformatics, from GPUs to compute clusters and more. * The Sample: This blog focuses on a range of topics of interest to clinical labs, including the adoption of molecular tools, issues related to lab management, in-depth coverage of the major reference labs, and more. GenomeWeb Premium Content All GenomeWeb premium content provides readers with in-depth, exclusive coverage in key technology or application areas. These publications include business, technology, and research news; patent and IP information; product launches and upgrades; and hirings, promotions, and other people news.
Autism research program that makes available post-mortem brain tissue to qualified scientists all over the world. Working directly with tissue banks, organ procurement agencies, medical examiners and the general public, this is the largest program dedicated to increasing and enhancing the availability of post-mortem brain tissue for basic research in autism. To date, the ATP has collected and stored more than 170 brains in their repositories at Harvard (US) and Oxford (UK). These brains are processed by formalin fixation and/or snap frozen to properly provide high quality tissue of all brain regions, in support of biological research in autism. The ATP is unique in that they diligently pursue all available clinical data (pre and post mortem) on tissue donors in order to create the most biologically relevant brain repository for autism research. These data, together with tissue resources from both banks and associated repositories, are presented to all interested researchers through their extensive web-based data portal (login required). The ATP is not a brain bank, but works directly with the Harvard Brain Tissue Resource Center in Boston (HBTRC), Massachusetts to serve as its tissue repository. This program augments brain bank functions by: * Creating the most biologically relevant brain tissue repository possible * Fully covering all costs associated with brain extraction and transfer to the repositories at Harvard (US and Canada) and Oxford (UK). * Providing scientific oversight of tissue distributions * Overseeing and managing all tissue grants * Clinically phenotyping and acquiring extensive medical data on all of their donors * Providing continuing family support and communication to all of their donors * Directly supporting researchers to facilitate autism research * Maintaining a robust web based data management and secure on-line global interface system * Developing and supporting ATP established scientific initiatives * Actively providing public outreach and education The ATP is not a clinical organ procurement agency, but rather they facilitate the wishes of donors and families to donate their tissue to autism research. Through the ATP's established international infrastructure, they work with any accredited tissue bank, organ procurement agency, or medical examiner that receives a family's request to donate their loved one's tissue to the program. Once contacted, the ATP will insure that the family's request to donate their loved one's tissue is faithfully met, covering all costs to the family and partnering agency as well as ensuring the tissues' proper and rapid transport to the ATP's repository at the Harvard Brain Tissue Resource Center (HBTRC) in Boston, Massachusetts.
Blogs for all things chemistry, hosted by Chemical & Engineering News (C&EN) magazine, where you will find blogs written by both C&EN staff and non-staff contributors on topics ranging from jobs to natural products chemistry to safety to the businesses of chemistry. CENtral Science currently includes the following blogs: * Artful Science: C&EN science writer Sarah Everts peers in to the laboratories that help museums and galleries authenticate, conserve, and restore art and artifacts. * Cleantech Chemistry: C&EN business writer Melody Voith looks at the business and technology strategies of companies that hope to serve the world's need for renewable energy, sustainable agriculture, clean water, and non-polluting manufacturing and transportation, among other cleantech sectors. * IYC 2011: CENtral Science's home for all things IYC 2011. * Just Another Electron Pusher: Contributors Christine Herman and Glenn Ernst profile people who've pursued professions away from the bench. They also write about their own personal quests for satisfying jobs that use their degrees but may not involve running any %$@& columns. * Newscripts: The companion blog to the like-named weekly C&EN column. Written primarily by C&EN science writers Lauren Wolf and Beth Halford, with contributions from the C&EN staff. * Terra Sigillata: Molecular cancer pharmacologist David Kroll writes about natural products, focusing on chemistry and pharmaceutical issues. * The Chemical Notebook: C&EN business writer Alex Tullo shares interesting tidbits from his reporter's notebook. * The Editor's Blog: The companion blog to the weekly print column by editor-in-chief Rudy Baum and deputy editor-in-chief Maureen Rouhi. * The Haystack: C&EN business writer Lisa Jarvis and science writer Carmen Drahl weed through pharma's molecular mountain to pluck out the drug developments worth noting. Also features frequent contributions from SeeArrOh, a Ph.D chemist working in industry. * The Safety Zone: C&EN science writer Jyllian Kemsley and safety consultant Russ Phifer cover chemical safety issues in academic and industrial research labs and in manufacturing. * Transition States: A blog about undergrads, by undergrads. Chiral Jones, a senior working on organic chemistry, and Sidechain Bob, a junior in the field of chemical biology, tell their stories of the graduate school experience. Over time, some blogs will retire and others will be added. Their blog network is intentionally a small one, and bloggers are added on an invitation basis. Proposals or blog suggestions may be submitted. It's not a community without your voice, so please contribute either as a commenter or a blogger.
Gene Ontology Normal Usage Tracking System
A wiki where users of the Gene Ontology can contribute and view notes about how specific GO terms are used. GONUTS can also be used as a GO term browser, or to search for GO annotations of specific genes from included organisms. The rationale for this wiki is based on helping new users of the gene ontology understand and use it. The GONUTS wiki is not an official product of the the Gene Ontology consortium. The GO consortium has a public wiki at their website, http://wiki.geneontology.org/. Maintaining the ontology involves many decisions to carefully choose terms and relationships. These decisions are currently made at GO meetings and via online discussion using the GO mailing lists and the Sourceforge curator request tracker. However, it is difficult for someone starting to use GO to understand these decisions. Some insight can be obtained by mining the tracker, the listservs and the minutes of GO meetings, but this is difficult, as these discussions are often dispersed and sometimes don't contain the GO accessions in the relevant messages. Wikis provide a way to create collaboratively written documentation for each GO term to explain how it should be used, how to satisfy the true path requirement, and whether an annotation should be placed at a different level. In addition, the wiki pages provide a discussion space, where users can post questions and discuss possible changes to the ontology. GONUTS is currently set up so anyone can view or search, but only registered users can edit or add pages. Currently registered users can create new users, and we are working to add at least one registered user for each participating database (So far we have registered users at EcoliHub, EcoCyc, GOA, BeeBase, SGD, dictyBase, FlyBase, WormBase, TAIR, Rat Genome Database, ZFIN, MGI, UCL and AgBase...
Retraction Watch is a blog of retractions in the scientific literature. It is maintained by Adam Marcus and Ivan Oransky and has been operating since August 2010.
University of New South Wales Embryology
A wiki / educational resource for learning concepts in embryological development with sections including medicine, science, movies - audio, human embryo, systems, abnormal and animals. Pages on developmental topics can be added by experts in that specific research area and the content subject to easy review and update. Students can also contribute and several undergraduate courses use content on this site. Editing of pages will be restricted to registered users and all changes are logged.
The Drugs.com mission is to be the Internets most trusted resource for drug and related health information. We will achieve this aim by presenting independent, objective, comprehensive and up-to-date information in a clear and concise format for both consumers and healthcare professionals. Their goal is to provide clear information about drugs sold in the USA, at a level everyone can comprehend. For consumers, we provide product information in non-technical language. Health professionals will find what they need in the FDA Product Label Professional Information database. The Care Guide provides information about the treatment of common illnesses and injuries. The Drug Interactions checker details drug-drug interaction mechanisms, severity and management, and also outlines drug-food interactions. Drugs.com is NOT an online pharmacy and does not condone the sale of prescription medicines over the Internet without a prescription. Drugs.com simply provides a free drug-information service to help you better understand how medicines work: their uses, side effects and potential to interact with other medicines. For information on purchasing prescription medicines online please visit the FDAs Buying Prescription Medicine Online: A Consumer Safety Guide. Drugs.com medical dictionary is powered by Stedmans. Since 1911, Stedmans Medical Dictionary has been the medical professions most trusted source for medical definitions. A complete medical terms dictionary, Steadmans Electronic Medical Dictionary contains over 107,000 medical terms taken directly from Stedmans Medical Dictionary, 28th Edition. Most search engines cover the entire Internet, and searches on these engines may produce many results that are not specific to your drug question. On Drugs.com, you can search by medical condition or by drug, and get the answer you need right away. Searches by drug can be made using the brand name or the generic name of the drug. Searches by medical condition will return a list of medications used to treat that condition. Sponsors: The Drugs.com drug information service is supported by donations and revenue from site advertisers. The Drugs.com staff endeavor to source ads that are medically or community-service oriented. All ads must be appropriate for all-age family viewing, and we screen banner ads for family-appropriate content before the ads go live.
News magazine for the European life sciences. The mixture of content, spirit and language works to make both Lab Times and www.labtimes.eu a good read as demonstrated by steadily rising reader counts and click rates, and the positive researcher feedback we've received, including an email from Tim Hunt, winner of the 2001 Nobel Prize in Physiology or Medicine, in which he stated, I like your magazine, and I wanted to let you know how much I enjoy reading it.
The PEDIATRIC BRAIN TUMOR CONSORTIUM (PBTC) is a multidisciplinary cooperative research organization devoted to the study of correlative tumor biology and new therapies for primary CNS tumors of childhood. PBTC's mission is to contribute rapidly and effectively to the understanding and cure of these tumors through the conduct of multi-center, multidisciplinary, innovative studies with designs and analyses based on uniformly high quality statistical science. While the primary mission of the PBTC is to identify through laboratory and clinical science superior treatment strategies for children with brain cancers, the PBTC investigators recognize their profound responsibility to meet the special needs of the children and families as they face this enormous challenge. Members are committed to working within their institutions and communities to improve support services and follow up care for these patients and their families. The PBTC's primary objective is to rapidly conduct novel phase I and II clinical evaluations of new therapeutic drugs, new biological therapies, treatment delivery technologies and radiation treatment strategies in children from infancy to 21 years of age with primary central nervous system (CNS) tumors. A second objective is to characterize reliable markers and predictors (direct or surrogate) of brain tumors' responses to new therapies. The Consortium conducts research on brain tumor specimens in the laboratory to further understand the biology of pediatric brain tumors. A third objective is to develop and coordinate innovative neuro-imaging techniques. Through the PBTC's Neuro-Imaging Center, formed in May 2000, research to evaluate new treatment response criteria and neuro-imaging methods to understand regional brain effects is in progress. These imaging techniques can also advance understanding of significant neuro-toxicity in a developing child's central nervous system. The Neuro-Imaging Center is supported in part by private sources - grants from foundations and non-profit organizations - in addition to the NCI. As an NCI funded Consortium, the Pediatric Brain Tumor Consortium (PBTC) is required to make research data available to other investigators for use in research projects. An investigator who wishes to use individual patient data from one or more of the Consortium's completed and published studies must submit in writing a description of the research project, the PBTC studies from which data are requested, the specific data requested, and a list of investigators involved with the project and their affiliated research institutions. A copy of the requesting investigator's CV must also be provided. Participating Institutions: Children's Hospital of Philadelphia, Children's National Medical Center (Washington, DC), Children's Memorial Hospital (Chicago), Duke University, National Cancer Institute, St. Jude Children's Research Hospital, Texas Children's Cancer Center, University of California at San Francisco, and University of Pittsburgh.
A software which can perform methylcytosine calling from BS-seq (WGBS and RRBS), and permits either unmapped reads (FASTQ) or mapped reads (SAM/BAM) to be used as the input data. Certain SNPs (C>A/G) can also be selected in the output.
A set of perl programs that correct errors in 454 pyrosequences by identifying and flagging poor quality insertions, deletions and substitutions within an alignment. The algorithm utilizes the inherent base quality in sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion errors. CorQ also takes uneven read mapping into account for correcting pyrosequencing miscall errors and it identifies and corrects carry forward errors.
A software program for source imaging Magnetoencephalographic data. Now MEG tools has added Imaged Coherence mapping, Talairach and MNI coordinates, Grainger Causality. MEG Tools also includes MR-FOCUSS, ECD, Beamformers and many other useful MEG tools. This is a Matlab-based software module that is used to image MEG data onto a patient's MRI. This software imports all MEG manufacture's data (4D-Neuroimaging/BTi, CTF and Neuromag/Elekta).
A resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year.
Southern California Earthquake Data Center
Archive of earthquake data for research in seismology and earthquake engineering in Southern California recorded or processed by the Southern California Seismic Network (SCSN). Users can access information on: * Recent earthquakes detected by the SCSN * Significant southern California earthquakes and faults * The southern California earthquake catalog, spanning from 1933 to present * Waveform and metadata files of SCSN seismic stations from 1977 to present * Data sets created by SCEC scientists to assist in ongoing and future research
NGS tools for the novice - Handy tools for processing of next generation sequencing (NGS) data
A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution.
A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.
Virginia Commonwealth University, Department of Pharmacology
VCU Department of Pharmacology and Toxicology
VCU Department of Pharmacology Toxicology
VCU School of Medicine; Department of Pharmacology and Toxicology
A graduate program for pharmacology and toxicology that is a component of the Virginia Commonwealth University. This organization also performs studies on medical disorders, and new pharmacology agents and their effects on human health.
Molecular Evolutionary Genetics Analysis
Molecular Evolutionary Genetics Analysis 4
Molecular Evolutionary Genetics Analysis 6
Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.
Tennenbaum Center for the Biology of Creativity
The purpose of this center is to study the molecular, cellular, systems and cognitive mechanisms that result in cognitive enhancements and explain unusual levels of performance in gifted individuals, including extraordinary creativity. Additionally, by understating the mechanisms responsible for enhancements in performance we may be better suited to intervene and reverse disease states that result in cognitive deficits. One of the key topics addressed by the Center is the biological basis of cognitive enhancements, a topic that can be studied in human subjects and animal models. In the past much of the focus in the brain sciences has been on the study of brain mechanisms that degrade cognitive performance (for example, on mutations or other lesions that cause cognitive deficits). The Tennenbaum Center for the Biology of Creativity at UCLA enables an interdisciplinary team of leading scientists to advance knowledge about the biological bases of creativity. Starting with a pilot project program, a series of investigations was launched, spanning disciplines from basic molecular biology to cognitive neuroscience. Because the concept of creativity is multifaceted, initial efforts targeted refinement of the component processes necessary to generate novel, useful cognitive products. The identified core cognitive processes: 1.) Novelty Generation the ability to flexibly and adaptively generate products that are unique; 2.) Working Memory and Declarative Memory the ability to maintain, and then use relevant information to guide goal-directed performance, along with the capacity to store and retrieve this information; and 3.) Response Inhibition the ability to suppress habitual plans and substitute alternate actions in line with changing problem-solving demands. To study the basic mechanisms underlying these complex brain functions we use translational strategies. Starting from foundational studies in basic neuroscience, we forged an interdisciplinary strategy that permits the most advanced techniques for genetic manipulation and basic neurobiological research to be applied in close collaboration with human studies that converge on the same core cognitive processes. Our integrated research program aims to reveal the genetic architecture and fundamental brain mechanisms underlying creative cognition. The work holds enormous promise for both enhancing healthy cognitive performance and designing new treatments for diverse cognitive disorders. Sponsors: The Tennenbaum Center for the Biology of Creativity was inspired by the vision and generosity of Michael Tennenbaum.
A post-alignment micro re-aligner for next-generation high throughput sequencing data.
A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations.
A variation browsing and analysis tool for variants derived from next-generation sequencing data.
bamseek - Browse large BAM and SAM alignment files.
A Large File Viewer for BAM and SAM alignment files.
University of Southampton Cancer Research UK Centre Tumour Bank
Collects and distributes human tissue for ethically approved studies to aid the study of cancer biology and other associated research. All tissue is collected with patient consent and tissue is distributed only to ethically approved studies. The purpose of the Tissue Bank is to source, organize, collect, prepare, store and distribute a diverse collection of human tissues and biological products. This valuable core resource is available to all local academics and researchers. The on-site bank allows for rapid access to a plethora of biological materials supported by an informatics system of databases acting as an inventory management system. In addition, the Tissue Bank provides a licensed facility to store surplus tissue when studies close. Tissues currently available include normal and malignant snap frozen blocks, freshly prepared spleen and lymph nodes, fresh biopsy tissues, blood products and biological fluids. Collections can be organized by bank staff or ran in parallel with current research activities and include a wide variety of cancer classifications. We currently hold over 38,000 vials. Tissue Availability: Lymphoma - solid tissue and cells - 843; Breast - solid tissue and cells - 540; Colon - solid tissue and cells - 238; Lung - solid tissue and cells - 43; Upper Gi - BIOPSY tissue - 114; Pleural fluid and cells - 14
The Guardian: Science Weekly with Alok Jha
Alok Jha and the Guardian's science team bring you the best analysis and interviews from the worlds of science and technology.
A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets.
EUCOMM - Tools for Functional Annotation of the Mouse Genome
EUCOMM: Tools for Functional Annotation of the Mouse Genome
Functional Annotation of the Mouse Genome, it will complete the International Knockout Mouse Consortium (IKMC) resource of mutations for all protein coding genes. Furthermore, it will maximize the utility of the conditional IKMC resource by generating up to 250 different, mostly inducible Cre driver mouse lines. In addition, EUCOMMTOOLS will develop novel tools to enhance the versatility of the IKMC resource. EUCOMMTOOLS vectors, mutant ES cells and mutant mice are distributed worldwide: EUCOMMTOOLS mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMMTOOLS mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Knockout-first Mutant Alleles: EUCOMMTOOLS will create 3500 C57Bl/6 conditional mutant alleles for single-exon (or otherwise previously conditionally untargeted) protein-coding mouse genes. These alleles will be made predominantly by introducing an "artificial intron", containing a standard EUCOMM promoter-driven targeting cassette, into the coding sequence of the single-exon gene. Cre Resources: EUCOMMTOOLS will engineer 500 new Cre C57Bl/6 ES cell lines by Cre knock-ins into genes with useful expression patterns. The resource will be made with inducible forms of Cre recombinase such as CreERT2. Up to 250 lines of Cre driver mice on a pure C57Bl/6N background will be generated and the Cre expression patterns documented and annotated in day P14 and P56. These mice will form a matched Cre driver resource for C57Bl/6N mice produced from conditional IKMC resources. Research, Technology and Complementary Reagents: EUCOMMTOOLS will develop novel technologies to add value, depth and flexibility to existing IKMC ES cell and mouse resources. Key areas include: * Development of novel recombinase based regulatory switches * Exploration of zinc-finger nuclease stimulated homologous recombination strategies in fertilized oocytes * Development and validation of complementary modular vector reagents which enable the construction of new useful knock-in alleles such as fluorescent and other reporters, site specific recombinases, and mutant cDNAs. These novel alleles can be constructed either by re-utilizing existing IKMC modular vector resources or directly modifying existing targeted IKMC ES cell lines by RMCE.
WHO Collaborating Centre for Drug Statistics Methodology
The official compendium for the Anatomical Therapeutic Chemical Classification System (ATC)-code descriptions. The Centre's main tasks are development and maintenance of the ATC/DDD system, including: * To classify drugs according to the ATC system. * Priority will be given to the classification of single substances, while combination products available internationally (i.e. important fixed combinations) will be dealt with as far as possible. * To establish DDDs for drugs which have been assigned an ATC code. * To review and revise as necessary the ATC classification system and DDDs. * To stimulate and influence the practical use of the ATC system by co-operating with researchers in the drug utilization field. Support: The WHO Collaborating Centre for Drug Statistics Methodology was established in 1982. The Centre is situated in Oslo at the Norwegian Institute of Public Health. The Centre is funded by the Norwegian government.
Software tool for detecting structural variations with single-base resolution using soft-clipping information from SAM files.
Free, online public record system for registration of clinical trials being conducted in India. Initiated as a voluntary measure, trial registration in the CTRI has been made mandatory by the Drugs Controller General (India) (DCGI) (http://www.cdsco.nic.in/). Moreover, Editors of Biomedical Journals of 11 major journals of India declared that only registered trials would be considered for publication. Today, any researcher who plans to conduct a trial involving human participants, of any intervention such as drugs, surgical procedures, preventive measures, lifestyle modifications, devices, educational or behavioral treatment, rehabilitation strategies as well as trials being conducted in the purview of the Department of AYUSH (http://indianmedicine.nic.in/) is expected to register the trial in the CTRI before enrollment of the first participant. Trial registration involves public declaration and identification of trial investigators, sponsors, interventions, patient population etc before the enrollment of the first patient. Submission of Ethics approval and DCGI approval (if applicable) is essential for trial registration in the CTRI. Multi-country trials, where India is a participating country, which have been registered in an international registry, are also expected to be registered in the CTRI. In the CTRI, details of Indian investigators, trial sites, Indian target sample size and date of enrollment are captured. After a trial is registered, trialists are expected to regularly update the trial status or other aspects as the case may be. After a trial is registered, all updates and changes will be recorded and available for public display. The CTRI is working with the WHO ICTRP to ensure that results of all trials registered with the CTRI are adequately reported and publicly available.
Weekly articles related to brain-based learning and learning styles, problem-solving and creativity, kids, families, and parenting, gifted and visual learners, dyslexia, attention deficit disorders, autism, and more.
detecttd - Tool to detect tandem duplications in NGS reads
Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone.
A software tool for removal of de novo duplicates in paired short DNA sequences.
Annotated list of online CME (continuing medical education) with links to, and descriptions of, Web Sites offering courses and CME credit specifically aimed at Canadian physicians. All Canadian Online CME offering MainPro-M1 credit includes an online group discussion format. You must participate in these discussions as well as go though the didactic material to earn credit.
Genetic European Variation in Health and Disease
Genetic European Variation in Health and Disease - A European Medical Sequencing Consortium
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world.
H2SO4 Hurts: And Other Pearls of Science Wisdom
Blog about technology, molecular biology, and editorial comments on the current state of science on the internet. Brian Krueger PhD, is the owner, creator and coder of LabSpaces by night and a Molecular biologist by day. His posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, his employer, or his educational institution.
TMAP - torrent mapping alignment program
Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.
BISMA: Analysis of primary bisulfite sequencing data manual
Bisulfite Sequencing DNA Methylation Analysis
An online tool for the analysis of bisulfite sequencing DNA methylation data. The software has specificity and quality control functions that allow the user to compile a set of sequences.
SOAP: short oligonucleotide alignment program
Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease
Consortium of Radiologic Imaging Study of PKD
A five-year prospective cohort study following 240 patients who have autosomal-dominant polycystic kidney disease (PKD) to determine whether changes in anatomic characteristics of their kidneys as measured by magnetic resonance imaging will be useful in providing surrogate measures for disease progression. CRISP's overall goal is to develop methods that would facilitate shortening the observation period necessary to determine efficacy of treatment interventions in PKD patients. Specific goals of this study are to: * Quantify cyst growth and ascertain severity of renal parenchymal involvement by sequential measurement of total kidney volume and the ratio of intact parenchyma to renal parenchyma occupied by cysts over time * Establish useful clinical correlations of imaging data with other markers of disease progression * Identify and test other potential markers or indices of disease progression, for example, assessment of loss of heterozygosity of renal cells shed in the urine, or other markers, in cohorts of patients with PKD * Gain information about the cost-effectiveness, patient acceptability, and advantages and disadvantages of different imaging techniques used serially in patients with PKD. Some experience has been gained in establishing that repeat imaging of the same PKD patient, using these techniques, yields reproducible estimates of kidney size and the proportion of renal parenchyma occupied by cysts. MRI may also have the advantage of permitting simultaneous estimation of GFR. Ultrasound has the advantage of being more cost-effective and perhaps more acceptable to patients for repetitive studies, but the measurements may be less accurate and reproducible. Nonetheless, there is very limited experience in applying these techniques to follow progression of the renal disease. Development of improved, reproducible imaging methods that assess cyst growth and provide markers of disease progression could markedly improve the feasibility of clinical trials. Participating clinical centers are Emory University, the Mayo Clinic, University of Kansas, and the University of Alabama at Birmingham. The data coordinating and imaging analysis center is at Washington University. (PI has since moved to University of Pittsburgh) The study found that kidney enlargement resulting from the expansion of cysts is continuous, quantifiable, and associated with the decline of renal function. Cystic expansion occurs at a consistent rate per individual, although it is heterogeneous in the population, and that larger kidneys are associated with more rapid decrease in renal function. These anatomic characteristics of patient kidneys may provide useful surrogate measures for disease progression, and hence enhance the development of targeted therapies for autosomal dominant PKD. CRISP III is a five-year prospective cohort study to follow ~170 remaining autosomal dominant polycystic kidney disease (ADPKD) patients who were part of the original CRISP cohort study. CRISP III will verify and extend the preliminary observations of CRISP to determine the extent to which quantitative (kidney volume and blood flow, and hepatic and kidney cyst volume) or qualitative (cyst distribution and character) structural parameters predict renal insufficiency and develop and test new metrics to quantify and monitor disease progression. Urine metabolites and the genome will be correlated with the progression of disease to look for new, predictive disease biomarkers. This information from CRISP III will help determine if the kidney enlargement, blood flow, cyst distribution, or urine metabolites can function as an informative surrogate measure for disease progression.
A software pipeline based on TopHat2 combined with a splice junction detection algorithm.
A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
PyNIfTI - Pythonic access to NIfTI and ANALYZE files
Pythonic access to NIfTI and ANALYZE files
PyNIfTI is no longer actively developed. At has been superseded by NiBabel -- a pure-Python package that provides everything that PyNIfTI could do, and a lot more. The PyNIfTI module is a Python interface to the NIfTI I/O libraries. Using PyNIfTI, one can easily read and write NIfTI and ANALYZE images from within Python. The NiftiImage class provides pythonic access to the full header information and for a maximum of interoperability the image data is made available via NumPy arrays.
Academy scientists, journalists, adventurers and other staff members are blogging their stories and inviting questions and comments. Read current science news, hear from researchers in the field (Philippines, Sao Tome, Papua New Guinea), ask a question of an Academy naturalist, and much more.
Software for short-read mapping to accurately map reads from the next-generation sequencing technology. It can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.
California National Primate Research Center Analytical and Resource Core
California National Primate Research Center Analytical Resource Core
The Analytical and Resource Core provides services and resources to the scientific research community in areas including hematology, clinical chemistry, genetics, immunology, endocrinology, flow cytometry, and pathogen detection. Available resources include biological specimens, viral stocks, DNA, and species-specific reagents. Scientists and staff associated with each of the seven Core Laboratories provide consultation in experimental design, sample collection, and data analysis, and offer assays that utilize species-specific reagents wherever possible. Core Laboratory scientists can also work with users to develop new assays to meet research needs. Training is available for all assays, and Core Laboratories equipment can be made available, typically on a recharge basis. Nonhuman primate resources developed at CNPRC are available to qualified individuals via the Resource Services component of the Core. * Clinical Laboratory * Endocrine Core Laboratory * Flow Cytometry Core Laboratory * Genetics Core Laboratory * Infectious Diseases Immunology Core Laboratory * Pathogen Detection Core Laboratory * Respiratory Disease Immunology Core Laboratory * Affiliated Laboratory: Clinical Proteomics Core Laboratory * Affiliated Laboratory: Microarray Core Facility * Resource Services: The following research resources of CNPRC are available to scientists on a recharge basis. ** Allergen: Characterized protein extracts of house dust mite (Dermatophagoides pteronyssinus and Dermatophagoides farinae) are available for allergen sensitization projects. ** Biological Specimens: Tissues collected at necropsy are available from rhesus monkeys (Macaca mulatta), cynomolgus monkeys (Macaca fascicularis), and titi monkeys (Callicebus cupreus). Contact: Biospecimens (at) primate.ucdavis.edu Blood samples are available through our blood donor program. ** Data: Data for colony animals are available from our computerized database. Data include birth records, weights, reproductive history, relocation history, etc. ** DNA: DNA extracted from peripheral blood mononuclear cells is available on animals of all age-sex classes from known pedigrees. ** Reagents and Samples: Reagents, controls, and known/unknown samples are available from the Pathogen Detection Core Laboratory. Samples include pedigreed sera/plasma, fixed tissues and DNA from macaques and various other species. Validated reagents for many pathogens are available, including SIV, SRV1-5, SFV, STLV, RRV, RhCMV, Herpes B, SV40, and LCV. More information is available at: http://pdl.primate.ucdavis.edu/PDLreagents.html. ** Shipping: Shipping services are available by trained staff who can properly document, package and ship critical experimental materials, including nonhuman primate samples. Assistance is also provided for obtaining CITES permits, required for international shipment of any nonhuman primate samples. ** Transformed B-Cell Lines: Cryopreserved Herpes papio - transformed B cell lines from over 300 rhesus monkeys in the CNPRC colony are available. Transformation of macaque B cells to establish a new cell line is available on request. ** Virus Stock: Rhesus Cytomegalovirus: A unique primary isolate, developed at CNPRC, is available. ** Virus Stock: Simian Immunodeficiency Virus: Aliquots of SIVmac251 and SIVmac239 virus stocks were prepared by propagation in peripheral blood mononuclear cells from rhesus macaques and contain approximately 100,000 50% tissue culture infectious doses per ml. As measured by the commercial SIV branched chain assay, SIVmac251 contains 2 x 109 copies of SIV RNA per ml and SIVmac239 contains 109 copies of SIV RNA per ml. These virus stocks are infectious for rhesus macaques by intravenous, intravaginal and oral routes of inoculation.
Semantic Web Applications in Neuromedicine (SWAN) Ontology
Semantic Web Applications in Neuromedicine Ontology
The SWAN (Semantic Web Applications in Neuromedicine) ontology is an ontology for modeling scientific discourse and has been developed in the context of building a series of applications for biomedical researchers, as well as extensive discussions and collaborations with the larger bio-ontologies community. Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to properly contextualize and integrate data and discourse in machine-interpretable form. This inherently limits the productivity of research and the progress toward cures for devastating diseases such as Alzheimer's and Parkinson's. The SWAN ontology is organized in three types of modules: * basic: basic modules represent the ontology building blocks. They cover topics that are general enough to be included in every ontology distribution. The current basic modules are: ** collections ** provenance, authoring and versioning (PAV) ** discourse relationships ** FOAF (in OWL-DL) ** SKOS (in OWL-DL) ** qualifiers ** scientific discourse * extension: extensions modules are covering topics (a) that can be related only to some fields of science (b) for which there could be more than one implementation (c) for which a temporary solution has been provided and it is possible to forecast its substitution. The current extensions modules are: ** life science entities ** citations ** qualifiers extension modules * distribution: distributions are modules that are including all the basic modules and extensions necessary for serving a specific domain (i.e. the SWAN ontology for the Alzheimer knowledge base or the generic distribution that is not binded to any specific scientific domain). The current available distributions are: ** swan-scientific-discourse ** swan-alzheimer
An information retrieval system that provides knowledge enriched searching facilities across the ever growing MEDLINE collection, the world's most comprehensive source of life sciences and biomedical bibliographic information. The semantic faceted search, using named entity recognition, can be accessed from your browser. By combining a selection of software services they can provide enhanced results through a process that identifies key entities within the text, such as gene names or proteins, and improves the querying method with unique identifiers by automatically including synonyms, spelling variants and even disambiguating acronyms. This combines with the traditional features found in other interfaces to provide a much needed solution to the growing problem of finding valuable information within the ever increasing volume of modern publications. The current available categories: * PROTEIN, GENE, METABOLITE, DISEASE, SYMPTOM, ORGAN, * DIAG_PROC, THERAPEUTIC_PROC, (diagnostic/therapeutic procedure, e.g. MRI, cerebral blood flow) * GENERAL_PHENOM, HUMAN_PHENOM, NATURAL_PHENOM, (Medical phenomenon or process, e.g. UV radiation ) * INDICATOR (Reagent or diagnostic aid, e.g. hydrogen peroxide, sulfhydryl reagent) * ACRONYM, AUTHOR, PUBLICATIONTYPE (e.g. Journal Article, Technical Report) Reference: C. Nobata, P. Cotter, N. Okazaki, B. Rea, Y. Sasaki, Y. Tsuruoka, J. Tsujii and S. Ananiadou. Kleio: a knowledge-enriched information retrieval system for biology. In Proc. of the 31st Annual International ACM SIGIR Conference, pp. 787--788, 2008
Andreas Vesalius De Humani Corporis Fabrica
Andreas Vesalius' De Humani Corporis Fabrica
English translation of Andreas Vesalius' Renaissance anatomical atlas On the Fabric of the Human Body (1543, 1555) and an explanation of the work in progress at Northwestern University to translate and annotate this historic work (by Daniel Garrison and Malcolm Hast). This detailed account of human anatomy transformed its subject and forever changed medical education in the West. Its woodcut illustrations became the basis of medical art and illustrations for generations to come, and continue to influence the way we look at the human body. * Book One -- The things that sustain and support the entire body, and what braces and attaches them all. (the bones and the ligaments that interconnect them) * Book Two -- All the ligaments and muscles, instruments of voluntary and deliberate motion * Book Three -- The series of veins and arteries throughout the body * Book Four -- The nerves * Book Five -- The organs of nutrition and generation * Book Six -- The heart and organs serving the heart (Chiefly the heart and lungs) * Book Seven -- The brain and organs of sense Note: Only introduction, images, and essays appear to be available.
A genetic testing company for rare and complex disorders and syndromes. The company specializes in retinal disorders, reproductive medicine and oncology. They also offer custom genotyping services.
Spinal Research committed to funding international research into cure for spinal cord paralysis. Charity that funds medical research for treating and curing spinal cord paralysis. Supports basic science, clinical research and funds PhD students. ISRT also hosts Annual Network Meetings.
A model evaluation method for training someone to read data. There are three methods: the holdout method, K-fold cross validation, and leave-one-out cross validation.
A web application framework that helps build applications or run protocols for the web. It allows the user to manage various tasks being run on the web both manually and through existing Perl modules.
A commercial company that sells affordable brain recording kits geared for neuroscience education purposes. Their products are meant to mimic electroencephalograms, a tool that measures the electrical activity of neurons.
An Australian brain bank which aims to collect, store, characterize and provide tissue to national and international researchers studying disorders of the brain such as alcohol-related brain damage and mental illness, like schizophrenia. The program encourages those who are medically healthy to donate.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Interactive database of Drosophila melanogaster nervous system. Used by drosophila neuroscience community and by other researchers studying arthropod brain structure.
Comprehensive Drug Self-administration and Discrimination Bibliographic Databases
Drug Self-administration and Discrimination Bibliographic Databases
Database of bibliographic details of over 9,000 references published between 1951 and the present day, and includes abstracts, journal articles, book chapters and books replacing the two former separate websites for Ian Stolerman's drug discrimination database and Dick Meisch's drug self-administration database. Lists of standardized keywords are used to index the citations. Most of the keywords are generic drug names but they also include methodological terms, species studied and drug classes. This index makes it possible to selectively retrieve references according to the drugs used as the training stimuli, drugs used as test stimuli, drugs used as pretreatments, species, etc. by entering your own terms or by using our comprehensive lists of search terms. Drug Discrimination Drug Discrimination is widely recognized as one of the major methods for studying the behavioral and neuropharmacological effects of drugs and plays an important role in drug discovery and investigations of drug abuse. In Drug Discrimination studies, effects of drugs serve as discriminative stimuli that indicate how reinforcers (e.g. food pellets) can be obtained. For example, animals can be trained to press one of two levers to obtain food after receiving injections of a drug, and to press the other lever to obtain food after injections of the vehicle. After the discrimination has been learned, the animal starts pressing the appropriate lever according to whether it has received the training drug or vehicle; accuracy is very good in most experiments (90 or more correct). Discriminative stimulus effects of drugs are readily distinguished from the effects of food alone by collecting data in brief test sessions where responses are not differentially reinforced. Thus, trained subjects can be used to determine whether test substances are identified as like or unlike the drug used for training. Drug Self-administration Drug Self-administration methodology is central to the experimental analysis of drug abuse and dependence (addiction). It constitutes a key technique in numerous investigations of drug intake and its neurobiological basis and has even been described by some as the gold standard among methods in the area. Self-administration occurs when, after a behavioral act or chain of acts, a feedback loop results in the introduction of a drug or drugs into a human or infra-human subject. The drug is usually conceptualized as serving the role of a positive reinforcer within a framework of operant conditioning. For example, animals can be given the opportunity to press a lever to obtain an infusion of a drug through a chronically-indwelling venous catheter. If the available dose of the drug serves as a positive reinforcer then the rate of lever-pressing will increase and a sustained pattern of responding at a high rate may develop. Reinforcing effects of drugs are distinguishable from other actions such as increases in general activity by means of one or more control procedures. Trained subjects can be used to investigate the behavioral and neuropharmacological basis of drug-taking and drug-seeking behaviors and the reinstatement of these behaviors in subjects with a previous history of drug intake (relapse models). Other applications include evaluating novel compounds for liability to produce abuse and dependence and for their value in the treatment of drug dependence and addiction. The bibliography is updated about four times per year.
Mouse Models For Alzheimer's Disease Research
An information resource about several models for mice to develop Alzheimer's-related characteristics as they age.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 09, 2013. A java tool to search published activation data. All data from papers submitted to the fMRI Data center are included, and may be referenced online or via flat file. Users may create their own data files, by saving subsets of original data or creating their own comma seperated value files (with simple formatting information included on the top row). Searches may be made based on coordinate space (MNI or T-space), anatomical area, author, and a number of other fields. Searched points may be displayed on a 3-d brain representation, as well.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A visualization tool for MRI images which handles several formats (.gipl,.mha,.hdr). It uses integrated coupled cursors to show the differences between images. It can load an overlay image and make screenshots.
A non-profit charity dedicated to providing education about animal research for the purpose of protecting medical and scientific progress. The organization seeks to provide accurate and incisive information to foster a balanced public debate on animal research issues. They work to do outreach by distributing timely and relevant news, information and analysis about animal rights extremism to the research community.
BRAINnet-Brain Research And Integrative Neuroscience Network
Brain Research And Integrative Neuroscience Network
A neuroscience network providing access to a database of brain, cognitive, genomic and clinical data for research and scientific publication. Data include genomic information, electrical measures of brain and body function, structural and functional MRI, and cognitive and medical history. All data are collected using a standardized assessment protocols. These data are from healthy people and those experiencing a range of brain-related illnesses.
NIH - Rapid Access to Interventional Development
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14, 2025.NIH-RAID makes available at no cost to researchers and organizations certain critical resources needed for the development of new therapeutic agents. This program, part of the Translational Research component of Reengineering the Clinical Research Enterprise, uses resources of NCI's Developmental Therapeutics Program and the National Heart Lung and Blood Institutes (NHLBI) Gene Therapy Resource Program. The services provided will depend upon the stage of the project and the strength of the preliminary data. Services available include: production, bulk supply, GMP manufacturing, formulation, development of an assay suitable for pharmacokinetic testing, and animal toxicology. Assistance also will be provided in the regulatory process, through access to independent product development planning expertise. Proposals in support of animal efficacy studies or synthesis and formulation of recombinant proteins or monoclonal antibodies will not be accepted. NIH-RAID is not a grant program. Successful projects will gain access to the governments contract resources, as well as the assistance of the NIH in establishing and implementing a product development plan. Funds to support individual projects will come both from the Roadmap and from individual Institutes, with Institutes assuming the bulk of support in the specific disease areas germane to their mission. This co-sponsorship is critical because of the resource and expertise needs and because NIH-RAID cannot support the full developmental pipeline; an Institute partnership may therefore be important for subsequent translational efforts. To obtain access to NIH-RAID resources, applications must be submitted electronically through Grants.gov using SF424. Applications are initially screened to determine whether the resources requested are appropriate for this program. Then they are reviewed by the NIH Center for Scientific Research. The results of that evaluation along with supplemental information from the lead investigator will guide final Institute and Roadmap resource allocation. The services provided will depend upon the stage of the project and the strength of the preliminary data. When a lead therapeutic agent has been selected and proposed for preclinical development, the following services are available: For small molecules, natural products, peptides, oligonucleotides, and gene vectors: Synthesis, Scale-up production, Development of analytical methods, Development of suitable formulations, Isolation and purification of natural products, Pharmacokinetic/ADME studies including bioanalytical method development, Range-finding initial toxicology, IND-directed toxicology, Manufacture of clinical trial supplies, Product development planning and advice in IND preparation For recombinant proteins and monoclonal antibodies: Pharmacokinetic/ADME studies including bioanalytical method development, Range-finding initial toxicology, IND-directed toxicology, Product development planning and advice in IND preparation When a lead therapeutic agent has not yet been selected and proposed for preclinical development, the following services are available: For small molecules, natural products, peptides, oligonucleotides, and gene vectors: Synthesis, Development of analytical methods, Isolation and purification of natural products, Preliminary Pharmacokinetic/ADME studies, including bioanalytical method development, Preliminary toxicology For recombinant proteins and monoclonal antibodies, Preliminary Pharmacokinetic/ADME studies, including bioanalytical method development, Preliminary toxicology In some cases the NIH-RAID program will support only one or two key steps for preclinical development, while in other cases it may be possible to provide assistance with most of the development tasks needed to file an Investigational New Drug (IND) application to the Food and Drug Administration (FDA). When the NIH-RAID program does not provide all of the remaining services required for IND submission, it is expected that other resources will be in place to complete development steps not supported by NIH-RAID. Funding Resource,.
A blog for peer-reviewed scientific papers taken from behind journal-subscription paywalls. It serves as a resource for those who cannot access these resources.
Oregon State University College of Pharmacy
The college of pharmacy at Oregon State University that offers professional education in pharmacy. The foundational goals are to provide professional education, foster research to contribute to public health initiatives and promote safe and affordable medication access.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A neuroscience program that provides research-based, rigorous training in neuroscience that prepares students for neuroscience-related graduate, masters or PhD programs. This program is competitive and only accepts a limited number of students each year.
Scripps Women's College, Neuroscience Department
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A neuroscience program that prepares the student for graduate work in biology, psychology, neuroscience, or preparation for medical school or a career in the health services.
A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends.
Stanford University Psychiatry and Behavioral Sciences
A Stanford-affiliated organization which is primarily concerned with the study and treatment of sleep disorders, the treatment of psychological illnesses, and the training of medical students, residents and research fellows in psychiatry and sleep medicine.
Temple University School of Medicine, Department of Neuroscience
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A department within the Temple University School of Medicine, which focuses on the education and research. This organization also hosts seminar series in neuroscience, sponsors annual lectures in neuroscience, and organizes bi-annual one-day workshops. This department has collaborative projects with researchers from the microbiology, immunology, pharmacology, radiology and the center for substance abuse research departments.
University of Texas Medical Branch Neurobiology
The University of Texas Medical Branch Neuroscience and Cell Biology
A department within the University of Texas which is concerned with researching basic and translational research in neuroscience and cell biology, as well as providing training in those disciplines for graduate, medical and post-doctoral students.
University of California, Irvine, Department of Anatomy and Neurobiology
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A department within UC Irvine which supports studies in anatomy and neurobiology, and provides education at the medical, graduate and postgraduate levels.
University of Miami, Department of Neuroscience
A department within the University of Miami which offers both undergraduate and postgraduate programs in neuroscience. The graduate program provides neuroscience research training in biological, behavioral, and physical sciences. This organization also conducts research through 55 active laboratories.
University of Vermont College of Medicine, Pharmacology
A department within the University of Vermont which offers a undergraduate minor, and a graduate program in pharmacology.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Biozon is a unified biological resource on DNA sequences, proteins, complexes and cellular pathways. It currently provides data on pairwise similarities between proteins, the domain structure of proteins, structural similarities, threading-based and profile-profile similarities between protein families. Additional information about 3D models, predicted protein-protein interactions, assignment of genes to pathways and expression data analysis, as well as local and global maps of the protein space will be gradually added to Biozon.
Perlegen/NIEHS National Toxicology: Mouse Genome Resequencing Project
THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Data, grouped by chromosome, available as flat files for download, of identified DNA polymorphisms (SNPs) in 15 commonly used strains of inbred laboratory mice. Perlegen's SNP, genotype (empirical and imputed), haplotype, trace, and PCR primer data has been compiled with NCBI Mouse Build information to produce data files for public use. Using high-density oligonuclueotide array technology, the study identified over 8 million SNPs and other genetic differences between these strains and the previously sequenced C57BL/6J reference strains (Phase 1). By leveraging data provided by Mark Daly's research team at the Broad Institute, genotypes were also predicted for 40 other common strains (Phase 2). Under an extension to the contract, Eleazar Eskin's group at UCLA has used this data to evaluate SNP associations with phenotypes from the Mouse Phenome Project (the Mouse Phenome Database), and to construct haplotype maps for a total of 94 inbred strains (the Mouse HapMap Project). SNP and genotype positions have been mapped from their original reference coordinates to NCBI Mouse Build 37 coordinates. Note that C57BL6/J strain was not selected for re-sequencing as this data would have been almost entirely redundant with the NCBI reference sequence. Since we did not actually determine genotypes for C57BL6/J, we did not submit genotypes for this strain to dbSNP. However, implicit genotypes for C57BL6/J can be obtained from the reference sequence at each SNP position (the reference allele is the first allele in the ALLELES column). The data is available for download in two different compressed file formats. The files are saved as both PC .zip files and Unix compressed .gz files. At this website, you can: * Learn more about the goals of the Perlegen mouse resequencing project. * Learn more about the array-based resequencing technology used in the project. * Download the SNPs, genotypes, and other data generated by the project, plus sequences of the long-range PCR primers used for SNP discovery. * Browse the mouse genome for SNPs. * View the haplotype blocks within the mouse genome. Mouse Genome Browser The Mouse Genome Browser can be used to visualize genes and the SNPs discovered in this study of genome-wide DNA variation in 15 commonly used, genetically diverse strains of inbred laboratory mice. The reference genome is the C57BL/6J strain NCBI build 37 mouse sequence. In addition to the experimentally-derived genotypes for the original 15 strains, the imputed genotypes for 40 additional inbred mouse strains can also be accessed. Mouse Haplotype Analysis The sequences of 16 commonly used, genetically diverse strains of inbred laboratory mice were analyzed to determine their haplotype structure. The Ancestry Browser shows which ancestral sequence each inbred strain most resembles, along with statistics on the pairwise similarity between the ancestral strains. The Haplotype Viewer shows the haplotype block boundaries and the pairwise similarity for all 56 strains: the 15 used for SNP discovery, the reference strain (C57BL/6J), and the 40 additional strains for which the genotypes were imputed.
An open-access Genomic Database for Lepidoptera. It includes all the Lepidoptera cDNA sequences available in NCBI's dbEST. Support for genomic-DNA sequences such as BACs and the Bombyx mori genome is being generated. Tools available on this website include BLAST search, Annotation search, Primer design, and Microsatellite repeat finders. Users can also download all data and sequences. Within the site, the Expressed Sequence Tag sequences are made with Trace2dbest from raw sequence data if available or downloaded from NCBI. We cluster them using PartiGene into gene-objects to reduce redundancy. Subsequently, we perform hierarchical BLAST searches to provide accurate similarity annotation and a robust protein translation protocol using prot4EST. Putative proteins objects have been further annotated with the Gene Ontology biological vocabulary (GO terms) and InterPro (EBI) domains to facilitate gene-hunters. The repository is open for all Lepidopteran researchers.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September23, 2022. Cancer GEnome Mine is a public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes. Within the website, users can browse microarray data or perform searches by hospital/disease classification/pathology/clinical presentation and other methods.
Cre-X-Mice: A Database of Cre Transgenic Lines
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Cre-X-Mice is a database of Cre transgenic mouse lines and mice genes. Users can search the database by anatomical area, cell type, stage, promoter locus, transgene type, or other properties. Users can also view anatomical areas by stage, or submit transgenic mouse lines.
Catalogue for Transmission Genetics in Arabs
The CTGA database is a database for genetic disorders in Arab populations. It hosts entries for Mendelian disorders and related genes, and currently contains nearly 1290 entries. Its goal is to facilitate further research on Arab genomic diseases.
DIMA, the Domain Interaction Map, aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains. The scope of the resource comprises both experimental data and computational predictions. Several methods and datasets have been integrated, already and inclusion of others is under way.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. EGO is a database of eukaryotic gene orthologs generated by pair-wise comparison between the Tentative Consensus (TC) sequences that comprise the Dana Farber Gene Indices from individual organisms.
Development of Validated Drosophila in vivo RNAi Models of Human Diseases
Database that provides free online tools to users to allow the retrieval of information related to the Drosophila genome and allows access to genome-wide and related cell-based screening of Drosophila at Harvard Medical School (for a fee) . Tools available include SnapDragon, and RNAi designer, a heat map tool for viewing screen data, and gene and amplicon search and download tools. The DRSC mainly exists to provide Drosophila genome screening services, including help with assay development and optimization, data and image analysis, and planning of follow-up assays.
FUGOID: a Database for Functional Genomics of Organelle Introns
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. FUGOID is a database for functional genomics of organelle introns. The taxonomically broad organelle intron database contains comprehensive functional and structural information on organellar (mitochondria and chloroplast) introns. FUGOID collects and integrates various structural and functional data on organellar (mitochondrial and chloroplast) introns, particularly functional information about intron splicing and mobility. It is implemented in a relational database management system and can be searched either by intron information or by a major reference. Data entry and revision systems have also been developed.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A data mining platform for the biogerontological-geriatric research community. It enables users to analyze, query, and visualize the aging-related genomic data. Our goal is to facilitate the digestion and usage of the public genomic data. A current focus is on integrative analysis of microarray gene expression data. We are establishing a central database for aging microarray data of six species: human (H. sapiens), rat (R. norvegicus), mouse (M. musculus), "fly" (D. melanogaster), "worm" (C. elegans), and yeast (S. cerevisiae). GAN is equipped with a set of bioinformatics tools for analysis of the microarray data sets, cross-platform and cross-species.
GOLD.db - Genomics Of Lipid-associated Disorders
Genomics Of Lipid-associated Disorders database
GOLD.db Genomics Of Lipid-associated Disorders
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 22, 2016. A database that integrates information on the function and properties of genes and their protein products relevant to lipid-associated disorders. GOLD.db provides information such as the biology, diagnosis management, treatment and prevention of such disorders like non-insulin dependent diabetes, various hyperlipedemias, high blood pressure and atherosclerosis. Resources include the biological pathways, data sets, microarray protocols and other experimental standards, analytical tools, and reagents.
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 22, 2016. A database of biomarkers for diagnosis, detection, protection and characterization of infectious diseases. It provides information on pathogens and biomarkers, such as nucleic acids, proteins, carbohydrates, and immune epitopes. The site links to global news and life science journal search engines as well as provides links to tool functions for gene sequence and protein structure analyses.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts.Includes geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; environmental genome browser with fast search functionalities; database with precomputed analyses for selected complete genomes; database and tool to classify metagenomic fragments based on oligonucleotide signatures.
A database of object-relational mitochondrial protein sequences, which contains both mitochondrial and nuclear encoded entries. This database that was generated from experimental evidence and other public databases. Each protein is annotated with data from external databases, including: Locuslink, Ensembl, OMIM, MINT, DIP, PFAM, InterPro, PRINTS and NCBI NR.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A database used for high throughput mapping of genes to QTL and comparative genome analysis between different humans, mice, and rats. This database is designed for the analysis of larger sets of data using genome-scale experimental approaches, and to organize information from various websites and publications.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A website that provides access to a database, nomenclature, fac sheets, downloadable slides, and other information regarding RB1 gene mutations.
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 22, 2016. A database on the proteome of rice that contains reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. It provides comprehensive interactive SNP annotation, as well as a selection and prioritization system for focused genotyping projects and/or analysis and interpretation of SNP data. The user can create one or more SNP lists and populate them by adding SNPs either directly or by picking genes, pathways, chromosomal locations or by uploading own SNP lists. Additionally, users can design one or more SNP scoring systems based on any available SNP annotations. After that, SNP scores can be computed for any user SNP list using any of the designed scoring systems. Those scores can be used to prioritize SNPs. Sorted/filtered SNP lists can be exported in tab-delimited text format. The SNP lists and scoring rules can be kept private or shared within the workgroup or made public.
VectorDB- Molecular Biology Vector Sequence Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. A database with information about a variety of vectors, including phage, plasmid, phagemid, phasmid, cosmid, virus and YAC vectors. It also contains information on drosophilia, C. elegans, yeast and drosophilia vectors, including vector functions, hosts and copy number.
A platform for posting and viewing videos related to all areas of neuroimaging.
A software application and database viewing system for genomic research, more specifically formulti-genome comparison and pattern discovery via genome self-comparison. Data are available for a range of species including Human Chr3, Human Chr12, Sea Urchin, Tribolium, and cow. The Genboree Discovery System is the largest software system developed at the bioinformatics laboratory at Baylor in close collaboration with the Human Genome Sequencing Center. Genboree is a turnkey software system for genomic research. Genboree is hosted on the Internet and, as of early 2007, the number of registered users exceeds 600. While it can be configured to support almost any genome-centric discovery process, a number of configurations already exist for specific applications. Current focus is on enabling studies of genome variation, including array CGH studies, PCR-based resequencing, genome resequencing using comparative sequence assembly, genome remapping using paired-end tags and sequences, genome analysis and annotation, multi-genome comparison and pattern discovery via genome self-comparison. Genboree database and visualization settings, tools, and user roles are configurable to fit the needs of specific discovery processes. Private permanent project-specific databases can be accessed in a controlled way by collaborators via the Internet. Project-specific data is integrated with relevant data from public sources such as genome browsers and genomic databases. Data processing tools are integrated using a plug-in model. Genboree is extensible via flexible data-exchange formats to accommodate project specific tools and processing steps. Our Positional Hashing method, implemented in the Pash program, enables extremely fast and accurate sequence comparison and pattern discovery by employing low-level parallelism. Pash enables fast and sensitive detection of orthologous regions across mammalian genomes, and fast anchoring of hundreds of millions of short sequences produced by next-generation sequencing technologies. We are further developing the Pash program and employing it in the context of various discovery pipelines. Our laboratory participates in the pilot stage of the TCGA (The Cancer Genome Atlas) project. We aim to develop comprehensive, rapid, and economical methods for detecting recurrent chromosomal aberrations in cancer using next-generation sequencing technologies. The methods will allow detection of recurrent chromosomal aberrations in hundreds of small (
Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona.
Vision Action and information manaGEment System in health
Research team focused on research and development of new algorithms in medical imaging, information processing and computer assisted intervention in the context of the pathologies of the central nervous system. Research team jointly affiliated to INSERM (National Institute of Health and Scientific Research), Inria (National Institute of Research in Computer Sciences and Automation) and IRISA / UMR CNRS 6074, University of Rennes I. Multidisciplinary team merging researchers in image processing and medical doctors.
This Wiki page provides information about Interactome of various species. An interactome of a species provides an important clues on how to interpret metabolic pathways of constituent enzymes and global protein network, which facilitates in turn to understand the mechanism responsible for the cellular functions.
Royal Institute of Technology: Research Project Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The KTH Research Project Database is intended to contain all the currently on-going projects at KTH. Sponsors: This resource is supported by the Royal Institute of Technology, Sweden,
The Salk Institute conducts research within three major areas of study: Molecular Biology and Genetics; Neurosciences; and Plant Biology. Six key areas represent strategic research priorities: Chemistry and Proteomics; Stem Cell Biology; Cell Biology; Regulatory Biology; Metabolic Research; and Computational and Theoretical Biology.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of genetic and gene expression data from the published literature on psychiatric disorders. Users can search the accumulated data to find the evidence in support of the involvement of a particular genomic region with a set of important psychiatric disorders, ADHD, autism, bipolar disorder, eating disorder, major depressive disorder, schizophrenia, and smoking behavior. It contains findings from manual reviews of 144 papers in psychiatric genetics, 136 primary reports and 8 meta-analyses. Disorders covered include schizophrenia (44 papers), autism (24 papers), bipolar disorder (24 papers), smoking behavior (24 papers), major depressive disorder and neuroticism (14 papers), ADHD (8 papers), eating disorders (3 papers), and a combined schizophrenia-bipolar phenotype (3 papers). The unbiased searches integrated into SLEP include genomewide linkage (117 papers), genomewide association (15 papers), copy number variation (9 papers), and gene expression studies of post-mortem brain tissue (3 meta-analyses courtesy of the Stanley Foundation). In total, SLEP captures 3,741 findings from these 144 papers. SLEP also contains over 70,000 SignPosts. These annotations derive from many different sources and are designed to try to capture current state of knowledge about disease associations in the human genome. SignPosts can be searched simultaneously with the psychiatric genetics literature in order to integrate these two bodies of knowledge. The SignPosts include: accumulated GWAS findings from the human genetics literature, the OMIM database, candidate gene association study literature, CNV location and frequency data, SNPs that influence gene expression in brain, genes expressed in brain, genes with evidence of imprinting and random monoalleleic expression, genes mutated in breast or colorectal cancer, and pathway data from BioCyc.
The database NPIDB (Nucleic acid Protein Interaction DataBase) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from Protein Data Bank (PDB) (1932 complexes in the end of 2007). It is equipped with a web-interface and a set of tools for extracting biologically meaningful characteristics of complexes. They are committed to satisfy all potential database users in order to: 1. Provide an essential information on structural features of DNA-protein and RNA-protein interaction for the users who need to get acquainted with the problem. 2. Give an effective access to the reasonably structured information about all DNA-protein and RNA-protein complexes containing in PDB. 3. Allow all visitors a quick access to our own research.
Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins.
A database of antibody structure containing sequences from Kabat, IMGT and the Protein Databank (PDB), as well as structure data from the PDB. It provides search of the sequence data on various criteria and display of results in different formats. For data from the PDB, sequence searches can be combined with structural constraints. For example, one can ask for all the antibodies with a 10-residue Kabat CDR-L1 with a serine at H23 and an arginine within 10A of H36. The site also has software for structure analysis and other information on antibody structure available.
Science Commons, OBO Foundry, and several other groups working with biological information on the Semantic Web have initiated an effort to establish shared community-maintained URIs for important data integration points such as life sciences database records (example: the record in the Entrez Gene database that has GeneID 1003064). We are attempting to determine the right technical and organizational recipe that will lead to the uptake of these URIs by a as many RDF-using bioinformatics projects as possible. Were this to be a success, one would be able to mash up information from multiple sources in a wide variety of ways, using the shared URIs to forge links between pieces. Information could be extracted from one source for inclusion in another; information could be combined in SPARQL queries using multiple FROM clauses; extractions from several triple stores could be combined to create a new one. Without shared URIs, this kind of integration would still be possible, but it would be significantly more difficult as it would require some kind of plumbing or mapping to get the two result sets to link up. Requirements We are limiting our concern for now to URIs for records in databases mentioned in external links from the Gene Ontology (GO), such as those from Enzyme or Pfam, with possible extension to other databases such as those in the LSRN (Life Science Resource Name) registry. The URIs we propose are meant to serve the community of Semantic Web-enabled bioinformatics projects that need URIs that refer to or denote database records. We identify the following requirements for URIs to serve a community and to be shared among Semantic Web projects: 1. It must be clearly stated what the intended referent of each URI is supposed to be, i.e. that the URI denotes some particular record from some particular database. 2. Information about the URI and its referent, including such a statement, must be made available, and in order to leverage existing protocol stacks, it must be obtainable via HTTP. (We'll call such information URI documentation.) 3. URI documentation must be provided in RDF. 4. Provision of URI documentation must be an ongoing concern. The ability to provide it may have to outlive the original database or the database's creator. 5. The provider of the URI documentation must be responsive to community needs, such as the need to have mistakes fixed in a timely manner. 6. URI documentation must be open so that it can be replicated and reused. Control of shared URIs should be in the hands of those who depend on them. This is the best way to ensure that the URIs serve the community in the ways listed above. Overall design The idea is to manage a server, or a set of servers, that can deliver appropriate RDF documents for the shared URIs. An HTTP GET of a URI would retrieve not the database record itself, but rather one of these RDF documents (perhaps via a 303 redirect). The RDF document will include the following: 1. Documentation specifying what the URI denotes (URI documentation), including an rdf:type, the database that the record comes from, and the record's identifier or key within that database. 2. Links to the various encodings of the record provided by the data provider, e.g. XML, ASN, HTML for the NCBI databases and so on. Each of these encodings would in turn have its own URI naming that particular encoding of the record, the main URI being the name of the record without commitment as to encoding. 3. Links as appropriate to corresponding resources belonging to semantic web projects participating in the common naming scheme, e.g. http://bio2rdf.org/pmid:15456405. 4. Links as appropriate to related external resources that build on the database record. For example, the RDF for PubMed record 15456405 could link out to the iHOP page for the article described by the PubMed record. 5. Other information related to the record that might be of use to a human reader or automated agent. External links can be represented rigorously in RDF, allowing programs that access the RDF to proceed deterministically not only to the various encodings but also to any of the various related resources. This might be accomplished by having a distinct property for each participating project, or in some other way. We do not generally expect the RDF to include any of the content of the database record, although there is no particular reason to rule this out (except in cases where license terms preclude it). science, commons, biological, bioinformatic, naming
AMPDB: Arabidopsis Mitochondrial Protein Database
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. The Arabidopsis Mitochondrial Protein Database is an Internet-accessible relational database containing information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana. This database, and the proteomic data contained in it for Arabidopsis mitochondria, have been accepted for publication in The Plant Cell.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This database is intended to serve as a learning tool to obtain curated information for the design of microarray targets to scan collecting duct tissues (human, rat, mouse). The database focuses on regulatory and transporter proteins expressed in the collecting duct, but when collecting duct proteins are a member of a larger family of proteins, common additional members of the family are included even if they have not been demonstrated to be expressed in the collecting duct. An Internet-accessible database has been devised for major collecting duct proteins involved in transport and regulation of cellular processes. The individual proteins included in this database are those culled from literature searches and from previously published studies involving cDNA arrays and serial analysis of gene expression (SAGE). Design of microarray targets for the study of kidney collecting duct tissues is facilitated by the database, which includes links to curated base pair and amino acid sequence data, relevant literature, and related databases. Use of the database is illustrated by a search for water channel proteins, aquaporins, and by a subsequent search for vasopressin receptors. Links are shown to the literature and to sequence data for human, rat, and mouse, as well as to relevant web-based resources. Extension of the database is dynamic and is done through a maintenance interface. This permits creation of new categories, updating of existing entries, and addition of new ones. CDDB is a database that organizes lists of genes found in collecting duct tissues from three mammalian species: human, rat, and mouse. Proteins are divided into categories by family relationships and functional classification, and each category is assigned a section in the database. Each section includes links to the literature and to sequence information for genes, proteins, expressed sequence tags, and related information. The user can peruse a section or use a search engine at the bottom of the web page to search the database for a name or abbreviation or for a link to a sequence. Each entry in the database includes links to relevant papers in the kidney and collecting duct literature. It uses links to PubMed to generate MEDLINE searches for retrieval of references. In addition, each entry includes links to curated sequence data available in LocusLink. Individual links are made to sequence and protein data for human, rat, and mouse. Links are then added as curated sequences become available for proteins identified in the renal collecting duct and for proteins identified in kidney and similar in function or homologous to proteins identified in the collecting duct.
Disease Genes Conserved Sequence Tags Database
A database of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts. Human and mouse genomic sequences were compared by BLASTZ. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity. The database can be accessed by gene, chromosomal location, graphic browser, DNA features, and coding regions.
A division of the Stanford University Libraries, which produces the online versions of journals and other scholarly content.
Histology World: Nervous System Histology
This website contains a lot of images and slides of the nervous system. Most images are of the central nervous system histology and peripheral nervous system histology. Computation Neuroscience
MAboya Gene Expression Patterns and Sequence Tags
MAboya Gene Expression Patterns and Sequence Tags (MAGEST)
A database for maternal gene expression information for ascidia, colloquially known as sea squirts. Information available includes DNA sequences, expression patterns of ESTs, and cDNA data from uncleaved fertilized eggs. The goal is to utilize the database to understand molecular mechanisms of establishment of embryonic body plans of chordates and to understand evolution from invertebrates to vertebrates in the future.
Basic Local Alignment with Successive Refinement
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html
CPODES is a numerical integrator for solving multibody dynamics problems using coordinate projection. It is based on the CVODES integrator which is part of the DOE Sundials suite. It is a multistep integrator providing variable order Adams (up to 12th order) and BDF (up to 5th order) methods for non-stiff problems and BDF (up to 5th order) for stiff problems. It uses CVODES to advance the ODE, and then performs coordinate projection back to the constraint manifold to exactly solve the DAE. The projection is also incorporated back into the error test where it permits larger steps. Binaries of this software are bundled with other SimTK Core modules.
Syndicated Universities Preparatory Research Educational Program
SUPREP MODEL LEARNING is a standardized credit earning academic exchange program that enables a student from any third world countries or technologically deficient institutions around the world, to attend and earn credits from the best traditional recognized accredited institutions globally, in which the credits earned are transferred to the home institution or SUPREP agency for aggregation towards successful graduation. :The goal of this program is to facilitate bringing students from the third world to reputable undergraduate and graduate neuroscience programs. Additionally, this program also aims t o grant Third World Neuroscience students Academic exchange programs worldwide.
NIH/Merck-Merial Summer Research Program
Program designed to expose students in their first or second year of veterinary school to all phases of biomedical research. This includes development of research ideas, preparation of research proposals, performance of biomedical research, and presentation of research results in written and oral formats. Students perform full time biomedical research during months of June, July, and August, participate in weekly seminars, and present their work in oral, poster, and written presentations. Students also attend the National Merial Scholars Conference. Summer Research Program has existed at Penn Vet since 1990. The program is currently funded by Merial and by an NIH training grant. Other sources of support include funds from the office of the dean, the four departmental chairs and the Marie Lowe Cancer Center. Students present poster of their work at the conference. In September, students prepare a written manuscript of their work in the form of a research paper. The following March, all participating students submit their work to the Penn Veterinary Student Research Day. Non-Penn Vet students can receive up to an additional $500 for relocation costs and will be offered reasonably priced housing options for the summer. It is anticipated that 18-24 students will be funded each year.
The Colour & Vision Research laboratory and database are based at the Institute of Ophthalmology, which is part of University College London. The Institute and CVRL are both closely associated with Moorfields Eye Hospital. The Institute is next door to Moorfields Eye Hospital near Old Street tube station (see directions). At the Colour & Vision Research laboratory, we investigate normal and clinical human visual perception. Our research focuses on questions about colour perception, light and dark adaptation, night-time vision, and the temporal and spatial properties of vision. Our primary goal is to understand the nature of the mechanisms that underlie visual perception, and to understand how those mechanism malfunction in clinical cases. More details about our research can be found by looking at the publications of members of the laboratory. The CVRL database, first set up in 1995, provides an annotated library of downloadable standard data sets relevant to colour and vision research. The focus of this site is primarily scientific and technical, but some introductory background information is also provided. A consistent set of functions for modeling colour vision based on the Stockman & Sharpe cone fundamentals and on our more recent luminous efficiency measurements are summarized under the category CVRL functions. These functions are tabulated in 0.1, 1 and 5 nm steps and can be returned as csv, xml, or tabular data or as dynamic plots. The Stockman & Sharpe cone fundamentals are the basis of a CIE proposal for physiologically-relevant colour matching functions. These functions, which are indentical to the CVRL functions, are summarized under the category CIE 2007 functions. The CIE functions are also tabulated in 0.1, 1 and 5 nm steps, and can also be returned as csv, xml, or tabular data or as dynamic plots. Significant additions to the database are the individual colour matching measurements made by Stiles & Burch. These have been compiled and cross-checked with the help of Boris Oicherman, Alexander Logvinenko, and Abhijit Sarkar from hard copies of the original data provided by Pat Trezona and Mike Webster. They can be obtained as Excel files and are available for both 2 and 10 colour matches. Other data sets, which are provided as csv files, include cone fundamentals, colour matching functions, chromaticity coordinates, prereceptoral filter density spectra, photopigment spectra, and CIE standards. Many of these data sets can also be viewed as dynamic plots. Sponsors: CVRL is funded by BBSRC The Wellcome Trust, Fight for Sight, National Eye Institute, and NIH.
Gemina is a web-based system designed to identify infectious pathogens and their representative genomic sequences through selection of associated epidemiology metadata. Gemina supports the development of DNA signature-based assays for the detection of pathogens or sets of pathogen through the Insignia Signature Pipeline at the University of Maryland. Sponsors: This resource is supported by the US Department of Homeland Security Science and Technology Directorate. [W81XWH-05-2-005, NBCH2070002].
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB).
A partnership that leads and inspires the world in achieving universal access to HIV prevention, treatment, care and support. UNAIDS publishes a new Report on the global AIDS epidemic every two years. The Report draws upon and publishes the best available data from countries and provides an overview and commentary on the epidemic and the international response. UNAIDS fulfills its mission by: :- Uniting the efforts of the United Nations system, civil society, national governments, the private sector, global institutions and people living with and most affected by HIV; :- Speaking out in solidarity with the people most affected by HIV in defense of human dignity, human rights and gender equality; :- Mobilizing political, technical, scientific and financial resources and holding ourselves and others accountable for results; :- Empowering agents of change with strategic information and evidence to influence and ensure that resources are targeted where they deliver the greatest impact and bring about a prevention revolution; and :- Supporting inclusive country leadership for sustainable responses that are integral to and integrated with national health and development efforts. Sponsors: This resource is supported by: Advocacy partners; Civil society; Donors; Global Coalition on Women and AIDS; Global Fund to Fight AIDS TB and Malaria; People living with HIV; Private sector, and UN Family.
Health 2.0 embraces the idea of bringing health care into the community of physicians, patients, and those in the health care industry together with technology and the Internet to provide the best possible health care environment.
Company focused on animal welfare and pest prevention in the wool industry.
A service for preparing genetically modified mice and rats for investigators at the University of Michigan. These mice models are typically used to study gene function, gene expression, gene regulation, and for the development of animal models of human disease and gene therapy reagents. TAMC provide access to their micromanipoulation and embryos stem cell workstations along with necessary reagents such as specialized plasmids, embryonic stem (ES) cell lines, FBS, and feeder cells certified for ES cell culture.
A visualization tool with microarray data and sample descriptions from the AtGenExpress project, which contains Affymetrix microarray data for Arabidopsis, a small flowering plant related to mustard and cabbage. This plant is used as a model organism in plant biology.
A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in.
An interactive computer system that utilizes cell phones and the Internet to collect real-time data about transmission rates of STDs, such as vaginosis among female sex workers, in Peru. This is tracked through the rates of precriptions of Metronidazole, an antibiotic used to treat bacterial infections of the vagina, stomach, skin, joints, and respiratory tract. Data from three communities is stored in an online database that can be accessed over secure Internet connection. This project has demonstrated that it is feasible to develop a public-health-surveillance system based on cell phones to collect data in real-time in Peru.
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. This site is built and maintained by the Madhani Lab, Dept. of Biochemistry and Biophysics at the University of California, San Francisco
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. Software designed to serve as a distributed computational framework to help perform mathematical simulations of muscle contraction. DEngine has a Windows PC, central controller PC and mathematical models that run as console applications on clients.
A suite of software tools designed for the rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data.
A database software for managing, analyzing and sharing information across multiple devices and people, both online and offline.
A portal for Maitreya Dunham's lab, which works on the genomic analysis of experimental evolution in yeast using microarrays and the chemostat. Research interests of the lab include experimental evolution of genetic networks in yeast, aneuploidy and copy number variation, comparative genomics, technology development and human genetics in yeast.
Understanding Human Disease Through Mouse Genetics
European Union Mouse Research for Public Health and Industrial Applications
A portal documenting a project for the development of novel approaches in phenotyping, mutagenesis and informatics to improve the characterization of mouse models for understanding human molecular physiology and pathology. EUMORPHIA has developed a new robust primary screening platform for determining the phenotype of mice: EMPReSS - European Mouse Phenotyping Resource for Standardised Screens. The project is also focused on training new young scientists by funding them to work in a variety of laboratories to gain a broader swathe of techniques. The project has also identified the need for more trained mouse pathologists. To address this, they are setting up training courses in pathology and working at a European level to establish more training.
A commercial vendor for science equipment and life science consumables. This company offers customer support such as: taking/tracking orders, product installation and training, application support, calibration services, and general product maintenance and repair.
Commercial vendor of visualization software, factory automation equipment and electric components.
Functional Annotation of the Mammalian Genome
Functional Annotation of the Mammalian Genome (FANTOM)
International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN.
A group dedicated to combining a variety of experimental and theoretical approaches to find general principles that explain the structure, behavior and evolution of cells and organisms. The center hosts a variety of fellows and faculty from various backgrounds such as biology, physics, chemistry, mathematics, computer science and engineering.
Portal of GEN2PHEN project, holistic approach to genotype-to-phenotype data. Aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality.
International Federation of Pharmaceutical Manufacturers and Associations Clinical Trials Portal
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. IFPMA Clinical Trials Portal is brought to you by IFPMA on behalf of its Member Companies and Associations. IFPMA Clinical Trials Portal ensures: a free and easy-to-use interface for patients and health professionals alike to ongoing clinical trials, clinical trial results and complementary information on related issues; non-promotional and reliable information; industry's commitment to the transparency of clinical trials. * Search by Medical Condition and Drug Name * Language Interfaces (En, Es, Fr, De, Jp) * Glossary and Easy Explanation of Medical Expressions * Geographical Search
A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research.
Veterans Health Information Systems and Technology Architecture
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A system of software applications that support patient care at Veterans Health Administration health care facilities. VISTA connects VHA facility workstations and PC's with nationally mandated and locally adapted software known as the Computerized Patient Record System (CPRS). Information is relevant to day-to-day operations for patients' medical and healthcare utilization histories such as data on demographics, episodes of care, medicines, practitioner information, diagnoses and procedures. All patients treated at VA Medical Centers are included in the files.
A school for education on community health sciences based out of the University of Nottingham. The school contains the divisions of epidemiology, public health, primary care, psychiatry, rehabilitation and aging. The common thread running through each of these divisions is that they all deal with communities, whether these be the entire populations of a region or country, or particular patient groups such as the mentally ill, people with disabilities, and elderly people.
Ronald M. Davis Tobacco Deposition and Trial Testimony Archive
A database of information from the Center for Tobacco Use Prevention and Research. Materials include depositions, trial testimony and opening and closing statements, expert reports, jury instructs, and verdicts. Some transcripts are rough copies and others may be marked as confidential although they no longer retain that status. This resource is in French.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. The SAGE Genie website provides highly intuitive, visual displays of human and mouse gene expression, based on a unique analytical process (Boon et al.) that reliably matches SAGE tags, 10 or 17 nucleotides in length, to known genes. Recently, with the construction and incorporation of a reference database of SNP-associated alternative tags into SAGE Genie (Silva et al.), the interpretation of tag to human gene mapping has been enhanced. Human SAGE Genie Tools The SAGE Anatomic Viewer visually displays the relative expression of a given gene in normal and malignant tissues of the human body. In addition, there is access to: o The Digital Northern, which shows the relative expression of the gene in each library. o The Ludwig Transcript (LT) Viewer, which visually represents a particular transcript with up to four possible virtual SAGE tag locations (starting from the 3' end) and locations of internally primed or alternatively polyadenylated transcripts. o Expanded access to brain, hES cells, and breast cell subtypes. * The SAGE Digital Gene Expression Displayer distinguishes significant differences in gene expression profiles between two pools of SAGE libraries. * The SAGE Experimental Viewer provides DGED results for pre-set pairs of libraries, one under control and the other under experimental conditions. * The SAGE Absolute Level Lister lists all SAGE libraries and links to the distribution of transcript expression levels in any given library. * The SAGE Library Finder tool searches for one or more tissue-specific libraries from the SAGE collection. * SAGE Genie Downloads provide files of genes, tags, datasets, mappings, and more. * SAGE Genomics Finder tool searches for genomics info for tags. * DKView tool for viewing Digital Karyotyping data. * DK Microbe tool searches for exact matches of 17 base-pair digital karyotyping tags in bacterial and viral genomes. * SAGE Tag Extraction tool to extract tags from sequence files. Mouse SAGE Genie Tools * The mSAGE Expression Matrix visually displays the relative expression of a given gene through stages of mouse development. In addition, there is access to: o The Digital Northern, which shows the relative expression of the gene in each library. o The Ludwig Transcript (LT) Viewer, which visually represents a particular transcript with up to four possible virtual SAGE tag locations (starting from the 3' end) and locations of internally primed or alternatively polyadenylated transcripts. * The mSAGE Absolute Level Lister lists all mouse SAGE libraries, organized by either tissue (normal or malignant) or developmental stage, and links to the distribution of transcript expression levels in any given library. * The mSAGE Digital Gene Expression Displayer distinguishes significant differences in gene expression profiles between two pools of mouse SAGE libraries. * The mSAGE Experimental Viewer automatically sets up the DGED with mouse libraries, prepared as stand alone experiments, for gene expression comparison. * The mSAGE Library Finder tool searches for one or more tissue-specific mouse libraries from the SAGE collection. * mSAGE Genie Downloads provide files of mouse genes, tags, datasets, mappings, and more. * SAGE Genomics Finder tool searches for genomics info for tags. * SAGE Tag Extraction tool to extract tags from sequence files. Notes: The majority of human libraries are short whereas the majority of mouse libraries are long. Several mouse developmental libraries are prepared by the SAGELite method. SAGELite is an extension of the long Sage protocol that includes a PCR-based amplification stage to allow the use of 10ng to 100ng of total RNA to produce a Sage library. However, it has been observed that a significant bias incurred by this amplification process. SAGE Genie was produced as part of the NCI CGAP SAGE project with collaborators from Johns Hopkins University, the Ludwig Institute for Cancer Research, Sao Paulo Branch, the University of Texas MD Anderson Cancer Center, and the Genome Sciences Center of the BCCRC.
A database of cytogenetic and clinical information on rare chromosomal disorders, including microdeletions and microduplications. The database is meant to be easily accessible for all participants, to improve patient care and collaboration between genetic centers, and collect the results of research and clinical features. The acronym ECARUCA stands for "European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations".
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 5, 2014. Keyose is a project designed and led by a family physician. We are not IT focused, but health-care focused. Technology is just a tool, not our purpose.
Sectional Atlas of Human Brain and Spinal Cord
Neuroanatomy Lab Resource Appendices Sectional Atlas
Sectional atlas featuring sections of the spinal cord and brain for a neuroanatomy course offered by Temple University. Labels may be turned on and off.
Ensembl Genomes project produces genome databases for important species from across taxonomic range, using Ensembl software system. Five sites are now available, one of which is Ensembl Metazoa, which houses metazoan species.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 13, 2012. Snippets of HTML that capture the information that is most important in a machine-readable, interlinked format, making it easier to see the big picture. aTags work with any Web text and can store and connect any textual element that is highlighted in a browser. The structure of the embedded RDF/OWL is decidedly simple: a very short piece of human-readable text that is "tagged" with relevant ontological entities. An aTag generator can be easily added to any web browser and allows researchers to quickly generate aTags out of key statements from web pages, such as PubMed abstracts. The resulting aTags can be embedded anywhere on the web, for example on blogs, wikis, or biomedical databases. aTag demonstrates how the resulting statements that are distributed over the web can be searched, visualized and aggregated with Semantic Web / Linked Data tools, and discusses how aTags can be used to answer practically relevant biomedical questions even though their structure is very simple. aTags are based on Semantic Web standards and Linked Data practices. Specifically, they make use of RDFa, the SIOC vocabulary and various domain ontologies and taxonomies that are available in RDF/OWL format. The autocomplete functionality is based on Apache Solr. Reference: Simple, ontology-based representation of biomedical statements through fine-granular entity tagging and new web standards Matthias Samwald and Holger Stenzhorn. Bio-Ontologies 2009., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Online Education for the International Research Community: AboutIntroduction to Clinical Drug and Substance Abuse Research Methods
THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 07, 2012. Decemeber 15, 2011 - Thank you for your interest in DrugAbuseResearchTraining.org. The site, courses, and resources are no longer available. Please send an email to inquiry (at) md-inc.com if you would like to be notified if the site or courses become available again. Introduction to Clinical Drug and Substance Abuse Research Methods is an online training program intended to introduce clinicians and substance abuse professionals to basic clinical research methods. The program is divided into four modules. Each module covers an entire topic and includes self-assessment questions, references, and online resources: * The Neurobiology of Drug Addiction * Biostatistics for Drug and Substance Abuse Research * Evaluating Drug and Substance Abuse Programs * Designing and Managing Drug and Substance Abuse Clinical Trials The learning objectives of this program are to help you: * Evaluate the benefits of alternative investigative approaches for answering important questions in drug abuse evaluation and treatment. * Define the proper levels of measurement and appropriate statistical methods for a clinical study. * Address common problems in data collection and analysis. * Anticipate key human subjects and ethical issues that arise in drug abuse studies. * Interpret findings from the drug abuse research literature and prepare a clinical research proposal. * Prepare research findings for internal distribution or publication in the peer reviewed literature. * Recognize drug addiction as a cyclical, chronic disease. * Understand and describe the brain circuits that are affected by addicting drugs, and explain to others the effects of major classes of addicting drugs on brain neurotransmitters. * Utilize new pharmacologic treatments to manage persons with drug addiction. Physicians can earn AMA PRA Category 1 Credit and purchase a high resolution printable electronic CME certificate(view sample); non-physicians can purchase high resolution printable electronic certificate of course participation that references AMA PRA Category 1 credit (view sample). This program does not offer printed certificates.
CPCTR: Cooperative Prostate Cancer Tissue Resource
Cooperative Prostate Cancer Tissue Resource
THIS RESOURCE IS NO LONGER IN SERVICE. Doumented on September 23,2022. The National Cancer Institute initially established the Cooperative Prostate Cancer Tissue Resource (CPCTR) to provide prostate cancer tissue samples with clinical annotation to researchers. The Resource provides access to formalin-fixed, paraffin-embedded primary prostate cancer tissue with associated clinical and follow-up data for research studies, particularly studies focused on translating basic research findings into clinical application. Fresh-frozen tissue is also available with limited clinical follow up information since these are more recent cases. The Resource database contains pathologic and clinical information linked to a large collection of prostate tissue specimens that is available for research. Researchers can determine whether the Resource has the tissues and patient data they need for their individual research studies. Consultation and interpretive services: Assistance is available from trained CPCTR pathologists. The CPCTR can provide consultative assistance in staining interpretation, and scoring, on a collaborative basis. Fresh Frozen and Paraffin Tissue: The resource has over 7,000 annotated cases (including 7,635 specimens and 38,399 annotated blocks). Tissue Microarrays (TMA): The CPCTR has slides from prostate cancer TMAs with associated clinical data. The information provided for each case on the arrays (derived from radical prostatectomy specimens) includes: age at diagnosis, race, PSA at diagnosis, tumor size, TNM stage, Gleason score and grade, and vital status and other variables.
A database of funding opportunities, professional conferences, calls for papers and other research-related materials. ResearchRaven is a public service provided by the Samaritan Health Services Center for Health Research and Quality.
Collaborative Informatics and Neuroimaging Suite
Collaborative Informatics Neuroimaging Suite
Mind Research Network - Collaborative Informatics and Neuroimaging Suite
A web-based neuroimaging and neuropsychology software suite that offers versatile, automatable data upload/import/entry options, rapid and secure sharing of data among PIs, querying and export all data, real-time reporting, and HIPAA and IRB compliant study-management tools suitable to large institutions as well as smaller scale neuroscience and neuropsychology researchers. COINS manages over over 400 studies, more than 265,000 clinical neuropsychological assessments, and 26,000 MRI, EEG, and MEG scan sessions collected from 18,000 participants at over ten institutions on topics related to the brain and behavior. As neuroimaging research continues to grow, dynamic neuroinformatics systems are necessary to store, retrieve, mine and share the massive amounts of data. The Collaborative Informatics and Neuroimaging Suite (COINS) has been created to facilitate communication and cultivate a data community. This tool suite offers versatile data upload/import/entry options, rapid and secure sharing of data among PIs, querying of data types and assessments, real-time reporting, and study-management tools suitable to large institutions as well as smaller scale researchers. It manages studies and their data at the Mind Research Network, the Nathan Kline Institute, University of Colorado Boulder, the Olin Neuropsychiatry Research Center (at) Hartford Hospital, and others. COINS is dynamic and evolves as the neuroimaging field grows. COINS consists of the following collaboration-centric tools: * Subject and Study Management: MICIS (Medical Imaging Computer Information System) is a centralized PostgreSQL-based web application that implements best practices for participant enrollment and management. Research site administrators can easily create and manage studies, as well as generate reports useful for reporting to funding agencies. * Scan Data Collection: An automated DICOM receiver collects, archives, and imports imaging data into the file system and COINS, requiring no user intervention. The database also offers scan annotation and behavioral data management, radiology review event reports, and scan time billing. * Assessment Data Collection: Clinical data gathered from interviews, questionnaires, and neuropsychological tests are entered into COINS through the web application called Assessment Manager (ASMT). ASMT's intuitive design allows users to start data collection with little or no training. ASMT offers several options for data collection/entry: dual data entry, for paper assessments, the Participant Portal, an online tool that allows subjects to fill out questionnaires, and Tablet entry, an offline data entry tool. * Data Sharing: De-identified neuroimaging datasets with associated clinical-data, cognitive-data, and associated meta-data are available through the COINS Data Exchange tool. The Data Exchange is an interface that allows investigators to request and share data. It also tracks data requests and keeps an inventory of data that has already been shared between users. Once requests for data have been approved, investigators can download the data directly from COINS.
A non-profit organization that supports the advance of healthy aging through biomedical research.
Sequenced genomes contain a treasure trove of information about how genes function and evolve. Getting at this information, however, is challenging and requires novel approaches that combine computer science and experimental molecular biology. My lab works at the intersection of both domains, and research in our group can be summarized as follows: generate hypotheses concerning gene function and evolution by computational means, and then test these hypotheses at the bench. This is easier said than done, as serious barriers still exist to using sequenced genomes and their annotations as starting points for experimental work. Some of these barriers lie in the computational domain, others in the experimental. Though challenging, overcoming these barriers offers exciting training opportunities in both computer science and molecular genetics, especially for those seeking a future at the intersection of both fields. Ongoing projects in the lab are centered on genome annotation and comparative genomics; exploring the relationships between sequence variation and human disease; and high-throughput biological image analysis. Current software tools available: VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology. MAKER 2 (updated 01-16-2012) MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. RepeatRunner RepeatRunner is a CGL-based program that integrates RepeatMasker with BLASTX to provide a comprehensive means of identifying repetitive elements. Because RepeatMasker identifies repeats by means of similarity to a nucleotide library of known repeats, it often fails to identify highly divergent repeats and divergent portions of repeats, especially near repeat edges. To remedy this problem, RepeatRunner uses BLASTX to search a database of repeat encoded proteins (reverse transcriptases, gag, env, etc...). Because protein homologies can be detected across larger phylogenetic distances than nucleotide similarities, this BLASTX search allows RepeatRunner to identify divergent protein coding portions of retro-elements and retro-viruses not detected by RepeatMasker. RepeatRunner merges its BLASTX and RepeatMasker results to produce a single, comprehensive XML-based output. It also masks the input sequence appropriately. In practice RepeatRunner has been shown to greatly improve the efficacy of repeat identifcation. RepeatRunner can also be used in conjunction with PILER-DF - a program designed to identify novel repeats - and RepeatMasker to produce a comprehensive system for repeat identification, characterization, and masking in the newly sequenced genomes. CGL CGL is a software library designed to facilitate the use of genome annotations as substrates for computation and experimentation; we call it CGL, an acronym for Comparitive Genomics Library, and pronounce it Seagull. The purpose of CGL is to provide an informatics infrastructure for a laboratory, department, or research institute engaged in the large-scale analysis of genomes and their annotations.
Open Biosystems - RNAi Gene Expression Antibodies
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Open Biosystems offers products that span Genomics, RNAi and Antibodies. Building on the rapid sharing model that is at the core of the Human Genome Project, Open Biosystems collaborates with some of the most innovative life science investigators working today. We partner with them to bring to market new productsthey have often pioneered the new resources in their own lab, and we prepare it for widespread use and then provide access to the research community. Delivery of genetic content is our most recent technological breakthrough. Recently, we brought to market the Tranz-vector system, the safest human-based lentiviral delivery technology. Further supplementing our already strong line of RNA interference (RNAi) and complementary DNA (cDNA) products, this technology provides investigators with superior delivery capabilities for high-quality cellular screening. The combination or our unique Tranz-vector system and whole genome RNAi and cDNA content enables our customers to perform drug target validation on a large scale. With our genomics resources, Open Biosystems provides the content investigators utilize to unlock the functions of human genes and their relationships to normal and disease development. We offer the most complete gene library in the industry. This novel library consists of several full length cDNA and open reading frame collections. Most prominently among these is the Mammalian Gene Collection (MGC), the industry's gold standard gene catalog. The discovery of RNA interference has revolutionized the way investigators approach the studies of gene expression, regulation and interactions, particularly as it relates to drug development. Our collaboration with Drs. Greg Hannon (CSHL) and Steve Elledge (Harvard) has led the way in the evolution of the short hairpin RNA (shRNA) technologies to provide the life science community with whole genome resources for human, mouse and rat with a multitude of technology and delivery advantages.
Neuroscience/psych blog by a neuroscientist in training. I mostly review articles and try to synthesize what I deem important/interesting. Enjoy!
Bork Group - Comparative Systems Analysis (EMBL)
The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin.
Project Hosting on Google Code provides a free collaborative development environment for open source projects.
DIAN - Dominantly Inherited Alzheimer Network
Dominantly Inherited Alzheimer Network (DIAN)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An international research partnership of leading scientists determined to understand a rare form of Alzheimers disease that is caused by a gene mutation and to establish a research database and tissue repository to support research on Alzheimers disease by other investigators around the world. One goal of DIAN is to study possible brain changes that occur before Alzheimers disease is expressed in people who carry an Alzheimers disease mutation. Other family members without a mutation will serve as a comparison group. People in families in which a mutation has been identified will be tracked in order to detect physical or mental changes that might distinguish people who inherited the mutation from those who did not. DIAN currently involves eleven outstanding research institutions in the United States, United Kingdom, and Australia. John C. Morris, M.D., Friedman Distinguished Professor of Neurology at Washington University School of Medicine in St. Louis, is the principal investigator of the project., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE)
Advanced Cognitive Training for Independent and Vital Elderly
Data set from a randomized controlled trial of cognitive interventions designed to maintain functional independence in elders by improving basic mental abilities. Several features made ACTIVE unique in the field of cognitive interventions: (a) use of a multi-site, randomized, controlled, single-blind design; (b) intervention on a large, diverse sample; (c) use of common multi-site intervention protocols, (d) primary outcomes focused on long-term, cognitively demanding functioning as measured by performance-based tests of daily activities; and (e) an intent-to-treat analytical approach. The clinical trial ended with the second annual post-test in January 2002. A third annual post-test was completed in December 2003. The area population and recruitment strategies at the six field sites provided a study sample varying in racial, ethnic, gender, socioeconomic, and cognitive characteristics. At baseline, data were collected by telephone for eligibility screening, followed by three in-person assessment sessions, including two individual sessions and one group session, and a self-administered questionnaire. At post-tests, data were collected in-person in one individual session and one group session as well as by self-administered questionnaire. There were four major categories of measures: proximal outcomes (measures of cognitive abilities that were direct targets of training), primary outcomes (measures of everyday functioning, both self-report and performance), secondary outcomes (measures of health, mobility, quality of life, and service utilization), and covariates (chronic disease, physical characteristics, depressive symptoms, cognitive impairment, psychosocial variables, and demographics). Phase I of ACTIVE was a randomized controlled, single-blind trial utilizing a four-group design, including three treatment arms and a no-contact control group. Each treatment arm consisted of a 10-session intervention for one of three cognitive abilities memory, reasoning, and speed of processing. Testers were blind to participant treatment assignment. The design allowed for testing of both social contact effects (via the contact control group) and retest effects (via the no-contact control group) on outcomes. Booster training was provided in each treatment arm to a 60% random subsample prior to first annual post-test. Phase II of ACTIVE started in July, 2003 as a follow-up study focused on measuring the long-term impact of training effects on cognitive function and cognitively demanding everyday activities. The follow-up consisted of one assessment to include the Phase I post-test battery. This was completed in late 2004.
NBDC - National Bioscience Database Center
National Bioscience Database Center (NBDC)
The National Bioscience Database Center (NBDC) intends to integrate all databases for life sciences in Japan, by linking each database with expediency to maximize convenience and make the entire system more user-friendly. We aim to focus our attention on the needs of the users of these databases who have all too often been neglected in the past, rather than the needs of the people tasked with the creation of databases. It is important to note that we will continue to honor the independent integrity of each database that will contribute to our endeavor, as we are fully aware that each database was originally crafted for specific purposes and divergent goals. Services: * Database Catalog - A catalog of life science related databases constructed in Japan that are also available in English. Information such as URL, status of the database site (active vs. inactive), database provider, type of data and subjects of the study are contained for each database record. * Life Science Database Cross Search - A service for simultaneous searching across scattered life-science databases, ranging from molecular data to patents and literature. * Life Science Database Archive - maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata in a unified format, and to access and download the datasets with clear terms of use. * Taxonomy Icon - A collection of icons (illustrations) of biological species that is free to use and distribute. There are more than 200 icons of various species including Bacteria, Fungi, Protista, Plantae and Animalia. * GenLibi (Gene Linker to bibliography) - an integrated database of human, mouse and rat genes that includes automatically integrated gene, protein, polymorphism, pathway, phenotype, ortholog/protein sequence information, and manually curated gene function and gene-related or co-occurred Disease/Phenotype and bibliography information. * Allie - A search service for abbreviations and long forms utilized in life sciences. It provides a solution to the issue that many abbreviations are used in the literature, and polysemous or synonymous abbreviations appear frequently, making it difficult to read and understand scientific papers that are not relevant to the reader's expertise. * inMeXes - A search service for English expressions (multiple words) that appear no less than 10 times in PubMed/MEDLINE titles or abstracts. In addition, you can easily access the sentences where the expression was used or other related information by clicking one of the search results. * HOWDY - (Human Organized Whole genome Database) is a database system for retrieving human genome information from 14 public databases by using official symbols and aliases. The information is daily updated by extracting data automatically from the genetic databases and shown with all data having the identifiers in common and linking to one another. * MDeR (the MetaData Element Repository in life sciences) - a web-based tool designed to let you search, compare and view Data Elements. MDeR is based on the ISO/IEC 11179 Part3 (Registry metamodel and basic attributes). * Human Genome Variation Database - A database for accumulating all kinds of human genome variations detected by various experimental techniques. * MEDALS - A portal site that provides information about databases, analysis tools, and the relevant projects, that were conducted with the financial support from the Ministry of Economy, Trade and Industry of Japan.
ZCre is a consortium of researchers who have a shared interest in developing Cre/lox based tools for use in the zebrafish model organism. ZCre plans to generate 15 or more tissue specific ERT2CreERT2 driver lines to be expressed in either differentiated cell types or precursor/stem cells, as well as 20 or more lines based upon multilox technology. One set of multilox transgenes will allow long-term permanent labelling of individual cells for lineage tracing and other applications. Another set will allow perturbation of single pathways within individual cells (PathM lines). In order to make these lines ZCre has developed a three-way cloning system using Gateway technology (Invitrogen). Once constructs are made they will be deposited at Addgene.org. Transgenic lines will be available from ZCre or from regional stock centers as requested.
Longitudinal Employer-Household Dynamics
Longitudinal Employer-Household Dynamics (LEHD)
A dataset that combines federal and state administrative data on employers and employees with core Census Bureau censuses and surveys, while protecting the confidentiality of people and firms that provide the data. This data infrastructure facilitates longitudinal research applications in both the household / individual and firm / establishment dimensions. The specific research is targeted at filling an important gap in the available data on older workers by providing information on the demand side of the labor market. These datasets comprise Title 13 protected data from the Current Population Surveys, Surveys of Income and Program Participation, Surveys of Program Dynamics, American Community Surveys, the Business Register, and Economic Censuses and Surveys. With few exceptions, states have partnered with the Census Bureau to share data. As of December 2008, Connecticut, Massachusetts, New Hampshire and Puerto Rico have not signed a partnership agreement, while a partnership with the Virgin Islands is pending. LEHD's second method of developing employer-employee data relations through the use of federal tax data has been completed. LEHD has produced summary tables on accessions, separation, job creation, destruction and earnings by age and sex of worker by industry and geographic area. The data files consist of longitudinal datasets on all firms in each participating state (quarterly data, 1991- 2003), with information on age, sex, turnover, and skill level of the workforce as well as standard information on employment, payroll, sales and location. These data can be accessed for all available states from the Project Website. Data Availability: Research conducted on the LEHD data and other products developed under this proposal at the Census Bureau takes place under a set of rules and limitations that are considerably more constraining than those prevailing in typical research environments. If state data are requested, the successful peer-reviewed proposals must also be approved by the participating state. If federal tax data are requested, the successful peer-reviewed proposals must also be approved by the Internal Revenue Service. Researchers using the LEHD data will be required to obtain Special Sworn Status from the Census Bureau and be subject to the same legal penalties as regular Census Bureau employees for disclosure of confidential information. Basic instructions on how to download the data files and restrictions can be found on the Project Website. * Dates of Study: 1991-present * Study Features: Longitudinal * Sample Size: 48 States or U.S. territories
A dataset of a prospective panel study of health and aging in Mexico. The study was designed to ensure comparability with the U.S. Health and Retirement Study in many domains, and the NHANES III. The baseline survey in 2001 is nationally representative of the 13 million Mexicans born prior to 1951. The six Mexican states which are home to 40% of all migrants to the U.S. were over-sampled at a rate of 1.7:1. Spouse/partners of eligible respondents were interviewed also, even if the spouse was born after 1950. Completed interviews were obtained in 9,862 households, for a total of 15,186 individual interviews. All interviews were face-to-face, with average duration of 82 minutes. A direct interview (on the Basic questionnaire) was sought, and Proxy interviews were obtained when poor health or temporary absence precluded a direct interview. Questionnaire topics included the following: * HEALTH MEASURES: self-reports of conditions, symptoms, functional status, hygienic behaviors (e.g., smoking & drinking history), use/source/costs of health care services, depression, pain, reading and cognitive performance; * BACKGROUND: Childhood health and living conditions, education, ability to read/write and count, migration history, marital history; * FAMILY: rosters of all children (including deceased children); for each, demographic attributes, summary indicators of childhood and current health, education, current work status, migration. Parent and sibling migration experiences; * TRANSFERS: financial and time help given to and received by respondent from children, indexed to specific child; time and financial help to parent; * ECONOMIC: sources and amounts of income, including wages, pensions, and government subsidies; type and value of assets. All amount variables are bracketed in case of non-response. * HOUSING ENVIRONMENT: type, location, building materials, other indicators of quality, and ownership of consumer durables; * ANTHROPOMETRIC: for a 20% sub-sample, measured weight, height; waist, hip, and calf circumference; knee height, and timed one-leg stands. Current plans are to conduct another two follow-up surveys in 2012 and 2014 and will field the 3rd and 4th waves of survey data collection in Mexico. For the 2012 wave, interviews will be sought for: every person who was part of the panel in 2003 and their new spouse / partner, if applicable, and a new sample of persons born between 1952 and 1962. For the 2014 wave, we will follow-up the whole sample from 2012. Interviews will be conducted person-to-person. Direct interviews will be sought with all informants, but proxy interviews are allowed for those unable to complete their own interview for health or cognitive reasons. A next-of-kin interview will be completed with a knowledgeable respondent for those who were part of the panel but have died since the last interview. A sub-sample will be selected to obtain objective markers such as blood sample and anthropometric measures. Data Availability: The 2001 baseline data, 2003 follow-up data, and documentation can be downloaded. * Dates of Study: 2001-2003 * Study Features: Longitudinal, International, Anthropometric Measures * Sample Size: 2001: 15,186 (Baseline) Link: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00142
Software Python module for electrophysiology data analysis.
A commercial supplier of custom synthetic molecules. They specialize in peptides, oligonucleotides, bioconjugation, molecular biology services, proteins and specialty chemistry.
A private antibody-producing corporation in Burlingame, California with subsidiaries in UK and Canada.
Repository of neural and cognitive models
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A repository of models of neuronal networks maintained by the Nengo (http://nengo.org) project. Most but not all models use Nengo. Nengo is a graphical and scripting based software package for simulating large-scale neural systems.
Boston University Mass Spectrometry Resource for Biology and Medicine
Boston University School of Medicine Mass Spectrometry Resource
Mass Spectrometry Resource for Biology and Medicine
Biomedical technology research center that conducts high-sensitivity structural determinations and analyses of biological compounds via mass spectrometry. The emphasis is on glycoconjugates, oligosaccharides and proteins.
Repository of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors, and ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in context of genetic and genomic data, using semantics and statistics. Discovery system provides basic and clinical science researchers, informaticists, and medical professionals with integrated interface and set of discovery tools to reveal genetic basis of disease, facilitate hypothesis generation, and identify novel candidate drug targets. Database that indexes authoritative information on experimental models of disease from MGI, RGD and ZFIN.
Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)
Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers.
Semiparametric QTL mapping in general pedigrees
Software application (entry from Genetic Analysis Software)
Software application for calculating the heterozygosity, PIC, and LIC values for polymorphic markers (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
power calculator for Extremely Discordant And Concordant sibpairs
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software application with implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Software application for combined segregation and linkage analysis, incorporating severity and diathesis. (entry from Genetic Analysis Software)
Case-control HAPLotype INference package
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Software application for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study. (entry from Genetic Analysis Software)
Software application for constructing multilocus linkage map (entry from Genetic Analysis Software)
Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software)
haplotype resolution using imperfect phylogeny
Software application that includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application that integrate genetic linkage map and physical map (entry from Genetic Analysis Software)
Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. Software application for inferring haplotypes from genotypes on pedigree data (entry from Genetic Analysis Software)
Software application providing a user freiendly way to perform QTL analysis. The software currently allows 3 types of QTL analysis: (1) single marker ANOVA. (2) marker regression. (3) interval mapping by regression. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. An interactive software program for radiation hybrid mapping (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Gene dropping simulation software. The program is a gzip'ed tar archive and is designed to run under UNIX/Linux operating system.
Sequential Oligogenic Linkage Analysis Routines
A flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of quantitative traits which may involve multiple loci (oligogenic analysis), dominance effects, and epistasis. (entry from Genetic Analysis Software)
Connectivity Informatics Technology Initiative Connectivity File Format
Standardizes file formats for the storage of connectivity data. These formats are developed by the Human Connectome Project and other interested parties. Use the MEDIAWIKI entry in the menu on the left for more information about the CIFTI file formats. Access the CIFTI discussion forum using the Forums entry in the menu on the left. Subscribe to the discussion forum and you will be informed about issues involving the CIFTI file formats via email.
Slicer3 module to provide a capability for performing white matter lesion classification and summary.
Construct and analyse brain network is a brain network visualization tool, which can help researchers to visualize construct and analyse resting state functional brain networks from different levels in a quick, easy and flexible way. Entrance parameter of construct and analyse brain network is export parameters of dparsf software.It would be greatly appreciated if you have any suggestions about the package or manual.
Generic classification tool for 3D images
A loose collection of programs and configuration options that intend to make working with data more transparent to formats. Currently available is a basic specification for NIfTI-1 for the UNIX file command and proof of concept code for the concept of treating data as an abstract concept and instantiating physical instances on demand.
A cross platform, open source gesture tracking program. You launch it from the web, and use it to streamline the way you communicate with the computer. It allows for a more natural method of issuing commands than with keyboard shortcuts or GUI buttons. GesTr supports simple XML files to customize recognized gestures and their corresponding actions. GesTr also has experimental support for the Wii Remote used with an infrared pen as an alternative input device.
Software for real-time parametric statistical analysis of functional MRI (fMRI) data. The system that combines a general architecture for sampling and time-stamping relevant information channels in fMRI (image acquisition, stimulation, subject responses, cardiac and respiratory monitors, etc.) and an efficient approach to manipulating these data, featuring incremental subsecond multiple linear regression. The advantages of the system are the simplification of event timing and efficient and unified data formatting. Substantial parametric analysis can be performed and displayed in real-time. Immediate (replay) and delayed off-line analysis can also be performed with the same interface. The system provides a time-accounting infrastructure that readily supports standard and innovative approaches to fMRI.
A reference MINC set of files that currently includes human head images only of standard modalities. The goal is to build a well curated collection of files that demonstrate the capabilities of MINC
An I/O library for Matlab/Octave Matlab and Octave library for reading and writing Nifti-1 files. cbiNifti is intended to be a small, self-contained library that makes minimal assumptions about what Nifti files should look like and allow users easy access to the raw data. cbiNifti handles compressed file formats for reading and writing, using Unix pipes for compression and decompression. More information and code examples at: http://www.pc.rhul.ac.uk/staff/J.Larsson/software.html
A software package for segmentation of structures using automated neual networks. This is the reference implementation using NAMIC software development best practices and the Insight Toolkit of the paper Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures. (PMID: 17904870). The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.
Configurable Pipeline for the Analysis of Connectomes
A configurable, open-source, Nipype-based, automated processing pipeline for resting state functional MRI (R-fMRI) data, for use by both novice and expert users. C-PAC was designed to bring the power, flexibility and elegance of the Nipype platform to users in a plug and play fashion?without requiring the ability to program. Using an easy to read, text-editable configuration file, C-PAC can rapidly orchestrate automated R-fMRI processing procedures, including: - quality assurance measurements - image preprocessing based upon user specified preferences - generation of functional connectivity maps (e.g., correlation analyses) - customizable extraction of time-series data - generation of local R-fMRI metrics (e.g., regional homogeneity, voxel-matched homotopic connectivity, fALFF/ALFF) C-PAC makes it possible to use a single configuration file to launch a factorial number of pipelines differing with respect to specific processing steps.
An R-based package to conduct brain connectivity analyses with a focus on a novel approach to conducting Connectome-Wide Association Studies (CWAS) using functional connectivity.
A platform-independent desktop tool for inspecting DICOM header fields, editing DICOM header fields, viewing DICOM images, and transferring DICOM files to a DICOM receiver. DicomBrowser includes scriptable header editing to support various de-identification protocols. DicomBrowser is written in Java and uses ImageJ for image viewing and the dcm4che toolkit for much of its DICOM implementation.
An instrumental supplier which provides researchers and clinicians with sophisticated All-in-One solutions in the field of neuroscience.
NeuroVigil: Revolutionizing Brain Analysis
Commercial company that produces simple EEG measurement devices compatible with phones.Develops proprietary non invasive brain monitors and advanced machine learning algorithms to detect constellation of biomarkers of pathologies in asymptomatic individuals, such as people with neurodegeneration, adverse drug side effects or brain cancer, and to ascertain intent including individuals who cannot otherwise communicate.
Net Station Software for EEG Acquisition and Physician and Review
APIs for Net Station data files. APIs are available for C++, C#, and Java.
A collection of functions with batch functionality for SPM: * user entered expression (one set of volumes); * binarize non-zero voxels; * binarize/threshold each image; * binarize non-zero voxels, sum, rebinarize; * voxelwise calculations on pairs (add sub mult div ... etc.); * flip sign of all non-zero voxels; * x-flip image along y = 0; * mask images to a template; * T-to-Z transform; * Winsorize (cap) extreme values; * Z-score transform of image relative to its global mean and SD; * write single voxels to a .nii; * create a cluster image; * split cluster image into constituent images; * write hemisphere masks from template; * homotopic calculations; * replace zeros with __; * pad image with extra voxels;
A laboratory dedicated to advancing health care through utilizing computation and imaging to new areas of medicine.
Harvard Children's Hospital Informatics Program
An applied research and education program at Children's Hospital in Boston. The program focuses on work done at the intersection of information science, health care and biomedical discovery. The field is inherently interdisciplinary, drawing on traditional biomedical disciplines, the science and technology of computing, data science, biostatistics, epidemiology, decision sciences, population health, omics, implementation science, and health care policy and management. This program's faculty are trained in medicine, data science, computer science, mathematics and epidemiology.
Core facility that provides the following services: Website development and hosting for research labs and studies requiring an online presence, interactive functionality, or site traffic tracking. The Health Communication Core offers a full range of creative communication services to support evidence-based recruitment and retention of study participants and intervention research. HCC serves researchers from diverse disciplines who need websites, logos, brochures, social media campaigns, publications, and interactive media targeted to the needs and preferences of specific audiences.
DF/HCC Specialized Histopathology Services Core
Core facility that provides the following services: Tissue trimming, cassetting, processing, and embedding, Cutting and staining of paraffin-embedded and cryostat sections, Immunohistochemistry for both routine and novel markers, In situ hybridization, using chromogenic or radioactive detection methods, Laser capture microdissection. Tissue analysis is critical to validation and evaluation of animal models of human cancer, and human cancer tissues serve as the operating system for translational research. The facility supports a wide spectrum of cancer-relevant research, from basic studies on pathogenic mechanisms in cancer to translational research focused on the development of new tests for biomarkers that stratify patients and direct therapy. The Specialized Histopathology (SHP) Core, was created in 2005 by consolidating five histopathology cores into a single unit with two performance sites: Longwood, Directed by Jon Aster and based at the Brigham and Women?s Hospital and MGH, Directed by Anat Stemmer-Rachamimov and based at Massachusetts General Hospital East in Charlestown. The SHP Core provides professional and technical research pathology services to DF/HCC investigators working in diverse organisms (e.g., rodents, fish, and monkeys) or human tissues. The Core also assists in experimental design and the development and interpretation of tests and their results. As of July 2012, the Longwood site offers CLIA Certified services.
Dartmouth College Clinical Pharmacology Shared Resource Core Facility
Dartmouth College DCC Clinical Pharmacology Shared Resource
DCC Clinical Pharmacology Shared Resource
Supports Dartmouth Cancer Center investigators in design, performance, data analysis, and interpretation of pharmacology objectives in preclinical, clinical and epidemiological studies.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A resource to develop shared resources for the implementation of geospatial analysis for cancer research at Dartmouth. Their goal is to provide expert consultation and collaboration for research projects of NCCC members in behavior, epidemiology, and health services research. The GeoSpatial Resource also strives to educate members of the community in different aspects of geospatial analysis by providing courses through TDI and at Dartmouth College.
Dartmouth College Optical Cellular Imaging Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2026. Core facility that provides the following services: Optical cellular imaging, Microscopy training. A Norris Cotton Cancer Center Shared Resource Facility. The Optical Cellular Imaging Shared Resource strives to provide reliable and affordable access to point scanning confocal microscopy, conventional bright field and fluorescence light microscopy, and image analysis resources. The facility provides individual and group training for operation of the light microscopes. Training is intended to provide an understanding of the basic light microscopy and digital imaging principles involved. Training for our microscope use and imaging consultation is open to all members of Dartmouth College, DMS, DHMC, and outside users.
Florida Agricultural and Mechanical University Drug Discovery Core Facility
A core facility at the Florida Agricultural and Mechanical University.
Flow Cytometry facility at Florida A&M University
A laboratory equipped with laser-based flow cytometric instruments, the main one being the Becton Dickinson two-laser FACScalibur analyzer. This facility provides a resource for analytical and preparative studies of cells using flow cytometry to the FAMU biomedical researchers. This facility offers FACS acquisition and analysis for detecting cell surface or intracellular proteins, measuring apoptosis, cell cycle, cellular physiology that have both biomedical and clinical applications.
A Java application programming interface (API) for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data.
HMS NERCE FACSCalibur Flow Cytometer Resource
Core facility that provides the following services: Flow cytometry assay service, Data management system. The BD FACSCalibur system combines unique dual-laser technology, an automated sample loader option, and powerful software to provide the high throughput necessary to meet productivity requirements of clinical laboratories. The modularity and innovative technology designed into the BD FACSCalibur system also offers investigators the performance and flexibility required for a variety of research applications. Please note that since the NERCE program will end in February 2014, our ability to support new requests for services is limited.
A lab facility that aims to accelerate research in the stem cell field by facilitating the derivation and distribution of induced pluripotent stem cell lines. Disease-specific pluripotent stem cell lines can provide the opportunity to study the mechanisms of disease and develop treatments. The core facility serves as a repository for iPS cells produced by HSCI scientists.
Harvard NeuroDiscovery Center - Biomarker Study
Core facility that provides the following services: Sample processing/storage. The Harvard NeuroDiscovery Center Biomarker Study aims to discover and validate biomarkers for neurodegenerative diseases.
Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility
The Partners HealthCare Center for Personalized Genetic Medicine
Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations.
A service facility with four main spectrometers. The facility consists of four NMR instruments: a JEOL GX-400, a Varian Inova 500, a Bruker Avance 500 equipped with a 13C-1H cryoprobe, and a Bruker Avance III 600 MHz spectrometer equipped with a cryoprobe. These spectrometers are utilized by scientists from Hunter College, as well as from the entire CUNY community. The large variety of available probes allows detection of virtually any MR-active nuclide. Data analysis is performed either at the spectrometer workstation with vendor software or off-line with third party software packages.
Jackson State University Environmental Toxicology Lab
A research laboratory and facility which supports research on environmental toxicology at Jackson State University.
A center dedicated to developing and applying morphometric methods to biomedical imaging data such as high-resolution MRI. The lab uses automated and semi-automated software such that MRI brain images are segmented into anatomical regions of interest. Projects in both basic and applied brain research include research on strokes and tumors; medical image processing research includes shape analysis of anatomical brain regions and measurement and analysis of brain volumes.
MGH Vector Development and Production Core Facility
A lab facility that provides viral vectors with custom-designed promoters and reporter genes and capacity for gene regulation. Services include DNA packaging and purification and titering and allocation of viral vectors.
A lab facility at Montana State University dedicated to utilizing MRI technologies to research applications of magnetic resonance microscopy (MRM) methods in the study of transport phenomena and material characterization. Research areas of this lab include: ceramics and foams, colloidal suspensions, biofilms, porous media, gels, and techniques and equipment.
Penn Diabetes Research Center Mouse Phenotyping Physiology and Metabolism Core
Core which provides researchers with resources for performing metabolic studies in mice. It also provides services, innovative techniques, and helpful consultation to both experienced and novice investigators with regards to metabolic questions.
A nonprofit machine shop at the University of Pennsylvania, Perelman School of Medicine. It aims to assist university faculty in the design and construction of both laboratory and clinical instrumentation. The shop's staff include both mechanical and optical specialists that have experience collaborating with scientists to design the custom clinical research instrumentation they needed.
Penn Small Animal Imaging Facility: PET/SPECT/CT Sub-Core
Core facility that provides the following services: PET/SPECT/CT image analysis.
Core facility that provides the following services: Biomarker quantification by mass spectrometry. This core provides sophisticated analytical services based on liquid chromatography-mass spectrometry.
A museum and center for insect identification and systematic research. The museum has workspace equipment, resources for taxonomic analysis and researchers from different laboratories that collaborate.
A lab and program dedicated to developing diagnostic tests, vaccines and biomarkers of infectious agents that are prevalent in the El Paso, Ciudad Juarez and McAllen Texas border communities. The BSL 3 lab's research interests include the West Nile virus and Myobacterium tuberculosis.
University of Texas at San Antonio Engineering Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025. Core facility located at the University of Texas at San Antonio.
Vanderbilt Flow Cytometry Core Laboratory
Core facility that provides the following services: FACS AriaCell Sorting, LSRII-Analytical Cytometry, AutoMacs-Magnetic Sorting, EasyCyte-Cell Counting/Viability. We enjoy state-of-the-art digital instrumentation maintained at the highest standards we can attain. This quality control allows researchers to sort cells at high efficiency and purity under the proper conditions or to run analytical experiments with as many as 17 different fluorochromes simultaneously. We are dedicated to providing the best service and training possible to ensure the best results attainable for our research scientists and physicians. Please investigate the pages of this website to address your scheduling needs and questions relating to flow cytometry research, methods and fees
Vanderbilt Diabetes Research and Training Center Islet Procurement and Analysis Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025.Core facility that provides access to isolated pancreatic islets from normal and diabetic models and performs islet functional analysis. The IPA Core also provides solutions for high-resolution whole slide imaging and access to image analysis tools for quantitative assessment of pancreatic islet morphology.
Vanderbilt X-Ray Photoelectron Spectroscopy Lab
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025.Lab with access to the PHI Versaprobe, a surface-sensitive analytical tool for identifying elemental composition and local bonding environment.
A core facility with access to imaging equipment and analysis software such as wide-field light microscopy, Total Internal Reflection Fluorescence microscopy (TIRF), confocal microscopy, Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), small animal imaging, spectroscopy, and flow cytometry.
XULA Materials Research - Shared Instrumentation Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025. Network of shared instrumentation facilities across Xavier University's research community.
A database of information about contaminants found at hazardous waste sites. The toxicological profiles are cataloged by chemical with the NTIS order number.
A database of scientific names in zoology. ZooBank is an online, open-access, community-generated registry for zoological nomenclature. It serves as a service to taxonomists, biologists, and the global diversity informatics community. It is the Official Register of the International Commission on Zoological Nomenclature (ICZN).
Developer of software tools for genomic research focused on computational methods of high throughput biomedical data analysis, including software to support next generation sequencing technologies, transcriptome analysis with RNASeq data, SNP detection and selection of disease specific SNP subsets. Provides custom genome annotation services.
Spike 2 software Cambridge Electronic Device
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. A data acquisition and analysis software package for electrophysiology data. Spike2 software offers multi-channel continuous data acquisition and analysis with a multitude of options. This offers flexible usage from a simple chart recorder to complex applications requiring stimulus generation, data capture, scrolling or triggered displays, control of external equipment, and custom analysis. Spike2 software can be used in many fields such as electrophysiology, neurophysiology, cardiovascular and respiratory studies, sports science and pharmacology.
Netherlands institute for permanent access to digital research resources. DANS encourages researchers to make their digital research data findable, accessible, interoperable and reusable. It does this by providing expert advice and certified services.
The Demographic and Health Surveys Program
A program that provides technical assistance for surveys that aim to advance global understanding of health and population trends in developing countries. The DHS program collects, analyzes, and disseminates accurate and representative data on population, health, HIV, and nutrition through more than 300 surveys in over 90 countries.
A comprehensive lexicon - a unified language of anatomic pathology terms - for standardized indexing and retrieval of anatomic pathology information resources.
Ontology that encompasses all knowledge about HIV
International Classification of Primary Care - 2 PLUS
Ontology of the international classification of primary care -2 PLUS
Ontology that is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.
Ontology of nursing interventions classification.
Archive of digital climate records, climate statistics, and monthly weather summaries on Alaska and the polar regions.
A commercial vendor of chemicals that provides custom synthesis of a wide variety of organic compounds. Frontier Scientific has capabilities for custom work in organoborons, organotins, porphyrins, silanes, halogenations, catalysts and cross couplings using Suzuki, Stille, and Kumada processes.
A commercial software laboratory notebook.
Non-profit charitable organization that benefits philanthropy, voluntarism and grantmaking foundations, focusing specifically on private independent foundations programs. (http://non-profit-organizations.findthebest.com/l/558154/Makray-Family-Foundation)
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. An ichtyological gene bank with data from fisheries in British Columbia, Canada.
Resource is currently not in service, documented July 29, 2016.
A blog that contains reviews and information on PCR methods, applications and technology. Topics include tips and advice, troubleshooting, optimization and up-to-date information on the polymerase chain reaction.
A blood bank that operates as the marketing arm for the family cord blood banking operations of Sheba Medical Center. It is the largest medical center in the Middle East with a 24/7 call center to answer questions. The center provides collection kits, supervises the collection process, and transports the collected blood to the Sheba Cord Blood Bank.
A blog about the origins of speech by Edmund Blair Bolles. The topics include book recommendations, commentary on linguistic theories, and other informational articles. Babel's Dawn is a book by Bolles that discusses the natural history of the origins of speech.
A database of gene transcription in neurons derived from Next Gen sequencing. Transcriptomes hosted on this database were designed and constructed at the University of Florida.
An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download.
A business that supplies livestock organisms and equipment to biomedical researchers and teachers. Examples of services include livestock such as sheep, goats, swine, and calves; materials such as blood, isolated tissue, feed, hay, equipment; and timed pregnancies and pre-delivery laboratory tests.
A podcast of neuroscience news in minute-intervals from the Scientific American. New episodes become available every Saturday.
A tissue bank which houses and supplies cancerous tissue for use by the research community. Along with tissue, the bank collects clinical history, lifestyle factors, breast pathology, treatment information, and follow up information.
A tissue donation bank based in Latvia. This resource is in Latvian.
A blog of up-to-the-minute insights into the innovative use of technology in further and higher education.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. The ENA Sequence Version Archive is a repository of all entries which have ever appeared in EMBL-Bank Sequence Database. You can browse the archive or use the batch retrieval form.
A database that provides primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens.
A network resource that aims to enhance and broaden understanding of how researchers in the UK create and use information resources. The network provides services of all kinds to support the development of effective policies and practices for researchers, institutions, funders, information professionals and everyone who is involved in the information landscape.
A neuroscience blog written by Noah Gray.
Bio-Job.org is a sister site to PROTOCOL-ONLINE.ORG and offers free job posting to not-for-profit employers such as universities, governments, research institutions/organizations. Currently industrial job listing is also free. * Employer's Services: Post a Job, Manage Jobs Posts, View Resumes * Jobseeker: Announce your availability and submit your resume to hundreds of Employers that visit this site. Employers can contact you directly as soon as a suitable position becomes available. Why is this site created: It's never been an easy job to recruit qualified people for employer or PI who runs a lab--Not only have you to pay a fee for job listing that could be as high as hundreds of dollars, you have to go through all the hassle of setting up an account, dealing with your account manager and making the payment. In an era when science is free, genome data is free, publications are free, and why is job posting not free? With this belief in mind, we created this site to allow free job posting for academia. What types of jobs can be posted here: Jobs in any scientific discipline and biotech jobs can be posted.
A blog that serves as a forum for disseminating the science, culture, and life of the Broad Institute. Broad Minded provides content that comes from the collaboration of the Broad community.
THIS RESOURCE IS NOT IN SERVICE, documented August 9, 2016. A genetic biobank in Taizhou, China which plans to collect five million samples in 10 years.
A portal with listings of continuing medical education opportunities such as radiology, pediatrics, and HIV/AIDS specializations.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 02, 2016.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 28, 2016.
A national tissue bank that provides management for database purposes, on-line ordering, guidelines, educational programs, policy making and certification of resources.
Banco de datos de biodiversidad del Ecuador
A searchable database of biology-related data based in Ecuador.
Comparative genomics software that assists in whole genome microsatellite search and investigation. The command line version is called SciRoKoCo. The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output.
Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings.
A service that provides low cost DNA sequencing. They utilize microfluidic technology.
Macquarie University Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Set of facilities based out of Macquarie University in New South Wales. Some facilities provide services such as proteome analysis or resources of various academic departments like engineering, biological sciences, and geography.
Macquarie University Department of Chemistry and Biomolecular Sciences NMR Facility
A facility that houses NMR spectroscopy services. It has a state-of-the-art facility including 400 and 600 MHz NMR spectrometers, the latter with a cryoprobe. All 1D and 2D NMR experiments are performed as per customer requests. They also offer a consultative service and spectral interpretation.
A university which provides programs in medical postgraduate studies as well as graduated health sciences.
The unification of three major universities in Finland - the Helsinki University of Technology, Helsinki School of Economics and the University of Art and Design Helsinki.
A public university in Denmark that offers degrees at the undergraduate and graduate level in fields such as engineering, nanotechnology, medicine and modern languages.
Aberystwyth University; Wales; United Kingdom
A public research university located in Wales, United Kingdom. The university offers degrees at the undergraduate and postgraduate level in fields from physics and earth sciences to creative writing and international politics.
The national academy of Taiwan that supports research activities in a wide variety of disciplines, ranging from mathematical and physical sciences, to life sciences, and to humanities and social sciences. The institution plays a particularly important role in the academic field of Chinese Studies.
An Australian government agency that allocates research funding to academics and researchers at Australian universities. The mission of the council is to deliver policy and programs that advance Australian research, spur innovation and benefit the community.
Austrian Academy of Sciences; Vienna; Austria
A national academy in Austria that promotes the sciences and humanities, especially in research. Resource is in German.
August Pi i Sunyer Biomedical Research Institute; Barcelona; Spain
August Pi i Sunyer Biomedical Research Institute
Institut d''Investigacions Biomediques August Pi i Sunyer
Institut d''Investigacions Biomèdiques August Pi i Sunyer
Institut d''Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
A biomedical research center in Barcelona. The institute focuses on encouraging translational research, innovation and technological progress, and the development of programs that address diseases with high morbidity and mortality.
Austrian Agency for Health and Food Safety
Austrian Agency for Health and Food Safety (AGES)
A company based in Austria that supports the management of federal agencies relating to public health, animal health, food safety, medical and drug safety, food security and consumer protection. They provide professional and scientific expertise.
Biomedical University Campus of Rome; Rome; Italy
A university in Rome that confers degrees in medicine, nursing, dieticians, the science of alimentation, and biomedical engineering.
A private, Ivy League research university in Rhode Island, USA. The university offers degrees at the undergraduate and graduate level in a wide variety of fields.
Catholic University of the Sacred Heart; Milan; Italy
An Italian private research university that offers undergraduate, graduate and postdoctoral level degrees in both Italian and English.
A private, non-profit foundation that operates a research center on biophysics, cell biology and oncology. The institute, located in Paris, France, is also home to a hospital that specializes in the treatment of cancer.
A higher education institute for advanced undergraduate and graduate studies in France. The institute has fourteen teaching and research departments that span the humanities and sciences.
Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland
Ecole Polytechnique Federale de Lausanne
Ecole polytechnique fédérale de Lausanne
École Polytechnique Fédérale de Lausanne
A research institute in Lausanne, Switzerland that specializes in the physical sciences and engineering.
Eidgenossische Technische Hochschule Zurich
Eidgenössische Technische Hochschule Zürich
Swiss Federal Institute of Technology Zurich
Public institute of technology in Zurich, Switzerland that specializes in science, technology, mathematics and management. École Polytechnique Fédérale de Lausanne is its sister university.
A government granting agency which consults with partnered programs through national authorities and food safety agencies. EFSA organizes its annual and multi-annual work program according to priorities agreed with the European Commission and other partners, taking into account available resources. EFSA staff may also produce scientific outputs on behalf of the agency, such as peer reviews of the assessment of active substances in pesticides, or responses to urgent requests for advice. EFSA staff also monitor and analyze information and data on biological hazards, chemical contaminants, food consumption and emerging risks.
Franklin and Marshall College; Pennsylvania; USA
A private, co-educational liberal arts college in Lancaster, Pennsylvania.
A public university in Shanghai, China that confers undergraduate and graduate degrees.
Genome Canada is a non-profit organization that is funded by the Government of Canada. The organization funds large-scale science and technology to fuel innovation regarding genomics in multiple sectors such as health, agriculture and agri-food, forestry, fisheries and aquaculture, environment, energy and mining. They create partnerships at the program and research project levels.
Greek General Secretariat of Research and Technology
General Secretariat for Research and Technology (GSRT)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 15,2025. Greek government funding agency for scientific research institutes for advanced ΙΤ systems and networks. The agency promotes the transfer and dissemination of advanced technologies throughout the country's productive sector through funding. This organization focuses on sectors important for the the improvement of the national economy by establishing new institutes and technological centers important for the development of the Greek economy.
Indian Council of Medical Research; New Delhi; India
A government-funded council for the promotion and coordination of biomedical research in India. The council focuses on specific diseases such as HIV/AIDS, tuberculosis, and leprosy in addition to national health priorities including the management of communicable diseases, fertility control, and mental health research.
Indian Institute of Science; Bangalore; India
A public research university for science and higher education in India. The university has six main divisions, including the biological sciences, chemical sciences, electrical sciences, mechanical sciences, physical and mathematical sciences, and interdisciplinary research.
Institute of Statistical Mathematics; Tokyo; Japan
The Institute of Statistical Mathematics (ISM) is a national research institute in Tokyo, Japan that conducts studies relating to theory and application of statistics and data science. IMS focuses on data-centric science, which includes fields of engineering involving massive data, statistical science, computer science, machine learning, and data mining.
International Institute of Molecular and Cell Biology; Warsaw; Poland
International Institute of Molecular and Cell Biology
International Institute of Molecular and Cell Biology (IIMCB)
International Institute of Molecular and Cell Biology creates partnerships with research centers within and outside Poland. This organization provides a base of administration, management of finances and resources, sharing space and equipment, grant writing and grant management procedures, etc. They organize workshops, training courses, conferences and other scientific events for researchers of various specialties and nationalities. Additionally, this organization commercializes results to provide biotechnological solutions with regards to the global economy and global research services deals.
Iowa State University (ISU) is an undergraduate, graduate and research institute. ISU has 100 majors and upwards of 800 student organizations.
Johns Hopkins University School of Medicine; Baltimore, Maryland; USA
Johns Hopkins University School of Medicine
Johns Hopkins University School of Medicine (JHM)
Johns Hopkins University School of Medicine is a medical graduate institution that provides physician, clinical fellowship and residency programs.
Jozef Stefan Institute; Ljubljana; Slovenia
A scientific research institute that is involved with a broad spectrum of basic and applied research. Some of the areas they focus on include production and control technologies, communication and computer technology, and energy utilization and environmental science. They also engage in collaborations to develop medical equipment and new diagnostic methods into clinical medicine.
Liverpool John Moores University; Liverpool; United Kingdom
Liverpool John Moores University provides undergraduate, masters, and doctorate programs.
Loma Linda University (LLU) is a Seventh-day Adventist educational health-sciences institution comprised of eight schools. Programs such as Allied Health Professions, Dentistry, Medicine, Nursing, Pharmacy, Public Health, Religion and Science and Technology are offered by the school. Curricula offered range from certificates of completion and associate in science degrees to doctor of philosophy and professional doctoral degrees. LLU also offers distance education.
Massachusetts Institute of Technology; Massachusetts; USA;
Massachusetts Institute of Technology (MIT)
Massachusetts Institute of Technology; Cambridge; USA;
MIT; Cambridge; Massachusetts; United States
Independent, coeducational, privately endowed university, organized into five schools: architecture and planning; engineering; humanities, arts, and social sciences; management; and science.
Max Planck Institute for Marine Microbiology; Bremen; Germany
max planck institut fur marine mikrobiologie
Max Planck Institute for Marine Microbiology
The Max Planck Institute for Marine Microbiology is an international university that offers the PhD programme International Max-Planck Research School (IMPRS) of Marine Microbiology (Marmic) together with the Alfred Wegener Institute for Polar and Marine Research, the University of Bremen and Jacobs University Bremen. Currently, the institute consists of four departments with several associated research groups: Microbiology, Biogeochemistry, Molecular Ecology, and Symbiosis.
Montana State University is a university institute has programs for undergraduate, master's and doctoral degrees. There are 54 master's degree options, 37 doctoral degree options including one specialist program, and 14 certificate options.
National Cheng Kung University; Tainan; Taiwan
National Cheng Kung University is a research-led comprehensive university in Tainan, Taiwan that has undergraduate, master's, and doctoral degree programs. This university has fields of: science, engineering, medicine, management, planning and design.
National Institute of Health Sciences; Tokyo; Japan
National Institute of Health Sciences (Japan)
National Institute of Health Sciences - Japan
Japanese national institute that conducts testing, research, and studies toward the proper evaluation of the quality, safety, and efficacy of pharmaceutical products, foods, and numerous chemicals in the living environment. Its major responsibilities involve extensive testing and research to ensure the quality, efficacy, and safety of chemical substances (including pharmaceuticals and food) that are closely related to people's lives.
National Institute on Chemical Dependency
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19, 2016.
National Taiwan University; Taipei; Taiwan
A national research university in Taipei, Taiwan. The university confers degrees at the undergraduate and graduate level bio-resources and agriculture, electrical engineering and computer science, engineering, law, liberal arts, management, medicine, public health, and the social sciences.
National University of Singapore; Singapore; Singapore
A public university located in Singapore that has a wide range of faculties and schools, including arts, business, computing, and dentistry.
A private research university in Tokyo, Japan that has undergraduate and graduate degree programs in a wide variety of fields, including in law, humanities, economics, and industrial technology.
NIH Office of Research on Women's Health; Bethesda; Maryland
NIH Office of Research on Women's Health
The Office of Research on Women's Health (ORWH) is part of the Office of the Director of NIH. ORWH works in partnership with the 27 NIH Institutes and Centers to ensure that women’s health research is part of the scientific framework at the NIH and throughout the scientific community.
Office of Research Services - Serving the NIH Community
The Office of Research Services (ORS) provides support to the NIH research mission by planning, directing and delivering scientific and regulatory activities, public safety, security, and services for the NIH community.
Netherlands Organization for Scientific Research
Netherlands Organization for Scientific Research (NWO) is a research institute and regional funding source in the Netherlands.
Ontario Ministry of Research and Innovation; Ontario; Canada
Ontario Ministry of Research and Innovation
Ministry that supports research, commercialization and innovation taking place across Ontario through a range of programs and services like the Ontario Research Fund, Innovation Demonstration Fund and Ontario Venture Capital Fund.
Pasteur Institute of Lille; Lille; France
Pasteur Institute of Lille is an international research institute in Lille, France focused on bettering human health by detecting risk factors in degenerative diseases.
Pontifical Catholic University of Argentina; Buenos Aires; Argentina
Pontifical Catholic University of Argentina
Pontificia Universidad Catolica Argentina
Pontifical Catholic University of Argentina is a part time MBA program university accredited by the London-based Association of MBAs (AMBA). It is located in Argentina with campuses in the cities of Buenos Aires, Santa Fe, Rosario, Parana, Mendoza and Pergamino.
Royal Institute of Technology; Stockholm; Sweden
Royal Institute of Technology is a university in Stockholm, Sweden that has undergraduate, master's, and doctoral degree programs.
Temple University is a university institute in Pennsylvania, USA that provides undergraduate, graduate and professional degree programs.
Private research university in Medford and Somerville, Massachusetts, United States, with additional facilities in Boston and Grafton, as well as Talloires, France. Provides undergraduate, graduate, and professional degree programs.
Tufts University School of Medicine; Massachusetts; USA
University in Massachusetts, USA that provides medical, physical assistant, master's, and health science degree programs.
University of Cambridge; Cambridge; United Kingdom
Public research university in Cambridge, United Kingdom. Founded in 1209 is second oldest university in English speaking world.
University of Dundee; Scotland; United Kingdom
University in Scotland, UK that provides undergraduate and doctoral degree programs.
University in Hawaii that provides undergraduate, master's, doctorate, and professional degree programs. Campuses are located in Manoa and in Hilo.
University of Melbourne; Victoria; Australia
University in Victoria, Australia that provides undergraduate and graduate degree programs.
University of San Diego; California; USA
Private university in San Diego, California that provides undergraduate, master's, doctoral, and professional degree programs.
University of Surrey; Surrey; United Kingdom
Public university in Surrey, UK that provides undergraduate, master's, doctoral, professional, and research degree programs.
University of Ulster; Ulster; Northern Ireland
Public university in Ulster, Northern Ireland that provides undergraduate, post graduate and post research degree programs.
Public university in Utah, USA that provides undergraduate, master's, post graduate, graduate, and professional degree programs.
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression.
Source code used to compress FASTQ files. FASTQ is DNA sequencing machine output.
A C++ application designed for compression of genome collections from the same species.
A compression tool for efficient storage of Genome Re-Sequencing data. GRS processes genome sequence data without use of reference SNPs and other variants. It can also automatically rebuild the individual genome sequence data using the reference genome sequence.
PREFAB - Protein Reference Alignment Benchmark
Downloadable data designed for testing multiple sequence alignment methods.
Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast.
An infrastructure as a service that lets you run your large-scale computing workloads on Linux virtual machines hosted on Google's infrastructure.
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data.
Borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available.
A method for non-parametric, empirical Bayesian-based analysis of RNA-seq count data.
A software tool for simulating fusion transcripts from a reference genome.
A comprehensive listing of companies and organizations involved with genomics and molecular biology. There are lists for genome software and services, genome institutions and supplies, and general institutions.
A base calling program for DNA sequence traces.
MassGenomics - Medical genomics in the post-genome era
Blog discussing next-generation sequencing and medical genomics in the post-genome era. Most posts are in-depth reviews of recent research publications or editorials.
A sequence alignment program for the output from Illumina GA-II clonal sequencers. It uses an algorithm that indexes the reference sequence as a series of 8-mers and then matches the genomic reads to the 8-mer index, in a mutation-tolerant way permitting identification of single-nucleotide substitutions and indels.
RPCI Gene Targeting and Transgenic Shared Resource
Roswell Park Cancer Institute Gene Targeting and Transgenic Facility
Roswell Park Cancer Institute Gene Targeting and Transgenic Shared Resource
RPCI Gene Targeting and Transgenic Facility
Facility which provides researchers with transgenic mouse technologies, methods, and animal models. Knockout mice, transgenic mice, and mice on multiple strain backgrounds are provided.
Contract research organization (CRO) that specializes in advanced tissue technologies. It offers services in histology, immunohistochemistry, digital pathology, and image analysis.
University of Oxford Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. An independent portal that lists the labs and facilities at the University of Oxford.
Peter MacCallum Cancer Centre - Cancer Therapeutics Program
Cancer research laboratory at the Peter MacCallum Cancer Centre which investigates biomarkers identification, compounds for activity as anti-cancer drugs, and small molecule targeted therapies.
Facility for performing and analyzing high-throughput biological assays. The facility provides advice and research service with a range of high-throughput assays. Analysis of microarrays, sequencing, QPCR, and flow cytometry are provided.
Life science consultancy and analysis service company. Analysis services include microarray analysis, next generation sequencing, experiment design, and biostatistics. Consultancy centers around experimental design in approaches involving large sets of patient-derived data.
Company which provides a suite of molecular biology and genomic services, including DNA sequencing by Sanger and Next Generation Sequencing. All services are offered at a research, GLP or clinical grade levels.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 14,2024. Core facility whose resources and services include confocal microscopy, wide field fluorescence microscopy, histology services, and phosphorimaging, among others. It also provides consultation on project design and image visualization and analysis.
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 15, 2016. A portal which lists and provides access to the labs and facilities at Indiana University.
Sanford-Burnham Medical Research Institute Labs and Facilities
Sanford Burnham Medical Research Institute Labs and Facilities
A portal which lists the various labs and facilities that are part of the Sanford-Burnham Medical Research Institute.
Washington University School of Medicine Genome Technology Access Center Core Facility
McDonnell Genome Institute Genome Technology Access Center
Washington University in St. Louis Genome Technology Access Center
Washington University in St. Louis McDonnell Genome Institute Genome Technology Access Center
Washington University in St. Louis School of Medicine Genome Technology Access Center Core Facility
Washington University McDonnell Genome Institute Genome Technology Access Center
Washington University School of Medicine GTAC
Washington University School of Medicine GTAC Core Facility
Genome Access Technology Center at the McDonnell Genome Institute offers comprehensive next generation sequencing, microarray, PCR and Bioinformatic services. In addition to generating high quality genomic, transcriptomic, and proteomic data, performs data analysis and provides technological support to users. Full service facility, from hypothesis to publication. Offers advanced analysis of microarray data. Provides free initial consultation to discuss project and offers several tiers of analysis packages to best suit your needs. NGS equipment includes NovaSeqs, Seqwell II, Oxford. Microarray expression and genotyping - all platforms.
Harvard University Bauer Core Laboratory
Harvard University Bauer Core Laboratory (FAS)
Core facility that provides the following services: Liquid handling, Long read sequencing, Cell sorting service, Cell analysis service, Imaging systems service, Microarrays service, Sequencing service, Genotyping service, Fragment analysis, Solexa DNA sequencing service, Solexa gene expression service, Solexa small RNA service, Solexa ChIP-Seq service, Real-time quantitative PCR service, Protein-molecule interaction service, Library replication service, Nucleic acid isolation service, Nucleic acid shearing service, DNA, RNA and protein sample analysis service. Their goal is to advance research efforts in the life sciences that cannot readily be accomplished in the traditional academic laboratory because of a need for expensive instrumentation or automation, scientific or organizational infrastructure, or multidisciplinary expertise. To promote cutting-edge research and to foster scientific collaborations, we make our extensive laboratory and computational resources available to scientists at Harvard. Our technical staff provide expertise and hands-on training in protocols and the use of instrumentation for a nominal fee. Researchers can sign up to use the instrumentation through an on-line scheduling system and conduct their experiments independently.
Chemical supplier that both curates and sells laboratory supplies and reagents.
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 15, 2016. Pathology Diagnostics Ltd is an independent GCLP accredited histopathology research organisation delivering tissue, laboratory, and diagnostics services to industry Research and Development scientists engaged in drug and biomarker development.
Universite de Sherbrooke Labs and Facilities
University of Sherbrooke Labs & Facilities
University of Sherbrooke Labs and Facilities
Universite de Sherbrooke Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 19,2024. Portal, Core facility
A specialized preclinical research organization that provides services for biological research and development on neural therapies. Renovo offers preclinical assays and 3D-electron microscopy services that provide routine and customized solutions for basic science, preclinical and clinical research, and drug development.
Arizona Bioindustry Association Core Labs
A core facility which provides fee-based sample imaging and analysis using analytical and microscopy equipment to technology incubator clients, university researchers, and industry.
A company which provides peptide nucleic acid products for use in research. It also provides engineered nuclease services to laboratories.
North Carolina State University Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15,2024. Online portal for the labs and facilities at North Carolina State University. Resources include a plant transformation lab, analytical instrumentation facility, and nuclear services center.
State University of New York at Buffalo Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2024. Portal listing the labs and facilities at SUNY at Buffalo.
A portal listing Miami University's labs and facilities which include the Center for Bioinformatics and Functional Genomics. The CBFG is the onsite core molecular biology and bioinformatics resource at Miami University that focuess mainly on DNA and protein analysis as well as expertise in robotics liquid handling.
Texas A and M University Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22,2024. Portal listing the Texas A and M University's labs and facilities, which include the TAMU Protein Chemistry Lab and the TIGM Transgenic Core.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Labs and facilities of the University of Utah, which include: Microarray and Genomic Analysis Core Facility, Flow Cytometry Core Facility, Mutation Generation and Detection Facility, and the Transgenic and Gene Targeting Core.
MS Bioworks - Protein Mass Spectrometry Services
A protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis.
A contract research organization based in India that provides services including Clinical Development, Contract Manufacturing and Informatics.
Ottawa Hospital Research Institute Labs and Facilities
Portal to research facilities and services within the Ottawa Hospital Research Institute. Facilities and services include access to their bioinformatics facility, flow cytometry facility, human pluripotent stem cell facility, and their clinical research lab.
Louisiana State University Labs and Facilities
Louisiana State University Labs & Facilities
Portal for Louisiana State University labs and facilities which include the AgCenter Biotechnology Laboratory, a core facility that provides basic and applied research expertise to support researchers in the LSU system as well as those in other academic institutions and industry. The ABL consists of three units: the Protein Facility, the Plant Transformation Facility and the Animal Cell Culture Facility.
Donald Danforth Plant Science Center Bioanalytical Chemistry Facility
Danforth Center Mass Spectrometry Facility
Danforth Center Proteomics and Mass Spectrometry Facility
Donald Danforth Plant Science Center Proteomics and Mass Spectrometry Facility
Proteomics and Mass Spectrometry Facility
Facility provides tools for high quality plant and biological sample analysis in proteomics, mass spectrometry, metabolomics, ionomics, and related analytical fields. It works with academic and commercial institutions and has established collaborations with many principle investigators.
University at Albany Center for Functional Genomics Proteomics Core Facility
University at Albany CFG Proteomics Core Facility
A core facility that provides services in the identification of individual proteins, characterization of entire protein complexes or biosimilars, and global analysis to discover changes in the proteomes of different samples. The core also specializes in the development of custom assays for quantitation of specific molecules in complex clinical samples.
A mobile application for real-time mobile polling on topics that include politics, ethics, pop culture, sports, health, and humor. Poll results can be filtered by gender, political party, age, or income range. The app is available for iPhone, iPad, Android devices, and Kindle Fire.
A biotechnology company that develops, manufactures and distributes molecular biology tool kits and laboratory consumable products. Services include DNA and RNA microarrays, PCR and transgenic genotyping, and DNA/RNA analysis and quality control.
Portal to the Duke University Model Systems Genomics facility equipped to perform molecular genetic research in Drosophilia. Equipment includes stereo microscopes for fly pushing and microdissection, a compound microscope and a microscope equipped to view GFP and RFP as well as two inverted microscopes for embryo injections.
ECRbase is the Database of Evolutionary Conserved Regions (ECRs), Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes created using ECR Browser alignments. Currently there are over 26 million ECRs available in the ECRbase that correspond to regions extracted from pairwise comparisons of all the available species.
UNC School of Medicine Metabolomics Laboratory
University of North Carolina at Chapel Hill School of Medicine Metabolomics Laboratory
Laboratory equipped for metabolite profiling from a wide range of biological samples. Equipment includes high-throughput robotic systems for the analysis of large sample sets. Data analysis software, both commercial and home built, is also available for discovery of biomarkers, metabolic signatures of disease, toxicity or other biological outcomes.
University of Colorado at Boulder Labs and Facilities
University of Colorado at Boulder Labs & Facilities
A portal for the core labs and facilities at the University of Colorado at Boulder.
University of Minnesota Histology and Immunohistochemistry Laboratory
University of Minnesota - Twin Cities Histology and Immunohistochemistry (IHC) Laboratory
University of Minnesota - Twin Cities Histology and Immunohistochemistry Laboratory
University of Minnesota Histology and Immunohistochemistry (IHC) Laboratory
Lab based at the University of Minnesota that provides histology services, including frozen sectioning, tissue grossing, fixation, and sectioning, optimization and performance of immunohistochemistry (IHC).
University of Illinois College of Medicine; Illinois; USA
University of Illinois at Chicago College of Medicine
University of Illinois at Chicago College of Medicine; Illinois; USA
University of Illinois College of Medicine at Chicago
The medical school division of the University of Illinois with four separate campuses. The school focuses on excellence in research, education and clinical work, diversity and innovation, and collaboration.
Northwestern University Feinberg School of Medicine; Illinois; USA
Northwestern University Feinberg School of Medicine
Medical school of Northwestern University which focuses on research initiatives, clinical affiliates, and global outlook.
A private Ivy League research university based in New Jersey that confers undergraduate and graduate degrees in the humanities, social sciences, natural sciences, and engineering. It offers professional degrees in international affairs, engineering and applied science, architecture, and finance
The United States federal government Department of Education, which oversees policies on federal financial aid for education, collecting data and disseminating research, and working to promote key educational discussions and equal access to education.
Virginia Commonwealth University School of Medicine; Virginia; USA
Medical school division of Virginia Commonwealth University.
A public co-educational university in Lexington, Kentucky that offers undergraduate, graduate and postgraduate degree programs in a variety of fields such as nursing, the arts, law and medicine.
Commercial supplier for biochemical reagents for manufacturing, development and distribution of products.
University at Buffalo School of Medicine and Biomedical Sciences; New York; USA
UB School of Medicine and Biomedical Sciences
University at Buffalo School of Medicine and Biomedical Sciences
Public university medical school located in Buffalo, New York.
An independent administrative institution dedicated to comprehensive research in science and technology and the dissemination of scientific research and technological developments to the public. RIKEN works in a range of fields, including physics, chemistry, medical science, biology, and engineering, covering the entire range from basic research to practical application.
Database constructed by merging mutation and polymorphism data from the published literature pertaining to Rett syndrome and related clinical disorders, and by incorporating unpublished mutation and polymorphism data that have been submitted directly. RettBase is updated on a very frequent basis manually by curators to ensure the validity of the data submitted., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.
R software that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA.
R package that contains functions to merge microRNA and respective targets using different databases.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software R package written for analysis of murine palate miRNA two-color expression data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software R package for the analysis of ChIP-chip data and Affymetrix tiling arrays. It provides functions for data import, quality assessment, and data visualization. The software provides tools for the efficient mapping of genomic sequences.
bsseq - Analyze manage and store bisulfite sequencing data
R package with tools for analyzing and visualizing bisulfite sequencing data.
R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining.
A coeducational public research university located in Oklahoma, USA. The institution confers undergraduate and graduate degrees in fields such as law, medicine, aviation, energy management, history of science, and Native American studies.
University of Adelaide; Adelaide; Australia
Public research university in Adelaide, South Australia. It is known for its focus on research and emphasis on moving towards commercialization of research.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount.
Medical College of Wisconsin; Wisconsin; USA
Private and freestanding medical school and graduate school of sciences in Milwaukee, Wisconsin. The institution offers medical degrees as well as masters and PhD-level studies in areas such as biochemistry, cell biology, and community and public health.
Center dedicated to providing statistical information to guide policies to improve the health of the American people. An affiliate of the Center for Disease Control and Prevention.
Commercial supplier of bioproducts for studies of inflammation, autoimmune disease, cancer, coronary disease, Alzheimer's Disease and more. These include antibodies, enzymes, coagulation factors, and assay kits.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. DOCUMENTED NOVEMBER 17, 2016: This program was removed on 03/18/15 and is not being monitored.A software visualization package for the symbolic display of functional neuroimaging datasets in an anatomical context. Written in IDL.
University of Florida College of Medicine Neuroscience
A department at the University of Florida's College of Medicine that offers programs of study on neural function and how it changes with injury and disease. The institution's research ranges from fundamental discovery to clinical application. These neuroscience programs are offered at the undergraduate, graduate, postdoctoral and resident level.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A suite of tools to generate the cortical surface of the brain. The surface is generated in the middle of grey matter and can be used to measure surface features including cortical depth and curvature.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A collection of latest articles published by Nature Publishing Group about the current state of next generation sequencing technologies.
A federally chartered, private, coeducational, nonsectarian, historically black university in Washington, D.C. Howard University has graduate schools in many fields, including business, nursing, engineering, and medicine.
Japan Society for the Promotion of Science
Research and outreach organization dedicated to promoting science, research and education. The society has four main objectives, including building international cooperative networks, enhancing education and research at universities, building evidence-based science-promotion systems and creating diverse world level knowledge.
Australian National University; Acton; Australia
A national research university in Canberra, Australia. It offers undergraduate and graduate degrees in fields such as law, medicine, business, arts and the social sciences.
Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.
Public research university based in Melbourne, Australia. The institution is divided into ten faculties, including art design and architecture, engineering, information technology, and medicine, nursing, and health sciences.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. The National B Virus Resource Center is located in the Viral Immunology Center of Georgia State Universitys Department of Biology. Their laboratory is studying viruses that directly affect the central nervous system of infected hosts. Current projects in the laboratory are focused on the molecular biology of human and nonhuman primate alphaherpesviruses and the diseases they cause, immune response characterization, antiviral strategies, including drug discovery and high-throughput drug screening within unique, high containment laboratory suites. They are also actively engaged in the study of unique reoviruses that have the capacity to infect the central nervous systems of non human primates, langur viruses, and a newly isolated mangaby herpesvirus. Alphaherpesviruses target the central nervous system of susceptible hosts, and subsequently establish latent infections generally without severely damaging the host. There may be an initial acute phase when the virus successfully replicates in peripheral tissue of the host. This replication, when it occurs, induces a series of specific immune functions that can serve as markers of infection. We use these markers to design, develop and implement diagnostic assays that will be useful during the management of clinical disease. Each herpesvirus coexists peacefully with the natural host in which it has co-evolved, but when the viruses for any reason find themselves no longer in the natural host, the usual host:parasite relationship may change dramatically. In some closely related hosts the virus can replicate and, in some cases, pathogenesis of the infection is radically more severe than that which occurs in the natural host. For example, this can be seen when New World monkeys are infected with humans herpesviruses, e.g., HSV-1 or HSV-2, or when humans are infected with B virus from a macaque, a member of the Old World monkey family. Their studies focus on the mechanisms by which virus kills the host and how that process can be circumvented with early identification, appropriate antiviral drugs, and in the future, effective vaccines. We continually screen the efficacy of existing as well as novel antiviral agents to inhibit the growth of viruses that can potentially cross into the human population, either through occupational exposure or through more subtle contact. Their laboratory provides a global resource funded by National Institutes of Healths National Center for Research Resources to assist in the identification of zoonotic disease transmissions and develop enhanced strategies to detect virus in macaques. They particularly focus on the transmission of B virus from Asian monkeys to humans who come in contact with them. Members of the genus Macaca include rhesus monkeys, cynomolgus macaques, snow macaques, as well as all other macaques. If the macaque is in the midst of the acute or recurrent infection with B, virus can be transmitted to people who handle these monkeys through cuts, scratches, splashes, bites, or even contaminated equipment or surfaces, i.e., fomites. To counter the effects of this virus, the NIH and Centers for Disease Control and Prevention have instituted a critical set of guidelines for institutions to follow in the event of exposures. Their laboratory provides immediate support to these cases to assist in the rapid diagnosis of B virus infections and to determine the efficacy of selected treatment. Lifetime patient monitoring is provided to identify possible reactivation disease and to better track this unique herpesvirus as it has begun its existence in the human populations. Sponsors: The viral immunology center is funded by National Institutes of Healths National Center for Research Resources.
A fast parallel error correction tool for short reads.
R package with tools for de novo motif discovery in large-scale genomic sequence data.
A software package for analyzing ChIP-seq (Chromatin ImmunoPrecipitation on sequencing) data that finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.
R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach.
R software that detects enriched regions of ChIP-seq data sets jointly.
Commercial supplier of biomaterials such as antibodies, antigens, lysates, and various assay kits.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 15,2025. Wiki of resources useful for researchers and clinicians interested in global health. All McGill faculty, clinicians, researchers, staff and students are encouraged to use and add to these resources. If members of the research community would like to contribute to this resource, but are not a member of the McGill community, the McGill community is available for contact. An account will be created for users.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that calculates an exact stratified test for HWE for diallelic markers, such as single nucleotide polymorphisms (SNPs), and an exact test for homogeneity of Hardy Weinberg disequilbrium. In addition, exact tests for HWE are calculated for each stratum. (entry from Genetic Analysis Software)
Proteomics Research Center for Integrative Biology
Proteomics Research Resource for Integrative Biology
Proteomics Resource for Integrative Biology
Biomedical technology research center that develops and integrates new proteomic technologies for collaborative and service studies, disseminating the new technologies and training scientists in their use.
Catholic University of Leuven; Flemish Brabant; Belgium
An independent, Catholic university in Belgium. The institution is Dutch-speaking but also offers several English programs.
Software for memory-efficient genome assembly. It utilizes sparse k-mer.
Commercial company that specializes in measurement science software, hardware and services. Their software products include a range of photogrammetric camera calibration, measurement and event logging software. Their hardware products include calibration cubes and underwater camera housings. Services include design, construction and calibration of vision measurement systems, software development and GIS consulting.
Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data.
A base-calling algorithm for Illumina DNA sequencing.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 15,2025. R software program for identifying differentially spliced genes from two groups of RNA-seq samples. It reads the count file and outputs the differences in the relative abundance of the isoforms of each gene in the annotation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided.
A software tool for comparative visualization of genomes. It is based in the GBrowse frameworks and integrates with the annotation features.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2.
Commercial antibody supply company that focuses on providing antibodies for research in cardiovascular and atherosclerosis.
Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database.
North Dakota State University; North Dakota; USA
Public research university in North Dakota, USA. It is a land-grant university that focuses on agriculture and the applied sciences. In addition, it offers undergraduate and graduate degrees in a wide variety of areas including engineering, science and mathematics, health professions, business, and agriculture and food systems studies.
A set of National Institutes of Health-funded programs for worker's training. Programs include the Hazardous Materials Worker Health and Safety Training and the HAZMAT Training at DOE Nuclear Weapons Complex training program. There are also Small Business Innovation Research (SBIR) Grants that fund research projects that further the development of e-learning products that support health and safety training of emergency responders, community and citizen engagement and the long-term health effects of environmental disasters.
Collection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies.
Human Genetics Laboratory: WFS1 Gene Mutation and Polymorphism Database
This web site lists the disease causing mutations and polymorphisms found in the Wolfram syndrome (WFS1) gene. Sponsors: This resource is supported by the University of Michigan at Ann Arbor.
An entry of the Cognitive Atlas which defines the term speech perception.
Ministry of Education of the People''s Republic of China
A governmental ministry that works on education reform, program development, and regulation and supervision of China's education system.
Transmission Disequilibrium Test Power Calculator
Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data.
FluView: A Weekly Influenza Surveillance Report
This page contains the Influenza Surveillance Report during 2008-2009 Influenza Season Week 15, ending April 18, 2009.
A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard.
Kyoto Encyclopedia of Genes and Genomes Expression Database
Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.
Server for SVM Prediction of Caspase Substrates Cleavage Sites
THIS RESOURCE IS NO LONGER IN SERVICE, documented December 12, 2016. CASVM is a web server for predicting caspase cleavage sites on protein sequences based on the SVM algorithms. It can also be used for predicting non-canonical caspase substrate cleavage sites. The server has a relational database containing experimentally verified caspase substrates retrievable using accession IDs, keywords or sequence similarity.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0 platforms. This software runs a clustering algorithm and generally should be run on a sample at least 50 times. It utilizes an Expectation-Maximization (EM) algorithm to produce genotypes and confidence scores for every individual at every SNP.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An eQTL visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments (entry from Genetic Analysis Software)
Orthologous and Paralogous Transcripts in Clades
Database and portal for the analysis of complete genomes in several clades. It includes orthologous and paralogous transcripts in clades for flies, nematodes, amniota, and yeasts. Users can browse and download the data within the database.
Coeducational public research university in West Virginia. Its undergraduate colleges include business, education, arts and media, health professions, information technology, liberal arts, and science. Its graduate colleges include schools of medicine and pharmacy.
statistical significance in Genomewide Association Studies in 2-stage
Software application for evaluating Statistical Significance in Two-Stage Genomewide Association Studies (entry from Genetic Analysis Software)
Commercial supplier which provides antibodies, assay kits, biomarkers, and proteins.
Commercial supplier and developer of mitochondrial antibodies and mitochondrial assays. The company focuses on supporting critical research areas in cancer, neurodegeneration and metabolic disorders.
IBL - America (Immuno-Biological Laboratories)
A commercial biomaterial supply resource for laboratory reagent assays. IBL-American provides resources to further research and clinical testing in various areas including autoimmunity, endocrinology, infectious disease, oncology and neuroscience among others.
A commercial company that provides a range of services from nucleic acid custom services to products and services for cloning, transfection, recombinant protein production and cell isolation.
A commercial antibody supplier that specializes in high-quality monoclonal antibodies and antigens for the diagnostic industry.
Commercial antibody supplier and developer for biomedical research. These products are compatible with use in flow cytometry and mass cytometry, immunoprecipitation and chip, western blotting, immunofluorescence microscopy, and quantitative multiplexing.
A French biotech company that specializes in the development of standardized flow cytometry kits in the field of haemostasis. It became part of the Stago group in 1994.
An antibody supplier that specializes in high-affinity custom chicken antibody production, providing clients with chicken IgY and other immunoreagents for biomedical research and antibody manufacturing.
An antibody supply company that provides reagents targeting all human proteins. Atlas Antibodies develops reagents and antibodies for mass-spectrometry-based quantitative proteomics as well. Their production and development is based on the Human Protein Atlas (HPA) project, which released a complete tissue-based map of human protein expression using antibodies.
Visualization and Analysis of Networks containing Experimental Data (VANTED)
Visualization and Analysis of Networks containing Experimental Data
Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data.
Commercial antibody supplier that provides reagents such as immunoassay kits, antibodies, and proteins as well as custom services such as antigen preparation, sequencing and engineering.
Software tool used to analyze diffusion tensor imaging. It produces three different diffusion-related images: the apparent diffusion coefficient map, a measurement of the general tendency of water protons to diffuse in the underlying voxel; the fractional anisotropy map, a measurement of whether water proton diffusion is equal in all directions or whether diffusion proceeds preferentially in certain directions; and directional map, a color map of the primary direction of diffusion.
Commercial antibody supplier that specializes in peptide-related products for research in obesity, cardiovascular disease, and diabetes.
A database of gene expression in mouse haematopoiesis, integrating 271 individual microarray experiments derived from 15 distinct studies done on most characterized mouse blood cell types. Gene expression information has been discretized to absent/present/unknown calls. It supports gene-centric searches to find out where a gene of interest is expressed, and what other genes follow the same (or a similar) pattern of expression. It also supports cell-centric searches to find out what genes are expressed in specific cell types/studies and not others.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17, 2023.Toolbook(tm) based, interactive graphical database which provides structural, molecular, and genetic information on the adult murine nervous system; and its relevance to human neurobiology. This resource is primarily designed as a platform for users to interact, each sharing knowledge on their own area of expertise, which is compiled to a master database. This hypertext atlas presently comprises more than 1000 pages and is designed to provide a flexible integrated resource for the description and discussion of all forms mammalian neurologic data. Version 4.0 of the NeuroMouse program extends the program's basic framework to include a number of areas in modern molecular neurobiology. This system provides an integrated resource for the characterization and description of mammalian neurological data. Major divisions include: Neural Atlas, Molecular Atlas, Genetics/Surgical Lesion Atlas. Neuromouse has been integrated into our strain-specific three dimensional MRI and surgical atlases of the murine CNS. Database contents: Neural Atlas: - Rotational representation of the murine brain. - Neural structures: visual and alphabetic point and click index of neural structures, pathways and systems. - Brain atlas:photographic serial sections in the coronal, sagittal, and horizontal planes (average plate distance - 300 um). Physical brain distances are also provided as are meta-index grids to allow rapid movement between different planes and regions. # Catalog of primary and immortalized neural cells indexed to relevant neural structures. Molecular Atlas: - Index of neurotransmitters: Acetylcholine, GABA, Glutamate, Aspartate, Glycine, Dopamine, Norepinephrine, Epinephrine, Serotonin (synthesis, distribution, degradation, molecular modules, receptors, subunits, agonists, antagonists, gene structure, localization, physical properties and transgenics are indicated for each item). - Index of neurotrophins / neurokines: NGF, BDNF, NT-3, NT-4/5, CNTF, LIF, Onostain M, IL-6, GDNF, FGF's, S100b (ligand, receptors, expression pattern, physical properties, homologous factors, transgenics/knockouts, chromosomal location, effects of agent, and effects of factors on agent are indicated for each item). - Index of additional neural agents: Bcl-2, TNF/Fas, TGF-beta, P53/Rb, PDGF, EGF family (ligand, receptor, expression patterns, physical properties, homologous factors, transgenics/ knockouts, chromosomal location, effects of agent, effects of factors on agent are indicated for each item). - Molecular biology: Molecular biology of important neural genes with integrated l links, plus selected neural topics (ex. programmed cell death, inducible gene systems, protein motifs, neural gene elements, and selected signal transduction pathways). Genetics Atlas: - Lesion paradigms: Index of common neuronal structural and chemical lesion paradigms. - Selected procedures: description of common neurosurgical, cell tracing, culturing and laboratory procedures. - Neurologic syndromes: Index of important human neurologic syndromes and appropriate animals models. - Neural mutant database: Index and description of naturally occurring and genetically modified murine neurologic mutations; including pages on double knockout animals. Interactive maps of each murine chromosome and human syntenic maps.
Reaper - Demultiplexing trimming and filtering sequencing data
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Software program for demultiplexing, trimming and filtering short read sequencing data.
Magnetic Resonance Microscopy of Mouse Embryo Specimens
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 14, 2013. A multidimensional, digital atlas based on magnetic resonance images of normal mouse embryos from 9.5 days after conception (E9) to the newborn (P0). The images include surface views and cross-sectional views from the transverse, coronal, and sagittal planes for each embryo. Several movies have also been included to demonstrate growth of the embryos and to present a variety of visualization tools available for studying and documenting embryonic anatomy. These images are organized as a reference for educators and researchers who want to understand better the embryological anatomy of their own specimens and to understand how their images relate to the whole embryo at many stages of development.
GimmeMotifs: a systematic de novo motif prediction pipeline
Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
BodyMap- human and mouse gene expression database
BodyMap-Xs: anatomical and taxonomical breakdown of animal EST
BodyMap: human and mouse gene expression database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008
Software that implements a set of C routines for robust, high-quality registration of two volumes, aligning according to a least-squares criterion which is well-suited to intramodal registration tasks. Programming skills are required to attach the ANSI-C routine to whichever system users have. It is available on Unix, Macintosh, and PC.
Insight Segmentation and Registration Toolkit
National Library of Medicine Insight Segmentation and Registration Toolkit (ITK)
Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
Earlier versus Later Levodopa Therapy in Parkinson Disease
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from the ELLDOPA study: a multicenter, placebo-controlled, randomized, dose-ranging, double-blind clinical trial of 361 early, mild Parkinson's disease (PD) subjects, not requiring symptomatic medications with a duration from time of diagnosis less than 2 years. A NINDS funded study. The multicenter, placebo-controlled, randomized, dose-ranging, double-blind clinical trial, called the Earlier versus Later Levodopa Therapy in Parkinson Disease (ELLDOPA) study was run by the Parkinson Study Group and sponsored by the National Institute of Neurological Disorders and Stroke (NINDS). The subjects (n=361) were enrolled between September 1998 and August 2001 at 33 sites in the United States and 5 sites in Canada. Despite the known benefit of levodopa in reducing the symptoms of Parkinsons disease, concern has been expressed that its use might hasten neurodegeneration. This study assessed the effect of levodopa on the rate of progression of Parkinsons disease.The primary analysis assessed the doseresponse relationship between the assigned doses and the worsening of parkinsonism, as indicated by the changes in the total score on the UPDRS between the baseline visit and week 42. Washout of study drug occurred during weeks 40-42.
skewer - A fast and sensitive adapter trimmer for illumina paired-end sequences
Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.
CISCRP- The Center for Information and Study on Clinical Research Participation
CISCRP is a resource for information on participation in, understanding of, and resources for clinical research participants and scientists. The mission of the Center is to educate, inform and empower patients, the public, medical and research professionals, the media and policymakers about clinical research participation and what it means to be an active participant in the clinical research process, promote greater awareness and understanding of clinical research participation and the role that it plays in public health, facilitate more effective collaboration among all members of the clinical research enterprise, and provide resources for the research community to better understand the study volunteer. To that end, the Center has developed a broad national awareness and education initiative in order to better inform the public at large about clinical study information. Furthermore, on its website, the Center offers program and event information related to clinical trials, an information center with facts, figures, informational resources, and FAQs for both patients and researchers, and a mailing list of clinical trial information. :The Center also maintains its own search engine website, : :searchclinicaltrials.org : : :, for those looking for further clinical trial information. The Center for Information and Study on Clinical Research Participation is located in Dedham, MA. :NIF thanks the : :Parkinson's Disease Foundation : : :for their referral of this resource to us.
NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study I
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from a multicenter, double-blind, futility study of minocycline and creatine in subjects with early untreated Parkinson's Disease (PD) or FS-I (Futility Study I). There were 65 subjects/treatment arm with 195 total randomized subjects from approximately 42 sites in the US and Canada. A NINDS funded study. A Multicenter, Double-Blind, Futility Study of Minocycline and Creatine in subjects with early untreated Parkinson's Disease (PD) (FS-1).The primary objective of the study was to assess the impact of minocycline and creatine on the progression of PD in order to assess whether it was non-futile to proceed with further study of these agents. The progression of PD was measured by the change in total UPDRS score between the baseline visit and month 12 or the time of sufficient disability to require symptomatic therapy (last visit before subject goes on dopaminergic therapy), whichever occurs first. The additional follow-up of subjects until 18 months addressed the secondary objectives. The FS-1 study was conducted by the NINDS funded Neuroprotection Exploratory Trials in PD (NET-PD).
NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study II
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from a multicenter, double-blind, pilot study of CoQ10 and GPI 1485 in subjects with early untreated Parkinson's Disease (PD) or FS-TOO (Futility Study II). There were 65 subjects/treatment arm with 195 total randomized subjects from approximately 42 sites in the US and Canada. A NINDS funded study. Multicenter, double-blind, pilot study of outpatients with early, untreated PD. De novo subjects were equally randomized to one of the three study arms: (1) active CoQ10 and placebo for GPI 1485, (2) active GPI 1485 and placebo for CoQ10 and (3) placebo for CoQ10 and GPI 1485. Subjects remained on blinded study drug for 12 months. The primary comparison of each drug was to historical control data, but a placebo group was included in order to ascertain concurrent control rates. The FS-TOO study was conducted by the NINDS funded Neuroprotection Exploratory Trials in PD (NET-PD).
flowWorkspace - Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore
Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.
khmer - k-mer counting and filtering FTW
khmer: k-mer counting filtering and graph traversal FTW
Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform.
massiR: MicroArray Sample Sex Identifier
Software that predicts the sex of samples in gene expression microarray datasets.
CenterWatch is an online resource for news, directories, analysis, and proprietary market research for clinical research professionals and patients. For patients, CenterWatch is committed to providing information on clinical trials, specific drugs, as well as other essential health and educational resources. On this website, patients can search clinical trials, receive e-mail notifications about specific clinical trials, review results from completed clinical trials, search drug information, learn about volunteering for a clinical trial, read an overview of the clinical trials process and find other health and educational resources. For researchers, CenterWatch offers a wide range of tools and resources to improve patient and investigator recruitment, remain current with industry trends and business practices, and strengthen organizational procedures. CenterWatch also offers information on grant opportunities, and a variety of educational books and publications. Researchers can provide the public with information about their clinical trials by using the Clinical Trials Listing Serviceprovided through CenterWatch, or look up more specific information on medicines and equipment using Drug and Device Pipeline News. Overall, the mission of CenterWatch is to be the leading source of news, directories, analysis, and proprietary market research for clinical research professionals and patients. It is located in Boston, MA. :NIF thanks the :Parkinson's Disease Foundation : :for their referral of this resource to us.
A search program to detect insertions of transposable element from short reads of next generation sequencer.
Software to manage the conversion of imaging data from one file format and convention to another. It consists of a graphical user interface to visually program the translations, and a data translation engine to read, sort and translate the input files, and write the output files to disk. The data translation engine: (1) Reads metadata from a set of image files on disk to identify the source that produced each file; (2) Groups the image files into user-defined collections using image metadata values; (3) Translates each image file collection by reading metadata and pixel data and mapping the data into the appropriate output file format through a programmable set of connected modules. The Debabeler uses the Java Image I/O Plugin Architecture to read and write a wide variety of common medical image file formats, including ANALYZE, MINC, and most variations of DICOM.
A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely.
Bachmann-Strauss Dystonia & Parkinson Foundation
The Bachmann-Strauss Dystonia and Parkinson Foundation
The Bachmann-Strauss Dystonia and Parkinson Foundation Inc.
A nonprofit organization whose goal is to find better treatments and cures for the movement disorders dystonia and Parkinson's disease. Funding opportunities are available through the collaborative research program between BSDPF and the Michael J. Fox Foundation.
International Essential Tremor Foundation
The IETF is an international nonprofit organization whose mission is to provide global educational information, services and support to those affected by essential tremor (ET) and to health care providers, while promoting and funding ET research. Services provided by the IETF include mailing or emailing a free information packet about ET upon request, maintaining an up-to-date listing of physicians specializing in ET, and assisting in forming and maintaining ET support groups. In addition, the IETF conducts several free educational events in cities across the United States every year, and an annual awareness campaign that runs in conjunction with the organization's largest fundraising activity, Tulips for Tremors. Every year, the IETF also funds basic research into the cause(s) of ET. Small grants are awarded to established scientists whose primary interest is tremor disorders. The IETF funds this program in the hope that these scientists will collect sufficient published data to help them qualify for future federal funding that will lead to better treatments and a cure. IETF members receive two copies a year of the member magazine, Tremor Talk and three copies of the research newsletter, The Scoop on Tremor. Articles in both publications are written for the non-medically trained person and discuss recent advances in research, coping techniques and topics of general interest to those with ET. Medical and research articles are written by physicians and researchers who work with patients with ET and/or study ET in laboratories. The International Essential Tremor Foundation is based in Lenexa, Kansas.
Software package that detects somatic single-nucleotide variants using statistical hypothesis testing with multiple testing correction. It uses Fisher's exact test along with multiple testing correction (Benjamini-Hochberg) to find significant differences between allele composition with a specified false discovery rate.
An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.
GenVision - Software for Publication-Quality Illustrations
A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. icyou is an internet resource of health-related video clips submitted by users. Health topics covered in videos can range anywhere from infectious diseases to fitness and exercise, with videos generally being shorter than 10 minutes in length. Videos also contain information on treatment and procedures, medical fields, and health politics and policy. These videos may or may not be authored by licensed medical personnel. All videos are searchable, and users can also choose to upload their own healthcare-related videos. In addition to gathering healthcare video from the best sources on the Web and beyond, icyou.com can call on its own award-winning health reporting team to cover the latest issues and trends. Through its parent company Benefitfocus, icyou.com has full access to the Benefitfocus Media Studio, a state-of-the-art HD facility located in Charleston, South Carolina. This studio is the only one of its kind devoted solely to creating healthcare-oriented video content. In it, the Benefitfocus Media team creates up-to-the-minute reports, tutorials, features and more that help illuminate its users about the complexities of the many facets of healthcare.
Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner.
Software implementing a supervised classification method for metagenomic samples that takes advantage of the natural structure of microbial community data encoded by phylogenetic trees.
A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions.
Clustering software which uses pairwise identity-by-descent (IBD) segments to infer multiple-haplotype IBD clusters. It expands clusters from seed haplotypes by adding qualified neighbors and extends clusters across sliding windows in the genome.
SplicePlot: a tool for visualizing alternative splicing
A software tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files.
A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species.
Identity-by-descent (IBD) association testing software for genome-wide association study analysis. It requires an IBD detection method such as Beagle FastIBD to run first. GraphIBD then builds upon the IBD information to test if the IBD segments show association to the traits.
rbsurv - Robust likelihood-based survival modeling with microarray data
Software package that selects genes associated with survival.
Skylign - Interactive logos for alignments and profile HMMs
A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position.
Software applying a quantitative prediction method to predict the effect of genetic variation using hidden Markov models.
Database of the variome of Mycobacterium tuberculosis (Mtb) comprising of over 29,000 single nucleotide variations created from re-analyzed data sets corresponding to over 400 isolates of Mtb. Using a systematic computational pipeline, potential functional variants and drug-resistance associated variants have been annotated. The database has an option to annotate variants from clinical re-sequencing of Mtb.
Short Tandem Repeat Variation Indentification from Paired-End Reads
STRViper: Short Tandem Repeat Variation Indentification from Paired-End Reads
Software tool for detection of short tandem repeat (STR) variations from paired-end next generation sequencing data. It makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats of size up to fragment length. This stratergy also helps avoiding false calls resulting from errors arised from sequencing of repeat DNA.
Breakway: Identify Structural Variations in Genomic Data
A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives.
Genometa - Rapid analysis of metagenomic short reads
A Java based bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence. The approach is based upon the established open source visualisation tool IGB and supported by the rapid alignment program bowtie. The Picard toolset for SAM files is also made use of.
CATCH - Unsupervised clustering of ChIP profiles
Software tool for exploring patterns in Chromatin Immuno Precipitation (ChIP) profiling data. The CATCH algorithm performs a hierachical clustering of the profile patterns with an exhaustive alignment at each step. The algorithm has a user-friendly graphical interface that makes it easy to browse results.
Dr. Donald Doherty''s Blog ActionPotential.com
Dr. Donald Doherty''s Blog: ActionPotential.com
Blog on neuroscience related topics by Dr. Donald Doherty. Donald Doherty, Ph.D., is a neuroscientist, software engineer, and entrepreneur with twenty-five years of experience delivering information technology based products in the health care and life sciences. During 2001, Donald founded and lead Brainstage Research, Inc. where he designed and built a Web platform that included a search engine, components to transform data into life science simulations, and a number of Semantic Web technologies. Brainstage Research, Inc. was sold in 2007 and reincorporated as Brainstage, Inc. Donald served as Chief Science Officer of Brainstage, Inc. where he continued to lead the development of its software platform until January 2010. Donald received his doctorate in Neuroscience from the University of California at Irvine.
A polymorphism discovery algorithm for short reads. To run it, you provide reads (and quality scores) from a "sample genome" as input, along with a vector sequence to trim from the reads, and a reference sequence for a related genome to compare to. VAAL produces as output a an assembly for the sample genome, together with a mask showing which bases are "trusted". It then deduces from that a list of differences between the sample and related genomes. Alternatively, it can be provided as input read data for two sample genomes, together with a reference sequence for a related genome. In this case, VAAL produces assemblies for each of the sample genomes, and compares them to each other, thereby deducing a list of differences between them. VAAL has been tested on bacteria, using single lanes of 36 bp unpaired reads from the Illumina platform. Note: This software package is no longer supported and information on this page is provided for archival purposes only.
Software that consists of two command-line utilities, slope_align (which finds the best split-read alignments to the reference genome) and slope_cluster (which clusters and outputs the alignments)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software for scanning reads from short-read sequenced genomes against a human breakpoint library to accurately identify structural variants (SVs). The library of breakpoints at nucleotide resolution were assembled from collating and standardizing ~2,000 published structural variants (SVs). For each breakpoint, its ancestral state (through comparison to primate genomes) was inferred and its mechanism of formation (e.g., nonallelic homologous recombination, NAHR).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 11, 2017. The Third Reviewer is a forum for scientists to share opinions about recently published research. Currently both microbiology and neuroscience papers in different journals are included. Third Reviewer allows anonymous commenting and provides a centralized location for commentary on papers from 11 major neuroscience venues.
Analysis pipeline that accurately detects and maps variations that are often missed by standard analysis algorithms. It uses direct de novo read overlap assembly to accurately detect and characterize SNPs (single nucleotide polymorphisms), indels, and SVs (structural variations). The pipeline uses existing Illumina HiSeq data and does not require additional library preparation. The algorithm is optimized for projects with at least 20x coverage per chromosome set (i.e. 40x for diploid).
A cloud-based infrastructure for managing, analyzing and sharing genomics datasets.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web-based portal and database aggregate of free and open source software for medical imaging. The programs are categorized and placed in a searchable database.
DNA motif discovery software adapted for ChIP-Seq data. It is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. It does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences
Software to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology. Tools for assembly, quality filtering, taxonomy based analysis and taxonomy independent analysis tools, and tools to convert the data to formats suitable for common ecological and statistical packages are available. For extremely large datasets, command line tools are available.
Chinese research university in Beijing, China that offers undergraduate and graduate degree programs in pure and applied sciences, social sciences and humanities, and sciences of management and education.
A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution.
Software to help users work with DICOM files by organizing, managing and analyzing them. Key features: * a smart DICOM viewer with 4 panel display, annotations, arrows, multimodality synchronization, etc... * an export wizard to the most common picture or movie file formats * an export wizard to Microsoft PowerPoint * the most simple and compatible DICOM CD-ROM reader * the most simple and smart DICOM CD-ROM WRITER * an archiving solution with lossless compression of the data * a DICOM creation module to dicomize images from any image source (even video capture) * e-mail or FTP import end export functions (teleradiology) * 16 native localized versions
Software program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations). Note: This software package is no longer supported and information on this page is provided for archival purposes only.
Software tool to evaluate de novo genome assemblies with RNA transcripts.
A fully automated and modular software package for mining sequence data to identify sequences of microbial origin. The pipeline was optimized for analysis of data generated by the Roche/454 next-generation sequencing platform but can be applied to longer sequences (Sanger sequencing data or assembled contigs) as well. Microbial sequences are identified on the basis of BLAST alignments and the taxonomic classification of the reference sequence(s) to which a read is aligned. Viruses are the focal point of VirusHunter as released, but it can be easily modified to generate parallel outputs for bacterial or parasitic species. To date, VirusHunter has been applied to thousands of specimens, including human, animal and environmental samples, resulting in the detection of many known and novel viruses.
seq2HLA - HLA typing from RNA-Seq sequence reads
Software for obtaining an individualXs HLA class I and II type and expression using standard NGS (Next-generation sequencing) RNA-Seq data. It comprises mapping RNA-Seq reads against a reference database of HLA alleles, determining and reporting HLA type, confidence score and locus-specific expression level.
High-throughput sequence alignment using Graphics Processing Units
Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer.
GeneMeta - MetaAnalysis for High Throughput Experiments
Software package providing a collection of meta-analysis tools for analysing high throughput experimental data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A next generation sequencing data analysis computer for biologists with or without IT background. It has an easy to-use graphical interface to analyze sequencing data in with only 15 clicks. A range of standard, add-on and custom applications help analyze and visualize data generated by Next Generation Sequencing machines. These are installed on each GenoMiner by default: * Reference assembly * De novo assembly * ChiP-Seq * BLAST * Hybrid de novo assembly * Hybrid reference assembly Add-on applications: * Quality assesment * RNA-Seq * Copy Number Variation (CNV) * Multiple Sequence Alignment * miRNA-Seq * Variant Calling
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Open source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing data.
Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species.
GenomicTools: a computational platform for developing high-throughput analytics in genomics.
A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. It implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address tasks from preprocessing and quality control to meta-analyses. The user can create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications. In addition to enabling rapid prototyping, the platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. The platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor.
An optional module in the Omixon Target application suite for HLA typing using NGS (next-generation sequencing) data that gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data.
Software application suite to help clinical labs adopt next generation sequencing for the analysis of diagnostic gene targets.
Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites.
QualiMap - Evaluating next generation sequencing alignment data
Software application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.
Software to address all aspects of Next Generation Sequencing data workflow.
Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.
BSSim: Bisulfite sequencing simulator for next-generation sequencing
Software to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD.
Software tool that delivers visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an user interface to make sure that your discovery process is fluid and streamlined.
A collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.
HiPipe - High Performance Pipelines for NGS Data Analysis
Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task.
TM4 Microarray Software Suite: MicroArray DAta Manager
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Data management software implemented in Java that facilitates the entry of data into a relational database. It guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results that are essential for the interpretation of expression results in downstream analyses. Canned reports provide information on RNA samples, studies, slide maps and other pertinent data and a general SQL query window allows freeform access to the underlying database. MADAM also serves as a platform for launching other data entry and management tools. Through the use of these integrated modules, users can view and score PCR plates, design experiments and studies, and track laboratory materials.
A commercial organization for pharmaceutical, biopharmaceutical, and medical device open-access capability and technology platform with global operations.
TM4 Microarray Software Suite: Microarray Data Analysis System
Application that provides users an interface to design analysis protocols combining one or more normalization and filtering steps. In this way, data from many individual hybridizations can be treated in a uniform and reproducible manner.
TM4 Microarray Software Suite: Automated Microarray Pipeline
THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis.
An ion channel focused Contract Research Organization (CRO) that does safety testing and screening for global pharma and biotech companies. ChanTest has developed a complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers. Services range from early functional screens for profiling drug candidates or ranking within profiles during the drug-discovery process to a complete set of in vitro GLP service products for cardiac risk assessment. ChanTest works in partnership with customers to speed the drug-development process, save time and money, and ultimately to help make better, safer drugs.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.
categoryCompare - Meta-analysis of high-throughput experiments using feature annotations
A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
A contract research organization providing drug development and animal testing services. Under the name Covance Research Products Inc., based in Denver, Pennsylvania, the company also deals in the import, breeding and sale of laboratory animals. It breeds dogs, rabbits, guinea pigs, non-human primates, and pigs, and runs the largest non-human primate laboratory in Germany. (Wikipedia)
metahdep - Hierarchical Dependence in Meta-Analysis
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.
Blog devoted to reporting, analyzing and interpreting the latest results in the field of brain imaging technologies, particularly at the levels of systems, circuits, single cells and below. The site content is produced by Andrew Hires.
Plantagora - a resource for plant genome assembly
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A web-based plant genome assembly simulation platform whose resources include out of the box scripts for analyzing assembly data, an on-demand web graphing tool to model your experiment, and a downloadable database with metrics and parameters from over 3,000 simulated genome assemblies.
QUAST: Quality Assessment Tool for Genome Assemblies
Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.
TileQC: A tile based approached to quality control
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,10, 2021.Software providing a visually oriented tile based approach to error detection for Solexa next-gen sequencing data. It is written in R and has both qualitative and quantitative error detection features. This software was written with the idea that the researcher's visual pattern recognition is the best way to detect novel errors and contains variety of ways to visualize that data. Once a new type of error is identified the data extraction features of the program may then be used as a starting point for the programmatic detection and/or filtration of similar errors. A supplementary role of tileQC is to convert the Eland and Q-score data contained within the Solexa "*_prb.txt" and "*_eland_results.txt" text files to a more flexible database form. Once in database form, tileQC simplifies the mechanics of interacting with that data and supplements standard SQL with an expression subsitution mechanism that allows R to be easily comingled with SQL. This system requires access to a mySQL server and the R package RMySQL as well as a few standard UNIX tools (also available on Windows and Macintosh).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists.
A C++ library for parsing and manipulating Variant Call Format (VCF) files, and many command-line utilities. The API provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.
Software that gives estimates of the structure and diversity of uncultured viral communities using metagenomic information.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025.Software to classify the function and phylogeny of reads as short as 30 bp. It is flexible, which can utilize multiple data modules and downstream analysis scripts. It is fast, reading in signature lists of 5-500 million peptide signatures in 1-15 minutes, and subsequently processes genomic fragments at the rate of 6 Gbp/hr. It parallelizes without significant increase in memory requirements until I/O bound on multiple input files; parallelization works well on 64 processors.
Genome Trax for Next Generation Sequencing
Service that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia.
Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API.
NGSUtils - Tools for next-generation sequencing analysis
A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis.
ChIP-seq - Tools for the analysis of ChIP-seq data
Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.
Knowledge Engineering from Experimental Design
Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable.
Tally - Deduplication of sequence fragments
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software program for deduplicating sequence fragments. It minimises memory usage by compressing sequences and using compact memory allocation techniques. A built-in parser allows a variety of input file formats and a simple specification language allows flexible output file formats. It can be made aware of paired-end reads, and it can handle degenerate sequence inserts intended to reveal amplification biases. Tally comes with reaper, a program for demultiplexing, trimming and filtering short read sequencing data.
mapDamage: tracking and quantifying damage patterns in ancient DNA sequences
Software for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
freeIbis - Improved Base Identification System
A software basecaller for Illumina sequencers with calibrated quality scores.
Software to detect short insertion / deletion variants (and SNPs) from population sequence data, i.e. sequence reads generated from a population of individuals. It uses a probabilistic model to utilize sequence reads from a population of individuals to automatically account for context-specific sequencing errors associated with indels. piCALL is implemented in C for use on Linux platforms and can be applied to sequence data from different sequencing platforms. However, the method requires each individual in a dataset to be sequenced using the same platform. The reads for each individual should be aligned to the same reference genome sequence. Note that the program will not be able to call indels from individual sequence datasets or data from a small number of individuals.
ERGO Genome Analysis and Discovery System
A web-based genome analysis platform that integrates proprietary functional genomic data, metabolic reconstructions, expression profiling, and biochemical and microbiological data with publicly available information. Focused on microbial genomics, it provides better and faster identification of gene function across all organisms. Building upon a comprehensive genomic database integrated with a collection of microbial metabolic and non-metabolic pathways and using proprietary algorithms, it assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products. . * Automated and manual annotation of genes and genomes * Analysis of metabolic and non-metabolic pathways to understand organism physiology * Comparison of multiple genomes to identify shared and unique features and SNPs * Functional analysis of gene expression microarray data * Data-mining for target gene discovery * In silico metabolic engineering and strain improvement
A collection of flexible and memory-efficient software programs for k-mer counting and indexing of large sequence sets. It is based on enhanced suffix arrays which gives a much larger flexibility concerning the choice of the k-mer size. It can process large data sizes of several billion bases.
Software utility for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. It scans the raw reads and produces a compact representation of all non-unique reads accompanied with number of their occurrences. The algorithm implemented makes use mostly of disk space rather than RAM, which allows to use KMC even on rather typical personal computers.
A k-mer counting software that can count k-mers of large Illumina datasets on laptops and desktop computers.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects.
BF Counter: Memory efficient K-mer counting Software
Software program for counting k-mers in DNA sequence data. It identifies all the k-mers that occur more than once in a DNA sequence data set using a Bloom filter, a probabilistic data structure that stores all the observed k-mers implicitly in memory with greatly reduced memory requirements.
snpStats: SnpMatrix and XSnpMatrix classes and methods
Software for classes and statistical methods for large single nucleotide polymorphism (SNP) association studies.
CNVtools - A package to test genetic association with CNV data
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.
CGEN - An R package for analysis of case-control studies in genetic epidemiology
Software R package for analysis of case-control studies in genetic epidemiology.
Ontology of a set of body-system terms used in the ICD (International Classification of Diseases) 11 revision
Software package for survival time prediction based on a piecewise baseline hazard Cox regression model. It is meant to help predict survival times in the presence of high-dimensional explanatory covariates.
iterativeBMAsurv - The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
Software package providing a variable selection method for applying survival analysis to microarray data.
multtest - Resampling-based multiple hypothesis testing
Software package for non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.
A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.
Software program suitable for genome-scale data which uses a Markov-hidden Markov model (MHMM) to estimate local ancestry. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel. One application is to perform admixture mapping without genotyping special ancestry-informative-marker panels.
A software package for the inference of locus-specific ancestry in recently admixed populations. LAMP-LD takes the genotypes of admixed individuals as well as reference haplotype panels approximating the mixing ancestral populations, and outputs the estimated number of alleles from each ancestry in each locus for each individual. The LAMP-LD package also includes the program LAMP-HAP, which processes haplotype data when high-quality phasing is available, and utilizes trio nuclear family designs to improve estimation accuracy. LAMP-LD is based on a window-based processing combined within a hierarchical Hidden Markov Model. It can process 2,3 or 5 mixing populations, and its short per-sample processing time makes it suitable for analyzing large datasets of dense SNP panels. The original program LAMP does not use the LD and therefore is not as accurate, but it is useful in cases where the SNP density is not high enough or when the ancestral haplotypes are unkown.
GemTools - A fast and efficient approach to estimating genetic ancestry
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software tools for modeling genetic ancestry based on the single nucleotide polymorphism (SNP) information. This package of functions helps the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy. It is completely written in R and runs on any platform that supports R.
MinimumDistance - A package for de novo CNV detection in case-parent trios
Software package for analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.
Synthetic Biology Open Language Visual Ontology
Ontology to represent standardized graphical notation for synthetic biology.
Iterative pruning Principal Component Analysis
Software implementing a population structure analysis algorithm which assigns individuals to subpopulations and infers the total number of subpopulations present. Additional functions have been included that result in improved population assignment accuracy. # Universal genotype data encoding scheme which allows the population analysis of all types of genetic markers; Single Nucleotide Polymorphism (SNP), Short Tandem Repeat (STR) and RFLP. # New termination criterion called ?EigenDev? which is more robust to population sampling, thus provides the better estimation of number of assigned subpopulations (K) and higher accuracy for the analysis of large complex population datasets.
A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. It uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software using a f frequentist approach for estimating individual ancestry proportion.
Mutascope - Analysis software designed for PCR-amplicon sequencing data
Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.
Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix.
VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
Software package that enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. It performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, it produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.
Software package using Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays.
Software package that contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open source R tools available at Bioconductor, including the R packages Biobase and oligo. This has numerous advantages, including the ability to build statistical models for SNP-level data that operate on instances of the class, and to communicate with other R packages that add additional functionality.
SMAP - A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
Software package providing functions and classes for DNA copy number profiling of array-CGH data.
Software package for quantile smoothing and genomic visualization of array data.
Benaroya Research Institute at Virginia Mason
Non-profit organization based out of Seattle, Washington that conducts medical research on autoimmune disease.
mBPCR - Bayesian Piecewise Constant Regression for DNA copy number estimation
Software package that estimates the DNA copy number profile to detect regions with copy number changes.
Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set.
genoset - Provides classes similar to ExpressionSet for copy number analysis
Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data.
exomeCopy - Copy number variant detection from exome sequencing read depth
Software package for detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.
A software application PDF reader which provides a modified method of reading scientific papers. Different programs are available with additional information concerning the PDF, including Altimetric, Mendeley, and SHERPA/RoMEO. Related, open access articles can be saved directly from Utopia Docs and terms within the PDF can be directly searched, with results appearing within the program.
CGHregions - Dimension Reduction for Array CGH Data with Minimal Information Loss
Software package for dimension Reduction for Array CGH Data with Minimal Information Loss.
CGHbase: Base functions and classes for arrayCGH data analysis
Software package that contains functions and classes that are needed by arrayCGH packages.
Software for ultra-fast base-calling of second-generation sequencing data by blind deconvolution.
beadarraySNP - Normalization and reporting of Illumina SNP bead arrays
Software package for importing data from Illumina SNP experiments and performing copy number calculations and reports.
Sequence Structure and Conservation profiler
Tool which can be used to identify novel miRNA gene candidates in the human genome.
Software program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.
Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.
SNP & Variation Suite (SVS) SNP Analysis
SNP Analysis software for basic to advanced analyses that incorporates a number of intuitive workflows to lead you beyond single marker associations. With support for case-control and quantitative traits, whole genome and candidate gene data, you can run a breadth of statistical tests under several genetic models. Advanced regression can further help elucidate even the most complex gene-gene and gene-environment interactions.
SNP & Variation Suite (SVS) CNV Analysis
A set of software tools for processing raw intensity data, identifying regions of copy number variation (CNV), visualizing copy number data, and performing association analyses on a variety of copy number covariates.
An American pharmaceutical company aiming to make a difference in the lives of people globally through their medicines, vaccines, biologic therapies and animal health products.
Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.
methylMnM - detect different methylation level (DMR)
Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison.
methyAnalysis - DNA methylation data analysis and visualization
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data.
les package: Identifying Differential Effects in Tiling Microarray Data
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.
ARRmNormalization - Adaptive Robust Regression normalization for Illumina methylation data
Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.
ChIPsim - Simulation of ChIP-seq experiments
Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.
Sherman - bisulfite-treated Read FastQ Simulator
Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments.
yaqcaffy - Affymetrix expression data quality control and reproducibility analysis
Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.
Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages.
Software package that provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.
Model-based software package for processing microarray images so as to estimate foreground and background intensities. The method starts with a very simple but effective automatic gridding method, and then proceeds in two steps. The first step applies model-based clustering to the distribution of pixel intensities, using the Bayesian Information Criterion (BIC) to choose the number of groups up to a maximum of three. The second step is spatial, finding the large spatially connected components in each cluster of pixels. The method thus combines the strengths of the histogram-based and spatial approaches. It deals effectively with inner holes in spots and with artifacts. It also provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three.
Software package that uses a modeling strategy especially designed for normalizing high-throughput genomic data. The premise is that your data is a function of study-specific variables which are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.
Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure
Specimen in a Corrected Optical Rotational Enclosure imaging
Narrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields.
Signal-to-Noise applied to Gene Expression Experiments
Software package that uses signal-to-noise ratios (SNRs) as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.
Simpleaffy - Very simple high level analysis of Affymetrix data
Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.
qcmetrics - A Framework for Quality Control
Software package that provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.
Optimised Local Intensity-dependent Normalisation
Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data.
Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments.
Software package for a Graphical User Interface for the limma Microarray package.
ffpe - Quality assessment and control for FFPE microarray expression data
Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).
dyebias - The GASSCO method for correcting for slide-dependent gene-specific dye bias
Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias.
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.
BeadDataPackR - Compression of Illumina BeadArray data
Software that provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.
Portal for a variety of web-based, educational information sources. Subjects include biotechnology, medical genetics, digestive systems and endocrine systems. Animations require a Java-enabled browser.
Light-weight software package for normalization and visualization of microarray data using only basic R data types. Software can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.
Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.
beadarray - Quality assessment and low-level analysis for Illumina BeadArray data
Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
arrayQuality - Assessing array quality on spotted arrays
Software functions for performing print-run and array level quality assessment.
Blood biobank for the Partners research program, which investigates the affects of genes, lifestyle and environment on human health.
arrayMvout - Multivariate outlier detection for expression array QA
Software package that supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.
affyQCReport - QC Report Generation for affyBatch objects
Software package to create a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.
affyPLM - Methods for fitting probe-level models
Software for fitting probe-level models and tools using these models. Probe-level models (PLM) based quality assessment tools.
Affymetrix linear modeling Graphical User Interface
R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11.
AffyExpress - Affymetrix Quality Assessment and Analysis Tool
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.
waveTiling - Wavelet-Based Models for Tiling Array Transcriptome Analysis
Software package to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.
A Java toolkit designed to convert DNA and RNA sequences into k-mers.
Gaussian Process Ranking and Estimation of Gene Expression time-series
Software R package for Gaussian Process Ranking and Estimation of Gene Expression time-series. The software fits two Gaussian processes (GPs) with an radial basis function (RBF) (+ noise diagonal) kernel on each profile. One GP kernel is initialized wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimized via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via receiver operating characteristic curves (ROC curves) is performed against Bayesian hierarchical model for the analysis of time-series (BATS) (Angelini et.al, 2007).
Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code.
A Swiss global health-care company that operates under two divisions: Pharmaceuticals and Diagnostics.
Wiki of chemical and preparatory experimental protocols.
Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models.
Software package for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays.
factDesign - Factorial designed microarray experiment analysis
Software package that provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.
Software for adaptive Gene Picking for Microarray Expression Data Analysis.
Bayesian Estimation of Temporal Regulation
Software package that implements the Bayesian Estimation of Temporal Regulation algorithm to identify differentially expressed genes in microarray time-course data.
Software for target enrichment performance for next-generation sequencing.
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Single-channel array normalization and Universal exPression Codes
A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A
Software package that generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Reports contain both general and platform-specific sections. Both one and two color array platforms are supported.
Web-based resource that provides an integrated set of tools for DNA sequence anlaysis, plasmid map creation, sequence viewing, and various biochemical calculations.
Imagescience: Imaging Conferences Database
Imagescience provides a database of scientific imaging conferences around the world. Sponsors: This database is supported by imagescience.org.
Software package that contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.
Differential Expression via Distance Summary
Differential Expression via Distance Summary for Microarray Data
Software library that contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements methodology (Differential Expression via Distance Summary) which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.
Harshlight - A corrective make-up program for microarray chips
Software package used to detect extended, diffuse and compact blemishes on microarray chips. It automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection.
MiChip Parsing and Summarizing Functions
Software package that takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.
Ocplus - Operating characteristics plus sample size and local fdr for microarray experiments
Software package that allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).
Bayesian Robust Inference for Differential Gene Expression
Software package to test for differentially expressed genes with microarray data. It can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. The model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space.
Factor Analysis for Robust Microarray Summarization
Software using a model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips. It is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise.
Preprocessing and analysis software for single microarrays and microarray batches.
An easy to use software tool for dual color microarray data. Its GUI-Tk based environment lets any non-experienced user perform a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.
Laplace Mixture Model in Microarray Experiments
Software to identify differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes.
maCorrPlot - Visualize artificial correlation in microarray data
Software that graphically displays correlation in microarray data that is due to insufficient normalization.
Significant Gene Expression Profile Differences in Time Course Microarray Data
A regression based software package to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments.
Software library that contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. It is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions.
Software package that uses functions to handle and analyze cDNA microarray data.
Mahalanobis Distance Quality Control for microarrays
A multivariate quality assessment software for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.
metaArray - Integration of Microarray Data for Meta-analysis
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) and combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform.
nnNorm - Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
Software package that allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.
Software to detect differential expression in microarray and proteomics datasets. Its use has been shown to improve the detection of differentially expressed genes or proteins in these datasets.
Software package that contains the function to assess the batch sourcs by fitting all sources as random effects including two-way interaction terms in the Mixed Model (depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book Batch Effects and Noise in Microarray Experiements, chapter 12.
Software package for robust estimation of cDNA microarray intensities with replicates. It uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance.
stepNorm - Stepwise normalization functions for cDNA microarrays
Software for stepwise normalization functions for cDNA microarray data.
Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows.
Software package that permits the user to combine raw data of different microarray platforms into one virtual array. It consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data combination and letting the user concentrate on analyzing the resulting virtual array.
NiLearn: Machine learning for Neuro-Imaging in Python
A software package to facilitate the use of statistical learning on NeuroImaging data. Namely NiLearn leverages the scikit-learn Python toolbox for multivariate statistics with applications such as predictive modelling, classification, decoding, or connectivity analysis.
Integrated DNA Technologies OligoAnalyzer
Web-based application for analyzing oligonucleotides. Analysis proceeds after the sequence has been entered and the calculations modified based on target type, oligo concentration, sodium ion concentration, magnesium ion concentration, and dNTP concentration.
Software library used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional "BH" or "BY" procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 14, 2016. The Australian Digital Futures Institute no longer exists. It has been replaced by the USQ Digital Life Lab. A portal for the Australian Digital Futures Institute, a cross-institutional, multidisciplinary Institute that focuses on software research for technology-enhanced innovation.
Public state university in West Bengal, India. There is a focus on interdisciplinary learning and research; the university features a variety of centers such as school of education technology, cognitive sciences, and natural product studies.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. An extensible, open-source platform for managing your digital objects. Using a variety of plugins, you can transform your digital objects into new formats, search and browse through your collection, collaborate through tagging and annotations, and create packages of information for publishing to all manner of systems. Written in Python.
MitoMiner - A database of the mitochondrial proteome
A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The Integrated Content Environment (ICE) is a free Word-processor based system that allows authors to work individually or collaboratively on material for the Web, CD and print. This free web content management system, produced by the University of Southern Queensland, was initially developed by staff at the university to produce course content for online and print delivery. It has also been used for general web site development, and to manage documents in project intranets.
Archive database for output data generated by next-generation sequencing machines including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, and others. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA). Please submit the trace data from conventional capillary sequencers to DDBJ Trace Archive., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Public Library of Science - Science Blog Network
PLoS Blogs has been set up to bring a select group of independent science and medicine bloggers together with the editors and staff who run our blogs. Our independent network is made up of writers who love science and medicine, and scientists and physicians that love to write. Here, you'll find an equal mix of blogs from journalists and researchers tackling diverse issues in science and medicine. There are three very distinct types of blogs on the PLoS Blogs network: the official PLoS blog, the PLoS journal blogs (collectively known as The PLoS Blogs), and blogs from the independent network (a.k.a. The PLoS Blogosphere) # The official PLoS blog: This content is produced, edited, and/or maintained by PLoS staff. # The journal blogs: This content is produced, edited, and/or maintained by PLoS journal staff: The current journal blogs are Speaking of Medicine (PLoS Medicine's blog) and everyONE (PLoS ONE's blog). # Our independent network of bloggers (The PLoS Blogosphere): This content is produced, edited, and/or maintained by the authors. * All of the content in The PLoS Blogosphere came from the minds of the authors. PLoS does not screen, edit, or otherwise meddle with content on the these blogs in any way. Our bloggers and our users are held to exactly the same standards, and the community guidelines apply to everyone that uses our site. If a blogger has posted content that you believe violates our site abuse policy, please contact PLoS. * Bloggers monitor their own comment threads: All comments will be reviewed by the author of the blog where you leave your thoughts. Just follow our simple community guidelines and we'll all get along just fine.
It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available.
Resource for Biocomputing Visualization and Informatics
Biomedical technology resource center that develops software and web-based resources for the visualization and analysis of molecular structure, and related data, at scales ranging from the atomic to the supramolecular. They create tools for handling and integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and networks. Their primary efforts are in the visualization and analysis of structures of molecules and molecular assemblies, enzyme sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. They provide technologies to enable identifying the molecular bases of disease and phenotypic variation, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. RBVI distributes software tools, including the popular UCSF Chimera visualization and analysis package, develops and hosts the Structure-Function Linkage Database, and provides access to state-of-the-art computational resources in support of research projects in these areas.
A database of hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities. The SFLD classifies evolutionarily related enzymes according to shared chemical functions and maps these shared functions to conserved active site features. The classification is hierarchical, where broader levels encompass more distantly related proteins with fewer shared features. It thus serves as the analysis and archive site for superfamilies targeted by the Enzyme Function Initiative, and is developed by the Babbitt Laboratory in collaboration with the UCSF Resource for Biocomputing, Visualization, and Informatics. The resource also provides a collection of tools and data for investigating sequence-structure-function relationships and hypothesizing function.
Mark up language for collecting and exchanging metadata in an automated, computer-based fashion, developed for neuroscience, specifically, neurophysiology experiments. In odML arbitrary metadata information is stored as extended key-value pairs in a hierarchical structure. Central to odML is a clear separation of format and content, i.e., neither keys nor values are defined by the format. This makes odML flexible enough for storing all available metadata instantly without the necessity to submit new keys to an ontology or controlled terminology. Common standard keys can be defined in odML-terminologies for guaranteeing interoperability.
THIS RESOURCE IS NO LONGER IN SERVICE, confirmed by curator 11/21/2018; Community of researchers attempting to build a comprehensive virtual cell model. The 3DVC will do for cell biology what the Large Hadron Collider (LHC) does for particle physics, but through a virtual rather than physical resource. It will bring together collaborators around a shared infrastructure to advance the field through efficient groundbreaking science and technology, the results of which will be broadly disseminated to an audience ranging from K12 to professionals. The 3DVC is committed to open science, yet strives for sustainability through new business models that leverages that open content.
Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password.
Blog focusing on cellular-level neuroscience for everyone. While a higher level of neuroscience, such as behavioral studies and human fMRI scans level of neuroscience is interesting to everyone, some people might want to focus a little closer in. That is what The Cellular Scale is for.
Knowledge management and engineering system software for experimental biomedical scientists permitting a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group derived on a local store of PDF files. Usability is especially emphasized within a laboratory so that this software could provide support to experimental scientists attempting to construct a personalized representation of their own knowledge on a medium scale. The BioScholar system uses a graphical interface to create experimental designs based on the experimental variables in the system. The design is then analyzed to construct a tabular input form based on the data flow. They call this methodology "Knowledge Engineering from Experimental Design" or "KEfED". The approach is domain-independent but domain-specific modules reasoning can be constructed to generate interpretations from the observational data represented in the KEfED model. The application is available for download as platform-specific installers including Linux, Unix, Mac OS, and Windows. The installer will install an application that will run the BioScholar server. This server uses Jetty as its integrated web server.
Sumatra: automated tracking of scientific computations
A software tool for managing and tracking projects based on numerical simulation or analysis to support reproducible research. It can be thought of as an automated electronic lab notebook for simulation/analysis projects. Sumatra consists of: a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the context, annotating these records, linking to data files, etc.; a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results; a LaTeX package and Sphinx extension for including Sumatra-tracked figures and links to provenance information in papers and other documents; and a Python API, on which smt and smtweb are based, that can be used in personalized scripts in place of using smt.
Community-based initiative to promote and co-ordinate open-source software development in neuroscience hosting a number of software projects for computational and systems neuroscience, including PyNN, NeuroTools, Brian, Neo, OpenElectrophy, libNeuroML and Sumatra. Some of the projects use their Trac installation, others are on GitHub. By grouping these projects together under the NeuralEnsemble umbrella, the aim is to maximize interoperability and build components that can easily be combined into powerful systems for brain simulations and advanced data analysis. An annual CodeJam workshop is organized, bringing together scientists, graduate students, and scientific programmers to share ideas, present their work, and write code together. These workshops have been hugely effective in catalyzing open-source neuroscience software development. There is a NeuralEnsemble Google group for discussion of collaborative neuroscience software development (mainly in Python, but users of other languages are welcome!) and to provide software support.
Open source Java library dedicated to semantic measures computation and analysis. Tools based on the SML are also provided through the SML-Toolkit, a command line software giving access to some of the functionalities of the library. The SML and the toolkit can be used to compute semantic similarity and semantic relatedness between semantic elements (e.g. concepts, terms) or entities semantically characterized (e.g. entities defined in a semantic graph, documents annotated by concepts defined in an ontology).
Biomedical technology resource center that develops new gamma-ray imaging instruments and techniques that yield substantially improved spatial and temporal resolutions. The Center makes its imagers and expertise available to a wide community of biomedical and clinical researchers through collaborative and service-oriented interactions. The collaborative research applies these new imaging tools to basic research in functional genomics, proteomics, cancer, cardiovascular disease and cognitive neuroscience, and to clinical research in tumor detection and other selected topics. There are five core research projects: * Detector technology research and development * Reconstruction algorithms and system modeling * Data acquisition, signal processing, and system development * Image-quality assessment and system optimization * Techniques for molecular imaging
Interactive software of a set of modular programs (each performing a specific task) that provide an integrated computing environment for data analysis and system modeling. Unique capabilities of LYSIS include input-output nonlinear system modeling and the novel methodology of Principal Dynamic Modes (PDMs). LYSIS is currently available in two versions: one for LYSIS 7.1 Windows and one for LYSIS 7.2 Matlab. Early versions are also available for UNIX environments, distributed as source code that can be compiled for each UNIX implementation (e.g., Solaris, HPUX, Linux). Specific features of LYSIS that cannot be found in commercially available packages include the efficient kernel estimation using Laguerre expansions and the use of Principal Dynamic Modes (PDMs). These enable input-output modeling of dynamic nonlinear systems with relatively short data-records (even in the presence of considerable noise). System Requirements * Operating System ** Windows XP/Vista/7 ** Sun/Unix: Solaris 2.x
ORCID and DataCite Interoperability Network
Service (Beta) that allows users to search the DataCite Metadata Store, and add their research outputs including datasets, software, and others to their ORCID profile. This should increase the visibility of these research data, and will make it easier to use these data citations in applications that connect to the ORCID Registry. In addition, the service is also providing formatted citations in several popular citation styles, supports COinS, links to related resources, and displays the attached Creative Commons license where this information is available. The DataCite Metadata Store of course also contains many text documents from academic publishers and services such as figshare or PeerJ Preprints, and these works can also be claimed. This tool is a collaborative effort by ORCID, CrossRef and DataCite.
Protocols and other training materials related to the CLARITY protocol, a technique for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable.
A repository of de-identified control arm data of patients from clinical studies of Alzheimer's disease and Mild Cognitive Impairment. It provides the ability to analyze the data online with the R statistical analysis program, create and download standard reports, run complex queries, or download data to a desktop for further analysis. Additional data will be added to the database over time. Critical Path Institute consortia members and qualified researchers may upload and work on scientific data relevant to biomarkers of drug toxicity, neurodegenerative diseases, and patient-reported outcomes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 8, 2022. Consortium developing new technologies and methods to accelerate the development and review of medical products for neurodegenerative diseases. It is focused on accelerating drug development for patients with chronic neurodegenerative disease, namely, Alzheimer's disease (AD) and Parkinson's disease (PD), by advancing drug development tools for evaluating drug efficacy, conducting clinical trials, and streamlining the process of regulatory review. The consortium focuses on sharing precompetitive patient-level data from the control arms of legacy clinical trials, developing new tools to be submitted to the regulatory agencies, and developing consensus data standards. CAMD has the following areas of focus: (1) qualification of biomarkers, (2) development of common data standards, (3) creation of integrated databases for clinical trials data, and (4) development of quantitative model-based tools for drug development. Regulatory milestones include a qualification opinion with EMA for the use of low baseline hippocampal volume for patient enrichment in pre-dementia trials, and most recently, positive regulatory decisions from the FDA and EMA for the use of a clinical trial simulation tool to aid in trials for mild to moderate stages of AD., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Common Data Element (CDE) Resource Portal
NIH Common Data Element (CDE) Resource Portal
A repository of Common Data Elements (CDE). The CDE is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. Forms in the Repository might be original, or might recreate the format of real-world data collection instruments or case report forms. NIH has endorsed collections of CDEs that meet established criteria. NIH-endorsed CDEs are designated with a gold ribbon. Users can Browse NIH-Endorsed CDEs, Browse All CDEs, or Browse Forms.
A set of modules that are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions. It models the dynamic interactions that take place among the various component mechanisms, including those involved in the chemical control of breathing, heart rate, and blood pressure, as well as the effects of changes in the sleep-wake state and arousal from sleep. PNEUMA includes the autonomic control of the cardiovascular system, chemoreflex and state-related control of breath-to-breath ventilation, state-related and chemoreflex control of upper airway potency, as well as respiratory and circulatory mechanics. The model is capable of simulating the cardiorespiratory responses to sleep onset, arousal, continuous positive airway pressure, the administration of inhaled carbon dioxide and oxygen, Valsalva and Mueller maneuvers, and Cheyne-Stokes respiration during sleep. In PNEUMA 3.0, we have extended the existing integrative model of respiratory, cardiovascular, and sleepwake state control, to incorporate a sub-model of glucoseinsulinfatty acid regulation. The extended model is capable of simulating the metabolic control of glucoseinsulin dynamics and its interactions with the autonomic nervous system. The interactions between autonomic and metabolic control include the circadian regulation of epinephrine secretion, epinephrine regulation on dynamic fluctuations in glucose and free fatty acids in plasma, metabolic coupling among tissues and organs mediated by insulin and epinephrine, as well as the effect of insulin on peripheral vascular sympathetic activity. This extended model represents a starting point from which further in silico investigations into the interaction between the autonomic nervous system and the metabolic control system can proceed. Features in PNEUMA 3.0 * Incorporates metabolic component based on prior models of glucose-insulin regulation and free fatty acid (FFA) regulation. * Changes in sympathetic activity from the autonomic portion of PNEUMA produce changes in epinephrine output, which in turn affects the metabolic sub-model. * Inputs from the dietary intake of glucose and external interventions, such as insulin injections, have also been incorporated. * Also incorporated is autonomic feedback from the metabolic component to the rest of PNEUMA: changes in insulin level lead to changes in sympathetic tone. System Requirements: PNEUMA requires Matlab R2007b or higher with the accompanying version of Simulink to be installed on your computer.
MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7
A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome.
NeuroMorpho.Org light species ontology is a customized taxonomy for species available in NeuroMorpho.Org. This file is created from the existing resources like NCBI Taxonomy, NIF organism, Rat strain ontology, and Jax mice catalogue. The OBO file can be explored and downloaded from the NCBO bioportal service. The current NCBI_NMOsp_v1.2.2.obo file consists of 887 concepts of which 24 unique classes are mapped onto species & strains data in NeuroMorpho.Org database.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).
Biospecimen and clinical data repository for researchers that includes tumor and normal tissue, blood samples, and other bio fluids. Samples are refrigerated, frozen, deep frozen, or frozen in liquid nitrogen. Four service lines are provided: ExpressBank offers access to biospecimens, which are collected under IRB-approved core protocol for future unknown research projects; Service Bank offers services such as biospecimen procurement, processing, and temporary banking; PathBank offers access to high-quality, annotated formalin-fixed paraffin-embedded (FFPE) tissues and H&E slides from Pathology department on fee-for-sample basis; and On-DemandBank allows targeted development of a temporary Biobank that strictly meets the specifications of an IRB-approved collection protocol of a sponsor on fee-for-service basis.
Online Neuroscience Lectures - Maintained by the Kilgard Lab
List of lectures, slides and videos concerning neuroscience and neurophysiology.
An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A database of over 700 retinal topography maps of a wide variety of species published in a diversity of journals. It has been assembled to assist vision and neuroscience researchers to locate and compare the distribution of retinal neurons within and across species. The maps can be searched by taxonomic or common name classification, cell type sampled, type of retinal specialization and staining/visualization method. Maps can be compared by selecting multiple maps and clicking the Compare Selected button. An interactive spreadsheet can be also downloaded.
Technology by Highly Oriented Research Center for Neuroinformatics
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Center hosting a number of related projects concerning neural networks, functional neuroimaging, multimedia signal processing, and biomedical signal processing. Neuroinformatics is a research field rooted in classical disciplines like signal processing, biology, physics, computer science and engineering. Neuroinformatics combines learning from the brain and learning about the brain. By studying information processing in the brain neuroinformatics invents new computing paradigms (e.g., artificial neural networks) with the objective of understanding the dynamics of the conscious mind. Artificial neural networks is an active neuroinformatics research field, which combines many approaches to adaptive signal processing in solving real world problems. They began using neural networks for general nonlinear adaptive signal processing. Since 1991 the CONNECT groups have participated in the development of neural computing as an advanced, non-linear statistical tool, which has been applied to forecasting within dynamical systems, pattern recognition, and medical image analysis, particularly functional neuroimages. While neural computing has largely been viewed as a black box approach, they have initiated research aimed at opening this black box, using hypertext, multimedia, and interactivity. Their key objective is to convert abstract models into intuitive knowledge through interactive visualization.
UCSD Center for NMR Spectroscopy and Imaging of Proteins
Center for NMR Spectroscopy and Imaging of Proteins
Resource for NMR Molecular Imaging of Proteins
Biomedical technology research center that develops new technology for NMR spectroscopy and makes it available to the biomedical research community for structure determination of proteins in biological supramolecular assemblies, such as membrane proteins or virus particles. The principal applications are to membrane-associated proteins; however, the approach is generally applicable to polypeptides that cannot be prepared in forms suitable for X-ray crystallography or multidimensional solution NMR spectroscopy. As a result, there are also applications to viruses and other biological systems. The principal instrumentation consists of high-field NMR spectrometers dedicated to high-resolution solid-state NMR spectroscopy. The spectrometers are capable of the full-range of multiple-resonance experiments on stationary and spinning samples; however, the major emphasis is on methods that utilize mechanically or magnetically oriented samples. Development encompasses preparation of samples, including: * Expression and purification of membrane proteins * Design and construction of instrumentation, especially probes * Implementation of new pulse sequences and other experimental protocols for solid-state NMR spectroscopy * Calculations for the processing of experimental data and protein structure determination from the orientational constraints derived from these data
weighted gene ontology term based subcellular locallization prediction
Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information.
Biobank which collects, preserves, and assesses gene information related to species of plants indigenous to Israel. The Bank's goal is to conserve representative gene pools of species whose economic potential has yet to be developed.
Resource Center for Medical Ultrasonic Transducer Technology
Resource on Medical Ultrasonic Transducer Technology
USC Resource Center for Medical Ultrasonic Transducer Technology
Biomedical technology research center focusing on the development of very high frequency (above 20 MHz) ultrasonic transducers/arrays for applications in medicine and biology that include ophthalmology, dermatology, vascular surgery, and small animal imaging. The research is pursued simultaneously in three directions: novel piezoelectric materials, very high frequency single element transducers and linear arrays, and finite element modeling and material property measurements. The Center also serves the community through collaborative efforts with investigators having a research interest in high-frequency ultrasound imaging. In addition, it performs the function of training and information dissemination by offering conferences, seminars and specialized courses at the University of Southern California. The Center has set forth a number of goals which define its mission: * Conduct novel research and development of very high frequency (>20MHz) ultrasonic transducers, arrays and imaging applications * Collaborate with other academic institutions, non-profit organizations, and small businesses supported by the NIH to further the development of these high-frequency applications and provide the expertise in transducers necessary for project success * Serve as an educational center for training scientists and engineers interested in ultrasonic transducer technology One of the primary goals of the Center is to provide service to outside investigators and small business. Often an investigator or company has a specific application in mind but is without the expertise to develop the necessary ultrasonic device. Investigators at academic institutions, research institutes, or small businesses supported by NIH grants who have a need for medical ultrasound transducers and are interested in a collaborative effort should contact Dr. Hyung Ham Kim or Dr. K. Kirk Shung. Ultrasound transducers and components can be fabricated either completely by center personnel or in a joint effort with other investigators. In addition, collaborators are encouraged to visit the facility for additional training in fabrication and assembly.
Hyperpolarized MRI Technology Resource Center
UCSF Hyperpolarized MRI Technology Resource Center
Biomedical technology research center developing, investigating, and disseminating new hyperpolarized MR techniques, new 13C agents and specialized analysis open-source software for data reconstruction and interpretation. The Technology Research & Development projects will leverage the extensive DNP facilities and experience of the project leaders to develop improved, robust hyperpolarized MRI methods. These technology developments will be driven by Collaborative Projects led by outstanding clinical and basic scientists who aim to use hyperpolarized 13C MRI to accomplish the scientific goals of their funded research. These technical developments will also be disseminated to the Service Project investigators for extramural feedback and then widely to the scientific community via a dedicated website and onsite training. This center will provide state-of-the-art training in this new metabolic imaging field and sponsor a yearly symposium focused on hyperpolarized MR technology development.
Center for Advanced Magnetic Resonance Technology
Biomedical technology research center that develops innovative technologies in five core research areas of magnetic resonance imaging and spectroscopy (MRI/MRS): # image reconstruction, fast imaging and radiofrequency (RF) pulse design methods, # R hardware development, # body imaging methods, # neuroimaging methods. # MR spectroscopy methods. In each of these areas, they capitalize on the long-standing, successful partnership and extensive experience in Stanford's Radiology and Electrical Engineering departments to improve and expand imaging technology for use in basic research and clinical care, and to provide cutting edge opportunities to the extramural community for biomedical research with MRI. Over its more than 18 years of existence, CAMRT has been motivated by and has served a wide base of extramurally sponsored collaborators and service users from leading medical and research institutions. Examples of collaborative projects are the development of real-time functional MRI biofeedback methods for neuroscience and clinical applications such as pain remediation, development of methods to mitigate metal artifacts in musculoskeletal imaging, development of novel RF pulses for many applications, and studies of breast cancer with efficient MRS methods.
A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs).
Pittsburgh NMR Center for Biomedical Research
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 19,2024. Biomedical Technology Research Center that develops methodologies for the acquisition of morphological, biochemical, cellular, and functional information in living animals using nuclear magnetic resonance imaging (MRI) and spectroscopy (MRS). Novel techniques utilizing multidimensional MR imaging, magnetic resonance microscopy (MRM), and multinuclear in vivo spectroscopy are being applied to a wide range of problems in the biomedical sciences.
Biomedical technology research center dedicated to the use of lasers and optics in biology and medicine with activities in technological research and development, collaborative research, service, training, and dissemination. One of the primary goals of LAMMP is to facilitate translational research by rapidly moving basic science and technology discoveries from blackboard to benchtop to bedside. This is accomplished by combining state of the art optical technologies with specialized resource facilities for cell and tissue engineering, histopathology, pre-clinical animal models, and clinical care. The resource center has been organized into 3 cores: * Microscopy and Microbeam Technologies (MMT) for high-resolution functional imaging and manipulation of living cells and tissues * Medical Translational Technologies (MTT) for non- and minimally-invasive monitoring, treating, and imaging pre-clinical animal models and human subjects, and * Virtual Photonics Technologies (VPT) for developing computational models and methods that advance the performance of biophotonic technologies, and enhance the information content derived from optical measurements. LAMMP cores contain complementary technologies that are capable of quantitatively characterizing, imaging, and perturbing structure and biochemical function in cells and tissues with scalable resolution and depth sensitivity ranging from micrometers to centimeters.
Center for EPR Imaging in Vivo Physiology
Center for Electron Paramagnetic Resonance (EPR) Imaging in Vivo Physiology
Center for Electron Paramagnetic Resonance Imaging in Vivo Physiology
Very Low Frequency ERP Imaging In Vivo Physiology
Biomedical technology research center that develops instrumentation, analysis techniques, spin probes and spin traps, and methodologies for imaging physiologically relevant aspects of tissue fluids, including high-resolution oxygen maps, with very low frequency electron paramagnetic resonance imaging (EPRI). Novel bridges and high-access, low-field magnet/gradient systems have produced physiologically relevant measurements and accommodate a number of resonant structures. The Center is a consortium between the University of Chicago, the University of Denver, the University of Maryland and Novosibirsk Institute of Organic Chemistry (NIOC), Russia.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 10, 2025. Semantic wiki with structured information, primarily from functional and molecular neuroimaging papers, but there are also other types of papers, e.g., from personality genetics. It lists results from neuroimaging studies, such as Talairach coordinates and brain volume measurements, as well as software packages and brain regions. SQL dumps of the structured information in the wiki is available so complex queries can be formed. The Brede Wiki templates store the structured information from neuroscience papers and editors may add free format text. Template definitions format the data so it is presented as tables on the formatted wiki-page. From a given PMID a web-service can format information from PubMed for inclusion in the Brede Wiki. A Matlab script can extract coordinates from SPM5 and format them in the Talairach coordinate template format.
MIT/ Harvard Center for Magnetic Resonance
MIT/ Harvard Center for Magnetic Resonance 900 MHz NMR Facility
MIT/ Harvard Center for Magnetic Resonance (CMR) 900 MHz NMR Facility
MIT/Harvard Center for Magnetic Resonance
Biomedical technology research center designated as a biotechnology nuclear magnetic resonance (NMR) resource that hosts research efforts into cancer, neurological diseases, and many other areas. The heart of the 900 MHz magnetic resonance instrument is a superconducting magnet with a field strength of 21 Tesla, the highest field currently available for magnetic resonance spectroscopy, roughly 400,000 times stronger than the earth's magnetic field. Magnetic resonance is a powerful tool for determining the structure of molecules, and has proven especially useful for elucidating the role of proteins in biological processes and diseases. The state of the art facility includes two 17.6 T magnets with a third to be delivered in 2000. With multiple 17.6 T NMR magnets, the CMR is a valuable resource in New England and will continue to serve this research community for years to come. The advent of high magnetic fields has placed demands on the hardware needed to run experiments in these very high fields. The CMR has recently produced new advances in NMR probe technology, in electron magnetic resonance, and in using microwaves to enhance NMR experiments. The results are powerful new methods for performing biological research and they are looking forward to the continued growth of these exciting new areas!
Computer Integrated Systems for Microscopy and Manipulation
UNC Chapel Hill Computer Integrated Systems for Microscopy and Manipulation
Biomedical technology research center that develops force technologies applicable over a wide range of biological settings, from the single molecule to the tissue, with integrated systems that orchestrate facile instrument control, multimodal imaging, and analysis through visualization and modeling. The Force Microscope Technologies Core designs instruments in an area of science where there are unusual opportunities: the measurement of forces and the integration with optical microscopy. Force technologies play the obvious role of both measuring events in the sample and modifying the sample during the experiment. It is through the microscope that the force data is correlated with simultaneous 3D optical images. The force technology development includes the magnetic bead technology in the 3D Force Microscope project, Atomic Force Microscopy in the nanoManipulator project, and Control Software to drive the instrumentation. This core is focused on providing the physical capability to perform the experiments and probe structure/property correlations. The Ideal User Interfaces core makes the connection between the user and the instrument, the model building, and the data. This includes control systems that allow the user to move the bead inside the cell culture with a handheld pen and the visualization techniques to view the optical microscope data as a rendered 3D image collocated with the force data. Using data to create, change, and understand a model is the focus of the Advanced Model Fitting and Analysis core. The quantitative reduction of images to structural, shape, and velocity parameters is the goal of Image Analysis. The immediate understanding of correlations across image fields and between data sets in the challenge of Visualization. The power of combining the strength of a computer science graphics group with a microscopy technology group is most evident in the Graphics Hardware Acceleration project, which seeks to harness the speed of graphics processors for microscope data analysis and simulation. The Advanced Technology core pushes the boundaries of the Human Computer Interface through the investigation of improved techniques for the interaction of users with virtual environments, the real time lighting of virtual settings, and the enabling of multi-person collaboration. These techniques are validated and evaluated through physiological measures in virtual environments effectiveness evaluation studies.
Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy.
Animal Models of Diabetic Complications Consortium
Consortium serving the diabetic complications community that sponsors annual meetings in complications-relevant scientific areas, solicits and funds pilot projects in high impact areas of complications research, and provides resources and data including animal models, protocols and methods, validation criteria, reagents and resources, histology, publications and bioinformatics for researchers conducting diabetic complications research.
National Resource for Imaging Mass Spectrometry
Biomedical technology research center with the focus on the application to biomedical research of a new generation of secondary ion mass spectrometer (SIMS), the Multi-Isotope Imaging Mass Spectrometer (MIMS). MIMS is an ion microscope and an ion counter. MIMS provides high mass separation at high transmission (M/lambdaM > 10,000), high spatial resolution (< 40 nm) and has the unique capability of simultaneously recording several atomic mass images. Of the utmost importance, MIMS makes it possible for the first time (and at the intracellular level) to simultaneously image the distribution and measure the accumulation of molecules labeled with any isotopes, in particular with stable isotopes, for example with 15N. Thus, MIMS allows one to study localization, accumulation and turnover of proteins, fats, sugars and foreign molecules in cellular microdomains, donor-receiver cellular trafficking, stem cell nesting and localization of drugs. Their aim is to be a technological, methodological, and intellectual resource for researchers from a variety of disciplines. They seek to explore and develop the unique capabilities of MIMS and to bring cutting-edge information to biology and medicine that is currently unobtainable using existing technologies.
Bio MicroElectroMechanical Systems (BioMEMS) Resource Center
Bio MicroElectroMechanical Systems Resource Center
Biomicroelectromechanical Systems (BioMEMS) Resource Center
Biomedical technology research center that provides biomedical investigators with novel microsystems engineering tools for biological discovery, diagnostic, prognostic, and therapeutic applications. Thrust areas of interest are the development of novel living cell-based, lab-on-a-chip type devices for sorting blood cells, for high-throughput biochemistry in small volumes, and for studying cellular behavior in controlled microenvironments.
Center for Biomedical OCT Research and Translation
Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware.
National Center for Image-Guided Therapy
National Center for Image Guided Therapy
Biomedical Technology Resource Center that serves as a national resource for all aspects of research into medical procedures that are enhanced by imaging. Its common goal is to provide more effective patient care. The center is focused on the multidisciplinary development of innovative image-guided intervention technologies to enable effective, less invasive clinical treatments that are not only more economical, but also produce better results for patients. The NCIGT is helping to implement this vision by serving as a proving ground for some of the next generation of medical therapies.
James Cook University; Townsville; Australia
Public university in Townsville, Australia that functions as a research and teaching institution. Some well-known divisions of the university include the division of Tropical Environments and Societies, Tropical Health and Medicine, and Research and Innovation.
Integrated Animals is a virtual database currently indexing available animal strains and mutants from: AGSC (Ambystoma), BCBC (mice), BDSC (flies), CWRU Cystic Fibrosis Mouse Models (mice), DGGR (flies), FlyBase (flies), IMSR (mice), MGI (mice), MMRRC (mice), NSRRC (pig), NXR (Xenopus), RGD (rats), Sperm Stem Cell Libraries for Biological Research (rats), Tetrahymena Stock Center (Tetrahymena), WormBase (worms), XGSC (Xiphophorus), ZFIN (zebrafish), and ZIRC (zebrafish).
Ontology for the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. It provides a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.
Center for Functional Neuroimaging Technologies
Biomedical technology research center that develops and applies innovative neuroimaging technologies and techniques to enable closer examination of the human brain, and thereby contribute to better understanding of the brain in health and disease. They develop new techniques and advance existing technologies for acquisition and analysis of functionally specific images of the working brain, with unprecedented physiological precision and spatiotemporal resolution. The research and development aims to improve and extend existing methods for non-invasive magnetic resonance image analysis and acquisition, electromagnetic source imaging, optical neuroimaging, and most recently, combined MR-PET neuroimaging. The Resource provides an essential interactive environment, within which an interdisciplinary team of highly skilled scientists, engineers, and clinicians with diverse expertise in multiple modalities and disciplines. The resource supports service use of the Center's facilities by neuroscientists throughout the country, provide extensive training opportunities for students, fellows, and staff scientists, and seek to advance the field of brain mapping through active dissemination of new knowledge and technology.
Integrated Technologies for Polymeric Biomaterials
Biomedical technology research center that works to develop integrated tools and technologies that advance the discovery of polymeric biomaterials for regenerative medicine, the delivery of biological agents, and the next generation of medical implants. To achieve its mission, RESBIO's research is focused on the development of combinatorial and computational approaches to biomaterials design and optimization. Within this framework, RESBIO employs and uses: * Advanced multi-photon confocal laser microscopy to explore, understand, and control the response of cells in contact with artificial surfaces * Electron microscopy techniques to study the effect of nano-scale surface morphological features on cell behavior RESBIO research emphasizes the integration of a strong synthetic effort to create new biomaterial candidates with the development of rapid screening techniques for key material and biological properties relevant to the performance of a biomaterial in a given medical application.
Radiological Research Accelerator Facility
Columbia University Radiological Research Accelerator Facility
Biomedical technology research center dedicated for radiobiological research with available ionizing radiations such as protons, alpha particles, and neutrons. RARAF is well-established and highly user-friendly. The focus of RARAF is the development of high-throughput single-cell/single-particle microbeams, which can deliver defined amounts of ionizing radiation into individual cells with a spatial resolution of a few microns or better. The ability of a microbeam to put double strand break damage at any specific known location in a given cell has allowed new approaches to the study of damage signaling.
Biomedical technology research center dedicated to the development of novel imaging methods for the basic scientist and the application of the methods to important biomedical questions. The CIVM has played a major role in the development of magnetic resonance microscopy with specialized MR imaging systems capable of imaging at more than 500,000x higher resolution than is common in the clinical domain. The CIVM was the first to demonstrate MR images using hyperpolarized 3He which has been moved from mouse to man with recent clinical trials performed at Duke in collaboration with GE. More recently the CIVM has developed the molecular imaging workbench---a system dedicated to multimodality cardiopulmonary imaging in the rodent. Their collaborators are employing these unique imaging systems in an extraordinary range of mouse and rat models of neurologic disease, cardiopulmonary disease and cancer to illuminate the underlying biology and explore new therapies.
Interactive infographic of a brain exploring more than 100,000 chemical reactions, highlighted by areas and explanations of what that area is known to do.
Center for Magnetic Resonance and Optical Imaging
Biomedical technology research center dedicated to the development and application of innovative, novel magnetic resonance and optical imaging techniques. The facility's core sections provide research and computing resources for numerous user, collaborative, and training projects. The focus of this resource is on developing instrumentation, methodologies, and data analysis techniques for the quantitative assessment of functional, structural, and metabolic parameters in humans with the use of multinuclear magnetic resonance, novel spectral, perfusion, functional, and optical imaging techniques. These technological developments are driven by collaboration with scientists from within and outside University of Pennsylvania, the primary institution. Specifically, the Resource is focused on the development of quantitative, noninvasive MR and optical imaging based biomarkers for studying tissue metabolism and function, with an eye towards clinical translation through early diagnosis. The Center also provides support in the development and evaluation of new therapies in a variety of diseases.
Southwestern NMR Center for In Vivo Metabolism
Southwestern NMR Center for in vivo Metabolism - NIBIB
Biomedical technology research center that develops and applies new methods for analysis of metabolic networks in intact tissues, animals and human patients. The importance of understanding abnormal metabolism in common diseases such as cancer, diabetes and heart disease has long been appreciated. Because of constraints in technology, however, much of this research has been conducted in isolated systems where clinical relevance may be uncertain. Progress in magnetic resonance technology provides a foundation for major advances towards new ways of imaging metabolism in patients. These new techniques offer the advantage of imaging biochemical pathways without radiation. The focus of this Resource is to bring these technologies to a level where clinical research is feasible through the development of new MR contrast agents, NMR spectroscopy at high fields, and imaging of hyperpolarized 13C.
National ESCA and Surface Analysis Center for Biomedical Problems
NESAC/BIO - National ESCA and Surface Analysis Center for Biomedical Problems
Biomedical technology research center that provides state-of-the-art surface analysis expertise, instrumentation, experimental protocols, and data analysis methods to address surface-related biomedical problems. NESAC/BIO develops and applies surface science methodologies that produce a full understanding of the surface composition, structure, spatial distribution, and orientation of biomaterials and adsorbed biomolecules. The NESAC/BIO program identifies areas where surface science must evolve to keep pace with the growth in biochemical knowledge and biomaterial fabrication technology, and develops instrumentation, experimental protocols, and data analysis methods to achieve this evolution. NESAC/BIO provides state-of-the-art surface analysis tools to researchers in the biomedical community. You can gain access to the NESAC/BIO facilities in one of the following ways: * Collaborative: Propose a project to collaborate on with NESAC/BIO. The project should be rewarding for both groups, and the results should reflect the utility of surface analysis for biomedical research * Service: Ask NESAC/BIO to analyze your biomaterial specimens. The spectra obtained from the analyses will be interpreted for you. * Training: Visit the University of Washington to receive training in surface analysis and personally run experiments for your individual research projects. These experiments should have a high probability for yielding useful information and should not involve the development of new ESCA techniques or methodologies.
A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components.
Colorado University at Boulder EM Services Core Facility
Boulder Electron Microscopy Laboratory Core
Colorado University Boulder Electron Microscopy Core Facility
Core provides access to instruments including:FEI Tecnai 12 Spirit TEM, FEI Tecnai F20 (200kV) FEG-TEM 200kV FEG-TEM,Gatan US4000 4k x 4k CCD, bottom-mount,CryoTEM and electron tomography,High-resolution TEM;FEI Tecnai F20 (200kV) FEG-TEM,300kV FEG-TEM,Gatan US4000 4k x 4k CCD, bottom-mount,CryoTEM and electron tomography,High-resolution TEM,FEI/Phillips CM100 (100kV) TEM,100kV, tungsten TEM,2k x 2k AMT CCD, bottom-mount.
National Center for X-ray Tomography: Cellular imaging at the mesoscale
Biomedical technology research center that develops novel cellular imaging technologies, specifically soft X-ray tomography, for visualizing and quantifying the internal structure of whole, hydrated cells, and high-numerical aperture fluorescence microscopy for locating the position of specific cellular molecules. Data from these two imaging modalities can be combined to form a single, correlated imaging view of a cell.
Anxiety Treatment Australia: Anxiety Disorder Help, Information and Psychologist List
Anxiety Treatment Australia provides information about anxiety disorders, the treatment options, psychologists around Australia who treat anxiety disorders, group therapy & workshops, support groups, articles, resources and links to other sites. Sponsors: his website is brought to you by Catherine Madigan, a Melbourne Clinical Psychologist who specializes in the treatment of Anxiety Disorders (ABN 51 109 368 630).
NIH Center for Macromolecular Modeling and Bioinformatics
NIH Center for Macromolecular Modeling & Bioinformatics
Resource for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Center for Macromolecular Modeling and Bioinformatics
Biomedical technology research center focusing on the structure and function of supramolecular systems in the living cell as well as on the development of new algorithms and efficient computing tools for physical biology. They bring the most advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance. They extend, refine and deliver these technologies in response to experimental progress and emerging needs of the wide biomedical research community. They magnify the impact of their work through direct collaboration with experimental researchers, the distribution of cutting-edge and user-friendly software, and via extensive training, service, and dissemination efforts. The multidisciplinary team is engaged in the modeling of large macromolecular systems in realistic environments, and has produced ground-breaking insights into biomolecular processes coupled with mechanical force, bioelectronic processes in metabolism and vision, and with the function and mechanism of membrane proteins. They are committed and work towards further advancement of * Molecular modeling tools which can integrate structural information with bioinformatics databases and molecular dynamics simulations, and which can be used by a wide audience; * High performance molecular visualization and simulation software, capable of modeling biomolecules in realistic environments of 100,000,000 atoms or more; * Conceptual and methodological foundations of molecular modeling in the fields of quantum biology, mechanobiology, and interactive modeling; * Biomedical science through collaborations between theoretical and experimental researchers; * Support of the entire research process and training through a web-enabled collaborative environment; and * Service, training, and dissemination by leveraging web-based molecular graphics and integrated modeling technologies.
Open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE. The repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. It includes proteomic data generated by the Yale NIDA Neuroproteomics Center (http://medicine.yale.edu/keck/nida/index.aspx). Sample descriptions are compatible with the evolving MIAPE standards.
Laboratory for Fluorescence Dynamics (LFD)
Biomedical technology research center and training resource that develops novel fluorescence technologies, including instrumentation, methods and software applicable to cellular imaging and the elucidation of dynamic processes in cells. The LFD's main activities are: * Services and Resources: the LFD provides a state-of-the-art laboratory for fluorescence measurements, microscopy and spectroscopy, with technical assistance to visiting scientists. * Research and Development: the LFD designs, tests, and implements advances in the technology of hardware, software, and biomedical applications. * Training and Dissemination: the LFD disseminates knowledge of fluorescence spectroscopic principles, instrumentation, and applications to the scientific community.
Communnity project to help support the efforts of investigators using Philips Healthcare systems. This clearingsite helps users find forums, mailinglists, etc. that support this community. If you have suggestions for inclusion, let the project admin know!
BioCARS: A Synchrotron Structural Biology Resource
Biomedical technology research center and training resource that is a state-of-the art, national user facility for synchrotron-based studies of dynamic and static properties of macromolecules by X-ray scattering techniques such as crystallography (specializing in time-resolved), small- and wide-angle X-ray scattering and fiber diffraction. BioCARS operates two X-ray beamlines, embedded in a Biosafety Level 3 (BSL-3) facility unique in the U.S. that permits safe studies of biohazardous materials such as human pathogens., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Biomedical technology research center and training resource for the study of the structure of partially ordered biological molecules, complexes of biomolecules and cellular structures under conditions similar to those present in living cells and tissues. The goal of research at BioCAT is to determine the detailed structure and mechanism of action of biological systems at the molecular level. The techniques used are X-ray fiber diffraction, X-ray solution scattering and X-ray micro-emission and micro-absorption spectroscopy, with an emphasis on time-resolved studies and the development of novel techniques.
Current Research Information System (CRIS)
U.S. Department of Agriculture Current Research Information System
A database of documentation and reporting for ongoing agricultural, food science, human nutrition, and forestry research, education and extension activities for the United States Department of Agriculture; with a focus on the National Institute of Food and Agriculture (NIFA) grant programs. Projects are conducted or sponsored by USDA research agencies, state agricultural experiment stations, land-grant universities, other cooperating state institutions, and participants in NIFA-administered grant programs, including Small Business Innovation Research and Agriculture and Food Research Initiative.
Macromolecular Crystallography Research Resource
Macromolecular Crystallography Research Resource at the National Synchrotron Light Source
Macromolecular Crystallography Research Resource at the NSLS
Research Resource for Macromolecular Crystallography at the National Synchrotron Light Source
Biomedical technology research center that creates optimal facilities and environments and support for macromolecular structure determination by synchrotron X-ray diffraction at the National Synchrotron Light Source for the benefit of outside and in-house investigators. The PXRR innovates new access modes such as Mail-in crystallography, builds new facilities, currently on the X25 undulator, advances automation, develops remote participation software, collaborates with outside groups, teaches novice users, and supports vising investigators with 7-day, 20-hours staff coverage.
MacCHESS Synchrotron Source for Structural Biology
MacCHESS Synchrotron Source for Structural Biology advances structural characterization of proteins and biomolecules critical for understanding key biological processes and properties through leveraging both established and emerging X-ray synchrotron technologies. Used to collect data that comprises all or part of research programs.
National Biomedical Center for Advanced ESR Technology
National Biomedical Center for Advanced Electron Spin Resonance Technology
Biomedical technology research center that develops methods, both experimental and theoretical, of modern electron spin resonance (ESR) for biomedical applications. Center technologies are applicable to the determination of the structure and complex dynamics of proteins. Principal areas of expertise: * Pulsed Fourier Transform and Two Dimensional ESR * High Frequency-High Field (HFHF) ESR * High Resolution ESR Microscopy * Theory and Computational Methods for Modern ESR Activities include: * making resources available to the biomedical community, * publishing results, * running workshops on the new methodologies, * addressing the need to bring these new technologies to other laboratories.
National Center for Macromolecular Imaging
Biomedical technology research center establishing the infrastructure for fast, routine, atomic structure determination of subcellular complexes by electron cryo-microscopy, computer reconstruction and modeling. Their emphasis is on specimens that cannot currently be studied by conventional structural techniques such as x-ray crystallography or NMR. The ultimate outcome of their research is a three-dimensional image of the complex that can be used for design of drugs and vaccines for a variety of diseases. The center is focused on extending the resolution, speed and flexibility of cryo-electron microscopy for the three-dimensional structure determination of biological macromolecular assemblies. Cryo-electron microscopy can visualize molecules under near-native conditions at resolutions ranging from 0.3 to 5 nm and can yield images of individual molecules in a range of different conformations as they exist in solution. Other cryo-electron mycroscopy techniques, such as cryo-electron tomography, are being developed to capture molecular structures in situ. The equipment, techniques and expertise developed are available to the research community through collaborative projects. The NCMI also provides training through workshops and other forms of dissemination via both traditional and modern Internet-based methods.
Database portal for science-based, 10-year national objectives resulting from a multiyear process that reflects input from a diverse group of individuals and organizations for improving the health of all Americans. 2020 Topics & Objectives are available in an A-Z format. DATA2020, the Healthy People 2020 interactive data tool, allows users to explore the data and technical information related to the Healthy People 2020 objectives. For 3 decades, Healthy People has established benchmarks and monitored progress over time in order to: * Encourage collaborations across communities and sectors. * Empower individuals toward making informed health decisions. * Measure the impact of prevention activities. Healthy People 2020 strives to: * Identify nationwide health improvement priorities. * Increase public awareness and understanding of the determinants of health, disease, and disability and the opportunities for progress. * Provide measurable objectives and goals that are applicable at the national, State, and local levels. * Engage multiple sectors to take actions to strengthen policies and improve practices that are driven by the best available evidence and knowledge. * Identify critical research, evaluation, and data collection needs.
Besluit Subsidies Investeringen Kennisinfrastructuur
Agency that is part of the Netherlands Ministry of Economic Affairs. The agency encourages entrepreneurs in sustainable, agrarian, innovative and international business. It helps with grants, finding business partners, know-how and compliance with laws and regulations.
National Resource for Automated Molecular Microscopy
Biomedical technology research center that develops, tests and applies technology aimed toward completely automating the processes involved in solving macromolecular structures using cryo-electron microscopy. The goal is to establish a resource that will serve both as a center for high-throughput molecular microscopy as well as for transferring this technique to the research community. Current Core Technology Research and Development is focused on 4 areas: improving grid substrates and specimen preparation; further automation and optimization of image acquisition; development of an integrated single particle analysis and processing pipeline; and the development of automated high throughput EM screening. NRAMM welcomes applications of both collaborative and service projects.
National Magnetic Resonance Facility at Madison
Provides access and developes NMR technology to advance range of applications and improves the efficiency, rigor and reproducibility of NMR data acquisition and analysis. Houses NMR spectrometers equipped with state-of-the-art probe technology and protocols to support acquisition of high-quality data. Spectrometers range from 500 MHz to 1100 MHz. Service is tailored to the needs of individual users and projects. Provides training and advice on experimental design, best practices for data acquisition, and data analysis. Experienced staff support users with training opportunities including workshops, video tutorials and protocols.
Vanderbilt University Medical Center Pharmacology
At the Department of Pharmacology at Vanderbilt University Medical Center we engage in scientific discovery to elucidate biological mechanisms and develop novel therapeutics. We provide training focused on critical thinking to promote innovation, scholarship and integrity. To this end, we foster creativity, collegiality, and leadership. The Department is one of the most distinguished Pharmacology departments in the country and have placed in the top two NIH ranking positions for sixteen of the last twenty years. Research interests in the Department include five major areas: signal transduction, neuroscience, bioactive lipid metabolism, genetic basis of cardiovascular dysfunction, and drug metabolism. Molecules under investigation include G-protein coupled receptors (rhodopsin, adrenergic, serotonin and receptors), heterotrimeric G-proteins, ion channels, transporters and regulatory proteins such as arrestins, protein kinases and protein phosphatases. A strength in our research and training environment is that Vanderbilt University has a world-acclaimed Division of Clinical Pharmacology, which links the Department of Medicine with the Department of Pharmacology. Faculty members in the Division of Clinical Pharmacology focus on human disease and clinical enigmas as the origin of their questions for research. Basic scientists who pursue their inquiries in this environment are continually informed by their colleagues of the pathophysiological and potential therapeutic relevance that can be achieved by appropriate focus of their efforts. We have created one of the first programs in the country to answer the call from the National Institutes of Health (NIH) for more scientists trained in the area of drug discovery and development. A unique feature of the department is our outstanding Ph.D. training program. Almost 60 scientists in training are addressing important issues in fields such neuroscience, cardiovascular development, receptor signaling, and drug metabolism. Scientists in these areas are linked by a common interest in, and understanding of, the basic principles of drug action and design. This perspective makes our trainees ideally suited for a wide range of careers and our program is committed to developing leaders in academia, industry, and regulatory affairs. Postdoctoral and other positions are available.
Collection of data sets on Kawasaki disease, a rare childhood illness that affects the blood vessels. The data includes biochemical measurements of myocardial strain, oxidative stress, and cardiomyocyte injury as well as protein level analysis.
EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. EEG base advances electrophysiology research by enabling access to public data, tools and results of research groups. The system essentially offers the following set of features (the set of accessible features depends on a specific user role): * User authentication * Storage, update, and download of EEG/ERP data and metadata * Storage, update and download of EEG/ERP experimental design (experimental scenarios) * Storage, update and download of data related to testing subjects * Fulltext search * Sharing of knowledge and working in groups The system is based on tree layer architecture (MVC pattern) consisting of persistent layer (relational database), application layer (object oriented code, object relational mapping from persistence layer) and presentation layer (JSP). The persistence layer uses Hibernate framework; Oracle 11g database server is used to ensure the processing of large data files. Application and presentation layers are designed and implemented using Spring technology. This framework supports MVC architecture, Dependency injection and Aspect Oriented Programming. There were no significant difficulties with integration of both frameworks, Hibernate and Spring MVC. Spring Security framework is used to ensure management of authentication and user roles. Since the system is thought to be finally open to the whole EEG/ERP community it is necessary to protect EEG/ERP data and metadata, and especially personal data of testing subjects stored in the database from an unauthorized access. Then a restricted user policy is applied and user roles are introduced. The complete overview of the system features and user roles (use case diagram) is available in (Pergler 2009). Concerning the architectural layers there is a question which layer is more feasible for mapping of its structure into ontology. Currently we have studied two possibilities: * Mapping from the persistence layer (relational database) * Mapping from the application layer (object oriented code) The mapping from the application layer to an ontology includes the precedent object relational mapping provided by Hibernate framework.
Wake Forest University School of Medicine: Department of Neurology
Department at the Wake Forest University's School of Medicine that hosts physicians who specialize in neurological topics such as neuromuscular disease, epilepsy, pediatric neurology, strokes, neuropsychology, neurosonology, and neurorehabilitaiton.
An interactive web application for visualizing genomic data of sequenced prokaryotic chromosomes. It allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences.
Entrez - The Life Sciences Search Engine
Search engine for the National Library of Medicine and the National Institutes of Health. It contains databases such as PubMed, EST, and BioSystems.
A collection of tools for flow cytometer and application setup, data acquisition, and data analysis that help streamline flow cytometry workflows. It provides features to help users integrate flow systems into new application areas, including index sorting for stem cell and single-cell applications, as well as automation protocols for high-throughput and robotic laboratories.
Cytoscape-driven Spanning tree Progression of Density normalized Events
CytoSPADE: Cytoscape-driven Spanning tree Progression of Density normalized Events
Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data.
Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder.
vsn - Variance stabilization and calibration for microarray data
Software package that implements a method for normalizing microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to normalized log-ratios. However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.
Database of information of spa-typing of MRSA, or Staphylococcus aureus, that can be used to collate and harmonize data from various geographic regions.
NIDDK Inflammatory Bowel Disease Genetics Consortium
Inflammatory Bowel Disease Genetic Consortium
Repository of biospecimen and phenotype data collected from Crohn's disease and ulcerative colitis cases and controls recruited at six sites throughout North America that are available to the scientific community. Phenotyping is performed using a standardized protocol, and lymphoblastoid cell lines are established for each subject. Phenotype data for each subject are collected by the Consortium's Data Coordinating Center (DCC), and phenotype data for all subjects with DNA samples are available. The resulting DNA samples have already been utilized by the Consortium to complete various association studies, including genome-wide association studies using dense genotyping arrays. Researchers can obtain DNA samples and phenotype, genotype, and pedigree data through the Data Repository. GWAS data must be requested through dbGAP. The IBDGC is involved with independent genetic research studies and actively works with members of the IBD and genetic communities on collaborative projects. They are also members of the International IBD Genetics Consortium. Phenotype Tools: The Consortium Phenotype Committee, led by Dr. Hillary Steinhart designed and validated paper forms to collect extensive phenotype data on Crohn's Disease and ulcerative colitis. Consortium phenotype tools are available for use by non-Consortium members.
Software tool as multi platform medical image processing and visualization software. Functionalities include 2D/3D/4D image visualization, image registration, diffusion MR processing and tractography, filtering.
UT Southwestern Acute Liver Failure Study Group
Clinical research network for gathering prospective data and bio-samples on acute liver failure in adults since 1998. Clinical histories and laboratory and outcome data are available. Sample types include serum, plasma, urine, DNA, and liver tissue.
Algorithms for Calculating Microarray Enrichment
A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.
A bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. It provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.
Collect, analyze, and communicate on comprehensive and current data on all islet/beta cell transplants in human recipients performed in North America, as well as some European and Australian centers to expedite progress and promote safety in islet/beta cell transplantation. This site serves as a repository for general information concerning protocols, clinical transplantation sites, publications, and other information of interest to the general community. Annual Reports are available. Islet/beta cell transplantation is a complex procedure with many factors contributing to the outcome. Compiling and analyzing data from all transplant centers in the US, Canada, as well as some European and Australian centers will accelerate the identification of both critical risk factors and key determinants of success and thereby guide transplant centers in developing and refining islet/beta cell transplant protocols. The inclusion of the term collaborative in the name of the Registry emphasizes the importance of collaboration in fulfilling the CITR mission and goals. Close collaboration with the transplant centers will ensure that relevant questions are addressed, that data submitted are accurate and complete, and that the needs of the transplant community are served. Information on how to participate as a CITR Transplant Center and to receive a transplant center application is available through the website. Progress in islet transplantation depends entirely on complete, high-quality medical data, including the information patients consented to report to the Collaborative Islet Transplant Registry. To make it as easy as possible to provide updated information about patient's health, an on-line questionnaire is available or patients can mail it to their transplant center. This information is very important in the continuing search for a cure for Type 1 diabetes.
Diabetes Prevention Trial--Type 1 (DPT-1) dataset
Data set and biosepecimens of a multi-center clinical trial to determine if treatment with beta-cell antigens can delay the onset of Type 1 Diabetes Mellitus (Type 1 DM) in non-diabetic relatives of persons with Type 1 DM. Insulin is a well characterized antigen specifically produced by beta-cells, and it was used for this purpose in the initial DPT-1 studies. The protocol for high risk subjects uses daily subcutaneous insulin injections and an annual course of intravenous insulin treatment, while the protocol for intermediate risk subjects uses daily doses of insulin administered orally. Neither injected nor oral insulin at the doses used were observed to delay or prevent diabetes, although further studies are needed to test whether oral insulin can delay diabetes in people in the intermediate risk group with high titers of insulin autoantibodies.
Epidemiology of Diabetes Interventions and Complications
Publications from a multi-center, longitudinal, observational study examining the risk factors associated with the long-term complications of type 1 diabetes. The study began in 1994 and follows the 1441 participants previously enrolled in the Diabetes Control and Complications Trial (DCCT), http://diabetes.niddk.nih.gov/dm/pubs/control/index.aspx. The primary aim of EDIC is to examine the long-term effects of conventional vs. intensive diabetes treatment received during the DCCT on the subsequent development and progression of microvascular, neuropathic and cardiovascular complications. This involves studying the influence of genetic factors and other factors such as HbA1c, blood pressure, lipid levels, and treatment modalities on the development and progression of these complications. Annual or biennial measurements (using DCCT methods, standardized protocols and central laboratories) of vascular events, albumin excretion, GFR, ECG, ankle-brachial BP index, serum lipids and HbA1c allows the following analyses: 1) continuation of intention-to-treat analyses to determine long-term effects of prior separation of glycemic levels; 2) risk factors for macrovascular outcomes; 3) correlation of progression of micro- and macrovascular outcomes. The current updated version of the EDIC Protocol is available for download. EDIC is made up of 28 clinical centers, one data coordinating center and one clinical coordinating center.
NIH Division of Nutrition Research Coordination
Division of Nutrition Research Coordination
Coordinates nutritional sciences-related research and research training across the National Institutes of Health (NIH) and among Federal Agencies by providing mechanisms to communicate research, research training, policy, and education initiatives. The DNRC facilitates the exchange of information, coordinates workshops and seminars on critical issues, encourages national and international research collaborations, and serves as the NIH primary point of contact for the Department of Health and Human Services (DHHS) and other agencies, departments, and organizations in matters pertaining to nutritional sciences and physical activity. Through its dedicated efforts to promote scientific policy reviews, innovative research, interagency collaboration, and technical advancements, the DNRC strives to define the increasing roles of nutritional sciences and physical activity in health promotion and disease prevention and treatment.
AnAge Database of Animal Ageing and Longevity
AnAge: The Animal Ageing and Longevity Database
Curated database of aging and life history in animals, including extensive longevity records and complementary traits for > 4000 vertebrate species. AnAge was primarily developed for comparative biology studies, in particular studies of longevity and aging, but can also be useful for ecological and conservation studies and as a reference for zoos and field biologists.
Human Nutrition Research Information Management
Federal Human Nutrition Research and Information Management (HNRIM) System Database
Federal Human Nutrition Research and Information Management System Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of human nutrition research and research training activities supported by the federal government. Information regarding trends in nutrition research, specific institutions and investigators involved in this research, or areas of agency emphases can be obtained from database searches or from published summary reports. Data for the system is prepared and submitted by participating agencies, and is updated annually. The database contains several thousand projects for each of fiscal years 1985present. Participating agencies include the Department of Health and Human Services, the U.S. Department of Agriculture, the Department of Veteran Affairs, the Agency for International Development, the Department of Defense, Department of Commerce, National Science Foundation, and the National Aeronautics and Space Administration.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Project portal housing NIA Mouse EST Project, NIA Mouse cDNA Clone Sets, a NIA Mouse Gene Index, NIA Mouse cDNA Database, and NIA Mouse Microarrays. Characteristics of NIA 15K Mouse cDNA Clone Set * ~15,000 unique cDNA clones were rearrayed among 52,374 ESTs from pre- and periimplantation embryos, E12.5 female gonad/mesonephros, and newborn ovary. * Up to 50% are derived from novel genes. * ~1.5 kb average insert size. * Clones were sequenced from 5' and 3' termini to obtain longer reads and verify sequence. Sequence information is available at this Web Site. Clone names are from H3001A01 to H3159G07. * Handling of NIA 15k cDNA Clone Set(June3, 2000) Characteristics of NIA mouse 7.4K cDNA Clone Set * ~7407 cDNA clones with no redundancy within the set or with NIA Mouse 15K. * ~1.5 kb average insert size for short insert clones and ~2.5-3.0 kb average insert size for long-insert enriched clones.. * Clones were sequenced from 5' and 3' termini to obtain longer reads and verify sequence. Sequence information is available at this Web Site. Clone names are from H4001A01 to H4079G07. * Handling of NIA mouse 7.4k cDNA Clone Set (similar to handling of NIA mouse 15K, to be updated) Individual Clones are available from ATCC and MRC geneservice, UK. To obtain Clone, search the database using either the rearrayed clone name or GenBank accession number at the Key Word Search page. Follow the link to the sequence information page for the rearrayed clone to obtain source clone ATCC number. Clicking the ATCC number will bring up the ATCC ordering page for the source clone. There is essentially no overlap between the two clone sets (7.4K and 15K) said Minoru S.H. Ko, M.D., Ph.D., head of the Developmental Genomics and Aging Section in the NIA's Laboratory of Genetics. In addition, all cDNA clones in the NIA 7.4K set were purified by single colony isolation and sequence-verified, and more than half were prepared by a new procedure that yields long full-length cDNAs (average size 3-4 kb). The NIA Mouse 15k and 7.4k Clone Set Data and Published Microarray Data are available for download. NIA Mouse Microarrays *Microarray Data Download * 60-mer Oligo Array Platform ** (A) NIA 22k Oligo Microarray Gene List (21939 gene features) ( Carter et al 2003 ) ** (B) Agilent Mouse Development Oligo Microarray Gene List ** ( Subset of Microarray (A): 20,280 gene features ) * Data Analysis Tools
Neuroscience Research Funding Contacts in the Federal Government
This resource provides a list of federal program officials in the neurosciences. An informal compendium of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units.
Private university located in Ankara, Turkey that offers undergraduate and graduate programs in fields that include economics, art and architecture, languages, and neuroscience.
International repository for importation, curation, genotypic and phenotypic validation, cryopreservation, and distribution of mouse stocks of value to the type 1 diabetes scientific community holding over 250 genetically modified or congenic mouse stocks that are being used to dissect genetic and biologic features of T1D. They provide extensive genotypic and phenotypic quality control and genetic stabilization for these strains, as well as incidence studies when available. An added value of T1DR stocks is their ability to propel advances in related areas of science, including research in non-T1D autoimmunity and infectious diseases. The staff provides information and technical assistance regarding selection and use of existing T1DR models, and will provide limited support for development of new models considered to be of high-value for the T1D community. The resource includes strains generated at the Jackson Laboratory as well as strains donated by external scientists. Investigators are highly encouraged to donate a strain to ensure its preservation and availability to other researchers.
Harvard - Oxford Cortical Structural Atlas
Harvard Oxford Cortical Structural Atlas
Harvard-Oxford cortical and subcortical structural atlases
Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis. T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented by the CMA using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label. Segmentations used to create these atlases were provided by: David Kennedy and Christian Haselgrove, Centre for Morphometric Analysis, Harvard; Bruce Fischl, the Martinos Center for Biomedical Imaging, MGH; Janis Breeze and Jean Frazier from the Child and Adolescent Neuropsychiatric Research Program, Cambridge Health Alliance; Larry Seidman and Jill Goldstein from the Department of Psychiatry of Harvard Medical School.
Federal government public education program that promotes diabetes prevention and control. They aim to reduce the morbidity and mortality associated with diabetes and its complications. The NDEP is jointly sponsored by the National Institutes of Health and the Centers for Disease Control and Prevention and over 200 partner organizations. Target audiences include people with diabetes and those at risk, including the racial and ethnic populations disproportionately affected by the disease, health care providers and payers and purchasers of health care.
Pediatric Acute Liver Failure (PALF) Study
Pediatric Acute Liver Failure (PALF) Study Group
Study group and network for a 2008 longitudinal study for the etiology, diagnosis, treatment, and outcome of acute liver failure in infants, children, and adolescents. Data from patients include urine, bile, serum, liver tissue, cell lines derived from fibroblast culture, and DNA.
Coordinated Gene Activity in Pattern Sets
Software that infers biological processes which are active in individual gene sets from corresponding microarray measurements. It achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets.
Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.
A virtual database of several model resources including: CellML Model Repository, ModelDB, Open Source Brain, SimTK, and ModelRun.
National Institutes of Health Chronic Prostatitis Symptoms Index
Questionnaire developed by physicians in NIDDK's Chronic Prostatitis Collaborative Research Network that can help physicians to accurately measure the severity of prostatitis symptoms and their impact on a patient's lifestyle. The CPSI questionnaire assesses pain, urination, and the effect of chronic prostatitis on daily activities. With this information, researchers and physicians can reliably evaluate whether potential treatments are working. The questionnaire was originally published in the Journal of Urology in August 1999 (Vol. 162, pages 369-375). It is available as a PDF document in English, Spanish, German and Korean.
Sequencing of Idd regions in the NOD mouse genome
Sequencing of Insulin-dependent diabetes regions in the NOD mouse genome
Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequences, such as their alignment, variation data and Ensembl gene coverage, can be obtained from the NOD mouse ftp site.
Job postings available to Bioinformatics.ca members. To become a member please sign up for an account. DISCLAMER: OICR and the Canadian Bioinformatics Workshops are not affiliated with and have not investigated the companies listing jobs on this site. OICR is not making any representations with respect to the positions and is not acting as an agent for the companies listed.
bioinformatics.ca Bioinformatics Experts
Investigators interested in Bioinformatics in Canada including practitioners as well as developers of algorithms, databases or resources. Principal investigators and group leaders from academia, government labs and industry are welcome on this page. All present have an interest in the development of bioinformatics resources in Canada.
Computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 micrometers) to coarse (20 micrometers). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the nose and mouth is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition.
National Science Foundation Graduate Research Fellowship Program
The National Science Foundation's Graduate Research Fellowship Program (GRFP) helps ensure the vitality of the human resource base of science and engineering in the United States and reinforces its diversity. The program recognizes and supports outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based master's and doctoral degrees in the U.S. and abroad. The NSF welcomes applications from all qualified students and strongly encourages under-represented populations, including women, under-represented racial and ethnic minorities, and persons with disabilities, to apply for this fellowship. Fellows share in the prestige and opportunities that become available when they are selected. Fellows benefit from a three-year annual stipend of $30,000 along with a $10,500 cost of education allowance for tuition and fees, a one-time $1,000 international travel allowance and the freedom to conduct their own research at any accredited U.S., or foreign institution of graduate education they choose. NSF Fellows are anticipated to become knowledge experts who can contribute significantly to research, teaching, and innovations in science and engineering. So that the nation can build fully upon the strength and creativity of a diverse society, the Foundation welcomes applications from all qualified individuals. Women, under-represented minorites and people with disabilities are encouraged to apply. Those with disabilities are additionally accommodated by the Foundation to provide for the most successful graduate experience possible. Sponsors: This program is supported by the National Science Foundation (NSF).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl.
A web tool that takes a 3D structure (a PDB input file) and generates an animated image which can be displayed using any browser without the need for any additional molecular visualization software.
Look AHEAD - Action for Health in Diabetes
16-center, randomized clinical trial investigating the long-term health consequences of an intensive lifestyle intervention program designed to achieve and maintain weight loss by decreased caloric intake and increased physical activity in overweight volunteers with type 2 diabetes. The Look AHEAD cohort comprises approximately 5,000 overweight or obese participants with type 2 diabetes, aged 45-76. Participants were randomized to one of two interventions: an intensive lifestyle intervention designed to produce and sustain weight loss over the long term or a diabetes support and education arm. Participants will be followed for a total of 11 to 13.5 years from randomization. The primary hypothesis is that the incidence rate of the first post-randomization occurrence of a composite outcome, which includes * cardiovascular death (including fatal myocardial infarction and stroke), * non-fatal myocardial infarction, * hospitalized angina, and * non-fatal stroke, over a planned follow-up period of up to 13.5 years will be reduced among participants assigned to the Lifestyle Intervention compared to those assigned to the control condition, Diabetes Support and Education. Look AHEAD will also test for reductions in the incidence of three secondary composite outcomes and examine the effect of the intervention on cardiovascular disease risk factors, diabetes control and complications, general health, and quality of life, and psychological outcomes. The cost and cost-effectiveness of the Lifestyle Intervention relative to Diabetes Support and Education will be assessed. The Look AHEAD intensive lifestyle intervention ended September, 2012. Participants continue to be followed to determine the long-term effects of the intervention on health outcomes.
Consortium established to capitalize on recent advances in immune profiling methods in order to create a novel public resource that characterizes diverse states of the human immune system following infection; prior to and following vaccination against an infectious disease; or prior to and following treatment with an immune adjuvant that targets a known innate immune receptor(s). Through this program, well-characterized human cohorts are studied using a variety of modern analytic tools, including multiplex transcriptional, cytokine, and proteomic assays; multiparameter phenotyping of leukocyte subsets; assessment of leukocyte functional status; and multiple computational methods. Centralized research resources and a comprehensive, centralized database will be constructed for use by the greater scientific community. The information gained from the program will provide a comprehensive understanding of the human immune system and its regulation, and will reveal novel associations between components of the immune system and other biological systems, identify novel immune mediators and pathways, establish predictors of vaccine safety in different populations, and enable the rapid evaluation of different vaccine formulations and administration regimens in human populations.
Teen-Longitudinal Assessment of Bariatric Surgery
Adolescent Bariatrics: Assessing Health Benefits and Risks
Adolescent Bariatrics: Assessing Health Benefits and Risks (Teen-LABS)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Consortium made up of five clinical centers and a data coordinating center. The goal of Teen-LABS is to conduct clinical, epidemiological, and behavioral research in adolescent bariatric surgery, through an observational prospective study protocol. Teen-LABS is an ancillary study to LABS, an observational study of adult bariatric surgery. Research staff, certified in standardized uniform data collection according to the protocol, collect data at pre-operative research visits, at surgery, 30 days and six months post-operative, and annual post-operative research visits at the five participating centers.
The Michael J Fox Foundation for Parkinson's Research
Portal for the Michael J. Fox Foundation dedicated to research on Parkinson's Disease.
Adult to Adult Living Donor Liver Transplantation Cohort Study
A2ALL: The Adult to Adult Living Donor Liver Transplantation Cohort Study
Study consisting of nine liver transplant centers with expertise in adult living-donor liver transplantation (LDLT) and a central data coordinating center to provide valuable information on the outcomes of adult to adult living donor liver transplantation (AALDLT) to aid decisions made by physicians, patients, and potential donors. The study will establish and maintain the infrastructure required to accrue and follow sufficient numbers of patients being considered for and undergoing AALDLT to provide generalizable data from adequately powered studies. The major aims of A2ALL are as follows: * Quantify the impact of choosing LDLT on the candidate for transplantation * Characterize the difference between LDLT and deceased donor liver transplant (DDLT) in terms of post-transplant outcomes, including patient and graft survival, surgical morbidity, and resource utilization on the recipient of a transplant * Determine the short- and long-term health and quality of life (QOL) impact of donation, including (a) morbidity after liver donation and (b) long-term health-related QOL of donors. * Standardize and assess the role of informed consent in affecting the decision to donate and satisfaction after living liver donation * Other aims include comparison of the severity of recurrence of hepatocellular carcinoma for DDLT versus LDLT, the systematic characterization of liver regeneration and function in donors and recipients, the evaluation of the differences in the immune response to LDLT versus DDLT, and the establishment of a robust data and sample repository on liver transplantation that may be used to study clinical and biological questions as new technologies and resources become available. Patients enrolled in the study will be followed and managed in a standardized fashion.
Behavior Enhances Drug Reduction of Incontinence
Multi-center randomized clinical trial to determine if the addition of behavioral treatment to drug therapy for the treatment of urge incontinence will make it possible to discontinue the drug and still maintain a reduced number of accidents. The most popular treatments for urge incontinence are drug therapy and behavior therapy, each with its own limitations. In this clinical study, the Urinary Incontinence Treatment Network (UITN) aims to determine differences with the addition of behavioral treatment to drug therapy alone.
Bypass Angioplasty Revascularization Investigation 2 Diabetes
Bypass Angioplasty Revascularization Investigation (BARI) 2 Diabetes
A multicenter randomized clinical trial that aims to determine the best therapies for people with type 2 diabetes and moderately severe cardiovascular disease. 2368 participants were randomized at 49 sites in 6 countries. All subjects were given intensive medical therapy to control cholesterol and blood pressure and given counseling, if needed, to quit smoking and to lose weight. Beyond that, they compared whether prompt revascularization, either bypass surgery or angioplasty, e.g. stents, was more effective than medical therapy alone. At the same time, they also looked at which of two diabetes treatment strategies resulted in better outcomes����??insulin-providing versus insulin-sensitizing - that is, increasing the amount of insulin or making the insulin work better. Only patients with known type 2 diabetes and heart disease that could be treated appropriately with a revascularization OR medical therapy alone were eligible for the trial. Patients entered the study between January 2001 ����?? March 2005 and were followed for an average of five years. When a patient entered the study, physicians first decided whether that patient should receive stenting or bypass surgery. The patient then received their randomization assignment. All patients were treated in BARI 2D for both their diabetes and heart disease, as well as other risk factors that might effect those diseases, regardless of which group they were in. Diabetes-specific complications including retinopathy, nephropathy, neuropathy, and peripheral vascular disease were monitored regularly. Tests, blood samples, urine samples, and treatment cost data were obtained periodically through the trial and examined by experts at 7 central laboratories and other research partners. Experts on risk factors routinely oversaw treatments of all patients at 4 central management centers. A panel of independent experts reviewed data every six months to make sure that all patients were receiving safe care.
Childhood Liver Disease Research and Education Network
Childhood Liver Disease Research and Education Network (ChiLDREN)
Database of clinical information and serum and tissue samples from children across the United States and Canada with Biliary Atresia, Idiopathic Neonatal Hepatitis, Cystic Fibrosis Liver Disease, Alagille Syndrome, Alpha-1 Antitrypsin Deficiency, Bile Acid Synthesis Defects, Mitochondrial Hepatopathies, and Progressive Familial Intrahepatic Cholestasis in order to facilitate research and to perform clinical, epidemiological, and therapeutic trials in these important pediatric liver diseases. Three NIDDK-funded consortia, Biliary Atresia Research Consortium (BARC), Cholestatic Liver Disease Consortium (CLiC), and the Cystic Fibrosis Liver Disease (CFLD) Network were consolidated to form ChiLDREN. Most of the ChiLDREN studies are natural history studies aimed at acquiring information and data that will provide a better understanding of these rare conditions. Participants will be asked to allow study personnel to obtain information from medical records and an interview, and to collect blood, urine, and tissue samples when clinically indicated, in order to understand the causes of these diseases and to improve the diagnosis and treatment of children with these diseases. All of the information obtained in these studies is confidential and no names or identifying information are used in the study.
A not-for-profit organization to increase awareness of and find a cure for Alpha-1 Antitrypsin Deficiency that has invested nearly $39 million to support Alpha-1 research at more than 70 institutions in North America, Europe and Australia. They are dedicated to providing the leadership and resources that will result in increased research, improved health, worldwide detection, and a cure for Alpha-1 Antitrypsin Deficiency. The Foundation has developed a solid infrastructure to promote research and the development of new therapies for improving the quality of life for those diagnosed with Alpha-1. It has fostered collaborations with investigators throughout the United States and Europe, working closely with the National Institutes of Health (NIH), the Food and Drug Administration (FDA), individuals affected by Alpha-1, and the pharmaceutical industry to expedite the development of improved therapies. The Foundation participates in industry and government liaison groups and develops strategic alliances with government, industry and other national and international health and research organizations. They're the source for all Alpha-1 and COPD-related info.
Standardization of C-peptide measurements
Standardization of c-peptide by calibrating C-peptide measurement to a reference method can increase comparability between laboratories. The C-peptide standardization program is supported to establish reliability in results and facilitate the conduct of international clinical trials. For c-peptide, purified or processed material shows significant matrix effects and cannot be used for calibration. The C-peptide program has evaluated the use of single donor and pooled specimens for use by manufacturers in the calibration of these assays and determined that this strategy will reduce C-peptide variability among different assay methods. The standardization process through manufacturer re-calibration is ongoing.
CKID A Prospective Cohort Study of Kidney Disease in Children
CKID: A Prospective Cohort Study of Kidney Disease in Children
Prospective, observational cohort study of children with mild to moderate chronic kidney disease (CKD) to: (1) determine risk factors for progression of pediatric chronic kidney disease (CKD); (2) examine the impact of CKD on neurocognitive development; (3) examine the impact of CKD on risk factors for cardiovascular disease, and; (4) examine the impact of CKD on growth. The CKiD study population will include a cohort of 540 children, age 1 16 years, expected to be enrolled over a 24-month period.
Multicenter clinical research study aimed at discovering whether modest weight loss through dietary changes and increased physical activity or treatment with the oral diabetes drug metformin (Glucophage) could prevent or delay the onset of type 2 diabetes in study participants. At the beginning of the DPP, all 3,234 study participants were overweight and had blood glucose levels higher than normal but not high enough for a diagnosis of diabetesa condition called prediabetes. In addition, 45 percent of the participants were from minority groups-African American, Alaska Native, American Indian, Asian American, Hispanic/Latino, or Pacific Islander-at increased risk of developing diabetes. The DPP found that participants who lost a modest amount of weight through dietary changes and increased physical activity sharply reduced their chances of developing diabetes. Taking metformin also reduced risk, although less dramatically. In the DPP, participants from 27 clinical centers around the United States were randomly divided into different treatment groups. The first group, called the lifestyle intervention group, received intensive training in diet, physical activity, and behavior modification. By eating less fat and fewer calories and exercising for a total of 150 minutes a week, they aimed to lose 7 percent of their body weight and maintain that loss. The second group took 850 mg of metformin twice a day. The third group received placebo pills instead of metformin. The metformin and placebo groups also received information about diet and exercise but no intensive motivational counseling. A fourth group was treated with the drug troglitazone (Rezulin), but this part of the study was discontinued after researchers discovered that troglitazone can cause serious liver damage. The participants in this group were followed but not included as one of the intervention groups. In the years since the DPP was completed, further analyses of DPP data continue to yield important insights into the value of lifestyle changes in helping people prevent type 2 diabetes and associated conditions. For example, one analysis confirmed that DPP participants carrying two copies of a gene variant, or mutation, that significantly increased their risk of developing diabetes benefited from lifestyle changes as much as or more than those without the gene variant. Another analysis found that weight loss was the main predictor of reduced risk for developing diabetes in DPP lifestyle intervention group participants. The authors concluded that diabetes risk reduction efforts should focus on weight loss, which is helped by increased exercise.
Diabetes Prevention Program Outcomes Study
Observational clinical trial studying the long term effect of diet and exercise and the diabetes medication, metformin, on the delay of type 2 diabetes in participants of the Diabetes Prevention Program (DPP). The Diabetes Prevention Program (DPP) was a multi-center trial examining the ability of an intensive lifestyle or metformin to prevent or delay the development of diabetes in a high risk population due to the presence of impaired glucose tolerance (IGT). The DPP has ended early demonstrating that lifestyle reduced diabetes onset by 58% and metformin reduced diabetes onset by 31%. The DPPOS is designed to take advantage of the scientifically and clinically valuable DPP participants. This group of participants is nearly 50% minority and represents the largest IGT population ever studied. Clinically important research questions remain that focus on 1)durability of the prior DPP intervention, 2) determination of the clinical course of precisely known new onset diabetes, in particular regarding CVD, CVD risk factors and atherosclerosis and microvascular disease, 3)close examination of these topics in men vs women and in minority populations. More than 87% of the original surviving DPP cohort has joined DPPOS as of December, 2007 and, to date, after 5 years of DPPOS and 10 years of combined DPP/DPPOS, 93% of the DPPOS cohort continue to attend annual follow-up visits. Interim analyses performed after 5 years of DPPOS have demonstrated a durable effect of diabetes prevention associated with the lifestyle and metformin interventions with 34 and 19% reductions in diabetes incidence, respectively, compared with the placebo group. Interim analyses also reveal significant reductions from baseline in CVD risk factors in the lifestyle intervention group, but with decreased utilization of glucose-lowering and lipid-lowering medications. Analyses of the participants in the placebo group who have developed diabetes during DPP/DPPOS, compared with those who have remained non-diabetic, reveal an increased frequency of retinopathy and microalbuminuria. The current, updated protocol describes the DPPOS including the revisions incorporated to complete the second five-years of the study. DPPOS participants have blood samples stored at the time of each annual visit. Specimens are stored at the study CBL until after the primary study outcomes are reported. DNA samples were previously collected and are stored at the NIDDKsample repository for DPP participants.
ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems
A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.
Multi-center placebo-controlled randomized clinical trial to assess the short-term and long-term efficacy of cognitive behavior therapy (CBT) for irritable bowel syndrome (IBS) using two treatment delivery systems: self administered CBT and therapist administered CBT. Long term project goals are to develop an effective self-administered behavioral treatment program that can enhance the quality of patient care, improve clinical outcomes, and decrease the economic and personal costs of one of the most prevalent and intractable gastrointestinal disorders.
Folic Acid for Vascular Outcome Reduction in Transplantation
Folic Acid for Vascular Outcome Reduction in Transplantation (FAVORIT)
Multi-center, randomized, double blind controlled clinical trial to determine whether treatment with a standard multivitamin augmented with high doses of folic acid, vitamin B6 and vitamin B12 reduces the rate of cardiovascular disease outcomes in renal transplant recipients relative to participants receiving a similar multivitamin that contains no folic acid. This study hopes to show that by reducing the level of homocysteine in the body, the risk of heart disease is also reduced among kidney transplant patients.
EuMMCR - European Mouse Mutant Cell Repository
Embryonic stem cell distribution unit that distributes material arising within European Conditional Mouse Mutagenesis Program consortium, currently targeting vectors and ES cells. Upon user request EUCOMM grow targeting vectors from glycerol stocks and prepare vector DNA. Identity of vector is verified by restriction mapping. Upon user request EUCOMM thaw, expand and re-freeze several aliquots of desired ES cell clone. Standard controls include PCR based assay. Upon additional request EuMMCR unit develops genotyping PCR, which can be used to genotype chimeric mice that may be generated using those ES cell clones.
Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Eyes Open Eyes Closed Sample
Data set of 48 healthy controls from a community (student) sample from Beijing Normal University in China with 3 resting state fMRI scans each. During the first scan participants were instructed to rest with their eyes closed. The second and third resting state scan were randomized between resting with eyes open versus eyes closed. In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 6-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information and information on the counterbalancing of eyes open versus eyes closed.
International network of researchers who are exploring ways to prevent, delay and reverse the progression of type 1 diabetes. It is conducting clinical trials with researchers from 18 Clinical Centers in the United States, Canada, Finland, United Kingdom, Italy, Germany, Australia and New Zealand. In addition, more than 150 medical centers and physician offices are participating in the TrialNet network. Studies are available for people newly diagnosed with type 1 diabetes, as well as for relatives of people with type 1 diabetes who are at greater risk of developing the disease. This NIH-sponsored clinical trials network conducts studies designed to evaluate new approaches to prevent or ameliorate type 1 diabetes specifically by interdicting the type 1 diabetes disease process. These include interventions designed to decrease beta-cell destruction and/or enhance beta-cell survival. Studies are conducted in non-diabetic persons at risk of type 1 diabetes in an effort to delay the development of type 1 diabetes as a clinical disease; or (if initiated prior to appearance of autoimmunity) in an effort to delay the appearance of autoimmunity; or in individuals with type 1 diabetes who are either newly diagnosed or have evidence of sustained beta cell function. Studies include long-term follow-up of subjects developing type 1 diabetes. The TrialNet network also supports natural history and genetics studies in populations screened for or enrolled in studies conducted by the TrialNet study group. In addition, TrialNet will evaluate methodologies that enhance the conduct of clinical trials interdicting the type 1 diabetes disease process.
A book adapted for the Web on the anatomy of the laboratory mouse by Margaret J. Cook, 143 pages, M.R.C. Laboratory Animals Centre, Carshalton, Surrey, England. Academic Press 1965. Mouse Externals, Skeleton, Viscera and Circulatory System are covered.
Provides investigators with the opportunity to obtain on-demand biological samples from selected individuals that TrialNet has developed through the longitudinal monitoring of individuals at risk for the development of type 1 diabetes within the Natural History study. Exploratory research is encouraged under this initiative. Studies must use TrialNet screened subjects, and cannot interfere with ongoing clinical trials or studies. Investigators can select the clinical characteristics needed for their study as well as the sample type and collection frequency. Although many Living Biobank studies may be implemented through cost-sharing with the TrialNet network, special sample collections and visits outside of the normal visit schedules will incur additional costs which should be covered by the approved applicant. In addition, some studies may require effort from the TrialNet coordinating center, with costs covered by the approved ancillary study. Living biobank studies will be evaluated with careful consideration for their potential impact on the objectives and performance of the TrialNet Natural History study. To protect the interests of TrialNet, each living biobank study must be reviewed and approved by the Ancillary Studies Committee before its initiation. All approved living biobank studies will be reviewed yearly to evaluate their progress, and impact on TrialNet as a whole. TrialNet welcomes the submission of living biobank studies as an adjunct to ongoing protocols.
Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework.
Diabetes Research in Children Network (DirecNet)
Network of clinical centers and a coordinating center that investigate the potential use of glucose monitoring technology and its impact on the management of type 1 diabetes in children. Specific goals for the network include the following: * Assess the accuracy of continuous monitoring devices in order to determine if these devices are useful in improving glycemic control and preventing hypoglycemia in children with T1DM. * Determine the optimal utilization of continuous glucose monitors in the management of T1DM in children. * Assess the impact of continuous glucose monitoring on quality of life for the child and family. * Develop tools for the child and parents to use for incorporating continuous glucose monitors into diabetes self-management. * To assess possible changes in neurocognitive function and how it relates to frequency of hypoglycemia in young children with type 1 diabetes. * Evaluate and develop distinct, age-appropriate treatment approaches to T1DM in children. * Use continuous glucose monitoring to characterize the glycemic profile of nondiabetic children. * Develop statistical methods for the analysis of continuous glucose monitoring data. Closed and active studies are listed along with the associated protocols, public datasets, and publications.
Freestanding, nonprofit coordinating center for multi-center clinical trials and epidemiologic research that focus on projects involving eye disorders or type 1 diabetes.
Diabetic Retinopathy Clinical Research Network
Diabetic Retinopathy Clinical Research Network (DRCR.net)
A collaborative network to facilitate multicenter clinical research of diabetic retinopathy, diabetic macular edema and associated conditions. It supports the identification, design, and implementation of multicenter clinical research initiatives focused on diabetes-induced retinal disorders. Principal emphasis is placed on clinical trials, but epidemiologic outcomes and other research may be supported as well. It currently includes over 109 participating sites (offices) with over 320 physicians throughout the United States. Closed and active studies are listed along with the associated protocols, public datasets, and publications.
Islet Transplantation Trials for Type 1 Diabetes
Network of centers to conduct studies of islet transplantation in patients with type 1 diabetes to improve the safety and long-term success of methods for transplanting islets. It is the aim of this trial to improve methods of isolating islets, to improve techniques for the administering those transplanted islets; and to develop approaches to minimize the toxic effects of immunosuppressive drugs required for transplantation.
Nebula - A web-server for advanced ChIP-seq data analysis
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web portal that allows users to analyze ChIP-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
This database contains gene expression patterns assembled from mouse nervous tissues at 4 time points throughout brain development including embryonic (e) day 11.5, e15.5, postnatal (p) day 7 and adult p42. Using a high throughput in situ hybridization approach we are assembling expression patterns from selected genes and presenting them in a searchable database. The database includes darkfield images obtained using radioactive probes, reference cresyl violet stained sections, the complete nucleotide sequence of the probes used to generate the data and all the information required to allow users to repeat and extend the analyses. The database is directly linked to Pubmed, LocusLink, Unigene and Gene Ontology Consortium housed at the National Center for Biotechnology Information (NCBI) in the National Library of Medicine. These data are provided freely to promote communication and cooperation among research groups throughout the world.
Web software which helps users create a website or blog. WordPress software can be downloaded and installed with an appropriate web host and minimum requirements. There is also a service called WordPress.com which allows users to get started with a new and free WordPress-based blog in seconds, though it varies in several ways and is less flexible than the self-installed WordPress. An array of plugins and themes are available to further customize a site.
Nonalcoholic Steatohepatitis Clinical Research Network
Clinical Research Network in Nonalcoholic Steatohepatitis
Nonalcoholic Steatohepatitis Clinical Research Network (NASH CRN)
Clinical research network to focus on the etiology, contributing factors, natural history, complications, and therapy of nonalcoholic steatohepatitis. They research the nature and underlying cause of Nonalcoholic Steatohepatitis (NASH) and conduct clinical studies on prevention and treatment. Approximately 1,500 pediatric and adult participants throughout the United States and Canada with nonalcoholic fatty liver disease (NAFLD) have enrolled into a database. The NASH CRN has recently reopened the database to enroll additional pediatric and adult participants with NAFLD. Serum, liver tissue, and genomic DNA samples are being collected and stored in the NIDDKrepository for ongoing as well as future studies. A three-arm randomized, placebo-controlled clinical trial of pioglitazone versus vitamin E completed enrollment in 2009. In addition to this adult trial, a similar trial in pediatric NASH patients randomized 180 children to receive treatment with vitamin E, metformin, or placebo.
BacPac Resources Center: BAC Clones Distribution Center
It is the distribution arm of their academic laboratory. They operate on a cost-recovery mechanism in order to make the resources generated in their laboratory available to the academic scientific community. While clones and screening services are widely available, library arrays are primarily available to researchers with a scientific need to analyze most clones in the library. This site contains information on currently available BAC and PAC genomic DNA libraries, BAC Clones, PAC Clones, Fosmid Clones, cDNA collections, high-density colony hybridization filters, and BAC and PAC cloning vectors. Protocols used in our laboratory for the hybridization-based screening of colony filters, purification of BAC and PAC DNA, and end-sequencing methodologies, are also provided. BPRC does not list clones, for two reasons: 1)most clones have not been characterized and lack specific data. 2)all clones are part of libraries and all clones from a particular library share common characteristics. Hence, to find out if BPRC has a particular clone, one needs either use Automatic Clone Validation or else find out if the clone is compatible with the range of clone names for a corresponding clone library. Typically (although not always), clone names are derived from the library name. BPRC uses the NCBI-recommended clone nomenclature & library nomenclature. Most arrayed libraries are available in frozen microtiter dish format to academic and non-academic users provided that there is a scientific need for complete-library access. (for instance to annotate, modify or analyze all BAC clones as part of a genome project).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for the insertion and modification of chemical information within Microsoft Word. Capabilities include inserting labels, formulas, and 2D depictions of chemical structures, as well as creating in-line chemical zones, rendering visual depictions of chemical structures, and the ability to store chemical information in a semantically rich manner.
Juvenile Diabetes Research Foundation International
Global funder of type 1 diabetes (T1D) research that aims to progressively remove the impact of T1D from people's lives until a world without T1D is achieved. JDRF collaborates with a wide spectrum of partners and is the only organization with the scientific resources, regulatory influence, and a working plan to better treat, prevent, and eventually cure T1D. More than 80 percent of JDRF's expenditures directly support research and research-related education. In 2012 Forbes magazine named JDRF one of its five All-Star charities, citing the organization's efficiency and effectiveness. The organization awards research grants for laboratory and clinical investigations and sponsors a variety of career development and research training programs for new and established investigators. JDRF also sponsors international workshops and conferences for biomedical researchers. Individual chapters offer support groups and other activities for families affected by diabetes.
MINT - the Molecular INTeraction database
A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.
Prospective and retrospective registry of well-characterized cases of drug-induced liver disease. The goals of Network include the development of standardized procedures to identify and fully characterize bona fide cases of drug- and complementary and alternative medicines (CAM)-induced liver injury, and to conduct controlled, clinical studies that will include extensive collection of data, serum, DNA, and tissue specimens. Cases of liver injury due to herbal medications are also included. The network will also develop terminology and standardized definitions for DILI, and to develop causality assessment instruments that are sensitive, specific, and reproducible. DILIN is funded by a cooperative agreement and includes five clinical centers and a central data coordinating center. The research goals of DILIN are to: * Create a registry of carefully documented DILI cases * Identify clinical, immunological, and environmental risk factors for drug- and CAM-mediated hepatotoxicity * Create a bank of biological specimens consisting of DNA, plasma, and immortalized lymphocytes to facilitate detailed genetic analyses * Characterize the natural history of drug- and CAM-induced DILI for at least six months following enrollment * Develop the capability to recontact these individuals over an extended period of time so that additional studies exploring DILI mechanisms can be performed Two studies are being initiated by the network. In the Retrospective Study, the implicated drugs are restricted to isoniazid, phenytoin, combination clavulanic acid/amoxicillin, and valproic acid (Depakote), Nitrofurantoin, Trimethoprim-sulfamethoxazole, Minocycline, and Quinolone antibiotics. These drugs were chosen because they are frequently administered to patients not receiving other hepatotoxic drugs, making it easier to establish causality. Patients must be alive, and the date of onset of the DILI episode must be on or after January 1, 1994. In the Prospective Study, all incident cases of drug- and CAM-induced liver injury are being considered. Initial presentation to a healthcare professional must be within the previous six months. A detailed medication history of the implicated DILI drug together with all prescription, OTC, and herbal medications is being recorded. Liver and serological tests are being performed to characterize the injury and to exclude competing causes of liver injury. A blood sample is also being drawn for plasma storage and DNA isolation. These cases will be followed longitudinally to characterize the long-term effects of the DILI episode. For both studies, documented, clinically significant DILI must be recorded in the patient's medical charts so that a causal determination can be made. Patients will be excluded if they are unwilling or unable to provide a blood sample or participate in the genetics component. Children under two years of age at the time of enrollment are excluded due to blood-volume requirements. If you have patients who are eligible to participate in either study, please contact one the DILIN clinical sites. As a general policy, the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) invites investigator-initiated research project applications for ancillary studies to ongoing, large-scale clinical trials, epidemiological studies, and disease databases supported by the Institute. These studies are focused on a wide range of diseases and conditions including diabetes, obesity, acute and chronic liver disease, chronic kidney disease, and benign prostatic hyperplasia, among others.
Family Investigation of Nephropathy of Diabetes
Family Investigation of Nephropathy & Diabetes
Family Investigation of Nephropathy and Diabetes (F.I.N.D.)
Multicenter observational study designed to identify genetic determinants of diabetic nephropathy. It is conducted in eleven U.S. clinical centers and a coordinating center, and with four ethnic groups (European Americans, African Americans, Mexican Americans, and American Indians). Two strategies are used to localize susceptibility genes: a family-based linkage study and a case-control study using mapping by admixture linkage disequilibrium (MALD). In the family-based study, probands with diabetic nephropathy are recruited with their parents and selected siblings. Linkage analyses will be conducted to identify chromosomal regions containing genes that influence the development of diabetic nephropathy or related quantitative traits such as serum creatinine concentration, urinary albumin excretion, and plasma glucose concentrations. Regions showing evidence of linkage will be examined further with both genetic linkage and association studies to identify genes that influence diabetic nephropathy or related traits. Two types of MALD studies are being done. One is a case-control study of unrelated individuals of Mexican American heritage in which both cases and controls have diabetes, but only the case has nephropathy. The other is a case-control study of African American patients with nephropathy (cases) and their spouses (controls) unaffected by diabetes and nephropathy; offspring are genotyped when available to provide haplotype data. The specific goals of this program: * Delineate genomic regions associated with the development and progression of renal disease(s) * Evaluate whether there is a genetic link between diabetic nephropathy and diabetic retinopathy * Improve outcomes * Provide protection for people at risk and slow the progression of renal disease * Help establish a resource for genetic studies of kidney disease and diabetic complications by creating a repository of genetic samples and a database * Encourage studies of the genetics of progressive renal disease
Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known.
Frequent Hemodialysis Network Daily Trial
Frequent Hemodialysis Network (FHN) Daily Trial
Randomized controlled clinical trial to understand how increasing hemodialysis to six times a week from the standard of three times a week may result in improved heart health. Subjects were recruited from dialysis units associated with designated Clinical Centers in the U.S. and Canada and followed for 1 year. Subjects will be randomized to either conventional hemodialyis Daily HD delivered for at least 2.5 hours (typically 3 to 4 hours), 3 days per week, or to more frequent hemodialysis delivered for 1.5 - 2.75 hours, 6 days per week. The study has two co-primary outcomes: 1) a composite of mortality with the change over 12 months in left ventricular mass by magnetic resonance imaging, and 2) a composite of mortality with the change over 12 months in the SF-36 RAND physical health composite (PHC) quality of life scale. In addition, main secondary outcomes have been designated for each of seven outcome domains: 1) cardiovascular structure and function (change in LV mass), 2) health-related quality of life/physical function (change in the PHC), 3) depression/burden of illness (change in Beck Depression Inventory), 4) nutrition (change in serum albumin), 5) cognitive function (change in the Trail Making Test B), 6) mineral metabolism (change in average predialysis serum phosphorus), and 7) clinical events (rate of non-access hospitalization or death). Hypertension and anemia are also main outcome domains, but without designation of single first priority outcomes.
Software for Next-Generation DNA sequencing, Sanger DNA analysis, and RNA sequencing. It contains sequence analysis tools which include reference-guided alignments, de novo assembly, variant calling, and SNP analyses. It has integrated the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data.
Polycystic Kidney Disease-Treatment Network
Consortium established to design and implement clinical trials of treatments that might slow the progressive loss of renal function in Polycystic Kidney Disease (PKD). Two multicenter randomized, double-blind, placebo controlled clinical trials are running concurrently to study the efficacy of renin-angiotensin-aldosterone system blockade on the progression of cystic disease (kidney volume) and on the decline in renal function in autosomal dominant polycystic kidney disease (ADPKD). Study A is to study whether intensive ACE-I/ARB blockade decrease the progression of cystic disease compared to ACE-I monotherapy patients with early disease, relatively preserved renal function, and high-normal BP or hypertension. Study B is to study whether intensive ACE-I/ARB blockade as compared to ACE-I monotherapy slow the decline in kidney function, end-stage of renal disease, or death in the setting of standard blood pressure control in hypertensive patients with moderately advanced disease.
Primary prevention trial conducted in 42 middle schools at 7 locations across the US to impact risk factors for type 2 diabetes in adolescents. Students were recruited at the start of 6th grade (fall 2006) and followed to the end of 8th grade (spring 2009). Half of the schools were randomized to receive an intervention that integrated four components: the school nutrition environment, physical education class activities, behavior change initiatives, and educational and promotional communications activities.
Network that brings together clinical centers with expertise in caring for patients with chronic hepatitis B virus (HBV) infection to conduct research in order to better understand the physiological effects of the disease and develop effective treatment strategies with the currently available therapies. The web site is designed to inform the public of the research activities conducted by the Hepatitis B Research Network. It is also a portal to support communications for their researchers and participants in their studies. The Hepatitis B Research Network is currently seeking patients for a multi-center prospective study of the natural history of chronic hepatitis B. Within the next few months treatment trials for various patients with chronic hepatitis B will also begin enrolling patients. Details of the entry criteria for these studies can be obtained from the clinical centers outlined on the website's map.
Data set of output of neuron models through the Trestles supercomputer.
Public doctoral university located in Manhattan, Kansas that is involved with research, especially agricultural.
Hepatitis C Antiviral Long-term Treatment against Cirrhosis
Hepatitis C Antiviral Long-term Treatment against Cirrhosis (HALT-C) Trial
Hepatitis C Antiviral Long-term Treatment against Cirrhosis Trial
Multi-center, randomized controlled study designed to determine if continuing interferon long term over several years will suppress the Hepatitis C virus, prevent progression to cirrhosis, prevent liver cancer and reduce the need for liver transplantation. Patient enrollment began in 2000 and was completed in 2003 at 10 clinical centers, which were supported by a data coordinating center, virological testing center, and central sample repository. Patients with chronic hepatitis C and advanced fibrosis or cirrhosis on liver biopsy who failed to respond to a previous course of interferon alfa were enrolled in this study. Patients were initially treated with a 24-week course of peginterferon alfa-2a and ribavirin. Patients who remained hepatitis C virus RNA positive were then randomized to receive maintenance, low-dose peginterferon or to be followed on no treatment. Liver biopsies were done before enrollment and after 2 and 4 years of treatment or follow-up. The endpoints were development of cirrhosis, hepatic decompensation, hepatocellular carcinoma, death, or liver transplantation. 1050 patients were randomized and followed through the 4 year randomized phase of the trial and as long as 4 years off treatment. Serum samples collected at multiple time points, DNA and liver tissue are available for scientific investigation.
International clinical research consortium dedicated to the clinical evaluation of novel tolerogenic approaches for the treatment of autoimmune diseases, asthma and allergic diseases, and the prevention of graft rejection. They aim to advance the clinical application of immune tolerance by performing high quality clinical trials of emerging therapeutics integrated with mechanism-based research. In particular, they aim to: * Establish new tolerance therapeutics * Develop a better understanding of the mechanisms of immune function and disease pathogenesis * Identify new biomarkers of tolerance and disease Their goals are to identify and develop treatment game changers for tolerance modulating therapies for the treatment of immune mediated diseases and disabling conditions, and to conduct high quality, innovative clinical trials and mechanistic studies not likely to be funded by other sources or to be conducted by private industry that advance our understanding of immunological disorders. In the Immune Tolerance Network's (ITN) unique hybrid academic/industry model, the areas of academia, government and industry are integral to planning and conducting clinical studies. They develop and fund clinical trials and mechanistic studies in partnership. Their development model is a unique, interactive process. It capitalizes on their wide-ranging, multidisciplinary expertise provided by an advisory board of highly respected faculty from institutions worldwide. This model gives investigators special insight into developing high quality research studies. The ITN is comprised of leading scientific and medical faculty from more than 50 institutions in nine countries worldwide and employs over 80 full-time staff at the University of California San Francisco (UCSF), Bethesda, Maryland and Benaroya Research Institute in Seattle, Washington.
Longitudinal Assessment of Bariatric Surgery
Longitudinal Assessment of Bariatric Surgery (LABS) Consortium
Longitudinal Assessment of Bariatric Surgery Consortium
Consortium comprised of six clinical centers and a data coordinating center to facilitate coordinated clinical, epidemiological, and behavioral research in the field of bariatric surgery, through the cooperative development of common clinical protocols and a bariatric surgery database that will collect information from participating clinical centers. LABS will help pool the necessary clinical expertise and administrative resources to facilitate the conduct of multiple clinical studies in a timely, efficient manner. Also, the use of standardized definitions, clinical protocols, and data-collection instruments will enhance the investigator's ability to provide meaningful evidence-based recommendations for patient evaluation, selection, and follow-up care. The consortium was funded in September 2003. The investigators have collaboratively developed a core database and clinical protocols, and subject enrollment began in early 2005. A repository of data and biological specimens for future research also will be collected by the centers participating in LABS. These will provide valuable resources for future study of obesity and its complications.
flowFP - Fingerprinting for Flow Cytometry
A Bioconductor software package for fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.
National Center for Integrative Biomedical Informatics
The Center develops conceptual models, computational infrastructure, an integrated knowledge repository, and query and analysis tools that enable scientists to effectively access and integrate the wealth of biological data. The National Center for Integrative Biomedical Informatics (NCIBI) was founded in October 2005 and is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan as a part of the Center for Computational Medicine and Biology (CCMB). NCIBI is composed of biomedical researchers, computational biologists, computer scientists, developers and human-computer interaction specialists organized into seven major core functions. They work in interdisciplinary teams to collectively develop tools that are not only computationally powerful but also biologically relevant and meaningful. The four initial Driving Biological Projects (prostate cancer progression, Type 1 and type 2 diabetes and bipolar disorder) provide the nucleation point from which tool development is informed, launched, and tested. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction that is a unique feature of this Center. Once tools are developed and validated the goal of the Center is to share and disseminate data and software throughout the research community both internally and externally. This is achieved through various mechanisms such as training videos, tutorials, and demonstrations and presentations at national and international scientific conferences. NCIBI is supported by NIH Grant # U54-DA021519.
Randomized Intervention for Children with Vesicoureteral Reflux
Randomized Intervention for Children With Vesicoureteral Reflux (RIVUR)
Randomized Intervention for Vesicoureteral Reflux
Multicenter, randomized, double-blind, placebo-controlled trial is designed to determine whether daily antimicrobial prophylaxis is superior to placebo in preventing recurrence of urinary tract infection (UTI) in children with vesicoureteral reflux (VUR). The basic eligibility criteria are: (1) age at randomization of at least 2 months, but less than 6 years, (2) a diagnosed first febrile or symptomatic UTI within 42 days prior to randomization that was appropriately treated, and (3) presence of Grade I-IV VUR based on voiding cystourethrogram (VCUG). Patients will be randomly assigned to treatment for 2 years with daily antimicrobial prophylaxis (trimethoprim-sulfamethoxazole) or placebo. The study is designed to recruit 600 children (approximately 300 in each treatment group) over an 18-24 month period. The primary endpoint is recurrence of UTI. In addition, patients will be evaluated for secondary endpoints related to renal scarring and antimicrobial resistance. Scarring will be determined based on renal scintigraphy by 99mTc dimercaptosuccinic (DMSA) scan. Quality of life, compliance, safety parameters, utilization of health resources, and change in VUR will be assessed periodically throughout the study.
National multi-center study aimed at understanding more about diabetes among children and young adults in the United States less than 20 years of age in six geographically dispersed populations that encompass the ethnic diversity of the United States. SEARCH has been helping to find answers about the types of diabetes, its complications, and how having diabetes affects the lives of children and young adults. There are more than 20,000 study participants representing all different racial and ethnic backgrounds who have helped SEARCH determine the extent of diabetes in the community and its impact on different populations. The SEARCH Study invites Investigators interested in childhood Diabetes Research to collaborate on matters of interest to the field of childhood Diabetes.
Schizophrenia and Bipolar Disorder Genetics Blog
This resource aims to provide information for the general public on the background and current progress of scientific research into the role of genetics in these disorders. Additionally, it also aims to provide a forum for the discussion of aspects of psychiatric genetics open to members of the research community.
Stress Incontinence Surgical Treatment Efficacy Trial
Clinical trial under the Urinary Incontinence Treatment Network to compare the treatment success for two surgical procedures that are frequently used and have similar cure rates, yet have not been compared directly to each other in a large, rigorously conducted randomized trial. The secondary aims of the trial are to compare other outcomes for the two surgical procedures, including quality of life, sexual function, satisfaction with treatment outcomes, complications, and need for other treatment(s) after surgery. Follow-up will be a minimum of two years and up to four years.
Group of collaborating investigators who conduct long-term studies and clinical trials of the most commonly used surgical, pharmacological, and behavioral approaches for management of urinary incontinence in women diagnosed with stress and mixed incontinence.
Study of Nutrition in Acute Pancreatitis
Randomized multi-center clinical trial designed to test whether duodenojejunal (DJ) feeding is more effective than nasogastric (NG) feeding in providing enteral nutrition to patients with severe acute pancreatitis. SNAP will enroll participants with severe acute pancreatitis admitted to the intensive care unit at eight clinical centers. Upon enrollment, participants are assigned to NG or DJ feeding and managed for up to 28 days or until weaned on to solid food. Follow-up continues until participants are discharged from the hospital or for a maximum of 60 days. Outcomes relate to feeding tolerance and failure, nutritional status, risk for life-threatening pancreatic/systemic complications, and hospital mortality.
Software that provides a comprehensive framework for the analysis of ChIP-seq data.
Targeting INflammation using SALsalate for Type 2 Diabetes
Targeting Inflammation Using Salsalate for Type 2 Diabetes-stage II
Nationwide, randomized, double blind, multi-center research study to determine whether the drug salsalate, a member of the commonly used Non-Steroidal Anti-Inflammatory Drug (NSAID) class, is effective in lowering sugars in patients with type 2 diabetes. The study is conducted in two stages. The primary objective of the first stage is to select a dose of salsalate that is both well-tolerated and demonstrates a trend toward improvement in glycemic control. The primary objective of Stage 2 of the study is to evaluate the effects of salsalate on blood sugar control in diabetes; the tolerability of salsalate use in patients with type 2 diabetes (T2D); and the effects of salsalate on measures of inflammation, the metabolic syndrome, and cardiac risk.
Treatment Options for type 2 Diabetes in Adolescents and Youth
Treatment Options for type 2 Diabetes in Adolescents & Youth
Randomized, double blind, nationwide clinical trial to compare the efficacy and safety of three interventions to treat adolescents and youth with type 2 diabetes (T2D): (1) metformin alone, (2) metformin plus rosiglitazone, and (3) metformin plus an intensive lifestyle intervention called the TODAY Lifestyle Program (TLP). The secondary aims are to: compare and evaluate the safety of the three treatment arms; compare the effects of the three treatments on the pathophysiology of type 2 diabetes (T2D) with regards to beta cell function and insulin resistance, body composition, nutrition, physical activity and aerobic fitness, cardiovascular risk factors, microvascular complications, quality of life, and psychological outcomes; evaluate the influence of individual and family behaviors on treatment response; and compare the relative cost effectiveness of the three treatment arms. The study recruits patients over a three-year period and follows patients for a minimum of two years. Patients are randomized within two years of the diagnosis of T2D. Materials that were used for the study are made publicly available: * The TODAY Standard Diabetes Education (TSDE) program, developed especially for youth with type 2 diabetes. (All participants received the TSDE program) * The TODAY Lifestyle Program (TLP) that was among the treatments tested.
Medical university in Stockholm, Sweden that offers more than fifty disciplines of medicine for study.
Study that compared the outcomes of two minimally invasive surgical procedures to treat stress urinary incontinence in women. These procedures are called mid-urethral slings. The procedures insert a mesh sling or hammock to support the bladder neck so that urine does not leak. Both procedures have been approved by the FDA and have been shown to be safe and successful in treating stress urinary incontinence. However, it is not known if one is better than the other. This study answers that question. The secondary aims of the trial are to compare other outcomes for the two surgical procedures, including quality of life, sexual function, satisfaction with treatment outcomes, complications, and the need for other treatments(s) after surgery. Follow-up will be a minimum of two years. Stress urinary incontinence is the accidental leakage of urine during activities such as coughing, laughing, sneezing, or lifting heavy objects.
Trial to Reduce IDDM in the Genetically at Risk
TRIGR - Trial to Reduce IDDM in the Genetically at Risk
International, randomized, double-blinded trial to determine whether weaning to a casein hydrolysate formula during the first 6-8 months of life in place of cow milk based formula reduces the incidence of autoimmunity and type 1 diabetes in genetically susceptible newborn infants. 2160 eligible infants were randomized to test or control formulas when mothers decide to wean from exclusive breastfeeding. The participants will be monitored up to the age of 10 years for the appearance of diabetes-predictive autoantibodies and clinical type 1 diabetes. The TRIGR trial will determine whether delayed exposure to intact food proteins will reduce the chances of developing type 1 diabetes later in life. All babies in the study received the recommendation to breastfeed for at least the first six months of life. If a mother was unable to exclusively breastfeed before the baby was 8 months of age, her child was randomly assigned to one of two groups. One group of these babies received a trial formula based on extensively hydrolyzed protein; the other group received another trial formula containing a smaller amount of hydrolyzed protein. In the hydrolyzed formula, the big protein molecules have been split into very small fragments to provide a source of nutritional amino acids, but the fragments are likely too small to stimulate the immune system. The TRIGR trial will also be able to analyze whether exclusive breastfeeding per se can reduce the risk of the children to develop type 1 diabetes.
NeuroPedia: Neuropeptide database and spectra library
A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species.
Karlsruhe Institute of Technology; Karlsruhe; Germany
Public research university in Germany for engineering and natural sciences.
Viral Resistance to Antiviral Therapy of Chronic Hepatitis C
Study of Viral Resistance to Antiviral Therapy of Chronic Hepatitis C
Study of Viral Resistance to Antiviral Therapy of Chronic Hepatitis C (Virahep-C)
Study designed to test the hypothesis that African-Americans respond less well to combination pegylated interferon and ribavirin therapy than Caucasian-Americans who have chronic hepatitis C genotype 1 and who were not previously treated with either interferon or ribavirin. Reasons for differences in response, regardless of race, will be studied. All patients were treated with combination therapy of pegylated interferon and ribavirin for 48 weeks, and were followed for an additional 48 week safter cessation of therapy. 400 patients, half African-American and half Caucasian American, from 8 clinical centers with the goals of establishing rates of response to optimal current therapy in the two ethnic groups, identify factors predictive of response, establish patterns of viral kinetics in response to antiviral therapy, and test hypotheses concerning viral and host factors determining response to therapy. Four ancillary studies designed to elucidate biological and virological basis for non-response are also included in Virahep-C. Additionally, the study has central facilitates for pathology, the virological testing laboratory and a serum/tissue repository.
GenitoUrinary Development Molecular Anatomy Project
Murine Atlas for Genitourinary Development
Project aggregates and provides experimental gene expression data from genito-urinary system. International consortium providing molecular atlas of gene expression for developing organs of GenitoUrinary (GU) tract. Mouse strains to facilitate developmental and functional studies within GU system. Experimental protocols and standard specifications. Tutorials describing GU organogenesis and primary data via database. Data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of developing mouse genitourinary (GU) system.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Consortium to advance the understanding of intestinal epithelial stem cell biology during development, homeostasis, regeneration and disease. Its immediate goals are to isolate, characterize, culture and validate populations of intestinal stem cells; answer major questions in stem cell biology of the intestinal epithelium; and accelerate research by making information and resources available to the research community. Resources include data sets, protocols, and a resource catalog. Long-term goals include: 1) laying the ground work for therapeutic manipulation of the intestinal epithelium 2) contributing to the greater understanding of stem cell biology through knowledge of the intestine as a model stem cell-driven system. Research Projects are housed at 8 institutions across the nation: Oregon Health & Science University, Stanford University, Stowers Institute for Medical Research, University of California, Los Angeles School of Medicine (UCLA) (partnered with the VA Greater Los Angeles), University of North Carolina, Chapel Hill (UNC), University of Oklahoma, University of Pennsylvania, and University of Pittsburgh.
Medical Therapy of Prostatic Symptoms (MTOPS)
Multi-center double-masked, placebo-controlled randomized clinical trial designed to evaluate the long-term efficacy of finasteride, or doxazosin, or the combination of both, in delaying or preventing the clinical progression of symptomatic benign prostatic hyperplasia (BPH). MTOPS was the largest and longest study to test whether drug therapy can prevent or delay the noncancerous growth of the prostate. A unique feature of MTOPS that has not been done in prior studies of pharmacotherapy of BPH is the biopsy substudy. A total of 1,082 volunteers from the 2,931 participants randomized during the full-scale phase are currently participating in this substudy. Biopsies of the prostate will be obtained on these volunteers at predetermined times during the course of the trial to evaluate the status of the prostate at key event times. The purpose of the substudy was to provide additional information regarding the histopathobiology of BPH and to test existing biomarkers for their prognostic ability regarding response to drug therapy.
Type 1 Diabetes Genetics Consortium (T1DGC)
Data and biological samples were collected by this consortium organizing international efforts to identify genes that determine an individual risk of type 1 diabetes. It originally focused on recruiting families with at least two siblings (brothers and/or sisters) who have type 1 diabetes (affected sibling pair or ASP families). The T1DGC completed enrollment for these families in August 2009. They completed enrollment of trios (father, mother, and a child with type 1 diabetes), as well as cases (people with type 1 diabetes) and controls (people with no history of type 1 diabetes) from populations with a low prevalence of this disease in January 2010. T1DGC Data and Samples: Phenotypic and genotypic data as well as biological samples (DNA, serum and plasma) for T1DGC participants have been deposited in the NIDDKCentral Repositories for future research.
Integrated software tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
KESMBA: Knife-Edge Scanning Microscope Brain Atlas
Knife-Edge Scanning Microscope Brain Atlas
A web-based, light-weight 3D volume viewer that serves large volumes (typically the whole brain) of high-resolution mouse brain images (~1.5 TB per brain, ~1 um resolution) from the Knife-Edge Scanning Microscope (KESM), invented by Bruce H. McCormick. Currently, KESMBA serves the following data sets: * Mouse: Whole-brain-scale Golgi (acquired 2008 spring): neuronal morphology: Choe et al. (2009) * Mouse: Whole-brain India Ink (acquired 2008 spring): vascular network: Choe et al. (2009); Mayerich et al. (2011); * Mouse: Whole-brain Golgi (acquired 2011 summer): neuronal morphology: Choe et al. (2011); Chung et al. (2011); * Mouse: Whole-brain Nissl (acquired 2009-2010 winter): somata (Choe et al. 2010) (Coming soon) They will ship you the full data set on a hard drive if you provide them with the hard drive and shipping cost.
GlyProt - In Silico Glycosylation of Proteins
Web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II, http://www.glycosciences.de/modeling/sweet2/doc/index.php
Web tool that allows drawing distances of equal r as a function of the appropriate F,Y coordinates using the nuclear Overhauser enhancement (NOE), which allows the detection of the proximity in space between protons that may be located in different, yet spatially neighboring residues of oligosaccharides. A single pair of contours drawn for the lower and upper limits of r for one NOE encloses a torus-like region which still covers an infinite number of F,Y conformations. Please note: This application only works if Java Script is activated in your web browser.
pdb-care: PDB CArbohydrate REsidue check
Tool that checks carbohydrate residues in pdb-files for errors, aiding experimentalists in detecting discrepancies in connectivities and nomenclature.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. A C#.NET/C++.NET 4.0 API multi-threaded, parallel class library with CUDA kernels for EEG predictive analytics gleaned from the ModelMaker 2 application. This web service and component library offers functionality to do univariate and multivariate nonlinear time series and frequency based predictive analysis for EEG / Ecog / MEG signals for gaming applications. Neural Maestro works with both EEGLab / BCILab and eConnectome as well as other MATLAB and R packages. It enables one to build highly sophisticated neuroscience applications with little effort in Windows applications.
The Biomedical Research Foundation - Current Research
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This laboratory facilities contain core research space for monoclonal antibody production, oligonucleotide and peptide synthesis, gene cloning, DNA sequencing, high performance liquid chromatography, tissue culture, positron emission tomography, magnetic resonance spectroscopy and electron microscopy.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This free neuropsychological evaluation software, Repeat, examines performance on a serial reaction time task thought to depend upon implicit memory. Participant's acquisition of a repeating stimulus sequence is assessed in this task. Repeat is a modification of procedures reported by Nissen and Bullemer (1987) and by Lewick, Hill and Bizot (1988). The computer screen is divided into quadrants. A single X, appears in one of the quadrants. The participant's task is either, depending on response modality, to strike as quickly as possible the key (4, 5, 1, 2 on the numeric keypad) corresponding to the quadrant in which the X appears or to position the mouse pointer over the quadrant and click it. The X then appears according to a repeating pre-programmed sequence in a different quadrant and the participant is required to respond as quickly as possible to that X. A trial is made up of a series of the repeating sequence. Sequence order and length and the number of iterations of the sequence are predetermined by the experimenter. CATs Repeat also allows for the interleaving of a randomly positioned X between each sequenced X. Alternatively a series of random presentations can be programmed to allow for assessment of the baseline speed of responding, that is a condition under which the participant can acquire no anticipatory information to enhance speed of responding. Repeat also contains a dual-task or split attention component modeled after a task reported by Nissen and Bullemer (1987). This task is identical to the one described above except that either a low or high tone is presented with each X presentation and the participant is asked to count the number of low tones they heard during a trial. The relative frequency of low tones is experimenter definable. Finally Repeat allows for the assessment of the explicit knowledge the participant may have acquired of the sequence. This component of the task is modeled after the generate procedure reported by Nissen and Bullemer (1987). At any point in the experiment the participant can be asked to begin predicting where the X will appear next. At this time no normative data is available for this test.
Service that automatically extracts carbohydrate information from pdb-files and displays it in LINUCS or IUPAC notation. Many pdb-files contain carbohydrate structures. Since there is not such a standard nomenclature like it exists for amino acids, it is difficult to find the carbohydrate information. Sometimes entire oligosaccharides are encoded in one single residue. Information about carbohydrate linkages is often missing, and if it is present, it is not in a unique format and therefore also difficult to find.
GlyVicinity: Analysis of Amino Acids in the Vicinity of Carbohydrate Residues contained in the Protein Data Bank (PDB)
Service to generate statistics about the amino acids present in the vicinity of carbohydrate residues. Besides the amino acids in sequential neighborhood of glycosylation sites (analysed by GlySeq), those in the spatial vicinity of carbohydrate residues determine the characteristics of glycoproteins. The latter ones are of special interest for the examination of carbohydrate-binding proteins. Since carbohydrate moieties are not covalently bound in these cases, sequence analysis comparable to that for glycosylation sites is not possible there. GlyVicinity performs statistical analyses on the types of amino acids around carbohydrate chains and on the atoms forming the closest contacts between protein and carbohydrate residues. Results are based on weekly updated datasets derived from the Protein Data Bank (PDB).
GlyTorsion: Analysis of Carbohydrate Torsion Angles found in the Protein Data Bank (PDB)
Service that performs a statistical analysis of carbohydrate torsion angles derived from the Protein Data Bank. Such as protein conformation can be described by the backbone torsion angles, a carbohydrate structure is mainly characterised by its linkage torsions. With the aid of pdb2linucs, a dataset of carbohydrate torsion angles was derived from from carbohydrate structures found in the PDB. This weekly updated dataset contains, besides linkage torsions, also ring torsions, omega torsions, N-acetyle group torsions and sidechain torsions of Asn residues involved in Glycan bonds. It can be queried by GlyTorsion.
GlySeq - Statistical Analysis of Glycoprotein Sequences
Service dedicated to statistically analyze the sequences around glycosylation sites. Glycosylation belongs to the most common and most important co- and postranslational modifications of proteins. Since it is often difficult to determine which potential glycosylation sites are in fact glycosylated, there is only few data available about glycoproteins. Sources from which such data can be retrieved are SwissProt and the Protein Data Bank (PDB). Data from the PDB is obtained using pdb2linucs and updated weekly. GlySeq is dedicated to statistically analyze these sequences, especially the areas around glycosylation sites.
Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms.
LInear Notation for Unique description of Carbohydrate Sequences
LINUCS: LInear Notation for Unique description of Carbohydrate Sequences
Service that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form. Input: A structure using the extended, non-graphic nomenclature (in ASCII writing) to describe complex carbohydrates as recommended by IUPAC. Output: A linear, unique notation. The source code (written in C), will be distributed so that software developers can easily implement their algorithm within their own application. LINUCS was chosen to fulfill to following conditions: * Input of extended, non-graphic nomenclature to describe carbohydrate structures. * Resulting linear code is closely related to notations and abbreviations recommended by IUPAC. * Number of additional rules to define the priority of the branches is low * Extended nomenclature of complex carbohydrates contains all information to define the hierarchy. * LINUCS is applicable to all types of carbohydrates (macrocyclic system are currently not implemented) . * Remaining unassigned linkage information are tolerated
Service that searches carbohydrate structures for motifs commonly used for carbohydrate classification, like N- and O-glycan cores, Lewis antigens, etc. Note: Sumo is currently under construction. Motif searches are a frequently used tool in proteomics. For carbohydrate structures, there are also many motifs classified in the literature, e.g. the Lewis antigens or the diverse O-glycan core structures. Sumo is a tool to locate such motifs in a carbohydrate structure given in LINUCS or in IUPAC nomenclature., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Service that calculates and displays the main fragments (Band C-, Z- and Y-, A- and X-ions) of oligosaccharides that should occur in MS-spectra. The extended ASCII nomenclature as recommended by IUPAC is used to input the sequence of complex oligosaccharides. However, some additional input rules have to be fulfilled. In case only the topology and composition of the oligosaccharide is known, a simpler way to input carbohydrate sequences is possible. Since the hydroxyl groups of synthetic carbohydrates are often the are protected they have included a way to indicate if sugar residue are persubstituted. Please have a look at the examples of valid input structures.
Manually curated, comprehensive repository of clusters of differentiation (CDs) which are a) defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids and b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins. The data base is generated by exhaustive search of literature and other online data banks related to carbohydrates and proteins. This data bank is the beginning of an effort to provide concise, relevant information of carbohydrate-related CDs in a user- friendly manner. For users convenience the data bank under menu browse of GlycoCD is arranged in two section namely carbohydrate recognition CDs (CRD CD) and glycan CD. The carbohydrate recognition CD part is the collection of proteins which recognize glycan structures by means of the CRDs. Glycan CD is the part in which CDs are summarized which characterize specific oligosaccharide structures. The GlycoCD databank has been developed with the aim to assist the immunologist, cell biologist as well as the clinician who wants to keep up with the present knowledge in this field of glycobiology.
A web-based gene list enrichment analysis tool that provides various types of visualization summaries of collective functions of gene lists. It includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes / proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries.
Benaroya Research Institute: Neurological Diseases
Benaroya Research Institute Neurological Diseases Research
BRI investigators study the molecular and genetic mechanisms which underlie some of the most devastating chronic neurological disorders, and conduct clinical trials for new innovative therapies. Neurological studies that are currently studied include Amyotrophic lateral sclerosis (ALS) or Lou Gehrig's Disease, Multiple Sclerosis, and Parkinson's Disease.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 application that interfaces with the Neural Maestro class library to perform Classical and Bayesian logistic polynomial regression analysis for multiple trial and experimental neuroscience / electrophysiological datasets. The idea is to build a neural feature extractor to plug into a neural recognition network based on recordings from patch clamps and/or brain computer interfaces. Frequency based feature sets are collected from the simulation of neuronal cell assemblies and examined for inclusion in combinatorial regressions using the Neural Maestro API. Regressions are evaluated based on different metrics. The application interfaces with a R and MATLAB API and produces a compendium to be published on CRAN.
Software that calls aberrations for array CGH data using a six state mixture model and several biological concepts. It is written in R.
Five data sets containing quasi-stationary, artifact-free EEG signals both in normal subjects and epileptic patients were put in the web by Ralph Andrzejak from the Epilepsy center in Bonn, Germany. Each data set contains 100 single channel EEG segments of 23.6 sec duration.
Rodrigo Quian Quiroga EEG ERP and single cell recordings database
Rodrigo Quian Quiroga - EEG ERP and single cell recordings database
5 EEG, ERP and single cell recordings data sets where each file corresponds to the recording on a different subject in the left occipital electrode (O1), with linked earlobes reference. Each file contains several artifact-free trials, each of them containing 512 data points (256 pre- and 256 post-stimulation) stored with a sampling frequency of 250 Hz. Trials are stored consecutively in a 1 column file. Data was pre-filtered in the range 0.1-70Hz. All trials correspond to target stimulation with an oddball paradigm. STAR R based Data Sets Used * Dataset # 1: Human single-cell recording * Dataset # 2: Simulated extracellular recordings * Dataset # 3: EEG signals from rats * Dataset # 4: Pattern visual evoked potentials. * Dataset # 5: Tonic-clonic (Grand Mal) seizures.
Data set from a large study to examine EEG correlates of genetic predisposition to alcoholism. It contains measurements from 64 electrodes placed on the scalp sampled at 256 Hz (3.9-msec epoch) for 1 second. There were two groups of subjects: alcoholic and control. Each subject was exposed to either a single stimulus (S1) or to two stimuli (S1 and S2) which were pictures of objects chosen from the 1980 Snodgrass and Vanderwart picture set. When two stimuli were shown, they were presented in either a matched condition where S1 was identical to S2 or in a non-matched condition where S1 differed from S2. There were 122 subjects and each subject completed 120 trials where different stimuli were shown. The electrode positions were located at standard sites (Standard Electrode Position Nomenclature, American Electroencephalographic Association 1990). Zhang et al. (1995) describes in detail the data collection process. There are three versions of the EEG data set. * The Small Data Set (smni97_eeg_data.tar.gz) contains data for the 2 subjects, alcoholic a_co2a0000364 and control c_co2c0000337. For each of the 3 matching paradigms, c_1 (one presentation only), c_m (match to previous presentation) and c_n (no-match to previous presentation), 10 runs are shown. * The Large Data Set (SMNI_CMI_TRAIN.tar.gz and SMNI_CMI_TEST.tar.gz) contains data for 10 alcoholic and 10 control subjects, with 10 runs per subject per paradigm. The test data used the same 10 alcoholic and 10 control subjects as with the training data, but with 10 out-of-sample runs per subject per paradigm. * The Full Data Set contains all 120 trials for 122 subjects. The entire set of data is about 700 MBytes.
THIS RESOURCE IS NO LONGER IN SERVICE, documented November 23, 2020; EEG data set, source code, and results from 7500 signal pairs from 5 epilepsy patients analyzed in the manuscript, Andrzejak RG, Schindler K, Rummel C. Nonrandomness, nonlinear dependence, and nonstationarity of electroencephalographic recordings from epilepsy patients. Phys. Rev. E, 86, 046206, 2012. All Matlab source codes are included in the file ASR_Sources_2012_10_16.zip. The clinical purpose of these recordings was to delineate the brain areas to be surgically removed in each individual patient in order to achieve seizure control.
Software package for normalizing and analyzing tiling arrays and ChIP-chip data. It is the R-version of a MAT program.
An efficient P300-based brain-computer interface for disabled subjects
A portal containing EEG datasets (in MATLAB format) and the MATLAB software that were used to produce the results in the paper named in the title of this resource. The files published can also be used as a basis for individual research on P300-based brain-computer interfaces. The system is based on the P300 evoked potential and is tested with five severely disabled and four able-bodied subjects. For four of the disabled subjects classification accuracies of 100% are obtained. The bitrates obtained for the disabled subjects range between 10 and 25 bits/min. The effect of different electrode configurations and machine learning algorithms on classification accuracy is tested.
Project BCI - EEG motor activity data set
EEG motor activity data sets used for Brain Computer Interface research project in Matlab MAT format. * Dataset 1 - 1D motion: This subject is a 21 year old, right handed male with no known medical conditions. The EEG consists of actual random movements of left and right hand recorded with eyes closed. Each row represents one electrode. The order of the electrodes is FP1 FP2 F3 F4 C3 C4 P3 P4 O1 O2 F7 F8 T3 T4 T5 T6 FZ CZ PZ. The recording was done at 500Hz using Neurofax EEG System which uses a daisy chain montage. The data was exported with a common reference using Eemagine EEG. AC Lines in this country work at 50 Hz. This info is also included in the MAT file. * Dataset 2 - 2D motion: This subject is a 21 year old, right handed male with no known medical conditions. The EEG consists of actual random movements of left and right hand recorded with eyes closed. Each row represents one electrode. The order of the electrodes is FP1 FP2 F3 F4 C3 C4 P3 P4 O1 O2 F7 F8 T3 T4 T5 T6 FZ CZ PZ. The recording was done at 500Hz using Neurofax EEG System which uses a daisy chain montage. The data was exported with a common reference using Eemagine EEG. AC Lines in this country work at 50 Hz. This data consists of the following movements # Three trials left hand forward movement # Three trials left hand backward movement # Three trials left hand forward movement # Three trials left hand forward movement # 1 trial imagined left hand forward movement # 1 trial imagined left hand backward movement # 1 trial imagined right hand forward movement # 1 trial imagined right hand backward movement # 1 trial left leg movement # 1 trial right leg movement
DEAP: A Dataset for Emotion Analysis using EEG Physiological and Video Signals
DEAPDataset: A Dataset for Emotion Analysis using EEG Physiological and Video Signals
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 12,2025. Multimodal dataset for emotion analysis using EEG, Physiological and Video Signals of human affective states. The electroencephalogram (EEG) and peripheral physiological signals of 32 participants were recorded as each watched 40 one-minute long excerpts of music videos. Participants rated each video in terms of the levels of arousal, valence, like/dislike, dominance and familiarity. For 22 of the 32 participants, frontal face video was also recorded. A novel method for stimuli selection was used, utilizing retrieval by affective tags from the last.fm website, video highlight detection and an online assessment tool. The dataset is made publicly available and other researchers are encouraged to use it for testing their own affective state estimation methods.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 WPF / OWL / REST / JSON / SPARQL multi-threaded, parallel desktop application enables the construction of biomedical knowledge through PubMed, ScienceDirect, EndNote and NIH Grant repositories for tracking the work of medical researchers for ranking and recommendations. Users can crawl web sites, build latent semantic indices to generate literature searches for both Clinical Translation Science Award and non-CTSA institutions, examine publications, build Bayesian networks for neural correlates, gene to gene interactions, protein to protein interactions and as well drug treatment hypotheses. Furthermore, one can easily access potential researcher information, monitor and evolve their networks and search for possible collaborators and software tools for creating biomedical informatics products. The application is designed to work with the ModelMaker, R, Neural Maestro, Lucene, EndNote and MindGenius applications to improve the quality and quantity of medical research. iBIOFind interfaces with both eNeoTutor and ModelMaker 2013 Web Services Implementation in .NET for eNeoTutor to aid instructors to build neuroscience courses as well as rare diseases. Added: Rare Disease Explorer: The Visualization of Rare Disease, Gene and Protein Networks application module. Cinematics for the Image Finder from Yale. The ability to automatically generate and update websites for rare diseases. Cytoscape integration for the construction and visualization of pathways for Molecular targets of Model Organisms. Productivity metrics for medical researchers in rare diseases. iBIOFind 2013 database now includes over 150 medical schools in the US along with Clinical Translational Science Award Institutions for the generation of biomedical knowledge, biomedical informatics and Researcher Profiles.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. Statistical and biomedical informatics software studio that develops neuroscience applications and brain computer interface games. They are dedicated to the integration of medical research, neuroscience, time series analysis, computer programming, statistics, sensor technologies, graphics design, artificial intelligence and entertainment to build gaming systems for neuroscientific research and intelligent tutoring in the classroom and lab. The current focus of The Cromwell Workshop/Neuronal Architects is on theoretical neuroscience and experimental modeling of psychological and neural processes that involve attention, emotion, motivation and executive functions that are impaired by neurological diseases. The outcome of this work is to use these results in the design of multiple genre brain computer interface gaming systems that can be used in both clinical and at home settings. If you would like to explore any collaborative opportunities to use their software or enhance your existing statistical products with their .NET, Java, R and Matlab code bases, let them know.
Software tool for microarray tile mapping. It utilizes ChIP-chip peak calling to identify genomic loci that show transcriptional activities and transcription factor binding patterns of interest.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. ASP.NET AJAX .NET 4, Telerik controls enabled application designed to be used with the books presented, papers and web content to help with the acceleration of learning and software development for the neurosciences. All content developed at The Cromwell Workshop is intended to accelerate the implementation of biomedical knowledge, help with EEG clinical certifications and provide the opportunity for students, software developers, neuroscientists, neurologists and neurosurgeons to collaborate globally with knowledge content. e-NeoTutor relies on a subscription model to build software components in multiple languages and access book material. Tutor designed to complement free online course content in neuroscience, work with the Society of Neuroscience, The Human Connectome Project and assist researchers with CNIM certification, biomedical informatics, neuroinformatics and neuroscience training programs.
Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files.
BigBrain: An ultrahigh-resolution 3D human brain model
Ultrahigh resolution 3D human brain model at nearly cellular resolution of 20 micrometers, based on reconstruction of histological sections. Provides considerable neuroanatomical insight into human brain, thereby allowing extraction of microscopic data for modeling and simulation. Enables testing of hypotheses on optimal path lengths between interconnected cortical regions or on spatial organization of genetic patterning, redefining traditional neuroanatomy maps such as those of Brodmann and von Economo.
Preliminary database of neuroanatomical connectivity reports specifically for the human brain, which have been manually curated. It includes details (based on manual literature curation) of tract tracing or related connectivity studies conducted in human brain tissue. This database and user interface will be expanded and improved in the near future.
HyperBrain: A Resource for Learning NeuroAnatomy
HyperBrain: An Online Neuroanatomy Tutorial
An online tutorial for human neuroanatomy designed as a supplement to textbook and class learning or as a lab substitute when human specimens, slides and models are not available. HyperBrain includes thousand of images and hundreds of linked illustrated glossary terms, as well as movies, quizzes and interactive animations. Last updated 2012.
Parkinson's Disease Data and Organizing Center
The Parkinson's Disease Data and Organizing Center
The Parkinson's Disease Data and Organizing Center (PD-DOC)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 02, 2011. Notice: This domain name expired on 10/29/11 and is pending renewal or deletion PD-DOC is a portal and a database resource, hosting a database and linking to other databases and data sets of clinical and translational data. PD-DOC functions to organize and facilitate clinical and translational research in Parkinson's disease. The PD-DOC Database contains standardized data collected by user institutions on large numbers of patients with Parkinsons disease and other parkinsonian disorders. In some cases, data is obtained at a single point in time, while in others data is collected repeatedly over time. The PD-DOC Database is composed of the Core Data Set (CDS) which consists of those variables required to be gathered for each subject whose data is entered into the PD-DOC database. In 2005, working groups of Udall Center and invited experts deliberated to establish the components of each CDS section (e.g. General Clinical, Cognitive/Behavioral, Postmortem Brain Neuropathological Findings). The PD-DOC CDS was established and designed to optimize data analyses and data mining for large numbers of subjects participating in a variety of research studies. In most cases corresponding DNA samples are available form the NINDS Human Genetic Repository (at Coriell). Much of the website is publicly available for viewing. To request access to sections of the website dealing with downloading or requesting data, requesting a consultation, or submitting data or other information you will need to register. Before registering, you should read the PD-DOC Policies. Note that PD-DOC data can be used for research purposes only. Once your registration is successfully completed you will be automatically logged into the website.
A topical portal which provides information about conditions that affect the nervous system (brain, spinal cord, nerves, and muscles), such as stroke (brain attack), Alzheimer's disease, and back pain. It is a physician developed and monitored source of neurology information for consumers. Additionally, it contains comprehensive condition and treatment information, as well as interactive tools.
Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.
big-PI Predictor: GPI Modification Site Prediction
Prediction tool locating potential GPI-modification sites in precursor sequences applied for large-scale protein sequence database searches. The composite prediction function (with separate parametrization for metazoan and protozoan proteins) consists of terms evaluating both amino acid type preferences at sequence positions near a supposed omega-site as well as the concordance with general physical properties encoded in multi-residue correlation within the motif sequence. The latter terms are especially successful in rejecting non-appropriate sequences from consideration. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set of fully annotated sequences from the SWISS-PROT database as well as with a newly created database big-Pi (more than 300 GPI-motif mutations extracted from original literature sources). The accuracy of predicting the effect of mutations in the GPI sequence motif was above 83 %.
Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
Cell: Expression Localization Development Anatomy
Structured vocabulary to organize cell-associated data and to place these data in clearly defined semantic relations to other biological facts. It describes cell types, their properties and origin and links this information to other existing ontologies like the Cell Ontology (CL), Foundational Model of Anatomy (FMA), Gene Ontology (GO), Mouse Anatomy and others using the top-level ontology BioTop.
A tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses. This is done by comparing the mass of the glycan to a list of pre-computed masses of glycan compositions. The program can be used with free or derivatised glycans and for glycopeptides where the peptide mass or protein is known. Compositional constraints can be applied to the output. Note: You can use GlycanMass to calculate the mass of an oligosaccharide structure from its oligosaccharide composition.
Access to Quicktime movies of histologic mouse anatomy including heart / lung, kidney, mammary gland, lymph node, prostate, spleen, liver, salivary glands, and 3-D wire model based on MRI sections; a Quicktime mouse radiographic atlas of skeletal anatomy containing a series of radiographic images with color overlays and labels; and a table containing a comparison between mouse and human anatomy. Special topics include the virtual necroscopy. Anatomic systems cover the central nervous system, male genital-urinary tract, female genital-urinary tract, mammary, kidney, skeletal, cardiovascular, gastrointestinal, and respiratory systems. The pathology and imaging section includes anatomy, histology, comparative imaging, physiology, pathology, comparative mammary, comparative prostate, GEM, and an image archive. These pages were put together as a pilot demonstration by Dr. Robert Cardiff, UCD Center for Comparative Medicine with the collaboration of Dr. Michael Paulus, Oak Ridge National Laboratories,MicroCat Group, Dr. Allan Johnson, Duke University Center for In Vivo Microscopy, and Drs. Steve Griffey, Gary Henderson and Tom Jue, University of California, Davis. This is a work in progress and for demonstration purposes.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2017. A resequencing package designed for mutation detection and analysis, SNP discovery and validation, pathogen sub-typing, allele identification and sequence confirmation.
Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms.
National Institute of Diabetes and Digestive and Kidney Disease Information Network
The NIDDK Information Network (dkNET) is a community-based network to serve needs of basic and clinical investigators that includes large pools of data and research resources relevant to mission of National Institute of Diabetes and Digestive and Kidney Disease.
Drosophila anatomy and development ontologies
A structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems.
Allows annotation of gene expression at all stages of development and tissue types (including sub cellular location) using standard Drosophila anatomy ontology. All methods of input use a controlled vocabulary to ensure data integrity.
Database that collects published lifespan data across multiple species. The entire database is available for download in various formats including XML, YAML and CSV.
A multi-species anatomy ontology for teleost fishes. It was originally seeded from ZFA, but covers terms relevant to other taxa. The TAO uses terms from the Common Anatomy Reference Ontology (CARO) as a template for its upper level nodes, and the Vertebrate Skeletal Anatomy Ontology (VSAO) for general skeletal anatomy classes. Growth of the TAO is enabled by contributions from data curators and the ichthyological community. The TAO can be browsed by using the NCBO BioPortal and data annotated using TAO terms can be queried using the Phenoscape Knowedgebase.
An ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichthys (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish. It contains (as of August 2010) over 38,500 names, and over 44,000 taxonomic synonyms. A majority of the taxonomic names and synonyms were made available from the Catalog of Fishes. In July 2010 they added nearly 15,000 common names provided by Fishbase. Additional names and synonyms are added as a result of their curation activities. The ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for their project's use for identifying evolutionary changes that match the phenotype of a zebrafish mutant.
Database of information on amphibian declines, natural history, conservation, and taxonomic information for every recognized species of amphibian in the world. Species accounts are being added regularly by specialists and volunteers and they contain species descriptions, life history information, conservation status, literature references, photos and range maps for many species. Some species have complete accounts; others as yet have only photographs or distributions. But all species can be queried for taxonomic, distributional and exact specimen data. AmphibiaWeb offers a powerful mapping tool by combining museum specimen data (via HerpNET) with expert opinion range maps (from Global Amphibian Assessment/IUCN) and overlaying these onto larger maps, allowing visualization in political, satellite, hybrid, or terrain map format. AmphibiaWeb currently (Aug 13, 2013) contains 7,160 species. They have 2,966 species accounts for 2,363 species, 6,517 literature references, 558 sound files, 109 video files, and 28,218 photos of 3,887 different amphibian species. These data come from numerous individuals--see acknowledgements. They have the ambitious goal of establishing a home page for every species of amphibian in the world. In order to accomplish this goal they encourage volunteers and specialists to help prepare species accounts. If you have special interest in a particular species, please contact them.
PhenoGen Informatics - The site for quantitative genetics of the transcriptome.
Website for analyzing microarray data. Software toolbox for storing, analyzing and integrating microarray data and related genotype and phenotype data. The site is particularly suited for combining QTL and microarray data to search for candidate genes contributing to complex traits. In addition, the site allows, if desired by the investigators, sharing of the data. Investigators can conduct in-silico microarray experiments using their own and/or shared data. There are five major sections of the site: Genome/Transcriptome Data Browser, Microarray Analysis Tools, Gene List Analysis Tools, QTL Tools, and Downloads. The genome/transcriptome data browser combines a genome browser with all the microarray, RNA-Seq, and Genomic Sequencing data. This provides an effective platform to view all of this data side by side. Source code is available on GitHub.
North American Conditional Mouse Mutagenesis Project
Large-scale research initiative focused on developing and distributing a library of mouse embryonic stem (ES) cell lines carrying single gene trapped or targeted mutations across the mouse genome. NorCOMM's large and growing archive of ES cells is publicly available on a cost-recovery basis from the Canadian Mouse Mutant Repository. As an international public resource, access to clones is unrestricted and nonexclusive. Through NorCOMM's affiliation with the Canadian Mouse Consortium (CMC), NorCOMM also provides clients with a single point of access to regional mouse derivation, phenotyping, genetic and archiving services across Canada. These value-added services can help your company harness NorCOMM's resources for drug discovery, target discovery and preclinical validation.
Texas A and M Institute for Genomic Medicine
Texas A&M Institute for Genomic Medicine
Resource for any researcher looking to obtain knockout mice and embryonic stem (ES) cells quickly and with favorable intellectual property (IP) terms. Our resources include the world’s largest gene trap library of ES cells in the C57BL/6N mouse strain and a constantly expanding repository of cryopreserved germplasm of knockout lines. TIGM provides both ES cell clones and mice as well as other transgenic core services including CRISPR/Cas9-based genome modifications within the Texas A&M system and to the public and private international research community.
A collection of free open courses. Subjects include Arts, Business, Education, Engineering & Computer Science, Health & Medical, Liberal Arts, Math and Science.
A simple sequence alignment editing tool, written in Java.
GTEx (Genotype-Tissue Expression) eQTL Browser
Database and browser that provides a central resource to archive and display association between genetic variation and high-throughput molecular-level phenotypes. This effort originated with the NIH GTEx roadmap project: however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets.
Expression Patterns for C. elegans promoter GFP fusions
Caenorhabditis elegans Expression Patterns
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of expression patterns of C. elegans promoter::GFP constructs. A text description of the observed pattern is provided, indicating the stage(s) and tissue(s) in which GFP is expressed. Also available for some strains are the corresponding 2D and 3D images. Investigators may browse the entire list, search by gene name, tissue, stage, and pattern. Search results may be downloaded in .csv and .txt formats. All of the strains in the expression pattern database are displayed in the browse page. The records are organized by gene; information such as locus name, genomic location (WormBase), the presence of images and videos, and the actual expression pattern are shown in a tabular format.
ADInstruments - Data Acquisition Systems for Life Science
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 19, 2018; A provider of computer-based data acquisition and analysis systems for life science. Products enable users to record and analyze life science data quickly and efficiently. ADInstruments product range is based on the PowerLab data acquisition system with LabChart software. The PowerLab system (also MacLab) is used in universities, hospitals, research institutes, pharmaceutical companies, contract research organizations and other private industry research sectors.
The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff
Curated database of known (published) gene lesions responsible for human inherited disease.
MATLAB -The Language of Technical Computing
Multi paradigm numerical computing environment and fourth generation programming language developed by MathWorks. Allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Used to explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance.
Atlas of Noncoding Conserved Regions in Animals
Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements.
A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq
Open source R package that provides web framework for building web applications using R. Used to create interactive web apps in native R, without needing to use HTML, CSS, or JavaScript.
Open source, platform-independent application for the visualization and analysis of complex, high-dimensional imaging data such as Diffusion Tensor Imaging (DTI) and High Angular Resolution Diffusion Imaging (HARDI). It has a plugin-based architecture which allows third parties to develop new plugins to extend the tool. Overview of the many features: * vIST/e is programmed in C++. It uses the Visualization Toolkit for visualization and pipelined data processing, as well as the cross-platform toolkit Qt Framework for an easy-to-use Graphical User Interface. * vIST/e introduces a powerful new plugin system, which allows for modular development with increased extensibility and stability. * Powerful GPU-based visualization techniques allow for smooth, real-time visualization of large data sets. Using custom ray tracing algorithms created with OpenGL, vIST/e can render DTI ellipsoids and HARDI spherical harmonics glyphs up to 4th order. The high frame rates offered by modern GPU technology allows for interactive exploration of this complex data. * Diffusion Tensor Imaging data can be visualized and interactively explored in a number of ways, including multiple cross-sections, volume rendering, and tensor glyphs. Derived scalar volumes, including various different anisotropy measures, can be computed and visualized. Data from other modalities, such as structural MRI, can be shown alongside the DTI data. * Various fiber tracking methods allow for fast and accurate reconstruction of fiber pathways. Interactively defined Regions of Interest (ROIs) can be used for seeding and filtering of fibers. Fibers are visualized either as lines, optionally using a powerful, GPU-based lighting engine, or as 3D structures such as tubes. * Scalar volumes, glyphs, and fibers can be colored using a wide array of coloring option. Customizable color loop-up tables allow for highly flexible visualization of scalar data. * Visualization and processing of various different HARDI formats is supported. HARDI data is interactively visualized using highly detailed glyphs rendered on the GPU. HARDI glyphs can be visualized in combination with DTI glyphs, for a better overview of complex diffusion data. * vIST/e includes support for NVIDIA's Compute Unified Device Architecture (CUDA), which enables highly parallel, GPU-based data processing, allowing for significant speed-up of computationally expensive algorithms.
Service to discover disease genes in GWAS using eQTL signature matching by simply submitting your list of GWAS associations (SNPs and p-values). It is important to upload all SNPs in your association study, not just the top hits. Sherlock may be able to group multiple lower-confidence SNPs to discover functionally-important genes.
Database of human SNPs in predicted miRNA-mRNA binding sites, based on information from dbSNP135 and mirBASE18. MirSNP is highly sensitive and covers most experiments confirmed SNPs that affect miRNA function. MirSNP may be combined with researchers' own GWAS or eQTL positive data sets to identify the putative miRNA-related SNPs from traits/diseases associated variants. They aim to update the MirSNP database as new versions of mirBASE and dbSNP database become available.
Public database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population.
Neuroscience Information Framework Web Services
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Representational State Transfer (REST) model based service for accessing a set of Neuroscience Information Framework (NIF) data through a fixed set of operations. They are defined by a WADL file which allows clients to automatically generate code for these services. The services (AnnotateService, FederationService, LdaService, LexicalService, LiteratureService, QueryService, SummaryService, VocabularyService) include the ability to: * Retrieve a federation summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/summary?q=* * Retrieve data records from a NIF federation source for a search, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nif-0000-00007-1?q=purkinje * Retrieve registry data records from NIF, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nlx_144509-1?q=miame * Retrieve a complete search summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/search?q=cortex * Retrieve NIF auto-complete suggestions, e.g., http://nif-services.neuinfo.org/servicesv1/v1/vocabulary?prefix=hippo * Use the NIF annotator for arbitrary text, e.g., http://nif-services.neuinfo.org/servicesv1/v1/annotate?content=The%20cerebellum%20is%20a%20wonderful%20thing These services are documented for developers in the WADL file (and client stubs should have the comments embedded in them). Visit, http://nif-services.neuinfo.org/servicesv1/ for more information
Database contating hydrothermal spring geochemistry that hosts and serves the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. It can accommodate published historical data as well as legacy and new data that investigators contribute.
Research Services Branch National Institutes of Mental Health
Research Services Branch National Institutes of Mental Health National Institutes of Neurological Disorders and Stroke
Portal for NIH, NIMH, and NINDS scientific and computer resources including Mac sites, PC sites, Linux sites, intramural programs, intranet and the NIH JumpStart and Directory.
Collection of isogenic human cell lines that are deficient for the expression of single genes. The current collection is based on the human cell line KBM-7 (Kotecki et al. Experimental Cell Research 1999), which is haploid for all chromosomes except chromosome 8 and a small part of chromosome 15. In these cells, genes are disrupted by the means of a retroviral gene trap. The collection is being expanded to cover the majority of expressed genes. The Human Gene Trap Mutant Collection is generated as a public-private partnership between CeMM (the Research Center for Molecular Medicine of the Austrian Academy of Sciences) and Haplogen.
Wellcome Trust Centre for Human Genetics Genome Scan Viewer
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database / display tool of genome scans, with a web interface that lets the user view the data. It does not perform any analyses - these must be done by other software, and the results uploaded into it. The basic features of GSCANDB are: * Parallel viewing of scans for multiple phenotypes. * Parallel analyses of the same scan data. * Genome-wide views of genome scans * Chromosomal region views, with zooming * Gene and SNP Annotation is shown at high zoom levels * Haplotype block structure viewing * The positions of known Trait Loci can be overlayed and queried. * Links to Ensembl, MGI, NCBI, UCSC and other genome data browsers. In GSCANDB, a genome scan has a wide definition, including not only the usual statistical genetic measures of association between genetic variation at a series of loci and variation in a phenotype, but any quantitative measure that varies along the genome. This includes for example competitive genome hybridization data and some kinds of gene expression measurements.
Database of raw data from people who have shared their direct-to-customer (DTC) genetic results from 23andMe, deCODEme or FamilyTreeDNA. Logged-In users can search the database for users with specific phenotypes and mass-download all corresponding SNP-datasets. This allows you to get datasets like All genotyping files of openSNP-users that have Alzheimer and the corresponding control group. They are currently working on providing API-access. You can also use JSON to get access to openSNP-data and some other ways: If you want to automate the file-downloads for a given phenotype the RSS-feeds could help you. Inside the RSS-XML there are 2 flags you could use to automatically create correct genotype-groups: gives you the variation of this user at the phenotype you are looking at and gives you the download link. If you were genotyped by 23andMe, deCODEme or FamilyTreeDNA (contact them regarding others) you can upload the raw genotype data which you can download from your DTC test provider. The data will then be openly available for the world to see and download. They also parse these SNPs and annotate them. For annotation they include the manually curated SNPedia and find Open Access primary publications which appear in the journals of The Public Library of Science (PLoS), an Open Access publishing group. Additionally they screen Mendeley, a crowd-sourced repository of scientific publications. You can also publish some of your phenotypes so some day it might get possible to associate some SNPs with phenotypes. You can also share your knowledge about SNPs and phenotypes with other users and can socialize.
Project to define a roadmap for diffusion MR imaging of traumatic brain imaging and design an infrastructure to implement the recommendations and tested to ensure feasibility, disseminate results, and facilitate deployment and adoption. The research roadmap and infrastructure development will concentrate on three areas: 1) standardization of diffusion imaging methodology, 2) trial design and patient selection for acute or chronic therapy, and 3) development of multi-center collaborations and repositories for evaluating whether advanced diffusion imaging does improve decision making and TBI patients' outcomes. # DTI MRI reproducability: One of the major areas of investigation in this project is to study the reproducibility of data acquisition and image analysis algorithms. Understanding reproducibility defines a base level of deviation from which scans can be analyzed with statistical significance. As part of this work they are also developing site qualification criteria with the intention of setting limits on the MR system minimal performance for acceptable use in TBI evaluation. # Infrastructure for image storage, analysis and visualization: There is a continuing need to refine and extend software methods for diffusion MRI data analysis and visualization. Not only to translate tools into clinical practice, but also to encourage continuation of the innovation and development of new tools and techniques. To deliver upon these goals they are designing and implementing a storage and computational infrastructure to provide access to shared datasets and intuitive interfaces for analysis and visualization through a variety of tools. A strong emphasis has been placed on providing secure data sharing and the ability to add community defined common data elements. The infrastructure is built upon a Software-as-a-Service model, in which tools are hosted and managed remotely allowing users access through well-defined interfaces. The final service will also facilitate composition or orchestration of workflows composed of different analysis and processing tasks (for example using LONI or XNAT pipelines) with the ultimate goal of providing automated no-click evaluations of diffusion MRI data. # Tool development: The final aspect of this project aims to facilitate and encourage tool development and contribution. By providing access to open datasets, they will create a platform on which tool developers can compare and improve and their tools. When tools are sufficiently mature they can be exposed in the infrastructure mentioned above and used by researchers and other developers.
Free, open-source, object-oriented software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping. The toolkit implements standard techniques, such as diffusion tensor fitting, mapping fractional anisotropy and mean diffusivity, deterministic and probabilistic tractography. It also contains more specialized and cutting-edge techniques, such as Monte-Carlo diffusion simulation, multi-fibre and HARDI reconstruction techniques, multi-fibre PICo, compartment models, and axon density and diameter estimation. Camino has a modular design to enable construction of processing pipelines that include modules from other software packages. The toolkit is primarily designed for unix platforms and structured to enable simple scripting of processing pipelines for batch processing. Most users use linux, MacOS or a unix emulator like cygwin running under windows. However, the core code is written in Java and thus is simple to call from other platforms and programming environments, such as matlab running under unix or windows.
Crowdsourcing site for annotating neuroimaging literature. Brainspell also allows for search across the literature.
University of California Davis Center for Neuroscience
Recognizing the importance of research in Neuroscience and its great promise, as well as the importance of educating the neuroscientists of the future, the University of California, Davis, in 1990, established The Center for Neuroscience. The Center has now become the focus of interdisciplinary studies in Cellular, Molecular, Systems, Cognitive and Translational Neuroscience, with a Faculty made up of world leaders in brain research. The Center occupies facilities especially designed to promote and foster interactions among the resident faculty, associated faculty, postdoctoral fellows, and graduate students, with state-of-the-art lab space and associated facilities such as cellular and molecular imaging, functional imaging of the human brain and extensive databasing facilities. The Center provides an attractive setting for seminar series that feature distinguished National and International guest speakers as well as speakers from the UC Davis community of scientists. The Center is home to a number of visiting scholars each year and enjoys a lively intellectual atmosphere.
Implemented under MATLAB, this DTI image processing toolbox provides import-filters for several MR file standards, a processing unit to calculate the diffusion tensors; several GUI based tools to calculate fiber tracks and to evaluate the DTI dataset. The results can be filed as images with 3D impression or can be logged in formatted ASCII files. Tools and features: * DTI Processing Unit: Calculates the diffusion tensors and their eigenvalues and eigenvectors. Different file formats are supported (like DICOM, Bruker, binary files, Matlab structures). The standard SIEMENS and GE diffusion encoding schemes are supported; other schemes have to be defined in a separate text, .m or .mat file. * FiberTracking: ** Fiber tracking is realized by using the FACT algorithm (Mori et al., Annal. Neurol 1999). ** Probabilistic tracking realized by using the PiCo (Parker et al., JMRI 2003) approach but with DTI data as basis. It is possible to extract pathways between two seeds by combining two maps (Kreher et al., NeuroImage 2008). ** Global Fiber Tracking on basis of HARDI or DTI data. The method is based on the approach reported in (Marco Reisert et al: Global fiber reconstruction becomes practical. NeuroImage 54(2):955-62) * FiberViewer: ** Visualization and Navigation through different data modalities like DTI maps, fiber tracks, diffusion main directions. ** Supports different kinds of DTI maps (e.g. FA, Trace, lambda images ) ** Creation and manipulation of mask based ROIs. ** Selection of streamline fibers ** Visualization of probabilistic fiber tracking results ** Documentation by logging statistics of ROIs and fiber tracks into text files. ** Import/Export from/to ANALYZE or Nifti * 3D Visualizer: Visualization of map slices, ROIs, and fiber tracks with 3D impression. * Batch Editor: Automatic processing of high amounts of data. Possibility to link processing with SPM8 easily.
A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation
A graphical toolbox developed in Matlab for exploratory diffusion (tensor) MRI and fiber tractography. It includes diffusion reconstruction approaches, analysis and visualization tools for fiber tractography, atlas based segmentation, and connectivity networks. It also provides a wide range of quality assessment and pre-processing tools. Main features: * Visualization of scalar and vector maps of various diffusion tensor properties * Display of principal diffusion vectors, cuboids, and ellipsoids with several color-encodings * Deterministic (streamline) and 'probabilistic' (wild-bootstrap) fiber tractography * Clustering of fiber tracts * Data quality assessment tools * HARDI reconstructions (Q-ball and spherical deconvolution imaging) * Tract-specific measurements * Tract-segment analysis * Motion / distortion correction (with B-matrix rotation!) * Other cool stuff... (see publication link)
A Python-based open source toolkit for magnetic resonance connectome mapping, data management, sharing, visualization and analysis. The toolkit includes the connectome mapper (a full DMRI processing pipeline), a new file format for multi modal data and metadata, and a visualization application.
Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble
An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.
An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.
Software that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries.
THIS RESOURCE IS NO LONGER IN SERVICE. Datasets described in the manuscript: "Global Epigenomic Reconfiguration During Mammalian Brain Development" (Science, 2013 - DOI: 10.1126/science.1237905. This study provides genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis.
Training materials including Web edition modules of the neuroanatomy coursebooks used by first-year medical students at the University of Wisconsin Medical School (UWMS), videos, and images. Topics include spinal cord, brain stem, Cerebellum, Thalamus, Cranial Nerves and National Board Review practice questions.
Comprehensive international bibliographic biomedical database that enables users to track and retrieve precise information on drugs and diseases from pre-clinical studies to searches on critical toxicological information. It contains bibliographic records with citations, abstracts and indexing derived from biomedical articles in peer reviewed journals, and is especially strong in its coverage of drug and pharmaceutical research. Embase can help with everything from clinical trials research to pharmacovigilance and is updated online daily and weekly. Its broad biomedical scope covers the following areas: * Drug therapy and research, including pharmaceutics, pharmacology and toxicology * Clinical and experimental (human) medicine * Basic biological science relevant to human medicine * Biotechnology and biomedical engineering, including medical devices * Health policy and management, including pharmacoeconomics * Public, occupational and environmental health, including pollution control * Veterinary science, dentistry, and nursing The Embase Application Programming Interface supports export, RSS feeds, and integration services, making it possible to share data with a wide range of systems.
Blog put out by the Neuroscience Information Framework covering a variety of neuroscience related topics including topics encountered by the Neuroscience Information Framework as a project.
Melvin Yahr International Parkinson's Disease Foundation
The Melvin Yahr International Parkinson's Disease Foundation
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2017. Foundation that helps junior physicians and neuroscientists continue their research on Parkinson's Disease and related disorders, with financial support for professional and intellectual development. It promotes an international community of researchers, focusing on the young enthusiastic investigators and clinicians who might otherwise be forced to abandon their ideas and efforts.
Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level.
Blog by Avery Gilbert, a sensory psychologist, taking a scientific sniff at the culture of smell. His specialty is olfaction --the strange and wonderful world of smell. He's worked in academia and the corporate world, published research in scientific journals, and written a book on the science of smell.
Annual Reviews: A Nonprofit Scientific Publisher
Annual Reviews offers comprehensive, timely collections of critical reviews written by leading scientists. It publishes authoritative, analytic reviews in 37 focused disciplines within the Biomedical, Life, Physical, and Social Sciences. The mission of Annual Reviews is to provide systematic, periodic examinations of scholarly advances in a number of fields of science through critical authoritative reviews. The comprehensive critical review not only summarizes a topic but also roots out errors of fact or concept and provokes discussion that will lead to new research activity. The critical review is an essential part of the scientific method. Sponsors: Annual Reviews is a non-profit organization created and managed by scientists to serve science by publishing reviews in 40 different scientific fields.
THIS RESOURCE IS NO LONGER IN SERVICE. Free access service resource dedicated to connect researchers creating scientific samples with scientists who need samples for their experiments. With Sample of Science researchers can submit samples, or contact scientists proposing sample for dissemination. Each disseminated sample also gets its description published in Sample of Science Bulletin, a dedicated open access journal. It acquires a Digital Object Identifier (DOI) and becomes a fully citable item. Because both adequate sample descriptions and mutually-agreed dissemination conditions are key factors for a fruitful dissemination that respects mutual interest, Sample of Science provides tools to elaborate, communicate, discuss, and refine both sample description and dissemination conditions. This process, termed peer-adoption process, results in the publication of disseminated sample descriptions in Sample of Science Bulletin, a dedicated open access publication. The publication in Sample of Science Bulletin is useful to provide adequate recognition to Sample Authors who contribute to the development of science by offering visibility to their disseminated samples. To the adopter it provides experimental details regarding the sample under the form of a citable reference useful for any future publications involving this sample. To a larger scientific community interested in material science, it provides a useful tool to stay abreast the activity of sample providers in their respective field of expertise.
Book with a downloadable version of the second edition of a practical introduction to the interdisciplinary field of computational neuroscience through the use of the GENESIS simulator. It is designed to be a step-by-step tutorial for professionals, researchers and students working in fields ranging from neuroscience to bioengineering, medicine, artificial neural networks and the cognitive sciences. Part I of the book teaches concepts in neuroscience and neural modeling by means of interactive computer tutorials on subjects ranging from neuronal membrane properties to cortical networks. These chapters, written by several contributors, allow the student to perform realistic simulations and experiments on model neural systems and provide the necessary background for understanding and using the tutorials. The simulations are user-friendly with on-line help and may be used without any prior knowledge of the GENESIS simulator or computer programming. Part II is intended to teach the use of the GENESIS script language for the construction of one's own simulations. This part will be useful for self-study by researchers who wish to do neural modeling, as well as students. It follows approximately the same sequence of topics as Part II, and uses parts of the tutorial simulations as examples of GENESIS programming. Several of these are based on recent research simulations which have been published in the neuroscience literature, but which have not been previously available for use outside the laboratories of the original researchers. Thus, the reader may modify these simulations and use them as a starting point for the development of original simulations. In addition to many revisions and additions to existing chapters, this second edition includes two new chapters on the modeling of biochemical signaling pathways and on the use of GENESIS on parallel computers and networks of workstations. Other new additions include a section describing ways to implement synaptic modification (learning), a section describing uses of a new method for modeling of a wide variety of voltage and ionic concentration dependent channels, a description of improvements in the procedure for implementing fast implicit numerical methods in GENESIS simulations, and descriptions of many new GENESIS commands and simulation components.
A web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document. It offers a comprehensive library on top of which more sophisticated systems can be built. The project provides an enhanced interactive environment that includes support for data visualization and facilities for distributed and parallel computation.
Public university in the capital of Thailand. Originally created to promote agricultural sciences, it now offers degrees in a range of fields including engineering, social sciences, business administration, and education.
An integrated resource for information on genes, QTLs and strains associated with diabetes. The portal provides easy acces to data related to both Type 1 and Type 2 Diabetes and Diabetes-related Obesity and Hypertension, as well as information on Diabetic Complications. View the results for all the included diabetes-related disease states or choose a disease category to get a pull-down list of diseases. A single click on a disease will provide a list of related genes, QTLs, and strains as well as a genome wide view of these via the GViewer tool. A link from GViewer to GBrowse shows the genes and QTLs within their genomic context. Additional pages for Phenotypes, Pathways and Biological Processes provide one-click access to data related to diabetes. Tools, Related Links and Rat Strain Models pages link to additional resources of interest to diabetes researchers.
Functional Anatomy of the Cerebro-Cerebellar System (FACCS)
Functional Anatomy of the Cerebro-Cerebellar System
Public neuroscience database providing a collection of published data describing structure and structure-function relationships in one of the largest projection systems of the brain: the cerebro-cerebellar system. It also gives access to a suite of tools that allow the user to visualize and analyze any selected combination of data sets. Contact them if you are interested in contributing data. The overall goal is to improve communication of results and permit re-use of previously published data in new contexts. FACCS is a part of the Rat Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union. The project is directed by Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
Reliable detection of directional couplings using rank statistics
Source code that allows you to calculate the different measures used in Chicharro D, Andrzejak RG (2009): Reliable detection of directional couplings using rank statistics. Physical Review E, 80, 026217.
Characterizing unidirectional couplings between point processes and flows
Source code that allows you to calculate the different measures used in Andrzejak and Kreuz 2011, http://iopscience.iop.org/0295-5075/96/5/50012
Detecting event-related time-dependent directional couplings
Source code that allows you to calculate the different measures used in Andrzejak et al 2006, http://iopscience.iop.org/1367-2630/8/1/006
Nonlinear time series analysis in a nutshell
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Source code that allows you to calculate the different measures used in Andrzejak RG (2011): Nonlinear time series analysis in a nutshell, http://www.dtic.upf.edu/~ralph/Kansas3.pdf. In: Osorio I, Zaveri H, Frei M, Arthurs S (eds.) Epilepsy: The Intersection of Neurosciences, Biology, Mathematics, and Engineering. CRC Press, Taylor & Francis Group, 125-138. http://www.taylorandfrancis.com/books/details/9781439838853/ The files allow you to calculate the nonlinear prediction error from some time series, you can generate a time series of an autoregressive process of order one and integrate the differential equation of the Lorenz dynamics.
This page provides quick access to the Comparative mapping functions available in the Map Viewer. Currently, comparative maps are calculated using HomoloGene orthology predictions. Once the gene pairs have been established, blocks of conserved syteny can be established using the positions of each gene object in their respective builds. Sponsors: This resource is supported by NCBI.
Time-resolved and time-scale adaptive measures of spike train synchrony
Source code that allows you to calculate the different measures used in Kreuz T, Chicharro D, Greschner M, Andrzejak RG (2011): Time-resolved and time-scale adaptive measures of spike train synchrony, http://www.sciencedirect.com/science/article/pii/S0165027010006564. Journal of Neuroscience Methods,195, 92-106 & Kreuz T, Chicharro D, Andrzejak RG, Haas JS, and Abarbanel HDI (2009) Measuring multiple spike train synchrony. Journal of Neuroscience Methods 183:287-299 http://www.sciencedirect.com/science/article/pii/S0165027009003616
SLqPCR - Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
Software functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH.
Association of American Medical Colleges
Not-for-profit association representing all 141 accredited U.S. and 17 accredited Canadian medical schools; nearly 400 major teaching hospitals and health systems, including 51 Department of Veterans Affairs medical centers; and 90 academic and scientific societies. Through these institutions and organizations, the AAMC represents 128,000 faculty members, 75,000 medical students, and 110,000 resident physicians. Through its programs and services, it strengthens the world's most advanced medical care by supporting the entire spectrum of education, research, and patient care activities conducted by member institutions. The AAMC and its members are dedicated to the communities they serve and steadfast in their desire to earn and keep the public's trust for the role they play in improving the nation's health. The vision of the AAMC and its members is a healthy nation and world in which: - America's system of medical education, through continual renewal and innovation, prepares physicians and scientists to meet the nation's evolving health needs. - The nation's medical students, biomedical graduate students, residents, fellows, faculty, and the health care workforce are diverse and culturally competent. - Advances in medical knowledge, therapies, and technologies prevent disease, alleviate suffering, and improve quality of life. - The nation's health system meets the needs of all. - Concern for compassion, quality, safety, efficacy, accountability, affordability, professionalism, and the public good guide the health care community.
The Ataxia Telangiectasia Children's Project, better known as the A-T Children's Project, was founded in late 1993 by a family in Florida with two young sons who have A-T. It is a public, tax-exempt, non-profit organization pursuant to Section 501(c)(3) of the Internal Revenue Code, and all gifts and donations to the Project are tax deductible. The A-T Children's Project was formed to raise funds through events and contributions from corporations, foundations and friends. These funds are then used to accelerate first-rate, international scientific research aimed at finding a cure and improving the lives of all children with ataxia-telangiectasia. - To encourage and support excellent laboratory research which will accelerate the discovery of a cure or possible therapies for ataxia-telangiectasia by: - awarding competitive research grants to top scientists using a peer-review board comprised of top scientists and physicians, - organizing and sponsoring workshops and symposiums in order to encourage cooperation among laboratories and to generate new research strategies, and - working with Congress and the National Institutes of Health to encourage the funding of active research on A-T by agencies of the U.S. government. - To improve the accurate and timely diagnosis of A-T patients by increasing public awareness and by educating physicians. - To develop and maintain an international patient registry of A-T patients with objective, neutral oversight, while leaving ultimate control in the hands of treating physicians, so that up-to-date clinical information about A-T patients can be obtained for researchers and so that when a treatment is developed, all patients can be reached through their physicians. - To support and oversee a clinical center and information clearinghouse at a top-rated, world-class medical center for the evaluation of A-T patients by a multidisciplinary team of specialists, and for the accumulation of experience in managing the many facets of A-T such as the ataxia, cancer and immune problems. - To develop quantitative endpoints for objectively measuring the progression rate and severity of the symptoms of A-T. - To maintain and enlarge a tissue/cell bank with objective, neutral oversight and control in order to ensure free access of existing and new researchers to A-T patient specimens. Sponsors: The A-T Children's Project is a non-profit organization that raises funds to support and coordinate first-rate biomedical research projects, scientific conferences and a clinical center aimed at finding a cure or life-improving therapies for ataxia-telangiectasia, a lethal genetic disease that attacks children, causing progressive loss of muscle control, immune system problems, and a strikingly high rate of cancer, especially leukemia and lymphoma.
Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.
Commercial antibody supplier based in Maryland.
An international working group dedicated to improving access to neuroimaging results in a free and open-access manner. It seeks to establish a universal coordinate database, including both past papers and future studies. Their current project involves the creation of a comprehensive database of neuroimaging results searchable based on standardized coordinates. Once complete, this will allow anyone to find all of the articles that report a coordinate, or set of coordinates, easily and without cost. Eventually, they hope to expand this database to include not only coordinates, but statistical parametric maps as well. Formation of such a database will increase the likelihood of relevant papers being found and cited, and also be a very useful tool for those interested in meta-analysis, and hopefully clarify structure-function relationships. They are interested in hearing from people who might be willing to contribute to their projects, particularly those with programming experience. The number of published neuroimaging studies is increasing rapidly and it is not feasible to read them all. If a computer database could store key information from published fMRI papers and make that information easier to search or share, this would have substantial benefits for the neuroimaging community. Projects like AMAT, Brainmap, Brede and SumsDB have started to tackle this problem. NIDAG wants to formalize and improve these databases so that they meet the needs of the neuroimaging community. Formal meta-analysis of published data is a valuable way to assess the consistency and reliability of experimental results. A database of neuroimaging results would facilitate meta-analyses, in conjunction with tools like GingerALE and Multi-level Kernel Density Analysis.
Genes to Cognition - Biological Resources
Biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6J
VHL is a library, a decentralized and dynamic information-source collection, designed to provide equitable access to scientific knowledge on health. This collection operates as an Internet network of products and services, structured to progressively meet the need for information on health on the part of authorities, administrators, researchers, professors, students, professionals, the media and the general public. It sets itself apart from other information sources available on the Internet due to its selection criteria and quality control. The Virtual Health Library is envisioned as the broad of scientific and technical knowledge based in health-entered, organized, and stored in electronic format in the countries of the Region, universally accessible on the Internet and compatible with international databases. The VHL is a common space shared by information users, producers and intermediaries. It is based on the information paradigm set by the Internet, where users may interact with networks of information sources and with other users. The most important consequence of this paradigm is the convergence of functions and activities of production, intermediation and use of information sources. It will also be possible to enrich, schedule, reformulate, and/or translate the basic information sources into new information products and services, with value added, in order to meet more efficiently the information needs of users from specific communities. BIREME has established a plan of action to implement the Virtual Health Library based on 5 lines of action: promotion and marketing; realignment of traditional products and services; production of electronic publications; development of tools for integrating and locating information; and development of other Virtual Health Library components. Sponsors: VHL is supported by the Latin-American and Caribbean Center on Health Sciences Information.
This is a database of 16S and 23S ribosomal RNA mutations reported in literature, expanded to include mutations in ribosomal proteins and ribosomal factors. Access to the expanded versions of the 16S and 23S Ribosomal RNA Mutation Databases has been improved to permit searches of the lists of alterations for all the data from (1) one specific organism, (2) one specific nucleotide position, (3) one specific phenotype, or (4) a particular author. Please send bibliographic citations for published work to be included in The Ribosomal Mutation Database to the curator via email. The database currently consists of 1024 records, including 485 16S rRNA records from Escherichia coli, 37 16S-like rRNA records from other organisms, 421 23S rRNA records from E. coli, and 81 23S-like records from other organisms. The numbering of positions in all records corresponds to the numbering in E. coli. We welcome any suggested revisions to the database, as well as information about newly characterized 16S or 23S rRNA mutations. The expanded database will be renamed to The Ribosomal Mutation Database and will include mutations in ribosomal proteins and ribosomal factors.
The Proteome 2D-PAGE Database system for microbial research is a curated database for storing and investigating proteomics data. Software tools are available and for data submission, please contact the Database Curator. Established at the Max Plank Institution for Infection Biology, this system contains four interconnected databases: i.) 2D-PAGE Database: Two dimensional electrophoresis (2-DE) and mass spectrometry of diverse microorganisms and other organisms. This database currently contains 4971 identified spots and 1228 mass peaklists in 44 reference maps representing experiments from 24 different organisms and strains. The data were submitted by 84 Submitters from 24 Institutes and 12 nations. It also contains various software tools that are important in formatting and analyzing gels and mass peaks; software include: *TopSpot: Scanning the gel, editing the spots and saving the information *Fragmentation: Fragmentation of the gel image into sections *MS-Screener: Perl script to compare the similarity of MALDI-PMF peaklists *MS-Screener update: MS-Screener can be used to compare mass spectra (MALDI-MS(/MS) as well as ESI-MS/MS spectra) on the basis of their peak lists (.dta, .pkm, .pkt, or .txt files), to recalibrate mass spectra, to determine and eliminate exogenous contaminant peaks, and to create matrices for cluster analyses. *GelCali: Online calibration of the Mr- and pI-axis of 2-DE gels with mathematical regression methods ii.)Isotope Coded Affinity Tag (ICAT)-LC/MS database: Isotope Coded Affinity Tag (ICAT)-LC/MS data for Mycobacterium tuberculosis strain BCG versus H37Rv. iii.) FUNC_CLASS database: Functional classification of diverse microorganism. This database also integrates genomic, proteomic, and metabolic data. iv.) DIFF database: Presentation of differently regulated proteins obtained by comparative proteomic experiments using computerized gel image analysis.
Biocatalogue - The Life Science Web Services Registry
Crowd-curated catalog of life sciences Web services with over 2400 service entries, thereby enabling users (people and programs) to discover and use these services easily. It provides a platform with several (standardized) interfaces and a suite of tools for registration of services by the community of users as well as empowers the community to extend and enhance the system. BioCatalogue provides a centralized biological web services market place which is accessible to the world as it is searchable and indexable to search engines. Additionally, it provides a quality of service standard for biological web services thereby enabling services to be classified and checked for availability, reliability and other quality measures. Primary goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Providers, Expert curators and Users will provide oversight, monitor the catalog and provide high quality annotations for services. * BioCatalogue is a place where the community can find contacts and meet the experts and maintainers of these services.
5 prime end Serial Analysis of Gene Expression Database
5'end Serial Analysis of Gene Expression Database
5end Serial Analysis of Gene Expression Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 30, 2012. A database that displays the observed frequencies of individual 5' end SAGE tags and previously unknown transcription start sites in the promoter regions, introns and intergenic regions of known genes. 5'SAGE will be useful for analyzing promoter regions and start site variation in different tissues, and is freely available.
Community standard for pathway data sharing. Standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Supports data exchange between pathway data groups and thus reduces complexity of interchange between data formats by providing accepted standard format for pathway data. Open and collaborative effort by community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in RDF/XML format.Uses W3C standard Web Ontology Language, OWL.
An Internet library offering the general public access to historical collections that exist in digital format including texts, audio, moving images, and software. Additionally it provides archived web pages in their collections, and specialized services for adaptive reading and information access for the blind and other persons with disabilities. Founded in 1996 and located in San Francisco, the Archive has been receiving data donations from Alexa Internet and others. In late 1999, the organization started to grow to include more well-rounded collections.
rSeqDiff: Detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test
An R package that can detect differential gene and isoform expressions from RNA-seq data of multiple biological conditions. The approach considers three cases for each gene: 1) no differential expression, 2) differential expression without differential splicing and 3) differential splicing.
Tools processing MRI data with a number of techniques from cvpr conference, including segmentation, matching, features, and classification.
The Brain Dynamics Centre (BDC) is a network of centers and units. It achieves a unique exploration of the healthy brain and disorders of brain function. It translates these insights into new ways to tailor treatments to the individual. There approach is: "integrative neuroscience" - bringing together clinical observations, theory, and modern imaging technologies. And it's theoretical framework derives from linking physiology, psychology and evolution. Additionally, BDC also actively researches ADHD and conduct disorder, stress and trauma-related problems, depression and anxiety, anorexia nervosa, psychosis (including early onset) and conversion disorders. The research facilities DBC include assessment, rooms, two cognition-brain function laboratories, genotyping and an MRI Suite with 1.5 and 3T GE systems. BDC is the coordinating site for an international network - BRAINnet. It has over 180 members, and coordinates access to the first standardized database on the human brain for scientific purposes: Brain Resource International Database.
Software designed to display most medical images, including MRI, CT, X-ray, and ultrasound. All versions of ezDICOM can automatically detect the format of a medical image and display it on the screen. The software is easy to use, mature, and can view a wide range of medical images including proprietary formats as well as images in the DICOM standard. The software will also automatically recognize and display Analyze, GE (LX, Genesis), Interfile, Siemens (Magnetom, Somatom) and NEMA images.
Conrad Prebys Center for Chemical Genomics
The Conrad Prebys Center for Chemical Genomics (CPCCG) uses advanced screening technologies to identify high level chemical probes that interact with proteins involved in cellular processes. Optimization of these probes using medicinal chemistry and informatics will form the basis of a new generation of medicines. CPCCG is 1 of 4 Comprehensive Centers chosen nationally to be a part of the Molecular Libraries Probe Program (MLP), which established the Molecular Libraries Probe Production Centers Network (MLPCN). The goal is to produce small molecule probes that allow research into health and disease on the cellular level. CPCCG core services span a range of biochemical and cell-based screens for obtaining hits and provide chemistry resources for optimizing hits into probes or drug development. - Full scale screening capabilities and technology which can provide rapid screening on a broad diversity of assays and detection platforms - Several fully-integrated industrial-scale high-throughput screening (HTS) workstations - HTS microscopy/HCS and novel algorithm development for image analysis - Full hit-to-probe chemistry and exploratory pharmacology - Powerful NMR based Chemical Fragment Screening - Highly integrated informatics infrastructure and efficient data mining capabilities - Protein production facility - Cell production facility for scale-up tissue culture The CPCCG Screening Core can screen 96, 384 or 1536 well formats using either biochemical or cell-based assays, and can process over 300,000 wells per day. Total throughput capacity will climb to over 2 million compounds per day following the opening of Burnhams east coast campus in Lake Nona, Florida.
Sanford-Burnham Neuroscience and Aging Research Center
Del E. Webb Neuroscience Aging and Stem Cell Research Center
Sanford-Burnham Del E. Webb Neuroscience Aging and Stem Cell Research Center
Center that translates basic science discoveries into new treatments to extend lifespan and to combat degenerative disorders associated with aging or development. Their researchers are discovering the etiological pathways as well as small-molecule and stem cell-based treatments to address the clinical unmet need of these patients. The Center uses a team based approach to apply their expertise in stem cells to develop therapies for new treatments for stroke and Parkinson's disease. They are also performing high-throughput screens to identify new molecules to protect the synapses of nervesthe connections between nerves that mediate movement, memory and cognition for Alzheimer's, Parkinson's and autism. By studying the links between Down syndrome and Alzheimer's disease, they are exploring new treatments to improve cognition in both disorders. Their collaborations with clinical partners enable them to test new discoveries in human trials, with a goal to improve the lives of patients and families affected by neurodegenerative disease and aging disorders.
Functional Image Processing software Computational Olio
Collection of software designed to analyze fMRI data using a series of processing steps. The input is the raw data, and the outputs are statistical brain maps showing regions of neural activation. Corrections for different systematic variations in the k-space (raw) data obtained from an fMRI session (head motion, ghosting, etc) are performed first. The image is then reconstructed (using the Fast Fourier Transform) and statistical analyses run. The user has a great deal of flexibility in choosing which corrections and statistics are executed. FIASCO emphasizes correct statistical models, for example for group comparisons.
AffinDB - Affinity Database For Protein-Ligand Complexes
Database of affinity data for protein-ligand complexes of the Protein Data Bank (PDB) providing direct and free access to the experimental affinity of a given complex structure. Affinity data are exclusively obtained from the scientific literature. As of Thursday, May 01st, 2014, AffinDB contains 748 affinity values covering 474 different PDB complexes. More than one affinity value may be associated with a single PDB complex, which is most frequently due to multiple references reporting affinity data for the same complex. AffinDB provides access to data in three different forms: # Summary information for PDB entry # Affinity information window # Tabular reports
FABA: Four-dimensional Ascidian Body Atlas
Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate.
Archaeal and Bacterial ABC Transporter Database
Archaeal and Bacterial ABC Systems database
ABCdb is a public resource devoted to the ATP-binding Cassette (ABC) transporters encoded by completely sequenced prokaryotic genomes. In order to establish, in a complete genome, the repertory of ABC systems, we have to: i) identify the different partners, ii) assemble the partners in putative systems, and iii) classify the system into the correct functional subfamily (Quentin et al., 2002). The main pitfalls were the identification of loosely conserved domains and the assembly of partners encoded by genes dispersed over the chromosome. In order to face the avalanche of newly sequenced genomes, we decided to also feed into the database the raw prediction issued by this automatic procedure, before time consuming review by an expert occurs. Therefore, the database comprises two sections: CleanDb, for data checked by an expert and AutoDb for raw data. The ABC proteins are involved in a wide variety of physiological processes in Archaea, Bacteria and Eucaryota where they are encoded by large families of paralogous genes. The majority of ABC domains energize the transport of compounds across membranes. In bacteria, ABC transporters are involved in the uptake of a wide variety of molecules, as well as in mechanisms of virulence and antibiotic resistance. In eukaryotes, most of them are involved in drug resistance and in human cell, many are associated with diseases. Sequence analysis reveals that members of the ABC superfamily can be organized into sub-families, and suggests that they have diverged from common ancestral forms. A typical ABC transporter system is composed of an assembly of protein domains that serve different functions: i) two Nucleotide Binding Domains (NBD) that energize transport via ATP hydrolysis, ii) two Membrane Spanning Domains (MSD) that act as a membrane channel for the substrate, and iii) for the importer, a Solute Binding Protein (SBP) that confers substrates specificity on the transporter. The different partners of an ABC system are generally encoded by neighboring genes. The database includes information on: * ABC transporters * Protein partners * Protein domains (NBD, MSD and SBP) * Classification of ABC transporters and their protein partners * Taxonomy of the species Each model Protein includes a link to the Peptide sequence, general information extracted from EMBL files, and specific tags to store results of predictions. The results of the annotation procedure are reachable through the class Prediction. The origin of the proteins is modeled as a path through the classes Chromosome, Strain, Species, and Taxon. Assembly and protein compilation tables are also provided for each of the chromosomes ( Assembly and Protein ).
A ChIP-seq peak caller for detection of megabase domains of enrichment.
A Classification of Mobile genetic Elements
ACLAME: A CLAssification of Mobile genetic Elements
A database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. Prophinder, a tool dedicated to the detection of prophages in sequenced bacterial genomes, is available on ACLAME.
Pedigree Editor for LInkage Computer ANalysis
Software utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN. It can read in and write out pedigree files, saving changes that have been made to the structure of the pedigree. Changes are made to the pedigree via a graphical display interface. The resulting display can be saved as a pedigree file and as a graphical image file.
Geospatial software for monitoring and modeling the Earth system. Includes tools for GIS, image processing, surface analysis, vertical applications for land change analysis and earth trends exploration, and more.
Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays
Cold Spring Harbor Protocols - Behavioral Assays
A bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format.
Public university in Ohio providing undergraduate and graduate degrees, as well as access to various institutes.
Cerebellar Gene Regulation in Time and Space Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Time-series data sets spanning twelve time-points between E12-P9 for exploring cerebellar development of the mouse in time and space. The database contains a number of mutant / wildtype microarray datasets including two complete wildtype microarray time-series (C57BL/6 and DBA/2J). The dataset also includes in situ hybridization and bioinformatic analyses. Exploration of this dataset will allow the investigator to assess differential gene expression profiles from a developing mutant cerebella, to assess the temporal changes in gene expression in the wildtype, and to verify the cellular expression of these genes in images from our in situ hybridization library. Using the database, the investigator can explore the developmental expression or differential expression patterns of a particular gene, or create lists of similarly expression genes by building simple search algorithms. These lists can then be mined across all the datasets in both space and time. Cb GRiTS's current datasets represent gene expression analyses from multiple cerebellar mutant and wildtype single time-point and developmental series.
THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Digital research archive for cerebellar research including mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation.
Chemistry Structures and 3D Molecules at 3Dchem.com
A to Z Index of Structures at 3Dchem.com
Chemistry Structures 3D Molecules (at) 3Dchem.com
Chemistry Structures & 3D Molecules (at) 3Dchem.com
A database that provides various information about more than 400 drugs, structures and molecules. Links are available for Molecules of the Month, A to Z Index of Structures, Top 50 Prescription Medicines, Gallery, Library of Inorganic Structures (over 1600 structures), Interactive 3D Periodic Table, 3D Stereo Glasses, Desktop Wallpaper, Medical advice and Search 3Dchem.com.
Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.
rlsim - a package for simulating RNA-seq library preparation with parameter estimation
Software package for simulating RNA-seq library preparation with parameter estimation.
VUIIS (Vanderbilt University Institute of Imaging Science) Image and Data Analysis Core's data processing tools written for MATLAB and, unless stated otherwise, capable of processing 2D/3D images (matrices). These tools are written for ease of use from within MATLAB.
Chilibot: Gene and Protein relationships from MEDLINE
Chilibot - Mining PubMed for relationships
Data analysis service that searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords using a NLP-based text-mining approach. The results are returned as a graph. The synonym database used in Chilibot is available, without fee, for academic use only. Several different search methods are supported including: * searching for relationship between two genes, proteins or keywords * searching for relationships between many genes, proteins, or keywords * searching for relationships between two lists of genes, proteins, or keywords Advanced options include: * Automated hypothesis generation (graph) * Restricting context using keywords * Providing your own synonyms * Modifying synonyms provided by Chilibot * Color coding nodes with gene expression values * Special search: modulation
unifiedWMWqPCR - Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.
The Phelan-McDermid Syndrome Foundation, established in 2002, is a 501(c)3 nonprofit group that provides support services for those who have family members affected by 22q13 Deletion Syndrome / Phelan-McDermid Syndrome. It also raises money to further awareness of the syndrome through research and sponsoring an international conference every two years that brings together families, researchers and therapists. The Foundation facilitates connections between families through networking, communications and support services. We also build alliances with other rare diseases groups to expand our reach and exposure. The syndrome, which affects families worldwide, is a rare genetic occurrence and is the result of a damaged or missing protein on the 22nd chromosome. Our Foundation works with researchers who are looking into the cause and possible cure for the syndrome. PMSF's grants and fellowships program is intended to encourage research projects that will advance the development of treatments and cures for PMS. Our mission is to bring together everyone affected by 22q13 Deletion Syndrome/Phelan-McDermid Syndrome to help them through the challenges they face every day and to raise awareness in the medical and research communities.
Database that provides 3-dim reconstructions of thalamic and neocortical neurons. These cells were reconstructed from 80-micron serial sections using a computerized tracing system, as well as a Neurolucida tracing system. The dendritic morphology and diameters were reconstructed in 3-dim using a X 100 objective and correction for tissue shrinkage was included, leading to a theoretical accuracy of 0.1 microns on dendritic diameters. The morphology and the modeling of these cells is described in the references given for each cell. The NEURON geometry of these cells are also available. Anyone is welcome to use these geometries in models.
DA works to relieve and to prevent depression by providing information and support services to those who are affected by it via their publications, supporter services and network of self-help groups for people affected by depression. Depression Alliances services help people to understand, work with and recover from symptoms associated with depression. Depression Alliance believes that the stigma and lack of accurate information surrounding depression continues to prevent people from seeking and finding appropriate and vital help when it is required. Early intervention and information are crucial in enabling those affected by depression to recover quickly and critically in preventing further episodes. Informed by the experiences of people with depression and by research, DA works extensively with government agencies and healthcare professionals to improve the service provision for those affected by depression. DA also campaigns to raise awareness amongst the general public about the realities of this severe and enduring illness by organizing a variety of events and initiatives.
A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software)
German Collection of Microorganisms and Cell Cultures
Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
The DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures) is the most comprehensive biological resource center in Europe. With more than 18.000 microorganisms, 1.200 plant viruses, 600 human and animal cell lines, 770 plant cell cultures and more than 7.100 cultures deposited for the purposes of patenting, DSMZ has demonstrated their obligation to serve science for decades. Main functions of DSMZ are: - to collect, maintain and store microorganisms and cell lines, as well as other biological material of relevance for applied biology, biotechnology, microbiology, teaching and other areas of research and general application; - to keep the scientific and industrial community informed on the contents of the collections by the means of catalogs, special lists, databases or electronic media; - to supply scientists and institutions with DSMZ cultures, in accordance with national and international laws such as the Infektionsschutzgesetz (Act dealing with protection against infection), the Genetic Engineering Act, the Foreign Trade Laws, the Convention on Biological Diversity as well as the DSMZ terms of supply; - to function as an internationally recognized collection center for the deposit of microorganisms, cell lines, and other biological material which have been cited in scientific literature or which are used in national or international test procedures (e.g. type strains, reference strains for national and international quality control regulations or susceptibility tests, strains with special properties, such as the production of enzymes, degradation of pollutants, host strains for plasmids, etc.); - to act as an International Depositary Authority (IDA) for the deposit of biological material for patent purposes according to the Budapest Treaty; - to act, in a confidential manner, as a center for the safe deposit of biological material; - to act as an advisory center for the scientific community and to offer teaching and service facilities. The DSMZ collections contain over 26 000 cultures (including 6500 patent deposits) representing more than 16 000 cultures of microorganisms (Archaea, Bacteria, plasmids, phages, yeasts, fungi), 750 plant cell cultures, 600 plant viruses, 700 antisera and 580 human and animal cell lines. Unique subcollections are held in the prokaryotes groups of acidophiles, alkaliphiles, halophiles, methanogens, phototrophs, thermophiles, and sulfate reducers. The research is focused on collection related fields which include: - Taxonomy - Evolution - Phylogeny - Microbial diversity and molecular assessment of diversity - Molecular systematics - Research on pathobiological aspects of leukemia-lymphoma cell lines applying classical and molecular genetics, immunological and cell biological methods * Development of cultivation and preservation methods for biological material * Characterization and identification of biological material
Duke University of North Carolina Brain Imaging and Analysis Center Core Facility
Brain Imaging and Analysis Center (BIAC)
Duke University of North Carolina Brain Imaging and Analysis Center
BIAC strives for excellence in its dual mission of research and service. BIAC faculty members are leaders in imaging methodology development, in analysis techniques, as well as in their application in cognitive and clinical neurosciences. In addition, BIAC offers imaging service to other imaging faculty members on campus and at the University of North Carolina in Chapel Hill.
Center for Advanced Magnetic Resonance Development
Department of Radiology: Center for Advanced Magnetic Resonance Development
Duke Center for Advanced Magnetic Resonance Development
DUMC Center for Advanced Magnetic Resonance Development
Research facility of the Department of Radiology at the Duke University Medical Center (DUMC) providing access to a whole-body, commercially manufactured 3 Tesla (Trio, Siemens Medical Systems) MR Imaging and Spectroscopy System with full research capability. The Center is fully equipped to perform clinical and research MR imaging or spectroscopy studies on humans or large animals. A full range of monitoring, anesthesia, RF coil development, computer and instrumental control facilities as well as MR research technologists and physics/chemistry consultation are available to Department of Radiology researchers and their collaborators.
A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)
Software package to apply the QL, QLShrink and QLSpline methods to quasi-Poisson or quasi-negative binomial models for identifying differentially expressed genes in RNA-seq data.
Duke University Medical Center: Duke Image Analysis Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Duke Image Analysis Laboratory (DIAL) is committed to providing comprehensive imaging support in research studies and clinical trials to various agencies. The capabilities of the lab include protocol development, site training and certification, and image archival and analysis for a variety of modalities including magnetic resonance imaging, magnetic resonance spectroscopy, computed tomography and nuclear medicine. DIAL uses the latest technologies to analyze Magnetic Resonance Imaging (MRI) data sets of the brain. Currently the lab is engaged in measurement of the hippocampus, amygdala, caudate, ventricular system, and other brain regional volumes. Each of these techniques have undergone a rigorous validation process. The measurements of brain structures provide a useful means of non-invasively testing for changes in the brain of the patient. Changes over time in the brain can be detected, and evaluated with respect to the treatment that the patient is receiving. Magnetic Resonance Spectroscopy (MRS) allows DIAL to obtain an accurate profile of the chemical content of the brain. This sensitive technique can detect small changes in the metabolic state of the brain; changes that vary in response to administration of therapeutic agents. The ability to detect these subtle shifts in brain chemistry allows DIAL to identify changes in the brain with more sensitivity than allowed by image analysis. In this respect, NMR spectroscopy can provide early detection of changes in the brain, and serves to compliment the data obtained from image analysis. Additionally, DIAL also contains SQUID (Scalable Query Utility and Image Database). It is an image management system developed to facilitate image management in research and clinical trials: SQUID offers secure, redundant image storage and organizational functions for sorting and searching digital images for a variety of modalities including MRI, MRS, CAT Scan, X-Ray and Nuclear Medicine. SQUID can access images directly from DUMC scanners. Data can also be loaded via DICOM CDs, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
eBioNews specializes in online information services and resource exchanges in the fields of life sciences and biotechnology. By applying its knowledge database and content management system (CMS), eBioNews offers readers and customers the organized and comprehensive information. eBioNews also provides a membership-based service to assist our customers in information and data search, processing, storage, and sharing. Generally, eBioNews covers the following areas: - life science frontiers - news and discussions - features and specials - resources and sourcing - career development - academic and industry - training and education Additionally, eBioNews information is organized into the following two clusters: - News Center: 1. Headlights 2. Research Frontiers 3. General Research 4. Clinical Development 5. Enterprise & Industry 6. Products & Services 7. Investment & Financials 8. Features 9. Newsletter The News Center consists of the elements and mechanisms that enable collecting, organizing, displaying, and delivering life science related information, data, and knowledge. - Resource Center: 1. eBioResources 2. Cooperation 3. Events 4. Human Resources 5. Intellectual Property 6. Finance & Legal 7. Operations 8. Organization 9. Publication The Resource Center is a system that hosts and facilitates the resource-related information between and among multiple parties, especially for promoting cooperation, collaboration, consortium, partnering, joint venture, licensing, out-sourcing, and trading. Sponsors: This resource is supported by eBioCenter Corporation.
Kent State University School of Biomedical Sciences; Ohio; USA
Graduate school in biomedical sciences at Kent State University with programs in neurosciences, physiology, biological anthropology, cellular molecular, and pharmacology.
sSeq - Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Software package to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.
Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
MCMC.qpcr: Bayesian analysis of qRT-PCR data
Software package that implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a classic model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results.
Arabidopsis GeneNet Supplementary DataBase
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 5, 2017.
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data
A software package that uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.
Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology
ENFIN is a virtual institute to enable systems-level integration of experimental results. It is committed to provide a Europe-wide integration of computational approaches in systems biology. Its objectives are: - To develop a shared approach between traditionally dry and traditionally wet researchers in the area of systems-level interpretation of experimental results - To develop a distributed computational platform this integration and analysis of experimental data - To directly prove that such an approach has scientific value - To encourage and participate in the critical assessment of systems-level approaches - To disseminate knowledge and techniques to other academic researchers worldwide - To disseminate knowledge and techniques to commercial researchers, in particular European SMEs - To train young European researchers from a variety of backgrounds in system-level informatics techniques. The ENFIN Network runs four major platforms: A Joint Research Program covering the fields of Discrete Function Prediction, Network Reconstruction, Systems-Level Modeling, a Provision of Analysis Tools - EnSUITE, a Platform for Data Integration - EnCORE, and training Courses and Workshops on Systems Biology. Sponsors: The ENFIN project is funded by the European Commission within its FP6 Programme, under the thematic area Life sciences, genomics and biotechnology for health,contract number LSHG-CT-2005-518254.
FunDO - Exploring Genes Using Functional Disease Ontology Annotations
Tool that takes a list of genes and finds relevant diseases based on statistical analysis of the Disease Ontology annotation database. It accepts Entrez gene ids or gene symbols, separated by tabs, newlines, or commas. This list of genes can be obtained by microarray, proteomics, sequencing or other high-throughput screening methods.
Tool for quantification of human miRNA-mRNA Interactions. TaLasso is also available as Matlab or R code.
Extracellular Matrix Interactions Database
MatrixDB: Extracellular Matrix Interactions Database
Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules.
A public curated compilation of allele frequency data on anthropologically defined human population samples linked to the molecular genetics-human genome databases. Only data on well defined population samples that are large enough to yield reasonably accurate frequencies and for polymorphisms sufficiently defined to be replicable can be included in ALFRED. Researchers wishing to have their data entered into ALFRED should contact them. Initially, ALFRED contained primarily data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data. Data from the published literature are being entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation. ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching. ALFRED provides easy searching options including versatile "Keyword search" and also has numerous summary tables providing quick overviews of contents by chromosome, population, average heterozygosity, Fst and others, all available under various tabs from the ALFRED homepage.
A collection of open source software tools for creating and managing genome-scale biological databases. GMOD is made up databases, applications, and adaptor software that connects these components together. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. At first GMOD just featured model organisms but now any organism with any kind of sequence associated with it is a good candidate as a subject for a GMOD database. There are GMOD databases with just protein sequence in them, with EST sequence only, those that are concerned primarily with gene expression, and even those dedicated to collections of RNA sequence. They have also heard of GMOD databases for oligonucleotides and plasmids.
Harvard Medical School, Department of Systems Biology: The Megason Lab - MegaCapture Software
MegaCapture is a VisualBasic macro developed for automating the acquisition of in toto image sets. It is useable on Zeiss microscopes using LSM v4.x software (pre-Zen). MegaCapture can automatically acquire image sets across any combination of dimensions including x, y, z, time, color, x-tile, y-tile, row, and column. Images are exported on the fly and can be compressed allowing very large (100,000 images) image sets to be captured. Sponsors: MegaCapture is supported by Harvard University.
Portal of neuroscience and neurology resources pertaining to the University of Eastern Finland.
Some of the alternate ORFs predicted to be genes by automatic annotation programs are subsequently culled by human curators; however, many escape even expert curation. AlterORF provides a database of such potentially mis-annotated ORFs. It has warehoused all alternate ORFs in fully sequenced microbial genomes that have significant hits with one or more of the protein features described in CDD, COG, KOG, PFAM, PRK and SMART in which the corresponding annotated genes that have been deposited in the databases have no such characteristics Some of the alternate ORFs that have significant protein features (CDD, COG, etc.) are associated with annotated genes that also have significant protein features, making it moot which is the real gene. Some of these instances are potentially dual function genes in which both ORFs may be expressed (e.g. ref). AlterORF identifies these possibilities for further computational and experimental investigation. All data present in AlterORF and database files and tables can be download in a compressed file. Please take in account that the complete database has ~ 300 GB. AlterORF operate 132 cpu cluster contributed by Microsoft as part of a sponsored research program. The Center for Bioinformatics and Genome Biology is a member of the Ibero- Latin American Bioinformatics Network (RIB), the Virtual Institute for Integrative Biology (VIIB) and the E-science Infrastructure Shared Between Europe and Latin America (EELA-2).
Provides informationa about Genome of California Purple Sea Urchin, one species (Strongylocentrotus purpuratus) of which has been sequenced and annotated by Sea Urchin Genome Sequencing Consortium led by HGSC. Reports sequence and analysis of genome of sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology.
Application programming interface that gives one programmatic access to the article level metrics data associated with articles and datasets collected by Altmetric. It extracts, disambiguates and collates mentions of scholarly works online, allowing one to focus on one's core product.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Integrated database of experiment data generated by participating research institutes and public databases relating to: 1) transcription starting position of human genes in the human genome, 2) conjunction to control region on transcriptional factors and the human genome 3) protein-protein interaction with a central focus on transcription factors organized for use in genome level research. Gene Search is the function to search the integrated database by using keywords and public IDs. The search results can be visualized by: * Genome Explorer : provides annotation of landmarks (genes, transcription start sites, etc.) aligned in accordance with their genome locations. * PPI Network : provides a graphical view of protein-protein interaction (PPI) network from the experimental data generated under the project and the public datasets. * Expression Profile : clusters genes by expression pattern and display the result with heatmap. The function provides genes which have relation of coregulation and anti-coregulation. * Comparison Viewer : This function gives the view to compare the genomic regions between human and mouse homologous genes. The viewer shows the distribution of transcription start sites (TSS) as the way of separable by tissues or time points with other landmarks on genome region. * Gene Stock : This is the function to save the gene list that you are interested until the session is closed.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R code for Bayesian modeling of paired RNA-seq experiments.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R software package for detecting and correcting biases in RNA-Sequencing data.
Linkage and Association Modeling in Pedigrees
Software for linkage and association modeling in pedigrees that uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.
George Mason University: Krasnow Institute for Advanced Study
The Krasnow Institute seeks to expand understanding of mind, brain, and intelligence by conducting research at the intersection of the separate fields of cognitive psychology, neurobiology, and the computer-driven study of artificial intelligence and complex adaptive systems. These separate disciplines increasingly overlap and promise progressively deeper insight into human thought processes. The Institute also examines how new insights from cognitive science research can be applied for human benefit in the areas of mental health, neurological disease, education, and computer design. It is this informed access to mind and brain that is the core of the mission of The Krasnow Institute. While their goals and tools are scientific, they also are fully cognizant of the applications of the results for the benefit of mankind, in areas like mental health, neurological diseases, and computer design. In asking the major questions they realized the necessity of being flexible, innovative, and trans-disciplinary. Therefore, they became dedicated to bringing together scholars from a wide variety of specialties and providing a milieu where they can be both productive and interactive. This institute will provide these researchers with the tools required to move ahead and create an environment of optimal scientific integrity coupling innovation with risk taking. The Krasnow institute is especially attuned to the deep insights from evolutionary biology, which is at the root of understanding all organismic functions including cognition; computer studies of complex systems, which present a revolution in our ability to deal with the world of interactive agents; and a long history of cognitive psychology, which provides a huge data base of human abilities and responses. It also continues to develop its long-term research program based on the contributions of George Mason University faculty holding joint appointments at Krasnow and other GMU academic departments. Additionally, the Krasnow Institute Department of Molecular Neuroscience, together with the College of Science (COS) and the College of Humanities and Social Sciences (CHSS), oversees the campus-wide Neuroscience Council in developing the Neuroscience PhD curriculum. Research groups in the Krasnow institute include: - Adaptive Systems Laboratory - Center for Neural Dynamics - Center for Social Complexity - Center for the Study of Neuroeconomics o Neuroeconomics Laboratory - Comparative Vertebrate Neurobiology Research Group - Center for Neuroinformatics, Neural Structures, and Neuroplasticity (CN3) o Computational and Experimental Neuroplasticity (CENlab) o Computational Neuroanatomy Group o Physiological and Behavioral Neuroscience in Juveniles (PBNJ) Lab - Receptor Complexes and Signaling Lab - Krasnow Investigations of Developmental Learning and Behavior (KIDLAB) - Neuro Imaging Core of the Krasnow Institute
Online portal of the software resources provided by Hanchuan Peng's lab. Program functions include 3D image rendering, MATLAB toolboxs, image annotator, and cell explorer atlas and building tools.
plateCore - Statistical tools and data structures for plate-based flow cytometry
Software that provides basic S4 data structures and routines for analyzing plate based flow cytometry data.
King's College London; London; United Kingdom
Public research university located in London, United Kingdom that offers undergraduate, graduate, and professional degree programs in medicine, economics, social sciences, etc.
This portal leads to the Internet Atlas of Histology. This atlas allows you to explore the complete set of histological specimens that features many excellent plastic sections prepared by Aulikki Kokko-Cunningham, M.D. Also called University of Illnois at Urbana-Champaign, the College of Medicine: Internet Atlas of Histology Over 1000 labeled histological features are labeled and have accompanying functional descriptions. All of this information is accessible though an alphabetical index and a search engine. This resource has images categorized in: - Slides: Links to all of the specimens - Objects:Index of histological features Sponsors: This resource is supported by UIUC.
Kidney and Urinary Pathway Knowledge Base
A collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made.
Online portal resource with hierarchically-organized list of links to web resources concerning neurological disorders.
Animal Quantitative Trait Loci (QTL) database
Database of trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into public databases before paper may be accepted for publication. User curator accounts are provided for direct data deposit. Users can download QTLdb data from each species or individual chromosome.
Data management software that runs the Pathway Commons web service. It makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Main features: * Import pipeline capable of aggregating pathway and interaction data sets from multiple sources, including: MINT, IntAct, HPRD, DIP, BioCyc, KEGG, PUMA2 and Reactome. * Import/Export support for the Proteomics Standards Initiative Molecular Interaction (PSI-MI) and the Biological Pathways Exchange (BioPAX) XML formats. * Data visualization and analysis via Cytoscape. * Simple HTTP URL based XML web service. * Complete software is freely available for local install. Easy to install and administer. * Partly funded by the U.S. National Cancer Institute, via the Cancer Biomedical Informatics Grid (caBIG) and aims to meet silver-level requirements for software interoperability and data exchange.
Database with quantitative binding data for peptides binding to various cells including MHC Ligand, TCR-MHC complexes, T-cell epitopes, TAP, B-cell, and immunological protein-protein interactions. Information in each entry includes peptide libraries, copy numbers, and diffusion coefficient data.
Medical Image Processing and Visualization in Virtual Environments
This resouce will centralize development of tools for interaction with medical imaging data in immersive virtual environments (based on the Vizard platform).
Online portal and image database of coronal sections of the sheep brain. Each image contains stained sections of cell bodies and myelinated fibers; nuclei and tracts are labeled.
Database for Antisense Oligonucleotides Selection and Design
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. AOBase is a database for antisense oligonucleotides (AOs) selection and design. AOBase is a database developed to facilitate Antisense Oligonucleotides (ODNs) selection for gene expression modulation and to provide a free data source for computer aided ODNs design. Information about valid and invalid ODNs reported in literature are collected and stored in the database, including oligo sequences, target sequences, secondary structures of the target sites, oligo activity measured, and the assay type used for activity measurement. The details on target RNA molecules and reference literature can be explored through the hyperlinks linked to GenBank and PubMed respectively. Each record can be searched for via two web retrieval interfaces: 1) TargetSearch interface, which allows users to query ODNs by name, accession number, or only imprecise descriptions of its target RNA; 2) AOSearch interface, which allows users to search ODNs with several parameters combined, such as oligo activity measured, oligo concentration applied, and motifs involved in oligo sequences. With these two retrieval interfaces, AOBase can be used to select effective ODNs for gene function exploration without expensive in vitro screening experiments, and contribute to mining rules for rational ODNs design. A user friendly interface to encourage data submission is provided.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19. 2022. Platform to promote studies on dynamic principles of brain functions through unifying experimental and computational approaches in cellular, local circuit, global network and behavioral levels. Provides services such as data sets, popular research findings and articles and current developments in field. This site has been archived since FY2019 and is no longer updated.
International Neuroinformatics Coordinating Facility: Blue Gene/L Access
Through this site, INCF provides he neuroinformatics community with access to an IBM Blue Gene/L supercomputer. INCF owns a share of a BlueGene/L (BG/L) supercomputer located at the Parallel Computer Center (PDC) at The Royal Institute of Technology (KTH) in Stockholm. Allocations are now available through the INCF Secretariat. During an initial evaluation phase, a limited numbers of large-scale computing projects will be selected, based on the suitability of the project for supercomputing. Research groups with limited access to supercomputers at their home institutions are given priority. Approved projects are regularly re-evaluated. New projects are approved based on availability and usage load of the BG/L. The Blue Gene/L supercomputer project is aimed at expanding the horizon of high-performance computing to unprecedented levels of scale and performance. Blue Gene/L is the first supercomputer in the Blue Gene family. The full Blue Gene/L consists of 64 racks containing 65,536 high-performance compute nodes. Each node (nodes and chips are the same in the Blue Gene system) contains two embedded 32-bit PowerPC processors. Furthermore, the same chip that is used for compute nodes is also used for the 1,024 I/O nodes. A three-dimensional torus network and a collective network are used to interconnect all nodes. The full system contains 33 terabytes of main memory; it is designed to achieve 183.5 teraflops peak performance using one of the processors of each node for computation and the other processor for communication, and 367 teraflops using both processors for computation. Another key architectural feature of this supercomputer is the link chip component and five Blue Gene/L networks, the PowerPC 440 core and floating-point enhancements, the on-chip and off-chip distributed memory system, the node- and system-level design for high reliability, and the comprehensive approach to fault isolation. One of the key objectives in Blue Gene/L design is to achieve cost/performance comparable to the COTS (Commodity Off The Shelf) approach, while at the same time incorporating a processor and network combination so powerful that it revolutionizes the performance of supercomputer systems. Sponsors: This resource is supported by the INCF.
Software that allows large scale neuron simulators to communicate during runtime. It allows exchange of data among parallel applications in a cluster environment, interconnects large-scale neuronal network simulators with each other or with other tools, participates in multi-simulations, and is continuously developed and extended. Three simulators currently have MUSIC interfaces: Moose, NEURON and NEST. Three applications execute in parallel while exchanging data via MUSIC. The software interface promotes interoperability by allowing models written for different simulators to be simulated together in a larger system. It enables re-usability of models or tools by providing a standard interface. As data are distributed over a number of processors, it is non-trivial to coordinate data transfer so that it reaches the correct destination at the correct time. Current and future simulators can make use of MUSIC - compliant general purpose tools and participate in multi-simulations, for example when: * Different parts of a complex nervous system model are optimally implemented in different simulators, and need to communicate with each other. * Post-processing of generated data is needed, where the amounts of data are too large for intermediate storage, and requires the simulator to pass the data directly to the post-processing module. A standard interface enables straight-forward independent third-party development and community sharing of interoperable software tools for parallel processing. * Library and utilities are written in C++, uses MPI. * It is possible to add a MUSIC interface to existing simulators. * Works independently, no assumptions are made about other applications to facilitate development of general purpose tools. * Performance Data transport with high bandwidth and low latency.
plink - Whole genome association analysis toolset
Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.
King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia
King Abdullah University of Science and Technology
Private research university in Thuwal, Saudi Arabia that offers undergraduate and graduate degree programs in Biological and Environmental Science and Engineering (BESE), Computer, Electrical, and Mathematical Science and Engineering (CEMSE), and Physical Science and Engineering (PSE).
A Markov Chain based software tool for haplotyping, genotype imputation and disease association analysis that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.
International Union of Physiological Sciences: Physiome Project
The Physiome Project is a worldwide public domain effort to provide a computational framework for understanding human and other eukaryotic physiology. It aims to develop integrative models at all levels of biological organization, from genes to the whole organism via gene regulatory networks, protein pathways, integrative cell function, and tissue and whole organ structure/function relations. Additionally, an important goal of the project is to develop applications for teaching physiology. Current projects include the development of: - ontologies to organize biological knowledge and access to databases - markup languages to encode models of biological structure and function in a standard format for sharing between different application programs and for re-use as components of more comprehensive models - databases of structure at the cell, tissue and organ levels - software to render computational models of cell function such as ion channel electrophysiology, cell signaling and metabolic pathways, transport, motility, the cell cycle, etc. in 2 & 3D graphical form - software for displaying and interacting with the organ models which will allow the user to move across all spatial scales Sponsors: This project is supported by the International Union of Physiological Sciences (IUPS), the IEEE Engineering. in Medicine and Biology (EMBS), and the International Federation for Medical and Biological Engineering (IFMBE)
Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis.
User-contributed list of biological databases available on the internet. Currently there are 1,801 entries, each describing a different database. The databases are described in a semi-structured way by using templates and entries can carry various user comments and annotations. Entries can be searched, listed or browsed by category. The site uses the same MediaWiki technology that powers Wikipedia, The Mediawiki system allows users to participate on many different levels, ranging from authors and editors to curators and designers. MetaBase aims to be a flexible, user-driven (user-created) resource for the biological database community. The main focuses of MetaBase are: * As a basic requirement, MB contains a list of databases, URLs and descriptions of the most commonly used biological databases currently available on the internet. * The system should be flexible, allowing users to contribute, update and maintain the data in different ways. * In the future we aim to generate more communication between the database developer and user communities.
Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution.
Intute: The Best Web Resources For Education and Research
Intute is a free online service that helps you to find the best web resources for your studies and research. It was created in response to users' needs and the changing Internet information environment. With millions of resources available on the Internet, it can be difficult to find useful material. The Intute subject specialists review and evaluate thousands of resources to help you choose the key websites in your subject. Intute can also help you develop your Internet research skills through our Virtual Training Suite tutorials, written by lecturers and librarians from universities across the UK. The discipline focus of their service is delivered through four new subject groups: * Science, Engineering and Technology (including geography) * Arts and Humanities * Social Sciences * Health and Life Sciences Intute is created by a consortium of seven universities, working together with a whole host of partners. The Intute consortium includes: * University of Birmingham * University of Bristol * Heriot-Watt University * The University of Manchester * Manchester Metropolitan University * University of Nottingham * University of Oxford Sponsors: Intute is funded by the Joint Information Systems Committee (JISC).
Aphid genome database. Facilitates community annotation of pea aphid genome by International Aphid Genomics Consortium (IAGC). It aims to store recently acquired genomic resources on aphids and compare them to other insect resources as functional annotation tools. AphidBase Information System designed to organize and distribute genomic data and annotations for large international community was constructed using open source software tools from Generic Model Organism Database (GMOD).
Java framework for building Semantic Web applications, it provides a collection of tools and Java libraries to help you to develop semantic web and linked-data apps, tools and servers. It provides extensive Java libraries for helping developers develop code that handles RDF, RDFS, RDFa, OWL and SPARQL in line with published W3C recommendations. Jena includes a rule-based inference engine to perform reasoning based on OWL and RDFS ontologies, and a variety of storage strategies to store RDF triples in memory or on disk. The Jena Framework includes: * an API for reading, processing and writing RDF data in XML, N-triples and Turtle formats; * an ontology API for handling OWL and RDFS ontologies; * a rule-based inference engine for reasoning with RDF and OWL data sources; * stores to allow large numbers of RDF triples to be efficiently stored on disk; * a query engine compliant with the latest SPARQL specification * servers to allow RDF data to be published to other applications using a variety of protocols, including SPARQL In April 2012, Jena graduated from the Apache incubator process and was approved as a top-level Apache project.
Finding Associated Concepts with Text Analysis
Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/
Prediction of Amyloid Structure Aggregation
Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence.
Journal of Cerebral Blood Flow and Metabolism
The Journal of Cerebral Blood Flow & Metabolism stands at the interface between basic and clinical neurovascular research, and features timely and relevant research highlighting experimental, theoretical, and clinical aspects of brain circulation, metabolism and imaging. The journal is relevant to any physician or scientist with an interest in brain function, cerebrovascular disease, cerebral vascular regulation and brain metabolism, including neurologists, neurochemists, physiologists, pharmacologists, anesthesiologists, neuroradiologists, neurosurgeons, neuropathologists and neuroscientists. On this website, you will find the full text of articles published online weekly, in advance of print, the current issue and an archive of previous issues. You can also find general information about the journal, and more detailed information for readers, authors, referees, librarians, advertisers, and journalists. Most articles are published online before they appear in print. New papers are uploaded weekly to the Advance online publication (AOP) page. The online publication date is specified for each paper; these versions are identical to the printed version in every respect and may be cited using the digital object identifier (DOI).
A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions.
Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.
An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An M software package for Clustering 16S rRNA sequences into operational taxonomic units (OTUs). The download link contain the package and some benchmark data sets.
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets
RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.
Neurolucida is advanced scientific software for brain mapping, neuron reconstruction, anatomical mapping, and morphometry. Since its debut more than 20 years ago, Neurolucida has continued to evolve and has become the worldwide gold-standard for neuron reconstruction and 3D mapping. Neurolucida has the flexibility to handle data in many formats: using live images from digital or video cameras; stored image sets from confocal microscopes, electron microscopes, and scanning tomographic sources, or through the microscope oculars using the patented LucividTM. Neurolucida controls a motorized XYZ stage for integrated navigation through tissue sections, allowing for sophisticated analysis from many fields-of-view. Neurolucidas Serial Section Manager integrates unlimited sections into a single data file, maintaining each section in aligned 3D space for full quantitative analysis. Neurolucidas neuron tracing capabilities include 3D measurement and reconstruction of branching processes. Neurolucida also features sophisticated tools for mapping delineate and map anatomical regions for detailed morphometric analyses. Neurolucida uses advanced computer-controlled microscopy techniques to obtain accurate results and speed your work. Plug-in modules are available for confocal and MRI analysis, 3D solid modeling, and virtual slide creation. The user-friendly interface gives you rapid results, allowing you to acquire data and capture the full 3D extent of neurons and brain regions. You can reconstruct neurons or create 3D serial reconstructions directly from slides or acquired images, and Neurolucida offers full microscope control for brightfield, fluorescent, and confocal microscopes. Its added compatibility with 64-bit Microsoft Vista enables reconstructions with even larger images, image stacks, and virtual slides. Adding the Solid Modeling Module allows you to rotate and view your reconstructions in real time. Neurolucida is available in two separate versions Standard and Workstation. The Standard version enables control of microscope hardware, whereas the Workstation version is used for offline analysis away from the microscope. Neurolucida provides quantitative analysis with results presented in graphical or spreadsheet format exportable to Microsoft Excel. Overall, features include: - Tracing Neurons - Anatomical Mapping - Image Processing and Analysis Features - Editing - Morphometric Analysis - Hardware Integration - Cell Analysis - Visualization Features Sponsors: Neurolucida is supported by MBF Bioscience.
Living Links: Center for the Advanced Study of Ape and Human Evolution
The primary mission of the Living Links Center is to study human evolution by investigating our close genetic, anatomical, cognitive, and behavioral similarities with great apes. The Living Links Center was established for primate studies that shed light on human behavioral evolution. It is an integrated part of the Yerkes National Primate Research Center, which is the nation's oldest and largest primate center. The Living Links Center is home to two socially housed groups of chimpanzees and two socially housed groups of capuchin monkeys. The research conducted in this center is broken down into four categories: - Chimpanzees: Chimpanzee research at the Living Links Center is conducted at the Yerkes Field Station, which is home to two socially housed chimpanzee groups known as FS1 and FS2. Each mixed gender group of 12 individuals lives in a large outdoor enclosure with wooden climbing structures and play objects attached to an indoor sleeping area. FS1 and FS2 can hear, but not see each other because their enclosures are ~200m apart and separated by a small hill. Chimpanzee research is conducted on a volunteer basis with members of each group. - Elephants: This newly found presence of mirror self-recognition in elephants, previously predicted due to their well-known social complexity, is thought to relate to empathetic tendencies and the ability to distinguish oneself from others. As a result of this study, the elephant now joins a cognitive elite among animals commensurate with its well-known complex social life and high level of intelligence. Although elephants are far more distantly related to us than the great apes, they seem to have evolved similar social and cognitive capacities making complex social systems and intelligence part of this picture. These parallels between humans and elephants suggest a convergent cognitive evolution possibly related to complex sociality and cooperation. - Capuchin Monkeys: Though there are several different species of capuchin monkey, the one most widely studied in captivity by Living Links, is the brown, or tufted, capuchin (Cebus apella). - Collaborative Projects: projects with collaborators around the world. Sponsors: This center is supported by the Yerkes National Primate Research Center.
RSVSim: an R/Bioconductor package for the simulation of structural variations
A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.
Note: ApiDots is currently unavailable. For data on apicomplexan EST assemblies, please see EuPathDB ApiDots is a database integrating mRNA/EST sequences from numerous Apicomplexan parasites. ESTs and mRNAs were clustered and further assembled to generate consensus sequences. These consensus sequences were then subjected to database searches against protein sequences and protein domain sequences. The underlying relational structure of this database allows researchers to analyze these data and pose biologically interesting questions.
TCC: Differential expression analysis for tag count data with robust normalization strategies
An R package that provides a series of functions for differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq).
Software package that provides the significance analysis of sequencing data with spike-in normalization. The statistical backgrounds and the benefits depend on SAMseq of the samr package.
The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection. Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds, and even entire organisms.
Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.
MEME Suite - Motif-based sequence analysis tools
Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.
PoissonSeq: Significance analysis of sequencing data based on a Poisson log linear model
Software package that implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data.
Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory
The In-Vivo Molecular Imaging Laboratory (IMIL) is a MSSM shared resource facility serving the research community of Mount Sinai with equipment and imaging expertise. State-of-the-art bioluminescent as well as fluorescent imaging modalities are supported for in-vivo monitoring of cellular and genetic activity. Investigators are provided with cutting edge imaging technologies as well as analysis techniques. The long-term goal is to establish a comprehensive SRF for in-vivo molecular imaging using micro-MRI, micro-PET and other modalities. IMIL houses a Xenogen IVIS-200 Series imaging system with the integrated fluorescent imaging options. Simultaneous dual reporter in-vivo imaging is possible with bioluminescence and fluorescence probes. The imaging chamber has a gas anesthesia manifold that can accommodate up to 5 mice for simultaneously image acquisition. Selectable field of views allow in-plane (X,Y) imaging resolutions of up to 60-microm. Integrated spectra filters allow for the determination of signal source depth (Z). IMIL will provide data acquisition services as well as analysis. IMIL has a dedicated imaging technologist for data acquisition. Investigators will bring their prepared animal to the lab and an IMIL imaging technologist will assist in sedating the animals and acquire imaging data. Typical imaging sessions last about an hour. Certified users who are trained in the use of the software will be able to perform their own analysis at the console. Usage of the imaging device is charged by the hour ($100/hour). Structural Imaging The IVIS-200 has the built-in capability of obtaining an image of the surface topography of the animal for 2D and 3D localization. If additional true 3D imaging data is required, micro MRI is available through the Imaging Science Laboratories (ISL). Image Analysis The IVIS-200 has an integrated image acquisition and analysis software (Living Image Software 2.50). Comprehensive data quantification is possible with this software. Raw data as well as analyzed results can be electronically transferred to the investigators. Support is also available for additional image analysis such as intermodality coregistration, 3D rendering, and group statistics. Additional software packages include MedX, SPM, Brainvoyager, Analyze, and in-house developed software.
A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.
Software to characterize the genetic variation of alternative splicing using a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. It takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data.
Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.
BEAGLE Genetic Analysis Software Package
Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).
R analysis and processing package for Illumina platform Chip-Seq data.
Mouse Genome Informatics: MouseCyc database
A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database.
Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions.
Database of proteins found in the nucleoli of Arabidopsis, identified through proteomic analysis. The Arabidopsis Nucleolar Protein database (AtNoPDB) provides information on the plant proteins in comparison to human and yeast proteins, and images of cellular localizations for over a third of the proteins. A proteomic analysis was carried out of nucleoli purified from Arabidopsis cell cultures and to date 217 proteins have been identified. Many proteins were known nucleolar proteins or proteins involved in ribosome biogenesis. Some proteins, such as spliceosomal and snRNP proteins, and translation factors, were unexpected. In addition, proteins of unknown function which were either plant-specific or conserved between human and plant, and proteins with differential localizations were identified.
Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs.
Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation.
National Center for e-Social Science: Obesity e-Lab
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Obesity e-Lab is a unique, secure environment for producing, sharing, communicating and finding obesity research between epidemiologists, public health researchers and social scientists. Features of e-Lab: - Tools to share: it enables social and biomedical researchers to share data, information and analytical tools for obesity research. First, it will create a portal to provide access to the platform and facilitate social networking. - Navigation tools: Second, it will generate search and navigation tools for researchers in academic, NHS or local government organizations to find data from administrative and secure data services, via social science views of health datasets, and health science views of social datasets. Within the NHS, e-Lab links records from a variety of administrative and health (and social) care sources for broadly-specified obesity research, and make pseudonymised extracts of NHS-linked datasets available via the portal. - Analytical tools: Third, it will develop analytical tools, focused on: i) easy, reliable and privacy-protecting transformation of geo-codes in health records to other geographies and area-based social and economic measures; ii) epidemiological extensions to geographical information systems; iii) growth-standardization of child obesity measures. The tool-building will employ as much existing software as possible, focusing on the provision of simple, intuitive interfaces to proven software to make it easy for social or biomedical researchers to use collaboratively.
Software for integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.
A Digital Warehouse of Auditory Models and Data
EarLab: A Digital Warehouse of Auditory Models and Data
EarLab: A Digital Warehouse of Auditory Models Data
Freely-accessible auditory databases as well as custom designed modeling and data analysis software tools. A fully functional online auditory modeling environment is also available, as well as downloadable models in several languages. The models cover many aspects of auditory function and at many different levels of detail ranging from multi-compartment celluar models to high-level abstractions of large portions of the auditory pathway. Currently a few models are available that can be run online and others are available for downloading. EarLab also provides custom cross-platform software for creating your own distributed auditory modeling environment, as well as software for analyzing the results from experimentation. A database of auditory modules is available for online use or download for the distributed auditory modeling environment, as well as instructions and specifications for creating your own modules. All these databases and custom software tools can be used in a wide variety of hearing research applications. This unique resource provides a wealth of information on auditory processing in humans and other animals. Mathematical models are also provided.
A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)
Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system.
Combinatorial Polyfunctionality Analysis of Single Cells
COMPASS - Combinatorial Polyfunctionality Analysis of Single Cells
COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells
Software for combinatorial polyfunctionality analysis of single cells. It is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. It uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.
Consensus Assessment of Sequence And VAriation
Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting
National Society of Genetic Counselors (NSGC)
Professional society of genetic counselors that promotes networking, continuing education opportunities, advocacy, and discussion of relevant issues in the field of genetics.
National Institutes of Health Stroke Scale
The National Institutes of Health Stroke Scale (NIHSS) is a systematic assessment tool that provides a quantitative measure of stroke-related neurological deficit. The NIHSS was originally designed as a research tool to measure baseline data on patients in acute stroke clinical trials. Now, the scale is also widely used as a clinical assessment tool to evaluate acuity of stroke patients, determine appropriate treatment, and predict patient outcome. The NIHSS can be used as a clinical stroke assessment tool to evaluate and document neurological status in acute stroke patients. The stroke scale is valid for predicting lesion size and can serve as a measure of stroke severity. The NIHSS has been shown to be a predictor of both short and long term outcome of stroke patients. Additionally, the stroke scale serves as a data collection tool for planning patient care and provides a common language for information exchanges among healthcare providers. Performing the scale takes between 5-8 minutes. Emergency physicians and nurses, neurologists, neuroscience nurses and other stroke team members are typical examples of who should be certified to perform the NIHSS. The NINDS/NIH training and testing DVD can be obtained from the National Institute of Neurological Disorders and Stroke. Sponsors: NIHSS is supported by the National Institute of Neurological Disorders and Stroke (NINDS).
Neural Engineering with Louisiana North Excellence Consoritium
This Consortiums objectives are to 1)synergistically enhance neuroscience research and neural engineering development activities in North Louisiana, 2) design and create via a multi-disciplinary team approach, better and more versatile techniques for studying and activating the nervous system, 3) refine these techniques in a collaborative and iterative manner; 4) use these techniques to advance our understanding of the nervous system in its normal, hypoxic and ischemic states; and 5) design neuroprostheses. By bringing engineers, life scientists, and clinicians together, the Consortium pursues a multimodal approach to neuroscience that enables a deeper understanding of normal and pathological neural conditions and opens new doors in the study and treatment of neurological impairment. It attacks a discrete set of problems that have been outside of the reach of neuroscience research, and propose solutions through the judicious application of neural engineering. And it is developing innovative techniques for minimally-invasive, fast-response, precisely localizable, wide-aperture, chronic measurement and stimulation of neural activity. These New Lanes are the novel methods and microdevices for monitoring and under-standing neural function, and providing potential functional replacements. By employing micro- and nano-system techniques, the NewLANE Consortium provides NewLANEs novel methods for monitoring various aspects of neuronal activity that are more sensitive, reliable, and versatile than currently available and novel met-hods for providing potential functional replacements all of which have direct applicability to the US veteran population. Sponsors: Funding comes from various sources including a VA Sr. Rehab. Research Career Scientist award.
Collection of tools to support all tasks associated with a neural simulation project, which are not handled by the simulation engine. NeuroTools is written in Python and works best with PyNN and other simulation engines with a Python front-end such as NEURON, NEST, PCSIM, BrainScaleS Neuromorphic VLSI, Brian, MOOSE/GENESIS, and Neurospaces/GENESIS. NeuroTools provides modules to facilitate simulation setup, parameterization, data management, analysis and visualization. The data-related tools are equally suited to analysis of experimental data.
flowClust - Clustering for Flow Cytometry
A Bioconductor software package for automated gating of flow cytometry data that implements a robust model-based clustering approach based on multivariate t mixture models with the Box-Cox transformation.
Neural Systems and Graphics Computing Laboratory: Atlas3D Software
A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.
A splice alignment software tool of RNA-Seq reads mapping.
SPADE - An analysis and visualization tool for Flow Cytometry
Spanning tree Progression of Density normalized Events
An analysis and visualization software tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes.
Neural Systems and Graphics Computing Laboratory: Micro3D Software
The Micro3D 2004 is a software for 3-D reconstruction, visualization, and analysis of neuronal populations and brain regions. Micro3D generates geometric models from line and point coded data sets, representing labeled objects such as cell bodies or axonal plexuses, and boundaries of brain regions in serial sections. Data are typically imported from image-combining computerized microscopy systems, such as Neurolucida (MicroBrightField, Colchester, VT). The models may be rotated and zoomed in real-time. Surfaces are re-synthesized on the basis of stacks of contour lines. Clipping is used for defining section-independent subdivisions of the model. Flattening of sheets of points in curved layers (e.g., neurons in a cortical lamina) facilitates inspection of complicated distribution patterns. Micro3D computes color-coded density maps, and allows production of mpeg videos. Micro3D 2004 runs on LINUX PCs equipped with Open Inventor. It performs operations similar to the Silicon Graphics based version that has been used in more than 25 investigations and in various species, ranging from insects to monkeys, at the LM- and EM-level. Sponsors:Micro 3D was developed with support from The Research Council of Norway and The Oslo Research Park / FORNY.
Brain Machine Interface Platform (BMI PF)
Databases of accumulating BMI (Brain Machine Interfaces)-related experimental data, mathematical models, and tools generated in neuroscience, computational theory, and robotics. Databases include: # Database of BMI (Brain Machine Interfaces)-related papers: More than 3500 BMI-related papers are registered. Each paper has original tags, for example, recording method and subject, for easy searching. # Database of original contents: BMI-related materials (Movie, Picture, Data, Program) provided by scientists. # Database of BMI-related research sites: 185 BMI-related research sites in the world (university, institute and company) are registered. The research site can be searched either by the location using clickable map or by the field of interest. # Database of BMI-related materials: Links to BMI-related materials (Movie, Picture, Document, Data, Program) are listed. You can easily find materials of your interest since each material is classified into research field. # BMI-related column: The columns are written by researchers specialized in BMI. Original contents include: * Neuronal activity during performance of a memory-guided movement * Reconstructed visual images from human fMRI activity * fMRI data and program for visual image reconstruction * Brain sections of monkeys, stained for several gene markers * Cortical Box Method: The Cortical box method is an analytical method that standardizes the serial coronal sections of rodent cortex for quantitative analysis. * Multineuron activity in monkey prefrontal cortex * Monkey Atlas: **Brain sections of monkeys, stained for AChE, ER81 mRNA and Sema3E mRNA - These pictures are low-resolution photos of serial brain sections of monkeys, stained for AChE as well as for ER81 and Sema3E mRNAs. The compressed file contains JPEG photos and html files for web browser navigation. Other materials are available at our website BraInSitu dedicated for in situ hybridization resources for brains. BraInSitu http://www.nibb.ac.jp/brish/indexE.html ** MRI Brain Atlas of Japanese Snow Monkey (Macaca Fuscata) at different ages - MRI Brain Atlas of Japanese Snow Monkey (Macaca Fuscata) at different ages ** The Stereotaxic MRI Brain Atlas of Japanese Snow Monkey - The Stereotaxic MRI Brain Atlas of Japanese Snow Monkey * Monkey M1 BMI ** m-file for checking the results of wrist angle estimation- This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/uln ** m-file for training of wrist angle estimation -This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation.ar deviation. ** M1 Neuronal Activity during monkey performing a motor task - video/x-ms-wmv ** Muscle tension - To estimate muscle tension from raw emg signal ** raw EMG signal - Raw EMG signal for 5 seconds ** training data of wrist angle and emg signal - This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation. ** Weight file of neural network - This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation. * Multineuron activity in monkey prefrontal cortex: Multineuron activity in monkey prefrontal cortex recorded by 3 tetrodes. Vertical 4 lines indicate one tetrode. Adjacent tetrodes are around 500 micron apart to each other.
Private non-sectarian and coeducational university based in Higashiosaka, Osaka, Japan.
Alternative Splicing transcriptional landscape visualization tool
Tool that extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, it detects the variations in their splicing structure and identifies all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. It provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase, etc.
CLUSTAG: Hierarchical Clustering and Graph Methods for Selecting Tag SNPs
Software application that uses hierarchical clustering and graph methods for selecting tag SNPs (single nucleotide polymorphisms). Cluster and set-cover algorithms are developed to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2 > C with at least one tag SNP, where C is specified by the user. The program is implemented with Java, and it can run in Windows platform as well as the Unix environment.
NLMorphologyConverter is a simple command-line program for converting between the various neuron morphology data formats which are used to describe the three-dimensional physical branching structure of biological neurons. The aim is to provide coverage of all formats, old and new, in which data is available online, and/or which are supported by free and commercial software packages (e.g. software for neuron reconstruction, generation, simulation, visualization, and analysis of neuron morphology). Permission is granted for this software to be freely copied. Main Features Currently 21 different morphology file formats fully or partially supported. Automatic detection of input file format. Faithful reproduction of output file formatting. Many command line options for manipulating the imported data Intensively tested using over 10000 publicly available morphology data files. Sponsors. This software is supported by NeuronLand.
NeuroExplorer: Neurophysiological Data Analysis Package
Data analysis software for neurophysiology with a multitude of features, including: * Import of native data files created by many popular data acquisition systems * All standard histogram and raster analyses * Shift predictors in crosscorrelograms and color markers in perievent rasters * Joint PSTH, burst analysis and many more analyses of timestamped data * Spectral analysis of spike and continuous data * 3D data view and animation * Fully customizable WYSIWYG graphics * Custom analysis and batch mode processing with internal scripting language * Direct data link to Matlab and Excel * Statistical tests via direct link to R-project
Neuroscience Postdoctoral Researcher Jobs
Interactive web site that brings together tools that graduate students can use to find jobs and that potential students can use to select graduate programs. The site also includes links to excellent resources on networking, writing a curriculum vita, interviewing and writing grants.
A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
A motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and DNase-Seq data.
Office of Research on Womens Health: Reseach
The mission of the Office of Research on Women's Health (ORWH) is to stimulate and encourage meritorious research on women's health, including the role of sex and gender in health and disease. The priorities signify approaches and areas for which there is a need to stimulate and encourage research on women's health, or sex/gender factors, and the advancement of women in biomedical research careers. These research priorities are not an exclusive list of research areas important to women's health; therefore other innovative or significant research areas should also be considered. The following four overarching themes are important for addressing research on women's health: Lifespan, Sex/Gender Determinants, Health Disparities/Differences and Diversity, ad Interdisciplinary Research. Special Areas of Emphasis - Prevention/Treatment: from basic biological factors, including identifying and validating biomarkers, to risk and its applications to disease prevention, early detection, and treatment. - Sex and Genetics/Pharmacogenomics: genetic, molecular, and cellular basis for action of pharmacologic agents known to have different effects in females than in males. Research on effects of sex as a modifier of gene function and response is under-investigated. Sponsors: This research is funded by the NAtional Institutes of Health.
Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages.
A place where people connected to cancer can share real-life experiences -- fears, insights, stories, and advice. Adding perspectives is easy, and every contribution builds the site into a more valuable and unique community resource. Content, resources, and support on wikiCancer: * Just been diagnosed with cancer? * Living with cancer * For cancer survivors * How to support someone with cancer * Connect with other cancer patients, survivors, family and caregivers
Online Encyclopedia for Genetic Epidemiology studies
OEGE - Online Encyclopedia for Genetic Epidemiology studies
Portal for researchers to locate information relevant to interpretation and follow-up of human genetic epidemiological discoveries, including: a range of population and case and family genetic epidemiological studies, relevant gene and sequence databases, genetic variation databases, trait measurement, resource labs, journals, software, general information, disease genes and genetic diversity.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. This is a directory of 5311 free online papers on consciousness in philosophy and in science, and of related topics in the philosophy of mind. The papers in this directory are drawn from PhilPapers, a database of both online and offline works in philosophy. Sponsors: Sponsored by the Joint Information Systems Committee as part of the Information Environment Programme.
Dindel: Accurate indel calls from short-read data
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems).
PDC operates leading-edge, high-performance computers on a national level. PDC offers easily accessible computational resources that primarily cater to the needs of Swedish academic research and education. PDC also takes part in major international projects to develop high-performance computing for the future and stay a leading national resource in parallel computing.
A model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any "thing", whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation.
FMRISTAT - A general statistical analysis for fMRI data
A Matlab toolbox for the statistical analysis of fMRI data. The fMRI data was first converted to percentage of whole volume. The statistical analysis of the percentages was based on a linear model with correlated errors. The design matrix of the linear model was first convolved with a hemodynamic response function modelled as a difference of two gamma functions timed to coincide with the acquisition of each slice. Temporal drift was removed by adding a cubic spline in the frame times to the design matrix (one covariate per 2 minutes of scan time), and spatial drift was removed by adding a covariate in the whole volume average. The correlation structure was modelled as an autoregressive process of degree 1. At each voxel, the autocorrelation parameter was estimated from the least squares residuals using the Yule-Walker equations, after a bias correction for correlations induced by the linear model. The autocorrelation parameter was first regularized by spatial smoothing, then used to "whiten" the data and the design matrix. The linear model was then re-estimated using least squares on the whitened data to produce estimates of effects and their standard errors. In a second step, runs, sessions and subjects were combined using a mixed effects linear model for the effects (as data) with fixed effects standard deviations taken from the previous analysis. This was fitted using ReML implemented by the EM algorithm. A random effects analysis was performed by first estimating the the ratio of the random effects variance to the fixed effects variance, then regularizing this ratio by spatial smoothing with a Gaussian filter. The variance of the effect was then estimated by the smoothed ratio multiplied by the fixed effects variance. The amount of smoothing was chosen to achieve 100 effective degrees of freedom. The resulting T statistic images were thresholded using the minimum given by a Bonferroni correction and random field theory, taking into account the non-isotropic spatial correlation of the errors.
PANDORA Matlab Toolbox and Other Utilities
Matlab toolbox for analyzing neuronal electrophysiology data and constructing databases.
A U.S. organization which funds Parkinson's disease research and provides materials and services to patients. PDF funds research through: research centers at major universities; early-career investigators that devote their talents to the study of Parkinsons; funding independent investigators through the International Research Grants Program; and collaboration with other organizations on innovative projects.
A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.
OrderedList - Similarities of Ordered Gene Lists
An R / bioconductor package for detecting similarity in ordered gene lists. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.
PathCase - Metabolic Pathway Database System
An integrated software system for storing, managing, analyzing, and querying biological pathways at different levels of genetic, molecular, biochemical and organismal detail. The system contains a pathways database and associated tools to store, compare, query, and visualize metabolic pathways. The aim is to develop an integrated database and the associated tools to support computational analysis and visualization of biochemical pathways. At the computational level, PathCase allows users to visualize pathways in multiple abstraction levels, and to pose predetermined and ad hoc queries using a graphical user interface. Pathways are represented as graphs, and implemented as a relational database. The available functional annotations include the identity of the substrate(s), product(s), cofactors, activators, inhibitors, enzymes or other processing molecules, GO-categories of enzymes (as well as GO hierarchy visualizations two-way-linked to PathCase enzymes), EC number information and the associated links, and synonyms and encoding genes of gene products.
Non-profit private university in Istanbul, Turkey that offers undergraduate and graduate degree programs in sciences, humanities, engineering, social sciences, medicine, and nursing.
PhosphoSitePlus: Protein Modification Site
A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published.
The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species. The system also aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data. Sponsors: ArkDB is funded by Biotechnology and Biological Sciences Research Council (BBSRC), UK. Cat, Chicken, Cow, Deer, Duck, Horse, Pig, Quail, Salmon, Sea Bass, Sheep, Turkey, QLT map, Linkage map, RH map, Farm animal, Genome map, Sequence, Mapping
Psychology Training - VA Fellowships and Internships
VA provides Internships, Postdoctoral Fellowships, and Practicum Training in many sites across the U.S. With about 470 internship positions at 93 locations and 260 postdoctoral fellowship positions at 65 sites funded each year, VA is the largest provider of training in Psychology in the nation. We have continued to expand our training opportunities and added 70 additional positions for the 2011-2012 academic year. These positions included additional internship and postdoctoral positions within existing training programs and the development of new internship programs in Boise ID, Canandaigua NY, Columbia SC, Huntington WV, Indianapolis IN, Madison WI, Philadelphia PA, Tuscaloosa AL, and West Palm Beach FL. In the meantime, the four internships started in 2008 (Anchorage AK, Asheville NC, Iowa City IA, and Richmond VA) have graduated their second classes and have now begun their third year. The internship program in Richmond is accredited through 2017. The other three programs do not yet have APA accreditation, but all have begun the accreditation process. In the interim, graduates of these programs will be eligible for employment as psychologists within the Department of Veterans Affairs just as are graduates from accredited programs. All existing VA Internship and many Postdoctoral Psychology training programs hold APA accreditation status.
Service and training support for academic, government, and private sector scientists worldwide in genomics, including laboratory experimentation, statistical analysis, and comprehensive bioinformatics support, including large-scale genome comparisons, algorithm and tools development, and database curation, annotation and hosting. The Centre for Applied Genomics hosts a variety of databases related to ongoing supported projects: *Autism Chromosome Rearrangement Database *Cystic Fibrosis Mutation Database *The Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database *Database of Genomic Variants *The Chromosome 7 Annotation Project *Human Genome Segmental Duplication Database *Non-Human Segmental Duplication Database Healthy control DNA samples from the Ontario Population Genomics Platform are available. The Biobanking and Databasing Facility provides DNA extraction from lymphoblasts, fibroblasts and other cell types, archiving of white cell pellets, preparation and immortalization of cell lines, and comprehensive databasing and tracking of samples and/or cell lines within the facility.
It aims to help researchers to utilize information more efficiently from the published association data. This database is freely accessible only for academic users under the GNU GPL PADB indexes the sentences containing "associat*" or "case-control*" or "cohort*" or "meta-analysis" or "systematic review" or "odds ratio*" or "hazard ratio*" or "risk ratio*" or "relative risk*" from PubMed abstracts and automatically extracts the numeric values of odds ratios, hazard ratios, risk ratios and relative risks data when available. PADB automatically identifies HUGO official symbols of human genes using NCBI Entrez Gene data, and each gene is linked to the UCSC genome browser and International HapMap Project database. Furthermore, molecular pathways listed in BioCarta or KEGG databases can be accessed through the link using CGAP gene annotation data. Also, each record in PADB is linked to GAD or HPLD if it is available from those databases. Currently, (Last Update of Database Contents : Dec. 20, 2006) PADB indexes more than 1,500,000 abstracts including about 190,000 risk values ranging from 0.00001 to 4878.9 and 3,442 human genes related to 461 molecular pathways. Sponsors: This work was supported by the Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea and a faculty research grant of Yonsei University College of Medicine for 2006, Seoul, Korea.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits.
THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
LinkHub: A Semantic Web System that facilitates cross-database queries and information retrieval in proteomics
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. LinkHub is a software system using Semantic Web RDF that manages the graph of identifier relationships and allows exploration with a variety of interfaces. It leverages Semantic Web standards-based integrated data to provide novel information retrieval to identifier-related documents through relational graph queries, simplifies and manages connections to major hubs such as UniProt, and provides useful interactive and query interfaces for exploring the integrated data. For efficiency, it is also provided with relational-database access and translation between the relational and RDF versions. LinkHub is practically useful in creating small, local hubs on common topics and then connecting these to major portals in a federated architecture; LinkHub was used to establish such a relationship between UniProt and the North East Structural Genomics Consortium. LinkHub also facilitates queries and access to information and documents related to identifiers spread across multiple databases, acting as connecting glue between different identifier spaces. LinkHub is available at hub.gersteinlab.org and hub.nesg.org with supplement, database models and full-source code. Sponsors: Funding for this work comes from NIH/NIGMS grant P50 GM62413-01, NIH grant K25 HG02378, and NSF grant DBI-0135442.
Laboratory that aims to understand the function of the cortical microcircuit by reverse-engineering of the cortical microcircuit using the mouse neocortex in vitro and in vivo as their experimental preparations. The techniques applied are electrophysiology, anatomy, and a variety of optical methods, including infrared-DIC, voltage- and ion-sensitive dye imaging with confocal, two-photon and second harmonic microscopy. They also use laser uncaging, biolistics, electroporation, electron microscopy and numerical simulations, and make extensive use of genetically modified mouse strains. They focus is on two major questions: (1) What is the function of dendritic spines? (2) What are the multicellular patterns of activity under spontaneous or evoked activation of the circuit? Resources include: * Cell Reconstructions: Cell Database, PDF Images, .DAT Files * Circuit Diagrams: Full Circuit Diagram, Inhibitory Circuit Diagram, Excitatory Circuit Diagram, Simplified Circuit Diagram, Layer to Layer Simplified Circuit, Circuit diagram references
Alt Event Finder: A tool for extracting alternative splicing events from RNA-seq data
Software tool for deriving data-driven alternative splicing (AS) events from RNA-seq data. It analyses the transcripts built by Cufflinks or Scripture and outputs AS event annotations which is compatible with MISO. It can be used for annotating novel AS events from a well-annotated species such as human. It can also be used for species of which known AS event annotation is not available. The current release (v0.1) supports skipped exon events only.
Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS.
MedMOLE improves the comprehension of microarray experimental results by grouping co-regulated genes on the basis of the informational content of MEDLINE documents. The tool relies on two components: a gene name extractor and a mining algorithm. The name extractor is based on existing dictionaries of gene names and aliases. The mining algorithm analyses the co-occurrences of words in the selected documents in order to automatically interpret the context, identify where the gene names appear, and map documents/genes into functional classes. DNA microarray technology is a high throughput method for gaining information on gene function. This large amount of data can be analyzed to identify groups of genes that share common expression characteristics, but the obtained results provide little information regarding the presence of functional biological correlations of genes within clusters. The published literature, on the other hand, provides a potential source of information to assist in interpretation of clustering results. We have developed a tool (MedMOLE) that improves the comprehension of microarray experimental results by grouping co-regulated genes on the basis of the informational content of MEDLINE documents. The tool relies on two components: a gene name extractor and a mining algorithm. The name extractor is based on existing dictionaries of gene names and aliases. The mining algorithm analyses the co-occurrences of words in the selected documents in order to automatically interpret the context, identify where the gene names appear, and map documents/genes into functional classes. Microarray transcriptional profiling is a powerful tool used in the study of transcriptional control mechanisms. An important point in the analysis of microarray data is the identification of hidden correlations between the differentially expressed genes generated upon some kind of cell stimulus. Functional annotation is an important topic for microarray data mining, however this is quite limited for complex organisms (e.g. H. sapiens, M. musculus) where a limited number of genes are well characterized and annotated. However, functional data are rapidly accumulating in the scientific literature and most of them are collected by MEDLINE, a database that contains over 11,000,000 biomedical journal citations. A microarray analysis usually generates few hundred of differentially expressed genes and, after statistical validation of the data and transcription profiles clustering, biologists try to identify genes functionally correlated by scientific literature analysis. Even if some tools have been recently developed to simplify information extraction on the MEDLINE database, reading every article requires too much time and labor. Therefore, it is necessary to have some kind of intelligent information extracting system that recognizes gene names inside the texts. The analysis of text documents (e.g. MEDLINE abstracts) can be approached by two different points of view: text mining and information extraction (I.E.). The former aims at the automatic identification of groups of documents that share the same patterns of words, and thus refer to the same topic or theme. The latter aims at providing a structured representation of the textual information and requires a pre-definition of entities and relationships to be looked for inside texts. Thus while the text mining algorithms are general purpose, the information extraction algorithms are specific to the application. Furthermore, the text mining approach is explorative and enables the discovery of new concepts and relations while information extraction only extracts those elements that have already been defined. These two approaches can be integrated: information extraction tools generate databases that can be analyzed using data mining techniques, and, on the other side, text mining tools might take advantage of specific domain information extracted using I.E. techniques. MedMOLE takes advantage of text mining techniques, and simplifies the extraction of functional knowledge by literature abstracts directly/indirectly related to differentially expressed genes identified by microarray technology. Sponsors: This work was partially supported by PRIN 2001 and FIRB 2002 grants.
A Systematic Annotation Package for Community Analysis of Genome
A systematic annotation package for community analysis of genomes
ASAP: a systematic annotation package for community analysis of genomes
Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Salk Institute for Biological Studies - Slesinger Lab
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This lab is investigating the molecular details of how potassium ion channels open and close (i.e. gating), the cellular regulation of potassium channels in nerve cells, and more recently, their role in drug addiction and mental disorders. There are currently two related areas of focus in the lab. One main area of research is investigating the G protein regulation of GIRK channels, utilizing structural, biochemical and electrophysiological strategies. The other area extends from the G protein regulation experiments to studies that examine the role of GIRK channels in the neural response to drugs of abuse, utilizing biochemical, electrophysiological and behavioral strategies.
Salk Institute for Medical Research: Laboratory for Cognitive Neuroscience
The Salk Institute's Laboratory for Cognitive Neuroscience (LCN) is dedicated to the study of the neural and genetic underpinnings of language and cognition. The LCN organizes its resources into two research foci: Linking Gene, Brain, and Cognition, and Language, Modality and the Brain. Linking Gene, Brain, and Cognition: Behavioral Neurogenetics: - This research is designed to increase the understanding of genetically based disorders, to investigate the consequences of genetic alterations on the development of the brain, and to explore the resulting alteration of cognitive capabilities. Language, Modality, and the Brain: - The focus of this research is to obtain a greater understanding of how language and cognition are represented in the brain. Sponsors: This resource is supported by LCN.
The Wellcome Trust is the largest charity in the UK. We fund innovative biomedical research, in the UK and internationally, spending over 600 million each year to support the brightest scientists with the best ideas. The Wellcome Trust is an independent charity funding research to improve human and animal health. Established in 1936 and with an endowment of around 13 billion, it is the UK's largest non-governmental source of funds for biomedical research. What we do We spend over 600 million every year both in the UK and internationally achieving our mission. Funding We support many different kinds of research and activities with the ultimate aim of protecting and improving human and animal health. This support is not restricted to UK researchers - we devote significant funding to international research too. Biomedical science Our biomedical science funding enables the investigation of health and disease in humans and animals. This includes funding for scientists, clinicians and veterinarians at different career stages. Technology transfer Our technology transfer funding supports the development of innovative, early-stage projects with potential medical applications. Medical humanities Our medical humanities funding supports research into biomedical ethics and the history of medicine. Public engagement Our public engagement funding promotes interest, excitement and debate around science and society. Capital funding Our capital funding is for large-scale construction or refurbishment projects in the UK that support science, public engagement, medical history, or the activities of learned societies. Strategic awards Our Strategic Awards provide flexible funding that adds value to excellent research groups. Managing a grant This area contains information and resources to help you manage a grant once it has been awarded, from the grant-start certificate to the end-of-grant report and beyond. Education Resources Teaching and education Resources to help promote contemporary science in the curriculum and to enable young people to engage with biomedical science. Tree of Life Darwin200 Big Picture Science Learning Centres Scientific animations Creative Encounters Courses and conferences Trust-run conferences, courses and workshops for scientists, historians, ethicists, social scientists, teachers, healthcare professionals and policymakers, held in the UK and overseas. Advanced Courses Scientific conferences Conference centres Retreats History of medicine Biomedical ethics Biomedical resources Tools, databases and information to support different areas of biomedical research, including genomics, post-genomics and developmental biology. Animal research Genomics Model organisms Microorganisms Post-genomics Tissues Researcher support Support and advice for all kinds of engagement activities to help you communicate your work in the most effective and rewarding way possible. About researcher support National opportunities Regional opportunities Highlights Publications Browse a wealth of publications covering all aspects of the work we fund. Wellcome Trust websites Explore a range of sites covering key biomedical topics and our public engagement activities.
Public research university in Edmonton, Alberta, Canada that offers degree programs in a variety of fields including business, arts, education, engineering, nursing, and medicine.
The San Diego County Medical Society (SDCMS) is a non-profit organization designed to address San Diego healthcare needs for all patients and physicians through innovation, education and service. The SDCMS Foundation is advancing several innovative programs and initiatives: - The Emergency Department Medical Home (EDMH) Project matches uninsured patients in the emergency department with public and private medical coverage and establishes a medical home for them at local community health centers. - Project Access San Diego (PASD) is a program that connects eligible, low-income, uninsured patients with physicians who provide deeply discounted or pro bono care. - The SDCMS Foundation has also established five medical student scholarships at the UCSD School of Medicine.
The San Diego Psychiatric Society is a local medical specialty society. It is the district branch of the American Psychiatric Association and the California Psychiatric Association. The physician members specialize in the diagnosis and treatment of mental and emotional disorders and substance abuse. The San Diego Psychiatric Society's organizational objectives include the advancement and improvement of care for persons with mental illness through public information, education, and awareness programs and material. The society represents over 400 psychiatrists, who are the primary mental health advocates for quality patient care. The organization works to improve the public's awareness of mental illness and increase legislative and financial support of psychiatric care. Members serve in community mental health organizations, and advise the legislature on mental health issues.
Founded in 1985, the San Diego Supercomputer Center (SDSC) enables international science and engineering discoveries through advances in computational science and data-intensive, high-performance computing. SDSC is considered a leader in data-intensive computing, providing resources, services and expertise to the national research community including industry and academia. The mission of SDSC is to extend the reach of scientific accomplishments by providing tools such as high-performance hardware technologies, integrative software technologies, and deep interdisciplinary expertise to these communities. From 1997 to 2004, SDSC extended its leadership in computational science and engineering to form the National Partnership for Advanced Computational Infrastructure (NPACI), teaming with approximately 40 university partners around the country. Today, SDSC is an Organized Research Unit of the University of California, San Diego with a staff of talented scientists, software developers, and support personnel. A broad community of scientists, engineers, students, commercial partners, museums, and other facilities work with SDSC to develop cyberinfrastructure-enabled applications to help manage their extreme data needs. Projects run the gamut from creating astrophysics visualization for the American Museum of Natural History, to supporting more than 20,000 users per day to the Protein Data Bank, to performing large-scale, award-winning simulations of the origin of the universe or how a major earthquake would affect densely populated areas such as southern California. Along with these data cyberinfrastructure tools, SDSC also offers users full-time support including code optimization, training, 24-hour help desk services, portal development and a variety of other services. As one of the NSF's first national supercomputer centers, SDSC served as the data-intensive site lead in the agency's TeraGrid program, a multiyear effort to build and deploy the world's first large-scale infrastructure for open scientific research. SDSC currently provides advanced user support and expertise for XSEDE (Extreme Science and Engineering Discovery Environment) the five-year NSF-funded program that succeeded TeraGrid in mid-2011.
Algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
SamSPECTRAL - Identifies cell population in flow cytometry data
Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample.
SeattleSNPs - Variation Discovery Resource
The SeattleSNPs PGA is focused on identifying, genotyping, and modeling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans. SeattleSNPs is focused on variation analysis in genes related to the inflammatory response. These gene targets are found in specific pathways and from interacting molecules contributing to this response. Available Resources: - Baseline assembled and complete genomic sequence and chromosomal location for candidate gene targets - Mapping of exon and repeat structure for candidate genes - Amplification primers and conditions - SNPs mapped by location in gene structure - SNPs with immediate surrounding sequence for genotype assay design - Genotypes and relative allele frequencies of the SNPs - Special features of SNPs - location (5', coding, etc.), amino acid substitutions, recurrent variation - Manuals on all protocols, data analysis procedures, and use of software tools - Workshop on genetic variation analysis and a gene submission program for variation analysis Sponsors: SeattleSNPs is funded as part of the National Heart Lung and Blood Institute's (NHLBI) Programs for Genomic Applications (PGA).
An algorithm that estimates the tumor purity and clonal / subclonal copy number aberrations directly from high-throughput DNA sequencing data.
Signal Transduction Knowledge Environment - Database of Cell Signaling
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. This database provides information on the components of cellular signaling pathways and their relations to one another, which are organized into pathways called Connections Maps, which serve as the graphical interface into the database. Access to the database is free. Scientists with expertise in a given field, designated as Pathway Authorities, provide the information. With canonical or general data about cell signaling, as well as specific data about particular signaling processes in specific organisms and cells, there is information for both novices to cell signaling and experts. The Connections Maps are dynamically generated graphical interface to a database of information on the components of cellular signaling pathways and their relations to one another. Information is provided by pathway authorities with expertise in a given field. These Maps provide information on Canonical Pathways -- idealized or generalized pathways that represent common properties of a particular signaling module or pathway. Sponsors: This database is supported by AAAS.
Simons Foundation Autism Research Initiative: Grant Resource
The mission of SFARI is to improve the diagnosis, treatment, and prevention of autism and related developmental disorders. SFARI explores neuroscience from multiple directions, including molecular, cellular, systems, immunological, cognitive, behavioral, genetic, theoretical and computational perspectives. Funding for innovative scientific research is available through a peer-reviewed proposal process at regular intervals. Research projects are reviewed by a scientific advisory board and managed by the scientific director and a highly qualified staff. Proposals in multiple research areas are sought, to reflect the complex nature of autism. The Foundation supports innovative scientific projects where our involvement will play an essential role. In the course of this support, The Foundation is interested in partnering with other entities, or providing matching support where appropriate. The Simons Foundation has historically accepted only solicited grant proposals. These grant decisions are made by the Trustees of The Simons Foundation, who review applications on an ongoing basis. In the area of autism research, requests for proposals are issued on an annual basis. The Simons Foundation does not give grants to individuals, except through their institutions.
Social Anxiety Disorder: Learn How to Cope with Anxiety
This site is about Social Anxiety Disorder, how to diagnose social anxiety, how to live and cope with social anxiety, and how to treat social anxiety. Additionally, this website also intends to educate, inform, promote self-help, and provide a way to facilitate dialog between those who suffer from social phobia.
Konrad Lorenz Institute for Evolution and Cognition Research; Altenberg; Austria
Institute for the study of theoretical biology with a focus on evolutionary developmental biology and cultural complexity.
Dendritica: Software Tools for Studying Dendritic Signaling
Dendritica is a program package for relating dendritic geometry and signal propagation. The programs are based on those used for the simulations described in the following paper: Vetter, P., Roth, A. & Husser, M. (2001). Action potential propagation in dendrites depends on dendritic morphology. Journal of Neurophysiology, 85: 926-937. Dendritica can functionally be divided into three main parts: - Interactive morphological analysis and electrophysiological simulation of single cells - Automated batch simulations across a set of morphologies using the same simulation parameters - Automated analysis of batch simulation runs Dendritica requires NEURON 4.1.1 with some modifications described in Appendix 1. It was tested for NEURON 4.1.1 on Linux and SGI IRIX. Some modifications to the Dendritica code may be necessary in order to run it on older or newer versions of NEURON. Sponsors: This work was supported by the Wellcome Trust, the European Community, the Max-Planck-Gesellschaft, the Wellcome Trust 4-year PhD Programme in Neuroscience.
Stony Brook University Medical Center: Neuropathology Primer
This is a primer of basic neuropathology- The Central Nervous System and Skeletal Muscle. It is organized in chapters by category of disease with a separate chapter for skeletal muscle. Many of the diseases could be included in more than one chapter because of overlapping pathophysiology; in each case the disorder is included in a single section in the interest of convenience. In order to recognize pathology one must have a basic foundation in normal structure, so the first chapter is an overview of basic regional central nervous system structure and anatomy. It includes an introduction to neurohistology. Other chapters address the pathophysiology of different categories of disease and provide examples of gross and microscopic pathology when they are available.
South African National Bioinformatics Institute: Resources
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. The South African National Bioinformatics Institute delivers biomedical discovery appropriate to both international and African context. Researchers at SANBI perform the highest level of research and provide excellence in education. Research at SANBI has set well recognized milestones in the field of computational biology. The tools and techniques used have not only been developed but also implemented across heterogeneous domains of advanced research. Local and international efforts have driven our discoveries. Until recently, the core of SANBIs research has focused upon gene expression biology. Methods developed and applied at SANBI revolve around a greater understanding of the underlying causes of diseases. SANBI approaches the problem by comparison of genes, genomes and transcriptomes. It uses computational gene expression biology to create novel biological insights and to provide biomarkers for experimental validation. It also performs analysis of human genome variation, transcriptional diversity on both the expression and splicing level and the unravelling of transcriptional regulatory networks. Resources - Hinv, STACKdb, Malaria resources and Trypanosome databases are available for on-line seaching. - SANBI offers WCD, STACKdb, stackPACK and eVOC and the eVOKE viewer as tools that can be downloaded. Sponsors: SANBI receives funding and support from a range of organisations in South Africa and Internationally. Organisations currently supporting SANBI include: South Africa * South African Medical Research Council * South African AIDS Vaccine Initiative * National Bioinformatics Network * National Research Foundation * Claude Leon Foundation * International Business Machines Inc. Europe * European Unions 6th Framework Programme * World Health Organization USA * US National Institutes of Health * Fogarty International Centre * Ludwig Institute for Cancer Research
Spike Train Analysis Software by Attila Szucs: Orbital Spike 4
Orbital Spike is a tool for time series analysis. It contains a wide range of methods to analyze data from point processes such as spike arrival times, heart beats or other behavioral episodes. It is optimized this program for spike trains but it works with other types of data, too. The program can analyze up to 8 channels recorded simultaneously each containing a maximum of 132,000 events (spikes). Assuming an average firing rate of 10 Hz for a neuron, you can then analyze a time series of approximately 3 and half hours long. There are up to 8 panels shown in the Orbital Spike desktop. The panels will contain the kind of data of interest. The graphs are associated with a bunch of parameters like window width, bin size, resolution, delay etc. All these parameters are listed in the parameter box, which appears on the right side of the desktop. It is pretty easy to change the parameters and what is nice, the corresponding graph(s) will be recalculated immediately. You can also use a dialog box to change parameters. There are a lot of functions, statistics, graphs and diagrams available. A few of them are: * Interspike interval sequences * ISI Poincar * maps or return maps Instantaneous firing rate * ISI histograms and probability densities * Joint ISI and MSI probability densitograms * Autocorrelation, crosscorrelation * Spike density functions using kernel estimators * Fourier-amplitude spectrum and spectogram * Symbolic maps, recurrence plots * Phase plots of spike density functions Sponsors: Support for this work came from the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Engineering and Geosciences, under Grants DE-FG03-90ER14138 and DE-FG03-96ER14592; from the Office of Naval Research under Grant N00014-00-1-0181; from the National Science Foundation under Grant PHY0097134; from the National Institutes of Health under Grants R01 NS-40110-01A2 and 1RO1 NS-40110; and from the Army Research Office under Contract DAAD19-01-1-0026. R. D. Pinto was supported by the State of Sao Paulo Research Foundation (FAPESP).
SPRUSTON / KATH LAB: Neuraling Modeling Database NEURAL MODELING DATABASE
This database contains morphologies of hippocampal pyramidal cells and interneurons (in Neurolucida, NEURON, and pdf formats) as well as data recorded from those cells. Sponsors:This work was supported by grants from the NIH (T32-GM-08061 to T.J.M., F32-NS-10532 to N.L.G., and R01-NS35180 and R01-NS 46064 to N.S. and W.L.K.) and NSF (IGERT fellowship to Y.K.). NS46064 is part of the NSF/NIH Collaborative Research in Computational Neuroscience Program
Sparse Learning with Efficient Projections
SLEP: Sparse Learning with Efficient Projections
Sparse Learning with Efficient Projections (SLEP)
Software package that provides functions for solving a family of sparse learning algorithms. The functions implemented enjoy the convergence rate of O(1/k^2), although the objective function is non-smooth. Main features: * First-Order Method. At each iteration, they only need to evaluate the function value and the gradient; and thus the algorithms can handle large-scale sparse data. * Optimal Convergence Rate. The convergence rate O(1/k^2) is optimal for smooth convex optimization via the first-order black-box methods. * Efficient Projection. The projection problem (proximal operator) can be solved efficiently. * Pathwise Solutions. The SLEP package provides functions that efficiently compute the pathwise solutions corresponding to a series of regularization parameters by the warm-start technique.
Korean Ministry of Education Science and Technology
Ministry of Education Science and Technology of Korea
THIS RESOURCE IS NO LONGER IN SERVICE, documented April 11, 2017. Division within the South Korean government that handled affairs of education and science. It has since been split into Ministry of Science, ICT and Future Planning and Ministry of Education.
AutDB: a Genetic Database for Autism Spectrum Disorders
Simons Foundation Autism Research Initiative Gene: Autism Database
Curated public database for autism research built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The genetic information includes data from linkage and association studies, cytogenetic abnormalities, and specific mutations associated with ASD. New gene submissions are welcome. Modules: * Human Gene: thoroughly annotated list of genes that have been studied in the context of autism, with information on the genes themselves, relevant references from the literature, and the nature of the evidence. Uniquely, SFARI Gene incorporates information on both common and rare variants. * Animal Model: information about lines of genetically modified mice that represent potential models of autism. This information includes the nature of the targeting construct, the background strain and, most importantly, a thorough summary of the phenotypic features of the mice that are most relevant to autism. * Protein Interaction (PIN): compilation of all known direct protein interactions for those gene products implicated in autism. It presents both graphical and tabular views of interactomes, highlighting connections between autism candidate genes. Each protein interaction is manually verified by consultation with the primary reference. * Copy Number Variant (CNV): a parallel resource providing genetic information about all known copy number variants linked to autism. * Gene Scoring: includes a "score" for each autism candidate gene, based on an assessment of the strength of human genetic evidence.
Stable Isotope Labeling with Amino Acids in Cell Culture
Stable isotope labeling with amino acids in cell culture (SILAC) is a simple and straightforward approach for in vivo incorporation of a label into proteins for mass spectrometry (MS)-based quantitative proteomics. SILAC relies on metabolic incorporation of a given "light" or "heavy" form of the amino acid into the proteins. The method relies on the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, 13C, 15N). In an experiment, two cell populations are grown in culture media that are identical except that one of them contains a "light" and the other a "heavy" form of a particular amino acid (e.g. 12C and 13C labeled L-lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of this particular amino acid will be replaced by its isotope labeled analog. Since there is hardly any chemical difference between the labeled amino acid and the natural amino acid isotopes, the cells behave exactly like the control cell population grown in the presence of normal amino acid. It is efficient and reproducible as the incorporation of the isotope label is 100%. SILAC Applications: - Differential expression of proteins and identification of disease biomarkers - Cell signaling dynamics - Analysis of yeast pheromone signaling pathway - Identification of methylation sites - Identification of protease substrates - Study of protein complexes/protein interactions - Analysis of signaling pathways and effect of pharmacological inhibitors - Subcellular proteomics Sponsors: Supported in part by an NIH Roadmap grant Technology Center for Networks & Pathways of Lysine Modification.
This resource hyperlinks to systematic analysis projects, resources, laboratories, and departments at Stanford University.
TCW: Transcriptome Computational Workbench
Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R.
A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)
Flybrain (at) Stanford - A warped brain is a good thing
Project content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer.
Degust - Take the time to digest and appreciate your Differential Gene Expression data
An interactive web tool for visualizing differential gene expression data.
flowUtils - Utilities for flow cytometry
Software that provides utilities for flow cytometry data.
A resource for viewing annotated genes arising from various Aspergillus sequencing and annotation projects, resulting from the merging of Central Aspergillus Data REpository (CADRE) and The Aspergillus Website, which took place in June 2008. The principal role of CADRE is to aid the Aspergillus research community by managing Aspergillus genome data and by providing visualization tools, ranging from relatively simple annotation displays to more complex data integration displays. In contrast, The Aspergillus Website provides a range of information to the medical community (i.e., clinicians, patients and scientists) regarding the genus Aspergillus and the diseases, such as Aspergillosis, that it can cause. CADRE has been implemented using the Ensembl v22 suite. This suite comprises: * a database schema, which has been devised for storing annotated eukaryotic genomes. The schema is implemented with the MySQL relational database management system. * several specialized programming modules for building interfaces (i.e., BioPerl and Ensembl API modules). * a series of programs (i.e., Perl CGI scripts using the API modules) for viewing genomic data within a web browser., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Database for Annotation Visualization and Integrated Discovery
The Database for Annotation Visualization and Integrated Discovery Bioinformatics Resources
Visualization and Integrated Discovery Bioinformatics Resources
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.
EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas
The Electronic Prenatal Mouse Brain Atlas, EPMBA, at present consists of two sets of annotated images of coronal sections from Gestational Day (GD) 12 heads and GD 16 brains of C57BL/6J mice. Ten micron thick sections were stained with hematoxylin and eosin. Images were prepared at various resolutions for annotations and for high resolution presentation. A subset of sections were annotated and linked to anatomical terms. Additionally, horizontal sections of a GD 12 head were aligned and re-assembled into a 3D volume for digital sectioning in arbitrarily oblique planes. These images were captured using a Nikon E800 stereomicroscope with a 10X objective. The resolution is 1.35 pixels/micrometer. The PC program used to grab the images, Microbrightfield's Neurolucida (version 6), stitched together a mosaic of between 10 and 50 high-res images for each tissue slice, while the user focused the scope for each mosaic tile. Since the nature of optic lenses is to focus on one central point, it was difficult to obtain a uniformly-focused field of vision; as such, small areas of these images are blurred. Images were then transferred to a Macintosh and processed in Adobe Photoshop (version 7). Color levels were adjusted for maximum clarity of the tissue, and areas surrounding the tissue were cleared of artifacts. Each image is approximately 3350 pixels wide by 2650 pixels high. A scale bar with a length of 1350 pixels/mm is visible in the lower right-hand corner of each image. The annotations have been completed for the Atlas of Developing Mouse Brain Gestational (Embryonic) Day 12 (7/5/07) as well as the Atlas of Developing Mouse Brain Embryonic Day 16 (4/26/07). The 3D EPMBA data set has been mounted on a NeuroTerrain Atlas Server (NtAS). (6/27/07).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Alternative Splicing and Transcript Diversity (ASTD) database project is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale. The current release of the human genome consists of: 16715 genes, 14101 have more than one splice isoform, with an average of 5.6 splice patterns per gene. 10831 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the mouse genome consists of: 16491 genes, 13028 have more than one splice isoform, with an average of 4 splice patterns per gene. 6011 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the rat genome consists of: 10424 genes, 6344 have more than one splice isoform, with an average of 2.6 splice patterns per gene. 1250 transcripts are annotated as full length with a transcription start site and a poly(A). Sponsors: The ASTD project at EBI is supported by a grant from the EC: Eurasnet Network of Excellence (LSHG-CT-2005-518238). It was also supported by the ASD grant from the EC (QLRT-CT-2001-02062) until November 2005 and the ATD grant from the EC (LSHG-CT-2003-503329) until May 2007.
Huntington's Disease Society of America - New England Region
New England Region of The Huntington's Disease Society of America
THIS RESOURCE IS NO LONGER IN SERVICE, documented April 12, 2016. The New England HDSA office provides education, advocacy, support, and care to people with Huntington's Disease and their families throughout New England. It funds research efforts and has an extensive education outreach program.
VideoCasting of special NIH events, seminars, conferences, meetings and lectures available to viewers on the NIH network and the Internet from the VideoCast web site. VideoCasting is the method of electronically streaming digitally encoded video and audio data from a server to a client. VideoCast is often referred to as streaming video. Streaming files are not downloaded, but rather are broadcast in a manner similar to television broadcasts. The videos are processed by a compression program into a streaming format and delivered in a staggered fashion to minimize impact upon the network and maximize the experience of the content for the viewer. When users request a streaming file they will receive an initial burst of data after a short delay (file latency). While content is being viewed, the streaming server machine and software continues to stream data in such a manner that the viewer experiences no break in the content. CIT can broadcast your seminar, conference or meeting live to a world-wide audience over the Internet as a real-time streaming video. The event can be recorded and made available for viewers to watch at their convenience as an on-demand video or a downloadable podcast. CIT can also broadcast NIH-only or HHS-only content.
ASTRAL Compendium for Sequence and Structure Analysis
The ASTRAL Compendium for Sequence and Structure Analysis
It provides databases and tools useful for analyzing protein structures and their sequences. It is partially derived from, and augments the SCOP: Structural Classification of Proteins database, a database created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. Most of the resources provided here depend upon the coordinate files maintained and distributed by the Protein Data Bank. Sponsors: This work is supported by grants from the NIH (1-P50-GM62412, 1-K22-HG00056) and the Searle Scholars Program (01-L-116), and by the US Department of Energy under contract DE-AC03-76SF00098.
Harvey Project: Open Course Collaboratories
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. It is an international collaboration of educators, researchers, physicians, students, programmers, instructional designers and graphic artists working together to build interactive, dynamic human physiology course materials on the Web. Sponsors: This work has received funding from the US National Science Foundation.
RchyOptimyx - Optimyzed Cellular Hierarchies for Flow Cytometry
RchyOptimyx: Optimyzed Cellular Hierarchies for Flow Cytometry
Software that constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 21, 2011. Database focusing on gene expression in the frog Xenopus laevis, it is the web companion to the research papers describing a large-scale in situ hybridization screening in Xenopus embryos. The goals of this large-scale in situ screen project are to identify genes by the characterization of their expression pattern, to partially sequence the corresponding cDNAs and to maintain a database collecting the results.
Johns Hopkins NIMH Research Center Novel Therapeutics of HIV-associated Cognitive Disorders
JHU NIMH Center for Novel Therapeutics of HIV-associated Cognitive Disorders
Johns Hopkins National Institute of Mental Health (NIMH) Center for Novel Therapeutics of HIV-associated Cognitive Disorders
Johns Hopkins National Institute of Mental Health Center for Novel Therapeutics of HIV-associated Cognitive Disorders
The Johns Hopkins NIMH Center is comprised of an interdisciplinary research team who has pooled their talents to study the nature of HIV-associated neurocognitive disorders (HAND). Their aim is to translate discoveries of the pathophysiological mechanisms into novel therapeutics for HAND. Objectives * To integrate aspects of ongoing research in HAND and SIV encephalitis * Develop high-throughput and screening assays for identifying novel therapeutic compounds * Use proteomics and lipidomics approaches to indentifying surrogate markers of disease activity * Disseminate information and education about HAND through existing and new educational systems, including the JHU AIDS Education Training Center and the JHU Center for Global Clinical Education * Facilitate the entry of new investigators into Neuro-AIDS research, and to catalyze new areas of research, particularly where relevant for drug discovery or the development of validated surrogate markers
Software package for Bayesian analysis of protein, DNA and RNA sequences. It utilizes multiple alignments, phylogenetic trees and evolutionary parameters to quantify uncertainty in these analyses. It is written in Java.
Software collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. ATGC stands for Alignable Tight Genomic Cluster, which is cluster of closely related prokaryotic genomes. ATGC is the principal notion of this web resource. The purpose of this web resource is to prepare ATGC-derived data sets for a variety of research projects in functional and evolutionary genomics. Unique features of ATGC include: * Reliable identification of orthologs (high degree of similarity between the genomes in the set allow an extensive use of synteny in ortholog identification); * Fine granularity of protein classification (in comparisons of more distant genomes, proteins belonging to families of paralogs are often lumped into a singlegroup; under the ATGC approach, comparison of genomic sequences from highly similar genomes allows one to track each set of orthologs separately); * Relative rarity of changes of any kind (in sequence, genome organization and gene content) allows the use of parsimony-related methods of analysis.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data. It stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, LAD provides interfaces for data retrieval, analysis, and visualization.
Arabidopsis thaliana Protein Interactome Database
Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.
The Microarray Gene Expression Data Society
Society that develop standards for biological research data quality, annotation and exchange. They facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. They promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis. Historically, FGED began with a focus on microarrays and gene expression data. However, the scope of FGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications.
The Microbial Protein Interaction Database
Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included.
A project of the Mind and Life Institute, fosters multidisciplinary communication about scientific research on meditation and other contemplative practices. It is dedicated to fostering dialog and research at the highest possible level between modern science and the great living contemplative traditions, especially Buddhism. It builds on a deep commitment to the power and value of both of these ways of advancing knowledge and their potential to alleviate suffering. Membership is free, and this loose affiliation of scientists, meditators, and people interested in research promotes opportunities for researchers and meditators to communicate together. All perspectives, scientific fields, and styles of meditation are welcome. The MLRN includes cognitive neuroscientists who skillfully use scientific methods in the study of meditation, meditation scholars interested in scientific interfaces, and people who can help support meditation research. MLRN members are likely to be recruited to serve as advisors, referees, participants, and collaborators in upcoming studies on meditation. The MLRN encompasses a variety of meditation practices, and incorporates both contemplative and scientific approaches. The MLRN includes a low-volume, moderated electronic announcement list. This list maintains a high signal-to-noise ratio by distributing infrequent but important messages to large numbers of recipients. Members of this announcement list receive bibliographic updates on recent publications, announcements of upcoming conferences, calls for papers for special-issue journals and conference symposia, synopses of recent meetings, announcements of relevant email lists, websites, and other resources, and other announcements appropriate for widespread distribution. Sponsors: The Hershey Family Foundation has been patron since 1990. This Institute has received generous financial support from the Fetzer Institute, The Nathan Cummings Foundation, Branco Weiss, Adam Engle, Michael Sautman, Mr. and Mrs. R. Thomas Northcote, Christine Austin, Dennis Perlman, Marilyn and the late Don Gevirtz, Michele Grennon, Klaus Hebben, Joe and Mary Ellyn Sensenbrenner, and Edwin and Adrienne Joseph.
University of California at San Diego, Department of Psychiatry Postdoctoral Positions
Postdoctoral positions within the UCSD Department of Psychiatry available for qualified candidates. The following are the available postdoctoral opportunities: - Post-Doctoral Position in Co-Occurring Disorders - Postdoctoral Positions in Behavioral Neuroscience in the areas of nicotine dependence, depression and schizophrenia - Postdoctoral Position in Neuroimaging and Twin Research - Postdoctoral Fellowship in Behavioral Neuroscience in the area of methamphetamine dependence and HIV
Database providing a sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on gene structure annotation. The current genome assembly displayed at AtGDB is version TAIR9. Annotated gene models are TAIR10. They have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing.
Korea Advanced Institute of Science and Technology; Daejeon; South Korea
Korea Advanced Institute of Science and Technology
Institute dedicated to research in science and technology in South Korea modeled after a research university.
The Online Brain Atlas Reconciliation Tool
Tool that provides an interactive method to examine quantitative relationships between brain regions defined by different digital atlases or parcellation methods. Its current focus is for human brain imaging, though the techniques generalize to other domains. The method offers a quantitative answer to the nomenclature problem in neuroscience by comparing brain parts on the basis of their geometrical definitions rather than on the basis of name alone. Thus far these tools have been used to quantitatively compare eight distinct parcellations of the International Consortium for Brain Mapping (ICBM) single-subject template brain, each created using existing atlasing methods. This resources provides measures of global and regional similarity, and offers visualization techniques that allow users to quickly identify the correspondences (or lack of correspondences) between regions defined by different atlases.
Software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets.
Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
Public datasets that have been transcoded into multiple formats. This library of valid file format conversions (DICOM->NIFTI, DICOM->PAR/REC, etc.) will provide a reference for tool developers seeking to support multiple sources of data.
Nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California with a sister facility in Jupiter, Florida, the institute has laboratories employing scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world.
Software toolbox that manages your RNA-Seq and ChIP-Seq data and also produces many different plots to visualize your data. It performs several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization. It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis. It also provides many ways to visualize data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots). A computer science background is not required to run it through a graphical interface and it can be run on any personal computer, yielding results within an hour for most queries.
A Java consistency based multiple sequence alignment software program.
University of Utah Genetic Science Learning Center - Learn Genetics
Genetic Science Learning Center - Learn Genetics
Genetic Science Learning Center - Learn.Genetics
University of Utah Genetic Science Learning Center
Educational resources that provide accurate and unbiased information about topics in genetics, bioscience and health for global and local audiences. They are jargon-free, target multiple learning styles, and often convey concepts through animation and interactivity. The Genetic Science Learning Center is a science and health education program located in the midst of the bioscience research being carried out at the University of Utah. Our mission is making science easy for everyone to understand. * Two websites, available free of charge to Internet users worldwide: ** Learn.Genetics delivers educational materials on genetics, bioscience and health topics. They are designed to be used by students, teachers and members of the public. The materials meet selected US education standards for science and health. ** Teach.Genetics provides resources for K-12 teachers, higher education faculty, and public educators. These include PDF-based Print-and-Go™ activities, unit plans and other supporting resources. The materials are designed to support and extend the materials on Learn.Genetics. *Professional development programs that update K-16 teachers' expertise in bioscience and health topics as well as prepare them to implement the materials on our websites. * Community programs that engage with diverse communities in discussions about genetics and health, and in developing culturally and linguistically-appropriate educational materials. Some topics in genetics and bioscience research are controversial. The Center does not take sides in political or ethical controversies. Rather, our goal is to provide comprehensive information that promotes a lively discussion of these topics, so that individuals can arrive at their own informed decisions.
Korean Ministry of Science ICT and Future Planning
Ministry of Science ICT and Future Planning
Ministry of Science ICT and Future Planning (MISP)
Division of the South Korea government responsible for formulating national science and technology policies and plans.
BioChemWeb.org - The Virtual Library of Biochemistry Molecular Biology and Cell Biology
BioChemWeb.org - The Virtual Library of Biochemistry Molecular Biology Cell Biology
This site is provided as a service to scientists, educators, students and others simply interested in the Biological subjects. While many of the resources listed on these pages are designed for scientific professionals, those that require little or no background are labeled as Beginner's Level. Topics include: Angiogenesis, Apoptosis, Carbohydrates, Cell Adhesion & ECM, Cell Cycle, Cell Senescence, Chemical Biology, Cytoskeleton & Motility, Development, Enzymes, Genes, Lipids & Membranes, Metabolism, Microscopy, Organelles, Proteins, Signaling, Structural Biology, Systems Biology Other available categories include: General Resources & Tutorials, Scientific Research Groups, Databases & Tools, Methods, Software, Vendors, Books, Journals, Literature Search, Career & Funding, Organizations & Meetings
Software tool to visualize and analyse high throughput mapped sequence data.
Center for advancing scientific understanding and improving the health and well-being of humans and nonhuman primates. The Center conducts research in microbiology and immunology, neurologic diseases, neuropharmacology, behavioral, cognitive and developmental neuroscience, and psychiatric disorders.
Ray - Parallel genome assemblies for parallel DNA sequencing
Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2.
Tropical Diseases Research to Foster Innovation & Knowledge Application
TropIKA.net (Tropical Disease Research to foster Innovation and Knowledge Application) was created as a global knowledge management electronic portal to share essential information and to facilitate identification of priority needs and major research gaps in the field of infectious diseases of poverty. This website also provides funding opportunities for researchers of tropical diseases. TropIKA.net is a web-based platform for the acquisition, review and sharing of current information and knowledge on: - Public health research needs and scientific opportunities - Research-based evidence in support of control and policy - High profile research activities and control projects - International research funding and support opportunities - Potential innovations for interventions and control of infectious diseases of poverty. The Primary goals of TropIKA.net are to - Present up-to-date content in a context that makes sense for health researchers and policy makers - Improve access to scientific information on infectious diseases of poverty - Facilitate broad-based participation of disease-endemic countries in discussions and the formulation of current and emerging research priorities and agenda setting - Provide health researchers and decision makers with a comprehensive resource about best practices and authoritative summaries of research findings that have implications for their efforts to meet the challenges of infectious disease control. - Be used as an interactive knowledge platform for infectious diseases of poverty at health forums Sponsors: This website is supported by The Special Programme for Research and Training in Tropical Diseases (TDR).
Software providing a HTML5/javascript based browser for visualizing RNA-seq results in the familiar track layout of common genome browser. But given the quantitative nature of RNA-seq data, in addition to visualizing sequence coverage, the browser quantitates transcript abundance across regions of interest. The HTML5 functionality is made of use to render all the tracks using the canvas drawing element. This greatly reduces the load on servers and allows for rich interactive graphics without the need for third-party plugins. Furthermore, this framework completely segregates data from visualization, making development much easier. The browser is designed to run on all modern browsers: Firefox, Safari, Chrome, Opera and Internet Explorer (though not recommended).
United Kingdom National Health Service: National Genetics Education and Development Centre
The NHS National Genetics Education and Development Centre is working with a range of groups throughout the UK to facilitate the integration of genetics education into all levels of education and training for all NHS health professionals. The key aims of this center: 1. Providing leadership in genetics education 2. Helping to raise awareness 3. Involving patients and their families in informing all aspects of our work 4. Identifying the genetics knowledge, skills and attitudes which are useful for clinical role 5. Developing a framework for competences in genetics 6. Facilitating the integration of genetics into curricula and courses 7. Identifying and developing resources appropriate to the needs of health professionals (and their trainers) 8. Supporting and disseminating learning from service development initiatives in genetics Sponsors: The Centre is funded by the Department of Health as one of the major initiatives of the 2003 Genetics White Paper, Our Inheritance, Our Future - Realising the potential of genetics in the NHS which set out the Governments strategy for ensuring that the potential benefits of genetics are realised by the NHS.
University of California at Berkeley: The Neural Prediction Challenge
The aim of the Neural Prediction Challenge is to accelerate the development of predictive models and to provide computational neuroscientists an opportunity to test their models objectively. The challenge is really quite simple: you will be given some (visual and/or auditory) stimuli and corresponding neural responses, and you must try to predict responses to other stimuli. Each data set will be divided in to two subsets: a fit set (90% of the data) that includes both the stimuli and the corresponding neuronal responses; and a validation set (10% of the data) that includes only stimuli (no responses). Your job is to use the fit set to fit your model and then to generate predicted responses based on the stimuli provided in the validation set. Once you have the predictions you should return them to us. We will compare your predicted responses to the responses actually observed in the validation set. Current data consist of recordings from visual and auditory neurons during naturalistic stimulation. Data are provided in simple ascii files that are easily readable in Matlab (or by any other modern programming language). Details on data formatting are provided with each data set. Predictions will be evaluated continuously as they are received and results will be posted in aggregate form. Individuals' names, prediction scores and models will not be posted without prior permission (though we may contact participants directly, see official rules). Please note that this is an academic research project, it is not a traditional contest. There is no real ending date, and there is nothing to win. Sponsors: This project is supported by the NIH Human Brain Project.
University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics
The UCLA-DOE Institute for Genomics and Proteomics carries out research in bioenergy, structural biology, genomics and proteomics, consistent with the research mission of the United States Department of Energy. Major interests of the 12 Principal Investigators and 9 Associate Members include systems approaches to organisms, structural biology, bioinformatics, and bioenergetic systems. The Institute sponsors 5 Core Technology Centers, for X-ray and NMR structural determination, bioinformatics and computation, protein expression and purification, and biochemical instrumentation. Services offered by this Institute: - Databases: * DIP (The Database of Interacting Proteins): The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. * ProLinks Database of Functional Linkages: The Prolinks database is a collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage. - Data-to-Structure Servers: * SAVEs Structure Verification Server * Merohedral Twinning Test Server * SER Surface Entropy Reduction Server * VERIFY3D Structure Verification Server * ERRAT Structure Verification Server - Structure-to-Function Servers: * ProKnow Protein Functionator * Hot Patch Functional Site Locator
Biomedical technology resource center specializing in novel approaches and tools for neuroimaging. It develops novel strategies to investigate brain structure and function in their full multidimensional complexity. There is a rapidly growing need for brain models comprehensive enough to represent brain structure and function as they change across time in large populations, in different disease states, across imaging modalities, across age and sex, and even across species. International networks of collaborators are provided with a diverse array of tools to create, analyze, visualize, and interact with models of the brain. A major focus of these collaborations is to develop four-dimensional brain models that track and analyze complex patterns of dynamically changing brain structure in development and disease, expanding investigations of brain structure-function relations to four dimensions.
AutoPSI database of predicted SCOP classifications
Automated Protein Structure Identification (AutoPSI) database
Automated Protein Structure Identification database
Searchable database for predicted protein sequences and structures. It has the ability to search through PDB ID, UniProt ID, and descriptive classifiers.
University of California at Los Angeles, School of Medicine: Neuro Imaging Lab of Thompson
The UCLA laboratory of neuroimaging is working in several areas to enhance knowledge of anatomy, including brain mapping in large human populations, HIV, Schizophrenia, methamphetamine, tumor growth and 4d brain mapping, genetics and detection of abnormalities.
University of California at Riverside Neuroscience Graduate Program
Neuroscience is a multidisciplinary approach to understanding nervous systems at levels ranging from the molecular and cellular to the whole organism. The goal of this Program is to prepare students for careers in research, teaching and/or scientific administration. Students are expected to learn the fundamentals of neuroscience, starting with a required core sequence, become knowledgeable concerning a range of research methods as taught in a required neuroscience laboratory course, and demonstrate capability in original research. Graduate student training ultimately reflects the research competence and specialties of the faculty, that is, the specific research training received by a graduate student is the responsibility of the major professor/mentor under whose guidance and in whose laboratory the student carries out the research projects leading to the degree. Students will benefit from an interdisciplinary training approach, tailored by the major advisor but enriched by the readily available expertise and laboratory facilities of program faculty with backgrounds ranging from chemistry to psychology. In addition to this training, it is our intention, through outside speakers and planned forums, to make students aware of alternate careers open to neuroscientists whose interests and talents might lead to areas such as biotechnology, science administration and the like. The Interdepartmental Ph.D Program in Neuroscience at UC Riverside is aimed at providing high quality graduate training for students who come from a variety of undergraduate backgrounds but share a commitment and an intense interest in nervous system research. We currently have nineteen faculty with expertise in various aspects of neuroscience and whose principal appointments are in the Departments of Biology, Cell Biology & Neuroscience, Chemistry, Entomology, and Psychology, and the Division of Biomedical Sciences. A major part of training in neuroscience is in supervised laboratory research, the student working with one or more of the neuroscience faculty.
UCSD Cognitive Science: The Future of Cognitive Science
This UCSD department, the first Cognitive Science Department in the world, provides a focus for the continued evolution of the discipline of cognitive science. Cognitive science is a diverse field unifying three broad categories: the brain, behavior and computation. It's the study of how people, animals and computers think, act and learn. In order to understand the mind/brain, cognitive science brings together the methods and discoveries from neuroscience, psychology, linguistics, anthropology, philosophy and computer science. The interdisciplinary aspects of cognitive science continue to flourish, and the participation of the broader cognitive science community on campus continues to be fundamental to cognitive science as practiced at UCSD. The interdisciplinary Ph.D. program continues to be offered as a degree option (in addition to the departmental Ph.D.), with participation by members of the Departments of Anthropology, Biology, Cognitive Science, Communication, Computer Science and Engineering, Linguistics, Music, Neuroscience, Philosophy, Psychiatry, Psychology, and Sociology. Cognitive Science is a relatively young field that focuses on conducting new research into the field or applying existing knowledge into new applications. This Department contains several research labs each specializing in different areas and the Department's faculty has also been published many times in various publications. Sponsors: This department is supported by the University of California at San Diego.
We have developed an integrated SNP discovery pipeline, which identifies SNPs from assembled EST sequences. The results are maintained in a custom relational database along with EST source and annotation information. The current database hosts data for the important crops rice, barley and Brassica. Users may rapidly identify polymorphic sequences of interest through BLAST sequence comparison, keyword searches of annotations derived from UniRef90 and GenBank comparisons, GO annotations or in genes corresponding to syntenic regions of reference genomes. In addition, SNPs between specific varieties may be identified for targeted mapping and association studies. SNPs are viewed using a user-friendly graphical interface. The implementation of autoSNPdb allows researchers to query the results of SNP analysis to characterize SNPs between specific groups of individuals or within genes with predicted function. The system is flexible and researchers may add additional levels of annotation, and perform novel queries specific to their area of interest. If you have sequence data you'd like to include please contact Dave Edwards.
Shiley-Marcos Alzheimer's Disease Research Center
University of California at San Diego Shiley-Marcos Alzheimer's Disease Research Center
The UCSD ADRC conducts a wide variety of research studies dedicated to understanding the causes, clinical features, and treatments for Alzheimer's disease and related memory disorders. The goal of the center is to discover ways to prevent and eradicate the disease. The Center aims to maintain research subjects, clinical resources, and clinical data to support ongoing and proposed research and to assist in the development of new clinical and interdisciplinary research. An Alzheimer's brain bank with well characterized cases, including Mild Cognitive Impairment and Lewy Body disease, is maintained at the Center.
University of California at San Diego, Center for Medicinal Cannabis Research
The Center for Medicinal Cannabis Research (CMCR) will conduct high quality scientific studies intended to ascertain the general medical safety and efficacy of cannabis products and examine alternative forms of cannabis administration. The Center will be seen as a model resource for health policy planning by virtue of its close collaboration with federal, state, and academic entities. The objectives of this center are: 1. To conduct and support focused controlled clinical trials on the efficacy of cannabis in patients diagnosed with HIV/AIDS, cancer, seizures or muscle spasms associated with a chronic debilitating condition, or any other serious condition providing sufficient theoretical justification. 2. To use prospective clinical trials to determine optimal dosage, timing, and modes of administration for cannabis in various medical disorders. 3. To conduct randomized trials to compare the efficacy and safety of various methods of cannabis administration. 4. To conduct observational studies and randomized trials to assess the safety and toxicity of cannabis in the medically ill. Such studies will evaluate the impact of treatment on daily functioning and on life quality. 5. To conduct limited pre-clinical studies with direct relevance to understanding cannabis as a therapeutic agent. 6. To facilitate the implementation of research by assisting investigators in securing relevant regulatory review and approval by state and federal agencies. 7. To establish a process of rigorous peer review of scientific proposals. 8. To secure external sources of funding to maximize the scope and size of cannabis studies. Sponsors: This resource is supported by the University of California at San Diego.
University of California at San Diego Computational Neuroscience
The Computational Neuroscience specialization is a new facet of the broader Neuroscience graduate program at UCSD. The goal of the specialization is to train the next generation of neuroscientists with the broad range of computational and analytical skills that are essential to understand the organization and function of complex neural systems. The specialization is intended for students with backgrounds in neuroscience, physics, chemistry, biology, psychology, computer science, engineering, and mathematics. This specialization allows Neuroscience students to concentrate on a focused program of rigorous course work in both the theoretical and experimental aspects of computational neuroscience. Students are encouraged to pursue thesis research that includes both an experimental and a computational component, often arranged by the student as a collaboration between two research groups. The program is focused on these major themes relevant for computational neuroscience research: - Neurobiology of Neural Systems - the anatomy, physiology, and behavior of systems of neurons, with emphasis on basic phenomenology. - Advanced Measurement Tools in Neuroscience - Advanced imaging and recording techniques reflecting the impact of experimental physics on neuroscience. - Algorithms for the Analysis of Neural Data - New algorithms and techniques for analyzing data obtained from physiological recording - Theoretical Basis for Collective Neural Dynamics - A synthesis of approaches from mathematics and physical sciences as well as biology will be used to explore the collective properties and nonlinear dynamics of neuronal systems. Sponsors: This program is supported by the University of California at San Diego.
University of California at San Diego Department of Psychiatry
The Department of Psychiatry at the University of California, San Diego is one of the most innovative and productive academic departments of psychiatry in the country. The guiding principle in this development has been that the educational and research programs of a psychiatry department must be at the cutting edge and encompass and integrate the most current innovations in the field with those approaches from the past which have proven to be valid and effective. The department has a strong commitment to the dynamic understanding of an individual's current social context and feelings, and past behaviors and experiences. We believe we have created one of the best available integrations of the biopsychosocial approaches to understanding normal and abnormal human behavior. By design, a rich diversity of scientific and clinical strategies are represented within the department, but the core organizing ethic of our educational and training programs is a profound commitment to our patients well being. It is the department's conviction that clinical psychiatry can only be learned in the context of meaningful interaction and contact with patients. The Residency Training Program is developmental in nature, appropriately challenging the residents at each level as they move from intensively supervised beginners to autonomous, confident, skilled clinicians and colleagues at graduation. The training occurs within the department's ambiance of collegiality, enthusiasm, openness of communication, intellectual and scientific rigor, and spirit of inquiry, which characterize our highly productive and energetic faculty. The UCSD faculty represent a virtual who's who of world-class basic and clinical scientists and clinicians, all of whom are available and participate in our residents training and experiences. The tradition at UCSD, both on the general campus and within the School of Medicine, is that of academic excellence. The department shares in this tradition and expects it from its faculty, trainees, and students. The goal of the residency program is to develop highly competent psychiatric physicians and leaders who are comprehensively trained in the most up-to-date diagnostic and treatment techniques which have proven effective for the full spectrum of mental disorders.
Commercial antibody supplier that specializes in the development and manufacture of viral antigens and anti-viral antibodies for diagnosis, monitoring, and treatment of significant viral infectious diseases.
Swartz Center for Computational Neuroscience
Computational neuroscience center that observes and models how functional activities in multiple brain areas interact dynamically to support human cognition, creativity and social interaction. Center research involves development computational methods and software, experimental methods and equipment, collection and analysis of human cognitive experiments, and collaborations to analyze data collected by other groups in such experiments. The Center has a 72-channel EEG recording system customized for use in the fMRI environment, and a very-high density Biosemi Active Two active-electrode EEG system, rapidly configurable either as a 256-channel system for a single subject or as two 136-channel systems for recording from two subjects simultaneously. In addition, UCSD now has a 306-channel MEG plus 128-channel EEG system (Neuromag/Elektra). Projects in the Center include studies of human cognitive processes including attention and memory, role of the anterior/posterior cingulate, time perception and emotional expression. Data acquisition includes high-density EEG, concurrent EEG and fMRI recording and analysis, and face video processing. Current analysis approaches include independent component and time-frequency analysis.
Bacteriome.org - Bacterial Protein Interaction Database
Database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Presently the resource offers access to two types of network: * A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework * Two networks of experimentally derived protein-protein interactions - a "core" network consisting of interactions deemed to be of "high quality"; and an "extended" network which extends the "core" network by including interactions for which experimental evidence is less strong.
National Center for Microscopy and Imaging Research: ImageJ Mosaic Plug-ins
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. 02111-1307, USA. Sponsors: ImageJ Mosaic Plug-Ins software presented here was produced at the National Center for Microscopy and Imaging Research at San Diego, which is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant P41 RR04050.
A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses.
RAVEN - Regulatory analysis of Variation in ENhancers
Regulatory analysis of Variation in Enhancers
Tool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles
National Center for Microscopy and Imaging Research: Jinx
Jinx was developed to aid in the 3D reconstruction of tomographic datasets acquired with one of the various electron microscopes available at the resource. Tomographic datasets consist of a series of 2D images from which objects of interest are segmented out for the 3D reconstruction. Jinx offers the user a graphical interface to step through each image of the series and facilities to manually trace out objects of interest. It relies on JadeDisplay to support the display of large images with graphical overlays and the JAI libraries for histogram functionality and other types of image manipulations. Jinx is currently under active development and future releases will offer semi-automated segmentation algorithms based on fuzzy logic, level set, and watershed algorithm. This software is free; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version. See the GNU General Public License for more details. For a copy of the GNU General Public License, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA. Sponsors: Jinx presented here was produced at the National Center for Microscopy and Imaging Research at San Diego, which is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant P41 RR04050. open source license, GNU general public license
A collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins. It is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Version 2.0 of the database incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. Within the resource, users can look at a list of all the alignments, download the whole database by ftp, get the "c" program to compare a test alignment with the BAliBASE reference (The source code for the program is freely available), or look at the results of a comparison study of several multiple alignment programs, using BAliBASE reference sets.
University of California at San Diego, Neurosciences Graduate Program
The Graduate Program in Neurosciences at the University of California, San Diego offers an outstanding opportunity for graduate training in one of the most highly interactive scientific environments available in the United States. Recently, our graduate program was named by the National Research Council of the National Academy of Sciences as the top-ranking neuroscience graduate program in the country. The faculty who participate in the Graduate Program in Neurosciences have been brought together from many campus departments, the School of Medicine and from a number of affiliated institutes, including the Salk Institute, the Scripps Research Institute, the Scripps Institute of Oceanography, the UCSD Medical Center, and the Veterans Administration Medical Center. Because there is an enormous breadth of neuroscience research interests represented among the faculty, students are able to pursue study in a wide range of neuroscience areas and they often carry out their dissertation research in collaboration with more than one laboratory. Sponsors: FUnding for this program comes from the University of California at San Diego.
University of California at San Diego, School of Medicine: Graduate Opportunities & Dual Degree Programs
The UCSD School of Medicine are dedicated to producing future leaders in all areas of medicine. As such, the School promotes the pursuit of dual degrees, either in the Medical School's own graduate degree programs or programs offered in other disciplines in the institution. In addition to the study of medicine, the School of Medicine actively encourages its student body to explore broadly in various scholarly areas related to the biomedical sciences. The goal of this additional training is to produce graduates who will bring fresh, innovative ideas to the research laboratory, the public health sector, the humanities and the social sciences, and the business environment. Students may elect to obtain advanced degrees in the following areas: * Biomedical Sciences * Masters in Bioengineering * Masters in Public Health * Masters in Leadership of Health Care Organizations * Masters of Advanced Studies in Clinical Research * Ph.D. Program in the Humanities and Social Sciences * Independent Ph.D. programs Opportunities for enrollment in research or degree programs outside of UCSD are also available, and students are encouraged to investigate these, if interested. Sponsors: This program is supported by the University of California at San Diego.
TEQC - Quality control for target capture experiments
An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.
Free and publicly accessible literature database for peer-reviewed primary and review articles in the field of human Biospecimen Science. Each entry has been created by a Ph.D. level scientist to capture relevant parameters, pre-analytical factors, and original summaries of relevant results.
Data analysis service to identify single nucleotide polymorphisms (SNPs) that may have an effect on the presence of one or more transcription factor binding sites (TFBSs). The input to regulatory SNPs (rSNPs) can consist of one or more genes, a genomic region, or a user-provided sequence. SNPs may be downloaded from dbSNP, entered manually by the user, or obtained by comparing two sequences. The result is a list of TFBSs whose score changes significantly as a consequence of the allele substitution caused by the SNP.
A MIAME/Plant-compliant and plant ontology enhanced expression database for Barley microarray data. It contains data from two Affymetrix genome arrays, Barley1 and Arabidopsis ATH1. Users can search based on experiment type, experimental factors, array design, or experimenter. They can also choose to browse lists of available data.
rSNPBase - A database for curated regulatory SNPs
Database for curated regulatory single nucleotide polymorphisms (SNPs) to assist researchers in selecting candidate SNPs for further genetic studies (especially for QTL studies), identifying causal variants of certain phenotypes, and exploring in-depth molecular mechanisms. It is characterized by several unique features: (i) To improve reliability, all SNPs in rSNPBase are annotated with reference to experimentally supported regulatory elements. (ii) rSNPBase focuses on rSNPs involved in a wide range of regulation types, including proximal and distal transcriptional regulation and post-transcriptional regulation, and identifies their potentially regulated genes. (iii) Linkage disequilibrium (LD) correlations between SNPs were analysed so that the regulatory feature is annotated to SNP-set rather than a single SNP. (iv) rSNPBase provides the spatio-temporal labels and experimental eQTL labels for SNPs.
The Center for Bio-Image Informatics is an interdisciplinary research effort between Biology, Computer Science, Statistics, Multimedia and Engineering. The overarching goal of the center is the advancement of human knowledge of the complex biological processes which occur at both cellular and sub-cellular levels. the center employs and develops cutting edge techniques in the fields of imaging, pattern recognition and data mining. Research also focuses on development of new information processing techniques which can afford us a better understanding of biological processes depicted in microscopy images of cells and tissues, specifically on the distributions of biological molecules within these samples. This is achieved by borrowing methods for information processing at the sensor level to enable high speed and super-resolution imaging. By applying pattern recognition and data mining methods to bio-molecular images, full automation of both the extraction of information and the construction of statistically-sound models of the processes depicted in those images was possible. At the heart of the center's reseach is the BISQUE system, an online repository for multidimensional bio-images, and testbed for new research techniques and methods. BISQUE: Online Semantic Query User Environment is an online database for managing up to 5 dimensional scientific images with associated metadata and a flexible, collaborative tagging system. Currently the system has more than 85,000 user-provided tags and 128006 2-D planes from over 6,000 biological images. BISQUE is much more than just a repository for scientific images- the system provides resources for complex scientific analysis over images, result visualization, user-extensible modules, customized organization of images, advanced search features, graphical annotations, textual annotations and compatible client-side applications. Sponsors: This work is supported in part by an NSF infrastructure award No. EIA-0080134 and IIS-0808772.
An Igor Pro XOP software tool collection for reading Heka Pulse/PM files and other tools for electrophysiologists.
Software for the analysis of neurophysiological patterns and measurements.
Biomedical technology resource center dedicated to the advancement of the state-of-the-art in biomedical modeling and simulation through Core and Collaborative Research projects, as well as the dissemination of this knowledge and related software through Service, Training and Dissemination activities aimed at the biomedical community at large. The BMSR includes four core research projects: * Pharmacokinetic/Pharmacodynamic Systems Analysis * Nonlinear Modeling of Complex Biomedical Systems * Modeling of Autonomic, Metabolic and Vascular Control Interactions * Nonlinear Modeling of the Hippocampus Fifteen Collaborative Research Projects serve as challenging test grounds for the Resource's methodologies and expertise.
Software MATLAB toolbox which implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) functional magnetic resonance imaging data. GIFT works on MATLAB 6.5 and higher. Many ICA algorithms were generously contributed by Dr. Andrzej Cichocki.
Database for exploring the function implication of single nucleotide polymorphism (SNP) alleles. It is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, it includes a search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, the system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments.
A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded.
University of Leeds - Computational Biology Group
The University of Leeds Computational Biology Group is an interdisciplinary research group based in the Faculty of Biological Sciences, and is part of the Centre for Nonlinear Studies. Research interests are at the interfaces of nonlinear dynamics, computational science and general physiology of excitable tissue (nervous system, cardiac and uterine muscle). A central theme is the reconstruction of tissue and organ physiology and pathologies from networks of intracellular, membrane and cellular models. Sponsors:
flowType - Phenotyping Flow Cytometry Assays
Software for phenotyping Flow Cytometry assays using multidimentional expansion of single dimentional partitions.
Hub of evaluated genetics-related teaching resources for teachers and learners in schools and higher education, health professionals and the general public. Suggest or submit a learning resource to the VGEC. Resources include: * simple experiments suitable for all ages * tutorial material * videos on useful techniques * current and relevant links to other evaluated resources The Virtual Genetics Education Centre (VGEC) * Provides information and genetics education resources for higher education, colleges, schools, health professionals and the general public. * Encourages collaboration in the development, evaluation and sharing of genetics education resources * provides links to, and evaluates, sources of information and educational material about genetics. * Explores innovative approaches to teaching and learning in genetics, such as the SWIFT project for example where Second Life is being used to teach some aspects of genetics in a virtual laboratory.
Institute dedicated to medical research to improve biomedical innovation and public health in South Korea.
Hierarchical Attribute Matching Mechanism for Elastic Registration
Software package that performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements. In order to make HAMMER as robust as possible to different acquisition protocols and conditions, they provide a distribution that assumes that images have been skull-stripped and segmented into gray matter, white matter, and ventricular CSF. We have other software tools that can perform these steps, including skull stripping, reorientation and reslicing, and segmentation tools. Importantly, they use 250 for WM, 150 for GM, 50 for Ventricles and 10 for CSF in the tissue-segmented brain images. Current modules used for group analysis: Labeling subject brain using a manually-labeled brain Model; Generating RAVENS map for each tissue (WM, GM, VN); Normalizing subject brain images
Center for Integrative Biomedical Computing
NIH/NIGMS Center for Integrative Biomedical Computing
Biomedical technology research center that produces open-source software tools for biomedical image-based modeling, biomedical simulation and estimation, and the visualization of biomedical data. The Center works closely with software users and collaborators in a range of scientific domains to produce user-optimized tools and provides advice, technical support, workshops, and education to enhance user success. Biological projects and collaborations drive their development efforts, all with a single unifying vision: to develop the role of image-based modeling and analysis in biomedical science and clinical practice. The CIBC has a strong, ongoing emphasis on software simulation of bioelectric fields, with clinically oriented collaborations in cardiac defibrillation and the diagnosis/treatment of epilepsy. In addition, the CIBC has expanded in recent years to include applications of statistical shape analysis and three-dimensional visualization to mouse genetics and neuroimaging and applications of image and geometry processing to cell biology.
Web application for blogging on WordPress that allows users to annotate in the margins of an online text.
Retrieve known single-nucleotide polymorphisms (SNPs) by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions.
Image acquisition software used to acquire images during magnetic resonance imaging.
Visible Human Transverse Section Through the Head
Portal for learning resources about the brain. It includes information and interactive images of transverse brain sections.
National Center for Posttraumatic Stress Disorder
We are the center of excellence for research and education on the prevention, understanding, and treatment of PTSD. Our Center has seven divisions across the country. Although we provide no direct clinical care, our purpose is to improve the well-being and understanding of American Veterans. We conduct cutting edge research and apply resultant findings to: Advance the Science and Promote Understanding of Traumatic Stress. The National Center has emerged as the world's leading research and educational center of excellence on PTSD. Its vision is to be the foremost leader in information on PTSD and trauma; information generated internally through its extensive research program, and information synthesized from published scientific research and collective clinical experience that is efficiently disseminated to the field. The Center is organized to facilitate rapid translation of science into practice, assuring that the latest research findings inform clinical care; and translation of practice into science, assuring that questions raised by clinical challenges are addressed using rigorous experimental protocols. By drawing on the specific expertise vested at each separate division (e.g., behavioral, neuroscientific, etc.), the National Center provides a unique infrastructure within which to implement multidisciplinary initiatives regarding the etiology, pathophysiology, diagnosis and treatment of PTSD.
Center for Imaging of Neurodegenerative Diseases
UCSF Center for Imaging of Neurodegenerative Diseases
Biomedical technology research center that develops and validates new imaging methods for detecting brain abnormalities in neurodegenerative diseases, including Alzheimer's disease, vascular dementia, frontotemporal dementia, Parkinson's disease, as well as epilepsy, depression, and other conditions associated with nerve loss in the brain. As people around the globe live longer, the impact of neurodegenerative diseases is expected to increase further with dire social and economical consequences for societies if no effective treatments are developed soon. The development at CIND is aimed to improve magnetic resonance imaging (MRI). The ultimate goal of the scientific program is to identify imaging markers that improve accuracy in diagnosing neurodegenerative diseases at early stages, achieve more reliable prognoses of disease progression, and facilitate the discovery of effective treatment interventions. In addition to addressing the general needs for studying neurodegenerative diseases, another focus of CIND concerns brain diseases associated with military service and war combat, such as post traumatic stress disorder (PTSD), brain trauma, gulf war illness and the long-term effects of these conditions on the mental health of veterans. The symbiosis between CIND and the Veterans Administration Medical Center in San Francisco makes this program uniquely suited to serve military veterans.
Neuroscience software that stores the results of numerous tracer studies in a standardized format and provides various tools for performing summaries and comparisons of these studies.
The Stars and Stripes Healthcare Network (VISN 4) Mental Illness Research
The mission of the VISN 4 MIRECC is the treatment and prevention of comorbid medical, mental health, and/or substance use disorders, with the aim of improving the health, quality of life, and outcomes of healthcare services for veterans with mental illness. This is accomplished through the integration of basic, clinical, and services research and educational and clinical programs. The objectives of this MIRECC are: * Develop new empirical knowledge that can be directly applied to improve the clinical care of veterans * Provide education to providers and trainees to enhance the delivery of high quality healthcare to veterans * Impact public health in terms of veterans' mental health and quality of life * Serve as a national resource in education, research, and treatment of patients with comorbidity, and as a replicable model of excellence in clinical and educational programs Examine causal factors in the development of comorbid conditions. Assess impact of comorbidity on: * the identification and classification of disorders * the development and implementation of treatments * access to treatment and the impact of treatments on outcomes Sponsors: This work is supported by the US Department of Veterans Affairs
Prediction of Activity Spectra for Substances
PASS is a computer program which predicts the biological activity spectrum for a compound on the basis of its structural formula. The result of prediction is displayed for free. PASS Inet predicts 3678 pharmacological effects, mechanisms of action, mutagenicity, carcinogenicity, teratogenicity and embryotoxicity. PASS gives you hits in the following: - Finding most probable new leads with required activity spectra among the compounds from in-house and commercial data bases. - Revealing new effects and mechanisms of action for the old substances in corporate and private data bases. - Providing the basis for selection of the most prospective compounds for high throughput screening from the set of available samples. - Determining the assays that are more relevant for a particular compound. Sponsors: This work is supported by the Russian Foundation for Basic Research (Grant # 03-07-90282).
Video Lectures: Exchange Ideas and Share Thoughts
VideoLectures.Net: Exchange Ideas & Share Thoughts
Award-winning free and open access educational video lectures repository. The lectures are given by distinguished scholars and scientists at the most important and prominent events like conferences, summer schools, workshops and science promotional events from many fields of Science. The portal is aimed at promoting science, exchanging ideas and fostering knowledge sharing by providing high quality didactic contents not only to the scientific community but also to the general public. All lectures, accompanying documents, information and links are systematically selected and classified through the editorial process taking into account also users' comments.
Wellcome Trust Case-Control Consortium (WTCCC)
Consortium of 50 research groups across the UK to harness the power of newly-available genotyping technologies to improve our understanding of the aetiological basis of several major causes of global disease. The consortium has gathered genotype data for up to 500,000 sites of genome sequence variation (single nucleotide polymorphisms or SNPs) in samples ascertained for the disease phenotypes. Analysis of the genome-wide association data generated has lead to the identification of many SNPs and genes showing evidence of association with disease susceptibility, some of which will be followed up in future studies. In addition, the Consortium has gained important insights into the technical, analytical, methodological and biological aspects of genome-wide association analysis. The core of the study comprised an analysis of 2,000 samples from each of seven diseases (type 1 diabetes, type 2 diabetes, coronary heart disease, hypertension, bipolar disorder, rheumatoid arthritis and Crohn's disease). For each disease, the case samples have been ascertained from sites widely distributed across Great Britain, allowing us to obtain considerable efficiencies by comparing each of these case populations to a common set of 3,000 nationally-ascertained controls also from England, Scotland and Wales. These controls come from two sources: 1,500 are representative samples from the 1958 British Birth Cohort and 1,500 are blood donors recruited by the three national UK Blood Services. One of the questions that the WTCCC study has addressed relates to the relative merits of these alternative strategies for the generation of representative population cohorts. Genotyping for this main Case Control study was conducted by Affymetrix using the (commercial) Affymetrix 500K chip. As part of this study a total of 17,000 samples were typed for 500,000 SNPs. There are two additional components to the study. First, the WTCCC award is part-funding a study of host resistance to infectious diseases in African populations. The same approach has been used to type 2,000 cases of tuberculosis (TB) and 2,000 cases of malaria, as well as 2,000 shared controls. As well as addressing diseases of major global significance, and extending WTCCC coverage into the area of infectious disease, the inclusion of samples of African origin has obvious benefits with respect to methodological aspects of genome-wide association analysis. Second, the WTCCC has, for four additional diseases (autoimmune thyroid disease, breast cancer, ankylosing spondylitis, multiple sclerosis), completed an analysis of 15,000 SNPs designed to represent a large proportion of the known non-synonymous coding SNPs across the genome. This analysis has been performed at the WTSI using a custom Infinium chip (Illumina). Data release The genotypic data of the control samples (1958 British Birth Cohort and UK Blood Service) and from seven diseases analyzed in the main study are now available to qualified researchers. Summary genotype statistics for these collections are available directly from the website. Access to the individual-level genotype data and summary genotype statistics is by application to the Consortium Data Access Committee (CDAC) and approval subject to a Data Access Agreement. WTCCC2: A further round of GWA studies were funded in April 2008. These include 15 WTCCC-collaborative studies and 12 independent studies be supported totaling approximately 120,000 samples. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC2 will perform genome-wide association studies in 13 disease conditions: Ankylosing spondylitis, Barrett's oesophagus and oesophageal adenocarcinoma, glaucoma, ischaemic stroke, multiple sclerosis, pre-eclampsia, Parkinson's disease, psychosis endophenotypes, psoriasis, schizophrenia, ulcerative colitis and visceral leishmaniasis. WTCCC2 will also investigate the genetics of reading and mathematics abilities in children and the pharmacogenomics of statin response. Over 60,000 samples will be analyzed using either the Affymetrix v6.0 chip or the Illumina 660K chip. The WTCCC2 will also genotype 3,000 controls each from the 1958 British Birth cohort and the UK Blood Service control group, and the 6,000 controls will be genotyped on both the Affymetrix v6.0 and Illumina 1.2M chips. WTCCC3: The Wellcome Trust has provided support for a further round of GWA studies in January 2009. These include 5 WTCCC-collaborative studies to be carried out in WTCCC3 and 5 independent studies, across a range of diseases. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC3 will perform genome-wide association studies in the following 4 disease conditions: primary biliary cirrhosis, anorexia nervosa, pre-eclampsia in UK subjects, and the interactions between donor and recipient DNA related to early and late renal transplant dysfunction. The WTCCC3 will also carry out a pilot in a study of the genetics of host control of HIV-1 infection. Over 40,000 samples will be analyzed using the Illumina 660K chip. The WTCCC3 will utilize the 6,000 control genotypes generated by the WTCCC2.
World Federation for Culture Collections
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Collects, authenticates, maintains and distributes cultures of microorganisms and cultured cells. Its aim is to promote and support the establishment of culture collections and related services, to provide liaison and set up an information network between the collections and their users, to organize workshops and conferences, publications and newsletters and work to ensure the long term perpetuation of important collections. The WFCC (through the activities of Professor Skerman, University of Queensland, Australia, and his colleagues in the 1960's) pioneered the development of an international database on culture resources worldwide. The result is the WFCC World Data Center for Microorganisms (WDCM). This data resource is now maintained at National Institute of Genetics (NIG), Japan and has records of nearly 476 culture collections from 62 countries. The records contain data on the organization, management, services and scientific interests of the collections. Each of these records is linked to a second record containing the list of species held. The WDCM database forms an important information resource for all microbiological activity and also acts as a focus for data activities among WFCC members.
Center for Computational Medicine and Biology
The CCMB was created to facilitate interdisciplinary research in computational medicine and biology and to forge collaborative relationships with faculty across campus and the US. Computational medicine and bioinformatics, is an emerging field that pursues biological questions using advanced computational technology such as complex merged datasets and powerful computing clusters. The Center currently has three components: The Bioinformatics Graduate Program (BGP), The Collaborative Computing & Data Unit, and The Interdisciplinary Research Program. Faculty from all areas of campus are affiliated with the center. The Bioinformatics Graduate Program (BGP) trains masters and Ph.D-level scholars, and oversees the research computing for four faculty members with partial appointments in the program. The Bioinformatics Graduate Program currently has 24 doctoral and 11 master-level students. The Collaborative Computing & Data Unit provides expert support for large cluster computing -- a necessary component for doing research in computational medicine and biology. This core also works with the UM Medical School and Office of the Vice President for Research (OVPR) to address long-term deficits in computing needs across campus. Finally, The Interdisciplinary Research Program oversees several NIH and state-funded projects, the largest being the National Center for Integrative Biomedical Informatics, whose goal is developing tools to facilitate biomedical research. The IDR also provides support to faculty applying for interdisciplinary grants in all areas of bioinformatics research.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a variety of graphical, tabular, computational formats. Biositemaps content allows such web browsers to pool resource-associated metadata from disparate and diverse sites and present it to the user in an integrated fashion. The Biositemaps protocol provides clues, information and directives for all Biositemap web harvesters that point to the existence and content of such biomedical resources at different sites.
Commercial company that develops and provides laboratory diagnostics and other medical research products.
International society dedicated to advancing understanding of anatomical and functional organization of human brain using neuroimaging. Primary function of society is to provide educational forums for exchange of up-to-the-minute and groundbreaking research across neuroimaging methods and applications. OHBM achieves this through its member led committees and Annual Meeting that is held in different locations throughout the world.
Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review.
Software that is a hierarchical genotype classifier of clonal pathogens.
ADaCGH2 - Analysis of big data from aCGH experiments using parallel computing and ff objects
Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.
Software package that functions as a de novo genome assembler based on the concept of string graphs. It is designed as a modular set of programs used to assemble large genomes from high coverage short read data.
Facility which provides instruments and instrument resources for analyzing DNA, RNA, protein, and radio-labeled substances.
American Society of Radiologic Technologists
Society of Radiologic Technologists to advance the medical imaging and radiation therapy profession and to enhance the quality of patient care, leading and serving its members, the profession, other health care providers and the public on all issues that affect the radiologic sciences. The mission of the ASRT is to foster the professional growth of radiologic technologists by expanding knowledge through education, research and analysis; promoting exceptional leadership and service; and developing the radiologic technology community through shared ethics and values. This portal offers information on Continuing Education opportunities, and has a variety of other resources including a marketplace, news, publications, events and conferences, career center, studies and surveys, professional resources, and much more. Scholarly Journals Members can earn CE credit through the Directed Readings program in the ASRT journals, Radiologic Technology and Radiation Therapist. By maintaining continuous membership, members can earn at least 12 Category A CE credits. Answer sheets for Directed Reading Quizzes can be completed on our Web site or mailed to the ASRT for grading. You will receive pass or fail notification immediately on the Web site or ASRT will notify you within 30 days if your completed quiz is mailed. A passing grade of 75 percent or better is required to receive the assigned Category A credit.
California Institute of Technology - Computation and Neural Systems
Portal offers information on people, research, seminars, academics, admissions, positions, and news, associated with interdisciplinary program to study problems arising at interface between neurobiology, electrical engineering, computer science, and physics. Applicants for Graduate Admissions should have undergraduate major in electrical engineering, biology, physics, mathematics, or computer science, and general background that will permit enrolling in advanced courses in other relevant disciplines. Admitted students will become affiliated with one of three participating divisions as appropriate to their background and interests. Post-doc positions are also available.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. Commercial antibody supplier. Imgenex has merged with Novus Biologicals.
This is a topical portal dedicated to the communication of news, science, and information of interest to the brain mapping community, and to sharing and promoting the science of brain mapping. The purpose and goal of brain mapping is to advance the understanding of the relationship between structure and function in the human brain. Scientists in this field seek to gain knowledge of the physical processes that underly human sensation, attention, awareness and cognition. These results are immediately applicable to surgical intervention, to the design of medical interventions and to the treatment of psychological and psychiatric disorders.
International Society for Magnetic Resonance in Medicine
The International Society for Magnetic Resonance in Medicine is an international, nonprofit, scientific association whose purpose is to promote communication, research, development, and applications in the field of magnetic resonance in medicine and biology and other related topics and to develop and provide channels and facilities for continuing education in the field. In addition to its large scientific meetings, the Society holds workshops and publishes two journals, Magnetic Resonance in Medicine and the Journal of Magnetic Resonance Imaging, and a newsletter, MR Pulse. It also sponsors study groups on specific areas of scientific interest and chapters based on geographical location. Its multidisciplinary membership of over 6,000 consists of clinicians, physicists, engineers, biochemists, and technologists. The ISMRMs inception, on January 1, 1994, resulted from a merger of the Society of Magnetic Resonance in Medicine and the Society of Magnetic Resonance Imaging forming the Society of Magnetic Resonance (now named the International Society for Magnetic Resonance in Medicine). The purposes of the Society are: (A) (i) To promote communication, research, development, applications, and the availability of information on magnetic resonance in medicine and biology and other related topics internationally; (ii) To develop and provide channels and facilities for continuing education and communication in the field, to publish and assist in the publishing of journals and other publications in the field; and (iii) To provide information and advice on those aspects of public policy which are concerned with magnetic resonance in medicine and biology and other related topics, and otherwise perform charitable, scientific and educational functions with respect to magnetic resonance applications in medicine and biology and other related topics. (B) To work with or for, and to co-operate with local, regional and national governments and governmental and private agencies, organizations, firms and institutions in efforts to accomplish one or more of the above purposes. (C) To ensure that scientists and clinicians working in the field have equal and fair opportunities to contribute to it. The site lists a partial list of NMR and MRI resources available on the World Wide Web. The content of these sites is not controlled or endorsed in any way by the ISMRM or SMRT. Sections devoted to MR safety and MRI information for patients is also available. Study groups are established to foster interaction among members with a common interest in topical and active areas of MR. If you are a member of the ISMRM or SMRT, you may become a member of any number of study groups; however, the cost of membership for each study group is US20. Recorded educational presentations, oral presentations, traditional posters, and electronic posters Available only to Meeting registrants - Now online
ISCBFM - International Society for Cerebral Blood Flow and Metabolism
International Society for Cerebral Blood Flow and Metabolism
International Society for Cerebral Blood Flow Metabolism
ISCBFM - International Society for Cerebral Blood Flow Metabolism
The International Society for Cerebral Blood Flow & Metabolism is a corporation operated exclusively for the purpose of promoting the advancement of education in the science of cerebral blood flow and metabolism throughout the world. The ISCBFM produces a quarterly newsletter, an official journal (Journal of Cerebral Blood Flow & Metabolism), have a yearly meeting, opportunities to host summer schools and a job board. ISCBFM members organize summer schools which are courses that have the aim to bring together young and experienced scientists for educational purposes. The biennial Brain Meetings also have a substantial part of the time allocated for educational purposes for young scientists interested in the field of cerebral blood flow and metabolism. Preference will be given to suggestions that are seen as a complement to scheduled courses in connection with the Brain Meetings and to courses that are given in between Brain Meetings.
The Cognitive Neuroscience Society (CNS) is committed to the development of mind and brain research aimed at investigating the psychological, computational, and neuroscientific bases of cognition. Since its founding in 1994, the Society has been dedicated to bringing its 2000 worldwide members the latest research and dialogues in order to facilitate public, professional and scientific discourse. The term cognitive neuroscience has now been with us for almost three decades, and identifies an interdisciplinary approach to understanding the nature of thought. Our members, who are engaged in research focused on elucidating the biological underpinnings of mental processes, form a network of scientists and scholars working at the interface of mind, brain and behavior research. The findings of this research are presented at our member-supported annual scientific conference. The three-day program of plenary speakers, symposia, posters and special events covers all aspects of cognitive neuroscience research. The Society also disseminates information regarding employment opportunities, training fellowships, research grants, and information on related scientific conferences in its monthly newsletter. Our members can receive the Journal of Cognitive Neuroscience at a substantial discount.
Portal for UC Berkeley's neuroscience research center. The group focuses on interdisciplinary collaboration between neuroscientists and members of UC Berkeley programs in engineering, chemistry, statistics, and computation. It also runs the neuroscience PhD program.
NARSAD: The Brain and Behavior Research Fund
NARSAD: The Worlds Leading Charity Dedicated to Mental Health Research
National Alliance for Research on Schizophrenia Depression
National Alliance on Research in Schizophrenia and Depression
The Brain and Behavior Research Foundation (formerly NARSAD, the National Alliance for Research on Schizophrenia and Depression) is committed to alleviating the suffering of mental illness by awarding grants that will lead to advances and breakthroughs in scientific research. Additionally, learn about brain and behavior disorders and upcoming events. 100% of all donor contributions for research are invested in NARSAD Grants leading to discoveries in understanding causes and improving treatments of disorders in children and adults, such as depression, bipolar disorder, schizophrenia, autism, attention deficit hyperactivity disorder, and anxiety disorders like obsessive-compulsive and post-traumatic stress disorders. Over a quarter of a century, we have awarded nearly $300 million worldwide to more than 3,000 scientists carefully selected by our prestigious Scientific Council. We receive no government funding. All of our work relies on contributions from families, foundations and other caring donors.
BioModels Database - A Database of Annotated Published Models
Repository of mathematical models of biological and biomedical systems. Hosts selection of existing literature based physiologically and pharmaceutically relevant mechanistic models in standard formats. Features programmatic access via Web Services. Each model is curated to verify that it corresponds to reference publication and gives proper numerical results. Curators also annotate components of models with terms from controlled vocabularies and links to other relevant data resources allowing users to search accurately for models they need. Models can be retrieved in SBML format and import/export facilities are being developed to extend spectrum of formats supported by resource.
Data set of manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the development and evaluation of segmentation methods by providing raw test and image data, human expert segmentation results, and methods for comparing segmentation results. Please see the MediaWiki for more information. This repository is meant to contain standard test image data sets which will permit a standardized mechanism for evaluation of the sensitivity of a given analysis method to signal to noise ratio, contrast to noise ratio, shape complexity, degree of partial volume effect, etc. This capability is felt to be essential to further development in the field since many published algorithms tend to only operate successfully under a narrow range of conditions which may not extend to those experienced under the typical clinical imaging setting. This repository is also meant to describe and discuss methods for the comparison of results.
Analysis methodology that allows simultaneous quantification and normalization of reverse phase protein array (RPPA) data.
XPP-Aut: X-Windows Phase Plane plus Auto
XPPAUT is a tool for solving differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations. It evolved from a chapter written by John Rinzel and me on the qualitative theory of nerve membranes and eventually became a commercial product for MSDOS computers called PHASEPLANE. It is now available as a program running under X11 and Windows. The code brings together a number of useful algorithms and is extremely portable. All the graphics and interface are written completely in Xlib which explains the somewhat idiosyncratic and primitive widgets interface. XPP contains the code for the popular bifurcation program, AUTO . Thus, you can switch back and forth between XPP and AUTO, using the values of one program in the other and vice-versa. I have put a ``friendly'' face on AUTO as well. You do not need to know much about it to play around with it. XPP has the capabilities for handling up to 590 differential equations. There are over a dozen solvers including several for stiff systems, a solver for integral equations and a symplectic solver. Up to 10 graphics windows can be visible at once and a variety of color combinations is supported. PostScript output is supported as well as GIF and animator GIF movies Post processing is easy and includes the ability to make histograms, FFTs and applying functions to columns of your data. Equilibria and linear stability as well as one-dimensional invariant sets can be computed. Nullclines and flow fields aid in the qualitative understanding of two-dimensional models. Poincare maps and equations on cylinders and tori are also supported. Some useful averaging theory tricks and various methods for dealing with coupled oscillators are included primarily because that is what I do for a living. Equations with Dirac delta functions are allowable. I have added an animation package that allows you to create animated versions of your simulations, such as a little pendulum moving back and forth or lamprey swimming. See toys! for examples. There is a curve-fitter based on the Marquardt-Levenberg algorithm which lets you fit data points to the solutions to dynamical systems. It is possible to automatically generate "movies'' of three-dimensional views of attractors or parametric changes in the attractor as some parameters vary. Dynamically link to external subroutines XPP has been successfully compiled on a SPARC II under OpenLook, a SPARC 1.5 running generic X, a NeXT running X11R4, a DEC 5000, a PC using Linux or Windows, and SGI and an HP 730. It also runs under Win95/NT/98 if you have an X-Server. I cannot vouch for other platforms but it has been compiled on the IBM RS6000. Building XPP requires only the standard C compiler, and Xlib. Look at the any README files that come with the distribution for solutions to common compilation problems.
Project portal for publishing, citing, sharing and discovering research data. Software, protocols, and community connections for creating research data repositories that automate professional archival practices, guarantee long term preservation, and enable researchers to share, retain control of, and receive web visibility and formal academic citations for their data contributions. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit. Hosts multiple dataverses. Each dataverse contains studies or collections of studies, and each study contains cataloging information that describes the data plus the actual data files and complementary files. Data related to social sciences, health, medicine, humanities or other sciences with an emphasis in human behavior are uploaded to the IQSS Dataverse Network (Harvard). You can create your own dataverse for free and start adding studies for your data files and complementary material (documents, software, etc). You may install your own Dataverse Network for your University or organization.
NIPS - Neural Information Processing Systems Conference
The Neural Information Processing Systems (NIPS) Foundation is a non-profit corporation whose purpose is to foster the exchange of research on neural information processing systems in their biological, technological, mathematical, and theoretical aspects. Neural information processing is a field which benefits from a combined view of biological, physical, mathematical, and computational sciences. The primary focus of the NIPS Foundation is the presentation of a continuing series of professional meetings known as the Neural Information Processing Systems Conference, held over the years at various locations in the United States and Canada.
A software tool for pairwise sequence alignment with a single gap.
Data and biospecimen from Rett Syndrome patients shared with the scientific community with the ability to visualize the list of available samples and select those with specific clinical and molecular features. It also contains information on biospecimen samples from x-linked retardation, microdeletion, duplication syndromes, autosomal MR, and retinoblastoma. The bank is active since 1998 and it is located in the Medical Genetics Unit, at the University Hospital of Siena. The bank is divided in three distinct sections: # Rett Syndrome. This section contains samples from patients affected by Rett syndrome, a neurodegenerative disease affecting almost exclusively girls with an estimated frequency of 1:10000-15000 live born. By accessing the section users can see a list of all patients available with their phenotype, the specific MECP2 or CDKL5 mutation if known and the kind of biological samples available for each patient. The availability of this large panel of patients is potentially important for the clarification of the molecular bases of Rett syndrome. In fact, a 20-30 of Rett cases do not have MECP2 or CDKL5 mutations. These patients might bear intronic/promoter MECP2 or CDKL5 mutations or they might have alterations in one or more genes different from MECP2 or CDKL5, as suggested by the identification of various chromosomal rearrangements. To confirm a causative role of these rearrangements, and to identify the relevant gene/s, it is important to collect a great number of patients in which to search for overlapping rearrangements or point mutations in candidate genes. # X-Linked Mental Retardation. This section contains samples collected by the centers belonging to the Italian network on X-linked mental retardation, which includes the laboratory of bank curators (for specific information on the network goals and organization, go to the section page). Mental retardation (MR) is the most frequent cause of serious handicap in humans with an estimated prevalence of 0,3-0,5 for moderate to severe MR (IQ<50) which increases to 1-1,5 when mild MR (IQ 50-70) is included. It is calculated that about 20-25 of mentally retarded males have a mutation in a gene on the X chromosome (X-linked mental retardation). X-linked mental retardation is a genetically heterogeneous condition. This is particularly true for the non-syndromic form (MRX), where MR is the only consistent clinical finding and no distinctive features between patients exist. In this situation the only possibility to group patients from different families is represented by linkage analysis, which needs the availability of large families. However, families linked to the same region demonstrate different causative genes. In these conditions, the number of patients available for analysis is a discriminating factor since a large number of patients need to be tested in order to fully confirm or exclude the involvement of a gene in MRX. # Other. This section of the bank contains biological materials and clinical data of patients with other genetic disorders (different from Rett and X-linked mental retardation). Part of this section is dedicated to Alport syndrome. Services: * Isolation of leukocytes from human peripheral blood samples * Establishment of EBV transformed lymphoblastoid cell lines from human peripheral blood leukocytes. * DNA extraction. * Plasma isolation. * Storage: ** Cryo-preservation of transformed cell lines and primary leukocytes at 135��C ** Storage of DNA at 20 degrees C ** Storage of plasma at 20 degrees C * Distribution of the stored biological samples.
Neural ElectroMagnetic Ontologies (NEMO) Project
THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. NIH funded project to create EEG and MEG ontologies and ontology based tools. These resources will be used to support representation, classification, and meta-analysis of brain electromagnetic data. Three pillars of NEMO are: DATA, ONTOLOGY, and DATABASE. NEMO data consist of raw EEG, averaged EEG (ERPs), and ERP data analysis results. NEMO ontologies include concepts related to ERP data (including spatial and temporal features of ERP patterns), data provenance, and cognitive and linguistic paradigms that were used to collect data. NEMO database portal is large repository that stores NEMO consortium data, data analysis results, and data provenance. EEG and MEG ontologies and ontology-based tools to support representation, classification, and meta-analysis of brain electromagnetic data. Raw EEG and ERP data may be uploaded to the NEMO FTP site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Website which allows data from completed clinical trials to be distributed to investigators and public. Researchers can download de-identified data from completed NIDA clinical trial studies to conduct analyses that improve quality of drug abuse treatment. Incorporates data from Division of Therapeutics and Medical Consequences and Center for Clinical Trials Network.
Tool for Rapid Annotation of Microbial SNPs
Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes
Tool for rapid annotation of microbial SNPs: a simple program for rapid annotation of genomic variation in prokaryotes
TRAMS: a simple program for rapid annotation of genomic variation in prokaryotes
A software program for functional annotation of genomic single nucleotide polymorphisms (SNPs) which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. It needs only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. It annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation. A workflow has also been developed for use in Galaxy to map short reads to a reference genome and extract and annotate the SNPs.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. Platform for Neuroscientists to describe neurons and neural circuitry. Registered users may edit. The ultimate goal is advance the field of Neuromics by creating an encyclopedia of neurons and neural circuitry. NOTE: The database is no longer being maintained due to lack of funding.
A Python and BioPython-based tool to generate metadata for single nucleotide polymorphisms (SNPs) for easy filtering, or submission to SNP databases. Information reported includes gene name, whether the SNP is coding or noncoding, and whether the SNP is synonymous or nonsynonymous. SNPMeta outputs in either a dbSNP submission report format, or a tab-delimited format. There is a also Web-based version available that only annotates with default settings, and only annotates a maximum of 20 SNPs at one time. The script may be downloaded for full functionality.
Laboratory for Neural Computation and Cognition
Lab that studies multiple levels of computational modeling and experimental work to understand the neural mechanisms underlying reinforcement learning, decision making and cognitive control.
Matlab toolbox that implements the wavelet-based image fusion technique for orthogonal images, introduced in (Aganj et al, MRM 2012).
Online portal with resources for education about hydrocephalus as well as community resources for those directly affected, family, and friends. The portal includes a community membership opportunity for people and families affected by hydrocephalus.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Online portal with educational resources such as videos, images, diagrams, and descriptions of basal ganglia activity. The model also includes interactions with areas of prefrontal cortex to examine BG roles in higher level cognitive functions such as working memory, attentional shifting, and decision making.
Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The NeuroFed resource is a listing of neuroscience research funding contacts in the Federal government. It is an informal compendium (PDF) of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units of the federal government. An electronic (PDF) version of the most recent update of this list is available on the Society for Neuroscience website at: http://www.sfn.org/index.aspx?pagename=professionalDevelopment_training. The list is updated annually by NIH personnel.
SNPAAMapper - A SNP Amino Acid Mapping tool
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take
Software application designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner. (entry from Genetic Analysis Software)
A not-for-profit, volunteer based charity whose purpose is to find a cure for Parkinson's disease through research, advocacy, education and support services. Parkinson Society Canadas leads initiatives that include: raising funds for research through national events; funding research, movement disorder clinics, and outreach programs across Canada; staffing a national Information and Referral Centre; developing educational and information materials; providing up to date detailed information about Parkinson's disease; and providing support for regional partners to better meet the needs of people living with Parkinson's services. Researchers can apply for various funding awards and fellowships by following the funding process outlined by Parkinson Society Canada.
An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software application that allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on.
The mission of the National Parkinson Foundation is to improve the quality of care for people with Parkinson's disease through research, education and outreach. NPF funds research through four main programs: the Centers of Excellence Network, which focuses on clinical studies of new therapeutic approaches; the Parkinson's Outcomes Project, a large clinical study of Parkinson's disease; the Grants/Clinical Research Fund, which provides funding to individual researchers; and fellowship awards, which are used to train neurologists in the movement disorder specialty.
A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms.
Pennsylvania State Hershey College of Medicine; Pennsylvania; USA
Penn State Hershey College of Medicine; Pennsylvania; USA
Pennsylvania State Hershey College of Medicine
Public, land-grant research university in Pennsylvania, USA. The College of Medicine offers professional degree programs in medicine.
The BioCurrents Research Center (BRC) is an integrated technology resource of the NIH:NCRR. The activities of the Center focus on molecular physiology as it relates to the cell function and disease. Our particular interest is how the dynamics of cell responses are reflected in the chemical profiles of microdomains surrounding single living cells. In order to measure complex cellular boundary layers, the BRC has specialized in the development of extremely sensitive signal acquisition and processing methods along with miniaturized electrochemical sensor designs. The technique is non-invasive and termed self-referencing. Since its establishment in 1996, the BRC has directed its technological research and development to the design and application of ultra-microelectrodes (tip diameters of less than 10m) tailored for the detection of specific chemicals. These have been successfully applied to the boundary layer profiles of many different cell types, with thematic strength in diabetes research, reproductive health and development (see collaborative profiles). More recently, it is changing its focus to technical developments, enhancing the integrative approach to cell function. To understand a cell as a dynamic and integrated whole, BRC must be able to examine responses from different domains as near to real time and as synchronously as possible. To this end, it is developing imaging capabilities to work in parallel with electrochemistry and conventional electrophysiological techniques. Imaging includes a spinning disc confocal, as well as a low light/luminescent imager designed and built within the BRC. The technologies developed or under development are in high demand within the biomedical community. Over 40 investigators work with the Center each year in a collaborative or service capacity. Over 80 of our visitor pool is NIH funded, representing approximately 25 NIH divisions and institutes. As part of our training and dissemination program we host occasional workshops at major national and international meetings, train a significant number of new investigators each year and host graduate students undertaking portions of their thesis dissertation using our technologies. In dissemination we advise on, and install, electrochemical systems in off campus research endeavors, both academic and industrial.
Online tool for utilizing a genotype calling algorithm for next-generation sequence data.
Parkinson's Disease Society of the United Kingdom
Parkinsons Disease Society of the United Kingdom
The Parkinsons Disease Society funds research, offers educational information, advice, and support from medical professionals, and runs campaigns with the goal of offering support, raising money, and finding a cure for Parkinsons disease. In addition to funding research, the Society offers a Helpline to support those suffering from Parkinsons and their caregivers, and also offers a range educational materials. The Society has a network of over 330 branches and support groups located across the UK. Additionally, the Society campaigns for and influences government policy and the development of high-quality services at a local and national level.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 06, 2013. Per the associated paper, Aguirre GK (2012) FIASCO, VoxBo, and MEDx: behind the code. Neuroimage 62: 765-7, the MedX software was discontinued. The website itself however, looks like you can still buy it (website last updated 2004). Highly optimized, portable, commercial software for the visualization, processing, and analysis of medical images. The packages include: SPM '99, FSL, DICOM Import/Export, ABLe, Functional Data Simulator. Designed especially for medical imaging researchers and system developers, MEDx brings multi-modality, multi-dimensional image processing functionality to the medical imaging research community. With MEDx, users display images and control menus using the industry-standard XWindow display system and Tcl/Tk interface language. MEDx transforms your computer into a powerful image processing workstation that displays, analyzes, and processes your medical image data in a myriad of innovative ways.
National VA Parkinson's Disease Consortium
The National VA Parkinson's Disease Consortium
A consortium created to support the provision of optimal care and education for veterans diagnosed with Parkinson's disease and related movement disorders through professional education, collaboration and advocacy.
SHARCGS - SHort read Assembler based on Robust Contig extension for Genome Sequencing
SHort read Assembler based on Robust Contig extension for Genome Sequencing
SHort read Assembler based on Robust Contig extension for Genome Sequencing (SHARCGS)
Software package for a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage.
PDtrials- Parkinsons Disease Clinical Trials
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A collaborative initiative of Parkinson's organizations dedicated to increasing education and awareness about clinical research. PDtrials provides up-to-date information on Parkinson's disease trials currently enrolling participants in the U.S. and Canada, as well as information about Parkinson's studies for people living with PD, their families and caregivers. Researchers can list their own trials on the PDtrials website. Patients can browse trial listings by type, location, symptom, or keyword.
Bgee: dataBase for Gene Expression Evolution
Bgee: dataBase Gene Expression Evolution
Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species. Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of gene expression.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. TheBrainMatters.org is a comprehensive resource for the public that provides information on on more than 250 neurologic disorders . This site combines important information from such credible sources as the American Academy of Neurology and the National Institute of Neurological Disorders and Stroke websites into one clean, organized, and user-friendly site designed specifically for users to become better informed about neurologic disorders.
DMETANALYZER - A tool for supporting pharmacogenomics data analysis
Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way.
Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot.
AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow
An open-source software pipeline for Affymetrix Axiom genotyping workflow.
WebPath - The Internet Pathology Laboratory for Medical Education
This popular web resource includes over 1900 images along with text, tutorials, laboratory exercises, and examination items for self-assessment that demonstrate gross and microscopic pathologic findings associated with human disease conditions. Content includes pathology cases (surgical pathology, autopsy, cytopathology, forensic pathology, clinical pathology) at the University of Utah Health Sciences Center and affiliated hospitals and laboratories, and from contributors at other institutions worldwide. The content at this web site will assist a medical student in achievement of an important goal: passing step 1 of the USMLE examination required to become licensed as a physician. This site was conceived from the necessity to create useful multimedia teaching resources for medical students at the University of Utah for use in the pathology courses given in the second year of the curriculum.
A nonprofit organization dedicated to providing an international forum for the latest scientific discoveries, medical practices and caregiver initiatives related to Parkinson's disease. It hosts the annual World Parkinson Congress, an event which focuses on bringing physicians, scientists, allied health professionals, caregivers and people diagnosed with Parkinson's disease together, in order to create a global dialogue that will help expedite treatment practices and the discovery of a cure .
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The World Parkinson's Disease Association is an alliance of members from all over the world who have come together to share information about Parkinson's disease. In order to further Parkinson's research and better the condition of those diagnosed with the disease, the Association: establishes computerized connections; takes part in and/or finances research activities; urges pharmaceutical companies and government institutions of the various countries to support the guidelines recommended by the associations of Parkinson's patients; and coordinates and promotes interchange of information among its members with the aim of solving problems of mutual interest.
Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome.
Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.
The Image Repository contains a collection of images produced by the research of John Clark's Eye Lab. Experiments include: Irradiated CP49 KO and wildtype, Hypothesis: CP49 KO mice will be more sensitive to X-irradiation than controls Huntington Mice Cataract ID, Hypothesis: Individuals can be identified by the pattern of their cataract. Alpha-Synuclein Mice, Hypothesis: Mice transgenic for the EGFP-tagged, mutant and WT strains of human alpha-synuclein gene, will provide a model for the testing of drugs on aggregation of the protein. alpha B Crystallin/SPARC DKO, Hypothesis: The absence of the chaperone protein, alpha B-Crystallin, causes a greater intensity and earlier onset in the opacifying effects of an absence of the matricellular protein, SPARC. Survey of SPARC KO and WT Survey of SPARC KO and WT Mice The repository is being built through a collaboration between the University of Washington's Department of Biological Structure, led by John Clark, and the Structural Informatics Group, led by Jim Brinkley. As an aim of the Biomedical Information Sciences Technology Initiative (BISTI), members of the Structural Informatics Group have been talking with biomedical researchers to find out their informatics needs. Tools such as this repository are being created in response to those needs. This web tool allows the researchers to add their images to a repository facilitating the organization and management of their data.
WIRM - Web Interfacing Repository Manager
WIRM is an innovative software toolkit that allows the creation of web applications that facilitate the acquisition, integration, and dissemination of multimedia biomedical data over the web, thereby reducing the cost of knowledge sharing. WIRM reduces the complexity of building custom biomedical web applications and it's visual modeling tools enable domain experts to describe the structure of their knowledge, from which WIRM automatically generates full-featured, customizable content management systems. WIRM is a Perl-based application server that provides a high-level programming environment for developing web information systems. WIRM consists of an object-relational database and a suite of Perl interfaces for visualizing, integrating and analyzing heterogeneous multimedia data. WIRM provides facilities for creating context-sensitive views over a multimedia database, allowing developers to rapidly build dynamic web sites that adapt their content and presentation to multiple classes of end-users. WIRM was developed by Rex Jakobovits as part of his PhD dissertation at the University of Washington Computer Science department, under the guidance of Dr. James F. Brinkley of the Department of Biological Structure. The system was generalized from work funded by NIH SBIR grant R43-MH61277-01 and Human Brain Project grant DC/LM02310.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented April 7, 2018. Online portal and searchable database with resources for the greater scientific community such as zoological records, nomenclature guides, and relevant scientific news stories and websites.
ISA Infrastructure for Managing Experimental Metadata
Investigation / Study / Assay (ISA) infrastructure
Investigation / Study / Assay infrastructure
Investigation/Study/Assay (ISA) infrastructure
Investigation/Study/Assay infrastructure
Desktop software suite targeted to curators and experimentalists that assists in the reporting and local management of experimental metadata, engages with minimum information checklists and ontologies and formats studies for submission to international public repositories. The ISA software suite is the product of an ongoing collaboration between various research and service groups from diverse life science domains. It represents an opportunity for the wider research community to start taking data management into their own hands by supporting graduated adherence to community standards and the efficient curation of experimental metadata at source, shielded from underlying complexities. The software suite is comprised of several platform-independent Java-based software components for local use, including a relational database, built around the ISA-Tab format. The components work both as stand-alone applications and as a unified system.
Minimum Information for Biological and Biomedical Investigations
MIBBI: Minimum Information for Biological and Biomedical Investigations
A common portal for minimum information (MI) checklists to act as a one-stop shop for those exploring the range of extant projects, foster collaborative development and ultimately promote gradual integration. Goals include * To increase the visibility of projects developing guidance for the reporting of biological and biomedical science. * To encourage appropriate collaborative development between projects to avoid duplication of effort or competition. * To promote the adoption of consensus guidance on reporting by journals and funders.
NIH Neuroscience Blueprint Cre Driver Network - Expression DB
NIH Neuroscience Blueprint Cre Driver Network Expression DB
Database of microarray analysis of twelve major classes of fluorescent labeled neurons within the adult mouse forebrain that provide the first comprehensive view of gene expression differences. The publicly available datasets demonstrate a profound molecular heterogeneity among neuronal subtypes, represented disproportionately by gene paralogs, and begin to reveal the genetic programs underlying the fundamental divisions between neuronal classes including that between glutamatergic and GABAergic neurons. Five of the 12 populations were chosen from cingulate cortex and included several subtypes of GABAergic interneurons and pyramidal neurons. The remaining seven were derived from the somatosensory cortex, hippocampus, amygdala and thalamus. Using these expression profiles, they were able to construct a taxonomic tree that reflected the expected major relationships between these populations, such as the distinction between cortical interneurons and projection neurons. The taxonomic tree indicated highly heterogeneous gene expression even within a single region. This dataset should be useful for the classification of unknown neuronal subtypes, the investigation of specifically expressed genes and the genetic manipulation of specific neuronal circuit elements. Datasets: * Full: Here you can query gene expression results for the neuronal populations * Strain: Here you can query the same expression results accessed under the full checkbox, with one additional population (CT6-CG2) included as a control for the effects of mouse strain. This population is identical to CT6-CG (YFPH) except the neurons were derived from wild-type mice of three distinct strains: G42, G30, and GIN. * Arlotta: Here you can query the same expression results accessed under the full checkbox, with nine additional populations from the dataset of Arlotta et al., 2005. These populations were purified by FACS after retrograde labeling with fluorescent microspheres. Populations are designated by the prefix ACS for corticospinal neurons, ACC for corticocallosal neurons and ACT for corticotectal neurons, followed by the suffix E18 for gestational age 18 embryos, or P3, P6 and P14 for postnatal day 3, 6 and 14 pups. For each successful gene query the following information is returned: # Signal level line plot: Signal level is plotted on Y-axis (log base 2) for each sample. Samples include the thirty six representing the twelve populations profiled in Sugino et al. In addition, six samples from homogenized (=dissociated and but not sorted) cortex are included representing two different strains: G42-HO is homogenate from strain G42, GIN-HO is homogenate from stain GIN. # Signal level raster plots: Signal level is represented by color (dark red is low, bright red is high) for all samples. Color scale is set to match minimum (dark red) and maximum (bright yellow) signal levels within the displayed set of probe sets. # Scaled signal level raster plots: Same as 2) except color scale is adjusted separately for each gene according to its maximum and minimum signal level. # Table: Basic information about the returned probe sets: * Affymetrix affyid of probe set * NCBI gene symbol, NCBI gene name * NCBI geneID * P-value score from ANOVA for each gene is also given if available (_anv column). P-value represents the probability that there is no difference in the expression across cell types.
Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models.
Protein Signalling Transcriptional Interactions & Inflammation Networks Gateway
Protein Signalling Transcriptional Interactions and Inflammation Networks Gateway
A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis.
Database of known and predicted functional associations between protein posttranslational modifications (PTMs) within proteins. In its first release it contains 13 different PTM types. PTM types are abbreviated in a two letter code as: Ph (phosphorylation), NG (N-linked glycosylation), Ac (acetylation), OG (O-linked glycosylation), Ub (ubiquitination), Me (methylation), SM (SUMOylation), Hy (hydroxylation), Ca (carboxylation), Pa (palmitoylation), Su (sulfation), Ni (nitrosylation) and CG (C-linked glycosylation). These PTMs are present in 25,765 proteins of 8 different eukaryotes. The database is focused on the exploration of the global post-translational regulation of proteins, not only by describing the set of its modifications, but by identifying the functional associations among the PTMs present in the protein. To do that, they combine five different evidence channels based on a literature survey, the modified residue co-evolution, their structural proximity, their competition for the same residue and the location within PTM highly-enriched protein regions (hotspots) and show the functional associations within the context of the protein architecture.
Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.
Software for targeted de novo assembly of microreads with mate pair information and sequencing errors.
NEI established NEHEP to increase awareness among healthcare professionals and the public of scientifically based health information that can be applied to preserving sight and preventing blindness. NEHEP works in partnership with a variety of public and private organizations that conduct eye health education programs. Program activities are designed to promote the importance of early detection and timely treatment of eye disease and the use of vision rehabilitation services using strategies that are culturally appropriate, health-literate, and evidence-based. NEHEP ensures that vision is a health priority by translating eye and vision research into public and professional education programs. NEHEP supports collaboration among eye health professionals, healthcare providers, patients, and the public. NEHEP programs provide healthcare professionals with information, materials, and resources to educate patients and the public about eye health and the importance of comprehensive dilated eye examinations. NEHEP is supported by a Planning Committee and a Partnership, which bring a vast array of knowledge about eye health and experience with populations at higher risk for eye disease. NEHEP Programs *Diabetic Eye Disease: The NEHEP Diabetic Eye Disease (DED) Education Program is designed to increase awareness about DED among people with diabetes, particularly those at higher risk. *Glaucoma: The NEHEP Glaucoma Education Program provides information about glaucoma to people at higher risk as well as those living with the disease. *Low Vision: The NEHEP Low Vision Education Program is designed to create awareness among adults, their families and friends, and the general public about vision rehabilitation services. *Ojo con su Vision: Ojo con su visin or Watch out for your vision is the Spanish-language program of NEHEP that targets the Hispanic/Latino community. Healthy Vision Program Healthy People 2010, the health promotion and disease prevention framework for the Nation, identifies the most significant risks to health and establishes national goals to reduce those risks. Focus area 28 of Healthy People 2010, Vision and Hearing, includes 10 vision objectives known as Healthy Vision. The Healthy Vision objectives identify national eye health concerns, and encourage individuals, organizations, and businesses to help address these concerns in their communities. *Healthy Vision 2010 Focusing on examination and prevention, eye diseases, injury and safety, and vision rehabilitation, Healthy Vision 2010 is designed to help you determine what you can do in your home, community, business, or state to help improve the Nation's eye health. *Healthy Vision Community Awards Program The Healthy Vision Community Awards Program provides awards of up to 10,000 for community-based eye health education programs. The program objectives address examinations and prevention, eye diseases, injury and safety, and vision rehabilitation. *Healthy Vision Month May is Healthy Vision Month, a national eye health observance sponsored by NEI and the National Eye Health Education Program Partnership. Healthy Vision Month is devoted to elevating vision as a public health priority. Each year focuses on a specific eye health topic. *Healthy Vision Community Programs Database The Healthy Vision Community Programs Database is a searchable collection of community-based vision health programs from the different U.S. states and territories. It stimulates ideas for creative eye health education projects and promotes networking among interested groups. Outlook Newsletter: Outlook is the electronic newsletter of the National Eye Health Education Program (NEHEP). Outlook provides quarterly updates on eye health education, disease prevention activities, and NEHEP activities and materials. Related Research: NEHEP represents an extension of the support that NEI provides to vision research, where results are disseminated to health professionals, patients, and the public.
Stanford Genomics Service Center Core Facility
Stanford Medicine Stanford Functional Genomics Facility
Stanford School of Medicine Stanford Functional Genomics Facility
Stanford University Functional Genomics Core Facility
Stanford Genomics formerly Stanford Functional Genomics Facility provides services for high throughput sequencing, single cell assays, gene expression and genotyping studies utilizing microarray and real time PCR, and related services. High throughput sequencing (Illumina HiSeq 4000, NextSeq 500, MiSeq and MiniSeq), microarray gene expression and genotyping services (Affymetrix, Agilent and Illumina). Provides 24/7 access to instruments, equipment and software utilized within genomics field.
POLYmorphism and de novo MUTaTion call in families with sequencing data
Software program that implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the (VCF) format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file. (entry from Genetic Analysis Software)
TissueNet - The Database of Human Tissue Protein-Protein Interactions
Database of human tissue protein-protein interactions (PPIs) that associates each interaction with human tissues that express both pair mates. This was achieved by integrating current data of experimentally detected PPIs with extensive data of gene and protein expression across 16 main human tissues. Users can query TissueNet using a protein and retrieve its PPI partners per tissue, or using a PPI and retrieve the tissues expressing both pair mates. The graphical representation of the output highlights tissue-specific and tissue-wide PPIs. Thus, TissueNet provides a unique platform for assessing the roles of human proteins and their interactions across tissues.
SAMHSAs National Clearinghouse for Alcohol and Drug Information
National Clearinghouse for Alcohol and Drug Information
SAMHSA's National Clearinghouse for Alcohol and Drug Information
THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/15/13. The Nation's one-stop resource for information about substance abuse prevention and addiction treatment offering more than 500 items to the public, many of which are free of charge. They distribute the latest studies and surveys, guides, videocassettes, and other types of information and materials on substance abuse from various agencies, such as the U.S. Departments of Education and Labor, the Center for Substance Abuse Prevention, the Center for Substance Abuse Treatment, the National Institute on Alcohol Abuse and Alcoholism, and the National Institute on Drug Abuse. They staff both English- and Spanish-speaking information specialists who are skilled at recommending appropriate publications, posters, and videocassettes; conducting customized searches; providing grant and funding information; and referring people to appropriate organizations. They are available 24 hours a day, 7 days a week to take your calls at 1-800-729-6686. NCADI services include: * an information services staff (English, Spanish, TDD capability) equipped to respond to the public's alcohol, tobacco, and drug (ATD) inquiries; * the distribution of free or low-cost ATD materials, including fact sheets, brochures, pamphlets, monographs, posters, and video tapes from an inventory of over 1,000 items; * a repertoire of culturally-diverse prevention, intervention, and treatment resources tailored for use by parents, teachers, youth, communities and prevention/treatment professionals; * customized searches in the form of annotated bibliographies from alcohol and drug data bases; * access to the Prevention Materials database (PMD) including over 8,000 prevention-related materials and the Treatment Resources Database, available to the public in electronic form; * rapid dissemination of Federal grant announcements for ATD prevention, treatment, and research funding opportunities.
An alphabetical listing of worldwide neural network research groups and resources.
Medical Image Processing and Visualization
MeVisLab: Medical Image Processing and Visualization
Modular framework for the development of image processing algorithms and visualization and interaction methods, with a special focus on medical imaging. It includes advanced medical imaging modules for segmentation, registration, volumetry, and quantitative morphological and functional analysis. The platform allows fast integration and testing of new algorithms and the development of application prototypes that can be used in clinical environments. In MeVisLab, individual image processing, visualization and interaction modules can be combined to complex image processing networks using a graphical programming approach. The algorithms can easily be integrated using a modular, platform-independent C++ class library. An abstract, hierarchical definition language allows the design of efficient graphical user interfaces, hiding the complexity of the underlying module network to the end user. JavaScript components can be added to implement dynamic functionality on both the network and the user interface level. MeVisLab is based on the Qt application framework, the OpenInventor 3D visualization toolkit and OpenGL. Several clinical prototypes have been realized on the basis of MeVisLab, including software assistants for neuro-imaging, dynamic image analysis, surgery planning, and vessel analysis. Feature Overview: :- Basic image processing algorithms and advanced medical imaging modules :- Full featured, flexible 2D/3D visualization and interaction tools :- High performance for large datasets :- Modular, expandable C++ image processing library :- Graphical programming of complex, hierarchical module networks :- Object-oriented GUI definition and scripting :- Full scripting functionality using Python and JavaScript :- DICOM support and PACS integration :- Intuitive user interface :- Integrated movie and screenshot generation for demonstration purposes :- Generic integration of the Insight Toolkit (ITK) and the Visualization Toolkit (VTK) :- Cross-platform support for Windows, Linux, and MacOS X :- Available for 64-bit operating systems
HUDSEN Electronic Atlas of the Developing Human Brain
Electronic Atlas of the Developing Human Brain
Interactive digital atlas and movies comprising 3-D reconstructions at all stages of human development from Carnegie Stage 12 (CS12; ~26 days post conception (dpc)) to CS23 (~ 56 dpc) and anatomical annotations of the 3-D models linked to an anatomical database. The 3D models are generated using Optical Projection Tomography (OPT; Sharpe et al 2002). The digital atlas is also linked to a gene expression database that has been developed from the Edinburgh Mouse Atlas Project gene expression database (EMAGE). In the future, the HUDSEN EADHB aims to provide the wider scientific and medical communities with a dynamic tool for documenting and analyzing gene expression patterns and morphological changes in the developing human brain.
Propagating Uncertainty in Microarray Analysis
Propagating Uncertainty in Microarray Analysis (PUMA)
Software program for developing probabilistic models for the analysis of microarray data.
Mammalian TRansient receptor potential channel-Interacting Protein Database
A manually curated database of protein-protein interactions (PPIs) for mammalian transient receptor potential (TRP) channels. The detailed summary of PPI data, fits into 4 categories: screening, validation, characterization, and functional consequence. These categorizations give answers for four basic questions about PPIs: how to identify PPIs (screening); how to confirm PPIs (validation); what are biochemical properties of PPIs (characterization); what are biological meaning of PPIs (functional consequence). Users can find in-depth information specified in the literature on relevant analytical methods, gene constructs, and cell/tissue types. The database has a user-friendly interface with several helpful features, including a search engine, an interaction map, and a function for cross-referencing useful external databases.
Washington University Neuromuscular Disease Center
Organization portal for neuromuscular disease community and contains comprehensive listing of biological and clinical aspects of neuromuscular disorders.This knowledge base contains information on the physiology, structure of ion channels, neurotransmitters, neuroreceptors, and associated diseases. Major categories include DISORDERS & SYNDROMES, INDEXES, NEUROMUSCULAR EVALUATION, ANTIBODY TESTING and NEUROMUSCULAR DIVISION.
A database of brain neuroanatomic volumetric observations spanning various species, diagnoses, and structures for both individual and group results. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses. Design strategy: The principle organizing data structure is the "publication". Publications report on "groups" of subjects. These groups have "demographic" information as well as "volume" information for the group as a whole. Groups are comprised of "individuals", which also have demographic and volume information for each of the individuals. The finest-grained data structure is the "individual volume record" which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be grouped into a "group volume" observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group.
Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.
Graphics software for a real-time approach to creating 3D graphics that offers a variety of intuitive, powerful design tools to create your 3D masterpiece. The graphics engine allows for a completely interactive environment, where all operations occur on solid objects in real time. A rendering engine allows you to produce stunning 3D imagery at virtually any resolution for Web, print, digital video, and film. Advanced capabilities include Radiosity rendering for photo-realistic scenes, Raytracing for true-to-life surface reflections and refractions, as well as variable smoke and lighting effects.
Arabidopsis Reactome - a curated knowledgebase of plant biological pathways
Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context.
A protein-protein interaction (PPI) database intending to bridge between the two communities most active in their characterization: structural biology and functional genomics researchers. It offers users access to binary subcomplexes, (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD. Selected web services are available to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms.
NeuralAct: A tool to visualize cortical activity on a 3D model of the cortex
Software to visualize electrocorticographic (ECoG) and possibly also other kinds of neural activity (EEG / EMG/ DOT) on a 3D model of the cortical surface. The tool has been used to produce cortical activation images and image sequences in several recent studies using ECoG. The tool is written in matlab. The package is thoroughly documented and includes a demo.
Automatic molecular interaction predictions
InteroPorc: Automatic molecular interaction predictions
Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.
PurBayes: Bayesian Estimation of Tumor Purity and Clonality
An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.
Cell Signaling and Neuroscience: Pathway Slides and Charts
Cell Signaling & Neuroscience Pathway Slides & Charts
Cell Signaling and Neuroscience Pathway Slides and Charts
Free, downloadable Cell Signaling and Neuroscience Pathway Slides with an overview of the pathway and its links to Your Favorite Gene. There you can explore dynamic pathways and locate products in the context of your research. Each overview contains helpful links to the biological pathways, interaction networks, gene details and related products. Slide Categories: *Apoptosis and Cell Cycle *Cytokines, Growth Factors and Hormones *Cytoskeleton and Extracellular Matrix *Gene Regulation and Expression *G Proteins and Cyclic Nucleotides *Immune Cell Signaling and Blood *Ion Channels *Lipids in Cell Signaling *Multi-Drug Resistance *Neurobiology *Neurotransmission *Nitric Oxide and Cell Stress *Protein Phosphorylation
Cell signaling pathways can be explored using PathFinder, the interactive, online graphical representation of cell signaling pathways. The user can use PathFinder to explore the relationships between different cell signaling pathway components while being presented with our high quality small molecules, antibodies, enzymes, siRNA for gene knockdown and qPCR components to aid them in their research.
Privately held company that develops and produces antibodies, ELISA kits, ChIP kits, proteomic kits, and other related reagents used to study cell signaling pathways that impact human health.
Warping tool for intersubject registration of brain images consisting of C functions for Unix systems plus Matlab visualization utility functions. Apart from warping there are also (command line) functions for ANALYZE header information, mirroring, translation, subsampling. The package cannot only be used as a preprocessing step in function neuroimaging but also as a step in deformation-based morphometry.
A software program to call short indels and SNPs for Ion Torrent and 454 data.
NeuronJ: An ImageJ Plugin for Neurite Tracing and Quantification
NeuronJ is an ImageJ plugin to facilitate the tracing and quantification of elongated structures in two-dimensional (2D) images (8-bit gray-scale and indexed color), in particular neurites in fluorescence microscopy images. Sponsors: The development of NeuronJ started while the primary developer ( Dr. Erik Meijering, PhD) was with the Biomedical Imaging Group (collaborating with people from the Laboratory of Cellular Neurobiology) of the Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland, and was finished while Dr. Meijering was with the Biomedical Imaging Group Rotterdam in the Netherlands.
flowViz - Visualization for flow cytometry
Software that provides visualization tools for flow cytometry data.
Database of the Human Proteotheque Initiative
The Human Proteotheque Initiative is a multidisciplinary project aimed at building a repertoire of comprehensive maps of human protein interaction networks. The information contained in the Proteotheque is made publicly available through an interactive web site that can be consulted to visualize some of the fundamental molecular connections formed in human cells and to determine putative functions of previously uncharacterized proteins based on guilt by association. The process governing the evolution of HuPI towards becoming a repository of accurate and complete protein interaction maps is described.
Database of annotations of functional units in proteins including multiple sequence alignment models for ancient domains and full-length proteins. This collection of models includes 3D structures that display the sequence/structure/function relationships in proteins. It also includes alignments of the domains to known three-dimensional protein structures in the MMDB database. The source databases are Pfam, Smart, and COG. Users can identify amino acids in protein sequences with the resources available as well as view single sequences embedded within multiple sequence alignments.
The GBG's mission is to manage and assess molecular interaction data obtained through multiple platforms, increase the understanding of the effect of those interactions on the chemosensitivity of cancer, and create tools that will facilitate that process. Translation of that information will be directed towards the recognition of diagnostic and therapeutic cancer biomarkers, and directed cancer therapy.
CASY Cell Counter and Analyser System Model TT
CASY Cell Counter + Analyser System Model TT
CasyTon Cell Counter and Analyser System
Tool for the qualitative and quantitative assessment of cell cultures including standardized cell counting methods, viability checks, aggregation correction, volumetric measurement with high measuring range dynamics. It enables to create optimal settings for measuring certain cell population numbers (based on size and gating strategies).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
SpliceAid-F: a database of human splicing factors and their binding sites
A database of human splicing factors and their RNA - binding sites. For each splicing factor (SF) the database reports its functional domains and its protein and chemical interactors. Furthermore, experimentally validated RNA-SF interactions are collected, including relevant information on the RNA binding sites such as the genes where these sites lie, their genomic coordinates, the splicing effects, experimental procedures, as well as the corresponding bibliographic references. Information from experiments showing no RNA-SF binding is also collected, at least in the assayed conditions. SpliceAid-F contains 4227 interactions, 2622 RNA binding sites and 1170 no-binding sites, including information on binding and no-binding specificity in different cellular contexts. SpliceAid-F can provide significant information to explain an observed splicing pattern as well as the effect of mutations in functional regulatory elements.
Vennt - Dynamic Venn diagrams for Differential Gene Expression
A web-tool to generate dynamic Venn diagrams for differential gene expression.
Integrating Network Objects with Hierarchies
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio-molecules that constitute signal transduction pathways or biological events in general. As most part of this knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form. The system provides pathway information as a composite of biological events, since functional knowledge is usually described as a set of fragmented processes. Each event is annotated with entries of a event ontology, which also has links to GO.
An index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. iRefIndex project has three long term objectives: # to facilitate exchange of interaction data between interaction databases. # to consolidate interaction data from multiple sources. # to provide feedback to source interaction databases. iRefIndex is made available in a number of formats: MITAB tab-delimited text files, iRefWeb interface, iRefScape plugin for Cytoscape, PSICQUIC Web services, and an interface for the R programming language environment.
A database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored. After submitting a query you can further refine the results using the new heat map retrieval tool to quickly find the entries that are most relevant to you. Text classification helps you find candidate peptides that are related to cancer, cardiovascular diseases, diabetes, apoptosis, angiogenesis and molecular imaging or peptides for which binding data exist.
Chemical Entities of Biological Interest
Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2017. Database of images depicting the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli. A number of different display and comparison tools are provided allowing patterns to be viewed from different perspectives, and descriptions of the methods and interpretations of these data are provided. Some of the more advanced tools require you to download software.
SA Instruments | Model 1025 MR-compatible Small Animal Monitoring and Gating System
MR-Compatible Model 1025 Monitoring and Gating System
Small Animal Monitoring and Gating System
Magnetic resonance compatible monitoring and gating system, including software, that enables monitoring rectal temperature, electrocardiogram and respiration rate during magnetic resonance imaging scan time. The PC displays multiple waveforms, measured values, trends and gating pulses. The data Acquisition modules are controlled by menu driven software from the PC. Data acquisition modules are available to measure the following parameters: ECG, respiration (three ways), temperature (two ways), pressure including invasive blood pressure (two ways), oxygen saturation and end-tidal CO2.
A toolset for the morphometric analysis and visualization of 3D models derived from electron microscopy image stacks. It is designed to import, analyze, and visualize mesh models. It has been designed specifically for the morphological analysis of 3D objects derived from serial electron microscopy images of brain tissue, although much of its functionality can be applied to any 3D mesh. These models can be generated by software that allows the images to be segmented so that 3D objects can be built. These objects can be generated by any 3D image segmentation software, such as ilastik or Fiji. The NeuroMorph toolset has been developed as a set of add-ons for Blender, a widely used free and open source 3D modeling software package.
SnPM - Statistical NonParametric Mapping - A toolbox for SPM
A toolbox for Statistical Parametric Mapping (SPM) that provides an extensible framework for voxel level non-parametric permutation/randomization tests of functional Neuroimaging experiments with independent observations. SnPM uses the General Linear Model to construct pseudo t-statistic images, which are then assessed for significance using a standard non-parametric multiple comparisons procedure based on randomization/permutation testing. It is most suitable for single subject PET/SPECT analyses, or designs with low degrees of freedom available for variance estimation. In these situations the freedom to use weighted locally pooled variance estimates, or variance smoothing, makes the non-parametric approach considerably more powerful than conventional parametric approaches, as are implemented in SPM. Further, the non-parametric approach is always valid, given only minimal assumptions. The SnPM toolbox provides an alternative to the Statistics section of SPM.
flowTrans - Parameter Optimization for Flow Cytometry Data Transformation
Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations.
Online platform for visualizing and editing the morphology of neurons. Written in Java.
Protein interaction and molecular information database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. PRIME is a developed version of Kinase Pathway Database which is an integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface. The protein-protein interactions are extracted by natural language processing (NLP) from abstracts using basic word pattern and protein name dictionary GENA: developed by our group. In this system, pathways are easily compared among species using protein interactions data more than 1,510,000 and orthologous tables. Further, using other organisms interaction data, interaction prediction is also possible.
Spliceosome Database - A source of information for the SLPICEOSOME: The large ribonucleoprotein complex responsible for pre-mRNA splicing
A database of proteins and RNAs that have been identified in various purified splicing complexes. Various names, orthologs and gene identifiers of spliceosome proteins have been cataloged to navigate the complex nomenclature of spliceosome proteins. Links to gene and protein records are also provided for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, tools were created to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes.
cisRED - Databases of genome-wide regulatory module and element predictions
Database for conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. The database offers information on atomic motifs, motif groups and patterns. In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, a base set of probabilistic ab initio discovery tools is used, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes. In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species.
THIS RESOURCE IS NO LONGER IS SERVICE. Documented on July,29,2022. Surface-based atlases of human, macaque, rat and mouse cerebral and cerebellar cortices derived from structural MRI volumes developed in the Van Essen laboratory can be downloaded by direct links on the SumsDB database and can be viewed using freely available Caret (offline) and WebCaret (online) software. The human and macaque atlases include a large and growing compendium of experimental data pertaining to the structural and functional organization of primate cerebral cortex.
Pathway Analysis Tool for Integration and Knowledge Acquisition
Pathway Analysis Tool for Integration and Knowledge Acquisition (PATIKA)
PATIKA - Pathway Analysis Tools for Integration and Knowledge Acquisition
The human pathway database which contains different biological entities and reactions and software tools for analysis. PATIKA Database integrates data from several sources, including Entrez Gene, UniProt, PubChem, GO, IntAct, HPRD, and Reactome. Users can query and access this data using the PATIKAweb query interface. Users can also save their results in XML or export to common picture formats. The BioPAX and SBML exporters can be used as part of this Web service.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A comprehensive collection of manually curated information from literature as well as public domain databases on signaling and metabolic pathways. PathArt includes a dynamic pathway articulator component, which builds molecular interaction networks from curated databases. PathArt provides a tool for analysis, biological interpretation and visualization of microarray data results in these curated pathways. In addition, PathArt provides a collection of high priority disease and physiology pathways with emphasis on pathway responsive genes and knockouts. The coverage is for pathways of Human, Rat and Mouse for cell specific, tissue specific and organism specific data. The present version of PathArt covers the following: -Includes 3527 regulatory and signaling pathways across diseases and physiologies. -Provides information on 39 high priority diseases, and pathway and disease responsive genes. -Provides pathway information on 23 diverse physiologies. -Covers information on ~8783 Knockouts and ~18000 mutation data points. -Coverage of pathways for Human, Mouse and Rat for cell specificity, tissue specificity and organism specific data.
Alternative Splicing Prediction Data Base
ASPicDB - A Database tool for alternative splicing analysis
A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.
Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013)
Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
HEXEvent - a database of Human EXon splicing Events
A free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser. This list can be restricted by the user to either only a specific region in the genome (by specifying the chromosome, the strand and the start and end position), to a whole chromosome or to a group of genes. Furthermore, exons can be filtered according to their splicing type (constitutive exons, cassette exons and exons with one or more alternative 3' and/or 5' splice sites). In order to extract a customized set of exons, the user-specific definitions of exon types can be fixed. The user needs to specify in what fraction of ESTs an exon is allowed to be alternatively spliced in order to still be called constitutive. Furthermore, the user can restrict the set of requested cassette exons by a certain upper inclusion level, which, for instance, is useful when only looking for low-inclusion exons.
A database of new exon boundaries induced by pathogenic mutations in human disease genes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web application used to exploration of protein pathways. It provides analysis and navigation within networks, overviews of biological connections between proteins, access to relevant literature and annotations, and comparisons of interaction and functional domains.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A comprehensive human kinase interactome and phospho-protein database. PhosphoPOINT also annotates any amino acids near the phosphorylation sites where a cSNP may cause a phosphorylation site to be lost, and at the same time identifies how such alteration of the phosphorylation site may lead to human disease. PhosphoPOINT integrates 4,195 phospho-proteins, 518 serine/threonine/tyrosine kinases, and their corresponding PPI datasets with the goal of delineating the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. PhosphoPOINT has integrated human protein kinases, phospho-proteins, and PPI datasets with the goal to delineate four kinds of links among kinases. These include their interacting proteins, substrates, and substrates as well as interacting phospho-proteins. Some of these interacting proteins for kinases are phospho-proteins, which might have the potential to serve as substrates for the interacting kinases.
Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.
It helps molecular cell biologists manage and test their increasingly complex mechanistic hypotheses. ProcessDB does this with a bio-savvy graphical user interface that helps users formulate, visualize, compare, modify, manage and test their own mechanistic theories of cellular function. All models in ProcessDB can be automatically combined with user-specified experimental protocols and exported to the Berkeley Madonna solver for testing against experimental data. ProcessDB allows investigators to know with precision what their theories predict, and speeds discovery of mechanisms that account for all of the available data. ProcessDB, which is accessable from any Internet-connected computer, offers a highly secure and professionally maintained tool that supports mechanistic knowledge management for research laboratories working on complex biological or biomedical problems.
Database of non-redundant sets of protein - small-molecule complexes that are especially suitable for structure-based drug design and protein - small-molecule interaction research. PSMB supports: * Support frequent updates - The number of new structures in the PDB is growing rapidly. In order to utilize these structures, frequent updates are required. In contrast to manual procedures which require significant time and effort per update, generation of the PSMDB database is fully automatic thereby facilitating frequent database updates. * Consider both protein and ligand structural redundancy - In the database, two complexes are considered redundant if they share a similar protein and ligand (the protein - small-molecule non-redundant set). This allows the database to contain structural information for the same protein bound to several different ligands (and vice-versa). Additionally, for completeness, the database contains a set of non-redundant complexes when only protein structural redundancy is considered (our protein non-redundant set). The following images demonstrate the structural redundancy of the protein complexes in the PDB compared to the PSMDB. * Efficient handling of covalent bonds -Many protein complexes contain covalently bound ligands. Typically, protein-ligand databases discard these complexes; however, the PSMDB simply removes the covalently bound ligand from the complex, retaining any non-covalently bound ligands. This increases the number of usable complexes in the database. * Separate complexes into protein and ligand files -The PSMDB contains individual structure files for both the protein and all non-covalently bound ligands. The unbound proteins are in PDB format while the individual ligands are in SDF format (in their native coordinate frame).
Database of Drosophila transcription factor DNA binding specificity using the bacterial one-hybrid method, DNase I or SELEX methods. The database provides community access to recognition motifs and position weight matrices for transcription factors (TFs), including many unpublished motifs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within the database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome. This database and its associated tools provide computational and experimental biologists with resources to predict interactions between Drosophila TFs and target cis-regulatory sequences.
Commercial supplier of antibodies, reagents, and dyes for research.
Protein families database of alignments and HMMs
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. iPfam is a resource that describes physical interactions between those Pfam domains that have a representative structure in the Protein DataBank (PDB). When two or more domains occur within a single structure, the domains are analysed to see if they form an interaction. If the domains are close enough to form an interaction, the bonds that play a role in that interaction are determined. The goal has been to re-calculate iPfam interaction data for each new Pfam release, so that, as Pfam changes, the information within iPfam remains up to date.
Protein Interactions by Structural Matching
It is a web-server that can be used to explore protein interfaces and predict protein-protein interactions. It is a website for protein interface analysis and prediction of putative protein-protein interactions. It is composed of a database holding protein interface structures derived from the Protein Data Bank (PDB). The server also includes summary information about related proteins and an interactive protein interface viewer. A list of putative protein-protein interactions obtained by running our prediction algorithm can also be accessed. These results are applied to a set of protein structures obtained from the PDB at the time of algorithm execution. Users can browse through the non-redundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of similar structures to these interfaces or see the results of interaction predictions for a particular protein. Another service provided is interactive prediction. This is done by running the algorithm for user input structures.
Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal.
The Protein Quaternary Structure file server ( PQS ) is an internet resource that makes available coordinates for likely quaternary states for structures contained in the Brookhaven Protein Data Bank that were determined by X-ray crystallography.
It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate.
National Center for Marine Algae and Microbiota
Provasoli-Guillard National Center for Culture of Marine Phytoplankton
Provasoli-Guillard National Center for Marine Algae and Microbiota
National marine phytoplankton collection, maintaining over 2700 strains from around the world, most are marine phytoplankton but they also have benthic, macrophytic, freshwater and heterotrophic organisms - now incorporating bacteria and viruses. Strain records have (when available): * collection and isolation information * culturing medium recipes and growth conditions * photographs * GenBank accession link * collection site map * link to the taxonomic database Micro*scope The deposition of new strains are welcome if the strains are a valuable addition to the collection. Examples include strains that are referred to in publications, contain interesting molecular, biochemical or physiological properties, are the basis for taxonomic descriptions, are important for aquaculture, or are from an unusual geographical location or ecological habitat. The NCMA offers a course in phytoplankton culturing techniques and facilities for visiting scientists are available at the new laboratories in East Boothbay, Maine. Services include: Mass Culturing DNA and RNA, Purification, Private Holdings, Culture Techniques Course, Visiting Scientists, Single Cell Genomics, Flow Cytometry, Corporate Alliances and Technology Transfer.
Databases that represent sets of pre-compiled information on biological relationships and associations, interactions and facts which have been extracted from the biomedical literature using Ariadne's MedScan technology. ResNet databases store information harvested from the entire PubMed in a formal structure that allows searching, retrieval and updating by Pathway Studio user. ResNet is seamlessly installed when Pathway Studio is installed. There are several available ResNet databases: *ResNet Mammalian Database includes data for Human, Rat, and Mouse *ResNet Plant Database has data on Arabidopsis, Rice and several other plants. Features of ResNet: *All extracted relations have linked access to the original article or abstract *Synonyms and homologs are included to maintain gene identity and to obviate redundancy in search results *Users can update ResNet as often as required using the MedScan technology built into all Ariadne products *Updates are made available by Ariadne every quarter To purchase Pathway Studio software with ResNet database, for information, or to schedule a web demonstration, call our sales department at (240) 453-6272, or (866) 340-5040 (toll free)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Biochemical Pathways Reaction Kinetics Database
System for Analysis of Biochemical Pathways Reaction Kinetics Database
System for the Analysis of Biochemical Pathways - Reaction Kinetics Database
A database based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modelers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. SABIO-RK contains and merges information about reactions such as reactants and modifiers, organism, tissue and cellular location, as well as the kinetic properties of the reactions. The type of the kinetic mechanism, modes of inhibition or activation, and corresponding rate equations are presented together with their parameters and measured values, specifying the experimental conditions under which these were determined. Links to other databases are provided for users to gather further information and to refer to the original publication. Information about reactions and their kinetic data can be exported to an SBML file. The reaction kinetics data are obtained by manual extraction from literature sources and curated.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. An online database of two-hybrid protein interactions in B. Subtilis. Interactions stored in SPID are either characterized by experimental evidence or by bibliographic references. A graphical user interface is provided to explore interaction networks as well as to view the details of each piece of evidence. The database contains 112 interactions between 79 proteins.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 29,2022. This database is an attempt to catalog in a convenient, searchable fashion the publicly available information about the identities of mammalian proteins that become covalently adducted by chemically-reactive metabolites of xenobiotic agents. At present all entries pertain to well-identified proteins that become adducted following defined exposures to known chemical agents in vivo or in cell culture experiments. Results from studies using enzymatic or chemical model systems have not been included but may be in the future. The search functions are relatively simple and intuitive, so most users can go straight to the Search page and begin searching. Additional explanations, examples and information about possible future expansions may be found.
The Liver Specific Gene Promoter Database
LSPD provides liver specific gene. It lists ~300 promoter regions responsible for liver specific transcriptions, collect ~400 experimentally verified regulatory regions and elements, provide information on transcription regulation of liver genes, compare transcription regulation of functionally or evolutionarily related genes, and retrieve sequences of the promoter region. Its regulatory elements provides information on transcription regulatory elements, reports the methods for verification of the elements, records binding affinity and regulatory function, and summarizes the site distribution and sequence consensus.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2022. InterPare is a database server for protein interaction interface information. It contains large-scale interface data of proteins whose 3D-structures are known. Protein interface information is derived from three different methods. InterPare introduces a large-scale protein domain interaction interface database called InterPare. InterPare uses three methods: 1) the Euclidean distance method for checking the distance among subunits in multidomain proteins, 2) Accessible Surface Area (ASA) for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, 3) the Voronoi diagram, a computational geometry method, that uses a mathematical definition of interface regions. InterPare includes tools with different display modes for viewing protein interior, surface, and interaction interfaces.
A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP.
The SEED is a framework to support comparative analysis and annotation of genomes. The cooperative effort focuses on the development of the comparative genomics environment and, more importantly, on the development of curated genomic data. Curation of genomic data (annotation) is done via the curation of subsystems by an expert annotator across many genomes, not on a gene by gene basis. From the curated subsystems we extract a set of freely available protein families (FIGfams). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free RAST-Server (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the Metagenomics-RAST-Server freely available. We also provide a SEED-Viewer that allows read-only access to the latest curated data sets. We currently have 58 Archaea, 902 Bacteria, 562 Eukaryota, 1254 Plasmids and 1713 Viruses in our database. All tools and datasets that make up the SEED are in the public domain and can be downloaded at ftp://ftp.theseed.org
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.The TFe provides details of transcription factor binding sites in close collaboration with Pazar, a public database of transcription factor and regulatory sequence information. The long-term goal of TFe is to create an online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes, combining a mixture of both expert-curated and automatically-populated content to provide users with a wide set of information relevant to a transcription factor protein of their interest.
Stress Responsive Transcription Factor Database
Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method.
Collection of eukaryotic promoters derived from published articles. Annotated non-redundant collection of eukaryotic POL II promoters, for which transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.
A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.
Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community.
Yeast consensus metabolic network - A consensus reconstruction of yeast metabolism
This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map that is periodically updated by a team of collaborators from various research groups. The first version of this reconstruction was published in Herrgrd, Swainston et al. (2008) A consensus yeast metabolic reconstruction obtained from a community approach to systems biology Nature Biotechnol. 26, 1155-1160 (you can access that network here). A second version has now been released and is awaiting publication. We plan on continuing to update this resource towards a complete metabolic network of yeast. All versions will remain accessible for historical purposes, however it is highly recommended that you always use the latest one since that is the most up to date. This effort started on the shoulders of a number of reconstructions of the metabolic network of yeast based on genomic and literature data that were published separately. (iMM904 and iLL672) However, due to the different approaches utilized in them, those earlier reconstructions had a significant number of differences. In addition they suffered from the use of non-standard names and overall they were not annotated with methods that are machine-readable. A community effort in 2007, led by the Manchester Centre for Integrative Systems Biology and the YSBN resulted in a consensus network representation of yeast metabolism, reconciling the earlier results. That effort is now ongoing under the leadership of the MCISB and with collaboration with colleagues under the UNICELLSYS FP7 project. Availability The network reconstruction is primarily assembled and provided as an SBML file enriched with MIRIAM-compliant annotations (which are embedded in the SBML through RDF). All small and macro- molecules are referenced to an authoritative database (e.g. Uniprot, ChEBI, etc.). All molecules and reactions are also annotated with appropriate publications that contain supporting evidence. Thus this network is entirely traceable and is presented in a computational framework. SBML is a format that is understood by a large number of software applications (see sbml.org). While the SBML file is the most efficient computational resource for these data, casual users also need access to the network. That is provided by a searchable relational database accessed directly from this website. The database pages also allow readers to add comments to any chemical species or reaction. Such comments are taken into consideration by the team collating new versions of the network and can lead to corrections and additions to the network. This reconstruction is provided in the following formats: :* an SBML file containing the reaction network and annotations, located to specific sub-cellular compartments :* an SBML file containing the reaction network and annotations without subcellular compartmentation (all reactions happening in a single compartment). :* a searcheable relational database, which uses the B-Net software from Pedro Mendes' group. The database version of this data set is managed with the B-Net software created in Pedro Mendes' group at the Virginia Bioinformatics Institute. B-Net's schema is a detailed representation of the underlying biochemistry and regulation. A number of reconstructions of the metabolic network of yeast based on genomic and literature data have been published. However, due to different approaches utilized in the reconstruction as well as different interpretations of the literature, the earlier reconstructions have significant number of differences. A community effort resulted in a consensus network model of yeast metabolism, combining results from previous models.
A curated database that strives to annotate gene promoters identified from ChIP-Seq experiment results. The long term goal of the database is to provide an integrated resource for mammalian gene transcriptional regulation and epigenetics. Users can search based on Enterz gene id/symbol, or by tissue/cell specific activity and filter results based on any combination of tissue/cell specificity, known/novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. It is also integrated with GBrowse genome browser for visualiztion of ChIP-seq profiles and display the annotations.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. It investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP.
Database of confirmed translation initiation sites (TISs) for prokaryotic genomes. The confirmed data has supporting evidence from different sources, including experiments records in the public protein database Swiss-Prot, literature, conserved domain search and sequence alignment among orthologous genes. Combing with predictions from the-state-of-the-art TIS predictor MED-Start/MED-StartPlus (in release 1.0 & 1.2) and TriTISA (since release 1.4) and annotations on potential regulatory signals, the database can serve as a refined annotation resource for the public database RefSeq.
Set of programs and Tk/Tcl scripts, with a GUI wrapper, for extracting the inner and outer cortical surfaces from a T1-weighted MR image of the human brain. It is based on the TFI C++ library and is written for a Unix-based environment (specifically 64-bit and 32-bit versions of Ubuntu). As a courtesy to Apple users a version for Apple/X11 is maintained but the OS X version will always lag the Linux version; also, because some of the third-party libraries SurfRelax relies on may not be supported in or compatible with future versions of OS X, there is no guarantee that the OS X version will be supported indefinitely. Although in principle SurfRelax could be run under Windows (using Cygwin), because of the difficulties of maintaining multiple platforms and the limited support libraries available under Cygwin, there will no longer be support for SurfRelax on this platform. The surfaces are guaranteed to be topologically equivalent to a sphere, thereby obviating the need for handle removal. SurfRelax requires no user intervention, although minor manual editing is recommended for optimal results (normally less than 10 minutes per hemisphere). SurfRelax has several properties that compare favorably with other software packages for surface reconstruction: * Free software - The binaries (written in C++ and Tcl/Tk) are in the public domain. The source code will be released once legacy code issues have been resolved (i.e. replacing with GPL code). * Uses standard public file formats: Analyze file format (SPM/FSL-compatible) for volumes and OOGL OFF binary format for surfaces (see www.geomview.org (http://www.geomview.org/docs/html/geomview_26.html#OOGLRef)) * Combines advantages of volumetric and surface-based methods for surface generation * Correct topology of output surface guaranteed * Requires little or no user intervention - no need for manual handle removal * Relatively robust to noise - multi-scale method compensates for partial volume effects and intensity inhomogeneities * Relatively fast (an entire brain is segmented, extracted and unfolded in less than 2 hours of CPU time) * Powerful editing and visualization tools for volumes and surfaces * Readily extendable - for instance for use with monkey brains or children's brains * Can be used to visualize functional data from SPM or FSL * Includes tools for integration with Stanford's VISTASOFT tools for FMRI data analysis (white.stanford.edu)
High resolution, compact and robust confocal that enables immunohistochemical colocalization analysis of florescent markers. Leica TCS SPE confocal point-scanning, spectral system for fluorescence imaging of live or fixed cells.
Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style.
A web-based application designed from a genetic epidemiology point of view to analyze association studies using single nucleotide polymorphisms (SNPs). For each selected SNP, you will receive: * Allele and genotype frequencies * Test for Hardy-Weinberg equilibrium * Analysis of association with a response variable based on linear or logistic regression * Multiple inheritance models: co-dominant, dominant, recessive, over-dominant and additive * Analysis of interactions (gene-gene or gene-environment) If multiple SNPs are selected: * Linkage disequilibrium statistics * Haplotype frequency estimation * Analysis of association of haplotypes with the response * Analysis of interactions (haplotypes-covariate)
Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium.
flowQB - Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q
flowQB: Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q
A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.
Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.
Database of unannotated short single-read primarily genomic sequences from GenBank including random survey sequences clone-end sequences and exon-trapped sequences. The GSS division of GenBank is similar to the EST division, with the exception that most of the sequences are genomic in origin, rather than cDNA (mRNA). It should be noted that two classes (exon trapped products and gene trapped products) may be derived via a cDNA intermediate. Care should be taken when analyzing sequences from either of these classes, as a splicing event could have occurred and the sequence represented in the record may be interrupted when compared to genomic sequence. The GSS division contains (but is not limited to) the following types of data: * random single pass read genome survey sequences. * cosmid/BAC/YAC end sequences * exon trapped genomic sequences * Alu PCR sequences * transposon-tagged sequences Although dbGSS sequences are incorporated into the GSS Division of GenBank, annotation in dbGSS is more comprehensive and includes detailed information about the contributors, experimental conditions, and genetic map locations.
Cinteny Server for Synteny Identification and Analysis of Genome Rearrangement
Online database for finding and analyzing syntenic regions across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.The goal of The Gene Index Project is to use the available Expressed Sequence Transcript (EST) and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these with information regarding the functional roles played by these genes and their products. The promise of genome projects has been a complete catalog of genes in a wide range of organisms. While genome projects have been successful in providing reference genome sequences, the problem of finding genes and their variants in genomic sequence remains an ongoing challenge. TGI has created an inventory that contains genes and their variants together with description. In addition, this resource is attempting to use these catalogs to find links between genes and pathways in different species and to provide lists of features within completed genomes that can aid in the understanding of how gene expression is regulated. DATABASES *Eukaryotic Gene Orthologues (formerly known as TOGA - TIGR Orthologous Gene Alignment): Eukaryotic Gene Orthologues (EGO) at DFGI are generated by pair-wise comparison between the Tentative Consensus (TC) sequences that comprise the Dana Farber Gene Indices from individual organisms. The reciprocal pairs of the best match were clustered into individual groups and multiple sequence alignments were displayed for each group. *GeneChip Oncology Database (GCOD):Cancer gene expression database is a collection of publicly available microarray expression data on Affymetrix GeneChip Arrays related to human cancers. Currently only datasets with available raw data (Affymetrix .CEL files) are processed. All processed datasets were subjected to extensive manual curation, uniform processing and consistent quality control. You can browse the experiments in our collection, perform statistical analysis, and download processed data; or to search gene expression profiles using Entrez gene symbol, Unigene ID, or Affymetrix probeset ID. *Gene Indices: As of July 1, 2008, there are 111 publicly available gene indices. They are separated into 4 categories for better organization and easier access. Animal: 41, Plant: 45, Protist: 15, Fungal: 10 *Genomic Maps: Human, mouse, rat, chicken, drosophila melanogaster, zebrafish, mosquito, caenorhabditis elegans, Arabidopsis thaliana, rice, yeast, fission yeast Dana-Farber Cancer Institute (DFCI) Gene Indices Software Tools: *TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets. *GICL: this package contains the scripts and all the necessary pre-compiled binaries for 32bit Linux systems. *clview: an assembly file viewer. *SeqClean:a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences. *cdbfasta/cdbyank: fast indexing/retrieval of fasta records from flat file databases. *DAS/XML Genomic Viewer The Genomic viewer borrows modules from http://www.biodas.org (lstein (at) cshl.org) & http://webreference.com.
Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
High Throughput Genomic Sequences Division
Database of high-throughput genome sequences from large-scale genome sequencing centers, including unfinished and finished sequences. It was created to accommodate a growing need to make unfinished genomic sequence data rapidly available to the scientific community in a coordinated effort among the International Nucleotide Sequence databases, DDBJ, EMBL, and GenBank. Sequences are prepared for submission by using NCBI's software tools Sequin or tbl2asn. Each center has an FTP directory into which new or updated sequence files are placed. Sequence data in this division are available for BLAST homology searches against either the htgs database or the month database, which includes all new submissions for the prior month. Unfinished HTG sequences containing contigs greater than 2 kb are assigned an accession number and deposited in the HTG division. A typical HTG record might consist of all the first-pass sequence data generated from a single cosmid, BAC, YAC, or P1 clone, which together make up more than 2 kb and contain one or more gaps. A single accession number is assigned to this collection of sequences, and each record includes a clear indication of the status (phase 1 or 2) plus a prominent warning that the sequence data are unfinished and may contain errors. The accession number does not change as sequence records are updated; only the most recent version of a HTG record remains in GenBank.
Informational portal that aggregates information about databases for next gen sequencing.
New Energy and Industrial Technology Development Organization
New Energy and Industrial Technology Development Database
A database of sequence data of cDNA clones from the Kazusa DNA Research Institute human spleen cDNA library, which was determined by the NEDO human cDNA sequencing project. The cDNAs supplied by Kazusa DNA Research Institute were generated by conventional methods and strictly size-selected from a cDNA library of adult human spleen. Consequently, not all of the cDNAs may be full-length, though all possess relatively long cDNA inserts, whose average size is about 4.5 kb. cDNAs having unknown end sequences and high protein-coding probability at their 5-prime ends were selected and sequenced. The physical maps were constructed on the basis of the sequence data of the cDNA clones. RepeatMasker, which is a program that screens DNA sequences for interspersed repeats known to exist in mammalian genomes, was applied to detect repeat sequences in cDNA sequences. The predicted protein sequences were examined for motifs present in the PROSITE database. Because weakly defined sequence motifs appear too many times in the HUGE database and are, thus, unlikely to be informative, several motifs were excluded from the analysis, including amidation site, N-glycosylation site, and cAMP- and cGMP-dependent protein kinase phosphorylation site.
neuRosim: Functions to Generate fMRI Data Including Activated Data Noise Data and Resting State Data
Software package that allows users to generate fMRI time series or 4D data. Some high-level functions are created for fast data generation with only a few arguments and a diversity of functions to define activation and noise. For more advanced users it is possible to use the low-level functions and manipulate the arguments.
Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits.
Sequence Tag Alignment and Consensus Knowledgebase Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index
Syzygy - SNP and indel calling for pooled and individual targeted resequencing studies
A targeted sequencing post processing analysis software tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant. (entry from Genetic Analysis Software)
Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins
TcoF - Dragon database of transcription co-factors and transcription factor interacting proteins
Database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions (transcription co-factors).
Benchtop high-performance cell sorter with multiple lazer, detector and fluoroscrome options. Allows detection of 12 parameters (10 color conjugates, forward and sideward scatter).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. This website contains a library of WD-repeat containing proteins in which the repeats appear as multi-aligned sets. WD-repeat-containing proteins are those that contain 4 or more copies of the WD-repeat (tryptophan-aspartate repeat), a sequence motif approximately 31 amino acids long, that encodes a structural repeat. This repeat is described by the following profile, where x is ANY amino acid. By clicking on each high-lighted character you will obtain the distribution of amino acids found at that position of the repeat among an aligned set of WD-repeat containing proteins. The tertiary structure of only one member of this family has been determined, that of the G protein beta subunit, which contains 7 WD-repeats. Each of the 7 repeats folds into a small antiparallel beta-sheet. The over-lines above indicate the position of these strands, with a being the strand closest to the central pore and d at the external surface of the folded protein. These sheets are arranged around a central pseudosymmetry axis into a beta propeller. The WD-repeat-containing proteins form a very large family that is diverse in both its function and domain structure. Within all these proteins the WD-repeat domains are thought to have two common features: the domain folds into a beta propeller; and the domains form a platform without any catalytic activity on which multiple protein complexes assemble reversibly. The fact that these proteins play such key roles in the formation of protein-protein complexes in nearly all the major pathways and organelles unique to eukaryotic cells has two important implications. It supports both their ancient and proto eukaryotic origins and supports a likely association with many genetic diseases.
The Structural Genomics Project aims at determination of the 3D structure of all proteins. It also aims to reduce the cost and time required to determine three-dimensional protein structures. It supports selection, registration, and tracking of protein families and representative targets. This aim can be achieved in four steps : -Organize known protein sequences into families. -Select family representatives as targets. -Solve the 3D structure of targets by X-ray crystallography or NMR spectroscopy. -Build models for other proteins by homology to solved 3D structures. PSI has established a high-throughput structure determination pipeline focused on eukaryotic proteins. NMR spectroscopy is an integral part of this pipeline, both as a method for structure determinations and as a means for screening proteins for stable structure. Because computational approaches have estimated that many eukaryotic proteins are highly disordered, about 1 year into the project, CESG began to use an algorithm. The project has been organized into two separate phases. The first phase was dedicated to demonstrating the feasibility of high-throughput structure determination, solving unique protein structures, and preparing for a subsequent production phase. The second phase, PSI-2, has focused on implementing the high-throughput structure determination methods developed in PSI-1, as well as homology modeling and addressing bottlenecks like modeling membrane proteins. The first phase of the Protein Structure Initiative (PSI-1) saw the establishment of nine pilot centers focusing on structural genomics studies of a range of organisms, including Arabidopsis thaliana, Caenorhabditis elegans and Mycobacterium tuberculosis. During this five-year period over 1,100 protein structures were determined, over 700 of which were classified as unique due to their < 30% sequence similarity with other known protein structures. The primary goal of PSI-1 was to develop methods to streamline the structure determination process, resulted in an array of technical advances. Several methods developed during PSI-1 enhanced expression of recombinant proteins in systems like Escherichia coli, Pichia pastoris and insect cell lines. New streamlined approaches to cell cloning, expression and protein purification were also introduced, in which robotics and software platforms were integrated into the protein production pipeline to minimize required manpower, increase speed, and lower costs. The goal of the second phase of the Protein Structure Initiative (PSI-2) is to use methods introduced in PSI-1 to determine a large number of proteins and continue development in streamlining the structural genomics pipeline. Currently, the third phase of the PSI is being developed and will be called PSI: Biology. The consortia will propose work on substantial biological problems that can benefit from the determination of many protein structures Sponsors: PSI is funded by the U.S. National Institute of General Medical Sciences (NIGMS),
University of Cantabria; Cantabria; Spain
Public university in Cantabria, Spain that offers undergraduate, graduate and post graduate degree programs in areas including sciences, humanities, law, medicine, and tourism.
A pairwise protein structure alignment software.
Repository providing free access to marine geophysical data (e.g. bathymetry, seismic data, magnetics, gravity, images) and related land-based data from NSF-funded research conducted throughout the global oceans. Data Portals include GeoPRISMS, MARGINS, Ridge 2000, Antarctic and Southern Ocean Data Synthesis, the Global Multi-Resolution Topography Synthesis, and Seismic Reflection Field Data Portal. Primary data types served are multibeam bathymetric data from the ocean floor, seismic reflection data imaging below the seafloor, and multi-disciplinary ship based data from the Southern Ocean. Other holdings include deep-sea photographic transects, and ultra-high resolution bathymetry, temperature probe data, biological species compilations, MAPR and CTD data. Derived data products and sets include microseismicity catalogs, images, visualization scenes, magnetic and gravity compilations, grids of seismic layer thickness, velocity models, GIS project files, and 3D visualizations. Tools to discover, explore, and visualize data are available. They deliver catalogs, maps, and data through standard programmatic interfaces. GeoMapApp, a standalone data visualization and analysis tool, permits dynamic data exploration from a map interface and the capability to generate and download custom grids and maps and other data. Through GeoMapApp, users can access data hosted at the MGDS, at other data repositories, and import their own data sets. Global Multi-Resolution Topography (GMRT) is a continuously-updated compilation of seafloor bathymetry integrated with global land topography. It can be used to create maps and grids and it can be accessed through several standard programmatic interfaces including GeoMapApp and Google Earth. The GMRT compilation can also be explored in 3D using Virtual Ocean. The MGDS MediaBank contains high quality images, illustrations, animations and video clips that are organized into galleries. Media can be sorted by category, and keyword and map-based search options are provided. Each item in the MediaBank is accompanied by metadata that provides access to a cruise catalog and data repository.
Web Genome Scannner for Terminators Database
WebGeSTer DB - A Transcription Terminator Database
Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed.
Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.
Potentially Functional SNP Search Engine
Search engine integrating various bio-informatic resources and algorithims to produce a one-stop resource for biologists to identify potentially functional SNPs. It caters to different groups of scientists interested in SNPs including those working in the following areas: * Whole-genome association studies * Gene-based association studies * Designing experiments to address the functionality of specific SNPs * Determining potentially functionally significant SNPs that are in LD with non-pfSNPs of interest. Users may add published SNP functions.
THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB.
Software package that provides a GUI interface for rTANDEM, an R/Bioconductor package for MS/MS protein identification. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files.
The Arabidopsis Gene Expression Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Arabidopsis gene Expression Database collects Arabidopsis gene expression data from genome-wide and gene-specific sources and integrative search tools are provided. Currently the database contains only root gene expression data, but has the capability to contain data from any part of the plant. The aim of Arabidopsis gene Expression Database is to: (1) Integrate genome-wide and gene-specific ("traditional") types of expression pattern data, using ontologies to describe data whenever possible, in particular to describe expression patterns. (2) Provide user-friendly search tools, for example to search for genes expressed with a certain pattern, or to search for the expression pattern of specific genes (from gene-specific experiments and from microarray data). Expression pattern predicted from the microarray data is called digital in situ.
NITRC Computational Environment in Amazon Marketplace
An on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. For a listing of current NITRC-CE packages visit: http://www.nitrc.org/ce-packages. You can also use the "public Amazon Machine Interface (AMI)" to conduct your analyses on the Amazon EC2 platform.
Genoscope - Centre National de Sequencage
Genoscope - Centre National de S�quen�age
Genoscope - French National Sequencing Center
French national sequencing center with the following resources: * Sequencing ** Genoscope Projects * Environmental genomics ** Microbial diversity in wastewater ** Metabolic genomics * Bioinformatics ** Atelier for comparative genomics ** Computational Systems Biology ** Servers resources *** GGB for Generic Genome Browser: graphic interface for various databases (sequence, annotation, syntenies...) for a given organism. *** MaGe for Magnifying Microbial Genomes: annotation system for microbial genomes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human. They have also manually curated metadata to ensure annotation consistency, and developed a user-friendly display matrix for quick navigation and retrieval of data for specific factors, cells, and papers. The community can contribute to this resource.
metaRNASeq: Meta-analysis of RNA-seq data
Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments.
Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.
The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. SOAPLAB, was developed in the European Bioinformatics Institute (EBI), and is a SOAP-based analysis web service that is used to wrap command-line applications so they can be used as web service. NASC provides most of its data via SOAPLAB.
flowPlots: analysis plots and data class for gated flow cytometry data
Software for analysis plots and data class for gated flow cytometry data.
Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Variant Annotation Analysis & Search Tool
Variant Annotation Analysis and Search Tool
A probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of phylogenetic conservation, amino acid substitution, and aggregative approaches to variant prioritization into a single unified likelihood-framework that allows users to accurately identify damaged genes and deleterious variants. The software can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. It can identify rare variants causing rare genetic diseases and can also use both rare and common variants to identify genes responsible for common diseases.
Algorithm for the Reconstruction of Accurate Cellular Networks
An algorithm, using microarray expression profiles, to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.
FR-HIT: Metagenome Fragment Recruitment at High Identity with Tolerance
Fragment Recruitment at High Identity with Tolerance
Metagenome Fragment Recruitment at High Identity with Tolerance
An efficient fragment recruitment software program for next generation sequences against microbial reference genomes. It produces similar sensitivity of BLASTN, but runs at a 100 times higher speed. The algorithm adopts a seeding heuristic strategy with overlapping k-mer hashing to locate candidate matching blocks on the reference sequences, and then apply an effective filtering within the candidate blocks to filter out blocks that do not meet the minimum criteria for containing an alignment with specified parameters. For each candidate block that passed the filter, the best matching sub-regions between a candidate block and a read are determined, and used subsequently by the banded Smith-Waterman algorithm to carry out the actual alignment efficiently, which will finally verify if this can be a valid recruitment hit.
A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.
flowPhyto - Methods for Continuous Flow Cytometry
An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.
Software tool that detects peaks of any type, any shape, any direction, and any size for neuroscientists who are studying spontaneous activities. Allows detection of virtually any kind of peaks including spontaneous miniature synaptic currents and potentials, action potential spikes, calcium imaging peaks, amperometric peaks, ECG peaks etc. It includes the complex and multiple peak detection algorithm. Has post-detection analyses including essential plots and statistical parameters. Group Analysis provides specialized and detailed analysis options for action potentials, decay fitting, fEPSP/population spikes, amperometry, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A premier bibliographic database that contains over 18 million references to journal articles in life sciences with a concentration on biomedicine. A distinctive feature is that the records are indexed with NLM Medical Subject Headings (MeSH). PubMed provides free access to MEDLINE and links to full text articles when possible. The great majority of journals are selected for MEDLINE based on the recommendation of the Literature Selection Technical Review Committee (LSTRC), an NIH-chartered advisory committee of external experts analogous to the committees that review NIH grant applications. Some additional journals and newsletters are selected based on NLM-initiated reviews, e.g., history of medicine, health services research, AIDS, toxicology and environmental health, molecular biology, and complementary medicine, that are special priorities for NLM or other NIH components. These reviews generally also involve consultation with an array of NIH and outside experts or, in some cases, external organizations with which NLM has special collaborative arrangements. MEDLINE is the primary component of PubMed, part of the Entrez series of databases provided by the NLM National Center for Biotechnology Information (NCBI). MEDLINE may also be searched via the NLM Gateway. Time coverage: generally 1946 to the present, with some older material. Source: Currently, citations from approximately 5,516 worldwide journals in 39 languages; 60 languages for older journals. Citations for MEDLINE are created by the NLM, international partners, and collaborating organizations.
Midas Platform - The Multimedia Digital Archiving System
Open-source toolkit that enables the rapid creation of tailored, web-enabled data storage and provides a cohesive system for data management, visualization, and processing. At its core, Midas Platform is implemented as a PHP modular framework with a backend database (PostGreSQL, MySQL and non-relational databases). While the Midas Platform system can be installed and deployed without any customization, the framework has been designed with customization in mind. As building one system to fit all is not optimal, the framework has been extended to support plugins and layouts. Through integration with a range of other open-source toolkits, applications, or internal proprietary workflows, Midas Platform offers a solid foundation to meet the needs of data-centric computing. Midas Platform provides a variety of data access methods, including web, file system and DICOM server interfaces, and facilitates extending the methods in which data is stored to other relational and non-relational databases.
Virtual database of individual data sources, maintained by SciCrunch participating groups. Database topics are varied, including animals, grants, software, brain gene expression, and clinical trials.
Community Inventory of EarthCube Resources for Geosciences Interoperability
A project constructing a community inventory and knowledge base on geoscience information resources to meet the challenge of finding resources across disciplines, assessing their fitness for use in specific research scenarios, and providing tools for integrating and re-using data from multiple domains. The project team envisions a comprehensive system linking geoscience resources, users, publications, usage information, and cyberinfrastructure components. This system would serve geoscientists across all domains to efficiently use existing and emerging resources for productive and transformative research.
National Oceanographic Data Center (NODC)
Accepts and provides access to biology data, buoy data, chlorophyll, nutrients, ocean currents, oxygen, plankton, profile data, salinity, satellite data, sea level, snow and ice, temperature, waves. Please note that routine underway oceanographic shipboard data collected with standard equipment aboard the UNOLS fleet (e.g. CTD, ADCP, XBT, MET, TSG) are routinely transmitted to NODC via Rolling Deck to Repository (R2R). NODC Provides: * The World's largest collection of freely available oceanographic data * Water temperatures dating back to the late 1700's and measuring thousands of meters deep * A State of the Ocean Climate from NODC's Ocean Climate Lab and Satellite Team's scientific analyses * Scientific journals, rare books, historical photo collections and maps through the NOAA Central Library, a division of NODC * Data management expertise including metadata training through NODC's National Coastal Data Development Center
Paleoecology database for plio-pleistocene to holocene fossil data with a centralized structure for interdisciplinary, multiproxy analyses and common tool development; discipline-specific data can also be easily accessed. Data currently include North American Pollen (NAPD) and fossil mammals (FAUNMAP). Other proxies (plant macrofossils, beetles, ostracodes, diatoms, etc.) and geographic areas (Europe, Latin America, etc.) will be added in the near future. Data are derived from sites from the last 5 million years.
Biological & Chemical Oceanography Data Management Office
Biological and Chemical Oceanography Data Management Office
Accepts and provides access to marine biogeochemical and ecological data sets from NSF-funded research programs. BCO-DMO is also the data repository for the US GLOBEC and JGOFS programs.
The Exomiser2: Annotate and Filter Variants
A Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF (Variant Call Format) file (version 4). The functional annotation code is based on Annovar and uses UCSCKnownGene transcript definitions and hg19 genomic coordinates. Variants are prioritized according to user-defined criteria on variant frequency, pathogenicity, quality, inheritance pattern, phenotype data from human and model organisms, and proximity in the interactome to phenotypically similar genes.
Antarctic and Southern Ocean Data Portal
Accepts and provides access to geoscience data, primarily marine, collected from oceanographic expeditions in the Antarctic region. The synthesis began in 2003 as the Antarctic Multibeam Bathymetry and Geophysical Data Synthesis (AMBS) with a focus on multibeam bathymetry field data and other geophysical data from the Southern Ocean collected with the R/V N. B. Palmer. In 2005, the effort was expanded to include all routine underway geophysical and oceanographic data collected with both the R/V N. B. Palmer and R/V L. Gould, the two primary research vessels serving the US Antarctic Program. Data available include seafloor bathymetry, subbottom profiling, trackline gravity and magnetics, meteorological, and water column data as well as basic cruise information for all Palmer and Gould expeditions. Seafloor bathymetry data are provided both as raw swath data as well as in gridded form through the Global Multi-Resolution Topography (GMRT) synthesis. This gridded compilation of seafloor bathymetry data can be accessed through GeoMapApp, Create Maps and Grids and through an OGC-compliant Web Map Service. GeoMapApp is an integrated mapping application that provides access to many additional regional bathymetric grids, seismic, radar, gravity and magnetics profiles as well as other map and grid compilations for the Antarctic continent including LIMA.
Seismic Reflection Field Data from the academic research community. Their partner Academic Seismic Portal at UTIG offers additional seismic resources, http://www.ig.utexas.edu/sdc/
National Center for Earth-Surface Dynamics
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Field, laboratory, and model data related to earth-surface dynamics created or compiled by NCED-funded scientists. NCED is a Science and Technology Center developed to predict the coupled dynamics and co-evolution of landscapes and their ecosystems in order to transform management and restoration of the Earth-surface environment.
Community Surface Dynamics Modeling System
Model repository and data related to earth-surface dynamics modeling. The CSDMS Modeling Tool (CMT) allows you to run and couple CSDMS model components on the CSDMS supercomputer in a user-friendly software environment. Components in the CMT are based on models, originally submitted to the CSDMS model repository, and now adapted to communicate with other models. The CMT tool is the environment in which you can link these components together to run new simulations. The CMT software runs on your own computer; but it communicates with the CSDMS HPCC, to perform the simulations. Thus, the CMT also offers you a relatively easy way of using the CSDMS supercomputer for model experiments. CSDMS deals with the Earth's surface - the ever-changing, dynamic interface between lithosphere, hydrosphere, cryosphere, and atmosphere. They are a diverse community of experts promoting the modeling of earth surface processes by developing, supporting, and disseminating integrated software modules that predict the movement of fluids, and the flux (production, erosion, transport, and deposition) of sediment and solutes in landscapes and their sedimentary basins. CSDMS: * Produces protocols for community-generated, continuously evolving, open software * Distributes software tools and models * Provides cyber-infrastructure to promote the quantitative modeling of earth surface processes * Addresses the challenging problems of surface-dynamic systems: self-organization, localization, thresholds, strong linkages, scale invariance, and interwoven biology & geochemistry * Enables the rapid development and application of linked dynamic models tailored to specific landscape basin evolution (LBE) problems at specific temporal and spatial scales * Partners with related computational and scientific programs to eliminate duplication of effort and to provide an intellectually stimulating environment * Supports a strong linkage between what is predicted by CSDMS codes and what is observed, both in nature and in physical experiments * Supports the imperatives in Earth Science research
Consortium of Universities for the Advancement of Hydrologic Science Hydrologic Information System
An internet-based system for sharing hydrologic data. It is comprised of databases and servers, connected through web services, to client applications, allowing for the publication, discovery and access of data.
A set of tools for deriving region of interest (ROI) atlases by whole brain clustering of task or resting state data. This resource also contains several atlases derived by parcellating publicly available resting state fMRI datasets. The initial release will include python scripts and ROI atlases developed to perform the analyses described in Craddock et. al., A whole brain fMRI atlas generated via spatially constrained spectral clustering, which is currently in revision in Human Brain Mapping. The scripts provide all of the tools necessary to derive an ROI atlases using spatially constrained Ncut spectral clustering. The scripts require python, numpy and scipy to run. Source code and parcellations now available! Go to http://ccraddock.github.io/cluster_roi/ for more information.
Data related to the National Critical Zone Observatory Program including in-situ environmental sensors, field instruments, remote sensing, and surface and subsurface imaging. The Program serves the international scientific community through research, infrastructure, data, and models. They focus on how components of the Critical Zone interact, shape Earth's surface, and support life. A primary goal is to develop high-resolution 4D datasets that inform our theoretical framework, constrain our conceptual and coupled systems models, and test our model-generated hypotheses. They are developing cross-CZO capabilities to easily share, integrate, analyze and preserve the wide range of multi-disciplinary data generated by CZOs.
Portal contains detailed information for Neisseria meningitidis MC58. Information include DNA molecule summary, primary annotation summary, and taxonomy. It is a tool that allows the researcher to access all of the bacterial genome sequences completed to date. Users may access information on all of the bacterial genomes or any subset of them. Information in the website about its DNA molecule includes: total number of DNA molecules, total size of all DNA molecules, number of primary annotation coding bases, and number of G + C bases. Its primary annotation summary include: total genes, protein coding genes, tRNA genes, and rRNA genes. Sponsors: The CMR was previously funded by two grants, one from the U.S. Department of Energy (DOE) and one from the National Science Foundation (NSF). It is currently partially funded by a Microbial Sequence Center (MSC) grant from the National Institute of Allergy and Infectious Diseases (NIAID)
Incorporated Research Institutions for Seismology
Passive and active source waveform data, event (earthquake) catalog, channel response data is available. This comprehensive data store of raw geophysical time-series data is collected from a large variety of sensors, courtesy of a vast array of US and International scientific networks, including seismometers (permanent and temporary), tilt and strain meters, infrasound, temperature, atmospheric pressure and gravimeters, to support basic research aimed at imaging the Earth's interior. IRIS also provides data and software for educational purposes. This consortium of over 100 US universities is dedicated to the operation of science facilities for the acquisition, management, and distribution of seismological data. IRIS programs contribute to scholarly research, education, earthquake hazard mitigation, and verification of the Comprehensive Nuclear-Test-Ban Treaty. Data is stored at the IRIS Data Management Center in Seattle, Washington. They currently manage a large archive from over tens of thousands of seismic stations and ship hundreds of terabytes of data yearly.
LEPR - Library of Experimental Phase Relations
Database of results of published experimental studies involving liquid-solid phase equilibria relevant to natural magmatic systems.
Tokyo Metropolitan Institute of Medical Science; Tokyo; Japan
Tokyo Metropolitan Institute of Medical Science
Scientific institute in Japan that promotes project-based research, targeted research initiatives for clinically-relevant questions on cancer, and dissemination of information to the research community and public.
Accepts and provides access to high-resolution (meter to sub-meter scale) Earth science-oriented topography data (e.g. LiDAR) and bathymetric data, and related tools and resources. The OpenTopography Tool Registry provides a community populated clearinghouse of software, utilities, and tools oriented towards high-resolution topography data (e.g. collected with LiDAR technology) handling, processing, and analysis. Tools registered range from source code to full-featured software applications. Contributions to the registry via the Contribute a Tool page are welcome. OpenTopography also hosts a dataset catalog to which users can register datasets hosted elsewhere; these entries are discoverable by users alongside OpenTopography hosted datasets. Lidar point cloud data are available in LAS, LAZ and ASCII formats. Raster datasets and derived products can be downloaded in Arc ASCII, IMG, and GeoTIFF formats. Derived products and visualizations are available in Google Earth KML format. The OpenTopography user community and advisory committee provides feedback to define the scope of collaborations on data hosting and cyberinfrastructure development
flowCore: Basic structures for flow cytometry data
A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions.
Experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets are generated in house while others are collected from the literature or deposited by academic labs, national centers, and the pharmaceutical industry. For the community to improve their approaches, they need exceptional datasets to train scoring functions and develop new docking algorithms. They aim to provide the highest quality data for a diverse collection of proteins and small molecule ligands. They need input from the community in developing target priorities. Ideal targets will have many high-quality crystal structures (apo and 10-20 bound to diverse ligands) and affinity data for 25 compounds that range in size, scaffold, and logP. It is best if the ligand set has several congeneric series that span a broad range of affinity, with low nanomolar to mid-micromolar being most desirable. They prefer Kd data over Ki data over IC50 data (no % activity data). They will determine solubility, pKa, logP/logD data for the ligands whenever possible. They have augmented some donated IC50 data by determining Kon/Koff and ITC data.
Accepts and makes available geochemical, geochronlogical, and petrological data (analytical and synthesis) through this community-driven effort to facilitate the preservation, discovery, access and visualization of data generated. * PetDB holds geochemical data from sub-oceanic igneous and metamorphic rocks generated at mid-ocean ridges including back-arc basins, young seamounts, and old oceanic crust. Data are compiled primarily from the published literature. * SedDB integrates marine and terrestrial sediment geochemical data compiled primarily from the published literature. * Deep Lithosphere Data Set contains geochemical and petrological data from lower crust and upper mantle xenoliths. (more info) * VentDB contains hydrothermal spring geochemistry that hosts and serves the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. * NAVDAT - The Western North American Volcanic and Intrusive Rock Database * Geochron is an application that helps with the onerous task of data management for geochronological and thermochronological studies. * EarthChemPortal is the one-stop-shop for geochemical data that gives users the ability to search federated databases PetDB, NAVDAT, and GEOROC simultaneously, integrated into a common output format. (more info) * The EarthChem Library is a repository for geochemical datasets (analytical data, experimental data, synthesis databases) and other digital resources relevant to the field of geochemistry, contributed by the geochemistry community. * SESAR - System for Earth SAmple Registration
Database / data repository for metamorphic petrology that is being designed and built by a global community of metamorphic petrologists in collaboration with computer scientists at Rensselaer Polytechnic Institute as part of the National Cyberinfrastructure Initiative.
Accepts and provides access to geochemical and petrological data for ocean floor igneous and metamorphic rocks, (whole rock, volcanic, glass, mineral, and melt inclusion analyses), and mantle and lower-crustal xenolith samples. Data are compiled primarily from the published literature. Authors are encouraged to submit their datasets and databases to EarthChem.
Geochemical database for marine and terrestrial sediments primarily from the published literature containing a full range of analytical values for sediment samples, primarily from marine sediment cores. It includes major and trace element concentrations, radiogenic and stable isotope ratios, and data for a plethora of materials such as organic and inorganic components, leachates, and size fractions. SedDB also archives a vast array of metadata relating to the individual sample.
UCL Medical School; London; United Kingdom
University College London Medical School
Medical school at the University College London that provides undergraduate and postgraduate medical education programs, educational research, and specializations in variety of medical subfields.
National facility for permanent curatorial preservation of rock collections from Antarctica and Southern Ocean. Repository preserves existing rock/dredge/unconsolidated/terrestrial core/photo archive collections for research use. Database allows online requests for sample loans. Mapping tool combines existing PRR database with high resolution satellite images of Antarctica, REMA or USGS topographic layers. PRR created Polar Rock Boxes for educators who are teaching about Earth science and Antarctica. Each Polar Rock Box contains samples with binder full of teaching information about Earth science and Antarctica. These boxes are freely available as short loans to US schools.
Antarctic Marine Geology Research Facility
National repository for geological materials collected in polar regions housing over 20,000 meters of deep-sea core sediment and over 5,000 kg of dredge, trawl, and grab samples, the largest such Southern Ocean collection in the world. These materials have been acquired from over 90 USAP research vessel cruises. The Facility also houses and curates nearly 3,000 meters of rotary cored geological material acquired by NSF supported drilling programs in the Antarctic. Replacement cost of this core inventory in terms of ship and ice-based drilling is conservatively estimated to be in the range of $150 to $200M. SESAR or the the System for Earth Sample Registration is a service provided by the IDEA. SESAR operates the registry that distributes the International Geo Sample Number IGSN. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search. Facility services include: * curation of the existing collections at the facility * onsite ship and land based curatorial services * receipt and processing of new cores * core description and publication of core descriptions * distribution of samples from the collection to authorized scientists * hosting of scientific meetings and workshops * tours, lectures, and student education and training in Antarctic geoscience * maintenance of: ** a core and sample database ** an Antarctic geology and marine geology reference library and a searchable End Note computer database of the entire collection ** a satellite IODP/MRC for nannofossils and diatoms
ARK-Genomics: Centre for Functional Genomics
Portal for studies of genome structure and genetic variation, gene expression and gene function. Provides services including DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing , Gene expression analysis using both microarrays and Next Generation Sequencing, High throughput genotyping of SNP and copy number variants, Data collection and analysis supported in-house high performance computing facilities and expertise, Extensive EST clone collections for a number of animal species, all of commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen, Parentage testing using microsatellites and smaller SNP panels. ARK-Genomics has developed network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to analysis of data often in conjunction with commercial partners.
Limnological Research Center LacCore Facility
Archive of almost 20,000 meters of high quality sediment cores from large and small expeditions to lakes all around the world. LacCore advocates for, coordinates, and facilitates core-based research on Earth's continents through collaborative support for logistics, field and laboratory, and data and sample curation and dissemination. They provide a wide variety of fee-based analytical services, as well as offer training and instrument time to lab visitors. They also develop Standard Operating Procedures (SOPs) for local training and adoption by individuals at other labs.
Core repository and one of the world's most unique and important collections of scientific samples from the deep sea. Sediment cores from every major ocean and sea are archived at the Core Repository. The collection contains approximately 72,000 meters of core composed of 9,700 piston cores; 7,000 trigger weight cores; and 2,000 other cores such as box, kasten, and large diameter gravity cores. They also hold 4,000 dredge and grab samples, including a large collection of manganese nodules, many of which were recovered by submersibles. Over 100,000 residues are stored and are available for sampling where core material is expended. In addition to physical samples, a database of the Lamont core collection has been maintained for nearly 50 years and contains information on the geographic location of each collection site, core length, mineralogy and paleontology, lithology, and structure, and more recently, the full text of megascopic descriptions. Samples from cores and dredges, as well as descriptions of cores and dredges (including digital images and other cruise information), are provided to scientific investigators upon request. Materials for educational purposes and museum displays may also be made available in limited quantities when requests are adequately justified. Various services and data analyses, including core archiving, carbonate analyses, grain size analyses, and RGB line scan imaging, GRAPE, P-wave velocity and magnetic susceptibility runs, can also be provided at cost. The Repository operates a number of labs and instruments dedicated to making fundamental measurements on material entering the repository including several non-destructive methods. Instruments for conducting and/or assisting with analyses of deep-sea sediments include a GeoTek Multi-Sensor Core Logger, a UIC coulometer, a Micromeritics sedigraph, Vane Shear, X-radiograph, Sonic Sifter, freeze dryer, as well as a variety of microscopes, sieves, and sampling tools. They also make these instruments available to the scientific community for conducting analyses of deep-sea sediments. If you are interested in borrowing any field equipment, please contact the Repository Curator.
Smithsonian Mineral Sciences Collections
Smithsonian Institution Mineral Sciences Collections
Smithsonian Institution National Museum of Natural History Mineral Sciences Collections
National facility for curating meteorite, rock, ore, gem, and mineral specimens that are available to the public via a standard web interface. New records and associated images are added continuously and are made available on an approximately monthly basis. There are currently over 350,000 records available. Every year hundreds of specimens are loaned to scientists around the world for research projects in geology, materials science, health, chemistry, physics, etc.
This matlab script and associated files will take resultant statistical images and essentially output everything you could ever want to know. It can work off of images that were previously corrected for multiple comparisons, but it can actually do the correction itself. This is because the cluster_correct script is incorporated within. It will iterate through atlases (borrowed from other software) to tell you the location of significant results. It outputs an extremely detailed report as well as a summary table for quick investigation. In addition, it will output statistics for each surviving cluster, and the image as a whole. Feedback would be much appreciated.
Antarctic Glaciological Data Center at NSIDC
Antarctic Glaciological Data Center at the National Snow and Ice Data Center
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Archives and distributes Antarctic glaciological and cryospheric system data collected by the U.S. Antarctic Program. The Data Catalog contains data sets collected by individual investigators and products assembled from many different PI data sets, published literature, and other sources. The catalog provides useful compilations of important geophysical parameters, such as accumulation rate or ice velocity. The NSF OPP Guidelines and Award Conditions for Scientific Data state that PIs should submit data collected as a result of their OPP grant to a designated data center as soon as possible, but no later than two years after the data are collected.
National data center / repository for snow and ice data including snow, ice, glaciers, frozen ground, and climate interactions that make up Earth's cryosphere. The center manages and distributes scientific data, creates tools for data access, supports data users, performs scientific research, and educates the public about the cryosphere. Users may explore the Earth's frozen places in the collection of photographs and images. Photographs from field research trips, images captured by satellites of the changing cryosphere, and photos and images are available. Data sets are organized into the following groups: sea ice, frozen ground, snow cover, snow hydrology, glaciers and ice sheets, arctic people.
U.S. Antarctic Program Data Coordination Center
Assists scientists in finding Antarctic scientific data of interest and submitting data for long-term preservation in accordance with their obligations under the National Science Foundation (NSF) Office of Polar Programs (OPP) Data Policy.
Sample Catalog and Registry for the International Geo Sample Number. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search.
Bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. Designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. Designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management.
flowMerge - Cluster Merging for Flow Cytometry Data
Software for merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework.
Software package that performs aggregation of ordered lists based on the ranks using several different algorithms: Borda count, Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force algorithm.
This script will take any .img file and correct it based on a cluster extent, cluster definition and voxelwise threshold. The threshold entered will be applied to positive and negative values separately, and separate pos and neg corrected images will be output. This script requires a license for the matlab image processing toolbox.
Software package for constructing longitudinal atlases, which are the necessary steps for many brain-related applications.
Database of biological collections in natural history museums, herbaria, and other biorepositories resulting from a merger of Index Herbariorum (IH), Biodiversity Collections Index (BCI) and biorepositories.org. It contains more than 14,000 records for biorepository institutions, their collections, and staff members. Their two main goals are to improve access to information about biorepositories, the collections and specimens they house, and the researchers and collection managers who work there; and to facilitate electronic linkages to this information through web services that will rely on unique identifiers assigned to biorepositories and collections. The Consortium for the Barcode of Life (CBOL) has developed and will manage GRBio in collaboration with IH and BCI and in consultation with GBIF and NCBI. GRBio includes four categories of data records that provide information on: * Institutional repositories such as museums, herbaria, botanical gardens, zoos, biomedical research institutes and culture centers; * Institutional collection records such as the bird, algal or insect collections within an institutional repository; * Personal collections such as field samples held by a researcher before they have been accessioned into an institutional collection, or privately owned specimens held by non-researchers; and * Staff members at institutional repositories GRBio operates as a moderated community-curated resource. The community is invited to check and update their records and to register institutions, collections and staff members that have not already been registered. GRBio offers registration of institutional collections, "personal" research collections that have not yet been accessioned into an institutional repository, and privately owned collections.
OpenBioinformatics.org: An open bioinformatis software repository
An open bioinformatis software repository with no tie to any organization or institution. Contact them to host your software.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28, 2025. Software tool that allows the user to operate on NIfTI image files from Matlab.
An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered.
Compilable Imaging Graphics and Analytical Language
Software program that provides accurate real-time stimulus control, behavioral and physiological recording, and synchronization with external devices. It can also provide continuous real-time feedback of task performance and physiological responses. Task programming typically involves a simple text file specifying basic parameter settings (e.g. screen color) and a list of stimulus events, which can include images, animated movies, sound files, text stimuli, video graphics, or commands that communicate with external hardware devices. Multiple video and auditory stimuli can be presented simultaneously. Multi-channel response recording and real-time feedback features require no user programming. Advanced users can add customized stimulus events using CIGAL's real-time programming capabilities. Output files can be automatically created in a variety of output formats (e.g. FSL 3-column files, XML Events files, CSV trial tables).
An EEGLAB plugin which adaptively estimates and removes sinusoidal artifacts from independent component analysis (ICA) components or scalp channels using a frequency-domain (multi-taper) regression technique with a Thompson F-statistic for identifying significant sinusoidal artifacts. This approach has been advocated by Partha Mitra and Hemant Bokil (Observed Brain Dynamics, Chapter 7.3.4., 2007) and CleanLine utilizes modified routines from the Mitra Lab's Chronux Toolbox (www.chronux.org). Sinusoidal noise can be a prominent artifact in recorded electrophysiological data. This can stem from AC power line fluctuations (e.g. 50/60 Hz line noise + harmonics), power suppliers (e.g. in medical equipment), fluorescent lights, etc. Notch filtering is generally undesirable due to creation of band-holes, and significant distortion of frequencies around the notch frequency (as well as phase distortion at other frequencies and Gibbs rippling in the time-domain).
Computational Morphometry Toolkit (CMTK)
A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished.
Ontology used to describe the experimental conditions within cognitive and behavioral experiments, primarily in humans for application and use in the functional neuroimaging community. CogPO has been developed through the integration of the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap Database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response.
University of Delaware Chick EST Database
University of Delaware Chick EST Project
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created.
A portal to different zebrafish resources such as jobs, book, journals, database, meetings, and K-12 programs. Most information leads to ZFIN: The Zebrafish Model Organism Database.
aBEAT: A Toolbox for Consistent Analysis of Longitudinal Adult Brain MRI
Adult Brain Extraction and Analysis Toolbox
A 4D adult brain extraction and analysis toolbox with graphical user interfaces to consistently analyze 4D adult brain MR images. Single-time-point images can also be analyzed. Main functions of the software include image preprocessing, 4D brain extraction, 4D tissue segmentation, 4D brain labeling, ROI analysis. Linux operating system (64 bit) is required. A computer with 8G memory (or more) is recommended for processing many images simultaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.
Software package for automatic processing of the one- and two- (typically, Cy3-green/Cy5-red) color images produced in cDNA, CGH (comparative genome hybridization) or protein microarray technologies. It incorporates the following modules: * The spot localization module (i) identifies the position of each spot on the array, so that the name of the spotted clone can be associated with the correspondent spot; and (ii) establishes the borders between the neighborhood spots letting one to perform further data processing procedures (i.e. to extract quantitative information) for each spot independently of the other neighborhood spots. Visually this results in the generation of a grid covering the image. The spot localization algorithm is fully automatic and robust with respect to deviations from perfect spot alignment and contamination. As an input, it requires only the common array design parameters: number of blocks and number of spots in the x and y directions of the array. * The spot quantification module for one-color images performs segmentation of the spots and estimates the averaged spot and local background intensities. The spot quantification module for two-color images estimates the ratio of the measured intensities in the two color channels at each spot reflecting differential gene (cDNA technology) or protein expression or a change in DNA copy number (CGH experiments) between the test and control samples for the corresponding gene. This module includes algorithms based on the linear regression and segmentation of the spots. A special procedure for detection and removal of the aberrant pixels has been developed to make ratio estimates more resistant to array contamination. It ensures more consistent ratio estimates obtained from different algorithms, and allows delivery of a single trustable ratio value. * The quality control module provides a value of spot quality reflecting the level of confidence in the obtained quantitative estimates at each spot. These quality values can be used either directly to flag out some spots with the quality lower than the user-defined threshold, or in the follow-up analysis as a weight controlling the contribution/influence of the obtained ratio estimates. The unique spot quality value for a spot is derived from a set of marginal quality parameters characterizing certain features of the spot. The contribution of each quality parameter in the overall quality is automatically evaluated based on the user visual classification of the spots, or using information available from the replicated spots, located at the same array or over a set of replicated arrays. * The image simulator allows the generation of a broad spectrum of microarray images with different types of contamination (like non-specific hybridization and dust) and noise. Since in simulation experiment the true values of the ratios are known exactly, it allows one to evaluate, to test and to compare different algorithms for microarray image processing objectively.
Massive, open, online courses (MOOCs) and interactive online classes in subjects including law, history, science, engineering, business, social sciences, computer science, public health, and artificial intelligence (AI). This non-profit was created by founding partners Harvard and MIT bringing the best of higher education to students around the world. Online courses are designed to be interesting, fun and rigorous. They are the best online courses, from the best professors and the best schools, spanning dozens of subjects. Some edX courses now offer ID verified Certificates of Achievement. A new way to demonstrate your achievement and showcase your knowledge.
Global, collaborative effort for neuroscience, medicine and computing to understand brain, its diseases and its computational capabilities. Goal is to obtain access to research, data sources, platforms and infrastructures offered by other organisations, and enabling organizations outside HBP to use HBP platforms to pursue their own research. Coordinating these activities is the responsibility of the European Research Programme.
A project producing datasets, software, and algorithms that is developing the technology to produce connectomes at the electron microscopic level of behaviorally-relevant neural circuits as well as the entire Drosophila nervous system. This technology will enable them to create a map of every neuron and synapse in the Drosophila nervous system, using novel approaches to electron microscopy (EM) as the foundation. In the same way that the fly genome paved the way for larger projects, including sequencing the human genome, Fly EM may ultimately contribute to our understanding of the human brain by establishing a fly "connectome" a map that shows how all neurons in the fly brain are connected to each other. They began their entry into EM reconstruction with the fly's adult visual system, where much is known about cell types from previous EM and histological studies, as well as ongoing studies in the Fly Light Project. In addition to establishing and publishing a fly connectome, Fly EM will make technology and methodology available that is needed to perform large-scale EM reconstructions. Fly EM will generally pursue an open policy with their datasets, software, and algorithms after relevant publications. When an EM reconstruction is published, the derived connectome and reconstructed neuronal skeletons will be made available online. The raw data and annotatations will be made available upon request as logistics dictate. To encourage further collaboration and scientific discovery, a small fraction of their raw data and corresponding segmentation will be made available independent of publication. Their goal is to enable others who wish to approach the many algorithmic challenges, but who do not have access to an EM facility, to have the data they need to support methods development, as well as their results to use as a benchmark. Fly EM emphasizes publication of supporting techniques and software approaches before major EM reconstruction releases to encourage rapid feedback from the community and adoption of their strategies. FlyEM maintains much of its software in the open-source repository GitHub:http://janelia-flyem.github.com. They will provide information on official release versions of these packages on git-hub when it reaches reasonable maturity.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Project mapping whole mouse brain connectivity using serial block face scanning electron microscopy (SBF-SEM) with a specially-designed whole-brain microtome (WBM). With any luck, the whole mouse brain will be mapped ultrastructurally in the near term, which will then open the door to more serious problems; reliable automated segmentation and circuit reconstruction. These will undoubtedly require advances in machine learning methods and their application. Connectomics Software and a Multiresolution Image Viewer (MIV) is also available.
NIMH Strategic Plan developing, for research purposes, new ways of classifying psychopathology based on dimensions of observable behavior and neurobiological measures. In brief, the effort is to define basic dimensions of functioning (such as fear circuitry or working memory) to be studied across multiple units of analysis, from genes to neural circuits to behaviors, cutting across disorders as traditionally defined. The intent is to translate rapid progress in basic neurobiological and behavioral research to an improved integrative understanding of psychopathology and the development of new and/or optimally matched treatments for mental disorders. The various domains of functioning, and their constituent elements, are being defined by an ongoing series of consensus workshops; input from the research community and other interested stakeholders is encouraged.
Commercial supplier of antibodies and assay kits for biomedical research.
Connectomic reconstruction of the inner plexiform layer in the mouse retina
Data set of the dense reconstruction of 950 neurons and their mutual contacts for the mouse inner plexiform layer--the main computational neuropil region in the mammalian retina. This was achieved by applying a combination of crowd-sourced manual annotation and machine-learning-based volume segmentation to serial block-face electron microscopy data. They characterize a new type of retinal bipolar interneuron and show that they can subdivide a known type based on connectivity. Circuit motifs that emerge from their data indicate a functional mechanism for a known cellular response in a ganglion cell that detects localized motion, and predict that another ganglion cell is motion sensitive. A Data browser is also available for download
A program of regional geochemical and geophysical surveys designed to attract the mineral exploration industry to an under-explored region of British Columbia between Williams Lake and Mackenize. The QUEST Project is focused on the Quesnel Terrane, which has good potential for copper and gold porphyry deposits, but in this region is covered by a thick layer of sand and gravel left behind by glaciers. Geoscience BC's QUEST Project included two airborne geophysical surveys: an airborne electromagnetic (EM) survey and an airborne gravity survey, which give insight into the conductivity and density of the rocks. The results of the two airborne surveys are an important tool for industry looking to understand the geology in the QUEST Project area. The QUEST Project also included the reanalysis of almost 5000 archived regional geochemical samples from parts of NTS sheets 93A, B, G, H, K and N, and the collection of 2200 new geochemical samples north and west of Prince George. This new geochemical data is helping industry to identify new exploration targets. Subsequent follow-up work has included analysis and inversion of datasets and updating the regional bedrock geology map.
A world-wide neuroscience competition for high school students that aims to motivate them to learn about the brain and to pursue neuroscience careers. Brain Bee tests knowledge of the human brain, including topics like intelligence, emotions, memory, sleep, vision, hearing, sensations, Alzheimer's disease, Parkinson's disease, stroke, schizophrenia, epilepsy, depression, addictions and brain research.
Simulation software for modeling the entire human brain by combining structural and functional data from empirical neuroimaging data. It can generate local field potentials, EEG, MEG and fMRI BOLD data based on neural mass models. The user can also modify the model parameters to match clinical conditions from focal lesions or degenerative disorders.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.
University of Alaska Fairbanks; Alaska; USA
Public research university in Fairbanks, Alaska that offers degree programs in engineering, liberal arts, fisheries and ocean sciences, and rural and community development.
Magnetic Resonance Connectome Automated Pipeline
MR Connectome Automated Pipeline (MRCAP)
Based on JIST and MIPAV, this pipeline combines structural magnetic resonance data with diffusion tensor imaging to estimate a connectome, which is a comprehensive description of the wiring diagram of the brain.
A dataset of 100 annotated papers for use in text mining applications, that includes the importance of each reference compared to other references. Useful for natural language processing, machine learning or bibliometrics. To collect the annotations, authors of a paper were asked to determine whether a given reference had a strong influence on their research. In a blog post on March 20th 2012, authors were invited to help create a gold-standard dataset of labeled references. Data are available for download.
CORUM - the Comprehensive Resource of Mammalian protein complexes
CORUM the Comprehensive Resource of Mammalian protein complexes
Database of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, but data from high-throughput experiments is excluded. The majority of protein complexes in CORUM originates from man (65%), followed by mouse (14%) and rat (14%)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks. It generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure.
National Human Genome Research Institute Dog Genome Project
The Dog Genome Project at the National Human Genome Research Institute is working to develop resources necessary to map and clone canine genes in an effort to utilize dogs as a model system for genetics and cancer research. The US National Human Genome Research Institute (NHGRI) agreed to fund a project to sequence the entire genome of a boxer dog named Tasha, because it recognized the value of the dog as an unrivaled model for the study of human disease. The National Human Genome Research Institute (NHGRI) led the National Institutes of Health's (NIH) contribution to the International Human Genome Project, which had as its primary goal the sequencing of the human genome. This project was successfully completed in April 2003. Now, the NHGRI's mission has expanded to encompass a broad range of studies aimed at understanding the structure and function of the human genome and its role in health and disease. To that end NHGRI supports the development of resources and technology that will accelerate genome research and its application to human health. A critical part of the NHGRI mission continues to be the study of the ethical, legal and social implications (ELSI) of genome research. NHGRI also supports the training of investigators and the dissemination of genome information to the public and to health professionals.
Database combining movies, animated schemata, interactive modules and pictures that will greatly facilitate the understanding of Drosophila development. The resource is aimed at university students and teachers of developmental biology classes. Contribute your own movies, images and illustrations to FlyMove. Illustrating developmental processes using first hand research data will allow students to gain a better understanding of the real organism, and it will allow you to draw their attention to your field of research and to your group. All donors of media integrated in FlyMove will be cited and links to their homepages will be made.
Kindai University School of Medicine; Osaka; Japan
Medical school division of Kindai University with a resident-centered approach to medicine.
MISO: An open source LIMS for small-to-large scale sequencing centres
MISO: An open-source LIMS for NGS sequencing centres
Open source software for a Laboratory Information Management System (LIMS) for NGS sequencing centres.
COSMIC - Catalogue Of Somatic Mutations In Cancer
Catalogue Of Somatic Mutations In Cancer
Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats. Some key features of COSMIC are: * Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types. * Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.
CPDB - the Circular Permutation Database
A database of circular permutation (CP) in proteins that provides resources for studying circular permutation (CP) and circular permutation relationships among protein structures. This site also offers viable CP site predictions in order to facilitate the application of CP in academic researches and biotechnological developments.<BR / The organizational principle of CPDB is a hierarchical categorization in which pairs of circular permutants are grouped into CP clusters, which are further grouped into folds and in turn classes. Additions to CPDB include a useful set of tools and resources for the identification, characterization, comparison and visualization of CP. Besides, several viable CP site prediction methods are implemented and assessed in CPDB. This database can be useful in protein folding and evolution studies, the discovery of novel protein structural and functional relationships, and facilitating the production of new CPs with unique biotechnical or industrial interests.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. These databases were constructed by extracting the organism specific ESTs from dbEST, removing polyA sequences from the ends and trimming 5' and 3' regions with greater than 25% N's in a 20 base pair window. These quality sequences were then aligned using the cap2 program and the consensus sequences thus generated put into a database that is available on the web. A number of parasitic organisms were chosen that have between 3000 and 15000 ESTs. The attempt here is to provide useful information and analyses to the scientific community without curating the results in any way. A total of 55192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, approximately 15%-20% represent putative homologs with a conservative cutoff of p < 10(-9), thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets.
A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.
Mouse Models of Human Cancers Consortium (MMHCC) Repository
Mouse Models of Human Cancers Consortium Repository
The NCI Mouse Repository cryoarchives and distributes strains of genetically engineered mice that are of immediate interest to the cancer research community. These are either gene-targeted or transgenic mice that display a cancer-related phenotype, or tool strains (e.g., cre transgenics) that can be used to develop new cancer models. You do not have to be a member of the NCI Mouse Repository or a recipient of NCI funding to have your mouse model distributed through the NCI Mouse Repository. NCI Mouse Repository strains are maintained as live colonies or cryoarchived as frozen embryos, depending on demand. Up to three breeder pairs may be ordered from live colonies. Cryoarchived strains are supplied as frozen embryos or recovery of live mice by the NCI Mouse Repository may be requested.
Genome of Takifugu, the Japanese puffer fish. The Fugu genome was sequenced and assembled using the whole genome shotgun method.
Data set of pictures representing genetic linkage maps of the rat resulting from the integration of two F2 intercrosses (SHRSP x BN and FHH x ACI). Markers in common between the two crosses are connected by a line to define integration points. There are a total of 4,786 markers on these maps; 4375 WIBR/MIT CGR markers; 223 markers from the previously released Mit/Mgh rat maps and 188 markers from the National Institute of Arthritis and Musculoskeletal and Skin Diseases Arb rat maps. Pictures are drawn to a scale of 5cm (Kosombi) per inch. The changes in color of the backbone of the chromosome for each cross represents the space between any two framework loci. Markers in blue type are framework loci. Markers in green type are unique placement loci. Markers in black type are bouncy placement loci.
The Rat Genome Program was launched after the National Institutes of Health (NIH) realized the potential of rat models in understanding basic biology and human health and disease. The purpose of this NIH Rat Genomics and Genetics web site is to serve as a central point for information on NIH sponsored and related rat genetic and genomic activities and resources. It will provide information on: the follow up to recommendations made to the NIH; funding opportunities for rat genomic and genetic tools and resources; major rat genomic resources available and/or produced in response to the NIH Rat Program; courses and meetings related to rat genomics and genetics; and selected reports and publications. These programs have produced a wide variety of resources and a way to link and capitalize upon the data and resources of other model organisms and the human. In conjunction with and in addition to these programs, the NIH, through the RGWG, has convened advisory groups and workshops to discuss the opportunities that rat models offer and provide recommendations on the investments that are needed to capitalize on these opportunities.
Rice Genome Research Program (RGP) is an integral part of the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Research Project. RGP now aims to completely sequence the entire rice genome and subsequently to pursue integrated goals in functional genomics, genome informatics and applied genomics. It is jointly coordinated by the National Institute of Agrobiological Sciences (NIAS), a government research institute under MAFF and the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), a semi-private research organization managed and supported by MAFF and a consortium of some twenty Japanese companies. The research is funded with yearly grants from MAFF and additional funds from the Japan Racing Association (JRA). It is now the leading member of the International Rice Genome Sequencing Project (IRGSP), a consortium of ten countries sharing the sequencing of the 12 rice chromosomes. The IRGSP adopts the clone-by-clone shotgun sequencing strategy so that each sequenced clone can be associated with a specific position on the genetic map and adheres to the policy of immediate release of the sequence data to the public domain. In December 2004, the IRGSP completed the sequencing of the rice genome. The high-quality and map-based sequence of the entire genome is now available in public databases.
flowMap - A probabilistic algorithm for matching and comparing multiple flow cytometry samples
Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process.
Package of software functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. Draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.
Washington University School of Medicine Neuroscience Tutorial
An illustrated guide to the essential basics of clinical neuroscience created in conjunction with the first-year course for medical students. Topics covered: * Coronal and horizontal sections * Basic visual pathway * Basic somatosensory pathway * Basic motor pathway * Eye and retina * Central visual pathways * Auditory and vestibular systems * Somatosensory pathways from the body * Somatosensory pathways from the face * Spinal motor structures * Brainstem nuclei of cranial nerves * Basal ganglia and cerebellum * Hypothalamus and autonomic nervous system * Medial temporal lobe and memory * Sleep and language * Where is...?
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The project aims to apply genome mapping research to sheep, utilizing previous research in sheep (in other countries) and in other species (in the UK and abroad) to the benefit of the UK sheep industry. The project itself uses existing breeding structures, knowledge of the sheep genome and experimental resources. It has three main aims: i) To use the Suffolk, Texel and Charollais Sire Referencing Schemes to detect and verify quantitative trait loci (QTLs) for growth and carcass composition traits ii) To investigate candidate genes and/or chromosomal regions for associations with production traits. iii) To investigate approaches for optimizing future genotyping strategies within the sire referencing schemes for practical and cost effective application of marker-assisted selection By using commercial breeding populations for the research, immediate application of beneficial results is possible. Potential benefits include increased genetic progress through marker assisted selection which utilizes the genotype information, correction of possible parentage errors (ultimately leading to additional genetic progress) and opportunities for using marker information for product certification. The project will benefit the UK sheep industry by the use of Marker Assisted Selection (MAS) utilizing QTL or gene variants identified in the project. Additional benefits may arise from parentage verification and correction of errors e.g. misallocation of lamb to ewe. In the longer term, opportunities may exist to use markers for quality control, tracing products to their source. The major advantage of the design of this project is that the results are immediately applicable to the breeding schemes within which the QTLs and/or genes are detected. The time lag in the application of the results that is often seen with experimental populations is minimized. The project requires close involvement with the Sire Reference Schemes, in return for their assistance the results have immediate benefit to animals within these groups.
Phenotype Driven Variant Ontological Re-Ranking Tool
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles.
Nonhuman Primate HIV/SIV Vaccine Trials Database
An overview of HIV and SIV vaccine trials and their outcomes. It was developed as a tool for compilation, search and comparison of published studies on SIV, HIV and SHIV vaccine trials in nonhuman primates. We used a set of criteria to scan Pubmed for relevant studies to enter into the database. In selecting studies for entry, priority was given to recently published studies in journals generally regarded as the primary source of information pertaining to HIV and SIV vaccine research in nonhuman primates. In most cases, we give priority to challenge studies, where the animals received a live virus to measure the "efficacy" of the immunogen(s) inoculated during the course of the investigation. The HIV Sequence Database focuses on five primary goals: *Collecting HIV and SIV sequence data (all sequences since 1987) *Curating and annotating this data, and making it available to the scientific community *Computer analysis of HIV and related sequences *Production of software for the analysis of (sequence) data *Publication of the data and analyses on this site and in a yearly printed publication, the HIV sequence Compendium, which is available free of charge
flowMeans - Non-parametric Flow Cytometry Data Gating
flowMeans: Non-parametric Flow Cytometry Data Gating
Software that identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.
ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters
A database of Annotated regulatory Binding Sites from orthologous promoters
Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented October 5, 2018. Digress.it is a tool (plugin) that offers paragraph-level commenting in the margins of a text. Digress.it is based on the WordPress blogging architecture, but is geared toward in-depth discussions of longer documents: article, essay or even book-length. Digress.it allows you run blog-style comment threads digressions, if you will off of individual paragraphs. To do this efficiently, we've re-jiggered the conventional post-discussion hierarchy of blogs, moving the comment area from beneath the post to beside it (floating to the right) hearkening back to the age-old practice of scribbling in page margins. We see great possibilities for educators, literary groups, political or civic activists, legal scholars, and pretty much anyone who wants to do a communal close reading. Since its initial launch Digress.it has been used by universities, publishers and governments across the world and is cited on various academic and scientific journals as an exemplary online collaboration tool. Digress.it is first an foremost a public service. The source code is completely free software and open to be used and customized by anyone without restriction. The hosting service is also free and has no ads. The project is primarily funded by grants, donations and people interested in seeing the project stay alive.
CTCFBSDB 2.0: A database for CTCF binding sites and genome organization
CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators
A comprehensive collection of experimentally determined and computationally predicted CCCTC-binding factor (CTCF) binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains. The CTCFBS Prediction Tool allows users to scan sequences for the single best match to CTCF position weight matrices. Currently (March 2014), the database contains almost 15 million experimentally determined CTCF binding sites across several species. CTCF binding sites were collected from published papers containing CTCF binding sites identified using ChIPSeq or similar methods, data from the ENCODE project, and a set of approximately 100 manually curated binding sites identified by low-throughput experiments. Users can browse insulator sequence features, function annotations, genomic contexts including histone methylation profiles, flanking gene expression patterns and orthologous regions in other mammalian genomes. Users can also retrieve data by text search, sequence search and genomic range search.
spliceR - Classification of alternative splicing and prediction of coding potential from RNA-seq data
An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
Automatic Generated Test-Sets Database for Protein-Protein Docking
Database providing automatic test cases for protein-protein docking. A consensus-type approach is proposed processing the whole PDB and classifying protein structures into complexes and unbound proteins by combining information from three different approaches. Out of this classification test cases are generated automatically. All calculations were run on the database. The information stored is available via a web interface. The user can choose several criteria for generating his own subset out of the test cases, e.g. for testing docking algorithms. In unbound protein--protein docking, the complex of two proteins is predicted using the unbound conformations of the proteins (Halperin et al.,2002). For testing of docking algorithms, two unbound proteins which form a known complex have to be identified, so that the result of the docking algorithm can be compared to the known complex. For the identification of test cases, the structures taken from the PDB have to be classified as unbound proteins or complexes and unbound proteins with a 100% sequence identity to one complex part have to be searched. By now, most groups use handpicked test sets. The largest collection of test cases used so far is described by Chen et al. (Chen et al.,2003) and contains 31 test cases for unbound docking. Because of the exponential growth of available protein structures in the PDB, automatic generation of test cases will become more and more important in the future.
International Neuroinformatics Coordinating Facility
The International Neuroinformatics Coordinating Facility
Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.
flowMatch - Matching and meta-clustering in flow cytometry
Software for matching cell populations and building meta-clusters and templates from a collection of flow cytometry (FC) samples.
A service created to allow healthcare professionals to access timely, relevant information within their respective fields. Users can subscribe to receive weekly emails with bibliographic lists about new scientific publications, personal web pages for one-time download of available abstracts, and an overview of the medical literature published in relevant journals over the past 12 to 24 months.
Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences.
flowFit - Estimate proliferation in cell-tracking dye studies
A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.
An interesting and exhaustive explanation of how the technology works and is applied. It is an online book on principles and practice of magnetic resonance imaging. This educational package requires a hyper text markup language (HTML) 3.0 compatible browser, such as Mozilla Firefox, Microsoft Internet Explorer, or Apple Safari. This type of browser allows the user to view frames. Three frames will be used in this package to simultaneously display text, graphics, and navigation aids. You are reading this in the text window. The graphics window is in the upper left hand corner of your screen. This window will be used to display animations, static figures, references, symbol definitions, and the glossary. The navigation window appears in the lower left corner of the screen and has one line of options. To experience the full potential of the frames, a screen capable of displaying at least 1024 by 768 pixels with 256 colors is recommended. You may be able to gain a few extra pixels in the vertical direction on your monitor by turning off the show toolbar, show location, and show directory buttons under options at the top of your browser. A computer mouse is necessary to access the contents of this package. The mouse allows you to move up and down in a frame by either moving the slider, or holding the mouse button down on the up or down arrows located at the right of the frame.
Annotated List of Online Continuing Medical Education (CME)
Online Continuing Medical Education (CME)
Links to, and descriptions of, every web site that offers AMA-approved Continuing Medical Education (CME) online. At this time, there are over 325 sites listed. These sites offer over 16,000 separate activities and over 26,000 hours of credit. Using this list, you can find online CME web sites arranged by their: # dominant medical specialty or medical topic; or # alphabetically by the first letter of the site name; or # you can scroll this list until you find a course or site of interest. Find sites by medical specialty or topic: Allergy, Anesthesia, Bioterrorism, Cardiology, Critical Care, Dermatology, Diabetes/Endocrinology, Ear, Nose and Throat, Emergency Medicine, Family Practice, Gastroenterology, Genetics, Geriatrics, Hematology / Oncology, HIV / Infectious Disease, Imaging / Radiology, Internal Medicine, Neurology, Neurosurgery, Obstetrics / Gynecology, Oncology/Hematology, Ophthalmology, Orthopedic Surgery, Pain Management, Pathology / Lab Medicine, Pediatrics, Psychiatry, Pulmonary, Quality/Management, Radiology / Imaging, Rheumatology, Surgery, Urology, Wellness / Prevention.
CYGD - Comprehensive Yeast Genome Database
MIPS Comprehensive Yeast Genome Database
MIPS Saccharomyces cerevisiae genome database
The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition, the data of various projects on related yeasts are used for comparative analysis.
Autosomal Recessive Polycystic Kidney Disease Mutation Database
Mutation Database Autosomal Recessive Polycystic Kidney Disease (ARPKD/PKHD1)
Catalog of all changes detected in PKHD1 (Polycystic Kidney and Hepatic Disease 1) in a locus specific database. Investigators are invited to submit their novel data to this database. These data should be meaningful for clinical practice as well as of relevance for the reader interested in molecular aspects of polycystic kidney disease (PKD). There are also some links and information for ARPKD patients and their parents. Autosomal recessive polycystic kidney disease (ARPKD/PKHD1) is an important cause of renal-related and liver-related morbidity and mortality in childhood. This study reports mutation screening in 90 ARPKD patients and identifies mutations in 110 alleles making up a detection rate of 61%. Thirty-four of the detected mutations have not been reported previously. Two underlying mutations in 40 patients and one mutation in 30 cases are disclosed, and no mutation was detected on the remaining chromosomes. Mutations were found to be scattered throughout the gene without evidence of clustering at specific sites. PKHD1 mutation analysis is a powerful tool to establish the molecular cause of ARPKD in a given family. Direct identification of mutations allows an unequivocal diagnosis and accurate genetic counseling even in families displaying diagnostic challenges.
demi: Differential Expression from Multiple Indicators
Differential Expression from Multiple Indicators
R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes.
Deja Vu: a Database of Highly Similar and Duplicate Citations
Deja Vu: a Database of Highly Similar Citations
Deja vu is a database of extremely similar Medline citations. Many, but not all, of which contain instances of duplicate publication and potential plagiarism. Deja vu is a dynamic resource for the community, with manual curation ongoing continuously, and we welcome input and comments. In the scientific research community plagiarism and multiple publications of the same data are considered unacceptable practices and can result in tremendous misunderstanding and waste of time and energy. Our peers and the public have high expectations for the performance and behavior of scientists during the execution and reporting of research. With little chance for discovery and decreasing budgets, yet sustained pressure to publish, or without a clear understanding of acceptable publication practices, the unethical practices of duplicate publication and plagiarism can be enticing to some. Until now, discovery has been through serendipity alone, so these practices have largely gone unchecked.
Functional Regression Analysis of DTI Tract Statistics
Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles.
Database of protein-ligand crystal structures that is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. The resolved protein crystal structures with clearly identified biologically relevant ligands are annotated with experimentally determined binding data extracted from literature. A viewer is provided to examine the protein-ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. The binding-affinity data ranges 13 orders of magnitude. The issue of redundancy in the data has also been addressed. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 best complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This collection of protein-ligand complexes will be useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques.
The BioAfrica HIV-1 Proteomics Resource is a website that contains detailed information about the HIV-1 proteome and protease cleavage sites, as well as data-mining tools that can be used to manipulate and query protein sequence data, a BLAST tool for initiating structural analyses of HIV-1 proteins, and a proteomics tools directory. HIV Proteomics Resource contains information about each HIV-1 gene product in regard to expression, post-transcriptional / post-translational modifications, localization, functional activities, and potential interactions with viral and host macromolecules. The Proteome section contains extensive data on each of 19 HIV-1 proteins, including their functional properties, a sample analysis of HIV-1HXB2, structural models and links to other online resources. The HIV-1 Protease Cleavage Sites section provides information on the position, subtype variation and genetic evolution of Gag, Gag-Pol and Nef cleavage sites.
Biological Magnetic Resonance Data Bank (BMRB)
Public depository that collects, annotates, archives, and disseminates important spectral and quantitative data derived from nuclear magnetic resonance spectroscopic investigations of biological macromolecules and metabolites. Provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR.
Blood Group Antigen Gene Mutation Database
BGMUT - Blood Group Antigen Gene Mutation Database
Blood Group Antigen Gene Mutation Database (BGMUT)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019.BGMUT was database that provided publicly accessible platform for DNA sequences and curated set of blood mutation information. Data Archive are available at ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive.
A collection of Pathway/Genome Databases which describes the genome and metabolic pathways of a single organism. The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. They also include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received. Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating. Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating. Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 967 DBs in Tier 3. The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site.
CampyDB is a database for comparative genome analysis of For Campylobacter, Helicobacter and Wolinella. The database contains information on: -Campylobacter coli RM2228 -Campylobacter concisus 13826 -Campylobacter curvus 525.92 -Campylobacter fetus subsp. fetus 82-40 -Campylobacter hominis ATCC BAA-381 -Campylobacter jejuni RM1221 -Campylobacter jejuni subsp. doylei 269.97 -Campylobacter jejuni subsp. jejuni 260.94 -Campylobacter jejuni subsp. jejuni 81-176 -Campylobacter jejuni subsp. jejuni 81-176 -Campylobacter jejuni subsp. jejuni 84-25 -Campylobacter jejuni subsp. jejuni CF93-6 -Campylobacter jejuni subsp. jejuni CG8486 -Campylobacter jejuni subsp. jejuni HB93-13 -Campylobacter jejuni subsp. jejuni NCTC 11168 -Campylobacter lari RM2100 -Campylobacter upsaliensis RM3195 -Helicobacter acinonychis str. Sheeba -Helicobacter hepaticus ATCC 51449 -Helicobacter pylori 26695 -Helicobacter pylori HPAG1 -Helicobacter pylori J99 -Thiomicrospira denitrificans ATCC 33889 -Wolinella succinogenes DSM 1740 Sponsors: The project was originally conceived in 2002 by Roy Chaudhuri and Mark Pallen at the University of Birmingham, as part of a BBSRC funded Exploiting Genomics (ExGen) consortium. CampyDB is developed and maintained by Nick Loman and Lori Snyder working in the Pallen Research Group at University of Birmingham and is supported by a 5 year BBSRC grant until Feburary 2012.
DBD: Transcription factor prediction database
Database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries. Benchmarks of the transcription factor predictions show they are accurate and have wide coverage on a genomic scale. The DBD consists of predicted transcription factor repertoires for 930 completely sequenced genomes.
Center for the Neural Basis of Cognition
CNBC is joint venture of University of Pittsburgh and Carnegie Mellon University. Our center leverages the strengths of the University of Pittsburgh in basic and clinical neuroscience and those of Carnegie Mellon in cognitive and computational neuroscience to support a coordinated cross-university research and educational program of international stature. In addition to our Ph.D. program in Neural Computation, we sponsor a graduate certificate program in cooperation with a wide variety of affiliated Ph.D. programs.
Major Histocompatibility Complex Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019 Database was open, publicly accessible platform for DNA and clinical data related to human Major Histocompatibility Complex (MHC). Data from IHWG workshops were provided as well., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The CGSC Collection contains only non-pathogenic BSL-1 laboratory strains, primarily genetic derivatives of Escherichia coli K-12, the laboratory strain widely used in genetic and molecular studies, but a few B strains. The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. The public version of the database includes this information and can be queried directly via this CGSC DB WebServer. The collection includes cultures of wild-type contributed from a number of laboratories and a few thousand derivatives carrying one or up to 29 mutations from among 3500 mutations in (or included in deletions spanning) more than 1300 different loci. Some combinations were constructed particularly for mapping purposes and are still used for teaching and for rapid localization, some for manifestation of a particular phenotype, some strains for transferring a particular region or for complementation analysis. Some plasmids, e.g., the Clarke and Carbon collection, F-primes, a number of toolkit plasmids, and a few classic plasmids are included, but it is not a comprehensive collection of plasmids. Additionally, we have recently acquired most of the strains from the Keio Collection of systematic individual gene knockout (deletion/kan insertion) strains.
A Java program that allows you to see, print, and edit DNA sequencing traces.
Consortium represents all publicly available gene trap cell lines, which are available on non-collaborative basis for nominal handling fees. Researchers can search and browse IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways, can find trapped genes of interest on IGTC website, and order cell lines for generation of mutant mice through blastocyst injection. Consortium members include: BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada), Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan), German Gene Trap Consortium provider (Germany), Sanger Institute Gene Trap Resource (Cambridge, UK), Soriano Lab Gene Trap Resource (Mount Sinai School of Medicine, New York, USA), Texas Institute for Genomic Medicine - TIGM (USA), TIGEM-IRBM Gene Trap (Naples, Italy).
A collection of chemical structure files in Protein Data Bank format that may be displayed in 3D by a plug-in called Chemscape Chime. These files may be saved locally and displayed outside of a browser with the programs RasMol or iMol. In addition, the cross-platform Java Viewer, Jmol, may be used to display the files locally or in web pages. Structures Collected at UW-Stevens Point Chemistry Department include: biochemical structures, amino acids, carbohydrates, coenzymes and vitamins, glycolysis enzymes and metabolites, krebs cycle enzymes and metabolites, neutral lipids, amphipathic lipids, isoprenoid lipids, nucleic acids, nucleotides, peptides and proteins, organic chemistry, aliphatic compounds, aromatic compounds, polymers, drugs, sweeteners, general chemistry, bioinorganic compounds, norganic compounds (crystals), and VSEPR structures
CIBEX: Center for Information Biology gene EXpression database
Center for Information Biology gene EXpression database
Gene expression database system in compliance with MIAME, which is a standard that the MGED Society has developed for comparing and data produced in microarray experiments at different laboratories worldwide. It serves as a public repository for a wide range of high-throughput experimental data in gene expression research, including microarray-based experiments measuring mRNA, serial analysis of gene expression (SAGE tags), and mass spectrometry proteomic data.
Software toolkit of a collection of scripts in which short reads (paired or unpaired), a fasta containing the sequences of transposable elements and a reference genome sequence, are the input and the output is a series of files containing the locations of TE insertions in the reference and short reads.
Clinicaltrials.gov: A Service Of The National Institutes Of Health
Registry and results database of federally and privately supported clinical trials conducted in United States and around world. Provides information about purpose of trial, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals.Offers information for locating federally and privately supported clinical trials for wide range of diseases and conditions. Research study in human volunteers to answer specific health questions. Interventional trials determine whether experimental treatments or new ways of using known therapies are safe and effective under controlled environments. Observational trials address health issues in large groups of people or populations in natural settings. ClinicalTrials.gov contains trials sponsored by National Institutes of Health, other federal agencies, and private industry. Studies listed in database are conducted in all 50 States and in 178 countries.
Expertly collected, well-curated data sets consisting of comprehensive clinical characterization and raw structural, functional and diffusion-weighted DICOM images in schizophrenia patients and gender and age-matched controls are now accessible to the scientific community through an on-line data repository (coins.mrn.org). This data repository will be useful to 1) educators in the fields of neuroimaging, medical image analysis and medical imaging informatics who need exemplar data sets for courses and workshops; 2) computer scientists and software algorithm developers for testing and validating novel registration, segmentation, and other analysis software; and 3) scientists who can study schizophrenia by further analysis of this cohort and/or by pooling with other data.
An efficient level set framework for multi-object segmentation. Its representation inherently prevents overlaps and gaps and it readily preserves object topology and object relationships. MGDM is efficient, storing only a fixed number of functions for any number of objects, and therefore scales well to segmentation problems with many classes and large images. It's representation also avoids some instabilities in other multi-class level set methods. MGDM is cross-platform; MATLAB wrappers, Java source and API are provided, with MIPAV plugins forthcoming.
Software toolkit that provides the following libraries and functions on linux platform: # Multi-resolution registration of MR images include T1, multimodality, and DTI images. # The registration model is B-spline, and users can custermize their own image similarity measures by writing a plugin function and recompile the program.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. Group providing a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems.
Cogprints: Cognitive Sciences EPrint Archive
An electronic archive for self-archive papers in any area of Psychology, neuroscience, and Linguistics, and many areas of Computer Science, Philosophy, Biology, Medicine, Anthropology, cognitive ethnology, archeology, paleontology, as well as any other portions of the physical, social and mathematical sciences that are pertinent to the study of cognition.
Medical Image Visualization and Analysis
Software package that is a powerful graphical interface that displays, segments, aligns, manipulates, and blends image (pixel) and geometry (real-world coordinates) data simultaneously. Several applications are directly built into MIVA. Registration modes include interactive affine transformations. Fiducial registration tools facilitate rapid alignments for inter-modality volumes. Interactive Region of Interst (ROI) and Volume-of-Interest (VOI) tools exist to segment medical images. Virtually unique to MIVA are its 3D geometry tools and their compatibility with pixel based medical images. A full 3D interactive rat brain atlas is in an fMRI module which walks one through the necessary steps of fMRI. A multiple material surface routine takes segmented medical slices and creates 3D triangulated surfaces that align along all region boarders without overlap or gaps. These surfaces are the direct input into the MIVA tetrahedral mesh generator.
A Matlab-based software library to perform independent component analysis on group white matter skeleton generated by FSL TBSS. The script produces stable estimates of the white matter tract or tract segments that resemble highly correlated variation profiles across a group of subjects.
A powerful and modular medical image viewer/editor. It should be particularly useful to Undergraduates, Postdocs and Researchers in Medical Imaging to visualize data and to easily make attractive figures (for papers or presentations). It will also in a near future offer a number of advanced algorithms for medical image processing. Look at the video to get an idea ! http://www.benoitscherrer.com/MisterI/videos.html
This simple visualization tool allows to load several images at the same time. The cursor across all windows are coupled and you can move/zoom on all the images at the same time. Very useful for quality control, image comparison.
flowCyBar - Analyze flow cytometric data using gate information
A software package to analyze flow cytometric data using gate information to follow population / community dynamics.
Provides pre-calculated evolutionary conservation profiles for proteins of known structure in the PDB. Enables flexibility in setting the parameters of the calculation, and accepts optional uploads of atomic coordinates, multiple sequence alignments, and phylogenetic trees for use in the calculation of conservation profiles.
Software tool that provides a convenient environment to simulate NMR diffusion in closed pores. It builds on the eigenfunction expansion of the magnetization.
dbRES: A web-oriented database for annotated RNA Editing Site
dbRES is a web-oriented comprehensive database for RNA Editing Site. dbRES contain only experimental validated RNA Editing Site. All the data in dbRES was manually collected from literatures reporting related experiment result or the GeneBank database. dbRES now contains all together 5437 RNA edit site data. dbRES covers altogether 95 organisms from 251 transcripts. RNA editing is a post-transcriptional modification of RNA and markedly increases the complexity of the transcriptome. RNA editing occurs in the nucleus, as well as in mitochondria and plastids. To date such changes have been observed in prokaryotes, plants, animals and virus. The diversity of this widespread phenomenon includes nucleoside modifications, nucleotide additions and insertions, either in coding or non-coding sequences of RNA, which can occur concomitantly with transcription and splicing processes.
NITRC Community Conferences Workshops and Meetings
NITRC / INCF Community Conferences Workshops and Meetings
Project to assist the community in the support of information about upcoming Conferences, Workshops and Meetings. Such support may be documents, news, files, etc. To see a listing of upcoming Events, please use the NITRC Community Events Page at http://www.nitrc.org/incf/event_list.php (and tab at right). To announce an Event, please use the Submit an Event at the NITRC Community Events Page, http://www.incf.org/Events/events/createObject?type_name=Event (and tab at right). Note, INCF account is currently required. All users are encouraged to check this site for upcoming meetings, and promote future meetings here.
Portal of glycoinformatics resources including databases and bioinformatics tools for glycobiology and glycomics research. Databases include a bibliography, structure, nuclear magnetic resonance (NMR), mass spectroscopy (ms) and a PDB search.
Free-to-view clinical trials register of clinical trials worldwide, it allows users to search, register and share information about randomized controlled trials. Publication services are also available via the range of open access peer-reviewed journals published by BioMed Central. Current Controlled Trials is run by an editorial and technical in-house team. It receives advice from an international Advisory Group, including academics, doctors and health care specialists of international renown. The Advisory Group provides valuable guidance on the current activities and possible new directions of Current Controlled Trials' two databases, the metaRegister of Controlled Trials (mRCT) and the International Standard Randomised Controlled Trial Number (ISRCTN) scheme.
Developmental and Reproductive Toxicology Database
Bibliographic database providing references to developmental and reproductive toxicology literature on the National Library of Medicine's Toxicology Data Network. It covers teratology and other aspects of developmental and reproductive toxicology. It contains over 200,000 references to literature published since 1965. DART/ETIC is easily accessible and free of charge. Search by subject terms, title words, chemical name, Chemical Abstracts Service Registry Number (RN), and author. Search results can easily be viewed, printed or downloaded. Search results are displayed in relevancy ranked order, but may be sorted by publication date, author or title.
A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.
Commercial supplier of antibodies, assay kits, conjugates and various toxins for biomedical research. ATS's product line is designed to assist scientists in the study of system functions, cell functionality, diseases and disorders.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 28, 2017. Software that performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation.
UPR Analysis Resource Center Confocal Microscopy Core Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE, documented June 26, 2017. Lab that provides resources for researchers such as image analysis and access to confocal microscopes.
Directory of Health Organizations Online
Directory of Information Resources Online
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 15, 2016. Database containing location and descriptive information about a wide variety of information resources including organizations, research resources, projects, and databases concerned with health and biomedicine. This information may not be readily available in bibliographic databases. Each record may contain information on the publications, holdings, and services provided. These information resources fall into many categories including federal, state, and local government agencies; information and referral centers; professional societies; self-help groups and voluntary associations; academic and research institutions and their programs; information systems and research facilities. Topics include HIV/AIDS, maternal and child health, most diseases and conditions including genetic and other rare diseases, health services research and technology assessment. DIRLINE can be searched using subject words (such as disease or condition) including Medical Subject Headings (MeSH) or for the name or location of a resource. It now offers an A to Z list of over 8,500 organizations.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An international collaboration between 46 labs from 20 different countries towards a low resolution canine marker map under the auspices of the International Society for Animal Genetics (ISAG). The map under development should achieve a resolution of about 20 cM and some of the markers should be mapped physically. The participants have agreed to use microsatellites as markers on a common panel of reference families which will provide the backbone of the marker map. It is foreseen to also include type I markers in the mapping effort and to produce cosmid derived microsatellites for physical mapping. For this purpose part of the effort focuses on the standardization of the canine karyotype. Special attention is payed to hereditary diseases where efforts are under way to establish resource families either by collecting families or by specific breeding. A point of emphasis of the DogMap project is the setting up of an internationally accessible database for handling the mapping data. The structure of the DogMap collaboration includes a managing committee and scientific advisers. The managing committee is responsible for the overall coordination of the activities within the collaboration, for the dissemination of relevant information to all of the participants and for the representation of DogMap outside the collaboration., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Repetitive motif detection by Assembly of Repetitive K-mers
Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome.
DoTS (Database Of Transcribed Sequences) is a human and mouse transcript index created from all publicly available transcript sequences. The input sequences are clustered and assembled to form the DoTS Consensus Transcripts that comprise the index. These transcripts are assigned stable identifiers of the form DT.123456 (and are often referred to as dots). The transcripts are in turn clustered to form putative DoTS Genes. These are assigned stable identifiers of the form DG.1234356. As of September 1, 2004, the DoTS annotation team has manually annotated 43,164 human and 78,054 mouse DoTS Transcripts (DTs), corresponding to 3,939 human and 7,752 mouse DoTS Genes (DGs). Use the manually annotated gene query to see the DoTS Transcripts that have been manually annotated. The focus of the DoTS project is integrating the various types of data (e.g., EST sequences, genomic sequence, expression data, functional annotation) in a structured manner which facilitates sophisticated queries that are otherwise not easy to perform. DoTS is built on the GUS Platform which includes a relational database that uses controlled vocabularies and ontologies to ensure that biologically meaningful queries can be posed in a uniform fashion. An easy way to start using the site is to search for DoTS Transcripts using an existing cDNA or mRNA sequence. Click on the BLAST tab at the top of the page and enter your sequence in the form provided. All the transcripts with significant sequence similarity to your query sequence will be displayed. Or use one of the provided queries to retrieve transcripts using a number of criteria. These queries are listed on the query page, which can also be reached by clicking on the tab marked query at the top of the page. Finally, the boolean query page allows these queries to be combined in a variety of ways. Sponsors: Funding provided by -NIH grant RO1-HG-01539-03 -DOE grant DE-FG02-00ER62893
DPDx: Laboratory Identification of Parasites of Public Health Concern
Parasite-related portal including concise reviews of parasites and parasitic diseases, an image library, a review of recommended procedures for collecting, shipping, processing, and examining biologic specimens, and a diagnostic assistance function, in which laboratorians and other health professionals desiring assistance in parasite identification can ask questions and/or send digital images of specimens for expedited review and consultation with DPD staff. This assistance is free of charge. The portal is hoped to strengthen diagnosis of, and enhance the capacity to address the global problem of parasitic diseases, both in the United States and abroad. Potential DPDx applications include: * training and continuing education of laboratorians, using material collected by CDC or contributed by other institutions * provision to health facilities worldwide of diagnostic assistance by CDC staff backed up when needed by experts from other institutions * diagnostic quizzes for self-assessment of laboratorians skills * informal, early detection of unusually clustered, atypical or emerging parasitic diseases
Table designed as a hypothesis testing, teaching and reference tool for physicians and researchers interested in drug interactions that are the result of competition for, or effects on the human cytochrome P450 system. The table contains lists of drugs in columns under the designation of specific cytochrome P450 isoforms. A drug appears in a column if there is published evidence that it is metabolized, at least in part, via that isoform. It does not necessarily follow that the isoform is the principal metabolic pathway in vivo, or that alterations in the rate of the metabolic reaction catalyzed by that isoform will have large effects on the pharmacokinetics of the drug., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.
dbSNP: Database for Short Genetic Variations
Entrez SNP - Single Nucleotide Polymorphism
NCBI Short Genetic Variations (SNV) database
Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.
DBSubLoc - Database of protein Subcellular Localization
A database of protein subcellular localization containing proteins from primary protein database SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross references to taxonomies and Gene Ontology database. Annotations were taken from primary protein databases, model organism genome projects and literature texts, and then were analyzed to dig out the subcellular localization features of the proteins. The proteins are also classified into different categories. Based on sequence alignment, nonredundant subsets of the database have been built, which may provide useful information for subcellular localization prediction. The database now contains >60 000 protein sequences including 30 000 protein sequences in the nonredundant data sets. Online download, SOAP server, Blast tools and prediction services are also available.
A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3
Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads.
Whole Genome Simulator for Next-Generation Sequencing.
Evolutionary Lineage Inferred from Structural Analysis
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ELISA is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function neighborhoods. The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). It introduces a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind.
Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
DBTBS: a database of Bacillus subtilis promoters and transcription factors
Database of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of Bacillus subtilis genes. The database allows the comparison of systematic experiments with individual experimental results in order to facilitate the elucidation of the complete B. subtilis gene regulatory network. The current version is constructed by surveying 947 references and contains the information of 120 binding factors and 1475 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs. The DBTBS database was reorganized to show operons instead of individual genes as the building blocks of gene regulatory networks. It now contains 463 experimentally known operons, as well as their terminator sequences if identifiable. In addition, 517 transcriptional terminators were identified computationally. (De Hoon, M.J.L. et al., PLoS Comput. Biol. 1, e25 (2005)). A new section was added under "Motif conservation", which presents hexameric motifs found to be conserved to different extents between upstream intergenic regions of genus-specific subgroups of homologous proteins.
Familial Hypertrophic Cardiomyopathy DNA Mutation Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of this locus-specific mutation database was to provide an online resource that contains summarized and updated information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data, for researchers and clinicians. It also serves as a means of publishing previously unpublished data, which could be of value in understanding genotype/phenotype correlations. This database contains mutations in various genes known to cause familial hypertrophic cardiomyopathy, a genetic disorder associated with defects in the sarcomere [1]. Only gene symbols approved by HUGO are used and mutations are reported in accordance with guidelines recommended by the Mutation Database Initiative of HUGO and EBI.
International Neuroinformatics Coordinating Facility Software Center
Software repository that makes it easy for neuroscientists to find, use and share software tools. The Software Center is accessible to everyone: you can browse and download available software tools without registering. However, by creating an account, you will be able to post comments, and request to join development teams. The INCF Software Center and the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) are sharing content. Software tools hosted by NITRC also appear at the INCF Software Center. Your software tool will be available to all users of the Software Center. You will be able to upload documentation, executables and related files; track use of your software; create a wiki; and establish a development team. Registered Software Center users will be able to comment on and post reviews about your software, and can request to join your development team. INCF's vision of the Software Center is that it will become a communication enabler for software users as well as developers. Accordingly, future system features to be added include communication and collaboration functions. We also plan to include support services to allow software developers organize their software, track the use, and receive feedback for further improvement and development. Further development of the Software Center will be strongly driven by the user needs. Please let us know what features you would like to see added.
Full-Malaria: Malaria Full-Length cDNA Database
FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan.
Minimum Information About a Microarray Experiment
Standard specification for the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment.
This website contains a list of five fungal genome databases from The J. Craig Venter Institute. Aspergillus genomes: -Aspergillus fumigatus (strain-Af 293) -Aspergillus clavatus -Neosartorya fischeri Other Fungal Genomes: -Cryptococcus neoformans (strain-JEC21) -Coccidioides posadasii
Project to improve the microarray and next-generation sequencing technologies and foster their proper applications in discovery, development and review of FDA regulated products by developing standards and quality measures. Microarrays and next-generation sequencing represent core technologies in pharmacogenomics and toxicogenomics; however, before these technologies can successfully and reliably be used in clinical practice and regulatory decision-making, standards and quality measures need to be developed. Everyone is invited to participate in the MAQC project.
NeuroHub: the information environment for Neuroscientists
Online aggregation portal of neuroscience research services that clients can use as a tool to contact, refer, and utilize such as medical services, neuropsychology assessments, and speech pathology.
Software providing a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.
DBTSS: Database of Transcriptional Start Sites
Database of transcriptional start sites (TSSs) representing exact positions in the genome based on a unique experimentally validated TSS sequencing method, TSS Seq. A major part of human adult and embryonic tissues are covered. DBTSS contains 491 million TSS tag sequences collected from a total of 20 tissues and 7 cell cultures. Also integrated is generated RNA-seq data of subcellular- fractionated RNAs and ChIP Seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. Also included is external epigenomic data, such as chromatin map of the ENCODE project. They associated those TSS information with public and original SNV data, in order to identify single nucleotide variations (SNVs) in the regulatory regions.
Commercial marketer, distributor and importer of industrial, medical, pharmaceutical and biological research and health innovation products.
Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.
GENESIS Neural Database and Modelers Workspace
GENESIS Neural Database and Modeler's Workspace
Software system to assist computational neuroscientists in interacting with databases of models and with neural simulation packages such as GENESIS. There are three components in the system: a user interface, a database server, and a global registry and repository. The collection of software tools with a graphical user interface enables users to interact over the WWW with databases of models and data. It provides facilities for searching multiple remote databases for model components based on various criteria; visualizing the characteristics of the components retrieved; creating new components, either from scratch or derived from existing models; combining components into new models; linking models to experimental data as well as online publications; and interacting with simulation packages such as GENESIS to simulate the new constructs. Although the initial version uses GENESIS as the simulator, the design permits the use of multiple simulation systems, with or without the use of a database. This allows modeling at multiple levels of scale from the molecular level, through the subcellular (e.g. ion channel), single cell, and network levels, to the systems level (e.g. relating models to fMRI studies). The system is intended to help users create and organize models and to interact with databases of models and neuronal simulation software. More specifically, the Modeler's Workspace is designed to provide the following: * Search and retrieval facilities for interacting with databases of models and other information; * Facilities for creating, editing and visualizing the characteristics of models; * Facilities for combining model components together and translating them into formats suitable for simulation systems such as GENESIS and NEURON; * Facilities for managing a personal database where a user can collect models and other objects; and * Collaboration facilities for connecting one or more users together, to allow them to simultaneously edit objects in a shared database and communicate with each other using real-time chat. The Modeler's Workspace is written in Java for portability and extensibility. It is modular in design and uses pluggable components for supporting different data formats, which means that new data types can be supported by loading an appropriate plug-in. To increase the probability that the Modeler's Workspace will be compatible with future databases and tools, they are using the eXtensible Markup Language (XML) as the interchange format for communicating with databases.
A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools.
Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases.
GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches.
A Bayesian image-based prediction algorithm that is based on the Relevance Vector Machine and Automatic Relevance Detection frameworks, which are popular approaches in Machine Learning. RVoxM adapts this framework to handle images and explicitly models the spatial smoothness in images. RVoxM can be used to learn to predict a binary or continuous variable from image data.
A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker).
International Organization for Standardization
An independent, non-governmental organization made up of members from the national standards bodies of 161 countries that develop and publish International Standards covering almost all aspects of technology and business. From food safety to computers, and agriculture to healthcare, ISO International Standards impact all our lives. The Central Secretariat in Geneva, Switzerland, coordinates the system. The standards are developed by the people that need them, through a consensus process. Experts from all over the world develop the standards that are required by their sector. This means they reflect a wealth of international experience and knowledge.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. A medical database with lists, or directories, of information in health and medicine and images of medical conditions. Users may search Hardin MD, browse through the Medical picture gallery, and sort search results by disease or alphabetical letter.
Haz-Map: Occupational Exposure to Hazardous Agents
Haz-Map: Information on Hazardous Chemicals and Occupational Diseases
Occupational health database designed for health and safety professionals and for consumers seeking information about the adverse effects of workplace exposures to chemical and biological agents. The main links in Haz-Map are between chemicals and occupational diseases. These links have been established using current scientific evidence. Haz-Map shows the diseases linked to each agent and the agents linked to each disease. Agents are chemical such as formaldehyde, or biological such as grain dust. Haz-Map links jobs and hazardous job tasks with occupational diseases and their symptoms. In Haz-Map, chronic occupational diseases are linked to both jobs and industries, while acute diseases and infectious diseases are linked only to jobs. Cancers are not linked to jobs, industries or findings. The information in Haz-Map comes from textbooks, journal articles, the Documentation of the Threshold Limit Values (published by ACGIH), and electronic databases such as NLM's Hazardous Substances Data Bank (HSDB). Haz-Map staff classifies, summarizes, and regularly updates the information found in the database.
Wikipedia offers a comparison of web annotation systems. Many of these systems require software to be installed to enable some or all of the features. This fact is only noted in footnotes if the software that is required is additional software provided by a third party.
Histology of Nervous Tissue Laboratory Course
Histology of Nervous Tissue Laboratories 9 and 10
A website for a neuroscience lab class from the University of South Carolina that contains images of different parts of the nervous system and allows students to identify each part and answer questions about it. You should be able to (a) recognize nervous tissue in routine histological sections; (b) distinguish peripheral nerves from dense CT and smooth muscle; (c) recognize the morphological differences between myelinated and unmyelinated nerves at both the light microscopic and electron microscopic levels; (d) recognize nerve cell bodies and their component parts; (e) identify and differentiate dendrites and axons; (f) understand and identify various types of neuroglia, including Schwann cells; (g) understand and identify the structural relationship of the Schwann cell cytoplasm and plasma membrane enveloping axons; (h) understand the general features of nerve synapses. You should be able to draw nerves, cell bodies, Nodes of Ranvier, synapses etc. as they would appear under both the electron and light microscopes.
MetaMorph Microscopy Automation and Image Analysis Software
Molecular Devices Metamorph Premier Software
Software tool for automated microscope acquisition, device control, and image analysis. Used for integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform analysis of acquired images. Offers user friendly application modules for analysis such as cell signaling, cell counting, and protein expression.
Histology atlas of different parts of the nervous system that corresponds with the laboratory exercises of the Cell & Tissue Biology course of the School of Medicine of the University of Kansas. Succinct explanations of the tissues to guide the first-year medical student in the use of their microscope is provided and subsequently serves as a permanent histology resource for all medical students and physicians. Sections of the brain that are included are: * Spinal Cord * Central Canal * White Matter * Gray Matter * Dorsal Root Ganglion * Cerebellum * Cerebrum * Astrocytes * Nerve * Node of Ranvier * Pacinian Corpuscle
A database providing detailed mortality and population data to those interested in the history of human longevity. For each country, the database includes calculated death rates and life tables by age, time, and sex, along with all of the raw data (vital statistics, census counts, population estimates) used in computing these quantities. Data are presented in a variety of formats with regard to age groups and time periods. The main goal of the database is to document the longevity revolution of the modern era and to facilitate research into its causes and consequences. New data series is continually added to this collection. However, the database is limited by design to populations where death registration and census data are virtually complete, since this type of information is required for the uniform method used to reconstruct historical data series. As a result, the countries and areas included are relatively wealthy and for the most part highly industrialized. The database replaces an earlier NIA-funded project, known as the Berkeley Mortality Database. * Dates of Study: 1751-present * Study Features: Longitudinal, International * Sample Size: 37 countries or areas
S.B.A.R.S - Spectral-Based Approach for Repeats Search
Spectral-Based Approach for Repeats Search
Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes.
Data Processing Assistant for Resting-State fMRI
A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely.
UniProtKB/Swiss-Prot Human Proteome Initiative
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP download, HTTP download or by using a mirroring program which automatically retrieves the file at regular intervals.
A toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel.
General purpose machine learning tool that is useful for supervised classification and regression problems as well as more generic problems such as patch-based segmentation.
This website contains animated 3D molecular models for amino acids, carbohydrates, and drugs. The amino acids listed are: -Alanine -Arginine -Asparagine -Aspartate -Cysteine -Glutamine -Glutamate -Glycine -Histidine -Isoleucine -Leucine -Lysine -Methionine -Phenylalanine -Proline -Serine -Threonine -Tryptophan -Tyrosine -Valine The categories of drugs included are: -Analgesics -Mood Elevators -Antacids -Psychedelics -Aphrodisiacs -Depressants -Stimulants -Intoxicants The carbohydrates listed are: -Fructose -Glucosamine -Glucose -Glyceraldehyde -Glycerol -Lactose -Maltose -Mannitol -Ribose -Ribulose -Sorbitol -Sucrose
International Committee on Taxonomy of Viruses
Virus Taxonomy: A community Knowledgebase Supporting Virus Research
International Committee on Taxonomy of Viruses (ICTV) is charged by the Virology Division of the International Union of Microbiological Societies (IUMS) with developing, refining, and maintaining the official, universal taxonomy of all viruses. The goal is to classify and name all known viruses into a single taxonomy that reflects their evolutionary relationships. It provides a variety of resources in support of that goal including online and downloadable versions of current and historical releases of the virus taxonomy.
IDbases are locus-specific databases for immunodeficiency-causing mutations. Our aim is to establish database for every immunodeficiency or provide links to those maintained elsewhere. IDbases contain in addition to gene mutation, also information about clinical presentation. Information has been collected from literature as well as received directly from researchers. It would be most glad if those analyzing mutations would send their information by using the interactive web submission available in each database. A number of articles have been published related to IDbases. IDbases are curated and distributed with proprietary MUTbase software suite.
Database of images from medical and natural history texts, most of which were printed before 1800. They are organized by theme: diagnostics, human body, imaging, instruments, physician-patient culture, portraits, public health, reproduction, reproduction instruments, therapeutics. The Clendening History of Medicine Library and Museum is the rare books and manuscripts library of the University of Kansas Medical Center. We actively collect rare books as well as current works in the history of medicine, nursing, and the allied professions. The Library also supports the biomedical ethics and medical humanities curriculum by collecting contemporary secondary works in these areas. Under the auspices of its Museum, the Library also owns hundreds of medical artifacts.
Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.
Online educational resource for human brain and spinal cord anatomy through images. Each image is annotated with major structures and coarse dissections.
Clinical and Laboratory Standards Institute
A not-for-profit membership organization that brings together the global laboratory community to foster excellence in laboratory medicine by facilitating the development of clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. CLSI is setting the standard for quality in clinical laboratory testing around the world.
DOE Joint Genome Institute Genome Portal
Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web.
Cancer Cytogenomics Microarray Consortium
Consortium promoting communication and collaboration among cancer cytogenomics laboratories, who are interested in applying microarray technologies to cancer diagnosis and cancer research. Their oals are to (1) establish platform-neutral and cancer specific microarray designs for diagnostic purposes, (2) share cancer microarray data between participating institutions for education purposes, (3) create a public cancer array database, and (4) carry out multicenter cancer genome translational research. Collaboration amongst the different laboratories and researchers will not only provide validation for the microarray design(s) but ultimately provide more comprehensive molecular information and more accurate interpretation to better serve cancer patients and further cancer research. The CGC was officially incorporated in June 2010 as a not-for-profit organization.
University of Amsterdam; Amsterdam; Netherlands
Public research university in the Netherlands that offers programs in humanities, social and behavioural sciences, economics and business, science, law, medicine, and dentistry.
Concierge: Personal Database Software for Digital Research Resources
Concierge: Personal Database Software for Managing Digital Research Resources
The Concierge Project: Personal Database Software for Digital Research Resources
A data management tool which stores, classifies and manages digital resources such as publications, experimental data, presentation files, etc, together with its metadata. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. It has a function of sharing data with open digital archives based on the XooNIps system, such as neuroinformatics platforms in operation and publicly available at J-Node (http://www.neuroinf.jp). The Concierge Project is a part of neuroinformatics research by Laboratory for Neuroinformatics in RIKEN Brain Science Institute. Concierge's primary goal is to encourage research resource sharing in neuroscience communities. A key feature of the software is its pluggable configuration. Based on the basic functions, various applications can be developed as plug-ins. It has already developed several application plug-ins specific to neuroscience research, e.g. literature manager, electronic laboratory notebook, etc.
BEAT - BS-Seq Epimutation Analysis Toolkit
Software that implements all bioinformatics steps required for the quantitative, high-resolution analysis of DNA methylation patterns from bisulfite sequencing data.
Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data.
A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu.
Groupwise and Longitudinal Image Registration Toolbox
Software for both groupwise registration and longitudinal registration, which are the necessary steps for many brain-related applications. Specifically, groupwise registration is important for unbiased analysis of a large set of MR brain images. Therefore, in this software package, they have included two of their recently-developed groupwise registration algorithms: 1) Improved unbiased groupwise registration guided with the sharp group-mean image, and 2) Hierarchical feature-based groupwise registration with implicit template (Groupwise-HAMMER for short). On the other hand, they also included their recently-developed groupwise longitudinal registration algorithm that aligns not only the longitudinal image sequence for each subject, but also align all longitudinal image sequences of all subjects to the common space simultaneously.
A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction.
Open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains. The curation effort aims at covering the interactions mediated by the following domains (SH3, SH2, 14-3-3, PDZ, PTB, WW, EVH, VHS, FHA, EH, FF, BRCT, Bromo, Chromo, GYF). The interactions deposited in DOMINO are annotated according to the PSI MI standard and can be easily analyzed in the context of the global protein interaction network as downloaded from major interaction databases like MINT, INTACT, DIP, MIPS/MPACT. It can be searched with a versatile search tool and the interaction networks can be visualized with a convenient graphic display applet that explicitly identifies the domains/sites involved in the interactions.
Educational resource to introduce users to the anatomy, physiology, histology, and pathology of the laboratory mouse, with an emphasis on the Genetically Engineered Mouse (GEM). It provides access to histological images, scanned at high resolution and browsable through Zoomify, movie loops and animations derived from MRI, correlated MRI and histology. It has CNS data but is focused on the whole body, e.g., physiological data is available for the heart in the form of wave patterns, histology, CNS, pathology, magnetic resonance imaging, neoplasms; animation, virtual histology, mouse, correlated imaging, necropsy, whole mouse. It may be useful to neuroscientists by relating brain anatomy to the rest of the body. There is a movie illustrating necropsy of the mouse. A link to a compendium of histological slices of brain neoplasms is provided under the Image Archive link. There is a CNS link under construction for anatomical system, which presumably will include detailed CT imaging. This site still appears to be under construction.
R Tutorial - An R Introduction to Statistics
R Tutorial (An R Introduction to Statistics)
Couple of introductory tutorials on basic R concepts that provides an introduction to the R programming language, and illustrates its use by solving elementary statistics textbook exercises. Beyond the basics, they also cover topics of GPU computing in R. An R Tutorial eBook is also available.
Online educational resource that provides introductory-level material for new R users who have basic experience with programming.
Online Information Center for Immunohistochemistry
This site provides access to a very wide variety of histological protocols either directly or through links. An entire section is devoted to neuroscience, including neurohistology and cell culture protocols.protocol, experimental technique.
Group Level Imputation of Statistic Maps
A software toolkit that performs multiple imputation for group level, single sample t-tests. Whole brain group level statistic maps from fMRI rarely cover the entire brain as a result of missing data. Missingness between subjects in fMRI datasets can result from susceptibility artifacts, bounding box (acquisition parameters), and small differences in post-normalized morphology. The toolkit consists of several interactive command line scripts that guide the user to map the spatial distribution of missing data across contrast images, calculate spatial neighborhood averages that help impute values, perform conventional and multiple imputed t-statistics, save the results to brain maps, and create result tables. The toolkit contains an instruction manual (pdf), two Matlab scripts and one R-Statistics script, which depend on functions defined in the popular SPM toolbox and functions defined in the MICE package for (R).
A magnetoencephalography facility hosted at NeuroSpin (CEA Saclay, France) equipped with a 306-channel MEG system from Elekta Neuromag, EEG and EGI systems, and an Eyelink 1000 eye-tracker from SR research. A large set of MEG data analysis tools are being used in the lab including mne-python, fieldtrip, brainstorm, spm, adjust and in-house techniques are also being developed.
DOMINE: Database of Protein Interactions
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014)
Public institution of higher learning in western France that offers programs four major areas: law, economics and business; arts, letters and languages; human and social sciences; and sciences, technology and health.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017. Database developed for storing, retrieving and cross-referencing neuroscience information about the connectivity of the avian brain. It contains entries about the new and old terminology of the areas and their hierarchy and data on connections between brain regions, as well as a functional keyword system linked to brain regions and connections.
Annotated magnetic resonance brain images, both slices and surface views, normalized to Talairach space, along with annotations and a nice tutorial on image normalization. A viewer for MRI images (MRicro) is available and is described in a separate entry. Series of coronal, axial and sagittal brain slices along with some rendered volumes with major brain structures delineated. Slices are presented as static series with partial overlap of slices, so they are not suitable for 3d reconstruction. This neuroanatomy atlas shows regions on normalized MRI scans. Normalization is the process of warping a brain to match a standard size, orientation and shape of other brains. You can normalize MRI scans using programs like AIR, FLIRT or SPM. Once normalized, the overall shape of your MRI scan will approximately match those in this atlas. However, normalization preserves the unique sulcal features of each brain, so there will be some variation between your image and the images shown in this atlas. There is a great deal of individual variability even after normalization, so any atlas is only a rough guide to the shape and location of structures in an individuals brain. As I have noted before, secondary and tertiary sulci are not found in all individuals (Ono et al. 1990, Atlas of Cerebral Sulci). Another benefit of normalizing brains is it makes it easy to complete an accurate "scalp stripping" with brain extracting software (my MRIcro software implements Steve Smith's BET for this task). You can then create a useful volume rendering of the cortical surface. Typically, it is much easier to identify cortical sulci and gyri by looking at a rendered image of the brain's surface. This atlas shows you how to recognize these landmarks on a rendered MRI scan.
mricron - magnetic resonance image conversion viewing and analysis
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Software package that provides solutions for registering two groups of images, which are the necessary steps for many brain-related applications.
The most comprehensive health sciences collection in Puerto Rico.
Software repository for tools used to create diploid FASTA files with containing snps, indels, duplications, deletions, and translocations. They can be used to create artificial genomes for next-gen sequencing simulations.
Rhetorical Document Structure Group HCLS IG W3C
This group aims to define a "rhetorical structure" for scientific papers, to use in authoring or mark-up tools. They are trying to come to a definition of such a format; have an intermediary proposal of their own and are beginning to make an overview of existing publisher's proposals. Objectives *O1: Study and develop a model -- set of elements -- (a core model plus additional domain-specific modules), that capture the rhetorical aspects of scientific publications at different granular levels. *O2: In the long run, integrate the developed model in different environments to improve the authoring, retrieving and browsing user experience. *O3: Make a mocked up annotated document collection using this element set for each use case. *O4: Disseminate these models and document systems to the rest of the W3C and the community at large.
Core facility that provides the following services: Classic confocal imaging experiments.
The DOSY Toolbox processing PFG-NMR diffusion data
Software toolbox for processing PFG NMR diffusion data that aims to incorporate many of the important processing schemes. It has a graphical user interface to make it easy to access a variety of different processing schemes (and a command mode for more advanced options). It is written in MATLAB, but can also be obtained as free standing compiled version that does not require a MATLAB installation. The MATLAB version runs on any platform, and the compiled version is presently available for Windows, Linux, and Mac.
Marine Biological Laboratory in Woods Hole
Private non-profit laboratory at the University of Chicago that works on scientific discovery of biodiversity, understanding the environment and exploring the human condition through education and research.
A complete browse and visualization tool for all types of paleoclimate and paleoecological data (Version 1.0 for Windows 3.1 and the Macintosh). Point and click to create queries, list site information, display or plot variables and data, or export the data for further processing and analysis. Note: PaleoVu is no longer maintained or supported. Data content is not being updated, and compatibility problems may exist with newer operating systems. PaleoVu is still suitable as a teaching tool, but our internet-based browsing tools are the most up to date source for paleoclimatic data.
Metabolomic Univariate and Multivariate Analysis
Metabolomics Univariate and Multivariate Analysis (MUMA)
Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY).
Database collection of known and predicted transcription factors of Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica. DRTF currently contains 2,025 putative transcription factors (TF) gene models in indica and 2,384 in japonica, distributed in 63 families. THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026.
VennDiagram: Generate high-resolution Venn and Euler plots
Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Neurons are characterized in terms of their morphological, physiological and gene expression profiles. Synaptic connections are characterized in terms of their physiological and anatomical profiles. Neuron morphology profiles are obtained from detailed morphometric breakdown of 3D reconstructed neurons (m-Profiles), neuron physiology profiles are obtained from detailed measurement of the electrophysiological responses to a series of stimulus protocols (e-Profiles), and neuron gene expression profiles are obtained from single cell RT-PCR data (g-Profiles) and in the near future from gene-chips. Synaptic connections are characterized by the identity of the pre and postsynaptic neurons (sn-Profile), the anatomy of synaptic connections as characterized by the axonal and dendritic location of light microscopically identified putative synapses (sm-Profile), and the physiology of synaptic connections as characterized by a profile of electrophysiological parameters obtained from a series of stimulation protocols applied to the presynaptic neuron (se-Profile).
University of Delaware Nervous Tissue Color Images
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. An image collection of tissue from the central nervous system and peripheral nervous system.
Training material created for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R to help you quickly access this language in your work. The book inspired by this site takes the material here and significantly expands upon it.
Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.
MCML is a Monte Carlo simulation program for Multi-layered Turbid Media with an infinitely narrow photon beam as the light source. The simulation is specified by an input text file called, for example, sample.mci, which can be modified by any simple text editor. The output is another text file called, for example, sample.mco. (The names are arbitrary.) CONV is a convolution program which uses the MCML output file to convolve for photon beams of any size in a Gaussian or flat field shape. CONV can provide a variety of output formats (reflectance, transmission, iso-fluence contours, etc.), which are compatible with standard graphics applications.
Realistic simulated MEG datasets ranging from basic sensory to oscillatory sets that mimic functional connectivity; as well as basic visual, auditory, and somatosensory empirical sets. The simulated sets were created for the purpose of testing analysis algorithms across the different MEG systems when the truth is known. MEG baseline recordings were obtained from 5 healthy participants, using three MEG systems: VSM/CTF Omega, Elekta Neuromag Vectorview, 4-D Magnes 3600. Simulated signals were embedded within the CTF and Neuromag 306 baseline recordings (4-D to be added). Participant MRIs are available. Averaged simulation files are available as netcdf files. Neuromag 306 averaged simulations are also available in fif format. Also available: single trials of data where the simulated signal is jittered about a mean value, continuous fif files where the simulated signal is marked by a trigger, and simulations with oscillations added to mimic functional connectivity.
UPR Department of Environmental Health Core Laboratory
Laboratory that provides physical space for equipment and research by faculty at the University of Puerto Rico.
Minimal Interval Resonance Imaging in Alzheimer's Disease
Minimal Interval Resonance Imaging in Alzheimer's Disease - public dataset
A database of volumetric MRI brain-scans of 46 Alzheimer's sufferers and 23 healthy elderly people. Many scans were collected of each participant at intervals from 2 weeks to 2 years, the study was designed to investigate the feasibility of using MRI as an outcome measure for clinical trials of Alzheimer's treatments. It includes a total of 708 scans and should be of particular interest for work on longitudinal biomarkers and image analysis.
NIH Toolbox - Assessment of Neurological and Behavioral Function
NIH Toolbox - Assessment of Neurological Behavioral Function
NIH Toolbox for Assessment of Neurological and Behavioral Function
NIH Toolbox for the Assessment of Neurological and Behavioral Function
An integrated set of tools for measuring cognitive, emotional, motor and sensory function. These tools are being validated for use in diverse cultures, ethnic and geographic groups, ages (3-85 years) and study types. The toolbox is expected to provide a more complete picture of neurological and behavioral health in large-scale longitudinal studies, epidemiological studies, and clinical trials; and to facilitate cross-study comparisons. Moreover, the toolbox will: * be minimally burdensome to subjects and investigators, * utilize state-of-the art psychometric approaches and technology, including computer-assisted evaluation, and * be dynamic and adaptable to changes in measurement and technology. * be available in English and Spanish Many clinical studies collect data on aspects of neurological and behavioral function. However, the neurological and behavioral tests currently available to researchers lack uniformity and often require specialized training to administer. These limitations make it difficult to compile data across the full range of normal neurological function, and to compare data across studies. The toolbox is royalty-free and is expected to be available online by summer 2012.
Tool to remove facial features from an MRI structural image for the purpose of de-identification.
2008 MICCAI MS Lesion Segmentation Challenge
Training material for the MS lesion segmentation challenge 2008 to compare different algorithms to segment the MS lesions from brain MRI scans. Data used for the workshop is composed of 54 brain MRI images and represents a range of patients and pathology which was acquired from Children's Hospital Boston and University of North Carolian. Data has initially been randomized into three groups: 20 training MRI images, 24 testing images for the qualifying and 8 for the onsite contest at the 2008 workshop. The downloadable online database consists now of the training images (including reference segmentations) and all the 32 combined testing images (without segmentations). The naming has not been changed in comparison to the workshop compeition in order to allow easy comparison between the workshop papers and the online database papers. One dataset has been removed (UNC_test1_Case02) due to considerable motion present only in its T2 image (without motion artifacts in T1 and FLAIR). Such a dataset unfairly penalizes methods that use T2 images versus methods that don't use the T2 image. Currently all cases have been segmented by expert raters at each institution. They have significant intersite variablility in segmentation. MS lesion MRI image data for this competition was acquired seperately by Children's Hospital Boston and University of North Carolina. UNC cases were acquired on Siemens 3T Allegra MRI scanner with slice thickness of 1mm and in-plane resolution of 0.5mm. To ease the segmentation process all data has been rigidly registered to a common reference frame and resliced to isotrophic voxel spacing using b-spline based interpolation. Pre-processed data is stored in NRRD format containing an ASCII readable header and a separate uncompressed raw image data file. This format is ITK compatible. If you want to join the competition, you can download data set from links here, and submit your segmentation results at http://www.ia.unc.edu/MSseg after registering your team. They require team name, password, and email address for future contact. Once experiment is completed, you can submit the segmentation data in a zip file format. Please refer submission page for uploading data format.
The EBI genomes pages give access to a large number of complete genomes including bacteria, archaea, viruses, phages, plasmids, viroids and eukaryotes. Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism. WGS data for a growing number of organisms are being submitted to DDBJ/EMBL/GenBank. Genome entries have been listed in their appropriate category which may be browsed using the website navigation tool bar on the left. While organelles are all listed in a separate category, any from Eukaryota with chromosome entries are also listed in the Eukaryota page. Within each page, entries are grouped and sorted at the species level with links to the taxonomy page for that species separating each group. Within each species, entries whose source organism has been categorized further are grouped and numbered accordingly. Links are made to: * taxonomy * complete EMBL flatfile * CON files * lists of CON segments * Project * Proteomes pages * FASTA file of Proteins * list of Proteins
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. Matlab code for two-factor (location and year) analysis-of-variance model for the calculation of climate anomalies, in which the reference interval is specified as the full length of the dataset. This scheme avoids the affects of shorter (e.g. 1961-1990) reference intervals on the temporal evolution of the spatial standard deviation of climate anomalies. Data files provided.
ABCDE Format - Publishing Semantic Conference Papers
Proposed format for papers to be machine-readable for computers and wikis. The goal is to make mining, integration, and consumption of published information by semantic browsers and wikis easier.
This toolbox is an EEGLAB plugin for performing Measure Projection Analysis. Measure Projection Analysis (MPA) is a novel probabilistic multi-subject inference method that overcomes EEG Independent Component (IC) clustering issues by abandoning the notion of distinct IC clusters. Instead, it searches voxel by voxel for brain regions having event-related IC process dynamics that exhibit statistically significant consistency across subjects and/or sessions as quantified by the values of various EEG measures. Local-mean EEG measure values are then assigned to all such locations based on a probabilistic model of IC localization error and inter-subject anatomical and functional differences.
EchoBASE: an integrated post-genomic database for Escherichia coli
A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium.
Vaganov-Shashkin-Lite Model of Tree-Ring Width
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. A simple, efficient, process-based forward model of tree-ring growth, requires as inputs only latitude and monthly temperature and precipitation.
Confocal Microscopy Image Gallery - Rat Brain Tissue Sections
An image gallery of the rat brain labeled via immunofluorescence in coronal, horizontal, and sagittal thick sections using laser scanning confocal microscopy.
Database for the bacterium Escherichia coli K-12 MG1655, the EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It offers short, structured reviews of proteins and protein families, especially leukocyte surface membrane molecules. Index of information available from PROW includes CD molecule, Alternate names, Current Guides, Past Guides, Entrez Gene and Assigning workshop. Current guides: expanded format including Summary Sentence and Abstract Past guides: older guides with excellent information, some data may be dated
object-oriented Transcription Factors Database
ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database. This database is aimed at capturing information regarding the polypeptide interactions which comprise and define the properties of transcription factors. ooTFD contains information about transcription factor binding sites, as well as composite relationships within transcription factors, which frequently occur as multisubunit proteins that form a complex interface to cellular processes outside the transcription machinery through protein-protein interactions. ooTFD contains information represented in TFD but also allows the representation of containment, composite, and interaction relationships between transcription factor polypeptides. It is designed to represent information about all transcription factors, both eukaryotic and prokaryotic, basal as well as regulatory factors, and multiprotein complexes as well as monomers.
Blog by evolutionary biologist and UC Davis professor Jonathan Eisen. Topics of his posts include microbiology, phylogenomics, product reviews, and a variety of miscellaneous topics.
EcoGene Database of Escherichia coli Sequence and Function
Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries.
Mindboggle (http://mindboggle.info) is open source software for analyzing the shapes of brain structures from human MRI data. The following publication in PLoS Computational Biology documents and evaluates the software: Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B, Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human brains. PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350
Complete set of free, publicly accessible, downloadable atlases, templates, and individual manually labeled brain image data, the largest collection of publicly available, manually labeled human brains in the world! http://journal.frontiersin.org/article/10.3389/fnins.2012.00171/full
Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization.
An open source Java-based project intended to provide a graphic user interface (GUI) for interactions between scientists (or enthusiasts) and their data. In its current (beta) form, mgui offers the following functionality: * Cross-platform functionality (with a Java Runtime installation, runs on Linux, Windows, Mac, or Solaris) * 2D rendering of data based upon Java2D, and 3D rendering based upon Java3D * The ability to organize complex datasets into intuitive mgui projects * A processing pipeline interface which allows users to process their datasets with any available Java or native software tools * An extensible I/O framework accommodating a variety of standard and non-standard file formats * Database connectivity using JDBC * Graph visualization based upon the JUNG library * An intuitive Swing-based GUI for managing, querying, and visualizing data * Various CAD-type tools for editing and creating geometry * A computational modelling framework
Multi-Modal MRI Reproducibility Resource
Scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease) intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic 1 hour session at 3T. Imaging modalities include MPRAGE, FLAIR, DTI, resting state fMRI, B0 and B1 field maps, ASL, VASO, quantitative T1 mapping, quantitative T2 mapping, and magnetization transfer imaging. All data have been converted to NIFTI format. Please cite: Bennett. A. Landman, Alan J. Huang, Aliya Gifford, Deepti S. Vikram, Issel Anne L. Lim, Jonathan A.D. Farrell, John A. Bogovic, Jun Hua, Min Chen, Samson Jarso, Seth A. Smith, Suresh Joel, Susumu Mori, James J. Pekar, Peter B. Barker, Jerry L. Prince, and Peter C.M. van Zijl. ?Multi-Parametric Neuroimaging Reproducibility: A 3T Resource Study?, NeuroImage. (2010) NIHMS/PMC:252138 doi:10.1016/j.neuroimage.2010.11.047
Annotated document corpus, containing PubMed identifiers and text spans of documents reviewed for consideration for the Neuron Registry by Kyle H. Ambert, PhD.
Public university in Antwerp, Belgium that offers programs in economics, engineering, arts, design sciences, and medicine and health.
A Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision. It supports NIfTI-1.1 format float, double and signed and unsigned byte, short, and integer formats and provides legacy support for Analyze 7.5 8 and 16 bit images. It provides image display, editing, delineation of structure boundaries, export of traced contours and generation of masked volumes. Images are displayed in 3 orthogonal views. Time series can be displayed as averaged or contrast images and time courses can be visualized graphically. Version 2 provides enhancements to the original MultiTracer feature set.
Multicomponent T2 estimation with stimulated echo correction
Software tool designed to assist users in the estimation of multiple relaxation components from MRI T2 weighted spin-echo data such as that produced by a Carr-Purcell-Meiboom-Gill (CPMG) sequence. This problem is important to study myelin content in white matter diseases such as multiple sclerosis. Stimulated echoes arising from non-ideal flip angles are accounted for using the Extended Phase Graph (EPG) algorithm. The distribution is modelled as a small number of discrete components and a Bayesian estimation algorithm is provided to determine the weights and locations of the components as well as the actual flip angle. This algorithm outperforms iterative gradient descent based approaches.
National Consortium on Alcohol and NeuroDevelopment in Adolescence: Data Integration Component
Manuals, training materials, and computational tools developed by the National Consortium on Alcohol and NeuroDevelopment in Adolescence (NCANDA) Data Component. The NCANDA consortium consists of an Administrative Component at UC San Diego, the Data Integration Component at SRI International, and five data collection sites, Duke University, Oregon Health & Sciences University, SRI International, University of Pittsburgh, and UC San Diego. Each collection site will collect data from about 150 adolescents, each of them seen for one baseline and three annual follow-up visits.
UNC Gene Therapy Center Joint Vector Laboratories
University of North Carolina Vector Core
Core facility to access a comprehensive range of resources and services for gene transfer research including vector production services for research, preclinical and clinical materials. Services include: * Adeno-associated Virus (AAV) Custom Production; * AAV In-Stock Aliquots: Reporters, Deisseroth, Boyden, Roth, Uchida, Shah; * Lentivirus Custom Production
EDAS - EST-Derived Alternative Splicing Database
EDAS: EST Derived Alternative Splicing Database
EST Derived Alternative Splicing Database
Databases of alternatively spliced genes with data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. It contains splicing information on human, mouse, dog (not yet functional) and rat (not yet functional). For each database, users can search by keyword or by overall gene expression. They can also view genes based on chromosomal arrangement or other position in genome (exon, intron, acceptor site, donor site), functionality, position, conservation, and EST coverage. Also offered is an online Fisher test.
Neuroelectromagnetic Forward Head Modeling Toolbox
Neuroelectromagnetic Forward Modeling Toolbox
A MATLAB Toolbox for generating realistic head models from available data (MRI and/or electrode locations), for computing numerical solutions for the forward problem of electromagnetic source imaging and for single dipole source localization. The NFT includes tools for segmenting scalp, skull, cerebrospinal fluid (CSF) and brain tissues from T1-weighted magnetic resonance (MR) images. The Boundary Element Method (BEM) and Finite Element Method (FEM) are used for the numerical solution of the forward problem. When a subject MR image is not available a template head model can be warped to measured electrode locations to obtain an individualized head model. Toolbox functions may be called either from a graphic user interface compatible with EEGLAB or from the MATLAB command line.
A modular structure for scientific articles in an electronic environment
This thesis proposes a modular form for Physics papers: by investigating a collection of papers, a more fine-grained structure for science papers and an extensive relationships taxonomy is proposed. Examples of modular articles are included.
University of Applied Sciences; Mecklenburg-Vorpommern; Germany
University of Applied Sciences of Stralsund
University of Applied Sciences Stralsund
Public university in Germany for vocational training in the applied sciences.
A complete software package for working with electroencephalography (EEG) and event-related potential (ERP) data. You can acquire, review, analyze, and now ?see? your participant with synchronized video. Net Station also offers specialized tools and workflow options for both clinical and research applications, allows you to save different combinations of view settings (called workspaces) and helps with your reporting requirements by letting you set up and print custom cover pages. For more specialized work, Net Station also provides an optional electrical source estimation module (GeoSource) and an optional sensor location digitizer (Geodesic Photogrammetry System).
Matlab toolbox for testing hypotheses about the human connectome. NBS has been widely used to identify connections and networks comprising the connectome that are associated with an experimental effect or a between-group difference. User provides a series of connectivity matrices from different cohorts, or from the same subject during different experimental conditions. Connectivity matrices are inferred from neuroimaging data using other packages that, for example, count the number of tractography streamlines that interconnect each pair of regions (diffusion-MRI), or measure the extent of inter-regional correlation in BOLD response (fMRI). User specifies hypothesis to be tested at every connection with the general linear model. Features include: graphical user interface; NBSview, a basic network viewer modeled on SPMresults; exchange blocks for repeated measures; options to measure network size with intensity or extent; false discovery rate (FDR) option. Developed by Zalesky, Fornito, Cocchi and Bullmore.
An advanced viewer for electrophysiological and behavioral data: it can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities.
eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups)
eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups
evolutionary genealogy of genes: Non-supervised Orthologous Groups
A database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). eggNOG's database currently counts 1.7 million orthologous groups in 3686 species, covering over 7.7 million proteins (built from 9.6 million proteins). (Jan 30, 2014)
A collection of tools that generate numerical fiber structures with the complexity of human white matter and simulate Diffusion-Weighted MR images that would arise from them. Its primary use is to enable the testing of tracking algorithms
Searchable portal for public non-coding RNA databases. The databases are classified by RNA family, information source, information content, and available search mechanisms.
Public research university in Tucson, Arizona that offers undergraduate and graduate degree programs in psychology, audiology, speech pathology, and medicine.
MRI Simulator that provides a realistic approximation of an actual MRI scanner to allow habituation and training of participants in an environment less daunting than a real scanner. Special populations such as children, the elderly, and psychiatric patients, are often prone to claustrophobia and anxiety in the bore of a magnet, and consequently have a much higher rate of terminating the experiment or scan session before its completion. Some centers that have dealt with these populations estimate a 50%-80% failure rate. With the use of the MRI Simulator this failure rate can often be reduced below 5%, improving cost effectiveness.
HIBAL Hydrologic Isotopic Balance Model for Paleolake Systems
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. FORTRAN code for a simple hydrologic-isotopic-balance model for application to paleolake d18O records. Inputs to the model include discharge, on-lake precipitation, evaporation, and the d18O values of these fluid fluxes. Benson and Paillet (2002)
Pharmabase - an open content cheminformatics resource linking physiology with pharmacology
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2015. Open content cheminformatics database linking physiology with pharmacology, it targets the action and use of pharmacological compounds in modifying protein function, while revealing molecular relationships and linking out to related databases and sites. Pharmabase has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds in cellular research. It has several navigational routes, including a graphics browser (shows graphics of cell types and pathways) and membrane transport, which also illustrates the diversity of mechanisms that are covered. Users have access to detailed compound records with interactive features, and a form to send comments to the editor. Investigators are encouraged to alert the editors to mistakes, omissions or new compound information available from their reading and research.
Database of CDC's pictures organized into hierarchical categories of people, places, and science, presented as single images, image sets, and multimedia files. Much of the information critical to the communication of public health messages is pictorial rather than text-based. Created by a Working Group at the Centers for Disease Control and Prevention (CDC), the PHIL offers an organized, universal electronic gateway to CDC's pictures. Public health professionals, the media, laboratory scientists, educators, students, and the worldwide public are welcome to use this material for reference, teaching, presentation, and public health messages.
Yloc - Interpretable Subcellular Localization Prediction
An interpretable web server for predicting subcellular localization. In addition to the predicted location, YLoc gives a reasoning why this prediction was made and which biological properties of the protein sequence lead to this prediction. Moreover, a confidence estimate helps users to rate predictions as trustworthy. YLoc+ is able to predict the location of multiple-targeted proteins with high accuracy. The YLoc webserver is also accessible via SOAP.
Software package of 2D and 3D restoration algorithms.Advanced image deconvolution and 3D visualization software for Life Science Researchers.
CAMERA - Collection of annotation related methods for mass spectrometry data
A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.
Sample Size Estimates for Well-Powered Cross-Sectional Cortical Thickness Studies
Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Bibliography for primate cortical connectivity. The page displays the articles by their year of publication and links to PubMed.
Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames.
iBEAT: Infant Brain Extraction and Analysis Toolbox
Infant Brain Extraction and Analysis Toolbox
A toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal (or single-time-point) multimodality (including T1, T2, and FA) (or single-modality) data can be processed using the toolbox. Main functions of the software (step by step) include image preprocessing, brain extraction, tissue segmentation and brain labeling. Linux operating system (64 bit) is required. A workstation or server with memory >8G is recommended for processing many images simutaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.
Liquid Publications: Scientific Publications meet the Web
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 08, 2014. Project proposing a "liquid" format for science papers that consists of a set of research objects, connected by links. The immediate targets are the scientific research communities including publishers that, in a liquid world, will need to develop novel services and business models. Results and additional reading material (case studies, surveys, and the like) will be made available. The project also is creating an open source development effort and a platform to manage liquid publications and their evaluation. Their current main effort is developing the Liquid Journal and Liquid Conference use cases.
WoLF PSORT - Protein Subcellular Localization prediction
Data analysis service for protein subcellular localization prediction.
Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available.
Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available.
Multi-modal imaging and multi-level characteristic with multi-classifier
A brain imaging classification tool, which can help researchers to discriminate patients from normal controls. The M3 includes three steps: feature selection, maximum uncertainty linear discriminant analysis (MLDA)-based classification and multi-classifier. A leave-one-out cross-validation (LOOCV) is further used to estimate the performance of the M3. Finally, the most discriminative features are identified.
Collection of software tools for simulating biological sequences, including simulations of genome fragment sampling, random genomic sequences, methylation levels, and NGS reads.
A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2
Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher.
Software for the detection and visualization of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy.
4D-PARSeR Pathological Anatomy Regression via Segmentation and Registration
4D-PARSeR (Pathological Anatomy Regression via Segmentation and Registration)
4D-Pathological Anatomy Regression via Segmentation and Registration
A tool for analyzing 4D images with pathology. Originally developed for processing longitudinal images of patients with traumatic brain injury, the tool contains new image analysis algorithms that combine registration and segmentation in a coherent framework, accounting for extreme changes due to extensive tissue damage.
An open source learning-based software that automatically learns how to transfer the output of a host segmentation tool closer to the user's manual segmentation using the image data and manual segmentation provided by the user. The motivation of this project is to bridge the gap between the segmentation tool developer and the tool users such that the existing segmentation tools can more effectively serve the community. More and more automatic segmentation tools are publicly available to today's researchers. However, when applied by their end-users, these segmentation tools usually can not achieve the performance that the tool developer reported. Discrepancies between the tool developer and its users in manual segmentation protocols and imaging modalities are the main reasons for such inconsistency.
A population-specific DTI template for young adolescent Rhesus Macaque (Macaca mulatta) monkeys using 271 high-quality scans. Using such a large number of animals in generating a template allows it to account for variability in the species. Their DTI template is based on the largest number of animals ever used in generating a computational brain template. It is anticipated that their DTI template will help facilitate voxel-based and tract specific WM analyses in non-human primate species, which in turn may increase our understanding of brain function, development, and evolution.
A self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.
Non-parametric Non-uniform intensity Normalization
The perl script nu_correct implements a novel approach to correcting for intensity non-uniformity in MR data that achieves high performance without requiring supervision. By making relatively few assumptions about the data, the method can be applied at an early stage in an automated data analysis, before a tissue intensity or geometric model is available. Described as Non-parametric Non-uniform intensity Normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. Preprocessing of MR data using N3 has been shown to substantially improve the accuracy of anatomical analysis techniques such as tissue classification and cortical surface extraction.
EPDnew databases are the result of merging Eukaryotic Promoter Database, EPD, promoters within house analysis of promoter specific high throughput data for selected organisms only. EPDnew is a set of species specific databases of experimentally validated promoters.
MRI Digital Projection System that uses Digital Light Processing (DLP) technology providing microsecond pixel rise times, outstanding contrast with all-digital fiber optic control that allows you to project crystal clear, sharp images. Includes: * High resolution (1024x768) DLP Projector with RF filtered enclosure, custom lens assembly, digital video (DVI) over fiber, high flow fans, internal thermal sensor * Control room device to perform DVI to Fiber conversion, remotely power down the projector, and allow use of projector remote control from control room * 30 meter fiber optic cable that runs between the projector and projector control station * Heavy duty, magnet compatible, projector stand (assembly required) * Heavy duty, magnet compatible mirror stand with mirror (assembly required) * High resolution, lenticular pitch rear projection screen for high quality image reproduction * Optional VGA to DVI converter (native DVI video cards on Windows or Macintosh recommended)
A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. These include * EC number * Recommended name * Alternative names (if any) * Catalytic activity * Cofactors (if any) * Pointers to the Swiss-Prot protein sequence entry(ies) that correspond to the enzyme (if any) * Pointers to human disease(s) associated with a deficiency of the enzyme (if any) We believe that the ENZYME database can be useful to anybody working with enzymes and that it can be of help in the development of computer programs involved with the manipulation of metabolic pathways. Available services include downloading ENZYME by FTP as well as report forms for a new ENZYME entry or for an error/update in an existing entry.
Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data.
A complete Python environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI).
Open-source utilities that are C++ based command line applications that allow image analysis and processing using ITK or VTK libraries. Specifically the following utilities are contained thus far: * ImageMath - the swiss army knife image modification * ImageStat - compute stats on images * IntensityRescaler - rescale/normalize intensities using a prior brain tissue segmentation * convertITKformats - convert 3D images in all ITK formats (NRRD, NIFTI, GIPL, Meta etc) * DWI_NiftiNrrdConversion - convert DWI and DTI from/to NRRD and NIFTI, works with UNC DTI tools and FSL * CropTools - crops 3D and 4D images * PolydataMerge - Merges VTK polydata files * PolydataTransform - Transforms polydata files * TransformDeformationField - concatenates or average deformation fields (H-fields or displacement fields) * DTIAtlasBuilder - Creates a DTI average from multiple DTI images
Commercial technology solutions for NIRS neuroscience imaging applications.
NIRx2nirs: A NIRx to .nirs data converter
A matlab script which takes near-infrared spectroscopy data recorded by NIRx system(s) and converts it to a .nirs file format for use with the HOMER2 NIRS processing pacakge.
Software program used to estimate allele frequency and SNP calling., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Support and community integration for the enhanced NITRC services of the Image Repository (IR) and the Computational Environment (CE). The NITRC Computational Environment, an on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. NITRC Image Repository is built upon XNAT and supports both NIfTI and DICOM images. The NITRC-IR offers 3,733 Subjects, and 3,743 Imaging Sessions searchable across seven projects to promote re-use and integration of valuable NIH-funded data.
Software repository of custom extensions to the GForge collaborative environment.
Non-rigid registration / distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI.
Neuroimaging Analysis Kit for Matlab and Octave
Software library of modules and pipelines for fMRI processing with Octave or Matlab(r) that can run in parallel either locally or in a supercomputing environment. Linux OS and MINC file format are supported. NIAK currently includes a preprocessing, a region growing and a connectome pipelines. NIAK features powerful pipeline management capabilities, including parallel computing, generation of detailed logs and automatic handling of pipeline failures or updates.
A Python package for reading and writing a variety of medical and neuroimaging file formats. This includes: ANALYZE (plain, SPM99, SPM2), NIfTI1, as well as MINC. NiBabel is the successor of PyNIfTI.
Software toolbox that includes reconstruction tools for emission and transmission imaging modalities, including Single Photon Emission Computed Tomography (SPECT), Positron Emission Tomography (PET), cone-beam X-Ray CT and parallel-beam X-Ray CT. At the core of NiftyRec are efficient, GPU accelerated, projection, back-projection and iterative reconstruction algorithms. The easy to use Matlab and Python interfaces of NiftyRec enable fast prototyping and development of reconstruction algorithms. NiftyRec includes standard iterative reconstruction algorithms such as Maximum Likelihood Expectation Maximisation (MLEM), Ordered Subsets Expectation Maximisation (OSEM) and One Step Late Maximum A Posteriori Expectation Maximisation (OSL-MAPEM), for multiple imaging modalities.
Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
AQnowledge Semantic Bookmarklet (Life Science)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Bookmarklet suitable for all main browsers, that, when invoked, highlights concepts of scientific significance in text and offers links to many open information resources about any concept highlighted.
Nipype: Neuroimaging in Python Pipeline and Interfaces
A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.
Software package for modeling Near-Infrared light transport in tissue and image reconstruction. This includes: Standard single wavelength absorption and reduced scatter, Multi-wavelength spectrally constrained models and Fluorescence models.
Nitime: time-series analysis for neuroscience
Software library for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.
Non-Rigid Image Registration Evaluation Project
Non-Rigid Image Registration Evaluation Project (NIREP)
Project to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations, using richly annotated image databases, using computer simulated data, and increasing the number and types of evaluation criteria. The goal of this project is to establish, maintain, and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore, these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms.
Normative Independent Component Analysis
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Software program, executable under any Windows32 OS, performs Group BSS (Blind Source Separation) analysis comparing two groups of individuals and it performs NICA (Normative ICA) analysis where individuals are compared individually to a (normative) group. All analysis is performed in the frequency domain, that is, for all frequencies. The program also performs all these analysis for qEEG, that is, at the electrode level, without any BSS. The program does all computations, saves and displays results. The rationale and methods used in this program are explained in all details in the following paper: Congedo M, John ER, De Ridder D, Prichep L (2010) Group Independent Component Analysis of Resting-State EEG in Large Normative Samples International Journal of Psychophysiology 78, 89-99.
A computerized, odor delivery device that can be used for basic research applications including mapping olfactory centers, cognitive / learning research, neuro-marketing among other uses. Additional products including tests for odor threshold, odor identification, odor discrimination and odor memory.
Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments.
Software with advanced visualization techniques and state-of-the-art volume rendering provide unparalleled insight into the details and properties of neurological data acquired by CT, micro-CT, MRI, PET, SPECT, microscopy and other modalities. With data fusion tools, intramodality and multimodality registration of MR/CT or PET/CT is easily accomplished, while semi-automatic VOI delineation on fused datasets can improve analysis. Standard formats, such as DICOM, RAW, JPEG, NIFTI, Analyze are supported and 3D/4D sequences can be played. Other features include MPR, oblique, CPR, volume clipping, and surface visualization of cortex, skull, and scalp models. Also standard are easy-to-use tools for voxel-based delineation of features and the measurement of properties, including areas, volumes, counts, and intensity profiles. Present your findings by creating annotated animations or high-resolution images for posters. An SDK is also available to create plug-ins that provide new workflows or functionalities.
A C++ package for low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG with very high accuracy.
PANDA (Pipeline for Analyzing braiN Diffusion imAges)
PANDA: a pipeline tool for diffusion MRI
PANDA: Pipeline for Analyzing braiN Diffusion imAges
Pipeline for Analyzing braiN Diffusion imAges
Software matlab toolbox for pipeline processing of diffusion MRI images. For each subject, PANDA can provide outputs in 2 types: i) diffusion parameter data that is ready for statistical analysis; ii) brain anatomical networks constructed by using diffusion tractography. Particularly, there are 3 types of resultant diffusion parameter data: WM atlas-level, voxel-level and TBSS-level. The brain network generated by PANDA has various edge definitions, e.g. fiber number, length, or FA-weighted. The key advantages of PANDA are as follows: # fully-automatic processing from raw DICOM/NIFTI to final outputs; # Supporting both sequential and parallel computation. The parallel environment can be a single desktop with multiple-cores or a computing cluster with a SGE system; # A very friendly GUI (graphical user interface).
Software that simulates PacBio reads by using either a model-based or sampling-based simulation.
PESTICA fMRI Physio Detection/Correction
Software tool to detect physiologic signals from the data itself as well as an adaptive physiologic noise removal tool (Impulse Response Function or IRF-RETROICOR) that zooms in on noise with only 6 regressors, getting all the noise that 5th order RETROICOR gets. These tools will allow you to correct your data for physiologic noise with what you currently have. These signals are equivalent to a parallel monitored pulse signal and a respiratory chest-bellows signal. Do you have 3D+time EPI data (BOLD or perfusion) but no usable physio signals for pulse and respiration? Are you concerned about the effect of physio noise on your data but don't know what to do but regress data-derived signals that mix unknown functional signal with possible physio noise signal? Are you concerned about the number of regressors you're incorporating once you add 5th order RETROICOR (20 more regressors!)? This is for you.
PHYCAA+: adaptive physiological noise correction for BOLD fMRI
Software algorithm that automatically estimates and removes physiological noise in BOLD fMRI data, including the effects of heartbeat and respiration. This algorithm (1) masks out high-variance CSF and vascular tracts that may otherwise confound analyses, and (2) regresses out noise timeseries in grey matter tissue, using an adaptive multivariate component decomposition (Canonical Autocorrelations Analysis). PHYCAA+ is an efficient, automated procedure that does NOT require external measures of physiology, nor does it require the user to manually identify noise components. Based on the peer-reviewed article: Churchill & Strother (2013). PHYCAA+: An Optimized, Adaptive Procedure for Measuring and Controlling Physiological Noise in BOLD fMRI. NeuroImage 82: 306-325
Public, co educational research university in Fayetteville, Arkansas.
Open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.
Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR)
Parkinson’s Disease Biomarkers Program Data Management Resource
PDBP: Parkinsons Disease Biomarkers Program
Common data management resource and web portal to promote discovery of Parkinson's Disease diagnostic and progression biomarker candidates for early detection and measurement of disease progression. PDBP will serve as multi-faceted platform for integrating existing biomarker efforts, standardizing data collection and management across these efforts, accelerating discovery of new biomarkers, and fostering and expanding collaborative opportunities for all stakeholders.
PennCNV: copy number variation detection
A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.
pIRS (profile based Illumina pair-end Reads Simulator)
profile based Illumina pair-end Reads Simulator
Software for de novo data simulation. It uses empirical distribution to reproduce Illumina pair-end reads with real distribution of substitution sequencing errors, quality values and GC%-depth bias.
Software providing a search engine independent platform for visualization of peptide and protein identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data.
Stimulus delivery and experiment control program. Stimuli include auditory, 2D and 3D visual, and multimodal and experimental data include fMRI, ERP, MEG, psychophysics, eye movements, single neuron recording, and reaction time measures.
University of Arkansas for Medical Sciences; Arkansas; USA
University of Arkansas for Medical Sciences
Division of medical sciences at a public research university in Arkansas. It focuses on education, research, and clinical programs with a specific goal to implement translational research in care.
Portal for documenting the Arrowsmith project and developing text mining tools for scientific, and specifically neuroscience, literature. It also contains a search functions that identifies similar concepts between two articles.
Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Pythagorean Displacement and Motion Regressors
Matlab script that uses the Pythagorean Theorem to calculate head motion and position, while preserving degrees of freedom. The motion parameters output by SPM (rp*.txt) estimate head position relative to the first volume in 3D translation and 3D rotation, which are often entered as a nuisance regressor during individual-level statistics. Regressing the total displacement and relative position can potentially explain more variance in voxel-level BOLD signals that is related to head movement during an fMRI experiment.
Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology.
Slicer3 modules for quantitative diffusion analysis. Modules include tools for clustering fiber tracts, summarizing measures over tract clusters, etc.
The package dti provides methods for structural adaptive smoothing of diffusion weighted data in the context of the diffusion tensor model. Through its edge preserving properties they reduce data noise without compromizing significant structures.
ShotGun: a Flexible Short Read Simulator to Facilitate Sequencing-based Study Designs
Software for short read simulating in order to facilitate sequencing-based study designs.
The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Computationally oriented experimental laboratory interested in the encoding of auditory information in the cerebral cortex and brainstem, and in the mechanisms of tinnitus and the effect of various drugs (Lidocaine, steroids, anti-oxidants) in relieving noise trauma induced tinnitus. The ferret (Mustela putorius) and the rat serve as their system model. Through chronic implants, they obtain electrophysiological data from awake behaving animals in order to investigate the response properties and functional organization of the auditory system, both in health and after noise trauma that induces tinnitus in rats. Projects: * Response Modulation to Ongoing Broadband Sounds in Primary Auditory Cortex * Neuronal Response Characteristics in the Inferior Colliculus of the Awake Ferret and Rat * Spectro-Temporal Representation of Feature Onsets in Primary Auditory Cortex * Targeting the changes in inferior colliculus induced by tinnitus
A stand-alone MATLAB-based toolkit for the rapid and flexible exploration of Region of Interest (ROI) response waveforms and other signals from across large fMRI datasets. An alpha-release is currently available for use with an example dataset and tutorial.
So far there is a lack for Random Field Theory (RFT) -based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley?s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer?s matlab subdirectory in the Matlab?s search path. In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171).
An automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping). Whole-brain segmentation is often the first component in neuroimage pipelines and therefore, its robustness is critical for the overall performance of the system. Many methods have been proposed in the literature, but they often: * work well on certain datasets but fail on others. * require case-specific parameter tuning ROBEX aims for robust skull-stripping across datasets with no parameter settings. It fits a triangular mesh, constrained by a shape model, to the probabilistic output of a supervised brain boundary classifier. Because the shape model cannot perfectly accommodate unseen cases, a small free deformation is subsequently allowed. The deformation is optimized using graph cuts.
Software application to visualize, segment, and quantify three-dimensional images. Multiple datasets may be loaded, displayed, fused, processed, and quantitatively analyzed simultaneously. Data may be imported from any DICOM-compatible three dimensional imaging modality. Regions-of-interest may be defined using a number of manual, semi-automatic, and automated tools to segment three-dimensional pixel volumes. They may also be imported from and exported to DICOM structure sets. This software has been applied to preclinical and clinical computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), and optical imaging data.
Project to discuss, debate, develop and deploy ontological practices for the fMRI community.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Database aimed at helping laboratory-based bacteriologists make best use of bacterial genome sequence data, with a particular emphasis on comparative genomics. The latest version, xBASE 2.0, now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy browser and a powerful full-text search facility. There are 2082 genomes in the database, 1062 complete and 1020 incomplete xSites: * coliBASE - a genome resource for the E. coli research community * campyDB - a genome resource for the Campylobacter research community * MycoDB - a genome resource for the Mycobacteria research community * RhizoDB - a genome resource for the Rhizobia research community * FtBASE - a genome resource for the Francisella research community * ClostriDB - a genome resource for the Clostridiales research community If you use xBASE in your work, please cite: xBASE2: a comprehensive resource for comparative bacterial genomics. Chaudhuri RR, Loman NJ, Snyder LA, Bailey CM, Stekel DJ, Pallen MJ. Nucleic Acids Res. 2008 Jan;36(Database issue):D543-6. Epub 2007 Nov 5.PMID: 17984072 This work is supported by the BBSRC, grant number BBE0111791, awarded to MJP and DJS.
A modified version of the Brain Extraction Tool (BET) that can process rodent brains.
An automatic cortical thickness measurement tool for rat brains. The pipeline consists of four steps: preprocessing to create binary mask and label map, thickness measurement which produces laplacian field and thickness map in order, run particle correspondence followed by statistical analysis resulting in mean thickness color map and t-test result. By running RodentThickness, you will need to fill in informations in a Graphical User Interface, and then compute. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a configuration file. The tool needs these other tools to work, so be sure to have these installed on your computer: * ImageMath * measureThicknessFilter * GenParaMeshCLP * ParaToSPHARMMeshCLP * ShapeWorksRun * ShapeWorksGroom * SegPostProcessCLP * BinaryToDistanceMap * MeshPointsIntensitysampling
S-rep Fitting Statistics and Segmentation
Software to fit s-reps to segmented anatomic objects, to compute probability distributions on these s-reps, to train and to apply classifiers between two classes of anatomic objects, and to apply hypothesis testing to determine which geometric or physiological features vary significantly between two classes. Software for object segmentation from medical images may also be included. S-reps are skeletal models for anatomic objects especially suited for computing probability distributions from populations of these objects and for providing object-related coordinates for the interior of these objects. They allow classification and hypothesis testing using their geometric features and physiological features derived from medical images. They also allow the definition of shape spaces, probability-based geometric typicality functions, and appearance models used for segmentation or registration. A variety of successful applications to objects in neuroimages have already been performed.
A Problem Solving Environment (PSE) for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.6.
SCRalyze - A matlab environment for model-based psychophysiology
A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models.
Society for Neuroscience: Brain Briefings
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 09, 2013. Brain Briefings is a newsletter series explaining how basic neuroscience discoveries lead to clinical applications. Brain Briefings is published during the academic year and prepared for a lay audience.
Spatially Organized Component Klassifikator
A software toolbox that can automatically identify many of the artifact components that are often present in independent component analysis (ICA) of functional MRI (fMRI). The method: * Does not require temporal information about the fMRI paradigm. * Does not require the user to train the algorithm. * Requires only the EPI images (additional acquisition of anatomical images is not required). * Is able to identify a high proportion of artifact-related ICs without removing components that are likely to be of neuronal origin. * Can be applied to resting-state fMRI. * Is automated, requiring minimal or no human intervention.
A matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics.
Software tool that computes point-based models using a parametric boundary description for the computing of Shape analysis. The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at speci?c locations. Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures.
Online word processor for scientific and scholarly papers. Write, share, cite, comment, export, and track changes of articles in one place.
X-ALD database initiated July 1999 by Hugo W. Moser, M.D. and Stephan Kemp, Ph.D. The primary aims of the database are: to catalogue and facilitate the analysis of X-ALD mutations; to provide background information on X-ALD; to provide links to X-ALD patient organizations; and to help with contacting and finding (local) X-ALD health care professionals. The purpose of the X-linked adrenoleukodystrophy database is to provide general educational information about X-ALD.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Server that allows you to explore a set of abstracts derived from a MEDLINE search. The system gives you the main associations between the words in groups of abstracts. Then, you can select a subset of your abstracts based on selected groups of related words and iterate your analysis on them. The only input needed is a set of abstracts (in one of the currently accepted input formats) or a definition of how to obtain them. XplorMed is recommended for cases in which you do not know exactly what are you expecting to find. Your interests may be modified by the results obtained, or you may want to inquire new questions as the analysis develops. Also, the results may suggest you additional words that should be used to expand your query in MEDLINE (e.g., unexpected abbreviations of a protein name, or synonyms of a disease).
Software to identify motifs, conserved regions, in DNA or protein sequences.
SRI24 Multi-Channel Atlas of Normal Adult Human Brain Structure
sri24-atlas - MRI-based brain atlas of normal adult human brain anatomy
An MRI-based atlas of normal adult human brain anatomy, generated by template-free nonrigid registration from images of 24 normal control subjects. The atlas comprises T1, T2, and PD weighted structural MRI, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal and transversal diffusivity), and two labels maps of cortical regions and subcortical structures. The atlas is provided at 1mm isotropic image resolution in Analyze, NIFTI, and Nrrd format. We are also providing an experimental packaging for use with SPM8.
A free volume processing segmenting tool that combines a flexible manual interface with powerful image processing and segmentation algorithms. Users can explore and label image volumes using slice windows and 3D volume rendering.
A Matlab demo for constructing a neuro-anatomical shape complex atlas from 3D MRI brain structures, based on the paper Ting Chen, Anand Rangarajan, Stephan J. Eisenschenk and Baba C. Vemuri, Construction of a Neuroanatomical Shape Complex Atlas from 3D MRI Brain Structures. In NeuroImage, Volume 60, Page 1778-1787, 2012
Statistical method and software for conducting image- and coordinate-based meta-analysis of neuroimaging studies investigating differences in brain activity (e.g. BOLD response in fMRI, metabolism in PET) or structure (e.g. gray matter volume in VBM, voxel-based or TBSS white matter fractional anisotropy in DTI, etcetera).
Software application that searches the BrainMap Database for papers of interest, reads their corresponding meta-data, and plots their results as coordinates on a standard glass brain in Talairach space.
Bamboo Dirt registry of digital research tools for scholarly use
Registry of digital research tools for scholarly use that makes it easy for digital humanists and others conducting digital research to find and compare resources ranging from content management systems to music OCR, statistical analysis packages to mindmapping software., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A viewer for medical imaging data that supports a variety of scientific file formats out-of-the-box (see https://github.com/xtk/X/wiki/X:Fileformats for a complete list). We think that the best way to render your files is without any necessary conversions. Just drop'em on a website and they are ready to render. Just drag'n'drop some medical imaging files on this website or try one of the four examples in the right corner. Then, play with the panels on the left and click, drag and rotate the 3d content. Slice:Drop uses WebGL and HTML5 Canvas to render the data in 2D and 3D. We use our own open-source toolkit to perform the rendering, called XTK ( http://goxtk.com ).
A single line of code to add your article pages to include the Altmetric score and donut graphic on your own site with minimal technical effort. Choose from an array of different badge styles, including the colourful and iconic Altmetric donut. Implement article level metrics into your pages in minutes. Their pricing is based on the number of journals you want covered, with significant discounts for larger portfolios. You can try out the badges for free and without any commitment - however, your visitors will only see a subset of activity for each article when they click through. See the technical documentation for details.
Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation. Note: these are for 3D Slicer version 3. There is now a version 4 of 3D Slicer available. Information about extensions for version 4 can be found at the following links: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/ExtensionsManager http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions
Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.
A GUI-enabled EEGLAB plugin for modeling and visualizing dynamical interactions between electrophysiological signals (EEG, ECoG, MEG, etc), preferably after transforming signals into the source domain. The toolbox consists of four modules: (1) Data Preprocessing, (2) Model Fitting and Connectivity Estimation, (3) Statistical Analysis, (4) Visualization, with a fifth Group Analysis module in development. Module 2 currently includes several adaptive multivariate autoregressive modeling (AMVAR) algorithms, including segmentation AMVAR and Kalman filtering. This subsequently allows the user to validate the model and estimate (in the time-frequency domain) a wide range of multivariate Granger-causal and coherence measures published to date. Module 3 includes routines for parametric and non-parametric significance testing. Module 4 contains routines for interactive visualization of dynamical interactions across time, frequency and anatomical source location.
Forum (Spanish) for sharing information and knowledge on this network, a collaboration between different research groups in Spain and national and international centres. (Foro para compartir datos y conocimiento sobre esta red. Se constituye el Spanish Resting State Network como una colaboracion entre distintos grupos de investigacion de Espa������a y centros nacionales e internacionales.)
A user-friendly, graphical user interface (GUI) that allows statistical and visual manipulations of real and simulated three-dimensional spatial point patterns. The analyses use files containing sets of X, Y, Z coordinates. These point patterns are frequently coordinates of cells of specific cell classes within in volumes of tissue derived from microscopy analyses. The analyses are scale independent so spatial analyses of coordinates from larger and smaller scale distributions are possible. The software can also generate sample sets of X, Y, Z coordinates for program exploration and modeling purposes.
University of Arkansas System; Arkansas; USA
The public university system in Arkansas, USA that includes 4-year institutions, 2-year colleges, and affiliated units for agriculture, public service and criminal justice programs.
Public research university and polytechnic education center in Aveiro, Portugal. It offers undergraduate, graduate and post-graduate degree programs in applied mathematics, physics, chemistry, telecommunications, robotics, bioinformatics, sea sciences, materials, design, business administration and industrial engineering.
University of Central Arkansas; Arkansas; USA
Public research university in Conway, Arkansas that offers degree programs in nursing, education, physical therapy, business, performing arts, and psychology.
Software simulator for a targeted resequencing generally known as exome sequencing. Wessim generates a set of artificial DNA fragments for next generation sequencing (NGS) read simulation.
Stereoscopic Atlas of Intrinsic Brain Networks
Stereoscopic Atlas of Intrinsic Brain Networks (SAIBN)
A 3D stereoscopic (anaglyph method) full brain functional connectivity atlas created using a parcellation atlas published by Craddock et al. (2012). Using 3D Slicer 3.6.3 and the two hundred Region of Interest (ROI) version of the Craddock atlas, 200 grayscale surface models were created using a z-stat threshold > 2.3, and each surface model was processed with a surface decimation algorithm, smoothed with the Taubin algorithm and without surface normals. For improved visualization of the functional connectivity networks and their relative anatomical position, the surface model of five subcortical anatomical structures (corpus callosum, bilateral caudate, pallidum, putamen, thalamus, amygdala and hippocampus) were included in SAIBN. These surfaces were created with 3D Slicer using the segmentation computed with Freesurfer v. 5.1. The viewer should use red-cyan glasses to see the 3D stereoscopic effect using 3D Slicer (version 3.6.3, http://www.slicer.org/pages/Special:SlicerDownloads).
3 atlases dedicated for neonates, 1-year-olds, and 2-year-olds. Each atlas comprises a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map. These atlases are constructed with the help of state-of-the-art infant MR segmentation and groupwise registration methods, on a set of longitudinal images acquired from 95 normal infants (56 males and 39 females) at neonate, 1-year-old, and 2-year-old.
Symmetric atlas of the primate brain created using 18 cases of rhesus macaques aged 16-34 months. It includes the T1-weighted image (with and without skull), and also tissue segmentation probability maps (white matter, gray matter, CSF, rest), subcortical structures segmentation (amygdala, caudate, hippocampus, pallidus, putamen), and a lobar parcellation map. You can find more details about the creation of this atlas in the following paper : M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8
XML-Based Clinical Experiment Data Exchange Schema
Data management software that provides an extensive metadata hierarchy for describing and documenting research and clinical studies. The schema organizes information into five general hierarchical levels: a complete project, studies within a project, subjects involved in the studies, visits for each of the subjects, the full description of the subject's participation during each visit.
peak_nii: Statistical image clustering peak detection and data extraction
Software toolbox for statistical image clustering, peak detection and data extraction developed to allow the user to have flexibility of clustering their data. Based on your threshold, it will cluster your data and find the peaks within each cluster. Additionally, it has been combined with a data extraction tool that allows one to extract the data from all the scans of the analysis from all the clusters, along with several other extraction options, with a single command.
Software Python package for working with DICOM files, made for inspecting and modifying DICOM data in an easy pythonic way. The modifications can be written again to a new file. As a pure python package, it should run anywhere python runs without any other requirements.
Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data.
University of Barcelona; Barcelona; Spain
Public university in Barcelona, Spain that offers degree programs in social sciences, engineering, and arts and humanities.
Mouse HapMap Imputation Genotype Resource
Genetic maps for 94 inbred strains of mouse and imputed genotypes using the NIEHS / Perlegen resequencing resource. Combining with the 13,094 Wellcome Trust SNPs (Single-nucleotide polymorphisms), a set of 132,285 SNPs was compiled and is available for download. Using the mouse HapMap resource, it is possible to accurately impute the genotypes of the 94 strains at the 8 million SNPs discovered by the NIEHS/Perlegen mouse resequencing project. They imputed the genotypes at the NIEHS/Perlegen SNPs from the mouse HapMap SNPs and an additional set of 7,570 gap-filling SNPs provided by NIEHS/Perlegen. Since each NIEHS/Perlegen SNP probe has different quality, they classified roughly half of the SNPs as "high-quality" SNPs, which do not have missing genotype at any of the 15 resequenced strains. The imputed genotypes are available for the high-quality SNPs, which has estimated error rate of 0.27% for high-confidence imputed genotypes. In addition, the imputed genotypes for all 8 million SNPs are also available for download. Their estimated error rate is 0.37% for high-confidence imputed genotypes.
scikit-learn: machine learning in Python
shapeAnalysisMANCOVA offers statistical shape analysis based on a parametric boundary description (SPHARM) as the point-based model computing method. The point-based models will be analyzed with the methods here proposed using multivariate analysis of covariance (MANCOVA). Here, the number of variates being tested is the dimensionality of our observations. Each point of these observations is a three dimensional displacement vector from the mean. The number of contrasts is the number of equations involved in the null-hypothesis. In order to encompass varying numbers of variates and contrasts, and to account for independent variables, a matrix computation is performed. This matrix represents the multidimensional aspects of the correlation significance and it can be transformed into a scalar measure by manipulation of its eigenvalues. Details of the methods can be found in its Insight Journal publication: http://hdl.handle.net/10380/3124
Vascular Modeling Toolkit in 3D Slicer 4
Provides series of modules which enable functions of Vascular Modeling Toolkit in 3D Slicer. Functionality includes vessel enhancement filtering, level set segmentation, centerline computation, network extraction and branch splitting.VMTK is available through the extension manager for 3D Slicer from version 4.6.2. Main difference to Slicer3 version is that now all VMTK modules come as one extension bundle. This should enhance the installation experience for users.
A question answer forum for scientists, focusing on methods in bioinformatics, computational genomics and biological data analysis. They welcome detailed and specific posts, written clearly and simply.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis.
Software tool for performing a per vertex statistical analysis across a population. The underlying statistical framework uses the R language.
Brain lesion segmentation tool using SVM
Brain lesion segmentation tool using Support Vector Machines
Segmentation tool that uses image analysis and machine learning techniques (Support Vector Machines). Image intensities from multiple MR acquisition protocols, after coregistration, are used to form a voxel-wise attribute vector which is used to perform the segmentation. Computer algorithms have started to complement expert-readings of MRI as they may improve throughput and consistency, in addition to providing more accurate quantitative measures of lesion type and volume. Computerized segmentation methods can also offer more precise measurements of longitudinal change of a lesion with disease progression or treatment response.
MBASED - Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
Meta-analysis Based Allele-Specific Expression Detection
Software package containing functions for allele-specific gene expression (ASE) analysis using meta-analysis based allele-specific expression detection.
Diffusion Tractography with Kalman Filter
Tractography with Unscented Kalman Filter
Software framework which uses an unscented Kalman filter for performing tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model. It is very easy to expand the framework and to implement new fiber representations for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be identical) and the other one uses a full tensor representation. The project is written in C++. It could be used both as a Slicer3 module and as a standalone commandline application.
A fast and robust software implementation of the popular Nonlocal Means for MRI-Rician denoising. It works by computing the non-local weights based on distances in a features space comprising the local mean value and gradients of the image. It can reach an acceleration factor of 20x over the original implementation, with an improved performance for medium-low SNR images. They use a bias correction step for Rician noise based on the well-known Conventional Approach. This software can be compiled either as a Slicer module or a stand-alone: http://www.nitrc.org/snapshots.php?group_id=518
FedBizOpps.gov: Federal Business Opportunities
The system is a web-based portal which allows vendors to review Federal Procurement Opportunities over 25,000. From the sites main navigation page, users can view opportunities and awards as well as view a variety of information and resources. FBO now contains Recovery and Reinvestment Act actions. Vendors / citizens may search, monitor, and retrieve opportunities. Government users may post, manage, and award opportunities when logged in using their password protected account.
Software application that uses a Monte Carlo algorithm to model the transport of photons through 3D volumes with spatially varying optical properties. Both highly-scattering tissues (e.g. white matter) and weakly scattering tissues (e.g. cerebral spinal fluid) are supported. Using the anatomical information provided by MRI, X-ray CT, or ultrasound, accurate solutions to the photon migration forward problems are computed in times ranging from minutes to hours, depending on the optical properties and the computing resources available.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Venue for discussing and defining standard web interfaces for sharing images, annotations, and analyses of multiscale biological images. The goal is to increase interoperability of code to share the burden of infrastructure, increase code reuse, and allow us to spend more time focused on scientific questions. Please visit our Wiki to start participating. Together we can develop a small group of interfaces which are easy to implement, extensible, and cover the major tasks of developing tools for multiscale data on the web.
Simultaneous Truth and Performance Level Estimation
STAPLE - Simultaneous Truth and Performance Level Estimation
An algorithm for the Simultaneous Truth and Performance Level Estimation, which estimates a reference standard and segmentation generator performance from a set of segmentations. It has been widely applied for the validation of image segmentation algorithms, and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation, by combination of the output of a group of segmentation algorithms, and for segmentation by registration and template fusion., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An automated online framework for performing validation studies of skull-stripping methods. Registered users may download 40 T1 MRI volumes, skull-strip them with the algorithm of their choice, and upload their segmentation results to the SVE website. The server will then compare the 40 skull-stripped results against a set of manually generated brain masks. The server computes a series of measures for the uploaded data, including Jaccard and Dice measures. It also produces images for visualizing the spatial location of the segmentation errors relative to a common space. The results are archived on the server, and the measures are viewable by visitors to the site.
Software package representing Spatial Statistical Parametric Mapping that includes two tools presently: MAGEE and FADTTS. MAGEE represents the Multiscale Adaptive Generalized Estimating Equation. It was developed specifically for analyzing multivariate neuroimaging data in 3-dimensional volume (or on 2-dimensional surface) from longitudinal neuroimaging studies. FADTTS represents Functional Analysis of Diffusion Tensor Tract Statistics. The aim of this tool is to implement a functional analysis pipeline, for delineating the structure of the variability of multiple diffusion properties along major white matter fiber bundles and their association with a set of covariates of interest, in various diffusion tensor imaging studies.
3D Slicer module for automated segmentation of the spine. This is an implementation of a novel model-based segmentation algorithm. This work was presented at the NA-MIC Week in Salt Lake City, Jan 2010.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. Software tools which can perform Stochastic Tractography and related analysis on DWMRI data. Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A collection of software tools used for processing and organizing MRI data. The Dicom Importer allows you to to view, assemble, and organize dicom files. Subject Library is a filesystem-based search and reporting tool that can be configured to work with many different organization schemes. This package also contains a python library that can be used to write scripts for custom tasks.
Tools for Advanced Parameterized Image Registration
A set of command line tools allowing 2D and 3D image registration, mainly for medical imaging (although also relevant to other image registration problems).
ESIP Data Management Short Course for Scientists
ESIP Commons Data Management Short Course for Scientists
ESIP Data Management Training for Scientists
Data Management Short Course for Scientists
ESIP Federation training courses to improve the understanding of scientific data management among scientists, emerging scientists, and data professionals. The ESIP Federation, in cooperation with NOAA, seeks to share the community's knowledge with scientists who increasingly need to be better data managers, as well as to support workforce development for new data management professionals.
An analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features: * Free to use and modify under the GPL licence. * Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis. * Cross platform, works on Windows, Linux and OSX. * Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters. * Includes both GUI and command line interface for one-off and batch analyses.
Commercial company that develops and sells flow cytometry assay development software and analytical cytology tools.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A lightweight C++ template library designed mainly for medical imaging processing. The design paradigm follows generic programming, and the purpose is to provide an easy-to-use and also ready-to-use library. The code is template-based, and only header files are needed to be included to the source code. This library provides the following functions: # DICOM (r), Analyze(r), Nifti (r/w), and MATLAB MAT V4 (r/w) # numerical: add, multiply, gradient. # interpolation: linear, gaussian radial basis # filters: mean, gaussian, laplacian, sobel, anisotropic diffusion # morphological processing: erosion, expansion, opening, closing # template-based Fourier transform # linear coregistration: rigid body, affine transform, least square fit, mutual information # nonlinear coregistration: The Large Deformation Diffeomorphic Metric Mapping (LDDMM)
An open-source software project for distributed Tetrahedral Mesh Modeling and Analysis (TMMA) of multidimensional data. Tetrahedra are 3D, space filling, geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images (e.g., 3D MRI brain images). Tetrahedra are a natural extension of lines (1D) and surface triangulations (2D) which enable finite element analysis of irregular shapes, and permit a greater range of morphometric characterization of multidimensional objects. A beta version of the program is available for download. Please see the very brief instructions on the "Docs" tab on the left.
Software application that includes R packages for reading, writing and visualising magnetic resonance images stored in Analyze, NIfTI and DICOM file formats (DICOM support is read only). It also contains functions specifically designed for working with diffusion MRI and tractography, including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software
Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images.
TurtleSeg - Interactive 3D Image Segmentation Software
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An interactive segmentation tool originally designed for 3D medical images. Accurate and automatic 3D medical image segmentation remains an elusive goal and manual intervention is often unavoidable. TurtleSeg implements techniques that allow the user to provide intuitive yet minimal interaction for guiding the 3D segmentation process.
Human brain atlases for adult, pediatric and elderly populations, by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images, tissue priors (WM,GM,CSF), lobar parcellation maps and subcortical structures. Current available atlases: * Adult atlas: Symmetric atlas generated from 50+ healthy adult subjects (20-59 year old). * UNC-MNI Pediatric 1-year-old atlas: Symmetric atlas generated from 104 1-year-old subjects, combining children at high familial risk of autism and controls. * Pediatric 4-year-old atlas: Symmetric atlas generated from 10 4-year-old healthy subjects. * Elderly atlas: Atlas generated from 27 healthy elderly subjects (60+ years old). Additional information and acknowledgment for their usage can be found by clicking on the release notes.
National and Kapodistrian University of Athens
Public university in Athens, Greece that offers degree programs in health sciences, law and economics, and theology.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. NOTE: VR Worlds 2 is no longer available as a standalone software. Software application designed for the creation and execution of neurobehavioral studies. The VR Worlds 2 platform allows accurate, real-time data collection of the navigation and interactions within a simulated environment. You are free to design and perform custom or predefined experiments tailored to your personal research or clinical needs. Create complex environments with meaningful content using VR Worlds 2?s user-friendly, drag-and-drop interface. Include triggers to launch simple or intricate events, such as a conversation between characters or a customizable rating scale. VR Worlds 2 provides several realistic simulations to immerse your subjects in context appropriate environments, including: * Residential/Urban Area * Hotel Lobby * Medical Office * Grocery Store * Neighborhood for drug and alcohol cue extinction treatment (featured on GMA, motion capture process) * Casino for gambling addiction research (featured on Canadian Discovery Channel) * Driving simulation for mild cognitive impairment research * Phobia scenarios * Spatial navigation mazes
Vaa3D: A Swiss army knife for bioimage visualization & analysis
Vaa3D: A Swiss army knife for bioimage visualization and analysis
A handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D/4D/5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Vaa3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to Vaa3D Plugins. Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, 28(4), pp.348-353) about Vaa3D and Vaa3D-Neuron, an order of magnitude of performance improvement (both reconstruction accuracy and speed) was achieved compared to other tools.
A command line voxel-wise statistical analysis software program for images. Images can be gray matter density, jacobian images, etc. The linear model is implemented, i.e. designs that can be modeled as Y=AB, where Y is a vector or matrix of dependent variables, B is a vector or matrix of parameters to be estimated, and A is a design matrix. Why use valmap? # Do not need a Matlab license to run. # Can incorporate a spatially varying independent variable (e.g., you have a perfusion map as your dependent variable, and you want to co-vary for gray matter at each voxel, so use a gray matter map as an independent variable). # Can use spatially invariant independent variables (e.g., you can have a cognitive test score as the dependent variable, and use jacobian maps as the independent variable). # Can have multiple dependent variables and do multivariate analyses (e.g., want to know the overall effect of disease on perfusion and structure, so use perfusion maps and jacobian maps as dependent variables).
Web application for real-time collaborative editing. It provides customizable options, a documented API and the ability to convert to various data exchange formats.
discovering Single Nucleotide Polymorphism
discovering Single Nucleotide Polymorphism (discoSNP)
Software designed for discovering Single Nucleotide Polymorphism (SNP) from raw sets of reads obtained with Next Generation Sequencers (NGS).
WFU Biological Parametric Mapping Toolbox
BPM - Integrated Tool for Biological Parametric Mapping
Software toolbox that performs SPM analysis with voxel-wise imaging covariates. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in Matlab with a user-friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely used T-field, has been implemented in the correlation analysis for more accurate results. Requirements: * SPM2 or SPM5 * MATLAB version 6.5 or higher
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. A fully automated software application for the processing of fMRI data using SPM. It is fully automated from the point of data acquisition at the MRI scanner. It incorporates tools for automated data transfer, archiving, real-time SPM5 batch script generation with distributed grid processing, automated error-recovery procedures, full data-provenance, email notifications, optional conversion back to DICOM (Digital Imaging and Communications in Medicine), and picture archiving and communications systems (PACS) insertion. The architecture allows for an infinite number of easily definable analyses that are fully automated from the point of acquisition. Requirements: * MATLAB 7.3 or greater with the Image Processing Toolbox * SPM5
University of Auckland; Auckland; New Zealand
Public university in New Zealand that offers degrees in areas such as the arts, business, education, medical and health science, and law.
National Toxicology Program: Department of Health and Human Services
The NTP is an interagency program whose mission is to evaluate agents of public health concern by developing and applying tools of modern toxicology and molecular biology. The program maintains an objective, science-based approach in dealing with critical issues in toxicology and is committed to using the best science available to prioritize, design, conduct, and interpret its studies. To that end, the NTP is continually evolving to remain at the cutting edge of scientific research and to develop and apply new technologies. More than 80,000 chemicals are registered for use in the United States. Each year, an estimated 2,000 new ones are introduced for use in such everyday items as foods, personal care products, prescription drugs, household cleaners, and lawn care products. We do not know the effects of many of these chemicals on our health, yet we may be exposed to them while manufacturing, distributing, using, and disposing of them or when they become pollutants in our air, water, or soil. Relatively few chemicals are thought to pose a significant risk to human health. However, safeguarding public health depends on identifying both what the effects of these chemicals are and at what levels of exposure they may become hazardous to humansthat is, understanding their toxicology. The program was created as a cooperative effort to: 1. Coordinate toxicology testing programs within the federal government. 2. Strengthen the science base in toxicology. 3. Develop and validate improved testing methods. 4. Provide information about potentially toxic chemicals to health, regulatory, and research agencies, scientific and medical communities, and the public. The need for a program like the NTP arose because of increasing scientific, regulatory, and Congressional concerns about the human health effects of chemical agents in our environment. Many human diseases were thought to be directly or indirectly related to chemical exposures; therefore, it was thought that decreasing or eliminating human exposures to those chemicals would help prevent some human disease and disability. Testing Information The NTP is an interagency program whose mission is to evaluate agents of public health concern by developing and applying the tools of modern toxicology and molecular biology. This involves conducting toxicological evaluations of substances of public health concern, developing and validating improved (sensitive, specific, rapid) testing methods, developing approaches and generating data to strengthen the science base for risk assessment, and communicating with all stakeholders. The NTP plays a critical role in providing needed scientific data, interpretations, and guidance concerning the appropriate uses of data to regulatory agencies and other groups involved with health-related research. Through its interactive relationship with regulatory agencies, the NTP plays an indirect, but important role in shaping public health policy. Study Data Searches The National Toxicology Program makes available data from more than 500 two-year, two species, toxicology and carcinogenesis studies collected by the NTP and its predecessor, the National Cancer Institute's Carcinogenesis Testing Program, are stored in a database at NIEHS. The NTP database also contains the results collected on approximately 300 toxicity studies from shorter duration tests and from genetic toxicity studies, which includes both in vitro and in vivo tests. In addition, test data from the immunotoxicity, developmental toxicity and reproductive toxicity studies are continually being added to this database. Partnerships Through relationships with regulatory agencies, the NTP has an indirect role in shaping public health policy. Federal and state government agencies rely on the scientific knowledge and its interpretation provided by the NTP to make credible decisions that protect public health and the environment. The NTP also plays a critical role in: 1. Fostering interagency collaborations in research and exposure assessment 2. Providing information to regulatory agencies about alternative methods for toxicity testing, interpretation 3. Exploring new technologies for evaluating how environmental agents cause disease NTP conferences and workshops provide an opportunity for researchers, regulatory, policy makers, and the public to examine issues together, exchange information, and reach agreement on future directions of toxicology and risk assessment. Postdoctoral Training Program Opportunities Applied Toxicology and Carcinogenesis Training Program Fellowship in Toxicological Pathology Fellowship in Laboratory Animal Medicine
A stand-alone axecutable under all main Windows OS for training the working memory. The WM Trainer looks and behaves a little bit like a video-game and has been specifically conceived for children attending the primary school. However, it can be used purposefully by people of any age, including adult and elderly. This application features highest graphic quality, a powerful adaptive engine for the difficulty level, a database of users and statistical tools to evaluate the progress. Currently English, French and Italian are supported, but any language can be easily supported.
Committee on Problems of Drug Dependence
The College on Problems of Drug Dependence (CPDD) is an interdisciplinary research society whose members address problems of drug dependence in the broadest range of scientific disciplines, including chemistry, basic biology, pharmacology, behavioral science, clinical research, sociology, psychology, anthropology, and history. CPDD serves as an interface among governmental, industrial and academic communities maintaining liaisons with regulatory and research agencies as well as educational, treatment, and prevention facilities in the drug abuse field. It also functions as a collaborating center of the World Health Organization. The Annual Scientific Meeting: Since 1938, a major focus of the CPDD's activities has been its sponsorship of an annual scientific meeting. This conference serves as a forum bringing together basic scientists and clinical investigators from industry, academia, and government. Representatives of regulatory agencies, as well as scientists and professionals in a number of diverse disciplines interested in the biochemical, behavioral, and public health aspects of drug dependence participate. Special Conferences: Periodically, the College sponsors conferences focused on timely topics of interest to researchers, government, industry, and the public. In recent years, CPDD has organized meetings on Abuse Liability Assessment of CNS Drugs; Drug Formulation and Abuse Liability; Pre-Clinical Abuse Liability Testing; Women and Smoking: Understanding Socioeconomic Influences; and Risk Management and Post-Marketing Surveillance for CNS-Acting Drugs. Consultation Activities: The CPDD provides consulting expertise in the area of epidemiology, treatment, prevention, and all the basic and clinical sciences related to drug dependence, drug abuse, and their behavioral and medical consequences. Sponsorship of Drug and Alcohol Dependence: The CPDD sponsors the journal Drug and Alcohol Dependence, published by Elsevier. A principal goal of the journal is to provide a source of quality, timely reports of scientific advances in substance abuse research. The journal is international in scope and interdisciplinary in coverage. The CPDD invites contributors. Donations Tax-deductible donations can be made to CPDD to support the Annual Scientific Meeting, testing facilities, drug assessment activities and Awards for Excellence.
Simple, menu-driven software toolbox for SPM 5/8 for exploratory data analysis for functional or structural images (.img / .nii) provides the user with several options: # a histogram of all non-zero voxel values in a brain image; # a scatter plot, Q-Q plot, or Bland-Altman plots comparing two images; # a surface plot of all voxel values at a particular axial slice; # easy Region of Interst (ROI)-based extraction of voxel values. Note: the toolbox calls various SPM 5/8 functions. The Q-Q plot function requires the MATLAB stats toolbox.
A free, distributable, easy-to-install software package of customizable, WordPress-based commons spaces for communities. This software project aimed at turning the infrastructure that successfully powers the CUNY (City University of New York) Academic Commons takes the complexity out of creating a Commons site, helping organizations create a space where their members can discuss issues, collaborate on projects, and share their work. CBOX also provides: * Out-of-the-box functionality with an intuitive set-up that guides site administrators through each step of installation. * A powerful, responsive, highly customizable theme developed for community engagement, based on PressCrew's Infinity Theming Engine. * Responsive design for easy viewing on many devices, including tablets and smartphones. * Collaborative document creation and file sharing. * Reply-By-Email functionality for quick, on-the-go communication. * Compatibility with many other WordPress and BuddyPress themes and plug-ins. * Expansive wiki options. CBOX will be useful to any organization that is looking for a shared space in which to build an engaged community of users and developers. Download their code, peruse their documentation, check out their project demo website, and join their community to find others using CBOX.
ESTerases and alpha / beta-hydrolase Enzymes and Relatives
ESTerases and alpha/beta-Hydrolase Enzymes and Relatives
Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
ckan - The open source data portal software
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A complete out-of-the-box data management software solution that makes data accessible by providing tools to streamline publishing, sharing, finding and using data. CKAN is aimed at data publishers (national and regional governments, companies and organizations) wanting to make their data open and available. It uses its internal model to store metadata about the different records, and presents it on a web interface that allows users to browse and search this metadata. It also offers a powerful API that allows third-party applications and services to be built around it. CKAN is built with Python on the backend and Javascript on the frontend, and uses the Pylons web framework and SQLAlchemy as its ORM. Its database engine is PostgreSQL and its search is powered by SOLR. It has a modular architecture that allows extensions to be developed to provide additional features such as harvesting or data upload. CKAN is currently used by governments and user groups worldwide to power both official and community data portals.
Free web application which guides users through the process of creating a data management plan (DMP) for a range of funders (NSF, NIH, etc.) and connect users with data management planning resources. The DMPTool allows users to edit, save, share, print, and download their data management plans. Institutions can customize the tool and configure Shibboleth login. Several universities and organizations are developing the DMPTool to help researchers meet these new requirements. In specific, the DMPTool will help researchers: * Create ready-to-use data management plans for specific funding agencies * Meet requirements for data management plans * Get step-by-step instructions and guidance for data management plan * Learn about resources and services available at your institution to fulfill the data management requirements of their grants
Provides comprehensive publication services for Univeristy of California affiliated departments, research units, publishing programs, and individual scholars who seek to publish original, open access journals, books, conference proceedings, and other scholarship. Content is delivered via research platform and is available to scholars worldwide.
Service that exports your Git repository to the new W3C PROV standard. Your Git repositories are a goldmine of provenance information, tracking the evolution of your code or data and the activities of the people involved. This information could be linked to other similar provenance data by exporting it in the provenance interchange W3C recommendation PROV (http://www.w3.org/TR/prov-overview/).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database to access gene information through common names and allows identification of homologs and paralogs for a given gene. This publicly available tool leverages public sequence data, gene metadata information, and other publicly available data to calculate and display orthologous and paralogous gene relationships for all genes from several species, including yeasts, insects, worms, vertebrates, mammals, and primates such as humans.
An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways.
Data set containing a gene-specific connectome file for each human gene and computer programs for ranking lists of genes within a gene-specific connectome, clustering and plotting the genes by the functional genomic alignment (FGA) approach, and generating gene-specific connectomes. The programs were developed and tested on Mac and Linux systems. The external software required for running these programs is open-source and free of charge. The HGC is the set of all biologically plausible routes, distances, and degrees of separation between all pairs of human genes. A gene-specific connectome contains the set of all available human genes sorted on the basis of their predicted biological proximity to the specific gene of interest. The HGC is a powerful approach for human genotype-phenotype high-throughput studies, for which it can be used to rank any list of genes within a gene-specific connectome for an experimentally validated core gene. Functional genomic alignment (FGA) is equivalent to traditional multiple sequence alignment (MSA), except that it clusters genes in trees on the basis of the functional biological distance between them predicted by HGC, rather than on the basis of molecular evolutionary genetic distance. This method is therefore more suitable for disease and phenotypic studies.
OMERO - Open Microscopy Environment Remote Objects
Open Microscopy Environment Remote Objects
Client-server software for management, visualization, and analysis of biological microscopy images. OMERO handles images in a secure central repository where users can view, organize, analyze and share data from anywhere with internet access. Work with images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software.
A web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go.
GROTOAP: GROTOAP: GROund Truth for Open Access Publications
GROTOAP: GROund Truth for Open Access Publications
Test set for training and performance evaluation of page segmentation and zone classification algorithms. Contains input articles in a digital form and corresponding ground truth files. The test set is based on articles obtained from DOAJ database published under CC-BY license. The whole test set is available under the same license.
A web application which provides altmetrics to help researchers measure and share the impacts of their research outputs. After making a profile, scientists can track which of their publications are most popular through number of citations, frequency of PDF downloads, etc. Information from research outputs such as journal articles, blog posts, datasets, and software contribute to a user's impact, which is viewable in their profile.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An extension for Chrome to see a version of a resource as it existed at some date in the past, by entering that URI in your browser and by specifying the desired date in a browser plug-in. Or you can actually browse the Web of the past by selecting a date and clicking. Whatever you land upon will be versions of Web resources as they were around the selected date. (This will only work if previous versions are available somewhere on the Web.)
Algorithm for single nucleotide variant detection using next-generation resequencing. It estimates the error rate at each base position in the reference sequence utilizing a command-line user interface through MATLAB.
OME-TIFF: Open Microscopy Environment Tagged Image File Format
Open Microscopy Environment Tagged Image File Format
A standardized file format for multidimensional microscopy image data. OME-TIFF maximizes the respective strengths of OME-XML and TIFF. It takes advantage of the rich metadata defined in OME-XML while retaining the pixel structure in multi-page TIF format for compatibility with many image-processing applications. An OME-TIFF dataset has the following characteristics: * Image planes are stored within one multi-page TIFF file, or across multiple TIFF files. Any image organization is feasible. * A complete OME-XML metadata block describing the dataset is embedded in each TIFF file's header. Thus, even if some of the TIFF files in a dataset are misplaced, the metadata remains intact. * The OME-XML metadata block may contain anything allowed in a standard OME-XML file. * OME-TIFF uses the standard TIFF mechanism for storing one or more image planes in each of the constituent files, instead of encoding pixels as base64 chunks within the XML. Since TIFF is an image format, it makes sense to only use OME-TIFF as opposed to OME-XML, when there is at least one image plane.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A high-resolution ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterized structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system.
Ontology to describe and categorize chemical biology and drug screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.
A catalog of gene-expression data collected from human cells treated with chemical compounds and genetic reagents. Computational methods to reduce the number of necessary genomic measurements along with streamlined methodologies enable the current effort to significantly increase the size of the CMap database and along with it, our potential to connect human diseases with the genes that underlie them and the drugs that treat them. The NIH has funded a large expansion of the Connectivity Map dataset through the Library of Integrated Network-based Cellular Signatures (LINCS). The Broad Institute's LINCS center aims to create a first installment of data generation and analysis for the LINCS program. Through these data LINCS intends to accelerate the discovery process by systematically revealing connections between genes/compounds discovered in screens and molecular pathways that underlie disease states.
Stowers Institute Original Data Repository
THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Open access repository of original, unprocessed data underlying work published by Stowers researchers to allow the scientific community to validate and extend the findings made by Stowers researchers. For papers first submitted for publication after November 1, 2011, the Stowers Institute requires its members to deposit original data files into the Stowers Original Data Repository or to repositories maintained by third parties at the time of publication. Access to the Stowers Original Data Repository is free, but you will be asked to register before you can download data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The Directory of Open Access Repositories - OpenDOAR
A quality-controlled directory of academic open access repositories that provides a simple repository list, and lets you search for repositories or search repository contents. Additionally, tools and support to both repository administrators and service providers in sharing best practice and improving the quality of the repository infrastructure are provided. The current directory lists repositories and allows breakdown and selection by a variety of criteria which can also be viewed as statistical charts. The underlying database has been designed from the ground up to include in-depth information on each repository that can be used for search, analysis, or underpinning services like text-mining.
Open source software made freely available to journals worldwide for the purpose of making open access publishing a viable option for more journals, as open access can increase a journal's readership as well as its contribution to the public good on a global scale. OJS assists with every stage of the refereed publishing process, from submissions through to online publication and indexing. Through its management systems, its finely grained indexing of research, and the context it provides for research, OJS seeks to improve both the scholarly and public quality of refereed research. OJS Features # OJS is installed locally and locally controlled. # Editors configure requirements, sections, review process, etc. # Online submission and management of all content. # Subscription module with delayed open access options. # Comprehensive indexing of content part of global system. # Reading Tools for content, based on field and editors' choice. # Email notification and commenting ability for readers. # Complete context-sensitive online Help support.
Repository of rejections of papers - letters and comments - that were ultimately accepted by a journal to educate others. Your rejection letters and comments are welcome. Some journals have begun including reviewers' comments with accepted papers to make the views of experts available to the reader. However, often the paper has been submitted to several journals and rejected before it is finally accepted. The rejection letters and comments are equally useful in helping to judge what kind of papers might be acceptable to a journal, and what kind of comments lead to rejections. Rather than hiding these low points in the trajectory of a scientific paper, this forum offers a place to publish these letters and comments to educate others.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Service that mashes up alt-metrics data from Altmetric with articles from the Public Library of Science (PLoS) that allows you to check which articles are seeing the most buzz from social media sites, newspapers and in online reference managers. Browse articles with mentions in the past: 1d, 3d, 1w, 1m, 3m or all time.
A Semantic content editor based on TinyMCE WYSIWYG editor. RDFaCE is created as a proof of concept for WYSIWYM (What You See Is What You Mean) concept. WYSIWYM aims to enable end-users to easily annotate their content using RDFa and Microdata markups. RDFaCE employs external NLP APIs to suggest namespaces, properties, URIs and to automatically annotate content.
Bibliographic database that brings together free, full-text scholarly articles from hundreds of universities and colleges worldwide. Curated by university librarians and their supporting institutions, the Network includes a growing collection of peer-reviewed journal articles, book chapters, dissertations, working papers, conference proceedings, and other original scholarly work. A central discipline wheel features ten color-coded disciplines: law, social and behavioral sciences, arts and humanities, life sciences, physical sciences and mathematics, education, engineering, medicine and health sciences, business, and architecture. The size of each color-coded area reflects the size of each discipline's collection relative to the rest of DCN. Users can click on any segment of any layer of the wheel, with the selected discipline, subdiscipline, or subject navigating users to their chosen commons area where they can then proceed to a list of full-text PDFs. To be clear, typing a couple of keywords into the Search Entire Network box, also located on the homepage, might be a more efficient method than mousing around on this graphical browsing element. If you would like to contribute your institution's research to the Digital Commons Network, Use the form provided, http://network.bepress.com/about/
Public university in Bari, Italy that offers a variety of degree programs including agricultural science, economics, education, and veterinary medicine.
A suite of automated tools that examine biological molecules and produces useful representations of the key biophysical and biochemical features of these structures that are critical for understanding function. The utility of this system extends from medical / pharmaceutical applications (model-based drug design, comparing pharmacological activities) to industrial applications (understanding structural stability, protein engineering). The FEATURE code is made available, without too much support, to any interested scientists. Audience: Researchers interested in identifying functional sites in protein structures. Long Term Goals and Related Uses: Enable improved functional site prediction.
An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies.
Blog featuring critical analysis of scholarly open-access journals by Jeffrey Beale. Good tool to consult if you have suspicions that a journal is less than legit. Jeffrey Beall works as a librarian at Auraria Library, University of Colorado Denver, in Denver, Colorado.
An open-source, web-based platform and suite of software tools for for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes - and collaborations between scientists. It preserves associations between them, along with information about the people and organizations involved. Underpinning SEEK is the ISA infrastructure, a standard format for describing how individual experiments are aggregated into wider studies and investigations. Within SEEK, ISA has been extended and is configurable to allow the structure to be used outside of Biology. SEEK is incorporating semantic technology allowing sophisticated queries over the data, yet without getting in the way of your users. Access to the RESTful API to access the data within SEEK is available.
An collaborative tool which allows users to edit LaTeX documents in their browser. Multiple users can simultaneously access and edit the same LaTeX document and see the changes in real time. The latest version is available online, and the built in chat helps communicate with others while editing.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 12, 2017. Dataset in Bilingual exposure optimizes left-hemisphere dominance for selective attention processes in the developing brain by Arredondo, Su, Satterfield, & Kovelman (XX) Does early bilingual exposure alter the representations of cognitive processes in the developing brain? Theories of bilingual development have suggested that bilingual language switching might improve children''s executive function and foster the maturation of prefrontal brain regions that support higher cognition. To test this hypothesis, we used functional Near Infrared Spectroscopy to measure brain activity in Spanish-English bilingual and English-monolingual children during a visuo-spatial executive function task of attentional control (N=27, ages 7-13). Prior findings suggest that while young children start with bilateral activation for the task, it becomes right-lateralized with age (Konrad et al., 2005). Indeed monolinguals showed bilateral frontal activation, however young bilinguals showed greater activation in left language areas relative to right hemisphere and relative to monolinguals. The findings suggest that bilingual experience optimizes attention mechanisms in the language hemisphere, and highlight the importance of early experiences for neurodevelopmental plasticity of higher cognition. These data are made available from Ioulia Kovelman''s Language and Literacy Lab at University of Michigan and may be exported through the NIF Data Federation. To cite these data please use this text Data were published by Arredondo et al. (XX) and made available via the NIF at XX
GlimmerHMM - Eukaryotic Gene-Finding System
A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).
National Center for Microscopy and Imaging Research
Biomedical technology research center that develops computer-aided, advanced microscopy for the acquisition of structural and functional data in the dimensional range of 1 nm to 100 um, a range encompassing macromolecules, subcellular structures and cells. Novel specimen-staining methods, imaging instrumentsincluding intermediate high-voltage transmission electron microscopes (IVEMs) and high-speed, large-format laser-scanning light microscopesand computational capabilities are available for addressing mesoscale biological microscopy of proteins and macromolecular complexes in their cellular and tissue environments. These technologies are developed to bridge understanding of biological systems between the gross anatomical and molecular scales and to make these technologies broadly available to biomedical researchers. NCMIR provides expertise, infrastructure, technological development, and an environment in which new information about the 3D ultrastructure of tissues, cells, and macromolecular complexes may be accurately and easily obtained and analyzed. NCMIR fulfills its mission through technology development, collaboration, service, training, and dissemination. It aims to develop preparative methods and analytical approaches to 3D microscopy applicable to neurobiology and cell biology, incorporating equipment and implementing software that expand the analysis of 3D structure. The core research activities in the areas of specimen development, instrument development, and software infrastructures maximize the advantages of higher voltage electron microscopy and correlated light microscopies to make ambitious imaging studies across scales routine, and to facilitate the use of resources by biomedical researchers. NCMIR actively recruits outside users who will not only make use of these resources, but who also will drive technology development and receive training.
National Biomedical Computation Resource
NBCR - National Biomedical Computation Resource
Biomedical technology research center that conducts, catalyzes and enables multiscale biomedical research, focusing on four key activities: 1) integrating computational, data and visualization resources in a transparent, advanced grid environment to enable better access to distributed data, computational resources, instruments and people; 2) developing and deploying advanced computational tools for modeling and simulation, data analysis, query and integration, three-dimensional image processing and interactive visualization; 3) delivering and supporting advanced grid/cyberinfrastructure for biomedical researchers; and 4) training a cadre of new researchers to have an interdisciplinary, working knowledge of computational technology relevant to biomedical scientists. NBCR enables biomedical scientists to address the challenge of integrating detailed structural measurements from diverse scales of biological organization that range from molecules to organ systems in order to gain quantitative understanding of biological function and phenotypes. Predictive multi-scale models and their driving biological research problems together address issues in modeling of sub-cellular biophysics, building molecular modeling tools to accelerate discovery, and defining tools for patient-specific multi-scale modeling. NBCR furthers these driving problems by developing tools and models based on rapid advances in mathematics and information technology, incorporating them into NBCR pipelines or problem solving environments, and addressing the inevitable changes in the underlying cyber-infrastructure technologies and continually adapting codes over time. Their technology focus integrates both the biological applications and the underlying support software into reproducible science workflows that can function across a number of physical infrastructures.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. CGHub gives scientific researchers the statistical power of large cancer genome datasets to attack the molecular complexity of cancer.
Program for Imaging & Cognitive Sciences
Program for Imaging and Cognitive Sciences
THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/28/13. Core facility of Columbia Neuroscience with the goal of establishing a collaborative and multi-investigator neuroimaging environment that is focused on the investigation of the neurocircuitry of the brain that underlies cognition, perception and action, and also the development of clinical applications that enhance the goals of personalized medicine. Within this environment the specific current research interests of the Hirsch group include several related directions of investigation. The first is conscious and subconscious neural processes that mediate emotion and cognition in healthy individuals and in patients with psychiatric disorders. This direction also includes neurocircuitry that is characteristic of disorders of consciousness such as minimally conscious or vegetative states, self and visual awareness, and attention. Neurocircuitry of other complex cognitive processes such as decisions, inductive and deductive reasoning, language, truthfulness and top-down influences of expectation, reward, and regulation on early visual and mid-level perceptual and emotional systems. On-going projects targeted for clinical applications include benefits for neurosurgery such as the development of task batteries to map the cortical locations of essential functions such as language, motor, sensation, memory, emotion and sensory functions including visions, audition and the chemical senses. Computational innovations for labeling correspondence between brain structure and specific functional regions are under development to achieve the highest interpretive precision. Current projects include integration of EEG and fMRI techniques to localize seizuregenic cortex in relation to eloquent and functioning cortex for neurosurgical planning; integration of TMS and fMRI to discriminate essential and associative language-sensitive cortical areas; and integration of VEP, EEG and fMRI to inform assessments of visual disease secondary to stroke or neural degeneration. Projects intended to refine and enhance diagnosis of psychiatric disorders such as anxiety, depression, and eating disorders include development of specialized paradigms to target dysfunctional neurocircuitry such as emotional systems (amygdala and basal ganglia) and control and regulatory systems (cingulate and pre-frontal cortex). Comparison of before-treatment images with after-treatment images to inform models of both treatment and disease and investigation of the hypothesis that individual genetic and functional differences have predictive value for treatment options and outcome are currently underway. The lab has pioneered techniques for functional mapping of single patients, and operates an active clinical service for mapping individuals for neurosurgical planning, assessments of the neurocircuitry that underlie acquired or inherited disabilities and the mechanisms of neuroplasticity that restore lost functions are actively investigated using both groups and single subject studies. :
MethylAid - Visual and interactive quality control of large Illumina 450k data sets
MethylAid: Visual and interactive quality control of large Illumina 450k data sets
Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.
National Institute of Technology and Evaluation Biological Resource Center
Collection of microbial resources and perform taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. NBRC is a member of WFCC, OECD Global BRC Network, ACM and JSCC. They are certified by quality management system ISO 9001. To provide attractive biological resources with useful information attached, they actively collect potentially useful biological resources (microorganisms and cloned genes) and distributes them to promote basic research as well as industrial applications. At the Biological Resource Center, they explore, isolate and identify microorganisms from various natural environments and at the same time accept scientifically and industrially useful microorganisms from researchers in academic and industrial sectors. The microbial DNA library constructed at the Biotechnology Development Center is also part of their collection. To improve and expand the collection, new methodologies for the isolation, identification and preservation of microorganisms and DNA will be investigated and developed so as to provide biological resources of higher quality. Their resources serve, for example, as the standard for determining antimicrobial activity, in aseptic tests as well as for the production of pharmaceutical substances and will be constantly reinforced for wider distribution to researchers in academia and industries. Please refer to the catalog shown at the NBRC website for details.
A source to FIND and APPLY for federal grants. The U.S. Department of Health and Human Services is proud to be the managing partner for Grants.gov, an initiative that is having an unparalleled impact on the grant community. All discretionary grants offered by the 26 federal grant-making agencies can be found on Grants.gov. Grants.gov was established as a governmental resource named the E-Grants Initiative, part of the President's 2002 Fiscal Year Management Agenda to improve government services to the public. The concept has its origins in the Federal Financial Assistance Management Improvement Act of 1999, also known as Public Law 106-107. Public Law 106-107 has since sunset and is now known as the Grants Policy Committee (GPC). For more information on the Grants Policy Committee, click here. Today, Grants.gov is a central storehouse for information on over 1,000 grant programs and provides access to approximately $500 billion in annual awards. You may find information on *What is a Grant? *Who is Eligible for a Grant? *Program highlights and accomplishments *Grants.gov in the News (Articles, press releases, milestones and events) *Program Status (Detailed information about our relationship with partner federal agencies, financial contributions, grant opportunities, fiscal reports, planning strategies and statistics.)
A interactive and highly effective educational resource and review for training in neuroscience and cognitive science. Supported by the Canadian institute of neurosciences, mental health and addiction; and Canadian institutes of health research.
Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
A flex/bison-based C++ Mascot Generic Format (MGF) parser library.
Enzyme database developed as a way to access the data of the IUBMB Enzyme Nomenclature List. The data, which are stored in a MySQL database, preserve the formatting of chemical names according to IUPAC standards. A simple, easy to use, web-based query interface is provided (Search), along with an advanced search engine for more complex queries (Advanced Search). Forms are provided to submit suggestions for new enzyme entries or to report errors in existing entries. Downloads of the database are available via FTP as SQL or XML.
Center for Research in Biological Systems
CRBS is a UCSD organized research unit (ORU) that exists to provide human resources, high technology equipment, and administrative services to researchers engaged in fundamental research on cell structure and function relationships in central nervous system processes, cardiovascular networking, and muscular contraction through multiple scales and modalities. CRBS scientists investigate these processes through invention, refinement, and deployment of sophisticated technologies, especially: - High-powered electron microscopes that reveal three-dimensional cell structures - State-of-the-art X-ray crystallography and magnetic resonance analysis that provide detail on protein structures at high-resolution - Laser-scanning and confocal light microscopes that reveal molecules tagged with fluorescent markers as they traffic within cells and pass transfer signals within and between cells - High performance computing and grid-based integration of distributed data CRBS facilitates an interdisciplinary infrastructure in which people from biology, medicine, chemistry, and physics can work with those from computer science and information technologies in collaborative research. Researchers share interests in the study of complex biological systems at many scales, from the structures of enzymes, proteins, and the body's chemical communications network at atomic and molecular levels, to an organism's physiology, strength, and support at cellular and tissue levels. The CRBS infrastructure integrates resources for high-performance computing, visualization, and database technologies, and the grid-integration of large amounts of archival storage data. The California Institute for Telecommunications and Information Technology (Cal-IT2) and the San Diego Supercomputer Center (SDSC) are collaborators in simulating the activity of biological systems, analyzing the results, and organizing the growing storehouse of biological information. CRBS is an entity evolving as research evolves. It forges interactions with biotechnology and biocomputing companies for technology transfer. Interaction, collaboration, and multiscale research produce new perspectives, reveal fruitful research topics, lead to the development of new technologies and drugs, and train a new generation of researchers in biological systems. Sponsors: CRBS is supported by the University of California at San Diego.
A free website for for neurologists, neurology residents, and medical students. Contains thousands of images, hundreds of multiple-choice review questions, dozens of educational videos, several user forums, and a couple of online courses. Created by a neurology resident, it is currently maintained by a neurologist and a neuropathologist, with contributions from people from around the world. FrontalCortex.com is a free resource for neurology education. The target audience is neurology residents and medical students. It features a bank of hundreds of boards-type review questions, all of which contain feedback and references to relevant articles or texts. It also has an image gallery with thousands of images, including EEGs, radiographs, illustrations, and over a thousand unique neuropathology images. Online courses in neuropathology and electrodiagnostic testing have been created on the site, and continue to be refined. These include dozens of educational videos. FrontalCortex.com was created by a neurology resident. That resident is now a neurologist, and the neurology program director at Marshall University, and continues to run the page, with the help of other physicians volunteering their time. All the content contributions are donated by volunteers, and are reviewed by physicians. Financial support for the page comes from advertisements on the page, and the occasional donation. No login is required, unless you want to contribute to the growing bank of educational resources, in which case you can create a free account. : :education, neurology, resident, neuropathology, board review, RITE exam : :
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. 3D image analysis software to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems. It is fully integrated for a seamless user experience.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An information and modeling database for families of proteins that function in the eye. Homologues are collected from all species and clustered according to tissue type, function and sequence similarity. A principal feature of the site is structural annotations, which range from experimentally solved structures to close structural neighbors to distant structure predictions. Many pre-generated homology models are provided. Other features include domain architecture analysis and pre-generated sequence alignments, and the site is extensively linked to other bioinformatic resources on the web.
Office of Scientific and Technical Information
The Office of Scientific and Technical Information's mission is to advance science and sustain technological creativity by making R&D findings available and useful to Department of Energy (DOE) researchers and the public. At OSTI you can find research results and science information from the Manhattan Project to the present, download documents, view energy citations, discover patents and e-prints, read about ongoing research projects and amazing accomplishments, search science conference proceedings and software, and connect to U.S. and global science portals. You can do this by using special online tools, such as: * Key Resources * DOE Science Accelerator * Science.gov * WorldWideScience.org Strategies for accomplishing the OSTI mission: * Collaborate within DOE through the Scientific and Technical Information Program to develop and maintain efficient, state-of-the-art access and delivery of research results. * Partner with others to facilitate alliances for national and international cooperation and information exchange. * Develop, deliver, and maintain customized information products and services for a variety of constituencies. * Implement Department-wide STI policy and best business practices. * Preserve STI, in tangible copies or electronically, as appropriate. * Accelerate the diffusion of knowledge to advance science. OSTI develops and maintains search tools that use a special technology called federated search. KEY RESOURCES Research Documents/Information Information Bridge Find DOE R&D full-text documents and bibliographic citations. DOE R&D Accomplishments Find information about the outcomes of past DOE R&D. DOE patents Find patents resulting from DOE-sponsored research and development. E-print Network Find e-prints in basic and applied sciences . Energy Citations Database (ECD) Find bibliographic records and full-text where available. Adopt-A-Doc? is an on-demand service that provides individuals the option to sponsor the digitization of full-text DOE technical reports. Science Conference Proceedings Find select science and technology conference papers and proceedings. EnergyFiles Find databases and websites of interest to DOE. Research Summaries DOE R&D Project Summaries Find R&D projects underway at DOE. Federal R&D Project Summaries Find R&D projects underway at federal agencies. Science Information from U.S. Agencies Science.gov Find selected science information provided by U.S. Government agencies. Science Information from Global Sources WorldWideScience.org Find science from participating nations of every inhabited continent. ETDEWEB Register for access to worldwide energy technology discoveries. International Nuclear Information System Find International bibliographic records related to peaceful applications of nuclear science and technology. Science Education Resources ScienceLab A portal listing numerous education resources within DOE and beyond Scientific Research Data About Scientific Research Data Learn about the Department of Energys data discovery tool as well as data centers, forums, and publications. DOE Data Explorer Find scientific research data - such as computer simulations, numeric data files, figures and plots, interactive maps, multimedia, and scientific images - generated in the course of DOE-sponsored research in various science disciplines. Scientific and Technical Software Energy Science and Technology Software Center Find federally funded scientific and technical software developed by the national laboratories, other facilities and DOE contractors. SCIENCE ACCELERATOR Science Accelerator is a gateway to science, including R&D results, project descriptions, accomplishments, and more, via resources made available by the Office of Scientific and Technical Information (OSTI), U.S. Department of Energy. Science Accelerator was developed and is made available by OSTI as a free public service. SCIENCE.GOV Science.gov searches over 40 databases and 1,950 selected websites, offering 200 million pages of authoritative U.S. government science information, including research and development results. WORLDWIDESCIENCE.ORG WorldWideScience.org is a global science gatewayaccelerating scientific discovery and progress through a multilateral partnership to enable federated searching of national and international scientific databases and portals.
Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes.
Database that combines detailed toxin data with comprehensive toxin target information. The database currently houses 3,053 toxins described by 32,276 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to 1,670 corresponding toxin target records. Altogether there are 37,084 toxin, toxin target associations. (March 2014) Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5,454 sources sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches
A software tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonetheless, ropeBWT2 is unique in that it may implicitly sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index.
Software tool to identify cancer driver genes based on linear annotations of biological regions such as protein domains.Uses information on three-dimensional structures of mutated proteins to identify specific structural features. Then algorithm analyzes whether these features are enriched in cancer somatic mutations and are candidate driver genes.
Connectome Wiki: collaborative neuroanatomy knowledge database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 6, 2012. Connectome Wiki is a knowledge base for macro- and mesoscale brain region and brain structural connectivity information across species. Employing modern semantic wiki technology, it serves as collaborative platform as well. What can I get? * Brain Regions: Plenty of information, including links to relevant literature and much more. * Brain Connections: Well established neuronal connections based mainly on neuronal tracer studies from the literature. * Abbreviations: Look up abbreviations and corresponding English and Latin names * Partition Schemes: Foundational and more partitions with their corresponding delineation criteria and protocols. * Species: Information about different species is available, using their binomial name as identifier. * External: Enhance the ConnectomeViewer with Volume-To-Ontology mappings. * Data Source: You can download the raw data in RDF or JSON. How can I contribute? If your research is in particular brain regions, or model organisms not yet registered, feel free to act as domain expert and add your knowledge. If you do any tracer studies, add findings with appropriate published papers. Incrementally building a mesoscale skeleton wiring diagram. Complete anything that is missing. See also PapersToAdd. Register your own partition scheme and link it semantically against known schemes. Adding brain region pages for your particular research organisms. Use ConnectomeWiki as knowledge backend for your application concerned with gross neuroanatomy. The goals of this wiki are: * A collaborative platform to collect, collate, manage and disseminate mesoscale nervous system region and connectivity information across various species * Authority for Brain Region Abbreviations * Representation of Brain Region Homologies * Interrelation of Brain Partition Schemes * Information source for the ConnectomeViewer application
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.
Digital image processing system where microscope settings and processing steps may be adjusted in single user interface. Can acquire images from variety of cameras. Includes software package for capturing, archiving and preparing images for publication. Allows users to visualize and present images in several dimensions. Functionality of imaging toolbox expands constantly with wide range of different modules that are tailored to specific applications or microscope accessories.
The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4. In FANTOM4 the focus has changed to understanding how these components work together in the context of a biological network. Using deepCAGE (deep sequencing with CAGE) we monitored the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1. This allowed us to identify active promoters, monitor their relative expression and define relevant regions for carrying out transcription factor binding site predictions. Computational methods were then used to build a network model of gene expression in this leukemia and the transcription factors key to its regulation. This work gives the first picture of the wiring between genes involved in acute myeloid leukemia and provides a strategy for identifying key factors that determine cell fates. In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome. TOOLS *Genome Browser: graphical display of genomic features, such as promoters, exon structures, H3K9 acetylation, transcription factors positioning on the genome, coupled with gene and promoter activities. *EdgeExpressDB: regulatory interactions, such as transcriptional regulation, post-transcriptional silencing with miRNA, and PPI, coupled with gene and promoter activities. *SwissRegulon: FANTOM4 TF regulation is predicted using Motif Activity Response Analysis (MARA) developed by Erik van Nimwegen at Biozentrum. Follow the link to carry out MARA on your own dataset. *Custom Tracks on the UCSC Genome Browser: FANTOM4 tracks on the UCSC Genome Browser Database. *The RIKEN integrated database of mammals: Integration of FANTOM4 data with other mammalian resources, in particular, produced by RIKEN.
Repository of geometric models collected from on-going and past research projects in the Cardiovascular Biomechanics Research Laboratory at Stanford University. The geometric models are mostly built from imaging data of healthy and diseased individuals. For each of the models, a short description is given with a reference. The geometric models are in VTK PolyData XML .vtp format. * Audience: Biomechanical and computational researchers interested in complex models of cardiovascular applications * Long Term Goals and Related Uses: Allow users to download geometric models for cardiovascular applications. These geometric models can be used for research purposes, such as meshing and scientific visualization. Users are welcome to contact the project administrator, join the project and contribute additional models.
A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.
An algorithm for identifying pathways that are known to exist between two regions within DTI data of anisotropic tissue, e.g., muscle, brain, spinal cord. The ConTrack algorithms use knowledge of DTI scanning physics and apriori information about tissue architecture to identify the location of connections between two regions within the DTI data. Assuming a course of connection or pathway between these two regions is known to exist within the measured tissue, ConTrack can be used to estimate properties of these connections in-vivo.
The goal of the neuromuscular models library is to provide a resource for students, researchers, and clinicians to access, use, test, and develop models. The majority of models in this library are for use with OpenSIM and/or SIMM. Users who contribute models to the database can set up a project page where they can track who is using the model and contact with them.
OpenSim is an open-source software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. The software provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through multi-institutional collaboration. The underlying software is written in ANSI C++, and the graphical user interface (GUI) is written in Java. OpenSim technology makes it possible to develop customized controllers, analyses, contact models, and muscle models among other things. These plugins can be shared without the need to alter or compile source code. Users can analyze existing models and simulations and develop new models and simulations from within the GUI.
Simbody(tm): SimTK Multibody Dynamics Toolset
This project is a SimTK Core toolset providing general multibody dynamics capability, i.e., the capability to solve Newton's 2nd law F=ma in any set of coordinates. The techniques of rigid body mechanics are used to provide results in Order(n) time for any set of n coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait. Simbody is provided as an open source, object-oriented C++ API and delivers high-performance, accuracy-controlled science/engineering-quality results. Binaries of this software are bundled with other SimTK Core modules.
sapFinder - A package for variant peptides detection and visualization in shotgun proteomics.
An R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. It automates (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.
SimVascular: Cardiovascular Modeling and Simulation
Open source software suite for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels. The suite also includes tools for physiologic boundary conditions, fluid structure interaction, and an accurate and efficient finite element Navier-Stokes solver. Commercial components have been used in the simulation process, and for these components, the project attempts to provide interfaces that allow substitution of open source components. The SimVascular project is derived from the ASPIRE2 software project and includes modified portions of PHASTA from RPI/SCOREC.
Knowledgebase for Addiction Related Genes
KARG: Knowledgebase for Addiction Related Genes
KARG: Knowledgebase for Addiction-Related Gene
Knowledgebase for Addiction-Related Gene
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database of data and knowledge linking genes and chromosome regions to addiction that were extracted from reviewing more than 1,000 peer-reviewed publications from between 1976 and 2006. This list of publications included review papers on addiction selected from results of PUBMED query "(addiction OR drug abuse) AND review" as well as research papers selected from PUBMED query "(addiction OR drug abuse) AND (gene OR microarray OR proteomics OR QTL OR population association OR genetic linkage)". The data spanned multiple technology platforms including classical hypothesis-testing of single genes, identification of significantly differentially expressed genes in microarray experiments, identification of significantly differentially expressed proteins in proteomics assays, identification of addiction-vulnerable chromosome regions in animal QTL studies, genetic linkage studies, population association studies, and OMIM annotations. From each publication they collected the genes, proteins, or chromosome regions linked to addiction, as well as metadata such as species, nature of the addictive substance, studied brain regions, technology platforms, and experimental parameters. In total, they collected 2,343 items of evidence linking 1,500 human genes to addiction. Among them 396 genes were supported by two or more items of evidence. The interface supports browsing of the genes by chromosome or pathways, advanced text search by gene ID, organism, type of addictive substance, technology platform, protein domain, and/or PUBMED ID, and sequence search by BLAST similarity. All data, database schema, and MySQL commands are freely available for download.
UMMC Center for Psychiatric Neuroscience Labs and Facilities
UMMC Center for Psychiatric Neuroscience Labs & Facilities
UMMC Center for Psychiatric Neuroscience Research Resource Cores
University of Mississippi Medical Center Center for Psychiatric Neuroscience
Core facility that provides access to psychiatrically characterized post-mortem brain specimens, state-of-the-art equipment, cutting-edge technologies and the technical advice of highly trained faculty members who serve as Core Directors. The sophisticated imaging systems and biotechnologically advanced molecular core resources are provided on a shared-use basis to CPN and UMMC researchers. The CPN Research Resources Cores include the Human Brain Collection Core, Animal Core, Imaging Core, Molecular Biology Core, and Information Technologies Core.
Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.
Synchronized Histological Image Viewing Architecture
Synchronized Histological Image View Arc
A Java-based visualization and analysis application that can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets. * Simultaneous visualization of multiple image volumes. * Tools for labeling and masking of structures. * Framework for the Mouse Atlas Project.
SuperPred: Drug classification and target prediction
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,2025. Publicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits.
Conditional random field (CRF) based transcription factor binding site (TFBS) finding system. The underlying CRF model can integrate features of different sources.
Wolfram Alpha Computational Knowledge Engine
Wolfram Alpha is a computational knowledge engine that to make all systematic knowledge computable. Although, this is not a specific neuroscience related resource, the computational and math element will be helpful. Wolfram Alpha's long-term goal is to make all systematic knowledge immediately computable and accessible to everyone. It aims to collect and curate all objective data; implement every known model, method, and algorithm; and make it possible to compute whatever can be computed about anything. It's goal is to build on the achievements of science and other systematizations of knowledge to provide a single source that can be relied on by everyone for definitive answers to factual queries. Wolfram Alpha aims to also bring expert-level knowledge and capabilities to the broadest possible range of peoplespanning all professions and education levels. It's goal is to accept completely free-form input, and to serve as a knowledge engine that generates powerful results and presents them with maximum clarity. Lastly, Wolfram Alpha is an ambitious, long-term intellectual endeavor that it intends to deliver increasing capabilities over the years and decades to come. With a world-class team and participation from top outside experts in countless fields, it's goal is to create something that will stand as a major milestone of 21st century intellectual achievement. As of now, Wolfram Alpha contains 10+ trillion pieces of data, 50,000+ types of algorithms and models, and linguistic capabilities for 1000+ domains. Built with Mathematicawhich is itself the result of more than 20 years of development at Wolfram ResearchWolfram Alpha's core code base now exceeds 5 million lines of symbolic Mathematica code. Running on supercomputer-class compute clusters, Wolfram Alpha makes extensive use of the latest generation of web and parallel computing technologies, including webMathematica and gridMathematica. Its knowledge base and capabilities already span a great many domains, and its underlying framework has the power and flexibility to support ready extension to essentially any domain that is based on systematic knowledge.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API
Java-based geometry viewer that supports file formats used by Center for Computational Biology (CCB) researchers and provides necessary viewing functions. ShapeViewer uses ShapeTools library support to read and display LONI Ucf, VTX XML, FreeSurfer, Minc Obj (both binary and ascii), Open Dx, Gifti, and OFF format data files.
Database for analyzing drug-target interactions, it integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present (May 2013), the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range.
Software library that is a collection of Java classes that enable Java programmers to model, manipulate and visualize geometric shapes and associated data values. It simplifies the creation of application programs by providing a ready-made set of support routines. * File format readers that implement ShapeIO interface (modeled after Java ImageIO) are automatically used when appropriate. * Storage of additional metadata of arbitrary type (other than shape vertices and interconnections) is enabled by the use of data attributes. * Shapes may contain a set of child shapes allowing for the construction and manipulation of complex hierarchies of shapes. * The various components of a shape are specified as interfaces with specific implementations, making it easy to create specialized implementations of a shape component when different performance characteristics are required.
Fast Fourier Transform (FFT) JavaLibrary
Java library used for the execution of discrete Fourier transforms in 1-D, 2-D and 3-D through the implementation of Fast Fourier Transform (FFT) algorithms. * The FFT library has been written in Java for portability across different platforms, integrated into a single jar file for easy implementation. * The FFT library provides forward and backward fast Fourier transforms in 1-D, 2-D and 3-D with an easy-to-use manner. * The FFT requires the length equal to a number with an integer power of two. This library automatically examines the input data and detects the length to prevent improper execution.
Public university in Basel, Switzerland that offers degree programs in theology, law, medicine, humanities and social sciences, science, psychology, and business and economics.
Bioinformatics and cheminformatics database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link.
Predicting allosteric communication in myosin via a conserved residue pathway
Software application and code base that allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space. The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins. It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or "walking" of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. They are investigating which residues are likely to participate in allosteric communication pathways. The application is a collection of C++/QT code, suitable for reproducing the computational results of the paper. (PMID 17900617) In addition, they provide input and alignment information to reproduce Figure 3 (a key figure) in the paper. Examples provided will show users how to use AlloPathFinder with other protein families, assumed to exhibit an allosteric communication. To run the application a multiple sequence alignment of representative proteins from the protein family is required along with at least one protein structure.
Public database of the structures of active ingredients in marketed drugs. It utilizes a web-query system with various search options, such as drug names, trade name, and synonyms.
Molecular Simulation Trajectories Archive of a Villin Variant
An archive of hundreds of all-atom, explicit solvent molecular dynamics simulations that were performed on a set of nine unfolded conformations of a variant of the villin headpiece subdomain (HP-35 NleNle). It includes scripts for accessing the archive of villin trajectories as well as a VMD plug-in for viewing the trajectories. In addition, all starting structures used in the trajectories are also provided. The simulations were generated using a distributed computing method utilizing the symmetric multiprocessing paradigm for individual nodes of the Folding_at_home distributed computing network. The villin trajectories in the archive are divided into two projects: PROJ3036 and PROJ3037. PROJ3036 contains trajectories starting from nine non-folded configurations. PROJ3037 contains trajectories starting from the native (folded) state. Runs 0 through 8 (in PROJ3036) correspond to starting configurations 0 through 8 discussed in the paper in J. Mol. Biol. (2007) 374(3):806-816 (see the publications tab for a full reference), whereas RUN9 uses the same starting configuration as RUN8. Each run contains 100 trajectories (named clone 0-99), each with the same starting configuration but different random velocities. Trajectories vary in their length of time and are subdivided into frames, also known as a generation. Each frame contains around 400 configurational snapshots, or timepoints, of the trajectory, with the last configurational snapshot of frame i corresponding to the first configurational snapshot of generation i+1. The goal is to allow researchers to analyze and benefit from the many trajectories produced through the simulations.
Software program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
A software application for animating and visualising RNA and other macromolecular structures. Users are able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another. It allow researchers to explore and manipulate molecular structures Imported from BiositeMaps registry, to better understand structure:function relationships, folding pathways, and molecular motion.
Semi-Automated Footprinting Analysis Software
A software package that anayzes the structral details of RNA molecules through rapid quantification of a footprinting gel. By automating many of the steps involved in gel analysis, approximately one entire gel with thousands of bands can be quantified in less than 10 minutes using SAFA. In general, all the automated features have a manual override, such that even difficult or exceptional gels can be analyzed with the package.
Brigham and Women's Hospital Research Imaging Core
Imaging Core facility that provides a comprehensive research imaging service to meet the needs of investigators and research subjects using imaging facilities at Brigham and Women's Hospital (BWH). A unique feature of BRIC is the complete anonymity of research subjects. Research image scheduling, image acquisition and image storage are all kept completely separate from BWH clinical Radiology systems. The BRIC provides the administrative infrastructure, customer service architecture and institutional support to promote investigative applications of imaging technologies.
NCBI database of Genotypes and Phenotypes (dbGap)
database of Genotypes and Phenotypes (dbGaP)
Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.
Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach.
University of Canterbury; Christchurch; New Zealand
Public university in New Zealand that offers degree programs in fields such as art, commerce, engineering, forestry, health sciences, and social work.
The Poldrack lab has developed software tools for fMRI data analysis (links on the site), experimental design, and informatics, in collaboration with several other groups. * pubbrain.org: Developed in collaboration with the UCLA Consortium for Neuropsychiatric Phenomics, this site is an automatic meta-analytic search aid that allows for visualizing PubMed searches based on published neuroanatomic findings. * LONI Probabilistic Atlas: Developed in collaboration with the UCLA Laboratory of Neuroimaging and Center for Cognitive Phenomics, this project provides free and open access to a probabilistic atlas of cortical structures in 40 healthy individuals, including all raw data. * fmripower.org: Software developed by Jeanette Mumford in the Poldrack lab for statistical power analysis for fMRI studies. * Automated ICA-based denoising: Toolbox developed by Jussi Tohka at the Tampere University of Technology in Finland in collaboration with our laboratory and the UCLA Laboratory of Neuroimaging. * Raw data diagnostics - An R program that reads in a 4-D data file and provides a diagnostic report. * Code to run various tasks used in the lab - all of these require MATLAB and the MATLAB Psychophysics toolbox: * - Stop signal task (for behavioral testing outside the scanner) * - File Stop signal task (for use in the scanner) * - File mixed gambles task (demo and scanning script)
Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.
Web service that tags gene, protein, and small molecule names in any web page. Clicking on a tagged term opens a small popup showing summary information, and allows the user to quickly link to more detailed information. For each protein or gene, Reflect provides domain structure, sub-cellular localization, 3D structure, and interaction partners. For small molecules, it provides the chemical structure and interaction partners. Reflect can be installed as a plugin to Firefox or Internet Explorer, or can be used by entering a URL in the field provided. It can also be accessed programmatically via a REST or SOAP API, and a Reflect button can easily be added to any web page using Javascript or using a CGI proxy. Reflect was first-prize winner out of over 70 submissions in the Elsevier Grand Challenge, an international competition for systems that improve the way scientific information is communicated and used. Reflect can be edited and improved by the community.
Software Python package for simulator-independent specification of neuronal network models. In other words, you can write the code for a model once, using the PyNN API, and then run it without modification on any simulator that PyNN supports (currently NEURON, NEST and PCSIM). The API has two parts, a low-level, procedural API (functions create(), connect(), set(), record(), record_v()), and a high-level, object-oriented API (classes Population and Projection, which have methods like set(), record(), setWeights(), etc.). The low-level API is good for small networks, and perhaps gives more flexibility. The high-level API is good for hiding the details and the book-keeping, and is intended to have a one-to-one mapping with FacetsML. The other thing that is required to write a model once and run it on multiple simulators is standard cell models. PyNN translates standard cell-model names and parameter names into simulator-specific names, e.g. standard model IF_curr_alpha is iaf_neuron in NEST and StandardIF in NEURON, while SpikeSourcePoisson is a poisson_generator in NEST and a NetStim in NEURON. Only a small number off cell models have been implemented so far.
A Windows (Win32) software application for montaging, aligning, tracing, measuring, and reconstructing objects from serial microscopic section images. The software is designed for microscopy in which section resolution is much less than section thickness, such as transmitted electron microscopy (EM) where the resolution is a few nanometers while the section thickness is many tens of nanometers. Reconstruct can easily handle series with hundreds of very large, high-resolution section images. It facilitates image cropping, scaling and alignment. Multiple images can be placed side-by-side to make a montage of a section from a mosaic of images. The alignment of adjacent sections can be rapidly compared by either blending the two sections or by flickering between them. Sections can be moved while blended. Reconstruct aids in the calibration of image size. Images taken at different magnifications can be combined, calibrated and aligned. Tools for tracing and editing of objects on sections are provided. Objects can be surfaced from the traces and previewed in an OpenGL-based 3D scene window. The 3D scene can be saved as a bitmap or as a VRML file.
Group service that provides expression profiling products and services. They manufacture DNA microarrays for gene expression and microRNA profiling.
A collection of downloadable central nervous system (CNS) images for teaching, presentations, articles, and other purposes. The following major categories of images are as follows: Brain anatomy, Brain physiology, Anxiety, Depression, Schizophrenia, Dementia, Parkinson's disease, Stroke, and Others.
Movement Disorder Virtual University (MDVU): Resource Library
THIS RESOURCE IS NO LONGER IN SERVICE, documented April 15, 2016. The Movement Disorder Virtual University (MDVU) Resource Library contains detailed movement disorder information and resources including rating scales, scoring sheets, patient fact sheets, teaching slide sets, research news, meeting reports, anatomical illustrations, movement disorder treatment and rehabilitation directory, a glossary, support organizations, drug package information, and a library of links.
NIH Neuroscience Blueprint CRE Driver Network
Project to provide Neuroscience Community with mouse strains that are suitable for tissue and cell-type-specific perturbation of gene function in nervous system. NIH Neuroscience Blueprint has established three centers in the USA for generation of genetically modified mice expressing CRE recombinases in nervous system on the C57BJ/6 genetic background. Mouse lines are generated at Cold Spring Harbor Lab, at Scripps Research Institute, and at Baylor College of Medicine.
Gene expression data and maps of mouse central nervous system. Gene expression atlas of developing adult central nervous system in mouse, using in situ hybridization and transgenic mouse techniques. Collection of pictorial gene expression maps of brain and spinal cord of mouse. Provides tools to catalog, map, and electrophysiologically record individual cells. Application of Cre recombinase technologies allows for cell-specific gene manipulation. Transgenic mice created by this project are available to scientific community.
A commercial facility handling induced pluripotent stem cell (iPSC) generation, cellular characterization, teratoma formation, karyotyping, and KO-mouse generation.
System control software used for data acquisition and analysis for microarray images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
RAD-seq: Restriction-site Associated DNA sequencing
Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq.
Database of Secondary Structure Assignments
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries. DSSP is distributed on a basis of trust and instructions are available on the site. * Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp > messages.txt * Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code. * FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command.
Database for scientists interested in fungal genomics. Multiple species are included, and the database provides information on DNA C-values and genomic size. It also gives information derived from electrophoresis experiments and genome sequencing projects. The database accepts data submissions. We appreciate receiving published offprints, preprints, and personal communications providing C-value estimates for fungi.
The Rodent Brain WorkBench is the portal to atlases, databases and tools developed by the Neural Systems and Graphics Computing Laboratory (NeSys) at the Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented database applications and tools. The main category of available data is high resolution mosaic images covering complete histological sections through the rat and mouse brain. A highly structured relational database system for archiving, retrieving, viewing, and analysing microscopy and imaging data, aiming at presentation in standardized brain atlas space, is used to present a series of web applications for individual research projects. * Brain Connectivity * Atlases of Mouse Brain Promoter Gene Expression * General Brain Atlas and Navigation Systems * Downloadable tools for 3-DVisualization Open Access: * Atlas 3D * Cerebro-Cerebellar I * Cerebro-Cerebellar II * Neurotransporter Atlas * Rat Hippocampus * Tet-Off Atlas I (PrP) * Tet-Off Atlas II (PrP/CamKII) * Whole Brain Connectivity Atlas The data presented have been produced in collaboration with a large number of laboratories in Europe and the United States.
Database which contains information pertaining to all currently known caspase substrates.
FunSimMat - Functional Similarity Matrix
FunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online tool
Software that measures average telomere length from whole genome or exome shotgun sequence data.
Automated recognition of brain region mentions in neuroscience literature.
Freely available corpus of manually annotated brain region mentions created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. We encourage you to test new methods and applications of the dataset. Please contact us if you do, we would like to hear about and link to your work. The abstracts are from PubMed/Medline, specifically The Journal of Comparative Neurology.
A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
SelectScience.net is a leading online resource for applied chemists, clinical chemists and life scientists. It provides up-to-date product and industry news, an extensive product directory and end-user product reviews, as well as the ability for visitors to review the products they use. Scientists can also use the site to search for jobs, application notes and scientific conferences. Sponsors: The company is run by independent scientists and funded from Government and Corporate sponsorship.
Neuroscience was implemented as a new interdisciplinary major in 1999, replacing the Psychobiology Program and providing a base of experiences in biology, chemistry and psychology. Our students benefit from being able to work in small classes and to experience investigative lab experiences even in their introductory courses. Wellesley's neuroscience majors graduate with a liberal arts background coupled with sufficient concentration in this specialized field to be competitive among students coming from exclusively research-oriented institutions. The best proofs of the success of this approach are its products: * 60% of our graduates proceed to medical school; * 15% of our graduates continue on with graduate work in neuroscience, psychology, or neuropsychology; * 10% of our graduates pursue careers that intersect with neuroscience - for example, patent law or work in the biotech industry. Neuroscience is the study of the structure and function of neurons and how they are assembled to produce behaviors. This topic uses a multidisciplinary approach that extends from the molecular, through the cellular, and to the behavioral level.
Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.
The department of Neuroscience was founded in 2001, resulting from a merger between the Physiology and Anatomy department. In 2008, the BNT department joined forces. At present we consist of about 150 people. Our research is dedicated to Plasticity and Dynamics of Sensori-Motor Systems, which we investigate at the physiological, anatomical end molecular level in 18 different research groups. We have teaching responsibilities within the whole bachelor's phase of the medical curriculum at the Erasmus MC, teaching both basic anatomy and physiology, as well as neuroscience. The department hosts its own Master of Neuroscience program. The department of Neuroscience is embedded in the ONWAR, Helmholtz, and MGC research school
An on-line database and query system based on Administration-on-Aging (AoA)-related data files and surveys, and includes population characteristics from the Census Bureau for comparison purposes. Four options or paths through AGID were designed to provide different levels of focus and aggregation of the data from individual data elements within Data-at-a-Glance, to State-level summaries in State Profiles, to detailed, multi-year tables in Custom Tables, and finally, to full database access within Data Files.
Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment.
International Graduate Program Medical Neurosciences
Program integrates basic laboratory research and the clinic in terms of faculty, students, course content and infrastructure. This university's rigorous and comprehensive Master program provides a structured education in basic neuroscience to medical students and trains students of the life sciences in medical topics and approaches concerning the central and peripheral nervous system. Besides in depth theoretical training, the MSc program emphasizes state-of-the art practical lab experience, preparing graduates for continued research as PhD students. The PhD program places a high emphasis on scientific excellence, provides a multidisciplinary research and learning environment and offers extensive supervision and tutoring allowing students to complete their projects within 3 years. The supervised research project stands in the center of the PhD program, complemented by colloquia, workshops and training in professional skills. Our PhD students are member of the undefined Humboldt-Graduate-School providing an excellent service and training in transferable skills.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 10, 2017. In the last few years the Berlin neuroscience community has been highly successful in creating new research projects. Not the least of these is the cluster of excellence, NeuroCure, which has brought nine new professors and their research groups to Berlin. Along with the increasing levels of research, a number of new neuroscience training programs have recently been established. In 2002 the International Graduate Program Medical Neurosciences was the only structured Masters and PhD program: as of 2009 Berlin hosts four neuroscience schools and several DFG funded research training groups. The purpose of this website to highlight the many projects and people involved in the Berlin neuroscience community. We hope that you, the reader, can benefit from this summary., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Stroke research group that performs disease-oriented basic research, clinical research, epidemiology and health services research.
Emotion Mining enables scientists to measure the emotions of subjects before, during, and after research protocols in a reliable, sensitive, and convenient manner. Furthermore, Emotion Minings easy to use online data collection methodology leads to deep insights into the problems facing respondents and their solutions. :Emotion Minings unique measurement of emotion is clarified emotion emotion from which normal research biases, including subject state and trait biases, are removed. Using "clarified" emotion, researchers can gain insight into what research subjects really feel beneath and beyond what they self-report. More specifically, Emotion Mining engages respondents in a game-like exercise that enables them to express their deep-seated idiosyncratic responses and emotions. Built-in consideration of all possible emotion words produces "whole" emotional profiles in Emotion Mining analyses. Emotion Mining is applicable to social, cognitive, and behavioral research challenges and goals. Because it can distinguish conscious, subconscious, and even unconscious emotional responses to an unlimited range of topics, it is particularly applicable to the following areas: Social Psychology Personality Psychology Cognition and Social Cognition Cognitive Neuroscience Behavioral Neuroscience Political Psychology Their online methodology provides an engaging, controlled environment where subjects feel free to express themselves. Emotion Mining collects vital emotional responses in a way that no other methodology can. Emotion Mining also allows: :- Identification of unappreciated but recognizable emotional responses :- Prioritization of most unique, least biased emotional responses :- Aggregation through structured emotion analysis :- Collection of rich emotional verbatim :- Keyword analysis of verbatim You can experience and determine the face validity of Emotion Mining for yourself by registering to use Emotion Mining for personal decision making. You may also wish to have your research group involved in a group test of this face validity. In setting up a collaborative or independent relationship with scientists at Emotion Mining Company, you will gain access to the following tools used for data collection, analysis, and reporting. High-speed Internet access is all that is required for this easy-to-use addition to your laboratory.
rBiopaxParser - Parses BioPax files and represents them in R
A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported.
Bird Base: A Database of Avian Genes & Genomes
Bird Base: A Model Organism Database for Birds
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Birdbase is a centralized resource for avian genomics and other aspects of avian biology. BirdBase Objectives: * Provide a community driven platform for information about bird genomes and genomics. * Stimulate scientific advancement by integrating information from a variety of bird species * Promote collaboration and cooperation between scientists using birds as model organisms and those studying agricultural traits of birds. * Help coordinate solutions to common issues such as gene nomenclature and ontology development * Provide a conduit for sharing reagents and protocols
Genes to Cognition (G2C) Online is about modern neuroscience. It focuses on cognitive disorders, cognitive processes, and research approaches. Use the dynamic network maps to explore our library of 750+ unique items. Or, use the linear Selected Items menu on top of each map to tour selected content. Read the G2C blog, use simple mapper, or the 3-D brain, an interactive model of the brain. Disorders included in this site: ADHD, Alzheimer's Disease, Autism, Bipolar Disorder, Depression, Schizophrenia Cognitive Processes include: Attention, Language, Learning and Memory, Perception, and Thinking Research Approaches include: Bioinformatics, Ethics, Gene Finding, Model systems, Neuroimaging, Psychology. Navigation: Interact with the dynamic Networks Maps to explore the full catalog of content. Roll-over a node on the map for a preview and click to open the content. Move on to other content by returning to the network map. Each node you visit on the map gets flagged. Follow the Selected Items Subway Line for an overview of a topic. Roll-over a subway node for a preview and click to open the content. Other Features: Most content items include links to Related Items, which allow you to explore further. The Glossary includes over 300 neuroscience keywords. Search for content using keywords or id number. Select a preferred network map to view the content in context. Open/close the History at the lower left to view visited content. Your history is stored until you clear it. Simple Mapper - We developed Simple Mapper to power this web site on the brain. Now, you can use it to organize what comes out of yours! With Simple Mapper create and save concept maps, network diagrams, or flowcharts for personal use or to share with others. 3-D Brain - The G2C Brain is an interactive 3-D model of the brain, with 29 structures that can be rotated in three-dimensional space. Each structure has information on brain disorders, brain damage, case studies, and links to modern neuroscience research. Ideal for students, researchers, and educators in psychology and biology. Also available for download: 3D Brain App for iPhone and iPod Touch!
Arthur Prochazka Laboratory, University of Alberta
University of Alberta Arthur Prochazka Laboratory
The lab of Arthur Prochazka, whose research focuses on routing electrical current from surface electrodes to deep-lying nerves using implanted conductors. His research mostly focuses on muscle physiology. Current fields of research: * Stimulus Router System: A new family of implanted neuroprostheses. It comprises an implanted lead that picks up some of the current delivered through the skin by a surface stimulator and delivers it to a target nerve via a nerve cuff. The SRS has the advantages of an implanted stimulator: selectivity, reproducibility and convenience, at a fraction of the cost * Bionic Glove: Hand opening and closing stimulator for C5-C6 tetraplegic people. It is based on Functional Electrical Stimulation (FES). * In-home Telerehabilitation: Providing exercise sessions over the internet. * Interactive Receptor Model: An online model explaining muscle spindles and tendon organs. * Spinal Motoneuron Activity During Gait * Robocats: Mathematical models for locomotion. * Rigidity Analyzer: A better means of assessing rigidity. * General Research: Fundamental questions in our field of neurophysiology. * Spinal Cord Microstimulation: Restoring bladder function after spinal cord injury.
Neurodynamic Utility Toolbox for Magnetoencephalography and Electroencephalography
Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms.
Stanley Neuropathology Consortium Integrative Database
A database of 1749 neuropathological markers measured in 12 different brain regions from 60 brains in the Consortium Collection from the Stanley Medical Research Institute combined with microarray data and statistical tools. Fifteen brains each are from patients diagnosed with schizophrenia, bipolar disorder, or major depression, and unaffected controls. The four groups are matched by age, sex, race, postmortem interval, pH, side of brain, and mRNA quality. A Repository of raw data is also included. Users must register for access.
Web application as free reference manager and academic social network to organize your research, collaborate with others online, and discover the latest research. Automatically generate bibliographies, Collaborate easily with other researchers online, Easily import papers from other research software, Find relevant papers based on what you're reading, Access your papers from anywhere online, Read papers on the go with the iPhone app. The software, Mendeley Desktop, offers: * Automatic extraction of document details * Efficient management of your papers * Sharing and synchronization of your library (or parts of it) * Additional features: A plug-in for citing your articles in Microsoft Word, OCR (image-to-text conversion, so you can full-text search all your scanned PDFs), etc The website, Mendeley Web, complements Mendeley Desktop by offering these features: * An online back up of your library * Statistics of all things interesting * A research network that allows you to keep track of your colleagues' publications, conference participations, awards etc * A recommendation engine for papers that might interest you.
Community Epidemiology Work Group (CEWG)
A network composed of researchers from major metropolitan areas of the United States and selected foreign countries which meet semiannually to discuss the current epidemiology of drug abuse. The primary mission of the Work Group is to provide ongoing community-level surveillance of drug abuse through analysis of quantitative and qualitative research data. Through this program the CEWG provides current descriptive and analytical information regarding the nature and patterns of drug abuse, emerging trends, characteristics of vulnerable populations and social and health consequences. Reports Reports are available from the biannual meetings at which the network members discuss current and emerging problems of substance abuse. At the meetings, CEWG members present data on drug abuse from a variety of city, State, Federal, and other sources. These data are enhanced with information gathered through ethnographic research, focus groups, interviews, and other qualitative methods. This integration of quantitative with qualitative data provides invaluable insight into emerging drug use trends. Book In 1998, the National Institute on Drug Abuse (NIDA) published the first edition of Assessing Drug Abuse Within and Across Communities: Community Epidemiology Surveillance Networks on Drug Abuse to share information on establishing drug abuse epidemiology networks at community and State levels. Its purpose is to provide guidelines for establishing epidemiology networks to monitor and assess drug abuse patterns and trends and emerging drug problems at community and State levels to provide a foundation of information for public health response. The second edition differs from the first in format. For each data source, there is a description of the source and database, followed by guidelines on how to access the data (including Web sites) and what to request, and examples of how the data have been used by epidemiology work groups or Federal agencies. NIDA hopes that this revised guide is helpful to agencies, organizations, and researchers that are involved in or wish to establish epidemiology networks in their communities or States.
Digital Repository Infrastructure Vision for European Research
Data infrastructure project that merged with OpenAIRE. Cohesive, robust and flexible, pan-European infrastructure for digital repositories, offering sophisticated services and functionalities for researchers, administrators and the general public. Access the network of freely accessible digital repositories with content across academic disciplines with over 3,500,000 scientific publications, found in journal articles, dissertations, books, lectures, reports, etc., harvested regularly from more than 295 repositories, from 38 countries. DRIVER has established a network of relevant experts and Open Access repositories. DRIVER-II will consolidate these efforts and transform the initial testbed into a fully functional, state-of-the art service, extending the network to a larger confederation of repositories. It aims to optimize the way the e-Infrastructure is used to store knowledge, add value to primary research data and information making secondary research more effective, provide a valuable asset for industry, and help bridging research and education. The objectives of DRIVER-II, the second phase of the project, include efforts to expand, enrich, and strengthen the results of DRIVER, in the following areas: * strategic geographic and community expansion by means of the DRIVER confederation * establish a robust, scalable repository infrastructure accompanied by an open source software package D-Net * broader coverage of content through the use of enhanced publications * advanced end-user functionality to support scientific exploration of complex digital objects * larger outreach and advocacy programs * continued repository support * guidelines for interoperability in the larger European digital library community
Society for Research on Nicotine and Tobacco
With over a thousand members, including many of the top experts on nicotine and tobacco from over 20 countries around the world, the Society for Research on Nicotine and Tobacco's mission is to stimulate the generation of new knowledge concerning nicotine in all its manifestations - from molecular to societal. The Society has the following goals: 1. To sponsor scientific meetings and publications fostering the exchange of information on the biological, behavioral, social, and economic effects of nicotine; these activities shall include basic research and research on mechanisms of action and the use of nicotine as a probe for studying nervous systems function as well as applied research on the behavioral and pharmacological aspects of tobacco use, nicotine dependence, the therapeutic uses of nicotine, and related areas. 2. To encourage scientific research on public health efforts for the prevention and treatment of cigarette and tobacco use. 3. To provide the means by which various legislative, governmental, regulatory, and other public agencies and the ethical drug industry can obtain expert advice and consultation on critical issues concerning tobacco use, nicotine dependence, and the therapeutic uses of nicotine. Membership dues will be used to plan an annual meeting, to publish a newsletter, to compile a directory, to conduct advocacy and liaison activities for nicotine research, and to begin work on professional publications such as a journal. Though the Society will meet at least once per year in North America and will be incorporated in the United States, the intent is to be international in scope, with co-sponsorship of meetings in other countries and active recruitment of members outside the United States. By clicking on the various links on the website you can gain access to further information about the society, its publications, activities and membership. In 2004, the Society for Research on Nicotine and Tobacco celebrated the tenth anniversary of its founding. During its first decade, the Society grew from around 100 to over 900 members, sponsored well-attended annual meetings and highly-influential satellite conferences to promote research, provided timely electronic and print services to increase the flow of information, and founded a new peer-reviewed journal (Nicotine and Tobacco Research: The Journal of SRNT) to facilitate communication of scientific advances. The record documents considerable progress in meeting the objective of the Society to stimulate new knowledge about nicotine in all its manifestations. As part of SRNT's Decade One celebration, two projects were developed to commemorate its achievements and help preserve its collective memory. The first is an article by two past presidents, Ovide Pomerleau and John Hughes, entitled With a little help from its friends: A brief history of the Society for Research on Nicotine and Tobacco, published in the Societys journal, Nicotine and Tobacco Research. The second is a series of e-interviews with each of SRNTs first ten presidents. A brief structured interview was designed, and the former presidents were invited to respond in writing to each question in as little or as much detail as desired. An open-ended question was provided at the end to allow for more free-form commentary. The results of this effort can be accessed via the links below.
Dispersion Shrinakge for Sequencing data
DSS - Dispersion shrinakge for sequencing data
Software R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.
Database that collects, integrates and links all relevant primary information from the GABI plant genome research projects and makes them accessible via internet. Its purpose is to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research. GreenCards is the main interface for text based retrieval of sequence, SNP, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensing agency are facilitated. * GreenCards: Text based search for sequence, mapping, SNP data etc. * Maps: Visualization of genetic or physical maps. * BLAST: Secure BLAST search against different public databases or non-public sequence data stored in GabiPD. * Proteomics: View interactive 2D-gels and view or download information for identified protein spots. Registered users can submit data via secure file upload.
Genomic Annotation from Time-couse Epigenomic data
Genomic Annotation from Time-couse Epigenomic data (GATE)
Model-based, open source software analysis tool for chromatin states prediction based on time-course epigenetic marks data. It uses a combinatory Finite Mixture model nested with HMM to model the time course marks data in which each single hidden markov model describes the hidden states for a region set across different time points.
NetPathMiner: R package for network path mining through gene expression
Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths.
Magnetic Resonance Metabolomics Database
MDL - The Magnetic Resonance Metabolomics Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An on-line database and publically accessible depository that is dedicated to the omics of small biomolecules.
SumsDB (Surface Management System Database) and WebCaret Online Visualization
SumsDB (Surface Management System Database) WebCaret Online Visualization
Surface Management System Database and WebCaret Online Visualization
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures
NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.
Washington National Primate Research Center
Center that aims to provide an environment to support biomedical research directed towards human health issues and nonhuman primate health and biology. To meet this mission, the WaNPRC supports biomedical research activities, professional research staff, specifically bred and maintained nonhuman primate colonies, and dedicated facilities and equipment required for nonhuman primate research protocols.
A database of high-quality protein-protein interactions in different organisms.
Software tool to rapidly search for short interactions between two long RNAs.
A Support Vector Machine-based classifier to assesses the protein-coding potential of a transcript based on six biologically meaningful sequence features. CPC can discriminate coding from noncoding transcripts with high accuracy and speed. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation. The coding potential calculator tool reads FASTA data format as input.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods.
Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on June 8, 2020.Macaque genomic and proteomic resources and how they are providing important new dimensions to research using macaque models of infectious disease. The research encompasses a number of viruses that pose global threats to human health, including influenza, HIV, and SARS-associated coronavirus. By combining macaque infection models with gene expression and protein abundance profiling, they are uncovering exciting new insights into the multitude of molecular and cellular events that occur in response to virus infection. A better understanding of these events may provide the basis for innovative antiviral therapies and improvements to vaccine development strategies.
National Gnotobiotic Rodent Resource Center
Material resource that provides germ-free and selectively colonized rodents to requesting investigators. Germ-free rodents are axenic, with no detectible bacteria, yeast, molds, parasites or viruses (except retroviruses).
The deer mouse (Peromyscus maniculatus) and congeneric species are the most common native North American mammal. Laboratory stock of both wild-type and genetically variant Peromyscus are used for investigations in which laboratory-based studies can be interfaced with those of natural populations. The major function of the Stock Center is to provide genetically characterized types of Peromyscus in limited quantities to scientific investigators. It provides a reliable source of genetically defined and virus-free animals and related materials to the scientific and educational communities. The center currently keeps nine species and more than 27 distinctive mutant and other genetically defined stocks. Included among the species maintained are P. californicus, P. leucopus, P. eremicus, P. aztecus, P. melanophrys as well as two subspecies each of P. maniculatus and P. polionotus and three inbred lines of P. leucopus. Among the mutant stocks are 17 with altered coat phenotypes, 3 with neurological symptoms, and 6 others with developmental/physiological effects. One of these is a line deficient in alcohol dehydrogenase that has been widely used in studies of alcohol metabolism. The stock center also supplies biological materials, including fresh, frozen, and preserved tissues; molecular probes, and libraries. The center functions as a clearinghouse for information regarding this genus by sponsoring an Internet database and the semi-annual Peromyscus Newsletter. The center maintains a collection of over 3,000 Peromyscus-related reprints of published articles, books, and journals-photocopies of which are available upon request. Continuation of the center is dependent upon significant external utilization, therefore potential users are encouraged to take advantage of this resource. Sufficient animals of the mutant types generally can be provided to initiate a breeding stock. Some what larger numbers, up to about 50 animals, can be provided from the wild-type stocks. A user fee of $25.00 per wild-type animal and $33.00 per mutant or other special types is charged. The user assumes the cost of air shipment. Animals lost in transit are replaced without charge. Tissues, blood, skins, etc. can also be supplied at a modest fee. Arrangements for special orders will be negotiated. :Sponsors: The peromyscus genetic stock center is supported by the University of South Carolina, :a grant from the Special Projects Program of the National Science Foundation and a P40 grant ( grant number: P40 RR014279) from the National Institutes of Health. physiological, Developmental, Biological, Animal,
New Science of Addiction: Genetics and the Brain
A physiologic and molecular look at drug addiction involving many factors including: basic neurobiology, a scientific examination of drug action in the brain, the role of genetics in addiction, and ethical considerations. Designed to be used by students, teachers and members of the public, the materials meet selected US education standards for science and health. Drug addiction is a chronic disease characterized by changes in the brain which result in a compulsive desire to use a drug. A combination of many factors including genetics, environment and behavior influence a person's addiction risk, making it an incredibly complicated disease. The new science of addiction considers all of these factors - from biology to family - to unravel the complexities of the addicted brain. * Natural Reward Pathways Exist in the Brain: The reward pathway is responsible for driving our feelings of motivation, reward and behavior. * Drugs Alter the Brain's Reward Pathway: Drugs work over time to change the reward pathway and affect the entire brain, resulting in addiction. * Genetics Is An Important Factor In Addiction: Genetic susceptibility to addiction is the result of the interaction of many genes. * Timing and Circumstances Influence Addiction: If you use drugs when you are an adolescent, you are more likely to develop lifetime addiction. An individual's social environment also influences addiction risk. * Challenges and Issues in Addiction: Addiction impacts society with many ethical, legal and social issues.
THIS RESOURCE IS NO LONGER IN SERVICE, Documented on March 24, 2014. A resource for gene expression studies, storing highly curated MIAME-compliant studies (i.e. experiments) employing a variety of technologies such as filter arrays, 2-channel microarrays, Affymetrix chips, SAGE, MPSS and RT-PCR. Data were available for querying and downloading based on the MGED ontology, publications or genes. Both public and private studies (the latter viewable only by users having appropriate logins and permissions) were available from this website. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format. RAD is part of a more general Genomics Unified Schema (http://gusdb.org), which includes a richly annotated gene index (http://allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. NOTE: Due to changes in technology and funding, the RAD website is no longer available. RAD as a schema is still very much active and incorporated in the GUS (Genomics Unified Schema) database system used by CBIL (EuPathDB, Beta Cell Genomics) and others. The schema for RAD can be viewed along with the other GUS namespaces through our Schema Browser.
La Jolla Interdisciplinary Neurosciences Center
La Jolla Interdisciplinary Neuroscience Center Core (Burnham-Salk-Scripps-UCSD)
Our NINDS Center Core Grant supports centralized resources and facilities shared by investigators with existing NINDS-funded research projects. Our Center is composed of three research cores, each of which will enrich the effectiveness of ongoing research, and promote new research directions. The three Core facilities support Electrophysiology, Neuropathology / Histology, and High-Throughput/High-Content Chemical and Genomic Library screening. By making these important Core Services available to the local Neuroscience community, the La Jolla Neurosciences Program hopes to promote the study of how the nervous system works and develop treatments for nervous system diseases. The cores and their services are available to La Jolla neuroscientists. Core services are available to NINDS-supported neuroscience projects from local investigators as well as young neuroscientists prior to obtaining their first NIH-funded grant. * Electrophysiology: SBMRI Electrophysiology ** The Electrophysiology Core consists of the Sanford-Burnham Electrophysiology Facility. This facility can perform patch-clamp intracellular and extracellular field recordings on a range of material including cultured cells and brain slices. The Sanford-Burnham facility emphasizes electrophysiological analysis of cultured cells and the detailed electrical properties of channels, receptors and recombinant proteins expressed in Xenopus oocytes or mammalian cells. * Neuropathology: UCSD Neuropathology ** The Neuropathology laboratory applies immunocytochemistry, neurochemistry, molecular genetics, transgenic models of disease, and imaging by scanning laser confocal microscopy to analysis of neurological disease in animal models. * Chemical Library Screening: SBIMR Assay Development, SBIMR Chemical Library Screening, SBIMR Cheminformatics, SBIMR High-content Screening ** The Chemical Library Screening core offers high-throughput screening (HTS) of biochemical and cell-based array using traditional HTS readouts and automated microscopy for high-content screening (HCS)> These facilities also offer array development and screening, as well as cheminformatics and medicinal chemistry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs and compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents.
Database of genomes at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation. Its primary goals are: 1) to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group, and 2) to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data.
Image processing software package that provides scientific image acquisition, visualization, analysis and laboratory automation in single package. Allows users to acquire grayscale and color images from most video cameras, variety of cooled CCD digital cameras and high resolution flatbed scanners. Capable of analyzing image data in seven different data types, this program can calculate integrated intensity, mean, min, and max values plus several morphometric parameters on object regions within images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Software tool for acquisition and device control for standard research applications, requiring four dimensional imaging. Provides access to advanced image capture, archiving, and analysis solutions that are easy-to-use and provide maximum workflow. Handles multi dimensional imaging with support for capture, display, data management, analysis and additional options for peripheral device control, and multi-dimensional acquisition. Provides advanced image processing options such as database capabilities and report generation, intensity over time measurement, and Extended Depth of Focus functionality.
Forum within psychiatry and neurology aimed at providing updated evidence-based educational resources and information for health care professionals including an opportunity to exchange knowledge and experiences online. The CNSforum includes Educational resources, Clinical resources, Patient Websites, Publications, and a Community forum. Educational resources: * Brain Explorer - A graphical and educational presentation of the brain and the disorders affecting it, aimed at GPs and specialists in training. * Image Bank - A collection of CNS images for download and free use in presentations. Expert Talks Online presentations by leading experts on scientific topics. * Journal Links - A collection of links to websites of scientific journals in neurology and psychiatry. * Film Forum - Specialists discuss mainstream films with a psychiatric or neurological element from an educational point of view. Clinical resources: * Psychiatry Quality Measurement, PQM PQM is and electronic patient database/journal for use by psychiatrists. * Psychotropics - A database of psychotropic and neurological drugs. Rating scales Descriptions of and references to central scales used in psychiatry and neurology as well as an introduction to the topic. * Commented Articles - Commented articles written for CNSforum by leading international specialists. Patient Websites: * DepNet - An online community and information website for people affected by depression. * DementiaNet - An online community and information website for people affected by dementia and their relatives. * Publications (A catalogue of The Lundbeck Institute's publications on topics of clinical relevance in psychiatry and neurology.) * Institute Books, Institute Magazine Community forum: available only for former seminar participants and other members of The Lundbeck Institute Network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Binding Inference from Nucleosome Occupancy Changes
Binding Inference from Nucleosome Occupancy Changes (BINOCh)
BINOCh - Binding Inference from Nucleosome Occupancy Changes
Software that infers the identity of transcription factors used to regulate cell response to stimulus or determine a program of differentiation. It uses genome wide information on enhancer proximal nucleosome occupancy, acquired using ChIP-seq targeting enhancer related histone modifications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
GeneSpeed- A Database of Unigene Domain Organization
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Database and customized tools to study the PFAM protein domain content of the transcriptome for all expressed genes of Homo sapiens, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans tethered to both a genomics array repository database and a range of external information resources. GeneSpeed has merged information from several existing data sets including the Gene Ontology Consortium, InterPro, Pfam, Unigene, as well as micro-array datasets. GeneSpeed is a database of PFAM domain homology contained within Unigene. Because Unigene is a non-redundant dbEST database, this provides a wide encompassing overview of the domain content of the expressed transcriptome. We have structured the GeneSpeed Database to include a rich toolset allowing the investigator to study all domain homology, no matter how remote. As a result, homology cutoff score decisions are determined by the scientist, not by a computer algorithm. This quality is one of the novel defining features of the GeneSpeed database giving the user complete control of database content. In addition to a domain content toolset, GeneSpeed provides an assortment of links to external databases, a unique and manually curated Transcription Factor Classification list, as well as links to our newly evolving GeneSpeed BetaCell Database. GeneSpeed BetaCell is a micro-array depository combined with custom array analysis tools created with an emphasis around the meta analysis of developmental time series micro-array datasets and their significance in pancreatic beta cells.
Software for aligning viewing and editing dna / aminiacid sequences, intuitive, fast and leightweight. It has been designed to meet the requirements of next generation sequencing era phylogenetic datasets.
A community-defined, uniform, generic description of the core attributes of biological databases. The BioDBCore checklist is overseen by the International Society for Biocuration (ISB), in collaboration with the BioSharing forum. A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them have been partly compiled with the support of Oxford University Press and Re3Data.org. Database providers are encouraged to either create or claim their BioDBCore entry and update it as appropriate., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
BioNumbers: The Database of Useful Biological Numbers
Database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. Along with the numbers, you'll find the relevant references to the original literature, useful comments, and related numbers. While always of importance to biologists, having numbers in hand is becoming increasingly critical for experimenting, modeling, and analyzing biological systems. BioNumbers was motivated by an appreciation of how long it can take to find even the simplest number in the vast biological literature. All numbers are taken directly from a literature source and that reference is provided with the number. BioNumbers is designed to be highly searchable and queries can be performed by keywords or browsed by menus. BioNumbers is a collaborative community platform where registered users can add content and make comments on existing data. All new entries and commentary are curated to maintain high quality.
Short Course on the Genetics and Epigenetics of Addiction National Institute on Drug Abuse: Archived Video
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An archived video on the web providing comprehensive and hands-on training in genetics and epigenetic methodology. The purpose of the course is to provide an introduction to approaches and tools for identifying genes that confer vulnerability to addiction and individual differences in responses to treatments. The course is targeted to those who are new to the field of addiction genetics. The course was held over 5 days with lectures and hands-on demonstrations given each day. Viewers of the course will gain familiarity with conceptual and practical approaches to complex disorders using relevant genetic and epigenetic databases, and appropriate statistical and empirical approaches. Topics covered Behavioral genetics, genetic epidemiology, twin and adoption studies, statistical genetic concepts and approaches for mapping complex traits, haplotype based approaches for association mapping, genome-wide scans for addictive disorders, application of linkage for mapping genes and genetic loci for addictive disorders, pharmacogenomics of treatment of addictive disorders, Baysian Methods for identifying gene-gene interactions, analysis of copy number variation, practical use of genetic databases, mapping of complex traits in mice, methods for analyzing gene expression, and methods for doing epigenetic analysis are covered. The course was held April 4, 2008, at the Bethesda North Marriott Hotel and Conference Center, 5701 Marinelli Road, Bethesda, MD 20852.
Group to provide a state-of-the art understanding and develop a roadmap in the area of provenance for Semantic Web technologies, development, and possible standardization., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Centre for Modeling Human Disease Gene Trap Resource
Centre for Modeling Human Disease (CMHD) Gene Trap Resource
Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Abbreviated reference atlas for the Embryonic 15.5 post conception day mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).
Abbreviated reference atlas for the P56 mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).
Abbreviated reference atlas for the P56 mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing is permitted between planes of sectioning thus allowing the most appropriate plane to be selected. Abbreviations are found in a list accessed by clicking the see abbreviation link at the bottom of each map. Alternatively, passing the cursor directly across the abbreviation on the map will result in the appearance of the appropriate term in the rider on top of the map panel. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).
A private philanthropy with principal interests in brain science, immunology, and education. The portal provides general information about the brain and current brain research, links to validated sites related brain disorders, education resources and lesson plans, and support for the training of in-school arts specialists. The Dana Foundation science and health grants support brain research in neuroscience and immunology and their interrelationship in human health and disease. The grant sections include brain and immuno-imaging, clinical neuroscience research, human immunology and neuroimmunology. The Foundation also occasionally sponsors workshops and forums for working scientists, as well as offering funding for selected young researchers to continue their education or to attend seminars and workshops elsewhere.
Software used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Statistical tools for the ANalyses of Deep Sequencing
Statistical tools for the Analyses of Deep Sequencing (ANDES)
Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.
A disease / disorder relationships explorer and a sample of a map-oriented scientific work. It uses the Human Disease Network dataset and allows intuitive knowledge discovery by mapping its complexity. The Human Disease Network (official) dataset, a poster of the data and related book (Biology - The digital era, ISBN: 978-2-271-06779-1) are available. This kind of data has a network-like organization, and relations between elements are at least as important as the elements themselves. More data could be integrated to this prototype and could eventually bring closer phenotype and genotype. Results should be visual, but also printable. Creating posters can enhance collaborative work. It facilitates discussion and sharing of ideas about the data. This website initiative is an invitation to think about the benefits of networks exploration but above all it tries to outline future designs of scientific information systems.
cognitive atlas - a collaboratively developed cognitive science ontology
Knowledge base (or ontology) that characterizes the state of current thought in cognitive science that captures knowledge from users with expertise in psychology, cognitive science, and neuroscience. There are two basic kinds of knowledge in the knowledge base. Terms provide definitions and properties for individual concepts and tasks. Assertions describe relations between terms in the same way that a sentence describes relations between parts of speech. The goal is to develop a knowledge base that will support annotation of data in databases, as well as supporting improved discourse in the community. It is open to all interested researchers. A fundamental feature of the knowledge base is the desire and ability to capture not just agreement but also disagreement regarding definitions and assertions. Thus, if you see a definition or assertion that you disagree with, then you can assert and describe your disagreement. The project is led by Russell Poldrack, Professor of Psychology and Neurobiology at the University of Texas at Austin in collaboration with the UCLA Center for Computational Biology (A. Toga, PI) and UCLA Consortium for Neuropsychiatric Phenomics (R. Bilder, PI). Most tasks used in cognitive psychology research are not identical across different laboratories or even within the same laboratory over time. A major advantage of anchoring cognitive ontologies to the measurement level is that the strategy for determining changes in task properties is easier than tracking changes in concept definitions and usage. The process is easier because task parameters are usually (if not always) operationalized objectively, offering a clear basis to judge divergence in methods. The process is also easier because most tasks are based on prior tasks, and thus can more readily be considered descendants in a phylogenetic sense.
A free tool to design effective RNAi molecules that includes the following target design options: Stealth RNAi siRNA, siRNA, miR RNAi, shRNA, siRNA to Stealth RNAi siRNA, and siRNA to shRNA.
Code Analysis Repository and Modelling for e-Neuroscience
Code Analysis Repository & Modelling for E-Neuroscience
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 14, 2023. Infrastructure for sharing data, tools and services, this virtual research environment (VRE) supports e-Neuroscience and is designed to provide services for data and processing of that data. While the system is initially focused on electrophysiology data (neural activity recordings are the primary data types), it is equally applicable to many domains outside neuroscience. The Portal Provides: * User login and customization. * Data upload/download. * Data handling including custom permissions for public, shared or private data. * The ability to invoke custom public, shared or private services that consume and produce data. For example, it would allow spike series to be run through a sorter, producing new data representing the sorted spikes. * The ability to host services written in a number of languages including, but not limited to Matlab, R, Python, Perl, Java. * A system to support metadata for data objects, which provides extensive support for entering metadata at the point of upload, and allows the generation of metadata from services to provide provenance information. * The ability to invoke additional visualization for the data, for example, via the Signal Data Explorer. A core part is the development of: (i) minimum reporting guidelines for annotation of data and other computational resources for the purpose of sharing, and; (ii) intermediate formats and APIs for translation between proprietary and bespoke data types. These recommendations are being implemented and the global community is encouraged both to engage in their specification and make use of them for their own data sharing systems. * MINI: Minimum Information about a Neuroscience Investigation - This framework represents the formalized opinion of the CARMEN consortium and its associates, and identifies the minimum reporting information required to support the use of electrophysiology in a neuroscience study, for submission to the CARMEN system. * NDTF: Neurophysiology Data Translation Format - This framework provides a vendor-independent mechanism for translating between raw and processed neurphysiology data in the form of time and image series. They are implementing NDTF in CARMEN but it may also be useful for third party applications.
PacmonsTR - Tandem Repeat Detection for Long Read Sequence Data
Software that implements a reference-based probabilistic approach to identify the Tandem Repeat (TR) region and estimate the number of these TR elements in long DNA reads.
Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
FisHiCal: Iterative FISH-based Calibration of Hi-C Data
Software that integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis.
Mutation Annotation and Genomic Interpretation
MAGI - A tool for Mutation Annotation and Genomic Interpretation
A tool for annotating, exploring, and analyzing gene sets that may be associated with cancer.
A Perl-based visualization software tool that generates circular figures of genome-associated data. Common uses of the tool include: * Displaying the sequence and/or genes in a GenBank flat file. * Highlighting differences and/or similarities in gene content between related organisms. * Comparing SNPs and indels between closely-related strains or serovars. * Comparing gene expression values across multiple samples or timepoints. * Visualizing coverage plots of RNA-Seq read alignments.
University of Southern California LONI Software
Portal provides list of software resources. LONI is leader in development of advanced computational algorithms and software for comprehensive and quantitative mapping of brain structure and function. Aims to encourage communication between users and LONI software engineers in order to improve effectiveness.
Web application for sequence analysis and the prediction of protein structure and function. The user interface intakes protein sequences or alignments and returned multiple sequence alignments, motifs, and nuclear localization signals., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
GenProtEC - E. coli genome and proteome database
GenProtEC- E. coli Genome and Proteome Database
GenProtEC is dedicated to the functions encoded by the Escherichia coli K-12 (strain MG1655) genome defined in the GenBank Accession No. NC_000913.2 deposit. All the data presented in GenProtEC is made easily accessible to the users through downloadable flat files in text format. GenProtEC presents information on the functions of E.coli K-12 MG1655 gene products from several points of view. E.coli proteins as single modules have been grouped in sequence similarity. Using the power of group membership of proteins of similar function, open reading frames within any group can be assigned the general function. In addition, the presence of domains of known function within E.coli proteins has been determined. Domain content permits annotation of some functional information to otherwise totally unknown sequences. The rich classification of cellular roles, MultiFun, has been applied, underlining the fact that many gene products have more than one cellular role. Our annotation work includes multiple types of information: 1. Sequence similarity to orthologues as defined by Darwin (start and end of aligned region, identity, and PAM distance). 2. Resolution of fused proteins into modular units with independent functions. 3. Identification of sequence similar protein groups within E. coli that are clustered by transitive relationships. The sequence similarity is limited to PAM 200 and an alignment of at least 83 amino acids. 4. Updated literature references. 5. Classification of gene products by their gene type and by their cellular role(s). The MultiFun classification system for cellular roles is used to assign gene products to one or more roles. MultiFun has been converted to Gene Ontology terms. 6. Familes of proteins related by structure and biochemical reaction mechanisms (work in progress). 7. SCOP superfamily identification and location (e.g. binding site domains) for E. coli proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
IMEx - The International Molecular Exchange Consortium
International Molecular Exchange Consortium
The International Molecular Exchange Consortium
Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data.
Group of 10 academic laboratories provide pancreatic islets of cGMP-quality to eligible investigators for use in FDA approved, IRB-approved transplantation protocols in which isolated human islets are transplanted into qualified patients afflicted with type 1 diabetes mellitus; optimize the harvest, purification, function, storage, and shipment of islets while developing tests that characterize the quality and predict the effectiveness of islets transplanted into patients with diabetes mellitus; and provide pancreatic islets for basic science studies. The centers are electronically linked through an Administrative and Bioinformatics Coordinating Center (ABCC). The ABCC manages a system with objectively defined criteria that establishes the order of priority for islet distribution. It also provides database and other informatics to track the utilization of pancreata and all distributed clinical grade islets for transplant and basic research, and supports the Islet Cell Resource Centers Consortium so that the research community has a single entry point to the program. Qualified researchers from domestic institutions may request islets by submitting a written application to the director of the ABCC. The ICRs will distribute Islets as appropriate for either clinical or basic science protocol use to eligible investigators who have received a favorable review and subsequent approval by the ICR Steering Committee (SC). The Administrative and Bioinformatics Coordinating Center (ABCC) manages the distribution according to a priority list. The ABCC will give preference to investigators who have peer-reviewed, NIH-funded research support.
Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps.
Computational Neurobiology Laboratory at the Salk Institute
The long range goal of this laboratory is to understand the computational resources of brains from the biophysical to the systems levels. The central issues being addressed are how dendrites integrate synaptic signals in neurons, how networks of neurons generate dynamical patterns of activity, how sensory information is represented in the cerebral cortex, how memory representations are formed and consolidated during sleep, and how visuo-motor transformations are adaptively organized. Additionally, new techniques have been developed for modeling cell signaling using Monte Carlo methods (MCell) and the blind separation of brain imaging data into functionally independent components (ICA).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. A data base system for the management of conformational maps and profiles, the system allows conformational maps to be archived in a standard format, and it provides search and comparison facilities. An interface to structures from Sweet-DB is implemented. GlycoMapsDB also offers scientists the possibility of adding their own publicized structures to the database via a web interface. GlycoMapsDB provides maps of 3D and 2D mono- and disaccharides. It provides users conformational information on carbohydrates and glycoproteins.
Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
Blind Source Separation and Independent Component Analysis
Blind Source Separation and Independent Component Analysis (ICA) algorithms including: An efficient batch algorithm: JADE and Adaptive algorithms: relative gradient algorithms. Associated papers / documentation are included as well as thoughts on Multi-dimensional independent component analysis. * An efficient batch algorithm: JADE - For off-line ICA, an algorithm has been developed based on the (joint) diagonalization of cumulant matrices. "Good" statistical performance is achieved by involving all the cumulants of order 2 and 4 while a fast optimization is obtained by the device of joint diagonalization. JADE has been successfully applied to the processing of real data sets, such as found in mobile telephony and in airport radar as well as to bio-medical signals (ECG, EEG, multi-electrode neural recordings). The strongest point of JADE for applications of ICA is that it works off-the-shelf (no parameter tuning). They advocate using the code provided as a plug-in replacement for PCA (whenever one is willing to investigate if such a replacement is appropriate). The weakest point of the current implementation is that the number of sources (but not of sensors) is limited in practice (by the available memory) to something like 40 or 50 depending on your computer. The JADE algorithm was originally developed to process complex signals, motivated by applications to digital communications. Another implementation is now available which is tuned to process more efficiently real-valued signals. * Adaptive algorithms: relative gradient algorithms - For adaptive source separation, they have developed a class of equivariant algorithms. This means that their performance is independent of the mixing matrix. They are obtained as stochastic relative gradient algorithms. * Multi-dimensional independent component analysis - Performing ICA on ECG signals with the JADE algorithm, it was realized that an interesting extension of the notion of independent component analysis would be to consider an analysis into linear components that would be "as independent as possible" as in ICA, but would be "livin" in subspaces of dimension greater than 1. This could be called "MICA" for Multi-dimensional Independent Component Analysis.
iontree: Data management and analysis of ion trees from ion-trap mass spectrometry
Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.
Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels.
A complete graphing and data analysis software package that provides a suite of features catering to the needs of scientists and engineers. Main features: * Drag-and-drop import of data and images * Save import settings to a worksheet or external files for repeated use * Use saved settings to re-import files with a single click * Post-process imported data * Import Wizard with visual feedback * Handle non-standard files by programming
Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat
Parahippocampal hippocampal connectivity
Interactive diagram containing existing knowledge of hippocampal-parahippocampal connections in which any connection can be turned on or off at the level of cortical layers. It includes references for each connection.
Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data.
Drug Information Portal - Quick Access to Quality Drug Information
The NLM Drug Information Portal gives users a gateway to selected drug information from the U.S. National Library of Medicine and other key U.S. Government agencies. At the top of the page are links to individual resources with potential drug information, including summaries tailored to various audiences. Resources include the NLM search systems useful in searching for a drug, NLM research resources, resources organized by audience and class, and other NIH and government resources such as FDA and CDC. The search box in the middle of the page lets you search many of these resources simultaneously. More than 34,000 drugs can be searched using this facility. The portal covers drugs from the time they are entered into clinical trials (Clinicaltrials.gov) through their entry in the U.S. market place (Drugs@FDA). Many drugs in other countries are covered, but not as thoroughly as U.S. drugs. The PubMed link provides medical literature describing research, and TOXLINE provides toxicology literature. Resources such as MedlinePlus provide easy to read summaries of the uses and efficacy of a drug. You may search by a drug's trade name or generic name. For example, the trade name Advil and the generic name ibuprofen will retrieve the same drug record. As you type in a name, suggestions are given beneath the search box. A spell checker gives suggestions if the name is not found. You can find embedded portions of names by using an asterisk at the beginning and/or end of a search term. You can also search by the general Category of usage of a drug by checking that radio button. Suggestions are given as you type here too. Once a drug is found, a summary of the drug's type and usage is given, as well as links leading to further information at one of the portal's resources. Outside links open in a new window. Within a given drug record, you may click on the drug category and retrieve drugs with the same or similar uses. * View drug category descriptions. * View top By Name searches (previous seven days). * View top By Category searches (previous seven days). * View top dispensed prescriptions in the US Market, 2010. * View common drug name list. * View category name list. * View list of resources searched. JavaScript must be enabled in your browser for the NLM Drug Information Portal to work properly.
Harvard NIEHS Center for Environmental Health Trace Metals Lab
Core facility that provides metals analytical capabilities to biomedical and non-biomedical researchers and serves as a source for study design consultation and sample QA/QC requirements. The transport, fate, exposure, and toxic effects of heavy metals is a primary focus of research at the Center. It operates as a modified fee-for-service laboratory. Researchers have the option of having the samples run by the Service staff, or of receiving instruction (for themselves or a doctoral or post doctoral trainee) on how to operate the analytical equipment and analyze their own samples. Both options have associated fees and, as with other services, facility access funds can be requested internal or external services when individual grant support is not yet available.
Automated software program for image analysis based on microarray based image application. Various output styles are available, including image overlay with warping and registration and scattered correlation plot with 2D or 3D spot profile. Outputs can be formatted in text, xml, excel, or custom format.
Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26.
Marginalia is an open source Javascript web annotation system that allows users of web applications to highlight text and write margin notes. Marginalia has been integrated into several web applications: * An extension to Moodle adds annotation to Moodle discussion forums. * A plug-in for Open Journal Systems allows readers to annotate journal articles. * Marginalia is part of the Bungeni parliamentary and legislative information system. * A stand-alone demo implementation provides a minimal sample implementation as a demonstration of how to integrate Marginalia with other web applications. The annotation feature supports recent versions of major browsers (Firefox, Safari, and IE), but works best and fastest in Firefox. The features are integrated into and work with a host web application with no need for special browser or other client software. Marginalia is the 2008 winner of the British Columbia Innovation Award in Educational Technology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Functional Magnetic Resonance Imaging of the Brain Software Library
Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.
Center to provide global research, training, and resources that will lead to the discovery of medically important toxins found in venoms. The Viper Resource Center (VRC) is located in the Natural Toxins Research Center at Texas A&M University-Kingsville.
Private, non-profit university in Utah. The university is a part of the Latter-day Saints Church Educational System.
A nonprofit devoted to fostering education, scientific research, and dissemination of information in the physiological sciences. Founded in 1887 with 28 members, the APS now has over 10,500 members. Most members have doctoral degrees in physiology and/or medicine (or other health professions). APS is governed by an elected Council consisting of a President, President-Elect, Past President, and nine Councillors. The National headquarters of the Society is based in Bethesda, Maryland, on the campus of the Federation of American Societies for Experimental Biology (FASEB). The American Physiological Society Awards program demonstrates the Society's dedication to its members and biomedical research by recognizing the research efforts of outstanding APS members. Awards are offered by the Society and the various APS Sections. For questions regarding the Society awards (including Student awards), please send an email to awards_at_the-aps.org. For questions regarding the Section awards please contact the individual Sections directly www.the-aps.org/sections/.
Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs.
It provides the communications/database network needed for efficient acquisition and sharing of existing captive primates and primate-related resources by investigators and institutions both nationally and internationally. The overall goal of this service is to maximize the use of existing captive primates, thereby reducing the total number of primates needed for research, and in turn, helping to promote the conservation of primate populations in the wild. Services Provided PRRS services include 1) Referral Service, an immediate, staff-operated service designed to match investigator inquiries/requests to the available resource listings maintained in the PRRS master database; 2) CURRENT LISTINGS, a twice-monthly newsletter listing current availability of, as well as needs for, primates, tissues, equipment, and services; 3) ANNUAL RESOURCE GUIDE (ARG), an annual publication that lists subscribing suppliers of primates, laboratories, equipment, and commercial services such as transportation and quarantine facilities; and 4) Web site, an interactive site that includes the full text of CURRENT LISTINGS as well as online forms for posting resource availabilities/needs and listing updates, the current ARG, a diagram of primate taxonomy with illustrative photographs, online renewal and feedback forms, general service information, and links to other sites of interest to the primate research community. The PRRS also maintains a database of colonies, primates, and primate materials to which notices of availability and need can be referred. Services are available without charge to government-supported researchers and other scientists in the United States and abroad using primates in their work. Sponsors: The PRRS is made possible by grant RR-01240 from the National Center for Research Resources, National Institutes of Health.
Gramene: A Resource for Comparative Grass Genomics
Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.
Database that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. LOC3d is a database of predicted subcellular localization for eukaryotic proteins of known 3-D structure taken from the Protein Databank. Subcellular localization is currently predicted using four different methods: predictNLS (nuclear localization signal), LOChom (using homology), LOCkey (using keywords) and LOC3d (neural network based prediction). The reported localization is based on the method which predicts localization of a given protein with the highest confidence. LOCtree is a novel system of support vector machines (SVMs) that predict the subcellular localization of proteins, and DNA-binding propensity for nuclear proteins, by incorporating a hierarchical ontology of localization classes modeled onto biological processing pathways. Biological similarities are incorporated from the description of cellular components provided by the gene ontology consortium (GO). GO definitions have been simplified and tailored to the problem of protein sorting. Technically the ontology has been implemented using a decision tree with SVMs as the nodes. LOCtree, was extremely successful at learning evolutionary similarities among subcellular localization classes and was significantly more accurate than other traditional networks at predicting subcellular localization. Whenever available, LOCtree also reports predictions based on the following: 1) Nuclear localization signals found by PredictNLS, 2) Localization inferred using Prosite motifs and Pfam domains found in the protein, and 3) SWISS-PROT keywords associated with a protein. Localization is inferred in the last two cases using the entropy-based LOCkey algorithm. Additional information can be found in the LOCtree manuscript and associated PredictNLS and LOCkey publications.
Private research university in Chicago, Illinois.
Public research university in Ohio that offers degree programs in a variety of fields such as business, music and arts, and medical and human service.
A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs.
A web-based analysis service for identifying exonic splicing enhancers in eukaryotic genes. ESEfinder accept sequences in the FASTA format. A typical mammalian gene is composed of several relatively short exons that are interrupted by much longer introns. To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently, in a process that requires the coordinated action of five small nuclear (sn)RNAs (U1, U2, U4, U5 and U6) and more than 60 polypeptides. The inaccurate recognition of exon/intron boundaries or the failure to remove an intron generates aberrant mRNAs that are either unstable or code for defective or deleterious protein isoforms. Exonic enhancers are thought to serve as binding sites for specific serine/arginine-rich (SR) proteins, a family of structurally related and highly conserved splicing factors characterized by one or two RNA-recognition motifs (RRM) and by a distinctive C-terminal domain highly enriched in RS dipeptides (the RS domain). The RRMs mediate sequence-specific binding to the RNA, and so determine substrate specificity, whereas the RS domain appears to be involved mainly in protein-protein interactions. SR proteins bound to ESEs can promote exon definition by directly recruiting the splicing machinery through their RS domain and/or by antagonizing the action of nearby silencer elements. Sponsors: ESEfinder is supported by the Cold Spring Harbor Laboratory.
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.
Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO.
A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids.
An online annotation, collaboration and indexing system for documents and images, supporting PDF and MS Office formats. Instead of emailing different versions of a document back and forth you can all comment on a single read-only copy online. Unlike online word processors, the document is displayed in high quality with fonts and layout just like the printed version. It is easy to use and runs in all common web browsers, with no software or plugins to install. Hosted solutions are available for individuals and workgroups. For enterprise users the full system is available for local installation. Special discounts apply for educational use. The FREE hosted solution offers single-user accounts for uploading up to 30 pages per month. Documents can be shared with any number of annotators.
A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence.
University of Coimbra; Coimbra; Portugal
Public university in Coimbra, Portugal that offers degree programs in a variety of fields including law, medicine, science and technology, pharmaceuticals, and sports sciences.
Studies of European Volunteer Twins to Identify Genes Underlying Common Diseases
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Study of genetic and life-style risk factors associated with common diseases based on analysis of European twins. The population cohorts used in the Genomeutwin study consist of Danish, Finnish, Italian, Dutch, English, Australian and Swedish twins and the MORGAM population cohort. This project will apply and develop new molecular and statistical strategies to analyze unique European twin and other population cohorts to define and characterize the genetic, environmental and life-style components in the background of health problems like obesity, migraine, coronary heart disease and stroke, representing major health care problems worldwide. The participating 8 twin cohorts form a collection of over 0.6 million pairs of twins. Tens of thousands of DNA samples with informed consents for genetic studies of common diseases have already been stored from these population-based twin cohorts. Studies targeted to cardiovascular traits are now being undertaken in MORGAM, a prospective case-cohort study. MORGAM cohorts include approximately 6000 individuals, drawn from population-based cohorts consisting of more than 80 000 participants who have donated DNA samples.
The National Academies Press (NAP) was created by the National Academies to publish the reports issued by the National Academy of Sciences, the National Academy of Engineering, the Institute of Medicine, and the National Research Council, all operating under a charter granted by the Congress of the United States. The NAP publishes more than 200 books a year on a wide range of topics in science, engineering, and health, capturing the most authoritative views on important issues in science and health policy. The institutions represented by the NAP are unique in that they attract the nation's leading experts in every field to serve on their award-winning panels and committees. This is the right place for definitive information on everything from space science to animal nutrition. Many books can be read on-line for free. NAP also offers many titles in electronic Adobe PDF format. Hundreds of these books can be downloaded for free by the chapter or the entire book, while others are available for purchase. Sponsors: This resource is supported by The National Academies.
Serves Drosophila research community by collecting and distributing DNA clones and vectors, cell lines, developing and testing genomics technologies.
Drosophila Genomics Resource Center at Indiana University
Serves Drosophila research community by collecting and distributing DNA clones and vectors; collecting and distributing Drosophila cell lines; developing and testing genomics technologies for use in Drosophila and assisting members of the research community in their use.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.
General Clinical Research Centers Program
General Clinical Research Centers (GCRC)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Through the General Clinical Research Centers (GCRC) program, NCRR funds a national network that provides settings for medical investigators to conduct safe, controlled, state-of-the-art, in-patient and out-patient studies of both children and adults. GCRCs also provide infrastructure and resources that support several career development opportunities.
This portal provides information about the Tribolium castabeum Genome Project. The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below. The red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University). Access to the Data :- Genome Assembly: The long term home of the Tribolium genome is Beetlebase. Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published. Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder. A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page. The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change. :- BLAST Searches: The BLAST link is located in the sidebar. :* Linearized chromosome and unplaced scaffold sequences :* Assembled contigs :* Bin0 unassembled reads and Repeat reads Traces are available from the NCBI Trace Archive by using the link in the sidebar, or by using NCBI MegaBLAST with a same species or cross species query. Sponsors: Funding for this project has been provided by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH), and the U.S. Department of Agriculture's Agricultural Research Service (USDA ARS Agreement No. 58-5430-3-338).
Software for the rapid development of psychological and neuroscientific experiments.
Ambystoma Resources for Model Amphibians Database
Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network.
This center provides routine behavioral/cognitive testing of mice with phenotypes that are expressed as a consequence of alterations at the level of gene function, and that are relevant to basic neuroscience and to animal models of neurological and psychiatric disorders. Current Research Behavioral testing within the center involves a collaborative component in which mice provided by users are assessed for behavioral/cognitive functions. All research includes behavioral assessment of a variety of genetically altered mice provided by users. Services Provided The objective of the center is to provide a link between genetic and molecular analysis of neural function and the study of integrative systems and clinical conditions through behavioral assessment of animal models, and mouse behavioral phenotypes generated by genetic modification. Sponsors: This resource is supported by the National Center of Research Resources (Grant Number: P40 RR017688).
Software for the automated evaluation of behavior in a range of pre-clinical and neuroscience applications in basic and clinical psychopharmacology. Applications include phenotype characterization and studying the behavioral effects of pharmacologic substances.
Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
BiGGR - Constraint based modeling in R using metabolic reconstruction databases
Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.
Virtual Physiological Human Network of Excellence
The VPH NoE is a project which aims to help support and progress European research in biomedical modeling and simulation of the human body. This project will improve our ability to predict, diagnose and treat disease, and have a dramatic impact on the future of healthcare, the pharmaceutical and medical device industries. The VPH Network of Excellence (VPH NoE) is designed to foster, harmonize and integrate pan-European research in the field of i) patient-specific computer models for personalised and predictive healthcare and ii) ICT-based tools for modeling and simulation of human physiology and disease-related processes. The main objectives of the VPH Network of Excellence are to support the: :- Coordination of research portfolios of VPH NoE partners through initiation of Exemplar integrative research projects that encourage inter-institution and interdisciplinary VPH research; :- Integration of research infrastructures of VPH NoE partners through development of the VPH ToolKit: a shared and mutually accessible source of research equipment, managerial and research infrastructures, facilities and services; :- Development of a portfolio of interdisciplinary training activities including a formal consultation on, and assessment of, VPH careers; :- Establishment of a core set of VPH-related dissemination and networking activities which will engage everyone from partners within the VPH NoE/other VPH projects, to national policy makers, to the public at large; :- Creation of Industrial, Clinical and Scientific Advisory Boards that will jointly guide the direction of the VPH NoE and, through consultation, explore the practical and legal options for real and durable integration within the VPH research community; :- Implementation of key working groups that will pursue specific issues relating to VPH, notably integrating VPH research worldwide through international physiome initiatives. Finally, by involving clinical and industrial stakeholders, VPH NoE also plans to lay a reliable ground to support sustainable interactions and collaboration between research and healthcare communities. Virtual Physiological Human lists, as its main target outcome, patient-specific computer models for personalized and predictive healthcare and ICT-based tools for modeling and simulation of human physiology and disease-related processes. Collaborative projects (IPs and STREPs) within the call will meet specific objectives, addressing: patient-specific computational modeling and simulation of organs or systems data integration and new knowledge extraction and clinical applications and demonstration of tangible benefits of patient-specific computational models. The networking action outlined within the call - the VPH NoE - should serve to connect these efforts, and lay the foundations for the methodological and technical framework to support such research. It should also build on previous EC investment in this field, including the outcomes of VPH type' projects funded within the EU Sixth Framework Programme, and through other National and International initiatives. The Virtual Physiological Human Network of Excellence (VPH NoE) has been designed with "service to the community" of VPH researchers as its primary purpose. Its aims range from the development of a VPH ToolKit and associated infrastructural resources, through integration of models and data across the various relevant levels of physiological structure and functional organization, to VPH community building and support. The VPH NoE aims to foster the development of new and sustainable educational, training and career structures for those involved in VPH related science, technology and medicine. The VPH NoE constitutes a leading group of universities, institutes and organizations who will, by integrating their experience and ongoing activities in VPH research, promote the creation of an environment that actively supports and nurtures interdisciplinary research, education, training and strategic development. The VPH NoE will lead the coordination of diverse activities within the VPH Initiative to help deliver: new environments for predictive, patient-specific, evidence-based, more effective and safer healthcare; improved semantic interoperability of biomedical information and contribution to a common health information infrastructure; facile, on-demand access to distributed European computational infrastructure to support clinical decision making; and increased European multidisciplinary research excellence in biomedical informatics and molecular medicine by fostering closer cooperation between ICT, medical device, medical imaging, pharmaceutical and biotech companies. The VPH NoE will connect the diverse VPH Initiative projects, including not only those funded as part of the VPH initiative but also those of previous EC frameworks and national funding schemes, together with industry, healthcare providers, and international organizations, thereby ensuring that these impacts will be realized. VPH NoE work packages and project structure The VPH NoE activities are divided between five main work packages (follow the links at the top of the page for more information on each). In brief, the focus of each work package is as follows: -Work package 1: Network Management -Work package 2: VPH NoE Exemplar Projects -Work package 3: VPH NoE ToolKit development -Work package 4: VPH NoE Training and Career Development -Work package 5: Spreading Excellence within the VPH NoE and VPH-I In view of its role as the networking action for the VPH Initiative, all VPH NoE activities have been designed to serve and interconnect not only the VPH NoE core members, but also the projects funded within the VPH call (VPH-I) and the wider research community. Key activities which the VPH NoE will pursue, in support of the development of a research environment which facilitates integrative, interdisciplinary and multilevel VPH research, are: -Support for integrative research -Training and dissemination activities -Networking activities Sponsors: VPH NoE is supported by The Directorate-General Research (DG RTD) and The Directorate-General Information Society and Media (DG INFSO).
mzR - parser for netCDF mzXML mzData and mzML and mzIdentML files
Software that provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
PAPi - Predict metabolic pathway activity based on metabolomics data
An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation.
Health Protection Agency Culture Collections
Public Health England Culture Collections
Archival database of cell lines and microbial strains. Maintained by Public Health England, the database is used by scientists to determine the effects of various substances on human cells as well as for controls for diagnostic and antimicrobial susceptibility tests.
Human Tissue and Organ for Research Resource (HTORR)
Human Tissue Organ Resource for Research
Human Tissues and Organs for Research (HTOR)
NDRI’s Human Tissue and Organs for Research Resource (HTORR) Program has been funded by the National Institutes of Health (NIH) for over 30 consecutive years to support research programs across multiple disciplines. It is through the HTORR program that NDRI provides academic biomedical investigators with donated normal and diseased human tissues and organs recovered from a diverse donor pool using customized procurement, processing, and preservation and distribution protocols. Our HTORR Program supports academic biomedical research investigators needs by providing: Access to a wide array of human biospecimens from any body system * Customized procurement in a variety of preservation formats including fresh, frozen, and fixed suitable for various analytical techniques * Reduced costs for tissue procurement * Technical support to design your studies utilizing human biospecimens * Letters of support and budgetary information for grant applications
A de novo peptide sequencing algorithm using complementary higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) tandem mass spectra.
Anatomical atlas about structural anatomy of Caenorhabditis elegans. Provides simple interface allowing user to easily navigate through every anatomical structure of worm. Contains set of images which can be sorted by different characteristics: sex, genotype, age, body portion or tissue type. Includes links to other major worm websites and databases. Application for viewing and downloading thousands of unpublished electron micrographs and associated data. These images have been generated by several labs in the C. elegans community, including the MRC, the Hall lab (Center for C. elegans Anatomy), and the Culotti and Riddle labs.
Provides vocabulary for performing several types of annotation - comment, entities annotation (or semantic tags), textual annotation (classic tags), notes, examples, erratum... - on any kind of electronic document (text, images, audio, tables...) and document parts. AO is not providing any domain ontology but it is fostering the reuse of the existing ones for not breaking the principle of scalability of the Semantic Web.
Hepatitis C Virus (HCV) Database Project
The Hepatitis C Virus (HCV) Database Project strives to present HCV-associated genetic and immunologic data in a user-friendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.
National Resource Center for Cephalopods
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The center serves the biomedical research community's increased needs for alternative invertebrate models by maintaining a consistent year-round supply of live cephalopod mollusks. These animals are suitable for a wide range of physiological and molecular biological investigations. Investigations are being conducted in the area of life history related to improved animal husbandry. Further studies focus on improving culture system design through development of computer automation and innovative water filtration technology. Current biomedical research on cephalopods includes neurophysiology of the giant axon; anatomy and neurophysiology of the equilibrium receptor organ as a comparative model of the vestibular system of invertebrates; chemoreception, basic nutrition, and protein metabolism; cellular receptor function; and brain, behavior, and learning. Services Provided: The center has built a computer-automated, environmentally controlled, recirculating seawater laboratory for the purpose of culturing cephalopods. The tank systems can be used to conduct a variety of experiments never before possible with cephalopods. Visiting researchers have access to dedicated facilities, including wet and dry laboratory space, office space, computer support and accommodations, as well as priority access to all available live animal resources. Off-site investigators can have live animals, dissected animal tissues/body fluids from all life stages, and a variety of molecular reagents (gene libraries and clones) delivered year-round. Staff expertise and an extensive literature library are available. All life stages of the squid (Sepioteuthis lessoniana) and the common cuttlefish (Sepia officinalis) are available year-round from laboratory culture populations. The sepiolid squid (Euprymna scolopes) can also be cultured on request. The squid Lolliguncula brevis is available year-round from local waters; the squids Loligo opalescens, L. pealeii, and L. plei can be obtained seasonally on request. The chambered nautilus, Nautilus pompilius, and Octopus bimaculoides are available on request. Animal costs vary by species and size. Any tissue or body fluid from these animals can also be provided. Fees for special services are negotiated on a case-by-case basis.
IBM SPSS Statistics:International Business Machines SPSS Statistics
Statistical Package for the Social Sciences
Software package used for interactive, or batched, statistical analysis in social science, health sciences and marketing. Software platform offers advanced statistical analysis, a library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and deployment into applications.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago.
Tuschl Laboratory: RNA Molecular Biology
RNA is not only a carrier of genetic information, but also a catalyst and a guide for sequence-specific recognition and processing of other RNA molecules. This lab investigates the regulatory mechanisms of RNA interference, RNA-mediated translational control, and nuclear pre-mRNA splicing. Classical and combinatorial biochemical techniques are used to analyze the function of the RNA- and protein-components involved in those processes.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 12, 2017. Web application for annotation and collaboration on web pages. Its features include the ability to highlight words, comment, and share annotated copies of the web page that can be annotated by other users.
Patterns of Gene Expression in Drosophila Embryogenesis
Database of embryonic expression patterns using a high throughput RNA in situ hybridization of the protein-coding genes identified in the Drosophila melanogaster genome with images and controlled vocabulary annotations. At the end of production pipeline gene expression patterns are documented by taking a large number of digital images of individual embryos. The quality and identity of the captured image data are verified by independently derived microarray time-course analysis of gene expression using Affymetrix GeneChip technology. Gene expression patterns are annotated with controlled vocabulary for developmental anatomy of Drosophila embryogenesis. Image, microarray and annotation data are stored in a modified version of Gene Ontology database and the entire dataset is available on the web in browsable and searchable form or MySQL dump can be downloaded. So far, they have examined expression of 7507 genes and documented them with 111184 digital photographs.
HERVd - Human Endogenous Retrovirus database
HERVd is compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects. We created a relatively simple and fast environment for screening human genome for Human endogenous retroviruses ( HERVs). The HERV database now contains retroviruses from more than 90 % of the human genome. Retroviral genomes or parts of their genomes are present in the DNA of many organisms. Studies of endogenous retroviral nucleotide sequences have become an important part of contemporary retrovirology as well as of molecular and cellular biology and genomics. Human endogenous retroviruses (HERVs) are of special interest also because their expression may be associated with several diseases, including cancer. Various groups of HERVs have been reported in the human genome. Their number can range from one copy to many thousand copies.
Commercial supplier of antibodies, reagents, PCR kits, and other materials for scientific research.
Wiki that provides a listing (and associated links) of various formats to store and export annotations. Apparently everyone uses his own proprietary format to store and export annotations. The FDF format (or better its XML variant XFDF) is or was used by Acrobat to store form values and annotations, but third-party implementations focus on the forms-part of FDF instead of the annotations-part. * XML Forms Data Format Specification (XFDF) 2.0 (2007). * iText classes (no full FDF/XFDF implementation) ** FdfReader ** FdfWriter ** XfdfReader * The commercial software Adobe Digital Editions explicitly supports external annotations. The FAQ says Digital Editions supports bookmarks, highlights, and text notes via its bookmarks panel. These annotations are stored in an open XML format separately from publications to enable seamless annotation across PDF- and EPUB-based publications. They will set the stage for future social networking features (such as sharing annotations within a community of readers). * Okular has its own annotation exchange format, similar to PDF annotation (comparison is needed) ** internal API documentation ** There is no file format documentation, but the source code is mainly in the methods AnnotationUtils storeAnnotation and Annotation store * Xournal is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations * Mendeley supports annotations, which can be synced independent from the PDF files they refer to, and exported together with PDFs. There is no documentation of the API and format they use to exchange annotations. * Evernote is worth a view. But proprietary and no Linux client. * iAnnotate seems to be popular on the iPad - can it export and import annotations? In which format? There is a good article by Scott McLeod with screenshots about his use of iAnnotate and Evernote to take notes (June 15, 2010). http://blogs.edweek.org/edweek/LeaderTalk/2010/06/tools_for_school_digital_docum.html
Toolbox at the European Bioinformatics Institute
The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics. These are subdivided into categories in the left menu for convenience. EBI has developed a large number of very useful bioinformatics tools. A few examples include: - Similarity & Homology - the BLAST or FASTA programs can be used to look for sequence similarity and infer homology. - Protein Functional Analysis - InterProScan can be used to search for motifs in your protein sequence. - Proteomic Services NEW - UniProt DAS server allows researchers to show their research results in the context of UniProtKB/Swiss-Prot annotation. - Sequence Analysis - ClustalW2 a sequence alignment tool. - Structural Analysis - MSDfold can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB). - Web Services - provide programmatic access to the various databases and retrieval/analysis services EBI provides. - Tools Miscellaneous - Expression Profiler a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Sponsors: This resource is sponsored by EBI.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine.
A portal to the on-line prediction services at Center for Biological Sequence Analysis. All of the servers are available as interactive input forms, and most of the servers are also available as stand-alone software packages with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services.
COnsensus-DEgenerate Hybride Oligonucleotide Primers
This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Brazilian Ministry of Science Technology and Innovation
Ministry of Science and Technology (Brazil)
Ministry of Science Technology and Innovation (Brazil)
Ministério da Ciência e Tecnologia - Brazil
Computational biology research at Memorial Sloan-Kettering Cancer Center (MSKCC) pursues computational biology research projects and the development of bioinformatics resources in the areas of: sequence-structure analysis; gene regulation; molecular pathways and networks, and diagnostic and prognostic indicators. The mission of cBio is to move the theoretical methods and genome-scale data resources of computational biology into everyday laboratory practice and use, and is reflected in the organization of cBio into research and service components ~ the intention being that new computational methods created through the process of scientific inquiry should be generalized and supported as open-source and shared community resources. Faculty from cBio participate in graduate training provided through the following graduate programs: * Gerstner Sloan-Kettering Graduate School of Biomedical Sciences * Graduate Training Program in Computational Biology and Medicine Integral to much of the research and service work performed by cBio is the creation and use of software tools and data resources. The tools that we have created and utilize provide evidence of our involvement in the following areas: * Cancer Genomics * Data Repositories * iPhone & iPod Touch * microRNAs * Pathways * Protein Function * Text Analysis * Transcription Profiling
Founded in 1976, the Dystonia Medical Research Foundation (DMRF) is a 501(c)3 organization dedicated to serving all people with dystonia and their families. Since its inception, the DMRF has grown from a small family-based foundation into a dynamic membership-driven organization led by a Board of Directors and network of volunteers with personal connections to dystonia. Because dystonia hits so close to home for our directors and volunteers, the DMRF leadership is motivated by an unrelenting drive to find a cure and an unwavering commitment to serving people affected by dystonia. Dystonia Medical Research Foundation (DMRF) prides itself on a long history of supporting dystonia research. Always the primary goal of the DMRF, research has led to a better understanding of dystonia as well as to breakthroughs in genetics and therapeutics.The funding which researchers obtain from the DMRF usually serves as seed money before generating even greater funding from the National Institutes of Health.Beyond the funding of research, the scientific program of the DMRF is multi-faceted, encompassing workshops, a residency elective program, and international medical symposiums, all to further the understanding of dystonia.
The Centre for Vision Research focuses on interdisciplinary research into human and machine vision and visual processes, into vision's interactions with other senses and with motor and cognitive processes, and in applications such as visually-guided robotics or clinical diagnosis and treatment. The Centre for Vision Research includes the following major research themes: - Human Visual Performance - Visual Human-Computer Interaction, Graphics and Virtual Reality - Visual Psychophysics - Eye Movements and Hand-Eye Coordination - Computational Modeling and Computer Vision - Electrophysiology - Clinical and Developmental Studies - Brain Imaging
Database designed for web-based examination of the human erythroid transcriptome. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology. Red blood cells in the circulation arise from hematopoietic stem cells that proliferate as erythroid progenitors and differentiate into erythroid precursor cells in response to the hormone erythropoietin. Messenger RNA was isolated from those cells and used to generate gene libraries. Sequencing several thousand expressed sequence tags (EST) from those libraries was then performed. Those EST and sequences encoding several hundred additional genes with known expression in erythroid cells are compiled here as a database of human erythroid gene activity. The database is organized and linked according to the location of these sequences within the human genome., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
A free set of Matlab and GNU/Octave functions for vision research. It makes it easy to synthesize and show accurately controlled visual and auditory stimuli and interact with the observer.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This interface is for exploring data collected as part of the NIF Neurodegenerative Disease Ontology project. Not generally intended for public consumption yet, but people are welcome to look - large caveat emptor applies. Sponsors: This resource is part of the NIF project.
The mission of Pathway Genomics is to empower you with the most secure, comprehensive and affordable personal genomic information available and to become your partner in utilizing that information to improve your health and wellness. Pathway is the only DNA testing service with an on-site federal and state CLIA-licensed laboratory. This means it offers: - Better Science: Its certified geneticists are on-staff and on-site in our own state-of-the-art laboratory in California. Their 10,600 square foot, high-complexity CLIA licensed lab facility is equipped with the latest high-throughput robotics and Affymetrix, Illumina and Sequenom genotyping equipment. As scientists committed to staying on the cutting-edge, they diligently monitor all new developments in the rapidly evolving DNA research field allowing us to provide you immediate access to more meaningful markers than any other DNA testing firm. - Better Security: Because Pathway Genomics has its own laboratory, your DNA never leaves the building, and is never shared with third parties. At Pathway Genomics the integrity of your genetic material and information are protected. Instead, enjoy the security of our proprietary DNA Lockbox. Everyone has the right to know the secrets hidden within their own DNA. That's why Pathway has created the most secure, comprehensive and affordable way to unlock those secrets. This way you can: - Identify genetic health and drug response - Personalize your medical care - Help your doctor help you - Uncover your ancestral path - Explore the traits that make you unique With Personal DNA Testing, you can take preventative steps to improve your future, and even extend your life. Pathway Genomics provides cutting-edge research and easy-to-read scientific information customized for you, and you alone, based on your genes and your lifestyle. For the first time in human history, modern science has made it possible for you to learn your genetic predisposition for more than 90 diseases and conditions, drug responses and pre-pregnancy carrier status. With this powerful knowledge and our easy-to-understand guidance, you can modify your health regime so that you may live a healthier, longer life. DNA testing will discover more about your personal heritage than you ever thought possible. We uncover your deep ancestry by taking giant leaps into the past, going back more than 10,000 years. We test both your mitochondrial DNA, which is passed down from mother to child and reveals your direct maternal ancestry; and your Y chromosome (males only), which is passed down from father to son and reveals your direct paternal ancestry. If you're like most people, you've always wondered about the genes you have inherited and what traits you will pass on to future generations. Discover your genetically inherited predispositions and characteristics and whether they are beneficial or potentially harmful. You may also find that some traits are simply fun to uncover.
Collection of images from cell type-specific protein expression in retina using BAC transgenic mice. Images from cell type-specific protein expression in retina using BAC transgenic mice from GENSAT project.
Resource of special strains of mice that are valuable tools for genetic analysis of complex diseases. They include panels of recombinant inbred (RI) and chromosome substitution (CS) strains.
An interactive web interface addressed to biologists, allowing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). Its strength is to make NGS analysis without software installation, login or long training period.
New England National Primate Research Center
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. A U.S. Regional Primate Research Center that focuses on AIDS, cancer, neuropsychiatric disorders, drug addiction, and neurodegenerative disease. The Division of Primate Resources provides researchers with the services and facilities to support biomedical research. It offers a broad spectrum of services ranging from analysis of tissue specimens to partnership investigations with leading biomedical research institutions. Outside investigators have access to tissue specimens, organs, blood, skeletal structures, and viral specimens. Services include veterinary services, animals and animal care, surgical and radiographic services, timed mating, biocontainment, pathology services, and professional and technical expertise. Additional diagnostic and research services at NEPRC include testing for antiviral antibodies, DNA cloning, and DNA sequencing. The colony of nine species includes rhesus macaques and other Old World monkeys and New World species including the common marmoset and squirrel monkey. Other species can be obtained. Animals with exceptional characteristics (specific-pathogen-free, timed pregnancy, surgically altered, etc.) can be made available if needed. Scientists wishing to conduct research at the center must have projects reviewed and approved by the center animal allocation committee.
Collaborative project to bring together biochemical pathway databases and research communities focused on plant metabolism. Used to build broad network of plant metabolic pathway databases. Central feature of PMN is PlantCyc, comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.The Human Gene and Protein Database presents SDS-PAGE patterns and other informations of human genes and proteins. The HGPD was constructed from full-length cDNAs. For conversion to Gateway entry clones, we first determined an open reading frame (ORF) region in each cDNA meeting the criteria. Those ORF regions were PCR-amplified utilizing selected resource cDNAs as templates. All the details of the construction and utilization of entry clones will be published elsewhere. Amino acid and nucleotide sequences of an ORF for each cDNA and sequence differences of Gateway entry clones from source cDNAs are presented in the GW: Gateway Summary window. Utilizing those clones with a very efficient cell-free protein synthesis system featuring wheat germ, we have produced a large number of human proteins in vitro. Expressed proteins were detected in almost all cases. Proteins in both total and supernatant fractions are shown in the PE: Protein Expression window. In addition, we have also successfully expressed proteins in HeLa cells and determined subcellular localizations of human proteins. These biological data are presented on the frame of cDNA clusters in the Human Gene and Protein Database. To build the basic frame of HGPD, sequences of FLJ full-length cDNAs and others deposited in public databases (Human ESTs, RefSeq, Ensembl, MGC, etc.) are assembled onto the genome sequences (NCBI Build 35 (UCSC hg17)). The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database (http://flj.hinv.jp/) constructed as a human cDNA sequence analysis database focusing on mRNA varieties caused by variations in transcription start site (TSS) and splicing.
The HGSC has sequenced the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. The genome sequence is being upgraded with additional sequence coverage. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social organization and behavioral traits. This project was proposed to the HGSC by a group of dedicated insect biologists, headed by Gene Robinson. Following a workshop at the HGSC and a honey bee white paper, the HGSC began the project in 2002. A 6-fold coverage WGS, BAC sequence from pooled arrays, and an initial genome assembly (Amel_v1.0) were released beginning in 2003. This has been a challenging project with difficulty in recovering AT-rich regions. The WGS data had lower coverage in AT-rich regions and BAC data from clones showed evidence of internal deletions. Additional reads from AT enriched DNA addressed these underrepresented regions. The current assembly Amel_4.0 was produced with Atlas and includes 2.7 million reads (1.8 Gb) or 7.5x coverage of the (clonable) genome. About 97% of STSs, 98% of ESTs, and 96% of cDNAs are represented in the 231 Mb assembly. About 2,500 reads were also produced from a strain of Africanized honey bee and SNPs were extracted. These were released in dbSNP and the NCBI Trace Archive. Analysis of the genome by a consortium of 20 labs has been completed. This produced a gene list derived from five different methods melded through the GLEAN software. Publications include a main paper in Nature and up to forty companion papers in Genome Research and Insect Molecular Biology. Sponsors: Sequencing of the honey bee is jointly funded by National Human Genome Research Institute (NHGRI) and the Department of Agriculture (USDA). Multiple drones from the same queen (strain DH4) were obtained from Danny Weaver of B. Weaver Apiaries. All libraries were made from DNA isolated from these drones. The honey bee BAC library (CHORI-224) was prepared by Pieter de Jong and Katzutoyo Osoegawa at the Children's Hospital Oakland Research Institute.
Commercial organization which provides life science services and products to researchers. They specialize in gene synthesis, peptide, protein, antibody and preclinical drug development service.
This portal leads to the numerous Wasserman Lab online software tools available for use. The following are list of active Software tools available: - ConSite: Transcription factor binding site detection using phylogenetic footprinting - dbMTN: Multiple Tissue Northern Blot Comparison Tool - Gene Set Builder: A tool for collation, curation and distribution of sets of genes - The Gene Characterization Index: a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described - JASPAR: Transcription Factor Binding Profile Database - MSCAN: Algorithm that detects clusters of transcription factor binding sites in genomic sequences - NHRscan: A computational predictor of nuclear hormone receptor binding sites - oPOSSUM: Web-based analysis of over-represented transcription factor binding sites - ORCA: Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite) - OrthoSeq: Alignment of DNA sequences - PAZAR: An open-access system for the collection and dissemination of regulatory sequence annotation - Phylofoot: Tools for phylogenetic footprinting - RAVEN: Regulatory analysis of Variation in ENhancers - SAGE2Splice: A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome - TFBS: Perl modules for transcription factor binding site detection and analysis - TFCat: TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. - TFe: An online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes - Ulysses: Protein Interactions Conserved Across Evolution
Human Immunodeficiency Virus Molecular Immunology Database
An annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites, plus related tools and information. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, tables and maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interfaces. Only responses to HIV-1 and HIV-2 are included in the database.
Framework for identifying, locating, relating, accessing, integrating, and analyzing information from neuroscience research. Users can search for and add neuroscience-related resources at NIF portal and receive and RRID to track and cite resources within scientific manuscripts.
Describes data from and access to permanent cell lines containing beta-arrestin fluorescent protein biosensors. This assay Bank provides plasmids, cells lines, and resulting data to the NIDA/NIH funded research community in order to better understand and combat addiction.
ORNIS is a database of bird specimens as well as a portal to connect the academic and museum communities involved with studying birds. This project expands on existing infrastructure developed for distributed mammal (MaNIS), amphibian and reptile (HerpNet), and fish (FishNet) databases. Over 5 million bird specimens are housed in North American collections, documenting the composition, distribution, ecology, and systematics of the world's estimated 10,000-16,000 bird species. Millions of additional observational records are held in diverse data sets. ORNIS addresses the urgent call for increased access to these data in an open and collaborative manner, and involves development of a suite of online software tools for data analysis and error-checking. This project expands on existing infrastructure developed for distributed mammal (MaNIS), amphibian and reptile (HerpNet), and fish (FishNet) databases. Improved access to avian data sets will allow predictive uses to reveal patterns and processes of evolutionary and ecological phenomena that have not been apparent heretofore. Along with similar infrastructures for other vertebrate groups, it also will enable detailed and synthetic knowledge of the earth's biodiversity for tracking climate change, emerging diseases (e.g., West Nile Virus), and other conservation challenges for species in the 21st century.
Neuroscience Education Resources Virtual Encycloportal
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Society for Neuroscience (SfN) provides this Web site, Neuroscience Education Resources Virtual Encycloportal (NERVE), to advance neuroscience teaching and educational efforts. SfN is a nonprofit association of more than 38,000 researchers and professionals, believes K-12 educators and vital partners for engaging the next generation of researchers. NERVE gives access to information and tools for teaching about the nervous system and related health issues. The goal of NERVE is to provide a gateway to credible information from government, nonprofit and other respected sources. Society scientists and educators have reviewed information for appropriateness but responsibility for content remains that of the originating author or organizations. NERVE gives access to information and tools for teaching about the nervous system and related health issues.
CODEHOP: COnsensus-DEgenerate Hybrid Oligonucleotide Primers
COnsensus-DEgenerate Hybrid Oligonucleotide Primers
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Service to design PCR primers from protein multiple sequence alignments. NOTICE: This version of CODEHOP is no longer maintained.
Schziophrenia Research Forum - A Catalyst for Creative Thinking
The mission of the SRF is to help in the search for causes, treatments, and understanding of the devastating disease of schizophrenia. Our goal is to foster collaboration among researchers by providing an international online forum where ideas, research news, and data can be presented and discussed. The website is intended to bring together scientists working specifically on schizophrenia, scientists researching related diseases, and basic scientists whose work can shed light on these diseases. In this way, we hope that the Schizophrenia Research Forum will be a catalyst for creative thinking in the quest to understand a deeply complex disease. It is our goal to create and maintain up-to-date content of the highest quality. The website is free of charge to users, independent of industry sponsorship, and open to the public. Though geared toward researchers, we welcome other visitorspeople with mental illnesses, families, the media, and others who need accurate information on research into schizophrenia. We do, however, require that users who wish to post comments and other materials be registered members. All such materials are subject to approval by the editorial team. As a forum, we encourage participation and welcome feedback from the community.
Development of a Specific-Pathogen-Free Baboon Colony
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Program developing a self-sustaining colony of baboons free of all known herpesviruses, four retroviruses, and SV40 for research. When the program is fully developed, they will provide healthy, behaviorally normal, SPF baboons that are free of all known herpes viruses, four retroviruses, and SV40. To accomplish this goal, the center has established in collaboration with co-investigators and consultants serological and PCR tests for each of the 11 target viruses. These baboon viruses include six herpesviruses (analogs of human HSV, VZV, CMV, HHV6, EBV, and HHV8), four retroviruses (simian foamy virus, SRV/D, SIV, and STLV), and SV40. Twenty-four infant baboons are being recruited into the SPF program in each of the first five years, for a final total of at least 66 SPF baboons. All infants will be repeatedly tested for each of the target viruses. At one month of age, larger social groups of 4-6 SPF animals are formed. Beginning at 2-3 years of age, SPF animals will be integrated into larger socially compatible groups. These groups will eventually mature into breeding harems of SPF animals. This approach provides infants with age-matched companions for socialization during their early period of development, minimizes opportunities for transmission of viruses to the infants from adult animals, and allows for the simultaneous elimination of many different viruses from SPF animals.
CNVassoc: Association analysis of CNV data
Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis.
An ontological representation of protein-related entities, explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. PRO encompasses three sub-ontologies: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).
Public university in Germany that offers degrees in law, management and business, the arts and humanities, and human sciences.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.The HIV Resistance Mutation Database is a resource that allows users to download HIV sequences and information on HIV drug resistance and mutations. Users must download the data from either of two files available on the site, as the online portion of the database is no longer available. The system requires Mac OS9 to work. The DATABASES folder contains the current versions of 2 databases copied from resdb: BestDefined, and resistrelated. The BestDefined database is a list of the Brander epitopes. The resistrelated database is a compilation of HIV drug resistance mutations. The Bib and biblio files are the associated references for these databases. The RESIST_HTML folder contains the html files used by the resistance database web site.
British charity and fundraiser for cardiovascular research.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. HIV Sequence Database is a database of annotated HIV sequences, plus a variety of tools and information for researchers studying HIV and SIV. The main aim of this website is to provide easy access to our sequence database, alignments, and the tools and interfaces we have produced. The HIV Sequence Database focuses on five primary goals: * Collecting HIV and SIV sequence data (all sequences since 1987) * Curating and annotating this data, and making it available to the scientific community * Computer analysis of HIV and related sequences * Production of software for the analysis of (sequence) data * The data and analyses on this site and published in a yearly printed publication, the HIV sequence Compendium, which is available free of charge.
The Lowe Syndrome Mutation Database is now being maintained by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. A database of mutations causing Lowe syndrome. Information on new mutations may be submitted online. Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. genetics
ISCoS promotes the highest standard of care in the practice of spinal cord injury for men, women and children throughout the world. Through its medical and multi disciplinary team of Professionals ISCoS endeavours to foster education, research and clinical excellence. ISCoS has a membership of over 1,000 Clinicians and Scientists from 87 countries. They regularly update their knowledge at the Annual Scientific Meeting held in a different country each year. Goals of ISCoS: :- Serve as an international impartial, non-political and non-profit making association whose purpose is to study all problems relating to traumatic and non-traumatic lesions of the spinal cord. This includes causes, prevention, basic and clinical research, medical and surgical management, clinical practice, education, rehabilitation and social reintegration. This society will function in close collaboration with other national and international bodies, thereby encouraging the most efficient use of available resources. :- Provide a scientific exchange among its members and others by collecting and disseminating information through publications, correspondence, exhibits, regional and international seminars, symposia, conferences and otherwise. :- Advise, encourage, promote and when requested, assist in efforts to co-ordinate or guide research, development and evaluation activities related to spinal cord lesions throughout the world. :- Advise, encourage, guide and support the efforts of those responsible for the care of patients involved and when requested, correlate these activities throughout the world. :- Advise, encourage, guide and support the efforts of those responsible for the education and training of medical professionals and professionals allied to medicine and when requested, correlate these activities throughout the world.
European Bioinformatics Institute - ClustalW2
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF.
University of Colorado is a four-campus system that includes the University of Colorado Boulder, the University of Colorado Colorado Springs, the University of Colorado Denver and the University of Colorado Anschutz Medical Campus.
University of Florida Labs and Facilities
Science Exchange University of Florida Labs and Facilities
Portal that lists and provides information on core facilities located at the University of Florida.
Database of mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. The mitochondrion plays a central role in cellular metabolism, and evidence of mitochondrial involvement in a number of different human diseases is increasing. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases. Mitochondrial DNA Sequence: A graphical tool was developed to visualize the human mitochondrial DNA sequences that highlight coding regions for RNAs and proteins. Disease susceptible mutations are also noted in the sequence. Mitochondrial DNA Polymorphism: Human mitochondrial sequences of different ethnic groups were obtained from the Human Mitochondrial Genome Database. A DNA sequence analysis tool was developed to compare polymorphisms of different human mitochondrial DNA sequences. This tool allows the user to select mitochondrial sequences from any two human populations and compare them for sequences variations. Mitochondrial proteins related diseases: Malfunction of mitochondrial proteins affect many cells from brain, heart, liver, skeletal muscles, kidney, and the endocrine and the respiratory systems which lead to many diseases. Relevant information for mitochondrial related diseases from OMIM, the Neuromuscular Disease Center and MITOMAP are gathered, and mitochondrion-associated diseases are grouped, categorized, and linked to OMIM. 3-D Structures of Mitochondrial proteins: The available 3D structures for mitochondrial proteins are presented through a custom-made interface. A concise HTML page is generated for reporting the structural details and the associated information obtained from relevant web sites (PDBREPORT, Interatomic Contacts of Structural Units (CSU), PROCHECK, Ligand Protein Contacts (LPC), PROMOTIF and CastP). References are linked to the PubMed site. The 3-D structures are presented through the use of a Kinemage.
MATLAB toolbox for deep-brain-stimulation (DBS) electrode reconstructions and visualizations based on postoperative MRI and computed tomography (CT) imaging. The toolbox also facilitates visualization of localization results in 2D/3D, analysis of DBS-electrode placement's effects on clinical results, simulation of DBS stimulations, diffusion tensor imaging (DTI) based connectivity estimates, and fiber-tracking from the VAT to other brain regions (connectomic surgery).
Simulation software that includes a parallel discrete event simulation kernel for running models of spiking neurons on a cluster of workstations. Models are specified using NeuroML, and visualized using Java2D. Simulation components are distributed across a parallel machine or network and communicate using timestamped events. The successor NEOSIM2 project under the NeuroGems umbrella at Edinburgh University (http://www.neurogems.org) continues to distribute the software, http://www.neurogems.org/neosim2/ The NEOSIM project includes: * a parallel discrete event simulation kernel for running models of spiking neural networks on clusters of machines. * a modules kit for extending the behavior of neurons and connectivity patterns. * a user interface for building and running simulations. OS: Linux, MS-Windows
ATGC: Montpellier bioinformatics platform
ATGC - South of France bioinformatics platform
A bioinformatics platform that is a joint project of several South of France laboratories with available services based on their expertise, issued from their research activities which involve phylogenetics, population genetics, molecular evolution, genome dynamics, comparative and functional genomics, and transcriptome analysis. Most of the software and databases on ATGC are (co)authored by researchers from South of France teams. Some are widely used and highly cited. South of France laboratories: * CRBM (transcriptomes and stem cells). * IBC (computational biology). * MiVEGEC (evolution and phylogeny). * LGDP (plant genomics). * LIRMM (computer science). * South Green (plant genomics).
CVXOPT - Python Software for Convex Optimization
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Software package for convex optimization based on the Python programming language. It can be used with the interactive Python interpreter, on the command line by executing Python scripts, or integrated in other software via Python extension modules. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Pythons extensive standard library and on the strengths of Python as a high-level programming language. Current version includes the following features: * efficient Python classes for dense and sparse matrices (real and complex), with Python indexing and slicing and overloaded operations for matrix arithmetic * an interface to most of the double-precision real and complex BLAS * an interface to LAPACK routines for solving linear equations and least-squares problems, matrix factorizations (LU, Cholesky, LDLT and QR), symmetric eigenvalue and singular value decomposition, and Schur factorization * an interface to the fast Fourier transform routines from FFTW * interfaces to the sparse LU and Cholesky solvers from UMFPACK and CHOLMOD * routines for linear, second-order cone, and semidefinite programming problems * routines for nonlinear convex optimization * interfaces to the linear programming solver in GLPK, the semidefinite programming solver in DSDP5, and the linear, quadratic and second-order cone programming solvers in MOSEK * a modeling tool for specifying convex piecewise-linear optimization problems. A platform-independent source package and a binary Windows installer are available from the Download section. CVXOPT is also available precompiled for the major platforms: * Debian Linux * Ubuntu Linux * Fedora Linux * Python(x,y) for Microsoft Windows CVXOPT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database
Lafora Progressive Myoclonus Epilepsy Mutation Polymorphism Database
The Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database
The Lafora Progressive Myoclonus Epilepsy Mutation Polymorphism Database
The Lafora database is a repository of information related to progressive myoclonus epilepsy mutation and polymorphism data. Users may view all mutations in the database(Mutations of EPM2A and NHLRC1(EPM2B)), click on individual exons for mutations, or search the database by keyword. Nucleotide and amino acids positions were assigned based on the GenBank reference sequence NM_005670 for EPM2A and NM_198586 for EPM2B. The data can be viewed using the XRT Table Browser, and where possible, links to external sources such as NCBI, PubMed are provided. At this time, the database is under development. The BioXRT (Cross-Referenced Tables) Table Browser is a highly configurable tool for viewing complex, table based information. The tables can be displayed using pre-set options, or customized to view arbitrary subsets of rows, columns or other features.
Hollywood.mit.edu - Alternatively spliced mRNA
Database built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags for human and mouse. It links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. A query tool allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser.
Assembly/Alignment/Annotation of 12 Related Drosophila Species
A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org.
A DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way.
Mass spectral peak labeling software developed for proteomics research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase.
Mind Research Network for Neuroscience Discovery
Non-profit organization focused on imaging technology that is dedicated to advancing the diagnosis and treatment of mental illness and brain injury. MRN consists of an interdisciplinary association of scientists located at universities, national laboratories and research centers around the world and is focused on imaging technology and its emergence as an integral element of neuroscience investigation. The MRNs initial plan called for the building of state-of-the-art magnetic resonance imaging (MRI) and magnetoencephalogram (MEG) neuroimaging systems to be applied to studies of mental illness. This important task was carried out by Minds initial collaborators: Massachusetts General Hospitals Martinos Biomedical Imaging Center (Harvard and MIT), the University of Minnesota, the University of New Mexico, and Los Alamos National Laboratory. Since both the Network and the mission have expanded beyond building neuroimaging tools, a comprehensive understanding of mental illness and more fundamental and systematic understanding of the brain, is possible. The MRN Mobile Imaging system is a custom designed one-of-a-kind facility.
Advanced Neuroscience Imaging Research Laboratory Software Packages
Advanced Neuroscience Imaging Research Software
Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.
An R package for array comparative genomic hybridization (aCGH) dye bias normalization.
Representative organization for postdoctoral scholars in the United States. It is member-driven and non-profit.
A software tool that can compare several search engines' results and combine them together.
Biotechnological company that produces and supplies materials to oxidative stress and aging researchers.
Charles University; Prague; Czech Republic
Research university located in Prague, Czech Republic.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2025. Database that provides access to population, housing, economic, and geographic data from several censuses and surveys about the United States, Puerto Rico and the Island Areas. Census data may be compiled into tables, maps and downloadable files, which can be viewed or printed. A large selection of pre-made tables and maps satisfies many information requests. By law, no one is permitted to reveal information from these censuses and surveys that could identify any person, household, or business. The following data are available: * American Community Survey * ACS Content Review * American Housing Survey * Annual Economic Surveys * Annual Surveys of Governments * Census of Governments * Decennial Census * Economic Census * Equal Employment Opportunity (EEO) Tabulation * Population Estimates Program * Puerto Rico Community Survey
Membership supported, nonprofit organization established dedicated to improving the lives of persons affected by ataxia through support, education, and research. The Foundation's primary purpose is to support promising ataxia research and to provide vital programs and services for ataxia families. The Foundation first began direct funding of ataxia research through the NAF Research Seed-Money Program. Since that time, the Foundation has established additional research programs which have included programs such as the NAF Young Investigator Award, the NAF Fellowship Award and other research initiatives. NAF research programs continue to fund promising ataxia research studies throughout the world. The Foundation supports research in dominant ataxia (including SCAs), recessive ataxia (including Friedreich's) and sporadic ataxia. The Foundation has developed an extensive library of NAF brochures, fact sheets, books, and videos on ataxia. Also available to its members is the Foundation's quarterly news publication, Generations. This 48 page ataxia news magazine provides the latest information on ataxia research, articles on living with ataxia, personal accounts from ataxia families throughout the United States, and much more.
Office of Intramural Training and Education
NIH Office of Intramural Training and Education
NIH Office of Intramural Training and Education (OITE)
Division of the Office of Intramural Research (OIR), Office of the Director (OD) which provides services to current trainees in programs in the NIH Intramural Research Program, potential applicants to training programs at the NIH, investigators and staff at the NIH, and trainees and investigators outside the NIH.
A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment.
CGHnormaliter - Normalization of array CGH data with imbalanced aberrations.
Software for normalization and centralization of array comparative genomic hybridization (aCGH) data with imbalanced aberrations. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).
AT&T Labs Research - software tools: labs research
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023.Software tools that have been developed by AT&T Labs researchers. In addition to the software tools available through Open Source and Non-Commercial licenses as listed on this page, AT&T has additional software and technology solutions available for licensing. Please reference the individual project web pages for specific license agreements. If an available license agreement does not meet your needs, please contact attip (at) att.com for assistance with a customized license. Open Source Licenses * AST: Advanced Software Technologies Open Source Collection * Cdt: Container Data Types Library * ECharts: A state machine-based programming language * GGobi: Data visualization for high-dimensional data * GSDjVu/DjVuDigital: Ghostscript driver to convert PS and PDF files to DjVu files * Graphviz: Tools for viewing and interacting with graph diagrams * PADS: Processing Arbitrary Data Streams * Sfio: Portable library for performing I/O * UWIN: Unix on Windows 95 and NT Machines * Vcodex: Software package for data transformation * WSP: Web Scraping Proxy * Yoix: The Yoix Scripting Language and Interpreter * iPlots: Interactive graphics for data analysis in R * vmalloc: Region Memory Allocator Non-Commercial Binary Licenses * BoosTexter: A general purpose machine-learning program * Hancock: A language for processing large-scale data Non-Commercial Source Licenses * ASDT: The AT&T Statistical Dialog Toolkit (ASDT) * Hancock: A language for processing large-scale data
Human Potential Tumor Associated Antigen database
To accelerate the process of tumor antigen discovery, we generated a publicly available Human Potential Tumor Associated Antigen database (HPtaa) with pTAAs identified by insilico computing. 3518 potential targets have been included in the database, which is freely available to academic users. It successfully screened out 41 of 82 known Cancer-Testis antigens, 6 of 18 differentiation antigen, 2 of 2 oncofetal antigen, and 7 of 12 FDA approved cancer markers that have Gene ID, therefore will provide a good platform for identification of cancer target genes. This database utilizes expression data from various expression platforms, including carefully chosen publicly available microarray expression data, GEO SAGE data, Unigene expression data. In addition, other relevant databases required for TAA discovery such as CGAP, CCDS, gene ontology database etc, were also incorporated. In order to integrate different expression platforms together, various strategies and algorithms have been developed. Known tumor antigens are gathered from literature and serve as training sets. A total tumor specificity penalty was computed from positive clue penalty for differential expression in human cancers, the corresponding differential ratio, and normal tissue restriction penalty for each gene. We hope this database will help with the process of cancer immunome identification, thus help with improving the diagnosis and treatment of human carcinomas.
HS3D - Homo Sapiens Splice Sites Dataset
HS3D (Homo Sapiens Splice Sites Dataset)
Data set of Homo Sapiens Exons, Introns and Splice regions extracted from GenBank Rel.123 with an aim of giving standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization. From the complete GenBank (Primate Sequences Division) Rel.123 (162,557 entries), entries of Human Nuclear DNA including Complete CDS and more than one Exon have been selected, and 4523 exons and 3802 introns have been extracted from these entries. Details about extracted exons and introns are reported (Locus, number, Start and End position in the entry, sequence, length, G+C content, presence of not AGCT data (nucleotide scan check)). Statistics are also reported (overall nucleotides, average G+C content, nucleotide scan check results, number of not GT starting / AG ending introns, minimum / maximum / average length, length standard deviation). 3799+3799 donor and acceptor sites, as windows of 140 nucleotides around each splice site have been extracted. After discarding sequences not including canonical GTAG junctions (65+74), including insufficient data (not enough material for a 140 nucleotide window) (686+589), including not AGCT bases (29+30), and redundant (218+226) there are 2796+ 2880 windows. Finally, there are 271,937 + 332,296 windows of false splice sites, selected by searching canonical GTAG pairs in not splicing positions. The false sites in a range of +/- 60 from a true splice site are marked as proximal.
A biopharmaceutical company engaged in the discovery and development of Nanobodies, a novel class of antibody-derived therapeutic proteins based on single-domain antibody fragments, for a range of serious life-threatening human diseases including inflammation, hematology, oncology and pulmonary disease.
Type-III-Secretion-System related database
Database aimed to annotate all bacterial Type III Secretion System (T3SS) related structure, effector, regulator, and auxiliary genes.
Open-source bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data. Users can choose from a variety of analysis protocols that utilize PacBio and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.
National Center for Toxicological Research
National Center for Toxicological Research (NCTR)
The National Center for Toxicological Research (NCTR), FDA's internationally recognized research center, plays a critical role in FDA's mission. The unique scientific expertise of NCTR is critical in supporting FDA product centers and their regulatory roles. The NCTR is an important research component of the FDA that plays a critical role in the missions of FDA and DHHS to promote and protect public health. * NCTRin partnership with researchers from government, academia, and industrydevelops, refines, and applies current and emerging technologies to improve safety evaluations of FDA-regulated products. * NCTR fosters national and international collaborations to improve and protect public health and enhance the quality of life for the American people. Through the training of scientists from around the world, as well as FDA staff, NCTR researchers spread the principles of regulatory science globally. * NCTR conducts FDA research with the goal to develop a scientifically sound basis for regulatory decisions and reduce risks associated with FDA-regulated products. NCTR represents the FDA on key committees of the National Toxicology Program (NTP), a program that evaluates the effects of chemicals on health. Over the past 30 years, the NTP and NCTR have conducted studies on FDA-nominated compounds, providing data to support science-based regulatory decisions.
Cross Platform Transcriptome Analysis (CPTRA)
Software package for analyzing transcriptome sequencing data from different sequencing platforms.
mtDB - Human Mitochondrial Genome Database
A database of human mitochondrial genomes containing mtDNA sequences, polymorphic sites, and the ability to search for specific variants. It contains 1865 complete sequences and 839 coding region sequences.
Research institute which investigates chronic disease and its triggers.
Human p53 Human hprt Rodent lacI and Rodent lacZ Databases
Human p53 Human hprt Rodent lacI and Rodent lacZ Databases and Software
Human p53 Human hprt Rodent lacI Rodent lacZ Databases
This site provides access to mutation databases and software including the human hprt database, Human p53 database, Transgenic lacZ database, and Transgenic lacI database. Other avaialble programs include Mutational spectra comparison and relational database data entry. The most recent hprt database contains information on over 2,300 mutations found in vivo and in vitro in the human hprt gene and runs under Windows. The version for evaluation on this homepage has fewer mutations and is a DOS program. The database contains information on the mutagen, dose, spontaneous and induced mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, cell type, citation, and other items. In addition, information regarding the cause and effect of mutations affecting splicing is given. Routines have been developed for the analysis of single base substitutions. The p53 database contains information on nearly 5,867 mutations found in the human p53 gene. The database itself has been updated in April of 1997. The database contains information on the cancer type, loss of heterozygosity, base position, amino acid position, amino acid change, local DNA sequence,citation, and other items. Routines have been developed for the analysis of single base substitutions. The Transgenic lacZ database contains information on 405 mutations found in vivo in the transgenic lacZ gene. It has last been updated in January of 1998. It provides information on the mutagen, dose, organ, mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, citation, and other items. The Transgenic lacI database contains information on over 1700 mutations found in vivo in the transgenic lacI gene and on nearly 8000 mutations in the lacI gene in native E. coli. The database was updated in January 1998. The database contains information on the mutagen, dose, organ, mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, citation, and other items. Routines have been developed for the analysis of single base substitutions for each of the databases. The software runs only on IBM-compatible PCs.
A community portal for sharing and integration of human protein data that allows research laboratories to contribute and maintain protein annotations. The Human Protein Reference Database (HPRD) integrates data that is deposited along with the existing literature curated information in the context of an individual protein. Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships can be submitted.
Database of interrupted coding sequences detected by a similarity-based approach in complete prokaryotic genomes. The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence. To facilitate the experimental characterization of ICDS, optimized primers are proposed for re-sequencing purposes. The database is accessible by BLAST search or by genome. 118 Genomes are available in the database.
AllerHunter: Cross-reactive Allergen Prediction Home
AllerHunter: Cross-reactive Allergen Prediction Program
A cross-reactive allergen prediction program built on a combination of Support Vector Machine (SVM) and pairwise sequence similarity. Cross-reactivity is based on similarity of proteins to allergens. However, not all proteins with similar sequence or structure to known allergens are cross-reactive allergens. AllerHunter aims to predict allergens and non-allergens with high sensitivity and specificity, without compromising efficiency at classification of proteins with similar sequence to known allergens. There are distinct differences between prediction of allergenicity and cross-reactivity of allergens. Allergenicity is the immunogenic potential of an allergen to induce IgE antibody production, whereas cross-reactivity is the potential of a substance to bind to IgE previously induced by a known allergen. It is difficult to predict allergenicity because causes of immunogenicity of allergens are still not completely clear. However it is possible to predict cross-reactivity since it implies similarity in IgE binding sites. Please provide protein sequence in fasta format.
AltAnalyze - Alternative Splicing Analysis Tool
Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.
Human Reference Genome - J. Craig Venter Institute
Database for the diploid genome sequence of J. Craig Venter as published in PLoS Biology. Its graphical interface depicts the haploid sequence with SNP and insertion/deletion DNA variants as identified by genome assembly and comparison methods, as well as represents the haplotype blocks from which diploid genome sequence can be inferred and gene annotations.
Mutant Mouse Resource and Research Center
National public repository system for mutant mice. Archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by biomedical research community. Includes breeding/distribution facilities and information coordinating center. Mice strains are cryopreserved, unless live colony must be established. Live mice are supplied from production colony, from colony recovered from cryopreservation, or via micro-injection of cell line into host blastocysts. MMRRC member facilities also develop technologies to improve handling of mutant mice, including advances in assisted reproductive techniques, cryobiology, genetic analysis, phenotyping and infectious disease diagnostics.
HvrBase++ is the improved and extended version of HvrBase. Extensions are made by adding more population-based sequence samples from all primates including humans. The current collection comprises 13,873 hypervariable region I (HVRI) sequences and 4940 hypervariable region II (HVRII) sequences. In addition, we included 1376 complete mitochondrial genomes, 205 sequences from X-chromosomal loci and 202 sequences from autosomal chromosomes 1, 8, 11 and 16. In order to reduce the introduction of erroneous data into HvrBase++, we have developed a procedure that monitors GenBank for new versions of the current data in HvrBase++ and automatically updates the collection if necessary. For the stored sequences, supplementary information such as geographic origin, population affiliation and language of the sequence donor can be retrieved. As a new key feature, HvrBase++ provides an interactive graphical tool to easily access data from dynamically created geographical maps.
An American global biotechnology company that manufactures drug therapies for cancer and inflammatory disorders. The company's major products are Thalomid (thalidomide), which is approved for the acute treatment of the cutaneous manifestations of moderate to severe erythema nodosum leprosum (ENL), as well as in combination with dexamethasone for patients with newly diagnosed multiple myeloma, and Revlimid (lenalidomide), for which the company has received FDA and EMA approval in combination with dexamethasone for the treatment of multiple myeloma patients who have received at least one prior therapy. Revlimid is also approved in the United States for the treatment of patients with transfusion-dependent anemia due to Low- or Intermediate-1-risk Myelodysplastic syndromes (MDS) associated with a deletion 5q cytogenetic abnormality with or without additional cytogenetic abnormalities. Both Thalomid and Revlimid are sold through proprietary risk-management distribution programs to ensure safe and appropriate use of these pharmaceuticals. Vidaza is approved for the treatment of patients with MDS. Celgene also receives royalties from Novartis Pharma AG on sales of the entire Ritalin family of drugs, which are widely used to treat Attention Deficit Hyperactivity Disorder (ADHD). (Adapted from Wikipedia) There are numerous clinical trials at major medical centers using compounds from Celgene. Investigational compounds are being studied for patients with incurable hematological and solid tumor cancers, including multiple myeloma, myelodysplastic syndromes, chronic lymphocyte leukemia (CLL), non-Hodgkin's lymphoma (NHL), glioblastoma, and ovarian, pancreatic and prostate cancer.
A freeware Macintosh program for simulating and testing polymerase chain reactions (PCRs) that can also be used as a tool for designing primers by evaluating candidates. It's a program to simulate the polymerase chain reaction. You specify a target sequence and primers, and it predicts the result. It's useful for planning experiments, testing primers and teaching about PCR. Amplify draws a diagram of the predicted results showing all expected primer matches and amplified fragments. Clicking on any of these objects gives additional information about them.
Database of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered predictions. It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available.
SHEsis: Analysis Tools For Random Samples
A powerful web-based platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci.
chimera - A package for secondary analysis of fusion products
A Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools. The current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, tophat-fusion-post and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools.
The Grass Foundation is a small, not-for-profit, private foundation chartered to support research and education in neuroscience. The hallmark program of The Grass Foundation is the Grass Fellowship Program at the Marine Biological Laboratory in Woods Hole, Massachusetts. This program provides a first opportunity for neuroscientists during late stages of predoctoral training or during postdoctoral years to conduct independent research for scientific discovery on their own at the MBL each summer. While sharing the Grass Laboratory, Fellows function as an intellectual and social group within the MBL community. The number of fellowships awarded varies annually. Additional programs supported by The Grass Foundation include the Robert S. Morison Fellowship, The Grass-MBL Faculty Grant Program, the Ricardo Miledi Program for Neuroscience Training, several neuroscience courses at the MBL, and yearly funding of a few lectureships and prizes. Please see our Program Grants section for more information.
An application for the automatic segmentation and tracing of three-dimensional neuronal images.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 23, 2013. Database for resting state functional connectivity studies. Functional connectivity has shown tremendous promise in mapping the intrinsic functional topography of the brain, evaluating neuroanatomical models, and investigating neurological and psychiatric disease. Brainscape includes a repository of public and private data and an analysis engine for exploring the correlation structure of spontaneous fluctuations in the fMRI BOLD signal. (DICOM data is the image format that can be uploaded.) With Brainscape you can upload, analyze, and share your own data. You can search for, download, and analyze studies in the repository of shared data. The analysis engine works by selecting one or more studies, typing in the coordinates of a brain region of interest, and the seed-region correlation engine computes the correlation structure across the whole brain. (T1, T2 and EPI data are the scan types Brainscape can process.) You decide who can access your data. You can keep it to yourself, share with select colleagues, or share it with everyone. The Brainscape database and analysis tools are open source and freely available.
Software tool as simulator for spiking neural network models that focuses on dynamics, size and structure of neural systems rather than on exact morphology of individual neurons. Used for any size spiking neurons networks including models of information processing, models of network activity dynamics, models of learning and plasticity.
International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.
Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets.
A peer reviewed, PubMed indexed journal devoted to the publication of biological research in a video format.
Australian New Zealand Clinical Trials Registry
Register of clinical trials being undertaken in Australia, New Zealand and elsewhere including trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. In 2007 the ANZCTR was one of the first three trial registries to be recognized by the World Health Organisation International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognizes registries as Primary Registries if they fulfill certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch Studies should be registered prospectively, i.e. before the first patient is recruited. The registry records a trial's * objectives * main design features * sample size and recruitment status * treatments under investigation * outcomes being assessed * principal investigator * contact person Key points about the ANZCTR * Publicly owned, managed by a not-for-profit organization * All details of trials registered on the ANZCTR are made publicly available * Registration is voluntary, but if a registrant chooses to register a trial, certain fields are mandatory * Registration is free of charge * Responsibility for registration lies with the Sponsor
Program for Population Genetics Software
A tool for SNP Search and downloading with local management. It also offers flanking sequence downloading and automatic SNP filtering. It requires Windows and .NET Framework.
Babelomics 4: Gene Expression and Functional Profiling Analysis Suite
An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool
University of Bergen Computational Biology Unit
An inter-department center that conducts bioinformatics research and expands the interface between bioinformatics and experimental biological and biomedical research. The unit is closely associated with the the Bioinformatics group at the Department of Informatics (II) and has tight links with the Sars Centre for Marine Molecular biology (SARS) and the Department of Molecular Biology (MBI). Six research groups are currently associated with CBU with projects that include sequence and structure analysis, molecular evolution, genome annotation and genomics data analysis. CBU also provides services and contributes to bioinformatics education primarily through training courses.
International ImMunoGeneTics/Human Leukocyte Antigen Database
Database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. It currently contains 9,310 allele sequences (2013) along with detailed information concerning the material from which the sequence was derived and data on the validation of the sequences. It is established procedure for authors to submit the sequences directly to the IMGT/HLA Database for checking and assignment of an official name prior to publication, this avoids the problems associated with renaming published sequences and the confusion of multiple names for the same sequence. The need for reasonably rapid publication of new HLA allele sequences has necessitated an annual meeting of the WHO Nomenclature Committee for Factors of the HLA System. Additionally they now publish monthly HLA nomenclature updates both in journals and online to provide quick and easy access to new sequence information. The IMGT/HLA Database is part of the international ImMunoGeneTics project. In collaboration with the Imperial Cancer Research Fund (ICRF) and European Bioinformatics Institute (EBI) they have developed an Oracle database to house the HLA sequences in such a way as to allow users to present complex queries about the sequence, sequence features, references, contacts and allele designations to the database via a graphical user interface over the web. The IMGT/HLA Database Submission Tool allows direct submission of sequences to the WHO HLA Nomenclature Committee for Factors of the HLA System. The IMGT/HLA Database provides an FTP site for the retrieval of sequences in a number of pre-formatted files.
Algorithm based on a Markov random field (MRF) model that uses additional gene coexpression data to enhance differential gene expression prediction power. It is able to call differentially expressed (DE) genes but also assign confidence scores to each inferred DE gene.
Brain Molecular Anatomy Project cDNA Resources
As part of BMAP gene discovery efforts, mouse brain cDNA libraries and Expressed Sequence Tags (ESTs) have been generated. Through this project a BMAP mouse brain UniGene set consisting of over 24,000 non-redundant members of unique clusters has been developed from EST sequencing of more than 50,000 cDNA clones from 10 regions of adult mouse brain, spinal cord, and retina (http://brainEST.eng.uiowa.edu/). In 2001, NIMH along with NICHD, NIDDK, and NIDA, awarded a contract to the University of Iowa ( M.B. Soares, PI) to isolate full-length cDNA clones corresponding to genes expressed in the developing mouse nervous system and determine their full-coding sequences. The BMAP mouse brain EST sequences can be accessed at NCBI's dbEST database (http://www.ncbi.nlm.nih.gov/dbEST/). Arrayed sets of BMAP mouse brain UniGenes and cDNA libraries, and individual BMAP cDNA clones can be purchased from Open Biosystems, Huntsville, AL (http://www.openbiosystems.com
mass spectrometry based proteomics information management system
ms-lims: mass spectrometry based proteomics information management system
Software that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.
Software tool to visualize and analyse ChIP-on-chip array data. Main features: * Import of data from Nimblegen arrays (other formats can be added if people send us examples) * Normalization of data (both per array and per probe) * Various data plotting options to assess data quality and the effectiveness of normalization * Creation of data groups for visualization and analysis * Visualization of data against an annotated genome. * Statistical analysis of data to find probes of interest * Creation of reports containing probes, data and genome annotation Note: This project is no longer being developed, but critical bug fixes will still be provided
Penn Induced Pluripotent Stem Cell Core Facility
Core facility that provides the following services: Induced pluripotent stem cell derivation, Characterization of induced pluripotent stem cells, Hands-on training course for embryonic / induced pluripotent stem cell culture. Additionally, the Core has several established human iPS cell lines for purchase for research purposes by non-profit institutions. Please contact the director for available cell lines. The goals of the Core are: * to facilitate derivation of induced pluripotent stem (iPS) cells from somatic cells; * to provide expertise and training to researchers in embryonic stem (ES)/iPS cell culture; * and to serve as a resource for sharing iPS cell lines and iPSC technology within the UPenn and the broader scientific community.
gel2de - Correlation analysis of gel electrophoresis data
Software application for performing pixel-by-pixel correlation analysis on a set of gel images from two-dimensional gel electrophoresis and a set of clinical parameters for a population. The application is written in C++, and has been tested on Windows, although it in principle should compile cross platform using CMake.
Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.
Elementary Objects of the Nervous System
EONS (Elementary Objects of the Nervous System)
EONS-The integrated synaptic modeling platform
Modeling platform to study the basic interactions between synaptic elements that allows the user to study qualitatively, and also quantitatively the relative contributions of diverse mechanisms underlying synaptic efficacy: the relevance of each and every element that comprises a synapse, the interactions between these components and their subcellular distribution, as well as the influence of synaptic geometry (presynaptic terminal, cleft and postsynaptic density). This platform consists of a graphical interface in which elements that comprise a single glutamatergic synapse (both pre- and post-synaptically), their behavior as well as the underlying synaptic geometry can be modified. For example, EONS offers the ability to study the effect of voltage-gated calcium channels density and distribution, the number and location of receptors and more. EONS is a parametric model of a generic glutamatergic synapse that takes into account pre-synaptic mechanisms, such as calcium buffering and diffusion, neurotransmitter release, diffusion and uptake in the cleft, and postsynaptic elements, such as ionotropic AMPA and NMDA receptors, their distribution and synaptic geometry, as well as metabotropic glutamate receptors. There are no complicated equations to write: all the models are predefined. This version is a great tool for first time users and students interested in learning about synapses, as well as for studying geometry and distribution hypotheses in a 2D rectangular geometry. System Requirements: EONS V1.2 is a Windows program but can be also successfully installed and run on Mac and Linux.
BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method. This is especially recommended when primers are designed to amplify the highly redundant bisulfite treated sequences. It has the unique property of analyzing the primer pairs for mispriming sites on the bisulfite-treated genome and determines potential non-specific amplification products with a new search algorithm. The options of primer-design and analysis for mispriming sites can be used sequentially or separately, both on bisulfite-treated and untreated sequences. In silico and in vitro tests of the software suggest that new PCR strategies may increase the efficiency of the amplification.
Edinburgh Mouse Atlas of Gene Expression
Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped.
An open source C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way. Its broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. It can also be used from the Chimera molecular modeling system, or via one of several web applications.
Allen Institute for Brain Science Sleep Study
Collection of gene expression data in mouse brain for five different conditions of sleep and wakefulness to understand sleep deprivation and dynamic changes underlying sleep and wake cycles. Platform to generate cellular resolution expression data.
Database of data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses. Users can search the Flu database, build queries, retrieve sequences, and apply analysis tools. This includes selecting influenza sequences by virus, subtype, host, and other criteria, finding complete genome sets, aligning sequence and others in the database (up to 1000 sequences), viewing clustering and phylogenetic trees, BLAST searching a flu sequence against the database, and more.
Automatic software program for microarray image quantification.
Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.
prorata - Quantitative Proteomics Software
ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation
A quantitative proteomics software program for accurate protein abundance ratio estimation with confidence interval evaluation.
BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Allen Brain Atlas Developing Mouse Brain
Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself.
Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python
IntEnz- Integrated relational Enzyme database
IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 08, 2013. A consortium of three facilities whose purpose is to establish, characterize, and distribute novel mutant mouse models with neural and/or behavioral phenotypes, and distribute them to the worldwide research community. Interested scientists are able to obtain information about mouse lines at all three sites in a single unified database. GOALS * Increase genomic and genetic tools for functional gene identification * Provide mice with mutations that alter the nervous system or behavior * Build collaborations between geneticists and neuroscientists The consortium is made up of three mutagenesis and phenotypic screening facilities, focused on identifying alterations in nervous system function and behavior, and established by NIH. They are the Neurogenomics Project at Northwestern University, the Neuroscience Mutagenesis Facility at The Jackson Laboratory, and the Neuromutagenesis Project of the Tennessee Mouse Genome Consortium. The NIH Neurogenomics Project at Northwestern University is directed by Dr. Joseph S. Takahashi, who also acts as the Director of the Neuromice.org consortium. Chemical mutagenesis is used to induce mutations throughout the genome and combined with phenotypic screens to detect mice with mutations. In order to maximize the genomic coverage and recover both dominant and recessive mutations, a dominant G1 screen and a recessive G3 screen are utilized. Phenotypic screens focus on five primary domains: learning and memory, behavioral responses to stress, responses to psychostimulants, circadian rhythmicity, and vision. The Neuroscience Mutagenesis Facility at the Jackson Laboratory is directed by Dr. Wayne N. Frankel. The Neuroscience Mutagenesis Facility is using a three-generation backcross breeding scheme to produce homozygous mutants and will thus recover dominant, semidominant, and recessive mutations. In addition, some mutagenesis will be done in ES cells followed by two generations of breeding. Phenotypic screens focus on identifying mutations affecting: motor function, seizure threshold, hearing, vision, and neurodevelopment. The Neuromutagenesis Project of the Tennessee Mouse Genome Consortium (TMGC) involves researchers throughout the state of Tennessee, under the direction of Dr. Daniel Goldowitz, Ph.D., at the University of Tennessee Health Science Center, Memphis. TMGC also includes researchers at Oak Ridge National Laboratory, Vanderbilt University, Meharry Medical College, University of Tennessee-Knoxville, St. Jude Children's Research Hospital, and the University of Memphis. The Project is using regional mutagenesis, covering regions on chromosomes 10, 14, 15, 19, and X, thus including approximately 15 of the genome in the screened region. Phenotypic screens include: motor and sensory function, learning and memory, neurohistology, aging, alcohol response, abused drug response, visual function, and social behavior. Neuromice.org has stopped taking orders online but mutants are orderable please contact the originating center for availability and pricing details. Live targeted mutant Fragile X model mice are now available for distribution.
A Swiss-led project with the aim of reverse engineering the mammalian brain and achieving a complete virtual human brain. The researchers have demonstrated the validity of their method by developing a realistic model of a rat cortical column, consisting of about 10,000 neurons. The eventual goal is to simulate systems of millions and hundreds of millions of neurons. The virtual brain will be an exceptional tool giving neuroscientists a new understanding of the brain and a better understanding of neurological diseases. In five years of work, Henry Markram's team has perfected a facility that can create realistic models of one of the brain's essential building blocks. This process is entirely data driven and essentially automatically executed on the supercomputer. Meanwhile the generated models show a behavior already observed in years of neuroscientific experiments. These models will be basic building blocks for larger scale models leading towards a complete virtual brain.
An R software package providing plotting and convenience functions.
MITOMAP - A human mitochondrial genome database
Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.
BRENDA: The Comprehensive Enzyme Information System
Database for functional enzyme and ligand-related information maintained as part of the German ELIXIR Node. Provides advanced query systems, evaluation tools, and various visualization options for the detailed assessment of enzyme properties. Enzyme data in BRENDA are classified according to the Enzyme Commission (EC) nomenclature of IUBMB.
Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator.
Allen Institute for Brain Science Transgenic Mouse Study
A comprehensive characterization of expression patterns of genetically-controlled markers or tool genes in the brains of transgenic mice generated by the Allen Institute as well as the broad scientific community. Providing standardized, detailed, anatomical profiling of transgene expression throughout the brain, this dataset is intended to reveal the potential of each transgenic mouse line and help researchers choose the appropriate tools for their studies. Transgenic mice are valuable tools to label selective neuronal or non-neuronal populations, modulate gene expression in these cells or manipulate activity of these cells for the study of neural circuits and brain function. The Allen Institute has launched a project to generate a variety of transgenic mouse lines, mainly using the Cre/lox system, to express fluorescent probes or neuronal activity manipulating tools in a variety of cell types in the brain. At the same time, utilizing Allen Institute's unique high-throughput capability, a pipeline is set up to characterize the ability in directing cell type specific expression in the brains of various transgenic mice generated by the Allen Institute as well as the broad scientific community. Through standardized, detailed, anatomical profiling of the transgene expression in the entire mouse brain, this dataset is intended to provide a comprehensive evaluation of the potential of each transgenic mouse line and help researchers choose the appropriate transgenic tools to study the function of different regions and/or cell types of the brain. This data release adds additional data to the existing set of new Cre-reporter lines generated at the Allen Institute that have stronger expression than other commonly used reporter lines are used to characterize approximately a dozen Cre-driver lines. The types of characterization data include digitized images (of sections sampling the entire brain) of colorimetric in situ hybridization (CISH), double fluorescent in situ hybridization (DFISH), native fluorescence of XFP (generic term for fluorescent proteins of different colors), and immunohistochemical (IHC) labeling of marker genes.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The mission of the C. elegans Gene Knockout Consortium is to facilitate genetic research of this important model system through the production of deletion alleles at specified gene targets. We choose targets based on investigator requests. Strains produced by the consortium are freely available with no restrictions to any investigator. At one time, our capacity dictated that we restrict requests to five per lab. This restriction no longer holds. Investigators are encouraged especially to register requests for functionally related groups of genes. Consortium strains are distributed by the C. elegans Genetic Center (CGC). In most cases, when you use the Consortium web site to request an existing allele, your request is forwarded automatically to the CGC. However, if you indicate that an existing allele is not satisfactory for your research, (for whatever reason), you may request that we generate another allele for the same target. Any information generated by the Consortium is entered into the official C. elegans data repository, WormBase.
Cambridge Cognition: Neuropsychological Cognitive Testing
Global commercial provider of cognitive assessment software for clinical trials, academic research and healthcare provision.
Software used for the identification of differentially expressed genes from count data or previously normalized count data. It empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene is likely to be part of the noise or represent a true differential expression.
Coddle-Codons Optimized to Discover Deleterious LEsions
Choosing codons to Optimize Discovery of Deleterious Lesions
Codons Optimized to Discover Deleterious LEsions
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Web-accessible program that identifies the region(s) of a user-selected gene and of its coding sequence (CDS) where the anticipated point mutations are most likely to result in deleterious effects on the gene's function. CODDLe separately handles 1) the prediction of changes which should truncate the protein and destabilize the RNA - nonsense changes and splice junction changes, and 2) the prediction of missense changes which should alter function of the gene product - those in conserved amino acid blocks in the CDS. Because the region(s) identified will be PCR amplified by the user and that amplicon will be used for polymorphism discovery, the application delivers primer pairs selected by Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998)Primer3.) After selecting a primer pair, CODDLe returns a window with the selected amplicon and tabulates the effects of all possible polymorphisms which could be detected in that amplicon. CODDLe will not identify the regions of a gene where polymorphisms are most likely to be discovered. Others have shown that naturally occurring SNPs are found more often in the untranslated regions of a gene.
A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines.
Network of ftp and web servers around world that store identical, up to date, versions of code and documentation for R. Package archive network for R programming language.
GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.
ADNI - Alzheimer's Disease Neuroimaging Initiative
Alzheimer's Disease Neuroimaging Initiative
Alzheimer's Disease Neuroimaging Initiative (ADNI)
Alzheimers Disease Neuroimaging Initiative
Database of the results of the ADNI study. ADNI is an initiative to develop biomarker-based methods to detect and track the progression of Alzheimer's disease (AD) that provides access to qualified scientists to their database of imaging, clinical, genomic, and biomarker data.
Peak-calling algorithm which analyzes changes in the location, fuzziness, and occupancy at each nucleosome or protein binding position.
GeneWeaver - A system for the integration of functional genomics experiments
Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.
Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes
Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.
A search engine system for automated peptide and protein identification from tandem mass spectra.
IPI provides a top level guide to the main databases (UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, RefSeq, Ensembl, TAIR, H-InvDB, Vega) that describe the proteomes of higher eukaryotic organisms. IPI: :1. effectively maintains a database of cross references between the primary data sources :2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) :3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. As previously announced, the closure of IPI has been proposed for some time. Replacement data sets are now available through UniProt for human and mouse; sets for the other species contained within IPI are expected to be included as part of the UniProt release 2011_07. To allow users time to transition to using the new UniProt data sets, IPI releases will continue to be produced throughout the summer. The final release will be made in September 2011. Thereafter, the IPI website will cease to be maintained, although previous releases of the dataset will continue to be available from the FTP site. We would like to thank our users for their support and interest in this service.
National voluntary specialty organization that serves its members, governments and public by Certifying individuals who provide medical genetics services, Establishing professional and ethical standards of medical genetics services, Establishing standards of medical genetics training, Providing professional and public education, Informing public policy.
Cognition and Brain Sciences Unit Imaging Wiki
MRC Cognition and Brain Sciences Unit Imaging Wiki
Portal where neuroimaging studies are carried out using a Siemens 3T Tim Trio Magnetic Resonance Imaging (or MRI) scanner that is wholly dedicated to studies in Cognitive Neuroscience. From emotions and memories to language and learning, functional neuroimaging is being applied in many different areas of Cognitive Neuroscience. In many cases, this research relies upon support from healthy volunteers although neuroimaging studies are also being conducted in various clinical populations, including depression, anxiety, Parkinson's disease and Alzheimer's disease.
Atlas of Gene Expression Patterns in Mouse Embryo
Digital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution.
CERAD - Consortium to Establish a Registry for Alzheimer's Disease
Consortium to Establish a Registry for Alzheimer's Disease
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Consortium that developed brief, standardized and reliable procedures for the evaluation and diagnosis of patients with Alzheimer's disease (AD) and other dementias of the elderly. These procedures included data forms, flipbooks, guidebooks, brochures, instruction manuals and demonstration tapes, which are now available for purchase. The CERAD assessment material can be used for research purposes as well as for patient care. CERAD has developed several basic standardized instruments, each consisting of brief forms designed to gather data on normal persons as well as on cognitively impaired or behaviorally disturbed individuals. Such data permit the identification of dementia based on clinical, neuropsychological, behavioral or neuropathological criteria. Staff at participating CERAD sites were trained and certified to administer the assessment instruments and to evaluate the subjects enrolled in the study. Cases and controls were evaluated at entry and annually thereafter including (when possible) autopsy examination of the brain to track the natural progression of AD and to obtain neuropathological confirmation of the clinical diagnosis. The CERAD database has become a major resource for research in Alzheimer's disease. It contains longitudinal data for periods as long as seven years on the natural progression of the disorder as well as information on clinical and neuropsychological changes and neuropathological manifestations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A community-driven knowledgebase of Alzheimer disease, in which researchers can annotate scientific claims, data, and information, putting these into the context of testable hypotheses and treatment discovery. This SWAN project adds a collection of hand-curated hypotheses to a research paper, which are then related through a set of discourse relationships. They can be browsed and relations between claims, as well as support networks for a specific claim, are made and visualized. AlzSWAN is where you explore scientific knowledge about Alzheimer disease and share your own ideas, comments and questions in a semantically structured system. AlzSWAN is enabled by Semantic Web technology, a new standard for knowledge organization and transfer on the Web. AlzSWAN organizes and manages knowledge using formal knowledge descriptions called ontologies. Using these formal knowledge descriptions, they can tie statements made in scientific publications or on the Web to scientific evidence, biological terminologies, and knowledgebases, and to claims and counterclaims made by other researchers.
Baffling Recursive Algorithm for Isotope distributioN
Baffling Recursive Algorithm for Isotopic distributioN calculations
Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S).
A cross-platform application for 3D brain visualization for multi-modality neuroimaging data written in Java/Java3D, that runs in both standalone and client-server mode. It supports basic data management capabilities, visualization of 3D surfaces (SPM's output or OFF files), volumes (Analyze, NIFTI or Minc) and label sets. MindSeer has 2 different modes: # Client/Server is designed to allow users to visualize data that is stored centrally and enhance collaboration. # Standalone mode is available to view local data and is built for more performance than Client/Server Both modes have the same interface and support the same features. It has a modular architecture and is designed to be extensible. Requirements: # Java 5.0 or above. # Java Web Start. # Java3D (installed automatically by Web Start).
Database of a list of insertion sequences isolated from eubacteria and archaea. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences. Although most of the entries have been identified as individual elements, a growing number are included from their description in sequenced bacterial genomes. The search engine permits the retrieval and display of individual and groups of ISs based on a combination of their general features. Two levels of search are available. The simple search option enables the user to sort elements using a limited number of basic items whereas the extensive search offers an additional set of possibilities such as comparisons of the sequences of terminal inverted repeats and a variety of different layout displays. Built in links are provided to: the EMBL sequence database, the NCBI taxonomy database and to the ESF plasmid database. At present, only individual sequences can be downloaded one by one for comparison. An on-line BLAST facility is available and in future versions direct access to additional analytical tools will be provided on line. Direct submission of ISs is encouraged using the on-line form provided.
JAX Neuroscience Mutagenesis Facility Protocols
Protocols of the Neuroscience Mutagenesis Facility
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The Neuroscience Mutagenesis Facility of the Jackson Laboratory (NMF) was established to produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The protocols are available. The impetus for the program resulted from the recognition that * the value of genomic data would remain limited unless more information about the functionality of its individual components became available, and * the task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e. N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. Protocols: * Genetics ** Production of Mice for a Genome-Wide ENU Mutagenesis Screen ** Production of Mice using Chemical Mutagenesis of Mouse ES Cells * Protocols ** Step by step procedures-- Mouse mutagenesis with ENU ** Step by step procedures-- ES Cell mutagenesis with EMS * Phenotyping: Overview * Protocols:(currently only screens marked * are in use) ** Acoustic startle response (ASR) ** Auditory brainstem response (ABR) ** CLAMSTM(former CCMS) ** Creatine kinase ** Developmental Screen * ** Eye and Vision * ** Gait Analysis ** Gustation ** Observation * ** Seizure threshold * ** Additional Background Information
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 6, 2016. This blog, which is maintained under the aegis of the Concept Web Alliance, is devoted to the Concept Web a dynamic, interactive fabric of concepts and their relationships. The Concept Web is constructed from, inter alia, research literature, Internet databases and other web sites together with off-line resources. The aim of creating the Concept Web is to remove both redundancy and ambiguity from available knowledge in order to help deal with information overload, to semantically "connect" concepts, and so to maximize the potential for knowledge discovery.
MicroArray and Gene Expression Markup Language
A language / data exchange format designed to describe and communicate information about microarray based experiments that is based on XML and can describe microarray designs, microarray manufacturing information, microarray experiment setup and execution information, gene expression data and data analysis results. MAGE-ML has been automatically derived from Microarray Gene Expression Object Model (MAGE-OM), which is developed and described using the Unified Modelling Language (UML) -- a standard language for describing object models. Descriptions using UML have an advantage over direct XML document type definitions (DTDs), in many respects. First they use graphical representation depicting the relationships between different entities in a way which is much easier to follow than DTDs. Second, the UML diagrams are primarily meant for humans, while DTDs are meant for computers. Therefore MAGE-OM should be considered as the primary model, and MAGE-ML will be explained by providing simplified fragments of MAGE-OM, rather then XML DTD or XML Schema. (from the description by Ugis Sarkans) The field of gene expression experiments has several distinct technologies that a standard must include. These include single vs. dual channel experiments, cDNA vs. oligonucleotides. Because of these different technologies and different types of gene expression experiments, it is not expected that all aspects of the standard will be used by all organizations. Given the massive amount of data associated with a single set of experiments, it is felt that Extensible Markup Language (XML) is the best way to describe the data. The use of a Document Type Definition (DTD) allows a well-defined tag set, a vocabulary, to describe the domain of gene expression experiments. It also has the virtue of compressing very well so that files in an XML format compress to ten percent of their original size. XML is now widely accepted as a data exchange format across multiple platforms.
Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
Portal for Recommendations on Biochemical and Organic Nomenclature, Symbols and Terminology. NC IUBMB,established by IUPAC-IUBMB Joint Commission, publishes standards on biochemical nomenclature, including enzyme nomenclature, in some cases jointly with the International Union of Pure and Applied Chemistry (IUPAC).
isopat: Calculation of isotopic pattern for a given molecular formula
Software function that calculates the isotopic pattern (fine structures) for a given chemical formula.
Software library for accessing data in HDF5 files produced by Pacific Biosciences sequencing machines. The R package supports accessing data from: cmp.h5, bas.h5, pls.h5, and trc.h5.
Software tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from cmp.h5 and bas.h5 files.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A repository for physical mapping data of the human X chromosome that aims at providing a global view of genomic data at a chromosomal level including an integrated physical, genetic, transcript and sequence map of the human X chromosome. This implies acquiring, understanding and formatting an enormous amount of experimental results and can only be accomplished progressively. We have chosen to start the integration process with YAC maps generated by the community. These provide the basis for future higher resolution physical maps, as well as emerging transcript and sequence maps. The current content of IXDB therefore reflects this situation, with the emphasis placed on YAC mapping data. Due to their immediate value, IXDB has also started to systematically include bacterial clone contig maps and EST data. Currently IXDB does not store sequence data, although links to nucleic sequence databases are provided.
An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results.
Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval.
Jenalib: Jena Library of Biological Macromolecules
Image library of biological macromolecules
IMB Jena Image Library of Biological Macromolecules
Jena Library of Biological Macromolecules
Database aimed at disseminating information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available. The JenaLib intends to fulfill both scientific and educational needs. Authors who are willing to make available images or coordinates to the scientific community via the Image Library of Biological Macromolecules are requested to contact the author. A PDB/SWISS-PROT cross-reference database combines information from both PDB and SWISS-PROT, thus providing significantly more cross-references than either PDB or SWISS-PROT. The existing brief descriptions of X-ray, NMR and FTIR methods for structure determination are supplemented by information on circular dichroism.
Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
enviPat: Isotope pattern profile and centroid calculation for mass spectrometry
Software for fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing.
A command-line utility for bigWig files designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Its functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted.
Produce resources to unravel the interface between insulin action, insulin resistance and the genetics of type 2 diabetes including an annotated public database, standardized protocols for gene expression and proteomic analysis, and ultimately diabetes-specific and insulin action-specific DNA chips for investigators in the field. The project aims to identify the sets of the genes involved in insulin action and the predisposition to type 2 diabetes, as well as the secondary changes in gene expression that occur in response to the metabolic abnormalities present in diabetes. There are five major and one pilot project involving human and rodent tissues that are designed to: * Create a database of the genes expressed in insulin-responsive tissues, as well as accessible tissues, that are regulated by insulin, insulin resistance and diabetes. * Assess levels and patterns of gene expression in each tissue before and after insulin stimulation in normal and genetically-modified rodents; normal, insulin resistant and diabetic humans, and in cultured and freshly isolated cell models. * Correlate the level and patterns of expression at the mRNA and/or protein level with the genetic and metabolic phenotype of the animal or cell. * Generate genomic sequence from a panel of humans with type 2 diabetes focusing on the genes most highly regulated by insulin and diabetes to determine the range of sequence and expression variation in these genes and the proteins they encode, which might affect the risk of diabetes or insulin resistance. The DGAP project will define: * the normal anatomy of gene expression, i.e. basal levels of expression and response to insulin. * the morbid anatomy of gene expression, i.e., the impact of diabetes on expression patterns and the insulin response. * the extent to which genetic variability might contribute to the alterations in expression or to diabetes itself.
Motif Statistics and Discovery - Sequence analysis toolkit for bioinformatics
Sequence analysis toolkit that contains a lot of sequence analysis algorithms, including methods for 1) motif statistics, e.g. compute the exact occurrence count distribution of a motif, 2) exact motif discovery: extraction of motifs with provably optimal p-value, 3) analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text, 4) statistics of fragment masses resulting from proteolytic cleavage of proteins, 5) computing the expectated read length of sequencing reads for a given dispensation order (for 454 or IonTorrent) and 6) analysing sensitivity of spaced alignment seeds.
tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions
Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins
This web-server takes a user-supplied sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA. Prediction can be performed using a profile of evolutionary conservation of the input sequence automatically generated by the web-server or the input sequence alone. Three prediction methods are run for each input sequence and consensus prediction is generated.
Cancer institute that provides expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. As an affiliate of Harvard Medical School and a Comprehensive Cancer Center designated by the National Cancer Institute, the Institute also provides training for new generations of physicians and scientists, designs programs that promote public health particularly among high-risk and underserved populations, and disseminates innovative patient therapies and scientific discoveries to their target community across the United States and throughout the world.
Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/
A database to support research on drugs for the treatment of different neurological disorders. It contains agents that act on neuronal receptors and signal transduction pathways in the normal brain and in nervous disorders. It enables searches for drug actions at the level of key molecular constituents, cell compartments and individual cells, with links to models of these actions.
Non-profit research center dedicated to the study of the human genome. Expert staff and pioneering programs in the fields of personalized medicine, cell biology, cytogenetics, genotyping, and biobanking drive our mission. The emerging field of personalized medicine draws upon a person's genomic information to tailor treatments and prescription drug dosing to optimize health outcomes. The Coriell Personalized Medicine Collaborative (CPMC) research study is seeking to understand the usefulness of genetic risk and pharmacogenomics in clinical decision-making and healthcare management. Coriell has a distinguished history in cell biology. We are building upon this expertise by playing an important role in induced pluripotent stem (iPS) cell research. These powerful cells, which can be made from skin cells or blood, are revolutionizing the way human disease is studied and how drugs are developed. The decline of neurons afflicted with Alzheimer's disease or pancreatic cells fighting diabetes can be studied in a Petri dish. By proving efficacy within the diseased environment prior to clinical trial, drugs can move through the pipeline quicker to reach patients sooner. In addition to pioneering cutting-edge research initiatives, Coriell offers custom research services including cell culture, cytogenetic analyses, and molecular biology to the scientific community. Furthermore, Coriell's Genotyping and Microarray Center is one of the nation's largest centers, with high-throughput DNA analysis systems from Illumina and Affymetrix. The Center is CLIA-certified in 48 states.
pacBioToCA (error correction via Celera Assembler)
A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads.
Department of Energy Joint Genome Institute
DOE Joint Genome Institute - Enabling Advances in Bioenergy & Environmental Research
Institute to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, the DOE JGI unites the expertise at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology. The facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.
DiNuP - A Systematic Approach to Identify Regions of Differential Nucleosome Positioning
Software that compares the nucleosome profiles generated by high-throughput sequencing between different conditions. It provides a statistical p-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the FDR as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise.
DaliLite Pairwise comparison of protein structures
DaliLite - Pairwise alignment of protein structures
Tool that computes optimal and suboptimal structural alignments between two protein structures. It will compare all chains in the first structure against all chains in the second (unless specific chain IDs are given). The resulting superimposed coordinate files can be downloaded or viewed interactively in Jmol. The Dali method optimizes a weighted sum of similarities of intramolecular distances. Suboptimal alignments do not overlap the optimal alignment or each other. Suboptimal alignments detected by the program are reported if the Z-score is above 2; they may be of interest if there are internal repeats in either structure. SOAP Web services are also available.
XNAT - The Extensible Neuroimaging Archive Toolkit
Extensible Neuroimaging Archive Toolkit (XNAT)
Software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Analytical tools. Archive files may be written in any format and may include explanatory figures, program sources, readme files, and other related files. The readme file describes the purpose and usage of the archive file. This data sharing framework allows users to improve the reproducibility of simulations. Users can browse the platform contents via branch sites (A catalogue of illusions, Visitope), which introduce user friendly view of items such as basic images and original artworks of visual illusions with high resolution. The items in Visiome Platform are useful not only for reproducing the published results, but also for advancing and expanding the research in Vision Science.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. BODB offers a way to document computational models of brain function by linking each model to Brain Operating Principles (BOPs), related brain regions, Summaries of Simulation Results (SSRs)and Summaries of Experimental Data (SEDs) used either to design or to test the model. Tools are provided to search for related models and to compare their coverage of SEDs. This allows automatic benchmarking of a model against a cluster of models addressing similar BOPs or SEDs or brain regions. Tools allow display of brain imaging results against a human brain applet; a new tool will link data to a macaque brain applet.
gutentag - A genetic sequence database for labs that can be browsed using tags
An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups that can be browsed using tags. The tool is Web 2.0-flavoured, allowing users to do more than just retrieve information. Its focus on user-editability is supported by the use of tags (metadata) associated with genetic sequences. Several methods of retrieving stored data are available including tag-clouds, BLAST and keyword searches. Also, sequence tags related to HGNC gene names, conserved domains (CDD) and GO terms can be automatically generated given sequence data. The tool is constructed using the high-level Python web framework, Django, with a SQLite3 backend.
Open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. It uses Cellular Potts Model to model cell behavior.
Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation).
survcomp - Performance Assessment and Comparison for Survival Analysis
R package providing functions to assess and to compare the performance of risk prediction (survival) models.
Ontology to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD), a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health.
SASqPCR: robust and rapid analysis of RT-qPCR data in SAS
All-in-one computer program for robust and rapid analysis of quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) data in SAS. It incorporates all functions important for RT-qPCR data analysis including assessment of PCR efficiencies, validation of internal reference genes and normalizers, normalization of confounding variations across samples and statistical comparisons of target gene expression in parallel samples. The program is highly automatic in data analyses and result output. The input data have no limitations for the number of genes or cDNA samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. The program is also extendable allowing advanced SAS users to develop particular statistical tests appropriate for their experimental designs. Thus users are the actual decision-makers controlling RT-qPCR data analyses. The program has to be used in SAS software; however, extensive SAS programming knowledge is not required.
Developmental Therapeutics Program NCI/NIH
Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Distant Regulatory Elements of co-regulated genes
Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.
enviPick: Peak picking for high resolution mass spectrometry data
Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.
GeneFisher2 - Interactive PCR Primer Design
A web-based program for designing degenerate primers. The procedure leads to isolation of genes in a target organism using multiple alignments of related genes from different organisms. The term gene fishing refers to the technique where PCR is used to isolate a postulated but unknown target sequence from a pool of DNA.
triplex - Search and visualize intramolecular triplex-forming sequences in DNA
Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.
Database of lipid related proteins representing human and mouse proteins involved in lipid metabolism. Collection of lipid related genes and proteins contains data for genes and proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio.
MPprimer: a program for reliable multiplex PCR primer design
A software program for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR. In addition, it provides a virtual electrophotogram to help users choose the best PSC. It is a valuable tool for designing specific, no dimer formation and amplicons size constrained PSCs to improve the multiplex PCR experiments.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The PDP++ software is a neural-network simulation system written in C++. It represents the next generation of the PDP software originally released with the McClelland and Rumelhart Explorations in Parallel Distributed Processing Handbook, MIT Press, 1987. It is easy enough for novice users, but very powerful and flexible for research use. The new version of PDP++, released 8/21/07, is now called Emergent.
A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file.
A fast thermodynamics-based software program for checking PCR primer specificity against genomic DNA and mRNA/cDNA sequence databases.
A software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguad (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.
family-specific degenerate primer design
Software program to design degenerate primers for PCR.
A community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results
ImageJ - Image Processing and Analysis in Java
Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
Sequence-based Ultra-Rapid Pathogen Identification
Software providing a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples.
Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools
Public image processing and analysis program for Macintosh.
NIDDK- National Institute of Diabetes and Digestive and Kidney Diseases Obesity Resources
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 23, 2017. This website contains resources for obesity researchers including: Obesity Databases, Registries and Information; Obesity Multicenter Clinical Research; Obesity Basic Research Networks; Obesity Reagents; Obesity Services; Obesity Standardization Programs; Obesity Tissues, Cells, Animals; Obesity Useful Tools.
Flytrap is an interactive database for displaying gene expression patterns, in particular P(GAL4) patterns, via an intuitive WWW based interface. This development consists of two components, the first being the HTML interface to the database and the second, a tool-kit for constructing and maintaining the database. The browser component of the project is entirely platform independent; based on javascript and HTML and therefore only requires a "standard" browser. This is to facilitate CD-ROM distribution and off-line browsing. Whether on-line or on CD, the basic browser structure does not reply on any server based scripts. Basic searching is now available. The search page uses javascript and will work off-line (i.e. from a CD-ROM copy). The construction tool-kit is UNIX based and requires an on-line web server. The tool-kit is used to compile the HTML browser interface from a simple database. The tool-kit part comprises a forms based HTML interface to the datasets allowing new information to b e added and updated very simply. We are also developing a java interface for the tool-kit that will enable us to edit and annotate images on-line. The basic browser interface is complete and a demonstration version can be accessed via the website. The first working version of the tool-kit is now on-line and is available for use.
A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.
MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation
MAPPER 2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation
Multi-genome Analysis of Positions and Patterns of Elements of Regulation
A platform composed of three modules: the Database, the Search Engine, and rSNPs, for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC and JASPAR data with the search power of profile hidden Markov models (HMMs). The Database contains putative TFBSs found in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each gene, they scanned the region from 10,000 base pairs upstream of the transcript start to 50 base pairs downstream of the coding sequence start against all their models. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs. The Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs.
Database for Drosophila melanogaster transcription profiling that allows users to search the Drosophilia genome, see sequence overviews, and look at various transcripts. The data were generated in conjunction with the recently developed high-throughput genome sequencer Illumina / Solexa using a newly developed 5'-end mRNA collection method. Approximately 25 million 25-27 nucleotide (nt) 5'-end mRNA tags from the embryos, larvae, young males, young females, old males, old females, and S2 (culture cell line) of D. melanogaster were collected. By arranging this vast amount of expression tag with other annotated data, they have built a one-stop service for Drosophila melanogaster transcription profiling.
Magnaporthe comparative genomics database
The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. It provides users the tools to BLAST search, browse genome regions (to retrieve DNA, find clones, and graphically view sequence regions), and provides gene indexes and genome statistics. We were funded to attempt 7x sequence coverage comprising paired end reads from plasmids, Fosmids and BACs. Our strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. Our specific aims are as follows: 1. Generate and assemble sequence reads yielding 7X coverage of the Magnaporthe oryzae genome through whole genome shotgun sequencing. 2. Generate and incorporate BAC and Fosmid end sequences into the genome assembly to provide a paired-end of average every 2 kb. 3. Integrate the genome sequence with existing physical and genetic map information. 4. Perform automated annotation of the sequence assembly. 5. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server and by deposition of the sequence assembly in GenBank.
The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations
Primer3Plus - pick primers from a DNA sequence
A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3.
Web tool that identifies sequence tagged sites (STSs) within DNA sequences. Using e-PCR, you can search for sub-sequences that closely match the PCR primers and have the correct order, orientation, and spacing. The software may also be downloaded to run locally.
A XML-based description language that provides a common data format for defining and exchanging descriptions of neuronal cell and network models. It facilitates the exchange of complex neural models, allows for greater transparency and accessibility of models, enhances interoperability between simulators and other tools, and supports the development of new software and databases. Exchange of network models will aid the investigation of structure-function relationships in neuroscience including theoretical studies relating connectivity patterns to normal and neurodegenerative network states. NeuroML is a free and open community effort developed with input from many contributors. They will need your help as the standards and tools continue to evolve.
Mammalian Mitochondrial Genomics Database
Database developed to assist the phylogeneticist user in retrieving individual gene sequence alignments for genes in complete mammalian mitochondrial genomes. Data retrieval in MamMiBase requires three stages. At the first stage, the user must select the mammalian species or group that (s)he wishes to study. In the second stage, the user will select the outgroup from a list that included all species selected in the first stage plus Xenopus laevis and Gallus gallus. Finally, at the third stage, the user will select individual mitochondrial gene alignments or a phylogenetic tree that (s)he wishes to download.
Eukarotic Linear Motif resource for Functional Sites in Proteins
Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.
A national mouse monoclonal antibody generating resource for biochemical and immunohistochemical applications in mammalian brain. NeuroMabs are generated from mice immunized with synthetic and recombinant immunogens corresponding to components of the neuronal proteome as predicted from genomic and other large-scale cloning efforts. Comprehensive biochemical and immunohistochemical analyses of human, primate and non-primate mammalian brain are incorporated into the initial NeuroMab screening procedure. This yields a subset of mouse mAbs that are optimized for use in brain (i.e. NeuroMabs): for immunocytochemical-based imaging studies of protein localization in adult, developing and pathological brain samples, for biochemical analyses of subunit composition and post-translational modifications of native brain proteins, and for proteomic analyses of native brain protein networks. The NeuroMab facility was initially funded with a five-year U24 cooperative grant from NINDS and NIMH. The initial goal of the facility for this funding period is to generate a library of novel NeuroMabs against neuronal proteins, initially focusing on membrane proteins (receptors/channels/transporters), synaptic proteins, other neuronal signaling molecules, and proteins with established links to disease states. The scope of the facility was expanded with supplements from the NIH Blueprint for Neuroscience Research to include neurodevelopmental targets, the NIH Roadmap for Medical Research to include epigenetics targets, and NIH Office of Rare Diseases Research to include rare disease targets. These NeuroMabs will then be produced on a large scale and made available to the neuroscience research community on an inexpensive basis as tissue culture supernatants or purified immunoglobulin by Antibodies Inc. The UC Davis/NIH NeuroMab Facility makes NeuroMabs available directly to end users and is unable to accommodate sales to distributors for third party distribution. Note, NeuroMab antibodies are now offered through antibodiesinc.
European Mouse Phenotyping Resource of Standardised Screens
European Mouse Phenotyping Resource of Standardized Screens
Database of validated Standard Operating Procedures (SOPs) for screens to determine the phenotype of a mouse, developed by the EUMORPHIA consortium. The SOP's cover all of the main body systems including: clinical chemistry, hormonal and metabolic systems, cardiovascular, allergy and infection, renal function, sensory function, neurological and behavioral function, cancer, bone and cartilage, and respiratory function. In addition, there are generic SOPs in histology, necropsy, pathology and gene expression. EMPReSS is a platform of individual tests. These can be performed as individual tests or grouped together in sequences, recommended in the EMPReSS database, to give more information on particular phenotype. Quick List of Current Pipelines: * EUMODIC Pipeline 1 * EUMODIC Pipeline 2 * GMC Pipeline * MGP Pipeline * Additional Tests * EUMODIC Pipeline 3
Repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project, part of the Arabidopsis Genome Initiative. It is moving towards becoming an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities. The aim is to create a comprehensive resource for Arabidopsis as a model that can then be used to transfer knowledge onto sequences from other species, including crop plants.
Tool that searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance. When successful, the search returns a sequence output file in fasta format containing all sequence in the database that lie between and include the primer pair. The fasta header describes the region in the database and the primers. The fasta body is capitalized in areas where the primer sequence matches the database sequence and in lower-case elsewhere. Sources and executables to run batch jobs on your own server are available free for academic, personal, and non-profit purposes. Non-exclusive commercial licenses are also available.
Neuro Systems and Graphics Computing Laboratory
This database contains axonal tracing data from the cerebro-ponto-cerebellar system in rats. Data are presented as 3-D coordinates in a common coordinate system for the pontine nuclei. It is presented through the Rodent Brain WorkBench.
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 6, 2017. Software to detect alternatively spliced exons between two conditions, for example, between two groups of treated and untreated patients in a typical clinical study.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.
EUROpean Saccharomyces Cerevisiae ARchive for Functional Analysis
Archive of yeast strains and plasmids that were generated during various yeast functional analysis projects.
Calculator for a variety of functions, including Cohen's d and the effect-size correlation, rYl, using means and standard deviations or independent groups t test values and df.
A tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications.
National Institute of General Medical Sciences: Research Funding
NIGMS places great emphasis on the support of individual, investigator-initiated grants within its scientific mission areas. Most grants are for research projects (R01), but NIGMS also funds program projects (P01) as well as some research resources. The Institute encourages research in certain scientific areas through requests for applications and program announcements. This website has information for upcoming grants, minority grants as well as training opportunities in medical research in the following disciplines: cell biology, biophysics, genetics, developmental biology, pharmacology, physiology, biological chemistry, bioinformatics, and computational biology.
Database of maps showing the sites of modified rRNA nucleotides. Access to the rRNA sequences, secondary structures both with modification sites indicated, 3D modification maps and the supporting tables of equivalent nucleotides for rRNA from model organisms including yeast, arabidopsis, e. coli and human is provided. This database complements the Yeast snoRNA Database at UMass-Amherst and relies on linking to some content from that database, as well as to others by colleagues in related fields. Therefore, please be very cognizant as to the source when citing information obtained herein. Locations of modified rRNA nucleotides within the 3D structure of the ribosome.
Central data repository for nematode biology including complete genomic sequence, gene predictions and orthology assignments from range of related nematodes.Data concerning genetics, genomics and biology of C. elegans and related nematodes. Derived from initial ACeDB database of C. elegans genetic and sequence information, WormBase includes genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. Maintains public FTP site where researchers can find many commonly requested files and datasets, WormBase software and prepackaged databases.
International Classification for Nursing Practice
Ontology of the international classification for nursing practice.
Database that summarizes diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models. It contains manually curated, highly detailed information about metabolic pathways in crop plants, including pathway diagrams, reactions, locations, transport processes, reaction kinetics, taxonomy and literature. It contains information about seven major crop plants with high agronomical importance and two model plants.
Database of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins.
Software package that implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity (qualitatively and quantitatively), and to borrow information across genes to estimate hyper-parameters from the data (empirical Bayes).
Software used to identify and classify alternative splicing events from RNA-Seq data. JuncBASE also uses read counts to quantify the relative expression of each isoform and identifies splice events that are significantly differentially expressed across two or more samples.
European Conditional Mouse Mutagenesis Program
Generate, archive, and distribute world-wide up to 12.000 conditional mutations across the mouse genome in mouse embryonic stem (ES) cells and Establish a limited number of mouse mutants from this resource. EUCOMM contributes the largest fraction of conditionally trapped and targeted genes in mouse C57BL/6N embryonic stem (ES) cells to the IKMC. EUCOMM vectors, mutant ES cells and mutant mice are distributed worldwide, enabling functional genomics research in a standardized and cost-effective manner by a much wider biomedical research community than has been possible previously. EUCOMM mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMM mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Mutagenesis Strategies * Conditional gene trapping - random approach for expressed genes * Conditional targeted trapping - directed approach, used for expressed genes * Conditional gene targeting - directed approach, used for non-expressed genes
Database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.
City University of New York; New York; USA
University system in New York City, New York. It is made up of 11 senior colleges, seven community colleges, The Macaulay Honors College, and five graduate and professional schools.
Set of plugins for the Eclipse platform which facilities note-taking and annotation of web-based works and non-web-based works.
MethDB - the database for DNA methylation and environmental epigenetic effects
Database that provides a resource to store DNA methylation data and to make these data readily available to the public. Future development of the database will focus on environmental effects on DNA methylation. No restriction applies on the type of data, i.e. as well as global estimations (e.g. HPLC) as data from high resolution analysis (i.e. sequencing) can be stored. As much background information as possible should be provided by the users. This includes the origin of the sample, phenotype, expression of the related gene, etc..
pairheatmap: A tool for comparing heatmaps
A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology.
Online conferences focused on the life sciences, laboratory animal sciences and clinical diagnostics community. BioConference Live brings together research scientists, veterinarians, clinicians, medical experts, thought leaders and professionals from around the world all exclusively online. * Receive CE Credits accredited by the AACC ACCENT and PACE. * No Cost or Travel. * Watch Live Streaming Sessions by Industry Experts. * Network with peers and professionals. * Explore a virtual exhibit floor showcasing advances in life sciences and medical technologies.
Integrated Grants is a virtual database currently indexing funded research resources including NIH Research Portfolio Online Reporting Tool (RePORT) (current grants, updated monthly) and ResearchCrossroads (1970-2008, defunct as of 2009).
An MRI data repository that holds a set of 7 Tesla images and behavioral metadata. Multi-faceted brain image archive with behavioral measurements. For each participant a number of different scans and auxiliary recordings have been obtained. In addition, several types of minimally preprocessed data are also provided. The full description of the data release is available in a dedicated publication. This project invites anyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging by documenting how much (scientific) value can be generated out of a single data release by publication of scientific findings derived from a dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and integration of new data.
Software that provides rapid incremental file transfer.
University of Colorado Boulder; Colorado; USA
Public university that offers degrees in the sciences, humanities, and social sciences.
Community portal for researchers and content management system for data and databases. Intended to provide common source of data to research community and data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. Central service where RRIDs can be searched and created. Designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas. Adds value to existing scientific resources by increasing their discoverability, accessibility, visibility, utility and interoperability, regardless of their current design or capabilities and without need for extensive redesign of their components or information models. Resources can be searched and discovered at multiple levels of integration, from superficial discovery based on limited description of resource at SciCrunch Registry, to deep content query at SciCrunch Data Federation.
Services for the long-term preservation and curation of America's digital data - data of any type or size, with minimal requirements on the data provider. It has the capacity to preserve hundreds of terabytes of digital data and comprises several partner organizations that provide a wide range of services. The project leverages high-speed networks, mass-scale storage capabilities, and the expertise of the partners in order to provide a geographically distributed, heterogeneous, and highly redundant archive system. Features of the project include: * Three geographically distributed copies of the data * Curatorial audit reporting * Development of best practices for data packaging and sharing Chronopolis is available to anyone who wants to have their data preserved. Storage is based on a yearly, per-terabyte charge. The smallest unit available is one terabyte; collections smaller than this will be charged the one terabyte rate.
An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).
Japanese Genotype-phenotype Archive (JGA)
A service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The JGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the JGA. Once processed, all data are encrypted. The JGA accepts only de-identified data approved by JST-NBDC. The JGA implements access-granting policy whereby the decisions of who will be granted access to the data resides with the JST-NBDC. After data submission the JGA team will process the data into databases and archive the original data files. The accepted data types include manufacturer-specific raw data formats from the array-based and new sequencing platforms. The processed data such as the genotype and structural variants or any summary level statistical analyses from the original study authors are stored in databases. The JGA also accepts and distributes any phenotype data associated with the samples. For other human biological data, please contact the NBDC human data ethical committee.
An open source JavaScript library of components for visualisation of biological data on the web.
A not for profit organization to accelerate research into aging by sharing resources: providing access to cost and time effective, aged murine tissue through a biorepository and database of live ageing colonies, as well as promoting the networking of researchers and dissemination of knowledge through its online collaborative environment; MiCEPACE. ShARM will provide valuable resources for the scientific community while helping to reduce the number of animals used in vital research into aging. The biobank of tissue and networking facility will enable scientists to access shared research material and data. By making use of collective resources, the number of individual animals required in research experiments can be minimized. The project also has the added value of helping to reduce the costs of research by connecting scientists, pooling resource and combining knowledge. ShARM works in partnership with MRC Harwell and the Centre for Intergrated Research into Musculoskeletal Ageing (CIMA).
Consortium serving to develop and qualify promising biomarkers in order to help accelerate the delivery of successful new technologies, medicines and therapies for prevention, early detection, diagnosis and treatment of disease. Current core disease areas of focus include Cancer, Inflammation and Immunity, Metabolic Disorders, and Neuroscience. One of the most difficult tasks facing biomarker assessment and evaluation is harmonizing the approaches of various stakeholders--government, industry, non-profits and foundations, providers, and academic institutions. Consortium founding members and other partners recognize the critical need for a coordinated cross-sector partnership effort. The Biomarkers Consortium brings together the expertise and resources of various partners to rapidly identify, develop, and qualify potential high-impact biomarkers. Biomarkers Consortium Goals: * Facilitate the development and qualification of biomarkers using new and existing technologies; * Help qualify biomarkers for specific applications in diagnosing disease, predicting therapeutic response or improving clinical practice; * Generate information useful to inform regulatory decision making; * Make consortium project results broadly available to the entire scientific community.
A multilingual application ontology aimed at the early detection of public health events in the media. It aims to describe the terms and relations necessary to detect and risk assess public health events in the grey literature at an early stage; and bridge the gap between the (multilingual) grey literature and existing standards in biomedicine. The BCO focuses on the usage of terms and relations within informal unstructured reports which are often made at a pre-diagnostic stage of a disease outbreak by non-medically trained reporters. This is done to provide monitoring and early warning about public health hazards from online media reports.
Biomedical Information Science and Technology Initiative
Biomedical Information Science & Technology Initiative
Biomedical Information Science Technology Initiative
BITSI - Biomedical Information Science and Technology Initiative
A consortium of representatives from each of the NIH institutes and centers. BISTI was established in May 2000 to serve as the focus of biomedical computing issues at the NIH. The mission of BISTI is to make optimal use of computer science and technology to address problems in biology and medicine by fostering new basic understandings, collaborations, and transdisciplinary initiatives between the computational and biomedical sciences. In support of this mission, the BISTI coordinates research grants, training opportunities, and scientific symposia associated with biomedical computing. Regular monthly meetings are conducted to discuss program status, future needs and directions, and topics of interest to the bioinformatics community.
Probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq and identifies differentially regulated isoforms or exons across samples.
FRAXA's mission is to accelerate progress toward effective treatments and ultimately a cure for Fragile X, by directly funding the most promising research. FRAXA also supports families affected by Fragile X and raises awareness of this important but relatively unknown disease. FRAXA was founded in 1994 by three parents of children with Fragile X, Katie Clapp, Michael Tranfaglia MD, and Kathy May, to support scientific research aimed at finding a treatment and a cure for Fragile X. Fragile X research is drastically underfunded, considering its high prevalence, prospects for a cure, and the promise that this research holds for advancing understanding of other disorders like autism, Alzheimer's disease, and X-linked mental retardation. FRAXA funds grants and fellowships at universities all over the world. We have funded more than $17 million dollars in top-notch science. FRAXA's management expenses have always been just 4% or less of income, as we have just one full-time staff, three part time staff, and hundreds of volunteer parents. Since FRAXA was founded, the Fragile X field has grown tremendously, due in large part to our grass-roots efforts. You can help us accomplish much more. FRAXA is a 501c3 tax-exempt organization; Tax ID 04-3222167
HYDEN - A Software for Designing Degenerate Primers
Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request).
Yale University Institution for Social and Policy Studies Data Archive
Data archive to assist in the sharing of research grade information pertaining to the social and economic sciences. The majority of digital content currently consists of social science research data from experiments, program files with the code for analyzing the data, requisite documentation to use and understand the data, and associated files. Access to the ISPS Data Archive is provided at no cost and is granted for scholarship and research purposes only. When possible, Data is linked to Projects and Publications, via the ISPS KnowledgeBase. ISPS operates in accordance with the prevailing standards and practices of the digital preservation community including the Open Archival Information System (OAIS) Reference Model (ISO 14721:2003) and the Data Documentation Initiative (DDI) standard. Accordingly, ISPS supports digital life-cycle management, interoperability, and preferred methods of preservation. The ISPS Data Archive is intended for use by social science researchers, policy-makers, and practitioners who are conducting or analyzing field (and other) experiments in various social science disciplines. Currently, Replication Files originate with ISPS-affiliated scholars.
micro-read substitution-only Fast Alignment Search Tool
mrsFAST: micro-read substitution-only Fast Alignment Search Tool
A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)
Multiple data sets, and associated publications, of electrophysiological data from the Computational Memory Lab, University of Pennsylvania. Separate requests must be made for each dataset. A collection of behavioral testing data is also available.
University of Colorado; Colorado Springs; USA
Public university that offers degrees in the social sciences, humanities, and natural sciences.
National Institutes of Health NeuroBioBank
National resource for investigators utilizing human post-mortem brain tissue and related biospecimens for their research to understand conditions of the nervous system. Federated network of brain and tissue repositories in the United States that collects, evaluates, stores, and makes available to researchers, brain and other tissues in a way that is consistent with the highest ethical and research standards. The NeuroBioBank ensures protection of the privacy and wishes of donors. Provides information to the public about the need for tissue donation and how to register as a donor.
South Texas Research Organizational Network Guiding Studies on Trauma and Resilience
A multidisciplinary and multi-institutional research consortium to develop and evaluate the most effective early interventions possible for the detection, prevention, and treatment of combatrelated posttraumatic stress disorder (PTSD) in activeduty military personnel and recently discharged veterans. Complementary investigations are focused on the root causes of PTSD, including biological factors that influence PTSD susceptibility and recovery; the influence of comorbid physical and psychological ailments; and the interaction of cognitive-behavioral therapies and pharmacologic treatments. The full cohort of STRONG STAR trials include: Treatment Studies, Biological Studies, Epidemiological Studies, and Preclinical Studies. STRONG STAR is currently conducting three clinical treatment trials at Carl R. Darnall Army Medical Center (CRDAMC). The studies are examining the effectiveness of Cognitive Processing Therapy (CPT), Prolonged Exposure Therapy (PE) and Cognitive Behavioral Therapy for Insomnia (CBTi) with active duty service members. Treatments are offered in individual, group, and online formats, and last from two to eight weeks. Study participants must be active duty service members who will remain in the Ft Hood area for at least 34 months to complete initial assessments and treatment programs. Referrals to the treatment studies can be made through a behavioral health provider or through selfreferral., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Prediction and Analysis of Nuclear Localization Signals
Software automated tool for analysis and determination of Nuclear Localization Signals (NLS). Predicts that your protein is nuclear or finds out whether your potential NLS is found in our database. The program also compiles statistics on the number of nuclear/non-nuclear proteins in which your potential NLS is found. Finally, proteins with similar NLS motifs are reported, and the experimental paper describing the particular NLS are given.
Data set developed to store, annotate and dsplay structural variant (SV) breakpoint events identified by PEMer and from other sources.
mrCaNaVaR - micro-read Copy Number Variant Regions
Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.
NovelSeq: Novel Sequence Insertion Detection
Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.
SRC - Better Science Through Better Stereology
A company of professionally trained stereologists, bioscientists, computer engineers, educators, and support personnel that provides comprehensive neurostereology products and services to the global bioscience community. These products and services include: stereology and image analysis software, digital imaging technology, turnkey stereologer solutions, comprehensive stereology and image analysis/image processing software, professional contract services, neurostereology workshops, basic stereology courses, and online stereology webinars. The Center also offers tissue processing (sectioning, staining, slide preparation) and stereology data collection services. Researchers may use equipment and facilities to complete projects with full confidentiality and according to Good Laboratory Practices guidelines.
PlantLoc: Plant Proteins Subcellular Localization Prediction Server
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif.
Primer3web - Pick primers from a DNA sequence
Tool used to design PCR primers from DNA sequence - often in high-throughput genomics applications. It does everything from mispriming libraries to sequence quality data to the generation of internal oligos.
A Functional Analysis and Selection Tool for SNP in Large Scale Association Study
FastSNP: A Functional Analysis and Selection Tool for SNP in Large Scale Association Study
Function Analysis and Selection Tool for Single Nucleotide Polymorphisms
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 9, 2016. A web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by deploying more Web wrapper agents. FASTSNP provides three options for users to submit requests. If users already have some candidate SNPs on a candidate gene, they may use Query by Candidate Gene to select the specific SNPs on the gene to perform prioritization. If users have a specified SNP or a list of SNP rsid's needs to be prioritized, they can use Query by SNP option and upload the SNP list in an Excel-format file. Finally, if users have a novel SNP sequence, FASTSNP provides Novel SNP analysis. FASTSNP will generate a SNP Function Report for each SNP. Users can export SNP data to an excel file for further genotyping processes. Other features of FASTSNP include SNP quality checking and haplotype LD information.
Neuroimaging Informatics Technology Initiative
Neuroimaging Informatics Technology Initiative (NIfTI)
NIfTI: Neuroimaging Informatics Technology Initiative
Coordinated and targeted service, training, and research to speed the development and enhance the utility of informatics tools related to neuroimaging. The initial focus will be on tools that are used in fMRI. If NIfTI proves useful in addressing informatics issues in the fMRI research community, it may be expanded to address similar issues in other areas of neuroimaging. Objectives of NIfTI * Enhancement of existing informatics tools used widely in neuroimaging research * Dissemination of neuroimaging informatics tools and information about them * Community-based approaches to solving common problems, such as lack of interoperability of tools and data * Unique training activities and research career development opportunities to those in the tool-user and tool-developer communities * Research and development of the next generation of neuroimaging informatics tools
Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.
Proteome Analyst Specialized Subcellular Localization Server
Web server specialized to predict the subcellular localization of proteins using established machine learning techniques.
Data analysis service that predicts subcellular location (either Nuclear, Nucleo-cytoplasmic, Cytoplasmic or Extracellular) of eukaryotic proteins using the predicted exposure value of their amino acids.
Commercial organization which provides reagents and services for molecular biology research. Its services include clone collections, microRNA solutions, genome editing, qPCR products, and fluorescent labeling and detection.
Software for detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment.
An NSF supported image repository of over 374,000 high-resolution photographs of approximately 4,000 species for research and education, used largely but not exclusively in the area of biodiversity research. Images can be annotated by users and browsed by specimen, view, taxonomy, location, collection, or annotation.
Biomedical technology research center that focuses on development of unique magnetic resonance (MR) imaging and spectroscopy methodologies and instrumentation for the acquisition of structural, functional, and biochemical information non-invasively in humans, and utilizing this capability to investigate organ function in health and disease. The distinctive feature of this resource is the emphasis on ultrahigh magnetic fields (7 Tesla and above), which was pioneered by this BTRC. This emphasis is based on the premise that there exists significant advantages to extracting biomedical information using ultrahigh magnetic fields, provided difficulties encountered by working at high frequencies corresponding to such high field strengths can be overcome by methodological and engineering solutions. This BTRC is home to some of the most advanced MR instrumentation in the world, complemented by human resources that provide unique expertise in imaging physics, engineering, and signal processing. No single group of scientists can successfully carry out all aspects of this type of interdisciplinary biomedical research; by bringing together these multi-disciplinary capabilities in a synergistic fashion, facilitating these interdisciplinary interactions, and providing adequate and centralized support for them under a central umbrella, this BTRC amplifies the contributions of each of these groups of scientists to basic and clinical biomedical research. Collectively, the approaches and instrumentation developed in this BTRC constitute some of the most important tools used today to study system level organ function and physiology in humans for basic and translational research, and are increasingly applied world-wide. CMRR Faculty conducts research in a variety of areas including: * High field functional brain mapping in humans; methodological developments, mechanistic studies, and neuroscience applications * Metabolism, bioenergetics, and perfusion studies of human pathological states (tumors, obesity, diabetes, hepatic encephalopathy, cystic fibrosis, and psychiatric disorders) * Cardiac bioenergetics under normal and pathological conditions * Automated magnetic field shimming methods that are critical for spectroscopy and ultrafast imaging at high magnetic fields * Development of high field magnetic resonance imaging and spectroscopy techniques for anatomic, physiologic, metabolic, and functional studies in humans and animal models * Radiofrequency (RF) pulse design based on adiabatic principles * Development of magnetic resonance hardware for high fields (e.g. RF coils, pre-amplifiers, digital receivers, phased arrays, etc.) * Development of software for data analysis and display for functional brain mapping.
NIH Human Pluripotent Stem Cell Registry
National Institutes of Health Human Pluripotent Stem Cell Registry
A listing of human embryonic cell lines that are eligible for use in NIH funded research. Those lines that carry disease-specific mutations are noted as such under the line name. Total Eligible Lines = 200. The purpose of the Registry is to provide investigators with: # a unique NIH Code for each cell line that must be used when applying for NIH funding and # contact information to facilitate investigators' acquisition of stem cells. Before submitting a new grant application and supporting materials for consideration of a human embryonic stem cell line, scientists may wish to see what lines are already under consideration: * Human embryonic stem cell lines submitted to NIH that are being reviewed to determine if they may be used in NIH-supported research, http://grants.nih.gov/stem_cells/registry/pending.htm President George W. Bush required that the name of the registry be changed in his Executive Order #13435, issued on June 20, 2007. As a result of this Executive Order, the former National Institutes of Health Human Embryonic Stem Cell Registry will now be called the National Institutes of Health Human Pluripotent Stem Cell Registry. The registry will now include both human embryonic stem cells that were derived consistent with the President's policy of August 9, 2001 and human pluripotent stem cells derived from non-embryonic sources.
ngLOC - A Bayesian method for predicting protein subcellular localization
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The downloadable version of this software with source code is freely available for academic use under the GNU General Public License.
An extensive high-performance subcellular protein localization prediction system that incorporates phylogenetic profiles and Gene Ontology terms to yield higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. A downloadable version of MultiLoc2 for local use is also available.
Central online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation.
A web service and web application for the annotation of microarray data providing integrated access to genomic information freely available from public data sources.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice.
Software tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching.
A database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3'-UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets. Furthermore, miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human. The cross-reference between the miRNA expression profiles and the expression profiles of its target genes can provide effective viewpoint to understand the regulatory functions of the miRNA.
Best Idea Grants (BIG) in Hyperphagia Research
Best Idea Grants in Hyperphagia Research
Request for Applications to fund the best ideas in the field of hyperphagia research. Institutions of Higher Education, Nonprofit organizations, For-profit companies are eligible.
The HUPO Proteomics Standards Initiative
Initiative to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The main organizational unit is the work group, with a Gel Electrophoresis (GEL) work group, a Mass Spectrometry (MS) work group, a Molecular Interactions (MI) work group, a Protein Modifications (MOD) work group, a Proteomics Informatics (PI) work group, and a Sample Processing (SP) work group. The Gel Electrophoresis (GEL) work group aims to develop reporting requirements that supplement the Minimum Information About a Proteomics Experiment (MIAPE) parent document, describing the minimum information that should be reported about gel-based experimental techniques used in proteomics. The group will also develop data formats for capturing MIAPE-compliant data about gel electrophoresis and informatics performed on gel images. The Mass Spectrometry Standards Working Group defines community data formats and controlled vocabulary terms facilitating data exchange and archiving in the field of proteomics mass spectrometry. A past achievement is the mzData standard, which captures mass spectrometry output data. mzData's aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into a single format. mzData has been released but is now deprecated in favor of mzML. The Molecular Interactions workgroup is concentrating on improving the annotation and representation of molecular interaction data wherever it is published, be this in journal articles, authors web-sites or public domain databases; and improving the accessibility of molecular interaction data to the user community. By using a common standard data can be downloaded from multiple sources and easily combined using a single parser. The protein modification workgroup focuses on developing a consensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications. The protein modification ontology (PSI-MOD) is available in OBO format or in OBO.xml. A spreadsheet containing the mapping of the descriptive labels used in various databases and search engines, the consensus list of proposed short name for protein modifications established by collaborative effort of mass spectrometry community, and the proposed rules and recommendations for this nomenclature are available. These short names are included in the ontology as synonyms of the corresponding terms. The Proteomics Informatics Standards Group (PSI-PI) goals are to provide a set of minimal reporting requirements which augment the MIAPE reporting guidelines with respect to analysis of data derived from proteomics experiments; to provide vendor-neutral and standard formats for representing results of analyzing and processing experimental data; to foster adoption of the format by highlighting efforts made by vendors and individuals that utilize the format in their products. The remit of the Sample Processing Working Group is to produce reporting guidelines, data exchange formats and controlled vocabulary covering all separation techniques not considered to be "classical" one- or two-dimensional gel electrophoresis (cf. the Gel WG home page), along with other kinds of sample handling and processing (for example, "tagging" proteins or peptides, splitting, combining and storing samples). Where possible we seek to develop our products in collaboration with all proteomics stakeholders and, where relevant, developers from other standards communities, most notably metabolomics. * Minimum reporting requirements: The evolving Minimum Information About a Proteomics Experiment (MIAPE) documents offer guidelines on how to adequately report a proteomics experiment. It is expected that these documents will be published, and that the requirements within will be enforced by journals, compliant repositories and funders (cf. MIAME). * XML formats for data exchange: Derived from the FuGE general object model, the formats developed by this workgroup are designed to function both as standalone files and as part of a "parent" FuGE-ML document. These formats will facilitate data exchange between researchers, and submission to repositories or journals. * Controlled vocabularies (CVs) and ontology: Lists of clearly defined terms are crucial for the construction of unambiguously worded data files. In addition to providing supporting CVs for the individual data capture formats as part of the integrated PSI CV, the Sample Processing WG will contribute terms to the Functional Genomics Ontology (FuGO).
Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism.
International Symposium on Objective Measures in Auditory Implants
8th International Symposium on Objective Measures in Auditory Implants
International Symposium on Objective Measures in Auditory Implants to explore what unique measures help us to achieve the best hearing outcome for each person who needs an auditory prosthesis.
American Association for the History of Medicine
A professional association of historians, physicians, nurses, archivists, curators, librarians, and others that promotes and encourages research, study, writing, and interest in the history of medicine and allied fields.
Software tool for detecting differential RNA processing from RNA-Seq data. It implements two statistical tests, rDiff.parametric and rDiff.nonparametric, to detect changes of the RNA processing between two samples.
A second-generation retrovirus producer lines for the generation of helper free ecotropic and amphotropic retroviruses. The lines are based on the 293T cell line (a human embryonic kidney line transformed with adenovirus E1a and carrying a temperature sensitive T antigen co-selected with neomycin). The unique feature of this cell line is that it is highly transfectable with either calcium phosphate mediated transfection or lipid-based transfection protocols-- up to 50% or higher of cells can be transiently transfected. The lines were created by placing into 293T cells constructs capable of producing gag-pol, and envelope protein for ecotropic and amphotropic viruses. The lines offered advantages over previous stable systems in that virus can be produced in just a few days. Academic and non-profit laboratories may obtain the Phoenix cells from either Allele Biotechnology or the National Gene Vector Bank. The vectors may be obtained from Addgene. They are no longer distributing these reagents from the lab.
Allele Biotechnology and Pharmaceuticals Inc
A private company offering a wide variety of Molecular Biology reagents, fluorescent proteins, luciferase assay substrates, genotyping kits, and various custom services. The company isalso in the RNAi field with its recent patents in Pol III promoter-driven siRNA, shRNA, and miRNA. They introduced high titer lentivirus, camelid antibodies, and cell based assays and also offer Baculovirus protein expression and Gryphon retrovirus systems.
Data analysis service to calculate free and total metals and chelators, Kds, complexes, and ionic contribution. You can evaluate chelators by having a non-zero value for any chelators you wish to evalute and at least one metal greater than zero. Kd's and ranges will appear at end. Only valid for metal-chelator combinations where there are constants.
MiST - Microbial Signal Transduction database
Microbial Signal Transduction database (MiST)
Database which contains the signal transduction proteins for complete and draft bacterial and archaeal genomes. The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes.
Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available.
Software package for the statistical language R, devoted to the analysis of next generation short read data of RNA-seq transcripts. It provides predictions of alternative exons in a single condition/cell sample, predictions of differential alternative exons between two conditions/cell samples, and quantification of alternative splice forms in a single condition/cell sample.
Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics.
Multichannel Acquisition Processor Software
Real-Time Acquisition System Programs for Unit Timing in Neuroscience
Real-Time Acquisition System Programs for Unit Timing in Neuroscience software
A suite of client / server programs that control spike sorting in the Multichannel Acquisition Processor (MAP) Data Acquisition System (MAP System) and provides real-time data visualization and analysis. Plexon's original program supporting multichannel data acquisition is a suite of programs referred to as the Real-Time Acquisition System Programs for Unit Timing in Neuroscience software (RASPUTIN). This combination of software and hardware enables users to view waveforms, acquire action potential waveforms around a voltage-threshold crossing, sort them in real time according to their shape, record continuous analog signals, such as field potentials, eye position, blood pressure, as well as capture external digital-event data, such as individual TTL lines or multi-bit strobed word data. RASPUTIN utilizes a client/server architecture on a Microsoft Windows operating system. The server program runs the MAP box and distributes the data among a set of cooperating client programs. The program can record analog signals and spike and digital-event data in a single data file, and supports 16, 32, 48, 64, 96 and 128 channel configurations. RASPUTIN's operation is based on two primary programs: Sort Client and MAP Server. The Sort Client is the primary control program for the MAP System hardware and may be used to adjust the MAP operating parameters (e.g., amplification, filtering) and to set the specific sorting parameters for each channel. MAP Server is the low-level interface for configuring the MAP, which transfers commands such as gain and filter changes or parameter settings from the various clients to the MAP box. MAP Server also accumulates data coming from the MAP box in a circular buffer memory. The client programs connect to MAP Server to gain access to that data. MAP Server also mediates communication between the clients, keeping them informed of commands sent to the MAP from other clients. RASPUTIN is not sold separately, but rather arrives pre-loaded on the MAP Control Computer with the purchase of any MAP System. As the MAP System has been replaced by the advanced OmniPlex D Neural Data Acquisition System, Plexon is no longer developing the RASPUTIN software program.
Software for evaluating the performance of bioinformatics pipelines for Next Generation re-Sequencing.
HuGE Navigator - Human Genome Epidemiology Navigator
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Knowledge base of genetic associations and human genome epidemiology including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. This tool explores HuGENet, the Human Genome Epidemiology Network, which is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. What does HuGE Navigator offer? *HuGEpedia - an encyclopedia of human genetic variation in health and disease, includes, Phenopedia and Genopedia. Phenopedia allows you to look up gene-disease association summaries by disease, and Genopedia allows you to look up gene-disease association summaries by gene. In general, HuGEpedia is a searchable database that summarizes published articles about human disease and genetic variation, including primary studies, reviews, and meta-analyses. It provides links to Pubmed abstracts, researcher contact info, trends, and more. *HuGEtools - searching and mining the literature in human genome epidemiology, includes, HuGE Literature Finder, HuGE Investigator Browser, Gene Prospector, HuGE Watch, Variant Name Mapper, and HuGE Risk Translator. *HuGE Literature Finder finds published articles in human genome epidemiology since 2001. The search query can include genes, disease, outcome, environmental factors, author, etc. Results can be filtered by these categories. It is also possible to see all articles in the database for a particular topic, such as genotype prevalence, pharmacogenomics, or clinical trial. *HuGE Investigator Browser finds investigators in a particular field of human genome epidemiology. This info is obtained using a behind-the-scenes tool that automatically parses PubMed affiliation data. *Gene Prospector is a gateway for evaluating genes in relation to disease and risk factors. This tool allows you to enter a disease or risk factor and then supplies you with a table of genes associated w/your query that are ranked based on strength of evidence from the literature. This evidence is culled from the HuGE Literature Finder and NCBI Entrez Gene - And you're given the scoring formula. The Gene Prospector results table provides access to the Genopedia entry for each gene in the list, general info including links to other resources, SNP info, and associated literature from HuGE, PubMed, GWAS, and more. It is a great place to locate a lot of info about your disease/gene of interest very quickly. *HuGE Watch tracks the evolution of published literature, HuGE investigators, genes studied, or diseases studied in human genome epidemiology. For example, if you search Trend/Pattern for Diseases Studied you'll initially get a graph and chart of the number of diseases studied per year since 1997. You can refine these results by limiting the temporal trend to a category or study type such as Gene-gene Interaction or HuGE Review. *Variant Name Mapper maps common names and rs numbers of genetic variants using information from SNP500Cancer, SNPedia, pharmGKB, ALFRED, AlzGene, PDGene, SZgene, HuGE Navigator, LSDBs, and user submissions. *HuGE Risk Translator calculates the predictive value of genetic markers for disease risk. To do so, users must enter the frequency of risk variant, the population disease risk, and the odds ratio between the gene and disease. This information is necessary in order to yield a useful predictive result. *HuGEmix - a series of HuGE related informatics utilities and projects, includes, GAPscreener, HuGE Track, Open Source. GAPscreener is a screening tool for published literature on human genetic associations; HuGE Track is a custom track built for HuGE data in the UCSC Genome Browser; and Open Source is infrastructure for managing knowledge and information from PubMed.
iLoc-Animal: Predicting subcellular localization of animal proteins with single or multiple sites
Data analysis service for predicting subcellular localization of animal proteins with single or multiple sites.
QDNAseq - Quantitative DNA sequencing for chromosomal aberrations
Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.
We define a simple method to detect cortical states that can be applied in real time for offline processing of large amounts of recorded data on conventional computers. Also, the online detection of up and down states will facilitate the study of cortical dynamics. An open-source MATLAB toolbox, and Spike 2-compatible version are made freely available. Intracellular recordings from different areas of the cerebral cortex were obtained from both in vitro and in vivo preparations during slow oscillations. A method that separates up and down states recorded intracellularly is defined and analyzed here. The method exploits the crossover of moving averages, such that transitions between up and down membrane regimes can be anticipated based on recent and past voltage dynamics. We demonstrate experimentally the utility and performance of this method both offline and online, the online use allowing to trigger stimulation or other events in the desired period of the rhythm. This technique is compared with a histogram-based approach that separates the states by establishing one or two discriminating membrane potential levels. The robustness of the method presented here is tested on data that departs from highly regular alternating up and down states. The neuronal cortical network generates slow (<1 Hz) spontaneous rhythmic activity that emerges from the recurrent connectivity. This activity occurs during slow wave sleep or anesthesia and also in cortical slices, consisting of alternating up (active, depolarized) and down (silent, hyperpolarized) states. The search for the underlying mechanisms and the possibility of analyzing network dynamics in vitro has been subject of numerous studies. This exposes the need for a detailed quantitative analysis of the membrane fluctuating behavior and computerized tools to automatically characterize the occurrence of up and down states.
WebServer that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins and genes, such as a set of disease-associated proteins and a set of differentially expressed disease genes, and a molecular interaction network (i.e., interactome). The output is a sparse, high-probability interactome sub-network connecting the two sets that is biased toward signaling pathways. This sub-network exposes additional proteins that are potentially involved in the studied condition and their likely modes of action. Computationally, it is formulated as a minimum-cost flow optimization problem that is solved using linear programming.
Commercial organization for research and development genomics services and technical support to researchers.
UCLA based service for research planning aimed to help users integrate and summarize large amounts of information into a searchable graphic format. The interactive features facilitates planning during writing of grants, research papers and reviews. ResearchMaps can also be used as a collaborative tool and as a catalyst for the creative process.
A comprehensive database for human surface and intracranial EEG data that is suitable for a broad range of applications e.g. of time series analyses of brain activity. Currently, the EU database contains annotated EEG datasets from more than 200 patients with epilepsy, 50 of them with intracranial recordings with up to 122 channels. Each dataset provides EEG data for a continuous recording time of at least 96 hours (4 days) at a sample rate of up to 2500 Hz. Clinical patient information and MR imaging data supplement the EEG data. The total duration of EEG recordings included execeeds 30000 hours. The database is composed of different modalities: Binary files with EEG recording / MR imaging data and Relational database for supplementary meta data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A curated database for synaptic proteins that provides adequate definitions of pre- and post-synaptic proteins, proteins present in sub-domains of the synapse, e.g. the synaptic vesicle and associated proteins, lipid rafts and postsynaptic density. In addition to data that was and will be gathered from the experiments conducted within SynSys - A European expertise Network on building the synapse, they have extracted and manually curated all relevant data on these proteins from other sources and provided an ontology for these. Novel splice forms are being identified that can be matched with proteomics data. Information on proteins, their 3D structure, binding small molecules Protein-Protein-Interactions (PPIs) and Compound-Protein-Interactions are integrated. Proteins or compounds can be searched and Interactive Networks can be visualized. The point Diseases present neurological diseases, to illustrate the role of SynSysNet in the medication.
Efficient paired-read overlap software program for use with Illumina sequencing.
A software application for such tasks as photo retouching, image composition and image authoring. It has many capabilities such as it can be used as a simple paint program, an expert quality photo retouching program, an online batch processing system, a mass production image renderer, an image format converter, etc. GIMP is expandable and extensible and designed to be augmented with plug-ins and extensions. The advanced scripting interface allows everything from the simplest task to the most complex image manipulation procedures to be easily scripted.
An automatic web server for protein molecular modelling. Starting with a query protein sequence, the server performs the homology modelling in six successive steps: (i) identify homologous proteins with known 3D structures by using PSI-BLAST; (ii) provide the user all potential templates through a very convenient user interface for target selection; (iii) perform the alignment of both query and subject sequences; (iv) extract geometrical restraints (dihedral angles and distances) for corresponding atoms between the query and the template; (v) perform the 3D construction of the protein by using a distance geometry approach and (vi) finally send the results by e-mail to the user. The strategy used in Geno3D is comparative protein structure modelling by spatial restraints (distances and dihedral) satisfaction.
A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
ProLinks Database of Functional Linkages
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage.
Web server to predict eukaryotic selenoproteins and SECIS (SElenoCysteine Insertion Sequences) elements along nucleotide sequences. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins.
Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families.
Software application to visualize and navigate large trees in hyperbolic space. Features include: * visualize large trees with hundreds of nodes or more * rotate and drag the display in cartesian space * search and select nodes * copy clusters for pasting into other programs * color-code branches * label branches (eg, common family members) * zoom in and out * view phylogenetic trees and other hierarchical clusters, such as gene expression profile clusters * run on several platforms: Mac, Windows, Unix/Linux
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. This site has a collection of cortical connectivity datasets and modeling software components that can be downloaded and used for modeling of cortical circuits. The toolbox combines Matlab functions and neuroanatomical data sets useful in the analysis of structural or functional brain networks. Several people have made contributions and if you wish to contribute yourself with a new function or set of functions please contact osporns_at_indiana.edu.The following is a collection of commonly used large scale cortical connectivity data sets compiled from tract-tracing studies. Hence nodes represent cortical areas and links represent large cortico-cortical tracts. * macaque71.mat (BD network). Macaque cortical connectivity: 71 nodes 746 links. Reference: Young (1993). Contributor: OS. Used in e.g. Sporns (2002). * fve30.mat; fve32.mat (BD networks). Two version the macaque visual cortex. fve30.mat: 30 nodes 311 links. fve32.mat: 32 nodes 320 links. Reference: Felleman and van Essen (1991). Contributor: OS. Used in e.g. Sportns et al. (2000) Sporns and Kotter (2004). * macaque47.mat (BD network). Large scale cortico-cortical connectivity matrix of the visual and sensorimotor areas in the macaque. 47 nodes; 505 links. Used in e.g. Honey et al. (2007). Contributor: RK. * cat.mat (WD networks). Connection matrices of cat cortex. CIJall contains all cortical and thalamic areas: 95 nodes 2126 links. CIJctx contains only 52 cortical areas: 52 nodes 820 links. Reference: Scannell et al. (1999). Contributor: OS. Used in e.g. Sporns and Zwi (2004) Sporns and Kotter (2004). * DSIhumanctx.mat (WU networks).
GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool
GOLEM An interactive graphical gene-ontology visualization navigation analysis tool
GOLEM An interactive graphical gene-ontology visualization navigation and analysis tool
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Welcome to the home of GOLEM: An interactive, graphical gene-ontology visualization, navigation,and analysis tool on the web. GOLEM is a useful tool which allows the viewer to navigate and explore a local portion of the Gene Ontology (GO) hierarchy. Users can also load annotations for various organisms into the ontology in order to search for particular genes, or to limit the display to show only GO terms relevant to a particular organism, or to quickly search for GO terms enriched in a set of query genes. GOLEM is implemented in Java, and is available both for use on the web as an applet, and for download as a JAR package. A brief tutorial on how to use GOLEM is available both online and in the instructions included in the program. We also have a list of links to libraries used to make GOLEM, as well as the various organizations that curate organism annotations to the ontology. GOLEM is available as a .jar package and a macintosh .app for use on- or off- line as a stand-alone package. You will need to have Java (v.1.5 or greater) installed on your system to run GOLEM. Source code (including Eclipse project files) are also available. GOLEM (Gene Ontology Local Exploration Map)is a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet.
GOToolBox Functional Investigation of Gene Datasets
GOToolBox - Functional Investigation of Gene Datasets
GOToolBox : Functional Investigation of Gene Datasets
The GOToolBox web server provides a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource. The web version of the GOToolBox is free for non-commercial users only. Users from commercial companies are allowed to use the site during a reasonable testing period. For a regular use of the web version, a license fee should be paid. We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license. Platform: Online tool
Project exploring the spectrum of genomic changes involved in more than 20 types of human cancer that provides a platform for researchers to search, download, and analyze data sets generated. As a pilot project it confirmed that an atlas of changes could be created for specific cancer types. It also showed that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale and develop an infrastructure for making the data publicly accessible. Its success committed resources to collect and characterize more than 20 additional tumor types. Components of the TCGA Research Network: * Biospecimen Core Resource (BCR); Tissue samples are carefully cataloged, processed, checked for quality and stored, complete with important medical information about the patient. * Genome Characterization Centers (GCCs); Several technologies will be used to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the Genome Sequencing Centers. * Genome Sequencing Centers (GSCs); High-throughput Genome Sequencing Centers will identify the changes in DNA sequences that are associated with specific types of cancer. * Proteome Characterization Centers (PCCs); The centers, a component of NCI's Clinical Proteomic Tumor Analysis Consortium, will ascertain and analyze the total proteomic content of a subset of TCGA samples. * Data Coordinating Center (DCC); The information that is generated by TCGA will be centrally managed at the DCC and entered into the TCGA Data Portal and Cancer Genomics Hub as it becomes available. Centralization of data facilitates data transfer between the network and the research community, and makes data analysis more efficient. The DCC manages the TCGA Data Portal. * Cancer Genomics Hub (CGHub); Lower level sequence data will be deposited into a secure repository. This database stores cancer genome sequences and alignments. * Genome Data Analysis Centers (GDACs) - Immense amounts of data from array and second-generation sequencing technologies must be integrated across thousands of samples. These centers will provide novel informatics tools to the entire research community to facilitate broader use of TCGA data. TCGA is actively developing a network of collaborators who are able to provide samples that are collected retrospectively (tissues that had already been collected and stored) or prospectively (tissues that will be collected in the future).
Inter-university Consortium for Political and Social Research (ICPSR)
Inter-university Consortium for Political Social Research (ICPSR)
Interuniversity Consortium for Political and Social Research
Interuniversity Consortium for Political Social Research
Data archive of more than 500,000 files of research in the social sciences, hosting 16 specialized collections of data in education, aging, criminal justice, substance abuse, terrorism, and other fields. ICPSR comprises a consortium of about 700 academic institutions and research organizations providing training in data access, curation, and methods of analysis for the social science research community. ICPSR welcomes and encourages deposits of digital data. ICPSR's educational activities include the Summer Program in Quantitative Methods of Social Research external link, a comprehensive curriculum of intensive courses in research design, statistics, data analysis, and social methodology. ICPSR also leads several initiatives that encourage use of data in teaching, particularly for undergraduate instruction. ICPSR-sponsored research focuses on the emerging challenges of digital curation and data science. ICPSR researchers also examine substantive issues related to our collections, with an emphasis on historical demography and the environment.
Commercial organization that provides services for assay development, research histopathology, and early stage project consultation.
ARC Centre of Excellence in Vision Science
ARC Center of Excellence in Vision Science
Australian Research Council Centre of Excellence in Vision Science
Centre of Excellence in Vision Science that brings together major vision research programs at the The Australian National University with cognate programs at the Universities of Queensland, Sydney and Western Australia. The research is focused on unravelling the cellular basis of visual sensing and processing; on revealing the algorithms that underlie the visual control of behavior and perception; and on discovering the cellular mechanisms that make the eye and retina stable, and whose breakdown causes blindness.
Data Federated Electronic Research Review Extraction and Tabulation Tool
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2025. A data analysis and extraction tool from the US Census Bureaus with recoding capabilities to customize federal, state, and local data to suit your requirements. DataFerret works with the DataWeb, a network of online data libraries and an infrastructure for intelligent browsing. TheDataweb provides easy access to data from disparate locations across the internet using DataFerrett as its interface. It brings together demographic, economic, environmental, health, and other datasets that are usually separated by geography and/or organization.Using DataFerrett, you can develop an unlimited array of customized spreadsheets that are as versatile and complex as your usage demands. For a listing/description of datasets available using the DataFerrett refer to the Datasets Available tab. DataFerrett helps you locate and retrieve the data you need across the Internet to your desktop or system, regardless of where the data resides. You can develop and customize tables and select the results to create a graph or map for a visual depiction of your data. You can also save your data in the databasket and save the table you have created for reuse. The DataFerrett tool can use a java applet through an internet browser or be installed as an application on your desktop. The DataFerrett Applet requires you to have popup windows enabled in your browser for this website to function properly.
An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results.
Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.
Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses.
A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Formerly a commercial organization for clinical diagnostics, blood screening, transplant products and research products, it had been acquired by Hologic in 2012.
Council of Scientific and Industrial Research
Council of Scientific & Industrial Research
Research and development organization that hosts a knowledgebase in diverse scientific areas. It also hosts a network of national Indian laboratories, outreach centres, and innovation complexes.
Phylogenetic Analysis with Space/Time Models
A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.
NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. 2012 workshop to establish a Central Resource of Data from Genome Sequencing Projects. The workshop addressed the challenges to aggregating and analyzing data sets from genome sequencing studies, such as: * Data sets being generally hard to access. * Data residing in various databases. * Variant and exposure/phenotype data not being comparable across studies. Participants in the workshop discussed options for dealing with these challenges, along with their costs and tradeoffs. Videos and accompanying slides from the workshop are available. Also available as a video playlist on GenomeTV
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 10, 2017. Sidewiki allows you to publish helpful information about any web page right in your browser, read insights in context from Sidewiki entries added by others, and share Sidewiki entries through Blogger, Facebook, Twitter and Google profiles. The toolbar with Sidewiki is free, installs in seconds and requires Internet Explorer 6+ or Firefox 2+; Windows XP SP2/Vista+. A Google Sidewiki extension is only available for Google Chrome 4.0+
EMDataBank - Unified Data Resource for 3DEM
Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods.
A tool for finding admixture proportions from next generation sequencing (NGS) data that is based on genotype likelihoods. It is a multithreaded c/c++ program.
QGene - Software for QTL data exploration
A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.
Statistical analysis and scientific graphing software for Windows OS.
Gemi - PCR oligos / primers design from multiple sequence alignments
Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences.
Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility.
Web application providing online database and workspace for evolutionary research, specifically systematics (the science of determining the evolutionary relationships among species). It enables researchers to upload images and affiliate data with those images (labels, species names, etc.) and allows researchers to upload morphological data and affiliate it with phylogenetic matrices. MorphoBank is project-based, meaning a team of researchers can create a project and share the images and associated data exclusively with each other. When a paper associated with the project is published, the research team can make their data permanently available for view on MorphoBank where it is now archived.
A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.
Glossary of Genetic Terms to help everyone understand the terms and concepts used in genetic research. In addition to definitions, specialists in the field of genetics share their descriptions of terms, and many terms include images, animation and links to related terms.
Wellcome-CTC Mouse Strain SNP Genotype Set
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34.
An official Digital Object Identifier (DOI) Registration Agency of the International DOI Foundation launched as a cooperative effort among publishers to enable persistent cross-publisher citation linking in online academic journals. The citation-linking network today covers over 65 million journal articles and other content items (books chapters, data, theses, technical reports) from thousands of scholarly and professional publishers around the globe. CrossRef does not aggregate full-text content but rather, it uses a system of distributed aggregation whereby full-text content is linked through a database consisting of minimal publisher metadata. Each record in the database is essentially a triplet: (metadata + URL+DOI). In addition to assigning DOIs to scholarly content, CrossRef has additional services: * Cited-By Linking * CrossRef Metadata Services * CrossCheck plagiarism screening (powered by iThenticate) * CrossMark update identification service * FundRef Funder identification service
Funder Registry and associated funding metadata allows everyone to have transparency into research funding and its outcomes. Open registry of persistent identifiers for grant-giving organizations around the world.
Database of Genomic Structural Variation
Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals.
Software toolbox for creating customized pediatric templates. It provides reference data based on imaging data from the NIH study of normal brain development. Using the general linear model, they statistically isolate the influence of external variables of interest on brain structure, allowing us to generate high-quality matched templates for any given group of subjects. The toolbox offers two options: # to create pediatric templates (T1) and tissue maps (GM, WM, and CSF) based on the objective 1 NIH data (n = 404), in the age range of 5-18 years, or # to assess a new reference population with regard to your variables of interest. Of note, this approach is generally applicable and in no way restricted to analyzing pediatric imaging data: for example, if you aim at investigating the effects of aging in elderly subjects, the toolbox will also allow you to create more appropriate reference (if your group is large enough to isolate such effects).
Minimum Information about a high-throughput SEQuencing Experiment
The Minimum Information about a high-throughput nucleotide SEQuencing Experiment that is needed to enable the unambiguous interpretation and facilitate reproduction of the results of the experiment. By analogy to the MIAME guidelines for microarray experiments, adherence to the MINSEQE guidelines will improve integration of multiple experiments across different modalities, thereby maximising the value of high-throughput research. The five elements of experimental description considered essential when making data available supporting published high-throughput sequencing experiments are as follows: # The description of the biological system, samples, and the experimental variables being studied # The sequence read data for each assay # The "final" processed (or summary) data for the set of assays in the study # General information about the experiment and sample-data relationships # Essential experimental and data processing protocols
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.
Tools for researchers to connect their data, code and computational methods to their published or soon to be published research in a convenient and easily citeable form. ResearchCompendia provides the tools to publish digital scholarly objects by hosting data, code, and methods in a form that is accessible, trackable, and persistent. They provide hosting and computational cloud resources for all researchers. Data and code should be citable and linked to the original publication.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. An online catalog for whole-exome sequencing (WES) results including mutations and gene-disease associations identified by WES. It is browsable and searchable by mutation, gene, study or publication. In addition, it centralizes all publications, software, platforms related to exome / whole genome sequencing.
SobekCM : Digital Content Management System
Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.
Community group working towards a common, RDF-based, specification for annotating digital resources. The effort began by trying to reconcile two proposals: the Annotation Ontology (http://code.google.com/p/annotation-ontology/) and the Open Annotation Model (http://www.openannotation.org/spec/beta/ ). Initially, editors of these proposals collaborated to devise a common draft specification that addresses requirements and use cases that were identified in the course of their respective efforts. This draft became available for public feedback and experimentation in the second quarter of 2012. The final deliverable is a specification, published under an appropriate open license, that is informed by the existing proposals, the common draft specification, and the community feedback.
A Mozilla project to teach and enable users on how to create on the web. Their tools, events and teaching guides allow webmakers to create the content that makes the web great and understand how the web works. They've built everything so you can see how it works, take it apart and remix it
A social writing platform, free for education, to easily create a classroom workspace where teacher and students can communicate and work on writing projects alone or in teams. Rich assessment tools give the power to measure student contribution and engagement in real-time. Wikispaces Classroom works great on modern browsers, tablets, and phones. For a fee it is also available to non-educators including companies, organizations, universities, groups, etc.
Mobile Diagnostic Rapid Test Strip Reader
Smart phone, tablet and mobile device software designed for highly sensitive real-time analysis and quantification of inexpensive rapid diagnostic test strips. The software allows anyone with a camera equipped device to take an image of a Rapid Diagnostic Test Strip and get back instant quantifiable results. It has the ability to run multiple tests at once and can be configured to read any lateral flow test strip.
RIKEN Arabidopsis Transposon mutants is a series of mutant lines which have a Ds transposon in the genome of Arabidopsis thaliana Nssen ecotype (background by Fedoroff and Smith). This web page provides information on the mutants produced in our laboratory. Each mutant line is assigned by stipulated line codes (ex. 13-4480-1). We determined the flanking sequences of Ds insertion for each independent line. Transposon insertion sites of mutants were estimated by a BLASTN homology against the genome sequence database of Arabidopsis thaliana Columbia ecotype. The closest genes (predicted by AGI) to the transposon insertion sites were picked up. The results of the BLASTP homology search against the nr database of NCBI for the closest genes have been collected for keyword searches.
Free software extension for MediaWiki that makes a wiki into an environment for collaborating on publication-quality manuscripts and software projects. It allows wiki users to work together on anything that can be done by using UNIX commands to transform textual source code into output. Researchers can use it to collaborate on programs written in R, python, C, or any other language, and there are special features to support easy work on LaTeX documents. It develops the potential of the wiki medium to serve as a combination collaborative text editor, development environment, revision control system, and publishing platform. Its potential uses are open-ended - its processing is controlled by makefiles that are straightforward to customize - and its modular design is intended to allow parts of it to be adapted to other purposes.
A collaboration tool which allows users to edit and publish scientific articles and papers. Overleaf utilizes the convenience of an easy-to-use WYSIWYG manuscript editor with real-time collaboration and structured, fully typeset output produced automatically. Authors can publish immediately and directly to their journal of choice while publishers can reduce their editorial and review turnaround times with powerful change tracking, commenting, and project lifecycle management features. It was formerly known as writeLaTex but changed its name to Overleaf in 2015.
Free software application for notetaking, sketching, keeping a journal using a stylus that runs on Linux (recent distributions) and other GTK+/Gnome platforms. It is similar to Microsoft Windows Journal or to other alternatives such as Jarnal, Gournal, and NoteLab. Note: is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations.
An open XML-based language used to describe the formatting of citations and bibliographies. CSL has become the standard way to add citation support to software.
An organization for universities and research institutions that is an information service and a forum for raising and discussing issues around the mission of modern universities and research institutions, particularly with regard to the creation, dissemination and preservation of research findings. Its aim is to further the opening up of scholarship and research that we are now seeing through the growing open access, open education, open science and open innovation movements. These, and other, "open" approaches to scholarship are changing the way research and learning are done and there are profound implications for universities and research institutions. EOS has been established to help guide developments and to assist others in understanding the issues and their implications. The context in which EOS has been established is that of increasing interest from governments, funders and the research community itself in opening up the way research is carried out and communicated. This interest is complemented by new research practices and processes that can work effectively only in an open, collaborative environment. Developments of relevance to the mission of EnablingOpenScholarship are reported on and news and details of forthcoming meetings, briefings and discussion sessions is provided.
Database of journal information that provides tools to search, sort, filter, compare, and evaluate scholarly journals. In addition to searching by journal name, category or publisher, authors can use title and abstract of paper to discover journals that have already published articles on similar topics. Data sources include major industry data sets, public resources, information submitted directly by journal editors, and real-life publishing experiences submitted by authors.
Commercial organization that supplies antibodies, proteins, ELISA kits, serum, and plasma to the research community.
Platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research.
Non-profit organization to increase the openness, integrity, and reproducibility of scientific research. COS priorities are to (1) make the entire scientific workflow accessible, (2) increase scientists' accountability, (3) facilitate good practices by scientists, (4) increase reward for good practices, and (5) promote reproducibility of scientific findings. COS has three primary activities: * Infrastructure development to support the scientific workflow and to connect technologies that support scientific research and communication, such as the Open Science Framework * Community building on open practices among open-source developers, open science researchers, and the broader scientific community, such as the Open Science Collaboration * Metascience, research on scientific practices, such as Reproducibility Project: Psychology and our partnership with Science Exchange, Reproducibility Project: Cancer Biology.
Private foundation whose funding activities are primarily centered around improving life in the United States. Its mission is to produce big and lasting changes in society over the long term. Their four areas of focus (2014) are: criminal justice, K-12 education, public accountability, and research integrity.
Child Language Data Exchange System (CHILDES)
Child language component of TalkBank system. TalkBank is system for sharing and studying conversational interactions. Includes software developed for speech recognition and analysis as well as behavior recognition. Database contains transcript and media data collected from conversations between young children and their playmates and caretakers. Conversations with older children and adults are available from TalkBank. All of data is transcribed in CHAT and CA/CHAT formats.
Databases of transcript and media data collected from conversations with adults and older children to foster fundamental research in the study of human and animal communication. Conversations with children are available from CHILDES. All of the data is transcribed in CHAT and CA/CHAT formats. Databases of the following types are included in the collection: Aphasia patient speech, Child speech, Study of Phonological Development, Conversation Analysis, and Bilingualism and Second Language Acquisition. TalkBank will use these databases to advance the development of standards and tools for creating, sharing, searching, and commenting upon primary materials via networked computers.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. MUGEN Mouse Database (MMdb) is a virtual and fully searchable repository of murine models of immune processes and immunological diseases. MMdb is being developed within the context of the MUGEN network of Excellence, a consortium of 21 leading research institutes and universities, and currently holds all mutant mouse models that were developed within the consortium. Its primary aim is to enable information exchange between participating institutions on mouse strain characteristics and availability. More importantly, it aims to create a mouse-centric international forum on modelling of immunological diseases and pave the way to systems biology of the mouse by correlating various genotypic and phenotypic characteristics. The basic categorization of models is based on three major research application categories: * Model of Human Disease * Model of Immune Processes * Transgenic Tool Mutant strains carry detailed information on affected gene(s), mutant alleles and genetic background (DNA origin, targeted, host and backcrossing background). Each gene/transgene index also includes IDs and direct links to Ensembl (EBI��s genome browser), ArrayExpress (providing expression profiles), Eurexpress II (for embryonic expression patterns) and NCBI��s Entrez Gene database. Phenotypic description is standardized and hierarchically structured, based on MGI��s mammalian phenotypic ontology terms, but also includes relevant images and references. Since version 2.1.0 MMdb is also utilizing PATO. Availability (in the form of live mice, cryopreserved embryos or sperm, as well as ES cells) is clearly indicated, along with handling and genotyping details (in the form of documents or hyperlinks) and all relevant contact information (including EMMA and JAX hyperlinks where available).
A biorepository and biomaterial supply resource which establishes, verifies, maintains, and distributes cells, cultures and DNA derived from cell cultures to the scientific community around the world. Scientists can browse the sample catalog and request specific cell lines for their research studies. An inventory of the remaining stock of each cell line and DNA preparation is presented in real time. Coriell's significant cell biobank collections include: NIGMS Human Genetic Cell Repository, NINDS Human Genetics DNA and Cell Line Repository, NIA Aging Cell Repository, NHGRI Sample Repository for Human Genetic Research, NEI Age-Related Eye Disease Study (AREDS) Genetic Repository, HD Community BioRepository, American Diabetes Association, GENNID Study, and Autism Research Resource. The repositories are ISO 9000-2001 compliant.
An ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. The project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies.
Oversight Committee appointed to monitor, coordinate and review the efforts of working groups (WG) in specialist areas (Biological context metadata WG, Chemical analysis WG, Data processing WG, Ontology WG, Exchange format WG) that will examine standardization and make recommendations.
Ontology for describing NMR experiments and acquisitions.
Catalog containing information about 547 biological pathway related resources and molecular interaction related resources. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.
Software for detection of differential splicing between two different conditions using RNA-Seq data.
RIKEN Tsukuba Institute RIKEN BioResource Center
RIKEN BRC contributes to advancement of life science research by collecting, preserving and distributing biological resources such as experimental animals, experimental plants, cultured cell lines, genetic materials (DNA), and associated bioinformatics. The RIKEN BRC develops novel bioresources to promote scientific research and new technologies to increase the value of bioresources, and also to implement effective procedures for the preservation, quality control and usage of bioresources. The RIKEN BRC is working closely with institutions in Japan and abroad.
Database with annotations for human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene.
Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.
Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed.
A structured controlled vocabulary for the phenotypes of Ascomycete fungi.
A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF).
Database for a curated classification and nomenclature that contains the names of all organisms that are represented in the public sequence databases with at least one nucleotide or protein sequence. Data provided encompasses archaea, bacteria, eukaryota, viroids and viruses. The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such.
Databases of protein sequences and 3D structures of proteins. Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
Radiotracer Chemistry Instrumentation and Biological Imaging
Radiotracer Chemistry and Instrumentation for Biological Imaging
Develop new scientific tools to image the movement of molecules in energy-relevant and environmentally-sensitive contexts in response to BER's call to explore the potential of radiotracer imaging in energy and environmentally-responsive contexts. Their goal is to visualize metabolic networks and regulatory systems underlying cellular communication in the living organism including plants and microbial communities. This has broad implications to DOE missions in energy and the environment and is very relevant to improvements in plant biomass for biofuel.
An application ontology built for the Beta Cell Genomics database aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc.
Gene Expression Profiling in Spinal Cord Injury
Database which provides on-line searching of microarray datasets generated from rat spinal cord after contusion injury. Both the primary injury site and a site 5 mm distal to the injury site were assayed. Tissue was obtained from Long Evans rats subject to spinal cord contusion injury using the MASCIS impactor (formerly known as the NYU impactor). RNA expression was assayed at the site of injury and distal to the site of injury using the Affymetrix Rat Neuro U34 chip.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 2, 2016. Database for defining official rat gene symbols. It includes rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. Rat Gene Symbol Tracker approves rat gene symbols by an automatic procedure. The rat genes are presented with links to RGD, Ensembl, NCBI Gene, MGI and HGNC. RGST ensures that each acclaimed rat gene symbol is unique and follows the guidelines given by the RGNC. To each symbol a status level associated, describing the gene naming process.
Ontology developed as an application ontology as part of the Biocode Commons project whose goal is to support the interoperability of biodiversity data, including data on museum collections, environmental and metagenomic samples, and ecological surveys. It includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of samples. Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.
Database of human brain images derived from a realistic phantom and generated using a sophisticated MRI simulator. Custom simulations may be generated to match a user's selected parameters. The goal is to aid validation of computer-aided quantitative analysis of medical image data. The SBD contains a set of realistic MRI data volumes produced by an MRI simulator. These data can be used by the neuroimaging community to evaluate the performance of various image analysis methods in a setting where the truth is known. The SBD contains simulated brain MRI data based on two anatomical models: normal and multiple sclerosis (MS). For both of these, full 3-dimensional data volumes have been simulated using three sequences (T1-, T2-, and proton-density- (PD-) weighted) and a variety of slice thicknesses, noise levels, and levels of intensity non-uniformity. These data are available for viewing in three orthogonal views (transversal, sagittal, and coronal), and for downloading.
Developer of enterprise-class software systems for workflow management of genetic analysis. Geospiza has established itself as the life science industry's top software developer for meeting the combined laboratory, data management and analytical needs of biotechnology and pharmaceutical companies, universities, researchers, contract core and diagnostic laboratories involved in genetic testing and manufacturing bio-therapeutics. Geospiza's products are designed and built by biologists, enabling researchers to focus on the science, not the software. *GeneSifter Analysis Edition: Access easy-to-use statistical, visualization and annotation tools for Microarray and Next Generation Sequencing data. *GeneSifter Lab Edition: Manage cross-platform core lab operations from a single interface out-of-the-box.
Serial histological sections of rat spinal cord at the lumbar and thoracic levels. Serial sections of rat spinal cord cut in the horizontal and sagittal planes. Also transverse and sagittal section series of the postnatal thoracic spinal cord immunolabeled for SMI-32.
A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data.
Nematode & Neglected Genomics (at) The Blaxter Lab
nematodes.org Nematode & Neglected Genomics (at) The Blaxter Lab
Nematode & Neglected Genomics (at) The Blaxter Lab is a nematode related portal including databases and services. Resources include genomic and transcriptomic databases for nematodes and other metazoan phyla and freely downloadable software tools for expressed sequence tag analysis, DNA barcode analysis and phylogenomics. Major categories include: * GenePool * 959 Nematode Genomes * Teaching * Research Projects * Bioinformatics Software Tools * Lab Personnel * Lab Wiki * Genomics Databases * NEMBASE4 * Tardigrada: Hypsibius dujardini * Earthworm: Lumbricus rubellus * MolluscDB * ArthropodDB * other Neglected Genomes
Database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified. It is curated from literature. Each NESbase entry contains information of whether NES was shown to be necessary and/or sufficient for export, and whether the export was shown to be mediated by the export receptor CRM1. The compiled information was used to make a sequence logo of the Leucine-rich NESs, displaying the conservation of amino acids within a window of 25 residues. Error reports and submissions of new data are most welcome!
An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.
Jackson Laboratory Cytogenetic Models Resource
Jackson Lab: Cytogenetic Models Resource
Maintains and distributes chromosome aberration stocks that provide primarily mouse models for Down syndrome. The Resource currently provides models for Down syndrome research, including: Rb(6.16)24Lub x Rb(16.17)7Bnr F1 hybrids that are used to produce Chr 16 trisomy (Ts16) embryos, which have many of the fetal developmental features of DS, and; Ts(1716)65Dn, segmental trisomy mice that survive to adulthood and have many of the features of DS. The Resource also includes stocks with selected reciprocal translocations involving Chr 16 and some Chr 16 transgenic stocks. In addition, a large number of Robertsonian chromosome stocks are held as frozen embryos in the Cryopreservation Resource. Each mouse chromosome is present in at least two different Robertsonian chromosomes in these strains so that specific trisomies for each of the 19 mouse autosomes can be produced. Breeding pairs and individual mice are provided.
Research Network in Early Experience and Brain Development
Research Network in Early Experience Brain Development
Research Network on Early Experience and Brain Development
Portal on how the experiences of early childhood are incorporated into the structures of the developing brain, and how, in turn, those changes in the structures of the brain influence behavior. The network explores how knowledge of brain development can guide us in understanding of behavioral development and vice versa. It focuses specifically on sensitive periods and neural plasticity, the reciprocal phenomena whereby (a) the brain is negatively affected if certain experiences fail to occur within a certain time period, and (b) the brain is altered by experience at virtually any point in the life span. Here we consider not only how the structure of experience is incorporated into the structure of the brain, but also how this knowledge can influence the decisions we make about intervening in the lives of children. Research and other projects conducted by the Network fall into four broad categories: * Effects of early experience on brain development * New methods for studying brain-behavior relations * Comparative studies of early brain-behavioral development * Impact on public policy: Educating educators and the media RESOURCES NimStim Face Stimulus Set The Research Network on Early Experience and Brain Development has developed a battery of 646 facial expression stimuli for use in its own and other studies of face and emotion recognition. Images include the following expressions, displayed by a variety of models of various genders and races: fearful, happy, sad, angry, surprised, calm, neutral, disgusted. They are making these stimuli available to the public free of charge with registration and acceptance of the terms and conditions to use the stimulus set.
An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. The ontology is a domain specialization of the broader Mental Functioning Ontology.
NLSdb: a database of nuclear localization signals
NLSdb - a database of nuclear localization signals
A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree
Software package for multidimensional data analysis and reproducible computational experiments. It aims to provide a powerful environment and a convenient technology transfer tool for researchers working with digital image and data processing in geophysics and related fields., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols.
Brain imaging data collected from a large population of normal, healthy children that have been used to construct pediatric brain templates, which can be used within statistical parametric mapping for spatial normalization, tissue segmentation and visualization of imaging study results. The data has been processed and compiled in various ways to accommodate a wide range of possible research approaches. The templates are made available free of charge to all interested parties for research purposes only. When processing imaging data from children, it is important to take into account the fact that the pediatric brain differs significantly from the adult brain. Therefore, optimized processing requires appropriate reference data be used because adult reference data will introduce a systematic bias into the results. We have shown that, in the in the case of spatial normalization, the amount of non-linear deformation is dramatically less when a pediatric template is used (left, see also HBM 2002; 17:48-60). We could also show that tissue composition is substantially different between adults and children, and more so the younger the children are (right, see also MRM 2003; 50:749-757). We thus believe that the use of pediatric reference data might be more appropriate.
Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).
A global biotechnology company manufacturing research tools, antibodies, and cGMP grade protein.
Software package for gene fusion discovery using RNA-Seq data. It uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries.
Xenbase: Xenopus laevis and tropicalis biology and genomics resource
Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics.
Psychoactive Drug Screening Program Ki Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Database of information on the abilities of drugs to interact with an expanding number of molecular targets. It serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes. The query interface is designed to let you search by any field, or combination of them to refine your search criteria. The flexible user interface also provides for customized data mining. The database is regularly updated. If you know of Ki data you would like to add, you can select Direct Ki Entry at the grey panel. If you would like, however, your own data (published or not) added, Send them a Reference at the grey panel, or send an email to Dr. Bryan Roth or Estela Lopez. Most common targets: 5-HT2A, DOPAMINE D1, DOPAMINE D2, 5-HT2C, 5-HT1A, Cholinergic, muscarinic M1, 5-HT Transporter, HISTAMINE H1, 5-HT2B, OPIOID Mu, 5-HT6, adrenergic Beta2, 5-HT7, OPIATE Delta, adrenergic Alpha1A, OPIOID Kappa, 5-HT3, m-AChR, adrenergic Beta1, adrenergic Alpha2A, 5-HT1, Acetylcholinesterase, AChE, Thromboxane A2, n-AChR, Opiate non-selective, CANNABINOID CB1, HERG, Dopamine, cocaine site, adrenergic Alpha2C, M3, Norepinephrine Uptake, Monoamine Oxidase A, Monoamine Oxidase B, 5-HT4, adrenergic Alpha1, 5-HT1E, B1 BRADYKININ, 5-HT2, 5-HT2C-INI, DOPAMINE D4, ANGIOTENSIN AT1, Neurokinin NK1, HISTAMINE H3, Sigma-1, VIP, Dopamine2-like, metabotropic glutamate 5, 5-HT2c VGI, Carbonic Anhydrase Isozymes, CA I, DOPAMINE D2 Long, adrenergic Alpha2, adrenergic Alpha2B, adrenergic Alpha2D, GABA A alpha1, CANNABINOID CB2, adrenergic Alpha1B, 5-HT5a, Melatonin, HISTAMINE H4, NMDA, 5-HT4a, Glucocorticoid, Interleukin 1-beta, Sodium Channel, Benzodiazepine central, Cholinergic, muscarinic M5, Neuropeptide Y1, GABA A alpha5, Galanin R2, Neurokinin NK3, 5-HT1B, M2, DOPAMINE D3, Angiotensin, Dopamine1-like, Neurokinin NK2, adrenergic Beta, Dopamine D1 high, Dopamine D1A, MAP kinase, ADENOSINE A2a, 5-HT7b, Nitrogen oxide synthase - neuronal, Sigma-2, CDK2, Neurotensin 2, DOPAMINE D2 Short, Multidrug Resistance Transporter MDR 1, GABA A Benzodiazepine, VEGF-R2, OPIATE Mu 2, Angiotensin II AT1, HISTAMINE H2, Angiotensin-converting enzyme, ACE, Sigma, beta-amyloid, ADENOSINE, ADENOSINE A2B, Adrenaline, Neurotensin 1
Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders
Project to generate human DNA promoters of less than 4 kb (MiniPromoters) to drive gene expression in defined brain regions of therapeutic interest for diseases such as Alzheimer, Parkinson, Huntington, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Spinocerebellar Ataxia, Depression, Autism, and Cancer. Project develops and shares tools like human MiniPromoters that drive region- and cell-specific gene expression in the mouse brain, expression constructs, mouse embryonic stem cell lines, and knock-in mice all of which carry brain-specific MiniPromoters. Project is daughter of Genome Canada Project, Atlas of Gene Expression in Mouse Development, within which mouse brain gene expression data have already been gathered. Project team has collaborated with International BioPharma Solutions Ltd., management and communications consulting company specializing in product development and commercialization advice. Project will explore challenging interface between science and journalism with focus on genomics and gene therapy.
Yale Rudd Center for Food Policy and Obesity
A non-profit research and public policy organization devoted to improving the worlds diet, preventing obesity, and reducing weight stigma.
Software to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Collection of individual databases on members of the steroid and thyroid hormone receptor superfamily. Although the databases are located on different servers and are managed individually, they each form a node of the NRR. The NRR itself integrates the separate databases and allows an interactive forum for the dissemination of information about the superfamily. NRR Components: Androgen receptor, Estrogen receptor, Glucocorticoid receptor, Peroxisome proliferator, Steroid receptor protein, Thyroid receptor, Vitamin D receptor.
An ontology that describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy; preparing and separating material for further analysis, such as sample ionization, chromatography, and electrophoresis; and synthesizing materials, such as epitaxy and continuous vapor deposition. It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).
NURSA - Nuclear Receptor Signaling Atlas
NURSA - The Nuclear Receptor Signaling Atlas
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 25, 2022.Software tool as knowledge environment resource that accrues, develops, and communicates information that advances understanding of structure, function, and role in disease of nuclear receptors (NRs) and coregulators. It specifically seeks to elucidate roles played by NRs and coregulators in metabolism and development of metabolic disorders. Includes large validated data sets, access to reagents, new findings, library of annotated prior publications in field, and journal covering reviews and techniques.As of March 20, 2020, NURSA is succeeded by the Signaling Pathways Project (SPP).
Revised database of O- and C-glycosylated proteins. The criteria for inclusion are at least one experimentally verified O- or C-glycosylation site. Each entry contains information about the glycan involved, the species, sequence, a literature reference and http-linked cross-references to other databases. Version 6.00 has 242 glycoprotein entries. The terminal sugar linked to serine or threonine is cited when known. The database is non-redundant in the sense that it contains no identical sequences, unless there is conflicting glycosylation data. Mucins have tandem repeat sequences, which are O-glycosylated. This result in some redundancy of the O-glycosylation sites. For prediction purposes they have also included a version of the database which contains no identical O-glycosylation sites (window=9) called O-Unique.seq. Data can no longer be retrieved by anonymous ftp. Only http is supported. New data, comments and suggestions are welcome.
Michigan State University Brain Biodiversity Bank
The Brain Biodiversity Bank refers to the repository of images of and information about brain specimens contained in the collections associated with the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, DC. Atlases and brain sections are available for a variety of mammals, and we are also developing a series of labeled atlases of stained sections for educators, students, and researchers. These collections include, besides the Michigan State University Collection, the Welker Collection from the University of Wisconsin, the Yakovlev-Haleem Collection from Harvard University, the Meyer Collection from the Johns Hopkins University, and the Huber-Crosby and Crosby-Lauer Collections from the University of Michigan. What we are doing currently at Michigan State is a series of demonstration projects for publicizing the contents of the collections and ways in which they can be used. For example, the images from the collection can be used for comparative brain study. We have prepared databases of the contents of the collections for presentation and use on this site, as well as for downloading by users in several formats. We are also developing a series of labeled atlases of stained sections for educators, students, and researchers. This internet site is associated with the Comparative Mammalian Brain Collections site. All of the images are in JPEG or GIF format.
An ontology that aims to establish a standard in representing chemical information including chemical structure and the ability to richly describe chemical properties, whether intrinsic or computed. It includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.
An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.
OmicCircos: High-quality circular visualization of omic data
An R software application and package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns.
The Surveillance Epidemiology and End Results (SEER) Program
The Surveillance Epidemiology and End Results (SEER) Program of the National Cancer Institute
Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data.
Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac
Software that designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. It is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. It incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for a particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for the data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species.
An ontology developed to facilitate interoperability between existing anatomy ontologies for different species, and to provide a template for building new anatomy ontologies.
A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X
Genedata Expressionist for Genomic Profiling
Software that provides data processing, analysis, management, and reporting of metabolomics, proteomics and biotherapeutics characterization studies based on mass spectrometry. It can process raw data from various MS instruments, serve MS processing, analysis and reporting needs, and ensure reproducibility and traceability of results.
Protege is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protege implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protege can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protege can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications. An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, database schemas, to fully axiomatized theories. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services. The Protege platform supports two main ways of modeling ontologies: * The Protege-Frames editor enables users to build and populate ontologies that are frame-based, in accordance with the Open Knowledge Base Connectivity protocol (OKBC). In this model, an ontology consists of a set of classes organized in a subsumption hierarchy to represent a domain's salient concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes - individual exemplars of the concepts that hold specific values for their properties. * The Protege-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C's Web Ontology Language (OWL). An OWL ontology may include descriptions of classes, properties and their instances. Given such an ontology, the OWL formal semantics specifies how to derive its logical consequences, i.e. facts not literally present in the ontology, but entailed by the semantics. These entailments may be based on a single document or multiple distributed documents that have been combined using defined OWL mechanisms (see the OWL Web Ontology Language Guide). Protege is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development.
Audiology - Arizona School of Health Sciences
Audiology; Arizona School of Health Sciences Audiology
Entry level program that teaches skills such as diagnostic, rehabilitative, habilitative, and related areas of the profession and practice of audiology. The program incorporates basic science education with clinical education through a combination of on-campus classes, clinical rotations, and computer-based education.
Database platform for cotton expressed sequence tag (EST)-related information, covering assembled contigs, function annotation, analysis of GO and KEGG, SNP, miRNA, SSR-related marker information.
Weighted Gene Co-expression Network Analysis
WGCNA: an R package for weighted correlation network analysis
Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Albert Einstein College of Medicine of Yeshiva University Department of Neuroscience
Albert Einstein College of Medicine of Yeshiva University; Department of Neuroscience
Albert Einstein College of Medicine; Department of Neuroscience
Yeshiva University; Albert Einstein College of Medicine; Department of Neuroscience
University department that oversees neuroscience research and graduate education.
Organization that provides biomedical researchers with online tools and a web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of the work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments.
Allegheny's neuroscience major formalizes an alliance dating back 25 years between the College's well-known biology and psychology departments. The major brings faculty and students together to study the brain and the nervous system using principles from the natural and social sciences. It requires a common core of biology, chemistry, and psychology courses. Students may choose from two tracks: "cellular neurobiology" or "behavioral and cognitive neuroscience", and they have the opportunity to explore interdisciplinary topics through the Junior Seminar and the year-long Senior Research Project.
An ontology designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.
Wellcome Trust Centre for Human Genetics
An international leader in genetics, genomics and structural biology, and research institute of the Nuffield Department of Medicine at the University of Oxford, whose objective is to extend our understanding on how genetic inheritance makes us who we are in order to gain a clearer insight into mechanisms of health and disease. Looking across all three billion letters of the human genetic code, they aim to pinpoint variant spellings and discover how they increase or decrease an individual's risk of falling ill. They collaborate with research teams across the world on a number of large-scale studies in these areas.
Software tools for read pair collation based algorithms on BAM files including * bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name * bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field * bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column * bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. * bamsort: reads BAM and writes BAM resorted by coordinates or query name * bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name
Dictyostelium Discoideum Anatomy Ontology
A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.
Software package that provides a simple and flexible way to generate Circos 2D track plot images for genomic data visualization. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.
NEI Retinal Degeneration Rat Model Resource
Supplier of fully penetrant rat models of the retinitis pigmentosa type of inherited retinal degeneration, including the following models: * Mutant rhodopsin transgenic rats ** P23H mutant rhodopsin transgenic rats -Three lines with different rates of photoreceptor degeneration ** S334ter mutant rhodopsin transgenic rats -Five lines with different rates of photoreceptor degeneration * RCS (Royal College of Surgeons) rats with inherited retinal dystrophy ** RCS pink-eyed inbred strain ** RCS pigmented congenic strain with slowed rate of retinal dystrophy ** RCS congenic control strains of both pigmentation types, wild-type at the retinal dystrophy (Mertk) genetic locus The resource has been supported by the National Eye Institute (NEI) for the past 19 years to produce and distribute breeding pairs of these animal models to vision scientists. Thus, the following apply: * Request for rats requires only a 1-page letter/e-mail addressing 4 questions * No charge for the animals or tissues (except for shipping costs) * No Material Transfer Agreement (MTA) required * No collaboration requirement (in most cases) The resource usually provides multiple breeding pairs of the rats to vision scientists to generate breeding stock. It can also provide extra animals to breed for immediate experimental work, animals of specific ages (depending upon availability), animals with prior exposure to different lighting conditions, eyes taken at specific ages instead of rats for pilot studies and other experiments (fresh, frozen, dissected in specific ways, or fixed with special fixatives or by different methods), or other tissues (e.g., liver, spleen, brain, testis, etc.) prepared different ways.
The U.S. National Institutes of Health Final NIH Statement on Sharing Research Data (NIH-OD-03-032) is now in effect. It specifies that all high-direct-cost NIH grant applications include plans for sharing of research data. To support and encourage collegial, enabling, and rewarding data sharing for neuroscience and beyond, the Laboratory of Neuroinformatics at Weill Medical College of Cornell University has established this site. A source of, and portal to, tools and proposals supporting the informed exchange of neuroscience data.
ggbio - Visualization tools for genomic data
An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. MedScan is a fast and flexible biomedical information extraction technology. It uses dictionaries to identify individual biomedical terms (proteins, cellular processes, small molecules, diseases, etc) referred to in literature articles, and applies advanced natural language processing techniques to detect the relationships within the article and extract these terms and the relationships; the overall process of detection, identification, extraction and assembling, is termed Information Harvesting. Information extracted by MedScan represents the multiple aspects of protein function, including protein modification, cellular localization, protein-protein interactions, gene expression regulation, molecular transport and synthesis, as well as association with diseases, and regulation of various cellular processes. This scope can be broadened by modifying information extraction rules and the dictionaries. Dictionaries can be assembled on any topic or area that is represented in the literature you wish to harvest. High-throughput data generation methodologies like microarray gene expression require new approaches for gathering information for data analysis. For the best results, computational approaches used for high-throughput data analysis require that biological information from the literature be a coherent and integrated part of the analysis software itself. Pathway Studio meets this challenge through its MedScan Technology and underlying ResNet database. All editions of Pathway Studio contain MedScan Technology to harvest information from the literature and to save this information in the Pathway Studio ResNet database ready for data analysis. MedScan is more than a web search engine. Indeed, the output of a Google search can be channeled into MedScan for example. Web searches, like Google, are excellent at finding items as a result of a query. A quick look at the output list usually locates the item for which you are looking. This approach however, is not well suited for information and knowledge gathering. Also, once information is gathered, where do you put it for later computational use? MedScan meets this challenge for the area of biomedical literature and biomedical online information. PubMed meets the needs for a central repository of biomedical literature. Researchers can go to PubMed and search for any topic and articles of interest, much like a web type of search. However, just like a web type of search, PubMed also provides a list of all the hits with a link to the articles. If a single article, or even just a few, are sought, this search approach is useful. Alternatively, MedScan will list all the articles of interest but additionally scans the text for relationships, highlights these relationships in the articles and then lists these relationships and the biological molecules and processes involved in the relationships in separate tables. The tables of relationships can be viewed graphically in Pathway Studio and can be saved into the ResNet database for use in experimental data analysis.
A formal ontology of phenotypes observed in fission yeast that is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource. Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.
Biomaterial supply resource that acquires, processes, stores, and distributes postmortem brain specimens for brain research. Various types of brain tissue are collected, including those with neurological and psychiatric disorders, along with their parents, siblings and offspring. The HBTRC maintains an extensive collection of postmortem human brains from individuals with Huntington's chorea, Alzheimer's disease, Parkinson's disease, and other neurological disorders. In addition, the HBTRC also has a collection of normal-control specimens.
The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
A structured controlled vocabulary used for various aspects of annotation by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them.
DAFGA: Diversity Analysis of Functional Gene Amplicons
Diversity analysis of Functional Gene Amplicons
A python script package which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. It provides gene-specific parameter sets for OTU clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME or Mothur.
Columbia University College of Physicians and Surgeons Department of Pharmacology
CU College of Physicians and Surgeons Dept. of Pharmacology
The spirit of the Department of Pharmacology is one of collaborative and synergistic science. As such, interests of the members of the Department span such diverse problems as the identification of molecular signals that determine whether a cell lives or dies to the discovery of new drugs that control cardiac rhythm in inherited and non-inherited heart disease. We at Columbia in general, and within the Department of Pharmacology in particular, are proud to be an integral part of the intellectual and cultural life of New York. In many ways the diversity of scientific interests within the Department reflect the diversity of the rich scientific environment of Columbia University and, in addition, the unique cultural and urban environment of New York City. Within the Graduate Programs in Mechanisms of Health and Disease, the Department of Pharmacology offers a Pharmacology and Molecular Signaling Program leading to the Ph.D. degree. Training is focused on both classical principles of pharmacology and more modern biophysical, genetic and computational approaches to the development of new and more specific therapeutic agents to manage human disease. The interdisciplinary training program in the molecular and genetic basis of cardiac arrhythmias is designed to provide training to post doctoral fellows with either M.D. or Ph.D. degrees to enable them to become independent researchers and leaders in the field as we enter a period of post genomic medical science. The overall aim of the program is to train researchers who will be well-grounded in molecular and cellular biology, but who also are trained in cardiovascular systems physiology/pharmacology in order to integrate the cellular and subcellular mechanisms (genotype) with the basis of human disease expressed at the systems level (phenotype).
PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees
Protein and Associated Nucleotide Domains with Inferred Trees
PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website.
Assessment test developed by the Autism Research Centre at the University of Cambridge, for assessing the severity of autism spectrum symptoms in children. This assessment is usually used with children aged from 4-11 years of age.
The Weill Medical College of Cornell University has a long tradition of neuroscience research. The faculty is large, and the research programs tackle the fundamental questions in the field at all levels - from genes to cells to systems to behavior. The neuroscience community at Weill Cornell spans two campuses. The main one, containing the medical school and associated hospitals, is located on the upper east side of Manhattan, adjacent to Rockefeller University and across the street from the Memorial Sloan-Kettering Cancer Center. The second campus, with the rapidly growing Burke-Cornell Research Institute, is located in White Plains. The following graduate programs are offered: Neuroscience PhD, Tri-Institutional MD-PhD, Physiology and Biophysics, and Tri-Institutional Graduate program in Computational Biology and Medicine.
MIPgen - One stop MIP design and analysis
Software for a fast, simple way to generate designs for MIP assays targeting hundreds or thousands of genomic loci in parallel. Packaged with MIPgen are scripts that aid in visualization of MIP designs and processing of MIP sequence reads to SAM files that can then be passed through any standard variant calling pipeline.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. A database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments.
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. It has been integrated into the National Cancer Informatics Program (NCIP). The National Cancer Institute launched the cancer Biomedical Informatics Grid (caBIG) to create a virtual network of interconnected data, individuals, and organizations that worked together to redefine how cancer research is conducted. caBIG capabilities allowed researchers and clinicians to collaborate more effectively so that complex research questions might be asked and answered faster and more effectively. The mission of caBIG was to develop a truly collaborative information network that accelerated the discovery of new approaches for the detection, diagnosis, treatment, and prevention of cancer, ultimately improving patient outcomes.
Glioma Molecular Diagnostic Initiative: Characterizing Brain Tumor Data
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. An initiative to develop a molecular classification schema that is both clinically and biologically meaningful, based on gene expression and genomic data from tumors (Gliomas) of patients who will be prospectively followed through natural history and treatment phase of their illness. The study will also explore gene expression profiles to determine the responsiveness of the patients and correlate with discrete chromosomal abnormalities. The initiative was designed to obtain a large amount of molecular data on DNA and RNA of freshly collected tumor samples that were collected, processed and analyzed in a standardized fashion to allow for large-scale cross sample analysis. The sample collection is accompanied by careful and prospective clinical data acquisition, allowing a variety of matched molecular and clinical data permitting a wide variety of analyses. GMDI has accrued fresh frozen tumors in the retrospective phase (all from the Henry Ford Hospital, without germline DNA) and fresh frozen tumors in the prospective phase (from a variety of institutions). In addition to characterizing the samples from patients enrolled in GMDI, the microarray group has generated genomic-scale analyses of the many human and canine glioma initiating cells/glioma stem cells (GIC/GSC) lines, as well as many canine and murine normal neural stem cell (NSC) lines produced in laboratory.
Gene expression data from published journal articles that test hypotheses relevant to neuroscience of addiction and addictive behavior. Data types include effects of particular drug, strain, or knock out on particular gene, in particular anatomical region. Focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data are available for query through NIF interface.Data submissions are welcome.
Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).
Arabidopsis Protein Phosphorylation Site Database
Database containing information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups. Specific information on the peptide properties as well as on the experimental and analytical context is given. The PhosPhAt service has a built-in plant specific phosphorylation site predictor trained on the experimental dataset for Serine, threonine and tyrosine phosphorylation (pSer, pThr, pTyr). Protein sequences or Arabidopsis AGI gene identifier can be submitted to the predictor. Users and researchers are encouraged to assist in keeping the database current by submitting either published data or unpublished data (MS/MS data required).
Creighton University Department of Pharmacology
Creighton University School of Medicine Department of Pharmacology
CU School of Medicine Department of Pharmacology
CU School of Medicine Dept. of Pharmacology
The primary instructional mission of the Department is to provide professional students with an understanding of the pharmacological basis of therapeutics. In addition to instruction of students in the medical, dental, pharmacy and nursing programs at Creighton, faculty are actively involved in both teaching and research training of graduate students. Ten departmental faculty work with an energetic group of graduate students, postdoctoral fellows and research staff in a congenial and collaborative environment. Faculty in the Department of Pharmacology at Creighton University School of Medicine reflect the complex scope of modern pharmacological research as they apply methods of systems and cell physiology, neuroscience, biochemistry, and cellular and molecular biology to better understand drug action. Departmental faculty are engaged in diverse areas of research including, but not limited to, G protein-coupled receptor signal transduction, regulators of G-protein signaling, regulation of receptor gene expression, control of neurotransmitter release, ion channel modulation, molecular pharmacology of excitatory neurotransmission, and cardiovascular and CNS drug discovery. These studies provide insight into the mechanisms of drug action and the means by which drug action is translated into responses in the cardiovascular system, the nervous system, exocrine glands and cancer cells.
A biopharmaceutical company applying its discoveries in human genetics to develop drugs and diagnostics for common diseases. They specialize in gene discovery - their population approach and resources have enabled them to isolate key genes contributing to major public health challenges from cardiovascular disease to cancer. The company's genotyping capacity is now one of the highest in the world. They have a large population-based biobank containing whole blood and DNA samples with extensive relevant phenotypic information from around 120.000 Icelanders. In the company's work in more than 50 disease projects, their statistical and informatics departments have established themselves in data processing and analysis. deCODE genetics is widely recognized as a center of excellence in genetic research.
MultIallelic Linkage Disequilibrium: a program for adjusted linkage disequilibrium (LD) calculations
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software).
Online educational tool that brings challenging clinical practice to your computer, providing medical education that is engaging, challenging and interactive. While there is no substitute for real-life direct contact with patients or colleagues, research has shown that interactive online education can be a highly effective and enjoyable method of learning many components of clinical medicine, including ethics, clinical management, epidemiology and communication skills. eDoctoring offers 25 simulated clinical cases, 15 interactive tutorials and a virtual library containing numerous articles, fast facts and video clips. Their learning material is arranged in the following content areas: * Ethical, Legal and Social Implications of Genetic Testing * Palliative and End-of-Life Care * Prostate Cancer Screening and Shared Decision-Making
Drexel University Neurobiology and Anatomy
Drexel University College of Medicine Department of Neurobiology and Anatomy
Drexel University College of Medicine Neurobiology & Anatomy
Drexel University College of Medicine Neurobiology and Anatomy
Neurobiology & Anatomy Department at DUCOM
Neurobiology and Anatomy Department at DUCOM
The Department of Neurobiology and Anatomy at the Drexel University College of Medicine provides an outstanding academic environment for pursuing multidisciplinary training and research in neuroscience. The department offers postdoctoral training through a NIH training grants and graduate student training through the Neuroscience program for outstanding individuals preparing for a research career in the biomedical sciences. The Department is also responsible for 3 major courses given to medical students that include Medical Neuroscience, Gross Anatomy and MicroAnatomy. Training can be obtained in all aspects of advanced microscopy and imaging, tissue culture, transplantation techniques, gene therapy and sequencing, behavioral neurobiology, kinematics, intracellular recording, patch clamping, computer modeling of neurobiological processes and robotics. The Department has well equipped shared facilities for confocal microscopy, electron microscopy, image acquisition and processing, small animal surgery, behavioral analysis, biochemistry and molecular biology. Research training is also supplemented by a seminar series featuring faculty, postdoctoral fellows and outside speakers. Journal clubs and discussions of research findings are scheduled regularly and often shared among individual laboratories.
Drexel University College of Medicine Pharmacology and Physiology
The Department of Pharmacology and Physiology offers graduate programs leading to the M.S. and the Ph.D. degrees. The programs require independent research under the direction of departmental faculty members who are engaged in highly active research programs involving molecular, cellular, and behavioral approaches to experimental pharmacology and physiology in a strongly collaborative environment. The disciplines of pharmacology and physiology touch on virtually every scientific discipline and clinical area within the biomedical sciences, thereby providing students with a range of opportunities into disease mechanisms and altered physiological processes, new pharmacological tools and new medications. We are unique in offering educational programs not only in the basic sciences of pharmacology and physiology but also in drug discovery and development, which provides students with a wealth of advantages in considering career opportunities within academic, biopharmaceutical, and pharmaceutical settings. Students in both the PhD and MS programs begin their coursework with a core curriculum in biomedical sciences, and immediately start laboratory rotations. Intensive graduate-level pharmacology and physiology courses round out the core programmatic courses. Specialization in ion channel physiology, smooth-muscle physiology, neuropharmacology, behavioral pharmacology, and signal transduction processes may involve the taking of several elective courses. Each program requires the defense of a thesis based on original research. For more information visit, http://www.drexel.edu/catalog/g-about/pharm.htm.
It studies epigenetic regulation of the genome and its dysregulation in disease. This lab has a long-standing interest in gene regulatory processes that extend over large regions of the genome and give rise to human diseases. Our major projects are centred on the discovery of DNA sequence characteristics that discriminate genes undergoing genomic imprinting, using these to find new imprinted genes that are candidates for causing human disease.
A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants)
Virtual microscope for viewing in situ images that show where a gene is used in an organism, sometimes down to cellular resolution. The user can examine cell-by-cell as well as tissue-by-tissue expression patterns. Users can retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection. Image set contributions are welcome. The following image collections are currently available for browsing: * High-quality high-resolution images of eight-week-old male mouse sagittal brain slices with reverse-complemented mRNA hybridization probes from the Allen Brain Atlas, courtesy of the Allen Institute for Brain Science * Mouse in situ images from the Jackson Lab Gene Expression Database (GXD) at MGI * Transcription factors in mouse embryos from the Mahoney Center for Neuro-Oncology * Mouse head and brain in situ images from NCBI' '''s Gene Expression Nervous System Atlas (GENSAT) database * Xenopus laevis in situ images from the National Institute for Basic Biology (NIBB) XDB project
Duke University, Pharmacology and Cancer Biology
Duke University Medical Center Pharmacology & Cancer Biology
Duke University Medical Center Pharmacology and Cancer Biology
Department of Pharmacology and Cancer Biology spans two overlapping and broad disciplines, one exploring how chemical agents impact living cells and one seeking to understand how inappropriate responses to environmental molecules and internal cellular cues can lead to development of Cancer. Occupying Levine Science Research Center, Pharmacology and Cancer Biology department is dedicated to mentoring and training of graduate students and postdoctoral fellows.Innovative undergraduate program also allows students majoring in Biology or Chemistry at Duke to complete area specialization in Pharmacology, as well as offering courses in Pharmacology and Neuropharmacology for undergraduates. Department trains also students working towards Ph.D.s in Molecular Cancer Biology. Moreover, students enter our department through several university-wide multi-disciplinary programs including the Toxicology, Cell and Molecular Biology Program and the University Program in Genetics and Genomics. Our 23 faculty members are remarkably diverse and use all of the tools available to biomedical scientists to address questions critical to fundamental biology and human health. The faculty members share the common goal of exploiting cellular signaling pathways to address a myriad of important scientific questions relevant to cancer, metabolism, nervous system function, drugs of abuse and environmental toxicants.
An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets
Source BioScience LifeSciences are European leaders in DNA sequencing, genomic services, bioinformatic analyses and offers a comprehensive portfolio of genomic reagents and antibodies. Source BioScience LifeScience is a CPA, GLP/GCP accredited and Illumina NGS CSPro certified genomic service provider and distributes a comprehensive range of biological products to companies and institutions worldwide. Source BioScience is proud to announce that Source BioScience imaGenes has joined it's LifeSciences group. This will enable us to bring our customers one unified website with our complete range of Products, Clones and Services. We have merged our clone libraries together so that can now offer you over 20 million clones! Add to this our excellent sequencing service and our range of over 100,000 antibodies and Source BioScience LifeSciences is your ideal outsourcing partner.
Duke University Trinity College of Arts and Sciences Undergraduate Neuroscience
DU Trinity College of Arts and Sciences Undergraduate Neuroscience
The major and minor in Neuroscience at Duke University was approved by the Arts and Sciences Council of Trinity College of Arts and Sciences on April 9, 2009. The program offers three academic plans: Bachelor of Science (B.S.) degree in Neuroscience, Bachelor of Arts (A.B.) degree in Neuroscience, and a Minor in Neuroscience. Although Neuroscience is a new major/minor, there is a rich and long-standing tradition of excellence in undergraduate neuroscience research and education at Duke. Groups of faculty in the Department of Psychology and Neuroscience and the Department of Biology, as well as the Department of Neurobiology in the Duke University School of Medicine, have been especially engaged in teaching neuroscience in undergraduate classes and hosting independent study projects in their research laboratories. Building upon this broad foundation, the new Undergraduate Studies in Neuroscience program is a truly interdisciplinary experience reflecting the diverse sources of knowledge that advance our understanding of the brain sciences. Undergraduate Studies in Neuroscience is a unique collaboration among many Departments and Schools , with administrative support provided by Trinity College of Arts and Sciences and the Duke Institute for Brain Sciences.
An application ontology established by a collaborative group of influenza researchers that includes consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)
Software for efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.
Proteins Interacting in the Nucleus Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 2, 2016. Relational database containing the compositions of multi-protein complexes in the nucleus of budding yeast and human cells. Its content is limited to information curated from the proteomics literature and primarily comprises of components of the general transcription and DNA repair machinery. In addition to database browsing and searching capabilities, the PINdb web portal also includes user-friendly interactive tools for comparative analysis of the composition of multiple protein complexes and for clustering and visualizing network of protein complexes. Currently, PINdb contains mostly protein complexes that may be involved in gene transcription. To facilitate comparative analyses and identification of protein complexes, the compositional information is integrated with standardized gene nomenclature, annotation and protein sequences from public databases. The PINdb web interface provides a number of tools for (1) comparison of protein complexes, (2) search for a protein complex by its published name or by a partial list of its components and (3) browsing specific subsets or a functional classification of the complexes.
An ontology that describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied.
East Tennessee State University, Department of Pharmacology
East Tennessee State University Quillen College of Medicine Department of Pharmacology
Faculty members of our Department are actively engaged in delivering outstanding teaching to undergraduate students, graduate students, medical students, and residents. Our Doctor of Philosophy (graduate) students matriculate to Pharmacology through the Biomedical Sciences Graduate Program at the Quillen College of Medicine. Students pursuing Master of Science and Doctor of Philosophy degrees may pursue a focus in Toxicology. Our faculty members are trained in several medical disciplines and our research applies methodological approaches that span molecular biology, cellular biology, systems biology, and human biology and pathology. Through research, our department strives to understand human disease pathology and use this understanding to develop new therapeutic entities (e.g. drugs) for the treatment of major human diseases. The primary foci of department research efforts are cardiovascular and neuropsychiatric diseases, although other areas of interest and activity exist. Our laboratories are funded by the National Institutes of Health, American Heart Association, the American Foundation for Suicide Prevention and a variety of other agencies and sources.
Emory University, Molecular and Systems Pharmacology
Emory Molecular and Systems Pharmacology Graduate Program
Emory University Molecular and Systems Pharmacology Graduate Program
The Molecular and Systems Pharmacology graduate program at Emory University offers broad training in the biomedical sciences for students interested in learning how the drugs of today work and how the novel therapeutics of tomorrow can be developed. The Program offers a specialization in toxicology. Emory University was recently rated by The Scientist magazine as the number 1 university in the world in terms of impact in pharmacology and toxicology research. Particular strengths within the MSP graduate school program at Emory include neuropharmacology, cancer biology, AIDS research, cardiovascular pharmacology, toxicology, and chemical biology. Ph.D. training in the Emory MSP program provides students with an ideal preparation for successful careers in the biotechnology and pharmaceutical industries as well as in academic research, teaching, government research, patent law and other disciplines that depend upon knowledge of fundamental pharmacological principles.
Protein Information Resource SuperFamily
A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF.
miR-PREFeR: microRNA PREdiction From small RNAseq data
miRNA PREdiction From small RNA-Seq data
An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.
Eindhoven University of Technology; North Brabant; Netherlands
Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. Niftilib currently has C, Java, MATLAB, and Python libraries; we plan to add some MATLAB/mex interfaces to the C library in the not too distant future. Niftilib has been developed by members of the NIFTI DFWG and volunteers in the neuroimaging community and serves as a reference implementation of the nifti-1 file format. In addition to being a reference implementation, we hope it is also a useful i/o library. Niftilib code is released into the public domain, developers are encouraged to incorporate niftilib code into their applications, and, to contribute changes and enhancements to niftilib. Please contact us if you would like to contribute additonal functionality to the i/o library.
George Washington University, Cognitive Neuroscience
The Cognitive Neuroscience Program provides graduate students with an intense and focused research experience in the areas of perception, attention, and memory, with emphasis on the neural bases of these capacities. The program utilizes diverse research methods such as patient-based testing, neuro-imaging, animal modeling, and psychophysical scaling, and computational modeling. The goal of the program is to train students for careers in academic and research institutions. At the undergraduate level, the program provides both entry level and advanced courses as well as honor seminars in special topics. The program boasts a high faculty / student ratio, reflecting a strong emphasis on close collaboration between faculty and students on joint research projects. The Washington, DC research environment is outstanding, with the National Institutes of Health, Georgetown University, the University of Maryland, Johns Hopkins University, George Mason University, and other research institutions all close by. GWU's other resources for cognitive neuroscience research include a major medical school, a teaching hospital with world-class Neurology, Neurosurgery and Neuroradiology Departments, and an intensive Neuroscience Program. GWU is located in the heart of Washington, DC, a beautiful city with a wide variety of national museums, historical sites, restaurants, and cultural events. The Cognitive Neuroscience program at GW is designed to train students to become independent scientists who do basic research in an academic setting. Please note that ours is not a clinical neuropsychology program -- we provide no training in diagnosing or treating any brain or neurological disorder.
A functional network for laboratory mouse based on integration of diverse genetic and genomic data. It allows the users to accurately predict novel functional assignments and network components. MouseNET uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the mouseNET algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. The graph may be explored further. As you move the mouse over genes in the network, interactions involving these genes are highlighted.If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed.
George Washington University, Department of Pharmacology and Physiology
GWU Department of Pharmacology & Physiology
GWU Department of Pharmacology and Physiology
GWU Dept. of Pharmacology and Physiology
The Department of Pharmacology & Physiology at the George Washington University provides unique research opportunities at the predoctoral and postdoctoral levels. They also offer courses in Pharmacology and Physiology for Medical and Health Sciences students, as well as a number of graduate-level courses. Our mission is to provide the highest quality of educational opportunities to our community, and to advance scientific knowledge and improve human health through leading-edge research in the biomedical sciences.
Annotated, non-redundant database of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s) (TSS) from various plant species. It contains 578 unrelated entries including 151, 396 and 31 promoters with experimentally verified TSS from monocot, dicot and other plants, respectively (April 2014). This DB presents the published promoter sequences with TSS(s) determined by direct experimental approaches and therefore serves as the most accurate source for development of computational promoter prediction tools.
A web service for fast microRNA-Seq data analysis in a GPU infrastructure.
An ontology that classifies algorithms available for the simulation of models in biology, their characteristics and the parameters required for their use.
Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
Georgetown University Medical Center; Department of Neuroscience
Faculty of the Department of Neuroscience participate in the teaching of courses in the Interdisciplinary Program in Neuroscience and the School of Medicine. A Ph.D. in Neuroscience is offered through the Interdisciplinary Program in Neuroscience. Support for graduate training is offered through the Department, the research grants of individual faculty, as well as through three NIH training grants directed by Neuroscience faculty. * Training in Recovery of Function after CNS Injury. Program Director: Barbara S. Bregman, Ph.D. * Training Program in Drug Abuse. Program Director: Barbara S. Bayer, Ph.D. * Training in Neural Injury and Plasticity. Program Director: Jean R. Wrathall, Ph.D. Scientists in the Department of Neuroscience participate in a wide array of research activities with a focus on understanding both the normal and injured nervous system. The theme of neuroplasticity characterizes much of the research in the Department. We study neuroplasticity during normal development and in the adult in response to activity (e.g., learning) or drugs. Our research is also focused on studying the plasticity that ensues after traumatic (such as spinal cord injury) or ischemic damage to the nervous system and over the course of developmental or neurodegenerative diseases (such as Specific Language Impairment, autism, or Parkinson's and Alzheimer's Diseases). The specific research interests of each of the principal investigators falls under four broad subheadings: *CNS disorders ( Faden, Mocchetti, Rebeck, Riesenhuber,Ullman) *Cognitive/Computational (Riesenhuber, Ullman) *Development, Regeneration and recovery of function after injury (Bregman, Faden, Kromer, Ullman, Wrathall) *Neuroimmunology and Drugs of Abuse (Bayer, Faden, Kromer, Mocchetti) Under this common theme, a variety of diverse techniques and models are employed by the faculty. They range from molecular studies of gene function to studies on humans using Event-Related Potentials (ERPs) and functional MRI. Experimental models include cell culture systems, rodent genetic and experimental models of nervous system injury and disorders, as well as the use of computer simulations to understand higher cortical processing.
Software tool to examine compositional high-throughput sequence data with Welch's t-test. A differential relative count abundance analysis for the comparison of two conditions. For example, single-organism and meta-rna-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs.
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PLPMDB: Pyridoxal-5'-phosphate dependent enzymes Mutants Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A searchable mutant database developed to provide access to relevant mutant information on pyridoxal-5'-phosphate dependent enzymes. All data have been extracted from publications and publicly available databases and organized to enable database searching. The database is a useful tool for planning mutant experiments and for interpretation of information from such experiments. PLPMDB includes mutation information from SWISS-PROT/TrEMBL, several web-based mutation data resources, and data extracted from the literature.
i2b2 Cross-Institutional Clinical Translational Research project
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A two year Clinical and Translational Science Award (CTSA) supplement that set up a SHRINE (Shared Health Research Informatics NEtwork) network to create an information exchange environment that successfully shared 4.2M deidentified patient records. The network successfully linked i2b2 sites at UW, UCSF, UC Davis and Harvard Catalyst. Recombinant Data Corporation was actively involved in this implementation. This is a collaborative information exchange pilot project to adapt and extend data discovery tools and processes to enhance research design and retrospective data study capabilities for clinical translational investigators. The novel approach of this project will be to incrementally build a common technical, semantic and appropriately secure and governed distributed system in close partnership with active researchers at three large and geographically distributed academic medical centers. This collaboration will extend the Informatics for Integrating Biology and the Bedside (i2b2) software architecture developed by the Harvard based National Center for Biomedical Computing (NCBC) to support multi-institution data query capabilities. The anticipated outcome of this two-year project is to make high-level anonymized descriptive characteristics of population-level data discoverable for research design, hypothesis generation and retrospective data studies.
Harvard Medical School Department of Neurobiology
The mission of the Department of Neurobiology is to promote research and teaching that leads to a better understanding of the normal and diseased brain. The Department faculty are committed to training leaders of the next generation of neuroscientists, including graduate and medical students. Candidates for the Ph.D. in Neurobiology are admitted to the graduate Program in Neuroscience. This interdepartmental training program links the Department of Neurobiology with faculty in the Harvard affiliated hospitals and with faculty in other basic science departments. The Program, established in 1981, now includes about 90 investigators who participate in the training of Ph.D. candidates. Approximately fifteen students are accepted each year so that the steady state enrollment is usually about 80-90. This Program in Neuroscience attracts superb students with a broad range of interests from all areas of the globe. The goals of our training are to produce scientists who have explored one area and one level of analysis in great depth, but who are familiar with the full scope of neuroscience. They should be able to move from one level to another in a critical and creative manner. We also try to develop an appreciation for translational research that bears on human brain disease. The Department of Neurobiology, established in 1966 with Stephen W. Kuffler as Chair, was the first of its kind. The intent was to bring together members of traditional departments- physiologists, biochemists, and anatomists- in order to understand the principles governing communication between cells in the nervous system. This interdisciplinary approach was revolutionary at the time, and the interdisciplinary theme has continued to permeate the evolution of the field of neuroscience ever since. The Program in Neuroscience is one of four programs administered by the Division of Medical Sciences (DMS). DMS, located at the medical school, is a division of the Faculty of Arts and Sciences of Harvard University.
An application ontology to cover all aspects of malaria (clinical, epidemiological, biological, etc) as well as the intervention attempts to control it, extending the infectious disease ontology (IDO).
Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology.
Computational Infrastructure for Geodynamics
Computational Infrastructure for Geodynamics (CIG)
Community-driven organization that develops and disseminates software for geophysics and related fields. They host codes in a wide range of disciplines in geodynamics and computational science including geodynamo, long-term tectonics, magma migration, mantle dynamics, seismology, and short-term crustal dynamics.
Tool for the identification of reliable and condition specific reference genes for RT-qPCR data normalization. RefGenes is available within Genevestigator.
An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms.
HTqPCR - Automated analysis of high-throughput qPCR data
Software package for the analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).
Interactive repository of mutations and other allelic variations of the genes involved in the DNA repair disorders, Xeroderma Pigmentosum (XP), Cockayne Syndrome (CS), Trichothiodystrophy (TTD), and other UV-sensitivity disorders. Any omitted data or new data may be submitted by using the on-line data submission form. There is a message board system to support discussions amongst those interested in XP and DNA Repair. RESOURCES * Educational module of the molecular biology of Nucleotide Excision Repair * Introduction to the DNA Repair disorders (XP, CS, TTD, UVs) * Background on each of the XP genes * A searchable database of mutations and sequence variations for the XP genes * Contact point for the submission of new mutation data * Discussion Forums and a Guest Book * Web Links to Additional Resources
Syracuse University; Institute for Sensory Research
The Institute for Sensory Research (ISR) defines itself as a world class research center dedicated to the discovery and application of knowledge of the sensory systems. Integration of engineering, life, and physical sciences, combining rigorous experimental methodology with mathematical analysis is stressed. Our multidisciplinary approach to bioengineering, sensory neuroscience, graduate, and undergraduate education, makes ISR a unique academic research center. At ISR, we study sensory systems, our gateways to the world. Our ears, eyes, skin, and mouth are channels through which we experience sound, light, texture, etc. These are functions that we usually take for granted until problems arise. Engineers, scientists, and students at ISR investigate both the basic sensory principles used by the brain, and also how the sensory systems can be best utilized, modified, and repaired if necessary to better communicate with our surroundings and with one another. In addition to basic research in hearing, touch, vision, and oro-facial biomechanics, recent projects include the design and testing of sensory-aid devices such as cochlear implants, hearing aids, ear protectors, and tactile aids for the visually and hearing impaired. Additional projects involve visual-depth perception, chewing and swallowing, oto-acoustic emissions, and personal care products such as oral rinses and skin lotions. Research * Auditory * Somatosensory * Vision
Statistics Online Computational Resource
A hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications. The tools and resources include a repository of interactive applets, computational and graphing tools, instructional and course materials. The core SOCR educational and computational components include the following suite of web-based Java applets: * Distributions (interactive graphs and calculators) * Experiments (virtual computer-generated games and processes) * Analyses (collection of common web-accessible tools for statistical data analysis) * Games (interfaces and simulations to real-life processes) * Modeler (tools for distribution, polynomial and spectral model-fitting and simulation) * Graphs, Plots and Charts (comprehensive web-based tools for exploratory data analysis), * Additional Tools (other statistical tools and resources) * SOCR Java-based Statistical Computing Libraries * SOCR Wiki (collaborative Wiki resource) * Educational Materials and Hands-on Activities (varieties of SOCR educational materials), * SOCR Statistical Consulting In addition, SOCR provides a suite of tools for volume-based statistical mapping (http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_AnalysesCommandLine) via command-line execution and via the LONI Pipeline workflows (http://www.nitrc.org/projects/pipeline). Course instructors and teachers will find the SOCR class notes and interactive tools useful for student motivation, concept demonstrations and for enhancing their technology based pedagogical approaches to any study of variation and uncertainty. Students and trainees may find the SOCR class notes, analyses, computational and graphing tools extremely useful in their learning/practicing pursuits. Model developers, software programmers and other engineering, biomedical and applied researchers may find the light-weight plug-in oriented SOCR computational libraries and infrastructure useful in their algorithm designs and research efforts. The three types of SOCR resources are: * Interactive Java applets: these include a number of different applets, simulations, demonstrations, virtual experiments, tools for data visualization and analysis, etc. All applets require a Java-enabled browser (if you see a blank screen, see the SOCR Feedback to find out how to configure your browser). * Instructional Resources: these include data, electronic textbooks, tutorials, etc. * Learning Activities: these include various interactive hands-on activities. * SOCR Video Tutorials (including general and tool-specific screencasts).
A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model.
Excel-based tool using pair-wise correlations for determination of stable housekeeping genes, differentially regulated target genes and sample integrity. It determines the best suited standards, out of ten candidates, and combines them into an index. The index can be compared with further ten target genes to decide, whether they are differentially expressed under an applied treatment. All data processing is based on crossing points.
NanoStringNorm: Normalize NanoString miRNA and mRNA data
Software package for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An XML-based language designed for metadescription of formats, used for digital storage of biomedical time series. Using SignalML, information on the structure of binary data files can be simply and efficiently coded. Once written, this information can be used by any software, which - owing to this metadescription - can read data files in the original format. This eliminates the need for conversions and duplication of data. signalml.org provides the following resources for interchange of relevant information and ideas: * SignalML wiki * Newsgroup / mailing list The main current software project is Svarog - a SignalML-compliant signal viewer, annotator, analyzer and (future) recorder. Svarog is written in Java and is currently best fitted for display of EEG and MEG signals. Also open platform for implementing advanced signal processing methods in user-friendly environment, at the moment interfacs for Java code, standalone executables and Matlab code via Matlab Builder for Java.
Non-profit biomedical research organization developing predictors of disease and accelerating health research through creation of open systems, incentives, and standards. Formed to coordinate and link academic and commercial biomedical researchers through Commons that represents new paradigm for genomics intellectual property, researcher cooperation, and contributor evolved resources.
An ontology of minimal set of terms for anatomy.
Ontology that describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive / behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Its aim is to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, experiment paradigms, and modalities (EEG/MEG).
NormFinder software - Determine the optimal normalization gene
Software for identifying the optimal normalization gene among a set of candidates. It ranks the set of candidate normalization genes according to their expression stability in a given sample set and given experimental design. It can analyze expression data obtained through any quantitative method e.g. real time RT-PCR and microarray based expression analysis. NormFinder.xla adds the NormFinder functionality directly to Excel. A version for R is also available.
NormqPCR - Functions for normalisation of RT-qPCR data
Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data.
Polymorphism in microRNAs and their TargetSites
Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions.
The Flicker image viewer is a Java applet which reads two images from the Internet and then displays them in the your Web browser. It allows you to enhance them in various ways and to compare them visually in a third window called the flicker window. The Open-source Flicker downloadable application is now available. The program uses the "flicker method" used in GELLAB with and with Xconf. The flicker method is the alternate display in the same visual space of two images being compared which are aligned by aligning similar morphologic features. Images may first be enhanced by spatial warping, pseudo 3-Dimensional projections, image sharpening, contrast enhancement and other transforms. The transformed images may then be presented using flickering. Flicker is a method for comparing images from different Internet sources on your Web browser. Scientists around the world often work on similar image data. More of this data is being published on the Internet each year. In the case of 2D protein electrophoretic gel images, maps identifying proteins in these gels are becoming increasingly available. Visually comparing 2D sample gels against these 2D gel database maps may suggest putative protein spot identification in many cases. Flicker was originally developed for comparing 2D protein gels across the Internet.
JHU SOM Dept. of Pharmacology and Molecular Sciences
John Hopkins Medicine Department of Pharmacology and Molecular Sciences
John Hopkins Medicine Pharmacology and Molecular Sciences
Johns Hopkins University; School of Medicine; Department of Pharmacology and Molecular Sciences
Johns Hopkins University; School of Medicine; Pharmacology and Molecular Sciences
The Department of Pharmacology and Molecular Sciences is proud of its history. Founded in 1893 by John J. Abel, the "Father of Pharmacology" in the United States, the Johns Hopkins Pharmacology Department's advances over the years have included the first crystals of insulin, the first measurement of a drug level in a human, discovery of both the insulin and opiate receptors, and discovery of a cancer preventive principle in broccoli. Many of these and other key contributions have been made by students pursuing advanced degrees in our Department. We are also proud of our track record in student training. Many of our graduates have gone on to become academic and industrial leaders in biomedical research throughout the country and world. Not resting on our laurels, we are continuing to maintain our strong commitment to creative scholarship and education. Additionally, there is an Anti-Cancer Drug Development Training Program for predoctoral and postdoctoral students as well ad other Postdoctoral research opportunities. Each of our faculty is engaged in cutting-edge research spanning many areas including: chemical biology, immunology, virology, cancer, and neuroscience. We believe the opportunities for discovering new drug targets and developing novel therapeutics have never been brighter and will continue to be lustrous for the century ahead. The Johns Hopkins University and School of Medicine provide an excellent scientific environment, with a friendly and supportive atmosphere, filled with energetic students, faculty, fellows, and staff.
Mouse Biomedical Informatics Research Network
Animal model data primarily focused on mice including high resolution MRI, light and electron microscopic data from normal and genetically modified mice. It also has atlases, and the Mouse BIRN Atlasing Toolkit (MBAT) which provides a 3D visual interface to spatially registered distributed brain data acquired across scales. The goal of the Mouse BIRN is to help scientists utilize model organism databases for analyzing experimental data. Mouse BIRN has ended. The next phase of this project is the Mouse Connectome Project (https://www.nitrc.org/projects/mcp/). The Mouse BIRN testbeds initially focused on mouse models of neurodegenerative diseases. Mouse BIRN testbed partners provide multi-modal, multi-scale reference image data of the mouse brain as well as genetic and genomic information linking genotype and brain phenotype. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder. BIRN's infrastructure is providing the collaborative tools to enable researchers with unique expertise and knowledge of the mouse an opportunity to work together on research relevant to pre-clinical mouse models of neurological disease. The Mouse BIRN also maintains a collaborative Web Wiki, which contains announcements, an FAQ, and much more.
VANO - Volume image object AnNOtation System
VANO is a Volume image object AnNOtation System for 3D multicolor image stacks, developed by Hanchuan Peng, Fuhui Long, and Gene Myers. VANO provides a well-coordinated way to annotate hundreds or thousands of 3D image objects. It combines 3D views of images and spread sheet neatly, and is just easy to manage 3D segmented image objects. It also lets you incorporate your segmentation priors, and lets you edit your segmentation results! This system has been used in building the first digital nuclei atlases of C. elegans at the post-embryonic stage (joint work with Stuart Kim lab, Stanford Univ), the single-neuron level fruit fly neuronal atlas of late embryos (with Chris Doe lab, Univ of Oregon, HHMI), and the compartment-level of digital map(s) of adult fruit fly brains (several labs at Janelia Farm, HHMI). VANO is cross-platform software. Currently the downloadable versions are for Windows (XP and Vista) and Mac (Intel-chip based, Leopard or Tiger OS). If you need VANO for different systems (such as 64bit or 32bit, Redhat Linux, Ubuntu, etc), you can either compile the software, or send an email to pengh (at) janelia.hhmi.org. VANO is Open-Source. You can download both the source code files and pre-complied versions at the Software Downloads page.
NIH MRI Study of Normal Brain Development
Data sets of clinical / behavioral and image data are available for download by qualified researchers from a seven year, multi-site, longitudinal study using magnetic resonance technologies to study brain maturation in healthy, typically-developing infants, children, and adolescents and to correlate brain development with cognitive and behavioral development. The information obtained in this study is expected to provide essential data for understanding the course of normal brain development as a basis for understanding atypical brain development associated with a variety of developmental, neurological, and neuropsychiatric disorders affecting children and adults. This study enrolled over 500 children, ranging from infancy to young adulthood. The goal was to study each participant at least three times over the course of the project at one of six Pediatric Centers across the United States. Brain MR and clinical/behavioral data have been compiled and analyzed at a Data Coordinating Center and Clinical Coordinating Center. Additionally, MR spectroscopy and DTI data are being analyzed. The study was organized around two objectives corresponding to two age ranges at the time of enrollment, each with its own protocols. * Objective 1 enrolled children ages 4 years, 6 months through 18 years (total N = 433). This sample was recruited across the six Pediatric Study Centers using community based sampling to reflect the demographics of the United States in terms of income, race, and ethnicity. The subjects were studied with both imaging and clinical/behavioral measures at two year intervals for three time points. * Objective 2 enrolled newborns, infants, toddlers, and preschoolers from birth through 4 years, 5 months, who were studied three or more times at two Pediatric Study Centers at intervals ranging from three months for the youngest subjects to one year as the children approach the Objective 1 age range. Both imaging and clinical/behavioral measures were collected at each time point. Participant recruitment used community based sampling that included hospital venues (e.g., maternity wards and nurseries, satellite physician offices, and well-child clinics), community organizations (e.g., day-care centers, schools, and churches), and siblings of children participating in other research at the Pediatric Study Centers. At timepoint 1, of those enrolled, 114 children had T1 scans that passed quality control checks. Staged data release plan: The first data release included structural MR images and clinical/behavioral data from the first assessments, Visit 1, for Objective 1. A second data release included structural MRI and clinical/behavioral data from the second visit for Objective 1. A third data release included structural MRI data for both Objective 1 and 2 and all time points, as well as preliminary spectroscopy data. A fourth data release added cortical thickness, gyrification and cortical surface data. Yet to be released are longitudinally registered anatomic MRI data and diffusion tensor data. A collaborative effort among the participating centers and NIH resulted in age-appropriate MR protocols and clinical/behavioral batteries of instruments. A summary of this protocol is available as a Protocol release document. Details of the project, such as study design, rationale, recruitment, instrument battery, MRI acquisition details, and quality controls can be found in the study protocol. Also available are the MRI procedure manual and Clinical/Behavioral procedure manuals for Objective 1 and Objective 2.
A plant promoter database that provides information on transcription start sites (TSSs), core promoter structure and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.
Software package providing an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. It requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The package implements a pipeline to collect, analyze and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.
Louisiana State University Health Sciences Center, Department of Pharmacology, Toxicology and Neuroscience
Louisiana State University Health Sciences Center Department of Pharmacology Toxicology Neuroscience
LSUHSC Shreveport; Department of Pharmacology Toxicology & Neuroscience
LSUHSC Shreveport; Department of Pharmacology Toxicology and Neuroscience
LSUHSCS Department of Pharmacology Toxicology & Neuroscience
LSUHSCS Department of Pharmacology Toxicology and Neuroscience
LSUHSCS Pharmacology Toxicology and Neuroscience
LSUHSCS Pharmacology Toxicology Neuroscience
A major emphasis of the Department of Pharmacology, Toxicology and Neuroscience is in the areas of neuropharmacology, neuroscience, and toxicology, with research in drug and alcohol addiction research, stress, neurotransmitter receptor function, oxidative mechanisms of toxicity, molecular regulation of toxicity and apoptosis, gene therapy, carcinogenesis and cancer chemoprevention. The Department offers graduate programs of study in neuroscience and toxicology and maintains an NIH training grant for its program of study in drug and alcohol addiction research. An MD/PhD Program and a Summer Undergraduate Pharmacology Research program are also offered.
BrainTrap: Fly Brain Protein Trap Database
This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download.
Loyola University Chicago Stritch School of Medicine; Neuroscience Graduate Program
LUC Stritch SOM Neuroscience Graduate Program
The Neuroscience Graduate Program at Loyola trains students to become the neuroscientists who will carry on exciting research. Since our program is interdepartmental and interdisciplinary, our students have an exceptionally broad choice of advisors and research topics on which to work. The neuroscience program offers a Ph.D., M.D./Ph.D., and Masters degree. Our students begin working towards their doctorate in neuroscience by first obtaining a broad base of knowledge in the whole field of neuroscience--brain anatomy, physiology, biochemistry, and pharmacology. After selecting a research advisor at the end of the first year, students usually take several electives in the advisor's home department to develop specialization and strength in one particular area. Each student is exposed to various situations where he or she learns how to express their ideas effectively, whether at a graduate seminar or as a teaching assistant in the medical neuroscience course. Throughout their training, students have the opportunity to interact and work closely with faculty and to receive individualized attention that continues until degree completion.
Loyola University Department of Molecular Pharmacology and Experimental Therapeutics
Loyola Stritch SOM Dept. of Pharmacology and Experimental Therapeutics
Loyola University Chicago Stritch School of Medicine Department of Molecular Pharmacology and Experimental Therapeutics
Loyola University Chicago Stritch SOM Department of Pharmacology and Experimental Therapeutics
Loyola University Chicago Stritch SOM Dept. of Pharmacology and Experimental Therapeutics
Loyola University Medical Center Department of Molecular Pharmacology and Experimental Therapeutics
Loyola University Medical Center Department of Pharmacology
LUC SSOM Department of Molecular Pharmacology and Experimental Therapeutics
Department committed to excellence in teaching and research offering degrees leading to Ph.D., M.S., M.D./Ph.D. and M.S./M.B.A. The commitment to teaching is exemplified by the innovative courses and programs that the department has developed, as well as a departmental emphasis on fostering student-faculty interactions. The department offers Summer Undergraduate Research Opportunities and Postdoctoral positions. Research in Pharmacology encompasses the understanding, prevention and treatment of human disease, and therefore is at the forefront in creating innovative therapeutic interventions to improve the human condition. Research interests of the Departmental faculty include Neuroscience, Cardiovascular, Hematology and Oncology.
GEOSS - Gene Expression Open Source System
GEOSS Gene Expression Open Source System
A complete software system used to store and analyze gene expression data.
Portal of geological information, including geology maps, reports, and GIS datasets, to help with the exploration, development and conservation of Alberta's resources.
Database that describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome. These modules represent the regulatory potential for 229 transcription factors families and are the first genome-wide / transcription factor-wide collection of predicted regulatory modules for the human genome. The algorithm used involves two steps: (i) Identification and scoring of putative transcription factor binding sites using 481 TRANSFAC 7.2 position weight matrices (PWMs) for vertebrate transcription factors. To this end, each non-coding position of the human genome was evaluated for its similarity to each PWM using a log-likelihood ratio score with a local GC-parameterized third-order Markov background model. Corresponding orthologous positions in mouse and rat genomes were evaluated similarly and a weighted average of the human, mouse, and rat log-likelihood scores at aligned positions (based on a Multiz (Blanchette et al. 2004) genome-wide alignment of these three species) was used to define the matrix score for each genomic position and each PWM. (ii) Detection of clustered putative binding sites. To assign a module score to a given region, the five transcription factors with the highest total scoring hits are identified, and a p-value is assigned to the total score observed of the top 1, 2, 3, 4, or 5 factors. The p-value computation takes into consideration the number of factors involved (1 to 5), their total binding site scores, and the length and GC content of the region under evaluation. Users can retrieve all information for a given region, a given PWM, a given gene and so on. Several options are given for textual output or visualization of the data.
Marquette University College of Health Sciences Biomedical Sciences Neuroscience Graduate Program
Marquette University College of Health Sciences Neuroscience Graduate Program
Marquette University Neuroscience Graduate Program
Neuroscience specialization in Graduate Program in Biological Sciences at Marquette University brings together researchers from Departments of Biological and Biomedical Sciences at Marquette to offer quality graduate education in the field of neuroscience with the goal of training students for careers as neuroscience researchers and educators. The specialization is for students who wish to pursue a Ph.D. degree. The collaborative and multi-disciplinary neuroscience research environment at Marquette is supported by the Integrative Neuroscience Research Center (INRC), a consortium of researchers committed to advancing neuroscience research and education at Marquette. The Neuroscience Graduate Program offers the opportunity to conduct research in a collaborative, intellectually rigorous environment, with access to the most modern research tools.
Ontology Development and Information Extraction
ODIE - Ontology Enrichment & Information Extraction
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. A software toolkit to code document sets with ontologies or to enrich existing ontologies with new concepts from the document set. It contains algorithms for Named Entity Recognition, Co-reference resolution, concept discovery, discourse reasoning and attribute value extraction. The project aimed to develop a toolkit that will provide the following functionality: * Build text processing pipelines that use ontologies to annotate documents. * Enrich ontologies with new concepts that are automatically discovered in documents. * Populate an information model automatically from information extracted from documents. ODIE is open source software released under the LGPL v3.0 License. ODIE is written in Java and uses the Eclipse RCP Framework for the UI. The source code is organized into Eclipse projects.
Software package for low-throughput real-time quantitative PCR data analysis. The package allows you to import easily qPCR data files. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors.
NanoStriDE - NanoString Differential Expression
Web application that accepts the raw count data produced by the NanoString nCounter analysis system, normalizes it according to guidelines provided by NanoString Technologies, performs differential expression analysis on the normalized data, and provides a heatmap of the results from the differential expression analysis.
DNA Array Core Facility GeneChip Operating Software
DNA Array Core Facility GeneChip Operating Software (GCOS)
Affymetrix has recently released a new software for the acquisition, management, and analysis of gene expression data. The new GeneChip Operating Software (GCOS) platform enables researchers to perform gene expression, SNP mapping and resequencing analysis with integrated data management and scalable client server configurations. * Compatible with additional Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip DNA Analysis Software (GDAS) * Supports Gene Expression, Resequencing and Genotyping Applications * Baseline Comparison Analysis Input: Affymetrix .DAT file Output: Affymetrix files (.CEL, .CHP, .RPT, .EXP, .TXT) Availability: The Core Facility has a copy of GCOS, as well as an older version of the Affymetrix software, Microarray Suite (MAS), available for use upon request.
THIS RESOURCE IS NO LONGER IN SERVICE documented June 4, 2013. Allows users to query across a number of caBIG data services, join on common data elements (CDEs), and view results in a user-friendly interface. With an initial focus on enabling outcomes analysis, caTRIP allows clinicians to query across data from existing patients with similar characteristics to find treatments that were administered with success. In doing so, caTRIP can help inform treatment and improve patient care, as well as enable the searching of available tumor tissue, enable locating patients for clinical trials, and enable investigating the association between multiple predictors and their corresponding outcomes such as survival caTRIP relies on the vast array of open source caBIG applications, including: * Tumor Registry, a clinical system that is used to collect endpoint data * cancer Text Information Extraction System (caTIES), a locator of tissue resources that works via the extraction of clinical information from free text surgical pathology reports. while using controlled terminologies to populate caBIG-compliant data structures * caTissue CORE, a tissue bank repository tool for biospecimen inventory, tracking, and basic annotation * Cancer Annotation Engine (CAE), a system for storing and searching pathology annotations * caIntegrator, a tool for storing, querying, and analyzing translational data, including SNP data Requires Java installation and network connectivity.
Laboratory portal, including software, web-based tools, databases and data sets, related to their research that focuses on the development and application of biophysical and bioinformatics methods aimed at understanding the structural and energetic origins of protein-protein, protein-nucleic acid, and protein-membrane interactions. Their work includes fundamental theoretical research, the development of software tools, and applications to problems of biological importance. In this regard they maintain an active collaborative computational and experimental research program on the molecular basis of cell-cell adhesion. Other problems of current interest include protein structure prediction, the organization of protein sequence/structure space, the prediction of protein function based on protein structure, the structural origins of specificity in protein-DNA interactions, RNA function and, more generally, the electrostatic properties of biological macromolecules.
PRIDE Archive - proteomics data repository
PRoteomics IDEntifications database (PRIDE)
Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester.
Compendium of protein fingerprints. Diagnostic fingerprint database.
GBSA - Genome-Wide Bisulfite Sequencing Analyser Software
Genome-Wide Bisulfite Sequencing Analyser Software
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Software for analyzing whole-genome bisulfite sequencing data.
This data resource is a genetic, molecular, and genomic toolkit that establishes one particular species, Pristionchus pacificus, as a major satellite system for evolutionary developmental biology. Users may download Pristionchus Sequences and use the Pristionchus pacificus genome browser where they may find gene or gene prediction data. Users can also use the BLAST feature, which allows users to search the assembly for position information of bacs, reads and contigs using the mapping tool. The center of the site's research is the evolutionary analysis of vulva formation. The general aim of the Department is to develop the nematode vulva as a suitable case study into the evolutionary alterations of developmental processes. By studying and comparing two distantly related species of the same phylum, such as P. pacificus and C. elegans, macroevolutionary alterations of developmental processes and mechanisms can be identified. The final goal of the Department is to achieve a comprehensive description of macro- and microevolutionary changes of developmental mechanisms at the molecular level in a phylogenetic and ecological context.
ASAP: the Alternative Splicing Annotation Project
Alternative Splicing Annotation Project database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases.
Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA
Children''s Hospital of Philadelphia - Research Institute
Children''s Hospital of Philadelphia - Research Institute; Pennsylvania; USA
Children's Hospital of Philadelphia (CHOP) Research Institute
Childrens Hospital of Philadelphia - Research Institute
Scientific organization dedicated to advancing pediatric medicine through translational research. Founded in 1922, it is currently one of the largest pediatric research programs in the United States.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A database of probes and microbes that can be searched for target organisms, probe names, probe sequences, probe accession numbers, and references. The search target site function can assist in the development of new rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization (FISH), while the match tool can be used to rapidly retrieve all published probes targeting your query sequences (e.g. from a rRNA gene clone library) without prior phylogenetic analysis. probeBase is hyperlinked with PubMed, RDP-II, and Greengenes to provide additional bibliographic information and up-to-date data on probe specificity. Ribosomal RNA (rRNA) targeted oligonucleotide probes are widely used for fluorescence in situ, dot blot, and microarray hybridization in culture-independent studies of microbial communities and for the identification of uncultured prokaryotes in clincal and environmental samples. probeBase is a comprehensive database containing published rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information.
An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns.
NAPPA: Performs the processing and normalisation of Nanostring miRNA and mRNA data
Software that enables the processing and normalization of the standard mRNA data output from the Nanostring nCounter software.
Data analysis software program that offers nCounter users the ability to QC, normalize, and analyze data without having to purchase additional software packages.
Meta-Analysis Gene-set Enrichment of variaNT Associations
A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input.
An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure.
The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways.
A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more.
China Agricultural University; Beijing; China
A reference ontology that models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.
Biomedical ontology in the domain of adverse events that aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO is a community-based ontology. Its development follows the OBO Foundry principles.
Software for meta-analysis of genome-wide SNP association results.
NeuroImaging Tools and Resources Collaboratory (NITRC)
Neuroimaging Informatics Tools and Resources Clearinghouse
Neuroimaging Informatics Tools Resources Clearinghouse
NeuroImaging Tools and Resources Collaboratory
NITRC - Neuroimaging Informatics Tools and Resources Clearinghouse
NITRC - Neuroimaging Informatics Tools Resources Clearinghouse
Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.
Database that provides experimentally determined thermodynamic interaction data between proteins and nucleic acids. It contains the properties of the interacting protein and nucleic acid, bibliographic information and several thermodynamic parameters such as the binding constants, changes in free energy, enthalpy and heat capacity.
For selected articles and letters Nature presents streaming videos featuring interviews with scientists behind the research and analysis from Nature editors. To view the videos you will need the free Flash browser plugin. You can also visit the Nature Video YouTube channel which enables you to easily embed and share our videos through websites, mobile devices, blogs and email.
Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms.
Substructure Index-based Approximate Graph Alignment
SAGA (Substructure Index-based Approximate Graph Alignment)
SAGA - Substructure Index-based Approximate Graph Alignment
SAGA: A Fast and Flexible Graph Matching Tool
SAGA (Substructure Index-based Approximate Graph Alignment) is a tool for querying a biological graph database to retrieve matches between subgraphs of molecular interactions and biological networks. SAGA implements an efficient approximate subgraph matching algorithm that can be used for a variety of biological graph matching problems such as the pathway matching SAGA uses to compare pathways in KEGG and Reactome. You can also use SAGA to find matches in literature databases that have been parsed into semantic graphs. In this use of SAGA, portions of PubMed have been parsed into graphs that have nodes representing gene names. A link is drawn between two genes if they are discussed in the same sentence (indicating there is potential association between the two genes). SAGA lets you match graphs between different databases even though the content is distinct and the databases organize pathways in different ways. This cross-database matching is achieved by SAGA's flexible approximate subgraph matching model that computes graph similarity, and allows for node gaps, node mismatches, and graph structural differences. Comparing pathways from different databases can be a useful precursor to pathway data integration. SAGA is very efficient for querying relatively small graphs, but becomes prohibitory expensive for querying large graphs. Large graph data sets are common in many emerging database applications, and most notably in large-scale scientific applications. To fully exploit the wealth of information encoded in graphs, effective and efficient graph matching tools are critical. Due to the noisy and incomplete nature of real graph datasets, approximate, rather than exact, graph matching is required. Furthermore, many modern applications need to query large graphs, each of which has hundreds to thousands of nodes and edges. TALE is an approximate subgraph matching tool for matching graph queries with a large number of nodes and edges. TALE employs a novel indexing technique that achieves a high pruning power and scales linearly with the database size.
Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters.
A database and annotation tool that provides a simple mechanism to allow scientists to add to the functional annotation of genes described in Gene. To be processed, a valid Gene ID must exist for the specific gene, or the Gene staff must have assigned an overall Gene ID to the species. The latter case is implemented via records in Gene with the symbol NEWENTRY.
Massachusetts Institute of Technology; Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology; Department of Brain Cognitive Sciences
MIT Department of Brain and Cognitive Sciences
MIT Dept. of Brain and Cognitive Sciences
MIT's Department of Brain and Cognitive Sciences stands at the nexus of neuroscience, biology and psychology. We combine these disciplines to study specific aspects of the brain and mind including: vision, movement systems, learning and memory, neural and cognitive development, language and reasoning. Together, MIT's Department of Brain and Cognitive Sciences offers extraordinary learning opportunities for undergraduate, graduate and postdoctoral students. Because the human brain is immensely complex in many different ways at once, we pursue every level of inquiry - from molecules to cells to circuits to the mystery of the mind itself. As we study its diseases and disorders, its development and daily feats, like vision, speech, movement and memory, we also integrate methods and insights from every area of brain research. This unusual diversity of expertise fosters an intensely creative atmosphere that sparks startling collaborations. Already known for remarkable contributions to the field, our faculty members continually stretch the limits of knowledge, and bring the same passion to educating our exceptional students. A key part of the BCS mission is to offer its graduate and undergraduate students an educational experience of the highest quality. Our graduate students benefit from the impressive range of our program, and from the ability to participate in research projects with faculty members who are leaders in their fields. The department's undergraduate program, which includes both neuroscience and cognitive science, is one of the fastest-growing majors at MIT.
A virtual biospecimen registry designed to support and facilitate basic science, clinical, and translational research that will advance understanding of mesothelioma pathophysiology with the goal of expediting the discovery of preventive measures, novel therapeutic interventions, and ultimately, cures for mesothelioma. The NMVB resource is designed to provide mesothelioma tissue samples with high-quality and well-characterized multimodal annotated data to researchers. The NMVB team strongly believes that progress in translational and clinical research - in cancer as well as other disease areas - depends on the ability of researchers to access high-quality tissue that is associated with meaningful annotation. MVB database version 3.0 has been released that provides researchers real-time access to demographic, epidemiologic, pathologic, genotype, and follow-up data associated with biospecimens at no cost. Researchers interested in utilizing NMVB samples for their research may submit an application. All researchers (academic or commercial, United States or foreign) may apply for NMVB tissue specimens. NMVB currently has 966 annotated cases and 1198 biospecimens including: * Paraffin Embedded Tissue * Fresh Frozen Tissue * Blood and DNA Samples The NMVB also has developed mesothelioma tissue microarrays (TMAs) with associated multimodal data annotation. Additional TMAs will be available shortly.
Ontology of Medically Related Social Entities
An ontology covering the domain of social entities that are related to health care, such as demographic information (social entities for recording gender (but not sex) and marital status, for example) and the roles of various individuals and organizations (patient, hospital, etc.)
Chinese University of Hong Kong; Hong Kong; China
Public research university in Sha Tin, New Territories, Hong Kong.
A distributed file storage system that you can upload files to and download files from. All files uploaded to the repository are replicated several times to protect against their accidental loss. Files uploaded to the repository can be of any size, can be of any file type, and can be encrypted with a passphrase of your choosing. The Proteome Commons Tranche repository is the first instance of a Tranche repository. Tranche, was created so that anybody can take it and make their own Tranche repository. This is the first implementation of the Tranche software, and is useful as a test bed for the software. This repository relies on educational institutions to provide the hardware and facilities for Tranche servers. While we maintain a set of servers, the continued growth of this public resource will rely on the generosity of the institutions that use the repository most.
A biomedical ontology in the area of vaccine adverse events aimed to represent and analyze various vaccine-specific adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO).
Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.
caTIES - Cancer Text Information Extraction System
Cancer Text Information Extraction System
Cancer Text Information Extraction System (caTIES)
The Cancer Text Information Extraction System (caTIES) provides tools for de-identification and automated coding of free-text structured pathology reports. It also has a client that can be used to search these coded reports. The client also supports Tissue Banking and Honest Broker operations. caTIES focuses on two important challenges of bioinformatics * Information extraction (IE) from free text * Access to tissue. Regarding the first challenge, information from free-text pathology documents represents a vital and often underutilized source of data for cancer researchers. Typically, extracting useful data from these documents is a slow and laborious manual process requiring significant domain expertise. Application of automated methods for IE provides a method for radically increasing the speed and scope with which this data can be accessed. Regarding the second challenge, there is a pressing need in the cancer research community to gain access to tissue specific to certain experimental criteria. Presently, there are vast quantities of frozen tissue and paraffin embedded tissue throughout the country, due to lack of annotation or lack of access to annotation these tissues are often unavailable to individual researchers. caTIES has three goals designed to solve these problems: * Extract coded information from free text Surgical Pathology Reports (SPRs), using controlled terminologies to populate caBIG-compliant data structures. * Provide researchers with the ability to query, browse and create orders for annotated tissue data and physical material across a network of federated sources. With caTIES the SPR acts as a locator to tissue resources. * Pioneer research for distributed text information extraction within the context of caBIG. caTIES focuses on IE from SPRs because they represent a high-dividend target for automated analysis. There are millions of SPRs in each major hospital system, and SPRs contain important information for researchers. SPRs act as tissue locators by indicating the presence of tissue blocks, frozen tissue and other resources, and by identifying the relationship of the tissue block to significant landmarks such as tumor margins. At present, nearly all important data within SPRs are embedded within loosely-structured free-text. For these reasons, SPRs were chosen to be coded through caTIES because facilitating access to information contained in SPRs will have a powerful impact on cancer research. Once SPR information has been run through the caTIES Pipeline, the data may be queried and inspected by the researcher. The goal of this search may be to extract and analyze data or to acquire slides of tissue for further study. caTIES provides two query interfaces, a simple query dashboard and an advanced diagram query builder. Both of these interfaces are capable of NCI Metathesaurus, concept-based searching as well as string searching. Additionally, the diagram interface is capable of advanced searching functionalities. An important aspect of the interface is the ability to manage queries and case sets. Users are able to vet query results and save them to case sets which can then be edited at a later time. These can be submitted as tissue orders or used to derive data extracts. Queries can also be saved, and modified at a later time. caTIES provides the following web services by default: MMTx Service, TIES Coder Service
Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions.
Software using a beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.
Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool
Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool (miniTUBA)
miniTUBA - Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool
The Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool
miniTUBA is a web-based modeling system that allows clinical and biomedical researchers to perform complex medical/clinical inference and prediction using dynamic Bayesian network analysis with temporal datasets. The software allows users to choose different analysis parameters (e.g. Markov lags and prior topology), and continuously update their data and refine their results. miniTUBA can make temporal predictions to suggest interventions based on an automated learning process pipeline using all data provided. Preliminary tests using synthetic data and laboratory research data indicate that miniTUBA accurately identifies regulatory network structures from temporal data. miniTUBA represents in a network view possible influences that occur between time varying variables in your dataset. For these networks of influence, miniTUBA predicts time courses of disease progression or response to therapies. minTUBA offers a probabilistic framework that is suitable for medical inference in datasets that are noisy. It conducts simulations and learning processes for predictive outcomes. The DBN analysis conducted by miniTUBA describes from variables that you specify how multiple measures at different time points in various variables influence each other. The DBN analysis then finds the probability of the model that best fits the data. A DBN analysis runs every combination of all the data; it examines a large space of possible relationships between variables, including linear, non-linear, and multi-state relationships; and it creates chains of causation, suggesting a sequence of events required to produce a particular outcome. Such chains of causation networks - are difficult to extract using other machine learning techniques. DBN then scores the resulting networks and ranks them in terms of how much structured information they contain compared to all possible models of the data. Models that fit well have higher scores. Output of a miniTUBA analysis provides the ten top-scoring networks of interacting influences that may be predictive of both disease progression and the impact of clinical interventions and probability tables for interpreting results. The DBN analysis that miniTUBA provides is especially good for biomedical experiments or clinical studies in which you collect data different time intervals. Applications of miniTUBA to biomedical problems include analyses of biomarkers and clinical datasets and other cases described on the miniTUBA website. To run a DBN with miniTUBA, you can set a number of parameters and constrain results by modifying structural priors (i.e. forcing or forbidding certain connections so that direction of influence reflects actual biological relationships). You can specify how to group variables into bins for analysis (called discretizing) and set the DBN execution time. You can also set and re-set the time lag to use in the analysis between the start of an event and the observation of its effect, and you can select to analyze only particular subsets of variables.
fade - Estimation of position specific methylation parameters in color or nucleotide space with NR optimization
A software package designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms.
Ontology that defines hierarchical display of different rat strains as derived from parental strains. Ontology Browser allows to retrieve all genes, QTLs, strains and homologs annotated to particular term. Covers all types of biological pathways including altered and disease pathways, and to capture relationships between them within hierarchical structure. Five nodes of ontology include classic metabolic, regulatory, signaling, drug and disease pathways. Ontology allows for standardized annotation of rat. Serves as vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within diagram or between pathways that in some fashion are globally related in pathway suites and suite networks.
The metafor package: A meta-analysis package for R
A free and open-source add-on for conducting meta-analyses with the statistical software environment R.
Einstein-Montefiore ICTR Research Informatics Core
Einstein-Montefiore Institute for Clinical & Translational Research - Research Informatics Core
Einstein-Montefiore Institute for Clinical and Translational Research - Research Informatics Core
Research Informatics Core - Einstein-Montefiore Institute for Clinical and Translational Research (ICTR)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Primary informatics resource for joint research efforts of the Albert Einstein College of Medicine and Montefiore Medical Center to facilitate the study and understanding of biological processes, clinical disorders, pathologic abnormalities, and the relationships among them, using a wide variety of informatics techniques, applications, and user training. Their services include: * Collaboration on research design to enable effective data management throughout all phases of a project * Provision of management capability for large volumes of data generated by microarrays and related technologies * Provision and supports a software toolchest for data capture, retrieval, and analysis * Design and implementation of custom interfaces to incorporate existing or separately designed databases into the central data management architecture * Support for data management for the Biorepository, to enhance specimen storage, identification, and linkage with clinical data * Ensuring conformity of data elements and structures to national standards via participation in standards organizations, facilitating intramural and extramural collaboration * Providing individualized support to end-users with bioinformatics training needs * Serving as a bioinformatics liaison to other research institutes and organizations * Providing data management support for clinical research * Providing a common, secure repository for clinical, experimental, and biosample storage data
T-profiler: Scoring the Activity of Pre-defined Groups of Genes Using Gene Expression Data
One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool
Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse
Research and development project at Stanford University to create a standards-based informatics platform supporting clinical and translational research. STRIDE consists of three integrated components: a clinical data warehouse, based on the HL7 Reference Information Model (RIM), containing clinical information on over 1.6 million pediatric and adult patients cared for at Stanford University Medical Center since 1995; an application development framework for building research data management applications on the STRIDE platform and a biospecimen data management system. STRIDE's semantic model uses standardized terminologies, such as SNOMED, RxNorm, ICD and CPT, to represent important biomedical concepts and their relationships. STRIDE receives clinical data for research use via HL7 feeds from both SUMC hospitals: Lucile Packard Children's Hospital and Stanford Hospital and Clinics. This clinical data is used to support a wide variety of translational research services including: * Anonymized Patient Research Cohort Discovery * Electronic Chart Review for Research * IRB-Approved Clinical Data Extraction * Biospecimen Data Management * Multimedia Research * Data Management and Research Registries STRIDE is a highly secure environment utilizing encryption, fine-grained access control, robust auditing and detailed data segregation. Additionally, STRIDE has a robust access control framework with well-defined access granting authorities and access control groups. Consequently STRIDE meets or exceeds the requirements of the HIPAA Privacy and Security regulations. Privacy protection is further enhanced by requiring IRB approval for all research projects using STRIDE clinical data. From a technology and standards perspective, STRIDE is hosted on the Oracle 11g database platform. STRIDE application software provides access to the web services of a three-tier infrastructures using SSL encryption with strong authentication. These programs are cross-platform, self-updating thick-client applications that provides a rich user interface for data entry, retrieval and review as well as image manipulation and annotation. STRIDE makes extensive use of XML technologies for representation of structured meta data, distributed systems technologies using JSON for secure remote communication between client and server, and Swing graphical interface components providing a rich widget-set as well as advanced imaging and graphing capabilities. Users of the STRIDE Research Desktop Client can perform rapid data entry into structured fields, compose complex queries, and interact securely with clinical, research and imaging data.
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 28, 2019. Core Facility provides the software and support for computer assisted protein and DNA sequence analysis and database access. The Genetics Computer Group GCG-Wisconsin package is currently available on PBRC's UNIX platform that is accessible via modem or direct connection. The package can be accessed via three interfaces: the command-line interface (UNIX C-shell), the web-based interface (SeqWeb) and the X-Windows based graphics interface (SeqLab). Applications in the package include sequence editing, alignment, comparison, primer design, restriction analysis, mapping, data presentation, database browsing, etc. In addition to local databases, access to remote databases (BLAST) is integrated into the package. The local databases are updated quarterly. Databases available include GenBank, EMBL, PIR-Protein, SWISS-PROT and Restriction Enzymes (REBASE).
Subset-quantile Within Array Normalization
Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package.
PROSITE - Database of protein domains families and functional sites
Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP.
Medical College of Georgia Department of Physiology
Department that trains independent, creative, productive scholars in the physiological sciences. The department offers programs leading to the Ph.D. degree. A combined M.D./Ph.D. or D.M.D./Ph.D. degree program is available for students who obtain prior or concurrent admission to the Schools of Medicine or Dentistry respectively. The primary research interests of the department are Cardiovascular Physiology, Endocrinology, and Neuroscience. Physiology faculty currently hold more than $7,000,000 in extramural funding, ranking 21st out of Medical School Physiology Departments nationally. Members of the Department teach in the Medical and Graduate Schools including Medical Physiology and Intergated Systems Biology, Neuroscience and advanced courses in cardiovascular and endocrine physiology.
Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP
A structured controlled vocabulary for the representation of plant environmental conditions.
A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.
An ontology that models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies, such as the Gene Ontology (GO), which covers biological processes, and the Phenotypic Quality Ontology (PATO).
A Web application development framework for Perl. Based on the MVC programming paradigm, it provides a sensible layout for Web applications that helps you write applications faster and with fewer mistakes. Solstice serves as the foundation for a suite of enterprise communication and collaboration tools used at the University of Washington. Many of these tools, such as the WebQ survey and quiz creation application, the UMail anonymous email form, and the CrowdControl module for managing groups of users, are available for download now. More are on the way. They will offer you rich starting points, examples, and solutions for your own applications. Solstice is designed to support large, complex applications that have a serious need for structured navigation. Its state-machine based navigation system ensures that users stay on the paths they need to follow within your Web application. With any mod_perl enabled Apache server, Solstice offers easy installation and proven scalability. Specifically, Solstice provides your application with: * a state-machine based navigation system, * integrated validation, * highly reusable and embeddable page elements, * session management, * user and group models for flexible, built-in authorization, * a development mode for realtime diagnostics, and * a focus on scalability. When you work with Solstice, you can also use Majere, a Web-based development tool that automates the creation of applications and manages their configuration. Majere frees you to focus on the more interesting parts of application development and is available along with Solstice on our Download page. Solstice provides support for RESTful development.
Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. These distribution sets contain software modules and/or data sets extracted from the Visualization and Analysis Software Tools (VAST) library developed at the Minneapolis VA Medical Center, the University of Minnesota and/or the International Consortium for Neuroimaging (INC) (partially funded by the Human Brain Project )
University of Toledo Health Sciences Campus; Neurosciences
University of Toledo Health Sciences Campus; Department of Neurosciences
UT Health Sciences Campus; Dept. of Neurosciences
UT Health Sciences Campus; Neurosciences
The Department of Neurosciences is highly committed to advancing the state of knowledge of nervous system structure and function through a tripartite mission of innovative research, state-of-the-art teaching methods, and dedicated service to the broader academic and surrounding communities. The teaching mission of our Department effectively communicates the current state of knowledge in neuroscience to the medical, graduate, and post-graduate students of the University using innovative methods. We are nationally known for using the most current technologies to teach human anatomy, embryology, and neurobiology to medical and graduate students. We teach critical thinking and problem solving skills and also provide opportunities for the students to excel in the laboratory and develop as life-long learners. Faculty participate in our Neurosciences and Neurological Disorders (NND) training track which awards both Ph.D. and M.S. degrees. We also train students towards the M.D./Ph.D and M.D./ M.S.B.S. joint degrees. Our research mission incorporates molecular, cellular, and systems neuroscience and cuts across the boundaries of traditional departments and disciplines. Our funded research in neurodevelopment, neurodegeneration, regeneration and repair, sensory function, and drug abuse comprise just a few of our interests. We employ cutting edge technologies and focus on the solution of fundamentally important problems pertinent to nervous system diseases and processes that can be translated feasibly to clinical issues. We work towards a synergistic interaction between the clinical and basic sciences that prompts unexpected discoveries of causes and novel treatments for the diseased nervous system. We also coordinate the Human Body Donation Program at the University of Toledo College of Medicine.
Montana State University, Department of Cell Biology and Neuroscience
Montana State University Department of Cell Biology and Neuroscience
Montana State University Department of Cell Biology Neuroscience
MSU Dept. of Cell Biology and Neuroscience
The academic programs and scientific research interests in our department cover a wide range of topics, with special emphasis on Cell Biology, Neurobiology, Developmental Biology, Physiology, Anatomy, Biophysics, and Neuroinformatics. Together, faculty and students in our department study biological processes that span the continuum from single cells to the entire human body. The Department of Cell Biology and Neuroscience offer both an Undergraduate and Graduate Program, which includes Ph.D. or M.S. degrees in Neuroscience or Biological Science. Two different undergraduate degree options are available within the Cell Biology and Neuroscience major: Biomedical Sciences and Cell Biology & Neuroscience. The Department of Cell Biology and Neuroscience offers exciting opportunities to work with nationally and internationally recognized faculty on a wide range of research topics, including cognitive neuroscience, neurophysiology, neuroinformatics, developmental biology, cell biology, biophysics and computational neuroscience.
Data set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available. Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice.
qPrimerDepot - A quantitative real time PCR primer database
A database that provides quantitative real time (qRT) PCR primers for 99.96% human RefSeq sequences. For 99% of intron-bearing genes, the PCR product will cross an exon-exon border which overlaps one of the largest introns. Primers are assumed to have a uniform annealing temperature of 60C, allowing them to be used in large-scale assays.
An ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs.
bpipe - A tool for running and managing bioinformatics pipelines
Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments.
A Python package to facilitate running tools with nested combinations of parameters and inputs. It provides three components: a module to build nested directory structures corresponding to choices of parameters; the nestrun script to run a given command using each set of parameter choices; the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. Also included is a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds.
BBID-Biological Biochemical Image Database
Database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics. The rationale for this collection is that: # Except in a few cases, information on most biological pathways in higher eukaryotes is non-existent, incomplete, or conflicting. # Similar biological pathways differ by tissue context, developmental stages, stimulatory events, or for other complex reasons. This database allows comparisons of different variations of pathways that can be tested empirically. # The goal of this database is to use images created directly by biomedical scientists who are specialists in a particular biological system. It is specifically designed to NOT use average, idealized or redrawn pathways. It does NOT use pathways defined by computer algorithm or information search approaches. # Information on biological pathways in higher eukaryotes generally resides in the images and text of review papers. Much of this information is not easily accessible by current medical reference search engines. # All images are attributable to the original authors. All pathways or other biological systems described are graphic representations of natural systems. Each pathway is to be considered a work in progress. Each carries some degree of error or incompleteness. The end user has the ultimate responsibility to determine the scientific correctness and validity in their particular biological system. Image/pathway submissions are welcome.
snakemake - A Python based language and execution environment for make-like workflows
A Python based language and execution environment for make-like workflows. The system supports the use of automatically inferred multiple named wildcards (or variables) in input and output filenames.
snape-pooled: Computes the minor allele frequency spectrum in pooled DNA (sequenced) samples
Software that computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.
Meharry Graduate Program in Pharmacology
Meharry Medical College School of Graduate Studies and Research; Graduate Program in Pharmacology
Meharry Medical College School of Graduate Studies and Research; Pharmacology
Meharry SOGSR Graduate Program in Pharmacology
Graduate Program in Pharmacology at Meharry Medical College embraces the broad definition of pharmacology as the study of how chemical agents affect living processes; the chemicals involved include agents such as endogenous hormones, neurotransmitters, and/or growth factors; toxic substances in our environment; and pharmaceutically developed drugs. The breadth of our scientific environment is manifested by faculty who study the fate of drugs once ingested and the variability of drug response in varying patient populations (a discipline known as pharmacokinetics), as well as faculty who study the mechanisms by which drugs and endogenous agents work (a discipline known as pharmacodynamics). A unique strength of our research and training environment is the inter-disciplinary nature of the program, which encompasses faculty from the four divisions of the Department of Biomedical Science and Departments of Internal Medicine and Neurology.
Next Generation Sequencing ANalysis for Enterprises
Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data.
Mercer University College of Pharmacy and Health Sciences; Department of Pharmaceutical Sciences
Mercer COPHS Dept. of Pharmaceutical Sciences
Mercer University COPHS Department of Pharmaceutical Sciences
The mission of the Department of Pharmaceutical Sciences is to make scholarly contributions to the discipline of pharmaceutical sciences and related fields. Education within the department offers a high quality learning environment that includes Ph.D. and Pharm.D./Ph.D. degree programs. Although not required for entry into pharmacy practice, a one-year residency is offered and affords the Pharm.D. graduate an opportunity to develop expertise in clinical pharmacy practice and specialty areas. The graduate program leading to the Ph.D. degree in pharmaceutical sciences is designed for students seeking teaching and research careers in academic institutions, the pharmaceutical industry and other health-related agencies. An interdisciplinary approach prepares graduates to perform independent research, to encourage scholarly development and to acquire teaching skills. Areas of specialization include pharmacology, pharmaceutics, toxicology, and medicinal chemistry. The Doctor of Pharmacy (Pharm.D.)/Doctor of Philosophy (Ph.D.) Degree Program enables highly qualified students to obtain both degrees in a shortened period of time. This Pharm.D./Ph.D. Degree program is designed primarily for students who are strongly motivated toward an academic/ research career in the pharmaceutical sciences. The Program is flexible enough to accommodate individuals of varied educational backgrounds.
National Institute of General Medical Sciences Image Gallery
Database of scientific photos, illustrations, and videos made available by the National Institute of General Medical Sciences.
A Java interface to the mzTab data exchange format for reporting a summary of proteomics results.
Software tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer.
Michigan State University, Department of Pharmacology and Toxicology
Michigan State University Department of Pharmacology and Toxicology
Michigan State University Department of Pharmacology Toxicology
MSU Dept. of Pharmacology and Toxicology
Michigan State Pharmacology and Toxicology
At the Department of Pharmacology & Toxicology at Michigan State University, we combine integrative research, active learning and intellectual enrichment to prepare the student for advancement and leadership in their chosen field. The Department provides courses for undergraduate students, graduate students, medical students of the allopathic, osteopathic and veterinary colleges, and nursing students. In addition, specialized courses of study are offered in areas of professional development and life-long learning. From molecular and cellular levels to organ systems and whole animal models, our graduate and undergraduate programs encompass multiple areas of study, empowering students to challenge the boundaries of knowledge and chart their own unique path in the biomedical sciences. The disciplines of pharmacology and toxicology play a momentous role in human health today, and their applications in the professional world are vast. The department offers: * Pharmacology & Toxicology Graduate Doctoral Program * Online MS Programs ** Online Professional Science Masters in Integrative Pharmacology ** Online Masters in Pharmacology * Undergraduate Courses in Pharmacology & Toxicology * Dual Major Graduate Program in Toxicology (joint Pharmacology & Toxicology/Environmental Toxicology graduate program) * NIGMS Integrative and Organ Systems Pharmacology Short Course * Summer Undergraduate Research Fellowships
Morehouse School of Medicine Neuroscience Institute
The mission of the Morehouse School of Medicine Neuroscience Institute (MSMNI) is to create a supportive and challenging environment for the investigation and teaching of the functional organization of the nervous system, and to seek ways to reduce suffering brought about by neurological disorders. Members of the MSM NI are involved in teaching graduate students, medical students, and health care professionals about researching and treating medical conditions that are caused by or are rooted in the central nervous system. Additionally, MSM NI offers an 8-week Summer Research Program to qualified undergraduate, post-baccalaureate and first-year medical school students. Funding and administrative support were secured from the National Institutes of Health Office on Research for Minority Health and the National Institute for Neurological Disorders and Stroke (NINDS), respectively. The Neuroscience Institute is composed of selected faculty members from the Department of Neurobiology and the Department of Pharmacology at Morehouse School of Medicine who are conducting grant supported research. MSMNI research areas cover a broad range of cellular and molecular neuroscience and include the molecular biology and physiology of circadian rhythm, mechanisms of sleep and sleep disorders, mechanisms of stroke and stroke prevention, photoreceptor and retinal physiology, glutamate receptor physiology and mechanisms of hyperexcitability in epilepsy. Investigators use a variety of experimental preparations including whole animals, the intact portions of the central nervous system, and simplified preparations, such as tissue slices and single cells, to study cellular activities and cell-cell communication under more controlled conditions.
Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.
Ontology that describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. It is built according to ontology development best practices (re-use of existing ontologies; formal definitions of terms; use of foundational ontologies). It describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil. Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their appropriate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration.
A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux.
Next-generation genome browser software designed for the latest generation of genome data.
A R package for multiple marker meta-analysis.
Harvard/MGH-UCLA Consortium: Human Connectome Project
Harvard/MGH-UCLA Human Connectome Project
MGH/UCLA Consortium: Human Connectome Project
A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.
Project facilitating the establishment and maintenance of standards systems and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The Human Variome Project produces two categories of recommendations: HVP Standards and HVP Guidelines. HVP Standards are those systems, procedures and technologies that the Human Variome Project Consortium has determined should be used by the community. These carry more weight than the less prescriptive HVP Guidelines, which cover those systems, procedures and technologies that the Human Variome Project Consortium has determined would be beneficial for the community to adopt. HVP Standards and Guidelines are central to supporting the work of the Human Variome Project Consortium and cover a wide range of fields and disciplines, from ethics to nomenclature, data transfer protocols to collection protocols from clinics. They can be thought of as both technical manuals and scientific documents, and while the impact of HVP Standards and Guidelines differ, they are both generated in a similar fashion. A document has been generated both as a guide for those collecting and distributing data and for those developing policy. Items should include those generated by HGVS/HVP collaborators as well as those generated by groups of individual Societies and Standards bodies in all relevant fields worldwide.
An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to).
A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1
A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.
Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.
A domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. It articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables the representation of pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables the representation of a patient and more largely a panel included in trials, and populations. SO-Pharm enables the representation of measured items on patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.
MultiPhen: a package for the genetic association testing of multiple phenotypes
Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).
Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.
Congress of Neurological Surgeons NeuroWiki
Wiki dedicated to neurosurgical topics, maintained by the Congress of Neurological Surgeons. Members can log in to contribute by adding or editing an article. A wiki is a collaborative technology for organizing information. Visitors can add, remove, and edit content. Like all other wikis, the CNS University's NeuroWiki allows linking among any number of pages. This ease of interaction and operation will engender collaborative authoring.
Brain Atlas of the Mozambique Tilapia Oreochromis mossambicus
Digital three-dimensional MRI atlas of the Mozambique tilapia brain, supported by Nissl staining. Images were viewed and analyzed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. The MRI atlas data (16-bit int) and delineation data (8-bit int) are provided in Raw data (file_name.raw), Amira format (file_name.am) and in Analyze format (file_name.img and file_name.hdr).
Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Short TR Sample
Dataset of resting state fMRI scans obtained using two different TR's in healthy college-aged volunteers. Specifically, for each participant, data is being obtained with a short TR (0.4 seconds) and a long TR (2.0 seconds). In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 8-minute resting-state fMRI scan (TR = 2 seconds, # repetitions = 240) * 8-minute resting-state fMRI scans (TR = 0.4 seconds, # repetitions = 1200) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information
Gene Cloud: Exploring Connections in the Mouse Genome
Gene Cloud is a novel tool presenting gene-gene associations based on the scientific literature. It was developed by the Knockout Mouse Repository (www.komp.org) to help our customers find products related to other products they chose. We have built a detailed graph model of gene-gene associations based on how many times two genes are cited in the same article. If two genes are cited in many papers together, they are considered strongly connected. Each instance of Gene Cloud is centered around a specific gene. A list of the top most related genes is plotted as a branching structure from the center. A secondary branch can occur if a gene in the graph is more related a non-central gene than it is to the center gene. The font size of a branched gene indicates the relative strength of connection--always to the center gene. The distribution of genes in space is randomized each time Gene Cloud is run so a different picture will result for the same central gene. Color is used to indicate the availability of Knockout Mouse products at the KOMP Repository. If a gene is colored green in the graph there are products (mutant ES cells, sperm, embryos, or mice) ready to be ordered. Blue colored genes do not yet have products available, but you can follow the links back to the KOMP Repository and register interest to be alerted when products do become available. Gene Cloud is driven by a database of gene-gene associations that currently contains 82,000 genes and other biotypes, 113,000 annotated publications, and 467 million connections. The latest gene symbols, names and gene-publication annotation information is updated daily from the Mouse Genome Informatics database. The graphing is accomplished through the use of a modified version of jsViz.
An online electronic lab notebook designed for lab scientists at research organizations that allows the creation and import research data, controlled sharing between lab members, and lets lab members communicate via messages and tasks. It also allows lab members to work from home or when travelling, in a secure, integrated collaborative environment.
A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. It provides: systematic and alternate names, atomic formulas and masses, enzyme activities generating the modifications, keywords, literature citations, Gene Ontology cross-references, Protein Information Resource (PIR) and SWISS-PROT protein sequence database feature table annotations, structure diagrams and molecular models. Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries.
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome
HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool.
Colorado Assessment Tests - Tower of London
CATs Tower of London test is a free, computer-based software test originally developed by Shallice (1982) to investigate problem solving in subjects with damage to the frontal lobes. The CATs Tower of London Test comes with one preprogrammed test along with extensive normative data for that test. You can also create a test using your design. Briefly, subjects are required to move colored beads from a window on the left (working area) until they achieve the arrangement in the window on the right (goal position). Subjects are instructed to try to achieve the goal arrangement in as few moves as possible. The software contains a Tower of London test. The test contains trials with 3 beads and 3 pegs, 4 beads and 4 pegs, and 5 beads and 5 pegs. You can use the Setup screen to create a test using your design. A test can contain 3, 4, and 5 bead problems with varying number of moves required for the optimal solution. In Shallice's initial investigation using the Tower of London, patients with damage to the left anterior frontal lobe demonstrated impaired planning (i.e., greater number of moves required for solution). Patients with damage to the right anterior, and left or right posterior areas of the frontal lobes were not impaired. Thus, results from this initial study provided support for the view that the left anterior frontal lobe area is involved in the planning required for solving the Tower of London test. Recent studies using neuroimaging techniques support this notion. Studies using regional cerebral blood flow (rCBF) imaging indicate an involvement of the left frontal lobes in the planning required for successfully completing the Tower of London puzzle. Studies of patients with damage to the frontal lobes indicate less cortical specificity, but are consistent with the view that the frontal lobes are involved in the planning required for solving this puzzle.
Oregon Health and Science University Neuroscience Graduate Program
The Neuroscience Graduate Program (NGP) at OHSU provides outstanding, multidisciplinary training in neuroscience in one of the best-recognized neuroscience programs in the United States. Our graduates are distributed at top research institutions throughout the world, and the success of our faculty ensures that graduates have ready access to their next step ����?? be it postdoctoral fellowships in academia or industry, or other science-related careers. The program is particularly strong in cellular neuroscience, neuronal signaling, gene regulation, biophysics of channels and transporters, sensory systems, and neuroendocrinology with increasing strength in developmental neuroscience and disease-oriented neuroscience research. Faculty members are located within research institutes at OHSU including the Vollum Institute, the Oregon National Primate Research Center (ONPRC), Oregon Hearing Research Center, Jungers Center and the Center for Research on Occupational and Environmental Toxicology (CROET); as well as the basic and clinical departments in the OHSU School of Medicine. As time spent in the lab is the most important component of graduate science training, our program is designed such that core coursework is completed in the first year. During that first year, students also are immersed in research through lab rotations in several labs, eventually choosing one that gives a mutual fit. Because of the relatively small number of students compared to the number of neuroscience laboratories at OHSU, students have many options for a thesis lab. Our well funded faculty provide state-of-the-art exposure to the concepts and technology of modern neuroscience. OHSU also offers certificate and degree programs, e.g. technology transfer and translational science, for advanced students in the NGP who want to broaden their career options.
Multiple Filters enhanced Genetic Ensemble System
Multiple Filters enhanced Genetic Ensemble System (MF-GE)
A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map.
Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment.
Computing resources structural biologists need to discover the shapes of the molecules of life, it provides access to web-enabled structural biology applications, data sharing facilities, biological data sets, and other resources valuable to the computational structural biology community. Consortium includes X-ray crystallography, NMR and electron microscopy laboratories worldwide.SBGrid Service Center is located at Harvard Medical School.SBGrid's NIH-compliant Service Center supports SBGrid operations and provides members with access to Software Maintenance, Computing Access, and Training. Consortium benefits include: * remote management of your customized collection of structural biology applications on Linux and Mac workstations; * access to commercial applications exclusively licensed to members of the Consortium, such as NMRPipe, Schrodinger Suite (limited tokens) and the Incentive version of Pymol; remote management of supporting scientific applications (e.g., bioinformatics, computational chemistry and utilities); * access to SBGrid seminars and events; and * advice about hardware configurations, operating system installations and high performance computing. Membership is restricted to academic/non-profit research laboratories that use X-ray crystallography, 2D crystallography, NMR, EM, tomography and other experimental structural biology technologies in their research. Most new members are fully integrated with SBGrid within 2 weeks of the initial application.
Software package contains methods for performing Phenome-Wide Association Study.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Visual span tests have been frequently used to assess non-verbal short-term memory. The free computer-based CATs Visual Span provides you with a flexible package for designing tests of visual spatial memory. You can create your own unique tests or variations on previously reported versions of the visual span test. For example in the Corsis Block-Tapping Test the examiner places nine blocks on a board and taps them in a designated sequence. The participant is required to repeat the sequence. Over trials the length of the sequence is increased (see Milner, 1971). The Knox Cube Imitation Test uses four blocks and essentially follows the same logic. The Wechsler Memory Scale - Revised includes a two part visual memory span test. In this test the examiner points at boxes on an eight box card in a prearranged sequence and the subject is required to repeat back the sequence. The initial trial starts with a sequence of two blocks and increases over trials. The two parts of this test are a forward visual span test and a reverse visual span test. Tests similar to these and more can be setup with the CATs Visual Span.
A web portal that aggregates information and educational materials about the brain and brain diseases. Resources such as videos, key brain concepts, and hands-on activities may be used and shared with the public.
Pennsylvania State University College of Medicine Neuroscience
PennState Hershey Neuroscience Institute
Pennsylvania State University Hershey Neuroscience Institute
Advances in our understanding of the brain are leading to new insights into how we think and to new opportunities to treat the devastating set of neurological diseases that affect all segments of our population. Penn State Hershey Neuroscience Institute integrates basic, translational and clinical neuroscience research; education of graduate students, medical students, postdoctoral fellows and residents; clinical care of patients with neurobehavioral diseases and disorders; and outreach to the local community, state, regional, national and international neuroscience organizations. With the neurosciences clearly established as a continuing priority in the overall strategic vision of Penn State Hershey, the leadership of the neuroscience community is seeking to establish the short and long term vision for excellence and continued growth in neuroscience. Those academic centers that can achieve the best collaboration and alignment among the various neuroscience disciplines will be best positioned to advance this field. We believe that the formation of Penn State Hershey Neuroscience Institute positions us to take a leading role in developing neuroscience knowledge and treatment.
Colorado Assessment Tests - Reaction Time
Reaction Time is free neuropsychological evaluation software designed to assess subject's speed of processing on three relatively simple tasks. Tasks include a simple reaction time test, a choice test, and a conditional choice test. Participants are shown a series of visual stimuli on a computer screen and asked to respond by pulling an appropriate trigger on a standard game pad. Both reaction time and the trigger pulled are recorded for subsequent analysis. Tasks to be used in the test, the average inter-stimulus interval and the number of stimuli presented for each task can be set by the investigator. The analysis includes means and standard deviations for response latencies for a single session, as well as the capability of evaluating a participant's performance on a particular session against their performance on a series of sessions. This test requires the use of a game pad that supports at least four buttons and provides a right and left trigger button. We have tested several different brands of inexpensive game pads and have found them acceptable; however we have standardized on Microsoft's SideWinder and have used it in collecting the normative data for this test.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The modifiable n-Back test is free software presumed to measure executive control of the updating of information in working memory. The task requires the participant to monitor some dimension (e.g. content, position, numerosity) of a temporally present sequence of items, responding when the currently presented item matches on the relevant dimension an item that was just recently presented. The match can be with an item present either 1 back, 2 back, 3 back or n back. Considerable flexibility is provided to the experimenter in specifying various parameters of the experiment (e.g. presentation rate, n back, content, position, color). The n-Back test is presumed to measure executive control of the updating of information in working memory. (Shimamura, 2000) Watter, Geffen and Geffen (2001) based on their work with the P300 event-related-potential have suggested that the n-Back is a dual task in that latencies of the P300 did not change with increasing task difficulty, that is memory load while amplitude did reflecting in their view a reallocation of attention and processing capacity away from the matching subtask. The n-Back task is one in which the participant is presented a series of stimuli at a constant rate. The task of the participant is to determine if the currently presented stimulus is similar (along some dimension) to one they have recently (usually one, two or three positions back) seen in the stream. Match criteria can be dimensions like material, position on the screen, color or some combination. CATs n-Back allows for substantial control over the position in which the material is presented (nine different positions), the nature of the material (any character or dingbat string, and any color. The experimenter can set the speed at which the sequence is presented including both the stimulus on time and the inter-stimulus interval. Participant responses can be made either using the keyboard or the mouse. At this time no normative data is available for this test.
An ontology that includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, they also incorporate taxonomic information across the vertebrates from the Paleobiology Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb) are incorporated to provide a more authoritative hierarchy and a richer set of names for specific taxonomic groups.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.Comprised of a large array of sophisticated programs, this comprehensive software package with tools based around the MINC file format. Utilities are provided for conversion, viewing, editing, registering, segmentation, and a wide array of analysis. Many programs are in Perl. MINC software tools for neurological imaging are free. Input format: Analyze, DICOM, Minc
Colorado Assessment Tests - Symptom Validity
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Memory impairment is one of the most common complaints after head injury, and accordingly, individuals may attempt to feign memory impairment or exaggerate symptoms of memory impairment. This free neuropsychological evaluation software contains some of the most common tests used to detect malingering of memory impairment. This software package contains a number of tests of declarative memory that assess recall of information that has a personal and temporal context. The typical example of declarative tests used for detecting malingering are the auditory verbal learning test and forced choice test. These tests are included in Symptom Validity along with other tests of declarative memory (e.g., prose recall, questionnaire tests). Unfortunately, classification of individuals is not completely accurate even with the use of multiple declarative memory tests. Thus, other tests that can complement previously used declarative memory measures by enhancing classification accuracy may be of great value to the neuropsychologist assessing the possibility of malingering. Your software contains two tests of nondeclarative memory that have been previously shown to be useful in the detection of malingered memory deficits (Davis et al., 1997a, 1997b). These tests take advantage of the general laypersons misunderstanding of the test performance of a truly memory impaired individual. That is, amnesic patients have been shown to perform normally on these nondeclarative memory tests and this is counterintuitive to the memory performance expectations of the general layperson. The nondeclarative tests included in Symptom Validity are two repetition priming tests of word stem completion and two tests of pattern categorization learning. Note: At this time this program will run only on Windows 98. We are currently working on a version that will run under the newer operating systems.
MiMi Web gives you an easy to use interface to a rich NCIBI data repository for conducting your systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research literature. The MiMI database comprehensively includes protein interaction information that has been integrated and merged from diverse protein interaction databases and other biological sources. With MiMI, you get one point of entry for querying, exploring, and analyzing all these data. MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases and augments this information from many other biological sources. MiMI merges data from these sources with deep integration into its single database with one point of entry for querying, exploring, and analyzing all these data. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in. MiMI gives you access to more information than you can get from any one protein interaction source such as: * Vetted data on genes, attributes, interactions, literature citations, compounds, and annotated text extracts through natural language processing (NLP) * Linkouts to integrated NCIBI tools to: analyze overrepresented MeSH terms for genes of interest, read additional NLP-mined text passages, and explore interactive graphics of networks of interactions * Linkouts to PubMed and NCIBI's MiSearch interface to PubMed for better relevance rankings * Querying by keywords, genes, lists or interactions * Provenance tracking * Quick views of missing information across databases. Data Sources include: BIND, BioGRID, CCSB at Harvard, cPath, DIP, GO (Gene Ontology), HPRD, IntAct, InterPro, IPI, KEGG, Max Delbreuck Center, MiBLAST, NCBI Gene, Organelle DB, OrthoMCL DB, PFam, ProtoNet, PubMed, PubMed NLP Mining, Reactome, MINT, and Finley Lab. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for MiMI. Access to this website is provided free of charge. The MiMI data is queryable through a web services api. The MiMI data is available in PSI-MITAB Format. These files represent a subset of the data available in MiMI. Only UniProt and RefSeq identifiers are included for each interactor, pathways and metabolomics data is not included, and provenance is not included for each interaction. If you need access to the full MiMI dataset please send an email to mimi-help (at) umich.edu.
OppNet - Basic Behavioral and Social Science Opportunity Network
OppNet: Basic Behavioral and Social Science Opportunity Network
OppNet is a trans-NIH initiative to expand the agency's funding of basic behavioral and social sciences research (b-BSSR). Basic-BSSR studies mechanisms and processes that influence behavior at the individual, group, community and population level. Research results lead to new approaches for reducing risky behaviors and improving the adoption of healthy practices. The mission of OppNet is to pursue opportunities for strengthening basic behavioral and social science research (b-BSSR) at the NIH while innovating beyond existing investments. * OppNet advances basic behavioral and social science research through activities and initiatives that build a body of knowledge about the nature of behavior and social systems. * OppNet prioritizes activities and initiatives that focus on basic mechanisms of behavior and social processes; that are relevant to the missions and public health challenges of multiple NIH Institutes, Centers and Offices (ICOs); and that build upon existing NIH investments without replicating them. All NIH Institutes and Centers (ICs) share the mission of supporting b-BSSR. OppNet will also develop a plan for focused multi-year programs across ICs to advance priority topics within b-BSSR.
Service that provides petabyte-scale cloud resources to analyze, manage, and share scientific data. It is designed to serve medium to large sized research projects by managing and operating a secure cloud computing infrastructure that can be shared across a project. This Science as a Service approach to research saves scientists and their funders valuable time and money. All of the software developed is open source and hosted on GitHub. The OSDC also has 1PB of public data in a wide variety of disciplines. The data sets can downloaded over the internet or high performance networks such as Internet2, as well as computed over directly on the OSDC.
Integrating Data for Analysis Anonymization and SHaring
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications.
Human Physiology is a featured book on Wikibooks because it contains substantial content, it is well-formatted, and the Wikibooks community has decided to feature it on the main page or in other places. Please continue to improve it and thanks for the great work so far! A printable and PDF version are available. You can edit its advertisement template. Contents: 1. Homeostasis 2. Cell Physiology 3. Integumentary System 4. The Nervous System 5. Senses 6. The Muscular System 7. Blood Physiology 8. The Cardiovascular System 9. The Immune System 10. The Urinary System 11. The Respiratory System 12. The Gastrointestinal System 13. Nutrition 14. The Endocrine System 15. The Male Reproductive System 16. The Female Reproductive System 17. Pregnancy and Birth 18. Genetics and Inheritance 19. Development: Birth through Death 20. Appendix 1: Answers to Review Questions 21. Authors 22. Further Reading
Software R package for RNA-Seq Differential Expression Analysis.
The MRC Laboratory of Molecular Biology (LMB) has long been, and remains, a world-class research laboratory. Our primary goal is to understand biological processes at the molecular level, through the application of methods drawn from physics, chemistry and genetics. This quest extends from structural studies of individual macromolecules, through their interactions and beyond to the functioning of subcellular systems, cells and multicellular systems in whole organisms, with the ultimate aim of using this knowledge to tackle specific problems in human health and disease. The LMB is one of the birthplaces of modern molecular biology. Many techniques were pioneered at the laboratory, most notably methods for determining the three-dimensional structure of proteins and DNA sequencing. Whole genome sequencing was initiated at the LMB. Another landmark discovery was the invention of monoclonal antibodies. Over the years, the work of LMB scientists has attracted 9 Nobel Prizes, shared between 13 LMB scientists, as well as numerous other prizes and scientific awards.
altmetrics is the creation and study of new metrics based on the Social Web for analyzing, and informing scholarship. No one can read everything. We rely on filters to make sense of the scholarly literature, but the narrow, traditional filters are being swamped. However, the growth of new, online scholarly tools allows us to make new filters; these alt-metrics reflect the broad, rapid impact of scholarship in this burgeoning ecosystem. We call for more tools and research based on alt-metrics. * Tools: Browse a directory of noteworthy altmetrics apps. * Media: Watch videos of altmetrics presentations.
An OWL representation of the data in PharmGKB, Comparative Toxicogenomics Database (CTD) and DrugBank and linked to related ontologies: ChEBI ontology, the Human Disease Ontology (DO), the Anatomical Therapeutic Chemical Classification System (ATC) and the Medical Subject Headings Thesaurus (MESH). The combined knowledge base can be exploited using the ELK reasoner.
An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. It includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX.
Brain Architecture Management System Cells
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein.
A coalescent simulation software program for a structured population including recombination, demographic structure and selection at a single diploid locus.
FSSP - Families of Structurally Similar Proteins
families of structurally similar proteins
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank. The database currently contains an extended structural family for each of 330 representative protein chains. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set (remote homologs, below 30%% sequence identity), as well as all structures in the Protein Data Bank with 70-30%% sequence identity relative to the search structure (medium homologs). Very close homologs (above 70 % sequence identity) are excluded as they rarely have marked structural differences. The alignments of remote homologs are the result of pairwise all-against-all structural comparisons in the set of 330 representative protein chains. All such comparisons are based purely on the 3D co-ordinates of the proteins and are derived by automatic (objective) structure comparison programs. The significance of structural similarity is estimated based on statistical criteria. The FSSP database is available electronically and by anonymous ftp (file transfer protocol).
The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA. Information provided for each nucleoside includes: the type of RNA in which it occurs and phylogenetic distribution; common chemical name and symbol; Chemical Abstracts registry number and index name; chemical structure; initial literature citations for structural characterization or occurrence, and for chemical synthesis. Both the structural diversity and extent of posttranscriptional modification in RNA is remarkable, with 107 different nucleosides presently known in all types of RNA. The discovery of new modified nucleosides as well as increasing knowledge of the array of functional roles of modification, based largely on extensive studies of tRNA, mandates a need for a comprehensive database of RNA nucleosides. The RNA Modification Database is maintained as an extension of the initial version published in mid-1994. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. The information provided permits access to the modified nucleoside literature through provision of both computer-searchable Chemical Abstracts registry numbers and key literature citations. This database also provides an historical record of the initial reports of occurrence, characterization and chemical synthesis of modified nucleosides from RNA. It is our judgement that the total number of RNA nucleosides listed, and the chemical structures reported, are very accurate. However, the distributions listed are in some cases a matter of concern, due primarily to the possibility of inhomogeneity of the RNA isolate and the use of methods of nucleoside identification that are not sufficiently rigorous. Reinvestigation of some of the unusual or single-report source distributions is warranted, and will likely lead to future refinements in the listings. The authors invite comments concerning new entries, errors or omissions and on the format presently used for electronic access to the database.
World's open biospecimen research database where biobanks and biomedical researchers meet to exchange human biospecimen needs and supply: whole blood, serum, plasma, solid tissue samples and more. The connection is accelerated so researchers save valuable time and money and tissue banks utilize inventory. The pace of specimen procurement remains unacceptably slow to the biomedical research community. Specimen Central is the foremost global resource to aid biomedical researchers in expediting their search for high quality human biospecimens, tissues, samples and specimens. They facilitate your search for blood, whole blood, buccal swab, DNA, RNA, protein, cell lines, plasma, serum, RBC, white cells, buffy coat, fluid, marrow, urine, stem cells, and solid tissue such as tumor, tumor and biopsy materials spanning all manner of common and rare pathologies and indications including Alzheimer's, basal cell carcinoma, bladder cancer, bone cancer, brain cancer, breast cancer, cerebrospinal fluid, amniotic fluid, colorectal cancer, colon cancer, hodgkins and non-hodgkins lymphoma, kidney/renal cancer, leukemia, liver cancer, lung cancer, melanoma, multiple sclerosis, myeloma neuroblastoma, neurodegenerative diseases, ovarian cancer, pancreatic cancer, prostate cancer, urinary cancer. This includes adult and pediatric indications. Specimen Central users specify a number of variables in their Specimen Requests, including preparation, preservation and handling requirements such as cryo-preserved, FFPE (Formalin-fixed paraffin-embedded), formalin, frozen, refrigerated, OCT, snap frozen, paraffin block, fresh, prospective, autopsy or cadaveric, etc. Many users require clinically annotated date associated with their specimens, as well as documentation of IRB or ethics committee approval and informed consents. For Researchers Most specimen databases require researchers to waste time and effort entering lengthy registrations and search queries that yield poor results, if anything. Specimen Central solves this problem by having tissue banks search for you. From years to months, months to weeks, and weeks to days, Specimen Central seeks to reduce delays and costs in the research & development life cycle by expediting connections between demand and supply. For Biobanks The capital costs of maintaining a biobank infrastructure are substantial and growing. Biobanks use Specimen Central as a marketing tool to augment their business development efforts. By routinely checking Specimen Central's Specimen Requests, biobanks can uncover market demand for their inventories and develop new connections and revenue streams to defray costs. Specimen Central supplements - not displaces - the efforts of your sales representatives, agents, brokers and commercial partners.
Neuro Bureau - Berlin Mind and Brain Sample
Neuro Bureau - Berlin: Mind & Brain Sample
Neuro Bureau/Berlin Mind and Brain Institute Sample
Neuro Bureau/Berlin Mind and Brain Sample
Dataset consisting of a community sample of individuals ranging in age from 18 to 60 years old with at least two 7.5-minute resting state fMRI scans. During the resting state scan participants were instructed to relax while keeping their eyes open. In part of the sample eye status was randomized between scans. The particular eye status for each scan is indicated in the phenotypic information. No visual stimulus was presented. A subset of participants completed the ICS and PANAS affective behavior scales. The following data are released for every participant: * Scanner Type: Siemens, 3T Trio Tim * 7.5-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * Demographic information, inluding ICS and PANAS scores (included in the release file).
Resting state datasets, including an anatomical as well as a resting state fMRI scan, collected from a community sample in Valencia, Spain. The first release includes data for 45 participants. Participants were instructed to keep their eyes open during the resting state scan, no visual stimulus was presented. The following data are released for every participant: * Scanner Type: Philips Achieva 3T-TX * One high-resolution T1-weighted mprage, defaced to protect patient confidentiality * At least one 6-minute resting state fMRI scan (R-fMRI), eyes open, no visual stimulus presented * Demographic Information
Christopher Newport University; Virginia; USA
Public university in Newport News, Virginia. Academic programs at CNU encompass more than 80 areas of study, from biology to business administration and political science to performing arts.
Open Rotterdam Glaucoma Imaging Data Sets
Data sets resulting from glaucoma research including visual fields, various imaging modalities and other data from both glaucomatous and normal subjects. The Longitudinal Glaucomatous Visual Fields data set contains IOP (Intraocular pressure) measurements and 24-2 Full Threshold visual fields obtained with a Humphrey Field Analyzer (Zeiss). Data of both eyes of 139 patients over a mean period of over 9 years is included, with on average more than 17 fields per eye. Local threshold and total deviation values are included.
Archive and access films from the field of Ophthalmology for free on highly secure servers for permanent access and citeability. A citeable identification number (specific addressing using DOI), allows for citation of individual films in journal publications. Films may be commented by the author either in speech, or in text. Key wording provided by the authors at the time of submission, make each film recognizable to internet search machines.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Sage Bionetworks video podcasts feature the plenary talks from the April 2011 Commons Congress in San Francisco. The Keynote and project update video posts are in reverse chronological order; the full agenda is available at www.sagecongress.org. There are also several excellent podcasts from the January 2011 Symposium on Human Data Interoperability. The podcasts are also available on iTunes where you can subscribe and receive new podcasts automatically when posted. Upcoming posts will feature presentations and interviews on network biology, genomics, healthcare and open science. All these podcasts feature research and thought leaders as well as policy advocates, scientists working at the coal-face and patients. The topics span technical and strategic issues and include fact and opinion. The goal is to engage, educate and inspire non-scientists and scientists alike.
Software tool that displays large genomics datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other biological processes.
TACMASS collects, preserves, and banks biospecimens obtained from Arizona Cancer Center surgical patients who are seen by University Medical Center surgeons and oncologists. Biospecimens collected at the time of surgery include fresh surgical tissue, blood and urine. Serum, plasma and genomic DNA are harvested from the whole blood. AZCC Members and collaborators may request the use of banked biospecimens through TACMASS. The patient's surgeon or oncologist is responsible for consenting the patient for submission of surgical specimens to the AZCC BioRepository (IRB #06-0609-04, Setsuko Chambers, PI). The surgeon and the Department of Pathology attending physicians and residents are responsible for identifying appropriate tissue for banking that will not compromise pathological diagnosis. Tumor and/or normal adjacent tissue, identified by gross examination, that will not be needed for pathological diagnosis are preserved by fixing in formalin, snap freezing, and/or fixing in RNALater. Histological diagnosis is rendered on each piece of formalin-fixed and snap frozen tissue by Hematoxylin and Eosin staining (H&E). Everyone involved in submitting specimens to the Tumor Bank must maintain a current CITI Certification.
A file format for graphs that consists of a language core to describe the structural properties of a graph and a flexible extension mechanism to add application-specific data. It is based on XML and is ideally suited as a common denominator for all kinds of services generating, archiving, or processing graphs. Its main features include support of * directed, undirected, and mixed graphs, * hypergraphs, * hierarchical graphs, * graphical representations, * references to external data, * application-specific attribute data, and * light-weight parsers.
Integrated Molecular Interaction Database
Database for molecular interaction information integrated with various other bio-entity information, including pathways, diseases, gene ontology (GO) terms, species and molecular types. The information is obtained from several manually curated databases and automatic extraction from literature. There are protein-protein interaction, gene/protein regulation and protein-small molecule interaction information stored in the database. The interaction information is linked with relevant GO terms, pathway, disease and species names. Interactions are also linked to the PubMed IDs of the corresponding abstracts the interactions were obtained from. Manually curated molecular interaction information was obtained from BioGRID, IntAct, NCBI Gene, and STITCH database. Pathway related information was obtained from KEGG database, Pathway Interaction database and Reactome. Disease information was obtained from PharmGKB and KEGG database. Gene ontology terms and related information was obtained from Gene Ontology database and GOA database.
Chung-Ang University; Seoul; South Korea
Private comprehensive research university in South Korea. Starting as a church-run kindergarten in 1918, CAU transformed into a school for female kindergarten teachers in 1922 and was granted university status in 1953.
Provides animal and human serums, plasmas, purified proteins, and antisera.
Program on Ontologies of Neural Structures
INCF Program on Ontologies of Neural Structures
Program consisting of three Task Forces and one Working Group to promote data exchange and integration in the neurosciences by developing terminology standards and formal ontologies for neural structures. Closely linked to the Program on Digital Brain Atlasing, the Program aims to establish a structured lexicon for the translation and definition of terms describing neural structures at multiple levels of granularity. The three Task Forces and one Working Group involved in the PONS effort: * Structural lexicon * Neuron registry * Representation and deployment * KnowledgeSpace Working Group Structural lexicon, Neuron registry, Representation and deployment, and KnowledgeSpace Working Group.
Software for automated anatomical labeling of activations in SPM (Statistical Parametric Mapping) using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. The software was used for an automated anatomical parcellation of the spatially normalized single-subject high-resolution T1 volume provided by the Montreal Neurological Institute (MNI) (D. L. Collins et al., 1998, Trans. Med. Imag. 17, 463468, PubMed). Using this parcellation method, three procedures to perform the automated anatomical labeling of functional studies were proposed: (1) labeling of an extremum defined by a set of coordinates, (2) percentage of voxels belonging to each of the anatomical volumes of interest (AVOI) intersected by a sphere centered by a set of coordinates, and (3) percentage of voxels belonging to each of the AVOI intersected by an activated cluster. An interface with the Statistical Parametric Mapping package is provided as a freeware to researchers of the neuroimaging community.
A listing of NIH supported data sharing repositories that make data accessible for reuse. Most accept submissions of appropriate data from NIH-funded investigators (and others), but some restrict data submission to only those researchers involved in a specific research network. Also included are resources that aggregate information about biomedical data and information sharing systems. The table can be sorted according by name and by NIH Institute or Center and may be searched using keywords so that you can find repositories more relevant to your data. Links are provided to information about submitting data to and accessing data from the listed repositories. Additional information about the repositories and points-of-contact for further information or inquiries can be found on the websites of the individual repositories.
Service that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. In particular, it formulates protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph.
International Classification for Patient Safety
Ontology network about Patient Safety Incident. This work has been carried out by the Ontological Engineering Group, using sources from the University of Saint Etienne and the Australian Patient Safety Foundation.
A web tool for descriptive analysis of microarray data. The analysis is performed by looking for descriptions of gene sets that are statistically significantly over- or under-expressed between different scenarios within the context of a genome-scale experiments (DNA microarray). Descriptions are defined by using the terms from the Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene-gene interactions found in the ENTREZ database. Gene annotations by GO and KEGG terms can also be found in the ENTREZ database. The tool provides three procedures for testing the enrichment of the gene sets (over- or under-expressed): Fisher's exact test, GSEA and PAGE, and option for combining the results of the tests. Because of the multiple-hypothesis testing nature of the problem, all the p-values are computed using the permutation testing method.
An international coalition formed to enable the sharing of genomic and clinical data to help unlock potential advancements in medicine and science. Bringing together more than 145 leading institutions working in healthcare, research, disease advocacy, life science, and information technology, the Global Alliance is working together to create and promulgate harmonized approaches to enable the responsible, voluntary, and secure sharing of genomic and clinical data.
WikiSurgery - The Free Surgical Encyclopedia
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A free surgical encyclopedia for surgeons and their patients. Contributions in the form of new articles and editing can be made by anyone at anytime anywhere in the world. With over 33,000 articles for surgeons and patients, including news, articles, operation scripts, biographies and images. The website is a "wiki" which allows for the collaborative editing and building of content. Contributions in the form of new articles and editing can be made by those who register on the site, confirm their email address and whose application is accepted by an administrator. Wikisurgery is more than just a depot of surgical knowledge, not just articles about facts but also articles about controversy, debates, with none of the usual editorial limits on space. Indeed we hope it will become a record of surgical thought, experience and progression. Key Topics: Operation Scripts, Basic Surgical Skills Training Program, Basic Laparoscopic Training Program, Operative Images, Patient Information; there is also a Featured Videos section.
Curated data set of a study that investigated the expression profiles of 347 primary invasive breast tumors on Affymetrix microarrays. Three separate breast cancer cohorts were analyzed: 1) Uppsala (n=249), 2) Stockholm (n=58), 3) Singapore (n=40). The Uppsala and Singapore data can be accessed in GSE4922. The Stockholm cohort data can be accessed at GEO Series GSE1456.
A US sperm bank that offers superior donor sperm and sperm banking services, including sperm storage and embryo storage. We provide the highest quality in the industry as one of the few sperm banks fully accredited by the American Association of Tissue Banks (AATB). Cryogenic Laboratories is fully compliant with FDA regulations. Extensive donor Information is downloaded FREE for ALL sperm donors. Searching for a donor is fun, easy and free of charge. Most other sperm banks require you to pay for each donor information product you view. So look and listen for free 24/7. Childhood photos, audio clips, medical and personal profiles are all free. Monthly specials are also there to make the process easier.
Partners HealthCare Center for Personalized Genetic Medicine Biorepository
Two biorepositories, operated by the Partners HealthCare Center for Personalized Genetic Medicine, to serve the research community at Partners HealthCare. The BioSample Services Facility (BSF) provides sample storage and processing services. The Partners Biorepository for Medical Discovery (PBMD) is an enterprise-wide repository of high-quality, consented samples available to foster genetic research and advance understanding of genetic causes of common, complex diseases. Services provided by these cores include assistance with the collection and processing of samples for research use, extraction of DNA and isolation of serum and or plasma with monitored cryogenic storage to provide stability and availability of the materials. After processing, and in conjunction with the BioSample Services Facility, the samples stored within the Biorepository for Medical Discovery may be arrayed for further processing via multiple molecular techniques such as - sequencing, genotyping, and expression profiling.
Integration framework for major open source packages in neuroimaging including SPM, FSL, FreeSurfer, EEGLAB, and Fieldtrip. Efficient neuroimaging workflows and parallel processing using Matlab and XML. Addresses challenges of processing multimodal datasets, like combining anatomy, functional MRI, diffusion, and EEG, to yield integrated views of brain. Allows to design, execute, and share pipelines utilizing multiple open source packages. Supports parallelized execution to address challenges of large cohort studies and provides quality control offering group statistics and reporting facilities to help identify outlier subjects and erroneous processing steps.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A machine learning toolbox written in Matlab and C that provides a general interface to support the integration of new statistical machine learning methods by writing high level wrappers. It allows complex methods to be built from simple building blocks and makes the use of cross-validation and permutation testing as easy as writing one line of Matlab code. The code requires at least Matlab distribution 7.6.0.324 (R2008a).
Phenome-wide association studies Catalog
Catalog of phenome-wide association study (PheWAS) results for 3,144 single-nucleotide polymorphisms (SNPs) present in the NHGRI GWAS Catalog as of 4/17/2012 in 13,835 European-ancestry individuals from five sites of the Electronic Medical Records and Genomics (eMERGE) network. A total of 1,358 EMR-derived phenotypes were analyzed for each SNP. This PheWAS replicated 66% (51/77) of sufficiently powered prior GWAS associations, and 210/751 of all prior GWAS associations. They also identified 63 potentially pleiotropic associations with p < 4.6x10-6 (false discovery rate < 0.1); the strongest of these novel associations replicated in an independent cohort (n=7,406). The catalog contains all associations with p < 0.05 (uncorrected)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A reference terminology and core biomedical ontology for NCI that covers approximately 100,000 key biomedical concepts with terms, codes, definitions, and more than 200,000 inter-concept relationships. It is the reference terminology for NCI, NCI Metathesaurus and NCI informatics infrastructure covering vocabulary for clinical care, translational and basic research, and public information and administrative activities. It includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available. It combines terminology from numerous cancer research related domains, and provides a way to integrate or link these kinds of information together through semantic relationships. NCIt features: * Stable, unique codes for biomedical concepts; * Preferred terms, synonyms, definitions, research codes, external source codes, and other information; * Links to NCI Metathesaurus and other information sources; * Over 200,000 cross-links between concepts, providing formal logic-based definition of many concepts; * Extensive content integrated from NCI and other partners, much available as separate NCIt subsets * Updated frequently by a team of subject matter experts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP).
Cure Alzheimer's Fund is a 501(c)(3) public charity. At Cure Alzheimer's Fund, our mission is to fund research with the highest probability of slowing, stopping or reversing Alzheimer's disease. This topical portal has a lot of information including news and blog. Cure Alzheimer's Fund is governed by a board of directors; administered by a small, full-time staff; and guided scientifically by a Research Consortium. A Scientific Advisory Board audits the research program to make sure it is consistent with the objectives of the foundation. Cure Alzheimer's Fund is a doing business as name for the Alzheimer's Disease Research Foundation, federal tax ID # 52-2396428.
A wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. NCIm features: * Maps 4,000,000 terms from more than 75 sources into 2,000,000 biomedical concepts that represent their meaning. * Displays preferred terms, synonyms, definitions, and other information from each source. * Links to NCI Thesaurus and other related information sources. * Contains 22,000,000 cross-links between content elements. * Updated frequently by a team of biomedical terminology and subject matter experts. NCIm contains most public domain terminologies from the National Library of Medicine's UMLS Metathesaurus, as well as many other biomedical terminologies created by or of interest to NCI and its partners. Some propriety terminologies are included, with permission, and have restrictions on their use. The current version of the NCI Metathesaurus, based on the UMLS build 2013AA, covers up to National Cancer Institute Thesaurus, 13.12d. A viewer for the UMLS changes document can be downloaded.
Small Python library containing a data structure and tools to represent and analyze neuronal morphologies stored in the de facto standard SWC format.
A manually curated resource of signal transduction pathways in humans. All pathways are freely available for download in BioPAX level 3.0, PSI-MI version 2.5 and SBML version 2.1 formats. The slim pathway models representing only core reactions in each pathway are available at NetSlim. All the NetPath pathway models are also submitted to WikiPathways., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.A manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. It currently contains 339 experimentally determined protein protein interactions.
An integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes. The multi-layered database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The website allows the interactive exploration of how each signaling protein is regulated. Features * experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; * combines manual curation with large-scale datasets; * provides confidence scores for each interaction; * operates a customizable download page with multiple file formats (e.g., BioPAX, Cytoscape, SBML).
Chungbuk National University; Cheongju; South Korea
An ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. HealthGrid is a wiki dedicated to grids for health. It is maintained as a dynamic knowledge resource for the healthgrid community. The HealthGrid community (a world-wide initiative) gathers individuals from the public and private domain world-wide who are actively exploring the beneficial impact of healthgrid technology on healthcare provision and research.
A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.
An application focused ontology modelling the experimental factors in ArrayExpress and Gene Expression Atlas. It has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology describes cross-product classes from reference ontologies in area such as disease, cell line, cell type and anatomy. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository and ArrayExpress Atlas. You may also browse the EFO in the NCBO Bioportal. Term submissions are welcome.
Corpus Callosum Thickness Profile Analysis Pipeline
An end-to-end pipeline for corpus callosum processing that provides automated midsagittal alignment, CC segmentation with a quality control tool, and thickness profile generation. Groupwise analysis is facilitated by permutation testing with FWER and FDR multiple comparison correction. Results display is facilitated by a display script that shows p-values on a 3D pipe representation of a CC. This pipeline is implemented in MATLAB and requires the Image Processing Toolbox. There are plans to implement it completely in Python.
Biomolecular Interaction Network Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. Designed to capture protein function, defined at molecular level as set of other molecules with which protein interacts or reacts along with molecular outcome. Archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions and phage display.
A portal into the 3D ultrastructure of the brain providing: Anatomy of astrocytes, axons, dendrites, hippocampus, organelles, synapses; procedures of 3D reconstruction and tissue preparation; as well as an atlas of ultrastructural neurocytology (by Josef Spacek), online aligned images, and reconstructed dendrites. Synapse Web hosts an ultrastructural atlas containing more than 500 electron micrographs (added to regularly) that identify unique ultrastructural and cellular components throughout the brain. Additionally, Synapse Web has raw images, reconstructions, and quantitative data along with tutorial instructions and numerous tools for investigating the functional structure of objects that have been serial thin sectioned for electron microscopy.
RNAdb 2.0 - A database of mammalian noncoding RNAs
A comprehensive mammalian noncoding RNA database containing sequences and annotations for tens of thousands of noncoding RNAs. These include a wide range of microRNAs, small nucleolar RNAs and larger mRNA-like ncRNAs. All raw data from the original RNAdb 2.0 database can be downloaded in XML or FASTA format. This website serves to archive the final snapshot of the RNAdb 2.0 datasets for legacy purposes. It will remain active indefinitely.
A structured controlled vocabulary for the annotation of mass spectrometry experiments.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity. By dynamically loading only data from the surround of the current view point, seamless navigation is not limited to datasets that fit into the available RAM but works with much larger dataset stored in a special format on disk. Currently, KNOSSOS is limited to 8-bit data. In addition to viewing and navigating, KNOSSOS allows efficient manual neurite annotation (''skeletonization''). KNOSSOS is being used mostly for reconstructing cell morphologies from 3D electron microscopic data generated by Serial Block-Face Electron Microscopy (SBEM), with an occasional application to 2-photon and confocal optical microscopy data.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 23, 2012. The National Neurologic AIDS Bank (NNAB) is a site of the HIV/CNS Tissue Network. Based in Los Angeles, which has the largest and most diverse AIDS population in the western United States, the NNAB provides researchers with well-characterized neural tissue from HIV-1-infected and seronegative control donors. The NNAB collaborates with the other designated sites, funding agencies, and outside experts to develop local and national tissue networks. There are plans to create a Network Steering Committee, a panel of outside advisers, and a protocol to recruit and characterize human donors. The NNAB collects pre- and post-mortem clinical data and neural tissues using a standardized autopsy protocol, and the bank stores, codes, catalogs, and distributes this tissue. An electronic database and an Internet-based application process that researchers can use to access the Network's resources are being designed.
Software package that constructs 2D and 3D datasets from 2D image mosaics using the nornir tools. This produces a set of images and transforms on disk which can be accessed via Viking, HTTP, or written as a stack of images.
A set of Python software packages that takes large sets of overlapping images in 2D and 3D and produces registered (aligned) 3D volumes at any size and scale. These tools were originally designed to construct 3D connectomics volumes from terabytes of image data for the Marc lab at the University of Utah Moran Eye Center.
Mount Sinai Allograft Technologies, a department of Mount Sinai Hospital formerly known as the The Rubinoff Bone Bank, has been a leader in advanced tissue innovations since 1972. We are committed to providing the highest quality bone and tissue allograft products as well as continued innovation in the development of allograft implants for transplantation. We are dedicated to meeting all surgical needs and to exceed all client expectations. We work closely with the Trillium Gift of Life Network to promote their mission of increasing donor awareness and to ensure that the wishes of Ontario donor families' are carried out with the utmost care and respect. Our allograft implants are 100% Ontario produced, human allograft tissues. To produce the safest and highest quality Canadian produced allograft implants, Mount Sinai Allograft Technologies leverages the expertise of a variety of medical experts, state-of-the art laboratory testing, proven bio-processing techniques, validated irradiation methods and preferred packaging systems.
Free, Java-based video coding and data visualization tool for collecting behavioral data from video. It supports all video formats that Quicktime or VLC can play, including .asf, .wmv, .avi, .flv, .mov, .mpf, .ogg, .mpg, .nsc, .wav, and .dts. It exports data in a variety of forms depending on analysis needs.
ALLBUS (Allgemeine Bev?lkerungsumfrage der Sozialwissenschaften) (German General Social Survey)
Allgemeine Bev?lkerungsumfrage der Sozialwissenschaften
Data set of up-to-date data on attitudes, behavior, and social structure in Germany. Every two years since 1980 a representative cross section of the population is surveyed using both constant and variable questions. The ALLBUS data become available to interested parties for research and teaching as soon as they are processed and documented.
Dartmouth Science Division Electronics Shop
Core facility that provides the following services: Printed circuit fabrication, Printed circuit board assembly, System design and fabrication. David Collins is NASA certified for electrical assembly.
DTU Center for Biological Sequence Analysis
Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics.
Web server to search for genes involved in given phenotypic difference between mammalian species. The mouse-referenced multiple alignment data files used to perform the forward genomics screen is also available. The webserver implements one strategy of a Forward Genomics approach aiming at matching phenotype to genotype. Forward genomics matches a given pattern of phenotypic differences between species to genomic differences using a genome-wide screen. In the implementation, the divergence of the coding region of genes in mammals is measured. Given an ancestral phenotypic trait that is lost in independent mammalian lineages, it is shown that searching for genes that are more diverged in all trait-loss species can discover genes that are involved in the given phenotype.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Database and atlas of transgenic mouse lines that are generated by random insertion of enhancer trap probes. The trapped lines have highly restricted expression of tet transcription activator (some lines also have Cre DNA recombinase), which enables genetic manipulations in specific cell types.
Database designed to capture experimental or inferential results that support submitter-provided annotation for sequence data that the submitter did not directly determine but derived from GenBank primary data. Records are divided into two categories: * TPA:experimental: Annotation of sequence data is supported by peer-reviewed wet-lab experimental evidence. * TPA:inferential: Annotation of sequence data by inference (where the source molecule or its product(s) have not been the subject of direct experimentation) TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information.
BCM Department of Neuroscience Andreas Tolias Lab
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Code and algorithms produced by the Andreas Tolias lab (Baylor College of Medicine, Department of Neuroscience) where the goal is to understand the rules by which networks of nerves cells in the neocortex orchestrate their activity to process information; to decipher the neural code.
Software library for manipulating neural data files generated in Andreas Tolias Lab.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6,2023. Code used for analysis of TwoPhoton data.
A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.
Organization to lead the integration of ocean, coastal, and Great Lakes observing capabilities, in collaboration with Federal and non-Federal partners, to maximize access to data and generation of information products, inform decision making, and promote economic, environmental, and social benefits to the nation and the world. This national-regional partnership is working to provide new tools and forecasts to improve safety, enhance the economy, and protect the environment. Integrated ocean information is available in near real time, as well as retrospectively. Easier and better access to this information is improving their ability to understand and predict coastal events - such as storms, wave heights, and sea level change. Such knowledge is needed for everything from retail to development planning. The Integrated Ocean Observing System (IOOS) program achieves its objectives by funding organizations through a competitive process.
EuroBioBank: European Network of DNA Cell and Tissue BioBanks for Rare Diseases
The EuroBioBank network is the first operating network of biobanks in Europe providing human DNA, cell and tissue samples as a service to the scientific community conducting research on rare diseases. It is the only network dedicated to rare disease research in Europe. By creating a critical mass of collections and facilitating the exchange of biological material, the EuroBioBank network helps accelerate research on these diseases. * Over 440,000 samples are available across the network and can be requested via the online catalogue. Approximately 13,000 samples are collected each year and 7,000 samples distributed in Europe and beyond. The biological samples are obtained from patients affected by rare diseases, including rare neuromuscular disorders. * The EuroBioBank Network is currently composed of 18 members, of which 16 biobanks from 8 European countries (France, Germany, Hungary, Italy, Malta, Slovenia, Spain and the United-Kingdom) as well as Israel and Canada. Goals * Identify and localize biological material of interest to researchers * Build a critical mass of rare disease sample collections * Distribute high quality material and associated data to users * Promote best-practice guidelines for biobanking activities * Disseminate knowledge and know-how to the scientific community through training courses * Enhance collaboration with the medical and scientific community in the field of rare diseases EuroBioBank acts as a clearing house or virtual bank, with all samples listed in the central online catalogue remaining in the possession of the member biobanks, where they are located and can be requested. The network was established by patients and researchers to facilitate research on rare diseases by guaranteeing quick and easy access to samples via an online catalogue. The catalogue lists the samples available throughout the EuroBioBank network by type of biomaterial. A search engine enables a search by disease or by bank contact. Once a sample has been located in the catalogue, it can be requested by email. Therefore, the biological material is exchanged faster. If a sample does not appear in the EuroBioBank catalogue, help can be provided to further search it at: eurobiobank (at) telethon.it Funding and Collaboration Originally funded by the EC between 2003-2006, the EuroBioBank received further EC support between 2007-2011 within the European Network of Excellence TREAT-NMD (FP6), which covered the cost sustained by Eurordis for the network coordination and website hosting. Each biobank of the network is financed by its own Institution or charitable organization. As of January 2012, the Fondazione Telethon provides the administrative support for coordinating the EuroBioBank network and hosting the website.
Developed as part of the BioText project at the University of California, Berkeley, the BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature. The system indexes all open access articles available at PubMed Central. New articles are indexed daily. The current collection consists of more than 300 journals, 40,000 articles, 100,000 figures, and 60,000 tables. The Full Text & Abstract view searches the full text of articles (in addition to title, author, and abstract information) and returns full-text excerpts that match users' queries. Three selection boxes at the top (ABSTRACTS, FULL-TEXT EXCERPTS and FIGURES allow users to choose what the view displays. The BioText Search Engine allows users to search in tables. When the table view is selected, BioText searches in article titles, table captions, and table contents. The Grid View allows users to search over captions. It returns figures and truncated captions in a grid arrangement.
NICHD Brain and Tissue Bank for Developmental Disorders
NICHD Brain Tissue Bank for Developmental Disorders
The objective of this human tissue repository is to systematically collect, store, and distribute brain and other tissues for research dedicated to the improved understanding, care, and treatment of individuals with developmental disorders. Brain sections are primarily frozen in isopentane / dry ice. Tissues are stored in 10% formalin and frozen at -85 degrees C. Of special interest are individuals with Down syndrome and other chromosomal defects, mitochondrial encephalopathies, phenylketonuria and other aminoacidopathies, maternal PKU, Rett syndrome, leukodystrophies, lysosomal disorders, dyslexia, autism, and other neurodevelopmental disorders. The brain and tissue banks have extensive experience in arranging for the rapid retrieval of tissue upon the death of individuals who die while at home, in hospitals or hospice care. As a special service, the brain and tissue banks are able to assist researchers who are working with patients who intend to donate tissues at the time of their death. Immediately after retrieval of the tissue, the brain and tissue banks will forward needed tissue to the referring investigators and ensure proper storage and cataloging of any additional tissues as part of the brain and tissue banks. The recipient of tissue and the brain and tissue banks are required to sign a Tissue Transfer Agreement before any tissues are transferred.
An R package designed to simulate RNA sequencing experiments with differential transcript expression. Given a set of annotated transcripts, it will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using a choice of downstream analysis tools. Polyester has a built-in wrapper function to simulate a case/control experiment with differential transcript expression and biological replicates. Users are able to set the levels of differential expression at transcripts of their choosing. This means they know which transcripts are differentially expressed in the simulated dataset, so accuracy of statistical methods for differential expression detection can be analyzed. Polyester offers several unique features: * Built-in functionality to simulate differential expression at the transcript level * Ability to explicitly set differential expression signal strength * Simulation of small datasets, since large RNA-seq datasets can require lots of time and computing resources to analyze * Generation of raw RNA-seq reads, as opposed to alignments or transcript-level abundance estimates * Transparency/open-source code
Knowledge Blog - Scientific Publishing for the Web Generation
Blog investigating a light-weight way of publishing scientific, academic and technical knowledge on the web where you can read about current events. It is used in a number of different ways: hosting tutorials on ontologies and bioinformatics; as a conference website; and as a mechanism for documenting Knowledge Blog. They also provide software for extending WordPress, enabling referencing, adding metadata to posts, and supporting mathematics on the web. Together, these pieces of software have had many thousands of downloads, representing 100s of installations; it can be used to provide a formal personal publication framework for the researcher. Finally, they provide Greycite, a service which provides bibliographic metadata for any website, supporting their referencing plugin, and helping authors to link to the many web archiving services, enabling increased digital preservation. Blogs and blog technology has been designed to allow people to discuss, share and disseminate their opinion in a simple and light-weight way. Adding a little formality to this, and we have a journal.
Agency for Healthcare Research and Quality
Agency for Healthcare Research and Quality (AHRQ)
Agency that produces evidence to make health care safer, higher quality, more accessible, equitable, and affordable. Funding opportunities, grants, and a large collection of longitudinal hospital care data in the United States including the Systematic Review Data Repository and data sources on healthcare cost, quality, and accessibility, emergency room visits, hospitalization, and medical insurance are available. It works within the U.S. Department of Health and Human Services and with other partners to make sure that the evidence is understood and used.
SET (Signature Evaluation Tool) - a Java tool to evaluate and visualize the sample discrimination abilities of gene expression signatures
SET - a Java tool to evaluate and visualize the sample discrimination abilities of gene expression signatures
A Java tool to evaluate and visualize the sample discrimination abilities of gene expression signatures. This tool provides a filtration function for signature identification and lies between clinical analyses and class prediction (or feature selection) tools.
National Brain Databank: Brain Tissue Gene Expression Repository
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. A publicly accessible data repository to provide neuroscience investigators with secure access to cohort collections. The Databank collects and disseminates gene expression data from microarray experiments on brain tissue samples, along with diagnostic results from postmortem studies of neurological and psychiatric disorders. All of the data that is derived from studies of the HBTRC collection is being incorporated into the National Brain Databank. This data is available to the general public, although strict precautions are undertaken to maintain the confidentiality of the brain donors and their family members. The system is designed to incorporate MIAME and MAGE-ML based microarray data sharing standards. Data from various types of studies conducted on brain tissue in the HBTRC collection will be available from studies using different technologies, such as gene expression profiling, quantitative RT-PCR, situ hybridization, and immunocytochemistry and will have the potential for providing powerful insights into the subregional and cellular distribution of genes and/or proteins in different brain regions and eventually in specific subregions and cellular subtypes.
Roswell Park Data Bank and BioRepository
Roswell Park Cancer Institute Data Bank and BioRepository
Roswell Park Cancer Institute Data Bank BioRepository
Roswell Park Cancer Institute DataBank and BioRepository
Collects and provides de-identified biospecimens and associated epidemiological and clinical data to meet the scientific needs of investigators. Newly diagnosed patients are asked to contribute data and specimens to the DBBR prior to treatment. Other patients with who have benign disease or advanced disease and have undergone treatment are also enrolled based on anticipated use of data and samples for research. Additionally, non-patients (family members and friends of patients and community members) with no personal history of cancer are asked to participate in the biorepository as controls. Specimens and data are procured with protected health information (PHI) and de-identified prior to distribution to investigators with hypothesis driven IRB reviewed studies. An extensive data collection and management system is in place to track informed consent, questionnaire collection and follow up, epidemiological questionnaire data, clinical data, biospecimens and their derivatives. Research Services * Availability of a bank of prospectively collected blood specimens (serum, plasma, buffy coat, red blood cells and DNA) from cancer patients, high risk individuals and healthy controls for research. * Collection, linking and distribution of epidemiologic and clinical data with biospecimens. * Study-specific biospecimen and data procurement to meet the needs of individual studies, including: ** Participant identification, eligibility screening and informed consent ** Serial biospecimen procurement prior to and throughout treatment ** Study specific collection of biospecimens other than blood (buccal cells, sputum, and urine) ** Procurement and distribution of fresh biospecimens ** Collection of extended clinical and risk factor data
Software tool that uses a machine learning (ML) approach to classify text, based on the Gene Ontology. It relies on a k-Nearest Neighbours algorithm, a simple algorithm which assigns to a new text the categories that are the most prevalent among the k most similar instances contained in the knowledge base. The ML classifier operates in two steps and combines two components. First, a related article search engine retrieves instances (i.e. abstracts) in the knowledge base that are the most similar to the input text (its nearest neighbours); second, a score computer infers the functional profile from the k most similar instances.
J-Express: Gene expression analysis software
Gene expression analysis software using Java.
Alaska Satellite Facility - Synthetic Aperture Radar Distributed Active Archive Center
Satellite facility that downlinks, processes, archives, and distributes remote-sensing data to scientific users around the world. Three major components: * Satellite Tracking Ground Station: Part of NASA?s Near Earth Network system of ground stations around the world. * Synthetic Aperture Radar Distributed Active Archive Center (SAR DAAC): ASF maintains the NASA archive of SAR data from a variety of satellites and aircraft, and provides these data and associated specialty support services to U.S. Government-approved researchers in support of NASA?s Earth Science Data and Information System project. * ASF Enterprise Center (ASFE): In support of UAF?s mission to be a student-centered research university, the ASF-E focuses on applications of remote-sensing data, specifically for UAF research. The ASF-E includes the GeoData Center (GDC), which provides data management and archive services for UAF principal investigators and maintains a variety of geophysical data collections in support of scientific research.
Aktuelle Wetterwerte deutscher Stationen
Data sets of current German weather stations updated hourly or every twelve hours. Data sets, in German, include: * Daily mean values ??of temperature, updated hourly. Daily archive since 29.1.2008 * Daily maximum and minimum temperature, updated every 12 hours. Daily archive since 21.7.2008 * Monthly mean values ??of temperature and deviation, updated daily . * Rainfall in the last 12 hours and monthly total, updated every 12 hours . * Monthly totals of precipitation and relative to langj. means in%, updated every 12 hours. Monthly Archive since Feb. 2008 * Air pressure and pressure tendency, updated hourly.
Resting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with autism spectrum disorder (ASD) and 573 typical controls. This initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites. This effort is expected to facilitate discovery science and comparisons across samples. All datasets are anonymous, with no protected health information included.
A virtual database indexing video and other multimedia content from: NIH VideoCasting and Podcasting, JoVE: Journal of Visualized Experiments, The Guardian: Science Videos, Biointeractive, goCognitive, UCSF Laboratory for Visual Neuroscience, and Clarity resources.
rOGED: Rat Ovarian Gene Expression Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. rOGED is a searchable database containing ovarian gene sequences, data, and images of ovarian genes expressed in rats. The site also provides customized gene expression profiles in the rat oviduct and uterus or mouse ovary. The database was constructed from total RNA isolated from intact ovaries, granulosa cells, or residual ovarian tissues collected from immature PMSG/hCG-treated rats at 0 (no PMSG), 12, and 48 h post-PMSG, as well as 6 and 12 h post-hCG. The total RNA was used for DNA microarray analysis using Affymetrix Rat Expression Arrays 230A and B. The microarray data was compiled and utilized for display of individual gene expression profiles through specially developed software. The final rOGED provides immediate analysis of temporal gene expression profiles for over 28,000 genes in intact ovaries, granulosa cells, and residual ovarian tissue during follicular growth and the preovulatory period. The accuracy of the rOGED was validated against the gene profiles for over 100 known genes. The utility of the rOGED was demonstrated by identifying seven genes which have not been described in the rat periovulatory ovary. The rOGED can be used as an instant reference for ovarian gene expression profiles, as well as reliable resource for identifying important yet, to date, unknown ovarian genes. Category: Microarray Data and other Gene Expression Databases
NIH Toolbox Dimensional Change Card Sort Test
Assessment test that measures the cognitive flexibility of patients. Two target pictures are presented that vary along two dimensions (e.g., shape and color). Participants are asked to match a series of bivalent test pictures (e.g., yellow balls and blue trucks) to the target pictures, first according to one dimension (e.g., color) and then, after a number of trials, according to the other dimension (e.g., shape). Switch trials are also employed, in which the participant must change the dimension being matched. For example, after 4 straight trials matching on shape, the participant may be asked to match on color on the next trial and then go back to shape, thus requiring the cognitive flexibility to quickly choose the correct stimulus. Scoring is based on a combination of accuracy and reaction time, and the test takes approximately 4 minutes to administer. This test is recommended for ages 3-85.
NIH Toolbox Flanker Inhibitory Control and Attention Test
Flanker Inhibitory Control and Attention Test
Assessment test that measures both a participant''s attention and inhibitory control. The test requires the participant to focus on a given stimulus while inhibiting attention to stimuli (fish for ages 3-7 or arrows for ages 8-85) flanking it. Sometimes the middle stimulus is pointing in the same direction as the flankers (congruent) and sometimes in the opposite direction (incongruent). Scoring is based on a combination of accuracy and reaction time, and the test takes approximately 3 minutes to administer. This test is recommended for ages 3-85.
NIH Toolbox Picture Sequence Memory Test
A measure for the assessment of episodic memory that involves recalling increasingly lengthy series of illustrated objects and activities that are presented in a particular order on the computer screen. The participants are asked to recall the sequence of pictures that is demonstrated over two learning trials; sequence length varies from 6-18 pictures, depending on age. Participants are given credit for each adjacent pair of pictures (i.e., if pictures in locations 7 and 8 and placed in that order and adjacent to each other anywhere such as slots 1 and 2 one point is awarded) they correctly place, up to the maximum value for the sequence, which is one less than the sequence length (if there are 18 pictures in the sequence, the maximum score is 17, because that is the number of adjacent pairs of pictures that exist). The test takes approximately 7 minutes to administer. This test is recommended for ages 3-85.
NIH Toolbox Auditory Verbal Learning Test (Rey)
NIH Toolbox Auditory Verbal Learning Test-Rey
Supplemental instrument that is a measure of immediate recall in which the participant is presented with a list of 15 unrelated words via audio recording and is asked to recall as many as he/she can. This process is repeated twice more, and the score is equal to the total number of words recalled across all three trials. This instrument is recommended for ages 8-85 as a supplement to the Picture Sequence Memory Test or as a potential alternative in cases where a participant's visual limitations would preclude administering the Picture Sequence Memory Test. The test takes approximately 3 minutes to administer. (The NIH Toolbox version of this test differs from some other available versions in that there are three rather than five learning trials and there is neither a delayed recall trial nor an interference trial.)
Software tools for the analysis of high-throughput small RNA data.
NIH Toolbox 9-Hole Pegboard Dexterity Test
Assessment test that measures manual dexterity recording the time required for the participant to accurately place and remove 9 plastic pegs into a plastic pegboard. The protocol includes 1 practice and 1 timed trial with each hand. Raw scores are recorded as time in seconds that it takes the participant to complete the task with each hand (a separate score for each). The test takes approximately 4 minutes to administer and is recommended for ages 3-85.
NIH Toolbox Oral Reading Recognition Test
Assessment test that measures the ability of patients to identify words and letters. The participant is asked to read and pronounce letters and words as accurately as possible. The test administrator scores them as right or wrong. For the youngest children, the initial items require them to identify letters (as opposed to symbols) and to identify a specific letter in an array of 4 symbols. The test is given in a computerized adaptive format and requires approximately 3 minutes. This test is recommended for ages 7-85, but is available for use as young as age 3, if requested. Separate but parallel reading tests have been developed in English and in Spanish.
NIH Toolbox Pattern Comparison Processing Speed Test
Pattern Comparison Processing Speed Test
Assessment test that measures speed of processing by asking participants to discern whether two side-by-side pictures are the same or not. Participants' raw score is the number of items correct in a 90-second period. The items are designed to be simple to most purely measure processing speed. The test overall takes approximately 3 minutes to administer. This test is recommended for ages 7-85, but is available for use as young as age 3, if requested.
A supplemental instrument that is a measure of speed of processing. The participant is presented with a set of nine symbols on the computer screen, each associated with a number 1-9, and is then presented with a series of symbols without numbers and is asked to orally say each number that should go with that symbol, without skipping any. The score is equal to the number of symbols correctly identified orally within two minutes. Recommended for ages 8-85 as a supplement to the Pattern Comparison Processing Speed Test or as a potential alternative in cases where a participant's motoric limitations would preclude administering the Pattern Comparison Processing Speed Test. Takes approximately 3 minutes to administer.
Data set that looked at religion, self-rated health, depression, and psychological well-being in a sample of older Blacks and older Whites (aged 65 and over) within the United States. Questions were asked regarding religious status, activities, and beliefs among those who currently practice the Christian faith, those who used to be Christian but are not now, and those who have never been associated with any religion during their lifetimes. Demographic variables include age, race, sex, education, and income. Wave II was collected in 2004 and reinterviewed 1,024 respondents. There were 75 respondents who refused to participate, 112 who could not be located, 70 that were too ill for participation, 11 who had moved to nursing homes and 208 were deceased. * Dates of Study: 2001- 2004 * Study Features: Longitudinal, Minority Oversample * Sample Size: 1,500
NIH Toolbox List Sorting Working Memory Test
Assessment test to measure the memory of patients using their ability to sort objects. It requires immediate recall and sequencing of different visually and orally presented stimuli. Pictures of different foods and animals are displayed with accompanying audio recording and written text (e.g., elephant), and the participant is asked to say the items back in size order from smallest to largest, first within a single dimension (either animals or foods, called 1-List) and then on 2 dimensions (foods, then animals, called 2-List). The score is equal to the number of items recalled and sequenced correctly, and the test takes approximately 7 minutes to administer. This test is recommended for ages 7-85, but is available for use as young as age 3, if requested.
Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A measure to assess static standing balance that involves the participant assuming and maintaining up to 5 poses for 50 seconds each. The sequence of poses is: eyes open on a solid surface, eyes closed on solid surface, eyes open on foam surface, eyes closed on foam surface, eyes open in tandem stance. Detailed stopping rules are in place to ensure participant safety with these progressively demanding poses. Postural sway is recorded for each pose using an accelerometer that the participant wears at waist level. This test takes approximately 7 minutes to administer and is recommended for ages 3-85.
Common Upper Mammalian Brain Ontology (CUMBO)
Ontology of formal definitions (i.e., machine processable) for the types of structures commonly described in neuroanatomy.
NIH Toolbox 2-Minute Walk Endurance Test
Assessment test that measures sub-maximal cardiovascular endurance by recording the distance that the participant is able to walk on a 50-foot (out and back) course in 2 minutes. The participant's raw score is the distance in feet and inches walked in 2 minutes. The test is adapted from the American Thoracic Society's 6-Minute Walk Test Protocol. The test overall takes approximately 4 minutes to administer (with instructions and practice). This test is recommended for ages 3-85.
NIH Toolbox 4-Meter Walk Gait Speed Test
Assessment test to measure gait speed where participants are asked to walk a short distance (4 meters) at their usual pace. Participants complete one practice and then two timed trials. Raw scores are recorded as the time in seconds required to walk 4 meters on each of the two trials, with the better trial used for scoring. The 4-Meter Walk Gait Speed Test is adapted from the 4-meter walk test in the Short Physical Performance Battery. The test takes approximately 3 minutes to administer (including instructions and practice). This test is recommended for ages 7-85.
Assessment test that measures grip strength. Participants are seated in a chair with their feet touching the ground. With the elbow bent to 90 degrees and the arm against the trunk, wrist at neutral, participants squeeze the Jamar Plus Digital dynamometer as hard as they can for a count of three. The dynamometer provides a digital reading of force in pounds. A practice trial at less than full force and 1 test trial are completed with each hand. This protocol is adapted from the grip strength testing protocol of the American Society of Hand Therapy. The test takes approximately 3 minutes to administer and is recommended for ages 3-85.
Assessment test to assess a person's ability to identify various odors. Participants use scratch 'n' sniff cards and after scratching them one at a time, are asked to identify which of four pictures on the computer screen matches the odor they have just smelled. Participants ages 10-85 are administered nine odor cards, while those ages 3-9 are administered five odor cards. Child participants (ages 3 -9 years) are first asked to identify the eight pictures that are used as answer choices, to ensure they can complete the task. Having identified the pictures, they are asked if they have tasted or smelled the objects or foods depicted. This test takes approximately 4 to 5 minutes to administer and is recommended for ages 3-85.
A self-report scale that measures the degree to which pain interferes with other activities in life in adults. Pain interference items were developed as part of the NIH PROMIS. This measure is administered as a computer-adaptive test and takes approximately three minutes. It is recommended for ages 8-85.
A measure that consists of a single item measuring immediate (i.e., acute) pain in adults. As part of Toolbox, a single pain intensity item measures immediate (a.k.a. acute) pain for use in adults. It takes less than one minute to administer and is recommended for ages 18-85.
NIH Toolbox Regional Taste Intensity Test
Assessment test that measures the perceived intensity of quinine (a bitter tastant) and salt administered in liquid solutions. The tastants are applied to the tip of the tongue as well as the whole mouth and rated on a generalized labeled magnitude scale (ranging from no sensation at all to strongest sensation of any kind). The test is recommended for administration to participants ages 12-85 and takes approximately six minutes to administer.
Resources for Enhancing Alzheimers Caregiver Health
Resources for Enhancing Alzheimer's Caregiver Health
Resources for Enhancing Alzheimer's Caregiver Health (REACH)
Data set from six research sites that examined the feasibility and outcomes of the most promising home and community-based intervention approaches for enhancing family caregiving for Alzheimers Disease (AD) and related disorders (ADRD). A unique feature is the examination of AD burdens and interventions in three ethnic groups (Caucasians, Hispanics, and African Americans). Caregiver/care recipient dyads are entered into the study using standardized eligibility criteria. The dyads are randomized at each intervention site using site-specific procedures. Standardized assessment batteries are administered at baseline, 6, 12, and 18 months. The five general types of REACH interventions are: Individual Information and Support strategies that increase caregivers' understanding of dementia and their particular caregiving situation; Group Support and Family Systems efforts that provide caregivers with multiple forms of social support; Psychoeducational and Skill-Based Training approaches that teach caregivers coping and behavioral management strategies; Home-Based Environmental interventions that modify the home environment's effect on the care recipient and support the caregiver; and Enhanced Technology Systems such as home-centered computer/telephone networks that are designed to reduce caregiver distress and isolation. REACH II was funded in 2001 to test a single multi-component intervention among family caregivers of persons with ADRD, building upon the findings of REACH. Recruitment for REACH II was completed in January 2004 with 642 participants entering the study across 5 participating sites.
A 50 question psychological assessment that measures the symptoms of autism in adults, children and adolescents.
Assessment test that is a measure of gaze stability, which helps identify individuals who may have a deficit of the vestibular system (which regulates internal balance). The NIH Toolbox Visual Acuity Test must be administered followed by the DVA Test. Participants are seated 12.5 feet from a computer monitor at eye level. For the DVA Test, participants wear lightweight headgear that contains a rate sensor, and are asked to move the head back and forth, as if saying no. Once the head is measured to be moving at greater than 180 degrees per second, an optotype flashes on the monitor, and the participant is asked to identify it. Smaller optotypes are displayed as the participant correctly identifies letters, and larger ones are displayed if the participant cannot correctly identify the letter shown, until the computer has calculated the smallest size that the participant can see with the head moving. This is calculated separately for head rotation leftward and rightward from center (though the participant continues shaking the head both ways), and this performance is compared to the participant's visual acuity when the head was stationary (the NIH Toolbox Visual Acuity Test score, sometimes referred to as static visual acuity in the context of the DVA test). The difference between static and dynamic visual acuity represents the vestibular contribution to gaze stability. The DVA Test takes approximately six minutes to administer and is recommended for ages 3-85.
Assessment test that directly measures participants' visual acuity, or distance vision. The participant is seated 12.5 feet away from a computer monitor at eye level, and letters (called optotypes) are displayed one at a time on the screen for the participant to identify, using both eyes at the same time. As the participant successfully identifies optotypes of a given size, smaller ones appear on the screen, until the computer program ascertains the smallest-size optotype the participant can successfully see. Conversely, the program displays larger optotypes if the participant cannot see the letter size that is first displayed, until a size that he/she can accurately see is found. For participants ages 3-7, only the letters H, O, T, and V are used, and children may point to a laminated card showing the letters if they cannot verbalize or cannot recall the letter names. For participants ages 8 and above, the entire set of optotypes is used, following a common protocol used in professional vision testing. This test takes approximately three minutes to administer and is recommended for ages 3-85.
Curated series of expression data for 159 tumors from which RNA could be collected in sufficient amounts and quality for analysis from breast cancer patients. Tissue material was collected from all breast cancer patients receiving surgery at Karolinska Hospital from 1994-1996.
Curated data set from a study that investigated 77 primary high-grade astrocytomas and 23 matched recurrences so that changes in gene expression related to both survival and disease progression can be identified. Samples in the study include WHO grade III and IV astrocytomas with a wide range of survival times.
Curated data set where gene expression profiling was performed on 60 prospectively collected samples of children with first relapse of acute lymphoblastic leukemia enrolled on the relapse trial ALL-REZ BFM 2002 of the Berlin-Frankfurt-Muenster study group.
Curated data set of gene expression data from 230 stage I-III breast cancers that were generated from fine needle aspiration specimens of newly diagnosed breast cancers before any therapy. The biopsy specimens were collected sequentially during a prospective pharmacogenomic marker discovery study between 2000 and 2008. These specimens represent 70-90% pure neoplastic cells with minimal stromal contamination. In the study, patients received 6 months of preoperative (neoadjuvant) chemotherapy including paclitaxel, 5-fluorouracil, cyclophosphamide and doxorubicin followed by surgical resection of the cancer.
Curated data set from gene expression profiles of 29 unique samples from uveal melanoma patients that were measured on Affymetrix microarray. In addition, expression of syntenin-1 was measured by RT-PCR and this data is also available in the study.
Curated data set from analyzed gene expression profiles in 19 pediatric patients with SoJIA during the systemic phase of the disease (fever and/or arthritis), 25 SoJIA patients with no systemic symptoms (arthritis only or no symptoms), 39 healthy controls, 94 pediatric patients with acute viral and bacterial infections (available under GSE6269), 38 pediatric patients with Systemic Lupus Erythematosus (SLE), and 6 patients with a second IL-1 mediated disease known as PAPA syndrome.
Curated data set from a study that developed biomarkers that may predict development of Clinically Isolated Syndrome (CIS) into a full multiple sclerosis. Expression data was taken from 37 CIS patients and 28 healthy controls at baseline. 34 CIS patients and 10 healthy controls were resampled at a second time point, approximately one year later. Patients were followed clinically for up to two years to determine the TTC (time to conversion to MS).
Curated data set from a gene expression profiling study investigating monozygotic twin pairs with various systemic autoimmune diseases. RNA microarray analyses (Agilent Human 1A(V2) 20K oligo arrays) quantified differential gene expression in blood from 20 monozygotic (MZ) twin pairs, to minimize polymorphic gene effects, discordant for SAID (six with systemic lupus erythematosus (SLE), six rheumatoid arthritis (RA), eight idiopathic inflammatory myopathies (IIM)) and 40 unrelated matched controls.
Curated data set from a study that contains a gene expression profile of peripheral blood cells (PBMCs) isolated from patients (248 in total) with rheumatoid arthritis (RA)/ systemic lupus erythematosus (SLE)/ polyarticular type juvenile idiopathic arthritis (polyJIA)/ Systemic onset juvenile idiopathic arthritis (sJIA) vs healthy children (HC) and healthy individual (HI).
Curated data set from a study that assessed the effects of epidermal growth factor and interleukin 1-beta stimulation, and the modulatory effects of glucocorticoids treatment and protein kinase A inhibition, on the airway smooth muscle transcriptome by microarray analysis. The samples from 4 donors were subjected to different stimulations by Il-1b and EGF (or both) with or without pre-treatment with fluticasone, and data was collected at different timepoints.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only.
A registry of stem cell lines that provides a searchable database that includes published and validated unpublished information on human embryonic (hESC) and disease-specific induced pluripotent (iPS) stem cell lines. The Registry will include information on cell lines from non-profit institutions, academic centers, stem cell banks and industry based in the United States and abroad. The International Stem Cell Registry is developed in partnership with and funded by the Massachusetts Life Sciences Center. The work of the registry is made possible by the MLSC and important collaborators, including the Harvard Stem Cell Institute.
Seattle Longitudinal Study (SLS) of Adult Cognitive Development
Seattle Longitudinal Study of Adult Cognitive Development
Data set from an ongoing, longitudinal-sequential study of adult-cognitive development, which began in 1956, that focuses on individual differences in age-related changes and differences across cohorts. The general purpose of the study is to examine the changes in intelligence and various abilities throughout adulthood. The data provide a normative base to determine the ages of detectable decrements in ability and the magnitudes of the decrements. The study also seeks to examine patterns of generational differences and age-related differences and to determine the effects of educational intervention on intellectual decline. This study is a mixed cross-sectional, longitudinal, and time-lag design. Included are family studies of cognitive similarity, prospective studies of early signs of dementia via psychological and genetic markers, as well as the investigation of personality and demographic variables that affect cognitive change in adults from young adulthood to advanced old age. Questionnaire topics include health behavior, behavioral rigidity, family environment, Life Complexity Inventory, CES-D Depression, and cognitive and neuropsychology batteries. Group Health Cooperative of Puget Sound Medical Records and Pharmacy Records. * Dates of Study: 1956-Present * Study Features: Longitudinal * Sample Size: 6,000+
Curated lists of genes associated to speech / language phenotypes and structural or functional abnormalities observed in patient populations. Entrez ID gene information, as well as gene expression profiles from the Allen Brain Atlas are available. You can also download expression data for a given gene in JSON or XML format.
Global Assessment of Functioning (GAF) Scale
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on October 6th, 2022. Assessment scale that considers psychological, social, and occupational functioning (how well they handle various problems in life) on a hypothetical continuum of mental health-illness. This does not include impairment in functioning due to physical (or environmental) limitations. The score received is usually given as a range (0-100) to patients. Scoring: * 91-100 No Symptoms * 81-90 Absent/Minimal Symptoms * 71-80 Symptoms are Present * 61-70 Mild Symptoms * 51-60 Moderate Symptoms * 41-50 Serious Symptoms * 31-40 Some Impairment * 21-30 Influenced behavior by Delusions or Hallucinations * 11-20 Some Danger of Hurting Self or Others * 1-10 Persistent Danger of Hurting Self or Others * 0 Inadequate Information on Patient
Assessment scale to measure the psychiatric symptoms of patients who might have psychiatric symptoms including depression, anxiety, hallucinations, and strange or unusual behaviors. The symptoms of the patient are rated between 1 and 7 and then the 18-24 items/symptoms are scored and combined to create the final score of the patient. This scale is similar to the PANSS, SANS, and SAPS.
Neuroscience data and knowledge from multiple scales and multiple data sources that has been extracted, linked, and organized to support comprehensive understanding of the brain. The core is the CAS Brain Knowledge base, a very large scale brain knowledge base based on automatic knowledge extraction and integration from various data and knowledge sources. The LND platform provides services for neuron data and knowledge extraction, representation, integration, visualization, semantic search and reasoning over the linked neuron data. Currently, LND extracts and integrates semantic data and knowledge from the following resources: PubMed, INCF-CUMBO, Allen Reference Atlas, NIF, NeuroLex, MeSH, DBPedia/Wikipedia, etc.
Data set of a crowd-sourced community effort to extract structured information from Wikipedia and make this information available on the Web. DBpedia allows you to ask sophisticated queries against Wikipedia, and to link the different data sets on the Web to Wikipedia data. It is hoped that this work will make it easier for the huge amount of information in Wikipedia to be used in some new interesting ways. Furthermore, it might inspire new mechanisms for navigating, linking, and improving the encyclopedia itself. The project extracts knowledge from 111 different language editions of Wikipedia. The DBpedia project maps Wikipedia infoboxes from 27 different language editions to a single shared ontology consisting of 320 classes and 1,650 properties. The mappings are created via a world-wide crowd-sourcing effort and enable knowledge from the different Wikipedia editions to be combined. The project publishes regular releases of all DBpedia knowledge bases for download and provides SPARQL query access to 14 out of the 111 language editions via a global network of local DBpedia chapters. In addition to the regular releases, the project maintains a live knowledge base which is updated whenever a page in Wikipedia changes. DBpedia sets 27 million RDF links pointing into over 30 external data sources and thus enables data from these sources to be used together with DBpedia data. Several hundred data sets on the Web publish RDF links pointing to DBpedia themselves and thus make DBpedia one of the central interlinking hubs in the Linked Open Data (LOD) cloud.
An technology innovator in database and application server software that has been a long time developer of database and semantic repository technologies on both single servers and clusters. This, combined with OpenLink's experience with SQL, gives an all round view of performance across many environments and workload profiles, from transactions to decision support or search. OpenLink also has extensive experience in developing scale-out parallel database technology. The cross-platform product portfolio addresses challenges such as: Universal Data Access, Data Virtualization & Management, Personal & Enterprise Data Spaces, and Implementation & Support.
Adult ADHD Self-Report Scale (ASRS-v1.1) Symptom Checklist
Adult ADHD Self-Report Scale Symptom Checklist
A self reporting scale to assess if adult patients are suffering from symptoms of attention deficit-hyperactivity disorder (ADHD). The Symptom Checklist is an instrument consisting of the eighteen DSM-IV-TR criteria. Six of the eighteen questions were found to be the most predictive of symptoms consistent with ADHD. These six questions are the basis for the ASRS v1.1 Screener and are also Part A of the Symptom Checklist. Part B of the Symptom Checklist contains the remaining twelve questions.
Assessment scale to assess the severity of symptoms of anxiety in adults, adolescents and children. The scale consists of 14 items, each defined by a series of symptoms, and measures both psychic anxiety (mental agitation and psychological distress) and somatic anxiety (physical complaints related to anxiety). Although the HAM-A remains widely used as an outcome measure in clinical trials, it has been criticized for its sometimes poor ability to discriminate between anxiolytic and antidepressant effects, and somatic anxiety versus somatic side effects. The HAM-A does not provide any standardized probe questions. Despite this, the reported levels of inter-rater reliability for the scale appear to be acceptable. The scale has been translated into: Cantonese for China, French and Spanish. An IVR version of the scale is available from Healthcare Technology Systems.
Hospital Anxiety and Depression Scale (HADS)
Assessment scale commonly used in hospitals to determine the anxiety and depression levels that a patient is experiencing. It contains 14 items, 7 of which are questions about anxiety and the other 7 are about depression.
Generalized Anxiety Disorder 7 Item (GAD-7)
Generalized Anxiety Disorder 7 Item Scale
A seven item assessment to measure the severity of a patient's anxiety. The test is self administered and cannot be used to replace a proper clinical assessment and additional evaluations.
Assessment scale to measure the severity of illness in patients with panic disorder (with or without agoraphobia). It is available in both clinician-administered and self-rating formats. It contains 5 sub-scales: panic attacks, agoraphobic avoidance, anticipatory anxiety, disability, and functional avoidance (health concerns). It rates the severity of symptoms over the past week.
Ontology of master drug data base, 2009_08_05
Private research university located in the Boston suburb of Waltham, Massachusetts. Founded in 1948 as a non-sectarian, coeducational institution sponsored by the Jewish community, Brandeis was established on the site of the former Middlesex University.
Collaborative framework that includes the NIH Office of the Director and the 14 NIH Institutes and Centers that support research on the nervous system. By pooling resources and expertise, the Blueprint identifies cross-cutting areas of research, and confronts challenges too large for any single Institute or Center. The Blueprint makes collaboration a day-to-day part of how the NIH does business in neuroscience, complementing the basic missions of Blueprint partners. During each fiscal year, the partners contribute a small percentage of their funds to a common pool. Since the Blueprint's inception in 2004, this pool has comprised less than 1 percent of the total neuroscience research budget of the partners. In 2009, the Blueprint Grand Challenges were launched to catalyze research with the potential to transform our basic understanding of the brain and our approaches to treating brain disorders. * The Human Connectome Project is an effort to map the connections within the healthy brain. It is expected to help answer questions about how genes influence brain connectivity, and how this in turn relates to mood, personality and behavior. The investigators will collect brain imaging data, plus genetic and behavioral data from 1,200 adults. They are working to optimize brain imaging techniques to see the brain's wiring in unprecedented detail. * The Grand Challenge on Pain supports research to understand the changes in the nervous system that cause acute, temporary pain to become chronic. The initiative is supporting multi-investigator projects to partner researchers in the pain field with researchers in the neuroplasticity field. * The Blueprint Neurotherapeutics Network is helping small labs develop new drugs for nervous system disorders. The Network provides research funding, plus access to millions of dollars worth of services and expertise to assist in every step of the drug development process, from laboratory studies to preparation for clinical trials. Project teams across the U.S. have received funding to pursue drugs for conditions from vision loss to neurodegenerative disease to depression. Since its inception in 2004, the Blueprint has supported the development of new resources, tools and opportunities for neuroscientists. For example, the Blueprint supports several training programs to help students pursue interdisciplinary areas of neuroscience, and to bring students from underrepresented groups into the neurosciences. The Blueprint also funds efforts to develop new approaches to teaching neuroscience through K-12 instruction, museum exhibits and web-based platforms. From fiscal years 2007 to 2009, the Blueprint focused on three major themes of neuroscience - neurodegeneration, neurodevelopment, and neuroplasticity. These efforts enabled unique funding opportunities and training programs, and helped establish new resources including the Blueprint Non-Human Primate Brain Atlas.
Panic Disorder Severity Scale - Self-Report
Panic Disorder Severity Scale (PDSS) Self-report
Panic Disorder Severity Scale - Self rated
A self-administered assessment used to detect possible symptoms of panic disorder and suggest the need for a formal diagnostic assessment. It consists of seven items (which are rated from 0-4). The items assess panic frequency, distress during panic, panic-focused anticipatory anxiety, phobic avoidance of situations, phobic avoidance of physical sensations, impairment in work functioning, and impairment in social functioning. The overall assessment is made by a total score, which is calculated by summing the scores for all seven items. The total scores range from 0 to 28. The PDSS-SR is used for screening and the scores 9 and above suggest the need for a formal diagnostic assessment. (Adapted from Wikipedia)
A 17 item self-reported questionnaire to assess the symptoms of posttraumatic stress disorder (PTSD) during the past 2 weeks. The 17 questions all describe symptoms of PTSD which patients rate (by severity) between 0-3, 0 meaning not at all or only once and 3 meaning almost all the time or at least five times a week. The end scores range from 0-51. Scoring: * 0-13 Likelihood of Little to No PTSD * 13-51 Likelihood of PTSD (Higher Score = More Severe)
A 17-item self-administered assessment questionnaire developed by the Psychiatry and Behavioral Sciences Department at Duke University effective in screening for and measuring the severity of social anxiety disorder. Each question is answered with one of 5 responses ranging from Not at All to Extremely. Each response is assigned a score and then totaled at the end. Scoring: * 0-20 Little or No Anxiety * 21-30 Mild Anxiety * 31-40 Moderate Anxiety * 41-50 Severe Anxiety * 51-68 Very Severe Anxiety
Polycystic Kidney Disease Outcomes Consortium
Polycystic Kidney Disease (PKD) Outcomes Consortium
Consortium to develop evidence supporting the use of imaging Total Kidney Volume (TKV) as a prognostic biomarker that predicts the progression of Autosomal Dominant Polycystic Kidney Disease (ADPKD) to select patients likely to respond to therapy into clinical trials. It aims to replace the currently used measurement of glomerular filtration rate (GFR). Scientists will use the data collected to develop a disease progression model that will evaluate the relationship between TKV and the known complications of ADPKD, including rate of loss of kidney function, hypertension, gross hematuria, kidney stones, urinary tract infections, development of end-stage renal disease, and mortality. These analyses will be used to support the regulatory qualification of TKV as an accepted measure for assessing the progression of ADPKD in clinical trials in which new therapies are tested. PKDOC has the following goals: # Develop standard clinical data elements and definitions that are specific to ADPKD # Create a database of aggregated data from existing multiple, longitudinal, and well-characterized research registries maintained over decades by the leading institutions in ADPKD clinical investigation # Advance and harmonize the missions of regulatory agencies by creating tools that help with the evaluation of new pharmaceutical compounds # Develop a quantitative disease progression model to examine the linkage between TKV and disease outcomes
THIS RESOURCE IS NO LONGER IN SERVICE, documented October 12, 2016. A brief self-report trauma screening tool, simple to administer and score, designed for trauma victims in general. This 10-items scale, all derived from the DSM-IV2 criteria, describes either a reexperiencing symptom of post-traumatic stress disorder (items 1 through 5) or an arousal symptom of PTSD (items 6 through 10). The result of the original study indicate that an excellent prediction of a PTSD diagnosis was provided by respondents endorsing at least 6x re-experiencing or arousal symptoms, for each sample of patients (rail crash survivors and crime victims). Scoring: 0-5 yes responses = Likelihood of No PTSD, 6-10 yes responses = likelihood of PTSD
Yale-Brown Obsessive Compulsive Scale (Y-BOCS)
Self-rating scale to assess the severity and type of symptoms in patients with obsessive-compulsive disorder (OCD). Each question is to be answered based on the average occurrence of each item over the past week. The first 5 questions relate to obsessive thoughts, the last 5 questions relate to compulsive behaviors. Scoring: * 07 Sub-Clinical * 815 Mild * 1623 Moderate * 2431 Severe * 3240 Extreme
A 10 question assessment to assess elderly patients for the possibility of dementia. The test has utility across a range of acute and outpatient settings. It takes five minutes to administer and must include all 10 questions. A score of less than 7 or 8 suggests cognitive impairment. Scoring: * 7-10 (correct) No Cognitive Impairment * 6-0 (correct) Cognitive Impairment, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Global CDR Assignment Based On Box Scores
Global Clinical Dementia Rating (CDR) Based on CDR Box Scores
A numeric scale used to quantify the severity of symptoms of dementia (i.e. its stage). Using a structured-interview protocol, a qualified health professional assesses a patient's cognitive and functional performance in six areas: memory, orientation, judgment and problem solving, community affairs, home and hobbies, and personal care. Scores in each of these are combined to obtain a composite score ranging from 0 through 3. (Adapted from Wikipedia)
General Practitioner Assessment of Cognition
Assessment test to screen a patient for cognitive impairment that takes less than four minutes for the cognitive test and less than two minutes for the informant interview. The cognitive test includes nine items: (1) time orientation, clock drawing: (2) numbering and spacing as well as (3) placing hands correctly, (4) awareness of a current news event and recall of a name and an address ( (5) first name, (6) last name, (7) number, (8) street, and (9) suburb). Each correct answer is valid one point leading to a maximum score of 9 (fewer points indicate more impairment). (Wikipedia) The informant interview asks six historical questions from an informant/next of kin who knows the patient well. He or she is asked to compare the patient's current function with his/her performance a few years ago. Areas that are covered in the informant interview include memory, word finding difficulties, trouble managing finances, difficulties managing medication independently and needing assistance with transportation. Scoring: * 9 No Significant Cognitive Impairment * 8-5 More Testing Required * 4-0 Cognitive Impairment
Informant Questionnaire on Cognitive Decline in the Elderly
Informant Questionnaire on Cognitive Decline in the Elderly (IQCODE)
Assessment questionnaire used as a screening test for dementia that is filled out by a relative or other supporter who knows the patient for a minimum of 10 years to determine whether that person has declined in cognitive functioning. It lists 26 everyday situations where a person has to use their memory or intelligence. The questions on the test compare the patient''s state of mind to 10 years ago using the scale of: Much Improved A Bit Improved Not Much Change A Bit Change A Bit Worse and Much Worse. If the person is found to have significant cognitive decline, then this needs to be followed up with a medical examination to determine whether dementia is present. Scoring: * 0-3 No Cognitive Impairment * >3 Cognitive Impairment
A 30 question assessment test to screen patients for cognitive impairment that is commonly used in medicine to screen for dementia. It is also used to estimate the severity of cognitive impairment and to follow the course of cognitive changes in an individual over time, thus making it an effective way to document an individual's response to treatment. It takes about 10 minutes and examines functions including arithmetic, memory and orientation.
Structured Clinical Interview for DSM-IV
A diagnostic exam used to determine DSM-IV Axis I disorders (SCID-I) (major mental disorders) and Axis II disorders (SCID-II) (personality disorders). An Axis I SCID assessment with a psychiatric patient usually takes between 1 and 2 hours, depending on the complexity of the subject's psychiatric history and their ability to clearly describe episodes of current and past symptoms. A SCID with a non-psychiatric patient takes 1/2 hour to 1-1/2 hours. A SCID-II personality assessment takes about 1/2 to 1 hour. The instrument was designed to be administered by a clinician or trained mental health professional. (Adapter from Wikipedia)
20-item clinical assessment to measure key aspects of hopelessness: feelings about the future, loss of motivation, and expectations. It takes 5 to 10 minutes is self-administered or verbally administered by a trained administrator.
Edinburgh Postnatal Depression Scale (EPDS)
A 10 item assessment scale developed to identify women who have postpartum depression (PPD). Items of the scale correspond to various clinical depression symptoms, such as guilt feeling, sleep disturbance, low energy, anhedonia, and suicidal ideation. Overall assessment is done by total score, which is determined by adding together the scores for each of the 10 items. Higher scores indicate more depressive symptoms. The EPDS may be used within 8 weeks postpartum and it also can be applied for depression screening during pregnancy. (Adapted from Wikipedia) Scoring: * 0-9 Not Likely to Have Depression * 10-30 Likely to Have Depression
A multiple question assessment scale used to provide an indication of depression and serves as a way to evaluate recovery in patients. It is designed for adults and is used to rate the severity of their depression by probing mood, feelings of guilt, suicide ideation, insomnia, agitation or retardation, anxiety, weight loss, and somatic symptoms. It was designed to be administered by a trained professional using a semi-structured interview. Although Hamilton's original scale had 17 items, other versions were developed to include up to 29 items (HRSD-29).(Adapted from Wikipedia) It takes about 20 minutes to complete the interview and score the results. Scoring: * 0-7 Normal * 8-13 Mild * 14-18 Moderate * 19-22 Severe * > or = 23 Very Severe
A psychological self-rating scale developed by Dalhousie University professor of psychiatry Stan Kutcher, to assess the level of depression in adolescents. While there are some variations, the 11-item version of the KADS is the most commonly used and most thoroughly verified for efficacy in monitoring outcomes in adolescents who are receiving treatment for major depressive disorder. Its items are worded using standard and colloquial terminology, and responses are scored on a simple 4 choice scale. There are ten questions about depression symptom frequency that the patient rates on a straight 4 point scale according to the following choices: hardly ever, much of the time, most of the time, all the time, and one question relating to the severity of suicidal ideation. Scores on the test range from 0 to 33. Unlike some rating scales, there is no threshold for sub-clinical presentation, or ranges for mild, moderate, and severe symptoms. Higher scores simply indicate more severe current depression symptoms. (Adapted from Wikipedia)
A 12 item self-report mood assessment developed by the World Health Organisation that is able to generate an ICD-10 or DSM-IV diagnosis of clinical depression in addition to an estimate of symptom severity. Scoring: * Mild depression: A score of 4 or 5 in two of the first three items. Plus a score of at least 3 on two or three of the last seven items. * Moderate depression: A score of 4 or 5 in two or three of the first three items. Plus a score of at least 3 on four of the last seven items. * Severe depression: A score of 4 or 5 in all of the first three items. Plus a score of at least 3 on five or more of the last seven items. * Major depression: The number of items is reduced to nine, as Item 4 is part of Item 5. Include whichever of the two items has the highest score (item 4 or 5). A score on at least five items is required, to be scored as follows: the score on the first three items must be at least 4, and on the other items at least 3. Either Item 1 or 2 must have a score of 4 or 5.
Montgomery-Asberg Depression Rating Scale
Montgomery����??����?sberg Depression Rating Scale
A ten-item diagnostic questionnaire which psychiatrists use to measure the severity of depressive episodes in patients with mood disorders. Higher MADRS score indicates more severe depression, and each item yields a score of 0 to 6. The overall score ranges from 0 to 60. The questionnaire includes questions on the following symptoms: 1. Apparent sadness 2. Reported sadness 3. Inner tension 4. Reduced sleep 5. Reduced appetite 6. Concentration difficulties 7. Lassitude 8. Inability to feel 9. Pessimistic thoughts 10. Suicidal thoughts. Scoring: * 0-6 Normal/Symptom Absent * 7-19 Mild Depression * 20-34 Moderate Depression * >34 Severe Depression (Adapted from Wikipedia)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27th, 2023. Cubist Pharmaceuticals was American biopharmaceutical company that targeted pathogens like MRSA. Company employed 638 people, mostly in Lexington, MA. On 8 December 2014, Merck acquired Cubist.
A self-rating scale to assess the level of depression for patients diagnosed with depressive disorder. There are 20 items on the scale that rate the rating affective, psychological and somatic symptoms associated with depression. There are ten positively worded and ten negatively worded questions. Each question is scored on a scale of 1 through 4 (based on these replies: a little of the time, some of the time, good part of the time, most of the time). Scores on the test range from 20 through 80. The scores fall into four ranges: Scoring: * 20-44 Normal Range * 45-59 Mildly Depressed * 60-69 Moderately Depressed * 70 and above Severely Depressed The Zung Self-Rating Depression Scale has been translated into many languages, including Arabic, Azerbaijani, Dutch, German, Portuguese, and Spanish. (Adapted from Wikipedia)
Anorectic Behavior Observation Scale (ABOS)
A thirty-item diagnostic scale devised to be answered by the parents, spouse or other family member of an individual suspected of having an eating disorder. The questions address three factors; unusual eating behavior, bulimic-type behavior and hyperactivity. The ABOS however does not address the frequency of the observed behavior. The ABOS is scored on a range of from 0-60. There are three possible answers provided per question, each assigned a numerical value: two points for yes, zero for no, and one for don't know. (Adapted from Wikipedia) Scoring: * 0-10 Non-Anorexic * 11-20 Retest Required in 2 Months * 21-30 Anorexic Eating Detected, More Testing Required * 31-60 Severe Anorexia, Seek Professional Guidance
A 16 item questionnaire used to assess the presence of binge eating behavior indicative of an eating disorder that was devised specifically for use with obese individuals. The questions are based upon both behavioral characteristics (e.g., amount of food consumed) and the emotional, cognitive response, guilt or shame. Each question has 3-4 separate responses assigned a numerical value. The score range is from 0-46: * < 17 Non-Binging * 18-26 Moderate Binging * 27 and greater Severe Binging (Adapted from Wikipedia)
A widely used standardized self-report measure of symptoms and concerns characteristic of eating disorders. The original 40-item version was developed for a study to examine socio-cultural factors in the development and maintenance of eating disorders. A 26-item refinement of the original test has been made and it has been translated into many different languages and used in hundreds of studies. The EAT-26 has been useful as a screening tool to assess eating disorder risk in high school, college and other special risk samples such as athletes. It can be used in a non-clinical as well as a clinical setting not specifically focused on eating disorders. It can be administered in group or individual settings and is designed to be administered by mental health professionals, school counselors, coaches, camp counselors, and others with interest in gathering information to determine if an individual should be referred to a specialist for evaluation for an eating disorder. It is intended primarily for adolescents and adults. The EAT-26 should be used as the first step in a two-stage screening process. According to this methodology, individuals who score 20 or more on the test should be interviewed by a qualified professional to determine if they meet the diagnostic criteria for an eating disorder. The tests are rated on a six-point scale in response to how often the individual engages in specific behaviors. (adapted from Wikipedia)
A self-report questionnaire used to assess the presence of eating disorders, anorexia nervosa, bulimia nervosa, and eating disorder not otherwise specified including Binge Eating Disorder (BED). The original questionnaire consisted of 64 questions, divided into eight subscales. There have been two subsequent revisions by Garner; Eating disorder inventory-two (EDI-2) and Eating disorder inventory-three (EDI-3). (Adapted from Wikipedia) The EDI-3 consists of 91 items organized into 12 primary scales: Drive for Thinness, Bulimia, Body Dissatisfaction, Low Self-Esteem, Personal Alienation, Interpersonal Insecurity, Interpersonal Alienation, Interoceptive Deficits, Emotional Dysregulation, Perfectionism, Asceticism, and Maturity Fears.
Critical Path to Tuberculosis Drug Regimens
A collaboration of international pharmaceutical companies, public health experts, civil society organizations, and U.S., European, and other regulatory authorities to speed the development of new and improved drug regimens for tuberculosis (TB). Its goals include creating innovative tools, including TB data standards and databases. The Initiative is built around four operating arms: Regulatory Science Consortium, Drug Development Coalition, Research Resources Group, and Drug Susceptibility Testing Group. The focus of the consortium is to: * Develop and integrate data standards * Qualify biomarkers through the Food and Drug Administration (FDA) / European Medicines Authority (EMA) * Develop quantitative disease progression (natural history) models * Create disease response metrics, develop target product profiles and supporting assays, and * Develop new pharmacokinetic/dynamic measures of drug interactions Accomplishments include: * Engaged the FDA, which has released updated regulatory guide-lines for developing new TB drug regimens with efforts to create a more favorable environment for combination regimen development * TB Alliance launched the first-ever clinical trial of a novel combination drug regimen for TB, validating the approach to regimen development set forth by CPTR, and is moving to a phase III clinical trial named STAND. * Developed and published TB data standards in collaboration with the Clinical Data Interchange Standards Consortium (CDISC). * Expanded scope to include the CPTR Rapid Drug Susceptibility Testing (RDST) Consortium and an expanded Modeling and Simulation development program. * Pursued several regulatory pathways with the FDA for the Hollow Fiber System Model for TB (HFS-TB). * Submitted a dossier to the EMA on the HFS-TB for qualification opinion consideration. * Submitted a "briefing book" to the FDA via the pre-IND process to review CPTR's data analysis plan and data inventory for liquid culture, with emphasis on time-to-positivity, as a quantitative measure of long-term outcome. * Initiated planning to develop a database supporting the RDST Consortium's goal to develop a rapid TB drug susceptibility test.
A 5-item self-reported diagnostic scale used to assess the presence and severity manic and hypomanic symptoms, most commonly in patients diagnosed with bipolar disorder. It assesses differences in normal or baseline levels in five subjective and behavioral areas: positive mood, self-confidence, sleep patterns, speech patterns / amount of sleep, and motor activity. Scores above a 5 are indicative of mania, or hypomania, with the severity of symptoms increasing with higher scores. Examining score changes over time is also used to determine the efficacy of a particular treatment in a clinical setting and to qualify whether the severity a manic episode is increasing or decreasing. (Adapted from Wikipedia) Scoring: * 0-5 Normal * 6-25 Probable Manic or Hypomanic Condition, Further Testing Recommended
An eleven-item, multiple-choice diagnostic questionnaire which psychiatrists use to measure the severity of manic episodes in patients. The scale was originally developed for use in the evaluation of adult patients who were suffering from bipolar disorder, but has since been modified for use in pediatric patients. A similar scale was then developed to allow clinicians to interview parents about their children's symptoms, in order to ascertain a better diagnosis of mania in children. Clinical studies have demonstrated the effectiveness of the parent version of the scale. The scale provided is in a slightly reworded form as a self-assessment. This may not be as accurate when self-administered, as people suffering from mania are often unable to properly assess relevant outward symptoms.
A test to measure narcissism as a personality trait in social psychological research. Although there are several versions, a forty-item forced-choice version (Raskin & Terry 1988) is the one most commonly employed in current research. It is based on the DSM-III clinical criteria for narcissistic personality disorder (NPD), although it was designed to measure these features in the general population. Thus, the NPI is often said to measure normal or subclinical (borderline) narcissism (i.e., in people who score very high on the NPI do not necessarily meet criteria for diagnosis with NPD). Raskin and Terry (1988) identified seven factors of the NPI (i.e., Authority, superiority, exhibitionism, entitlement, vanity, exploitativeness and self-sufficiency), mapping roughly onto the DSM criteria for NPD. Since then, several studies have further examined the factor structure of the NPI with varying results. It should take most people five to ten minutes to complete.
4-item questionnaire, where the name is an acronym of its four questions, that can indicate potential problems with alcohol abuse and has been extensively validated for use in identifying alcoholism. It has been determined that CAGE test scores >=2 had a specificity of 76% and a sensitivity of 93% for the identification of excessive drinking and a specificity of 77% and a sensitivity of 91% for the identification of alcoholism. The most important question in the questionnaire is the use of a drink as an Eye Opener, so much so that some clinicians use a yes to this question alone as a positive to the questionnaire; this is due to the fact that the use of an alcoholic drink as an Eye Opener denotes abuse since the patient is going through withdrawal in the morning, hence the need for a drink as an Eye Opener.(Adapted from Wikipedia) Scoring: * 2 (or more) yes responses indicates the possibility of alcoholism
Standardized Mini-Mental State Examination
Standardized Mini-Mental State Examination (SMMSE)
Assessment test imposing strict guidelines for administration and scoring to improve the reliability of the Mini-Mental State Examination (MMSE), a screening test for the purpose of evaluating cognitive impairment in older adults.
Social Environment and Biomarkers of Aging Study in Taiwan
Social Environment and Biomarkers of Aging Study (SEBAS) in Taiwan
Data sets of information regarding the health and well-being of older persons in Taiwan (from 2000 and 2006), in particular the relationship between life challenges and mental and physical health, the impact of social environment on the health and well-being of the elderly, and biological markers of health and stress. The study collected self-reports of physical, psychological, and social well-being, plus extensive clinical data based on medical examinations and laboratory analyses. Examination of health outcomes included chronic illnesses, functional status, psychological well-being, and cognitive function. Questions regarding life challenges focused on perceived stress, economic difficulties, security and safety, and the consequences of a major earthquake. Biological markers were used to identify cardiovascular risk factors, metabolic process measures, immune-system activity, the hypothalamic-pituitary adrenal axis, and sympathetic nervous system activity. The study design consists of face-to-face interviews with participants drawn from a random sub-sample of participants from 27 PSUs from the 1999 Survey of Health and Living Status of the Middle Aged and Elderly in Taiwan. Hospital visits and blood and urine specimens also were collected. A second wave of SEBAS was conducted in 2006 using a similar protocol to SEBAS 2000, but with the addition of performance assessments conducted by the interviewers at the end of the home interview. * Dates of Study: -2000, 2006 * Study Features: Longitudinal, International, Anthropometric Measures * Sample Size: 27 PSUs
Project that aims to provide structure and clarity to the research-by-consortium model, presenting both the consortia framework and partnership components in an effort to guide and inform emerging and existing collaborative efforts. Their goal is to ensure that research-by-consortium efforts are at their highest performance and achieving the best possible outcomes. A consortium will thrive if its leadership and governance structure is able to define a mission that's shared by all stakeholders and articulate the desired outcomes of the effort early in the process. For collaborative efforts to move forward, consortia must recognize and leverage the unique strengths and resources that each partner can contribute and bring to fruition. They have found that managing expectations and establishing transparency measures are essential to building trust among all participating stakeholders. Transparency curbs potential conflicts of interest and creates a culture that allows for open sharing of data and a responsible approach to intellectual property negotiations. They found that for collaborations in the medical research and development ecosystem to be effective and sustainable, they must be driven by the ultimate goal of delivering a medical solution that could improve or save lives. Through the project, they are creating several tools for the biomedical research community: * Framework report: This series of reports analyzes a diversity of existing consortia to understand the operational management and framework used to initiate and manage these complex collaborations. * Consortium database * Landscape analysis trends and intended output * Educational webinars and spotlights
Academic Drug Discovery Consortium (ADDC)
A collaborative network among university-led drug discovery centers and programs to allow scientists to exchange technical expertise on drug discovery and development strategies as well as form partnerships with each other, biopharma companies, and drug discovery-focused contract service organizations and consultants. The website will also serve as a repository for drug discovery events, educational material, job postings, and partnership opportunities. Through active member participation this website will become a valuable tool for every scientist working in the drug discovery arena. In addition, involvement of members will enable them to effectively advocate to the NIH and other funding agencies to increase the awareness of the growing number of academic drug discovery scientists and their success as well as their needs.
Elements of Morphology: Human Malformation Terminology
Data set of standardized terms used to describe human morphology including definitions of terms for the craniofacies in general, the major components of the face, and the hands and feet. This provides a uniform and internationally accepted terms to describe the human phenotype.
Project designing, prototyping, optimizing, and evaluating a learning health system to improve clinical practice, patient self-management, and disease outcomes of patients with chronic illness. This open, peer production system combines the collective input of patients, clinicians and researchers. It combines large clinical data registries with patient entered data and makes them accessible and interactive. A platform allows researchers to design, test and implement new knowledge and innovations in patient care. To test their platform approach, C3N is working on a model of treating children with Inflammatory Bowel Disease using the ImproveCareNow Network of pediatric clinics. Following this demonstration phase, the goal is to apply the social, scientific and technical platform to transform the care of a variety of chronic illnesses. The C3N effort has the following goals: # Deploy and optimize an integrated set of engagement tools to make it easier for patients and care providers to collect and use the right information during the clinical encounter and in between visits. # Prototype novel interventions to re-design care delivery by promoting the development of tools for real-time and dynamic population management, "just-in time" scheduling of visits, virtual clinic visits, and measuring the impact of these interventions on health, care, and cost. # Pilot and deploy patient-focused technology to improve the flow of data between patients, clinicians and scientists to enable faster learning and improvement.
Predictive Safety and Testing Consortium Drug-induced Nephrotoxicity Biomarkers
PSTC NWG Drug-induced Nephrotoxicity Biomarkers
Urinary kidney biomarkers (KIM-1, albumin, total protein, 2-microglobulin, cystatin C, clusterin and trefoil factor-3) that are considered acceptable biomarkers for the detection of acute drug-induced nephrotoxicity in rats and can be included along with traditional clinical chemistry markers and histopathology in toxicology studies. These biomarkers may be used voluntarily as additional evidence of nephrotoxicity in nonclinical safety assessment studies to complement the standard data (BUN and sCr). In ROC analyses, some of these biomarkers showed better sensitivity and specificity than BUN and sCr relative to histopathological alterations considered to be the gold standard when tested with a limited number of nephrotoxicant and control compounds.
Center for Integration of Medicine and Innovative Technology
Center for Integration of Medicine & Innovative Technology
Center for Integration of Medicine and Innovative Technology (CIMIT)
A non-profit consortium of Boston academic medical centers and universities (and growing) to accelerate the healthcare innovation cycle by fostering interdisciplinary, inter-institutional collaboration among experts in translational research, medicine, science, engineering, healthcare implementation and entrepreneurship in concert with industry, foundations and government to rapidly improve patient care. It concentrates on early stage, high-risk ideas, projects and supports them through to a commercial exit from academia. It provides innovators with resources to explore, develop and implement novel technological solutions for today's most urgent healthcare problems. CIMIT is dedicated to helping develop medical technology that will help both military and civilian patients.
Consortium to identify, fund and support breakthrough technologies that will significantly enhance biopharmaceutical R&D productivity and accelerate the development of new safe and efficacious drugs. CQDM is a neutral ground that brings patient groups, academia, governments, biotech and the pharma industry together to work collaboratively on complex medical challenges. Projects supported by the consortium are highly relevant to the pharmaceutical sector and typically address: * Opportunity for new therapeutic approaches and research * Safe and effective new drug development * Enhancing the efficacy of already existing drugs * Reducing costs, time and risks associated with the discovery and development of new drugs Funded projects typically involve multidisciplinary collaborations between research teams that represent both the academic and the private sector, who are mentored by industry scientists provided by the consortium sponsors.
Project to develop a drug safety database from the pharmaceutical industry legacy toxicology reports and public toxicology data; innovative in silico strategies and novel software tools to better predict the toxicological profiles of small molecules in early stages of the drug development pipeline. The project is creating this pharmaco-toxicological database with an aim to: * Reduce the number of animal tests * Decrease the attrition rates of new drug candidates * Increase the success rate of new molecular entities becoming drugs * Improve the safety of drugs on the market The project consists of three different systems, * eTOX VITIC Database a unified database containing all confidential and non-confidential data collected in eTOX (historical data from the pharmaceutical industry) * ChOX Database a unified database containing public data (literature and public database) * eTOXsys Query and Prediction System an interface providing a uniform access to the two databases (VITIC and ChOX) and to all developed prediction models and systems
Investigation of Serial Studies to Predict Your Therapeutic Response With Imaging And moLecular Analysis 2
A collaboration to test an adaptive clinical trial model that would assess the efficacy of a candidate therapeutic earlier than traditional clinical trials, potentially enabling drugs to be developed and approved using fewer patients, less time and fewer resources. This trial focuses on women with newly diagnosed locally advanced breast cancer to test whether adding investigational drugs to standard chemotherapy is better than standard chemotherapy alone. It uses genetic and biological markers from individual patients' tumors to screen several promising new treatments simultaneously and allows doctors to quickly measure the effectiveness of the treatment prior to removing the tumor. The experimental adaptive trial design uses patient outcomes to immediately inform treatment options for subsequent trial participants. The trial has 5 components that differentiate it from conventional clinical trial models. # I-SPY2 uses tissue and imaging biomarkers from individual cancer patients' tumors to determine eligibility, guide/screen promising new treatments and identify which treatments are most effective in specific tumor subtypes. # The trial's adaptive design allows the Team to learn as they go, enabling researchers to use data from patients early in the trial to guide decisions about which treatments might be more useful for patients who enter the trial earlier. I-SPY2 provides a scientific basis for researchers to eliminate ineffective treatments and graduate effective treatments more quickly. # The neoadjuvant treatment approach - in which chemotherapy is given to patients prior to surgery - allow the team to evaluate tumor response with MRI before removal. This approach is safe as treating after surgery, allowing tumors to shrink, and more importantly, it enables critical learning early on about how well treatments work. # The ability for the team to screen multiple drug candidates developed by multiple companies. New agents will be selected and added as those used initially and either graduate to Phase III, or are dropped, based on their efficacy in targeted patients. # The trials informatics system allows data to be collected, verified, and shared in real-time. This allows data to be assessed early and in an integrated fashion - with an aim to enhance and encourage collaboration
Drug Development Tools Qualification Programs
Drug Development Tools (DDT) Qualification Programs
To support Drug Development Tools development efforts, FDA established qualification programs for animal models for use under Animal Rule, biomarkers, and clinical outcome assessments. DDTs are methods, materials, or measures that have potential to facilitate drug development. Examples of DDTs may include, but are not limited to biomarker2 used for clinical trial enrichment, clinical outcome assessment used to evaluate clinical benefit, and animal model used for efficacy testing of medical countermeasures under regulations commonly referred to as Animal Rule3.
Hungarian Neurological-Psychiatric Biobank
Hungarian Neurological - Psychiatric Biobank
Hungarian Neurological - Psychiatric Biobank - NEPSYBANK
The Hungarian Society of Clinical Neurgenetics established a nationwide collaboration for prospective collection of human biological materials and databases from patient with neurological and psychiatric diseases. The basic triangle of the NEPSYBANK is the sample, the information and the study management. The present participants of the NEPSYBANK are the Department of Neurology and Psychiatry of the four Medical Universities (in Budapest, Debrecen, Pecs, Szeged) and the National Institute of Psychiatry and Neurology in Budapest. The NEPSYBANK is a disease based biobank collecting both phenotypical and environmental data and biological materials such as DNA/RNA, whole blood, plasma, cerebral spinal fluid, muscle / nerve / skin biopsy, brain, and fibroblast. The target of the diseases is presently (Phase I): stroke syndromes, dementias, movement disorders, motoneuron diseases, epilepsy, multiple sclerosis, schizophrenia, alcohol addiction. In the near future (Phase II.) it is planned to enlarge the scale with headaches, disorders of the peripheral nerves, disorders of neuromuscular transmission, disorders of skeletal muscle, depression, anxiety. DNA/RNA is usually extracted from whole blood, but occasionally different tissues such as muscle, brain etc. can be used as well. The extracting procedures differ among the institutes, but in all cases the concentration and the quality of the DNA/RNA must be registered in the database. Participating institutional biobanks have committed themselves to follow common quality standards, which provide access to samples after prioritization on scientific grounds only. In every case the following data are registered. 1. General data: main bank categories, age, sex, ethnicity, body height, body weight, economic stats, education, type of place of living, marital status, birth complications, alcohol, drugs, smoking. 2. Sample properties (sample ID, type of sample, date of extraction, concentration, and level of purity). General patient data as blood pressure, heart rate, internal medical status, ECG, additional diseases. Disease specific question e.g. in schizophrenia the diagnosis after DSMIV and ICD 10, detailed diagnostic questions after both classification, detailed psychiatric and neurological status, laboratory findings, rating scales, data of neuroimaging, genetic tests, applied medication (with generic name, dose, duration), adverse drug effects and other treatments. The Biobank Information Management System (BIMS) is responsible for linkage of databases containing information on the individual sample donors. If you want to have samples from the NEPSYBANK an application must be submitted containing the following information: short research plan including aims and study design, ethic application with a positive decision, specific demands regarding the right of disposition, agreements with grant organizations which regulate immaterial property, information about financing (academic grants, support from industry). All participants have the right to withdraw their samples through a simple order.
ILSI HESI Drug-induced Nephrotoxicity Biomarkers
HESI Drug-induced Nephrotoxicity Biomarkers
ILSI / HESI Nephrotoxicity Working Group Drug-induced Nephrotoxicity Biomarkers
International Life Sciences Institute / Health and Environmental Sciences Institute Nephrotoxicity Working Group Drug-induced Nephrotoxicity Biomarkers
Urinary kidney biomarkers, Clusterin and Renal Papillary Antigen-1 (RPA-1), that sponsors may use to determine more conservative NOAELs for estimating starting doses in the initial human clinical trial of a drug that displays nonclinical nephrotoxicity as determined by histopathology. When tested with a limited number of nephrotoxic compounds, the Receiver Operating Characteristic (ROC) analyses showed that urinary clusterin and renal papillary antigen-1 (RPA-1) have better sensitivity and specificity than BUN and creatinine for the detection of specific kidney pathologies in male rats. Clusterin and RPA-1 provide additional and complementary information to BUN, serum creatinine (sCr), and histopathology for the detection of acute drug-induced nephrotoxicity in safety assessment studies.
O'Brien Reagan York and Jacobsen Drug-induced Cardiotoxicity Biomarkers
Serum / plasma biomarkers, Cardiac troponins T (cTnT) and I (cTnI), in safety assessment studies for rats, dogs, and monkeys are qualified biomarkers for the following contexts of use: # When there is previous indication of cardiac structural damage with a particular drug, cardiac troponin testing can help estimate a lowest toxic dose or a highest non-toxic dose to help choose doses for human testing. In this case, cardiac troponins may serve as a clinical chemistry correlate to the histology. For example, in a safety assessment study, lower doses without increases in cardiac troponins may be used to support a no observed effect level (NOEL) identified by histology. # When there is known cardiac structural damage with a particular pharmacologic class of a drug and histopathologic analyses do not reveal structural damage, circulating cardiac troponins may be used to support or refute the inference of low cardiotoxic potential. # When unexpected cardiac structural toxicity is found in a nonclinical study, the retroactive (reflex) examination of serum or plasma from that study for cardiac troponins can be used to help determine a no observed adverse effect level (NOAEL) or lowest observed adverse effect level (LOAEL). The results of this testing may support inclusion of cardiac troponin testing in subsequent safety assessment studies.
Exacerbations of Chronic Pulmonary Disease Tool
Exacerbation of Chronic Pulmonary Disease Tool Patient Reported Outcome (EXACT-PRO) Instrument
Exacerbation of Chronic Pulmonary Disease Tool Patient Reported Outcome Instrument
Exacerbations of Chronic Pulmonary Disease Tool (EXACT)
An electronically administered patient-reported outcome (PRO) measure that is a qualified measure of symptoms of acute bacterial exacerbation of chronic bronchitis in patients with chronic obstructive pulmonary disease (ABECB-COPD), for use in phase 2 trials. Refer to the proposed context of use, http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/DrugDevelopmentToolsQualificationProgram/UCM399682.pdf. Its intent to quantify frequency, severity, and duration of acute exacerbations in clinical trials of COPD including those with chronic bronchitis. It is designed as an electronic diary made up of fourteen items to be completed by the patient each evening just prior to bedtime. (An item-reduction statistical analysis narrowed the questions from 23 to 14.) For more information see, http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/DrugDevelopmentToolsQualificationProgram/UCM386248.pdf
Medaka Fish Anatomy and Development Ontology
A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.
European Multicenter Study about Spinal Cord Injury
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A clinical spinal cord injury network that provides a database of clinical assessment data from spinal cord injured patients. The EMSCI assessment scheme currently consists of the so called core sets: neurological (ISNCSCI), functional (10MWT, 6MWT, TUG, WISCI2) measurements and independence measures (SCIM3). Additional assessments are: neurophysiology (MEP, SSEP, NCV), pain, hand function and an urodynamics.
Multiple Myeloma Research Foundation (MMRF) - CoMMpass Study
Relating Clinical Outcomes in MM to Personal Assessment of Genetic Profile
Relating Clinical Outcomes in Multiple Myeloma to Personal Assessment of Genetic Profile Study
A personalized medicine initiative to discover biomarkers that can better define the biological basis of multiple myeloma to help stratify patients. This effort hopes to obtain samples from approximately 1,000 multiple myeloma patients and follow them over time to identify how a patient's genetic profile is related to clinical progression and treatment response. As a partnership between 17 academic centers, 5 pharmaceuticals and the Department of Veterans Affairs, the goal of this eight year study is to create a database that can accelerate future clinical trials and personalized treatment strategies. MMRF's CoMMpass Study has the following goals: * Create a guide to which treatments work best for specific patient subgroups. * Share data with researchers to accelerate drug development for specific subtypes of multiple myeloma patients. In order to facilitate discoveries and development related to targeted therapies, the comprehensive data from CoMMpass is placed in an open-access research portal. The data will be part of the Multiple Myeloma Research Foundation's (MMRF) Personalized Medicine Platform combines CoMMpass data with those collected from MMRF's Genomics Initiative. It is hoped that the longitudinal data, combined with the annotated bio-specimens will help provide insights that can accelerate personalized therapies.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Database providing access and limited analysis to the MMGP portal data sets. These include the MMRC funded reference array comparative genomic hybridization (aCGH) and gene expression data and additional public multiple myeloma datasets. The MMGP will be updated with new features such as additional data and analysis tools as they become available.
A non-profit foundation that funds basic research and is focused on accelerating the development of myelin repair therapeutics for multiple sclerosis. They have defined a 15-year research plan to develop a drug or drugs and believes its Accelerated Research Collaborative (ARC) model can subsequently be used to accelerate the treatment for all diseases. The ARC framework coordinates and manages the entire therapeutic development continuum from discovery biology to FDA approval. The model works by coordinating multi-disciplinary basic research from academic and government laboratories, systematically validating and derisking potential compounds/targets, and collaborating with pharma partners to increase the probability of successful programs.
Observational Medical Outcomes Partnership
Observational Medical Outcomes Partnership (OMOP)
Initiative to improve the safety of drugs on the market that utilized information drawn from patient medical record databases and health insurance claims to develop and test methods to detect and evaluate drug safety issues over time. The OMOP pilot project focused on the following objectives: * Defining and evaluating analytical methods that can be used to identify associations between drugs and health-related conditions. * Developing tools for organizing access to and evaluating the usefulness of multiple observational datasets. * Study how information from analyses of observational data can be used to inform ongoing pharmacovigilence efforts. The software tools - packaged as the OMOP Web RL Platform was developed and made available to the public, https://github.com/OMOP . In addition to these data tools, this collaborative research effort discovered methods for using data to reliably identify correlations between individual medical interventions and specific health outcomes. These insights are being used to help inform the FDA Sentinel Initiative as part of the Innovation in Medical Evidence Development and Surveillance (IMEDS) program. The achievements of the program include: * Establishment of a common data model and creation of data characterization tools, and vocabulary mappings * Implementation of Health Outcome of Interest definitions, including a program to implement these definitions as part of the Regularized Identification of Cohorts (RICO) * Release of 14 analysis methods to evaluate the performance of methods and data in identifying drug safety issues
Medical Diagnostic Categories - Diagnosis Related Groups
Ontology of Medical Diagnostic Categories-Diagnosis Related Groups
Initiative to advance oncology research by enabling collaborative sharing of historical oncology clinical trial data through a universal platform (database). The initiative aims to network all stakeholders in the cancer community researchers, industry, academia, advocacy, and other organizations to share insights and collaborate on issues that could not be solved individually. To do this, they have made efforts to address issues of data privacy, security, intellectual property, resources, and incentives as part of its effort to maximize participation. Data contributions include control arms of clinical trials, and the platform uses data-security precautions and analytics to pool multiple studies associated with the same diagnosis in a manner that seeks to protect the privacy of patients and the security of the data contributed.
A public-private partnership to identify new and improved translational safety testing methods for use in nonclinical and clinical studies and submit them for formal regulatory qualification by the FDA (Food and Drug Administration), EMA (European Medicines Agency), and PMDA (Japanese Pharmaceutical and Medical Devices Agency). The current 19 corporate members of the consortium share internal experience with nonclinical and clinical safety biomarkers in six working groups: cardiac hypertrophy, nephrotoxicity, hepatotoxicity, skeletal myopathy, testicular toxicity, and vascular injury. The ultimate goal of the consortium is to improve the current approach to drug safety testing and offer assurance to the drug developers that these approaches will be accepted by the regulatory authorities in their drug development programs. Through PSTC, members are able to share their expertise, resources, data, and internally developed approaches in a neutral, precompetitive, confidential environment. There are more than 250 participating scientists and C-Path serves as the trusted third party, leading the collaborative process by collecting and summarizing the data, and leading the interactions with global health authorities.
Non-profit research organization aiming to accelerate drug development by increasing the quality and efficiency of clinical studies through the development of shared tools, methods, and platforms. Consortium partnerships are limited to pharmaceutical and biotechnology companies with research & development operations, although there are collaborations with external organizations such the Clinical Data Interchange Standards Consortium (CDISC). Its current focus is to collaborate on: * Standardizing risk-based monitoring * Development of methods to qualify and train clinical trial sites * Development of a common investigator web portal * Development of clinical data standards on efficacy, and methods for comparator drug trials It currently has 5 projects: # Standardized Approach for High-Quality, Risk-Based Monitoring program aims to develop an industry-wide standard and approach for risk-based monitoring of clinical trials in order to enhance patient safety and ensure the quality of clinical trial data. # Shared Site Qualification and Training program aims to standardize GCP training and site qualification credentials in order to realize efficiencies and accelerate study start-up timelines. # Common Investigator Site Portal is a platform designed to streamline investigator and site access through harmonized delivery of content and services. # Data Standards project is a partnership with CDISC to develop industry-wide data standards in priority therapeutic areas to support the exchange and submission of clinical research and meta-data, improving patient safety and outcomes. # Comparator Drugs project aims to establish reliable, rapid sourcing of quality products for use in clinical trials through a comparator supply model enabling accelerated trial timelines and enhanced patient safety.
A French world-class cluster dedicated to therapeutic innovations, it is the one-stop contact to optimize any R&D development or business project in Europe, both in drug development and medical technologies. Located in Alsace region, part of the famous French-German-Swiss BioValley and with a unique concentration of international life sciences & healthcare players, Alsace BioValley helps any Life Sciences & Healthcare companies interested in new projects and partnerships in Europe: * to search outstanding scientific or industrial partners to develop very innovative R&D projects * to find the best innovative technology, patent or scientific expertise * to set up and locate in Alsace region
Business-Led Networks of Centres of Excellence
Business-Led Networks of Centres of Excellence Program
Funds large-scale collaborative research networks that bring a wide range of research expertise to bear on specific challenges identified by an industrial sector. Led by a not-for-profit consortium of industrial partners, networks enhance private sector innovation by blending academic expertise with the private sector''s drive to respond to real-world challenges. BL-NCEs increase private sector investments in Canadian research, support training of skilled researchers, and accelerate the transfer of ideas from the laboratory into solutions needed by the private sector.
Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus
Accelerating Medicines Partnership - Arthritis
Accelerating Medicines Partnership - Autoimmune
Accelerating Medicines Partnership - Autoimmune Diseases
Accelerating Medicines Partnership - Autoimmune Diseases of Rheumatoid Arthritis and Lupus
AMP Autoimmune Diseases of Rheumatoid Arthritis and Lupus
The autoimmune disease arm of the Accelerating Medicine Partnership (AMP), which aims to identify and validate the most promising biological targets of disease for new diagnostic and drug development, that is focused on rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). They seek to identify shared common flaws in inflammation, particularly those that are shared with a larger number of autoimmune disorders which can cause severe disability, greatly affect quality of life, and are associated with an increased risk of death. This project aims to reveal biomarkers and biological targets for drug development, matching existing drugs to patients with specific molecular profiles who are most likely to benefit. The research plan proposes a 5 year process. Year one will include startup activities such as validation of tissue acquisition processes and analytic technologies, and the development of operating procedures. The second year will focus on identification of disease specific pathways by comparing data from patients and healthy individuals. Years 3-5 will expand the scale to include comparisons of different subsets of patients with RA or lupus to allow molecularly based patient stratification for precise treatment. The final 12 months (2019) will also include preliminary target validation. The data will be made publicly available through an internet-based information portal.
An information integration software tool that enables users to integrate data from a variety of data sources including databases, spreadsheets, delimited text files, XML, JSON, KML and Web APIs. Users integrate information by modeling it according to an ontology of their choice using a graphical user interface that automates much of the process. Karma learns to recognize the mapping of data to ontology classes and then uses the ontology to propose a model that ties together these classes. Users then interact with the system to adjust the automatically generated model. During this process, users can transform the data as needed to normalize data expressed in different formats and to restructure it. Once the model is complete, users can publish the integrated data as RDF or store it in a database.
A worldwide competitiveness cluster centered on pharmaceutical activities including the fight against human and animal infectious diseases and cancers. Designed as a tool interface and public / private approximation, the division has implemented measures to encourage collaborative R & D, help in setting up projects and find funding, increase strategic and financial partnerships for economic development and international companies, provide access to reception areas, technological shared platforms such as the Infectious Diseases Center Lyonbiop��le. It aims to strengthen the competitiveness of the sector health and the attractiveness of the Rh��ne-Alpes area, mainly on the Lyon-Grenoble axis. (adapted from the translated Wikipedia)
Organization that drives the development of Ontario's economy by helping create new jobs, products, services, technologies and businesses by bridging academia and industry. The program suite covers almost all stages of business development and career advancement, covering three key areas: Industry-Academic R&D Collaboration; Commercialization; and Entrepreneurship. Other key initiatives are the IBM Smart Computing Initiative and Colleges Ontario Network for Industry Innovation (CONII). In partnership with industry, OCE co-invests to commercialize innovation originating in the province's publicly funded colleges, universities and research hospitals. They also support and invest in early-stage projects, where the probability of commercial success and potential total return on innovation are substantial. Another expanding focus for OCE is the development of the next generation of innovators through their entrepreneurship fellowships and programs for students and youth across Ontario. Their efforts are focused on sectors of the economy with the greatest potential to drive Ontario's future prosperity and global competitiveness: energy and environment (including water); advanced manufacturing; advanced health technologies; and information, communications technologies and digital media. A trusted partner of government in program delivery, they are committed to advancing a whole-of-government approach as a means of streamlining funding application processes for companies and entrepreneurs.
A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile.
A not-for-profit research and development laboratory focused on the design, development, and deployment of advanced technological solutions for the nation's most challenging and important problems in security, space exploration, healthcare, and energy. Their expertise includes the areas of guidance, navigation, and control systems; fault-tolerant computing; advanced algorithms and software solutions; modeling and simulation; and MEMS and multichip module technology. With a strong commitment to delivering working solutions to their sponsors, they apply their expertise to a variety of domains, including autonomous air, land, sea, and space systems; information integration; distributed sensors and networks; precision-guided munitions; and biomedical engineering; chemical/biological defense; and energy system modeling and management. When appropriate for the needs of their sponsors, they will work with commercial partners to transition their technology to commercial production.
A dropbox like model cloud-based, commercial data management and collaboration system designed specifically for research scientists. It helps manage and annotate data, track provenance and share this with colleagues.
Mar Institute of Medical Research Foundation
Fundacio Institut Mar d'Investigacions Mediques
Fundació Institut Mar d'Investigacions Médiques
Fundación Instituto Mar de Investigaciones Médicas
A private non-profit independent organization that supports and manages research at the Municipal Institute for Medical Research (IMIM) in Barcelona. Its main roles include managing and monitoring research projects and grant requests, promoting quality research, ensuring the observance of ethical principles of professional practice, disseminating the results of research activities, and encouraging specialized teaching and continuous training by and for professionals in the field of Health Sciences. The Foundation is responsible for managing the Institute's resources, and plays an especially relevant role in managing European projects, services abroad and grants for research projects and cooperative research networks from the Carlos III Health Institute. The expertise of the Project Office team covers: project management; financial management; legal assessment; exploitation and intellectual property rights management; knowledge management; validation and assessment; business planning; and training, dissemination and communication strategies design and implementation.
A nonprofit devoted to spreading ideas, usually in the form of short, powerful talks (18 minutes or less). TED began as a conference where Technology, Entertainment and Design converged, and today covers almost all topics - from science to business to global issues - in more than 100 languages. Meanwhile, independently run TEDx events help share ideas in communities around the world.
Anti-Biopharmaceutical Immunization: Prediction and Analysis of Clinical Relevance to Minimize the Risk
A consortium that seeks to provide an integrated approach to anti-drug immunization by evaluating immunogenicity in hemophilia A, multiple sclerosis, and inflammatory diseases, and exploring new tools for protein drug immunogenicity. The data collected will be pooled in a single immunogenicity databank and will be standardized and used to develop models of anti-drug antibodies. By examining the correlation between patient and clinical factors and the incidence of immunogenicity, it hopes to reduce the regulatory and resource burdens of immunogenicity testing. The objectives of the consortium are: # Access to large cohorts of patients treated with marketed biopharmaceutical products # Complementary expertise for anti-drug antibodies (ADA) assays; standardization and characterization of ADA # Novel integrated approaches to characterize anti-drug lymphocyte responses # Development and validation of innovative prediction tools # Collection and integration of immunogenicity-related data and clinical relevance of ADA ABIRISK is grouped into five working projects, which communicate with one another and provide each other with results and data for analysis. The five working projects are: ADA assay development and validation and cohort management; cellular characterization and mechanisms of the AD immune response; evaluation and development of technologies for predicting immunogenicity; establishment of database, data analyses and integration; and project management and communication.
Advanced Immunization Technologies (ADITEC)
A consortium that aims to accelerate the development of immunization technologies for the next generation of human vaccines. The goals are to characterize the mode of action and conduct comparative effectiveness studies of: adjuvants, vectors, formulations, delivery devices, routes of immunization, homologous and heterologous primeboost schedules, on vaccine efficacy. As part of these clinical trials, the consortium will also investigate the impact of host factors such as age, gender, genetics and pathologies. The consortium hopes to use insights gained from their projects to advance the development of next-generation vaccines, using tools such as standardized animal models to select promising immunization technologies. The intended outcome of this partnership is to improve the vaccine development process by advancing: basic research, new technology development, and clinical trial methods. Scientific objectives: # Development of adjuvants, vectors, formulations, and delivery devices # Selection of candidates, routes of immunization, and prime-boost combinations in animal models # Assessment of the impact of host factors in response to vaccination # Development of concepts and tools from human immunization # Development of concepts and tools to address regulatory and ethical issues posed by novel immunization technologies # Creation of an internationally recognized training program for translational immunology and vaccinology. Data is shared across the research partners within and between the different workstreams. Additionally, the consortium has plans to create a clinical database that combines phenotypic and clinical information to study the immune response to influenza vaccination at a population level, in an effort to advance studies into the effects of genetic background, gender, and disease on vaccine response.
Accelerating Medicines Partnership - Alzheimers
Accelerating Medicines Partnership - Alzheimer's
Accelerating Medicines Partnership - Alzheimer's Disease
Accelerating Medicines Partnership Alzheimer's Disease
The Alzheimer's disease arm of the Accelerating Medicines Partnership (AMP) that will identify biomarkers that can predict clinical outcomes, conduct a large scale analysis of human AD patient brain tissue samples to validate biological targets, and to increase the understanding of molecular pathways involved in the disease to identify new potential therapeutic targets. The initiative will deposit all data in a repository that will be accessible for use by the biomedical community. The five year endeavor, beginning in 2014, will result in several sets of project outcomes. For the biomarkers project, tau imaging and EEG data will be released in year two, as baseline data becomes available. Completed data from the randomized, blinded trials will be added after the end of the five year studies. This will include both imaging data and data from blood and spinal fluid biomarker studies. For the network analysis project, each project will general several network models of late onset AD (LOAD) and identify key drivers of disease pathogensis by the end of year three. Years four and five will be dedicated to validating the novel targets and refining the network models of LOAD, including screening novel compounds or drugs already in use for other conditions that may have the ability to modulate the likely targets.
Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D)
Accelerating Medicines Partnership Type 2 Diabetes
Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal
Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.
Biomarkers for Enhanced Vaccine ImmunoSafety
Biomarkers for enhanced vaccines immunosafety
BioVacSafe - Biomarkers for enhanced vaccines immunosafety
Project focused on developing cutting edge tools to speed up and improve the testing and monitoring of vaccine safety, both before and after release to the market. The three specific objectives of the project are: * the characterization of early inflammation induced by vaccines currently on the market and the identification and validation of biomarkers of early inflammation and allergic responses; * the identification and validation of early biomarkers of autoimmunity and their use to help identifying population at risk of developing autoimmunity; * the analysis of the incidence and epidemiology of autoimmune disease in the general population and the link to genetic background or previous events in the life of patients, including severe effects, such as anaphylactic shock.
Consortium bringing together academic and industry researchers to advance the understanding of disease causing factors and disease progression in Rheumatoid Arthritis (RA), with a focus on accelerating the development of new drugs. The efforts under this consortium aim to develop: (1) animal models; (2) human biobanks, databases and technologies; (3) research network to address critical biologic and clinical questions; (4) community to network patients and companies. The focus will be the development of new diagnostic methods to discover the early forms of RA as well as tools to separate the different forms of RA, where different molecular mechanisms are involved and where different therapies may be required. The ultimate goal for therapeutic development is to identify the disease-causing molecular events early in the disease and then influence immunity and inflammation so that functional deterioration is halted, immunity is re-regulated and the disease is cured. Samples from biobanks will be analysed in vitro and models will be aligned with different variants of human arthritis. In addition, new models will be established using similar molecular pathways as the relevant human arthritis subsets, leading to the understanding of the etiology and early pathology of the disease for a program aimed at early and curative treatment of RA and RA-like diseases. A major focus of these efforts will be to understand and subsequently alter the adaptive immune reactions in patients from a disease-inducing mode into either a protective mode against the disease or become asymptomatic.
A three-year consortium that brings together insurers and health care providers to share information from approximately 9 million patients, with a goal that insights from the data will bring down healthcare costs and improve outcomes. It aims to be one of the largest health information exchanges in the country, with the goal of better connecting the vast, often disparate healthcare landscape across California. The database that will house patient data will be overseen by Orion Health, an independent eHealth software company. The information will only be used for clinical purposes. Academic research institutions can apply to use the Cal INDEX de-identified data for research to benefit the public good, such as population health initiatives. Cal INDEX has five main goals: * Improve the quality of care by providing clinicians with a unified statewide source of integrated patient information * Provide patients with a seamless transition between health plans or across various healthcare professionals and hospitals * Improve efficiency and reduce the cost of healthcare * Encourage healthcare technology innovation * Improve public health by providing de-identified data for medical research. Cal INDEX plans to launch at the end of 2014 with approximately 9 million health information records from combined members of Dignity Health and Blue Shield of California and Anthem Blue Cross. Cal INDEX is open to any health data contributor. Cal INDEX will establish a bi-directional data interface with providers to exchange data with EMRs and other hospital and office-based systems.
An American multinational beverage corporation and manufacturer, retailer and marketer of nonalcoholic beverage concentrates and syrups, which is headquartered in Atlanta, Georgia. (Wikipedia) It is the world's largest beverage company, refreshing consumers with more than 500 sparkling and still brands.
Nclamp - data acquisition software for electrophysiology
Data acquisition software that runs in conjunction with neuromatic. configured to work with Igor Pro on PC or Mac, instrutech or national instrument acquisition devices. Funded by The Medical Research Council (UK) Compatibility with WaveMetrics Igor Pro 5 and 6. Compatibility with Mac or PC. NIDAQ interfacing multifunction DAQ boards from National Instruments. Requires Igor NIDAQ Tools MX. ITC interfacing - data acquisition systems from InstruTech / Heka. Requires Igor ITC XOPs. Episodic acquisition (stim and sample). Continuous acquisition (currently for ITC users only). Online analysis, with ability to create your own analysis functions. Notes and Log Files which can be displayed within a table or notebook. Automatic saving of data and log folders to your hard drive. Flexible stimulus pulse generator with ability to use your own pulse waveforms. Instant accessibility to all of NeuroMatics and Igor Pros pre-existing data analysis functions.
Medical Dictionary for Regulatory Activities
Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA)
St. John's College of Pharmacy and Allied Health Professions
St. John's University College of Pharmacy and Health Sciences
St. Johns College of Pharmacy and Allied Health Professions
The College of Pharmacy and Allied Health Professions equips students with the education, training and support they need to meet the present and future demands professionals encounter as pharmacists, physician assistants, clinical laboratory scientists, toxicologists and radiologic technologists. The College is committed to helping students: * Focus on the responsibilities of public health and service * Appreciate the ever-changing character of the health professions * Enjoy a broad, general education * Pursue graduate study in specialized fields of interest Facilities Laboratory facilities in the College of Pharmacy and Allied Health Professions include state-of-the-art equipment used in pharmacology/toxicology, medicinal chemistry, industrial pharmacy and drug information. Our facilities include: GC-mass spectrophotometers; transmission and scanning electron microscopes; Mrs.; capillary GCs; preparative and analytical HPLCs; liquid scintillation and gamma counters; luminometers; dissolution apparatus; membrane potentiometers; atomic absorption spectrophotometers; polygraphs; high-speed and ultracentrifuges. In addition, we have sophisticated tissue-cultures laboratories, molecular pharmacology and molecular biology laboratories, as well as an AAALAC accredited animal facility. In addition to the main University computer, a fully equipped microcomputer laboratory is located adjacent to the main science complex.
Global Health Innovative Technology Fund
A consortium that focuses their efforts on discovering and developing new pharmaceutical drugs, vaccines (both preventive and therapeutic) and diagnostics against the infectious diseases that are prevalent in developing countries. The initial targets are those disorders designated by WHO as neglected tropical diseases prevalent in developing nations. The consortium aims to facilitate international partnerships that enable Japanese technology, innovations, and insights to play a more direct role in improving global health. Another goal of GHIT is to develop a new drug-discovery screening platform to assist the screening of compound libraries housed within Japanese companies and academic institutions. The vision is to have Japanese research organizations donate compounds, with the Fund reimbursing screening costs and leveraging screening programs of existing product-development partners.
Initiative to improve health by speeding up the development of, and patient access to, innovative medicines, particularly in areas where there is an unmet medical or social need. It does this by initiating and managing consortia composed of the key players involved in healthcare research, including universities, the pharmaceutical and other industries, small and medium-sized enterprises (SMEs), patient organizations, and medicines regulators. IMI is a public-private partnership between the European Union and the European pharmaceutical industry, represented by the European Federation of Pharmaceutical Industries and Associations (EFPIA), with a timeframe separated into two phases (2008-2013, 2014-2024) that are each defined by unique research agendas. The first phase (2008 2013) had four pillars that defined the focus of its research agenda: * Predicting safety: evaluating the safety of a compound during the pre-clinical phase of the development process and the later phases in clinical development. * Predicting efficacy: improving the ability to predict how a drug will interact in humans and how it may produce a change in function. * Knowledge management: utilization of information and data for predicting safety and efficacy. * Education and training: closing existing training gaps in the drug development process. Some of the consortia managed under IMI focused on specific health issues while others focused on broader challenges in drug development. Additionally, IMI launched a number of education and training projects during its first phases. The goal of the second phase (IMI2, 2014-2024) is to develop next generation vaccines and drugs. The focus is on delivering the right prevention and treatment for the right patient at the right time. There is a strong focus on the development of new medicines with an emphasis on tools and methods that accelerate patient access to new medicines. IMI2's agenda can be defined by four axes of research: * target validation and biomarker research (efficacy and safety) * adoption of innovative clinical trial paradigms * innovative medicines * patient-tailored adherence programs As part of its distinct goals, IMI2 aims to deliver: * 30% better success rate in clinical trials of priority medicines identified by the WHO; clinical proof of concept in immunological, respiratory, neurological and neurodegenerative diseases in five years; * new and approved diagnostic markers for four of these diseases and at least two new medicines which could either be new antibiotics or new therapies for Alzheimer's disease.
bioMARkers and molecular tumor classification for non-genotoxic CARcinogenesis
MARCAR - towards novel biomarkers for cancer risk assessment
Consortium to identify early biological indicators (biomarkers) that can be used to predict the development of cancer, as an unintended and adverse response to a new drug. The use of these biomarkers that detect early carcinogenicity will hopefully accelerate drug development and increase patient safety. The project focuses on non-genotoxic carcinogenesis (NGC) specifically looking at the role of epigenetic effects that could be caused as unintended consequences of new drugs. Using a combination of molecular analysis technologies, the consortium combines expertise in the field of biomarkers, human and rodent cancer models, imaging, molecular profiling and bioinformatics. Participants will focus on liver tumors, the organ most affected by non-genotoxic carcinogenesis, during the preclinical safety evaluations of candidate-medicines. Their findings aim to facilitate tumor identification in other organs as well, in hopes of providing insights in the mechanisms of tumor growth. The main objectives of the consortium are to: * Identify early biomarkers for predicting which compounds have a potential for later cancer development * Improve the scientific basis for assessing carcinogenic potential of non-genotoxic (NGC) drugs * Identify the molecular response to NGC exposure that underpins development of early exposure biomarkers * Improve drug safety and the efficiency of drug development by advancing the development of alternative research methods
Commercial organization developing a disruptive, proprietary technology platform for the direct, electronic analysis of single molecules. The instruments GridION and MinION are adaptable for the analysis of DNA, RNA, proteins, small molecules and other types of molecule. Consequently, the platform has a broad range of potential applications, including scientific research, personalized medicine, crop science and security / defence.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A base caller for pyrosequences from the 454 Life Sciences sequencing machines.
A not-for-profit organization that initiates and manages drug development consortia that involve the pharmaceutical industry, academia, and the Dutch Government. The aim of all their consortia is to conduct pre-competitive research while strengthening the Netherlands' international reputation for drug development. The consortia are focused on addressing therapeutic areas that are listed as priority areas by the World Health Organization including: autoimmune diseases, cardiovascular diseases, cancer, infectious diseases, and diseases of the brain. The consortia are also focused on enabling: therapeutic target discovery, validation, and animal models; lead selection and in-silico modeling; predictive drug disposition and toxicology; biomarkers and biosensors; drug formulation, delivery, and targeting; and, production technologies. TI Pharma consortia aim to improve the efficiency of the drug-development process, with a focus on advancing regulatory science. In addition to research, TI Pharma also has objectives to train and educate scientists in the Netherlands on the drug discovery and development processes, as well as on entrepreneurship. Participants include: all Dutch universities and academic medical centers, more than 30 industrial partners, small-to-medium sized companies, and representatives from the Dutch Medicines Evaluation Board (Netherlands regulatory body for drugs).
Center for Healthy Aging Stein Institute for Research on Aging
Sam and Rose Stein Institute for Research on Aging
UCSD Stein Institute for Research on Aging
Portal dedicated to the development and application of the latest advances in biomedical and behavioral science knowledge to issues of successful, healthy aging and the prevention and reduction of the burden of disability and disease in late life. Additionally, they provide numerous grants to junior faculty, as well as education programs for doctors and researchers through monthly Grand Rounds. From studying memory to identifying genes with important roles in aging, Stein Institute scientists are continuously pushing the boundaries of knowledge. One of their most promising ongoing projects is the Successful AGing Evaluation (SAGE) Study. SAGE is the only large-scale study on successful aging that considers the impact of positive psychological traits, such as resilience and wisdom, in addition to biological factors, providing a much more complete picture of older adults. Their monthly public lectures presented by renowned physicians and scientists are broadcast on UCSD-TV and have been viewed more than one billion times. This year they partnered with the Clinical and Translational Research Institute and the Osher Lifelong Learning Institute to organize Making Sense of Science, a course for older adults interested in science and health. In addition, They distribute a free monthly newsletter and work extensively with the community, participating in numerous events and conferences.
Stein Institute for Research on Aging News
A list of articles published related to aging produced by the Center for Healthy Aging, Stein Institute for Research on Aging.
Stein Institute for Research on Aging Video Archive
Videos and podcasts presenting the latest innovative research being conducted by the Stein Institute for Research on Aging medical faculty, with the aim of promoting healthy aging. Additionally, many of the public lectures from the Public Lecture Series are also available on UCSD-TV's website video on demand programming. The Lecture series allows affiliated faculty members of the Stein Institute for Research on Aging and other scientists from the UCSD School of Medicine, as well as individuals from surrounding academic and research institutions, to present the latest findings in their respective fields of expertise and share their present work with the general community. All of these lectures focus on topics related to healthy aging or age-related diseases.
University of California San Diego Television
A University of California San Diego based station, including television, blogs, videos and podcasts, with access to people and events that impact both the campus community and the greater San Diego region. The station's non-commercial status gives it the autonomy to create content based strictly on relevance, interest and merit and is able to devote significant airtime to in-depth coverage of new ideas, key issues and emerging talent.
Markup language for encoding raw spectrometer output. From 2005-2008 there has existed two separate XML formats for encoding raw spectrometer output: mzData developed by the PSI and mzXML developed at the Seattle Proteome Center at the Institute for Systems Biology. It was recognized that the existence of two separate formats for essentially the same thing generated confusion and required extra programming effort. Therefore the PSI, with full participation by ISB, has developed a new format by taking the best aspects of each of the precursor formats to form a single one. It is intended to replace the previous two formats. This new format was originally given a working name of dataXML. The final name is mzML.
University of Connecticut; Connecticut; USA
University of Connecticut is a public land-grant research university system with its main campus in Storrs, Connecticut, United States. It was founded in 1881 as the Storrs Agricultural School, named after two benefactors. In 1893, the school became a public land grant college, then took its current name in 1939.
European Translational Information & Knowledge Management Services
European Translational Information and Knowledge Management Services
Research informatics and analytics platform for the IMI OncoTrack consortium.
Consortium to accelerate the search for new, more effective combinations of treatments to tackle Tuberculosis and address pre-clinical research barriers to the discovery and development of new TB drug combinations. To overcome the challenges in Tuberculosis drug development they will create tools to accelerate PK-PD (Pharmacokinetic / Pharmacodynamic) analysis that are connected to clinical outcomes. By addressing the gaps in preclinical information, the consortium aims to provide a framework and tools to facilitate the transition of the best combinations of drugs to late phase development. They aim to develop an integrated set of laboratory-based models that will provide much-needed data to indicate the most appropriate doses and combinations of drugs for patients. In addition, the project will generate a comprehensive database of patient data from previous and on-going clinical trials for use as a reference for evaluating the performance of combination anti-TB drug regimens in these newly developed laboratory models. Ultimately, they aim to enable researchers to be able to use the information generated by the novel models to design better clinical trials involving TB patients. The aims of the consortium: * To systematically evaluate two successive panels of representative anti-tuberculosis drugs (licensed and novel) using a suite of standard, novel and enhanced preclinical model systems, with respect to performance in clinical trials * To refine the set of preclinical systems on the basis of these results in order to identify and define the currently optimal critical path in discovery and pre-clinical development for tuberculosis. * To develop an integrated PK-PD / Disease modelling and simulation framework for tuberculosis which will facilitate prediction of optimal combinations and design of clinical studies.
OncoTrack - Methods for systematic next generation oncology biomarker development
An international consortium to develop and assess novel approaches to identify and characterize biological markers for colon cancer that will deepen the understanding of the variable make-up of tumors and how this affects the way patients respond to treatment. They will use cutting edge laboratory-based genome sequencing techniques coupled to novel computer modelling approaches to study both the biological heterogeneity of colon cancers (i.e. patient to patient variability) as well as tumor variation within the patient for example, by comparing primary tumors with metastases. This five year project brings together top scientists from European academic institutions offering a wide range of expertise, and partners them with pharmaceutical companies. The project is based on the premise that this genetic and epigenetic information, combined with a description of the molecular pathology of the tumor, will allow OncoTrack to generate a more accurate in-silico model of the cancer cell. This will facilitate the identification of predictive markers that can be used to guide the optimal therapy strategy at the level of the individual patient - and will also provide on-going prognostic guidance for the clinician. This project will not only advance understanding of the fundamental biology of colon cancers but will provide the means and approach for the identification of previously undetected biomarkers not only in the cancer under study, but potentially also in other solid cancers and, in doing so, open the door for personalized management of the oncology patient.
Alcohol and Alcohol Problems Science Database
Alcohol Alcohol Problems Science Database
Portal to support researchers and practitioners searching for information related to alcohol research including links to a number of databases, journals, and Web sites focused on alcohol research and related topics. Also included is a link to the archived ETOH database, the premier Alcohol and Alcohol Problems Science Database, which contains over 130,000 records and covers the period from 1972 through 2003. Included in ETOH are abstracts and bibliographic references to journal articles, books, dissertation abstracts, conference papers and proceedings, reports and studies, and chapters in edited works. ETOH's scope reflects the multidisciplinary nature of the alcohol research field. The range of subject areas contained in ETOH includes: medicine, biochemistry, psychology, psychiatry, epidemiology, sociology, anthropology, treatment, prevention, education, accidents and safety, legislation, criminal justice, public policy, and health services research. The ETOH database is indexed with vocabulary from the Alcohol and Other Drug Thesaurus: A Guide to Concepts and Terminology in Substance Abuse and Addiction (AOD Thesaurus), Third Edition. More than 5,000 terms in the AOD Thesaurus are used as ETOH descriptors. The Databases/Resources section includes databases and resources for alcohol researchers and practitioners. It includes an introduction to the National Library of Medicine's PubMed and some sample searches on alcohol to run in the PubMed database; descriptions of and links to the various databases of the National Clearinghouse for Alcohol and Drug Information (NCADI); a selection of alcohol and other drug databases with their descriptions and links; links to peer-reviewed journals most often used by alcohol researchers; and links to a selection of Web sites pertinent to the substance abuse field.
Japanese pharmaceutical company formed from the merger of Yamanouchi Pharmaceutical Co., Ltd. and Fujisawa Pharmaceutical Co., Ltd. Astellas' franchise areas are urology, immunology (transplantation), dermatology, cardiology, and infectious disease. Priority areas for R&D are infectious diseases, diabetes, gastrointestinal diseases, oncology, and diseases of the central nervous system. The company's headquarters are in Tokyo, with research centers in Tsukuba and Osaka. Clinical development is centered in Northbrook, Illinois and Leiderdorp, Netherlands. Combined revenues of the two pre-merger companies were $7.9 billion in 2004. Worldwide the company employs about 17,000 people. (Wikipedia)
Science People: how people do Science - interviews with neuroscientists
SciPle.org uses a two-step data-driven approach to foresee future trends in neuroscience. 1. We build profiles of neuroscientists by collecting interviews with them. 2. These profiles are combined with trends in neuroscience literature to gain insight into the evolution of the "next big thing". SciPle.org merges these two approaches to build an objective model of the neuroscience system, which will allow us to better understand and predict evolving topics and the role played by neuroscientists in shaping and following the current and future trends in neuroscience. We build profiles of neuroscientists by collecting interviews with them: neuroscientists are the agents shaping the neuroscience field. Their interests, drives, motivations and dreams drive their research. Neuroscientists exist in an ecosystem of hidden emergent forces which result from their interactions with thousands of other neuroscientists. Our approach consists in sampling a large pool of neuroscientists. Having a large enough sample (across a reasonable time lag) will allow the building of representative profiles of neuroscientists. * Future: We are aggregating interviews from a large pool of neuroscientists asking them what they envisage for the future of neuroscience. SciPle algorithm will parse those interviews and produce a visualization of the most likely future scenario of the neuroscience field. * Connectivity: We are developing algorithms that will allow profiling of neuroscientists (on the basis of their interviews) and track links (common views on the future and present of neuroscience) between scientists. 1. You send us back SciPle's questionnaire 2. We discover who are the fellows who share the same vision as yours on the future of neuroscience 3. Meet your fellows at conferences and find out whether SciPle was right!
EPITARGET - Targets and biomarkers for antiepileptogenesis
A multidisciplinary project focused on the process leading to epilepsy, epileptogenesis, in adults. Their main hypothesis is that there are combinations of various causes, acting in parallel and/or in succession, that lead to epileptogenesis and development of seizures. Their central premise and vision is that a combinatorial approach is necessary to identify appropriate biomarkers and develop effective antiepileptogenic therapeutics. The project will focus on: * identifying novel biomarkers and their combinations for epileptogenesis after potentially epileptogenic brain insults in clinically relevant animal models, such as traumatic brain injury (TBI) and status epilepticus (SE); * exploring multiple basic mechanisms of epileptogenesis and their mutual interactions; * and translating these findings towards the clinic by validating biomarkers in human samples accessible to the consortium.
Image-Based Meta-Analysis toolbox for SPM. Implementation of z-based statistics: Fisher's, Stouffer's.
International Association for the Exchange of Students for Technical Experience
An independent, non-profit and non-political student exchange organization that provides students in technical degrees (primarily Science, Engineering and the applied arts) with paid, course-related, training abroad and employers with highly skilled, highly motivated trainees, for long or short term projects.
Consortium for Reliability and Reproducibility
Consortium for Reliability and Reproducibility (CoRR)
Consortium that has aggregated resting state fMRI (R-fMRI) and diffusion imaging data from laboratories around the world, creating an open science resource for the imaging community, that facilitates the assessment of test-retest reliability and reproducibility for functional and structural connectomics. Given that this was a retrospective data collection, they have focused on basic phenotypic measures that are relatively standard in the neuroimaging field, as well as fundamental for analyses and sample characterization. Their phenotypic key is organized to reflect three classifications of variables: 1) core (i.e., minimal variables required to characterize any dataset), 2) preferred (i.e., variables that were strongly suggested for inclusion due to their relative import and/or likelihood of being collected by most sites), and 3) optional (variables that are data-set specific or only shared by a few sites). CoRR includes 33 datasets consisting of: * 1629 Subjects * 3357 Anatomical Scans * 5093 Resting Functional Scans * 1302 Diffusion Scans * 300 CBF and ASL Scans
A not-for-profit membership organization and educational charity that facilitates collaborative data sharing projects in the pharmaceutical, cosmetics and chemistry-related industries specializing in the development of expert computer systems for toxicity and metabolism prediction. They provide a number of extensive and continually updated knowledge bases and the software needed to interrogate them. Its charitable aims include the sponsorship of activities that advance scientific knowledge and understanding and they regularly support computational chemistry events and initiatives that are of interest to Lhasa Limited members and the wider scientific community. All applications for sponsorship will be considered on their individual merits.
Software for an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.
Minimal Information for a Phylogenetic Analysis
Central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard.
Neuroflocks is an unique tool to navigate tweets from the past SfN meeting and find out the hot topics tweeted during the conference (SfN-2010). We have collected all tweets using the hashtag #sfn10 and made them browsable via a simple visual search interface. Type in the word you want to search for and only tweets containing that word will light up! You can click on single tweets, browse the tweet content, click on the Twitter user and find new Neuroscience-enthusiast twitterers! You can also find out what was really HOT during the conference (Re-Tweeted tweets, RT have been color coded). Moreover, the tweets follow a time gradient from the inside out: the spiral's center contains tweets from the beginning of the meeting while tweets on the outside of the spiral were tweeted at the end of the meeting. Enhanced versions of neuroflocks are currently under development !!!
Sciencewise Expert Resource Centre for Public Dialogue In Science and Innovation
Sciencewise-ERC is the UK's national center for public dialogue in policy making involving science and technology issues. It provides co-funding and specialist advice and support to Government departments and agencies to develop and commission public dialogue activities in emerging areas of science and technology. It consists of a comprehensive online resource of information, advice and guidance together with a wide range of support services aimed at policy makers and all the different stakeholders involved in science and technology policy making, including the public. Sciencewise-ERC works with central Government and its agencies, and executive, advisory and non-departmental public bodies. Some of the Government departments include the Department for Environment, Food and Rural Affairs (Defra), the Department of Energy and Climate Change (DECC) and most recently HM Treasury.
A for-profit health data-sharing platform that can transform the way patients manage their conditions, change the way industry conducts research and improve patient care. PatientsLikeMe aligns patient and industry interests through data-sharing partnerships. They work with trusted nonprofit, research and industry Partners who use this health data to improve products, services and care for patients. They take the information patients share about their experience with the disease and sell it to their partners (i.e., companies that are developing or selling products to patients). These products may include drugs, devices, equipment, insurance, and medical services. Except for the restricted personal information entered when registering for the site, participants should expect that every piece of information submitted (even if it is not currently displayed) may be shared with their partners and any member of PatientsLikeMe, including other patients. They do not rent, sell or share personally identifiable information for marketing purposes or without explicit consent. Because they believe in transparency, they tell members exactly what they do and do not do with their data. Patients have the opportunity to share both personal stories and health data about their conditions to help uncover great ideas and new knowledge. By sharing information on the site, they can put their disease experiences in context and find answers to the questions they have. Every partnership we develop must bring them closer to aligning patient and industry interests. Their end goal is improved patient care and quality of life.
November 2020, Onyx merged with Legacy Acquisition Corp. to form PARTS iD, Inc. Our data intelligence, integrated platforms, product cataloging, digital marketing expertise, and virtual warehousing have ensured our continued leadership in the competitive marketplace.
Product development company focused on therapeutic products and diagnostic devices targeting misfolded protein diseases. On July, 2015 the company name was changed to ProMIS Neurosciences, Inc.
Organization that develops methods, works with leaders and teams, and provides education and training to help organizations improve their products and services and to build their capability for on-going improvement.
Minimal Standard Terminology of Digestive Endoscopy
Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy. Bethesda, MD: National Library of Medicine, 2001.
Subsidiary of Eli Lilly and Company who develops new molecular imaging agents capable of changing the medical management of significant, chronic human diseases by identifying the first stages of pathological change, potentially assisting in earlier diagnosis, and better management and development of new therapies. The company has developed a radioactive tracer called florbetapir (18F). Florbetapir can be used to detect beta amyloid plaques in patients with memory problems using positron emission tomography (PET) scans, making the company the first to bring to market an FDA-approved method that can directly detect this hallmark pathology of Alzheimer's disease.
German multinational chemical company and largest chemical producer in the world. BASF Group comprises subsidiaries and joint ventures in more than 80 countries and operates six integrated production sites and 390 other production sites in Europe, Asia, Australia, the Americas and Africa.
Foldit is a revolutionary new multiplayer online computer game that engages non-scientists in solving hard prediction problems, enabling you to contribute to important scientific research. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy. Here are the basic principles to keep in mind when folding proteins. Your score on each protein is based on how well you do with these three things: # Pack the protein: The smaller the protein, the better. More precisely, you want to avoid empty spaces (voids) in the structure of the protein where water molecules can get inside. So you want the atoms in the protein to be as close together as possible. Certain structures, such as sheets, will even connect together with hydrogen bonds if you line them up right and get them close together. This is also good. Key word: Compact. # Hide the hydrophobics: Hydrophobics are the sidechains that don't want to be touching water, just like oil or wax. Since most proteins float around in water, you want to keep the hydrophobics (orange sidechains) surrounded by as many atoms as possible so the water won't get to them. The other side of this rule is that hydrophilics (blue sidechains) do want to be touching water, so they should be exposed as much as possible. Key word: Buried. # Clear the clashes: Two atoms can't occupy the same space at the same time. If you've folded a protein so two sidechains are too close together, your score will go down a lot. This is represented by a red spiky ball (clash) where the two sidechains are intersecting. If there are clashes, you know something is wrong with your protein. So make sure everything is far enough apart. Key word: Apart. The current series of Science Puzzles, the Grand Challenges, are meant to generate the evidence needed to prove that human protein folders can be more effective than computers at certain aspects of protein structure prediction. That's what all the puzzles in Foldit are about right now: predicting the structure of a protein based on its amino acid sequence. The three rules mentioned above describe the characteristics of correct protein structures.
Pennsylvania-based company supporting pharmaceutical and medical device innovation with imaging core lab, EDC, IVR / IWR, CTMS, and supply chain forecasting and optimization. Its initial service was medical imaging for clinical trials. It is used to capture, collect, control quality, provide blinded reading services to the final delivery to the sponsor company and to the FDA or EMEA if required for medical images in a wide range of imaging modalities. (Wikipedia)
Global biotechnology company based in Cambridge, Massachusetts, specializing in discovering, developing, and delivering important therapies for the treatment of neurodegenerative, hematologic and autoimmune diseases to patients worldwide.
Company that provides testing and manufacturing services to pharmaceutical and biopharmaceutical companies that span the product cycle from early pre-clinical development to licensed production.
Charles River Laboratories International Inc.
Commercial organism provider selling mice, rats and other model animals. American corporation specializing in a variety of pre-clinical and clinical laboratory services for the pharmaceutical, medical device and biotechnology industries. It also supplies assorted biomedical products and research and development outsourcing services for use in the pharmaceutical industry. (Wikipedia)
A computationally-oriented biotech company located in Barcelona that is focused on the drug discovery and development areas. Chemotargets' goal is to help the biopharma industry fast-forward the process of bringing new medicines to market, speeding up drug discovery and development programs and making them more cost-efficient. To this end, they have designed, and continue to develop, an integrated technology platform involving a broad spectrum of cutting-edge computational methodologies.
An American multinational energy corporation headquartered in San Ramon, California, and active in more than 180 countries, that is engaged in every aspect of the oil, gas, and geothermal energy industries, including exploration and production; refining, marketing and transport; chemicals manufacturing and sales; and power generation. Chevron is one of the world's largest oil companies; as of 2013, it ranked third in the Fortune Global 500-2014 list of the world's largest companies. (Adapted from Wikipedia)
University of Geneva; Geneva; Switzerland
Jmol: an open-source Java viewer for chemical structures in 3D
An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component.
A family of databases covering the 3D features of monos, di, oligo, polysaccharides, glycosyltransferases, lectins, monoclonal antibodies and glycosaminoglycan-binding proteins. Other databases are also made available that completes the picture of glycan 3D structure decoding. that are made freely available to the scientific community. A search engine has been developed that scans the full content of all the data bases for queries related to sequential information of the carbohydrates or other related descriptors. This database ensemble offers a unique opportunity to characterize the 3D features that a given oligosaccharide can assume in different environments.
A non-governmental, non-profit public database for paleontological data providing researchers and the public with information about the entire fossil record. It has been organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. Its purpose is to provide global, collection-based occurrence and taxonomic data for organisms of all geological ages, as well data services to allow easy access to data for independent development of analytical tools, visualization software, and applications of all types. The Database's broader goal is to encourage and enable data-driven collaborative efforts that address large-scale paleobiological questions. Paleontological data files are accepted for upload. However, PaleoBioDB needs some basic data types to be included in order to perform an upload. The Application Programming Interface (API) gives scientists, students, and developers programmatic access to taxonomic, spatial, and temporal data contained within the database.
Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions.
Minimum Information About a Simulation Experiment
A set of guidelines (community effort) suitable for use with any structured format for simulation experiments to identify the Minimal Information About a Simulation Experiment necessary to enable the reproducible simulation experiments. The Guidelines list the information that a modeller needs to provide to enable the execution and reproduction of a numerical simulation experiment, derived from a given set of quantitative models. MIASE is designed to help modelers and software tools to exchange their simulation settings and to foster collaboration. In 2011, he MIASE guidelines were accepted by researchers from 19 different institutes.
Assembling the Tree of Life: Phylogeny of Spiders
Project whose aim is to produce a robust phylogeny of all the deepest branches within a mega-diverse group, the spiders, by combining a massive amount of newly generated comparative genomic data with a substantial set of new and re-assessed data on morphology and behavior. They propose to collect a huge amount of genomic information in order to test and improve the results achieved by over 50 detailed morphological cladistic analyses conducted by more than 30 investigators during the past 15 years. The insignificant amount of genomic work to date on spiders has been uncoordinated and of little utility for broad-scale phylogenetic investigation. The advent of high-throughput DNA sequencing, however, makes it feasible to examine substantial parts of the genome across a dense sampling of spider taxa. They propose to sequence at least 50 loci (genome samples of 500-1,000 or more base pairs that can be sequenced as single pieces in both directions simultaneously) for representatives of at least 500 genera of spiders and their closest relatives (the whipscorpion orders Amblypygi, Uropygi, and Schizomida). These genera will be carefully selected by a sampling strategy designed to maximize the resolution of deep branches within spider phylogeny, and will purposefully include all the previously most-favored study organisms of ethologists, ecologists, physiologists, and developmental and molecular biologists, thus integrating and contextualizing their research. Data matrices will be produced that combine the new genomic data with a new, comprehensive survey of morphological and behavioral homologies, offering a unique index to all comparative data on one large group. New computer software, designed in large part by members of their group and using massively parallel processing to achieve supercomputing capability, makes such analyses feasible.
A non-governmental organization aimed at raising awareness of all forms of dementia by creating a common European platform through co-ordination and co-operation between Alzheimer organizations throughout Europe. Alzheimer Europe is also a source of information on all aspects of dementia.
Since 1990 Telethon, along with millions of Italians, has stepped up to the challenge of beating muscular dystrophy and the other genetic diseases. It is a marathon against time, because there are many people who live with these rare disorders, and the resources to deal with them have to be carefully measured out because there is not much public or private funding invested in this field of research, and the path to finding cures is often long and tortuous. The foundation In order to guarantee as much research funding as possible into muscular dystrophy and other genetic diseases, the Telethon team works throughout the year and has adopted a management system for the donated funds that is strict and efficient. For every euro raised by Telethon, about eighty euro cents reach the cutting edge laboratories and excellent research centers. Scientific area The selection of the best research projects, the funding of dedicated researchers and the foundation and maintenance of its research institutes make Telethon a point of Italian excellence in the world. Along with recognition from the international scientific community, Telethon's world of research is the biggest ally of all the people who live with muscular dystrophy or other genetic disorders every day. The online database provides complete information about the projects funded by Telethon from 1991 to the present. The archive contains information about all the Foundation's efforts in the field of biomedical research. In addition to a search by disease, it is possible, using the advanced search function, to interrogate the database by groups of disorders, by the name of a researcher or research institute, or by the town, province, or region where projects are based. The use of another search filter makes it possible to check which research projects are ongoing and which have come to an end.
An on-demand archiving system for webreferences (cited webpages and websites, or other kinds of Internet-accessible digital objects), which can be used by authors, editors, and publishers of scholarly papers and books, to ensure that cited webmaterial will remain available to readers in the future. Users make a local copy of the cited webpage / webmaterial and archive the cited URL to enable readers permanent access to the cited material. If cited webreferences in journal articles, books etc. are not archived, future readers may encounter a 404 File Not Found error when clicking on a cited URL. It's free and takes only 30 seconds. A WebCite-enhanced reference is a reference which contains - in addition to the original live URL (which can and probably will disappear in the future, or its content may change) - a link to an archived copy of the material, exactly as the citing author saw it when he accessed the cited material.
A question answering web site and forum that focuses on neuroinformatics and neuroscience. Initially conceived by Istvan Albert's highly successful BioStar website within the Bioinformatics community, NeuroStars is born as an experiment to engage the Neuroinformatics community after some unfruitful attempts in StackExchange's Area51. Posts that are detailed and specific, written clearly and simply are welcome.
NeuroVault - A public repository of unthresholded brain activation maps
Data repository where researchers can publicly store and share unthresholded statistical brain activation maps produced by MRI and PET studies.
An information management framework for comprehensive ion channel information. It is a knowledge base system centered on genetically expressed ion channel models and it encourages researchers of the field to contribute, build and refine the information through an interactive wiki-like interface. It is web-based, freely accessible and currently contains 187 annotated ion channels with 50 Hodgkin-Huxley models (September 2014). Channelepdia provides an ideal platform to collectively build ion channel knowledge base by accommodating both structured and unstructured data. The current version of Channelpedia contains the following sections : Introduction, Genes, Ontologies, Interactions, Structure, Expression, Distribution, Function, Kinetics and Models. Newly published literature related to ion channels is automatically queried every week from PubMed and added to respective categories. Currently, Channelpedia contains ~180,000 abstracts related to ion channels from Pubmed.
A private subsidiary of the French National Institute of the Health and Medical Research (Inserm), dedicated to technology transfer (from invention disclosure to industrial partnership). It manages European and International research projects, supports large scale projects in epidemiology and public health. It has run a proof of concept fund. The company is also committed to seed financing in the biotech sector, through its dedicated seed fund company Inserm Transfert Initiative. www.inserm-transfert.fr
A collective international initiative to construct a framework intended to implement tools to recognize and measure the use of bioresources for research. A BRIF would make it possible to trace the quantitative use of a bioresource, the kind of research using it and the efforts of the people and institutions that construct it and make it available. It targets 4 main objectives that are currently ongoing: # the assignment of a unique and persistent identifier to the bioresource by an independent international institution or body, # the construction of the BRIF algorithm on the basis of a number of agreed parameters for the follow-up of the use of bioresources, # the modification of editorial guidelines in order to integrate coherently the citation and acknowledgement of the bioresources used in scientific articles and # the assessment of incentives for bioresources access and sharing policies.
Biobank Standardisation and Harmonisation for Research Excellence
Biobank Standardisation and Harmonisation for Research Excellence in the European Union
A consortium of leading biobanks and international researchers from all domains of biobanking science to ensure the development of harmonized measures and standardized computing infrastructures enabling the effective pooling of data and key measures of life-style, social circumstances and environment, as well as critical sub-components of the phenotypes associated with common complex diseases. The overall aim is to build upon tools and methods available to achieve solutions for researchers to use pooled data from different cohort and biobank studies. This, in order to obtain the very large sample sizes needed to investigate current questions in multifactorial diseases, notably on gene-environment interactions. This aim will be achieved through the development of harmonization and standardization tools, implementation of these tools and demonstration of their applicability. BioSHaRE researchers are collaborating with P3G, the Global Alliance for Genomics and Health, IRDiRC (International Rare Diseases Research Consortium), H3Africa and other organizations on the development of an International Code of Conduct for Genomic and Health-Related Data Sharing. A draft version is available for external review. Generic documents have been prepared covering areas of biobanking that are of major importance. SOPs have been finalized for blood withdrawal (SOPWP5001blood withdrawal), manual blood processing (SOPWP5002blood processing), shipping of biosamples (SOPWP5003shipping) and withdrawal, processing and storage of urine samples (SOPWP5004urine).
Open source project providing a collaborative layer of knowledge over academic publications by allowing users to share real-time highlights and annotations. Participate in open discussion that drives ideas and academia forward. It provides a supportive space to learn about research and ask questions of peers and experts. Follow authors and other users to understand their perspectives, make connections, and discover new ideas.
THIS RESOURCE IS NO LONGER IN SERVICE; REPLACED BY NEPHROSEQ; A growing database of publicly available renal gene expression profiles, a sophisticated analysis engine, and a powerful web application designed for data mining and visualization of gene expression. It provides unique access to datasets from the Personalized Molecular Nephrology Research Laboratory incorporating clinical data which is often difficult to collect from public sources and mouse data. Please note, Nepromie has become Nephroseq in 2016.. http://dx.doi.org/10.1016/j.kint.2016.01.015.
EURORDIS is a non-governmental patient-driven alliance of patient organizations and individuals active in the field of rare diseases, dedicated to improving the quality of life of all people living with rare diseases in Europe. It is a not-for-profit organization and represents more than 479 rare disease organizations in 45 different countries (of which 25 are EU Member States), covering more than 4,000 rare diseases. It is therefore the voice of the 30 million patients affected by rare diseases throughout Europe. EURORDIS aims at improving the quality of life of people living with rare diseases in Europe through advocacy at the European level, support for research and drug development, networking patient groups, raising awareness and other actions designed to fight against the impact of rare diseases on the lives of patients and family. EURORDIS' training programs and resources are designed to strengthen the capacity of rare disease patients' representatives. Training empowers patients' representatives to advocate effectively for rare diseases at both the local and EU level. Key issues affecting patients of Rare Diseases on which we actively work: * Sustaining rare diseases as an EU public health priority * Making Rare Diseases A Public Health Priority In All Member States * Rare Diseases: An International Public Health Priority * Improving Access To Orphan Drugs * Improving Access To Quality Care * Promoting cross-border healthcare and patient mobility * Bridging Patients And Research * Genetic testing and newborn screening
Charity that aims to significantly reduce the number of asthma deaths, hospitalizations and living lives compromised by asthma helping over five million people with asthma in the UK through research, campaigning, health promotion and engagement with the asthma community. Asthma UK is a significant investor in asthma research within the UK and to date has invested over 50 million pounds into research for better treatments and ultimately a cure for asthma.
A human writeable and human readable language to express the information required to describe pharmacometric models and tasks using these models. The specification of the MDL offers a standard for coding models and associated objects and defining how to execute tasks. The standards for defining MDL objects are independent of any specific target modelling software. This allows the user to specify the model in a consistent manner and facilitates understanding of the model and associated tasks, regardless of the software used to build the model. New modelling applications may take advantage of the standard without having to re-invent how to describe common modelling processes.
Collection of structures and annotations of biologically relevant lipids that contains unique lipid structures. Structures of lipids from : LIPID MAPS Consortium's core laboratories and partners; lipids identified by LIPID MAPS experiments; biologically relevant lipids manually curated from LIPID BANK, LIPIDAT, Lipid Library, Cyberlipids, ChEBI and other public sources; novel lipids submitted to peer-reviewed journals; and computationally generated structures for appropriate classes. All the lipid structures adhere to the structure drawing rules proposed by the LIPID MAPS consortium. A number of structure viewing options are offered: gif image (default), Chemdraw (requires Chemdraw ActiveX/Plugin), MarvinView (Java applet) and JMol (Java applet). All lipids have been classified using the LIPID MAPS Lipid Classification System. Each lipid structure has been assigned a LIPID MAPS ID (LM_ID) which reflects its position in the classification hierarchy. In addition to a classification-based retrieval of lipids, users can search using either text-based or structure-based search options.
Unit studying human cognition and the brain with about 90 researchers and postgraduate students investigating topics such as attention, emotion, language and memory. They are developing new treatments for depression, improving hearing through cochlear implants, and helping children to overcome memory problems. With a large collection of scientists engaged in both basic and translational research on the mind and brain, the Unit provides an exceptional training and academic environment that benefits postgraduate students and researchers at all levels. A significant part of their research makes use of brain imaging and they have excellent on-site facilities for magnetic resonance imaging (MRI) magnetoencephalography (MEG) and electroencephalography (EEG). They also have clinical facilities at Addenbrooke's Hospital. The Unit has close links both with the hospital and with Cambridge University.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9,2023. Project portal for a cross European study designed to find biomarkers, or tests, for Alzheimer's disease. Its objectives are to produce and improve experimental models of Alzheimer's for biomarker discovery and to identify a biomarker for Alzheimer's disease suitable for diagnosis, prediction, and monitoring disease progression for use in clinical trials and in clinical practice. The baseline dataset database was scheduled to be completed and locked in 2008 and become available to researchers by 2009. Requests to access the data will be reviewed by the scientific projects committee.
European Federation of Pharmaceutical Industries and Associations
Federation representing the pharmaceutical industry operating in Europe. Through its direct membership of 33 national associations and 40 leading pharmaceutical companies, it is the voice on the EU scene of 1,900 companies committed to researching, developing and manufacturing new medical treatments. In addition, it is active in partnering in EU Research programmes, such as the IMI (Innovative Medicines Initiative), Europe's largest public-private partnerships. They also work on corporate social responsibility initiatives with others healthcare stakeholders, such as patient groups and healthcare professionals. EFPIA has specialized committees and task forces focused on key areas of activity. EFPIA also includes two specialized groups focusing on vaccines and biotechnology, respectively: * Vaccines Europe (formerly European Vaccine Manufacturers, EVM) produces approximately 80% of vaccines used worldwide * European Biopharmaceutical Enterprises (EBE) harness biotechnology to develop approximately one-fifth of new medicines
Private research university in Rochester, New York. University grants undergraduate and graduate degrees, including doctoral and professional degrees.
A bio-pharmaceutical company with a focus on research and development of new targets & therapies against proliferative diseases. Its current development program is based on inecalcitol, a vitamin D receptor agonist being studied in three potential indications: * alone in chronic lymphocytic leukaemia * in combination with imatinib in chronic myeloid leukaemia * in prostate cancer, for use with current standards of care Hybrigenics'' research program investigates the action of enzymes called Deubiquitinating Enzymes (DUBs) in the recycling of onco-proteins and the utility of proprietary patented DUB inhibitors against various cancer indications. Hybrigenics Services, a Hybrigenics subsidiary, markets very specialized scientific services to researchers in all areas of life sciences who want to identify, validate and inhibit protein interactions in animal, plant or microbiological cells.
Organization that drives the development of disease-modifying treatments against Alzheimer's, Parkinson's, Diabetes and other protein misfolding disorders through two independently managed business units: * Contract Research: The in-vivo Contract Research Organization (CRO) helps its clients to assess the pharmacokinetics and -dynamics of their experimental treatments against Alzheimer's disease. The main focus is on efficacy testing of candidate drugs in reMYND's proprietary Alzheimer mouse models expressing the clinical APP-London allele as single transgene or in combination with clinical alleles of human PS1 and TAU. * Drug Discovery: The Drug Discovery and Development Unit (DDD) focuses on disease-modifying treatments against protein-misfolding disorders, such as Alzheimer's disease (tau), Parkinson's disease (-synuclein), and Diabetes. In addition, reMYND grants licenses and markets commercial kits of RadarScreen, a technology for rapid and cost-effective identification of genotoxic liabilities in early stage drug discovery. reMYND has been substantially supported by grants from IWT and from The Michael J Fox Foundation.
Consortium focused on identifying the foundational pathways responsible for the aging of the brain, with a focus on Late Onset Alzheimer's disease. They aim to identify the interactions through which the aging phenotype develops in normal and in disease conditions; modeling novel pathways and their evolutionary properties to design experiments that identify druggable targets. As early steps of neurodegenerative disorders are expected to impact synapse function the project will focus in particular on pre- or postsynaptic protein networks. The concept is to identify subsets of pathways with two unique druggable hallmarks, the validation of interactions occurring locally in subregions of neurons and a human and/or primate accelerated evolutionary signature. The consortium will do this through six approaches: * identification of interacting protein networks from recent Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) data, * experimental validation of interconnected networks working in subregion of a neuron (such as dendrites and dendritic spines), * inclusion of these experimentally validated networks in larger networks obtained from available databases to extend possible protein interactions, * identification of human and/or primate positive selection either in coding or in regulatory gene sequences, * manipulation of these human and/or primate accelerated evolutionary interacting proteins in human neurons derived from induced Pluripotent Stem Cells (iPSCs) * modeling predictions in drosophila and novel mouse transgenic models * validation of new druggable targets and markers as a proof-of-concept towards the prevention and cure of aging cognitive defects. The scientists will share results and know-how on Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) gene discovery, comparative functional genomics in mouse and drosophila models, in mouse transgenic approaches, research on human induced pluripotent stem cells (hiPSC) and their differentiation in vitro and modeling pathways with emphasis on comparative and evolutionary aspects. The four European small to medium size enterprises (SMEs) involved will bring their complementary expertise and will ensure translation of project results to clinical application.
Commercial organization that builds software for collection, management, and analysis of complex data, most typical in biomedical domain. The solutions are generic and can be used for multitude of uses and application domains.
Airway Disease Predicting Outcomes through Patient Specific Computational Modelling
Consortium focused on developing computer and physical models of the airway system for patients with asthma and chronic obstructive pulmonary disease (COPD). Developing accurate models will better predict how asthma and COPD develop, since current methods can only assess the severity of disease. They aim to bridge the gaps in clinical management of airways-based disease by providing reliable models that predict disease progression and the response to treatment for each person with asthma or COPD. A data management platform provides a secure and sustainable infrastructure that semantically integrates the clinical, physiological, genetic, and experimental data produced with existing biomedical knowledge from allied consortia and public databases. This resource will be available for analysis and modeling, and will facilitate sharing, collaboration and publication within AirPROM and with the broader community. Currently the AirPROM knowledge portal is only accessible by AirPROM partners.
Medical University of South Carolina; South Carolina; USA
Public medical school in Charleston, South Carolina. Opened in 1824 as small private college aimed at training physicians. One of the oldest continually operating schools of medicine in the United States and the oldest in the Deep South.
Consortium focused on making electronic health data more interoperable, both within and outside of Europe, with the intention to create, validate, and disseminate standard methods to test and certify electronic health solutions and services. In particular it will: Drive the adoption of recognized sets of profiles and underlying standards for eHealth interoperability, and improve the impact of the EU and International eHealth standards development process; Define and validate testing guidelines and common approaches on Interoperability Labelling and Certification processes at European and at National / Regional level. Four work packages were created to provide guidelines, recommendations and frameworks based on a set of use cases, related profiles and standards, Interoperability Quality Management System, testing guidelines and Certification process. All the deliverables will be presented for validation and promotion by organizing workshops across Europe.
Minimal Standard Terminology of Digestive Endoscopy - French
Minimal Standard Terminology of Digestive Endoscopy French
Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation, 2001
European Collaborative Project on Inflamation and Vascular Wall Remodelling in Atherosclerosis - AtheroRemo
Project targeting vulnerable plaques causing unexpected acute myocardial infarcts and sudden cardiac deaths by identifying and validating novel drug targets as well as devising and validating diagnostic tests. It has been designed to advance the present knowledge on the role of inflammatory remodeling in the different stages of atherosclerosis. It will also provide important knowledge for the development of strategies for prevention and clinical management of vascular diseases.
Consortium to generate complete catalogs of somatic mutations in 500 breast cancers, of the ER+ve HER2- subclass, under the International Cancer Genome Consortium model by high coverage, shotgun genome sequencing of both tumor and normal DNA. The strategy is to collect, store, review, quality control and extract DNA and RNA from breast cancer and normal tissues from 500 ER+, HER2- breast cancer cases which will be subjected to a coordinated series of genomic analyses including whole genome shotgun sequencing, genome-wide copy number analysis, mRNA expression analysis, miRNA expression analysis and genome-wide methylation analysis. A comprehensive catalogue of somatic mutations will be generated from each cancer. Somatic mutation catalogues from the 500 cancers will be analysed and integrated with expression and methylation data to identify novel cancer genes, characterize subverted biological pathways that are operative, describe patterns of somatic mutation and explore early translational applications of personalized somatic genomic data for patients with ER+, HER2- breast cancer. The results will impact the understanding of the causes and biology of breast cancer and will lead to major advances in detection, prevention and treatment in one of the most common diseases and causes of death in the developed world. The Consortium has completed a number of investigative exercises into the experimental protocols and technological practices relating to whole genome sequencing, epigenetics and transcriptomics including: * Completion of extensive testing of current RNA-seq protocol. * Designed and implemented a new, improved RNA-seq protocol which utilizes RNA samples regardless of their RNA Integrity Number. * Completed pilot testing of the Infinium 450k array and associated bi-sulfite sequencing. * Refined the whole genome sequencing library production protocols to produce more robust libraries. * Improved the primary variant-calling algorithms (for substitutions, insertions / deletions and rearrangements) * Developed new analytical algorithms to explore the resulting high-quality variants. As such, variant calling of whole genome sequencing data and secondary downstream analysis can begin in earnest in a trackable and automated fashion.
BetaBat - Development of novel treatment strategies based on knowledge of cellular dysfunction in diabetes
Development of novel treatment strategies based on knowledge of cellular dysfunction in diabetes
Development of novel treatment strategies based on knowledge of cellular dysfunction in diabetes (BetaBat)
Project that aims to develop new treatment strategies based on knowledge of cellular dysfunction in diabetes. They will perform a detailed organelle diagnosis based on both focused and systems biology approaches, which will provide the scientific rationale for the design of specific interventions to boost the capacity of beta cells and brown adipocytes to regain homeostatic control. They propose that only by understanding the complex molecular mechanisms triggering cellular dysfunction in diabetes, and by integrating this knowledge at the systems level, will it be possible to develop interventional therapies that protect and restore beta cell and (Brown adipose tissue) BAT function. The ultimate goal is to offer individual therapeutic choices based on both genetic information and organelle diagnosis.
Swiss Institute of Allergy and Asthma Research
Originally established as a research institute for tuberculosis, it now performs applied, basic research in the field of allergies and asthma. Research activities are focused on immune-pathological mechanisms of allergic, asthmatic and cutaneous inflammations and the structural basis and peculiarities of allergens, as well as development of novel tools for the diagnosis and treatment of allergic disease.
Ontology that provides a reference for describing an exercise in terms of functional movements, engaged musculoskeletal system parts, related equipment or monitoring devices, intended health outcomes, as well as target ailments for which the exercise might be employed as a treatment or preventative measure.
BIG Project - Big Data Public-Private Forum
A consortium working towards the definition and implementation of a clear strategy that tackles the necessary efforts of Big Data (in terms of research and innovation) while also providing supporting actions for the successful implementation of the Big Data economy. Building an industrial community around Big Data in Europe is the priority of this project, together with setting up the necessary collaboration and dissemination infrastructure to link technology suppliers, integrators and leading user organizations.
Biohybrid templates for peripheral nerve regeneration
Consortium with the goal of repairing damaged nerve trunks that will engage in the preclinical development of an artificial biohybrid nerve device for the regenerative treatment of traumatic injuries of peripheral nerves. Based on the extensive basic and clinical experience within this consortium the artificial nerve device will be developed together with standardized application and evaluation parameters. A key objective of this study is to generate a protocol that serves as a template for future clinical trials in the regenerative therapy of damaged peripheral nerves. The results of the multidisciplinary research will feed into the establishment of artificial biohybrid devices as stand alone alternatives to accepted standard procedures and tools. Furthermore, standardized application guidelines and evaluation parameters will be set up to enable continuous progress and evaluation of the outcome of clinical application.
A structured controlled vocabulary of the anatomy of mosquitoes.
Developing imaging technologies for therapeutic interventions in rare diseases
Developing imaging technologies for therapeutic interventions in rare diseases (BIOIMAGE-NMD)
Project whose objective is to deliver combined structural and molecular imaging biomarkers with proven utility for the detection of therapeutic effects in patients with rare neuromuscular diseases (NMD). The project has three specific objectives: # To develop a new generation of muscle diffusion Magnetic Resonance Imaging (MRI). This diffusion imaging technology will be used to augment a state of the art simultaneous MRI / Magnetic Resonance Spectroscopic Imaging (MRSI) protocol for quantitative muscle imaging. # To provide a proof of principle in Duchenne Muscular Dystrophy (DMD) that simultaneous MRI/MRSI can be used as a biomarker to monitor therapeutic efficacy in clinical trials in neuromuscular diseases. # To develop a novel simultaneous Positron Emission Tomography (PET)/MRI technology to advance innovative drug development programs for personalized medicines based on Antisense Oligonucleotide technology
Biomarker for Cardiovascular Risk Assessment in Europe
Biomarker for Cardiovascular Risk Assessment in Europe (BIOMARCARE)
EU funded consortium including over 30 partner from academia and industry. BiomarCaRE aims to determine the value of established and emerging biomarkers to improve risk estimation of cardiovascular disease in Europe. BiomarCaRE relies on an exceptional resource of large scale epidemiological cohorts with long term follow-up and available bio specimens based on the population of the MORGAM Project as well as several cardiovascular disease cohorts and clinical trials.
Foundation with aim of bringing together patients, the public and respiratory professionals to positively influence lung health and respiratory medicine. ELF aims to communicate respiratory science to those outside of the respiratory field, to ensure that people with lung diseases and the general public have a chance to influence respiratory research and guidelines at a European level.
Pedigree Plotting Program for the Pedfile Format (entry from Genetic Analysis Software)
BLUEPRINT - A BLUEPRINT of Haematopoietic Epigenomes
Consortium to further the understanding of how genes are activated or repressed in both healthy and diseased human cells with a focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukemic counterparts. They will generate at least 100 reference epigenomes and study them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. Reference epigenomes will be generated by state-of-the-art technologies from highly purified cells for a comprehensive set of epigenetic marks in accordance with quality standards set by International Human Epigenome Consortium (IHEC). Access to the data is provided as well as the protocols used to collect the different blood cell types, to perform the different types of epigenomic analyses, etc.). This resource-generating activity will be complemented by hypothesis-driven research into blood-based diseases, including common leukemias and autoimmune disease (Type 1 Diabetes), by discovery and validation of epigenetic markers for diagnostic use and by epigenetic target identification. Since epigenetic changes are reversible, they can be targets for the development of novel and more individualized medical treatments. The involvement of companies will energize epigenomic research in the private sector by the development of smart technologies for better diagnostic tests and by identifying new targets for compounds. Thus the results of the project may lead to targeted diagnostics, new treatments and preventive measures for specific diseases in individual patients, an approach known as "personalized medicine". The Blueprint Data Access Committee will consider applications for access to data sets stored in the European Genome-phenome Archive (EGA) when authorized to do so by the Blueprint consortium and the holders of the original consent documents. Access is conditional upon availability of samples and/or data and signed agreement by the researcher(s) and the responsible employing Institution to abide by policies related to publication, data disposal, ethical approval and confidentiality. At EBI, the ftp site with the data can be found. You can either opt to link to the track hubs yourself or you can add the track hub to a genome browser - UCSC or ENSEMBL. Also Meta Data files and README are available. The data can also be accessed via the BIOMART system.
CALLIOPE - Creating a European coordination network for eHealth interoperability implementation
Creating a European coordination network for eHealth interoperability implementation
Creating a European Coordination Network for eHealth Interoperability Implementation (CALLIOPE)
Consortium to act as a forum for the diversity of stakeholders in the implementation of electronic health systems. It comprises a dedicated forum where decision makers, implementers, professionals, patients and other stakeholders can share visions, experiences and good practices on how to establish interoperable eHealth services. The process of consensus-building has reached six main achievements. # Offering support to European decision-makers with regard to EU level actions on eHealth. # Enlarging active representation of EU and European Free Trade Association (EFTA) activities. CALLIOPE established a roster of 22 national members in 2010 # Enlarging active involvement of European eHealth stakeholder organizations. # Developing and validating an open working method among stakeholders # Creating a working collaboration method between the appropriate eHealth large-scale pilot(s) and a wider range of Member States & and sta-keholders CALLepSO collaboration # Building an eHealth Interoperability roadmapping process. A full iterative cycle of the Roadmapping process has been now completed and the second issue of the EU eHealth Interoperability Roadmap has been delivered.
Canadian Consortium on Neurodegeneration in Aging
Canadian Consortium on Neurodegeneration in Aging (CCNA)
Consortium that will be the premier research hub for all aspects of research involving neurodegenerative diseases that affect cognition in aging - including Alzheimer's disease. They will promote high impact, inter-institutional and interdisciplinary collaboration through a pan-Canadian approach, and will position Canadian researchers to lead and participate in a new wave of national and international initiatives with congruent goals. The consortium focuses research into the basic mechanisms of neurodegenerative diseases, accelerating the development of tools that can be used to assist in the diagnosis and treatment of the diseases. The intended outcome of these tools is to improve the quality of life and services patients with neurodegenerative diseases. As part of the Canadian contribution to the International Collaborative Research Strategy for Alzheimer's disease, the consortium brings together Canadian government agencies (federal and provincial), foundations, pharmaceutical companies, philanthropists and international stakeholders to identify if there are common causes and risk factors to neurodegenerative diseases. The consortium is focused on three themes: * Primary Prevention aimed at preventing the disease from developing * Secondary Prevention focused on delaying the clinical manifestations of the already developing disease * Quality of Life designed for helping individuals, caregivers and the health system in the context of a clinically developed disease.
The UK's leading dementia research charity that funds world-class, pioneering scientists at leading universities to find preventions, treatments and a cure for dementia.
Chemical Manufacturing Methods for the 21st Century Pharmaceutical Industries
Chemical Manufacturing Methods for the 21st Century Pharmaceutical Industries (Chem21)
A European public-private consortium examining ways to make chemical research and the pharmaceutical industry more sustainable and environmentally friendly with the aim of developing sustainable biological and chemical alternatives to finite materials, such as precious metals, which are currently used as catalysts in the manufacture of medicines. The project has looked at the industry and identified needs and barriers, and is now working to develop methods to navigate around them to reduce costs for companies and thus reduce prices for patients. Chem21 also involves an educational training component that will help instill the project's results in the next wave of scientists. The project has four focus areas that are driving it toward the desired impact on the 21st century pharmaceuticals industry: * New, more efficient catalyst classes made available for greening processes and the generation of novel molecules * Alternative methodologies clearly described to allow broader use * New modified microorganisms for preparing pharma building blocks disclosed * Training materials developed for driving longer-term innovation
Systematized Nomenclature of Medicine - International Version
Systematized Nomenclature of Medicine International Version
Ontology of systematized nomenclature of human and veterinary medicine: SNOMED International. Cote, Roger A., editor. Northfield (IL): College of American Pathologists; Schaumburg (IL): American Veterinary Medical Association, Version 3.5, 1998.
Collaboration on the optimisation of macromolecular pharmaceutical access to cellular targets
Collaboration on the Optimization of Macromolecular Pharmaceutical Access to Cellular Targets
Consortium to reduce delivery and targeting bottlenecks for developing novel innovative biopharmaceutical based medicines. The project aims to shed new light on the obstacles biopharmaceuticals (medicines based on biological molecules such as proteins, peptides or nucleic acids) need to overcome to get to where they are needed in the body. The team will then use this information to develop and validate biopharmaceutical formulations to deliver these novel drugs to their targets. By finding more effective ways of administering these biopharmaceutical drugs, and improving their ability to travel through the body to where they are needed, COMPACT will allow more patients to benefit from biopharmaceuticals. Furthermore, designing less invasive administration routes and reducing the dose (and therefore the side effects) and frequency of administration will help to improve patient compliance with treatments.
DDMoRe project to develop common standards and tools to allow scientists to share their models. Developed model repository which enables access to curated and shared knowledge for benefit of model informed drug discovery.
Modelling Description Language - Integrated Development Environment
Modelling Description Language Integrated Development Environment
Software framework within which files containing Modelling Description Language (MDL) code can be created and edited offering a user-friendly, customizable modelling experience including syntax highlighting and on-demand model formatting. MDL model development is enhanced by productivity features such as the support for templates (re-usable blocks of MDL code that can be parameterised for ease of inclusion in multiple models) and content assist (the automatic display of possible alternatives based on the current editing location in the model). Common operations are supported by wizards which provide a step-by-step guide through the necessary functionality, while an advanced validation engine immediately highlights any inconsistencies or errors detected in the model and offers a list of suggested options to correct the problem. The MDL-IDE includes in-built functionality to convert an MDL model into the equivalent NM-TRAN control stream (.ctl file). Organizationally, it can support multiple distinct projects within a workspace, offering a natural separation between disparate models but retaining the ability to switch between the models quickly and easily. Additionally a large main window with a tabbed layout allows multiple models to be open for editing or viewing simultaneously.
Commercial organization that manufactures Vacuum Electron Devices and Associated RF Circuits for Communications, Science, Radar, Industry & Directed Energy Applications. Other products include photo-detectors for scientific and medical applications and specialized material processing and plating services.
European Asthma Research and Innovation Partnership
European Asthma Research and Innovation Partnership (EARIP)
Consortium that convenes asthma experts from across Europe to define research gaps to reduce the impact of asthma. The project activities range from basic cell science research, to assessing and improving European healthcare systems. Their activities include workshops, prioritization exercises, consensus strategies, and the development and publication of a set of recommendations about what's needed to reduce asthma deaths and hospitalizations. The eventual goal is to have a comprehensive R&D roadmap for asthma. EARIP will target a number of asthma research areas to ensure a comprehensive overview of all current research strategies from across Europe is included in the project road map. These include: * Research into biological targets, aiming to discover new targets and better define the role of existing biological targets * Identify new systems, models and tools for phenotypic stratification * Develop better and more efficient healthcare systems across Europe * Define and develop new diagnostic tools * Assess and improve patient self-management systems and provide suggestions for how these can be developed * Identify how to establish a European Innovation Partnership (EIP) for the management of asthma * Establish a European research network of clinical asthma research facilities
European Federation of Allergy and Airways Diseases Patients Associations
European Federation of Allergy & Airways Diseases Patients Associations
European Federation of Allergy and Airways Diseases Patients' Associations
A non-profit network of allergy, asthma and Chronic Obstructive Pulmonary Disease (COPD) patients' organisations, representing 35 national associations in 22 countries and over 400,000 patients. They're dedicated to making Europe a place where people with allergies, asthma and COPD have the best quality care and a safe environment, live uncompromised lives and are actively involved in all decisions influencing their health. They work on behalf of patients to: * Promote awareness of allergies and airways diseases among policymakers and the general public. * Broaden our understanding of these conditions by increased collaboration between national patient associations. * Share knowledge and experience to beneficially educate both the public and EFA members. * Promote patient concerns and opinions within the European institutions and enable national patient associations to gain representation at EU level. * Improve their health and quality of life.
EBiSC - European Bank for induced pluripotent Stem Cells
European Bank for induced pluripotent Stem Cells
Consortium to address the increasing demand by researchers for quality-controlled, disease-relevant research grade induced Pluripotent Stem Cell (iPSC) lines, data and cell services by demonstrating an operational banking and distribution service of iPSC lines after 3 years and establishing subsequently for Europe a centralized, not-for-profit bank providing all qualified users with access to scalable, cost-efficient and customized products. The main facility will be at the Babraham Research Campus (Cambridge, UK) and will undertake cell expansion, QC and characterization. The European Cell Culture Collection (ECACC) of Public Health England (Department of Health, UK) will coordinate cell line distribution. The Fraunhofer IBMT (Saarbr��cken, Germany) will provide comprehensive operational back up. In a phased business strategy EBiSC will hot-start distribution of lines contributed by iPSC Centres in 2014, lines collected based on specified user demand, will reach full scale operations in 2016, and with extended funding will become self-sustaining as a not for profit banking operation by 2019. EBiSC will spearhead Europe in the international standardization of iPSC banking by forging collaborative links with similar endeavors in the USA and Asia. It will also provide training to encourage adoption and use of the bank. The project has up to one year after completion to disseminate intellectual property or data created by the project.
Organization that supplies undifferentiated, clinical grade, human pluripotent stem cell lines to the life science community, and works with academic, clinical and commercial colleagues to enable and facilitate the use of these high grade cells in the development of new reagents, drugs and cellular therapeutics. They also seek to drive the economic development of the stem cell sector in Scotland. Their products can act as a valuable tool in supporting clients' drug discovery, development and clinical research programmes.
Consortium that promotes the discovery of novel small molecule candidates suitable for subsequent optimization either to drug candidates or to high-quality pharmacological tools for the experimental validation of targets using open innovation and crowd sourcing. It is designed to provide best-in-class resources and funding-in-kind, to academics or small and medium enterprises (SMEs) who are working on promising biology targets or chemistry scaffolds. Screening of compounds to assess their activity is also funded and performed by the EU Lead Factory, with collaboration to help develop an Improved Hit List from the Qualified Hit List. They will provide collaborative screening of previously safeguarded, high quality corporate compounds. Around 300,000 compounds in the EFPIA Compound Collection, contributed by EFPIA members, will be screened against both commercially contributed biology targets and targets from public sources. The second phase of the consortium is to build a substantial new Public Compound Collection of around 200,000 compounds. Together, the EFPIA and Public compound collections will form a 500,000-strong Joint European Compound Collection. Target program owners and compound contributors will receive a Qualified Hit List (QHL) of up to 50 compounds complete with relevant information to help in the development of an Improved Hit List (IHL). Target program owners, will have exclusive access to threshold active compounds in their QHL. After the three-year exclusivity period, QHL/IHL information will be made public. Milestone payments are due if direct exploitation proceeds, not for research use. And owners and contributors will give EFPIA participants the right to submit a first bid (which they do not have to accept).
European Gram Negative AntiBacterial Engine
European Gram Negative Antibacterial Engine (ENABLE)
European Gram-negative Antibacterial Engine
Consortium working to advance the development of potential antibiotics against Gram-negative bacteria, such as Escherichia coli. The project creates and manages a drug discovery engine for testing and optimizing molecules that are still in the earlier stages of drug discovery but have the potential to become future drug candidates capable of treating resistant Gram-negative infections. The project will focus on the discovery and pre-clinical stages of drug development, as well as (potentially) phase 1 clinical trials. ENABLE will run several drug discovery programs in parallel and the consortium seeks external hit and lead programs to join, through a series of open calls during the project. Researchers who have interesting molecules will have the opportunity to collaborate with a diverse range of experts in microbiology, pharmacology and chemistry to help advance their molecule through the drug development process until it is an attractive candidate for clinical testing. Specifically, the project is working towards: # identifying three antibacterial lead molecules which, following extensive testing, have been identified as having promising antimicrobial activity; # identifying two antibacterial clinical candidate molecules # advancing at least one compound into preclinical and phase 1 clinical studies, i.e. early clinical safety testing in humans.
University of Cincinnati Research and Training in Cardiovascular Biology
University of Cincinnati Research Training in Cardiovascular Biology
UC Research and Training in Cardiovascular Biology
Our 24 faculty members approach the Research and Training in Cardiovascular Biology program from different subspecialties that include genetics, metabolism, development, cellular biology, systems biology, structural biology, biophysics, pharmacology, molecular biology, bioinformatics and biochemistry. While these subspecialties are clearly diverse, our faculty collaboratively leverages these areas toward the common goal of understanding cardiovascular disease from the gene all the way up to integrated organism function (systems biology). This diverse array of subspecialties provides a truly unique training environment that few centers can match. Another critical aspect of our training program is our steadfast commitment to a superior and nurturing training environment for our predoctoral trainees, postdoctoral trainees and clinician-scientists. Our training faculty are uniformly committed to monitoring our personnel for success in every way possible, to not only ensure their future placement in the academic ranks but to also build a stronger cardiovascular community around the country. The current National Institutes of Health-sponsored Research and Training in Cardiovascular Biology was instituted in 1978 by Arnold Schwartz, MD, PhD. This program has trained more than 120 scientists, who have pursued independent research careers and are holding prominent scientific positions worldwide. Our trainees have been distinguished as chairs of basic science departments, directors of centers or pharmaceutical companies, clinical directors and tenured faculty members in academic research. The overall emphasis continues to focus on integrative training and well-rounded knowledge of the fundamentals in biochemical, molecular, physiological and pharmacological underpinnings of cardiovascular disease. Dr. Schwartz has been a constant guiding force since the program was established. The University of Cincinnati, with Cincinnati Children's, has also developed a reputation as a leading center for the generation and analysis of genetically modified mouse models for interrogation of gene-disease relationships in the heart. This theme has been expanded to incorporate molecular genomics, proteomics and bioinformatics, as we continue to be among the leaders in the nation in molecular pathway analysis associated with single gene manipulations in the hearts of mice. Most faculty and trainees are using these approaches, but they are also well-versed in many other aspects of cardiovascular science, including excellence in basic physiology, pharmacology, biochemistry, structural biology and molecular biology. Thus, we are a rare conglomeration of faculty in which all aspects of cardiovascular biology are practiced, starting with cutting-edge molecular and genetic approaches, spanning more traditional cellular and whole animal approaches to build an integrated network of functional and disease-relevant data and extending to translational research incorporating cell therapy.
European Autism Interventions - A Multicentre Study for Developing New Medications
Consortium aiming to generate tools that will enhance understanding of autism spectrum disorders (ASD) and pave the way for the development of new, safe and effective treatments for use in both children and adults. For example, the team will gather samples from people bearing certain mutations associated with ASD; this will pave the way for the generation of cell lines that can be used to test treatments. Elsewhere, the researchers will advance the use of brain scans as a tool to boost ASD drug discovery and also identify which people with ASD might respond best to a given drug. The project will also create a pan-European network of clinical sites. As well as making it easier to run clinical trials, this network will create an interactive platform for those with ASD and professionals. By the end of the 5 year project they expect to provide novel validated cellular assays, animal models, new fMRI methods with dedicated analysis techniques, new PET radioligands, as well as new genetic and proteomic biomarkers for patient-segmentation or individual response prediction. They will provide a research network that can rapidly test new treatments in man. These tools should provide their EFPIA partners with an added competitive advantage in developing new drugs for ASD.
Consortium that aims to improve the efficiency of the medicine development process by better incorporating estimates of relative effectiveness into drug development and to enrich decision-making by regulatory authorities and health technology assessment (HTA) bodies through: * Bringing together regulators, HTA bodies, academics, companies, patients and other societal stakeholders; * Assessing existing processes, methodologies, and key research issues; * Proposing innovative (and more pragmatic) trial designs and assessing the value of information; * Proposing and testing innovative analytical and predictive modelling approaches; * Assessing operational, ethical, regulatory issues and proposing and testing solutions; * Creating new decision making frameworks, and building open tools to allow for the evaluation of development programs and use in the assessment of the value of new medicines; * Sharing and discussing deliverables with, among others, Pharmaceutical companies, regulatory authorities, HTA / reimbursement agencies, clinicians and patient organizations; * Developing training activities for researchers, decision makers and societal stakeholders in the public and private sector in order to increase knowledge about various aspects of relative effectiveness. The expected impact is that it will contribute to the knowledge base, particularly to inform clinical decision making and improve the efficiency of the R&D process. GETREAL will help to generate a consensus on best practice in the timing, performance and use of real life clinical studies in regulatory and reimbursement decision-making. It will also help to create a strong platform for the communication of results and for future discussions in this important area.
A non-profit collection of biological samples and detailed associated clinical data, designed to facilitate medical research into vitiligo, a devastating skin disease that is much neglected. They collect, store and analyze biological samples throughout the network of collaborators in 11 countries, using standard collection protocols and unified patient record, which are then made available to the scientific community and research organizations investigating pathogeneses, diagnostics, new treatments, and ultimately a cure for vitiligo. The core asset is a large collection of well-organized hair, blood, serum and DNA samples, integrated with comprehensive and anonymized patient records.
Mosquito Insecticide Resistance Ontology
Application ontology for entities related to insecticide resistance in mosquitos
IMIDIA - Innovative Medicines Initiative for Diabetes: Improving beta-cell function and identification of diagnostic biomarkers for treatment monitoring in Diabetes
Innovative Medicines Initiative for Diabetes
Consortium aiming to improve pancreatic beta-cell function and identification of diagnostic biomarkers for treatment monitoring in diabetes. It brings together academic teams, pharmaceutical companies, and a Small to Medium Enterprises (SMEs), which provides a unique blend of expertise and forms a strong basis for a successful enterprise to ultimately improve industrial competitiveness and Public Health in Europe. The program aims at delivering: * Novel tools for the study of human beta-cell development, function and survival; their modulation by potential therapeutic compounds; and for in vivo beta-cell imaging. * Biomarkers for the diagnosis and prognosis of beta-cell failure and for monitoring diabetes progression and treatment. * Knowledge on novel molecular pathways and sites that control beta-cell life & death as well as mass and function.
Cross-Pharmaceutical Investigator Databank
Consortium between several pharmaceutical companies to develop a database that shares clinical trial investigator information that each company has on file to reduce administrative burden for investigators and to increase visibility of qualified investigators to research sponsors. Hosted by a 3rd party, DrugDev, it is the one place where pharmaceutical companies can share investigator and site information and investigators can view, edit, and comment on their own information. Industry members will be able share information from their clinical trial management systems including investigator / site contact details, GCP training records, past trial participation, and recruitment history. Upon investigator opt-in, this information is used by each participating company to identify sites for upcoming studies; to help set recruitment targets and timelines; and to share start-up documents such as CV, GCP, and site profile forms. The Databank has grown to include nearly 180,000 investigators (May 2014) and is already bringing benefits to its member companies in identifying qualified investigators for their studies. It also reported the inclusion of 7,335 protocols and 50K sites, representing a patient population around 1.9M.
University of Manitoba; Manitoba; Canada
Project whose goal is to improve understanding of how potential drugs bind with their target, and develop methods and tools to allow researchers to study drug-target interactions with greater ease. These tools would help researchers to determine whether a drug candidate is likely to be safe and effective much earlier in the drug development process. The first goal of the team is to enhance understanding of binding kinetics; exactly how do small molecules interact with their targets? Ultimately, the project aims to develop a range of robust techniques, methods and models that could be easily incorporated into the drug development pathway and enable scientists and drug designers worldwide to reliably predict a molecule's kinetic properties (its "kinotype"). This information will allow drug developers to more easily determine the safety and efficacy of a molecule and will weed out ineffective or unsafe molecules earlier in the drug development process. Eventually, the project also hopes to raise awareness of the importance of considering the kinetic aspects of drug-target interactions throughout drug development.
Consortium that brings together the kidney community (patient advocacy groups, industry, government agencies, and professional organizations) to overcome existing challenges, including regulatory and nonregulatory barriers, and optimize the development and safety of products that impact kidney health including drugs, devices, biologics, and food products. The goals of the consortium are to: * Facilitate dialogue and research that informs regulatory processes with regard to the kidney health of patients being treated for kidney-related as well as other diseases. * Assess current medical therapies and diagnostics to identify areas in need of greater innovation and/or better defined regulatory pathways. * Develop innovative and efficient trial designs appropriate to answer the most important questions related to kidney health. * Establish expert consensus around common terminology and key definitions related to kidney health. * Develop approaches to the systematic collection of retrospective or prospective data, such as registries and/or global databases, and establishment of data standards. * Coordinate think tanks, public forums, educational exchanges, and other events to promote discussion and updates on topics in kidney health pertaining to drug, device, biologics, and food product development and evaluation. * Create transparent infrastructure and processes that facilitate collaboration and communication among the greater nephrology community and the FDA, including: * Seek input from all stakeholders (including nephrologists and other health professionals, patient groups, industry, the National Institutes of Health, the Centers for Medicare and Medicaid Services, the Health Resources and Services Administration, and other federal agencies). * Leverage previously conducted and ongoing clinical studies, research infrastructure, and databases. * Create an open and efficient mechanism for encouraging and objectively evaluating potential projects submitted to KHI. * Involve consortium members in the selection and execution of projects. * Establish systems to optimize post-market surveillance of products that affect kidney health, either intentionally or via adverse drug reactions. * Author journal articles and white papers regarding key issues, describing opportunities and challenges and proposing solutions, as well as promoting execution of these solutions.
Mechanism based Integrated systems for the Prediction of Drug Induced Liver Injury
Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Injury
Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Injury (MIP-DILI)
Consortium that brings together Europe's top industrial and academic experts to develop new tests that will help researchers detect potential liver toxicity issues much earlier in drug development, saving many patients from the trauma of liver failure. The team aims to deepen the understanding of the science behind drug-induced liver injury, and use that knowledge to overcome the many drawbacks of the tests currently used. A major focus will be on a systematic and evidence-based evaluation of both currently available and new laboratory test systems, including cultures of liver cells in one-dimensional and three dimensional configurations. The project will also develop models that take into account the natural differences between patients. This is important because factors such as certain genes, the liver's immune response, and viral infections have all been associated with an increased risk of DILI. The project will seek to address the current lack of human liver cells available to researchers by using induced pluripotent stem cells (iPSCs) generated from patients who are particularly sensitive to DILI. Another strand of the project will develop computer models to unravel the complex, often inter-related mechanisms behind DILI. Finally, the team will assess how accurate the results of laboratory tests are at predicting actual outcomes in patients.
A global organization that helps Philips introduce innovations that improve people's lives by providing technology options for innovations in the area of health and well-being, targeted at both developed and emerging markets. Positioned at the front-end of the innovation process, they work on everything from spotting trends and ideation to proof of concept and - where needed - first-of-a-kind product development.
NEWMEDS - Novel Methods leading to New Medications in Depression and Schizophrenia
Novel Methods leading to New Medications in Depression and Schizophrenia
Consortium that will develop new models and methods to enable novel treatments for schizophrenia and depression including three important missing tools that will facilitate the translation of scientific findings into benefits for patients. The project will focus on developing new animal models which use brain recording and behavioral tests to identify innovative and effective drugs for schizophrenia. The project will develop standardized paradigms, acquisition and analysis techniques to apply brain imaging, especially fMRI and PET imaging to drug development. It will examine how new genetic findings (duplication and deletion or changes in genes) influence the response to various drugs and whether this information can be used to choose the right drug for the right patient. And finally, it will try and develop new approaches for shorter and more efficient trials of new medication - trials that may require fewer patients and give faster results.
DepressionTools.org Clinical Significance Calculator
Online instrument that estimates whether a biomarker predicting outcome of depression treatment is likely to be clinically significant.
Pharmacological Imaging and Pattern Recognition toolbox
Pharmacological Imaging and Pattern Recognition
Software toolbox designed to provide machine learning methods for pre-processed imaging data allowing for two (or more) class classification in the context of drug development. The Toolbox includes implementations of Gaussian Process Classification, Support Vector Machines, Ordinal Regression and Sparse Multinomial Logistic Regression for fMRI, Structural and ASL imaging data.
A web-based tool to screen for duplicate patients in clinical trials within and across studies, sponsors and therapeutic areas.
orbito - Innovative Tools for Oral Biopharmaceutics
Project that aims to increase understanding of how orally-administered drugs are taken up from the gastrointestinal tract into the body, and apply this knowledge to create new laboratory tests and computer models that will better predict the performance of these drugs in patients over a range of clinically relevant conditions. The integration of in vitro and in silico approaches will provide a biopharmaceutics toolkit, validated using clinical data, to accelerate drug development. Ultimately, the project will help to facilitate and speed up the formulation development process and significantly reduce the need for animal experiments in this area as well as for human clinical studies in the future. For patients, the main benefit will be in the form of high quality medicines where the dose required is well calculated and is released in a way that consistently provides an optimal clinical effect.
A three-member pharmaceutical industry consortium that aims to provide a new platform to improve access to information about clinical trials for patients and providers. The platform aims to enhance the existing clinicaltrials.gov by providing more detailed and patient-friendly information about available trials and embedding a machine-readable target health profile to improve the ability of healthcare software to match individual health profiles with applicable clinical trials. Using clinicaltrials.gov as its foundation and Eli Lilly' '''s Application Programming Interface (API), the consortium is focused on creating an open platform to make this data more amenable to patients and providers, as well as creating an opportunity to integrate a patient' '''s electronic health record into the clinical trial matching service. This feature will allow patients to search for trials using their own Blue Button data. The following features are planned add-ons to clinicaltrials.gov: * Target Profile is a machine readable query, that can be executed against an electronic file (or record) with patient health data such as an Electronic Health Record (EHR), an Electronic Medical Record (EMR) or Personally Controlled Health Record (PCHR) * Augmented Content is public, IRB approved information about the study that has not been published on clinicaltrials.gov, and that is shared with / targeted for patients with a matching Target Profile. The following are the incremental goals of the consortium: * Advancement of the Lilly API platform to support read/write interaction and additional data objects and information. * The initial 3 sponsor organizations - Lilly, Pfizer and Novartis - will upload Target Profiles for a select set of clinical trials. A Target Profile is a machine interpretable description of the characteristics of patients who may qualify for that trial i.e. a query that can be executed against a patient' '''s electronic health record or personal health record. Additionally, sponsors of clinical research studies will also be able to upload Augmented Content to the Lilly Platform to supplement information on clinicaltrials.gov with additional, patient-focused information about the study, e.g., a study brochure and practical information on how to contact investigational sites. * A matching service, developed by Corengi, will compare Target Profiles to a de-dentified personally controlled health record (PCHR), represented by patient' '''s Blue Button Plus CCDA XML document. * Integration into a patient community platform from Avado for providing the patient PCHR and presenting the results of the match service. The patient will be able to explore the respective matching studies for additional information and next steps such as contacting a nearby investigator clinic or hospital. The first demo of the prototype was made available on June 2014, built on a database of anonymized patient health records from different clinical research studies sponsored by Lilly, Novartis, and Pfizer. Other website: http://portal.lillycoi.com/
Prediction of cognitive properties of new drug candidates for neurodegenerative diseases in early clinical development
Project aiming to tackle bottlenecks in Alzheimer' '''s disease research and drug discovery by developing and validating new tools to test candidate drugs for the treatment of symptoms and disease in a faster and more sensitive way. They will provide the tools needed to define more precisely the potential of a drug candidate, reduce the development time of new medicines and thus accelerate the approvals of promising new medicines. By bringing together databases of previously conducted clinical trials and combining the results from blood tests, brain scans and behavioral tests, the scientists will develop a ' '''signature' ''' that gives more accurate information on the progression of the disease and the effect of candidate drugs than current methods do. The scientists will conduct parallel studies in laboratory models, healthy volunteers and patients in order to better predict good new drugs as early as possible. This will enable them, for instance, to find out how memory loss in Alzheimer' '''s disease can be simulated in healthy volunteers, for example with sleep deprivation or drugs that temporarily affect the memory, in order to test the effect of candidate-medicines early in the drug development process.
Ontology of experimental design for high-throughput mouse analysis pipelines.
Consortium to develop efficient and safe strategies for the production of clinical-grade protein pharmaceuticals in plants, and to define the procedures needed for the production of these proteins in compliance with the strict regulatory standards that govern the manufacture of all pharmaceuticals. Ultimately the consortium aimed to take a candidate product all the way through the development pipeline culminating in a phase I human clinical trial. The consortium has a wide range of expertise spanning the areas of molecular biology, plant biology, immunology, recombinant protein expression technology, vaccinology, and plant biotechnology. The objectives listed at the beginning of the Pharma-Planta project are as follows: # To produce a recombinant pharmaceutical molecule in transgenic plants, which will be developed through all regulatory requirements, GMP (good manufacturing practice) standards and pre-clinical toxicity testing. This will then be evaluated in Phase I human clinical trials. # To develop robust risk assessment practices for recombinant pharmaceutical molecules produced in plants, based on health and environmental impact, working with regulatory authorities within the EU as well as public groups to ensure that the production systems are as safe and as acceptable as possible, and that they comply with all biosafety regulations. # To define and carry out a coordinated program for securing and managing intellectual property that will facilitate the availability of high priority plant-derived recombinant pharmaceuticals to the poor in developing countries while simultaneously allowing the products to be developed commercially in Europe and North America. # To develop and refine new strategies for the expression of recombinant pharmaceuticals in plants, which can be used on a generic basis for molecules that are normally expressed poorly. # To develop and generate transgenic plants expressing a second generation of recombinant molecules that will be used in future clinical trials. In 2011 they reached their benchmark for success launching a phase I clinical study of an antibody that neutralizes HIV, produced in and isolated from tobacco plants. This antibody could one day become an inexpensive component of a microbicide used to prevent the spread of HIV/AIDS. The project has also spun off many additional technologies that are being adopted by researchers all over the world, and has resulted in more than 100 publications in peer-reviewed scientific journals.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. InBase is a curated database devoted to inteins. It developed by a commercial laboratory, New England BioLabs, that also provides products related to enzyme digests on the same website. Users can access the Intein Registry, to discover properties of individual inteins. They can also submit intein data, browse intein motfis, and view mechanisms and introductions to protein splicing.
PRECISESADS - Molecular reclassification to find clinically useful biomarkers for systemic autoimmune diseases
A project that will study 2,500 people with various systemic autoimmune diseases (SADs), gathering data on the molecular causes of their disease as well as their clinical symptoms, enabling them to pave the way for a new classification of these diseases. The goal is to use OMICs and bioinformatics to identify new classifications for diseases known to share common pathophysiological mechanisms. Results will be shared to deliver a new molecular taxonomy of systemic autoimmune diseases. In order to achieve this, PRECISEADS is informing on a regular basis on the project implementation and results, and involving stakeholders from Europe in its activities in order to broaden the project impact and increase opportunities for cooperation.
Preclinical evaluation of drug efficacy in common solid tumours
Predect New models for preclinical evaluation of drug efficacy in common solid tumours
Project that aims to create more appropriate in vitro platforms for target validation and drug discovery for breast, prostate and lung cancers. Laboratory platforms to validate whether target modulation would provide a clinical benefit are usually highly reductionist, often using long-established cell lines growing in 2 dimensions in vitro. These models do not reflect the complexity and heterogeneity of a tumor in situ, where biochemical pathways are wired with connections to the complex tumor environment provided by the stroma. PREDECT has the goal of comparing the pathological and molecular profiles of novel in vitro platforms with those of human tumors. Because obtention of clinical material presents both logistics and quality problems for ongoing and intense studies of target validation, PREDECT aims to use material from genetically engineered mouse models, and some advanced xenografts, whose pathology and molecular profiles closely match cohorts of human tumors. PREDECT hopes to provide more appropriate in vitro platforms both for target validation and subsequent preclinical studies which will replace a current cascade of tests which are poorly predictive of clinical activity. The project is expected to shift paradigms in cell biology as well as in preclinical target validation where it should permit greater predictivity of drug efficacy in patient cohorts.
READNA - REvolutionary Approaches and Devices for Nucleic Acid analysis
REvolutionary Approaches and Devices for Nucleic Acid analysis
Consortium to accelerate new breakthrough DNA sequencing technologies and methods to enhance existing analysis methods. The ultimate aim is to advance DNA sequencing technologies to a level where a human genome can be analyzed at high resolution for less than 1000 euros in less than one day. The goals of the consortium are to revolutionize nucleic acid analysis methods by improving elements necessary to use the currently emerging generation of nucleic acid sequencers in a meaningful and accessible way, providing methods that allow in situ nucleic acid analysis and methods capable of selectively characterizing mutant DNA in a high background of wildtype DNA, combining RNA and DNA analysis in a single analytical device, providing technology to efficiently analyze DNA methylation (genome-wide, with high resolution and in its long-range context), implementing novel concepts for high-throughput HLA-screening, developing fully integrated solutions for mutational screening of small target regions (such as for screening newborns for cystic fibrosis mutations), developing a device for screening multiple target regions with high accuracy and implementing strategies for effective and high-resolution genotyping of copy number variations. READNA was awarded the Stars of Europe prize in December 2013.
TRANSFoRm Clinical Data Integration Model
A global mediation model expressed as an ontology for use in the primary care domain. It uses a realist approach employing Basic Formal Ontology (BFO v1.1) as an upper ontology. Other ontologies were imported or specialized to give deeper definition to the concepts in the domain. These included OGMS, IAO and VSO. The CDIM ontology includes concepts that are especially important to primary care (e.g. episode of care or reason for encounter), but also others to handle temporality in queries (e.g. the start and beginning of processes). The owl file provided for download is the merged file created directly in Prot��g�� through the Refactor/Merge ontologies tool in order to facilitate the load of CDIM in LexEVS for use in the unified interoperability framework.
A Unified Approach to Evaluating Cellular Immunotherapy in Solid Organ Transplantation
The ONE Study - A Unified Approach to Evaluating Cellular Immunotherapy in Solid Organ Transplantation
Consortium aiming to produce regulatory T cells that are compatible with a kidney transplant patient' '''s immune system, as a measure to suppress the body' '''s natural immune response against a transplanted organ. If successful, this approach will reduce a transplantation patient' '''s life-long dependency on immune suppressing drugs, many of which are often associated with undesirable side effects and can limit the patient' '''s daily routine. The consortium goals are to develop and conduct clinical trials of various immunoregulatory T-cell-based products in organ transplantation recipients, allowing a direct comparison of the safety, clinical practicality and therapeutic efficacy of each cell type. The central focus of the project is to: # Production and manufacture of distinct populations of hematopoietic immunoregulatory T cells # Comparatively study the tolerogenic characteristics of these regulatory cell types # Test these cell therapy products side by side in a clinical trial living donor renal transplant recipients The first workstream will work with different T regulatory cell, tolerogenic DC and suppressive macrophage cell products that are currently in development. In addition to these therapeutics, another goal of this workstream is to develop a cell tracking technology that assesses pharmacodynamics and pharmacokinetics of these cell-based therapies. The second workstream is focused on designing and conducting a cell therapy based clinical trial in renal transplantation, taking into consideration ethics, concurrent immunosuppressive drug use, state-of-the-art immune monitoring, innovative all-in-one data capturing systems, and pharmacovigilance. The goal is to have a comparative evaluation of hematopoietic cell therapy safety in renal transplantation. The third workstream aims to learn more about the specific comparative characteristics of suppressive cell types and to use this knowledge to improve later trial designs and foster novel ideas for new or improved suppressive / tolerogenic cell population.
University of Sherbrooke; Quebec; Canada
Translational Research and Patient Safety In Europe
Project to develop a ''rapid learning healthcare system'' driven by advanced computational infrastructure that can improve both patient safety and the conduct and volume of clinical research in Europe. Three carefully chosen clinical ''use cases'' will drive, evaluate and validate the approach to the ICT (information and communications technology) challenges. The project will build on existing work at international level in clinical trial information models (BRIDG and PCROM), service-based approaches to semantic interoperability and data standards (ISO11179 and controlled vocabulary), data discovery, machine learning and electronic health records based on open standards (openEHR). TRANSFoRm will extend this work to interact with individual eHR systems as well as operate within the consultation itself providing both diagnostic support and support for the identification and follow up of subjects for research. The approach to system design will be modular and standards-based, providing services via a distributed architecture, and will be tightly linked with the user community. Four years of development and testing will end with a fifth year that will be dedicated to summative validation of the project deliverables in the Primary Care setting. In order to support patient safety in both clinical and research settings, significant ICT challenges need to be overcome in the areas of interoperability, common standards for data integration, data presentation, recording, scalability, and security., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
TRANSFoRm Clinical Research Information Model
A clinical research information model for the integration of clinical research covering randomized clinical trials (RCT), case-control studies and database searches into the TRANSFoRm application development. TRANSFoRm clinical research is based on primary care data, clinical data and genetic data stored in databases and electronic health records and employs the principle of reusing primary care data, adapting data collection by patient reported outcomes (PRO) and eSource based Case Report Forms. CRIM was developed using the TRANSFoRm clinical use cases of GORD and Diabetes. Their use case driven approach consisted of three levels of modelling drawing heavily on the clinical research workflow of the use cases. Different available information models were evaluated for their usefulness to represent TRANSFoRm clinical research, including for example CTOM of caBIG, Primary Care Research Object Model (PRCOM) of ePCRN and BRIDG of CDISC. The PCROM model turned out to be the most suitable and it was possible to extend and modify this model with only 12 new information objects, 3 episode of care related objects and 2 areas to satisfy all requirements of the TRANSFoRm research use cases. Now the information model covers Good Clinical Practice (GCP) compliant research, as well as case control studies and database search studies, including the interaction between patient and GP (family doctor) during patient consultation, appointment, screening, patient recruitment and adverse event reporting.
Charity registered in United Kingdom whose mission is to accelerate research in new areas of human biology and drug discovery.Not for profit, public-private partnership that carries out basic science of relevance to drug discovery whose core mandate is to determine 3D structures on large scale and cost effectively targeting human proteins of biomedical importance and proteins from human parasites that represent potential drug targets.
Mouse Gross Anatomy and Development Ontology
A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).
A set of three models, which in conjunction with the semantic mediator enables the execution of queries formulated through the eligibility representation of the Clinical research information model (WT6.4). An ontology-driven mechanism was developed to enable linkage and integration of phenotypic and genotypic data from multiple distributed data sources. It makes use of the Clinical Data Integration Model (CDIM, WT6.5), the Data Source Model (DSM, WT6.6) and the CDIM-DSM mapping model (WT6.6). Queries formulated through the CDIM and vocabulary service (WT7.2) are translated to local queries by the mediator using the individual source instances of the DSM and CDIM-DSM models.
National Ataxia Foundation Ataxia Tissue Donation
National Ataxia Foundation Tissue Donation Program
National Ataxia Foundation: Ataxia Tissue Donation
A website where users can find information on donating tissue for ataxia research.
Fondazione Centro San Raffaele; Milan; Italy
A non-profit organization to support the research of the IRCCS San Raffaele Hospital with the aim of helping the development of science in the service of medicine. To make progress and achieve new successes, which may also be of benefit to future generations, the Fondazione Centro San Raffaele Hospital supports through participation in invitations to national and international research and fundraising activities to individuals and businesses. The lines of research in 2013 which focuses on the activities of the Foundation, in synergy with the San Raffaele hospital: # Molecular and functional approaches to the study of neurological and psychiatric disorders # Molecular and cellular therapies for regenerative medicine # Study and modulation of innate and adaptive immune response # Cellular and molecular approaches to the study of solid tumors and blood # Molecular and cellular approaches to the study and treatment of cardiovascular and metabolic diseases # Genetic mechanisms, molecular and cellular disease and aging # Genomics and post-genomics for the study of the mechanisms of disease and response to drugs # Molecular and cellular imaging for the study of oncological diseases and molecular imaging of cardiovascular disease
A high technology company that is a developer and supplier of photonic and laser systems for microelectronics manufacturers. They manufacture a variety of products for testing and repairing equipment, and particularly products designed for use by manufacturers of other high-tech products. These include laser trimming systems. (Adapted from Wikipedia)
An independent owner-operated contract research organization providing clinical research services to the biopharmaceutical industry and life science organizations. If you are looking for data management, biostatistics and EDC solutions or plan to conduct a high quality phase I-IV or non-interventional study in and outside of Germany KOEHLER eClinical is your partner in study planning, conduct, evaluation and publication.
A matchmaker portal for the pharmaceutical industry worldwide offering a directory and contact platform. This includes a database of ten thousands of profiles of companies offering pharma services as well as a selection of companies including niche providers delivering the service of interest. The platform is used to search for human medicinal products, veterinary medicinal products, cosmeceuticals, nutriceuticals, medical devices, and diagnostics. The company''s platform also enables users to post their service requests, service offers, and APIs/intermediates; and interact with other users. In addition, it offers advice and operational support services for outsourcing and inlicensing processes, such as strategic, scientific, and regulatory advice related to due diligence and decision making of research and development, sourcing, and M and A processes; conduct of third party GMP and pharmacovigilance audits; customized interim solutions; and qualified person functions for GMP and pharmacovigilance. The company also serves various sectors of the life science industry, such as contract manufacture, laboratory investigations and contractual testing, clinical research organizations and pre-clinical research organizations, consulting and legal counseling, logistics and distribution, education, marketing, IT, and investment and financing sectors; and small and medium enterprises/pharma, academic, public institutions, and freelancers. (Bloomberg Businessweek)
A service-provider company specialized in developing and managing scientific research projects. Its mission is to support research activities from the idea to the realization of project. ALTA assists in finding the proper strategy, building European Consortia and putting science in the most appropriate administrative and management framework.
Commercial organization that produces products for biomarker research and development. Their goal is to help customers and collaborators to improve clinical decisions through the use of molecular biomarkers. Their tools bring new insights into disease processes, improve disease detection, and contribute to a better understanding of biology.
Commercial organization that discovers, validates & analyzes genomic biomarkers with a focus on body fluid samples. Take advantage of their proven expertise in biomarker signature development and speed up your biomarker studies.
A biotechnology company that has developed technology for synthesizing custom microarrays, the FlexArrayer. Its is a desk-top sized instrument which allows the researcher to generate, in their own laboratory, either a custom oligonucleotide array in a single day or oligonucleotide pool in a few days. Recent developments in synthesis chemistry allows many modifications to be incorporated or for alternative chemistries to be considered., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A development-stage diagnostics company whose mission is to curb the spread of hospital-acquired infections and anti-microbial resistance by developing a small-footprint, inexpensive, and automated diagnostic instrument that will quickly deliver patient-specific information on 50+ genetic markers. With their on-chip, high-multiplex approach, they expect to offer a higher-performing, lower-cost, and more versatile solution versus bacterial culture and competing approaches in development.
Pharmaceutical company with a mission to discover and develop innovative medicines that ease patients'' suffering, and solve the most important unmet medical needs of our time. As one of the Janssen Pharmaceutical Companies, their strategy is to identify the biggest unmet medical needs and match them with the best science, internal or external, to find solutions for patients worldwide. They leverage their world-class discovery and development expertise, and operational excellence, to bring innovative, effective treatments in five therapeutic areas: cardiovascular and metabolism, immunology, infectious diseases and vaccines, neuroscience, and oncology.
Public Health England; London; United Kingdom
Health Protection Agency; England; United Kingdom
An executive agency of the Department of Health in the United Kingdom to protect and improve the nation''s health and well-being, and reduce health inequalities. It employs 5,500 staff, who are mostly scientists, researchers and public health professionals. They have 15 local centers and 4 regions (north of England, south of England, Midlands and east of England, and London). They work closely with public health professionals in Wales, Scotland and Northern Ireland, and internationally. Its formation came as a result of reorganization of the National Health Service (NHS) in England. It took on the role of the Health Protection Agency, the National Treatment Agency for Substance Misuse and a number of other health bodies. They are responsible for: * making the public healthier by encouraging discussions, advising government and supporting action by local government, the NHS and other people and organisations * supporting the public so they can protect and improve their own health * protecting the nation''s health through the national health protection service, and preparing for public health emergencies * sharing information and expertise with local authorities, industry and the NHS, to help them make improvements in the public''s health * researching, collecting and analyzing data to improve our understanding of health and come up with answers to public health problems * reporting on improvements in the public''s health so everyone can understand the challenge and the next steps * helping local authorities and the NHS to develop the public health system and its specialist workforce
Commercial organization specializing in bacterial detection including tuberculosis, therapeutic protein and protein aggregation diseases. * Tools for rapid and simple bacteria and virus extraction including tuberculosis * Seprion technology for the detection and study of protein aggregates and protein aggregation diseases * LiMA technology for the ultra sensitive detection of bacteria and bacterial contamination
Organization that provides academic and industrial clients access to functional genomics technologies, services and partnering solutions including genome-wide expression, copy number profiling, miRNA expression, DNA-protein interaction (ChIP-on-chip), Illumina high-throughput sequencing including nucleic acid quality and quantity assessment. For gene silencing and ectopic expression purposes, they offer high-titer shRNA and ORF lentiviruses targeting genes of interest. They also offer customized services e.g. preparation of gain or loss-of-function cell lines and protein interactomics-based services (yeast two-hybrid). In addition, they provide access to wide array of computational data analyses. BMGen also offers partnering deals for clients interested in customized integration of several technologies.
Non-profit organization that facilitates co-operation between professionals in biotechnology and the life sciences all over Europe bringing research groups, universities, SMEs, large companies and indeed all actors in biotechnology together to build and deliver partnerships.
Human Induced Pluripotent Stem Cells Initiative
A UK national induced pluripotent stem (iPS) cell resource that will create and characterize more than 1000 human iPSCs from healthy and diseased tissue for use in cellular genetic studies. Between 2013 and 2016 they aim to generate iPS cells from over 500 healthy individuals and 500 individuals with genetic disease. They will then use these cells to discover how genomic variation impacts on cellular phenotype and identify new disease mechanisms. Strong links with NHS investigators will ensure that studies on the disease-associated cell lines will be linked to extensive clinical information. Further key features of the project are an open access model of data sharing; engagement of the wider clinical genetics community in selecting patient samples; and provision of dedicated laboratory space for collaborative cell phenotyping and differentiation.
A commercial organization with expertise and multiple departments that focus on both fish physiology and molecular cell biology. ZF-pharma has developed patented technology for the automated in vivo high-throughput screening of pharmaceutical drug candidates against diseases. They seek industrial partners that are interested in obtaining a license for this technology or, alternatively, would prefer to outsource screening of TB drugs to ZF-pharma. NewCatch BV has developed a tool for use in sustainable aquaculture. The tool will first be used for reproduction of the highly valued fish species eel, pikeperch and sole. They seek industrial / aquaculture partners interested in obtaining a license for ZF-implants in other fish species. NewCatch BV carries out fish reproductive research, for instance European eel (Anguilla anguilla), exploring maturation and reproduction. ZF-Genomics offers multiple sequencing services, including mRNAseq and microRNA analysis and de novo and reference genome assemblies. In addition they also offer the bioinformatics services that are needed to make sense of the sequence data. In addition, they perform Next generation sequencing tasks for (inter)national research project partners and for external customers.
A globally operating Finnish developer, manufacturer and marketer of human and veterinary pharmaceuticals, active pharmaceutical ingredients and diagnostic tests. They are continuously developing new drugs and treatment methods. Pharmaceutical RD focuses on central nervous system drugs, oncology and critical care drugs, and Easyhaler pulmonary drugs.
Academic cancer research center, a postgrad college, and a charity in the United Kingdom that is making discoveries that defeat cancer. With their partners The Royal Marsden NHS Foundation Trust they form the largest comprehensive cancer center in Europe and perform high quality and original basic research and translational studies, with the aim of developing better treatments for the benefit of cancer patients worldwide. The ICR offers comprehensive, modern facilities for research and studentships supported by the Wellcome Trust, MRC, CRUK and EPSRC and the ICR''s own resources which are awarded on a competitive basis. The ICR offers postgraduate research degrees (MPhil, PhD and MD (Res)) and a modular postgraduate taught degree in oncology aimed at clinicians undertaking specialist training in the field of Clinical or Medical Oncology leading to a Postgraduate Certificate, Postgraduate Diploma or MSc in Oncology.
Each month our podcast team will be broadcasting the very latest breakthroughs and discoveries in neurosciences, psychiatry and psychology.
VTT Technical Research Centre of Finland
A multitechnological applied non-profit research organisation in Northern Europe that provides high-end technology solutions and innovation services. They enhance their customers'' competitiveness, thereby creating prerequisites for society''s sustainable development, employment, and well-being. VTT has ISO9001:2008 certificate and ISO14001:2004 certificate.
Systematized Nomenclature of Medicine - Clinical Terms
Ontology of SNOMED (Systematized Nomenclature of Medicine) clinical terms.
Commercial organization that develops pre-competitive solutions to the knowledge challenges facing drug discovery by connecting companies, leading academics and biotech specialists. It provides the bandwidth, knowledge and experience to successfully deliver pre-competitive projects through leadership, technical consulting, workflow expertise and software production. They possess over 30 years collective experience of large pharma drug discovery, computational science and knowledge management experience.
Fundaci�� Institut d''Investigaci�� Biom��dica de Bellvitge
Institut d''Investigacio Biomedica de Bellvitge
Institut d''Investigacio Biomedica de Bellvitge (IDIBELL)
Institut d''Investigaci�� Biom��dica de Bellvitge
Institut d''Investigaci�� Biom��dica de Bellvitge (IDIBELL)
A research center focused on cellular medicine, where the basic research focuses and works on relevant clinical matters and fosters economic development. The center manages the research of the Bellvitge University Hospital, the Institut Catal�� d''Oncologia (Catalan Institute of Oncology) and the University of Barcelona. It is one of the first five Spanish research centers accredited as health research institute by the Instituto de Salud Carlos III (Health Institute Carlos III).
Advanced Laboratories of Translational Health
A biomedical company in Spain focused on the development of new tools for diagnosis and personalized treatment of oncological diseases and precancerous. It has three areas of activity in permanent innovation: Assistance in Diagnosis / Prognosis in solid and hematological tumors, Translational Research covering the gap between basic and clinical research and advanced radiotherapy treatments based image-guided single dose (SD-IGRT). Their objectives are: * Provide an integrated tissue and tumor molecular phenotype analysis using the most advanced technologies in diagnosis, to guide the most appropriate treatment for each patient. * Discover and validate molecular patterns by molecular systems and platforms including pathology, to generate predictive algorithms through computational biology, evolution and determining the response of patients with a particular tumor profile. Althia has laboratories equipped with the most advanced equipment and technologies in Barcelona and Granada Genyo Center, with offices in Madrid.
A Swiss service and consulting company specialized in the computational analysis of biomarker data from clinical trials. Their technical expertise spans across multiple biomaker technological platforms such as genetics, transcriptomics, protein assays and cellular assays. Quartz Bio is a spin-off of Merck Serono with the capital of the company entirely owned by its employees.
Centre for Genomics and Oncological Research
Pfizer-University of Granada-Junta de Andaluc??a Centre for Genomics and Oncological Research
Pfizer-University of Granada-Junta de Andaluc??a Centre for Genomics and Oncological Research (GENYO)
Center for excellence research in genomic medicine, focusing on the comprehensive study and understanding of the genetic basis of human diseases in general, placing special emphasis on cancer and its genetic disorders related to inheritance. GENYO was created as a multidisciplinary research space, where different professionals from the healthcare, university and business areas interact, making it possible to generate new systems to diagnose, prevent and treat diseases based on the joint and coordinated application of first-rate knowledge in the different areas of genetics. The center is the benchmark center of the Andalusian Program for Research in Clinical Genetics and Genomic Medicine, a program which, together with those of Cell Therapy and Regenerative Medicine, and Nanomedicine have the main objective of supporting and fostering translational research in Advanced Therapies. The activities performed within these three research programs are developed in coordination with the Andalusian Initiative for Advanced Therapies (IATA), an initiative of the Andalusian Government promoted by the Regional Ministries of Health and Innovation, Science and Enterprise.
NeuroTrends - Uncovering methodological trends in Functional MRI research
Service that extracts and analyzes methodological information from thousands of published studies across the functional neuroimaging literature. It currently offers searching articles by methodological choices, visualization of methods trends over time, and extraction of methods information from text. It currently includes 282,476 methodological details about 21,562 articles, published between 1992 and 2014. (2014) * Search for articles by title, authors, and methods. * Interactive visualizations of methodological parameters over time, by author, and more. * All data are programmatically accessible through a simple application programming interface. It''s simple to re-analyze the data or integrate with your own application.
WU-Minn HCP 500 Subjects MR and MEG Release
WU-Minn HCP 500 Subjects MR + MEG Release
Behavioral and 3T MR imaging data from over 500 healthy adult participants with 14 subjects also scanned in resting-state MEG (rMEG) and task MEG (tMEG). Highlights: * Behavioral and demographic data on 550 subjects. * MR imaging data preprocessed using updated pipelines (structural pipeline v3.1, functional pipeline v3.1, diffusion pipeline v3.1, task analysis pipeline v3.3). * Updates to pipelines include a new intersubject registration method called MSMSulc. All MR data from Q1-Q3 releases have been reprocessed. HCP strongly advises against mixing data from this release with previously-released data. * Individual task fMRI grayordinate-based analysis results (available at 2mm, 4mm, 8mm, and 12mm smoothing levels) and volume-based analysis results (4mm smoothing) are available for all complete 500 Subjects tfMRI data, using an updated task analysis pipeline v3.3. * New extensively processed 100- and 400+-subject group-average functional MR data. * Updates to MEG data and access in ConnectomeDB. Structural MRI-based MEG anatomical models and MR data for the 14 MEG1 Release subjects. * Improvements to behavioral data organization and data dictionary, including the addition of previously unreleased restricted behavioral and demographic data. * All imaging data soon to be available on the cloud through Amazon S3. (More information to come!)
GENSAT at NCBI - Gene Expression Nervous System Atlas
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 19, 2012. Due to budgetary constraints, the National Center for Biotechnology Information (NCBI) has discontinued support for the NCBI GENSAT database, and it has been removed from the Entrez System. The Gene Expression Nervous System Atlas (GENSAT) project involves the large-scale creation of transgenic mouse lines expressing green fluorescent protein (GFP) reporter or Cre recombinase under control of the BAC promoter in specific neural and glial cell populations. BAC expression data for all the lines generated (over 1300 lines) are available in online, searchable databases (www.gensat.org and the Database of GENSAT BAC-Cre driver lines). If you have any specific questions, please feel free to contact us at info_at_ncbi.nlm.nih.gov The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques. Search criteria include gene names, gene symbols, gene aliases and synonyms, mouse ages, and imaging protocols. Mouse ages are restricted to E10.5 (embryonic day 10.5), E15.5 (embryonic day 15.5), P7 (postnatal day 7), and Adult (adult). The project focuses on two techniques * Evaluation of unmodified mice lines for expression of a given gene using radiolabelled riboprobes and in-situ hybridization. * Creation of transgenic mice lines containing a BAC construct that expresses a marker gene in the same environment as the native gene
Treatable Intellectual Disability Endeavor in B.C.
A collaborative care and research initiative with a focus on prevention and treatment of Intellectual disability (ID) that is due to inborn errors of metabolism (IEM), which can be treated with diet or drugs. Health care policy and institutional culture is still operating under the old premise that all ID is incurable and thus, many children born with treatable ID are at risk of not being treated. To acknowledge the multidisciplinary scope and the ways in which health care professionals and researchers will collaborate, the goals of the TIDE BC project are demonstrated within a framework of 7 Work Packages: * Implementation of a new Protocol for diagnostic evaluation of ID, focusing of treatable conditions; * Development of infrastructure to facilitate implementation, evaluation and sustainability of the Protocol; * Investments into next generation genomic technologies; * Improving evidence of and access to treatments; * Evaluation and health economy; * Knowledge dissemination; * Education and Mentoring. The objectives addressed in all Work Packages reflect a highly integrated cluster combining clinical care, research, evaluation, and knowledge dissemination.
Funding resource that raises funds to support BC Children's Hospital, Sunny Hill Health Centre for Children and the Child and Family Research Institute. The Foundation also works with Sunny Hill's Board of Directors to manage the Sunny Hill Foundation for Children. In 2013, BC Children's Hospital Foundation received donations from more than 150,000 people and had revenues of over $83 million.
Polymun Scientific Immunbiologische Forschung GmbH
A private commercial company generating revenues by contract development and manufacturing biopharmaceuticals as well as creating liposomal formats of drugs for contract partners. These revenues are invested in the proprietary product pipeline and the further development of technology platforms. The R&D projects and technologies are open for co-development and licensing. Polymun operates in accordance with current GMP guidelines and holds an Austrian production license for pharmaceuticals (??63 Austrian Pharmaceutical Law) thus meeting the EU requirements for drug manufacturing. Its core competence is the development and manufacture of biopharmaceuticals, using both mammalian and microbial cell technology. A fine example are Polymun''s broadly neutralizing HIV-1 antibodies produced in CHO cells. Other examples are recombinant human and porcine trypsin produced in yeast. Cell culture was also the basis for the development of a live attenuated influenza vaccine produced in Vero cells which led to the further investigation in genetically modified influenza viruses used as carrier for foreign epitopes (HIV, TB). Also the innovative liposome technology was initiated in order to optimize the formulation of the pharmacologically potent enzyme SOD, produced by Polymun in E. coli. Today, Polymun can apply this drug delivery platform to all kinds of pharmaceutically active ingredients. The industrial applicability in scale and price is a common focus throughout all projects and technologies.
Data.gov Science and Research Data Catalog
A catalog of high-value public science and research data sets from across the Federal Government.
Systems Chemical Biology and Chemogenomics Ontology
Ontology for Systems Chemical Biology and Chemogenomics
Italian National Agency for New Technologies Energy and Sustainable Economic Development
l''Agenzia nazionale per le nuove tecnologie l''energia e lo sviluppo economico sostenibile
Italian national agency for new technologies, energy and sustainable economic development with the following main research issues: * Energy Efficiency * Renewable Energy Sources * Nuclear Energy * Climate and the Environment * Safety and Health * New Technologies * Electric System Research The Agency''s activities are devoted to: * basic, mission-oriented, and industrial research exploiting wide-ranging expertise as well as experimental facilities, specialized laboratories, advanced equipment; * new technologies and advanced applications; * dissemination and transfer of research results, thus promoting their exploitation for production purposes; * provide public and private bodies with high-tech services, studies, measurements, tests and assessments; * training and information activities aimed at broadening sector expertise and public knowledge and awareness. The Agency''s multidisciplinary competences and great expertise in managing complex research projects are put at the disposal of the Country system.
A diabetes company active in the field of pharmaceutical development. The Company develops the diabetes vaccine Diamyd with the active ingredient GAD, which has the potential to become a key piece of the puzzle of a future solution to prevent, treat or cure type 1 diabetes and other forms of diabetes. Diamyd Medical has independently pursued the development of the diabetes vaccine Diamyd to global Phase III trials, leading to one of Sweden''s largest biotech agreements ever. The company has secured an exclusive license for a patent application for the specific combination therapy GAD plus the endogenous substance GABA, which has demonstrated favorable results in preclinical trials. The license also encompasses rights for the therapeutic use of GABA to treat diabetes and other inflammation-related disorders.
A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows.
bioRxiv - the preprint server for biology
A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 21, 2014. Commercial organization that provides technology, tools, and services for the development and production of biologics from therapeutics and drugs, food ingredients, and agriculture products. The company specializes in biologics separation and purification. Its products are used for industrial process chromatography applications. (Businessweek)
Commercial organization that provides laboratory and process technologies and equipment. Their products and services help customers around the globe implement complex and quality-critical processes in biopharmaceutical production and laboratory environments in a time- and cost-efficient way. Sartorius operates its own production facilities in Europe, Asia and America, and also has sales offices and local representatives in more than 110 countries.
LIFE search engine contains data generated from LINCS Pilot Phase, to integrate LINCS content leveraging semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to Harvard Medical School and Broad Institute and other LINCS centers, who provide more information including experimental conditions and raw data. Please visit LINCS Data Portal.
Greek Association of Alzheimers Disease and Related Disorders
Greek Association of Alzheimer Disease and Related Disorders
Greek Association of Alzheimer Disease and Relative Disorders
Greek Association of Alzheimer's Disease and Related Disorders
A non-profit organization whose aim is to offer advice concerning the care of Alzheimer' '''s disease patients, information and services for the people affected and their families. Also, to offer mutual help to the family members of the patients in order to reduce the social, economic and emotional cost deriving from the long care of people suffering from dementia. Lastly, the association attempts to publicize the social needs of the population affected and to inform the public in order to be acquainted with the problem. The mission of the Greek Association of Alzheimer' '''s Disease is * the early diagnosis of dementia by scientists * the promotion of research * education and training for all the stakeholders * the development of Care Units for patients with Alzheimer' '''s Disease * the provision of useful information and advise (24 hour help-line) on dementia problems (caring, legal or financial issues) * the presentation of lectures by health professionals and informal carers, covering all aspects of Alzheimer Disease * and the development of professional seminars during the whole year.
A public Solr index for the Gene Ontology. This index will replace some of the query functionality for GOOSE as well as become the new backend for AmiGO 2 and other services.
A contract research organization (CRO) that are mitochondrial experts, operating mitochondrial function screening platforms by using accepted pharmaceutical innovative technologies. The dynamic analysis of several typical markers of central and mitochondrial metabolism, redox status, or mitochondrial biogenesis are included in the determination of bioenergetic balance in living cells of human origin. These platforms are used to validate the activity of pharmaceuticals, cosmetics and environmental assets xenobiotics on mitochondrial targets associated with the activity or toxicity of these products under the selected models. They specialize in the selection of drugs affecting the progression of neurodegenerative diseases and offer proven models of Huntington's disease, Parkinson's and Alzheimer's, using primary cells of human origin. They have developed and use technology cellulomique and proteomics to identify early response profiles and clinical safety of pharmaceutical products for diseases of the CNS.
A Research as a Service (RaaS) Company founded by a Clinical Pharmacologist and Neuropsychiatrist that offers to its partners (health products industries and public research), 3 platforms: * Clinical research (CRO and SMO) * Scientific & regulatory consulting * Online surveys (Web portal) Their Research & Development profile allows them to propose innovative concepts such as : * Patient-Leader studies * Translational research studies (fMRI, innovative biomarkers, modeling, ...) * Behavioral parameters as biomarkers studies Qualissima also proposes proof of concept studies, proof of activities studies, medical devices studies and observational studies.
A comprehensive, free, and interactive platform to help individuals discover more about clinical trials that may be appropriate for them for a variety of diseases. The platform allows stakeholders within the clinical trials community (investigators, site personnel, sponsors, and disease advocates) to engage with potential enrollees and educate them about specific clinical trials. They have identified some of the most commonly used criteria for the clinical trials in each disease. Using these criteria, they developed a questionnaire for a single disease. Then, looking at just those questions, they can start to get a sense of which clinical trials might be appropriate for a particular person which is a helpful to start to narrow down the list of potentially appropriate trials. All clinical trials that are posted on www.clinicaltrials.gov for the diseases that Corengi covers will be on the website.
Repository where scientists and organizations can share, store, manipulate, and publish biological network data. Users can also run their own copies of NDEx Server software in cases where stored networks must be kept in highly secure environment (such as for HIPAA compliance) or where high application load is incompatible with shared public resource. Open source software system that is part of Cytoscape family. Project of Cytoscape Consortium in conjunction with Ideker lab at UCSD School of Medicine. Public forum where biologists can exchange and publish computable network models in many types and formats. NDEx is based on REST web API which can be accessed by any application, including NDEx website and NDEx Cytoscape App. NDEx networks are assigned stable, globally unique URIs and so can be referenced by publications, by other networks, and by analytic applications.
Research based company providing predictive pharmacokinetic and pharmacodynamic tools, workshops and consultancy services. Their user-friendly simulator and databases predict drug absorption, clearance, distribution and metabolic drug-drug interactions from in vitro data. Simcyp's clients include major global pharmaceutical and bioscience companies, leading academic institutes and regulatory authorities. These clients form the Simcyp Consortium, which together with independent International Scientific Advisory Board, guide scientific development at Simcyp.Simcyp was acquired by Certara in 2012.
Organization that designs and manufactures analytical instrumentation to measure physicochemical parameters for the pharmaceutical and biotech industry, as well as offers physicochemical data and consultancy services. Their instruments provide accurate and reliable values for pKa, log P, log D, solubility and dissolution, particle size and shape analysis. These critical physicochemical parameters are important in drug formulation, and also influence the ability of New Chemical Entities to cross biological membranes such as the gastro-intestinal tract, blood-brain barrier, skin and cell walls. Sirius also offers an analytical service for high quality PhysChem outsourcing, used by hundreds of clients worldwide.
Commercial developer of Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) and Physiologically-Based Pharmacokinetic (PBPK) modeling and simulation software for the pharmaceutical and biotechnology, industrial chemical, cosmetic, herbicide, and food ingredient industries. Their software allows pharmaceutical scientists to predict certain key potential endpoints and dynamics, in silico, thereby reducing research & development costs and helping clients make better projects decisions sooner. Consulting services: Their team of highly-skilled scientists is available to assist with your discovery and development activities on a project-by-project basis. They now offer expanded pharmacodynamic modeling services, NONMEM analysis, and regulatory report writing assistance. Their ultimate goal is to develop tools and systems which bridge PBPK modeling with clinical trial data analysis. Training workshops & User Groups: they offer hands-on introductory and advanced training workshops in the United States, Europe, and Asia throughout the year.
A pharmaceutical company committed to provide valuable medicines through their own R&D efforts, licenses and collaborations. Through seeking innovative medicines they aim to become a relevant player in respiratory and dermatology diseases with also a strong interest in gastroenterology and pain. The company is headquartered in Barcelona, Spain, and has 14 affiliates in Europe and North America and trading capacity in 22 countries.
A pharmaceutical chemical group in Spain with a presence worldwide. It operates in the pharmaceutical sector by researching and developing new drugs, marketing a wide range of ethical and OTC products, generics, vaccines and also products for hospital and veterinary use. Through its subsidiary Esteve Qu??mica is also present in the Active Pharmaceutical Ingredients sector.
Commercial provider of software solutions for drug discovery applications offering tools, services, and research collaborations. The software portfolio ranges from design, over screening, to the visualization of ligand libraries, for hit identification, optimization, and scaffold hopping. With a stellar scientific advisory board and founders from academia who intensely collaborate with pharma, BioSolveIT catalyzes products off of university research successes with proven pharmaceutical industry application. They provide software products within the areas of ligand and structure-based drug design and is the pioneer of computational fragment-based ligand design. BioSolveIT innovate break-throughs in drug discovery by supplying smooth, user-centered designed tools bringing different researchers together for efficient multidisciplinary drug design.
A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes
Company committed to development, characterization and manufacture of antibody and ELISA type assays for academic, biopharmaceutical and clinical research.
An informatics service focusing on competitor intelligence and text-mining within the life sciences. It mines a diverse array of scientific content to look for mentions of targets, indications, companies, drugs and technologies of interest to those involved in human health and drug discovery. A free newsletter service is provided to allow everyone to explore the therapeutic landscape and stay informed and a range of professional products and services are offered for those who need more in-depth analysis of the therapeutic landscape. Its text-mining engine can be configured to a variety of different use cases and performs with very high throughput. SciBite has a number of big-pharma and scientific publishers as current customers. SciBITES is free on the website but for extended functionality, including a data mining API and access to internal or commercial documents, you may wish to consider an installation of the SciBITES server software within your organization.
Commercial organization that uses next generation sequencing technologies coupled with computational modeling of tumor and somatic tissues in order to identify individualized therapies for cancer patients. The company also uses these technologies to help pharmaceutical partners stratify patients for their clinical trials. Alacris has an exclusive worldwide commercial license for the computational modeling of tumors and somatic tissues using proprietary computational systems modeling technologies ModCell developed at the Max Planck Institute for Molecular Genetics (MPI-MG) in Berlin coupled with next generation sequencing and genotyping technology developed at Harvard Medical School in Boston. The company also is building up the first next generation sequencing center in Europe for clinical operations.
Experimental Pharmacology and Oncology Berlin-Buch
EPO - Experimental Pharmacology & Oncology GmbH
Experimental Pharmacology & Oncology Berlin-Buch
Experimental Pharmacology & Oncology Berlin-Buch GmbH
Experimental Pharmacology & Oncology GmbH
A small and medium-sized enterprise (SME) that has expertise in preclinical pharmacology, pharmacokinetics, and toxicology for the characterization of novel anticancer therapeutics and predictive biomarkers like: cytostatics, biologicals (peptides, antibodies), (anti)-hormones, immunomodulators (cytokines), and gene therapeutics. EPO has modern laboratories licensed for animal experiments and gene technology (S2) and a broad panel of murine and human tumor models growing in immunocompetent (SPF-quality, syngeneic strains) or immunodeficient mice (nude, SCID, NOD/SCID). EPO has established imaging technologies to monitor in vivo tumor growth.
THIS RESOURCE IS OUT OF SERVICE, documented on July 23, 2021.Commercial organization with expertise in European research and innovation that provide both science providers (researchers) and technology users (Industry including SMEs, public authorities, Universities, clusters, etc.) tailor-made services to give the highest possible European added value to their project.
GABO:mi Gesellschaft f??r Ablauforganisation :milliarium mbH & Co. KG
GABO:mi Gesellschaft f??r Ablauforganisation:milliarium mbH & Co KG
GABO:mi Gesellschaft f??r Ablauforganisation:milliarium mbH & Co. KG
GABO:mi Gesellschaft fur Ablauforganisation :milliarium mbH & Co. KG
GABO:mi Gesellschaft fur Ablauforganisation:milliarium mbH & Co. KG
THIS RESOURCE IS OUT OF SERVICE, documented on July 23, 2021. Small and medium-sized enterprise (SME) that is expert in management of research projects. Initially, they provide support with help and advice when applying for European research grants - free of charge. From project start, they take over contract negotiations, financial management, reporting to the EC, meeting organization, public relations and much more. ARTTIC Innovation GmbH took over GAVBO:mi.
A professional and scientific society that provides leadership, education, advocacy, and resources enabling clinical pharmacists to achieve excellence in practice and research. Their membership is composed of practitioners, scientists, educators, administrators, students, residents, fellows, and others committed to excellence in clinical pharmacy and patient pharmacotherapy. The Practice and Research Networks (PRNs) represent focused interest groups of ACCP members, providing a means for clinical pharmacists with common practice and research interests to gather for professional interaction, networking, and continuing education. Activities within individual PRNs may vary depending on the interests and perceived needs of their members. All PRNs conduct educational programs within their interest areas at the ACCP Annual Meeting and the Spring Practice and Research Forum.
Coordinating center for infectious diseases
Commercial organization focused on the development and exploitation of novel biomarkers for psychiatric illnesses. They provide industrial and academic partners with comprehensive biomarker discovery services in commercial and collaborative projects. They operate in the field of psychiatric disorders and their products and services are designed to excel biomarker research. In 2010, Psynova Neurotech and its partner company Rules-Based-Medicine Inc (now MyriadRBM) conducted a beta launch of a blood test aiding in the diagnosis of schizophrenia (http://www.veripsych.com/). They are now refining the test and have shifted their focus to the development of new blood-based biomarker tests that aid in the diagnosis, prognosis and differential diagnosis of schizophrenia, bipolar disorder and major depression. They offer not only their pre-selceted Multiple Reaction Monitoring (MRM) and Multiplex Immunoassay products, but also custom build panels. If they are provided with a list of analyses to evaluate, they can produce an analytical panel according to individual needs utilizing either MRM or Multiplex Immunoassay technologies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS OUT OF SERVICE, documented on July 23, 2021. Company focusing on stem cell derived products and services for drug discovery, toxicity testing and applications within regenerative medicine. The company leverages long-standing experience in stem cell handling and scale up together with leading expertise in differentiation of cells into mature and functional human cells. The laboratories are prepared to meet the EU and US guidelines for current Good Manufacturing Practice (cGMP). Now part of Takara Bio Inc.
Commercial organization that provides preclinical services and expertise, specializing in investigative toxicology, exploratory and discovery toxicology, metabolism and pharmacokinetics. CXR Biosciences is now Concept Life Sciences.
Centers for Medicare and Medicaid Services
Centers for Medicare & Medicaid Services
Commercial organization that offers human and animal hepatocyte products as well as other products derived from liver tissue, kits and media. Services they offer include in vitro metabolism, in vitro toxicology and cell therapy.
Commercial organization that is a worldwide provider of drug transporter technology, assays and reagents. Leveraging their expertise in efflux and uptake transporters, they generate quality reports for submission to FDA / EMA. From small molecules to protein therapeutics, SOLVO can test all transporter needs. Drug transporter Services and Products include: * Over 100 solutions for a wide range of transporters * Uptake transporter assays * Efflux transporter assays in cellular and membrane-based models * Transporter Consultancy Services * FDA- and EMA-ready reports * Ready-to-use Kits * In vitro and in vivo methods for studying transporters in the BBB, intestine, liver and kidney * Custom assay development
Association of kidney patients focused on patient-centered education, advocacy and community. They share educational pieces covering every level of kidney disease, advocate for improved access to high-quality health care through regulatory and legislative reform at the federal level, and make an effort to bring kidney patients together to promote community, conversations and to seek out services that help maximize patients'' everyday lives.
American Nephrology Nurses'' Association
Non-profit professional association that represents nurses who work in all areas of nephrology including hemodialysis, chronic kidney disease, peritoneal dialysis, acute care, and transplantation. Most members work in freestanding dialysis units, hospital outpatient units, and hospital inpatient units. ANNA develops and updates standards of clinical practice, educates practitioners, stimulates and supports research, disseminates knowledge and new ideas, promotes interdisciplinary communication and cooperation, and monitors and addresses issues encompassing the breadth of practice of nephrology nursing.
An organization of physicians, scientists, and allied health professionals whose mission is to advance apheresis medicine for patients, donors and practitioners through education, evidence-based practice, research and advocacy. ASFA represents a broad range of professionals involved in: donor apheresis, apheresis in transplantation & therapeutic apheresis.
American Society of Diagnostic and Interventional Nephrology
American Society of Diagnostic & Interventional Nephrology
Society that aims to promote the proper application of new and existing procedures to improve the care of patients with kidney disease. They promote education, research, public policy and clinical practice initiatives relating to diagnostic and interventional procedures. ASDIN works closely with other societies and programs to achieve its goals. All professionals involved in the care of patients with kidney disease are welcome to join and become active in the Society. Activities of the Society include: * the establishment of practice standards, * certification of physicians in specific procedures, * accreditation of training programs in specific procedures, * development of training tools and techniques, * sponsoring symposia and training courses, * and the dissemination of information through periodic meetings and through print and other media.
American Society of Pediatric Nephrology
An organization of pediatric nephrologists and affiliated health care professionals to promote optimal care for children with kidney disease through advocacy, education and research; and to disseminate advances in clinical practice and scientific investigation.
An organization of transplant professionals dedicated to advancing the field of transplantation and improving patient care by promoting research, education, advocacy, and organ donation.
Biopharmaceutical company focused on developing and commercializing products to treat serious diseases associated with inflammation and autoimmune diseases.
University Renal Research and Education Association
A not-for-profit research organization committed to improve patient care through research that shapes medical policies and practice. In particular, they conduct health outcomes research on chronic disease and end-stage organ failure, with expertise in biostatistical analysis, clinical practice, health economics, public policy, database management and integration, and project coordination. Through research projects that are national and global in scope, their scientific collaborations provide valuable and timely information to the worldwide health care community. They are a leader in interdisciplinary health outcomes and policy research focused on reducing the health and economic burden of chronic diseases and improving the delivery of care.
Association for the Advancement of Medical Instrumentation
A nonprofit organization made up of a diverse community of healthcare technology professionals that support the healthcare community in the development, management, and use of safe and effective medical technology. It is the primary source of consensus and timely information on medical instrumentation and technology. * AAMI is the primary resource for the industry, the professions, and government for national and international standards. * AAMI provides multidisciplinary leadership and programs that enhance the ability of the professions, healthcare institutions, and industry to understand, develop, manage, and use medical instrumentation and related technologies safely and effectively. * AAMI helps members: contain costs, keep informed of new technology and policy developments, add value in healthcare organizations, and improve professional skills and enhance patient care. * AAMI provides a unique and critical forum for members who cover a complete range of interests, from clinical and biomedical engineers and technicians, physicians, nurses, and hospital administrators, to educators and researchers, manufacturers, distributors, government representatives and other healthcare professionals with an interest in medical devices. * AAMI fulfills its mission through: ** continuing education, conferences ** certification of healthcare technical specialists ** the publication of technical documents, periodicals, books, software.
A global healthcare company with expertise in medical devices, pharmaceuticals and biotechnology. Through its subsidiaries, they develop, manufacture and market products that save and sustain the lives of people with hemophilia, immune disorders, infectious diseases, kidney disease, trauma, and other chronic and acute medical conditions. BioScience Baxter is a manufacturer of recombinant and plasma-based proteins to treat hemophilia and other bleeding disorders; plasma-based therapies to treat immune deficiencies, alpha 1-antitrypsin deficiency, burns and shock, and other chronic and acute blood-related conditions; products for regenerative medicine, such as biosurgery products; and vaccines. Baxter''s Medical Products business manufactures products used in the delivery of fluids and drugs to patients. These include intravenous (IV) solutions and administration sets, premixed drugs and drug-reconstitution systems, IV nutrition products, infusion pumps and inhalation anesthetics. The business also provides products and services related to pharmacy compounding, drug formulation and packaging technologies. In addition, Baxter''s Medical Products business is a leader in Renal home-based therapies, such as peritoneal dialysis, and offers other products and services for people with end-stage kidney disease.
A multinational developer, manufacturer, and marketer of medical technologies specializing in the manufacture of vascular, urology, oncology and surgical specialty products. BARD pioneered the development of single-patient-use medical products for hospital procedures; today BARD is dedicated to pursuing technological innovations that offer superior clinical benefits while helping to reduce overall costs. Bard is perhaps best known for having introduced the Foley catheter. (Adapted from Wikipedia)
A biopharmaceutical company focused exclusively on discovering, developing and commercializing orally-administered therapeutics to treat autoimmune diseases, inflammatory disorders and cancer. Each drug candidate is a small molecule designed to target a specific chemokine or chemo-attractant receptor, thereby blocking the inflammatory response driven by that particular chemokine while leaving the rest of the immune system unaffected., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Neuroscience Information Framework (NIF) Cell Ontology
Neuroscience Information Framework Cell Ontology
Software program for filtering duplicate 454 sequences by comparing flowgram information.
THIS RESOURCE IS OUT OF SERVICE, documented on July 23, 2021.Organization that uses metabolomics to provide pharmaceutical companies with clinically relevant and practical insight into drug response and safety for renal and cardiovascular diseases, obesity and diabetes. Their combination of skills to achieve exhaustive understanding of a disease along with detailed clinical insights, signature panel of urine-based metabolomic biomarkers, proprietary metabolomics and computational expertise will accelerate the speed and success rate of drug development. ClinMet helps drug developers to efficiently transform promising compounds into safe and effective medicines. Their efficacy and toxicity indices enable pharmaceutical companies to make better clinical trial-related decisions and provide an increased understanding of a drug''s mechanism of action.
Healthcare company. Commercial dialysis provider with offerings that include in-center hemodialysis, in-center nocturnal dialysis, peritoneal dialysis, home hemodialysis, vascular access management, chronic kidney disease education, and renal diet assistance. Information on dialysis and chronic kidney disease, including informative articles and animated learning modules, and recipes for the dialysis diet are also available. Take advantage of their discussion forum, Find a Dialysis Center tool, DaVita GFR Calculator and more.
A nationwide, non-profit, patient-led organization with membership open only to dialysis and pre-dialysis patients and their families working to improve the quality of life for all dialysis patients through education and advocacy. They are dedicated to developing awareness of dialysis issues, advocating for dialysis patients, promoting favorable public policy and improving the partnership between patients and caregivers. Their policies and their mission are guided solely by their membership.
European Renal Association - European Dialysis & Transplant Association
European Renal Association - European Dialysis and Transplant Association
An association of European kidney specialists whose objective is advancement of medical science and of clinical work in nephrology, dialysis, renal transplantation, hypertension and related subjects. They aim at providing up-to-date knowledge, exclusively based on scientific data, independent from governments'' policies and from any influence of the industry. It is registered in England and Wales, but its area of activity mainly covers Europe and the Mediterranean area.
A clinical stage company developing a timely, precise, and convenient method for measuring plasma volume and glomerular filtration rate (GFR). They focus on development and commercialization of a patented technology for quantifying clinically relevant parameters that have been challenging or impossible to measure in the past. The company is currently developing technology for quantifying volume status and kidney function in a clinically actionable timeframe. Their technology could have a significant impact on the treatment of patients with acute kidney injury (AKI) and chronic kidney disease (CKD).
Global specialty biopharmaceutical company that focuses on developing treatments for conditions where the impact of their medicines can make an immediate and tangible difference for patients. They provide treatments in Neuroscience, Rare Diseases, Gastrointestinal, and Internal Medicine. This might be a therapy to treat an extremely rare and life-threatening disease like Hunter syndrome or Fabry disease; or a medicine for a specialist condition like ADHD or ulcerative colitis which if not treated effectively, can dramatically affect the lives of the patient and their whole family.Shire was acquired by Takeda Pharmaceutical company on January 8, 2019.
American global pharmaceutical and medical device company with headquarters in Lake Forest, Illinois.Provider of injectable drugs and infusion technologies and global leader in biosimilars. From September 2015 Hospira is part of Pfizer.
An independent global pharmaceutical company that produces specialty pharmaceutical products including generic drugs and imaging agents. They manufacture and distribute products used in diagnostic procedures and in the treatment of pain and related conditions. This includes the development, manufacture and distribution of specialty pharmaceuticals, active pharmaceutical ingredients, contrast products and radiopharmaceuticals. They are the largest U.S. supplier, by prescription, of opioid pain medications and the largest U.S. supplier of the medical isotope technetium-99m. The company is among the top 10 generic pharmaceuticals manufacturers in the United States. The company is also the largest producer of bulk acetaminophen. Mallinckrodt also produces cocaine derived from the Coca-Cola coca leaves, extracted by the Stepan Company. (Adapted from Wikipedia, 10/2014)
A commercial optical diagnostic company focused on providing clinicians with critical information to improve patient care. The Optical Renal Function Monitor (ORFM) is their first product platform and is focused on real-time, easy to use, and cost-effective monitoring of kidney function. Their non-invasive monitoring technology works in a similar fashion to pulse oximetry by using a light sensor placed on the skin. After the sensor has been placed, a proprietary biocompatible tracer is administered. The system can then monitor the patient''s real-time point-of-care kidney function. This information will allow for earlier detection of renal issues enabling clinicians to provide earlier, and hence more effective interventions. MediBeacon has created a research grade technique that is clinically applicable for real-time point-of-care Glomerular Filtration Rate measurement (mGFR). MediBeacon has invented a fluorescent tracer agent (MB-102) that is removed from the blood exclusively by the GFR mechanism of the kidneys. Together with their non-invasive detection device, this will deliver a real-time point-of-care measurement of GFR.
Medical technology company that develops and manufactures devices and therapies to treat more than 30 chronic diseases, including heart failure, Parkinson's disease, urinary incontinence, Down syndrome, obesity, chronic pain, spinal disorders, and diabetes. A Commercial healthcare organization for both patients and healthcare professionals. For professionals, it provides products, therapy and procedure solutions, and services.
Centers for Disease Control and Prevention
Government granting agency that works 24/7 to protect America from health, safety and security threats, both foreign and in the U.S. CDC Office of Financial Resources aids in achieving CDC’s mission by quickly and effectively allocating funds to where they are needed.
Organization in the U.S. dedicated to the awareness, prevention and treatment of kidney disease. Initiatives include public and professional education, kidney health screenings, research, and patient services. They publish a number of scientific journals including the American Journal of Kidney Diseases, Advances in Chronic Kidney Disease and the Journal of Renal Nutrition. The NKF also publishes the Kidney Dialysis Outcomes Quality Initiative K/DOQI, a comprehensive set of clinical practice guidelines. (Adapted from Wikipedia)
National Renal Administrators Association
A nonprofit organization representing dialysis facilities and centers throughout the United States. It supports members from all types of providers including freestanding, hospital-based and national chains through the weekly e-mail newsletter, Renal Watch, the Annual Meeting, periodic workshops and other meetings. NRAA members include dialysis provider companies and management consulting companies and other companies involved in the End Stage Renal Disease (ESRD) industry and supportive of the purposes of NRAA. Individuals not directly employed or otherwise involved in companies that are NRAA members may join as individual Associate Members. The purposes for which the NRAA is organized are as follows: # To provide renal administrators the opportunity for gaining continuing education, obtaining peer recognition and expanding development in the profession. # To promote and encourage education and training for renal administrators. # To recognize individuals who have done or are doing noteworthy service in the field of renal administration. # To educate the public and members of governing bodies of health care organizations to understand the issues surrounding the practice of renal administration. # To represent the professional interests of renal administrators as a national representative spokesperson for the development and implementation of public policy. # To act as a resource on local and national ESRD issues.
Nonprofit organization committed exclusively to support research seeking the cause of the potentially debilitating kidney disease Focal Segmental Glomerulosclerosis (FSGS) and Nephrotic Syndrome, improve treatment and find a cure. NephCure Kidney International is: * Committed to funding research around the globe that will continue to move us closer to an improved treatment and a cure. * The primary source of information on Nephrotic Syndrome and FSGS. * Leading the charge for legislative action to provide more federal funding for research into Nephrotic Syndrome and FSGS. * Working to attract researchers to this field. * Educating the public and raising awareness about Nephrotic Syndrome and FSGS.
Nephrology Nursing Certification Commission
Organization that established credentialing mechanisms to promote patient safety and to improve the quality of care provided to nephrology patients. There is a diversity of examinations providing the opportunity for certification at various levels of education, experience, and areas of practice within nephrology nursing. All of the certification examinations are endorsed by American Nephrology Nurses' ''' Association (ANNA). The Commission recognizes the value of education, administration, research, and clinical practice in fostering personal and professional growth and currently provides six examinations to validate clinical performance: * The Certified Dialysis Nurse examination * The Certified Dialysis LPN/LVN examination * The Certified Nephrology Nurse examination * The Certified Clinical Hemodialysis Technician * The Certified Clinical Hemodialysis Technician - Advanced * The Certified Nephrology Nurse - Nurse Practitioner
Commercial service interpreting renal biopsies using 14 board-certified, fellowship-trained pathologists with decades of experience. They provide doctors with a high quality, clinico-pathologic discussion by the pathologist that read the case. It is their goal to help equip doctors with the results they need to deliver the most effective patient care possible. That is why they deliver same-day biopsy results, including EM, because they know that time often has a critical effect on the outcome of many renal diseases. Nephropath also offers PLA2R serum testing and will soon be offering neuropathology services including muscle and nerve biopsy services.Nephropath is now Arkana Laboratories.
Data management platform and data repository based on the CKAN tool for managing and publishing collections of data. It enables the user to search for data, register published datasets, create and manage groups of datasets, and get updates from datasets and groups of interest.
A biotechnology corporation that uses human genetic information to discover, develop, manufacture and commercialize medicines to treat patients with serious or life-threatening medical conditions.
Private and statutory Ivy League research university in Ithaca, New York. Founded in 1865 by Ezra Cornell and Andrew Dickson White, the university was intended to teach and make contributions in all fields of knowledge—from the classics to the sciences, and from the theoretical to the applied.
A distributed framework and cyberinfrastructure for open, persistent, and secure access to Earth observational data. It ensures the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program. The DataONE Investigator Toolkit is a collection of software tools for finding, using, and contributing data in DataONE. DataONE currently hosts three Coordinating Nodes that provide network-wide services to enhance interoperability of the Member Nodes and support indexing and replication services. Coordinating Nodes provide a replicated catalog of Member Node holdings and make it easy for scientists to discover data wherever they reside, also enabling data repositories to make their data and services more broadly available to the international community. DataONE Coordinating Nodes are located at the University of New Mexico, the University of California Santa Barbara and at the University of Tennessee (in collaboration with Oak Ridge National Laboratory). DataONE comprises a distributed network of data centers, science networks or organizations. These organizations can expose their data within the DataONE network through the implementation of the DataONE Member Node service interface. In addition to scientific data, Member Nodes can provide computing resources, or services such as data replication, to the DataONE community.
A medical device company that develops, manufactures and markets innovative dialysis systems for the treatment of end-stage renal disease, or ESRD, and acute kidney failure.
An independent, not-for-profit consortium to accelerate research, and improve treatment for patients affected with the most commonly-diagnosed cancers in Asia by generating a genomic data resource for the most prevalent cancers in Asia. ACRG is focusing its initial efforts on Asian liver, gastric and lung cancers. Goals * Generate comprehensive genomics data sets for Asia-prevalent cancers * Conduct all research under good clinical practices and in accordance with local laws * Uncover key mutations and pathways for developing targeted therapies * Discover molecular tumor classifiers for patient stratification * Discover prognostic markers to identify high-risk patients * Freely share resulting raw data with scientific community to empower researchers globally and enable development of new diagnostics and medicines * Publish data analysis results jointly in prominent scientific journals Over the next two years, Lilly, Merck and Pfizer have committed to create an extensive pharmacogenomic cancer database that will be composed of data from approximately 2,000 tissue samples from patients with lung and gastric cancer that will be made publicly available to researchers and, over time, further populated with clinical data from a longitudinal analysis of patients. Comparison of the contrasting genomic signatures of these cancers could inform new approaches to treatment. Lilly has assumed responsibility for ultimately providing the data to the research public through an open-source concept managed by Lilly' '''s Singapore research site. Moreover, Lilly, Merck and Pfizer will each provide technical and intellectual expertise. One dataset can be found at http://gigadb.org/dataset/100034
Repository to host data and tools associated with articles published by GigaScience & GigaByte journals. GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support an article or study. Through their association with DataCite, each dataset will be assigned a DOI that can be used as a standard citation for future use of these data in other articles by the authors and other researchers. Datasets in GigaDB all require a title that is specific to the dataset, an author list, and an abstract that provides information specific to the data included within the dataset. Detailed information about the dataset is curated by dedicated biocurators in collaboration with the article authors at the time of publication of the associated manuscript to ensure full transparency and reproducibility of all journal articles published in GigaScience and GigaByte journals.
Analgesic Anesthetic and Addiction Clinical Trial Translations Innovations Opportunities and Networks
A public-private partnership with the United States Food and Drug Administration (FDA) to identify, prioritize, sponsor, coordinate, and promote innovative activities - with a special interest in optimizing clinical trials - that will expedite the discovery and development of improved analgesic, anesthetic, and addiction medications and to more generally accelerate the development of treatments with improved efficacy and safety. This multi-year, multi-phase initiative is closely aligned with the FDA' '''s Critical Path Initiative. The key objectives of ACTTION involve initiating and supporting strategic collaborations among a broad spectrum of stakeholders - including, but not limited to, academia, the FDA and other government agencies, industry, professional organizations, patient advocacy groups, foundations, and philanthropic organizations - with the goals of sharing data and innovative thinking about the development of novel therapeutics. These strategic collaborations involve a wide range of research projects and other activities, for example, scientific workshops, consensus meetings, and in-depth analyses of clinical trial data to determine the effects of research methods on study assay sensitivity and efficiency. ACTTION launched an initiative to develop training materials for clinical trial subjects (and staff) to be used with pain rating scales and other pain-related patient reported outcomes. Once materials have been developed and evaluated, proof-of-concept trials will be conducted to test the hypothesis that patient and staff training can improve the assay sensitivity of analgesic trials.
Alzheimer''''s Disease Genetics Consortium
Alzheimer''''s Disease Genetics Consortium (ADGC)
Consortium to conduct genome-wide association studies (GWAS) to identify genes associated with an increased risk of developing late-onset Alzheimer' '''s disease (LOAD). The goal of the ADGC is to identify genetic variants associated with risk for AD. It plans to do this through the following collaborative goals: # Identify genes responsible for AD susceptibility # Identify AD sub-phenotype genes rate-of-progression plaque / tangle load / distribution biomarker variability # Generate a genetic data resource for the AD research community Data generated by ADGC is available at the following website: https://www.niagads.org/content/alzheimers-disease-genetics-consortium-adgc-collection
Ontology to organise a 2009 set of over 200 NHS quality indicators from different sources. Relationships between indicators, a basic set of inclusion / exclusion criteria, clinical pathway, clinical code and purpose (per 1992 Institute of Medicine, originally intended to categorise clinical guidelines) are identifies and made searchable.
Towards novel translational safety biomarkers for adverse drug toxicity
Consortium to develop novel in vitro predictive screening tools and in vivo translational models and biomarkers to improve adverse drug reaction (ADR) hazard identification. This project studies the metabolic effects of eight drugs (among which are paracetamol and diclofenac ) with known side effects in the liver. By looking into the mechanics on a level ranging from the molecule to the patient, the researchers in this project aim to find biomarkers and develop tools for the early prediction of side effects of drugs. One of the breakthroughs in the project is the discovery that a person' '''s genetic profile appears to be one of the mechanics that have an influence on the resistance to adverse drug reactions. The ability to identify adverse effects in an early stage will prevent much discomfort in patients and economic loss. Several PhD theses have been written from this project.
Alzheimers Association Research Roundtable
Alzheimer's Association Research Roundtable
A consortium aiming to facilitate the development and implementation of new treatments for Alzheimer's disease by collectively addressing obstacles to research and development, clinical care and public health education. The Roundtable convenes twice each year for a two-day presentation and discussion of specific topics within Alzheimer's research. Topics are selected from a list proposed and voted on by members. Roundtable members explore a broad range of Alzheimer's science topics, including: * New data and technologies that may improve the diagnosis of Alzheimer's disease, especially in its earliest and mildest stages. * Neuropsychological testing, genetic factors, and biochemical and neuroimaging biomarkers that could contribute to an earlier and more accurate Alzheimer's diagnosis. * Lessons learned about clinical trial design that may help shape future clinical trials of drugs aimed at slowing or stopping the progression of Alzheimer's. * The pros and cons of various scales as outcomes measures of clinical trials. The outputs of Roundtable meetings are published as articles in the Alzheimer's Association's journal, Alzheimer's & Dementia. The Research Roundtable also sponsors Alzheimer's Association grants. The chosen project is named Research Roundtable Sponsored Grant and the principal investigator of the project is invited to give a progress report at a Roundtable meeting.
Lions Eye Institute for Transplant and Research
Lions Eye Institute for Transplant & Research
A nonprofit ocular research center with the largest eye bank in the world that provides eye tissue for research and transplantation to ophthalmic specialists and surgeons nationwide. They empower researchers to conduct real-time studies of healthy and diseased ocular tissue leading to a greater understanding of the events that lead to blindness. Their mission is to improve visual outcomes and quality of life for those who are blind or visually impaired through innovative ocular endeavors.
International Age-related Macular Degeneration Genetics Consortium
Consortium aiming to identify the remaining genetic risk variants for Age-related Macular Degeneration (AMD). To increase the statistical power needed to identify genes that have small, yet significant contributions to AMD, the consortium is conducting a meta-analysis on 15 Genome Wide Association Studies (GWAS) pooled from consortium members representing over 8,000 patients with advanced AMD (dry type, neovascular, or both) and 50,000 controls. In addition to verifying known genes, the consortium identified 19 new gene variants. The genes identified in these studies function in the immune system, cholesterol transport and metabolism, and formation and maintenance of connective tissue. This study provides a nearly complete picture of genetic heritability for AMD.
JDRF Artificial Pancreas Project Consortium
JDRF/NIDDK Artificial Pancreas Project Consortium
Consortium aiming to accelerate the development of systems for automated control of blood glucose in patients with diabetes. Consortium investigators seek to research and develop strategies, which can be commercialized, that will confer the long-term benefits of improved glycemic control by combining novel automated control algorithms and hormone therapies with continuous glucose monitors and pump devices. The field of closed-loop artificial pancreas research requires expert diabetologists partnering with expert mathematicians and engineers. Consortium investigators include endocrinologists and control theorists at research institutions in the US and in Europe. Many of the diabetes device manufacturers have also participated, providing pumps and sensors with enhanced capabilities that allow for closed-loop experiments to be performed. The goals of the consortium include: * Design, optimization, and clinical testing of multiple algorithmic approaches to closed-loop control * An in silico simulation platform, accepted by the FDA, for validating candidate closed-loop control algorithms in place of animal trials * Reusable templates for constructing the Investigational Device Exemption regulatory documents that must be approved by the FDA prior to any in-clinic, computer-assisted, closed-loop control research involving people * A modular software platform-the Artificial Pancreas System-with a protocol-independent user interface and hooks to incorporate an arbitrary control algorithm and control various continuous glucose monitors and pump devices * A secure consortium Web site with a central repository for experimental data and interfaces to submit candidate control algorithms for centralized validation and to upload or download clinical data sets * the first outpatient studies of an overnight controller * the first outpatient studies of a hypoglycemia minimization strategy * the development and testing of a modular treat-to-range closed-loop approach * multiple studies of dual hormone (insulin and glucagon) devices and a means to improve insulin kinetics Ongoing and recently completed in-clinic studies at the end of 2011 include investigations into hypoglycemia prediction and avoidance as well as fully-automated closed-loop control investigations using MPC and PID/PD-based algorithms. The most recent developments include the first-ever feasibility trials of portable, outpatient-based closed-loop control systems.
European Organisation for Research and Treatment of Cancer Clinical trials
A database that contains information about EORTC (European Organisation for Research and Treatment of Cancer) clinical trials but also clinical trials from other organizations, in which EORTC has been/is participating. The protocol database may be browsed by EORTC Research Group, tumor site, treatment, or drug.
NYU Health Sciences Library Data Catalog
A searchable data catalog that facilitates researchers'' access to large datasets available either publicly or through institutional or individual licensing. Dataset records include information about the content of the dataset, how to access the dataset, and local experts within NYULMC and NYU to assist in the use of these datasets. The data catalog will expand to include internally generated datasets from NYULMC and NYU in the near future. Use the contact form if you are interested in submitting a dataset to the data catalog.
A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation.
Consortium of pharmaceutical companies and clinical research organizations, plus one regional association, that are pooling their resources to deliver quality training courses for clinical research professionals in the Asia Pacific region. The collaborative training initiatives aim to resolve issues of redundant and duplicate trainings, less than optimal class sizes and lower than ideal training frequencies, all of which are prevalent in the region. ATC also hopes to significantly enhance the number and quality of professionals to meet the resource demands of the globalized industry. The first target audience would be clinical trial investigators and clinical trial management staff - with priorities provided to clinical trial associates, clinical trial project managers, and clinical research managers. As of 2014, 900 days of ATC courses have been taught in classrooms throughout Asia. The ATC''s Foundations of Clinical Project Management is a regularly offered in Shanghai and is available on-line in English and Mandarin.
Biomarkers Across Neurodegenerative Diseases
Consortium that launched a Request for Applications (RFA) to stimulate analyses across the Alzheimer's disease (AD) and Parkinson's disease (PD) research enterprises to engage in further data analysis of existing cohorts, including, but not limited to, biomarker discovery, standardization of assays, genetic profiles, and imaging modalities. The RFA aims to build on existing momentum to leverage similar activities and increase impact across the neurodegenerative disease spectrum. It also builds on recent evidence suggesting substantial overlap between AD, PD, and other neurodegenerative diseases pathologically, but also potentially biologically. The RFA is designed to enable preliminary pilot research or proof-of-principle studies utilizing data and/or samples from two large biomarker studies, the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Parkinson's Progression Markers Initiative (PPMI), in order to garner further research support from other funding agencies. Application Deadline: March 19, 2014. Efforts under BAND include studies that: * analyze datasets to test hypotheses related to aging and neurodegenerative disorders; * seek to identify panels or pathways that may play a role in disease mechanisms, such as around inflammation; * pursue shared or disparate biochemical markers of disease risk, onset or progression; * assess potential commonalities across the disease spectrum, including around other neurological disorders such as Lewy body dementia. Recent data reported at the 2013 Alzheimer's Association's International Conference stimulated discussion in the research community about the possible cross talk between AD and PD. For example, underlying pathologies / biomarkers, such as cerebrospinal fluid (CSF) alpha-synuclein, have been measured in the sample sets collected for both diseases to help understand similarities and differences in these diseases. Furthermore, similar imaging modalities, such as MRI and PET, are being employed to interrogate changes that occur with disease progression. As therapeutic approaches are developed that may be disease-modifying for several neurodegenerative diseases, stratification of clinical trial populations based on biomarker profiles may increase the probability of success in demonstrating a beneficial effect.
Canadian granting agency to address the existing translational funding gap in neurodegenerative research of the aging population with a goal of accelerating the development of therapeutics and to encourage innovation in the granting process. To achieve this they address gaps and inefficiencies in the funding market by supporting high-risk, high-reward projects independent of commercial potential, while leveraging world-class business and scientific expertise to build a fast and flexible granting process. The Weston Brain Institute is committing up to $10 million in funding across Canada, each year, through various programs and partnerships. The Weston Brain Institute has ongoing collaborative relationships with the Alzheimer's Drug Discovery Foundation - Canada, Brain Canada, the Michael J. Fox Foundation, as well as a group of scientific advisors chaired by Dr. Andres Lozano.
Foundation that gives grants in Canada for the benefit of Canadians and directs its resources to specific organizations in Education, Land Conservation and Science in Canada''s North. In addition, it provides funds to further Canada''s research in neuroscience. These programs are director-initiated and the Foundation therefore does not accept applications for funding. By law, the Foundation is only able to support Canadian charities that are registered with the Canadian Revenue Agency. These charities must have a CRA charitable number and offer programs benefiting Canadians in Canada.
biomedical and healthCAre Data Discovery and Indexing Ecosystem
Project to facilitate the construction of a Data Discovery Index. The data discovery index (DDI) is to do for data what PubMed (and PubMed Central) did for the literature. Biomedical researchers and healthcare institutions should be enabled to share their data in a way that advances science and protects privacy. They will find ways to facilitate structuring, discovery, and accessing of data without requiring people to understand complex standards that only a few specialized groups can decipher. bioCADDIE will pursue the following aims: # Provide ease in finding accessible data of interest according to disease, data modality (e.g., imaging, molecular measurements), and/or demographics through simple and intuitive computer interfaces that allow quick ranking, visualization, and summarization of data resources - this requires methods for automated indexing (i.e., creation of metadata), tools that allow free text searches, accessibility tools that decode consent requirements, etc. # Assist data producers on how to publish data for maximal discoverability and assessment of impact of disseminated data through data citation networks; and # Train data producers and data users in relevant tools related to biomedical data sharing. This will be done through online resources, workshops, and dissemination of best practices through publication of articles about data discovery in different venues (a) scholarly publications, and (b) lay press news articles.
Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations
Biomarkers of Anti-TNF- Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients
Biomarkers of Anti-TNF- Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients (BATTER-UP)
Biomarkers of Anti-TNF-alpha Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients
A consortium evaluating a new biomarker screening test that might help identify patients with rheumatoid arthritis (RA) who are unlikely to benefit from anti-tumor necrosis factor-alpha (TNFalpha) medications. BATTER-UP will enroll around 1,000 patients being treated by one of several marketed anti-TNF RA drugs: Enbrel, Remicade, Humira, Simponi, or Cimzia. Through data analyses and predictive response modeling, the consortium aims to better understand which patients with RA will derive the greatest benefit from TNF inhibitors. The investigators in this observational study will attempt to validate an 8-gene biomarker set based on work by Biogen Idec researchers as likely to predict anti-TNF responsiveness in patients with RA. In preliminary results, the 8-gene biomarker set predicted with 89% accuracy individuals who did not reach European League Against Rheumatism (EULAR) Disease Activity Score (DAS)-28 good response after 14 weeks of treatment. The 8 genes included in the screen are CLTB, MXRA7, CXorf52, COL4A3BP, YIPF6, FAM44A, SFRS2, and PGK1. Biological samples and clinical outcome information will be used to confirm and extend the utility of previously published biomarkers that can predict response to anti-TNF agents. These data may also generate new hypotheses for further testing. The BATTER-UP samples and data will be established as a reference set for investigation of personalized medicine in RA. The study will be a resource of DNA and other biological materials that can be investigated for biomarkers in the future as new technologies arise.
Center aiming to be a catalyst for regenerative medicine by facilitating collaboration, supporting research, and promoting awareness of the field. The center includes 15 scientists at five Toronto hospitals, as well as the University of Toronto, currently working to accelerate the development of more effective treatments for conditions such as heart disease, diabetes, respiratory disease and spinal cord injury. They collaborate with many other research institutions throughout North America, Europe and the Asia / Pacific region. The research is powered by a team of recent doctoral graduates recruited from around the world that are selected through a competitive process. They are a critical tool for supporting the work of McEwen Centre, allowing them to find medical breakthroughs faster.
DanStem - The Center for Stem Cell Research
Center consisting of 9 research groups who all address basic questions in stem cell and developmental biology with the overall aim of developing new stem cell-based therapeutic approaches for diabetes and cancer. DanStem comprises two sections: * The Novo Nordisk Foundation Section for Basic Stem Cell Biology (BasicStem) * The Section for Strategic Translational Stem Cell Research and Therapy (TransStem) DanStem was established as a result of a series of international recruitments coupled with internationally recognized research groups focused on insulin producing beta cells and cancer research already located at the University of Copenhagen. They all have well-established, international collaborations and actively participate in several international scientific consortia. DanStem is also active in training undergraduates, PhD students and postdocs.
An academic-business-clinical partnership that sponsors research programs focused on the development of next-generation biomedical diagnostic devices. They aim to transform healthcare by pioneering advances in the science and technology of diagnostics and by translating these advances into clinical use. Building on key scientific insights, the BDI will now apply its established capabilities to create integrated Point-of-Care solutions, which will have major impacts on diagnosing disease and sustaining human health.
Commercial organization that offers medicinal chemistry services and consulting consisting of the combination of structure based drug design and computational chemistry with multi-disciplinary expertise. A proven track record exists in the identification and the delivery of successful drug candidates. They offer solutions within small molecule drug discovery and outsourcing project management.
A drug discovery company utilizing its methodologies to evaluate the interaction of molecules in order to generate novel therapeutics. They offer expertise and services in the area of surface plasmon resonance (SPR) biosensor-based small molecule interaction analysis and partnerships for fragment-based lead generation using their proprietary Sprint platform.
A consortium that aims to transform cancer research through collaborative oncology trials that leverage the scientific and clinical expertise of the Big Ten universities. The goal is to align the conduct of cancer research through collaborative, hypothesis-driven, highly translational oncology trials that leverage the scientific and clinical expertise. The clinical trials that will be developed will be linked to molecular diagnostics, enabling researchers to understand what drives the cancers to grow and what might be done to stop them from growing. The consortium also leverages geographical locations and existing relationships among the cancer centers. One of the consortium's goals is to harmonize contracts and scientific review processes to expedite clinical trials. The consortium will only focus on phase 0 to II trials because larger trials - even a randomized phase II trial - are difficult to conduct at a single cancer center.
An independent nonprofit cancer research organization that provides full-service clinical trial management and support, from conception and study design through project completion and publication. Established to explore and develop leading edge cancer treatments across the United States and internationally, their clinical trials, developed in collaboration with academic and community oncologists, are conducted within a member network of more than 130 clinical research sites. Their vision and mission is to form unparalleled relationships between academic, community, pharmaceutical, and biotech partners with the goal of advancing cancer research, education, and patient advocacy. There are no costs to become a member.
Consortium formed to improve global health by overcoming obstacles to the development and implementation of biomedical innovation. CBI provides a safe and transparent environment for collaborative research among industry, academia, and government, and draws on the expertise of the Massachusetts Institute of Technology' '''s (MIT) Schools of Engineering, Science, and Management, as well as the Harvard-MIT Division of Health Sciences and Technology (HST). The center manages several consortia addressing a variety of challenges in the global biomedical industry by developing, testing, and disseminating new knowledge and tools designed for real world application through the following programs: the Biomanufacturing Program (BioMAN), the Consortium on Adventitious Agents in Biomanufacturing (CAACB), and New Drug Development Paradigms (NEWDIGS). The consortia managed by CBI include: * Biomanufacturing (BioMAN): a collaborative research and educational program in biotherapeutic manufacturing. The objective is to develop new knowledge, science, technologies and strategies that advance the manufacture and global delivery of high quality biopharmaceuticals. BioMAN activities bring together thought leaders from industry, the government/FDA and academia and involve faculty from across the Schools of Science, Engineering and Management at MIT * Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB): Their mission is to develop a comprehensive understanding of adventitious agents encountered in biomanufacturing, the sources of such agents, and a systematic, risk-based analysis of the most effective strategies and technologies to prevent contamination. * NEW Drug Development ParaDIGmS (NEWDIGS): focuses on transforming the current global pharmaceutical innovation ecosystem to more reliably and sustainably deliver new, better, affordable drugs to the right patients faster. System re-engineering projects are designed and executed with input from industry; regulators from US, Europe, Singapore, and Canada; payers and health technology assessment officials; providers, patients, and academic researchers from MIT, Harvard and other leading academic institutions.
Exploring and Understanding Adverse Drug Reactions by Integrative Mining of Clinical Records and Biomedical Knowledge
Consortium that created the capability to detect Adverse Drug Response (ADR) signals by creating the infrastructure for large-scale monitoring of drug safety using electronic health records (EHR). The platform leverages EHR' '''s comprising demographics, drug use and clinical data of over 30 million patients from several European countries. Special attention was given to patient groups that are not routinely involved in clinical trials, for ethical or practical reasons (e.g. pregnant women, elderly people, people using many drugs simultaneously, and children). This project also studies and compares a number of different techniques that all aim to detect unexpected or disproportional rates of events. The algorithms that they studied originate not only from the field of (pharmaco)epidemiology, but also from fields such as bio-terrorism, machine learning, and classical signal detection. EU-ADR specific objectives are: To detect events, To relate these events to drugs, To develop hypothesis that explain adverse events, To detect adverse events earlier, and To avoid false positives. The web-based platform is available at https://bioinformatics.ua.pt/euadr/ EU-ADR has contributed to the ability to conduct better drug safety studies based on the re-use of healthcare data. By facilitating the early detection of adverse drug reactions, but also providing key information on populations at risk, potential drug interactions, potential underlying mechanisms and intervening pathways in adverse events, etc., the project will allow for improved and more complete information to be available for drug and healthcare delivery, leading to increased patient safety and its associated cost savings. The EU-ADR system can be considered as a complementary tool to already existing pharamcovigilance systems. Should the system be widespread in the long term, it has the potential to contribute to the development of future electronic health record systems, insofar as the expected benefits of these IT tools are only fully attainable when EHRs develop themselves in consistency, richness and formats that allow them to be subject of such tools. In anticipation, EU-ADR has been designed to be modular and scalable, so that different EHR databases (other than those participating in the Consortium) can be progressively enlisted in the future, adopt the software for data extraction and therefore become susceptible of exploitation by the system, for maximum global effect.
International Genomics of Alzheimers Project
International Genomics of Alzheimer's Project
Consortium to discover and map the genes that contribute to Alzheimer's disease and completely understand the role inheritance plays. To achieve this goal, they will work to identify all the genes that contribute to the risk of developing this disease. Investigators will have access to combined genetic data from a large number of Alzheimer's disease subjects and compare it to genetic data from an equally large number of elderly people who do not have Alzheimer's. In the initial phase of the work, more than 20,000 people with Alzheimer's and about 20,000 healthy elderly subjects will be compared. As the study progresses, 10,000 additional people with Alzheimer's and the same number of healthy elderly subjects will be added to the study. The subjects for these studies come from different Alzheimer research project locations across Europe, the UK, the US, and Canada. Data is available from their 2014 publication in Translational Psychiatry at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944635/ (http://www.ncbi.nlm.nih.gov/pubmed/24495969) Currently, there is no public access to the raw individual level genetic data because of privacy considerations. Researchers working with US cohorts deposit data in the database of genotypes and phenotypes (dbGaP), where it is available to all researchers who can show that they are able to guarantee the security of the data. After scanning the DNA of over 74,000 patients and controls from 15 countries, the IGAP consortium reported 11 new regions of the genome involved in late-onset Alzheimer's disease. IGAP published its results in Nature Genetics on October 27, http://www.ncbi.nlm.nih.gov/pubmed/24162737
Ben-Gurion University of the Negev; Beer-Sheva; Israel
Ben-Gurion University of the Negev; Beersheva; Israel
Public research university in Beersheba, Israel. Ben-Gurion University of the Negev has five campuses: the Marcus Family Campus, Beer Sheva; the David Bergmann Campus, Beer Sheva; the David Tuviyahu Campus, Beer Sheva; the Sede Boqer Campus, and Eilat Campus.
National Institute of Health and Medical Research; Rennes; France
A non-profit registered French charity that provides a research on Alzheimer's disease and related disorders program with the following goals: * create a dynamic national and international collaborative research of the fundamental absorptions, * densify the network of public and private researchers with an attractive policy * install infrastructure basic, clinical and laboratory performing research * promote interaction with the health industries to reduce development time. At the national level the Foundation has implemented measures Research Plan, through: * animation fabric French medical and scientific research, * coordination of research initiatives * the implementation of actions, * support for specific projects. Internationally, the Foundation is at the origin of an international mobilization of researchers, initiated during the French Presidency of the European Union. Called Joint Programming, this pilot initiative involves 23 countries will coordinate their efforts at European level research on neurodegenerative diseases, especially Alzheimer's disease.
French Muscular Dystrophy Association (AFM)
Disease-related portal with the objective to defeat neuromuscular diseases which are devastating muscle-wasting diseases. It has set itself two missions: curing neuromuscular diseases and reducing the disabilities they cause.
Cohorts for Heart and Aging Research in Genomic Epidemiology
Consortium formed to facilitate genome-wide association study meta-analyses and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies. A bibliography of CHARGE publications is available. Its founding member cohorts include: * Age, Gene, Environment, Susceptibility Study -- Reykjavik * Atherosclerosis Risk in Communities Study * Cardiovascular Health Study * Framingham Heart Study * Rotterdam Study Additional core cohorts include: * Coronary Artery Risk Development in Young Adults * Family Heart Study * Health, Aging, and Body Composition Study * Jackson Heart Study * Multi-Ethnic Study of Atherosclerosis
A multi-national pharmaceutical and diagnostics company that develops, manufactures, and distributes an extensive array of diagnostics and therapeutics for a wide range of indications and conditions. They focus on production of cardiovascular products, vaccines, hormones, antibiotics, gastrointestinal products, and eye care. The company operates in the U.S., Chile, Israel, Mexico, Uruguay, and Spain. (Adapted from Wikipedia)
Healthcare company that oversees all pharmaceutical and medical device commercial activities of Otsuka Group (Otsuka) in North America. Products with emphasis on neuroscience, oncology, cardio-renal, and medical device markets.
A biopharmaceutical company developing pharmaceuticals for patients with renal and vascular diseases. Their ongoing Phase 3 clinical trial is evaluating whether a single treatment of PRT-201 can reduce vascular access failure, one of the most serious problems experienced by patients with chronic kidney disease (CKD) undergoing hemodialysis. PRT-201 is an investigational drug that may inhibit neointimal hyperplasia, the growth of tissue inside blood vessels that can result in vessel narrowing and reduced blood flow. PRT-201 has received fast track and orphan drug designations for hemodialysis vascular access indications.In September 2019, Proteon Therapeutics merged with ArTara Therapeutics.
Company developing peritoneal dialysis disinfection system to improve quality of life for dialysis patient by reducing infections related to peritoneal dialysis (PD) and saving time through improved, simplified connection of PD catheters. While decreasing dependence on patient compliance, the goal is to keep patients well protected and healthy throughout the efficient dialysis process.
Quintiles Global Clinical Research Organization
Contract research organization, clinical trial services, and pharmaceutical consulting service company. Now IQVIA after merger of Quintiles and IMS Health, Inc.
Pharmaceutical company focused on investigating experimental oral antioxidative and anti-inflammatory drugs, which dually activate the antioxidative transcription factor Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) and inhibit the pro-inflammatory transcription factor NF-B (nuclear factor kappa-light-chain-enhancer of activated B cells). The antioxidative and anti-inflammatory compounds bardoxolone methyl and RTA 408 are the lead clinical development compounds in their portfolio.
Cancer Research UK is UK's largest charity funding cancer research. Cancer Research UK is a registered charity in England and Wales (1089464) and in Scotland (SC041666). Registered as a company limited by guarantee in England & Wales No. 4325234.
The R-fMRI Network (RFMRI.ORG): A network for supporting resting-state fMRI related studies!
The R-fMRI Network - a network for supporting resting-state fMRI related studies
The R-fMRI Network a network for supporting resting-state fMRI related studies
A network for supporting resting-state fMRI (R-fMRI) related studies. It connects R-fMRI researchers (as nodes) by their sharings (as edges). Through the network, ideas, comments, resources, tools, experiences, and data can be shared. Researchers (nodes) with basic neuroscience, methodological, or clinical backgrounds can connect with each other in the network. It also contains a preprint server that allows neuroscientists to share their preprints, comment on each others research and get back valuable information about their experiments from their colleagues. This is based on the arXiv model. Ultimately, the network aims to enhance collaborations among researchers, especially to translate knowledge of basic neuroscience and methodology to clinical applications (bench to bedside).
International Alzheimer's Disease Research Portfolio
International Alzheimers Disease Research Portfolio
Database that brings together funded Alzheimer's disease (AD) research supported by public and private organizations both in the US and abroad all categorized using the Common Alzheimer's Disease Research Ontology or CADRO. Launched as a joint collaboration between the National Institute on Aging (NIH) and the Alzheimer's Association, IADRP enables users the ability to assess the portfolios of major organizations (currently 30) for areas of overlap as well as areas of opportunities in which to collaborate and coordinate in a collective effort to advance AD research.
A flexible, extensible and modular XML-based data exchange standard for seismological data which is intended to cover a broad range of fields.
National Institute of Mental Health Educational Resources
Common Alzheimer''s Disease Research Ontology
Common Alzheimer's Disease Research Ontology (CADRO)
A classification system developed by the National Institute on Aging and the Alzheimer's Association that can be used to integrate and compare Alzheimer's disease (AD) research portfolios from public and private organizations supporting AD research in the US and abroad. The CADRO was constructed as a three-tier classification system organized around seven major categories: five in research and two resource-related: * Category A. Molecular Pathogenesis and Pathophysiology of Alzheimer's Disease * Category B. Diagnosis, Assessment and Disease Monitoring * Category C. Translational Research and Clinical Interventions * Category D. Epidemiology * Category E. Care, Support and Health Economics of Alzheimer's Diseases * Category F. Research Resources * Category G. Consortia and Public Private Partnerships * Category H. Alzheimer's Disease - Related Dementias Using information from project abstracts and research aims, the above categories were stratified into research topics and these were further divided into research themes. The three levels of classification are meant to enable a fine-grained portfolio analysis that can inform strategic planning and funding decisions. The CADRO was developed as a dynamic portfolio analysis tool that can be used to: (i) capture the changing landscape of AD research funded by different organizations, (ii) identify opportunities for coordination of support for AD research, and (iii) identify funding gaps as well as areas of overlap within and across organizations.
Biopharmaceutical company focused on development and commercialization of non-absorbed polymeric drugs to treat disorders in areas of renal, cardiovascular and metabolic diseases.February 2021 - Relypsa changed its name to Vifor Pharma. Company is focused on development and commercialization of late stage medicines that will change treatment paradigms and improve patients lives.
An association representing and serving nephrology practitioners in the United States whose members are committed to improving the care of patients with chronic kidney disease (CKD) and related disorders. RPA educates policymakers about issues that affect both patients and nephrology practices. They also work with the Centers for Medicare & Medicaid Services (CMS) on regulatory policies. (Adapted from Wikipedia) Programs focus in the areas of practice management, public policy and quality patient care. They provide timely and relevant programs along with current nephrology tools and resources to make certain members maintain their highest level of professional satisfaction.
A nonprofit, patient-focused, patient-run organization that provides non-medical services to those affected by chronic kidney disease (CKD). RSN strives to help patients develop their personal coping skills, special talents, and employability by educating and empowering them and their family members to take control of the course and management of the disease. RSN plays a vital role in providing lawmakers and policymakers with the patient''s perspective on the needs and capabilities of people with CKD.
A fully-integrated biopharmaceutical company targeting end-stage renal disease (ESRD) and chronic kidney disease (CKD) with products and services for the treatment of iron deficiency anemia, secondary hyperparathyroidism and hemodialysis.
Company provides specialist diagnostic products to clinicians and laboratory professionals worldwide. Specialist protein company committed to research, development, manufacture and distribution of immunodiagnostic assays for global laboratory market. Specialized in antibody specificity technology, Binding Site gives clinicians and laboratory staff tools to significantly improve diagnosis and management of those patients with specific cancers and immune disorders. Binding Site manufactures wide range of products for plasma protein analysis including Freelite, Hevylite and SPAplus.
Private, clinical stage biotherapeutics company focused on delivering new solutions to individuals affected by kidney disease. They are committed to developing novel approaches to protect, treat and restore kidney function for this patient group. Company has designed specific class of peptide compounds that have shown excellent results in controlling experimental kidney diseases, notably, models of diabetic nephropathy (kidney damage associated with diabetes), and acute kidney injury. These proprietary peptides may therefore be able to prevent and treat acute kidney injury, as well as slow and possibly reverse the progression of diabetic nephropathy. They act to control apoptosis (programmed cell death), inflammation and fibrosis (formation of scar tissue).
Public research university founded in 1945 in Łódź, Poland, as a continuation of educational institutions functioning in Łódź in the interwar period — the Teacher Training Institute, the Higher School of Social and Economic Sciences and a division of the Free Polish University.
Private research university in Boston, Massachusetts. The university is nonsectarian but maintains its historical affiliation with the United Methodist Church. It was founded in 1839 by Methodists with its original campus in Newbury, Vermont, before moving to Boston in 1867.
A data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas.
A society to raise interest in the field of hemodialysis vascular access, to promote and conduct basic and clinical research and to organize congresses, meetings and courses. The VAS is a multidisciplinary society which is of interest to nephrologists, surgeons, interventional radiologists, dialysis, nurses, vascular and radiological technologists. The VAS organizes an International Congress every two years in one of the countries in Europe. Every year a Vascular Access Course will be held in a European City. The multidisciplinary council of the VAS consists of nephrologists, surgeons and radiologists and representatives from each European country will be asked to join the board.
NCRI - National Cancer Research Institute
The National Cancer Research Institute (NCRI) is a UK-wide partnership between the government, charity and industry which promotes co-operation in cancer research among the 22 member organizations for the benefit of patients, the public and the scientific community. Cancer affects everyone. One third of people in the UK get cancer at some time in their lives and a quarter of all people die from it. This means that even if we don''t have cancer ourselves, we know someone who does, or soon will.
Society devoted to the advancement of the field of dialysis access through research, education and advocacy for patients with end stage kidney disease. They provide vascular access education for physicians, nurses, and other health care professionals and advocate for evidenced-based best clinical practices.
An international organization for patients with vasculitis, their families, friends and the health care professionals who care for them, supporting and empowering them through education, awareness and research. The Foundation advocates for early diagnosis and leading edge treatment for all. The Foundation also partners with researchers around the world to determine the cause and discover the cure for vasculitis.
An American manufacturing company specializing in products derived from fluoropolymers that focuses its efforts in four main areas: electronics, fabrics, industrial and medical products.
Commercial organization that aims to bridge the gap between academia and the life-sciences industry with a wide ranging experience in pharmaceutical industry R&D covering multiple target classes and therapeutic areas. This deep scientific insight and established links with world class research institutions is applied across their business groups: * Drug Discovery * Biomarker and Translational Research * Enabling Technologies * R&D Information Technologies They measure their performance by successful outcomes for their collaborators, and recognize that an authentic partnership approach is essential in achieving the goal of converting outstanding science into high quality starting points for new medicines.
In 2018 Bruker acquired Sierra Sensors GmbH, based in Hamburg, Germany. Sierra develops and manufactures innovative analytical biosensors based on Surface Plasmon Resonance (SPR) detection. Driven by patented technologies in the areas of SPR detection and microfluidic sample delivery, Sierra instruments are setting a new standard in high-throughput and high-performance label-free analysis.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.This project attempts to establish a platform for spike sorting with two different goals: First, to provide a sophisticated benchmark data set which could be used for future publications on this topic. Second, to give researchers using spike sorting software the possibility to evaluate their data under different conditions and compare their results to other spike sorters. Extracellular recordings are a standard procedure to analyzing the activity of neurons. A problem with this kind of recording is the simultaneous recording of not a single neuron but a small local population of neurons. It is not straight-forward to reconstruct the single neuronal activities. To estimate the single neuron activity (the so called spike train) from this multi neuron activity, spike sorting is applied. Many different algorithms for spike sorting were proposed. However, despite many efforts to tackle this problem, it is still difficult to tell under which circumstances which spike sorting algorithm is the best. If you are interested in some basic reading about spike sorting please consult the following references. A review of methods for spike sorting: the detection and classification of neural action potentials M. S. Lewicki (1998), Network: Computation in Neural Systems, Vol. 9, No. 4. (1998), pp. 53-78 Towards reliable spike-train recordings from thousands of neurons with multielectrodes. Einevoll GT, Franke F, Hagen E, Pouzat C, Harris KD (2011), Curr Opin Neurobiol. 2011 Oct 22.
Organization founded to meet a growing, urgent need for streamlining clinical trials that brings together an online network of clinical trial sites, the leading investigator identification and start-up platform, the industry''s best trial optimization system, and the leading grants payment capabilities to transform the way drug developers find, engage and pay doctors to run clinical trials. Specialties include: Site Identification, Protocol Feasibility, Building Investigator Communities, Site Startup, Investigator Payments, Contracts and Essential Documents, Investigator Budget Development
Quantitative Enrichment of Sequence Tags
Quantitative Enrichment of Sequence Tags: QuEST
A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments.
Curriculum materials for an Introduction to Neurobiology course for undergraduate and graduate students. The course focuses on the analysis of neurons and neural circuits for behavior using the fundamental principles of neuroscience. From the online course syllabus, the 24 units that make up the course may be directly accessed. Each unit contains a reading, links to at least one simulation, and a problem set. A list of all available simulations can be found here: https://neurowiki.case.edu/wiki/Simulations. * 25 simulations are written in JavaScript and will run in any browser. Source code: https://github.com/CWRUChielLab/JSNeuroSim * Pre-compiled executables (Windows, Mac, Linux) are available for 1 desktop simulation, the Nernst Potential Simulator. Source code: https://github.com/CWRUChielLab/Nernst Structure of the Course * Solving problems based on simulations of neuronal components, neurons, and simple circuits to understand how they work. * For advanced students, writing a neuroscience Wikipedia article, critical review, or grant, in stages.
This resource no longer in service. Documented on August 12, 2021. French biotech company dedicated to human endocrine cell line production with a first focus on human pancreatic beta cell. Other cell types are being prepared like glucagon cells. The material will be powerful tools for drug discovery, toxicology and cell replacement therapy. Achievements to date * Generated tumoral and non-tumoral human beta cell lines which closely resemble human primary pancreatic beta cells (using technologies which have been first developed and validated using immortalized rat beta cell lines). World first. * Established a robust technology platform which will be used to develop other human endocrine cell lines.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. An aggregated data platform for genome sequencing data created by a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data set provided on this website spans 61,486 unrelated individuals sequenced as part of various disease-specific and population genetic studies. They have removed individuals affected by severe pediatric disease, so this data set should serve as a useful reference set of allele frequencies for severe disease studies. All of the raw data from these projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects. They ask that you not publish global (genome-wide) analyses of these data until after the ExAC flagship paper has been published, estimated to be in early 2015. If you''re uncertain which category your analyses fall into, please email them. The aggregation and release of summary data from the exomes collected by the Exome Aggregation Consortium has been approved by the Partners IRB (protocol 2013P001477, Genomic approaches to gene discovery in rare neuromuscular diseases).
A complete guide to antibody research and suppliers. Serving the scientific community since 1997, the Antibody Resource Page is a guide designed by scientists for scientists to find companies that sell catalog antibodies and custom monoclonal and polyclonal antibodies. See our other pages on antibody-related databases, software, and educational websites. If you wish to suggest or update a link, please see our FAQ.
European Organisation for Research and Treatment of Cancer
European Organization for Research and Treatment of Cancer
An independent pan-European clinical research organization to improve the standards of cancer care through the multidisciplinary multinational efforts of basic scientists and clinicians. The efforts include the testing of more effective therapeutic strategies based on drugs, surgery and/or radiotherapy that are already in use. They also contribute to the development of new drugs and other approaches in partnership with the pharmaceutical industry which is accomplished mainly by conducting large, multicenter, prospective, randomized, phase III clinical trials. The EORTC Network comprises over 300 hospitals and cancer centers in over 30 countries which include some 2,500 collaborators from all disciplines involved in cancer treatment and research. The EORTC Headquarters staff handle some 6,000 new patients enrolled each year in cancer clinical trials, approximately 30 protocols that are permanently open to patient entry, over 50,000 patients who are in follow-up, and a database of more than 180,000 patients. Intergroup collaboration is also promoted to face current challenges of clinical trials aiming at targeted therapies in order to recruit a large number of patients within a reasonable period of time.
Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea
Korea Research Institute of Bioscience & Biotechnology
Korea Research Institute of Bioscience & Biotechnology (KRIBB)
Korea Research Institute of Bioscience and Biotechnology
KRIBB - Korea Research Institute of Bioscience & Biotechnology
A research- and development-oriented company based in Berlin that engineers and markets technology for animal behavior research offering unique, automated instrumentation. This includes specialized applications of virtual reality and touch screen technology for animal behavior environments and RFID (transponder) operated devices in home cage environments. Their experimental systems are used for behavioral phenotyping, brain research, experimental psychology, and the diagnostic characterization of animal models for translational medicine.
International Alliance of Patients Organizations
International Alliance of Patients'' Organizations
A global alliance representing patients of all nations across all disease areas and promoting patient-centered healthcare across the world. They represent people who suffer from diseases, disabilities, illnesses, impairments or syndromes and work with communities of patients to get their voices heard by all involved in healthcare. With the help of their members and collaborating organizations, they work towards patient-centered healthcare throughout the world.
Commercial organization that develops tools and systems for measurement and analysis of animal and human behavior. They develop instrumented home cage systems, in which rodent behavior and ultrasonic vocalizations can be measured in a non-intrusive manner. Furthermore, they develop computer vision and pattern recognition technology for automated behavior detection. They believe that this approach has significant potential in research on animal models for Autism Spectrum Disorder.
A project manager service focused on creating progress in life science innovation. They can assist in IMI and H2020 proposal preparation, obtaining funding for Small to Medium Enterprises (SMEs), leading a consortium, and have an established network - they know who best can help you.
Blog on how to increase your return on the effort you invest in collaboration. You''ll learn about ways you can maximize your operational efficiency and ways to increase what you get in return.
Commercial provider of advanced software and solutions that helps R&D teams make discoveries. They provide organizations with the technology they need to securely capture, manage, share and exploit structured and unstructured data. Their technology and domain expertise enables users to link data to data, data to people and people to people to drive innovation, achieve faster time to market and improve margins. Their diverse customer list includes R&D driven international companies in pharmaceuticals, biotechnology, agricultural sciences, chemicals, consumer goods, energy, engineering, food and beverage, and healthcare.
Performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.
Fundaci��n Centro de Excelencia en Investigaci��n de Medicamentos Innovadores en Andaluc��a Medina
Fundaci��n MEDINA (Centro de Excelencia en Investigaci��n de Medicamentos Innovadores en Andalucia)
A non-profit research center established through a public-private alliance between the Regional government of Andalusia, the pharmaceutical company Merck Sharp & Dohme Spain S.A. (MSD), and the University of Granada, that is focused on: # Discovery of new compounds and therapies as new leads for drug development # Contract Research Services: High throughput screening services for lead discovery, ADME/TOX, bioanalysis and metabolomics MEDINA offers 1) natural products screening services for lead discovery on therapeutic targets developed by the customers and 2) compound profiling services for their drug candidates, using a counterscreening panel designed to determine potential risks in cardiovascular safety and drug-drug interactions.
Neurophysiology imaging core facility that provides anatomical and functional MRI scanning for researchers in the National Institute of Mental Health (NIMH), the National Eye Institute (NEI), and the National Institute for Neurological Disorders and Stroke (NINDS). The shared intramural resource centers on a cutting-edge 4.7T vertical bore scanner dedicated to imaging of nonhuman primates.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 12, 2021. Technology based company in Madrid that offers consulting services on Bioinformatics in areas of research, diagnostics and pharmaceutical industry.
Commercial organization supplying topoisimerase products and services to the pharmaceutical industry and academia to aid research in the anti-infectives and anti-cancer markets. Their aim is to provide pharmaceutical companies, and others involved in drug development, with the necessary tools to develop and screen novel anti-infective and anti-cancer compounds. Products All their proteins are expressed as the native sequences without additional tags. The only exception is the M. tuberculosis gyrase which is currently produced with a C-terminal His tag. An untagged version of this protein will be available soon. * Topoisomerase Enzymes and Assay Kits * Specific Gyrase Protein Domains * DNA Substrates and Markers * Antibodies Services * Gel Based Assays * Medium / High Throughput Assay * Investigation protein DNA interaction ReDCaT chip
Based in Washington, D.C., the American Psychological Association (APA) is a scientific and professional organization that represents psychology in the United States. With more than 154,000 members, APA is the largest association of psychologists worldwide. The mission of the APA is to advance the creation, communication and application of psychological knowledge to benefit society and improve people''s lives. The American Psychological Association aspires to excel as a valuable, effective and influential organization advancing psychology as a science, serving as: * A uniting force for the discipline * The major catalyst for the stimulation, growth and dissemination of psychological science and practice * The primary resource for all psychologists * The premier innovator in the education, development, and training of psychological scientists, practitioners and educators * The leading advocate for psychological knowledge and practice informing policy makers and the public to improve public policy and daily living * A principal leader and global partner promoting psychological knowledge and methods to facilitate the resolution of personal, societal and global challenges in diverse, multicultural and international contexts * An effective champion of the application of psychology to promote human rights, health, well being and dignity APA and its affiliate organizations provide a diverse range of scholarships, grants, and awards with the aim of advancing research in psychology. Using our specialized search tool, you can find funding by type, sponsor, topic area, recipient type, and deadline date.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 12, 2021. Commercial organization with expertise in lead generation, such as compound selection, iterative screens, fragment based lead generation (FBLG), HTS evaluation (clustering, scoring and actives selection), development of clusters into lead series (expansion via compound libraries, scaffold hopping and multi-parameter optimization), management of secondary screens (physical properties, ADMET), project management and presentation for customers or scientific committees. Synthetic organic chemistry is an important area of lead generation which is why both single compound synthesis and compound library synthesis are integrated. The scientists are skilled in predictive models including target modelling, virtual screening, high quality compound library design, compound triage and design, compound synthesis (including parallel synthesis) and automated purification. KeytoLead management team also has experience in leadership, line management, international collaborations, intellectual property and continuous improvement.
Commercial organization providing the GRID software to scientists working on the field of drug design. All the products are based on the GRID force field, which is used in connection with experimental design and multivariate analysis tools to transform information into knowledge. The main field of application is drug discovery, property design and prediction by merging molecular modelling techniques and Quantitative structure-activity relationship (QSPR) methods into 3D-QSPR models. The same strategies can also be used in virtual screening, ADME prediction and profile and prediction of human drug metabolism, where selection or prioritization of candidates is required from large collections of compounds to minimize drug failures. Molecular Discovery offers training courses on all MD programs. Workshops and seminars on Drug Design methodologies, DMPK prediction and QSPR are also offered. Consulting agreements are also offered in research areas related with chemometrics and drug discovery. Products * GRID, a program for rational or structure-based design using molecular interaction fields * MetaSite, a program for predicting metabolic hotspots or soft spots and subsequent metabolite formation * Mass-MetaSite, a program for identifying metaoblites based on experimental LC-MSMS data * WebMetaBase, a program for storing, visualising, and data-mining the results from Mass-MetaSite * VolSurf+, a program for modelling pharmacokinetic or ADME properties * SHOP, a program for scaffold replacement * MoKa, a program for modelling pKa and tautomerisation * Pentacle, a program for 3D-QSAR (an update of Almond) * FLAP, a program for virtual screening, pharmacophore modelling, docking, water prediction, and 3D-QSAR
A Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
Full service Clinical Research Organization (CRO) in Hamburg, Germany, mainly focusing on phase-I and phase-IIa clinical trials. MPS owns 72 bed research clinic with 6 physicians and 15 nurses as permanent staff. MPS is experienced in performing all kind of early stage clinical trials, including first-in-man-trials, medical-devices-trials, nutraceutical and consumer-goods-trials. MPS holds active database of more than 17,000 healthy volunteers, plus hundreds of patients in special populations.
A chemistry contract research organization (CRO) that offers synthetic and analytical chemistry services performed by a team of predominately PhD. level chemists with pharma backgrounds. * Synthesis Services: Their main areas of expertise are in Medicinal Chemistry (SAR exploration, parallel chemistry, patent examples), synthesis of reference compounds, metabolites and labeled compounds (including radio-labeled compounds). OT Chemistry also offers drug Development Support chemistry expertise in route scouting and process optimization. * Analytical and Pre-clinical Services: They provide a wide range of analytical and pre-clinical services such as bioanalysis (non-GLP and GLP utilizing UPLC MS/MS), MTS solubility, protein binding studies, stability and degradation studies, metabolic profiling, formulation development, autoradiography and mass balance studies.
A non-profit partnership and global research network providing high quality vaccine safety information. Their mission is to enhance the science of vaccine research by providing standardized, validated, and objective methods for monitoring safety profiles and benefit to risk ratios of vaccines. Products and services to promote high quality vaccine safety research include: * Standardized case definitions of adverse events following immunization * Guidelines for collection, analysis, and presentation of vaccine safety data * Template protocols for vaccine safety research * Automatic Case Classification Tool (ABC tool) * Library of vaccine safety publications * Links to high quality vaccine safety resources * Vaccine Safety Quarterly - Newsletter
EuroRec - European Institute for Health Records
An independent not-for-profit organization promoting in Europe the use of high quality Electronic Health Record systems (EHRs). One of its main missions is to support, as the European authorized certification body, EHRs certification development, testing and assessment by defining functional and other criteria. EuroRec is organized as a permanent network of National ProRec centers and provides services to industry (developers and vendors), healthcare providers (buyers), policy makers and patients.
Synapse Research Management Partners S.L.
Commercial organization specialized in the high quality management of complex research and development projects in the biomedical sector. Synapse partners with national and international organizations, both public and private. Their company goes beyond classical project management and brings in added value capabilities in team management, vision management, strategic thinking and project intelligence. Synapse's expertise extends to market knowledge, business planning and valorization of research results.
Fondazione PENTA - for the Treatment and Care of Children with HIV-ONLUS
A Level 1 network for pediatric infectious disease in Europe recognized by the European networks of paediatric research at the European Medicines Agency (EnprEMA) whose activities vary from clinical trials, to cohort studies and training. It is currently developing a portfolio of clinical trials in antimicrobials in children, including antibiotics, antivirals and antifungals.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A population based database collecting incident cases of cancer diagnosed since January 1998 in the population of the Federal state of Bremen. The Registry provides data for the analysis of * age specific time trends and geographical patterns of cancer incidence in men and women * cancer causes (e.g. work-related, environmental and personal risk factors) * epidemiological evaluation of screening programs * survival analysis of cancer patients. Since the incidence year of 2001, the Registry has a completeness level of > 95 %, based on expected values provided by the Robert Koch Institute.
Leibniz Institute for Prevention Research and Epidemiology Biobank
Biobank that contains more than 50,000 blood, urine and saliva samples as well as tissue materials from epidemiological field studies. The samples and DNA collected in various studies are increasingly being used for the investigation of genetic, environmental and life-style associated factors in the etiology and prognosis of cancer and other chronic diseases such as obesity, diabetes and metabolic syndrome.
Korea University is a private research university in Seoul, South Korea. Established in 1905, Korea University is one of the nation oldest and most prominent institutions of higher education. The student body consists of over 20,000 undergraduate students and over 10,000 graduate students. Korea University consists of the Seoul Campus, Sejong Campus and three auxiliary hospitals (Anam Hospital, Guro Hospital, Ansan Hospital).
Three-dimensional digital connectome atlas of the C57Black/6J mouse brain and catalog of neural tracer injection cases, which will eventually cover the entire brain. Serial sections of each case are available to view at 10x magnification in the interactive iConnectome viewer. The Image Gallery provides a glimpse into some of the highlights of their data set. Representative images of multi-fluorescent tracer labeling can be viewed, while more in depth examination of these and all other cases can be performed in the iConnectome viewer. Phase 1 of this project involves generating a physical map of the basic global wiring diagram by applying proven, state of the art experimental circuit tracing methods systematically, uniformly, and comprehensively to the structural organization of all major neuronal pathways in the mouse brain. Connectivity imaging data for the whole mouse brain at cellular resolution will be presented within a standard 3D anatomic frame available through the website and accompanied by a comprehensive searchable online database. A Phase 2 goal for the future will allow users to view, search, and generate driving direction-like roadmaps of neuronal pathways linking any and all structures in the nervous system. This could be looked on as a pilot project for more ambitious projects in species with larger brains, such as human, and for providing a reliable framework for more detailed local circuitry mapping projects in the mouse.
Chimera - an Extensible Molecular Modeling System
UCSF Chimera - an Extensible Molecular Modeling System
Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials.
Resource Identification Initiative Portal
Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource.
Commercial organization specialized in the management of EU-funded research projects in the HEALTH area. They carry out the non-scientific tasks of funded research projects and provide support and consultancy services for scientists and researchers at universities, in businesses and research institutes from the first project idea to the successful completion. As the project office, it is the point of reference for funded research projects. They support you with the following services: * Fund-raising and project planning * Project management * Financial management * Conference services * Dissemination and project marketing * Training organization
A private limited company that specializes in data protection solutions for eHealth. They are a trusted and reliable Trusted Service Provider (TSP) in the Healthcare sector providing both consultancy and technical privacy protection solutions. Its data protection services are supported by a combination of high-level technical and legal expertise in privacy protection and e-security and a sound experience with a number of advanced e-security solutions such as PKI, VPN, Web Services security frameworks, time-stamping and more. Custodix helps businesses deal with all security and privacy related aspects of modern data management (cf. European Data Protection Directive 95/46/EC, 2001/20/EC, 2005/28/EC, the US HIPAA Privacy Rule, the WHO GCP, GPMP/ICH/135/95, ...) by offering end-to-end solutions for data protection in e-Clinical Trials, disease management and other longitudinal studies. Custodix has an international customer-base, deploying services in Europe, Asia and Australia. Customers are both commercial companies and governmental research organizations. Specialties: CATS - Custodix Anonymization Tool services, TriTob - clinical TRIal TOolBox, PIMS - Patient Identity Management System, PESF - Privacy Enhanced Storage Framework, TTPS - Trusted Third Party Services, FP7 EU Research
A commercial company specialized in the field of clinical governance, research and clinical-epidemiological analysis and development of services and software applications for healthcare. Products and Services * Analysis and development software solutions, web, e-learning * Design and Implementation APP for Smartphone and Tablet (iOS, Android, Windows Phone) * Clinical Intelligence & Clinical Decision Support Systems (CDSS) * Data center services and Application Server Provider * Epidemiology, Surveillance and Health Promotion - Development of studies and epidemiological research
A collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive, quantitative descriptions of individual species including: * Their subcellular organization, * Their chromosome sequences, * The essentiality, location, length, direction, and homologs of each gene, * The organization and promoter of each transcription unit, * The expression and degradation rate of each RNA gene product, * The specific folding and maturation pathway of each RNA and protein species including the localization, N-terminal cleavage, signal sequence, prosthetic groups, disulfide bonds, and chaperone interactions of each protein species, * The subunit composition of each macromolecular complex, * Their genetic code, * The binding sites and footprint of every DNA-binding protein, * The structure, charge, and hydrophobicity of every metabolite, * The stoichiometry, catalysis, coenzymes, energetics, and kinetics of every chemical reaction, * The regulatory strength of each transcription factor on each promoter, * Their chemical composition, and * The composition of its typical SP-4 laboratory growth medium. WholeCellKB currently contains a single database of Mycoplasma genitalium, an extremely small gram-positive bacterium and common human pathogen. This database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. Users can download the WholeCellKB source code and content to create and customize - including the content, data model, and user interface - their own model organism database.
PHARMO Institute for Drug Outcomes Research
An independent scientific research organization dedicated to the improvement of the use, quality and cost-effectiveness of pharmaceuticals. They collect, maintain and perform research on patient-centric data to derive real-life insights for tailoring of medicines. They maintain a large and high quality database network and work closely with (inter)national medical universities and European databases. Through its studies with longitudinal and real-life patient data, they contribute to risk management, outcomes research and provides solutions for decision makers in market access, health economics and health outcomes domains. Academics from Dutch universities or research institutes are granted the opportunity to perform scientific studies using the PHARMO Database Network.
Commercial company delivering content for personalized medicine in the areas of Biomarker Services, Biomarker Assays, Isobaric and Isotopic Reagents and Proprietary Biomarkers. A global leader in applied proteomics, they use high sensitivity proprietary technologies to detect biomarkers (differentially expressed proteins in diseases) and to develop rapid assays for testing. The biomarkers discovered in body fluids or tissues are validated, developed and commercialized as diagnostic, prognostic or therapeutic products through strategic alliances and out-licensing.
Independent network and system used to collect epidemiological information for clinical research from family paediatricians in Italy. It is based on the transmission of specific data from computerised clinical files. Such data is collected anonymously by a central server in Padua, where it is validated and elaborated.
National university in Kyoto, Japan. It is the second oldest Japanese university, one of Asia highest ranked universities and one of Japan National Seven Universities.
A commercial software and service company operating in Spain, France and Colombia whose main stakeholder is Indra and its main product is the G platform, on top of which they have developed several vertical applications for various industry sectors like banking, healthcare, government and SMB. Since its constitution, gn??bila has constituted an international reference in the development and deployment of Network Service Infrastructures and Platforms for Businesses, Organizations and Individuals, facilitating communication, collaboration and the coordination of applications, data and information. gn??bila Products: * Cloud Application Platform * Cloud TP Platform * Platform as a Service * Development Platform
Commercial organization that specializes in compound management, compound logistic services, screening compound collection, and compound storage and retrieval. BioAscent enables drug discovery innovation; increasing lead finding opportunities through access to new chemical space; and providing compound management and logistics services that increase the value of existing collections.
Commercial organization that provides cheminformatics software platforms, applications and services to optimize the value of chemistry information in life science and other R&D. This software enables structure visualization and management, property predictions and calculations, virtual synthesis, screening, clustering and drug design.
A commercial medicinal chemistry company dedicated to the design and synthesis of natural product-mimetic screening compounds, Hit-to-Lead & Lead Optimization projects and Custom Synthesis. Aiming at the acceleration of the lead discovery and optimization process in pharma and biotech research organizations, EDELRIS uses its validated chemistry and drug discovery expertise to provide novelty to its customers with exclusive or non-exclusive small molecules and with efficient hit-to-lead optimization capabilities. EDELRIS has a wide range of services and based on its experience in various and complementary fields, the team is capable to deliver innovative solutions to synthetic and medicinal chemistry problems faced by clients.
Commercial organization active in the field of pharmaceutical research that transforms promising early-stage projects into leads with initial proof-of-concept in animals. Focusing on small molecules, the LDC conducts drug discovery projects originating primarily from academic groups and sustains a preferred partnership with the Max Planck Society. Projects are developed in close collaboration with the project owner. LDC offers core expertise in Automation & Screening, Cellular Biology, Pharmacology and Medicinal Chemistry.
Privately owned European contract research organization offering innovative chemistry, medicinal chemistry and early process research services to accelerate drug discovery and development. They provide a wide range of chemical services specializing in exclusive synthetic and process chemistry services to support research and development programs of companies across the globe. Name changed to Symeres after merger of Mercachem and Syncom., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Commercial organization dedicated to open innovation, providing automated cellular and biochemical in-vitro screening experiments, and ultra-High Throughput Screening (uHTS) services. The Pivot Park facilities include MSD''s former screening centre which comprise two unique robotic systems for in-vitro screening. Because the new screening centre was able to retain a significant number of the original screening staff, it offers a wealth of experience in assay development, screening and automation in a new, open setting.
DCI Tissue and Blood Procurement Shared Resource
DCI Tissue Blood Procurement Shared Resource
Duke Cancer Institute Tissue and Blood Procurement Shared Resource
Duke Cancer Institute Tissue Blood Procurement Shared Resource
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Over 10,000 patient consents, 5,000 banking events, and 40,000 biospecimens have been processed to date with storage of both formalin fixed paraffin embedded (FFPE) tissue and frozen tissue located within multiple freezers spanning temperatures in the range of -80 degrees to -180 degrees C depending on protocol requirements. Considerable effort continues to be expended to assure compliance with IRB, NIH and HIPAA best practices and guidelines on banking human tissues. The biorepository in place today is the result of the combined efforts of the Duke Cancer Institute (DCI) Breast SPORE, DCI Shared Resource for Tissue and Blood Procurement, and the Duke University School of Medicine Research Foundation (DUSOM-RF). The DCI and the School of Medicine Research Foundation (SOMRF) have funded the collection of frozen and fixed tissues, both malignant and benign, under an ?????????????????excess tissue????????????????? protocol that utilizes freshly excised tissue that is available for research after the needs of the pathologic workup are met. This program procures tissues from many anatomic sites including breast. Recently Duke''s Institute of Genome Science & Policy (IGSP), under the direction of Drs. Geoff Ginsburg and Tom Burke, initiated a blood collection program that spans several departments and institutes. The Breast SPORE blood collection program served as the pilot for this much larger effort. The Breast SPORE tissue and blood collection effort utilizes much of the same infrastructure and personnel that are also supported by the DCI, SOMRF, and IGSP.
Independent commercial provider of integrated drug discovery with core capabilities including medicinal chemistry, in vitro bioscience, computational chemistry and informatics. They also provide ADME (absorption, distribution, metabolism, and excretion), in vitro toxicology, early safety pharmacology, in vivo efficacy models, ion channel expertise, protein production and X-ray crystallography according to our clients'' specific needs, via long-term strategic alliance partners. They undertake complete drug discovery programs and hit finding, hit-to-lead and lead optimization projects.
Syncom: Contract Research in Organic Chemistry
Independent contract research organization / small and medium sized enterprise (CRO/SME) that assists pharma and biotechnology companies with medicinal chemistry programs, providing tailor-made custom synthesis solutions. Primary activities include synthesis of key building blocks, route scouting services, process research activities, scale up, medicinal chemistry services and hit-to-lead optimization. On custom basis they also synthesize metabolites, impurities, reference standards and stable labelled compounds. Their services are backed up by state-of-the-art analytical technologies such as HPLC, GC, LC-MS, GC-MS and NMR. These technologies can be offered as stand-alone analytical services as well. Syncom also has expertise in chiral technology. The firm has designed and synthesized numerous unique scaffolds, yielding many patent applications and clinical candidates. Name changed to Symeres after merger with Mercachem., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An independent contract research company that serves the needs of pharmaceutical, chemical, agrochemical and biotech companies, operating state-of-the art lab facilities and supporting the diverse needs of its customers in efficient drug discovery, medicinal chemistry and classical synthetic chemistry. Taros'' scientists combine more than 140 years industrial organic chemistry experience and over 60 years of active drug discovery experience from big pharmas and biotechs. They have expertise across a broad range of therapeutic areas (oncology, respiratory, CNS, cardiovascular, inflammation, pain, metabolism and infectious) and in all small molecule target classes. They have developed TarosGate, a unique software suite putting cost, time and chemistry information at a Project Leader''s finger tips.
Ontology that is a subset of GO directed for neurological and immunological systems. It was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains.
Organization which develops and maintains a centralized database on rare disease clinical research supported by the NIH. It also stimulates rare disease research by supporting scientific workshops and symposia, responds to requests for information on highly technical matters and matters of public policy, provides information to the Office of the Director on matters relating to rare diseases and orphan products, and coordinates and serves as a liaison with Federal and non-Federal national and international organizations.
Digital Access to Scholarship at Harvard
Harvard University''s central service for sharing and preserving work. In addition to the scholarly journal articles targeted by Harvard''s several open access resolutions, DASH maybe used to self-archive manuscripts and materials. DASH supports a variety of file formats, and users are encouraged to deposit related materials with manuscripts (including data, images, audio and video files, etc.) When users deposit their work in DASH, it becomes visible to colleagues around the world by virtue of metadata harvesting, Google Scholar, and other indexing services. Higher visibility leads to higher rates of citation and impact. When users post early versions of their work, before publication, they establish intellectual priority sooner. Users act in their own best interests by taking part in the University''s mission to share and preserve the knowledge produced there. Because Harvard now has a prior, non-exclusive license to faculty journal articles in schools with open access policies, those faculty members are required to act accordingly when publishing journal articles, either by attaching an addendum to their publication agreement or obtaining a waiver. They then must deposit the publication in DASH.
FlyTF.org - The Drosophila Transcription Factor Database
A database of genomic and protein data for Drosophila site-specific transcription factors.
An experimental course and blog offered by the Harvard-Smithsonian Center for Astrophysics John G. Wolbach Library and the Harvard Library to train librarians to respond to the growing data needs of their communities. Data science techniques are becoming increasingly important to all fields of scholarship. In the hands-on course, librarians learn the latest tools for extracting, wrangling, storing, analyzing, and visualizing data. By experiencing the research data lifecycle themselves, librarians develop the data savvy skills that can help transform the services they offer. Material will be made available via the DST4L website as it progresses.
SHared Access Research Ecosystem (SHARE)
A higher education and research community initiative to ensure the preservation of, access to, and reuse of research outputs. SHARE will develop solutions that capitalize on the compelling interest shared by researchers, libraries, universities, funding agencies, and other key stakeholders to maximize research impact, today and in the future. SHARE aims to make the inventory of research assets more discoverable and more accessible, and to enable the research community to build upon these assets in creative and productive ways. ARL, AAU, and APLU strongly believe that ensuring broad and continuing access to research is central to the mission of higher education. Research publications, research data, other research outputs, along with their associated metadata, should be publicly accessible and available for reuse, text mining, data mining, and machine reading. This accelerates further research and discovery.
A wiki knowledge base for the life sciences that combines the collaborative and largely altruistic possibilities of wikis with explicit authorship. Authors are provided credit even while the knowledge can evolve via continual revision and traditional peer review into a rigorous scientific tool.
Committee on Coherence at Scale for Higher Education
Committee to foster strategic thinking about how to more rigorously manage the transition from analog to digital in higher education to ensure the programmatic, concerted, and efficient development of large-scale projects that, if built as coherent elements of an emerging digital environment, will significantly enhance scholarly productivity and enrich teaching. The Committee will produce a blueprint for this new environment that is cost effective and sustainable by focusing on the following activities: research and analysis of key large projects and the technology requisite for their correlation; business plans necessary for a coherent, sustainable digital ecology of enormous scale in service to education and the public good; and return on investment, that is, the benefits and transformational aspects of such an undertaking.
A partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world. Their goals are: * To build a reliable and increasingly comprehensive digital archive of library materials converted from print that is co-owned and managed by a number of academic institutions. * To dramatically improve access to these materials in ways that, first and foremost, meet the needs of the co-owning institutions. * To help preserve these important human records by creating reliable and accessible electronic representations. * To enable the digital archive to be accessible to persons who have print disabilities. * To stimulate redoubled efforts to coordinate shared storage strategies among libraries, thus reducing long-term capital and operating costs of libraries associated with the storage and care of print collections. * To create and sustain this public good in a way that mitigates the problem of free-riders. * To create a technical framework that is simultaneously responsive to members through the centralized creation of functionality and sufficiently open to the creation of tools and services not created by the central organization.
Repository for all research outputs from across all fields of science in any file format as well as both positive and negative results. They assign all publicly available uploads a Digital Object Identifier (DOI) to make the upload easily and uniquely citeable. They further support harvesting of all content via the OAI-PMH protocol. They promote peer-reviewed openly accessible research, and curate uploads. ZENODO allows users to create their own collection and accept or reject all uploads to it. They allow for uploading under a multitude of different licenses and access levels.
Semantic Automated Discovery and Integration
SADI - Semantic Automated Discovery and Integration
Semantic Automated Discovery and Integration (SADI)
Framework for discovery of, and interoperability between, distributed data and analytical resources. It combines GET/POST-based Web Services with standards from the W3C Semantic Web initiative. The objective is to make it easy for data and analytical tool providers to make their resources available on the Semantic Web with minimal disruption to their usual practices. It simply defines an open set of best-practices and conventions, within the spectrum of existing standards, that allow for a high degree of semantic discoverability and interoperability between participating services.
Portal to research centers and core facilities specifically support obesity research and better understand the relationship between health and nutrition.
IMHRO: International Mental Health Research Organization
International Mental Health Research Organization
International Mental Health Research Organization (IMHRO) is a 501(c)3 organization committed to raising awareness and funding research to find preventions and cures for schizophrenia, depression and bipolar disorder within a generation. We are families and individuals whose lives have been touched by these brain diseasesand who have seen how far mental health research has come in the last decade. Contributors to IMHRO have played a major part. The $135 million they have helped to raise has funded stunning scientific discoveries to help people now and tomorrow.
3DSwap - Knowledgebase of proteins involved in 3D domain swapping
3DSwap: Knowledgebase of 3D Domain Swapping in Proteins
Curated knowledegbase of protein structures that are reported to be involved in 3-dimensional domain swapping. 3DSwap provides literature curated information and structure related information about 3D domain swapping in proteins. Information about swapping, hinge region, swapped region, extent of swapping, etc. are extracted from original research publications after extensive literature curation.
Stanford University, Center for Interdisciplinary Brain Sciences Research
Stanford Center for Interdisciplinary Brain Sciences Research
The Center for Interdisciplinary Brain Sciences Research (CIBSR) at the Stanford University School of Medicine is dedicated to research that will improve the lives and well-being of individuals with disorders of the brain and improve knowledge of healthy brain and behavioral development. CIBSR research staff are dedicated to identifying biological and environmental risk factors, understanding disease pathophysiology and developmental outcomes, and developing new treatments for neurodevelopmental, neurogenetic and neuropsychiatric disorders of childhood onset. Our research studies are truly multi/interdisciplinary as they bring together experts from the fields of psychiatry, neurology, psychology, computer science, biostatistics and genetics to explore and seek answers for complex questions related to brain-behavior relationships. Active research at CIBSR includes: * Mutlimodal imaging of the brain utilizing anatomical and functional magnetic resonance imaging (MRI), diffusion tensor imaging (DTI) and magnetic resonance spectroscopy (MRS). * Behavioral, cognitive, and physiological assessment to address questions concerning the influence of biological and environmental factors on outcome. * The development of new biological and cognitive-behavioral treatments. * Development of brain image analysis methods and software.
This is a facility for UK-based research into leukemia and other related disorders. The Bank contains viable cells and DNA from children diagnosed with acute leukemia. (diagnostic, treatment and relapse samples) and also HLA- typed normal cord blood donations. Samples can only be obtained from the Cell Bank for approved peer-reviewed and fully costed research projects. To view further information about the Cell Bank, or for instruction on how to apply for samples, please register.
Cleveland Clinic Genomic Medicine Biorepository
Cleveland Clinic Genomic Medicine Institute Biorepository
Genomic Medicine Institute Biorepository
A biorepository is a place where investigators can deposit and store biological material, in this case samples derived from patients. Moreover, the Genomic Medicine Institute (GMI) takes this basic concept and elevates it to make the Genomic Medicine Biorepository (GMB) a full-service processing and banking laboratory that serves as the foundation for evidence-based research for the GMI, the Cleveland Clinic, and our collaborators. The process relies on a team of multi-disciplinary professionals coordinating their efforts in order to streamline medical research. This begins with dedicated physicians and genetic counselors identifying individuals with specific medical conditions indicating the possibility of genetic involvement. Once identified, biological material (e.g. blood, tissue, or saliva) is collected under the care of the patient''s doctor or by our clinicians and sent to the GMB. Once in the lab, the patient and their samples are assigned a unique identifier (to protect the patient''s personal information) and logged into a central database. This unique identifier accompanies all samples processed and banked for that individual. The specimens are then processed into research-relevant samples using proven laboratory techniques and state-of-the-art quality control practices. These samples include the isolation of DNA and RNA from white blood cells for genetic studies; collection of plasma for proteomic studies; and initiated immortalized cell lines from lymphocytes for in-vitro studies and biochemical research. These cell lines are able to be indefinitely stored in cryogenic suspension and are invaluable as a renewable resource for genetic and biochemical research. The GMB also processes genetic material from various tissues (both fresh and archived). Charis Eng, MD, PhD, Chair and Director of the GMI, has been the faculty oversight person of a human biorepository for the last eight years. Since then, our biorepository has received, cataloged, processed, and banked, in excess of 25,000 specimens. These samples are of numerous tissue types from patients and their family members located all over the world. Our biorepository has managed samples that have resulted in more than 150 original peer reviewed articles and greater than $25 million total direct costs in extramural funding over the last four years alone.
THIS RESORUCE IS NO LONGER IN SERVICE. Documented on April 27,2023. CCLG is an association of healthcare professionals involved in the treatment and care of children and younger teenagers with cancer, and underpins all the activity in pediatric oncology in the British Isles. CCLG is committed to research and development in the treatment of cancer in this age group, the ultimate goal of which is to maximize cure while minimizing the early and late side effects of treatment. Provision of information for patients and families is a core activity. The Children''s Cancer and Leukaemia Group was formed in 2006 as a result of the merger of the UK Children''s Cancer Study Group and the UK Childhood Leukaemia Working Party, both of which had been in existence since the 1970s.
Sunnybrook Research Institute Tumor bank
Sunnybrook Research Institute Tumour bank
Sunnybrook Research Institute''s tumour bank provides a mechanism for the optimal collection, storage and distribution of human tissue for investigative purposes. We collect both freshly frozen and formalin-fixed paraffin-embedded tumour and normal samples, retrospectively and prospectively (informed consent and confidential consent is obtained from patients before sample collection). We offer the 1. Distribution of tissue and data to interested investigators after approval from the institutional research ethics board and 2. Collaboration with various research investigators. Our mandate is to design, implement and manage the structures and processes to ensure the timely provision of tissue samples and associated data. We are currently building bank on four disease sites: breast, prostate, colorectal, gynecological. We are also creating and maintaining a database with a tissue tracking and inventory system, using TissueMetrix software.
Platform for storing, finding and accessing data that provides a service for data centres to mint DOIs and store associated metadata. Their goals are to establish easier access to scientific research data on the Internet, increase acceptance of research data as legitimate, citable contributions to the scientific record and support data archiving that will permit results to be verified and re-purposed for future study. DataCite is global, with member institutions offering services and advice directly where they are needed by the researchers. While datasets are shared and accessed globally, researchers work within national funding and organizational frameworks. It therefore operates globally, with national representation. The DataCite Metadata Scheme is a list of core metadata properties chosen for the accurate and consistent identification of data for citation and retrieval purposes, along with recommended use instructions.
A freely available online personalized cancer medicine knowledge resource for physicians, patients, caregivers and researchers that gives up-to-date information on what mutations make cancers grow and related therapeutic implications, including available clinical trials. It is a one-stop tool that matches tumor mutations to therapies, making information accessible and convenient for busy clinicians.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. Stem cell research, particularly human embryonic stem cell (hESC) research, holds tremendous promise to discover therapeutic options and perhaps cures for insidious diseases such as cancer, juvenile diabetes, Alzheimer's and Parkinson's. The Massachusetts Human Stem Cell Bank provides the biomedical research community with expertly maintained human ES (hES) and reprogrammed (iPS) cell lines to facilitate studies into the properties and potential therapeutic applications of pluripotent stem cells. The Bank cultures, characterizes and distributes quality controlled hES and iPS cell lines derived in Massachusetts and beyond. The Bank is a 15,000 square foot facility that contains research and training space for visiting investigators. In addition, the Education and Training division provides technical training and programs to educate the community.
Parkinson's Disease Mouse Model Resource
The Parkinson's Disease Mouse Model Resource (PDMMR) is funded by the Michael J Fox Foundation to provide genetically engineered mice and information useful for their selection and use. The resource also serves as an archive of genetically stable mouse models. The Repository distributes Parkinson's disease models that are useful for the study of the basic pathophysiology of PD, and for testing new therapies. Also available are research tool strains including transgenics that express marker genes in affected brain regions, and strains with systems for regulating gene expression (e.g. Cre recombinase and tet-inducible promoters) in specific types of neurons.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. It has been incorporated with the LBIH Biobank. The Liverpool Tissue Bank (LTB) collects biological samples (tissue surplus to diagnostic requirement and blood) from patients undergoing surgery or biopsy procedure for the treatment and diagnosis of a wide variety of medical conditions. The main focus of the LTB is collecting samples from patients where cancer is a confirmed or likely diagnosis. These samples are banked to provide an invaluable resource for research groups investigating the molecular mechanisms involved in a range of medical conditions with the aim of devising new treatments and therapies. The Liverpool Tissue Bank (LTB) was formerly known as the Cancer Tissue Bank Research Centre (CTBRC) and changed to the LTB in late 2009. The Tissue Bank was established in 1991 from a charitable donation by the Candis Club, the charitable arm of Candis Magazine. It is a University of Liverpool resource located within the Department of Pathology, School of Cancer Studies. The LTB operates a cost recovery scheme where a charge is made to researchers to cover the costs involved in the collection, storage and processing of biosamples.
A reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Part of the Surgery Program, The Moncton Hospital''s Tissue Bank is a support service that recovers, processes, stores and distributes bone for transplantation. Approximately 175 surgical bone donors and 25 cadaver donors are received by The Moncton Hospital Tissue Bank each year. The Tissue Bank consolidates the recovery, processing, testing, storage and distribution of tissues for transplantation to: * Improve the health of individuals; * Provide the required tissue to surgeons for their patients; * Provide the highest quality tissue for transplantation; * Ensure the safety, efficacy and economy in all aspects of tissue banking practice; * Ensure that the quantity and range of tissue meets the clinical demand; * Develop and use outcome measures to ensure quality and safety of tissue provided; * Contribute to the development and implementation of national standards; and * Provide a clinical support service to clinicians in order for them to help the patients achieve their optimum level of functioning. While South-East Regional Health Authority has led the province of New Brunswick in organ donation for decades, only in 2002 did the health authority officially embark on working towards achieving accreditation. In October, 2006, the American Association of Tissue Banks awarded the prestigious accreditation to the Dr. Donald MacLellan Tissue Bank, making this the sixth tissue bank in Canada to hold this achievement. This service will enable SERHA to provide better care to New Brunswicker''s in the event of a trauma or the need for reconstructive surgery.
International Anesthesia Research Society
The International Anesthesia Research Society is a nonpolitical, not-for-profit medical society founded in 1922 to advance and support scientific research and education related to anesthesia, and to improve patient care through basic research. The IARS contributes nearly $1 million annually to fund anesthesia research; provides a forum for anesthesiology leaders to share information and ideas; maintains a worldwide membership of more than 15,000 physicians, physician residents, and others with doctoral degrees, as well as health professionals in anesthesia-related practice; sponsors the SmartTots initiative in partnership with the FDA; and publishes the monthly Anesthesia & Analgesia journal in print and online. The IARS mission is to encourage, stimulate, and fund ongoing anesthesia-related research projects that will enhance and advance the specialty, and to disseminate current, state-of-the art, basic and clinical research data in all areas of clinical anesthesia, including perioperative medicine, critical care, and pain management. The IARS is focused solely on the advancement and support of education and scientific research related to anesthesiology. To fulfill this mission the Society publishes a monthly scientific journal, Anesthesia & Analgesia, conducts an annual clinical and scientific meeting, funds anesthesia-related research, and sponsors the SmartTots research initiative.
Sasakawa Memorial Health Foundation (SMHF) was established in 1974, with Mr. Ryoichi Sasakawa, founder and first chairman of the Nippon Foundation (TNF) as President, and Professor Morizo Ishidate, father of chemotherapy of Hansen''s Disease (HD) in Japan, as chair. The principal objective of SMHF is to eliminate HD, a disease which has struck fear into human beings for millennia and stigmatized those it touched. SMHF approaches HD not only as a public health problem but also as a social and human issue. Apart from HD, the work of SMHF covers many of issues within the realm of basic health needs. In doing so SMHF has always respected the ownership by the people, of their own health related needs. SMHF believes in sharing resources and knowledge, rather than creating a situation in which the ''haves'' give to the ''have-nots''. Through this we would like to share with you the joy of working together across national borders for the benefit of people in need. Sasakawa Memorial Health Foundation provides grants to projects implemented by non-profit organizations based outside of Japan. Funding Areas: Hansen''s disease (HD), Neglected Tropical Diseases (NTDs), and Palliative Care (For Japan based Applicants Only)
A non-profit organization dedicated to saving lives through organ and tissue donation in the seven-county greater Los Angeles area. With more than 200 hospitals, 12 transplant centers and a diverse population of 19 million, OneLegacy is the largest organ and tissue recovery organization in the world. OneLegacy saves and heals lives through organ, eye and tissue donation, comforts the families we serve, and inspires our communities to Donate Life. With each day comes a chance for people to say yes to donation and help those on the other side of the bridge, one legacy at a time.
Japanese national university located in Fukuoka, in the island of Kyushu.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.
COBALT: Constraint-based Multiple Alignment Tool
Constraint-based Multiple Alignment Tool
NCBI Constraint-based Multiple Alignment Tool
COBALT is a multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. Pairwise constraints are then incorporated into a progressive multiple alignment. A Linux executable for COBALT, and CDD and PROSITE data used is available at ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt/ COBALT has reasonable runtime performance and alignment accuracy comparable to or exceeding that of other tools for a broad range of problems.
The UK''s leading MS charity that provides information and support, funding research and fighting for change. We''re a democratic organization: one member, one vote. We fund research, give grants, campaign for change, provide information and support, invest in MS specialists and lend a listening ear to those who need it. The UK''s biggest MS charity. * 38,000 members have a say in how we''re run. * 9000 volunteers give a million hours every year. * 550 staff work in all four nations of the UK. * Over 300 branches support people with MS locally. * One aim: to beat MS. Our national offices in England, Scotland, Wales and Northern Ireland and our network of 300 branches support people affected by MS locally.
Pathosystems Resource Integration Center
A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available.
BioPharma Storage Facility - Masy Systems
Safe and secure environmentally controlled storage for the biotech, pharmaceutical and medical device industries. Masy provides same-day retrieval and shipping of your biomaterials. Our cost-effective repository space is comprised of multiple chamber styles, from walk-in refrigerators / freezers for large containers, to single-shelf storage units for individual vials. Segregated & unsegregated storage is available. Our sophisticated inventory management system utilizes a precise bar-code inventory track-and-trace system with data safely stored on dedicated servers. Critical data access is secured by password protection. Environmental storage condition information and sample access is limited to customer approved personnel only. Our in-house Validation and Calibration teams allow us to offer unique storage conditions. And, we now offer GMP labeling and distribution of clinical samples. Masy is ISO 9001:2009 Certified and NVLAP ISO/IEC 17025:2005 Accredited. Our state-of-the-art facility is conveniently located less than an hour from Metro-Boston, just 15 minutes from the Devens Commerce Park.
Demystifying Depression is a wiki book on depression that is downloadable as a PDF file. This book may not have been written by a doctor. The recommendations are not referenced to actual research except in a bibliography. This document should in no way serve as a substitute for medical advice. Experts are welcome to add their comments. Depression is a mood disorder, so start many descriptions of the illness. That is a gross understatement. Depression does indeed seriously affect your mood, but that is just the tip of the iceberg. A clinical depression can be an incapacitating illness, affecting your ability to perform tasks that require concentration and rendering you unable to work. By writing this document we hope to provide you with the knowledge everyone should have about their mental well-being. Depression is not an unavoidable fate. It is physical.
Brain Tumour Foundation of Canada is a dedicated team of volunteers, patients, survivors, family members, health care professionals and staff, determined to make the journey with a brain tumor one full of hope and support. We work collaboratively to serve the needs of those Canadians affected by all types of brain tumors. Information, education and support is available and research continues into the cause of and a cure for brain tumors. Every year, thousands of Canadians affected by brain tumors find emotional support and comfort while gaining a better understanding and knowledge of their disease through a range of programs and services available across the country. This includes: up-to-date brain tumor information material, numerous education events and support groups. Important brain tumor research is also supported through annual grants, a fellowship and the brain tumour tissue bank. We welcome donations, large or small. Charitable Registration #BN118816339RR0001
Cre expressing mice under the control of promoters with a design focus on the brain. Each promoter is derived from human sequence, but the resulting expression is assessed in the mouse for the activation of a LacZ reporter gene by the Cre activity. Promoters tested as large MaxiPromoters (BACs inserted into the mouse genome) and MiniPromoters (plasmid-based sequences inserted either into the mouse genome or introduced within AAV viruses). The Cre-related project continues from the Pleiades Promoter Project. Here is the list of genes for which icre/ERT2 mice are currently in development: AGTR1, CARTPT, CLDN5, CLVS2, CRH, GABRA6, HTR1A, HTR1B, KCNA4, KDM5C, MKI67, NEUROD6, NKX6-1, NOV, NPY2R, NR2E1, OLIG2, POU4F2, SLITRK6, SOX1, SOX3, SOX9,, SPRY1, VSX2
ProMPT - Prostate Cancer Mechanisms of Progression and Treatment
Prostate Cancer Mechanisms of Progression and Treatment
Prostate Cancer: Mechanisms of Progression and Treatment
The MRC and Cancer Funders'' Forum (now National Cancer Research Institute, NCRI) established two cancer collaboratives in 2002, ProMPT and the Southern Collaborative. Their purpose was to increase the critical mass of basic and translational cancer researchers working on prostate cancer. The Collaboratives have both been successful in raising external grant income over the past 5 or 6 years and the current funding is very much geared around infrastructure to help with bio-marker development. This includes the establishment of biorepositories and tissue collections together with appropriate epidemiological and clinical information. The ProMPT collaborative is organized by Professor David Neal, Chair of Surgical Oncology in Cambridge. The other institutions include the Universities of Bristol, Manchester, Newcastle upon Tyne, Sheffield and York. The collaborative is very much working on translational aspects of prostate cancer research and has available to it a wide range of models. The Bristol group is working on epidemiological aspects and IGF, the Manchester group is working on stem cells, the Newcastle group is focused on target identification and validation and new drug development. Sheffield is working on model systems, bone metastasis and angiogenesis, York''s expertise is stem cells, structural biology and prostate specific gene targeting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations.
NeuroImaging Tools and Resources Collaboratory Image Repository
Data repository for neuroimaging data in DlCOM and NIFTI formats. It allows users to search for and freely download publicly available data sets relating to normal subjects and those with diagnoses such as: schizophrenia, ADHD, autism, and Parkinson's disease.XNAT-based image registry that supports both NIfTI and DICOM images to promote re-use and integration of NIH funded data.
A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.
PublicationsList.org exists to let researchers and research organizations maintain a reliable web-based record of their academic output without any fuss. Free for individual use; subscription for additional services and institutional sites. PublicationsList.org was set up to streamline the process of maintaining a professional academic publications list online with an easy to use web front end which any researcher can use to maintain their own, professional looking list of publications, which can be hosted on publicationslist.org, or embedded within a departmental web page. Links to full text preprints, or versions in open access repositories and journal websites can be included. Publicationslist.org now offers solutions for research groups and universities to archive and disseminate their research output. The emphasis on ease of use and intuitive user interaction that appeals so much to individuals provides an effective means for organizations to gather and manage research content without having to worry about user interface design themselves. There is a built in PubMed search interface for finding publications matching your name and selecting and importing the ones you want. All the fields will be fetched automatically from MedLine, including the abstract and keywords where available. In the data entry page there is an area where you can paste an entry from the reference management software and have the form automatically populated. You can also upload a complete bibliography file to add all the papers in one go. The supported formats are: EndNote, Reference Manager, BibTeX, ProCite, US Library of Congress XML (MODS), ISI, with conversions performed by bibutils.
GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center. GenomeNet was established in September 1991 under the Human Genome Program of the then Ministry of Education, Science and Culture (Monbusho). The GenomeNet service has been developed by the Kanehisa Laboratory in Kyoto University as part of the research projects. GenomeNet is operated using the Supercomputer System of the Institute for Chemical Research, Kyoto University. LinkDB is supported by the National Bioscience Database Center of the Japan Science and Technology Agency.
Collection of full text archive of biomedical and life sciences journal literature at U.S. National Institutes of Health National Library of Medicine (NIH/NLM). With PubMed Central, NCBI is taking lead in preserving and maintaining open access to electronic literature. Value of PubMed Central, in addition to its role as an archive, lies in what can be done when data from diverse sources is stored in common format in single repository. All articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access.
SeWeR - SEquence analysis using WEb Resources
Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C.
Tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. It is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research.
Document Metadata Organizer Web Annotation Toolkit
domeo - (Document Metadata Organizer) Web Annotation Toolkit
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. The DOMEO (Document Metadata Organizer) Annotation Tool, is an extensible web component enabling users to visually and efficiently create and share ontology-based stand-off annotation metadata on HTML or XML document targets - and soon images - , using the Annotation Ontology (AO) RDF model. The tool supports manual, fully automated, and semi-automated annotation with complete provenance records, as well as personal or community annotation with access authorization and control. DOMEO is just one of the components of a bigger architecture - The Annotation Framework - that uses Annotation Ontology (AO) as communication mechanism within the platform and with the external world. Acknowledgements Special thanks to Marco Ocana for his valuable contribution in bootstrapping the DOMEO project.
British Columbia Gynaecologic Tissue Bank
The OvCaRe Tissue Bank is housed within the Vancouver General Hospital Department of Pathology and the British Columbia Cancer Agency. This bank contains tumour samples from over 1100 patients. The tissue samples in the bank are collected from consenting patients within 30 minutes of surgical excision and stored in a variety of forms, including snap frozen, formalin fixed, and as live cells. As of 2007, serum, plasma, and buffy coat are also being collected for every case within the tissue bank. In addition to providing research material for OvCaRe researchers, the OvCaRe Tumour Bank is more active than any other tumour bank in sending samples to research collaborators and has already contributed to 43 national and international research projects. This and other tissue banks provide the foundation for translational research in medicine. In order for these samples to be used by current technologies such as Illumina whole transcriptome sequencing, the samples must be of extremely high quality. We have currently sent a selection of our samples to The Cancer Genome Atlas Project for analysis and were told by researchers there that our samples were among the best quality that they had encountered around the world. Serum Bank The OvCaRe serum bank is located at the British Columbia Cancer Agency. This bank contains over 10,000 serum samples that have been submitted for CA-125 testing as well as samples collected from patients who have consented to have their tumours submitted to the OvCaRe Tumour Bank. Like the tumour bank, these resources are available to collaborating researchers. Ovarian Cancer Tissue Microarrays The ovarian cancer tissue microarray facility from all available early ovarian cancer cases in the province for the period 1984-2000 (541 samples) was created by Dr. Blake Gilks and is the largest tissue microarray of early ovarian cancer samples. This population based series was generated in the Genetic Pathology Evaluation Center (GPEC), a laboratory supported by a Michael Smith Foundation for Health Research Unit Grant and is being used by over 20 different local and international collaborative studies. Two other ovarian cancer tissue microarrays are also built and are available to interested collaborators. All samples in the tissue microarray are linked to clinical outcomes at the Cheryl Brown Ovarian Cancer Outcomes Unit.
eBIRT - Biomedical Interactive Resource Tool
Electronic Biomedical Interactive Resource Tool
Venue for research resource discovery offering resource providers a platform to advertise their services and products, as well as investigators a means to locate services for their use. Search results may be refined by resource type, research area or institution.
INMEX - INtegrative Meta-analysis of EXpression data
INtegrative Meta-analysis of EXpression data
A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner.
CFC International is a volunteer, not-for profit, self-help support group for persons and families dealing with Cardio-Facio-Cutaneous Syndrome. Incorporated in 1999 in the state of New York, its membership has grown from 21 families in mainly the USA to now include persons from all around the world. Our mission is to strive to help each other cope with the challenges of raising a child with a rare and often medically involved disorder. We act as a clearinghouse of information on all aspects of CFC Syndrome. We publish a quarterly newsletter, produce a brochure and CFC Parent' '''s Guide, private address book, host a private family computer list serve and also host a website. We host International family conferences and clinics open to families from all over the globe. Our goal is to educate the general public, the medical profession, and government agencies by disseminating information on CFC Syndrome. We work to facilitate research on this very rare syndrome. We have a medical/scientific advisory board consisting of doctors from different regions of the world who have a committed interest in our CFC children. We maintain the most extensive registry for CFC Syndrome patients in the world. The Registry provides resources for the study of CFC Syndrome. It maintains centralized information records on CFC Syndrome cases from around the world. Confidentiality of personal information regarding incidence, genetics, clinical course, and prognosis is provided to professionals and families. The Registry also serves to improve communication of ideas among interested researchers, and to assure rapid distribution of any new information that may benefit patients or their families. As part of this medical registry we are founding members of the Genetic Alliance BioBank. The BioBank contains the largest collection of DNA and tissue samples from CFC patients and their parents.
A program to eliminate artifactual reads from next-generation sequencing data sets.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
Web-based, searchable portal of three interlinked registries, containing both in-house and crowdsourced manually curated descriptions of standards, databases and data policies, combined with integrated view across all three types of resource. By registering your resource on FAIRsharing, you gain credit for your work, increase its visibility outside of your direct domain, reduce potential for unnecessary reinvention and proliferation of standards and databases.
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. The Unified Library Database, or UniLib, takes a library-level view of the EST and SAGE libraries present in NCBI's dbEST, UniGene and SAGEmap resources. This database was initially developed by NCBI in order to track and annotate libraries being generated by NCI's CGAP project. The query bar of the UniLib Library browser provides the most friendly way to navigate through these libraries. When matches to the Library browser query are returned as summaries, full library records can be retrieved through the linked Record retriever.
Friedrich Miescher Institute for Biomedical Research
The Friedrich Miescher Institute is devoted to fundamental biomedical research aimed at understanding the basic molecular mechanisms of health and disease. We communicate and patent our findings to enable their translation into medical application. The FMI focuses on the fields of Epigenetics, Signaling & Cancer, and Neurobiology. In these fields, the FMI has gained international recognition as a center of excellence in innovative biomedical research. Training young scientists The Friedrich Miescher Institute contributes to the training of graduate students and postdoctoral fellows. Through its PhD program, which was established as early as 1970, the FMI attracts top international students. The FMI is affiliated with the University of Basel, where most of the graduate students are enrolled and where it contributes to the teaching program. Many FMI alumni have gone on to pursue successful careers in Novartis, in other pharmaceutical companies, or in academic research. Exciting environment for academic and applied research Staff at FMI benefit from a unique scientific environment, allowing researchers, specialists and students to pursue questions that yield new scientific insights. As part of the Novartis Research Foundation, the FMI receives strong core support from the foundation. Funding is supplemented by competitive fellowships and awards from national and international funding agencies. This provides an optimal environment for both academic and applied biomedical research.
NIH Topic Maps - A Topic Database of NIH Funded Grants
There is a great demand for practical tools that enable scientists to understand the organization of the fields of research of interest to them. This project is an ''unofficial'' (i.e., non-supported by NIH itself) web-based system that helps researchers understand the ''funding landscape'' of a particular field through the use of statistical analysis of the language used in grant applications'' abstracts. Our system is available at https://app.nihmaps.org/, providing both a query- and mapping- based interface for funded NIH-grants from 2007-2010. From its conception, this project has been a highly collaborative team effort. The project''s main driving force has been provided by Ned Talley but has involved ideas, technical support, academic contributions and funding from multiple sources and people.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.Digital collection of images, with themes ranging from medical and social history to contemporary healthcare and biomedical science. The collection contains historical images from the Wellcome Library collections, Tibetan Buddhist paintings, ancient Sanskrit manuscripts written on palm leaves, beautifully illuminated Persian books and much more. The Biomedical Collection holds over 40 000 high-quality images from the clinical and biomedical sciences. Selected from the UK''s leading teaching hospitals and research institutions, it covers disease, surgery, general healthcare, sciences from genetics to neuroscience including the full range of imaging techniques. They are always looking for new high quality biomedical images from scientific researchers, clinical photographers and artists in any field of science or medicine. As a contributor you retain your original material and copyright, and receive commission and full credit each time your images are used. The annual Wellcome Images awards (previously known as Biomedical Images Awards) reward contributors for their outstanding work and winners are chosen by a panel of experts. The resulting public exhibitions are always extremely popular and receive widespread acclaim. All images on the Wellcome Images site are available free for use in: * private study and non-commercial research * examination papers * criticism and review, this applies only where there are no multiple copies made * theses submitted by a student at a higher or further education institution for the purposes of securing a degree * personal use by private individuals
biological Process Inference from eXperimental Interaction Evidence
bioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data. This novel system for biological data integration and visualization, allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. The system is based on a Bayesian algorithm for identification of biological networks based on integrated diverse genomic data. To start using bioPIXIE, enter your genes of interest into the search box. You can use ORF names or aliases. If you enter multiple genes, they can be separated by commas or returns. Press ''submit''. bioPIXIE uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the bioPIXIE algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. As you move the mouse over genes in the network, interactions involving these genes are highlighted. If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. You may need to download the Adobe Scalable Vector Graphic (SVG) plugin to utilize the visualization tool (you will be prompted if you need it).
Guthy-Jackson Repository for Neuromyelitis Optica
Special collection of Neuromyelitis Optica (NMO) biological samples and data to foster scientific collaboration for NMO Spectrum Disease that will lead to the prevention, clinical treatment programs and a potential cure for Neuromyelitis Optica (NMO) Spectrum Disease. In this initiative, people with NMO can enroll into the repository at ACP''s collection sites located in leading neurology clinics across the US. Participants provide blood samples and information, which will in turn be used by qualified scientists whose research will contribute to the diagnosis, prevention, treatment, and/or cure of NMO. NMO subjects are primarily enrolled through the efforts of a study nurse employed by UTSW. Accelerated Cure Project (ACP), University of Texas Southwestern (UTSW), and Guthy-Jackson will work together to invite people with NMO to participate in the repository. Participants can enroll by visiting one of the ACP repository sites or by accepting an enrollment visit from the UTSW nurse.
Biorepository Alliance of Georgia for Oncology
Bio-Repository Alliance of Georgia for Oncology
Bio-Repository Alliance of Georgia for Oncology Tissue and Tumor Bank
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The Georgia Cancer Specimen and Tissue Bank is committed to a safe and reliable supply of tissue and cell products for research purposes. Work has begun already to build the state tumor bank initiative with operating sites in several locations through the state. We are confident that our results will yield a strong program that will benefit all Georgians and contribute to significant advances in cancer research and knowledge.
An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data.
NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into Sets and Groups, NeuroMatic makes it relatively easy to compute transformations and statistical analyses on their data, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, rise-time computations, etc. Being open source and modular designed, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Note, if you have reached this page in search of a freeware tool for neuronal reconstructions, you are more likely to be interested in Neuromantic, a software package that sounds like NeuroMatic, but is not quite the same. Features of NeuroMatic Include * Sorting, Scaling, Averaging, Interpolation * Max / Min / Mean / Level / Rise Time / FWHM / Slope Measurements * Stability / Stationarity Analysis * Event Detection * Waveform Template Matching * Spike Raster Plots * Interspike-Interval and Peri-Stimulus Time (PST) Histograms * Compact Easy-to-Use Interface * Modular design as a basis for your own procedures * Extra space for your own buttons and controls * Import functions for Axograph and Pclamp data * Automatic macro generation for batch processing Supporting Agencies: MRC, Wellcome Trust Spike, Event, Fit, NClamp, Acquisition, spike train, EPSP, IPSP, IPSC, EPSC
Functional Interpretation of Differential Expression Analysis
A web server for the functional interpretation of differential expression analysis. It can: * Calculate overrepresentation statistics using KEGG, Interpro, Gene Ontology Molecular Function, Gene Ontology Biological Process, Gene Ontology Cellular Component and GoSlim classifications; * Analyze down-regulated and up-regulated DE genes separately or together as a single set; * Provide interactive graphs and tables that can be modified on the fly according to user defined parameters; the user can set a fold change filter and interactively see the effects on the gene set under examination; * Output publication-ready plot of the graph; * Compare the results of several experiments in any combination.
SeqMap is a generalized tool to characterize insertion sites that have been predicted from LM/LAM PCR methods. It will automatically identify genome insertion sites and nearby genes characterizing their function. This is an important tool as insertion site analysis is required for gene therapy clinical trials that are using retroviral and lentiviral vectors.
Evaluation of Genomic Applications in Practice and Prevention
Evaluation of Genomic Applications in Practice and Prevention (EGAPP)
Initiative to develop a systematic, evidence-based process for evaluating genetic tests and other applications of genomic technology that are rapidly moving from research to use in clinical practice. A key objective of this process is to provide objective, timely, and credible information that is clearly linked to the scientific evidence on specific applications of genetic and genomic tests. The primary focus of EGAPP activities is an independent, nonfederal expert panel, the EGAPP Working Group. Other components of the EGAPP initiative include a federal interagency, the CDC staff and consultants, and an EGAPP initiative evaluation team.
RatMine integrates data from RGD, UniProtKB, NCBI, KEGG and other sources to form a web-based data warehouse and tool set tailored for rat based data research. Search RatMine by entering names, identifiers, or keywords for genes, proteins, pathways, papers, etc. Additionally, we support programmatic access to our data through Application Programming Interface - choose from Perl or Java API. RatMine is a data warehouse that integrates many diverse biological data sets. The main focus is R. norvegicus genomics and proteomics. By integrating such data into one place it is possible to construct queries across domains of biological knowledge. The RatMine user interface is designed to go beyond simply looking up an identifier and viewing a report page. Some of the features include: * Quick Search is available just like on other sites, type in an identifier to see a report page. * Template queries are ''canned'' queries that provide a simple form to perform a specific task. You can create your own templates if you log in. * Lists lets you operate on whole lists of data at once. You can upload lists or save them from results tables. We also create useful public lists for everyone to use. * MyMine lets you create an account to save your own queries, bags and templates, as well as marking public templates as favorites.
Greenville Hospital System Cancer Biorepository
Institute for Translational Oncology Research Biorepository
Institute for Translational Oncology Research Biorepository Services
From the type of mutation causing cancer to specific gene expression levels, genetic biomarkers are becoming an indispensable tool for developing new treatment models for cancer. The ITOR Biorepository Services tissue bank initiatives are critical to the continued development of an organized research infrastructure that will attract leading biotechnology and pharmaceutical companies interested in developing the next generation of cancer therapies. Ultimately, by linking the laboratory and clinical settings through innovative research investigations, USC, Greenville Hospital System University Medical Center, and private partners can identify the most novel ways to find and couple these biomarkers to patient drug trials and eventually, the most effective treatments & cures for cancer. The ITOR Biorepository Services Department ����?����������?? in conjunction with the Greenville Hospital System''s surgical oncologists, pathologists and staff ����?����������?? have developed tissue bank sample processing guidelines for frozen tissue, fresh tissue and peripheral blood and include flash freezing in liquid nitrogen within 15 minutes of harvest to maximize cell viability for basic science research. The department has a dedicated staff, including two research nurses and a data coordinator, which facilitate the logistics of tissue handling and submit outcomes data on participating patients. The ITOR Biorepository staff is in the process of adopting a universal consent for all patients of the Greenville Hospital System to have the option of donating excess tissue for research, should they desire. ITOR of GHS has several tissue-based patient initiatives & programs under development and ongoing. At the forefront of cancer care are two specific programs, Total Cancer Care and Caris Target Now.
The Canadian Tumour Repository Network (CTRNet) is a not-for-profit consortium of leading provincial tumor banks and programs that furthers Canadian health research. CTRNet provides interested researchers with a streamlined process to obtain quality human tissue and human tissue products from member tumor banks. The benefits of working with CTRNet.ca include: * The ability for researchers to search for quality controlled tissue samples from Canada' '''s leading tumor banks in one central location and for biobanks to display and make their biospecimens available for research users. * Learning opportunities in tissue handling, research design and relevant technology training and innovations. * Invitation to CTRNet workshops and conferences. * A resource for current news links and discussion forums about cancer research and tumor banking. The vision of CTRNet is to create new opportunities for translational cancer research that will improve cancer outcomes in Canada and beyond. Through the creation and maintenance of an online pan-Canadian network, researchers will gain unprecedented access to a new and comprehensive source of tissue and clinical data. The network is a sustainable resource and operates according to the highest scientific and ethical standards for research to benefit all Canadians. Currently CTRNet has the following member banks: * CBCF Tumor Bank Alberta * Manitoba Tumour Bank * Ontario Tumour Bank * British Columbia Cancer Agency Tumour Tissue Repository (BCCA-TTR) * Le r��seau de recherche en cancer du FRSQ * NCIC Clinical Trials Group
One Mind: One Voice Bio-repository Cosmic Landscape
International registry of biomaterial supply resources both for transplantation and research. Contributions to this resource are welcome. The database is searchable through NIF and is updated regularly.
Progeria Research Foundation Cell and Tissue Bank
Progeria Research Foundation Cell Tissue Bank
The PRF Cell & Tissue Bank provides medical researchers with genetic and biological material from Progeria patients and their families, so that research on Progeria and other age-related diseases can be performed. We''ve been hard at work with the families and their physicians to gather these precious biological materials. As you know, Hutchinson-Gilford Progeria Syndrome is an extremely rare condition. Thus while access to cell lines is essential for studying the biology and genetics of the disorder, there are very few cell lines in existence. Because an integral part of PRF''s mission is to stimulate interest in, and NIH funding opportunities for, Progeria research, there is an increased need for cell lines. The PRF Cell Bank will ensure that need is met! The goals of The PRF Cell & Tissue Bank are to promote: * Sufficient availability of cells for approved research projects * Incentive for new research projects * Study of the biochemical basis for Hutchinson-Gilford Progeria Syndrome * Discoveries leading to new treatments for children with Progeria * Discovery of a cure for Progeria
An ISO 9001 certified designer, manufacturing and distributing orthopedic implants and instrumentation worldwide for over 50 years. Wright''s product offerings include large joint implants for the hip and knee; extremity implants for the shoulder, elbow, hand, wrist and foot; and both synthetic and tissue-based bone graft substitute materials. Since its inception, Wright has introduced a number of products that represent new standards in orthopedic technology. From new material technologies to advanced products and instrumentation, Wright is committed to finding solutions to the challenges that face today''s orthopedic professionals.
Division of Cancer Treatment and Diagnosis
Division of NCI that takes prospective cancer detection and treatment leads, facilitates their paths to clinical application, and expedites the initial and subsequent large-scale testing of new agents, biomarkers, imaging tests, and other therapeutic interventions (radiation, surgery, immunotherapy) in patients. DCTD, like all of NCI, supports many programs that could not be done without government funding - investigators supported by the division engage in scientifically sound, high-risk research that may yield great benefits for patients with cancer, but are too difficult or risky for industry or academia to pursue. This includes a particular emphasis on the development of distinct molecular signatures for cancer, refined molecular assays, and state-of-the-art imaging techniques that will guide oncologic therapy in the future. The division has eight major programs that work together to bring unique molecules, diagnostic tests, and therapeutic interventions from the laboratory bench to the patient bedside: * Cancer Diagnosis Program * Cancer Imaging Program * Cancer Therapy Evaluation Program * Developmental Therapeutics Program * Radiation Research Program * Translational Research Program * Biometrics Research Branch * Office of Cancer Complementary and Alternative Medicine
NIF Integrated Brain Gene Expression View
Virtual database indexing brain region gene expression data from mice from: Gene Expression Nervous System Atlas (GENSAT), Allen Mouse Brain Atlas, and Mouse Genome Institute (MGI).
Proteomics Standards Initiative Protein Modifications
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The protein modification workgroup focuses on developing a consensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications. The protein modification ontology (PSI-MOD) is available in OBO format or in OBO.xml. A spreadsheet containing the mapping of the descriptive labels used in various databases and search engines, the consensus list of proposed short name for protein modifications established by collaborative effort of mass spectrometry community, and the proposed rules and recommendations for this nomenclature are available. These short names are included in the ontology as synonyms of the corresponding terms.
EVOLUTIONARY FOUNDATIONS FOR THE HUMAN FOREBRAIN
First Periodic Table for the Neurosciences
Portal on the evolution of the Human Forebrain with schematically depicted sequential age levels of cortical evolution: Staggered Dual Parameter Grid, Growth Rings of the Neocortex, Growth Shells of Thalamus, Major Nuclei of the Thalamus, Dual Parameter - Grid, Types of Neocortical Lamination, and Rolf Hasslers Hexa-Partition of Unit Thalamic Inputs. The cytoarchitectonic subdivisions of both the thalamus and the neocortex are topographically defined in terms of the variables of phylogenetic age and input specificity. The cortical and thalamic parcellations of Brodmann, von Economo and Hassler are each quantitatively correlated to a specific Cartesian coordinate value designating discrete levels for both age and input basic parameters. The variable of phylogenetic age is represented in the cortex by the five circumferential growth rings demonstrated by Sanides, plus an additional growth ring detected intermediate to the fifth and sixth age levels and designated as prekoniocortex. The paleocortex and the archaecortex are the two primordial neocortical precursors that form the mammalian neocortex. In contrast to the arrangement in the planar cortex, six phylogenetically distinct growth shells are detected in the three-dimensional thalamus and are designated after the corresponding schematic levels of Rolf Hassler''s paradigm of hexapartition of unit-thalamic inputs. The subthalamus and the epithalamus analogously represent the primordial diencephalic precursors of the mammalian dorsal thalamus, Both the neocortex and the dorsal thalamus evolved in response to the necessity for a more comprehensive blending of inputs from differing neuraxial levels. Unlike the age variable, the parameter of input specificity is most readily apparent in the dorsal thalamus; which is the site of termination for each major forebrain input. Accordingly, the fourteen individual units of the parameter of input specificity are designated after each of the specific input classifications projecting discretely to circumscribed thalamic sectors, An identical complement of input parameter levels also occurs in the cortex by way of thalamic relay across the internal capsule. Furthermore, each thalamic nucleus of specific parameter coordinates directs its main projection to cells of the cortex displaying identical coordinate values, establishing forebrain interconnectivity as an additional function of the dual parameter paradigm.
DC-Research.eu - Dendritic Cell Research Knowledge Portal
An open knowledge resource for the dendritic cell research community, this index of research assets and expertise is designed to support translational research by providing annotations and interrelations on materials, datasets, tools, techniques, persons and organizations. The content of DC-RESEARCH.EU can be accessed by researchers through its website and can be accessed programmatically: the information in DC-RESEARCH.EU is represented through machine processable languages, proper of the Semantic Web (RDF and RDFa). To submit to the dc-thera directory please contact: dc-research_at_leafbioscience.com
A portal that provides a province-wide, population-based cancer control program for the residents of British Columbia and the Yukon. The BC Cancer Agency''s mandate covers the spectrum of cancer care, from prevention and screening, to diagnosis, treatment, and through to rehabilitation. The BC Cancer Agency''s mandate is driven by a three-fold mission: 1. To reduce the incidence of cancer; 2. To reduce the mortality rate of people with cancer; 3. To improve the quality of life of people living with cancer. This mission drives everything we do, including providing screening, diagnosis and care, setting treatment standards, and conducting research into causes of, and cures for, cancer. The BC Cancer Agency operates five regional cancer centers, providing assessment and diagnostic services, chemotherapy, radiation therapy, and supportive care. Each of the BC Cancer Agency''s centers delivers cancer treatment based on provincial standards and guidelines established by the Agency. We work in partnership with communities to provide a network of chemotherapy clinics so patients can receive care closer to home. Research is an essential part of the BC Cancer Agency''s mission to not only find the causes of cancer, but to find better treatments for prolonged life and better quality of life. With direct links between the BC Cancer Agency''s physicians and researchers at our five centers, the Deeley Research Centre (located in Victoria) and the BC Cancer Agency''s Research Centre (located in Vancouver), we can quickly translate new discoveries into clinical applications. The BC Cancer Agency''s Research Centre includes eight specialty laboratories including the Genome Sciences Centre, and the Terry Fox Laboratory. The BC Cancer Foundation raises funds for cancer research and enhancements to care at the BC Cancer Agency.
Medical Education and Research Institute - MERI
Medical Education and Research Institute
A nonprofit medical teaching and training school in Memphis, Tennessee qualified under section 501 (c) (3) of the Internal Revenue Code. The MERI conducts state-of-the-art, hands-on educational courses for physicians, nurses and other medical professionals from across the country and around the world. At the MERI, medical professionals are introduced to the latest innovations in medicine, and have the opportunity to learn first-hand about the most up-to-date medical techniques and technologies. The MERI supports research in all specialties by providing the sponsor with the most effective environment for achieving maximal outcomes for their studies. Through our Mobile MERI unit, we are proud to provide courses and support to our sponsors off-site anywhere in the continental United States. Our dedicated course specialists offer customer service, provide safe and efficient transport of equipment and ensure a quality training and educational experience at the off-site location.
Software application that uses genotyping data from SNP arrays for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data. (entry from Genetic Analysis Software)
University at Buffalo SMBS Department of Pharmacology and Toxicology
UB SMBS Dept. of Pharmacology and Toxicology
The Department of Pharmacology and Toxicology strives to maintain excellence in the areas of research, teaching and service to the School, University, and Community. The Department offers a program of didactic course work and research training leading to the degree of Doctor of Philosophy in Pharmacology, either through the Interdisciplinary Graduate Program in Biomedical Sciences (IGPBS) or through the Medical Scientist Training Program (MSTP). Pharmacology and Toxicology have similar basic principles and often utilize similar experimental methods and approaches to address a wide range of biomedical and health-related questions. Both are sciences that are basic not only to medicine, but also to pharmacy, nursing, dentistry, public health, and veterinary medicine. Additional programs are offered for the Bachelor of Science, or a combined Bachelor of Science / Master of Science in Pharmacology and Toxicology, and a Master of Arts in Pharmacology. The graduate programs are structured to provide the candidate with a broad training in basic areas of pharmacology as well as a degree of expertise in one research area including: Neuropharmacology, Psychopharmacology, Toxicology, Molecular and Cellular Pharmacology, Clinical Pharmacology
Boston University Medical Campus; Massachusetts; USA
The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.
A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.
A repository of biological samples and data from people with multiple sclerosis, selected other demyelinating diseases, and unaffected controls. The repository not only provides much-needed samples and data to researchers studying MS and other diseases, but also aggregates the results from all of these studies so that they can be analyzed collectively, leading to new findings and breakthroughs. The repository collects blood, DNA, and imaging once per year. The repository currently includes samples and data from over 2,700 subjects with Multiple Sclerosis, Neuromyelitis Optica, Acute Disseminated Encephalomyelitis, Transverse Myelitis, Optic Neuritis, and Clinically Isolated Syndromes, as well as controls. Blood samples are provided as aliquots as serum, plasma, DNA, RNA, and lymphocytes and each sample is accompanied by more than 40 pages of clinical and epidemiological data contributed by the subject and the enrolling neurologist.
Software that implements the full regularization path optimization algorithm for training a support vector machine. The support vector machine algorithm has a single hyperparameter C that regularizes the learned model. Recently, Hastie et al. (2004) described an algorithm for finding the SVM solution for all possible values of this regularization parameter. An efficient C++ implementation of this algorithm is presented. For large values of C, it is often faster to find the entire regularization path than to train a single model.
Online Nucleosomes Position Prediction by Genomic Sequence
This tool allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model that we developed in these papers: * Segal et al., A Genomic Code for Nucleosome Positioning, Nature 2006 * Field et al., Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals, PLoS Comp Biol. 2008 * Kaplan et al., The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome, Nature 2008 We recommend using the latest version of the model (Version 3), which is applicable to all species. Paste in a sequence to analyze or upload file. You can provide multiple sequences in fasta format (separate sequences by lines starting with ''>'' followed by the sequence name). The length of each sequence must be between 147bp and 40kb bp. Note: Due to boundary effects, we highly recommend that you add at least 5000 bp of flanking sequence around your sequence of interest. You can generate the nucleosomes positioning predictions on your own machine using our executable and wrapping Perl scripts.
An independent, not-for-profit biobanking and biotechnology foundation designed to facilitate new, high quality medical research. The IBBL collects, stores, and analyzes biological samples and associated data, which are then made available to research organizations investigating new treatments for diseases. It houses a biospecimen collection and biorepository that contains high quality tissues and maintains quality control of the specimens and the clinical data associated with the tissue samples, while maintaining biobanking ethical standards. It also provides biorefinery analyses and research services that can make analytes from tissues (e.g. DNA, RNA and protein), maintains technology for high throughput gene sequencing and gene expression, and conducts biospecimen research. An informatics platform maintains the clinical and biospecimens data in a secure fashion for additional analysis. Samples are collected by IBBL personnel from hospitals in a targeted manner. The IBBL collaborates with research and health organizations in North America, Europe and the Middle East, and with the major international biobanking societies.
International Biologics is a fully accredited American Association of Tissue Banks (����??AATB����??) Tissue Bank and Processing Facility --- Accreditation #00162. It receives 100% of it''s donor tissue from federally licensed Organ Procurement Organizations (OPO����??s) and other AATB accredited donor sources. International Biologics provides multitudinous bone and soft tissue allografts. Clinical applications for these products include: Orthopedic, Spine, Joint Restoration, Oral Maxillofacial, Podiatry, Periodontal, Urology, Trauma The collection and distribution of donated tissue including soft tissue, bone tissue and organ donation of kidneys, livers and hearts (collectively tissue) are controlled by the Government. Organ Procurement Organizations (OPOs) have long been established in every state to recover tissue from donors. Because there is a very short period following death before tissue breaks down rendering it useless for implantation, OPOs maintain round-the-clock presences in hospitals including grief counseling through procurement personnel. OPO tissue is heavily federally regulated and is therefore the most highly sought tissue because it is universally understood to be the safest tissue for transplant. International Biologics has long-term high-volume OPO tissue supply contracts making it one of the largest recipients of cadaveric bone and soft tissue in the world. International Biologics processes its tissue within a state-of-the-art facility located in Scottsdale, Arizona. The facility includes nine -86C ultra low temperature freezers, 14 tray lyophilization, and four validated class 1000 clean rooms including CNC.
Biosample processing, management, storage and retrieval infrastructure that operates on a cost-recovery basis to investigators. Services are available to Research Ethics Board (REB) approved studies. They accept any human tissue from appropriately consented subjects for processing to DNA, RNA, serum, plasma, peripheral blood cells, fixed tissue, and tissue blocks. Once your samples have been collected and processed, CBSR will provide short and long-term sample storage, and retrieval(typically within 24hrs) upon request. Their storage services include robust robotic systems for sample aliquoting, tracking, storage, and retrieval to ensure chain of custody on all samples. Their temperature monitoring system ensures that all samples are maintained at the chosen temperature, and provides regulatory-grade audit trail for all samples.
Canadian Breast Cancer Foundation Tumor Bank
Canadian Breast Cancer Foundation Alberta Research Tumor Bank
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 18, 2022. A tumor bank that provides a large collection of cancer specimens, from breast and other cancers, annotated with clinical information. The CBCF TB enables researchers to address unanswered questions concerning the prognosis and treatment of breast cancer and other cancers. The CBCF TB website is also directed to participants interested in donating tumor tissue or blood. Biological specimens such as blood, urine, bone marrow, and ascites (fluid that sometimes collects in the abdomen) contain genetic information, just as tumor tissue does. These samples can be used in studies that may help researchers see how people with certain genetic make-ups respond to certain treatments. It can also explain why different people have different health problems. CBCF TB, formerly ARTB, was created by a merger of components of two existing Tumor-banking initiatives, the CLS Repository in Calgary and the Tumor bank of the PolyomX Program in Edmonton.
The Canadian Breast Cancer Foundation is the leading national volunteer-based organization in Canada dedicated to creating a future without breast cancer. Established in 1986 by a dedicated group of volunteers, the Foundation works collaboratively to fund, support and advocate for: * Relevant and innovative research, * Meaningful education and awareness programs, * Early diagnosis and effective treatment * A positive quality of life for those living with breast cancer. Our fundraising through our annual Canadian Breast Cancer Foundation CIBC Run for the Cure, special events, corporate sponsorship and donations has enabled the Foundation to allocate millions of dollars in grants for breast cancer projects and services since our inception. Addressing the needs of Canadians from coast to coast, the Canadian Breast Cancer Foundation has regional offices in British Columbia/Yukon Territory, Prairies/NWT, Ontario and the Atlantic Region. The Foundation''s central office is located in Toronto. Charitable Registration No. 12799 3608 RR0001
ACSR - AIDS and Cancer Specimen Resource
A biorepository for HIV-infected human biospecimens from a wide spectrum of HIV-related or associated diseases, including cancer, and from appropriate HIV-negative controls. The ACSR has formalin-fixed paraffin embedded biospecimens, fresh frozen biospecimens, malignant cell suspensions, fine needle aspirates, and cell lines from patients with HIV-related malignancies. It also contains serum, plasma, urine, bone marrow, cervical and anal specimens, saliva, semen, and multi-site autopsy speicmens from patients with HIV-related malignancies including those who have participated in clinical trials. The ACSR has an associated databank that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. The ACSR database contains more than 300,000 individual biospecimens with associated clinical information. Biospecimens are entered into the ACSR database by processing type, disease category, and number of cases defined by disease category.
University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA
University of North Carolina at Chapel Hill School of Medicine
University of North Carolina School of Medicine
Database of three-dimensional structures of macromolecules that allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships. * Macromolecular structures: The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. It is possible, for example, to find 3D structures for homologs of a protein of interest by following the Related Structure link in an Entrez Protein sequence record. * Conserved domains and protein classification: Conserved domains are functional units within a protein that act as building blocks in molecular evolution and recombine in various arrangements to make proteins with different functions. The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, in addition to NCBI-curated domains that use 3D-structure information explicitly to define domain boundaries and provide insights into sequence/structure/function relationships. * Small molecules and their biological activity: The PubChem project provides information on the biological activities of small molecules and is a component of NIH' '''s Molecular Libraries Roadmap Initiative. PubChem includes three databases: PCSubstance, PCBioAssay, and PCCompound. The PubChem data are linked to other data types (illustrated example) in the Entrez system, making it possible, for example, to retrieve information about a compound and then Link to its biological activity data, retrieve 3D protein structures bound to the compound and interactively view their active sites, and find biosystems that include the compound as a component. * Biological Systems: A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. The NCBI BioSystems Database provides centralized access to biological pathways from several source databases and connects the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system. BioSystem records list and categorize components (illustrated example), such as the genes, proteins, and small molecules involved in a biological system. The companion FLink icon FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems.
BrainSpan - Exon microarray summarized to genes
Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, Exon microarray summarized to genes, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis.
Diabetes Wiki is a wiki where people with diabetes share personal stories, and build a database of helpful information. Categories include News, What is Diabetes?, Managing Diabetes, Impact of Diabetes, and more. Additionally, contribute to blog posts and the forum.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. The mission of the Canadian Virtual Brain Tumour Bank (CVBTB) is to facilitate clinical, molecular and translational research through the provision of well-characterized tissue linked to clinical data and to become a standardized national tissue resource whereby scientific needs are met, addressed and accelerated through a common public accessible core the CVBTB. Recognizing the need to encourage systemic banking of brain tumor tissues throughout the country and to link banks of brain tumor tissue samples with academic and scientific institutions that require these samples, the CVBTB was established. Under the sponsorship of Schering Plough Canada Inc. and in association with the Canadian Brain Tumour Consortium (CBTC), the CVBTB looks to act as a resource for all researchers to provide them with information on the types of brain tumor tissue samples available and to direct them to the tumor tissue banking sites holding these samples. The CVBTB also looks to provide information on standard operating procedures regarding aspects of tumor tissue banking such as tissue accrual, storage and shipment and the processing of blood samples such as serum and lymphocytes. The CVBTB currently consists of four brain tumour tissue banking sites (Toronto Western Hospital - Toronto, Ontario; London Health Sciences Centre - London, Ontario; McGill University - Montreal, Quebec; University of Calgary - Calgary, Alberta) and is continuously looking for more institutions to be a part of the CVBTB. If your institution would like to become a part of the CVBTB, please contact the CVBTB coordinator.
UAB Comprehensive Cancer Center Tissue Procurement Shared Facility
The Tissue Procurement Shared Facility (TPSF) of the Comprehensive Cancer Center operates as a prospective service to collect, from UAB associated hospitals, normal, malignant, benign, and diseased fresh human tissues and fluids which are then preserved appropriate to protocol. The TPSF can provide normal, malignant, benign, or diseased remnant human tissues and/or fluids from surgical resections, autopsies, or clinical procedures for IRB-approved researchers. The preservation can include fresh storage in media or saline, snap-frozen storage in liquid nitrogen, freezing in OCT for frozen section preparation, or preservation in a fixative of choice. The TPSF can also provide procurement of control tissues including uninvolved tissues or matched tissues from patients with benign disease processes. The histology laboratory can provide paraffin blocks and/or stained or unstained slides. In addition, investigators can obtain access to rare tissues through the national Cooperative Human Tissue Network (CHTN). Although the facility operates as a prospective service specializing in the preparation of samples to protocol, limited banked frozen and paraffin-embedded samples may be available. Investigators are required to complete an application and provide a copy of their IRB approval as well as a brief description of the project for which the requested samples will be utilized. Samples are provided for research purposes only. Processing fees are to offset processing costs and should be included in all grant applications.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.
The Alberta Cancer Foundation is more than a charity. It''s a movement for cancer-free lives today, tomorrow and forever. It''s a movement of those who know a cancer-free future is possible and who won''t settle for some day. It''s a movement of those who stand with Albertans who have no choice but to stand up to cancer. It''s a movement of those who know something can be done and are willing to do it. For those facing cancer today, in honour of those lost to cancer, and for generations to come, we promise progress. Our mission is to deliver progress in cancer research, prevention, treatment and care by generating community investment for Alberta''s coordinated research strategy, the Cross Cancer Institute, Tom Baker Cancer Centre and 15 other cancer centres throughout the province. The Alberta Cancer Foundation is a Registered Charity - Business Number 11878 0477 RR0001. Your dollar fights cancer on every front: research, prevention, screening, early diagnosis, education, treatment and care.
R��seau de recherche sur le cancer du FRSQ
An infrastructure to allow Quebec researchers to have at their disposal tumor banks and the services that support large scale research in genomics and proteomics. The database and the tissue bank of the research network was created to allow rapid access to biological samples and their clinical data. It is spread out over many hospital institutions (in Montreal, Quebec and Sherbrooke). The members of the RRCancer-BTD supply normal, benign and malignant samples from routine surgeries and blood tests. Blood and tissue samples are collected by the provincial biobanks on a regular basis and are coded, classified and stored. The samples can be supplied to a researcher either fresh or frozen or blocks of paraffin or on slices. The sharing of information and biological material is managed according to ethical rules and contributes to increasing the value of research in Quebec. The network has mobilized a significant number of researchers in the area of cancer that unite their efforts to pursue high caliber multidisciplinary research. They are a group of researchers from many different Qu��bec Universities all working in the branch of cancer research. They are located in four hospital centers in Quebec, namely the University of Montreal Hospital Centre (CHUM), the University of Quebec Hospital Centre (CHUQ), the University of Sherbrooke Hospital Centre (CHUS) and the McGill University Hospital Centre (CUSM), as well as in the affiliated research and university centers (Sacr��-Coeur, Maisonneuve-Rosemont and the Montreal Jewish Hospital). The collaborative efforts created and maintained in this network have allowed transfer of knowledge and the sharing of cutting edge technologies. RRCancer favors multidisciplinary cancer research in both fundamental and clinical scopes. The network is based on the desire researchers to work together to prevent cancer and improve therapeutic strategies, all the while continuing the very important task of raining new specialists and graduate students.
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)
BBMRI: Biobanking and Biomolecular Resources Research Infrastructure
BBMRI: Biobanking Biomolecular Resources Research Infrastructure
Biobanking and Biomolecular Resources Research Infrastructure
Biobanking Biomolecular Resources Research Infrastructure
Biobanking Biomolecular Resources Research Infrastructure (BBMRI)
BBMRI is a pan-European and internationally broadly accessible research infrastructure and a network of existing and de novo biobanks and biomolecular resources. The infrastructure will include samples from patients and healthy persons, representing different European populations (with links to epidemiological and health care information), molecular genomic resources and biocomputational tools to optimally exploit this resource for global biomedical research. During the past 3 years BBMRI has grown into a 53-member consortium with over 280 associated organizations (largely biobanks) from over 30 countries, making it the largest research infrastructure project in Europe. During the preparatory phase the concept of a functional pan-European biobank was formulated and has now been presented to Member States of the European Union and for associated states for approval and funding. BBMRI will form an interface between specimens and data (from patients and European populations) and top-level biological and medical research. This can only be achieved through a distributed research infrastructure with operational units in all participating Member States. BBMRI will be implemented under the ERIC (European Research Infrastructure Consortium) legal entity. BBMRI-ERIC foresees headquarters (central coordination) in Graz, Austria, responsible for coordination of the activities of National Nodes established in participating countries. BBMRI is in the process of submitting its application to the European Commission for a legal status under the ERIC regulation, with an expected start date at the end of 2011. Major synergism, gain of statistical power and economy of scale will be achieved by interlinking, standardizing and harmonizing - sometimes even just cross-referencing - a large variety of well-qualified, up-to date, existing and de novo national resources. The network should cover (1) major European biobanks with blood, serum, tissue or other biological samples, (2) molecular methods resource centers for human and model organisms of biomedical relevance, (3) and biocomputing centers to ensure that databases of samples in the repositories are dynamically linked to existing databases and to scientific literature as well as to statistical expertise. Catalog of European Biobanks www.bbmriportal.eu Username: guest / Password: catalogue The catalogue is intended to be used as a reference for scientists seeking information about biological samples and data suitable for their research. The BBMRI catalogue of European Biobanks provides a high-level description of Europe''s biobanks characteristics using a portal solution managing metadata and aggregate data of biobanks. The catalogue can be queried by country, by biobank, by ICD-groups, by specimen types, by specific strengths, by funding and more. A search function is available for all data.
Human Brain Tissue Repository of Bangalore
A National Facility to promote research in Neurobiology using human nervous tissues. The brain tissues collected with informed consent of close relatives within 4-24 hours following death are frozen for Biochemical, Immuno-histochemical and Molecular Biological studies. A large number of formalin fixed brain tissues from various Neurological, Neurosurgical and Psychiatric disorders are also available for study.
The world''s largest collection of tick cell lines, enabling scientists to carry out advanced research. This biobank is establishing a collection of all the continuous cell lines derived from ixodid and argasid ticks of medical and veterinary importance available worldwide now and in future. Ticks are blood feeding arthropods which transmit many human and animal diseases. Research into prevention and cure of these diseases, which are caused by viruses, bacteria and protozoa, is greatly assisted by the use of cell culture systems which enable study of both how tick cells function, and how and why ticks transmit these disease-causing pathogens. Cell lines will always be shipped to recipient laboratories as growing cultures, since we cannot guarantee successful resuscitation of frozen stabilates. Tick cells in culture can tolerate the range of temperatures experienced during transit by air for up to a week. Training: We will provide training in tick cell line care and maintenance. This is an essential component of successful transfer of tick cells to, and their establishment in, laboratories with little or no previous experience of tick cell culture. Recipient scientists (preferably the person who will actually look after the cells) can visit the biobank for between 2 days and 2 weeks, depending on their level of previous experience, to be trained in the specific approach and methods for tick cell cultivation. Establishment of new cell lines: In response to requests and on receipt of suitable starting material (engorged female or moulting nymphal ticks), we will attempt to establish new cell lines from tick species or strains which are not already represented in the collection. Deposition of new tick cell lines: We invite researchers anywhere in the world who have established new tick cell lines to deposit samples for safekeeping free of charge and, if requested, for distribution alongside the existing biobank portfolio.
An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.
Phelan-McDermid Syndrome International Registry
International registry that consolidates information from individuals with Phelan-McDermid Syndrome into a single database, which will be utilized by researchers to understand Phelan-McDermid Syndrome better. In order to accelerate translational efforts (moving from basic laboratory research to meaningful health outcomes, such as therapies and treatments) related to Phelan-McDermid Syndrome, PMSF is funding the Phelan-McDermid Syndrome International Registry. The Registry is important for characterizing and understanding the syndrome better. Not only will the Registry provide valuable information for families and doctors to make the best care decisions possible, it will be important to help researchers decide what are the most important challenges to address. The Registry will also help scientists find out if there are any PMS patients who might be a good match for their research studies. Collecting information from PMS patients is very important, but protecting the privacy of people affected by PMS is also extremely important. In order to protect your privacy, Patient Crossroads (the company that designed the registry software) has designed many safeguards. Your child''s information will be de-identified so no one who looks at the data can identify you or your child. Your child''s information will be assigned a code. If a researcher is interested in learning more about your child, the researcher will ask the Patient Crossroads/PMSIR genetic counselor to contact you. A scientist will not be able to receive any identifying information about your child unless you give explicit consent for your child''s identity to be released to that researcher. BE PART OF OUR INTERNATIONAL REGISTRY The Registry will provide valuable information for families and doctors to make the best care decisions possible, and it will help researchers decide what are the most important challenges to address in PMS. Establishing the registry addresses two important scientific needs. First, scientists studying PMS need accurate, firsthand information to understand how PMS affects people. Second, scientists who are ready to start studies, such as those that test new treatments, will be able to access The Registry to identify people that may be eligible to participate in studies. In either case, your privacy is assured while the cause of research is advanced. While raw data about PMS will be available to scientists, they won''t have access to any identifying information about your child unless you agree to have your child''s identity released.
An automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. The analysis pipeline is deployed in local hardware and the Amazon Web Services cloud via the DNAnexus platform.
Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go.
Stem cell company focused on developing and marketing products to treat medical conditions in the inflammatory, autoimmune, orthopedic and cardiovascular areas. Now part of Smith and Nephew.
Society in Science - The Branco Weiss Fellowship
Society in Science: The Branco Weiss Fellowship
Society in Science The Branco Weiss Fellowship provides young researchers around the world with a generous personal grant, giving them the freedom to work on whatever topic they choose anywhere in the world, for a maximum duration of five years. This research funding is designed to support postdoctoral researchers after their PhD and before their first faculty appointment. Those in current postdoctoral positions are also eligible. Society in Science was initiated and financed by the Swiss entrepreneur Dr. Branco Weiss, who passed away in October 2010. The program is coordinated by the Swiss Federal Institute of Technology Zurich (ETH).
Certified by the federal government, LifePoint is the designated Organ Procurement Organization (OPO) for organ recovery services in South Carolina, excepting Aiken and Edgefield counties. LifePoint actively provides organ, tissue and ocular donor services to 62 hospitals throughout the state. We offer professional education about donation to the hospital staff members in order to maximize the amount and quality of donated organs and tissues. LifePoint also helps support and educate families at an emotionally devastating time, so they can make well-informed decisions about organ and tissue donation. Whether they decide for or against donation, our aim is to assure that they will feel they have made the right decision in the months and years to come.
National program to improve the diagnosis and assessment of cancer by moving scientific knowledge into clinical practice by coordinating and funding resources and research for the development of innovative in vitro diagnostics, novel diagnostic technologies and appropriate human specimens. The Cancer Diagnosis Program is divided into four branches: Biorepository and Biospecimen Research Branch (BBRB), Diagnostic Biomarkers and Technology Branch (DBTB), Diagnostics Evaluation Branch (DEB), and the Pathology Investigation and Resources Branch (PIRB).
A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline.
CURE - Digestive Diseases Research Center
Center whose interests and activities encompass several facets of gastrointestinal regulatory physiology and cell biology. It provides an infrastructure to support basic, translational and clinical research and to facilitate interdisciplinary research and training activities in digestive diseases.
A set of software tools created to rapidly build scientific data-management applications. These applications will enhance the process of data annotation, analysis, and web publication. The system provides a set of easy-to-use software tools for data sharing by the scientific community. It enables researchers to build their own custom-designed data management systems. The problem of scientific data management rests on several challenges. These include flexible data storage, a way to share the stored data, tools to curate the data, and history of the data to show provenance. The Yogo Framework gives you the ability to build scientific data management applications that address all of these challenges. The Yogo software is being developed as part of the NeuroSys project. All tools created as part of the Yogo Data Management Framework are open source and released under an OSI approved license.
Radio National''s weekly foray into all things mental a program (podcast) about the mind, brain and behavior, hosted by Lynne Malcolm (previously by Natasha Mitchell). From dreaming to depression, addiction to artificial intelligence, consciousness to coma, psychoanalysis to psychopathy, free will to forgetting ��All in the Mind��explores the human condition through the mind''s eye. All in the Mind brings together unexpected voices, themes and ideas and engages with both leading thinkers and personal stories. Psychology and human behavior are only part of the equation. The program''s scope is considerably broader and explores themes in science, religion, health, philosophy, education, history and pop culture, with the mind as the key focus.
American Donor Services (ADS) is an independent, non-profit organization specializing in tissue donation. Its mission is to improve lives through the gift of donation. ADS honors the spirit of donation by providing caring support to donor families, employing competent staff, and partnering with organizations that are dedicated to the innovative use of tissue for transplantation and research. We are registered with the Food and Drug Administration (FDA). ADS is also accredited with the American Association of Tissue Banks (AATB) and employs dedicated and experienced leadership and staff to sustain our program. The fundamental objective of ADS is to provide the opportunity of donation to individuals who have designated themselves as a donor and families who have the inclination and the potential to have their loved one become a tissue donor. ADS is dedicated to the cause of all donations and as such will support all other organizations in their parallel undertakings. We are committed to providing the best possible serivce to our Donor Families, Hospitals, Medical Donate Life Examiners, Coroners and Funeral Professionals.
Life Alaska Donor Services is the tissue donation organization serving the state of Alaska, offering the option of donation to families who have suffered a death in Alaska. Life Alaska was established in 1991 as the state''s tissue donation program. Since that time, Life Alaska has had many donors and has supplied thousands of tissues for transplantation to Alaskan patients. Life Alaska works in partnership with the federally designated Organ Procurement Organization in Washington (LifeCenter Northwest) to provide education on tissue and organ donation throughout the state. Tissue donations have taken place across the state, from Barrow to Ketchikan. The age criteria for transplantable tissues and organs are generally from birth to 80 years of age, with patients of any age being candidates for research. Tissues donated to Life Alaska are first offered to Alaskan patients and physicians before being made available outside the state. Organs are shared using the federally mandated national sharing system operated by the United Network for Organ Sharing and are first offered to transplant centers in the Pacific northwest.
AIDS and HIV Research is a disease-related portal that includes Articles, News, Jobs, Free Journals, Links, Forum, Structures, Labs & Rankings. * AIDS and HIV research links are profiled and rated. You can rate each website and view the websites in a number of categories including portals, blogs, databases, software and several other categories. Below you will find the top 10 rated AIDS and HIV research links. * Recent AIDS and HIV research literature is highlighted. We have taken the entire set of AIDS and HIV research articles and arranged them according to their previous or expected citation rate. This allows you to quickly identify the most important articles in the field. * Recent AIDS and HIV research news and press releases are highlighted. We scour over 20,000 news sources to bring you the latest AIDS and HIV research news. * AIDS and HIV research laboratories are featured. We have actually profiled nearly 99% of all AIDS and HIV research laboratories. We have also ranked all labs based upon the citation rating of the papers of the principal investigator. Laboratories may alter information on each lab page including picture, publications, affiliation, and biography. You will find the top 20 AIDS and HIV research laboratories.
University of North Carolina at Charlotte; North Carolina; USA
University of North Carolina at Charlotte
Public research university in Charlotte, North Carolina.
Biobank Graz is a non-profit central Medical University of Graz (MUG) service facility that provides the logistics and infrastructure to optimally support MUG research teams in the collection, processing and storage of biological samples and their associated data. In the course of this, special attention is given to sample and data quality and to the protection of the individual rights of patients. Samples from selected patients at the Graz LKH-University Clinical Centre, who have signed an informed consent declaration, are deposited in Biobank Graz. This means that excess tissue and blood samples are collected and placed in storage. The samples are harvested in the course of routine interventions undertaken by the different departments and institutes of the Graz LKH-University Clinical Centre and approved for use in research projects only after the completion of all necessary laboratory and histopathological analyses. No additional material is removed: in other words, there are no associated drawbacks whatsoever for the patients involved. Biobank Graz operates a quality management system according to ISO 9001:2008 and offers the following services for the processing and storage of biological samples and the handling of data: * Consistently high sample quality through the processing of samples using standardized methods in accordance with written working instructions (SOPs) * Efficient use of resources through the building of shared infrastructure and the development of optimized processes * A high degree of reliability provided by the storage of samples in 24/7 - monitored storage systems. * Processing and storage of all data in accordance with data protection legislation. Biobank Graz comprises both population-based and disease-focused collections of biological materials. It currently contains approx. 3.8 mio samples from approx. 1.2 mio patients representing a nonselected patient group characteristic of central Europe. Because the Institute of Pathology was, until 2003, the exclusive pathology service provider for major parts of the province of Styria, including its capital Graz (population approx. 1.2 mio people), samples from all human diseases, treated by surgery or diagnosed by biopsy, are included in the collection at their natural frequency of occurrence and thus represent cancers and non-cancerous diseases from all organs, and from all age groups. The scientific value of the existing tissue collection is, thus, not only determined by its size and technical homogeneity (all samples have been processed in a single institute under constant conditions for more than 20 years), but also by its population-based character. These features provide ideal opportunities for epidemiological studies and allow the validation of biomarkers for the identification of specific diseases and determination of their response to treatment. Prospectively collected tissues, blood samples and clinical data comprise, on the one hand, randomly selected samples from all diseases and patient groups to provide sufficient numbers of samples for the evaluation of the disease-specificity of any gene or biomarker. On the other hand, Biobank Graz adopts a disease-focused approach for selected diseases (such as breast, colon and liver cancers as well as some metabolic diseases) through the collection of a range of different human biological samples of highest quality and detailed clinical follow-up data. Graz Medical University established the Biobank to provide improved and sustainable access to biological samples and related (clinical) data both for its own academic research and for external research projects of academic and industrial partners. It is a major interest of the university to initiate co-operative research projects. Biological samples and data are available to external institutions performing high-quality research projects which comply with the Biobank''s ethical and legal framework according to the access rules (Contact: COO Karine Sargsyan, MD, PhD).
Kickstarter is the world''s largest funding platform for creative projects. Every week, tens of thousands of amazing people pledge millions of dollars to projects from the worlds of music, film, art, technology, design, food, publishing and other creative fields. A new form of commerce and patronage. This is not about investment or lending. Project creators keep 100% ownership and control over their work. Instead, they offer products and experiences that are unique to each project. All or nothing funding. On Kickstarter, a project must reach its funding goal before time runs out or no money changes hands. Why? It protects everyone involved. Creators aren''t expected to develop their project without necessary funds, and it allows anyone to test concepts without risk. Each and every project is the independent creation of someone like you. Projects are big and small, serious and whimsical, traditional and experimental. They''re inspiring, entertaining and unbelievably diverse. We hope you agree... Welcome to Kickstarter!
Statistical Ranking of ANotated Genomic Experimental Results
StRAnGER (Statistical Ranking of ANotated Genomic Experimental Results) is a web application for the automated statistical analysis of annotated gene profiling experiments, exploiting controlled biological vocabularies, like the Gene Ontology or the KEGG pathways terms. Starting from annotated lists of differentially expressed genes StRAnGER repartitions and reorders the initial distribution of terms to define a new distribution of elements where each element pools terms holding the same enrichment score. The elements are then prioritized according to StRAnGER' '''s algorithm and, by applying bootstrapping techniques, a corrected measure of the statistical significance of these elements is derived, enabling the selection of terms mapped to these elements, unambiguously associated with respective significant gene sets. Besides their high statistical score, another selection criterion for the terms is the number of their members, something that incurs a biological prioritization in line with a Systems Biology context. Platform: Online tool
The DNA Bank accepts the clinical samples from projects that have been approved by the Committee on Human Research (CHR). Genomic DNA isolation is performed utilizing standardized and quality controlled Gentra Systems'' PureGene DNA isolation system or Qiagen Kits. The quantity and quality of the genomic DNA isolate is determined by 260/280 UV spectrophotometery. Following isolation and quality assessment, DNA can be aliquoted into a normalized concentration. The preparation of aliquots serves to allow ready distribution of DNA samples to both the client laboratory and their collaborators and to preclude excessive routine freezing and thawing of the primary DNA isolate, a practice which is well known to result in notable degradation of genomic DNA stocks. All samples are stored in alarmed Revco ultra-low freezers at -80����?����?����?��������C. All of the ultra-low freezer units utilized by the DNA Bank are monitored by a temperature sensitive alarm system that provides 24 hour oversight. In the event of a power outage, all freezers are on an emergency back-up electrical generator.
BSRD - Bacterial Small Regulatory RNA Database
A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets.
R package for differential expression analysis of RNA-seq data.
Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.
Provia Laboratories Inc. offers Store-A-Tooth, the industry-leading dental stem cell banking service for preserving the stem cells found in baby teeth and wisdom teeth. Store-A-Tooth is a service that provides you the opportunity to store the stem cells inside of teeth that come out. Eligible teeth include baby teeth, wisdom teeth, and other healthy teeth that need to be surgically extracted during the normal course of dental care. Store-A-Tooth has been available since 2006 from dentists across the U.S. At the core of our tooth transport device is the Save-A-Tooth device, which is FDA-approved and ADA accepted for the preservation of avulsed teeth. We use Save-A-Tooth for tooth collection and transport to ensure optimal viability of your sample for processing and cryopreservation. Our laboratory is FDA-registered, CLIA-certified, and AABB-accredited.
Interactive graphical browser for biological networks and molecular interaction data. The N-Browse server at NYU currently provides access to a variety of large-scale functional genomic datasets from several species.
Webvision - The Organization of the Retina and Visual System
Webvision - The Organization of the Retina Visual System
Online textbook that has evolved into an interactive, dynamic blog that covers all things related to the bioscience of the visual system. It summarizes recent advances in knowledge and understanding of the visual system through dedicated chapters and evolving discussion to serve as a clearing house for all things related to retina and vision science.
UC San Diego Moores Cancer Center Biorepository
University of California San Diego Moores Cancer Center Biorepository
The Biorepository contains plasma, serum, RNA stabilized buffy coat, urine, viable tumor samples, and formalin-fixed paraffin-embedded tumor; all with associated clinical information. These can be provided to investigators with Cancer Sample Banking Committee approval (IRB approval is also required for projects requesting ongoing sample collection or clinical annotation.) Urine and blood-derived specimens are available from a wide variety of cancer cases and cancer-free controls. Tumor sample availability is more limited and predominately from breast and gastrointestinal malignancies. Samples are collected from consented subjects and de-identified clinical information on the subjects is collected over time. Subjects are consented for research germ line genotyping. Access to the clinical annotation is determined based on need as justified in each investigator''s request or protocol. Anonymized samples from the biorepository are available compliant with UCSD HRPP exempt category 4.
HHMI Center for integrated teams of lab scientists and tool builders to share methods, results, and tools with the scientific community. Janelia Research campus is a research campus of the Howard Hughes Medical Institute located in Ashburn, Virginia.
South Texas Accelerated Research Therapeutics Tumor Bank
Biospecimen repository for tumor specimens, available to all researchers actively engaged in cancer research whether they are in University, Academic, or Pharmaceutical industry, with a goal to accelerate the discovery and development of new agents for the treatment and cure of cancer. The START tumor bank was created to make tumor tissue gifted by patients receiving care or treatment at The START Center available to all researchers involved in developing a better understanding of the biology of cancer or those engaged in the discovery of new therapies. The START Tumor Bank is a department within the PK Department and handles skin and tumor biopsies required by clinical trial protocols. A member of the PK Department is present during biopsy procedures for immediate processing of the sample for the trial. Additionally, the Tumor Bank collects and banks the tumor tissues of patients who consent. This tissue is then stored for future use by researchers developing new therapies.
Biomedical technology research center that develops new algorithms, visualizations and conceptual frameworks to study biological networks at multiple levels and scales, from protein-protein and genetic interactions to cell-cell communication and vast social networks. They are developing freely available, open-source suite of software technology that broadly enables network-based visualization, analysis, and biomedical discovery for NIH-funded researchers. This software is enabling researchers to assemble large-scale biological data into models of networks and pathways and to use these networks to better understand how biological systems operate under normal conditions and how they fail in disease. The National Resource for Network Biology is organized around the following key components: Technology Research and Development, Driving Biomedical Projects, Outreach, Training and Dissemination of Tools. The NRNB supports several types of training events, including both virtual and live workshops; tutorials sessions for clinicians, biologists and bioinformaticians; presentations and demonstrations at conferences; online tutorials and webcasts; and annual symposium.
The Broadband Forum is the central organization driving broadband wireline solutions and empowering converged packet networks worldwide to better meet the needs of vendors, service providers and their customers. They develop multi-service broadband packet networking specifications addressing interoperability, architecture and management. Their work enables home, business and converged broadband services, encompassing customer, access and backbone networks. Keywords: Vendor, Service, Broadband, Wireline, Forum, Network,
SFARI - Simons Foundation Autism Research Initiative
Simons Foundation Autism Research Initiative
Launched in 2005, the Simons Foundation Autism Research Initiative (SFARI) is a research campaign within the Simons Foundation''s overall suite of programs. SFARI''s mission is to improve the diagnosis and treatment of autism spectrum disorders by funding, catalyzing and driving innovative research of the greatest quality and relevance. Although SFARI''s priority is to benefit individuals challenged by these disorders, its efforts are certain to yield insights into the neural mechanisms of fundamental human capabilities, thereby promoting the broader mission of the Simons Foundation to advance the frontiers of research in the basic sciences and mathematics. Autism spectrum disorders are a set of complex developmental disorders characterized by persistent deficits in social communication and interaction, as well as restricted behaviors, interests or activities. The Centers for Disease Control and Prevention estimates that roughly 1 in 110 children in the U.S. have autism, with many more boys affected than girls. These disorders cost the U.S. economy an estimated $35 billion dollars each year in direct care costs and lost productivity, and extract an incalculable human toll.
TFSEARCH: Searching Transcription Factor Binding Sites
TFSEARCH: DNA Transcription Factor Binding Site Prediction
The TFSEARCH searches highly correlated sequence fragments against TFMATRIX transcription factor binding site profile database in the "TRANSFAC" databases developed at GBF-Braunschweig, Germany. The TFSEARCH program was written by Yutaka Akiyama (Kyoto University, currently at RWCP) in 1995.
The GO Consortium coordinates an effort to maximize and optimize the GO annotation of a large and representative set of key genomes, known as ''reference genomes''. The goal of the Reference Genome Annotation project is to completely annotate twelve reference genomes so that those annotations may be used to effectively seed the automatic annotation efforts of other genomes. With more and more genomes being sequenced, we are in the middle of an explosion of genomic information. The limited resources to manually annotate the growing number of sequenced genomes imply that automatic annotation will be the method of choice for many groups. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO''s logical structure and biological content. All GO annotations from this project are included in the gene association files that each group submits to GO. Annotations can also be viewed using the GO search engine and browser AmiGO. Annotated families can be viewed with the homolog set browser.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 22, 2022. Data set collected at the Children''s Hospital Boston, of EEG recordings from pediatric subjects with intractable seizures. Subjects were monitored for up to several days following withdrawal of anti-seizure medication in order to characterize their seizures and assess their candidacy for surgical intervention. All signals were sampled at 256 samples per second with 16-bit resolution. Most files contain 23 EEG signals (24 or 26 in a few cases).
Donor Alliance is one of 58 not-for-profit organ recovery organizations federally designated by the U.S. Department of Health & Human Services to facilitate the donation and recovery of organs for people needing transplants. Additionally, Donor Alliance is a recognized leader in facilitating the donation and recovery of transplantable tissues in Colorado and most of Wyoming. Our goal is to save the lives of people in need. To achieve this, Donor Alliance employs effective family approach and recovery programs in more than 100 hospitals in Colorado and Wyoming. Additionally, Donor Alliance dedicates time, funding and effort toward increasing the number of registered organ and tissue donors through active public awareness and educational programs and grassroots public relations campaigns.
Every week, John Horgan takes a puckish, provocative look at breaking science. A former staff writer at Scientific American, he is the author of four books, the most recent of which is The End of War (to be published by McSweeney''s Books January 17, 2012). He currently directs the Center for Science Writings at Stevens Institute of Technology. He lives in New York State''s Hudson Highlands, where he plays ice hockey each winter to hone his cross-checking skills.
Artemis: Genome Browser and Annotation Tool
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.
A peak-calling software program for DNAseI-seq data.
Medpedia is an open platform connecting people and information to advance medicine. This wiki is the collaborative encyclopedia and resource for information about health, medicine and the body. Only physicians and Ph.D.s are allowed to edit the Articles on Medpedia after they create an account and are approved as an Editor. Non-Editors can create an account and then suggest changes that must be approved by an Editor before going live on the site. To suggest changes, click the link Suggest Changes at the top of Article Pages. Intended Uses and Benefits: * Reference source for both medical professionals and the lay-public covering information about health, medicine and the body * Forum for individuals and groups to be recognized for their areas of expertise * Clearinghouse of bio-medical journal articles, data, research, and educational materials * Forum for debating emerging issues * Platform for advancing medical knowledge Medpedia Portals - Adult Primary Care, Allergy and Immunology, Anatomy, Cardiology, Emergency Medicine, Endocrinology, Epidemiology, Gastroenterology and Hepatology, General Medicine, Infectious Diseases, Internal Medicine, Neurology & Neurobiology, Nutrition, OB/GYN and Reproductive Health, Oncology, Orthopedics, Pathology, Pediatrics, Pharmacology, Psychiatry, Public Health, Pulmonology, Rheumatology, Women''s Health In association with Harvard Medical School, Stanford School of Medicine, Berkeley School of Public Health, University of Michigan Medical School and other leading global health organizations, Medpedia will be a commons for the gathering of the information and people critical to health care.
University of Minnesota Tissue Procurement Facility
Procure and distribute human tissue and other biological samples in support of basic, translational, and clinical cancer research at the University of Minnesota. The TPF is a centralized resource with standardized patient consent, sample collection, processing, storage, quality control, distribution, and electronic record maintenance. Since the 1996 inception of the TPF, over 61,000 tissue samples including well-preserved samples of malignant and benign tumors, organ-matched normal tissue, and other types of diseased tissues, have been collected from surgical specimens obtained at the University of Minnesota Medical Center-Fairview (UMMC-F) University Campus. Surgical pathologists are intellectually engaged in TPF functions, providing researchers with specimen-oriented medical consultation to facilitate research productivity. Prior to surgery, TPF personnel identify and consent patients for procurement of tissue, blood, urine, saliva, and ascites fluid. Within the integrated working environment of the surgical pathology laboratory, freshly obtained tissues not needed for diagnosis are selected and provided by pathologists to TPF personnel. Tissue samples are then assigned an independent code and processed. TPF staff can also work with researchers to individualize the procurement of tissues to fit specific research needs.
Northeast ALS Consortium Sample Repository
Repository of serum, plasma, cerebrospinal fluid (CSF), whole blood, extracted DNA, and urine samples from NEALS and Massachusetts General Hospital Neurology Clinical Trials Unit (NCTU) research studies of amyotrophic lateral sclerosis (ALS). Samples from this repository are available to researchers for the purpose of furthering the understanding of ALS or developing disease biomarkers. Applications will be accepted at any time, but the committee meets bi-monthly to review applications. The application requires a brief description and scientific justification for the use of the samples. Priority will be given to members of NEALS and investigators from sites that participated in the collection of samples. Investigators must provide IRB approval from their institution. Applications may be submitted to: mghneuroclinicaltrialsunit (at) partners.org (please cc: tlincoln (at) partners.org) NEALS collects an administrative fee of $1,000 at the time of application submission to offset processing costs. If an application for samples is denied, 80% of the administrative fee will be returned. The administrative fee is waived for NEALS members. Checks may be made payable to: The Northeast ALS Consortium.
A non-profit, community resource that works with volunteer donors to provide the highest quality blood and tissue components to patients. They collect and test more than 200,000 components of life-saving blood and tissue each year from volunteers all over South Texas. Because patients are in constant need of blood, blood components, and/or tissue, donors are essential. By using cutting-edge technology, the team of dedicated professionals have helped save hundreds of thousands of lives over more than 35 years. They are a member of the American Association of Blood Banks (AABB); American Association of Tissue Banks (AATB) and America''s Blood Centers (ABC). We are also one of the first blood centers in the country to be registered by the International Standards Organization.
New Life Generation is a not-for-profit tissue agency headquartered in Indianapolis, Indiana. We recognize our responsibility to recover, process, store and distribute human tissues in a professional manner that is of service to the medical community, ensures safety of transplantable tissue, and increases the availability of quality allograft tissue. While our primary focus is tissue donation, we recognize that donation also includes organ, bone marrow, blood, and blood products.
Transplant Services Center is a clinical and academic service center of UT Southwestern Medical Center which completes the Circle of Care from donation to transplantation by providing a full service tissue bank which procures, processes, stores and distributes tissue allografts. These transplantable tissues include corneas, sclera, skin, musculoskeletal and cardiovascular allografts, which restore function, improve the quality of life and in some cases even save lives. Transplant Services Center provides services to hospitals and physicians throughout Texas, the nation and on occasion worldwide. The mission of the Transplant Services Center is to * provide quality tissue grafts for transplantation, teaching, research and medical need that is responsive and appropriate to both the recipient need and the donor family; * to promote public and professional education to increase donor awareness; * and to contribute to advancements in transplantation technology.
University of Pennsylvania; Philadelphia; USA
University of Pennsylvania is private Ivy League research university located in University City neighborhood of Philadelphia, Pennsylvania. Established in 1740, UPenn has 4 undergraduate schools and 12 graduate schools.
Nevada Donor Network (NDN) is a federally designated, not-for-profit organ, tissue, and eye procurement organization. NDN is responsible for the coordination, recovery, and distribution of donated human organs and tissues for transplantation and medical research throughout the Las Vegas area. In addition, NDN participates in national organ and tissue sharing in an effort to meet the ever-growing needs of patients awaiting transplantation therapy. NDN is one of the few organ procurement agencies in the country to manage the recovery of organs, tissues, and eyes in the same facility, making Nevada progressive in the field of organ and tissue procurement. NDN is certified by the Department of Health and Human Services and the Center for Medicare and Medicaid Services (CMS). The Network is accredited by the Eye Bank Association of America (EBAA), the American Society for Histocompatibility and Immunogenetics (ASHI), the Clinical Laboratory Improvement Act (CLIA), and the American Association of Tissue Banks (AATB).
Atlas of high resolution Nissl stained digital images of the brain of the zebra finch, the mainstay of songbird research. The cytoarchitectural high resolution photographs and atlas presented here aim at facilitating electrode placement, connectional studies, and cytoarchitectonic analysis. This initial atlas is not in stereotaxic coordinate space. It is intended to complement the stereotaxic atlases of Akutegawa and Konishi, and that of Nixdorf and Bischof. (Akutagawa E. and Konishi M., stereotaxic atalas of the brain of zebra finch, unpublished. and Nixdorf-Bergweiler B. E. and Bischof H. J., A Stereotaxic Atlas of the Brain Of the Zebra Finch, Taeniopygia Guttata, http://www.ncbi.nlm.nih.gov.) The zebra finch has proven to be the most widely used model organism for the study of the neurological and behavioral development of birdsong. A unique strength of this research area is its integrative nature, encompassing field studies and ethologically grounded behavioral biology, as well as neurophysiological and molecular levels of analysis. The availability of dimensionally accurate and detailed atlases and photographs of the brain of male and female animals, as well as of the brain during development, can be expected to play an important role in this research program. Traditionally, atlases for the zebra finch brain have only been available in printed format, with the limitation of low image resolution of the cell stained sections. The advantages of a digital atlas over a traditional paper-based atlas are three-fold. * The digital atlas can be viewed at multiple resolutions. At low magnification, it provides an overview of brain sections and regions, while at higher magnification, it shows exquisite details of the cytoarchitectural structure. * It allows digital re-slicing of the brain. The original photographs of brain were taken in certain selected planes of section. However, the brains are seldom sliced in exactly the same plane in real experiments. Re-slicing provides a useful atlas in user-chosen planes, which are otherwise unavailable in the paper-based version. * It can be made available on the internet. High resolution histological datasets can be independently evaluated in light of new experimental anatomical, physiological and molecular studies.
DNA barcode data with an online workbench that supports data validation, annotation, and publication for specimen, distributional, and molecular data. The data platform consists of three main modules, a data portal, a database of barcode clusters, and data collection workbench. The Public Data Portal provides access to all public barcode data which consists of data generated using the Workbench module as well as data mined from other sources. The Barcode Index Number (BIN) system assigns a unique identifier to each sequence cluster of COI, providing an interim taxonomic system for species in the animal kingdom. The workbench module integrates secure databases with analytical tools to provide a private collaborative environment for researchers to collect, analyze, and publish barcode data and ancillary DNA sequences. This platform also provides an annotation framework that supports tagging and commenting on records and their components (i.e. taxonomy, images, and sequences), allowing for community-based validation of barcode data. By providing specialized services, it aids in the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. Public data records include record identifiers, taxonomy, specimen details, collection information and sequence data. Data that has been publicly released through BOLD can be retrieved manually through the BOLD public interface or automatically through BOLD web services. BOLD analytical tools are available for any data set that exists in BOLD (including publicly available data). Analytical tools can be accessed through the BOLD Project Console under the headings Sequences Analysis or Specimen Aggregates. Some examples include Taxon ID Tree, Alignment Viewer, Distribution Maps, and Image Library.
Scholarometer (beta) is a social tool to facilitate citation analysis and help evaluate the impact of an author''s publications. It is a social (crowdsourcing) application that leverages the wisdom of the crowds. Scholarometer makes visualization of author and discipline networks available on the web site. It requires users to tag their queries with one or more discipline names, choosing from predefined ISI subject categories or arbitrary tags. This generates annotations that go into a database, which collects statistics about the various disciplines, such as average number of citations per paper, average number of papers per authors, etc. This data is publicly available. Scholarometer users can save the finding into formats appropriate for local reference management software (e.g., EndNote), or for social publication sharing systems (e.g., BibSonomy). Currently, our system supports the following export formats: BibTex (BIB), RefMan (RIS), EndNote (ENW), comma-separated values (CSV), tab-separated values (XLS), and BibJSON. Export data is dynamically generated in response to any filter, merge or delete actions performed by the user. Since Scholarometer is a browser extension that provides a smart interface for Google Scholar, it does not have the limitations of server based citation analysis tools that sit between the user and Google Scholar. At the same time Scholarometer is not an application, such as Publish or Perish, and therefore it is platform independent and runs on every system that supports the Firefox or the Chrome browser. Still, Scholarometer uses Google Scholar, which provides the most comprehensive source of citation data across the sciences and social sciences. Scholarometer provides a RESTful web API so that other developers can make use of our crowdsourced data. Select the method on the left panel to see corresponding documentation. The extension/add-on code is available in the Mozilla Firefox Add-ons and Google Chrome Extensions repositories. Additional server-side code is not available at this time.
OECI - Tubafrost: The European Human Frozen Tissue Bank
Tubafrost - The European Human Frozen Tissue Bank
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. In this web site you will find the central European database of OECI-TuBaFrost collecting the information of biobanks or in the project support environment on human material; i.e., frozen tumor tissue specimens, pathology blocks, blood samples in different forms, cell lines, Tissue Micro Arrays, etc. Our goal is by centralizing the tumor tissues information to facilitate the search of doctors / researchers for tumor materials, which they need for their cancer research there with facilitating cancer research. OECI members only can participate in the OECI-TuBaFrost exchange platform, or those introduced by an OECI member. We are a group of pathology and research departments as well as bio-bankers in clinical based biobanking based in comprehensive cancer centers or hospitals with a competence in comprehensive cancer care across Europe. Each participating institute is involved in cancer research resulting in innovative procedures, new drugs, improved diagnosis and new insights in disease development. The overall result is better care and treatment for cancer patients. To maximize the scientific value of the human tissue samples, information about the clinical status of the patient in combination with the quality and type of samples is very important. A TuBaFrost electronic database will securely store all this information. Within the closed project supporting environments, the data collected will include: * Diagnosis - identification of the type of cancer * Type of tissue collected - the origin, i.e. breast, skin, colorectal * Quality of tissue collected - collection and storage details The tissue is stored in the hospital where the donor was diagnosed/treated. It stays there until it is used or sent to another hospital or research center within the TuBaFrost group. The electronic database will track samples throughout the network. The tissue is not sold. The exchange of tissue to other hospitals is regulated by a contract, which uses the national regulations of the country supplying the tissue. Tissue samples within the TuBaFrost collection will only be used for research, which has been approved by ethics committees. This ensures that the tissue is only used for the best quality research and only for the specific reasons given to the ethics committee.
Cincinnati Children's Hospital Medical Center Discover Together Biobank
Provides access to services for standardized and centralized acquisition, processing, storage and distribution of biospecimens for research. Services include biospecimen storage, serum and plasma processing, preparation of kits for sample collection and shipping, automated DNA/RNA extraction from blood, saliva, tissue and other materials, biofluid collection, processing and storage, tissue collection, processing and storage.Home to Better Outcomes for Children (BofC) biorepository.
Oregon Health and Science University Biolibrary
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.A Joint Project between Oregon Clinical and Translational Research Institute (OCTRI) and the Knight Cancer Institute, the OHSU Biolibrary provides information on campus collections of biospecimens originating from OHSU patients. The Biolibrary Search Engine is a user-friendly, online search tool that allows OHSU researchers to search for suitable biospecimen samples. As of October 2010, the Biolibrary Search Engine contains data on over 500,000 biospecimens. The Search Engine accesses data from the OHSU Cancer Registry, the Department of Pathology, and the OCTRI Research Data Warehouse. You must be connected to the OHSU network to access the Search Engine. The Search Engine is accessible on Internet Explorer through WTS connection to the OHSU network.
Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts
Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).
The OBO Relation Ontology is an ontology of core relations for use by OBO Foundry ontologies. To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena. The OBO Relation ontology is undergoing substantial changes: * Core domain-independent relations will live in BFO * Biology specific relations (defined in terms of core relations) will live in RO
Commercial antibody vendor which supplies antibodies and other products to life science researchers.
The primary blood supplier for Ochsner Medical Center, Ochsner Health Center - Kenner, Ochsner Health Center - West Bank, Ochsner Baptist Health Center, Ochsner St. Anne General Hospital and Lady of the Sea General Hospital in Cut Off. In addition, Ochsner Blood Bank participates in blood-resource sharing with other local community hospitals. Ochsner Blood Bank''s mission is to provide an adequate and safe blood supply for the hospitals and communities Ochsner serves. More than 45,000 blood components were transfused just last year. There''s also supporting information that indicates there will be a significant increase in transfusions for the current year. Blood replacement removes some of the costs of blood, but more importantly it provides patients with a safe and adequate blood supply. It''s likewise insurance that blood will be readily available should the need arise. If you happen to need blood during a hospital stay, please consider asking your family and friends to replace the blood that was transfused. Ochsner offers a blood replacement plan that takes care of everything. It even provides coverage for your family members, or other designated individuals, to receive the replacement units for up to one year should they need them.
Wikikidney.org is an effort to prevent kidney diseases and achieve better outcomes in those who have end stage renal disease. Our mission is to use this medium to make the public more aware of kidney disease in a sincere effort to prevent it when we can, and to help our colleagues achieve good outcomes in those who already have end stage renal disease. Our role is to provide as much information as possible to patients, professionals and the general public, with the hopes that this education will be a motivating factor in making the necessary changes to prevent or stall chronic kidney disease. After nearly two decades of seeing patients with end stage renal disease, it is apparent that much of what we deal with can be delayed or prevented altogether. Several medical trials and innovations in the last several years have confirmed these observations, and form the basis of this website. A major element in preventing renal illness is simply early detection, and for this one needs education. As the Internet expands and becomes more and more a tool of everyday life, we will have the ability to access and distribute information like no other generation before us. Qualified readers are encouraged to contribute to existing articles and to create articles of their own. Contents * 1 Kidney Resources - NIC * 2 Especially for Patients * 3 General Kidney Resources * 4 Issues in Nephrology * 5 Clinical Wiki Projects * 6 Be an author, editor or reviewer on wikikidney * 7 Clinical Trials * 8 Newsdesk Top Stories * 9 Essential Physician Resources * 10 Organizations * 11 Government Agencies * 12 Vendor and other Sites * 13 Patents * 14 Index
Brown University Rhode Island Biobank Core Facility
Brown University Rhode Island Biobank Cryogenic Core Facility
Cryogenic facility for human tissue and fluid samples under management of Brown University Division of Biology and Medicine and supports biomedical research on Brown campus and across affiliated hospitals of Warren Alpert Medical School.
KLI Theory Lab: A powerful scientific database
The primary aim of the KLI Theory Lab is to highlight interconnections between topics of problems of research on evolution and cognition that look theoretically or methodologically promising. Quite often such correlations remain unrecognized because of the disciplinary closure that characterizes the organization of the scientific enterprise. * Introductory Resources: Introductory texts to various relevant disciplines, provided by the Konrad Lorenz Institute include: ** Introduction to Artificial Intelligence ** Introduction to Artificial Life ** Introduction to Cognitive Science ** Introduction to Cultural Evolution ** Introduction to Developmental Biology ** Introduction to Epistemology & Philosophy of Science ** Introduction to Ethology & Sociobiology ** Introduction to Evolutionary Biology ** Introduction to Evolutionary Epistemology ** Introduction to Genetic Epistemology ** Introduction to History and Social Sciences ** Introduction to Normative Issues ** Introduction to Philosophy of Biology ** Introduction to Philosophy of Mind ** Introduction to Theoretical Biology * Reference Database: The KLI Theory Lab contains a vast collection of research papers that have been selected based on their significance and quality. ** Search references: The search page allows you to search for references and to narrow down your search based on keywords. Results are ordered by relevance. ** Browse references: All references in the database, ordered by date of publication.
Multiple Myeloma Research Constortium Tissue Bank
Until recently, a scarcity of high-quality myeloma tissue has posed one of the greatest challenges in advancing myeloma research and drug development. Now, with the successful establishment of the MMRC Tissue Bank, researchers for the first time have access to the critical mass of high-quality tissue needed to rapidly validate novel and combination therapies for myeloma. The MMRC Tissue Bank is the only resource of its kind that integrates myeloma tissue samples with corresponding genomic and clinical data. To date, the MMRC Tissue Bank has accrued more than 2,700 samples with matching peripheral blood samples, with ongoing collection of tissue samples at Member Institutions nationwide. To further accelerate accrual, the MMRC has also launched a direct-to-patient program to enable myeloma patients to donate their tissue to the MMRC Tissue Bank. Notably, all tissue accrued into the MMRC Tissue Bank is uniformly collected and stored in adherence with Good Laboratory Practices (GLP) standards and under the governance of more than 50 standard operating procedures. The MMRC has also established a quality assurance unit that performs weekly internal quality assurance reviews and issues quarterly quality assurance reports. In addition, the MMRC Tissue Bank has been audited twice by external organizations since its inception last year. With these stringent practices in place, the MMRC has ensured that all tissue samples in the MMRC Tissue Bank are of the very highest-quality and, as such, has quickly become the premier resource for industry seeking fresh tissue samples to initiate strong validation work.
Open-source software for network visualization and analysis helping data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluterize, manipulate and export all types of networks. Gephi runs on Windows, Linux and Mac OS X. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps. It is open-source and free (GNU General Public License). Applications: * Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time. * Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks. * Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks. * Biological Network analysis: representing patterns of biological data. * Poster creation: scientific work promotion with hi-quality printable maps. Gephi 0.7 architecture is modular and therefore allows developers to add and extend functionalities with ease. New features like Metrics, Layout, Filters, Data sources and more can be easily packaged in plugins and shared. The built-in Plugins Center automatically gets the list of plugins available from the Gephi Plugin portal and takes care of all software updates. Download, comment, and rate plugins provided by community members and third-party companies, or post your own contributions!
Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Our robust searchable Tissue Bank database at US Biomax contains normal, non-cancerous disease and cancer samples, just a fraction of total paraffin tissue bank. Use advanced search function to define your search. Some of them have H&E images. Our tissue repository, tissue bank has huge paraffin tissue blocks, a large selection of histology tissue section slides of human cancer, normal tissue, rhesus and cynomolgus normal fresh frozen tissue as well as paraffin blocks and slides. It has also normal human organs in paraffin embedded tissue blocks as well as rhesus and cynomolgus monkey normal organ tissues. Snap frozen (fresh frozen) tissue of rhesus/cynomolgus monkey are also available. We also provide tissue array, custom tissue microarray (with samples you provided or from our tissue bank) as well as OEM services. Other products/services available include tissue microarray, paraffin tissue sections, histology services and quantitative telomerase detection kit.
St. Louis University Department of Neurology and Psychiatry
SLU Department of Neurology & Psychiatry
St. Louis University Department of Neurology & Psychiatry
St. Louis University Department of Neurology Psychiatry
The Department of Neurology & Psychiatry aims to 1) provide the best psychiatric and neurological care to patients and their families, 2) discover and investigate new treatments for psychiatric and nervous system disorders, 3) study psychosocial processes in psychiatric and neurological illness, and 4) educate the next generation of practitioners, as well as our patients and the lay community. The Department of Neurology & Psychiatry (DNP) was established on June 1, 2007. The Department has 34 faculty members and is planning continued expansion. There are 7 psychiatrists, 18 neurologists, 4 child neurologists, and 5 NIH-supported PhD investigators. The DNP is one of five departments in the country that combines the disciplines of neurology and psychiatry. We are unique in having two strong residency programs and are the only that attempts to establish a new paradigm in care of patients with neurological and psychiatric disease through co-management initiatives. * Division of Psychiatry: The Psychiatrists work within four areas: Adult, Geriatric, Community, and Forensic Psychiatry. * Division of Neurology: The division has an extremely active stroke/intensive care and general neurology service. We are expanding services in neurocritical care and interventional neurology. * Education: The DNP has approximately 25 residents/fellows in each discipline. * Research: The DNP has robust programs in clinical, basic, and translational research. We emphasize 3 areas in this overview of the DNP. ** Clinical Research Unit ** Psychosocial Processes Group ** Translational Neuromuscular Disease VISION STATEMENT All members of the Saint Louis University Department of Neurology & Psychiatry will collaborate to support state-of-the-art neurological and psychiatric education, compassionate patient care, and a growing research enterprise. The Department will develop the most exciting intellectual environment in the Nation for investigation, treatment, and training in psychiatry and neurology. We will fulfill this Vision in an environment of mutual respect and collaboration.
LifeShare Transplant Donor Services of Oklahoma
LifeShare Transplant Donor Services of Oklahoma strives to recover healthy, transplantable organs and tissues through careful screening and management of donors to provide the maximum number of lifesaving/life-enhancing organs and tissues for patients awaiting transplantation in Oklahoma. It is committed to providing a better quality of life for those people who require organ or tissue transplantation, while respecting and honoring those families who share the gift of life. LifeShare emphasizes a person''s decision to be an organ and tissue donor and whenever possible will honor the decision of the individual to donate. It works hard to provide education to the state of Oklahoma about organ, eye and tissue donation. Education is provided to medical professionals who identify and care for potential organ and tissue donors, and recognize donation as continuing to care for the patient and their family. LifeShare strongly supports research and development to improve the quality and availability of organs and tissues for transplantation and the success of human transplantation in general. It is also committed to providing support and comfort to grieving families who have suffered great loss.
The taxonomy database of the International Sequence Database Collaboration contains the names of all organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The database is available via the EBI SRS server of ftp.
The Alzheimer Society of Ireland is the leading dementia specific service provider in Ireland. The Society is a company limited by guarantee and a registered charity - CHY 7868. The Society was founded in 1982 by a small group of people who were caring for a family member with Alzheimer''s Disease or a related dementia. Today, it is a national voluntary organization with an extensive national network of branches, regional offices and services that aims to provide people with all forms of dementia, their families and carers with the necessary support to maximize their quality of life. As the major dementia-specific service provider in Ireland, The Society''s network includes over 100 dementia specific services such as day care centers, home care services, carer support groups, social clubs, a national respite center and an advocacy service. The Society also operates the Alzheimer National Helpline Service offering information and support to anyone affected by Alzheimer''s disease / dementia at 1800 341 341. For a full list of services in your area please see the We Can Help section. The Society comprises over 2,500 members, 300 volunteers and over 700 full and part-time staff. The Society has 6 regional offices and a network of Branches around the country. A number of core functions are operated through our national office including information, policy and research, fundraising, public relations, training and finance.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 21, 2013. Laboratory portal of Ray Truant, PhD. It provides an image gallery and videos.
At BioStorage Technologies, our mission is to provide our clients with world class, biorepository services, exceeding clients����?? expectations of service, value and quality while setting the industry standard for the storage, management & logistics of samples. Offering onsite or outsourced management of sample assets, BioStorage Technologies manages the complete life-cycle of samples. With a team of global sample experts, state-of-the-art temperature-controlled storage facilities, and a real-time web-based sample intelligence and tracking system, the company supports customers in maximizing opportunities, minimizing risk and reducing the cost of sample management. The unique advantages of BioStorage Technologies * Consulting����??Expert consulting on Good Storage Practices, global transport standards, standard operating procedures and business continuity planning to mitigate risk and optimize your resources * Consolidation����??Comprehensive management of the sample lifecycle through consolidation of sample data into one technology system for faster retrieval, more flexible tracking and enhanced security * Control����??Enhanced control of sample asset data within one technology system, ISISS, for faster go/no-go decisions and expansion into future research * Compliance����??Improved chain of custody of your samples and easier audit trail tracking for adherence to quality and regulatory compliance standards in order to support product approvals * Cost-Reduction����??Reduced cost of sample management and increased project ROI through more efficient sample and data management processes, enabling you to refocus resources on your core competencies BioStorage Technologies, Inc. was founded in 2002 and is privately held and headquartered in North America in Indianapolis, Indiana with an additional full-service site in Europe near Frankfurt, Germany.
Alzheimer''s Disease International (ADI) believes that the key to winning the fight against dementia lies in a unique combination of Global Solutions and local knowledge. As such, it works locally, by empowering Alzheimer associations to promote and offer care and support for people with dementia and their carers, while working globally to focus attention on dementia. Our board is composed of people from around the world, and our staff team is based in London. ADI is the international federation of Alzheimer associations around the world, in official relations with the World Health Organization. Each member is the Alzheimer association in their country who support people with dementia and their families. ADI''s vision is an improved quality of life for people with dementia and their families throughout the world. ADI runs the Alzheimer University, a series of practical workshops aimed at helping the staff and volunteers of Alzheimer associations build and strengthen their organisations. ADI holds an annual international conference which is the longest running international conference on dementia. The conference is a unique multi-disciplinary event which unites people with an interest in dementia from around the world. World Alzheimer''s Day, celebrated on September 21 each year, is an opportunity to raise global awareness about dementia and its impact on families and the important work of our members throughout the world. Medical research is also important, and some of ADI''s member Alzheimer associations actively support research in their own countries. More information about research can be found on the web sites of Alzheimer''s Association (USA), Alzheimer''s Society (UK), Alzheimer Society of Canada, or the association in your country. For the fourth year, the Fondation M��d��ric Alzheimer and ADI are running Alzheimer''s Awards for evidence-based psychosocial interventions for people with dementia and their carers.
Duke Translational Research Institute Biobanking
The Duke Biobank is an institutional resource that combines well-annotated clinical data with a standardized, regulation compliant, cost efficient repository for both fluid and tissue, connected via information systems to a large scale, long-term biobank in Kannapolis, in order to foster breakthroughs in research; while ensuring the strictest adherence to ethical standards and regulations. Our goal is to work with investigators to maintain biorepository collections which are in compliance with all relevant local, regional and national and IRB biobanking standards. Capabilities * Provide expert consultation in planning and design of biobanking programs * Access, process, aliquot, store and distribute a wide array of liquid and tissue biological samples * Maintain informatics capabilities to accurately and efficiently track samples and link to clinical and laboratory assay data * Use the Duke Biobanking Guidelines document (in development) as guidance on scientific, ethical/legal, and operational to ensure quality and standardization of biospecimen collection * Minimize redundancy of infrastructure, as appropriate, across Duke Medicine. Duke University offers both on- and off-campus options for investigators seeking biobanking services. Our biobanking facilities are: * The Center for Human Genetics (CHG). Serves as the primary on-campus biobank for liquid sample storage for Duke Medicine, and as a portal between Duke and the LabCorp Biobank. * Duke Hospital South Tissue Bank. Serves as a sample portal for the Duke Biobank, and as the primary facility for tissue storage for Duke Medicine. ** DCCC Tissue & Blood Procurement ** IGSP Biospecimen Repository * LabCorp Biorepository. Located in Kannapolis, NC, this is the preferred storage center for large-scale, infrequently accessed sample collections
University of Alabama at Birmingham Alzheimer's Disease Center
The UAB Alzheimer's Disease Center provides comprehensive treatment for Alzheimer's patients while also promoting research for the prevention and cure of Alzheimer's disease and related disorders. The ADC is an interdisciplinary program of scientists working in areas including neurology, psychiatry, genetics, and psychology. The Center provides comprehensive treatment and promotes research for the prevention and/or cure of Alzheimer's disease and other related disorders with memory loss and impaired cognition. A major emphasis of research is the maintenance of a clinical research database comprised of neurological, medical, and neuropsychological test data from participants seen in the ADRC Clinical study since 1999, many of whom have been followed for several years in the study.
The Duke Institute for Genome Sciences & Policy (IGSP), in partnership with the Duke University School of Medicine Research Foundation and Department of Pathology (SOMRF), has established the Duke IGSP Biospecimen Repository as a centralized and accessible biological resource for Duke Investigators and research programs. The Repository is a standardized, regulatory-compliant and privacy protected repository for fluid and tissue biospecimens, and enables Duke investigators to reduce costs, and eliminate redundancies and significant risks associated with alternative biobanking practices, while facilitating integration of clinical trials and translational research programs with molecular profiling technologies. In order to ensure sample and data integrity and comparability, the Biorepository is developing, evaluating, and implementing evidence-based biobanking ''best practices''. Centralization of activities to a dedicated and expert staff and facility allows small and large research programs to reduce costs through elimination of redundancies and achieving efficiencies and economies of scale. The Duke-IGSP Biorepository is committed to ensuring appropriate consent, approved use, and protection of privacy through compliance with HIPAA regulations and IRB guidelines. The Duke-IGSP Biospecimen Repository will facilitate the integration of clinical research programs with molecular profiling technologies, enabling large-scale ''omic'' research programs that will inform and drive the development of new generations of targeted diagnostics, therapies, and preventions, which in turn will transform clinical outcomes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documentedt on January 10, 2023. Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Favorite and most desired neuroscience books, and books in fields related to neuroscience, listed by Neuroscience News staff members. You may search for books or browse by category. If you don''t see your favorite neuroscience books, or related science books for sale on the site, they want you to let them know which neuroscience books they should include.
qvality - Nonparametric estimation of posterior error probabilities
qvality estimates q-values and posterior error probabilities directly from score distributions. The method can be accessed via a web interface or downloaded as stand-alone software (C++ source code and binaries are available under MIT license). The qvality web server allows you to use qvality to compute posterior error probability and q-values for your data. There are two input modes: *Input the empirical score distribution and a corresponding null score distribution. The two inputs do not have to contain the same numbers of scores. *Input only the empirical p-value distribution. In this case, you must use p-values rather than raw scores. In either mode, the output is the same: a three-column file in which the first column contains sorted observed scores, the second column contains estimated q-values, and the third column contains estimated posterior error probabilities. Qvality is a C++ program for estimating two types of standard statistical confidence measures: the q-value, which is an analog of the p-value that incorporates multiple testing correction, and the posterior error probability (PEP, also known as the local false discovery rate), which corresponds to the probability that a given observation is drawn from the null distribution. In computing q-values, qvality employs a standard bootstrap procedure to estimate the prior probability of a score being from the null distribution; for PEP estimation, qvality relies upon non-parametric logistic regression. Relative to other tools for estimating statistical confidence measures, qvality is unique in its ability to estimate both types of scores directly from a null distribution, without requiring the user to calculate p-values.
As of 12th March 2009, GeneDB provides access to the transcriptome of the Tsetse fly Glossina morsitans morsitans, the biological vector of African trypanosomiases. The current data set includes: >>7,015 contigs comprised of ESTs from Trypanosoma brucei infected midgut tissue (Lehane et al, Genome Biol. 2003;4(10):R63) >>7,493 contigs comprised of ESTs from salivary gland tissue >>18,404 contigs comprised of EST pooled from a range of different tissue- and developmental stage-specific libraries: head (2,700 ESTs), midgut (21,662 ESTs), reproductive organs (3, 438 ESTs), salivary gland (27,426 ESTs), larvae (2,304 ESTs), pupae (2,304 ESTs), fatbody (20,257 ESTs) (Attardo et al, Insect Molecular Biology 2006, 15(4):411-424), male and female whole bodies (19,968 ESTs). These data include the midgut and salivary gland ESTs used in the library specific clustering for the contig sets listed above. Initial automated annotations of product descriptions were manually revised by participants in two community annotation jamborees held under the auspice of the International Glossina Genome Initiative (IGGI) with funding by TDR. A Glossina morsitans morsitans genome project is currently also underway. To date, 2.4M capillary shotgun reads have been produced and the initial assembly is available to download via the ftp server and for blast analysis.
Biorepository promoting the safe handling, receipt, processing, storage, inventory control, packaging and distribution for all types of infectious and non-infectious biological specimens and reagents. The facility houses ultra-low mechanical freezers, vapor-phase liquid nitrogen freezers and mechanical walk-in freezer and cold rooms. A multi-purpose computerized security system provides around-the-clock secure access, intrusion and fire detection, and electronic monitoring of all freezers and critical building functions. In the past, KamTek managed NIH-NIAID Reference reagent Repository that stored and distributed over 2000 different reagent products including antisera against a wide variety of viruses and other infectious organisms, as well as viral antigens, allergenic, mycoplasma, and immunologic reagents. The NIAID Repository was designated World Health Organization (WHO) Collaborating Center for Antiviral Drugs and Interferon and responsible for the international distribution of the WHO Interferon reference standards. In addition, other government agencies and private sector clients use our repository and there is provision to accommodate new clients as well. BIO-SPECIMEN REPOSITORY SERVICES: * Bio-specimen Acquisition * Bio-specimen Processing * Cryo-preservation * Cryo-storage and Maintenance of Bio-Repository * Shipments * Inventory of stored biological samples * Database management of inventory for each project
The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.
UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries. There are 10 categories of keywords: Biological process Cellular component Coding sequence diversity Developmental stage Disease Domain Ligand Molecular function Post-translation modification Technical term You may browse by hierarchy, search in Keywords, or list all keywords. By default, searching the keywords will look for matches in both name and definition.
A provider for commercial products for analyzing neuronal morphology, stereology, etc.
Charge Czar: Peptide charge state determination for low-resolution tandem mass spectra
Charge Czar is a software tool that uses a support vector machine to discriminate between +2- and +3-charged tandem mass spectra, with the goal of reducing database search time by eliminating the need to search twice with each spectrum. Charge Czar is written in Python and ANSI C. Source code for the latest version, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded after you have agreed to the license agreement. Mass spectrometry is a particularly useful technology for the rapid and robust identification of peptides and proteins in complex mixtures. Peptide sequences can be identified by correlating their observed tandem mass spectra (MS/MS) with theoretical spectra of peptides from a sequence database. Unfortunately, to perform this search the charge of the peptide must be known, and current charge-state-determination algorithms only discriminate singly- from multiply-charged spectra: distinguishing +2 from +3, for example, is unreliable. Thus, search software is forced to search multiply-charged spectra multiple times. To minimize this inefficiency, we present a support vector machine (SVM) that quickly and reliably classifies multiply-charged spectra as having either a +2 or +3 precursor peptide ion. By classifying multiply-charged spectra, we obtain a 40% reduction in search time while maintaining an average of 99% of peptide and 99% of protein identifications originally obtained from these spectra.
A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.
Center for Organ Recovery and Education - CORE
Transplant Organ Procurement Foundation of Western Pennsylvania
The Center for Organ Recovery & Education (CORE) is one of 58 federally designated agencies in the United States known as a not-for-profit organ procurement organization (OPO). CORE is dedicated to promoting donation, education and research for the purpose of saving and improving the quality of life through organ, tissue and corneal transplantation. An innovative, responsive OPO, CORE plays a pivotal role between potential donors and patients awaiting transplantation. In addition to talking with families about the opportunity to donate, CORE coordinates the surgical recovery of organs, tissue and corneas, as well as the computerized matching of donated organs and placement of corneas. In 1995, CORE created the first donor card database in Pennsylvania. In 1996, the organization added tissue recovery and eye banking services to its organ recovery component. It enhanced its line of services by opening an internal laboratory in 1997, where CORE performs the necessary tests to help determine if the organs, tissue and corneas are healthy for transplantation. Since its inception more than 30 years ago, CORE has helped to provide more than 300,000 organs, tissue and corneas for transplantation. The chances for renewed health provided through CORE would not be possible without those who have said yes to donation.
UVA Center for Research in Reproduction Ligand Assay and Analysis Core
This Core at the University of Virginia employs state-of-the-art methods to quantitate peptide and steroid reproductive hormones in blood and tissue. It also develops new methodology, prepares labeled reagents for immunoassays, immunocytochemistry and binding studies and assists in the transfer of technology to participating investigators. Available services: AMH ELISA, 3-ALPHA DIOL G ELISA (ON HOLD), ANDROSTENEDIONE RIA, CORTISOL HUMAN IMMULITE, CORTICOSTERONE RIA, DHEA ELISA, DHEA-SO4 HUMAN IMMULITE, DHT NON EXTRACTION RIA (ON HOLD), ESTRADIOL HUMAN & MOUSE BECKMAN COULTER RIA, ESTRADIOL RAT SIEMENS RIA, ESTRONE- RIA, FSH HUMAN IMMULITE, IGF-1 HUMAN IMMULITE, INHIBIN-A ELISA, INHIBIN-B ELISA, INSULIN HUMAN IMMULITE, LH HUMAN IMMULITE, MOUSE FSH RIA, MOUSE LH SANDWICH IRMA, PROGESTERONE RIA, PROINSULIN RIA, PROLACTIN HUMAN IMMULITE, 17a-OH-PROGESTERONE RIA, RAT FSH RIA, RAT LH SANDWICH IRMA, SHBG HUMAN IMMULITE, TESTOSTERONE RIA, SENSITIVE ESTRADIOL HUMAN & RAT RIA, SENSITIVE PROGESTERONE RIA, SENSITIVE TESTOSTERONE - RIA
Established in 1990 as a long term storage cryobank, ReproTech, Ltd. is dedicated to offering safe and effective shipment and long term storage of reproductive tissue that has been originally cryopreserved at another laboratory or cryobank. It is the intent of RTL to provide the physician and client depositors with quality services that fully comply with industry and government Standards and/or Regulations. Our Locations: Florida, Minnesota, Nevada, US Network Administration ReproTech, Ltd. (RTL) is a one-stop resource specializing in effective solutions to the challenges faced in today''s ever changing field of Reproductive Medicine. ReproTech''s experienced staff provides expert consultation services for long term storage of reproductive tissues and donor program management to assist in compliance with regulatory agencies.
physics-based Simulation of Biological Structures
Simbios - NIH Center for Biomedical Computation at Stanford
Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions. Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, protein folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating with Simbios can apply for NIH funding. To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with https://simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repositories. Simbios is developing and disseminating the SimTK core simulation toolkit, (simtk.org/home/simtkcore). SimTK core is open-source software developed by experienced professionals. The software includes advanced capabilities for modeling the geometry and physics of biological systems. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists. Simbios has developed OpenSim, an application for advanced neuromuscular modeling that uses the SimTK toolkit, and is making it openly available at simtk.org/home/opensim. Simbios also publishes the Biomedical Computation Review, a magazine devoted to the science and tools in biocomputation, aimed at the community which encompasses the diverse biocomputation disciplines. To help researchers find high quality software and tools Simbios has also establishes the Simbiome an inventory of high-quality commercial and academic bio-simulation tools. Simbios has recurring openings for postdoctoral researchers.
Database containing information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug-target relations. The SIDER Side Effect Resource represents an effort to aggregate dispersed public information on side effects. To our knowledge, no such resource exist in machine-readable form despite the importance of research on drugs and their effects. The creation of this resource was motivated by the many requests for data that we received related to our paper (Campillos, Kuhn et al., Science, 2008, 321(5886):263-6.) on the utilization of side effects for drug target prediction. Inclusion of side effects as readouts for drug treatment should have many applications and we hope to be able to enhance the respective research with this resource. You may browse the drugs by name, browse the side effects by name, download the current version of SIDER, or use the search interface.
Ludwig Boltzmann Gesellschaft Tumor Bank
As a basis for the experimental cluster projects, and for further future projects a collection of various biological specimens of cancer patients shall be established. All participating Ludwig Boltzmann Institutes (LBIs) are supplying biological specimens from tumor patients and clinical documentation. At the LBI for Gynecology and Gynecologic Oncology a tumor bank for biological specimens from gynecologic cancer patients already exists. All the procedures for sample processing and storage are well established. Existing equipment for storing tissue specimens at -196 degrees C can be used. Materials from the following malignant diseases are collected: Breast cancer Colorectal cancer Neuroendocrine tumors (NET) (Small cell lung cancer (SCLC) and Carcinoid tumors) Types of biological materials: Tissue (fresh frozen) Bone marrow Blood (serum/plasma/cell fractions) Pleural effusions Ascitic fluids Sputum Bronchial lavage Stool The biological specimens are initially processed at the respective LBIs or at their connected lab facilities. Enrichment of blood samples for disseminated tumor cells is done at the LBI for Gynecology and Gynecologic oncology. Long time storage of all materials is done at appropriate temperatures at the same institution. This LBI also coordinates the logistics. All relevant sample-specific and clinical data are surveyed at the respective LBIs and stored centralized in an on-line data bank in anonymized form, respecting all relevant regulations on data protection and security.
Wardwiki is a wiki designed to give free advice to foundation doctors (also know as interns) to help with practical issues as they arise on hospital wards. Despite the proliferation of medical websites and expensive courses there remains a large gap in provision of practical, experience based guidance to help foundation doctors survive the first two years on the wards. You may search for topics of interest but there are also sections including Popular Topics, Popular Categories, Top 25 articles, and Featured article. It is the responsibility of each foundation doctor to ensure their actions, referrals and prescriptions are accurate. These pages are written and maintained to the best ability of the contributing authors. We encourage any contributions be well founded, accurate, in good faith, without endorsement of medical products or opinions, and not to breach existing copyright. WardWiki cannot accept liability for adverse events that may arise directly or indirectly from advice given.
Russia 2045: Brain Reverse Engineering Lab
The internet-laboratory will present records (publications) of the group of theorist researches, who joined their efforts for collective intellectual works with the goal to understand the mechanisms of operation of human brain in general and in all details, which are necessary for the subsequent artificial re-creation of these mechanisms. The main initial task of the laboratory will be creation of open-access scientific, technological and engineering internet-resource in a form of a specialized database of knowledge on mechanisms of brain work. It is supposed that as a result of the planned work at the end of 2015 the project''s team will elaborate the full detailed description of the mechanisms of human brain. It will be possible to use this description to make (in yrs. 2018-2020) a full scale working analog of the human brain, based on technological (not biological) informational elements and devices. At the present stage the team for the project is under formation. It will include 21 persons of an advanced research level with background in physics and biophysics. The whole work will be divided into overlapping zones of responsibility. All basic elements of the project will be discussed in detail at general sessions of the team and in local group consultations. * Preliminary stage (2011-2012): The main working instrument of the project at this stage will be the internet-laboratory. * The working stage (2013-2015): The forming of the program and of the methods of work will proceed in the course of the preliminary stage of the project. To apply for taking part in the project please write to: shkolamozg (at) ru.ru (Only serious suggestions will be considered).
Lifesharing Tissue Services provides the opportunity to improve and extend lives through the procurement, processing, storage and distribution of human tissue for transplantation and research. Originally established in 1984 to support the Burn Center at UCSD Medical Center, Lifesharing Tissue Services is a non-profit organization serving San Diego and Imperial counties in Southern California. The majority of tissues recovered by Lifesharing Tissue Services stay in this region to enable physicians to provide the best possible care for critically ill patients. Tissue grafting not only reduces pain and speeds recovery, but it also improves a patient''s quality of life. Fully accredited by the American Association of Tissue Banks (AATB) and the Food and Drug Administration (FDA), Lifesharing Tissue Services works to ensure the highest quality of tissue and technical service. Lifesharing is a member of the United Network for Organ Sharing (UNOS).
A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB)
Biospecimens / Biorepositories: Rare Disease-HUB
Biospecimens/Biorepositories: Rare Disease-HUB
A database of biospecimens collected, stored, and distributed by biorepositories in the United States and around the globe. Its goals are: To help and assist interested parties and investigators search, locate, and identify desired biospecimens needed for their research; to facilitate collaboration and sharing of material and data among investigators across the globe; to accelerate research to facilitate the discovery of new treatments, therapeutics and eventually cures for rare diseases as well as common diseases; to identify, locate and increase the awareness of existing biorepositories across the globe; and to link the RD-HUB with the Global Rare Diseases Patient Registry and Data Repository (GRDR).
Repository for all data, figures, theses, publications, posters, presentations, filesets, videos, datasets, negative data in a citable, shareable and discoverable manner with Digital Object Identifiers. Allows to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow. Features integration with ORCID, Symplectic Elements, can import items from Github and is a source tracked by Altmetric.com. Figshare gives users unlimited public space and 1GB of private storage space for free. Data are digitally preserved by CLOCKSS. Supported by Digital Science, a division of Macmillan Publishers Limited, as a community-based, open science project that retains its autonomy.
NeuroPod is the neuroscience podcast from Nature, produced in association with the Dana Foundation. Each month, join us as we delve into the latest research on the brain, from its molecular makings to the mysteries of the mind. We''ll also be bringing you the latest news from neuroscience conferences around the globe, along with special reports on hot areas in neuroscience.
Donor Network of Arizona is the federally designated, not-for-profit, organ procurement organization for the state of Arizona and a tissue and eye recovery organization. DNA serves five organ transplant centers in Arizona with the combined capacity to perform heart, lung, kidney, pancreas and liver transplants. * Our Mission: We make the most of life through the gift of organ and tissue donation. * Our Vision: We challenge ourselves and others everyday to realize Arizona''s potential to save and improve lives. DNA shares organs regionally and nationally through the United Network for Organ Sharing''s (UNOS) national network. DNA is accredited by the Association of Organ Procurement Organization, American Association of Tissue Banks and the Eye Bank Association of America.
The Wales Cancer Bank aims to collect samples of tumour, normal tissue and blood from all patients in Wales who are undergoing an operation to remove tissue where cancer is a possible diagnosis. These samples will be banked to build up a research resource that will be used by research groups to help understand the molecular mechanisms involved in cancer and work towards the selection of optimum targeted treatment for individuals. The Wales Cancer Bank is licensed by the Human Tissue Authority (license 12107) to store human tissue for research and has ethics approval from the Wales Multicentre Research Ethics Committee to collect and issue samples for cancer related research.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The M2Gen Biorepository offers the world's largest cancer-focused tissue biobank linked to longitudinal clinical and molecular data. We provide well-annotated, high quality tissue and clinical data to support research and clinical partnerships. M2Gen's Biorepository team includes dedicated pathologists, biobanking specialists and licensed laboratory staff. Quality control assessment is performed by board-certified pathologists.
Genopole is France''s leading biotech-and biotherapy-dedicated science and business park. The Genopole project was initiated in 1998 in the town of Evry-Corbeil, under the impetus of the French government, Ile-de-France Regional Council, Essonne County Council and the French Muscular Dystrophy Association (Association Francaise contre les Myopathies, AFM); the goal was to create France''s first ever science and business park dedicated to genomics, genetics and biotech and help the country to catch up with its international rivals in these fields. Its threefold mission is 1. to develop a high-level research campus in genomics and post-genomics, focused on gene therapy in collaboration with the University Evry Val d''Essonne; 2. encourage the start-up and foster the development of biotech companies in the Paris region by providing personalized advice and support, including financial assistance and 3. create a biopark in Evry-Corbeil in collaboration with the research campus. In addition to constant support from its founding members and other partners, Genopole''s success is largely based on the novelty of its approach: bringing together public-and private-sector research labs, university teaching facilities and life science start-ups on a single campus in EvryCorbeil. In collaboration with France''s national research institutes and the Paris Ile-de-France region''s universities, Genopole hosts and equips academic research units specializing in genetics, genomics and related sciences. Genopole also stimulates scientific life on the biopark by coordinating and organizing high-level teaching & training programs, seminars, symposia, business clubs and much more.
Nathan S. Kline Institute for Psychiatric Research; New York; USA
Nathan Kline Institute for Psychiatric Research
Nathan S. Kline Institute for Psychiatric Research
New York State-funded research Institute, located in Orangeburg, New York.
Stony Brook University Department of Neurobiology and Behavior
SBU Department of Neurobiology and Behavior
The Department of Neurobiology currently has 18 faculty with substantial research strengths in neural development, circuit function, computation, cellular communication through receptors, channels and synapses and neurological and psychiatric diseases. The Department offers a university-wide predoctoral training program designed to provide broad training opportunities for students interested in careers in the neurosciences. Students can enter from their undergraduate training or through the MD/PhD program. The graduate program provides a broad educational background in neurobiology, experience in teaching, and the opportunity to pursue original doctoral research in one of over 40 laboratories. The program includes scientists at SUNY Stony Brook, recently ranked number two in the Graham/Diamond study of public research institutions, at Cold Spring Harbor Laboratories, an internationally renowned private research institute, and at Brookhaven National Laboratory, a multidisciplinary research facility of the U.S. Department of Energy. Total research grant funding for the primary faculty of $6.8 million dollars was received in FY 2008. Under the direction of Dr. Lorna Role, who arrived as Chair in April 2008, the department looks forward to continued growth, expansion and innovation. If you consider yourself a Postdoc in training, regardless of your title, you are welcome to participate in our program.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The MCG Tumor Tissue and Serum Repository or tumor bank, located in the Department of Pathology, Murphey Pathology Building, was established with support from the Georgia Cancer Coalition (GCC). Its mission is to provide researchers access to high quality annotated specimens, an essential requirement for cancer research. The repository collection includes a variety of specimen types, such as tumor tissue and cells, blood and other biofluids as well as normal specimens used as controls. The quality of all specimens is reviewed by a pathologist, and the information is captured in the tumor bank''s database. An imaging system will be used in the future to capture this information. Human-derived specimens are a very precious resource, and therefore the operations of the tumor bank are overseen by an advisory board, representing GHSU and other stakeholders, to ensure that the specimens are properly utilized and the privacy of specimen donors is protected.
Xenopus anatomy and development ontology
A structured, controlled vocabulary of the anatomy and development of the African clawed frogs (Xenopus laevis and tropicalis), organized in a graphical structure. Tissues are shown as being part of other tissues and the timing of their development is indicated by start and end stages. The lineage of tissues is represented by develops from relationships between different tissues at different developmental stages. Many items have been classified according to the Common Anatomy Reference Ontology. The Xenopus Anatomical Ontology will be used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes. Its robust developmental map will enable powerful database searches and data analyses. They encourage community recommendations for updates and improvements to the ontology.
Duke Cancer Institute: A National Cancer Institute-designated Comprehensive Cancer Center
One of 40 centers in the country designated by the National Cancer Institute (NCI) as a comprehensive cancer center, it combines cutting-edge research with compassionate care. Its vision is to accelerate research advances related to cancer and improve Duke''s ability to translate these discoveries into the most advanced cancer care to patients by uniting hundreds of cancer physicians, researchers, educators, and staff across the medical center, medical school, and health system under a shared administrative structure.
Private human tissue processing and storage bank in the UK based in Plymouth on the medical campus of Derriford Hospital, Europe''s 4th largest teaching hospital. The company was set up to serve the UK and private health sectors looking to outsource the processing and storage of human tissue to an accredited, trusted and experienced expert. Storing for human application, they now process and store human tissue for organizations all over the world, including the Plymouth Hospitals NHS Trust. They are also the only private tissue bank of any true scale in the UK with the ability to store well over 1 million human tissue samples on one site. BioVault has achieved a number of accreditations and forged relationships with numerous bodies since 2002, all designed to test the robustness of our internal procedures and reassure clients they are being given the highest levels of quality and service. Many of BioVault''s pioneering systems have been designed to exceed the criteria set out by the Human Tissue Authority (HTA) with whom we work closely. The HTA is the competent authority under the European Tissue and Cell Directive and sets the standards for regulating human tissue application establishments.
Platform to facilitate sharing, discovery, and secure access to UCSF biomedical data. It''s powered by the Dataverse Network platform, which supports a variety of data types, as well as attribution and licensing needs. Researchers may share datasets, discover data from other labs, and reuse data. Links to tools and information that help scientists properly organize, manage, and document their datasets are also provided.
SchistoDB is a genomic database for the parasitic organism Schistosoma mansoni, one of the major causative agents of schistosomiasis worldwide. It currently incorporates sequences and annotation for S. mansoni in a single user-friendly database. Several genomic scale analyses are available as well as ESTs, oligonucleotides, metabolic pathways and drugs. Make your data available: If you''d like to have your updates and/or datasets integrated in SchistoDB, drop us an email.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Two types of tools are presently available, widgets and RSS. Widgets are code-bearing graphic elements that allow you add Department of Health and Human Services (HHS) content or functionality to your Web product. RSS are syndication feeds that allow you to automatically import HHS content into your Web product. You may search by keyword, HHS Agency and/or type. New tools are being added regularly. The links below will take you to Data.gov where you can access the data set, rate it, and view additional details.
WikiPatient is the independent patient information & news source that anyone can edit. With 71,700 Textbook Chapters and News Articles in English, this wiki is all about Care, Community, and Co-Creation. Major sections include WikiPatient: Patient Resources, WikiPatient News: Today in Medicine, Diseases/Disease States and Care Centers. WikiPatient is available in other languages including Español, Français, Polski, Русский, Română, 中文, and Türkçe.
Comprehensive neuroscience directory that places Neuroscience websites in a relevant category within the internet''s oldest directory. Search engines rely on these listings when evaluating where to place your website in their results. A listing in the BOTW Neuroscience Directory makes your website pop so be sure to take advantage of this opportunity and submit your site today! Currently major categories include: * Neuroanatomy (at) * Neurobiology * Neurochemistry * Blogs (at) * Education * Neuroscientists * News and Media * Organizations * Research See Also: * Kids and Teens: Science and Math: Science: Living Things: Human Body: Nervous System * Health: Conditions and Illness: Neurological Disorders * Health: Medicine: Medical Specialties: Neurology * Health: Medicine: Surgery: Neurosurgery
Cellular Technology Ltd Cryopreserved PBMC
Cellular Technology Limited Cryopreserved PBMC
Cellular Technology Limited Cryopreserved Peripheral Blood Mononuclear Cells
CTL Cryopreserved Peripheral Blood Mononuclear Cells
No longer functioning as an independent charity, onCore UK is a national cancer biobanking organization. Our mission is to serve as an action team that informs, coordinates and develops cancer biobanking to enable research towards the discovery and development of new interventions against cancer. We also offer advice to researchers who need to collect and store samples for their own specific projects. Our main strategic objectives are: * To empower research using human biosamples to find new and effective means of preventing, detecting or treating cancer. * To improve access by researchers to the human biosamples they require for their work. * To facilitate an environment in which patients, the public, health professionals, researchers, funders of research, policy makers and regulators can work together to support cancer biobanking and the research it underpins. * To provide practical information, coordination and development for current and future people and organizations involved in cancer biobanking to ensure that they are not unnecessarily hindered in their work. * To provide an accurate and regularly updated picture of the cancer biobanking provision in the UK that will inform future decisions by funders supporting research using donated human biosamples. * To distribute the human biosamples that onCore UK has in its custody. onCore UK conducts its business within the overall scope of the National Cancer Research Institute (NCRI) and for the benefit of cancer research. In the past we have also worked with selected NHS hospitals in different parts of the country to collect biosamples and relevant clinical data donated by cancer patients. These biosamples are stored in a secure repository and researchers can apply to use them. We make anonymized biosamples and data available for scientifically and ethically approved research on a cost-recovery basis. onCore UK works with other cancer biobanks in the UK via the NCRI Confederation of Cancer Biobanks (CCB), and with other biobanks internationally, to improve access for researchers to larger numbers of high quality biosamples, to harmonize how biobanks work and to share expertise for the benefit of all involved.
BiblioSpec enables the identification of peptides from tandem mass spectra by searching against a database of previously identified spectra. This suite of software tools is for creating and searching MS/MS peptide spectrum libraries. BiblioSpec is available free of charge for noncommercial use through an interactive web-site at http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/bibliospec.php The BiblioSpec package contains the following programs: * BlibBuild creates a library of peptide MS/MS spectra from MS2 files. * BlibFilter removes redundant spectra from a library. * BlibSearch searches a spectrum library for matches to query spectra, reporting the results in an SQT file. In addition to the primary programs, the following auxiliary programs are available: * BlibStats writes summary statistics describing a library. * BlibToMS2 writes a library in MS2 file format. * BlibUpdate adds, deletes, or annotates spectra. * BlibPpMS2 processes spectra (bins peaks, removes noise, normalizes intensity) as done in BlibSearch and prints the resulting spectra to a text file. Several reference libraries are available for download. These libraries are updated regularly and are for use under the Linux operating system. You will find libraries for * Escherichia coli * Saccharomyces cerevisiae * Caenorhabditis elegans
The community-based Doheny Eye & Tissue Transplant Bank has become a pioneer and leader in providing eye and tissue banking services to patients, surgeons and hospitals in southern California for more than 40 years. The mission of the Doheny Eye & Tissue Transplant Bank is to relieve human suffering by providing human tissue for transplant, research, and medical education in our community and around the world. The non-profit, non-governmental Doheny Eye & Tissue Bank is a member of the TBI/Tissue Banks International non-profit network of vision and certified by Eye Bank Association of America.
Discovery and Reconstruction of Unannotated Transcripts
Software for Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data.
Dana-Farber/Harvard Cancer Center Pathology Specimen Locator
Pathology Specimen Locator: deidentified human specimens for translational cancer research
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The Dana-Farber/Harvard Cancer Center Pathology Specimen Locator (PSL) is a core developed to facilitate translational research requiring human specimens. The PSL is a distributed network of databases containing de-identified pathology reports and other specimen information from IRB-approved repositories within Dana-Farber/Harvard Cancer Center affiliated institutions. Using the PSL, researchers can work with the pathology departments to find appropriate specimens for their research. The Harvard VLS currently contains approximately two million de-identified pathology reports from the four main Harvard Teaching Hospitals.
Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux.
Rocky Mountain Multiple Sclerosis Center
The Rocky Mountain MS Center is a patient-centered organization dedicated to changing the way we think about and treat MS in order to protect the futures of those living with the disease. Our mission is to improve the lives of people with Multiple Sclerosis (MS) and their families through care, support, education and research. * Medical Care and Support: We offer a comprehensive care approach that maximizes and enhances the brain''s ability to protect and repair itself and to promote quality of life for patients and their families. We incorporate wellness, exercise, diet and stress management, and supportive services in addition to the most progressive medical care. * Education: We empower patients, families and health care providers by sharing what we know. There are 10,000 peer reviewed articles published annually; we sort through that information and share the latest advances. * Research: We are pursuing new treatment approaches to save the brain. We are leading the way to assure that we prevent the silent but ongoing brain damage that results in disability. This means treating early and treating aggressively.
KI Biobank is an accredited core facility offering sample collection services. KI Biobank is located at the Department of Medical Epidemiology and Biostatistics. KI Biobank offer infrastructure for pre analytical sample handling and provide researchers guidance on how samples should be taken and labeled. The processes comprise registration, handling, storage and distribution of samples. KI Biobank also offers DNA-extraction from blood and saliva. In order to insure complete traceability on samples and belonging information all processes are controlled by a Laboratory Information Management System (LIMS). For every new study a contract is established describing the study and the disposition rights. We also help in writing Biobank agreements including multicenteravtal and Material Transfer Agreement. KI Biobank is, according to the Biobank law, responsible for all sample collections handled within the core facility and those that are stored on the departments on KI campus. Clinical sample collections are handled by the Biobank units at the respective hospitals within the Stockholm County Council. Besides the samples that are stored centrally at KI Biobank, KI Biobank is also the administrative biobank for research sample collections at Karolinska Institutet that are stored and administrated at the departments. All research sample collections must be reported to KI Biobank. The following types of sample collections are registered in the biobank; sample collections taken within the regular health care that has been transferred to Karolinska Institutet with an agreement of transfer, samples taken from healthy individuals or other persons out of the regular health care and samples that have been taken abroad.
Free, up-to-date and reliable encyclopaedia covering the rapidly advancing field of echocardiography. Anyone may contribute but articles will be reviewed by an European Association of Cardiovascular Imaging (EACVI) board of echocardiography experts. Watch out for the EACVI logo which indicates approved articles!
Open-Content Textbook of Emergency Medicine
Emergency Medicine is an Open-Content Textbook of Emergency Medicine. This wikibook is intended to be a collaborative communication between physicians, nurses, physician assistants, paramedics, EMTs and other healthcare providers. It is not intended for the general public. It is under development and inevitably contains many errors and omissions. As the information in this textbook can be edited by anyone, regardless of whether they are medically trained or not, it should not be used as a guide to treating yourself or anyone else! Contents * 1 SYMPTOMS AND PRESENTATIONS ** 1.1 GENERAL SYMPTOMS ** 1.2 HEAD AND NECK SYMPTOMS ** 1.3 CHEST SYMPTOMS ** 1.4 ABDOMINAL SYMPTOMS * 2 TOPICS ** 2.1 ABDOMINAL AND GASTROINTESTINAL DISORDERS ** 2.2 CARDIOVASCULAR DISORDERS ** 2.3 CUTANEOUS DISORDERS ** 2.4 DISASTER MEDICINE ** 2.5 ENDOCRINE, METABOLIC, AND NUTRITIONAL DISORDERS ** 2.6 ENVIRONMENTAL DISORDERS ** 2.7 HEAD, EAR, EYE, NOSE, THROAT DISORDERS ** 2.8 HEMATOLOGIC DISORDERS ** 2.9 IMMUNE SYSTEM DISORDERS ** 2.10 INFECTIOUS DISORDERS ** 2.11 MUSCULOSKELETAL DISORDERS (NONTRAUMATIC) ** 2.12 NERVOUS SYSTEM DISORDERS ** 2.13 OBSTETRICS AND GYNECOLOGY ** 2.14 RENAL AND UROGENITAL DISORDERS ** 2.15 THORACIC-RESPIRATORY DISORDERS ** 2.16 TOXICOLOGIC DISORDERS ** 2.17 TRAUMATIC DISORDERS * 3 TESTS ** 3.1 Imaging ** 3.2 Lab Investigations ** 3.3 Point of Care Testing * 4 TREATMENT ** 4.1 Procedures ** 4.2 Resuscitation ** 4.3 Other Treatment * 5 SPECIAL POPULATIONS * 6 PRACTICE AND ADMINISTRATION * 7 KNOWLEDGE AND COMMUNICATION
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 7, 2022. Functional Genomics Data Society - FGED Society, founded in 1999 as the MGED Society, advocates for open access to genomic data sets and works towards providing concrete solutions to achieve this. Our goal is to assure that investment in functional genomics data generates the maximum public benefit. Our work on defining minimum information specifications for reporting data in functional genomics papers have already enabled large data sets to be used and reused to their greater potential in biological and medical research. We work with other organizations to develop standards for biological research data quality, annotation and exchange. We facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. We promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis.
Throughout the past 25 years, John Theurer Cancer Center at Hackensack University Medical Center has become one of the largest and most comprehensive cancer centers in the United States. Today, we are a top 50 U.S. News and World Report Best Hospitals for cancer the only cancer center in New Jersey with this prestigious designation. Its mission is to deliver extraordinary care that is multidisciplinary, personalized, innovative, and at the appropriate cost with superior outcomes to the most satisfied patients. Year after year, we have harnessed the newest technologies and retained world-class physicians, nurses and scientists to help service the needs of our patients within our 14 specialized cancer divisions.
National Autonomous University of Mexico; Mexico City; Mexico
National Autonomous University of Mexico
Founded in 1551, this research university features murals by Diego Rivera and other famous artists.
Rocky Mountain Multiple Sclerosis Center Tissue Bank
Scientists throughout the world depend on the Rocky Mountain MS Center Tissue Bank to supply high quality human brain tissue and cerebral spinal fluid to support their research. Funded in part by the National MS Society, the Tissue Bank is one of only four MS-related tissue banks in the nation. The Tissue Bank has distributed specimens to more than 160 investigators worldwide and over 1,600 people have consented to be donors after death. Tissue banks provide a unique bridge between those who live with MS and the scientific community. Studies conducted with samples from the Center have led to several important discoveries and 130 publications. While deeply personal, the decision to donate has far-reaching effects as scientists unlock the mysteries of multiple sclerosis. If you would like to donate, arrangements must be made in advance because it is important that tissue is taken within a few hours of death. For more information on making a donation, visit the How To Donate section of this website and contact the Rocky Mountain MS Center Tissue Bank at 303.788.4030 x111.
Viral Informatics Resource for Metagenome Exploration
Viral Informatics Resource for Metagenome Exploration - VIROME
A web-application designed for scientific exploration of metagenome sequence data collected from viral assemblages occurring within a number of different environmental contexts. The VIROME informatics pipeline focuses on the classification of predicted open-reading frames (ORFs) from viral metagenomes. The portal allows you to submit your viral metagenome to be processed through the VIROME analysis pipeline, and enable you to investigate your data via the VIROME user interface., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
MultiFun: a cell function assignment schema
MultiFun: a cellfunction assignment schema
MultiFun is a multifunctional classification scheme for Escherichia coli K-12 gene products. In the classification scheme, cellular functions are divided into 10 major categories: Metabolism, Information Transfer, Regulation, Transport, Cell Processes, Cell Structure, Location, Extra-chromosomal Origin, DNA Site, and Cryptic Gene. These major categories are further sub-divided into a hierarchical scheme. Two thousand nine hundred twenty-two gene products of E. coli K-12 were assigned to one or more functions depending on the role they play in the cell. Functional assignments were made to 66% of E. coli gene products, ranging from 1 to 16 assignments per gene product. The expansion of cellular function categories and the assignment to more than one category (multifunction) provides a more complete description of the gene products and their roles and hence better reflects the functional complexity of organisms. We believe this classification system will be useful in the field of genome analysis, both for annotation purposes and for comparative studies. The functional classification scheme and the cellular function assignments made to E. coli gene products can be accessed from the web at the databases GenProtEC (http://genprotec.mbl.edu) and EcoCyc (http://www.ecocyc.org).
A nonprofit organization offering research and clinical grade pluripotent stem cell lines, cytogenetic testing, quality control testing and cell banking services to researchers worldwide. The organization is focused on enhancing and expanding the study of human pluripotent stem cells by supporting basic research; establishing research protocols; creating and distributing cell lines; providing training to scientists worldwide; and supporting efforts to unlock the therapeutic potential of stem cell technologies. As home to the Wisconsin International Stem Cell (WISC) Bank, and previously the first US National Stem Cell Bank, WiCell serves the worldwide scientific stem cell community through banking, characterization, and distribution of stem cell lines as well as providing technical support. WiCell also offers cytogenetic services, quality control testing services and clinical grade cell lines to researchers across the globe.
Web based service that offers software developers centralized online location to control and manage free and open source software projects. Open source software tool and business public software platform.
Organization within the United States Department of the Navy responsible for the science and technology programs of the U.S. Navy and Marine Corps.
Sterol and Isoprenoid Research Consortium
A consortium which represents a collaborative group of investigators along with their academic medical centers and the National Institutes of Health, patient advocacy groups, and clinical research programs. Members of the STAIR Consortium are dedicated to participating in clinical research regarding disorders related to cholesterol and other sterol and isoprenoid metabolism. The overall objective of the Sterol and Isoprenoid Research Consortium (STAIR) is to study a group of diseases bound by common biochemistry, impact on health, and rarity. STAIR will conduct several clinical studies, support a full-scale training program in the field of sterol and isoprenoid diseases, and engage several patient advocacy groups in consortium activities. Researchers interested in partnering with STAIR may contact its Administrative Director.
Marshfield Clinic Personalized Medicine Research Project bio-bank
Personalized Medicine Research Project bio-bank
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A large collection of biological samples and health information collected for the Personalized Medicine Research Project (PMRP) for use in biological research. Genetic information from 20,000 participants forms a database enabling scientists to study which genes cause disease, which genes predict reactions to drugs, and how environment and genes work together to cause disease. The goal of this project is to learn how to apply genetic science to human health. This knowledge will help researchers develop new medications and diagnostic tests, and will enable physicians to prescribe medications that work best for a particular person. Marshfield Clinic Personalized Medicine Research Project (PMRP) resources currently available: DNA, plasma, serum, questionnaire, electronic medical records to construct phenotypes; ability to recontact subjects for additional information (where they have given consent for recontact); stored pathology specimens collected for clinical purposes; 51 clinically relevant polymorphisms; Illumina 660 quad for ~4200 subjects aged 50+.
Rare Diseases Clinical Research Network Patient Contact Registry
A portal specifically for patients (and their families) with sterol and other related disorders where they can register themselves with STAIR in order to be contacted in the future about clinical research opportunities and updated on the progress of the STAIR research projects. An online Registry form exists for all the BVMC disorders currently being studied.
Vanator-CVR - A metagenomics & virus discovery pipeline
Vanator-CVR: A metagenomics and virus discovery pipeline
Virus Alignment de Novo Assembly and Taxonomy On Reads
A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples.
RETICULUM - Neuroscience History Resources
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. RETICULUM is a gateway to Internet resources for history and historians of basic, clinical, and behavioral neuroscience. Links to existing sites are reviewed for salience and accuracy, organized by topic for convenient access, and regularly tested for availability. Comments, questions, and additional resource suggestions and submissions are welcomed. Major categories include: Calendar/Announcements, Professional societies and associations, Internet forums, Placement opportunities, Funding opportunities, Education opportunities, Repositories and collections, Catalogs and indexes, Texts on the Internet, Images on the Internet, Exhibits on the Internet, Periodicals, Commercial resources, Subject guides, Internet introductions, tutorials and tools, Questions-Comments-Suggestions-Submissions, Credits
The Rare Diseases Clinical Research Network (RDCRN) was created to facilitate collaboration among experts in many different types of rare diseases. Our goal is to contribute to the research and treatment of rare diseases by working together to identify biomarkers for disease risk, disease severity and activity, and clinical outcome, while also encouraging development of new approaches to diagnosis, prevention, and treatment. The Rare Diseases Clinical Research Network (RDCRN) is made up of 19 distinctive consortia that are working in concert to improve availability of rare disease information, treatment, clinical studies, and general awareness for both patients and the medical community. The RDCRN also aims to provide up-to-date information for patients and to assist in connecting patients with advocacy groups, expert doctors, and clinical research opportunities.
The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms. You may search in subcellular locations or list them all along with their definitions (490). By default, searching the subcellular locations will look for matches in both name and definition.
A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl.
Genetic code prediction tool FACIL: Fast and Accurate genetic Code Inference and Logo
Genetic code prediction tool that infers the genetic code directly from any set of nucleic acid sequences and assigns a Random Forest-based reliability score to its predictions.
FishBase: A Global Information System on Fishes
A global species database and encyclopedia of over 32,800 species and subspecies of fishes that is searchable by common name, genus, species, geography, family, ecosystem, references literature, tools, etc. It links to other, related databases such as the Catalog of Fishes, GenBack, and LarvalBase. It is associated with a partner journal, Acta Ichthyologica et Piscatoria. It is available in English, Greek, Spanish, Portuguese, French, Dutch, Italian, and German. Photo and video submissions are welcome. FishBase 2004 is also available on DVD or CD-ROMs with full information on 28,500 species. It comes together with the FishBase 2000 book and can be ordered for 95 US$ including air-mail.
Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria.
Ontology of pneumology (french version) developped by Audrey Baneyx, under the direction of Jean Charlet about knowledge engineering expertise and by Francois-Xavier Blanc in collaboration with Bruno Housset about medical expertise.
The Lymphoma Research Foundation (LRF), in collaboration with American Type Culture Collection (ATCC), has created a Mantle Cell Lymphoma (MCL) Cell Bank. The Cell Bank is a collection of various MCL lines created by scientists from all over the world. The idea for the Cell Bank was generated by the scientists that make up the MCL Consortium (MCLC). It was created to provide a single, centralized location where scientists can easily acquire high-quality, well-characterized MCL cell lines in an effort to accelerate discoveries in MCL. LRF has acquired 8 different MCL cell lines (July 2010): Mino, Z-138, JVM-2, JVM-13, REC-1, NCEB-1, JeKo-1, and Maver-1. The Cell Bank is chaired by Dr. Owen O''Connor of New York University Langone Medical Center and is housed at ATCC, the world''s largest biological resource center and the most comprehensive source of reference cultures and reagents used by researchers in the academic and industry laboratories. The Cell Bank was made possible by the scientists who generously agreed to share their resources, including, Dr. Elias Campo, Dr. Zeev Estrov, Dr. Richard Ford, Dr. Junia Melo and Dr. Alberto Zamo.
Aims to carry out an integrated (epi)genomic analysis of the NET BioBank established at the Royal Free and UCL Hospitals to identify new biomarkers for translation into diagnostics and therapeutics. The Neuroendocrine Tumour (NET) Unit at the Royal Free Campus of UCL Hospitals has an international reputation for the management of neuroendocrine tumor patients. It currently receives around 10 new referrals per month and has an active patient cohort of over 800 patients. We receive referrals from across the UK as well as from abroad. It is the designated center for NETs within the North London Cancer Network. In order to improve both treatment and outcome in Neuroendocrine Tumors (NETs), better understanding of their biology and the biological pathways involved is imperative (reviewed in (Modlin et al., 2008)). Currently, the use of targeted treatments is limited and management challenging due to the lack of knowledge of the molecular pathogenesis and mechanistic regulation of these tumors (Barakat et al., 2004). Due to the rarity of NETs and difficulty in obtaining fresh tissue and archival samples, very little is known about the (epi)genetic and germline mutations associated with neuroendocrine tumors ����?? which encompass a clinically and genetically heterogeneous group. To date, studies have been small and under-powered. Clinical trials have included small patient numbers and are often non-randomized phase II trials comparing a new therapy against a non-standardized first line treatment. Initially we will undertake genome-wide methylation analysis on our entire cohort of neuroendocrine tumors in order to determine the methylation profiles of differing NET types. This will improve diagnostic accuracy and potentially identify new therapeutic targets and biomarkers. These studies will be performed on high-throughput analysis platforms based on micoarrays and next-generation sequencing. In parallel, we will analyze the mRNA expression profiles of these tumors to enable integrated (epi)genomic analysis of these intriguing tumors.
WikiHealth is a collaborative online health and wellness community where your participation makes a difference! WikiHealth''s goal is to offer the most comprehensive, current and insightful information to help anyone and everyone achieve optimal health. Our belief is that your knowledge matters--- and you can help others by sharing what you know. WikiHealth is a collaborative writing project aiming to build an extensive and valueable repository on a variety of health and wellness topics. Our mission is to bring free, accesible and thorough information on health and wellness into the homes of every individual worldwide. The goal is for new articles on any health and wellness topic to be added regularly and for existing articles to be improved by volunteer contributors. In time, we envision WikiHealth to be the best health resource to come to for unbiased information as well as prescriptive advice on any health or wellness topic. Please join us by writing a new article or editing an existing one.
Case Comprehensive Cancer Center Biorepository and Tissue Processing Core Facility
Biorepository and Tissue Processing Core Facility of the Case Comprehensive Cancer Center
Biorepository Tissue Processing Core Facility
Case CCC Biorepository Tissue Processing Core Facility
Case Comprehensive Cancer Center Biorepository Tissue Processing Core Facility
Case Western Biorepository and Tissue Processing Core Facility
Case Western Reserve University: Biorepository and Tissue Processing Core Facility
CWRU CCC Biorepository Tissue Processing Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Case Comprehensive Cancer Center''s Biorepository and Tissue Processing Core Facility (BTPC) serves two primary functions: 1. To build an inventory of remnant human tissues, blood and other body fluids (collectively termed biospecimens) targeted towards cancer and other medical research, for later assignment to investigators; and 2. To provide long term, controlled storage of biospecimens for specific researchers. These samples are for research purposes only and may not be used for clinical diagnosis or implantation into humans. Clinical information relating to the samples and donors are collected and maintained in a secure database. Samples and data are de-identified or de-linked before release to the researcher unless he/she has specific IRB approval to gain access to this information. Remnant biospecimens are prospectively collected from surgical procedures, autopsies and clinical laboratories for the BTPC by the Human Tissue Procurement Facility (HTPF), which operates under UH-IRB Protocol 01-02-45. Blood and bone marrow specimens are collected for the BTPC by the Hematopoietic Stem Cell Core Facility (HSCC), which operates under UH-IRB Protocol 09-90-195. The Division of Surgical Pathology at University Hospitals Case Medical Center (UHCMC) has clinical archives of paraffin blocks that can be made available through the BTPC for retrospective research studies under the approval of the Vice Chair for Clinical Affairs at UHCMC. Surgical Pathologists associated with the BTPC are responsible for determining which blocks can be made available and how much material can be removed from the blocks. Types of Tissue Available * Malignant, benign, diseased, normal and normal human tissues * Normal adjacent tissues available paired with tumor specimens in many cases * Tissues are collected from over 50 anatomic sites * Frozen specimens, OCT-embedded and paraffin-embedded tissues * Large array of paraffin-embedded specimens from clinical archives of paraffin blocks and QC research blocks maintained by the HTPF * Peripheral blood and bone marrow samples from initial visits and follow-up procedures are processed to obtain serum and cell fractions for storage * No samples are collected from individuals with known infectious illnesses * Fetal biospecimens are not collected due to state and local statutes
SNiPer-HD: Improved genotype calling accuracy
Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.
The Maryland Brain Collection (MBC), a resource of the Maryland Psychiatric Research Center (MPRC), is dedicated to promoting research with brain tissue obtained post-mortem from individuals with schizophrenia or related disorders. The primary goal of the MBC is to provide high-quality tissue, along with comprehensive clinical information, for hypothesis-driven research. The MBC is not conceptualized as a Brain Bank with open access but is maintained and funded through collaborative research. The Maryland Brain Collection is managed by researchers at the Maryland Psychiatric Research Center (MPRC). MPRC scientists are dedicated to understanding the causes and improving the treatment of mental illness. The Maryland Brain Collection is associated with the Office of the Chief Medical Examiner for the State of Maryland and other donor sources. MPRC scientists collaborate with scientists from around the world to understand how abnormalities in brain tissue relate to mental illness. The purpose of the MBC is to study the following: Schizophrenia, Bipolar Disorder, Depression, Suicide/Teen suicide, Substance Abuse.
Software to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells.
Health Data and Tools Available on Data.gov
Public, high-value federal datasets, tools, and applications using data about health and health care gathered from agencies across the U.S. government.
Case Western Reserve University Case Comprehensive Cancer Center
Core is a partnership organization supporting all cancer-related research efforts at CWRU, University Hospitals Case Medical Center, and the Cleveland Clinic. The Case CCC is organized into 9 interdisciplinary scientific programs plus one program initiative. Research programs of the Case CCC are extending into CWRU affiliated hospitals including MetroHealth Medical Center (the region's county hospital), Louis Stokes Veterans Affairs Hospital, and 13 community medical centers operated by University Hospitals and Cleveland Clinic. The Center operates an NCI-supported Cancer Information Service (CIS) serving the northern half of Ohio as part of the Midwest consortium and has an active outreach program for clinical practice-based prevention and screening initiatives, educational programs, minority recruitment, and facilitation of patient referrals. Case CCC is a member of NCI's CaBIG initiative and is actively pursuing electronic databases for clinical trials, tissue repositories, and related bioinformatics.
Howard Hughes Medical Institute BioInteractive
Collection of biology-focused teaching materials created and administered by the Howard Hughes Medical Institute including free lectures, videos and animations for science education. Many of the resources are also available on DVD and CD-ROM. In addition to the resources on the website, BioInteractive offers DVDs of HHMI''s annual Holiday Lectures on Science and CD-ROMs of the Virtual Lab series. These materials are available to educators for free and can be ordered from the catalog at http://catalog.hhmi.org. Each Holiday Lectures on Science is a set of four one-hour lectures presented each December at the headquarters of the Howard Hughes Medical Institute in Chevy Chase, Maryland . The lectures give students and teachers the opportunity to learn about cutting-edge biomedical research directly from some of the world''s leading scientists. Intended to inspire young students to pursue careers in science, the lectures bring the latest developments in a rapidly moving field of research into the classroom. The lectures are primarily geared to high school students in honors and Advanced Placement biology classes. Other high school students and undergraduates can certainly benefit from the content of the lectures. Some of the related materials on the biointeractive website (http://www.biointeractive.org/) are aimed at a broader audience. With a teacher''s guidance, middle school students can also enjoy learning about the topic. Holiday Lectures are webcast live at http://www.hhmi.org/biointeractive/hl/. Following the live event, they are available as on-demand streaming video at the same Web address. Webcasts of all past Holiday Lectures are available as on-demand streaming video at http://www.hhmi.org/biointeractive/lectures/index.html. Holiday Lectures are also available as podcasts from http://www.hhmi.org/biointeractive/podcast_popup.html
ORION is our neuron reconstruction software package developed for the morphological reconstruction of neurons from confocal and multiphoton microscopy data. It accepts raw neuron stack data as input and it is capable of reconstructing the neuron structure, visualizing the output, and exporting the reconstruction in a variety of formats. We are developing tools that will enable Neuroscientists to explore single neuron function via sophisticated image analysis. Advanced optical imaging can produce both structural and functional data and is at the forefront of experimentally exploring the fast, small-scale dynamics of living neurons. Further, compartmental modeling of neuronal function enables rapid testing of hypotheses and estimating experimentally inaccessible parameters. Combining these two techniques will afford unprecedented capabilities in the study of single neuron function. Our software utility bridges the two Neuroscience techniques by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.
Angioma Alliance DNA/Tissue Bank and Patient Registry
Cerebral Cavernous Malformations (CCM) DNA & Tissue Bank
Cerebral Cavernous Malformations (CCM) DNA and Tissue Bank
Cerebral Cavernous Malformations DNA and Tissue Bank
Angioma Alliance has established a DNA/Tissue Bank and matching clinical database for cerebral cavernous malformations (CCM, cavernous angioma, cavernoma). Our goal is to create the world''s largest collection of CCM genetic samples with matching clinical data to be used as a resource to drive research. We are recruiting individuals with a history of cerebral cavernous malformations to participate in the study. Qualified participants donate a blood sample and complete a comprehensive questionnaire or interview. Blood donation kits will be sent in the mail for participants to take to their doctor, clinic or blood draw center to have their blood drawn. The kit is then mailed to a private lab where the sample is processed. If a surgery is scheduled, the Angioma Alliance DNA/Tissue Bank will work with the participant, the surgeon, and the hospital to coordinate tissue donation. If surgery scheduling allows, dry ice will be shipped to the hospital facility along with a tissue collection kit for use and return to the private lab. The Angioma Alliance DNA/Tissue Bank will attempt to acquire Institutional Review Board approvals at facilities where this is required. The Angioma Alliance BioBank will follow up with participants on a yearly basis to update their clinical information. If the participant has not already had documented genetic testing, we will test their DNA sample for possible CCM1, CCM2, or CCM3 mutation or CCM2 exon 2-10 deletion. If additional causative genes are identified for the illness, we will also test for mutations on these. Participants will not be informed of the results of testing, but if a mutation or deletion is found, they will be informed that results can be released to a diagnostic laboratory in order to obtain follow-up confirmatory clinical diagnostic testing. This could mean a substantial cost savings to the patient whose insurance does not cover genetic testing or who is uninsured. All researchers requesting the use of DNA and/or Tissue samples from Angioma Alliance must complete an application form and material transfer agreement.
National Cancer Institute Office of the Director
CAMO (Cell Adhesion Molecule Ontology) is a set of standard vocabulary that provide a hierarchical description of cell adhesion molecules and their functions. We compiled a list for cell adhesion molecules by integrating Gene Ontology annotations, domain structure information, and keywords query against NCBI Entrez Gene annotations. Totally 496 unique human genes were identified to function as cell adhesion molecules, which is by far the most comprehensive dataset including cadherin, immunoglobulin/FNIII, integrin, neurexin, neuroligan, and catenin families. CAMO was constructed as a directed acyclic graph (DAG) using DAG-Edit to input, manage and update data. We annotated each term with name, definition and source references, as well as the relationship to other terms, based on manual reviews of domain architecture and functional annotations. If vertices represent terms and the relationships between terms are represented by edges, the terms in a DAG can be connected via a directed graph without cycles. CAMO thus provides a hierarchical description of functions of CAMs with five top-level categories: CAM gene families, CAM genetics, CAM regulation, CAM expression and CAM diseases. Each top-level term is further divided into several categories to describe the functions in detail.
Dbfetch is an acronym for database fetch. Dbfetch provides an easy way to retrieve entries from various databases at the EBI in a consistent manner and allows you to retrieve up to 50 entries at a time from various up-to-date biological databases. It can be used from any browser as well as well as within a web-aware scripting tool that uses wget, lynx or similar. From the browser, follow these instructions... * Select a database: If you are using the first form to paste your search items: choose a database name from this form. If you are using the second form to upload your search items: the database name is included at the beginning of each line line of the upload file followed by a colon. * Enter search terms: These MUST BE in the appropriate database format, up to 200 search items can be queried in one run. If you are using the first form: separate search items with a comma or space. If you are using the second form: separate search items with a new line. * Choose an output format: Here you can choose the simpler fasta format, or the databases' ''' default format for the chosen database. * Style: You can get your results as text or html. * Retrieve! - You are now ready to fetch your results, by pressing the Retrieve button.
Segtools is a Python package designed to put genomic segmentations back in the context of the genome! Using R for graphics, Segtools provides a number of modules to analyze a segmentation in various ways and help you interpret its biological relevance. Segmentations should be in BED4+ or GFF format, with the ''name'' field of each line used specifying the segment label of that line. The Segtools commands allow you to compare the properties of the segment labels with one another.
Biomedical Research Institute UCA - CONICET
The Biomedical Research Program (PIB) of the School of Medical Sciences was created in 2007, after a Collaboration Protocol was established between UCA and the National Council of Scientific and Technical Research (CONICET). Research at PIB aims at unraveling the molecular, biochemical and genetic aspects of human diseases, therefore contributing to understanding complex pathologies. Research Groups include: * Molecular and Cell Biology Lab (LBCM) - Group leader: Tom��s A. Santa Coloma, Ph.D. * Nanotechnology Lab - Group leader: Tom��s A. Santa Coloma, Ph.D. * Molecular Neurobiology Lab - Group leader: Francisco J. Barrantes, Ph.D.
This database contains the three sequenced Sulfolobus genomes and the sequenced extrachromosomal elements belonging to Sulfolobales. Users can browse, export, and compare sequences in addition to utilizing BLAST searching.
MPI Research exists to provide comprehensive discovery, safety evaluation, bioanalytical, and analytical services that meet the requirements of biopharmaceutical, medical device, animal health, and chemical companies as we partner globally to bring safer and more effective products to the world. Our goal is to exceed the expectations of our Sponsors and maintain the highest respect in our industry by providing customized, responsive, and on-time services that add value to our Sponsors'' efforts to discover, develop, and enhance products in regulated international environments. We excel as a high performance, high quality organization because of our scientific knowledge and experience, integrity, trust, teamwork, and dedication to strong and enduring Sponsor relationships. MPI Research has conducted thousands of drug safety, discovery, bioanalytical, and analytical studies. We offer extensive support and resources including, but not limited to * A wide and diverse range of classes of compounds * All routes of administration except inhalation * Studies with numerous species and models * Comprehensive reporting capabilities Flexibility and ample capacity enable us to * Accommodate multiple requirements simultaneously * Adjust schedules readily * Produce results quickly Responding to a broad spectrum of research needs: Working in partnership with pharmaceutical, biotech, medical device, and chemical companies, we conduct customized preclinical research throughout the discovery and development process, from early proof of concept testing to regulatory submissions, including IND, EPA/OPPTS, NDA, PMA, and 510K.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. High quality, well characterized pluripotent stem cell lines for distribution to researchers worldwide. Offerings include human embryonic and induced pluripotent stem cell lines, as well as modified cell lines tailored to specific research needs. *Human Embryonic Stem Cell Lines *Modified Cell Lines *Induced Pluripotent Stem Cells (iPS) *Clinical Grade (cGMP) Human ES Cell Banks
MAGNet - Multiscale Analysis of Genomic and Cellular Networks
Center for the Multiscale Analysis of Genomic and Cellular Networks
The mission of the Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) is to develop novel Structural and Systems Biology methods and tools for the dissection of molecular interactions in the cell and for the interaction-based elucidation of cellular phenotypes. These tools are made freely available to the the members of the research community. They are also validated in the context of the Center' '''s own research program through collaborative projects with experimental biologists. MAGNet is one of 7 National Centers for Biomedical Computing (NCBC). These Centers, in conjunction with individual investigator awards, are creating a networked effort to build the computational infrastructure for biomedical computing in the nation. The NCBC program is devoted to all facets of biomedical computing, from basic research in computational science to providing the tools and resources that biomedical and behavioral researchers need to do their work. In addition to carrying out fundamental research the NCBCs play a major role in educating and training researchers to engage in biomedical computing. MAGNet is also one of 12 inter-disciplinary Centers for Cancer Systems Biology (CCSBs), a component of the National Cancer Institute' '''s Integrative Cancer Biology Program. The CCSBs provide a core framework for applying systems biology approaches to cancer research through the development and implementation of computational models of processes relevant to cancer prevention, diagnostics and therapeutics. The CCSBs seek to integrate experimental biology with mathematical modeling to foster new insights in the biology and new approaches to the management of cancer. MAGNet' '''s Training Core ensures that the methods developed by the Center are integrated into the educational offerings of Columbia University' '''s Medical School.
For 35 years, Mid-America Transplant Services (MTS) has served as the regional organ and tissue procurement organization for eastern Missouri, southern Illinois, and northeast Arkansas, serving 4.3 million people in 84 counties. From our founding goal to assist in the coordination of kidney donations, we have grown to become a multi-faceted organization dedicated to saving lives and enhancing the quality of all donated organs and tissues currently available for transplant. MTS''s primary service offering is to facilitate and coordinate the organ and tissue donation process. With a mission to save lives through excellence in organ and tissue donation, we have been at the forefront of enhancing the quality of organs and tissue for transplant. Throughout our history, we have relentlessly pursued our core values of compassion, quality, teamwork, and honesty to create a positive donation experience for Donor Families, which is at the heart of what matters most to MTS. Located in Saint Louis, Missouri, MTS is one of 58 federally designated organizations of its kind in the United States. Incorporated in the State of Missouri, MTS is a private, not-for-profit 501(c)(3). To fulfill our mission, we work closely with the four transplant centers and over 110 donor hospitals located within our service area.
Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note.
Anopheles gambiae (African malaria mosquito) genome view
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A database for the Anopheles gambiae str. PEST genome that was sequenced using a whole genome shotgun approach. The database aims to contribute to the understanding of mosquito genome structure and organization and will assist the development of malaria control strategies and improved anti-malarial drugs and vaccines. Sequences were generated and assembled into contigs for submission to GenBank.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A private repository of clinical and genetic information on families with autism. Genetic and clinical data are obtained from families that have more than one family member diagnosed with an Autism Spectrum Disorder. The biological samples, along with the accompanying clinical data, are made available to AGRE-approved researchers worldwide. As they become available, additional family pedigrees will be posted in the online catalog. Cell lines have been established for the majority of families in this collection and serum/plasma is available on a subset of the subjects until stocks are depleted. The diagnosis of autism has been made using the standard Autism Diagnostic Interview-Revised (ADI-R) algorithm and the Autism Diagnostic Observation Scale (ADOS-G). Detailed birth and medical histories (including basic dysmorphology assessments) on children as well as family and medical information for parents and unaffected siblings, are available for nearly all families. DNA, cell lines, serum, plasma and clinical information are made available to AGRE-approved researchers for analysis.
Neuroscience News: Neuroscience Lab Equipment
Neuroscience Lab Equipment offers a few neuroscience lab products available for purchase including lab coats, oscilloscopes, neuroscience research software, electrophysiology equipment, micromanipulators, centrifuges, lab glassware, pipettes, neuroscience charts and much more. Take a look around and if you don''t find what you need, let us know and we will try to update our Neuroscience Lab Equipment area to sell it.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters.
A central tissue repository at Moffitt specializing in protocol-driven human tissue collection, storage, processing and dissemination. Tissue Core provides investigators with access to high quality, well-annotated human specimens obtained from representative of the patient populations. The advent of powerful molecular technologies has opened the door to developing more effective treatments of patients with cancer. Access to high quality specimens with associated clinical, treatment, recurrence outcome data will be critical to developing and validating the tests needed for diagnosis and prediction of response to therapy. Since its commencement in 1993, the Tissue Core has collected more than 8,000 cases of human liquid cancers and solid primary and metastatic tumors both malignant and benign with adjacent normal, from variety of sites and diagnoses. Collected samples are mostly remnant tissues obtained from patients undergoing therapeutic surgical procedures at the Center. The core also ensures tissue release compliance with USF-IRB and Privacy Board recommendations. * Protocol driven sample collection, processing and distribution * Collection of sample and patient demographic information. * Nucleic acid extractions from tissue sections, FNA, core biopsies blood and bone marrow. * Histology services: H&E slides, staining, sectioning, paraffin blocks, OCT blocks, sample microdissection * WBC, plasma and serum isolation. * Project development and support: Facility staff provides advice and guidance to researchers.
National Drug Abuse Treatment Clinical Trials Network
A collaboration in which the National Institute on Drug Abuse, treatment researchers, and community-based service providers cooperatively develop, validate, refine, and deliver new treatment options to patients in Community Treatment Programs (CTPs). The partnership between CTPs and academic research leaders aims to achieve the following objectives: * Conducting studies of behavioral, pharmacological, and integrated behavioral and pharmacological treatment interventions of therapeutic effect in rigorous, multisite clinical trials to determine effectiveness across a broad range of community-based treatment settings and diversified patient populations; and * Ensuring the transfer of research results to physicians, clinicians, providers, and patients. The CTN, with its core of CTPs engaging diverse populations, is also designed to provide a platform for other studies, which would be funded under separate research grants. Three important ways to use the CTN are: to conduct ancillary studies in connection with CTN protocols; to utilize CTN Node facilities as a platform for investigations; and for Nodes to serve as home bases for NIH Training Centers and individual researchers who have NIH fellowships or career development awards.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Catalog of Fishes is the authoritative reference for taxonomic fish names, featuring a searchable on-line database. The Catalog of Fishes covers more than 53,000 species and subspecies, over 10,000 genera and subgenera, and includes in excess of 16,000 bibliographic references. The Catalog of Fishes consists of three hardbound volumes of 900-1000 pages each, along with a CD-ROM. The online database is updated about every 8 weeks and is now about twice the size of the published version. It is one of the oldest and most complete databases for any large animal group. References are over 30,000. Valid species are over 30,000. This work is an essential reference for taxonomists, scientific historians, and for any specialist dealing with fishes. Entries for species, for example, consist of species/subspecies name, genus, author, date, publication, pages, figures, type locality, location of type specimen(s), current status (with references), family/subfamily, and important publication, taxonomic, or nomenclatural notes. Nearly all original descriptions have been examined, and much effort has gone into determining the location of type specimens. The Genera are updated from Eschmeyer''s 1990 Genera of Recent Fishes. Both genera and species are listed in a classification using recent taxonomic schemes. Also included are a lengthy list of museum acronyms, an interpretation of the International Code of Zoological Nomenclature, and Opinions of the International Commission involving fishes.
Open Biological and Biomedical Ontologies Relationship Types
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Ontology that defines core relations used in all OBO ontologies. Obsolete. Replaced with RO.
The Lymphoma Research Foundation (LRF) is the nation''s largest non-profit organization devoted exclusively to funding innovative lymphoma research and providing people with lymphoma and healthcare professionals with up-to-date information about this type of cancer. LRF''s mission is to eradicate lymphoma and serve those touched by this disease. LRF was formed in November 2001 by the merger of the Cure for Lymphoma Foundation (CLF) and the Lymphoma Research Foundation of America (LRFA). Both organizations were founded by lymphoma advocates who sought to use their personal experiences with lymphoma to benefit others with the disease. CLF was founded in 1994 in New York City by Jerry Freundlich, a non-Hodgkin lymphoma survivor, and his wife Barbara Freundlich. LRFA was founded in 1991 by Ellen Glesby Cohen, who lost her own battle with non-Hodgkin lymphoma in August 2000. Our goal is to change the future for everyone whose life has been affected by a lymphoma diagnosis. We are dedicated to funding biomedical research focused on the origins, treatment and identification of a cure for lymphoma; to raising public awareness of the disease; and providing support and services to people with lymphoma, their families and caregivers.
PROCURE Qu��������bec Prostate Cancer Biobank
PROCURE proposes to enable the collection and storage of standardized high volumes of prostatic tissues, blood, urine, clinical information and socio-demographic data from men undergoing prostate cancer screening and surgery across the province of Quebec and facilitate access to these resources. PROCURE will make the Biobank materials and information available to the global scientific community to facilitate the implementation of studies at an accelerated pace. Informed consent, upholding full confidentiality, will be sought from the thousands of men already undergoing prostate biopsies and radical prostatectomies in Quebec each year. Quebec is an ideal location to conduct this initiative with its diverse ethnic groups and low migration. The low migration will allow for repeated follow-up with individuals. This large collection of biospecimen and information will be used for biochemical and genetic analysis with great statistical power and will facilitate learning about the manifestation and progression of prostate cancer over time. Additional benefits include the acceleration of clinical trials, better prevention, earlier detection and diagnosis, the development of personalized medicine, more efficacious treatment, and follow-up care. The Biobank is a collaborative organization with long term partnerships established between PROCURE, the four Qu��������bec universities (McGill University, Universit�������� de Sherbrooke, Universit�������� Laval, Universit�������� de Montr��������al), with the Fonds de recherche en sant�������� du Qu��������bec and other key groups to be confirmed over time.
SCPD - Saccharomyces cerevisiae promoter database
SCPD - The Promoter Database of Saccharomyces cerevisiae
A promoter database of Saccharomyces cerevisiae. Users can explore the promoter regions of ~6000 genes and ORFs in yeast genome, annotate putative regulatory sites of all genes and ORFs, locate intergenic regions, and retrieve sequence of the promoter region. In regards to regulatory elements and transcription factors, users can provide information on transcriptionally related genes, browse matrix and consensus sequences, view the correlation between elements, observe binding affinity and expression, and look at genomewise distribution. SCPD also provides some simple but useful tools for promoter sequence analysis. Gene, consensus and matrix records may be submitted.
GASSST : Global Alignment Short Sequence Search Tool
Global Alignment Short Sequence Search Tool
Software that finds global alignments of short DNA sequences against large DNA banks. It is able to perform fast gapped alignments and works well for both short and longer reads. It has been tested for reads up to 500bp.
AcaWiki enables graduate students and researchers to share summaries of academic papers online. There are currently over 600 Creative Commons licensed summaries of academic papers on AcaWiki. Browse summaries in economics, psychology, sociology, business, or computer science among other fields. AcaWiki enables you to easily post summaries and literature reviews of peer-reviewed research. Many summaries on AcaWiki come up high on Google results. If you want to find summaries or literature reviews of peer-reviewed research, you can either browse summaries or search.
Harvard Stem Cell Institute Blood Genomics
Harvard Stem Cell Institute Blood Program
Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development.
A dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens serving imagery for more than 750 specimens contributed by almost 150 collaborating researchers from the world''s premiere natural history museums and universities. Browse through the site and see spectacular imagery and animations and details on the morphology of many representatives of the Earth''s biota. Digital Morphology, part of the National Science Foundation Digital Libraries Initiative, develops and serves unique 2D and 3D visualizations of the internal and external structure of living and extinct vertebrates, and a growing number of ''invertebrates.'' The Digital Morphology library contains nearly a terabyte of imagery of natural history specimens that are important to education and central to ongoing cutting-edge research efforts. Digital Morphology visualizations are now in use in classrooms and research labs around the world and can be seen in a growing number of museum exhibition halls. The Digital Morphology site currently presents: * QuickTime animations of complete stacks of serial CT sections * Animated 3D volumetric movies of complete specimens * Stereolithography (STL) files of 3D objects that can be viewed interactively and rapidly prototyped into scalable physical 3D objects that can be handled and studied as if they were the original specimens * Informative introductions to the scanned organisms, often written by world authorities * Pertinent bibliographic information on each specimen * Useful links * A course resource for our ''Digital Methods for Paleontology'' course, in which students learn how to generate all of the types of imagery displayed on the Digital Morphology site
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 27, 2012. The National Cancer Institute established centers in the United States and its territories for the collection and distribution of tissues, blood and secretions from patients with clinically-characterized AIDS related malignancies in 1994. The AIDS Malignancy Bank makes these tissues available to qualified investigators in the United States for research on AIDS malignancies. It is hoped that by providing access to these high-quality specimens, research in AIDS-related malignancies will be encouraged and expanded. The AMB contains formalin-fixed paraffin-embedded tissues, fresh-frozen tissues, malignant-cell suspensions, fine-needle aspirates, and cell lines from AIDS-related malignancies. The bank also contains serum, plasma, urine, bone marrow, cervical secretions, anal swabs, saliva semen and multi-site autopsy tissues from patients with AIDS-related malignancies who have participated in clinical trials. The bank has an associated database that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. Researchers pay for preparation and shipping of specimens.
University of Chicago Human Tissue Resource Center Biospecimen Banking
Biospecimen banking (BSB) involves collecting, processing, storing and distributing of human or animal tissues and body fluids of molecular grade. Human tissues and body fluids are banked in compliance with IRB approved protocols without compromising the diagnostic process and maintaining donor confidentiality (HIPAA compliant). Investigator-driven biobanking initiatives are of paramount importance at the University. The BSB provides investigators with the infrastructure to establish organ-specific biobanks in a centralized location. This arrangement allows for minimal duplication of costs, as well as establishing a working template for all tissue collections. The BSB has grown exponentially, and has a strong team of experienced personnel banking tissues for clinical trials, investigator-driven projects, and future biospecimen-based research. In addition, the BSB now collects and stores saliva, urine, blood, plasma, serum, and derivatives. The BSB is a complex process, requiring multiple interacting systems to ensure the scientific quality of procured tissue, and body fluids, patient confidentiality, adherence to good clinical practices, and regulated disbursement of biospecimens to approved investigators. They are also aware that policies, HIPAA guidelines, and federal and state tissue procurement regulations may change, and will be fully compliant with all new regulations.
A biomaterial supply resource which stores and provides ovarian, breast, pancreatic, and cervical tissue samples and fluids to cancer researchers. The UAB Tissue Collection and Banking Facility collects tissue samples for the UAB Ovarian, Breast, Pancreatic, and Cervix SPORE banks. Samples from the former Ovarian SPORE bank are available to UAB Cancer Center members via the Tissue Procurement Shared Facility, and to other researchers via the Cooperative Human Tissue Network.
A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.
The Childhood Brain Tumor Foundation (CBTF), an all-volunteer organization, was founded in 1994 by families, friends and physicians of children with brain tumors. Our mission is to raise funds for scientific research and heighten public awareness of this most devastating disease and to improve prognosis and quality of life for those that are affected. Founded and incorporated in Virginia, relocated to Maryland in 1998, the Foundation (a 501(c) (3), strives to meet the goals of our mission. Friends, families, and physicians brought CBTF together and are dedicated to serving the needs of families and children with brain tumors, in hopes of improving the quality of life and find cures for pediatric brain tumors. Annually, CBTF funds basic science or clinical research for pediatric brain tumors; conferences and other programs. We provide informational materials on our website and mail other information (nationally and internationally) upon request. The Childhood Brain Tumor Foundation (CBTF) has funded state-of-the-art research and supported conferences for pediatric brain tumors over the past 17 years. Grants submissions are reviewed thoroughly by our dedicated renown team of scientific advisors to ensure that CBTF selects the highest quality research for pediatric brain tumors. Each year, we receive so many outstanding applications and it is through the support of private and public donations that this is all possible. With your support, together, we will strive to find a cure for children''s brain tumors.
Children''s Brain Tumor Foundation, a non-profit organization, was founded in 1988 by dedicated parents, physicians and friends. Our mission is to improve the treatment, quality of life and the long term outlook for children with brain and spinal cord tumors through research, support, education, and advocacy to families and survivors. Knowledge is critical for families to access expert care and ensure quality of life. Our free publication A Resource Guide for Parents of Children with Brain and Spinal Cord Tumors is now in its fourth edition, and is full of practical information to sort out the complexities of medical procedures, interruptions in school and social life, and uncertainty about the future. CBTF co-sponsors conferences for families, survivors and health care professionals, offering the latest information about research, treatments and strategies for living. Only scientific research will identify the causes and lead to effective treatments for brain tumors in children. CBTF funds cutting-edge research by scientists at top academic medical centers. Their discoveries hold the promise of improving the lives of affected children today and discovering the means of prevention for future generations. CBTF has awarded over $5 million in grants for basic and clinical research related to pediatric brain and spinal cord tumors. Also, over $625,000 has been given out in Quality of Life Grants.
The Danish Multiple Sclerosis Center (DMSC) comprises the MS Clinic and the MS Research Unit including the Neuroimmunology Laboratory. The main research areas are: clinical research including investigator driven trials of new therapies in MS, neuroimaging, neuropsychology and rehabilitation; pathogenesis of MS with focus on immunology, biomarkers and treatment response; as well as studies in the pathology and genetics of MS. DMSC is part of the Department of Neurology, Rigshospitalet, and the Faculty of Medicine, University of Copenhagen. The research facilities are located in sections 6311 and 9392 at the hospital site. DMSC constitutes one of the European MS Centers of Excellence and has extensive collaboration with institutions in Denmark, in other European countries, as well as overseas. DMSC is supported by both national and international grants.
Central repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway.
This is a wiki on diagnostic radiology. Major topics include General Types of Radiology, Imaging Modalities, Radiography, CT scanning, Sonography, MRI Magnetic Resonance Imaging, Nuclear medicine, Normal Radiological Anatomy, Imaging of Specific Anatomic Regions, Diagnosis of Specific Anatomic Regions, Imaging in Pediatric Radiology, and External resources. Radiology is the branch of medical science dealing with medical imaging. It may use x-ray machines or other such radiation devices. It also uses techniques that do not involve radiation, such as MRI and ultrasound. The medical information provided on Wikibooks is, at best, of a general nature and cannot substitute for the advice of a medical professional (for instance, a qualified doctor/physician, nurse, pharmacist/chemist, and so on). Wikibooks is not a doctor.
To meet the strategic objectives of ongoing and future scientific and medical research, Biostor Ireland designed and constructed a technologically advanced repository for storage and distribution of biological materials. It offers secure, certified realtime biostorage of valuable biological materials for medical / scientific research, healthcare, medical device, pharmaceutical and biopharmaceutical sectors. This facility has been inspected by the Irish Medicines Board (IMB) and complies with the requirements of the EU Directive 2004/23/EU for storage and distribution of Human Tissues and Cells. Biostor also complies with the principals of current Good Manufacturing Practice (GMP), FDA requirements 21 CFR Part 1271 and ISBER (International Society of Biological and Environmental Repositories) Best Practices for Repositories. Outsourcing biostorage makes sense * Increase Workspace * Reduce Storage Costs * Peace of Mind * Expand your Business * Reduce Labor Costs * Uniform Maintenance * Improve Productivity * Tailored Storage * Delegate
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. In the Open HHS Blog, Chief Technology Officer, Todd Park, writes about harnessing the power of data, technology and innovation to improve the health and welfare of the nation.
An ontology for describing the nature of reference citations in scientific research articles and other scholarly works, both to other such publications and to Web information resources, and for publishing these descriptions on the Semantic Web. Citation are described in terms of the factual and rhetorical relationships between citing publication and cited publication, the in-text and global citation frequencies of each cited work, and the nature of the cited work itself, including its publication and peer review status. CiTO is useful both for the annotation of bibliographic reference lists and for the visualization of citation networks. CiTO is written in the Web Ontology Language OWL, uses the namespace http://purl.org/net/cito/, and is available from http://purl.org/net/cito/. This site uses content negotiation to deliver to the user an OWLDoc Web version of the ontology if accessed via a Web browser, or the OWL ontology itself if accessed from an ontology management tool such as Protege 4 (http://protege.stanford.edu/). Collaborative work is under way to harmonize CiTO with other ontologies describing bibliographies and the rhetorical structure of scientific discourse.
Privately held company that develops and produces antibodies, ELISA kits, ChIP kits, proteomic kits, and other related reagents used to study cell signaling pathways that impact human health., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Bone Bank Allografts is the distributor of the SteriGraft line of high quality bone and soft tissue allografts to medical professionals. The company has been in existence for over 13 years and has helped doctors and their patients with over one hundred thousand successful transplantations. Bone and soft tissue allografts in the SteriGraft line are validated to a sterility assurance level (SAL) of 10(-6) in accordance with ISO 11137-2 Method 1. Bone Bank Allografts was founded in 1993 in response to a growing need for allograft tissue in South Texas. Since 1993, Bone Bank Allografts'' distribution network has grown to cover Texas, the country and the globe, fulfilling surgical needs for allograft tissue in more than 175,000 successful transplantations. Located in San Antonio, Texas, Bone Bank Allografts is dedicated to a just, equitable and fair distribution of cadaveric tissue to surgeons, hospitals, surgicenters and dental offices. Over the years, our customers have come to rely on the superior quality of our tissue products as well as the unmatched service of our well trained, certified Tissue Bank Specialists (CTBS) and our knowledgeable distribution staff. With accreditation from the American Association of Tissue Banks (AATB), registration with the U.S. Food and Drug Administration (FDA) and compliance with the FDA''s Good Tissue Practices, Bone Bank Allografts continues to pursue our mission: To enhance the quality of patient care by providing safe, high quality allograft tissues to health care professionals for transplant and research. Most recently, Bone Bank Allografts has taken the next important step in tissue banking by developing a powerful partnership with Texas Human Biologics (THB) in order to process donated human tissue.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. Gray Matters is a radio series on brain topics that has been produced since 1994 by Public Radio International in association with the Dana Alliance. More than 25 programs have been created on topics ranging from stress, neuroethics, learning throughout life and sports, fitness and the Brain. Dana Alliance members serve as advisers to Gray Matters programming and are interviewed during the programs. The transcripts are also available.
National Database for Autism Research (NDAR)
National Institute of Mental Health Data Archive
The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI).
Allograft Innovations was formed in 2006 to facilitate quality biologic grafts for surgery. We are committed to providing quality tissue to enhance patients'' health, mobility and quality of life nationwide and across the globe. Our goal is to provide the safest, most clinically effective allografts available. The health of tissue recipients is top priority to us, and we take every possible step to ensure safety and integrity during all processes. Allograft Innovations partners with federally designated OPO''s (Organ Procurement Organization), as well as Tissue recovery agencies that comply with all 21 CFR 1270 and 1271 FDA Standards, and have achieved AATB accreditation.
An open source and domain independent Workflow Management System ����?? a suite of tools used to design and execute scientific workflows and aid in silico experimentation. Taverna Workbench now has support for service sets, offline workflow editing, workflow validation, improved workflow run monitoring, and the pausing and canceling of workflow runs. The command line tool allows you to run workflows outside of the workbench and is available as a stand-alone download or bundled with the Taverna Workbench 2.2.0 download. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick execution of workflows from a terminal. Taverna 2.2.0 includes * Copy/paste, shortcuts, undo/redo, drag and drop * Animated workflow diagram * Remembers added/removed services * Secure Web services support * Secure access to resources on the web * Up-to-date R support * Intermediate values during workflow runs * myExperiment integration * Excel and csv spreadsheet support * Command line tool
NIDDKConsortium Interconnectivity Network
THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO).
MindSpec: Informatics for Neurodevelopmental Conditions
MindSpec - Informatics for Neurodevelopmental Disorders
MindSpec is a nonprofit organization that utilizes innovative bioinformatics strategies to accelerate research on common neurodevelopmental disorders. With our research we hope to foster discovery and development of treatments that alleviate the symptoms of affected individuals. Our core mission at MindSpec is to advance research on neurodevelopmental conditions. Founded in 2006, MindSpec is an independent, non-profit research organization established to facilitate the discovery of a cure for autism. Although the initial focus was autism, we have gradually expanded our scope to other neurological disorders. We develop bioinformatics strategies using current information technology platforms to build disease specific databases. At MindSpec we place a strong emphasis on translational research, that is, closing the gap between basic science discoveries and practical treatments with the potential of benefiting people who have autism. Goals: * Build an integrated, up-to-date, relevant, searchable resource on autism, AutDB. * Build a community of scientists, practitioners, educators, policymakers and people affected by autism to share and disseminate knowledge of autism. * Identify gaps in autism research around the world. * Identify priority areas in autism research based on real-world needs. * Build an autism dictionary and digital information library. * Address cultural differences in treatments for autism, a social disease. * Build knowledge about autism for immediate use.
Qiqqa is a free reference management tool that provides all the tools you need to manage your documents and notes effectively, visualize your ideas, and find insights you would have missed otherwise. Engineered by academics, its mission is to make your research life easier. Qiqqa allows users to annotate PDF''s, assign tags, share documents and offers cloud storage for a nominal fee. We help academics, researchers, and professionals manage all their PDFs and get more out of them, with our award winning Qiqqa software. * PDF management, OCR, reading, annotation * Unique tools to understand and discover * Cloud sync, cite, and much much more * Free. Trusted by academia and industry for all five stages of the knowledge lifecycle. Add all your papers, and it helps you do all the rest, quicker. # Organize # Discover # Review and Understand # Collaborate # Create
The Guthy-Jackson Charitable Foundation is dedicated to funding basic science research to find answers that will lead to the prevention, clinical treatment programs and a potential cure for Neuromyelitis Optica (NMO) Spectrum Disease. The decision to create our Foundation came from a personal family crisis. Our daughter was officially diagnosed with NMO in June 2008. Since that time, we have met with many clinicians and researchers in order to understand what this means for our beautiful daughter and our family. Additionally, we have gathered and read every piece of information and NMO research article that is available on the Web. We are now beginning to understand that NMO is not only considered an orphan disease, but that very little research is available. We met with the All Greater Good Foundation in early July 2008 when it became clear that there is little-to-no funding available to research this rare and often misunderstood disease. We joined hands with the All Greater Good Foundation to immediately begin our work, and thus, The Guthy-Jackson Charitable Foundation was born. The Guthy-Jackson Charitable Foundation is dedicated to funding biomedical research in the search to understand the pathophysiology and biochemistry of NMO Spectrum Disease. It is our greatest hope that together we will reverse the effects of NMO and eventually cure this disease.
Louisiana Organ Procurement Agency - LOPA
The Louisiana Organ Procurement Agency (LOPA) is the federally-designated organ procurement organization for the State of Louisiana. The agency focuses on educating the medical community and the general public about organ and tissue donation issues, working with families through the donation process, recovering donated organs and tissue, and placing the organs and tissue for transplant. Our mission is to save and enhance lives through organ and tissue donation. We envision a world in which no one suffers due to a lack of donor organs or tissues. LOPA has its main office in Metairie, with regional offices in Lafayette, and Shreveport. Additionally, LOPA has representatives in Baton Rouge, Alexandria, Lake Charles, and Monroe.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches. It includes ''resource_type'', ''area of research'', and ''activity''. It is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The biositemaps site is no longer available but the biomedical resource ontology is still available via bioportal Biomedical Resource Ontology (BRO).
University of Pennsylvania Alzheimer's Disease Center
A national Alzhiemer's disease research center funded by the National Institute on Aging, and the research arm of the Penn Memory Center.
EDAR study: biomarkers for Alzheimer's disease
Early Diagnosis of AD and as marker of treatment response
Early Diagnosis of AD and as marker of treatment response (EDAR study)
A European collaborative study to develop and validate new biomarkers for Alzheimer's disease. Central in the project is the development of an assay for the measurement of beta amyloid oligomers in cerebrospinal fluid and plasma. In order to validate the assay for beta amyloid oligomers, cerebrospinal fluid and plasma will be repeatedly collected in subjects with Alzheimer's disease, other types of dementia, mild cognitive impairment, and control subjects.
The Cancer Diagnosis Program of the National Cancer Institute (NCI) initiated the Cooperative Human Tissue Network (CHTN) in 1987 to provide increased access to human tissue for basic and applied scientists from academia and industry to accelerate the advancement of discoveries in cancer diagnosis and treatment. This unique resource provides remnant human tissues and fluids from routine procedures to investigators who utilize human biospecimens in their research. Unlike tissue banks, the CHTN works prospectively with each investigator to tailor specimen acquisition and processing to meet their specific project requirements. Because the CHTN is funded by the NCI, the CHTN is able to maintain nominal processing fees for its services. The CHTN is comprised of five adult divisions and one pediatric division. Each of the adult divisions coordinates investigator applications/requests based upon the investigator's geographic location within North America. The Pediatric Division manages all investigators who request pediatric specimens only. The CHTN divisions share coordination for requests from outside North America. The CHTN divisions work both independently with individual investigators and together as a seamless unit to fulfill requests that are difficult to serve by any single division. The CHTN's unique informatics system allows each division to effectively communicate and network the needs of its investigators to all CHTN divisions. The Network as a whole can then help fulfill an investigator's request. Biospecimens from surgeries, autopsies and other routine procedures: Malignant, Benign, Diseased, Normal, Biofluids (urine, serum, plasma, buffy coat) High quality specimens at LOW processing fees: Fresh, Frozen, Floating in fixative, RNAlater, Paraffin embedded or and/or unstained slides, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
UMass Cancer Center Tissue and Tumor Bank
The UMass Cancer Center Tissue and Tumor Bank is a dynamic tissue procurement service: Collection, Storage, Annotation, and Distribution of Human Biologic Specimens. Our goal is to facilitate basic science, clinical research and translational studies by providing researchers with the ability to obtain and study human tissues using a dynamic collection, storage, annotation, and distribution service. * Fresh, diseased tissue is collected and processed immediately after surgery. ** When possible, surrounding healthy tissue is collected as a matched normal control. ** Anonymous, de-identified clinical and pathologic data are linked to the specimens in a secure database. * Bone marrow and blood specimens are collected and available as fresh cell isolates, frozen cell isolates or unprocessed. * A variety of services are available including routine histology, fresh tissue for cell culture, frozen sections, as well as DNA and RNA extraction. * Specific study needs can be met. * Consultation during study design is available and recommended. Contact Us * Assistance in the IRB approval process is offered. ** New: IRB approval is required only if you need identifiable private clinical information and/or patient follow-up for your study. The UMass Cancer Center Tissue and Tumor Bank is an open access biorepository. Specimens are available to investigators both internal and external to UMass. The Tumor Bank ships specimens to researchers worldwide. Please contact us to determine if we have specimens that meet your research needs.
Epilepsy Research Ireland is a non-profit organization (Charity CHY17527), run by a group of volunteers, who are dedicated to find cure for epilepsy by raising awareness and money for research. We can say cure now with much more confidence than we could even 10 years ago because recent advances in genetics, brain imaging and drug therapy, all hold out the promise of that holy grail the cure. We can also say with confidence that you can be part of that push by participating in this new foundation since we have collaborations with doctors and scientists all over Europe, the US and Australia, all of whom share the same goal. Epilepsy research, conducted by Epilepsy Research Ireland, is essential and will deliver benefits across the board. Research planned and already underway by Epilepsy Research Ireland will help develop and improve clinical skills; it will provide a knowledge base to develop new ways to manage and treat epilepsy; it will help in the evaluation of new medical advances. Ultimately we can improve the quality of care and provide greater understanding, better and more accurate diagnosis and more tailored treatments. Ireland is uniquely well-positioned, given its relatively homogenous population to make the goal, of making real discoveries in epilepsy research that will directly improve the lives of people with epilepsy, a realistic one.
ProFunc - prediction of protein function from 3D structure
ProFunc: Analysis of a protein''''s 3D structure to help identify its likely biochemical function
The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein' '''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time.
The Crimson Biospecimen Core prospectively collects discarded clinical materials matching investigator-defined criteria. Queries are run against real-time data on recently received clinical samples, including ICD.9 codes and results of clinical laboratory testing. Studies using the core must either (1) have an IRB-approved protocol for discarded clinical materials and anonymized information or (2) a protocol to allow collection of discarded samples from patients consented for their study. Collected samples may be additionally processed, aliquotted, or tested per the menu of tests available within the BWH and MGH Clinical Laboratories and Partners Genomics Center. Services: * Collection of discarded clinical specimens including serum, plasma, CSF, urine and microbiological isolates for IRB-approved studies. * Processing or additional clinical testing of collected materials. * Ability to receive consented patient samples for processing and clinical testing. * Online interface to manage collected sample inventories, associated test results, and study users/workgroup per IRB-approval.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A pan European network for virtual tissue archiving aimed at supporting clinical trials, biomarker research, tissue microarray analysis and virtual slide based education. NIVTA has state-of-the-art digital scanning systems including an Aperio CS system, Aperio OS system (one of only two currently available in Europe) and a Hamamatsu system with fluorescent scanning capability.
An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy' '''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket.
The National Psoriasis Foundation (NPF) is a non-profit, voluntary health agency dedicated to finding a cure for psoriasis and psoriatic arthritis and eliminating their devastating effects through research, advocacy and education. Founded in 1966, the Psoriasis Foundation has evolved to become the leading patient advocacy group for the 7.5 million Americans living with psoriasis and psoriatic arthritis. As emerging research continues to demonstrate the serious, systemic effects of these chronic autoimmune diseases, our highest priority is to find a cure. Guided by our five year-strategic plan, we are moving towards this goal with an integrated approach that leverages the work of members, health care providers, advocates and scientists in four critical areas: * Research: ** Directly supporting the most promising early-stage research and emerging researchers. ** Hosting the world''s largest bank of psoriasis DNA samples. * Advocacy: ** Advancing a public policy agenda to secure more federal funding for psoriasis research. ** Improving access to care for patients. * Education: ** Providing extensive patient education. ** Keeping health care professionals up to date on psoriasis treatment. * Connection: ** Online communities, support networks, mentorship programs. ** Building a grassroots network of volunteers and advocates. * Leadership: ** A volunteer Board of Trustees steers the strategic direction of the National Psoriasis Foundation. ** Our Medical Board, made up of leading national psoriasis experts, provides medical guidance, leadership and advocacy. ** An executive staff of seasoned non-profit leaders drives the organization to achieve its strategic plan goals.
A parallel short read assembler for large genomes using de Bruijn graphs.
Provides an comprehensive workflow of analyzing data from plant microRNA (miRNA) deep sequencing.
Science Care''s whole body donation program supports medical research, training and professional education, which provides enormous benefits to humankind. Given the increasing advancements in medical technologies, donation is of greater importance than ever. A life-affirming choice, donation is also a highly individual decision. In every way possible, Science Care honors that decision by adhering to the strictest guidelines and providing the most compassionate care. Science Care was founded in 2000 with the vision to become the world''s leading whole body donor program. Under the leadership of James Rogers, Founder and CEO, Science Care has accelerated research on many fronts leading to the development of new medical devices and safer, more effective treatments for patients. At Science Care, we provide the opportunity to make a final choice with control and dignity. Our donors know that their last act was donating to the welfare of humankind, and their gift provides a lasting legacy.
St. James Hospital Cryobiology Laboratory Stem Cell Facility
St. James''s Hospital Cryobiology Laboratory Stem Cell Facility
St. James''s Hospital Stem Cell Facility
The Cryobiology laboratory is a stem cell processing laboratory, preparing clinical grade haemopoietic (bone marrow or peripheral blood) stem cells for transplant. The Laboratory supports the National Adult Stem Cell Transplant Programme based in St James Hospital treating Leukemia and related disorders. Approximately 100 Transplants are carried out annually. The Tissue Establishment is part of a network of hospitals carrying out stem cell transplant. Stem cells are imported from abroad and exported world wide for stem cell transplantation. The Laboratory is a GMP Tissue Establishment and is licensed by the Irish Medicines Board to process cells under the EU tissue directive.
Scientific focus articles and general resources for scientists within the pharmaceutical and biotechnology industries that take a comprehensive look at the industry and the tools that are in use to speed drug discovery and development. Resources include a forum, courseware, and a listing of professional societies, associations and companies/organizations. In addition to features on classical drug discovery, NetSci will address biotechnology, genomic research, and materials design as well as subjects suggested by readers. Network Science has collected an extensive list of professional societies and associations and companies/organizations that are a part of the world-wide efforts in drug discovery and development. These organizations were selected based upon the fact that they contribute to pharmaceutical research and development and healthcare throughout the world. The forum for experts to explore and discuss current applications of science and technology with their colleagues world-wide, permits publication of scientific data without the delays inherent in traditional printed media and encourages immediate dialog using hypertext (a contextual linkage of related information sources), multimedia, interactive electronic feedback forms, and automatic electronic mail connections which are not available within any other media. CourseWare provides a collection of materials which examine the pharmaceutical industry and the use of technology in drug discovery. Topics range from an introduction to the drug development process to an in-depth examination of the tools and techniques used in pharmaceutical research and development. If your would like to see a topic added to this collection, or know about companies and products that you feel would be of interest to the readers, would like to add your organization to the list or correct the listing that is on-line, please contact us.
National Alliance for Medical Image Computing
The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary team of computer scientists, software engineers, and medical investigators who develop computational tools for the analysis and visualization of medical image data. The purpose of the Center is to provide the infrastructure and environment for the development of computational algorithms and open-source technologies, and then oversee the training and dissemination of these tools to the medical research community. Electronic resources provided by NA-MIC include software, data, tutorials, presentations, and more.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 7, 2022. Consortium of 19 brain banks across Europe with an aim to harmonize neuropathological diagnostic criteria and develop gold standards for quality, safety and ethics standards for brain banking. BrainNet Europe also contributes to research on rare diseases, such as: Pick''s disease or other rare forms of dementia, as well as to questions after the events in the aging brain. Anyone can be a donor - irrespective of disease of the central nervous system or not, because for research purposes, one does not only need tissue samples from ill donors, but also from healthy ones for comparison.
Spliced Transcripts Alignment to a Reference (STAR)
Spliced Transcripts Alignment to Reference
Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
Essential Tremor Centralized Brain Repository
Finding a cure for any neurological disorder begins with the scientific study of the disorder''s causes, processes, and development in the brain. For essential tremor (ET), rigorous study of this kind had not been undertaken until 2003, when the Essential Tremor Centralized Brain Repository (ETCBR) was established at Columbia University. For the past five years, brain tissue from ET donors has been collected, processed and compared alongside age-matched control brains at the ETCBR, and already several significant findings have been made. However, there is still much to learn and a severe shortage of ET brains for scientific study. If you have been diagnosed with essential tremor, donating your brain tissue in the hours immediately after your death is of utmost importance in providing crucial information about what causes ET. Direct analysis of the shape and number of nerve cells and their content will provide medical researchers with the information they need in order to understand this complex illness. By advancing our medical knowledge of ET, the gift of brain tissue is a central piece of the puzzle in the search to develop better treatments and find a cure.
Through the South Dakota Lions Eye Bank, donors can provide the gift of sight and health through the donation of bone, connective tissue, heart valves, veins, skin, and corneas. The option of donation is available to both men and women, up to the age of 95. Since 1990, the South Dakota Lions Eye Bank has restored sight to over 5500 people world wide. In recent statistics the South Dakota Lions Eye Bank has transplanted 2217 corneas since 2001; 1237 transplanted in the United States and 980 transplanted overseas. It is the fondest hope of the South Dakota Lions Eye Bank that you will become an eye, tissue and organ donor and pass along to someone the greatest gift of all, Life.
Iowa State University Neuroscience Program
The Neuroscience Program at Iowa State University has a philosophy based on the balanced combination of mentoring, general curriculum and frontier collaborative research to teach graduate students essential theoretical, research, teaching, writing and presentation skills and to prepare students for the competitive environment in academia and industry. The program reflects the structure of contemporary neuroscience which has become a diverse and inter-disciplinary field. Students of diverse educational, ethnic and national backgrounds are encouraged to apply to the program. Participating Departments in Neuroscience * Animal Science * Biochemistry, Biophysics and Molecular Biology * Biomedical Sciences * Chemical and Biological Engineering * Chemistry * Computer Science * Genetics, Development and Cell Biology * Kinesiology * Psychology
Estonian Genome Center University of Tartu
The Estonian Biobank is the population-based biobank of the EGCUT. The project is conducted in accordance with the Estonian Genes Research Act and all participants have signed a broad informed consent form (www.biobank.ee <http://www.biobank.ee/> and Metspalu 2004, Drug Dev. Res.). As of December 2011, the biobank contains 51,515 participants (gene donors). The database of genotypic, phenotypic, health and genealogical information represents about 5% of Estonia''s adult population, and is the largest cohort ever gathered in Estonia. The age, sex and geographical distribution of this cohort reflect the structure of the adult population in Estonia. The database enables to conduct research in order to find links between genes, environmental factors, lifestyles and complex diseases or other traits. Active use of the biobank has started and although the first users are researchers all over the world with hundreds of different projects currently underway, industry is also interested. At the international level, the EGCUT will join the BBMRI follow-up program (ERIC) and through this channel provide service (biobanking, genotyping, sequencing and data analysis) for the centers in Europe who need it. Currently, the first follow-up study is underway and the molecular information of the cohort will be increased. For example, we have over 12 000 DNA samples analyzed by high density genotyping arrays and over 10 000 plasma samples analyzed by NMR scans, over 1000 individuals with RNA expression arrays, 2000 individuals with clinical laboratory analysis (over 40 tests) and over 60 full genomes are under deep sequencing. The infrastructure of the EGCUT includes a laboratory for DNA genotyping and next generation sequencing all based on Illumina platforms (HiScanSQ, HiSeq2000 and robotics), an IT unit (databases) with required computing power and storage space (1.2PB), data analysis team (bioinformatics and statistical genetics) and last but not least, a patient recruitment unit (health records, lifestyle and environmental information and biological samples ����?����������?? DNA, plasma and WBC from all 51515 gene donors). This is all located on 1000m2 in a brand new laboratory building, Riia str 23, Tartu, Estonia.
Cureline BioPathology: Research Histology Laboratory
Cureline BioPathology is a research histology laboratory providing high-quality human and animal tissue processing, preparation and analysis. In collaboration with Cureline, Cureline BioPathology offers a complete portfolio of services in human tissue research, including human tissue acquisition, biospecimen storage, tissue processing and comprehensive tissue analysis using special stains and immunohistochemical methods. The laboratory was founded in San Francisco Bay area by Cureline, Inc., to leverage already established relationships with clinical sites and biotechnology companies. Cureline has extensive experience in human tissue procurement, preservation and biospecimen management, and has been providing effective human tissue research services to pharmaceutical and biotechnology clients since 2003. Our experienced and motivated team is dedicated to providing support to academia and industry clients in all aspects of human and animal tissue processing, target profiling, antibody cross-reactivity studies, and toxicology.
A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.
Feinstein Institute for Medical Research
The Feinstein Institute for Medical Research is the research branch of the North Shore-Long Island Jewish Health System. Biomedical research has been a vital aspect of its two academic medical centers North Shore University Hospital and Long Island Jewish Medical Center since their establishment in the early 1950''s. Through its connection to the hospital system, the Institute bridges the gap between biomedical research and patient care, accessing hundreds of thousands of patients in the health system''s 15 hospitals, four long-term care facilities, three trauma centers, six home health agencies and dozens of outpatient facilities. Institute scientists collaborate with clinicians throughout the system to shed light on basic biological processes underlying disease. This knowledge is used to develop new therapies and diagnostics. Currently, more than 800 scientists and investigators are conducting research in oncology, immunology and inflammation, genetics, psychiatry, neurology, pediatrics, surgery, urology, obstetrics/gynecology and many other specialties. In 2008, the Feinstein received funding from the National Institutes of Health in excess of $28 million, and an additional $10 million from other federal sources. Total annual research funding from all sources exceeded $44 million in 2008. We stand at the threshold of an extraordinary time in medicine. Over the last 100 years, biomedical science has progressed very rapidly. Advances coming from the integration of genomics, proteomics and bioinformatics into the biomedical toolkit hold the promise that this transformation will continue well into the 21st century. The Feinstein Institute for Medical Research is a growing force in research innovation, education and progress.
Roswell Park Comprehensive Cancer Center
Cancer research and treatment center located in Buffalo, New York. Founded by surgeon Roswell Park in 1898, the center was the first in the United States to specifically focus on cancer research. The center is usually called Roswell Park in short.
Infrastructure for sharing cardiovascular data and data analysis tools. Human ExVivo heart data set and canine ExVivo normal and failing heart data sets are available. Canine hearts atlas and human InVivo atlases are available.
Intergovernmental organisation funded by public research money from its member states in Europe. Groups and laboratories perform basic research in molecular biology and molecular medicine, training for scientists, students and visitors. Provides development of services, new instruments and methods, data and technology in its member states.
WikiHealthCare is The Joint Commission''s interactive forum for health care professionals. It is designed to enable and encourage discussion and collaboration among all users for the purpose of improving health care quality. While The Joint Commission provides the forum, users of the site control its content. The WikiHealthCare Quality Improvement forum is a collaborative network for health care professionals, researchers, and other health care stakeholders. Within this forum, you can freely exchange information, describe your implementation experiences and create and share performance improvement solutions. Registered members of the WikiHealthCare community are free to use this forum to create new web pages, initiate blogs, and dialogue with other members of the community.
WHO International Clinical Trials Registry Platform
International Clinical Trials Registry Platform
International Clinical Trials Registry Platform (ICTRP)
Public database of information about all clinical trials involving humans, this global initiative provides a single point of access to information about ongoing and completed clinical trials. It contains the trial registration data sets made available by data providers around the world meeting criteria for content and quality control. It also aims to: * To improve the comprehensiveness, completeness and accuracy of registered clinical trial data * To communicate and raise awareness of the need to register clinical trials * To ensure the accessibility of registered data * To build capacity for clinical trial registration * To encourage the utilization of registered data * To ensure the sustainability of the ICTRP The mission of the WHO International Clinical Trials Registry Platform is to ensure that a complete view of research is accessible to all those involved in health care decision making. This will improve research transparency and will ultimately strengthen the validity and value of the scientific evidence base. The registration of all interventional trials is a scientific, ethical and moral responsibility. The ICTRP: * Publishes the ICTRP Search Portal * Supports the WHO Registry Network * Supports countries and regions wanting to establish WHO-compliant clinical trial registries or policies on trial registration.
An accredited cord blood bank and stem cell bank in Europe. Services offered include family cord blood banking, public banking, directed allogeneic transplantation, umbilical cord tissue banking and HLA typing.
NEWT is the taxonomy database maintained by the UniProt group. It integrates taxonomy data compiled in the NCBI database and data specific to the UniProt Knowledgebase. Browse by hierarchy, List all, or Complete proteomes. Organisms are classified in a hierarchical tree structure. Our taxonomy database contains every node (taxon) of the tree. UniProtKB taxonomy data is manually curated: next to manually verified organism names, we provide a selection of external links, organism strains and viral host information. Species with protein sequences stored in the UniProt Knowledgebase are named according to UniProt nomenclature. We endeavour to maintain a list of manually curated species names for which protein sequence data is available. In particular, we have adopted a systematic convention for naming viral and bacterial strains and isolates. Links to external sites are chosen by the UniProt taxonomy team and show pictures and various scientific data of interest (taxonomy, biology, physiology,...).
CFC International INTERNATIONAL REGISTRY
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016.
Systems Biology for Micro-Organisms Database
Systems Biology of Micro-Organisms Database
SysMO-DB is a project that is creating a web-based platform, and tooling, for finding, sharing and exchanging Data, Models and Processes in Systems Biology. It was designed to support the SysMO Consortium (Systems Biology for Micro-Organisms), but the principles and methods employed are equally applicable to other multi-site Systems Biology projects. All code is open source and available for download. SEEK, a component of SysMO-DB, is a private community collaboration and asset sharing platform for Systems Biology models, data and protocols serving 120 research institutions throughout Europe. SEEK is the main web-based access point to the system and provides an access control layer to enable researchers to restrict access to collaborators, colleagues or other individuals until they are ready to share with the whole consortium or the wider community. The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that: * facilitates and maximizes the potential for data exchange between SysMO research groups; * maximizes the ''shelf life'' and utility of data generated by SysMO; * provides an integrated platform for the dissemination of the results of the SysMO projects to the scientific community; and * facilitates standardization of practices in Systems Biology for the interfacing of modeling and experimentation. We follow several key principles: * exploit what is already available, both within the consortium and outside it, and do not reinvent; * identify the least we can do to make a benefit and do this incrementally. SysMO-DB will soon be opening it up to the wider scientific community, but for now it is currently only available for those within the SysMO consortium.
Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae
While many data sharing programs exist worldwide, widespread sharing of raw data has not yet won across-the-board acceptance in the scientific community, and the very existence of all these databases makes the approach fractured at best. The Data Sharing Project, launched last year by University of California-San Francisco Professor Michael Weiner, has two goals: One is to make widespread raw data sharing a reality initially in the realm of medicine through creation of a repository system accessible to all researchers; the second goal is to foster broad scientific support for this move and its adoption in other fields of research. With major projects such as the Human Genome Project demonstrating the tremendous scientific breakthroughs made possible by data sharing and with the decline of technological barriers impeding such efforts, the time has come to work to achieve widespread sharing of raw data worldwide. The Data Sharing Project proposes to further this goal initially in the field of medicine by working to create a raw data sharing program that will serve as a model to other disciplines attempting to make their own way in this arena. The Northern California Institute for Research and Education (NCIRE) together with the University of California-San Francisco and support from the Michael J. Fox Foundation is now in the process of canvassing the scientific community to analyze the best possible data sharing program and practices to establish in the field of medicine.
Database of neurobehavioral and physiological data of adult zebrafish models, complementing the available repositories for zebrafish genetic information, by providing a dynamic, open-access data repository of comprehensive, curated collection of results from zebrafish neurobehavioral experiments. As of May 2012, it contains over 4,500 experimental results, from over 75 unique physiological and behavioral tests and 330 different drug treatments. ZNP incorporates validated and curated data from work published in this field, to improve the accessibility of current knowledge to researchers interested in using adult zebrafish models. Overall, this program will allow investigators to rapidly review data, to direct their research using these models. Data and protocol submissions are now being accepted.
Visualization and Analysis of Microbial Population Structure
A publicly-accessible website to measure and visualize similarities and differences between molecular profiles of complex microbial communities. The project includes visualization tools such as heat maps that simultaneously compare the taxonomic distributions of multiple datasets and 3-D charts of the frequency distributions of 16S rRNA tags. Analytical tools include Chao diversity estimates and rarefaction curves. As a service to the community, researchers have the opportunity to upload their own data to the site for private viewing with the full range of data and analysis tools. Public data can be downloaded for further analysis locally.
Microarray and Gene Expression Data Ontology
An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.
Arnold Arboretum of Harvard University: Weld Hill Microscopy Lab
Microscopists at Weld Hill will find a range of tools from the simple hand lens to the confocal microscope for 3-D reconstructions.
Free online electrocardiography (ECG) course and textbook via a wiki where anyone can contribute and changes are supervised by physicians. Learn from cases and examples. It designed for medical professionals such as cardiac care nurses and physicians. All content is freely accessible. The information on this site should NOT be used as a substitute for the advice of an appropriately qualified and licensed physician or other health care provider. For questions like these we advise you to contact your physician.
An open-access portal for discussion, information sharing, and collaboration among those working to advance the rapidly developing field of clinical research informatics (CRI). We hope that you find the content useful and that you use our interactive features to contribute your knowledge and experience for the benefit of our community. Research Informatics.org Contents include: * CRI Initiatives * CRI News * CRI Events * CRI Resources * CRI Wiki * CRI Forum * CRI Blog
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. LifeTek is a full service International Tissue Bank, with recovery and processing partners in the United States, Spain and Mexico. Our goal is to provide safe, quality allograft implants, therefore serving donor families, physicians and recipients. Following regulations established by state and federal agencies, including the United States Food and Drug Administration, specific steps are taken to ensure donor suitability, including serologic testing performed by CLIA certified laboratories. LifeTek aseptically process tissues in Class 100 Cleanrooms, significantly reducing the risk of airborne contaminants. Equipment and reagents used are sterilized in steam autoclaves. Grafts are further processed and sterilized using Clearant Technology. LifeTek allografts are provided either freeze-dried or frozen. Freeze-dried allografts are stored at ambient temperatures, while frozen allografts are stored at -40 degrees C or colder. Freeze-dried allografts are provided with a maximum of two years expiration, frozen allografts are provided with a maximum of five years expiration.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17,2021. Manufacturer of allograft tissue grafts in the United States in the ortho-biologics field of medicine. They develop new products for the patients they serve, including the UltraGraft non-irradiated & sterile line of allograft tissue implants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run.
Podcast, hosted by Dr. Ginger Campbell, featuring the latest books about neuroscience as well as interviews with leading scientists from around the world. In this podcast, she shares recent discoveries from the world of neuroscience in a way that people of all backgrounds can enjoy. Dr. Campbell is an experienced emergency physician with a long-standing interest in mind-body medicine, the brain, and consciousness. She believes that understanding how the brain works gives us insight into what makes us human. She is also committed to showing how the scientific method has unraveled many long-standing mysteries. Brain Science Transcripts are also available.
Software program to compute highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs.
Foundation for the National Institutes of Health
A public charity whose mission is to support the NIH in its mission to improve health, by forming and facilitating public-private partnerships for biomedical research and training. Its vision is Building Partnerships for Discovery and Innovation to Improve Health. The FNIH draws together the world''s foremost researchers and resources, pressing the frontier to advance critical discoveries. They are recognized as the number-one medical research charity in the countryleveraging support, and convening high level partnerships, for the greatest impact on the most urgent medical challenges we face today. Grants are awarded as part of a public-private partnership with the National Heart, Lung, and Blood Institute (NHLBI) on behalf of The Heart Truth in support of women''s heart health education and research. Funding for the Community Action Program is provided by the FNIH through donations from individuals and corporations including The Heart Truth partners Belk Department Stores, Diet Coke, and Swarovski. Successful biomedical research relies upon the knowledge, training and dedication of those who conduct it. Bringing multiple disciplines to bear on health challenges requires innovation and collaboration on the part of scientists. Foundation for NIH partnerships operate in a variety of ways and formats to recruit, train, empower and retain their next generation of researchers. From lectures and multi-week courses, to scholarships and awards through fellowships and residential training programs, their programs respond to the needs of scientists at every level and stage in their careers.
HelioScan is a versatile control software for microscopes written in the intuitive graphical programming language LabVIEW. It solves a number of problems observed with custom-built image acquisition systems by providing the following features: * Extendability: both hardware components and software functionality are encapsulated in exchangeable, software components. Additional components can be implemented easily and plugged in at run-time. Components can be independently developed, allowing multiple developers to work in parallel. * Flexibility: Components are independently configurable; each component can have an unlimited number of configurations. * Understandability: The LabVIEW code is well-structured, commented and documented. * High speed: The software supports FPGA-based hardware that enables intelligent and extremely fast signal acquisition and generation. FPGA logic can be easily programmed using LabVIEW. * Tailored to in vivo brain imaging: The software is especially suited for 2-photon Calcium imaging, but can in principle be used for any kind of microscopy. The out-of-the-box software supports different imaging modalities (camera, galvanometric scan mirrors, acusto-optic deflectors) and imaging modes (camera video acquisition, intrinsic optical imaging, two-photon frame scan and tilted frame scan, 2D line scan, 3D spiral scan) and can easily be extended to other imaging modalities (e.g., resonance scanners), imaging modes (e.g., 2D and 3D arbitrary line scans) and associated hardware (e.g., stimulation devices). * Open file-format with extensible meta-data schema: HelioScan saves data in the OME-TIFF file format, which contains image data as multipage TIFF and meta-data as human-readable XML in the TIFF description tag according to the OME schema.
Consortium conducting meta-analyses of genome-wide genetic data for psychiatric disease. Focused on autism, attention-deficit hyperactivity disorder, bipolar disorder, major depressive disorder, schizophrenia, anorexia nervosa (AN), Tourette syndrome (TS), and obsessive-compulsive disorder (OCD). Used to investigate common single nucleotide polymorphisms (SNPs) genotyped on commercial arrays, structural variation (copy number variation) and uncommon or rare genetic variation. To participate you are asked to upload data from your study to central computer used by this consortium. Genetic Cluster Computer serves as data warehouse and analytical platform for this study . When data from your study have been incorporated, account will be provided on central server and access to all GWAS genotypes, phenotypes, and meta-analytic results relevant to deposited data and participation aims. NHGRI GWAS Catalog contains updated information about all GWAS in biomedicine, and is usually excellent starting point to find comprehensive list of studies. Files can be obtained by any PGC member for any disease to which they contributed data. These files can also be obtained by application to NIMH Genetics Repository. Individual-level genotype and phenotype data requires application, material transfer agreement, and informed consent consideration. Some datasets are also in controlled-access dbGaP and Wellcome Trust Case-Control Consortium repositories. PGC members can also receive back cleaned and imputed data and results for samples they contributed to PGC analyses.
Ricopili is a tool for visualizing regions of interest in select GWAS data sets. How it works Choose a data set and enter a genomic location or a gene name in the form below. A .pdf plot will be generated, as well as a text file with single SNP results. You can also specify the following options: * Clumping: Independent regions will be colored differently, to highlight LD. If you request more than one clump, be sure to have at least one SNP passing the specified p-value-threshold (for performance reasons.) * SNP: SNPs in the region are colored by LD to this index SNP. * Anonymity: Frequency information is from HapMap to protect anonymity. * NHGRI results: Results from the NHGRI GWAS catalog will be included in the plot. Finally, please note that this tool is in development (it was released on September 19th, 2011) and should be considered beta. In particular, our development server is not equipped for high traffic. If the server fails to respond to your request, please try again at a later time.
A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events.
University of Ljubljana; Ljubljana; Slovenia
A pharmacovigilance ontology to connect known facts on drugs, disease, ADEs, and their molecular mechanisms.
An accurate and reliable method for identifying athletes with head trauma, and a strong candidate rapid sideline screening test for concussion. The test is able to capture impairments of eye movement, attention, language and other symptoms of impaired brain function. It is a physical method of evaluating visual tracking and saccadic eye movements is based on the time to perform rapid number naming. It involves reading aloud a series of single digit numbers from left to right on three test cards. Participants are asked to read the numbers on each card from left to right as quickly as possible but without making any errors. The sum of the three test card time scores constitutes the summary score for the entire test. The test is a proven indicator of oculomotor inefficiencies regarding eye movements during reading. Published medical studies have determined that deficiencies in saccadic eye movements can be an indicator of mild Traumatic Brain Injury (mTBI) or concussions. Studies have shown that there is a significant relationship between poor oculomotor functions and learning disabilities (including dyslexia detection). Saccadic eye movement deficiencies can be improved with training and correspondingly reading performance also can be improved. Simply put, subjects who don''t perform well on this test are not efficient readers, although because there are many reasons for poor reading unrelated to eye movements, some poor readers do fine on the test. They believe that the test should be in the hands of teachers in order to help them determine if a student''s poor reading performance is related to deficiencies in their ability to move their eyes efficiently.
Istituto di Linguistica Computazionale Antonio Zampolli
ILC-CNR has been one of the major promoters of the notion of language resources as the central component of the linguistic infrastructure (aware also of its cultural, economical and political implications), has coordinated the major initiatives relating to language resources and standardization and has often been the promoter of new paradigms in the field. ILC-CNR has coordinated numerous international, European and national strategic initiatives and projects. ILC-CNR has designed and built several types of corpora and lexicons and the respective ontologies, has developed a complete chain of tools for a robust processing of the Italian language, for the acquisition of information from corpora and for word-sense disambiguation and has developed technologies for several application domains (question answering, information retrieval, text mining, monolingual and multilingual terminology extraction, ontology acquisition and structuring, summarisation, filtering of Web documents, preservation of the cultural heritage through digital image processing and digital libraries techniques etc.). The research fields of the Institute are: Models and methods for natural language processing, and mono- and multilingual application prototypes. Design of international standards and development of computational language resources. Design and implementation of architectures and infrastructures for language resources and language technologies. Computational methods and tools for humanistic research, particularly in linguistic, literary, and philological disciplines, and in lexicography.
Regional Biobank Centre Southern Health Care Region
Swedish Regional Biobank Center Southern Health Care Region
To meet the law requirements and regulations of the National Board of the Southern Health Care Region, Region Skane and Lund University agreed to establish a common biobanking center for Southern healthcare region. Regional biobanksrcentrum will develop and maintain systems for quality assurance and integrity protected using biobanks. The Regional Biobank center is responsible for matters relating to the collection, storage and use of samples stored in biobanks in the Southern healthcare region. Regional Biobank center operations consist of: * to promote the use of biobank material is in accordance with legal requirements biobank * to promote integrity protected and safe storage of repository material * to provide information about the biobank law and biobank materials used for individual sample donors, health professionals, researchers and the public * to handle requests for modified consent and desire to destroy or de test * maintaining a current and privacy protected records of repository material in the region * work to the individual''s integrity will be strengthened in relation to research on biobank material. Tissue samples available to other parties, by surrendering, or by sending tissue samples for analysis, requiring the return or destruction, after completion of the analysis. Regional Biobank Centre (RBC) for the southern healthcare region was established in 2004 and was until 2010 in the Oncology Centre. As of January 1, 2011 it is under the management of RBC Labmedicin Skane.
Stem cell banking is a unique opportunity to store the precious building blocks of the human body; cord blood, cord tissue and fat tissue are just some sources of stem cells ready to provide the foundation for more than 70 treatments of blood, blood related diseases and future applications in regenerative medicine. To not consider the storage or donation of these precious stem cells could be a missed opportunity! Cryo-Save is officially recognized as the largest family stem cell bank in Europe. With more than 180,000 samples stored and four fully-owned storage facilities throughout the world, Cryo-Save has over ten years'' experience and state-of-the-art technical know-how, providing the basis for a strong and reliable organization. An ethical approach, scientific professionalism and customer-focused care are the core elements of our daily activities, as we strive to be an active player in life-science development in over 40 countries. Our company was established in 2000, is headquartered in the Netherlands and successfully active in 40 countries across four continents. We are officially accredited by the regulatory authorities and set the highest quality standards in everything we do. We follow a dual storage system, meaning that the stem cells are stored independently in two separate storage tanks within our state-of-the-art facility. Our dedication to research in collaboration with universities, physicians and stem cell scientists has put us at the forefront of technological developments.
Defense and Veterans Brain Injury Center
Defense and Veterans Head Injury Program
The Defense and Veterans Brain Injury Center (DVBIC) is a congressionally mandated collaboration of the Department of Defense (DoD) and Veterans Affairs (VA) health centers serving patients with traumatic brain injury (TBI). Its mission is to serve active duty military, their beneficiaries, and veterans with traumatic brain injuries (TBIs) through state-of-the-art clinical care, innovative clinical research initiatives and educational programs. DVBIC fulfills this mission through ongoing collaboration with military, VA and civilian health partners, local communities, families and individuals with TBI. In 2008, DVBIC''s mission expanded to include Force Health Protection and Management. This encompasses the following Department of Defense (DoD) programs: * TBI Surveillance * TBI Registry * Pre-deployment neurocognitive testing * Family Caregiver Curriculum * 15 year longitudinal study of TBI * Independent study of automated neurocognitive tests DVBIC has been named the Office of Responsibility or Executive Agency for these programs. The DVBIC multi-site network includes a growing number of DoD and VA hospitals as well as civilian TBI rehabilitation programs. Each DVBIC site works collaboratively to provide and improve TBI care for active duty military, veterans and their eligible beneficiaries. DVBIC''s multi-center network design and collaborations with forward medical commands allows for clinical innovation along the entire continuum of care: from initial injury in the war zone through to medical evacuation, acute care, rehabilitation and ultimately a return to community, family, and work or continued duty when possible. WHAT WE DO * Develop and provide advanced TBI-specific evaluation, treatment and follow-up care for military personnel, their beneficiaries, and veterans with mild to severe TBIs * Conduct clinical research that defines optimal care and treatment for individuals with TBI * Develop and deliver effective educational materials and programming for the prevention, assessment and treatment of TBI including the management of its continuing effects. DVBIC is specifically committed to the effort to prevent, treat, and provide education on TBI for US military members currently on active duty, National Guard and reservists recently injured in the line of duty, their beneficiaries, and retired military personnel. * Oversee congressionally-mandated DoD TBI programs All of the above are done through innovative collaborations among the Armed Forces, VA, federal agencies, and coordinating academic institutions.
National Surgical Adjuvant Breast and Bowel Project Tissue Bank
National Surgical Adjuvant Breast Bowel Project Tissue Bank
The NSABP (National Surgical Adjuvant Breast and Bowel Project) Tissue Bank is the central repository of tissue samples (stained and unstained slides, tissue blocks, and frozen tissue specimens) collected from clinical trials conducted by the NSABP. The main scientific aim of the NSABP Division of Pathology is to develop clinical context-specific prognostic markers and predictive markers that predict response to or benefit from specific therapeutic modality. To achieve this aim, the laboratory collects the tumor and adjacent normal tissues from cancer patients enrolled into the NSABP trials through its membership institutions, and maintain these valuable materials with clinical follow-up information and distribute them to qualified approved investigators. Currently, specimens from more than 90,000 cases of breast and colon cancer are stored and maintained at the bank. Paraffin embedded tumor specimens are available from NSABP trials. We currently do not bank frozen tissues. All blocks are from patients enrolled in prospective NSABP treatment protocols and complete clinical follow up information as well as demographic information is available. Depending on the project, unstained tissue sections of 4-micrometer thickness, tissue microarrays, or stained slides are provided to the investigators in a blinded study format. Any investigators with novel projects that conform to the research goals of NSABP may apply for the tissue. Please refer to the NSABP Tissue Bank Policy to determine if your project conforms to these goals. Priority is given to NSABP membership institutions who regularly submit tissue blocks.
A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.
University of Virginia Tissue Culture Facility
University of Virginia School of Medicine Tissue Culture Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 11,2024. Tissue Culture Facility provides mycoplasma testing, baculovirus titer measurements, growing of cultured cells and cell storage, to University of Virginia researchers. The Facility also supplies cell culture reagents and supplies. Training and access to facilities is also available. Products and services are only available to users at the University of Virginia.
SPecies Identification by Insertions/Deletions
SPInDel - Species identification by insertions/deletions
A multifunctional workbench for species identification using insertion/deletion variants. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species.
Cooperative Health Research in the Region of Augsburg-gen
KORA-gen is infrastructure to provide phenotypes, genotypes and biosamples for collaborative genetic epidemiological research. From all four surveys that have been conducted so far, the following biological material is on hand: genomic DNA, blood serum, blood plasma and EBV immortalized cell lines (form KORA S4 only). These have been extracted from blood samples and are stored in nitrogen tanks and -80 degrees C refrigerators. Genomic DNA from more than 18.000 adult subjects from Augsburg and the surrounding counties is available at present. So far, EBV immortalized cell lines from 1.600 participants are cultivated. To meet the manifold demands of researchers with genetic and molecular questions KORA-gen fulfills the following prerequisites for successful genetic-epidemiological research: * representative samples from the general population, * well characterized disease phenotypes and intermediate phenotypes, * information on environmental factors, * availability of genomic DNA, serum, plasma and urine, as well as EBV immortalized cell lines. In total, four population based health surveys have been conducted between 1984 and 2000 with 18000 participants in the age range of 25 to 74 years, and a biological specimen bank was established in order to enable scientists to perform epidemiologic research with respect to molecular and genetic questions. The KORA study center conducts regular follow-up investigations and has collected a wealth of information on sociodemography, general medical history, environmental factors, smoking, nutrition, alcohol consumption, and various laboratory parameters. This unique resource will be increased further by follow-up studies of the cohort. The assessment of statistical questions covers the definition of the study design and the calculation of statistical power. Furthermore, we offer assistance in data analysis. Kora-gen can be used by external partners. Interested parties can inform themselves interactively via internet about the available data and rules of access. The genotypic data base is a common resource to all partners.
The WHO World Mental Health Surveys: Global Perspectives on the Epidemiology of Mental Disorders
The WMH Survey Initiative is a project of the Assessment, Classification, and Epidemiology (ACE) Group at the World Health Organization coordinating the implementation and analysis of general population epidemiologic surveys of mental, substance use, and behavioral disorders in countries in all WHO Regions. Reported are the first results of the WHO World Mental Health (WMH) Survey Initiative, a highly ambitious series of cross-national psychiatric epidemiological surveys. The general population surveys in the WMH series span 17 countries in all parts of the world. In many of these countries the WMH surveys provide the first community epidemiological data ever available on mental disorders in the population. The detailed information on lifetime prevalence, age of onset, course, correlates, and treatment of mental disorders in this volume provides mental health professionals and healthcare policy planners with an unprecedented reference on the cross-national descriptive epidemiology of mental disorders. The WHO Global Burden of Disease Study estimates that mental and addictive disorders are among the most burdensome in the world and their burden will increase over next decades. However, these estimates and projections are based largely on literature reviews and limited and isolated studies rather than on cross-national epidemiologic surveys. In order to move forward with public health initiatives aimed at addressing the global burden of mental disorders the WMH Survey Initiative carried out rigorously implemented general population surveys that estimate the prevalences of mental disorders, evaluate risk factors for purposes of targeting interventions, study patterns of and barriers to service use, and validate estimates of disease burden world-wide. The WMH Survey Initiative aims to obtain accurate cross-national information about the prevalences and correlates of mental, substance, and behavioral disorders. Included in studies of correlates will be analyses of impairments, other adverse social consequences, and patterns of help-seeking. The WMH Survey Consortium includes nationally or regionally representative surveys in 28 countries, representing all regions of the world, and with a total eventual sample size in excess of 154,000. ISBN:9780521884198
EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens.
Nucleosome-Occupancy Study for Cis-elments Accurate Recognition
One-class SVM for Cis-elements Accurate Recognition
Software tool to identify binding sites of known transcription factors on promoter regions. The algorithm is based on one-class support vector machine (One-class SVM). OSCAR uses the sequential composition of known binding sites, and further incorporates the locational preferences of binding events. Nu-OSCAR (Nucleosome-Occupancy Study for Cis-elments Accurate Recognition) is a program that can be used to identify binding sites of known transcription factors, which further incorporates nucleosome occupancy around sites on promoter regions, thereby improving the accuracy of prediction. The derivation of the the algorithm is based on a biophysical view of interactions between protein factors and nucleosome DNA.
Controlled vocabulary for soybean field growth stages (Soybean Whole Plant Growth Ontology), plant structure names (Soybean Structure Ontology), development (Soybean Development Ontology) and plant traits (Soybean Trait Ontology). These are only a suggestion. Input from the community will be necessary to update and extend the ontologies. Because of this, these ontologies should also be considered a work in progress. Where applicable, soybean specific terms have been associated with their Plant Ontology (PO) and Gramene Plant Trait Ontology (TO) synonyms to facilitate cross species comparisons. Please feel free to contact them for corrections, additions, and questions.
Banyan Biomarkers was founded in 2002 by Ron Hayes, PhD , Kevin Wang, PhD, and Nancy Denslow, PhD to create the first Point of Care (POC) Blood Test to diagnose traumatic brain injury (TBI) and to diagnose neurological diseases. Initially inspired by research conducted at the University of Florida and The Evelyn F. and William McKnight Brain Institute, Banyan Biomarkers has made significant progress in developing and clinically validating novel enzyme linked immunosorbent assays (ELISAs) for traumatic brain injury (TBI). Banyan scientists have created an extensive pipeline of potential biomarkers and the company has a robust intellectual property portfolio. Jackson Streeter, Banyan''s CEO, has extensive experience in development of medical devices for acute brain injury. Currently no blood test exists for use by physicians to detect the presence and severity of brain trauma. Banyan Biomarkers'' research has identified unique and proprietary biomarkers present in the patient''s blood following injury to the brain. The detection and quantification of these biomarkers may provide early indications of brain trauma essential for earlier intervention and management. Banyan Biomarkers, Inc. offers preclinical and clinical sample analyses with a proven panel of neurological, psychiatric, neurodegenerative disease, and organ toxicity biomarker assays. The company provides analytical services to a wide range of customers including pharmaceutical companies, biotechnology companies and investigators at academic research institutes.
With expertise in the preservation of biological specimens, Swiss Biobank is a biobank of cell therapy products (stem cells, progenitor). Strategically located in Suisse Romande, the center is accessible 7J/7J, 365 days / year. The laboratories and technology platforms are tailored to international standards. Service is prompt, courteous, and responsive to your needs. The first opportunity to harvest adult stem cells, which is the only type at Swiss Biobank, occurs just after the birth of a baby. The umbilical cord blood and placenta are rich in hematopoietic stem cells and can regenerate all cells in the bloodstream. The cord and placenta tissues themselves contain mesenchymal cells that can be used for the regeneration of connective tissue. The standardized procedures for collecting cord blood units are made ����??����??by the medical staff of the hospital / clinic according to international standards. The sample is transported by a courier Swiss Medical Biobank in which it is prepared and cryo-preserved by qualified personnel within 24 hours. In the case of public biobanking, cells, tissues, organs are donated and can be used with consent of the donor, a third person for transplantation, or as part of clinical research. The HLA (Human Leukocyte Antigen) is a group of proteins on the cell surface, and specific to each individual. This allows the immune system to distinguish our own cells for foreign elements (pathogens) that are likely to be attacked. Histocompatibility between the donor and recipient is of primary importance in organ transplantation, tissues and / or cells, to minimize the chances of rejection. There is one chance in four that two siblings have the same HLA code.
Highly characterized cell lines and high quality DNA for cell and genetic research representing a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations. The NIGMS Repository contains more than 10,600 cell lines, primarily fibroblasts and transformed lymphoblasts, and over 5,500 DNA samples. The NIGMS Repository has a major emphasis on heritable diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, and many apparently healthy controls. Human induced pluripotent stem cell lines, many of which were derived from NIGMS Repository fibroblasts, have recently become available through the NIGMS Repository. Sample donation facilitates all areas of research by making available well-characterized materials to any qualified researcher who might have otherwise been unable to invest the time and resources to collect needed samples independently. Donations to the Repository have created a resource of unparalleled scope. Samples from the collection have been used in more than 5,500 publications and are distributed to scientists in more than 50 countries. This resource is continuously expanding to support new directions in human genetics.
Ontology for standard measures related to complex diseases, phenotypic traits and environmental exposures
Eye mutant resource - The Jackson Laboratory
The Eye mutant resource lists and describes mouse models for ocular research available from The Jackson Laboratory and provides continuing results from a Jackson Laboratory screening program to identify genes and new mutations that affect vision. It also provides a list of known mouse mutations that affect vision and presents updated information on the cloning of vision-related genes. The primary focus is on the mouse as a model of human inherited vision disorders. The number of known serious or disabling eye diseases in humans is large and affects millions of people each year. Yet research on these diseases frequently is limited by the obvious restrictions on studying pathophysiologic processes in the human eye. Likewise, many human ocular diseases are genetic in origin, but appropriate or available families often are not easy for genetic studies. Mouse models of inherited ocular disease provide powerful tools for quick genetic analysis and characterization. The mouse eye is remarkably similar in structure to the human eye, and many developmental or invasive experiments can be done in mice that are impossible in human beings. Comparative mapping and sequencing between human and mouse genomes shows that knowing the gene location in either man or mouse allows for the same gene to be found more quickly in the other. Finally, the use of inbred strains, where all mice in the strain are alike genetically except for the mutation being studied, is a powerful tool for linkage analysis, and assures phenotypic reproducibility of any model found in a strain. The virutal identity of mice in an inbred strain also allows for fewer numbers of mice to be studied clinically. Mouse models of retinal degeneration have been investigated for many years in the hope of understanding the causes of photoreceptor cell death. 16 naturally occurring mouse mutants that manifest degeneration of photoreceptors in the retina with preservation of all other retinal cell types have been found: retinal degeneration (formerly rd , identical with rodless retina, r, now Pde6b rd1); Purkinje cell degeneration (pcd); nervous (nr); retinal degeneration slow (rds, now Prph Rd2); retinal degeneration 3 (rd3 ); motor neuron degeneration (mnd); retinal degeneration 4 (Rd4 ); retinal degeneration 5 (rd5); vitiligo (vit , now Mitf mi-vit); retinal degeneration 6 (rd6 ); retinal degeneration 7 (rd7); neuronal ceroid lipofuscinosis ( nclf ); retinal degeneration 8 (rd8 ); retinal degeneration 9 ( Rd9 ); retinal degeneration 10 (rd10); and cone photoreceptor function loss (cpfl1).
NINDS Human Genetics DNA and Cell Line Repository
NINDS Human Genetics DNA Cell Line Repository
The NINDS Human Genetics DNA and Cell Line Repository
The NINDS Human Genetics Resource Center
Open resource of biological samples (DNA, cell lines, and other biospecimens) and corresponding phenotypic data to promote neurological research. Samples from more than 34,000 unique individuals with cerebrovascular disease, dystonia, epilepsy, Huntington's Disease, motor neuron disease, Parkinsonism, and Tourette Syndrome, as well as controls (population control and unaffected relatives) have been collected. The mission of the NINDS Repository is to provide 1) genetics support for scientists investigating pathogenesis in the central and peripheral nervous systems through submissions and distribution; 2) information support for patients, families, and advocates concerned with the living-side of neurological disease and stroke.
DOAJ - Directory of Open Access Journals
Database providing access to quality controlled Open Access Journals. For a journal to be included it should exercise quality control on submitted papers through an editor, editorial board and/or a peer-review system. It is not be limited to particular languages or subject areas. Offering free online access to high quality full text content, plus excellent search tools, the portal enables researchers to find, use and re-use a vast range of materials with ease. The content of DOAJ will be even more visible and disseminated through this portal. The aim of the Directory is to increase the visibility and ease of use of open access scientific and scholarly journals thereby promoting their increased usage and impact. As of April 2014, DOAJ has 9,709 journals, 5,624 journals searchable at article level, 133 Countries and 1,600,991 articles. The database may be browsed by title or subject, or searched through the interface to for journals or articles.
kdetrees: Nonparametric method for identifying discordant phylogenetic trees
R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.
National Ophthalmic Disease Genotyping Network
National Ophthalmic Disease Genotyping Network (eyeGENE)
National Ophthalmic Disease Genotyping Network (eyeGENETM)
National network of research laboratories for genetic testing of eye disease. They offer testing for affected individuals coupled to registry of clinical information available through patient registry. Large data set for investigators to identify additional genetic risk factors and to explore relationship between genetic disease (genotype) and its clinical manifestation (phenotype).
A medical, nonprofit, educational wiki created to support a collective online memory for physicians, nurses, and medical students. Users can publish review articles, clinical notes, pearls, and medical images on the site. Anyone with a medical background can contribute to or edit medical articles. Images include: EKG, x-ray, coronary angiograms, peripheral angiograms, structural angiograms, searchable angiograms, echocardiograms, and radiology. Tutorials include: EKG tutorials, coronary angiography tutorials, and ventriculography tutorials.
The Pathology Informatics Curriculum Wiki is a public wiki based on community-based, continually updated online resources. It is about computers and information technology as tools within the field of pathology. Its content includes information management and communication (e.g. meetings on quality, electronic medical records, electronic order entry, reporting critical values, etc.) The goals of the Pathology Informatics Curriculum Wiki are four-fold: 1. To increase interest among pathology residents in pathology informatics; 2. To become a shared educational resource for pathology training programs to supplement or develop their own local curriculum in pathology informatics; 3. To increase research activities in the field; and 4. To connect pathology residents to experts in pathology informatics. We encourage contributors to (1) use the the wiki format to improve and extend this curriculum; (2) help edit and maintain the pathology informatics related pages in Wikipedia that are linked to this curriculum, and (3) create new pathology informatics pages in Wikipedia and link them to this website. In each of the lessons of the curriculum, we highlight areas where we feel that there is need for new or updated articles in Wikipedia relating to that topic.
The mission of the American Diabetes Association (ADA) is to prevent and cure diabetes and to improve the lives of all people affected by diabetes. We lead the fight against the deadly consequences of diabetes and fight for those affectedby diabetes. * We fund research to prevent, cure and manage diabetes. * We deliver services to hundreds of communities. * We provide objective and credible information. * We give voice to those denied their rights because of diabetes.
Immunology is a wikibook with the following contents: * Introduction * Organs of the Immune System * Cells of the Immune System * Antigens * Antibodies * Immune System Genetics * Antibody/Antigen Interactions * Major Histocompatibility Complex * Antigen Processing and Presentation * T Cells * B Cells * Cell-Mediated Immune Response * Cytokines * The Complement System * Inflammation * Hypersensitivity * Infectious Disease * Immunodeficiency * Autoimmunity * Transplants * Cancer * Vaccines * Experimental Methods in Immunology You may download as a PDF or print it.
NHGRI Sample Repository for Human Genetic Research
Sample Repository for Human Genetic Research
DNA samples and cell lines from fifteen populations, including the samples used for the International HapMap Project, the HapMap 3 Project and the 1000 Genomes Project (except for the CEPH samples). All of the samples were contributed with consent to broad data release and to their use in many future studies, including for extensive genotyping and sequencing, gene expression and proteomics studies, and all other types of genetic variation research. NHGRI led the contribution of the NIH to the International HapMap Project, which developed a haplotype map of the human genome. This haplotype map, called the HapMap is a publicly available tool that allows researchers to find genes and genetic variations that affect health and disease. The samples from four populations used to develop the HapMap were initially housed in the Human Genetic Cell Repository of the National Institute of General Medical Sciences (NIGMS). Except for the Utah CEPH samples that were in the NIGMS Repository before the initiation of the HapMap Project and remain there, the NHGRI Repository now houses all of the HapMap samples. The NHGRI repository also houses the extended set of HapMap samples, which includes additional samples from the HapMap populations and samples from seven additional populations. All of the samples were collected with extensive community engagement, including discussions with members of the donor communities about the ethical and social implications of human genetic variation research. These samples were studied as part of the HapMap 3 Project. The NHGRI repository also houses the samples for the International 1000 Genomes Project. This Project is lightly sequencing genome-wide 2500 samples from 27 populations. This project aims to provide a detailed map of human genetic variation, including common and rare SNPs and structural variants. This map will allow more precise localization of genomic regions that contribute to health and disease. The 1000 Genomes Project includes many of the samples from the HapMap and extended set of HapMap samples, as well as samples being collected from additional populations. Currently, samples from five additional populations are available; the others will become available during 2011 and 2012. No identifying or phenotypic information is available for the samples. Donors gave broad consent for use of the samples, including for genotyping, sequencing, and cellular phenotype studies. Samples collected from other populations for the study of human genetic variation may be added to the collection in the future. The NHGRI Repository distributes high quality lymphoblastoid cell lines and DNA from the samples to researchers. DNA is provided in plates or panels of 70 to 100 samples or as individual samples. Cell cultures and DNA samples are distributed only to qualified professional persons who are associated with recognized research, medical, educational, or industrial organizations engaged in health-related research or health delivery.
Ontology that extends the Ontology for Biomedical Investigations (OBI) to support consistent annotation of Bioinformatics Web services.
Biobank of Hospital Clinic Barcelona IDIBAPS
Hospital Clinic Barcelona - IDIBAPS biobank
A biobank of repositories which works to obtain, store, manage and distribute large collections of human biological samples of phenotypes and diseases of marked interest for researchers. The biobank sample collection is made up of three extensive repositories. The Neurological Tissue Biobank is a nervous tissue repository (brain and spinal cord) created from donations from cadavers with or without neurological conditions. It helps facilitate research in neurological illnesses. The Tumour Biobank and Anatomical Pathologies Collections is a repository of tumorous tissue and samples from cancer patients. The Blood and Fluid Biobank is a repository which contains samples of metabolic, inflammatory bowel, hepatic, digestive and maternal and foetal diseases, among others. It houses a large range of samples of scientific interest, primarily DNA, serum and plasma.
ProTECT III - Progesterone for Traumatic Brain Injury: Experimental Clinical Treatment: Phase III Clinical Trial
Recently, our team completed an NINDS-funded, Phase IIa double-blinded, placebo-controlled pilot clinical trial that examined the pharmacokinetics, safety, and activity of progesterone, a steroid found to have powerful neuroprotective effects in multiple animal models of brain injury. Our pilot study demonstrated a 50% reduction in death among severe TBI patients and less disability among moderate TBI patients treated with progesterone. Based on these promising results and supportive preclinical data, we are conducting a large, phase III clinical trial (ProTECT III) to definitively assess the safety and efficacy of this treatment for adults with moderate to severe acute TBI. The study is slated to begin August 2008. WHY Progesterone: Although progresterone is widely considered a sex steroid, it is also a potent neurosteroid. Progesterone is naturally synthesized in the CNS. A large and growing body of animal studies indicate that early administration of progesterone after TBI reduces cerebral edema, neuronal loss, and behavioral deficits in laboratory animals. Certain properties of progesterone make it an ideal therapeutic candidate. First, in contrast to most drugs tested to date, progesterone rapidly enters the brain and reaches equilibrium with the plasma within an hour of administration. Second, unlike other experimental agents, progesterone has a long history of safe use in humans. Finally, the findings of our pilot clinical trial (presented in the Preliminary Data Section, below) indicate that progesterone has consistent and predictable pharmacokinetic properties, is unlikely to produce harm, and may be efficacious for treating acute TBI in humans.
Standards-based Infrastructure with Distributed Resources
A searchable public data repository for multi-assay studies in the field of high-throughput biology. Studies are annotated and curated using ontologies and controlled vocabularies according to the recommendations of the OBO foundry (Open Biological and Biomedical Ontologies) and the NCBO bioportal. Each data set is assigned a digital object identifier (DOI) provided by DataCite. In addition, the SIDR team has developed an ISA-XML (ISA-ML) version of the ISA-TAB format and the mapping to the FuGE object model (ISA-TABtoFuGE); these improvements should facilitate further tool integration, including web services. SIDR contributes to the proof-of-concept addressing the critical success factor for data integration. The SIDR team will continue to put in place the building blocks for giving access to interoperable data through a world-wide network of national hubs in the context of the community-based ISA infrastructure.
tred: web-based visualization and editing of phylogenetic trees
Software tool to visualize and edit phylogenetic trees. It combines a browser-based Javascript client with a Python (web2py) server. Trees are rendered in SVG using Raphael.
The Regional Biobank of Central Norway, henceforth called the Biobank, is a research facility which contains a collection of human biological material such as blood, tissue and urine samples, and a database which stores relevant information about the samples and the patients from whom the samples originate, as well as information obtained from analysis of the material. The material is collected as part of medical examinations, diagnosis or treatment. The Biobank is foreseen to give an increased knowledge about causes for diseases and their mechanisms, and thereby contributing to improve prophylactic health work, diagnostics and treatment. The Biobank is owned and operated by official authorities on a no commercial profit basis. The Biobank was established in collaboration between the Central Norwegian Regional Health Authority (data management and administration) and the Faculty of Medicine at the Norwegian University of Science and Technology (economics and personnel). The Biobank is approved by The Data Inspectorate of Norway, and by the Regional Committee for Medical Research Ethics, and all information in the Biobank is handled according to the guidelines of the Data Inspectorate.
SeraCare Lifesciences: Sample Storage Management and Processing Services
SeraCare Lifesciences: Sample Storage Management Processing Services
SeraCare Sample Storage Management and Processing Services
SeraCare stores and manages over 19 million samples in our state-of-the-art biobank, and is supported by a range of processing and characterization services. Security. Backup. On-line inventory. Next day sample access. Analysis. Characterization. Anonymization. Transformation. Restoration. Compliance. Coordination. We handle your samples all the way through. SeraCare is well-equipped to perform a wide range of sample storage, management, and processing services. We have longstanding customer relationships with clinical and research laboratories, biopharma, and public health agencies, including the National Institutes of Health, the Centers for Disease Control, and the US Food and Drug Administration. * Our scientists have expertise in virology, immunology, molecular biology, and biochemistry * We have a proven legacy of custom assay design and custom product development to meet your specifications
NEI Age-Related Eye Disease Study Genetic Repository
The NEI-AREDS Genetic Repository is a collection of genetic material submitted by participants in the Age-Related Eye Disease Study (AREDS) which was sponsored by the National Eye Institute (NEI). The Repository stores DNA for use by investigators conducting genetics research into the causes of eye disease. The Age-Related Eye Disease Study was designed to learn about macular degeneration and cataract, two leading causes of vision loss in older adults. The study looked at how these two diseases progress and what their causes may be. In addition, the study tested certain vitamins and minerals to find out if they can help to prevent or slow these diseases. Participants in the study did not have to have either disease. (Enrollment was completed in January 1998.) Eleven medical centers in the United States took part in the study, and more than 4,700 people across the country were enrolled in AREDS. The study was supported by the National Eye Institute, part of the Federal government''s National Institutes of Health. The clinical trial portion of the study also received support from Bausch & Lomb Pharmaceuticals and was completed in October 2001. Data from AREDS is publicly available in the Database of Genotypes and Phenotypes (dbGaP). Genetic samples from 600 AREDS participants (200 controls, 200 Neovascular AMD cases, and 200 Geographic Atrophy cases) were selected using data available in March 2005 and then were genotyped using the Illumina 100K and the Affymetrix 100K gene chips. These genotype data are available in the dbGaP. DNA samples are distributed only to qualified professional persons who are associated with recognized research, medical, educational, or industrial organizations engaged in health-related research or health delivery. All orders for DNA samples must be submitted using the online catalog.
The AIDS And HIV Research Lab Registry is a registry of lab heads ranked by total citation score. You may sort the rankings by total score, mean score, publication number and last 365 days. Results presented are Rank, Name, Affiliation, and Total score/Last 365 days. Clicking on the name of the lab head provides additional information including a picture, affiliation, citations, the researcher''s home page, and collaborative biography.
Software resource including non-EEG related Matlab functions, Neuron''s simulation files, C/C++ functions, Java, Unix tips, Flash 5 buttons and movies, Publishing photo albums using Linux (external page), and Publishing digital camera movies using Linux (external page). Non-EEG related Matlab functions *Qsubfunc *Gui Matlab functions *Function keyword input/output arguments processing *Web and Matlab help *Others C/C++ functions *Convolution *Chono *Format_biblio *Image processing library *Fusion sort Java *Simple scroll *Rebound scroll *Spiking neurons Unix tips *Send a mail automatically in non-interactive mode *Log in remotely and redirect/assess resources *Schedule automatically a task (for instance to check your quota)
Cooperative Huntington's Observational Research Trial Repository
A repository of information related to Huntington's disease and its causes, progression, treatments, and possible cures. It stores and accepts data and specimens to accelerate research on Huntington's disease and provides scientists with prospectively collected clinical data and biological specimens. The COHORT sample includes individuals which manifest Huntington's disease (HD), unaffected individuals known to carry the HD gene or who are at risk of carrying the HD gene, and family members who have no risk for HD (control subjects). Clinical data includes demographics, clinical features, family history, and genetic characteristics. Biological specimens include blood with a potential of collecting urine or other samples in the future. The COHORT biological specimen repository will provide research specimens for current and future scientific research aimed at developing useful biomarkers of HD.
The J.P. McCarthy Cord Stem Cell Bank at the Karmanos Cancer Institute is a public, non-profit stem cell bank with over 1,200 umbilical cord blood units in its inventory. The bank was founded in 2001 and is one of only 21 internationally recognized cord stem cell banks affiliated with the National Marrow Donor Program. The only bank of its kind in Michigan, it was created in anticipation of providing life-saving hope to people who have been diagnosed with cancer and serious blood disorders. Karmanos collects, processes and stores donated umbilical cord blood that becomes a readily available source of hematopoietic stem cells for transplant in children and adults with leukemia, lymphoma, sickle cell disease or other life-threatening conditions. The J.P. McCarthy Cord Blood Bank and Carls Processing Laboratory is also accredited by the Foundation for the Accreditation of Cellular Therapy (FACT). The accreditation signifies the highest standards of practice in collection, processing and transplantation. Karmanos is the only FACT accredited cord blood bank in Michigan and one of only nine in the United States. In the Detroit Metropolitan area, the number of hospitals participating in the collection of cord blood is rapidly increasing. Please consider donating your baby''s cord blood if you are delivering at one of our participating hospitals: Henry Ford Wyandotte Hospital in Wyandotte, MI, Providence Park Hospital in Novi, MI, St. Joseph Mercy Hospital in Ann Arbor
The Michigan Neonatal Biobank (Biobank) is a storage and management facility for The Michigan Department of Community Health''s archive of dried blood spot cards. A 501(c)3 non-profit charitable organization, the Biobank is contracted to serve as the repository for storage and management of the samples in a temperature controlled facility at Wayne State University''s Biobanking Center of Excellence in Tech Town. The Biobank''s roots are planted in the State''s Newborn Screening Program which began in 1965 in the Department of Community Health. Newborn screening is a public health program required by Michigan law to find babies with rare but serious disorders that require early treatment. A few drops of blood taken from the baby''s heel are sent to the State Public Health Laboratory and are tested for 49 disorders. Each year more than 200 Michigan babies are found to have a disorder detected by Newborn Screening. Once screening in the State laboratory is complete, residual dried blood spot samples that are no longer needed for testing are each assigned a unique code which assures anonymity for the sample and its donor. The samples are then sent for storage in the Michigan Neonatal Biobank.
Selectome: a Database of Positive Selection
Database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees.
It is the aim of the SepNet initiative to establish a central facility, essential to data and sample quality and homogeneity, that comprises a structured and easily accessible sample bank with probes of homogeneous quality originating from a well-characterized patient population enrolled in independent, innovative and internationally competitive prospective clinical sepsis trials. The SepNetBiobank is a core facility of SepNet. The object of this central sample resource is to organize and handle all relevant aspects of sampling, storage and delivery of samples in the SepNet collaboration to ensure homogeneity of the samples in terms of specimen quality and maintaining sampling standards. This will be achieved through central handling of samples collected in peripheral nationwide 17 regional centers and an additional 36 associated centers according to an agreed sampling scheme and pre-set standards for sample quality, sample handling and banking; quality assurance and all relevant parts of sample handling will be in the hands of the core unit, minimizing pre-analytical steps in the heterogeneous environment of the different regional centers. In the next few months a fully automated sample storage system will be implemented that allows handling of more than 200.000 individual aliquots expected after completion of the different ongoing and planned SepNet Trails. In the next six months a fully automated -80 degree C sample storage system will be implemented. After completion of the plannend and ongoing SepNet trials more than 59.710 expected primary samples (218.040 aliquots) will be stored in this system. This outstanding sample resource will provide the basis for scientific projects aming at improving patient care with sepsis e.g. advancement in diagnostics, risk stratification, therapy and outcome.
A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.
Central repository of information on neuronal cell types mainly accumulating information on: Genetically labeled cell types in mouse brain and genetically engineered mouse lines for cell type research. Mouse lines are annotated with * Atlas for examining transgene expression patterns * Information on construct used to generate transgene * Associated publications * Anatomical regions where transgene is expressed (based on Atlas) * Information on where to obtain the animals Currently, the mouse lines in the database are mostly generated at Cold Spring Harbor Lab, Scripps Research Institute, Baylor College of Medicine and Brandeis University with few other exceptions. In the future, they will incorporate more mouse lines useful for neuronal cell type research. Cell types are annotated with * Anatomical region * Properties (frequently used terms in neuroscience research) * Mouse line used to define the cell type * Genome wide transcriptome data (if available) * Specific (marker) genes (if available) * Marker immunostaining data (if available) * Associated publications * Electrophysiological characterizations (when available) * Morphological characterizations (when available)
Established in 1985, LifeLink Tissue Bank is a not-for-profit organization dedicated to serving patients in need of transplantation therapy. It is one of five divisions of the LifeLink Foundation and the largest not-for-profit tissue bank in the Southeast and one of the largest in the United States. LifeLink Tissue Bank is inspected and accredited by The American Association of Tissue Banks (AATB). Our goal is to provide the safest, most clinically effective allografts while remaining cognizant of the rising cost of medical care. Donors and their families are the core of our organization. We treat them with respect, show them compassion, and offer them comfort in knowing that their confidentiality is protected and their gifts optimally utilized. Our allografts are utilized by surgeons and hospitals that trust LifeLink to provide them with safe and clinically effective allografts. Every effort is made to ensure that our allografts are placed back in the hospitals of the communities that we serve with organ and tissue recovery services.
OpenAnesthesia.org is a wiki promoting evidence-based medicine in anesthesiology, critical care and pain management. It is divided into several, major Units (Anesthesia Text, Critical Care Manual, Practice-Changing Articles, Controversies in Anesthesia, ABA keywords, Audio/Video Archives, CME, GME, Pharmacology...), each of which is subdivided into Chapters (or in some cases, even smaller subdivisions, such as sections, individual key words, topics, points of interest, or bibliographic references). The goal of Anasthesia Text is to collect and distribute evidence-based information regarding all aspects of anesthesia. This section is similar to a traditional textbook in the broad range of topics covered, but different in that it will provide this information in the form of a wiki (i.e. anyone can edit, add, or subtract to it). OpenAneshesia.org provides anesthesia residents with GME credit and Program Directors with a tool to document core competency activities for Accreditation Council for Graduate Medical Education (ACGME)-mandated learning portfolios. Residents are invited invited to read the Anesthesia & Analgesia article of the month and listen to an interview with one of the article''s authors. During the interview, the author will discuss the specifics of the article as well as general topics geared towards improving each resident''s appreciation of basic or clinical research. After listening to the podcast and reading the article, residents can answer 5 questions in order to demonstrate their mastery of the topics discussed (similar to the Anesthesia & Analgesia Continuing Medical Education (CME) section). Like the CME section, after demonstrating proficiency, a resident will receive a printable certificate that will specify which ACGME core competencies were addressed in the article and interview. The certificates can be put in each resident''s ACGME-required learning portfolio.
Samaritan Health Services (SHA) is a non-profit network of hospitals, physician clinics and health services caring for the communities of the mid-Willamette Valley and central Oregon Coast. We''ve joined together to provide innovative medicine and world-class quality in a way that''s consistent with the values of the places we serve. That includes care and compassion for everyone, regardless of the ability to pay. Samaritan Health Services is a values-driven, church-related organization governed by community members, physicians and other health care providers. We seek to be the first choice of consumers in the region and to lead collaborative efforts among those who share similar goals.
Encefalus: Studying the complex interaction between brain
This is a blog that combines an update of the current scientific research on psychology (and all its related disciplines) along with criticism, personal thoughts and commentary. Since psychology, along with its many other facets, is a social science I consider its connection with society to be an essential part of it. Therefore, the criticism and the commentary I make will often take things to the larger scale of society whether the research concerns neurology, cognitive psychology or anything else. Holding true to this spirit, this blog will many times incorporate current news from all over the world in an attempt to establish the missing link that differentiates mainstream psychology from the real out-of-the-lab world. I hope that this blog really brings something different to just a simple updating of the current research, because there are, indeed, many blogs that do this job. The author describes this blog as some occasional psycho-rant by a former student (now graduate) of psychology (and post graduate in artificial intelligence), while combining of course an update on the current research with a critical view and the occasional satiric spirit.
This project explores the use of a wiki as an online collaborative tool for improving and updating peer-reviewed systematic reviews. Posted on this wiki is a copy of the article: Second-line therapy in patients with type 2 diabetes inadequately controlled with metformin monotherapy: A systematic review and mixed treatment comparisons meta-analysis. Readers are invited to edit the article by adding to, deleting or modifying its contents.
Established in 2004, SPH Biorepository was built to create a centralized facility for many research programs, as well as for new ones; more effective use of the available storage space; development of new database management tools; and quality control of sample processing and banking. While maintaining ultimate control of the samples accumulated in their research projects, PIs will have the assurance of competent handling of their biological samples, reliable access, safe storage, and expert advice from the Biorepository personnel. In the long-term, the Biorepository will provide: * Safe and orderly storage of banked samples * Samples diversification in case of a major disaster *Leverage for additional funding for the new projects Over 145,000 thousands of various biological and environmental samples have been stored and archived through the CHAMACOS, Vitamin, FACES, IBD, and other projects. The Biorepository (Holland - Director) has accumulated substantial expertise in the development of customized databases to barcode and monitor sample location, transfer, and use.
Cardio-Facio-Cutaneous Syndrome International Biobank
Cardio-Facio-Cutaneous International BioBank
CFC International holds the world''s largest collection of blood and tissue from people affected by CFC and their immediate relatives. It is the only centralized repository in the world. The CFC BioBank provides medical researchers with genetic and biological material from CFC patients and their families, so that research on CFC and other related syndromes can be performed. CFC International joined the Genetic Alliance BioBank in 2004 to make certain that your privacy and confidentiality are protected and your samples are available to any approved research project. The bank serves as a resource for researchers around the world who are willing to search to find the gene(s) responsible for the Cardio-Facio-Cutaneous Syndrome. As you know, Cardio-Facio-Cutaneous Syndrome is an extremely rare condition. Thus while access to cell lines is essential for studying the biology and genetics of the disorder, there are very few cell lines in existence. Because an integral part of CFC''s mission is to stimulate interest in CFC research, there is an increased need for cell lines. The CFC BioBank will ensure that need is met! The goals of The CFC BioBank are to promote: * Sufficient availability of cells for approved research projects * Incentive for new research projects * Study of the biochemical basis for CFC Syndrome * Discoveries leading to new treatments for children with CFC Syndrome If you are interested in donating to the CFC BioBank please call 607-772-9666, or e-mail us at bconger_at_cfcsyndrome.org and indicate your interest. Researchers with an interest in either donating CFC Syndrome cell lines or in applying to use material from the bank should also call or write.
Welcome to the website of the Fourth International Conference on Science in Society, to be held at the University of California, Berkeley, USA from 17 to 19 November 2012. This Conference will address disciplinary and interdisciplinary challenges in the sciences, and in particular the relationships of science to society. Key themes addressed by the Conference include the social impacts of science, the values and ethics of science, the pedagogies of science, the knowledge-making processes of science, the politics of science and the economics of science. At first glance, the scope and concerns of the Conference are enormous. However, in contrast to conferences with a specialist disciplinary focus, this Conference aims to explore, in an interdisciplinary spirit, linkages between different areas of concern and practices of investigation. We welcome presentation proposals which range from broad explorations of philosophical, theoretical, methodological and policy questions, to proposals which present finely grained evidence of the connections of science to society in microcosms of research, teaching and practice. Participants at the Conference will include researchers, teachers, administrators and policy makers from the basic natural-physical sciences, the applied sciences, the social sciences, history and philosophy of science, the humanities, and the professions. Plenary speakers will include some of the world's leading thinkers in the various fields which are concerned with the relationships of science to society, as well as numerous paper, colloquium and workshop presentations by practitioners, teachers and researchers. Participants are welcome to submit a presentation proposal either for a 30-minute paper, 60-minute workshop, or a jointly presented 90-minute colloquium session. Parallel sessions are loosely grouped into streams reflecting different perspectives or disciplines. Each stream also has its own talking circle, a forum for focused discussion of issues. For those unable to attend the Conference in person, virtual participation is also available. We encourage all presenters to submit written papers to The International Journal of Science in Society, a fully refereed academic Journal. Virtual participants may also may also submit papers for consideration by the Journal. All Conference participants who have finalized their registration will receive a complimentary online subscription to the Journal. This subscription is valid until one year after the Conference end date. If you would like to know more about this Conference, bookmark the Science in Society site and return for further information-the site is regularly updated. You may also wish to subscribe to the Conference and Journal Newsletter.
An affiliation of organ and tissue recovery organizations across the United States that is committed to saving and improving lives by connecting one life to another through donation and transplantation. DCI Donor Services (DCIDS) supports families who have sustained the loss of a loved one by providing an opportunity for organ, eye and tissue donation and by facilitating the recovery and transplantation of these gifts to help others in need. They also provide after-care support to donor families while at the same time working to inspire universal acceptance of donation throughout the hospitals and communities we serve to ensure every person in need receives the Gift of Life.
Established in 1987, LifeGift is a not-for-profit organ procurement organization that recovers organs and tissue for individuals needing transplants in 109 Texas counties in North, Southeast and West Texas. Our Role * Help grieving families consider the decision to give the gift of life. Inform families of registered donors of their loved ones����?? wishes to donate. * Coordinate the organ and tissue recovery process with surgeons, other transplant professionals and transplant centers. Collect data for use in transplantation research. * Partner with hospitals to continually develop effective, government-regulated donation systems to help increase the number of donated organs available for transplant. * Educate the public about the need for organ and tissue donation. Serve the African-American, Latino and Asian minority communities with specific educational programs. * Continue to support and maintain contact with donor families following the donation process, facilitating communication between recipients and donor families, if both parties desire.
The IBC Research Foundation BioBank is a secure, privacy-protected collection of biological specimens from ibc-diagnosed patients (cases, and, unlike the former George Washington University IBC Registry, ibc patients who have died, those who are under legal age, and those living but unable to make decisions for themselves, may be consented to participate in the IBC Research Foundation BioBank by their authorized representative) and from those not diagnosed with ibc (controls), volunteering following a consent decision making process, and signing an Informed Consent. Clinical Data and a comprehensive questionnaire will also be obtained for those diagnosed with ibc. The Inflammatory Breast Cancer Research Foundation (ibcRF) has established a BioBank and Clinical Database. The BioBank contains non-tumor RNA and DNA, tumor RNA and DNA, blocks and slides from diagnostic pathology, and medical records describing clinical and pathologic findings at diagnosis.
Software package provides statistical tools. Derives copy number and BAF from variety of NGS data including WES, WGS, targeted panel, and shallow sequencing as well as Microarray data. Multifaceted desktop software for rapid discovery of genomic alterations. Accepts data from various manufacturers and technologies including Infinium GSA and CytoScan XON.
CAS REGISTRY - The gold standard for substance information
CAS REGISTRY, the gold standard for substance information, is the only integrated, comprehensive source of chemical information from a full range of disclosed material including patents, journals, and reputable web sources. When you need to positively identify a chemical substance, you can rely on the authoritative source for chemical names and structures of CAS REGISTRY. CAS databases are curated and quality-controlled by CAS scientists, and recognized by chemical and pharmaceutical companies, universities, government organizations, and patent offices around the world as authoritative. By combining these databases with advanced search and analysis technologies (SciFinder, STN, and Science IP products and services), CAS delivers the most current, complete, and cross-linked secure digital information environment for scientific discovery. You can identify your substance of interest by its CAS Registry Number, which is the best way to identify a substance, regardless of what name you have for it. You can also use CAS REGISTRY to locate * literature references to the substance * experimental and predicted property data (boiling and melting points, etc.) * commercial availability * preparative methods * spectra * regulatory information from international sources
Resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. PGN comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project. However, it accepts submission from other sources. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database. The current datasets on PGN come from the floral genome project and includes the following species: Acorus americanus, Amborella trichopoda, Asparagus officinalis, Cucumis sativus, Eschscholzia californica, Eschscholzia californica, Illicium parviflorum, Ipomopsis aggregata, Liriodendron tulipifera, Mesembryanthemum crystallinum, Mimulus guttatus, Nuphar advena, Papaver somniferum, Persea americana, Prymnesium parvum, Ribes americanum, Saruma henryi, Stenogyne rugosa, Vaccinium corymbosa, Welwitschia mirabilis, Yucca filamentosa, Zamia fischeri. For functional annotation, blast is used to compare find the best match of each unigene sequence to in the Genbank NR database, and the in complete coding sequences from Arabidopsis. These annotations are stored in the database and serve as the primary source of annotation. The annotation framework will be extended to Gene Ontology annotations in the future.
Established in 1970, the University of Miami Tissue Bank (UMTB) is the oldest academic institution of its kind in the United States. UMTB came about and evolved in an effort to provide safe and effective bone and soft tissue grafts to patients long before allograft bone transplantation was widely accepted. UMTB has always been focused on safety and the advancement of knowledge in allograft use. More scientific peer-reviewed articles, book chapters and innovations have come from UMTB either directly or indirectly than from any other organization of its kind. UMTB continues to be a leader in transplantation research and has maintained an impeccable safety record. As the only university-run tissue bank, UMTB works closely with surgeons and basic science investigators to advance the field of bone and soft tissue transplantation. Our scientific endeavors include clinical trials to confirm and improve graft efficacy for oral surgery, orthopedic tumor and spine surgery, and sports injuries. When warranted, we engage commercial entities for these studies. As a multidisciplinary organization of surgeons, pathologists, scientists and technicians, we have safely recovered, processed, distributed and implanted aseptically processed bone, cartilage and soft tissue grafts in thousands of patients. We make extraordinary efforts to ensure aseptic recovery and processing to protect the biologic activity, integrity, bio attributes, and safety of the graft. We believe that the American Association of Tissue Banks (AATB) has adopted appropriate guidelines for Tissue Banking in the United States and the University of Miami is a proud member of this organization.
OSCAR is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries. This tool for shallow, chemistry-specific parsing of chemical documents identifies (or attempts to identify): * Chemical names: singular nouns, plurals, verbs etc., also formulae and acronyms, some enzymes and reaction names. * Ontology terms: if you can do it by string-matching, you can get OSCAR to do it. * Chemical data: Spectra, melting/boiling point, yield etc. in experimental sections. In addition, where possible the chemical names that are detected are annotated with structures, either via lookup or name-to-structure parsing (OPSIN), and with identifiers from the chemical ontology ChEBI Current work on OSCAR3 by Peter Corbett focuses on its use in SciBorg, a framework for the deep parsing of chemical text. OSCAR3 also includes the Oscar Server, a Jetty-powered set of servlets. These provide the following services: * Parsing of text/HTML by OSCAR. * Text/InChI/SMILES/SMILES substructues/SMILES similarity search of papers, coupled with keyword and ontology-based search, using Lucene and the CDK. * List of all names found / all names that co-occur with a search term or terms. * Online management of a chemical/stopword lexicon. * Manual editing of SciXML fragments containing named entities, for creating of gold standards and training data. Oscar3 can be found on SourceForge: http://sourceforge.net/projects/oscar3-chem/
Language Map Experiment Management System
UW Integrated Brain Project Language Map Experiment Management System
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. An experiment management system for researchers studying language organization in the brain. Data from thirteen patients are available as a public demo. Language Map EMS
Draft release 3 for genome-wide SNP genotyping and targeted sequencing in DNA samples from a variety of human populations (sometimes referred to as the HapMap 3 samples). This release contains the following data: * SNP genotype data generated from 1184 samples, collected using two platforms: the Illumina Human1M (by the Wellcome Trust Sanger Institute) and the Affymetrix SNP 6.0 (by the Broad Institute). Data from the two platforms have been merged for this release. * PCR-based resequencing data (by Baylor College of Medicine Human Genome Sequencing Center) across ten 100-kb regions (collectively referred to as ENCODE 3) in 712 samples. Since this is a draft release, please check this site regularly for updates and new releases. The HapMap 3 sample collection comprises 1,301 samples (including the original 270 samples used in Phase I and II of the International HapMap Project) from 11 populations, listed below alphabetically by their 3-letter labels. Five of the ten ENCODE 3 regions overlap with the HapMap-ENCODE regions; the other five are regions selected at random from the ENCODE target regions (excluding the 10 HapMap-ENCODE regions). All ENCODE 3 regions are 100-kb in size, and are centered within each respective ENCODE region. The HapMap 3 and ENCORE 3 data are downloadable from the ftp site.
The Handbook of Genetic Counseling is a wikibook designed as an introduction to the discipline and practice of genetic counseling. The text provides an introduction to genetic counseling as a clinical practice and includes sample counseling outlines and letters for students of genetic counseling. Additional outline and letter examples are highly encouraged. Wikibooks contains books on many medical topics; however, no warranty whatsoever is made that any of the books are accurate.
Founded in 1982 and headquartered in Virginia Beach, VA, LifeNet Health Inc., is a leading biomedical alloengineering organization and organ and tissue donation agency whose mission is saving lives and restoring health. LifeNet Health of Florida is a fully owned subsidiary dedicated to the recovery of tissue in Northern Florida, improving the awareness of tissue donation and educating the public about donation in the Northern Florida Community. Our mission is to improve upon the awareness of tissue donation within the community as well as to provide human tissue for transplant. We strive to give back to the community by providing an extensive public education program regarding donation, as well as being involved and making contributions that we feel will benefit the local community as a whole. Our efforts with total quality management have solidified our belief that LifeNet Health of Florida, Inc., must be driven by excellence in service and uncompromising quality. By the continuous improvement of processes and services leading to a better understanding of the entire donor process for both hospital personnel and members of our community.
emedicinehealth: Dementia Due to HIV Infection
A narrative resource that provides a wealth of information on topic including: * Dementia Due to HIV Infection Overview * Dementia Due to HIV Infection Causes * Dementia Due to HIV Infection Symptoms * Exams and Tests * Dementia Due to HIV Infection Treatment * Self-Care at Home * Medical Treatment * Next Steps * Follow-up * Prevention * Outlook * Support Groups and Counseling * For More Information * Web Links * Multimedia * Synonyms and Keywords Additional information includes: * HIV AIDS Myths and Facts Slideshow Pictures * Take the HIV/AIDS Quiz * AIDS Retrospective Slideshow Pictures
WebMD has created an organization that we believe fulfills the promise of health information on the Internet. We provide credible information, supportive communities, and in-depth reference material about health subjects that matter to you. We are a source for original and timely health information as well as material from well known content providers. The WebMD content staff blends award-winning expertise in journalism, content creation, community services, expert commentary, and medical review to give our users a variety of ways to find what they are looking for. And that, we believe, requires dedicated, full-time staff professionals with state-of-the-art expertise in: * Health news for the public * Creating and maintaining up-to-date medical reference content databases * Medical imagery, graphics, and animation * Communities * Live web events * User experience * Interactive tools Our board-certified physicians, award-winning journalists, and trained community moderators are solely dedicated to your daily information experience on WebMD. Our content staff includes individuals who hold advanced degrees in journalism, medical illustration, health communications, clinical informatics, nursing, and medicine. WebMD verifies the qualifications of all medical professionals on the site; including health professionals, experts, editorial professionals and contributors with a specialty license. You may search for information or use the Health A-Z option. Additionally, Drugs & Supplements, Living Healthy, Eating & Diet, Parenting & Pregnancy, Teen Health, and Pet Health tabs are available.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.The mission of the Human Antibody Initiative (HAI) aims to promote and facilitate the use of antibodies for proteomics research. The initiative consists of two separate activities; (1) the generation of a catalogue of validated antibodies from many different sources and (2) a protein atlas for the expression and localization of human proteins in normal and disease tissue. The two separate activities have as their primary deliverables to generate databases with free public accessibility. The Antibody Resource database (www.antibodypedia.org) is aimed to produce a comprehensive catalogue of validated antibodies towards human proteins. This initiative depends on input from a large number of academic groups and commercial companies. The Protein Atlas initiative (www.proteinatlas.org) is aimed to provide comprehensive and annotated database of high-resolution images showing tissue profiles in normal and cancer tissues. Both databases will be open to the public without restriction (no passwords).
SysMO JERM Ontology of Systems Biology for Micro-Organisms
An ontology to describe the entities and relationships in the SEEK database, a Systems Biology environment for the sharing and exchange of data and models. The SysMO-SEEK database contains the work of the SysMO consortium (Systems Biology of Micro-Organisms) https://seek.sysmo-db.org/
CCTS Biomedical Informatics Group at UTHealth BioBank
Clinical and Translational Sciences BioBank
UTHealth Clinical and Translational Sciences BioBank
The University of Texas Health Science Center at Houston (UTHealth) Clinical and Translational Sciences (CCTS) BioBank employs a federated rather than a centralized model which encourages participation by sample owners who are concerned about guaranteeing their ownership of samples and sample information about patients, samples and related clinical data. In a federated model, individual sites agree on shared policies and procedures for data and sample sharing and oversight. Samples remain with and are governed by the contributing principal investigator at each site. The contributing investigator has final authority whether or not to collaborate or to release samples to qualified researchers. The goal of SLED (Sample Location and Enhanced Distribution) is to help researchers overcome two of the biggest obstacles preventing their research from beginning: 1) location of samples and related data, and 2) requesting of samples and related data. Prior to SLED''s inception the existing system was limited to providing links to samples and data and relying on phone calls to sample owners to facilitate sharing. Collaboration between the CTSA Biobank Consortium and the informatics team at the University of Texas School of Biomedical Informatics is ongoing during this effort. The initial design was constructed using best practices offered by NIH, NCI, and other biobank industry leaders to support and to improve synergy and interaction among various research efforts. Through SLED, researchers will be able to search for samples using a variety of criteria including availability, clinical data, consent criteria, patient demographics, patient diagnoses, study data, and sample type at local and national biobank sites.
Software tool that allows scripting of simple modifications to pedigree files. (entry from Genetic Analysis Software)
SubMito is the first computational system for predicting protein submitochondria locations from its primary sequence. SubMito is designed and implemented with Java. This site is a web-like front end for SubMito system. Users can access SubMito on the server side by uploading a FASTA file or entering sequence below. The prediction result will be saved on server, and a link to the result file will be provided. Since there may be several sessions running at the same time on the server, the responding of the server side SubMito may be very slow. Another way to use SubMito is to download a local version of the software. The online service can accept 2 forms of input. One is single sequence, the other is uploaded FASTA file. If you want to predict submitochondria location for a single sequence, you can paste your sequence in the text box. Optionally, you can choose to write some remarks in the text field labeling Enter your remark. Then, press the Submit button to perform the prediction. The result will be saved in a FASTA format file, and you can download it at any time in the coming 48 hours.
TETRA - Fragment assignment by intrinsic tetranucleotide frequencies
Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences.
Canceropole Grand Sud-Ouest Virtual Tumour Bank
Canc��rop��le Grand Sud-Ouest Virtual Tumour Bank
Tumorotheque Virtuelle du Canceropole GSO
The Virtual Tumour Bank of the Canceropole Grand Sud-Ouest''s mission is to federate the cancer research of four French regions: Aquitaine, Languedoc-Roussillon, Limousin and Midi-Pyrenees. This site allows access to an inventory of the specimens stored in the tumor banks of the Greater South-West region, within the laboratories of Pathology of the University Hospital Centers and Cancer Centers of Bordeaux, Limoges, Montpellier, Nimes and Toulouse. You may search by disease or multiple criteria. These specimens are removed from patients primarily to confirm and accurately characterize their cancer diagnosis, and are therefore stored by the tumor bank for diagnostic and/or therapeutic purposes. These samples can be re-qualified for scientific research pending that a number of conditions are met, including the absence of refusal from the person (in compliance with French regulations). So far, the tumor bank is a major tool for cancer treatment and research. This inventory is a further evidence of the coordination effort between the eight concerned tumor banks that have been mobilized at the service of patients and research within the framework of the Canceropole Grand Sud-Ouest programs. These biological resources are made available to research groups that conduct basic or translational programs in the field of oncology. They will not be made available for projects in fields other than oncology.
Alien_hunter: Interpolated Variable Order Motifs for Identification of Horizontally Acquired DNA
Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer.
Southern Alberta Organ and Tissue Donation Program
The Southern Alberta Organ and Tissue Donation Program is an integrated donation program for organs, occular tissue and non-occular tissue. These services are provided by the Southern Alberta Organ Donation Program, Lions Eye Bank & the Southern Alberta Tissue Program. This service provides: * coordination of donation, allocation, recovery and distribution of organs for transplantation for Southern Alberta; * recovery, processing, storage and distribution of occular and non-occular tissues for transplantation; * public , professional education and awareness; * research and statistics; * bereavement support.
Blood and Tissue Center of Central Texas
Travis County Medical Society Blood Bank
The Blood and Tissue Center of Central Texas is a 501(c)(3) not-for-profit organization. Its mission is to safeguard the community''s gifts of blood and tissue with uncompromising quality and excellence in customer service. The Center is licensed by the US Food and Drug Administration, accredited by the American Association of Blood Banks and American Association of Tissue Banks, and is a proud member of America''s Blood Centers. The Blood and Tissue Center today is the exclusive provider and guardian of the community blood supply for more than 37 medical facilities in a ten-county service area of Central Texas. In 2010, over 56,000 whole blood donations and 7,700 apheresis platelet donations were collected. These donations are tested extensively to assure suitability for transfusion and processed into life saving components: red blood cells, plasma, and platelets, which go to help Central Texas patients. The Center works with the Marrow Donor Program of Central and South Texas to increase the number of Central Texans on the National Marrow Donor Registry. The Tissue Services division was established in 1985 due to the increasing demand for allograft tissue. Today, The Tissue Center surgically recovers tissue from approximately 300 donors each year and assists with donor family services. The Tissue Center''s main facility is located in Austin with a satellite office in Corpus Christi.
Psychology wiki is an up-to-date, authoritative statement of knowledge, theory, and practice in the whole field of psychology reflecting generally accepted academic standards. A topic covered in this wiki portal includes Neuroinformatics. The Neuroinformatics wiki page currently offers the following categories: overview, history, collaboration with other disciplines, research programs and groups, technologies and developments, references, external links, research centers, and more. Neuroinformatics is a research field that encompasses the development of neuroscience data, knowledge and application of computational models and analytical tools for the integration and analysis of experimental data and for improving existing theories about nervous system and brain. Neuroinformatics provides tools, databases, models, networks technologies and models for the clinical and research purposes in the neuroscience community and other fields.
Alabama Head Injury Foundation: Improving Life After Traumatic Brain Injury
The Alabama Head Injury Foundation (AHIF) was founded in 1983 to increase public awareness of Traumatic Brain Injury (TBI) and to stimulate the development of supportive services. Today, AHIF is among the largest state brain injury associations in the nation with model programs and statewide services. Its mission is to improve the quality of life for people who have survived traumatic brain injuries and for their families. Whether the injury is mild or severe the life of the injured person and their family is changed forever. The impact can be both emotionally and financially devastating. AHIF provides the information to help clients and families understand the results of injury. AHIF helps access available resources and provides services and programs which meet the unique needs of individuals with traumatic brain injury (TBI) as well as spinal cord injury (SCI) in certain programs.
University of Texas MD Anderson Cancer Center Clone Bank
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The MD Anderson Cancer Center Clone Bank consists of 802 murine cDNA clones, purchased from Research Genetics, Inc. These clones were sequence verified. A listing of the following are available: * Currently available clones (xls) * Top five blast hits for incorrect sequences (xls)
Community Tissue Services (CTS), a not-for-profit tissue bank, was founded in Dayton, Ohio in 1986 as a division of the Community Blood Center. The tissue bank was established to help patients in need of life saving or life enhancing tissue grafts. CTS'' goal is to educate the community of the importance of tissue donation so that families can make informed decisions about the options of donation. CTS serves the public through recovery, processing and distribution of human tissue grafts used for transplantation. Since 1994, CTS has expanded its Dayton, Ohio operations into Texas, Oregon, California, Indiana, Pennsylvania and Tennessee, with over 300 employees nationwide. CTS is an accredited member of the American Association of Tissue Banks and CTS-CTIR is ISO 13485 certified. Strongly committed to providing the highest quality of tissues for transplantation, the tissue bank complies with all federal and state regulations. CTS is currently one of the largest US tissue banks, distributing nearly 10% of the tissue grafts in the United States. CTS is the largest nonprofit provider of skin grafts to surgeons for severe burn patients.
The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. Links to the library''s holdings in LocatorPlus, NLM''s online public access catalog, are also provided.
The GEO Profiles database stores gene expression profiles derived from curated GEO DataSets. Each Profile is presented as a chart that displays the expression level of one gene across all Samples within a DataSet. Experimental context is provided in the bars along the bottom of the charts making it possible to see at a glance whether a gene is differentially expressed across different experimental conditions. Profiles have various types of links including internal links that connect genes that exhibit similar behaviour, and external links to relevant records in other NCBI databases. GEO Profiles can be searched using many different attributes including keywords, gene symbols, gene names, GenBank accession numbers, or Profiles flagged as being differentially expressed.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023.The Linked Clinical Trials (LinkedCT) project aims at publishing the first open Semantic Web data source for clinical trials data. The data exposed by LinkedCT is generated by (1) transforming existing data sources of clinical trials into RDF, and (2) discovering links between the records in the trials data and several other data sources. You may download static data dumps. The LinkedCT data space is published according to the principles of publishing Linked Data. These principles greatly enhance adaptability and usability of data on the web. Each entity in LinkedCT is identified by a unique HTTP dereferenceable Uniform Resource Identifier (URI). When the URI is looked up, related RDF statements about the entity is returned in HTML or RDF/XML based on the user''s agent. Moreover, a SPARQL endpoint is provided as the standard access method for RDF data.
DISCO: Extensible Web resource DISCOvery
registration and interoperation framework
DISCO is an information integration approach designed to facilitate interoperation among Internet resources. It consists of a set of tools and services that allows resource providers who maintain information to share it with automated systems such as NIF. NIF is then able to harvest the information and keep those sets of information up-to-date. How is this accomplished? By using a series of files and/or scripts which are then placed in the root directory of the resource developer''s resource. (NIF can also host the files on its servers and crawl for changes there.) Once the files of the resource providers are in place, and DISCO is notified, the DISCO server can then recognize and consume the information shared, providing machine understandable information to NIF Integrator Servers (also known as Aggregators) about your resource. What can DISCO do for my resource? * Inform search engines about your resource and keep your NIF Registry resource description up-to-date. * Expose your data (semi-structured datasets or fields within your structured database) through NIF''s Data Federation you choose what data will be shared. * Create links from an NCBI database (e.g., PubMed, Protein, Nucleotide, etc.) to your data records in NIF using Entrez LinkOut. * Advertise your terminology or ontological information. * Share your resource''s news with the NIF community., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Open-Source Robotic Biorepository and Informatics Technology
The Open-Source Robotic Biorepository & Informatics Technology is a platform that aims to make blood samples and health related information available to researchers. This resource is intended to help researchers understand human biology so they can develop treatments that are effective for each individual. In the simplest terms, ORBIT is a large library of blood specimens. Patient recruitment for ORBIT is being rolled out of Aurora''s 13 hospitals and 120 clinics in eastern Wisconsin, starting with its Milwaukee facilities. So far, more than 70 percent of patients have agreed to participate. If patients agree to participate, blood left over from their medical tests is sent to the ORBIT lab. Here a robot extracts the DNA from the blood, bar codes the sample and stores it in a freezer. The barcode allows the informatics technology to link each sample with the appropriate privacy-protected electronic medical record. The open source aspect of ORBIT is intended to expand scientific discovery. Researchers who use ORBIT specimens will return their research results to ORBIT to minimize study repetition and to allow researchers from around the world to build on previous results.
The baseline NCS, fielded from the fall of 1990 to the spring of 1992, was the first nationally representative mental health survey in the U.S. to use a fully structured research diagnostic interview to assess the prevalences and correlates of DSM-III-R disorders. The baseline NCS respondents were re-interviewed in 2001-02 (NCS-2) to study patterns and predictors of the course of mental and substance use disorders and to evaluate the effects of primary mental disorders in predicting the onset and course of secondary substance disorders. In conjunction with this, an NCS Replication survey (NCS-R) was carried out in a new national sample of 10,000 respondents. The goals of the NCS-R are to study trends in a wide range of variables assessed in the baseline NCS and to obtain more information about a number of topics either not covered in the baseline NCS or covered in less depth than we currently desire. A survey of 10,000 adolescents (NCS-A) was carried out in parallel with the NCS-R and NCS-2 surveys. The goal of NCS-A is to produce nationally representative data on the prevalences and correlates of mental disorders among youth. The NCS-R and NCS-A, finally, are being replicated in a number of countries around the world. Centralized cross-national analysis of these surveys is being carried out by the NCS data analysis team under the auspices of the World Health Organization (WHO) World Mental Health Survey Initiative. In order to provide an easily accessible database which can be updated and checked on a regular basis, we have created a public use file system containing all the documents from the NCS and NCS-R programs. These file systems can be accessed through the Internet and either downloaded onto a disk or printed. We will update the system on a regular basis to add newly completed paper abstracts and other documents. In addition, the NCS and NCS-R data can be accessed through ICPSR (Inter-university Consortium for Political and Social Research). Any updates to the data to correct coding or classification errors will be made available along with written documentation of the changes in ICPSR''s quarterly newsletter.
Sapien Games is a blog at the intersection of Nicholas Saij Horton''s interests in Evolutionary Science and Political Theory. He is a graduate student in mathematics at Portland State University. His areas of study are Quantum Game theory and Mathematical Modeling in the Behavioral Sciences including Biological Evolution, Economics, and Political Science.
National Tsing Hua University; Hsinchu; Taiwan
National Tsing Hua University; Hsinchu City; Taiwan
Research university in Hsinchu City, Taiwan. Public institution that traces its roots back to 1911, when it was established in Beijing as Tsing Hua Academy.
Human Biological Data Interchange (HBDI)
Database of medical history and genealogical data on over 6700 families who are affected by type 1 diabetes and a repository of DNA and immortalized cell lines collected from 500 families. This database and repository was originally created to help researchers uncover the genetic causes of type 1 diabetes but today, it is also used by researchers who study type 2 diabetes, diabetic complications, autoimmune diseases, kidney disease, and other disorders. The following resources and services are available to researchers through HBDI: * International Type 1 Diabetes Database: This database includes more than 6700 families with diabetes, related complications and other genetic diseases. There are extensive genealogical and medical histories for more than 90,000 individuals. NDRI conducts searches of the database for approved research requests. * HBDI Catalog: The catalog contains 503 family pedigrees with associated cell lines, DNA, and serum for research. Also available are HLA-typing and auto-antibody test results for diabetes families in the catalog. * HBDI Repository: The HBDI repository contains cell lines, DNA, and HLA typing information from 480 families, and frozen buffy coats from 23 families, all with Type 1 diabetes. They have recently expanded the repository to include specimens from individuals with rare diseases. * Customized Collections: NDRI will collect data from patients and physicians, conduct phone interviews and collect blood and other specimens for research on request., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The Genome Properties system consists of a suite of Properties which are carefully defined attributes of prokaryotic organisms whose status can be described by numerical values or controlled vocabulary terms for individual completely sequenced genomes. The system has been designed to capture the widest possible range of attributes and currently encompasses taxonomic terms, genometric calculations, metabolic pathways, systems of interacting macromolecular components and quantitative and descriptive experimental observations (phenotypes) from the literature. You may search the Genome Properties Database in 1 of 3 ways: * Search For Predicted Properties in the CMR: The Genome Property Search allows you to search the Genome Property database for state information for selected genomes and properties. * Perform a Keyword Search for a Specific Property: Lists all Genome Properties that match a specific text string. You can choose to search All Fields within a genome property or the Property Name. * Browse Top Level Genome Properties: Click on the properties to see the specific genome property report page. The Genome Properties system presents key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties.
WSDbfetch is a webservice implementation of Dbfetch, a generic DB retrieval system that allows you to retrieve entries from various up-to-date biological databases using entry identifiers or accession numbers. It aims to provide programmatic access for sequence retrieval. This involves a service running on a SOAP server responding to remote client invocations. This is equivalent to the CGI based dbfetch service and like the CGI service a request can return a maximum of 200 entries.
BIO - OPTIONS provides human tissues and biological materials to researchers and scientists for molecular and genomic research. These high quality, well characterized biological specimens are available for drug and biomarker discovery, validation of drug targets and development of diagnostic tests and devices. BIO - OPTIONS specializes in providing fresh tumor tissue, blood and other biological fluids delivered the same day or overnight for your studies. We collect specimens from virtually all disease states through our extensive network of physicians, hospitals, and clinical laboratories. All of our specimens are collected at facilities located in the United States in compliance with all applicable federal and state laws and regulations and ethical guidelines. Collection facilities are located on the East and West coasts and Midwest. The officers of BIO - OPTIONS consist of licensed physicians with extensive medical training and experience. This enables us to work directly with physicians and support staff to insure that collection protocols provide the high quality specimens needed for research without compromising patient care. Protocols are designed to work within the workflow of physician offices and hospital operating rooms so that specimens are timely processed and preserved and well characterized.
EyeWiki is an ophthalmic wiki where ophthalmologists, other physicians, patients and the public can view an eye encyclopedia of content written by ophthalmologists covering the vast spectrum of eye disease, diagnosis and treatment. Any qualified ophthalmologist, or ophthalmologist in training, is invited to contribute content to the wiki and post it immediately. Categories: *Cataract / Anterior Segment *Cornea / External Disease *Glaucoma *Miscellaneous *Neuro-ophthalmology / Orbit *Oculoplastics / Orbit *Oncology / Pathology *Pediatric Ophthalmology / Strabismus *Refractive Management / Intervention *Retina / Vitreous *Uveitis
Cancer Center Tissue Bank - Fudan University
Institutional Tissue Bank of Fudan University Shanghai Cancer Center
The Institutional Tissue Bank (ITB) of Fudan University Shanghai Cancer Center was established in 2006 with the goal of serving as a central repository for human tissue samples for cancer research and possible personalized medicine for the institution. The Institutional Research Board oversees the fulfilling of informed consent of each patient whose samples are collected. The ITB''s collection procedures meet the global quality standards and provide high quality tissue samples. The quality control for morphology, RNA, DNA and protein has been set up to ensure the sample quality. Routine frozen section from tissue aliquot is made for every piece of sample to ensure the component of tumor tissue and the pathological feature is the same as the diagnosed tumor. Agilent 2100 Bioanalyzer was used to provide RNA and DNA quality parameters. The Tissue Bank occupies 500 m2, with sufficient space for sample preparation and storage, data registration, data tracking/access, related equipments and monitor system. Variant samples including blood, tumor tissue, and body fluids are collected and serve as alternative permanent patient tissue records. Annotation of collected samples is captured through linking the medical record and pathological report system to tissue bank software. Frequent tumor types such as lung cancer, breast cancer, gastric cancer, urological tumors, gynecological tumors and esophageal cancers, head & neck cancers, as well as infrequent cancer types such as malignant soft tissue sarcomas, pancreatic cancer, gall bladder cancer, and other rare cancers are all collected and stored. Tumor tissues are stored with matched normal tissues. Serum and plasma are isolated from coagulation plus and coagulation minus blood samples. White blood cells are stored as well. Tissues are stored both in RNALater at -20 degrees C and -80 degrees C after snap frozen. Samples have been increased from 4,000 in 2008 to 10,783 in 2009. To the end of September 2010, over 30,000 samples has been processed and stored in our tissue bank. As planned, 50,000 samples will be stored dynamically. Over 50 funded projects have used the samples from our tissue bank. Productive papers have been published in the past years by using the samples. More and more projects will be approved to get research resources from tissue bank in the future. The tissue bank of FUSCC has been designated as the key subject and successful model by Shanghai municipal government.
British Columbia Tumour Tissue Repository
BC Cancer Agency Tumor Tissue Repository
BC Cancer Agency Tumour Tissue Repository
A provincial biobank resource to support translational cancer research at the BC Cancer Agency, across Canada and internationally. This biobank collects biospecimens (tissues and blood), and clinical information and processes these to create anonymous cases that can be studied by cancer researchers to understand how cancer develops, how it grows, how it spreads, and how it responds to treatment. These tissues and data are obtained from patients who undergo surgery to treat a tumor and who have generously provided their consent for the TTR to collect tissues that are unused after diagnosis has been completed. The TTR is a provincial program that currently comprises a core biobank at the Vancouver Island Center, Victoria, that offers participation in the program to patients in Victoria and Nanaimo. The TTR works with other banks and expert translational research groups in BC, to create expanded capacity for collection and opportunities for research access to tissue resources. The TTR operates under the management and oversight of the director, a scientific advisory board, and the UBC BCCA Research Ethics Board. The TTR operates within organizational policies and a commitment to protection of donor privacy that is embodied in all standard operating procedures and aspects of the repository. The TTR is also a founding member and contributor to the development of provincial (BC BioLibrary) and national (CTRNet) initiatives to promote biobanking.
The BioReliance Biorepository offers secure cell storage of eukaryotic, prokaryotic and viral biological materials. Our vapor phase liquid nitrogen and -80����??C freezers offer complete flexibility and protection. Each bank is certified free from mycoplasma and tested for sterility prior to storage and then divided and stored in separate validated vessels. Our continuously monitored facilities in US and UK follow cGMP.
A software for binning and annotating short paired-end reads.
Science website dedicated strictly to neuroscience research news including brain research news, neuroscience jobs, neuroscience forums, social network, student resources and events. They scour news sources every weekday and choose only neuroscience research related news headlines and links to post. They attempt to link to the original neuroscience research news release as much as possible to enable readers to bypass opinion and get straight to the news. In a few cases, the original neuroscience research article is not available without registration, so they will link to a secondary source to ensure that readers get the neuroscience news as soon as possible. Neuroscience News staff encourages visitors to submit neuroscience research articles, brain research news, neuroscience article reviews, breaking neuroscience news tips, original neuroscience blog posts, neuroscience book reviews and suggestions to be reviewed, implemented and possibly published on Neuroscience News.
Database listing of jobs where neuroscience students, neuroscience research professionals, neuroscience professors and anyone looking for a neuroscience job can use the interface to find jobs in their area or post neuroscience jobs needing to be filled. Neuroscience News members are encouraged to use the resources for neuroscience job information and also consider joining up to our Neuroscience Jobs Group. Members of the Neuroscience Jobs group are allowed to post jobs available and job positions sought. Neuroscience jobs offers, job listings, neuroscience resumes, networking and more can be found in the group.
SI 622 is a Masters-level Human-Computer Interaction course taught in the School of Information at the University of Michigan on a yearly basis during the Winter semester. Students learn and apply a number of methods for assessing the usability and usefulness of interactive systems such as websites or software applications. The course is based around a semester-long group project in which groups of 3-4 students select a system to study and then proceed to conduct a series of evaluations and other analyses, generating reports and recommendations along the way. If you would like to obtain a free, high-quality assessment of your website or software product, you can submit a proposal for a course project. If a student group chooses your project, they will perform a series of evaluations of your product and give you detailed and actionable feedback on the usability problems they find.
Structural variant discovery by integrated paired-end and split-read analysis
Integrated structural variant prediction software that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout genome.
Established nearly 30 years ago, the New York Firefighters Skin Bank is the only comprehensive skin bank in New York State, providing allograft skin grafts to patients throughout the region. Allograft skin grafts enable burn victims to fight infection, maintain their fluids and body heat, and control pain. The Skin Bank also provides cryopreservation services so that patients can bank their own skin for future autologous transplantation.
Golden State Donor Services (GSDS) is the nonprofit, federally designated transplant donor network serving two and a half million people in the greater Sacramento area. We are committed to saving and improving lives by connecting one life to another through donation and transplantation. We support potential donor families in their time of loss, provide care for them through the donation process and coordinate the recovery of organs and tissues for transplant. We also provide after-care support to donor families while at the same time working to inspire universal acceptance of donation to ensure every person in need receives the ����??Gift of Life.����?? GSDS'' designated service area includes 11 counties in Northern California, (Amador, Calaveras, Colusa, El Dorado, Nevada, Placer, Sacramento, Sierra, Sutter, Yolo, and Yuba), as well as the communities of Santa Rosa and Reno. Currently GSDS has agreements with 30 hospitals. In Golden State Donor Services'' area, more than 1000 people now wait for an organ transplant, (heart, liver, lungs, kidneys, intestine or pancreas).
Simply put ganfyd is an evolving textbook of medicine: a free medical knowledge base that anyone can read and any registered medical practitioner may edit. This collaborative medical reference by medical professionals and invited non-medical experts is based around the wiki format, enabling true sharing of knowledge. Please join and help us to create a great source of information and experience! Ganfyd is the first of its type and relies on your contributions to make it a truly world-class resource. Contents: * Medical Specialties * Surgical Specialties * Primary Care * Public Health * Laboratory-based specialties * Imaging Specialties * Basic Medical Sciences * Miscellaneous * Women''s health * Survival Guides * How-tos & Practical Advice * Resources for Trainees * Computing * Medical Dictionary
The Scientist: Magazine of the Life Sciences
The Scientist is the magazine for life science professionalsa print and digital publication dedicated to covering a wide range of topics central to the study of cell and molecular biology, genetics, and other life-science fields. Through innovative print articles, online stories, and multimedia features, the magazine explores the latest scientific discoveries, trends in research, innovative techniques, new technology, business, and careers. It is read by leading researchers in industry and academia who value penetrating analyses and broad perspectives on life-science topics both within and beyond their areas of expertise. Written by prominent scientists and professional journalists, articles in The Scientist are concise, accurate, accessible, and entertaining.
A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services.
Procures brain, spinal cord and other tissues bequeathed by donors and makes them available to scientists investigating the cause and treatment of multiple sclerosis. The Tissue Bank achieves this aim by addressing the following objectives: # Increasing the awareness of the importance of human tissue to research amongst the MS and scientific communities. # Being sensitive to the needs of the tissue donor and responsive to the requirements of scientists when collecting and processing donated tissue. # Making available high quality, well-documented samples of tissue to research scientists working to better understand MS. There are approximately 85 000 people with multiple sclerosis in the United Kingdom. The varied symptoms experienced by all these people result from damage taking place within their brain and spinal cord. Understanding the exact nature of this damage is essential if we are to better treat the condition. Vital information about how the brain and spinal cord are damaged in multiple sclerosis can be obtained by using a multitude of experimental approaches to study the affected tissue from people with MS and ''control'' tissue from people without the disease. The donation of tissue for research is therefore fundamental to furthering our understanding of the causes of multiple sclerosis and to developing more effective treatments for the disease. The UK Multiple Sclerosis Tissue Bank welcomes requests for tissue samples for use in research into the cause and treatment of multiple sclerosis. It has available post mortem, cryopreserved brain and spinal cord tissue both fixed and unfixed, and cerebrospinal fluid from patients with and without a history of multiple sclerosis. Freshly dissected tissue samples, or those preserved using unconventional techniques may also be made available by prior arrangement.
UCL/UCLH Biobank for Studying Health and Disease
UCL / UCLH Biobank for Studying Health Disease
UCL/UCLH Biobank for Studying Health Disease
UCL Biobank for studying Health and Disease
The UCL/UCLH Biobank for Studying Health and Disease has been primarily established to support the Research Programme and scientific needs, of the Pathology Department UCLH & the UCL Cancer Institute. The establishment of the core programme enables a centralised approach to the management and integration of all research groups working within these institutions, providing appropriate structure and support. The biobank has policies and guidelines to guarantee compliance with HTA legislation and to ensure quality standards will be maintained. The biobank stores normal and pathological specimens, surplus to diagnostic requirements, from relevant tissues and bodily fluids, as well as human tissue used in xenograft experiments. Stored tissues include; snap-frozen or cryopreserved tissue, formalin-fixed tissue, paraffin-embedded tissues, and slides prepared for histological examination. Tissues include resection specimens obtained surgically or by needle core biopsy. Bodily fluids include; whole blood, serum, plasma, urine, cerebrospinal fluid, milk, saliva and buccal smears and cytological specimens such as sputum and cervical smears. Fine needle aspirates obtained from tissues and bodily cavities (eg. pleura and peritoneum) are also collected. Where appropriate the biobank also stores separated cells, protein, DNA and RNA isolated from collected tissues and bodily fluids described above. Some of the tissue and aspirated samples are stored in the diagnostic archive.
Tumorbank Bern - TBB collects high quality clinical samples since 2003 for translational research selected by expert pathologists under controlled conditions of normal and diseased tissue from different origin. The Tumor Bank is approved by the Ethical Commission of Bern, we only collect samples with written informed patient consent. Origin of Tissue: Thoracic Surgery, Gynecology, Urology, Visceral Surgery, Orthopedic Surgery, Head and Neck Surgery, Neurosurgery Tumorbank Bern TBB holds 12,000 samples from 3600 Patients. Please contact us to check if we have samples for your field of research.
OSU College of Pharmacy Bachelor of Science in Pharmaceutical Sciences (BSPS) Program Overview
OSU Bachelor of Science in Pharmaceutical Sciences
OSU College of Pharmacy Bachelor of Science in Pharmaceutical Sciences (BSPS) Program
OSU College of Pharmacy Bachelor of Science in Pharmaceutical Sciences Program
Bachelor of Science in Pharmaceutical Sciences (BSPS) provides training for success in variety of healthcare or research-oriented/non-clinical graduate programs and careers. Emphasizes integrated science learning, hands-on laboratory experiences and career development.
Leishmania major strain Friedlin homepage on GeneDB
Leishmania major strain Friedlin on GeneDB
Database of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.
IPBIR - Integrated Primate Biomaterials and Information Resource
Integrated Primate Biomaterials and Information Resource
Integrated Primate Biomaterials Information Resource
IPBIR - Integrated Primate Biomaterials Information Resource
The purpose of the IPBIR - Integrated Primate Biomaterials and Information Resource is to assemble, characterize, and distribute high-quality DNA samples of known provenance with accompanying demographic, geographic, and behavioral information in order to stimulate and facilitate research in primate genetic diversity and evolution, comparative genomics, and population genetics. Further research in these areas will advance our understanding of human origins, the biological basis of cognitive processes, evolutionary history and relationships, and social structure, and will provide critical scientific information needed to facilitate conservation of biological diversity. The derived DNA will be openly available to the broad scientific community who agree to restrict use to non-commercial purposes. DNA and cell culture samples are distributed only to qualified professional persons who are associated with recognized research, medical, or educational organizations engaged in research.
The Stanford Tissue Bank was established with seed funding from the Bio-X Program and the Department of Pathology, and currently receives support from the Stanford Cancer Institute. The goal of the Tissue Bank is to facilitate biomedical research using tissues at Stanford, by providing services for the procurement, storage, distribution, and study of tissues. Current Tissue Bank activities and services include collecting and banking freshly-frozen tissue specimens from excess surgical material and from autopsy, providing fresh tissue specimens for viable cell studies, processing and banking blood components, maintaining a tissue database with links to clinicopathological data, performing histological staining and pathological review, and coordinating patient consent and assuring regulatory compliance. As a centralized shared resource, the Tissue Bank adds value through experience, efficiency, standardization, accountability, protection of patient confidentially, and timely completion of research. An oversight committee serves to guide policies, prioritize resources, and review service requests to ensure equitable usage.
Ontology designed for neuroscience. Includes complete set of concepts that describe parts of rat nervous system, growing set of concepts that describe neuron populations identified in different brain regions, and relationships between concepts.
Amino Acid-Nucleotide Interaction Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. AANT, the Amino Acid-Nucleotide Interaction Database, contains information derived from all of the protein/nucleic acid complexes with experimentally determined structures in the Protein Data Bank. You can visualize the AANT models using the simple web interface, which relies on the Chime plug-in. You can also download these models for further analysis using publicly available tools for manipulating PDB structures. The software that generates AANT uses HBPLUS to predict hydrogen bond interactions between single bases and single amino acid residues within these complexes. The AANT software uses this information to break down a single PDB structure into scores of individual interactions between either the base, sugar, or phosphate of a nucleotide and the side chain or peptide backbone of a amino acid. The software then superimposes all the interactions between a particular moiety of a nucleotide and a particular moiety of a amino acid residue into a single 3D model, centering on a particular point in the base, sugar, or phosphate. The AANT software then groups geometrically similar interactions into clusters.
Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.
A DNA-composition-based binning algorithm for classifying metagenomic reads. It has the ability to accurately bin raw sequence reads without need for assembly or training. It applies principal component analysis to project the data into an informative lower-dimensional space, and then uses the normalized cut clustering algorithm on this filtered data set to classify sequences into taxon-specific bins.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. Search engine that integrates over 100 curated and publicly contributed data sources and provides integrated views on the genomic, proteomic, transcriptomic, genetic and functional information currently available. Information featured in the database includes gene function, orthologies, gene expression, pathways and protein-protein interactions, mutations and SNPs, disease relationships, related drugs and compounds.
HD Community BioRepository is a secure, centralized repository that stores and distributes quality-controlled, reliable research reagents. This repository currently provides access to huntingtin DNAs, polyclonal antibodies (with antigenic peptides) and cell lines. Monoclonal antibodies and hybridomas will be added in the near future. Working together with the Coriell Institute for Medical Research, CHDI Foundation established this secure, centralized repository to store and distribute quality-controlled and reliable research reagents to give research scientists unobstructed access to biomaterials and to support the discovery of therapeutics that will slow or prevent Huntington's disease. Huntington's disease is a fatal, familial disease caused by a mutation in the huntingtin gene. The mutation causes brain cells to malfunction, resulting in cognitive and physical impairments that, over the course of the disease, isolate and constrain the individual. There is currently no way to stop or reverse the course of Huntington's disease. Researchers currently not collaborating with CHDI Foundation may request these Huntington's disease resources from the HD Community BioRepository through the website; CHDI collaborators are asked to contact Mithra Mahmoudi at CHDI Management. Materials will be sent after completing a simple online MTA. Recipients are asked to cover the costs of shipping and handling. Persons with Huntington's disease bioresources interested in making them available to the research community through the HD Community BioRepository should also contact CHDI Management.
A private, not-for-profit research organization that serves as an international collaborative enabler in order to discover drugs that slow the progression of Huntington's disease (HD). The activities of CHDI extend from exploratory biology to the identification and validation of therapeutic targets, and from drug discovery and development to clinical studies and trials. CHDI works with biotech and pharmaceutical companies and funds and works with academic HD researchers at universities.
A genetic resource to support the study of autism in families where more than one child is affected or where one child is affected and one demonstrates another significant and related developmental disorder. An open bank of anonymously collected materials documented by a detailed clinical diagnosis forms the basis of this growing database of information about the disease. The Autism Resource is housed at the Coriell Institute for Medical Research in New Jersey, which holds the world''s largest collection of human cells for use in genetic research. The Autism Research Resource has been built through a full collaboration between Coriell and clinical services at the UMDNJ-Robert Wood Johnson Medical school, New Brunswick campus, which provides clinical information and diagnosis. All clinical interviews were conducted face-to-face. Further multiplex families will be added to the resource in a continuing program of diagnosis and Repository development. The Autism Research Resource includes cell lines and DNA from families with more than one child who meets criteria for autistic disorder. An additional group of families is included in which monozygotic twins meet all criteria for autistic disorder. Also included in this resource, however, are families in which one child meets the criteria for autistic disorder while another child displays behavior with a broader phenotype of falling within the spectrum of autistic disorder. A small number of multiplex families is included in which one child meets all criteria for autistic disorder and a second has a behavioral disorder falling outside the autism spectrum. Pedigrees are provided for each family. Where clinical statements are noted for individuals other than the affected children and parent(s), these should be judged as reported. All family relationships have been verified by confirming the molecular identities, established using a panel of six microsatellite markers.
Yerkes Collection Non-Human Primate Resource
The Yerkes National Primate Research Center of Emory University is an international leader in biomedical and behavioral research. For more than seven decades, the Yerkes Research Center has been dedicated to advancing scientific understanding of primate biology, behavior, veterinary care and conservation, and to improving human health and well-being. The Yerkes Non-Human Primate Resource at Coriell includes viable and contaminant-free Pan troglodytes cell cultures and high quality DNA samples derived from these cultures, both subjected to rigorous quality control.
Web server that predicts protein transmembrane topology and signal peptides. Hidden Markov models (HMM) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. They expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBN). Their model, Philius, is inspired by a previously published HMM, Phobius, and combines a signal peptide sub-model with a transmembrane sub-model. They introduce a two-stage DBN decoder which combines the power of posterior decoding with the grammar constraints of Viterbi-style decoding. Philius also provides protein type, segment, and topology confidence metrics to aid in the interpretation of the predictions.
Hollings Cancer Center Tissue Biorepository and Research Pathology Services Shared Resource
Hollings Cancer Center Tissue Biorepository Research Pathology Services Shared Resource
The Hollings Cancer Center Tissue Biorepository & Research Pathology Services Shared Resource provides investigators with a centralized infrastructure that promotes biomedical research involving the use and study of human biospecimens. The shared resource is comprised of four integrated components: Biospecimens and data bank, Laser Capture Microdissection, Tissue Microarray, and Research Pathology Services. These components, along with extensive staff expertise, offer a comprehensive means by which researchers can utilize valuable human biospecimens and cutting edge technology to support basic, translational and clinical research. Services: * Biospecimen and Data Bank ** Collecting, processing, and banking of tissue, saliva, urine, blood, plasma, serum, and other tissue derivatives; including those for protocol driven studies ** Retrieval of banked specimens linked to clinicopathologic data, while maintaining patient confidentiality, for research use ** Quality control of collected tissue by the Tissue Biorepository Director, a trained pathologist: verification of diseased state and assessment of tumor purity, etc ** Quality control of DNA/RNA/protein isolated from collected tissue using the Agilent Bioanalyzer * Laser Capture Microdissection ** Identification, localization, and microdissection of targeted cell populations (from human and animal tissue sources) ** Extraction of DNA/RNA/protein from microdissected samples. ** Quality analysis and quality control of isolated nucleic acid using Agilent Bioanalyzer * Tissue Microarray ** Create custom and standard TMAs ** Consultation and technical support in the construction and analyses of TMA * Research Pathology Services ** Macrodissection of tissue prior to isolation of DNA/RNA/protein to increase tumor purity ** Immunohistochemistry and In-situ hybridization ** Quantitative image analysis on conventional and TMA sections, including tissue scoring, Ki-67 labeling index, microvascular density counting, and tissue microarray scoring, etc. * Bio-molecular Assessment ** Cellular DNA, RNA and protein prepared by the Tissue Repository from banked specimens or any other biomolecules submitted by investigators can be qualitatively assessed by Agilent Bioanalyzer, prior to use for downstream applications such as microarray and/or qRT-PCR analysis
Washington Regional Transplant Community - WRTC
Washington Regional Transplant Community
Founded in 1986, Washington Regional Transplant Community (WRTC) is federally designated as the organ procurement organization (OPO) for Washington, DC, Northern Virginia and suburban Maryland since 1988. This non-profit organization provides full-service organ, tissue and eye recovery. WRTC responds to potential donors at more than 44 area healthcare institutions and serves approximately 5.13 million Washington-area residents. It coordinates with all five area transplant centers and the United Network for Organ Sharing (UNOS). WRTC provides support to more than 4,000 donor family members and acts as the community and professional education resource for organ and tissue donation in the Washington, DC, region.
Estimate average coverage and create Nonpareil curves for metagenomic datasets.
Nucleotide database as collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
Drug discovery company providing pharma with protein and antibody therapeutics in the fields of Oncology and Immunology.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. BioVU is a research resource providing a View into biology at the level of DNA and other important macromolecules. BioVU has two major components. The first is a repository of DNA samples (extracted from discarded blood samples) that are coded solely by a Research Unique Identifier (RUI) derived from the Medical Record Number (MRN) using a one-way hash function. This is a computer algorithm that creates a transformation of each MRN such that the resulting RUI (which is in this instance is a 512 byte identifier) is unique, and has the property that it is not possible to infer or compute the MRN that generated it. As of early 2009, over 50,000 DNA samples were in the biobank, with new samples being added at the rate of approximately 700 per week. The second component of the resource is the creation of a database known as the Synthetic Derivative which is a collection of de-identified information extracted from VUMC''s electronic clinical information systems, indexed by the same one-way RUI used to track samples, and with content changed by deletion or permutation of all identifiers contained within each record. The Synthetic Derivative search interface is available to Vanderbilt researchers via the StarBRITE research portal created and maintained by the Vanderbilt Institute for Clinical and Translational Research. This user interface enables investigators meeting protocol approval criteria and other user agreement requirements to receive protocol-specific sets of data derived from DNA samples and from the Synthetic Derivative., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels.
FslAtlasIntegration is a documentation site for FSL coordinate reporting and atlas integration. Links to references are available to internal FMRIB systems. Some of this material is drawn from Matthew Brett' '''s webpages on MNI-Talairach Atlas Differences and Localization in Brain Mapping. http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml
SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank (PDB). The resultant multiple alignment can be colored according to different structural features and the matching 3D structures can be superimposed and viewed in RasMol. Use the form to identify your protein sequence of interest by: a) providing a PDB code, b) providing a UniProt code or accession number, c) pasting in your sequence, or d) uploading a PDB file. By default the whole PDB will be searched, but you can restrict the search using the Search Option box at the bottom.
Software providing a framework for genomic data analysis using Apache Pig and Hadoop.
Central England Haemato-Oncology Research Biobank
Central England Haemato-Oncology Research Biobank (CEHRB)
The Central England Haemato-Oncology Research Biobank stores excess material from oncology samples referred for diagnostic testing and disease monitoring at the West Midlands Regional Genetics Laboratory (WMRGL). The bank is housed within the WMRGL. Types of material stored include viable cells, fixed cell suspensions, DNA, RNA / cDNA, and plasma. The material is made available to all cancer research groups both locally and nationally. Excess sample (mainly from blood and bone marrow) is stored from diagnostic patient material and from samples received throughout their disease course. The WMRGL serves a population of about 5.5 million and is the largest UK NHS genetic Lab. Due to the large patient population CEHRB is able to collate sufficient research material from all classifications of neoplastic haematological disorders including those that are rare.
Johns Hopkins University; Undergraduate Neuroscience Program
Johns Hopkins University; Undergraduate Program in Neuroscience
Undergraduate Program in Neuroscience offers broad overview of field, as well as more advanced training in one of four specialized areas: cellular and molecular, cognitive, computational, or systems neuroscience.
Since its creation in 1990, the mission of the Genethon''s DNA and Cell Bank is to promote advances in genetic research by providing the scientific community with a high quality cell and human tissue products resource. Europe''s leading bank for genetic diseases, it serves the whole of the medical and scientific community. Each year, Genethon''s DNA and Cell Bank: * Produces approximately 2,000 lymphoblastoid cell lines * Performs approximately 3,000 DNA extractions * Prepares primary myoblast and fibroblast cultures from approximately 100 biopsies Genethon has developed a computer database for ensuring sample management and traceability, which has been submitted to and approved by the CNIL. The Genethon DNA and Cell Bank has been AFNOR certified, according to French biological research center standard NF S 96-900. The activities of the DNA and Cell Bank are as follows: * Collecting blood or DNA from patients affected with genetic diseases and their families with the minimum identification data necessary for the monitoring and follow-up of samples. * Processing the samples in order to make them available to the scientific community and perpetuating DNA preservation (serum isolation and DNA extraction), isolating lymphocytes and establishing lymphoblastoid B lines and primary cultures (mainly myoblasts and fibroblasts). * Storing samples for future research and preserving the genetic heritage by ensuring the long-term physical security of the preserved samples. * Distributing samples as necessary for ongoing research while complying with the principles and laws of bioethics and using the best available technologies at minimum cost.All these activities are carried out following Standard Operating Procedures (SOP) validated by the Quality Assurance department at Genethon. The Bank is open to researchers in France or abroad wishing to store samples or use the services provided (extraction, establishment of cell lines etc.). Each sample received at Genethon is coded in order to guarantee confidentiality, in accordance with the rules established by the CNIL (French Data Protection Authority). All requests for collaboration with the DNA and Cell Bank should be made in writing to Dr Safaa SAKER-DELYE.
University of Michigan Autism and Communication Disorders Center
At the UMACC our mission is to improve the lives of individuals with autistic spectrum disorders and their families through the education of current and future leaders in the field, research that enhances the understanding of causation, intervention, prevention, and course, and provision of clinical services to individuals, families and the community. At UMACC, research and training initiatives strengthen clinical services by incorporating the latest research findings and sharing this information with families. At the same time, families have the opportunity to be a part of the research studies-and help expand scientific knowledge through their participation.
Job board for science professionals worldwide. You may search through international listings in science and research or post your job listing for free. Advanced filters are available and you may also research jobs by field. Currently, fields include: Agricultural Science, Anthropology, Biology, Chemistry, Computer Science, Design, Economics, Education, Engineering, Entertainment and Arts, Geoscience, History, Law, Linguistics, Literature, Mathematics, Medicine, Other, Philosophy, Physics, Political Science, Psychology, Religious Studies, Social Science, Space Science
A database of three-dimensional protein models calculated by comparative modeling. ModBase is organized into datasets, which are either available to the public, to the academic community, or to specific users. 20 unique amidohydrolase and 41 unique enolase structures have been determined have been included in the database.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 24,2025. In 2009, the Medical School and the Michigan Institute for Clinical & Health Research (MICHR) unveiled a new biorepository for U-M researchers in need of a controlled storage environment for biological samples. MICHR is pleased to be able to add to its many services for the research community a centralized biological repository for controlled storage of biological samples, and related services (including DNA, RNA, and other downstream preparation) within the U-M campus. The biorepository, located in the CAP/CLIA-certified Michigan Center for Translational Pathology (MCTP) laboratory at the U-M Traverwood facility on Huron Parkway, will store biologic material, including blood and urine. Sample accessioning and tracking will be accomplished using the caTISSUE suite of programs, and samples will be processed and stored in compliance with CAP/CLIA guidelines. Initially, all samples will be used only with the authorization of the individual investigator who directed the project under which the samples were obtained. Samples will be used in accordance with the relevant informed consent. Long-term plans include federating the database in order to facilitate sharing of data and samples between research teams.
Repository of genetic samples from approximately 3,000 families, each of which has one child affected with an Autism Spectrum Disorder (ASD) and parents unaffected with ASD. A central database characterizing all of the study subjects is available to any qualified researcher and biospecimens are freely available to SFARI grant holders, and to other researchers on a modest fee-for-use basis. Each genetic sample will have an associated collection of data that provides a precise characterization of the individual (phenotype). Rigorous phenotyping will maximize the value of the resource for a wide variety of future research projects into the causes and mechanisms of autism. The Simons Simplex Collection is operated by SFARI in collaboration with twelve university-affiliated research clinics.
University of Texas at Dallas School of Behavioral and Brain Sciences
University of Texas at Dallas School of Behavioral Brain Sciences
UT Dallas School of Behavioral and Brain Sciences
Mission of the School of Behavioral and Brain Sciences is to understand the intersection of mind, brain and behavior; enhance the health, education, and quality of life of children and families; and create and implement technologies and therapies that repair and strengthen human abilities. The School is housed in Green Hall on the main UT Dallas campus in Richardson. It also has satellite research centers and facilities in downtown Dallas.
Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads.
Free, collaborative 3D, interactive encyclopedia of proteins and other molecules, it collects, organizes and disseminates structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules, in a manner that is relevant and broadly accessible to students and scientists. With a free user account, users can edit pages in Proteopedia. Click on the green links to change the 3D image or click and drag the molecules. Categories include Diseases & Related Topics, Enzymes, Gene Expression & Replication, Metabolism, Signaling & Transport, Structural Biology and Miscellaneous. Currently, Proteopedia has 93,912 articles (pages), and 2,366 registered users (May 2013). Among other pages, Proteopedia contains one page (or article) for every entry in the World Wide Protein Data Bank. Proteopedia is updated weekly with new entries shortly after they are released by the Protein Data Bank. Most of these pages, which are titled with a four-character PDB identification code, are seeded automatically to include a default view of the asymmetric unit, the abstract of the publication, green links to sites and ligands, and molecule-specific links to other viewers and databases. When you go to a random page, you nearly always get one of these automatically-seeded, PDB-code-titled pages (click Random Page in the navigation box at the upper left), because of their abundance. In addition to one article about each entry in the Protein Data Bank (PDB identification code-titled articles), there are articles titled with the name of a molecule or a subject, instead of a PDB identification code. Some of these articles that have substantial content are listed at Topic Pages, or you can browse a complete list of articles not titled with a PDB identification code. There are also articles About Macromolecular Structure.
An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community.
ScienceNOW - UP TO THE MINUTE NEWS FROM SCIENCE
ScienceNOW is science headline news from all realms of science, including biology, genetics, medicine, stem cells, evolution, animals, climate change, the environment, physics, astronomy, and science policy. This free content is produced by Science Magazine''s award-winning team of journalists.
THIS RESOURCE IS NO LONGER IN SERVICE, documented Jan 13, 2022; To enhance the understanding of the evolution of the Kingdom Fungi, 1500+ species were sampled for eight gene loci across all major fungal clades, plus a subset of taxa for a suite of morphological and ultrastructural characters with resulting data: AFTOL Molecular Database (generated by WASABI - Web Accessible Sequence Analysis for Biological Inference), Blast search the AFTOL Database (generated by WASABI), AFTOL primers (generated by WASABI), AFTOL primers by species (generated by WASABI), AFTOL alignments, and the AFTOL Structural and Biochemical Database. Users may submit samples to the AFTOL project. AFTOL is a collaboration centered around four universities in the United States: Duke University (Francois Lutzoni and Rytas Vilgalys), Clark University (David Hibbett), Oregon State University (Joey Spatafora), and University of Minnesota (David McLaughlin). Participants throughout the world have donated vouchers, taxon samples, and gene sequences. The aim of the project is to reconstruct the fungal tree of life using all available data for eight loci (nuclear ribosomal DNA: LSU, SSU, ITS (including 5.8s, ITS1 and ITS2); RNA polymerase II: RPB1, RPB2; elongation factor 1-alpha; mitochondrial SSU rDNA, and mitochondrial ATP synthase protein subunit 6). A further objective of this study is to summarize and integrate current knowledge regarding fungal subcellular features within this new phylogenetic framework. The name of the bioinformatic package developed for AFTOL is WASABI which provides an efficient communication platform to facilitate the collection and dissemination of molecular data to (and from) the laboratories and participants. All molecular data can be viewed, downloaded, verified, and corrected by the participants of AFTOL. A central goal of the WASABI interface is to establish an automated analysis framework that includes basecalling of newly generated chromatograms, contig assembly, quality verification of sequences (including a local BLAST), sequence alignment, and congruence test. Gene sequences that pass all tests and are finally verified by their authors will undergo automated phylogenetic analysis on a regular schedule. Although all steps are initially carried out noninteractively, the users can verify and correct the results at any step and thus initiate the reanalysis of dependent data.
Gift of Life Donor Program, the nonprofit organization serving the eastern half of Pennsylvania, southern New Jersey and Delaware, is responsible for recovering and distributing organs and tissues used in life-saving and life-enhancing transplants. Founded in 1974 by the Greater Delaware Valley Society of Transplant Surgeons, Gift of Life is one of the oldest and largest of 58 organ procurement organizations (OPO) in the United States. Gift of Life is part of the nationwide organ and tissue sharing network run by the United Network for Organ Sharing (UNOS). In addition, Gift of Life coordinates life-enhancing tissue transplants for area residents who are in need of corneas for sight-restoring procedures, as well as skin, tissue and bone to repair injuries. Gift of Life partners with 150 acute care hospitals to offer families from around the region the option of donation.
Queen Square Brain Bank for Neurological Disorders
A brain bank which holds an archive of brains donated by individuals with neurodegenerative disease and others who serve as neurologically normal controls. It specializes in parkinsonian movement disorders, including Parkinson's disease and multiple system atrophy, and holds the national collection of brains donated by individuals with progressive supranuclear palsy (PSP). Recently the collection has been developed to include donated brains from prospectively studied people with familial dementias. The QSBB also banks brains donated by people with dystonia and Gilles de la Tourette syndrome. The Brain Bank aims to provide brain tissue for neuropathological studies and for scientific research both in the UK and worldwide. The large collection of tissue is backed up by clinical documentation and all material is fully evaluated by the neuropathologists at QSBB. Brain tissue is stored as formalin-fixed, wax embedded blocks and is frozen, either at -20 degrees C or at -80 degrees C (flash-frozen). Tissue can be provided as slide-mounted sections, or as small blocks for neurochemistry, proteomics and DNA and RNA analysis. Flash-frozen material has excellent histological preservation and is suitable for in situ hybridization and immunohistochemistry. Case-control studies are matched for post-mortem delay and agonal status and are supplied blind.
Egon Willighagen''s blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference! Egon Willighagen is a postdoctoral research associate at the Karolinska Institute in Stockholm. Open source programming is my main hobby resulting in participation in, amongst many others, Bioclipse, CDK and Jmol. This blog is personal and may not reflect university''s views.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A biorepository containing thousands of biosamples from international pharmas, biotechs, hospitals, medical centers, private physicians and universities. As a part of our custodial activities, we have on-site power generators, extra supplies of liquid nitrogen and regular inspections. Sample tracking is handled by our LIMS system, which is connected to our laboratory service work, ensuring integrity of sample tracking and sample identification. Our biorepository group also handles sample collection kits, constructing kits with relevant tubes, accession sheets and barcode labels. The group also tracks expiration of tubes. Having a biorepository is also major advantage for serving the needs of clinical trials. It decreases costs, as there is lesser need for shipping samples. It mitigates the risk associated with sample transfer and handling. It simplifies trial management, fewer partners to manage. It simplifies chain of custody, sample transfer occurs under a single LIMS at a single site with teams that work together each day. It simplifies processing any sample repeats, no tracking, cost or risks associated with inter-company transfers. We can also supply sample collection kits complete with accession sheets and matched barcode labels.
Progressive Supranuclear Palsy Association
The PSP Association is dedicated to the support of people with Progressive Supranuclear Palsy (PSP) and those who care for them. We also support those with the related, but rarer, disease Cortico Basal Degeneration (CBD). We fund research to better understand the possible causes of PSP and CBD, to find ways to achieve earlier and better diagnosis and to develop treatments that could potentially slow down, or even halt, the progression of these diseases. We support patients, families and carers through the services we offer on a UK-wide basis, through our Nurse Specialist helpline, our Local Support Groups, our publications (including the comprehensive Carers'' Information Pack) and our Annual Symposium for carers and therapists. We raise awareness of PSP and CBD on a local and national level and work in partnership with the relevant bodies and umbrella organisations in the UK to seek to make a positive difference to the lives of people with PSP and CBD. Registered charity numbers: England & Wales 1037087 / Scotland: SC041199.
The Daily Scan - What''s Worth Reading on the Web
A roundup of the most interesting mainstream media articles, blog posts, and peer-reviewed literature relevant to genomic and proteomic scientists. Published daily online and by e-mail bulletin.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 17, 2021.Convenient, cost-effective and reliable storage solutions including maintaining, storing and monitoring your biological samples. Avoid costly purchases of ultra-low temperature freezers, sample tracking LIMS, and layers of emergency back-up infrastructure. Enjoy peace of mind in the knowledge that your critical samples are safe, secure, and readily available to you. Service Features * Real-time sample tracking and monitoring, with 24/7 accessibility. * GLP compliant repository with cold chain of custody. * Numerous storage options, from ambient temperature to -170 degrees C. * Hazardous specimen storage capabilities. * Redundant emergency back-up systems. * Secure-access facility. * At Temperature back-up freezers. * Rapid domestic & international shipping. As a full-service contract genomics provider, SeqWright is able to offer our BioRepository customers the additional benefit of a broad portfolio of regulated services for testing of samples, as and when required, and then returning the samples back to our BioRepository for further storage. Contact us for your customized solution.
Network of non profit association of Italian repositories to form catalogue of biospecimens and associated data. Used to collect, process, preserve and distribute biological samples and related clinical data from individuals affected by rare diseases, their relatives or from healthy control individuals, with standards complying with Italian laws and international recommendations. You may browse sample catalogue by diagnosis or use advanced search option. Request for samples is granted only if project is in agreement with TNGB mission and after receiving signed material transfer agreement form.
The New York Organ Donor Network is the nonprofit, federally designated organ procurement organization (OPO) for the greater New York Metropolitan area. Established in 1978, the Donor Network is the second largest OPO in the United States, serving a culturally and ethnically diverse population of 13 million people. Working closely with transplant centers and hospitals, we: * Coordinate organ, tissue and eye donation for transplant in the New York region * Educate the public and health care professionals about donation and transplantation * Promote the importance of signing up on the New York State Donate Life Registry. We work closely with 10 transplant centers, more than 90 hospitals, and various tissue and eye banks. The Donor Network is accredited by the Association of Organ Procurement Organizations (AOPO) and a member of the United Network for Organ Sharing (UNOS), which oversees the organ transplant waiting list in the U.S.
Collection of cell lines developed by Wistar scientists that includes a group of hybridomas that produce monoclonal antibodies that are useful in influenza research and vaccine development, melanoma cell lines derived from patients with diseases ranging from mild dysplasia to advanced metastatic cancer and a range of human endothelial cell lines.
US Immunodeficiency Network DNA and Cell Repository
US Immunodeficiency Network DNA Cell Repository
The USIDNET DNA and Cell Repository has been established as part of an NIH-funded program - the US Immunodeficiency Network - to provide a resource of DNA and functional lymphoid cells obtained from patients with various primary immunodeficiency diseases. These uncommon disorders include patients with defects in T cell, B cell and/or granulocyte function as well as patients with abnormalities in antibodies / immunoglobulins, complement and other host defense mechanisms. All samples in this Repository have been de-identified to protect the privacy of the individual donors. The USIDNET also operates a Patient Data Registry in addition to this Repository and certain clinical data relating to a specific sample may be available through the Registry for some of the patient samples in the Repository collection. Materials in the collection are being made available at modest cost to qualified investigators in academic and commercial organizations in an effort to stimulate research to increase understanding of these orphan diseases and to promote development of new treatments. Requestors are required to complete a Statement of Research Intent briefly describing their proposed use of materials obtained from the Repository and must sign an Assurance agreeing to conditions established by USIDNET for distribution of samples from its collection. Requestors wishing to obtain additional clinical data specific to individual samples in the Repository collection must make a separate application for that information to the Registry (see www.usidnet.org) Physicians or Patients wishing to submit cell samples for the Repository collection should first contact Coriell to arrange for the Repository to send them the correct sample collection tubes as well as prepaid mailers for returning the collected sample(s) to Coriell. Separate collection and shipping procedures may be involved depending on how many samples are to be shipped at one time and whether the shipment will involve freshly obtained blood or already established cell lines.
University of Colorado Denver; Colorado; USA
University of Colorado Denver Anschutz Medical Campus
University of Colorado Denver Anschutz Medical Campus;Colorado; USA
University of Colorado Health Sciences Center
University of Colorado Health Sciences Center; Colorado; USA
University of Colorado Denver is a public research university in Denver. It is part of the University of Colorado system.
The distributed annotation system (DAS) is a client-server system in which a single client integrates information from multiple servers. The UniProt DAS server provides access to sequence and annotation from UniProt, UniParc and IPI. Researchers can then provide annotation of their own results in the context of UniProt annotation, IPI annotation and UniParc cross references through the use of suitable DAS client such as Dasty2, the Ensembl DAS client or SPICE. The server also gives access to Gene Ontology Annotation of UniProt sequences (GOA) and theoretical tryptic digests of protein sequences in UniProt and IPI. An extremely useful resource for users of DAS is the DAS Registration Server that supports registry and discovery of DAS services. The datasources provided by the UniProt DAS server are all registered with this service.
Brain Bank for Autism & Related Developmental Research
Brain Bank for Autism and Related Developmental Research
Encourages and facilitates brain tissue donation for use in the best scientific studies to better understand the biological basis of autism down to the cellular and molecular levels and through that understanding bring about the development of effective interventions for those affected by autism spectrum disorders. To ensure the best co-ordinated use of brain tissue, the UK Brain Bank for Autism works in collaboration with the Autism Tissue Program in the US and shares the same Tissue Advisory board. The Brain Bank for Autism & Related Developmental Research was established in 2009. It is an initiative to develop a similar program in the UK to the Autism Tissue Program, which has been developed in the US since 1998. Our Brain Bank is the first extension outside the US of the Autism Tissue Program and is integrated with it. The Brain Bank is based at Oxford University, where it forms part of the Thomas Willis Oxford Brain Collection. It operates in accordance with all UK legal and ethical requirements. The donation of post-mortem brain tissue for this research program is of fundamental importance to our understanding of the causes of autism and to help us develop more effective diagnostic measures and interventions. A separate brain bank for autism is necessary because we need to understand how, in autism, the brain develops over time and how the brain functions as a whole. However, our Brain Bank will promote close cooperation across all relevant brain banks in order to take the research forward. Our research focuses on: * people within the autism spectrum or their family members * people not affected by autism but who are affected by epilepsy * individuals without autism or epilepsy.
The Living Legacy Foundation of Maryland
The Living Legacy Foundation is the non-profit organ and tissue donation program serving the state of Maryland, with the exception of three counties (Charles, Montgomery, and Prince Georges). We facilitate the life-saving process of organ and tissue donation, celebrate the generous gifts of organ and tissue donors, support our donor families and educate others about the importance of registering as a donor. Our organization was incorporated in 1990, consolidating the former Maryland Organ Procurement Center and the Maryland Tissue Bank. The U.S. Department of Health and Human Services, Centers for Medicare and Medicaid Services accredits us as an organ procurement organization, and the State of Maryland licenses us as a Tissue Bank. Our tissue bank is accredited by the American Association of Tissue Banks. We are governed by a 25 member Board of Directors, which includes general public members, transplant recipient representatives and donor family members. Our Board also includes transplant physicians, surgeons and administrators from the two Baltimore organ transplant centers (the University of Maryland Medical Center and The Johns Hopkins Hospital).
BioBank is a new Beaumont research center that is focused on developing innovative methods for early detection of disease and personalized treatment plans through leading edge analysis techniques and state of the art technologies. Biomarkers from tissue, blood or fluids, are used to develop the next generation of care management, taking it from bench to bedside. Beaumont BioBank will work to: * collect high-quality biological specimens from any specialty at Beaumont * store, analyze and record specimens in an efficient, organized and accessible manner using leading-edge technologies * connect specialties and specialists with each other across traditional hospital or laboratory departments to provide a multidisciplinary research structure * facilitate translational research that links molecular laboratory techniques that enable us to apply biomarker discoveries to clinical outcome studies in a speedy and direct manner
Central Biomaterial Bank - German Heart Failure Network
Competence Network Heart Failure Central biomaterial bank
Heart Failure Competence Network Central biomaterial bank
The goal of this project is the creation of an extensive biomaterials bank. Materials (blood, serum, plasma, DNA) from all patients who participate in studies in the network will be collected for this purpose. The objective is a consistently high quality standard for the processing, storage and management of all samples. The biomaterials bank is an investment in the future by the network. It enables the competence network and the research community in general to acquire new scientific knowledge about the development, progression and prognosis of the different forms of heart failure. Each time a patient is documented in a study in the competence network, blood (EDTA whole blood and serum) is drawn from the patient, sent by post to the central biomaterials bank and processed there in the central incoming sample laboratory according to specified standards. In the first two subsidization periods, a total of 100,000 samples from approximately 10,000 patients was documented and processed (aliquoting, DNA extraction). These samples are stored in climate-controlled rooms used especially for this purpose at the biomaterial bank of the Experimental and Clinical Research Center (ECRC) in Berlin-Buch at temperatures between -20 and -80 degrees C. As the central infrastructure project for all samples, the biomaterials bank is deeply involved in the networking. There are also intensive collaborations with other competence networks (e.g. the Competence Network for Congenital Heart Defects) and biobanks. The biomaterial bank of the Heart Failure Competence Network also participates in domestic and European pilot projects for networking biomaterial banks (BBMRI, ESFRI, etc.). The goal of these projects is to develop uniform methods for sample processing and use.
PXE International BioBank and Clinical Data Registry
The PXE International BioBank and Clinical Data Registry is the centralized sample repository and registry for pseudoxanthoma elasticum (PXE). It enables translational research and treatment discovery. PXE International, Inc. holds the world' '''s largest collection of blood and tissue from people affected by PXE and their families. It is the only centralized repository for PXE samples in the world. The PXE International BioBank has tens of thousands of samples, including DNA, tissue from every organ in the body, full body donations postmortem, and many special samples such as eyes, urine, breast tumor tissue and so on. The PXE International Clinical Data Registry ties the biological samples to the clinical record and stores self reported data (surveys and questionnaires), medical records (from any specialist), images (CT scans, MRIs and so on) and anything else that can be scanned or typed in. We are using these samples for genetic research ������?? examining the many mutations, the effect of the mutations on the cell and the future of possible interventions. PXE International established the PXE International Blood and Tissue Bank to make certain that your privacy and confidentiality are protected and your samples are available to any approved research project. Researchers interested in either donating PXE DNA, tissue and cell lines or in applying to use material from the bank should call 202.362.9599 or email Sharon Terry.
A tool for taxonomic classification of DNA fragments, as they are typically obtained in metagenome projects. The classification is based on taxon-specific DNA base composition characteristics (genomic signatures). Classification of query sequences is achieved by mapping the query sequences to the genomic signatures of sequences with known taxonomic affiliations. The mapping is done via the Self-Organizing Map (SOM) algorithm. TaxSOM offers two modes of operation: * mapping query sequences to a pre-calculated SOM * mapping query sequences to a custom SOM
University of Colorado School of Medicine; Colorado; USA
University of Colorado Denver School of Medicine
University of Colorado School of Medicine
One of the medical schools in the U.S., consistently ranked among the top in the nation.
The Systems Biology Graphical Notation (SBGN) project aims to develop high quality, standard graphical languages for representing biological processes and interactions. Each SBGN language is based on the consensus of the broad international SBGN community of biologists, curators and software developers. Over the course of its development many individuals, organizations and companies made invaluable contributions to the SBGN through participating in discussions and meetings, providing feedback on the documentation and worked examples, adopting the standard and spreading the word. Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. A list of software packages known to provide (or have started to develop) support for SBGN notations is available.
Research consortium to advance scientific research in the primary immune deficiency diseases (PIDD) and: * Assemble and maintain a registry of patients with primary immunodeficiency diseases to provide a minimum estimate of the prevalence of each disorder in the United States. Provide a comprehensive clinical picture of each disorder and act as a resource for clinical and laboratory research. * Establish a multifaceted mentoring program to introduce new investigators into the field and stimulate interest and research in primary immune deficiency diseases. * Establish an advisory/review committee to maintain a cell/DNA Repository of biologic material from well-characterized PIDD patients for the advancement of scientific research USIDNET operates a large database of patient information for your use. The purpose and scope of this project is to assemble and maintain a registry of residents with primary immunodeficiency diseases. The project was started with the Registry of U.S. Residents with Chronic Granulomatous Disease. Since then, the registry has been expanded and now collects data on all primary immunodeficiency disorders. The following are just a few of the diseases housed in the registry: Chronic Granulomatous Disease, Common Variable Immunodeficiency Disease, DiGeorge Anomaly, Hyper IgM Syndrome, Leukocyte Adhesion Defect, Severe Combined Immunodeficiency Disease, Wiskott-Aldrich Syndrome, X-Linked Agammaglobulinemia Physicians who would like to register their patients or access the registry are encouraged to contact Onika Davis or Lamar Hamilton, USIDNET team, at odavis (at) primaryimmune.org, or lhamilton (at) primaryimmune.org
National non-profit patient organization dedicated to improving the diagnosis, treatment and quality of life of persons with primary immunodeficiency diseases through advocacy, education and research. One of the greatest challenges faced by individuals diagnosed with primary immunodeficiency disease is finding the right information and resources when they need it. With knowledge and foresight from their personal experience, the Immune Deficiency Foundation (IDF) was founded by families of children with primary immunodeficiency diseases and their physicians to help meet those needs. It is with the spirit and energy of this keen perspective that IDF exists today, thriving as an organization dedicated to individuals living with primary immunodeficiencies. Since 1980, IDF has provided accurate and timely information for the nearly quarter-million Americans who have been diagnosed with a primary immunodeficiency disease. Governed by a Board of Trustees and supported by a Medical Advisory Committee comprised of some of the world''s leading clinical immunologists, as well as hundreds of grassroots volunteers and a compassionate, professional staff IDF has provided individuals and their families with vital knowledge and made tremendous strides in: * Helping the patient and medical community gain a broader understanding of primary immunodeficiency diseases through education and outreach efforts; * Promoting, participating, and funding research that has helped characterize primary immunodeficiency diseases and given patients and physicians substantially improved treatment options; * Addressing patient needs through public policy programs by focusing on issues such as insurance reimbursement, patient confidentiality, ensuring the safety and availability of immune globulin therapy, and maintaining and enhancing patient access to treatment options. Today, thousands of individuals and families affected by primary immunodeficiency diseases depend on IDF for advocacy, education and empowerment.
The Southeast Tissue Alliance recovers tissues and provides them to leading tissue processing companies. One of the most important aspects of this process is ensuring that donor families understand tissue donation and are fully supported as they make the gifts that change the lives of others. To promote tissue donation, we also work throughout the community to increase awareness, educate health professionals and further donation-related research. The Southeast Tissue Alliance is accredited by the American Association of Tissue Banks, which ensures that our services are of the highest quality and are provided in the most professional manner.
Software application using multipoint IBD method for partitioning genetic variance of quantitative traits to specific chromosome regions using data on nuclear families. (entry from Genetic Analysis Software)
National University of Ireland; Galway; Ireland
Located in the city of Galway in Ireland.
Brain Research Trust is a Registered Charity (no. 1137560) and a Company Limited by Guarantee (no. 7345516) promoting and supporting vital research. With the help of our donors, Brain Research Trust supports world-class research at University College London' '''s Institute of Neurology (IoN), London. We were able to provide a record 2.3m pounds to research grants in the 09/10 financial year and has been supporting its vital research program for almost 40 years. Brain Research Trust comprises a dedicated fundraising team, a supportive Board of Trustees and a knowledgeable Scientific Advisory Panel who all work together closely to ensure your money goes towards the best neurological research projects. Some of the conditions into which we fund research include: Alzheimer' '''s Disease, Ataxia, Brain Tumours, Creutzfeldt-Jakob Disease, Dystonia, Epilepsy, Huntington' '''s Disease, Migraine, Motor Neurone Disease, Multiple Sclerosis, Parkinson' '''s Disease, Progressive Supranuclear Palsy, Stroke. The Institute of Neurology also carries out research into Autism, Aphasia, Guillain-Barre Syndrome, M��ni��re' '''s Disease, Multiple Systems Atrophy (MSA), Myasthenia Gravis, Niemann-Pick Disease, Shy-Drager Syndrome, Tay-Sachs Disease and Tourette Syndrome.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023.To guarantee the top level of expertise in modern genetic and biological analyses, we have built an infrastructure that facilitates the collection of genome-wide information on the genetic background of diseases as well as functional information on the molecules that are critical in the disease process. Furthermore we have established the necessary storage, database and computational resources for the expert analyses of the massive amount of collected biological information. Our scientific expertise, technology platforms and large nationwide sample collections facilitate a highly competitive environment for research and education in molecular medicine of the 21st century. The biobanking wet lab effort is concentrated to KTL/Biomedicum Large scale DNA extraction and storage facility. The facility presently houses DNA from more than 200 000 individuals and is co-ordinated by National Public Health Institute. It is equipped with state of the art bar coding system for sample tracking, an automated Gentra DNA extraction equipment, liquid handling robots, storage facilities, and tailor made data management tools for optimal confidentiality and quality control.
Centers for Disease Control and Prevention Cell and DNA Repository
A repository which houses DNA samples prepared from reference cell lines and are available for use in molecular genetic testing. The CF samples contain mutations associated with unique populations, combinations of IVS8 poly-thymidine tract variants, and mutations not previously available. Three DNA samples with homozygous MTHFR-related mutations are available. Hemochromatosis-associated samples include a compound HFE heterozygote and other combinations of HFE alleles. DNA samples with triplet repeats at the intermediate-range are available for HD and Fragile X syndrome. Mutations were confirmed in all cell lines from which the DNA has been prepared by reference testing and multi-laboratory pilot testing. Control DNA samples negative for all mutations are also available. Laboratories are encouraged to contact Coriell Cell Repositories to inquire about obtaining samples or donating samples as possible candidates for transformation.
ILSbio LLC (Integrated Laboratory Services - Biotech)
ILSbio: Wolrd''s Most Comprehensive Tissue Collection Network
Integrated Laboratory Services - Biotech
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 17, 2021.Biospecimens and support services to advance translational research including a wide range of specimen types, including matched sets of normal and diseased tissue, Formalin-Fixed, Paraffin-Embedded (FFPE), blood, and serum, focusing primarily on cancer. They stock a wide range of sample formats to help meet research goals quickly and on budget. Collections are preformed to be ideal for a wide range of studies including genomic, proteomic, molecular and histologic analysis. ILSbio provides tissue and tissue derivatives that are high quality, cost effective and procured in compliance with current and anticipated regulations. The company obtains its clinical specimens under strict IRB approved protocols with informed consent and the utmost attention to issues of patient safety, anonymity and confidentiality. Clinical and pathological data is available for all specimens. Researchers use the tissue products at all levels of scientific study ranging from large pharma and biotech organizations to small labs and university research facilities. They also participate in wholesale distribution to other bio-banking organizations.
An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset.
Founded in 1977, California Cryobank (CCB) is a full-service sperm bank providing a comprehensive resource for frozen donor sperm, private semen cryopreservation, and specialized reproductive services (including egg and embryo storage and artificial insemination guidance). We are extremely proud of our 30 years of reproductive success. The demand for expert services has grown exponentially as discussion of reproductive challenges has continued to become more mainstream. At California Cryobank we understand that regardless of how much information and education you bring to the process, there can still be significant apprehension accompanying such big steps as sperm donation and donor insemination. CCB''s commitment to making our clients as comfortable as possible is what sets us apart and makes us so much more than just another sperm bank. Our services are entirely patient-centric; from the education that we provide����??answering questions and providing step-by-step timetables that let patients know what to expect in the weeks and months to come from donor sperm selection through insemination����??to the guidance that we offer. Our team is comprised of physicians, lab technicians, genetic counselors, Client Service Consultants, and Donor Matching Consultants. Every facet of our services is completely and expertly led by one of our experienced and compassionate team members. And while our sperm donor program is the foundation of our service, California Cryobank provides a full range of services for our clients including cord blood banking and access to our CCB Sibling Registry.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Develop, manufacture and market proprietary, nanocrystalline calcium-phosphate-based biomaterials that promote the repair and regeneration of bone damaged by trauma or disease. ETEX focuses on expanding applications through combinations with cells, biologics, or therapeutic agents delivered in minimally invasive and easy to use systems.
LMS Leiomyosarcoma Cell and DNA Repository
The Leiomyosarcoma Cell and DNA Repository has been established with an award from the National Leiomyosarcoma Foundation. This foundation provides leadership in supporting research of Leiomyosarcoma, improving treatment outcomes of those affected by this disease as well as fostering awareness in the medical community and general public. The resources available include highly-characterized, viable, and contaminant-free cell cultures and high quality, well-characterized DNA samples derived from these cultures, both subjected to rigorous quality control. Leiomyosarcoma is a rare form of cancer, which affects about four people in every million. It spreads through the blood stream and can affect the lungs, liver, blood vessels, or any other soft tissue in the body. Presently there is no cure, only remission if it can be attained, and this rare cancer can reappear anywhere at any time. Because of its rarity, few doctors know how to treat it and it attracts very little research. Cell cultures or DNA are distributed only to qualified professional persons who are associated with recognized research, medical, educational, or industrial organizations engaged in health-related research or health delivery. Before cell cultures or DNA samples can be shipped, the principal investigator must sign an ASSURANCE FORM (Material Transfer Agreement) detailing the terms and conditions of sale. This agreement must be renewed annually. In addition, before receiving lymphoblast or other virus-transformed cell cultures users should read the MINIMUM SAFETY GUIDELINES RECOMMENDED FOR WORKING WITH HUMAN CELL CULTURES.
This article is an appeal to technically-oriented library staff to initiate collaborative, bottom-up data-analysis efforts across their libraries. We discuss successful strategies used at North Carolina State University (NCSU) Libraries for initiating cross-departmental outreach for data-analysis work, as well as structuring and storing data, and disseminating findings. We present several specific examples of collaborative data-analysis projects undertaken at NCSU Libraries. Although the primary goal of the Code4Lib Journal is to provide practical solutions for technologists working in libraries, it has a lot to offer non-technologists. Technology affects all of the work that our libraries are doing and will define what the future of libraries will look like.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. SEVENS summarizes GPCR (G-protein coupled receptor) genes that are identified with high accuracy from 43 eukaryote genomes, by a pipeline integrating such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. This treats a larger data space (than that in currently available other databases), which should include not only the expressed sequences but also the newly identified sequences that cannot be detected by in vivo experiments, although they definitely exist on the genome sequence and are just waiting for the opportunity to express their functions. SEVENS provides the infrastructure of general information of GPCR universe for comparative genomics. We developed an automatic system for identifying GPCR (G-protein coupled receptor) genes from various kinds of genomes, by integrating such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. SEVENS enables us to perform a genome-scale overview of the GPCR universe using sequences that are identified with high accuracy (99.4% sensitivity and 96.6% specificity). Using this system, we surveyed the complete genomes of 7 eukaryotes and 224 prokaryotes, and found that there are 4 to 1016 GPCR genes in the 7 eukaryotes, and only a total of 16 GPCR genes in all the prokaryotes. Our preliminary results indicate that 11 subfamilies of the Class A family, the Class 2(B) family, the Class 3(C) family and the fz/smo family are commonly found among human, fly, and nematode genomes. We also analyzed the chromosomal locations of the GPCR genes with the Kolmogorov-Smirnov test, and found that species-specific families, such as olfactory, taste, and chemokine receptors in human and nematode chemoreceptor in worm, tend to form clusters extensively, whereas no significant clusters were detected in fly and plant genomes. How we found GPCR sequences: Candidate GPCR genes were collected from 32 eukaryote genomes by using the GPCR gene discovery pipeline, composed of two stages: (1) the gene finding stage, and (2) the GPCR gene screening stage. 1)Gene finding stage (i.e., translation of genomic sequences into amino acid sequences). 2)GPCR gene screening stage of GPCR candidates by assessing genes with sequence search, motif- and domain assignment, and transmembrane helix (TMH) prediction. Details available at the website. Acknowledgment: We are pleased to acknowledge the use of the BLAST package from NCBI, the SOSUI from Dr. T. Hirokawa, the ALN from Dr. O. Gotoh, the HMMER from Dr. A. Bateman. This work was supported by KAKENHI (208059) (Grant-in-Aid for Publication of Scientific Research Results) of Japan Society for the Promotion of Science (JSPS).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17,2021. An Antibody supplier
Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 15, 2011. The Spanish HIV BioBank was created with the objectives of processing, storing and providing distinct samples from HIV/AIDS patients, categorized according to strictly defined characteristics, free of charge to research projects. Strict compliance to ethical norms is always guaranteed. HIV BioBank possesses nearly 50,000 vials containing different prospective longitudinal study sample types. More than 1,700 of these samples are now used in 19 national and international research projects. (2009) The HIV BioBank represents a novel approach to HIV research that might be of general interest not only for basic and clinical research teams working on HIV, but also for those groups trying to establish large networks focused on research on specific clinical problems. It also represents a model to stimulate cooperative research among large numbers of research groups working as a network on specific clinical problems. The HIV BioBank is able to very efficiently release samples to different research project not only in Spain but also in other countries.
A volunteer, not for profit organization providing leadership in supporting research of LeioMyoSarcoma, improving treatment outcomes of those affected by this disease as well as fostering awareness in the medical community and general public. All dollars go to research and awareness. Leiomyosarcoma is a rare form of cancer, which affects about four people in every million. It spreads through the blood stream and can affect the lungs, liver, blood vessels or any other soft tissue in the body. Presently there is no cure, only remission if it can be attained, and this rare cancer can reappear anywhere and at any time. Because of its rarity, few doctors know how to treat it and it attracts little research. The National LeioMyoSarcoma Foundation hosts several Fundraising events throughout the year.
Human Reference Genetic Material Repository
J. Craig Venter Institute Human Reference Genome (HuRef)
The Human Reference Genetic Material Repository makes available DNA from a single individual, J. Craig Venter, whose genome has been sequenced and assembled. The DNA samples are prepared from a lymphoblastoid cell line established at Coriell Cell Repositories from a sample of peripheral blood. The DNA samples are available in 50 microgram aliquots. The lymphoblastoid cell line is not available for distribution. The human DNA sample provided is that of J. Craig Venter whose DNA from white blood cells and sperm was sequenced using Sanger chemistry (ABI Capillary Electrophoresis Platforms 3700 and 3730xl), assembled using the Celera Assembler and was published in PLoS Biology . J. Craig Venter, born on 14 October 1946, is a Caucasian male of self-reported European-American ancestry. The data available on this sample, whose genome assembly is referred to as HuRef, includes: * Whole Genome Shotgun Sequencing data * Sequence trace set deposited by JCVI in the NCBI trace archive * Human Genome Browser displaying sequence assembly, DNA variants and gene annotations Additional data sets from this study include: * Full set of Sanger reads used for genome assembly * SNP and insertion/deletion variant on the human genome sequence coordinates (NCBI version 36) * Affymetrix 500K GeneChip data * Illumina HumanHap650Y Genotyping BeadChip data Given the amount of data publicly available the genomic content of this sample, HuRef will be useful as a reference for many genetic studies.
A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available.
Toronto Public Library Health Information
Consumer Health Information Service Wiki
Toronto Public Library Health and Wellness
Toronto Public Library Health and Wellness Wiki
Toronto Public Library''s Health and Wellness Wiki
This site, created and maintained by the Business, Science & Technology Department of the Toronto Public Library, is designed to help you find reliable, understandable health information for you and your family. It can help you access a wide range of health and medical information online, and supports people in gaining greater control over their own health through access to health information. Resources include articles, books, health guides, reading list and websites.
Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury
Defense Centers of Excellence for PH and TBI
The Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury (DCoE) was established in November 2007 to integrate knowledge and identify, evaluate and disseminate evidence based practices and standards for the treatment of psychological health and TBI within the Defense Department. DCoE is part of the Military Health System, which provides a ''continuum of care'' from initial accession to deployment to discharge. DCoE works across the entire continuum of care to promote resilience, rehabilitation and reintegration for warriors, families and veterans with psychological health concerns and traumatic brain injuries. DCoE leads a groundbreaking collaborative effort that includes the Department of Veterans Affairs (VA), civilian agencies, community leaders, advocacy groups, clinical experts and academic institutions that are dedicated to expanding the state of knowledge of psychological health and TBI. In addition, DCoE''s Real Warriors Campaign is working to encourage help-seeking behavior for warriors with post-traumatic stress or mTBI. DCoE brings together six directorates and three centers. Their joint goal is to maximize opportunities for warriors and families to thrive through a collaborative global network to promote resilience, recovery and reintegration for PH and TBI.
A network of specialized rehabilitation programs serving Veterans and Service Members with both combat and civilian related Traumatic Brain Injury (TBI) and polytrauma. Services available include: interdisciplinary evaluation and treatment, development of a comprehensive plan of care, case management, patient and family education and training, psychosocial support, and application of advanced rehabilitation treatments and prosthetic technologies.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Urgencyclop?die is a wiki in French about first aid, rescue and emergency medicine. Anyone who registers may contribute.
University of Texas MD Anderson Cancer Center
The mission of The University of Texas MD Anderson Cancer Center is to eliminate cancer in Texas, the nation, and the world through outstanding programs that integrate patient care, research and prevention, and through education for undergraduate and graduate students, trainees, professionals, employees and the public. VISION: We shall be the premier cancer center in the world, based on the excellence of our people, our research-driven patient care and our science. We are Making Cancer History.
Hema-Quebec''s mission is to efficiently provide adequate quantities of safe, optimal blood components, substitutes, human tissues and cord blood to meet the needs of all Quebecers; provide and develop expertise along with specialized and innovative services and products in the fields of transfusion medicine and human tissue transplantation. Hema-Quebec is driven by the commitment, support and recognition of its employees as well as the trust of its partners to remain the standard of quality and innovation with respect to the safe procurement of blood products, human tissues and stem cells.
The MIGHEALTHNET wiki has been set up to gather information about the health of migrants and ethnic minorities in the United Kingdom. It forms part of the project MIGHEALTHNET, currently being carried out in 16 countries and co-funded by DG SANCO, the Health and Consumer Protection Directorate-General of the European Commission. We invite you to add your contributions to it and to pass on the address of this site to others who may be interested. This website is part of an EU Project that aims to give professionals, policy makers including health authorities, researchers, educators and representatives of migrant and minority groups easy access to a dynamically evolving body of knowledge and a virtual network of expertise. It will stimulate the formation of networks of individuals and organizations concerned with migrant and minority health.
LifeSource is the non-profit organization dedicated to saving lives through organ and tissue donation in the Upper Midwest. We serve more than 6 million people in communities across Minnesota, North Dakota, South Dakota and portions of western Wisconsin. As the federally-designated organization that manages organ and tissue donation in our region, we are dedicated to working with our hospital and community partners to support donor families, facilitate the donation of organs and tissues to transplant recipients and encourage the people in our communities to register as donors.
An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations.
Repository of molecular brain neoplasia data
REMBRANDT (Repository of Molecular Brain Neoplasia Data)
REMBRANDT - Repository of Molecular Brain Neoplasia Data
REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients' ''' response to various treatments. Clinical trials' ''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
National Temporal Bone Pathology Resource Registry
National Institute on Deafness and Other Communication Disorders National Temporal Bone Hearing Balance Pathology Resource Registry
NIDCD National Temporal Bone Hearing & Balance Pathology Resource Registry
NIDCD National Temporal Bone Hearing and Balance Pathology Resource Registry
A non-profit organization that promotes research on hearing and balance disorders. The Registry database allows researchers to perform simple searches to locate specimens of interest. The results show the laboratories where specimens that match the query are located. Investigators should contact the individual laboratories for studying the specimens or for access to the sections. The Registry also serves the public and the scientific community through the dissemination of public information on temporal bone donation and research, enrollment of temporal bone donors, publication of The Registry, a newsletter for researchers, conservation of existing human temporal bone collections, and professional educational activities for physicians and scientists.
Blood Borne Pathogens Surveillance Project
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. To develop a method to look for known and emerging blood borne diseases, a secure bank of samples has been established to test for known blood borne infectious agents and genetic changes causing or modifying the clotting disease, and to be available for testing for newly discovered viruses and clotting gene changes as they are found. The objectives of this project are: * To collect blood samples for a sample bank of plasma, DNA, and RNA to screen for known and emerging blood borne diseases. * To identify the mutation leading to each consenting patient''s bleeding disorder, and to characterize other known and yet to be discovered genes that affect blood coagulation. * To collect encoded, non-nominal data into a central database from an electronic chart known as CHARMS, which is currently kept in each hemophilia clinic in Canada to correlate with results from 1 and 2.
Tissue Bank at the IU Simon Cancer Center
The goals of the Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center are to acquire biomolecule and tissue specimens from the entire continuum of breast development: puberty to menopause and to make these specimens or the digital data derived from them available and accessible to researchers across the globe.
ProViDE: Program for Viral Diversity Estimation
A similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A multiple-sample, technology-aware SNP and indel caller.
The NCBI Related Structures tool allows you to find 3D structures from the Molecular Modeling Database (MMDB) that are similar in sequence to a query protein. Although the query protein may not yet have a resolved structure, the 3D shape of a similar protein sequence can shed light on the putative shape and biological function of the query protein. CBLAST is a tool that compares a query protein sequence against all protein sequences from resolved 3D structures by using protein BLAST against the PDB data set. The purpose is to find representative 3D structures for the query and/or its homologs, as available. Each record in the Entrez Protein database has been CBLAST''ed and the search results are available as Related Structures in the Links menu of Entrez Protein records. You can also enter a protein query sequence directly into the CBLAST search page in order to find its sequence-similar 3D structure records. The search results can be viewed in Cn3D (hence the name CBLAST), which displays an alignment of the query protein to the related structure''s sequence and allows you to interactively examine the sequence-structure relationship.
Catalog of data sets that are generated and held by the Federal Government, including data, tools and resources to conduct research, develop web and mobile applications, design data visualizations, etc. Data.gov provides descriptions of the Federal datasets (metadata), information about how to access the datasets, and tools that leverage government datasets. The data catalogs will continue to grow as datasets are added. Federal, Executive Branch data are included in the first version of Data.gov.
Manually annotated reaction database where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. The database has been populated with the reactions found in the Enzyme Commission (EC) list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalyzed reactions, other biochemical reactions are also included. Rhea is a manually annotated resource and it provides: stable reaction identifiers for each of its reactions; directionality information if the physiological direction of the reaction is known; the possibility to link several reactions together to form overall reactions; extensive cross-references to other resources including enzyme-catalyzed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; and chemical substructure and similarity searches on compounds in Rhea.
HTRN Biorepository & Biospecimen Resource
HTRN Biorepository and Biospecimen Resource
Human Tissue Resource Network Biospecimen Bank
The HTRN biospecimen bank is comprised of samples for the Ohio State University Cancer and Leukemia Group B Pathology Coordinating Office (CALGB-PCO) and the Ohio State University Midwestern Division of the Cooperative Human Tissue Network (CHTN). The CALGB-PCO banks biospecimens donated by patients enrolled in clinical trials. Samples can include tumor and normal tissue, plasma, serum, whole blood and white blood cells and urine. All of these samples are used later in correlative studies. The Midwestern Division of the CHTN stores a temporary biospecimen bank of tumor and normal tissue, tissue slides and paraffin embedded tissue blocks for research investigators throughout the country and Canada who are trying to find a cure for cancer. As part of the HTRN biospecimen bank, a Rees Scientific equipment monitoring system helps to secure the integrity and quality of samples stored in the biorepository. Scientific research within the HTRN is currently underway to determine the best methods in tissue storage for long term use. The NCI First-Generation Guidelines for NCI-Supported Biorepositories and the NCI Best Practices for Biospecimen Resources are continuously reviewed and adapted by the HTRN.
Orthopaedic Surgery is a collaborative wikibook of orthopedic surgery. *Preface *Chapter 1: Basic Sciences *Chapter 2: Upper Limb *Chapter 3: Foot and Ankle *Chapter 4: Spine *Chapter 5: Hand and Microsurgery *Chapter 6: Pediatric Orthopedics *Chapter 7: Adult Reconstruction *Chapter 8: Sports Medicine *Chapter 9: Musculoskeletal Tumors *Chapter 10: Injury *Chapter 11: Surgical Procedures *Chapter 12: Rehabilitation *Chapter 13: Practice
Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application for parentage inference using molecular data from diploid codominant markers (entry from Genetic Analysis Software)
Patient-Reported Outcomes Measurement Information System
Patient Reported Outcomes Measurement Information System
Repository of person centered measures that evaluates and monitors physical, mental, and social health in adults and children.
Enter your science video, website, or multimedia for a chance to win this year''s multimedia awards! It''s time for you to send us your best videos, interactive multimedia, websites, blogs, or any other techie creation meant for sharing the latest in life science research with the world. You only have until May 6th (2011) to enter, so post your submission today! We''re calling all scientists, research groups, teachers, and bio-enthusiasts who''ve gone the extra mile to communicate their work in style. The entries will be rated by a panel of judges and the winners will be announced in our September issue. We''ll also ask you, our readers, to pick your favorites. All entries must be created with funding from an individual or single research grant (no entries created with funding from a corporation or research institution will be accepted). All videos must be 10 minutes or less, and all entries must relate to the life sciences. Entries will be judged on scientific content, concept/originality, entertainment value, and production quality. Winners will be featured in a full-length article in the September issue of The Scientist, complete with a presentation of their multimedia mastery on our website.
A semi-supervised metagenomic fragment classification software program that utilizes the genome signatures to characterize the DNA sequences and taxonomic classification is based on an information theoretic measure referred as Relative Abundance Index (RAI). A DNA sequence of unknown source is classified and taxonomically labeled based on the phylogenetic profiles of the previously sequenced genomes. The profiles are iteratively updated using the unknown DNA sequences and the classification results. After a few cycles, the metagenome is classified into operational taxonomic units.
The Alabama Organ Center (AOC) is the federally designated organ procurement organization for the state of Alabama. We work with all of the hospitals in the state to coordinate their donation services. Like all organ procurement organizations, the AOC is a non-profit organization. We provide a variety of services: * Hospital education * Public education * Screening of potential donors * Coordination of the donation process * Family support The AOC is committed to providing a better quality of life for those who require an organ or tissue transplant, while respecting the families who share the gift of life.
Human DNA Polymerase Gamma Mutation Database
Database that lists all known mutations in the coding region of the POLG gene and describes the associated disease. Human DNA polymerase is composed of two subunits, a 140 kDa catalytic subunit encoded by the POLG on chromosome 15q25, and a 55kDa accessory subunit encoded by the POLG2 gene on chromosome 17q23-24. A number of mutations have been mapped to the gene for the catalytic subunit of DNA polymerase, POLG, and found to be associated with mitochondrial diseases. The nucleotide changes are numbered from the initiation Methionine codon and are based on the cDNA (accession U60325.1) and gene sequence (accession AF497906.1).
Transforming Research and Clinical Knowledge in Traumatic Brain Injury Network
Transforming Research and Clinical Knowledge in Traumatic Brain Injury: Multicenter Implementation of the TBI Common Data Elements
Network evaluating consensus-based common data elements (CDE) for traumatic brain injury (TBI) and psychological health (TBI-CDE, www.commondataelements.ninds.nih.gov/TBI.aspx) while extensively phenotyping a cohort of TBI patients across the injury spectrum from concussion to coma. Institutions that participate in the TBI Network will be able to track the outcomes of patients through a 3, 6 and 12-month followup program and compare outcomes with other participating institutions. For the three acute care centers, patients were enrolled that presented to the emergency department within 24 hours of head injury and required computed tomography (CT). For the rehabilitation center, referrals from acute hospitals were enrolled. Patients were consented to participate in components: clinical profile; blood draws for measurement of proteomic and genomic markers; 3T MRI within 2 weeks; three-month Glasgow Outcome Scale-Extended (GOS-E); and six-month TBI-CDE Core outcome assessments. A web-enabled database, imaging repository, and biospecimen bank was developed using the TBI-CDE recommendations. A total of 605 patients were enrolled. Of these subjects, 88% had a GCS 13-15, 5% had a GCS 9-12, and 7% had a GCS of 8 or less. Three-month GOS-E''s were obtained for 78% of the patients. Comprehensive 6-month outcome measures, including PTSD assessment, are ongoing until September 2011. Blood specimens were collected from 450 patients. Initial CTs for 605 patients and 235 patients with 3T MRI studies were transferred to an imaging repository. The TRACK TBI Network will provide qualified institutions access to a web-based version of key forms in tracking TBI outcomes for Quality Improvement and institutional benchmarking.
National University of Malaysia; Selangor; Malaysia
UKM affirms integration of faith in Allah and constructive knowledge along with amalgamation of theory and practice as core fundamentals in advancement of knowledge, building of educated society and development of university.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17, 2011. The US government contract funding the National Stem Cell Bank (NSCB) ended on February 28, 2010. A repository for the pluripotent stem cells lines listed on the NIH Human Pluripotent Stem Cell Registry. These cells were derived prior to August 2001 using excess IVF embryos and were eligible for use in federally funded research under previous presidential policy. The eligibility of these lines will not be known until the NIH issues final stem cell guidelines in July 2009. The goal of the NSCB is to grow, characterize and distribute the cell lines listed on the registry, and to provide comprehensive technical support to stem cell researchers around the world. Starting February 2, 2010, these materials can be ordered from the Wisconsin International Stem Cell Bank (the WISC Bank) operated by WiCell Research Institute, for delivery after February 28, 2010.
A database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).
European Molecular Biology Laboratory - European Bioinformatics Institute
Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.
BioreclamationIVT - The complete resource for all biologicals
BioIVT, formerly BioreclamationIVT, is global provider of biological specimens and services. Provides biological and in vitro products specializing in control and disease state matrices manufactured from human and animal whole blood, plasma, serum, tissues and other fluids which are used in drug discovery, compound development, clinical and research diagnostics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The ZFIN Antibody Database is a database of zebrafish gene expression antibodies.
International Mission for Prognosis and Analysis of Clinical Trials in TBI Prognostic Calculator
A calculator that calculates the prediction models for 6 month outcome after Traumatic Brain Injury. Based on extensive prognostic analysis the IMPACT investigators have developed prognostic models for predicting 6 month outcome in adult patients with moderate to severe head injury (Glasgow Coma Scale <=12) on admission. By entering the characteristics into the calculator, the models will provide an estimate of the expected outcome at 6 months. We present three models of increasing complexity (Core, Core + CT, Core + CT + Lab). These models were developed and validated in collaboration with the CRASH trial collaborators on large numbers of individual patient data (the IMPACT database). The models discriminate well, and are particularly suited for purposes of classification and characterization of large cohorts of patients. Extreme caution is required when applying the estimated prognosis to individual patients. The sequential prediction models may be used as an aid to estimate 6 month outcome in patients with severe or moderate traumatic brain injury (TBI). However, the prediction rule can only complement, never replace, clinical judgment and can therefore be used only as a decision-support system.
A secure repository of biological samples and data dedicated for medical and research purposes. These biological samples are linked to consenting patient relative data. Biobanque de Picardie provides quality and traceability services for establishment, conservation and use of biological samples collections. It houses collections of human tissue in a variety of areas of disease. Samples are used in basic research and translational studies, physiopathology of diseases and identification of new diagnostic, and as prognostic or therapeutic biomarkers. Biobanque de Picardie also develops healthy or pathological human primary stem cell banks, such as: mesenchymal stem cells in umbilical cord (HUC-MSC), primary hepatocytes (HPH), peripheral blood mononuclear cells (PBMC), and fibroblasts. Biological samples are stored at - 80 degrees C in electric freezers, at - 196 degrees C in liquid nitrogen or -130 degrees C in nitrogen vapor.
The Ontario Tumour Bank is a province-wide biorepository and data bank focused on collection of tumor-related human biospecimens. It provides academic and industry cancer researchers with a diverse selection of high quality tumor-related specimens and data obtained directly by dedicated tumour bank staff, who follow a stringent set of procedures and ethical guidelines. The biospecimens and clinical data are an important resource for scientists engaged in translational research who are developing better diagnostic tools and new drug therapies. Researchers depend on the Ontario Tumour Bank to provide research biospecimens of high quality, diversity, and integrity. Operating at state-of-the-art hospitals and cancer centers across Ontario, the Ontario Tumour Bank coordinates the collection, storage, analysis, annotation, and distribution of tumor and peripheral blood samples. Working in collaboration with local pathologists, medical oncologists, surgeons and other hospital personnel, specially trained staff obtain patient consent, collect tissues and assemble comprehensive clinical information about each donor and the corresponding samples.
The Brain Tumor Action Network is a not-for-profit 501(c)(3) organization established to bring awareness to the general public about brain tumors and to educate and empower brain tumor survivors, their families and friends. We foster grassroots advocacy on federal and state legislative issues affecting brain tumor survivors, their families and friends by providing information on brain tumor-related public issues and effective advocacy. BTAN has the following goals: * To encourage those living with brain tumors, their families and friends to become advocates for brain tumor awareness. * To foster grassroots advocacy on federal and state legislative issues affecting brain tumor survivors, their families and friends by providing information (and training) on brain tumor related public issues and effective advocacy. * To work independently and in collaboration with other brain tumor related organizations on behalf of the brain tumor community family. * To increase brain tumor awareness nationally through the Hidden Under Our Hats, National Brain Tumor Awareness Project in Washington, DC and at various treatment centers, conferences and fund raisers. * To raise funds to support specific research projects. * To create a PILOT respite care program for brain tumor survivors and their families at Moffitt Cancer Center & Research Institute (Tampa, FL). The respite care fund would assist brain tumor patients and their family members with additional care and support from home health care workers.
Albert Einstein College of Medicine Department of Pathology
An educational and research department at the Albert Einstein College of Medicine. Research is mainly focused on genomics and cancer biology, immunopathology, infectious disease, and neuropathology.
Brain Tumor Foundation For Children Inc.
Established in 1983 in Atlanta, GA, the Brain Tumor Foundation for Children (BTFC) was the first nonprofit organization in the United States to focus on pediatric brain tumor disease. The mission of the Brain Tumor Foundation for Children is to provide financial assistance, social support, and information for families of children with brain and spinal cord tumors; fund research projects that improve treatment options and search for a cure; and raise public awareness of the disease and advocate on behalf of children who are affected.
Software package providing distributed string mining for High-Throughput Sequencing data that provides a content-based exploration and retrieval method for whole metagenome sequencing samples.
pplacer: phylogenetic placement and downstream analysis
Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
The UK Stem Cell Bank was established to provide a repository of human embryonic, fetal and adult stem cell lines as part of the UK governance for the use of human embryos for research. Its role is to provide quality controlled stocks of these cells that researchers worldwide can rely on to facilitate high quality and standardized research. It is also ready to prepare stocks of ''clinical grade'' cell lines as seed stocks for the development of therapies. The bank exists to establish and make available fully characterized and quality-controlled cell banks. These will be supplied to scientific research teams and eventually to pharmaceutical companies, to enable the development of broad-ranging cell therapies. The bank will support the development of stem cell therapy in the UK by: * Creating and growing a supply of well-characterized stem cell lines for researchers in the UK and abroad. This will allow the research teams to establish the basis for therapeutic applications. * Creating, a bank of stem cell lines, under conditions consistent for the preparation of pharmaceutical products which provide cultures that could be supplied for the production of medicines for human use. For researchers deriving human embryonic stem cell lines in the UK, it is a condition of the Human Fertilization and Embryology Authority (HFEA) license that a sample of all human embryonic stem cell lines derived in the UK must be deposited in the UK Stem Cell Bank. The UK Stem Cell Bank does not collect, process, store or distribute Umbilical Cord Blood either for its own use or on behalf of others. A catalog of currently available stem cells is available or you may search for a particular stem cell.
The mission of the Florida Brain Tumor Association (FBTA) is to provide hope, support and education to brain tumor survivors, their families and friends; to conquer brain tumors by funding research into their causes and cures; and to enrich the quality of life of those touched by brain tumors. In October, 1991, the Florida Brain Tumor Association (formerly South Florida Brain Tumor Association) began due to a desperate need from brain tumor survivors and families who were searching for support and a safe place to share their life changing experiences. Beginning in Boca Raton, Florida, as a grass roots organization and a handful of people, the first support group was conceived. Today, there are many additional FBTA support groups, from coast to coast in the state of Florida. The Florida Brain Tumor Association (FBTA) has become a major force in the brain tumor community. We host many fundraisers yearly, donating funds for research to brain tumor centers. The FBTA has hosted over 20 three day conferences, seminars and meetings, attracting thousands of survivors, families and health care professionals in the United States and Canada. Many of the most renowned physicians in the world travel from far and near to present at FBTA conferences. We are proud and grateful for their commitment and dedication to our cause. The FBTA is a not-for-profit 501(c)(3) organization that is supported by contributions from individuals, corporations, and foundations. We are the only organization of this kind, relying on the strength and dedication of our members, who are brain tumor survivors, family members and friends. Our Medical Advisory Board is also voluntary; we are very thankful to them for their generous gifts of time.
Term-Preterm ElectroHysteroGram DataBase
It was obtained from 1997 to 2005 at the University Medical Centre Ljubljana, Department of Obstetrics and Gynecology. The records were obtained during regular check-ups either around the 22nd week of gestation or around the 32nd week of gestation. The women participating in the study represented a sample of the general population. In all, almost 1300 records were obtained during these years, and a preliminary database was built and used for studies by Ivan Verdenik, Gorazd Kavek, Marjan Pajntar and iva Novak-Antoli
Autism Speaks has grown into the nation''s largest autism science and advocacy organization, dedicated to funding research into the causes, prevention, treatments and a cure for autism; increasing awareness of autism spectrum disorders; and advocating for the needs of individuals with autism and their families. We are proud of what we''ve been able to accomplish and look forward to continued successes in the years ahead. In addition to putting money into new and cutting edge research, we also fund resources and programs such as the Autism Speaks Autism Treatment Network, Autism Speaks������?? Autism Genetic Resource Exchange and several other scientific and clinical programs. Autism Speaks was founded in February 2005 by Bob and Suzanne Wright, grandparents of a child with autism. Their longtime friend Bernie Marcus donated $25 million to help financially launch the organization. At Autism Speaks, our goal is to change the future for all who struggle with autism spectrum disorders. We are dedicated to funding global biomedical research into the causes, prevention, treatments, and cure for autism; to raising public awareness about autism and its effects on individuals, families, and society; and to bringing hope to all who deal with the hardships of this disorder. We are committed to raising the funds necessary to support these goals. Autism Speaks aims to bring the autism community together as one strong voice to urge the government and private sector to listen to our concerns and take action to address this urgent global health crisis. It is our firm belief that, working together, we will find the missing pieces of the puzzle.
As one of three primary databases of PubChem (Pcsubstance, Pccompound, and PCBioAssay), PubChem Substance Database contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay. If the contents of a chemical sample are known, the description includes links to PubChem Compound. A PubChem FTP is available and new data is accepted into the repository. Pcsubstance contains more than 81 million records (2011).
Accelerated Cure Project for Multiple Sclerosis
A national nonprofit organization dedicated to accelerating the cure of MS by facilitating research that determines the causes and mechanisms of MS. Our main effort is the creation of a large-scale, multidisciplinary MS Repository of blood samples and data from people with MS and matched controls. We make these samples available to researchers investigating the causes of MS and other demyelinating diseases. In exchange for access to the repository, researchers agree to return the data they generate from the samples so that results from disparate experiments can be combined. We are also developing a Cure Map to establish and document what is known and what is not known about the causes of MS. From the Cure Map, Accelerated Cure Project will facilitate the research most likely to reveal the causes of MS in the shortest time through use of our MS Repository.
National Brain Tumor Society (NBTS) is a nonprofit organization committed to finding a cure for brain tumors. We aggressively drive strategic research, advocate for public policies that meet the critical needs of the brain tumor community, and provide patient information. Headquartered in Watertown, Massachusetts, with offices in San Francisco, California and Wilmington, Delaware, we host activities throughout the United States. Formed in 2008 by the merger of two leading organizations that had served the brain tumor community, the National Brain Tumor Foundation and the Brain Tumor Society, the National Brain Tumor Society is now the largest brain tumor nonprofit organization in the country. Both legacy organizations had been formed in the 1980s by parents and other people who were committed to increasing both research funding and access to resources specific to brain tumors. In 2010, the Kelly Heinz-Grundner Foundation, a Delaware-based organization, joined NBTS as a wholly-owned subsidiary. Founded in 2005, after the death of Kelly Heinz-Grundner to a brain tumor, the group has contributed to NBTS''s efforts to pursue research and public policies that benefit the brain tumor community. NBTS grant programs are effective for academic researchers, inclusive of industry expertise, and promising for the patient community. All funding is open to both the domestic and international research communities. The Innovation Research Grant Program supports catalytic transformative projects that will significantly move the field forward. These may include out-of-the-box projects or research that is critical to move therapies down the pipeline. Research that represents an incremental advance is not considered innovative. NBTS will accept Innovation Letters of Intent throughout the year. Researchers in academic or industry labs and at all stages of their career may be funded through this program.
A virtual database currently indexing software and tools from the SciCrunch Registry, Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform, and Genetic Analysis Software (GAS).
Fox Chase Biosample Repository Core Facility
Fox Chase Cancer Center Biosample Repository
Fox Chase Cancer Center Biosample Repository Core Facility
Fox Chase has developed a facility dedicated to the collection and distribution of human subject biosamples and supporting personal and family cancer history data. In response to announcement (CA-00-025; P30 CA06927S2), the Fox Chase Cancer Center''s Biosample Repository (BR) and Tumor Bank Facility (TBF) is making blood specimens (i.e., whole blood, plasma, platelet-rich plasma, platelet homogenates, red blood cells, leukocytes, lymphoblastoid cell lines, and DNA isolated from leukocytes) and tumor tissues (i.e., multi-tissue microarrays and tumor DNAs) collected by our facilities available for research. Request for blood and tissue will be reviewed by a panel of scientists and ranked. Priority will be given to those investigators with current NIGH/NCI funding, but will be made available as recommended by the internal and external advisory committees. * Blood Inventory: Plasma, Serum, Whole Blood, Lymphocytes, DNA * Tissue Inventory: Tumor and Normal Adjacent Tissue, Fresh-Frozen, Formalin-Fixed Paraffin-Embedded Tissue, OCT Embedded Tissue, Ethanol-fixed Tissue
deStruct - Bioinformatics tool for identifying structural variation in tumour genomes
A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing.
The Oklahoma Brain Tumor Foundation (OKBTF) is a nonprofit organization that provides education, advocacy and support for Oklahomans with brain tumors and their families to improve their quality of life and help find a cure. Founded by Nancy Thomason after the death of her son Cade Thomason to a brain stem PNET tumor on February 17, 2000, she vowed to fight the disease in honor and memory of her son Cade. OKBTF is dedicated to meeting the needs of Oklahoma families, caregivers and patients affected by primary brain or central nervous system tumors. We work to provide for needs through education, advocacy, research and service. Whatever your needs, whether financial, physical, mental or spiritual, we will work with you to fight the battle. Here you will find many of the services we offer in support of families just like yours, who are confused, hurting and just wanting straight answers. Feel free to browse around, get to know us, see what we are doing to help and send us your comments or questions... We are here for you.
Platform for Interactive Learning by Genomics Results Mining
PILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis.
A controlled vocabulary thesaurus that consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH, in machine-readable form, is provided at no charge via electronic means. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as Anatomy or Mental Disorders. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as Ankle and Conduct Disorder. There are 27,149 descriptors in 2014 MeSH. There are also over 218,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, Vitamin C is an entry term to Ascorbic Acid. In addition to these headings, there are more than 219,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world' '''s leading biomedical journals for the MEDLINE/PubMED database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic.
Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy.
Language Resources Evaluation Conferences
The LREC conference has become a major event in the field of language engineering, and constitutes a milestone in the life of Human Language Technologies (HLT). The International Conference on Language Resources and Evaluation is organized by ELRA biennially with the support of institutions and organizations involved in HLT, and brings together a large number of people working and interested in HLT.
A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Specimen Resource Locator is a database to help researchers locate human specimens (tissue, serum, DNA/RNA, other specimens) for cancer research. It includes tissue banks and tissue procurement systems with access to normal, benign, precancerous and cancerous human tissue from a variety of organs. Researchers specify the types of specimens, number of cases, preservation methods and associated data they require. The Locator will then search the database and return a list of tissue resources most likely to meet their requirements. When no match is obtained, the researcher is referred to the NCI Tissue Expediter (tissexp@mail.nih.gov). The Tissue expediter is a scientist who can help researchers identify appropriate resources and/or appropriate collaborators.
The Pediatric Brain Tumor Foundation (PBTF) is a nonprofit organization dedicated to eradicating childhood brain tumors and providing support to families. It is a 501(c)(3) nonprofit charitable organization that seeks to * find the cause of and cure for childhood brain tumors by supporting medical research * increase public awareness about the severity and prevalence of childhood brain tumors * aid in the early detection and treatment of childhood brain tumors * support a national database on all primary brain tumors * provide educational and emotional support for children and families affected by this life-threatening disease. As the world''s largest non-governmental source of funding for childhood brain tumor research, we''re dedicated to not only eradicating this disease, but to providing support to families. Our educational resources deliver comfort and hope to families in need of information, and our college scholarship program gives brain tumor survivors a boost for the future. Through our efforts to raise public awareness, more attention has been focused on this deadly disease. Whether addressing congressional briefings or funding international conferences, the PBTF is an unwavering advocate. Together, we''re making a difference in the lives of children with brain tumors. And with your continued help, we will cure the kids!
The Compass of Pleasure: Vice virtue and the brain''s pleasure circuits
A blog written by David J. Linden, Ph.D., professor of Neuroscience at the Johns Hopkins University School of Medicine, focusing on the brain''s pleasure circuits. Topics covered include exercise, pleasure and the brain; and understanding the biology of runners high. The Compass of Pleasure: How Our Brains Make Fatty Foods, Orgasm, Exercise, Marijuana, Generosity, Vodka, Learning, and Gambling Feel So Good is also a book and available for purchase. David J. Linden, Ph.D., is a professor in the Department of Neuroscience at the Johns Hopkins University School of Medicine. His laboratory has worked for many years on the cellular substrates of memory storage in the brain and a few other topics. He has a longstanding interest in scientific communication and serves as the Chief Editor of the Journal of Neurophysiology. He has written two books for a general audience about the biological basis of mental function: The Compass of Pleasure (Viking Press, 2011) and The Accidental Mind (Harvard/Belknap, 2007).
Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion.
Pediatric Low Grade Astrocytoma Foundation
The Pediatric Low Grade Astrocytoma (PLGA) Foundation is the largest, and only, non-profit organization dedicated to providing hope to children, parents, and families fighting Pediatric Low Grade Astrocytomas (PLGAs). We were founded in August 2007, as a 501(c)(3) foundation made up of families and friends dedicated to helping children who are struggling with brain tumors. To date, families associated with the Pediatric Low Grade Astrocytoma (PLGA) Foundation have raised over $6 million for DEDICATED PLGA research and funded over a dozen new research projects targeted specifically at children''s brain tumors or PLGA''s. These funds have supported the launch of the Dana Farber Cancer Institute''s PLGA Research Program as well as numerous grants distributed by the Brain Tumor Society, and other fine institutions. The PLGA Foundation awards 100% of funds to education and research in the search for more effective, less toxic treatment options for this potentially devastating childhood brain tumor. The PLGA Foundation actively promotes partnerships with other non-profit organizations, private individuals and government entities and has collaborated on fund raising, education and grant allocations in order to leverage resources and funds. Our goal at the Pediatric Low Grade Astrocytoma (PLGA) Foundation, also known as Fight Juvenile Pilocytic Astrocytoma (FightJPA.org), is to UNITE families around the country and around the world in the FIGHT for the lives of our children who suffer from PLGAs - childhood brain tumors. We can defeat childhood brain tumors through a united effort on all fronts to increase awareness, education, fundraising and research of pediatric low grade astrocytomas.
User software contributions for XNAT - The Extensible Neuroimaging Archive Toolkit, http://www.xnat.org
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Archiving services, insertional site analysis, pharmacology and toxicology resources, and reagent repository for academic investigators and others conducting gene therapy research. Databases and educational resources are open to everyone. Other services are limited to gene therapy investigators working in academic or other non-profit organizations. Stores reserve or back-up clinical grade vector and master cell banks. Maintains samples from any gene therapy related Pharmacology or Toxicology study that has been submitted to FDA by U.S. academic investigator that require storage under Good Laboratory Practices. For certain gene therapy clinical trials, FDA has required post-trial monitoring of patients, evaluating clinical samples for evidence of clonal expansion of cells. To help academic investigators comply with this FDA recommendation, the NGVB offers assistance with clonal analysis using LAM-PCR and LM-PCR technology.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17, 2021. An Antibody supplier.
The Gerry & Nancy Pencer Brain Trust is a not-for-profit organization with a mandate to make a difference in the quality of life of people living with brain tumors. This registered charity is the primary source of funding for The Gerry & Nancy Pencer Brain Tumor Centre, and carries out annual fundraising events to support its'' ongoing research and patient care activities. The Gerry & Nancy Pencer Brain Tumor Centre is located in Toronto, Canada at the world-renowned Princess Margaret Hospital. The Centre provides multidisciplinary care, treatment, support, and education for brain tumor patients and their families, and promotes brain tumor research in the hopes of one day finding a cure for brain cancer. All of this is made possible through your very generous donations.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019, The National Gene Vector Biorepository offers an informational toxicology database as a resource to gene therapy investigators. The database contains information on animal studies that have been conducted to study the biodistribution of vector to different target organs and to evaluate potential toxic effects associated with the use of various vector systems. Studies within the database have been submitted to the US FDA in support of gene therapy clinical trials. The purpose of the database is to inform gene therapy investigators about the conclusions of prior toxicology studies and to facilitate the cross-referencing of relevant studies in support of new Investigational New Drug Applications (INDs) applications. The studies are generally small, randomized single dose or dose escalation studies consisting of various animal models from mouse to non-human primate. The study parameters capture the test system, vector information, dose procedures, clinical observations, macroscopic/microscopic pathology, histopathology, tissue collection for PCR analysis, clinical pathology: hematology/chemistry analysis and a summary of the relevant findings. Investigators have agreed to allow submission of their data into this database. The database is also accessible to any investigator in the gene therapy field who would like to share their data. The database is being expanded to include non-GLP studies submitted to the FDA in support of an IND. These studies are conducted under careful compliance parameters and can be critical to platform studies in the development of novel vectors.
At Brain Injury Alliance of Kentucky (BIAK), a 501(c)(3) non-profit agency, our sole mission is to serve Kentucky citizens whose lives have been affected by brain injury. We do this through advocacy, education, prevention, research, service and support. BIAK links survivors of brain injury and their families to support from others with similar experience; provides them with education and information about living and coping with brain injury; assists them in locating resources for financial assistance; and seeks to connect people with sources of emotional support. BIAK began as an outgrowth of a Lexington area support group in the early 1980s. Family members, medical staff and others felt the need to expand the services and support to reach statewide. The state office was moved to Louisville and incorporated in 1986. BIAK now has offices and staff in Louisville and Lexington. BIAK seeks to share its philosophy, experience and skills with survivors, family members, students, caregivers, administrators, health professionals, legislators, the lay community and all those who desire to make a difference in the life of individuals with brain injuries and their families. At BIAK you will find information about brain injury. We define brain injury as any injury to the brain including injury received from a fall, a stroke, trauma, anoxia, infection, and tumors or other illnesses. Each year, a growing number of Kentucky citizens are affected by brain tumors. These may range from benign tumors to aggressive cancers. The Michael Quinlan Brain Tumor program recently joined BIAK to provide service and support to individuals and families who have been affected by brain tumors. There is always help available to you and your family.
A simulation tool to identify positions of nucleosomes from Next Generation Sequencing data.
National University of Sciences and Technology; Islamabad; Pakistan
National University of Sciences & Technology
National University of Sciences and Technology
Loma Linda University Cancer Center Biospecimen Laboratory
LLU Cancer Center Biospecimen Laboratory
The Loma Linda University Cancer Center Biospecimen Laboratory provides specimens for researchers as they search for the causes of cancer, and look for new means of prevention and treatment. The specimens include tissues, blood products (blood cell, plasma and serum) and bone marrow cells. Researchers interested in gaining access to the Biospecimen Laboratory''s samples should email Dr. Saied Mirshahidi, requesting access. The number and types of samples we have available for research can be viewed, http://www.llu.edu/catissuesummary/. Use the Biospecimen Laboratory Tissue Request Form to request specimens for research studies.
Founded in 1995, the Southeastern Brain Tumor Foundation (SBTF), a 501c3 not-for-profit charitable foundation, is devoted to improve the quality of life for brain tumor patients and their families. By offering information, education and support services, we aspire to instill hope, knowledge and comfort to all involved. The Southeastern Brain Tumor Foundation also raises funds for research and medical personnel so that a cure can be found. For over a decade, the SBTF has become a well-known fundraising entity supporting critical, cutting edge brain tumor research at major medical centers in the Southeast. Our annual Race for Research held in Atlanta, Georgia each summer, is our main fundraising event popular throughout Atlanta and the surrounding metropolitan area and has funded over $1.2 million dollars in research grants to leading researchers at major medical centers throughout the Southeast over the past decade. We are proud of our dedicated, all volunteer Board of Directors who meet monthly. Our Board is a diverse group comprised of individuals who''ve been touched by brain tumors in many different ways. Ranging from patients and family members to healthcare professionals; we are all committed to promoting the awareness of brain tumors in the community, communicating with patients and families and raising critical funds for research grants furthering advancements in the treatment of brain tumors. Our monthly support group, lead by a nurse practitioner, welcomes patients and their families to sit side by side with each other, share their experiences, communicate and receive support. As a neurosurgeon-scientist focused on the treatment of patients with brain tumors, I am committed to advancing the mission of SBTF forward in the fight against brain tumors. Our ability to serve the brain tumor community is dependent on each of you. Whether you support us with a financial donation in our fundraising efforts or with your time as a volunteer, each of you are a vital and integral part of our success and we thank you.
GENEticS is arap video about genetics. So let''s talk about genes, and I don''t mean trousers, go the lyrics to this catchy rap video created for The GAMY (Genetics and Merthyr Youth) Project. It is one of the many videos, games, and digital media used by researchers at the University of Glamorgan in the United Kingdom use to engage local teenagers in a conversation about genetics. Video produced by Jon Chase (aka Oort Kuiper).
Database of genes regulated by pain derived from published manuscripts describing results of pain-relevant knockout studies. The database has two levels of exploration: across-gene and within-gene. The across-gene level, the PainGenesdbSelector, is encountered first. All genes in the database can be accessed and sorted by their gene name, protein name, common names and acronyms, or genomic position (by navigating a graphic representation of the mouse genome). The gene and protein names can be selected from an alphabetical list, or by typing a text string into a search box.
Webserver for taxonomic classification of metagenomic reads.
University of Lausanne; Lausanne; Switzerland
The Barth Syndrome Registry and Repository (BRR) at the University of Florida and Children''s Hospital Boston was created to provide additional information about this rare disorder. By collecting information directly from families and abstracting medical information from patient records, we hope to build a large anonymized database that is useful for answering scientific research questions and that is a source of medical information. Additionally, we are collecting blood samples for DNA isolation and storage and for the development of special cell lines. These tools will allow researchers to better understand the cellular and genetic nature of this disease and how these abnormalities may impact the clinical variability of Barth syndrome patients. Currently available data from the Barth Syndrome Registry and Repository includes self-reported data. This includes basic demographics, age at diagnosis of Barth Syndrome, reason for diagnosis, family history; symptoms, presence or absence of a history of cardiomyopathy, history regarding hospitalizations, cardiac transplant or listing for transplant, presence or absence of a history of neutropenia; history of infections, medical therapy and basic developmental history. We are in the process of abstracting medical data to build a more complete medical database and may be able to provide additional data with a specific request. Currently the DNA bank has data from 65 patients, genomic DNA from 50 patients, lymphoblast lines from 41 patients, fibroblast lines from 3 patients, and myocardium/autopsy from 3 patients. However, this is increasing as new patients enroll in the Registry. Please contact us with questions and specific requests about data or specimens.
Biomet and Interpore Cross are on the cutting edge of technology in the orthopedic biomaterials market. Our focus is developing and providing truly innovative products, which meet the rapidly expanding needs of orthopedic surgeons both today and in the future. Our Pro Osteon resorbable bone graft material is derived from an abundant non-decorative coral. Pro Osteon is available in a selection of fully resorbable sterile granules and blocks, in a variety of shapes and sizes. Our InterGro DBM products combine the osteoinductivity of DBM with a natural, non-soluble carrier that won''t wash away, delivering a unique bone graft that offers superior handling and performance characteristics. This highly-moldable composite graft can be easily formed to fit any shape fracture or defect.
SVMerge - Enhanced structural variant and breakpoint detection
Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available.
One of the largest financiers of research in Sweden that promotes scientific research, teaching and/or education beneficial to the Kingdom of Sweden. 20-30 percent of the Foundation''s grants relate to high-value research equipment for use within the technical, natural sciences and biomedical fields, and about 50 percent relate to major research projects and substantial scientific networks. Universities, academies and similar research and educational institutions are eligible for grants within the following fields: * Expensive scientific equipment * Fellowship programs initiated by the Foundation * Selected research projects of significant potential * Larger educational research projects Applications may be submitted by individual scientists, or research groups affiliated to a Swedish university or equivalent institution. An application may also be submitted by the management of a university, university college, scientific academy, or national research associations. Applications from private individuals without connection to a scientific institution are not considered.
BrainPod is the podcast from the journal Neuropsychopharmacology. Join us as we delve into the latest basic and clinical research that advance our understanding of the brain and behavior, featuring highlighted content from a top journal in fields of neuroscience, psychiatry, and pharmacology.
At the Website of the Causal Cognition Group (CCG) of the University of M��laga, you may read information about our group, its members, our research, main activities, and more. Our main interests are cognitive psychology and learning, and more recently cognitive neuroscience, physiological correlates of learning and cognitive control. This site is in constant evolution... though there are things that hardly change: Cognitio rei per causas.
Arnold Arboretum of Harvard University: Weld Hill Molecular Lab
The molecular lab at Weld Hill is well equipped for modern molecular studies, from RNA expression studies to phylogenetic analyses.
Ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. The new PATO differs from the old in that the system of attributes and values has been abandoned in favor of a single hierarchy of qualities. PATO is designed to be used in conjunction with ontologies of quality-bearing entities. An example of such an entity is an insect eye (taken from the fly_anatomy ontology), which could be the bearer of the quality ''red'' (PATO:0000322). This combination is the red eye phenotype. We say that the phenotype term is ''post-coordinated'', as it is formed by coordinating two terms together. This is in contrast to ontologies of pre-coordinated phenotypes, such as the Mammalian Phenotype (MP) ontology. PATO is independent of any exchange format or database schema. One way of expressing phenotype annotation using PATO is pheno-syntax, or pheno-xml. They will also post recommendations for representing phenotypes using OWL. All representations share the same basic formal underpinnings, a combination of quality-bearing entity and a quality (the EQ model).
University of Alabama at Birmingham Traumatic Brain Injury Model System
This website offers educational materials and information on services of the UAB Traumatic Brain Injury Model System (UAB-TBIMS) along with links to national organizations, government agencies, and educational resources related to traumatic brain injury. The UAB-TBIMS is one of 16 national TBI Model Systems Centers working to maintain and improve a cost-effective, comprehensive service delivery system for people who incur a traumatic brain injury. A Model System must demonstrate outstanding care to individuals with traumatic brain injury, from the emergency medical services, to acute care in the hospital, to rehabilitation. The UAB TBIMS * conducts research, * distributes their research findings to both clinical and consumer audiences * collaborates with other clinical research programs and * participates in the Model Systems Database. This Center, operates within the UAB Department of Physical Medicine and Rehabilitation, which is located at Spain Rehabilitation Center in the UAB Hospital complex. Here it establishes and maintains links with emergency medical service agencies throughout the state, with state vocational rehabilitation and long-term follow-up programs.
mouseMAP: Tissue-specific functional networks for the laboratory mouse
In collaboration with several research groups at Jackson Laboratory, we mapped the tissue-specific functional relationship networks in the laboratory mouse by simulating the natural tissue specificity realized by differential protein expression between tissues. MouseMAP is an interface that allows browsing networks of different tissues and the comparison between them. The current version of MouseMAP includes one global network as an extension of mouseNET (http://mousenet.princeton.edu) and 107 tissue-specific networks organized into 15 different major body systems. The interface has the following features (their usage are detailed in Help and FAQ page): 1. Single graph query with one or multiple genes of interests. 2. Expansion/shrinking of query results through edge or node cutoffs. 3. Comparison of local networks between different tissues. 4. Dynamic generation of figure legend to facilitate manuscript writing.
Ohio Tissue Procurement Shared Resources
Collect, bank, and distribute human tissue and fluid specimens by uniting tissue-based research resources within the OSU Department of Pathology and promoting collaborative research within the OSU Medical Center and related national human research projects. The HTRN is comprised of the Pathology Core Facility (PCF), Tissue Archive Service (TAS), Tissue Procurement Service (TPS), AIDS and Cancer Specimen Resource (ACSR), the Cancer and Leukemia Group B Pathology Coordinating Office (CALGB - PCO), and an Adenoma Polyp Tissue Bank (APTB).
Trypanosoma brucei TREU927 homepage on GeneDB
Database of the most recent sequence updates and annotations for the T. brucei genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. T. brucei possesses a two-unit genome, a nuclear genome and a mitochondrial (kinetoplast) genome with a total estimated size of 35Mb/haploid genome. The nuclear genome is split into three classes of chromosomes according to their size on pulsed-field gel electrophoresis, 11 pairs of megabase chromosomes (0.9-5.7 Mb), intermediate (300-900 kb) and minichromosomes (50-100 kb). The T. brucei genome contains a ~0.5Mb segmental duplication affecting chromosomes 4 and 8, which is responsible for some 75 gene duplicates unique to this species. A comparative chromosome map of the duplicons can be accessed here (PubmedID 18036214). Protozoan parasites within the species Trypanosoma brucei are the etiological agent of human sleeping sickness and Nagana in animals. Infections are limited to patches of sub-Saharan Africa where insects vectors of the Glossina genus are endemic. The most recent estimates indicate between 50,000 - 70,000 human cases currently exist, with 17 000 new cases each year (WHO Factsheet, 2006). In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.
California Transplant Services (CTS) is a full service eye and tissue bank headquartered in Carlsbad, California. CTS is a California non-profit public benefit corporation qualified by the IRS as a section 501(c)3 public charity, licensed by the California Department of Public Health as a Tissue Bank and registered and inspected by the United States Food and Drug Administration. We were also inspected by the American Association of Tissue Banks in September of 2003 and awarded Accreditation in December 2003. California Transplant Services is a Member of the Eye Bank Association of America. We are registered in California with the Office of Charitable Trusts. Most of CTS California Transplant''s fulltime staff are Certified Tissue Bank Specialists (CTBS) by the AATB or Certified Eye Bank Technicians (CEBT) by the Eye Bank Association of America. CTS staffing includes fulltime and part time tissue procurement specialists. CTS helps tissue banks by providing 24 hour tissue placement services from it''s west coast USA distribution center. CTS has provided cornea and bone tissue placement services nationwide since 1994.
National Cancer Institute Biorepositories
National Cancer Institute Biological Testing Branch Services
National Cancer Institute Biorepositories provides information on the tumor repository, animal production program, and access to other NIH Repositories. A catalog of in vitro cell lines, transplantable animal and human tumors and microarrays, including ordering information, is available. In the Animal Production Program, rodents are supplied to Federal Institutions and to grantees/contractors with a current OLAW Assurance on file. Requests from international entities seeking rodent strains solely available from the NCI Animal Production Program must have an OLAW Assurance or current AAALACi accreditation and will be evaluated on a case-by-case basis. In general, the rodents are supplied to the following: * Researchers at NCI-Frederick * NIH on-campus laboratories * NIH/NCI funded research contracts * NIH/NCI funded grantees * Other government agencies To meet the above needs, animal production contracts plus quality control contracts are used. The animal production contracts are used to propagate the NIH sublines of the strains. Many of the strains produced are not available commercially and the NCI program is the sole source of several lines.
Ohio State University Comprehensive Cancer Center
Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute
Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Solove Research Institute
OSUCCC - The James Cancer Hospital and Solove Research Institute
As the Midwest''s first and Ohio''s only fully dedicated cancer hospital and research institute, The Ohio State University Comprehensive Cancer CenterArthur G. James Cancer Hospital and Solove Research Institute (OSUCCC-James) is one of the nation''s premier cancer centers for the prevention, detection and treatment of cancer. The OSUCCC-James is one of only 40 centers in the United States designated by the National Cancer Institute a Comprehensive Cancer Center. In addition, the OSUCCC-James is a founding member of the National Comprehensive Cancer Network (NCCN), an alliance of 21 of the world''s leading cancer centers that develops clinical practice guidelines to improve the quality and effectiveness of care provided to patients with cancer. The Ohio State cancer program is part of The Ohio State University, the largest public university in the nation. We are affiliated with The Ohio State University Medical Center, one of the largest and most diverse academic medical centers in the nation and the only academic medical center in central Ohio. The cancer program at Ohio State encompasses more than 200 comprehensive cancer center members from 13 of the 18 colleges at The Ohio State University and includes physicians from 16 specialties. The OSUCCCJames'' singular focus on cancer has led to multiple accomplishments that have changed the standards of care with respect to prevention, diagnosis and treatment, in a way that substantially improves outcomes for cancer patients.
Phylogenetic analysis of metagenomics sequence data
Data analysis service that analyzes DNA sequences and determines their most likely phylogenetic origin. Its main use is in metagenomics projects, where DNA is isolated directly from natural environments and sequenced (the organisms from which the DNA originates are often entirely undescribed). It will search such sequences for suitable marker genes, and will use maximum likelihood analysis to place them in the ' '''Tree of Life' '''. This placement is more reliable than simply assessing the closest relative of a sequence using BLAST. More importantly, MLTreeMap decides not only who is the closest relative of your query sequence, but also how deep in the tree of life it probably branched off. Additionally, MLTreeMap searches the sequences for genes, which are coding for key enzymes of important functional pathways, such as RuBisCo, methane monooxygenase or nitrogenase. In case of a positive hit, MLTreeMap uses maximum likelihood analysis to place them in the respective ' '''gene-family tree' '''.
Surgical Procedures is a wikibook on surgical procedures. It is by no means intended to be a guide to at-home surgery. Surgical illness should only be managed by a professional medical expert (e.g Surgeon). Topics include: 1. Abdominoplasty 2. Adenoidectomy 3. Amputation 4. Melanoma 5. Mandibular Fractures 6. General Surgery Guidelines 7. Abdominal Surgery A. Cholecystectomy * Open Cholecystectomy * Lap Cholecystectomy B. Cholecystitis C. Cholecystography D. Cholelithiasis E. Choledocholithiasis 8. General Surgery 9. Acid Base Disorder 10. Plastic Surgery
LifeCenter Organ Donor Network, A Donate Life Organization, encourages and coordinates the donation of human organs and tissues for transplantation. In 1981 LifeCenter began operating as an independent, not-for-profit organ procurement organization (OPO) with a mission to save, enhance and change lives through organ and tissue donation. LifeCenter is accredited by the Association for Organ Procurement Organizations (AOPO) and the American Association of Tissue Banks (AATB), and has been approved and designated by the Centers for Medicare and Medicaid Services (CMS) as the primary OPO serving eight counties in Southwestern Ohio, six counties in Northern Kentucky and two counties in Southeastern Indiana. LifeCenter is an institutional member of the United Network for Organ Sharing (UNOS) and follows all the guidelines for organ sharing. The population of LifeCenter''s service area is approximately two million people. Within this area there are 30 hospitals that LifeCenter works with to facilitate and coordinate organ and tissue donation. The clinical staff provides 24-hour service for referrals, case management, recovery and organ placement. Our education staff provides programs for schools, civic and community groups, religious institutions and healthcare professionals. Additional services offered by LifeCenter include bereavement services for donor families, volunteer opportunities, and donor drives for area businesses and organizations that facilitate the enrollment of donors.
Cardiovascular Gene Ontology Annotation Initiative
Full Gene Ontology annotation to genes associated with cardiovascular processes. Every GO annotation made, is attributed to an identified source, such as a publication identifier (PMID), and an indication of the type of evidence which supports the association between the gene product and the GO term. Over 4,000 cardiovascular associated genes have been identified. A variety of tools have been provided to enable cardiovascular scientists to review the annotation of their ' '''favorite' ''' gene and suggest information that may be missing, inaccurate or incomplete in these annotations. Annotation suggestions can be sent through the feedback form or by email. The Gene Ontology (GO) vocabulary is the established standard for the functional annotation of gene products. By using GO to curate scientific literature and by integrating results from high-quality high-throughput experiments they will create an information-rich resource for the cardiovascular-research community, enabling researchers to rapidly evaluate and interpret existing data and generate hypotheses to guide future research.
RIKEN Brain Science Institute (BSI) has a mission to produce innovative research and technology leading to scientific discoveries of the brain. In addition, BSI aims to develop domestic and international brain researchers by creating an environment that will integrate various intellectual disciplines and from that convergence find solutions that will ultimately benefit society in the realms of medicine, engineering, business, and education. In striving toward this goal, BSI has become a leading international center for brain research with a reputation for discovery, innovation, training, and globalization of the scientific enterprise. Brain science is valuable not only for the advancement of science but also because it can greatly impact our society and economy. To meet these expectations, the Brain Science Institute (BSI) was established in 1997 as part of RIKEN, an independent research institution supported by the Japanese government.
Pedigree Drawing/ Window Pedigree Drawing (MS-Window and X-Window version of PEDRAW)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A pedigree drawing program using LINKAGE data files (entry from Genetic Analysis Software)
Code4Lib Journal WordPress Customizations
WordPress plugins for Anti-Spam, Metadata, Presentation, URLs, and Workflow from the Code4Lib community, a group of computer programmers and library technologists who largely work for and with libraries. Anti-Spam *Akimset - Filters out spam-link comments based on their content *reCAPTCHA - Requires users to copy a distorted word before they can comment Metadata *COinS Quicktags Button - In the non-WYSIWYG editor, can be used to build a basic COinS tag. This has been abandoned in favor of the generator at http://generator.ocoins.info/. *unAPI Server - Provides information about articles. Useful for Zotero users. Presentation *SyntaxHighlighter - Makes code pretty. *C4LJ Custom the_author()- Replaces the text returned by the_author() with the value of the author custom field. Necessary since articles are entered by their editors, but we want author information to appear on the articles and in the syndication feeds. URLs *C4LJ Remove Parents - A customization of http://wordpress.org/extend/plugins/remove-parents/. Prettifies category URLs so that issues appear at http://journal.code4lib.org/issues/issue1 instead of http://journal.code4lib.org/issues/issues/issue1. *FeedBurner FeedSmith - Redirects the main feed and the general comments feed to FeedBurner Workflow *Issue Manager - Enables one-click publishing of new issues, and prevents articles from being published until their associated issue is published. *Role Manager - Allows creation of custom roles and editing of roles' permissions. Used to create the Reviewer role, which can read Private articles, so that authors can see their articles before publication, and to prevent editors from publishing articles on accident.
Dresden University of Technology; Saxony; Germany
Public research university founded in 1828. One of the largest Universities of Technology in Germany.
Database of apo and holo structure pairs of proteins before and after binding. Various protein functions have been shown directly associated with conformational transitions triggered by binding other molecules. Tertiary structures determined in the unbound and bound state are usually named apo and holo structures, respectively. AH-DB is the largest database of apo-holo structure pairs and provides a sophisticated interface to search and view the collected data. It contains 746314 apo-holo pairs of 3638 proteins from 702 organisms.
Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project' '''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP.
Digital Enterprise Research Institute (DERI)
The Digital Enterprise Research Institute is an internationally recognized institute in semantic web research, education and technology transfer. DERI brings together academic and industrial partners to boost innovation in science and technology, which directly contributes to the Irish government''s plan of transforming Ireland into a competitive knowledge economy.
Collects, processes, and distributes human blood products to hospitals and research-related organizations. They operate donor centers and mobile donor vehicles to collect transfusable blood products from healthy donors, and offer human-derived blood products to research organizations. HemaCare also provides blood related services, principally therapeutic apheresis procedures, stem cell collection and other blood treatments, to patients and in connection with clinical trials.
Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions.
Daniel Mietchens demo wiki: What would scholarly communication look like if it were invented today?
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. Wiki serving as a demo for integrating wikis with scientific workflows, extending peer review and open access from formal scholarly publishing to the whole research cycle. Just imagine you could browse science as it happens. It is intended to be launched, as a prototype, in early 2011, and any help with it is welcome just create an account and mention here how you would like to get involved. In the initial phase, the platform will primarily be used to simply archive copies of scholarly articles that were formally published under an Open license. This WikiRepository shall provide a unified front-end to search, discover and sort all these Open Access papers, and to annotate, share, bookmark and discuss them. Later on, it is intended to be complemented by a formal publishing platform, WikiJournal. From the start on, emphasis will be placed on updatability of published research, on placing new research in the context of existing knowledge as well as ongoing and even planned research on the matter, and of the communities concerned.
The University of Texas at San Antonio''s (UTSA) Neurobiology Podcast, showcasing the current research of internationally renowned guest Neuroscientists. Each episode features a moderated discussion with a cross section of UTSA Neurobiology faculty, highlighting the featured guest''s research, and the state of the art in the field at hand.
A cross-database search service for Drosophila gene expression data, including microarray data from FlyAtlas and in situ images from BDGP and Fly-TED. The applications provide different ways to search for and compare gene expression data for the fruit fly Drosophila melanogaster. You may Search Gene Expression Data by Gene, Gene Batch, and by Tissue Expression Profile. A number of Web services (SPARQL endpoints) are provided from this site which may be queried programmatically for data.
SEQanswers: the next generation sequencing community
An information resource and user-driven community focused on all aspects of next-generation genomics. They hope to become the central location for next generation sequencing technology discussion and education. The site will always attempt to cater to everyone, regardless of scientific background or knowledge. The High-Throughput Sequencing Map site was conceived by James Hadfield (Cancer Research UK, Cambridge) and built by Nick Loman (University of Birmingham). The database is as only as good as you, the users.
Bio-Mixer is a web-based environment that supports the flexible exploration of biomedical ontologies. The concepts in the ontologies and their mappings can be explored in different views such as graph views, lists and timeline views. Drag-and-drop interaction can be used to show items and collections in different views, to create filtered views and to synchronize selections. Bio-Mixer enhances drag and drop with a new drop target highlighting and preview approach to make working with multiple collections and views easy. Bio-Mixer also provides support for ontology annotation and workspace sharing between collaborators. For more information, visit code.google.com/p/bio-mixer/
Wiki forum providing an extensive catalogue of manually categorized analysis tools, technologies and information about service providers, maintained by the members of the SEQanswers community. * Minimum Information about a high-throughput Sequencing Experiment * Software Hub: The place to add to, edit or browse the software database on SEQwiki. * Service Providers: Browse or edit the list of NGS service facilities. * How-to Hub: Mini reviews for the most used tools broken down by common tasks. * Developers Hub: The place to discuss the development of the SEQwiki site and its associated data. See also publishing SEQ*. * Publications: Publication about SEQwiki and selected citations.
Human Brain and Spinal Fluid Resource Center
Human Brain and Spinal Fluid Resource Center (HBSFRC)
Human Brain Spinal Fluid Resource Center
The Human Brain and Spinal Fluid Resource Center (HBSFRC)
A biomaterial supply resource which collects, stores, and distributes donated tissue to research scientists around the world. Collection occurs through the an anatomical donor program which accepts tissue donation from people with neurological/ psychiatric disorders. The Center also provides a continuous boost to biomedical research by providing high quality and quantity of pre- and post-mortem brains, spinal cords, cerebrospinal fluid (CSF), serum, blood cells and urine to use in investigations of neurological and psychiatric diseases. Scientists without a clinical site may use the Center''s readily available, high quality banked specimens.
Software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. It is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events.
A software pipeline for the analysis of microRNA Deep Sequencing data.
An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples.
Alaska Traumatic Brain Injury Advisory Board
The Alaska Brain Injury Network, Inc (ABIN) is a non-profit organization dedicated to Alaskans whose lives have been changed by brain injury. The ABIN mission is to educate, plan, coordinate, and advocate for services for the survivors of traumatic brain injury and their families. ABIN''s Board of 18 directors represents all regions of Alaska, and at least 50 percent are TBI survivors or family members. ABIN has two primary functions: TBI Advisory Board and TBI Resource Navigation Agency. Advisory Board -Visit both urban and rural communities, and listen to the stories that the public shares about the issues facing Alaskans with brain injuries. -Collaborate with our partner boards to affect changes in policies to improve programs and services. -Advocate for safety legislation, in-state brain injury rehabilitation, and TBI Waiver services. -Bring TBI professional training to Alaska. -Conduct ''needs assessment'' surveys of survivors, family members, and health workers. -Maintain up to date information on emerging issues identified through callers, public testimony, and the media. Resource Navigation (Information and Referral) -Respond to requests for assistance, information, resources, and referral. -Distribute a brain injury resource directory with statewide and local resources and supports available to individuals, families, friends, professionals, caregivers and the general public. -Work to establish a TBI hotline and brain injury support groups. -Distribute educational and informational resources to the public.
Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, gene expression studies, SNP discovery, genome mapping, and gene silencing. Probe records contain information on reagent distributors, probe effectiveness, and computed sequence similarities. The database is constantly updated, with over 11,000,000 probes available. Users may deposit their data into NCBI Probe Database.
TrackVis is software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. It does NOT perform actual fiber tracking. Diffusion Toolkit is a set of tools that reconstruct diffusion imaging data and generate fiber track data for TrackVis to visualize. Because these two sets of tools were developed and maintained separately and each has distinguished funtionalities, they decided to distribute them as two separate programs for the ease of maintenance and upgrade. You do need both of them to perform complete diffusion data processing and analysis. Features of TrackVis include: * Cross-platform. Works on Windows, Mac OS X and Linux with native look and feel. * A variety of track filters (track selecting methods) allowing users to explore and locate specific bundles with ease. * Multiple rendering modes with customizable scalar-driven color codes. * Real-time parameter adjustment and 3D render. * Open format of the track data file allowing users to integrate customized scalar data into the track file and visualize and analyze it. Save and restore scenes in XML style scene file. * Statistical scalar analysis of tracks and ROIs. * Synchronized real-time multiple dataset analysis and display allowing time-point and/or subject comparison. Synchronized analysis and display on same dataset can also be performed in real-time remotely over the network. * Upfront in-line parameter adjustment in real-time. No tedious pop-up dialogs. TrackVis works with Track File created by Diffusion Toolkit. Diffusion Toolkit processes raw DICOM, Nifti format and ANALYZE images. TrackVis and Diffusion Toolkit are cross-platform software. They can run on Windows XP, Mac OS X as well as Linux.
A small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains. BFO is a genuine upper integration in scientific and other domains. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences.
Private research university with its main campus in Macon, Georgia. Founded in 1833 as Mercer Institute and gaining university status in 1837.
The MiND: Metadata in NIfTI for DWI framework enables data sharing and software interoperability for diffusion-weighted MRI. This site provides specification details, tools, and examples of the MiND mechanism for representing important metadata for DWI data sets at various stages of post-processing. MiND framework provides a practical solution to the problem of interoperability between DWI analysis tools, and it effectively expands the analysis options available to end users. To assist both users and developers in working with MiND-formatted files, we provide a number of software tools for download. * MiNDHeader A utility for inspecting MiND-extended files. * I/O Libraries Programming libraries to simplify writing and parsing MiND-formatted data. * Sample Files Example files for each MiND schema. * DIRAC LONI''s Diffusion Imaging Reconstruction and Analysis Collection is a DWI processing suite which utilizes the MiND framework.
Fellowship for Interpretation of Genomes
Fonstein, Kogan, Osterman, Overbeek and Vonstein found the non-profit Fellowship for Interpretation of Genomes (FIG) to follow their vision of seeking advances in understanding through comparative analysis of the growing body of genomic data. The team at FIG began a new open source comparative genomics environment, the SEED. The Project to Annotate 1000 Genomes is a central goal of FIG. FIG is a nonprofit organization devoted to providing support for those analyzing genomes. It focuses on organizing the data needed to support interpretation of genomes, providing the infrastructure needed by the world community in its efforts to achieve understanding. FIG offers the key services required to architect and implement a comparative framework for interpreting genomes. In addition, we pick specific, critical problems and attempt to actively participate in the unraveling of the secrets within these amazing entities. It is only by merging the work of building infrastructure with the applications that use it that we will more deeply understand what is needed at each step.
Banner Sun Health Research Institute Brain and Body Donation Program
Banner Sun Health Research Institute Brain and Tissue Bank
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. An autopsy-based, research-devoted brain bank, biobank and biospecimen bank that derives its human donors from the Arizona Study of Aging and Neurodegenerative Disease (AZSAND), a longitudinal clinicopathological study of the health and diseases of elderly volunteers living in Maricopa county and metropolitan Phoenix, Arizona. Their function is studied during life and their organs and tissue after death. To date, they have concentrated their studies on Alzheimer's disease, Parkinson's disease, heart disease and cancer. They share the banked tissue, biomaterials and biospecimens with qualified researchers worldwide. Registrants with suitable scientific credentials will be allowed access to a database of available tissue linked to relevant clinical information, and will allow tissue requests to be initiated., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Life Extension is a global authority on nutrition, health and wellness as well as a provider of scientific information on anti-aging supplements and therapies. We supply only the highest quality nutritional supplements, including minerals, vitamins, herbs and hormones. Life Extension publishes the very latest information on anti-aging and wellness in its monthly publication, Life Extension Magazine, the Disease Prevention and Treatment book of integrative health protocols, the Life Extension Update e-mail newsletter and the Daily Health Bulletin, and at this website. All to support more informed health choices. In addition to a wealth of information, Life Extension offers 300+ premium-quality vitamins, minerals, hormones, diet and nutritional supplements, and even skin care products, which are often the fruits of research reported on or funded by the Life Extension Foundation.
This program is developed for predicting a query sequence with hairpin structure as a real miRNA precursor or not. The triplet-SVM classifier analyzes the triplet elements of the query and predicts it using a SVM classifier. The SVM classifier is previously trained based on the triplet element features of a set of real miRNA precursors and a set of pseudo-miRNA hairpins. triplet-SVM classifier was written by Chenghai Xue and is free to all users but without any warranty.
University of Freiburg; Baden-Wurttemberg; Germany
Public research university located in Freiburg im Breisgau, Baden-Württemberg, Germany.
National Yang-Ming University; Taipei; Taiwan
Kings College London Infectious Diseases BioBank
King''s College London Infectious Diseases BioBank
Centralized specimen archiving and molecular analysis facility that assists researchers wishing to undertake cohort-based projects in areas such HIV/AIDS, HCV infection or MRSA. Its aim is to make medical research easier, more efficient and faster to perform. The IDB collects valuable clinical samples from patients with infections who are attending their partner NHS-Trust clinics. Their core collections include blood samples from patients infected with human immunodeficiency virus (HIV), hepatitis B (HBV) & hepatitis C (HCV) viruses or methicillin resistant Staphylococcus aureus (MRSA). Blood samples are separated so that patients������?? DNA, plasmas (cell-free blood) and lymphocytes (white blood cells) can be frozen into a comprehensive library. Medical researchers can access complete sets of samples to answer important clinical questions, if their research project is approved by the IDB''s Management Committee. For this reason they are actively recruiting ''medically interesting'' patients who are infected with HIV, for example: those who remain well ������?? despite being infected for many years; others who are exposed to HIV but remain uninfected; others who develop AIDS very quickly; and, those who are in the process of sero-converting.
Health++ (HealthPlusPlus) is a wiki about health, also a medical knowledge base, an online medical encyclopedia. We are making this wiki unique with adding relevant videos, links, resources and communities. Please join us in this effort to make this wiki the most useful and comprehensive medical wiki resource site. Some of the initial content on this page may be incorporated in part from copyleft sources in the public domain including wikis such as Wikipedia and AskDrWiki. Drug information for patients came from the The National Library of Medicine. Infectious disease information may have come from the Centers for Disease Control (CDC). * Health care in the United States * List of common health issues * List of RSS feeds on health * List of encyclopedias on medicine * MedlinePlus Health News * List of medical websites * List of medical wikis * List of online medical encyclopedia * List of online medical dictionaries * List of hospitals
iHOP - Information Hyperlinked over Proteins
Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.
Data management platform that houses all data generated by the Human Connectome Project - image data, clinical evaluations, behavioral data and more. ConnectomeDB stores raw image data, as well as results of analysis and processing pipelines. Using the ConnectomeDB infrastructure, research centers will be also able to manage Connectome-like projects, including data upload and entry, quality control, processing pipelines, and data distribution. ConnectomeDB is designed to be a data-mining tool, that allows users to generate and test hypotheses based on groups of subjects. Using the ConnectomeDB interface, users can easily search, browse and filter large amounts of subject data, and download necessary files for many kinds of analysis. ConnectomeDB is designed to work seamlessly with Connectome Workbench, an interactive, multidimensional visualization platform designed specifically for handling connectivity data. De-identified data within ConnectomeDB is publicly accessible. Access to additional data may be available to qualified research investigators. ConnectomeDB is being hosted on a BlueArc storage platform housed at Washington University through the year 2020. This data platform is based on XNAT, an open-source image informatics software toolkit developed by the NRG at Washington University. ConnectomeDB itself is fully open source.
International Federation of Digital Seismograph Networks (FDSN) Web service that returns event (earthquake) information from the catalogs submitted to the Incorporated Research Institutions for Seismology (IRIS) Data Management Center (DMC). Events may be selected based on location, time, catalog, contributor and internal identifiers. By default, events are retrieved from the NEIC PDE catalog for recent events and then the ISC catalog when it becomes available. These default results include only that catalog''s primary origin and primary magnitude for each event, they may optionally include all available origin and magnitude estimates. By default results are returned as XML in QuakeML format but may also be requested in text formats. This service is an implementation of the FDSN web service specification version 1.
Conticabase - European Sarcoma Database and Tumour Bank
Conticabase - European Sarcoma Database Tumor Bank
Conticabase - European Sarcoma Database Tumour Bank
This database contains anonymized information describing the tumor, treatment and follow-up as well as tumor sample availability and molecular biology analyses for mesenchymal tumors except GIST and bone tumors. The query tool allows users to ask questions about the overall content of the database in order to evaluate the feasibility of specific collaborative studies. We hope this database will become an important tool for increasing our knowledge on these rare tumors and for developing joint research programs. The tool can be used as a local center database thanks to its rules for access to patient data and material. Conticabase currently contains the following data from 31 out of the 48 registered centers (Last modification on 28/03/2012): * 11518 Patients * 11562 Tumors * 13897 Samples (13636 Paraffin and 5773 Frozen) Use of conticabase data At anytime, a data manager can export data of patients from his (her) Centre or group according to his (her) level of rights. To obtain data from another Centre, a partner should ask the coordinator of the corresponding Centre for these data. To use data for a cooperative study, a member should write a short text describing the project and send it to partners of interest. Each partner may decide whether to participate or not and therefore, whether to send or not the corresponding data to the project leader. In the event that the data from the conticabase result in a publication, acknowledgement is required. Use of tumour material entered in the ConticaBank To obtain material from another Centre for a cooperative study, a partner should write a short text describing the project and send it to the partners of interest. Each partner may decide whether to participate or not and, therefore, whether to send or not the corresponding material to the project leader. In the event that the material used result in a publication, acknowledgement is required.
Neuroscience Information Framework Data Federation
Service that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Podcasts View * Integrated Software View * Integrated Video View * Integrated Jobs * Integrated Blogs For a listing of the Federated Databases see, http://neuinfo.org/mynif/databaseList.php or refer to the Resources Listed by NIF Data Federation table below.
UNYTS: Upstate New York Transplant Services
Leading procurement organization in the United States and one of the only eight centers nationwide to house organ, tissue and eye procurement in one location. With the addition of Community Blood Service, Upstate New York Transplant Services has become the first organization of its kind nationwide. It operates as a non-profit serving the eight counties of Western New York and works to assist donor families, coordinate the donation process and increase knowledge and awareness within the community regarding transplantation. Upstate New York Transplant Services is ranked as one of the top procurement organizations nationwide. In 1997, Upstate New York Transplant Services had just 200 donors; in 2007 the organization surpassed 1,000. In the summer of 2007, Upstate New York Transplant Services added community blood banking services - bringing both a significant savings to area hospitals and assurance to Western New York donors that their blood donations remain local.
A privately held spinal company that is driving significant technological advancements across a complete suite of spinal products. Founded in 2003, Globus'' single-minded focus on advancing spinal surgery has made it the fastest growing company in the history of orthopedics. Globus is driven to utilize superior engineering and technology to achieve pain free, active lives for all patients with spinal disorders. The ultimate goal at Globus is to deliver innovation by utilizing superior engineering and technology to help improve patients'' lives. This clinical inspiration is central to every endeavor we undertake. We have developed a Spine Innovation Engine to focus our efforts on delivering industry leading solutions to surgeons and their patients. Our Spine Innovation Engine has developed a portfolio that includes a comprehensive line of technologically-advanced spine products. To date we have released over 50 major products and have over 30 more in various stages of development. Clinical Studies are the foundation for advancing innovative spine care and Globus is committed to a robust investment into prospective and retrospective clinical trials to evaluate the safety and efficacy of our products. Globus is currently conducting several FDA-approved Investigational Device Exemption (IDE) clinical studies.
A video resource containing short, scientific videos which can be browsed or searched for. The videos are based on published papers, talks or posters. It is free to use and disseminates research findings to the world wide web. SciVee enables researchers to combine video with documentation and data in a media rich format, enhancing journal articles with pubcasts by linking and synchronizing video explanations to their published text. Similarly, video summaries can be associated and synchronized with scientific posters to create postercasts highlighting the key finding of the research.
Donor Services of Indiana (DSI) in Fort Wayne is the nonprofit tissue bank established to provide high-quality human tissue and eye tissue for transplant to patients in our region, and for use in medical research. The program depends on contributions made by generous people who have consented to donation after the death of a family member. Bone, tendons, skin grafts and heart valves can significantly improve the quality of life for transplant recipients by preventing amputation, restoring mobility, relieving pain and sometimes saving lives. DSI adheres to the strict guidelines of the American Association of Tissue Banks and is widely recognized for its leadership in tissue banking. Transplant tissue provided by DSI is from regional donors evaluated and procured by our clinical staff, tested under our rigorous protocols, and distributed, tracked and followed by our professionals. DSI provides tissues back to the community from which they came and is equipped to deliver needed tissues on an urgent basis for medical emergencies, surgeries and procedures.
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. Patent Abstracts is a set of biology-related abstracts of patent applications derived from data products of the European Patent Office (EPO). Patent documents from Europe (EP), USA (US) and World (WO) are included. Abstracts are extracted from the ESPACE ACCESS and GlobalPat CD/DVD products according to the International Patent Classification (IPC) classes covering biology topics. The data are transformed to a common XML format and combined into one SRS dataset.
Minnesota Liver Tissue Cell Distribution System
Liver Tissue Cell Distribution System (LTCDS)
Liver Tissue Procurement and Distribution System
University of Minnesota Liver Tissue Cell Distribution System
Tissue bank that provides human liver tissue from regional centers for distribution to scientific investigators throughout the United States. These USA regional centers have active liver transplant programs with human subjects approval to provide portions of the resected pathologic liver for which the transplant is performed.
A large selection of complex network measures in Matlab that are increasingly used to characterize structural and functional brain connectivity datasets. Several people have contributed to the toolbox, and if you wish to contribute with a new function or set of functions, please contact Olaf Sporns. All efforts have been made to avoid errors, but users are strongly urged to independently verify the accuracy and suitability of toolbox functions for the chosen application. Please report bugs or substantial improvements.
Susan G. Komen for the Cure is the global leader of the breast cancer movement, having invested more than $1.9 billion since inception in 1982. As the world''s largest grassroots network of breast cancer survivors and activists, we''re working together to save lives, empower people, ensure quality care for all and energize science to find the cures. Thanks to events like the Susan G. Komen Race for the Cure and the Susan G. Komen 3-Day for the Cure, and generous contributions from our partners, sponsors and fellow supporters, we have become the largest source of nonprofit funds dedicated to the fight against breast cancer in the world.
Research Tissue Repository - University of Connecticut
Research Tissue Repository Core Facility
UConn Health Center Research Biorepository
University of Connecticut Health Center Research Tissue Repository Core Facility
The UConn Health Center Research Biorepository consists of de-identified tissue and/or blood samples and patient data obtained from consented patients coupled with a database of clinical and laboratory data. Identified samples are available to researchers with IRB approval. Our goal is to develop a comprehensive resource that will procure, characterize and distribute high quality human specimens according to rigid protocols and ethical guidelines. We are sponsored by the Carole and Ray Neag Comprehensive Cancer Center and work closely with clinical and basic science investigators concentrating on translational research. The Biorepository is one of the many core facilities that receives support from the Health Center Research Advisory Committee (HCRAC). Our services include consenting of eligible patients, coordination for specimen collection, storage, data management and specimen distribution. We offer H & E, unstained and frozen sections on slides as well as paraffin and OCT curls. RNA and DNA isolation from specimens are also available, using methods that preserve the integrity of the nucleic acids. Logged in investigators can browse the catalogue for a detailed description of our services and prices on the Research Store and see an inventory of our samples using the link on this page titled ����??Sample Inventory����??. The inventory is updated on a regular basis.
SMPDB (The Small Molecule Pathway Database)
An interactive, visual database containing more than 350 small molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes / protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB''s mapping interface. All of SMPDB''s images, image maps, descriptions and tables are downloadable.
The Mount Sinai Biobank is a large collection of DNA and plasma samples that are stored in a way that protects patients'' privacy while allowing research to be performed on de-identified clinical information from Mount Sinai''s data warehouse system. The Biobank''s goal is to acquire samples from a total of 100,000 donors over a period of several years. Mount Sinai is one of only a handful of places nationwide establishing biobanks on such a large scale. Funded by the Charles R. Bronfman Institute for Personalized Medicine, the Biobank project is a research project that is approved by the Mount Sinai Institutional Review Board and is continuously reviewed. Biobank Facts: * 17947 donors between 18 and 89 years of age have already participated in Biobank. * 194111 aliquots of DNA and * 212005 aliquots of plasma are available for future research.
Public bibliographic database that provides access to citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include fields of biomedicine and health, covering portions of life sciences, behavioral sciences, chemical sciences, and bioengineering. Provides access to additional relevant web sites and links to other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to full-text of articles at journal web sites using LinkOut.
The Rocky Mountain Tissue Bank is a Colorado, 501c3 non-profit corporation, established in 1980. It is governed by a Board of Directors and is an independent tissue processing facility with no affiliation with any other tissue bank. It develops and produces irradiated allogenic cancellous bone and marrow for human transplantation. This product stimulates bone regeneration in patients with bone loss due to trauma, disease, or genetic malformation and provides a foundation for dental implants. The primary distribution network is through Periodontists, and Oral Surgeons and clinicians specializing in implant dentistry.
MetaPhyler - Estimating Bacterial Composition from Metagenomic Sequences
A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database.
Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.
Metagenomic AND rDNA Taxonomic Assignment
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Java-based software that blasts each sequence that you provide it, and then looks for a consensus taxon among the top-hits returned from blast. MARTA uses NCBI''s megablast program to align your sequence(s) against a local installation of blast. Then MARTA uses GenInfo Identifiers from the top-hits to retrieve taxonomic information from NCBI''s taxonomy database. Using your thresholds/cutoffs, MARTA ''votes'' to find a taxonomic assignment by consensus; MARTA might resolve some sequences to species level, and others to kingdom or to no level, depending on the taxonomic information held within your tag or sequence.
Database of images, specimen records, and natural history information on ants including Search Tools, Regional Lists, In Depth Information, Ant Image Comparison Tool, PDF Field Guides, Maps on AntWeb and Google Earth, and Ant Genera of the World Slideshow. It is community driven and open to contribution from anyone with specimen records, natural history comments, or images. As of February of 2013, AntWeb has 97,814 ant images, of 23,272 specimens representing over 10,549 species. AntWeb provides tools for submitting images, specimen records, annotating species pages, and managing regional species lists. AntWeb contains information on the ant faunas of several areas in the Nearctic and Malagasy biogeographic regions, and global coverage of all ant genera. AntWeb provides tools for exploring the diversity and identification of ants (Hymenoptera: Formicidae). These tools have been developed to encourage the study of ants, to facilitate the use of ants in inventory and monitoring programs, and to provide ant taxonomists with access to images of type specimens. AntWeb illustrates the diversity of ants by providing information and high quality color images of many of the approximately 10,000 known species of ants. AntWeb currently focuses on the species of the Nearctic and Malagasy biogeographic regions, and the ant genera of the world. Over time, the site will grow to describe every species of ant known.
Mercer University College of Pharmacy; Georgia; USA
Mercer University College of Pharmacy and Health Sciences
One of four health sciences units within Mercer Health Sciences Center. Provides the first pharmacy program in the region to offer the Doctor of Pharmacy degree as its sole professional degree. The College offers the Doctor of Pharmacy (Pharm.D.) degree and the Doctor of Philosophy (Ph.D.) degree in pharmaceutical sciences, as well as four combined degree programs – Pharm.D./M.B.A, Pharm.D./M.P.H., Pharm.D./Ph.D. and Pharm.D./M.S. in Health Informatics.
siDirect 2.0 provides functional and off-target minimized siRNA design for mammalian RNAi. The previous version of our software designed functional siRNAs by considering the relationship between siRNA sequence and RNAi activity, and provided them along with the enumeration of potential off-target gene candidates by using a fast and sensitive homology search algorithm. In the new version, the siRNA design algorithm is extensively updated to eliminate off-target effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability, or the melting temperature (Tm), of the seed-target duplex, which is formed between the nucleotides positioned at 2-8 from the 5'' end of the siRNA guide strand and its target mRNA. Selection of siRNAs with lower seed-target duplex stabilities (benchmark Tm < 21.5 degrees C) followed by the elimination of unrelated transcripts with nearly perfect match should minimize the off-target effects. siDirect 2.0 provides functional, target-specific siRNA design with the updated algorithm which significantly reduces off-target silencing. When the candidate functional siRNAs could form seed-target duplexes with Tm values below 21.5 degrees C, and their 19-nt regions spanning positions 2-20 of both strands have at least two mismatches to any other non-targeted transcripts, siDirect 2.0 can design at least one qualified siRNA for > 94% of human mRNA sequences in RefSeq. Enter an accession number and retrieve sequence or Paste in a nucleotide sequence.
Database containing descriptions of biological source materials used in experimental assays. Sources include: GenBank, Sequence Read Archive (SRA), Coriell, ATCC. Submissions are supported by a web-based Submission Portal that guides users through a series of forms for input of rich metadata describing their samples. As the capacity and complexity of biological data sets expands, databases face new challenges in ensuring that the information is adequately organized and described. The NCBI BioSample database is being developed to help address the challenges by providing the means by which data generators can organize and describe a broad range of sample types, and link to corresponding sets of experimental data in archival databases.
Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome.
Database that aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI' '''s assay databases such as ArrayExpress, the European Nucleotide Archive or PRoteomics Identificates DatabasE. It provides links to assays for specific samples, and accepts direct submissions of sample information. The goals of the BioSample Database include: # recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; # minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and # supporting cross database queries by sample characteristics. The database includes a growing set of reference samples, such as cell lines, which are repeatedly used in experiments and can be easily referenced from any database by their accession numbers. Accession numbers for the reference samples will be exchanged with a similar database at NCBI. The samples in the database can be queried by their attributes, such as sample types, disease names or sample providers. A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples (at) ebi.ac.uk. Current data sources: * European Nucleotide Archive (424,811 samples) * PRIDE (17,001 samples) * ArrayExpress (1,187,884 samples) * ENCODE cell lines (119 samples) * CORIELL cell lines (27,002 samples) * Thousand Genome (2,628 samples) * HapMap (1,417 samples) * IMSR (248,660 samples)
Brodmann Areas in the Human Brain with an Emphasis on Vision and Language
Brodmann Areas in the Human Brain with an Emphasis on Vision Language
Reference atlas of Brodmann Areas in the Human Brain with an Emphasis on Vision and Language. Other Pages include: Flat Brodmann Maps, Brodmann Area Names (with locational Descriptions), Flat Visual Area Maps, Language Areas, PopUp Gyri Maps
Data set of over 1500 one- and two-minute EEG recordings, obtained from 109 volunteers. Subjects performed different motor/imagery tasks while 64-channel EEG were recorded using the BCI2000 system (http://www.bci2000.org). Each subject performed 14 experimental runs: two one-minute baseline runs (one with eyes open, one with eyes closed), and three two-minute runs of each of the four following tasks: # A target appears on either the left or the right side of the screen. The subject opens and closes the corresponding fist until the target disappears. Then the subject relaxes. # A target appears on either the left or the right side of the screen. The subject imagines opening and closing the corresponding fist until the target disappears. Then the subject relaxes. # A target appears on either the top or the bottom of the screen. The subject opens and closes either both fists (if the target is on top) or both feet (if the target is on the bottom) until the target disappears. Then the subject relaxes. # A target appears on either the top or the bottom of the screen. The subject imagines opening and closing either both fists (if the target is on top) or both feet (if the target is on the bottom) until the target disappears. Then the subject relaxes. The data are provided here in EDF+ format (containing 64 EEG signals, each sampled at 160 samples per second, and an annotation channel).
Stanley Medical Research Institute Online Genomics Database
The Stanley Online Genomics Database uses samples from the Stanley Medical Research Institute (SMRI) Brain Bank. These samples were processed and run on gene expression arrays by a variety of researchers in collaboration with the SMRI. These researchers have performed analyses on their respective studies using a range of analytic approaches. All of the genomic data have been aggregated in this online database, and a consistent set of analyses have been applied to each study. Additionally, a comprehensive set of cross-study analyses have been performed. A thorough collection of gene expression summaries are provided, inclusive of patient demographics, disease subclasses, regulated biological pathways, and functional classifications. Raw data is also available to download. The database is derived from two sets of brain samples, the Stanley Array collection and the Stanley Consortium collection. The Stanley Array collection contains 105 patients, and the Stanley Consortium collection contains 60 patients. Multiple genomic studies have been conducted using these brain samples. From these studies, twelve were selected for inclusion in the database on the basis of number of patients studied, genomic platform used, and data quality. The Consortium collection studies have fewer patients but more diversity in brain regions and array platforms, while the Array collection studies are more homogenous. There are tradeoffs, the Consortium results will be more variable, but findings may be more broadly representative. The collections contain brain samples from subjects in four main groups: Bipolar Schizophrenia, Depression, and Controls Brain regions used in the studies include: Broadman Area 6, Broadman Area 8/9, Broadman Area 10, Broadman Area 46, Cerebellum The 12 studies encompass a range of microarray platforms: Affymetrix HG-U95Av2, Affymetrix HG-U133A, Affymetrix HG-U133 2.0+, Codelink Human 20K, Agilent Human I, Custom cDNA Publications based on any of the clinical or genomic data should credit the Stanley Medical Research Institute, as well as any individual SMRI collaborators whose data is being used. Publications which make use of analytic results/methods in the database should additionally cite Dr. Michael Elashoff. Registration is required to access the data.
Database of nucleotide sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI''s Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. Cn3D is a tool for visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Can be used to display MMDB structures, superpositions of VAST related structures, and conserved core motifs identified in conserved domains.
DiScRIBinATE: Distance Score Ratio for Improved Binning and Taxonomic Estimation
Distance Score Ratio for Improved Binning and Taxonomic Estimation
Software for accurate taxonomic classification of metagenomic sequences using a similarity based binning method. User needs to perform a similarity search of the input metagenomic sequences (reads) against the nr protein database using BLASTx search. The generated blastx output is then taken as the input by the DiScRIBinATE program.
University of Leeds; West Yorkshire; United Kingdom
Public research university in Leeds, West Yorkshire, England. It was established in 1874 as the Yorkshire College of Science. In 1884 it merged with the Leeds School of Medicine and was renamed Yorkshire College.
PubOnto: Open Biomedical Ontology-Based Medline Exploration
We developed an ontology-based interactive Medline exploration solution called PubOnto to enable the interactive exploration and filtering of search results through the use of multiple ontologies from the OBO foundry. The PubOnto program is a rich internet application based on the FLEX platform. It contains a number of interactive tools, visualization capabilities, an open service architecture, and a customizable user interface. Effective Medline database exploration is critical for the understanding of high throughput experimental results and the development of novel hypotheses about the mechanisms underlying the targeted biological processes. While existing solutions enhance Medline exploration through different approaches such as document clustering, network presentations of underlying conceptual relationships and the mapping of search results to MeSH and Gene Ontology trees, we believe the use of multiple ontologies from the Open Biomedical Ontology can greatly help researchers to explore literature from different perspectives as well as to quickly locate the most relevant Medline records for further investigation.
A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies.
Magazine published by Simbios, a National NIH Center for Biomedical Computing, covering the latest research wherever computation, biology, and medicine intersect. In addition to disseminating information about the latest research in biomedical computation, they aim to foster community amongst the wide audience interested in any and all aspects of biomedical computing. Whether you are a long time researcher in this area or new to it, please consider joining those who have already started to participate in Biomedical Computation Review. You are encouraged to: * Write a letter to the editor on any relevant topics * Suggest your favorite topics that should receive more attention * Suggest an idea for a feature article * Propose an idea for an Under the Hood tutorial * Tell us any other way in which we can better serve this community
South Texas Accelerated Research Therapeutics
South Texas Accelerated Research Therapeutics (START) directs clinical trials of novel anticancer agents using a high quality and innovative information technology infrastructure to ensure accurate and rapid clinical trials in a setting that emphasizes personalized and compassionate clinical care. START''s head office is located in San Antonio, Texas, in the heart of the South Texas Medical Center. With centers located in San Antonio, Texas and Madrid, Spain, START conducts the world''s largest Phase I medical oncology program putting more than 400 patients per year on Phase I trials. Patients travel from all over the world to participate in one or more of our Phase I drug trials. START consists of a team of highly trained physicians and staff with extensive experience in Phase I clinical trials research and are nationally recognized as thought leaders in cancer research and drug development. The mission of START is to accelerate the development of new anticancer drugs that will improve the quality of life and survival for patients with cancer. Our drug development program is not only furthering cancer research, but also offers hope to patients facing the toughest cancer battles.
LifeCenter Northwest is one of 58 federally designated nonprofit organ procurement organizations (OPO) in the United States. LifeCenter Northwest works together with families, medical professionals, and communities in Alaska, Montana, North Idaho, and Washington to save lives through organ and tissue donation. LifeCenter Northwest provides the following services: * Hospital Development ** support of donor families throughout and after the donation process ** development of strong relationships between hospitals and LifeCenter Northwest ** helping hospitals stay compliant with federal and state regulations ** ongoing education of hospital staff on donation laws and programs * Organ Recovery Services ** on-site referral response to hospitals ** evaluation of patient medical suitability for donation ** management of patient care through the allocation and recovery of organs ** placement of organs, working with the United Network for Organ Sharing (UNOS) ** coordination of transplant team transportation and arrival at donor hospitals ** surgical recovery and transportation of organs * Tissue Recovery Services ** telephone referral response to hospitals ** evaluation of patient medical suitability for donation ** surgical recovery and transportation of tissues
PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System
Protein ANalysis THrough Evolutionary Relationships
Protein ANalysis THrough Evolutionary Relationships Classification System
System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.
International Histocompatibility Cell and DNA Bank
International Histocompatibility Cell DNA Bank
International Histocompatibility Working Group Cell and DNA Bank
International Histocompatibility Working Group Cell DNA Bank
The IHWG Cell and DNA Bank was established as a shared resource to support the scientific projects of the 13th International Histocompatibility Workshop (IHWS). The Research Cell Bank (RCB), located in Fred Hutchinson Cancer Research Center in Seattle, WA, maintains the IHWG inventory. This comprehensive inventory includes B-Lymphoblastoid Cell Lines (B-LCL) from previous International Workshops, HLA heterozygous and homozygous donors, selected families, and individuals of diverse population groups. The RCB maintains stocks of purified DNA derived from these cell lines, as well as DNA reference panels that provide an extensive array of HLA and HLA-related sequence polymorphisms. The RCB also provides cloned HLA genes and B-LCL transfected with selected HLA genes, which are available on a limited basis.
The Regional Tissue Bank (RTB), in Halifax Nova Scotia, is a non-profit service dedicated to providing Canadian health care teams with safe high quality allograft tissue and tissue products in support of optimal patient outcomes. It is accredited with the American Association of Tissue Bank (AATB) for all aspects of screening, procurement, processing, storage and distribution for cardiovascular, bone and skin tissues. The RTB is also in compliance with the Eye Bank Association of America (EBAA) and the draft Canadian Standards for Tissue Donation and Transplantation. It also supports autologous tissue transplantation, the bone marrow transplantation program and provides perfusion and preservation service to the Multi-Organ Transplant Program kidney and liver procurement teams. The mission of the Regional Tissue Bank is to ensure all Nova Scotians are offered the option of tissue donation and to provide safe high quality tissue products to Nova Scotian surgical programs and patients. It has expanded its activities with New Brunswick, in collaboration with Health Care Regions, to support tissue donation and transplantation in New Brunswick. The RTB also provides tissue to centers throughout Canada when requested; under the condition that meeting these requests would not disadvantage Atlantic Canadians.
Mount Desert Island Biological Laboratory
Non-profit research institution that studies marine and non-marine organisms to learn about the basic biology of life. Our scientists make critical discoveries about how organisms adapt to their environment and how environment, health, and genetics are related. They study a wide range of organisms such as sharks, skates, and sea urchins to learn about development and regeneration. They investigate the root causes of diseases like cystic fibrosis, and they examine the mechanisms that make living creatures age. Research at MDIBL takes place within three centers: the Center for Regenerative Biology and Medicine, the Martha and Wistar Morris Center for Environmental Health Sciences, and the John W. and Jean C. Boylan Center for Cellular and Molecular Physiology. Scientists at each center include both permanent MDIBL faculty and adjunct faculty who come to MDIBL for a few weeks or an entire season, often year after year. Short courses, symposia, and fellowships provide research experience and training to students and scientists at all levels, from high school and college through medical school and senior investigators. Our education programs are always hands-on and engage students in meaningful research. MDIBL is the lead institution for the Maine IDeA Network for Biomedical Researcha research and education network linking MDIBL with The Jackson Laboratory and ten Maine colleges and universities.
Medical Library Association - Hospital Libraries Section
Sponsored by the Hospital Libraries Section of the Medical Library Association, the Hospital Librarians Wiki provides the structure in which we can all share best practices. Everyone is invited to participate and can add content to existing pages by Editing This Page. You do not have to be a member of HLS/MLA. To add a new page, click on Join in the upper left corner, wait for your request to be accepted (generally within 24 hours), then click on New Page in the upper left corner. You may add links to the left Navigation bar.
Northwest Tissue Services is the only fully accredited non-profit tissue bank in this region. As a non-profit tissue bank, we provide all allograft and tissue products at the lowest possible cost consistent with high quality. Our accreditation by the American Association of Tissue Banks (AATB) is a testament to the quality and safety of tissue we have provided to hospitals and patients in this region for over twenty years. As the most knowledgeable and experienced tissue resource in the Northwest, we work hard every day to provide high quality tissue products and services.
RNA Assessment; WUSTL Tissue Procurement Core Facility and Tumor Bank
Washington University Tissue Procurement Core Facility and Tumor Bank
Washington University Tissue Procurement/Tumor Bank
The Tissue Procurement Core Facility and Tumor Bank is a collaborative effort between the Siteman Cancer Center and the Department of Pathology and Immunology. This shared resource facility provides the resources, infrastructure, and technologies for biospecimen-based translational pathology research. Services include: Tissue Procurement, Processing, and Storage; Archival Frozen Tissue Bank; and Laser Capture Microdissection. * Tissue Procurement, Processing, and Storage: For investigators initiating new protocols that involve biospecimen collection (e.g. solid tissues, blood, bone marrow), the Core can provide model consent forms and personnel to collect specimens through the Division of Surgical Pathology and other clinical sites on campus. Solid tissues are usually snap frozen in the surgical pathology suite, although investigators may request alternate preservation methods. Blood specimens are generally processed to frozen serum aliquots and peripheral leukocyte cell pellets. Other specimens (e.g. lymph node needle aspirations) that may be obtained in a variety of other patient care areas can be collected and processed immediately by a staff member who is on call at all times to receive specimens. * Archival Frozen Tissue Bank: For investigators desiring immediate access to material for molecular and histological studies, an archive of over 18,000 frozen human biospecimens is available. Specimens include solid tumors, patient-matched non-malignant tissue, serum, and peripheral blood leukocytes. Each specimen is accompanied with basic patient demographic information and pathology diagnostic data. Generally, each frozen tissue specimen is reviewed to confirm that the specimen is representative of the written pathology diagnosis. Investigators may request frozen tissue sections for immunohistochemical analysis, genomic DNA, protein extracts, or cellular RNA derived from any specimen in the archive. * RNA Assessment: Cellular RNA prepared by the Core from banked specimens or any other RNA submitted by investigators can be qualitatively assessed by Agilent Bioanalyzer capillary microelectrophoresis and quantified by fiberoptic spectrophotometry, prior to use for downstream applications such as microarray or qRT-PCR analysis. * Laser Capture Microdissection: Pure cell populations are often needed for clonality, loss of heterozygosity (LOH), gene mutation, and mRNA expression analysis studies. The Core''s Pixcell II Laser Capture Microdissection (LCM) instrument can be used to dissect pure populations of cells from heterogeneous tissue sections. The instrument greatly enhances the speed and ease of dissection as compared to traditional manual methods. The instrument is available for use to investigators who wish to microdissect cells from either specimens stored in the Tissue Procurement Core or their own sets of collected tissue specimens.
UniGe, is one of the largest universities in Italy. It is located in the city of Genoa and regional Metropolitan City of Genoa, on the Italian Riviera in the Liguria region of northwestern Italy. The original university was founded in 1481.
Capital Biosciences: innovative solutions for life sciences
Biological products including Cell Immortalization Products, Clinically Defined Human Tissue, cDNA ORF Clones, Premade Adenoviruses, Purified Proteins, Viral Expression Systems and others as well as services like Custom Recombinant Adenovirus Production, Custom Recombinant Lentivirus Production, Protein Detection and Quantification and Stable Cell Line Production for academic and governmental research institutes, pharmaceutical and biotechnology industry. Capital Biosciences offers most types of human tissues, normal and diseased, with extensive clinical history and follow up information. Standard specimen format: Snap-frozen(flash-frozen), Formalin fixed and paraffin embedded (FFPE) tissues, Blood and blood products, Bone marrow, Total RNA, Genomic DNA, Total Proteins, Primary cell cultures, Viable frozen tissue. Tumor tissue samples include: Bladder cancer, Glioblastoma, Medulloblastoma, Breast Carcinoma, Cervical Cancer, Colorectal Cancer, Endometrial Cancer, Esophageal Cancer, Head and Neck (H&N) Carcinoma, Hepatocellular Carcinoma (HCC), Hodgkin's lymphoma, Kidney, Renal Cell Carcinoma, Lung Cancer, Non-Small Cell (NCSLC), Lung Cancer, Small Cell (SCLC), Melanoma, Mesothelioma, non-Hodgkin's Lymphoma, Ovarian Adenocarcinoma, Pancreatic Cancer, Prostate Cancer, Stomach Cancer.
Frederick National Laboratory for Cancer Research
NCI Frederick National Laboratory for Cancer Research
A federally funded research and development center dedicated to biomedical research. NCI-Frederick partners with university, government, and corporate scientists to speed the translation of laboratory research into new diagnostic tests and treatments for cancer and HIV/AIDS. NCI-Frederick is comprised of more than 2,800 government- and contractor-employed biomedical researchers, laboratory technicians, and support staff and several cancer research centers. The FNLCR provides quick response capabilities and meets special long-term research and development needs for NCI that cannot be met as effectively by existing in-house or contractor resources.
Lawson Health Research Institute Brain Tumour Bank
Lawson Health Research Institute Brain Tumour Tissue Bank
To aid researchers, the Brain Tumour Tissue Bank, located located in London Health Sciences Centre in London, Ontario, Canada has been collecting human brain tumor specimens and matching clinical data for neuro-oncology research in Canada and internationally since its establishment in 1991. A wide variety of primary and secondary brain tumors, spinal tumors, peritumors and normal brain tissues are available for molecular, protein, enzyme and immunohistochemical studies. Interested researchers can review the information provided at the website and can contact the tissue bank for information about what is currently available. In order to complete a request, an application must be completed.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11,2023. SuperCAT hosts typing databases for the Bacillus cereus group of bacteria. The databases contain MultiLocus Sequence Typing (MLST), MultiLocus Enzyme Electrophoresis (MLEE), and Amplified Fragment Length Polymorphism (AFLP) phylogenetic data. multilocus, sequence, Bacillus cereus, bacteria, Genomics, non-vertebrate, taxonomy, identification
Organ Procurement and Transplantation Network
Organ Procurement Transplantation Network
The only national patient waiting list and an online database system, called UNet, that links all of the professionals involved in the donation and transplantation system for the collection, storage, analysis, and publication of all OPTN data pertaining to the patient waiting list, organ matching, and transplants. The system contains data regarding every organ donation and transplant event occurring in the U.S. since October 1, 1987. UNet is a fail-safe, 24/7, secure Internet-based transplant information database created to enable the nation' '''s organ transplant institutions to: * register patients for transplants * match donated organs to waiting patients * manage the time-sensitive, life-critical data of all patients, before and after their transplants Data reports are available by type: National Data, Regional Data, State Data, Center Data, Build Advanced Report, and Annual Report Data. UNet is being used right now by all of the nation' '''s organ transplant programs, organ procurement organizations, and histocompatibility (tissue typing) laboratories working cooperatively to efficiently share a limited number of donated organs among thousands of patients.
hyfi: software suite for binding site search
This collection of software is designed to rapidly identify identifies primer and microarray probe binding sites for a query sequence in genomic DNA. This software suite has four main programs:1. A program for indexing a sequence file to speed up the binding site search. 2. A program for retrieving the binding sites of a query sequence. 3. A program for identifying sites where PCR primers could co-operate to exponentially amplify a sequence 4. A program for analyzing a set of binding sites to tailor the search for different reaction conditions. This software is implemented in C.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Located in Spain, the Andalusian Regional Tumour Bank is a regional tumor bank. In the last decades cancer knowledge is growing exponentially due human genome knowledge and technological advantages. However, this disease is the biggest problem of health in Europe, with more than 2,5 million new cases per year. The diagnosis and treatment of cancer is now allowing to identify the characteristics that the disease has on each person. The next step is meant to be a great revolution in the treatment of cancer. This scientific development is dependent on the availability of human tumour samples preserved in demanding conditions. Current technology requires the availability of tissue morphological and molecular conditions similar to those that had the sample before being removed. Tumor banks are responsible for these new quality requirements to foster the development of research and health care of patients.
IBIS: Inferred Biomolecular Interactions Server
Inferred Biomolecular Interactions Server
NCBI Inferred Biomolecular Interactions Server
A web server and database that organizes, analyzes and predicts interactions between proteins and other biomolecules. For a given protein sequence or structure query, it reports protein-protein, protein-small molecule, protein nucleic acids and protein-ion interactions observed in experimentally-determined structural biological assemblies. It also infers/predicts interacting partners and binding sites by homology, by inspecting the protein complexes formed by close homologs of a given query. To ensure biological relevance of inferred binding sites, the IBIS algorithm clusters binding sites formed by homologs based on binding site sequence and structure conservation.
Neurology Podcast is a weekly podcast of content from Neurology, the official journal of the American Academy of Neurology. The Neurology podcast is introduced by Editor-in-Chief Robert A. Gross, MD, PhD, who discusses several highlighted articles in the current issue of the journal. The podcast features an interview with the author of an article in the current issue that summarizes the paper and discusses the main findings and clinical implications for neurologists. It concludes with the Lesson of the Week, a short segment on a topic such as a laboratory technique, statistical methods, or historical neurology.
An anatomy digital health sciences library to educate patients, healthcare providers, and students in a free and anonymous manner while using current, authoritative, trustworthy health information. Anatomy Atlases addresses the continuum of anatomy education and may be of use primarily to three distinct populations. It is written for and intended primarily for use by Medical Students, Residents, Fellows, or Attending Physicians studying anatomy. Other Health Care Providers studying anatomy should find it useful. Finally, Patients (including patient''s family members or friends) may find it helpful. Anatomy Textbooks and Anatomy Atlases: * Atlas of Human Anatomy * Atlas of Human Anatomy in Cross Section * Illustrated Encyclopedia of Human Anatomic Variation * Atlas of Microscopic Anatomy - A Functional Approach: Companion to Histology and Neuroanatomy: Second Edition * Anatomy of First Aid - A Case Study Approach * Lessons From a Bone Box Lessons From a Bone Box
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. The National Biobank Program is a joint national program of two Swedish investments on functional genomics, Swegene and Wallenberg Consortium North. This web-site is intended as an information resource on biobanks in Sweden, where knowledge about the Swedish biobanking system is mediated and the progress of the National Biobanking Program is presented. You will also find a list of individual Swedish biobanks. The main objectives of the National Biobank Program are: * to increase the knowledge of the Swedish biobanking system * to increase the quality of Swedish biobanks * to increase usability and availability of samples stored in Swedish biobanks for use in research, diagnosis and treatment * to increase the safety of the providers of samples by stimulating increased protection of the personal integrity and increased ethical awareness The National Biobank Program works through financing of strategic investments to improve biobanking systems of national interest. The program has a budget of SEK 26.4 million for the period of 2002 to 2003.
EEG / ERP data available for free public download
A collection of 32-channel EEG / ERP data from 14 subjects (7 males, 7 females) acquired using the Neuroscan software (3.6 Gb), made available by the laboratory of Arnaud Delormes, along with electrode files and images presented in the experiment. Subjects are performing a go-nogo categorization task and a go-no recognition task on natural photographs presented very briefly (20 ms). Images are only available for viewing. Each subject responded to a total of 2500 trials. Data is CZ referenced and is sampled at 1000 Hz (total data size is 4Gb). Alternate datasets are also compiled including one from the EEGLAB software tutorial.
Repository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them.
A virtual database currently indexing authoritative information on disease and treatment options from NINDS Disorder List and PubMed Health.
Protein Biotechnologies Inc., a San Diego, California based company, provides global pharmaceutical, biotechnology, government and academic institutions with human clinical specimen derivatives and high-throughput protein and tissue microarrays. With the largest collection of ready-to-use, clinically defined, pathology-validated human specimen derivatives on the market, Protein Biotechnologies facilitates biomedical research and drug discovery efforts for cancer, neurodegenerative diseases, cardiovascular diseases, diabetes / obesity and autoimmune disease research. To facilitate high-throughput screening of human clinical specimens, Protein Biotechnologies provides its tissue lysate library on ready-to-use protein microarrays. And, for protein localization, immunohistochemical and in-situ hybridization studies, Protein Biotechnologies'' tissue microarrays are an ideal method for studying multiple human cancer / normal tissues in a single assay. Key Products & Services: * Reverse Phase Protein Microarrays * Human Clinical Tissue Lysates * Tissue Microarrays * Primary & Secondary Antibodies * Supplemental Research Reagents * Protein, RNA and DNA Isolation and Purification * Peptide Synthesis * Custom Protein and Peptide Microarray Design and Manufacturing * Custom Antibody Production
These Brainbow 1.0 (founder line L) mice allow labeling of individual neuronal types (specifically hippocampal neuron cell bodies, and including motor neurons, dentate gyrus granule cells, pyramidal neurons of the cortex and CA1 area) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainbow strains (Stock No. 007901, Stock No. 007911, Stock No. 007921) for neurobiological studies. These Thy1-Brainbow 1.0 (line L) transgenic mice are viable and fertile. The mice possess multiple fluorescent protein sequences uniquely flanked with pairs of incompatible Lox sites alternated to create mutually exclusive recombination events; allowing stochastic expression of multiple fluorescent proteins from a single transgene. Prior to Cre-mediated recombination, the fluorescent protein immediately adjacent to the promoter, dTomato (RFP), is expressed in peripheral and central neurons. When bred to Cre recombinase expressing mice, the resulting offspring can have one of three expression outcomes for each transgene in each cell of the cre expressing tissue(s): dTomato (RFP) (no recombination), mCerulean (CFP), or mYFP. Integration of tandem transgene copies yields combinatorial fluorescent protein expression in each cell, and thus many possible cell colors, providing a way to distinguish adjacent neurons and visualize other cellular interactions. Of note, the single FRT site inserted in the transgene allows tandem transgene copy number reduction through Flp-mediated recombination if desired. These Brainbow 1.0 (founder line L) mice were found to have multiple transgene copies that allow labeling of individual neuronal types (specifically hippocampal neuron cell bodies, and including motor neurons, dentate gyrus granule cells, pyramidal neurons of the cortex and CA1 area) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainbow strains (Stock No. 007901, Stock No. 007911, Stock No. 007921) for neurobiological studies. This mouse can be used to support research in many areas including: Neurobiology Research * Cre-lox System (loxP-flanked Sequences) * Fluorescent protein expression in neural tissue Research Tools * Cre-lox-System (loxP-flanked Sequences: Test/Reporter) * Developmental Biology Research (Cre-lox system) * Developmental Biology Research (transplantation marker for embryonic and adult tissue) * FLP-FRT System (FRT-flanked Sequences) * Fluorescent Proteins * Genetics Research (Mutagenesis and Transgenesis: Cre-lox system) * Genetics Research (Tissue/Cell Markers: Cre-lox system) * Genetics Research (Tissue/Cell Markers: astrocyte-specific marker) * Genetics Research (Tissue/Cell Markers: astrocytes) * Genetics Research (Tissue/Cell Markers: astrocytes, neurons) * Genetics Research (Tissue/Cell Markers: glial cells) * Genetics Research (Tissue/Cell Markers: multiple) * Genetics Research (Tissue/Cell Markers: neurons) * Genetics Research (Tissue/Cell Markers: transplantation marker for embryonic and adult tissue) * Neurobiology Research (astrocyte-specific marker) * Neurobiology Research (cell marker) * YFP related Research Tools * Fluorescent Proteins Control: 000664 C57BL/6J (approximate)
RTI Donor Services is a not-for-profit, American Association of Tissue Banks (AATB) accredited organization, working with organ and tissue agencies to provide responsible stewardship of the gift of donation. By working with RTI Donor Services, you will receive the benefit of the science, safety and innovation of RTI Biologics, Inc. (RTI). While RTI Biologics and RTI Donor Services are separate but affiliated organizations, our missions are symbiotic ����?? both are aimed at improving the lives of others with a focus on maximizing the gift of tissue donation, providing safe tissue implants for recipients, and providing education and support programs to donor families and the donation community. Please visit http://www.rtidonorservices.org/about_rti_donor_services for more information.
Database of Genomic Variants Archive (DGVa)
Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA).
Wikipedia is a free, web-based, collaborative, multilingual encyclopedia project supported by the non-profit Wikimedia Foundation. Its 19 million articles (over 3.6 million in English) have been written collaboratively by volunteers around the world, and almost all of its articles can be edited by anyone with access to the site. As of July 2011, there were editions of Wikipedia in 282 languages. Wikipedia was launched in 2001 by Jimmy Wales and Larry Sanger and has become the largest and most popular general reference work on the Internet, ranking around seventh among all websites on Alexa and having 365 million readers. The name Wikipedia was coined by Larry Sanger and is a combination of wiki (a technology for creating collaborative websites, from the Hawaiian word wiki, meaning quick) and encyclopedia. Wikipedia''s departure from the expert-driven style of encyclopedia building and the large presence of unacademic content has been noted several times. Some have noted the importance of Wikipedia not only as an encyclopedic reference but also as a frequently updated news resource because of how quickly articles about recent events appear. Although the policies of Wikipedia strongly espouse verifiability and a neutral point of view, critics of Wikipedia accuse it of systemic bias and inconsistencies (including undue weight given to popular culture), and allege that it favors consensus over credentials in its editorial processes. Its reliability and accuracy are also targeted. A 2005 investigation in Nature showed that the science articles they compared came close to the level of accuracy of Encyclopedia Britannica and had a similar rate of serious errors.
Inflammatory Breast Cancer Research Foundation
The Inflammatory Breast Cancer Research Foundation is a non-profit corporation dedicated to the support of research and public awareness. It is dedicated to researching the cause of Inflammatory Breast Cancer, also known as IBC, an advanced and accelerated form of breast cancer usually not detected by mammograms or ultrasounds. Inflammatory breast cancer requires immediate aggressive treatment with chemotherapy prior to surgery and is treated differently than more common types of breast cancer. Our mission is to assist scientists and researchers in their quest to determine the definitive causes of inflammatory breast cancer. The Inflammatory Breast Cancer Research Foundation seeks to assist them in their work so effective and meaningful detection and diagnosis, prevention and treatment can be pursued and achieved. Our Goals Include: * To ignite interest in the study and research of inflammatory breast cancer at every level. From researchers to physicians, educators and scientists, the IBC Research Foundation seeks to support and inspire those seeking to identify the cause(s) of inflammatory breast cancer. * To support research, the purpose of which is to reach an unambiguous definition of inflammatory breast cancer. The clinical/pathological definition in use since the late 1800s with little change in the 1900s is ambiguous and doesn''t result in a diagnosis of all cases of IBC. By using research methods available in the 21st Century, an unambiguous definition is now possible, assuring with high certainty that all cases of IBC will be correctly diagnosed, and possible sub-types of IBC identified, which may lead to better treatment outcomes. * To increase awareness of IBC for primary care physicians, nursing professionals, and medical technicians in order to minimize the time from presentation of symptoms to correct diagnosis of inflammatory breast cancer. * To increase public awareness in an effort to encourage women to seek medical attention for common inflammatory breast cancer symptoms soon after they appear and to empower patients, caregivers, families and friends to pursue meaningful paths in support of diagnosis and treatment of inflammatory breast cancer.
Key Driver Analysis (KDA) is an analysis tool, as both an R package and Cytoscape plugin, for identifying key regulators of a gene regulatory network. It takes as input a gene network N (directed or undirected) and a gene set (module) G. The gene set is any subset of genes from the network N (e.g. pathway, module, ontology), permitting focus on a particular biological context. The KDA archive contains the plugin source, the plugin jar file, and several example datasets. Prerequisites: *Java, 5.0+ (www.javasoft.com) *Cytoscape, 2.6+ (www.cytoscape.org)
University of Leicester; Leicester; United Kingdom
Public research university based in Leicester, England. Famous for the discovery of genetic fingerprinting and contributing to the discovery and identification of the remains of King Richard III.
The University Andrology Laboratory provides physicians and their patients with all forms of male infertility testing, as well as operating a Patient Sperm Banking Program. This full-service facility is dedicated to the diagnosis and treatment of the infertile male using the highest standard of quality of care. Patients can either visit the main laboratory facility on the University of Illinois at Chicago Medical Center campus or visit our satellite laboratory on North Michigan Avenue. Now available through the University Andrology Laboratory is the OverNiteMale Program. The OverNiteMale Program is particularly convenient for patients who are unable to make a personal visit to one of our laboratories to produce a sample. Patients can now produce a sample in the privacy of their own home from any location in the U.S.A. and send it via Federal Express directly to our laboratory. In-patients can also take advantage of the OverNiteMaleTM Program during their hospital stay. The University Andrology Laboratory was originally introduced at Michael Reese Hospital in Chicago in 1982 and relocated in 1996 to the University of Illinois at Chicago Medical Center, Department of Urology. The laboratory meets the highest standard of quality control and quality assurance. The operation of the University Andrology Laboratory has been under the direction of Gail S. Prins, Ph.D., HCLD, from its inception to the present.
Cancer Control using Population-based Registries and Biobanks
Cancer Control using Population-based Registries Biobanks
CCPRB (Cancer Control using Population-based Registries and Biobanks)
CCPRB (Cancer Control using Population-based Registries Biobanks)
CCPRB - Cancer Control using Population-based Registries and Biobanks
CCPRB (Cancer Control using Population-based Registries and Biobanks) is a Network of Excellence project within the sixth framework programme of the European Union. It is aiming at improved control of cancer by facilitating research linking biobanks and cancer registries. The project involves a systematic quality assurance and continuous development of standards and norms for human sample biobanks in Europe, as well as development of improved integrity-protection standards in the handling of sensitive information in connection with biobank-based research. The samples in the biobanks will be used in large-scale cancer research searching for genetic and infectious causes to cancer, in particular in the areas of breast and colorectal cancer and childhood leukemia. Project objectives: * Provide the study base for uniquely large population-based prospective studies on cancer * Define and implement a generally applicable European Quality Standard for Biobanking that will include improved data and specimen standardization, acquisition and analysis, reliable and standardized statistical analysis as well as improved management and co-ordination of European biobanks. * Define and promote the implementation of integrity-proof methods for biobank-based research involving well defined and secure third party code-keeping systems. * Enable large-scale, population-based research on: ** evaluation of cancer treatment and role of molecular markers in treatment selection ** use over-generation registry linkages applied to large biobank cohorts to identify and evaluate genetic predisposition associated with increased cancer risk as well as interactions with common environmental exposures. ** use over-generation registry linkages applied to large biobank cohorts to explore and evaluate intrauterine exposures associated with increased cancer risk ** exploit the power of large population cohorts for design of optimal strategies for cancer prevention and its evaluation. * Establish a Europe-wide network for spreading the awareness of i) the data, samples and knowledge generated European biobank-based research ii) possibilities for future biobank-based research and iii) the best practice quality standards for biobank-based research.
The mission of the Biospecimens Interest Group is to serve as an educational and tutorial vehicle for disseminating information, best practices, regulations, and ethical/legal information formulated and issued by various NIH offices, federal agencies and other leading biospecimens organizations. Please join our listserv so we can inform you about the date, time and the place for future meetings, speakers, website and other activities --- https://list.nih.gov/cgi-bin/wa?SUBED1=biospecimens&A=1. Meetings and seminars are videocast. Vision: #. To create a place where all stakeholders may exchange scientific data, ideas, and information concerning the creation and use of high quality biospecimens for research, assay validation, technology development and other appropriate uses. #. To promote and facilitate interaction between NIH intramural and extramural stakeholders who are interested in and involved with a variety of clinically-oriented, translational research projects using high quality biospecimens. #. To encourage leading stakeholders to address critical elements in study design and statistical analysis of data to facilitate the production of accurate, optimal, and clinically meaningful results (best outcome). #. To educate stakeholders about the potential barriers and obstacles that may obstruct the sharing and collaboration between stakeholders across different organizations and countries. #. To increase the awareness for the necessity of high quality biospecimens and the harmonization, and when appropriate, standardized procedures (best practices, SOPs) for annotating, collecting, transporting, processing, storing, and sharing biospecimens to ensure optimal reproducibility of outcomes and the privacy of the patients (donors) through adherence to the ethical and legal requirements associated with the use of biospecimens. #. To provide the connectivity to various biorepositories and biospecimens around the world, especially those containing rare and difficult to get biospecimens.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures (entry from Genetic Analysis Software)
Virginia Bioinformatics Institute Microbial Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Database covering a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at Virginia Bioinformatics Institute. The data comes from different sources and has genomes of 3 oomycetes pathogens: Phytophthora sojae, Phytophthora ramorum and Hyaloperonospora arabidopsidis. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. Two different statistical methods were used to validate these gene models, Fickett' '''s and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum could be assigned. An easy-to-use genome browser was created to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs.
Laboratory of Experimental Neuropathology
UCSD Experimental Neuropathology Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The Laboratory of Experimental Neuropathology is engaged in the study of neurodegenerative disease, including Alzheimer's, Parkinson's, and the dementia of HIV encephalitis. It contains a large bank of materials available to fellow investigators including images, publications, and lab safety. Fellow Investigators and Collaborators may request materials from the brain bank. Technologies employed by the laboratory include immunocytochemistry, neurochemistry, molecular genetics, transgenic models of disease, and imaging by scanning laser confocal microscopy.
Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories.
BioBank that collects, stores, processes and distributes biospecimens and the associated data. The biospecimens are human and non-human genetic materials, proteins, cells, tissues and biofluids. The data are the biological information associated to the samples and, in the case of human samples, the clinical information pertaining to the donor. The da Vinci European BioBank (daVEB) is a multicenter biobank with a centralized IT infrastructure and a main repository located at the Polo Scientifico (Scientific Campus of the University of Florence) in Sesto Fiorentino (Florence, Italy). Hosted by the Magnetic Resonance Center (CERM), an expert center on protein structure and metabolomics, daVEB's aim is to host as rich as possible biological human sample collections, stored accordingly to EU guidelines, in order to offer a powerful tool in the study of complex diseases. At the end of July 2011, the da Vinci European BioBank of the Pharmacogenomics FiorGen Onlus Foundation has been audited and got the quality certification according to UNI EN ISO 9001:2008 for Collection, storage and distribution of biological samples and the associated data for scientific research. Besides the samples stored at da Vinci European BioBank in Sesto Fiorentino (Florence), the daVEB is also the administrative biobank for research sample collections that are stored in the delocalized repositories. All the sample collections must be registered in the biobank: * sample collections taken within the regular health care * samples taken from healthy individuals or other persons out of the regular health care * samples that have been taken in hospitals within research protocols on specific pathologies all transferred to daVEB endowed with a transfer agreement signed by the donor. The Research Units actually afferent to daVEB are delocalized in the Florence, Prato, Pisa and Siena provinces. Delocalized repositories are under construction in Tuscany.
ELRA is the driving force to make available the language resources for language engineering and to evaluate language engineering technologies. In order to achieve this goal, ELRA is active in identification, distribution, collection, validation, standardization, improvement, in promoting the production of language resources, in supporting the infrastructure to perform evaluation campaigns and in developing a scientific field of language resources and evaluation. ELRA''s missions are to promote language resources for the Human Language Technology (HLT) sector, and to evaluate language engineering technologies. To achieve these two major missions, we offer a range of services, listed below and described in the Services around Language Resources section: - Identification of language resources - Promotion of the production of language resources - Production of language resources - Validation of language resources - Evaluation of systems, products, tools, etc., related to language resources - Distribution of language resources - Standardization The promotion of the production of language resources also includes our support of the infrastructure for evaluation campaigns and our support in developing a scientific field of language resources and evaluation, e.g. via the LREC conference. ELRA also regularly conducts market studies and surveys in the field of HLT, and publishes a quarterly newsletter, distributed not only to its members but also to a large number of people in the HLT community.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 2,2026. A non-profit program providing tissue procurement services to the state of Wisconsin. The Wisconsin Tissue Bank handles organ donation, works with organ donors, provides organ donation information and organ transplantation. The Wisconsin Tissue Bank staff provides service to hospitals, Medical Examiners/Coroners and Funeral Directors throughout the state of Wisconsin for the recovery of bone, related soft tissue, veins, skin, and cardiovascular tissue for donation and transplantation. The Wisconsin Tissue Bank is dedicated to the education of health care professionals and the public to promote organ and tissue donation. The Wisconsin Tissue Bank promotes an environment sensitive to the physical, emotional, spiritual, social and economic needs of both those served and those who provide the service.
An integrated text mining / natural language processing system based on the Unstructured Information Management Architecture (UIMA) Framework. It allows interoperability of text mining tools and allows the creation of text mining workflows, comparison and visualization of tools. U-Compare can be launched straight from the web or downloaded. As the name implies comparison of components and workflows is a central feature of the system. U-Compare allows sets of components to be run in parallel on the same inputs and then automatically generates statistics for all possible combinations of these components. Once a workflow has been created in U-Compare it can be exported and shared with other users or used with other UIMA compatible tools and so in addition to comparison, U-Compare also functions as a general purpose workflow creation tool. It contains a repository of 50+ biomedical text mining components. These components are included in the U-Compare single-click-to-launch package, ready to use by just drag-and-drop. You can also use this repository independent from the U-Compare system. Link with Taverna It has a link with Taverna for scientific workflows, http://bioinformatics.oxfordjournals.org/content/26/19/2486.abstract, where you can use U-Compare and its workflow from within the Taverna workflow. There are two ways, the U-Compare Taverna plugin and the U-Compare command line mode as a Taverna activity. We have recently integrated it with Peter Murray-Rust' '''s OSCAR for Chemistry (see http://www.nactem.ac.uk/cheta/) Web Demo: http://www.nactem.ac.uk/software/cheta/
Indiana Organ Procurement Organization - IOPO
Indiana Organ Procurement Organization Inc.
IOPO - Indiana Organ Procurement Organization
Indiana Organ Procurement Organization (IOPO) is the non-profit health service dedicated to advancing organ, tissue, and eye donation throughout Indiana. Its mission is to save and enhance the quality of life through organ, tissue and eye donation. IOPO''s vision is to create the most effective and influential donation and transplantation delivery model in health care. IOPO, as a health services organization, is regulated by several agencies of the US government and maintains accreditations and compliance with regulatory requirements by strict adherence to quality.
University of California San Francisco Laboratory for Visual Neuroscience
Devise better ways to prevent and treat vision loss due to amblyopia and strabismus, and to advance medical science by understanding the human visual system. Various Images, Videos and Talks related to the research are available. In the Laboratory for Visual Neuroscience at the University of California, San Francisco, we are seeking to discover how visual perception occurs in the human brain. The function of the visual system is to guide our behavior by providing an efficient means for the rapid assimilation of information from the environment. As we navigate through our surroundings, a continuous stream of light images impinges on our eyes. In the back of each eye a light-sensitive tissue, the retina, converts patterns of light energy into electrical discharges known as action potentials. These signals are conveyed along the axons of retinal ganglion cells to the lateral geniculate body, a relay nucleus in the thalamus. Most of the output of the lateral geniculate body is relayed directly to the primary visual cortex (striate cortex, V1), and then to surrounding visual association areas. To understand the function of the visual pathways, our research is focused on 5 major themes: * Organization of Primary Visual Cortex * Mapping of Extrastriate Visual Cortex * Amblyopia and Visual Development * Strabismus and Visual Suppression * The Human Visual Cortex
Health Blog offers news and analysis on health and the business of health. The blog is written by Katherine Hobson and includes contributions from staffers at The Wall Street Journal, WSJ.com and Dow Jones Newswires. A searchable interface allows the user to find topics of interest. Katherine Hobson has been writing about health and business for more than 15 years, including stints covering cancer, nutrition, exercise science, the U.S. economy and the U.K. beer industry.
MetaPhlAn - Metagenomic Phylogenetic Analysis
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes identified from reference genomes.
Banque de Cellules Leuc��������miques du Qu��������bec
The primary objective of the Quebec Leukemia Cell Bank is to support basic and clinical blood cancer research. It also serves to provide an infrastructure and services aimed at facilitating the work of researchers in various fields, such as oncology, hematology and immunology in particular. Several researchers have already benefited from this infrastructure in the course of their work. The main missions of the Quebec Leukemia Cell Bank are : * To set up a bank of well-characterized human blood tumor cells. The constitutional DNA is also stored for the majority of samples. A computerized databank includes all laboratory tests performed on these specimens, as well as the corresponding clinical data. Before this bank was created, the absence of access to adequate blood tumor specimens severely hampered our researchers'' efforts to competitively pursue their work. Also, the availability of these specimens now makes it possible to establish an essential link between the basic and clinical research communities. * Provide chromosomal analysis by conventional cytogenetics and spectral karyotyping (SKY) for human and mouse cells. * Contribute to the training of specialized staff and students. The Quebec Leukemia Cell Bank is a provincial program that groups together hematologists, researchers and clinical scientists from four Quebec universities (Universit�������� Laval, McGill, Sherbrooke, Montr��������al) and Quebec research centers. The cell bank has been in operation since 2001. The purpose of this website is to raise awareness about our cell bank so we can continue to help an increasing number of researchers.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26, 2019.An international Non-Profit Organization that advocates Open Access for never-before-published research papers on the web and provides Self-Archiving platform to enable better knowledge sharing in a way that''s easy to publish. They collect scientific material (not only publications), e.g., Journal Articles, Theses or Dissertations, Departmental Bulletin Papers, Conference Papers, Presentations, Books, Technical Reports, Research Papers, Articles, Preprints, Learning Materials, Others. If you have such a paper and would like to add a Creative Commons license to your work, or if your working organization has no Institutional Repository (IR), Open your archives to spread them to the world. How to use: 1. Sign in with Twitter 2. Select PDF and add a Creative Commons license 3. Publish and Share on Social Media Video tutorial: http://myopenarchive.org/whatsmyoa
Lifebanc is the nonprofit organ and tissue recovery organization for Northeast Ohio. As one of the original seven independent organ procurement organizations in the United States, Lifebanc serves nearly four million people and works with 80 hospitals in 20 counties. We are a member of the Organ Procurement and Transplantation Network (OPTN), which has been managed by the United Network for Organ Sharing (UNOS) since 1986. We also work closely with local partners, as well as the other Organ Procurement Organizations in the state of Ohio to educate the public and healthcare professionals about the benefits of and need for organ, tissue and eye donations. These organizations include Lifeline of Ohio; LifeCenter and Life Connection of Ohio. Along with serving the public, professional community and donor hospitals, Lifebanc provides life-saving organs to two transplant centers: The Cleveland Clinic and University Hospital Case Medical Center. Recovered tissue is transplanted countless times in hospitals throughout the region. Last year, Lifebanc helped to heal and save more than 25,000 lives. Additionally, it was instrumental in helping to perform the nation''s first near-total face transplant and establishing the world-record for lungs transplanted in a year.
HMP Data Analysis and Coordination Center
Data Analysis and Coordination Center for the Human Microbiome Project
Human Microbiome Project Data Analysis and Coordination Center
Common repository for diverse human microbiome datsets and minimum reporting standards for Common Fund Human Microbiome Project.
Biomarkers for Spinal Muscular Atrophy Data Portal
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A publicly available tool that contains data from the BforSMA clinical study ( ClinicalTrials.gov, NCT00756821 ), a pilot study to identify candidate biomarkers in blood or urine from a wide range of Spinal Muscular Atrophy (SMA) patients that associate with disease severity. It is hoped that the identification of candidate biomarkers will lead to clinical efficacy and longitudinal natural history studies to verify these markers and enable their use as validated pharmacodynamic markers, longitudinal progression markers, or surrogate endpoint measures in clinical trials.
NIMH Chemical Synthesis and Drug Supply Program
NIMH Chemical Synthesis Drug Supply Program
A program that synthesizes, purifies, and distributes otherwise unavailable essential compounds to stimulate basic and clinical research in psychopharmacology relevant to mental health in areas such as the molecular pharmacology and signaling of CNS receptors, longitudinal studies to evaluate the molecular, biochemical, and behavioral actions of psychoactive compounds, and functional brain imaging in both primates and humans. WHAT IS AVAILABLE: * Ligands for CNS receptors, radiolabeled compounds for autoradiography and neuroimaging, biochemical markers, drug analogs and metabolites, and reference standards * Synthesis (including GMP) of promising compounds for mental health research, including preclinical toxicology and safety studies, especially compounds for PET neuroimaging * A listing of currently available NIMH CSDSP compounds is available online at www.nimh-repository.rti.org. RTI International scientists can provide investigators with technical assistance and additional information about the compounds on request. Data sheets containing purity, storage, and handling information are supplied with all NIMH CSDSP compounds. WHO IS ELIGIBLE: Investigators involved in basic or clinical research relevant to mental health are eligible to submit requests. To learn more about current NIMH research areas, please visit the NIMH website at www.nimh.nih.gov. NIMH CSDSP compounds are free to qualified academic investigators, but payment may be required from nonacademic requestors. Investigators interested in obtaining radiolabeled compounds but uncertain about what type of label or specific activity would work best for them may obtain help by communicating with the technical contacts listed on the website.
Cliniques Universitaires Saint-Luc Cancer Centre
Centre du Cancer Cliniques Universitaires St-Luc
Cliniques Universitaires Saint-Luc Cancer Center
An essential reference center in Europe and a leader in French-speaking Belgium that treats all types of adult and childhood cancer. They fight against cancer while giving patients comprehensive and humane care. Their quest for excellence is in three main academic fields: clinical care, research and teaching.
A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI.
Alzheimer's and Dementia Resource Center
The Alzheimer's and Dementia Resource Center (ADRC) facilitates tissue donations for the Brain Bank Research Program in order to help find better treatments, more diagnostic tools and a cure for Alzheimer's disease and dementia. The Brain Bank Program is administered by Mount Sinai Medical Center in Miami Beach and under contract with the Florida Department of Elder Affairs. ADRC also provides caregivers with the educational resources, spiritual comfort and emotional support. The ADRC facilitates training for professional caregivers that meets requirements for the Florida Department of Elder Affairs.
NeuroDevNet, a Canadian Network of Centres of Excellence (NCE), is dedicated to helping children overcome neurodevelopmental disorders. Network investigators seek to understand the causes of neurological deficits, and to transfer this knowledge to health care professionals, policy makers, and communities of interest. NeuroDevNet works with its partners in academia, the community, not-for-profit sector, industry, and government, and across traditional disciplinary boundaries and sectors, to ensure generated knowledge is translated into tangible diagnostic, preventative, therapeutic, social, economic, and health benefits for all. NeuroDevNet supports transformative research, provides training to build a new generation of Canadian researchers, strengthens communities with the right tools and information, and translates research findings into early diagnostic, preventative, and therapeutic strategies for children with neurological disorders to live healthier lives. Currently, the network''s research focuses on autism spectrum disorder, cerebral palsy, and fetal alcohol spectrum disorder. These demonstration projects are supported by NeuroDevNet''s central infrastructure and cores, including Neuroethics, Neuroinformatics, and Knowledge Translation.
Stanford Research Institute International
Independent, nonprofit research institute conducting client sponsored research and development for government agencies, commercial businesses, foundations, and other organizations. SRI also brings its innovations to the marketplace by licensing its intellectual property and creating new ventures. SRI was founded as Stanford Research Institute in 1946 by a group of West Coast industrialists and Stanford University. SRI formally separated from the University in 1970, and we changed our name to SRI International in 1977.
Tayside Tissue Bank is a secure bio-repository which holds small samples of surplus tissue and other specimens generously donated by patients who have undergone surgery or other more minor medical procedures during the course of their investigations and treatment. Such samples are vital for medical researchers seeking to improve the detection and treatment of many different diseases as well as advance our understanding of how and why they arise. This website is for both patients who wish to know more about how their tissue is used and for researchers who wish to explore the possibility of utilising the donations kindly made by patients to advance medical research. It also explains some of the additional services the Tissue Bank provides to assist researchers with their investigations including: embedding and cutting sections, standard histological staining, immunohistochemistry (IHC), nucleic acid extraction, protein extraction, and generation of Tissue Microarrays. Donations made to the Bank are held within ultra-low temperature (ULT) freezers within the University of Dundee Medical School at Ninewells Hospital, Dundee. The freezers are alarmed and their temperature continuously monitored. The Bank''s location adjacent to the Pathology Department means it is ideally situated for prompt processing and storage of tissue samples after they have been examined by a pathologist. In addition to collecting, logging and storing tissue samples the bank also holds blood specimens and other materials collected as part of national trials. It also plays a role in administering access to the Tayside Type II diabetes cohort. The Bank contains in the region of 30,000 fresh frozen tissue samples from around 6000 different patients. There are also in excess of 5000 blood samples. Storage of the samples is split between separate, continuously monitored freezers. In addition the Bank has access to the Pathology Department''s Histopathology Archive (30,000 new specimens annually).
Collaboration environment for sharing variable sets and statistical methods for analysis across social science survey data. MethodBox enables you to browse and download datasets, share methods and scripts, find fellow researchers with similar interests and share your knowledge. MethodBox source available on Google code. Finding the variables you need to support a particular research question can be time consuming. Wading through hundreds of pages of PDF documents, codebooks and metadata and then trying to find the exact column in a huge spreadsheet can be very frustrating. MethodBox gets you to the variables faster and lets you download only the data you need. You can also share your scripts with others to allow them to adopt best practice quicker than before.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd, 2023. Sequence composition based classifier for metagenomic sequences. It works by capturing signatures of each sequence based on the sequence composition. Each sequence is modeled as a walk in a de Bruijn graph with underlying Markov chain properties. ClaMS captures stationary parameters of the underlying Markov chain as well as structural parameters of the underlying de Bruijn graph to form this signature. In practice, for each sequence to binned, such a signature is computed and matched to similar signatures computed for the training sets. The best match that also qualifies the normalized distance cut-off wins. In the case that the best match does not qualify this cut-off, the sequence remains un-binned.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2012. (no longer being funded) The NIH Microarray Consortium provides for-fee services to a community of NIH grantees, together with a more limited set of services to the public. The primary goal of this consortium is to move basic and translational research forward through acquisition and dissemination of high quality genomic data. This site includes a repository of microarray data sets and offers one-click links to public projects. These datasets were generated by various researchers on these platforms: Affymetrix, Agilent, Ambion, cDNA, Illumina, and Operon. The species currently covered are: Arabidopsis, Bovine, chicken, C. Elegans, Drosophila, Human, Macaca mulatta (Rhesus macaque), Mouse, Rat, Songbird, Xenopus, Yeast, and zebra finch. Basic search functions allows users to choose multiple options for finding the projects that interest them, and raw data files can also be downloaded after user registration. Web-based data analysis tools are also available. Scientists can analyze microarray data from the consortium repository or investigators can upload outside data for analysis.
Open University; Milton Keynes; United Kingdom
Public research university and the largest university in the UK for undergraduate education. The majority of the OU's undergraduate students are based in the United Kingdom and principally study off-campus; many of its courses can also be studied anywhere in the world.
ScienceOnline2012 is the sixth annual international meeting on science and the Web. The agenda includes more than 70 discussion sessions and workshops over three full days, and additional demonstrations, science lab tours, a museum reception & a dose of comedy. ScienceOnline2012 #scio12 across social media will take place January 19-21, 2012 on the campus of NC State University in the spacious McKimmon Center, with some 450 participants. Every January since 2007, the Research Triangle area of North Carolina has hosted scientists, students, educators, physicians, journalists, librarians, bloggers, programmers and others interested in the way the World Wide Web is changing the way science is communicated, taught and done. As in all the previous years, the meeting will be held in an ''unconference'' style the program is built beforehand with the help of participants on the planning wiki, and the sessions are designed to foster conversations and discussions among everyone in the room rather than a traditional one-before-many lecture approach. Help us continue the success of past conferences by familiarizing yourself with the plans for ScienceOnline2012, volunteering to help, offering your organization''s or company''s sponsorship or in-kind support, and, above all, engaging with the online science community before, during and after the conference.
A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions.
Affiliated with Harvard School of Dental Medicine and Harvard Medical School and has collaborations with university and research organizations around the world. Dedicated to advancing human health and wellbeing through scientific discovery and education. Independent non-profit organization.
The foundation biobank-suisse (BBS) is a collaborative network of existing and future research biobanks in Switzerland. The primary goals are: 1. to provide researchers a quick overview of available human biospecimens (by using the web query interface) and up to date person related data; and 2. to provide biobankers with services to further improve the quality of biobanks in Switzerland (e.g. information about up-to-date IT and database software for biobanking; solutions for ethical, legal, and social issues; develop common platform for biobankers; etc.). We maintain a database with data about patients and biospecimens. The database can be queried from our web-site. Once the researcher has found suitable biospecimens we will bring him in contact with the biobanks, which have collected the biospecimen. The researcher and the biobank manager will then discuss the next step without further participation of the foundation biobank-suisse. We provide advice and support to biobank manager, who are in the process to start a biobanking activity for material from humans. Well established biobanks can benefit from our help in realizing specific projects to improve their operations. BBS was founded in December 2005 as an initiative of Oncosuisse and SWISS BRIDGE with the goal to build a collaborative network of existing and future biobanks for research in Switzerland. BBS has currently information from about 60 000 biospecimens and 10 000 patients. This information is provided by the biobanks shown under the Partner biobank menu item and include: * Institut de Pathologie, Centre hospitalier universitaire vaudois (CHUV) * Institut f��r Pathologie Universit��tsspital Basel * Institut f��r Pathologie der Universit��t Bern BBS has entered in a closed collaboration with SAKK''s (Swiss Working Group on Clinical Cancer Research) IT department. BBS''s server is run by SAKK and technical support is provided by the SAKK IT department. BBS is an active member of ISBER (International Society of Biological and Environmental Repositories) the international society of biobanks. BBS also joint BBMRI (an European initiative to build an pan-European network of biobanks.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A service and research oriented network of statewide regional brain bank sites. The intent of the brain bank program is to study brains of persons clinically diagnosed with dementia and provide tissue for research after their deaths. Mt. Sinai Medical Center contracts annually with the State of Florida to operate the primary brain bank. Coordinators at regional brain bank sites in Orlando, Tampa and Pensacola assist in recruiting participants and act as liaisons between the brain bank and participant families. Alzheimer's disease respite care program providers, memory disorder clinics, and model day care programs also recruit brain bank participants. The Florida Brain Bank supports collaborative research programs related to Alzheimer's disease and other degenerative disorders of the brain.
Protocol Online - Your labs reference book
Protocol Online Your lab''s reference book
Database of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert).
A software tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. Allowing an incorporation of ''gene models'' already at the alignment stage almost doubles the number of transcripts that can be measured reliably.
Saskatoon Arabidopsis T-DNA mutant population SK Collection
Population of almost 50,000 activation tagged Arabidopsis thaliana lines that have been archived as individual lines to the T3 generation. The population is an excellent tool for both reverse and forward genetic screens and has been used successfully to identify a number of novel mutants. Flanking sequence tags (FST) have been generated and mapped for 15,507 lines to enable further application of the population, while providing a clear distribution of T-DNA insertions across the genome. The population is being screened for a number of biochemical and developmental phenotypes. The population provides an additional tool for plant researcher's to assist with determining gene function for the many as yet uncharacterized genes annotated within the Arabidopsis genome sequence. The presence of enhancer elements on the inserted T-DNA element (pSKI015) allows both knock-out and dominant activation phenotypes to be identified for traits of interest.
Florida Alzheimer's Disease Research Center
A statewide consortium dedicated to Alzheimer's disease research to better understand the disease and related memory disorders. It includes Alzheimer's researchers and clinicians from institutions across Florida such as USF Health, Mayo Clinic Jacksonville, and Mount Sinai Medical Center. The purpose of the ADRC is to assist institutions in developing an infrastructure (cores) that can be used for various research projects with the goal of better understanding Alzheimer's disease and related disorders. The Florida ADRC is comprised of six cores, three projects and three pilot projects among other collaborations that utilize these cores.
Pennsylvania State University Huck Institutes of the Life Sciences Neuroscience Graduate Program
Huck Institutes Neuroscience Graduate Program
Program provides preparation for students seeking careers in academia, education and industry. Students are usually admitted with the intent of obtaining a PhD degree in Neuroscience but the MS degree may be sought as part of the doctoral program.
State of Florida Alzheimer's Disease Initiative
A program that provides services to meet the needs of individuals with Alzheimer's disease, and similar memory disorders, and their families. The Alzheimer's Disease Initiative (ADI) of Florida provides caregiver respite services and support which include in-home, facility-based, emergency, and extended care for caregivers who serve patients with memory disorders. Additionally, the ADI includes services provided by Memory Disorder Clinics (MDCs).
Power and Sample-Size Calculations for the TDT and ASP Tests
Software application for power and sample-size calculations for the TDT and ASP tests under a wide variety of ascertainment schemes. Uses the flexible genetic model of McGinnis. Most calculations are exact rather than asymptotic. (entry from Genetic Analysis Software)
The European Genome-phenome Archive (EGA)
Web service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers. The EGA''s role is to provide secure access to the data that otherwise could not be distributed to the research community. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. As an example, only members of the EGA team are allowed to process data in a secure computing facility. Once processed, all data are encrypted for dissemination and the encryption keys are delivered offline. The EGA also supports data access only for the consortium members prior to publication.
The Erasmus MC Virtual Tissue Bank is embedded in the department of Pathology. The collection is meant for medical research purposes only. This concerns a typical clinical based pathology biobank. Tissue samples left over from surgical resection specimen are stored under liquid nitrogen and can be requested by Erasmus MC scientists for medical scientific experiments. An application has been developed to enable scientists to search the collection on-line and request tissue samples over the Erasmus MC Intranet. Every request shall be judged according to procedures determined by the Erasmus MC Tissue Bank. A growing need is anticipated for large collections of well-diagnosed fresh frozen tumor tissue and, if available, corresponding pre-malignant and normal tissue samples. Scientific research on patient residual material has to comply with strict rules and regulations. Equipment The Erasmus MC Tissue bank manages the PALM microdissection laser for the center for Biomics, which is available through the center for Biomics ONLY after having followed an introduction course. Additionally, a complete TMA (Tissue Micro Array) platform, fully funded by the Josephine Nefkens Stichting, consisting of a Beecher Automated Tissue Arrayer ATA 27 and a Virtual Microscope or Nanozoomer from Hamamatsu and Medical Solutions with TMA analyses software strongly supports translational research on tissue samples. Complete histologic Images from the Virtual Microscope are available within the Erasmus MC Intranet or available on the Internet either by overview or a direct example.
UniProtKB Sequence/Annotation Version Archive
The UniProtKB Sequence/Annotation Version Archive (UniSave) is a repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions. Entries can be retrieved by entering a primary accession number or an entry name and pressing the Go! button. The result of the query is a list of entry versions with the UniProtKB database name, entry status, primary accession number, entry name, entry version, sequence version, release number and the release date, ordered by the release date, the latest version first. The entry version status can be ' '''incorporated' ''', ' '''active' ''', ' '''changed' ''', ' '''replaced' ''' or ' '''deleted' '''. An incorporated entry version is the first entry version added into UniProtKB, an active entry version is part of the latest public release, a changed entry version has been superseded by a newer entry version, a replaced entry has become secondary to another entry, and a deleted entry has been removed from the UniProtKB without becoming secondary to any other entry. For replaced entry versions, the status ' '''Replaced' ''' can be clicked to return all entries, which have the given entry as a secondary entry. If a date is provided as part of the query then only the version of the entry that was current at that date is displayed. Entries can be viewed by clicking ' '''View' ''' in the query results table. The ' '''<< Earlier' ''' and ' '''Later >>' ''' links can be used to access the earlier and later entry versions. The ' '''Back to List' ''' link returns the user to the query results table. Selecting ' '''UniProtKB' ''' or ' '''Fasta' ''' and pressing ' '''Save' ''' downloads the entry in flat file or fasta format. Comparison between entry versions is straightforward: selecting two entries and clicking the ' '''Compare Selected' ''' button will show the differences between the two entries. Whenever comparisons are made a Smith-Waterman sequence alignment is computed using SSEARCH, and displayed at the bottom of the entry. The actual alignment is displayed only when the sequences are not identical.
ArchSchema - graphs of related Pfam domain architectures
ArchSchema is a java webstart application that generates dynamic plots of related Pfam domain architectures. The protein sequences having each architecture can be displayed on the plot and separately listed. Where there is 3D structural information in the PDB, the relevant PDB codes can be shown on the plot. Sequences can be be filtered by organism, or the output can be limited to just those protein sequences for which there is structural information in the PDB. Search by UniProt sequence id, or by Pfam domain id. Red underlines indicate the extent to which 3D structures of the domains and architectures are available in the PDB. Left-clicking on a node shows a panel containing information about the constituent domains, the protein sequences having the given architecture, and any sequences that have whole or partial structures in the PDB. You can display protein sequence (or, alternatively, the protein structures) associated with each architecture. You can download ArchSchema to run locally from your own machine. Note, however, you only download the code and not the data. Thus you will need to be connected to the Internet whenever you perform a search from within ArchSchema. The search initiates a call to the EBI which returns the data to ArchSchema for graphing.
A virtual database currently indexing multiple podcast resources including: The Brain Science Podcast, Nature Podcast, NeuroPod, Science Podcast, The American Journal of Psychiatry Podcast, 60-Second Mind, and Science Talk.
Tufts University Graduate School of Biomedical Sciences Graduate Programs
Graduate school provides training of highly educated biomedical scientists through collaborative and interdisciplinary research. Provides degree programs in Cell, Molecular and Developmental Biology; Genetics; Immunology; Molecular Microbiology; Neuroscience; Clinical and Translational Science; Pharmacology and Drug Development.
Database documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. The nomenclatural novelties will each be allocated a unique MycoBank number that can be cited in the publication where the nomenclatural novelty is introduced. These numbers will also be used by the nomenclatural database Index Fungorum, with which MycoBank is associated and will also serve as Life Science Identifiers (LSIDs). Nomenclatural experts will be available to check the validity, legitimacy and linguistic correctness of the proposed names in order to avoid nomenclatural errors; however, no censorship whatsoever, (nomenclatural or taxonomic) will be exerted by MycoBank. Deposited names will remain -when desired- strictly confidential until after publication, and will then be accessible through MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives, where they will further be linked to other databases to realize a species bank that eventually will link all databases of life. MycoBank will (when applicable) provide onward links to other databases containing, for example, living cultures, DNA data, reference specimens and pleomorphic names linked to the same holomorph. Authors intending to publish nomenclatural novelties are encouraged to contribute to this new initiative. For the moment 2 search engines are available from the MycoBank website. The first one permits to search for fungal names (at any rank level), the authority or the MycoBank unique number. The second is dedicated to bibliographic queries related to fungal name' '''s publications. MycoBank users willing to deposit their data will have to register so that they willbe able to contact the depositor for specific information (e.g. MycoBank number, possible points of attention regarding the name, actual publication, etc), and to avoid fake entries.
Portal and tools for sharing and editing neurophysiological and behavioral data for brain-machine interface research. Users can search for existing data or login with their Google, Facebook, or Twitter account and upload new data. Their main focus is on supporting brain-machine interface research, so we encourage users to not just provide recordings of brain activity data, but also information about stimuli, etc., so that statistical relationships can be found between stimuli and/or subject behavior and brain activity. The Matlab tools are for writing, reading, and converting Neuroshare files, the common file format. A free, open source desktop tool for editing neurophysiological data for brain-machine interface research is also available: https://github.com/ATR-DNI/BrainLiner Since data formats aren' '''t standardized between programs and researchers, data and analysis programs for data cannot be easily shared. Neuroshare was selected as the common file format. Neuroshare can contain several types of neurophysiological data because of its high flexibility, including analog time-series data and neuronal spike timing. Some applications have plug-ins or libraries available that can read Neuroshare format files, thus making Neuroshare somewhat readily usable. Neuroshare can contain several types of neurophysiological data, but there were no easy tools to convert data into the Neuroshare format, so they made and are providing a Neuroshare Converter Library and Simple Converter using the library. In future work they will make and provide many more useful tools for data sharing. Shared experiments include: EMG signal, Takemiya Exp, Reconstruct (Visual image reconstruction from human brain activity using a combination of multi-scale local image decoders), SPIKE data, Speech Imagery Dataset (Single-trial classification of vowel speech imagery using common spatial patterns), Functional Multineuron Calcium Imaging (fMCI), Rock-paper-scissors (The data was obtained from subject while he make finger-form of rock/paper/scissors). They also have a page at https://www.facebook.com/brainliner where you can contact us
Pythia is an open source thermodynamically oriented primer design python module. Pythia can be used in two ways. 1. Executable binaries only: under windows with cygwin and python 2.5 (built with mingw, that comes with the cygwin release). These executables allow the user to index DNA files for primer specificity search, design one primer pair per region, and tile regions with PCR amplicons. 2. A python module: under windows with cygwin, python2.5, numpy, swig, and mingw, or under linux with python2.4 or later, numpy, and swig (everything but numpy should be pre-installed on a normal linux system). The module gets you everything that the binaries get you, in a more pythonic framework. This package also includes modules for computing DNA binding and folding energies using the partition function approach with publicly available thermodynamic data. Usage documentation is in the downloads.
Homology derived Secondary Structure of Proteins
Homology-derived Secondary Structure of Proteins
HSSP - Homology derived Secondary Structure of Proteins
HSSP - Homology-derived Secondary Structure of Proteins
HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. Homologues are very likely to have the same 3D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of sequence aligned sequence families, but it is also a database of implied secondary and tertiary structures. Likely secondary structure are carried over from the PDB protein to each homologous protein. Tertiary structure models can be built by fitting the sequence of the homologue as aligned into the 3D template of the protein of known structure. Special software is needed to construct 3D models by homology, such WHATIF by Gert Vriend or MaxSprout by Liisa Holm and Chris Sander. The command rsync can be used to obtain a local copy of the HSSP. We appreciate receiving an Email from people who do so, but there are no strings attached. Everybody can freely download the files, academia and industry alike. If your institute''s firewall doesn''t allow you to use the (preferred) rsync way of obtaining HSSP files, feel free to work with FTP. The files are in that case available from: ftp://ftp.cmbi.ru.nl//pub/molbio/data/hssp/
Public research university with its main campus in Athens, Georgia. Founded in 1785, it is one of the oldest public universities in the United States.
Public reference database supporting the XML family of markup language standards, XML vocabularies, and related structured information standards. It promotes and enables the use of open, interoperable, standards-based solutions which protect digital information and enhance the quality of data processing. The Cover Pages web site provides reference material on enabling technologies compatible with SGML/XML descriptive markup language standards and applications: object modeling, semantic nets, ontologies, authority lists, document production systems, and conceptual modeling. It also supplies references for social aspects of distributed and public sector concerns: privacy, open standards, patented technology embedded in standards, etc. NB. This statement and the resource itself are works in progress, subject to continuous revision.
The Tissue Bank stores tissue, blood, and bone marrow samples that have been taken from patients who have given their consent after they have undergone biopsies, surgery, or other procedures for cancer at the John Theurer Cancer Center. Our scientists use these samples to analyze and study multiple types of human cancer, with a goal toward learning more about how cancer develops, developing innovative new treatments, and determining how well a treatment is working. Our Tissue Bank is overseen by our program and medical director, Andre Goy, M.D., M.S., who is also deputy director of the Cancer Center and chief of the Division of Lymphoma; and our scientific director, K. Stephen Suh, Ph.D. Currently, 30 percent of our Tissue Bank team members work in our clinics, and 70 percent of our team works ����?��������??behind the scenes,����?��������?? conducting important scientific research without meeting patients.
Understanding and Curing the Healthcare Crisis: A Wise Way to Better Outcomes and Lower Costs
Wellness Wiki is offered to help clarify the complex problems plaguing the U.S. healthcare system and develop sustainable ways to improve the health and well-being of all people. This virtual encyclopedia of the healthcare crisis and potential remedies welcomes your comments! The Wellness Wiki Book (Understanding & Curing American Healthcare: A Wise Way to Better Outcomes and Lower Costs) is available for purchase as a softcover book or pdf download. Table of contents: *Introduction & Executive Summary *Defining the Problem *Examining Three Proposed Solutions *Introducing a New Solution - Overview and Benefits, Wellness-Plus Solution Tactics, Barriers and Drivers to Implementing the Wellness-Plus Solution *Conclusion & Epilogue *Appendix *Wellness Model Technology Blueprint
Founded by the physician partners of ACORN, Inc. (Accelerated Community Oncology Research Network), World BioBank embraces forward-thinking technology and a strong commitment to the advancement of bioscience. The World BioBank collects cancer samples, normal samples, and other non-neoplastic diseases. Data available include sample-specific data, patient-specific data, and study-related data. * SOLID TISSUES (snap frozen and matched formalin-fixed paraffin embedded diseased and normal internal controls) from: Surgical resections, Image-guided biopsies, Bone marrow biopsies, Endoscopic biopsies * LIQUID TISSUES: Peripheral blood, Genomic DNA (from buffy coat), Plasma, Serum World BioBank is committed to marrying samples to a wealth of longitudinal medical data and tissue-specific data.
University of Zurich SCRM - Cell-and Tissue Biobank
University of Zurich SCRM - Cell and Tissue Biobank
University of Zurich SCRM - Cell Tissue Biobank
University of Zurich Swiss Center for Regenerative Medicine Cell-and Tissue Biobank
UZH Swiss Center for Regenerative Medicine Cell-and Tissue Biobank
The SCRM-CTBB offers state-of-the-art infrastructure and technologies (e.g. cryogenic work bench, semiautomatic cryogenic storage system, uninterrupted cooling chain) and is structured into two areas, including research and a GMP/GCP regulated therapeutic applications. Research: For pre-clinical studies, the SCRM-CTBB provides researchers guidance regarding cell and tissue cryo-preservation, comprising registration, handling, storage and distribution. In order to ensure complete traceability on samples and belonging information all processes are controlled by a Laboratory Information Management System (LIMS) and Quality Assurance (QA) system. The SCRM Biobank is designed to create database that allows connection with other biobanks nationally and internationally. This meta-data file will enable a unique scientific resource for interdisciplinary research. For every new study a contract is established describing the study and the disposition rights. Assistance in writing Biobank Agreements (BAs) and Material Transfer Agreements (MTAs) is provided. Therapeutical applications: As a new feature, apart from research, the SCRM Biobank enables the asservation and preservation of cells and tissues under GMP conditions for later therapeutic use. A special focus will be on a conceptional combination of private and public umbilical cord blood banking (hybrid banking), which allows autologous and/or allogeneic cell applications.
XP-CLR (Chen et al. 2010) uses allele frequency differentiation at linked loci to detect selective sweeps. Source code and documentation are available.
Since 1995 the Tumorbank Basel Foundation (German: Stiftung Tumorbank Basel) is a non-for-profit foundation acting in cancer translation research. The purpose of the Tumorbank Basel Foundation is to support in promoting optimization of decision making process for the management of solid cancer personalized treatment modalities to the benefit of the patient. Our Aims: * Acquisition and storage of biological material and clinical data of patients suffering of solid cancer diseases in particular breast and prostate cancer. * Promoting and supporting cancer research using the acquired material and data for clinical studies and translational research. * The development of molecular tumor analyses / tools for cancer patients and the performance of the resulting diagnostic services for personalized treatment modalities. The Tumorbank Basel Foundation has acquired * Data about more than 10''000 breast cancer patients * Data comprise clinical and pathological (histology & IHC) characteristics and biochemical (continuous quantified protein expression levels) features, which are available for almost all samples as well as clinical follow-ups now available for more than 2''000 patients * The RNA expression level of 65 genes has been assessed in >800 samples by Real-Time PCR (317 retrospectively in cases with follow-up, the remaining on a routine basis, prospectively since 2004) The Tumorbank Basel Foundation is storing in Freezers at - 80 degrees C * Ca. 6''000 fresh frozen tissue samples of breast cancer patients * Ca. 9''000 particulate fractions (cytosol / membrane) of all samples analyzed * Ca. 1''000 paired non-malignant adjacent tissue material samples * More than 1''000 extracted RNA samples of good quality * Serum and plasma collection from patients has been started since 2005 All data are stored in a relational SQL data bank using an application. The Tumorbank Basel Foundation is collaborating with several pathology institutes allowing to perform studies correlating results obtained from fresh frozen and paired paraffin embedded tissue samples. The Tumorbank Basel Foundation has started a prostate carcinoma project in Collaboration with the ZeTuP (www.zetup.ch) and pathology institute of St. Gallen. Fresh frozen samples of more than 150 prostate carcinoma patients have been collected and are under investigation.
D2R Server - Publishing Relational Databases on the Semantic Web
D2R Server is a tool for publishing relational databases on the Semantic Web. It enables RDF and HTML browsers to navigate the content of the database, and allows applications to query the database using the SPARQL query language. Data on the Semantic Web is modeled and represented in RDF. D2R Server uses a customizable D2RQ mapping to map database content into this format, and allows the RDF data to be browsed and searched the two main access paradigms to the Semantic Web. D2R Server''s Linked Data interface makes RDF descriptions of individual resources available over the HTTP protocol. An RDF description can be retrieved simply by accessing the resource''s URI over the Web. Using a Semantic Web browser like Tabulator (slides) or Disco, you can follow links from one resource to the next, surfing the Web of Data. The SPARQL interface enables applications to search and query the database using the SPARQL query language over the SPARQL protocol. Requests from the Web are rewritten into SQL queries via the mapping. This on-the-fly translation allows publishing of RDF from large live databases and eliminates the need for replicating the data into a dedicated RDF triple store. The latest source code is available from the project''s CVS repository and can be browsed online.
An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563).
EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction.
International group of researchers interested in providing standardized gene nomenclature for chicken genes. A Chicken Gene Annotation Tool is available from CGNC-UK which assigns chicken nomenclature based on predicted orthology to human genes. The CGNC-US database includes CGNC-UK information and adds manually biocurated from biocurators and interested contributors. A Human Chicken Ortholog Predictions Search is available. Both resources are part of a united CGNC effort and nomenclature data is shared and co-ordinated between these two resources. They strongly encourage researchers with domain knowledge to participate in this nomenclature effort by requesting a login and providing gene nomenclature for their genes of interest. Please contact them for further information or assistance. The AGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees, including the Chicken Gene Nomenclature Committee (CGNC). The Avian and Chicken nomenclature efforts are co-ordinated and chicken data is shared between these two groups.
LifeLink Foundation is a non-profit community service organization dedicated to the recovery of life-saving and life-enhancing organs and tissue for transplantation therapy. The Foundation works in a sensitive, diligent, and compassionate manner to facilitate the donation of desperately needed organs and tissues for waiting patients, support research efforts to enhance the available supply of organs and tissue for transplant patients, improve clinical outcomes of patients post transplantation and works closely with the United Network For Organ Sharing (UNOS) to support its goals. We are committed to inspiring the public to save lives through organ donation. To make organ transplant a reality, LifeLink Foundation focuses its attention in a number of areas: Immunology Laboratory, Public Education, Fundraising, Organ Recovery.
Gift of Hope Organ and Tissue Donor Network
Gift of Hope Organ & Tissue Donor Network
Gift of Hope Organ & Tissue Donor Network is proud to serve as the federally designated not-for-profit agency that coordinates organ and tissue donation and supports families of donors in the northern three-quarters of Illinois and northwest Indiana. Since our inception in 1986, we have coordinated donations that have saved the lives of 17,000 organ transplant recipients and helped hundreds of thousands of other patients receive needed tissue transplants. As one of 58 organ procurement organizations (OPOs) that make up the nation''s organ donation system, we work with 179 hospitals in our donation service area. In managing the recovery, care and transportation of donated organs to transplant patients, we work closely with Illinois'' nine transplant centers, which operate 32 transplant programs. We also work with other transplant centers and other OPOs through the United Network for Organ Sharing (UNOS) to provide lifesaving organs for patients awaiting them. UNOS is the federally mandated registration center for organ transplant candidates in the United States. UNOS'' computer-based system matches donated organs with patients in need, in accordance with strict federal guidelines intended to ensure equitable distribution.
Spatially unbiased atlas template of the cerebellum and brainstem
A spatially unbiased atlas template of the cerebellum and brainstem
A spatially unbiased atlas template of the cerebellum and brainstem (SUIT)
A spatially unbiased atlas template of the cerebellum brainstem
A spatially unbiased atlas template of the cerebellum brainstem (SUIT)
Spatially unbiased atlas template of the cerebellum brainstem
High-resolution atlas template of the human cerebellum and brainstem, based on the anatomy of 20 young healthy individuals. The atlas is spatially unbiased, i.e. the location of each structure is equal to the expected location of that structure across individuals in MNI space. At the same time, the new template preserves the anatomical detail of cerebellar structures through a nonlinear atlas-generation algorithm. By using automated nonlinear normalization methods, a more accurate intersubject-alignment than current whole-brain methods can be achieved. The toolbox allows you to: * Automatically isolate cerebellar structures from the cerebral cortex based on an anatomical image * Achieve accurate anatomical normalization of cerebellar structures * Normalize functional imaging data for fMRI group analysis * Normalize focal cerebellar lesions for lesion-symptom mapping * Use Voxel-based morphometry (VBM) to determine patterns of cerebellar degeneration or growth * Use a probabilisitc atlas in SUIT space to assign locations to different cerebellar lobuli in an unbiased and informed way * Automatically define ROIs for specific cerebellar lobuli and summarize function and anatomical data * Improve normalization of the deep cerebellar nuclei using an ROI-driven normalization. The suit-toolbox requires Matlab (Version 6.5 and higher) and SPM. The newest version only supports SPM8, although it likely runs under SPM2 or 5 as well. A standalone version for the suit-toolbox is not planned. Usage of the isolation or normalization functions, however, does not require that the analysis is conducted under SPM.
Peer Review Radio is a weekly radio show and podcast that portions the tastiest science and prepares it for public consumption. The end goal of this program is to provide an outlet where anyone and everyone can understand current scientific issues and generate their own informed opinions. In addition, Peer Review Radio promotes careers in research and science and serves as a training ground for future scientists to acquire invaluable communication skills. Peer Review Radio was established by a group of motivated graduate students with a desire to spread their love of science. By breaking down complicated concepts into bite-sized morcels, the ''Peers'' hope to spark the curiosity of their listeners with relevant, reliable information. Our producers determine content and coordinate the activities of the journalists. To ensure variety of content, graduate students are enlisted to act as advisers in their fields of expertise and direct literature research for necessary episode scripts. Then, we get together with professors, industrial scientists, post doctoral fellows and graduate students to talk about issues in science. Also, we supplement each episode with ''what if''-type questions, critiquing of science in film, profiles of alternative careers in science, book reviews and more! Our weekly radio show will air on CHUO 89.1 FM in Ottawa, Ontario, Canada starting this Fall 2010, and with each episode we hope to address another hot topic in science without frying your frontal cortex.
St. Gallen Lung Biopsy Biobank - An interdisciplinary collaboration in pulmonary medicine
St. Gallen Lung Biopsy Biobank is a tissue and blood sample collation (biobank) of all patients willing to give informed consent, who are undergoing bronchoscopy and/or surgical lung resection in their diagnostic pathway for any pulmonary disease. The special feature of the proposed biobank is the collection of endobronchial biopsies, blood, and molecularly defined cell populations from tumor tissue in a quality suitable for mRNA and other protein expression techniques, which is not possible by standard biobanks.
UniProt Non-redundant Reference database
Various non-redundant databases with different sequence identity cut-offs created by clustering closely similar sequences to yield a representative subset of sequences. In the UniRef90 and UniRef50 databases no pair of sequences in the representative set has >90% or >50% mutual sequence identity. The UniRef100 database presents identical sequences and sub-fragments as a single entry with protein IDs, sequences, bibliography, and links to protein databases. The two major objectives of UniRef are: (i) to facilitate sequence merging in UniProt, and (ii) to allow faster and more informative sequence similarity searches. Although the UniProt Knowledgebase is much less redundant than UniParc, it still contains a certain level of redundancy because it is not possible to use fully automatic merging without risking merging of similar sequences from different proteins. However, such automatic procedures are extremely useful in compiling the UniRef databases to obtain complete coverage of sequence space while hiding redundant sequences (but not their descriptions) from view. A high level of redundancy results in several problems, including slow database searches and long lists of similar or identical alignments that can obscure novel matches in the output. Thus, a more even sampling of sequence space is advantageous. You may access NREF via the FTP server.
University of Lincoln; Lincoln; United Kingdom
Public research university in Lincoln, England. The University has origins that trace back to 1861, and obtained university status in 1992 and its present name and structure in 2001.
Fox Chase Cancer Center is the region''s only hospital devoted entirely to cancer treatment, research and prevention. Our 100-bed hospital, located in Philadelphia, is consistently ranked by U.S. News and World Report among the top cancer centers in the nation. Our nationally and internationally recognized staff provides consultations and treatment recommendations for all types of adult cancer. Fox Chase Cancer Center is an independent, nonprofit institution formed in 1974 by the union of American Oncologic Hospital (one the the nation''s first cancer hospitals, established in 1904) and the Institute for Cancer Research (founded in 1927). Fox Chase was also among the first institutions to be designated a National Cancer Institute Comprehensive Cancer Center in 1974. In September 2000, the Hospital of Fox Chase Cancer Center became the nation''s first comprehensive cancer center and Pennsylvania''s first hospital to receive Magnet status for nursing excellence from the American Nurses Credentialing Center, which renewed this honor in 2004 and again in 2009, making it the first hospital in Pennsylvania to have achieved two successful Magnet renewals. The Women''s Cancer Center builds on Fox Chase''s world-renowned expertise in breast and gynecologic cancers. The Center offers women a place where they can receive coordinated, state-of-the-art care, support services, and education all under one roof.
Public university ranked established in 1972. Courses taught entirely in English, related to the world of business, engineering, culture, art and Spanish society.
United Network for Organ Sharing (UNOS) is the private, non-profit organization that manages the nation''s organ transplant system under contract with the federal government. UNOS is involved in many aspects of the organ transplant and donation process: * Managing the national transplant waiting list, matching donors to recipients 24 hours a day, 365 days a year. * Maintaining the database that contains all organ transplant data for every transplant event that occurs in the U.S. * Bring together members to develop policies that make the best use of the limited supply of organs and give all patients a fair chance at receiving the organ they need, regardless of age, sex, ethnicity, religion, lifestyle or financial/social status. * Monitoring every organ match to ensure organ allocation policies are followed. * Provides assistance to patients, family members and friends. * Educates transplant professionals about their important role in the donation and transplant processes. * Educating the public about the importance of organ donation. UNOS was first awarded the national Organ Procurement and Transplantation Network (OPTN) contract in 1986 by the U.S. Department of Health and Human Services. UNOS continues as the only organization ever to operate the OPTN. As part of the OPTN contract, UNOS has: * established an organ sharing system that maximizes the efficient use of deceased organs through equitable and timely allocation * established a system to collect, store, analyze and publish data pertaining to the patient waiting list, organ matching, and transplants * informed, consulted and guided persons and organizations concerned with human organ transplantation in order to increase the number of organs available for transplantation
Database of dermatology cases and browsable by diagnosis, category or body site with 12,176 images, 583 contributors and dermatology links. You may retrieve images using any diagnosis, disease category, body site, pigmentation, image contributor, patient age, image name, and/or key words. You are welcome submit images or to download images for lectures and other teaching purposes - or with permission for other uses. Additionally, you may search DermAtlas from your website. Add YOUR Link On the DermAtlas' ''' Add a Link Page you can associate your link with as many diagnoses as you like. Case submission If you have a high quality image that you would like to submit to DermAtlas, submit the requested information, and upload the image. The data and image will automatically be sent to the editors for review. You will be notified within one week of submission of images. In order for an image to be considered for inclusion into this collection, consent must be obtained from the patient or his/her legal guardian. Contributors are solely responsible for obtaining consent.
WikiDoc is the Original Medical Wiki / Encyclopedia. 71,700 Textbook Chapters and News Articles in English are available and anyone may edit this medical news service and textbook of medicine. Major sections include WikiDoc News: Today in Medicine, Co-Author The World''s Largest Textbook of Medicine, Community, and Care. WikiDoc is available in other languages including Espa��ol, Fran��ais, Polski, , Rom��n, , and T��rk��e.
Association of physicians, scientists, academics, research institutes and self-help groups that provides and nurtures interdisciplinary cooperation between research and primary, secondary and tertiary health care. Many internationally renowned heart failure researchers and working groups live and work in Germany. Nevertheless, there is insufficient cooperation of the respective working groups and research projects in this area. In order to remain internationally competitive in the heart failure research community, excellent implementation of large scale clinical and genetic trials is indispensable. Further, deficits in the effective presentation and transfer of research findings into clinical practice need to be addressed. An adequate translation of guidelines into practical, tangible instructions can facilitate clinical practice both in primary and tertiary care fundamentally. The need for action to address the research-practice-gap is obvious.
A software pipeline for analyzing deep sequencing maps of chromatin structure.
The AIDS Specimen Bank (ASB) provides repository services to cohort studies such as the Women''s Interagency HIV Study (WIHS), Primary HIV Infection Study, Staying Well Study, clinical trials performed at UCSF, and others. The majority of ASB clients are HIV investigators, but the bank also processes and stores specimens collected from some non-HIV studies. The ASB is also the Specimen Bank Core for the UCSF/GIVI Center for AIDS Research. The mission of the AIDS Specimen Bank is to provide the following: * Processing and handling of specimens * Short-term or long-term storage (includes ultra-low temperatures and liquid nitrogen) * Data management * Well-characterized specimens to qualified investigators for translational research * Consultation to investigators inquiring about specimen collection and storage * International resource for HIV research * Networking tool within the research community All body fluids����??sera, plasma, saliva, vaginal lavage, etc.����??are stored as 1-milliliter aliquots in ultra-low freezers (-70��������C). PBMCs are processed and stored in liquid nitrogen. All equipment involved with the processing of specimens (centrifuges and Coulter counter) is calibrated by trained technicians. The ASB is a participant in the Adult AIDS Clinical Trials Group PBMC Cryopreservation and Viability Panel, in which sets of processed and frozen PBMCs are sent to the Immunology Quality Assessment Program (IQA) testing lab for viability and cell counts. Our laboratory has participated in the IQA program for three years, and all samples have proven to be acceptable to their standards. The ASB is compliant with Good Laboratory Practices guidelines.
Stem cell and bone marrow register in the United Kingdom, managing and recruiting donors internationally for patients who require stem cell transplants. A database of tissue-typing results of all prospective donors is maintained. A national cord blood program consisting of both a cord blood bank and a research institute provides donated umbilical cord blood for use in clinical transplants and research. Research is conducted in immunogenetics, immunotherapy, bioinformatics (curating the World Health Organisation HLA Nomenclature database, ensuring that all new tissue types are consistently documented), and immune reconstitution.
MD Anderson Pancreatic Cancer Study Group Human Tumor Bank and Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. A clinical database and PTB were created in 1990 and 2000, respectively, to collect clinical information and biospecimens from patients with suspected or confirmed pancreatic cancer, other pancreatic diseases, and tumors of the duodenum, ampulla of Vater, and distal bile duct. Standard procedures for biospecimen collection and data entry were developed. The use of human tissue for research is an invaluable tool to understand the basic mechanisms of tumor biology, which will hopefully lead to the development of new therapeutic approaches to pancreatic cancer treatment. The cornerstone of any large translational research program is the development of an accurate and comprehensive tumor bank. All tumors removed in the operating room are sampled for careful pathologic study and the remainder of the tumor is promptly stored in our Pancreas Tissue Bank (PTB) to be used for research. Other samples, including blood, pancreatic juice and biopsy material, can also be utilized to identify early markers for pancreatic cancer. The molecular profile of tumors in the PTB can be linked to information in our clinical database to provide insight on the relationship between molecular events and clinical outcome. Patients may contribute to the tissue banking effort by choosing to participate in select research protocols. Protecting patient privacy is of great importance and thus, to maintain the confidentiality of health information, the PTB complies with all federal and institutional regulations governing research with human participants.
Fred Hutchinson Cancer Research Center and Seattle Cancer Care Alliance (SCCA) have merged to form Fred Hutchinson Cancer Center, unified adult cancer research and care center. Independent, nonprofit organization is clinically integrated part of UW Medicine and is UW Medicine’s cancer program.
The Nervous System In Action by Michael D. Mann, Ph.D. is a textbook on nervous system physiology. Available here is the web accessible version of of this textbook. An Adobe Acrobat (PDF) version is also supplied for better printing. You will need Acrobat Reader to see and print it. The textbook consists of the following: Preface (1) Neurophysiology, An Overview (2) Human Behavior (3) 1. Diffusion and Transport (4) 2. Control Systems and Homeostasis (5) 3a. Properties of Excitable Membranes: The Membrane Potential (6) 3b. Properties of Excitable Membranes: The Spike (7) 4a. Receptor Properties: Receptor Potentials and Coding (8) 4b. Sensory Receptors II (9) 5. Somesthesia--Peripheral Mechanisms (0) 6. Somesthesia--Central Mechanisms (a) 7. Vision (b) 8. Audition (c) 9. The Vestibular System (d) 10.Gustatory and Olfactory Senses (e) 11. Muscle Receptors (f) 12. Peripheral Nerves (g) 13. Synapses (h) 14. Muscle Contraction (i) 15. Reflexes (j) 16. Initiation and Control of Movement (k) 17. Activities Involving the Cerebral Hemispheres (l) 18. The Clinical Implications of Neurophysiological Concepts (m) 19. Learning and Memory Appendix: Common abbreviations (n) Glossary (o) Index (p)
A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 17, 2021. Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world. The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser.
Portal touching on all aspects of neuroscience from molecules to the mind, from the laboratory bench to the patient's bedside. Members study the normal structure and workings of the nervous system, its development, its cognitive functions, its derangement by disease and injury, and the means of its repair and protection. Projects span traditional disciplinary boundaries, as do graduate and postdoctoral training programs. Its major achievement has been to foster and improve multidisciplinary collaborations which has increasingly permitted the identification of pathogenic mechanisms and the formulation of new therapeutic approaches.
MiTCR - T-cell receptor repertoire analysis software
An open source software package aimed at extraction of information on repertoire of T-cell clones from Next Generation Sequencing (NGS) data. It is designed with the knowledge of the critical challenges arising in everyday processing of immunological data.
Kentucky Organ Donor Affiliates (KODA) is dedicated to saving lives through organ and tissue donation and transplantation. An independent, non-profit organ and tissue procurement agency, KODA was formed to establish a statewide educational and procurement network. Its services include evaluation of organ/tissue donor suitability; coordination of organ recovery; organ placement; tissue recovery; family support and aftercare; hospital staff education; public education. Like all OPOs, KODA is federally designated by the U.S. Department of Health and Human Services (HHS). As a licensed tissue bank, KODA Tissue Operations is regulated by the Food & Drug Administration (FDA). KODA is a member of the United Network of Organ Sharing (UNOS), a government-chartered nationwide network operating the Organ Procurement and Transplantation Network (OPTN) under federal contract with the U.S. Department of Health and Human Services (HHS). Founded in 1987 (Originated as a combination of existing organ and tissue procurement programs at the University of Kentucky and the University of Louisville), it now serves 114 counties in Kentucky, 4 counties in southern Indianan and 2 counties in western West Virginia. (Six northern Kentucky counties are served by LifeCenter in Cincinnati). Its major clients are 112 hospitals, 3 transplant centers and a multicultural population of 4 million people.
German biobank registry containing names, addresses of the contact persons, web links and basic information of the biobanks. The Registry is available in German and English and is organized by content and by region. The goal is to create public awareness and understanding of the objectives and functions of biobanks, and to arrange collaborations between scientists. The registry cooperates with the European initiative Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). Currently the first phase is implemented as an open access registry. A further expansion is planned with the possibility of online data entry and correction. The German Biobank Registry should help scientists and researchers, but also the interested public as an information gateway to serve. The functions of the registry are: * providing a publicly available registry of the medically relevant biobanks in Germany * improving the national and international visibility of German biobanks; * provision of partners for cooperation; * networking among biobanks; * promoting the exchange of information and of samples between research groups and institutions (hospitals, research institutes and pharmaceutical and biotech companies) operating biobanks; * improved use of existing resources; * promotion of transparency and understanding of the objectives and functions of biobanks in the general public; * Establishing a community to develop common solutions for legal and regulatory issues and thus avoiding redundant expenses for the individual researcher; * provide a planning basis for selective and efficient investments in new biobanks and the expansion of the existing infrastructure. The TMF is cooperating with the European BBMRI project to improve the biobank infrastructure in Europe. Data collection for the national registry is consistent with the survey of BBMRI project. You have to sample the data of your biobank only once and your biobank will be visible nationally and internationally. On the last page of the questionnaire you can give your consent for the use and publication of data for both projects (TMF and BBMRI) specifically. If you participate in the survey that has been harmonized for use throughout Europe by the BBMRI your biobank will be presented to the scientific community, potential partners for cooperations, funding organizations and sponsors. Furthermore, the survey provides an overview of the existing biobank infrastructure in Germany, and by this supports plans to ensure the sustainability and international competitiveness of German biobanks and the necessity of further financial support.
Tennessee Donor Services (TDS) is a nonprofit, independent organization authorized by the Federal Government to accept anatomical gifts for transplantation and research. Its mission is to support families in our communities who have sustained the loss of a loved one by providing an opportunity for organ, eye and tissue donation and by facilitating the recovery and transplantation of these gifts to help others in need. In our area (TN & VA), over 4,600 people now wait for an organ transplant, (heart, liver, lungs, kidneys, intestine or pancreas). Annually, our service area has approximately 300 people who donate one or more organs upon death and over 900 who donate corneas and/or tissues annually. The need for transplants far exceeds the number of donations in the area covered by TDS, and across the nation. Currently, in the United States, more than 108,000 people wait for an organ transplant. One third of them will die waiting for a transplant. TDS'' designated service area includes 84 counties in Tennessee, 10 counties in Virginia, 3 counties in Georgia and 1 county in Kentucky.
Technology Methods and Infrastructure for Networked Medical Research
Technology Methods Infrastructure for Networked Medical Research
TMF - Technology Methods and Infrastructure for Networked Medical Research
As an umbrella organization for medical research networks, the TMF is responsible for improving the organization and infrastructure of medical research in networked structures. It supports researchers at the various locations in jointly identifying and solving problems of an organizational, legal and technical nature that are often not associated with the particular clinical problem or research focus. The network not only focuses on legal and ethical frameworks for networked medical research but also on the development of IT infrastructure, quality management activities for science-initiated trials and questions on the intermeshing of research and patient care. Under the umbrella organization of the TMF, expert opinions, studies, concepts, requirements specifications, services and tools are created. The products of the cooperation within the TMF are available to the research community. The aims of joint work in the TMF are: * Improvement of medical research in terms of quality, organization and cooperation * Solution of questions spanning networked medical research, e.g. on the collection, processing and exchange of research data * Clarification of the legal and ethical foundations for performing medical research * Issues of quality assurance and quality management * Development and extension of efficient IT infrastructures and their implementation in cross-institutional networked structures * Realization of cross-location solutions * Contributions to sustainable and efficient health research by means of the improved transfer of research findings to patient care
BBMRI Wiki: For a global biomedical research
Biobanking and Biomolecular Resources Research Infrastructure Wiki
Biobanking Biomolecular Resources Research Infrastructure Wiki
The BBMRI Wiki is intended to help establish a standard vocabulary within the European BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) project. This Wiki also facilitates the definition and updating of new terms as well as the Minimum Information About BIobank data Sharing: MIABIS. MIABIS represents the minimum information required to enable the exchange of biological samples and data between biobanks.
M-pick: a modularity-based clustering method for OTU picking
A modularity-based clustering software for Operational Taxonomic Unit (OTU) picking of 16S rRNA sequences. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance or variance levels to define OTUs.
University of Manchester; Manchester; United Kingdom
Public research university in Manchester, England, formed in 2004 by merger of University of Manchester Institute of Science and Technology and Victoria University of Manchester. Second largest university in United Kingdom by enrollment.
Commercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services.
UC Davis Center for Childrens Environmental Health
Center for Children''s Environmental Health
Center for Children''s Environmental Health and Disease Prevention
UC Davis School of Vet Med: Center for Children''s Environmental Health
The Center for Children''s Environmental Health and Disease Prevention is a multi-disciplinary collaborative research organization established to examine how toxic chemicals may influence the development of autism in children. The Center''s goal is to contribute knowledge about autism that will lead to new strategies for the prevention and treatment of this mysterious condition. Parents and health professionals have raised concerns about how environmental factors such as pesticides, a variety of chemicals, or even some ingredients included in vaccines may effect the development of the disorder. We are the first center to examine the roles of a wide range of toxic chemicals, genetic predisposition, and the interplay between these two in altering brain development during early life and leading to abnormal social behavior in children. Scientists in the CCEH study the effects of the environment on children''s health, with a particular focus on autism. Researchers come from all fields including molecular biology, medicine, nutrition, psychology, animal behavior, and genetics. The Center''s research is guided by an Advisory Board with representatives including parents, activists, non-profits, government agencies, and concerned citizens. This Center is one of several children''s centers throughout the nation funded by the U.S. EPA and NIEHS.
CARMA - Characterizing Short Read Metagenomes
A software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes. The software was originally designed for the analysis of environmental metagenomes obtained by the ultra-fast 454 pyrosequencing system.
The mission of the Cancer Center Biorespository is to provide high quality, well-characterized cancer-related human tissue specimens and biological materials to collaborators. The specific objectives of the shared resource are: * The procurement, preparation, and preservation of malignant, benign, and normal human specimens in a centralized repository * To provide high quality annotated data (pathological and clinical) using a secure and interactive database system * To facilitate compliance with all mandated regulatory processes (IRB, HIPAA, SRC) thereby promoting ethical research by UC Davis researchers * To provide pathologic consultation to investigators using human specimens for scientific correlation * To efficiently prioritize, disperse, and track specimens via a rapid and standardized approval and monitoring process * To provide TMA consultation and services for cancer center investigators and their collaborators
A database-based neuron simulation tool. An innovative approach to large-scale, biologically plausible, neural-network simulation library. Based on data structures and methods directly coded into database, information flow implying separation of data representing neurons, conceived to share load on multiple machines and calibrating operational load on each machine.
A free repository for oncology information, chemotherapy protocols, and cancer treatment regimens. It is meant for Healthcare providers working in the field of Oncology.
SLiQ: Simple linear inequalities based Mate-Pair reads filtering and scaffolding
Software for simple linear inequalities based Mate-Pair reads filtering and scaffolding. A set of simple linear inequalities (SLIQ) derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a pre-processing step for any scaffolding algorithm. This tool filters mate pairs and then produces a Directed Contig Graph (contig diGraph). Also provided is a Naive scaffolder that can then produce scaffolds out of the contig diGraph.
MD Anderson Gynecologic Cancer Tissue Bank
MD Anderson Cancer Center Gynecologic Cancer Tissue Bank
MD Anderson Cancer Center Gynecologic Cancer Translational Research Tissue Bank
Multidisciplinary Gynecologic Cancer Translational Research Tissue Bank
The purpose of the Multidisciplinary Gynecologic Cancer Translational Research Tissue Bank is to provide investigators with primary human tissue for research projects relating to gynecologic cancer. Priority for samples is given to the MD Anderson scientific community. This tissue bank handles the consent, collection, processing, storage and distribution of primary gynecologic tumor samples as well as ascites, blood and urine of gynecologic cancer patients.
Alamo Tissue Service, headquartered in San Antonio, Texas, is a distributor of high quality tissue allografts to physicians, hospitals, surgical clinics and tissue banks. We are a licensed tissue bank and our quality assurance program meets both the Federal Food & Drug Administration (FDA) regulations and American Association of Tissue Bank (AATB) Standards. A list of allografts processed from donated human tissue include: * Fresh frozen ligaments, tendons, and traditional grafts. * Freeze-dried (lyophilized) tissue, cancellous, cortical, femoral shaft, cloward dowel, tricortical block, tibial shaft, unicortical block, fibula section, femoral ring, patella tricortical, radius section, costal cartilage, fascia, femoral head. Alamo Tissue Service is dedicated to providing the highest quality tissue available and our ability to network with the finest accredited Tissue Banks in the United States allows us to help you with those hard to find specialty grafts. Alamo Tissue is available 24 hours a day through our toll-free or local telephone numbers. We look forward to working with you and your facility. Alamo Tissue Service would like to thank all donor families during their time of grief for remembering the needs of others.
DNAPlotter: circular and linear interactive genome visualization
Software application used to generate images of circular and linear DNA maps to display regions and features of interest. The images can be inserted into a document or printed out directly. As this uses Artemis it can read in the common file formats EMBL, GenBank and GFF3.
Medical University of Vienna; Vienna; Austria
The Wikiversity School of Medicine is a free online educational resource for the study of medicine. It is a member of the Faculty of Life Sciences and aims to maximize collaboration with other schools within the faculty and elsewhere. Prospective students may study medicine at Wikiversity by registering with the site and joining the school. Students may study via the proposed curriculum pathway, by picking and choosing modules or lessons from the different departments or by joining the school in creating lessons. The school''s medical course is currently divided into pre-clinical and clinical sets of modules. Access to these modules is via the school curriculum. This resource is available in other languages including Deutsch, Espa��ol, Fran��ais, Italiano, Portugu��s, and .
Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample.
University of Ioannina; Ioannina; Greece
University was founded in 1964, as a charter of the Aristotle University of Thessaloniki and became an independent university in 1970.
Public research university in Iowa City, Iowa. Founded in 1847, it is the oldest and the second-largest university in the state.
Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.
Competence Network on Parkinson's Disease
A medical network comprised of university clinics, special clinics, and special practices working together to collect data, gene samples, and execute clinical trials in order to bring about diagnoses and therapy methods. Research projects are done in cure research, diagnostic and therapeutic research. The care network includes university clinics, town clinics, special clinics for Parkinson's disease, specialists, and general practitioners.
A brain bank which collects brain tissue from patients who died from various neurological and psychiatric diseases. These tissues are available for biochemical, molecular biological, and other work groups with the aim of supporting research on the pathogenesis, diagnosis, and therapy of these diseases. Collected brains are clinically and neuropathologically well-characterized. The collection and distribution of brain tissue samples is an ongoing process. NeuroBiobank Munich offers help with the organization and implementation of autopsies as well as with the neuropathologic diagnostics. The thematic emphasis of the NeuroBiobank Munich is Parkinson's disease and demential degenerative disorders such as Alzheimer's disease or Creutzfeldt-Jakob disease. NeuroBiobank Munich coordinates the German national brain tissue bank (BrainNet) and the European brain tissue bank (BrainNet Europe).
A wiki which provides information on neurodegenerative diseases to caregivers, students, and researchers.
Short Time-series Expression Miner (STEM)
The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category or user defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While STEM is designed primarily to analyze data from short time course experiments it can be used to analyze data from any small set of experiments which can naturally be ordered sequentially including dose response experiments.) Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 28,2022. A network of several university centers in Germany that classifies neurological and psychiatric disorders neuropathologically and collects and provides brain tissue for research. The aim and task of the Brain-Net are: the collection of clinically and neuropathologically well-characterized brain tissue samples; the standardization of neuropathological diagnoses according to internationally accepted criteria; and providing a basis for future research projects using genetic, epidemiological, biometric and other issues to neurological and psychiatric disorders.
Nationwide organ and tissue donor registry that is a private, non-profit organization dedicated to the enhancement of organ and tissue donation. They educate the community about the urgent need for donors so no one dies or suffers for lack of donation, honor donors and support organ recipients, living donors and their families. They are cognizant of the many challenges ahead before the day comes when no one will die because a donor organ was not available at the time of need. The Board and Staff of The Living Bank dedicate their efforts to increase the number of registered-informed donors. The programs and services of The Living Bank are: # The Living Donor Bank Program advocates and supports living donors before, during and after the donation process. # Travel Stipend/Donor Support Program assists living donors in arranging transportation and provides stipends if they must travel to donate. # Donor Education Program educates the public regarding the donation and use of organs and tissues and provide donor cards.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Neurologic AIDS Research Consortium (NARC) is supported by the National Institutes of Health to design and carry out clinical trials to improve the therapy for HIV induced neurologic disease, and neurologic conditions associated with the AIDS virus. This consortium was established in 1993 when the NARC grant submitted by David B. Clifford, M.D. of Washington University School of Medicine was funded by the National Institute of Neurologic Disorders and Stroke (NINDS) to establish the consortium. Since that time the grant has supported studies of the natural history of neurologic performance in advanced AIDS, treatment of HIV associated peripheral neuropathy, progressive multifocal leukoencephalopathy, and cytomegalovirus.
An Operational Taxonomic Unit (OTU) clustering software for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that calculates the sample size required for obtaining a prescribed power against a specified alternative for TDT. (entry from Genetic Analysis Software)
Duke University Kathleen Price Bryan Brain Bank
A research repository of human brains with neurological disorders and normal controls, recruited through the Autopsy and Brain Donation Program coordinator. The Kathleen Price Bryan Brain Bank contains brains from patients with Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis, Huntington's disease, Muscular Dystrophy, and other neurological and dementing disorders. The brain tissue is subjected to a detailed neuropathological evaluation and then stored as fixed and frozen hemispheres, paraffin blocks and histological slides. After receipt of an IRB approved request, tissue is supplied to investigators at Duke University, major medical centers and pharmaceutical companies across the United States and worldwide.
For over 20 years Fairfax Cryobank has provided the highest quality donor sperm that has led to the creation of many happy healthy families. We provide the caring and sensitive support you need, the high quality donor sperm you require, and are accredited by the AATB (American Association of Tissue Banks) and fully compliant with FDA regulations governing reproductive tissue banks. Fairfax Cryobank offers a large selection of high quality donors; only 1 in 200 applicants make it through our rigorous screening process to become donors. We perform the most extensive genetic and infectious disease testing of all sperm banks. Fairfax Cryobank is dedicated to supplying updated verified and accurate medical and personal information on our donors. We have a caring, sensitive and knowledgeable Client Services Team ready to assist you in your choices. Fairfax Cryobank provides a variety of services that will support your process of selecting your perfect donor match including photo matching and a clear and user friendly donor search. We appreciate the importance of finding the right match, the total package, and so we offer incentives and specials that allow you to purchase donor sperm and accompanying products at reduced cost. We have a long-standing reputation of excellence with over two decades of satisfied physicians and patients. Trust, credibility, and quality are the basis of our success.
A specialized hardware platform that will perform cortex-scale emulations while offering software-like flexibility. With sixteen 12x14 sq-mm chips (Neurocores) assembled on a 6.5x7.5 sq-in circuit board that can model a slab of cortex with up to 16x256x256 neurons - over a million! The chips are interconnected in a binary tree by 80M spike/sec links. An on-chip RAM (in each Neurocore) and an off-chip RAM (on a daughterboard, not shown) softwire vertical and horizontcal cortical connections, respectively. It provides an affordable option for brain simulations that uses analog computation to emulate ion-channel activity and uses digital communication to softwire synaptic connections. These technologies impose different constraints, because they operate in parallel and in serial, respectively. Analog computation constrains the number of distinct ion-channel populations that can be simulatedunlike digital computation, which simply takes longer to run bigger simulations. Digital communication constrains the number of synaptic connections that can be activated per secondunlike analog communication, which simply sums additional inputs onto the same wire. Working within these constraints, Neurogrid achieves its goal of simulating multiple cortical areas in real-time by making judicious choices.
Joseph and Kathleen Bryan Alzheimer's Disease Research Center
Bryan Alzheimer's Disease Research Center
Joseph & Kathleen Bryan Alzheimer's Disease Research Center
An Alzheimer's disease center (ADC) that offers support services for families caring for persons with memory disorders, community outreach and education programs, in addition to its clinical and basic research activities. Information on current scientific and clinical findings is offered to the general public, medical and scientific community. An important emphasis of the Bryan ADRC is to advance basic medical discovery concerning AD and related dementias. This basic science mission is facilitated through the DNA cell repository located in the Institute of Genome Sciences and Policy (IGSP) and the Bryan ADRC brain donation program of the Kathleen Price Bryan Brain Bank. These affiliated Bryan ADRC programs provide a source of fresh brain tissue.
Simple Modular Architecture Research Tool
Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.
An independent, non-profit organization, Lifeline of Ohio (LOOP), promotes and coordinates the donation of human organs and tissue for transplantation. Its mission is to educate and empower central and southeastern Ohioans about organ and tissue donation while also facilitating the donation process. Lifeline of Ohio, a Donate Life Organization, has been approved by the Centers for Medicare and Medicaid Services (CMS) as the designated organ procurement organization (OPO) serving 37 Ohio counties along with Wood and Hancock counties in West Virginia. Accredited by both the Association of Organ Procurement Organizations (AOPO) and the American Association of Tissue Banks (AATB), Lifeline of Ohio provides services to 70 hospitals and the communities they serve through its procurement and tissue coordinators, and other professional staff.
University of Pittsburgh Brain Tissue Donation Program
Conte Center Brain Tissue Donation Program
Conte Center for the Neuroscience of Mental Disorders Brain Tissue Donation Program
University of Pittsburgh Medical Center Brain Tissue Donation Program
UPMC Center for the Neuroscience of Mental Disorders and Translational Neuroscience Program Brain Tissue Donation Program
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 19,2024. Brain tissue donation is a valuable contribution to mental health research. It enables scientists to investigate how the normal brain works, and how the brain is disturbed when it is affected by schizophrenia, depression, bipolar (manic depressive) disease or other related disorders. The Department of Psychiatry at the University of Pittsburgh has established a brain tissue bank to which brain tissue can be donated at no expense. The gift of brain tissue enables scientists to conduct research designed to understand causes, to develop new treatments, and ultimately to find cures for diseases that affect the brain. Brain tissue donation is a gift that makes it possible for researchers to study various types of mental disorders. Donations of brain tissue from individuals without these disorders are also needed to establish comparisons with brain samples from individuals who have these disorders. Any legally competent adult or guardian may indicate during life their interest in donating brain tissue after death. Next-of-kin either of healthy individuals or of those with psychiatric disorders may give consent to donate brain tissue following the death of a loved one. Brain tissue is removed during autopsy at a morgue or hospital and is transported to the University of Pittsburgh Medical Center for examination and study.
Medical University of Vienna Institute of Neurology
The (Clinical) Institute of Neurology (IN) of the Medical University Vienna was founded in 1882 by Heinrich Obersteiner. It is the oldest institution embracing the multidisciplinarity of neurosciences and has served as model for the establishment of similarly designed institutions in many countries. The original location of the then Neurological Institute in Vienna was at Schwarzspanierstrasse. Since 1993, IN is located in the Vienna General Hospital in top-class laboratory facilities. IN is committed to its proud tradition as Obersteiner Institute and to a promising future of a nationally and internationally leading institution in the clinical neurosciences. Our work aims to translate the understanding of nervous diseases to the development of novel therapeutics and diagnostics. IN' '''s tasks include diagnostic patient service, research and graduate / postgraduate teaching in neuropathology, neurochemistry, and neuro-molecular biology in an integrated way. Neuropathology is a recognized medical specialty in Austria. It analyzes structural changes of nervous tissues in disease. Diagnostic neuropathology makes use of most modern morphological techniques applied to diseased central, peripheral and vegetative nervous tissues and fluids, and muscle. Neuropathological diagnoses are a basis for disease classification and rational therapies. Neurodegenerative disorders, in particular prion diseases, virus diseases affecting the nervous system, and brain tumors (neuro-oncology) are research priorities. In the highly publicized area of prion diseases, IN has developed into a national and international center of excellence and expertise that leads several European, EU-funded networks in prion research. As an indispensable asset, the IN possesses a large brain bank that has systematically collected neuropathological specimens since 1948. Most samples are fixed and paraffin-embedded tissue only, but in a part of neurosurgical, nerve and muscle biopsies and autopsies, also fresh tissue is obtained, frozen and stored at -80 degrees C. Occasionally blood and CSF are also available. The unique neuropathological collection of histological slides, paraffin blocks and formol-fixed nervous tissues now comprises about 16.000 brain autopsies, 30.000 neurosurgical and 7.500 nerve/muscle biopsies. Also a number of cell cultures have been stored, mainly fibroblasts from patients with rare neurometabolic diseases, and primary cultures of brain tumors. IN participates in the EU-supported European Network of Brain Banks BrainNet Europe.
Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.
FlyAtlas: the Drosophila gene expression atlas
FlyAtlas gives you a quick answer to the question: where is my gene of interest expressed/enriched in the adult fly? For each gene and tissue, you''re given the mRNA SIGNAL (how abundant the mRNA is), the mRNA ENRICHMENT (compared to whole flies), and the Affymetrix PRESENT CALL (out of 4 arrays, how many times it was detectably expressed). The dataset so far comprises 44 Affymetrix Dros2 expression arrays, each mapping the expression of 18770 transcripts - corresponding to the vast majority of known Drosophila genes. The dataset thus contains over 822800 separate datapoints. This website is intended to make the data easily accessible and comprehensible to mere mortals. FlyAtlas provides the most comprehensive view yet of expression in multiple tissues of Drosophila melanogaster. Meta-analysis of the data shows that a significant fraction of the genome is expressed with great tissue specificity in the adult, demonstrating the need for the functional genomic community to embrace a wide range of functional phenotypes. Well-known developmental genes are often reused in surprising tissues in the adult, suggesting new functions. The homologs of many human genetic disease loci show selective expression in the Drosophila tissues analogous to the affected human tissues, providing a useful filter for potential candidate genes. Additionally, the contributions of each tissue to the whole-fly array signal can be calculated, demonstrating the limitations of whole-organism approaches to functional genomics and allowing modeling of a simple tissue fractionation procedure that should improve detection of weak or tissue-specific signals.
New Mexico Donor Services (NMDS) is committed to saving and improving lives, connecting one life to another through donation and transplantation. NMDS and New Mexico hospitals share responsibility to ensure that an individual''s decision to be a donor is followed or their family is given the option to donate organs and/or tissue. Hospitals identify potential donors, make timely referrals, and manage the patients to allow NMDS to evaluate the patient for donor suitability and check donor status on their driver''s license or ID. Organs are distributed to waiting recipients through the national organ transplant list maintained by the United Network for Organ Sharing (UNOS) based on medical factors such as blood type, size and tissue match. It is illegal to distribute organs based on wealth or celebrity status. Tissue is distributed based on patient need, medical criteria and availability.
The South Carolina Biorepository System (SCBS), directed by Dr. Phil Buckhaults, School of Medicine, is a statewide tissue bank working with health care facilities across South Carolina to collect tumor and matched normal tissue samples from patients with cancer, and providing these samples to researchers statewide. All specimens are de-identified to protect patient privacy, but are annotated with essential, detailed clinical data. Currently, the SCBS inventory includes specimens from the leading types of cancers in South Carolina: breast, colorectal, lung, and prostate, as well as many other cancer sites. The ultimate goal is to improve the lives of cancer patients and their families.
SOPRA - Statistical Optimization of Paired Read Assembly
Statistical Optimization of Paired Read Assembly
Software tool to exploit the mate pair/paired-end information for assembly of short reads from high throughput sequencing platforms, e.g. Illumina and SOLiD.
A biological medical device company that focuses on the development of implantable biological devices, surgical adhesives, and biomaterials for use in cardiac and vascular for patients of all ages. The Company''s research and development efforts are focused on Protein Hydrogel Technologies, such as BioFoam Surgical Matrix for parenchymal organ sealing. The Company is also investigating additional applications for its SynerGraft decellularization technology. CryoLife provides surgeons with multiple tissue options for cardiovascular reconstruction. CryoLife preserved allografts have helped save the lives and limbs of patients for 20 years. CryoLife''s tissue, along with BioGlue and BioFoam offer a wide range of Life Restoring Technologies for cardiac and vascular surgeons. CryoLife provides innovative products that will benefit patients around the world by working with other pioneering companies and by continuous investment in research and development.
Non-profit organization dedicated exclusively to education and support for the issues of prevention and recovery of brain injury in the state of Utah. The Brain Injury Association of Utah provides Help, Hope and Healing through Education, Facilitation and Advocacy. If you are one of the thousands of people who are faced with traumatic brain injury, you may be scared, and confused. We have resources, connections and programs that can help offer hope, clarity and sense of direction when it comes to living life to the fullest possibilities after traumatic brain injury. You are not alone. Together, we will not only survive, but thrive through the challenges ahead. At the Brain Injury Association of Utah you will find: * What To Expect * Basics of Brain Injury * Continuum of Care * Emotional Stages after Brain Injury * Facts About Brain Injury * Cognitive Brain Skills & Clues About Brain Injury * Glascow and Ranchos Coma Scale * Types and Levels of Brain Injury BIAU has coalitions with major hospitals, governmental agencies, and rehabilitation centers to provide a network of support, information, and help. Your support will strengthen this network and make a significant difference in the lives of those who have suffered a brain injury.
Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets
Percolator post-processes the results of a shotgun proteomics database search program, re-ranking peptide-spectrum matches so that the top of the list is enriched for correct matches. Shotgun proteomics uses liquid chromatography-tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of peptide identifications from a collection of tandem mass spectra. Percolator uses semi-supervised machine learning to discriminate between correct and decoy spectrum identifications, correctly assigning peptides to 17% more spectra from a tryptic dataset and up to 77% more spectra from non-tryptic digests, relative to a fully supervised approach. The yeast-01 data is available in tab delimetered format. The SEQUEST parameter file and target database for the yeast and worm data are also available.
TBI/Tissue Banks International is a non-profit network of medical eye and tissue banks dedicated to the relief of human suffering through transplantation. More than 100,000 patients are treated with TBI tissue annually. TBI is a recognized innovator in the field of eye and tissue banking and has led advancements in recovery, processing, and distribution of allograft tissue. Each person who chooses to become an eye and tissue donor can help more than a dozen people through their gift. Sight can be restored with a cornea, mobility enabled with a ligament, pain eased with a spinal implant made of bone, burns treated with skin, and lives saved with heart valves. The largest provider of ocular tissue in the world, TBI started as a single eye bank in 1962, and has grown to a network that covers the United States and reaches around the globe. Each year, more than 130,000 TBI tissues are used in transplant surgery, with thousands more utilized in research and medical education.
Allen Institute Neurowiki: Biological Linked Data Map
Allen Neurowiki: Biological Linked Data Map
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. The Allen Institute Neurowiki is a joint project between Vulcan Inc. and the Allen Institute to build a Semantic Wiki mapping genetic instances. It is a finished prototype testing the import pipelines and display componenets for combining 5 major RDF datasets from 4 different sources. Current planning includes mapping complete datasets, curating a better ontology, and creating multiple ontology management for a user class. Biological Linked Data Map: * Open, public online access * Data from multiple RDF data stores * Complete import pipeline using LDIF framework * Outlines of each imported instance embedding inline wiki properties and providing views of imported properties from original RDF datasets * Charting tools that ' '''pivot' ''' SPARQL queries providing several views of each query * Navigation and composition tools for accessing and mining the data Where did we get the data? * KEGG: Kyoto Encyclopedia of Genes and Genomes: KEGG GENES is a collection of gene catalogs for all complete genomes generated from publicly available resources, mostly NCBI RefSeq * Diseasome: The Diseasome website is a disease / disorder relationships explorer and a sample of an innovative map-oriented scientific work. Built by a team of researchers and engineers, it uses the Human Disease Network dataset. * DrugBank: The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information. * Sider: Sider contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. Every piece of content on every instance page is generated by Semantic Result Formatters interpreting SPARQL results.
NDRI actively recovers a diverse range of normal and diseased human tissues for biomedical researchers. We have recently implemented a new program to make human dorsal root ganglia (DRG) available for your research studies. The dorsal root ganglia contain cell bodies of afferent (inbound) neurons, and transmit pain and temperature sensations from the body. DRGs from C5 through L5 regions will be available. DRGs will be recovered under operating room conditions with a low post mortem interval to preservation and can be shipped at 4 degrees C, snap-frozen or fixed. Detailed medical-social history information is provided for each donor. If you are interested in obtaining these specimens, please contact me at your earliest convenience. Current NDRI researchers can immediately request these samples. Non-NDRI researchers need to submit a researcher application. * The program provides a reliable source of human DRG neurons that can be utilized for: Electrophysiology analysis, Live cell imaging studies * Low PMI yields high quality samples that are suitable for rigorous molecular applications: Deep sequencing analysis, In situ hybridization, Micro-array analysis * DRGs from C5 through L5 regions will be available. * The tissue fee for this program is 500 dollars per DRG * Customizable-- the researcher determines the DRG location and quantity that is needed for their research.
Platform for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels that includes two interactive databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities: * The open public image database, here, providing in situ hybridization data mapping gene expression across the anatomic structures inherent in glioblastoma, as well as associated histological data suitable for neuropathological examination * A companion database (Ivy GAP Clinical and Genomic Database) offering detailed clinical, genomic, and expression array data sets that are designed to elucidate the pathways involved in glioblastoma development and progression. This database requires registration for access. The hope is that researchers all over the world will mine these data and identify trends, correlations, and interesting leads for further studies with significant translational and clinical outcomes. The Ivy Glioblastoma Atlas Project is a collaborative partnership between the Ben and Catherine Ivy Foundation, the Allen Institute for Brain Science and the Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment.
ESPRIT-Tree: Hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time
Software for hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. In this database data can be searched and browsed. Very few SSU rRNA modification maps are believed to be complete, i.e., with all sites and structures of modified nucleosides unambiguously established. The exception is perhaps E. coli, the subject of investigation for many years; Lingering discrepancies were mostly resolved upon completion of the gene sequence, with the final modified residue (Y-516) placed in 1994. When using the present compilation, the reader should be aware of several major sources of incomplete listings for some organisms. The first is that only portions of the rRNA molecule may have been sequenced, thus giving the (possibly incorrect) appearance in comparative alignments that portions of the rRNA are unmodified. For example in the case of B. stearothermophilus only the 52 3'-terminal nucleotides were sequenced, but which produces an incomplete picture when B. stearothermophilus is aligned with the E. coli map, which is complete. An additional source of incomplete listings lies in data derived from RNase T1 catalogs in the earlier literature. Most such studies were made for the purpose of establishing patterns of phylogenetic relatedness. For this reason most reported catalog sequences purposely omitted short sequences, some of which were undoubtedly modified, because they were of less use in establishing unique "signature" sequences. The extent of this problem in judging modification map completeness is difficult to judge unless a total modification assay (as from HPLC or LC/MS analysis of a complete nucleoside digest) has been carried out in order to determine the identities and approximate numbers of modifications. A third source of incompleteness may result from the method used for detection of modification. For instance pseudouridine residues (which are abundant in eukarya) would not be reported if the 14C-methionine method, resulting in labeled methyl groups, were used. Similarly, maps reporting locations of pseudouridine have in recent years often been based on the modification-reverse transcriptase method of Ofengand, and was thus not intended to detect ribose methylation. Reference to the original citations will usually be required to establish whether the methodology used would have influenced the reported modification distribution. Supported by: National Institute of General Medical Sciences, grant GM29812.
Huazhong University of Science and Technology; Wuhan; China
Huazhong University of Science & Technology
Huazhong University of Science & Technology; Hubei; China
Huazhong University of Science and Technology
Public research university located in Guanshan Subdistrict, Hongshan District, Wuhan, Hubei province, China.
University of Texas Medical Branch Human Tumor Bank Core
UTMB Sealy Center for Cancer Cell Biology Human Tumor Bank Core
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016.
Database containing a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. Users may submit a Popset using Sequin.
Open PHACTS - Open Pharmacological Space
Open Pharmacological Concepts Triple Store
Project that developed an open access discovery platform, called Open Pharmacological Space (OPS), via a semantic web approach, integrating pharmacological data from a variety of information resources and tools and services to question this integrated data to support pharmacological research. The project is based upon the assimilation of data already stored as triples, in the form subject-predicate-object. The software and data are available for download and local installation, under an open source and open access model. Tools and services are provided to query and visualize this data, and a sustainability plan will be in place, continuing the operation of the Open PHACTS Discovery Platform after the project funding ends. Throughout the project, a series of recommendations will be developed in conjunction with the community, building on open standards, to ensure wide applicability of the approaches used for integration of data.
Uniformed Services University of the Health Sciences, Department of Pharmacology
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 18,2021.Research in the Department of Pharmacology addresses fundamental questions relevant to understanding the actions of drugs, hormones, neurotransmitters, and growth factors at the molecular and cellular level, as well as their effects on the whole organism. Current areas of focus, employing a wide variety of approaches and model systems, are neuropharmacology and mechanisms of signal transduction. Seminars, Journal Clubs and Interest Groups create a stimulating, supportive and collegial environment in which intra and interdepartmental collaborations flourish. Postdoctoral fellows and graduate students from the interdisciplinary Molecular and Cell Biology and Neuroscience training programs enrich this environment, and faculty are actively encouraged to participate all aspects of graduate education. In addition to modern, well-equipped laboratories within the Department, the Biomedical Instrumentation Center provides core facilities for imaging, flow cytometry, proteomics and protein and DNA sequencing. Other University resources, as well as our proximity to the National Institutes of Health, provide easy access to additional state-of the-art technologies that enhance the research programs of our faculty.
A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead.
Brain Canada is a national non-profit organization that develops and supports collaborative, multidisciplinary, multi-institutional research across the neurosciences. Through partnering with the public, private and voluntary sectors, Brain Canada connects the knowledge and resources available in this area to accelerate neuroscience research and funding and maximize the output of Canada''s world-class scientists and researchers. Brain Canada was created to address the twin challenges of increasing the scale of brain research funding in Canada and widening its scope to encourage interdisciplinary collaboration to produce insights for treating multiple disorders. Brain Canada is built on the successes and model of NeuroScience Canada (NSC). Established in 1999, NSC raised more than $11.5 million, leveraged over $20 million with partnered funding, and funded 100 individual and teams of researchers in Canada. Brain Canada is the new vision for Canadian brain researchthe voice for the brain and the grouping of brain disorders, raising awareness about their prevalence and impact on individuals, families, the economy and society. But most important, through the research we are funding, we are giving hope to the millions of Canadians who are directly or indirectly touched by diseases, disorders, and injuries of the brain, spinal cord and nervous system.
Created by the Government of Canada in 1997 to undertake world-class research and technology development to benefit Canadians by investing in facilities and equipment, universities, colleges, research hospitals and non-profit research institutions to attract and retain the world's top talent, training the next generation of researchers, supporting private-sector innovation and creating high-quality jobs.
miRNA targets by weighting immunoprecipitation-enriched parameters
mirWIP - miRNA Targets by Weighting RISC-IP Enriched Parameters
Tool to search for targets of conserved microRNAs in Caenorhabditis elegans by weighting RISC-immunoprecipitation-enriched parameters.
A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads.
An Antibody supplier, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University of Kerala, formerly the University of Travancore, is an affiliating university located in Thiruvananthapuram, capital of the state of Kerala, India.
An open web-accessible resource for gene functional annotations in the plant sciences to facilitate improvement, consolidation and visualization of gene annotations across several plant species. It is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis, potato, tomato, rice, and tobacco are included. The main features are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes.
Ontodog: A Web-based Ontology View Generator
Ontodog is a web-based ontology view generator. It can generate inSubset annotation ontology, user preferred label annotation ontology and subset of source ontology. Simply provide Ontodog input term file (Microsoft Excel file or tab-delimited text file), select one source ontology or enter your own source ontology and SPARQL endpoint, then set the settings for Ontodog output files and get the OWL (RDF/XML) Output files. Ontodog performs the basic ontology modularization-like function, i.e.,it automatically extracts all axioms and related terms associated with user-specified signature term(s). In addition, Ontodog includes extra features: (1) extracting all instance data associated with the retrieved class terms and annotations; and (2) recursively extracting all axioms and related terms indirectly associated with signature terms. More features are being added to Ontodog, such as relabeling preferred names for various ontology terms to fit in with the needs from a specific community. The Ontodog input data requires a source ontology and a list of user-specified signature terms in tab-delimited format. Ontodog provides the template files for generating the signature terms as the input terms file to download. There are several output options that the users can choose based on their needs. With more and more ontologies being developed, Ontodog offers a timely web-based package of solutions for ontology view generation. Ontodog provides an efficient approach to promote ontology sharing and interoperability. It is easy to use and does not require knowledge of SPARQL, script programming, and command line operation. Ontodog is developed to serve the ontology community for ontology reuse. It is freely available under the Apache License 2.0. The source code is made available under Apache License 2.0.
A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries.
NNG: Neuron Navigator - A Database of Drosophila Brain Neurons
Neuron Navigator (NNG) integrates a 3D neuron image database into an easy-to-use visual interface. Via a flexible and user-friendly interface, NNG is designed to help researchers analyze and observe the connectivity within the neural maze and discover possible pathways. With NNG''s 3D neuron image database, researchers can perform volumetric searches using the location of neural terminals, or the occupation of neuron volumes within the 3D brain space. Also, the presence of the neurons under a combination of spatial restrictions can be shown as well. NNG is a result of a multi-discipline collaboration between neuroscientists and computer scientists, and NNG has now been implemented on a coordinated brain space for the Drosophila (fruit fly) brain. Account is required.
University of Iowa Carver College of Medicine; Iowa; USA
Roy J. and Lucille A. Carver College of Medicine
University of Iowa Carver College of Medicine
Medical school of the University of Iowa, located in Iowa City, in the U.S. state of Iowa.
Center that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species.
German Federal Ministry of Education and Research
Bundesministerium für Bildung und Forschung
Federal Ministry of Education and Research
Federal Ministry of Education and Research (Germany)
Service to align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool. Note: Submission is currently limited to at most 1000 sequences of at most 6000 bases each. If your requirements exceed this limitation, get Opens internal link in current windowSINA for local installation.
Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.
Digital Brain Atlas of the Common Marmoset
Web-accessible digital brain atlas of the common marmoset (Callithrix jacchus), prepared from histological sections of the marmoset brain using various staining techniques.
Assembly Guided by Optical Restriction Alignment
An algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. AGORA takes as input two data structures: OpMap ? an ordered list of fragment sizes representing the optical map; and Edges ? a list of de Bruijn graph edges with their corresponding sequences.
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies
A generic algorithm for scaffolding next-generation sequencing assemblies.
A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer.
Scaffolding Reads with Practical Algorithms
SCARPA: scaffolding reads with practical algorithms
A stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data.
Public research university with its main campus in Lawrence, Kansas, and several satellite campuses, research and educational centers, medical centers, and classes across the state of Kansas.
NCIR - Non-Canonical Interactions in RNA
This website provides several different RNA databases for researchers. The first, the Non-canonical Base Pair Database, provides access to all the RNA structures in which a particular rare base pair has been found. Another, the Prokaryotic 16S rRNA Signature Database, offers local sequence segments that are highly characteristic of particular organisms or groups of organisms. The third, the Prokaryotic 16S rRNA Signature Database II, provides generalized ribosomal RNA data.
Environmental Protection Agency Data Standards
U.S. Environmental Protection Agency Data Standards
EPA data standards are a means to promote the efficient sharing of environmental information among US EPA, states, Tribes, local governments, the private sector, and other information trading partners. EPA''s Data Standards are managed by the Data Standards Branch (DSB) within the Office of Environmental Information (OEI). DSB works closely with Federal agencies, states, tribes, and other information trading partners to develop data standards. By its nature the program is a part of EPA''s Enterprise-wide Data Architecture and EPA''s Quality Systems. The use of data standards across EPA''s multiple program offices provides consistently defined and formatted data elements and sets of data values which provide the public access to more meaningful data. The benefits of EPA''s data standards are those as are applicable to any standard: * They are developed by subject matter experts coming to common consensus on how to solve business problems so represents the best solution * They are harder to develop than non-standards, but are more economical in the long term because you can use the same code or presentation and publishing mechanisms to provide access to information * They enable transparency and understanding use of standards promotes common, clear meanings for data that is often reused * They enable access - the same well understood terms, codes, and data structures can be used for data retrieval * They encourage and enable reuse of data and software for multiple purposes * Mappings to standards allow comparisons even when data isn''t standardized solves the environmental interest problem between programs and states * They provide consistent results during data retrieval Standards also promote quality EPA''s goal is high quality information delivered in an efficient way to the people who need it.
The Earth Observing System Data and Information System (EOSDIS) is a major core capability within NASA''s Earth Science Data Systems Program. EOSDIS ingests, processes, archives and distributes data from a large number of Earth observing satellites. EOSDIS consists of a set of processing facilities and Earth Science Data Centers distributed across the United States and serves hundreds of thousands of users around the world, providing hundreds of millions of data files each year covering many Earth science disciplines. In order to serve the needs of a broad and diverse community of users, NASA''s Earth Science Data Systems Program is comprised of both Core and Community data system elements. Core data system elements reflect NASA''s responsibility for managing Earth science satellite mission data characterized by the continuity of research, access, and usability. The core comprises all the hardware, software, physical infrastructure, and intellectual capital NASA recognizes as necessary for performing its tasks in Earth science data system management. Community data system elements are those pieces or capabilities developed and deployed largely outside of NASA core elements and are characterized by their evolvability and innovation. Successful applicable elements can be infused into the core, thereby creating a vibrant and flexible, continuously evolving infrastructure. NASA''s Earth Science program was established to use the advanced technology of NASA to understand and protect our home planet by using our view from space to study the Earth system and improve prediction of Earth system change. To meet this challenge, NASA promotes the full and open sharing of all data with the research and applications communities, private industry, academia, and the general public. NASA was the first agency in the US, and the first space agency in the world, to couple policy and adequate system functionality to provide full and open access in a timely manner - that is, with no period of exclusive access to mission scientists - and at no cost. NASA made this decision after listening to the user community, and with the background of the then newly-formed US Global Change Research Program, and the International Earth Observing System partnerships. Other US agencies and international space agencies have since adopted similar open-access policies and practices. Since the adoption of the Earth Science Data Policy adoption in 1991, NASA''s Earth Science Division has developed policy implementation, practices, and nomenclature that mission science teams use to comply with policy tenets. Data System Standards NASA''s Earth Science Data Systems Groups anticipate that effective adoption of standards will play an increasingly vital role in the success of future science data systems. The Earth Science Data Systems Standards Process Group (SPG), a board composed of Earth Science Data Systems stakeholders, directs the process for both identification of appropriate standards and subsequent adoption for use by the Earth Science Data Systems stakeholders.
MBCluster.Seq: Model-Based Clustering for RNA-seq Data
Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data.
National Aeronautics and Space Administration Science
National Aeronautics Space Administration Science
NASA leads the nation on a great journey of discovery, seeking new knowledge and understanding of our planet Earth, our Sun and solar system, and the universe out to its farthest reaches and back to its earliest moments of existence. NASA's Science Mission Directorate (SMD) and the nation's science community use space observatories to conduct scientific studies of the Earth from space to visit and return samples from other bodies in the solar system, and to peer out into our Galaxy and beyond. NASA's science program seeks answers to profound questions that touch us all: * How and why are Earth's climate and the environment changing? * How and why does the Sun vary and affect Earth and the rest of the solar system? * How do planets and life originate? * How does the universe work, and what are its origin and destiny? * Are we alone? This is NASA's science vision: using the vantage point of space to achieve with the science community and our partners a deep scientific understanding of our planet, other planets and solar system bodies, the interplanetary environment, the Sun and its effects on the solar system, and the universe beyond. In so doing, we lay the intellectual foundation for the robotic and human expeditions of the future while meeting today's needs for scientific information to address national concerns, such as climate change and space weather. At every step we share the journey of scientific exploration with the public and partner with others to substantially improve science, technology, engineering and mathematics (STEM) education nationwide.
cortex_var - for variant and population assembly
A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for variants that distinguish one set of samples (eg phenotype=X, cases, parents, tumour) from another set of samples (eg phenotype=Y, controls, child, normal). cortex_var features * Variant discovery by de novo assembly - no reference genome required * Supports multicoloured de Bruijn graphs - have multiple samples loaded into the same graph in different colours, and find variants that distinguish them. * Capable of calling SNPs, indels, inversions, complex variants, small haplotypes * Extremely accurate variant calling - see our paper for base-pair-resolution validation of entire alleles (rather than just breakpoints) of SNPs, indels and complex variants by comparison with fully sequenced (and finished) fosmids - a level of validation beyond that demanded of any other variant caller we are aware of - currently cortex_var is the most accurate variant caller for indels and complex variants. * Capable of aligning a reference genome to a graph and using that to call variants * Support for comparing cases/controls or phenotyped strains * Typical memory use: 1 high coverage human in under 80Gb of RAM, 1000 yeasts in under 64Gb RAM, 10 humans in under 256 Gb RAM
IUPAC CPEP Subcommittee on Electronic Data Standards
International Union of Pure and Applied Chemistry Committee on Printed and Electronic Publications Subcommittee on Electronic Data Standards
IUPAC Committee on Printed and Electronic Publications Subcommittee on Electronic Data Standards
Joint Committee on Atomic and Molecular Physical Data
Joint Committee on Atomic Molecular Physical Data
An International Union of Pure and Applied Chemistry (IUPAC) subcommittee that deals with individual projects related to technique-specific data standards as well as generic issues. There are worrying gaps in the coverage of known chemistry by reference spectroscopic databases, which are unlikely to be filled by the activities of the commercial sector alone. The IS-DB offers the scientific community the opportunity to share their spectra and develop a vital resource for future generations. Such a collection of spectra will help to provide significant improvements in human health, new materials, environmental protection, sustainable development and educational progress. XML in Chemistry is a new IUPAC initiative to bring a degree of regulation to this important and rapidly expanding field. They aim to facilitate the validation of data dictionaries for various groups developing ontologies expressed in XML in the broad field of Chemistry. This will help to reduce duplication of effort around the world and allow development projects to build on the work previous groups concentrating on their own innovative goals rather than wasting time and effort re-inventing wheels. IUPAC encourages the submission of projects in all areas of chemistry relevant to its work. If you believe there is a need for a new scientific data standard in your field and wish to know more about how to form a limited term task group to get the standard developed please contact the subcommittee.
Data files for a high resolution three dimensional (3D) structure of the rat hippocampus reconstructed from histological sections. The data files (supplementary data for Ropireddy et al., Neurosci., 2012 Mar 15;205:91-111) are being shared on the Windows Live cloud space provided by Microsoft. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files. * Hippocampus Nissl Images: The high resolution histological Nissl images obtained at 16 micrometer inter-slice distance for the Long-Evans rat hippocampus can be downloaded or directly viewed in a browser. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files. * Hippocampus Layer Tracings: The seven hippocampus layers ''ML, ''GC'', ''HILUS'' in DG and ''LM'', ''RAD'', ''PC'', ''OR'' in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded. * Hippocampus VoxelDB: The 3D hippocampus reconstructed is volumetrically transformed into 16 micrometer sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file was split into three rar archive files. Please note that the three rar archive files should be downloaded and decompressed in a single directory in order to obtain the single voxel data file (Hippocampus-VoxelDB.txt). * 3D Surface Renderings: This is a rar archive file with a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene. * 3D Hippocampus Movie: This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites.
International Union of Pure and Applied Chemistry
International Union of Pure Applied Chemistry
IUPAC: International Union of Pure and Applied Chemistry
Recognized as the world authority on chemical nomenclature, terminology, standardized methods for measurement, atomic weights and many other critically evaluated data, this scientific, international, non-governmental and objective body addresses many global issues involving the chemical sciences. It serves to advance the worldwide aspects of the chemical sciences and to contribute to the application of chemistry in the service of Humankind. The Union sponsors major international meetings that range from specialized scientific symposia to CHEMRAWN meetings with societal impact. * Projects: IUPAC encourages the submission of projects in all areas of chemistry relevant to its work. * Publications: IUPAC publishes books, journals, electronic resources, and issues many reports in all areas of chemistry * Conferences: Each year IUPAC sponsors a large number of symposia that cover a wide range of specialized topics in chemistry. * Members and bodies: Chemists throughout the world are engaged on a voluntary basis in the scientific work of IUPAC.
PDBML: Protein Data Bank Markup Language
Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available.
DCC Dissemination of InFormal and Formal Useful Specifications and Experiences Standards Frameworks
DCC DIFFUSE Standards Frameworks is a browsable database with information on both standards and the organizations which sponsor them. Entries can currently be browsed either by category, alphabetically by title or by sponsoring body. Although no further work on DIFFUSE is planned, frameworks that were created remain an accessible and relevant resource. These include frameworks developed from existing publications or specifications as well as those developed specifically for the DIFFUSE project. The DCC DIFFUSE Standards Frameworks were developed in partnership with a number of organizations with the aim of presenting searchable frameworks of standards relevant to digital curation and preservation. DCC DIFFUSE Standards Frameworks provides information about sets of standards, used by specific domains, which enable curation and preservation of, and access to, data across all stages of the DCC Curation Lifecycle Model. The project maintains information about current and emerging standards and specifications which are used. Entries for individual standards and specifications include: * Links to database entries concerning sponsoring bodies * Links to the official documentation * Links to additional documentation such as user guides, tutorials, implementation profiles and registers, XML DTD or Schema * A description of the scope of the standard or specification * A description of the development of the standard or specification * Practical examples of the standard or specification in use Entries for sponsoring bodies include: * Contact details * Organizational objectives * Areas of activity * Membership details DCC DIFFUSE includes published standards which are included in frameworks used for curation and preservation of access to digital material, for example: * Standards ratified by national or international standards organizations or bodies * Standards developed by, or ratified by, professional organizations * Publicly available specifications developed by, or ratified by, a consortia or fora
The Digital Curation Centre (DCC) is a world-leading centre of expertise in digital information curation with a focus on building capacity, capability and skills for research data management across the UK''s higher education research community. The Digital Curation Centre provides expert advice and practical help to anyone in UK higher education and research wanting to store, manage, protect and share digital research data. The DCC provides access to a range of resources including our popular How-to Guides, case studies and online services. Our training programmes aim to equip researchers and data custodians with the skills they need to manage and share date effectively. We also provide consultancy and support with issues such as policy development and data management planning.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Software that aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts. The simulation pipeline models different steps as modules, each with a minimal set of parameters that can be estimated by experimental parameters. The first step is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are simulated by in silico library preparation and sequencing.
Restless Legs Syndrome Foundation Brain Bank
RLS Foundation Brain Bank Tissue Collection
The Restless Legs Syndrome Foundation established the RLS Foundation Brain Bank at the Harvard Brain Tissue Resource Center in 2000. A part of the Harvard University medical system, the Center (housed at McLean Hospital and commonly referred to as The Brain Bank) began in 1978 as a centralized resource for the collection and distribution of human brain specimens for research and diagnostic studies. Over the years, hundreds of scientists from the nation''s top research and medical centers have requested tissue from The Brain Bank for their investigations. Because most of these studies can be carried out on a very small amount of tissue, each donated brain provides a large number of samples for many researchers. For comparative purposes, brain tissue is needed from healthy individuals, as well as from those who had RLS. When possible, a small portion of frozen tissue taken from each brain donated to the RLS Foundation Collection will be kept available to serve as a resource for future genetic testing. The process of donating your brain to RLS research is broken down into 5 steps. To view these steps, please read our Process Steps in RLS Brain Tissue Collection. To read about the process of donating brain tissue for research, visit our Brain Bank Tissue Donation page.
Benchmarker for Evaluating the Effectiveness of RNA-Seq Software
Benchmarker for Evaluating the Effectiveness of RNA-Seq Software (BEERS)
A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl.
A database for phenotyping human single nucleotide polymorphisms (SNPs)that primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. They provide a detailed variant analysis using their tools such as: * TANGO to predict aggregation prone regions * WALTZ to predict amylogenic regions * LIMBO to predict hsp70 chaperone binding sites * FoldX to analyse the effect on structure stability Further, SNPeffect holds per-variant annotations on functional sites, structural features and post-translational modification. The meta-analysis tool enables scientists to carry out a large scale mining of SNPeffect data and visualize the results in a graph. It is now possible to submit custom single protein variants for a detailed phenotypic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Mutation Mapping Analysis Pipeline for Pooled RNA-seq
A software analysis pipeline for mapping mutations using RNA-seq that works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome. In addition, it compensates for the considerable amount of noise in RNA-seq datasets and simultaneously identifies the region where the mutation lies and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can utilize RNA-seq datasets from isolated tissues or whole organisms that are often generated for phenotypic analysis and gene network analysis in novel mutants.
Transcriptome Atlas Database for Mouse Embryo
Genome transcriptome atlas by RNA in situ hybridization on sagittal sections of developing mouse at embryonic day 14.5. Consists of searchable database of annotated images that can be interactively viewed. Anatomy based expression profiles for coding genes and microRNAs, tissue specific genes. Expression data generated by using human and murine tissue arrays.
GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options.
A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology.
SoyBase and the Soybean Breeder''s Toolbox
SoyBase and the Soybean Breeder''s Toolbox: Integrating Genetics and Molecular Biology for Soybean Researchers
Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome.
Software providing a Hadoop-based genomic structural variation (SV) caller for Illumina paired-end DNA sequencing data. It contains a full pipeline for aligning data in the form of FASTQ files using alignment pipelines that generate many possible mappings for every read, in the Hadoop framework. It then contains Hadoop jobs for computing genomic features from the alignments, and for calling insertion and deletion variants from those features.
SPEED- Searchable Prototype Experimental Evolutionary Database
Searchable Prototype Experimental Evolutionary Database
A new, relational database to be used for disease gene discovery, gene annotation and reporting, and searching for genes for future studies in model organisms. It incorporates 5 layers of information about the genes residing in it- the expression information from a gene (as reported in Unigene), the cytological location of the gene (if available), the ortholog of each gene in the available species within the database, the divergence information between species for each gene, and functional information as reported by OMIM and the Enzyme Commission (EC) reference number of genes. Tables have also been created to help record polymorphism data and functional information about specific changes within or between species, such as measured by Granthams distance (1) or model organism studies.
The Alfred P. Sloan Foundation is a philanthropic, not-for-profit grantmaking institution based in New York City. Established in 1934 by Alfred Pritchard Sloan Jr., then-President and Chief Executive Officer of the General Motors Corporation, the Foundation makes grants in support of original research and education in science, technology, engineering, mathematics and economic performance. * Promotes research in science, technology, engineering, mathematics, and economic performance * Offers two-year long research fellowships for early career researchers
A database of mRNA alternative splicing in the human genome. Within it, several modes of mRNA alternative splicing, such as exon skipping, alternative 5''-splicing sites, alternative 3''-splicing sites and mutually exclusive exons are computationally derived and extracted. Finally, for each type of alternative splicing, the flanking intronic sequences are collected and then exploited by motif discovery tools. The tissue-specific information and gene functionalities that correspond to the selected regions are also considered. The database provides a means of investigating alternative splicing and can be used for identifying alternative splicing - related motifs, such as the exonic splicing enhancer (ESE), the exonic splicing silencer (ESS) and other intronic splicing motifs.
comrad - Discovery of gene fusions using paired end RNA-Seq and WGSS
A novel algorithmic framework for the integrated analysis of RNA-Seq and Whole Genome Shotgun Sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as expressed or not expressed and accurate classification of the genomic or non-genomic origin of aberrant transcripts. A major benefit of Comrad is its ability to accurately identify aberrant transcripts and associated rearrangements using low coverage genome data. As a result, a Comrad analysis can be performed at a cost comparable to that of two RNA-Seq experiments, significantly lower than an analysis requiring high coverage genome data.
American Academy of Neurology Research Fellowship Program
AAN Foundation Research Fellowship Program
The Research Fellowship Program of the AAN Foundation is focused on one critical need that crosses all disciplines: the need to recruit and train clinical researchers in neurology. This program funds research in neurological sciences and offers clinical research fellowships and young investigators fellowships; professional development awards. The scientific and medical communities have called the shortage of investigators a crisis that will impact far more than the 50 million Americans currently suffering from a neurological disease. Recognizing this critical need for neurology research, the AAN Foundation has dedicated its grant making efforts toward investing in young researchers. NIH funding for neurologic research has remained the same for the last four years and competition for NIH funds has intensified. The increase in AAN''s fellowships have kept the dream alive for many of our young clinician-researchers. For several years in a row, AAN fellowship recipients have gone on to receive NIH funding at record levels. AAN fellowships are the first step to a broader base of support. The AAN Foundation has identified and developed several funding mechanisms to help achieve this goal: Opportunities * Clinical Research Training Fellowships are mentored awards designed for relatively new investigators in the early-to-mid stages of their training in clinical research methodology. * Clinician-Scientist Development Awards are three-year awards to support clinical research leading to discovery of new therapies in specific disease areas. * Practice Research Training Fellowships are two-year awards to support training in clinical practice research and are intended to create unique training opportunities, previously difficult to access for neurologists. * AHA/ASA/AANF Lawrence M. Brass M.D. Stroke Research Postdoctoral Fellowship A two year award offers support to a postdoctoral fellow with a preference for trainees in vascular neurology, stroke, neurocritical care, or outcomes research.
International Federation of Digital Seismograph Networks (FDSN) Web Service dataselect
International Federation of Digital Seismograph Networks Web Service dataselect
Web service to access seismic time-series data for specified channels and time ranges that are selected using SEED time series identifiers (network, station, location & channel). Data are returned in miniSEED format. This service is an implementation of the International Federation of Digital Seismograph Networks (FDSN) web service specification version 1.
The Brain Tumor Funders'' Collaborative is a partnership among five private philanthropic and advocacy organizations: American Brain Tumor Association, Brain Tumour Foundation of Canada, Children''s Brain Tumor Foundation, James S. McDonnell Foundation, and Sontag Foundation. This Collaborative promotes research directly relating to brain tumors and offers grants to professors and institutions to conduct research.
A single nucleotide variant caller optimised for identifying somatic variants in low cellularity cancer samples.
The Damon Runyon Cancer Research Foundation funds early career cancer researchers who have the energy, drive and creativity to become leading innovators in their fields. We identify the best young scientists in the nation and support them through four award programs: our Fellowship, Pediatric Cancer Fellowship, Clinical Investigator and Innovation Awards. Damon Runyon awards give young scientists: * Freedom to follow their own ideas, explore new paths and take risks * A prestigious endorsement that attracts further funding, advances their careers and accelerates their research * Guaranteed financial support, sparing them hours applying for grants Since 1946, Damon Runyon has invested more than $240 million in the best young minds in the nation. Our alumni include 11 Nobel Laureates and leaders of major cancer centers across the United States. Many of our 3,300 scientists have gone on to make breakthroughs in the way we prevent, diagnose and treat many forms of cancer. The Damon Runyon Cancer Research Foundation is a registered nonprofit with 501(c)(3) status.
Tool for calling indels in Tumor-Normal paired sample mode.
Software program to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255) that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and 255 means there is a probability of 1 ? 10(255/-10) that the genotypes are different between tumor and normal. This is consistent with how the SAM format reports such probabilities. It is currently available as source code via github or as a Debian APT package.
Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. Strelka2 germline and somatic small variant caller.
RNA-seq tool that uses the Dirichlet distribution and a transformation to identify genes that exhibit small within-condition and large between-condition variance.
Leona M. and Harry B. Helmsley Charitable Trust
Leona M. Harry B. Helmsley Charitable Trust
The Leona M. and Harry B. Helmsley Charitable Trust supports a broad spectrum of healthcare and medical research-based programs. The areas supported include Type 1 Diabetes, Digestive Diseases, Rural Healthcare, Cardiology, and a range of other programs and institutions.
The HFSP supports novel, innovative and interdisciplinary basic research focused on the complex mechanisms of living organisms; topics range from molecular and cellular approaches to systems and cognitive neuroscience. A clear emphasis is placed on novel collaborations that bring biologists together with scientists from fields such as physics, mathematics, chemistry, computer science and engineering to focus on problems at the frontier of the life sciences. The Trust provides funding for research regarding complex biological systems. It offers research grants, post doc fellowships, career development fellowships, and short- long- and cross- disciplinary fellowships. HFSP funding programs are strictly project-related and begin at the postdoctoral level. We have no support for PhD students nor for travel grants to scientific meetings. Nor do we provide sponsorship or funds to organizers of scientific meetings. Research Grants Research Grants are awarded for novel collaborations involving extensive collaboration among teams of scientists working in different countries and in different disciplines. Two types of grants are available: Young Investigators Grants and Program Grants. Postdoctoral Fellowships Postdoctoral Fellowships are available for scientists who wish to work in foreign laboratories, with emphasis on individuals early in their careers who wish to obtain training in a different field of research. Fellows who return to their home countries or move to an HFSP member country that is different from the Fellowship host country are eligible to apply for a Career Development Award. Long-Term Fellowships are for scientists with a Ph.D. degree in the life sciences who wish to broaden their experience through postdoctoral training abroad. Cross-Disciplinary Fellowships are intended for postdoctoral fellows with a Ph.D. degree in the physical sciences, chemistry, mathematics, engineering and computer sciences who wish to receive training in biology. Career Development Awards Career Development Awards are for former HFSP Long-Term or Cross-Disciplinary Fellows who return to their home country or move to an HFSP member country that is different from the host country of their HFSP Fellowship. The award provides support for initiating the fellows'' first independent laboratory., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The Kavli Foundation, based in Oxnard, California, is dedicated to advancing science for the benefit of humanity, promoting public understanding of scientific research, and supporting scientists and their work. The Foundation''s mission is implemented through an international program of research institutes, professorships, symposia and other initiatives in the fields of astrophysics, nanoscience, neuroscience and theoretical physics. The Foundation is also a founding partner of the Kavli Prizes, which recognize scientists for their seminal advances in astrophysics, nanoscience and neuroscience. To date, The Kavli Foundation has made grants to establish Kavli Institutes on the campuses of the University of California Santa Barbara, Stanford University, the California Institute of Technology, the University of Chicago, Columbia University, Yale University, Cornell University, the University of California San Diego, Delft University of Technology in the Netherlands, the Massachusetts Institute of Technology, Peking University, the Chinese Academy of Sciences, Harvard University, the University of Cambridge and the Norwegian University of Science and Technology. In addition to the Kavli Institutes, six Kavli professorships have been established: two at the University of California Santa Barbara, one at University of California Los Angeles, one at the University of California Irvine, one at Columbia University, and one at the California Institute of Technology. The Kavli Futures Symposia a series of high quality scientific symposia on topics of emerging importance in the fields of astrophysics, nanoscience and neuroscience. The Frontiers of Science symposia bring together some of the very best young scientists across many disciplines to share and discuss exciting advances and opportunities in their fields. Videos and feature pieces have been created for teachers and students. This includes video interviews with acclaimed researchers Eric Kandel, M.D. and Edvard and May-Britt Moser, a video introduction and panel discussion on neuroscience, feature stories, written science overview, institute profiles and other materials. The Kavli Foundation is a private foundation qualified under IRC Section 501 (c) (3).
The Albert and Mary Lasker Foundation and its programs are dedicated to the support of biomedical research toward conquering disease, improving human health and extending life. The Foundation''s mission is to foster the prevention and treatment of disease and disabilities by honoring excellence in basic and clinical science, by educating the public, and by advocating for support of medical research. The Lasker Awards The Lasker Foundation''s Awards Program recognizes the contributions of scientists, physicians, and public servants who have made major advances in the understanding, diagnosis, treatment, cure or prevention of human disease. Other Programs Although the Lasker Foundation is not a grant-giving organization, it does support select initiatives that raise awareness of medical discoveries and their benefits to human health, and that increase support for the medical science enterprise. These initiatives have included study groups, Congressional briefings, innovative web-based programs, educational forums, and scholarly studies.
In the belief that innovation and discovery occur in direct proportion to quality of training, the Life Sciences Research Foundation administers an international program of postdoctoral fellowships in all areas of the life sciences. Since it was established, in 1981, the Foundation has attracted support from a wide variety of sponsors. The mission of the Life Sciences Research Foundation (LSRF) is to establish partnerships between those who support research in the life sciences and academic institutions for their mutual benefit. The simple vehicle for achieving this partnership is a highly competitive postdoctoral fellowship program. Fellowship Eligibility. Three-year fellowships will be awarded on a competitive basis to graduates of medical and graduate schools in the biological sciences holding M.D., Ph.D., D.V.M. or D.D.S. degrees. Awards will be based solely on the quality of the individual applicant''s previous accomplishments, and on the merit of the proposal for postdoctoral research. Persons doing a second postdoc are eligible only if they are transferring to a different supervisor''s laboratory and embarking on a new project not connected to their previous research. All U.S. citizens are eligible to apply with no geographic restriction on the laboratory of their choice. Foreign applicants will be eligible for study in U.S. laboratories. LSRF fellows must carry out their research at nonprofit institutions. LSRF fellows may change projects, laboratories, and/or institutions during the fellowship as long as the eligibility rules listed here are not violated. A person holding a faculty appointment is not eligible to apply for an LSRF fellowship. The LSRF solicits monies from industry, foundations and individuals to support postdoctoral fellowships in the life sciences. Active solicitation of funds continues, for which we need the assistance of all concerned individuals. We recognize that discoveries and the application of innovations in biology for the public''s good will depend upon the training and support of the highest quality young scientists in the very best research environments. LSRF awards fellowships across the spectrum of the life sciences: biochemistry; cell, developmental, molecular, plant, structural, organismic population and evolutionary biology; endocrinology; immunology; microbiology; neurobiology; physiology; virology. Note: There may be no more than one LSRF fellow in any one laboratory at a time.
UnoSeq - Expression profiling with next generation sequencing without a reference genome
A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists.
An integrated database for the genomics of the Lepidoptera Spodoptera frugiperda. It provides access to expressed sequence tags (EST) from Spodoptera frugiperda. ESTs from five independent cDNA libraries, prepared from three different S. frugiperda tissues (hemocytes, midgut and fat body) and from the Sf9 cell line, are deposited in the database. These tissues were chosen because of their importance in biological processes such as immune response, development and plant/insect interaction. So far, the SPODOBASE contains 29,325 ESTs, which are cleaned and clustered into non-redundant sets (2294 clusters and 6103 singletons). The SPODOBASE is constructed in such a way that other ESTs from S. frugiperda or other species may be added. User can retrieve information using text searches, pre-formatted queries, query assistant or blast searches. Annotation is provided against NCBI, UNIPROT or Bombyx mori ESTs databases, and with GO-Slim vocabulary.
SPROUTS- Structural Prediction for Protein Folding Utility System
Structural Prediction for Protein Folding Utility System
SPROUTS is a database of predicted protein folding related data. It was designed to gather all the results from a study concerning the comparison between tools devoted to the prediction of stability changes upon point mutations. The second aim of this database is to offer simple and user-friendly tools to better visualize and analyze the results obtained. We are now able to propose three ways of visualization and analysis: the first one consists in getting raw Delta Delta G values in a table. The second one is a 2D graph representation of a computed stability score for each residue of a given sequence and for each tool. The last one is based on a Jmol applet (Jmol) with the possibility to represent the 3D structure of a given protein with symbols representing the information stored in the database. We assume that each visualization mode offers a different look on the data stored in the database and will suit to every scientists willing to query the database whether they are more used to handle 3D protein structure or 1D/2D sequence problems. Finally, the ultimate objective is to integrate these data and their analysis with other structural bioinformatic concepts in order to improve other methods that may be related to this concept. We are currently working at adding the information extracted from our other projects related to the prediction of protein folding nucleus in order to obtain a meta server devoted to the characterization of the folding core of proteins. As of today, this database has grown up and consists in more than 100 structures which have been computed for a total of around 16500 amino acids.
Transcripts in gRAPHs - Traph: A tool for transcript identification and quantification with RNA-Seq
A software tool for transcript identification and quantification with RNA-Seq. The method has a two-fold advantage: on the one hand, it translates the problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers; on the other hand, it is general enough to encompass many of the previous proposals under the least sum of squares model.
Java software which computes a series of quality control metrics for RNA-seq data and can compare sequencing quality across different samples or experiments to evaluate different experimental parameters. The input can be one or more BAM files, and the output consists of HTML reports and tab delimited files of metrics data.
Sting Report is a database of amino acid sequences, structures, functions, and parameters. It allows users to easily extract from the Blue Star Sting Database detailed but focused information about an individual amino acid, which belongs to a structure described in a PDB file. The extracted information is presented as a series of GIF images and a table, which are generated by Blue Star Sting modules and contain values of up to 125 sequence/structure/function descriptors/parameters. The HTML page resulting from a query on Sting Report, containing the GIF images and the table, is printable, and can also be composed and visualized at a computer platform with elementary configuration.
The M. J. Murdock Charitable Trust seeks to enrich the quality of life in the Pacific Northwest by providing grants and enrichment programs to non-profit organizations that seek to strengthen the region''s educational, spiritual, and cultural base in creative and sustainable ways. In addition to a special interest in education and scientific research, the Trust partners with a wide variety of organizations that serve the arts, public affairs, health and medicine, human services, leadership development, and persons with disabilities. Eligibility for scientific research grants is limited. Select public research universities and medical institutes located within the five-state region (Pacific Northwest: Alaska, Washington, Oregon, Idaho, Montana) are typically considered for funding. The Trust prefers requests for projects in the natural sciences where the main objective is the acquisition of new knowledge. However, requests for research in engineering and medicine are also eligible. Training students in conducting research is an important consideration.
The National Academy of Sciences (NAS) is a private, non-profit society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the public good. An Act of Congress, signed by President Abraham Lincoln in 1863 at the height of the Civil War, calls upon the NAS to provide independent advice to the government on matters related to science and technology. The National Research Council was created under the NAS charter in 1916 to extend the scope of the NAS in its advisory role. The National Academy of Engineering and the Institute of Medicine were organized under the NAS charter in 1964 and 1970, respectively. Since 1863, the nation''s leaders have turned to the National Academy of Sciences for advice on the scientific and technological issues that frequently affect policy decisions. Most of the institution''s science policy and technical work is conducted by the National Research Council (NRC), which was created expressly for this purpose and which provides a public service by working outside the framework of government to ensure independent advice on matters of science, technology, and medicine. The NRC enlists the nation''s top scientists, engineers, and other experts, who volunteer their time to study specific issues. The reports that result from their deliberations have led to some of the most significant and lasting improvements in the health, education, and welfare of all Americans. The Academy''s service to government has become so essential that Congress and the White House have issued legislation and executive orders over the years that reaffirm its unique role. NAS Award in the Neurosciences - Established by the Fidia Research Foundation Awarded in recognition of extraordinary contributions to progress in the fields of neuroscience, including neurochemistry, neurophysiology, neuropharmacology, developmental neuroscience, neuroanatomy, and behavioral and clinical neuroscience. The award is given every three years and will be awarded again in 2013
Subscribe to the National Academy of Sciences podcasts to learn more about scientists and their work, the latest in research, and key findings of National Research Council reports. * InterViews: InterViews provides first-person accounts of the lives and work of National Academy of Sciences members. In this series of one-on-one conversations, scientists talk about what inspired them to pursue the careers they chose and describe some of the most fascinating aspects of their research. * Science Sessions: The Proceedings of the National Academy of Sciences offers brief, 5-minute, nontechnical conversations with cutting-edge researchers, including members of the National Academy of Sciences, and policymakers as they discuss topics relevant to today''s scientific community. Learn the behind-the-scenes story of work published in PNAS, plus a broad range of scientific news about discoveries that affect the world around us. * News from the National Academies: Listen to the latest news conferences and public briefings on National Research Council and Institute of Medicine reports. * Sounds of Science: This informative and entertaining series puts a spotlight on the high-impact work of the National Research Council. Focusing on a wide range of critical issues in science, engineering, and medicine, these short episodes are a quick and easy way to tune in our key findings and important recommendations. * Cultural Programs: The Cultural Programs of the National Academy of Sciences presents public exhibitions, lectures, and other programs exploring the intersections of art, science, and culture. The podcast features audio recordings of past lectures and other events. * Engineering Innovation: This weekly podcast from the National Academy of Engineering highlights exciting developments in engineering and provides technical context to stories in the news. The 40-second episodes demonstrate how engineers are making an impactin energy, health, the environment, sports, and more.
The Arthur M. Sackler Colloquia address scientific topics of broad and current interest that cut across the boundaries of traditional disciplines. Each year, three to four colloquia are scheduled, typically two days in length and international in scope. Each colloquium is organized by a member of the NAS, often with the assistance of an organizing committee, and feature presentations by leading scientists in the field and discussions among one hundred or more researchers with an interest in the topic. Colloquia are held at the Arnold and Mabel Beckman Center in Irvine, California, unless noted otherwise. Papers resulting from Sackler colloquia are often published as a collection in Proceedings of the National Academy of Sciences (PNAS). Colloquium papers printed in from January 1, 1996 forward are available free online. PDFs of colloquium papers published in PNAS since 1997 are also available free online through the National Academies Press, (NAP) or reprints may be purchased through the NAP online bookstore. These colloquia are made possible by a generous gift from Jill Sackler in memory of her husband, Arthur M. Sackler.
This is the Sackler Colloquia YouTube channel. The Arthur M. Sackler Colloquia of the National Academy of Sciences address scientific topics of broad and current interest, cutting across the boundaries of traditional disciplines. Each year, several colloquia are scheduled, typically two days in length and international in scope. Each colloquium is organized by a member of the Academy, often with the assistance of an organizing committee, and feature presentations by leading scientists in the field and discussions with a hundred or more researchers with an interest in the topic. These colloquia are made possible by a generous gift from Jill Sackler, in memory of her husband, Arthur M. Sackler.
University of Kiel; Schleswig-Holstein; Germany
Regions Hospital Alzheimer's Research Center
A national research center that conducts research for Alzheimer's disease, stroke and other nervous system disorders. The mission of the Center is to improve the treatment and prevention of Alzheimer's disease and other neurologic disorders by advancing scientific knowledge through creative and collaborative research.
A brain bank which has obtained brains from individuals who suffered from some form of dementia. Clinical records and a family history are obtained for each donor in order to better understand each dementing illness and to work towards the improvement of diagnosing, treating, and preventing these diseases.
sRNAMap is a collection of sRNAs, regulators, and targets in microbial genomes. It provides valuable information on sRNAs, such as their secondary structure, expressed conditions, the expression profiles, the transcriptional start sites, and cross-links to other biological databases. Various textual and graphical interfaces were also designed and implemented to facilitate the data access in sRNAMap. Overall, this work presents an integrated database, namely sRNAMap, to collect the sRNA genes, the transcriptional regulators of sRNAs and the sRNA target genes by integrating a variety of biological databases and by surveying literature. It currently contains 397 sRNAs, 62 regulators/sRNAs and 60 sRNAs/targets in seventy microbial genomes.
A quick and simple pipeline for the analysis of transposable element (TE) insertions in (natural) populations using next generation sequencing. It calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions. PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences (fasta-file).
St. Louis University Alzheimer's Brain Bank
Saint Louis University Alzheimer’s Brain Bank
Saint Louis University Medical Center Alzheimer's Disease Brain Bank
A brain bank which provides brain tissue for interdisciplinary research in neurochemical, anatomical, epidemiological and clinical aspects of Alzheimer's disease. It provides brain tissue from Alzheimer's patients and healthy elderly brain donors to investigators who are helping further the understanding of Alzheimer's disease through research. It also gives family members of Alzheimer's patients the opportunity to obtain a confirmed diagnosis through brain autopsy. Through this program, families of individuals with either a clinical diagnosis, or those with suspected Alzheimer's disease, grant permission for a brain autopsy to be performed immediately after death.
A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available. RetroSeq is a two phase process, the first being the read pair discovery phase where discorandant mate pairs are detected and assigned to a TE class (Alu, SINE, LINE, etc.) by using either the annotated TE elements in the reference and/or aligned with Exonerate to the supplied library of viral sequences.
Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data.
Brain Atlas of the Common Marmoset Callithrix jacchus jacchus
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 1, 2019. The first brain atlas for the common marmoset to be made available since a printed atlas by Stephan, Baron and Schwerdtfeger published in 1980. It is a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. For the present atlas, an adult female was perfused through the heart with PBS followed by 10% formalin. The brain was then sent to Neuroscience Associates of Knoxville, TN, who prepared the brain for histological analysis. The brain was cut in the coronal (frontal) plane at 40 microns, every sixth section stained for Nissl granules with thionine and every seventh section stained for myelinated fibers with the Weil technique. The mounted sections were photographed at the NIH (Medical Arts and Photography Branch). The equipment used was a Nikon Multiphot optical bench with Zeiss Luminar 100 mm lens, and scanned with a Better Light 6100 scan back driven by Better Light Viewfinder 5.3 software. The final images were saved as arrays of 6000x8000 pixels in Adobe Photoshop 6.0. A scale in mm provided with these images permitted construction of the final Nissl atlas files with a horizontal and vertical scale. Some additional re-touching (brightness and contrast) was done with Adobe Photoshop Elements 2.0. The schematic (labeled) atlas plates were created from the Nissl images. The nomenclature came almost exclusively from brainmaps.org, where a rhesus monkey brain with structures labeled can be found. The labels for the MRI images were placed by M. R. Zametkin, under supervision from Dr. Newman.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 1, 2015. Consortium that aims to facilitate interdisciplinary collaborations to advance the understanding of pancreatic islet development and function, with the goal of developing innovative therapies to correct the loss of beta cell mass in diabetes, including cell reprogramming, regeneration and replacement. They are responsible for collaboratively generating the necessary reagents, mouse strains, antibodies, assays, protocols, technologies and validation assays that are beyond the scope of any single research effort. The scientific goals for the BCBC are to: * Use cues from pancreatic development to directly differentiate pancreatic beta cells and islets from stem / progenitor cells for use in cell-replacement therapies for diabetes, * Determine how to stimulate beta cell regeneration in the adult pancreas as a basis for improving beta cell mass in diabetic patients, * Determine how to reprogram progenitor / adult cells into pancreatic beta-cells both in-vitro and in-vivo as a mean for developing cell-replacement therapies for diabetes, and * Investigate the progression of human type-1 diabetes using patient-derived cells and tissues transplanted in humanized mouse models. Many of the BCBC investigator-initiated projects involve reagent-generating activities that will benefit the larger scientific community. The combination of programs and activities should accelerate the pace of major new discoveries and progress within the field of beta cell biology.
sparse linear modeling of RNA-Seq data for isoform discovery and abundance estimation
Software package that takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample. It is based on a linear model with a design matrix that models the sampling probability of RNA-Seq reads from different mRNA isoforms. To tackle the model unidentifiability issue, SLIDE uses a modified Lasso procedure for parameter estimation. Compared with deterministic isoform assembly algorithms (e.g., Cufflinks), SLIDE considers the stochastic aspects of RNA-Seq reads in exons from different isoforms and thus has increased power in detecting more novel isoforms. Another advantage of SLIDE is its flexibility of incorporating other transcriptomic data such as RACE, CAGE, and EST into its model to further increase isoform discovery accuracy. SLIDE can also work downstream of other RNA-Seq assembly algorithms to integrate newly discovered genes and exons. Besides isoform discovery, SLIDE sequentially uses the same linear model to estimate the abundance of discovered isoforms.
A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required.
A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases.
Distinctive Voices highlights innovations, discoveries, and emerging issues in an exciting and engaging public forum. Do you wonder how things work? What the future holds? If you are curious about the science and technology behind today''s hot topics, Distinctive Voices is for you! Spend an evening gaining insights on significant advances in medicine, biotechnology, energy, the environment, space exploration, and more. Learn from some of the best minds in the world including members of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicinein presentations geared to the general public. Events are held in Irvine, California and Woods Hole, Massachusetts, with videos of past Distinctive Voices events available on our YouTube channel. Distinctive Voices was created in 2006 as a program of the National Academy of Sciences Communication Initiative to increase science literacy. The live programming hosted at the Beckman Center in Irvine, California received major funding from the Arnold and Mabel Beckman Fund of the National Academy of Sciences and National Academy of Engineering. Additional support is provided by The Edward Lifesciences Fund and Pacific Life Foundation. The program at the Jonsson Center in Woods Hole, Massachusetts is supported by the Frank Press Fund of the National Academy of Sciences, the Thomas Lincoln Casey Fund of the National Academy of Sciences, the Arthur L. Day Fund of the National Academy of Sciences, and the Kellogg Fund of the Institute of Medicine.
An easy-to-use webserver that analyses the structural effects of your mutation of interest. The server allows you to submit a protein sequence and the mutation. Project HOPE will then collect and combine available information from a series of webservers and databases and will produce a mutation report complete with results, figures and animations. Where available Project HOPE will use the 3D structure of the protein but the server can also build a homology model if necessary. Other information sources include the Uniprot database and a series of DAS prediction servers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
It provides aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP. SRPDB assists the study of structure and function of signal recognition particles (SRP), and provides annotated SRP, RNA, and SRP protein sequences phylogenetically ordered and aligned. Included are representative RNA secondary structure diagrams where each base pair is proven by comparative sequence analysis, information about other proteins that play a role in SRP-mediated protein translocation, as well as structural information about components of SRP. Where possible, links to primary sources were established.
Non-profit organization providing the latest information about Restless Legs Syndrome (RLS). Its goals are to increase awareness, improve treatments, and through research, find a cure for RLS, a condition which severely affects the lives of millions of individuals. By educating healthcare providers about RLS symptoms, diagnosis, and treatment, the RLS Foundation helps patients receive the quality care they both need and deserve. In recent years the Foundation has provided information to healthcare providers at many exhibit meetings, including the American Academy of Neurology, the American College of Obstetricians and Gynecologists, and the American Academy of Nurse Practitioners. The Foundation continually strives to be the most reputable source of information on RLS. Their renowned Medical Advisory Board, composed of leading RLS experts from all over the world, has written several publications on the diagnosis and treatment of RLS. These include our comprehensive RLS Medical Bulletin, their patient brochure, and their brochures on special topics including concerns for surgery, depression, pregnancy, and children. The Foundation has taken giant strides to further RLS research, funding grants for 27 research projects. Among the most distinguished research projects the Foundation has put its resources behind is the ongoing Stanford Epidemiology Project. Although it is still underway, the Foundation recognizes that the highly anticipated results of the Stanford Epidemiology Project, including the creation of a world standard questionnaire used to accurately diagnose RLS, could be spectacular. Eventually this questionnaire may help researchers understand the health consequences of RLS and identify other conditions and diseases that are associated with or exacerbated by RLS. In addition, the RLS Foundation helped fund a study led by Dr. David Rye and deCODE Genetics in Iceland which recently announced the discovery of a gene for RLS.
PANTHER Evolutionary analysis of coding SNPs
Data analysis service that estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. To analyze many SNPs, download the PANTHER Coding Snp Analysis tool from the downloads page.
SSToSS - Sequence-Structural Templates of Single-member Superfamilies
SSToSS is a database that provides sequence-structural templates of single member protein domain superfamilies. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies. The templates are mapped on the sequence using different color code. Sequence-structural templates can be visualized within the three dimensional structure of the superfamily member by using molecular graphics program like CHIME or RASMOL Spatial orientation of the templates in terms of distance and angle is provided for each set of templates. Templates are also presented in a Dendrogram based on the inter motif spatial distances using PHYLIP. The sequences of the sequence-structural motif regions are also provided.In the SSToSS database we incorporated related sequence search option based on multiple-pattern matching combined with a search for statistically significant sequence similarity. The specificity of the search engine is increased by utilizing the inter-motif spacing and pair wise global alignment of the query and hits. SSToSS database also utilizes an alignment algorithm to provide multiple alignment of the similar sequences identified by multiple-motif based database search. It allows the user to obtain a control over the alignment by providing sequence-structure template regions as input to the alignment program to achieve a more structurally relevant and functionally useful alignment of protein sequences. The algorithm employs local conserved regions of the sequences to be fixed and aligns the rest based on normal progressive alignment. The chances of global misalignment are thereby reduced and the possibility of obtaining overall better alignment is increased. We also provide three dimensional model structures of the similar sequences identified by multiple-motif based similarity search as potential member of each SSToSS superfamily. 3D models are built using the program MODELLER based on the structure of superfamily member protein Currently, this database contains structural motifs for 613 single member superfamilies of PASS2 database.
Washington University Knight Alzheimer's Disease Research Center Multimedia Presentations
Videos of Knight ADRC related events for educational and informational purposes. A link to additional Center produced media is provided to access the Knight ADRC YouTube Channel. Videos are in HTML5 mp4 format and are available in 1080p or 4K resolution.
UMKC Neuroscience Brain Tissue Bank and Research Laboratory
UMKC Neuroscience Brain Tissue Bank & Research Laboratory
UMKC Neuroscience Brain Tissue Bank Research Laboratory
University of Missouri-Kansas City Neuroscience Brain Tissue Bank & Research Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The UMKC Neuroscience Brain Tissue Bank and Research Laboratory has been established to obtain, process, and distribute human brain tissue to qualified scientists and clinicians dedicated to neuroscience research. No other living organ approaches the human brain in complexity or capacity. Healthy, it astounds and inspires miracles. Diseased, it confounds and diminishes hope. The use of human brain tissue for research will provide insight into the anatomical and neurochemical aspects of diseased and non-diseased brains. While animal models are helpful and necessary in understanding disease, certain disorders can be more efficiently studied using human brain tissue. Also, modern research techniques are often best applied to human tissue. We also need samples of brain tissue that have not been affected by disease. They help us to compare a 'normal' brain with a diseased one. Also, we have a critical need for brain donations from relatives who have genetically inherited disorders. Tissue preparation consists of fresh quick-frozen tissue blocks or coronal slices (nitrogen vapor frozen; custom dissection of specific anatomic regions) or formalin-fixed coronal slices (custom dissection of specific anatomic regions).
STCDB - Signal Transduction Classification Database
STCDB is a database of signal transduction pathways and classifications. Signal transduction classifications are listed in signal transduction number order. Each entry provides a link to details of that signal transduction. Alternatively, if looking for a specific signal transduction used in the classification of the broad outline defined by the first two numbers are given as a tree representation. Each of these subclass entries is linked to a location where the category is subdivided to sub-subclasses. These in turn are linked to a list of recommended names for each signal transduction in the sub-subclass. The links are to a list of sub-subclasses which in turn list the signal transductions linked to separate files for each signal transduction.
rQuant: quantitative detection of alternative transcripts with RNA-Seq data
Software for quantitative detection of alternative transcripts with RNA-Seq data. The method, based on quadratic programming, estimates biases introduced by experimental settings and is thus a powerful tool to reveal and quantify novel (alternative) transcripts.
naturejobs.com - The premier science jobs recruitment website
Search for the widest range of science jobs with thousands of vacancies advertised globally on the site. Employers range from top international pharmaceutical and biotechnology companies to highly respected academic and government institutions. Job seekers can find a wide range of scientific career information and news as well as expert advice, all free to access. What''s more, employers can post jobs for free.
The editors of Scientific American regularly encounter perspectives on science and technology that we believe our readers would find thought-provoking, fascinating, debatable and challenging. The guest blog is a forum for such opinions. The views expressed belong to the author and are not necessarily shared by Scientific American.
StellaBase: Nematostella vactensis genomics database
StellaBase is a genomics database of Nematostella vectensis. It allows users to query the assembled Nematostella genome, a confirmed gene library, and a predicted genome using both keyword and homology based search functions. Data provided by these searches will elucidate gene family evolution in early animals. Unique research tools, including a Nematostella genetic stock library, a primer library, a literature repository and a gene expression library will provide support to the burgeoning Nematostella research community. Supported by: National Science Foundation (Grant No. 0212773 to JRF)
International job board for careers in academic, research, science and related professions in the UK, Europe, Australasia, Africa, America and Asia & Middle East. Launched by the University of Warwick, they have grown to become the top recruitment site in their sector, attracting the most qualified and talented people from the UK, Europe and across the world. Users may subscribe to Jobs by Email for vacancies in universities, colleges, research institutions, commercial and public sector, schools and charities. You may upload your CV to give yourself an advantage by making your CV visible to top employers now!
At New Scientist Jobs you can search our database for hundreds of Science and Technology jobs from across the globe. Registration is free and you can upload your resume, set up email job alerts, subscribe to RSS feeds and apply for Science and Technology jobs online. Employers can post jobs. We also work in partnership with the science and academic community to help them recruit the right Science and Technology candidates for their vacancies online.
The journal Science is one of the most prestigious and widely cited scientific journals in the world. Founded by Thomas Edison in 1880, Science has been publishing breaking news and seminal research for more than 125 years. Science Careers is the careers component of Science that scientists rely on for career information and job postings. Science Careers offers a wide variety of content designed to assist scientists of all disciplines, backgrounds and experience levels navigate their career path. This includes over 3,000 job listings that are updated daily, thousands of career advice articles written by the Science Careers editorial staff, graduate program information, meetings and event information, funding opportunities on GrantsNet, and a Career Forum where scientists can join a community of experts and peers engaging in real time discussions around career issues. For employers, Science Careers provides multiple platforms for recruiting scientists and extending their employment brand including job postings, banner advertisements, email and newsletters and sponsorships.
A leading online job board for scientists, Access-ScienceJobs.co.uk was initially launched in July 2005 from an existing scientific recruitment platform with the sole aim to provide employers a more cost-effective recruitment advertising solution, and for jobseekers a one-stop portal for finding their ideal scientific position. For Jobseekers We work with some of the UK''s leading recruitment agencies and direct employers to bring you an extensive selection of scientific jobs across all related industry sectors. Start your job search here or find a direct employer or agency in our companies a-z directory. Don''t miss our articles section, with useful careers, reviews and news articles written by respected recruitment and cv specialists. * Apply Online - fast, securely & professionally * Save your Job Alerts and manage them easily within your control panel * Create an effective CV Profile and let recruiters find you For Recruiters Looking to fill a job vacancy? We attract a wide range of Scientists within the UK through various forms of job distributions, networks and media coverage. * Post your Science related Jobs to our network of qualified Scientists * Edit, Repost & Expire your Job postings, anytime * Find professional Science Candidates when you CV Search online * Post your Career & News Articles to enhance your Employer brand * List your Profile for FREE in our Companies A-Z Directory
ScienceBlogs posts about Brain & Behavior.
TheScienceJobs.com: Vacancies in Academic Research and Management fields
An international career website for vacancies in academic, research and related professions in Science, Technology and Engineering. Announcements on upcoming conferences, workshops, training courses, etc are also available in the site. Job seekers can subscribe for email alerts on latest jobs/event postings. Employers can post jobs free of cost. The site can be viewed in about 35 world languages. About 500 jobs, fellowships and conference announcements are made available to the site every month. Users belong to more than 120 countries.
Annotating Sequence Ontology of Variants in Ruby
ASOoViR - Annotating Sequence Ontology of Variants in Ruby
A set of Ruby modules to annotate consequence terms, defined by the Sequence Ontology, of variants (SNP/SNVs, INDELs, SVs, CNAs) using Ensembl gene sets. Prior to annotation of variants an Ensembl gene set and reference coding sequences are loaded into memory from a database file, which can be downloaded or generated by the user from reference files. This allows rapid annotation of variants, making it suitable for annotation of whole genome scale calls. Annotation is performed on a transcript level basis, identifying associated sequence ontology terms for affected and nearby transcripts. Default output can be obtained on a gene basis, summarising the consequences for each gene affected, or on a transcript level basis. Output information is also readily customisable using user-generated scripts.
Tropical Botanic Garden and Research Institute
Jawaharlal Nehru Tropical Botanic Garden and Research Institute
Tropical Botanic Garden & Research Institute
Tropical Botanic Garden & Research Institute (TBGRI)
Tropical Botanic Garden Research Institute
Tropical Botanic Garden & Research Institute (TBGRI) is an autonomous Institute established by the Government of Kerala on 17th November 1979 and registered on 23rd November 1979 under the Travancore-Cochin Literary, Scientific and Charitable Societies Registration Act, 1955. It functions under the umbrella of the Science, Technology and Environment Department, Government of Kerala. Prof. A. Abraham, a visionary and a great Botanist, conceived the idea of establishing a Botanic Garden and Research Institute to study and conserve the rare and vanishing wild plant genetic resources of the country. Kinded by the spirit of his concept, the Government of Kerala took a far sighted decision resulting in the establishment of Tropical Botanic Garden & Research Institute (TBGRI) as an autonomous organization at Thiruvananthapuram, the capital City of Kerala. In the beginning, the Institute functioned at Thiruvananthapuram city on a rented duplex building. Thanks to the Forests & Wildlife Department, the land for establishment of the garden was allotted in 1983 and the foundation stone was laid on 27th May 1983 by the then Chief Minister, Shri K. Karunakaran. The then Education Minister, the late C. H. Mohammed Koya laid the foundation stone for the construction of the Visiting Scientists'' Guest House. The meeting was presided over by the Minister for Forests, Shri K. P. Noorudeen. With the recruitment of a skeletal scientific and technical staff, the Institute made a modest beginning. Biotechnology and Taxonomy were the two subjects considered to have immediate relevance to the development of the garden. While taxonomists prepared a flora of the garden documenting the native plant wealth before mass introduction and face lift which subsequently followed, the bio-technologists mass multiplied plants of commercial importance, especially orchids for cultivation and distribution to the public. The Royal Botanic Gardens (RBG), Kew played an exemplary and significant role in shaping and design of garden lay out of TBGRI in its formative stages. RBG, Kew not only lent its best men to train our technical staff in gardening and landscaping but also generously supplied books and living plants as gifts to enrich the respective collections. Undoubtedly, the continuing support of RBG, Kew is of special mention in the development of the Garden.
Biomedical Informatics Research Network - The Conduit for Biomedical Research
BIRN - The Conduit for Biomedical Research
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. National initiative to advance biomedical research through data sharing and online collaboration that provides data sharing infrastructure, software tools, strategies and advisory services. Groups may choose whether to share data internally or with external audiences. Hardware and data remain under control of individual user groups.
A Matlab toolbox for fMRI data analysis using Independent Component Analysis (ICA). It provides an integrated environment to manage, process and analyze fMRI data in a single framework so that users can complete the analysis without switching between software. In addition, it provides an interactive Matlab graphic user interface (GUI). All the necessary processes to apply ICA to fMRI data and review its results can be run from the graphic interface. The FMRLAB processing flow is straightforward. Custom analyses can be performed with Matlab scripts using the FMRLAB functions and data structure. Since fMRI data analysis is a complex enterprise, including digital image processing, statistical analysis and data visualization, an integrated framework combining processing elements is desired eagerly by users in the neuroimaging community. Recently, large number of software tools for data analysis and visualization have been developed for this purpose. However, most of these tools use model-based statistical methods which assume that the users know the hemodynamic response (HR) for their paradigm in advance and can specify a reasonable HR model. Often, however, accurate or reasonable response HR models are unavailable. An alternative data-driven method, infomax ICA (McKeown et al., 1998), does not require that an a priori HR model, instead deriving HRs of spatially independent components of the entire data set from the higher-order statistics of the data themselves. FMRLAB is a toolbox running under Matlab containing necessary components for data-driven fMRI data analysis using the highly reliable infomax ICA algorithm (Bell & Sejnowski, 1995), normalized (Amari, 1999), extended (Lee, Girolami and Sejnowski, 1999) and automated by Makeig et al. FMRLAB has been developed under Matlab 6.1 running on Red Hat Linux. FMRLAB Features * Graphic user interface * Flexible data importing * Interactive data plotting * Computationally efficient * Defined FMRI data structure * Independent component browser * Smooth, transparent component exporting and spatial normalization process * Interface with other software for further analysis or visualization. * SPM-style component plots (MIP, 2-D slice overlay and 3-D)
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 25,2022.NOTE:Blogs hosted on Nature Network have now moved to new homes in the Nature Publishing Group network of blogs. We' '''ve made these changes so that our bloggers can take advantage of improvements in blogging technology, and so that we can offer a better service to our colleagues and those who choose to blog with us. We are no longer hosting blogs on Nature Network itself. Nature Network Blogs are blogs posted by members of Nature Network, the professional networking website for scientists around the world. All features on Nature Network are completely free. All you need to do is create a profile.
Latest science news, comment, analysis and features from guardian.co.uk, the world''s leading liberal voice.
Software designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data.
A computational pipeline for analyzing bisulfite sequencing data.
LabSpaces.net is a social network for the scientific community designed to spread scientific news, maintain and create friendships, and harbor collaboration through the internet. The site serves as a web profile for researchers and labs, and is also a community for active communication in the sciences. Current Features LabSpaces offers a wide range of features that will attract and engage researchers. Some of these features include: A Science News feed updated daily with ~40 news articles, UserProfiles, Friends, A Messaging system, Groups, Lab Profiles with Lab members, Lab Picture albums, Collaboration Profiles, Science Discussion Forum, Publication Database, Protocol Database, and free Blogs upon request.
Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time.
University of Konstanz; Baden-Wurttemberg; Germany
University of Konstanz; Baden-W�rttemberg; Germany
University in the city of Konstanz in Baden-Württemberg, Germany. Its main campus was opened on the Gießberg in 1972 after being founded in 1966.
Annotation Visualization and Impact Analysis
An interactive web-based tool to explore and interpret large sets of genomic variations (single nucleotide variations and insertion/deletions) to help guide and summarize genomic experiments. The tool is based on coupling a comprehensive annotation pipeline with a flexible visualization method. They leveraged the ANNOVAR (Wang et. al, 2010) framework for assigning functional impact to genomic variations by extending its list of reference annotation databases (RefSeq, UCSC, SIFT, Polyphen etc.) with additional in-house developed sources (Non-B DB, PolyBrowse). Further, because many users also have their own annotation sources, they have added the ability to supply their own files as well. The results can be obtained in tabular format or as tracks in whole genome circular views generated by the Circos application (Krzywinski et. al, 2009). Users can also select different sets of pre-computed tracks, including whole genome distributions of different genomic features (genes, exons, repeats), as well as variations analysis tracks for the 69 CGI public genomes for reference.
A webtool which helps in characterizing Single Nucleotide Polymorphisms (SNPs) that are located in the vicinity of an SNP of interest (start SNP). Along with the computation of the maximal Linkage Disequilibrium (LD) region around the start SNP. CandiSNPer provides additional information with respect to the molecular consequences of the SNPs and the genes located in the LD region.
chaos - Annotation analysis and visualization of variants from high-throughput sequencing experiments
A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization.
Comparison of variants and functional annotation
COVA - Comparison of variants and functional annotation
A variant annotation and comparison tool for next-generation sequencing. It annotates the effects of variants on genes and compares those among multiple samples, which helps to pinpoint causal variation(s) relating to phenotype.
ScienceBlogs posts about Medicine & Health.
An R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A database for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Version 2.0 is based on the Gencode release 9 / Ensembl version 64 and includes a total of 87,347,043 nsSNVs and 2,270,742 essential splice site SNVs. It compiles prediction scores from six prediction algorithms (SIFT, Polyphen2, LRT, MutationTaster, MutationAssessor and FATHMM), three conservation scores (PhyloP, GERP++ and SiPhy) and other related information including allele frequencies observed in the 1000 Genomes Project phase 1 data and the NHLBI Exome Sequencing Project, various gene IDs from different databases, functional descriptions of genes, gene expression and gene interaction information, etc. Some dbNSFP contents (may not be up-to-date though) can also be accessed through variant tools, ANNOVAR, KGGSeq, UCSC Genome Browser''s Variant Annotation Integrator, Ensembl Variant Effect Predictor and HGMD.
A software package and a pipeline for identifying causal mutations for rare congenital diseases by next-generation sequencing. Features * one-stop solution for identifying causal mutations of rare genetic diseases * detect wide-spctrum variants, including medium and large sized indels, and tandem repeats * annotate and filter variants * prioritize candidate variants
Software tool set for calculating the biological consequences of genomic variations. The suite of perl modules compares genomic variations with reference genome annotations and generates the possible effects each variant may have on the transcripts it overlaps. It evaluates each variation/transcript combination and describes the effects in the mRNA, CDS and protein sequence contexts. It provides details of the sequence and position of the change within the transcript / protein as well as Sequence Ontology terms to classify its consequences.
Software tool to help study pre-mRNA splicing and to better understand intronic and exonic mutations leading to splicing defects. To calculate the consensus values of potential splice sites and search for branch points, new algorithms were developed. Furthermore, they have integrated all available matrices to identify exonic and intronic motifs, as well as new matrices to identify hnRNP A1, Tra2-? and 9G8.
A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A ?Model_Annotations? field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species.
A tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. Genomic Annotations, Protein Annotations, and Cancer Annotations are aggregated from many resources. A standalone version of Oncotator is being developed.
A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest.
SNPdat - A Simple High Throughput Analysis Tool for Annotating SNPs
A simple and easy to use high through-put analysis tool which can provide comprehensive annotation of both novel and known single nucleotide polymorphisms (SNPs) for any organism with a draft sequence and annotation. SNPdat makes possible analyses involving non-model organisms that are not supported by the vast majority of SNP annotation tools currently available. It is especially intended for use by researchers with limited bioinformatic experience.
ORMAN : Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms
A software tool for resolving multi-mappings within an RNA-Seq SAM file.
Software package containing tools to process bam files in order to evaluate and analyze de novo assembly / assemblers and identify Structural Variations suspicious genomics regions. The tools have been already successfully applied in several de novo and resequencing projects. This package contains two tools: # FRCbam: tool to compute Feature Response Curves in order to validate and rank assemblies and assemblers # FindTranslocations: tool to identify chromosomal rearrangements using Mate Pairs
SNPdbe - nsSNP database of functional effects
A database to fill the annotation gap left by the high cost of experimental testing for functional significance of protein variants. It joins related bits of knowledge, currently distributed throughout various databases, into a consistent, easily accessible, and updatable resource. It currently covers over 155,000 protein sequences which come from more than 2,600 organisms. Overall more than one million single amino acid substitutions (SAASs) are referenced consisting of natural variants, SAASs from mutagenesis experiments and sequencing conflicts. SNPdbe offers the following pieces of information (if available) on each SAAS: * Experimentally derived functional and structural impact * Predicted functional effect * Associated disease * Average heterozygosity * Experimental evidence of the nsSNP * Evolutionary conservation of wildtype and mutant amino acid * Link-outs to external databases A convenient webinterface to query SAASs on the following levels is offered: * Protein and gene identifiers and keywords * Disease keywords * Protein sequence on different sequence identity thresholds * Variant identifier (dbSNP rs, SwissVar, PMD) or specific mutant like XposY and specified sequence They offer the possibility to submit protein sequences along with experimentally substantiated mutations in order to predict their functional effect and inclusion into our database.
SnpEff - Genetic variant annotation and effect prediction toolbox
Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs.
A web server for functional annotation of novel and publicly known genetic variants that was developed to assess the potential significance of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models in order to identify the phenotypically important variants. A broader range of variations have been incorporated such as insertions / deletions, block substitutions, IUPAC codes submission and region-based analysis, expanding the query size limit, and most importantly including additional categories for the assessment of functional impact. SNPnexus provides a comprehensive set of annotations for genomic variation data by characterizing related functional consequences at the transcriptome/proteome levels of seven major annotation systems with in-depth analysis of potential deleterious effects, inferring physical and cytogenetic mapping, reporting information on HapMap genotype/allele data, finding overlaps with potential regulatory elements, structural variations and conserved elements, and retrieving links with previously reported genetic disease studies.
SPOT - Biological prioritization after a SNP association study
A web-based tool for using biological databases to prioritize single nucleotide polymorphisms (SNPs) after a genome-wide association study (GWAS). The site allows users to upload a list of SNPs and GWAS P-values and returns a prioritized list of SNPs using the GIN method. Users can specify candidate genes or genomic regions with custom levels of prioritization. The results can be downloaded or viewed in the browser where users can interactively explore the details of each SNP, including graphical representations of the genomic information network (GIN) method. For investigators interested in incorporating biological databases into a post-GWAS SNP selection strategy, the SPOT web tool is an easily implemented and flexible solution.
Analysis tool that can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. It not only reports the obvious functional effects in the coding regions but also analyzes noncoding SNVs situated both within the gene and in the neighborhood that could affect different regulatory motifs, splicing signals, and other structural elements. These include: Jaspar regulatory motifs, miRNA targets, splice sites, exonic splicing silencers, calculations of selective pressures on the particular polymorphic positions, etc. Software analysis pipelines used in the analysis of NGS data are highly modular, heterogeneous, and rapidly evolving. VARIANT can easily be incorporated into a NGS resequencing pipeline either as a CLI or invoked a webservice. It inputs data directly from the most widely used programs for SNV detection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
From the editors and reporters of Scientific American, this blog delivers commentary, opinion and analysis on the latest developments in science and technology and their influence on society and policy. From reasoned arguments and cultural critiques to personal and skeptical takes on interesting science news, you''ll find a wide range of scientifically relevant insights here.
A database for comparative genomics of group A and group B streptococci. It is based on OGeR (Open Genome Resource for comparative analysis of prokaryotic genomes) and includes all sequenced GAS and GBS strains and serovars available as EMBL genome review or NCBI GenBank files. Strepto-DB identifies the homologous proteins deduced from the genomes of interest. It allows for the elucidation of the GAS and GBS core- and pan-genomes via genome-wide comparisons. Moreover, an intergenic region analysis tool provides alignments and predictions for transcription factor binding sites in the non-coding sequences. An interactive genome browser visualizes functional annotations. Strepto-DB (http://oger.tu-bs.de/strepto_db) was created by the use of OGeR, the Open Genome Resource for comparative analysis of prokaryotic genomes. OGeR is a newly developed open source database and tool platform for the web-based storage, distribution, visualization and comparison of prokaryotic genome data. The system automatically creates the dedicated relational database and web interface and imports an arbitrary number of genomes derived from standardized genome files.
From climate change to intelligent design, HIV/AIDS to stem cells, science education to space exploration, science is figuring prominently in our discussions of politics, religion, philosophy, business and the arts. New insights and discoveries in neuroscience, theoretical physics and genetics are revolutionizing our understanding of who are are, where we come from and where we''re heading. Launched in January 2006, ScienceBlogs is a portal to this global dialogue, a digital science salon featuring the leading bloggers from a wide array of scientific disciplines. Today, ScienceBlogs is the largest online community dedicated to science. We believe in providing our bloggers with the freedom to exercise their own editorial and creative instincts. We do not edit their work and we do not tell them what to write about. We have selected our 80+ bloggers based on their originality, insight, talent, and dedication and how we think they would contribute to the discussion at ScienceBlogs. Our role, as we see it, is to create and continue to improve this forum for discussion, and to ensure that the rich dialogue that takes place at ScienceBlogs resonates outside the blogosphere. ScienceBlogs is always interested in bringing new contributors into our community. If you''re interested in blogging with us, please fill out our application, and we''ll be in touch.
Software to estimate purity / ploidy, and from that compute absolute copy-number and mutation multiplicities. When DNA is extracted from an admixed population of cancer and normal cells, the information on absolute copy number per cancer cell is lost in the mixing. The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles.
Expanding Ploidy and Allele Frequency on Nested Subpopulations
Software that characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results.
HIVCD - Informatics tool for contamination screening in the HIV sequencing lab
Informatics software tool to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage.
A blog that explores local science, nature, and environment issues & experiences in Northern California. A collaborative effort, our many writers come from local museums, zoos, science centers and research institutions, as well as KQED''s TV and Radio producers covering stories in the field.
A computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner. This process is composed of a subtractive phase in which input reads are subtracted by alignment to human reference sequences, and an analytic phase in which the remaining reads are aligned to microbial reference sequences (viral, fungal, bacterial, archaeal) and de novo assembled. PathSeq is currently available in a cloud computing environment via Amazon Web Services The typical approach one would take to pathogen discovery with PathSeq: RNA or DNA is extracted from the tissue of interest and sequencing libraries are constructed to be run on the next-generation DNA sequencing platform of choice. The resulting sequence data is run through the PathSeq pipeline in a cloud computing environment. PathSeq reports potential microbes in the sequence data as well as the complete set of reads that could not be identified as human or microbial sequences.
A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets.
Software tool for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. Specifically, it detects virus infection, co-infection with multiple viruses, virus integration sites in host genomes, as well as mutations in the virus genomes. It also facilitates virus discovery by reporting novel contigs, long sequences assembled from short reads that map neither to the host genome nor to the genomes of known viruses. VirusFinder 2 works with both paired-end and single-end data, unlike the previous 1.x versions that accepted only paired-end reads. The types of NGS data that VirusFinder 2 can deal with include whole genome sequencing (WGS), whole transcriptome sequencing (RNA-Seq), targeted sequencing data such as whole exome sequencing (WES) and ultra-deep amplicon sequencing.
An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input.
Software for reconstructing haplotypes from next-generation sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Science news and technology updates from Scientific American.
qure - software for viral quasispecies reconstruction from next-gen seq. data
A software program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) next-generation sequencing (NGS) data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral variants overlapping across the genome division. QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions.
An award-winning multimedia science and environment series created by KQED, San Francisco, the public media station serving Northern California. Launched in February 2007, by the end of its fourth season (in September 2010), QUEST had reached approximately 36 million viewers and listeners through its traditional TV and radio broadcasts and its growing Web audience. QUEST''s ultimate aim is to raise science literacy in the San Francisco Bay Area and beyond, inspiring audiences to discover and explore science and environment issues for themselves. Every season, KQED''s QUEST produces: * half-hour television episodes episodes that air weekly, exploring the cutting-edge work of Northern California scientists and researchers (QUEST airs Wednesdays 7:30pm on KQED Public Television 9); * weekly radio reports covering urban environmental issues which often include multimedia slide shows, and interactive online maps (QUEST airs Mondays 6:30am and 8:30am on KQED Public Radio 88.5 FM); * Educational resources, for use by formal and informal educators; QUEST also provides professional development for science educators to support multimedia and technology integration in science classrooms and programs; * 20 six-minute stories for its new web only series, Science on the SPOT, which takes a fresh, fast and curious look at science with stories about albino redwoods, the science of fog and banana slugs, to name a few. (launched in 2010); * A daily science blog written by Northern California scientists, QUEST producers and science enthusiasts; * Exclusive web extras, featuring extended interviews with scientists; Flickr photos, and science hikes. Formal and informal Educators who would like to become involved withthe educational outreach program should contact: ScienceEd (at) kqed.org.
ShoRAH - Short Reads Assembly into Haplotypes
A software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.
A software tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. It combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. V-Phaser can reliably detect rare variants in diverse populations that occur at frequencies of <1%. V-Phaser 2 is a complete rewrite of the original V-Phaser. It contains a new model for length polymorphisms (indels) and incorporates paired end read information in its phasing model. The data access and probability computation sections of the code have also been highly optimized, resulting in substantial improvements in running time and memory usage.
Nonnegativity and Sparsity constrained Maximum A Posteriori
NSMAP: A Method for Spliced Isoforms Identification and Quantification from RNA-Seq
Software designed to identify and quantify isoforms from RNA-seq by incorporating a sparsity term into expression level estimation to enable isoform structure prediction and expression estimation simultaneously.
University of Eastern Finland at Kuopio; Kuopio; Finland
University of Eastern Finland was formed through merger of two formerly independent universities, the University of Joensuu and the University of Kuopio.Public University of Eastern Finland Kuopio Campus is located in the Savilahti area.
Hi. I''m genegeek (aka Catherine Anderson). I realized during my PostDoc that I preferred learning and explaining new results to doing science so I started a non-traditional career of teaching and outreach. I''ll be using this space to explore public perception of genetics and other cool molecular biology stuff. I hope to add to the great discussions re: new science discoveries and general understanding of genetics. I''ve been running an outreach program and enjoy talking to non-experts about their opinions and understanding. I hope my enthusiasm for the topics can come through the screen. My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.
Science 3.0 - the community for the advancement of science
Science 3.0 is a community for the advancement of online science. Science 3.0 is constantly trying to use and develop web 2.0 tools to make online science more efficient. Community projects include FigShare, COASPedia, ScienceSeeker, and Science 3.0 Open Data. Science 3.0 combines the hypothesis based inquiry of laboratory science with the methods of social science research to understand and improve the use of new human networks made possible by today''s digital connectivity. This website is a community where those interested in the advancement of research can share ideas, tools and build connections. This website is designed to be a neutral, impartial community where people can discuss the pros and cons of each application so that they can be developed in the most efficient manner. The site is not designed to be a place where all science researchers from all disciplines meet and share results. The site is for those who wish to develop science online, or have an interest in science online. We do not have the answers to all of the problems associated with open access and bringing science to the masses. We are the place where like minded people can collaborate to generate these answers.
The Science Blogs section covers every science post from every large English-speaking science blog as they are published. You can click to see archives of specific bloggers or sites and view whats trending in science blogging right now. The S3.0 Blogregator is a great way to view all the blogs covering specifically ''Online Science'' as they are updated. The team of Science 3.0 bloggers who blog predominantly about ''Science Online'' and ''Open Access'' are also available. You can start your own blog on the site which we will help you set up free of charge.
Read the latest science news and views from Oxford University in the Oxford Science Blog. The blog gives you the inside track on science at Oxford University: the projects, the people and what''s happening behind the scenes. Curated by Pete Wilton, science writer and OU Press Officer.
Sciblogs brings together the best science bloggers in the country (New Zealand) on one website, creating a hub for scientific analysis and discussion and facilitating reader interaction. The website is for scientists who want to reach out to a general audience to explain their science and how it relates to society. Some Sciblog contributors spend most of their time in the lab or buried in research. Others are authors or entrepreneurs. All of them know what they are talking about and have an interest in engaging in discussion on the big science-related issues facing society. Over time more bloggers will be added to the Sciblogs roster. If you would like to inquire about hosting a blog on Sciblogs contact us. You can easily keep an eye on new Sciblogs posts by subscribing via RSS or email or by following our Twitter feed. Alternatively, there is a Facebook page as well as a Facebook group feel free to join in! Categories: * Science * Agriculture * Technology * Health and Medicine * Environment and Ecology * Science and Society
The New York Times Well is a blog by Tara Parker-Pope on the latest medical research and societal trends affecting your health. Healthy living doesn''t happen at the doctor''s office. The road to better health is paved with the small decisions we make every day. It''s about the choices we make when we buy groceries, drive our cars and hang out with our kids. Join columnist Tara Parker-Pope as she sifts through medical research and expert opinions for practical advice to help readers take control of their health and live well every day.
SciLogs - The daily storyline of science
The SciLogs combine the strengths of both science culture and the medium blog. They provide scientists and lay people with the opportunity to interact in interdisciplinary discussions about science in all its facets: research, applications, ethics, values, politics etc. Good Science is transparent and provides us with new knowledge about the world and ourselves. As an important part of our culture and society, science is never isolated. Informing about new results and recent developments as well as the dialogue with the public are characteristics of good science. Good blogs are personalized, authentic and active. Oftentimes, they provide unique perspectives. Blog posts are serious invitations for dialogue, readers are potential partners, invited to comment and ask the bloggers questions. The SciLogs are not a closed community. Every user is invited to comment, and new bloggers are welcome, too. Please submit your blog or blog idea to blog@scilogs.de - and we will check if we fit together.
University of KwaZulu-Natal; Durban; South Africa
University with five campuses in the province of KwaZulu-Natal in South Africa. It was formed on 1 January 2004 after the merger between the University of Natal and the University of Durban-Westville.
Search Tool for the Retrieval of Interacting Genes/Proteins
STRING - Known and Predicted Protein-Protein Interactions
Database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations and are derived from four sources: Genomic Context, High-throughput experiments, (Conserved) Coexpression, and previous knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently covers 5''214''234 proteins from 1133 organisms. (2013)
FlowSim - a simulation pipeline for pyrosequencing data
A suite of tools for simulating the 454 pyrosequencing process. It is based on the characteristics of real 454 data, and attempts to model the known aspects of the process.
Clinical and Translational Science Awards Connect
CTSAconnect: A Linked Open Data approach to represent clinical and research expertise activities and resources
THIS RESOURCE IS NO LONGER IS SERVICE. Documented on December 5th, 2022. Semantic framework to integrate information about research activities, clinical activities, and scientific resources to facilitate the production and consumption of Linked Open Data about investigators, physicians, biomedical research resources, services, and clinical activities. The goal is to enable software to consume data from multiple sources and allow the broadest possible representation of researchers' ''' and clinicians' ''' activities and research products. Current research tracking and networking systems rely largely on publications, but clinical encounters, reagents, techniques, specimens, model organisms, etc., are equally valuable for representing expertise. CTSAConnect will provide linkage between semantic representations of a wide range of clinical and research data using controlled vocabularies mapped to the Unified Medical Language System (UMLS) as a bridge between the two subject areas. The data sources include data from Medicaid, hospital billing systems, CTSAShareCenter, and other CTSA resource data, eagle-i and VIVO. It allows institutions to leverage existing tools and data sources by making the information they contain more discoverable and easier to integrate. For instance, with the ISF, researchers can be characterized by organizational affiliations, grant and project participation, research resources that they have generated, and publications that they have (co)-authored. Clinicians can be characterized by training and credentials, by clinical research topic, and by the kinds of procedures and specialization that can be inferred from encounter data. LOD refers to data that has been given a specific Uniform Resource Identifier (URI), for the purpose of sharing and linking data and information on the Semantic Web. While a large amount of data is published as LOD, there remains a significant gap in the representation of research resources and clinical expertise. Researchers can be characterized by the organization to which they belong, the grants and research in which they have participated, the research topics and research resources (reagents, biospecimens, animal models) they have generated, as well as the publications they have (co)-authored. Clinician profiles on the other hand, can be defined by their credentials, clinical research topics, and the kinds of procedures and specialization that can be inferred from clinical encounter data. They believe that integrating and relating this diversity of information sources and platforms requires addressing the overlap between research resources and the attributes and activities of researchers and clinicians. CTSAconnect aims to promote integration and discovery of research activities, resources, and clinical expertise. To this end, they will publish their ontologies and LOD via their website, which will also illustrate repeatable methods and examples of how to extract, consume, and utilize this valuable new LOD using freely available tools like VIVO, eagle-i, and Google APIs. CTSAconnect is a collaboration between Oregon Health & Science University, Stony Brook University, Cornell University, Harvard University, University at Buffalo, and the University of Florida, and leverages the work of eagle-i (eagle-i.net), VIVO (vivoweb.org), and ShareCenter (ctsasharecenter.org).
SimRare - A program to generate and analyze sequence-based data for rare variant association studies of quantitative and qualitative traits
A stand-alone executable software with user-friendly graphical interface implemented in Python/C++ for rare variant association studies. It is designed as a unified simulation framework to provide an unbiased and easy manner to evaluate association methods, including novel methods, under a broad range of choice of biological contexts. It consists of three modules, variant data simulator, genotype/phenotype generator and association method evaluator. SimRare generates variant data for gene regions using forward-time simulation which incorporates realistic population demographic and evolutionary scenarios. For phenotype data it is capable of generating both case-control and quantitative traits. The phenotypic effects of variants can be detrimental, protective or non-causal. SimRare has a graphical user interface which allows for easy entry of genetic and phenotypic parameters. Simulated data can be written into external files in a standard format. For novel association method implemented in R it can be imported into SimRare, which has been equipped built in functions to evaluate performance of new method and visually compare it with currently available ones in an unbiased manner.
Provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
MiTie: Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples
Software framework for simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples. They define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data, and show how to find the optimal solution using Mixed Integer Programming. MiTie can a) take advantage of known transcripts, b) reconstruct and quantify transcripts simultaneously in multiple samples, as well as c) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction.
Science, Technology, Education, Government, and anti-woo. Cassandra had the gift of seeing the future, but the curse of having no one believe her.
BioPortfolio is a leading news, information and knowledge resource covering the global life science industries impacted on by biotechnology. The site aims to provide the lay person, the researcher and the management executive with a single location to source core information on specific bio-related topics, to collate relevant data associated with each topic and to point the user to relevant knowledge resources. We publish up to the minute news (see biotechnology news categories) and regularly update content across our information databases. BioPortfolio promotes and sells market research and management reports from 30+ publishers. In addition our unique corporate database lists 40,000+ companies and organizations. BioPortfolio aims to bring together high quality information about marketed drugs - medication and relevant clinical trials, research papers and recent news from PubMed, ClinicalTrials.gov, and DailyMed. Additionally, resources include biotech, pharma and medical job listings. When the BioPortfolio site was launched in February 1997 the company aimed to provide a global free-to-use resource with defined aims and mission statement: to meet the increasing demand of consumers, scientists, investors, commerce and government for timely, accurate and commercially useful information and intelligence on biotechnology companies, technologies and products world-wide. Driven by the success of the site we have made major investments and improvements to enhance our content and to apply the latest web technologies to improve functionality and site utility. We believe this unique depth and breadth of content is supporting individuals, organizations and policy-makers to become more aware of the role of biotechnology on the global economy. With 97,000 users visiting the site more than once per month we are confident that we are providing information our users need. We hope you the users find the site of value for both personal and professional reasons. Please enjoy this free resource and email your comments!
GeneTalk - The Professional Network and Online Tool for Geneticists
A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. VCFs (Variant Call Formats) are preprocessed and annotated, you can filter them, access all databases and provide your expertise to the community by creating annotations.
An algorithm for the simultaneous isoform reconstruction and abundance estimation. In addition to modelling novel isoforms, multi-mapped reads and read duplicates, this method takes into account the possible presence of unspliced pre-mRNA and intron retention. iReckon only requires a set of transcription start and end sites, but can use known full isoforms to improve sensitivity. Starting from the set of nearly all possible isoforms, iReckon uses a regularized EM algorithm to determine those actually present in the sequenced sample, together with their abundances. iReckon is multi-threaded to increase efficiency in all its time consuming steps.
NIH established expectations for sharing data obtained through NIH-funded genome-wide association studies (GWAS) with the implementation of the GWAS Policy. Information and resources related to the GWAS Policy can be found on this website.
Science Navigation Group - Services for the Biomedical Community Maps & Navigation
Science Navigation Group - Services for the Biomedical Community Maps and Navigation
Science Navigation Group - Services for the Biomedical Community Maps Navigation
The Science Navigation Group is a group of independent companies that collaborate closely with each other to publish and develop information and services for the professional biomedical community and for the consumer market. Our products run the gamut from journals to websites, databases, maps and audiovisuals, and cater to clients as various as physicians, scientists, pharmaceutical companies, patients, students and the general public. We have created the UK''s largest entertainment listings database, developed the leading mobile phone navigation software platform and publish one of the most respected biomedical literature awareness services. * Faculty of 1000 Ltd: F1000 - the online post-publication peer review service for biology and medicine * Current BioData Ltd: Publisher of evaluated information on target proteins that supports the development of safe and effective new medicines * Global DataPoint Ltd: Global DataPoint - International data services for mobile, new media, press and publishing * Wozzon Ltd: Dedicated web service of information on all types of events taking place in the UK and internationally * Web of Stories Ltd: The Web of Stories site is where you can record your own stories and watch stories that others have recorded. The Group has its head office in London (UK), with additional offices in New York, New Jersey, Geneva, Amsterdam and Tel Aviv.
IsoformEx: Isoform level gene expression estimation using non-negative least squares from mRNA-Seq data
Software that estimates transcript expression levels and gene expression levels from mRNA-Seq data. Technically speaking, IsoformEx parses bowtie alignment files in a project directory (e.g. ~yourid/isoformex/xxx, where xxx is the project name) and generates two files: (1) xxx/xxx_transcript_1.txt: expression levels of all transcripts, (2) xxx/xxx_gene_1.txt: expression levels of all genes.
The SSD has been developed to address the need for resources and tools for understanding large sets of superpositions in order to understand evolutionary relationships and to make predictions of function. We have therefore created the Structure Superposition Database (SSD) for accessing, viewing and understanding large sets of structure superposition data. It contains the results of pairwise, all-by-all superpositions of a representative set of 115 (beta/alpha) barrel structures (TIM barrels). The initial implementation of the SSD contains the results of pairwise, all-by-all superpositions of a representative set of 115 (/alpha)8 barrel structures (TIM barrels). Future plans call for extending the database to include representative structure superpositions for many additional folds. The SSD can be browsed with a user interface module developed as an extension to Chimera, an extensible molecular modeling program. Features of the user interface module facilitate viewing multiple superpositions together.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Featured Job Postings from the Web. Polygenic Pathways Jobs Job Site includes the latest jobs from polygenic.jobamatic.com. Post a job - only $5 for 100 days.
IQSeq - Integrated Isoform Quanti?cation Analysis based on A Partial Sampling Framework
Software for integrated Isoform Quanti?cation Analysis based on A Partial Sampling Framework.
Now at NEJM - A blog for physicians about NEJM
A blog produced by the NEJM publishing communications team about new and innovative content in the New England Journal of Medicine (NEJM.org). Our goal is to inform you about what''s new and provide some additional context to complement the content published in NEJM. Each week we post a piece under Insights about one of the latest research papers in NEJM, discussing its clinical significance, where it may lead us in practice and research, and often giving an editor''s thoughts about why it was important to publish. We pose questions to stimulate your thinking and discussion. The idea is to make it easy for you to give us your views on a particular topic and make the conversation accessible to other doctors and physicians-in-training. Posts contain links to the full article, which will be free to all visitors for a limited time. We also feature two posts from the Resident e-Bulletin each week, with an article summary, Clinical Pearls, and Morning Report Questions teaching points that many of you find so useful in your roles as teachers or trainees. The blog gives us a new way to distribute and store this educational information on the social web, again, inviting comment and discussion. You''ll also hear about new products and applications as we bring them out, such as new Interactive Medical Cases, or iPhone applications, like NEJM This Week and the Image Challenge. We link to videos on the NEJMvideo channel on YouTube, share our Twitter feed, and links to NEJM in the News, too. We''d like this to be an open forum, complementary to the core content of NEJM, engaging you in a new experience beyond the journal page in a more interactive community.
Enhanced Read Analysis of Gene Expression
Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models.
California Academy of Sciences Family Science
Family Science - Fun activities to do at home, on the web, in the Academy and more. The program serves San Francisco''s fourth and fifth grade teachers, students and their families. The Rock Program We are excited to welcome you, your students and their families to the Enhanced Museum Visits for Students Program. Generously funded by Arthur and Toni Rembe Rock, this program is open to all 4th and 5th grade classes within San Francisco County lines. Each of the following FREE features are built into the field trip program to support and enrich the museum experience for teachers, students and families: * Bus transportation - if needed * Teacher workshops that highlight exhibit themes and educational resources (required for first time participants, optional for repeat teachers) * Educational programs designed to enhance the museum visit fieldtrip for your students * A student pass entitling each student unlimited free admission through August * A one-time free family pass with a science activity book for each student valid through the end of August.
An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. FusionMap runs under both Windows and Linux (requiring MONO) environments. Although it can run on 32 bit machine, it is recommended to run on 64-bit machine with 8GB RAM or more. If you have an ArrayStudio License, you can run the fusion detection easily through its GUI.
Scientific American, the oldest continuously published magazine in the U.S., has been bringing its readers unique insights about developments in science and technology for more than 160 years. It is the leading source and authority for science, technology information and policy for a general audience. In an era of rapid innovation, Scientific American founded the first branch of the U.S. Patent Agency, in 1850, to provide technical help and legal advice to inventors. A Washington, D.C., branch was added in 1859. By 1900 more than 100,000 inventions had been patented thanks to Scientific American. * Read in print by 3.5 million worldwide consumers * On average, 2.7 million unique users visit ScientificAmerican.com every month * 14 local language editions worldwide, including the U.S. edition of Scientific American, read in more than 30 countries, with a worldwide audience of more than 5 million people * A third of Scientific American readers hold postgraduate degrees * 144 Nobel Prize Scientists have contributed 234 articles to Scientific American * Part of Macmillan Publishers, owned by Holtzbrinck Group of companies; acquired by Holtzbrinck in 1986 * Three Scientific American features in the Federal Record * Scientific American won the 2011 National Magazine Award for General Excellence.
Project to use bioinformatics-based research activities in high schools that provides teachers and students training materials to support the teaching of Life Sciences, particularly in the area of Biology. Their aims include new ways to learn biology, adapting Bioinformatics exercises to the curricula of practical classes, and encouraging the acquisition of new scientific and technological knowledge.
VIVO - enabling national networking of scientists
Open source semantic web application that enables the discovery of research and scholarship across disciplines at a particular institution and across institutions by creating a semantic cloud of information that can be searched and browsed. Participants include institutions with local installations of VIVO or those with research discovery and profiling applications that can provide semantic web-compliant data. The information accessible through the national network' '''s search and browse capability will therefore reside and be controlled locally within institutional VIVOs or other semantic web applications. The VIVO ontology provides a set of types (classes) and relationships (properties) to represent researchers and the full context of their experience, outputs, interests, accomplishments, and associated institutions. https://wiki.duraspace.org/display/VIVO/VIVO-ISF+Ontology VIVO is populated with detailed profiles of faculty and researchers including information such as publications, teaching, service, and professional affiliations. It also supports browsing and a search function which returns faceted results for rapid retrieval of desired information. The rich semantically structured data in VIVO support and facilitate research discovery. Examples of applications that consume these rich data include: visualizations, enhanced multi-site search through VIVO Search, and applications such as VIVO Searchlight, a browser bookmarklet which uses text content of any webpage to search for relevant VIVO profiles, and the Inter-Institutional Collaboration Explorer, an application which allows visualization of collaborative institutional partners, among others. Institutions are free to participate in the national network by installing and using the application. The application provides linked data via RDF data making users a part of the semantic web! or any other application that provides linked data can be used. Users can also get involved with developing applications that provide enhanced search, new collaboration capabilities, grouping, finding and mapping scientists and their work.
Clinical Translational Science Awards ShareCenter
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5th, 2022. An open-source platform designed for organic sharing and collaborative work, it provides the CTSA Consortium with a convenient web platform for networking, exchanging resources, and collaborating. Created and maintained as a tool for the CTSA Consortium, it can be implemented by organizations, either in a standalone installation or via cloud-based hosting provided by Zaloni, Inc. The installation package is available at http://www.getsharecenter.org/, including a package optimized for research networks. ShareCenter integrates with VIVO and is a demonstration site for the new CTSAconnect project that will coalesce the VIVO and eagle-i ontologies. CTSA personnel can use ShareCenter to connect and share with each other, while CTSAs can (a) set up the open-source package, which includes a version optimized for research networks or (b) easily create their own private ' '''channel' ''' on CTSA ShareCenter. * Search for resources and people. * Contribute your institute' '''s gems. * Look cool for being a top contributor! ShareCenter Features * Easy search and access: Find content easily using faceted search. * Team based workspaces: Easily create and manage private collaboration spaces. * Connect with other users and follow their activities: Connect with other CTSA members. Follow their activities. * Subscriptions and Notifications: Subscribe to interesting content and receive notifications when your requests are filled. * Sophisticated categorization of information: Content can be categorized by key function areas, taxonomy and keywords. * Incentives for sharing: Reward users for sharing resources, ideas, expertise, skills.
phenoman - Phenotypic data exploration selection management and quality control for association studies of rare and common variants
An interactive software program that integrates phenotypic data exploration, selection, management and quality control using a unified platform for association studies of rare and common variants.
Models of SHM Targeting and Substitution
S5F - Models of SHM Targeting and Substitution
A targeting model that defines where mutations occur (by specifying the relative rates at which DNA motifs in the Ig sequence are mutated), and a nucleotide substitution model that defines the resulting mutation (by specifying the probability of each base mutating to each of the other three possibilities as a function of the surrounding bases).
Werblin Lab: Division of Neurobiology; Department of Molecular and Cell Biology
The goal of our research is to uncover the neural circuitry that mediates some of the remarkable processing capabilities of the retina. The retina to operates at high spatial and temporal resolution over more than 7 orders of magnitude, to detect the direction of motion, to blank and then recover after saccades, to generate at least a dozen different abstract representations of the visual world. How is all of this, and much more, possible in this tissuepaper-thin array of neurons? Videos and images describing this include: * The retinal hypercircuit. * How the Retina Works * Take a Tour through the Retina * Cartoon of the retina showing layering of neurons * Directional Selectivity * Feedback and Crossover inhibition * Multiple Representations of the Visual Scene ** Pseudo Array Recording Methods ** Multiple Representations of the Visual World ** Regions of Frequency Space * Regions of space/time frequency * Space-time rasters for ON and OFF cells * Patching a neuron in a retinal slice * Targeting Retinal Neuron Subregions with Arficial Rhodopsins
Kepler is a software application for analyzing and modeling scientific data. Using Kepler''s graphical interface and components, scientists with little background in computer science can create executable models, called scientific workflows, for flexibly accessing scientific data (streaming sensor data, medical and satellite images, simulation output, observational data, etc.) and executing complex analyses on this data. Kepler is developed by a cross-project collaboration led by the Kepler/CORE team. The software builds upon the mature Ptolemy II framework, developed at the University of California, Berkeley. Ptolemy II is a software framework designed for modeling, design, and simulation of concurrent, real-time, embedded systems. The Kepler Project is dedicated to furthering and supporting the capabilities, use, and awareness of the free and open source, scientific workflow application, Kepler. Kepler is designed to help scien��tists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines. Kepler can operate on data stored in a variety of formats, locally and over the internet, and is an effective environment for integrating disparate software components, such as merging R scripts with compiled C code, or facilitating remote, distributed execution of models. Using Kepler''s graphical user interface, users simply select and then connect pertinent analytical components and data sources to create a scientific workflowan executable representation of the steps required to generate results. The Kepler software helps users share and reuse data, workflows, and compo��nents developed by the scientific community to address common needs. Kepler is a java-based application that is maintained for the Windows, OSX, and Linux operating systems. The Kepler Project supports the official code-base for Kepler development, as well as provides materials and mechanisms for learning how to use Kepler, sharing experiences with other workflow developers, reporting bugs, suggesting enhancements, etc. The Kepler Project Leadership Team works to assure the long-term technical and financial viability of Kepler by making strategic decisions on behalf of the Kepler user community, as well as providing an official and durable point-of-contact to articulate and represent the interests of the Kepler Project and the Kepler software application. Details about how to get more involved with the Kepler Project can be found in the developer section of this website.
A tool that implements an algorithm for optimal alignment of sequences with Structural Variations (SVs).
A fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). With current NGS single-end sequencing data, the output regions by Breakpoint mainly contain the approximate breakpoints of indels and a limited number of large SVs. Notably, Breakpointer can uncover breakpoints of insertions which are longer than the read length. Breakpointer also can find breakpoints of many variants located in repetitive regions. The regions can be used not only as a extra support for SV predictions by other tools (such as by split-read method), but also can serve as a database for searching variants which might be missed by other tools. Breakpointer is a command line tool that runs under linux system. Breakpointer takes advanage of two local mapping features of single-end reads as a consequence of indel/SVs: 1) non-uniform read distribution (depth skewness) and 2) misalignments at the boundaries of indel/SVs. These features are summarized as breakpoint signature. Breakpointer proceeds in three stages in capturing this signature. It is implemented in C++ and perl. Input is the file or files containing alignments of single-end reads against a reference genome (in .BAM format). Output is the predicted regions containing potential breakpoints of SVs (in .GFF format). To be able to read in .BAM files, Breakpointer requires bamtools API, which users should install beforehand.
CLEVER - Clique Enumerating Variant Finder
A collection of tools to discover and genotype structural variations in genomes from paired-end sequencing reads. The main software is written in C++ with some auxiliary scripts in Python.
clippers - Deletion Identification Program using Periodic Spaced Seed
A software program designed to identify long deletions of a genome as well as the RNA splicings using long Illumina reads. Currently, Clippers is implemented for long reads Illumina, ex: 75bp or 100bp, allowing mismatches and a single deletion/splicing. Clippers is a sister tool of PerM, our short reads aligner. Users are strongly suggested to use PerM to initially mapped reads and identify the deletion/splicing with the initially unmapped reads. We plan to extend it to ABI SOLiD reads in the near future. Clippers outputs gap-alignments in SAM format. You can use SAMtools or other program to interpret the deletion/splicing. The input files are a reference in fasta format and the reads is in fasta or fastq format.
An algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. CREST uses pieces of DNA called soft clips to find structural variations. Soft clips are the DNA segments produced during sequencing that fail to properly align to the reference genome as the sample genome is reassembled. CREST uses the soft clips to precisely identify sites of chromosomal rearrangement or where pieces of DNA are inserted or deleted.
A software tool for calling short indels in next generation sequencing data.
GASVPro: Geometric Analysis of Structural Variants
Software tool combining both paired read and read depth signals into probabilistic model which can analyze multiple alignments of reads. Used to find structural variation in both normal and cancer genomes using data from variety of next-generation sequencing platforms. Used to predict structural variants directly from aligned reads in SAM/BAM format.Combines read depth information along with discordant paired read mappings into single probabilistic model two common signals of structural variation. When multiple alignments of read are given, GASVPro utilizes Markov Chain Monte Carlo procedure to sample over the space of possible alignments.
Software that detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose signatures corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments. Hydra does not attempt to classify SV breakpoints based on the mapping distances and orientations of each breakpoint cluster, it merely detects and reports breakpoints. This is an intentional decision, as it was observed that in loci affected by complex rearrangements, the type of variant suggested by the breakpoint signature is not always correct. Hydra does report the orientations, distances, number of supporting read-pairs, etc., for each breakpoint. It is suggested that downstream methods be used to classify variants based on the genomic features that they overlap and the co-occurrence of other breakpoints. For example, they developed BEDTools for exactly this purpose and the breakpoints reported by Hydra are in the BEDPE format used by BEDTools. Future releases of Hydra will include scripts that assist in the classification process.
inGAP-sv: structural variation detection and visualization
integrative next-generation genome analysis pipeline
Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations.
VelociMapper - Accelerated Reference Alignment Mapping Tool
Accelerated alignment tool for mapping data from next-generation DNA sequencing systems. It runs on TimeLogic''s newest FPGA-based DeCypher J-Series Similarity Search Engine Accelerator to provide fast and reliable results that significantly outperform software-only or GPU-accelerated alternatives.
Software package as computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from novel genome.
SPLITREAD - Split read based INDEL/SV Caller
Software for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions that are within the coding regions from the exome sequencing data. It also can be applied to the whole genome sequencing data.
McConnell Brain Imaging Center MNI Macaque Atlas
A reference atlas of standard macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual macaque monkeys and studies. We have used MRI volumes from a group of 25 normal adult macaque monkeys (18 Macaca fascicularis, 7 Macaca mulatta) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous macaque brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the MNI macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.
A Java application to investigate alternative mRNA splicing patterns in data from high-throughput mRNA sequencing studies. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing. This tool may be used on a single RNASeq sample to identify genes with multiple spliceforms, on a pair of samples to identify differential splicing between the two, or on groups of samples to identify statistically significant group level differences in splicing patterns. SpliceSeq can be run from the install page as a java web start application to explore the sequencing data on their server or can be installed locally to analyze your own mRNA-Seq data.
The Subviral RNA database facilitates the research and analysis of viroids, satellite RNAs, satellite viruses, the human hepatitis delta virus, and related RNA sequences. It integrates a large number of Subviral RNA sequences, their respective RNA motifs, analysis tools, related publication links and additional pertinent information to allow users to efficiently retrieve and analyze relevant information about these small RNA agents. The Subviral RNA Database contains 2877 sequences indexed in 83 species and 4 main groups.
Software for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.
OSA: a super-fast and accurate alignment tool for RNA-Seq data
A fast and accurate alignment tool for RNA-Seq data.
Using robotic devices to investigate human motor behavior, this group develops computational models to understand the underlying control and learning processes. By simulating novel objects or dynamic environments they study how the brain recalibrates well-learned motor skills or acquires new ones. These insights are used to design fMRI studies to investigate how these processes map onto the brain. They have developed a number of novel techniques of how to study motor control in the MRI environment, and how to analyze MRI data of the human cerebellum. They also study patients with stroke or neurological disease to further determine how the brain manages to control the body.
Software focusing on calling indels from the next-generation paired-end sequencing data.
Software aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models.
SEECER - SEquencing Error CorrEction for Rna reads
Algorithm for sequencing error correction of RNA-seq data sets. SEECER removes mismatch and indel errors from the raw reads and improves downstream analysis of the data.
Software package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models.
The core mission of the AXA Research Fund is to finance basic research contributing to understand and prevent risks. We support innovative and cutting-edge projects within three areas: environmental, life, and socio-economic risks. Only research institutions may submit applications. * Funding for research projects, postdoc and graduate fellowships, and long and short term projects * Encourages international applicants and research around the world Research projects funded by the Fund must fall within the scope of one of the themes identified by the AXA Scientific Board. The themes for 2011 are identified below: * Life risks ** Aging & Long-term care ** Biomedical risks ** Addictions and risky behaviors * Socio-economic risks ** Geopolitical risks ** Macroeconomic and financial systemic risks ** Individual and collective behaviors when facing uncertainties ** Large corporate risks * Environmental risks ** Climate change ** Natural hazards ** Human driven environmental changes
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 9, 2025. A database which retains extensive clinical information about study subjects recruited by the Alzheimer's Disease Research Center Clinical Core, as well as other individuals with neurological diseases. In addition to clinical information, the database has basic demographics, medical history (including risk factors such as smoking), and a detailed family history from all subjects. Some entries have neuropsychological measures. Users can access a Summary Database which contains the most commonly requested variables. A data dictionary describing the variables in the Summary Database is available.
A database of haptens. It compiles 2D/3D structures, physicochemical properties and references for about 7500 haptens and 25,000 synonyms. Commercial availability is documented for about 6300 haptens and 450 related antibodies, enabling experimental approaches on cross-reactivity. The immune system protects organisms from foreign proteins, peptide epitopes and a multitude of chemical compounds. Among these, haptens are small molecules, eliciting an immune response when conjugated with carrier molecules. Known haptens are xenobiotics or natural compounds, which can induce a number of autoimmune diseases like contact dermatitis or asthma. Furthermore, haptens are utilized in the development of biosensors, immunomodulators and new vaccines. Although hapten-induced allergies account for 6-10% of all adverse drug effects, the understanding of the correlation between structural and haptenic properties is rather fragmentary. We have developed a manually curated hapten database, SuperHapten, integrating information from literature and web resources. The current version of the database compiles 2D/3D structures, physicochemical properties and references for about 7500 haptens and 25,000 synonyms. The commercial availability is documented for about 6300 haptens and 450 related antibodies, enabling experimental approaches on cross-reactivity. The haptens are classified regarding their origin: pesticides, herbicides, insecticides, drugs, natural compounds, etc. Queries allow identification of haptens and associated antibodies according to functional class, carrier protein, chemical scaffold, composition or structural similarity. keywords: hapten
DTI white matter atlases with different data sources and different image processing. These include single-subject, group-averaged, B0 correction, processed atlases (White Matter Parcellation Map, Tract-probability maps, Conceptual difference between the WMPM and tract-probability maps), and linear or non-linear transformation for automated white matter segmentation. # Adam single-subject white matter atlas (old version): These are electronic versions of atlases published in Wakana et al, Radiology, 230, 77-87 (2004) and MRI Atlas of Human White Matter, Elsevier. ## Original Adam Atlas: 256 x 256 x 55 (FOV = 246 x 246 mm / 2.2 mm slices) (The original matrix is 96x96x55 (2.2 mm isotropic) which is zerofilled to 256 x 256 ## Re-sliced Adam Atlas: 246 x 246 x 121 (1 mm isotropic) ## Talairach Adam: 246 x 246 x 121 (1 mm isotropic) # New Eve single-subject white matter atlas: The new version of the single-subject white matter atlas with comprehensive white matter parcellation. ## MNI coordinate: 181 x 217 x 181 (1 mm isotropic) ## Talairach coordinate: 181 x 217 x 181 (1 mm isotropic) # Group-averaged atlases: This atlas was created from their normal DTI database (n = 28). The template was MNI-ICBM-152 and the data from the normal subjects were normalized by affine transformation. Image dimensions are 181x217x181, 1 mm isotropic. There are two types of maps. The first one is the averaged tensor map and the second one is probabilistic maps of 11 white matter tracts reconstructed by FACT. # ICBM Group-averaged atlases: This atlas was created from ICBM database. All templates follow Radiology convention. You may need to flip right and left when you use image registration software that follows the Neurology convention.
Johns Hopkins Laboratory of Brain Anatomical MRI
Johns Hopkins Medical Institute Laboratory of Brain Anatomical MRI
The goal of our laboratory is to develop new MR technologies to improve the resolution and contrast of MRI and apply them to observe brain anatomy to answer various types of biological questions. Currently we have three major research targets: Characterization of mouse brain development; Human white matter anatomy and development; and Development of diffusion tensor imaging technique and technology dissemination. The DTI database (Under the DTI Download Tab) contains raw and processed DTI data of normal population. Currently we have 2.5 mm isotropic resolution images and 2.2 mm isotropic resolution images. Only 2.5 mm data are available from this site. If you are interested in the high-resolution images, please contact susumu @ mri.jhu.edu. This database is open to public once the user is registered. Basic imaging parameters can be also downloaded.
A linear average model atlas produced by the International Consortium for Brain Mapping (ICBM) project. A set of full- brain volumetric images from a normative population specifically for the purposes of generating a model were collected by the Montreal Neurological Institute (MNI), UCLA, and University of Texas Health Science Center at San Antonio Research Imaging Center (RIC). 152 new subjects were scanned using T1, T2 and PD sequences using a specific protocol. These images were acquired at a higher resolution than the original average 305 data and exhibit improved contrast due predominately to advances in imaging technology. Each individual was linearly registered to the average 305 and a new model was formed. In total, three models were created at the MNI, the ICBM152_T1, ICBM152_T2 and ICBM152_PD from 152 normal subjects. This resulting model is now known as the ICBM152 (although the model itself has not been published). One advantage of this model is that it exhibits better contrast and better definition of the top of the brain and the bottom of the cerebellum due to the increased coverage during acquisition. The entirely automatic analysis pipeline of this data also included grey/white matter segmentation via spatial priors. The averaged results of these segmentations formed the first MNI parametric maps of grey and white matter. The maps were never made publicly available in isolation but have formed parts of other packages for some time including SPM, FSL AIR and as models of grey matter for EEG source location in VARETTA and BRAINWAVE. Again, as these models are an approximation of Talairach space, there are differences in varying areas, to continue our use of origin shift as an example, the ICBM models are approximately 152: +3.5mm in Z and +-co-ordinate -3.5mm and 2.0mm in Y as compared to the original Talairach origin. In addition to the standard analysis performed on the ICBM data, 64 of the subjects data were segmented using model based segmentation. 64 of the original 305 were manually outlined and a resulting parametric VOI atlas built. The native data from these acquisitions was 256x256 with 1mm slices. The final image resolution of this data was 181x217x181 with 1mm isotropic voxels. Refer to the ICBM152 NonLinear if you are fitting an individual to model and do not care about left/right comparisons. A short history of the various atlases that have been produced at the BIC (McConnell Brain Imaging Center, Montreal Neurological Institute) is provided.
A commercial database of the substructures of natural compounds. Their conformers are available for purchase. Although tremendous effort has been put into synthetic libraries, most drugs on the market are still natural compounds or derivatives thereof. There are encyclopaedias of natural compounds, but the availability of these compounds is often unclear and catalogues from numerous suppliers have to be checked. To overcome these problems we have compiled a database of approximately 50,000 natural compounds from different suppliers. To enable efficient identification of the desired compounds, we have implemented substructure searches with typical templates. Starting points for in silico screenings are about 2500 well-known and classified natural compounds from a compendium that we have added. Possible medical applications can be ascertained via automatic searches for similar drugs in a free conformational drug database containing WHO indications. Furthermore, we have computed about three million conformers, which are deployed to account for the flexibilities of the compounds when the 3D superposition algorithm that we have developed is used.
Oxford Centre for Functional MRI of the Brain
Functional Magnetic Resonance Imaging of the Brain Center
Functional Magnetic Resonance Imaging of the Brain Centre
Oxford Functional Magnetic Resonance Imaging of the Brain Center
Oxford Functional Magnetic Resonance Imaging of the Brain Centre
The FMRIB Centre is a multi-disciplinary neuroimaging research facility, which focuses on the use of Magnetic Resonance Imaging (MRI) for neuroscience research, along with related technologies such as Transcranial Magnetic Stimulation, transcranial Direct Cortical Stimulation and EEG. FMRIB is composed of research groups in all aspects of brain imaging research, including physics, analysis, basic science and clinical neuroscience. We were recently awarded 8 million pounds by the MRC, EPSRC, Wolfson Foundation and University of Oxford to purchase and install new 7T and 3T leading-edge MRI systems to enable us to image brain structure and function at even higher resolution than currently possible.
A sample script on how to map some numbers to brain regions, using the Talairach-Tournoux Atlas database. For example, put the value 0.379 in each hippocampus voxel, and the value 0.666 in each superior temporal gyrus voxel.
A database of scents. Users can search their structure or by scent tree, and can also add or search for specific scents by name. The database SuperScent was established to supply users with detailed information on the variety of odor components. The version of the database presented here comprises the 2D/3D structures of approximately 2100 volatiles and around 9200 synonyms as well as physicochemical properties, commercial availability and references. The volatiles are classified according to their origin, functionality and odorant groups. The information was extracted from the literature and web resources. SuperScent offers several search options, e.g. name, Pubchem ID number, species, functional groups, or molecular weight.
Analysis-tool which identifies singular node motifs in a network. Network nodes can be described by node-motifs. It is an improvement to the method described in Costa et al. (2009).
A biomedical research institute that aims to understand and develop more effective treatments for human disease, focusing on critical research areas such as heart disease, cancer, lupus and Alzheimer's disease.
Computer Assisted Brain Injury Rehabilitation Ontology
A web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living.
A portable software infrastructure designed to analyze massive genomics datasets produced by contemporary and emerging technologies, in particular Next Generation Sequencing (NGS) platforms. It consists of a comprehensive suite of infrastructure tools focused on enabling the end-to-end analysis of sequence data ? from from raw base calling to analyzed variants ready for interpretation by users. SeqWare is tool agnostic, it is a framework for building analysis workflows and does not provide specific implementations out-of-the-box. You use SeqWare to create high-throughput infrastructure for NGS analysis using whatever analysis tools you like. SeqWare currently provides 5 main tools specifically designed to support massively parallel sequencing technologies. All tools can be used together or separately: * MetaDB: provides a common database to store metadata used by all components. * Portal: a LIMS-like web application to manage samples, record computational events, and present results back to end users. * Pipeline: a workflow engine that is capable of wrapping and combining other tools (BFAST, BWA, SAMtools, etc) into complex pipelines, recording metadata about the analysis, and facilitates automation of pipelines based on metadata. * Web Service: a programmatic API that lets people build new tools on top of the project * Query Engine: a NoSQL database designed to store and query variants and other events inferred from sequence data.
CloVR - Automated Sequence Analysis from Your Desktop
A desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing.
A web-based tool that supports more than 50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is Given X, find all Y''s where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences.
PheKB - a knowledgebase for discovering phenotypes from electronic medical records
Collaborative environment of building and validating electronic phenotype algorithms using electronic medical records (EMRs) and natural language processing (NLP) for use in genome-wide association studies (GWAS). On this site you can: View existing algorithms, Enter or create new algorithms, Collaborate with others to create or review algorithms, View implementation details for existing algorithms. The Electronic Medical Records and Genomics Network (eMERGE) has investigated whether data captured through routine clinical care using electronic medical records (EMRs) can identify disease phenotypes with sufficient positive and negative predictive values for use in genome-wide association studies (GWAS). Most EMRs captured key information (diagnoses, medications, laboratory tests) used to define phenotypes in a structured format; in addition, natural language processing has also been shown to improve case identification rates. PheKB is an outgrowth of that validation effort. Phenotype algorithms can be viewed by data modalities or methods used: CPT codes, ICD 10 codes, ICD 9 codes, Laboratories, Medications, Vital Signs, Natural Language Processing Algorithms can also be viewed by: * Implementation results (positive predictive value, sensitivity, publications) * Institution * Work Group
An encyclopedia that is dedicated to a ligand and binding site oriented view of the protein structural space. SuperSite integrates evolutionary information in the proteins as well as predicted binding sites from LigsiteCSC. A point set match algorithm is implemented that allows to screen the surface of a protein for the occurrence of possible binding sites as well as a similarity screen for similar compounds based on fingerprints. SuperSite allows users to discover the ligand space of the PDB, check for evolutionary conservation of residues using HSSP files, display possible binding sites of proteins via the LigsiteCSC algorithm, similarity screen for ligands contained in the SuperSite, and screen a protein for the possible similarity of binding pockets towards certain known drug binding sites.
mirpara - know and novel miRNA prediction software
A SVM (support vector machine-based software tool for prediction of most probable microRNA coding regions in genome scale sequences.
A commercial service organization from Zyagen.
Protein Interaction information Extraction the search
A web service to extract Protein-protein interaction (PPI)-relevant articles from MEDLINE that provides protein interaction information (PPI) articles for biologists, baseline system performance for bio-text mining researchers and a compact PubMed-search environment for PubMed users. It accepts PubMed input formats including All Fields, Author, Journal, MeSH Terms, Publication Date, Title, and Title/Abstract with Boolean operations (AND, OR, and NOT). However, the output is the list of articles prioritized by PPI confidence rates. Some words (mostly gene/protein names) which contributed for PPI prediction are underlined and linked to Entrez or Entrez Gene. Even though our system focuses on a PubMed search environment, it also provides a CGI access for bio-text mining researchers. Using the CGI program, a list of PubMed IDs can be obtained as a query result, thus it can be utilized as a baseline system performance. PIE the search is based on a winning approach in the BioCreative III ACT competition (BC3)1. For input queries, MEDLINE articles are first retrieved through the PubMed service. PPI scores are calculated for the retrieved articles, and the articles are re-ranked based on scores. To effectively capture PPI patterns from biomedical literature, their approach utilizes both word and syntactic features for machine learning classifiers. Dependency parsing, gene mention tagging, and term-based features are utilized along with a Huber classifier.
Einstein-Montefiore Institute for Clinical and Translational Research Biorepository
Einstein-Montefiore Bio-Repository Databank
Einstein-Montefiore Bio-Repository Databank (EM-BRED)
Einstein-Montefiore Institute for Clinical & Translational Research Biorepository
Einstein-Montefiore Institute for Clinical Translational Research Biorepository
Patient-derived specimens are essential to research in genomics, proteomics, and biomarkers. We provide banking for biological fluid and tissue specimens as well as human DNA and RNA. We provide secure archival sample storage as well as clinically-annotated specimen biobanks for defined research projects. The core serves the human research blood and tissue banking needs of clinical and translational researchers. Samples can be banked by an individual PI or by a consortium of investigators. All samples are tracked and archived using a secure tracking database, the Einstein-Montefiore Bio-Repository Databank (EM-BRED), http://informatics30.aecom.yu.edu/em-bred/default.aspx. EM-BRED provides qualified investigators with a solution to securely link patient specimens to clinical and pathological data. It consists of a user-friendly query engine that allows for comprehensive specimen search, and ultimately to build clinical annotations of relevance. The facility works under the best practices set out by NCI and ISBER (2006) for collection, storage, and retrieval of human biological materials for research.
A database thatprovides access to information about toxic compounds (names, synonyms and structures). It is primarily designed for pharmacists, biochemists, and medical scientists, but also researchers working in cognate disciplines. SuperToxic predicts the toxicity of compounds, informs about potential targets in biochemical pathways and shows potential binding partners. The database also includes links to suppliers, where the compound can be obtained for further investigations. The current version of this database compiles approx. 60,000 compounds with about 100,000 synonyms. These molecules are classified according to their toxicity based on more than 2,500,000 measurements.
Software that performs a morphology-based approach for the automatic identification of outlier neurons based on neuronal tree structures. This tool was used by Zawadzki et al. (2012), who reported on and its application to the NeuroMorpho database. For the analysis, each neuron is represented by a feature vector composed of 20 measurements, which are projected into lower dimensional space with PCA. Bivariate kernel density estimation is then used to obtain a probability distribution for cells. Cells with high probabilities are understood as archetypes, while those with the small probabilities are classified as outliers. Further details about the method and its application in other domains can be found in Costa et al. (2009) and Echtermeyer et al. (2011). This version requires Matlab (Mathworks Inc, Natick, USA) and allows the user to apply the workflow using a graphical user interface.
University of Delaware Skate Genome Project
Core facility provides a model for collaborative approaches to use specialized resources and expertise in an integrated process. Core builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form NECC. The Skate Genome Annotation Workshops and Jamborees offer training and opportunities for faculty and students to work with and annotate genome sequences. Workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea.
Computer Retrieval of Information on Scientific Projects Thesaurus
Ontology of Computer retrieval of Information on Scientific Projects (CRISP).
Portal supporting the North East Bioinformatics Collaborative''s project to sequence the genome of the Little Skate. Provided is a clearinghouse for Little Skate Genome Project and other publicly available Skate and Ray (Batoidea) genome data, and tools for data visualization and analysis. Little Skate Genome Project The little skate (Leucoraja erinacea) is a chondrichthyan (cartilaginous) fish native to the east coast of North America. Elasmobranchs (Skates, Rays, and Sharks) exhibit many fundamental vertebrate characteristics, including a neural crest, jaws and teeth, an adaptive immune system, and a pressurized circulatory system. These characteristics have been exploited to promote understanding about human physiology, immunology, stem cell biology, toxicology, neurobiology and regeneration. The development of standardized experimental protocols in elasmobranchs such as L. erinacea and the spiny dogfish shark (Squalus acanthias) has further positioned these organisms as important biomedical and developmental models. Despite this distinction, the only reported chondrichthyan genome is the low coverage (1.4x) draft genome of the elephant shark (Callorhinchus milii). To close the evolutionary gaps in available elasmobranch genome sequence data, and generate critical genomic resources for future biomedical study, the genome of L. erinacea is being sequenced by the North East Bioinformatics Collaborative (NEBC). As close evolutionary relatives, the little skate sequence will facilitate studies that employ dogfish shark and other elasmobranchs as model organisms. Skate tools include the SkateBLAST and the Skate Genome Browsers: Little Skate Mitochondrion, Thorny Skate Mitochondrion, and Ocellate Spot Skate Mitochondrion.
miRdSNP - a database of disease-associated SNPs and microRNA target sites on 3''UTRs of human genes
A database of manually curated dSNPs on the 3''UTRs of human genes from available publications in PubMed. The advanced web interface allows users to perform proximity searches between miRNA target sites and dSNPs by gene name, miRbase ID, target prediction algorithm, disease, and any nucleotide distance between dSNPs and miRNA target sites. The web interface displays detailed sequence views showing the relationship between dSNPs, miRNA target sites, and SNPs. An interactive visualization tool shows the chromosomal distribution of dSNPs, miRNA target sites (from TargetScan), and SNPs. miRdSNP provides a comprehensive data source of dSNPs and robust tools to capture their spacial relationship with miRNA target sites on the 3''UTRs of human genes. miRdSNP enables researchers to further explore the molecular mechanism of gene dysregulation for dSNPs at posttranscriptional level.
SUPFAM is a database that consists of clusters of potentially related homologous protein domain families, with and without three-dimensional structural information, forming superfamilies. The present release (Release 3.0) of SUPFAM uses homologous families in Pfam (Version 23.0) and SCOP (Release 1.69) which are examples of sequence -alignment and structure classification databases respectively. The two steps involved in setting up of SUPFAM database are * Relating Pfam and SCOP families using a new profile-profile alignment algorithm AlignHUSH. This results in identifying many Pfam families which could be related to a family or superfamily of known structural information. * An all-against-all match among Pfam families with yet unknown structure resulting in identification of related Pfam families forming new potential superfamilies. The SUPFAM database can be used in either the Browse mode or Search mode. In Browse mode you can browse through the Superfamilies, Pfam families or SCOP families. In each of these modes you will be presented with a full list which can be easily browsed. In Search mode, you can search for Pfam families, SCOP families or Superfamilies based on keywords or SCOP/Pfam identifiers of families and superfamilies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
HMMER - biosequence analysis using profile hidden Markov models
Tool for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
Service that automatically extracts mutation-gene pairs from MEDLINE abstracts for a given disease.
SysCall - Distinguishing heterozygous sites from systematic errors
A logistic regression based classifier distinguishing heterozygous sites from systematic errors. Given a list of candidate heterozygous genomic locations and a sam file of sequenced reads SysCall classifies each genomic location as either a heterozygous site or a systematic error and outputs according lists, along with the assigned posterior probabilities.
The Synergizer database is a growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a namespace) to another. The Synergizer is a service for translating between sets of biological identifiers. It can, for example, translate Ensembl Gene IDs to Entrez Gene IDs, or IPI IDs to HGNC gene symbols, and much more. Unlike some other tools for this purpose, The Synergizer is simple and easy to learn. The Synergizer works via a web interface (for users who are not programmers) or through a web service (for programmatic access).
Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values.
University of Colorado at Boulder, Department of Neuroscience
University of Colorado at Boulder Neuroscience
The University of Colorado at Boulder offers a Ph.D. in Neuroscience, as well as graduate and undergraduate Certificates in Neuroscience that can be combined with a variety of majors. The Neuroscience Community at the University of Colorado at Boulder is made up of over 80 faculty and research associates rostered in 13 departments and institutes. Neuroscience activities on the campus are coordinated by the Center for Neuroscience.
KGGSeq: A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data
A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data.
Fungal genomics database and interactive analytical tools that integrates all fungal genomes for diverse fungi that are important for energy and environment, the focus of the JGI Fungal program. It integrates genomics data from the DOE JGI and its users and promotes user community participation in data submission, annotation and analysis. Over 100 newly sequenced and annotated fungal genomes from JGI and elsewhere are available to the public through MycoCosm, and new annotated genomes are being added to this resource upon completion of annotation. MycoCosm offers web-based genome analysis tools for fungal biologists to ''navigate'' through sequenced genomes and explore them in the context of ''genome-centric'' and ''comparative views''.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. The SV40 T antigen database lists viruses and plasmids expressing mutant forms of large T antigen. Each entry contains information regarding the mutant designation, mutant type, virus strain, nucleotide change, amino acid change and pertinent references. Category: Human Genes and Diseases Subcategory: Cancer gene databases
A web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species. The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts. By selecting relevant sentences and highlighting the biomedical terminology EBIMed enhances your ability to acquire knowledge, relate facts, discover implications and, overall, have a good overview economizing the effort in reading.
Plant Genomics Program - Capturing Light to Fuel Our Future
The goal of the DOE JGI Plant Genome Program is to shed light on the fundamental biology of photosynthesis and transduction of solar to chemical energy. Other areas of interest include characterizing: * Ecosystems and the role of terrestrial plants and oceanic phytoplankton-in carbon sequestration. * The role of plants in coping with toxic pollutants in soils by hyper-accumulation and detoxification. * Feedstocks for biofuels, e.g., biodiesel from soybean; cellulosic ethanol from perennial grasses. * The ability to respond to environmental change (e.g., loss of diversity from monoculture produces vulnerabilities; nitrogen fixing nodules in legumes reduce fertilizer need). * The generation of useful secondary metabolites (produced largely for disease resistance)- for positive/negative control in agriculture, with attendant influence on global carbon cycle. The Plant Genome Program accomplishes the above through the following activities: # Sequence. Produce genome sequences of key plant (and algal) species to accelerate biofuel development and understand response to climate change. # Function. Develop datasets (and synthetic biology tools) to elucidate functional elements in plant genomes, with special focus on handful of flagship genomes. # Variation. Characterize natural genomic variation in plants (and their associated microbiomes), and relate to biofuel sustainability and adaptation to climate change. # Integration. Provide a centralized hub for the retrieval and deep integrated analysis of plant genome datasets.
Service that partners with independent scholarly publishers, societies, associations, and university presses to facilitate the digital dissemination of 1779 journals, reference works, books, and proceedings. It also offers a complete manuscript submission, tracking, peer review, and publishing system for journal editors.
The Gene Wiki is a project that facilitates transferring information on human genes to Wikipedia article stubs with the goal of promoting collaboration and expansion of the articles. Number of gene articles The human genome contains an estimated 20,00025,000 protein-coding genes. The goal of the Gene Wiki project is to create seed articles for every notable human gene, that is, every gene whose function has been assigned in the peer-reviewed scientific literature. Approximately half of human genes have assigned function, therefore the total number of articles seeded by the Gene Wiki project would be expected to be in the range of 10,000 - 15,000. To date, approximately 10,271 articles have been created or augmented to include Gene Wiki project content. Expansion Once seed articles have been established, the hope and expectation is that these will be annotated and expanded by editors ranging in experience from the lay audience to students to professionals and academics. Proteins encoded by genes The majority of genes encode proteins hence understanding the function of a gene generally requires understanding of the function of the corresponding protein. In addition to including basic information about the gene, the project therefore also includes information about the protein encoded by the gene. Stubs for the Gene Wiki project are created by a bot and contain links to the following primary gene/protein databases * HUGO Gene Nomenclature Committee official gene name * Entrez Gene database * OMIM (Mendelian Inheritance in Man) database that catalogues all the known diseases with a genetic component * Amigo Gene Ontology * HomoloGene gene homologs in other species * SymAtlasRNA gene expression pattern in tissues * Protein Data Bank 3D structure of protein encoded by the gene * Uniprot (universal protein resource) a central repository of protein data
The MAKER Web Annotation Service (MWAS) is an easily configurable web-accessible genome annotation pipeline. It' '''s purpose is to allow research groups with small to intermediate amounts of eukaryotic and prokaryotic genome sequence (i.e. BAC clones, small whole genomes, preliminary sequencing data, etc.) to independently annotate and analyze their data and produce output that can be loaded into a genome database. MWAS is build on the stand alone genome annotation pipeline MAKER, and users who wish to annotate larger datasets and whole genomes are free to download MAKER for use on their own systems. MWAS identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MWAS can also automatically train popular gene prediction algorithms for use on new genomes for which pre-existing information is limited. MAKER is a member of the Generic Model Organism Database (GMOD) project and output produced by this site can be directly used with other GMOD tools. Annotations can be directly viewed online by the user via GBrowse, JBrowse, and Apollo, or they can be downloaded for local analysis and integration into a genome database. MWAS also supplies summary statistics on sequence features via the Sequence Ontology tool SOBA. MWAS should prove especially useful for emerging model organism genome projects with minimal bioinformatics expertise and computer resources, since a user can produce final genome annotations without having to install and configure any software locally.
Community built database about RNA / DNA or Peptide aptamers. The Aptamer Base is a collaborative knowledge base about aptamers, their interactions and detailed experimental conditions with citations to primary scientific literature. Aptamers are short single-stranded nucleic acids or amino acid polymers that recognize and bind to targets with high affinity and selectivity. Nucleic acid aptamers are typically isolated from large combinatorial libraries through the application of SELEX. For more information visit http://aptamerbase.semanticscience.org
German Institute of Economic Research; Berlin; Germany
Deutsches Institut fur Wirtschaftsforschung
Deutsches Institut f�r Wirtschaftsforschung
Deutsches Institut f�r Wirtschaftsforschung Berlin
The German Institute for Economic Research or more commonly DIW Berlin is a economic research institute in Germany, involved in basic research and policy advice.
WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation
WebApollo - A Web-Based Sequence Annotation Editor for Community Annotation
WebApollo is an extensible web-based sequence annotation editor for community annotation. No software download is required and the annotations are saved to a centralized database with real-time annotation updating. (The edit server mediates annotation changes made by multiple users.) The Web based client uses JBrowse, is fast and highly interactive. WebApollo accesses many types of genomic data including access to public data from UCSC, Ensembl, and GMOD Chado databases. Source code (BSD License) * Client source code: https://github.com/berkeleybop/jbrowse * Annotation editing engine: http://code.google.com/p/apollo-web * Data model and I/O layer: http://code.google.com/p/gbol * Trellis server code: http://code.google.com/p/genomancer
Statistical Tracking of Ontological Phrases
Statistical Tracking of Ontological Phrases (STOP)
STOP is a multi-ontology enrichment analysis tool. It is intended to be used to help from hypothesis about large sets of genes or proteins. The annoations used for enrichment analysis are obtained automatically applying text descriptions of genes and proteins to the NCBO annotator. Text for genes is found using NCBI entrez gene, and text for proteins is found using UniProt. The text is then run though NCBO annotator with all the available ontologies. For more information about the NCBO annotator please visit: http://bioportal.bioontology.org/ The goal of National Center for Biomedical Ontology (NCBO) is to support biomedical researchers in their knowledge-intensive work, by providing online tools and a Web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of our work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments. This work is an expansion of the work of Rob Tirrell and others on RANSUM This probject would not be possible without the contributions of Emily Howe, Uday Evani, Corey Powell, Mathew Fleisch, Tobias Wittkop, Ari Berman, Nigam Shah and Sean Mooney An account is required.
Service to access comprehensive information on diseases, drugs, treatments and medical biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to drill down to specific details. Search results are presented in a dashboard format comprized of panels containing various categories of information ranging from introductory sources to the latest scientific articles.
Program that rapidly converts the primary sequence of a complex carbohydrate, as defined by standard nomenclature, directly into a reliable 3D molecular model by linking together preconstructed 3D molecular templates of monosaccharides in the manner specified by the sequence and then optimizing the 3D structure using the MM3 force field. The user interaction is supported by an input spreadsheet consisting of a grid of sugar symbol and connection type cells. Several ways to visualize and to output the generated structures and related information are implemented.
NYS Office for People With Developmental Disabilities
New York State Office for People With Developmental Disabilities
The OPWDD''s mission is to help people with developmental disabilities live richer lives. OPWDD operates 13 Developmental Disabilities Services Offices (DDSOs) responsible for providing programs in one or more counties. These offices seek to provide specially designed person-centered assistance to each individual with developmental disabilities as requested by that person or by his or her family. In partnership with individuals, families, staff, private providers and local governments, these offices seek to improve the quality of life of individuals and their families through the provision of quality, cost-effective housing, employment and family support services.
Software using a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid discovery of errors and comparisons between similar assemblies.
Text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. It allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs.
R package for identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.
A Web service that annotates textual metadata (e.g. journal abstract) with relevant ontology concepts. NCBO uses this Web service to annotate resources in the NCBO Resource Index. They also provide this Web service as a stand-alone service for users. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Their service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.
CHiP-seq ANalytics and Confidence Estimation
A standalone software package for ChIP-seq quality control and protocol optimization.
phantompeakqualtools - Computes quick but highly informative enrichment and quality measures and fragment lengths for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data
Software package that computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
CoIN: A network exploration for document triage
A web-based system that assess articles according to their term correlations among sentences. It employs the co-occurrence relations and their network centralities to evaluate the influence of biomedical terms from Comparative Toxicogenomics Database (CTD)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format.
FORCE11 - the Future of Research Communications and e-Scholarship
A collaboration which works to transform scholarly communications through advanced use of computers and the Web. FORCE11 advocates the digital publishing of papers in order to enable more effective scholarly communication. The virtual community also advocates the publication of software tools and research communication by means of social media channels. As such, FORCE11 provides access to information and tools for the wider scientific community.
A database of bodily fluid proteome data. It contains information on proteins from humanplasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid. Our body fluid protein database, Sys-BodyFluid, contains 11 body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid. Over 10,000 proteins are included in the Sys-BodyFluid. These body fluid proteome data come from 50 peer-review publications of different laboratories all over the world. Protein annotation are provided including protein description, Gene ontology, Domain information, Protein sequence and involved pathway. User can access the proteome data by protein name, protein accession number, sequence similarity. In addition, user could perform query cross different body fluids to get more comprehensive understanding. The difference and similarity between these 11 body fluids are also analyzed. Thus , the Sys-BodyFluid database could serve as a reference database for body fluid research and disease proteomics. plasm, serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid, protein, proteomics
AGNOSIA APHASIA APRAXIA and Related Terms for Cognitive Behavioral and Neurological Disorders
AGNOSIA APHASIA APRAXIA Related Terms for Cognitive Behavioral Neurological Disorders
Compilation terms with definitions that describe altered states that are associated with brain injury (e.g., trauma, stroke, tumor) or with developmental deficits. Although the list deals with primarily CNS-associated disorders, in some cases the term does not distinguish between a CNS cause or a peripheral or neuromuscular cause. Terms that are primarily psychiatric diagnoses (e.g., schizophrenia) are not included. AGNOSIA is a general term for a loss of ability to recognize objects, people, sounds, shapes, or smells; that is, the inability to attach appropriate meaning to objective sense-data. It usually is used when the primary sense organ involved is not impaired. APHASIA is a general term relating to a loss of language ability. APRAXIA is a general term for disorders of practice. These conditions are usually caused by brain injury due to trauma, stroke and/or tumor. Many of these terms have two synonymous forms that differ in whether the word starts with a- or with dys- such as alexia and dyslexia. Here the a- form is usually defined and the other is noted as syn:, except when the dys- form is the more common usage. (If you cannot find a term in one of these forms, look for it in the other. All other synonyms are defined in both forms.) Sources: These definitions are paraphrased from definitions in a large number or print and online dictionaries. Thus this list is not meant to be considered my own, but rather is a compilation. Note: When a word appears in italics, that indicates it is defined elsewhere in this list.
Web application, API and widget able to recognize and annotate biomedical concepts in text.Provides annotations for isolated, nested and intersected entities.Identifies concepts from multiple semantic groups, providing preferred names and enriching them with references to public knowledge resources.
The CEI Science & Technology Network (S&TN), launched at the beginning of 2004, is composed of sevenTrieste-based research centres and their partners in the CEI region. With the aim to strengthen scientific and technological cooperation, the S&TN provides financial support for the organization of seminars, conferences, workshops and training courses. Young scientists from CEI countries, especially non-EU member States, are offered the opportunity to attend such activities and carry out scientific research on various topics in one of the seven Lead Institutions (LIs). The area of cooperation of each Lead Institution is separately defined in a three-year Protocol complemented by an annual Work Programme. During 2004-2009, the Network''s Lead Institutions implemented a number of activities, some of which in partnership with other institutions from CEI countries. This cooperation started up the Secondary Network whose further enhancement will be the main challenge in the future years. The CEI Research Fellowship Programme The CEI Research Fellowship Programme was established in 2005 to enable mobility across the CEI region by giving selected scientists the possibility of carrying out research in one of the Network''s Lead Institutions. In the time-frame 2005 - 2009, the request for fellowships has constantly increased and witnessed the effectiveness of the Programme. Taking this into account, in 2008 the CEI-ES started to explore EU funding opportunities in order to develop its Research Fellowship Programme. A joint proposal named CERES (CEI Research Fellowship Programme) was submitted to the European Commission under the Seventh Framework Programme for Research and Technological Development (FP7). CERES was approved and is currently under implementation. EU Funding opportunities for the CEI Science & Technology Network Following the successful experience of CERES, the CEI-ES, along with the Network''s Lead Institutions, will continue to look into funding opportunities offered by the EU with the ultimate aim to support mobility of researchers across the CEI area and promote significant progress in the S&T sector.
GEM: ChIP-Seq and ChIP-exo analysis tool
Genome wide Event finding and Motif discovery
Java software for studying protein-DNA interaction using ChIP-seq / ChIP-exo data. It links binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence, resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution. GEM reciprocally improves motif discovery using binding event locations, and binding event predictions using discovered motifs.
A web based search tool to help you gain an overview of the set of articles (up to 25,000 most recent articles) retrieved by a PubMed query. Once you enter a query, you can select different types of summary information to view: Important words, Topics, Authors, Affiliations, Journals, Year, Clustered by topic.
National Ataxia Foundation Patient Registries
A portal presenting the patient registries and databases of the National Ataxia Foundation. The registries include: Ataxia Patient Registry at CoRDS, Friedreich's Ataxia Research Alliance Patient Registry; the Fragile X Research Registry; Autosomal recessive spastic ataxia of Charlevoix-Saguenay ARSACS; and, Ataxia-Telangiectasia (A-T) Children's Project Family Data Base.
(at)Note2 - A workbench for Biomedical Text Mining
THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 18, 2017. Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. It aims to provide support to three different usage roles: biologists, text miners and application developers. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels.
University of Rochester Program for Brain Tumors and Spinal Tumors
University of Rochester Brain Tumor and Spinal Tumor Program
URMC Program for Brain and Spinal Tumors
Collaborative neuro-oncology research program with a tissue repository (tumor bank) containing a wide range of clinical specimens, which they make available to researchers in order to study the effects of new drugs on a large number and wide range of tumor specimens. They provide highly coordinated, complex care in neurosurgery, radiation oncology, medical oncology, and neurology to patients afflicted with tumors of the brain and spine by combining the newest technologies and treatments available anywhere in the world. The program is formed from a multidisciplinary group with a goal of helping patients navigate the complex issues surrounding brain and spinal cancer care. The researchers are working to increase the number of targets that could be considered for anti-angiogenesis therapy. Many of their studies focus on the blood vessel cells (endothelial cells) themselves, which, unlike tumor cells, rarely mutate and so might be less likely to become resistant to therapy and are also more easily reached through the bloodstream. Their researchers are also attempting to better understand the changes in the blood-brain barrier (BBB) that are associated with fluid accumulation and brain swelling (edema) in neuro-oncology patients. Normal brain tissue is shielded from the rest of the body by the BBB. This barrier is composed of very tight blood vessels that prevent most substances from entering the brain. Brain tumors have a leaky BBB ����?? this feature can be used to identify tumors on MRI scans. They have identified specific molecules that appear to be associated with the leaky, abnormal vessels while the normal blood vessels with intact BBB produce these molecules at very low levels or not at all. Inhibiting the function of these molecules may help control or prevent disruption of the BBB and limit cerebral edema in brain tumor patients, as well as patients suffering from stroke or traumatic brain injury.
Case Western Reserve Tissue Procurement and Histology Core Facility
Case Western Reserve Tissue Procurement and Histology Core Facility (TPHC)
Case Western Reserve Tissue Procurement Histology Core Facility
CWRU Tissue Procurement and Histology Core Facility (TPHC)
CWRU Tissue Procurement Histology Core Facility (TPHC)
A combined tissue bank and core facility which provides annotated human tissue samples for research purposes. The facility also offers high quality tissue procurement, tissue microarray, histology, immunohistochemistry, photomicroscopy, and laser capture microdissection services for both human and animal tissues to biomedical investigators conducting non-clinical research studies. The TPHC offers instruction to researchers on how to incorporate human tissue into research activities and how to work within the boundaries of patient confidentiality and other regulatory issues. The purpose of the TPHC is to provide tissue collection and processing services to intramural and extramural researchers studying cancer and other diseases. Normal, diseased, benign and malignant tissues are obtained, and matched normal adjacent tissues and tissues from different organ sites from the same donor can also be provided when available. Tissue samples are prepared according to user-specified protocols and can be fresh in a medium of choice, fixed in formalin, quick frozen in the vapor phase of liquid nitrogen or snap-frozen by plunging the sample into liquid nitrogen. Frozen tissues are held in the vapor phase of the liquid nitrogen. Tissues can also be embedded, cut and mounted on slides, and stained upon request. Tissue Microarray (TMA) services are offered for the design and construction of TMAs meeting specific project needs. Basic demographic data (age, race, gender) and histopathologic data from Surgical Pathology Reports are provided by the TPHC with the tissues.
University of Cincinnati Neuroscience Institute
Leading treatment, research and teaching center for complex neurological conditions based at the University Hospital and the UC College of Medicine. Its physicians and researchers have created national models for evidence-based treatment and research of complex conditions, including ischemic and hemorrhagic stroke, brain aneurysms, brain and spinal cord trauma, brain tumors, Parkinson's disease, epilepsy and seizure disorders, multiple sclerosis, trigeminal neuralgia, Alzheimer's disease and memory disorders, mood disorders, and neuromuscular disorders. UCNI includes a team of more than 100 experts from 15 specialties who collaborate across disciplines to provide the most comprehensive diagnoses and treatments possible.
Charles R. Drew University of Medicine and Science; California; USA
Charles R. Drew University of Medicine and Science
A private, nonprofit, nonsectarian, Historically Black College and University and a Minority Serving Institution located in Willowbrook, unincorporated Los Angeles County, California, United States.
UC College of Medicine Department of Psychiatry and Behavioral Neuroscience
UC College of Medicine Department of Psychiatry Behavioral Neuroscience
UC College of Medicine Psychiatry & Behavioral Neuroscience
UC College of Medicine Psychiatry and Behavioral Neuroscience
University of Cincinnati Department of Psychiatry and Behavioral Neuroscience
University of Cincinnati Department of Psychiatry Behavioral Neuroscience
UC Psychiatry and Behavioral Neuroscience
Founded in 1942, the UC Department of Psychiatry and Behavioral Neuroscience is transforming behavioral health care through basic, clinical and translational research programs. Our vision is to be leaders in advancing the understanding and treatment of psychiatric disorders.
A software program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.
FaBox - an online fasta sequence toolbox
Tools for splitting, joining and otherwise manipulating FASTA format sequence files. The first tools in the toolbox is for manipulating fasta headers, cropping alignments and doing some sequence comparison allowing users to combine the description of data (often in excel spreadsheets) with the actual data (often DNA sequences). Also, producing correct input files for a range of programs seems to be problematic for the average user. Hence, some converters in some of the services have been included as well as some stand-alone converters. The converters are not necessarily meant to provide the final input file, but you''ll get a valid input file for Arlequin, MrBayes etc. - that you may further edit so it suit your needs. This means that you may need to combine several of the tools to finish your handling - but it keeps it relatively simple to use. Please note that FaBox is written in PHP and ONLY RUNS ON A WEBSERVER.
University of Colorado School of Medicine Department of Neurology
CU School of Medicine Department of Neurology
University of Colorado at Denver Health Sciences Center Department of Neurology
The Department is part of the University of Colorado Anschutz Medical Center and is one of the largest Academic Medical Centers between Chicago and the West Coast. The School of Medicine is in the top 25 schools nationally in NIH funding and includes numerous nationally recognized affiliated hospitals. Our Department is composed of over 30 primary faculty members whose clinical and research interests and activities encompass virtually all aspects of neurology. Faculty are integrated into functional units including Behavioral Neurology, Cerebrovascular Diseases, Epilepsy and Sleep Disorders, Infectious Disease, Movement Disorders, Multiple Sclerosis, Neuromuscular Disorders, Neuro-oncology, and Neuro-ophthalmology each of which strives to provide cutting-edge diagnostic and therapeutic services to patients and families dealing with neurological disease. Our faculty have clinical activities at four affiliated teaching hospitals (The Childrens Hospital, Denver Health Medical Center, Denver Veterans Affairs Medical Center, University Hospital), each of which brings unique clinical, educational, and research strengths to our program. Clinical, research and educational programs are closely linked to the Division of Pediatric Neurology of the Department of Pediatrics. The educational mission of the Department includes primary responsibility for the training of medical students in required neurology clerkships, an ACGME accredited Neurology Residency Training Program (16 positions), Clinical Fellowships (Behavioral Neurology, Cerebrovascular Disease, CNS Infections, Epilepsy, Movement Disorders, Neuromuscular Disease, MS) and both clinical and laboratory based fellowships in neurology research. The clinical enterprise includes busy outpatient, inpatient and consultation services, as exemplified by over 12,000 outpatient visits and over 800 annual admissions at UH.
Small and very fast utility to calculate X-coverage from Next-Generation-Sequencing data.
University of Delaware Behavioral Neuroscience Graduate Program
UD Behavioral Neuroscience Graduate Program
Ph.D. program in Behavioral Neuroscience is committed to training exceptional students for independent neuroscience research careers in academic, governmental, or industrial settings. Our program provides training in biological foundations of behavior, with particular focus on sensation, learning and memory, affect, development, and neural plasticity.
An online tool that takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation includes 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish.
In the early nineties it became evident that HIV infection was spreading widely in India and the national efforts for control of HIV infection needed to be backed by quality research. It was also realized that AIDS, being a multifaceted disease, needed multi-disciplinary research involving virology, immunology, microbiology, clinical research, epidemiology, field based trials and social and behavioral research. An Institute devoted exclusively to HIV/ AIDS that could undertake research of such a diversity and magnitude was established to meet this requirement. National AIDS Research Institute (NARI) was established in October 1992 in Bhosari, Pune on a seven acre plot. The Institute has progressively expanded its activities in various aspects of research on HIV and AIDS through infra-structural development, capacity building & research programmes. The activities of NARI are supported by the ICMR & numerous extramural agencies. For the fiscal year 2005-2006 the ICMR allocated 5.66 crores for NARI. Additionally, over 13 crores have been generated through extramural sources. The Institute''s research activities are guided by a Scientific Advisory Committee which includes eminent scientists from varied disciplines. All research projects are reviewed & approved by the Ethics Committee which also ensures that research is conducted with highest ethical standards. Establishment of a Community Advisory Board which acts as an interface between the community and the researchers is a pioneering effort by NARI.
AIDS.gov works to increase HIV testing and care among people most at-risk for, or living with, HIV, by using emerging communication strategies to provide access to Federal HIV information, policies (e.g. the National HIV/AIDS Strategy), programs, and resources. Objectives # Expand visibility of timely and relevant Federal HIV policies, programs, and resources to the American public. # Increase use of new media tools by government, minority, and other community partners to extend the reach of HIV programs to communities at greatest risk. # Increase knowledge about HIV and access to HIV services for people most at-risk for, or living with, HIV. Unless otherwise noted, material presented on the AIDS.gov Web site is considered Federal government information and is in the public domain. That means this information may be freely copied and distributed. We request that you use appropriate attribution to AIDS.gov. AIDS.gov receives planning guidance from a cross agency planning group and uses a logic model (70 KB) and Communications Plan (702 KB) to guide AIDS.gov activities.
A neuroscience collaboratory that supports open neuroscience, which basically encompasses the unrestricted sharing of: analytic tools, computational resources, data, and knowledge. Its goal is to establish a spirit and forum for open neuroscience, and to facilitate the translation of that ethos into action by conducting successful large open interdisciplinary collaborative efforts such as releasing the preprocessed version of the ADHD-200 competition dataset. The Brain-Art Competition is likewise an effort to bring attention to the more aesthetically-oriented aspects of their field, and to publicize and encourage creative developments taking place at the nexus of art and neuroimaging.
A grassroots initiative dedicated to accelerating the scientific community' '''s understanding of the neural basis of ADHD through the implementation of open data-sharing and discovery-based science. They believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice. The ADHD-200 Global Competition invited participants to develop diagnostic classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging (MRI) of the brain. Applying their tools, participants provided diagnostic labels for previously unlabeled datasets. The competition assessed diagnostic accuracy of each submission and invited research papers describing novel, neuroscientific ideas related to ADHD diagnosis. Twenty-one international teams, from a mix of disciplines, including statistics, mathematics, and computer science, submitted diagnostic labels, with some trying their hand at imaging analysis and psychiatric diagnosis for the first time. The data for the competition was provided by the ADHD-200 Consortium. Consortium members from institutions around the world provided de-identified, HIPAA compliant imaging datasets from almost 800 children with and without ADHD. A phenotypic file including all of the test set subjects and their diagnostic codes can be downloaded. Winner is presented. The ADHD-200 consortium included: * Brown University, Providence, RI, USA (Brown) * The Kennedy Krieger Institute, Baltimore, MD, USA (KKI) * The Donders Institute, Nijmegen, The Netherlands (NeuroImage) * New York University Medical Center, New York, NY, USA (NYU) * Oregon Health and Science University, Portland, OR, USA (OHSU) * Peking University, Beijing, P.R.China (Peking 1-3) * The University of Pittsburgh, Pittsburgh, PA, USA (Pittsburgh) * Washington University in St. Louis, St. Louis, MO, USA (WashU)
A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts.
An annual Brain-Art Competition to recognize the beauty and creativity of artistic renderings emerging from the neuroimaging community. Submission deadline: June 1st, 2012. Awards will be announced on June 11th during the OHBM conference in Beijing. (You need not be present to win) Countless hours are devoted to creation of informative visualizations for communicating neuroscientific findings. This competition once again aims to recognize the artistic creativity of our community that often goes underappreciated in the publication process. We are inviting researchers to submit their favorite unpublished works for entry. Both team and single-person entries are welcomed. The competition will have five award categories: # Best Representation of the Human Connectome # Best Abstract Brain Illustration # Best Educational Brain Illustration # Best Humorous Brain Illustration # Best Video Illustration of the Brain Submissions will be evaluated based on their aesthetic merit
Functional Connectomes Project International Neuroimaging Data-Sharing Initiative (FCP/INDI)
International Neuroimaging Data-Sharing Initiative
Collection of resting state fMRI (R-fMRI) datasets from sites around world. It demonstrates open sharing of R-fMRI data and aims to emphasize aggregation and sharing of well-phenotyped datasets.
1200+ ''resting state'' functional MRI (R-fMRI) datasets independently collected at 33 sites and donated by the principal investigators for the purpose of providing the broader imaging community complete access to a large-scale functional imaging dataset. Age, sex and imaging center information are provided for each of the datasets. In accordance with HIPAA guidelines, all datasets are anonymous, with no protected health information included. We anticipate this data-sharing effort will equip researchers with a means of exploring and refining R-fMRI approaches, and facilitate the growing ethos of sharing and collaboration. Disclaimer: The ''1000 Functional Connectomes Project'' datasets are provided freely without assurance of quality or appropriateness for usage.
Boston University Biospecimen Archive Research Core
Biospecimen Archive Research Core Boston University Medical Center
Boston University Biospecimen Archive Research Core (BARC)
Boston University Medical Center Biospecimen Archive Research Core
Biospecimen repository of normal and diseased human material from a variety of tissues and conditions along with clinical annotation. Both frozen aliquots and paraffin embedded tissue are available. Biospecimens are available to qualified researchers with IRB approval. * Preliminary inquires please contact Cheryl Spencer at cheryl.spencer (at) bmc.org
This is a demo store. Any orders placed through this store will not be honored or fulfilled. The Open Biobank is a network of bio-banks, collaborators, and consumers supplying or acquiring samples that are proactively acquired for future testing, analysis, and/or replenishment for human life. Our goal is to supply quality samples to clinicians and researchers with making their ordering experience convenient, accessible, and available 24/7. Suppliers that we distribute for are Bio-Banks, Tissues Banks, and Seed Banks who supply samples to the open life science community. Samples are stored in bio-repositories, physical and data storage facilities with various controlled environments normally containing associated data history on the sample(s) sourced. We have a policy to provide all consumers with documentation from suppliers on the state, procedures, protocols, and historical data on sample handling and testing analysis on samples ordered from suppliers. In choosing samples to order, suppliers categorize the usage, handling, environment, and application of samples to properly supply samples to users. However, users expect information on sample handling, collection or harvesting, storage, management, shipment, and other logistical considerations that may affect sample quality and impact sample use. The Amazon-like storefront saves lives by sourcing samples from all bio-banks around the world. This is how it works: * Choose a supplier you trust. Find the sample you need. Select samples from search results and place an order. Payment systems by Amazon are reliable. Choose your shipper and method of delivery. Track your orders from multiple vendors. Query reports of all orders place by your staff. Rate the samples you ordered and view the ratings of your peers. * Market your Biospecimen and Data on the Open Biobank
Translational Genomics Research Institute Podcasts
Podcasts (Audio and video files over the internet) form the Translational Genomics Research Institute.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The Adenoma Polyp Tissue Bank (APTB) receives whole blood from patients enrolled in the Prevention of Sporadic Colorectal Adenomas with Celecoxib clinical trial. We have reached our accrual on blood submissions, so we will no longer be receiving blood specimens The objectives of this trial are as follows: A. To determine the efficacy and safety of celecoxib versus placebo in preventing the occurrence of newly detected colorectal adenomas in subjects at increased risk for colorectal carcinoma. In addition to incidence, other established risk factors will be evaluated for their association with occurrence of new colorectal adenomas, including cancer family history and adenoma size, histopathologic grade, multiplicity and location. Primary assessment of treatment efficacy will be the reduction in the number of subjects with adenomas at colonoscopy after Year 1 and Year 3 of study drug use. Secondary assessments of treatment efficacy will be 1) the number of adenomas 2) the histopathologic grade of adenomas and 3) the size of adenomas, also measured after one year and three years of study drug use. These factors will be incorporated into a risk model for predicting adenoma occurrence and response to celecoxib. B. To determine the efficacy of celecoxib versus placebo in modulating one or more of a panel of biomarkers for colorectal cancer at the cellular and molecular level sampled in a subset of subjects at selective sites at baseline and after Year 1 and Year 3 of study drug use. These biomarkers will include measurements of aberrant crypt foci (ACF), proliferation (index and crypt distribution), apoptosis (index and crypt distribution), COX expression and activity. If modulation of one or more mucosal biomarkers occur, we will explore whether it correlates with the development of incident colorectal neoplasia (adenomas/carcinomas), thereby attempting to validate the surrogacy of that biomarker. C. To develop a specimen bank. Serum and white blood cells are isolated from whole blood and adenoma tissue blocks and slides are banked. Banked specimens will become available for use in correlative science studies at a later point. This project began in 1999 and will be extended through 2006. The lead principal investigator is Monica M. Bertagnolli, MD, Brigham and Women''s Hospital, Boston, MA, and the APTB Director is Scott Jewell, Ph.D., Department of Pathology, The Ohio State University. The APTB is supported by the NIH, NCI Division of Cancer Prevention, in connection with the Strang Cancer Prevention Center, Cornell University, New York., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of information on bacterial phages. It contains multiple phage genomes, which users can BLAST and MegaBLAST, and also hosts a Phage Forum in which users can discuss phage data. Interactive browsing of completed phage genomes is available using the program. The browser allows users to scan the genome for particular features and to download sequence information plus analyses of those features. Views of the genome are generated showing named genes BLAST similarities to other phages predicted tRNAs and other sequence features.
Database with 2797 unique DNA-binding proteins (mostly transcription factors, TFs), 4196 Position Weight Matrices (PWMs) and 13161 DNA Binding Sites extracted from the literature and other repositories. The binding interfaces of (most) proteins in the database are inferred from the collection of protein-DNA complexes described in 3D-footprint. The database predicts transcription factors which bind a specific DNA site or motif and DNA motifs or sites likely to be recognized by a specific DNA-binding protein.
Public university in French community of Belgium. International university spreads out over 4 campuses. Its official language is French.
The mission of the HIV Neurobehavioral Research Center (HNRC) is to increase our understanding of how HIV and other diseases affect the human nervous system. The HNRC conducts local, national, and international research devoted to advancing our knowledge of the prevention, diagnosis and treatment of HIV-related diseases as they affect the brain and nervous system, and result in impairment of everyday functioning. Research areas of the Center include: - The incidence, prevalence, and features of neurocognitive impairment caused by HIV - The attributes of the virus, host, and host-virus interactions that determine the presentation of HIV-associated neurocognitive disorders - Possible molecular and cellular mechanisms of nervous system impairment, including the mechanisms by which host-virus factors generate neural injury and neurobehavioral disorders - The cerebrospinal fluid (CSF) as a window on CNS events * The role of co-pathogens and comorbidities in neuroAIDS (e.g., hepatitis C infection, methamphetamine abuse) - Real life implications of neurocognitive impairment in terms of work, daily life, and survival - The effects of HIV disease and neurocognitive impairment on family and social adaptation - NeuroAIDS in resource limited settings - Treatments for neurocognitive impairment and behavioral interventions HNRC also has a Developmental Grants Program (DGP), the primary goal of which is the initiation of innovative studies by junior faculty and trainees at UCSD or affiliated institutions with the following objectives: 1. Recruitment to neuroAIDS research of new investigators or established investigators without prior experience in the field; 2. Generation and pilot testing of new research initiatives; 3. Fostering collaboration among investigators from throughout Southern California. The program provides to qualified investigators and trainees any appropriate combination of the following forms of support: 1. Small, 1-2 year grants to support pilot studies; 2. Access to HNRC core resources such as data, specimens, participants, equipment, administrative support, or expert consultation and technical assistance. Lastly, The the NHRC Mentored Investigator Program recruits, supports, and follows the progress of graduate students, postdoctoral (Ph.D. or M.D.) fellows, and junior faculty in disciplines relevant to HNRC research. The HNRC is committed to tailoring our training opportunities to the backgrounds and interests of candidates from a variety of disciplines who join us with various levels of training and experience in research. We have and will continue to provide training and mentoring of medical students, doctoral students in clinical psychology, and postdoctoral fellows in Medicine, Psychiatry, Neurology, and Psychology. Sponsors: The Center is supported by public funding from the National Institutes of Health, the State of California, and other sources.
The Invitrogen Clone Collection: * Ultimate ORF Clones: Full-insert sequenced human and mouse open reading frames (ORFs) in a Gateway entry vector offering the highest utility for your downstream analysis needs. * GeneStorm Clones: GeneStorm Clones are human ORFs cloned and tested for expression in a mammalian, insect, or bacterial expression system. They are sequenced for identity and classification and are not guaranteed at the nucleotide level. * Full-Length Clones: An unparalleled repository of clones enriched for full-length inserts, derived from both public and proprietary sources. * BAC/PAC Clones: Invitrogen offers several genomic libraries from a selection of tissues and sources to facilitate your research and discovery. These collections are available in a variety of formats including clones, plates, pools and high-density colony membrane filters. * Yeast Deletions: Each yeast deletion represents a unique gene-knockout of the S. cerevisiae genome. Each open reading frame is knocked out using a PCR-based gene deletion strategy. Yeast deletions are available as clones, pools, plates and complete collections. * Yeast GFP Clones: The Yeast GFP Clone Collection of S. cerevisiae tagged open reading frames were generated by Dr. Erin O''Shea and Dr. Jonathan Weissman at University of California-San Francisco. The GFP fusion proteins are integrated into the yeast chromosome through homologous recombination and are expressed using endogenous promoters.
MolBioLib: C++11 framework for rapid develop and deploy of bioinformatic tasks
A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++.
Software to assist a bioinformatician to organize, document, share, execute and repeat workflows in a command line environment without losing any of the flexibility of the command line, and, at all times giving the user full access to all aspects of the workflow.
University of Georgia College of Pharmacy, Department of Pharmaceutical and Biomedical Sciences
UGA College of Pharmacy & Biomedical Sciences
UGA College of Pharmacy and Biomedical Sciences
UGA College of Pharmacy Biomedical Sciences
University of Georgia College of Pharmacy Department of Pharmaceutical and Biomedical Sciences
University of Georgia College of Pharmacy Department of Pharmaceutical Biomedical Sciences
Department of Pharmaceutical and Biomedical Sciences research focus is on the cutting edge of pharmaceutical sciences. Provides training at professional, master, doctoral and post-doctoral levels in wide range of disciplines, including medicinal chemistry, pharmaceutics, toxicology, drug delivery, pharmacology and many other related biomedical sciences.
Predicting Regulatory Information from Single Motifs
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Knime4Bio: custom nodes for the interpretation of Next Generation Sequencing data with KNIME
A set of custom nodes for the KNIME (The Konstanz Information Miner) graphical workbench, for analysing next-generation sequencing (NGS) data without the requirement of programming skills.
ergatis: workflow creation and monitoring interface
A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level.
Medical Research Council Mammalian Genetics Unit
It is now widely known that animals share many genes with humans and can suffer from the same diseases, for example diabetes or deafness. Investigating these diseases in animals can provide vital leads to understanding both their causes and ways to treat them in humans. This approach to medical research lies at the heart of work at the MRC Mammalian Genetics Unit (MGU) at Harwell in Oxfordshire. In 1995 the MRC Radiobiology Unit was reconstituted to form two new units, the Radiation and Genome Stability Unit and the MGU. These opened in January 1996, together with the UK Mouse Genome Centre which is now part of MGU, making MRC Harwell a unique campus for multi-disciplinary genetics research. Since MGU's Director Steve Brown took the reins in 1996, the unit has dramatically expanded its scientific scope and increased its personnel from 40 to over 100. It now has 13 research programs encompassing molecular genetics, genomics, genetic manipulation and data analysis at all levels, from single genes to the whole genome. With a combination of cutting-edge facilities and expertise unrivaled in Europe, MGU Harwell has become firmly established as one of the world's leading academic centres for mouse genetics.
Series of tutorial material covering a broad selection of topics in bioinformatics. Categories include: Bioinformatics APIs, Data integration, Events, Grid and Cloud Computing, Metabolic modelling, Reviews, Software Comparisons, Statistics, Systems Biology, Transcriptomics, Tutorials.
Knowledge Blog for descriptive, tutorial and explanatory material about building, using and maintaining ontologies, as well as the social processes and technology that support this. Ontogenesis features over 20 articles written by leading academics, and has attracted over 17,000 page reads. Articles are peer-reviewed. Following publication as reviewed, articles are stable and can be cited by stable URL or DOI. Ontogenesis is now archived by the British Library as part of the UK Web Archive and is indexed by Google Scholar. The initial idea for Ontogenesis came from Phillip Lord. You can read the original manifesto that they wrote, describing the purpose of this blog. Ontogenesis is the first and main example of a Knowledgeblog, a flexible and light-weight process for scientific publication. It has received funding from JISC. They are currently open to submissions. Please contact them if you want further information, or would like to offer articles for publication., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Taverna Knowledge Blog: Designing, Executing and Sharing Scientific workflows
NBIA Disorders Association: from discovery to cure
The NBIA Disorders Association, formerly known as Hallervorden-Spatz Syndrome Association, (HSSA) was originally founded in 1996 by President, Patricia Wood. The goals of the association are to raise funds to support research pertinent to NBIA; to provide emotional support to those afflicted with NBIA and their families; and to raise public awareness of NBIA. The NBIA Disorders Association is accepting applications for one-year grants for clinical and translational research studies related to the early detection, diagnosis, or treatment of patients with NBIA. Neurodegeneration with Brain Iron Accumulation (NBIA) is a group of rare, genetic, neurological disorders characterized by the accumulation of iron deposits in the brain and progressive degeneration of the nervous system. It typically first appears in childhood. Presenting signs and symptoms may include difficulty walking, loss of balance, and problems related to speech. Those affected suffer a progressive loss of muscle control, sudden involuntary muscle spasms, and uncontrolled tightening of the muscles. Symptoms may also include disorientation, seizures, and deterioration of intellectual ability. Approximately half of the cases diagnosed have been linked to a mutation of a gene known as PANK2. At the present time, symptoms may be treated but there is no cure. The purpose of the NBIA Disorders Association Research Grant Program is to encourage meritorious research studies designed to improve the diagnosis or treatment of NBIA. The research can be conducted in the United States, countries of the European Union, Canada, Australia, New Zealand, Brazil, Argentina, Chile, South Africa, Japan, or Israel, and in other countries where adequate supervision of grant administration is possible. Grants will be awarded to qualified researchers to initiate pilot studies, the results of which are intended to be used to obtain larger multi-year grant funding. Evaluation of proposals will follow NIH guidelines and include careful consideration of experimental or protocol design, objectivity or relevance of parameters measured, and statistical analysis plan. Proposals that address the following areas will be given priority: * Therapeutics Development: ** Development of pantethine and its derivatives ** Development of other rational therapeutics * Animal & Cellular Models: ** Development of a new rodent disease model by targeted insertion of a ''human disease'' mutation into Pank2 ** Development of induced pluripotent stem cell lines. *** Development of animal and cellular models will be considered for multi-year funding with adequate budget justification. Proposals should detail a research plan and a budget for the initial phase of the work, with the option to contract further work out to a commercial enterprise. * Biomarker Discovery and Assay Development: ** Metabolomics ** Coenzyme A / acyl coenzyme A measurement using accessible (peripheral and central) tissue/fluid * New NBIA gene discovery
International Society for Biological and Environmental Repositories
International Society Biological Environmental Repositories
International Society for Biological and Environmental Repositories (ISBER)
ISBER - International Society for Biological and Environmental Repositories
Global biobanking organization that creates opportunities for networking, education, and innovation. ISBER provides a community for harmonizing approaches to emerging challenges in repositories, as well as fostering ideas to create new solutions.
Neuroscience Information Framework Integrated Jobs
A virtual database currently indexing the following scientific Job resources: Naturejobs, Monster, Indeed, Hays, jobs.ac.uk, New Scientist Jobs, Science Careers, Access-ScienceJobs.co.uk, TheScienceJobs.com, ScienceBlogs: Jobs, and It Takes 30.
A Comprehensive Bioinformatics Scientific Workflow Module for Distributed Analysis of Large-Scale Biological Data that is distributed on top of the core Kepler scientific workflow system.
Neuroscience Information Framework Integrated Blogs
Neuroscience Information Framework Integrated News
A virtual database created by the Neuroscience Information Framework currently indexing Scientific Blog and News resources such as: Nature Network Blogs, Wired Science Blogs, The Guardian: Science, It Takes 30, Scientific American Cross-Check, Scientific American Bering in Mind, Research Blogging, CENtral Science, ScienceBlogs: Medicine and Health, American Guest Blog, Scientific American Observations, LabSpaces, RetractionWatch.com, Wired Science, Genomes Unzipped, PLoS Blogs, Daring Nucleic Adventures - genegeek, H2SO4Hurts - Brian Krueger PhD, and Sciblogs.
A literature search and visualization tool that allows end users to enter any PubMed query and see that query rendered as a heatmap illustrating which regions of interest are most commonly mentioned within the search results. To use PubBrain, simply enter any valid PubMed search in the search box.
The Gulf of Mexico Oil Spill Incident has impacted many aspects of the coastal environment and the people living in the coastal states. The general public, government officials, and journalists would like to get a general, big picture of the impact, and Gulf-based researchers would like to investigate the fate and effects of oil, dispersed oil, and dispersant on the ecosystems of the Gulf of Mexico and affected coastal states. The topic map we have developed serves to facilitate not only the understanding of the impacts of the incident but also knowledge discovery through interdisciplinary knowledge fusion. Although the topic map focuses on the Gulf of Mexico Oil Spill Incident, it also covers oil spill incidents and concerns elsewhere. A topic map has three constructs: (1) topics (or concepts), (2) associations (or relationships, links) between the topics, (3) information resources relevant to a given topic. You will be able to see all three of these on the topic map. By scanning the topics and their relationships, you can get a big picture of the topics and focus on the information resources that relate most significantly to your interest, and hopefully discover new knowledge by integrating the knowledge from multiple disciplines. Please visit our User Guides to get an idea of how to navigate through the topic map, and its textual interface. The topic map is posted at: http://topicmap.lsu.edu The project is funded by Gulf of Mexico Research Initiative through Louisiana State University.
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool designed for efficient and accurate variant detection in high throughput sequencing data. Haplotype based variant caller for next generation sequence data.
An atlas of normal and abnormal brain images intended as an introduction to basic neuroanatomy, with emphasis on the pathoanatomy of several leading central nervous system diseases that integrates clinical information with magnetic resonance (MR), x-ray computed tomography (CT), and nuclear medicine images. A range of brain abnormalities are presented including examples of certain brain disease presented with various combinations of image type and imaging frequency. Submissions of concise, exemplary, clinically driven examples of neuroimaging are welcome.
Emage (e-Mouse Atlas of Gene Expression)
A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without.
Brown Alpert Medical School Brain Tissue Resource Center
A tissue resource center which facilitates research into the relationship between Alzheimer's disease and other brain disorders such as strokes and mental illnesses. Most donations have been obtained from Alzheimer's patients. Normal controls are available, many of which are from subjects with close relatives with Alzheimer's. The Brown BTRC also supports a collection of brain tumor cases that were harvested from patients who underwent surgery and who were enrolled in a clinical trial for the development of new treatments for brain cancer.
NEURON for empirically-based simulations of neurons and networks of neurons
NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties. NEURON has benefited from judicious revision and selective enhancement, guided by feedback from the growing number of neuroscientists who have used it to incorporate empirically-based modeling into their research strategies. NEURON's computational engine employs special algorithms that achieve high efficiency by exploiting the structure of the equations that describe neuronal properties. It has functions that are tailored for conveniently controlling simulations, and presenting the results of real neurophysiological problems graphically in ways that are quickly and intuitively grasped. Instead of forcing users to reformulate their conceptual models to fit the requirements of a general purpose simulator, NEURON is designed to let them deal directly with familiar neuroscience concepts. Consequently, users can think in terms of the biophysical properties of membrane and cytoplasm, the branched architecture of neurons, and the effects of synaptic communication between cells. * helps users focus on important biological issues rather than purely computational concerns * has a convenient user interface * has a user-extendable library of biophysical mechanisms * has many enhancements for efficient network modeling * offers customizable initialization and simulation flow control * is widely used in neuroscience research by experimentalists and theoreticians * is well-documented and actively supported * is free, open source, and runs on (almost) everything
PING - Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference for Nucleosome Positioning
Software program for probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.
International Neuroinformatics Coordinating Facility Training in Neuroinformatics
The International Neuroinformatics Coordinating Facility (INCF) Training in Neuroinformatics section provides a broad listing of educational and training opportunities in fields related to neuroinformatics.
BETA - Binding and Expression Target Analysis
A software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (1) to predict whether the factor has activating or repressive function; (2) to infer the factor' '''s target genes; and (3) to identify the motif of the factor and its collaborators which might modulate the factor' '''s activating or repressive function. BETA requires ~2GB RAM and 1h for the whole procedure. BETA may run on the web server at Cistrome or may be downloaded.
An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet.
J. Craig Venter Institute Comprehensive Microbial Resource
Database of all of the publicly available, complete prokaryotic genomes. In addition to having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes. CMR offers a wide variety of tools and resources, all of which are available off of our menu bar at the top of each page. Below is an explanation and link for each of these menu options. * Genome Tools: Find organism lists as well as summary information and analyses for selected genomes. * Searches: Search CMR for genes, genomes, sequence regions, and evidence. * Comparative Tools: Compare multiple genomes based on a variety of criteria, including sequence homology and gene attributes. SNP data is also found under this menu. * Lists: Select and download gene, evidence, and genomic element lists. * Downloads: Download gene sequences or attributes for CMR organisms, or go to our FTP site. * Carts: Select genome preferences from our Genome Cart or download your Gene Cart genes. The Omniome is the relational database underlying the CMR and it holds all of the annotation for each of the CMR genomes, including DNA sequences, proteins, RNA genes and many other types of features. Associated with each of these DNA features in the Omniome are the feature coordinates, nucleotide and protein sequences (where appropriate), and the DNA molecule and organism with which the feature is associated. Also available are evidence types associated with annotation such as HMMs, BLAST, InterPro, COG, and Prosite, as well as individual gene attributes. In addition, the database stores identifiers from other centers such as GenBank and SwissProt, as well as manually curated information on each genome or each DNA molecule including website links. Also stored in the Omniome are precomputed homology data, called All vs All searches, used throughout the CMR for comparative analysis.
A free, fully featured, powerful, configurable and easy to maintain bioinformatics workstation that provides more than 500 bioinformatics programs on an Ubuntu Linux 12.04 LTS base. Install it or run it live. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can run a Bio-Linux system on Amazon EC2 or other cloud computing architectures by using CloudBioLinux.
Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch have assigned RRIDs which are used to cite resources in scientific manuscripts. SciCrunch Registry, formerly NIF Registry, provides resources catalog. Allows to add new resources. Allows edit existing resources after registration. Curators are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping contents current.
Neuroscience Information Framework Literature
Simultaneous search across multiple literature indices, including PubMed and Open Access literature, it is one of the core resources of NIF accessed through the NIF search interface. Literature results are displayed under the Literature tab. Features: * Facet by Year, Author, and / or Journal * Option to search open access literature only * Sort by relevance or year * Snippets from the full text of the paper are included in search results where search term was found * LinkOuts are now provided for some papers. These mean that someone associated a reagent, piece of data, note/blog, etc., with this specific publication. * Searching within sections of articles is now possible within the open access literature. For more info, see, http://neuinfo.org/about/release_notes_4.5.shtm#search. * Annotate papers. Any user can submit a public comment or annotation of an open access paper through the DOMEO tool. For more information, see http://neuinfo.org/about/release_notes_4.5.shtm#annotate
A freely editable semantic wiki for community-based curation of the terms used in Neuroscience. Entries are curated and eventually incorporated into the formal NIFSTD ontology. NeuroLex also includes a Resource branch for community members to freely add neuroscience relevant resources that do not become part of NIFSTD ontology but rather make up the NIF Registry. As part of the NIF, we provide a simple search interface to many different sources of neuroscience information and data. To make this search more effective, we are constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g., neuron is a cell. These categories provide the means to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that we use to describe our data, e.g., anatomical terms, techniques, organism names. Because wikis provide an easy interface for communities to contribute their knowledge, we started the NeuroLex.
Data analysis service for gene-list enrichment analysis against a manual database. It allows users to input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The database integrates interaction data from ChIP-chip, ChIP-seq, ChIP-PET and DamID studies and contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes.
A database for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs (snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase currently includes millions of transcription factor binding sites (TFBSs) among 6 species. ChIPBase provides several web-based tools and browsers to explore TF-lncRNA, TF-miRNA, TF-mRNA, TF-ncRNA and TF-miRNA-mRNA regulatory networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Data portal that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations (May 2013). Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update.
A software library for analyzing DNase-seq data.
A database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains >2000 samples from >500 ChIP-seq and ChIP-chip experiments, representing a total of >170 proteins and >10,000,000 protein-DNA interactions (March 2014). A web server provides an interface for database query. Protein-DNA binding intensities can be retrieved from individual samples for user-provided genomic regions. The retrieved intensities can be used to cluster samples and genomic regions to facilitate exploration of combinatorial patterns, cell type dependencies, and cross-sample variability of protein-DNA interactions.
IARC Recommendations and Protocols for Biobanking
IARC Recommendations Protocols for Biobanking
International Agency for Research on Cancer Recommendations and Protocols for Biobanking
The IARC Working Group Reports contain common minimum technical standards and protocols for Biological Resource Centres dedicated to Cancer Research. * Cover Page * Table of Contents * Working group participants * Preamble * Definitions * Roles of biological resource centres in cancer research * Recommendations for BRCs * Selected protocols * Annexes
Homo Sapiens Comprehensive Model Collection
Homo Sapiens Comprehensive Model Collection (HOCOMOCO) of transcription factor (TF) binding models
Homo Sapiens Comprehensive Model Collection of transcription factor binding models
A comprehensive collection of human transcription factor binding sites models. DNA sequences of TF binding regions obtained by both pregenomic and high-throughput methods were collected from existing databases and other public data. The ChIPMunk software was used to construct positional weight matrices. Four motif discovery strategies were tested based on different motif shape priors including flat and periodic priors associated with DNA helix pitch. A quality rating was manually assigned to each model based on known binding preferences. An appropriate TFBS model was selected for each TF, with similar models selected for related TFs. In any case only one model per TF was selected unless there was additional evidence for two distinct binding models or different stable modes of dimerization. All TFBS models and initial binding segments data used for motif discovery were mapped to UniPROT IDs.
Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
TFinDIT: Transcription Factor-DNA Interaction Data Depository
Transcription Factor-DNA Interaction Data Depository
A database and web service for structural bioinformatics studies of transcription factor (TF)-DNA interactions. Various datasets can be generated based on one or more search options specified by users.
Arabidopsis thaliana Promoter Binding Element Database
AtProbe: Arabidopsis thaliana Promoter Binding Element Database
Arabidopsis thaliana promoter binding element database that focuses on specific binding elements on known genes, found with experimental methods.
Database of transcription factors with alignments and primers
A database of transcription factors from 13 plant species, and PCR primers for around 90% of them.
Neuroscience Information Framework (NIF) Standard Ontology
Neuroscience Information Framework Standard Ontology
The NIF Standard Ontology (NIFSTD) is a collection of modular ontologies that provides an extensive set of terms and concepts important for the domains of neuroscience and biology, as well as the data and resources relevant for the life sciences. It is a core component of the Neuroscience Information Framework (NIF) project, a semantically enhanced portal for accessing and integrating neuroscience data, tools and information.
Public research university in Lisbon, and the largest university in Portugal. It was founded in 2013, from the merger of two previous public universities located in Lisbon, the former University of Lisbon and the Technical University of Lisbon.
International Neuroinformatics Coordinating Facility Funding
International Neuroinformatics Coordinating Facility (INCF) Funding is an overview of funding opportunities for neuroinformatics research and infrastructure. This list is not comprehensive and we are continually adding to it.
A web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.
BrainImmune - Reference Source for Bridging Neurosciences and Immunology
BrainImmune is a free web-based reference that provides comprehensive and up-to-date information on the broad spectrum of medical research related to brain-immune interactions and their impact on health and disease. BrainImmune is written collaboratively by experts in the field from all around the world. Here, concise summaries of basic and clinical research describe how the brain and the immune system ''talk'' to each other in order to maintain homeostasis. BrainImmune is continually updated, with articles and opinions on history, the present state of the art, and new ideas and conceptual frameworks for the neurohormonal- and stress-immune interactions and their implications for common human diseases. Our goal in developing BrainImmune is to facilitate and advance neuroendocrine-immunology research, and the communication and collaborations in this vast interdisciplinary area.
The mission of AIS is to improve the health of the community by setting the standard of stress management in education, research, clinical care and the workplace. The American Institute of Stress educates medical practitioners, scientists, health care professionals and the public; conducts research; and provides information, training and techniques to prevent human illness related to stress.
From time to time the Editor of Health and Stress interviews leaders in the field of stress management on a variety of topics for inclusion in our publications. Some interviews are listed below. For a complete list of interviews and content, you must be a member of AIS and access the Archives.
Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology.
International Agency for Research on Cancer
IARC - International Agency for Research on Cancer
The International Agency for Research on Cancer (IARC) is part of the World Health Organization. IARC''s mission is to coordinate and conduct research on the causes of human cancer, the mechanisms of carcinogenesis, and to develop scientific strategies for cancer prevention and control. The Agency is involved in both epidemiological and laboratory research and disseminates scientific information through publications, meetings, courses, and fellowships.
TOBFAC: The database of tobacco transcription factors
Database of transcription factor sequences from a single plant species (over 2,500 genes). It is possible to search: # 1,159,022 gene-space sequence reads (GSRs) obtained by methylation filtering from the Tobacco Genome Initiative (TGI). # The DFCI Tobacco Gene Index (Release 4.0 July 5, 2008) that contains 163,524 tobacco EST sequences and 2,288 expressed transcripts (ETs). # The complete TOBFAC database of tobacco transcription factors. It is also possible to search multiple libraries in a single search. They have incorporated tools for downloading all of the sequences from the blast results and also a contig tool to assemble any or all of the resulting sequences. They are also improving the TOBFAC sequences by extending the original contigs using a contig extension tool designed by Ryan Thompson. This has allowed them to refine the predicted genes. These will be updated on a gene family basis as the improved data become available.
University of Liverpool; Liverpool; United Kingdom
Public university based in the city of Liverpool, England. Founded as a college in 1881, it gained its Royal Charter in 1903 with the ability to award degrees and is also known to be one of the six original 'red brick' civic universities.
A software tool for spliced and unspliced alignments and SNP detection of short sequence reads.
American Society for Investigative Pathology
American Society for Investigative Pathology (ASIP)
The American Society for Investigative Pathology (ASIP) is a society of biomedical scientists who investigate mechanisms of disease. Investigative pathology is an integrative discipline that links the presentation of disease in the whole organism to its fundamental cellular and molecular mechanisms. It uses a variety of structural, functional, and genetic techniques and ultimately applies research findings to the diagnosis and treatment of diseases. ASIP advocates for the practice of investigative pathology and fosters the professional career development and education of its members. The mission of the Society is to promote the discovery, advancement, and dissemination of basic and translational knowledge in experimental pathology and related disciplines. This shall be achieved by fostering investigation into the pathogenesis, classification, diagnosis, and manifestations of disease through meetings, publications, and educational activities. ASIP welcomes basic and clinical biomedical research scientists as active members.
Neuroskeptic - A thought experiment gone horribly wrong
Neuroskeptic - International Brain of Mystery
A blog by a neuroscientist (United Kingdom) that takes a skeptical look at his own field, and beyond.
BSeQC: Quality Control of bisulfite sequencing experiments
A quality control software package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing.
A blog about functional MRI from a lab at UC Berkeley.
SKIPPY - A Tool for the Detection of Exonic Variants that Modulate Splicing
A Web-based tool that allows users to input a set of exonic variants to score them for a number of features (such as changes in splicing regulatory elements) that have been shown to be predictive of known genome variations that cause exon skipping or activation of ectopic splice sites. In this way, variants can be either prioritized for further splicing-based functional analysis or the results can be used as further genomic evidence in cases in which the causative variant is already known.
A database of maize genomic sequences, searchable by BLAST, by repeat sequences, and sequence name, gene name, locus, or other landmark. TIGR is a member of the Consortium for Maize Genomics. The Consortium received a funding award from the National Science Foundation in September 2002, to evaluate two gene-enrichment techniques, methylation filtration and high Cot selection, to sequence the maize 'genespace'. Draft assemblies of 287 maize BAC clones selected by the maize community and the Consortium were also produced in the Consortium project. We have recently developed an improved version of the TIGR annotation pipeline optimized for maize genomic assemblies. The latest maize genomic assemblies obtained by gene-enrichment (AZM5) and the 287 maize draft BAC assemblies have been annotated using the improved pipeline. Gene model annotation and functional annotation can be accessed via the TIGR maize BLAST server or the TIGR maize gbrowse display. The first version of the Maize Repeat Database contained 485 characterized maize repeat sequences from the TIGR Cereal Repeat Database. To these we added repetitive sequences downloaded from GenBank and a file of retrotransposon sequences compiled by Phillip SanMiguel (Purdue University). In addition we searched our maize genomic assemblies (AZMs) to identify new repeats. Any sequence within an AZM that showed at least 80% identity over a minimum stretch of 100 bp with an entry in the TIGR Cereal Repeat Database was coded accordingly and added to the Maize Repeat Database.
C software program for displaying sequence statistics for next generation sequencing. Works with large fasta, fastq and SAM/BAM files.
International Neuroinformatics Coordinating Facility Blog
The International Neuroinformatics Coordinating Facility (INCF) Neuroinformatics blog.
Ministry of Education and Science of the Russian Federation
Russian Ministry of Education and Science
Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.
Videos uploaded to YouTube by the Whole Brain Catalog.
International Neuroinformatics Coordinating Facility - YouTube
Videos uploaded to YouTube by the International Neuroinformatics Coordinating Facility (INCF).
A software package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. This QC pipeline supplies a fast, easy-to-use, and parallel processing approach to accomplish the comprehensive QC steps, which could be applied widely to almost all kinds of NGS reads, including genomic, transcriptomic and metagenomic data.
Bis-SNP - A bisulfite space genotyper & methylation caller
Bis-SNP - A bisulfite space genotyper and methylation caller
A software package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol. It contains the following key features: * Call and summarize methylation of any cytosine context provided (CpG, CHH, CHG, GCH et.al.); * Work for single end and paired-end data; * Accurtae variant detection. Enable base quality recalibration and indel calling in bisulfite sequencing; * Based on Java map-reduce framework, allow multi-thread computing. Cross-platform; * Allow multiple output format, detailed VCF files, CpG haplotype reads file for mono-allelic methylation analysis, simplified bedGraph, wig and bed format for visualization in UCSC genome broswer and IGV browser. BisSNP uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
bisulfighter - A pipeline for accurate detection of methylated cytosines and differentially methylated regions
A software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data.
CpG_MPs: identification of CpG methylation patterns of genomic regions
Tool for identification and analysis of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. It may identify the unmethylated and methylated regions for a single sample, the conserved and differential methylation regions with different methylation patterns for paired or multiple samples. It includes four main modules as follows: # Normalization of the sequencing reads of cytosines following guanines; # Identification of the unmethylated (methylated) regions using hotspot extension algorithm; # Identification of conservatively and differentially methylated regionsby combining the combinatorial algorithm for determination of potentially functional regions with the algorithm of analysis of variance (ANOVA) for assess the statistical significance of differentially methylated regions; # Extraction of sequence features and visualization of these potentially functional regions.
Cytosine Methylation Analysis Tool for Everyone
A web application that allows you to perform a quick and comprehensive methylation analysis of cytosine sites in DNA sequences.
Web application that facilitates the management and analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins.
A web-based tool for bisulfite sequencing analysis that was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species.
Brain-Computer Interfaces University of Zaragoza - YouTube
Videos uploaded to YouTube by the Brain-Computer Interfaces (BCI) research team, University of Zaragoza.
High-Quality methylation maps and SNV calling from BS-Seq experiments
A user friendly software tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation.
The human brain has the remarkable ability to adapt in response to changes in the environment over the course of a lifetime. This is the mechanism for learning, growth, and normal development. Similar changes or adaptations can also occur in response to focal brain injuries, e.g., partially-adapted neighboring brain regions or functionally-related brain systems can either substitute for some of the lost function or develop alternative strategies to overcome a disability. Through ongoing research, the Music and Neuroimaging Laboratory''s mission is to: * Reveal the perceptual and cognitive aspects of music processing including the perception and memory for pitch, rhythmic, harmonic, and melodic stimuli. * Investigate the use of music and musical stimuli as an interventional tool for educational and therapeutic purposes. * Reveal the behavioral and neural correlates of learning, skill acquisition, and brain adaptation in response to changes in the environment or brain injury in the developing and adult brain. * Reveal the determinants and facilitators for recovery from brain injury. Project topics include: Aphasia Therapy, Singing and Speaking, Tone Deafness / Congenital Amusia, Motor Recovery Studies, Music and Emotions, Music and Autism, Children and Music Making, Brain Stimulation, Adult Musician Studies, Absolute Pitch Studies, Acute Stroke Studies
A simple integrated software tool for handling MAP (methyltransferase accessibility protocol) and MAP-IT (MAP individual templates) footprinting projects. It can process sequence data (*.txt, *.ab1 and *.scf) derived from the use of up to four different DNA methyltransferases.
A software tool to simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels from BS-seq, oxBS-seq and TAB-seq experiments. It generates consistent estimates across experiment types.
A classification software for DNA methylation profiling with bisulphite next-generation sequencing data.
German Rheumatism Research Centre Berlin; Berlin; Germany
Deutschen Rheuma-Forschungszentrum Berlin
German Rheumatism Research Centre Berlin
Institute in the field of immunology, experimental rheumatology and rheumatism epidemiology.
Resource:F1000: Faculty of 1000 Post-Publication Peer Review
Faculty of 1000 - YouTube is a YouTube video resource highlighting some of F1000''s top articles in biology and medicine -- selected and evaluated by our Faculties of more than 10,000 expert scientists and clinical researchers. If you wish to blog, twitter or otherwise communicate or disseminate the results or discussion in these videos to any third parties, blogs, message boards or other public online resources, you must contact the presenting author first to obtain their permission.
International Foundation for Music Research
National Association of Music Merchants Foundation
The NAMM Foundation is a non-profit organization with the mission of advancing active participation in music making across the lifespan by supporting scientific research, philanthropic giving and public service programs from the international music products industry. FOUNDATION ACTIVITIES: * Research: The NAMM Foundation provides support for projects that explore the impact of active music making during various stages of life and on human experience and conditions. The Foundation then promotes this research through the media to educate people of all ages about the proven benefits of playing music. * Program Grants: The NAMM Foundation supports innovative community-based music learning programs that allow more people the opportunity to experience the proven benefits of active music making. In 2010, the NAMM Foundation provided close to $600,000 in grants to worthy organizations and programs. * Wanna Play Fund: Wanna Play? is a public education campaign designed by NAMM in 2006 to raise awareness of the many benefits of music making and inspire people of all ages and talent levels to become active music makers. Initiated in September 2009, the Foundation''s Wanna Play Fund seeks public donations for programs and activities that expand access to music education and participation in music making for people of all ages. Donations to the Wanna Play Fund will be used to provide musical instruments to schools that are expanding or re-instating music education programs. * The Museum of Making Music: The mission of the Museum of Making Music is to celebrate the rich history and encourage the future of music making. The one-of-a-kind museum invites all NAMM Members to tour the Museum FREE of charge. Located in the NAMM Industry Headquarters in beautiful Carlsbad, Calif., the museum is a great way to experience first-hand the impact of the music products industry over the last 100 years. For more information about the museum or its activities, call 877-551-9976 or visit www.museumofmakingmusic.org. * SupportMusic Coaltion and Music Education Advocacy: The NAMM Foundation seeks to strengthen music education in schools and communities nationwide through its SupportMusic Coalition and website. Music and the arts are vital to every child''s education. SupportMusic provides tools and resources to advance community support for music education with the idea that local parents, teachers, students and advocates CAN make a difference! The NAMM Foundation also annually releases a list of the ������??Best Communities for Music Education������?? honoring schools that demonstrate a strong commitment to music and arts as part of a well-rounded education for every child.
PReprocessing and INformation of SEQuences
A publicly available tool that is able to filter, reformat and trim your genomic and metagenomic sequence data and provide you summary statistics for your sequence data. The interactive web interface facilitates visualizations of the results and export functionality for subsequent data processing. The standalone lite version is written in Perl and does not require any non-core Perl modules. The lite version is primarily designed for data preprocessing and does not generate summary statistics in graphical form., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The primary mission of the Nancy Lurie Marks (NLM) Family Foundation is to help people with autism lead fulfilling and rewarding lives. The Foundation is committed to understanding autism from a scientific perspective, increasing opportunities and services available to the autism community and educating the public about autism. In pursuit of its mission, the Foundation develops and provides grants to programs in research, clinical care, policy, advocacy and education. Founded by Nancy Lurie Marks over 25 years ago, the NLM Family Foundation is one of the largest supporters of initiatives in these areas. The principal goal of the scientific program is to achieve a deeper understanding of the biological basis of autism, focusing on genetics, synaptic chemistry, the neurobiology of communication, systems biology and the physiology of movement. The Foundation funds peer-reviewed research, the development of collaborative investigator projects, and research fellowship programs. Through sponsorship of scientific conferences, symposia and workshops, the Foundation seeks to encourage innovation and provide a springboard to generate new avenues of shared inquiry. The NLM Family Foundation supports programs which focus on novel ways to improve the communication and social abilities of those with autism. Other programs are designed to increase advocacy for legal rights and access to support services for persons with autism, and to increase community understanding and openness to inclusion through education and documentary films.
The Lurie Center for Autism is a highly successful program designed to evaluate and treat children and adults with a wide variety of developmental and handicapping conditions. Our mission is to provide the highest quality clinical, social and support services to those diagnosed with autism, pervasive developmental disorders and other developmental disabilities. The Lurie Center for Autism is unique because of the population it serves and because it uses a multidisciplinary approach that begins with comprehensive medical evaluations and extends to supporting the well-being of patients and families. Nurses, social workers, speech pathologists, occupational therapists, physical therapists, neuro-psychologists, special education professionals and family members are involved in the treatment processes in addition to physicians. Each has a depth of expertise in his/her respective field. The team, as a unit, plays an integral role in the continuum of care for individuals diagnosed with developmental disabilities. Our services and therapies include: * Extensive diagnostic evaluations * Medical, cognitive and behavioral interventions including speech and language * Speech therapy, occupational therapy, occupational with sensory integration therapy and physical therapy; psychological evaluation and counseling; * Parent skills training and family empowerment * Referral support for additional medical and educational resources at locations near each patient''s home and throughout the New England region The Lurie Center for Autism is committed to improving the medical, social and psychological well-being of children, adolescents, adults and families. To this end, our goals and objectives are to: * Provide a stable, consistent and structured environment within a medical context * Provide opportunities for each individual to achieve * Develop self control, social skills and self esteem in each individual * Support and educate families in order to transfer the learned skills to home, school, work and community environments * Provide teaching to physicians and professionals in training and to pursue research related to the treatment and causes of autism, pervasive developmental disorders and other devlopmental disorders of the central nervous system
VolumeRover (a.k.a VolRover) is an interactive multi-purpose image processing software that can visualize three dimensional imaging data of any size (as big as terabyte) in a commodity PC or workstation and additionally supports the following image processing operations. Image Contrast Enhancement, Filtering/Noise Reduction, Image Segmentation, Isocontouring, Symmetry Detection (for Virus Maps, Boundary-free Image Skeletonization. VolRover provides a user interface to a number of CVC software packages including Segmentation, Contrast Enhancement, and Motif Elucidation.
Free University of Brussels; Brussels; Belgium
French speaking research university in Brussels, Belgium. ULB is one of the two institutions, which trace their origins to the Free University of Brussels, founded in 1834 by Belgian lawyer Pierre-Théodore Verhaegen.The split occurred along linguistic lines, forming the French-speaking ULB in 1969, and Dutch-speaking Vrije Universiteit Brussel (VUB) in 1970.
Next Generation Sequencing Quality Control
NGSQC: Next Generation Sequencing Quality Control
Software pipeline that provides a set of novel quality control measures for quickly detecting a wide variety of quality issues in deep sequencing data derived from two dimensional surfaces, regardless of the assay technology used. It also enables researchers to determine whether sequencing data related to their most interesting biological discoveries are caused by sequencing quality issues. NGSQC can help to ensure that biological conclusions, in particular those based on relatively rare sequences, are not caused by low quality sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
It assists in the compilation and identification of repeat sequences in plant genomes. All of the repetitive sequences in the database are coded for the convenience of future analyses. In plants, ploidy levels and repetitive sequences contribute significantly to genome size. A number of different repetitive sequences have been reported in the plant genome and these can be classified into super-classes, classes, and subclasses based on structure and sequence composition. The transposable element (TEs) super-class includes retrotransposons, transposons, and miniature inverted-repeat transposable elements (MITEs). Other repetitive sequences are associated the centromere and telomere. Another super-class of repetitive sequences are rDNAs which encode the structural RNA components of ribosomes.
A software toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Videos uploaded to YouTube by the Laboratory of Neuro Imaging (LONI). The Laboratory of Neuro Imaging at UCLA strives to improve our understanding of the brain in health and disease. LONI is a leader in the development of advanced computational algorithms and scientific approaches for the comprehensive and quantitative mapping of brain structure and function.
Society for Neuroscience Video - YouTube
The Society for Neuroscience (SfN) is a nonprofit membership organization of scientists and physicians who study the brain and nervous system. SFNVideo - YouTube are videos uploaded to YouTube by the Society for Neuroscience (SfN). Since inception in 1969, the Society has grown from 500 members to more than 41,000. Today, SfN is the world''s largest organization of scientists and physicians devoted to advancing understanding of the brain and nervous system.
Brain Blogger - Topics from Multidimensional Biopsychosocial Perspectives
With a team of over 80 contributors, this award winning collaborative health and science blog covers topics from multidimensional biopsychosocial perspectives. We review the most impactful news and research related to neuroscience / neurology, psychology / psychiatry, and health / healthcare. Our blog serves as a beacon for attracting new minds beyond the basic sciences of brain and into the biopsychosocial model. Founded in 2005 by Dr. Shaheen Lakhan, Brain Blogger is an official undertaking of the Global Neuroscience Initiative Foundation (GNIF) an international charity for the advancement of neurological and mental health patient welfare, education, and research. Brain Blogger is one of the most effective mediums for the GNIF to raise awareness of neuro-related topics. We are a proud member of the 9rules Network and the Scientific American Partner Network a handful of selected blogs that share similar interests and readership. Also, our commitment to ethical biomedical journalism is exemplified by successfully undergoing annual voluntary certification by HONcode the oldest and the most used ethical and trustworthy code for medical and health related information available on internet. Moreover, we are a member of the Healthcare Blogger Code of Ethics. Under the editorship of Dr. Shaheen Lakhan, Brain Blogger hosts a team of over 80 contributors from diverse academic, professional, and social backgrounds: including neurosurgeons (Dr. McCleary), psychotherapists (Mr. Yourell), forensic psychologists (Dr. MacHovec), registered nurses (Mrs. Jones), clinical pharmacists (Dr. Gibson), patient advocates (Mrs. Wilson-Herndon), and general citizens concerned about neurological and mental health (Mr. McIntyre). To join our team, please follow the simple instructions to sign-up online.
NextClip - Nextera Long Mate Pair analysis and processing tool
A software tool for analysing reads from Long Mate Pair (LMP) libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads.
Streamlined microsatellite genotyping for quick analysis
Free plugin that imports ABI fragment analysis ?les and allows you to visualize traces, ?t ladders, call peaks, predict bins, display alleles in a tabular format and export your data.
National Institute of Mental Health Multimedia
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Audio and video available from the National Institute of Mental Health (NIMH).
Global Neuroscience Initiative Foundation
Global Neuroscience Initiative Foundation (GNIF)
The GNIF is a non-profit charity organization for the advancement of neurological and mental health patient welfare, education, and research. We aim to further brain related studies, end mental health stigmatization and discrimination, improve the well-being of afflicted individuals, promote the free and open-access distribution of brain related information, and institute universal and multidisciplinary distance educational programs. The paramount GNIF mission is the betterment of neurological and mental health patient welfare, education, and research. With the development of novel free and open-access Therapeutic Recreational Centers, health promotion campaigns, and other charitable activities throughout the world, this organization can aid diagnosed individuals and their advocates. By presenting free and open-access information and educational courses via a distance, the GNIF aims to educate clinicians, teachers, scientists, patients, and the general public on neuroscience, medicine, psychology, biotechnology, and computer science. Moreover, the GNIF supports a variety of sound research programs ranging from biomedical to spiritual studies on the nature of the mind-body connection, biopsychosocial model of health and disease, and health psychology/behavioral medicine practices. The Global Neuroscience Initiative Foundation (GNIF) offers several projects and partnerships adherent to its missions. The following is an alphabetical listing of the GNIF Project Directory: * Brain Blogger * Brain Sciences & Neuropsychiatry * Distance Education Division * Ethics in Mental Health * Knowledge Center * Living with a Brain Disorder * Neuropsychiatry for Kids * Surgical Webcasts * Therapeutic Recreational Centers * Visual Brain Application
BrainBlogger - YouTube are videos uploaded to YouTube by Brain Blogger. Brain Blogger covers topics from multidimensional biopsychosocial perspectives. It reviews the latest news and stories related to neuroscience, psychiatry, and neurology. It serves as a focal point for attracting new minds beyond the science of the mind-and-brain and into the biopsychosocial model.
The TIGR database is a collection of plant transcript sequences. Transcript assemblies are searchable using BLAST and accession number. The construction of plant transcript assemblies (TAs) is similar to the TIGR gene indices. The sequences that are used to build the plant TAs are expressed transcripts collected from dbEST (ESTs) and the NCBI GenBank nucleotide database (full length and partial cDNAs). "Virtual" transcript sequences derived from whole genome annotation projects are not included. All plant species for which more than 1,000 ESTs or cDNA sequences are available are included in this project. TAs are clustered and assembled using the TGICL tool (Pertea et al., 2003), Megablast (Zhang et al., 2000) and the CAP3 assembler (Huang and Madan, 1999). TGICL is a wrapper script which invokes Megablast and CAP3. Sequences are initially clustered based on an all-against-all comparisons using Megablast. The initial clusters are assembled to generate consensus sequences using CAP3. Assembly criteria include a 50 bp minimum match, 95% minimum identity in the overlap region and 20 bp maximum unmatched overhangs. Any EST/cDNA sequences that are not assembled into TAs are included as singletons. All singletons retain their GenBank accession numbers as identifiers. Plant TA identifiers are of the form TAnumber_taxonID, where number is a unique numerical identifier of the transcript assembly and taxonID represents the NCBI taxon id. In order to provide annotation for the TAs, each TA/singleton was aligned to the UniProt Uniref database. For release 1 TAs, a masked version of the Uniref90 database was used. For release 2 and onwards, a masked version of the UniRef100 database is used. Alignments were required to have at least 20% identity and 20% coverage. The annotation for the protein with the best alignment to each TA or singleton was used as the annotation for that sequence. Additionally, the relative orientation of each TA/singleton to the best matching protein sequence was used to determine the orientation of each TA/singleton. Some sequences did not have alignments to the protein database that met our quality criteria, and those sequences have neither annotation nor orientation assignments. The release number for the plant TAs refers to the release version for a particular species. For the initial build, all TA sets are of version 1. Subsequent TA updates for new releases will be carried out when the percentage increase of the EST and cDNA counts exceeds 10% of the previous release and when the increase contains more than 1,000 new sequences. New releases will also include additional plant species with more than 1,000 EST or cDNA sequences that have become publicly available.
Called The Marquis de fMRI by Dr. Anon, NeuroPsyDoctor8 is about neurolaw and related moral cognition research, by someone who has a forensic psych type biz in NYC & then decided to pursue a neuropsych PhD. Now she uses fMRI and a side of bourbon to figure it all out.
The Beautiful Brain explores the latest findings from the ever-growing field of neuroscience through monthly long-form essays, reviews, galleries, short-form blog posts and more, with particular attention to the dialogue between the arts and sciences. The site illuminates important new questions about creativity, the mind of the artist, and the mind of the observer that modern neuroscience is helping us to answer, or at least to provide part of an answer. Instances where art seeks to answer questions of a traditionally scientific nature are also of great interest, and for that reason you will hear from artists as well as scientists on The Beautiful Brain. The Beautiful Brain Podcast also explores the latest findings from the ever-growing field of neuroscience, with particular attention to the dialogue between the arts and sciences. In this monthly program, host Noah Hutton reports on news from the world of brain science, interviews important thinkers about their work, and reviews new literature in the field. The show illuminates important new questions about creativity, the mind of the artist, and the mind of the observer that modern neuroscience is helping us to answer, or at least to provide part of an answer. Instances where art seeks to answer questions of a traditionally scientific nature are also of great interest, and for that reason you will hear from artists as well as scientists on The Beautiful Brain. Subscribe today to receive a brand new episode each month.
A user-friendly software pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster. It is designed to be easily implemented by researchers who do not have expert knowledge of bioinformatics. As it does not have any dependencies, it provides full flexibility and control to the user. The user can use any version of a compatible mapper and any reference genome assembly. There is no need to maintain the mapper, reference or DistMap source code on each of the slaves (nodes) in the Hadoop cluster, making maintenance extremely easy.
PRIMEGENS - High-throughput Primer and Probe Design
A Web-based Tool for High-throughput Primer and Probe Design. The program has its different utilities available on its web server. A standalone version is also available. Algorithms: * SSPD - Sequence Specific Primer Design: to design primers for each of the specific sequences given by the user in the query input file against any alternate potential hybridization with any of the sequences given in the database input file. * PSPD - Probe Specific Primer Design: to design primers it selects the gene-specific fragments (probes) to design primer pairs for their PCR amplification. * FSPD Fragment Specific Primer Design: primer design algorithm used when there is a very long query sequence for which multiple primers are required for its amplification. * Check Binding Specificity * Probe Design Only: Probe design algorithm could be used to find sequence-specific probes, which doesn''t show any blast hit against database. Such probe design has been used for targeted sequencing like agilent sure-select technology with next-generation sequencing.
Python package for analysing immune receptor sequences (antibodies and T cell receptors).
Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
Cache ASsisted Hash Search with Xor logic
Cache ASsisted Hash Search with Xor logic Pipeline
Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G.
neurosphere - neuroscience in everything
This blog belongs to me, Dave J Hayes PhD, a Neuroscientist at the University of Ottawa''s Institute of Mental Health Research. My research focuses on the neuroscience of motivation and emotion particularly regarding how brains and people respond to aversive and rewarding things in their environment. A neurosphere is a free-floating group of neural stem cells which can multiply, outside of their natural environment, and retain the ability to differentiate into functional brain cells. I don''t work on neurospheres. However, i like the metaphor of a group of people coming together, outside of their natural environment, through their interest in all things neuro which, incidentally, is everything. The sphere of human thought.
Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome.
Software program (based on CUSHAW2) designed and optimized for Kepler-based GPUs, but still workable on earlier-generation Fermi-based ones.
Oscillatory Thoughts - Thoughts of a Neuroscientist
Bradley Voytek' '''s blog is where he tries out new ideas. He will often be wrong, but that' '''s the point. He is a Neuroscientist studying human cognition, neuroplasticity, and brain computer interfacing. Into really geeky stuff. World zombie neuroscience expert. Also runs brainSCANr.com with his wife, Jessica.
Genomic Next-generation Universal MAPper
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A software program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. By using the posterior probability of mapping a given read to a specific genomic loation, we are able to account for repetitive reads by distributing them across several regions in the genome. In addition, the output of the program is created in such a way that it can be easily viewed through other free and readily- available programs. Several benchmark data sets were created with spiked-in duplicate regions, and GNUMAP was able to more accurately account for these duplicate regions.
Genomic Short-read Nucleotide Alignment Program
Software to align single and paired end reads as short as 14 nt and of arbitrarily long length. Can detect short and long distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or database of known splice sites. Permits SNP-tolerant alignment to reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for study of methylation state.
Kraken: A set of tools for quality control and analysis of high-throughput sequence data
A set of software tools ( Reaper, Tally and Sequence Imp) designed to streamline the analysis of next-generation sequencing data. Although designed with small RNA sequence analysis in mind the tools can be used to address issues facing next-generation sequencing in general.
Maq: Mapping and Assembly with Qualities
A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.
A reference-guided assembler comprising of two main modular programs: MosaikBuild and MosaikAligner. MosaikBuild converts various sequence formats into Mosaik?s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences and produces BAMs as outputs. At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BAM format. Unlike many current read aligners, MOSAIK produces gapped alignments using the Smith-Waterman algorithm. MOSAIK is written in highly portable C++ and currently targetted for the following platforms: Microsoft Windows, Apple Mac OS X, FreeBSD, and Linux operating systems. Other platforms can easily be supported upon request. MOSAIK is multithreaded. If you have a machine with 8 processors, you can use all 8 processors to align reads faster while using the same memory footprint as when using one processor. MOSAIK supports multiple sequencing technologies. In addition to legacy technologies such as Sanger capillary sequencing, our program supports next generation technologies such as Roche 454, Illumina, AB SOLiD, and experimental support for the Helicos Heliscope.
mrFAST - Micro Read Fast Alignment Search Tool
Software designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient mannerl. Currently Supported Features: * Output in SAM format * Indels up to 8 bp (4 bp deletions and 4 bp insertions) * Paired-end mapping ** Discordant option to generate mapping file ready for VariationHunter to detect structural variants. * One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq * Matepair library mapping (long inserts with RF orientation). Planned Features: * Multithreading
Nextgenmap - A mapping method for Next Generation Sequencing reads
A mapping program for Next Generation Sequencing reads that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. NextGenMap uses a memory efficient index structure (hash table) to store the positions of all 13-mers present in the reference genome. This index enables a quick identification of potential mapping regions for every read. Unlike other methods, NextGenMap dynamically determines for each read individually how many of the potential mapping regions have to be evaluated by a pairwise sequence alignment. Moreover, NextGenMap uses fast SIMD instructions (SSE) to accelerate the alignment calculations on the CPU. If available NextGenMap calculates the alignments on the GPU (using OpenCL/CUDA) resulting in a runtime reduction of another 20 - 50 %, depending on the underlying data set.
A collection of software programs for population genetics analyses from NGS (Next-Generation Sequencing) data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP (Single Nucleotide Polymorphism) or genotype calling, and are particularly suitable for low sequencing depth data.
PASS: a program to align short sequences
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 19, 2020.A program to align short sequences that has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by ILLUMINA, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the compare-and-swap CPU instruction to increase parallelism. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the jellyfish dump command., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Deric Bownds'' Mindblog reports new ideas and work on mind, brain, and behavior - as well as random curious stuff. Deric Bownds, retired Univ. Wisc. Professor, studies brain and mind. My laboratory research of ~35 years contributed to our understanding of how vision works. This work was gradually phased out in the 1990''s as I devoted increasing time to studying the evolution, development, and function of humans brains.
Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site.
A software to map short sequencer reads to reference genomes. It is able to detect not only mismatches but also insertions and deletions. Furthermore, it is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.
SeqMap - A Tool For Mapping Millions Of Short Sequences To The Genome
A software tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions / deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process. A typical mapping can be done in a few hours on an ordinary PC.
A software package for aligning genomic reads against a target genome.
Wisconsin?s High-throughput Alignment Method
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. High-throughput sequence alignment tool that aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Feature list for the current version (v 0.1.5) of WHAM: * Supports paired-end reads * Supports up to 5 errores * Supports alignments with gaps * Supports quality scores for filtering invalid alignments, and sorting valid alignments * finds ALL valid alignments * Supports multi-threading * Supports rich reporting modes * Supports SAM format output
Software that aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads.
National Institutes of Health SciEd Blog
A blog put out by the NIH Office of Science Education.
University based in Lleida, Spain. It was the first university in Catalonia and the whole Crown of Aragon. It was founded in 1300, using the name of Estudi General de Lleida.Leading institution in Spain for research and education in the fields of Agronomy, Food Technology and Forestry.
SNAP - Scalable Nucleotide Alignment Program
A sequence aligner software program that is 10-100x faster and simultaneously more accurate than existing tools like BWA, Bowtie2 and SOAP2. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. GPU-based software for aligning short reads with a reference sequence. It can find all alignments with k mismatches, where k is chosen from 0 to 3.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software package for the mapping of short reads from illumina sequencing machines onto a reference genome. It''s recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features: * Maps single, paired-end and mate pair Illumina reads to a reference genome * Fast: about 20 Gbase per hour in hybrid mode (using BWA) * Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome * High sensitivity for indels and divergent reads, up to 10-15% * Low mapping bias for reads with SNPs * Well calibrated mapping quality scores * Input: Fastq and Fasta; gzipped or plain * Output: SAM, Maq''s map file * Optionally calculates per-base alignment posteriors * Optionally processes part of the input * Handles reads of up to 4500 bases
A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. Mouse brains displayed in the Microsoft Silverlight PivotViewer from the Mouse Brain Library (MBL) which consist of high-resolution images of brains from many genetically characterized strains of mice. PivotViewer makes it easier to interact with massive amounts of data on the web in ways that are powerful, informative, and fun. By visualizing thousands of related items at once, users can see trends and patterns that would be hidden when looking at one item at a time. Because PivotViewer leverages Deep Zoom, it displays full, high-resolution content without long load times, while the animations and natural transitions provide context and prevent users from feeling overwhelmed by large quantities of information. This simple, inviting interaction model encourages exploration and longer audience engagement times, and applies broadly to a variety of content types.
MicrobesOnline is designed specifically to facilitate comparative studies on prokaryotic genomes. It is an entry point for operon, regulons, cis-regulatory and network predictions based on comparative analysis of genomes. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.
Stroke Patient Recovery Research Database (SPReD)
Stroke Patient Recovery Research Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 28,2025. The Stroke Patient Recovery Research Database (SPReD) initiative creates the infrastructure needed for the collection of a wide range of data related to stroke risk factors and to stroke recovery. It also promotes the analysis and management of large brain and vessel images. A major goal is to create a comprehensive electronic database Stroke Patient Recovery Research Database or SPReD and populate it with patient data, including demographic, biomarker, genetic and proteomic data and imaging data. SPReD will enable us to combine descriptions of our stroke patients from multiple projects that are geographically distributed. We will do this in a uniform fashion in order to enhance our ability to document rates of recovery; to study the effects of vascular risk factors and inflammatory biomarkers; and to use these data to improve their physical and cognitive recovery through innovative intervention programs. This comprehensive database will provide an integrated repository of data with which our researchers will investigate and test original ideas, ultimately leading to knowledge that can be applied clinically to benefit stroke survivors.
Latin American Brain Mapping Network (LABMAN)
On March 8, 2008 in Havana, the Latin American Network for Brain Mapping (LABMAN) was created with participants from Argentina, Brazil, Colombia, Cuba and Mexico. The focus of LABMAN is to promote neuroimaging and systems neuroscience in the region through the implementation of training and exchange programs, and to increase public awareness of the Latin American potential to contribute both to basic and applied research in human brain mapping. The immediate LABMAN goals are to: * Train specialists in all major imaging techniques. * Expedite the transfer of new scientific and technical knowledge from abroad. * Increase the scientific productivity of the region. * Drastically increase the awareness of local governments, international organizations and of the general public of brain mapping results on potential. * Organize multinational projects in areas of special relevance to the region, e.g. nutrition, pediatric development, neurodegeneration. Latin American Brain Mapping Network (LABMAN) participants : * Cuban Neuroscience Center * University of Buenos Aires * University of Sao Paulo * Universidad del Valle, Cal��, Colombia * UAM Iztapalapa, Mexico City, Mexico
IdCheck: A tool for genotype and gene expression sample identity checking
Software that allows assessment of concordance between genotype (from SNP arrays or DNA sequencing) and gene expression (RNA-seq) samples. IDCheck compares the identity of RNA-seq reads and SNP genotypes using a likelihood based method. Based on maximum likelihood estimates of relevant parameters, we can detect sample contamination and identify correct sample pairs when swapping occurs.
The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. BMDExpress is a Java application used to analyze dose-response data from microarray experiments. The program was designed to perform a stepwise analysis on microarray data that combines bench mark dose (BMD) calculations with gene ontology (GO) classification analysis. The combination provides dose estimates at which different cellular processes are altered at a defined increase in risk based on expression levels in the untreated controls. The fitting of the data to the statistical models (linear, 2 polynomial models, 3 polynomial, and power models) is performed using source code borrowed from the U.S. Environmental Protection Agency' '''s BMDS software. The MPPD model is a computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 m) to coarse (20 m). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the head is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition. Eight tutorials are provided so that the user can learn to interact with the software.
A flexible software platform for distributed processing, analysis, exchange and visualization of brain imaging data. The expected result is a middleware platform that will render the processing environment (hardware, operating systems, storage servers, etc...) transparent to a remote user. Interaction with a standard web browser allows application of complex algorithm pipelines to large datasets stored at remote locations using a mixture of network available resources such as small clusters, neuroimaging tools and databases as well as Compute Canada's High Performance Computing Centers (HPC). Though the focus of CBRAIN is providing tools for use by brain imaging researchers, the platform is generalizable to other imaging domains, such as radiology, surgical planning and heart imaging, with profound consequences for Canadian medical research. CBRAIN expanded its concept to include international partners in the US, Germany and Korea. As of December 2010, GBRAIN has made significant progress with the original three partners and has developed new partners in Singapore, China, India, and Latin America. CBRAIN is currently deployed on 6 Compute Canada HPC clusters, one German HPC cluster and 3 clusters local to McGill University Campus, totaling more than 80,000 potential CPU cores.
HTSeq: Analysing high-throughput sequencing data with Python
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.
ENIGMA: Enhancing Neuro Imaging Genetics Through Meta-Analysis
Enhancing Neuro Imaging Genetics Through Meta-Analysis
Network that brings together researchers in imaging genomics, to understand brain structure and function, based on MRI, DTI, fMRI and genomewide association scan (GWAS) data. The ENIGMA Network has several goals: * to create a network of like-minded individuals, interested in pushing forward the field of imaging genetics * to ensure promising findings are replicated via member collaborations, in order to satisfy the mandates of most journals * to share ideas, algorithms, data, and information on promising findings or methods * to facilitate training, including workshops and conferences on key methods and emerging directions in imaging genetics. Data sharing with other members of the ENIGMA Network is optional and by no means a requirement of joining the network. Genetics and Imaging Protocols are available.
A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF.
French Ministry of Foreign Affairs and International Development
The Ministry of Foreign Affairs and is the ministry in the government of France that handles France's foreign relations.
A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base resolution border detection. 4) Border matching.
OECI - Organisation for European Cancer Institutes
OECI - Organization for European Cancer Institutes
Organisation for European Cancer Institutes
Organisation for European Cancer Institutes European Economic Interest Grouping
Organization for European Cancer Institutes
The OECI is a non-government, non-profit organization founded in Vienna in 1979. The primary objectives of its 68 associated European Cancer Centres are to improve communication and to increase collaborative activities among European cancer institutes. These goals are achieved by promoting and strengthening Comprehensive Cancer Centres in Europe to reduce cancer incidence and mortality, and supporting cancer patients. The OECI leadership has demonstrated its active involvement in the promotion of a European approach to cancer management as a partner with UICC in the series of European Cancer Management Meetings organized with support from the European Union (Antwerp, 2000; Paris 2001). OECI members are leading Cancer Centres throughout Europe, encompassing the full spectrum of Cancer activities and national considerations. In order to facilitate the activities of their members and the definition of common programs of international interest and to facilitate the participation in European projects and programs the GEIE-LINC and the OECI in 2001 decided to set-up 9 specific Working Groups active in the following fields: Guidelines, Registration & Data Evaluation, Cost-Benefit, Pre-Clinical and Clinical Research, Education, Communication, Telematics & Telemedicine, Pathology, New Technologies
Texas A and M Health Science Center MSC Distribution
Institute for Regenerative Medicine at Scott & White MSC Distribution
Texas A M Health Science Center MSC Distribution
Texas A&M Health Science Center College of Medicine Institute for Regenerative Medicine MSC Distribution
Texas A&M Health Science Center MSC Distribution
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Center for cell line distribution and stock at Texas A&M Health Science Center College of Medicine Institute for Regenerative Medicine. Scott & White have received a grant funded by the NIH to provide well-characterized human adult stem cells, rat stem cells, and mouse stem cells to academic researchers worldwide upon request.
Software to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory.
FreClu - Efficient Frequency-based de Novo Short Read Clustering
An algorithm for efficient frequency-based de novo short read clustering for error trimming in next-generation sequencing. It organizes erroneous short sequences originating in a single abundant sequence into a tree structure such that each child sequence is considered to be derived stochastically from its more abundant parent sequence because of sequencing errors.
Governmental agency of Italy. Its headquarters are in Rome and is led by the Italian Minister of Health.
TMAD- Stanford Tissue Microarray Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd,2023. TMAD stores raw and processed data from Tissue Microarray experiments along with their corresponding stained tissue images. In addition, TMAD provides methods for data retrieval, grouping of data, analysis and visualization as well as export to standard formats. Researchers at the Stanford University School of Medicine and their collaborators worldwide have constructed many tissue microarrays for use in basic research.
This blog highlights and comments on current research and hypotheses relating to how the brain wires itself up during development, how the end result can vary in different people and what happens when it goes wrong. It includes discussions of the genetic and neurodevelopmental bases of traits such as intelligence and personality characteristics, as well as of conditions such as schizophrenia, autism, dyslexia, epilepsy, synaesthesia and others.
Phenologs - Systematic discovery of non-obvious disease models and candidate genes
Database for identifying orthologous phenotypes (phenologs). Mapping between genotype and phenotype is often non-obvious, complicating prediction of genes underlying specific phenotypes. This problem can be addressed through comparative analyses of phenotypes. We define phenologs based upon overlapping sets of orthologous genes associated with each phenotype. Comparisons of >189,000 human, mouse, yeast, and worm gene-phenotype associations reveal many significant phenologs, including novel non-obvious human disease models. For example, phenologs suggest a yeast model for mammalian angiogenesis defects and an invertebrate model for vertebrate neural tube birth defects. Phenologs thus create a rich framework for comparing mutational phenotypes, identify adaptive reuse of gene systems, and suggest new disease genes. To search for phenologs, go to the basic search page and enter a list of genes in the box provided, using Entrez gene identifiers for mouse/human genes, locus ids for yeast (e.g., YHR200W), or sequence names for worm (e.g., B0205.3). It is expected that this list of genes will all be associated with a particular system, trait, mutational phenotype, or disease. The search will return all identified model organism/human mutational phenotypes that show any overlap with the input set of the genes, ranked according to their hypergeometric probability scores. Clicking on a particular phenolog will result in a list of genes associated with the phenotype, from which potential new candidate genes can identified. Currently known phenotypes in the database are available from the link labeled ''Find phenotypes'', where the associated gene can be submitted as queries, or alternately, can be searched directly from the link provided.
BrainEthics - Consequences of Brain Science
There are a lot of fine blogs out there covering the avalance of current neuroscience research. With this blog Thomas Rams��y & Martin Skov want to highlight the many consequences of this growing understanding of the human brain. We are especially interested in two types of consequences: Tinkering with the brain and What is it like to be a human being? * Tinkering with the brain: First and foremost, with an understanding of how the brain works comes the possibility of tinkering with it. We already use billions of dollars every year on psychopharmocologia trying to treat depression, schizophrenia, obsessive-compulsive disorder and other mental diseases. But should we also use our knowledge of the brain to treat undesirable mental traits such as pedophilia or sociopathy? And what about enhancing normal brains? Clearly, evolution hasn''t endowed us with the most efficient brain imaginable. Shouldn''t we do something about its many shortcomings? * What is it like to be a human being?: Secondly, our view of human behavior is sure to change with our improved understanding of the human brain. Our knowledge of core human faculties such as language, social reasoning, aesthetics, and economics is already being challenged by modern neuroscience, yielding multiple hard questions. Do we have a free will? Is the mind innate or plastic? If people are not responsible for their actions (since all actions are caused by blind molecular processes) does our legal system still make sense? In short, will modern neuroscience come to completely redefine human nature? We try to discuss contemporary research literature, not just news reports. Although we will occasionally also target popular science reports, since we believe they play an important role in dissemining lessons from the lab. And in the future we plan to also post interviews with interesting researchers, as well as link to our own publications in journals and books. Additionally, the latest and most important books in the multidisciplinary field of neuroscience, cognition, psychology, ethics and economics are presented.
Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.
French Ministry of Higher Education and Research
Ministere de i''Enseignement Supereur et de la Recherche
Ministere de l''Enseignement Supérieur et de la Recherche
Ministry of Higher Education, Research and Innovation, France is one of the 900 Higher Education-related Organizations and Associations.
How do the recent developments in neuroscience affect psychology and society? Today, many new findings challenge the way we think about ourselves and others. These changes impact on how we should think about issues such as the self, mentality, psychology, free will, morale, law and society. Through interviews of prominent scholars in the fields of neuroscience and beyond, the BrainEthics Podcast provides updated, novel and comprehensive news and views from the world of neuroscience, and how the world responds to it. We provide a full list of all podcast episodes. Although we are hosting all episodes, you can also subscribe to the podcast on all major podcasting directories.
FASTQ/A short-reads pre-processing tools
Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
The mission of AIDS.ORG is to help prevent HIV infections and to improve the lives of those affected by HIV and AIDS by providing education and facilitating the free and open exchange of knowledge at an easy-to-find centralized website. AIDS.ORG makes access to important AIDS information easier and faster. We provide prevention, testing, and treatment information currently to well over 4 million people a year. AIDS.ORG has been awarded the Health on the Net Foundation Code of Conduct (HONcode) seal for reliability and credibility of information in the field of healthcare. Additionally, every year over 2.4 million young people under the age of 25 turn to AIDS.ORG, making us an important resource since over 50% of all new HIV infections in the USA occur in this age group. AIDS.ORG, Inc. is a nonprofit 501(c) (3) educational organization, and maintains a very strict privacy policy. We make it our goal to be the best starting point for someone looking for AIDS information on the Internet. Our intent is that users be directed to the best information on the topic they''re investigating. We bring people together to share knowledge and experiences. In the past, we also provided the very first Internet-based program of accredited AIDS education for medical professionals, allowing doctors in rural and isolated areas to better serve AIDS patients.
TMBETA-GENOME- Annotation of Beta-Barrel Membrane Proteins in Genomic Sequences
A collection of amino acid sequences for all the completed genomes and the annotated trans beta-barrel membrane proteins (TMBs) using different discrimination algorithms. For each genome, the calculations have been performed with statistical methods and machine learning techniques and the results are accumulated in the database. TMBETA-GENOME has the feasibility of selecting the organism from the three kingdoms of life, archaea, bacteria and eukaryote. Further, users have the option to select any of the methods or their combinations, and display the results with/without amino acid sequence information.
The tmRDB is a tool in the study of the structures and functions of the tmRNA (earlier called 10S RNA). As the name implies, tmRNA has properties of tRNA and mRNA combined in a single molecule. The tmRDB provides aligned, annotated and phylogenetically ordered tmRNA sequences. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Where possible, we established direct links to primary sources. We acknowledge support provided by the National Institutes of Health and the Danish Technical Research Council. tRNA, mRNA, trans-translation, rescue, ribosome, broken mRNA, bacteria, mitochondria chloroplasts, cyanelles, bacteriphage, phylogenetic
A software program to identify artificial duplicates from raw 454 sequencing reads, including exact duplicates and near identical duplicates.
modelcrop.org - Comparative genomics using the model grass Brachypodium distachyon
modelcrop.org - The Brachypodium distachyon comparative genomics resource
A Brachypodium distachyon comparative genomics resource offering a genome browser, BLAST server, download capabilities, Brachypodium physical map, Comparative maps, and comparison with rice and Sorghum chromosomes. * Genome browser >>> Browse the v1.0 genome assembly and the v1.0 gene predictions from JGI/MIPS. Also displays JIC FST data (T-DNA lines) and alignments of ESTs from wheat, barley and Brachypodium. * BLAST server >>> BLAST your sequences against the Brachypodium sequence assembly and the predicted proteome. * Download sequence >>> Download sequence from the brachy assembly (limited to 50kb regions). Download complete assembly file as FASTA. Download sequence and additional data from the v1.0 annotated assemblyincluding protein-coding sequences as FASTA, translated coding sequences as FASTA, gene sequences as FASTA, and COS markers. PLEASE NOTE: The published genome analysis is based on the v1.0 annotation. The v1.2 annotation can be downloaded from MIPS. * Brachypodium physical map >>> Brachypodium physical map data displayed using SyMAP. (view in genome browser) * Comparative maps >>> Brachypodium genetic and physical maps aligned to rice and wheat. * Comparison with rice and Sorghum chromosomes >>> Dotplots of the Brachypodium assembly aligned to rice and Sorghum chromosomes.
BioOntology.ch - Interlinked bio-ontologies for knowledge-based data-driven science
BioOntology.ch is a blog on the interlinked bio-ontologies for knowledge-based data-driven science. * Bio-ontology is standards: Modern research generates data at unprecedented rates. Where such data are described and labelled using unconstrained text, different terminology is often used for similar or identical things. Such terminological variance is normal and reflects natural language; usually humans have no difficulty resolving ambiguous usages of terminology and discrepant labels. However, due to the sheer volumes of research data being generated, it is necessary to develop computational methods of aggregating and aligning like with like. One approach to addressing this issue is to adopt shared standards for the categorisation of data. Agreement in annotation across different databases increases the value of a standardised terminology, allowing for easier cross-domain integration and querying. * Bio-ontology is knowledge representation: Modern biomedical ontologies harness the formal semantics underlying the Web Ontology Language (OWL), which allows complex logical expressions to be built that define knowledge about the domain, in such a fashion that computers can perform automatic reasoning for tasks such as hierarchy management and consistency checking / error detection. OWL is based on Description Logics, a family of decidable logical languages optimised for the expression of large-scale terminological knowledge such as is found within large biomedical vocabularies. * Bio-ontology is interdisciplinarity: Increasingly, research in the life sciences needs to integrate knowledge and results from multiple disparate fields and methodological approaches in order to gain insight into underlying biological mechanisms. This is the case, for example, when studying the genetic and epigenetic factors in understanding behavioural phenotypes, or in the development of predictive models to enable personalised and translational medicine. Research results from diverse disciplines such as genetics, molecular biology, physiology, chemistry, psychology and medicine have to be integrated in order to build a coherent picture of what is known in order to address key research gaps.
Phospho3D is a database of three-dimensional structures of phosphorylation sites which stores information retrieved from the phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database also collects the results of a large-scale structural comparison procedure providing clues for the identification of new putative phosphorylation sites.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 24, 2017. Platform to enable dissemination of scientific findings, foster open peer commentary and promote collaboration among the research community. Widespread participation in OneLab will increase the quality, transparency and reproducibility of data thus accelerating the pace of scientific discoveries. The result will be a streamlined process from the bench to the clinic with tremendous benefits for the well-being of the general public. OneLab is a private professional network that mirrors the hierarchy of real world research laboratories. Users are designated as either principal investigators (PI) or lab members. PIs can invite lab members to join and data posted by lab members cannot be shared without PI approval. In this way the PI retains FULL CONTROL over the dissemination of scientific content thus safeguarding the primacy of authorship. This professional network will serve as a backdrop for sharing scientific findings, promote collaborations, and provide a basis for open peer commentary. Semantic Search of Structured Content OneLab implements a powerful search functionality that is based on structured content. Users describe their Single Figure Posts (SFPs) using defined fields such as model organism, genes, proteins and assay. This additional layer of structure provides the basis for a smarter and more accurate search engine that understands searcher intent and therefore generates more relevant results. Structured content allows OneLab to go one step further by offering recommendations based on similarities that might not be intuitive, thus increasing potential collaborations among scientists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
TomatEST DB is a collection of tomato EST sequences downloaded from dbEST. Gene indices are created by grouping overlapping EST sequences into clusters. Each cluster corresponds to a unique gene. A cluster can consist in one or multiple contigs. In the case of a cluster of multiple contigs each contig share similarities with the others in the cluster because of i) putative alternative transcription; ii) paralogy; iii) domain sharing.
Open-source software package for the analysis of neural data. Chronux routines may be employed in the analysis of both point process and continuous data, ranging from preprocessing, exploratory and confirmatory analysis. The current release is implemented as a MATLAB library. Chronux offers several routines for computing spectra and coherences for both point and continuous processes. In addition, it also offers several general purpose routines that were found useful such as a routine for extracting specified segments from data, or binning spike time data with bins of a specified size. Since the data can be continuous valued, point process times, or point processes that are binned, methods that apply to all these data types are given in routines whose names end with ' '''c' ''' for continuous, ' '''pb' ''' for binned point processes, and ' '''pt' ''' for point process times. Thus, mtspectrumc computes the spectrum of continuous data, mtspectrumpb computes a spectrum for binned point processes, and mtspectrumpt compute spectra for data consisting of point process times. Hybrid routines are also available and similarly named - for instance coherencycpb computes the coherency between continuous and binned point process data.
Transmission Disequilibrium Test and Sib Transmission Disequilibrium Test
Software program that provides separate results for TDT, S-TDT, and the combined (overall) test, as appropriate. (entry from Genetic Analysis Software)
HC2 is an EU funded project that aims to promote, support and help define future lines of research in Human Computer Confluence (HCC). HCC is the study of the intersection of HCI, Cognitive Neuroscience, VR/AR, Presence, Pervasive Computing and how they can enable new forms of sensing, perception, interaction and understanding. In a sense it is the study of the disappearing interface. HCC, Human-Computer Confluence, is an ambitious research program studying how the emerging symbiotic relation between humans and computing devices can enable radically new forms of sensing, perception, interaction, and understanding. The horizontal character of HCC makes it a fascinating and fertile interdisciplinary field, but it can also compromise its growth, with researchers scattered across disciplines and groups worldwide. To address this we are building a community of HCC researchers. There are lots of ways you can join in. Add your name to the HCC Players Map, take advantage of our Exchange Program to work with colleagues at your favorite lab, sign up for our Summer School or just follow us on Twitter and LinkedIn to see what''s happening. In order to foster interdisciplinary research and promote HCC research we have set up an Exchange Program. Students that wish to apply for financial support from our Exchange Program should follow the steps provided. The Exchange Program is open to all graduate students (Masters and PhD). A maximum of 500 Euro support will be provided per student.
CGAT - A Comparative Genome Analysis Tool
A comparative genome analysis tool for detailed comparison of closely related bacterial-sized genomes. It visualizes precomputed pairwise genome alignments on both dotplot and alignment viewers. Users can add information on this alignment, such as existence of tandem repeats or interspersed repetitive sequences and changes in codon usage bias, to facilitate interpretation of the observed genomic changes. Besides visualization functionalities, it also provides a general framework to process genome-scale alignments using various existing alignment programs. CGAT employs a client-server architecture, which consists of AlignmentViewer (client; a Java application) and DataServer (a set of Perl scripts). The DataServer package contains data construction scripts and CGI scripts and the AlignmentViewer program visualizes the alignment data obtained from the server thorough the HTTP protocol.
Starlab - Where science turns into the technologies of the future
Starlab''s mission is to transform science into technologies with a profound and positive impact on society. We achieve this by identifying social needs and the market opportunities they create. Then we reach to science and engineering to propose or provide technical solutions, products and services for governments, industry and downstream markets. Starlab Research carries out interdisciplinary R&D focusing on two areas: Space and Applied Neuroscience. Our vision is to make science more useful, alive, vibrant, faster. Our staff consists of a team of scientists, engineers and economists from different nationalities working together to provide our clients with breakthrough technologies that create business opportunities. The growing Starlab team (now more than 28 on staff) includes 5 nationalities spanning knowledge in physics, engineering, oceanography, computer science, neuroscience and economics. Circa 50% of our staff have a PhD, and more than 80% a Master or PhD. We target technology and applications: the development of new sensors and efficient algorithms to extract information from data, identification of platforms and deployment opportunities, as well as the development of services and products. Interdisciplinarity is a key aspect of our research. Space R&D develops payloads, algorithms and mission feasibility studies. We have demonstrated experience in GNSS technologies, radar altimetry and space astronomy. Earth Observation applications include technologies such as GNSS-R, SAR and multi-spectral analysis for environmental and energy applications. We have demonstrated expertise in the development of innovative sensors and systems in both the Space and Applied Neuroscience areas, signal-processing algorithms, with a strong specialization in electrophysiology algorithms, software and hardware. It will also manage the project and prospect potential commercial impact.
An interactive reference atlas providing a systematic overview of cyto- and chemoarchectonical features of the hippocampus proper, fasciola, and associated parahippocampal cortices. This atlas system has been developed to serve the need to integrate detailed descriptions of structures and criteria defining boundaries and atlas images in which the underlying histological features can be explored. Features * Alphabetical and hierarchical overview of 18 hippocampal structures * Detailed, illustrated descriptions of 63 boundaries * Interactive image repository with ~100 coronal histological images stained for NeuN, calbindin, and parvalbumin * Triple image viewer in which differently stained neighboring sections can be interactively compared * Graphical overlay of substructures based on described boundary criteria * Bidirectional links between structure descriptions and image repository The atlas is based on histological material from an adult Long Evans rat, stained for NeuN, calbindin, and parvalbumin. The system is intended for researchers working in the field, as well as students interested in this brain region. The atlas is accessed through the structure index or image viewer. Re-use of data from this repository is allowed provided that reference is given to the publication.
Command-line software tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
Resource Discovery System is a web-accessible and searchable inventory of biomedical research resources. Powered by the Resource Discovery System (RDS) that includes a standards-based informatics infrastructure * Biositemaps Information Model * Biomedical Resource Ontology Extensions * Web Services distributed web-accessible inventory framework * Biositemap Resource Editor * Resource Discovery System Source code and project documentation to be made available on an open-source basis. Contributing institutions: University of Pittsburgh, University of Michigan, Stanford University, Oregon Health & Science University, University of Texas Houston. Duke University, Emory University, University of California Davis, University of California San Diego, National Institutes of Health, Inventory Resources Working Group Members
Massachusetts Institute of Technology OpenCourseWare
A web-based publication of virtually all MIT course content for free. OCW is open and available to the world and is a permanent MIT activity. Materials include free lecture notes, exams, and videos from MIT. No registration required. MIT OpenCourseWare is a free publication of MIT course materials that reflects almost all the undergraduate and graduate subjects taught at MIT. * OCW is not an MIT education. * OCW does not grant degrees or certificates. * OCW does not provide access to MIT faculty. * Materials may not reflect entire content of the course. A site overview is available for MIT OpenCourseWare. You can also browse courses by department or use the advanced search to locate a specific course or topic. High school students and educators should check out Highlights for High School.
Genome Institute of Singapore; Singapore; Singapore
The NIH Chemical Genomics Center (NCGC) was created in 2008 as a Comprehensive Screening Center in the Molecular Libraries Probe Production Centers Network, part of the NIH Molecular Libraries Common Fund Program. The goals of NCGC in the NCATS Division of Pre-Clinical Innovation are to translate the discoveries of the Human Genome Project into biological and disease insights and ultimately new therapeutics for human disease through small molecule assay development, high-throughput screening, cheminformatics and chemistry. NCGC programs include Assay Development and High-Throughput Screening, Chemistry Technology and RNAi. In addition, NCGC is one of 12 centers that make up the National Cancer Institute''s Chemical Biology Consortium. These centers use the consortium''s high-throughput screening, informatics and chemistry resources to work on select cancer biology projects and move them through the therapeutics development pipeline, eventually into the clinic. Through such programs, NCGC produces a variety of pre-clinical research tools, from informatics and software tools to an assay guidance manual and more than 200 molecular probes.
The NIH Chemical Genomics Center plays a role within the NIH Molecular Libraries Initiative (MLI), mandated to bring advanced technologies and expertise to researchers who lack the means to perform high-throughput screens and follow-up medicinal chemistry efforts as a means of identifying and optimizing small molecule probes of novel, unexplored cellular targets. These reagents offer the research community much-needed proof-of-concept pharmacological tools that may serve as starting points for therapeutic development into clinical agents. Results from these projects are disseminated to the scientific community through the publicly accessible PubChem database and via peer-reviewed publications. This highly collaborative program merges academic researchers'' wide-ranging expertise within the study of new biochemical targets and pathways with the translational infrastructure of NCATS. To date, NCATS scientists, in collaboration with hundreds of extramural scientists, have developed more than 60 probes that are freely accessible to the scientific community. A number of these probes are highlighted below: * Project: Activators for Human Pyruvate Kinase M2 (hPK) as Leads in Cancer Therapeutics * Project: Inhibitors of Caspase 1 for the Treatment of Numerous Autoimmune and Inflammatory Diseases * Project: Inhibitors of 12-Human Lipoxygenase (12-hLO) for the Treatment of Diabetes and Clotting * Project: Inhibitors of Cruzain as Therapeutic Leads for Chagas Disease * Project: Inhibitors of NAD+-Dependent 15-Hydroxyprostaglandin Dehydrogenase (HPGD) for the Study of Prostaglandin''s Role in Inflammation * Project: Inhibitors of Cdc2-Like Kinase 4 (Clk4) to Elucidate the Mechanism and Controlling Gene Splicing * Project: Agonists of the Thyroid Stimulating Hormone Receptor for the Treatment of Graves'' Disease * Project: Identification of Inhibitors of the N370S Mutant Form of Glucocerebrosidase as a Potential Therapy for Gaucher Disease * Project: Identification of SMN Modulators for Potential SMA Disease Therapeutics * Project: Inhibitors of Platelet Integrin IIb3 * Project: Identification of Novel Small Molecule Antagonists of the Neuropeptide-S Receptor * Project: Inhibitors of Schistosoma mansoni Redox Cascade
Bio-Image Semantic Query User Environment
Bio-Image Semantic Query User Environment Database
Open source database for exchange and exploration of biological images. Used to store, visualize, organize and analyze images in cloud. Centered around database of images and metadata.
Short Course on the Genetics of Addiction
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This course emphasizes genetic applications and approaches to drug addiction research through methodological instruction based on literature, data sets and informatics resources drawn from studies of addiction related phenotypes. The course includes plenary sessions on major progress in addiction genetics, and discussion sessions in which students present their work for discussion on applications of genetic methods. Students will leave the course able to design and interpret genetic and genomic studies of addiction as they relate to their specific research question, and will be able to make use of current bioinformatics resources to identify research resources and make use of public data sources in their own research.
University of London; London; United Kingdom
Core facility that provides the following services: Cell immortalization through retroviral or lentiviral vectors service, Microscopy training, User-based microscopy service.
A blast oriented interface that allows you to retrieve families of polymorphic sequences. It aims to help molecular evolutionary biologists and population geneticists in their research.
Bisque - Bio-Image Semantic Query User Environment
A scalable web-based system for biological image analysis, management and exploration. The Bisque system incorporates many features useful to imaging researchers from image capture to extensible image analysis and querying. At the core, bisque maintains a flexible database of images and experimental metadata. Image analyses can be incorporated into the system and deployed on clusters and desktops. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content. New features and testing of Bisque version: 0.5.1, among many others are: # Parallel execution of datasets # Rich interfaces for autogenerated module UI # Abstracted storage system for local, irods, etc.. They are using Mercurial for their source control system. This should be installed before proceeding. Browse source on-line, http://biodev.ece.ucsb.edu/projects/bisquik/browser Bisque Installation, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/InstallationInstructions05 Bisque DOWNLOAD, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/download, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Central location for voluntary submission of genetic test information by providers including the test''s purpose, methodology, validity, evidence of the test''s usefulness, and laboratory contacts and credentials. GTR aims to advance the public health and research into the genetic basis of health and disease. GTR is accepting registration of clinical tests for Mendelian disorders, complex tests and arrays, and pharmacogenetic tests. These tests may include multiple methods and may include multiple major method categories such as biochemical, cytogenetic, and molecular tests. GTR is not currently accepting registration of tests for somatic disorders, research tests or direct-to-consumer tests.
Repository of Cre Driver lines and related information resources. Their services include analysis of Cre line excision function in both target and non-target tissues using Cre reporter lines and presenting the annotated data in the expression data portion of this website, http://cre.jax.org/data.html.
Donate a strain to The Jackson Laboratory Repository
Donate a strain to The Jackson Laboratory Repository. Why donate a strain? * Donating reduces your costs of maintaining strains, lab personnel, shipping and resources. * Each donated strain is cryopreserved, protecting against accidental loss and genetic contamination. * Each donated strain is rederived to a high health status and may be resupplied to donors (up to 3 breeder pairs as long as we have live mice available) * Donating fulfills NIH obligations to share mice. How strain donation works: Strains are submitted by investigators for distribution to the scientific community. All repository strains are cryopreserved. All strains are evaluated monthly by the Genetic Resource Committee (GRC). The GRC is made up of staff scientists and resource managers from The Jackson Laboratory. The GRC recommends which strains are most appropriate to include in the Repository. You will be notified by email after your strain has been reviewed. Donation evaluation criteria * Importance of its current use for research, publication history, and current demand * Importance of its anticipated or potential future use * Difficulty of maintenance relative to scientific value * Existence and reliability of other resources that would ensure its survival * Difficulty of re-creating the strain relative to the time and effort required for its importation and preservation
A cross-platform graphical DNA trace viewer and editor that displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. TraceEdit is freely available and designed to operate on Windows and UNIX platforms.
A tool for mapping and performing quality control on Hi-C data.
Jackson Laboratory Neurobiology Resource
A laboratory that researches neurological diseases, including amyotrophic lateral sclerosis, Alzheimer's disease, glaucoma, retinitis pigmentosa, epilepsy, and hearing disorders. The Laboratory offers courses that train and update neuroscience researchers. It distributes JAX Mice models suitable for neuroscience research. Also available are research tools for neurobiology.
Project is providing critical tools for understanding gene function and genetic causes of human diseases. Project KOMP is focused on generating targeted knockout mutations in mouse ES cells. Second phase, KOMP2, relies upon successful generation of strains of knockout mice from these ES cells. Information from JAX about their contributions to KOMP project.
topographic mapping of Single Nucleotide Polymorphism
A topographic database for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of proteins. These include disease- associated nsSNPs derived from the Online Mendelian Inheritance in Man (OMIM) database and other nsSNPs derived from dbSNP, a resource at the National Center for Biotechnology Information that catalogs SNPs. TopoSNP further classifies each nsSNP site into three categories based on their geometric location: those located in a surface pocket or an interior void of the protein, those on a convex region or a shallow depressed region, and those that are completely buried in the interior of the protein structure. These unique geometric descriptions provide more detailed mapping of nsSNPs to protein structures. It also includes relative entropy of SNPs calculated from multiple sequence alignment as obtained from the Pfam database (a database of protein families and conserved protein motifs) as well as manually adjusted multiple alignments obtained from ClustalW. These structural and conservational data can be useful for studying whether nsSNPs in coding regions are likely to lead to phenotypic changes. TopoSNP includes an interactive structural visualization web interface, as well as downloadable batch data.
An online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The individual modules, or Bricks, are unified under a standardized interface, with a consistent look-and-feel and can flexibly be put together to comprehensive workflows. The workflow management is intuitively handled through a simple drag-and-drop system. With this system, you can edit the predefined workflows or compose your own workflows from scratch. Your own Bricks can easily be added as scripts or plug-ins and can be used in combination with pre-existing analyses. GeneXplain GmbH provides a number of state-of-the-art bricks; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field.
Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children' '''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs.
Georgetown University; Washington D.C.; USA
Georgetown University is a private research university in the Georgetown neighborhood of Washington, D.C. The oldest Catholic and Jesuit institution of higher education in the United States.
An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters.
Advanced Sequence Automated Pipeline (ASAP)
Software developed to provide a framework for building and executing a pipeline to preprocess next generation sequence data and variant calls.
A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality.
Seqtrace - User-friendly software for viewing and processing DNA sequencing trace files
A software application for viewing and processing DNA sequencing chromatograms (trace files) that makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA. SeqTrace also includes a full-featured trace file viewer and editor. You can view your sequencing chromatograms at a variety of scales and zoom levels, simultaneously view matching forward and reverse traces, edit the called bases, and export individual DNA sequences as well as forward/reverse alignments. SeqTrace supports popular trace file formats, including ABIF, SCF, and ZTR.
BrainBlog is news about our knowledge of the brain and behavior from Anthony Risser, Ph.D. Anthony Risser, Ph.D. is a consulting neuropsychologist. My interests include online and distributed applications in medicine, clinical trials, professional training, and undergraduate/graduate education.
Childrens Hospital Oakland Research Institute
Children''s Hospital Oakland Research Institute
Children''s Hospital Oakland Research Institute (CHORI)
CHORI is the internationally renowned biomedical research institute of Children''s Hospital and Research Center at Oakland. With world-class scientists and research centers known both nationally and internationally in multiple fields, CHORI is 5th in the nation for National Institutes of Health pediatric research funding. Bridging basic science and clinical research in the treatment and prevention of human disease, CHORI is a leader in translational research, providing cures for blood diseases, developing new vaccines for infectious diseases, and discovering new treatment protocols for previously fatal or debilitating conditions. Striving to provide the highest standard of excellence and innovation, CHORI brings together a multidisciplinary collaborative of distinguished investigators in six different Centers of Research: The Center for Cancer Research, The Center for Genetics, The Center for Immunobiology & Vaccine Development, The Center for Nutrition & Metabolism, The Center for Prevention of Obesity, Cardiovascular Disease & Diabetes, and The Center for Sickle Cell Disease & Thalassemia. Within these major areas of focus, CHORI pushes the frontiers of science and of excellence beyond their borders. Among the leading biotech enterprises in the Bay Area, CHORI produced 25 patents in the last 5 years alone. In addition to providing world-class research, CHORI is also a teaching institute, offering unique educational opportunities to high school, college, doctoral and post-doctoral students.
MethylomeDB - the Brain Methylome Database
A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database.
Chromatogram viewer that can display an entire trace in a scalable multi-pane view, allows raw data views, BLAST searching and the ability to reverse complement sequences and traces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A Windows Explorer clone dedicated to DNA sequence analysis and manipulation. View, edit, and convert chromatograms. Trim low quality ends automatically. The Lite version of Chromatogram Explorer is freeware.
tranSMART is a knowledge management platform that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data, and assessing their analytical results in the context of published literature and other work. tranSMART is licensed through GPL 3. The integration, normalization, and alignment of data in tranSMART permits users to explore data very efficiently to formulate new research strategies. Some of tranSMART''s specific applications include: * Revalidating previous hypotheses * Testing and refining novel hypotheses * Conducting cross-study meta-analysis * Searching across multiple data sources to find associations of concepts, such as a gene''s involvement in biological processes or experimental results * Comparing biological processes and pathways among multiple data sets from related diseases or even across multiple therapeutic areas Data Repository The tranSMART Data Repository combines a data warehouse with access to federated sources of open and commercial databases. tranSMART accommodates: * Phenotypic data, such as demographics, clinical observations, clinical trial outcomes, and adverse events * High content biomarker data, such as gene expression, genotyping, pharmacokinetic and pharmaco-dynamics markers, metabolomics data, and proteomics data * Unstructured text-data, such as published journal articles, conference abstracts and proceedings, and internal studies and white papers * Reference data from sources such as MeSH, UMLS, Entrez, GeneGo, Ingenuity, etc. * Metadata providing context about datasets, allowing users to assess the relevance of results delivered by tranSMART Data in tranSMART is aligned to allow identification and analysis of associations between phenotypic and biomarker data, and it is normalized to conform with CDISC and other standards to facilitate search and analysis across different data sources. tranSMART also enables investigators to search published literature and other text sources to evaluate their analysis in the context of the broader universe of reported research. External data can also be integrated into the tranSMART data repository, either from open data projects like GEO, EBI Array Express, GCOD, or GO, or from commercially available data sources. Making data accessible in tranSMART enables organizations to leverage investments in manual curation, development costs of automated ETL tools, or commercial subscription fees across multiple research groups. Dataset Explorer tranSMART''s Dataset Explorer provides flexible, powerful search and analysis capabilities. The core of the Dataset Explorer integrates and extends the open source i2b2 application, Lucene text indexing, and GenePattern analytical tools. Connections to other open source and commercial analytical tools such as Galaxy, Integrative Genomics Viewer, Plink, Pathway Studio, GeneGo, Spotfire, R, and SAS can be established to expand tranSMART''s capabilities. tranSMART''s design allows organizations flexibility in selecting analytical tools accessible through the Dataset Explorer, and provides file export capabilities to enable researchers to use tools not accessible in the tranSMART portal.
Chromaseq: a package for processing chromatograms and sequence data in Mesquite
A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap.
National Institute of Mental Health Image Library
Database of photographs and illustrations of general biomedical research and research tools, mental health specific research, and treatment related images that are available, copyright free, to the public at no cost. Many images are available in low, medium, and high resolutions. Formats include jpg, gif, and png. NIMH images may not be used to state or imply the endorsement by NIMH or by an NIMH employee of a commercial product, service, or activity, or use in any other manner that might mislead. No fee is charged for using the images. However, credit must be given to the National Institute of Mental Health, National Institutes of Health, Department of Health and Human Services unless otherwise instructed to give credit to the photographer or other source., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
WaNPRC Pathology and Tissue Distribution Program
Washington National Primate Research Center Pathology & Tissue Program
Washington National Primate Research Center Pathology and Tissue Program
Washington National Primate Research Center Pathology Tissue Program
A comparative pathology unit offering pathology support, training programs, and a Tissue Distribution Program (TDP). The TDP provides a wide variety of nonhuman primate tissues to investigative groups within and outside the Washington National Primate Research Center (WaNPRC). Tissue and pathology services (ACVP board certified Veterinary Pathologists), full histology services (including immunohistochemistry and frozen sectioning), and protocol development consultation are available. The Pathology and Tissue Program is an integration of comparative pathology activities occurring at the Washington National Primate Research Center and those occurring within the University of Washington Department of Comparative Medicine ((DCM). Using this model, Washington National Primate Research Center pathologists provide routine pathology support for Washington National Primate Research Center animals, with ancillary support, expertise, and guidance provided by DCM pathologists and mission-dedicated technicians and laboratories. This integrated comparative pathology unit also provides an excellent training opportunity for students such as those enrolled in the Department of Comparative Medicine post-doctoral training program, which offers training in laboratory animal medicine and comparative pathology. A particularly important function of this comparative pathology unit is support of the Tissue Distribution Program. The TDP provides a wide variety of nonhuman primate tissues to investigative groups within and outside the WaNPRC. This program is an extremely valuable method of conserving the nonhuman primate resource. NHP tissues and biological materials are collected in preparation for RNA/DNA isolation, cell culture, immunohistochemistry/histology, anatomic dissection, and cell sorting. Capabilities of the TDP include, but are not limited to flash frozen preservation, sterile preparation, perfusion, technical surgical dissections, and OCT embedding. In conjunction with the Histology and Imaging core of the University of Washington DCM, research capabilities post-collection include in situ hybridization, confocal and fluorescent microscopy, live cell imaging (DeltaVision), and whole slide scanning with image analysis (Visiopharm, Nikon Elements, and Image Pro). Centralized coordination of nonhuman primate tissue requests with animal availability allows support for a large number of biomedical programs with significantly decreased impact on the animal resource.
Cognitive Behavioral Therapy in Northern Ireland - Solve Therapies
Solve Therapies Cognitive Behavioral Therapy In Northern Ireland
Our hope and aims are to empower those affected by common life difficulties such as Anxiety, Depression, low Self-Esteem etc to overcome their obstacles and achieve their full and true potential. Our core approach is client-centred and we aim to convey to each client the ''core conditions'' of empathy, congruence and unconditional positive regard. Using Compassion focused Cognitive Behavioral Therapy (CBT), Acceptance and Commitment Therapy (ACT) among other approaches we gear all therapy treatments towards clients unique needs and goals. Passionate about research in all therapeutic and associated fields, we want to continue to keep our fingers on the pulse of developments in this area of work. We at Solve Therapies strive to empower all of our clients to choose helpful, rational thoughts and actions and to do so with less shame and self-criticism through the use of Cognitive Behavioural Therapy and Compassion-focused techniques. We offer a confidential, professional therapeutic service using Cognitive Behavioural Therapy and other forms of counseling/psychotherapy. All therapists are accredited and regulated by the British Association of Counselling & Psychotherapy (BACP) and/or British Association of Behavioural and Cognitive Psychotherapy (BABCP), the professional bodies who regulate, inform and ensure ethical practice. We also provide useful information on common difficulties and on how you can learn how to become your own therapist and manage your difficulties in the long term, with counselling venues throughout Northern Ireland including Belfast, Portrush, Antrim and Portglenone in order to provide flexibility for client appointments. ' ''' ''S' ''' ''olution-focused ' ''' ''O' ''' ''ptions ' ''' ''L' ''' ''ife-change ' ''' ''V' ''' ''alidation ' ''' ''E' ''' ''mpathy
A suite of programs aimed at developers of alignment methods rather than end-users to assess the accuracy of multiple sequence alignment methods. It includes a reference database of protein multiple sequence alignments that were generated by consideration of protein three-dimensional structure.
Learn About SMA is a resource for spinal muscular atrophy (SMA) patients, families and researchers. The site includes stories of living with SMA and recent advances in the understanding and potential treatment of SMA. Learn About SMA is divided into five sections with video interviews, animations, and narrative. What is SMA? includes interviews with doctors and patients, plus an animation explaining the cause, inheritance and diagnosis of SMA. SMA Science provides an introduction to the genes and mechanisms involved with SMA, including 2-D and 3-D animations and interviews with Nobel Laureates. * In SMA Therapies doctors discuss current and potential treatments for SMA and a father describes the daily routine of physical therapies for his daughter, who has SMA. Antisense Therapy for SMA includes videos and animations to explain antisense therapy for SMA. In Living with SMA four SMA families describe daily routines, disease progression, children''s understanding of SMA, and grieving.
Sybil: Web-based software for comparative genomics
A web-based software package for comparative genomics.
National Institute of Mental Health Video
A provider for videos available from the National Institute of Mental Health (NIMH). Visitors may sort by topic and/or subscribe to RSS feeds.
A web-based application for the management and storage of tissue microarray (TMA) images and the associated metadata. The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis.
Tissue microarray (TMA) Software used for Biomarker Discovery that allows TMA experiments to be performed anytime, anywhere, reducing administrative costs and time. It is designed to support TMA scoring workflow and allows configuration of experiments in minutes. Access and view clinical metadata, the TMA core, scoring criteria and the TMA map all on a single interface.
A high performance, intuitive client viewer with integrated reporting functionality that can be used as a standalone viewer for accessing slides locally, or connected to Digital Image Hub for remote review.
Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays.
A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement.
A Simple Software Tool to Permit Analysis of Replicate Cores on Tissue Microarrays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.
Software tool for biomarker assessment and outcome based cut point optimization.
National Institutes of Health Office of Science Education
The NIH Office of Science Education (OSE) coordinates science education activities at the NIH and develops and sponsors science education projects in house. These programs serve elementary, secondary, and college students and teachers and the public. Activities * Develop curriculum supplements and other educational materials related to medicine and research through collaborations with scientific experts at NIH * Maintain a website as a central source of information about NIH science education resources * Establish national model programs in public science education, such as the NIH Mini-Med School and Science in the Cinema * Promote science education reform as outlined in the National Science Education Standards and related guidelines The OSE was established in 1991 within the Office of Science Policy of the Office of the Director of the National Institutes of Health. The NIH is the world''s foremost biomedical research center and the U.S. federal government''s focal point for such research. It is one of the components of the Department of Health and Human Services (HHS). The Office of Science Education (OSE) plans, develops, and coordinates a comprehensive science education program to strengthen and enhance efforts of the NIH to attract young people to biomedical and behavioral science careers and to improve science literacy in both adults and children. The function of the Office is as follows: (1) develops, supports, and directs new program initiatives at all levels with special emphasis on targeting students in grades kindergarten to 16, their educators and parents, and the general public; (2) advises NIH leadership on science education issues; (3) examines and evaluates research and emerging trends in science education and literacy for policy making; (4) works closely with the NIH extramural, intramural, women''s health, laboratory animal research, and minority program offices on science education special issues and programs to ensure coordination of NIH efforts; (5) works with NIH institutes, centers, and divisions to enhance communication of science education activities; and (6) works cooperatively with other public- and private-sector organizations to develop and coordinate activities.
Software tool to map bisulfite converted sequence reads and determine cytosine methylation states. Flexible aligner and methylation caller for Bisulfite-Seq applications. Used to map bisulfite treated sequencing reads to genome of interest and perform methylation calls in single step.
jmhc - software for analyzing and visualization of the results of deep amplicon sequencing
Software for analyzing and visualization of the results of deep amplicon sequencing.
Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, and ongoing research that helps us better understand and treat disorders. Mental disorders are common. You may have a friend, colleague, or relative with a mental disorder, or perhaps you have experienced one yourself at some point. Such disorders include depression, anxiety disorders, bipolar disorder, attention deficit hyperactivity disorder (ADHD), and many others. Some people who develop a mental illness may recover completely; others may have repeated episodes of illness with relatively stable periods in between. Still others live with symptoms of mental illness every day. They can be moderate, or serious and cause severe disability. Through research, we know that mental disorders are brain disorders. Evidence shows that they can be related to changes in the anatomy, physiology, and chemistry of the nervous system. When the brain cannot effectively coordinate the billions of cells in the body, the results can affect many aspects of life. Scientists are continually learning more about how the brain grows and works in healthy people, and how normal brain development and function can go awry, leading to mental illnesses. Brain Basics will introduce you to some of this science, such as: * How the brain develops * How genes and the environment affect the brain * The basic structure of the brain * How different parts of the brain communicate and work with each other * How changes in the brain can lead to mental disorders, such as depression.
An open-source de novo genome assembly software tool, which is run from the Unix command line, providing a multi-platform graphical front-end for the Velvet de novo assembler. VAGUE is implemented in JRuby and targets the Java Virtual Machine.
Collaborative Research in Computational Neuroscience
Collaborative Research in Computational Neuroscience - Data sharing
Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources.
Neuroscience and Psychiatry Module 1: Translating Neural Circuits into Novel Therapeutics
Neuroscience and Psychiatry Module 1 - Translating Neural Circuits into Novel Therapeutics
Neuroscience Psychiatry Module 1: Translating Neural Circuits into Novel Therapeutics
Translating Neural Circuits into Novel Therapeutics
This is the first in a series of modules on neuroscience and psychiatry. This module explores research on cognitive deficits, a core feature of schizophrenia and the single best predictor of functional outcomes in this disorder for which we currently have no treatments. This module is an example of how translational neuroscience can provide clues for the development of promising novel therapeutics.
Database of computationally predicted Transcription Factors and binding sites in gamma-proteobacterial genomes. The user may browse a map containing all known E. coli transcription factors and regulatory interactions that connect them, and retrieve information on the conservation of each regulatory interaction across the 30 organisms included in the database. Downloading the information is straightforward, and navigation tabs added to dynamic pages ease navigation between the five interfaces of the database. The original prediction approach, based on the representation of binding sites through statistical models was complemented by a new approach that uses known E. coli regulatory sites as the basis for a pattern matching search of regulatory sites. The use of both approaches together resulted in a more intensive exploration of the sequence space of each regulator's binding site. These data should aid researchers in the design of microarray experiments and the interpretation of their results. They should also facilitate studies of Comparative Genomics of the regulatory networks of this group of organisms.
Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice.
A set of lessons for students used to gain insight into the biological basis of mental illnesses and how scientific evidence and research can help us understand its causes and lead to treatments and, ultimately, cures. Both the Web version and the free supplement are available. It is a creative, inquiry-based instruction program designed to promote active learning and stimulate student interest in medical topics. This curriculum supplement aims to help students experience the process of scientific inquiry and develop an enhanced understanding of the nature and methods of science.
National Institute of Mental Health Clinical Trials
NIMH supports research studies on mental health and disorders. Participate, refer a patient or learn about results of studies in ClinicalTrials.gov, the NIH/National Library of Medicine' '''s registry of federally and privately funded clinical trials for all disease. Find NIH-funded studies currently recruiting participants in the following mental health topics: * Anxiety Disorders ** Generalized Anxiety Disorder ** Obsessive-Compulsive Disorder (OCD) ** Panic Disorder ** Post-traumatic Stress Disorder (PTSD) ** Social Phobia (Social Anxiety Disorder) * Attention Deficit Hyperactivity Disorder (ADHD, ADD) * Autism Spectrum Disorders (Pervasive Developmental Disorders) * Bipolar Disorder (Manic-Depressive Illness) * Borderline Personality Disorder * Depression * Eating Disorders * HIV/AIDS * Schizophrenia * Suicide Prevention Information Resources for NIMH Researchers Conducting Clinical Trials * Limited Access Datasets from NIMH-Supported Clinical Trials * NIMH Policy for Recruitment of Participants in Clinical Research * NIMH Policy on Data and Safety Monitoring in Extramural Investigator-Initiated Clinical Trials * Register a study with ClinicalTrials.gov
Limited Access Datasets From NIMH Clinical Trials
Available Limited Access Datasets From NIMH Clinical Trials
A listing of data sets from NIMH-supported clinical trials. Limited Access Datasets are available from numerous NIMH studies. NIMH requires all investigators seeking access to data from NIMH-supported trials held by NIMH to execute and submit as their request the appropriate Data Use Certification pertaining to the trial. The datasets distributed by NIMH are referred to as limited access datasets because access is limited to qualified researchers who complete Data Use Certifications.
CATIE - Clinical Antipsychotic Trials in Intervention Effectiveness
Clinical Antipsychotic Trials in Intervention Effectiveness
Clinical Antipsychotic Trials in Intervention Effectiveness - Schizophrenia
The NIMH-funded Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) Study was a nationwide public health-focused clinical trial that compared the effectiveness of older (first available in the 1950s) and newer (available since the 1990s) antipsychotic medications used to treat schizophrenia. These newer medications, known as atypical antipsychotics, cost roughly 10 times as much as the older medications. CATIE is the largest, longest, and most comprehensive independent trial ever done to examine existing therapies for this disease. Schizophrenia is a brain disorder characterized by hallucinations, delusions, and disordered thinking. The course of schizophrenia is variable, but usually is recurrent and chronic, often causing severe disability. Previous studies have shown that taking antipsychotic medications consistently is far more effective than taking no medicine and that the drugs are necessary to manage the disease. The aim of the CATIE study was to determine which medications provide the best treatment for schizophrenia. Additional information may be found by following the links, http://www.nimh.nih.gov/trials/practical/catie/index.shtml, http://www.clinicaltrials.gov/ct/show/NCT00014001?order=1
A free open source software platform consisting of the 3D Slicer application software, a number of tools and toolkits such as VTK and ITK, and a software engineering methodology that enables multiplatform implementations. It also draws on other best practices from the community to support automatic testing for quality assurance. The NA-MIC kit uses a modular approach, where the individual components can be used by themselves or together. The NA-MIC kit is fully-compatible with local installation (behind institutional firewalls) and installation as an internet service. Significant effort has been invested to ensure compatibility with standard file formats and interoperability with a large number of external applications. Users of the NAMIC Kit will typically use a combination of its many modular components. * 3D Slicer is a general purpose application. Biomedical researchers will typically use this software tool to load, view, analyze, process and save image data. Slicer has been implemented to interoperate with many other tools, including XNAT, which is an open source image database. * Slicer modules, which are dynamically loaded by Slicer at run-time, can be used to extend Slicer' '''s core functionality including defining graphical user interfaces. Modules are typically used by algorithms and application developers. * Application and algorithms developers may also use NA-MIC Kit toolkits and libraries. For example, the Insight Segmentation and Registration Toolkit ITK can be used to develop slicer modules for medical image analysis. The Visualization Toolkit can be used to process, visualize and graphically interact with data. KWWidgets is a 2D graphical user interface toolset that can be used to build applications. Teem is a library of general purpose command-line tools that are useful for processing data. Finally, those individuals wishing to create and manage complex software, the NAMIC-Kit software process is available as embodied in CMake, CTest, CPack, DART and the various documentation, bug tracking and communication tools.
Core facility that provides the following services: Training Service, TEM Analysis Service. ?The Nanoscale Analytical Facility is equipped with Jeol 2100 EDAX operated at 200kV. Nanomaterial containing samples of inorganic as well as organic building blocks, macromolecular constructs, metallic nanoparticles, metal oxide nano-powders are often imaged.
A software tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses.
3D Slicer: A multi-platform free and open source software package for visualization and medical image computing
A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.
Manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. Used to predict potential transcription factor binding sites.
The Office of Extramural Research (OER) presents conversations with NIH staff members. Designed for investigators, fellows, students, research administrators, and others, we provide insights on grant topics from those who live and breathe the information. In mp3 and updated monthly. Transcripts are also available. So You Wanna... Keep Up with What' '''s Hot? Prepare a Successful Grant Application? Suggest a Topic? Understand How Your Grant is Reviewed? Be an NIH Investigator?
Systems Transcriptional Activity Reconstruction
Systems Transcriptional Activity Reconstruction Genome Browser
A next-generation web-based application that aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets.
Software package for analysis of microarray images. Microarray spot detection and characterization software package which extracts numerical information from cDNA microarrays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
NIMH Resources for Research Training and Career Development
NIMH Research Training Career Development and Related Programs
NIMH Resources for Research Training Career Development
Research Training Career Development and Related Programs
A portal to the National Institute of Mental Health''s Research Training, Career Development, and Related Programs. Topics cover Resources for Applicants, Individual Fellowship Programs, Individual Career Development Programs, Institutional Training Programs, Additional Career Development/Training-Related Opportunities, and Training Programs to Increase Workforce Diversity.
A web-based application for alignment visualization, browsing and analysis of genome sequence data.
Humboldt University of Berlin; Berlin; Germany
Public research university in central borough of Mitte in Berlin, Germany.University Library is responsible for editing and curating Persistent Identifiers PIDs, such as organisation identifiers of the University.
e-Source: Behavioral and Social Sciences Research
e-Source: Behavioral & Social Science Research
e-Source: Behavioral & Social Sciences Research
e-Source: Behavioral and Social Science Research
e-Source: Behavioral Social Sciences Research
Inside e-Source you will find 20 interactive chapters with authoritative answers to methodological questions on behavioral and social science research. With contributions from a team of international experts, this anthology provides the latest information on addressing emerging challenges in public health. Book contents include: Setting the Scene, Describing How, Explaining Why, What Works, Emerging Issues. Tables, Figures, Exercises and Examples are included. Login for enhanced functionality. Contents: * Appropriate Research Methods * ''Science'' in the Social Sciences * Design Decisions in Research * Theory Development * Social and Behavioral Theories * Sample Surveys * Social Survey Data Collection * Administrative Data Systems * Observational Studies * Qualitative Methods * Conversation Analysis * Software and Qualitative Analysis * Clinical Trials * Cluster Unit Randomized Trials * Ethical Challenges * Multilevel Modeling * Objective Measurement of Subjective Phenomena * Measuring Socioeconomic Status * Evaluating the Quality of Health Care * Patient-Reported Outcomes
The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation.
A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
NIMH Psychoactive Drug Screening Program
National Institute of Mental Health Psychoactive Drug Screening Program
This service provides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters. Bryan Roth MD, PhD (University of North Carolina Chapel Hill) will perform pharmacological and functional screening of novel compounds as a contractor to NIMH. Screening of compounds is provided to qualified academic investigators at no cost. * Assays using for a large number of cloned human or rodent cDNAs for CNS receptors, channels and transporters. For a list of current receptors/transporters go to:clones.html * Ki determinations * Functional assays to determine effects on second messenger systems, channel activity and transporter function * Cloned receptors are also available at no cost to qualified investigators. * Assays are now available for bioavailability predictions (CaCo2, MDR-1) and cardiovascular toxicity predictions (HERG, 5-HT2B) Who is eligible * Academic investigators involved in basic or clinical research relevant to mental health. * Projects from research and development areas in small businesses relevant to mental and behavioral science. * Areas of interest to NIMH include the design and development of new chemical entities and small molecules as research tools, probes, targeted drug delivery systems, and PET ligands for brain imaging. * Research areas of interest are described in the Division of Basic and Clinical Neuroscience Research webpage, http://www.nimh.nih.gov/about/organization/dnbbs/index.shtml.
NIMH Toxicological Screens of Novel Ligands
NIMH Toxicological Screens of Novel Ligands Program
Toxicological Evaluation of Novel Ligands Program
Toxicological Evaluation of Novel Ligands
The purpose of the NIMH Toxicological Evaluation of Novel Ligands Program is to accelerate the discovery, development, and application of novel ligands for PET, SPECT, and MRI imaging in humans by providing toxicology and safety assessment of promising, target-selective compounds. The program will also provide limited assessment of novel psychoactive agents for clinical research and as potential therapeutics. Toxicology and safety data generated by the program will be used to support an Investigational New Drug (IND) application to the Food and Drug Administration (FDA), or for Radioactive Drug Research Committee (RDRC) evaluation of a compound for human studies. The contract will evaluate toxicity and safety of compounds submitted for testing which may include, but are not limited to, novel chemical entities, structural analogs of compounds with an IND, or analogs of FDA-approved drugs. The services available under this program fall under four general phases: (1) analytical, (2) pharmacokinetics, (3) preliminary safety, and (4) IND-directed toxicity including safety pharmacology. What is available A broad range of tasks are available for assessing the safety and/or pharmacokinetics of each ligand. Specific capabilities available to investigators include: * Validation of the analytical methods for quantitating drug concentrations in dosing solutions, biological fluids, and tissues, as required. Determination of plasma drug levels in animals administered the agent under study, and calculation of pharmacokinetic parameters derived from these data. * Determination of bioavailability of the drug after different routes of administration, including oral, intravenous (i.v.), subcutaneous (s.c.), intramuscular (i.m.), or intraperitoneal (i.p.), as needed. Calculation of the pharmacokinetic parameters from the derived data. * In vitro evaluation of hepatotoxicity in human and animal liver cells. * Preclinical acute toxicity evaluations on lead compounds, evaluating clinical observations, body weights, clinical pathology, histopathology, and plasma drug levels in rodents and non-rodent species. Other toxicology endpoints may be selected if needed. * Subacute and subchronic toxicity evaluations in rodents and large animal species, evaluating clinical observations, body weights, clinical pathology, and histopathology. * Genotoxicity assessments using a battery of appropriate assays. Since these preclinical studies are needed to demonstrate to the FDA that a candidate medication or imaging agent is understood well enough for designing appropriate clinical treatment regimens, most of the work to be conducted to achieve these objectives must be performed and the resulting data analyzed and reported in strict compliance with the FDA''s GLP regulations for nonclinical laboratory studies (21 CFR 58). These data must be obtained by carefully planned and skillfully executed methods that are specific, accurate, and precise. The applicable portions of the accumulated safety data will be included in documents submitted to the FDA in support of regulatory applications. Who is eligible Academic investigators involved in basic or clinical research relevant to mental health. Research areas are described on the NIMH website.
Mapping and Assembly with Qualities Viewer
A graphical read alignment viewer specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. It is highly efficient in speed, memory and disk usage. Maqview is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy.
GORetriever is used to find all of the GO annotations corresponding to a list of user-supplied protein identifiers. GORetriever produces a list of proteins and their annotations and a separate list of entries with no GO annotation. Platform: Online tool
A publicly available database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. Using TranspoGene the user can learn about the many aspects of the effect these TEs have on their hosting genes, such as: exonization events (including alternative splicing-related data), insertion of TEs into introns, exons, and promoters, specific location of the TE over the gene, evolutionary divergence of the TE from its consensus sequence and involvement in diseases. TranspoGene database is quickly searchable through its website, enables many kinds of searches and is available for download. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome.
Bridging Interventional Development Gaps
NIH Rapid Access to Intervention Development
Rapid Access to Intervention Development
on a competitive basis, successful applicants receive access to NIH contractors who conduct preclinical studies at no cost to the investigator for the development of new therapeutic agents. In general, synthesis, formulation, pharmacokinetic and toxicology services in support of investigator-held Investigational New Drug (IND) applications to the Food and Drug Administration are available. Contract costs are supported by the NIH Common Fund and collaborating NIH Institutes and Centers. Access to contracts is based upon a peer-reviewed application process. The number of awards made will depend on the number of applications received, their scientific merit, and the availability of NIH funds. BrIDGs is not a complete drug development program or an unconditional commitment to develop a particular compound for the clinic. In some cases the program supports one or two key steps for preclinical development, while in other cases it assists with most of the development tasks needed to file an IND. The services provided by the program depend upon the stage of a given project and need for additional data. Once a project is approved, NIH staff work with principal investigators to develop a plan for the conduct of proposed studies. Contractors perform tasks approved by BrIDGs under the direction of NIH staff. Development proceeds sequentially in most cases and the start of one segment of the project (e.g., toxicology) may depend on satisfactory completion of preceding segments (e.g., formulation). Insurmountable difficulties in one segment may force the discontinuation of an entire project. BrIDGs supports projects proposed by academic institutions, not-for-profit organizations, and SBIR-eligible businesses. Foreign academic and non-profit institutions may also apply. Potential therapies for any disease or disorder may be submitted to BrIDGs. All proposed therapeutic agents should have demonstrated pharmacological activity in an appropriate in vivo disease model before applying.
SCSORS - Semi-Custom Synthesis On-line Request System
Semi-Custom Synthesis On-line Request System
ChemNavigator has extended its agreement with NCI to include the development of a new Semi-Custom Synthesis On-line Request System (SCSORS), funded mostly by NCI with additional financial support from the NIH Chemical Genomics Center (NCGC). The new SCSORS project will provide the NIH access to the world''s supply of synthetic chemistry available for drug discovery. Once fully formed, SCSORS will provide a strategy for all NIH scientists to circulate requests for specific chemical samples among thousands, if not tens of thousands, of synthetic chemists at suppliers registered in the system. Sample quantities will range from milligram up to kilogram scale requests. Suppliers will be provided tools that allow them to review these requests and make proposals to NIH scientists for the synthesis of substances. It is expected that using the SCSORS strategy will allow the NIH to acquire chemical samples at less than 10% of the internal cost of synthesis while offering access to world wide chemical expertise and diversity. Once fully implemented, SCSORS will become an archive of commercially accessible custom chemistry products for pharmaceutical research. It is expected that this database of commercially accessible substances will grow to over 250 million substances in the coming two years.
A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.
A centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools. It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web.
Hunan Normal University; Changsha; China
University founded in 1938, is a higher education institution in Changsha, Hunan Province. The university is a national 211 Project university, one of 100 key universities in the 21st century that enjoy priority in obtaining national funds.
Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes.
Software which performs accurate and fast mapping of bisulfite-treated short reads. Supplementary information and examples are provided on the site.
MRI Research Safety and Ethics: Points to Consider
NIMH recognizes the need to consider safety and ethical issues related to both the administration of MR (magnetic resonance) facilities and the use of these facilities for research. This document summarizes the points to consider discussed by the National Advisory Mental Health Council (NAMHC) Workgroup. Examples of safe and ethical practices are discussed in relation to several issues. These examples are intended to be illustrative and should not be interpreted as an exhaustive or exclusive list. This document was presented to the full NIMH Council on September 15, 2006 and approved unanimously. By making the points to consider document available publicly, NIMH intends to provide a resource for researchers and institutions that use MRI in research. The agenda was organized into six topics, which provide the organization for the points to consider that follow: A. MRI screening B. Training, operating, and emergency procedures C. Physical facilities D. Scanning/participant health variables E. Context- Specific Considerations: University vs. medical settings F. Additional data needs and updating The NIMH believes that investigators, institutions and facilities can use this document as a resource for the development, administration, evaluation, and use of MRI research facilities.
TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available. For each organism, its complete membrane transport complement was identified, classified into protein families according to the TC classification system, and functional predictions are provided.For each organism, a summary page is available, overviewing the whole transporter system, including transporter types and individual transporter families. For individual transporter types, a detailed list of transporters with their possible substrates is shown with links to individual protein page which contains protein sequence and annotation information. You can also compare the transporter system from two or more different organisms. A search engine is set up for easy search in our transporter database for transporter type, family, individual proteins and their substrates. You can also blast search your protein sequence against our transporter database.With the rapid development of genomic sequencing both in TIGR and in other institutes, more and more genomes are available for the analysis of their transporter system. We will keep updating this site with the newly published genomes. If you have any suggestions, corrections, or comments on our site, please contact us. We are currently working on providing additional functionality for this database.
MATRICS - Measurement And Treatment Research to Improve Cognition in Schizophrenia
Measurement And Treatment Research to Improve Cognition in Schizophrenia
Measurement Treatment Research to Improve Cognition in Schizophrenia
Cognitive deficits -- including impairments in areas such as memory, attention, and executive function -- are a major determinant and predictor of long-term disability in schizophrenia. Unfortunately, available antipsychotic medications are relatively ineffective in improving cognition. Scientific discoveries during the past decade suggest that there may be opportunities for developing medications that will be effective for improving cognition in schizophrenia. The NIMH has identified obstacles that are likely to interfere with the development of pharmacological agents for treating cognition in schizophrenia. These include: (1) a lack of a consensus as to how cognition in schizophrenia should be measured; (2) differing opinions as to the pharmacological approaches that are most promising; (3) challenges in clinical trial design; (4) concerns in the pharmaceutical industry regarding the US Food and Drug Administration''s (FDA) approaches to drug approval for this indication; and (5) issues in developing a research infrastructure that can carry out clinical trials of promising drugs. The MATRICS program will bring together representatives of academia, industry, and government in a consensus process for addressing all of these obstacles. Specific goals of the NIMH MATRICS are: * To catalyze regulatory acceptance of cognition in schizophrenia as a target for drug registration. * To promote development of novel compounds to enhance cognition in schizophrenia. * Leverage economic research power of industry to focus on important but neglected clinical targets. * Identify lead compounds and if deemed feasible, support human proof of concept trials for cognition in schizophrenia.
Dartmouth SYNERGY Clinical Research Unit
The SYNERGY Clinical Research Unit (CRU) is an outpatient research support unit that offers investigators a full array of services for the conduct of clinical research. The CRU is available to any Dartmouth faculty or researcher wishing to access dedicated space and staff resources for the efficient conduct of clinical research.
WIthin-SamplE COpy Number aberration DetectOR
A set of python scripts that detects fetal chromosomal and subchromosomal duplications and deletions in maternal blood samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
UCSF Center for AIDS Prevention Studies (CAPS)
Center for AIDS Prevention Studies (CAPS) - Responding to the Challenge of HIV
Established in 1986, the Center for AIDS Prevention Studies (CAPS) at the University California, San Francisco (UCSF) is the world''s largest research center dedicated to social, behavioral, and policy science approaches to HIV. The mission of the CAPS is to conduct research to prevent new HIV infections, improve health outcomes among those infected, and reduce disparities. This is how we do it: * CAPS provides core support for multidisciplinary and high-impact HIV research, enhances the excellence of research projects, trains a new generation of HIV scientists, and assists implementing partners. * Our Administrative Core provides strong leadership and management to stimulate innovative research and ensure scientific rigor and sound fiscal operations. * Our Developmental Core fosters innovative, high-impact, multidisciplinary HIV research by providing funds for innovative pilot work, sponsoring training and education, and ensuring the scientific excellence of research. * Our Methods Core provides comprehensive methodological training and consultation in research design, qualitative and quantitative analysis, and state-of-the-art data collection and management. * Our Policy and Ethics Core stimulates and supports policy-relevant research, identifies and analyzes the policy and ethics implications of research, and ensures the highest ethical conduct of research. * Our Technology and Information Exchange (Domestic Response) Core responds to the domestic epidemic by disseminating information, fostering community collaborative research, providing technical assistance and capacity-building to community-based organizations, and learning from community expertise. * Our Global Response Core responds to the global epidemic by fostering collaborative research with scientists in developing countries, completing and disseminating Cochrane Collaborative scientific reviews, and providing technical assistance, capacity building, and an evidence base to implementing partners.
MagicViewer: Integrated Solution for Next-generation Sequencing Data Visualization and Genetic Variation Detection and Annotation
Software to easily visualize the short reads alignment, identify the genetic variation and associate with the annotation information of reference genome. MagicViewer provides a user-friendly interface in which large-scale short reads and sequencing depth can be easily visualized in zoomable images under user definable color scheme through an operating system-independent manner with the implement of Java language. Meanwhile, it holds a versatile genetic variation annotation and visualization interface, providing details of the query options, functional classifications, subset selection, sequence association and primer design.
Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format
A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. Bambino may be launched online via Java Web Start or downloaded and run locally.
A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)
DiProGB - The Dinucleotide Properties Genome Browser
Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand.
By collecting and analyzing blood samples from Geisinger''s large patient population, MyCode will help unlock the mysteries of some of the most devastating and debilitating diseases. Blood samples are obtained from patients of certain Geisinger specialty clinics to study specific conditions, such as obesity and cardiovascular disease, and also from patients of Geisinger primary care clinics to provide a representative sample of the regional population. More than 60,000 samples from over 23,000 Geisinger patients have been collected so far, and sample collection is ongoing. MyCode researchers use the blood samples to study the genetic causes of diseases and certain disease-related molecular mediators. Knowledge gained from these studies will allow researchers to pursue innovative approaches to disease prevention, diagnosis and treatment. To be of value for Genomic Medicine research, bio-banked samples must be connected to clinical data: MyCode allows genetic and molecular data about the samples to be connected to medical data in a way that protects patient identity. When a patient agrees to participate in MyCode, blood samples for the MyCode Project are collected during blood draws ordered as part of the patient''s routine medical care. After the sample is drawn and labeled, a staff member from the Weis Center for Research transports the blood to the Geisinger Clinic Genomics Core (GCGC) where it is processed for storage. At this stage, all personal identification markers are removed and the samples are assigned a randomly-selected identification number. A secure key is maintained that allows approved researchers to connect the samples to the clinical data for genomic studies in a way that ensures confidentiality of the information. To maintain confidentiality of MyCode data the code linking the research numbers and the electronic health records are kept in a password-protected files accessible only to MyCode team members. Additionally, all results generated from the samples are reported as a group so that individuals are not identified. The samples are stored indefinitely.
Literature-derived human gene-disease network
A text mining derived database with focus on extracting and classifying gene-disease associations with respect to several biomolecular conditions. It uses a machine learning based algorithm to extract semantic gene-disease relations from a textual source of interest. The semantic gene-disease relations were extracted with F-measures of 78. More specifically, the textual source utilized here originates from Entrez Gene' '''s GeneRIF (Gene Reference Into Function) database (Mitchell, et al., 2003). LHGDN was created based on a GeneRIF version from March 31st, 2009, consisting of 414241 phrases. These phrases were further restricted to the organism Homo sapiens, which resulted in a total of 178004 phrases. We benchmark our approach on two different tasks. The first task is the identification of semantic relations between diseases and treatments. The available data set consists of manually annotated PubMed abstracts. The second task is the identification of relations between genes and diseases from a set of concise phrases, so-called GeneRIF (Gene Reference Into Function) phrases. In our experimental setting, we do not assume that the entities are given, as is often the case in previous relation extraction work. Rather the extraction of the entities is solved as a subproblem. Compared with other state-of-the-art approaches, we achieve very competitive results on both data sets. To demonstrate the scalability of our solution, we apply our approach to the complete human GeneRIF database. The resulting gene-disease network contains 34758 semantic associations between 4939 genes and 1745 diseases. The gene-disease network is publicly available as a machine-readable RDF graph. We extend the framework of Conditional Random Fields towards the annotation of semantic relations from text and apply it to the biomedical domain. Our approach is based on a rich set of textual features and achieves a performance that is competitive to leading approaches. The model is quite general and can be extended to handle arbitrary biological entities and relation types. The resulting gene-disease network shows that the GeneRIF database provides a rich knowledge source for text mining.
Hungarian Academy of Sciences; Budapest; Hungary
The Hungarian Academy of Sciences is the most important and prestigious learned society of Hungary. Its seat is at the bank of the Danube in Budapest, between Széchenyi rakpart and Akadémia utca.
A database providing access to mRNA sequences and associated regulatory elements. Users can obtain data relating to translation (by species in a non-redundant format), search for regulatory elements in a defined set, or search their own sequence for known regulatory elements. The mRNA sequences are processed from Genbank, including complete genomes. They are divided into biologically relevant sections 5' UTRs and 3' UTRs, initiation and termination regions and the full CDS sequences. This data or your own sequences can be searched for defined regulatory elements. Recent Developments The web interface has been revised to allow users to analyse their own sequences. All motifs description have been revised new specific patterns have been added. Transterm data was updated with Genbank 122 (Feb 2001). Acknowledgements Health Research Council of New Zealand Marsden Fund of New Zealand translation, translational control of protein synthesis, mRNA, biologically relevant mRNA regions, GenBank, taxonomy, initiation codon (Kozaks consensus or Shine Dalgarno sequences), termination codon, coding regions or 3' flanking regions, Nucleotide Sequence, Transcriptional regulator, transcription factor
Quantitative Measurements in MR Brain Images
Neuromorphometrics provides brain labeling and measurement services. Given raw MRI brain scans, we make precise quantitative measurements of the volume, shape, and location of specific neuroanatomical structures. Web tool for brain measurement services. Used for modeling living human brain and make quantitative measurements of volume, shape, and location of specific neuroanatomical structures using given MRI brain scans. Automated analyses are manually guided, inspected and certified by a neuroanatomical expert. Resource of neuroanatomically labeled MRI brain scans database. Resource for neuroanatomical localization and identification: NeuAtlas.
Human Electrophysiology Anatomic Data & Integrated Tools
Human Electrophysiology Anatomic Data & Integrated Tools (HeadIT) Resource
Human Electrophysiology Anatomic Data & Integrated Tools Resource
Human Electrophysiology Anatomic Data and Integrated Tools (HeadIT) Resource
Platform for sharing, download, and re-analysis or meta-analysis of sophisticated, fully annotated, human electrophysiological data sets. It uses EEG Study Schema (ESS) files to provide task, data collection, and subject metadata, including Hierarchical Event Descriptor (HED) tag descriptions of all identified experimental events. Visospatial task data also available from, http://sccn.ucsd.edu/eeglab/data/headit.html: A 238-channel, single-subject EEG data set recorded at the Swartz Center, UCSD, by Arnaud Delorme, Julie Onton, and Scott Makeig is al.
TRbase: A Database Of Tandem Repeats In The Human Genome
This TRbase is a relational tandem repeat database that relates tandem repeats to gene locations and disease genes of the human genome. The TRbase stores both perfect and imperfect repeats of 1 to 2000 bp unit lengths that were identified using the Tandem Repeat Finder program. Disease information for all 24 chromosomes was retrieved from the Online Mendelian Inheritance in Man (OMIM) database. There are five main search forms by which the user may query the database: 1. The Advanced tandem repeat search: This allows a complete search for tandem repeats using a combination of criteria, such as total tandem repeat length, repeat unit length, copy number of the repeats, percentage matches and the consensus repeat pattern. On submission, the number of repeats and the detailed tandem repeat characteristics of each repeat that match the user query are tabulated. 2. The Main search: This relates tandem repeat data to genes and diseases. The user may specify a gene of interest to view details of all repeats associated with it or search for tandem repeats present in a particular disease by entering the name/keyword for the disease or the MIM number of the disease gene. 3. The Composite search: This more advanced search allows the user to query specifically for repeats present in exons, introns or intergenic regions of a gene or disease gene. 4. The Gene Search: Further information on genes can be available by a simple gene name search on this page. 5. The Disease search: This allows extensive information on disease genes on all chromosomes of the human genome. Searching for a MIM number, or keyword searches specifying the features of the disease, will retrieve the information on the disease and the chromosome in which the disease gene occurs. Each entry retrieved is linked to the OMIM database for detailed literature and gene map information on the disease.
A public repository of information on tandem repeats in genomic DNA and contains a variety of tools for their analysis. These currently include the Tandem Repeats Finder algorithm, query and filtering capabilities for finding particular repeats of interest, repeat clustering algorithms based on sequence similarity, polymorphism prediction based on common patterns of mutation, PCR primer selection, and data download in a variety of formats. In addition, TRDB serves as a centralized research workbench, provides storage space for results of analysis, and permits collaborators to privately share their data and analysis.
Audio clips that highlight research efforts at the National Institute on Drug Abuse and include interviews with prominent NIDA scientists. To listen to these clips, just click Listen Now under the clip summary. You must have Real Media Player or Windows Media Player installed to download these clips. To view a printable transcript of a clip, click View Transcript under the clip summary.
Transcriptional Regulatory Element Database
Collects mammalian cis- and trans-regulatory elements together with experimental evidence. Regulatory elements were mapped on to assembled genomes. Resource for gene regulation and function studies. Users can retrieve primers, search TF target genes, retrieve TF motifs, search Gene Regulatory Networks and orthologs, and make use of sequence analysis tools. Uses databases such as Genbank, EPD and DBTSS, and employ promoter finding program FirstEF combined with mRNA/EST information and cross-species comparisons. Manually curated.
Gene Ontology Browsing Utility (GOBU) (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable software architecture. Users may interact with the Gene Ontology and user-defined hierarchy data of genes, and then use its plugins to (and not limited to) (1) browse the GO hierarchy with user defined data, (2) browse GO-oriented expression levels in the user data, (3) compute GO enrichment, and/or (4) customize data reporting. A set of classes and utility functions has been established so that a customized program can be made as a plugin or a command-line tool that programmically manipulate the Gene Ontology and specified user data. See the source code repository for examples. Reference Lin WD, Chen YC, Ho JM, Hsiao CD. GOBU: Toward an Integration Interface for Biological Objects. Journal of Information Science and Engineering. 2006 22(1):19-29. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Web-service providing access to database that brings together information from broad range of resources. Web application for functional annotation and statistical hypothesis testing. Provides tools for analysis of genomic and microarray data. Collection of tools include Bibliographic Information,Databases,Gene Annotation,Gene Regulation, Microarray,Proteins,Sequence Manipulation - Nucleic Acids,Sequence Manipulation - Protein, Systems Biology.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. KI Biobank - Gallstone aims at investigating genetics of gallstone disease on Swedish Twins. Types of samples * EDTA whole blood * DNA * Plasma Number of sample donors: 82
Service to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs.
go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Network Ontology Analysis (NOA) (abbreviated to NOA) is a freely available collection of Gene Ontology tools aiming to analyze functions of gene network instead of gene list. Network rewiring facilitates the function changes between conditions even with the same gene list. Therefore, it is necessary to annotate the specific function of networks by considering the fundamental roles of interactions from the viewpoint of systems biology. NOA is such a novel functional enrichment analysis method capable to handle both dynamic and static networks. The application of NOA in biological networks shows that NOA can not only capture changing functions in rewiring networks but also find more relevant and specific functions in traditional static networks. Platform: Online tool
OBO-Edit is an open source, platform-independent application written in Java for viewing and editing any OBO format ontologies. OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes. The UI components are cleanly separated from the data model and data adapters, so these can be reused in other applications. The oboedit foward-chaining reasoner can also be used independently (for example, for traversing ontology graphs). OBO-Edit uses the OBO format flat file. See the GO wiki, http://wiki.geneontology.org/index.php/OBO-Edit:_Getting_the_Source_Code, for instructions on downloading the source code. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Since focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the GO nomenclature. Compare commercially available microarrays based on GO. User account required. Platform: Online tool
The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independently of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. We demonstrated the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer data sets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms (Draghici et.al, Genomics, 81(2), 2003). Other results obtained with Onto-Express can be found in Khatri et.al., Genomics. 79(2), 2002. Custom level of abstraction of the Gene Ontology. User account required. Platform: Online tool
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. Short reads mapping software for bisulfite sequencing reads.
An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM).
A collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups.
OntoVisT: A General purpose Ontological Visualization Tool
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. Web based ontological visualization tool for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor. It takes any ontology file in OBO format as input and generates output as DAG hierarchical graph for the chosen query. To enhance the navigation capabilities of complex networks, we have embedded several features such as search criteria, zoom in/out, center focus, nearest neighbor highlights and mouse hover events. The application has been tested on all 72 data sets available in OBO format through OBO foundry. The results for few of them can be accessed through OntoVisT-Gallery.
Software Tool for Rapid Annotation of Proteins
STRAP - Software Tool for Rapid Annotation of Proteins
Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible
Cancer Genome Anatomy Project GO Browser
With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool
COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
National Institute of General Medical Sciences - YouTube
YouTube videos provided by the National Institute of General Medical Sciences (NIGMS).
Gene Class expression: analysis tool of Gene Ontology terms with gene expression data
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. Gene Class Expression allows functional annotation of SAGE data using the Gene Ontology database. This tool performs searches in the GO database for each SAGE tag, making associations in the selected GO category for a level selected in the hierarchy. This system provides user-friendly data navigation and visualization for mapping SAGE data onto the gene ontology structure. This tool also provides graphical visualization of the percentage of SAGE tags in each GO category, along with confidence intervals and hypothesis testing. Platform: Online tool
GeneInfoViz: Constructing and Visualizing Gene Relation Networks
GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG. Platform: Online tool
GOfetcher: a database with complex searching facility for gene ontology
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. We developed a web application, GOfetcher, with a very comprehensive search facility for the GO project and a variety of output formats for the results. GOfetcher has three different levels for searching the GO: Quick Search, Advanced Search, and Upload Files for searching. The application includes a unique search option which generates gene information given a nucleotide or protein accession number which can then be used in generating gene ontology information. The output data in GOfetcher can be saved into several different formats; including spreadsheet, comma-separated values, and the Extensible Markup Language (XML) format. Platform: Online tool
Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Service that provides a summary of GO annotations available for each species. The user provides a taxon id and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided.
GOanna is used to find annotations for proteins using a similarity search. The input can be a list of IDs or it can be a list of sequences in FASTA format. GOanna will retrieve the sequences if necessary and conduct the specified BLAST search against a user-specified database of GO annotated proteins. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match. Platform: Online tool
Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris
Pandora - Protein ANnotation Diagram ORiented Analysis
Protein ANnotation Diagram ORiented Analysis
With PANDORA, you can search for any non-uniform sets of proteins and detect subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA supports GO annotations as well as additional keywords (from UniProt Knowledgebase, InterPro, ENZYME, SCOP etc). It is also integrated into the ProtoNet system, thus allowing testing of thousands of automatically generated protein families. Note that PANDORA replaces the ProtoGO browser developed by the same group. Platform: Online tool
The Arabidopsis Information Resource Keyword Browser
TAIR Keyword Browser searches and browses for Gene Ontology, TAIR Anatomy, and TAIR Developmental stage terms, and allows you to view term details and relationships among terms. It includes links to genes, publications, microarray experiments and annotations associated with the term or any children terms. Platform: Online tool
TreeBASE - A Database of Phylogenetic Knowledge
Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review.
Wandora is a general purpose information extraction, management and publishing application based on Topic Maps and Java. Wandora has graphical user interface, layered and merging information model, multiple visualization models, huge collection of information extraction, import and export options, embedded HTTP server with several output modules and open plug-in architecture. Wandora is a FOSS application with GNU GPL license. Wandora is well suited for constructing ontologies and information mashups. Wandora is capable of extracting and converting a wide range of open data feeds to topic map formats. Beyond topic map conversion, this feature allows Wandora user to aggregate multidimensional information mashups where information from Flickr interleaves with information from GeoNames and YouTube, for example. Wandora is a software application to build, edit, publish and visualize information graphs, especially topic maps. Wandora is written in Java and suits for * Collecting, combining, aggregating, managing, refining and publishing information and knowledge graphs * Designing information, information modeling and prototyping * Information mashups * Ontology creation and management * Mind and concept mapping * Language technology applications * Graph visualizations * Knowledge format conversions * Digital preservation * Data journalism * Open data projects * Linked data projects Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
BIIT - Bioinformatics Algorithmics and Data Mining Group
BIIT - Bioinformatics Algorithmics Data Mining Group
BIIT Group - Institute of Computer Science
The Bioinformatics, Algorithmics, and Data Mining group BIIT lead by prof. Jaak Vilo is a joint research group between the Department of Computer Science (University of Tartu), Quretec, and the Estonian Biocenter. Our main research topics and capabilities include the gene regulation, gene expression data analysis, biological data mining, systems biology, combinatorial pattern matching, developing software for biomedical research databases, as well as partnering in stem cell and cancer related projects. Software * MEM - Multi-Experiment-Matrix -- large-scale gene expression data queries and mining (Genome Biology 2009) * g:Profiler family of tools for functional assessment of gene groups, gene ID mappings, orthology and expression similarity searches. (NAR web server issue 2007) * KEGGanim - visualisation of high-throughput data on biological pathway charts (Bioinformatics, 2007) * GraphWeb - a tool for mining large biological networks (NAR Web server issue 2008) * FunGenES data atlas * More software tools
Principe Felipe Research Centre; Valencia; Spain
Centro de Investigaci��n Pr��ncipe Felipe
The Pr��ncipe Felipe Research Centre (CIPF), which was inaugurated by their Royal Highnesses the Prince and Princess of Asturias on 17th March 2005, is a centre dedicated to biomedical research, with the aim of taking on new challenges in the field of basic research and encouraging scientific works of excellence. The construction of the Centre was carried out thanks to the Regional Development Funds from the European Union, and from the Regional Government (Generalitat Valenciana) through its Ministry of Health. The current financing of the CIPF comes mainly from the investment made by the Generalitat Valenciana through the Ministry of Health, as well as the Regenerative Medicine Programme, the fruit of an agreement between the Institute of Health Carlos III and the Ministry of Health for basic and translation research in this field. The CIPF takes the research tradition from the then Valencian Cytological Research Institute and the Valencian Biomedical Research Foundation, with the aim of consolidating and expanding this research. Therefore the activity in the CIPF can be divided into three main strategic work areas: The Regenerative Medicine area focuses its research on cellular therapy and interdisciplinary research in human embryonic and adult stem cells, with the aim of regenerating damaged organs to improve human health. The Chemical and Quantative Biology area aims to understand, through the application of (bio) chemical, genetic, and bioinformatic methods, to understand the molecular mechanisms that control the biological processes and alterations that lead to pathological conditions. The Biomedicine area focuses on understanding the molecular bases of human pathologies that require new diagnostic and clinical procedures for their identification and treatment, pathologies such as cancer, neurological pathologies and rare illnesses.
CIPF Bioinformatics and Genomics Department
Biomedicine can only be understood in the context of genomics and with the concourse of bioinformatics. Our department aims to tackle biomedical problems from a system's biology perspective. Following this, the general objective we seek through the main lines of research is to relate the mutations (Pharmacogenomics and Comparative Genomics) to their effect at cellular and phenotypic level (Functional Genomics) trying to understand the mechanism of action (Structural Genomics). Systems Biology Genes operate within an intricate network of interactions that we have only recently started to envisage. Many higher-order levels of interaction are continuously being discovered. In this scenario we are interested in developing methods and tools which can help to understand large-scale experiments from a systems biology perspective. Comparative genomics We are interested in the analysis of patterns and processes occurred during the evolution of our genome, and in the application of the evolutionary thought in human health and disease. * Adaptive Human Evolution * Evolutionary Pharmacogenetics * SNP's and Human Disease Structural genomics Our Unit aims to develop and apply computational methods for understanding the molecular mechanisms of cell regulation beyond proteins. In particular, we apply our methods to study the interaction of small chemical compounds with proteins and to characterize their molecular actions. We are also developing methods for RNA 3D structure prediction with the aim of applying them to understand the effects of non-coding RNA molecules. Finally, in collaboration with experimentalists, we are working in determining the first ever 3D structure of a genomic domain in human.
A pipeline for analyzing whole genome bisulfite sequencing (WGBS) data.
Virtual Biology Lab portal from the University of Nice Sophia Antipolis; Nice; France. Offered are a variety of software including: * GenBank2Treedyn: Extract annotations from GenBank files for: ** More convenient alignments and phylogeny (replace def line of fasta file by GI number) ** Extremely powerful annotations of phylogenetic trees with TreeDyn. * THEA: Analyses of DNA chip data with ontologies * Blast2Tree: Blast server for the identification of procaryotes * Dashboard: e-Tool for data exchanges among partners, DNA chips design and developement * Oligo Heat Map: Check thermodynamical parameters for PCR primers and compute graphical representation to show specificity of target sequences * EmblEx: A cgi tool to parse and extract data from EMBL entries to various formats * Miscellaneous software ** Jane plugin: Add a small panel to Jane server to retrieve PMID of publications ** EtBlast plugin: Add a small panel to EtBlast server to retrieve PMID of publications ** Oligo Builder: Get the oligomers from a set of target sequences by avoiding non-target sequences
A dataset of an on-going multi-level longitudinal survey in Indonesia that collects extensive information on socio-economic and demographic characteristics of respondents, as well as extremely comprehensive interviews with local leaders about community services and facilities. The survey is ideally suited for research on topics related to important dynamic aging processes such as the transition from self-sufficiency to dependency, the decline from robust health to frailty, labor force and earning dynamics, wealth accumulation and decumulation, living arrangements and intergenerational transfers. The first wave of IFLS was fielded in 1993 and collected information on over 30,000 individuals living in 7,200 households. The sample covers 321 communities in 13 provinces in Indonesia and is representative of about 83% of the population. These households were revisited in 1997 (IFLS2), 2000 (IFLS3), and 2007-8 (IFLS4). A 25% sub-sample of households was re-interviewed in 1998 (IFLS2+). Special attention is paid to the measurement of health, including the measurement of anthropometry, blood pressure, lung capacity, a mobility test and collection of dry blood spots by a nurse or doctor. In addition to comprehensive life history data on education, work, migration, marriage and child bearing, the survey collects very detailed information on economic status of individuals and households. Links with non co-resident family members are spelled out in conjunction with information on borrowing and transfers. Information is gathered on participation in community activities and in public assistance programs. Measurement of health is a major focus of the survey. In addition to detailed information about use of private and public health services along with insurance status, respondents provide a self-reported assessment of health status. Detailed information on the local economy and prices of goods and services are also collected. These data may be matched with the individual and household-level data. Considerable attention has been placed on minimizing attrition in IFLS. In each re-survey, about 95% of households have been re-contacted. Around 10-15% of respondents have moved from the location in which they were interviewed in the previous wave. In addition, individuals who split-off from the original households have been followed. They have added around 1,000 households to the sample in 1997 and about 3,000 households in 2000. Data Availability: IFLS1 data are available through ICPSR as study number 6706. Data from subsequent waves of the IFLS can be accessed from the RAND project Website. * Dates of Study: 1993-2008 * Study Features: Longitudinal, International, Anthropometric Measures, Biomarkers * Sample Size: ** 1993: 22,000 (IFLS1) ** 1997: 33,000 (IFLS2) ** 1998: 10,000 (IFLS2+) ** 2000: 37,000 (IFLS3) ** 2008: 44,103 (IFLS4) Links: * IFLS1 ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06706 * IFLS ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00184
Clemson Computational Biophysics and Bioinformatics
Clemson Computational Biophysics Bioinformatics
Clemson Computational Biophysics & Bioinformatics
The research in the lab focuses on computational modeling of biological macromolecules and their assemblages and predicting biophysical quantities associated with them. The main focus of the lab is the development and maintenance of the popular software package DelPhi, which calculates electrostatic potential and energies of systems comprised of biological macromolecules. In addition, we are interested in modeling disease-causing missense mutations, pKa''s of amino acids and nucleic groups and pH-dependence of stability and binding. In parallel with in silico modeling, the lab actively collaborates with experimetalists to better understand molecular mechanisms of biological reactions and interactions. The combination of the methods of Computational Biophysics and Bioinformatics with experimental results is an essential approach utilized in our research.
NYU Bioinformatics Lab - Courant Institute of Mathematical Sciences
NYU Bioinformatics group applies algorithmic, statistical, and mathematical techniques to solve problems of interest to biology, biotechnology and biomedicine. The group focuses on bioinformatics, computational biology and systems biology with many active projects in areas ranging from single molecules to entire populations: Analysis of Single-Molecule/Single-Cell Data, SPM-based Transcriptomic Profiling, Whole-Genome Haplotype Sequencing using SMASH (Single Molecule Approaches to Haplotype Sequencing), SUTTA (Scoring and Unfolding Trimmed Tree Assembler) assembly algorithm, Analysis of Spatio-Temporal Data, Model Checking and Model Building for Systems Biology, GOALIE-based Phenomenological Models and their Verification, Causality Analysis, Causal Models and their Verification, Analysis of EHR (Electronic Health Record Data) and Disease Models (e.g., Chronic Fatigue Syndrome, Congestive Heart Failure, Deep Vein Thrombosis, etc.), Models of Cancer, Applications to Pancreatic Cancer, Polymorphisms and Biomarkers, Strategies for Group Testing, Epidemiological and Bio-Warfare Models, Planning with Large Agent Networks against Catastrophes (PLAN C), Population Genomics, and Genome Wide Association Studies (GWAS). The group has received its funding from Air Force, Army, CCPR, DARPA, NIH, NIST, NSF, NYSTAR, etc. and various other governmental and commercial entities. Currently, the group is part of an NSF funded Expedition in Computing project (CMACS: Center for Modeling and Analysis of Complex Systems at CMU) and collaborates widely, both nationally and internationally. The group is highly multi-disciplinary, attracting researchers and students from mathematics, statistics, computer science, and biology who team up with physicians, physicists, and chemists as well as professionals in their own disciplines. This group is led by Prof. Bud Mishra, a professor of computer science and mathematics at NYU''s Courant Institute of Mathematical Sciences.
Stanford Center for Biomedical Informatics Research
Mark Musen''s laboratory studies components for building knowledge-based systems, controlled terminologies and ontologies, and technology for the Semantic Web. For more than two decades, Musen''s group has worked to elucidate reusable building blocks of intelligent systems, and to develop scalable computational architectures for systems with significant applications in biomedicine. Informatics is the study of information: its structure, its communication, and its use. As society becomes increasingly information intensive, the need to understand, create, and apply new methods for modeling, managing, and acquiring information has never been greater especially in biomedicine. BMIR is home to world class scientists and trainees developing cutting-edge ways to acquire, represent, process, and manage knowledge and data related to health, health care, and the biomedical sciences. Our faculty, students, and staff are committed to ensuring the biomedical community is properly equipped for the information age, and believe our efforts will provide the structure for the burgeoning revolution of health care and the biomedical sciences.
Proteomic Mass Spectrometry Lab at The Scripps Research Institute
The Scripps Research Institute -Yates Lab
Yates Lab at The Scripps Research Institute
Scientists at the Yates Lab at The Scripps Research Institute (TSRI) rely on information yielded by tandem mass spectrometry to identify proteins from complex mixtures. Using this powerful technique, researchers draw upon a cross section of fields to increase the scope, sensitivity, and throughput of technologies for practical proteomics. Biologists provide the questions that drive our research. By identifying complexes that are poorly understood or organism-wide issues requiring further exploration, we gain a theoretical understanding of issues that are tractable only through proteomic strategies. Analytical chemists and biochemists improve our tools for revealing the proteins present in biological samples. Targets for optimization include the isolations used to obtain proteins, the steps to generate peptides from these proteins, and the separation of peptides en route to the mass spectrometer. Chemistry is vital to increasing power of proteomic technology. Computer science yields tools on two scales. First, the sequence corresponding to each peptide''s tandem mass spectrum must be identified. Once those identifications have been completed, additional tools are needed to summarize and organize these identifications.
The research of the group concentrates on the molecular biology of Gram-positive bacteria, with Bacillus subtilis and Lactococcus lactis as the main model organisms. A number of important (human) pathogens are also investigated: Bacillus cereus, Streptococcus pneumoniae and Enterococcus faecalis. The nature of the research is both fundamental and application-oriented. Transcript- and protein profiling by high-throughput technologies such as DNA microarrays and proteomics tools are being used. The very large data sets generated are analyzed by employing existing and novel bioinformatics tools. Major lines of research are in the field of functional genomics of these organisms, using systems- and synthetic biology approaches.
UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core
UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics and Computational Biology Core
UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Computational Biology Core
The Biostatistics Core provides statistical support for cancer-related research at UCSF, focusing particulary on applications in clinical trials and population studies. The Computational Biology Core supports applications to genomics, genetics and molecular biology. Core faculty have expertise in study design, protocol and proposal development and review, data analysis, and publication of results. Support for Cancer Center investigators participating in established Site Committees is typically handled by the faculty member assigned to that committee. Other requests can be directed to the consulting service request page maintained by the UCSF Clinical & Translational Science Institute (CTSI). These requests will then be assigned to a Core faculty member. Basic consulting services are generally provided free of charge to Cancer Center Members. Members requiring frequent assistance are encouraged to provide regular salary support to a Core statistician when possible to support more extensive requests and for long-term projects. Services: * Study Design * Guidance on Study Conduct * Data Analysis and Reporting of Study Results * Teaching resources
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.
Cincinnati Children's Research Foundation
Foundation scientists and physicians conduct breakthrough research to improve care for children as well as train the next generation of investigators. Cincinnati Children's Research Foundation is dedicated to advancing basic, translational, clinical and outcomes-based research. Why choose our cores for your research? We can provide you with cutting-edge, cost-effective technology and data analysis that would be unattainable on an individual research basis. Our fee-for-service program also offers unique studies that you can't find anywhere else. Our faculty also has access to the research cores hosted at the University of Cincinnati College of Medicine. * Animal Behavioral Core * Cardiovascular Imaging Core * Cell Manipulations Laboratory * Cell Processing Core * Cincinnati Biobank * Cincinnati Center for Nutritional Research and Analysis * Comprehensive Mouse and Cancer Core * Gene Expression Microarray Core * Genetic Variation and Gene Discovery Core * Imaging Research Center * Laser Capture Microdissection Microscopy * Lenti-shRNA Library Core * Pathology Research Core * Pluripotent Stem Cell Facility * Research Flow Cytometry Core * Stem Cell Processing Core Lab * Transgenic and Gene Targeting Core * Translational Core Labs * Translational Trials Development and Support Laboratory (TTDSL) * Vector Production Facility * Veterinary Services * Viral Vector Core Support Services: We provide expert consultation, including grant proposal design, data management and regulatory compliance, to investigators at Cincinnati Children's. Research Education and Training: The Cincinnati Children's Research Foundation offers research-based education and training options for scientists, often in conjunction with the University of Cincinnati. High School Programs, Undergraduate Programs, Graduate Degree Programs, Medical Student Program, Postgraduate Programs, Postdoctoral Programs
University of Barcelona Statistics and Bioinformatics Research Group
University of Barcelona Statistics Bioinformatics Research Group
UB Statistics and Bioinformatics Research Group
The Statistics and Bioinformatics research group has as its main objectives the development of methods and tools to deal with problems appearing in the interface between Statistics and Bioinformatics. We started focusing in DNA microarrays but we are also interested in statistical methods for ''omics'' data integration and next generation sequencing (NGS). Our group collaborates with different research groups in the fields of biology and biomedicine, to whom it offers statistical support for problems which are specifically statistic in nature, such as experimental design or microarray data analysis, and also in more general aspects, such as modeling, analysis or data mining. After a first period of collaboration agreements with the Fundaci�� Vall d''Hebr��n Institut de Recerca we contributed to the creation of the Statistics and Bioinformatics Unit (UEB) which provides statistical and bioinformatical support to VHIR researchers.
University of Lorraine; Lorraine; France
Private Methodist affiliated university with its main campus in Stockton, California, and graduate campuses in San Francisco and Sacramento.
GUMC Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab
Georgetown University Medical Center Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab
Georgetown University Medical Center Liu Lab
GUMC Department of Biostatistics Bioinformatics Biomathematics - Liu Lab
Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Computational Biology and Bioinformatics Group at ORNL
Computational Biology at Oak Ridge National Laboratory
Computational Biology Bioinformatics Group at ORNL
We are the Computational Biology and Bioinformatics Group of the Biosciences Division of Oak Ridge National Laboratory. We conduct genetics research and system development in genomic sequencing, computational genome analysis, and computational protein structure analysis. We provide bioinformatics and analytic services and resources to collaborators, predict prospective gene and protein models for analysis, provide user services for the general community, including computer-annotated genomes in Genome Channel. Our collaborators include the Joint Genome Institute, ORNL''s Computer Science and Mathematics Division, the Tennessee Mouse Genome Consortium, the Joint Institute for Biological Sciences, and ORNL''s Genome Science and Technology Graduate Program.
The Roth Laboratory is designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease. Software for research focused on a specific research goal is available. Current experimental interests: * Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription. * Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance. * Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism. Current computational interests: * Systematic analysis of genetic interaction to reveal redundant systems and order of action in genetic pathways * Integrating large-scale studies - including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns - to quantitatively assign function to genes and guide experimentation and disease association studies. * Alternative splicing and its relationship to protein interaction networks.
As part of its multimedia outreach, the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health -- the United States'' medical research agency -- offers audio and video podcasts and other multimedia resources that explore the exciting world of basic biomedical research.
UT Southwestern Medical Center Department of Pathology
University of Texas Southwestern Medical Center Department of Pathology
The Department of Pathology at UT Southwestern Medical Center is committed to its missions in diagnostics, research, teaching, and resident and fellowship training. Our facilities include approximately 54,000 square feet of lab and office space. Our Department comprises more than 100 of the most outstanding faculty in the country and more than 50 residents and fellows. We are home to more than a dozen graduate students at any given time. The Department of Pathology offers comprehensive, in-depth training in all of the various pathology disciplines, as well as a complete array of subspecialty fellowship programs. It is our view that a strong academic environment with access to state-of-the-art and newly emerging diagnostic technologies is essential to the preparation of any pathologist for professional life in the 21st century, regardless of the ultimate practice setting. Therefore, basic training in our program is enhanced by extensive exposure to modern molecular diagnostics, advanced flow cytometric analysis, and molecular cytogenetics. The Department provides diagnostic services in a variety of clinical settings that include a large county hospital (Parkland Memorial Hospital), two private University Hospitals (Zale-Lipshy and St. Paul), a tertiary care private pediatric hospital (Children''s Medical Center), a large university outpatient clinic (Aston Clinic), and the Dallas VA Medical Center, exposing our residents, fellows, and faculty to the full spectrum of human adult and pediatric disease.
TRIPLES- a database of TRansposon-Insertion Phenotypes Localization and Expression in Saccharomyces
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. TRIPLES provides full public access to the data and reagents generated from ongoing functional analysis of the yeast genome. Using a novel transposon-tagging approach, we have analyzed disruption phenotypes, gene expression, and protein localization on a genome-wide scale in Saccharomyces. The data generated from this study may be accessed through our database, TRIPLES ; additionally, all reagents generated in this study are freely available from on-line order forms (linked to TRIPLES as well). multipurpose, mini-transposon, mutant alleles, phenotypes, protein localization, gene expression, Saccharomyces cerevisiae, Web-accessible database, transposon-mutagenized yeast strains, downloaded, tab-delimited, text file, protein localization data, fluorescent micrographs, staining patterns, indirect immunofluorescence analysis of indicated epitope-tagged proteins, subcellular localization of the yeast proteome, visual library, Nucleic Acid Sequence Data Library (GenBank), clone report, graphic map, transposon insertions (represented as flags)
BIOTEC - Biotechnology Center TU Dresden
The Biotechnology Center (BIOTEC) of the Technische Universit��t Dresden is a unique interdisciplinary center focusing on research and teaching in molecular bio-engineering. The BIOTEC hosts top international research groups working on genomics, proteomics, biophysics, cellular machines, molecular genetics, tissue engineering, and bioinformatics. The Biotechnology Center (BIOTEC) was founded in 2000 as a central scientific unit of the Technische Universit��t Dresden. The center is an essential part of implementing the Biotechnology-Offensive of the Free State of Saxony within the TU Dresden. The main goal in establishing and developing this center was to link the revolutionary change within molecular and cell biology to Dresden''s traditionally strong background in engineering. Dresden''s aspired innovation advantages as a location for developing state-of-the-art biotechnology are already visible in some parts. The BIOTEC plays a central role in the Molecular Bioengineering and Regenerative Medicine profile of the TU Dresden, fostering developments in the new field of Biotechnology/Biomedicine. Establishing and developing a strong and internationally competitive research center molecular bioengineering required a powerful nucleus. The BIOTEC started with five professorships and one junior research group recruited within the Biotechnology-Offensive of the Free State of Saxony. Through the interdisciplinary work of these researchers from different fields and faculties, the development of the center was catalyzed, and the main goal of building an internationally competitive research structure is now well underway. Today, the BIOTEC houses six professorships and seven junior research groups. Their work has given rise not only to novel discoveries in modern life sciences, but the translation of these finding into economically useful innovations. The BIOTEC is located within the BioInnovation Center in Dresden, which has provided an atmosphere essential for its development. In accordance with its motto Science and Economy under one roof, the BioInnovation Center offers a unique opportunity for knowledge and technology transfer between the research center and start-ups working on biotechnology and related fields of cutting-edge technology. The BIOTEC has about 230 members from over 35 countries, including Eastern and Western Europe, Asia, Australia, and the Americas. These researchers have diverse backgrounds, covering biology, medicine, physics, chemistry, computer science, and engineering. The BIOTEC offers excellent lab facilities and infrastructure, as well as close links to companies residing in the same building.
A database that manages genetic and genomic information about tropical crops studied by Cirad. The database is organised into crop specific modules. Each module includes data on genetic ressources (agro-morphological data, parentages, allelic diversity), information on molecular markers, genetics maps, result of QTL analyses, data from physical mapping, sequences, genes, as well as corresponding references. GENE DB interface has been designed to allow quick consultations as well as complex queries. Nine modules are presently on line.
GlycomeDB - A carbohydrate structure metadatabase
GlycomeDB is a database of all known carbohydrate structures. This was achieved by crosslinking several other databases of carbohydrate structures by using the GlycoCT XML language specification. We have analyzed all of the existing public databases and defined a sequence format based on XML (GlycoCT) capable of storing all structural information of carbohydrate sequences. We have implemented a library of parsers for the interpretation of the different encoding schemes for carbohydrates. With this library we have translated the carbohydrate sequences of all freely available databases (CFG , KEGG, GLYCOSCIENCES.de, BCSDB and Carbbank) to GlycoCT, and created a new database (GlycomeDB) containing all structures and annotations. During the process of data integration we found multiple inconsistencies in the existing databases which were corrected in collaboration with the responsible curators. With the new database, GlycomeDB, it is possible to get an overview of all carbohydrate structures in the different databases and to crosslink common structures in the different databases. Scientists are now able to search for a particular structure in the meta database and get information about the occurrence of this structure in the five carbohydrate structure databases.
The Hepatitis C Virus Database (HCVdb) is a cooperative project of several groups with the mission of providing to the scientific community studying the hepatitis C virus a comprehensive battery of informational and analytical tools. The Viral Bioinformatics Resource Center (VBRC), the Immune Epitope Database and Analysis Resource (IEDB), the Broad Institute Microbial Sequencing Center (MSC), and the Los Alamos HCV Sequence Database (HCV-LANL) are combining forces to acquire and annotate data on Hepatitis C virus, and to develop and utilize new tools to facilitate the study of this group of organisms.
The National Hellenic Research Foundation (NHRF) is a multidisciplinary Research Centre established by Royal Decree on 9th October 1958. Its purpose is the organisation, finance and support of high-level research projects in the humanities and the natural sciences. The Humanities Institute cover a wide spectrum of study and research fields in Greek history and culture, contributing substantially and critically to the knowledge and promotion of Greek identity. The Natural Sciences Institutes perform basic and applied research in leading edge areas of science such as health, pharmaceuticals, environment, biotechnology and new materials. They develop innovative methods for solving complex problems facing Greek industry and they provide specialised services and know-how both to the public and private sector. The NHRF is governed by the Board of Directors and the Central Administration under the Director/Chairman of the Board.
GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: selection of entity sets, comparison of sets of Pfam families, semantic comparison of sets of GO terms, functional comparison of sets of gene products. This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Software resource that extends the functionality of go-perl (on which it depends) with GO Database access functionality. go-db-perl comes bundled with various scripts and a shell command line interface that can be used as standalone tools. Installation is more involved than for go-perl; you will need a MySQL database plus the requisite DBI and DBD Perl modules. Full installation instructions are included in the download. go-db-perl is in use both to drive AmiGO and internally within Ensembl. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Onto-Miner (OM) provides a single and convenient interface that allows the user to interrogate our databases regarding annotations of known genes. OM will return all known information about a given list of genes. Advantages of OM include the fact it allows queries with multiple genes and allows for scripting. This is unlike GenBank which uses a single gene navigation process. Scripted search of the Onto-Tools database for gene annotations. User account required. Platform: Online tool
Transcription Regulatory Regions Database
TRRD is a unique information resource, accumulating information on structural and functional organization of transcription regulatory regions of eukaryotic genes. Only experimentally confirmed information is included into TRRD. Transcription Regulatory Regions Database (TRRD) is developed for accumulation of experimental information on the structure-function features of regulatory regions of eukaryotic genes. Each entry of TRRD corresponds to a particular gene. The annotated part of an entry includes the structure-function description of gene regulatory regions composed by regulatory units (promoters, silencers, enhancers, etc.), individual transcription factor binding sites that constitute these regulatory units, and transcription factors that bind to these sites. In addition, the entry contains the gene expression patterns and references to original publications.
SeqGSEA - Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Software package that provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene''s differential expression and splicing, respectively.
In the annotation world, the same piece of information can be stored and viewed differently across different databases. For instance, more than one Affymetrix probe ID can refer to the same GenBank sequence (accession number) and more than one nucleotide sequence from GenBank can be grouped in a single UniGene cluster. The result of Onto-Express depends on whether the input list contains Affymetrix probe IDs, GenBank accession numbers or UniGene cluster IDs. The user has to be aware of relations between the different forms of the data in order to interpret correctly the results. Even if the user is aware of the relationships and knows how to convert them, most existing tools allow conversions of individual genes. Onto-Translate is a tool that allows the user to perform easily such translations. Affymetrix probe IDs, etc., translate GO terms into other identifiers like GenBank accession number, Uniprot IDs. User account required. Platform: Online tool
ToppGene Suite is a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. ToppGene Suite is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. The similarity scores from individual features are combined into an overall score using statistical meta-analysis.
Db for Dummies! (DBD) is a flexible, lightweight, memory-resident database. DBD manages any conceivable data structure including lists, tables, multi-rooted hierarchies, graphs and complex networks. Unlike traditional databases, DBD stores data as a network of nodes. DBD has four interfaces to manage data: * The Graphical User Interface (GUI) allows users to manage data mainly via a tree and grid. * The Natural Language Interface (NLI) allows users to mangage data via English-like expressions. * The Remote User Interface (RUI) allows users to manage data via a remote computer. * The Application Programmer Interface (API) allows programmers to manage data via a Dynamic Link Library (DLL). DBD is useful for applications where: # Data structure is complex and highly varied (non-uniform). # Data structure changes frequently. # Data structure is unknown in advance. # Minimum impact on existing code and data is desirable in adapting to new requirements. These characteristics may make DBD useful for Artificial Intelligence applications.
Db for Dummies! is a small database that imports the Generic GO Slim. It allows data to be viewed in a tree. The Gene Ontology describes gene products in terms of their associated biological processes, cellular components and molecular functions. The Generic Slim Gene Ontology is a subset of the whole Gene Ontology. The slim version gives a broad overview and leaves out specific/fine grained terms. This example stores the slim version of the Gene Ontology (goslim_generic_obo) that can be downloaded from www.geneontology.org/GO.slims.shtml. Platform: Windows compatible
HOLLOW - Volume Filling of Protein Structures
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures
HOLLOW facilitates the production of surface images of proteins. HOLLOW is a portable command-line utility written in Python 2.4-2.7; it does not have any other dependencies (although running under the PyPy JIT interpreter, it runs much faster). The input is a PDB file. The output is a PDB file of dummy water atoms that forms a cast of the voids and channels of a protein. HOLLOW generates a surface from a cast of the protein surface. HOLLOW fills the interior spaces of a protein structure with dummy atoms defined on an overlapping grid. The surface generated by these dummy atoms can be shown to reproduce the surface of the protein at the ideal limit. The use of the surface of the dummy atoms allows us to focus on a specific piece of the interior surface. Simply by deleting dummy atoms, the interior surface can be trimmed to produce a custom portion of the interior space. For advanced coloring of the surface, the B-factor of the dummy atoms can be calculated as the average of the B-factor of the protein atoms surrounding the dummy atoms. This allows various colorings of the surface to be conveyed through the B-factor field of the PDB files. The volume filling representation facilitated by HOLLOW is meant to complement other programs that identify voids, pockets and channels, such as SPHGEN and CASTp, which identify binding sites but cannot produce output that can be rendered in standard molecular graphics software. HOLLOW can be used to help render these binding pockets.
go-perl is a set of Perl modules for parsing, manipulating and exporting ontologies and annotations. It includes parsers for the OBO and GO gene association file formats. It has a graph-based object model with methods for graph traversal. For more details, see the documentation included with the modules. go-perl comes bundled with XSL (Extensible Stylesheet Language) transforms (which can also be used independently of Perl, provided you have files in OBO-XML format), as well as scripts that can be used as standalone tools. Installation should be simple, provided you have some experience with Perl and CPAN; see the INSTALL file for details. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
ONTO-PERL is a collection of Perl modules to handle OBO-formatted ontologies (like the Gene Ontology). This code distribution gathers object-oriented modules (for dealing with ontology elements such as Term, Relationship and so forth), scripts (for typical tasks such as format conversions: obo2owl, owl2obo; besides, there are also many examples that can be easily adapted for specific applications), and a set of test files to ensure the suite' '''s implementation quality. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
OWLTools (aka OWL2LS - OWL2 Life Sciences) is a java API for accessing ontologies in either OBO or OWL. OWLTools provides a bio-ontologies friendly wrapper on top of the Manchester OWL API. It provides many features, including: * convenience methods for OBO-like properties such as synonyms, textual definitions, obsoletion, replaced_by * simple graph-like operations over ontologies * visualization using the QuickGO graphs libraries Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Biomedical Logical Programming (Blip) is a research-oriented deductive database and prolog application library for handling biological and biomedical data. It includes packages for advanced querying of ontologies and annotations. Blip underpins the Obol tool. Here are some distinguishing characteristics of Blip * Lightweight. Bloat-free: Blip only has as many modules as it needs to do its job. * Fast. * Declarative. Say what you want to do, not how you want to do it * Blip can be Query-oriented: specify your data sources and ask your query * Blip can be Application-oriented: it is designed to be used as an application library used by other bioinformatics tools * Mature and fully functional ontology module for handling both OBO-style ontologies and OWL ontologies. * Modules for handling biological sequences and sequence features. (currently limited functionality, added as needed) * A systems biology module for querying pathway and interaction data. (currently limited functionality, added as needed) * Relational database integration. SQL can be viewed as a highly restricted dialect of Prolog. Although the SWI-Prolog in-memory database is fast and scalable, sometimes it is nice to be able to fetch data from an external database. Blip contains a generic SQL utility module and predicate mappings for the GO database, Ensembl and Chado * Integration with a variety of bioinformatics file formats. SWI-Prolog has a variety of fast libraries for dealing with XML, RDF and tabular data files. Blip provides bridges from bio file formats encoded using these syntaxes into its native models. For other syntaxes, Blip seamlessly integrates other packages such as BioPerl and go-perl. Although these dependencies require extra installation, there is no point reinventing the wheel * Rapid development of web applications. Blip extends SWI-Prolog' '''s excellent http support with a simple and powerful logical-functional-programming style application server, serval. This has been used to prototype a fully-featured next-generation replacement for the GO project amigo browser. * Scalable. Blip is not intended to be a toy system on toy data (although it is happy to be used as a toy if you like!). It is intended to be used as an application component and a tool operating on real-world biological and biomedical data Blip is written in SWI-Prolog, a fast, robust and scalable implementation of ISO Prolog. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
The OWL API is a Java API and reference implementation for creating, manipulating and serializing OWL Ontologies. The latest version of the API is focused towards OWL 2. The OWLAPI underpins ontology browsing and editing tools and platforms such as SWOOP and Protege4. Note that this API, or any other OWL-based API, can be used without an integrated OWL parser if you download a pre-converted OWL file generated from OBO. See OBO Ontologies List for all OBO ontologies converted to OWL (we do not list the full complement of OWL-based APIs here, only those of direct relevance to GO). The OWL API includes the following components: * An API for OWL 2 and an efficient in-memory reference implementation * RDF/XML parser and writer * OWL/XML parser and writer * OWL Functional Syntax parser and writer * Turtle parser and writer * KRSS parser * OBO Flat file format parser * Reasoner interfaces for working with reasoners such as FaCT++, HermiT, Pellet and Racer Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
CLENCH: A program for calculating cluster enrichment using the Gene Ontology
Cluster Enrichment (CLENCH) allows A. thaliana researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using GO slim term lists (which can be edited by the user) and a local installation of GO. Platform: Windows compatible, Linux compatible,
BiNGO: A Biological Networks Gene Ontology tool
The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape' '''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
CateGOrizer takes batch input of GO term IDs in a list format or unformatted plain text file, allows users to choose one of the available classifications such as GO_slim, GOA, EGAD, MGI_GO_slim, GO-ROOT, or a self-defined classification list, find its parental branch and performs an accumulative classification count, and returns the results in a sorted table of counts, percentages, and a pie chart (if it takes longer than standard time out period, it will email the user with a URL link to the results). This tool is comprised with a set of perl CGI programs coupled with a MySQL DBMS that stores the GO terms DAG data. Platform: Online tool
FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products
Functional Semantic Similarity Measure between Gene Products (FuSSiMeG)
Functional Semantic Similarity Measure between Gene-Products
FuSSiMeG is being discontinued, may not be working properly. Please use our new tool ProteinOn. Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) provides a functional similarity measure between two proteins using the semantic similarity between the GO terms annotated with the proteins. Platform: Online tool
SocioPatterns is an interdisciplinary research collaboration that adopts data-driven methodology with the aim of uncovering fundamental patterns in social dynamics and coordinated human activity. To achieve its scientific goals, the SocioPatterns collaboration also contributes to the development of new technologies for collecting relevant data. In particular, the collaboration supports the development of the SocioPatterns sensing platform, which uses wireless wearable sensors to gather longitudinal data on human mobility and face-to-face proximity in real-world environments. The SocioPatterns team also works on developing tools and techniques to represent, analyze and visualize the collected data. We increasingly use digital media and computational devices in our daily activities, and leave behind a sizable amount of digital traces while doing so. The proliferation of mobile devices, and the incorporation of various sensing technologies in these devices, will further add to this growing trail of data. The possibility to mine and analyze these data, and the scale at which this can be done on contemporary computer systems, affords a novel, data-driven approach in the investigation of various aspects of human behavior. The following collection of datasets obtained through the SocioPatterns sensing platform are available: * Infectious SocioPatterns dynamic contact networks * Hypertext 2009 dynamic contact network * Primary school cumulative networks * Infectious SocioPatterns
ProteInOn - Protein Interactions and Ontology
ProteInOn calculates semantic similarity between GO terms or proteins annotated with GO terms. It also calculates term enrichment of protein sets, by applying a term representativity score, and gives additional information on protein interactions. The query compute protein semantic similarity returns the semantic similarity scores between all proteins entered, in matrix format. The option Measure allows users to choose one of several semantic similarity measures: Resnik, Lin, or Jiang & Conrath's measures with or without the DCA approach, plus the graph-based simUI and simGIC measures. These measures are listed by order of performance as evaluated with protein sequence similarity. The option GO type allows users to choose one of the aspects of GO: molecular function, biological process and cellular component. The option Ignore IEA limits the query to non-electronic annotations, excluding evidence types: IEA, NAS, ND, NR.
ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions free molecules and ions, and orientation of free molecules. Any generalized coordinate may be kept fixed. Molecules and fragments that are not expected to undergo significant conformational changes may be treated as rigid bodies. Popular molecular modeling programs usually work in the space of Cartesian coordinates of atoms. During energy minimization of a big system, many Cartesian coordinates-variables move collectively. For example, rotation of a benzene ring around the C-Ph bond in the Cartesian-coordinates space involves collective motion of 33 variables. In the generalized-coordinates space, this rotation involves variation of just one torsion angle. In ZMM, any fragment of a molecular system may be treated as either rigid or flexible. The generalized-coordinates method saves large computational resources if only a small part of a system is considered flexible. Examples are ligand-protein and protein-protein interactions. The savings occur because the sampling space is reduced and because molecular interactions within rigid fragments are not computed. * ZMM runs on Windows 95, 98, 2000, XP, UNIX, and Linux * ZMM can be used via the command-line interface * ZMM can also be used at Windows via a graphical user interface
ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity. ESTScan takes advantages of the bias in hexanucleotide usage found in coding regions relative to non-coding regions. This bias is formalized as an inhomogeneous 3-periodic fifth-order Hidden Markov Model (HMM). Additionally, the HMM of ESTScan has been extended to allows insertions and deletions when these improve the coding region statistics.
Public research university in Lafayette, Louisiana. It has the largest enrollment within the nine-campus University of Louisiana System and the second largest enrollment in Louisiana.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
SIMBioMS - System for Information Management in BioMedical Studies
System for Information Management in BioMedical Studies
SIMBioMS (System for Information Management in BioMedical Studies) is a multi-module solution for data management in biomedical studies. Any research concerning human samples and/or utilizing high-throughput technologies yields such amount of information that conventional data storage solution might not be sufficient. We offer here three software modules: * Sample Information Management System (SIMS), * Assay Information Management System (AIMS) * Sample avAILability system (SAIL) * Emanta Administration tool (Emanta) All three software modules were developed as a part of the integrated EU project MolPAGE (Molecular Phenotyping to Accelerate Genomic Epidemiology) and the collaborative research project ENGAGE (European Network of Genomic and Genetic Epidemiology). SIMS and AIMS can work either as united system or as two completely independent components. In turn, SAIL is an independent web-based system for indexing of phenotypes availability in different cohorts and collections. All systems are packaged in such a way that they can easily be installed either as local (e.g. on a laptop) or as centralized databases (to be used by a group of people). SIMS and AIMS benefit from customizable interface, editable vocabularies and a choice of options for tackling data confidentiality issues. The systems provides a user with efficient means of control over data exchange process and at the same time helps to format the metadata in compliance with the standards accepted in functional genomics. Since SIMBioMS is an open source project, source files can be downloaded and changed by the user if needed.
GraphWeb allows the detection of modules from biological, heterogeneous and multi-species networks, and the interpretation of detected modules using Gene Ontology, cis-regulatory motifs and biological pathways. GraphWeb is a public web server for graph-based analysis of biological networks that: * analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; * integrates multiple diverse datasets into global networks; * incorporates multispecies data using gene orthology mapping; * filters nodes and edges based on dataset support, edge weight and node annotation; * detects gene modules from networks using a collection of algorithms; * interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs. Platform: Online tool
A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Public research university in Louisville, Kentucky. It is part of the Kentucky state university system.
omniBiomarker: Knowledge-Driven Biomarker Identification and Data Combination
omniBiomarker is a web-application for analysis of high-throughput -omic data. Its primary function is to identify differentially expressed biomarkers that may be used for diagnostic or prognostic clinical prediction. Currently, omniBiomarker allows users to analyze their data with many different ranking methods simultaneously using a high-performance compute cluster. The next release of omniBiomarker will automatically select the most biologically relevant ranking method based on user input regarding prior knowledge. The omniBiomarker workflow * Data: Gene Expression * Algorithms: Knowledge-Driven Gene Ranking * Differentially expressed Genes * Clinical / Biological Validation * Knowledge: NCI Thesaurus of Cancer, Cancer Gene Index * back to Algorithms
Opasnet is a wiki-based website and workspace for helping societal decision making. The website collects, synthesizes, and distributes people''s values and scientific information. Opasnet welcomes anyone who wants to promote science-based decision-making in any field. The specialty is that the information is structured for both scientific scrutiny and for policy use at the same time. In practice, you can do original research, store data, make models, and perform policy assessments and discuss all of that work in one workspace. Originally, the developers of Opasnet came from the environmental health, i.e. a research field that studies the impacts of environment on human health. We are actively working, among other things, on climate change and air pollution, but you can also start a new assessment about a decision of your own interest, or participate in an existing assessment. Opasnet is a website that has basically two parts. One part is a wiki site (called Opasnet wiki or simply Opasnet) that has descriptive pages with text, figures, and tables; it also contains files. The other part is a database called Opasnet Base that contains quantitative estimates about anything that is described in Opasnet. The majority of information is openly available. However, both Opasnet wiki and Opasnet Base have a protected area for working with material that is non-public for some reason.
CLASSIFI - Cluster Assignment for Biological Inference
Cluster Assignment for Biological Inference
Cluster Assignment for Biological Inference (CLASSIFI)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 10, 2012. Cluster Assignment for Biological Inference (CLASSIFI) is a data-mining tool that can be used to identify significant co-clustering of genes with similar functional properties (e.g. cellular response to DNA damage). Briefly, CLASSIFI uses the Gene Ontology gene annotation scheme to define the functional properties of all genes/probes in a microarray data set, and then applies a cumulative hypergeometric distribution analysis to determine if any statistically significant gene ontology co-clustering has occurred. Platform: Online tool
The Human Adenovirus Type Classification coordinates the naming of candidate new types, prior to manuscript submission for peer review. This resource contains a method of submitting candidate HAdV, criteria for a new HAdV type, and a Serotyping tool, which displays all potential types corresponding to the query serotype entered by a user. The criteria are based on discussions at the International Adenovirus Meeting (Dobog��k, Hungary; 26-30 April, 2009) and the NIH Human Adenovirus Working Group Workshop (Bethesda, MD. USA; 3 February 2011), which are summarized in a Letter to the Editor.
A database of oncogenes and tumor suppressor genes. Users can search by genes, chromosomes, and keywords. The coAnsensus domain analysis tool functions to identify conserved protein domains and GO terms among selected TAG genes, while the “oncogenic domain analysis” can analyze oncogenic potential of any user-provided protein based on a weighed term frequency table calculated from the TAG proteins. The completion of human genome sequences allows one to rapidly identify and analyze genes of interest through the use of computational approach. The available annotations including physical characterization and functional domains of known tumor-related genes thus can be used to study the role of genes involved in carcinogenesis. The tumor-associated gene (TAG) database was designed to utilize information from well-characterized oncogenes and tumor suppressor genes to facilitate cancer research. All target genes were identified through text-mining approach from the PubMed database. A semi-automatic information retrieving engine was built to collect specific information of these target genes from various resources and store in the TAG database. At current stage, 519 TAGs including 198 oncogenes, 170 tumor suppressor genes, and 151 genes related to oncogenesis were collected. Information collected in TAG database can be browsed through user-friendly web interfaces that provide searching genes by chromosome or by keywords. The “consensus domain analysis” tool functions to identify conserved protein domains and GO terms among selected TAG genes. In addition, the “oncogenic domain analysis” can analyze oncogenic potential of any user-provided protein based on a weighed term frequency table calculated from the TAG proteins. This study was supported by grant from National research program for genomic medicine (NRPGM) and personnel from Bioinformatics Center of Center for Biotechnology and Biosciences in the National Cheng Kung University, Taiwan.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets.
American Cancer Society - The Official Sponsor of Birthdays
The American Cancer Society is the nationwide, community-based, voluntary health organization dedicated to eliminating cancer as a major health problem by preventing cancer, saving lives, and diminishing suffering from cancer, through research, education, advocacy, and service. Together with our millions of supporters, the American Cancer Society (ACS) saves lives and creates a world with less cancer and more birthdays by helping people stay well, helping people get well, by finding cures, and by fighting back. Headquartered in Atlanta, Georgia, the ACS has 12 chartered Divisions, more than 900 local offices nationwide, and a presence in more than 5,100 communities.
MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition
Multiobjective Analyzer for Genetic Marker Acquisition
Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem.
he Open Protein Structure Annotation Network
TOPSAN - The Open Protein Structure Annotation Network
Collect, share, and distribute information about protein three-dimensional structures. It serves as a portal for the scientific community to learn about protein structures solved by SG centers, and also to contribute their expertise in annotating protein function. The premise of the TOPSAN project is that, no matter how much any individual knows about a particular protein, there are other members of the scientific community who know more about certain aspects of the same protein, and that the collective analyses from experts will be far more informative than any local group, let alone individual, could contribute. They believe that, if the members of the biological community are given the opportunity, authorship incentives, and an easy way to contribute their knowledge to the structure annotation, they would do so. Therefore, borrowing elements from successful, distributed, collaborative projects, such as Wikipedia (the free encyclopedia anyone can edit) and from other open source software development projects, TOPSAN will be a broad, collaborative effort to annotate protein structures, initially, those determined at the JCSG. They believe that the annotation of proteins solved by structural genomics consortia offers a unique opportunity to challenge the extant paradigm of how biological data is collected and distributed, and to connect structural genomics and structural biology to the entire biological research community. TOPSAN is designed to be scalable, modular and extensible. Furthermore, it is intended to be immediately useful in a simplistic way and will accommodate incremental improvements to functionality as usage becomes more sophisticated. Their annotation pages will offer the end user a combination of automatically generated as well as expert-curated annotations of protein structures. They will use available technology to increase the speed and granularity of the exchange of scientific ideas, and use incentive mechanisms that will encourage collaborative participation.
pepr-chip-seq: A ChIP-Seq analyzing program for biological replicates
A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions.
Comparative Anatomy of Marmoset and Mouse Cortex from Genomic Expression
Comparative Anatomy of Marmoset Mouse Cortex from Genomic Expression
Database of gene expression in the marmoset brain.Comparative anatomy of marmoset and mouse cortex from genomic expression. Atlas comparing brain of neonatal marmoset with mouse using in situ hybridization.
ALCHEMY - An automated population genetic model driven SNP genotype calling method
ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.
MutationAssessor - functional impact of mutations
MutationAssessor - functional impact of protein mutations
mutationassessor.org - functional impact of protein mutations
A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The PeptideMapper Web-Service provides alignments of peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence. The PeptideMapper Web-Service can be used interactively or as a web-service using either HTTP or SOAP requests. Results of HTTP requests can be returned in a variety of formats, including XML, JSON, CSV, TSV, or XLS, and in some cases, GFF or BED; results of SOAP requests are returned as SOAP responses. The PeptideMapper Web-Service maps at most 20 peptides with length between 5 and 30 amino-acids in each request. The number of alignments returned, per peptide, gene, and sequence type, is set to 10 by default. The default can be changed on the interactive alignments search form or by using the max web-service parameter.
The Peptide Sequence Database contains putative peptide sequences from human, mouse, rat, and zebrafish. Compressed to eliminate redundancy, these are about 40 fold smaller than a brute force enumeration. Current and old releases are available for download. Each species'' peptide sequence database comprises peptide sequence data from releveant species specific UniGene and IPI clusters, plus all sequences from their consituent EST, mRNA and protein sequence databases, namely RefSeq proteins and mRNAs, UniProt''s SwissProt and TrEMBL, GenBank mRNA, ESTs, and high-throughput cDNAs, HInv-DB, VEGA, EMBL, IPI protein sequences, plus the enumeration of all combinations of UniProt sequence variants, Met loss PTM, and signal peptide cleavages. The README file contains some information about the non amino-acid symbols O (digest site corresponding to a protein N- or C-terminus) and J (no digest sequence join) used in these peptide sequence databases and information about how to configure various search engines to use them. Some search engines handle (very) long sequences badly and in some cases must be patched to use these peptide sequence databases. All search engines supported by the PepArML meta-search engine can (or can be patched to) successfully search these peptide sequence databases.
A portal for hormone-related health information for the public, physicians, allied health professionals and the media. It serves as a resource for the public by promoting the prevention, treatment and cure of hormone-related conditions through outreach and education. It provides free educational materials, public forums, physician referral service, and media education campaigns. It offers a library of educational materials and programs covering a wide range of endocrine topics, including adrenal disorders, breast cancer, diabetes, osteoporosis, stress, thyroid disease and cancer.
To test a sample population of genes for overrepresentation of GO terms, the R/BioC function GOHyperGAll computes for all GO nodes a hypergeometric distribution test and returns the corresponding p-values. A subsequent filter function performs a GO Slim analysis using default or custom GO Slim categories. Basic knowledge about R and BioConductor is required for using this tool. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
GlycoPeptideSearch (GPS) simplifies data interpretation of N-glycopeptide CID MS/MS datasets by searching for glycopeptide results consistent with MS/MS spectra. Results are tabulated in Excel format. Accelerate and simplify interpretation of N-glycopeptide CID MS/MS spectra using GlycoPeptideSearch (GPS). This tool is designed for tandem mass-spectra acquired from proteolytic digests of purified glycoproteins modified with N-glycans and analyzed by LC-MS/MS and CID. The search yields an Excel spreadsheet of N-glycopeptide matches consistent with the spectra. GPS requires two files as input - an mzXML (or other open spectral format) file of glycopeptide CID tandem mass-spectra and a text file (.txt) of peptide sequences containing the N-linked glycosylation motif NXS/T. Spectral datafiles must be converted from raw vendor formats, such as .RAW or .wiff, to an open peak list format (mzXML preferred). In addition to these two input files, the user must specify one or more glycan databases (provided in the software package). The database(s) selected by the user will be used to match glycan structures in the glycopeptide spectra. The output is an Excel spreadsheet with one or more rows for spectra within the dataset that contain evidence of glycoprotein fragmentation, paired with one or more proposed glycopeptide matches for each spectrum. Glycopeptide matches consist of a peptide-glycan pair, with the peptide drawn from the user-supplied peptide file, and the glycan selected from a glycan database(s). The human subset of the GlycomeDB glycan database is provided, and N-linked glycans are automatically selected from it. GPS interprets glycopeptide CID MS/MS spectra by first requiring MS/MS spectra contain evidence of glycopeptide fragmentation - the oxonium ion peaks (m/z 204 - Hex, m/z 366 - HexNAc), and N-glycopeptide core specific peaks (peptide, peptide + HexNAc, peptide + HexNAc-HexNAc, peptide + HexNAc-HexNAc-Hex). For spectra that meet these initial criteria, for a particular peptide, a mass-based search of one or more glycan databases looks for glycans which capture the remaining mass of the spectral precursor. Additional spectral information may be used to narrow the number of matches, and equivalent glycan topologies may be collapsed to a single peptide-glycan pair. GPS also provides N-glycan compositions with the necessary additional mass, even if no glycan with the composition is present in the glycan database(s). GPS can either be run from the command-line or by using its graphical user interface. We recommend the msconvert (or MSConvertGUI) software from the ProteoWizard project to convert spectral datafiles from vendor formats such as .wiff and .RAW into mzXML.
FuncAssociate: The Gene Set Functionator
A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool
American College of Medical Genetics and Genomics
American College of Medical Genetics Genomics
An organization composed of biochemical, clinical, cytogenetic, medical and molecular geneticists, genetic counselors and other health care professionals committed to the practice of medical genetics to Improve Health Through Medical Genetics. The American College of Medical Genetics and Genomics will: * Define and promote excellence in the practice of medical genetics and genomics in the integration of translational research into practice; * Promote and provide medical genetics and genomics education; * Increase access to medical genetics and genomics services and integrate them into patient care; * Advocate for and represent providers of medical genetics and genomics services and their patients; and * Maintain structure and integrity of ACMG and its value to members and the public.
GOdist is a Matlab program that analyzes Affymetrix microarray expression data implementing Kolmogorov-Smirnov (KS) continuous statistics approach. It also implements the discrete approach using Fisher exact test employing a two-tailed hypergeometric distribution. GOdist enables detection of both kinds of changes within specific GO terms represented on the array in relation to different populations: the global array population, the direct parents of the analyzed GO term and the global parent of it (e.g. biological process, molecular function or cellular component). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
UCbase & miRfunc: Ultraconserved Sequences and miRNA Funciton Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. UCbase & miRfunc is a database of (i) human, mouse and rat microRNAs and (ii) Ultraconserved elements providing information about function, expression and correlation between these classes of non-coding RNAs and the disorders related to their aberrant expression. The genomics interface allows the user to explore where whole-genome collections of miRNAs and UCRs are located with respect to annotation sets such as band, disorders and known genes. The Blast interface provides a web tool for matching miRNAs/UCRs elements against any given sequence and providing specific functional information on the results. 481 Ultraconserved sequences (UCRs) longer than 200 bases were discovered in the genomes of human, mouse and rat. These are DNA sequences showing 100 percent identity among the human, mouse and rat genomes. UCRs are frequently located at genomic regions involved in cancer, differentially expressed in human leukemias and carcinomas and in some instances regulated by microRNAs (miRNAs), the most extensively studied category of non-coding RNAs (ncRNAs). Here we present the first database which links UCRs and miRNAs with the related human disorders and genomic properties.
The Burroughs Wellcome Fund is an independent private foundation dedicated to advancing the biomedical sciences by supporting research and other scientific and educational activities. Within this broad mission, BWF has two primary goals: * To help scientists early in their careers develop as independent investigators * To advance fields in the basic biomedical sciences that are undervalued or in need of particular encouragement BWF''s financial support is channeled primarily through competitive peer-reviewed award programs. * BWF''s endowment: $586.8 million at the end of FY 2009 * BWF approved $26.4 million in grants during FY 2009 BWF makes grants primarily to degree-granting institutions on behalf of individual researchers, who must be nominated by their institutions. To complement these competitive award programs, BWF also makes grants to nonprofit organizations conducting activities intended to improve the general environment for science. A Board of Directors comprising distinguished scientists and business leaders governs BWF. BWF was founded in 1955 as the corporate foundation of the pharmaceutical firm Burroughs Wellcome Co. In 1993, a generous gift from the Wellcome Trust in the United Kingdom, enabled BWF to become fully independent from the company, which was acquired by Glaxo in 1995. BWF has no affiliation with any corporation.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 11, 2012. FuncExpression is a web-based resource for functional interpretation of large scale genomics data. FuncExpression can be used for the functional comparison of plant, animal, and fungal gene name lists generated from genomics and proteomics experiments. Multiple gene lists can be classified, compared and visualized. FuncExpression supports two way-integration of plant gene functional information and the gene expression data, which allows for further cross-validation with plant microarray data from related experiments at BarleyBase. Platform: Online tool
FunCluster is a genomic data analysis algorithm which performs functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis aims to detect co-regulated biological processes through a specially designed clustering procedure involving biological annotations and gene expression data. FunCluster' '''s functional analysis relies on Gene Ontology and KEGG annotations and is currently available for three organisms: Homo Sapiens, Mus Musculus and Saccharomyces Cerevisiae. FunCluster is provided as a standalone R package, which can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix). Download it from the FunCluster website, or from the worldwide mirrors of CRAN. FunCluster is provided freely under the GNU General Public License 2.0. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Centre de Recherche des Cordeliers; Paris; France
Organization focusing on the regulation of important functions and the roles of the deregulation of these functions in the genesis and progression of diseases. Nineteen teams are structure in 2 departments, Physiology, Metabolism, Differenciation and Immunology, Cancer, Inflammation. This 2 departments are joined by a Therapeutic Innovations coordinated by a team manager. Through a strong synergism between scientists, clinicians and industry, the CRC has created the means of success of translational research. Several teams are involved in innovation in various fields such as imaging, identifications of genetic, protein or cellular prognostic markers, the production of molecules (monoclonal antibody) or generation of cells (dendritic cells or macrophage) for therapeutic use. The CRC has developed important core facilities including a modern animal facility with a transgenic service, a small animals imaging platform, a core facility for in vivo and ex vivo studies of renal functions, an ex vivo cell imaging facility with a confocal microscopy service, flow cytometry, electron microscopy and laser micro dissection. These facilities under the management of highly competent scientists and engineers work for the transfer of competence toward the students and ensures the continued formation through regular organization of scientific day meetings. The CRC participates in the research and academic training. On the campus is located the faculty of medicine Paris Descartes, the Pierre and Marie Curie Institute of Doctoral training and the school of physiology and pathophysiology. About a hundred PhD students belonging to 8 different Doctoral Schools are hosted in 36 doctoral training teams. Students from technical, bachelor and masters levels are also being trained. In addition, young pupils from secondary and high school participate regularly in the programs for initiation to research conceptions and technology. Seminars as well as meetings at national and European levels and scientific debates on various important contemporary topics, and open-door programs are conducted regularly in the Center.
FIVA - Functional Information Viewer and Analyzer
FIVA - Functional Information Viewer Analyzer
Functional Information Viewer and Analyzer
Functional Information Viewer and Analyzer (FIVA)
Functional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
American Society of Hematology Video Library
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. ASH's video library includes a number of films produced on various topics, including ASH''s history and award winners, Society programs such as the Clinical Research Training Institute, and a trailer and clips from the hematology documentary Blood Detectives, which aired on Discovery Health. These videos were created for educational purposes, and we encourage members of the hematology community to share them with others.
Genomic Analysis and Rapid Biological ANnotation
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 12, 2012. GARBAN is a tool for analysis and rapid functional annotation of data arising from cDNA microarrays and proteomics techniques. GARBAN has been implemented with bioinformatic tools to rapidly compare, classify, and graphically represent multiple sets of data (genes/ESTs, or proteins), with the specific aim of facilitating the identification of molecular markers in pathological and pharmacological studies. GARBAN has links to the major genomic and proteomic databases (Ensembl, GeneBank, UniProt Knowledgebase, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications. Source may be shared: e-mail garban (at) ceit.es. Platform: Online tool
THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible
University of California at Santa Cruz Genome Browser
Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.
OMGN - Oomycete Molecular Genetics Research Collaboration Network
Oomycete Molecular Genetics Research Collaboration Network
The Oomycete Molecular Genetics Research Collaboration Network (OMGN) is a network for research collaboration for investigators interested in oomycete molecular genetics and genomics. The goals of the OMGN is to facilitate the integration of these investigators into the community and to further strengthen the cooperative culture of this community. A particular emphasis is placed on training and integrating junior faculty and faculty from institutions under-represented in the U.S. research infrastructure. Because of their economic impact as plant pathogens, molecular, genetic and genomics studies are well advanced in many oomycete species. These organisms have served as lead species for the entire Stramenopiles lineage, a major radiation of crown eukaryotes, distinct from plants, animals and fungi. The oomycete molecular genetics community has a strong culture of collaboration and communication, and sharing of techniques and resources. With the recent blossoming of genetic and genomic tools for oomycetes, many new investigators, from a variety of backgrounds, have become interested in oomycete molecular genetics and genomics. The proposed network is open to all researchers with an interest in oomycete molecular genetics and genomics, either at an experimental or a computational level. Investigators new to the field are always welcome, especially those interested in saprophytes and animal pathogens. Goals of OMGN # Provide training to o��mycete molecular genetics researchers, especially those from smaller institutions, in the use of bioinformatics and genomics resources. # Promote the entry, participation and training of new investigators into the field of o��mycete genomics, particularly junior faculty and faculty from institutions under-represented in the U.S. research infrastructure. # Promote communication and collaboration, and minimize duplication of effort, within the worldwide o��mycete genomics community. # Support an O��mycete Genomics Resources Center to maintain and distribute training and research materials produced by community genomics projects. The network''s activities have been supported by two grants from the NSF Research Collaboration Networks in Biology program.
Aims to explore heritability for clinically confirmed chronic obstructive lung disease (COPD), estimate the heritability for lung function and investigate interactions between smoking and genes including the genetic effect on smoking habits. Study participants have been recruited from the Swedish Twin Registry. Types of samples * EDTA whole blood * DNA * Plasma * Serum Number of sample donors: 386 (sample collection completed)
biopieces - Biopieces is a bioinformatic framework of tools easily used and easily created
A collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis. The advantage of the Biopieces is that a user can easily solve simple and complex tasks without having any programming experience. Moreover, since the data format used to pass data between Biopieces is text based, different developers can quickly create new Biopieces in their favorite programming language - and all the Biopieces will maintain compatibility. Finally, templates exist for creating new Biopieces in Perl and Ruby. There are currently ~190 Biopieces (March 2014).
The GO Slim Mapper (aka GO Term Mapper) maps the specific, granular GO terms used to annotate a list of budding yeast gene products to corresponding more general parent GO slim terms. Uses the SGD GO Slim sets. Three GO Slim sets are available at SGD: * Macromolecular complex terms: protein complex terms from the Cellular Component ontology * Yeast GO-Slim: GO terms that represent the major Biological Processes, Molecular Functions, and Cellular Components in S. cerevisiae * Generic GO-Slim: broad, high level GO terms from the Biological Process and Cellular Component ontologies selected and maintained by the Gene Ontology Consortium (GOC) Platform: Online tool
GOArray is a Perl program which inputs a lists of genes annotated as of interest (GOI) or not, and determines if any associated GO terms have an overrepresentation of GOI. A permutation test is optionally used to assess confidence in the results. Output includes multiple visualizations and supplementary information and, for future reference, a summary of the statistical methods used. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Developer tools, APIs and resources. Search developers.google.com and code.google.com.
Univeristy of Minnesota Biocatalysis/Biodegradation Database
University of Minnesota Biocatalysis and Biodegradation Database
University of Minnesota Biocatalysis/Biodegradation Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2014. Database containing information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. Its goal is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes. The present database has been successfully used to teach enzymology and use of biochemical Internet information resources to advanced undergraduate and graduate students, and is being expanded primarily with the help of such students. In addition to reactions and pathways, this database also contains Biochemical Periodic Tables and a Pathway Prediction System. * Search the UM-BBD for compound, enzyme, microorganism, pathway, or BT rule name; chemical formula; chemical structure; CAS Registry Number; or EC code. * Go to Pathways and Metapathways in the UM-BBD * Lists of 203 pathways; 1400 reactions; 1296 compounds; 916 enzymes; 510 microorganism entries; 245 biotransformation rules; 50 organic functional groups; 76 reactions of naphthalene 1,2-dioxygenase; 109 reactions of toluene dioxygenase; Graphical UM-BBD Overview; and Other Graphics (Metapathway and Pathway Maps and Reaction Mechanisms).
A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans.
GoSurfer uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics. Platform: Windows compatible
GOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online tool
MAPPFinder is an accessory program for GenMAPP. This program allows users to query any existing GenMAPP Expression Dataset Criterion against GO gene associations and GenMAPP MAPPs (microarray pathway profiles). The resulting analysis provides the user with results that can be viewed directly upon the Gene Ontology hierarchy and within GenMAPP, by selecting terms or MAPPs of interest. Platform: Windows compatible
A tool for assisting the GO annotation of UniProt entries by linking the GO terms present in the uncurated annotations with evidence text automatically extracted from the documents linked to UniProt entries. Platform: Online tool
Icahn School of Medicine at Mount Sinai; New York; USA
Icahn School of Medicine at Mount Sinai, formerly Mount Sinai School of Medicine, is graduate medical school in Manhattan, New York City. Leader in medical and scientific training and education, biomedical research and patient care.
MetaGeneProfiler on the WEB - Web service for significance test of differentially-expressed Meta Genes
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Meta Gene Profiler (MetaGP) is a web application tool for discovering differentially expressed gene sets (meta genes) from the gene set library registered in our database. Once user submits gene expression profiles which are categorized into subtypes of conditioned experiments, or a list of genes with the valid pvalues, MetaGP assigns the integrated p-value to each gene set by combining the statistical evidences of genes that are obtained from gene-level analysis of significance. The current version supports the nine Affymetrix GeneChip arrays for the three organisms (human, mouse and rat). The significances of GO terms are graphically mapped onto the directed acyclic graph (DAG). The navigation systems of GO hierarchy enable us to summarize the significance of interesting sub-graphs on the web browser. Platform: Online tool
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 13, 2012. OntoGate provides access to GenomeMatrix (GM) entries from Ontology terms and external datasets which have been associated with ontology terms, to find genes from different species in the GM, which have been mapped to the ontology terms. OntoGate includes a BLAST search of amino acid sequences corresponding to annotated genes. Platform: Online tool
ProfCom - Profiling of complex functionality
Profiling of Complex Functionality (ProfCom)
Profiling of Complex Functionality (ProfCom) is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of complex function. A complex function is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes. Platform: Online tool
SerbGO is a web-based tool intended to assist researchers determine which microarray tools for gene expression analysis which make use of the GO ontologies are best suited to their projects. SerbGO is a bidirectional application. The user can ask for some features by checking on the Query Form to get the appropriate tools for their interests. The user can also compare tools to check which features are implemented in each one. Platform: Online tool
SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool
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The Ontologizer is a Java webstart application for GO term enrichment analysis that provides browsing and graph visualization capabilities. The Ontologizer allows users to analyze data with the standard Fisher exact test and also the parent-child method and topology methods. The tool can be started directly from the web using Java webstart. For graph visualizations, users need to install the GraphViz library. The tool is freely available to all, and source code is available at SourceForge. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
THEA - Tools for High-throughput Experiments Analysis
Tools for High-throughput Experiments Analysis
THIS RESOURCE IS NO LONGER IN SERVICE, on documented July 16, 2012. An integrated information processing system dedicated to the analysis of post-genomic data. It allows automatic annotation of data issued from classification systems with selected biological information (including the Gene Ontology). Users can either manually search and browse through these annotations, or automatically generate meaningful generalizations according to statistical criteria (data mining). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Universal PBM Resource for Oligonucleotide Binding Evaluation
Universal Protein Binding Microarray Resource for Oligonucleotide Binding Evaluation
Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences.
CureHunter - Real-Time Evidence Based Medicine
CureHunter is the only fully integrated scientific search, data retrieval and analysis engine on the web that can read the entire US National Library of Medicine Medline Archive and automatically extract and quantify the evidence for successful clinical outcomes of all known drugs for all known human diseases. * For patients we provide low-cost Summary PDF Reports with all drug evidence for all known cures or symptom improvement * For medical professionals CureHunter on-line access delivers decision support in 10-20 seconds of real clinical time to make an evidence check as SOP as a BP or Temp * For pharma research scientists we offer powerful data export functions that deliver over 1.5 million specific clinical outcome data points to new drug discovery software Use the CureHunter Research Interface: * Discover new potential off-label applications * Export data and apply custom analytics * 1-click drug performance meta-analyses * Keep up-to-date on the latest developments in your field * Optimize formularies with total evidence-based objectivity * RSS Feeds for Tracking Pharma Products
A database of human molecular interaction networks that integrates human protein-protein and transcriptional regulatory interactions from 15 distinct resources and aims to give direct and easy access to the integrated data set and to enable users to perform network-based investigations. The database includes tools (i) to search for molecular interaction partners of query genes or proteins in the integrated dataset, (ii) to inspect the origin, evidence and functional annotation of retrieved proteins and interactions, (iii) to visualize and adjust the resulting interaction network, (iv) to filter interactions based on method of derivation, evidence and type of experiment as well as based on gene expression data or gene lists and (v) to analyze the functional composition of interaction networks.
The Generic GO Term Mapper finds the GO terms shared among a list of genes from your organism of choice within a slim ontology, allowing them to be binned into broader categories. The user may optionally provide a custom gene association file or slim ontology, or a custom list of slim terms. The implementation of this Generic GO Term Mapper uses map2slim.pl script written by Chris Mungall at Berkeley Drosophila Genome Project, and some of the modules included in the GO-TermFinder distribution written by Gavin Sherlock and Shuai Weng at Stanford University, made publicly available through the GMOD project. GO Term Mapper serves a different function than the GO Term Finder. GO Term Mapper simply bins the submitted gene list to a static set of ancestor GO terms. In contrast, GO Term Finder finds the GO terms significantly enriched in a submitted list of genes. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
GREAT: Genomic Regions Enrichment of Annotations Tool
Genomic Regions Enrichment of Annotations Tool
Genomic Regions Enrichment of Annotations Tool (GREAT)
Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool
GoBean - a Java application for Gene Ontology enrichment analysis
GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible
BiGG - a Biochemical Genetic and Genomic knowledgebase
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.
BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2). These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database. The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API.
A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper.
TXTGate is a literature index database and is part of an experimental platform to evaluate (combinations of) information extraction and indexing from a variety of biological annotation databases. It is designed towards the summarization and analysis of groups of genes based on text. By means of tailored vocabularies, selected textual fields and MedLine abstracts of LocusLink and SGD are indexed. Subclustering and links to external resources allow for an in-depth analysis of the resulting term profiles. You need to be registered in order to use the TXTGate application. Platform: Online tool
Hierarchical optimization of enriched GO terms
GO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online tool
IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures
Integrated Tool for IC-based GO Semantic Similarity Measures
Integrated Tool for IC-based GO Semantic Similarity Measures (IT-GOM)
The Integrated Tool for IC-based GO Semantic Similarity Measures (IT-GOM) integrates the currently known GO semantic similarity measures into a single tool. It provides the information content (IC) of GO terms, semantic similarity between GO terms and GO-based protein functional similarity scores. The specificity of GO terms and the similarity of biological content between GO terms or proteins are transformed into numeric values for protein analyses at the functional level. The integration of the different measures enables users to choose the measure best suited to their application and to compare results between different semantic similarity measures. Platform: Online tool
G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools
Gene Semantic Similarity Analysis and Measurement Tools
Gene Semantic Similarity Analysis Measurement Tools
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2,2025. G-SESAME contains a set of tools. They include: tools for measuring the semantic similarity of GO terms; tools for measuring the functional similarity of genes; and tools for clustering genes based on their GO term annotation information. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. The database contains 17,705 diseases, consolidated from 28 sources.
Database that contains publicly available protein sequences with stable and unique identifiers (UPI) which are never removed, changed or reassigned. UniParc tracks sequence changes in the source databases and archives the history of all changes. Information other than protein sequence must be retrieved from the UniParc source databases using the database cross-references.
FSST - Functional Similarity Search Tool
Functional Similarity Search Tool (FSST)
The Functional Similarity Search Tool (FSST) has been implemented for comparing user defined sets of annotated entities. FSST supports the computation of functional similarity scores based on an individual ontology and of combined scores. Its multi-threaded Java implementation takes advantage of symmetric multi-processing computers, decreasing runtime considerably. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis
A Galaxy framework-based online pipeline for reliable analysis of data generated by three types of CLIP-seq protocols: HITS-CLIP, PAR-CLIP and iCLIP. It provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.
GOChase: correcting errors from gene ontology-based annotations for gene products
GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations. # GOChase-History resolves the whole modification history of GO IDs. # GOChase-Correct highlights merged GO IDs and redirects to the correct primary term into which the secondary ID was merged. For obsolete GO terms, the nearest non-discarded parent term is recommended by GOChase. This function may be used by GO browsers such as AmiGO and QuickGO to fix broken hyperlinks. # A whole database (such as LocusLink) as a flat file can be loaded into GOChase, reporting the annotation errors and GOChase corrections. # When one inputs a GO ID, GOChase will resolve all gene products annotated with the GO ID across all the major databases. Platform: Online tool
A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user' '''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool
A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text.
REViGO - Reduce & Visualize Gene Ontology
REViGO - Reduce + Visualize Gene Ontology
REViGO - Reduce and Visualize Gene Ontology
Web server that summarizes lists of Gene Ontology terms by removing redundant terms and visualizing the remaining ones in scatterplots, interactive graphs, treemaps, or tag clouds. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Short IN/DEL Prediction by Large deviation Inference and Non-linear True frequency Estimation by Recursion
Software that detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples.
WEGO - Web Gene Ontology Annotation Plot
BGI WEGO - Web Gene Ontology Annotation Plotting
Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool
An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher' '''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. PubSearch is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. PubSearch can be downloaded from GMOD. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Tool for helping people identify and locate online repositories of research data. Users and bibliographers create and curate records that describe data repositories that users can search. * What repositories are appropriate for a researcher to submit his or her data to? * How do users find appropriate data repositories and discover datasets that meet their needs? * How can librarians help patrons locate and integrate data into their research or learning? Databib attempts to address these needs for the research community, including: * data users * data producers * publishers and professional societies * librarians * research funding agencies Are you familiar with a data repository that isn''t included in Databib? Please consider submitting a new record. You can suggest a repository for us to catalog by simply entering its title, URL, authority, and a subject for it... and we''ll do the rest!
Public data warehouse for searching cell line data extracted from both ATCC and HyperCLDB. The knowledge base uses the Cell Line Ontology, created with the Protege ontology editing tool from the National Center for Biomedical Ontologies (NCBO) and merges concepts from other ontologies, including the Cell Type Ontology. The Cell Line Knowledge Base uses our Cell Line Ontology as the underlying data model. The ontology defines the following cell line attributes: Cell Line ID, Organism, Tissue, Pathology, Growth Mode, MeSH ID. To report errors in the data or to add cell line data to the knowledge base, please email: clbk-data (at) umich.edu
PIDFinder is a tool for the exploration of the Primary Immunodeficiency Disease Ontology. Apart from browsing the knowledge contained in the ontology, it can also be used for the identification of PIDs based on a set of observed Phenotypes. The PidFinder web application is a developing prototype application that allows non-bioinformaticians to quickly view and use the knowledge contained in the Primary Immunodeficiency Disease Ontology. The application consists of a number of components: * The PIDFinder: allows the selection of a set of phenotypes and subsequently compares the set with the canonical set of phenotypes defined in the PID Ontology. The phenotypes, that can be selected are grouped by biomarker and are thus available in a number of different facets. Once phenotypes have been selected, the application compares them to canonical phenotypes associated with PIDs in the PID Ontology, by computing a semantic similarity measure. The similarity is determined using a Tanimoto Distance - the more closely related an observed phenotype is to a canonical ontology phenotype, the closer the calculated Tanimoto Distance is to 1 - with increasing dissimilarity, the Tanimoto Coefficient tends towards 0. * The Phenotype Explorer: a rudimentary browser for phenotypes currently contained in the PID Ontology. The browser allows the user to find phenotypes based on biomarker categories and provides some basic definitions (not all definitions are available at this stage) and disease association information. * A Heatmap comparing the phenotypic overlap of PIDs: In essence, the heatmap is a many-to-many comparison of the phenotypic overlap between all Primary Immunodeficiency Diseases contained in the PID Ontology. Again, overlap is calculated using a Tanimoto Distance. The heatmap is a matrix, plotting the Tanimoto coefficients for every PID/PID pair. Increased off-diagonal overlap between PIDs most likely indicates genes in the same pathway. * A Phenotype Frequency Visualization: The phenotype frequency visualization is a simple bar chart indicating how often a particular phenotype is associated with a Primary Immunodeficiency Disease in the Ontology. * A PID Expert map: All of the phenotypes and knowledge contained in the Primary Immunodeficiency Disease Ontology has been extracted from primary clinical or research literature. To construct the map, we have extracted the affiliations and locations of the authors of the literature sources and overlayed them on a map. The hope is that this will facilitate the identification of (local) experts on primary immunodeficiency diseases.
PIDO - Primary Immunodeficiency Disease Ontology
pido - The Primary Immunodeficiency Disease Ontology
Primary Immunodeficiency Disease Ontology
The Primary Immunodeficiency Disease Ontology Project is developing an ontology for the phenotypic description of Primary Immunodeficiency Diseases. The ontology can be used for integrative research in both biomedical and clinical research. Primary Immunodeficiency Diseases (PIDs) are Mendelian diseases, caused by defects or deletions of genes involved in the development, regulation and maintenance of the immune system. They usually affect newborns and toddlers, but can also manifest much later in life. Information about PIDs is often widely scattered across the research literature and a number of databases. PIDO is an attempt to develop both a machine- as well as a human-comprehensible representation of these diseases, starting with a phenotypic descriptions of disease.
Major depressive disorder neuroimaging database
Major Depressive Disorder Neuroimaging Database (MaND)
The Major Depressive Disorder Neuroimaging Database (MaND) contains information of 225 studies which have investigated brain structure (using MRI and CT scans) in patients with major depressive disorder compared to a control group. 143 studies and 63 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website.
AMAT is a Matlab-based, open source interface for searching fMRI coordinates together with a simple database of coordinates. The AMAT database is deliberately designed to be minimal. Effectively, the database reproduces the tables of XYZ coordinates which are common in fMRI papers. Each coordinate is associated with the anatomical label given by the authors of the original paper, a ag for Talaraich or MNI coordinates, a very brief description of the description of the functional task or contrast which activated this coordinate, and the PubMed ID of the published paper. The latter links directly to the abstract in PubMed and allows the user to retrieve the original publication. Anatomical information labeling a coordinate as a particular Brodmann area or functional region is optional, and is normally only included if the authors of the original paper included these labels. No other information is stored.
University of Maryland School of Medicine; Maryland; USA
University of Maryland School of Medicine
Medical school of the University of Maryland, Baltimore and is affiliated with the University of Maryland Medical Center and Medical System. Located in Baltimore City, Maryland, U.S.
brain-development.org at imperial college
brain-development.org hosts data and resources used in computational analysis of brain development, including MRI data sets of developing human, software tools, atlases, protocols and software. Several different atlas datasets are available including: * Adult * Pediatric * Neonatal (T2 Templates, Probability Maps) * Neonatal (High-definition, T1 and T2 Templates, Probability Maps) * Fetal (High-definition, T2 Templates, Probability Maps) * Atlas software Anatomical segmentation protocols are available, as well as an Image Registration Toolkit.
Information eXtraction from Images dataset
Data set of nearly 600 MR images from normal, healthy subjects, along with demographic characteristics, collected as part of the Information eXtraction from Images (IXI) project available for download. Tar files containing T1, T2, PD, MRA and DTI (15 directions) scans from these subjects are available. The data has been collected at three different hospitals in London: * Hammersmith Hospital using a Philips 3T system * Guy''s Hospital using a Philips 1.5T system * Institute of Psychiatry using a GE 1.5T system
A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Its focus is on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. The CLO development has become a community effort with international collaborations. The development consortium includes experts from all over the world: the USA, Europe, and Japan.
Brain Networks: Code to perform network analysis on brain imaging data.
Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.
Neurofitter is software for parameter tuning of electrophysiological neuron models. It automatically searches for sets of parameters of neuron models that best fit available experimental data, and therefore acts as an interface between neuron simulators, like Neuron or Genesis, and optimization algorithms, like Particle Swarm Optimization, Evolutionary Strategies, etc.
Software package for haplotype block identification, visualization and htSNP selection. It can also compare the haplotype block structure with local LD pattern. The program can be either run as a web service, or standalone executables on local machine. (entry from Genetic Analysis Software)
University of Pittsburgh Bioinformatics Resources Collection
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System at the University of Pittsburgh. The OBRC containing 1542 major online bioinformatics databases and software tools was constructed using the HSLS content management system built on the Zope? Web application server. To enhance the output of search results we further implemented the Vivsimo Clustering Engine? which automatically organizes the search results into categories created dynamically based on the textual information of the retrieved records. As the largest online collection of its kind and the only one with advanced search results clustering OBRC is aimed at becoming a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. OBRC is available at the University of Pittsburgh's Health Sciences Library System.
Cell Press publishes monthly podcasts featuring interviews with leading scientists from around the world. You can subscribe to the Cell podcast via iTunes, listen directly by using the audio player, or download the individual podcast.
Brains Matter - The Podcast on Science Curiosities and General Knowledge. Brains Really Do Matter!
Welcome to the Brains Matter podcast where brains really do matter. A discussion of science, trivia, history, and general knowledge. The show started in September 2006, and includes discussion on various topics, as well as interviews with experts in their field. You can subscribe to the show via iTunes, a standard RSS reader, or listen to the individual MP3 shows from the ''flash player'' on the website, or direct download.
iBioSeminars - Bringing the World''s Best Biology to You
iBioSeminars - Bringing the Worlds Best Biology to You
iBioSeminars offers: * Free, on-demand lectures: Many universities/colleges have limited access to high profile leaders in biological research. Our goal is to add 15-20 seminars per year, of similar quality to outstanding lectures that are currently in this library. Access, through web streaming or download, is completely free-of-charge. * Targeting a broad audience: iBioSeminars start with an extended introduction, making them accessible to non-specialists and students, and then progress to cover current research. Senior scientists and students can view and enjoy these lectures. * Education: iBioSeminars are being used by undergraduate and graduate teachers to augment their classroom material. We have now added an education component to this web site (including lecture notes, questions/answers and short video clips for teaching). * International communication: iBioSeminars have viewers in 115 countries and they are being internally promoted in several countries as an educational tool and scientific resource. * Goodwill: Lecturers generously donate their time to prepare these lectures. The project, largely funded by HHMI, is a grass roots efforts with time invested by several individuals at UCSF, HHMI and ASCB.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. So far there is only limited knowledge about possible genetic influences in acute spinal cord injuries (SCI). In this project DNA is collected prospectively from persons with SCI admitted to the acute SCI rehabilitation unit of the Karolinska University Hospital. Trauma is the cause of injury in a majority of the patients. Other causes of injury are spinal abscesses, tumors or spinal infarctions. The aim of the project is to create a sufficiently large DNA biobank with samples from 200-400 individuals from clinically well characterized patients to allow for studies of association between candidate genes and clinical outcome parameters.
An NIGMS magazine that showcases the exciting ways that scientists are using the power of computers to expand our knowledge of biology and medicine. From text messaging friends to navigating city streets with GPS technology, we''re all living the computing life. But as we''ve upgraded from snail mail and compasses, so too have scientists. Computer advances now let researchers quickly search through DNA sequences to find gene variations that could lead to disease, simulate how flu might spread through your school and design three-dimensional animations of molecules that rival any video game. By teaming computers and biology, scientists can answer new and old questions that could offer insights into the fundamental processes that keep us alive and make us sick. This booklet introduces you to just some of the ways that physicists, biologists and even artists are computing life. Each section focuses on a different research problem, offers examples of current scientific projects and acquaints you with the people conducting the work. You can follow the links for online extras and other opportunities to learn aboutand get involved inthis exciting new interdisciplinary field.
Visit ChemHealthWeb for research highlights, chemist profiles, games and videos and other Web extras. The NIGMS Chemistry of Health booklet describes basic chemistry and biochemistry research that spurs a better understanding of human health.
The NIGMS Inside Life Science series brings you inside the science of health. Each story shows how basic biomedical researchfrom the history of a field to the people doing cutting-edge work todaylays the foundation for advances in disease diagnosis, treatment and prevention. Through explorations of how the body works and highlights from recent studies, you''ll discover even more on what scientists have found and are finding about fundamental life processes. NIGMS supported all of the featured research.
TogoTV - distributing tutorial videos of bioinformatcs resources
TogoTV - distributing tutorial videos of bioinformatcs resources. Categories include: Catalog, DBCLS, Gene expression, Genome analysis, Lecture, Natural Language Processing, Sequence analysis , Visualization, Workflow, YouTube
Ontology for the description of student health records. Student health records are created for entering college students in order to provide better health services will be formed. This file contains various sections such as history of disease, family history of disease, public examinations and ... .
The mission of the American Liver Foundation (ALF) is to facilitate, advocate and promote education, support and research for the prevention, treatment and cure of liver disease. These values guide our work as volunteers and staff of the American Liver Foundation as we move toward our ultimate goal of a world without liver disease. By living these values every day, we offer hope to all those affected by liver disease. * Research: Research is integral to the work of American Liver Foundation and is essential to improving treatment and finding cures. * Education: Many forms of liver disease are preventable, and many more can be cured if detected early. Yet tens of thousands of people in the U.S. are living with liver disease and don''t even know it. * Advocacy: American Liver Foundation takes a leadership role in advocating on behalf of the millions of Americans living with liver disease and their families.
SBUR - Society for Basic Urologic Research
Society for Basic Urologic Research (SBUR)
The Society for Basic Urologic Research (SBUR) is a society of scientists whose expertise includes the study of urologic cancers (prostate, bladder, kidney, testis, penis), the biology of prostate growth, kidney and bladder function, autoimmune urologic diseases, infectious diseases, neuro-urologic diseases, male reproductive biology, infertility and erectile dysfunction. Members include molecular biologists, immunologists, epidemiologists, oncologists, biochemists and clinical urologic scientists. SBUR members serve on a wide variety of advisory panels, study sections, editorial boards and in the pharmaceutical industry. The SBUR organizes two annual meetings to share new findings at a multidisciplinary level, to promote interaction among members and other interested scientists and to highlight new areas of research and funding opportunities. The Society was organized to address the following: * To provide a forum for the presentation and discussion of basic scientific topics related to urology * To develop educational forums concerning scientific advancements related to the field of urology * To promote collaborative investigations among member scientists with an emphasis on the interchange of expertise among clinical and basic scientists * To promote the communication and interests of urologic disease investigators with national funding agencies, industry representatives and academic institutions with regards to urology related research * To serve as a resource for research information and expertise to clinical urologists through the American Urological Association
A website containing the complete sequenced genome of the medaka fish. It presents a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination4, 5, 6 and developmental genetics7. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approx2,900 new genes, using 5&rsquo;-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approx 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.
Digestive Disease Week (DDW) is the world''s largest gathering of physicians and researchers in the fields of gastroenterology, hepatology, endoscopy and gastrointestinal surgery. Claim CME for DDW - Certificate of Attendance
The American Urological Association (AUA), founded in 1902, is the premier professional association for the advancement of urologic patient care, and works to ensure that its more than 18,000 members are current on the latest research and practices in urology. The AUA also pursues its mission of fostering the highest standards of urologic care by providing a wide range of servicesincluding publications, research, the Annual Meeting, continuing medical education (CME) and the formulation of health policy.
American Urological Association - YouTube channel
AmerUrological's channel - YouTube are videos put out by the American Urological Association.
R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Semantic Interoperability of Metadata and Information in unLike Environments
SIMILE, a joint project conducted by the MIT Libraries and MIT CSAIL, was focused on developing robust, open source tools that empower users to access, manage, visualize and reuse digital assets. SIMILE seeks to enhance interoperability among digital assets, schemata/vocabularies/ontologies, metadata, and services. A key challenge is that the collections which must inter-operate are often distributed across individual, community, and institutional stores. We seek to be able to provide end-user services by drawing upon the assets, schemata/vocabularies/ontologies, and metadata held in such stores. SIMILE will leverage and extend DSpace, enhancing its support for arbitrary schemata and metadata, primarily though the application of RDF and semantic web techniques. The project also aims to implement a digital asset dissemination architecture based upon web standards. The dissemination architecture will provide a mechanism to add useful views to a particular digital artifact (i.e. asset, schema, or metadata instance), and bind those views to consuming services. To guide the SIMILE effort we will focus on well-defined, real-world use cases in the libraries domain. Since parallel work is underway to deploy DSpace at a number of leading research libraries, we hope that such an approach will lead to a powerful deployment channel through which the utility and readiness of semantic web tools and techniques can be compellingly demonstrated in a visible and global community. The SIMILE Project and its members are fully committed to the open source principles of software distribution and open development and for this reason, it releases the created intellectual property (both software and reports) under a BSD-style license. The SIMILE Project Team Members gladly welcome community efforts.
A database of Alzheimer's disease and dementia clinical trials currently in progress at centers throughout the U.S.
The Andrew W. Mellon Foundation currently makes grants in five core program areas: * Higher Education and Scholarship * Scholarly Communications and Information Technology * Art History, Conservation, and Museums * Performing Arts * Conservation and the Environment Within each of its core programs, the Foundation concentrates most of its grantmaking in a few areas. Institutions and programs receiving support are often leaders in fields of Foundation activity, but they may also be promising newcomers, or in a position to demonstrate new ways of overcoming obstacles to achieve program goals. Our grantmaking philosophy is to build, strengthen and sustain institutions and their core capacities, rather than be a source for narrowly defined projects. As such, we develop thoughtful, long-term collaborations with grant recipients and invest sufficient funds for an extended period to accomplish the purpose at hand and achieve meaningful results.
DSpace open source software is a turnkey institutional repository application. DSpace is the software of choice for academic, non-profit, and commercial organizations building open digital repositories. It is free and easy to install out of the box and completely customizable to fit the needs of any organization. DSpace preserves and enables easy and open access to all types of digital content including text, images, moving images, mpegs and data sets. And with an ever-growing community of developers, committed to continuously expanding and improving the software, each DSpace installation benefits from the next. Top Reasons to Use DSpace * Largest community of users and developers worldwide * Free open source software * Completely customizable to fit your needs * Used by educational, government, private and commercial institutions * Can be installed out of the box * Can manage and preserve all types of digital content
DuraSpace sustains and grows its flagship repository platforms--Fedora and DSpace--while expanding into new technologies. DuraSpace is the independent 501(c)(3) not-for-profit born from a vision to help save our shared scholarly, scientific and cultural record. We are dedicated to sustaining and improving Fedora and DSpace, two of the most dominant open source repository solutions. We continue to lead the development and improvement of open technologies that provide long-term, durable access to your digital assets. Our new technology, DuraCloud, will exploit digital preservation support services in the cloud. We are also expanding into new areas that include exploring strategies on how to manage the ''data deluge'' and addressing the challenge of converting the overwhelming amount of data produced by scholars and scientists into useful information. DuraSpace is committed to providing leadership and innovation in the development and deployment of open technologies that promote durable, persistent access to digital data. We collaborate with academic, scientific, cultural, and technology communities in creating practical solutions to help ensure that current and future generations have access to our collective digital heritage. Our values are expressed in our organizational byline, open technologies for durable digital content.
A pattern growth algorithm based pileline for splice site detection in paired-end RNA-Seq data.
UTRdb/UTRsite is a portal to other databases, including Nucleotide Sequence Databases, Protein Sequence Databases, other Sequence databanks, Untranslated Nucleotide Sequence Databases, Mitochondrial Databases, Mutation Databases, and others. The site also allows users to start long-term permanent projects or just to do quick searches, depending on the user''s needs.
Trichophyton rubrum Expression Database (TrED)
TrED is a database of Trichophyton rubrum, a fungus. The database contains strains, cDNA libraries, pathways, and microarray data as well as a directed set of literature. Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It' '''s a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs) and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies. All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST. TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes.
ccPDB - Compilation and Creation of datasets from PDB
ccPDB - Compilation Creation of datasets from PDB
Compilation and Creation of datasets from PDB
ccPDB (Compilation and Creation of datasets from PDB) is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links. * Compilation of Datasets: Datasets at ccPDB can be classified in two categories, i) datasets collected from literature and ii) datasets compiled from PDB. We are in process of collecting PDB datasetsfrom literature and maintaining at ccPDB. We are also requesting community to suggest datasets. In addition, we generate datasets from PDB, these datasets were generated using commonly used standard protocols like non-redundant chains, structures solved at high resolution. * Creation of datasets: This module developed for creating customized datasets where user can create a dataset using his/her conditions from PDB. This module will be useful for those users who wish to create a new dataset as per ones requirement. This module have six steps, which are described in help page. * Web Services: We integrated following web services in ccPDB; i) Analyze of PDB ID service allows user to submit their PDB on around 40 servers from single point, ii) BLAST search allows user to perform BLAST search of their protein against PDB, iii) Structural information service is designed for annotating a protein structure from PDB ID, iv) Search in PDB facilitate user in searching structures in PDB, v)Generate patterns service facility to generate different types of patterns required for machine learning techniques and vi) Download useful information allows user to download various types of information for a given set of proteins (PDB IDs). * Important Links: One of major objectives of this web site is to provide links to web servers related to functional annotation of proteins. In first phase we have collected and compiled these links in different categories. In future attempt will be made to collect as many links as possible.
CharProtDB: Characterized Protein Database
The Characterized Protein Database, CharProtDB, is designed and being developed as a resource of expertly curated, experimentally characterized proteins described in published literature. For each protein record in CharProtDB, storage of several data types is supported. It includes functional annotation (several instances of protein names and gene symbols) taxonomic classification, literature links, specific Gene Ontology (GO) terms and GO evidence codes, EC (Enzyme Commisssion) and TC (Transport Classification) numbers and protein sequence. Additionally, each protein record is associated with cross links to all public accessions in major protein databases as ��synonymous accessions��. Each of the above data types can be linked to as many literature references as possible. Every CharProtDB entry requires minimum data types to be furnished. They are protein name, GO terms and supporting reference(s) associated to GO evidence codes. Annotating using the GO system is of importance for several reasons; the GO system captures defined concepts (the GO terms) with unique ids, which can be attached to specific genes and the three controlled vocabularies of the GO allow for the capture of much more annotation information than is traditionally captured in protein common names, including, for example, not just the function of the protein, but its location as well. GO evidence codes implemented in CharProtDB directly correlate with the GO consortium definitions of experimental codes. CharProtDB tools link characterization data from multiple input streams through synonymous accessions or direct sequence identity. CharProtDB can represent multiple characterizations of the same protein, with proper attribution and links to database sources. Users can use a variety of search terms including protein name, gene symbol, EC number, organism name, accessions or any text to search the database. Following the search, a display page lists all the proteins that match the search term. Click on the protein name to view more detailed annotated information for each protein. Additionally, each protein record can be annotated.
The Terry Fox Foundation is responsible for supporting close to $20 million in discovery based research each year in Canada - all monies raised outside Canada must be distributed to (a) an institute approved by the Foundation and its advisors or (b) remitted to Canada. The Terry Fox Research Institute (TFRI) is a recipient of TFF funding for translational research. TFRI is an exciting new initiative whose goal is to translate rapidly today''s best science into better cancer treatment and diagnosis for all Canadians. The Institute will bring scientists and clinicians together across the country into a functionally integrated, geographically dispersed Institute with nodes in several provinces. Terry Fox was diagnosed with osteogenic sarcoma (bone cancer) in his right leg in 1977 and had his leg amputated 15 cm (six inches) above the knee. While in hospital, Terry was so overcome by the suffering of other cancer patients that he decided to run across Canada to raise money for cancer research. He called his journey the Marathon of Hope. Terry''s Marathon of Hope took place in 1980 with the simple objective of informing Canadians of the importance of finding a cure for cancer. With fierce determination, he ran an average of 42 kilometres (26 miles) every day for 143 days. Terry was forced to end his run on September 1, 1980 when the cancer spread to his lungs. By February 1, 1981, Terry''s dream of raising $1 for every Canadian was realized - the Terry Fox Marathon of Hope fund totaled $24.17 million. Terry died in June 1981. On May 26, 1988, The Terry Fox Run became a Trust, independent from the Canadian Cancer Society, and received tax-exempt charitable registration as a public foundation. In addition to our signature and long-standing National Terry Fox Run Day in September of each year, The Terry Fox Foundation is proud to include in its events portfolio The National School Run Day. The Foundation recognizes the duality of its mandate. Not only does it raise money for research, but it also continues to share the story of Terry Fox. The Terry Fox Foundation strives to maintain the heroic effort and integrity that Terry embodied. It is a grassroots organization that does not allow the Terry Fox name or likeness to be commercialized or conjoined with other worthy causes. To date, over $600 million has been raised worldwide for cancer research in Terry''s name.
Database of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers. It currently contains ~291204 entries (July 2014) in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality. Deposit your data: An interface allows you to upload, validate and edit CIF files before submitting them for deposition.
University of Neuchatel; Neuchatel; Switzerland
French-speaking university based in Neuchâtel, Switzerland. The university has four faculties and more than a dozen institutes, including arts and human sciences, natural sciences, law and economics.
National Archive of Computerized Data on Aging (NACDA)
National Archive of Computerized Data on Aging
Archive of data relevant to gerontological and aging research. Used to advance research on aging. Subjects include demographic, social, economic, and psychological characteristics of older adults, physical health and functioning of older adults, and health care needs of older adults. NACDA staff represents team of professional researchers, archivists and technicians who work together to obtain, process, distribute, and promote data relevant to aging research.
This database is intended as a comprehensive resource for UTR (Untranslated Region) biology in C. elegans. The database provides detailed information on UTR structures for all protein-coding mRNAs, and includes annotations extracted from other databases (such as WormBase and PicTar) as well as new annotations generated as part of the NYU UTRome project (including preliminary characterization of UTR clones, USTs (UTR sequence tags), curated sequences, and computational and experimental analysis of functional elements). Examples of functional elements within UTRs include predicted and validated microRNA (miRNA) binding sites (responsible for post-transcriptional gene regulation), putative consensus signals for polyA addition, and predicted secondary structures (which may influence the biological activity of UTRs). The UTRome project is part of the ModEncode Consortium, an NIH initiative to characterize at a genomic scale functional sequence elements encoded in the worm (C. elegans) and fly (D. melanogaster) genomes. UTRs are important portions of mRNAs required for post-transcriptional regulation by interacting with proteins or non-coding RNAs (e.g. microRNAs). To study the role of UTRs we are building a UTR database for C. elegans.
North Texas Traumatic Brain Injury Model System
North Texas Traumatic Brain Injury Model System (NT-TBIMS)
The 16 affiliated Model System centers throughout the United States are responsible for gathering and submitting the core data set to the national database as well as conducting research studies on traumatic brain injury (TBI) both in collaboration with the other centers and within our own site. Through our research we hope to learn more about TBI and about the issues and concerns of people with TBI. Our goals are to improve the outcome and quality of life for people who have had brain injuries and for those who are caring for the person with a TBI. The North Texas Traumatic Brain Injury Model System (NT-TBIMS) pools the efforts and talents of individuals from the Departments of Neurosurgery, Neurology, Physical Medicine and Rehabilitation, Psychiatry (Neuropsychiatry), and Neuroradiology of the two leading medical institutions in the North Texas region. To be a patient involved in the research being conducted by the North Texas Traumatic Brain Injury Model System you must have suffered a TBI, be at least 16 years of age, have received initial treatment for the TBI at either Parkland Health and Hospital System or Baylor University Medical Center and then have received rehabilitative care at either Parkland, University Hospital Zale-Lipshy, or Baylor Institute for Rehabilitation. The patient must also be able to understand and sign an informed consent to participate or, if unable, have a family member or a legal guardian who understands the form sign the informed consent for the patient.
It consists of a Genome Browser, an LD Search System, and the VaryGene 2 system. The Generic Genome Browser is a combination of database and interactive Web page for manipulating and displaying annotations on genomes, while LDSearchSystem is a search system for linkage disequilibrium (LD) bins. VaryGene 2 is a system to search, display, and download our research results on human polymorphism based on publicly available data and annotations of transcripts presented by H-InvDB. VaryGene 2 provides information about single nucleotide polymorphisms (SNPs), deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), and their relations to the genome, transcripts, and functional domains. Users can search by polymorphisms, transcripts, STRs/SARs, and CNVs.
The Finnish Cancer Registry maintains a nation-wide database on all cancer cases in Finland going back to 1953. It is also an internationally active institute for statistical and epidemiological cancer research. The Mass Screening Registry is a department of the Finnish Cancer Registry, and is responsible of planning and evaluating national cancer screening programs in Finland. The site contains information on cancer research and up to date statistics on the prevalence of different types of cancer in Finland, the Nordic countries and on a global level. The web pages include information for participants in cancer screening and for professionals involved in organizing such screening.
University of Nevada at Reno; Nevada; USA
Public land-grant research university in Reno, Nevada.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. An integrated resource hosting combined EST data from Oomycetes. It also separates Soybean ESTs from compatible P.sojae infection libraries. Public soybean unigenes and publicly available soybean infection libraries are also part of this database. Currently in this database we have placed 10 libraries from P.sojae(sHA,sHB,sMA,sML,sMY,sMC,sZG,sZO,sZS,iMY) having 33350 raw sequences. Additionally, there are 99,320 EST sequences from P.infestans from NCBI. For P.infestans sequences cleaning information is not available. These sequences are clustered and assembled and data analysis was performed by us. We have separated Soybean ESTs from P.sojae libraries using insillico methods. The soybean libraries are named as gHA and gHB based on their origin from sHA or sHB. All publicly available soybean unigenes(37,465) are added to this database. For public soybean sequences we did not perform any cleaning or assembly. The unigenes were annotated prior to storing. Recently, we added 37492 ESTs from Hyaloperonospora parasitica. All the ESTs are clustered into unigenes and annotated using blastx to nr database, interproscan, TMHMM and SignalP. Annotations are updated every 3 months.
This file describes a selection of the behavioral paradigms that have been useful in behaviorally phenotyping mouse mutants.
The Janus Serum Bank has blood samles from 317 000 Norwegians. The biobank is reserved for cancer research, and is internationally unique regarding size and number of cancer cases. The Janus Serum Bank is a population based biobank reserved for cancer research. The specimens are collected during the period from 1972-2004 and are stored at 25 degrees Celsius. The samples originate from 317 000 persons in Norway who have participated in health studies and also from blood donors in and around Oslo. Today, samples are only collected from earlier donors in the Janus Serum Bank who have developed cancer. The Bank is internationally unique regarding size and number of cancer cases. Annual linkage to the Cancer Registry shows that 52 500 donors are diagnosed with cancer as of December 31, 2009. The main goals of the biobank are to make the material available to cancer researchers over the whole world and deliver quality assured samples and data. The Janus Serum Bank is registered in the Biobank Register (Notification number 737)
Authoring tool to create, share, and collaborate on the web with documents, spreadsheets, presentations, and more in real time. All your changes are saved automatically in Drive.
Zebrafish Anatomy and Development Ontology
A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). It includes a list of structures, organized hierarchically into an ontology, with descriptions of each structure. The current version is being written by a consortium of researchers, each serving as an expert for a particular set of anatomical structures. Additional anatomical information derived from the current literature is provided by the ZFIN curation group. Development of a complete and uniform anatomical ontology for the zebrafish is vital to the success of zebrafish science. The anatomical ontology is necessary for: * Effective data dissemination and informatics. * A reference framework. * Interoperability.
Information and Communication Technologies Center
Information and Communication Technologies Centre
Information Communication Technologies Centre
CSIRO''s hub for innovative information and communication technologies applied across the breadth of CSIRO''s engagement with industry and society. Our Labs * Autonomous systems - CSIRO is developing autonomous technologies to monitor the environment and infrastructure and improve safety and operating efficiency in the mining, manufacturing and agricultural industries. * Information engineering - Science and technology for finding, integrating, managing and delivering services and information in a trusted and secure way. * Wireless & networking - CSIRO is working on enabling technologies for future mobile and wireless communications networks and developing next generation imaging and sensing systems. CSIRO is developing improved communications systems and sensors for innovative medical and industrial applications. * Australia e-Health Research Centre - Through the Australian e-Health Research Centre, CSIRO invests significantly in using information and communication technologies to improve healthcare and clinical treatment for all Australians. * Tasmanian ICT Centre - The Tasmanian ICT Centre has developed a world-class ICT research capacity and conducts innovative applied research in the areas of sensor networks and data management.
Citation-Sensitive In-Browser Summarizer
CSIBS: The Citation-Sensitive In-Browser Summarizer
A software tool designed to aid researchers in browsing through scientific literature. As one reads an online article and encounters a citation that looks important, CSIBS creates a preview summary of the cited document. The key innovation is the contextual tailoring of the automatically generated summaries using the citation and its surrounding text. As this context changes, so too does the citation-specific summary portion of the preview, which contains contextually-relevant sentences extracted from the cited document. The CSIBS preview presents relevant information required to appraise the citation, containing meta-data about the reference, the abstract and the citation-specific summary. Thus, CSIBS, alleviates information overload by enabling the reader to determine whether or not to invest time in exploring the cited article further. Reference, http://www.sciencedirect.com/science/article/pii/S1570826810000181
A manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker's yeast and Brewer's yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases. YMDB contains metabolites arising from normal S. cerevisiae metabolism under defined laboratory conditions as well as metabolites generated by S. cerevisiae when used in baking and in the production of wines, beers and spirits. YMDB currently contains 2027 small molecules with 857 associated enzymes and 138 associated transporters. Each small molecule has 48 data fields describing the metabolite, its chemical properties and links to spectral and chemical databases. Each enzyme/transporter is linked to its associated metabolites and has 30 data fields describing both the gene and corresponding protein. Users may search through the YMDB using a variety of database-specific tools. The simple text query supports general text queries of the textual component of the database. By selecting either metabolites or proteins in the search for field it is possible to restrict the search and the returned results to only those data associated with metabolites or with proteins. Clicking on the Browse button generates a tabular synopsis of YMDB's content. This browser view allows users to casually scroll through the database or re-sort its contents. Clicking on a given MetaboCard button brings up the full data content for the corresponding metabolite. A complete explanation of all the YMDB fields and sources is available. Under the Search link users will find a number of search options listed in a pull-down menu. The Chem Query option allows users to draw (using MarvinSketch applet or a ChemSketch applet) or to type (SMILES string) a chemical compound and to search the YMDB for chemicals similar or identical to the query compound. The Advanced Search option supports a more sophisticated text search of the text portion of YMDB. The Sequence Search button allows users to conduct BLASTP (protein) sequence searches of all sequences contained in YMDB. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported. YMDB also supports a Data Extractor option that allows specific data fields or combinations of data fields to be searched and/or extracted. Spectral searches of YMDB's reference compound NMR and MS spectral data are also supported through its MS, MS/MS, GC/MS and NMR Spectra Search links. Users may download YMDB's complete textual data, chemical structures and sequence data by clicking on the Download button.
BLASTatlas - Mapping of whole genome homology
The BLASTatlas is a tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms using either blastp, blastn, tblastn, or blastx. DNA structural information is also included in the atlas to visualize the DNA chromosomal context of regions. Additional information can be added to these plots. The tool is SOAP compliant and WSDL (web services description language) files are available with programming examples available in Perl. The resolution is per-residue or per nucleotide depending on the regime of the blast search: For each annotation in the reference genome, the best hit in the database genome is found using one of the above algorithms. Each matching or mismatching residue/nucleotide of the best hit (based on BLAST score) is then mapped back to the genome sequence, using the coordinates provided in the annotations. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence enabling automation of repeated tasks. This tool can be relevant in many pangenomic as well as in metagenomic studies, by giving a quick overview of clusters of insertion sites, genomic islands and overall homology between a reference sequence and a data set.
Integrated Automatically Extracted Annotation
NIF Integrated Auto-Extracted Annotation
NIF Integrated Auto. Extracted Annotation
NIF Integrated Automatically Extracted Annotation
A virtual database that indexes both BioNOT for negation data, and the Resource Discovery Pipeline: an automated resource discovery and semi-automated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. This virtual database currently indexes the following resources: * BioNOT, http://snake.ims.uwm.edu/bionot/index.php?searchterm=mecp2+autism&submit=Search * Resource Discovery Pipeline, http://lucene1.neuinfo.org/nif_resource/current/
The study subjects invited to participate is chosen from the Swedish national Multiple Sclerosis registry and will number around 10 000 individuals to be included during two to three years. The same number of matched controls will also be included in the study. A pilot study with around 100 participants was performed during 2009, and the large scale study started in November 2009. Multiple sclerosis (MS) is a neurological disease that affects the central nervous system. It affects young people and the debut age is between 20 and 40 years. The disease comes with exacerbations but further on leads to disability. The incidence in Sweden is around 5 per 100 000 per year and the prevalence is 125 per 100 000 inhabitants. In total there are estimated around 13000 cases in Sweden and today 9000 of them are registered in the Swedish National Multiple Sclerosis register. Sample types * EDTA whole blood * DNA * Plasma Number of sample donors: 5592 (June 2010)
XuvTools (pronounced ex-you-vee-tools) is a fully automated 3D stitching software for biomedical image data, typically confocal microscopy images. XuvTools runs on Microsoft Windows XP and Vista, Linux and Apple Mac computers. It supports 32 and 64bit operating systems (with 64bit highly preferred). The goal of XuvTools is to provide tools, that combine multiple microscopic recordings to obtain a larger field of view (stitching) and a higher dynamic range (HDR recombination), or better resolution (multi view reconstruction), and to make these tools publicly available. What XuvTools can do: * Full 3D Stitching * Scaling, if the voxel sizes are known from image data * Fully automatic stitching modes * Manual pre-alignment modes * Arbitrary large datasets * Reads stage coordinates if available * free, no hidden costs * Reads many many input formats via LOCI Bio-Formats and Dmitry Fedorov''s BioImage. Limitations of XuvTools: (current limitations, we are working on it!) * No 2D Stitching: stacks need 4 Z-slices or more * No memory management: You need lots of RAM * No rotational alignment * The only supported output formats are: Imaris, HDF5 (No TIFF output support)
ViBE-Z: The Virtual Brain Explorer for Zebrafish
An imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae. ViBE-Z contains a database with precisely aligned gene expression patterns (1����m^3 resolution), an anatomical atlas, and a software. This software creates high-quality data sets by fusing multiple confocal microscopic image stacks, and aligns these data sets to the standard larva. The ViBE-Z database and atlas are stored in HDF5 file format. They are freely available for download. ViBE-Z provides a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. ViBE-Z enhances the data quality through fusion and attenuation correction of multiple confocal microscope stacks per specimen and uses a fluorescent stain of cell nuclei for image registration. It automatically detects 14 predefined anatomical landmarks for aligning new data with the reference brain. ViBE-Z performs colocalization analysis in expression databases for anatomical domains or subdomains defined by any specific pattern. The ViBE-Z database, atlas and software are provided via a web interface.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Project creating a DNA biobank from persons admitted to the neurointensive care unit of the Karolinska University Hospital to study possible genetic influences in traumatic brain injuries (TBI). Serum and cerebrospinal fluid sampled during the subacute phase are also collected. Samples were collected prospectively from clinically well characterized patients to allow for studies of association between candidate genes and clinical outcome parameters or biomarkers for relevant disease processes. The aim is to collect samples from 200-400 individuals. Samples will be collected from TBI patients at up to three different occasions. At first sampling, whole blood, serum and liquor will be collected and at the second and third occasions only serum and liquor.
Epidemiological Investigation of risk factors for Multiple Sclerosis
A multi-center population based epidemiological investigation of risk factors for Multiple Sclerosis (MS), where lifestyle- and environmental factors are examined systematically with concurrent genetic information. Newly diagnosed cases of MS in a geographically defined population and randomly chosen controls are identified and asked to answer a questionnaire on lifestyle, previous exposures at work, home and during spare time activities. For both cases and controls blood samples are taken for analysis of putative risk genes since environmental exposures probably contributes to disease only in individuals with certain genotypes. Exposures of interest are different sociodemographic factors, smoking, sunlight exposure, oral contraceptives / hormonal factors, butyrophilin (a milk protein), vaccinations, infections, atopic disease, organic solvents, mineral oils and a number of different psychosocial factors, such as critical lifetime events. Data from more than 1600 cases and 3200 controls are currently collected. (August 2014) The intention is to continue with the data collection over several years in order to analyse how genes and environment interact. The study is a collaboration between different institutions at Karolinska Institutet and neurological centers from 38 different hospitals in Sweden. Sample types * EDTA whole blood * DNA * Plasma * Serum
KI Biobank - Immunomodulatory Drugs in Multiple Sclerosis
Immunomodulatory drugs in multiple sclerosis (IMSE) is a nation-wide pharmacoepidemiological and genetic study on persons treated with Tysabri. The study focuses on response to treatment and development of neutralizing antibodies, and to perform large-scale genetic studies. Sample types * EDTA whole blood * DNA * Plasma Number of sample donors: 1293 (June 2010)
University of Texas at Austin; Texas; USA
Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts.
Oak Ridge National Laboratory Distributed Active Archive Center Data Product Citation Policy
Data Product Citation Policy of including a bibliographic citation for the products that were used in publications to acknowledge the scientists who have provided archived ORNL DAAC (Oak Ridge National Laboratory Distributed Active Archive Center) data products. Such citations will help others find the products and see how they have been used. Citation information is provided in the documentation that accompanies all data products. ORNL DAAC is operated by the ORNL Environmental Sciences Division and is responsible for data archival, product development and distribution, and user support for biogeochemical and ecological data and models. The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemcial dynamics is one of the NASA Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project, which is responsible for providing scientific and other users access to data from NASA''s Earth Science Missions.
Publisher that specializes in academic and professional book and journal publishing, mostly in the field of biodiversity science and natural history. They are academic publishers based in Eastern Europe with more than 600 books and e-books published so far. They largely perform their activities in English, with only a minor fraction of publications being in French, German, Russian and Bulgarian. Pensoft is also involved as a publisher in several European Union Fp5, FP6 and FP7 projects where they have specialized in dissemination, communication and publishing; as well as in creating and maintaining websites and Internal Communication Platforms (ICP), designing of logos, flyers, leaflets and posters. Open-access journals include ZooKeys, BioRisk, and PhytoKeys. ZooKeys is a journal in biodiversity science and has implemented several innovations in digital publishing and dissemination including developing and implementing an XML-based submission, editorial, publication and dissemination workflow. The TRIADA platform, for publishing, disseminating and marketing of printed books, e-books and open access journals, provides a linked environment for content, authors, reviewers, editors and customers through four independent classifications (taxonomic, subject, geographical, and geological time scale) as well through tagging and semantic mark-up. TRIADA uses a one-time registration process which allows users to submit, review or edit manuscripts, to subscribe for E-mail and RSS alerts, and to purchase Pensoft''s products. Web services: Metadata and journal content can be harvested.
GBIF - Global Biodiversity Information Facility
Global Biodiversity Information Facility
The Global Biodiversity Information Facility (GBIF) was established by governments in 2001 to encourage free and open access to biodiversity data, via the Internet. Through a global network of countries and organizations, GBIF promotes and facilitates the mobilization, access, discovery and use of information about the occurrence of organisms over time and across the planet. GBIF provides three core services and products: # An information infrastructure an Internet-based index of a globally distributed network of interoperable databases that contain primary biodiversity data information on museum specimens, field observations of plants and animals in nature, and results from experiments so that data holders across the world can access and share them # Community-developed tools, standards and protocols the tools data providers need to format and share their data # Capacity-building the training, access to international experts and mentoring programs that national and regional institutions need to become part of a decentralized network of biodiversity information facilities. GBIF and its many partners work to mobilize the data, and to improve search mechanisms, data and metadata standards, web services, and the other components of an Internet-based information infrastructure for biodiversity. GBIF makes available data that are shared by hundreds of data publishers from around the world. These data are shared according to the GBIF Data Use Agreement, which includes the provision that users of any data accessed through or retrieved via the GBIF Portal will always give credit to the original data publishers. * Explore Species: Find data for a species or other group of organisms. Information on species and other groups of plants, animals, fungi and micro-organisms, including species occurrence records, as well as classifications and scientific and common names. * Explore Countries: Find data on the species recorded in a particular country, territory or island. Information on the species recorded in each country, including records shared by publishers from throughout the GBIF network. * Explore Datasets: Find data from a data publisher, dataset or data network. Information on the data publishers, datasets and data networks that share data through GBIF, including summary information on 10028 datasets from 419 data publishers.
Database that gathers, generates, and shares taxa, images, videos, and sounds to freely provide knowledge about life on earth to increase awareness and understanding of living nature. Free EOL memberships are ranked so members have greater authority and editorial abilities based on their level of expertise.
Service and open API to tag the people, places, facts and events in your content. You hand the Web Service unstructured text (like news articles, blog postings, your term paper, etc.) and it returns semantic metadata in RDF format. Using natural language processing and machine learning techniques, the Calais Web Service examines your text and locates the entities, facts, and events. Calais then processes the entities, facts and events extracted from the text and returns them to the caller in RDF format. * Calais Tagaroo: If you are on WordPress, this plug-in automatically tags content as you type. It can also fetch images from Flickr and videos from Google Video. * Calais Marmoset: To manipulate your search results appearance in Google and Yahoo!, which is simple javacode you embed in your site pages. It will collect the metadata from your page (in the form of RDFa) and hand it over to Google Rich Snippets> and Yahoo! Search Monkey so that you can customize the way your search results appear. * Semantic Proxy: If you want to extract metadata from Web pages using URLs * Calais Collection: For the open source platform Drupal, you can find a complete Calais Collection of modules for easy integration. * OpenPublish: for building a new site from the ground up, this free Content Management System is based on Drupal. OpenPublish bakes-in OpenCalais from the ground up to semantify your site and automate the creation of ''related reading'' widgets, ''topic hubs'' and more.
Vector database is a digital collection of vector backbones assembled from publications and commercially available sources. This is a free resource for the scientific community that is compiled by Addgene. Only the plasmids deposited at Addgene are available for purchase through this website.
DBETH - Database for Bacterial ExoToxins for Humans
Database for Bacterial ExoToxins for Humans
Database of Bacterial ExoToxins for Human is a database of sequences, structures, interaction networks and analytical results for 229 exotoxins, from 26 different human pathogenic bacterial genus. All toxins are classified into 24 different Toxin classes. The aim of DBETH is to provide a comprehensive database for human pathogenic bacterial exotoxins. DBETH also provides a platform to its users to identify potential exotoxin like sequences through Homology based as well as Non-homology based methods. In homology based approach the users can identify potential exotoxin like sequences either running BLASTp against the toxin sequences or by running HMMER against toxin domains identified by DBETH from human pathogenic bacterial exotoxins. In Non-homology based part DBETH uses a machine learning approach to identify potential exotoxins (Toxin Prediction by Support Vector Machine based approach).
Java Enrichment of Pathways Extended To Topology
A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results.
International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies.UC system is member organization of Dryad general subject data repository.
NESCent - National Evolutionary Synthesis Center
The National Evolutionary Synthesis Center (NESCent) is a nonprofit science center dedicated to cross-disciplinary research in evolution. NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries. Synthetic research in evolutionary science takes many forms but includes integrating novel data sets and models to address important problems within a discipline, developing new analytical approaches and tools, and combining methods and perspectives from multiple disciplines to answer and even create new fundamental scientific questions. NESCent facilitates such synthetic research by providing an environment for fertile interactions among scientists. Our Science and Synthesis program sponsors postdoctoral fellows and sabbatical scholars as resident scientists, and two kinds of meetings, working groups and catalysis meetings. Catalysis meetings provide a novel mechanism for bringing together diverse research communities and cultures to identify common interests, while working groups provide an opportunity for scientists to work together intensively on fundamental synthetic questions over a several-year period. These activities are community driven through our application process and evaluated by an external advisory board. Our Informatics program provides state of the art informatics tools to visiting and in-house scientists and aims to take the lead in assembling novel databases and developing new analytical tools for evolutionary biology. Finally it is sponsoring a major initiative to provide a digital data repository for work in evolutionary biology. NESCent''s Education and Outreach group communicates the results of evolutionary biology research to the general public and scientific community, provides outreach to groups who are underrepresented in evolutionary biology and works to improve evolution education.
Standard: Universal Numerical Fingerprint
The Standard: Universal Numerical Fingerprint
Citation standard that offers proper recognition to authors as well as permanent identification through the use of global, persistent identifiers in place of URLs, which can change frequently. Use of universal numerical fingerprints (UNFs) guarantees to the scholarly community that future researchers will be able to verify that data retrieved is identical to that used in a publication decades earlier, even if it has changed storage media, operating systems, hardware, and statistical program format.
Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads.
Adaptive Information Disclosure Application Toolkit
A generic set of components that can perform a variety of tasks, such as learn new pattern recognition models, perform specialized search on resource collections, and store knowledge in a repository. W3C standards are used to make data accessible and manageable with semantic web technologies such as OWL, RDF(S), and SKOS. The AIDA Toolkit is directed at groups of knowledge workers that cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. The server offers services for: text indexing and statistics, metadata storage and querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, and model learning.
FastFig is a computational tool that lets users seamlessly combine numerical models so that using science is easier than ever. Sign up now for our limited beta release to be among the first to experience FastFig. At Fig Labs, Inc. we develop solutions for scientific data management, analysis and distribution. We specialize in scientific computing solutions and information management systems. Currently, we are developing a web application called FastFig that helps engineers and scientists to collaboratively create, solve and share numerical models. With FastFig you can: * Perform numerical analysis on everything from simple equations to complex models using our dynamic online interface. * Share the functions that you have built along with documentation so that others can use your function. * Search and browse functions to discover what people are calculating all over the world.
The study will collect 1,500 cases with schizophrenia and 1,500 well-matched controls ascertained via high-quality Swedish national hospitalization and population registries. Both cases and controls will be population-based and of Scandinavian ancestry. Types of samples * EDTA whole blood * DNA Number of donors: 10 820 (June 2010)
VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens
Bioinformatics Resource Center for invertebrate vectors. Provides web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases.
SynDB is an online resource of proteins known or predicted to be related to the synapse or synaptic activity, and extensive information on the proteins'' functions, sequences, structures, expression, pathways, interactions, and disease associations. It is intended to be a repository of current knowledge and data as well as a starting point for future proteomics research in neurobiology. SynDB is the first focused database of the molecular biology of the synapse proteome. It contains the most comprehensive collection of proteins (13809 unique proteins spanning 1979 species and 104 protein domains, Aug 2006) that are known or predicted to be associated with synaptic activities. It integrates extensive information on protein functions, sequences, structures, expression, pathways, interactions, and disease associations. SynDB was generated using a combination of automated approaches, including keyword- and domain-based searches, and manual curation. It serves as a starting point for future neurobiology, neuropharmacology, and neuroinformatics research. Synapse ontology is a set of standard vocabulary which help to describe all synaptic gene products in a consistant way. As in common ontology, synapse ontolgy is composed of all the terms in a hierarchical structure, but specifically restricted to the function and structure annotation of synapse related gene products. Synapse ontology is a callaborative fruit of bioinformatists and neural biologists. Synapse ontolgy is aimed to describe all the synaptic molecules in terms of structure/biochemistry of synapse and physiology/function at synapse in a specied-independent manner. The controled vocabularies are hierarchically structured, so you can browser the related gene products in different levels: for example, you can find all the gene products of synaptic vesicle cycling or ion channels and receptors, or you can zoom in on all the gene products playing roles in the priming step of synaptic vesicle cycling.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19,2022. The St G??ran Bipolar Study (SBP) is a prospective naturalistic study of patients suffering from bipolar disorder. Consenting patients are enrolled when diagnosed with any of Bipolar I, II, NOS disorder, cyclothymia, or schizoaffective disorder. At baseline, medical and social history is meticulously reviewed and the clinical diagnosis is established using a structured diagnostic instrument. Types of samples * EDTA whole blood * DNA * Plasma * Serum * Cerebrospinal fluid Number of sample donors: 371 (June 2010)
STAGE - Attention Deficit Hyperactivity Disorder
Swedish Twin study of Adults: genes and Environment - ADHD
Swedish Twin study of Adults: genes and Environment - Attention Deficit Hyperactivity Disorder
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Study to investigate symptoms of Attention Deficit Hyperactivity Disorder (ADHD) according to DSM-IV in adults with special focus on attention deficit. Information is used from the Swedish Twin study of Adults: genes and Environment (STAGE) from the Swedish Twin Registry. ADHD-discordant and concordant samples of pairs of twins for ADHD are selected from STAGE for studies of brain structure and function with Functional Magnetic Resonance Imaging (fMRI).
This study will include 5000 individuals recruited from The National Quality Register for Bipolar Disorder (Bipol��R) and The National Patient Register (Patientregistret) from which subjects with two or more hospitalizations with bipolar disorder will be eligible for inclusion. Bipolar disorder (manodepressive illness) is an often devastating neuropsychiatric disorder associated with considerable morbidity, mortality, human suffering, and societal costs. Genetic epidemiological studies provide indirect evidence of the importance of inheritance as bipolar disorder is clearly familial. Sample types * EDTA whole blood * DNA * Plasma Number of sample donors: 915 (June 2010)
KI Biobank - Schizophrenia Twins and Relatives
Schizophrenia and Bipolar Disorder: Neural endophenotypes genetic liability and adverse fetal environment
Large, ongoing, multifactorial study based on nation-wide ascertainment of patients with schizophrenia and bipolar disorder through the Swedish Twin Registry to include both neuroimaging data, neurocognitive function, molecular genetic data and early adverse environmental factors in the same model in a genetic sensitive design. Swedish schizophrenia research will benefit from this large study database of in total 240 affected and healthy twin pairs collected over a 5 year period. The specific aims are: * To elucidate neural endophenotypes for schizophrenia and bipolar disorder and to clarify the extent of overlap in these features between the two syndromes. * To investigate candidate genes and genomic regions for linkage and association with neural endophenotypes for schizophrenia and bipolar disease. * To determine the contributions of adverse prenatal and perinatal conditions to neural changes associated with schizophrenia and bipolar disease. Types of samples * EDTA whole blood * DNA * RNA Number of sample donors: 251 (June 2010)
DIG IT - Database of Immunoglobulins and Integrated Tools
Database of Immunoglobulins and Integrated Tools
Database of Immunoglobulins Integrated Tools
DIG IT - Database of Immunoglobulins Integrated Tools
DIG IT! Database of Immunoglobulins and Integrated Tools
DIG IT! Database of Immunoglobulins with Integrated Tools
The Database of Immunoglobulins and Integrated Tools (DIG IT) is an integrated resource storing sequences of annotated immunoglobulin variable domains of NCBI database and enriched with tools for searching and analyzing them. It contains 145759 heavy chain sequences and 71404 light chain sequences (47168 kappa type and 24236 lambda type) with assigned canonical structures for the hypervariable loops and the data on the type of antigen as well as the pairing information of immunoglobulin heavy and light chains (9672 total pairs). The user can input the immunoglobulin variable domain sequence (amino acid or nucleotide) of interest (heavy chain variable domain sequence; light chain variable domain sequence or both) to retrieve the closest sequences (sorted according to e-value) with complete annotation. The user can also directly query the database by antigen type, canonical structure, germline family in accordance to the requirements.
aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data
An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation.
Catalogue of Domain-specific Data Standards
Catalogue to: 1, centralize community-developed bioscience standards, linking to policies, other portals, open access resources and lists of tools and databases implementing the standards; 2. develop and maintain a set of criteria for assessing the usability and popularity of the standards, also the interoperability and relations among them; 3. foster interoperability, addressing overlaps and duplication of efforts that hamper their wider uptake and interfere with the creation of standards-compliant systems. Research community, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated. Similar trends in both the regulatory arena and commercial science. The BioSharing catalogue classifies standards into three types: * reporting requirements (minimal information checklists to report of the same core set of information) * terminological artifacts (such as controlled vocabularies and ontologies to describe the information) * exchange formats (to communicate the information) You can sort columns and browse the reporting guidelines content, or you can view all the standards, or reporting guidelines, or terminological artifacts or exchange formats only. Contribute and help build the catalogue.
Set of (mostly) C programs that run on X11+Unix-based platforms (Linux, Mac OS X, Solaris, etc.) for processing, analyzing, and displaying functional MRI (FMRI) data defined over 3D volumes and over 2D cortical surface meshes. AFNI is freely distributed as source code plus some precompiled binaries.
Distributed repository of anatomo-functional data and of simulation algorithms, fully integrated into a seamless simulation environment and directly accessible. This infrastructure will be used to create the physiome of the human musculo-skeletal system.
An ontology to describe Dictyostelium where the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle is defined. There are two main goals for this new tool: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes (already in use), and in the future, of gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning. To this end, all terms are defined. The complete ontology can be browsed using EBI''s ontology browser tool. (http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=DDANAT)
Shuttleworth Foundation is supporting exceptional people to change the world. We provide funding for dynamic leaders who are at the forefront of social change. We identify amazing people, give them a fellowship grant, and multiply the money they put into their projects by a factor of ten or more. We are looking for social innovators who are helping to change the world for the better and are looking for some support through an innovative social investment model.
DRCAT Resource Catalogue - Bioinformatics Web-based Data Resources
Data resource catalog that collates metadata on bioinformatics Web-based data resources including databases, ontologies, taxonomies and catalogues. An entry includes information such as resource identifier(s), name, description and URL. ' '''Query' ''' lines are defined for each resource that describe what type(s) of data are available, in what format, how (by what identifier) the data can be retrieved and from where (URL). DRCAT was developed to provide more extensive data integration for EMBOSS, but it has many applications beyond EMBOSS. DRCAT entries (including ' '''Query' ''' lines) are annotated with terms from the EDAM ontology of common bioinformatics concepts.
Genetic Regulation of the End-Stage Clotting Process that leads to Thrombotic Stroke
Genetic Regulation of the End-Stage Clotting Process that leads to Thrombotic Stroke (EuroClot)
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The study Genetic Regulation of the End-Stage Clotting Process that leads to Thrombotic Stroke (EuroClot) aims specifically to identify the major genes involved in variations of the end-stage clotting process and investigate the role of these novel genes (and existing candidate genes) in the pathogenesis of stroke across Europe. EuroClot will study stroke intermediate phenotypes in 4500 twins from GenomEUtwin project involving 8 countries and 1000 subjects from extended families from the GAIT2 (Spain) and EuroHead (Finland) studies. Types of samples * EDTA whole blood * DNA * Plasma * Serum Number of sample donors: 601 (sample collection completed)
nanopub.org - People Tools and Knowhow for Datapublishing
Format for creating, finding, using and citing nanopublications. A nanopublication has two basic elements: * The Assertion: An assertion is a minimal unit of thought, expressing a relationship between two concepts (called the Subject and the Object) using a third concept (called the Predicate). * The Provenance: This is metadata providing some context about the assertion. Provenance means, ' '''how this came to be' ''' and includes Supporting metadata (like methods) and Attribution metadata (such as authors, institutions, time-stamps, grants, links to DOIs, URLs). Nanopublications can be serialized using existing ontologies and RDF, allowing nanopublications to be machine readable and opening the door to universal interoperability. In turn, this allows extremely large, heterogeneous and decentralized data to be analyzed for the discovery of new associations that would otherwise be beyond the capacity of human reasoning. Nanopublication infrastructure is administered by the Concept Web Alliance, and are based on open standards. They anticipate the community-driven evolution of nanopublication formats to fit the changing needs of authors and publishers.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of the study is to estimate the importance of genetic (primary) and environmental factors for economic behavior by conducting a series of standard behavioral economics experiments on a sample of twins from the Swedish Twin Registry.
Public research university in Denton, Texas.
Database of biomedical literature citations, harvested from the reference lists of all open access articles in PubMed Central that reference ~20% of all PubMed Central papers (approx. 3.4 million papers), including all the highly cited papers in every biomedical field. All the data are freely available for download and reuse. The web site allows these bibliographic records and citations to be browsed, individual articles to be selected, and its citation network to be visualized in a variety of displays. Details of each selected reference, and the data and diagrams for its citation network, may be downloaded in a variety of formats, while the entire Open Citations Corpus can be downloaded from our source data page in several formats including RDF and BibJSON. Their aim for the future is to work with publishers to make available the reference lists from many more current and recent journal articles, starting with the biomedical literature, and to make the citations contained within them available as Open Linked Data in the manner demonstrated by the existing exemplar data available here.
A lightweight provenance vocabulary to provide terms to enable practitioners of data publishing to publish their data responsibly. It is closely based on the community provenance data model, the Open Provenance Model (OPM). Since release 1.0 OPMV becomes a profile of OPM. OPMV can be used together with other provenance-related RDF/OWL vocabularies/ontologies, such as Dublin Core, FOAF, the Changeset Vocabulary, and the Provenance Vocabulary. As being grounded on OPM, the OPMV aims to assist the interoperability between provenance information on the Semantic Web. The Open Provenance Model Vocabulary is defined as an OWL-DL ontology and it is partitioned into a core ontology and supplementary modules. In order to avoid making the core ontology too complex, the core module only implements structures defined in OPM and the supplementary modules provide less frequently used terms and a broad range of specializations of the core terms. * Classes: Agent, Artifact, Process * Properties: used, wasControlledBy, wasDerivedFrom, wasEncodedBy, wasEndedAt, wasGeneratedAt, wasGeneratedBy, wasPerformedAt, wasPerformedBy, wasStartedAt, wasTriggeredBy, wasUsedAt
Working group to support the widespread publication and use of provenance information of Web documents, data, and resources. The Working Group will publish W3C Recommendations that define a language for exchanging provenance information among applications. The Working Group is based on an extensive review and roadmap developed by a prior incubator group. Specifications: * PROV Primer * PROV Ontology * PROV Data Model * PROV Notation * PROV Constraints * PROV Access and Query
Project to addresses challenges associated with the preservation of scientific experiments in data-intensive science, including: * The definition of models to describe, in a standard way, scientific experiments by means of workflow-centric Research Objects, which comprise scientific workflows, the provenance of their executions, interconnections between workflows and related resources (e.g., datasets, publications, etc.), and social aspects related to such scientific experiments. * The collection of best practices for the creation and management of Research Objects. * The analysis and management of decay in scientific workflows. To address these challenges they are creating an architecture and tooling for the access, manipulation, sharing, reuse and evolution of Research Objects in a range of disciplines. This will result into the next generation RO-enabled myExperiment.
Software tool for viewing, analyzing, and registering volumetric medical imaging data sets. It has been written on top of GTK+ and runs on any system that supports this toolkit (Linux, Windows, Mac OS X, etc.). The program incorporates automatic non-orthogonal data reslicing, allowing multiple data set to be fused without imposed constraints on the dimensions, anisotrophy, or voxel sizes of the data. Additional features include 3D ROI (ellipses, cylinders, boxes, and isocontours), multi-slice viewing, volume rendering, and data importing through the (X)MedCon library.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\ \\\\\\ An Antibody supplier
Disease Meth-The Human Disease Methylation Database
Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases.
Diseases and Traits In Linkage Disequilibrium
Diseases and Traits In Linkage Disequilibrium blocks
The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database performs three important tasks: # published GWAS are collected from several sources and linked to standardized, international disease codes ICD10 codes) # data from the International HapMap Project are analyzed to define linkage disequilibrium (LD) blocks onto which SNPs and genes are mapped # the web interface makes it easy to query and visualize disease-associated SNPs and genes within LD blocks. Users can query the database by diseases, SNPs or genes. No matter which of the three query modes was used, an intermediate page will be shown listing all the studies that matched the search with a link to the corresponding publication. The user can select either all studies related to a certain disease or one specific study for which to view the related LD blocks. The DistiLD resource integrates information on: * Associations between Single Nucleotide Polymorphisms (SNPs) and diseases from genome-wide association studies (GWAS) * Links between SNPs and genes based on linkage disequilibrium (LD) data from HapMap For convenience, we provide the complete datasets as two (zipped) tab-delimited files. The first file contains GWAS results mapped to LD blocks. The second file contains all SNPs and genes assigned to each LD block.
A tool for automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs.
CATSS - Child and Adolescent Twin Study in Sweden
CATSS - Child Adolescent Twin Study in Sweden
Child and Adolescent Twin Study in Sweden
Child and Adolescent Twin Study in Sweden (CATSS)
Data and biomaterial from a study investigating how both genetic and environmental effects influence health and behavior in children and adolescents. In this study parents to all Swedish twins turning 9 or 12 years are asked to complete a telephone interview concerning the health and behavior of their twins. The interview screens for several different health (e.g., asthma, allergies, diabetes) and behavior (e.g., attention, social interaction) problems. Some of the families will be followed up with additional questionnaires, as well as with genotyping and clinical interviews. The response frequency of the telephone interview is 80%. By November 2008, 7408 interviews had taken place. Types of samples * Saliva alt. EDTA whole blood * DNA Number of sample donors: 10 721 (June 2010)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 03, 2014. A study that is a follow-up of the CATSS study and includes 15-year old twins who have been identified with autism, ADHD, learning-, eating-, tics disorders, compulsion-, defiance-, conduct- or motor control problems. The study also includes the co-twin, controls and the parents. DNA will be collected from the twins and the parents. For the twins, both a saliva sample and capillary blood samples will be collected, and for the parents, a saliva sample will be collected. Types of samples * Saliva alt. capillary blood * DNA Number of sample donors: 764 (June 2010)
Ontology for knowledge representation related to computer-based decision support in rehabilitation; concepts and relationships in the rehabilitation domain, integrating clinical practice, the ICD (specifically its 11th revision), the clinical investigator record ontology, the ICF and SNOMED CT.
Scholarly Electronic Publishing Bibliography
Bibliography with over 3,800 selected English-language articles, books, and other printed and electronic sources that are useful in understanding scholarly electronic publishing efforts on the Internet. It covers a wide range of topics, such as digital copyright, digital libraries, digital preservation, digital repositories, e-books, e-journals, license agreements, metadata, and open access. It includes Scholarly Electronic Publishing Resources, a selective directory of related Web sites, and the Scholarly Electronic Publishing Weblog, a frequently updated list of new publications and other resources that may be of interest to bibliography readers. Most sources have been published from January 1, 1990 through October 30, 2011; however, a limited number of earlier key sources are also included. The bibliography includes links to freely available versions of included works. It does not include digital media works (such as MP3 files), editorials, e mail messages, letters to the editor, daily newspaper articles, presentation slides or transcripts, or weblog postings. An archive of prior versions of SEPB is available as a downloadable compressed file (.zip) that includes all versions of the bibliography. The Scholarly Electronic Publishing Bibliography 2010 is available as a paperback (466 pages, $18.95, ISBN-10: 1456453289 and ISBN-13: 9781456453282) and an open access PDF file.
ROARMAP: Registry of Open Access Repositories Mandatory Archiving Policies
International registry of institutional open access mandates. Total Mandates to Date (by type) (2013): * Institutional Mandates (166) * Sub-Institutional Mandates (36) * Multi-Institutional Mandates (4) * Funder Mandates (80) * Thesis Mandates (101) * Proposed Institutional Mandates (6) * Proposed Sub-Institutional Mandates (4) * Proposed Multi-Institutional Mandates (6) * Proposed Funder Mandates (11)
Listing of institutional repositories for depositing preprints of published materials with the aim of promoting the development of open access by providing timely information about the growth and status of repositories throughout the world. Open access to research maximizes research access and thereby also research impact, making research more productive and effective. Repository Types: * Research Institutional or Departmental * Research Multi-institution Repository * Research Cross-Institutional * e-Journal/Publication * e-Theses * Database/A&I Index * Research Data * Open and Linked Data * Learning and Teaching Objects * Demonstration * Web Observatory * Other Repository Software: * ARNO * Bepress * CDS Invenio * ContentDM by OCLC * DIGIBIB * DigiTool * DiVA * DoKS * DSpace * EDOC * EPrints * Equella * ETD-db * Fedora ** Fez * Greenstone * HAL * i-Tor * IntraLibrary * Keystone DLS * MiTOS * MyCoRe * Open Journal System * Open Repository * OPUS (Open Publications System) * Other softwares (various) * PMB Services * SBCAT * SciX * SobekCM * WIKINDX * Zentity
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 8, 2017. Service that aggregates altmetrics: diverse impacts from articles, datasets, blog posts, and more, to create a measure of the impact of scholarly output. * view metrics: Point to research products in Slideshare, GitHub, and Dryad. Import items from Google Scholar profiles or a BibTex file and the output is a metrics report that can be viewed and shared. * embed anywhere: Use the full-featured API to add metrics to projects. Or drop the embeddable Javascript widget into a publishing platform''s HTML. * Free - metrics data (and source code). They believe open altmetrics are key for building the coming era of Web-native science.
Conditioned Taste Aversion: An Annotated Bibliography
A searchable, keyword-indexed bibliography on conditioned taste aversion learning, the avoidance of fluids and foods previously associated with the aversive effects of a variety of drugs. The database includes articles as early as 1951, and papers just published given that the database is ongoing and constantly updated. In the mid 1950''s, John Garcia and his colleagues at the Radiological Defense Laboratory at Hunters Point in San Francisco assessed the effects of ionizing radiation on a myriad of behaviors in the laboratory rat. One of their behavioral findings was that radiated rats avoided consumption of solutions that had been present during radiation, presumably due to the association of the taste of the solution with the aversive effects of the radiation. These results were published in Science and introduced to the literature the phenomenon of conditioned taste aversion learning (or the Garcia Effect). Subsequently, Garcia and his colleagues demonstrated that such learning appeared unique in a number of respects, including the fact that these aversions were acquired often in a single conditioning trial, selectively to gustatory stimuli and even when long delays were imposed between access to the solution and administration of the aversive agent. Together, these unique characteristics appeared to violate the basic tenets of traditional learning theory and along with a number of other behavioral phenomena (e.g., bird song learning, species-specific defense reactions, tonic immobility and schedule-induced polydipsia) introduced the concept of biological constraints on learning that forced a reconceptualization of the role evolution played in the acquisition of behavior (Garcia and Ervin, 1968; Revusky and Garcia, 1970; Rozin and Kalat, 1971). Although the initial investigations into conditioned taste aversion learning focused on these biological and evolutionary issues and their relation to learning, research in this area soon assessed the basic generality of the phenomenon, specifically, under what conditions such learning did or did not occur. With such research, a wide variety of gustatory stimuli were reported as effective conditioned stimuli and an extensive list of drugs with diverse consequences were reported as effective aversion-inducing agents. Aversions were established in a range of strains and species and under many experimental conditions. Research in this area continues to extend the conditions under which such learning occurs and to demonstrate its biological, neurochemical and anatomical substrates. Although the conditions under which aversion learning are reported to occur appear to generalize from the specific conditions under which they were originally reported, a number of factors including sex, age, training and testing procedures, deprivation level and drug history, all affect the rate of its acquisition and its terminal strength (Riley, 1998). In addition to these experimental demonstrations and assessments of generality, research on conditioned taste aversions has expanded to include investigations into its research and clinical applications (Braveman and Bronstein, 1985). In so doing, taste aversion learning has been applied to the characterization and classification of drug toxicity, the demonstration of the stimulus properties of abused drugs, the management of wildlife predation, the assessment of the etiology and treatment of cancer anorexia, the study of the biochemistry and molecular biology of learning, the etiology and control of alcohol use and abuse, the receptor characterization of the motivational effects of drugs, the occurrence of drug interactions, the characterization of drug withdrawal, the determination of taste psychophysics, the treatment of autoimmune diseases and the evaluation of the role of malaise in drug-induced satiety and drug-induced behavioral deficits. The speed with which aversions are acquired and the relative robustness of this preparation have made conditioned taste aversion learning a widely used, highly replicable and sensitive tool. In 1976, we published the first of three bibliographies on conditioned taste aversion learning. In this initial publication (see Riley and Baril, 1976), we listed and annotated 403 papers in this field. Subsequent lists published in 1977 (Riley and Clarke, 1977) and 1985 (Riley and Tuck, 1985) listed 632 and 1373 papers, respectively. Since that time, we have maintained a bibliography on taste aversion learning utilizing a variety of journal and on-line searches as well as benefiting from the generous contribution of preprints, reprints and pdf files from many colleagues. To date, the number of papers on conditioned taste aversion learning is approaching 3000. The present database lists these papers and provides a mechanism for searching the articles according to a number of search functions. Specifically, it was constructed to provide the reader access to these articles via a variety of search terms, including Author(s), Key Words, Date, Article Title and Journal. One can search for single or multiple items within any specific category. Further, one can search a single or combination of categories. The database is constantly being updated, and any feedback and suggestions are welcome and can be sent to CTALearning (at) american.edu.
DataVer is the premier data management verification service for scientific data. DataVer''s data management plan (DMP) Compliance Review and the companion Star Ratings will bring transparency to the investigator''s compliance with data management and sharing guidelines on a grant by grant basis. DataVer will accomplish this through 1) open publication of its review standards and procedures that it applies to all submitted grants and 2) openly report the results of its findings through its web portal so anyone can look up the compliance history of an investigator or lab. The Data Management Plan. The NIH and the NSF typically require a DMP detailing data types and quantity, its storage duration, and plans for making the data accessible to fellow scientists. The DMP is supposed to meet their published guidelines outlining the data management and sharing requirements to which the PI must agree as a condition of funding. The compliance record to date is less than ideal.. Institutional funders may not require a specific DMP as such but many have specific requirements for data management and post-grant data availability. While a specific DMP as such may not be produced for these grants, the data management and sharing is expected to comport with the funders'' guidelines. To date, there are no standardized or uniform means to track or assess the compliance of the investigator with the DMP or published guidelines. While individual institutions have tasked program managers with monitoring the compliance, the process is not uniform and the data stays within the specific institute, unavailable for other granting institutes or foundations. What DataVer does. DataVer offers two services with variations. First, it offers a DMP (or funder guideline) compliance review. For this DataVer compares the actual data management and data sharing of the grant funded data to the approved DMP and with the guidelines its funding agency(s). Second, DataVer rates the actual usability and accessibility of the data based on its own published standards on a three star rating scale. This indicates at a glance how well the data is organized and whether it''s available for reuse by an outside investigator. These procedures give the funders and the scientific community accurate, standardized and timely reports on an investigators'' data storage and data sharing in a publicly available database. We at DataVer believe this light, cast on actual data openness, will further encourage increased care in data management and archiving as well as increased data sharing. This openness and transparency will be a positive means to increase data management plan and guideline compliance, and will stimulate increased attention to the accessibility and usability of the data, so important to its reuse. We will offer a means by which universities, investigators, research facilities, and data repositories can obtain a compliance certification for consistently setting a high standard of data accessibility and usability across multiple grants. This certification is a means by which these stakeholders can demonstrate their achievement in support of data sharing. Grantors will be able to see an institution or facility''s pattern of compliance when deciding where to spend their limited resources.
A database which collects virus data from miRBase and ICTV, VirGne, VBRC., etc, including known viral miRNAs and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also provides effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons. Additionally, multiple functions and graphical web interface are designed and implemented to help users to investigate the microRNA roles in viral existence., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Database of European clinical trials containing information on interventional clinical trials on medicines. The information available dates from 1 May 2004 when national medicine regulatory authorities began populating the EudraCT database, the application that is used by national medicine regulatory authorities to enter clinical trial data. The EU Clinical Trials Register website launched on 22 March 2011 enables users to search for information which has been included in the EudraCT database. Users are able to: * view the description of a phase II-IV adult clinical trial where the investigator sites are in European Union member states and the European Economic Area; * view the description of any pediatric clinical trial with investigator sites in the European Union and any trials which form part of a pediatric investigation plan (PIP) including those where the investigator sites are outside the European Union. * download up to 20 results (per request) in a text file (.txt). The details in the clinical trial description include: * the design of the trial; * the sponsor; * the investigational medicine (trade name or active substance identification); * the therapeutic areas; * the status (authorized, ongoing, complete).
UMAS University Hospital - Biobanks of the Department of Clinical Pathology and Cytology
UMAS University Hospital - Biobanks of the Department of Clinical Pathology Cytology
Biobanks of the Department of Clinical Pathology and Cytology
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 6th, 2022. The biobank comprises paraffin blocks of surgical and autopsy tissue samples and corresponding histological slides as well as cytological material consisting of slides of vaginal smears, fine needle aspiration biopsies and exfoliative cytological material. The tissue samples date back until 1944 and most of the cytological samples until 1970. A subunit of the bank constitutes the National Tissue Microarray Centre. This center is supported by SWEGENE with the purpose to organize and construct tissue microarrays (TMA:s) for high throughput molecular pathology research on various kinds of tumors and other diseases. By linking the TMA.s to long-term and complete clinical follow-up data, prognostic and predictive studies will be facilitated. Biobank content: * Approximately 2,4 million paraffin blocks of surgical tissue specimens, * 1,1 million paraffin blocks of tissue samples from autopsies, * 3,8 million histological slides and * 1,6 million cytology slides. At present, the Tissue Microarray Centre includes: * A consecutive series of all invasive breast cancers (n=600) diagnosed in Malmo between 1988 and 1992. * All incident breast cancers within the Malmo Diet and Cancer cohort (n=400). * A subgroup of 600 pre-menopausal primary breast cancers within the nationwide, population-based randomized tamoxifen trial SBII:2. * 180 primary breast cancers from post-menopausal women included in a similar study. * A set of 120 extremely well characterized primary breast cancer samples with a clinical follow-up of 10 years. More than 40 relevant tumor biological parameters have been recorded in this material and it is therefore useful for a first screening of a marker in order to identify associations to other gene products. * 350 renal cell carcinomas (In collaboration with NUS). We provide researchers with state-of-the-art population based tissue microarrays with long-term and complete follow-up data on survival and treatment. With the TMA-technology, valuable biobank material will be preserved, allowing high throughput in-situ analyses of various tumors and other diseases with a minimal waste of tissue.
DOMMINO - Database Of MacroMolecular INteractiOns
DOMMINO is a comprehensive structural database on macromolecular interactions. As of June, 2011, it contains more than 407,000 binary interactions. The distinctive features of DOMMINO are: # Automated updates: DOMMINO is fully automated and is designed to update itself on a weekly basis, one day after a PDB weekly update. Thus, the community will be able to study macromolecular interactions almost immediately after they are released by PDB. # Coverage of non-domain mediated interactions: In addition to domain-domain and domain-peptide interactions the database characterizes the interaction between domains and unstructured protein regions that are not parts of a domain, such as inter-domain linkers and N- and C-termini. The interactions that involve the latter unstructured parts of proteins have been included to the database for the first time providing additional ~186,000 interactions (~45% of the total number of interactions, as of June, 2011). # Coverage of new structural domains: DOMMINO employs one of the most accurate structural classifications of proteins, SCOP. In addition to the existing SCOP-annotated domains, we employ a state-of-the-art machine learning approach to classify newer protein structures into existing SCOP families. With the progress of structural genomics, we do not expect a significant growth of the number of structurally novel folds or protein families and therefore our method allows covering almost all new protein structures. In total, using this predictive approach has allowed us to add more than 261,000 new interactions, almost twice as many as existing SCOP-annotated interactions. # The web-interface is designed to give the user a possibility of a flexible search as well as the capability to study macromolecular interactions in a PDB structure at the interaction network level and at the individual interface level. The web interface of the DOMMINO database includes a comprehensive list of help topics linked to the specific actions. In addition, we have designed a step-by-step tutorial that covers all aspects of working with the data from DOMMINO using the web interface.
The dbRBC database provides an open, publicly accessible platform for DNA and clinical data related to the human Red Blood Cells (RBC). A new bioinformatics resource, dbRBC, has been installed at the National Center of Biotechnology Information (NCBI). This resource combines the well established Blood Group Antigen Gene Mutation Database (BGMUT) with tools and interlinked resources developed at the NCBI. The main task of dbRBC is to provide access to publicly available genomic, protein and structural information linked to the red blood cell antigens. The site offers a number of resources: * BGMUT Database * Alignment Viewer * SBT Tool * Probe/Primer Resource * Typing Kit Interface * Obstacle
MIT Edgerton Center - High Speed Imaging
The Edgerton Center for High Speed Imaging
The MIT Edgerton Center carries on the legacy of Doc Edgerton''s research and teaching by providing the Institute with a continuing expertise in high-speed and scientific imaging. Our facilities include a large studio space, a photographic darkroom, and a digital imaging studio equipped with an array of scanners, digital cameras, printers and plotters, and Macintosh computers. In addition, we have several technical digital cameras, including: * Redlake MASD PCI Motionscope, monochrome high-speed video at up to 8,000 images per second. * Concurrent analog data acquisition via a National Instruments A/D card. * Midas 2.0 motion analysis software from Xcitex, Inc. * NAC Model color high-speed camera (in process of donation). * Redlake MASD Ektapro 1012 high-speed video, monochrome, up to 12,000 images per second. * Redlake MASD Megaplus 1.4i scientific still camera These systems are available for use by interested MIT researchers and instructors, and by students pursuing hands-on projects. Each summer we offer a week-long course on high-speed imaging through the MIT Professional Institute. This subject (6.51s) is designed for scientists, engineers, and photographers who need to gather data on rapidly moving subjects and events for study, motion analysis, and trouble-shooting. Mornings are spent in the lecture hall learning the fundamentals for lighting, imaging technologies, and motion analysis. Afternoons are spent making high-speed images in the laboratory. For MIT students, we offer the popular Strobe Project Lab (6.163) to 24 students each term, where students learn the fundamentals of high-speed imaging and apply these techniques to final projects of their own choosing. Two subjects are offered that investigate digital imaging and image manipulation, SP.757 in Fall terms, and SP.747 in Spring terms.
Dynamic and interactive view of 222 world wide available mouse resources, classified in 22 categories. The massive generation of data has led to the propagation of mouse resources and databases and the concomitant need for formalized experimental descriptions, data standardization and database interoperability and integration. In this context and with these goals, information is collected through an online questionnaire and/or manual curation. All mouse resource data in MRB are broken up in four sections and presented in four tabs: * The General section/tab contains information such as URL(s), contact information, database description and categorization and related links. * The Ontologies & Standards tab indicates controlled vocabularies and data representation standards adopted by each resource, such as ontologies and minimum information standards. A hyperlink to an index of OBO and non-OBO ontologies can be found here; an index of minimum information standards can be found here. * The Technical tab holds technical information for each resource such as the server technology used, relational database management system(s) utilized, programming language(s) of implementation, schema descriptive documents or actual database dumps and most importantly information on each resource''s programmatic access, the integration and interoperability services. Additionally and through the integration with Molgenis, MRB is capable of generating a SOAP API for hosted resources. * The final section on Database Description Framework (DDF) Criteria, describes the compliance of each resource to the CASIMIR database criteria, which aim to capture key technical data about a database in a formal framework. All data in MRB are freely available to interested users through downloadable weekly database dumps. Programmatic access to some of MRB''s data is feasible via MRB''s SOAP web service. MRB is the front end of a relational, fully normalized PostgreSQL database. The source code is available under the GNU general public license (GPL) as a binary download and via cvs.
Edgerton Digital Collections (EDC) project
Edgerton Digital Collections: ''Doc'' Edgerton
Over 22,000 still images of Harold Doc Edgerton materials, 150 restored and digitized films and video, access to approximately 8,000 digitized pages from Doc Edgerton''s hand-written laboratory notebooks, and hundreds of high-speed photographic images constituting the material record of an extraordinary man, great pioneer, inventor, professor emeritus at MIT, who shaped public perception about science and technology. The collections include a social dimension, including you, and the committed community of MIT alumni, faculty, students, staff, and aficionados who share Doc Edgerton''s philosophy of Work hard. Tell everyone everything you know. Close a deal with a handshake. Have fun! The Edgerton Digital Collections (EDC) project is an ambitious and collaborative publishing venture, documenting the history of science and technology. This project celebrates the spirit of a great pioneer and provides the first online access to Harold Edgerton''s research notebooks held by MIT, constituting the material record of an extraordinary man. The collection is a work in progress. Since this project began, we have inventoried, analyzed, cleaned, repaired, cataloged, photographed, titled, annotated, sorted, and organized tens of thousands of Edgerton artifacts, and enabled the public viewing of Doc''s research notebooks, still and moving images.
BLESS - Bloom-filter-based Error Correction Tool for NGS reads
BLoom-filter-based Error correction Solution for high-throughput Sequencing reads
Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory.
Review of Clinical and Functional Neuroscience
Review of Clinical and Functional Neuroscience - Swenson
Review of Clinical Functional Neuroscience
On line textbook of basic clinical and functional neuroscience, developed by Rand S. Swenson, D.C., M.D., Ph.D., Dartmouth Medical School Chapter Index * Introduction * Cellular organization * Peripheral nervous system * Development * Spinal cord * Brain stem organization * Sensory systems * Motor systems * Limbic system * Thalamic organization * Cerebral cortical organization * Nutrition of the brain * Conclusions
Dr.VIS - Human Disease-Related Viral Integration Sites
Database of Human Disease-related Viral Integration Sites
Dr. VIS - Database of Human Disease-related Viral Integration Sites
Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free.
KI Biobank - Swedish Adoption/Twin Study of Aging
SATSA - The Swedish Adoption/Twin Study of Aging
Longitudinal twin study to understand individual differences in aging with corresponding data and biological samples. The twin design and the inclusion of twins reared apart makes it possible to study the importance of genetic and environmental factors that may underlie differing aging outcomes. Further, the broad spectrum of biological, psychological, and social domains assessed across the life span makes it possible to study patterns of change within and across domains and how these predict health and diseases of aging. The study is comprised of several longitudinal components including, a comprehensive questionnaire that was sent to all twins in the Swedish Twin Registry who were separated at an early age and reared apart and a control sample of twins reared together. The questionnaires include items concerning rearing, family, adult, and working environment, health status, health related behaviors (e.g. alcohol, tobacco, and dietary habits) as well as relationships, and personality measures. The questionnaires were sent again at 3 year intervals in 1987, 1990, 1993 and after a break again in 2004, 2007, and 2010. Thus far more than 2,000 twins have responded to at least one of the seven questionnaire assessments conducted between 1984 and 2010. Additionally there is information about midlife life style factors from the Swedish Twin Registry that were collected about twenty years before SATSA started. In the second component a subsample of 861 individuals have participated in at least one wave of in-person testing (IPT). The first IPT started in 1986 and since then eight IPTs have been collected and the last wave will be collected during 2012-2013. The IPT includes a health examination, structured interviews, tests of functional capacity, and memory and thinking abilities. To date, over 76% of the sample has participated in 3 or more measurement waves. At IPT9 a third component was added to SATSA, a measure of day-to-day fluctuations in memory and thinking abilities, and emotions. Information about social interactions is also collected. After the visit by the research nurses the twins fill out the day-to-day booklet during the next five days. This procedure will be repeated in IPT10. This will add information about small and short-term changes and more changes are supposed to indicate the beginning of poor health. Data from SATSA can be used to study various aspects of aging. For example, the relative importance of genetic and environmental factors for individual differences in aging especially in cognitive and physical domains has been studied. A further main focus is to study changes within and across domains and which genetic and life style factors predict these changes. Given the wide spectrum of data from measured genes to social relationships collected over more than two decades they dare to say that SATSA is a unique study, with the possibility to answer many questions within gerontology and geriatrics. Types of samples * Serum * DNA Number of sample donors: 674 (June 2010)
Atlas of the Brain - Structure with functional correlates
On line labeled atlas of the human brain developed by Dr. Rand Swenson of Dartmouth Medical School. It includes gross anatomical and MRI-generated slices (Axial T1-weighted MRI and Coronal T2 MRI weighted, along with Magnetic resonance arteriogram (MRA) and Magnetic resonance venogram (MRV)images. Labels may be turned on and off. A companion on-line textbook is also available. The site says it is still under construction, although the copyright is 2009. * Atlas of Gross Brain Topography * Atlas of the Brain Stem in Cross Section * Atlas of the Brain in Axial Slices * Atlas of the Brain in Coronal Slices * Atlas of the Head in Axial Slices * Axial T1-weighted MRI * Axial T2-weighted MRI * Coronal T1 MRI * Coronal T2 MRI * Magnetic resonance arteriogram (MRA) * Magnetic resonance venogram (MRV)
Software program that allows researchers to perform citation analysis and calculate various impact metrics. It uses Google Scholar to obtain the raw citations, then analyzes these and presents the following statistics: * Total number of papers * Total number of citations * Average number of citations per paper * Average number of citations per author * Average number of papers per author * Average number of citations per year * Hirsch''s h-index and related parameters * Egghe''s g-index * The contemporary h-index * The age-weighted citation rate * Two variations of individual h-indices * An analysis of the number of authors per paper. The results are available on-screen and can also be copied to the Windows clipboard (for pasting into other applications) or saved to a variety of output formats (for future reference or further analysis). The Publish or Perish software is a Microsoft Windows application that can also be installed and used on Apple Mac OS X and GNU/Linux computers, with the aid of a suitable emulator such as Wine or CrossOver Mac.
A virtual database currently indexing clinical trials databases including EU Clinical Trials Register and Clinicaltrials.gov.
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI.
One of eight Bioinformatics Resource Centers nationwide providing comprehensive web-based genomics resources including a relational database and web application supporting data storage, annotation, analysis, and information exchange to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. These centers serve the scientific community and conduct basic and applied research on microorganisms selected from the NIH/NIAID Category A, B, and C priority pathogens that are regarded as possible bioterrorist threats or as emerging or re-emerging infectious diseases. The VBRC provides a variety of analytical and visualization tools to aid in the understanding of the available data, including tools for genome annotation, comparative analysis, whole genome alignments, and phylogenetic analysis. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.
Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics.
Object-Oriented Development Interface for NMR
Object Oriented Development Interface for NMR
ODIN - Object-Oriented Development Interface for NMR
A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms.
EPI-images of 25 participants gathered during rest as well as anonymized anatomical images of the same participants. The resting-state fMRI images were collected on several occasions: # the first resting-state scan in a scan session # 5-11 months after the first resting-state scan # about 30 (< 45) minutes after 2. Each scan occasion is released as a new version release of the resource. ---Caution: Participants here are part of the NewYork_a contribution to the 1000 Functional Connectomes Project. DO NOT combine datasets.
A collection of software plug-ins developed for the automatic segmentation of magnetic resonance brain images. The tools include multiple published algorithms developed at Johns Hopkins University. The SPECTRE algorithm performs brain extraction. The TOADS algorithm generates a topology-preserving tissue classification into cortical, subcortical, and cerebellar structures. The CRUISE algorithm produces inner, central, and outer cortical surfaces suitable for computing thickness and other geometric measures. Tools are also included for performing gyral labeling, lesion segmentation, thickness computation, surface visualization, and surface file conversion. All tools are released as plug-ins for the MIPAV software package and were developed using the Java Image Science Toolkit (both available at NITRC: http://nitrc.org). They are therefore cross-platform and compatible with a wide variety of file formats.
Public knowledge base specialized in the management and analysis of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. It contains high quality and up-to-date information gathered and curated from public databases (VirusMint, Intact, HIV-1 database). It allows users to search by host gene, host/viral protein, gene ontology function, KEGG pathway, Interpro domain, and publication information. It also allows users to browse viral taxonomy.
A free, user-friendly software package that allows researchers to record and analyze hand movements traveling toward potential responses on the screen (via the x, y coordinates of the computer mouse). By looking at the dynamics of how participants' hand movements settle into a response alternative--and how they may be partially pulled toward other alternatives--researchers glean valuable information about real-time cognitive processing. It's like opening up a single reaction time into a continuous stream of rich cognitive output. MouseTracker has impressive temporal resolution, comparable to eye-tracking and event-related brain potential (ERP) measures. Experiments can incorporate images, letter strings, sounds, and videos. Once recorded, mouse trajectories can be visualized, averaged, and explored, and measures of attraction/curvature, complexity, velocity, and acceleration can be computed. Precise characterizations of mouse trajectories' temporal and spatial dynamics are available, and these can shed light on a variety of important empirical questions across psychology, cognitive science, and beyond.
HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration
Hierarchical Attribute Matching Mechanism for Elastic Registration and White matter lesion Modules for 3D Slicer
A software plugin for 3D Slicer that matches morphological signatures of medical images automatically. HAMMER is an acronym for Hierarchical Attribute Matching Mechanism for Elastic Registration (Dinggang Shen, Christos Davatzikos, HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration, IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002) - an elastic registration algorithm for medical images, matching morphological signatures of images in a hierarchical multi-scale regime. White matter lesion (WML) segmentation is a novel multi-spectral WML segmentation protocol via incorporating information from T1-w, T2-w, PD-w and FLAIR MR brain images. (Zhiqiang Lao, Dinggang Shen, Dengfeng Liu, Abbas F Jawad, Elias R Melhem, Lenore J Launer, Nick R Bryan, Christos Davatzikos, Computer-Assisted Segmentation of White Matter Lesions in 3D MR images, Using Pattern Recognition, Academic Radiology, 15(3):300-313, March 2008).
A comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput.
Cold Spring Harbor Laboratory - Hannon Lab
The Hannon laboratory comprises a broad spectrum of programs in small RNA biology, mammalian genetics and genomics. We study RNAi and related pathways in a wide variety of organisms to extract common themes that define both the mechanisms by which small RNAs act and the biological processes which they impact. Currently, we focus on microRNAs, endogenous siRNAs and piRNAs and their roles in gene regulation, cancer biology, stem cell biology and in defense of the genome against transposons. In collaboration with Steve Elledge (Harvard) and Scott Lowe (CSHL), we develop genome-wide shRNA tools for RNAi-based genetics in mammalian cells, and we are now producing similar collections of artificial microRNAs for Arabidopsis with Detlef Weigel (MPI), Dick McCombie (CSHL) and Rob Martienssen (CSHL) as part of the 2010 project (see 2010.cshl.edu). Our genomic efforts include the application of RNAi-based genetic screens to cancer biology and stem cells. We also make heavy use of next generation sequencing methodologies for probing small RNA populations, in part as a member of the ENCODE consortium (with Tom Gingeras, CSHL). Finally, we develop (with Dick McCombie) and apply focal re-sequencing methods for identifying disease relevant mutations, for probing the epigenetic landscape and for the study of human evolution.
R software package for the detection of gross chromosomal abnormalities from gene expression microarray data.
API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service
A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications.
A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome.
Software toolkit for the visualization, segmentation, registration and analysis of multidimensional biomedical imaging data. With Analyze, both anatomic structure and associated function can be studied and fused together for synergistic display and measurement of important structure-to-function relationships.
An end-to-end application allowing individual regional analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line. * Operating System: MacOS, Linux * Programming Language: C++ * Supported Data Format: ANALYZE, Nrrd, Other Format * build requires: Insight Toolkit
A toolbox for SPM to improve fMRI analysis of high motion pediatric and clinical subjects. The toolbox includes special algorithms for motion adjustment, data repair, and noise filtering, and methods to find outlier subjects in group studies. Visualization tools are included for quality checking the data, including a movie format for viewing all data and all contrast estimates on every voxel of every subject. Methods are included to quantify results into percent signal change. * Operating System: OS Independent * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 * execution requires: SPM
Database of high-quality craniofacial anthropometric normative data for the research and clinical community based on digital stereophotogrammetry. Unlike traditional craniofacial normative datasets that are limited to measures obtained with handheld calipers and tape measurers, the anthropometric data provided here are based on digital stereophotogrammetry, a method of 3D surface imaging ideally suited for capturing human facial surface morphology. Also unlike more traditional normative craniofacial resources, the 3D Facial Norms Database allows users to interact with data via an intuitive graphical interface and - given proper credentials - gain access to individual-level data, allowing users to perform their own analyses.
Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.
ART ' '''acpcdetect' ''' program for automatic detection of the AC and PC landmarks and the mid-sagittal plane on 3D structural MRI scans. ART ' '''brainwash' ''' program for automatic multi-atlas skull-stripping of 3D structural MRI scans. ART ' '''3dwarper' ''' program of non-linear inter-subject registration of 3D structural MRI scans. Software (art2) for linear rigid-body intra-subject inter-modality (MRI-PET) image registration. Data resource: The ART projects makes available corpus callosum segmentations of 316 normal subjects from the OASIS cross-sectional database. ART ' '''yuki' ''' program for fast, robust, and fully automatic segmentation of the corpus callosum on 3D structural MRI scans.
Toolbox for post-processing fMRI data. Includes software for comprehensive analysis of sources of artifacts in timeseries data including spiking and motion. Most compatible with SPM processing, but adaptable for FSL as well. * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A probabilistic algorithm that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome.
Automatic Segmentation of Hippocampal Subfields
A software package for automatic segmentation of hippocampal subfields in magnetic resonance imges. Given a pair of T1-weighted and T2-weighted images (the latter acquired using a protocol tuned for hippocampus imaging), ASHS will automatically label main subfields of the hippocampus, and some extra-hippocampal structures, using multi-atlas segmentation. The main method is described in the Yushkevich et al. 2011 Neuroimage paper (http://tinyurl.com/cffrp3p). * execution requires: Advanced Normalization Tools, FSL
Tool box for arterial spin labeled perfusion MRI data processing. It is based on SPM and Matlab. More detailed documentation can be found in asl_perf_subtract.m, the main function for calculating CBF value. It supports 3D or 4D Analyze or Nifiti format and PASL, CASL, and PCASL data. It contains the code for calculating CBF and a set of SPM batch scripts for preprocessing and statistical analysis.
FaceBase - A Resource For Craniofacial Researchers
A web portal that provides access to data, tools and materials that will aid in craniofacial research. Included is access to genomic and imaging based data sets from a variety of species, including zebrafish, human and mouse.
OCDM - Ontology of Craniofacial Development and Malformation
OCDM - Ontology of Craniofacial Development Malformation
Ontology of Craniofacial Development and Malformation (OCDM)
Ontology of Craniofacial Development Malformation (OCDM)
To satisfy the need for standardized terminologies several ontologies, we are developing the Ontology of Craniofacial Development and Malformation. When complete, this ontology will describe several realms of anatomy and development relevant to FaceBase, including: * Human craniofacial anatomy, including developmental progressions * Craniofacial malformations * Mouse craniofacial anatomy * Mappings between mouse and human anatomy These ontologies are currently undergoing active development. As a result, these files should be considered very preliminary. They may not work correctly, and contents will almost certainly undergo significant change. Five (sub) ontologies in this zip archive correspond to the categories described above. * OCDM - Ontology of Craniofacial Development and Malformation: currently imports the CHO, CMO, and the CHMMO. * CHO - Craniofacial Human Ontoloogy: normal adult human craniofacial anatomy derived from the FMA. * CMO - Craniofacial Mouse Ontology: normal adult mouse craniofacial anatomy * CHMMO - Craniofacial Human-Mouse Mapping Ontology: mappings of classes in the * CHO to related (homologous) structures in the CMO. CFMO - Craniofacial Malformation Ontology: abnormal human anatomy, includes the CHO All ontologies are in Protege Frames format (requires Protege 3.x). Ontologies refer to other ontologies via the Protege include mechanism. The CHMMO includes the CHO and the CMO. The OCDM (which is the umbrella ontology) includes all of the rest. Future releases will include translations to the OWL language.
MetaQC: Objective Quality Control and Inclusion / Exclusion Criteria for Genomic Meta-Analysis
MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis
Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision.
THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. FaceBase Biorepository is now collecting biological samples from people with cleft lip/palate and their family members. Information for Prospective Cases: Clefts of the lip and/or palate can be caused by a wide range of genetic, environmental and other factors. The FaceBase Biorepository will serve as a common source of both biological samples and information that can be made available to investigators trying to determine the underlying cause of these common birth defects. Genetic studies, in particular, will benefit from both family history information and having samples from affected individuals as well as their family members. DNA is the information containing molecules found in all the cells of our body and can be easily obtained from material such as blood or saliva samples. As part of the FaceBase Biorepository, we are requesting families to submit biological samples from specific family members as well as information from other family members that might be affected with either the same condition or a similar condition. The medical and family history information that is collected includes other relevant information such as exposure to possible environmental causes during pregnancy. The biorepository is managed by Nichole Nidey, a research study coordinator, and Jeff Murray, a pediatric clinical geneticist and researcher. They are available to speak with family members regarding questions they may have, including providing information about the biorepository and making arrangements for the collection of samples for those who wish to participate. All participation is voluntary. Your name or other personally identifiable information (name, address, etc) will be removed before information is placed in the biorepository. Summary data to show how the database itself has been used overall as well as updates on whether specific findings might have been made using this database will be available on the FaceBase website at www.facebase.org. A newsletter containing this information will also be given to families and referring clinicians so that they may discuss the specifics with the families if there appears to be information that might be relevant in a particular case. Families will also need to sign a consent form that has been approved by the Institutional Review Board at the University of Iowa. Also, any submitted samples or data can also be removed from the database at any time should the family no longer wish to participate. Investigators interested in requesting DNA samples or for more information, please contact cleftresearch (at) uiowa.edu, Nichole Nidey, nichole-nidey (at) uiowa.edu or (319) 353-4365, or Jeff Murray, jeff-murray (at) uiowa.edu.
University of Michigan Department of Neuroscience Graduate Program
University of Michigan Neuroscience Graduate Program
The Graduate Program at the University of Michigan was constituted in 1971, making it the longest-standing neuroscience graduate program in the United States. We are a collegial and interactive group of 75 students and 115 faculty that perform research across the breadth of the neuroscience field. Neuroscience graduate students on this campus form a cohesive group, which promotes interactions among the faculty, making the Graduate Program the nexus of the neuroscience community. Graduates receive a Ph.D. in Neuroscience, which provides tremendous flexibility in choosing one's career path. There are more than 100 alumni of our Program, and these graduates work in academic research, industrial research and development, academic medicine and biotechnology. Our program captures the excitement and interaction intrinsic to the field of neuroscience. Students can seek admission to the Neuroscience Program by three different routes direct application to the Neuroscience Program, application via the Program in Biomedical Sciences and application via the Medical Scientist Training Program.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The SALTY study will contact approximately 25 000 twins born 1943 - 1958. One of the main purposes with the study is to continue to build up the Swedish Twin Biobank which was established by the Twin Gene project.
STAGE - Swedish Twin Studies of adults: Genes and Environment
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. The Swedish twin registry has recently examined all twins in Sweden born between 1959-1985. 25,000 individuals participated in the study. The twins had to implement a Web-based survey on the Internet or a telephone interview where we had to answer questions about, among other things, about the diseases they have, or have had, behaviors, eating and drinking habits, smoking habits, etc. The aim of the study is to extend the information in the Swedish twin registry. Our goal with twin studies are, inter alia, to study the relative importance of the heritage and environment for the emergence of various diseases. The responses from the study is currently the basis for a number of analyses regarding how inheritance and environment affects disease and tobacco habits. Currently third follow-up STAGE where 10,000 twins that had previously taken part are contacted again. The purpose of alteplase randomized controlled trials is to follow up the same individuals one year after the first and second questionnaire replies were received to see if anything has changed. The issues we are interested in the follow-up to include changes in general health, working and living situation, your weight, smoking habits, etc. Study Results The results we have so far come to and which we can present here are figures on the prevalence of certain diseases. The figures give a rough estimate of the incidence of these diseases will look for all individuals, born in Sweden in 1959-1985. The figures are based on the questions on the questionnaire which the twins themselves had to answer whether they have or have had various diseases.
Voronoia is a program suite to analyse and visualize the atomic packing of protein structures. It is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. Voronoia is also targeted to detect locations of putative internal water or binding sites for ligands. Accordingly, Voronoia is beneficial for a broad range of protein structure approaches. It is applicable as a standalone version coming with a user friendly GUI or, alternatively, as a Pymol Plugin. Finally, Voronoia is also available as an easy to use webtool to process user defined PDB-files or to asses precalculated packing files from DOPP, the regularly updated Dictionary of Packing in Proteins.
In collaboration with GenomeEUtwin, the TwinGene project investigates the importance of quantitative trait loci and environmental factors for cardiovascular disease. It is well known that genetic factors are of considerable importance for some familial lipid syndromes and that Type A Behavior pattern and increased lipid levels infer increased risk for cardiovascular disease. It is furthermore known that genetic factors are of importance levels of blood lipid biomarkers. The interplay of genetic and environmental effects for these risk factors in a normal population is less well understood and virtually unknown for the elderly. In the TwinGene project twins born before 1958 are contacted to participate. Health and medication data are collected from self-reported questionnaires, and blood sampling material is mailed to the subject who then contacts a local health care center for blood sampling and a health check-up. In the simple health check-up, height, weight, circumference of waist and hip, and blood pressure are measured. Blood is sampled for DNA extraction, serum collection and clinical chemistry tests of C-reactive protein, total cholesterol, triglycerides, HDL and LDL cholesterol, apolipo��protein A1 and B, glucose and HbA1C. The TwinGene cohort contains more than 10000 of the expected final number of 16000 individuals. Molecular genetic techniques are being used to identify Quantitative Trait Loci (QTLs) for cardiovascular disease and biomarkers in the TwinGene participants. Genome-wide linkage and association studies are ongoing. DZ twins have been genome-scanned with 1000 STS markers and a subset of 300 MZ twins have been genome-scanned with Illumina 317K SNP platform. Association of positional candidate SNPs arising from these genomscans are planned. The TwinGene project is associated with the large European collaboration denoted GenomEUtwin (www.genomeutwin.org, see below) which since 2002 has aimed at gathering genetic data on twins in Europe and setting up the infrastructure needed to enable pooling of data and joint analyses. It has been the funding source for obtaining the genome scan data. Types of samples: * EDTA whole blood * DNA * Serum Number of sample donors: 12 044 (sample collection completed)
BIOAIR - BIOmarkers in severe Chronic AIRway Disease
BIOmarkers in severe Chronic AIRway Disease
BIOmarkers in severe Chronic AIRway Disease (BIOAIR)
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Longitudinal Assessment of Clinical Course and BIOmarkers in severe Chronic AIRway Disease (BIOAIR) is a study within the European Network For Understanding Mechanisms Of Severe Asthma (ENFUMOSA). BIOAIR study involves studies of severe asthma. The 10% of all asthmatics who have the most difficult disease has a 5-year survival in level with severe cancer diseases, as well as account for half of the costs to society of asthma. Mechanisms for the development of severe asthma, however, is unknown. BIOAIR the project characterizes clinical Phenotype and biomarkers in a study involving 12 centers in nine European countries. In a longitudinal study comparing severe asthmatics with mild asthmatics and patients with COPD (Chronic obstructive pulmonary disease). Clinical data and medicine consumption are collected daily in over a year with the help of modern IT technology. Blood tests, urine samples, upphostningsprover and bronkialbiopsier are collected repeatedly and tested for a wide range of possible pathogenetic factors, including genotype.
OLIN - Obstructive Lung disease in Northern Sweden
Obstructive Lung disease in Northern Sweden
OLIN (Obstructive Lung disease in Northern Sweden)
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Longitudinal studies that consist of more than 40 000 subjects that have been followed since 1986 to be used in studies on how hereditary factors influence the development and progression of Chronic Obstructive Pulmonary Disease (COPD). Its overall objective to find ??tg??rdbara determinants of especially asthma and COPD but also allergy and OSAS (obstructive sleep apnea syndrome). Research is carried out in two huvudforskningslinger; population studies among adults of asthma, allergies, COPD, chronic bronchitis and OSAS. The second main line of longitudinal studies on asthma and allergies among schoolchildren with measurement of incidence, remission and morbidity. The study followed annually all 3500 schoolchildren since 1996 when they went in first and second class in Kiruna, Lulea and Pitea. In addition to questionnaire studies contained in methods, as well as in the adult studies, mainly respiratory function, BMI, skin prick test and clinical interview. Main fragestallningen of risk factors for incident asthma and allergy.
neuro Visualization Imagemapping Information System for Analysis and Simulation
An open framework for integrative data analysis, visualization and population simulations for the exploration of network dynamics on multiple levels. This generic platform allows the integration of neuroontologies, mapping functions for brain atlas development, and connectivity data administration; all of which are required for the analysis of structurally and neurobiologically realistic simulations of networks. What makes neuroVIISAS unique is the ability to integrate neuroontologies, image stacks, mappings, visualizations, analyzes and simulations to use them for modelling and simulations. Based on the analysis of over 2020 tracing studies, atlas terminologies and registered histological stacks of images, neuroVIISAS permits the definition of neurobiologically realistic networks that are transferred to the simulation engine NEST. The analysis on a local and global level, the visualization of connectivity data and the results of simulations offer new possibilities to study structural and functional relationships of neural networks. neuroVIISAS provide answers to questions like: # How can we assemble data of tracing studies? (Metastudy) # Is it possible to integrate tracing and brainmapping data? (Data Integration) # How does the network of analyzed tracing studies looks like? (Visualization) # Which graph theoretical properties posses such a network? (Analysis) # Can we perform population simulations of a tracing study based network? (Simulation and higher level data integration) neuroVIISAS can be used to organize mapping and connectivity data of central nervous systems of any species. The rat brain project of neuroVIISAS contains 450237 ipsi- and 175654 contralateral connections. A list of evaluated tracing studies are available. PyNEST script generation does work using WINDOWS OS, however, the script must be transferred to a UNIX OS with installed NEST. The results file of the NEST simulation can be visualized and analyzed by neuroVIISAS on a WINDOWS OS.
eQuilibrator - biochemical thermodynamics calculator
Web interface designed for thermodynamic analysis of biochemical systems. eQuilibrator enables free-text search for biochemical compounds and reactions and provides thermodynamic estimates for both in a variety of conditions. It can provide estimates for compounds in the KEGG database, and individual compounds and enzymes can be searched for by their common names (water, glucosamine, hexokinase). Reactions can be entered in a free-text format that eQuilibrator parses automatically. eQuilibrator also allows manipulation of the conditions of a reaction - pH, ionic strength, and reactant and product concentrations.
The mission of the Doris Duke Charitable Foundation is to improve the quality of people''s lives through grants supporting the performing arts, environmental conservation, medical research and the prevention of child abuse, and through preservation of the cultural and environmental legacy of Doris Duke''s properties. Established in 1996, the foundation supports four national grant-making programs. It also supports three properties that were owned by Doris Duke in Hillsborough, New Jersey; Honolulu, Hawaii; and Newport, Rhode Island. The foundation is headquartered in New York and is governed by a board of 12 Trustees. DDCF''s activities are guided by the will of Doris Duke, who endowed the foundation with financial assets that totaled approximately $1.6 billion as of December 31, 2010. The foundation regularly evaluates and modifies its allocation of resources from the endowment to support the programs and properties and to respond to fluctuations in portfolio returns. The foundation awarded its first grants in 1997. As of December 31, 2011, the foundation has awarded grants totaling more than $1 billion. DDCF awards grants in four core program areas: * The Arts Program supports performing artists with the creation and public performance of their work. * The Environment Program supports efforts that enable communities to protect and manage wildlife habitat and create efficient built environments. * The Medical Research Program seeks to contribute to the prevention and cure of disease by supporting clinical research. * The Child Abuse Prevention Program seeks to protect children from abuse and neglect in order to promote their healthy development. In the fall of 2007, DDCF also launched the African Health Initiative, with the goal of strengthening health systems in sub-Saharan Africa. The Building Bridges Program, which seeks to increase public understanding of Islamic cultures through media and the arts, is funded through the Doris Duke Foundation for Islamic Art and is headquartered in DDCF''s offices in New York. The Properties In her will, Doris Duke requested that several operating foundations manage the properties listed below. She also expressed her wishes that the properties be opened for public visitation and used for educational programs. The operating foundations receive funding from the Doris Duke Charitable Foundation. * The Duke Farms Foundation manages a 2,700-acre property in Hillsborough, New Jersey, which is known as Duke Farms and has a mission of environmental stewardship. * The Doris Duke Foundation for Islamic Art manages Doris Duke''s home in Honolulu, Hawaii, which is known as Shangri La and serves as a center for the study of Islamic art and cultures. * The Newport Restoration Foundation preserves historic houses in Newport, Rhode Island, and operates Doris Duke''s home in Newport known as Rough Point, which is also a public museum.
FungiDB is a database for functional and evolutionary comparison of fungal genomes. FungiDB is a functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center (http://EuPathDB.org). FungiDB uses the same infrastructure and user interface as EuPathDB, which allows for sophisticated and integrated searches to be performed using an intuitive graphical system. The current release of FungiDB contains genome sequence and annotation from 18 species spanning several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal "Zygomycete" lineage Mucormycotina. Additionally, FungiDB contains cell cycle microarray data, hyphal growth RNA-sequence data and yeast two hybrid interaction data. The underlying genomic sequence and annotation combined with functional data, additional data from the FungiDB standard analysis pipeline and the ability to leverage orthology provides a powerful resource for in silico experimentation.
FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme' '''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms.
Combines collections of genetic variants (GVs) from GWAS and their comprehensive functional annotations, as well as disease classifications. Used to maximize utilility of GWAS data to gain biological insights through integrative, multi-dimensional functional annotation portal. In addition to all GVs annotated in NHGRI GWAS Catalog, we manually curate GVs that are marginally significant (P value < 10-3) by looking into supplementary materials of each original publication and provide extensive functional annotations for these GVs. GVs are manually classified by diseases according to Disease Ontology Lite and HPO (Human Phenotype Ontology) for easy access. Database can also conduct gene based pathway enrichment and PPI network association analysis for those diseases with sufficient variants. SOAP services are available. You may Download GWASdb SNP. (This file contains all of the significant SNP in GWASdb. In the pvalue column, 0 means this P-value is not reported in the study but it is significant SNP. In the source column, GWAS:A represents the original data in GWAS catalog, while GWAS:B is our curation data which P-value < 10-3)
Provides standardized vocabulary of phenotypic abnormalities encountered in human disease. Structured and controlled vocabulary for phenotypic features encountered in human hereditary and other disease. HPO is being developed in collaboration with members of OBO Foundry (Open Biological and Biomedical Ontologies), and logical definitions for HPO terms are being developed using PATO and a number of other ontologies including FMA, GO, ChEBI, and MPATH.
Hemorrhagic Fever Viruses (HFV) Database
Hemorrhagic Fever Viruses (HFV) Database Project
The Hemorrhagic Fever Viruses (HFV) sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide.
wFleaBase provides gene and genomic information for species of the genus Daphnia - commonly known as the water flea. It contains the genome of Daphnia pulex and other species, including bulk data files, and all gene pages, plus genomics tools including microsatellites, cDNA, Cosmid and BAC libraries, GSS and ESTs, and microarrays. It also contains maps of the Daphnia genome, and genome annotation tools. The freshwater crustacean Daphnia is a model system for ecology, evolution and the environmental sciences. The rapidly growing genomic data for this organism is stimulating interdisciplinary research to understand the complex interplay between genome structure, gene expression, individual fitness, and population-level responses to chemical contaminants and environmental change.wFleaBase includes data from all species of the genus, yet the primary species are D. pulex and D. magna, because of the broad set of genomic tools that have already been developed for these animals. A complete sequence for Daphnia pulex is now available at this site. Please observe this Data release policy. The data is a first characterization of the crustacean genome, which was made possible by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) in collaboration with the Daphnia Genomics Consortium (DGC) whose members were funded by the National Science Foundation. Category: Genomics Databases (non-vertebrate) Subcategory: Invertebrate genome databases
Los Alamos hepatitis C sequence database
The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. This central website provides annotated sequences and analysis tools that will be helpful to HCV scientists worldwide. Things you can do: * Find sequences in the database * Download sequences from the database * Retrieve data about the sequences * Analyze sequences * Work with the sequences using our tools * Download ready-made alignments The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses.
Wnt proteins form a family of highly conserved secreted signaling molecules that regulate cell-to-cell interactions during embryogenesis. Insights into the mechanisms of Wnt action have emerged from several systems: genetics in Drosophila and Caenorhabditis elegans; biochemistry in cell culture and ectopic gene expression in Xenopus embryos. Mutations in Wnt genes or Wnt pathway components lead to specific developmental defects, while various human diseases, including cancer, are caused by abnormal Wnt signaling.As currently understood, Wnt proteins bind to receptors of the Frizzled and LRP families on the cell surface. Through several cytoplasmic relay components, the signal is transduced to beta-catenin , which then enters the nucleus and forms a complex with TCF to activate transcription of Wnt target genes. Protein sequence databases, Databases of individual protein families, Metabolic and Signaling Pathways, Protein-protein interactions
ACTREC - Advanced Centre for Treatment Research and Education in Cancer
Advanced Centre for Treatment Research and Education in Cancer
The Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) is the new state-of-the-art R&D satellite of the Tata Memorial Centre (TMC), which also includes under its umbrella the Tata Memorial Hospital (TMH), the largest cancer hospital in Asia. ACTREC has the mandate to function as a national centre for treatment, research and education in cancer. TMC is an autonomous grant-in-aid institution of the Department of Atomic Energy (DAE), Government of India. It is registered under the Societies Registration Act (1860) and the Bombay Public Trust Act (1950). Its Governing Council is headed by the Chairman, Atomic Energy Commission, Government of India. ACTREC comprises of 2 arms - one for basic research and another for clinical research. The basic research building was inaugurated in March 2002 at the new site of ACTREC in Kharghar, Navi Mumbai. In August 2002, the Cancer Research Institute (CRI) shifted in toto from its Parel campus in Mumbai to serve as the basic research arm of ACTREC. The clinical research arm of ACTREC comprising of the Clinical Research Centre (CRC) has become functional from March 2005. ACTREC also has a 50-bed hospital fully equipped with state-of-the-art diagnostic and therapeutic facilities. Research investigations at CRI currently focus on molecular mechanisms responsible for causation of major human cancers relevant to India. It is envisaged that in the future, ACTREC will play a greater role in drug development and emerging therapies for treatment and prevention of cancer.
HotRegion - A Database of Cooperative Hotspots
HotRegion: A database of cooperative hot spots
HotRegion: a database of predicted hot spot clusters
Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot regions are important for the stability of protein complexes, as well as providing specificity to binding sites. HotRegion provides the hot region information of the interfaces by using predicted hot spot residues, and structural properties of these interface residues such as pair potentials of interface residues, accessible surface area (ASA) and relative ASA values of interface residues of both monomer and complex forms of proteins. Also, the 3D visualization of the interface and interactions among hot spot residues are provided. The number of interfaces in the database is 147909 and still growing.
YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses
Software providing a simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms.
Exploratory Software for Confidence Intervals
ESCI (pronounced ''esky'') is a set of interactive simulations that run under Microsoft Excel. The set of Excel files lets students explore some key concepts in statistical and quantitative reasoning, including effect sizes, confidence intervals, and meta analysis. These are key concepts in the neuroscience toolkit, but can be particularly difficult to foster in undergraduate and graduate students. With ESCI you can: * explore many Confidence Interval (CI) concepts * calculate and display CIs for your own data, for some simple designs * calculate CIs for Cohen''s standardized effect size d * explore noncentral t distributions and their role in statistical power * use CIs for simple meta-analysis, using original or standardized units * explore all these concepts via vivid interactive graphical simulations. The simulations are free, excellent, and come with detailed supporting materials. Cumming also has a printed textbook companion which is quite good. Cumming, G. (2012). Understanding The New Statistics: Effect Sizes, Confidence Intervals, and Meta-Analysis. New York: Routledge * Explains estimation, with many examples. * Designed for any discipline that uses statistical significance testing. * For advanced undergraduate and graduate students, and researchers. * Comes with free ESCI software. * May be the first evidence-based statistics textbook. * Assumes only prior completion of any intro statistics course. * See the dance of the confidence intervals, and many other intriguing things. The Excel files truly stand on their own, though, with good feedback from their use in a basic stats class for psych and neuroscience majors. Finally, if you are like me and learned the ''old school'' statistics of null-hypothesis testing, here''s a great article by Gerd Gigerenzer to kick you into the ''new school'' of confidence intervals and effect sizes. Learn the dirty secrets of null hypothesis testing: Gigerenzer G, Kraus S & Vitouch O. (2004). The null ritual: What you always wanted to know about significance testing but were afraid to ask. The Sage Handbook of Quantitative Methodology for the Social Sciences, p. 391-408: http://library.mpib-berlin.mpg.de/ft/gg/GG_Null_2004.pdf
The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets.
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria
ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community.
IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature
IDEAL - Intrinsically Disordered proteins with Extensive Annotations Literature
Intrinsically Disordered proteins with Extensive Annotations and Literature
IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature, is a collection of knowledge on experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites together with references and structural domain assignments. Protean segment One of the unique phenomena seen in IDPs is so-called the coupled folding and binding, where a short flexible segment can bind to its binding partner with forming a specific structure to act as a molecular recognition element. IDEAL explicitly annotates these regions as protean segment (ProS) when unstructured and structured information are both available in the region. Access to the data All the entries are tabulated in the list and individual entries can be retrieved by using the search tool at the upper-right corner in this page. IDEAL also provides the BLAST search, which can find homologs in IDEAL. All the information in IDEAL can be downloaded in the XML file.
Database that integrates and disseminates the data from the cloning of complete set of predicted protein-encoding ORFs of Caenorhabditis elegans. It also allows the community to search for availability and quality of cloned ORFs. So far, ORF sequence tags (OSTs) obtained for all individual clones have allowed exon structure corrections for ORFs originally predicted by the C. elegans sequencing consortium. The database contains this OST information along with data pertinent to the cloning process.
X:Map is a project for mapping between Affymetrix Exon Arrays and their corresponding genome data. It consists of a website for general visualisation of Gene/Transcript/Exon/Probeset relationships, and an R package exonmap to support statistical analysis of Exon Array experiments. Affymetrix exon arrays aim to target every known and predicted exon in the human, mouse or rat genomes, and have reporters that extend beyond protein coding regions to other areas of the transcribed genome. This combination of increased coverage and precision is important because a substantial proportion of protein coding genes are predicted to be alternatively spliced, and because many non-coding genes are known also to be of biological significance. In order to fully exploit these arrays, it is necessary to associate each reporter on the array with the features of the genome it is targeting, and to relate these to gene and genome structure. X:Map is a genome annotation database that provides this information. Data can be browsed using a novel Google-maps based interface, and analysed and further visualized through an associated BioConductor package.
Study to surveyed structures of protein-protein interfaces in PDB to carry out structural comparisons of interfaces. Structural comparisons of protein-protein interfaces.
Simulator for Neural Networks and Action Potentials
SNNAP (Simulator for Neural Networks and Action Potentials) is a tool for rapid development and simulation of realistic models of single neurons and neural networks. It includes mathematical descriptions of ion currents and intracellular second messengers and ions. In addition, you can simulate current flow in multicompartment models of neurons by using the equations describing electric coupling. SNNAP also includes mathematical descriptions of intracellular second messengers and ions, and simulate the modulation of membrane currents and synaptic transmission, , either enhancement or inhibition. Other advantages of SNNAP include: * Written in JAVA and can run on virtually any type of computer system. * Graphical user interface * Ability to simulate common experimental manipulations. * Modular organizations of input files. Agencies: NCRR, FOSR grant F49620-93-1-0272, as well as NIH grants R01-RR11626 and P01-NS38310
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. We have completed the recruitment of this population-based prostate cancer case-control study, one of the largest prostate cancer case-control study populations available so far. This study population was recruited in two phases. The inclusion and exclusion criteria were the same for the first (CAPS1) and second phase (CAPS2), except for the timeframe. In total, 3,030 cases and 1,960 controls participated in CAPS donating blood samples and answering a questionnaire during 2001-2003. In addition we have detailed clinical information on all 3,000 cases. With data generated from CAPS we have 25 published papers and 10 manuscripts since 2004. During 2006 we completed a record linkage to the Cause of Death Registry to determine the cause of death for all participants. We could conclude that 347 of the cases in CAPS had died of prostate cancer. The CAPS study has provided data to several new studies on markers on prostate cancer progression. Sample types: * EDTA whole blood * DNA Number of sample donors: 5015 (sample collection completed)
Saliva taken from participants in a study investigating the association between environmental exposures and brain tumors in children aged 7-19 years and the interaction between these risk factors and genetic polymorphisms, which may confer susceptibility to effects of exogenous agents. Sample types: * Saliva Number of sample donors: 886 (sample collection completed)
ICAP - Integrated analysis of prostate cancer
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd, 2023. The ICAP - Integrated analysis of prostate cancer study aims at identifying a set of biomarkers with high prognostic value for prostate cancer progression. These biomarkers will be used to customize treatment and to identify patients with high risk of recurrent disease. Sample types: * EDTA whole blood * DNA Number of sample donors: 505 (sample collection completed)
LIBRO-1: Individualized prediction and prevention of breast cancer
LIBRO-1: Individualized prediction prevention of breast cancer
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Libro-1 is a study with the overall aim to identify prognostic factors for breast cancer. The study comprise women in the Stockholm-Gotland region that were diagnosed with breast cancer between the years 2001-2008. Register data (tumor characteristics and treatment), lifestyle factors and blood samples have been collected from the participants.
ChiCTR - Chinese Clinical Trial Registry
National clinical trial registry by Ministry of Health of China to join World Health Organization International Clinical Trial Registration Platform (WHO ICTRP Primary Registry), and the approved Primary Registry of WHO ICTRP. It registers both Chinese and global clinical trials, receives data from Partner Registers certified by the WHO ICTRP, and submits data to the WHO ICTRP Central Repository for global search. Moreover, based upon the talent and technical platform, consisting of Chinese Evidence-based Medicine Centre of Ministry of Health of China, Virtual Research Centre of Evidence-Based Medicine of Ministry of Education of China, Chinese Cochrane Centre, UK Cochrane Centre and International Clinical Epidemiology Network Resource and Training Centre in West China Hospital, Sichuan University (INCLEN CERTC), ChiCTR is responsible for providing consultations on trial design, central randomization service, guidance on the writing of clinical trial reports and relevant training. WHO takes the lead in establishing the global clinical trial registration system, which is agreed upon by governments from all over the world. There are both ethical and scientific reasons for clinical trial registration. Trial participants expect that their contributions to biomedical knowledge will be used to improve health care for everyone. Open access to information about ongoing and completed trials meets the ethical duty to trial participants, and promotes greater trust and public confidence in clinical research. Furthermore, trial registration ensures that the results of all trials can be tracked down and should help to reduce unnecessary duplication of research through greater awareness of existing trials and results. The mission of ChiCTR is to Unite clinicians, clinical epidemiologists, biostatisticians, epidemiologists and health care managers both at home and abroad, to manage clinical trials in a strict and scientific manner, and to promote their quality in China, so as to provide reliable evidences from clinical trials for health care workers, consumers and medical policy decision makers, and also to use medical resources more effectively to provide better service for Chinese people and all human beings. Any trial performed in human beings is considered as a clinical trial, and should be registered before its implementation. All the registered clinical trials will be granted a unique registration number by WHO ICTRP.
PROCAP is a study of the importance of lifestyle and genetic factors in the progression of localized cancer of the prostate. Our study hypothesis is that the likelihood of disease recurrence of prostate cancer is modified or determined by genetic variation in the human genome and/or lifestyle factors. To be able to test our hypothesis, we are using a large, population-based cohort of men with localized prostate cancer in Sweden, recruited in 1997-2002, from which detailed clinical information and data on progression already have been collected. From this cohort, we are collecting lifestyle data and blood samples from 8,500 men. If men with progressive prostate cancer could be identified on their genetic make-up, they could be given additional therapies targeted specifically at prostate cancer progression or monitored even more frequently so that progressions could be treated even earlier. If lifestyle factors are important, these results have an impact on recommendations given to men with newly diagnosed prostate cancer. In the study, we are asking the study persons to fill in an Internet-based questionnaire focusing on diet and physical activity and we ask them to leave 2 test tubes of blood at their local urologist/health care center. The pilot study has recently been completed and evaluated and the remaining 7,500 men in the cohort will be included during 2007 and 2008. So far, we have a response rate of approximately 85% on the blood samples. The response rate for the questionnaire is approximately 80% (both in the web based and paper based versions combined). Genotyping and analysis will begin in the fall of 2008. Sample types: * EDTA whole blood * Plasma * DNA Number of sample donors: 5492 (sample collection completed)
h5vc - Managing alignment tallies using a hdf5 backend
h5vc - Scalable nucleotide tallies with HDF5
Software package that contains functions to interact with tally data from Next-Generation Sequencing (NGS) experiments that is stored in HDF5 files.
SCALE (Scandinavian lymphoma etiology) study
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The original aim of this study was to increase our understanding of the etiology of malignant lymphomas, especially in view of the increasing trend in incidence. Malignant lymphoma (including non-Hodgkin lymphoma, NHL, Hodgkin lymphoma, HL, and chronic lymphocytic leukemia, CLL) constitute a heterogeneous group of malignancies with regard to histology, molecular characteristics and clinical course. Etiological factors may also vary by lymphoma subtype. The incidence of NHL, the most common lymphoma group, has increased dramatically during the past decades in Sweden and in many other Western countries. The reasons for this increase as well as for the majority of all new cases is not well understood. Well established risk factors for lymphoma overall include hereditary and acquired disorders of strong immune dysfunction such as HIV/AIDS and organ transplantation, but they explain few new cases in the population. Approach: Population-based case-control study in Sweden and Denmark. The study includes in total 3740 patients and 3187 controls in both countries recruited during the period October 1999 to October 2002. Through a rapid case ascertainment system, the cases were identified shortly after diagnosis. The controls were randomly selected from national population registers and frequency-matched to the expected number of cases by sex and age group. Both cases and controls were interviewed by telephone based on a standardized questionnaire to obtain detailed information on potential risk factors for lymphoma such as medical history including infectious diseases, drug use and blood transfusions, socio-economic factors and life-style. Blood samples were also collected and stored as serum, plasma, DNA and live lymphocytes. In addition, written questionnaires about dietary habits or work exposures were sent out in Sweden. Tumor material from the cases was re-examined and uniformly classified according to the REAL classification. Status The data collection ended in 2002 and data analysis has been ongoing since then. We have primarily analyzed a range of environmental factors in relation risk of malignant lymphoma subgroups including sun exposure, body mass index, family history of hematopoietic cancer, allergy, autoimmune disorders and mononucleosis. We have also assessed specific genetic determinants in a subgroups of patients with follicular lymphoma and controls. Study results have so far been presented in 14 publications in peer-reviewed journals. In addition to new analyses on other environmental factors, we now also work to understand genetic susceptibility and gene-environmental interaction and risk of lymphoma. Also, prognostic studies have been initiated in collaboration with other research groups with regard to in CLL, HL and T-cell lymphoma.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. Recently it has been discovered that specific Single Nucleotide Polymorphisms (SNPs) may elevate the risk of developing prostate cancer. This study aims at investigating whether it is possible to use these SNPs in a clinical setting in order to sharpen the diagnostic tools when investigating if a man has prostate cancer. By collecting blood from men who have undergone a needle biopsy of the prostate and do a SNP analysis of their genes and compare this with the result of the biopsy and PSA result we hope to be able to develop a test that is more specific than the routine that is being used today. Sample types: * EDTA whole blood * DNA Number of sample donors: 5321 (June 2010)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 4, 2014. Tissue Biobank collects samples from different types of cancers patients prospectively. Blood samples are being sent to KI Biobank for DNA extraction and storage. Number of sample donors: 611 (June 2010)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. CEFAM: Risk factors for atherosclerosis and cardiovascular disease, a randomized controlled study among women from the Middle East and Latin America. The study aims to analyze how two different physical activity programs in overweight and sedentary immigrant women influence changes in biomarkers related to glucose- and lipid metabolism, stress related hormone production, sub clinical inflammation, chronic cyclooxygenase mediated inflammation and oxidative stress.
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. Cardiovascular disease and periodontitis are common diseases, causing considerable suffering and costs. Despite strong links between the two diseases it is unclear if periodontitis causes cardiovascular disease. The primary aims are to investigate whether periodontitis is a risk factor for the development of myocardial infarction and if periodontitis increases the risk for new cardiovascular events such as myocardial infarction, stroke and death in patients with a previous myocardial infarction. PAROKRANK is a case control study. Cases (n=1500) are patients with a first myocardial infarction and controls population derived people without cardiovascular disease(n=1500). Both groups are subjected to predefined dental examinations, analyses of a variety of risk factors and a biobank of blood and dental samples will be established. Information is collected from available registries (RIKS-HIA and SEPHIA) and study specific records.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. Software package used to simulate brain images with local growth / atrophy within a prescribed spherical region. Specifically, given an input image and its segmented image, the location of the center of the spherical region, and the radius of that sphere, it simulates new images that have tissue growth or shrinkage within that pre-specified brain region according to given rates (atrophy for rates less than one and growth for rates greater than one). The algorithm uses an iterative procedure that tries to achieve the given level of volumetric change for brain tissues within the region, by seeking a smooth deformation field, whose Jacobian determinants match the prescribed volume change rate within the region. Note that in the current software, the simulation of growth or atrophy for brain tissue requires that the input spherical region has to cover some CSF or background regions.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. Secondary prevention of ischemic heart disease in primary care, a randomized controlled intervention study. The study aims to elucidate if an early, active, group-oriented intervention at the primary care level can decrease the probability of developing a new cardiovascular event within three years, when compared to primary care according to standard protocols. The study also aims at analyzing how the intervention affects parameters as physical activity, eating habits, quality of life, blood pressure, waist measure, and smoking habits. Furthermore, changes in biochemical markers related to glucose- and lipid metabolism, stress related hormone production and sub clinic inflammatory activity as well as the presence of DNA polymorphism in the IL-6- and adiponutrin (ADPN) genes, will be investigated. Types of samples * EDTA whole blood * DNA Number of sample donors: 102 (sample collection completed)
Integrated Genomic Database of Non-Small Cell Lung Cancer
IGDB.NSCLC database is aiming to facilitate and prioritize identified lung cancer genes and microRNAs for pathological and mechanistic studies of lung tumorigenesis and for developing new strategies for clinical interventions. We integrated and curated various lung cancer genomic datasets to present # lung cancer genes with somatic mutations, experimental supports and statistic significance in association with clinicopathological features; # genomic alterations with copy number alterations (CNA) detected by high density SNP arrays, gain or loss regions detected by arrayed comparative genome hybridization (aCGH), and loss of heterozygosity (LOH) detected by microsatellite markers; # aberrant expression of genes and microRNAs detected by various microarrays. IGDB.NSCLC database provides user friendly interfaces and searching functions to display multiple layers of evidence for detecting lung cancer target genes and microRNAs, especially emphasizing on concordant alterations: # genes with altered expression located in the CNA regions; # microRNAs with altered expression located in the CNA regions; # somatic mutation genes located in the CNA regions; and # genes associated with clinicopathological features located in the CNA regions. These concordant altered genes and miRNAs should be prioritized for further basic and clinical studies.
An on-line assessment tool for cognitive strengths and weaknesses compared to the normal standards as found in the Brain Resource database. Available to clinicians and employers. The assessment takes approximately 30 minutes and the completed report is then provided within minutes to the individual''s clinician, providing detailed analysis of cognitive strengths and weaknesses., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
IndelFR - Indel Flanking Region Database
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions.
Software platform that allows researchers to easily collaborate on research and share reagents, antibodies, cell lines and more. It is designed to increase scientific collaboration across disciplines and geographical boundaries. Among the institutions now using the platform include Yale University, U of Pennsylvania, U of Chicago, Washington U, Cambridge University, University College London. The platform is licensed to select institutions. ResearchAccelerator.org allows researchers to form targeted, data driven collaborations. Researchers can search for data based on gene, disease and pathway, and they can post data which would otherwise be orphaned. The resulting collaborations, which are likely to be transdisciplinary, can greatly amplify impact and research productivity.
University of Massachusetts Amherst; Massachusetts; USA
A campus of the University of Massachusetts system, located in Pioneer Valley of Western Massachusetts.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management.
InterEvol database is designed for the analysis of co-evolution events at the interface of known structures of hetero- and homo-oligomers. The database can be search and analyzed through 3 interconnected levels of analysis: * From a Keyword or the PDB entry of a complex, you can browse: ** structural homologs for every chain in other complexes ** structural interologs for every interface ** retrieve pre-computed sequence alignments in diverse species * From 1 or 2 sequences of interacting partners: ** build 2 multiple sequence alignments with the same species ordered in each ** query the InterEvol database with alignments using profile-profile comparison method * Visualize structure vs sequence alignment at the complex interface ** A dedicated Pymol plugin is provided ** Alignment views in Pymol are interactively restricted to the residues selected at the interface
Read Codes Clinical Terms Version 3 (CTV3)
Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre
The Genome Foundation (AKA Genome Research Foundation) is a fully government accredited and registered non-profit research foundation. GRF aims to provide genome philosophy, science, and technology. GRF is a nonprofit publisher, and research and advocacy organization to promote completely free publication of knowledge with minimum restriction. Our core objectives are to: * Provide ways to overcome unnecessary barriers to immediate availability, access, and use of research * Pursue a publishing strategy that optimizes the openness, quality, and integrity of the publication process * Develop innovative approaches to the assessment, organization, and reuse of ideas and data Genome Foundation Research * Personalized Medicine * Personal Genomics * AngioGenesis drug * Bioinformatics * RNA expression * Protein structure * Human Genome Rights Projects at Genome Foundation * The Human Genome Rights * Human Genome Rights Petition * Free Personal Genome Sequencing Project * Free Personal Genome Sequencing Petition * Tiger Genome Initiative: Amur Tiger and big cat genomes * Whale Genome Project
Software based on evolutionary conservation of expression profiles, implemented in R, for identification of poor quality arrays in dataset composed of arrays from many independent experiments.
Major Intrinsic Protein superfamily Models
MIPModDB - Major Intrinsic Protein superfamily Models
This is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. The nearly completed sets of MIPs have been identified from the completed genome sequence of organisms available at NCBI. The structural models of MIP proteins were created by defined protocol. The database aims to provide key information of MIPs in particular based on sequence as well as structures. This will further help to decipher the function of uncharacterized MIPs. For each MIP entry, this database contains information about the source, gene structure, sequence features, substitutions in the conserved NPA motifs, structural model, the residues forming the selectivity filter and channel radius profile. For selected set of MIPs, it is possible to derive structure-based sequence alignment and evolutionary relationship. Sequences and structures of selected MIPs can be downloaded from MIPModDB database.
NeuroGems is a collection of neuroinformatics software modules for data and modelling in neuroscience. The emphasis is on tools for collaboration, visualisation and use of open XML standards. The project was an escience pilot project funded by the UK MRC and BBSRC and based at the Universities of Edinburgh, Newcastle and UCL running from 2002 - 2005. Software Applications available: Textensor, Axiope, NeuroML, neuroConstruct, NClamp, RatBrain, 3D Atlas, Catacomb, Protsim1, Protsim2, Neosim1, Neosim2, Growth, Marching, Voxel, Patterns.
mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. quantitative real-time PCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. This database aims to be useful to anyone investigating the role of microRNAs in shaping plant development, organ formation and response to different biotic and abiotic stresses. To start exploring the database just press the "Browse Atlas" button or search for a particular microRNA record by typing at least two numbers from its ID in the window.
Atlantic Canada Conservation Data Centre
Comprehensive lists of plant and animal species, with a rarity rank and legal status for each. It has has over 635,000 geo-located records of species occurrences and over 40,000 records of extremely rare to uncommon species in the Atlantic region, including New Brunswick, Nova Scotia, Prince Edward Island, Newfoundland, and Labrador. The Atlantic CDC also maintains biological and other types of data in a variety of linked databases. The CDC welcomes inquiries from those who would like to contribute data about plant or animal species at risk or rare communities in Atlantic Canada. Its mission is to assemble and provide objective and understandable data and expertise about species and ecological communities of conservation concern, including those at risk, and undertake field biological inventories to support decision-making, research, and education in Atlantic Canada. The Atlantic CDC develops species location data, known as element occurrence records. Occurrence precision (accuracy) ranges from quite precise (within meters) to less precise (within counties) but most commonly it is within 1 5 km. Element occurrence (EO) refers to one or more locations considered important to the continued existence of a species or ecological community. For species, over 30 types of data: taxonomy, biology, etc. are typically examined when identifying EOs. An EO is generally the habitat occupied by a local population. However, occurrence varies among species and some species have more than one type of occurrence (e.g., breeding and winter occurrences). Breeding colonies, breeding ponds, denning sites, and hibernacula are general examples of different types of animal EOs. For an ecological community, an EO may be the area containing a patch of that community type.
The Foundation for Polish Science (FNP), formed in 1991, is an independent, self-financing, non-profit, non-governmental organization, with a mission of supporting science in Poland. It is the largest source of science funding in Poland outside the state budget. The main objectives of FNP are: * to support excellent scientists and research teams, * to facilitate technology transfer, * to support various investment initiatives serving science in Poland. The Foundation realizes these objectives by: * awarding individual prizes and scholarships to scientists, * awarding grants for the modernization of scientific facilities and the protection of scientific collections, * grants for the transfer of scientific achievements to industry, * otherwise supporting important undertakings in the service of science (e.g. through conferences and publishing programs). The Foundation also plays an increasingly active role in supporting international scientific cooperation, taking actions to facilitate the exchange of scientific ideas, and increasing the scientific independence of the younger generation of scientists.
2D mouse brain atlas of high quality coronal Nissl- and myelin-stained sections with labels, 3D images of hippocampal formation and limited other brain structures. The data for this digital atlas are based on the Atlas of the Mouse Brain and Spinal Cord, authored by Richard L. Sidman, Jay. B. Angevine and Elizabeth Taber Pierce, published as a hard cover book by Harvard University Press in 1971 and currently out of print. C57BL/6J strain adult specimens were used in creating the atlas.
MMMDB - Mouse Multiple tissue Metabolome DataBase
Mouse Multiple tissue Metabolome DataBase
MMMDB, Mouse Multiple tissue Metabolome DataBase, is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided.
MOPED - Model Organism Protein Expression Database
Multi-Omics Profiling Expression Database
An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions.
Software application for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program. (entry from Genetic Analysis Software)
University of Nebraska Medical Center Pharmacology
University of Nebraska College of Medicine; Department of Pharmacology and Experimental Neuroscience
UNMC Department of Pharmacology and Experimental Neuroscience
There are over 120 faculty, postdoctoral fellows, graduate students and support staff collaborate in state-of-the-art research facilities on the University of Nebraska Medical Center campus. The Department of Pharmacology and Experimental Neuroscience is rapidly growing, not only in terms of facilities, personnel and research support, but in terms of national and international reputation as well. The department offers graduate education in pharmacology and neurosciences, and a summer undergraduate research program. Pharmacology continues to be among the most dynamic of the biomedical sciences. Neuroscience research has been a major emphasis of the Department of Pharmacology at UNMC from its earliest days. This has been expanded with the 2004 merger of UNMC''s internationally recognized Center for Neurovirology and Neurodegenerative Disorders (CNND) into the Department of Pharmacology and Experimental Neuroscience.
A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs.
A database housing EST information from nine mollusc species, including Lymnaea stagnalis, the pond snail. Co-curated with Angus davison of Nottingham University.
NEMBASE4 - Nematode Transcriptome Analyses
NEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets.
As part of our effort in PhyloGenomics, we have developed the PartiGene ARTHROPODA Database. In these databases, we have analyzed the EST datasets for sixty different arthropod species. To aid searching we have split the interface between four class-based views: Chelicerata, Hexapoda, Crustacea, Myriapoda. Amongst other analyses, we have included Alfried Vogler's lab's PartiGene analysis of ~30 different arthropod species ESTs. A separate access point for that dataset is also available.
This database presents a PartiGene analysis of the Bombus terrestris worker caste normalised Sanger ESTs produced by Sadd et al.
Newt-omics is a database, which enables researchers to locate, retrieve and store data sets dedicated to the molecular characterization of newts. Newt-omics is a transcript-centered database, based on an Expressed Sequence Tag (EST) data set from the newt, covering ~50,000 Sanger sequenced transcripts and a set of high-density microarray data, generated from regenerating hearts. Newt-omics also contains a large set of peptides identified by mass spectrometry, which was used to validate 13,810 ESTs as true protein coding. Newt-omics is open to implement additional high-throughput data sets without changing the database structure. Via a user-friendly interface Newt-omics allows access to a huge set of molecular data without the need for prior bioinformatical expertise. The newt Notopthalmus viridescens is the master of regeneration. This organism is known for more than 200 years for its exceptional regenerative capabilities. Newts can completely replace lost appendages like limb and tail, lens and retina and parts of the central nervous system. Moreover, after cardiac injury newts can rebuild the functional myocardium with no scar formation. To date only very limited information from public databases is available. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive annotations, expression data and experimentally verified peptide sequences with yet no homology to other publicly available gene sequences. The goal is to obtain a detailed understanding of the molecular processes underlying tissue regeneration in the newt, that may lead to the development of approaches, efficiently stimulating regenerative pathways in mammalians. * Number of contigs: 26594 * Number of est in contigs: 48537 * Number of transcripts with verified peptide: 5291 * Number of peptides: 15169
University of New Mexico; New Mexico; USA
Public research university in Albuquerque, New Mexico. Founded in 1889, UNM offers bachelor's, master's, doctoral, and professional degree programs.
ProQuest Dissertation Publishing has been publishing dissertations and theses since 1938. In that time, we have published over 2 million graduate works from graduate schools around the world. We have over 700 active university publishing partners, and publish more than 70,000 new graduate works each year. In addition to publishing, we provide access to graduate works for thousands of libraries around the world. Based on your interests, you should find the information you need below: * Authors - Information for authors on why and how to publish their graduate work with us. * Grad Schools & Libraries - Learn about the benefits of publishing, and why to submit online. * Researchers - We can help you find the dissertation or thesis you need.
Yeast Search for Transcriptional Regulators And Consensus Tracking
A curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references. It also includes the description of 326 specific DNA binding sites shared among 113 characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains a total of 7130 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA algorithm. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database.
This database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. It contains a complete, curated list of yeast genes encoding mitoproteins. The ORF name for each mitoprotein is linked to a page presenting a summary of the Baysian prior-based profile for conserved segments of that protein and statistics describing profile quality. The page also contains a list of homologs identified by the profile that span the widest possible taxonomic breadth. A multi-domain diagram at the bottom of the page displays the relationships between the conserved segments of different homologs and shows any additional sequence domains. Clicking on these initiates BLAST searches against the database of all fully sequenced genomes. A clickable button accesses a full multiple alignment of the profile-matched segments for the homolog set. Phylogenetic trees based on these alignments can also be displayed by clicking appropriate buttons (See How to use YMPD). A complete list of the known mitoproteins classified by functional category has links to the pages for individual mitoproteins in each category
NRG-CING presents a complete validation report for all 9,000+ wwPDB NMR entries including remediated experimental data such as chemical shifts from BMRB and restraints from NRG . These CING reports are compiled from internal analyses and those by CCPN, DSSP, PROCHECK-NMR/Aqua, ShiftX, Talos+, Vasco, Wattos, and WHAT_CHECK. The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. (See website for more information on CING.) In case the underlying experimental data is available, these have been cleaned up and made syntactically and semantically correct and homogeneous. For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available.
OGEE - Online GEne Essentiality database
Online GEne Essentiality database containing genes that were tested experimentally for essentiality and their features; it also provides a set of tools to systematically explore and analyze these data. The main purpose of this project is to better understand gene essentiality by facilitating the comparisons of the differences and similarities between essential and non-essential genes. This is achieved by collecting not only experimentally tested essential and non-essential genes, but also associated gene features such as expression profiles, duplication status, conservation across species, evolutionary origins and involvement in embryonic development. We focus on large-scale experiments and complement our data with text-mining results. Genes are organized into data sets according to their sources. Genes with variable essentiality status across data sets are tagged as conditionally essential, highlighting the complex interplay between gene functions and environments. Linked tools allow the user to compare gene essentiality among different gene groups, or compare features of essential genes to non-essential genes, and visualize the results. Why is it different from existing databases? * we included both essential and non-essential genes so that we could better understand the gene essentiality by comparing the similarities and differences between the two gene sets; * we compiled a list of features for each gene, including whether they are duplicates or involved in development, the number of other homologous genes in the same genome, as well as their earliest expression stages during development. These features are keys to understand the essentiality of genes; * we also provide a set of tools to explore our data and visualize the results. For example, users can simply divide genes into two groups according to whether they are duplicates, calculate the proportion of essential genes (PE%) in each group and then visualize the results in a bar plot; or they can classify genes into multiple groups according to their earliest expression stages during evolution, compare the essentiality of genes that were expressed earlier with those were latter, and plot the results in a line chart.
The Foundation is dedicated to advancing environmental conservation, scientific research, and patient care, as well as helping to improve quality of life in the San Francisco Bay Area--Gordon and Betty Moore''s home for more than 70 years. The Foundation is devoted to the inspirational vision articulated by our founders: creating positive outcomes for future generations. This vision guides our mission: to achieve significant, lasting and measurable results in environmental conservation, science, patient care, and the San Francisco Bay Area. A set of core valuesimpact, integrity, disciplined approach, and collaborationdirects our work. The Foundation carries out its work through the following frameworks: * Programs. The enduring management unit designed to achieve transformational change in a selected field of interest through a portfolio of integrated interventions. * Initiatives. Initiatives are built around well-developed strategies for concentrated investments, focused on the long-term and achieving significant impact. Initiatives are characterized by a portfolio approach to grantmaking, and other engagements of the Foundation, to pursue ambitious, large-scale outcomes. * Program grants. The Foundation devotes some of its grantmaking to experimentation, focused innovation, and agile response to time-sensitive, high-impact opportunities in its areas of focus. Across all initiatives and program grants, the Foundation''s grantees and partners seek to make positive changes in the world. The Foundation''s headquarters are in Palo Alto, in a building renovated with an emphasis on the environment and sustainability.
ZiFDB is a database of zinc finger arrays and zinc finger proteins organized for use by molecular biologists. ZiFDB organizes information on both individual zinc finger modules and engineered ZFAs. There are currently four sets of zinc finger modules available: 1) Sangamo BioScience researchers have identified fingers recognizing all 5''-GNN-3'' and a few of 5''-ANN-3'', 5''-CNN-3'' and 5''-TNN-3'' triplets using phage display, targeted mutagenesis and SELECT methods (Liu et al., 2002); 2) the Barbas group constructed another set of models, which recognize all 5''-GNN-3'', most 5''-ANN-3'', 5''-CNN-3'' and a few 5''-TNN-3'' triplets (Dreier et al., 2001; Dreier et al., 2005; Dreier et al., 2000;); 3) Toolgen, Inc. isolated a set of naturally-occurring zinc finger modules from human transcription factors (Bae et al., 2003); 4) the Joung lab has made a large number of ZFAs by OPEN, and the constituent zinc fingers are included in the database. For the engineered ZFAs, we have collected information on 3-finger ZFAs, since this is the architecture advocated by the Zinc Finger Consortium (http://www.zincfingers.org), a group of academic laboratories dedicated to the development of improved methods to engineer zinc finger proteins. Currently, all ZFAs in ZiFDB are described in the published literature. In the future, unpublished ZFAs will also be included. It is hoped that the information in this database will help molecular biologists develop zinc finger reagents that meet their needs for genome modification. Further, we hope the analysis of the collected information will aid in improving modular design.
nature.com blogs is the new home for blogs written by Nature Publishing Group editors, staff and occasional guest bloggers. If you''re looking for the nature.com blogs catalogue of science blogs, this has been temporarily taken offline. In the meantime, the data in the catalogue is still accessible via the blogs API. If you''d like to submit your blog to the catalogue or suggest someone else''s, please email blogs (at) nature.com All nature.com blogs * Nature News Blog * Of Schemes and Memes Blog * Spoonful of Medicine * The Sceptical Chymist * Nature Jobs Blog * Trade Secrets * Stepwise * Soapbox Science * London Blog * Boston Blog * New York Blog * House of Wisdom * Indigenus * Methagora * Action Potential * Free Association * The Seven Stones Archived blogs * Climate Feedback * In The Field * Inherently Responsive * Nascent * Nature''s Journal Club * Nautilus * Peer-to-Peer * The Niche
Videos from the National Center for Biotechnology Information including presentations and tutorials about NCBI biomolecular and biomedical literature databases and tools.
A free, open source authoring and publishing platform that is designed to make it easy for authors to write long-form, born-digital scholarship online. Scalar enables users to assemble media from multiple sources and juxtapose them with their own writing in a variety of ways, with minimal technical expertise required. This semantic web authoring tool brings a considered balance between standardization and structural flexibility to all kinds of material including a built-in reading interface as well as an API that enables Scalar content to be used to drive custom-designed applications. Scalar also gives authors tools to structure essay- and book-length works in ways that take advantage of the unique capabilities of digital writing, including nested, recursive, and non-linear formats. The platform also supports collaborative authoring and reader commentary.
Randomized Axelerated Maximum Likelihood
Software program for phylogenetic analyses of large datasets under maximum likelihood.
International Standard Randomised Controlled Trial Number Registry
International Standard Randomized Controlled Trial Number Register
A primary clinical trial registry which houses proposed, ongoing, and completed clinical research studies. An ISRCTN is a simple numeric system for the unique identification of randomized controlled trials worldwide. The registry provides content validation and curation and the unique identification number necessary for publication. Submitted studies range from cancer to urological diseases.
The Hereditary Disease Foundation (HDF) aims to cure genetic illness by supporting basic biomedical research. The HDF was started by Dr. Milton Wexler in 1968 when his wife was diagnosed with Huntington''s disease (HD). The Foundation uses a variety of strategies - workshops, grants, fellowships, and targeted research contracts - to solve the mysteries of genetic disease and develop new treatments and cures. Huntington''s disease is a fatal, dominantly inherited, genetic, neurological disorder causing involuntary movements, severe emotional disturbance and progressive cognitive loss over ten to twenty years. Each child of an affected parent has a 50% risk of inheriting HD, usually in the third or fourth decade of life, though children as young as two years and adults in their eighties may also develop symptoms. The Hereditary Disease Foundation uses Huntington''s disease as a model for hereditary disease research because it is triggered by a mutation of one single gene. Progress toward treatment or a cure could be instrumental in finding ways to treat other illnesses with more complex genetics, including Parkinson''s, Alzheimer''s, Lou Gehrig''s disease (ALS), depression, schizophrenia, and cancer. The Hereditary Disease Foundation has given over $50 million to support pioneering research in genetics, gene therapy, molecular and cell biology, cell survival and death, animal models, neurophysiology, neuropharmacology and other areas relevant to understanding inherited diseases. * Milton Wexler Workshop Program: A centerpiece of the Foundation is the interdisciplinary Workshop Program which sponsors Workshops held many times during the year. Milton Wexler began the Program to bring scientists together from different academic disciplines to brainstorm - without prepared lectures or slides - and explore new directions for research. They often share unpublished data. * Funding Opportunities ** The Basic Research Grants Program supports projects that contribute to identifying and understanding the fundamental defects in Huntington''s disease and related disorders. ** The John J. Wasmuth Postdoctoral Fellowships are named in honor of the late John Jacob Wasmuth, an essential member of the Huntington''s Disease Collaborative Research Group. Our hope is that those granted fellowships bearing his name will seek John''s level of imagination, rigor, creativity and spirit. ** The Lieberman Award is presented annually to a worthy scientist, thanks to the generosity of Harry Lieberman, a trustee of the Hereditary Disease Foundation. ** The Milton Wexler Postdoctoral Fellowship Award is named after the founder of the Hereditary Disease Foundation. The Hereditary Disease Foundation restricts this annual award to research highly relevant to curing Huntington''s disease. * Giving to the Hereditary Disease Foundation - Donations are accepted by check, credit card, etc.
MIALAB, headed by Dr. Vince Calhoun, focuses on developing and optimizing methods and software for quantitative analysis of structure and function in medical images with particular focus on the study of psychiatric illness. We work with many types of data, including functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI), electroencephalography (EEG), structural imaging and genetic data. Much of our time is spent working on new methods for flexible analysis of brain imaging data. The use of data driven approaches is very useful for extracting potentially unpredictable patterns within these data. However such methods can be further improved by incorporating additional prior information as constraints, in order to benefit from what we know. To this end, we draw heavily from the areas of image processing, adaptive signal processing, estimation theory, neural networks, statistical signal processing, and pattern recognition.
Software toolbox to facilitate quick and easy import, visualization and measurement for Event Related Potential (ERP) data. The toolbox can open and visualise ERP averaged data (Neuroscan, ascii formats), 2D/3D electrode coordinates and 3D cerebral tissue tesselations (meshes). All the features can be explored quickly and easily using the example data provided in the toolbox. The GUI interface is simple and intuitive.
XSEDE - Extreme Science and Engineering Discovery Environment
Extreme Science and Engineering Discovery Environment
XSEDE - Extreme Science Engineering Discovery Environment
XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services things like supercomputers, collections of data and new tools to improve our planet. XSEDE resources may be broadly categorized as follows: High Performance Computing, High Throughput Computing, Visualization, Storage, and Data Services. Many resources provide overlapping functionality across categories. Scientists, engineers, social scientists, and humanists around the world - many of them at colleges and universities - use advanced digital resources and services every day. Things like supercomputers, collections of data, and new tools are critical to the success of those researchers, who use them to make our lives healthier, safer, and better. XSEDE integrates these resources and services, makes them easier to use, and helps more people use them. XSEDE supports 16 supercomputers and high-end visualization and data analysis resources across the country. Digital services, meanwhile, provide users with seamless integration to NSF''s high-performance computing and data resources. XSEDE''s integrated, comprehensive suite of advanced digital services will federate with other high-end facilities and with campus-based resources, serving as the foundation for a national cyberinfrastructure ecosystem. Common authentication and trust mechanisms, global namespace and filesystems, remote job submission and monitoring, and file transfer services are examples of XSEDE''s advanced digital services. XSEDE''s standards-based architecture allows open development for future digital services and enhancements. XSEDE also provides the expertise to ensure that researchers can make the most of the supercomputers and tools.
The John Templeton Foundation serves as a philanthropic catalyst for discoveries relating to the Big Questions of human purpose and ultimate reality. We support research on subjects ranging from complexity, evolution, and infinity to creativity, forgiveness, love, and free will. We encourage civil, informed dialogue among scientists, philosophers, and theologians and between such experts and the public at large, for the purposes of definitional clarity and new insights. Our vision is derived from the late Sir John Templeton''s optimism about the possibility of acquiring new spiritual information and from his commitment to rigorous scientific research and related scholarship. The Foundation''s motto, How little we know, how eager to learn, exemplifies our support for open-minded inquiry and our hope for advancing human progress through breakthrough discoveries. Our Core Funding Areas cover the full range of the Foundation''s activities and grantmaking. Science and the Big Questions is the largest of these Core Funding Areas and is further divided into several subfields. The descriptions and illustrative grants attached to the Core Funding Areas are not meant to be exhaustive, but they should give potential applicants a general understanding of the sorts of activities that the Foundation does and does not fund. Core Funding Areas: * Science and the Big Questions ** Mathematical and Physical Sciences ** Life Sciences ** Human Sciences ** Philosophy and Theology ** Science in Dialogue * Character Development * Freedom and Free Enterprise * Exceptional Cognitive Talent and Genius * Genetics
Service that helps users navigate the research journey, connecting people and information from dissertations to governmental and cultural archives to news, in all its forms. Its role is essential to libraries and other organizations whose missions depend on the delivery of complete, trustworthy information. ProQuest''s massive information pool, built through partnerships with content creators, is navigated through technological innovations that enable users to quickly find just the right information. The ProQuest platform moves beyond navigation to empower researchers to use, create, and share contentaccelerating research productivity. The Summon web-scale discovery service is a boon to academic libraries worldwide. ProQuest expanded into corporate and government markets, with the ProQuest Dialog service and acquiring Congressional Information Services and University Publications of America. It acquired ebrary, expanding ProQuest''s content base to include e-books and adding to the technology expertise resident across the enterprise, which also includes such units as Serials Solutions, RefWorks-COS, and Bowker.
University of New South Wales; New South Wales; Australia
An ontology for sequence annotations and how to preserve them with reference sequences.
Web Platform Docs is a new community-driven site that aims to become a comprehensive and authoritative source for web developer documentation. Anyone can contribute and each person who does makes us stronger. Together we can continue to drive innovation on the Web to serve the greater good. WebPlatform project, supported by various stewards between 2012 and 2015, has been discontinued. Static archived version of github is available.
This Week in Virology (TWiV) is a podcast - or netcast, as some prefer to call them, since you don''t need an iPod to listen - about viruses - the kind that make you sick. Professors Vincent Racaniello, Dickson Despommier, Rich Condit and science writer Alan Dove and guests deconstruct viruses, how they cause illness, and how you can prevent infections. It was begun in September 2008 by Vincent Racaniello and Dick Despommier, two science Professors at Columbia University Medical Center. Their goal was to have an informal yet informative conversation about viruses which would be accessible to everyone, no matter what their science background. We wanted to eventually bring other virologists into the conversation, to make it more varied and interesting. Alan Dove, a science writer, joined us late in 2008; Rich Condit, a poxvirologist, joined in 2009, and Kathy Spindler, an adenovirologist, joined in 2012. We''ve had quite a few guests on the show and we''re always trying to get more. Transcripts A few readers have been kind enough to produce transcripts for several TWiV episodes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. This Week in Microbiology (TWiM) is a new podcast about unseen life on Earth hosted by Vincent Racaniello and friends. Following in the path of his successful shows ''This Week in Virology'' (TWiV) and ''This Week in Parasitism'' (TWiP), Racaniello and guests produce an informal yet informative conversation about microbes which is accessible to everyone, no matter what their science background. As a science Professor at Columbia University, Racaniello has spent his academic career directing a research laboratory focused on viruses. His enthusiasm for teaching inspired him to reach beyond the classroom using new media. TWiM is for everyone who wants to learn about the science of microbiology in a casual way. While there are no exams or pop quizzes, TWiM does encourage interaction with the audience via comments on specific episodes, via email and voicemail at 908-312-0760. Listeners can also use MicrobeWorld to suggest topics for the show by submitting articles or papers to the site and tagging them with TWiM. Each week Racaniello will view the tagged content and select items for discussion. Co-hosts on TWiM include Ronald Atlas, Jo Handelsman, Margaret McFall-Ngai, Stanley Maloy, Elio Schaechter, and Michael Schmidt. Music used on TWiM is composed and performed by Ronald Jenkees and used with permission.
PyMVPA - Multivariate Pattern Analysis in Python
A Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run. Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. This Python-based, cross-platform, open-source software toolbox software toolbox for the application of classifier-based analysis techniques to fMRI datasets makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages.
University of North Carolina at Chapel Hill; North Carolina; USA
University of North Carolina at Chapel Hill
The University of North Carolina at Chapel Hill, also known as UNC-Chapel Hill, Chapel Hill, North Carolina, or simply Carolina is a public research university in Chapel Hill, North Carolina. It is the flagship of the 17 campuses of the University of North Carolina system.
CMHD - Centre for Modeling Human Disease
Multidisciplinary collaboration undertaking genome-wide mutagenesis to functionally annotate the mouse genome and develop new mouse models relevant to human disease. To achieve these goals two major research platforms are carried out: Gene trapping and ENU Mutagenesis. A new challenge is faced in the post-genomic era - the assignment of biological function to the human genome sequence and projecting that assignment into understanding of human health and disease. The Centre for Modeling Human Disease (CMHD) was established to take part in the worldwide initiative to address these challenges. At the CMHD, two fundamentally different, yet complimentary methods are employed to generate mutant mouse models of human disease: chemical mutagenesis by ethylnitrosourea (ENU), and gene trap insertional mutagenesis. The Centre contributes its resources to similar international efforts and is the first of its kind in Canada. The Center is also actively developing other mutagenic strategies including pharmacologic and genetic modifier screens to dissect disease pathways, and novel mutagenic techniques using embryonic stem cells. ENU Database * Statistics for Mouse Physiological Parameters * Search Mutants by Phenotype * Search Mutants by Heritability Gene Trap Database * Search by in vitro Expression Pattern * Search by Gene Trap Sequences CMHD Members Only (must register and login) * Search Mouse Line * Histopathology * Sperm, Tissue, Slide Archiving * CMHD Database Download CMHD Services * Phenotyping * Genetic Mapping * Pathology * Pathology Service Charges
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 27,2023.Interactive multimedia educational outreach resource promoting awareness and understanding of key microbiological issues to adult and youth audiences, and showcases the significance of microbes in our lives. It is an online community for sharing the latest news, blog posts, videos, podcasts, images, research and resources related to microbiology and the life sciences. Join today and help contribute to the fastest growing networks for science information on the web. The anthrax attacks of 2001 and the ensuing focus on bioterrorism, the potential of viral and bacterial infections for victims of Hurricane Katrina, the emergence of avian flu, and the public''s growing interest in alternative fuel sources have thrust microbes into unprecedented prominence in the headlines. MicrobeWorld informs the public about how science works. The various outreach methods feature the process of discovery, historical changes in research, and a variety of scientific careers in industry, academia, and government. One of the first MicrobeWorld Radio podcasts explained how microbes enter the initially sterile bodies of infants just hours after birth, establishing the microbial communities that stay with them for life. Other topics have included why the overuse of antibiotics is a growing problem, how microbes are key in the making of chocolate, and how microbiologists are on the front line in the war against infectious diseases that threaten human and animal health. Objectives * Leverage emerging communications technologies to promote the science of microbiology to the public and provide educational resources for all levels. * Repurpose the American Society for Microbiology''s resources for the wired generation. * Increase public understanding and appreciation of the vital role microbes play on our planet. * Use new technology to promote ASM''s resources to students, educators and other potential members of the Society. * Establish ASM as a leader in online science content.
The W. M. Keck Foundation was established in 1954 in Los Angeles by William Myron Keck, founder of The Superior Oil Company. Our Foundation is one of the nation''s largest philanthropic organizations, with assets of more than $1billion. Mr. Keck envisioned a philanthropic institution that would provide far-reaching benefits for humanity. By taking a bold, creative approach to grantmaking, he created a legacy that the Foundation proudly upholds today. In recent years, the Foundation has focused on Science and Engineering Research; Medical Research; Undergraduate Education; and Southern California. Each of our grant programs invests in people and programs that are making a difference in the quality of life, now and for the future. Supporting pioneering discoveries in science, engineering and medical research has been our mandate for a half-century. By funding the work of leading researchers, the establishment of unique laboratories and research centers, and the purchase of sophisticated instruments, we are laying the groundwork for breakthrough discoveries and new technologies that will save lives, provide innovative solutions to complex problems and add immeasurably to our understanding of life on Earth and our place in the universe. We believe that a high-quality, well-rounded college education is vital for tomorrow''s leaders. The Foundation''s undergraduate education program promotes inventive approaches to instruction and effective involvement of students in research at colleges across the nation. Our support of Southern California-based organizations enriching the lives of our region''s residents has expanded and deepened over the years. We place a special emphasis on children, youth and their families, with the goal of providing safe, healthy, supportive environments that prepare children to succeed in school and in life.
Brain Atlas Database of Japanese Monkey for WWW
Atlas of magnetic resonance images and histological sections of a Japanese monkey brain, Rhesus monkey and human. The Brain Explorer allows for display, magnification, and comparison these images. Other formats include a collection of .jpg images, Quicktime VR (allow user to zoom in), and EmonV, a voxel viewer for MacOS X.
RIO-DB (Research Information Database) is a multimedia one concerning various research information which is developed and accumulated through many AIST R&D projects. RIO-DB project aims to contribute to the creation and promotion of new businesses from academic society to industrial community by spreading the research information via internet. This is a portal to many database resources in the following categories: * Standard * Chemistry * Earth sciences * Energy * Biology * Material * Information Technology * Safety
A topical portal and providers of brain injury rehabilitation services. Resources * Pharmacology Guide * Glossary of Brain Injury Terms * Brain Injury Research Articles * Common Brain Injury Assessment Tools / Rating Scale * Certified Continuing Education Courses * Links to Resource Sites
Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software.
VIRsiRNAdb - Database of Viral siRNA / shRNA
VIRsiRNAdb is a curated database of experimentally validated viral siRNA / shRNA targeting diverse genes of 42 important human viruses including influenza, SARS and Hepatitis viruses. Submissions are welcome. Currently, the database provides detailed experimental information of 1358 siRNA/shRNA which includes siRNA sequence, virus subtype, target gene, GenBank accession, design algorithm, cell type, test object, test method and efficacy (mostly quantitative efficacies). Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. The database has facilities like search, advance search (using Boolean operators AND, OR) browsing (with data sorting option), internal linking and external linking to other databases (Pubmed, Genbank, ICTV). Additionally useful siRNA analysis tools are also provided e.g. siTarAlign for aligning the siRNA sequence with reference viral genomes or user defined sequences. virsiRNAdb would prove useful for RNAi researchers especially in siRNA based antiviral therapeutics development.
POcket Similarity Search Using Multiple-Sketches
Pocket Similarity Search using Multiple-Sketches (PoSSuM)
PoSSuM - POcket Similarity Search Using Multiple-Sketches
Relational database of all the discovered similar pairs in a huge number of protein-ligand binding sites with annotations of various types (e.g., CATH, SCOP, EC number, Gene ontology). They used a tremendously fast algorithm called SketchSort that enables the enumeration of similar pairs in a huge number of protein-ligand binding sites. They conducted all-pair similarity searches for 3.4 million known and potential binding sites using the proposed method and discovered over 24 million similar pairs of binding sites. PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures. Basically, the users can search similar binding pockets using two search modes: # Search K is useful for finding similar binding sites for a known ligand-binding site. Post a known ligand-binding site (a pair of PDB ID and HET code) in the PDB, and PoSSuM will search similar sites for the query site. # Search P is useful for predicting ligands that potentially bind to a structure of interest. Post a known protein structure (PDB ID) in the PDB, and PoSSuM will search similar known-ligand binding sites for the query structure.
A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model.
The Prokaryotic Operon DataBase (ProOpDB) constitutes one of the most precise and complete repository of operon predictions in our days. Using our novel and highly accurate operon algorithm, we have predicted the operon structures of more than 1,200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved including: i) organism name, ii) metabolic pathways, as defined by the KEGG database, iii) gene orthology, as defined by the COG database, iv) conserved protein motifs, as defined by the Pfam database, v) reference gene, vi) reference operon, among others. In order to limit the operon output to non-redundant organisms, ProOpDB offers an efficient protocol to select the more representative organisms based on a precompiled phylogenetic distances matrix. In addition, the ProOpDB operon predictions are used directly as the input data of our Gene Context Tool (GeConT) to visualize their genomic context and retrieve the sequence of their corresponding 5�� regulatory regions, as well as the nucleotide or amino acid sequences of their genes. The prediction algorithm The algorithm is a multilayer perceptron neural network (MLP) classifier, that used as input the intergenic distances of contiguous genes and the functional relationship scores of the STRING database between the different groups of orthologous proteins, as defined in the COG database. Nevertheless, the operon prediction of our method is not restricted to only those genes with a COG assignation, since we successfully defined new groups of orthologous genes and obtained, by extrapolation, a set of equivalent STRING-like scores based on conserved gene pairs on different genomes. Since the STRING functional relationships scores are determined in an un-bias manner and efficiently integrates a large amount of information coming from different sources and kind of evidences, the prediction made by our MLP are considerably less influenced by the bias imposed in the training procedure using one specific organism.
ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization--from the genome to the ecosystem--embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light-dark cycle reveals the choreography of gene expression in cells in a ''natural'' state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included.
ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats' corresponding codons.
University of Nice Sophia Antipolis; Nice; France
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19, 2021.University of Nice Sophia Antipolis was university located in Nice, France and neighboring areas. It was founded in 1965 and was organized in eight faculties, two autonomous institutes and engineering school. It was merged in 2019 into the University of C�te d'Azur.
ProtChemSI - the database of protein-chemical structural interactions
ProtChemSI: protein-chemical interaction database
Protein-Chemical Structural Interactions
The database of protein-chemical structural interactions includes all existing 3D structures of complexes of proteins with low molecular weight ligands. When one considers the proteins and chemical vertices of a graph, all these interactions form a network. Biological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein would bind the other. The current version includes data from the Protein Data Bank as of August 2011. The database is updated monthly.
PSCDB - Protein Structural Change DataBase
Protein Structural Change DataBase (PSCDB)
Database for protein structural change upon ligand binding that are classified into 7 classes in terms of the ligand binding sites and the location where the dominant motion occurs. # Coupled Domain motions are the domain motions induced upon ligand binding. # Independent Domain motions are the observable domain motions regardless of ligand binding. # Coupled Local motions are the local motions induced upon ligand binding. # Independent Local motions are the observable local motions regardless of ligand binding. # Burying ligand motions are imaginable motions required to hold ligand protein-inside. # No significant motions mean just nothing happen. # Other motions are motions unclassified into domain and local motions. Proteins are flexible molecules that undergo structural changes to function. The Protein Data Bank contains multiple entries for identical proteins determined under different conditions, e.g. with and without a ligand molecule, which provides important information for understanding the structural changes related to protein functions. We gathered 839 protein structural pairs of ligand-free and ligand-bound states from monomeric or homo-dimeric proteins, and constructed the Protein Structural Change DataBase (PSCDB). In the database, we focused on whether the motions were coupled with ligand binding. As a result, the protein structural changes were classified into seven classes, i.e. coupled domain motion (59 structural changes), independent domain motion (70), coupled local motion (125), independent local motion (135), burying ligand motion (104), no significant motion (311) and other type motion (35). PSCDB provides lists of each class. On each entry page, users can view detailed information about the motion, accompanied by a morphing animation of the structural changes.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database for corrected read counts and genome mapping on NCBI's Short Read Archive. The corrected count was done using RECOUNT and the mapping with LAST. We also provide information of reference genome to which we aligned the short reads. We focus on transcriptomic data, specifically TSS-Seq and RNA-Seq. Because this is the type of data for which sequence count correction is most important. Hence we do not include the genomic reads. The current version contains 2,265 entries from 45 organisms, with read lengths from 17 to 100bp. Via a searchable and browseable interface users can obtain corrected data in formats useful for transcriptomic analysis. We provide the data grouped according to the genome, type of studies and submitter in TAB , PSL and BAM format. They contain the mapping position and annotation of reads observed and corrected counts.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on 5/29/14. An Expectation Maximization error correction tool for next generation sequencing data (Solexa/Illumina). The main features of RECOUNT: * Uses quality score to estimate the correct counts, hence potentially more accurate. * It does not use reference genome. * Memory efficient. Next generation sequencing technologies enable rapid, large-scale production of sequence data sets. Unfortunately these technologies also have a non-neglible sequencing error rate, which biases their outputs by introducing false reads and reducing the quantity of the real reads. They have applied RECOUNT to several types of Solexa/Illumina reads from mouse embryo, 5''-end SAGE, and bacterial metagenomic reads. They found that the correction by the tool not only increases the number of mappable reads, but also makes a real difference in the biological interpretation of next generation sequencing data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
RNA Characterization of Secondary Structure Motifs
RNA Characterization of Secondary Structure Motifs (RNA CoSSMos)
RNA CoSSMos - Characterization of Secondary Structure Motifs
Znosko Lab RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database
Database to search through the nucleic acid structures from the Protein Data Bank and examine structural motifs, including (a)symmetric internal loops, bulge loops, and hairpin loops. They have compiled over 2,000 three-dimensional structures, which can now be searched using different parameters, including PDB information, experimental technique, sequence, and motif type. RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop' '''s structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is updated weekly.
Catalog of over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors (TFs). They've curated 11 literature sources, benchmarked the published position-specific scoring matrices against in-vivo TF occupancy data and TF deletion experiments, and combined the most accurate models to produce a single collection of the best performing weight matrices for Saccharomyces cerevisiae. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors. Enter a TF name to find the recommended matrix for a particular TF, or enter a nucleotide sequence to identify all TFs that could bind a particular region.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2019. Analyzing protein structure projection on exon-intron structure of corresponding gene through years led to several fundamental conclusions about structural and functional organization of the protein. According to these results we decided to map the protein functional sites. So we created the database SitEx that keep the information about this mapping and included the BLAST search and 3D similar structure search using PDB3DScan for the polypeptide encoded by one exon, participating in organizing the functional site. This will help: # to study the positions of the functional sites in exon structure; # to make the complex analysis of the protein function; # to exposure the exons that took part in exon shuffling and came from bacterial genomes; # to study the peculiarities of coding the polypeptide structures. Currently, SitEx contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms.
A tool to bridge the gap between tabular formats and linked data by transforming data tables to RDF datasets, it is able to process spreadsheets, csv files, but also other tabular formats: statistical oriented ones (PC-Axis), analysis tool formats, shapefiles (GIS) and so on. The aim is to provide means to discover and to surface the data structures hidden in tables, and to enable users to combine data over and above the limits of files and formats. By transforming data tables to RDF datasets, the information integration achieves a new dimension. Raw data transcends into a world of linked resources brimming with enrichment and entity reconciliation opportunities. Tabels is not a mere transformation tool, but it facilitates end-user exploitation of data by supplying front-end interactive mechanisms. Moreover, Tabels offers the possibility to disambiguate terms extracted from the input files against online datasets such as DBPedia, publishing and relating information from offline sources to the Linked Data cloud. Furthermore, the RDF datasets generated by Tabels can be extended or manipulated by means of declarative directives (based on the Jena rules engine and the SPARQL 1.1 interface). Tabels is more than a transformation tool and it is geared with data-sensitive front-end widgets to facilitate end users the exploitation and exploration of data: namely, chart views, faceted views, interactive charts and maps and sparql endpoint.
Regulation of Gene Expression Ontolology
An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.
Wiki investigating human genetics including information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. It is based on a wiki model in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. As the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we' '''ll all want to know more - a lot more - about the meaning of these DNA variations and SNPedia will be here to help. SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being. For more information see the Wikipedia page, http://en.wikipedia.org/wiki/SNPedia * Download URL: http://www.SNPedia.com/index.php/Bulk * Web Service URL: http://bots.SNPedia.com/api.php
THIS RESOURCE IS NO LONGER IN SERVICE. Documented October 5, 2017. Database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large. The HID can be extended to contain relevant information concerning experimental subjects, assessments of subjects, the experimental data collected, the experimental protocols, and other metadata normally included with experiments.
Original NMR (nuclear magnetic resonance) data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED) respectively as described in the references. There are 9,672,968 parsed constraints in 7159 entries. (Mar. 2013)
The UMD-BRCA1/BRCA2 databases have been set up in a joined national effort through the network of 16 diagnostic laboratories to provide up-to-date information about mutations of the BRCA1 and BRCA2 genes identified in patients with breast and/or ovarian cancer. These databases currently contain published and unpublished information about the BRCA1/BRCA2 mutations reported in French diagnostic laboratories. This database includes 28 references and 5530 mutations (1440 different mutations and 786 protein variants) The databases of BRCA1 and BRCA2 mutations were built using the Universal Mutation Database tool. For each mutation, information is provided at several levels: * at the gene level: exon and codon number, wild type and mutant codon, mutation event, mutation name and, * at the protein level: wild type and mutant amino acid, binding domain, affected domain. If you want to submit a mutation, please contact R. Lidereau., S. Caputo. or E. Rouleau.
Science 2.0 is a blog created in 2006 to modernize science communication, publishing, collaboration and public participation. In creating Science 2.0 we set out to accomplish the following: * Create a place where world-class scientists write articles and discuss issues without being filtered by size or editorial limitations, where there are no political or cultural agendas, and the audience can read great science directly from the sources and maybe learn some new things. * Create an infrastructure where actual collaboration can occur using customized tools. * Create an open publishing model. The old model of subscriptions is no longer viable, since government has taken control of academic research - taxpayers have paid for the research so they should be allowed to read it without paying. Open access, where the cost burden is shifted to scientists instead, is a good first step but Science 2.0 embraces a true open publishing model, where readers do not have to pay to read and scientists do not have to pay to publish. * Encourage increased participation in the science endeavor by those outside science. SETI (at)home, GalaxyZoo, Fold.it and other tools show the public will help if the tools are there. See The FAQ for more information written by our community moderators. * Science 2.0, Scientific Blogging and The world''s best scientists, the Internet''s smartest readers are registered trademarks of ION Publications LLC.
Curated database of experimentally supported data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent functions that cause disease. Information such as EntrezGeneID, gene genomic sequence, mutation (nucleotide substitutions, deletions and insertions), mutation location within the gene, organism, detailed description of the splicing mutation and references are also given. Users are able to submit new entries to the database. This database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, they manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference PubMed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. They standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, they give direct links of the entry to the respective position/region in the genome browser.
Michigan State University Brain Biodiversity Bank - Human Brain Atlas
MSU Brain Biodiversity Bank - Human Brain Atlas
A labeled three-dimensional atlas of the human brain created from MRI images. In conjunction are presented anatomically labeled stained sections that correspond to the three-dimensional MRI images. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies. The MRI subject was a 22-year-old adult male. Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process. The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp
The CreZOO database is the European virtual repository of Cre and other targeted conditional driver strains. CreZOO is being developed in the context of the CREATE consortium, a core of major European and international mouse database holders and research groups involved in conditional mutagenesis. Its aim is to capture and disseminate extant and new information on Cre driver strains. CreZOO also aims to contribute data to the CREATE portal for worldwide access of related information. All transgenic strains carry detailed information on the promoter, specificity (using Adult Mouse Anatomy terms and Theiler Stages) and expressed gene(s) including IDs and direct links where available. Allele details are also presented, in addition to strain, background and availability (in the form of live mice, cryopreserved embryos or sperm etc) information (including EMMA, MGI, MMRRC etc hyperlinks where available). Handling and genotyping details (in the form of documents or hyperlinks) together with all relevant publications are clearly presented with PMID(s) and direct PubMed links.
CREATE (Coordination of resources for conditional expression of mutated mouse alleles)
CREATE (Coordination of resources for conditional expression of mutated mouse alleles) project
CREATE - Coordination of resources for conditional expression of mutated mouse alleles
The CREATE consortium represents a core of major European and international mouse database holders and research groups involved in conditional mutagenesis, primarily to develop a strategy for the integration and dissemination of Cre driver strains for modelling aspects of complex human diseases in the mouse. Collectively the participants have amassed a significant number of these strains in their respective databases. Therefore one of the goals of CREATE is to provide a unified portal for worldwide access to these critical resources. The portal can either be searched through an advanced BioMart interface, by driver name, or by anatomical site of expression using Embryonic Mouse Anatomy Project (EMAP) and Mouse Anatomy (MA) ontology terms. Search results link back to the original source of the data for more detailed information and to IMSR to order mice if available. The ontology browser is particularly useful as it enables the CREATE consortium to identify cell and tissues that are not currently covered by existing lines. CREATE also aims to coordinate the production of suitable lines by the Cre generation projects described above. Through the CREATE portal, the CREATE consortium aims to develop a strategy for the production, integration and dissemination of new Cre driver strains for modelling aspects of complex human diseases in the mouse. CREATE is also developing a roadmap for harnessing emerging technologies and methods for improving Cre-mediated recombination in vivo through targeted, intensive workshops and discussion forums on the portal. This will entail review of construct design options for classical transgenic constructs (promoter/enhancer used, small size <2025 Kb) vs large transgenic constructs (BAC, P1, YAC etc.); methods used for Cre transgenic lines including random vs targeted integration, position independent expression loci, or replacement of endogenous coding sequences with Cre recombinase under the control of the endogenous locus. CREATE provides a platform for discussion of additional issues specific to inducible Cre strategies including background activity before induction, inducibility (kinetics), efficiency, and protocols used for induction of Cre recombinase activity. Additional components of the technology roadmap will be the cataloguing of other existing methodologies (rtTA, FLP, Dre) of mouse genome modification, sharing information on validated Cre mutant lines as well as identification and assessment of new methods of mutagenesis such as RNAi and other emerging technologies. Other discussion topics addressed through surveys on the CREATE portal include the characterization of Cre lines (specificity of expression/deletion; efficiency of expression/ deletion; reproducibility of deletion from animal to animal for the same floxed allele; reproducibility with different floxed alleles; timing of expression/deletion, etc.), the extent to which Cre expression changes upon backcrossing to specific genetic backgrounds through variegation and silencing; potential phenotypes caused by either integration- mediated mutagenesis or Cre ''toxicity''; and other factors affecting the specificity of Cre-mediated expression/deletion. CREATE regularly integrates common fields from the Cre-X, CreZOO and the MGI recombinase portal resources described below. The data in common consists of: * Transgene or Knock-in name. * MGI ID of allele. * Driver. * Anatomical site of expression. * Pubmed ID. * IMSR strain name and link. * Inducibility (YES/NO).
National Resource for Cell Analysis and Modeling
National Resource of Cell Analysis & Modeling (NRCAM)
National Resource of Cell Analysis and Modeling
National Resource of Cell Analysis and Modeling (NRCAM)
The National Resource for Cell Analysis and Modeling
Biomedical technology research center that develops new technologies for modeling cell biological processes. The technologies are integrated through Virtual Cell, a problem-solving environment built on a central database and disseminated as a Web application for the analysis, modeling and simulation of cell biological processes. NRCAM resides at the Center for Cell Analysis and Modeling, CCAM, and provides a vast array of laboratory equipment that can be used for obtaining experimental data needed to create and enhance Virtual Cell models. Microscopy instrumentation includes three confocal laser scanning microscopes including UV excitation, nonlinear optical microscopy utilizing a titanium sapphire pulsed laser, confocal-based fluorescence correlation spectroscopy, wide-field imaging workstation with cooled CCD and rapid excitation filter wheel, and dual-wavelength spectrofluorometer. Access to the facilities and technical staff is open to all researchers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A genome-scale method for predicting mitochondrial proteins
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution.
Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide.
Federation of International Mouse Resources
Federation of International Mouse Resources (FIMRe)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7, 2022. Federation of International Mouse Resources (FIMRe) is a collaborating group of Mouse Repository and Resource Centers worldwide whose collective goal is to archive and provide strains of mice as cryopreserved embryos and gametes, ES cell lines, and live breeding stock to the research community. Goals of the Federation of International Mouse Resources: * Coordinate repositories and resource centers to: ** archive valuable genetically defined mice and ES cell lines being created worldwide ** meet research demand for these genetically defined mice and ES cell lines * Establish consistent, highest quality animal health standards in all resource centers * Provide genetic verification and quality control for genetic background and mutations * Provide resource training to enhance user ability to utilize cryopreserved resources
Video library of curated educational videos, many of which represent collaborations between talented educators and animators nominated through the TED-Ed platform. This platform also allows users to take any useful educational video, not just TED''s, and easily create a customized lesson around the video. Users can distribute the lessons, publicly or privately, and track their impact on the world, a class, or an individual student. TED-Ed''s videos aim to capture and amplify the voices of the world''s greatest educators.
A multiplatform, highly modular image processing and visualization application which is under development by the Center for Interdisciplinary Brain Sciences Research. The goal of this project is provide a framework application for neuroimaging which facilitates the interchange of software tools developed by researchers. BrainImageJava can: * Delineate ROIs in slices along X, Y, or Z axes, with 3D feedback in the other axes. * Create and display triangular mesh surfaces from MRI volumes. * Draw Surfaces-of-Interest (SOIs) in 3D, and edit them in a planar display. * Set Talairach grid on a volume, export an AC/PC stack, and measure the values within each grid unit. This 3D image processing and analysis program for the Apple Macintosh PowerPC is based on the public domain application, NIH Image. It includes interactive procedures for 3D MRI quantification including semi-automated procedures for removing non-brain tissues from images, fuzzy segmentation of tissue compartments, global or local parcellation (based on the Talairach atlas), region-growing, etc. The last version of the software included multiplatform capability, volume visualization and advanced image analysis tools.
An Antibody supplier who also provides assay services and products.
Pathbase - European mutant mouse pathology database
Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development)
TraDES - Trajectory Directed Ensemble Sampling
With Trajectory Directed Ensemble Sampling (TraDES) create large ensembles of high-quality protein structures quickly, ranging from near-native to partially unfolded to intrinsically unfolded. TraDES is a system for directly controlling and sampling protein conformational space. TraDES has been previously used for measuring the vastness of protein conformational space and testing the hypothesis of a brute force solution to the protein folding problem. Over 10 Billion protein structures have been produced by TraDES software in previous distributed computing experiments. The package is comprised of binary executable programs and accessory programs and scripts as well as protein structure data files that map out protein conformational space in a probabilistic way. The main programs are: * trades - generates protein structures following the Trajectory Distribution (see below) * seq2trj - makes Trajectory Distributions from sequences for sampling * str2tr - makes Trajectory Distributions from 3D structures for sampling Trajectory Distributions - Controlling the Sampling of Conformational Space The concept of the trajectory distribution may be new to many protein scientists. A trajectory distribution is simply a map of available conformational space at an amino acid residue. NMR scientists are the primary users of the TraDES package.
The Toronto Centre for Phenogenomics (TCP) is an innovative, scientific collaboration between four research hospitals to operate a centralized, state-of-the-art research-enabling mouse facility. We conduct and support genetic research involving generation of mutant mice, physiological phenotyping, behavioural analysis, imaging, pathology and cryopreservation for storage and distribution. This joint project involving Mount Sinai Hospital, The Hospital for Sick Children, University Health Network and St. Michael''s Hospital pools resources and expertise to achieve excellence and economies of scale. The TCP opened for operations in October 2007. The centre functions as a regional, national and international resource for mouse models of human disease. This 120,000 square foot facility is located at 25 Orde Street, Toronto, and occupies four floors two below ground and two above. It houses specialized laboratories for mouse generation and analysis and, when fully occupied, it will contain approximately 36,000 cages (180,000 mice). The world-renowned scientific staff studies mammalian gene function, identifies genetic components of complex human disease, produces new mouse models of human disease, develops and tests new cell-based and gene-based therapies, and develops technologies for genome manipulation and phenotypic analysis. The TCP offers state-of-the-art mouse holding and facility support services to academic stakeholders and strategic private sector partners. It houses the Centre for Modeling Human Disease (CMHD), the Canadian Mouse Mutant Repository (CMMR), and the Mouse Imaging Centre (MICe) to provide an array of pre-clinical research services to clients. TCP Services * Phenotyping * Genetic Mapping * Pathology * Cryopreservation * Imaging * Genetically Engineered Mouse Models * Mouse Holding and Technical Services
Central repository for the physical archive and distribution of cryopreserved ES cells, spermatozoa, ova, embryos, and non-germ cell tissue DNA generated by Canada' '''s mouse genome effort. The CMMR acts in coordination with other repositories worldwide and is establishing a nation-wide network of repository nodes to house sub-sets of the resources generated across Canada. The CMMR is the repository and distribution center for the North American Conditional Mouse Mutagenesis project (NorCOMM). The CMMR also collects and stores somatic tissue from mouse models in a variety of formats (fixed, embedded, and glass-slide mounted) enabling world wide access to specimens from established mouse models. Services include: * Embryo cryopreservation and recovery * Ovary cryopreservation and recovery * Ovary transplant * Sperm cryopreservation and recovery * Strain services, including rederivation by IVF, speed expansion and strain rescue * NorCOMM ES cell withdrawal * Non-NorCOMM ES cell expansion
A unique resource and comprehensive imaging facility combining the latest state-of-the-art digital medical imaging technologies for the characterization of mouse functional genomics. The goals of the Mouse Imaging Centre are: * To provide a variety of medical imaging technologies adapted to studying genetically modified mice. These technologies include magnetic resonance (MR) imaging, micro computed tomography (micro-CT), ultrasound biomicroscopy (UBM), and optical projection tomography (OPT). * To screen large numbers of mice for models of human diseases. * To image an individual mouse over time to observe development, disease progression and responses to experimental treatment. * To develop an exciting team of investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. * To work by collaboration with researchers throughout the world. When we look for human diseases in the human population, we make extensive use of medical imaging. Therefore, it makes sense to have available the same imaging capabilities as we investigate mice for models of human disease. The Mouse Imaging Centre (MICe) has developed high field magnetic resonance imaging microscopy, ultrasound biomicroscopy, micro computed tomography, and optical techniques. With these imaging tools, MICe is screening randomly mutagenized mice to look for phenotypes that represent human diseases and is taking established human disease models in mice and using imaging to follow the progression of disease and response to treatment over time. It is clear that imaging has a major contribution to make to phenotyping genetic variants and to characterizing mouse models. MICe is staffed by an exciting new team of about 30 investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. The Mouse Imaging Centre (MICe) is not a fee-for-service facility but works through collaborations. Services include: * Projects involving MicroCT are available as a fee for service. * We will eventually move to the same model above with MRI. * Ultrasound Biomicroscopy is used for cardiac, embryo and cancer studies and is available as fee for service at $100 per study or in some cases on a collaborative basis. * Optical Projection Tomography has only limited availability on a collaborative basis. Mouse Atlas As our images are inherently three-dimensional, we will be able to make quantitative measures of size and volume. With this in mind, we are developing a mouse atlas showing the normal deviation of organ sizes. This atlas is an important resource for biologists as it has the potential to eliminate the need to sacrifice as many controls when making comparisons with mutants. Mouse Atlas Examples: * Variational Mouse Brain Atlas * Cerebral Vascular Atlas of the CBA Mouse * Neuroanatomy Atlas of the C57Bl/6j Mouse * Vascular Atlas of the Developing Mouse Embryo * Micro-CT E15.5 Mouse Embryo Atlas
University of Washington School of Medicine; Washington; USA
University of Washington School of Medicine
Public medical school in the northwest United States, located in Seattle and affiliated with the University of Washington.
The Journal Lab is a service that aims to improve dialog about published science allowing the community of professional scientists to openly and anonymously discuss peer-reviewed research and share one''s insights. Users can leave their most insightful comments, risk free. Begin by entering a few terms that you regularly search on PubMed. Then sign up to save your feeds and start sharing your insights. You can use them to discover and discuss the latest research. We are working hard to help top-tier scientists: * Read papers more efficiently. * Share opinions about those papers. * Benefit from the aggregated knowledge of experts in their field. We''re ready for science to change. Retraction rates are on the rise, peer review is becoming increasingly political, negative data is ignored, and reproducibility has become optional, not the standard. It''s time to close the gap between what science is and what it is supposed to be. Let''s put the impact back in impact factor. Solid science does not equal high impact publication. High impact publication does not equal solid science. Sad but true. Together, we can change that. Help us build a world where science is critiqued for its integrity, not its splash.
The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos.
Mouse models for the study of human and animal disease for Australian and international researchers. It has reduced the cost to researchers of accessing mouse models of disease, and provides equipment and expertise to undertake characterization and further research of these models. The APN brought together mouse production, strain storage and pathology capabilities, later extending the core services of the network, and include new services (RNAi and genomics services). Twelve Australian facilities and institutions currently constitute the APN. The APN partners contribute their expertise and infrastructure for the production of mouse models, as well as providing cryopreservation and pathology services. * Walter and Eliza Hall Institute of Medical Research * Monash University * Queensland Institute of Medical Research * Animal Resources Centre * Institute of Medical and Veterinary Science * University of Melbourne * Institute of Molecular Bioscience * Menzies Research Institute * Peter MacCallum Cancer Centre * Australian National University * Western Australian Institute of Medical Research * Centenary Institute In addition, the APN is working with the Atlas of Living Australia to develop a framework for Australia' '''s e-science infrastructure to improve the capture, annotation and dissemination of research data. The APN' '''s core expertise and infrastructure is also extended by key national and international partnerships. These include the Garvan Institute, the National Institutes of Health (United States), the Wellcome Trust (United Kingdom), and the University of Manitoba (Canada). Services * ES Cell to Mouse: Create a mouse model from embryonic stem cells * RNAi: Screen full genomes to identify novel gene targets * ENU Mutagenesis - Produce chemically-induced mouse models * Pathology - Investigate mouse models using clinical and histopathology * Genomics - Further mouse mutant identification via new discovery pipeline * NHMRC Australian PhenomeBank - a non-profit repository of mouse strains used in Medical Research.
National Center for Biotechnology Information Epigenomics
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.
A C / C++ command line toolbox for structural variation (SV) detection that reports mobile element insertions (MEI). It takes advantage of both read-pair and split-read algorithms and is extremely fast and memory-efficient. Powered by the Bamtools API, it can call SV events on multiple BAM files (a population) simutaneously to increase the sensitivity on low-coverage dataset.
Collection of human reference epigenomes and results of their integrative and comparative analyses. Successive releases of the Atlas will provide progressively more detailed insights into locus-specific epigenomic states, including histone marks and DNA methylation marks across specific tissues and cell types, developmental stages, physiological conditions, genotypes, and disease states. The Human Epigenome Atlas is produced by the NIH Epigenomics Roadmap Consortium.
GoCognitive - Educational tools for cognitive neuroscience
Free access to materials for students, educators, and researchers in cognitive psychology and cognitive neuroscience. Currently there are about a dozen demonstrations and more than 30 videos that were produced over the last two years. The basic philosophy of goCognitive rests on the assumption that easy and free access to high-quality content will improve the learning experience of students and will enable more students to enjoy the field of cognitive psychology and cognitive neuroscience. There are a few parts of goCognitive that are only available to registered users who have provided their email address, but all of the online demonstrations and videos are accessible to the everyone. Both new demonstrations and new video interviews will continually be added to the site. Manuals for each of the demonstration are being created and available as pdf files for download. Most of the demonstrations are pretty straightforward - but in some cases, especially if you would like to collect data - it might be a good idea to look over the manual. There are different ways in which you can get involved and contribute to the site. Your involvement can range from sending us feedback about the demonstrations and videos, suggestions for new materials, or the simple submission of corrections, to the creation or publication of demonstrations and videos that meet our criteria. Down the road we will make the submission process easier, but for now please contact swerner (at) uidaho dot edu for more information. NSF student grant Undergraduate students can apply through goCognitive for an $1,100 grant to co-produce a new video interview with a leading researcher in the field of cognitive neuroscience. The funding has been provided by the National Science Foundation.
MacArthur Foundation Research Network on Law and Neuroscience
Blog that provides an on-line forum where the members of the MacArthur Foundation Research Network on Law and Neuroscience can share their ideas and interact with not only other researchers but also with the interested public more generally. One of the main goals of the blog is to provide a resource with information about cutting edge research at the cross-roads of neuroscience, law, and philosophy.
PhenExplorer - Explore the Human Phenotype Ontology
The PhenExplorer allows you to browse the Human Phenotype Ontology (HPO) in different ways, using the tabs ' '''by features' ''', ' '''by disease' ''', ' '''by ontology' ''' or ' '''by genes' '''. Clicking on a particular phenotypic feature (HPO-term) you can get a list of disease entries that are linked to it (i.e. diseases that are annotated with this HPO-term). You can also visualize this term in the context of the ontological structure. Finally, a lists of genes can be displayed, that are known to cause (when mutated) the linked diseases mentioned above. For each disease you can get the list of linked HPO-terms and genes. You can also search for specific genes and explore to which HPO-terms and diseases they are linked.
Phenomizer - Clinical Diagnostics with Similarity Searches in Ontologies
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 31,2026. Phenomizer offers three different approaches to find the appropriate term for a phenotypic abnormality, indicated by the three tabs on the left hand side: Feature, Disease and Ontology. The Phenomizer is intended to be used by qualified and licensed physicians in order to provide assistance in reaching the correct diagnosis in patients with hereditary diseases and for use as a teaching aid. The Phenomizer does not make diagnoses. Rather, it produces a ranked list of possibilities that can be used by physicians as a part of the diagnostic workup. The Phenomizer does not contain information about all possible diagnoses or even all possible hereditary diseases. The Phenomizer should not be used to make medical decisions without the advice of a physician.
International Mouse Phenotyping Consortium (IMPC)
IMPC - International Mouse Phenotyping Consortium
International Mouse Phenotyping Consortium
Center that produces knockout mice and carries out high-throughput phenotyping of each line in order to determine function of every gene in mouse genome. These mice will be preserved in repositories and made available to scientific community representing valuable resource for basic scientific research as well as generating new models for human diseases.
Ontology that describes the different types of associations between a gene and a disease. It was developed to integrate information from different databases that contain gene-disease associations such as UniProt, CTD, Orphanet, the GWAS Catalog, GAD, MGD, RGD, and LHGDN.
IMPReSS - International Mouse Phenotyping Resource of Standardised Screens
International Mouse Phenotyping Resource of Standardised Screens
Contains standardized phenotyping protocols essential for the characterization of mouse phenotypes. IMPReSS holds definitions of the phenotyping Pipelines and mandatory and optional Procedures and Parameters carried out and data collected by international mouse clinics following the protocols defined. This allows data to be comparable and shareable and ontological annotations permit interspecies comparison which may help in the identification of phenotypic mouse-models of human diseases. The IMPC (International Mouse Phenotyping Consortium) core pipeline describes the phenotype pipeline that has been agreed by the research institutions. IMPReSS has a SOAP web service machine interface. The WSDL can be accessed here: http://www.mousephenotype.org/impress/soap/server?wsdl
Create knockout alleles in protein coding genes in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing, with the aim to cover them all. Each allele created is analyzed for morphological differences and published on the ZMP site. Transcript counting is performed on alleles with a morphological phenotype. Alleles generated are archived and can be requested from this site through the Zebrafish International Resource Center (ZIRC). You may register to receive updates on genes of interest, or browse a complete list, or search by Ensembl ID, gene name or human and mouse orthologue.
Clearinghouse and exchange portal for gene variant (mutation) data produced by diagnostics laboratories, offering users a portal through which to announce, discover and acquire a comprehensive listing of observed neutral and disease-causing gene variants in patients and unaffected individuals. Cafe Variome is not a ' '''database' ''' for the hosting/display/release of data, but a shop window for finding data. As such, it holds only core info for each record, and uses this merely to enable holistic searching across resources. Diagnostics laboratories routinely assess DNA samples from patients with various inherited disorders, and so produce a great wealth of data on the genetic basis of disease. Unfortunately, those data are not usually shared with others. To address this gross deficiency, a novel system has been developed that aims to facilitate the automated transfer of diagnostic laboratory data to the wider community, via an internet based Cafe for routinely exchanging genetic variation data. The flow of research data concerning the genetic basis of health and disease is critical to understanding and developing treatments for a range of genetic diseases. Overall, the project aims to lower the barriers and provide incentives for a willing community to share data, and thereby facilitate the broader exploitation of diagnostic laboratory data. Cafe Variome aims to address the above data flow problems by: # Minimizing the effort required to publish variant data # Ensuring attribution for data creators working in diagnostic laboratories Key elements of the project strategy are: * Data publication will be automated by endowing standard analysis tools used by laboratories with an online data submission function. Submissions will be received by a central Internet depot, which will serve as a place where published datasets are advertised, and subsequently discovered by diverse 3rd parties. * Each dataset will be unambiguously linked with the data submitter' '''s identity, and systems devised to facilitate citation of published variant datasets so they can be cited in the literature. Data creators will thus be credited for their contributions. Data submitters can use Cafe Variome to simply announce or publicize their data to the world. To enable this, only core, non-identifiable data is submitted to the central repository, enabling users to search and discover records of interest in the source repository. The data are not automatically handed on to the user (unless intended by the submitters). Hence, the concept is used to deal with the challenge of maximally sharing data whilst fully respecting ethico-legal considerations.
A fully-automated PDF-to-XML converter service for scientific articles. It takes a full-text PDF article as input and outputs the hierarchy of its distinct logical elements in an XML format. The elements that PDFX can currently extract are: * Front Matter ** title, abstract, author, author footnote * Body Matter ** body text, h1, h2, h3, image, table, figure/table caption, figure/table reference, bibliographic item, bibliographic reference (citation) * Extras ** header, footer, side note, page number, email, URI Note: This system has been designed for processing scientific articles. While virtually any PDF file is acceptable input, quality of the processing output might be degraded e.g. for entire books, slide presentations or spreadsheet/strictly tabular data. There are two ways in which you can use PDFX: * via a web browser * via any other HTTP client, such as the curl command-line tool
KNIME (Konstanz Information Miner) is a user-friendly and comprehensive Open-Source data integration, processing, analysis, and exploration platform. KNIME (naim) is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualization and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. KNIME can be downloaded onto the desktop and used free of charge. KNIME products include additional functionalities such as shared repositories, authentication, remote execution, scheduling, SOA integration and a web user interface as well as world-class support. Robust big data extensions are available for distributed frameworks such as Hadoop. KNIME is used by over 3000 organizations in more than 60 countries. The modular data exploration platform, initially developed at the University of Konstanz, Germany, enables the user to visually create data flows, execute selected analysis steps, and later investigate the results through interactive views on data and models. KNIME is a proven integration platform for tools of numerous vendors due to its open and modular API. The KNIME.com product pipeline includes an Enterprise Server, Cluster Execution, Reporting solutions, and professional KNIME support subscriptions. KNIME.com also offer services such as data analysis, hands-on training and the development of customized components for KNIME.
PhenomeNet - Cross Species Phenotype Network
PhenomeNet is a cross-species phenotype similarity network. It contains the experimentally observed phenotypes of multiple species as well as the phenotypes of human diseases. PhenomeNet provides a measure of phenotypic similarity between the phenotypes it contains. The latest release (from 22 June 2012) contains 124,730 complex phenotype nodes taken from the yeast, fish, worm, fly, rat, slime mold and mouse model organism databases as well as human disease phenotypes from OMIM and OrphaNet. The network is a complete graph in which edge weights represent the degree of phenotypic similarity. Phenotypic similarity can be used to identify and prioritize candidate disease genes, find genes participating in the same pathway and orthologous genes between species. To compute phenotypic similarity between two sets of phenotypes, we use a weighted Jaccard index. First, phenotype ontologies are used to infer all the implications of a phenotype observation using several phenotype ontologies. As a second step, the information content of each phenotype is computed and used as a weight in the Jaccard index. Phenotypic similarity is useful in several ways. Phenotypic similarity between a phenotype resulting from a genetic mutation and a disease can be used to suggest candidate genes for a disease. Phenotypic similarity can also identify genes in a same pathway or orthologous genes. PhenomeNet uses the axioms in multiple species-dependent phenotype ontologies to infer equivalent and related phenotypes across species. For this purpose, phenotype ontologies and phenotype annotations are integrated in a single ontology, and automated reasoning is used to infer equivalences. Specifically, for every phenotype, PhenomeNet infers the related mammalian phenotype and uses the Mammalian Phenotype Ontology for computing phenotypic similarity. Tools: * PhenomeBLAST - A tool for cross-species alignments of phenotypes * PhenomeDrug - method for drug-repurposing
lapdftext: Layout-Aware Text Extraction from Full-text PDF of Scientific Articles
Layout-Aware Text Extraction from Full-text PDF of Scientific Articles
Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise.
International Standards for Cytogenomic Arrays (ISCA) Consortium
International Standards For Cytogenomic Arrays Consortium
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 22, 2022. A rapidly growing group of clinical cytogenetics and molecular genetics laboratories committed to improving quality of patient care related to clinical genetic testing using new molecular cytogenetic technologies including array comparative genomic hybridization (aCGH) and quantitative SNP analysis by microarrays or bead chip technology. They improve clinical care by providing a large publicly available database and forum where clinicians and researchers can share knowledge to expedite the understanding of copy number variation (CNV) in an abnormal population. The ISCA database contains whole genome array data from a subset of the ISCA Consortium clinical diagnostic laboratories. Array analysis was carried out on individuals with phenotypes including intellectual disability, autism, and developmental delay. Efforts of the Consortium include: # Clinical Utility: The ISCA Consortium has made recommendations regarding the appropriate clinical indications for cytogenetic array testing (Miller et al. AJHG 2010, PMID: 20466091). Currently, discussions are focused on pediatric applications for children with unexplained developmental delay, intellectual disability, autism and other developmental disabilities. A separate committee has been developed to address appropriate cancer genetic applications (http://www.urmc.rochester.edu/ccmc/). # Evidence-based standards for cytogenomic array design: The Consortium will develop recommendations for standards for the design, resolution and content of cytogenomic arrays using an evidence-based process and an international panel of experts in clinical genetics, clinical laboratory genetics (cytogenetics and molecular genetics), genomics and bioinformatics. This design is intended to be platform and vendor-neutral (common denominator is genome sequence coordinates), and is a dynamic process with input from the broader genetics community and evidence-based review by the expert panel (which will evolve into a Standing Committee with international representation). # Public Database for clinical and research community: It is essential that publicly available databases be created and maintained for cytogenetic array data generated in clinical testing laboratories. The ISCA data will be held in dbGaP and dbVar at NCBI/NIH and curated by a committee of clinical genetics laboratory experts. The very high quality of copy number data (i.e., deletions and duplications) coming from clinical laboratories combined with expert curation will produce an invaluable resource to the clinical and research communities. # Standards for interpretation of cytogenetic array results: Using the ISCA Database, along with other genomic and genetics databases, the Consortium will develop recommendations for the interpretation and reporting of pathogenic vs. benign copy number changes as well as imbalances of unknown clinical significance.
Archive of aggregated information about sequence variation and its relationship to human health. Provides reports of relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. Collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about submitter, and other supporting data. Alleles described in submissions are mapped to reference sequences, and reported according to HGVS standard.
Human Genome Variation database of Genotype to Phenotype information
Publicly available database of summary level findings from genetic association studies in humans, including genome wide association studies (GWAS). Previously named HGBASE, HGVbase and HGVbaseG2P.
Deciphering Developmental Disorders (DDD)
The Deciphering Developmental Disorders (DDD) study aims to find out if using new genetic technologies can help doctors understand why patients get developmental disorders. To do this we have brought together doctors in the 23 NHS Regional Genetics Services throughout the UK and scientists at the Wellcome Trust Sanger Institute, a charitably funded research institute which played a world-leading role in sequencing (reading) the human genome. The DDD study involves experts in clinical, molecular and statistical genetics, as well as ethics and social science. It has a Scientific Advisory Board consisting of scientists, doctors, a lawyer and patient representative, and has received National ethical approval in the UK. Over the next few years, we are aiming to collect DNA and clinical information from 12,000 undiagnosed children in the UK with developmental disorders and their parents. The results of the DDD study will provide a unique, online catalogue of genetic changes linked to clinical features that will enable clinicians to diagnose developmental disorders. Furthermore, the study will enable the design of more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with developmental disorders. Over time, the work will also improve understanding of how genetic changes cause developmental disorders and why the severity of the disease varies in individuals. The Sanger Institute will contribute to the DDD study by performing genetic analysis of DNA samples from patients with developmental disorders, and their parents, recruited into the study through the Regional Genetics Services. Using microarray technology and the latest DNA sequencing methods, research teams will probe genetic information to identify mutations (DNA errors or rearrangements) and establish if these mutations play a role in the developmental disorders observed in patients. The DDD initiative grew out of the groundbreaking DECIPHER database, a global partnership of clinical genetics centres set up in 2004, which allows researchers and clinicians to share clinical and genomic data from patients worldwide. The DDD study aims to transform the power of DECIPHER as a diagnostic tool for use by clinicians. As well as improving patient care, the DDD team will empower researchers in the field by making the data generated securely available to other research teams around the world. By assembling a solid resource of high-quality, high-resolution and consistent genomic data, the leaders of the DDD study hope to extend the reach of DECIPHER across a broader spectrum of disorders than is currently possible.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 10th,2023. Commercial provider of cognitive assessments, including their proprietary database, the Brain Resource International Database (BRID) that allows users to quantify individual differences in brain function, compare individual performance against peers, and provide a robust frame of reference for clinical assessment and treatment decisions. Database provides evidence for brain behavior connection so important to reliably enabling optimal solutions for mental health and wellbeing. It powers all Brain Resource products.
Integrated Gene-Disease Interaction View
NIF Integrated Gene-Disease Interaction View
Virtual database currently indexing interaction between genes and diseases from Online Mendelian Inheritance in Man (OMIM) and Comparative Toxicogenomics Database (CTD).
A web utility providing a direct interface to perform SQL queries directly on the GO database, allowing users to run custom queries without having to install a copy of the GO database locally. GOOSE includes many sample queries to aid novice users and allows results to be retrieved as a web page or as tab-delimited text. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Provides information and tools to help consumers stay healthy including resources on a wide range of health topics selected from over 1,600 government and non-profit organizations to provide the best, most reliable health information possible.
Mammalian Adult Neurogenesis Gene Ontology
Database of genes concerning adult neurogenesis mapped to cell types and processes that have been curated from the literature. In its present state, the database is restricted to neurogenesis in the hippocampus.
International Federation of Digital Seismograph Networks (FDSN) Web Service Station
International Federation of Digital Seismograph Networks Web Service Station
Web service that returns International Federation of Digital Seismograph Networks (FDSN) station metadata in FDSN StationXML format or as delimited text. Results are available at multiple levels of granularity: network, station, channel and response. Metadata may be selected based on channel descriptors, time ranges, geographic regions, and more. This service is an implementation of the FDSN web service specification version 1.
Database and discovery platform containing publicly available collections of genes and variants associated to human diseases. Integrates data from curated repositories, GWAS catalogues, animal models and scientific literature.
Building data bridges between biological and medical infrastructure in Europe (BioMedBridges)
Building data bridges between biological and medical infrastructures in Europe
Building data bridges from biology to medicine in Europe
Consortium of 12 Biomedical sciences research infrastructure (BMS RI) partners to develop a shared e-infrastructure to allow interoperability between data and services in the biological, medical, translational and clinical domains (providing a complex knowledge environment comprising standards, ontologies, data and services) and thus strengthen biomedical resources in Europe. The BMS RIs are on the roadmap of the European Strategy Forum on Research Infrastructures (ESFRI). Connecting several European research infrastructures brings a diversity of ethical, legal and security concerns including data security requirements for participating e-Infrastructures that are storing or processing patient-related data (or biosamples): EATRIS, ECRIN, BBMRI, EuroBioImaging and EMBL-EBI. In addition, INSTRUCT is interested in secure sample transport and in intellectual property rights; Infrafrontier stores high-throughput data from mice. BBMRI with its focus on the availability of biomaterials is currently emphasizing aspects like k-anonymity and metadata management for its data. Sharing of imaging data by Euro-BioImaging poses challenges with respect to anonymisation and intellectual property. Therefore, an ethical, regulatory and security framework for international data sharing that covers these diverse areas and different types of data (e.g. clinical trials data, mouse data, and human genotype and DNA sequence data) is of crucial importance. The outcomes will lead to real and sustained improvement in the services the biomedical sciences research infrastructures offer to the research community. Data curation and sample description will be improved by the adoption of best practices and agreed standards. Many improvements will emerge from new interactions between RIs created by data linkage and networking. Ensuring access to relevant information for all life science researchers across all BMS RIs will enable scientists to conduct and share cutting-edge research.
University of Athens Biophysics and Bioinformatics Laboratory
Biophysics and Bioinformatics Laboratory at University of Athens
Biophysics and Bioinformatics Laboratory of the Department of Cell Biology and Biophysics of the University of Athens
University of Athens Biophysics & Bioinformatics Laboratory
Laboratory focuses on research related to the elucidation of the principles governing protein structure and function, under the supervision of Professor Stavros J. Hamodrakas. In particular, original research is carried out along two main axes: # Algorithm development for the prediction of protein structure, function and interactions from amino acid sequence as well as construction of relevant databases. # Application of a variety of Biophysical methods and techniques for protein structure determination and for structural studies of complex, physiologically important, Biological tissues such as insect chorion and cuticle. More than 15 individuals (including post-doctoral researchers, PhD students, MSc and undergraduate students) are currently involved in several ongoing research projects. Apart from research, our lab offers undergraduate courses in Bioinformatics and Molecular Biophysics, which are elective for the degrees (BSc) in Biology (Faculty of Biology) and Physics (Faculty of Physics) of the University of Athens. At the same time, our lab is actively involved in the organization and co-ordination of the MSc Programme in Bioinformatics of the Faculty of Biology.
PRED-SIGNAL - Prediction of Signal Peptides in Archaea with Hidden Markov Models
A web tool for prediction of signal peptides in archaea. Computational prediction of signal peptides (SPs) and their cleavage sites is of great importance in computational biology; however, currently there is no available method capable of predicting reliably the SPs of archaea, due to the limited amount of experimentally verified proteins with SPs. We performed an extensive literature search in order to identify archaeal proteins having experimentally verified SP and managed to find 69 such proteins, the largest number ever reported. A detailed analysis of these sequences revealed some unique features of the SPs of archaea, such as the unique amino acid composition of the hydrophobic region with a higher than expected occurrence of isoleucine, and a cleavage site resembling more the sequences of gram-positives with almost equal amounts of alanine and valine at the position-3 before the cleavage site and a dominant alanine at position-1, followed in abundance by serine and glycine. Using these proteins as a training set, we trained a hidden Markov model method that predicts the presence of the SPs and their cleavage sites and also discriminates such proteins from cytoplasmic and transmembrane ones.
Database containing cDNA clone information of the brains of songbirds. These clones are annotated with behavioral information, as well as links to information of homologous genes of other species. The database includes over 91,000 zebra finch brain cDNAs (2009) sequenced by Duke, ESTIMA, and Rockefeller research groups. The project is a collaborative effort of the Jarvis Laboratory of Duke University, Duke Bioinformatics, and The Genomics group of RIKEN, with Erich D. Jarvis as P.I. and Kazuhiro Wada as Co-P.I. Microarrays with the cDNAs in this database are available at Duke http://mgm.duke.edu/genome/dna_micro/core/spotted.htm and through the NIH Neurosciences Microarray Consortium http://arrayconsortium.tgen.org/np2/public/overview.jsp
Michael J. Fox Foundation for Parkinsons Research
Michael J. Fox Foundation for Parkinson's Research
A Parkinson's research foundation dedicated to finding a cure for Parkinson's disease and to ensuring the development of improved therapies. Pipeline Programs fund investigator-initiated proposals focused on the following critical points along the translational pathway to new therapies for Parkinson's disease.
Training Programs in Epidemiology and Public Health Interventions Network
Created in 1997, Training Programs in Epidemiology and Public Health Interventions Network (TEPHINET) is a professional network of field epidemiology training programs (FETPs) located in 53 countries around the world. TEPHINET aims to strengthen international public health capacity by training field epidemiologists through an applied apprenticeship program. Trainees of FETPs master a set of core competencies that are vital to the practice of public health, while providing a valuable public health service to their countries and regions.
AMYL-PRED: A Consensus Method for Amyloid Propensity Prediction
A web tool using the consensus prediction method for identifying possible amyloidogenic regions in protein sequences. This tool uses an assortment of different methods that have been found or specifically developed to predict features related to the formation of amyloid fibrils. The consensus of these methods is defined as the the hit overlap of at least two out of five methods and it is the primary output of the program. However, the individual predictions of these methods are also made available in the form of a text file, maintained on the server for 1 (one) day. Consequently, the tool predicts probable amyloidogenic determinants for a given amino acid sequence of a peptide or protein.
HMM-TM: Prediction of Transmembrane Alpha-Helical Proteins
A web tool using the Hidden Markov Model method for the topology prediction of alpha-helical membrane proteins that incorporates experimentally derived topological information. Hidden Markov Models (HMMs) have been extensively used in computational molecular biology, for modelling protein and nucleic acid sequences. In many applications, such as transmembrane protein topology prediction, the incorporation of limited amount of information regarding the topology, arising from biochemical experiments, has been proved a very useful strategy that increased remarkably the performance of even the top-scoring methods. However, no clear and formal explanation of the algorithms that retains the probabilistic interpretation of the models has been presented so far in the literature. We present here, a simple method that allows incorporation of prior topological information concerning the sequences at hand, while at the same time the HMMs retain their full probabilistic interpretation in terms of conditional probabilities. We present modifications to the standard Forward and Backward algorithms of HMMs and we also show explicitly, how reliable predictions may arise by these modifications, using all the algorithms currently available for decoding HMMs. A similar procedure may be used in the training procedure, aiming at optimizing the labels of the HMM''s classes, especially in cases such as transmembrane proteins where the labels of the membrane-spanning segments are inherently misplaced. We present an application of this approach developing a method to predict the transmembrane regions of alpha-helical membrane proteins, trained on crystallographically solved data. We show that this method compares well against already established algorithms presented in the literature, and it is extremely useful in practical applications.
PRED-LIPO: Prediction of Lipoprotein and Secretory Signal Peptides in Gram-positive Bacteria with Hidden Markov Models
A web tool using the Hidden Markov Model method for the prediction of lipoprotein signal peptides of Gram-positive bacteria, trained on a set of 67 experimentally verified lipoproteins. The method outperforms LipoP and the methods based on regular expression patterns, in various data sets containing experimentally characterized lipoproteins, secretory proteins, proteins with an N-terminal TM segment and cytoplasmic proteins. The method is also very sensitive and specific in the detection of secretory signal peptides and in terms of overall accuracy outperforms even SignalP, which is the top-scoring method for the prediction of signal peptides.
CW-PRED: A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria
A web tool for the prediction of Cell Wall-Anchored Proteins in Gram+ Bacteria. Gram-positive bacteria have surface proteins that are often implicated in virulence. A group of extracellular proteins attached to the cell wall contains an LPXTG-like motif that is target for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A new Hidden Markov Model (HMM), an extension to the HMM model from Litou et al., http://www.ncbi.nlm.nih.gov/pubmed/18464329, was developed for predicting the LPXTG and LPXTG-like cell-wall proteins of Gram-positive bacteria. An analysis of 177 completely sequenced genomes has been performed as well. We identified in total 1456 cell-wall proteins, from which 1283 have the LPXTG motif, 39 the NPXTG motif, 53 have the LPXTA and 81 the LAXTG motif.
Web-based tool to create claims, hypotheses, or statements, and relate these to other claims using an open set of relationships. It is usable for science, but also for structuring online debates on other topics. The visual tool allows users to create, connect and share Ideas. Back them up with websites. Support or challenge them. Embed them to spread virally. Discover who - literally - connects with your thinking.
PRED-TMBB: A Hidden Markov Model method capable of predicting and discriminating beta-barrel outer membrane proteins
A web tool, based on a Hidden Markov Model, capable of predicting the transmembrane beta-strands of the gram-negative bacteria outer membrane proteins, and of discriminating such proteins from water-soluble ones when screening large datasets. The model is trained in a discriminative manner, aiming at maximizing the probability of the correct prediction rather than the likelihood of the sequences. The training is performed on a non-redundant database consisting of 16 outer membrane proteins (OMP''s) with their structures known at atomic resolution. We show that we can achieve predictions at least as good comparing with other existing methods, using as input only the amino-acid sequence, without the need of evolutionary information included in multiple alignments. The method is also powerful when used for discrimination purposes, as it can discriminate with a high accuracy the outer membrane proteins from water soluble in large datasets, making it a quite reliable solution for screening entire genomes. This web-server can help you run a discriminating process on any amino-acid sequence and thereafter localize the transmembrane strands and find the topology of the loops.
estMOI - Estimating multiplicity of infection using parasite deep sequencing data
A per-based software to estimate multiplicity of infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data. It requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. # Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. # Single Nucleotide Polymorphisms (SNPs) are then identified using SAMTools/BCFtools and stored in the VCF format. # The reference FASTA file is expected to be indexed using ''samtools faidx'' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.log) and a summary for all chromosomes (file with name *.txt).
A tool that predicts the coupling specificity of G-protein coupled receptors to G-proteins. We present a method that combines hidden Markov models and a feed-forward artificial neural network to overcome these limitations, while producing the most accurate predictions currently available. Using an up-to-date curated dataset, our method yields a 94% correct classification rate in a 5-fold cross-validation test. The method predicts also promiscuous coupling preferences, including coupling to G12/13, whereas unlike other methods avoids overpredictions (false positives) when non-GPCR sequences are encountered. * The PRED-COUPLE 2.00 system predicts coupling specificty of GPCRs to all families of G-proteins (including G12/13). * Coupling to more than one G-protein families can also be predicted with this tool. * No membrane topology information is required. Furthermore, no membrane topology prediction is executed by this method. * The method is based on a refined library of highly-discriminative Hidden Markov Models. Hits from individual profiles are combined by a feed-forward Artificial Neural Network to produce the final output. * Seven (7) transmembrane receptor signatures from the Pfam database version 17.00 are also applied in order to verify a true GPCR sequence. When a query sequence is not recognized as a 7 transmembrane receptor a message is shown.
A web tool for the Consensus Prediction of TransMembrane Beta-Barrel Proteins. Prediction of the transmembrane strands and topology of beta-barrel outer membrane proteins is of interest in current bioinformatics research. Several methods have been applied so far for this task, utilizing different algorithmic techniques and a number of freely available predictors exist. The methods can be grossly divided to those based on Hidden Markov Models (HMMs), on Neural Networks (NNs) and on Support Vector Machines (SVMs). In this work, we compare the different available methods for topology prediction of beta-barrel outer membrane proteins. We evaluate their performance on a non-redundant dataset of 20 beta-barrel outer membrane proteins of gram-negative bacteria, with structures known at atomic resolution. Also, we describe, for the first time, an effective way to combine the individual predictors, at will, to a single consensus prediction method. We assess the statistical significance of the performance of each prediction scheme and conclude that Hidden Markov Model based methods, HMM-B2TMR, ProfTMB and PRED-TMBB, are currently the best predictors, according to either the per-residue accuracy, the segments overlap measure (SOV) or the total number of proteins with correctly predicted topologies in the test set. Furthermore, we show that the available predictors perform better when only transmembrane beta-barrel domains are used for prediction, rather than the precursor full-length sequences, even though the HMM-based predictors are not influenced significantly. The consensus prediction method performs significantly better than each individual available predictor, since it increases the accuracy up to 4% regarding SOV and up to 15% in correctly predicted topologies.
fcros: FCROS for detecting differentially expressed genes
A fold change ranks ordering statistics based software for detecting differentially expressed genes.
PRED-GPCR: GPCRs Family classification from sequence alone
A prediction tool for GPCR Family Classification from sequence alone based on a probabilistic method that uses family-specific profile Hidden Markov Models. The PRED-GPCR system is based on a probabilistic method that uses family specific profile HMMs in order to determine to which GPCR family a query sequence belongs or resembles. The approach proposed in this method exploits the descriptive power of profile HMMs along with an exhaustive discrimination assessment method to select only highly selective and sensitive profiles, for each family. The collection of these profiles constitutes a signature library, which is scanned, for significant matches with a given query sequence. The output report for a query sequence consists of two sections: * A ranked list of the profile HMM matches, below the selected individual motif E-value cutoff, along with their corresponding family. * A ranked list of the Combined P-values, E-values as well as the number of profiles matched for each family. To cross-evaluate your results you can browse through Swiss-Prot, Trembl, Pfam and Prosite family related entries.
Guide by the Australian National Data Service (ANDS) regarding data citation for eResearch infrastructure support providers and researchers with the aim of enabling more researchers to re-use research data more often. It is not so much a guide to how to cite data, but a guide to the issues around it, and activities underway to change the culture around data citation in order to support improved data management and sharing. ANDS is engaged in activities that will make it easier to share data, to recognize the importance of making data available and to make data citation a standard procedure.
MCMBB: Markov Chain Model for Beta Barrels
A web tool used in the discrimination of beta-barrel outer membrane proteins with a Markov chain model. MCMBB is a fast algorithm, which discriminates beta-barrel outer membrane proteins from globular proteins and from alpha-helical membrane proteins. The algorithm is based on a 1st order Markov Chain model, which captures the alternating pattern of hydrophilic-hydrophobic residues occurring in the membrane-spanning beta-strands of beta-barrel outer membrane proteins. The model achieves high accuracy in discriminating outer membrane proteins, since it can discriminate beta-barrel outer membrane with a correct classification rate of 90.08% and the globular proteins with a correct classification rate of 92.67%. When submitting alpha-helical membrane proteins, the method shows an accuracy of 100%. A score greater than zero, indicates that the protein is more likely to be a beta-barrel outer membrane protein, whereas a result lower than zero, indicates that the protein is probable not a beta-barrel. You may enter up to 1000 sequences in Fasta format.
waveTM: Wavelet-based transmembrane segment prediction
A web tool for the prediction of transmembrane segments in alpha-helical membrane proteins. A sliding window of 20 residues is used in order to calculate an average residue hydrophobicity profile, using a hydrophobicity scale. Discrete Wavelet Transform is applied on the average residue hydrophobicity signal and the different frequency coefficients produced are adaptively thresholded so that a denoised signal is reconstructed. A dynamic programming algorithm processes the denoised signal to provide the optimal model for the number, the length and the location of membrane-spanning segments. The end points of the predicted segments are extended to include flanking hydrophobic residues. Topology prediction can also be obtained in conjunction with OrienTM (Liakopoulos et al, 2001). Analysis of a non-redundant test set, provides a ~95% per segment accuracy and ~90% per residue accuracy. Now, you can: * Run waveTM on a sequence * Browse the results obtained with the algorithm * View additional material concerning the hydrophobicity scale
A blog on the neural organization of language moderated by Greg Hickok and David Poeppel. Essays, comments on new papers, and job openings. Greg Hickok is Professor of Cognitive Sciences, and Director of the Center for Cognitive Neuroscience at UC Irvine. David Poeppel, after several years as Professor of Linguistics and Biology at the University of Maryland, College Park, is now Professor of Psychology at NYU. Hickok and Poeppel first crossed paths in 1991 at MIT in the McDonnell-Pew Center for Cognitive Neuroscience where Hickok was a post doc, and Poeppel a grad student. Meeting up again a few years later at a Cognitive Neuroscience Society Meeting in San Francisco, they began a collaboration aimed at developing an integrated model of the functional anatomy of language. Research in both the Hickok and Poeppel labs is supported by NIDCD.
An ontology consisting of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending the GO process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms. The prime application of NBO is to provide the vocabulary that is required to integrate behavior observations within and across species. It is currently being applied by several model organism communities as well as in the description of human behavior-related disease phenotypes. The main ontology is available in both the OBO Flatfile Format and the Web Ontology Language (OWL).
Publish over 230 plus peer-reviewed open access journals. These free-to-view online journals cover all major disciplines of science, technology, medicine and social sciences. Bentham OPEN offers its ''Complimentary Membership'' to International R & D organizations, institutes and universities. This opportunity will entitle authors from different member institutes to a special discount of 30% in the open access publication fee for submission of articles to Bentham OPEN journals. Additionally, input and contributions from associate institutes would also be recognized and a link to their respective Website would be displayed on the Bentham OPEN membership page. The member institution''s logo will also be published on the same page. Bentham Open Membership provides the following advantages: * Possibility to explore 73 distinct disciplines by means of publishing in 239 open access journals. * Free access to all provides prospects of higher citations. * Author(s) own the copyrights to their published articles. * High standard criteria for peer-review. * Unbound right to read, download or print open access articles. * Access to a range of articles in printed form such as short communications, full length research articles, reviews or conference proceedings. * Simple steps from submission to publication, leading to fast turn-around. * Possibility of archiving published articles. The complimentary membership is valid for a span of one year and upon completion of the prescribed period, it is renewed by mutual interest and agreement. If you find the above mentioned details relevant, then kindly contact us via e-mail at membership_at_benthamscience.org or oa_at_benthamscience.org.
PRED-TMR: A novel method for predicting transmembrane segment in proteins based on a statistical analysis of the SwissProt database
A web server that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The algorithm refines a standard hydrophobicity analysis with a detection of potential termini (edges, starts and ends) of transmembrane regions. This allows both to discard highly hydrophobic regions not delimited by clear start and end configurations and to confirm putative transmembrane segments not distinguishable by their hydrophobic composition. The accuracy obtained on a test set of 101 non homologous transmembranes proteins with reliable topologies compares well with that of other popular existing methods. Only a slight decrease in prediction accuracy was observed when the algorithm was applied to all transmembrane proteins of the SwissProt database (release 35).
A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions.
PRED-TMR2: Prediction of Transmembrane regions in proteins
A web server that classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment and analysis of open reading frames (ORF''s) identified in complete genomes and, especially, those ORF''s that correspond to proteins with unknown function. The network has a simple hierarchical feed-forward topology and a limited number of neurons which makes it very fast. By using only information contained in 11 protein sequences, the method was able to identify, with 100% accuracy, all membrane proteins with reliable topologies collected from several papers in the literature. Applied to a test set of 995 globular, water-soluble proteins, the neural network classified falsely 23 of them in the membrane protein class (97.7% of correct assignment). The method was also applied to the complete SWISS-PROT database with considerable success and on ORF''s of several complete genomes. The neural network developed was associated with the PRED-TMR algorithm (Pasquier,C., Promponas,V.J., Palaios,G.A., Hamodrakas,J.S. and Hamodrakas,S.J., 1999) in a new application package called PRED-TMR2.
model organism ENCyclopedia Of DNA Elements
National Human Genome Research Institute model organism ENCyclopedia Of DNA Elements
NHGRI model organism ENCyclopedia Of DNA Elements
A comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. The entire modENCODE data corpus is now available on the Amazon Web Services EC2 cloud. What this means is that virtual machines and virtual compute clusters that you run within the EC2 cloud can mount the modENCODE data set in whole or in part. Your software can run analyses against the data files directly without experiencing the long waits and logistics associated with copying the datasets over to your local hardware. You may also view the data using GBrowse, Dataset Search, or download the data via FTP, as well as download pre-release datasets.
A clustering and visualization tool that enables the interactive exploration of genome-wide data, with a specialization in epigenomics data. Spark is also available as a service within the Epigenome toolset of the Genboree Workbench. The approach utilizes data clusters as a high-level visual guide and supports interactive inspection of individual regions within each cluster. The cluster view links to gene ontology analysis tools and the detailed region view connects to existing genome browser displays taking advantage of their wealth of annotation and functionality.
Human Epigenome Browser at Washington University
Software tool for visualizing and interacting with whole-genome datasets. Browser hosts Human Epigenome Atlas data produced by Roadmap Epigenomics project, but its use of advanced, multi-resolution data formats and its user-friendly interface make it possible for investigators to upload and visualize their own data as custom tracks. Developed and maintained by Epigenome Informatics Group at Washington University in St. Louis.
A visualization hub displaying sequencing data from the Roadmap Epigenomics project. It hosts high volume of tracks from ENCODE and Roadmap Epigenomics projects, supports multiple organisms, visualizes chromatin-interaction data (e.g. Hi-C), performs gene set view, gene plot, and many others. All delivered on the web at high performance.
University of Nottingham; Nottingham; United Kingdom
Public research university in Nottingham, United Kingdom. It was founded as University College Nottingham in 1881, and was granted a royal charter in 1948.
A JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of poor annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. GeneViTo has already been applied to visualize the genomes of two microbial organisms: the bacterion Chlamydia trachomatis and the archaeon Methanococcus jannaschii. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment (Java 1.4.1) is already installed in the system.
A portal of online studies that encourage community participation to tackle the most challenging problems in neuropsychiatry, including attention-deficit / hyperactivity disorder, schizophrenia, and bipolar disorder. Our approach is to engage the community and try to recruit tens of thousands of people to spend an hour of their time on our site. You folks will provide data in both brain tests and questionnaires, as well as DNA, and in return, we will provide some information about your brain and behavior. You will also be entered to win amazon.com gift cards. While large collaborative efforts were made in genetics in order to discover the secrets of the human genome, there are still many mysteries about the behaviors that are seen in complex neuropsychiatric syndromes and the underlying biology that gives rise to these behaviors. We know that it will require studying tens of thousands of people to begin to answer these questions. Having you, the public, as a research partner is the only way to achieve that kind of investment. This site will try to reach that goal, by combining high-throughput behavioral assessment using questionnaires and game-like cognitive tests. You provide the data and then we will provide information and feedback about why you should help us achieve our goals and how it benefits everyone in the world. We believe that through this online study, we can better understand memory and attention behaviors in the general population and their genetic basis, which will in turn allow us to better characterize how these behaviors go awry in people who suffer from mental illness. In the end, we hope this will provide better, more personalized treatment options, and ultimately prevention of these widespread and extremely debilitating brain diseases. We will use the data we collect to try to identify the genetic basis for memory and impulse control, for example. If we can achieve this goal, maybe we can then do more targeted research to understand how the biology goes awry in people who have problems with cognition, including memory and impulse control, like those diagnosed with ADHD, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorders. By participating in our research, you can learn about mental illness and health and help researchers tackle these complex problems. We can''t do it without your help.
Raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive.
deepSNV - Detection of subclonal SNVs in deep sequencing experiments
Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants).
An ontology written in OWL 2 DL to enable the metadata properties of the DataCite Metadata Kernel Specification version 2.2 (http://test.datacite.org/schema/meta/kernel-2.2/index.html) to be described in RDF. This version of the DataCite Ontology has been completely revised and significantly expanded to permit accurate mapping of this new version of the DataCite Metadata Kernel Specification to RDF.
PRED-CLASS - Classification of proteins into one of four possible classes
A system of cascading neural networks that classifies any protein, given its amino acid sequence alone, into one of four possible classes: membrane, globular, fibrous, mixed.
CoPreTHi - A Java-program which Combines the results of several methods (available throught the Internet ) that Predict Transmembrane regions in proteins in a joint prediction Histogram
A Java based web application, which combines the results of methods that predict the location of transmembrane segments in protein sequences into a joint prediction histogram. Clearly, the joint prediction algorithm, produces superior quality results than individual prediction schemes.
orienTM - Orientation of TransMembrane proteins
A computer software that utilizes an initial definition of transmembrane segments to predict the topology of transmembrane proteins from their sequence. It uses position-specific statistical information for amino acid residues which belong to putative non-transmembrane segments derived from a statistical analysis of non-transmembrane regions of membrane proteins stored in the SwissProt database. Its accuracy compares well with that of other popular existing methods.
Secondary Structure Prediction of Proteins
A tool to Predict the Secondary Structure of a protein from its amino acid sequence alone. The SecStr package uses six different secondary structure prediction methods (Nagano, Garnier et al., Burges et al., Chou and Fasman , Lim and Dufton and Hider). The results of those methods are combined into a Joint Prediction Histogram (JPH) as described by Hamodrakas, 1988 and Hamodrakas et al., 1982. As previously mentioned, the SecStr package contains computer programs making use of the secondary structure prediction methods of Nagano, Garnier et al., Burges et al., Chou and Fasman, Lim and Dufton and Hider. These programs were written in Fortran. The results of individual prediction methods are combined as described by Hamodrakas (1988), using a Perl program, to produce joint prediction histograms (JPH), for three types of secondary structure, which may be presented separately on a Java Applet. The output may be given either in text or graphics mode. For the latter a Java capable browser is required.
OMPdb - A database of Beta-barrel outer membrane proteins from Gram-negative bacteria
A database of Beta-barrel outer membrane proteins from Gram-negative bacteria. The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for text search within the database''s protein entries or run BLAST searches against the database. The most up-to-date version of the database (as well as all past versions) can be downloaded in various formats (flat text, XML format or raw FASTA sequences). For constructing OMPdb, multiple freely accessible resources were combined and a detailed literature search was performed. The classification of OMPdb''s protein entries into families is based mainly on structural and functional criteria. Information included in the database consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. Along with the database, a collection of profile Hidden Markov Models that were shown to be characteristic for Beta-barrel outer membrane proteins was also compiled. This set, when used in combination with our previously developed algorithms (PRED-TMBB, MCMBB and ConBBPRED) will serve as a powerful tool in matters of discrimination and classification of novel Beta-barrel proteins and whole-genome analyses., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
LepChorionDB - Lepidoptera chorion protein database
A relational database of Lepidoptera chorion proteins. The proteinaceous Lepidopteran chorions are used in our lab, as a model system towards unraveling the routes and rules of formation of natural protective amyloids. Therefore, we constructed LepChorionDB a relational database, containing all Lepidoptera chorion proteins identified to date. Lepidoptera chorion proteins can be classified in two major protein families, A and B. This classification was based on multiple sequence alignments of conserved key residues, in the central domain of, well characterized, silkmoth chorion proteins. These alignments were used to build Hidden Markov Models in order to search various DataBases. This work was a collaboration of the Department of Cell Biology and Biophysics, University of Athens and the Centre of Immunology & Transplantation Biomedical Research Foundation, Academy of Athens.
Human-gpDB: A database of human GPCRs G-proteins Effectors and their interactions
A publicly accessible, relational database of human G-Proteins and their interactions with human GPCRs and Effectors. Advanced data integration techniques make Human-gpDB very rich in context since all of the bioentities are linked to a rich variety of external data sources. High quality visualization methods make the networks more informative and the extraction of information easier. Human-gpDB is currently a very useful tool for drug targeting investigation. The sequences of G-Proteins and GPCRs are classified according to a hierarchy of different classes, families and sub-families, whereas the Effectors sequences are classified in families, subfamilies and types, based on extensive literature search. The classification of GPCRs follows the IUPHAR classification, while the Effectors classification is a unique feature and is based on their function. The database currently holds information about 713 human GPCRs, 36 human G-Proteins and 99 human Effectors. The collection of the information about the interactions between these molecules was done manually and the current status of Human-gpDB reveals information about 1663 connections between GPCRs and G-Proteins and 1618 connections between G-Proteins and Effectors.
Heuristic Pairwise alignment for Transmembrane Proteins
hPATM - heuristic pairwise alignment for transmembrane proteins
A web tool, based on a heuristic transformation of the original global pairwise and local pairwise alignment algorithms, offers objective alignments for transmembrane protein sequences. hPATM takes advantage of the information offered by the knowledge of the position of transmembrane segmets, by experiment or prediction. The heuristic approach may reveal similarities between diverge sequences with low percentages of identity and similarity. The produced alignments, based on common structural scaffolds derived by the transmembrane segments of the sequence, can be used to spot conserved non-transmembrane segments or as a basis for the production of 3-D models via homology modelling. The hPAFAG algorithm is based on the heuristic transformation of the Needleman & Wunsch and Smith & Waterman algorithms, featuring affine gap penalties. The heuristic transformation is based on two extra features: * a heuristic bonus, added to the score when two amino acids that belong to transmembrane segmens are aligned. * a heuristic gap penalty, substracted from the score when a gap is opened in a transmembrane segment. This way transmembrane segments are anchored (not by force, but by more strict alignment) together, allowing the pairwise alignment to focus on non-transmembrane segments. This web server offers a friendly interface for the hPATM command line version. The algorithm was implemented in PERL and the source code of the command line version is available on request by the authors.
A web tool to select biological sequences from a given set, with similarity / homology less than a user-defined level. This web-based application takes as input a set of N sequences and outputs a set of sequences of user-determined redundancy. Initially, the algorithm runs an all-against-all BLAST alignment on the input data set and creates an NxN matrix of pairwise distances defined by the similarity percentages. In the next step, the algorithm removes the sequence with the largest number of neighbors, causing that sequence not to be counted as a neighbor of any other sequence during the next iterations. It then reassesses the number of neighbors of each sequence and repeats the previous step until the sequences left over have no more neighbors. The user can specify the similarity (%) threshold and the minimum coverage length of the alignments. Sequences with a similarity below the threshold or a smaller coverage than the minimum length are not considered to be neighbors.
An integrated environment designed to support protein sequence and structure analysis on the web.
SCAR - Structure Creation and Representation
A web tool to create, display and manipulate structures of small molecules, proteins and DNA.
FT - Study of Residue Periodicities in Sequences
A web program that can locate residue periodicities in either amino acid or DNA sequences. It is based on an algorithm of Dr. A.D. McLachlan (1977). NOTE: You must use a Java compatible browser to run the application.
NeuroLogica Blog - Your Daily Fix of Neuroscience Skepticism and Critical Thinking
A blog by the accomplished Yale Neurologist Steven Novella, MD, covering news and issues in neuroscience, but also general science, scientific skepticism, philosophy of science, critical thinking, and the intersection of science with the media and society. Dr. Novella is an academic clinical neurologist at Yale University School of Medicine. He is the president and co-founder of the New England Skeptical Society. He is the host and producer of the popular weekly science podcast, The Skeptics'' Guide to the Universe. He is also a senior fellow and Director of Science-Based Medicine at the James Randi Educational Foundation (JREF), a fellow of the Committee for Skeptical Inquiry (CSI) and a founding fellow of the Institute for Science in Medicine. Dr. Novella also contributes every Sunday to The Rogues Gallery, the official blog of the SGU, every Monday to SkepticBlog, and every Wednesday to Science-Based Medicine, a blog dedicated to issues of science and medicine.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. An annotated and searchable collection of protein sequences for the families of DNA-binding proteins. DnaProt maximizes family information retrieval and helps reveal the relationships within the various functional binding classes. This classification system, implemented in an web-based management resource, is available for online DNA-binding pattern search and specific DNA-binding record retrieval. The database contains 3238 full-length sequences (retrieved from the SWISS-PROT database, release 38) that include, at least, a DNA-binding domain. Sequence entries are organized into families defined by PROSITE patterns, PRINTS motifs and de novo excised signatures. Combining global similarities and functional motifs into a single classification scheme, DNA-binding proteins are classified into 33 unique classes, which helps to reveal comprehensive family relationships. To maximize family information retrieval, DnaProt contains a collection of multiple alignments for each DNA-binding family while the recognized motifs can be used as diagnostically functional fingerprints. All available structural class representatives have been referenced. The resource was developed as a Web-based management system for online free access of customized data sets. Entries are fully hyperlinked to facilitate easy retrieval of the original records from the source databases while functional and phylogenetic annotation will be applied to newly sequenced genomes.
DELSA: Data-Enabled Life Sciences Alliance
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 1, 2022. Organization whose mission is to build and promote a sustainable ecosystem of professional societies, funding agencies, foundations, companies, and citizens together with life science researchers and innovators in computing, infrastructure and analysis with the expressed goal of translating new discoveries into tools, resources and products.
University of Western Brittany; Brest; France
French university, located in Brest, in the Academy of Rennes.
A software infrastructure, course and tool set for teaching bioinformatics, and biology through the use of models. This platform for learning bioinformatics through problem solving aims to make learning bioinformatics fun and easy. Learning bioinformatics usually requires solving computational problems of varying difficulty that are extracted from real challenges of molecular biology. Rosalind offers an array of intellectually stimulating problems that grow in biological and computational complexity; each problem is checked automatically, so that the only resource required to learn bioinformatics is an internet connection. Rosalind also promises to facilitate improvements in standard bioinformatics education by providing a vital teaching aid and a central homework resource. Rosalind is inspired by Project Euler, Google Code Jam, and the ever growing movement of free online courses. The project''s name commemorates Rosalind Franklin, whose X-ray crystallography with Raymond Gosling facilitated the discovery of the DNA double helix by Watson and Crick. We hope that Rosalind will inspire a new generation of bioinformatics students by attracting biologists who want to develop vital programming skills at their own pace in a unique environment as well as programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication.
Extensible Neuroimaging Archive Toolkit CENTRAL
Online repository of open access images including MR Sessions, MRI, Freesurfer APARC, Freesurfer ASEGs, Clinical Assessments, Atlas Scaling Factors, and Fast Segmentations data. CENTRAL currently contains 374 Projects, 3808 Subjects, and 5174 Imaging Sessions (June 2014). Central is powered by XNAT (The Extensible Neuroimaging Archive Toolkit), an open source software platform designed to facilitate management and exploration of neuroimaging and related data. XNAT includes a secure database backend and a rich web-based user interface.
A blog about neuromarketing, a research methodology born of the fusion of neuroscience and research techniques of conventional marketing in Spanish by Sergio Monge. If you want to read it in English, Google translate does a good job. A good way to learn about practical applications of neuroscience to a field with little exposure in conventional neuroscience academia. The neuromarketing is a branch of market research that uses biometric measurement systems in their studies (EEG, MRI, galvanic skin response, eye-tracking, heart rate ...). One of the most significant differences with conventional research neuromarketing is not content with the verbal statements of the subjects, but aims to go further, unraveling the effect of the unconscious and emotions in decision-making. The author of Neuromarca is Sergio Monge, Degree in Advertising and Public Relations and PhD in Audiovisual Communication and Advertising from the University of the Basque Country / Euskal Herriko Universitatea. Sergio has experience in the field of Corporate Communications and is familiar with the blogosphere and the Internet communication environment. He currently teaches full time for the UPV / EHU and offers some services such as communications and marketing consultant. The interest of the author of this blog by neuroscience and neuromarketing longstanding but his attendance Neuro Connections conference, held from 5 to 7 febreo 2009 in Krakow (Poland), is the main reason he began writing Neuromarca. The intention is that Neuromarca is a repository of articles in Spanish about neuromarketing, so that could be a reference to the Hispanic blogosphere in this emerging discipline.
NeuroDojo - Brains behaviour and evolution
A blog by Zen Faulkes, an invertebrate neuroethologist at The University of Texas-Pan American.
An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.
Wellcome Trust Sanger Institute Mouse Resources Portal
Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute' '''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute' '''s primary screen.
Software for statistical analysis of peptide microarrays. It uses an integrated analytical method for analyzing peptide microarray antibody binding data, from normalization through subject-specific positivity calls and data integration and visualization.
EnzyMiner automatically identifies the PubMed abstracts that contain information on the impact of a protein level mutation on the stability or the activity of a given enzyme. For querying EnzyMiner, please choose an enzyme from the list and specify if you are interested in disease related abstracts or non-disease related abstracts. For disease related abstracts, the mutation list and direct links to the abstracts will be displayed. For those abstracts that are related to non-diseases, in addition to having the mutation list, the abstracts are also categorized into two groups. These two groups determine whether the mutation has an effect on the enzyme''s stability or functionality. If your target enzyme is not in the list, please write the enzyme name to the query box. We will run the EnzyMiner for the desired enzyme and add the results to our database. EnzyMiner has been developed by Computational Biology Lab of Sabanci University.
Pathway and Network Oriented GWAS (Genome-Wide Association Study) Analysis
Pathway and Network Oriented GWAS Analysis
Pathway and Network-Oriented GWAS Analysis
A web server to devise functionally important pathways through the identification of single nucleotide polymorphism (SNP)-targeted genes within these pathways. The strength of the methodology stems from its multidimensional perspective, where evidence from the following five resources is combined: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein-protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways.
InterSpecies Analysing Application using Containers
Interspecies Analysing Application using Containers - ISAAC
ISAAC (Interspecies Analysing Application using Containers)
ISAAC - InterSpecies Analysing Application using Containers
Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups.
A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems.
Reproductive Trait and Phenotype Ontology
Ontology for livestock reproductive traits and phenotypes
A free, open-source extension to MediaWiki - the wiki software that powers Wikipedia - that helps to search, organize, tag, browse, evaluate, and share the wiki''s content. While traditional wikis contain only text which computers can neither understand nor evaluate, SMW adds semantic annotations that allow a wiki to function as a collaborative database. Semantic MediaWiki introduces some additional markup into the wiki-text which allows users to add semantic annotations to the wiki. While this first appears to make things more complex, it can also greatly simplify the structure of the wiki, help users to find more information in less time, and improve the overall quality and consistency of the wiki. A large number of related extensions have been created that extend the ability to edit, display and browse through the data stored by SMW: the term Semantic MediaWiki is sometimes used to refer to this entire family of extensions.
A personal weblog of developmental cognitive neuroscience by Craig Bennett in the Department of Psychology at the University of California, Santa Barbara.
A collection of population life tables covering a multitude of countries and many years. Most of the HLD life tables are life tables for national populations, which have been officially published by national statistical offices. Some of the HLD life tables refer to certain regional or ethnic sub-populations within countries. Parts of the HLD life tables are non-official life tables produced by researchers. Life tables describe the extent to which a generation of people (i.e. life table cohort) dies off with age. Life tables are the most ancient and important tool in demography. They are widely used for descriptive and analytical purposes in demography, public health, epidemiology, population geography, biology and many other branches of science. HLD includes the following types of data: * complete life tables in text format; * abridged life tables in text format; * references to statistical publications and other data sources; * scanned copies of the original life tables as they were published. Three scientific institutions are jointly developing the HLD: the Max Planck Institute for Demographic Research (MPIDR) in Rostock, Germany, the Department of Demography at the University of California at Berkeley, USA and the Institut national d''��tudes d��mographiques (INED) in Paris, France. The MPIDR is responsible for maintaining the database.
University of Oklahoma College of Medicine; Oklahoma; USA
University of Oklahoma College of Medicine
College of Medicine is the largest component of the University of Oklahoma Health Sciences Center and is at the center of OU Health. OU College of Medicine offers Physician Associate Program and MD/PhD dual degree program to meet unique interests of medical students. The college also offers students the option to take MPH coursework.
A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Baylor College of Medicine; Department of Pharmacology
The Department of Pharmacology at Baylor College of Medicine is dedicated to research and education in modern pharmacology. Our research interests cover a broad spectrum of topics including chemical biology, drug discovery, clinical pharmacology, computational biology, molecular genetics, protein chemistry, protein design, psychopharmacology and structural biology. Our accomplished faculty and well equipped laboratories offer graduate students outstanding opportunities to begin successful careers. Learn more about earning a graduate degree at Baylor College of Medicine by visiting Graduate School of Biomedical Sciences.
A publicly accessible database containing data on Affymetrix DNA microarray experiments, and Serial Analysis of Gene Expression, mostly on human and mouse stem cell samples and their derivatives to facilitate the discovery of gene functions relevant to stem cell control and differentiation. It has grown in both size and scope into a system with analysis tools that examine either the whole database at once, or slices of data, based on tissue type, cell type or gene of interest. There is currently more than 210 stem cell samples in 60 different experiments, with more being added regularly. The samples were originated by researchers of the Stem Cell Network and processed at the Core Facility of Stemcore Laboratories under the management of Ms. Pearl Campbell in the frame of the Stem Cell Genomics Project. Periodically, new expression data is submitted to the Gene Expression Omnibus (GEO) repository at the National Center for Biotechnological Information, in order to allow researchers to compare the data deposited in StemBase to a large amount of gene expression data sets. StemBase is different from GEO in both focus and scope. StemBase is concerned exclusively with stem cell related data. we are focused in Stem Cell research. We have made a significant effort to ensure the quality and consistency of the data included. This allows us to offer more specialized analysis tools related to Stem Cell data. GEO is intended as a large scale public archive. Deposition in a public repository such as GEO is required by most important scientific journals and it is advantageous for a further diffusion of the data since GEO is more broadly used than StemBase.
An intelligent search engine to retrieve biomedical correlations from MEDLINE, based on indexing by Natural Language Processing and Text Mining techniques. You can find abstracts/sentences in MEDLINE by specifying semantics of correlations; for example, What activates p53 and What causes colon cancer. Semantic search uses a semantic query for finding biomedical correlations. Input a subject, a verb, and an object of a concept (or either of them) into a form. Results of the query will be shown in a second. (E.g., What does p53 activate? (subject=p53, verb=activate)) Reference: Miyao, Yusuke, Tomoko Ohta, Katsuya Masuda, Yoshimasa Tsuruoka, Kazuhiro Yoshida, Takashi Ninomiya and Jun' '''ichi Tsujii (2006) Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. Proceedings COLING-ACL 2006. Sydney, Australia, pp. 1017--1024.
A project that observes the processes of adaptive evolution in nature, and tests evolutionary hypotheses, by studying populations of guppies on the Caribbean island of Trinidad. Darwin thought that evolution by natural selection occurred very slowly, over hundreds if not thousands of years. Evolutionary biologists now know that evolutionary changes in species can happen very quickly, over a relatively few generations. The National Science Foundation (NSF), through its Integrative Biological Research (FIBR) program, is funding a 5-year study by 13 biologists from colleges, universities, and research institutions throughout the United States and Canada, to study the relationship of adaptive evolution and environmental circumstances. The Trinidadian guppy (Poecilia reticulata) is an excellent species for these purposes because: * It matures rapidly (one generation = 3-4 months) * It inhabits different ecological environments that can be easily manipulated On Trinidad, guppies live in streams, or portions of streams, that can differ in the species of predators that the guppies have to contend with. Some streams are high-predation environments, others low-predation. Different predation environments are often right next to one another, separated by a waterfall (which neither guppies nor predators can cross). Guppies from high-predation environments experience much higher mortality rates than do guppies in low-predation environments. High mortality is associated with the following characteristics, all of which have a genetic basis: * Earlier maturity * Greater investment of resources in reproduction * More and smaller offspring. We have found that mortality rates can be manipulated by: * Transplanting guppies from high-predation localities into sites from which they and their predators had previously been excluded by natural waterfalls, thus lowering mortality rates; * Introducing predators into low-predation sites, thus increasing mortality rates. Such experiments have shown that species evolve as predicted by theory. We have also found that evolution by natural selection can be remarkably fast, on the order of four to seven orders of magnitude faster than had been inferred from the fossil record.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19,2021. A model of peer review, providing independent and standardized peer review that can be accepted and shared across all types of journals and distribution systems. Rubriq can provide rigorous reviews by the same qualified peers who review for journals, but with a standardized scorecard that can be used in any publishing model. The system will enable faster, more consistent reviews, and will help match papers with the right journals. Authors, reviewers and journal editors are encouraged to sign up in the earliest phases, so you can be among the first to participate and provide feedback.
Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix.
Database storing and integrating genomic data of diamondback moth (DBM), Plutella xylostella (L.). It provides comprehensive search tools and downloadable datasets for scientists to study comparative genomics, biological interpretation and gene annotation of this insect pest. DBM-DB contains assembled transcriptome datasets from multiple DBM strains and developmental stages, and the annotated genome of P. xylostella (version 2). They have also integrated publically available ESTs from NCBI and a putative gene set from a second DBM genome (KONAGbase) to enable users to compare different gene models. DBM-DB was developed with the capacity to incorporate future data resources, and will serve as a long-term and open-access database that can be conveniently used for research on the biology, distribution and evolution of DBM. This resource aims to help reduce the impact DBM has on agriculture using genomic and molecular tools.
A video production and hosting resource designed to help scientists record and share lab protocols. The site also makes video protocols available.
Computerized Anatomical Reconstruction and Editing Toolkit
Computerized Anatomical Reconstruction Editing Toolkit
Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems.
Open-source scientific workflow and provenance management system that provides support for simulations, data exploration and visualization. It was designed to manage these rapidly-evolving workflows. VisTrails has a comprehensive provenance infrastructure that maintains detailed history information about the steps followed and data derived in the course of an exploratory task: VisTrails maintains provenance of data products, of the workflows that derive these products and their executions. This information is persisted as XML files or in a relational database, and it allows users to navigate workflow versions in an intuitive way, to undo changes but not lose any results, to visually compare different workflows and their results, and to examine the actions that led to a result. It also enables a series operations and user interfaces that simplify workflow design and use, including the ability to create and refine workflows by analogy and to query workflows by example. VisTrails supports the creation and execution of workflows. It allows the combination of loosely-coupled resources, specialized libraries, grid and Web services. The released version comes with support for several packages including, VTK, Image Magick, Web Services, and pylab. You can also download packages contributed by users, as well as create your own packages/modules. Workflows can be run interactively, through the VisTrails GUI, or in batch using a VisTrails server. VisTrails is written in Python and it uses the multi-platform Qt library for its user interface. It runs on Mac, Linux and Windows. Provenance-rich results derived by VisTrails can be included in LaTeX, Wiki, Microsoft Word and PowerPoint documents.
SpliceDB: canonical and non-canonical splice site sequences in mammalian genes
Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs.
RUVSeq: Remove Unwanted Variation from RNA-Seq Data
Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.
Project to enhance online research articles across all of the RSC journals by identifying the compounds and subject terms to make it easier for users to find the articles that are most relevant to them, as well as providing downloadable information about compounds. RSC editors annotate compounds, concepts and data within articles and link these to additional electronic resources such as biological databases. This will transform the free text within an article to add new ways of identifying, retrieving and presenting the information within RSC publications. Text mining is used to attach structural information (InChI, SMILES and CML) to chemical names, especially chemical names which have never been seen before, and extensions handle terms defined in the Gold Book and ontology entries. The text mining is reviewed by skilled Technical Editors before publication.
Moss Aphasia Psycholinguistics Project Database
A database of experimental behavioral data from > 170 aphasia patients who exhibited language impairments secondary to chronic left hemisphere stroke. The core of the database is individual-trial performance data from picture naming. Picture naming is a primary test of lexical processing. The task taps a critical juncture in the language system because naming mediates between high-level conceptual and syntactic processing and low-level phonological processing. Difficulty in this task is present to varying degrees in nearly all aphasic individuals. This site allows researchers to search through naming data from over 170 patients. Searches can narrow in on data subsets based on patient characteristics (e.g. time since aphasia onset, clinical diagnosis), stimulus characteristics (e.g. semantic category, lexical frequency) and task performance (e.g. error type). The data available on this site can be used to test hypotheses about naming impairment and aphasic impairment generally. Once the basic analysis tools of the site are exhausted, users can export the raw data for further analysis and visualization. The web database represents years of data collection. Most were recruited to the research program at Moss Rehabilitation Research Institute (MRRI).
An ontology for the description of biological and clinical investigations built with international, collaborative effort. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This includes a set of universal terms that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. Currently OBI is being built under the Basic Formal Ontology (BFO). This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project.
ROM is an on-line Registry of Outcome Measures and associated tools designed to give guidance, information and assistance to international collaborative teams of reviewers undertaking the crucial task of choosing the right outcome measures (OMs) for neuromuscular disease trials and studies. It is also hoped that the Registry will reduce duplication of effort in this area. Outcome measures are the tests that investigators perform to decide whether a treatment being tested in a clinical trial is having any effect. These can come in many different forms from assessing how far a patient can walk in six minutes to looking at changes in their muscle through a biopsy and using the right outcome measure is a vital step in making sure a trial can really prove whether or not a treatment works. The searchable Registry contains information about OMs, such as a description, details of validation, availability, contact details for providers, and references to related documents including manuals and training videos. Review teams can record OMs by category as being considered for a specific study or trial and benefit from seeing the OM choices being considered by other review teams. A manual gives advice on how to assess and select OMs. Information contained in ROM may also prove useful to doctors, clinicians, physiotherapists, industry and other organizations with an interest in OMs relevant to NMD research.
The NeuroSys Data Management System is a set of software tools created to enhance the process of data annotation, analysis and web publication. The system provides a set of easy to use software tools for data sharing by the scientific community. It enables researchers to build their own custom designed data management systems. Another branch of the system provides tools for viewing anatomical and physiological data. The initial implementation of the software, simply called NeuroSys, allowed users to create XML databases. Centered on a Java-based client application, it provided a way to design and construct custom GUI screens for data entry, data query and retrieval. It also automatically created a controlled vocabulary and supported the extension and/or migration of that vocabulary to whatever standard might be chosen at a later date. Most importantly, it empowered end-users to carry out all of these operations without the expertise and expense of trained database programmers. Right now a transition is underway, converting NeuroSys into a web-based application called Yogo. Yogo will retain all of functionality of NeuroSys, while adding new features. The new features will include automated data import from laboratory devices (such as microscopes and amplifiers), and a limited scope HTML editor to make data collections available on the web. Another component of the system is MIEN, a suite of data visualization and analysis tools. MIEN is intended for viewing anatomical and physiological data, and for annotating neuronal models.
Public flagship research university in Eugene, Oregon, United States.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 13, 2012. Cell Press continues to evolve the way scientific information is conveyed, and has made Article of the Future available for all review article formats, in addition to the research article format launched in January. With this latest release, all articles are also now more customizable, giving users added flexibility and control over how they read research and reviews. Readers can now: * Adjust the widths of the text and figure panels using a horizontal slider, allowing text and figures to be viewed side-by-side in a way that best suits the readers' needs. (Available in the Summary and Main Text tabs for reviews, and in the Results tab for research articles) * Easily identify proteins and small molecules and access additional information about these compounds with Reflect, winner of the 2009 Elsevier Grand Challenge * Reveal greater detail in figures with improved zoom functionality * Search across all tabs within an article * View the article in the standard, linear format with one click
A biomedical ontology in the vaccine domain
HyBrow: A prototype system for computer-aided hypothesis evaluation
A prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. It consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology, and programs to perform hypothesis design and evaluation. There are five key components involved in making HyBrow work. # The Event-based ontology for representing biological knowledge # The Discreet Event Systems based conceptual framework which provides the theory that allows us to make statements in a context free formal language (made up of the ontology) and evaluate the statements for validity using constraints declared on existing data # The rule library that provides the steps to apply those constraints and decide support, contradiction or no comment. # The relational database that stores existing information structured into the ontology. # The user interface.
An open-membership International community to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data. Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards: * the implementation of new genomic standards * methods of capturing and exchanging metadata * harmonization of metadata collection and analysis efforts across the wider genomics community
NeuroElectro: organizing information on cellular neurophysiology
A database of elecrophysiological properties text-mined from the biomedical literature as a function of neuron type. Specifically, NeuroElectro seeks to extract information about the electrophysiological properties (e.g. resting membrane potentials and membrane time constants) of diverse neuron types from the existing literature and place it into a centralized database. There are 252 neurons currently available, with the naming convention established in NeuroLex.
University in Norway, located in Oslo. Its faculties include Lutheran Theology, Law, Medicine, Humanities, Mathematics, natural sciences, social sciences, Dentistry, and Education.
University of Otago; Dunedin; New Zealand
Collegiate university based in Dunedin, Otago, New Zealand.
Children''s Tumor Foundation NF Registry
A patient registry to identify people with neurofibromatosis (NF) who are interested in participating in clinical trials, as well as determining the commonality of specific characteristics of NF. The NF Registry is committed to secure methodologies and pioneering research that will lead to improving the health and well-being of individuals and families affected by NF. This registry has been created to collect data on large numbers of people with NF. This has never existed before and will help: * Identify people who may be eligible for clinical trials or other research studies being conducted in the field of NF. New clinical trials are launched each year yet challenges identifying participants too often mean that these studies finish late or never really get started. Today, 80 percent of trials fail to recruit enough volunteers within planned timelines. Under enrollment is one of the most significant problems facing NF drug development. Together, we can solve it. * Determine the commonality of specific NF characteristics. This will help researchers and doctors devise better ways to care for people with NF If you or your child has been diagnosed with neurofibromatosis (NF) please join the NF Registry today. It''s quick, it''s easy, and it matters. The key to treatments lies within you researchers can''t deliver treatments without committed volunteers.
Collaborative Annotation Toolkit for Massive Amounts of Image Data
A toolkit designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy. The interface is inspired by GoogleMaps, with which it shares basic navigation concepts, enhanced to allow the exploration of 3D biological image data acquired by optical or physical sectioning microscopy techniques. The interface enables seamless sharing of regions of interest through bookmarks and synchronized navigation through multiple registered data sets. With massive biological image data sets it is unrealistic to create a sustainable centralized repository. A unique feature of CATMAID is its partially decentralized architecture where the presented image data can reside on any Internet accessible server and yet can be easily cross-referenced in the central database. In this way no image data are duplicated and the data producers retain full control over their images. CATMAID is intended to serve as data sharing platform for biologists using high-resolution imaging techniques to probe large specimens. Any high-throughput, high-content imaging project such as gene expression pattern screens would benefit from the interface for data sharing and annotation. Features: * Fast terabyte-scale image data browsing * Collaborative microcircuit reconstruction and annotation * Flexible hierarchical semantic annotation * Multiple linked image stack display * Neuron Catalog * SVG and WebGL-based neuronal morphology viewer * Open source software
A trusted third-party gatekeeper of patient data from participants in a rare disease ecosystem, collecting and managing the information in a scalable, cost-effective manner. Each patient registry provides critical disease knowledge which makes that disease easier to study, increasing the probability a treatment can be developed. PatientCrossroads takes a network approach to patient registry programs. Unlike companies that merely sell registry software, we offer a full range of administration, management, and genetic curation services. What does this consolidated, patient-centric approach to patient registries mean? * Patients can more easily find registries and provide their valuable data (including locations of blood and tissue samples as well as reports of diagnoses, disease symptoms, treatment usage, and lifestyle activities) * Patients can be confident in the privacy of their de-identified data and the knowledge that PatientCrossroads does not sell patient data * Researchers and pharmaceutical companies have a larger, more easily accessible pool of potential patients for research studies and clinical trials targeting specific rare diseases * Pharmaceutical companies can collect post-market surveillance data in a more scalable and cost-effective manner * Rare disease advocacy and research foundations can more easily organize their global patient populations for inclusion in trials and studies
Children's Tumor Foundation: Ending Neurofibromatosis Through Research
A non-profit dedicated to ending neurofibromatosis (NF) through research. It is the leading nonprofit funding source of NF research in the world. The mission of The Children''s Tumor Foundation is to: * Encourage and support research and the development of treatments and cures for neurofibromatosis types 1 and 2, schwannomatosis, and related disorders (hereafter collectively referred to as NF); * Support persons with NF, their families, and caregivers by providing thorough, accurate, current, and readily accessible information; * Assist in the development of clinical centers, best practices, and other patient support mechanisms (but not including direct medical care) to create better access to quality healthcare for affected individuals; and, * Expand public awareness of NF to promote earlier and accurate diagnoses by the medical community, increase the non-affected population''s understanding of the challenges facing people with NF, and encourage financial and other forms of support from public and private sources. Through the implementation of the Foundation''s research initiatives, progress is being made on all fronts and for all types of NF; from discovery studies understanding the molecular signaling deficits that cause the manifestations of NF to the growth of preclinical drug screening initiatives and the emergence of a growing number of clinical trials. The Foundation advances research through strategically integrated programs that speed therapies from the lab to the patient.
Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases.
Software application for inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. (entry from Genetic Analysis Software)
Database that allows scientists without specialized training to effectively utilize Molecular Libraries Program (MLP) data. It allows the research community to utilize and develop new chemical probes to explore biological functions by building a central, permanently accessible link to all aspects of chemical biology data and analyses. The project is split into two basic segments, the first segment delivering functionality for a data dictionary, as well as assay protocol and data entry tools. The second builds a data warehouse for analysis and visualization, accessible through a public RESTful API. They will initially deploy two clients that will use this API - a web-based interface and a desktop application. Advanced access to data and the platforms will also be available to support plug-in development and the repackaging of data by others. Initially the project will focus on small molecule assays. Features: * allow scientists to annotate assay data using a common, shared language * provide facile access to data, integrating existing chemical biology and computational resources * enable meaningful analysis and interpretation of discovery data by the research community * support hypothesis generation for iterative probe- and drug-discovery projects * inform the entire small molecule discovery and development process, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
International Neuroinformatics Coordinating Facility Swiss Node
Portal to promote the activities of Swiss research groups working in the field of neuroinformatics, and encourage and facilitate collaborations both between them and with the wider International Neuroinformatics Coordinating Facility community. The initial focus is on neural reconstruction as a theme, both from image data acquired via light microscopy and electron microscopy; these data are invaluable for identifying neural circuits and the simulation and modelling of these systems. Open Source software packages developed for neuroinformatics in Switzerland and useful data sets provided by groups in Switzerland are freely available for use, subject to appropriate attribution.
Access to semantically processed full-text of the open-access subset of PubMed Central. The RDF model and resulting dataset make extensive reuse of existing ontologies and semantic enrichment services. The entire enriched data set is available for download or via REST services. A SPARQL query interface to 10,000 enriched articles is available. The entire collection of RDF documents is available for download as a collection of ZIP files. Each document consists of three RDF files serialized as XML.
An open source data sharing and visualization platform for neuroimaging data, that uses the OntoNeuroLOG ontology. Shanoir (Sharing NeurOImaging Resources) is an open source neuroinformatics platform designed to share, archive, search and visualize neuroimaging data. It provides a user-friendly secure web access and offers an intuitive workflow to facilitate the collecting and retrieving of neuroimaging data from multiple sources and a wizard to make the completion of metadata easy. Shanoir comes with many features such as anonymization of data, support for multicenter clinical studies on subjects or group of subjects. Shanoir offers an ontology-based data organization (OntoNeuroLOG). Among other things, this facilitates the reuse of data and metadata, the integration of processed data and provides traceability trough an evolutionary approach. Shanoir allows researchers, clinicians, PhD students and engineers to undertake quality research projects with an emphasis on remote collaboration. As a secured J2EE web application, it therefore allows you safely store and archive, with no more requirements than a computer with an internet connection. Furthermore, Shanoir is not only a web application: it is also a complete neuroinformatics platform in which you can easily integrate your existing processing tools or develop your own ones: see ShanoirTk. Shanoir is a project carried out by the VisAGeS Team, based at IRISA (INRIA Rennes - Bretagne Atlantique Research Centre). This software is released under QPL 1.0 license.
A semantic web-powered knowledge management framework, aiming at a streamlined application development cycle and following a semantic web in a box approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. It is targeted at rapid application deployment of new applications in any research field, supported by a comprehensive integration engine and an advanced data distribution API.
Multidimensional Magnetic Resonance Histology Atlas of the Wistar Rat Brain
Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage.
KCCMR Chimpanzee Biomedical Research Resource
Keeling Center for Comparative Medicine and Research Chimpanzee Care Center
One of only four NCRR-supported centers with the capability to conduct biomedical research in the chimpanzee, it offers chimpanzee-derived cell lines, antibodies and other biological materials, along with a registry of biologic reagents that are known to work in the chimpanzee. The Resource and Management Core is responsible for providing animal resources, tissues/biological fluids, cell lines, expert advice and research support to NIH extramural and intramural programs, other federal agencies and private sponsors. The Resource-Related Research Core conducts research to improve the health of the animals maintained, with special emphasis on studies that will enhance the usefulness of the chimpanzee as a model for studies of human disease. Resource-related research will focus on characterization of the immune system of the chimpanzee, expansion of our understanding of chimpanzee cardiomyopathy as a potential human disease model and comparisons of the physiologic and immunological consequences of research manipulations on chimpanzees trained to voluntarily cooperate with research procedures. By expanding the resources available, conducting resource-related research and containing costs, the CBRR will continue to provide a critically important, highly specialized research resource to address important human health issues.
Owl Monkey Breeding and Research Resource
KCCMR Owl Monkey Breeding and Research Resource
Keeling Center for Comparative Medicine and Research Owl Monkey Breeding and Research Resource
Owl Monkey research portal that is a national resource providing owl monkeys of known genetic background, tissues, cell lines and biological fluids from owl monkeys, and a registry of normal values and reagents that can be used in studies that utilize owl monkeys. This is the only such resource for owl monkeys available to the NIH extramural grantee community and has expanded the mission of the Keeling Center's Neotropical Primate Breeding and Research Resource (NPBRR) to a second New World monkey genus. This resource helps meet the needs of the National Institute for Allergy and Infectious Diseases (NIAID) intramural malaria research program. The longer term goal, to create a self-sustaining breeding resource of owl monkeys, is being accomplished by applying expertise that has been developed at the NPBRR for owl monkeys with resource-related research that specifically focuses on reducing adult mortality and improving reproductive efficiency of the owl monkey. This project is helping address the need for resources of alternative primate species to reduce the demand for rhesus monkeys, which are in critically short supply. The OBMRR meets the needs of the biomedical research community in three ways: * It provides a national resource for laboratory-born owl monkeys. The resource provides tissues and biological fluids to investigators throughout the country, thus reducing the need for living animals for these studies. * It has an active research component that continues to add new information about the biology of the owl monkey, with a particular emphasis on reproduction and colony management. * The resource is a source of expertise for owl monkey biology, management and husbandry that can be accessed by anyone anytime.
Squirrel Monkey Breeding and Research Resource
KCCMR Squirrel Monkey Breeding and Research Resource
Keeling Center for Comparative Medicine and Research Squirrel Monkey Breeding and Research Resource
SMBRR maintains the only self-sustaining national research resource of laboratory-born squirrel monkeys, their tissues and other biological materials, as well as the expertise to carry out research on this animal. Scientists with NIH grants utilize squirrel monkeys to study many diseases that threaten human health including Alzheimer's disease and other disorders of the central nervous system, drug addiction, malaria, and viral diseases. Center that carries out research on squirrel monkey biology and its research uses. It meets the needs of the biomedical research community in three ways: providing national resource for laboratory-born squirrel monkeys, having active research component that continues to add new information about the biology of the squirrel monkey with a particular emphasis on reproduction and colony management, and acts as a source of expertise for squirrel monkey biology, management and husbandry.
Schizophrenia related portal that aims to solve the mystery of genetic predisposition to psychosis, develop new methods for early diagnosis and prevention, and discover new treatments that will cure people suffering from it. Our objectives are to fully characterize: # neurobiological mechanisms related to susceptibility genes for schizophrenia and related clinical disorders; # genetic variation in aspects of cognition and emotionality associated with schizophrenia; and # small molecular targets for novel therapies. A unique feature of this Program is that its diverse scientific resources will be focused on a highly specific scientific agenda, that is to acquire the critical biological information about the susceptibility genes associated with schizophrenia and related illnesses. Our mission and goal, to understand the basic mechanisms of serious mental illness, has again guided us into new areas of research and to new insights. We have found evidence of new genes implicated in the cause of schizophrenia and involved in brain functions related to cognition and emotion and we have begun to explore how genes interact with each other and with the environment to individualize risk for these conditions. We are working now with over 20 genes related to schizophrenia. One of the key developments in our research over the past year has been the emergence of some targets for the development of novel therapeutics. We have discovered a new schizophrenia susceptibility gene, KCNH2, which represents the first clear target for the development of novel treatments. Just in this past year, for example, we published the first extensive statistical analysis of how schizophrenia genes may vary in their risk effects based on different genetic background (Nicodemus et al Hum Gen 2006), the first studies of schizophrenia genes interacting in effecting gene expression in brain (Lipska et al Hum Mol Genetics 2006a, Lipska et al Hum Mol Gen 2006 b); the first evidence that the mechanism of genetic association of NRG1 with schizophrenia involves a novel isoform of the gene in human brain (Law et al PNAS 2006), and the first evidence that MAOA may be linked to mood and impulse control because it effects critical mood regulatory neural networks (Meyer-Lindenberg et al PNAS 2006).
Shared Health Research Informatics NEtwork
Software providing a scalable query and aggregation mechanism that enables federated queries across many independently operated patient databases. This platform enables clinical researchers to solve the problem of identifying sufficient numbers of patients to include in their studies by querying across distributed hospital electronic medical record systems. Through the use of a federated network protocol, SHRINE allows investigators to see limited data about patients meeting their study criteria without compromising patient privacy. This software should greatly enable population-based research, assessment of potential clinical trials cohorts, and hypothesis formation for followup study by combining the EHR assets across the hospital system. In order to obtain the maximum number of cases representing the study population, it is useful to aggregate patient facts across as many sites as possible. Cutting across institutional boundaries necessitates that each hospital IRB remain in control, and that their local authority is recognized for each and every request for patient data. The independence, ownership, and legal responsibilities of hospitals predetermines a decentralized technical approach, such as a federated query over locally controlled databases. The application comes with the SHRINE Core Ontology but it can be used with any ontology, even one that is disease specific. The Core Ontology is designed to enable the widest range of studies possible using facts gathered in the EMR during routine patient care. SHRINE allows multiple ontologies to be used for different research purposes on the same installed systems.
A social visualization repository for the scientific workflow management system VisTrails providing a platform for sharing and executing computational tasks. It adopts the model used by social Web sites and that integrates a set of usable tools and a scalable infrastructure to provide an environment for scientists to collaboratively analyze and visualize data. crowdLabs aims to foster collaboration but was specifically designed to support the needs of computational scientists, including the ability to access high-performance computers and manipulate large volumes of data. By providing mechanisms that simplify the publishing and use of analysis pipelines, it allows IT personnel and end users to collaboratively construct and refine portals. This lowers the barriers for the use of scientific analyses and enables broader audiences to contribute insights to the scientific exploration process, without the high costs incurred by traditional portals. In addition, it supports a more dynamic environment where new exploratory analyses can be added on-the-fly.
Multidisciplinary data repository for a consortium of universities in the Netherlands housing over datasets with a focus on scientific and technical data. Most data were produced by Dutch researchers including datasets from doctoral research. Users can deposit up to 1G by completing an upload form. Collection development foci include applied sciences, biomedical technology, earth sciences, and technology and construction. 4TU.Datacentrum is a collaboration of the libraries of the three leading technical universities - Delft University of Technology, Eindhoven University of Technology and the University of Twente.
Complete three-dimensional data set of reference magnetic resonance microscopy (MRM) images of the human embryo representing 10 stages of development for each of 18 human embryos representing Carnegie stages 10 through 23, a critical embryonic time period for organogenesis. The users of the collection are able to manipulate the data on their own personal computers to view any slice from any plane of sectioning. Dynamic rotational views of whole embryos and time-lapse views of the growing embryo are accessible. Each embryo was imaged with three magnetic resonance pulse sequences to obtain fully-registered T1-weighted, T2-weighted, and diffusion-weighted image datasets. A complete set of coronal, sagittal, and axial images were produced from each image data set. Several major organs were isolated from each T1-weighted embryo data set using image segmentation methods and separate image data sets were created to represent each of these organs. Additionally, each embryo was optically photographed under a low-power microscope. The formalin-fixed specimens came from the highly respected Carnegie Collection of Human Embryos. This is the first distributable work to document in three dimensions the anatomy of the human embryonic time period. Pseudo- time-lapse movies were created using morphing software to represent the fourth dimension (time). Carnegie stages are a system used by embryologists to describe the apparent maturity of embryos. An embryo is assigned a Carnegie stage (numbered from 1 to 23) based on its external features. This staging system is not dependent on the chronological age nor the size of the embryo. The stages, are in a sense, arbitrary levels of maturity based on multiple physical features. Embryos that might have different ages or sizes can be assigned the same Carnegie stage based on their external appearance because of the natural variation which occurs between individuals. Postovulatory age is frequently used by clinicians to describe the maturity of an embryo. It refers to the length of time since the last ovulation before pregnancy. Postovulatory age is a good indication of embryonic age because the time of ovulation can be determined and fertilization must occur close to the time of ovulation. The terms gestation, pregnancy, and conception are usually avoided in describing embryonic age because fertilization is not universally accepted as the commencement of development (some consider implantation as the beginning of development). MRM was performed at the Center for In-vivo Microscopy at Duke University. Image processing and data managment was performed at the School of Art and Design, University of Michigan.
Embryo Images Normal and Abnormal Mammalian Development
Embryo Images Normal & Abnormal Mammalian Development
Tutorial that uses scanning electron micrographs (SEMs) as the primary resource to teach mammalian embryology. The 3-D like quality of the micrographs coupled with selected line drawings and minimal text allow relatively easy understanding of the complex morphological changes that occur in utero. Because early human embryos are not readily available and because embryogenesis is very similar across mammalian species, the majority of micrographs that are utilized in this tutorial are of mouse embryos. The remainder are human. This tutorial is divided into units that may be studied in any order. All of the images have a legend that indicates the age of the embryo. If it is a mouse embryo, the approximate equivalent human age is indicated. To minimize labeling, color-coding is widely used. To view the micrographs without color, the cursor may be placed on the image. The SEMs used in this tutorial are from the Kathleen K. Sulik collection. The line drawings have been used with permission from Lippincott Williams & Wilkins and are from the 6th and 7th editions of Langman''s Medical Embryology by T.W. Sadler.
Software package for the analysis of recombination rates from population genetic data (entry from Genetic Analysis Software)
Non-profit professional society dedicated to advancement of the field of developmental biology. Excellence in research and education in developmental biology is fostered; advice and resources on careers in developmental biology is provided; and information for the public on relevant topics in developmental biology is provided. Perhaps most importantly, a communication hub for all developmental biologists is provided. The SDB is associated with the journal Developmental Biology; the SDB organizes scientific meetings that focus on developmental biology; the SDB has established programs to interface with the international community of developmental biologists; and the SDB maintains this society web site that covers all aspects of developmental biology. Membership includes developmental biologists at all stages of their careers from around the world.
Brad Smith Magnetic Resonance Imaging of Embryos
Data set of image collections and movies including Magnetic Resonance Imaging of Embryos, Human Embryo Imaging, MRI of Cardiovascular Development, and Live Embryo Imaging. Individual MRI slice images, three-dimensional images, animations, stereo-pair animations, animations of organ systems, and photo-micrographs are included.
One of the largest universities in Finland, located in the city of Oulu. It was founded on July 8, 1958.
A de novo assembly program targeting populations with high mutation rates.
Argumentative Zoning: Information Extraction from Scientific Articles
Simone Teufel''s thesis introducing a rhetorical-level analysis of scientific research articles called Argumentative Zoning that aims to provide an intelligent library search tool for researchers. This could include the summarization of single or multiple articles, and also improved citation indexes. A construct called a citation maps could help people grasp relationships between papers. The definition of the argumentative Zones is given by the sentential-rhetorical speech act of single, important sentences (landmark sentences, e.g. in the paper they develop a method for or in contrast to REFERENCE, their approach uses ...). That means, she is particularly interested in the rhetorical status of that sentence with respect to the communicative function of the whole paper. The zones, each associated with one or more sentences, are the following: * BKG: General scientific background (yellow) * OTH: Neutral descriptions of other people''s work (orange) * OWN: Neutral descriptions of the own, new work (blue) * AIM: Statements of the particular aim of the current paper (pink) * TXT: Statements of textual organization of the current paper (in chapter 1, we introduce...) (red) * CTR: Contrastive or comparative statements about other work; explicit mention of weaknesses of other work (green) * BAS: Statements that own work is based on other work (purple) The thesis looks at how humans perform the analysis, how much they agree or disagree (they agree pretty much!) and how an automatic, rather shallow process can apply the analysis, based on machine learning and sentential features.
NEMO (NEuron MOrphological analysis tool)
Software to handle and process large numbers of optical microscopy image files of neurons in culture or slices in order to automatically run batch routines, store data and apply multivariate classification and feature extraction using 3-way principal component analysis (PCA). This freeware for semi automated quantitative and dynamic analysis of neuron morphometry incorporates the most important microstructural quantification methods, such as fractal and sholl analysis with statistical and classification tools to provide an integrated image processing environment which enables fast and easy feature identification. It includes: * Friendly interactive graphical user interface * Image pre-processing * Morphological analysis * Topological analysis * Cell counting * 3-way PCA analysis (also available as an ImageJ plugin) * Plot of variables Sequential images of labeled or unlabelled neurons or tissue slices can be uploaded batch-wise in order to create a 3 axis (time, image coordinate) data base and a datamatrix of variables for 3-way Principal Component Analysis*.
Database characterizing and comparing pluripotent human stem cells. The growth and culture conditions of all 21 human embryonic stem cell lines approved under the August 2001 Presidential Executive Order have been analyzed. Available to the scientific community are the results of our rigorous characterization of these cell lines at a more advanced level.
AREDS2: The Age-Related Eye Disease Study 2
Study designed to assess the effects of oral supplementation of high doses of macular xanthophylls (lutein and zeaxanthin) and/or omega -3 LCPUFAs (DHA and EPA) for the treatment of AMD and cataract.
A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.
Software program for constructing linkage disequilibrium (LD) maps. (entry from Genetic Analysis Software)
Congress of Neurological Surgeons University of Neurosurgery
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19,2021.Designed with the neurosurgeon in mind, this portal contains everything you need to acquire new skills and techniques, including courses, an image database, and the world''s largest neurosurgical wiki reference - NeuroWiki. The new University of Neurosurgery includes: * More than 40 new online courses - in all neurosurgical subspecialties. * Archived webinars. * Lectures from the CNS Annual Meetings. * Neurosurgical image database. We are continuing to add new content - check back often.
Congress of Neurological Surgeons Online Image Database
Congress of Neurological Surgeons Image Database
University of Neurosurgery Image Database
University of Neurosurgery Online Image Database
Data set of almost 2,000 neurosurgical images using a variety of search options.
BioCreAtIvE - Critical Assessment for Information Extraction in Biology
Critical Assessment of Information Extraction systems in Biology
Community-wide effort (Challenge) for evaluating text mining and information extraction systems applied to the biological domain. It is focused on the comparison of methods and the community assessment of scientific progress, rather than on the purely competitive aspects. There is a considerable difficulty in constructing suitable gold standard data for training and testing new information extraction systems which handle life science literature. Thus the data sets derived from the BioCreAtIvE challenge - because they have been examined by biological database curators and domain experts - serve as useful resources for the development of new applications as well as helping to improve existing ones. Two main issues are addressed at BioCreAtIvE, both concerned with the extraction of biologically relevant and useful information from the literature. The first one is concerned with the detection of biologically significant entities (names) such as gene and protein names and their association to existing database entries. The second one is concerned with the detection of entity-fact associations (e.g. protein - functional term associations ).
Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software)
Images and movies of plant organelle dynamics that were obtained from plant research, based on the Plant Organelles Database. This educational tool is written in layman' '''s terms to engage members of the non-scientific community such as students and school teachers. Additional content: ' '''What happens, if organelle functions become defective ' ''' was added in anticipation that readers will be interested in this subject. The Scientific Research of Priority Areas on Organelle Differentiation as the Strategy for Environmental Adaptation in Plants was started on 2004 to promote a comprehensive understanding of plant organelle research, and research with plant scientists all over Japan has been conducted for the past five years. The Plant Organelles Database (PODB), which contains images and movies of various plant organelles that were obtained from this project' '''s research was constructed but was designed for scientists. ' '''The Plant Organelles World' ''' was created for the non-scientific community to understand. Plants have developed mechanisms to adapt to the environment, which is different from the mammalian system of adaption. From recent plant research, the small compartments in cells, ' '''organelles' ''', have been shown to be involved in various responses to environmental changes. The dramatic development of bio-imaging analysis tools such as green fluorescent protein (GFP), which won a Nobel prize for chemistry in 2008, has contributed to recent plant science, because it has become easier to biotechnologically introduce GFP and its derivatives into cells, leading to convenient methods of observing the inside of cells. As a result, we can analyze organelle dynamics and obtain insights related to understanding the way plants live, as well as forming a deeper understanding of organelles.
Johns Hopkins Guides: Antibiotic HIV and Diabetes Guides
Authoritative, need-to-know information from Johns Hopkins available for mobile devices and the web. Guides provide up to date information and break down details of diagnosis, drug indications, dosing, pharmacokinetics, side effects and interactions, pathogens, management, and vaccines into frequently-updated, quick-read entries. Available for infectious disease (ABX), diabetes, and HIV.
Woods Hole Oceanographic Institution; Massachusetts; USA
The world''s largest private, nonprofit ocean research, engineering and education organization.
General purpose simulation platform developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models. As such, GENESIS, and its version for parallel and networked computers (PGENESIS) was the first broad scale modeling system in computational biology to encourage modelers to develop and share model features and components. User contributed GENESIS models and simulations are available. You may to contribute a model or simulation. Educational tutorials for instruction in both neurobiology and computational methods have been developed. These tutorials and GENESIS are now being widely used in graduate and undergraduate instruction. These uses include full semester courses in computational neuroscience or neural modeling, short intensive courses or workshops, an option for a course project, and short units on computational neuroscience within courses on artificial neural nets. They also have a repository of user-contributed tutorials and materials for use in neuroscience education. If you have course descriptions, syllabi, exercises, tutorials, or short HOWTO documents, please upload them to Education.
Agri-environmental Research Data Repository
Data repository to preserve and provide access to agricultural and environmental data produced during research projects undertaken at the University of Guelph including datasets on topics such as crop yield, soil moisture, weather and agroforestry. A special emphasis is placed on research funded by Ontario Ministry of Agriculture and Food (OMAF) and MRA.
A multidisciplinary repository of public data sets such as the Human Genome and US Census data that can be seamlessly integrated into AWS cloud-based applications. AWS is hosting the public data sets at no charge for the community. Anyone can access these data sets from their Amazon Elastic Compute Cloud (Amazon EC2) instances and start computing on the data within minutes. Users can also leverage the entire AWS ecosystem and easily collaborate with other AWS users. If you have a public domain or non-proprietary data set that you think is useful and interesting to the AWS community, please submit a request and the AWS team will review your submission and get back to you. Typically the data sets in the repository are between 1 GB to 1 TB in size (based on the Amazon EBS volume limit), but they can work with you to host larger data sets as well. You must have the right to make the data freely available.
University of Ottawa often referred to as uOttawa or U of O, is a bilingual public research university in Ottawa, Ontario, Canada.
Centre is committed to free and open exchange of scientific data and is working collaboratively with international centres, networks and scientists to build sustainable polar data commons. Delivers professional data management and analysis services to Antarctic scientists and environmental managers. Supports logistical operations of Australian Antarctic Program. Data held in AADC data stores are qualified with metadata and discoverable through Catalogue of Australian Antarctic and Sub-antarctic Metadata (CAASM http://data.aad.gov.au/aadc/metadata) or through customized applications accessible via the website. All data is archived in AADC to permit its re-use. AADC has capability to create DOIs for datasets.
Web-based linked data server and browser specifically designed for ontology terms, it supports ontology visualization, query, and development. Ontobee provides a web interface for displaying the details and hierarchy of a specific ontology term. Meanwhile, Ontobee provides a RDF source code for the particular web page, which supports remote query of the ontology term and the Semantic Web. Ontobee provides an efficient and publicly available method to promote ontology sharing, interoperability, and data integration.
The Australian Repositories for Diffraction ImageS
Dissemination of public datasets containing raw crystallography data (known as ''diffraction images''), along with rich metadata for search and persistent handles for citation in publications. Storage is federated, meaning the public index contains no data itself and merely points to data stored in external labs and institutions. TARDIS is scheduled to be replaced by the Bioscience Data Platform (https://www.nectar.org.au/bioscience-data-platform-tardis-cloud)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Lists2Networks: Integrated analysis of gene/protein lists
A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system.
Forum for researchers in human developmental biology and related fields to meet and establish links.
HUDSEN Human Gene Expression Spatial Database
Database of a set of standard 3D virtual models at different stages of development from Carnegie Stages (CS) 12-23 (approximately 26-56 days post conception) in which various anatomical regions have been defined with a set of anatomical terms at various stages of development (known as an ontology). Experimental data is captured and converted to digital format and then mapped to the appropriate 3D model. The ontology is used to define sites of gene expression using a set of standard descriptions and to link the expression data to an ' '''anatomical tree' '''. Human data from stages CS12 to CS23 can be submitted to the HUDSEN Gene Expression Database. The anatomy ontology currently being used is based on the Edinburgh Human Developmental Anatomy Database which encompasses all developing structures from CS1 to CS20 but is not detailed for developing brain structures. The ontology is being extended and refined (by Prof Luis Puelles, University of Murcia, Spain) and will be incorporated into the HUDSEN database as it is developed. Expression data is annotated using two methods to denote sites of expression in the embryo: spatial annotation and text annotation. Additionally, many aspects of the detection reagent and specimen are also annotated during this process (assignment of IDs, nucleotide sequences for probes etc). There are currently two main ways to search HUDSEN - using a gene/protein name or a named anatomical structure as the query term. The entire contents of the database can be browsed using the data browser. Results may be saved. The data in HUDSEN is generated from both from researchers within the HUDSEN project, and from the wider scientific community. The HUDSEN human gene expression spatial database is a collaboration between the Institute of Human Genetics in Newcastle, UK, and the MRC Human Genetics Unit in Edinburgh, UK, and was developed as part of the Electronic Atlas of the Developing Human Brain (EADHB) project (funded by the NIH Human Brain Project). The database is based on the Edinburgh Mouse Atlas gene expression database (EMAGE), and is designed to be an openly available resource to the research community holding gene expression patterns during early human development.
MRC-Wellcome Trust Human Developmental Biology Resource
Collection of human embryonic and fetal material (Tissue and RNA) ranging from 3 to 20 weeks of development available to the international scientific community. Material can either be sent to registered users or our In House Gene Expression Service (IHGES) can carry out projects on user' '''s behalf, providing high quality images and interpretation of gene expression patterns. Gene expression data emerging from HDBR material is added to our gene expression database which is accessible via our HUDSEN (Human Developmental Studies Network) website. A significant proportion of the material has been cytogenetically karyotyped, and normal karyotyped material is provided for research.
PredictSNP - Consensus classifier for prediction of disease-related mutations
Consensus classifier tool that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database. A stand-alone version is also available.
Worcester Polytechnic Institute; Massachusetts; USA
Private research university in Worcester, Massachusetts, focusing on the instruction and research of technical arts and applied sciences.
Collection of high resolution images and movies of mouse and human embryos produced using high resolution episcopic microscopy (HREM). Each data set is a series of block-face images generated during sectioning through an entire embryo, typically cut at 2-3 micrometers. Datasets are organized by approximate developmental stage and each embryo has been assigned a specimen ID (SID) for identification. This is an ongoing project funded by the Wellcome Trust to provide comprehensive imaging of normal and mutant mouse embryos that will complement the standard anatomical texts and form the basis for systematic phenotyping. * Movies: A 3D reconstruction shows each embryo, and lower resolution movies created through each orthogonal plane enable you to quickly review the data set. * Image Stacks: In the stack viewer, you can step through the images in sequence, zoom in to see fine details and adjust the image contrast. * NEW: Embryo Comparison: Two image stacks can now be compared in the stack viewer.
University of Neurosurgery Video Theatre
Congress of Neurological Surgeons Video Theatre
The Congress of Neurological Surgeons presents surgical videos on a variety of topics: Cerebrovascular, Pain, Pediatric, Peripheral Nerves, Spine, Functional/Epilepsy, and Tumor. You must have QuickTime player installed to view the videos but you can download this from the site. Cerebrovascular * Contralateral Microsurgical Approach to Multiple Aneurysms * Microsurgical Exosure and Clipping of an Ophthalmic Clinoidal Aneurysm Pain * Motor Cortex Stimulation for Chronic Pain * Pain Surgery * Spinal Cord Stimulation for Failed Back Syndrome * Treatment of Chiari I Malformation Pediatric * Occipitocervical Fusion in a Pediatric Patient:Use of a New Device Peripheral Nerves * Brachial Plexus Schwannoma in the Upper Trunk * Mini Open Carpal Tunnel Release * Ulnar Nerve Neurolysis and Subcutaneous/Submuscular Transposition Spine * Bilateral Thoracoscopic Sympathectomy * En Bloc Resection of Primary Cervical Spine Tumors * Endoscopic Thoracic Stabilization * Occipitocervical Fusion in a Pediatric Patient:Use of a New Device * Spinal Cord Stimulation for Failed Back Syndrome * Surgical Management of Spinal Cord Ependymomas * Thoracoscopic Discectomy * Treatment of Chiari I Malformation Functional/Epilepsy * Anteromedial Temporal Resection * STN Deep Brain Stimulation for Parkinson''s Disease Tumor * En Bloc Resection of Primary Cervical Spine Tumors * Insular Tumor Resection * Surgical Management of Spinal Cord Ependymomas * Surgical Resection of Brain Metastasis
Open source software written in R that tracks a single animal walking in a homogenous environment (Buritrack) and analyzes its trajectory. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. Buritrack is a program to track individual Drosophila fruit flies online with any camera as they walk in Buridan's paradigm. The program extracts the coordinate locations of the fly and stores them in a text file.
Plugins can extend WordPress to do almost anything you can imagine. In the directory you can find, download, rate, and comment on all the best plugins the WordPress community has to offer. Search for res-comms for Beyond the pdf related plugins. WordPress can host your plugin and give it some exposure. You'll be able to: # Keep track of how many people have downloaded it. # Let people leave comments about your plugin. # Get your plugin rated against all the other cool WordPress plugins. # Give your plugin lots of exposure in this centralized repository.
Funds patient-focused research on gliomas to develop better diagnostics and treatments that lead to long-term survival and a high quality of life for patients with brain tumors. The goal is to decrease the suffering of patients with brain tumors. With an ultimate goal to cure brain cancer, their immediate goal is to improve diagnostics and treatment. They are dedicated to improving the lives of all patients with brain cancer by funding research that they hope will lead to the doubling of life expectancy of patients with brain cancer. Their goal is to do this within the next seven years. Since 2005 they''ve committed more than $50 million to research into brain tumors, with the expectation that this will lead to better diagnostics and therapies. They are dedicated to this search because funding leads to answers, and answers lead to hope.
A federated data sharing platform and infrastructure that provides access to real-time clinical, imaging and biospecimen data across jurisdictions, institutions and diseases. The web-based platform provides a secure infrastructure that advances health research by linking privacy-protected and ethically approved data among a wide network of health collaborators. Access to de-identified health records data is granted to authorized researchers after an application process so patient privacy and intellectual property are protected. BioGrid Australia''s approved researchers are provided access to multiple institutional databases, via the BioGrid interface, preventing gaps in patient records and research analysis. This legal and ethical arrangement with participating collaborators allows BioGrid to connect data through a common platform where data governance and access is managed by a highly skilled team. Data governance, security and ethics are at the core of BioGrid''s federated data sharing platform that securely links patient level clinical, biospecimen, genetic and imaging data sets across multiple sites and diseases for the purpose of medical research. BioGrid''s infrastructure and data management strategies address the increasing need by authorized researchers to dynamically extract and analyze data from multiple sources whilst protecting patient privacy. BioGrid has the capability to link data with other datasets, produce tailored reports for auditing and reporting and provide statistical analysis tools to conduct more advanced research analysis. In the health sector, BioGrid is a trusted independent virtual real-time data repository. Government investment in BioGrid has facilitated a combination of technology, collaboration and ethics approval processes for data sharing that exist nowhere else in the world.
Wrangler is an interactive tool for data cleaning and transformation. Spend less time formatting and more time analyzing your data. Why wrangle? * Too much time is spent manipulating data just to get analysis and visualization tools to read it. Wrangler is designed to accelerate this process: spend less time fighting with your data and more time learning from it. * Wrangler allows interactive transformation of messy, real-world data into the data tables analysis tools expect. Export data for use in Excel, R, Tableau, Protovis, ... * Want to learn more about Wrangler''s design? Take a look at our research paper. * Wrangler is still a work-in-progress. Please share your feedback and feature requests!
Software application for performing unsupervised machine learning and visualization with a focus on the clustering (separating data into groups) and dimensionality reduction (finding low dimensional structure in high dimensional data) subfields of machine learning. For visualization we provide support for both the whole dataset (e.g. a scatter plot) and points (e.g. transforming a particular point into an image). * Endlessly extensible. Every clusterer, reducer, point visualizer and dataset visualizer in Divvy is a plugin. We''ve provided a few big ones (K-means, PCA, scatter plot, &c.) and we''re hoping the community will use our plugin protocol to build many more. Each plugin defines its own UI, so your algorithm can look and behave the way that you want it to without top-down constraints. * Have lots of cores? Divvy is both task and data parallel. No longer will you be waiting for one algorithm to complete before you start another. Start as many as you want and keep using the UI. Only started one? With data parallelism we''ll still push your new MacBook Pro to 800% CPU utilization. * Part of your workflow: Export your clusterings and reductions to .csv and your visualizations to .png. Use your Matlab or R data with our Matlab/R to Divvy export tools available at http://github.com/jmlewis/divvy.
Nature Network is the professional networking website for scientists around the world. It''s an online meeting place where you and your colleagues can gather, share and discuss ideas, and keep in touch. It''s also where you can consult the community for answers to scientific questions or offer your expertise to help others. Additionally, using the Workbench, you can collate your online scientific tools or widgets together in a customizable workspace, allowing you to group your most important tools and information in the way that works best for you. Scientists can also benefit from interactions at the local level whether discussing local news, looking for jobs or finding out about events nearby. All features on Nature Network are completely free. To get the most out of the site, all you need to do is create a profile. You can also use your nature.com account details if you have one. Once you''re set up, here''s a selection of what you can do: *Manage My Profile *Manage My Contacts *Join or Start Groups *Join or Start Forums *Blog *Join a Hub *Customize Your Workbench *Ask a Question or Submit an Answer to Q&A
Funding resource that supports research into A-T (Ataxia Telangiectasia) and other debilitating, degenerative diseases plaguing human kind, including cancer and neuro-degeneration associated with auto-immunity and aging. Researchers share their findings and collaborate with each other. The research must lead to practical, near-term treatments and cures to receive funds. The researchers have found treatments and cures that are the first of their kind in the world. Over $850,000 in direct research grants have been made. These grants have leveraged over $9 million in research resources contributed by partner institutions. We pay the research institutions for direct costs only. We pay no administrative, indirect, or overhead costs.
Yale School of Medicine; Connecticut; USA
A software tool providing a Web interface and a database back-end for collecting clinical symptoms and physical findings observed in patients with genetic disorders. The main goals of this software are * To allow for collecting patient data in standard formats, enabling effortless data exchange and automated search in annotated gene and disease databases, and * To provide advanced functionalities and a friendly user interface that help reduce the clinician' '''s workload, permitting seamless use of this application within the clinician' '''s routine. PhenoTips uses the Human Phenotype Ontology (HPO) to express clinical phenotypes, and provides a friendly interface with error-tolerant, predictive search of phenotypic descriptions. PhenoTips closely mirrors clinician workflows: observations can be recorded directly during the patient encounter, and the interface is compatible with any device that runs a modern Web browser. The clinician can record demographic information, family history, medical history, various standard measurements, phenotypic abnormalities detected in the patient, pertinent indications that were not observed and that can be helpful for differential diagnosis, relevant images depicting manifestations of the patient' '''s disorders, and additional notes for each of these categories. The software automatically plots growth curves, selects phenotypes reflecting abnormal measurements, instantly finds OMIM disorders matching the phenotypic description and suggests other symptoms to investigate in order to reach a more accurate diagnosis.
Supports research and scholarship to improve the quality of life by providing funding for grants in three program areas: studying complex systems, understanding human cognition, and mathematical and complex systems approaches for brain cancer. Types of awards include Fellowship Awards, Scholar Awards, and Collaborative Awards. * Studying Complex Systems: This program supports scholarship and research directed toward the development of theoretical and mathematical tools that can be applied to the study of complex, adaptive, nonlinear systems. It is anticipated that research funded in this program will address issues in fields such as biology, biodiversity, climate, demography, epidemiology, technological change, economic development, governance, or computation. * Understanding Human Cognition: This program supports research studying how neural systems are linked to and support cognitive functions and how cognitive systems are related to an organism's (preferably human) observable behavior. Studies with model organisms should justify why such models were selected and how data obtained from models advances our understanding of human cognition. * Mathematical & Complex Systems Approaches for Brain Cancer: (Collaborative Activity Awards grant type only.) Despite some recent cause for optimism for advancing the clinical treatment of brain cancers, for many patients brain tumor remains a devastating diagnosis. Progress against this disease has been stymied by limited understandings of the molecular, metabolic, and physiological characteristics of human brain cancers across multiple temporal and spatial scales and by the failure of many preclinical models to predict patient responses.
Martin Fenner''s blog is about a WordPress plugin that he created that automatically creates ePub files from blog posts - they are created in the background when you save a blog post. The plugin can be installed directly from your WordPress installation. For now the plugin, ePub Export, only stores the text and images, but the next version should allow embedding of all kinds of files, most importantly data. ePub is a very interesting document format for scholarly publishing and has several advantages over PDF, including: * ePub can be used for all steps in the creation of a scholarly document, including data collection, authoring, annotating and peer review. There is no need for time-consuming and expensive format conversions. Currently most manuscripts are submitted in Microsoft Word or LateX formats, and then converted first to XML and then to HTML and PDF. Metadata such as author identifiers, digital object identifiers and semantic information can be added early on and don''t get lost in a format conversion. * ePub makes it easy to include supplementary material, e.g. video and other multimedia content, the datasets used in the publication (particularly the data used for tables and figures), all cited references in BibTeX format, etc. * ePub is much better suited for reading on mobile devices, as the format allows reflowing of content. Most articles today are printed from the PDF and then read, but this behavior is rapidly changing.
A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.
University of South Florida Department of Molecular Pharmacology and Physiology
USF Department of Molecular Pharmacology & Physiology
USF Department of Molecular Pharmacology and Physiology
USF Molecular Pharmacology and Physiology
The Department of Molecular Pharmacology and Physiology supports the vision and goals of USF Health and the School of Biomedical Sciences. Our mission is to offer outstanding educational opportunities to medical students, graduate students, and fellows and to perform innovative biomedical research. Research in the Department is focused on interdisciplinary approaches to the study of the nervous and cardiovascular systems and related disorders, including Alzheimer''s disease and other neurodegenerative disorders, cardiovascular disease and stroke, diabetes, and neuropsychiatric disorders such as depression and drug addiction.
Recon x - Reconstruction of The Human Genome
Recon x Reconstruction of The Human Genome
Recon x: Reconstruction of The Human Genome
A comprehensive biochemical knowledge-base on human metabolism, this community-driven, consensus metabolic reconstruction integrates metabolic information from five different resources: * Recon 1, a global human metabolic reconstruction (Duarte et al, PNAS, 104(6), 1777-1782, 2007) * EHMN, Edinburgh Human Metabolic Network (Hao et al., BMC Bioinformatics 11, 393, 2010) * HepatoNet1, a liver metabolic reconstruction (Gille et al., Molecular Systems Biology 6, 411, 2010), * Ac/FAO module, an acylcarnitine/fatty acid oxidation module (Sahoo et al., Molecular bioSystems 8, 2545-2558, 2012), * a human small intestinal enterocytes reconstruction (Sahoo and Thiele, submitted). Additionally, more than 370 transport and exchange reactions were added, based on a literature review. Recon 2 is fully semantically annotated (Le Nov��re, N. et al. Nat Biotechnol 23, 1509-1515, 2005) with references to persistent and publicly available chemical and gene databases, unambiguously identifying its components and increasing its applicability for third-party users. Here you can explore the content of the reconstruction by searching/browsing metabolites and reactions. Recon 2 predictive model is available in the Systems Biology Markup Language format.
Foundation to help all people lead healthy, productive lives, this funding and job resource is focused on health, poverty, and opportunity. They work with partner organizations worldwide to tackle critical problems in four program areas. Their Global Development Division works to help the world''s poorest people lift themselves out of hunger and poverty. Their Global Health Division aims to harness advances in science and technology to save lives in developing countries. Their United States Division works to improve U.S. high school and postsecondary education and support vulnerable children and families in Washington State. And their Global Policy & Advocacy Division seeks to build strategic relationships and promote policies that will help advance their work. Our approach to grantmaking in all four areas emphasizes collaboration, innovation, risk-taking, and, most importantly, results. The foundation is unable to make grants directly to individuals. The majority of our funding is proactive and made to U.S. tax-exempt organizations that are independently identified by our staff.
Global-Multi Resolution Topography Image Service
Global-Multi Resolution Topography (GRMT) Image Service
API for requesting images from Global-Multi Resolution Topography (GRMT).
Society for Neuroscience Membership Directory Search
This directory contains proprietary and confidential information belonging to the Society for Neuroscience. It is designated a service to and for personal, noncommercial and information use only of its members and granting agencies. Note that links to individual websites are provided by SfN members and are in no way endorsed by the Society for Neuroscience. SfN reserves the right to remove any member information or web links which are contrary in nature to professional, scientific content. The Society for Neuroscience retains all ownership and proprietary rights in the directory and the information contained in the directory. Any commercial use or other solicitation is strictly prohibited. By continuing with your search inquiry, you are hereby agreeing to these provisions. This system is not intended for wholesale searches of large institutions, or of cities, states or countries. To prevent abuse, the system is set to return results only when the number of matching members is 200 or less. Searches returning a large number of matching members will have to be refined so that they return 200 or less.
Piedmont Health Survey of the Elderly (PHSE) Ten-Year Follow-up of the North Carolina EPESE
Data set of a follow-up study (one of four Established Populations for Epidemiologic Studies of the Elderly - EPESE) that obtains information on four primary outcome variables (cognitive status, depression, functional status, and mortality) and four primary independent variables (social support, social class, social location, and chronic illness); and examines the relationships between social factors and chronic disease on the one hand and health outcomes on the other. This data set complements the other three sites providing a population which is both urban and rural and contains approximately equal numbers of black and white participants across a broad socioeconomic base. The Duke site was originally funded by the NIA Epidemiology, Demography and Biometry Program (EDBP) to complete seven waves of data collection (three in-person and four telephone interviews) in order to examine the health of a sample of 4,162 persons aged 65+, and factors that influence their health and use of health services. The cohort was originally interviewed in 1986/87 and followed annually for 6 years thereafter. The study design consisted of a random stratified household sample with an over-sampling of blacks. Questionnaire topics include the following: Demographics, Alcohol Use, Independence, Health condition, Cognition, Personal mastery, Health Service Utilization, Activity of daily living, Social Support, Hearing and Vision, Incontinence, Social Interaction, Weight and Height, Smoking, Religion, Nutrition, Life Satisfaction, Self Esteem, Sleep, Medications, Economic Status, Depression, Life Changes, Blood pressure. National Death Index files have been searched and death certificates obtained for the members of this study. Sample members have been matched with Medicare Part A files to obtain information on hospitalizations, and will be matched on Medicare Part B (outpatient) files. Data from the first wave of the survey is in the public domain and can be obtained from NACDA or from the National Archives, Center for Electronic Records in Washington, DC. * Dates of Study: 1996-1997 * Study Features: Longitudinal, Oversampling * Sample Size: 1986-1988: 4,162 Links: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/02744 * National Archives: http://www.archives.gov/research/electronic-records/
Web server to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). A standalone command line version is also available, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Web based Java implementation of biological neuron model networks.
Private Ivy League research university in New Haven, Connecticut. Founded in 1701 as the Collegiate School, it is the third-oldest institution of higher education in the United States and one of the nine Colonial Colleges chartered before the American Revolution.
An open-source, open-process, open-access scholarly authoring and publishing platform based on WordPress. Its objectives are to develop a simple, robust, easy-to-use authoring system to create and edit scholarly articles, and to deliver an editorial review and publishing system that can be used to submit, review, and publish scholarly articles. Software and source code are also available. Annotum will build upon the WordPress platform as a foundation, filling in the gaps by providing the following additional features: * Rich, web-based authoring and editing: ** What you see is what you get (WYSIWYG) authoring with rich toolset (equations, figures, tables, citations and references) ** coauthoring, comments, version tracking, and revision comparisons * Strict conformance to a subset of the NLM journal article publishing tag set * Multiple import and export formats ** Export to PDF and XML formats ** Import XML and WXR formats for round-tripping of content ** Articles can be cited, exported, imported across systems/sites * Simple editorial workflow for authoring and reviewer/editor approval * Features specific to scholarly publishing: ** Equations, figures, tables ** References including citation search features ** Auto-generation and registration of CrossRef DOIs
Software application to create Open Data from your Google Drive spreadsheets. # Create a spreadsheet in Google Drive. Share, collaborate and refine your data as usual. # Design the template in EasyOpenData. Format your data the way you want it - any markup, any schema. # Publish your Open Data feed. Feeds update automatically when your spreadsheet is changed.
Expansive collection of high-quality wholeslide images
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Project to advance understanding of the neural mechanisms of vocal learning by providing a quantitative description of the relationship between physiological variables and vocal performance over the course of development in a songbird, the zebra finch. They propose to study vocal learning dynamically across neuronal and peripheral subsystems, using a novel collaborative approach that will harness the combined expertise of several investigators. Their proposed research model will 1) provide simultaneous measurements of acoustic, articulatory and electrophysiological data that will document the detailed dynamics of the vocal imitation process in a standardized learning paradigm; and 2) incorporate these measurements into a theoretical/computational framework that simultaneously provides a phenomenological description and attempts to elucidate the mechanistic basis of the learning process.
Remote Annotation and Multichannel Boundary Observer in 3D
A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels.
Databases and portal to data and ordering mouse strains from MRC Harwell including mouse stocks in FESA (Frozen Embryo and Sperm Archive), mutants from the mutagenesis screen, the ENU DNA archive, standardized phenotyping procedures, imprinting genes and chromosome anomalies. The portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide added value information above and beyond what is available through other routes such as IMSR (International Mouse Stain Resource). MouseBook can be searched either using an intuitive Google-style free text search or using the Mammalian Phenotype Ontology (MP) tree structure. Text searches can be on gene, allele, strain identifier (e.g. MGI ID) or phenotype term and are assisted by automatic recognition of term types and autocompletion of gene and allele names covered by the database. Results are returned in a tabbed format providing categorized results identified from each of the catalogs in MouseBook. Individual results lines from each catalog include information on gene, allele, chromosomal location and phenotype and provide a simple click-through link to further information as well as ordering the strain. The infrastructure underlying MouseBook has been designed to be extensible, allowing additional data sources to be added enabling other sites to make their data directly available through MouseBook.
Public university in Asturias. It is the only university in the region. It has three campus and research centres, located in Oviedo, Gijón and Mieres.
Collection of chemical structures. Provides access to structures, properties and associated information from hundreds of data sources to find compounds of interest and provides services to improve this data by curation and annotation and to integrate it with users applications.
University of Oxford; Oxford; United Kingdom
Collegiate research university in Oxford, England. Teaching as early as 1096, making it the oldest university in English speaking world and world second oldest university in continuous operation.
A community owned repository of concepts used to define all concepts unambiguously. Users can edit and add their own concepts to the wiki.
Database of key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services, including electronic health records. This set of files and software brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems. Users can use the UMLS to enhance or develop applications, such as electronic health records, classification tools, dictionaries and language translators. The UMLS has three tools, which we call the Knowledge Sources: * Metathesaurus: Terms and codes from many vocabularies, including CPT, ICD-10-CM, LOINC, MeSH, RxNorm, and SNOMED CT * Semantic Network: Broad categories (semantic types) and their relationships (semantic relations) * SPECIALIST Lexicon and Lexical Tools: Natural language processing tools We use the Semantic Network and Lexical Tools to produce the Metathesaurus. Metathesaurus production involves: * Processing the terms and codes using the Lexical Tools * Grouping synonymous terms into concepts * Categorizing concepts by semantic types from the Semantic Network * Incorporating relationships and attributes provided by vocabularies * Releasing the data in a common format Although we integrate these tools for Metathesaurus production, you can access them separately or in any combination according to your needs. The UMLS Terminology Services (UTS) provides three ways to access the UMLS: Web Browsers, Local Installation, and Web Services APIs.
Repository of peer reviews of antibodies to help scientists find the right tools fast. Researchers from schools including Stanford, Harvard, John Hopkins have contributed reviews of over 1500 antibodies. Most of these reviews contain experimental details that are hard to find in publications and yet crucial for the success of antibody usage. In addition, scientists are enabled to connect through knowledge of expertise, as members are required to use their real names and lab affiliations. BenchWise is currently open to a select list of leading research institutes and is completely free. Scientists waste over 100 hours a year on either bad antibodies or finding out the right antibody usage condition, despite the fact that someone, somewhere likely has already done the same. They want to solve this problem by enabling scientists to share their product usage knowledge. Antibody records that are documented in spreadsheets are also accepted and will be parsed into individual reviews and uploaded to save you time.
Neuroscience-related portal that has launched a free textbook project on a wiki that will provide a free, accurate and comprehensive introduction to neuroscience for both educators and students. This is being accomplished through an online collaborative environment where the next generation of neuroscientists - and anyone who would like to help - will have the opportunity to work with colleagues from all over the world. The textbook is provided in three different formats: A downloadable app from the IOS and android market, a downloadable .pdf, and a physical copy that can be ordered at cost. Articles and a blog are also available from the portal.
Summary of recordings of spike trains available for analysis and guide to their context and means for their analysis
This is a data resource of recordings of spike activity from about 5000 neurons along the auditory pathway from the cochlear nuclei to the neocortex, cerebellum, and elsewhere. There is also an analysis program that averages histograms of spike activity and concurrent electromyographic (EMG) activity obtained from the orbicularis oculi (eyeblink) and levator oris (nose twitch) muscles. No search interface; distribution consists of a collection of Microsoft Office and Windows executable files. Each recording contains the response to a 70 dB click* (produced by applying a 1 ms rectangular pulse to a loudspeaker) before or after conditioning blink responses to the click as a CS. A discriminative acoustic stimulus, a 70 dB hiss DS, was also presented at a time apart from the click. There are guides to the regions from which each recording was made and to the associated behavioral states as well as a tutorial on how to use the analysis program. There is an appendix listing the data format. Sufficient indexes and examples are available here to understand the data. The data can be downloaded (voluminous) or borrowed on CD (5) from the UCLA Biomedical Library and copied. There is also an analysis program that averages histograms of spike activity and concurrent electromyographic (EMG) activity obtained from the orbicularis oculi (eyeblink) and levator oris (nose twitch) muscles. Each recording contains the response to a 70 dB click (produced by applying a 1 ms rectangular pulse to a loudspeaker) before or after conditioning blink responses to the click as a CS. A discriminative acoustic stimulus, a 70 dB hiss DS, was also presented at a time apart from the click. There are guides to the regions from which each recording was made and to the associated behavioral states as well as a tutorial on how to use the analysis program. There is an appendix listing the data format. There is a second appendix (12. Appendix 2) with downloadable, self-executable data files of the complete database. Also available are copies of the original lab notebooks with depths of the recordings. WHAT THE ANALYSIS PROGRAM DOES 1. Averages four groups of specified spike or EMG files. 2. Graphs the current averages as peri-stimulus time histograms (PSTHs). (Check the ppt files.) 3. Adjusts scaling to specification. 4. Prints or copies the graphs to slides. 5. Creates super averages from specified averages or data from many units 6. Graphs, scales, prints and copies super averages 7. Batch processing as yet not ready for use 8. Provides detailed reports of all useful information contained within the current averages raw data files or general information about the super averages 9. Provides error messages concerning the analyses.
Database facilitating information integration and mining within the pig and across species of all genomics / genetics research results accumulated over the years including pig gene expression, quantitative trait loci (QTL), candidate gene, and whole genome association study (WGAS) results. The key functions developed so far include pig gene pages (a centralized gene search tool), a local copy of Biomart (for customizable genome information queries), genome feature alignment tools (Pig QTLdb and Gbrowse), integrated gene expression information (ANEXDB and ESTdb), a dedicated pig genome and gene set BLAST server, and virtual comparative map database and tools (VCmap). By developing the PGD, it is our aim to collaboratively utilize existing databases and tools via networked functions, such as web services, database API, etc., to maximize the potential of all related databases through the PGD implementation.
An atlas that facilitates fMRI analysis understanding by providing access to all of the functions that have been associated with each of the 52 Brodmann's areas or corresponding gyri. Links to main publications supporting the findings are provided in PubMed ID format. Brodmann's areas with similar functions and locations have been collapsed into a single page. The word left or right has been added indicating a lateralized function. All the abstracts published on PubMed on fMRI and brain PET studies in which the Brodmann's area or its anatomical correlate were mentioned have been reviewed up to August 2008. Abstracts with poorly described experimental methods or findings clearly conflicting with established knowledge provided by the clinical model were excluded. Studies on patients were also excluded.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 27,2025. Compact 3rd edition of The Rat Brain Atlas of Paxinos & Watson published in 1997, it is the most widely used stereotaxic reference system for rat brain. The illustrations and nomenclature of the atlas have become standard tools used by almost all research neuroscientists who deal with anatomy, physiology, or function. It has been subsequently updated, with the 6th edition being the most recent. The 3rd edition is the most recent one available online for free. The program runs in Adobe Acrobat Reader.
Human Nervous System - Disease and Injury
A collection of images of the human nervous system focusing on disease and injury.
Data set of images of the human nervous system focusing on neuroanatomy.
Maintains breeding colony of Mexican axolotls (Ambystoma mexicanum) that distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. Their mission is to serve biology research programs and educators by providing experimental material and expertise and by encouraging and facilitating the exchange of information and ideas.
Web-based, open access scientific networking system providing one-stop shopping for investigators seeking collaborators at Columbia University Medical Center in New York City. Contact information, grants, and publications are integrated to facilitate searches by topic or person.
Italian university located in city of Padua, region of Veneto, northern Italy. University of Padua was founded in 1222 by group of students and teachers from Bologna. Padua is the second oldest university in Italy.
Fly Circuit - A Database of Drosophila Brain Neurons
FlyCircuit - A Database of Drosophila Brain Neurons
FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain.
The Open Annotation Collaboration project aims to facilitate the emergence of a Web and Resource-centric interoperable annotation environment that allows leveraging annotations across the boundaries of annotation clients, annotation servers, and content collections. To this end, interoperability specifications will be devised. Additionally, this project will demonstrate through implementations an interoperable annotation environment enabled by the interoperability specifications in settings characterized by a variety of annotation client/server environments, content collections, and scholarly use cases and will seed widespread adoption by deploying robust, production-quality applications conformant with the interoperable annotation environment in ubiquitous and specialized services, tools, and content used by scholars -- e.g.: Zotero, AXE, LORE, Co-Annotea, Pliny; JSTOR, AustLit, MONK. Alpha3 Data Model: The Open Annotation Data Model specifies an approach for associating annotations with resources, using a methodology conformant with the Architecture of the World Wide Web and the Linked Data initiative. It draws on the Annotea model, as well as more recent extensions of that model.
BrainColor: Collaborative Open Labeling Online Resource
Collaborative Open Labeling Online Resource
This resource was created to host descriptions of protocols, definitions and rules for the reliable identification and localization of human brain anatomy and discussions of best practices in brain labeling. Project for manual anatomical labeling of human brain MRI data, and the visual presentation of labeled brain images.
Carolina Data Acquisition & Reporting Technology
Carolina Data Acquisition and Reporting Technology
CDART - Carolina Data Acquisition & Reporting Technology
CDART - Carolina Data Acquisition and Reporting Technology
Data management tool designed to support multicenter research studies including key components needed in a full-featured research data management application. It is web based and builds on mysql, xml, and tomcat components. Key features include: * Support for complex, highly customized case report forms (XML based configuration) * Security and access at the site, user, and form levels * User management * Management of multiple studies from a single instance * CDISC Operational Data Model (ODM) data extraction for input to analysis software * Longitudinal data collection They are working on major revisions to improve performance and add important new features. Version 2 should be available by mid-2013. They are making this version available now so that other centers with multisite study and/or complex form needs can leverage CDART for their needs. CDART will have a higher support requirement than REDCap and is not intended to replace REDCap for single site studies. Files are provided to assist in setting up an instance of CDART.
Clinical Text Analysis and Knowledge Extraction System
cTAKES - clinical Text Analytics and Knowledge Extraction System
An open-source natural language processing system for information extraction from electronic medical record clinical free-text. This is a system through which one creates one or more pipelines to process clinical notes and to identify clinical named entities. It processes clinical notes, identifying types of clinical named entities, drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures. Each named entity that is found is given attributes for the text span, the ontology mapping code, the context (family history of, current, unrelated to patient), and negated/not negated. cTAKES is built on the UIMA framework. cTAKES 2.5 does not provide a GUI of its own for installation or processing. The cTAKES documentation shows how to use the GUIs provided by the UIMA framework, and how to run cTAKES from a command line. Before using cTAKES you need to know that cTAKES does not provide any mechanisms of its own to handle patient data securely. It is assumed that cTAKES is installed on a system that can process patient data, or that any data being processed by cTAKES has already been through a deidentification step in order to comply with any applicable laws. The tool has been developed and deployed at Mayo Clinic since early 2000.
Clinical and Translational Sciences Award Intellectual Property
Database that aggregates and markets technologies from CTSA institutions as well as those of the National Institutes of Health, with the goal of enhancing research activity and private partnerships across the CTSA consortium. Regular, automatic updating with a standardized template facilitates broad participation by CTSA consortium members. Currently, there are over a dozen CTSAs contributing information on their technologies to the site. CTSA-IP Mission * Intellectual Property information exchange * Links publicly available licensing opportunities from CTSI Institutions in an easily searchable format that connects providers & users. * Aim of creating a consortium view of IP, licensing & sponsored research opportunities. * Stimulus to collaboration and partnering with and between CTSA member institutions.
A single library software prototype transitioning to a to an open-source platform ready for adoption and extension at other institutions wishing to provide research data sharing and discovery services. Datastar' '''s ability to expose metadata about research datasets in a standard semantic format called Linked Data will be enhanced to support selective interchange of related information with VIVO, an open-source semantic researcher networking tool gaining prominence through adoption at multiple U.S. universities, in the federal government, and internationally.
Repository of digital research and educational materials created and used by the Rutgers University community and its strategic collaborators. The goal of the repository is to advance research and learning at Rutgers, to foster interdisciplinary collaboration, and to contribute to the development of new knowledge through the archiving, preservation, and presentation of digital resources. Original research products and papers of the faculty and administrators and the unique resources of the libraries will be permanently preserved and made accessible with tools developed to facilitate and encourage their continued use. RUcore''s developing collection includes * Primary source materials-manuscripts, photographs, maps, and multimedia, from the libraries'' special collections. * Resources about New Jersey, from the state''s libraries, museums, archives and historical societies from the New Jersey Digital Highway collection. * Electronic theses and dissertations, in collaboration with the Rutgers University graduate schools. * Faculty and Departmental publications: pre-prints, postprints, presentations, technical reports, etc.
Federated Utah Research and Translational Health Electronic Repository
FURTHeR - Federated Utah Research and Translational Health Electronic Repository
Data and knowledge management infrastructure for the new Center for Clinical and Translational Science (CCTS) at the University of Utah. This clinical cohort search tool is used to search across the University of Utah clinical data warehouse and the Utah Population Database for people who satisfy various criteria of the researchers. It uses the i2b2 front end but has a set of terminology servers, metadata servers and federated query tool as the back end systems. FURTHeR does on-the-fly translation of search terms and data models across the source systems and returns a count of results by unique individuals. They are extending the set of databases that can be queried.
Open source software platform for building powerful Web portals that support scientific discovery, learning, and collaboration. Some refer to such web sites as collaboratories supporting team science. They call them hubs because each site becomes a focal point for its user community. HUBzero includes a powerful content management system built to support scientific activities. Users of a HUB can work together in projects, publish datasets and computational tools with Digital Object Identifiers (DOIs), and make these publications available for others to use--not as dusty downloads, but as live, interactive digital resources. Simulation/modeling tools published on a hub can be accessed with the click of a button. They run on cloud computing resources, campus clusters, and other national high-performance computing (HPC) facilities and serve up compelling visualizations. Projects can create public or private groups for collaboration and take advantage of over 10,000 Joomla! software extensions that provide additional functionality.
GeneTerm Linker - post enrichment functional association by non-redundant reciprocal linkage
Web application that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. It can also be accessed through its web service.
Patient Refined Information Services Manager
Software application that supports the execution of multivariable prediction models with patient-specific characteristics so that personalized estimates of outcomes, often as a function of alternative treatments, can be generated within the routine flow of patient care. This can support evidence-based, shared medical decision-making to improve the safety, outcomes and cost-effectiveness of care. The current application is in the setting of generating individualized informed consent documents for PCI. However, the tool can support that translation of novel biomarkers, genetics and pharmacogenomic interactions into clinical care. The platform gives healthcare providers instantaneous access to the latest clinical prediction models coupled with rich visualization tools. These models may come from national organizations, outcomes researchers or a specific institution. In addition to decision support applications, it can be used to rapidly create personalized educational materials, patient letters, informed consent documents and a broad array of other items that can help elevate the quality of healthcare delivery.
Free and secure registry to bring together two groups of people who are looking for one another: (1) people who are trying to find research studies, and (2) researchers who are looking for people to participate in their studies. It has been developed by major academic institutions across the country who want to involve you in the mission of helping today' '''s studies make a real difference for everyone' '''s health in the future. Anyone can join ResearchMatch. Many studies are looking for healthy people of all ages, while some are looking for people with specific health conditions. ResearchMatch can help ' '''match' ''' you with any type of research study, ranging from surveys to clinical trials, always giving you the choice to decide what studies may interest you.
Services Pricing & Application for Research Center
Services Pricing and Application for Research Center
Web-based research management system that provides a one-stop-shop to researchers and their study teams to browse services and submit service and pricing requests to research service providers with a focus on billing compliance and proposal and budget development. Upgrades in process include work fulfillment data collection, invoicing and billing features, and outcome metrics using grant and publication data.
Protemics Standard Initiative Common QUery InterfaCe
Web service with well defined methods to enable programmatic access to molecular interactions. Standard for computational access to molecular interaction data resources.
CGAT - Computational Genomics Analysis Tools
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 3, 2023. A collection of tools for the computational genomicist written in the python language to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy. Please note that the tools are part of a larger code base also including genomics and NGS pipelines. Everyone who uses parts of the CGAT code collection is encouraged to contribute. Contributions can take many forms: bugreports, bugfixes, new scripts and pipelines, documentation, tests, etc. All contributions are welcome.
Integrated Nervous System Connectivity View
Neuroscience Information Framework Integrated Nervous System Connectivity
NIF Integrated Nervous System Connectivity View
A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references.
Open Repository for the deposition and sharing of protocols for scientific research. These protocols are posted directly on the Protocol Exchange by their authors and hence have not been further styled, peer reviewed or copy edited. Rather they are made freely available to the scientific community for use and comment. The Protocol Exchange strives to facilitate rapid and unencumbered distribution of protocols for scientific research. They welcome Protocols from any branch of science however we focus particularly on Protocols being used to answer outstanding biological and biomedical science research questions, which includes methods grounded in physics and chemistry with a practical application to the study of biological problems. The content of Protocol Exchange is currently classified under the following broad subject categories: Biochemistry; Cell biology; Cell culture; Chemical modification; Computational biology; Developmental biology; Epigenomics; Genetic analysis; Genetic modification, Genomics; Imaging; Immunological techniques; Isolation, Purification and Separation; Lipidomics; Metabolomics; Microbiology; Model organisms; Nanotechnology; Neuroscience; Nucleic acid based molecular biology; Pharmacology; Plant biology; Protein analysis; Proteomics; Spectroscopy; Structural biology; Synthetic chemistry; Tissue culture; Toxicology; and Virology. If your protocol does not fall into any of these categories please contact us at protocol.exchange (at) nature.com before uploading.
MATLAB toolbox for performing functional connectivity analyses includes many of the most commonly-used approaches researchers have utilized to date for the identification of condition-dependent functional interactions between fMRI time-series obtained from two or more brain regions. The approaches are either bivariate or multivariate methods defined in time or frequency domains that emphasize distinct features of relationships among the time-series.
Platform where academic researchers from around the world collaborate to propose and conduct basic research projects with the support of funding provided by the broader online community. The OSSP hopes to transform how academic research is funded and increase the accessibility of academic research. * Researchers pay a monthly subscription to create and maintain public profiles * Researchers alone (or in teams) submit proposed research studies - each study is peer reviewed, and (if approved) is then posted online * Investors browse through posted studies, and invest in them via small grants (microinvestments). The OSSP doesn''t charge any transaction fees or commissions * Researchers whose studies are funded conduct their research and publish their results It is in the best interest of each researcher to make their case to as many citizens as possible to ensure that they are aware of the work the researcher is engaged in - and of its importance. It is to help academic researchers make this case, and invite the broader non-research community to play a more active role in the academic research process, that The OSSP has developed this unique platform. Through the tools and resources offered by The OSSP, academic researchers may: * Create publicly-accessible profiles * Interact and exchange ideas with peers and colleagues * Manage scholarly publications/bibliographies * Secure research funding (in the form of microgrants provided by the broader non-research community) Simultaneously non-researchers, by registering as ''investors'', may: * Read through cutting-edge (peer-reviewed) research proposals * Interact and exchange ideas with academic researchers * Fund academic research projects
Public registry of antibodies with unique identifiers for commercial and non-commercial antibody reagents to give researchers a way to universally identify antibodies used in publications. The registry contains antibody product information organized according to genes, species, reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones). Data is provided in many formats so that authors of biological papers, text mining tools and funding agencies can quickly and accurately identify the antibody reagents they and their colleagues used. The Antibody Registry allows any user to submit a new antibody or set of antibodies to the registry via a web form, or via a spreadsheet upload.
Software package that performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data and also includes a randomised algorithm which is more efficient for larger data sets.
A computational tool for analyzing multiple gene expression time series data sets for the same organism. The goal is to determine if there is evidence for gene regulatory mechanisms that are shared by multiple different expression responses.
Software to control Type-I error inflation in partially sequenced data for rare variant association testing. It is typically used to combine sequence and genotype data for the two stage design, in which individuals sequenced in stage one for variant detection are solely or predominantly cases then in stage two the discovered variants are genotyped in the remaining individuals. BETASEQ can work with any existing rare variant association methods that use genotypes or imputed genotypes as input.
PhyloBayes - phylogenetic reconstruction using infinite mixtures
A Bayesian Monte Carlo Markov Chain (MCMC) sampler software for phylogenetic reconstruction. Its main distinguishing feature is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Molecular Evolutionary Genetics Analysis - Mutation Diagnosis
Molecular Evolutionary Genetics Analysis software with mutational diagnosis
Software to forecast the deleteriousness of non-synonymous single nucleotide variants (nsSNVs) using multiple methods and explore them in the context of the variability permitted in the long-term evolution of the affected positions. A web version (MEGA-MDW) is also available.
CGARS: Cancer Genome Analysis by Rank Sums
Software package to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations (SCNA) across a set of tumor specimens or cell lines.
MAGIC - MAize Gene expressIon Compendium
Web based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress.
epigenomix - Epigenetic and gene expression data normalization and integration with mixture models
Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.
QCGWAS: Quality Control of Genome Wide Association Study results
Quality Control of Genome Wide Association Study
Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies.
Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.
Software that facilitates accurate estimation for sampling-induced read duplication in deep sequencing experiments.
Socrates - SOft Clip re-alignment To idEntify Structural variants
Socrates: Identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads
SOft Clip re-alignment To idEntify Structural variants
Software for detecting genomic rearrangements in tumors that utilizes only split-read data. It features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It takes advantage of parallelism for efficient use of resources.
CMGRN - constructing multi-level gene regulatory networks using ChIP-seq and gene expression data
Constructing Multi-level Gene Regulatory Networks
A web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data.
Global-Multi Resolution Topography Grid Service
API service for requesting data on topography grid applications.
SNPdryad - Deleterious Non-Synonymous SNP Predictions for Human
Service to predict deleterious non-synonymous human Single Nucleotide Polymorphisms (SNPs) using only orthologous protein sequences.
Dartmouth Shared Instruments Core Laboratory
Core facility that provides the following services: 7500 fast Q-PCR service, MALDI MS service, Agilent 2100 bioanalyzer service, NanoDrop 1000 service.
A community building portal dedicated to understanding Alzheimer's disease and related disorders, it reports on the latest scientific findings from basic research to clinical trials, creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across disciplines.
A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype.
A C++ software program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples.
TSSer: a computational pipeline to identify transcription start sites in bacterial genomes
A computational pipeline to analyze differential RNA sequencing (dRNA-seq) data to determine transcription start sites genome-wide.
Infrastructure for manipulating intervals on sequences
Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible.
The LBDA is a Lewy Body Disease (LBD) information resource for lewy body patients, caregivers, and medical professionals. It provides general information on LBD, including diagnosis, symptoms, treatments, etc., as well as providing links to support resources and an LBD online community. For professionals, the site also provides information on patient care, current LBD research and publications, and diagnostics information. LBDA offers many support resources for those affected by LBD and for their loved ones. These resources include local support group meeting information, online support groups, and user forums where users can find information or ask any questions they may have about the disease. A portion of the site is also dedicated to those who wish to help, either through participation in clinical trials, donations, or volunteering. LBDA also offers information on upcoming LBD-related events. LBDA is located Atlanta, GA. :NIF thanks the : :Parkinson''s Disease Foundation : : :for their referral of this resource to us.
Develops innovative products to advance proteomic research. We specialize in discovering peptides and proteins with novel biological properties, designing and developing enzyme activity assays for diverse screening applications, and producing innovative protein analysis tools for biomarker identification and characterization.
SILVA - high quality ribosomal RNA databases
High quality ribosomal RNA databases providing comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Supplementary services include a rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. Alignment tool, SINA, is available for download as well as available for use online.
American Society of Nephrology Kidney Tube
American Society of Nephrology Kidney Tube - YouTube
ASN Kidney Tube - YouTube are videos hosted at YouTube put out by the American Society of Nephrology (ASN).
Chordoma Foundation Resource & Data Repository
Chordoma Foundation Resource and Data Repository
U-CH1 and U-CH2 are sacral-chordoma derived cell lines created by the lab of Dr. Peter Moeller at the University of Ulm, Germany. The Chordoma Foundation maintains a repository of these cell lines and makes them available to academic and industry investigators. Additionally, Notochordal tissue is available from the Congenital Defects Lab at the University of Washington. (Contact us for more information.) The following data is available: * Xenographs: The U-CH1 cell line forms tumors that resemble chordomas in NSG mice. A protocol for creating a xenograft using U-CH1 was developed by Dr. Adrienne Flanagan. * Tissue Microarrays (sacral, spine, skull base, lumbar, cervical, mobile spine, etc.) * Gene Expression Data: EBI Array Express Experiment E-MEXP-353: transcription profiling of human mesenchymal and some possibly neural crest derived neoplasms using the Affymetrix GeneChip? Human Genome HG-U133A. This data set was generated by the University College London Cancer Institute and contains 96 tissue samples including 4 chordomas. * Comparative Genomic Hybridization Data: Gene Expression Omnibus Series GSE9023: DNA copy number analysis of 21 fresh frozen chordoma biopsies, and the respective relapse in four of them, using 32k and 1Mb array CGH. Cases 1-11 were analyzed using 32k array CGH and male genomic DNA (Promega) was used as reference. Cases 17-26, and the respective relapse in four of these tumors, were analyzed with 1 Mb array CGH, using sex matched controls. All cases showed copy number alterations and primarily deletions of chromosomal regions were found. Particularly, the CDKN2A and CDKN2B loci in 9p21 were homo- or heterozygously lost in 70% of the tumors.
California National Primate Research Center
Center for investigators studying human health and disease, offering the opportunity to assess the causes of disease, and new treatment methods in nonhuman primate models that closely recapitulate humans. Its mission is to provide interdisciplinary programs in biomedical research on significant human health-related problems in which nonhuman primates are the models of choice.
Manually curated database of all conditions with known genetic causes, focusing on medically significant genetic data with available interventions. Includes gene symbol, conditions, allelic conditions, inheritance, age in which interventions are indicated, clinical categorization, and general description of interventions/rationale. Contents are intended to describe types of interventions that might be considered. Includes only single gene alterations and does not include genetic associations or susceptibility factors related to more complex diseases.
The fundraising partner of the BC Cancer Agency and the largest charitable funder of cancer research in this province. We enable donors to make contributions to leading-edge research that has a direct impact on improvements to cancer care for patients in British Columbia. By connecting philanthropy and research, we support the revolutionary advances that will help us achieve our vision of a world free from cancer. Our Cause: Supporting world-renowned cancer research in BC One in three British Columbians will be diagnosed with cancer in their lifetime. Because the BC Cancer Agency integrates research and treatment, the process from discovery to treatment is shorter, and researchers are asking questions focused on the needs of patients in BC. The BC Cancer Agency excels at translating exciting discoveries from the researcher' '''s bench to the patient' '''s bedside. This is the quickest and most effective way to impact cancer care, and it makes the Agency an international leader in cancer research. Our Donors: Leading the way in helping us advance our cause Our unique relationship with the BC Cancer Agency allows our donors to be part of research discoveries made right here in BC. We invite donors to become more connected to the BC Cancer Agency' '''s world-leading research that is shaping the future of patient care. At the BC Cancer Foundation we are funding the areas of greatest priority and promise. We know, because we ask the scientists and clinicians at the BC Cancer Agency to identify the priorities and needs that will have the most significant and timely impact on cancer care and treatment. We then partner with our donors to raise the necessary funds in support of this life-saving work. Together we are funding and finding solutions that are having a direct impact on improving care for cancer patients in British Columbia.
University of Florida Department of Pharmacology and Therapeutics
UF Department of Pharmacology Therapeutics
University of Florida Department of Pharmacology Therapeutics
UF Department of Pharmacology & Therapeutics
UF Department of Pharmacology and Therapeutics
Department fosters independent but interactive research programs in the areas of neuro-pharmacology, cancer pharmacology, cardiovascular pharmacology, retinopathy, inflammation, obesity, aging and gene therapy. A significant number of faculty are actively involved in new drug development. Extramural research support is provided from federal, private and industrial sources.Trainees include undergraduate and graduate students, postdoctoral fellows and M.D., Ph.D. students. Graduate education and training is through the College of Medicine Interdisciplinary Program in Biomedical Sciences. Professional education includes medical, physician assistants and dental students.
Biobank Ireland Trust promotes the development of an Irish Hospital Biobank Network to coordinate collection of small samples of cancer and normal tissue and coded patient data from those having a cancer operation. This will facilitate international molecular research collaborations, which may help identify the best treatment for each individual patient - personalized medicine. Biobank Ireland is promoting the development of a Hospital Biobank Network throughout the island of Ireland as a bridge between cancer research and care. This new infrastructure will facilitate large national and international translational research collaborations that will raise Ireland''s research profile and benefit those with cancer. Researchers will have online access to samples and to restricted patient data from participating hospitals and an equitable withdrawal process for scientifically and ethically approved projects. Important research results will be explained to the public. Other Objectives: * To facilitate (inter)national translational research collaborations that may lead to new tests and better, less toxic treatments for those with cancer * To enable molecular research on cancer tissue from clinical trials patients identify the best treatment for each individual patient ������??personalized medicine������?? * Researchers will have online access to samples and restricted patient data from participating hospitals, and a fair release process for scientifically and ethically approved projects * Biobank Ireland recognizes the need to have harmonization in biobanking around the world * Important research results will be explained to the public * Biobank Ireland will seek to have the hospital-based Biobank Network funded by government as standard of care
Parkinson's Progression Markers Initiative
An observational longitudinal clinical study partnership to identify and validate biomarkers of Parkinson disease (PD) progression and provide easy and open web-based access to the comprehensive set of correlated clinical data and biospecimens, information, and biosamples acquired from PD and age and gender matched healthy control subjects to the research community. The data and specimens have been collected in a standardized manner under strict protocols and includes clinical (demographic, motor and non-motor, cognitive and neurobehavioral), imaging (raw and processed MRI, SPECT and DAT), and blood chemistry and hematology subject assessments and biospecimen inventories (serum, plasma, whole blood, CSF, DNA, RNA and urine). All data are de-identified to protect patient privacy. PPMI will be carried out over five years at 21 clinical sites in the United States and Europe and requires the participation of 400 Parkinson's patients and 200 control participants. The PPMI database provides researchers with access to correlated clinical and imaging data, along with annotated biospecimens, all available within an open access system that encourages data sharing (http://www.ppmi-info.org/access-data-specimens/). The website hosts an Ongoing Analysis section to keep the scientific community apprised of analyses being completed, in hopes of stimulating collaborations between researchers who are using PPMI data and specimens.
Freely available desktop applications including KegHier: Java application for browsing BRITE hierarchy files, KegArray: Java application for microarray data analysis, and KegDraw: Java application for drawing compound and glycan structures. They run on the Mac OS X, Windows, and Linux platforms.
An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database.
Provides a compact storage of de Bruijn subgraphs representing the k-subwords of a set of strings.
OMIA - Online Mendelian Inheritance in Animals
Describes phenotype relationships with between breeds and genes. Catalogue/compendium of inherited disorders, other (single-locus) traits, and genes in 245 animal species. Database of genes, inherited disorders and traits in animal species other than human, mouse, and rats. Database contains textual information and references, as well as links to relevant records from OMIM, PubMed and Gene.
OMIM - Online Mendelian Inheritance in Man
The Online Mendelian Inheritance in Man Morbid Map
Online catalog of human genes and genetic disorders, for clinical features, phenotypes and genes. Collection of human genes and genetic phenotypes, focusing on relationship between phenotype and genotype. Referenced overviews in OMIM contain information on all known mendelian disorders and variety of related genes. It is updated daily, and entries contain copious links to other genetics resources.
Mouse Party is an interactive website that teaches how various drugs disrupt the synapse by taking a look inside the brains of mice on drugs! Every drug of abuse has its own unique molecular mechanism. Where applicable, this presentation primarily depicts how drugs interact with dopamine neurotransmitters because this website focuses on the brain''s reward pathway. Mouse Party is designed to provide a small glimpse into the chemical interactions at the synaptic level that cause the drug user to feel ''high''. The simplified mechanisms of drug action presented here are just a small part of the story. When drugs enter the body they elicit very complex effects in many different regions of the brain. Often they interact with many different types of neurotransmitters and may bind with a variety of receptor types in a variety of different locations. For example, THC in marijuana can bind with cannabinoid receptors located on the presynaptic and/or postsynaptic cell in a synapse.
NIST - National Institute of Standards and Technology
National Institute of Standards and Technology
Founded in 1901, NIST (National Institute of Standards and Technology) is a non-regulatory federal agency within the U.S. Department of Commerce. NIST''s mission is to promote U.S. innovation and industrial competitiveness by advancing measurement science, standards, and technology in ways that enhance economic security and improve our quality of life. NIST carries out its mission through the following programs: * the NIST Laboratories, conducting world-class research, often in close collaboration with industry, that advances the nation''s technology infrastructure and helps U.S. companies continually improve products and services; * the Hollings Manufacturing Extension Partnership, a nationwide network of local centers offering technical and business assistance to smaller manufacturers to help them create and retain jobs, increase profits, and save time and money; and * the Baldrige Performance Excellence Program, which promotes performance excellence among U.S. manufacturers, service companies, educational institutions, health care providers, and nonprofit organizations; conducts outreach programs; and manages the annual Malcolm Baldrige National Quality Award which recognizes performance excellence and quality achievement; * From 2007 to 2011, NIST provided cost-shared grants through the Technology Innovation Program, and between 1990 and 2007, it managed the Advanced Technology Program. NIST measurements support the smallest of technologiesnanoscale devices so tiny that tens of thousands can fit on the end of a single human hairto the largest and most complex of human-made creations, from earthquake-resistant skyscrapers to wide-body jetliners to global communication networks. We invite you to explore our web site to learn about our current projects, to find out how you can work with us, or to make use of our products and services. From the smart electric power grid and electronic health records to atomic clocks, advanced nanomaterials, and computer chips, innumerable products and services rely in some way on technology, measurement, and standards provided by the National Institute of Standards and Technology. NIST funds industrial and academic research in a variety of ways. The Small Business Innovation Research Program funds R&D proposals from small businesses. We also offer other grants to encourage work in specific fields: precision measurement, fire research, and materials science. Grants/awards supporting research at industry, academic, and other institutions are available on a competitive basis through several different Institute offices. For general information on NIST grants programs, please contact Christopher Hunton at christopher.hunton@nist.gov and (301) 975-5718.
Standard specification to reduce inter-laboratory variation in creatinine assay calibration and therefore enable more accurate estimates of glomerular filtration rate (eGFR). Created by NKDEP' '''s Laboratory Working Group in collaboration with the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) and the European Communities Confederation of Clinical Chemistry (now called the European Federation of Clinical Chemistry and Laboratory Medicine), the effort is part of a larger NKDEP initiative to help health care providers better identify and treat chronic kidney disease in order to prevent or delay kidney failure and improve patient outcomes. Recommendations are intended for the USA and other countries or regions that have largely completed standardization of creatinine calibration to be traceable to an isotope dilution mass spectrometry (IDMS) reference measurement procedure. The program' '''s focus is to facilitate the sharing of information to assist in vitro diagnostic manufacturers, clinical laboratories, and others in the laboratory community with calibrating their serum creatinine measurement procedures to be traceable to isotope dilution mass spectrometry (IDMS). The program also supports manufacturers' ''' efforts to encourage their customers in the laboratory to coordinate use of standardized creatinine methods with implementation of a revised GFR estimating equation appropriate for use with standardized creatinine methods. Communication resources and other information for various segments of the laboratory community are available in the Creatinine Standardization Recommendations section of the website. Also available is a protocol for calibrating creatinine measurements using whole blood devices. The National Institute for Standards and Technology (NIST) released a standard reference material (SRM 967 Creatinine in Frozen Human Serum) for use in establishing calibrations for routine creatinine measurement procedures. SRM 967 was validated to be commutable with native serum samples for many routine creatinine procedures and is useful to establish or verify traceability to an IDMS reference measurement procedure. Establishing calibrations for serum creatinine methods using SRM 967 not only provides a mechanism for ensuring more accurate measurement of serum creatinine, but also enables more accurate estimates of GFR. For clinical laboratories interested in independently checking the calibration supplied by their creatinine reagent suppliers/manufacturers, periodic measurement of NIST SRM 967 should be considered for inclusion in the lab' '''s internal quality assurance program. To learn more about SRM 967, including how to purchase it, visit the NIST website, https://www-s.nist.gov/srmors/quickSearch.cfm
Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
Glomerular Filtration Rate (GFR) Calculator
Glomerular Filtration Rate (GFR) calculators to estimate kidney function for adults (MDRD GFR Calculator) and children (Schwartz GFR Calculator). In adults, the recommended equation for estimating glomerular filtration rate (GFR) from serum creatinine is the Modification of Diet in Renal Disease (MDRD) Study equation. The IDMS-traceable version of the MDRD Study equation is used. Currently the best equation for estimating glomerular filtration rate (GFR) from serum creatinine in children is the Bedside Schwartz equation for use with creatinine methods with calibration traceable to IDMS. Using the original Schwartz equation with a creatinine value from a method with calibration traceable to IDMS will overestimate GFR.
Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources.
Cancer-specific High-throughput Annotation of Somatic Mutations
CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning.
Louisiana State University School of Medicine Neurosciences Center
Health Sciences Center: Neurosciences Center
Louisiana State University Health Sciences Center School of Medicine at New Orleans; Neuroscience Center of Excellence
Louisiana State University School of Medicine at New Orleans
Research center that takes multidisciplinary approach to neuroscience education and research. Research programs on molecular and cellular bases of neural diseases are the center of the innovative educational programs. Primary mission is to foster and conduct science that advances understanding of brain function and diseases that affect nervous system.
Mouse Genome Informatics: The Gene Ontology Project
This resource is part of the Gene Ontology Consortium which seeks to provide controlled vocabularies for the description of the molecular function, biological process, and cellular component of gene products. These terms are to be used as attributes of gene products by collaborating databases, facilitating uniform queries across them. GO team members at MGI participate in ontology development, outreach, and functional curation of mouse gene products. The GO vocabularies have a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low level, highly specific terms. This broad range is useful both in annotating genes and in searching for gene information using these terms as search criteria. GO terms are defined, allowing all databases to use the terms consistently and properly. GO annotations in the databases additionally include the publication reference which allowed the association to be made and an evidence statement citing how the association was determined.
HTQC - Quality control and filtration for illumina sequencing data
A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc..
Founded in 1916, The Endocrine Society is the world''s oldest, largest, and most active organization devoted to research on hormones and the clinical practice of endocrinology. The Society works to foster a greater understanding of endocrinology amongst the general public and practitioners of complementary medical disciplines and to promote the interests of all endocrinologists at the national scientific research and health policy levels of government. The Endocrine Society publishes four world-renowned journals and a monthly news magazine, holds scientific conferences, provides educational programs for physicians, issues clinical practice guidelines, promotes careers in endocrinology, and advocates for appropriate funding of scientific research in endocrinology and public policies that support the practice of clinical endocrinology. The Hormone Health Network, the Society''s public education affiliate, is a leading source of hormone-related health information for the public, physicians, allied health professionals and the media. The Endocrine Society is an international body with more than 15,000 members from over 100 countries. The Society''s diverse membership represents medicine, molecular and cellular biology, biochemistry, physiology, genetics, immunology, education, industry and allied health fields. Members of The Endocrine Society represent the full range of disciplines associated with endocrinologists: clinicians, researchers, educators, fellows and students, industry professionals and health professionals who are involved in the field of endocrinology. These professionals are dedicated to the research and treatment of the full range of endocrine disorders: diabetes, reproduction, infertility, osteoporosis, thyroid disease, obesity/lipids, growth hormone, pituitary tumors, and adrenal insufficiency.
ermineJ: Gene Ontology analysis for high-throughput data
Data analysis software for gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are doing something interesting in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Major features include: * Implementation of multiple methods for gene set analysis: ** Over-representation analysis ** A resampling-based method that uses gene scores ** A rank-based method that uses gene scores ** A resampling-based method that uses correlation between gene expression profiles (a type of cluster-enrichment analysis). * Gene sets receive statistical scores (p-values), and multiple test correction is supported. * Support of the Gene Ontology terminology; users can choose which aspects to analyze. * User files use simple text formats. * Users can modify gene sets or create new ones. * The results can be visualized within the software. * It is simple to compare multiple analyses of the same data set with different settings. * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results. * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Autoimmune Lymphoproliferative Syndrome Information
Autoimmune Lymphoproliferative Syndrome (ALPS)
NIAID Autoimmune Lymphoproliferative Syndrome
NIAID Autoimmune Lymphoproliferative Syndrome (ALPS)
A disease-related portal about Autoimmune Lymphoproliferative Syndrome (ALPS) including research in the following categories: Medical and Genetic Description, Database of Mutations, Database of ALPS-FAS Mutations, and Molecular Pathways. Autoimmune Lymphoproliferative Syndrome (ALPS) is a recently recognized disease in which a genetic defect in programmed cell death, or apoptosis, leads to breakdown of lymphocyte homeostasis and normal immunologic tolerance. It is an inherited disorder of the immune system that affects both children and adults. In ALPS, unusually high numbers of white blood cells called lymphocytes accumulate in the lymph nodes, liver, and spleen, which can lead to enlargement of these organs. Database of Mutations * All existing ALPS-FAS mutations (NIH Web site) * ALPS-FAS * ALPS Type Ia (most common type) ** Reported FAS (TNFRSF6) mutations causing ALPS ** Distribution of FAS (TNFRSF6) mutations ** FAS (TNFRSF6) polymorphisms * ALPS Type II
National Institute of Standards and Technology Standard Reference Data
For over 40 years, NIST has provided well-documented numeric data to scientists and engineers for use in technical problem-solving, research, and development. These recommended values are based on data which have been extracted from the world''s literature, assessed for reliability, and then evaluated to select the preferred values. These data activities are conducted by scientists at NIST. NIST Data Gateway-provides easy access to many (currently over 80) of the NIST scientific and technical databases. These databases cover a broad range of substances and properties from many different scientific disciplines. The Gateway includes links to free online NIST data systems as well as to information on NIST PC databases available for purchase.
The Science Podcast takes you on a tour of some interesting stories in the journal and online. * MP3 of this show * Transcript of this show * Subscribe to the Science Podcast RSS Feed
Library of Integrated Network-based Cellular Signatures
Database that contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents and experimental and data analysis protocols. Experimental reagents include small molecule perturbagens, cells, antibodies, and proteins.
GeneNetworkBuilder - Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
Software application for discovering direct or indirect targets of transcription factors (TFs) using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, it generates a regulatory network of the TF.
Congressionally Directed Medical Research Program
Fund the best research to eradicate diseases and support the warfighter to benefit the American Public. They promote innovative research, recognizing untapped opportunities, creating partnerships, and guarding the public trust. Research Program topics include: * Amyotrophic Lateral Sclerosis * Autism * Bone Marrow Failure * Breast Cancer * Defense Medical Research and Development Program * Duchenne Muscular Dystrophy * Gulf War Illness * Lung Cancer * Multiple Sclerosis * Neurofibromatosis * Ovarian Cancer * Peer Reviewed Cancer * Peer Reviewed Medical * Peer Reviewed Orthopaedic * Prostate Cancer * Psychological Health / Traumatic Brain Injury * Spinal Cord Injury * Tuberous Sclerosis Complex
Bloomington Drosophila Stock Center at Indiana University
Collects, maintains and distributes Drosophila melanogaster strains for research. Emphasis is placed on genetic tools that are useful to a broad range of investigations. These include basic stocks of flies used in genetic analysis such as marker, balancer, mapping, and transposon-tagging strains; mutant alleles of identified genes, including a large set of transposable element insertion alleles; defined sets of deficiencies and a variety of other chromosomal aberrations; engineered lines for somatic and germline clonal analysis; GAL4 and UAS lines for targeted gene expression; enhancer trap and lacZ-reporter strains with defined expression patterns for marking tissues; and a collection of transposon-induced lethal mutations.
A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure.
International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.
Software for accurate indel prediction using paired-end short reads.
The Office of Public Health Genomics (OPHG) aims to integrate genomics into public health research, policy, and programs. Doing so could improve interventions designed to prevent and control the country''s leading chronic, infectious, environmental, and occupational diseases. OPHG''s efforts focus on conducting population-based genomic research, assessing the role of family health history in disease risk and prevention, supporting a systematic process for evaluating genetic tests, translating genomics into public health research and programs, and strengthening capacity for public health genomics in disease prevention programs. Goals: To improve public health interventions of diseases of major public health importance, including chronic, infectious, environmental, and occupational diseases, through six major initiatives: * Evaluation of Genomic Applications in Practice and Prevention (EGAPP), * Human Genome Epidemiology Network (HuGENet), * NHANES Collaborative Genomics Project, * Family History Public Health Initiative, * Genomics Translation Research and Programs, and, * Genomic Applications in Practice and Prevention Network (GAPPNet).
Global online employment solution for people seeking jobs and the employers who need great people. They''ve been doing this for over ten years, and have expanded from their roots as a job board to a global provider of a full array of job seeking, career management, recruitment and talent management products and services.
LeadDiscovery: Providing Information to the Drug Discovery Sector
LeadDiscovery was founded by life scientists to expedite drug discovery and pharmaceutical development. Based on a solid background of experience from within the pharmaceutical research and development sector, the aim of this resource is to help companies optimize drug discovery and product pipelines through the identification of breaking research and the in depth and expert evaluation of selected therapeutic areas. At the same time it also provides a showcase for pharmaceutical, biotechnology and academic organizations wishing to increase the exposure of their research to the drug development community. LeadDiscovery sits at the center of this sector helping companies to identify commercially viable R&D options from within small biotechs and the public sector. Additionally, it supports the drug discovery and pharmaceutical development community through three key services: DailyUpdates, UpdatesPlus and PharmaReports - DailyUpdates: Launched in 2002 this popular e-mail alert service delivers information on breaking research, new clinical trials, drug development news and recently published market research and pipeline analysis reports. Registration to receive the service is available here - UpdatesPlus: Developed in 2007 as an extension of DailyUpdates, UpdatesPlus provides a monthly in depth analysis of breaking research and development activity in high profile therapeutic areas. - PharmaReports: LeadDiscovery offers a wide range of in depth pharmaceutical reports. It''s reports include market research reports and pipeline analyses. You can search our entire portfolio using LeadDiscovery''s search engine. Alternatively as it are one of the few information providers that has extensive research and development experience, LeadDiscovery occupys a unique position of being able to source reports that accurately meet your needs. If we don''t have a report that fits your requirements, it can produce one through its pharmaceutical consultancy services. LeadDiscovery offers full reports in selected areas of the pharmaceutical and biotech sector. Each of the reports below has been especially selected by LeadDiscovery and categorized into relevant areas: - Oncology - Cancer Immunotherapy - Immunology & Inflammatory Diseases - Infectious Diseases - Psychiatric, Addictive & Sleep Disorders - Pain - Neurodegenerative & Neuroelectrophysiological Disorders - Metabolic & Hormonal Disorders - Cardiovascular Disorders - GenitoUrinary Tract Disorders - Technology - Diagnostics & Devices - Other Theraputic Areas, Pharmaceutical Strategy and Development
Kabat Database of Sequences of Proteins of Immunological Interest
The Kabat Database determines the combining site of antibodies based on the available amino acid sequences. The precise delineation of complementarity determining regions (CDR) of both light and heavy chains provides the first example of how properly aligned sequences can be used to derive structural and functional information of biological macromolecules. The Kabat database now includes nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules, and other proteins of immunological interest. The Kabat Database searching and analysis tools package is an ASP.NET web-based portal containing lookup tools, sequence matching tools, alignment tools, length distribution tools, positional correlation tools and much more. The searching and analysis tools are custom made for the aligned data sets contained in both the SQL Server and ASCII text flat file formats. The searching and analysis tools may be run on a single PC workstation or in a distributed environment. The analysis tools are written in ASP.NET and C# and are available in Visual Studio .NET 2003/2005/2008 formats. The Kabat Database was initially started in 1970 to determine the combining site of antibodies based on the available amino acid sequences at that time. Bence Jones proteins, mostly from human, were aligned, using the now-known Kabat numbering system, and a quantitative measure, variability, was calculated for every position. Three peaks, at positions 24-34, 50-56 and 89-97, were identified and proposed to form the complementarity determining regions (CDR) of light chains. Subsequently, antibody heavy chain amino acid sequences were also aligned using a different numbering system, since the locations of their CDRs (31-35B, 50-65 and 95-102) are different from those of the light chains. CDRL1 starts right after the first invariant Cys 23 of light chains, while CDRH1 is eight amino acid residues away from the first invariant Cys 22 of heavy chains. During the past 30 years, the Kabat database has grown to include nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules and other proteins of immunological interest. It has been used extensively by immunologists to derive useful structural and functional information from the primary sequences of these proteins.
University of British Columbia Department of Pharmacology
UBC Department of Anesthesiology Pharmacology Therapeutics
University of British Columbia Department of Anesthesiology Pharmacology and Therapeutics
UBC Department of Anesthesiology Pharmacology and Therapeutics
University of British Columbia Department of Anesthesiology, Pharmacology and Therapeutics is an amalgamation of three very important areas of medicine: anesthesiology, pharmacology, and therapeutics. Although we are a joined department with many common interests, each of the sections named above, bring special areas of expertise and learning to the mix. We welcome your interest in our department and look forward to the recruitment of outstanding anesthesiology residents, pharmacology grad students, anesthesiology fellows, and pharmacology post-graduate students. Information on the residency program and postgraduate programs can be found on the appropriate link. Our department now extends across the Province of British Columbia.
Online repository of information about Australian plants, animals, and fungi. Development started in 2006. The Commonwealth Scientific and Industrial Research Organisation is organisation significantly involved in development of ALA.
THIS RESOURCE IS NO LONGER IN SERVCE, documented on August, 19, 2021. Antibody supplier.
Overview of the genetics of hereditary hearing impairment for researchers and clinicians. The site lists data and references for all known gene localizations and identifications for nonsyndromic hearing impairment, and several for syndromic hearing loss. For syndromic hearing impairment, only a few of the most frequent forms are covered. An atlas of cochlea with genes listed can be accessed from this site.
Journal of Comparative Neurology Antibody database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. It was integrated with Antibody Registry. The JCN antibody database is a listing of all antibodies used in JCN papers from 2006 onward. The catalog numbers and vendor information is included for all antibodies listed, and with a new collaboration with NIF' '''s AntibodyRegistry, a unique identifier is also listed for each antibody. The Journal of Comparative Neurology requires rigorous characterization for all antibodies that are used in JCN papers. The antibodies in the The Journal of Comparative Neurology antibody database have in nearly all cases been described and characterized adequately according to the provided guidelines. This information can be used to identify a particular target immunohistochemically or to design an experiment using the antibody information. If you are looking for an antibody to identify a particular target immunohistochemically, this list is a good place to begin your search. We suggest you then look up the paper in which the antibody was used, to make sure that it will meet your needs and to verify its characterization. (The characterization of antibodies in JCN papers often goes well beyond the material published by the manufacturer, so that examining this information before you order an antibody can be very useful.) While we do not guarantee that these antibodies will identify only the intended target (that is a function of the actual experiment and controls), this is the most carefully verified list of antibodies that we are aware of, and we wanted to share this resource with our readers and authors.
A listing of all current openings across the NIH. You may search for NIH Jobs, browse job descriptions, view all descriptions or use the quick links.
National Center for Biotechnology Information
NCBI - National Center for Biotechnology Information
A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.
A production service that gives researchers the ability to create and manage long-term identifiers so that they can to track usage, get credit for their work, share their data, and have the data reused for additional research. As a result, EZID identifiers also make it possible to increase citations, to build on previous work, to conduct new research, and avoid duplicating previous efforts. EZID identifiers provide a simple but powerful way to track research materials, including datasets, throughout their life cycle. In this way, researchers can share their data, get more citations, and track their results.
Autism Chromosome Rearrangement Database: A database of structural variants in autism spectrum disorder
Autism Chromosome Rearrangement Database
The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, including phenotypes, organized by chromosome, related to autism, taken from publicly available literature: databases and unpublished data. The database welcomes submission of data and comments regarding the database from the research community. The database is continuously updated with information from in-house experimental data as well as data from published research studies.
Current Topics in Genome Analysis lecture series
NHGRI: Current Topics in Genome Analysis
Current Topics in Genome Analysis lecture series consists of 13 lectures on successive Wednesdays, with a mixture of local and outside speakers covering the major areas of genomics. In this tenth edition of the series, rather than splitting the lectures into laboratory-based and computationally-based blocks, we have intermingled the lectures by general subject area. We hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future. The lectures are geared at the level of first year graduate students, are practical in nature, and are intended for a diverse audience. Handouts will be provided for each lecture, and time will be available at the end of each lecture for questions and discussion. All lectures are held on Wednesday mornings from 9:30 a.m. to 11:00 a.m. in the Lipsett Amphitheatre of the National Institutes of Health Clinical Center (Building 10). Course Directors: Andy Baxevanis, Ph.D., Eric Green, M.D., Ph.D., Tyra Wolfsberg, Ph.D. Lectures in this series will be available on the GenomeTV channel of YouTube viewing shortly after the live lecture and also includes all of the handouts. Lectures will not be Webcast live. The lecture series archives (available from 2005-) covers important milestones in genetics. CME Credits: This activity has been approved for AMA PRA Category 1 Credits. The intended audience includes clinicians, clinical geneticists, social and behavioral scientists, genetic counselors, those involved with genetics and public policy, health educators, and other biomedical and clinical scientists with an interest in genetics, genomics and personalized medicine. No prior expertise on the part of the audience will be required and the lecturers will be instructed to provide any relevant background as part of their lectures.
American Society for Pharmacology & Experimental Therapeutics
American Society for Pharmacology and Experimental Therapeutics
The American Society for Pharmacology and Experimental Therapeutics
Scientific society whose members conduct basic and clinical pharmacological research in academia, industry and the government developing disease-fighting medicines and therapeutic agents. ASPET publishes five journals: Drug Metabolism and Disposition, Journal of Pharmacology and Experimental Therapeutics, Molecular Pharmacology, Pharmacological Reviews, and Molecular Interventions. ASPET''s membership newsletter is The Pharmacologist. ASPET''s annual meeting is part of Experimental Biology. There are numerous career opportunities in the field of pharmacology available to graduates of advanced training programs. The Society''s web site lists university departments of pharmacology that have established Web sites describing their graduate study programs but it is unlikely that their listing will be complete. ASPET supports nine Divisions, each of which is governed by an Executive Committee. * Division for Behavioral Pharmacology * Division for Cardiovascular Pharmacology * Division for Drug Discovery and Development * Division for Drug Metabolism * Division for Integrative Systems, Translational and Clinical Pharmacology * Division for Molecular Pharmacology * Division for Neuropharmacology * Division for Pharmacology Education * Division for Toxicology
British Association for Tissue Banking (BATB)
The BATB is open to individuals who are involved or interested in Tissue Banking, research, clinical or donor-related activities. Corporate membership is available for organizations that supply technology/services to tissue banks (or have an interest in the use of human tissue for research, bio-engineering or other medical purposes). The Association is instituted for the advancement of tissue banking: * to contribute to the preparation and maintenance of professional standards for the practice of tissue banking in the United Kingdom * to facilitate the interchange of information between members * to provide opportunities for the discussion of all aspects of tissue banking practice * to encourage relevant research and development: to provide informed comment to external agencies * to foster education and training in tissue banking: to maintain national and international links with relevant bodies * to make knowledge in the field of tissue banking available to any person for the general good of the community
Cure PSP: Society for Progressive Supranuclear Palsy
CurePSP+ is an organization dedicated to increasing awareness of progressive supranuclear palsy, corticobasal degeneration, and related disorders, advancing research toward a cure, educating health professionals, and providing support, education and hope for persons with PSP, CBD and their families. PSP provides a number of resources, including a research grants/funding program, support for patients and families, educational materials, and PSP-related events. Patient and family support services include an online magazine, a resources guide, an educational center that provides The Guide for Persons with PSP, videos, support group meetings, and outreach and education brochures and conferences. In addition, CurePSP offers ART2CURE, a program of CurePSP (The Society for Progressive Supranuclear Palsy) that helps to generate essential revenue for research, advocacy, outreach, education and operating through the promotion and sale of artwork provided by various artists throughout the country. CurePSP is located in Hunt Valley, Maryland. :NIF thanks the : :Parkinson''s Disease Foundation : : :for their referral of this resource to us.
Wired Science Blogs is new network of all-star science bloggers.
Software that finds and displays approximate tandem repeats in DNA sequences.
Pathpedia.com - Online pathology resource
Pathpedia.com is web-based wiki on human anatomical, clinical, and experimental pathology created for pathologists. This collaborative portal includes news, education, jobs, meetings, forums and links. The Education tab includes access to journals, books, CME / SAM/ CMIL, WikiBooks, eAtlas, etc. The eAtlas module allows you post unusual and difficult pathology cases to be reviewed by other pathologists across the globe. This module may help in identifying previously unreported entities and unusual / variant examples of known entities. Categories include Histopathology, Gross pathology, Normal histology, Image quiz and Case sharing. Immunopedia - A clinically useful web-based database on the immunohistochemical and flow cytometric evaluation of neoplasms. 1. Large database 2. Regular updates 3. Quality citations 4. Exquisite modules *Data included for both neoplastic & non-neoplastic tissues/cells *Clones indicated wherever applicable along with their markers *References cited for each piece of data on markers or diseases *Option provided to merge data of discrete disease categories Online case sharing *Share unusual cases with pathology community *Help identify previously unreported entities *Get expert reviews and comments from your peers
Xavier University of Louisiana; Louisiana; USA
A private, coeducational, liberal arts college with the distinction of being the only historically black Roman Catholic institution of higher education located in the Gert Town section of New Orleans, Louisiana, USA.
Gene Ontology For Functional Analysis (GOFFA)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Software tool developed for ArrayTrack that takes a list of genes and identifies terms in Gene Ontology associated with those genes. GOFFA provides tools to view/access the following: GO term hierarchy, full listing of GO terms annotated with the genes associated with a given term, Fisher's exact test p-value providing the probability of identifying that many genes for a given term by chance alone, and relative enrichment factor (E-value) giving the enrichment of a GO term for genes in the submitted list relative to the frequency of genes assigned to that term from the full set of GOFFA annotated genes for a particular species.
The COLT-Cancer database is a collection of shRNA dropout signatures profiles, covering ~16000 human genes, and derived from more than 70 Pancreatic, Ovarian and Breast human cancer cell-lines using the microarray detection platform developed in the COLT (CCBR-OICR Lentiviral Technology) facility at the Moffat Lab. All shRNA dropout profiles are freely available through download or queries via this website.
A collection of small sequence processing utilities that are modeled after the Unix command line text processing utilities so every utility tries to perform a specific task and most of them take a sequence file as input and create a new processed sequence file as output. This design encourages the assembly of the seq_crumbs utilities with Unix pipes to create complex pipelines.
Listing of scientific conferences from across the globe and provides you with the tools to get the most out of them: post, follow, discuss - all for free.
With the MGI GO Browser, you can search for a GO term and view all mouse genes annotated to the term or any subterms. You can also browse the ontologies to view relationships between terms, term definitions, as well as the number of mouse genes annotated to a given term and its subterms. The MGI GO browser directly accesses the GO data in the MGI database, which is updated nightly. Platform: Online tool
CWA is an open collaborative community that is actively addressing the challenges associated with the production of unprecedented volumes of academic and professional data. This international effort seeks to organize the massive amounts of information flooding the biological sciences and other scientific disciplines. Challenges include storage, interoperability and analysis of such massive and disparate data sets. CWA''s agreed approach is a ''Semantic Web'' strategy, meaning that disparate data on the internet are now structurally connected to each other. As the amount of scholarly communication increases, it is increasingly difficult for specific core scientific statements to be found, connected and curated. Additionally, the redundancy of these statements in multiple fora makes it difficult to determine attribution, quality, and provenance. To tackle these challenges, the Concept Web Alliance has promoted the notion of nanopublications (core scientific statements with associated context) in a manner allowing for meaningful Web-wide interconnectivity. The notion of a ''nanopublication'' is basically a general scientific assertion, written using semantic-web standard formats with additional meta-data concerning provenance.
Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain.
Unique - The Rare Chromosome Disorder Support Group
Unique is a source of information and support to families and individuals affected by any rare chromosome disorder and to the professionals who work with them. Unique is a UK-based charity but welcomes members worldwide. Unique' '''s Karyotype Database allows users to search the Registered Chromosome Disorders by chromosome, arm and disorder. You may have been given a diagnosis or indication of a chromosome disorder by a geneticist or other medical professional and they may have used a medical term which is unfamiliar to you. So to help you decide if Unique is the appropriate organization for you, we thought it would be useful to describe the different categories of rare chromosome disorder. Rare chromosome disorders can be grouped as structural disorders, numerical disorders and other miscellaneous disorders. Unique: * acts as an international family support group * produces a newsletter three times each year * works to promote awareness of rare chromosome disorders * arranges for families to assist in research into rare chromosome disorders * links families whose children have similar clinical and/or practical problems * works to ensure that the public at large are aware of rare chromosome disorders * works to raise funds to support the group activities and produce literature to make others more aware of our children' '''s conditions * assists relevant research projects and the centralisation of information, at all times observing the need for total confidentiality * sets up local groups throughout the UK for families affected by any rare chromosome disorders and to give support and encouragement to each other * develops and maintains a comprehensive computerised database detailing the life-time effects of specific chromosome disorders on affected members * aims to hold an annual conference where families and relevant specialists can meet and be informed of the latest medical, technical and practical developments * liaises and works in co-operation, with other similar support groups and professionals world-wide for the benefit of families and individuals affected by rare chromosome disorders * ensures that hospitals, doctors, health authorities, genetic clinics and other professionals are aware of the group so that we may have early contact with families where required Membership of Unique is free but the group receives no government funding and is heavily reliant on donations and fundraising to continue its work. Please help us in whatever way you can.
International Neuroinformatics Coordinating Facility News
International Neuroinformatics Coordinating Facility Newsroom
Find all news and updates about INCF and neuroinformatics in the International Neuroinformatics Coordinating Facility (INCF) Newsroom.
Ontology and database that links plant anatomy, morphology and growth and development to plant genomics data.Plant Ontology Consortium develops, curates and shares controlled vocabularies (ontologies) that describe plant structures and growth and developmental stages, providing semantic framework for meaningful cross species queries across databases. PO is under active development to expand to encompass terms and annotations from all plants.
Commercial organization that provides products for basic and applied research in the neurophysiology, hearing, and speech sciences as well as for general data acquisition applications. It offers a complete line of modular DSP-based data acquisition and stimulus generation systems, ranging in complexity from a simple audio stimulator to a complete multichannel sensory and behavioral neurophysiology system for awake, behaving subjects.
Google App Engine: Platform as a Service
Platform as a service that provides a fully-integrated application environment that permits web applications to run on Google''s infrastructure. The environment includes: dynamic web serving, with full support for common web technologies, persistent storage with queries, sorting and transactions, automatic scaling and load balancing, APIs for authenticating users and sending email using Google Accounts, and a fully featured local development environment. Project Hosting on Google Code is a free service to the open source community. Easy to build, Easy to scale, Easy to maintain * Zero to sixty: Scale your app automatically without worrying about managing machines. * Supercharged APIs: Supercharge your app with services such as Task Queue, XMPP, and Cloud SQL, all powered by the same infrastructure that powers the Google services you use every day. * You''re in control: Manage your application with a simple, web-based dashboard allowing you to customize your app''s performance.
OBO Tracker: Plant Ontology (PO) TERM requests
Source Forge OBO Plant Ontology (PO) term request tracker
SourceForge.net: Open Biomedical Ontologies: Plant Ontology (PO) TERM requests
Tracker: Plant Ontology (PO) TERM requests
Open Biomedical Ontologies Tracker that allows users to browse the Plant Ontology (PO) term requests and view their status. Details include a summary, ID, status, Date opened, assignee, submitter, resolution and assigned priority. New requests are accepted from logged in users.
GeneAnswers provide an integrated tool for given genes biological or medical interpretation. It includes statistical test of given genes and specified categories. Microarray techniques have been widely employed in genomic scale studies for more than one decade. The standard analysis of microarray data is to filter out a group of genes from thousands of probes by certain statistical criteria. These genes are usually called significantly differentially expressed genes. Recently, next generation sequencing (NGS) is gradually adopted to explore gene transcription, methylation, etc. Also a gene list can be obtained by NGS preliminary data analysis. However, this type of information is not enough to understand the potential linkage between identified genes and interested functions. The integrated functional and pathway analysis with gene expression data would be very helpful for researchers to interpret the relationship between the identified genes and proposed biological or medical functions and pathways. The GeneAnswers package provides an integrated solution for a group of genes and specified categories (biological or medical functions, such as Gene Ontology, Disease Ontology, KEGG, etc) to reveal the potential relationship between them by means of statistical methods, and make user-friendly network visualization to interpret the results. Besides the package has a function to combine gene expression profile and category analysis together by outputting concept-gene cross tables, keywords query on NCBI Entrez Gene and application of human based Disease ontology analysis of given genes from other species can help people to understand or discover potential connection between genes and functions. Sponsors: This project was supported in part by Award Number UL1RR025741 from the National Center for Research Resources.
City of Hope CpG Island Analysis Pipeline
COHCAP - City of Hope CpG Island Analysis Pipeline
An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.
Electronic archive and distribution server for research articles providing open access to more than 850,000 e-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics. Users can retrieve papers via the web interface. Registered authors may use the web interface to submit their articles to arXiv. Authors can also update their submissions if they choose, though previous versions remain available. Listings of newly submitted articles in areas of interest are available via the web interface, via RSS feeds, and by subscription to automatic email alerts.
Indiana University School of Medicine Department of Pharmacology and Toxicology
Indiana University School of Medicine; Department of Pharmacology and Toxicology
Indiana University School of Medicine; Department of Pharmacology Toxicology
IU Department of Pharmacology and Toxicology
IU Department of Pharmacology Toxicology
IUSM Department of Pharmacology and Toxicology
IUSM Department of Pharmacology Toxicology
IUSM Dept. of Pharmacology and Toxicology
Department of Pharmacology and Toxicology
Mission of Department of Pharmacology and Toxicology is to perform research to advance understanding of interactions of chemicals and drugs with living systems and to assist in development of new therapeutics and strategies to treat disease.
University of Perpignan Via Domitia; Perpignan; France
F1000 Posters: The Open Poster Repository for Biology and Medicine
An open access repository of conference posters from across the life sciences and medicine. It provides a permanent, structured environment for the deposition of posters as well as a trustworthy venue for ongoing discussion and development of the information being presented. You can browse posters by Topic or Section or by conference. Please note that most posters on this site present work that is preliminary in nature and has not been peer reviewed. The most interesting posters are selected for evaluation by our expert Faculty and you will receive ideas and feedback. Widen your audience ����?? top performing posters receive 800+ views in a month!
Louisiana State University School of Medicine Health Sciences Center Department of Pharmacology and Experimental Therapeutics
LSUHSC Department of Pharmacology and Experimental Therapeutics
LSUHSC School of Medicine at New Orleans; Department of Pharmacology and Experimental Therapeutics
LSUHSC School of Medicine Department of Pharmacology and Experimental Therapeutics
Department of Pharmacology and Experimental Therapeutics faculty provide professional instruction in schools of Medicine, Dentistry, Nursing, Allied Health and Graduate Studies. Department offers Ph.D. and M.D./Ph.D. degrees and graduate and post doctoral training.
A professional, social network and publication database geared to researchers where the latest field specific publications can be read, publications with other specialists can be discussed, and collaboration with colleagues is facilitated. They provide researchers with access to around 40 million abstracts and tens of thousands of Full texts, uploaded by the authors themselves. Researchers can search through 7 of the largest databases simultaneously, such as PubMed, IEEE & CiteSeer.
Electron Microscopy Data Bank at PDBe (MSD-EBI)
Electron Microscopy Data Bank at Protein Data Bank in Europe
Repository for electron microscopy density maps of macromolecular complexes and subcellular structures at Protein Data Bank in Europe. Covers techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.
A comparative platform for green plant genomics. Families of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology / paralogy relationships as well as clade specific genes and gene expansions. As of release v9.1, Phytozome provides access to forty-one sequenced and annotated green plant genomes which have been clustered into gene families at 20 evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Neuroinformatics: Exploring the Human Brain
This resource''s long-term goal is to develop informatics methodologies and tools that will increase the creativity and productivity of neuroscience investigators, as they work together to use shared human brain mapping data to generate and test ideas far beyond those pursued by the data''s originators. This resource currently has four major projects supporting this goal: * Database tools: The goal of the NeuroServ project is to provide neuroscience researchers with automated information management tools that reduce the effort required to manage, analyze, query, view, and share their imaging data. It currently manages both structural magnetic resonance image (MRI) datasets and diffusion tensor image (DTI) datasets. NeuroServ is fully web-enabled: data entry, query, processing, reporting, and administrative functions are performed by qualified users through a web browser. It can be used as a local laboratory repository, to share data on the web, or to support a large distributed consortium. NeuroServ is based on an industrial-quality query middleware engine MRALD. NeuroServ includes a specialized neuroimaging schema and over 40 custom Java Server Pages supporting data entry, query, and reporting to help manage and explore stored images. NeuroServ is written in Java for platform independence; it also utilizes several open source components * Data sharing: DataQuest is a collaborative forum to facilitate the sharing of neuroimaging data within the neuroscience community. By publishing summaries of existing datasets, DataQuest enables researchers to: # Discover what data is available for collaborative research # Advertise your data to other researchers for potential collaborations # Discover which researchers may have the data you need # Discover which researchers are interested in your data. * Image quality: The approach to assessing the inherent quality of an image is to measure how distorted the image is. Using what are referred to as no-reference or blind metrics, one can measure the degree to which an image is distorted. * Content-based image retrieval: NIRV (NeuroImagery Retrieval & Visualization) is a work environment for advanced querying over imagery. NIRV will have a Java-based front-end for users to issue queries, run processing algorithms, review results, visualize imagery and assess image quality. NIRV interacts with an image repository such as NeuroServ. Users can also register images and will soon be able to filter searches based on image quality.
Xiamen University, colloquially known as Xia Da in Mandarin Chinese or Ha Tai in Xiamen dialect, is public research university in Xiamen, Fujian, China with strengths in economics and management, fine arts, law, chemistry, journalism, communication, and mathematics.
Nine centers that conduct clinical trials and basic research on new immune-based therapies for autoimmune diseases. This program enhances interactions between scientists and clinicians in order to accelerate the translation of research findings into medical applications. By promoting better coordination and communication, and enabling limited resources to be pooled, ACEs is one of NIAID' '''s primary vehicles for both expanding our knowledge and improving our ability to effectively prevent and treat autoimmune diseases. This coordinated approach incorporates key recommendations of the NIH Autoimmune Diseases Research Plan and will ensure progress in identifying new and highly effective therapies for autoimmune diseases. ACEs is advancing the search for effective treatments through: * Diverse Autoimmunity Expertise Medical researchers at ACEs include rheumatologists, neurologists, gastroenterologists, and endocrinologists who are among the elite in their respective fields. * Strong Mechanistic Foundation ACEs augment each clinical trial with extensive basic studies designed to enhance understanding of the mechanisms responsible for tolerance initiation, maintenance, or loss, including the role of cytokines, regulatory T cells, and accessory cells, to name a few. * Streamlined Patient Recruitment The cooperative nature of ACEs helps scientists recruit patients from distinct geographical areas. The rigorous clinical and basic science approach of ACEs helps maintain a high level of treatment and analysis, enabling informative comparisons between patient groups.
Pictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users' ''' own PDB format files and generates a private set of analyses for each uploaded structure.
Database of authoritative health information about diseases, conditions, and wellness issues that offers reliable, up-to-date health information for free. It contains the latest treatments, information on drugs and supplements, the meanings of words, and medical videos and illustrations. Links to the latest topic or disease specific medical research or clinical trials are also offered. * MedlinePlus pages contain carefully selected links to Web resources with health information on over 900 topics. ** The MedlinePlus health topic pages include links to current news on the topic and related information. You can also find preformulated searches of the MEDLINE/PubMed database, which allow you to find references to latest health professional articles on your topic. * The A.D.A.M. medical encyclopedia brings health consumers an extensive library of medical images and videos, as well as over 4,000 articles about diseases, tests, symptoms, injuries, and surgeries. * The Merriam-Webster medical dictionary allows you to look up definitions and spellings of medical words. * Drug and supplement information is available from the American Society of Health-System Pharmacists (ASHP) via AHFS Consumer Medication Information, and Natural Medicines Comprehensive Database Consumer Version. ** AHFS Consumer Medication Information provides extensive information about more than 1,000 brand name and generic prescription and over-the-counter drugs, including side effects, precautions and storage for each drug. ** Natural Medicines Comprehensive Database Consumer Version is an evidence-based collection of information on alternative treatments. MedlinePlus has 100 monographs on herbs and supplements. * Interactive tutorials from the Patient Education Institute explain over 165 procedures and conditions in easy-to-read language. An XML File for the MedlinePlus Health Topics is available, http://www.nlm.nih.gov/medlineplus/xmldescription.html. The ontology is available through Bioportal, http://bioportal.bioontology.org/ontologies/MEDLINEPLUS
MethylSeekR - Segmentation of Bis-seq data
A software package for the discovery of regulatory regions from Bis-seq data.
Blog about molecules, minds and everything in between, written by Mo, a molecular and developmental neurobiologist turned science writer. He aims to produce well-written and easily accessible articles about all aspects of neuroscience, so that he might help to improve public understanding of it. This blog has been featured for two consecutive years in the Open Lab annual anthologies of the best science blogging. AFTER four years at ScienceBlogs.com, Neurophilosophy has moved to a new home. It is now hosted by The Guardian.
Public archive providing a comprehensive record of the world' '''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.
Streamlined Analysis and Annotation Pipeline for reduced representation bisulfite sequencing
Database supports use of mouse model system for human cancer by providing comprehensive resource for data and information on various tumor models.
unite: A molecular database for the identification of fungi
A fungal rDNA internal transcribed spacer (ITS) sequence database (although additional genes and genetic markers are also welcome) to facilitate identification of environmental samples of fungal DNA. Additional important features include user annotation of INSD sequences to add metadata on, e.g., locality, habitat, soil, climate, and interacting taxa. The user can furthermore annotate INSD sequences with additional species identifications that will appear in the results of any analyses done. UNITE focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. In addition, it also holds all fungal ITS sequences in the International Nucleotide Sequence Databases (INSD: NCBI, EMBL, DDBJ). Both sets of sequences may be used in any analyses carried out. UNITE is accompanied by a project management system called PlutoF, where users can store field data, document the sequencing lab procedures, manage sequences, and make analyses. PlutoF intends to make it possible for taxonomists, ecologists, and biogeographers to use a common platform for data storage, handling, and analyses, with the intent of facilitating an integration of these disciplines. A user can have an unlimited number of projects but still make analyses across any project data available to him.
Louisiana State University School of Medicine, Health Sciences Center: Epilepsy Center
LSU Health Sciences Center School of Medicine at New Orleans; Epilepsy Center
LSUHSC School of Medicine at New Orleans; Epilepsy Center
LSUHSC School of Medicine; Epilepsy Center
The LSU Epilepsy Center of Excellence is dedicated to providing state-of-the-art, comprehensive epilepsy treatment, enhancing access to epilepsy education for patients and physicians, and promoting multidisciplinary epilepsy research in pharmacology, neuroelectrophysiology, neuroimaging, neurosurgery, neuropsychology, biomedical engineering and public health. The center''s team of professionals offers diagnostic and presurgical monitoring, the strategic use of antiepileptic medications, specialized epilepsy neuroimaging, vagus nerve stimulator implantation, ketogenic diet management, neuropsychological testing, psychiatric support and epilepsy surgery for adults and children. The Center also hosts several clinical research trials each year for investigational medications and devices. The following are the treatment methods currently available at this center: - Epilepsy Brain Implants - Responsive Neurostimulator (RNS) - Medications - Medication blood level monitoring - Vagus Nerve Stimulators (VNS) - Epilepsy Surgery - Ketogenic Diet - Psychiatric Services - Radiosurgery Epilepsy Center Sections: *Electrophysiology *Neuroimaging *Neuropsychology *Neuroscience *Neurosurgery *Pharmacology *Psychiatry *Research
Database of images, movies, and protocols to promote a comprehensive understanding of plant organelle dynamics, including organelle function, biogenesis, differentiation, movement, and interactions with other organelles. It consists of 5 individual parts, ''Perceptive Organelles Database'', ''The Organelles Movie Database'', ''The Organellome Database'', ''The Functional Analysis Database'', and ''External Links to other databases and Web pages''. All the data and protocols in ''The Organelle Movie Database'', ''The Organellome Database'' and ''The Functional Analysis Database'' are populated by direct submission of experimentally determined data from plant researchers. Your active contributions by submission of data and protocols to our database would also be appreciated. * Perceptive Organelles Database: This database contains images and movies of organelles in various tissues during different developmental stages in response to environmental stimuli. * Organelles Movie Database: This database contains time-lapse images, Z slices and projection images of organelles in various tissues during different developmental stages, visualized using fluorescent and non-fluorescent probes. * Organellome Database: This database contains images for cellular structures that are composed of organelle images in various tissues during different developmental stages, visualized with fluorescent and non-fluorescent probes. * Functional Analysis Database: This database is a collection of protocols for plant organelle research. * External Links: Access to biological databases.
Matlab routines for analyzing psychophysical data * sychometric function fitting * Multi-condition model fitting * Adaptive procedures * Signal detection measures * Maximum likelihood difference scaling * Model comparisons
A database of miRNA-mRNA interactions. The interaction data is obtained from various external data sources and in some cases computed in-house by algorithms implemented for miRNA target prediction.
The Transverse Myelitis Association was established in 1994 as an organization dedicated to advocacy for those who have these rare neuroimmunologic diseases. It was incorporated as a not-for-profit organization in 1996. It facilitates support and networking opportunities amongst families; provides educational information; functions as a clearinghouse for articles and research literature; and investigates, advocates for and supports research and innovative treatment efforts. Transverse Myelitis is a rare neurological disorder that is part of a spectrum of neuroimmunologic diseases of the central nervous system. Other disorders in this spectrum include, Acute Disseminated Encephalomyelitis (ADEM), Optic Neuritis, and Neuromyelitis Optica (Devic''s disease). The membership of The Transverse Myelitis Association includes persons with all of these disorders, their family members and caregivers and the medical professionals who treat people with these disorders. The TMA publishes a newsletter for our members twice a year, which contains articles by physicians and health care providers. There are also articles written by people with the rare neuroimmunologic disorders. A membership directory is published and distributed annually. The TMA assists in the development of local support groups and is involved in various fund-raising efforts, such as Reading for Rachel, to raise awareness and funds for research. The TMA supports and conducts various symposiums and workshops involving both professionals and patients for the exchange of information regarding research and treatment strategies for persons with the rare neuroimmunologic disorders of the central nervous system.
SRAdb - A compilation of metadata from NCBI SRA and tools
Software package to make access to the compilation of metadata from NCBI SRA and tools associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.
Java toolset for working with next generation sequencing data in the BAM format.
THIS RESOURCE IS NO LONGER IN SERVICE; documented April 28, 2016. A blog which seeks to inform users on different neurological conditions. These conditions include Alzheimer's, brain tumors, epilepsy, Parkinson's disease, sleep disorders, psychiatric conditions, stroke, and spine conditions.
National Kidney Disease Education Program
NKDEP: National Kidney Disease Education Program
Educational resource to increase awareness of kidney disease and its risk factors, improve early detection of chronic kidney disease (CKD), reduce the burden of CKD, facilitate identification of patients at greatest risk for progression to kidney failure, stress the importance of testing those at risk, promote evidence-based interventions to slow progression of CKD, and support the coordination of Federal responses to CKD. Target audiences include individuals at risk, particularly those with diabetes, high blood pressure, and a family history of kidney disease, and primary care providers.
The Neurocritic is a blog deconstructing the most sensationalistic recent findings in Human Brain Imaging, Cognitive Neuroscience, and Psychopharmacology. Born in West Virginia in 1980, The Neurocritic embarked upon a roadtrip across America at the age of thirteen with his mother. She abandoned him when they reached San Francisco and The Neurocritic descended into a spiral of drug abuse and prostitution. At fifteen, The Neurocritic''s psychiatrist encouraged him to start writing as a form of therapy.
Mimas is an organization of experts. Our role is to support the advancement of knowledge, powering world-class research and teaching. Technology is at the heart of everything we do. As a nationally designated data center, we host a significant number of the UK''s research information assets. But our core expertise is building applications that enable a wide range of users to make the most of this rich resource from students and researchers working with census data to investigate social inequalities, to scientists using satellite imagery to survey and protect our environment. We have a longstanding relationship with JISC, developing services that support teaching, learning and research and strong connections with research councils, especially the Economic and Social Research Council (ESRC). We also have partnerships with commercial groups, universities and colleges, government agencies, and national libraries and archives. * An organization of experts: We''re experts in technological development, information management, user support, training, project management, and applied research. * What we do: We maintain and support quality services, develop applications and software, provide data hosting and storage, and share our learning. * What we stand for: Four main principles guide our activities: commitment to our users, technological experimentation and innovation, communication within our community, and investment in staff.
Comparative Toxicogenomics Database (CTD)
CTD - Comparative Toxicogenomics Database
A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks.
Database and data set of known mutations in connexins related to deafness with associated information including published work and classification scheme. Users may submit new mutations. A large number of subjects are affected by hearing impairment. In developed countries deafness has an important genetic origin and at least 60% of the cases are inherited. The pattern of inheritance can be dominant, recessive, X-linked and mitochondrial. Many genes are involved in the different types of deafness (syndromic and non-syndromic). Non-syndromic hereditary deafness is mainly (80%) due to recessive genes (or mutations). It is believed that more than one hundred genes could be involved in hearing impairment. Several of these genes have been identified recently by positional cloning or positional candidate gene approaches. Despite the fact that more than 20 loci have been described for non-syndromic autosomal recessive deafness (DFNB), a single locus, DFNB1, accounts for a high proportion of the cases, with variability depending on the population. The gene involved in this type of deafness is GJB2, which encodes the gap junction protein connexin 26(Cx26). NEW Recent data indicates that DFNB1 can also be due to a deletion of 342Kb involving GJB6, a gene that is very close to GJB2. This deletion has been reported to cause deafness both in the homozygous status and in heterozygosity with a GJB2 point mutation in trans (see big deletions affecting connexin genes...). Connexins are transmembrane proteins that form channels allowing rapid transport of ions or small molecules between cells. There are two types of connexins, alpha and beta, named GJA or GJB followed by a number. Connexins are expressed in many different tissues. Other connexin genes are also involved in deafness. These are GJB1 (Cx32), which is also responsible for X-linked Charcot-Marie-Tooth disease type I; GJB3 (Cx31), involved in both deafness or a skin disease, erythrokeratodermia variabilis, depending on the location of the mutation; GJB6 (Cx30), which has been related to a dominant type of deafness in an Italian family and NEW GJA1 (Cx43), which has recently been shown to be involved in recessive deafness.
Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols.
World class research center that undertakes top-class basic and translational science to tackle some of the most pressing issues in animal health and welfare, their implications for human health and for the role of animals in the food chain. Roslin provides holistic solutions to global challenges in human and veterinary medicine and the livestock industry. Its mission is to gain fundamental understanding of genetic, cellular, organ and systems bioscience underpinning common mechanisms of animal development and pathology, and to drive this into prevention and treatment of important veterinary diseases and develop sustainable farm animal production systems. The Roslin Institute aims to enhance the lives of animals and humans through world class research in animal biology. The principal objectives are to: * Enhance animal health and welfare through knowledge of genetic factors affecting resistance to disease. * Enhance sustainability and productivity of livestock systems and food supply chains through understanding of reproductive and developmental biology. * Enhance food safety by understanding interactions between disease causing organisms and animals. * Enhance human health through an understanding of basic mechanisms of health and disease and comparative biology of animal species. * Identify of new and emerging zoonoses and understand how pathogens might cross from animals to humans. * Enhance quality of life for animals by studying the mechanisms and behaviors associated with optimizing their environment and life experiences.
Private research university with four campuses in New York City.
This module implements pseudo-random number generators for various distributions. For integers, uniform selection from a range. For sequences, uniform selection of a random element, a function to generate a random permutation of a list in-place, and a function for random sampling without replacement. On the real line, there are functions to compute uniform, normal (Gaussian), lognormal, negative exponential, gamma, and beta distributions. For generating distributions of angles, the von Mises distribution is available. Sponsors: This resource is supported by ASTi logo Advanced Simulation Technology Inc. (ASTi); Array BioPharma Inc.; BizRate.com; Canonical Ltd.; CCP Games; cPacket Networks; EarnMyDegree.com; Enthought Inc.; Exoweb Ltd.; Google; HitMeister Inc.; IronPort Systems; KNMP; Lucasfilm; Madison Tyler LLC.; Merfin, LLC.; Microsoft; OpenEye Scientific Software; Opsware, Inc.; O''Reilly & Associates, Inc.; PropertySold.ca; Rogue Wave; SEO Moves; Strakt Holdings, Inc.; Sun Microsystems; Tabblo; ZeOmega, LLC., and Zope Corporation.
Computational-based software that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies to improve the quality of sample-derived datasets.
F1000: Faculty of 1000 Post-Publication Peer Review
Service that identifies and evaluates the most important articles in biology and medical research publications. The selection process comprises a peer-nominated global ''Faculty'' of the world''s leading scientists and clinicians who rate the best of the articles they read and explain their importance. Faculty Members and their evaluations are organized into over 40 Faculties (subjects), which are further subdivided into over 300 Sections. On average, 1500 new evaluations are published each month; this corresponds to approximately the top 2% of all published articles in the biological and medical sciences. F1000 is a subscription service paid for by academic and corporate institutions. Users at subscribing institutions automatically receive full access to the F1000 service when using internet facilities provided by their institution.
A set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina' '''s Solexa, Roche' '''s 454 and Applied Biosystems' ''' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format.
Community database that collects and integrates the gene expression information in MGI with a primary emphasis on endogenous gene expression during mouse development. The data in GXD are obtained from the literature, from individual laboratories, and from large-scale data providers. All data are annotated and reviewed by GXD curators. GXD stores and integrates different types of expression data (RNA in situ hybridization; Immunohistochemistry; in situ reporter (knock in); RT-PCR; Northern and Western blots; and RNase and Nuclease s1 protection assays) and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development. GXD also maintains an index of the literature examining gene expression in the embryonic mouse. It is comprehensive and up-to-date, containing all pertinent journal articles from 1993 to the present and articles from major developmental journals from 1990 to the present. GXD stores primary data from different types of expression assays and by integrating these data, as data accumulate, GXD provides increasingly complete information about the expression profiles of transcripts and proteins in different mouse strains and mutants. GXD describes expression patterns using an extensive, hierarchically-structured dictionary of anatomical terms. In this way, expression results from assays with differing spatial resolution are recorded in a standardized and integrated manner and expression patterns can be queried at different levels of detail. The records are complemented with digitized images of the original expression data. The Anatomical Dictionary for Mouse Development has been developed by our Edinburgh colleagues, as part of the joint Mouse Gene Expression Information Resource project. GXD places the gene expression data in the larger biological context by establishing and maintaining interconnections with many other resources. Integration with MGD enables a combined analysis of genotype, sequence, expression, and phenotype data. Links to PubMed, Online Mendelian Inheritance in Man (OMIM), sequence databases, and databases from other species further enhance the utility of GXD. GXD accepts both published and unpublished data.
University of Picardie Jules Verne; Amiens; France
Public university organized into five main faculties. One of the top 60 universities of France.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A database of completed or in-progress sequenced plant genomes. The list of plant sequencing projects in this page includes those that have reached the stage where active sequence determination is currently producing, or is expected to produce in the near future. In addition, GenBank accession are provided toward the goal of determining the sequence of that plant genome.
National Institute of Diabetes and Digestive and Kidney Diseases Central Repository
NIDDK Central Repositories are two separate contract funded components that work together to store data and samples from significant, NIDDK funded studies. First component is Biorepository that gathers, stores, and distributes biological samples from studies. Biorepository works with investigators in new and ongoing studies as realtime storage facility for archival samples.Second component is Data Repository that gathers, stores and distributes incremental or finished datasets from NIDDK funded studies Data Repository helps active data coordinating centers prepare databases and incremental datasets for archiving and for carrying out restricted queries of stored databases. Data Repository serves as Data Coordinating Center and website manager for NIDDK Central Repositories website.
CTE and Post-traumatic Neurodegeneration: Neuropathology and Ex Vivo Imaging
Chronic Traumatic Encephalopathy and Post-traumatic Neurodegeneration: Neuropathology and Ex Vivo Imaging
Initiative to assemble a multicenter team of expert neuroscientists to evaluate the late effects of Traumatic brain injury (TBI), including single and repetitive TBI of varying severity, and Chronic Traumatic Encephalopathy (CTE), using histological examination of postmortem bio specimens and neuroimaging tools as a foundation to develop in vivo diagnostics. As a first aim, this proposal will bring together a team of 5 accomplished neuropathologists in neurodegenerative disease to establish consensus criteria for the post-mortem diagnosis of CTE. This team will also define the stages of CTE pathology, the features that differentiate CTE from other neurodegenerations and the effects of substance abuse, and the characteristics of posttraumatic neurodegeneration after single TBI. As a second aim, this proposal will establish a national bio specimen and data bank for TBI (Understanding Neurological Injury and Traumatic Encephalopathy (UNITE) bio bank) by developing a nationwide brain donor registry and hotline to acquire high quality bio specimens and data. The UNITE bank will use strictly standardized protocols and a web-based interface to ensure that tissue and data are readily available to qualified investigators. Comprehensive retrospective clinical data including clinical symptoms, brain trauma and substance abuse history, and medical records (including common data elements) will be entered into a secure database. Behavioral/ mood dysfunction, cognitive changes, substance abuse and traumatic exposure will be correlated with quantitative assessment of the multifocal tauopathy, Ass deposition and axonal injury. As a third aim, neuroimaging signatures of the neuropathology will be determined in post-mortem tissue using high spatial resolution diffusion tensor imaging (DTI) and autoradiography using a highly selective PET ligand for tau. Quantitative assessment of axonal injury, tau, and Ass will be correlated with ex vivo DTI abnormalities and tau ligand autoradiography. Pilot neuroimaging studies of individuals at high risk for the development of CTE will also be conducted in the final 2 years of the proposal. This proposal will determine the clinical and neuroimaging correlates of CTE and posttraumatic neurodegeneration and create the groundwork for establishing their incidence and prevalence. This study will have a tremendous impact on public health of millions of Americans and greatly increase our understanding of the latent effects of brain trauma.
HOMSTRAD - Homologous Structure Alignment Database
A curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER. These structure-based alignments are annotated with JOY and examined individually.
Database of information resources on geothermal energy from a national network of data providers. Data are contributed by academic researchers, private sector participants, and state and federal agencies, primarily the Department of Energy. Access, view, and download data with this free and easy online search tool.
A human tissue bank that collects, processes, stores and gives out research specimens for future scientific studies. Presently, the VABBB is obtaining neurologic tissue specimens from Veterans who suffer from amyotrophic lateral sclerosis (ALS) and other illnesses that affect Veterans, along with relevant clinical data, essential for research. Currently, neither the cause nor prevention of ALS is known. Medical researchers are currently examining environmental, toxic, genetic, traumatic, medical, and occupational influences as possible contributors to the development and progression of ALS. Veterans have a higher risk of developing ALS compared with non-Veterans; however, the reasons for this higher risk are currently unknown. Any Veteran with ALS in the U.S. may enroll in the VABBB.
OER serves as a vital interface between the NIH and the biomedical research community by guiding investigators through the process of attaining grants funding and helping them understand and navigate through federal policies and procedures. OER supports extramural research by providing policy and guidance to the 24 NIH Institutes and Centers that award grants. Extramural grants account for approximately 84 percent of NIH''s 29 billion budget. These are awarded to investigators throughout the U.S. and abroad. Approximately 10 percent of the NIH budget supports NIH intramural investigators, NIH staff who conduct research.
Software tool that stores definitions of views of data, along with the ontology concepts they represent. This is a part of the Neuroscience Information Framework (NIF) code stack.
flybase A Drosophila Genomic and Genetic Database
FlyBase: A Database of Drosophila Genes & Genomes
FlyBase: A Database of Drosophila Genes and Genomes
Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.
Metabolism and Transport Drug Interaction Database
Metabolism & Transport Drug Interaction Database
Metabolism Transport Drug Interaction Database
The Database is a research and analysis tool developed at the University of Washington, in the Department of Pharmaceutics. It contains in vitro and in vivo information on drug interactions in humans from the following sources: * 9648 peer-reviewed journal articles referenced in PubMed * 102 New Drug Applications (NDAs) * 411 excerpts of FDA Prescribing Information * In-depth analyses of drug-drug interactions in the context of 40 diseases / co-morbidities. In addition, the database also provides PK Profiles of drugs, QT Prolongation data, including results of TQT studies from recent NDAs, as well as Regulatory Guidances and Editorial Summaries/Syntheses relevant to advances in the field of drug interactions. Access to the Database is licensed by UW Center for Commercialization (C4C) to organizations interested in in-depth information on drug interactions. The Database is particularly useful to scientists/clinicians working in drug discovery and drug development. Database users can search for information using several families of pre-formulated queries based on drug name, enzyme name, transporter name, therapeutic area, and more.
The American Society for Microbiology is the oldest and largest single life science membership organization in the world. Membership has grown from 59 scientists in 1899 to more than 39,000 members today, with more than one third located outside the United States. The members represent 26 disciplines of microbiological specialization plus a division for microbiology educators. Eligibility for Full Membership is open to any person who is interested in microbiology and holds at least a bachelor''s degree or equivalent experience in microbiology or related field. Many members hold advanced degrees, including a large number at the master''s, PhD, ScD, DrPH and MD level. A regularly matriculated student of microbiology or a related field is eligible to become a student member. There are also separate membership categories for postdoctoral fellows and for transitional scientists in the early years of a career. Microbiologists study microbes--bacteria, viruses, rickettsiae, mycoplasma, fungi, algae and protozoa--some of which cause diseases, but many of which contribute to the balance of nature or are otherwise beneficial. Microbiological research includes infectious diseases, recombinant DNA technology, alternative methods of energy production and waste recycling, new sources of food, new drug development, and the etiology of sexually transmitted diseases, among other areas. Microbiology is also concerned with environmental problems and industrial processes. Microbiology boasts some of the most illustrious names in the annals of science--Pasteur, Koch, Fleming, Leeuwenhoek, Lister, Jenner and Salk--and some of the greatest achievements for mankind. Within the 20th century, a third of all Nobel Prizes in Physiology or Medicine have been bestowed upon microbiologists. The mission of the American Society for Microbiology is to advance the microbiological sciences as a vehicle for understanding life processes and to apply and communicate this knowledge for the improvement of health and environmental and economic well being worldwide. To achieve these goals, ASM will: * Support programs of education, training and public information; * Publish journals and books; convene meetings, workshops and colloquia; * Promote the contributions and promise of the microbiological sciences; * Recognize achievement and distinction among its practitioners; * Set standards of ethical and professional behavior.
Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources
Database of Chromosomal Imbalance Phenotype in Humans using Ensembl Resources
DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources
Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center' '''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes.
Consortium that puts sequences into a chromosome context and provides the best possible reference assembly for human, mouse, and zebrafish via FTP. Tools to facilitate the curation of genome assemblies based on the sequence overlaps of long, high quality sequences.
Office of Behavioral and Social Sciences Research
NIH Office of Behavioral Social Sciences Research
Office of Behavioral Social Sciences Research
An NIH office devoted to the study of the role of behavioral and social factors in illness and health. Its mission is to stimulate behavioral and social sciences research throughout NIH and to integrate these areas of research more fully into others of the NIH health research enterprise, thereby improving our understanding, treatment, and prevention of disease. To provide the OBSSR with counsel in fulfilling its mission, the Behavioral and Social Sciences Research Coordinating Committee (BSSR CC) serves as an internal advisory board. The Office of Behavioral and Social Sciences Research (OBSSR) opened officially on July 1, 1995. The major responsibilities of the office and its director, set forth in its formal mission statement, are: * To provide leadership and direction in the development, refinement, and implementation of a trans-NIH plan to increase the scope of and support for behavioral and social sciences research. * To inform and advise the NIH director and other key officials of trends and developments having significant bearing on the missions of the NIH, DHHS, and other federal agencies. * To serve as the principal NIH spokesperson regarding research on the importance of behavioral, social, and lifestyle factors in the causation, treatment, and prevention of diseases; and to advise and consult on these topics with NIH scientists and others within and outside the federal government. * To develop a standard definition of behavioral and social sciences research, assess the current levels of NIH support for this research, and develop an overall strategy for the uniform expansion and integration * of these disciplines across NIH institutes and centers. * To develop initiatives designed to stimulate research in the behavioral and social sciences arena, integrate a bio-behavioral perspective across the research areas of the NIH, and encourage the study of behavioral and social sciences across NIH''s institutes and centers. * To initiate and promote studies to evaluate the contributions of behavioral, social, and lifestyle determinants in the development, course, treatment, and prevention of illness and related public health problems. * To provide leadership in ensuring that findings from behavioral and social sciences research are disseminated to the public. * To sponsor seminars, symposia, workshops, and conferences at the NIH and at national and international scientific meetings on state-of-the-art behavioral and social sciences research. Funding Opportunities Announcements (FOA) Since opening its doors in 1995, The Office of Behavioral and Social Sciences Research (OBSSR) has worked to achieve the goals of its authorizing legislation by effectively highlighting and supporting the scientific opportunities that exist in basic and applied behavioral and social sciences research. Guided by its Strategic Plan, OBSSR has been working actively with its IC partners to develop funding opportunities in the behavioral and social sciences. Although OBSSR does not have grant-making authority, it has been active in organizing and funding (through transfers to NIH Institutes and Centers) a variety of trans-NIH research programs. Scientific Areas The Office of Behavioral and Social Sciences Researchs (OBSSR) leadership is crucial at a time when exciting scientific opportunities, persistent public health needs, and emergent public health challenges face our nation. The vision of the office is to bring together the biomedical, behavioral, and social science communities to work more collaboratively to solve complex pressing health challenges. Notable areas of research where OBSSR has led efforts and encourages research include: * Biopsychosocial Interactions * Methodology (including Systems Science and CBPR) * Genes, Behavior and Environment * Social and Cultural Factors in Health * Health and Behavior * Translation OBSSR Training & Education Opportunities The Office of Behavioral and Social Sciences Research (OBSSR) develops and coordinates training and career development opportunities with the NIH Institutes and Centers.
Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations.
The Neurotechnology Industry Organization (NIO) is a non-profit trade association that represents companies involved in neuroscience (neuropharmaceuticals, cell-based therapeutics, neurodevices and neurodiagnostics), academic neuroscience research centers, and brain-illness advocacy groups across the United States and throughout the world. NIO was formed to provide a unified voice for the commerical neuroscience community. NIO advocates for its member organizations on a range of issues related to neurotechnology research and business development including favorable changes in the tax code, intellectual property issues, neuroethics, public policy, reimbursement and patient advocacy. Thank you for taking the time to read this brief introduction to the Neurotechnology Industry Organization (NIO), the recently formed trade association representing companies involved in neuroscience (drugs, devices and diagnostics), brain research centers, patient advocacy groups, and research foundations worldwide. NIO was founded in August 2006 and has attracted over 80 member organizations. NIO''s mission is to accelerate treatments and cures for brain and nervous system illnesses by: * Advocating neurotech''s position to government and regulatory officials * Promoting the industry''s progress and contributions to quality of life * Providing industry development services for our members NIO is spearheading several innovative programs that will benefit your company including: National Neurotechnology Initiative - a new $200M/year Federal initiative aimed at accelerating translational neuroscience innovation and improving the effectiveness of the FDA review process for neuroscience drugs, devices and diagnostics NIO/FDA private-public working group - an initiative to work collaboratively with the FDA to improve the efficiency of the evaluation process for neuroscience products and to increase communication and clarity during the regulatory process Partnering, investment and policy events - networking events with other members of the global commercial neuroscience community at events such as the annual public policy tour in March in Washington D.C. and the Neurotech investing and partnering conference in Spring National Visibility - NIO actively outreaches to global media outlets to encourage coverage of Neurotech that will foster great investor, policymaker and consumer interest. As a member of NIO you will enjoy the following benefits: * Influence in the industry''s overall development agenda * Access to key opinion leaders in Congress, regulatory agencies, media * Participation in FDA and CMS working groups, stakeholder meetings * Expanded networking at neurotech investing and partnering events throughout the year * Participation in neuroscience education awareness initiatives, public awareness campaigns * Industry leadership through participation in driving innovative legislation, new projects NIO''s programs increase awareness of commercial neuroscience products, reduce barriers to innovation, support industry growth and will benefit your company and industry. I hope that you will consider joining NIO in support of our mission to give the brain a voice..
Standard Windows interoperability suite of programs for Linux and Unix that provides secure, stable and fast file and print services for all clients using the SMB/CIFS protocol, such as all versions of DOS and Windows, OS/2, Linux and many others. Samba is an important component to seamlessly integrate Linux/Unix Servers and Desktops into Active Directory environments using the winbind daemon.
Prize4Life is a 501(c)(3) nonprofit organization dedicated to accelerating the discovery of treatments and cures for ALS (amyotrophic lateral sclerosis, also known as Lou Gehrig''s disease). Our mission is to accelerate the discovery of a treatment and a cure for ALS by using powerful incentives to attract new people and new ideas and to leverage existing efforts and expertise in the ALS field. Our Values: * Patients first. Avichai Kremer, one of the Harvard Business School students who founded Prize4Life, was diagnosed with ALS in 2004. We therefore know the disease firsthand and have a sense of urgency to find a treatment. We value patients and their viewpoints. Patients, please tell us what you think. * Global awareness. We plan to push ALS to the forefront of fatal disease issues. We need your help in order to do this. Get involved. * New people and new ideas. We believe important breakthroughs in ALS may reside in the minds and laboratories of people who are not currently researching the disease. Our platform is a bridge for reaching these people. Enter the competition. * Results. Research is traditionally funded upfront, before an idea is even tested. Our prize model ensures that only clear research results, vetted by a team of scientific advisors, are rewarded. grants; funding resource;.
Registry Builder Data Harmonization and Aggregation Tool
Software to harmonize the data that you have in different Excel files, databases, repositories, biospecimen applications, etc. and maps it to one common registry. Remedy Informatics' platform aggregates data from multiple sources, harmonizes the data via Ontology, and provides data visualization and pattern recognition and querying tools.
Provides clinically relevant and medically actionable information for inherited conditions in standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families. Searchable book of expert-authored, peer-reviewed disease descriptions presented in standardized format and focused on clinically relevant and medically actionable information on diagnosis, management, and genetic counseling of patients and families with specific inherited conditions.
emedicinehealth:experts for everyday emergencies
eMedicineHealth.com is a consumer health information site that was launched in May 2003. The site contains over 900 health and medical articles written by physicians for patients and consumers. If you are interested in authoring one or more articles, or if you are interested in becoming a medical editor for eMedicineHealth, please see our Medical Writer and Medical Editor submission form for more information. You may search for information or use the Topics from A-Z option. Additionally, Slideshow pictures, Image gallery, Medications, Quizzes, and Medical Dictionary sections are available. eMedicineHealth.com''s main office is in San Clemente, California, and the corporate office is in New York, New York.
Medical College of Wisconsin Cell Biology Neurobiology and Anatomy
Our mission is to conduct fundamental research in the areas of cell biology, developmental biology and neurobiology, and to provide a first rate educational experience for students of the Medical College of Wisconsin and its Graduate School of Biomedical Sciences. Current research in the department is strong in two major areas; developmental biology and neurobiology. Postdoctoral research opportunities are available. In developmental biology there is a focus on growth, regeneration and transcription mediated pathways in such systems as neural crest differentiation, heart development, liver development and in the area of muscle atrophy and plasticity. In neurobiology there is a strength in vision with special focus on photoreceptor cell biology, color vision, plasticity in the visual cortex, and functional MRI of the visual system. The department is currently expanding its research efforts in both areas. Faculty in the department also participate in interdisciplinary graduate education through the Graduate Programs in Neuroscience and Biomedical Sciences, and through management of an interdisciplinary Graduate Program in Cell and Developmental Biology. The department also plays an essential role in medical education through its first year medical courses in Cell and Tissue Biology, Developmental Biology, and Clinical Human Anatomy. In addition, the department is a principal participant in an interdisciplinary neuroscience course which includes faculty from other departments within the medical college.
ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. ViralZone project is handled by the virus program of SwissProt group. Proteins popups were developed in collaboration with Prof. Christian von Mering and Andrea Franceschini, Bioinformatics Group , Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, funded in part by the SIB Swiss Institute of bioinformatics. All pictures in ViralZone are copyright of the SIB Swiss Institute of Bioinformatics.
NAGRP Bioinformatics Coordination Program
NAGRP NRSP-8 Bioinformatics Coordination Program
National Animal Genome Research Program Bioinformatics Coordination Project
National Animal Genome Research Program NRSP-8 Bioinformatics Coordination Program
USDA NRSP-8 Program Bioinformatics Coordination Project
We at NRSP-8 bioinformatics coordination program strive to serve the animal genomics research community to better use computer tools and methods, to best utilize available resources, and in working with researchers in the community, to effectively share, combine, manage, manipulate, and analyze information from genomics/genetics studies. This site is designed as an information center to serve the national animal genome research projects of cattle, chicken, pigs, sheep, horse, and aquaculture species. This is home to databases and web sites (being) built for structural, functional and application oriented studies of the animal genomics, to serve the purpose of research, education and related activities in the scientific, industrial and educational communities in the states and world wide. The challenges in bioinformatics support/research for animal genomics may involve * Effective data collection, organization and management * Rapid development of most needed bioinformatics tools and resources * Efficient use of these tools for innovative data analysis Projects: * Animal Trait Ontology (ATO) Project * Virtual Comparative Genomics * The Past, the Current, and the Potentials * Collaborative and Hosted Works
An online open-access open-data journal, publishing ''big-data'' studies from the entire spectrum of life and biomedical sciences whose publication format links standard manuscript publication with its affiliated database, GigaDB, that hosts all associated data, provides data analysis tools, cloud-computing resources, and a DOI assignment to every dataset. GigaScience covers not just ''omic'' type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale sharable data. Supporting the open-data movement, they require that all supporting data and source code be publicly available in a suitable public repository and/or under a public domain CC0 license in the BGI GigaScience database. Using the BGI cloud as a test environment, they also consider open-source software tools / methods for the analysis or handling of large-scale data. When submitting a manuscript, please contact them if you have datasets or cloud applications you would like them to host. To maximize data usability submitters are encouraged to follow best practice for metadata reporting and are given the opportunity to submit in ISA-Tab format.
Freely available tool for Gene-centered collection and display of DNA variations. It also provides patient-centered data storage and storage of Next Generation Sequencing (NGS) data, even of variants outside of genes. Please note that LOVD provides a system for storage of information on genes and allelic variants. To obtain information about any genes or variants, do not download the LOVD package. This information should be obtained from the respective databases, http://www.lovd.nl/2.0/index_list.php In total: 2,507,027 variants (2,208,937 unique) in 170,935 individuals in 62619 genes in 88 LOVD installations. (Aug. 2013) LOVD 3.0 shared installation, http://databases.lovd.nl/shared/genes To maintain a high quality of the data stored, LOVD connects with various resources, like HGNC, NCBI, EBI and Mutalyzer. You can download LOVD in ZIP and GZIPped TARball formats.
Plasmodium falciparum homepage on GeneDB
Database of the most recent sequence updates and annotations for the P. falciparum genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Plasmodium research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. The P. falciparum 3D7 nuclear genome is 23.3 Mb in size, with a karyotype of 14 chromosomes. The G+C content is approximately 19%. The P. falciparum genome is undergoing re-annotation. This process started in October 2007 with a weeklong workshop co-organized by staff from the Wellcome Trust Sanger Intistute and the EuPathDB team. Ongoing curation and sequence checking is being carried out by the Pathogen Genomics group. Plasmodium falciparum is the most deadly of the five Plasmodium species that cause human malaria. Malaria has a massive impact on human health; it is the worlds second biggest killer after tuberculosis. Around 300 million clinical cases occur each year resulting in between 1.5 - 2.7 million deaths annually, the majority in sub-saharan Africa. It is estimated that 3,000 children under the age of five years fall victim to malaria each day. Around 40% of the worlds population are at risk. In collaboration with EuPathDB, genomic sequence data and annotations are regularly deposited on PlasmoDB where they can be integrated with other datasets and queried using customized queries.
Adult Mouse Anatomical Dictionary Browser
Anatomical Dictionary for the Adult Mouse
MGI Adult Mouse Anatomical Dictionary Browser
Ontology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display.
International Neuroinformatics Coordinating Facility - Japan Node: The Portal System for Neuroinformatics in Japan
International Neuroinformatics Coordinating Facility Japan Node
The Japan Node of the INCF coordinates neuroinformatics activities within Japan and represents Japanese efforts in INCF. This site provides information about Japanese neuroinformatics platforms (NI Platforms) and the techniques and tools available from the International Neuroinformatics Coordinating Facility (INCF). The Neuroinformatics Japan Center (NIJC) will also supply techniques and tools developed at RIKEN BSI and at other research groups in Japan. INCF expects each national node to: 1. Actively formulate and implement the INCF Work Programs, 2. Coordinate and facilitate local neuroinformatics research activities at the national level, 3. Encourage neuroinformatics data sharing that conforms with INCF standards, and 4. Promote neuroinformatics development that supports the goals of INCF. The Neuroinformatics Japan Center (NIJC) represents the Japan Node. Together with the Japan Node Committee and the Platform Subcommittees, we promote domestic activities of neuroinformatics. Platform Subcommittee members collaborate to develop databases that are available for use on the website. Standing at the intersection of neuroscience and information science, the field of neuroinformatics develops the tools to house, share and analyze neuroscientific data, and to create computational models of brain. NIJC supports researchers developing and maintaining neuroscience databases, provides a portal for these databases and Neuroinformatics, and is designing the infrastructure for Neuroinformatics. It is also developing database technologies, and facilitates cooperation and distribution of the information stored in those databases. The activities of the Japan Node * Shaping domestic neuroinformatics research and directions (Japan Node Committee) * Advising on Intellectual Property Rights and protecting experimental subjects (Japan Node Committee) * Developing and publishing brain science databases (Platform Subcommittee) * Coordinating database management (Platform Subcommittee) * Disseminating neuroinformatics information via the web portal * Developing the infrastructure for brain science information and neuroinformatics * Supporting the development and diffusion of neuroinformatics technology
Common Fund Protein Capture Reagents Program
NIH Common Fund Protein Capture Reagents Program
Program that is developing new resources and tools to understand the critical role the multitude of cellular proteins play in normal development and health as well as in disease. These resources will support a wide-range of research and clinical applications that will enable the isolation and tracking of proteins of interest and permit their use as diagnostic biomarkers of disease onset and progression. The program is being implemented in phases, with three Funding Opportunity Announcements (FOAs): * FOA 1: Antigen Production (RFA-RM-10-007) To produce human transcription factor antigens for making monoclonal antibodies or other affinity capture reagents; this effort is already underway. * FOA 2: Anti-Transcription Factor Antibodies Production (RFA-RM-10-017) To optimize and scale anti-transcription factor capture reagent production to develop a community antibody resource. * FOA 3: New Reagent Technology Development and Piloting (RFA-RM-10-018) To develop improvements in the reagent production pipeline with regard to quality, utility, cost, and production scalability. To understand what makes a cell function normally and what may go awry in disease, we need better tools and resources, such as renewable protein capture reagents and probes, to study how proteins work in isolation and how they interact with other proteins, carbohydrates, or DNA regions within a cell. Ideally, this resource would allow us to identify and isolate all proteins within cells, in their various forms the so called proteome to ensure broad application in research and clinical studies aimed at understanding, preventing, detecting and treating disease. Existing protein capture reagents, such monoclonal antibodies, have been developed for a number of protein targets, although these represent only a subset of all proteins comprising the human proteome. In addition, many monoclonal antibodies lack the desired level of specificity and do not reliably target only the protein of interest. This is particularly problematic given the multiple forms of any one protein and the broad range of protein types in the body. The Protein Capture Reagents Program is organized as a pilot program using transcription factors as a test case to examine the feasibility and value of generating a community resource of low cost, renewable affinity reagents for all human proteins. The reagents must be specifically designed for high quality and broad experimental utility in order to meet the growing demands of biomedical researchers. Based on what is learned from these funding initiatives, the program may expand to a larger production effort to provide a broad community resource of human protein capture reagents.
PsychoPy - Psychology software in Python
Open source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It is intended as a free, powerful alternative to Presentation or e-Prime.
A blog presented by Faculty of 1000 highlighting and linking to the latest, greatest research recommended by F1000. Contributors include F1000 staff, freelance journalists, and scientists. We encourage readers to participate in the conversation via email to suggest topics and contribute guest posts.
DrugPort provides an analysis of the structural information available in the Protein Data Bank (PDB) relating to drug molecules and their protein targets. The drug-target data comes from the DrugBank database. You can search the entries by identifier, test or by protein sequence, or you can use the browse options in the menu on the left.
University College London Institute of Neurology
The Institute of Neurology is a specialist postgraduate institute of UCL. The Institute is closely associated in its work with the National Hospital for Neurology & Neurosurgery, University College London Hospitals'' NHS Foundation Trust, and in combination they form a national and international centre at Queen Square for teaching, training and research in neurology and allied clinical and basic neurosciences. The Institute of Neurology has eight academic departments encompassing clinical and basic research within in each theme: Neurodegenerative Disease; Molecular Neuroscience, incorporating the Reta Lila Weston Institute of Neurological Studies; Clinical and Experimental Epilepsy; Motor Neuroscience and Movement Disorders; Imaging Neuroscience; Brain Repair and Rehabilitation, Neuroinflammation and Clinical Neurosciences, Royal Free campus. In parallel there are currently six divisions representing professional affiliations: Clinical Neurology; Neurosurgery; Neurophysiology; Neuropathology; Neuropsychiatry and Neuropsychology; and Neuroradiology and Neurophysics. The Institute employs a total of around 500 staff, occupies some 6,451 sq m of laboratory and office space in five buildings, and has a current annual turnover of 33m pounds. The Institute currently holds over 250 active grants, supporting research into the causes and treatment of a wide range of neurological diseases, including movement disorders, multiple sclerosis, epilepsy, brain cancer, stroke and brain injury, muscle and nerve disorders, cognitive dysfunction and dementia, and the work of the Institute''s clinical academic staff is closely integrated with the Hospital''s care of patients. UCL Neuroscience is currently rated second in the world by ISI Essential Science Indicators, and four of the top twelve most highly cited authors working worldwide in neuroscience and behaviour are based at the IoN. There are seven Fellows of the Royal Society at Queen Square.
Yeungnam University; North Gyeongsang; South Korea
Private research university located in Gyeongsan, North Gyeongsang, South Korea. University includes colleges of Law and Medicine and teaching hospital.
Cochrane Central Register of Controlled Trials
A bibliographic database that provides a highly concentrated source of reports of randomized controlled trials. Records contain the list of authors, the title of the article, the source, volume, issue, page numbers, and, in many cases, a summary of the article (abstract). They do not contain the full text of the article. Cochrane Groups maintain and update Specialized Registers, which are collections of controlled trials relevant to the groups. CENTRAL is comprised of these Specialized Registers, relevant records retrieved from MEDLINE and EMBASE, and records retrieved through handsearching (planned manual searching of a journal or conference proceedings to identify all reports of randomized controlled trials and controlled clinical trials). The Cochrane Collaboration contracts a technology company, Metaxis, to merge the records from the sources outlined above and provide a data feed to the publisher. New and changed data are delivered to the publisher on a monthly basis.
National Institute of Neurological Disorders and Stroke CDEs
NINDS NINDS Common Data Elements: Harmonizing information. Streamlining research.
The purpose of the NINDS Common Data Elements (CDEs) Project is to standardize the collection of investigational data in order to facilitate comparison of results across studies and more effectively aggregate information into significant metadata results. The goal of the National Institute of Neurological Disorders and Stroke (NINDS) CDE Project specifically is to develop data standards for clinical research within the neurological community. Central to this Project is the creation of common definitions and data sets so that information (data) is consistently captured and recorded across studies. To harmonize data collected from clinical studies, the NINDS Office of Clinical Research is spearheading the effort to develop CDEs in neuroscience. This Web site outlines these data standards and provides accompanying tools to help investigators and research teams collect and record standardized clinical data. The Institute still encourages creativity and uniqueness by allowing investigators to independently identify and add their own critical variables. The CDEs have been identified through review of the documentation of numerous studies funded by NINDS, review of the literature and regulatory requirements, and review of other Institute''s common data efforts. Other data standards such as those of the Clinical Data Interchange Standards Consortium (CDISC), the Clinical Data Acquisition Standards Harmonization (CDASH) Initiative, ClinicalTrials.gov, the NINDS Genetics Repository, and the NIH Roadmap efforts have also been followed to ensure that the NINDS CDEs are comprehensive and as compatible as possible with those standards. CDEs now available: * General (CDEs that cross diseases) Updated Feb. 2011! * Congenital Muscular Dystrophy * Epilepsy (Updated Sept 2011) * Friedreich''s Ataxia * Parkinson''s Disease * Spinal Cord Injury * Stroke * Traumatic Brain Injury CDEs in development: * Amyotrophic Lateral Sclerosis (Public review Sept 15 through Nov 15) * Frontotemporal Dementia * Headache * Huntington''s Disease * Multiple Sclerosis * Neuromuscular Diseases ** Adult and pediatric working groups are being finalized and these groups will focus on: Duchenne Muscular Dystrophy, Facioscapulohumeral Muscular Dystrophy, Myasthenia Gravis, Myotonic Dystrophy, and Spinal Muscular Atrophy The following tools are available through this portal: * CDE Catalog - includes the universe of all CDEs. Users are able to search the full universe to isolate a subset of the CDEs (e.g., all stroke-specific CDEs, all pediatric epilepsy CDEs, etc.) and download details about those CDEs. * CRF Library - (a.k.a., Library of Case Report Form Modules and Guidelines) contains all the CRF Modules that have been created through the NINDS CDE Project as well as various guideline documents. Users are able to search the library to find CRF Modules and Guidelines of interest. * Form Builder - enables users to start the process of assembling a CRF or form by allowing them to choose the CDEs they would like to include on the form. This tool is intended to assist data managers and database developers to create data dictionaries for their study forms.
Anxiety Disorders Association of America
The Anxiety Disorders Association of America (ADAA) is a national nonprofit organization dedicated to the prevention, treatment, and cure of anxiety disorders and to improving the lives of all people who suffer from them. It is the leader in education, training, and research for anxiety and stress-related disorders. ADAA leads the way, improving the lives of millions of people: * Promotes professional and public awareness of anxiety and related disorders and their impact on people''s lives. * Encourages the advancement of scientific knowledge about causes and treatment of anxiety and related disorders. * Links people who need treatment with the health care professionals who provide it. * Helps people find appropriate treatment and develop self-help skills. * Works to reduce the stigma surrounding anxiety and related disorders. ADAA was founded in 1980 as the Phobia Society of America by a diverse group of clinicians and patients. The term anxiety disorder had not yet been coined. Most anxiety disorders were simply called phobias. That changed as researchers discovered links between panic attacks and abnormal blood flow in the brain, learned that anxiety disorders are associated with pervasive social and health consequences, and discovered and tested various therapies and medications to treat anxiety disorders. ADAA adopted its new name in 1990 to reflect the changing and growing field. Over the years ADAA has launched several national educational campaigns to promote awareness about anxiety disorders and encourage people to seek treatment. ADAA has also funded more than $1.5 million in anxiety disorder research. Today ADAA continues to be the voice for those affected by anxiety and anxiety-related disorders. The organization is frequently cited by the media and also provides information and treatment referrals to tens of thousands each year by phone, e-mail, and through this website.
LIPID Metabolites And Pathways Strategy database
Multi-institutional supported website and database that provides access to large number of globally used lipidomics resources. Internationally led the field of lipid curation, classification, and nomenclature since 2003. Produces new open-access databases, informatics tools and lipidomics-focused training activities will be generated and made publicly available for researchers studying lipids in health and disease.
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit
Gene Ontology Enrichment Analysis Software Toolkit
Gene Ontology Enrichment Analysis Software Toolkit (GOEAST)
Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) is a web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results, especially for results from microarray hybridization experiments. The main function of GOEAST is to identify significantly enriched GO terms among give lists of genes using accurate statistical methods. Compared with available GO analysis tools, GOEAST has the following unique features: * GOEAST supports analysis for data from various resources, such as expression data obtained using Affymetrix, illumina, Agilent or customized microarray platforms. GOEAST also supports non-microarray based experimental data. The web-based feature makes GOEAST very user friendly; users only have to provide a list of genes in correct formats. * GOEAST provides visualizable analysis results, by generating graphs exhibiting enriched GO terms as well as their relationships in the whole GO hierarchy. * Note that GOEAST generates separate graph for each of the three GO categories, namely biological process, molecular function and cellular component. * GOEAST allows comparison of results from multiple experiments (see Multi-GOEAST tool). The displayed color of each GO term node in graphs generated by Multi-GOEAST is the combination of different colors used in individual GOEAST analysis. Platform: Online tool
University of Florida DNA and Tissue Bank
UF Alpha-1 Foundation DNA and Tissue Bank
The Alpha-1 Foundation DNA and Tissue Bank, established in 2000 by the Alpha-1 Foundation, is a repository specifically for medical information (hyperlink to data points) and tissue samples (DNA, plasma, lung/liver) for alpha-1-antitrypsin deficient individuals, their family and friends. The Bank serves the international scientific community. Currently the Bank has the largest collection of DNA in the world for Alpha-1-antitrypsin research studies. The Alpha-1 Foundation has established a Tissue Bank Advisory Committee which includes a wide representation of physicians, ethicists, attorneys, consumers as well as international experts in tissue banking. Collectively this Advisory Committee reviews requests for research. At this time the Bank has over 2400 members who have provided valuable medical and/or tissue samples. For investigators interested in obtaining tissue samples with phenotypes from the Bank, please contact the Alpha-1 Foundation or our research staff at the University of Florida.
Laser and Biomedical Technology Laboratories
Biomedical technology research center and training resource that develops time-resolved laser technologies and instrumentation, with a focus on 2-D IR spectroscopy. The technologies enable atomic-level measurements of the fastest steps in biological processes to elucidate structure and dynamics in biological macromolecules, assemblies and cells. The Center makes most of its instrumentation available for service research projects to outside users nation-wide.
Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes by the reactions they catalyze. Also included are links to individual documents and advice is provided on how to suggest new enzymes for listing, or correction of existing entries. The common names of all listed enzymes are listed, along with their EC numbers. Where an enzyme has been deleted or transferred to another EC number, this information is also indicated. Each list is linked to either separate entries for each entry or to files with up to 50 enzymes in each file. A start has been made in showing the pathways in which enzymes participate. For other enzymes a glossary entry has been added which may be just a systematic name or a link to a graphic representation. The glossary from Enzyme Nomenclature, 1992 may also be consulted. This has been updated with subsequent glossary entries. Each enzyme entry has links to other databases. Enzyme Subclasses provide links to a list of sub-subclasses which in turn list the enzymes linked to separate files for each enzyme, or to a list as part of a file with up to 50 enzymes per file.
Curated data about all recombinase-containing transgenes and knock-ins developed in mice providing a comprehensive resource delineating known activity patterns and allows users to find relevant mouse resources for their studies.
Schizosaccharomyces pombeGenome Sequencing Project
Model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation, mailing lists, and welcomes data submissions.
A utility, whose output is a PostScript file of aligned sequences with graphical enhancements. Its main input is an ascii file of pre-aligned sequences. Optional files allow further rendering. The program calculates a similarity score for each residue of the aligned sequences. The output shows: * Secondary Structures * Aligned sequences * Similarities * Accessibility * Hydropathy * User-supplied markers * Intermolecular contacts In addition, similarity score can be written in the bfactor column of a pdb file, to enable direct display of highly conserved areas. You can run ESPript from this server with the HTML interface. It is configured for a maximum of 1,000 sequences. Links to webESPript * ENDscript: you can upload a PDB file or enter a PDB code such as 1M85. The programs DSSP and CNS are executed via the interface, so as to obtain an ESPript figure with a lot of structural information (secondary structure elements, intermolecular contacts). You can also find homologous sequences with a BLAST search, perform multiple sequence alignments with MULTALIN or CLUSTALW and create an image with BOBSCRIPT or MOLSCRIPT to show similarities on your 3D structure. * ProDom: you can enter a sequence identifier to find homologous domains, perform multiple sequence alignments with MULTALIN and click on the link to ESPript. * Predict Protein: you can receive a mail in text (do not use the HTML option when you submit your request in Predict Protein) with aligned sequences and numerous information including secondary structure prediction. Click on a special html link to upload your mail in ESPript. * NPS(at): you can execute the programs BLAST and CLUSTALW to obtain multiple alignments. You can predict secondary structure elements and click on the link to ESPript. This program started in the laboratory of Dr Richard Wade at the Institut de Biologie Structurale, Grenoble. It moved later to the Laboratory of Molecular Biophysics in Oxford, then to the Institut de Pharmacologie et de Biologie Structurale in Toulouse. It is now developed in the Laboratoire de BioCristallographie of Dr Richard Haser, Institut de Biologie et de Chimie des Prot��������ines, Lyon and in the Laboratoire de Biologie Mol��������culaire et de Relations Plantes-Organismes, group of Dr Daniel Kahn, Institut National de la Recherche Agronomique de Toulouse.
Ontology that provides a comprehensive and formal representation of the different domain concepts involved in documenting the full complexity of the skeletal dysplasia domain. It captures and combines the genetic features that discriminate the bone dysplasias with the multitude of phenotypic characteristics manifested by patients and required to be taken into account in order to support the diagnosis process.
Network of Minority Health Research Investigators
Network of Minority Health Research Investigators (NMRI)
Communication network of current and potential biomedical research investigators and technical personnel from traditionally under-served communities: African American, Hispanic American, American Indian, Alaskan Native, Native Hawaiian, and other Pacific Islanders. The major objective of the network is to encourage and facilitate participation of members of underrepresented racial and ethnic minority groups in the conduct of biomedical research in the fields of diabetes, endocrinology, metabolism, digestive diseases, nutrition, kidney, urologic and hematologic diseases. A second objective is to encourage and enhance the potential of the underrepresented minority investigators in choosing a biomedical research career in these fields. An important component of this network is promotion of two-way communications between network members and the NIDDK.
Pseudomonas Genome Database - Improving Disease Treatment Through Genome Research
Database of peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome expanded to include all Pseudomonas species to facilitate cross-strain and cross-species genome comparisons with high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP (Pseudomonas aeruginosa Community Annotation Project) participating researchers. If you are interested in participating, you are invited to get involved. Many annotations, DNA sequences, Orthologs, Intergenic DNA, and Protein sequences are available for download.
A high-performance nonlinear finite element solver. A key feature is the option of GPU-based execution, which allows the solver to significantly out-perform equivalent commercial packages.
BoDD is an electronic re-incarnation of BOTANICAL DERMATOLOGY by John Mitchell & Arthur Rook. This updated on-line version is made available to users with the kind permission of the original authors. The original edition has been digitized by Google Books. Although BoDD is actively being updated, updates are uploaded to the website only at about monthly intervals. A vast body of information collected by the Editor (Richard J. Schmidt PhD) awaits addition to the database. Users should be aware that some of the information that is currently accessible is neither accurate nor up-to-date. None of the information presented in BoDD should be regarded as a recommendation to treat any disease or disorder. The following are databases that are present in BoDD: -Balsaminaceae -Elaeagnaceae -Gelsemiaceae -Gentianaceae / Potaliacaceae -Hydroleaceae -Loganiaceae / Spigeliaceae / Strychnaceae -Martyniaceae -Orobanchaceae -Phrymaceae -Sabiaceae -Tamaricaceae
Software tools for global and local image registration. The algorithm used for global registration is based on a block matching approach enabling robust registration (outliers rejection). The local registration implementation uses a cubic B-Spline parametrisation (Free-Form Deformation). All registration algorithms are based on symmetric approaches where forward and backward transformations can be optimised concurrently. NiftyReg has been implemented for both CPU and GPU (through the use of CUDA).
NIMS: Neurobiological Image Management System
A scientific data management system specifically designed for neuroimaging data. NIMS automatically reaps data from the measurement instrument (e.g., MR scanner), sorts and organizes the data based on header information, does some basic processing on the data, and makes the data available to authorized users through a web-based interface. The data are also available from the command-line through a FUSE-based filesystem.
Bone and Cartilage Tissue Engineering Ontology
Ontology that describes the field of Tissue Engineering for what concerns bone and cartilage tissues.
Interactive and programmatic interfaces to query, browse and navigate an increasing number of biomedical ontologies and controlled vocabularies. It provides a web service interface to query multiple ontologies from a single location with a unified output format. It can integrate any ontology available in the Open Biomedical Ontology (OBO) format. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A weekly MySQL database export file can be downloaded from the EBI public FTP directory.
Articles published by guardian.co.uk Science about: Science + Video
Database of mapped validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development. CellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text. Operated under the Open Source/Access model, community and scientific networking applications will allow users to store and retrieve their data and to explore cells and their interactions on singular and complex resolution levels. The involvement of stem cell registries and banks will allow direct access to selected cells. The set up the stem cell data repository will involve three lines of action: * the acquisition of scientific data and contents * the standardized description of this data, its organization with the help of ontologies and technical implementation * the integration of existing sources/logistics and to ensure sustainable long-term operation
Academic Careers Understood through Measurement and Norms
European research collaboration aimed at understanding the ways in which researchers are evaluated by their peers and by institutions, and at assessing how the science system can be improved and enhanced. This FP7 project is a cooperation among nine European research institutes with Professor Paul Wouters (CWTS ����?? Leiden University) as principal investigator.
Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images.
National Biomedical Electron Paramagnetic Resonance Center
Biomedical technology research center focusing on technological innovation and application of new techniques to biological problems. The main areas of research are free radicals, spin labeling, metal complexes, and metallo proteins. Spectrometers are available for S-, X-, L-, Q- , and W-band EPR, many with ENDOR, ELDOR, saturation-transfer, saturation-recovery, and multiquantum capabilities. * Development of multiquantum Q- and W-band spectrometers, including multiquantum ELDOR, development of time-locked sub-sampling (TLSS) for broadband detection of periodically modulated signals * Development of loop-gap resonators using finite element modeling of Maxwell''s equations * Application of multifrequency (1 to 100 GHz) electron paramagnetic resonance (EPR) to characterize paramagnetic centers * Study of relaxation processes using multifrequency pulse saturation recovery * Use of nitroxide radical spin labels to measure translational and rotational diffusion in biological systems, site-directed spin labeling (SDSL), and use of EPR for the detection of nitric oxide and oxy radicals
Botryllus schlosseri anatomy and development ontology
Ontology describing the anatomy and the development of Botryllus schlosseri.
brainline.org: preventing treating and living with traumatic brain injury (TBI)
BrainLine is a national multimedia project offering information and resources about preventing, treating, and living with TBI. BrainLine includes a series of webcasts, an electronic newsletter, and an extensive outreach campaign in partnership with national organizations concerned about traumatic brain injury. BrainLine serves anyone whose life has been affected by TBI. That includes people with brain injury, their families, professionals in the field, and anyone else in a position to help prevent or ameliorate the toll of TBI. Through BrainLine, we seek to provide a sense of community, a place where people who care about TBI can go 24 hours a day for information, support, and ideas. BrainLine is funded by the Defense and Veterans Brain Injury Center, the Primary Operational TBI Component of the Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury, through a subcontract award with the Henry M. Jackson Foundation for the Advancement of Military Medicine.
Immune Epitope Database and Analysis Resource (IEDB)
Immune Epitope Database and Analysis Resource
Repository contains antibody/B cell and T cell epitope information and epitope prediction and analysis tools. Immune epitopes are defined as molecular structures recognized by specific antigen receptors of the immune system, namely antibodies, B cell receptors, and T cell receptors. Immune epitopes from infectious diseases, excluding HIV, and immune-mediated diseases and the accompanying biological information are included.
The Wake Forest Cynomolgus Breeding Colony (CBC) is a colony of cynomolgus macaques (crab-eating macaques, Macaca fascicularis). The cynomolgus colony is designed to produce specific pathogen free (SPF) cynomolgus monkeys for use in biomedical research. The colony, supported by a grant from the NCRR, addresses the growing need for investigators to use in their protocols animals defined for the absence of specific diseases including CHV-1 (Herpes B), simian immunodeficiency virus, and simian retroviruses. An additional important characteristic of this colony is that, unlike many breeding colonies, the NHPs will be fed two defined diets. The first diet is a soy-free diet, not commercial monkey chow. The second diet has the same macronutrients but the protein source is from soy; similar in isoflavone content. A drawback of chow diets is that the exact nutritional product composition is unknown from lot to lot. However, they are always rich in soy bean meal, isoflavones and other constituents of soy bean meal that are known confounders of several types of research projects. All research using the cynomolgus colony must be reviewed and approved by the colony''s scientific board and the Wake Forest Animal Care and Use Committee (ACUC) before any work can be initiated. The scientific board meets regularly to assess the scientific value of each request and to determine whether or not animals/samples/data can be made available. This includes all requests for: # The purchase of animals for use outside the colony # The use of animals within the colony for the collection of blood/tissue samples, behavioral observations or other kinds of testing # The use of the CBC sample/tissue repository # The use of the CBC data repository
Database and data analysis system dedicated to glossary, nomenclature, classification, information search, prediction, design, and statistics of Antimicrobial peptides and beyond. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually in the past several years. Peptides will be registered into this database if: # they are from natural sources (bacteria, protozoa, fungi, plants, and animals); # their antimicrobial activities are demonstrated (MIC
National Center on Addiction and Substance Abuse
National Center on Addiction and Substance Abuse at Columbia University
A science-based organization focused on developing effective solutions to address the disease of addiction and reduce the risks associated with substance use. CASAColumbia works to: * Close the gap between what is known about addiction and what is actually done to prevent and treat it * Incorporate addiction prevention and treatment into routine health care and medical practice * Explore the possibility of finding a cure Founded by Former U.S. Secretary of Health, Education, and Welfare Joseph A. Califano, Jr., CASA remains the only national organization that assembles under one roof all of the professional skills needed to research and develop proven, effective ways to prevent and treat substance abuse and addiction to all substances - alcohol, nicotine as well as illegal, prescription and performance enhancing drugs - in all sectors of society. CASAColumbia is committed to understanding the science of addiction and its implications for health care, public policy and public education.
A database of drug-gene relationships that provides drug-gene interactions and potential druggability data given list of genes. There are about 15 data sources that are being aggregated by DGIdb, with update date and these data sources are listed on this page: http://dgidb.genome.wustl.edu/sources, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Database that provides the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. RAP-DB contains clone positions, structures and functions of genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison.
Database of Osteogenesis Imperfecta and Type III Collagen Variants
Database integrating collagen biological and physicochemical properties with known variants. Web-based, interactive, graphical user interface displays data as annotations on collagen protein sequences. Collagen gene-level data are provided as custom tracks for display in the UCSC genome browser. COLdb currently includes 35,582 data points spanning collagen types I, II, and III, and, importantly, users can add their own data to the display. The database is the first comprehensive integration of disparate functional information on the three major fibrillar collagens, and the first electronic collection of mutations in the COL2A1 gene. Sponsors: This data base is supported by University of Leicester.
TREAT-NMD is a network for the neuromuscular field that is creating the infrastructure to ensure that the most promising new therapies reach patients as quickly as possible. Since its launch in January 2007 the network''s focus has been on the development of tools that industry, clinicians and scientists need to bring novel therapeutic approaches through preclinical development and into the clinic, and on establishing best-practice care for neuromuscular patients worldwide.
casper - Characterization of Alternative Splicing based on Paired-End Reads
Characterization of Alternative Splicing based on Paired-End Reads
Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.
Software tools for quality control, visualization and processing for High-Throughput Sequencing data. These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.
This project will develop an approach and mechanism to address the construction and propagation of linked data in the context of research and academic endeavour. The proposed work will build experiments in previous projects (Claddier, StoreLink) to develop a peer-to-peer protocol to underpin the construction of a web of linked data. This set of semantically annotated links between data resources forms a graph of citation and provenance and the project will build value added services to exploit these features. The project will address the following specific objectives: * To specify and implement the Intercom Protocol so that it can communicate a range of types of semantic links between resources via a secure communication mechanism. * To develop a practical working scenario involving data repositories, publication repositories, open science notebooks and publishers. * To develop aggregation techniques supporting added value services in search and impact analysis. * To evaluate of the approach with the identified stakeholders groups.
Global Proteome Machine Database (GPM DB)
The Global Proteome Machine Organization
The Global Proteome Machine Organization: Proteomics Database and Open Source Software
The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists.
Brain Research - Analysis of Images Networks and Systems
Medical image processing software suite for brain analysis.
Database providing integrated access to genome sequence, expression data and literature curation for Tuberculosis (TB) that houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. (July 2010) To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data.
EDAM Ontology - Bioinformatics operations types of data topics and data formats
An ontology of bioinformatics operations (tool, application, or workflow functions), types of data including identifiers, topics (application domains), and data formats. The applications of EDAM are within organizing tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.
British Psychological Society Research Digest
Research Digest - Blogging on brain and behaviour
The British Psychological Society''s award-winning Research Digest blog provides original, authoritative reports on the latest psychology research papers. Plus we publish a few other fun features too. The Digest doesn''t just pick up on the same studies covered by the mainstream media. The editor trawls hundreds of peer-reviewed journals looking for the latest findings from across the breadth of psychological science. The aim is to write accessible, accurate reports on those studies that make an important contribution, that are relevant to real life, timely, novel or thought-provoking. We want to demonstrate how interesting and useful psychological science can be, whilst also casting a critical eye over the methods used. We also hope you''ll use the comments function to have your say on the new research reported here. There are also ''Extras'' posts with links to eye-catching studies that didn''t make the final cut, and the ''Special Issue Spotter'' with links to the latest journal special issues in psychology. Over the years there have also been a number of special guest features - look out for more in the future. In 2010 the Digest was voted best psychology blog in the inaugural Research Blogging awards.
MeshValmet: Validation Metric for Meshes
A tool that measures surface to surface distance between two triangle meshes using user-specified uniform sampling. Thus, users can choose finer sampling level to calculate errors to gain more accuracy in theerror space, or sparser sampling to gain speed and get an approximate feeling of error distribution between boundaries. Besides its pleasant visualization using the VTK library, MeshValmet also provides useful histogram and statistical information based on the sample errors, such as mean and median distance, root mean square distance, mean square distance, mean absolute distance, Hausdorff distance, 95 percentile, 68 percentile, etc. MeshValmet is based on the work of Nicolas Aspert, etc.: MESH: Measuring Errors between Surfaces using the Hausdorff distance in the proceedings of the IEEE Int. Conf. on Multimedia and Expo 2002 (ICME), vol. I, pp. 705-708. The calculation of the Dice's Coefficient is calculated by Joshua Stough using the concept of a Riemannian sum.
Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data.
It facilitates the search for and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS). Use the Search Page to search for a compound of your interest, using the name, mass, formula, InChI etc. as query input. Additionally, a Library Search service enables the search of user submitted mass spectra within the GMD. In parallel to the library search, a prediction of chemical sub-groups is performed. This approach has reached beta level and a publication is currently under review. Using several sub-group specific Decision Trees (DTs), mass spectra are classified with respect to the presence of the chemical moieties within the linked (unknown) compound. Prediction of functional groups (ms analysis) facilitates the search of metabolites within the GMD by means of user submitted GC-MS spectra consisting of retention index (n-alkanes, if vailable) and mass intensities ratios. In addition, a functional group prediction will help to characterize those metabolites without available reference mass spectra included in the GMD so far. Instead, the unknown metabolite is characterized by predicted presence or absence of functional groups. For power users this functionality presented here is exposed as soap based web services. Functional group prediction of compounds by means of GC-EI-MS spectra using Microsoft analysis service decision trees All currently available trained decision trees and sub-structure predictions provided by the GMD interface. Table describes the functional group, optional use of an RI system, record date of the trained decision tree, number of MSTs with proportion of MSTs linked to metabolites with the functional group present for each tree. Average and standard deviation of the 50-fold CV error, namely the ratio false over correctly sorted MSTs in the trained DT, are listed. The GMD website offers a range of mass spectral reference libraries to academic users which can be downloaded free of charge in various electronic formats. The libraries are constituted by base peak normalized consensus spectra of single analytes and contain masses in the range 70 to 600 amu, while the ubiquitous mass fragments typically generated from compounds carrying a trimethylsilyl-moiety, namely the fragments at m/z 73, 74, 75, 147, 148, and 149, were excluded.
The program of medical genome research is a large-scale biomedical research project which extends the national genome research net (NGFN) and will be funded by the federal ministry of education and research (BMBF) from 2008-2013. Currently the program includes two fields: * Research ** NGFN-Plus: With the aim on combating diseases that are central to health policy, several hundred researchers are systematically investigating the complex molecular interactions of the human body. They are organized in 26 Integrated Genome Research Networks. * Application ** NGFN-Transfer: The rapid transfer of results from medical genome research into medical and industrial application is the aim of the scientists from research institutes and biomedical enterprises that cooperate in eight Innovation Alliances. AREAS OF DISEASE * Cardiovascular disease * Cancer * Neuronal diseases * Infections and Inflammations * Environmental factors
LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
European website providing information about orphan drugs and rare diseases. It contains content both for physicians and for patients. Reference portal for rare diseases and orphan drugs to help improve diagnosis, care and treatment of patients with rare diseases.
Physiopedia is a resource utilizing collaborative wiki technology for rehabilitation professionals throughout the world, offering a place for physiotherapists and physical therapists to contribute, share, gain and build knowledge to develop a global understanding. The content of Physiopedia is driven by experts and represents an evidence-based approach to patient care. Physiopedia explores a plethora of clinical specialities and encompasses many aspects of each speciality. Physiopedia includes clinically relevant information that clinicians will find useful in their practice and in the provision of good patient care. sharing As an international site, Physiopedia works to unite physiotherapists and physical therapists globally and collaboratively promote our profession. For educators Physiopedia offers an opportunity to involve their students in this knowledge creation process as part of an educational program. This clinical reference for patient care, educational framework and professional development platform is intended for physiotherapists, physical therapists, Rehabilitation Specialists, and Allied Health Professionals.
Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project
Mouse Gene Expression Information Resource Project
A unified resource that combines text-based and 3D graphical methods to store, display, and analyze mouse developmental gene expression information. The Mouse Gene Expression Information Resource resource will integrate the following components: * Gene Expression Database (GXD) - Integrates different types of expression data and provides links to many other resources to place the data into the larger biological and analytical context. * Anatomy Database - Provides the standard nomenclature for developmental anatomy. * 3D Atlas / Graphical Gene Expression Database - Provides a high-resolution digital representation of mouse anatomy reconstructed from serial sections of single embryos at each representative developmental stage enabling 3D graphical display and analysis of in situ expression data.
Stanford University HIV Drug Resistance Database
The Stanford University HIV Drug Resistance Database is a curated public database designed to represent, store, and analyze the different forms of data underlying HIVs drug resistance. HIVDB has three main types of content: (1) Database queries and references, (2) Interactive programs, and (3) Educational resources. Database queries are designed primarily for researchers studying HIV drug resistance. The interactive programs and educational resources are designed for both researchers and those wishing to learn more about HIV drug resistance. 1.DATABASE QUERY AND REFERENCE PAGES Genotype-Treatment Correlations This Genotype-Treatment section of the database links to 15 interactive query pages that explore the relationship between treatment with HIV-1 antiretroviral drugs (ARVs) and mutations in HIV reverse transcriptase (RT), protease, and integrase. There are five types of interactive query pages: Treatment Profiles (Protease and RT inhibitors) Mutation Profiles (Protease and RT mutations) Detailed Treatment Queries (Protease, RT, and integrase inhibitors) Detailed Mutation Queries (Protease, RT, and integrase mutations) Mutation Prevalence According to Subtype and Treatment Genotype-Phenotype Correlations The main page of the Genotype-Phenotype Correlations section links to four interactive query pages: three dynamically updated data summaries and one regularly updated downloadable dataset. Drug Resistance Positions Query for levels of resistance associated with known drug resistance mutations Detailed Phenotype Queries Queries for levels of resistance associated with individual mutations or mutation combinations at all positions of protease, RT, and integrase Patterns of Drug Resistance Mutations Downloadable Reference Dataset Genotype-Clinical Correlations This part of the database has two main sections: Clinical Trials Datasets Summaries of Clinical Studies References This part of the database has two main sections: one with summaries of the data from each of the references in HIVDB and one in which every primate immunodeficiency virus sequence in GenBank is annotated according to its presence or absence in HIVDB. Studies in HIVDB GenBank <=> HIVDB New Submissions Approximately every three months, the New Submissions section lists the studies that have been entered into HIVDB. The study title links to the introductory page of the study in the References section. Database Statistics (http://hivdb.stanford.edu/pages/HIVdbStatistics.html) 2. INTERACTIVE PROGRAMS HIVDB has seven main interactive programs. 1. HIVdb Program Mutation List Analysis Sequence Analysis HIVdb Output Sierra Web Service Release Notes Algorithm Specification Interface (ASI) 2. HIValg Program 3. HIVseq Program 4. Calibrated Population Resistance (CPR) tool 5. Mutation ARV Evidence Listing (MARVEL) 6. ART-AiDE 7. Rega HIV-1 Subtyping tool Three programs in the HIV Drug Resistance Database share a common code base: HIVseq, HIVdb, and HIValg. HIVseq accepts user-submitted protease, RT, and integrase sequences, compares them to the consensus subtype B reference sequence, and uses the differences as query parameters for interrogating the HIV Drug Resistance database (Shafer, D Jung, & B Betts, Nat Med 2000; Rhee SY et al. AIDS 2006). The query result provides users with the prevalence of protease, RT and integrase mutations according to subtype and PI, nucleoside RT inhibitor (NRTI), non-nucleoside RT inhibitor (NNRTI), and integrase inhibitor (INI) exposure. This allows users to detect unusual sequence results immediately so that the person doing the sequencing can check the primary sequence output while it is still on the desktop. In addition, unexpected associations between sequences or isolates can be discovered by immediately retrieving data on isolates sharing one or more mutations with the sequence. There are three ways in which the HIVdb program can be used: (i) entering a list of protease and RT mutations, (ii) entering a complete sequence containing protease, RT, and/or integrase, and (iii) using a Web Service. HIVdb is an expert system that accepts user-submitted HIV-1 pol sequences and returns inferred levels of resistance to 20 FDA-approved ARV drugs including 8 PIs, 7 NRTIs, 4 NNRTIs, and - with this update - one INI. In the HIVdb system, each HIV-1 drug resistance mutation is assigned a drug penalty score and a comment; the total score for a drug is derived by adding the scores of each mutation associated with resistance to that drug. Using the total drug score, the program reports one of the following levels of inferred drug resistance: susceptible, potential low-level resistance, low-level resistance, intermediate resistance, and high-level resistance. HIValg is designed for users interested in comparing the results of different algorithms or who are interested in comparing and evaluating existing and newly developed algorithms. The ability to develop new algorithms that can be run on the HIV Drug Resistance Database depends on the Algorithm Specific Interface (ASI) compiler (Shafer & Betts JCM 2003). Submission of Sequences and Mutations For each of the three programs, sequences can be entered using either the Sequence Analysis Form or the Mutation List form. 3. EDUCATIONAL RESOURCES HIVDB contains several regularly updated sections summarizing data linking RT, protease, and integrase mutations and antiretroviral drugs (ARVs). These sections include (i) tabular summaries of the major mutations associated with each ARV class, (ii) detailed summaries of the major, minor, and accessory mutations associated with each ARV, (iii) the comments used by the HIVdb program, (iv) the scores used by the HIVdb program, (v) clinical studies in which baseline drug resistance mutations have been correlated with the virological response (clinical outcome) to a specific ARV, (vi) mutations that can be used for drug resistance surveillance, and (vii) a two-page PDF handout. 1. Drug Resistance Summaries Tabular Drug Resistance Summaries by ARV Class Detailed Drug Resistance Summaries by ARV Drug Resistance Mutation Comments Used by the HIVdb Program Drug Resistance Mutation Scores Used by the HIVdb Program Genotype-Clinical Outcome Correlation Studies 2. Surveillance Drug-Resistance Mutation List Section 3. PDF Handout Grant Support 1. National Institute for Allergy and Infectious Diseases (NIAID, NIH): Online HIV Drug Resistance Database (PI: Robert W. Shafer, MD, 1R01AI68581-01A1), 04/01/06 - 3/31/11 2. National Institute for Allergy and Infectious Diseases (NIAID, NIH) supplement to the grant Identification of Multidrug-Resistant HIV-1 Isolates (PI: Robert W. Shafer, MD, AI46148-01): Supplement provided 1999-2005. 3. NIH/NIGMS Program Project on AIDS Structural Biology Program Project: Targeting Ensembles of Drug Resistant Protease Variants (PI: Celia Schiffer, PhD, University of Massachusetts): 2002-2007 4. University-wide AIDS Research Program (CR03-ST-524). Community collaborative award: Optimizing Clinical HIV Genotypic Resistance Interpretation: Principal Investigators: Robert W. Shafer, MD and W. Jeffrey Fessel MD (Kaiser Permanente Medical Care Program): 2004-2005 5. Stanford University Bio-X Interdisciplinary Initiative: HIV Gene Sequence Analysis for Drug Resistance Studies: A Pharmacogenetic Challenge Principal Investigators: Robert W. Shafer, MD and Daphne Koller, Ph.D. (Computer Science): 2000-2002
A system for identifying content objects in the digital environment. DOI names are assigned to any entity for use on digital networks. They are used to provide current information, including where they (or information about them) can be found on the Internet. Information about a digital object may change over time, including where to find it, but its DOI name will not change. The DOI System provides a framework for persistent identification, managing intellectual content, managing metadata, linking customers with content suppliers, facilitating electronic commerce, and enabling automated management of media. DOI names can be used for any form of management of any data, whether commercial or non-commercial. The DOI System is an ISO International Standard. Using DOI names as identifiers makes managing intellectual property in a networked environment much easier and more convenient, and allows the construction of automated services and transactions.
A database which provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. It specifically contains information on quality-controlled, aligned and annotated bacterial and archaean 16S rRNA sequences, fungal 28S rRNA sequences, and a suite of analysis tools for the scientific community. Most of the RDP tools are now available as open source packages for users to incorporate in their local workflow.
DroID - Drosophila Interactions Database
DroID - The Drosophila Interactions Database
A gene and protein interactions database designed specifically for the model organism Drosophila including protein-protein, transcription factor-gene, microRNA-gene, and genetic interactions. For advanced searches and dynamic graphing capabilities the IM Browser and a DroID Cytoscape plugin are available.
CCUG: Culture Collection; University of Goteborg; Sweden
CCUG: Culture Collection; University of Gothenburg; Sweden
The CCUG holds a broad range of bacteria and the most demanded test strains of filamentous fungi and yeasts. We do not hold extremophils or intracellular organisms and we do not distribute hazard group 3 organisms. Cultures are freeze-dried and may be sent abroad promptly under controlled forms. Our identification service has been active for 43 years. CCUG has huge databases and they are pleased to share the information with you through their search engine.
An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components.
Down Syndrome Research and Treatment Foundation
The Down Syndrome Research and Treatment Foundation is dedicated to finding a treatment to improve cognition including learning, memory and speech for individuals with Down syndrome. Since our founding in 2004 we have become the leading private source of funding in the United States for Down syndrome cognition research. The mission of DSRTF is to stimulate biomedical research that will accelerate the development of treatments to significantly improve cognition, including memory, learning and speech, for individuals with Down syndrome in order that they: * participate more successfully in school; * lead more active and independent lives; * and avoid the early onset of Alzheimer''s Disease. DSRTF is funding research that applies the information, tools and techniques resulting from the genome project along with recent advances in brain research to the study of cognition in Down syndrome. Our goal is the development of treatments that will improve learning, memory, and speech, and therefore enhance the lives of those with Down syndrome and their families. The majority of individuals with Down syndrome fall into the mild to moderate range of cognitive impairment. For many of these individuals, a 10%-20% improvement in cognitive ability would provide them with the ability to live independently, hold a job and be fully integrated within their communities.
Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.
The country''s oldest and largest nationwide brain injury advocacy organization. We are dedicated to increasing access to quality health care and raising awareness and understanding of brain injury through advocacy, education and research. With a nationwide network of more than 40 chartered state affiliates and hundreds of local chapters and support groups, we provide help, hope and healing for individuals who live with brain injury, their families and the professionals who serve them. Brain injury is not an event or an outcome. It is the start of a misdiagnosed, misunderstood, under-funded neurological disease. Individuals who sustain brain injuries must have timely access to expert trauma care, specialized rehabilitation, lifelong disease management and individualized services and supports in order to live healthy, independent and satisfying lives.
Yong Loo Lin School of Medicine; Singapore; Singapore
The Influenza Research Database (IRD) serves as a public repository and analysis platform for flu sequence, experiment, surveillance and related data.
One of our goals at Autism Speaks is to identify and support promising research with the hope that results from these efforts will produce significant findings that will be reported in peer-reviewed journals. We also hope that grants we fund will lead to additional research support from government or other funding agencies. Since 1997, the organizations combined have committed more than $89 million to fund more than 737 research projects and fellowships. The investment in these research grants alone has been leveraged into nearly $153 million in NIH and other funding for the continuation of these scientific studies. Grants: Each year Autism Speaks holds a variety of investigator-initiated grant calls. We are pleased to be able to support many different types of projects, each critical for advancing all phases of autism research, from basic to clinical to treatment. These grants are crucial for allowing investigators to gain enough data to be able to attract even larger, multi-year commitments from the NIH and other traditional medical research funding organizations. Our grants include pilot grants, basic and clinical grants, augmentation and bridge grants, treatment and technology grants. Fellowships: Fellowships provide the necessary resources to support and encourage the development of young scientists who benefit from the mentorship of prominent researchers. We believe the investment in autism research training will grow exponentially as many of our fellows later assume teaching roles and join departments around the country and the world, many of which currently have no representation in autism research. Please note that in addition to our investigator-initiated grants and fellowships, we also support research through funding of proactive initiatives, including collaborative projects, resources and meetings.
Dictyostelium discoideum genome database
Model organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ' '''reference genome' ''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries.
A report incorporating current and retrospective data on all aspects of the epidemiology, practice patterns, costs, and impact of urologic diseases in the United States and is intended for use by public officials, nongovernment organizations, the media, academic researchers, health professionals, and the public. The UDA compendium consists of data tables annotated in chapters that amplify the data analyses. The objectives of the UDA project include: secondary data analyses of: changes in the overall healthcare burden for individual urologic diseases, in physician practice patterns for each urologic disease, and in demographics of persons with urologic disease, the impact of specific urologic diseases, especially diseases of the prostate, on the minority populations of the U.S., and documentation of new and evolving therapies for urologic disease and their cost.
Ontology that provides a normalized naming system for generic and branded drugs and a tool for supporting semantic interoperation between drug terminologies and pharmacy knowledge base systems. It contains the names of prescription and many over-the-counter drugs available in the United States and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software. It can mediate messages between systems not using the same software and vocabulary. * RxNorm Download Files - contain data consistent with the 2013AB UMLS Metathesaurus Release Files. * RxNorm API - web service for accessing the current RxNorm data set. * RxNorm Browser (RxNav) - a browser for several drug information sources, including RxNorm, RxTerms and National Drug File - Reference Terminology (NDF-RT) . * Current Prescribable Content - subset of currently prescribable drugs found in RxNorm. * RxTerms Drug Interface Terminology - a drug interface terminology derived from RxNorm for prescription writing or medication history recording
bedtools - a swiss army knife for genome arithmetic
bedtools: a flexible suite of utilities for comparing genomic features
A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
Fully customizable, comprehensive genetic pedigree and clinical data management software including a multi-user relational database with an integrated pedigree drawing component to manage genetic and pedigree data in one database. Manage Pedigrees, Individuals, SNPs, STRs, Samples, Plates, Genotypes and exports to multiple analysis platforms. (entry from Genetic Analysis Software) * LIMS software, providing advanced sample tracking and management (including functionality to generate and record barcodes) and configurable workflows for your specific environment. * Full genotype management gives users the ability to track not only family-based studies, but Whole Genome Association studies containing 1000''s of samples with large arrays.
A hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.
Founded in 1973, the American Brain Tumor Association (ABTA) was the first national nonprofit organization dedicated solely to brain tumors. For nearly 40 years, the Chicago-based ABTA has provided critical funding to researchers working toward breakthroughs in brain tumor diagnosis, treatment and care, and is the only national organization providing comprehensive resources and serving the complex supportive care needs of brain tumor patients and caregivers from diagnosis through treatment and beyond.
TIGAR: Transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference
Software to estimate transcript isoform abundances from RNA-Seq data by variational Bayesian inference. The statistical method can handle gapped alignments of reads against reference sequences so that it allows insertion or deletion errors within reads.
Software to recontruct abundances of known transcript forms from RNAseq data. The algorithm works by distributing the reads mapping to a given exonic region (or splice junction) among the transcripts including the exon (or splice junction). The input is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome. From the reference annotation, splicing graphs are produced and reads are mapped to corresponding edges in these graphs according to the position where they align in the genomic sequence. The resulting graph with edges labelled by the number of reads can be interpreted as a flow network where each transcript representing a transportation path from its start to its end and consequently each edge a possibly shared segment of transportation along which a certain number of reads per nucleotide -- i.e., a flux -- is observed. Given a density function of reads along a transcript, the expected participation of each transcript in an edge under consideration can be estimated. The basic idea is to cast back from these latter participations and the observed number of reads - allowing for a certain amount of noise - to the original transcript abundancies. To do so, a linear constraint is formalized for each edge, and an optimal solution for the complete set of constraints is found by a standard linear program solver.
A simple interface to simulate Brownian motion in arbitrary, complex environments. The analysis routines enable visualization of these models with DTI, q-space, and higher order diffusion weighted MRI.
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.
European Monitoring Centre for Drugs and Drug Addiction
The European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) is the central source of comprehensive information on drugs and drug addiction in Europe. It was set up to provide factual, objective, reliable and comparable information concerning drugs, drug addiction and their consequences. Mission and work programme Just over a decade ago, Europes capacity for monitoring its drug problem was extremely limited. National approaches to the topic varied greatly and there was a lack of reliable and comparable information at European level concerning drugs, drug addiction and their consequences. In other words, it was impossible to talk with confidence about patterns and trends in drug use across the EU. The European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) was founded in 1993 to change that. Inaugurated in Lisbon in 1995, the EMCDDA is the hub of drug-related information in the European Union. It exists to provide the EU and its Member States with a factual overview of European drug problems and a common information framework to support the drugs debate. The EMCDDA consists of a 90-strong team of specialists representing some 20 nationalities. Today it offers policy-makers the scientific evidence base they need for drawing up drug laws and strategies and helps professionals and researchers pinpoint best practice and new areas for analysis. Improving the comparability of drug information in the EU is central to the agencys work. To achieve this, the EMCDDA coordinates and relies on a network of some 30 national monitoring centres (Reitox network) to gather and analyse country data according to common data-collection standards and tools. The results of this national monitoring process are fed to the Lisbon centre for analysis and are ultimately released in the Annual report on the state of the drugs problem in Europe one of its many outputs. The EMCDDA has many working partners in Portugal. These include technical bodies primarily the Instituto da droga e da toxicodependncia which furnish the agency with the Portuguese drugs picture, and political bodies which use EMCDDA information when taking decisions on drug-related issues. In addition to cooperating with partners at national level, the EMCDDA also collaborates with its peers worldwide, having signed agreements with European and international organisations working in the drugs field. Over time, the EMCDDA has become not only Europes central reference point on drugs but also a respected authority globally. This interest has been reflected in visits by Heads of State and high-ranking politicians from all world regions and in requests from several non-EU countries for cooperation, whether in the area of technical assistance or the exchange of data and expertise. While the EMCDDA monitors the drug situation today, it is ever vigilant for new drugs and emerging trends that may pose a threat to Europes citizens tomorrow. With the production of cocaine and heroin at historically high levels and with around 7,000 Europeans dying every year of drug overdoses, constant monitoring is imperative. Public access to documents Citizens of the European Union and natural or legal persons residing or having their registered office in a Member State have the right of access to EMCDDA documents under Article 255(1) of the EC Treaty and Article 2(1) of Regulation (EC) No 1049/2001 in accordance with detailed rules laid out in the implementing rules adopted by the Management Board on 24 February 2006. This right to access concerns documents held by the EMCDDA, that is to say, documents drawn up or received by it and in its possession. Pursuant to article 2(2) of Regulation (EC) No 1049/2001, citizens of third countries not residing in a Member State and legal persons not having their registered office in one of the Member States shall enjoy the right of access to EMCDDA documents on the same terms as the beneficiaries referred to in Article 255(1) of the EC Treaty and Article 2(1) of Regulation (EC) No 1049/2001. All applications for access to a document should be sent by mail, fax or email, clearly stating the reference Application for access to EMCDDA documents. Funding The EMCDDA receives stable funding under Commission budget line B3-441 of the general budget of the European Union. Each year, a preliminary draft budget is presented by the Centre''s Director to the Management Board which may modify the draft before adopting it and submitting it to the European Commission. On this basis, the Commission presents its proposal for the annual funding to the EMCDDAs budget, to be adopted by the European Parliament and the Council. The implementation of the EMCDDA budget is subject to the external audit of the European Court of Auditors. The political responsibility for the execution of the budget rests with the EMCDDA''s Management Board, which adopts its own internal financial rules, based on the financial regulation applicable to the general budget of the European Communities.
International Union of Pure and Applied Chemistry Nomenclature
This site is intended primarily to provide information on IUPAC nomenclature recommendations (Organic & Biochemical Nomenclature, Symbols & Terminology etc.). As the author has been primarily involved in the preparation of organic and biochemical material most work will be in that field. Other material will be provided as it becomes available, either from this site or by links to other locations.
DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. The start and end positions of each feature (gene, non-translated region and the like) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the website) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses. The public sequence databases contain vast amounts of data on virus genomes but accessing and comparing the data, except for relatively small sets of related viruses can be very time consuming. The procedure is made difficult because some of the sequences on these databases are incorrectly named, poorly annotated or redundant. The NCBI Reference Sequence project (1) provides a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA) and protein products, for major research organisms. This now includes curated information for a single sequence of each fully sequenced virus species. While this is a welcome development, it can only deal with complete sequences. An important feature of DPV is the opportunity to access genes (and other features) of multiple sequences quickly and accurately. Thus, for example, it is easy to obtain the nucleotide or amino acid sequences of all the available accessions of the coat protein gene of a given virus species or for a group of viruses. To increase its usefulness further, DPVweb also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA (ssDNA) genome. Sponsors: This site is supported by the Association of Applied Biologists and the Zhejiang Academy of Agricultural Sciences, Hangzhou, People''s Republic of China.
Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.
Ontology that assigns a grade to a tumor starting from the 3 criteria of the NGS
University of Pittsburgh; Pennsylvania; USA
Public research university in Pittsburgh, Pennsylvania. Pitt was founded by Hugh Henry Brackenridge in 1787 as the Pittsburgh Academy.
Brain Innovation: Home of the BrainVoyager Product Family
Brain Innovation B.V. is developing scientific software in the field of human and animal brain imaging, neural network simulation and computer-based experimental control. Our current major product, BrainVoyager QX, is a commercially available cross-platform neuroimaging tool, which is used in hundreds of labs across the planet. Turbo-BrainVoyager is an easy to use program for real-time data analysis, which allows to observe a subject''s or patient''s brain activity during an ongoing functional MRI scanning session. TMS Neuronavigator provides the hard- and software to navigate a TMS coil to desired anatomical or functionally defined brain regions. We also provide free software products. BrainVoyager Brain Tutor allows to learn about brain areas by clicking on rotatable 3D brain models. StimulDX is a powerful stimulation software based on Microsofts DirectX API, which we will make available for free download in the near future.
Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center
Cooperative Human Tissue Network - Western Division
The Cooperative Human Tissue Network- Western Division at Vanderbilt University Medical Center is one of six institutions throughout the country funded by the National Cancer Institutes to procure and distribute remnant human tissues to biomedical researchers throughout the United States and Canada. CHTN operates through a shared networking system which allows investigators greater access to available research specimens. CHTN offers a variety of preparation and preservation techniques to ensure investigators are receiving the quality specimens needed for research. Remnant tissues are obtained from surgical resections and autopsies and are procured to the specifications of the investigator.
A versatile web-server application for the analysis and visualization of array-CGH data.
MSU Rice Genome Annotation Project Database and Resource
Database and resource that provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 75 tracks of annotation. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads. Rice is a model species for the monocotyledonous plants and the cereals which are the greatest source of food for the world''s population. While rice genome sequence is available through multiple sequencing projects, high quality, uniform annotation is required in order for genome sequence data to be fully utilized by researchers. The existence of a common gene set and uniform annotation allows researchers within the rice community to work from a common resource so that their results can be more easily interpreted by other scientists. The objective of this project has always been to provide high quality annotation for the rice genome. They generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines. They have provided a resource to extend the annotation of the rice genome to other plant species by providing comparative alignments to other plant species. Analysis/Tools are available including: BLAST, Locus Name Search, Functional Term Search, Protein Domain Search, Anatomy Expression Viewer, Highly Expressed Genes
NCI Breast and Colon Cancer Family Registries
The Breast Cancer Family Registry (Breast CFR) and the Colon Cancer Family Registry (Colon CFR) were established by the National Cancer Institute (NCI) as a unique resource for investigators to use in conducting studies on the genetics and molecular epidemiology of breast and colon cancer. Known collectively as the CFRs, they share a central goal: the translation of research to the clinical and prevention settings for the benefit of Registry participants and the general public. The CFRs are particularly interested in: * Identifying and characterizing cancer susceptibility genes; * Defining gene-gene and gene-environment interactions in cancer etiology; and * Exploring the translational, preventive, and behavioral implications of research findings. The CFRs do not provide funding for studies; however, researchers can apply to access CFR data and biospecimens contributed by thousands of families from across the spectrum of risk for these cancers and from population-based or relative controls. Special features of the CFRs include: * Population-based and clinic-based ascertainment; * Systematic collection of validated family history; * Epidemiologic risk factor , clinical, and followup data; * Biospecimens (including tumor blocks and Epstein-Barr virus (EBV)-transformed cell lines); * Ongoing molecular characterization of the participating families; and * A combined informatics center.
Vanderbilt Energy Balance Core Laboratory
Core facility that provides the following services: Energy Expenditure Assessment, Body Composition Assessment, Physical Activity Assessment. This component of the core utilizes existing institutional resources for measurement of energy balance and provides personnel support that permit assessment of research in energy balance and nutrition assessment.
PDGene - A database for Parkinsons disease genetic association studies
The PDGene database aims to provide a comprehensive, unbiased and regularly updated collection of genetic association studies performed on Parkinson's disease (PD) phenotypes. Eligible publications are identified following systematic searches of scientific literature databases, as well as the table of contents of journals in genetics, neurology, and psychiatry. The database can be searched either by a variety of dropdown menus or by specific keywords. For each gene, summary overviews are provided displaying key characteristics for each publication, including links to genotype distributions of the polymorphisms studied, random-effects allelic meta-analyses, and funnel plots for an assessment of publication bias. The PDGene database, developed by Massachusetts General Hospital/Harvard Medical School, The Michael J. Fox Foundation and the Alzheimer Research Forum, is supported by a grant from The Michael J. Fox Foundation in partnership with the Alzheimer Research Forum.
A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme
SUB-cellular location database for Arabidopsis proteins II
SUBA provides a powerful tool to investigate subcellular localization in Arabidopsis. SUBA houses large scale proteomic and GFP localization sets from cellular compartments of Arabidopsis, and also contains pre-compiled bioinformatic predictions for protein subcellular localizations. The Database functions through the unification of disparate datasets and through the provision of a web accessible interface for the construction of user based queries resulting in a one-stop-shop for protein localization in this model plant. Subcellular localization information can contribute towards our understanding of protein function, protein redundancy and of biological inter-relationships. In an attempt to get a clearer picture of our experimental data and to more generally understand subcellular partitioning we have brought together various data sources to build SUBA.
Private research university in Seoul, South Korea. Particularly respected in studies of medicine and business administration.
British Columbia Breast Cancer Tumour Bank
British Columbia Breast Cancer Tumor Tissue Repository
British Columbia Breast Cancer Tumour Tissue Repository
The Molecular Oncology department hosts the breast cancer tumour tissue repository (BREAST-TTR), a project within the agency-wide tumour tissue repository. The BREAST-TTR comprises several important banks of breast tissues, contemporaneous as well as archival. The main banks are: * 3000 frozen breast cancers, linked to 15 year outcomes data from the BCCA Breast Cancer Outcomes Unit. This archival bank consists of frozen tissue, DNA and RNA, and a tissue microarray of the cases. * Live-cryopreserved cancers. At present around 50 individual cases of metastatic breast cancer, with tumour material cryopreserved for subsequent cell culture/xenograft work. * Comptemporary bank. Between the TTR in Victoria and the accrual site in Vancouver, approximately 1300 contemporaneous (within last 4 years) breast cancers with matched normal DNA and outcomes linkages.
Free, immediate and permanent online access to the full text of all articles published within its portfolio of over 200 peer-reviewed journals, and through its open access waiver fund, ensuring that scientific authors in low-income countries do not face financial barriers to publishing in open access journals. Open access provides a way for researchers from low-income countries to participate more fully in the international research community, and so BioMed Central has created a set of initiatives designed to increase the visibility and output of scientific research from these countries.
Gastroparesis Clinical Research Consortium
Gastroparesis Clinical Research Consortium (GpCRC)
Perform clinical, epidemiological, and therapeutic research in gastroparesis and provide an infrastructure that can rapidly and efficiently design and conduct clinical trials for effective medical, surgical, or other interventions to improve treatment of patients with gastroparesis. The GpCRC studies comprise well characterized individuals with diabetic, surgical, and idiopathic gastroparesis.
University of Pittsburgh School of Medicine; Pennsylvania; USA
University of Pittsburgh School of Medicine
Web server to provide germplasm information about plants, animals, microbes, invertebrates and access to databases that maintain passport, characterization, evaluation, inventory, and distribution data for the management and utilization of national germplasm collections. Under control of the U.S. Department of Agriculture's Agricultural Research Service to support the National Genetic Resources Program (NGRP). Operated by the Database Management Unit of the National Germplasm Resource Laboratory in Beltsville, Maryland.
Peptide Resource Page: Your Complete Guide to Peptide Research and Suppliers
A guide to peptide-related research and products including custom peptide suppliers, peptide synthesis reagent suppliers that provide resins, coupling reagents, and protected amino acids as well as biologically active peptides and substrates, peptide synthesizers for solution or solid phase peptide synthesis, peptide sequence analysis services, software to calculate the chemical or biochemical properties of peptides, including the prediction of antigenicity or difficult-to-synthesize sequences. There is an additional section on Proteomics Tools for the identification of proteins from peptide sequences determined by mass spectrometry. The site also contains a set of links to educational materials about peptide related research topics.
Micro-array Database at the National Cancer Institute
Microarray data management and analysis system for NCI / Center for Cancer Research scientists / collaborators. Data is secured and backed up on a regular basis, and investigators can authorize levels of access privileges to their projects, allowing data privacy while still enabling data sharing with collaborators.
Wake Forest School of Medicine Vervet Research Colony
NIH funded national research resource to provide biomedical research community with access to US born, known age, pedigreed, genomically sequenced, pathogen free Caribbean origin vervet monkeys also known as African green monkeys. Provides access to animals, extensive multisystem clinical phenotyping, sample and data repositories, expertise in use of nonhuman primate models for translational studies, serves as platform for training veterinarians and other professionals in biomedical research, husbandry, clinical care, and the colony behavioral management.
DMEAS - DNA Methylation Entropy Analysis Software
DNA Methylation Entropy Analysis Software
A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data.
Ribonuclease P is responsible for the 5''-maturation of tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria (and some Archaea) the RNA subunit alone is catalytically active in vitro, i.e. it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models and accessory information. The database contains information on bacterial, archaeal, and eukaryotic RNase P. The RNase P and protein sequences are available from phylogentically-arranged lists, individual sequences, or aligned in GenBank format. The database also provides secondary structures and 3D models, as well as movies, still images, and other accessory information.
National Endocrine and Metabolic Diseases Information Service
Information dissemination service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) providing information about endocrine and metabolic diseases in easy-to-understand language: online, in booklets and fact sheets, by email, and over the phone to patients, health professionals and the public. The NEMDIS provides the following informational products and services: * Response to inquiries about endocrine and metabolic diseases, ranging from information about available patient and professional education materials to referrals to patient support organizations. Assistance is available by phone (8:30 a.m. to 5 p.m. eastern time, M-F), fax, mail, and email. * Publications about endocrine and metabolic diseases, provided free of copyright, in varying reading levels. Available online or in hard copy. NEMDIS also sends publications to health fairs and community events. * Referrals to health professionals through the National Library of Medicine' '''s MEDLINEplus, which includes a consumer-friendly listing of organizations to assist in the search for physicians and other health professionals.
Induced Pluripotent Stem Cell (iPSC) and Source Cells available for distribution for postnatal-to-adult human control and patient-derived cells and their reprogrammed derivatives in support of stem cell research relevant to mental disorders. This includes but is not limited to anxiety disorders, attention deficit hyperactivity disorder, autism spectrum disorders, bipolar disorder, borderline personality disorder, depression, eating disorders, obsessive-compulsive disorder, panic disorder, post-traumatic stress disorder, and schizophrenia. The capabilities of the repository range from derivation and banking of primary source cells from postnatal through adult human subject tissue to more comprehensive banking and validation of induced pluripotent stem cells (iPSCs) or similar reprogrammed / de-differentiated cells. Please send a message with the Contact page if you wish to contribute source cells or iPSC.
SoftSearch - Detecting Structural Variations Using Split Reads and Discordant Read Pairs
A sensitive structural variant (SV) detection software tool for Illumina paired-end next-generation sequencing data. It simultaneously utilizes soft-clipping and read-pair strategies for detecting SVs to increase sensitivity. Soft clips are proxies for split-reads that indicate part of the read maps to the reference genome, but the other part is not localized at the same place (e.g. breakpoint spanning reads). Discordant read-pairs refer to a read and its mate, where the insert size is greater (or less than) the expected distribution of the dataset ? or ? where the mapping orientation of the reads is unexpected (e.g. both on the same strand). SoftSearch looks for areas with soft-clipping in the genome that have discordant read pairs supporting the anomaly. Once areas with both these conditions are identified, the read and mate information is extracted directly from the BAM file containing the discordant reads, obviating the need for time-consuming and error-prone complex alignment strategies. Only a small number of soft-masked bases discordant read-pairs are necessary to identify an SV, which on their own would not be sufficient to make an SV call, thus highlighting SoftSearch?s improved sensitivity. SoftSearch is well suited to be ?plugged in? to most sequence analysis workflows, since it requires standard file inputs, such as a BAM file using almost any aligner and a reference genome FASTA file. Because SoftSearch requires soft-masked bases, the only requirement is that the aligner must have this functionality, which is usually turned on by default by many standard aligners (e.g. BWA, Novoalign, etc).
Musculoskeletal Transplant Foundation - MTF
The Musculoskeletal Transplant Foundation is a non-profit service organization dedicated to providing quality allograft tissue through a commitment to excellence in education, research, recovery and care for recipients, donors and their families. We are a national consortium comprised of academic medical institutions, organ procurement organizations and tissue recovery organizations. MTF was created as a charitable organization with a mission that is dedicated to the needs of donors, donor families, patients and surgeons. We focus on respectful stewardship of the donated gift while advancing the science and practice of bone, ligament, cartilage and skin transplantation. Since our inception in 1987, MTF has recovered more than 60,000 donors and distributed more than 3 million grafts for transplantation. We also support research to expand the science of transplantation, and we encourage the efforts of our members and non-member clients to improve the understanding of donation and transplantation among the medical community and the public at large. Our policies are developed and implemented by MTF' '''s Medical Board of Trustees, Donation Board of Trustees and Board of Directors, composed of physicians and recovery agency representatives who are dedicated to the mission of the Foundation. This fundamental commitment enables us to set and maintain the highest levels of safety assurance and quality control in all phases of our operations.
Web game that provides an innovative infrastructure for labeling to enable an alternative to expert raters for medical image labeling through statistical analysis of the collaborative efforts of many, minimally-trained raters. Statistical atlases of regional brain anatomy have proven to be extremely useful in characterizing the relationship between the structure and function of the human nervous system. Typically, an expert human rater manually examines each slice of a three-dimensional volume. This approach can be exceptionally time and resource intensive, so cost severely limits the clinical studies where subject-specific labeling is feasible. Methods for improved efficiency and reliability of manual labeling would be of immense benefit for clinical investigation into morphological correlates of brain function.
Ontology covering a comprehensive list of cell lines derived from breast tissue, both normal and pathological. The ontology in built in OWL with cross relation to classes- genetic variation, pathological condition, genes, chemicals and drugs. The relations built enable semantic query across different classes
MPact: Representation of Interaction Data at MIPS
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It provides a common access point to interaction resources at MIPS. It is designed to support the PSI-MI standard, for both downloading and uploading data. It provides the user with intuitive query forms to quickly retrieve the interactions of interest. Graphical representations allow an easy navigation through the protein interaction networks.
Consensus Measures for Phenotype and Exposure
Consensus Measures for Phenotypes and Exposures
Consensus Measures for Phenotypes Exposure
Consensus Measures for Phenotypes Exposures
PhenX (consensus measures for Phenotypes and eXposures)
PhenX - consensus measures for Phenotypes and eXposures
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 05 01 2025. PhenX is a project to prioritize Phenotype and eXposure measures for Genome-wide Association Studies (GWAS). Leaders of the scientific community will assess and prioritize a broad range of domains relevant to genomics research and public health. The PhenX Steering Committee (SC), chaired by Dr. Jonathan Haines, provides leadership in the selection of domains and domain experts. Members of the SC include outstanding scientists from the research community and liaisons from the Institutes and Centers of the National Institutes of Health. Consensus measures for GWAS will have a direct impact on biomedical research and ultimately on public health. During the course of this project, up to 20 research domains will be examined, with up to 15 measures being recommended for use in future GWAS and other large-scale genomic research efforts. The goal is to maximize the benefits of future research by having comparable measures so that studies can be integrated. Each selected domain will be reviewed by a Working Group (WG) of scientists who are experts in the research area. A systematic review of the literature will guide the WGs selection of up to 15 high priority measures with standardized approaches for measurement. Selection criteria for the measures include factors such as validity, reproducibility, cost, feasibility, and burden to both investigators and participants. The scientific community will be asked to provide input on proposed measures. Consensus development is a key component of the project.
Embryonic gene expression Database as a Biomedical Research Source
Embryonic Gene Expression Database for Biomedical Research Source
Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System.
Ontology describing kidney and urinary pathways cell, anatomy, and disease.
Antidepressant Therapy for Functional Dyspepsia
Functional Dyspepsia Treatment Trial (FDTT)
Multi-center, randomized, placebo-controlled trial evaluating the tricyclic antidepressant, amitriptyline and the selective serotonin reuptake inhibitor (SSRI), escitalopram to placebo in patients with functional dyspepsia. The purpose of this study is to determine whether amitriptyline and escitalopram are more efficacious than placebo in relief of the symptoms of functional dyspepsia, adjusting for psychological and psychiatric co-morbidities.
WormBook The Online Review of C. Elegans Biology
WormBook: The Online Review of C. Elegans Biology
WormBook is a comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to the biology of Caenorhabditis elegans and other nematodes. Wormbook also contains WormMethods, a collection of protocols for nematode researchers, and the Worm Breeder''s Gazette, an informal, non-refereed, biannual newsletter for the interchange of ideas and information related to C. elegans and other nematodes. WormBook is the online text companion to WormBase, the C. elegans model organism database. WormBook contains original reviews on all aspects of C. elegans biology and up-to-date descriptions of technical procedures used to study this animal. WormBook Sections: *Genetics and genomics *Molecular biology *Biochemistry *Cell biology *Developmental control *Post-embryonic development *Sex determination *The germ line *Signal transduction *Neurobiology and behavior *Evolution and ecology *Disease models and drug discovery
BACTIBASE - database dedicated to bacteriocins
Data repository of bacteriocin natural antimicrobial peptides and includes data collected from published literature as well as high-throughput datasets. The database provides a manually curated annotation of bacteriocin sequences. New bacteriocin submissions are welcome. Various tools have been incorporated for bacteriocin analysis, such as homology search, multiple sequence alignments, Hidden Markov Models, molecular modelling and retrieval through our taxonomy Browser. BACTIBASE should be a useful tool in food preservation or food safety applications and could have implications for the development of new drugs for medical use. BACTIBASE contains calculated or predicted physicochemical properties of 218 bacteriocins produced by both Gram-positive (194) and Gram-negative bacteria (19). They also note the presence of three bacteriocins from the Archaea domain. The database now comprises 31 genera (2009).
InterPro protein sequence analysis and classification
InterPro: protein sequence analysis & classification
Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ' '''Add your annotation' ''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries.
A software tool primarily proposed for mapping SOLiD reads or Illumina reads to a reference genome. It was based on seeding techniques adapted to the statistical characteristics of the reads: the default seeds are for example designed (using the Iedera software) to comply with the properties of the SOLiD color encoding, or Illumina more classical encoding as well as the observed reading error distribution along the read., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A set of online services created in support of MIRIAM, a set of guidelines for the annotation and curation of computational models. The core of MIRIAM Resources is a catalogue of data types (namespaces corresponding to controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources. Access to this data is made available via exports (XML) and Web Services (SOAP). MIRIAM Resources are developed and maintained under the BioModels.net initiative, and are free for use by all. MIRIAM Resources are composed of four components: a database, some Web Services, a Java library and this web application. * Database: The core of the system is a MySQL database. It allows us to store the data types (which can be controlled vocabularies or databases), their URIs and the corresponding physical URLs, and other details such as documentation and resource identifier patterns. Each entry contains a diverse set of details about the data type: official name and synonyms, root URI, pattern of identifiers, documentation, etc. Moreover, each data type can be associated with several resources (or physical locations). * Web Services: Programmatic access to the data is available via Web Services (based on Apache Axis and SOAP messages). In addition, REST-based services are currently being developed. This API allows one to not only resolve model annotations, but also to generate appropriate URIs, based upon the provision of a resource name and accession number. A list of available web services, and a WSDL are provided. A browser-based online demonstration of the Web Services is also available to try. * Java Library: A Java library is provided to access the Web Services. The documentation explains where to download it, its dependencies, and how to use it. * Web Application: A Web application, using an Apache Tomcat server, offers access to the whole data set via a Web browser. It is possible to browse by data type names as well as browse by tags. A search engine is also provided.
Center for Collaborative Genomic Studies on Mental Disorders
NIMH Repository and Genomics Resources (NRGR)
NIMH: Center for Collaborative Genetic Studies
Collaborative venture between the National Institute of Mental Health (NIMH) and several academic institutions. Repository facilitates psychiatric genetic research by providing patient and control samples and phenotypic data for wide-range of mental disorders and Stem Cells.Stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. RGR database likewise links to other repositories holding data from same subjects, including dbGAP, GEO and NDAR. Allows to access these data and biospecimens (e.g., lymphoblastoid cell lines, induced pluripotent cell lines, fibroblasts) and further expand genetic and molecular characterization of patient populations with severe mental illness.
Annual report, standard analysis files and an online query system from the national data registry on the end-stage renal disease (ESRD) population in the U.S., including treatments and outcomes. The Annual Data Report is divided into two parts. The Atlas section displays data using graphs and charts. Specific chapters address trends in ESRD patient populations, quality of ESRD care, kidney transplantation outcomes, costs of ESRD care, Healthy People 2010 objectives, chronic kidney disease, pediatric ESRD, and cardiovascular disease special studies. The Reference Tables are devoted entirely to the ESRD population. The RenDER (Renal Data Extraction and Referencing) online data query system allows users to build data tables and maps for the ESRD population. National, state, and county level data are available. USRDS staff collaborates with members of Centers for Medicare & Medicaid Services (CMS), the United Network for Organ Sharing (UNOS), and the ESRD networks, sharing datasets and actively working to improve the accuracy of ESRD patient information.
A method for using massively parallel paired-end transcriptome sequencing for ''alternative expression analysis''.
Comprehensive and authoritative global index of species of animals, plants, fungi and micro-organisms. It consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.3 million species. This figure continues to rise as information is compiled from diverse sources around the world. There are two distinct versions of the Catalogue of Life: the Dynamic Checklist and the Annual Checklist. Choose the version most suited to your needs. If you have a taxonomic database and would like to join the Species 2000 federation of databases in the Catalogue of Life please contact the Species 2000 Secretariat: all candidate databases go through a peer review process. The Annual Checklist Exchange Format defines the format for exchanging data.
National Diabetes Information Clearinghouse
National Diabetes Information Clearinghouse (NDIC)
Information dissemination service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) established to increase knowledge and understanding about diabetes among patients, health care professionals, and the general public: online, in booklets and fact sheets, by email, and over the phone. To carry out this mission, NDIC works closely with NIDDK' '''s Diabetes Research and Training Centers; the National Diabetes Education Program (NDEP); professional, patient, and voluntary associations; Government agencies; and State health departments to identify and respond to informational needs about diabetes and its management. NDIC provides the following informational products and services: * Response to inquiries about diabetes, ranging from information about available patient and professional education materials to statistical data. By phone (8:30 a.m. to 5 p.m. eastern time, M-F), fax, mail, and email. * Publications about diabetes, provided free of copyright, in varying reading levels. Available online or as booklets and brochures. NDIC also sends publications to health fairs and community events. * Referrals to health professionals through the National Library of Medicine' '''s MEDLINEplus includes a consumer-friendly listing of organizations that will assist you in your search for physicians and other health professionals. * Exhibits at professional meetings specific to diabetes, as well as cross-cutting professional meetings. NDIC exhibits at 12 professional meetings, each year, including American Diabetes Association Postgraduate Course, American College of Physicians, CDC Diabetes Translation Conference, American Academy of Physician Assistants, American Diabetes Association, American Association of Diabetes Educators, and American Dietetic Association.
Digestive Diseases Statistics for the United States
Digestive Diseases in the United States: Epidemiology and Impact
A collection of statistics about specific digestive diseases, including prevalence, mortality, care delivery and cost.
Berkeley Bioinformatics Open-Source Projects
The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including the Gene Ontology, OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project. Our group is focused on the development, use, and integration of ontolgies into biological data analysis. Software written or maintained by BBOP is accessible through the site.
methVisual - Methods for visualization and statistics on DNA methylation data
Software package that allows the visualization of DNA methylation data after bisulfite sequencing.
A non-profit university-governed consortium that facilitates geoscience research and education using geodesy. It rovides access to and submission of Geodetic GPS / GNSS Data, Geodetic Imaging Data, Strain and Seismic Borehole Data, and Meteorological Data. Data access web services/API provides the ability to use a command line interface to query metadata and obtain URLs to data and products. UNAVCO also provides a variety of software, including web applications, and desktop utilities for scientists, instructors, students, and others. Web-based data visualization and mapping tools provide users with the ability to view postprocessed data while web-based geodetic utilities provide ancillary information. Downloadable stand-alone software utilities include applications for configuring instruments, managing data collection, download and transfer, and performing computations on the raw data, e.g., data pre-processing or processing. The UNAVCO Facility in Boulder, Colorado is the primary operational activity of UNAVCO and exists to support university and other research investigators in their use of geophysical sensor technology for Earth sciences research. The Facility performs this task in part by archiving GNSS/GPS data and data products for current and future applications. Other data types that scientists use for Earth deformation studies are also held in the UNAVCO Archive collections. UNAVCO operates a community Archive, which provides long-term secure storage and easy retrieval of GNSS data, strain data, various derived products and related metadata. The Archive primarily stores high-precision geodetic data used for research purposes, collected under National Science Foundation and NASA sponsored projects. UNAVCO provides many learning opportunities including: Short Courses and Workshops, Educational Resources, RESESS Research Student Internships, and Technical Training.
University of Puerto Rico; Puerto Rico; USA
Main public university system in the U.S. Commonwealth of Puerto Rico and a government-owned corporation.The oldest and largest higher learning institution in the Caribbean.
Army Study To Assess Risk and Resilience in Servicemembers
Study of mental health risk and resilience factors ever conducted among military personnel. The purpose of Army STARRS is to identify as quickly as possible factors that protect or pose risks to Soldiers'' emotional well-being and overall mental health so that the Army may apply the knowledge to its ongoing health promotion, risk reduction, and suicide prevention efforts. Army STARRS investigators will use four separate study components the Historical Data Study, New Soldier Study, All Army Study, and Soldier Health Outcomes Study to identify factors that help protect a Soldier''s mental health and factors that put a Soldier''s mental health at risk. Army STARRS is a five-year study that will run through 2014. Findings will be reported as they become available, so that the Army may apply them to its ongoing health promotion, risk reduction, and suicide prevention efforts. Given its length and scope, Army STARRS will generate a vast amount of information and will allow investigators to focus on periods in a military career that are known to be high risk for psychological problems. The information gathered from volunteer participants throughout the study will help researchers identify not only potentially relevant risk factors, but potential protective factors as well. Because promoting mental health and reducing suicide risk are important for all Americans, the findings from Army STARRS will benefit not only servicemembers but the nation as a whole. NIMH has assembled a group of renowned experts to carry out this research including teams from the Uniformed Services University of the Health Sciences (USUHS), the University of California, San Diego, University of Michigan, Harvard Medical School, and NIMH. Additional Army and NIMH program staff will contribute to the oversight and implementation of the study. This research team brings together international leaders in military health, health and behavior surveys, epidemiology, suicide, and genetic and neurobiological factors involved in psychological health.
ASN: Leading the Fight Against Kidney Disease
Society leading the fight against kidney disease by educating health professionals, sharing new knowledge, advancing research, and advocating the highest quality care for patients. To accomplish its mission, ASN will: # Educate health professionals by increasing the value of ASN education. # Share new knowledge by improving the quality and expanding the reach of ASN''s communications, including maintaining the premier publications in kidney disease. # Promote the highest quality care by serving as the professional organization informing health policy in kidney disease. # Advance patient care and research in kidney disease by strengthening the pipeline of clinicians, researchers, and educators. To accomplish this goal, ASN will: ## Implement a strategy to increase interest in nephrology careers, which includes promoting diversity within the nephrology workforce. ## Help fund travel to ASN educational activities for physicians and researchers training in the field of kidney disease. ## Use the ASN Grants Program to support outstanding research and foster career development. # Continue to bolster the ASN infrastructure, which includes: ## Increasing diversityincluding age and experience, ethnicity, and genderat all levels of the society. ## Providing avenues for helping ASN members facilitate professional exchange. ## Expanding ASN membership. ## Increasing the ASN Council-Designated Endowment Fund (independent of operational budget) to support grants and other priorities
Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.
One Mind for Research''s plan to work smarter and share resources through public and private partnerships has the power to help us make more progress on every brain disorder from schizophrenia to traumatic brain injury. In the process, we will increase the investment in research by $1.5 billion each year for the next 10 years. And achieve a minimum 10% reduction in the cost of brain disease per year. This is how neurological cures that once seemed beyond our reach begin to take shape. When we''re all of one mind working toward the same goal, anything can be accomplished. $8 billion a year is spent on brain research, but the minimum cost of brain disease is one hundred times that. Yet amazingly, unlocking the mysteries of the human brain has less to do with resources than it does their coordination. Because though there is science, it exists in many different silos. There has never been a single organization that brings together the science, technology, financial resources and knowledge required to create an unprecedented understanding of brain disease. Until now. The One Mind for Research Forum began on May 23, 2011 and over the course of 2 days, the best and brightest from around the world gathered as part of a national collaboration of research universities, scientists, and the National Institutes of Health (NIH) Directors as they imagined an ambitious 10-year plan for neuroscience research. One Mind believes that new treatments and cures for neurological and psychiatric diseases that afflict one in three Americans, from children with autism to senior citizens with Alzheimer''s disease, are all within reach.
Molecular Imaging and Contrast Agent Database
Molecular Imaging and Contrast Agent Database (MICAD)
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Searchable book regarding molecular imaging and contrast agents (under development, in clinical trials or commercially available for medical applications) that have in vivo data (animal or human) published in peer-reviewed scientific journals prior to June 30 of 2013. 1444 agents are currently listed and there will be no more updates. Also available is a downloadable list of FDA approved contrast agents (Latest update: January 2013) and a Molecular Imaging Probes and Contrast Agents List (MIP & CA List) created by the MICAD staff by screening the PubMed / MedLine databases and other appropriate sources of such information. Only agents used in animal or human studies yielding in vivo data were selected for inclusion in the list. The list is by no means considered complete. No one imaging modality has been given preference over the others and the omission of any agent(s) or the introduction of any errors in the list is purely unintentional. The MIP & CA List is subject to the same copyright and disclaimers as the rest of the MICAD content. The database includes, but is not limited to, agents developed for positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), ultrasound (US), computed tomography (CT), optical imaging, planar radiography, and planar gamma imaging. The information on each agent is summarized in a book chapter format containing several sections such as Background, Synthesis, in vitro studies, Animal Studies (with sub-sections: rodents, other non-human primate animals, and human primates), Human Studies, and References. In addition, the references are linked to PubMed for retrieval of the publication abstract. Also, each chapter contains links to resources at the National Center for Biotechnology Information (NCBI) and other relevant databases regarding the target of the imaging probe or contrast agent.
An R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.
A Knowledge Resource for Innate Immunity Interactions and Pathways
InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways
InnateDB: Systems Biology of the Innate Immune Response
Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice.
samscope - A lightweight OpenGL SAM/BAM viewer
A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments.
National Resource for Quantitative Functional MRI
Resource for Quantitative Functional Magnetic Resonance Imaging
Resource for Quantitative Functional MRI
Biomedical technology research center that provides expertise for the design of quantitative magnetic resonance imaging (MRI) and spectroscopy (MRS) data acquisition and processing technologies that facilitate the biomedical research of a large community of clinicians and neuroscientists in Maryland and throughout the USA. These methods allow noninvasive assessment of changes in brain anatomy as well as in tissue metabolite levels, physiology, and brain functioning while the brain is changing size during early development and during neurodegeneration, i.e. the changing brain throughout the life span. The Kirby Center has 3 Tesla and 7 Tesla state of the art scanners equipped with parallel imaging (8, 16, and 32-channel receive coils) and multi-transmit capabilities. CIS has an IBM supercomputer that is part of a national supercomputing infrastructure. Resources fall into the following categories: * MRI facilities, image acquisition, and processing * Computing facilities and image analysis * Novel statistical methods for functional brain imaging * Translating laboratory discoveries to patient treatment
Genome wide map of putative transcription factor binding sites in Arabidopsis thaliana genome.Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites.Integrated transcriptional and post transcriptional data.Provides web tools for analysis and identification of co-regulated genes. Provides web tools for database assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana.
A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format
The UMD TP53 Mutation Database is a novel web site exclusively dedicated to mutant TP53. The following datasets, analytical tools and software are available. * The TP53 UMD mutation database in human cancer (2012 release). This novel release (35,000 mutations, 3,600 publications) has been highly curated using an original and novel statistical procedure (See Edlung et al. PNAS 2012). * TP53MUTLOAD (MUTant Loss Of Activity Database), a novel database dedicated to detailed analysis of the properties of each TP53 mutant, ranging from transactivation to cell growth properties, change of conformation, localization or various gains of functions. The database contains more than 110,000 different entries. * TP53 Mut assessor, a novel stand-alone software available for both Windows and Mac users. Check your favorite TP53 mutants and get an instant identity card. Very useful to analyze any newly discovered TP53 mutants, as the software checks for every possible TP53 mutation. * MUT-TP53 2.0, an accurate and powerful tool that automatically manages p53 mutations and generate tables ready for publication, decreasing the risk of typing errors. MUT-TP53 2.0 also provides specific information for each TP53 mutation, allowing the user to assess the quality of the data. Up to 500 TP53 mutations can be managed simultaneously.
Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support.
Zebrafish Atlas - A Lifespan Atlas of the Zebrafish
Atlas containing 2- and 3-dimensional, anatomical reference slides of the lifespan of the zebrafish to support research and education worldwide. Hematoxylin and eosin histological slides, at various points in the lifespan of the zebrafish, have been scanned at 40x resolution and are available through a virtual slide viewer. 3D models of the organs are reconstructed from plastic tissue sections of embryo and larvae. The size of the zebrafish, which allows sections to fall conveniently within the dimensions of the common 1 x 3 glass slide, makes it possible for this anatomical atlas to become as high resolution as for any vertebrate. That resolution, together with the integration of histology and organ anatomy, will create unique opportunities for comparisons with both smaller and larger model systems that each have their own strengths in research and educational value. The atlas team is working to allow the site to function as a scaffold for collaborative research and educational activity across disciplines and model organisms. The Zebrafish Atlas was created to answer a community call for a comprehensive, web-based, anatomical and pathological atlas of the zebrafish, which has become one of the most widely used vertebrate animal models globally. The experimental strengths of zebrafish as a model system have made it useful for a wide range of investigations addressing the missions of the NIH and NSF. The Zebrafish Atlas provides reference slides for virtual microscopic viewing of the zebrafish using an Internet browser. Virtual slide technology allows the user to choose their own field of view and magnification, and to consult labeled histological sections of zebrafish. We are planning to include a complete set of embryos, larvae, juveniles, and adults from approximately 25 different ages. Future work will also include a variety of comparisons (e.g. normal vs. mutant, normal vs. diseased, multiple stages of development, zebrafish with other organisms, and different types of cancer)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
SLIF - Subcellular Location Image Finder
SLIF finds fluorescence microscope images in on-line journal articles, and indexes them according to cell line, proteins visualized, and resolution. Images can be accessed via the SLIF Web database. SLIF takes on-line papers and scans them for figures that contain fluorescence microscope images (FMIs). Figures typically contain multiple FMIs, to SLIF must segment these images into individual FMIs. When the FMI images are extracted, annotations for the images (for instance, names of proteins and cell-lines) are also extracted from the accompanying caption text. Protein annotation are also used to link to external databases, such as the Gene Ontology DB. The more detailed process includes: segmentation of images into panels; panel classification, to find FMIs; segmentation of the caption, to find which portions of the caption apply to which panels; text-based entity extraction; matching of extracted entities to database entries; extraction of panel labels from text and figures; and alignment of the text segments to the panels. Extracted FMIs are processed to find subcellular location features (SLFs), and the resulting analyzed, annotated figures are stored in a database, which is accessible via SQL queries.
Christopher Hogues Research Lab at the National University of Singapore
Christopher Hogue''''s Research Lab at the National University of Singapore
This website is a life-sciences research wiki hosted on Google Sites and managed by Principal Investigator Christopher Hogue at the National University of Singapore' '''s Department of Biological Sciences on behalf of the Mechanobiology Institute of Singapore. Mechanobiology is the study of cellular and molecular systems that either respond to or generate forces. One of the major efforts of the Mechanobiology Institute is THE MANUAL OF CELLULAR AND MOLECULAR FUNCTION, a Wiki inspired online text resource. Brief History: Between 1997-2007 the Hogue Laboratory was located at Mount Sinai Hospital in Toronto where we developed BIND and other bioinformatics resources. Dr. Hogue was affiliated with the University of Toronto as a non-tenure track Associate Professor. Facing funding and staffing cutbacks in 2005, the intellectual property amassed by the group was sold by Mount Sinai Hospital & founders to Thomson-Reuters Scientific in March of 2007. In late 2007 Dr. Hogue moved to Singapore where he is now tenure-track faculty in Southeast Asia' '''s Premiere Research University - the National Unviversity of Singapore.
Antibody and density gradient media supplier.
ELSA - English Longitudinal Study of Ageing
English Longitudinal Study of Ageing (ELSA)
An interdisciplinary data resource on health, economic position and quality of life as people age. Longitudinal multidisciplinary data from a representative sample of the English population aged 50 and older have been collected. Both objective and subjective data are collected relating to health and disability, biological markers of disease, economic circumstance, social participation, networks and well-being. Participants are surveyed every two years to see how people''s health, economic and social circumstances may change over time. One of the study''s aims is to determine the relationships between functioning and health, social networks, resources and economic position as people plan for, move into and progress beyond retirement. It is patterned after the Health and Retirement Study, a similar study based in the United States. ELSA''s method of data collection includes face-to-face interview with respondents aged 50+; self-completion; and clinical, physical, and performance measurements (e.g., timed walk). Wave 2 added questions about quality of health care, literacy, and household consumption, and a visit by a nurse to obtain anthropometric, blood pressure, and lung function measurements, as well as saliva and blood samples, and to record results from tests of balance and muscle strength. Another new aspect of Wave 2 is the ''Exit Interview'' carried out with proxy informants to collect data about respondents who have died since Wave 1. This interview includes questions about the respondents'' physical and psychological health, the care and support they received, their memory and mood in the last year of their life, and details of what has happened to their finances after their death. Wave 3 data added questions related to mortgages and pensions. The intention is to conduct interviews every 2 years, and to have a nurse visit every 4 years. It also is envisioned that the ELSA data will ultimately be linked to available administrative data, such as death registry data, a cancer register, NHS hospital episodes data, National Insurance contributions, benefits, and tax credit records. The survey data are designed to be used for the investigation of a broad set of topics relevant to understanding the aging process. These include: * health trajectories, disability and healthy life expectancy; * the determinants of economic position in older age; * the links between economic position, physical health, cognition and mental health; * the nature and timing of retirement and post-retirement labour market activity; * household and family structure, social networks and social supports; * patterns, determinants and consequences of social, civic and cultural participation; * predictors of well-being. Current funding for ELSA will extend the panel to 12 years of study, giving significant potential for longitudinal analyses to examine causal processes. * Dates of Study: 2002-2007 * Study Features: Longitudinal, International, Anthropometric Measures * Sample Size: ** 2000-2003 (Wave 1): 12,100 ** 2004-2005 (Wave 2): 9,433 ** 2006-2007 (Wave 3): 9,771 ** 2008-2009 (Wave 4): underway Links * Economic and Social Data Service (ESDS): http://www.esds.ac.uk/longitudinal/about/overview.asp * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00139#scope-of-study
A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3?/5? splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.
Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants' ''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly.
Database of Locus Specific Mutation Databases. Fields include HGNC Gene symbol / OMIM No., Database name / Internet address, and Curators. If you wish to add an LSDB please go to the LSDB Submission Page.
Genome Assembler Reconcilation and Merging
A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies.
Software suite for analysis of T cell receptor repertoire data. Used for fast, efficient analysis of T cell receptor (TcR) repertoire samples, designed to be accessible to those with no previous programming experience.
A graph-based statistical method to detect differential transcription using RNA-seq data.
The American Society of Hematology (ASH) is the world''s largest professional society concerned with the causes and treatments of blood disorders. The mission of the Society is to further the understanding, diagnosis, treatment, and prevention of disorders affecting the blood, bone marrow, and the immunologic, hemostatic and vascular systems, by promoting research, clinical care, education, training, and advocacy in hematology.
Simons Foundation - Advancing Research in Basic Science and Mathematics
The Simons Foundation is a private foundation based in New York City, incorporated in 1994 by Jim and Marilyn Simons. The Simons Foundation''s mission is to advance the frontiers of research in mathematics and the basic sciences. We sponsor a range of programs that aim to promote a deeper understanding of our world. The primary focus of the foundation''s Mathematics & the Physical Sciences (MPS) program is on the theoretical sciences radiating from mathematics: in particular, the fields of mathematics, theoretical computer science and theoretical physics. Although we have supported basic research in mathematics and physics for years at institutions around the globe, the mode of our support entered an important new phase in fall 2009 with the introduction of grant opportunities with open application procedures. It is intended that this will become our primary mode of operation. In 2010, the MPS program issued its first requests for grant applications. These requests offered grants to establish post-doctoral fellowships, grants to promote collaboration between researchers, grants to create professorships that combine mathematics with other fields, and a grant to endow an institute for theoretical computer science. Other projects are under way, including the Africa Mathematics Project, intended to bolster mathematics scholarship on the African continent, and an oral history project: a series of interviews with renowned mathematicians and scientists which will be made available to the public for viewing. The Simons Foundation''s initial support of life sciences work has tended to focus on research that promotes synergy between biology and mathematics. Such projects have included quantitative biology programs at Cold Spring Harbor Laboratory, the Institut des Hautes ��tudes Scientifiques, the Institute for Advanced Study, and The Rockefeller University. The Life Sciences program is expected to expand in scope over the next two to three years. To date, the Simons Foundation''s single largest initiative has been in autism research. The Simons Foundation Autism Research Initiative (SFARI) program seeks to improve the diagnosis and treatment of autism spectrum disorders by funding, catalyzing, and driving innovative research of the greatest quality and relevance. In 2007, SFARI issued its first Request for Applications, its goal being to attract the best researchers to the field. In the years since, SFARI has given grants to 150 investigators in the United States and abroad. Additionally, to facilitate the field as a whole, SFARI has created the Simons Simplex Collection of extensive genetic and phenotypic data from almost 3,000 families with a child affected by autism. Although SFARI''s immediate priority is to benefit individuals challenged by autism spectrum disorders, the program''s research is expected to yield insights into the neural mechanisms of fundamental human capabilities, complementing the mission of the Simons Foundation to advance research in the basic sciences and mathematics.
Traumatic Brain Injury Model Systems National Data and Statistical Center
The Traumatic Brain Injury Model Systems National Data and Statistical Center (TBINDSC) located at Craig Hospital in Englewood, Colorado, is a central resource for researchers and data collectors within the Traumatic Brain Injury Model Systems (TBIMS) program. The primary purpose of the TBINDSC is to advance medical rehabilitation by increasing the rigor and efficiency of scientific efforts to longitudinally assess the experience of individuals with traumatic brain injury (TBI). The TBINDSC provides technical assistance, training, and methodological consultation to 16 TBIMS centers as they collect and analyze longitudinal data from people with TBI in their communities, and as they conduct research toward evidence-based TBI rehabilitation interventions. The project design includes * The first prospective, longitudinal multi-center study ever conducted which examines the course of recovery and outcomes following the delivery of a coordinated system of acute neurotrauma and inpatient rehabilitation. * Includes large scale follow-up to 20 years post-injury. Available from this site are links to the TBIMS Presentation and TBIMS Update, which has information about the individual model systems and descriptions of the injury and followup data that are being collected. 2007-2012 Project Priorities * Improved long-term outcomes of individuals with TBI by conducting 1-2 site-specific research projects to test innovative approaches that contribute to rehabilitation interventions and evaluating TBI outcomes in accordance with the focus areas identified in NIDRR''s Long-Range Plan. * Improved outcomes for individuals with TBI by participating in at least one collaborative research module project, which may range from pilot research to more extensive studies. * Continued assessment of long-term outcomes of TBI by enrolling at least 35 subjects per year into the longitudinal portion of the TBIMS database. * In carrying out research activities, each Center may select from the following research domains: Health and Function, Employment, Participation and Community Living, and Technology for Access and Function. In addition, each Center must: * Provide a multidisciplinary system of rehabilitation care specifically designed to meet the needs of individuals with TBI. The system must encompass a continuum of care, including emergency medical services, acute care services, acute medical rehabilitation services, and post-acute services; and * Coordinate with the NIDRR funded Model Systems Knowledge Translation Center to provide scientific results and information for dissemination to clinical and consumer audiences.
A free award-winning educational program that teaches you knowledge about the human brain through interactive exploration of rotatable 3D models. The models have been computed with BrainVoyager QX using original data from magnetic resonance imaging (MRI) scans. Besides having fun with the rotatable 3D models, the program contains information about the major lobes, gyri, sulci and Brodmann areas of the cerebral cortex. The program runs on Windows XP, Vista and Windows 7.
The first publicly-funded text mining center in the world that provides text mining services in response to the requirements of the UK academic community. You can find pointers to sources of information about text mining such as links to: * text mining services provided by NaCTeM * software tools, both those developed by the NaCTeM team and by other text mining groups * seminars, general events, conferences and workshops * tutorials and demonstrations * text mining publications NaCTeM is operated by the University of Manchester with close collaboration with the University of Tokyo.
A community-based data facility to support, sustain, and advance the geosciences by providing data services for observational solid earth data from the Ocean, Earth, and Polar Sciences. IEDA systems enable these data to be discovered and reused by a diverse community now and in the future. Data services include data access, data analysis, data compliance, data publication, DOI search, and web services. Desktop apps GeoMapApp and Virtual Ocean are available to explore, visualize and analyze your own data within the context of hundreds of other earth science data from around the world. IEDA is a partnership between EarthChem and the Marine Geoscience Data System (MGDS). EarthChem and MGDS systems include the geochemical databases PetDB and SedDB, the geochemistry data network EarthChem, the Ridge2000 and MARGINS Data Portals, the Academic Seismic Portal field data collection, the Antarctic and Southern Ocean Data System, the Global Multi Resolution Topography synthesis, and the System for Earth Sample Registration SESAR.
University of Quebec Hospital Centre; Quebec; Canada
Centre hospitalier universitaire de Quebec
Centre hospitalier universitaire de Qu�bec
Network of three teaching hospitals affiliated with the medical school of Université Laval and several specialized institutions in Quebec City.
fitGCP - Fitting genome coverage distributions with mixture models
Software providing a framework for fitting mixtures of probability distributions to genome coverage profiles.
NCMRR - National Center for Medical Rehabilitation Research
National Center for Medical Rehabilitation Research
Foster development of scientific knowledge needed to enhance the health, productivity, independence, and quality-of-life of people with disabilities. A primary goal of Center-supported research is to bring the health related problems of people with disabilities to the attention of the best scientists in order to capitalize upon the myriad advances occurring in the biological, behavioral, and engineering sciences. The NCMRR uses seven research priorities to help guide its research and research priorities. The research initiatives and opportunities recommended in the Research Plan (PDF - 223 KB) for the National Center for Medical Rehabilitation Research are discussed in terms of seven cross-cutting areas in which increased research effort is needed. Those areas are: * improving functional mobility * promoting behavioral adaptation to functional losses * assessing the efficacy and outcomes to medical rehabilitation therapies and practices * developing improved assistive technologies * understanding whole body system responses to physical impairments and functional changes * developing more precise methods of measuring impairments, disabilities, and societal and functional limitations * training research scientists in the field of rehabilitation In addition, the NCMRR has its own National Advisory Board on Medical Rehabilitation Research that meets twice a year to discuss the Center''s portfolio and research directions. Programs/Program Areas * Behavioral Sciences and Rehabilitation Technologies (BSRT) Program * Biological Sciences and Career Development (BSCD) Program * Pediatric Critical Care and Rehabilitation (PCCR) Program * Spinal Cord and Musculoskeletal Disorders and Assistive Devices (SMAD) Program * Traumatic Brain Injury (TBI) and Stroke Rehabilitation (TSR) Program * Various Supported Networks, Programs, and Initiatives
Nearly one million people die of malaria every year, mostly infants, young children, and pregnant women, and most of them in Africa. Finding effective ways to control and eventually eradicate the disease is a high priority of NIAID. For the latest in NIAID-supported malaria research, NIAID Strategic Plan for Malaria Research, NIAID Research Agenda for Malaria, Quick Facts, Transmission, Symptoms, Diagnosis, Treatment, Prevention, Publications, News and Events please refer to this site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A core synthesis facility dedicated to the preparation of imaging probes, initially for intramural NIH scientists, and later, for the extramural scientific community. The IPDC provides a mechanism for the production of sensitive probes for use by imaging scientists who cannot obtain such probes commercially. The probes to be made will encompass all major imaging modalities including radionuclide, magnetic resonance, and optical. Nearly all of these imaging probes are not commercially available, nor are they viable commercial products, and most are new compositions-of-matter (http://nihlibrary.ors.nih.gov/ipdcdb/IPDCDB_Search.asp). The IPDC was born from the realization that imaging technologies will be crucial in basic, translational, and clinical research in the 21st century, and that the synthetic chemistry required to reliably produce imaging probes lies at the heart of research within imaging technologies. To this end, the IPDC has recruited the equipment and expertise to concurrently synthesize multiple types of imaging probes for bioscientists with diverse research interests, encompassing all imaging modalities, including optical, radionuclide, ultrasound, and magnetic resonance. The IPDC embodies an exciting new approach to apply and combine chemistry and imaging sciences toward specific problems in biology and medical sciences, and will be a truly interdisciplinary effort aimed at maximizing returns from the revolutionary new discoveries being described in modern imaging. A significant part of the IPDC will also be directed, independently, to the discovery of new imaging approaches and compositions. The IPDC houses scientific staff, mostly chemists, who have interests and expertise in one or more aspects of molecular imaging. The IPDC is generating known and novel imaging probes for targeting receptors, cells, and tissues, and for preclinical in vivo evaluations by its intramural collaborators. Many such interesting agents have been described in the scientific literature, but are often not explored further due to lack of a reliable supply of reagent. One aspect of the IPDC''s mission is to rectify this situation. IPDC-supplied reagents will not be limited to one imaging modality, but will include the flexible application of diverse technologies. Also, the IPDC will seek to develop novel state-of-the-art imaging probes in collaboration with biological and biomedical intramural scientists who can provide or suggest suitable targeting agent/receptor pairs. The Imaging Probe Development Center (IPDC) was initiated in the incubator space of the Common Fund and has transitioned to the intramural program of the National Heart, Lung, and Blood Institute.
The EB-eye Search system is developed on top of the Apache Lucene project framework, which is an Open-source, high-performance, full-featured text search engine library written entirely in Java. It uses this technology to index EBI databases in various formats (e.g. flatfiles, XML dumps, OBO format, etc.) and provides very fast access to the EBI''s data resources. The system allows the user to search globally across all EBI databases or individually in selected resources by using an Advance search.
SPAR - Semantic Publishing and Referencing Ontologies
Semantic Publishing and Referencing Ontologies
Semantic Publishing and Referencing Ontologies (SPAR)
Semantic Publishing Referencing Ontologies
SPAR - Semantic Publishing and Referencing
SPAR - Semantic Publishing Referencing Ontologies
A suite of orthogonal and complementary ontology modules for creating comprehensive machine-readable RDF metadata for all aspects of semantic publishing and referencing. The ontologies can be used either individually or in conjunction. The component ontologies within SPAR: * Semantic Publishing ** FaBiO - FRBR-aligned Bibliographic Ontology ** PRO - Publishing Roles Ontology ** PSO - Publications Status Ontology ** PWO - Publishing Workflow Ontology * Referencing ** CiTO - Citation Typing Ontology ** BiRO - Bibliographic Reference Ontology ** C4O - Citation Counting and Context Characterization Ontology ** DoCO - Document Components Ontology Each is encoded in the Web ontology language OWL 2.0 DL. Together, they provide the ability to describe far more than simply bibliographic entities such as books and journal articles, by enabling RDF metadata to be created to relate these entities to reference citations, to bibliographic records, to the component parts of documents, and to various aspects of the scholarly publication process. Where appropriate, the SPAR ontologies, specifically FaBiO, the FRBR-aligned Bibliographic Ontology, and BiRO, the Bibliographic Reference Ontology, employ the FRBR (Functional Requirements for Bibliographic Records) classification model, a conceptual entity-relationship model developed by the International Federation of Library Associations and Institutions (IFLAI) as a generalized view of the bibliographic universe, intended to be independent of any cataloging code or implementation. FRBR distinguishes Works, Expressions, Manifestations and Items.
Everything Added to Food in the United States
PAFA contains administrative, chemical and toxicological information on over 2000 substances directly added to food. In addition, the database contains only administrative and chemical information on less than 1000 such substances. The more than 3000 total substances together comprise an inventory often referred to as Everything Added to Food in the United States (EAFUS). The EAFUS list of substances contains ingredients added directly to food that FDA has either approved as food additives or listed or affirmed as GRAS. Nevertheless, it contains only a partial list of all food ingredients that may in fact be lawfully added to food, because under federal law some ingredients may be added to food under a GRAS determination made independently from the FDA. The list contains many, but not all, of the substances subject to independent GRAS determinations. :Sponsors: This information is generated from a database maintained by the U.S. Food and Drug Administration (FDA) Center for Food Safety and Applied Nutrition (CFSAN) under an ongoing program known as the Priority-based Assessment of Food Additives (PAFA).
Web-based tools for working with functional genomics and other data, including Gene Expression and Protein Tools, Molecular Markers and Mapping Tools, and Other Genomic Tools. Most are designed with the plant (mainly Arabidopsis) researcher in mind, but a couple of them can be useful to the wider research community, e.g. Mouse eFP Browser or BlastDigester. The associated paper for most tools is available.
AlzGene: Field Synopsis of Genetic Association Studies in AD
The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer''s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data. In addition to identifying the epsilon4 allele of APOE and related effects, we pinpointed over a dozen potential Alzheimer disease susceptibility genes (ACE, CHRNB2, CST3, ESR1, GAPDHS, IDE, MTHFR, NCSTN, PRNP, PSEN1, TF, TFAM and TNF) with statistically significant allelic summary odds ratios (ranging from 1.11-1.38 for risk alleles and 0.92-0.67 for protective alleles). Our database provides a powerful tool for deciphering the genetics of Alzheimer disease, and it serves as a potential model for tracking the most viable gene candidates in other genetically complex diseases.
Podcasts from AIDS.gov, featuring information from the Federal government about HIV/AIDS prevention, testing, research, treatment, and using new media in response to HIV/AIDS. Categories include: Basic HIV information, New Media, Federal Programs and Policies, HIV/AIDS Awareness Days, and Real Stories.
EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data
Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
POLGUI - Matlab GUI for Polhemus Fastrak
An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows)
A set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of seven orthogonal vocabularies defining: the roles of reaction participants (eg. substrate), quantitative parameters (eg. Michaelis constant), a precise classification of mathematical expressions that describe the system (eg. mass action rate law), the modeling framework used (eg. logical framework), and a branch each to describe entity (eg. macromolecule) and interaction (eg. process) types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. A programmatic access to the content of the Systems Biology Ontology is provided by Web Services.
A compilation and assessment of epidemiologic, public health, and clinical data on diabetes and its complications in the United States. Published by the National Diabetes Data Group of the National Institute of Diabetes and Digestive and Kidney Diseases, the book contains 36 chapters organized in five areas: * the descriptive epidemiology of diabetes in the United States based on national surveys and community-based studies, including prevalence, incidence, sociodemographic and metabolic characteristics, risk factors for developing diabetes, and mortality * the myriad complications that affect patients with diabetes * characteristics of therapy and medical care for diabetes * economic aspects, including health insurance and health care costs * diabetes in special populations, including African Americans, Hispanics, Asian and Pacific Islanders, Native Americans, and pregnant women. Diabetes in America, 2nd Edition, has been designed to serve as a reliable scientific resource for assessing the scope and impact of diabetes and its complications, determining health policy and priorities in diabetes, and identifying areas of need in research. The intended audience includes health policy makers at the local and Federal levels who need a sound quantitative base of knowledge to use in decision making; clinicians who need to know the probability that their patients will develop diabetes and the prognosis of the disease for complications and premature mortality; persons with diabetes and their families who need sound information on which to make decisions about their life with diabetes; and the research community which needs to identify areas where important scientific knowledge is lacking.
Software that supports browsing and inspecting essential BrainVoyager data files as well as the header and content of DICOM files. The Viewer supports standard image files (JPEG, GIF, PNG, TIFF, BMP) allowing to inspect snapshots, figures or photos. Users can prepare a folder with selected data of a subject (VMRs, SRFs, Maps, snapshot images), which allows participants of fMRI measurements to browse their brain data and to show it to others. The Viewer can be handed over to colleagues not having a BrainVoyager license together with relevant data. This will allow them to view and explore your analyzed data files.
Data resource that includes a large collection of genome-wide ChIP-Seq experiments performed on transcription factors (TFs), histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression.
Database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them.
neuroade - A Cognitive Neuroscience Laboratory
At neuroade, a Cognitive Neuroscience Laboratory, we study change in brain and behavior across multiple time-scales. Researchers in the lab combine a variety of methodologies to answer specific questions about typical and atypical behavior and development. We use functional magnetic resonance imaging (fMRI), peripheral psychophysiology (such as skin conductance responses), behavioral testing, genotyping analysis, and computational modeling. Most of our work takes place at the Centre for Integrative Neuroscience and Neurodynamics (CINN), and we all live in the Department of Psychology at the University of Reading. Our research is divided into several distinct yet highly interlinked themes, all converging in their application to understanding psychopathology -- summarised here in no particular order: * Decision-making and the Evaluation of Decision Outcomes * Dimensions of Impulsivity as a Foraging Strategy * Adolescent Development * Computational Modeling Probes of Individual Differences
NeuroNEXT - Network for Excellence in Neuroscience Clinical Trials
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 26,2022. A unique clinical trial network open to studies of more than 400 neurological diseases, allowing investigators to more efficiently pursue new therapies based on scientific opportunity. The network has a centralized IRB serving 25 sites, which will allow trials to move faster, without the need to coordinate IRBs at each individual site. It is not necessary to be part of the NeuroNEXT infrastructure to propose and conduct a study within the network. The Network for Excellence in Neuroscience Clinical Trials, or NeuroNEXT, was created to conduct studies of treatments for neurological diseases through partnerships with academia, private foundations, and industry. The network is designed to expand the National Institute of Neurological Disorders and Stroke''s (NINDS) capability to test promising new therapies, increase the efficiency of clinical trials before embarking on larger studies, and respond quickly as new opportunities arise to test promising treatments for people with neurological disorders. The NeuroNEXT program aims to: * Provide a robust, standardized, and accessible infrastructure to facilitate rapid development and implementation of protocols in neurological disorders affecting adult and/or pediatric populations. The network includes multiple Clinical Sites, one Clinical Coordinating Center (CCC) and one Data Coordinating Center (DCC). * Support scientifically sound, possibly biomarker-informed, Phase II clinical trials that provide data for clear go/no-go decisions. * Energize and mobilize federal, industry, foundations and patient advocacy partners by leveraging existing relationships between NINDS and NeuroNEXT to organize high impact Phase II clinical trials for neurological disorders. * Expand the pool of experienced clinical investigators and research staff who are prepared to be leaders of multicenter clinical research trials. * Working with NeuroNEXT is a cooperative venture between NINDS, the NeuroNEXT network and the applicant.
NeuroNetwork - a professional network dedicated to the study of the brain
Professional networking site dedicated to those working, studying, or simply interested in the science of the brain. Those with personal and professional interests in neuroscience, neurology, psychology, and all related areas -- those studying neural activities in invertebrates up to the human brain, including brain-like systems and networks are welcome. The NeuroNetwork was built to allow students and researchers to find and interact with each other in a professional environment. You may create searchable profiles with your research interests; start a blog; upload poster presentations and videos; post and search job listings; form a virtual group based on your interests, geographical location, etc.; and view, post, and RSVP to upcoming meetings. And don''t just create a profile for yourself -- create one for your organization, institute, society, or even your lab as well.
Software that implements a greedy algorithm and uses graph theory to link and orient assembled existing contigs quickly and accurately using mate pair information.
Software to determine most stable reference (housekeeping) genes from set of tested candidate reference genes in given sample panel. From this, gene expression normalization factor can be calculated for each sample based geometric mean of user-defined number of reference genes.
Database of information on nervous systems and behavior of various species of invertebrates and a large body of ancillary material to promote the use of invertebrate systems in research and education and facilitate information transfer to engineers that are looking for mechanisms that may be useful to solve a wide range of technological problems. The database is linked to explanations of the contents to allow users to familiarize themselves with the data and the context in which they were obtained. The platform has four entrance points tailored to different target user groups. The first entrance point is designed for users that are interested in using invertebrates for research purposes, in particular in the field of neuroscience, to assist them in initiating research projects. This includes databases of sensory systems, brains, and behavior of invertebrates, especially insects. The databases contain sensory organ structure and function, photographs and movies documenting insect behavior, data acquisition equipment and other instrumentation, software, material for eduction, and bibliography. A second entrance point is available for those that are concerned with implementations of design principles of invertebrate nervous systems and behavior in industrial applications. The third portal is destined for providing quick access for instructors that intend to use invertebrates for educational purposes and the remaining entrance point facilitates obtaining general comparative information on sensory and central nervous systems and behavior of invertebrates.
GASiC - Genome Abundance Similarity Correction
A method to correct read alignment results for the ambiguities imposed by similarities of genomes.
Database of genomes that are in the process of being annotated are provided as an early access site for users. Genomes are here when the initial BLAST analysis on a new assembly has been done but the gene build has not been completed. Owing to the preliminary nature of the data, Pre-Ensembl provides views of the assembly, BLAST against the assembly and download of portions of the assembly - and little else. A number of ready-made tools for processing your data are also available. In general a full Ensembl release takes months depending on how complex the data are and the time constraints of people in the team. Occasionally a more complete gene build will be released on this site, but without any comparative genomics, variation or other additional data. Many other species with fully annotated genomic data, more website features and documentation are available at www.ensembl.org
The NIH Pain Consortium was established to enhance pain research and promote collaboration among researchers across the many NIH Institutes and Centers that have programs and activities addressing pain. To this end, the following goals have been identified for the Pain Consortium: * To develop a comprehensive and forward-thinking pain research agenda for the NIH - one that builds on what we have learned from our past efforts. * To identify key opportunities in pain research, particularly those that provide for multidisciplinary and trans-NIH participation. * To increase visibility for pain research - both within the NIH intramural and extramural communities, as well as outside the NIH. The latter audiences include our various pain advocacy and patient groups who have expressed their interests through scientific and legislative channels. * To pursue the pain research agenda through Public-Private partnerships, wherever applicable. This underscores a key dynamic that has been reinforced and encouraged through the Roadmap process.
Manual of Cellular and Molecular Function
MBInfo: A modular approach to cellular functions
Portal that deals with the process of mechanotransduction, providing in-depth, regularly updated reviews on the mechanics of cellular and molecular function. Each review is written by scientists and subsequently peer reviewed by experts in the field to ensure the content is accurate, reliable and up to date. Each review emphasizes the functional and mechanical aspects of a process, rather than the genetic aspects, with the aim of making this resource accessible to a wider audience. MBInfo is an ideal resource for scientists working in alternative fields, individuals working in industries where products are based on biological principles or students seeking a reliable introduction to a given cellular process. Each topic is written in a pyramid structure. The top of the pyramid is represented by an overview page, providing a basic description of a given function or process. These pages target a broad spectrum of readers and assume only a basic understanding of biology. Further down the pyramid, the reader will encounter the steps involved in the process described and functional modules that address specific mechanical aspects. These pages outline the protein complexes involved and the mechanisms by which they achieve the given process or function. These pages assume the readers have a more in-depth knowledge of scientific terms and principles. For every topic, a series of graphics and/or animations are available. These supplement the reviews, clarify information and guide the reader through complex processes pictorially. This makes MBInfo an ideal teaching resource, whether in the classroom or for clients trying to understand your product. All images and text are copyright protected and are for personal use only. Current Topics include: * Cellular Structures in Mechanosensing and Cell Motility * Methods in the Study of Mechanobiology * Nuclear Mechanotransduction Almost 100 stand alone Glossary Terms are now available. These include short definitions or summaries of proteins and processes that relate to broader topics discussed within the site. Browse an extensive range of figures, tables and videos in our resources section. New quizzes and other interactive content can also be found.
Automated Detection and Analysis of ProTrusions
Software tool as plug-in developed for ImageJ/FIJI platform to automatically detect and analyse cell migration and morphodynamics. Provides whole cell analysis of multiple cells, while also returning data on individual membrane protrusion events.
Brain Research through Advancing Innovative Neurotechnologies Initiative
NIH Brain Research through Advancing Innovative Neurotechnologies Initiative
Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts.
National Digestive Diseases Information Clearinghouse
National Digestive Diseases Information Clearinghouse (NDDIC)
Information dissemination service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) established to increase knowledge and understanding about digestive diseases among people with these conditions and their families, health care professionals, and the general public: online, in booklets and fact sheets, by email, and over the phone. To carry out this mission, NDDIC works closely with a coordinating panel of representatives from Federal agencies, voluntary organizations on the national level, and professional groups to identify and respond to informational needs about digestive diseases. NDDIC provides the following informational products and services: * Response to inquiries about digestive diseases - ranging from information about available patient and professional education materials to statistical data. By phone (8:30 a.m. to 5 p.m. eastern time, M-F), fax, mail, and email. * Publications about specific digestive diseases, provided free of copyright, in varying reading levels. Available online or as booklets and brochures. NDDIC also sends publications to health fairs and community events. * Referrals to health professionals through the National Library of Medicine' '''s MEDLINEplus includes a consumer-friendly listing of organizations that will assist you in your search for physicians and other health professionals. * Exhibits at professional meetings specific to digestive diseases, as well as cross-cutting professional meetings. NDDIC exhibits at nine professional meetings each year, including Digestive Diseases Week, American College of Gastroenterology, Society of Gastroenterology Nurses and Associates, American Academy of Family Physicians, American Academy of Physician Assistants, American Nurses Association, and the National Conference for Nurse Practitioners.
High-dose Ursodiol Therapy of Primary Sclerosing Cholangitis
High-dose Ursodiol Therapy of Primary Sclerosing Cholangitis (HUSC)
Multicentered Randomized Trial of High-dose Urso in Primary Sclerosing Cholangitis
Trial of High-dose Urso in Primary Sclerosing Cholangitis
Multi-center, placebo-controlled trial of ursodiol in primary sclerosing cholangitis (PSC). A total of 150 patients with previously untreated PSC without cirrhosis were randomly assigned to receive high doses of ursodiol (20-25 mg/kg/day) or placebo for two years. Patients underwent medical evaluation, endoscopic retrograde cholangiography, and liver biopsy before randomization and again at two-year intervals. The endpoints of therapy were progression of hepatic fibrosis, liver decompensation, liver transplantation, or death. The treatment phase of the study was stopped for futility in June 2008; however, patients continue to be followed. Ongoing mechanistic studies are underway.
Ensembl Genomes: Extending Ensembl across the taxonomic space
Database portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualization platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community - essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimized data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualized in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.
Offers one and two week short courses in bioinformatics, genomics and proteomics in response to an identified need for a skilled bioinformatics workforce in Canada. For eight years, the series offered short courses in bioinformatics, genomics and proteomics in various cities across Canada. Taught by top faculty from Canada and the US, the courses offered small classes and hands-on instruction. The CBW initiated development of a new format and series of exciting workshops focusing on training the researchers of these advanced technologies on the latest approaches being used in computational biology to deal with the new data. Past workshop content is available under a Creative Commons License.
Queries and unique database alignment inferred by clustering homologs
A software package for local sequence alignment for next-generation sequencing (NGS) data. It generates the pairwise local alignments between a query dataset against a database. The main design purpose of qudaich is to focus on datasets from next generation sequencing. These the datasets generally have hundreds of thousand sequences or more, and so, the input database should contain large number of sequences. Qudaich is flexible and its algorithmic structure imposes no restriction on the absolute limit of the acceptable read length, but the current version of qudaich allow read length <2000 bp. Qudaich can be used to align DNA, translated DNA and protein sequences.
Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology
Resource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology
A controlled vocabulary of ontology class structures and entities of observed phenotypic terms for primary immunodeficiency diseases (PIDs) that facilitate global sharing and free exchange of PID data with users'' communities
Next Generation Sequencing - Standardization of Clinical Testing
Next Generation Sequencing: Standardization of Clinical Testing
Next Generation Sequencing: Standardization of Clinical Testing Working Groups
National workgroup to define platform-independent approaches for establishing technical process elements of a quality management system (QMS) to assure the analytical validity and compliance of next-generation sequencing (NGS) tests with existing regulatory and professional quality standards. The workgroup identified and addressed gaps in quality practices that could compromise the quality of both clinical laboratory services and translational efforts needed to advance the implementation and utility of NGS in clinical settings. The workgroup was composed of experts with knowledge of and experience with NGS and included clinical laboratory directors, clinicians, platform and software developers and informaticians, as well as individuals actively engaged in NGS guideline development from accreditation bodies and professional organizations. Representatives from US government agencies also participated. These guidelines address four topics that are components of quality management in a clinical environment: (i) test validation, (ii) quality control (QC) procedures to assure and maintain accurate test results, (iii) the independent assessment of test performance through proficiency testing (PT) or alternative approaches and (iv) reference materials (RMs). Discussions were limited to the analytic and informatics processes required for accurate variant calling. The workgroup did not address how variants are prioritized, interpreted or reported.
Chemical Effects in Biological Systems (CEBS)
Repository for toxicogenomics data, including study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. Data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. Data relating to environmental health, pharmacology, and toxicology. It is not necessary to have microarray data, but study design and phenotypic anchoring data are required.CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Biomedical Investigation Database is another component of CEBS system. used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee. BID has been shared with Health Canada and the US Environmental Protection Agency.
The BioBricks Foundation (BBF) is dedicated to advancing synthetic biology to benefit all people and the planet. To achieve this, we must make engineering biology easier, safer, equitable, and more open. We do this in the following ways: by ensuring that the fundamental building blocks of synthetic biology are freely available for open innovation; by creating community, common values and shared standards; and by promoting biotechnology for all constructive interests. We envision a world in which scientists and engineers work together using BioBric parts freely available standardized biological parts to create safe, ethical solutions to the problems facing humanity. We envision synthetic biology as a force for good in the world. We see a future in which architecture, medicine, environmental remediation, agriculture, and many other fields are using the technology of synthetic biology. Our supporters are many and include corporations, individuals, institutions, foundations, government, corporations, and others. Currently, the BBF''s key programs include: * BIOFAB * BioBrick Public Agreement * Technical Standards Framework * Conferences and Workshops * BBF Global Network * OpenWetWare
A Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha). The important features of Virmid are: * Estimation of accurate proporation of control sample in a (mixed) disease sample * Improved SNP and somatic mutation calling with regard to the estimated proportion
A quality assessment software package for next-genomics sequencing data.
re3data.org: Registry of Research Data Repositories
Global registry of research data repositories from all academic disciplines that allows the easy identification of appropriate research data repositories, both for data producers and users. Information icons display principal attributes of a repository that can be used for multi-faceted searches. Repository operators can suggest their infrastructures to be listed via a simple application form. A repository is indexed when the minimum requirements are met, i.e. mode of access to the data and repository, as well as the terms of use.
Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database.
Bioinformatics Named Entity Recogniser for Databases and Software
Bioinformatics Named Entity Recognizer for Databases and Software
A named entity recognizer for the recovery of bioinformatics databases and software from primary literature. The entity recognizer achieved an F-measure of between 63% and 91% on different datasets (63%78% at the document level). Results from full-text literature analysis for both Genome Biology and BMC Bioinformatics journals are available as well as a full list of references and links for the various major resources mentioned. Data generated data can be used for exploration of bioinformatics database and software usage. This tool makes heavy use of GATE (version 6.1). It can be run in sandbox mode, which means a installation of GATE is not a prerequisite, but you will instead need to point the config to a unzipped gate_plugins directory instead (located in the bin/BMC_Files directory).
mubiomics - Scripts for processing next-gen sequencing data
A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier.
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit
Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish.
Peginterferon and Ribavirin for Pediatric Patients with Chronic Hepatitis C
Peginterferon and Ribavirin for Pediatric Patients with Chronic Hepatitis C (Peds-C)
Pegylated Interferon +/- Ribavirin for Children With Hepatitis C
Multi-center, randomized controlled trial that studied peginterferon therapy, with or without ribavirin, in children with chronic hepatitis C. Approximately 120 children were randomly assigned to receive peginterferon alfa-2a alone or peginterferon with ribavirin for 48 weeks. Samples of blood, genomic DNA, and liver tissue are stored in the NIDDKrepositories. A long-term follow up study of the clinical trial participants is underway.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. This Week in Parasitism (TWiP) is a podcast about eukaryotic parasites hosted by Vincent Racaniello and Dick Despommier. Following in the path of their successful podcast ''This Week in Virology'' (TWiV), they strive for an informal yet informative conversation about parasites which is accessible to everyone, no matter what their science background. As science Professors at Columbia University, they have spent their entire academic careers directing research laboratories focused on parasites (Dick) and viruses (Vincent). Their enthusiasm for teaching inspired them to reach beyond the classroom with new media. TWiP is for everyone who wants to learn about parasites in a relaxing way. Music used on TWiP is composed and performed by Ronald Jenkees and used with permission.
REDfly Regulatory Element Database for Drosophilia
Regulatory Element Database for Drosophilia
Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome.
EBCall (Empirical Baysian mutation Calling)
A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies.
It is a collection of selected human-focused cellular pathways implicated in cancer that are linked to visualization and analysis tools. Biologists can browse and search the Cancer Cell Map pathways and view gene expression data on any pathway. All data is freely available. Computational biologists can download all pathways in BioPAX format for global analysis. Software developers can build software on top of the Cancer Cell Map using the web service API. Download and install the cPath pathway database software to create a local mirror of the Cancer Cell Map. Cancer Cell Map pathways were selected based on the scientific interests of research labs at Memorial Sloan-Kettering Cancer Center. Effort was made not to duplicate information in other public pathway databases. Available pathways include: Alpha6Beta4Integrin, AndrogenReceptor, EGFR1, Hedgehog, ID, KitReceptor, NOTCH, TGFBR, TNF alpha/NF-kB, Wnt. Each pathway has around 100-400 interactions.
ENCODE + Epigenomics Roadmap Combined Data Browser
Encyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome.
canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research. This cancer research and drug discovery resource was developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification and 3D structural data. Scientists can, in a single place, rapidly identify biological annotation of a target, its structural characterization, expression levels and protein interaction data, as well as suitable cell lines for experiments, potential tool compounds and similarity to known drug targets. canSAR has, from the outset, been completely use-case driven which has dramatically influenced the design of the back-end and the functionality provided through the interfaces. The Web interface provides flexible, multipoint entry into canSAR. This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data.
A biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium.
HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.
A NIfTI visualizer for statistical brain images (fMRI, VBM, etc) the iPad. The visualizer displays these images as overlay on the MNI standard brain. You can use it to store all your statistical images from your fMRI / VBM / TBSS studies and visualise them in 2D and 3D. Use NeuroPub as a library for your statistical images. It's the perfect app to bring to meetings, conferences, etc, and show your latest results.
Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image.
GBS barcode splitter - PERL script for split GBS reads by barcode
PERL script used to split barcode of Illumina sequencing data created by GBS protocol (www.maizegenetics.net). The barcode has variable size. Paired-end reads are supported.
sickle - A windowed adaptive trimming tool for FASTQ files using quality
Software tool for windowed adaptive trimming for fastq files using quality. Supports quality values like Illumina, Solexa, and Sanger. Takes the quality values and slides a window across them whose length is 0.1 times the length of the read.
Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded.
Cooperative Study Group for Autoimmune Disease Prevention
Collaborative network of investigators with a focus on prevention of autoimmune disease, defined as halting the development of autoimmune disease prior to clinical onset by means other than global immunosuppression, and an emphasis on Type 1 diabetes. Its mission is to engage in scientific discovery that significantly advances knowledge for the prevention and regulation of autoimmune disease. The specific goals enunciated in pursuit of this mission are: * To create improved models of disease pathogenesis and therapy to better understand immune mechanisms that will provide opportunities for prevention strategies * To use these models as validation platforms with which to test new tools applicable to human studies * To encourage core expertise and collaborative projects designed for rapid translation from animal to human studies, emphasizing the development of surrogate markers for disease progression and/or regulation which can be utilized in the context of clinical trials
Software that implements a probabilistic graphical model to analyze sequence data from tumor / normal pairs. The model draws statistical strength by analysing both genome jointly to more accurately classify germline and somatic mutations. It effectively reduces false positive somatic mutation predictions in tumour-normal pair sequencing data. It is highly recommended to post-process results with mutationSeq in order to filter technical artifacts.
Diabetes Control and Complications Trial
DCCT and EDIC: The Diabetes Control and Complications Trial and Follow-up Study
Clinical study that showed that keeping blood glucose levels as close to normal as possible slows the onset and progression of eye, kidney, and nerve diseases caused by diabetes. EDIC is a follow-up study of people who participated in DCCT. The DCCT involved 1,441 volunteers, ages 13 to 39, with type 1 diabetes and 29 medical centers in the United States and Canada. Volunteers had to have had diabetes for at least 1 year but no longer than 15 years. They also were required to have no, or only early signs of, diabetic eye disease. The study compared the effects of standard control of blood glucose versus intensive control on the complications of diabetes. Intensive control meant keeping hemoglobin A1C levels as close as possible to the normal value of 6 percent or less. The A1C blood test reflects a person' '''s average blood glucose over the last 2 to 3 months. Volunteers were randomly assigned to each treatment group. DCCT Study Findings * Intensive blood glucose control reduces risk of ** eye disease: 76% reduced risk ** kidney disease: 50% reduced risk ** nerve disease: 60% reduced risk When the DCCT ended, researchers continued to study more than 90 percent of participants. The follow-up study, called Epidemiology of Diabetes Interventions and Complications (EDIC), is assessing the incidence and predictors of cardiovascular disease events such as heart attack, stroke, or needed heart surgery, as well as diabetic complications related to the eye, kidney, and nerves. The EDIC study is also examining the impact of intensive control versus standard control on quality of life. Another objective is to look at the cost-effectiveness of intensive control. EDIC Study Findings * Intensive blood glucose control reduces risk of ** any cardiovascular disease event: 42% reduced risk ** nonfatal heart attack, stroke, or death from cardiovascular causes: 57% reduced risk
Efficacy and Mechanisms of Glutamine Dipeptide in the Surgical Intensive Care Unit
Efficacy and Mechanisms of GLN Dipeptide in the SICU
Efficacy and Mechanisms of GLN Dipeptide in the SICU (GLND)
Phase III Study on the Efficacy of Glutamine Dipeptide-Supplemented Parenteral Nutrition in Surgical ICU Patients
Multi-center, double-blind, placebo-controlled, intent-to-treat Phase III trial, designed to determine the effect of parenteral glutamine (GLN) dipeptide on important clinical outcomes in patients requiring surgical intensive care unit (SICU) care and parenteral nutrition (PN) after cardiac, vascular, or intestinal surgery. Patients who required PN and SICU care will receive either standard glutamine (GLN)-free PN (STD-PN) or isocaloric, isonitrogenous alanyl-glutamine dipeptide (AG)-PN until enteral feedings are established. The study will determine whether AG-PN decreases hospital mortality, nosocomial infection and other important indices of morbidity and will obtain mechanistically relevant observational data in the subjects on whether AG-PN a) increases serial blood concentrations of glutathione (GSH), heat shock proteins (HSP)-70 and -27, and glutamine; b) decreases the serum presence of the bacterial products flagellin and lipopolysaccharide (LPS) and the adaptive immune response to these mediators; and c) improves key indices of innate and adaptive immunity.
AEO represents the Adverse Event Ontology, a community-driven ontology developed to standardize and integrate data on biomedical adverse events (e.g., vaccine adverse events) and support computer-assisted reasoning. The AEO also can be found in BioPortal, http://bioportal.bioontology.org/ontologies/45534?p=terms
An application ontology for the domain of Sleep Medicine.
Web server for functional enrichment analysis and conversions of gene lists. Web based tool for functional profiling of gene lists from large scale experiments. Has web interface with powerful visualization. Used for analyzing data from any organism.
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
A statistical software package for identifying protein-associated transcripts from RIP-seq experiments. Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.
A structured controlled vocabulary of the development of Caenorhabditis elegans.
Thompson Center for Autism and Neurodevelopmental Disorders
MU Thompson Center for Autism and Neurodevelopmental Disorders
Thompson Center for Autism Neurodevelopmental Disorders
The mission of the Thompson Center is to improve the lives of individuals and families affected by autism and neurodevelopmental disorders through world class programs that integrate research, clinical service delivery, education and public policy. The Thompson Center''s vision is to become a recognized national center of excellence that serves as a model of interdisciplinary practice, research and training in the field of autism and neurodevelopmental disorders. At the MU Thompson Center, education and training activities are a key part of our mission. Our goal is to teach others about the needs of persons with autism and other neurodevelopmental disorders and their families. In addition, we strive to help learners acquire skills needed to improve the outcomes of individuals with developmental differences. These skills include evidence-based assessment and intervention strategies, interdisciplinary approaches to service delivery, research methods, and policy development. The Thompson Center offers a range of health, educational and behavioral services in one location for individuals with autism and other developmental concerns. Professionals from different disciplines strive to deliver family-centered care that is comprehensive and coordinated. Autism recently has been recognized as a national public health concern, and federal research funding in this area has increased substantially. Faculty members engage in research that will lead to early identification, treatment and ultimately prevention of autism spectrum disorders (ASD). How findings may eventually translate into improved outcomes in clinical and community settings is a primary goal of our research.
ShortRead - Classes and methods for high-throughput short-read sequencing data.
Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats.
TANGO: Taxonomic Assignment in Metagenomics
Software tool for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy.
A software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data. mutationSeq has the advantages of integrating different features (e.g., base qualities, mapping qualities, strand bias, and tailed distance features), and validated somatic mutations to make predictions. Given paired normal/tumour bam files, mutationSeq will output the probability of each candidate site being somatic.
University of Rostock; Mecklenburg-Vorpommern; Germany
Public university located in Rostock, Mecklenburg-Vorpommern, Germany. Founded in 1419.
National Hematologic Diseases Information Service
Information dissemination service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) providing information about certain hematologic diseases in easy-to-understand language: online, in booklets and fact sheets, by email, and over the phone to patients, health professionals and the public. The NHDIS provides the following informational products and services: * Response to inquiries about hematologic diseases, ranging from information about available patient and professional education materials to referrals to patient support organizations. Assistance is available by phone (8:30 a.m. to 5 p.m. eastern time, M-F), fax, mail, and email. * Publications about hematologic diseases, provided free of copyright, in varying reading levels. Available online or in hard copy. NHDIS also sends publications to health fairs and community events. * Referrals to health professionals through the National Library of Medicine' '''s MEDLINEplus, which includes a consumer-friendly listing of organizations to assist in the search for physicians and other health professionals.
This project (CheTA) will integrate Cambridge''s chemical text mining tool OSCAR with the U-Compare workflow infrastructure developed by NaCTeM and others. This integration adds chemistry to the world''s largest public collection of interoperable text mining tools and will be highly valued by influential stakeholders both in the JISC community and the wider chemistry community. There is a web interface (beta), http://www.nactem.ac.uk/software/cheta/, or you may download. As part of CheTA, OSCAR has been refactored into different workflows (a sequence of individual components to perform a certain task, in this case named entity recognition of chemical elements).
Software package that provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
QUASR - Cross-platform NGS processing and analysis pipeline in Python
A lightweight software pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal, demultiplexing, primer-removal, quality-assurance (QA) graphing, quality control (QC), consensus-generation, minority-variant determination, minority-variant graphing.
An interactive analysis program that searches neurophysiological data and plots the results. MatOFF was developed especially for dealing with the complexities common to behavioral neurophysiological experiments. It runs under Windows 2000 or XP and relies on MATLAB version R11.1 (or above) for all operations. MatOFF searches a data file to locate and plot epochs (trials) of special interest to the investigator. Appropriate input data files have time-stamped event codes, usually including neuron action potential firing events (spikes), and digitized analog data. The user specifies a list of event code numbers that uniquely identify a sequence of events. MatOFF uses this sequence to search the raw data file, select the epochs that meet the criteria, time-shift the trials to align them on a common event, order the epochs based on user-selected criteria, and plot the results based on a collection of page formatting specifications. MatOFF will also save extracted data and some statistics to disk. Features: * Powerful, interactive searching tools for locating relevant experimental events * Compatible with Cortex data acquisition program * Compatible with Plexon data acquisition system * Flexible, publication-quality graphical display and printing * Comprehensive scripting language * Supports learning and other dynamic behavior * Integrated interface to MATLAB functions * Automatic alignment of trial data and generation of histograms * Large variety of options for selecting and ordering trial data * Descriptive and non-parametric statistics * XY analog displays * Data export with flexible format control * Up to 72 plots per page * Display templates can be saved and reloaded * Free for public or private use * Adaptable to almost any data file format
Simulate High-Throughput Sequencing Data
Software that given a reference sequence, will create a large set of short nucleotide reads, simulating the output from today''s high-throughput DNA sequencers, such as the Illumina Genome Analyzer II.
Bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.
East Carolina University Department of Pharmacology and Toxicology
East Carolina University Brody School of Medicine Department of Pharmacology & Toxicology
East Carolina University Brody School of Medicine Department of Pharmacology and Toxicology
ECU BSOM Dept. of Pharmacology & Toxicology
ECU BSOM Dept. of Pharmacology and Toxicology
ECU Dept. of Pharmacology and Toxicology
Department of Pharmacology and Toxicology in Brody School of Medicine at East Carolina University prepares students to begin career related to studying biological actions of chemicals. Department offers Ph.D. program and combined M.D./Ph.D. program available through School of Medicine.
Blog by Brian E. Moore, MD, discussing issues pertaining to the practice of neuropathology -- including nervous system tumors, neuroanatomy, neurodegenerative disease, muscle and nerve disorders, ophthalmologic pathology, neuro trivia, neuropathology gossip, job listings and anything else that might be of interest to a blue-collar neuropathologist. Brian E. Moore, MD: Neuropathologist, Memorial Medical Center in Springfield, Illinois. Co-Chair, Southern Illinois University School of Medicine Department of Pathology.
This MATLAB toolbox implements a data fitting routine for Neurite Orientation Dispersion and Density Imaging (NODDI). NODDI is a new diffusion MRI technique for imaging brain tissue microstructure. Compared to DTI, it has the advantage of providing measures of tissue microstructure that are much more direct and hence more specific. It achieves this by adopting the model-based strategy which relates the signals from diffusion MRI to geometric models of tissue microstructure. In contrast to typical model-based techniques, NODDI is much more clinically feasible and can be acquired on standard MR scanners with an imaging time comparable to DTI.
1000 Genomes: A Deep Catalog of Human Genetic Variation
International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes
A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions.
An open-source general packing algorithm that packs 3D objects onto surfaces, into volumes, and around volumes. It provides a general architecture to allow various packing algorithms to interoperate efficiently in the same model. autoPack can incorporate any packing solution into its modular python program architecture, but is currently optimized to provide a novel solution to the loose packing problem which places objects of discrete size into place (compared to advancing front, popcorn, or other fast tight-packing solutions that allow objects to scale to arbitrary masses.) Most popular 3D software programs now contain robust physics engines based on Bullet that can separate small collections of overlapping objects or allow volumes to be filled by pouring shapes from generators, but these approaches fails for large complex systems and result in either overlapping geometry, crashed software, or non-random gradients. Most packing algorithms are designed to position objects as efficiently as possible, but autoPack allows the user to select from random loose packing to highly organized packing methods����??even to choose both methods at the same time. autoPack positions 3D geometries into, onto, and around volumes with minimal to zero overlap. autoPack mixes several packing approaches and procedural growth algorithms. autoPack can thus place objects with forces and constraints to allow a high degree of control ranging from completely random distributions to highly ordered structures. * zero to minimal overlaps depending on the method used * accuracy vs speed parameters selected by the user * zero edge effects * complete control, from fully random to fully ordered distributions * agent-based interaction, weighting, and collision control
A specialized version of autoPack designed to pack biological components together. The current version is optimized to pack molecules into cells with biologically relevant interactions to populate massive cell models with atomic or near-atomic details. Components of the algorithm pack transmembrane proteins and lipids into bilayers, globular molecules into compartments defined by the bilayers (or as exteriors), and fibrous components like microtubules, actin, and DNA.
seqbias - Estimation of per-position bias in high-throughput sequencing data
Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.
PDQ - NCI''s Comprehensive Cancer Database
NCI''s comprehensive cancer database that contains summaries on a wide range of cancer topics; a registry of 8,000+ open and 19,000+ closed cancer clinical trials from around the world; a directory of professionals who provide genetics services; the NCI Dictionary of Cancer Terms, with definitions for 6,800+ cancer and medical terms; and the NCI Drug Dictionary, which has information on 2,300+ agents used in the treatment of cancer or cancer-related conditions. The PDQ cancer information summaries are peer reviewed and updated monthly by six editorial boards comprised of specialists in adult treatment, pediatric treatment, supportive care, screening and prevention, genetics, and complementary and alternative medicine. The Boards review current literature from more than 70 biomedical journals, evaluate its relevance, and synthesize it into clear summaries. Many of the summaries are also available in Spanish.
This web server makes predictions of family, superfamily and fold level classifications of proteins based on the Structural Classification of Proteins (SCOP) hierarchy using the Support Vector Machine (SVM) learning algorithm. SVM-FOLD detects subtle protein sequence similarities by learning from all available annotated proteins, as well as utilizing potential hits as identified by PSI-BLAST. Predictions of classes of proteins that do not have any known example with a significant pairwise PSI-BLAST E-value can still be found using SVMs.
A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.
Action Potential is a forum operated by neuroscience editors at Nature for the entire neuroscience community. We''ll discuss what''s new and exciting in science, be it in our journals or elsewhere, as well as science policy and publishing and provide updates from major meetings. Although we provide the opportunity to comment as a service to the community, we do not endorse all viewpoints represented here. To contact the contributors directly with confidential questions or suggestions for future entries, please e-mail n.gray (at) us.nature.com.
Software and Hardware for Neurophysiology: The home of NIMH Cortex
A program developed by the NIMH Laboratory of Neuropsychology for data acquisition and experimental control of neurophysiological experiments. The purpose of this website is to make it easier to access new versions of NIMH CORTEX and its supporting documents. Ultimately, it is also hoped that these pages will make it easier for users to report bugs, request enhancements, and obtain help. Download the latest version and unzip it into a new sub-directory. Then read the on-line documentation. For the new user, the User''s Manuals are invaluable in specifying system requirements and giving an overview of the features and necessary hardware. The Function reference goes into more detail about how to write experiments using NIMH CORTEX. The Demos reference is a good place for new and experienced users to start to get an idea of what NIMH CORTEX can do these days.
BTRIS: NIH Biomedical Translational Research Information System
Biomedical Translational Research Information System
Provides NIH clinical investigators with access to identifiable data for the subjects on their own active protocols, while providing all NIH investigators with access to de-identified data across all protocols. BTRIS provides users with advanced search, filtering, and aggregation methods to create data sets to support ongoing studies and stimulate ideas for new research. BTRIS is two distinct but interrelated applications, BTRIS Data Access and BTRIS Preferences. * BTRIS Data Access is the data repository where principal investigators or their designee create reports on their active protocols with identified subject data. Reports include the IRB Inclusion Enrollment Report, demographics, patient lists, laboratory and microbiology results, vital signs, medication orders and administration, diagnoses, and radiology reports (with links to images in the CC PACS system). * BTRIS Preferences is a Web based application that allows principal investigators or their designees to verify subject enrollment in their protocol(s). This ensures that reports created in BTRIS Data Access include all subjects. It also allows the principal investigator to designate an alternate investigator from the protocol to manage subject enrollment and create reports in BTRIS Data Access. BTRIS contains subject data from CRIS/MIS (the Clinical Center Medical Information Systems) and research data from NIAID (Crimson), NIAAA, and NCI. Data are available from 1976 to the present.
A Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections' ''' properties and it offers easy integration with matplotlib for plotting the results. The geometry can be saved using NeuroML and the computational results in a customized and extensible HDF5 format; the results can then be reload in the software and analyzed in a later stage, without re-running the simulation. Featuring 3D visualization of the model with the possibility to change it runtime; creation of vectors to record any variables present in the section; pylab integration to plot directly the result of the simulation; exploration of the timecourse of any variable among time using a color coded scale; saving the results simulation for later analysis; automatic download and running of models in ModelDB.
The Epilepsy Genetic Association Database (epiGAD) is an online repository of data relating to genetic association studies in the field of epilepsy. It summarizes the results of both published and unpublished studies, and is intended as a tool for researchers in the field to keep abreast of recent studies, providing a bird''s eye view of this research area. The goal of epiGAD is to collate all association studies in epilepsy in order to help researchers in this area identify all the available gene-disease associations. Finally, by including unpublished studies, it hopes to reduce the problem of publication bias and provide more accurate data for future meta-analyses. It is also hoped that epiGAD will foster collaboration between the different epilepsy genetics groups around the world, and faciliate formation of a network of investigators in epilepsy genetics. There are 4 databases within epiGAD: - the susceptibility genes database - the epilepsy pharmacogenetics database - the meta-analysis database - the genome-wide association studies (GWAS) database The susceptibility genes database compiles all studies related to putative epilepsy susceptibility genes (eg. interleukin-1-beta in TLE), while the pharmacogenetics studies in epilepsy (eg. ABCB1 studies) are stored in ''phamacogenetics''. The meta-analysis database compiles all existing published epilepsy genetic meta-analyses, whether for susceptibility genes, or pharmacogenetics. The GWAS database is currently empty, but will be filled once GWAS are published. Sponsors: The epiGAD website is supported by the ILAE Genetics Commission.
Collaborative Studies on Genetics of Alcoholism
Database and biorepository from a multi-site, multi-disciplinary study characterizing the familial transmission of alcoholism and related phenotypes and identifying susceptibility genes using genetic linkage. Investigators have assembled a collection of over 300 extended families densely affected by alcoholism (more than 3000 individuals), including clinical, neuropsychological, electrophysiological, biochemical, and genetic data, and established a repository of immortalized cell lines from these individuals, to serve as a permanent source of DNA for genetic studies. NIAAA has funded the Collaborative Studies on Genetics of Alcoholism (COGA) since 1989, with the goal of identifying the specific genes underlying this vulnerability. Data and biomaterials are available to qualified investigators in the broader scientific community. Recipients of data and biomaterials will be responsible for defraying the cost of their distribution. Pedigrees densely affected with alcoholism (DSM-III-R) have been ascertained at six sites (SUNY Downstate Health Sciences Center, University of Connecticut, Indiana University, Washington University, University of Iowa, and The University of California at San Diego). Diagnoses of alcohol dependence according to several diagnostic systems (e.g., DSM-III-R, Feighner, ICD-10) are made based on examination of medical records and direct assessment using the Semi-Structured Assessment for Genetics of Alcoholism (SSAGA). Nuclear and extended pedigrees containing at least two alcohol-dependent first-degree relatives in addition to an alcohol dependent proband (with all affected individuals meeting both DSM-IIIR and Feighner criteria) have been ascertained. Clinical data comprises anonymous data on family structure, age, sex, vital status, psychopathology, diagnosis, other clinically relevant information, are stored, maintained, and distributed by Washington University. Research data, consist of data on blood biochemistry and psychological test performance, which are stored, maintained, and distributed by Washington University, and brain electrophysiological data, which are stored, maintained, and distributed by SUNY. Genetic analysis data, consisting of marker genotypes, along with results of previous genetic analyses of COGA data, are stored, maintained, and distributed by Washington University. Biomaterials, consisting of lymphoblastoid cell lines and DNA from participating subjects are stored, maintained, and distributed by Rutgers University. Researchers may gain access to clinical data, research data, genetic analysis data, and biomaterials, subject to NIAAA approval, by completing an application details available from the website. After access certification, the principal investigator will be given access to electronic data files and other documentation.
National Kidney and Urologic Diseases Information Clearinghouse
National Kidney and Urologic Diseases Information Clearinghouse (NKUDIC)
Information dissemination service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) established to increase knowledge and understanding about diseases of the kidneys and urologic system among people with these conditions and their families, health care professionals, and the general public: online, in booklets and fact sheets, by email, and over the phone. To carry out this mission, NKUDIC works closely with a coordinating panel of representatives from Federal agencies; voluntary organizations on the national level; professional groups; and State health departments to identify and respond to informational needs about kidney and urologic diseases. NKUDIC provides the following informational products and services: * Response to inquiries about kidney and urologic diseases-ranging from information about available patient and professional education materials to statistical data. By phone (8:30 a.m. to 5 p.m. eastern time, M-F), fax, mail, and email. * Publications about specific kidney and urologic diseases, provided free of copyright, in varying reading levels. Available online or as booklets and brochures. (See our Publications Catalog.) NKUDIC also sends publications to health fairs and community events. Please contact us for more information. * Referrals to health professionals through the National Library of Medicine' '''s MEDLINEplus includes a consumer-friendly listing of organizations that will assist you in your search for physicians and other health professionals. * Exhibits at professional meetings specific to kidney and urologic diseases, as well as cross-cutting professional meetings. NKUDIC exhibits at 11 professional meetings, each year, including Society of Urologic Nurses and Associates, American Urologic Association, American Society of Nephrology, National Kidney Foundation, Polycystic Kidney Disease Research Foundation, American Academy of Family Physicians, American Academy of Physician Assistants, American Nurses Association, and the National Conference for Nurse Practitioners.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. Chromosome maps are labeled by name of the originating organism, the map title, total markers, total UniSTSs and links to view maps as well as research documents available through PubMed, another NCBI database. The search functions within UniSTS allow the user to search by gene marker, chromosome, gene symbol and gene description terms to locate markers on specified genes. A representation of the UniSTS datasets is available by ftp. NOTE: All data from this resource have been moved to the Probe database, http://www.ncbi.nlm.nih.gov/probe. You can retrieve all UniSTS records by searching the probe database using the search term unists(properties). (use brackets insead of parenthesis). Additionally, legacy data remain on the NCBI FTP Site in the UniSTS Repository (ftp://ftp.ncbi.nih.gov/pub/ProbeDB/legacy_unists).
Funds innovative research and development in Washington state to promote life sciences competitiveness, enhance economic vitality, and improve health and health care. Its grantmaking opportunities are designed to leverage the state''s investment in research and development by achieving three goals: promoting health; making the life sciences sector more competitive; and strengthening Washington''s economy. LSDF currently offers two different types of granting mechanisms for both for-profit and non-profit organizations in Washington: * Proof of Concept grants to enhance the commercial viability of intellectual property developed by non-profit organizations or enhance the competitiveness of early-stage companies for private equity investment. (This grant mechanism combines the Commercialization and PreCede mechanisms offered in prior years.) * Opportunity grants to fund extraordinary research and development proposals having the ability to significantly leverage LSDF dollars against those from other sources.
A selection of image analysis algorithms for the processing of diffusion-weighted MR images. Features & Highlights * Tensor and q-ball reconstruction * Glyph visualization * Quantification and partial volume clustering of tensor and q-ball images * Global fiber tractography, visualization, and tract post-processing * Brain network statistics and visualization (connectomics) * Interactive exploration of Tract-based spatial statistics (TBSS) results * Intra-voxel incoherent motion (IVIM) estimation * Synthetic data generation Additional system specific requirements: * Windows: If you have problems running the Windows application, please install the Microsoft Redistributable Packages for VS 2008: 32 bit or 64 bit * Linux: the Qt framework, version 4.6.2 or later Tested systems: Windows 7, Windows Vista; Ubuntu 12.04 and newer; OS X 10.6 (Snow Leopard), OS X 10.8 (Mountain Lion) The OS X 10.6 installer is compatible with OS X 10.7 (Lion) so there is no dedicated disk image build under 10.7. The MITK Diffusion application is based on the MITK research platform and the most of it is open-source. The available code is embedded into the source code of MITK as a module and can be accessed through the public git repository.
Nonhuman Primate Transplantation Tolerance Cooperative Study Group
Non-human Primate Transplantation Tolerance Cooperative Study Group
Cooperative program for research on nonhuman primate models of kidney, islet, heart, and lung transplantation evaluating the safety and efficacy of existing and new treatment regimens that promote the immune system' '''s acceptance of a transplant and to understand why the immune system either rejects or does not reject a transplant. This program bridges the critical gap between small-animal research and human clinical trials. The program supports research into the immunological mechanisms of tolerance induction and development of surrogate markers for the induction, maintenance, and loss of tolerance.
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool
Gene Ontology enRIchment anaLysis and visuaLizAtion tool
GOrilla: Gene Ontology Enrichment Analysis Visualization Tool
A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes.
VarScan - variant detection in massively parallel sequencing data
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
National Institute on Drug Abuse Media Guide
The latest findings on the science of drug abuse and addiction and commonly abused drugs, and lists resources for more information. They are committed to bringing timely, factual information on addiction and treatment to the press and public. NIDA''s Public Information and Liaison Branch (PILB) is part of NIDA''s Office of Science Policy and Communications. Linking scientists, the scientific community, and the media, PILB supports the rapid dissemination of research information to inform policy and to improve practice. NIDA''s goal is to ensure that science - not ideology or anecdote - forms the foundation of public information on drug abuse and addiction. NIDAs online MEDIA GUIDE provides answers on how to find what you need to know about drug abuse and addiction, including information on the basics (The Science of Drug Abuse and Addiction and Commonly Abused Drugs), resources (Where to Find Nationwide Trends and Statistics, NIDA Resources, and Other Government Web Sites for Health and Science Information), NIDAs history and background, a glossary and relevant contact information. NIDA is pleased to offer this guide to the important findings that are emerging as a result of research on addiction and its treatment. NIDA, part of the National Institutes of Health under the U.S. Department of Health and Human Services, supports most of the world''s research on drug abuse and addiction, including basic and behavioral science research that addresses fundamental and essential questions relevant to drug abuse, ranging from its causes and consequences to its treatment and prevention. The purpose of this guide is to give journalists fast and user-friendly access to the latest scientific information but it is useful for anyone interested in how to access accurate information about drug abuse and addiction. In more than three decades as a researcher, I have seen the impact that science and health journalists have had in bringing scientific research to the public. It is through information that Americans gain hope and understanding. I have come to know many of you over the years and remain committed to releasing scientific information as quickly as possible for rapid dissemination to the public. Please keep this guide nearby as a useful tool and let us know how NIDA''s public liaison staff can help you reach your information and deadline needs. A PDF version is available for download.
Database of Chemical Compounds and Reactions in Biological Pathways
KEGG LIGAND contains knowledge of chemical substances and reactions that are relevant to life. It is a composite database consisting of COMPOUND, GLYCAN, REACTION, RPAIR, and ENZYME databases, whose entries are identified by C, G, R, RP, and EC numbers, respectively. ENZYME is derived from the IUBMB/IUPAC Enzyme Nomenclature, but the others are internally developed and maintained. The primary database of KEGG LIGAND is a relational database with the KegDraw interface, which is used to generated the secondary (flat file) database for DBGET.
A software collaboration platform that provides: Bug tracking, Code hosting using Bazaar, Code reviews, Ubuntu package building and hosting, Translations, Mailing lists, Answer tracking and FAQs, and Specification tracking. Launchpad can host your project''s source code using the Bazaar version control system.
The Millennium Cohort Study is the largest prospective health project in military history. It is designed to evaluate the long-term health effects of military service, including deployments. The Department of Defense recognized after the 1991 Gulf War that there was a need to collect more information about the long-term health of service members. The Millennium Cohort Study was designed to address that critical need, and the study was launched by 2001. Funded by the Department of Defense, and supported by military, Department of Veterans Affairs, and civilian researchers, almost 150,000 people are already participating in this groundbreaking study. As force health protection continues to be a priority for the future of the United States military, the Millennium Cohort Study will be providing critical information towards enhancing the long-term health of future generations of military members. Participants include Panel 1 (enrolled beginning in 2001), Panel 2 (enrolled beginning in 2004), and Panel 3 (enrolled beginning in 2007). A Panel 4 will be invited to participate throughout the upcoming survey cycle, and we expect to have over 200,000 participants total upon completion of the cycle. Participants are asked to complete one questionnaire (by mail or online) every three years, through 2022.
National Swine Resource and Research Center
Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research.
Federal Interagency Traumatic Brain Injury Research Informatics System
Federal Interagency Traumatic Brain Injury Research (FITBIR) Informatics System
Platform for Traumatic Brain Injury relevant data. System was developed to share data across entire TBI research field and to facilitate collaboration between laboratories and interconnectivity between informatics platforms. FITBIR implements interagency Common Data Elements for TBI research and provides tools and resources to extend data dictionary. Established submission strategy to ensure high quality and to provide maximum benefit to investigators. Qualified researchers can request access to data stored in FITBIR and/or data stored at federated repositories.
A teaching, training and test tool app, designed for both iPhone and iPad, for the vestibulo-ocular reflex (VOR) system and its disorders, including Benign paroxysmal positional vertigo (BPPV). It demonstrates eye saccades, including those caused by canalithiasis (free-floating particles in the canals), and both functioning and dysfunctional VOR. It shows how BPPV is caused and treated. aVOR demonstrates how head movement has an automatic influence on eye direction, the impact of dysfunction of the semicircular canals, their size, shape and location in the head, and the causes of nystagmus. The application includes a Test Mode which presents the symptoms of various types of VOR dysfunction for the student to diagnose. It is designed for college-level neuropsychology students and medical professionals, and incorporates the latest research. Compatible with iPhone, iPod touch, and iPad. Requires iOS 3.2 or later Languages: English, Chinese, German, Italian, Japanese, Russian, Spanish
Transdisciplinary Tobacco Use Research Centers
A transdisciplinary approach to the full spectrum of basic and applied research on tobacco use to reduce the disease burden of tobacco use, including: * Etiology of tobacco use and addiction * Impact of advertising and marketing * Prevention of tobacco use * Treatment of tobacco use and addiction * Identification of biomarkers of tobacco exposure * Identification of genes related to addiction and susceptibility to harm from tobacco Goals * Increase the number of investigators from relevant disciplines who focus on the study of tobacco use as part of transdisciplinary teams. * Generate basic research evidence to improve understanding of the etiology and natural history of tobacco use. * Produce evidence-based tobacco use interventions that can translate to the community and specific understudied or underserved populations. * Increase the number of evidence-based interventions that are novel, including the development, testing and dissemination of innovative behavioral treatments and prevention strategies based upon findings from basic research. * Train transdisciplinary investigators capable of conducting cutting-edge tobacco use research. * Increase the number of peer-reviewed publications in the areas of tobacco use, nicotine addiction, and treatment.
An information-rich viewer for next-generation genome assembles with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation. EagleView is a multi-platform application developed with C++ and is available for all three major platforms: Windows, Linux, and Mac OS.
NIMH Division of Intramural Research Programs
Division of Intramural Research Programs at the National Institute of Mental Health
National Institute of Mental Health Intramural Research Program
The Division of Intramural Research Programs (DIRP) at the National Institute of Mental Health (NIMH) is the internal research division of the NIMH. NIMH DIRP scientists conduct research ranging from studies into mechanisms of normal brain function, conducted at the behavioral, systems, cellular, and molecular levels, to clinical investigations into the diagnosis, treatment and prevention of mental illness. Major disease entities studied throughout the lifespan include mood disorders and anxiety, schizophrenia, obsessive-compulsive disorder, attention deficit hyperactivity disorder, and pediatric autoimmune neuropsychiatric disorders. Because of its outstanding resources, unique funding mechanisms, and location in the nation''s capital, the DIRP is viewed as a national resource, providing unique opportunities in mental health research and research training. Training is conducted in all the Institute''s clinical branches and basic neuroscience laboratories located on the 305-acre National Institutes of Health campus in Bethesda, Maryland. In addition to individualized trainee/mentor-driven postdoctoral training opportunities in the clinical and basic sciences, the DIRP offers Postbaccalaureate Research Training Awards, a Clinical Electives Program, as well as a variety of Summer Research Fellowships and an Undergraduate Internship Program. The mission of the division is to plan and conduct basic, clinical, and translational research to advance understanding of the diagnosis, causes, treatment, and prevention of mental disorders through the study of brain function and behavior; conduct state-of-the-art research that, in part, complements extramural research activities and exploits the special resources of the National Institutes of Health; and provide an environment conducive to the training and development of clinical and basic scientists. In addition the DIRP fosters standards of excellence in the ethical treatment and the provision of clinical care to research subjects; serve as a resource to the NIMH in responding to requests made by the Administration, members of Congress, and citizens'' groups for information regarding mental disorders; and analyzes and evaluates national needs and research opportunities and provides advice to the Institute Director on matters of scientific interest. Core Facilities: * Functional MRI Core * Magnetic Resonance Core * Magnetoencephalography Core * Microarray Core * Neurophysiology Imaging Facility * Non-Human Primate Core * Scientific and Statistical Computing Core * Section on Instrumentation Core * Transgenic Core * Veterinary Medicine Resources
Type 1 Diabetes Preclinical Testing Program
NIDDKType 1 Diabetes Preclinical Testing Program
Type 1 Diabetes Preclinical Testing Program (T1D-PtP)
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Investigator access is provided to the established facilities and expertise needed to extend, enhance and validate preclinical studies of promising new therapeutics in cases where additional preclinical testing is needed to validate potential therapies under disease-specific conditions and in multiple animal models before therapeutics can enter the Type 1 Diabetes Rapid Access to Intervention Development (T1D-RAID) development pipeline. The T1D-RAID program provides resources for pre-clinical development of drugs, natural products, and biologics that will be tested as new therapeutics in type 1 diabetes clinical trials. The T1D-RAID program is not currently accepting applications. The T1D-PTP program currently supports two contracts, which are separate from each other and from the T1D-RAID NCI contract resources, to assist in preclinical development of therapeutics for T1D: * Agents to be tested for Preclinical Efficacy in Prevention or Reversal of Type 1 Diabetes in Rodent Models. Type 1 Diabetes Preclinical Testing Program (T1D-PTP) (NOT-DK-09-006) * Needs for Preclinical Efficacy Testing of Promising Agents to Prevent or Reverse Diabetic Complications (NOT-DK-09-009) The T1D-RAID and T1D-PTP are programs intended to remove the most common barriers to progress in identification and development of new therapies for Type 1 Diabetes. The common goal of these programs is to support and provide for the preclinical work necessary to obtain proof of principle establishing that a new molecule or novel approach will be a viable candidate for expanded clinical evaluation.
It is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. CASP-DB is fully browsable and searchable and is regularly updated. The regions of the polypeptide chain immediately preceding or following a helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived for cappings but the structural motifs associated to them are still unclassified. CAPS-DB is a database of clusters of structural patterns of different capping types. The clustering algorithm is based in the geometry and the space conformation of these regions. CAPS-DB is a relational database that allows the user to search, browse, inspect and retrieve structural data associated to cappings. The contents of CAPS-DB might be of interest to a wide range of scientist covering different areas such as protein design and engineering, structural biology and bioinformatics. CapsDB v4.0 * PDB structures: 4591 * Number of clusters: 859 * Number of caps: 31452
National Center for Research Resources - Primate Resources
THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 16, 2013. NCRR has been absorbed into other parts of the National Institutes of Health. This organizational structure is no longer available. Provides laboratory scientists and clinical researchers with the resources and tools they need to understand, detect, treat and prevent a wide range of diseases. Animal models, such as nonhuman primates, are a critical component of biomedical research, having profound implications for public health. Scientists depend on laboratory animals and other nonhuman models for investigating biological processes, studying the causes of diseases and testing promising new therapies. Nonhuman primates, in particular, are important for translational research because of their close physiological similarities to humans. They enable discoveries that have direct application to human studies, bridging the gap between basic science and human medicine. Discoveries in animal models are helping scientists test treatments for human conditions such as drug addiction, obesity, malaria, HIV/AIDS and neurodegenerative diseases, accelerating the pace at which these research advances can be translated into treatments for patients. Through its Division of Comparative Medicine, NCRR offers a wide variety of primate resources for NIH-funded scientists across the nation. Additionally, funding opportunities are available to National Primate Research Centers. Eight National Primate Research Centers (NPRCs) located throughout the country provide animals, facilities and expertise in all aspects of nonhuman primate biology and husbandry. These facilities and resources enable collaborative research among NPRC staff scientists, investigators from the NPRC host institution and other NIH-funded researchers. Major areas of research benefiting from the primate centers include AIDS, avian flu, Alzheimer''s disease, Parkinson''s disease, diabetes, asthma and endo-metriosis. The centers????????????????? specialized resources are intended to support investigators who receive their primary research project funding from NIH, but they also may be used by investigators who are funded by other federal, state and local agencies, as well as by research foundations and the private sector. Together the primate centers have more than 28,000 nonhuman primates of 20 different species. This portal covers the following topics: * National Primate Research Centers * Monkey Research Resources * Chimpanzee Research Resources * Chimpanzee Management Program * Specific-Pathogen-Free Macaque Resources * Nonhuman Primate Research Reagents
HIA - Hybrid Index based sequence Alignment
A sequence alignment tool to align both short and long reads to a reference genome. HIA has two indexes, a hash table index and a suffix array index. The hash table is capable of the direct lookup of a q-gram and the suffix array is very fast in the lookup of a variable length q-gram. Our experiments show that the hybrid of hash table and suffix array is useful at the perspective of speed to map NGS sequencing reads to a reference genome sequence.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 27, 2016. Curated database of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. All interactions are assembled into pathways, and can be accessed by performing searches for biomolecules, or processes, or by viewing predefined pathways. This was a collaborative project between the NCI and Nature Publishing Group (NPG) from 2006 until September 22nd, 2012, and is no longer being updated. PID is aimed at the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. The database focuses on the biomolecular interactions that are known or believed to take place in human cells. It can be browsed as an online encyclopedia, used to run computational analyses, or employed in ways that combine these two approaches. In addition to PID' '''s predefined pathways, search results are displayed as dynamically constructed interaction networks. These features of PID render it a useful tool for both biologists and bioinformaticians. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of interest. In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is supplemented by a concise editorial section that includes specially written synopses of recent important research articles in areas related to cancer research, and specially commissioned Bioinformatics Primers that provide practical advice on how to make the most of other relevant online resources. The database and editorial content are updated monthly, and users can opt to receive a monthly email alert to stay informed about new content. Note: as of September 23, 2012 the PID is no longer being actively curated. NCI will maintain the PID website and data for twelve months beyond September 2012 to allow interested parties to obtain the previously curated data before the site is retired in September 2013.
Software R package to quickly scan reads and gather statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected.
Growing library of software for physiologic signal processing and analysis, detection of physiologically significant events using both classical techniques and novel methods based on statistical physics and nonlinear dynamics, interactive display and characterization of signals, creation of new databases, simulation of physiologic and other signals, quantitative evaluation and comparison of analysis methods, and analysis of nonequilibrium and nonstationary processes. A unifying theme of the research projects that contribute software to PhysioToolkit is the extraction of hidden information from biomedical signals, information that may have diagnostic or prognostic value in medicine, or explanatory or predictive power in basic research. Contributions of software to PhysioToolkit are welcome, http://physionet.org/guidelines.shtml#software-contributions
Virginia Commonwealth University Medical Center, Center for Molecular Imaging
The Center for Molecular Imaging integrates molecular imaging and molecular medicine with systems biology approaches to understand disease complexity, promising to provide predictive, preventative and personalized medicine that will transform health care. The multi-modality molecular imaging program is composed of individual but overlapping research themes with specific projects under each theme. As all projects are underpinned by methodology development in the chemistry, biology, physics and bioengineering of imaging, there is always a strong overlap and cross feed in terms of methods and assays. The research themes include: * Biomarker pharmacodynamic imaging of metabolism, proliferation, cell death and vascular perfusion * Molecular genetic imaging in developing multi-modal reporter gene-based probes * Molecular imaging of angiogenesis and its relation to tumor hypoxia * Multi-modal nanoparticle probes for drug delivery and molecular imaging, including cell and immune-based therapies * Radiolabeled drug pharmacokinetics and studies of drug discovery and structural biology using molecular imaging strategies * Development of nanotechnology molecular imaging systems * Imaging proteomic mass spectrometry * Molecular imaging and molecular pathology diagnostic research The Center for Molecular Imaging fosters collaborative research, bringing together the advances being made in technology-driven research such as bioengineering, chemical genomics and nanotechnology with biomedical research groups studying cell and molecular biology and radiobiology, biologically targeted therapeutics, immuno-based mechanisms, and drug and biomarker discovery. The aim is to develop and validate multi-modality molecular imaging tools that will facilitate the advancement of translational medicine and clinical science research in oncology and neuroscience as well as other clinical research areas. The center is equipped with laboratories for radiochemistry, analytical chemistry, molecular biology, nanotechnology and animal imaging, as well as a dedicated facility for translational clinical imaging. Imaging technologies within the center include Positron Emission Tomography/Computed Tomography (preclinical and clinical), Single Photon Emission Computed Tomography, optical imaging, autoradiography and multi-modality nanotechnology imaging. Molecular probe developments underpin the biological and biomedical research conducted using the above modalities.
A group blog providing expert, independent commentary on the personal genomics industry. The goal of the project is to provide genetic testing consumers with independent and informed analysis of developments in the field of genetics and the genetic testing industry. Members of Genomes Unzipped include active researchers in various fields of genetics, as well as specialists in the legal and public health issues surrounding new genomic technologies. Many of us have also been extensively involved in public communication about genetics. Members of the group have had their DNA tested with a variety of products. We have released all of these genetic data openly to the public, both as raw data and in a custom genome browser. As the project proceeds we plan to obtain more genetic tests ����?? up to and including whole genome sequencing ����?? and to continue to release these data to the world. The group is also performing analyses of our own raw genetic data to illustrate fundamental concepts in genetics, using software written both by group members and other collaborators; and we����??ll be releasing the code for that software in our new code repository. As the project expands, we����??ll be looking to add data from other volunteers to the project, as well as to collaborate with other ����??genome hackers����?? on the development of new tools for exploring genetic data.
The Protein Research Foundation has collected information related to amino acids, peptides and proteins and created several databases. The website is partially commerical and some databases are available only for a fee, although all can be accessed for a brief period as a guest account as well. They provide a literature search database, a Peptide/Protein Sequence Database, and a Synthetic Compounds Database.
Institute for Laboratory Animal Research
The mission of ILAR is to evaluate and disseminate information on issues related to the scientific, technological, and ethical use of animals and related biological resources in research, testing, and education. Using the principles of refinement, reduction, and replacement (3Rs) as a foundation, ILAR promotes high-quality science through the humane care and use of animals and the implementation of alternatives. Through the reports of expert committees, the ILAR Journal, web-based resources, and other means of communication, ILAR functions as a component of the National Academies to provide independent, objective advice to the federal government, the international biomedical research community, and the public. ILAR supports the responsible use of animals in research, testing, and education as a key component to advancing the health and quality of life of humans and animals. It promotes high-quality science and humane care and use of research animals based upon the principles of refinement, replacement, and reduction (the 3Rs) and high ethical standards. It fosters best practices that enhance human and animal welfare by organizing and disseminating information and by facilitating dialogue among interested parties. It has developed a unique Search Engine to search for animal models and strains. This search engine surveys all the websites of vendors and repositories of laboratory animals and biological material on our Links page. The ILAR develops guidelines on laboratory animal care and use and conducts conferences, symposia, and workshops on important laboratory animal problems. ILAR publishes the ILAR Journal on a quarterly basis, as well as conference proceedings and special reports prepared by committees of experts. A list of ILAR publications on issues related to laboratory animal research is available on the Web site. As part of the Animal Models and Genetic Stocks Information Exchange Program, ILAR staff members answer direct telephone and mail inquiries and maintain a Web page containing a database on animal models and genetic stock. The Web site also offers a comprehensive search engine that enables users to find information on the existence and location of special animal models, correct nomenclature to identify animals, and related topics such as diseases of animals and relevant publications. Sponsors: ILAR receives funding from the following sponsors: -Abbott Laboratories -Abbott Fund -American College of Laboratory Animal Medicine (ACLAM) -American Society of Laboratory Animal Practitioners (ASLAP) -Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) -Bristol-Myers Squibb Co. -Charles River -Charles River Laboratories Foundation -Covance -Federation of American Societies for Experimental Biology (FASEB) -GlaxoSmithKline -Merck & Co., Inc. -National Science Foundation (NSF) -Pfizer -Scientists Center for Animal Welfare (SCAW) -U.S. Department of Agriculture (USDA) -U.S. Department of the Army -U.S. Department of Health and Human Services (DHHS) :*National Institutes of Health (NIH) :*Office of Research Integrity (ORI) -U.S. Department of the Navy -U.S. Department of Veterans Affairs -Wellcome Trust -Wyeth Pharmaceuticals
eXpress - Streaming quantification for high-throughput sequencing
THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018. From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/. Software for streaming quantification for high-throughput DNA/RNA sequencing. Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them.
National Institutes of Health Research Portfolio Online Reporting Tool
A database of federally funded biomedical research projects conducted at universities, hospitals, and other research institutions that provides a central point of access to reports, data, and analyses of NIH research. The RePORTER has replaced the CRISP database. The database, maintained by the Office of Extramural Research at the National Institutes of Health, includes projects funded by the National Institutes of Health (NIH), Substance Abuse and Mental Health Services (SAMHSA), Health Resources and Services Administration (HRSA), Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDCP), Agency for Health Care Research and Quality (AHRQ), and Office of Assistant Secretary of Health (OASH).
Marine Geosciences Data System MediaBank
A collection of high-quality images and videos for education and outreach from the Integrated Earth Data Applications Facility. Albums include: Ridge2000, MARGINS, GeoMapApp, GeoPRISMS, Antarctic and Southern Ocean, Global Multi-Resolution Topography. To contribute your media to Media Bank, you are asked to supply metadata with each image/video supplied.
Human Genome Variation Society: Databases and Other Tools
A list of various databases freely available to the public, including several mutation and variation resources, such as education resources for teachers students provided by the Human Genome Variation Society. Databases listed include: * Locus Specific Mutation Databases * Disease Centered Central Mutation Databases * Central Mutation and SNP Databases * National and Ethnic Mutation Databases * Mitochondrial Mutation Databases * Chromosomal Variation Databases * Other Mutation Databases ( i.e. your round holes don' '''t fit our square pegs) * Clinical and Patient Aspects Databases * Non Human Mutation Databases * Artificial Mutations Only * Other Related Databases * Education Resources for Teachers and Students
The Loom is a blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer. Carl Zimmer writes about science regularly for the New York Times and magazines such as Discover, where he is a contributing editor and columnist.
BrainMaps.org: High Resolution Brain Atlases
BrainMaps: An Interactive Multiresolution Brain Atlas
An interactive multiresolution brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and integrated with a high-speed database for querying and retrieving data about brain structure and function. Currently featured are complete brain atlas datasets for various species, including Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, Tyto alba and many other vertebrates. BrainMaps is currently accepting histochemical, immunocytochemical, and tracer connectivity data, preferably whole-brain. In addition, they are interested in EM, MRI, and DTI data.
HIV-1 Human Protein Interaction Database
HIV-1: Human Protein Interaction Database
Human immunodeficiency virus type 1 human protein interaction database at NCBI
A database of interactions between HIV-1 and human proteins published in the peer-reviewed literature. The goal is to provide a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. For each HIV-1 human protein interaction the following information is provided: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * PubMed identification numbers (PMIDs) for all journal articles describing the interaction. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the ''HIV-1 protein interactions'' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication.
Artfastqgenerator - Ouputs artificial FASTQ files derived from a reference genome
Software to evaluate and improve the accuracy of sequencing error under different experimental conditions. It can identify which components of a system may be suboptimal and which regions of the genome may be problematic.
A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies.
It Takes 30 - a blog from the Department of Systems Biology (at) Harvard Medical School
Blog about the interests of the Department of Systems Biology at Harvard Medical School. They use tools from physics, mathematics and computer science to help us better understand the behavior of biological systems, large and small. Jobs and postdoc positions are available under the corresponding categories. Interests: * Methods for quantitative measurement, and for data analysis. Although much is said about the flood of new data in biology, nearly every time you want to understand a biological system at a mathematical or mechanical level you find that the numbers you need most are missing. Measuring and extracting the parameters that describe key features of the system is a major interest. * Theoretical and computational methods that can cope with the special features of biological systems. Issues such as combinatorial complexity, stochasticity, and variation from individual to individual and tissue to tissue are hard to deal with using conventional tools. * Philosophies of modeling. How do we represent what we know about the system what level of abstraction is appropriate for a given question, what is important and what can be ignored? What are models useful for? * Evolution. One of the more useful tools to identify what''s important is evolution a comparison across species helps to show what is allowed to change and what is not. * Synthetic biology. If I understand it, can I build it? (And in any case, can I build useful stuff?) They will post thoughts about recent papers in the literature that they find interesting, news about the Department, and information about Department Alumni. Please check back frequently, and feel free to comment.
HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site
Haemophilia A Mutation Structure Test and Resource Site
Haemophilia A Mutation Structure Test Resource Site
HAMSTeRS - The Haemophilia A Mutation Structure Test Resource Site
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2019. Database for those interested in the consequences of Factor VIII genetic variation at the DNA and protein level, it provides access to data on the molecular pathology of haemophilia A. The database presents a review of the structure and function of factor VIII and the molecular genetics of haemophilia A, a real time update of the biostatistics of each parameter in the database, a molecular model of the A1, A2 and A3 domains of the factor VIII protein (based on the crystal structure of caeruloplasmin) and a bulletin board for discussion of issues in the molecular biology of factor VIII. The database is completely updated with easy submission of point mutations, deletions and insertions via e-mail of custom-designed forms. A methods section devoted to mutation detection is available, highlighting issues such as choice of technique and PCR primer sequences. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequences from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Their intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. To submit your mutants to the Haemophilia A Mutation Database email the details. (Refer to Submission Guidelines)
National Cancer Research Institute''s Confederation of Cancer Biobanks
The Confederation of Cancer Biobanks (CCB) is a consortium of organisations based in the UK that are involved in the development, management and use of biobank resources for cancer research. The Confederation aims to promote and disseminate a collective view on best practices for biobanks and to promote transfer of knowledge and experiences between banks. While individual banks retain their full autonomy, membership leads to mutual benefit, ensures complementarities, avoids unnecessary competition and ensures a coordinated approach to cancer biosample provision. This will benefit all involved by allowing the sharing of expertise and information, the establishment of harmonized standards for the operation of cancer biobanks and provide a means to access a larger pool of biosamples from the confederated banks. The initial achievements of the NCRI Confederation of Cancer Biobanks were the drafting of a Memorandum of Understanding for the founder members of the Confederation, and a document outlining the Guiding Principles for the management and operation of a tissue bank / biobank in the contemporary ethical and legal setting. Any organization based in the UK, which collects and distributes biosamples for cancer research (not necessarily in the UK), may apply to join. CCB Members receive: * access to the Members Area of the web site containing shared resources * inclusion in email discussion fora with other members * networking opportunities with other members * inclusion in a collective voice to research funders, policy makers, legislators and others * inclusion in the NCRI''s new on-line sample directory * one free registration for each CCB workshop * a future opportunity to pursue accreditation/quality endorsement for the bank * a potential future opportunity for your donors to join a donor forum, which provides patients/sample donors with a mechanism of keeping in touch with research biobanking activities.
A mini-collection of human gait data that was constructed as a teaching resource for an intensive course (The Modern Science of Human Aging, conducted at MIT) that includes walking stride interval time series from 15 subjects: 5 healthy young adults (23 - 29 years old), 5 healthy old adults (71 - 77 years old), and 5 older adults (60 - 77 years old) with Parkinson's disease. For each subject, two columns of data are included. The first column is time (in seconds) and the second is the stride interval (variously known as stride time, gait cycle duration, and time between successive heel strikes of the same foot). The same data are also available as standard PhysioBank-format annotation (.str) and header (.hea) files, for viewing or analysis using PhysioToolkit software from this site. Subjects walked continuously on level ground around an obstacle-free path. The stride interval was measured using ultra-thin, force sensitive resistors placed inside the shoe. The analog force signal was sampled at 300 Hz with a 12 bit A/D converter, using an ambulatory, ankle-worn microcomputer that also recorded the data. Subsequently, the time between foot-strikes was automatically computed. The method for determining the stride interval is a modification of a previously validated method that has been shown to agree with force-platform measures, a gold standard. Data were collected from the healthy subjects as they walked in a roughly circular path for 15 minutes, and from the subjects with Parkinson's disease as they walked for 6 minutes up and down a long hallway.
Androgen Receptor Gene Mutations Database
Androgen Receptor Gene Mutations Database World Wide Web Server
Comprehensive listing of androgen receptor gene mutations published in journals and meetings proceedings. The majority of mutations are point mutations identified in patients with androgen insensitivity syndrome. Information is included regarding the phenotype, the nature and location of the mutations, as well as the effects of the mutations on the androgen binding activity of the receptor. In light of the difficulty in getting new AR mutations published the curator will now accept new mutations that have not been published, provided that it is from a reputable research or clinical laboratory. The database incorporates information on the exon 1 CAG repeat expansion disease, spinobulbar muscular atrophy (SBMA), as well as CAG repeat length variations associated with risk for female breast, uterine endometrial, colorectal, and prostate cancer, as well as for male infertility. The possible implications of somatic mutations, as opposed to germline mutations, in the development of future locus-specific mutation databases (LSDBs) is discussed. The database now provides information on the external genitalia and on sex - of - rearing. Additionally, the new version of the database has an entry to show if pathogenicity has been proven. A pdf and fully searchable version of the Database is available for download.
TerMine is a Term Management System which identifies key phrases in text. This freely available service may be used from your browser for lightweight uses, through a batch service for processing documents larger than 2MB, via a SOAP Service for integrating TerMine with your applications, or by using the TerMine Plugin for Prot��g�� to access TerMine from within Prot��g�� to help populate your OWL ontologies. Technical terms are important for knowledge mining, especially in the bio-medical area where vast amount of documents are available. The amount of terms (e.g., names of genes, proteins, chemical compounds, drugs, organisms, etc) is increasing at an astounding rate in the bio-medical literature. Existing terminological resources and scientific databases cannot keep up-to-date with the growth of neologisms. A domain independent method for term recognition is very useful to automatically recognize terms from documents. TerMine is the terminological management system with the C-Value term extraction and AcroMine acronym recognition integrated. As a freely available service from the academic domain, it is necessary to limit server load and give preference to individual users. Please contact us in advance if you plan to use the service for bulk processing. Excessive server load may result in IP addresses or institutions being blocked from using the TerMine service. There is a limit enforced on how many times unregistered users may use this service per day. Reference: Frantzi, K., Ananiadou, S. and Mima, H. (2000)Automatic recognition of multi-word terms. International Journal of Digital Libraries 3(2), pp.117-132.
A read mapping software program with adjustable sensitivity based on counting q-grams. RazerS 3 supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers? bit-vector algorithm for verification, memory saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular long reads with many errors.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019. A database that integrates not only RIKEN' '''s original large-scale mammalian databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists' ''' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.
Database that contains measures of gait from 93 patients with idiopathic PD (mean age: 66.3 years; 63% men), and 73 healthy controls (mean age: 66.3 years; 55% men). The database includes the vertical ground reaction force records of subjects as they walked at their usual, self-selected pace for approximately 2 minutes on level ground. Underneath each foot were 8 sensors (Ultraflex Computer Dyno Graphy, Infotronic Inc.) that measure force (in Newtons) as a function of time. The output of each of these 16 sensors has been digitized and recorded at 100 samples per second, and the records also include two signals that reflect the sum of the 8 sensor outputs for each foot. This database also includes demographic information, measures of disease severity (i.e., using the Hoehn & Yahr staging and/or the Unified Parkinson's Disease Rating Scale) and other related measures (available in HTML or xls spreadsheet format). A subset of the database includes measures recorded as subjects performed a second task (serial 7 subtractions) while walking, which shows excerpts of swing time series from a patient with PD and a control subject, under usual walking conditions and when performing serial 7 subtractions. Under usual walking conditions, variability is larger in the patient with PD (Coefficient of Variation = 2.7%), compared to the control subject (CV = 1.3%). Variability increases during dual tasking in the subject with PD (CV = 6.5%), but not in the control subject (CV = 1.2%).
A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs/ligands directed at each of these targets. Also included in this database are links to relevant databases that contain information about the function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and related literatures of each target.This database currently contains 1535 targets and 2107 drugs/ligands. Queries can be submitted by entering or selecting the required information in any one or combination of the five fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field.
Yeast Transcription Factor Specificity Compendium
YeTFaSCo: The Yeast Transcription Factor Specificity Compendium
Collection of all available transcription factor (TF) specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. The specificities are evaluated for quality using several metrics. With this website, you can scan sequences with the motifs to find where potential binding sites lie, inspect precomputed genome-wide binding sites, find which TFs have similar motifs to one you have found, and download the collection of motifs. Submissions are welcome.
Summer School in Computational Sensory-Motor Neuroscience
2012 Summer School in Computational Sensory-Motor Neuroscience
This unique summer school focuses on computational techniques integrating the multi-disciplinary nature of sensory-motor neuroscience through combined empirical-theoretical teaching modules and a focus on the use of databases of movement data (NSF CRCNS). Major breakthroughs in brain research have been achieved through computational models. The goal of the Summer School in Computational Sensory-Motor Neuroscience is to provide cross-disciplinary training in mathematical modelling techniques relevant to understanding brain function, dysfunction and treatment. In a unique approach bridging experimental research, clinical pathology and computer simulations, students will learn how to translate ideas and empirical findings into mathematical models. Students will gain a profound understanding of the brain''s working principles and diseases using advanced modelling techniques in hands-on simulations of models during tutored sessions by making use of data / model sharing. This summer school aims at propelling promising students into world-class researchers. Dates: August 5-19, 2012 Location: Northwestern University Chicago (Evanston campus), Illinois, USA Deadlines: * April 22, 2012: Application due, including letters of reference (extended!!!) * May 1, 2012: Notification of acceptance * May 20, 2012: Attendance confirmation of applicants and registration payment This summer school is directed at graduate students and post-doctoral fellows from multi-disciplinary backgrounds, including Life Sciences, Psychology, Computer Science, Mathematics and Engineering. We will also accept highly motivated outstanding under-graduate students. There are no formal prerequisites, but basic knowledge in calculus, linear algebra, neuroscience and the Matlab simulation environment is expected. Enrollment will be limited to 40 participants.
The official source of information about Google Scholar. Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research.
Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates.
Evaluating Predictors and Interventions in Sphincter of Oddi Dysfunction
Evaluating Predictors & Interventions in Sphincter of Oddi Dysfunction
Evaluating Predictors & Interventions in Sphincter of Oddi Dysfunction (EPISOD)
A prospective, double-blind, randomized, sham-controlled, multi-center clinical trial that enrolls subjects who have received a prior cholecystectomy and are diagnosed with the clinical syndrome of Sphincter of Oddi Dysfunction III (SOD III) as defined by the Rome III criteria. The goal of the study is to asses the value of endoscopic sphincterotomy as a treatment for adult subjects categorized as SOD III suffering from pain after cholecystectomy and to define the role of manometry in treating these patients.
PrimerBank: PCR Primers for Gene Expression Detection and Quantification
Database of human and mouse primer pairs for gene expression analysis by polymerase chain reaction (PCR) and quantitative PCR (qPCR). A total of 306,800 primers covering most known human and mouse genes can be accessed from the PrimerBank database, together with information on these primers such as T(m), location on the transcript and amplicon size. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. All primers in PrimerBank were carefully designed to ensure gene specificity. All experimental validation data for mouse primers are available from PrimerBank. You can submit your primers. They will be added to the database once they are properly QCd.
Database that integrates large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. LifeDB integrates data regarding full length cDNA clones and data on expression of encoded protein and their subcellular localization on mammalian cell line. LifeDB enables the scientific community to systematically search and select genes, proteins as well as cDNA of interest by specific database identifiers as well as gene name. It enables to visualize cDNA clone and subcellular location of proteins. It also links the results to external biological databases in order to provide a broader functional information. LifeDB also provides an annotation pipeline which facilitates an improved mapping of clones to known human reference transcripts from the RefSeq database and the Ensembl database. An advanced web interface enables the researchers to view the data in a more user friendly manner. Users can search using any one of the following search options available both in Search gene and cDNA clones and Search Sub-cellular locations of human proteins: By Keyword, By gene/transcript identifier, By plate name, By clone name, By cellular location. * The Search genes and cDNA clones results include: Gene Name, Ensemble ID, Genomic Region, Clone name, Plate name, Plate position, Classification class, Synonymous SNP''s, Non- synonymous SNP''s, Number of ambiguous positions, and Alignment with reference genes. * The Search sub-cellular locations of human proteins results include: Subcellular location, Gene Name, Ensemble ID, Clone name, True localization, Images, Start tag and End tag. Every result page has an option to download result data (excluding the microscopy images). On click of ''Download results as CSV-file'' link in the result page the user will be given a choice to open or save result data in form of a CSV (Comma Separated Values) file. Later the CSV file can be easily opened using Excel or OpenOffice.
diARK- a resource for eukaryotic genome resources
diArk provides access to eukaryotic sequencing projects that have resulted in genome assemblies or cDNA/EST datasets. It gives users a comprehensive search module, as well as detailed options and three different views of the selected data. We have done our best to include all eukaryotic sequencing projects in the world that provide assembled genomic data or a considerable amount of cDNA/EST data.
Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology
Issues guidelines for nomenclature and classification of human biological targets, including targets of current and future prescription medicines. Works to facilitate interface between discovery of new sequences from Human Genome Project and designation of derived entities as functional biological targets and potential drug targets. Developes database which provides access to data on all known biological targets.
Surveillance Epidemiology and End Results
Surveillance Epidemiology and End Results (SEER) Program
Surveillance Epidemiology End Results (SEER) Program
SEER collects cancer incidence data from population-based cancer registries covering approximately 47.9 percent of the U.S. population. The SEER registries collect data on patient demographics, primary tumor site, tumor morphology, stage at diagnosis, and first course of treatment, and they follow up with patients for vital status.There are two data products available: SEER Research and SEER Research Plus. This was motivated because of concerns about the increasing risk of re-identifiability of individuals. The Research Plus databases require more rigorous process for access that includes user authentication through Institutional Account or multiple-step request process for Non-Institutional users.
pythonxy - Scientific-oriented Python Distribution based on Qt and Spyder
y) - Scientific oriented Python Distribution based on Qt and Spyder
Scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment. Used to interpreted languages (such as MATLAB or IDL) or compiled languages (C/C++ or Fortran) to switch to Python.
VU National Research Resource for Imaging Mass Spectrometry
Vanderbilt University National Research Resource for Imaging Mass Spectrometry
National Research Resource for Imaging Mass Spectrometry
Biomedical technology research center that advances the technology of Imaging Mass Spectrometry, facilitates the application of this novel imaging modality to problems of biological and clinical significance, and promotes the adoption of these technologies by a larger community of scientists and clinicians. Technical innovations include next-generation hardware, software and methods. Technology development is conducted by an interdisciplinary team of scientists and engineers, both within the Resource and through collaborative relationships with other universities, research institutes, and private industry. Development milestones are guided by Driving Biological Projects that require specific advancements in Imaging Mass Spectrometry in order to address biological problems. By working together, they anticipate new insights into these biological systems and a better understanding of health and disease at the molecular level that translates to improved patient care. The training mission of the Resource is accomplished through a variety of educational programs where Resource scientists and collaborators share their knowledge and experience with those interested in learning more about the technology.
An open source tool to help researchers document, manage, and archive their tabular data that integrates with Microsoft Excel. The tool will parse .xlsx or .csv file to detect the presence of potential issues that do not comply with data management best practices, assign a unique identifier to a data set and deposit it within the DataONE repository system.
Software programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits.
UCSD-Nature Signaling Gateway Molecule Pages
Alliance for Cellular Signaling Molecule Pages Database
Molecule Pages: A comprehensive signaling database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Relational database of all significant published qualitative and quantitative information on cell signaling proteins. The Molecule Pages database was developed with the specific aim of allowing interactions, and indeed whole pathways, to be modeled. The goal is to filter the data to present only validated information. In addition, the Gateway is the home of Signaling Update, which provides a one-stop overview of the latest and hottest research in cell signaling for both the specialist and non-specialist alike.
Pattern Recognition for Neuroimaging Toolbox
PRoNTo (Pattern Recognition for Neuroimaging Toolbox)
PRoNTo - Pattern Recognition for Neuroimaging Tool
A software toolbox based on pattern recognition techniques for the analysis of neuroimaging data. Statistical pattern recognition is a field within the area of machine learning which is concerned with automatic discovery of regularities in data through the use of computer algorithms, and with the use of these regularities to take actions such as classifying the data into different categories. In PRoNTo, brain scans are treated as spatial patterns and statistical learning models are used to identify statistical properties of the data that can be used to discriminate between experimental conditions or groups of subjects (classification models) or to predict a continuous measure (regression models).
National Center for Advancing Translational Sciences Pharmaceutical Collection
National Institutes of Health Chemical Genomics Center Pharmaceutical Collection
NIH Chemical Genomics Center Pharmaceutical Collection
The NCGC Pharmaceutical Collection (NPC) is a comprehensive, publically-accessible collection of approved and investigational drugs for high-throughput screening that provides a valuable resource for both validating new models of disease and better understanding the molecular basis of disease pathology and intervention. The NPC has already generated several useful probes for studying a diverse cross section of biology, including novel targets and pathways. NCGC provides access to its set of approved drugs and bioactives through the Therapeutics for Rare and Neglected Diseases (TRND) program and as part of the compound collection for the Tox21 initiative, a collaborative effort for toxicity screening among several government agencies including the US Environmental Protection Agency (EPA), the National Toxicology Program (NTP), the US Food and Drugs Administration (FDA), and the NCGC. Of the nearly 2750 small molecular entities (MEs) that have been approved for clinical use by US (FDA), EU (EMA), Japanese (NHI), and Canadian (HC) authorities and that are amenable to HTS screening, we currently possess 2,400 as part of our screening collection. The NPC resource currently consists of (i) the physical collection suitable for high throughput screening (HTS) and (ii) the informatics browser and database. Putting together the physical collection has been surprisingly challenging in terms of the time and effort required in the informatics, compound management and synthetic chemistry related activities required for this endeavor. We provide access to the NPC screening library through collaboration. Please contact our Scientific Director Dr. Chris Austin for additional information. The other half of the NPC resource is the NPC browser. This is a self-contained software that is actively developed and maintained by the informatics group to provide electronic access to the NPC content. The latest version of the NPC browser for various platforms can be downloaded.
The collection of chapters in this eBook is written to provide guidance to investigators who are interested in developing assays useful for the evaluation of collections of molecules to identify probes that modulate the activity of biological targets, pathways, and cellular phenotypes. These probes may be candidates for further optimization and investigation in drug discovery and development. Originally written as a guide for therapeutic project teams within a major pharmaceutical company, this manual has been adapted to provide guidelines for scientists in academic, non-profit, government and industrial research laboratories to develop potential assay formats compatible with High Throughput Screening (HTS) and Structure Activity Relationship (SAR) measurements of new and known molecular entities. Topics addressed in this manual include: * Development of optimal assay reagents. * Optimization of assay protocols with respect to sensitivity, dynamic range, signal intensity and stability. * Adopting screening assays from bench scale assays to automation and scale up in microtiter plate formats. * Statistical concepts and tools for validation of assay performance parameters. * Secondary follow up assay development for chemical probe validation and SAR refinement. * Data standards to be followed in reporting screening and SAR assay results. * Glossaries and definitions. This manual will be continuously updated with contributions from experienced scientists from multiple disciplines working in drug discovery & development worldwide. An open submission and review process will be implemented in the near future on this eBook website, hosted by the National Library of Medicine with content management by the National Center for Advancing Translational Sciences (NCATS, http://ncats.nih.gov/), the newest component of the National Institutes of Health (NIH).
University of Tennessee Memphis School of Medicine Department of Pharmacology, Addiction Science, and Toxicology
The Department of Pharmacology, a dynamic scholarly environment dedicated to teaching, training, and fundamental discovery, is engaged in numerous collaborations that enhance our research efforts and broaden our training opportunities. To meet the research objectives of our students and faculty, the Department has acquired advanced technologies that enable investigators to take integrative and molecular approaches to their work.
LOLA is a web driven database of published and manually curated (public), and user-specific (private) gene lists derived from genome-wide approaches such as expression profiling and proteomics. LOLA allows researchers to measure the similarity of gene lists in order to identify genes that are robustly changed across laboratories, studies, and platforms, and within and between species. Furthermore, LOLA compares lists at a gene-level so that probes mapping to the same gene are not considered different.
Noise Enhancement of Sensorimotor Function
Data set of postural sway measurements for 15 healthy young (mean age 23, standard deviation 2), and 12 healthy elderly (mean age 73, standard deviation 3) volunteers. Each subject''s postural sway was recorded during a test of 10 minutes for the young subjects, or 5 minutes for the elderly subjects, in all cases with a 2-minute seated break midway through the test. Each test was divided into 30-second trials, and each file of the database contains data for one of these 30-second trials.
A multilingual database that provides large time-series and cross sectional data relating to hunger, food, agriculture, nutrition, fisheries, forestry and food aid by country and region from 1961 to present. Data can be searched, browsed, analyzed and downloaded.
Adult Blood Lead Epidemiology and Surveillance Interactive Database
Adult Blood Lead Epidemiology and Surveillance (ABLES) Interactive Database
Interactive data set on lead exposure (Blood Lead Concentrations greater than or equal to 25 micrograms per deciliter) of adults in the United States. The data comes from laboratory-reported elevated blood lead levels. Recent research has led to increased concerns about the toxicity of lead at low doses. Reflecting this increased concern, the ABLES program updated its case definition for an elevated BLL to a blood lead concentration greater than or equal to 10 micrograms per deciliter in 2009. This new case definition has also been: (1) recommended by the Council of State and Territorial Epidemiologists in 2009; (2) included in CDC''s list of nationally notifiable conditions in 2010; and (3) adopted as the Healthy People 2020 Occupational Safety and Health Objective 7. Given this new case definition, NIOSH will update the ABLES Charts and Interactive Database to include lead exposures to blood lead level greater than or equal to 10 micrograms per deciliter in the near future.
CROP: Clustering 16S rRNA For OTU Prediction
A clustering tool designed mainly for Metagenomics studies, which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU). By using a Gaussian Mixture model, CROP can automatically determine the best clustering result for 16S rRNA sequences at different phylogenetic levels without setting a hard cutoff threshold as hierarchical clustering does. Yet, at the same time, it is able to manage large datasets and to overcome sequencing errors.
BioCarta Pathways allows users to observe how genes interact in dynamic graphical models. Online maps available within this resource depict molecular relationships from areas of active research. In an open source approach, this community-fed forum constantly integrates emerging proteomic information from the scientific community. It also catalogs and summarizes important resources providing information for over 120,000 genes from multiple species. Find both classical pathways as well as current suggestions for new pathways.
SIU CADRD Dementia Brain Autopsy Program
SIU School of Medicine Dementia Brain Autopsy Program
A brain autopsy program developed to serve the needs of Illinois families and individuals affected by dementing diseases and to advance dementia research by providing tissue to researchers studying dementing diseases. The SIU School of Medicine (SIU-SM) Dementia Brain Autopsy Program facilitates the postmortem process for families wishing to obtain an autopsy for a loved one. A brain autopsy provides family members with accurate information regarding the exact nature of their relative's dementia. This includes information about the possibility of an inherited disorder which may affect other family members. The brain autopsy also helps clinicians improve their clinical skills by identifying the precise cause of the clinical dementia.
A package that implements several semantic similarity measures. It is both a library and an end-user application, featuring an intuitive graphical user interface (GUI). It has been implemented with the aim of being fast, expandable, and easy to use. It allows the user to work with the most updated version of GO database and customizable annotation corpora. It provides a set of logically-organized classes that can be easily exploited to both integrate semantic similarity into different analysis pipelines and extend the library with new measures. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
The NICHD Study of Early Child Care and Youth Development
It is the most comprehensive child care study conducted to date to determine how variations in child care are related to children''s development. The NICHD SECCYD is a longitudinal study initiated by The National Institute of Child Health and Human Development (NICHD) in 1989 to answer the many questions about the relationship between child care experiences and characteristics and children''s developmental outcomes. After a thorough scientific review, the NICHD selected a research team located at universities across the U.S., and at the NICHD, together providing multiple perspectives on and interests in child care research. The network was led and managed by a Steering Committee which included an independent chairperson, one representative from each of the grantee sites, one representative from the data center and one representative from NICHD. The Steering Committee established policies and procedures that governed the operations of the network, including its publication procedures. The progress of the study was monitored by NICHD and by the Steering Committee with guidance from an Advisory Board which was nominated by the Director of NICHD. This team of researchers worked cooperatively to design and implement the study, and in 1991, enrolled a very diverse sample of children and their families at 10 locations across the U.S. The NICHD SECCYD is characterized by a complex and detailed study design which takes into account many variables, including characteristics of the child care and the family environment. Researchers assessed children''s development using multiple methods (trained observers, interviewers, questionnaires, and testing) and measuring many facets of children''s development (social, emotional, intellectual, language development, behavioral problems and adjustment, and physical health). The 1,364 children and their families enrolled in the study were followed from birth to age 3 years during Phase I of the study from 1991-1994. Phase II of the study was conducted between 1995-2000 to follow the 1226 children and families continuing to participate from age 54 months through their second year in school. Phase III of the study was conducted between 2000 - 2005 to follow over 1100 of the children through their seventh year in school. Phase IV was conducted between 2006 2007 to follow over 1000 of the original families through age 15. The NICHD SECCYD was conducted by a network of investigators, the NICHD Early Child Care Research Network. You may view information regarding data assessments, study publications, as well as a listing of the study researchers and committee members on the study website located at http://secc.rti.org. Qualified researchers are able to become affiliates with the study to utilize data from all phases of the study. As of January 2009, the Inter-University Consortium for Political and Social Research (ICPSR) at the University of Michigan assumed responsibility for the administration of data use agreements for the Phase I IV data. The ICPSR Data Use Agreement can be found at the following location: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/21940/documentation. If you have questions regarding the ICPSR process, please contact Russel Hathaway at rhataway (at) umich.edu.
A digital image database of serially sectioned human embryos from the Carnegie Collection originally developed as a collaboration between embryologist Dr. Raymond Gasser at Louisiana State University Health Science Center (LSUHSC) and the Human Developmental Anatomy Center (HDAC) in Washington D.C. The aim of the project is to increase understanding of human embryology and to encourage study of human embryonic development by providing students and researchers with reliable resources for human embryo morphology. The VHE project has several components: * DREM: The Digitally Reproduced Embryonic Morphology (DREM) project, with funding from NICHD, project has produced 27 image databases of labeled serial sections from representative human embryos at each of the 23 Carnegie stages. These databases, together with animations and reconstructions of the embryos are available on DVD and CD. * HEIRLOOM: The HEIRLOOM Collection (Human Embryo Imaging and Reconstruction, Library Of Online Media) was funded by the National Library of Medicine to provide greater access to the DREM databases. NLM provided funding to set up this website and to produce additional 3D-reconstructions and animations that are included on the DREM disks. Original website, http://virtualhumanembryo.lsuhsc.edu/HEIRLOOM/heirloom.htm * EHD: Starting in 2011, The Endowment for Human Development (EHD) will also host the VHE databases. They have made the project accessible to everyone and include a comprehensive cataloging of all the terms used to label the embryos. Their website enables users to browse through the complete VHE atlas of human embryology, http://www.ehd.org/virtual-human-embryo/
Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.
Service that disambiguates acronyms from Medline in text through your browsers; or use the RESTful Service for integrating it with your applications. Reference: Okazaki, N., Ananiadou, S. and Tsujii, J. (2010). Building a High Quality Sense Inventory for Improved Abbreviation Disambiguation.Bioinformatics, Oxford University Press.
A structured controlled vocabulary of Caenorhabditis elegans phenotypes.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. Software tool that facilitates the analysis of the 3D structure of spine insertions in dendrites, providing insight on spine distribution patterns. Dispine depends on python 2.6, PyQt4, numpy, python wrappers of VTK and pygame. If you want to test the tool, a test set is provided.
A computational pipeline bringing together numerous software packages to perform a full analysis of MeDIP-seq data, including sequence alignment, quality control (QC), and determination and annotation of DMRs.
It is a Brazilian face database that contains a set of face images taken between June 2005 and March 2006 at the Artificial Intelligence Laboratory of FEI in So Bernardo do Campo, So Paulo, Brazil. There are 14 images for each of 200 individuals, a total of 2800 images. All images are colourful and taken against a white homogenous background in an upright frontal position with profile rotation of up to about 180 degrees. Scale might vary about 10 and the original size of each image is 640x480 pixels. All faces are mainly represented by students and staff at FEI, between 19 and 40 years old with distinct appearance, hairstyle, and adorns. The number of male and female subjects are exactly the same and equal to 100. Figure 1 shows some examples of image variations from the FEI face database. In addition, we provide a subset of the FEI face database composed of only frontal face images previously aligned to a common template so that the pixel-wise features extracted from the images correspond roughly to the same location across all subjects. In this manual alignment, we have randomly chosen the frontal image of a subject as template and the directions of the eyes and nose as a location reference. All these frontal images were then cropped to the size of 360x260 pixels. Since the number of subjects is equal to 200 and each subject has two frontal images (one with a neutral or non-smiling expression and the other with a smiling facial expression), there are 400 full frontal face images manually registered to evaluate experiments on a controlled environment. More recently, with the support of CNPq under the grant 472386/2007-7, we have proposed and implemented a sequence of image processing steps to automatically normalize frontal face images. A computational tool has been developed to minimize image variations due to the acquisition protocol. Figure 2 shows the average face images of the neutral (left) and smiling (right) facial expressions before and after the normalization. We believe that this additional set of frontal face images is particularly useful for evaluating experiments on synthesizing realistic expressions and aging estimation in 2D face data sets.
Arabidopsis Gene Regulatory Information Server
An information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB).
Diabetes Autoantibody Standardization Program
Diabetes Autoantibody Standardization Program (DASP)
Program that develops materials and methods to improve measurements of autoantibodies that are predictive of type 1 diabetes. These are the most sensitive and meaningful measures for predicting this disease. Historically, autoantibody measures have been variable among laboratories; therefore, this program, in collaboration with the Immunology of Diabetes Society, was established. The goals of DASP are to improve laboratory methods, evaluate laboratory performance, support the development of sensitive and specific measurement technologies, and develop reference methods. Currently, 48 key laboratories from 19 countries participate in DASP.
A database of sequence alignments and phylogenetic trees for chordates and embryophytes. The Adaptive Evolution Database (TAED) was first presented as a collection of branches from chordate and embryophyte gene families with fast evolutionary rates mapped onto the NCBI taxonomy (1,2). The original gene families were from the Master Catalog and are proprietary (3). A new version of TAED is now presented as a taxonomic shell together with a gene family database. In addition to multiple sequence alignments and phylogenetic trees for all families of chordate and embryophyte sequences, the ratio of non-synonymous to synonymous nucleotide substitution rates (Ka/Ks) is provided for each branch of every phylogenetic tree. This ratio, when significantly greater than 1, is an indicator of positive selection and potentially a change of function of the encoded protein. With a gene tree to species tree mapping, the branches significantly greater than 1 are collated together in a phylogenetic context. The framework is expandable to incorporate other genomic-scale information in a phylogenetic context. Ultimately, the database is designed both to provide high-quality gene families with multiple sequence alignments and phylogenetic trees for chordates and embryophytes, and to enable asking the question, What makes each species unique at the molecular genomic level?
ImMunoGeneTics/Laboratoire d''ImmunoGenetique Moleculaire-Database
IMGT/LIGM-DB is a comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate species (270). IMGT/LIGM-DB includes all germline (non-rearranged) and rearranged IG and TR genomic DNA (gDNA) and complementary DNA (cDNA) sequences published in generalist databases. IMGT/LIGM-DB allows searches from the Web interface according to biological and immunogenetic criteria through five distinct modules depending on the user interest. Users can search the catalogue by accession number, mnemonic, definition, creation date, length, or annotation level. They also have the option to search through taxonomic classification, keywords, and annotated labels. For a given entry, nine types of display are available including the IMGT flat file, the translation of the coding regions and the analysis by the IMGT/V-QUEST tool (see parent org. below). IMGT/LIGM-DB distributes expertly annotated sequences. The annotations hugely enhance the quality and the accuracy of the distributed detailed information. They include the sequence identification, the gene and allele classification, the constitutive and specific motif description, the codon and amino acid numbering, and the sequence obtaining information, according to the main concepts of IMGT-ONTOLOGY. They represent the main source of IG and TR gene and allele knowledge stored in IMGT/GENE-DB and in the IMGT reference directory., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
DARC - Database for Aligned Ribosomal Complexes
Database for Aligned Ribosomal Complexes
Database for Aligned Ribosomal Complexes (DARC)
A database for aligned ribosomal complexes that provides a resource for directly comparing the structures. A collection of files deposited in the RCSB protein data bank and the Electron Microscopy Data Bank have been aligned so as to make direct comparison of the structures possible. An easy-to-use, searchable interface allows users to access and download >130 cryo-EM maps and >300 atomic models in the format of brix and pdb files, respectively. The aligned coordinate system substantially simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.
Ocean Biogeographic Information System Marine
Accepts and provides access to biogeographic data collected throughout the global oceans. The datasets are integrated so you can search them all seamlessly by species name, higher taxonomic level, geographic area, depth, and time; and then map and find environmental data related to the locations. Created by the Census of Marine Life, OBIS is now part of the Intergovernmental Oceanographic Commission (IOC) of UNESCO, under its International Oceanographic Data and Information Exchange (IODE) programme
A web-based, interactive brain atlas viewer, containing a growing number of atlas templates for various species, including mouse, macaque and human. Standard features include fast brain region lookup, point and click to select a region and view its full 3D extent, mark a stereotaxic coordinate and view all regions in a hierarchy. Built-in extensions are the CoCoMac plugin, which provides a spatial display of Macaque connectivity, and a service to transform stereotaxic coordinates to and from the INCF Waxholm space for the mouse. Three dimensional renderings of brain regions are available through a Matlab interface (local installation of Matlab required). The SBA is designed to be customizable. External users can create plugins, hosted on their own servers, to interactively attach images or data to spatial atlas locations. This fully web-based display engine for brain atlases and topologies allows client websites to show brain region related data in a 3D interactive context. Currently available atlases are: * Macaque: The Paxinos Rhesus Monkey atlas (2000) * Macaque: Various templates available through Caret, registered to F99 space: Felleman and Van Essen (1991), Lewis and Van Essen (2000), Regional Map from K��tter and Wanke (2005), Paxinos Rhesus Monkey (2000) * Macaque: The NeuroMaps Macaque atlas (2008) * Mouse: The INCF Waxholm Space for the mouse (2011). Previous versions available. * Mouse: The Allen Mouse Brain volumetric atlas (ABA07) * Human: The LPBA40 parcellation, registered to SRI24 space A variety of services are being developed around the templates contained in the Scalable Brain Atlas. For example, you can include thumbnails of brain regions in your own webpage. Other applications include: * Analyze atlas templates in Matlab * List all regions belonging to the given template * List of supported atlas templates * Find region by coordinate * Color-coded PNG (bitmap) or SVG (vector) image of a brain atlas slice * Region thumbnail in 2D (slice) or 3D (stack of slices) The Scalable Brain Atlas is created by Rembrandt Bakker and Gleb Bezgin, under supervision of Rolf K��tter in the NeuroPhysiology and -Informatics group of the Donders Institute, Radboud UMC Nijmegen.
Open source software system for capturing, storing and analyzing raw phenotyping data from SOPs contained in EMPReSS, it provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centers. Mutants of interest can be identified by searching the gene or the predicted phenotype. You can also access phenotype data from the EMPReSSlim Pipeline for inbred mouse strains. Initially EuroPhenome was developed within the EUMORPHIA programme to capture and store pilot phenotyping data obtained on four background strains (C57BL/6J, C3H/HeBFeJ, BALB/cByJ and 129/SvPas). EUMORPHIA (European Union Mouse Research for Public Health and Industrial Applications) was a large project comprising of 18 research centers in 8 European countries, with the main focus of the project being the development of novel approaches in phenotyping, mutagenesis and informatics to improve the characterization of mouse models for understanding human molecular physiology and pathology. The current version of EuroPhenome is capturing data from the EUMODIC project as well as the WTSI MGP, HMGU GMC pipeline and the CMHD. EUMODIC is undertaking a primary phenotype assessment of up to 500 mouse mutant lines derived from ES cells developed in the EUCOMM project as well as other lines. Lines showing an interesting phenotype will be subject to a more in depth assessment. EUMODIC is building upon the comprehensive database of standardized phenotyping protocols, called EMPReSS, developed by the EUMORPHIA project. EUMODIC has developed a selection of these screens, called EMPReSSslim, to enable comprehensive, high throughput, primary phenotyping of large numbers of mice. Phenovariants are annotated using a automated pipeline, which assigns a MP term if the mutant data is statistically different to the baseline data. This data is shown in the Phenomap and the mine for a mutant tool. Please note that a statistically significant result and the subsequent MP annotation does not necessarily mean a true phenovariant. There are other factors that could cause this result that have not been accounted for in the analysis. It is the responsibility of the user to download the data and use their expert knowledge or further analysis to decide whether they agree or not. EuroPhenome is primarily based in the bioinformatics group at MRC Harwell. The development of EuroPhenome is in collaboration with the Helmholtz Zentrum Munchen, Germany, the Wellcome Trust Sanger Institute, UK and the Institut Clinique de la Souris, France.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The T-DB contains millions of structural alignments between all proteins in the PDB as of July 2005 found by the TOPOFIT method. Structural neighbors to the query protein structure can be retrieved by the PDB code and chain id. Pairwise or multiple structural alignments can be visualized in 3D with the FRIEND software. In the TOPOFIT method, similarity of protein structures is analyzed using three-dimensional Delaunay triangulation patterns derived from backbone representation. It has been found that structurally related proteins have a common spatial invariant part, a set of tetrahedrons, mathematically described as a common spatial sub-graph volume of the three-dimensional contact graph derived from Delaunay tessellation (DT). Based on this property of protein structures we present a novel common volume superimposition (TOPOFIT) method to produce structural alignments of proteins. The superimposition of the DT patterns allows one to uniquely identify a common number of equivalent residues in the structural alignment, in other words, TOPOFIT identifies a feature point on the RMSD/Ne curve, a topomax point, until which two structures correspond to each other including backbone and inter-residue contacts, while the growing number of mismatches between the DT patterns occurs at larger RMSD (Ne) after topomax point. The topomax point is present in all alignments from different protein structural classes; therefore, the TOPOFIT method identifies common, invariant structural parts between proteins. The TOPOFIT method adds new opportunities for the comparative analysis of protein structures and for more detailed studies on understanding the molecular principles of tertiary structure organization and functionality. It helps to detect conformational changes, topological differences in variable parts, which are particularly important for studies of variations in active/binding sites and protein classification.
Genetic factors contribute significantly to ASD. AutismKB is an evidence-based knowledgebase of Autism spectrum disorder (ASD) genetics. The current version contains 2193 genes (99 syndromic autism related genes and 2135 non-syndromic autism related genes), 4617 Copy Number Variations (CNVs) and 158 linkage regions associated with ASD by one or more of the following six experimental methods: # Genome-Wide Association Studies (GWAS); # Genome-wide CNV studies; # Linkage analysis; # Low-scale genetic association studies; # Expression profiling; # Other low-scale gene studies. Based on a scoring and ranking system, 99 syndromic autism related genes and 383 non-syndromic autism related genes (434 genes in total) were designated as having high confidence. Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder with a prevalence of 1.0-2.6%. The three core symptoms of ASD are: # impairments in reciprocal social interaction; # communication impairments; # presence of restricted, repetitive and stereotyped patterns of behavior, interests and activities.
Schizophrenia Research Forum: Published Candidate Genes for Schizophrenia
SZGene(SchizophreniaGene): Field Synopsis of Genetic Association Studies in SZ
The SZGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in schizophrenia. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data. Eligible publications are identified following systematic searches of scientific literature databases, as well as the table of contents of journals in genetics and psychiatry. The database can be searched either by a variety of dropdown menus or by specific keywords. For each gene, summary overviews are provided displaying key characteristics for each publication, including links to genotype distributions of the polymorphisms studied, random-effects allelic meta-analyses, and funnel plots for an assessment of publication bias.
This genomic tRNA database contains tRNA gene predictions made by the program tRNAscan-SE (Lowe & Eddy, Nucl Acids Res 25: 955-964, 1997) on complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been inspected for agreement with published literature. Transfer RNAs (tRNAs) represent the single largest, best-understood class of non-protein coding RNA genes found in all living organisms. By far, the major source of new tRNAs is computational identification of genes within newly sequenced genomes. To organize the rapidly growing collection and enable systematic analyses, we created the Genomic tRNA Database (GtRNAdb). The web resource provides overview statistics of tRNA genes within each analyzed genome, including information by isotype and genetic locus, easily downloadable primary sequences, graphical secondary structures and multiple sequence alignments. Direct links for each gene to UCSC eukaryotic and microbial genome browsers provide graphical display of tRNA genes in the context of all other local genetic information. The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group. Inevitably with automated sequence analysis, we find exceptions to general identification rules, isoacceptor type predictions (esp. due to variable post-transcriptional anticodon modification), and questionable tRNA identifications (due to pseudogenes, SINES, or other tRNA-derived elements). We attempt to document all cases we come across, and welcome feedback on new or unrecognized discrepancies.
Southern Illinois University School of Medicine Department of Pharmacology
Pharmacology research teams and faculty study mechanisms of disease, develop and test novel drug therapies and seek to understand and prevent drug interactions. They also educate and train medical students, graduate students, residents and fellows in field of pharmacology.
Collection of tools developed by GO Consortium and by third parties. Tools are listed by category or alphabetically and continue to be improved and expanded.
Project to map the neural pathways that underlie human brain function for several modalities of neuroimaging data including fMRI. The purpose of the Project is to acquire and share data about the structural and functional connectivity of the human brain. It will greatly advance the capabilities for imaging and analyzing brain connections, resulting in improved sensitivity, resolution, and utility, thereby accelerating progress in the emerging field of human connectomics. Altogether, the Human Connectome Project will lead to major advances in the understanding of what makes us uniquely human and will set the stage for future studies of abnormal brain circuits in many neurological and psychiatric disorders. The sixteen institutes and centers of the NIH Blueprint for Neuroscience have funded two major grants that will take complementary approaches to deciphering the brain's amazingly complex wiring diagram. An 11-institution consortium led by Washington University in St. Louis and the University of Minnesota received a 5-year grant to enable development and utilization of advanced Magnetic Resonance Imaging (MRI) methods to chart brain circuitry. A consortium led by Massachusetts General Hospital and the University of California at Los Angeles received a grant to enable building and refining a next-generation 3T MR scanner that improves the quality and spatial resolution with which brain connectivity data can be acquired at this field strength.
GeneCodis - Gene annotations co-ocurrence discovery
Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available.
CPTAC Proteomics Pipeline Infrastructure Ontology
A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project
A database of proteins identified by various 2-D PAGE and SDS-PAGE reference maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data (isoelectric point, molecular weight, amino acid composition, peptide masses) and bibliographical references. In addition to this textual data, SWISS-2DPAGE provides several 2-D PAGE and SDS-PAGE images showing the experimentally determined location of the protein, as well as a theoretical region computed from the sequence protein, indicating where the protein might be found in the gel. Using the database, users can locate these proteins on the 2-D PAGE maps or display the region of a 2-D PAGE map where one might expect to find a protein from UniProtKB/Swiss-Prot.
An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries .
Minnesota Center for Twin and Family Research
Composed of many projects, including the Minnesota Twin Family Study (MTFS) and The Sibling Interaction and Behavior Study (SIBS), this research center seeks to identify genetic and environmental influences on development and psychological traits. Both projects are longitudinal research studies including twins, siblings, and parents. Over 9800 individuals have contributed to these exciting projects! By studying twins and siblings and their families, we can estimate how genes and environment interact to influence character, strengths, vulnerabilities and values. Participants in the MTFS include families with same-sex identical or fraternal twins who were born in Minnesota. The SIBS study is comprised of adoptive and biological siblings and their parents. Most participants partake in day-long visits to the MCTFR, and due to the longitudinal nature of our projects, they return every 3-4 years for follow-up visits.
Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them.
A Monte Carlo (MC) solver for photon migration in 3D turbid media. Different from existing MC software designed for layered (such as MCML) or voxel-based media (such as MMC or tMCimg), MMC can represent a complex domain using a tetrahedral mesh. This not only greatly improves the accuracy of the solutions when modeling objects with smooth/complex boundaries, but also gives an efficient way to sample the problem domain to use less memory. The current version of MMC support multi-threaded programming and can give a almost proportional speed-up when using multiple CPU cores.
Myrna: Cloud-scale differential gene expression for RNA-seq
A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.
FunSpec is a web-based tool for statistical evaluation of groups of genes and proteins (e.g. co-regulated genes, protein complexes, genetic interactors) with respect to existing annotations, including GO terms. FunSpec (an acronym for Functional Specification) inputs a list of yeast gene names, and outputs a summary of functional classes, cellular localizations, protein complexes, etc. that are enriched in the list. The classes and categories evaluated were downloaded from the MIPS Database and the GO Database . In addition, many published datasets have been compiled to evaluate enrichment against. Hypertext links to the publications are given. The p-values, calculated using the hypergeometric distribution, represent the probability that the intersection of given list with any given functional category occurs by chance. The Bonferroni-correction divides the p-value threshold, that would be deemed significant for an individual test, by the number of tests conducted and thus accounts for spurious significance due to multiple testing over the categories of a database. After the Bonferroni correction, only those categories are displayed for which the chance probability of enrichment is lower than: p-value/#CD where #CD is the number of categories in the selected database. Without the Bonferroni Correction, all categories are displayed for which the same probability of enrichment is lower than: p-value threshold in an individual test Note that many genes are contained in many categories, especially in the MIPS database (which are hierarchical) and that this can create biases for which FunSpec currently makes no compensation. Also the databases are treated as independent from one another, which is really not the case, and each is searched seperately, which may not be optimal for statistical calculations. Nonetheless, we find it useful for sifting through the results of clustering analysis, TAP pulldowns, etc. Platform: Online tool
Cancer Research and Management ACGT Master Ontology
Ontology to represent the domain of cancer research and management in a computationally tractable manner.
A computational pipeline for the analysis of MethylSeq experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Provide quality human tissue grafts for transplantation, research or education through the compassionate support of families, outreach and education to communities. The Allograft Resources Tissue Bank was developed to fill a particular need within a single hospital in the San Antonio area. The tissue industry, as a whole, had persistently struggled with fulfilling the need for cryopreserved heart valves for the pediatric Cardiothoracic program at University Hospital. The region serviced by the University of Texas Health Science Center at San Antonio medical school and the University Hospital has a high population of pediatric patients with cardiothoracic anomalies which require pediatric heart surgery. From this need the Allograft Resource Program was developed and has continued to grow rapidly. The Allograft Resource Program has continued to add services as demanded by the local community and now offers a vast array of services to include compliance assistance, recovery services, bereavement support, and location and delivery of difficult to find grafts for implantation.
Mental Illness Research Education and Clinical Center
The Mental Illness Research, Education and Clinical Centers (MIRECC) were established by Congress with the goal of researching the causes and treatments of mental disorders and using education to put new knowledge into routine clinical practice in the VA. Congress established MIRECCs in October 1996 through Public Law 104-262. There are currently 10 MIRECCs. Each MIRECC focuses on mental illnesses or conditions that are common in Veterans. MIRECCs investigate the causes of mental illness, develop new treatments for mental illness, and evaluate both established and new treatments with the goal of identifying best practices. The MIRECCs also develop educational and training initiatives to implement best practices into the clinical settings of the VA. Each MIRECC works with all the facilities in its network (region) on research, education and clinical initiatives, evaluating services offered to the Veteran and helping the networks implement improved treatments, services, or practices. Several educational products are posted on this site on the Products page. These materials are in the public domain and available for your use. Many MIRECCs have additional materials that can be downloaded from their web sites or are available by request.
This is MATLAB library to create Neuroshare data format. You can convert your own data into Neuroshare format file.
NIMH DIRP Scientific and Statistical Computing Core
DIRP Scientific and Statistical Computing Core
NIMH DIRP Scientific Statistical Computing Core
Scientific and Statistical Computing Core
Scientific and Statistical Computing Core of the NIMH Intramural Research Program supporting functional neuroimaging research at the NIH. This includes development of new data analysis techniques, their implementation in the AFNI software, advising researchers on the analysis methods, and instructing them in the use of software tools. Support methods: A. Provision of software for analysis for FMRI data (AFNI package: http://afni.nimh.nih.gov) * AFNI has been developed for the last 10 years by Dr Cox, et al. (6 years in Milwaukee, 4 years at NIMH) * Formal and informal instruction in the use of AFNI, including outlines of the statistical methods used in the programs * Installation of AFNI on NIH computers (Mac OS X, Unix, Linux) approximately 120 NIH systems have used AFNI in the last month (80 NIMH, 20 NINDS, 20 other) * Realtime monitoring of FMRI data at scanners * Continuing development of new modules for AFNI to meet needs of NIH researchers B. Consulting with NIH researchers about FMRI data analysis issues, concerns, and methods
Minimum Information about a Genotyping Experiment
Standard specification for the information required to report a genotyping experiment, covering: study and experiment design, subject information, genotyping procedure, and data analysis methods. The goal is to set a reporting standard for adoption by the research community to facilitate consistent data interpretation and independent validation/reproduction, and to serve as guidance for database design for storing genotyping experiment data. MIGen is being developed as a collaborative project involving international domain experts and is a registered project under MIBBI: Minimum Information for Biological and Biomedical Investigations.
Comprehensive differentially methylated regions (DMR) analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization.
A U.S. nonprofit organization, in partnership with The Tuchman Foundation. It was formed to foster philanthropic activities to raise funds for the most promising Parkinson's disease research that will help find the cure. The Parkinson Alliance is dedicated to raising donations through special fundraising events. The Parkinson Alliance is also devoted to improving the quality of life in the DBS community through informational means and by funding promising research within the DBS field.
Database of disease genes and risk factors and of host pathogen/interactomes. Lists genes, pathways and environmental risk factors positively associated with diseases and conditions such as Alzheimer's disease, schizophrenia, multiple sclerosis, childhood obesity, anorexia nervosa, HIV-1/AIDS, and helicobacter pylori. Details of polymorphisms as well as negative/positive association data can be found via Useful links. Throughout the site are links to Entrez Gene and Pubmed.
PLEXdb - Gene expression resources for plants and plant pathogens
PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets.
IMGT/GENE-DB is the comprehensive IMGT genome database for immunoglobulin (IG) and T cell receptor (TR) genes from human and mouse, and, in development, from other vertebrates. IMGT/GENE-DB is the international reference for the IG and TR gene nomenclature and works in close collaboration with the HUGO Nomenclature Committee, Mouse Genome Database and genome committees for other species. IMGT/GENE-DB allows a search of IG and TR genes by locus, group and subgroup, which are CLASSIFICATION concepts of IMGT-ONTOLOGY. Short cuts allow the retrieval gene information by gene name or clone name. Direct links with configurable URL give access to information usable by humans or programs. An IMGT/GENE-DB entry displays accurate gene data related to genome (gene localization), allelic polymorphisms (number of alleles, IMGT reference sequences, functionality, etc.) gene expression (known cDNAs), proteins and structures (Protein displays, IMGT Colliers de Perles). It provides internal links to the IMGT sequence databases and to the IMGT Repertoire Web resources, and external links to genome and generalist sequence databases. IMGT/GENE-DB manages the IMGT reference directory used by the IMGT tools for IG and TR gene and allele comparison and assignment, and by the IMGT databases for gene data annotation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
This site exists to document developments in the field of personal archiving, and to support a broad community practitioners working to ensure long term access for various personal collections and archives. The Personal Digital Archiving 2011 Conference to be held February 24 & 25, 2011 at The Internet Archive, San Francisco. The full conference schedule is at http://www.personalarchiving.com/2011-schedule/ Register for the conference at http://pda2011.eventbrite.com/. Early bird rates end February 1.
A vocabulary that is able to describe and semantically interconnect the different paradigms of the cancer chemoprevention domain.
Array Information Library Universal Navigator
Re-annotated gene expression / proteomics data from GEO by relating all probe IDs to Entrez Gene IDs once every three months, enabling you to find data from GEO, and compare them from different platforms and species. Platform Annotations adds the latest annotations to any uploaded probe / gene ID list file. Platform Comparison compares any two platforms to find corresponding probes mapping to the same gene. Cross-species mapping maps platform annotations to other species. Gene Search finds deposited platforms and samples in GEO that contain a list of genes. GPL ID Search finds the GPL ID (GEO platform ID) for your array. You can also download the latest annotations files for all arrays and their comprehensive universal gene identifier table, which relates all types of gene / protein / clone identifiers to Entrez Gene IDs for all species. Note: The database was last updated on 4/30/2011. They have successfully mapped 54932732 individual probes from 385099 GEO samples measuring 3519 GEO platforms across 217 species.
FunNet - Transcriptional Networks Analysis
Functional Analysis of Transcriptional Networks
Functional Analysis of Transcriptional Networks (FunNet)
Functional Analysis of Transcriptional Networks (FunNet) is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes. FunNet is provided both as a web-based tool and as a standalone R package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can be downloaded from the FunNet website, or from the worldwide mirrors of CRAN. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Comprehensive set of protein domain families automatically generated from UniProt Knowledge Database. Automated clustering of homologous domains generated from global comparison of all available protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae, it allows storing, retrieving, visualizing and data mining the quantitative single-cell measurements extracted from micrographs of the temperature-sensitive (ts) mutant cells. PhenoM allows users to rapidly search and retrieve raw images and their quantified morphological data for genes of interest. The database also provides several data-mining tools, including a PhenoBlast module for phenotypic comparison between mutant strains and a Gene Ontology module for functional enrichment analysis of gene sets showing similar morphological alterations. About one-fifth of the genes in the budding yeast are essential for haploid viability and cannot be functionally assessed using standard genetic approaches such as gene deletion. To facilitate genetic analysis of essential genes, we and others have assembled collections of yeast strains expressing temperature-sensitive (ts) alleles of essential genes. To explore the phenotypes caused by essential gene mutation we used a panel of genetically engineered fluorescent markers to explore the morphology of cells in the ts strain collection using high-throughput microscopy. The database contains quantitative measurements of 1,909,914 cells and 78,194 morphological images for 775 temperature-sensitive mutants spanning 491 different essential genes in permissive temperature (26* C) and restrictive temperature (32* C). The morphological images were generated by high-content screening (HCS) technology.
A set of tools to perform diffusion-weighted MRI white matter tractography in the presence of crossing fibres, using Constrained Spherical Deconvolution (Tournier et al.. 2004; Tournier et al. 2007), and a probabilisitic streamlines algorithm (e.g. Behrens et al., 2003; Parker et al., 2003). These applications have been written from scratch in C++, using the functionality provided by the GNU Scientific Library, and gtkmm. The software is currently capable of handling DICOM, NIfTI and AnalyseAVW image formats, amongst others. Installation * Unix/Linux * Microsoft Windows * Mac Os X, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Database of human histone variants, sites of their post-translational modifications and various histone modifying enzymes. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes of modifying enzymes. Many data fields are hyperlinked to other databases (e.g. UnprotKB/Swiss-Prot, HGNC, OMIM, Unigene etc.). Additionally, this database also provides sequences of promoter regions (-700 TSS +300) for all gene entries. These sequences were extracted from the UCSC genome browser. Sites of post-translational modifications of histones were manually searched from PubMed listed literature. Current version contains information for about ~50 histone proteins and ~150 histone modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics (CoEE), Indian Institute of Science Education and Research (IISER), Pune.
A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.
Resource out of service. Documented on May, 5th, 2021.The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB). The structural neighborhoods and alignments are automatically maintained and regularly updated using the Dali search engine. The Dali Database contains structural alignments of PDB90 versus the full PDB using DaliLite. The data can be viewed interactively here, or downloaded in its entirety Users may search by PDB identifier or keyword.
MABMIS: Multi-Atlas Based Multi-Image Segmentation
Multi-Atlas Based Multi-Image Segmentation
This software package implements an algorithm for accurate and consistent segmentation / labeling on a group of images. The images should be in Analyze format with paired header and image files. All images should be preprocessed so that they have been affinely aligned together.
Sleep Recordings and Hypnograms in European Data Format
Sleep Recordings and Hypnograms in European Data Format (EDF)
Sleep EEG dataset from 8 subjects in European Data Format (EDF) including original recordings and their hypnograms as described in B Kemp, AH Zwinderman, B Tuk, HAC Kamphuisen, JJL Obery��. Analysis of a sleep-dependent neuronal feedback loop: the slow-wave microcontinuity of the EEG. IEEE-BME 47(9):1185-1194 (2000). The recordings were obtained from Caucasian males and females (21 - 35 years old) without any medication; they contain horizontal EOG, FpzCz and PzOz EEG, each sampled at 100 Hz. The sc* recordings also contain the submental-EMG envelope, oro-nasal airflow, rectal body temperature and an event marker, all sampled at 1 Hz. The st* recordings contain submental EMG sampled at 100 Hz and an event marker sampled at 1 Hz. The 4 sc* recordings were obtained in 1989 from ambulatory healthy volunteers during 24 hours in their normal daily life, using a modified cassette tape recorder. The 4 st* recordings were obtained in 1994 from subjects who had mild difficulty falling asleep but were otherwise healthy, during a night in the hospital, using a miniature telemetry system with very good signal quality.
BitterDB is a free and searchable database of bitter compounds. It currently holds over 550 bitter compounds obtained from the literature and from Merck index and their associated 25 human bitter taste receptors (hT2Rs). BitterDB provides several ways to investigate the bitter world: search for bitter compounds by different criteria, search for bitter molecules with structure similar to a query compound, blast bitter receptors and more. New! 2D plots of bitter receptors are available in the receptors pages. The alignment contains the sequences of the 25 human bitter taste receptors. The alignment shows the secondary structure for each receptor as predicted by TOPCONS. In each trans-membrane helix X, the most conserved residue (X.50 in Ballesteros-Weinstein numbering) is indicated. The alignment was generated using ClustalW2.
PBmice: PiggyBac Mutagenesis Information CEnter
Database for storing, retrieving, and displaying the information derived from piggyBac (PB) insertions (Insert) and their characterizations in the mouse genome with piggyBac transposon system. Quick Search and Advanced Search tools have been provided to find information in the PBmice database, the result is centered on Inserts and provides information related to the Inserts. A mapping database is linked to PBmice too. This mapping database allows row experiment data to be inputted in. All the mature data can be allowed publish to PBmice. PBmice Source Code is available with a License Agreement.
Gait Dynamics in Neuro-Degenerative Disease Data Base
Gait Dynamics in Neuro-Degenerative Disease DataBase
Gait Dynamics in Neurodegenerative Disease
Database of records from patients with Parkinson's disease (n = 15), Huntington's disease (n = 20), or amyotrophic lateral sclerosis (n = 13). Records from 16 healthy control subjects are also included here. The raw data were obtained using force-sensitive resistors, with the output roughly proportional to the force under the foot. Stride-to-stride measures of footfall contact times were derived from these signals.
It is a publicly available web-based database that aims to provide further understanding of protein-ligand interactions. It''s a resource containing biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes. The PLD contains biomolecular data including calculated binding energies, Tanimoto ligand similarity scores and protein percentage sequence similarities. The database has potential for application as a tool in molecular design.
A Matlab package for working with graphs that uses the Boost Graph Library to efficiently implement the graph algorithms. MatlabBGL is designed to work with large sparse graphs with hundreds of thousands of nodes.
Open Archives Initiative - Object Reuse and Exchange Initiative
Initiative which defines standards for the description and exchange of aggregations of Web resources. The intent of the effort is to develop standards that generalize across all web-based information including the increasing popular social networks of web 2.0. The goal of these standards is to expose the rich content in these aggregations (sometimes called compound digital objects, they may combine distributed resources with multiple media types including text, images, data, and video) to applications that support authoring, deposit, exchange, visualization, reuse, and preservation. The specific aim of the ORE effort is to promote (through creation or endorsement) effective and consistent mechanisms which: facilitate discovery of compound digital objects; reference (or link to) these objects (as well as parts thereof); obtain a variety of disseminations of these objects; aggregate and disaggregate objects; and enable processing of objects by automated agents.
Data analysis service and software program that perform Operantional Taxonomic Units (OTUs) finding. It uses a three-step clustering for identifying OTUs. The first-step clustering is raw read filtering and trimming. The second step is error-free reads picking.. At the last step, OTU clustering is done at different distanct cutoffs (0.01, 0.02, 0.03... 0.12).
A Whole Genome Admixture Scan for Type 2 Diabetes in African Americans
Genomic data set on Type 2 Diabetes in African-Americans derived via admixture mapping, a method for genome-wide association analysis based on admixture-generated linkage disequilibrium. This collaborative group has identified 1,478 African Americans with Type 2 Diabetes (T2D) from the Jackson Heart Study and Multiethnic Cohort Study, as well as 498 controls from the Jackson Heart Study who are normoglycemic despite high body mass index and older age. All samples were genotyped (using the Illumina BeadLab platform) for 1,291 polymorphic markers chosen to be extremely different in frequency between west Africans and European Americans. Evidence for association to diabetes at each marker as reported by the ANCESTRYMAP software are reported in the downloadable table. They calculate that this study has statistical power to detect loci where African or European ancestry on average confers multiplicative increased risk of 1.35-fold or more. The fact that they did not detect a statistically significant signal of association in the scan suggests that any genetic risk factors for T2D do not confer different risks due to ancestry that differ by this factor. The genome scan results are publicly available (Excel file) prior to publication so that researchers interested in the genetics of T2D can use the results of the scan to prioritize follow-up of any regions of interest.
African American Study of Kidney Disease and Hypertension
African American Study of Kidney Disease and Hypertension (AASK) Clinical Trial and Cohort Study
African American Study of Kidney Disease and Hypertension Clinical Trial and Cohort Study
Clinical trial investigating whether a specific class of antihypertensive drugs (beta-adrenergic blockers, calcium channel blockers, or angiotensin converting enzyme inhibitors) and/or the level of blood pressure would influence progression of hypertensive kidney disease in African Americans. The initiative consisting of 21 clinical centers and a data-coordinating center is followed by a Continuation of AASK Cohort Study to investigate the environmental, socio-economic, genetic, physiologic, and other co-morbid factors that influence progression of kidney disease in a well-characterized cohort of African Americans with hypertensive kidney disease. Only patients who were previously in the randomized trial are eligible for the cohort study. A significant discovery was made in the treatment strategy for slowing kidney disease caused by hypertension. Angiotensin-converting enzyme (ACE) inhibitors, compared with calcium channel blockers, were found to slow kidney disease progression by 36 percent, and they drastically reduced the risk of kidney failure by 48 percent in patients who had at least one gram of protein in the urine, a sign of kidney failure. ACE inhibitors have been the preferred treatment for hypertension caused by diabetes since 1994; however, calcium channel blockers have been particularly effective in controlling blood pressure in African Americans. The AASK study now recommends ACE inhibitors to protect the kidneys from the damaging effects of hypertension. The Continuation of AASK Cohort Study will be followed at the clinical centers. The patients will be provided with the usual clinical care given to all such patients at the respective centers. Baseline demographic information, selected laboratory tests, and other studies are being obtained at the initiation of the Continuation Study. The patients will be seen quarterly at the centers, and some selected studies done at these visits. Samples will be obtained and stored for additional studies and analyses at a later date.
Neural Connections - How circuitry can unravel the mind
Blog is first and foremost dedicated to circuitry, all the way from a small cluster of connections in a small brain area to wide-spread circuitry between several brain areas (local, regional and functional connectivity). My Philosophy (on neuroscience): I do not think that functions of the brain (and/or mind) can be localized to certain areas (modular zones). This is a distributed, interactive function in a neural network. Second, there is usually an underlying tone that relates to the hippocampus, and/or the post has a systems-level approach to it. Postings will most likely be in a review-esque fashion. This is really meant to be an information resource. I hope to get more opinion pieces in there sometime. Posts are usually what I am currently researching, interested in, or what I have previously done research on at one time. I also want to build a community of professionals and others interested in neuroscience and/or psychology (philosophy of mind, too!). The blog, in general, helps everything (the information) stay fresh in my mind.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 29,2019. Locus-specific database listing variants of the SCN1A gene. To provide a continued platform that is in keeping with the latest data, this web site has been set up where all information can be accessed and downloaded. A Mutation submission form encourages data submissions. Over the past ten years, mutations in voltage-gated sodium channels (Navs) have become closely associated with inheritable forms of epilepsy. One isoform in particular, Nav1.1 (gene symbol SCN1A), appears to be a superculprit, with virtually hundreds of mutations. The associated phenotypes range from benign febrile seizures to extremely serious conditions like Dravet syndrome (a.k.a. severe myoclonic epilepsy in infancy or SMEI). Despite the wealth of information, mutational analyses are cumbersome, owing to inconsistencies among the Nav1.1 sequences to which different research groups refer. Splicing variability is the core problem: Nav1.1 exists in the brain in 3 different isoforms: full-length (2009 AA) as well as two shorter versions that lack 11 or 28 amino acids compared to the former. This online database ?????? SCN1A infobase ?????? establishes a standardized nomenclature for Nav1.1 variants so as to provide a platform from which future mutation analyses can be started without up-front data normalization.
BacMap: An Interactive Atlas for Exploring Bacterial Genomes
An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes. It uses a visualization tool (CGView) to generate high-resolution circular genome maps from sequence feature information. Each map includes an interface that allows the image to be expanded and rotated. In the default view, identified genes are drawn to scale and colored according to coding directions. When a region of interest is expanded, gene labels are displayed. Each label is hyperlinked to a custom ''gene card'' which provides several fields of information concerning the corresponding DNA and protein sequences. Each genome map is searchable via a local BLAST search and a gene name/synonym search. A complete listing of the species and strains in the BacMap database is available on the BacMap homepage. Below each species/strain name is a list of the sequenced chromosomes and plasmids that are available. Some features of BacMap include: * Maps are available for 2023 bacterial chromosomes. * Each map supports zooming and rotation. * Map gene labels are hyperlinked to detailed textual annotations. * Maps can be explored manually, or with the help of BacMap''s built in text search and BLAST search. * A written synopsis of each bacterial species is provided. * Several charts illustrating the proteomic and genomic characteristics of each chromosome are available. * Flat file versions of the BacMap gene annotations, gene sequences and protein sequences can be downloaded. BacMap can be used to: * Obtain basic genome statistics. * Visualize the genomic context of genes. * Search for orthologues and paralogues in a genome of interest. * Search for conserved operon structure. * Look for gene content differences between bacterial species. * Obtain pre-calculated annotations for bacterial genes of interest.
agriGO -- GO Analysis Toolkit and Database for Agricultural Community
A web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
It was created to host functional genomic information gathered as part of a large NSF funded rice kinase proteomics project. The goal is to integrate disparate data sets into a logical, user friendly format. To accomplish this, they have developed a platform to display user selected functional genomic data on a phylogenetic tree. The RKD also includes an interactive chromosomal map showing the positions of all rice kinases and an interactive protein-protein interaction maps.
I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France
Infrastructure Informatique Interop��rable pour les CRB
Project to improve data and sample exchanges and to facilitate large scale analysis of data by improving interoperability of French Biological Resources Centres (BRC or biobanks) IT systems and biological databases. The work done in this project will be linked to other national (IBiSA, ANR, R��seau des Biobanques, Club 3C-R), European (BBMRI, ELIXIR) or international project (P3G). In the preliminary phase (2009-2010) I3-CRB has developed a directory of French Biological Resource Centres / Biobanks where one may register their French BRC or perform a search across all of them. Detail by overall data or kingdom is provided as well as many filtering options. Access to biological samples is provided by the participating BRC' '''s. Biological Resources Centres (BRC or biobanks) collect annotated biological samples from various sources (human, animal, plant, bacteria...). The type of samples depends on the collection and the associated thematic (DNA, proteins, cells, tissues, blood, serum, organisms...). The aims of these centers are to collect, to store, to transform and to distribute the biological samples. They constitute a vital infrastructure for life science and health research. Goals of the French Biobanks/Biological Resource Centres: * List French biobanks and their biological collections * Improve sample exchanges * Improve the international visibility of the French biological collections MeSH terms have been integrated: Domains, diseases, and location of the disease (Anatomy). Collections/species are based on NCBI Taxonomy.
Maryland Genetics of Interstitial Cystitis
Maryland Genetics of Interstitial Cystitis (MaGIC)
Clinical study that investigated several hundred families with two or more blood relatives with interstitial cystitis in order to understand the molecular genetic basis of this condition. The study sought to find changes in genes that are found far more commonly in family members who have interstitial cystitis than in those who do not have the disease. Identifying these genes should lead to a better understanding of the cause of interstitial cystitis. This is a national study which is conducted by telephone and mail, and in which participants could participate entirely from their home.
SAPIENTA - Automating the Semantic Annotation of Papers
Semantic Annotation of Papers: Interface & ENrichment Tool Automated
Software to help researchers process scientific papers faster and get the information they are interested in out of them. This is achieved by automating the recognition of core scientific concepts such as Motivation, Method, Result, Conclusion in papers and uses them to generate automatic summaries. This SAPIENTA tool adds additional functionality to the SAPIENT tool, an annotation tool implemented as a web application which enables experts to annotate scientific papers, sentence by sentence manually, according to the Core Scientific Concept (CSC) schema.
National Library of Health: Medical Literature Analysis and Retrieval System Online Fact Sheet
MEDLINE (Medical Literature Analysis and Retrieval System Online) is the U.S. National Library of Medicine''s (NLM) premier bibliographic database that contains over 16 million references to journal articles in life sciences with a concentration on biomedicine. MEDLINE is the primary component of PubMed, part of the Entrez series of databases provided by NLM''s National Center for Biotechnology Information (NCBI). MEDLINE may also be searched via the NLM Gateway. Currently, citations from approximately 5,200 worldwide journals in 37 languages; 60 languages for older journals. Citations for MEDLINE are created by the NLM, international partners, and collaborating organizations. The subject scope of MEDLINE is biomedicine and health, broadly defined to encompass those areas of the life sciences, behavioral sciences, chemical sciences, and bioengineering needed by health professionals and others engaged in basic research and clinical care, public health, health policy development, or related educational activities. MEDLINE also covers life sciences vital to biomedical practitioners, researchers, and educators, including aspects of biology, environmental science, marine biology, plant and animal science as well as biophysics and chemistry. Sponsors: Services/products providing access to MEDLINE data are also developed and made available by organizations that lease the database from NLM.
A knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on: 1. primary sequence 2. known or predicted secondary structure 3. known or predicted tertiary contacts (optional) Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures. NAST uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate large numbers of plausible 3D structures that satisfy the constraints given on the secondary and tertiary structure. It then filter these structures based on agreement to the experimental data (if available). This results in a model of the molecule which satisfies all the known residue-resolution data. Imported from BiositeMaps registry
Criminal Justice Drug Abuse Treatment Studies
Criminal Justice-Drug Abuse Treatment Studies
A cooperative research program to explore the issues related to the complex system of offender treatment services. Nine research centers and a Coordinating Center were created in partnership with researchers, criminal justice professionals, and drug abuse treatment practitioners to form a national research infrastructure. The establishment of CJ-DATS is an outstanding example of cooperation among Federal agencies with the research community... We need to understand how to provide better drug treatment services for criminal justice offenders to alter their drug use and criminal behavior. - Dr. Nora Volkow, Director of NIDA. CJ-DATS PHASE I In 2002, NIDA launched the National Criminal Justice����������Drug Abuse Treatment Studies (CJ-DATS). CJ-DATS is a multisite research program aimed at improving the treatment of offenders with drug use disorders and integrating criminal justice and public health responses to drug involved offenders. From 2002 through 2008, CJ-DATS researchers from 9 research centers, a coordinating center, and NIDA worked together with federal, state, and local criminal justice partners to develop and test integrated approaches to the treatment of offenders with drug use disorders. The areas that were studied included: * Assessing Offender Problems * Measuring Progress in Treatment and Recovery * Linking Criminal Justice and Drug Abuse Treatment * Adolescent Interventions * HIV and Hepatitis Risk Reduction * Understanding Systems CJ-DATS PHASE II In 2008, CJ-DATS began to focus on the problems of implementing research-based practices drug treatment practices. This research concerns the organizational and systems processes involved in implementing valid, evidence-based practices to reduce drug use and drug-related recidivism for individuals in the criminal justice system. 12 CJ-DATS Research Centers are conducting implementation research in three primary domains: * Research to improve the implementation of evidence-based assessment processes for offenders with drug problems * Implementing effective treatment for drug-involved offenders * Implementing evidence-based interventions to improve an HIV continuum-of-care for offenders
Database of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. This website enables users to explore: * The set of genes that are potentially regulated by a particular microRNA. * The implied cooperativity of multiple microRNAs on a particular mRNA. * MicroRNA expression profiles in various mammalian tissues. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation. The microRNA Target Detection Software, miRanda, is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Carbon Dioxide Information Analysis Center
The primary climate-change data and information analysis center of the U.S. Department of Energy (DOE) and includes the World Data Center for Atmospheric Trace Gases, serving the climate change-related data and information needs of users worldwide. CDIAC''s data holdings include estimates of carbon dioxide emissions from fossil-fuel consumption and land-use changes; records of atmospheric concentrations of carbon dioxide and other radiatively active trace gases; carbon cycle and terrestrial carbon management datasets and analyses; and global/regional climate data and time series. CDIAC provides scientific and data management support for projects sponsored by a number of agencies, including the AmeriFlux Network, continuous observations of ecosystem level exchanges of CO2, water, energy and momentum at different time scales for sites in the Americas; the Ocean CO2 Data Program of CO2 measurements taken aboard ocean research vessels; DOE-supported FACE experiments, which evaluate plant and ecosystem response to elevated CO2 concentrations; and the HIPPO project, which is analyzing the atmospheric carbon cycle and greenhouse gas concentrations from pole to pole over the Pacific Ocean. For those wishing to contribute data to the CDIAC data collection, review the guide and then contact one of the CDIAC staff members to discuss further data submission plans. Data providers may submit data in a variety of ways including via email, direct deposit to a secure CDIAC File Transfer Protocol (FTP) server, on transfer media (e.g. CD-ROM), or by having CDIAC mirror a location at the investigator''s institution.
Collection of curated structural variation in the human genome. Catalogue of human genomic structural variation identified in healthy control samples for studies aiming to correlate genomic variation with phenotypic data. It is continuously updated with new data from peer reviewed research studies. The Database is no longer accepting direct submission of data as they are currently part of a collaboration with two new archival CNV databases at EBI and NCBI, called DGVa and dbVAR, respectively. One of the changes to DGV as part of this collaborative effort is that they will no longer be accepting direct submissions, but rather obtain the datasets from DGVa (short for DGV archive). This will ensure that the three databases are synchronized, and will allow for an official accessioning of variants.
A Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units (GPU) based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card (14MP/114Cores), the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470.
Substance Abuse and Mental Health Data Archive
Substance Abuse & Mental Health Data Archive
Database of the nation''s substance abuse and mental health research data providing public use data files, file documentation, and access to restricted-use data files to support a better understanding of this critical area of public health. The goal is to increase the use of the data to most accurately understand and assess substance abuse and mental health problems and the impact of related treatment systems. The data include the U.S. general and special populations, annual series, and designs that produce nationally representative estimates. Some of the data acquired and archived have never before been publicly distributed. Each collection includes survey instruments (when provided), a bibliography of related literature, and related Web site links. All data may be downloaded free of charge in SPSS, SAS, STATA, and ASCII formats and most studies are available for use with the online data analysis system. This system allows users to conduct analyses ranging from cross-tabulation to regression without downloading data or relying on other software. Another feature, Quick Tables, provides the ability to select variables from drop down menus to produce cross-tabulations and graphs that may be customized and cut and pasted into documents. Documentation files, such as codebooks and questionnaires, can be downloaded and viewed online.
Comparative Sequencing of Plant Small RNAs
This project has developed a sequence dataset of plant small RNAs based on the hypothesis that most if not all plants utilize important small RNA signaling networks. Different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles. Comparative genomics approaches can be applied to distinguish potential miRNAs from siRNAs and to match the miRNAs to the target sequences. This project develops an unparalleled resource of millions of plant small RNAs for comparative analyses. The project includes sequencing of small RNAs from a diverse and agronomically-relevant set of plant species, focused analyses of important members of the Solanaceae and Poaceae, and development of a small RNA database and web interface for public access and analysis of data. These data will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, and will be tremendously useful to a broad set of plant biologists interested in development, stress responses, epigenetics, evolution, RNA biology and other traits impacted by small RNAs. We offer a variety of tools to query the small RNA data set, with options to identify sequences based on homology, expression levels, conservation, or potential function: 1. Small RNA mapping tool: searches for small RNAs perfectly matching a genomic sequence provided by the user. 2. Small RNA mismatch tool: searches the database for small RNAs or other short sequences provided by the user, allowing mismatches. 3. Library-comparison tool to identify conserved small RNAs. 4. Library-comparison tool to identify differentially regulated small RNAs. 5. Reverse Target Prediction.
30 sections from a serial section Transmission Electron Microscopy (ssTEM) data set of the Drosophila first instar larva ventral nerve cord (VNC). The microcube measures 2 x 2 x 1.5 microns approx., with a resolution of 4x4x50 nm/pixel. The images are representative of actual images in the real-world: there is a bit of noise; there are image registration errors; there is even a small stitching error in one section. None of these led to any difficulties in the manual labeling of each element in the image stack by an expert human neuroanatomist. A software application that aims at removing or reducing human operation must be able to cope with all these issues. Each labeled object has a unique id and fits into the overall datastructure of the data set. For example, each mitochondria is represented by a unique Arealist object, containing a list of labeled areas, one per section. All membranes have been highlighted as one unique object. All neurites (and glia) have been highlighted each as its own independent object, delimited by membrane and non-overlapping with membrane and with each other. On the other hand, mitochondria, noise and synapses overlap with membranes, neurites and glia; hence, they are offered as independent tif stacks.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. A command line program in Unix to convert images to a variety of formats (PNG, TIFF, JPEG, PPM..etc). It is uniquely different from other programs such as Adobe Photoshop or ImageMagick because it is designed for dealing with the high-resolution images with file sizes of several gigabytes. Image Converter does not require any additional RAM or virtual memory to run. Also, run-time is relatively fast for high resolution data.
Software tool to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes. The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats. The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines.
The WWW Virtual Library: Model Organisms
Catalog of internet resources relating to biological model organisms, and is part of the Biosciences area of the Virtual Library project. The main Model Organisms Library discussed in this website are: * E. coli (bacterium) * Yeasts (Saccharomyces cerevisiae, and other species) * Dictyostelium discoideum (slime mold) * Drosophila melanogaster (fruit fly) * Xenopus laevis (African clawed frog) Many aspects of biology are similar in most or all organisms, but it is frequently much easier to study particular aspects in particular organisms - for instance, genetics is easier in small organisms that breed quickly, and very difficult in humans! The most popular model organisms have strong advantages for experimental research, and become even more useful when other scientists have already worked on them, discovering techniques, genes and other useful information.
University of Wurzburg; Bavaria; Germany
Julius-Maximilian''s University of Würzburg
DynGO: a tool for visualizing and mining of Gene Ontology and its associations
DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations (which requires more disk and memory to handle the semantic retrieval). The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. Requirements: Java Platform: Windows compatible, Linux compatible, Unix compatible
Software program that analyzes patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. An open source, downloadable, 3d atlas of the mouse brain and its cellular constituents that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework. This next generation open environment has been developed to connect members of the neuroscience community to facilitate solutions for today's intractable challenges in brain research through cooperation and crowd sourcing. The client-server platform provides rich 3-D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. An open-source, 3-D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations. Within the Catalog, researchers can view and contribute a wide range of data including: * 3D meshes of subcellular scenes or brain region territories * Large 2D image datasets from both electron and light level microscopy * NeuroML and Neurolucida neuronal reconstructions * Protein Database molecular structures Users of the Whole Brain Catalog can: * Fit data of any scale into the international standard atlas coordinate system for spatial brain mapping, the Waxholm Space. * View brain slices, neurons and their animation, neuropil reconstructions, and molecules in appropriate locations * View data up close and at a high resolution * View their own data in the Whole Brain Catalog environment * View data within a semantic environment supported by vocabularies from the Neuroscience Information Framework (NIF) at http://www.neuinfo.org. * Contribute code and connect personal tools to the environment * Make new connections with related research and researchers 5 Easy Ways to Explore: * Explore the datasets across multiple scales. * View data closely at high resolution. * Observe accurately simulated neurons. * Readily search for content. * Contribute your own research.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 2, 2019. Ontology-based segmentation and analysis tools for electron tomographic data.
Open Source MATLAB toolbox and EEGLAB plugin for the design, prototyping, testing, experimentation with, and evaluation of Brain-Computer Interfaces (BCIs), and other systems in the same computational framework. It facilitates the design and development of new methods for cognitive state estimation and their use in both offline data analysis and real-time applications. BCILAB includes an easily extensible collection of currently over 100 methods from the literature (covering signal processing, machine learning and BCI-specific methods). Aside from supporting advanced BCI research, a special aim of BCILAB is to facilitate the adoption of machine learning and advanced statistical modeling for functional neuroimaging purposes in tandem with the EEGLAB platform. The toolbox offers multiple different interfaces which link to the same backend functionality, including a GUI, scripting support (MATLAB-based), APIs for real-time processing, and a variety of extension component interfaces. MATLAB programming is not strictly necessary, as most BCILAB features can be accessed from the GUI, although it is required for batch scripting and custom extensions. The strength of MATLAB-based software lies in its resources for leading-edge scientific computing, as well as in the good support for rapid prototyping, but BCI systems developed in it can be used for real-time out-of-lab experimentation, and can in principle be deployed without the need for a MATLAB license. However, due to the complexity and overhead of the MATLAB environment, the system is best used as a research platform, and not as a product development environment -- end-user software is ideally re-implemented in a compiled language, after a suitable approach has been identified and extensively tested. The process of identifying and testing an approach involves more than just computation, but also data exploration and investigation - an area which is helped by the deep integration with the EEGLAB platform. In the future, this integration will be further strengthened, bringing rich statistical learning and signal processing into routine EEG analysis workflows. The toolbox has been developed by C. Kothe at the Swartz Center, inspired by the preceding PhyPA BCI toolbox created by C. Kothe and T. Zander at the Chair for Human-Machine Systems, Berlin Institute of Technology.
Frequent Hemodialysis Network Nocturnal Trial
Frequent Hemodialysis Network (FHN) Nocturnal Trial
Frequent Hemodialysis Network: Nocturnal Trial
Randomized controlled clinical trial where subjects will be randomized to conventional hemodialysis delivered three days per week home arm or to the six times per week nocturnal home hemodialysis arm which will follow any dialysis prescription provided their prescribed standardized Kt/V is at least 4.0 and treatment time is at least 6.0 hours, six times per week. Subjects were recruited from dialysis units associated with designated Clinical Centers in the U.S. and Canada and followed for 12 months. Primary Outcome Measures: * composite of 12 month mortality and the change over 12 months in left ventricular mass by cine-MRI, * a composite of 12 month mortality and the change over 12 months in the SF-36 RAND physical health composite Secondary Outcome Measures: * cardiovascular structure/funct (change in LV mass over 12 mos), health-related QoL/phys funct (change over 12 mos in PHC), * depression / dis burden (change over 12 mos in Beck Depression Inv.), nutrition (change over 12 mos in serum albumin, cognitive funct (change over 12 mos in TrailMaking Test B), mineral metabolism (change over 12 mos in aveg pre-dialysis serum phosphorus), * clin events (rate of non-access hospital or death * hypertension, anemia
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Software application that is a web-based tool for viewing and annotating images. The application is based on the open source Google Web Toolkit (GWT) version 1.7, which generates Javascript code that runs on the user''s web browser. No special installation or software other than a Javascript-enabled web browser is required for use. Images to be viewed or annotated are preprocessed into multi-resolution tiles by either the commercial Zoomify preprocessor application or a locally written `zoomify_create'' tool, which produces lossless Portable Network Graphics (PNG) tiles. The WebImageBrowser application reads and manages tiled images in a manner similar to Google Maps or similar applications, allowing viewing of images of arbitrarily large size. The source code is available at https://github.com/OpenCCDB/WebImageBrowser . It requires a build. If you want the annotation function to be enabled, then you will need to install the CCDB schema in the Postgres database.
neurospy is a free software for functional imaging of fast neuronal activity. neurospy is a modular cross-platform application framework written in Java for the NetBeans Platform. At this time it runs on Windows XP-based LeCroy oscilloscopes and drives acousto-optic scanners via USB using the Analog Devices 9959 Direct Digital Synthesis chip. This combination makes one of the most powerful systems for scanning microscopy available today at any price. neurospy is very easy to port to other kinds of acquisition and scanning hardware.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Software to support registering brain images to the stereotaxic coordinate system of a brain atlas. It was specifically designed to work with the large scale brain mosaics. When data are uploaded to the CCDB, users may launch Jibber, a custom tool for defining correspondence points between the image and an atlas overlay. Jibber automatically downsamples the data, so that users can define the warping and scaling parameters with good interactive performance on the smaller copy. Once the warping transformation is computed, the original image and the transformation matrix are sent to a cluster of computers for warping. The current version of Jetsam is running on a 30 Sun V20 nodes and the execution time is roughly about 20 minutes per GB. The warped images are then automatically registered with an image web server that supports spatial queries based on stereotaxic coordinates. These servers generate optimized downsampled images, which can be displayed by standard online clients regardless of the size of the original image.
ABSORB: Atlas Building by Self-Organized Registration and Bundling
ABSORB: Atlas Building by Self-Organized Registration Bundling
Atlas Building by Self-Organized Registration and Bundling
Atlas Building by Self-Organized Registration Bundling
This software package implements an algorithm for effective groupwise registration. The required input is a set of 3D MR intensity images (in Analyze format with paired .hdr and .img files) with a text file (.txt) listing all header file (.hdr) names. The output is the set of registered images together with the corresponding dense deformation fields. This software has been tested on Windows XP (32-bit) and Linux (64-bit, kernel version 2.6.18-194.el5). The images should be pre-processed before applying ABSORB: * All brain MR images used as inputs to ABSORB should be in the same situation (e.g., skull-stripped or not, cerebellum removed or not, etc.). * The input images should be in Analyze format with paired header and image files. This software was developed in IDEA group in UNC-Chapel Hill.
Computational Linguistics And Information Retrieval Library
A suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA). Its architecture also allows for external software to be plugged in with very little effort. The latest version of clairlib is 1.06 which was released on March 2009 and includes about 130 modules implementing a wide range of functionalities. Clairlib is distributed in two forms: * Clairlib-core, which has essential functionality and minimal dependence on external software, and * Clairlib-ext, which has extended functionality that may be of interest to a smaller audience. Much can be done using Clairlib on its own. Some of the things that Clairlib can do are: Tokenization, Summarization, Document Clustering, Document Indexing, Web Graph Analysis, Network Generation, Power Law Distribution Analysis, Network Analysis, RandomWalks on Graphs, Tf-IDF, Perceptron Learning and Classification, and Phrase Based Retrieval and Fuzzy OR Queries.
Public land grant research university in Laramie, Wyoming.
Stanford University Center for Narcolepsy
The Stanford Center for Narcolepsy was established in the 1980s as part of the Department of Psychiatry and Behavioral Sciences. Today, it is the world leader in narcolepsy research with more than 100 articles on narcolepsy to its name. The Stanford Center for Narcolepsy was the first to report that narcolepsy-cataplexy is caused by hypocretin (orexin) abnormalities in both animal models and humans. Under the direction of Drs. Emmanuel Mignot and Seiji Nishino, the Stanford Center for Narcolepsy today treats several hundred patients with the disorder each year, many of whom participate in various research protocols. Other research protocols are conducted in animal models of narcolespy. We are always looking for volunteers in our narcolepsy research studies. We are presently recruiting narcoleptic patients for genetic studies, drug clinical trials, hypocretin measurement studies in the CSF and functional MRI studies. Monetary gifts to the Center for Narcolepsy are welcome. If you wish to make the ultimate gift, please consider participating in our Brain Donation Program. To advance our understanding of the cause, course, and treatment of narcolepsy, in 2001 Stanford University started a program to obtain human brain tissue for use in narcolepsy research. Donated brains provide an invaluable resource and we have already used previously donated brains to demonstrate that narcolepsy is caused by a lack of a very specific type of cell in the brain, the hypocretin (orexin) neuron. While the brain donations do not directly help the donor, they provide an invaluable resource and a gift to others. The real answers as to what causes or occurrs in the brain when one has narcolepsy will only be definitively understood through the study of brain tissue. Through these precious donations, narcolepsy may eventually be prevented or reversible. We currently are seeking brains from people with narcolepsy (with cataplexy and without), idiopathic hypersomnia and controls or people without a diagnosed sleep disorder of excessive sleepiness. Control brains are quite important to research, as findings must always be compared to tissue of a non-affected person. Friends and loved ones of people who suffer with narcoleps may wish to donate to our program to help fill this very important need. Refer to the Movies tab for movies of Narcolepsy / Cataplexy.
Target genes of Wnt/beta-catenin signaling
A list of target genes of Wnt/beta-catenin signaling. Suggestions for additions are welcome. Direct targets are defined as those with Tcf binding sites and demonstrating that these sites are important.
NIH initiative to support production of cDNA libraries, clones and 5'/3' sequences and to provide set of full-length (open reading frame) sequences and cDNA clones of expressed genes for Xenopus laevis and Xenopus tropicalis. Clones distribution is outsourced to for profit companies. Project concluded in September 2008. Resources generated by XGC are publicly accessible to biomedical research community. All sequences are deposited into GenBank.Corresponding clones are available through IMAGE clone distribution network. With conclusion of XGC project, GenBank records of XGC sequences will be frozen, without further updates. Since knowledge of what constitutes full-length coding region for some of genes and transcripts for which we have XGC clones will likely change in future, users planning to order XGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).
NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).
Bipolar Disorder Neuroimaging Database (BiND)
Database of 141 studies which have investigated brain structure (using MRI and CT scans) in patients with bipolar disorder compared to a control group. Ninety-eight studies and 47 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website.
Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains. The Motifscanner program utilizes an entropy approach that assesses the probability of a site matching the motif using the selectivity values and sums the logs of the probability values for each amino acid in the candidate sequence. The program then indicates the percentile ranking of the candidate motif in respect to all potential motifs in proteins of a protein database. When available, percentile scores of some confirmed phosphorylation sites for the kinase of interests or confirmed binding sites of the domain of interest are provided for comparison with the scores of the candidate motifs.
Database that represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.
VAMCA: Visualization And Meta-analysis on Cortical Anatomy
Visualization And Meta-analysis on Cortical Anatomy
A stand-alone, open source human cortical meta-analysis and visualization toolbox for MatLab. It projects stereotaxic coordinates to a mean cortical surface by using an anatomical database of 60 young adults to provide multiple mappings of normalized cortical surfaces into MNI space. VAMCA performs the following analyses: # Multi-Fiducial Projection Mapping: Map stereotaxic 3D coordinates to the normalized cortical location for each of 60 database subjects. # Computing Centroid Locations for groups of foci both on a mean cortical surface and in MNI space. # Comparing Two Groups of Foci for differences in location (surface or 3D) of their group centroids and computing the groups' overlap extent using permutation tests. # Detecting Significant Densities of Foci or Density Differences of Two Groups within anatomical ROIs on a mean cortical surface by using Monte Carlo analyses. Coordinate weights allow fixed or random effects type analyses.
The goal of this project is to aid genetic association studies of addiction by creating a resource of biologically relevant genes, pathways and single nucleotide polymorphisms (SNPs). The primary users of the NeuroSNP resource are investigators conducting genome-wide association studies (GWASs) of addiction-related phenotypes. NeuroSNP will allow investigators to identify biologically relevant genes for addiction based on curated expert knowledge, and assess the coverage of these genes provided by commercial SNP microarrays. If investigators wish to ensure the coverage of certain addiction-related genes is optimal, NeuroSNP provides a mechanism for supplementation. While commercial SNP microarrays offer affordable and comprehensive coverage of the human genome, some diseases have biologically relevant genomic regions that may require additional coverage. Addiction, for example, is believed to be influenced by complex interactions involving several genes and pathways. NIDA has assembled a number of investigators specializing in fields such as genetics, pharmacogenetics, bioinformatics and neurobiology through a Request for Information. These investigators have pooled their expert knowledge to produce a database of addiction-related genes and SNPs. Commercial SNP microarrays, such as those offered by Affymetrix and Illumina, are then analyzed to determine how well certain addiction-related genes are covered. When the coverage is less than optimal, a SNP prioritization scheme is used to supplement the commercial array with the most biologically informative markers. For example, SNPs in coding regions, promoters, and evolutionary conserved regions are selected first.
UK Parkinson's Disease Society Tissue Bank
UK Parkinson's Disease Society Tissue Bank at Imperial College London
A brain bank of the United Kingdom which collects human brains for Parkinsons disease research. The collection is comprised of brain, spinal cord and a sample of cerebrospinal fluid from people with and without Parkinson's after death. Researchers can fill out a brain tissue request form to order samples from the bank.
SAMHSA National Survey on Drug Use & Health
NSDUH is the primary source of statistical information on the use of illegal drugs, alcohol, and tobacco by the U.S. civilian, noninstitutionalized population aged 12 or older. Conducted by the Federal Government since 1971, the survey collects data through face-to-face interviews with a representative sample of the population at the respondent''s place of residence. Correlates in OAS reports include the following: age, gender, pregnancy status, race / ethnicity, education, employment, geographic area, frequency of use, and association with alcohol, tobacco, & illegal drug use. NSDUH collects information from residents of households and noninstitutional group quarters (e.g., shelters, rooming houses, dormitories) and from civilians living on military bases. The survey excludes homeless persons who do not use shelters, military personnel on active duty, and residents of institutional group quarters, such as jails and hospitals. Most of the questions are administered with audio computer-assisted self-interviewing (ACASI). ACASI is designed to provide the respondent with a highly private and confidential mode for responding to questions in order to increase the level of honest reporting of illicit drug use and other sensitive behaviors. Less sensitive items are administered by interviewers using computer-assisted personal interviewing (CAPI). The 2010 NSDUH employed a State-based design with an independent, multistage area probability sample within each State and the District of Columbia. The eight States with the largest population (which together account for about half of the total U.S. population aged 12 or older) were designated as large sample States (California, Florida, Illinois, Michigan, New York, Ohio, Pennsylvania, and Texas) and had a sample size of about 3,600 each. For the remaining 42 States and the District of Columbia, the sample size was about 900 per State. The design oversampled youths and young adults; each State''s sample was approximately equally distributed among three age groups: 12 to 17 years, 18 to 25 years, and 26 years or older.
MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery
MRM NeAt (Neurological Atlas) Image Gallery
Image Gallery of a 3D MRI Atlas of an Adult C57BL/6J Mouse Brain showing Slice Animation and 3D Animation including Axial, Coronal, Sagittal views. RealPlayer or Windows Media Player needs to be installed for viewing these animations.
Standard software package for genetic linkage called LINKAGE. Genetic linkage analysis is statistical technique used to map genes and find approximate location of disease genes.
A categorized list of bookmarks concerning neurobiology assembled by Professor Mark Dubin, Dept. of Molecular, Cellular and Developmental Biology, University of Colorado. Major categories include anatomy, computing, mental and physical conditions, general knowledge, mind, physiology, psychology, senses, and techniques.
Database of animal toxins, this most recent release (2009) focused on constructing a global-scale animal toxin-channel interaction network based on literature and database annotations through the integration of an ion channel database into ATDB 2.0. Most ion channel sequences were categorized and annotated with a hierarchic controlled term system (Ion Channel Ontology). More than 55,022 possible T-C interactions were extracted by text mining which link the toxin and ion channel database. These interaction data were classified carefully based on evidence type, in which 9,193 high confidence interactions were annotated in active site level. A web-based T-C interaction network view was build to visualize and make data access easy. The features and updates of ATDB 2.0 are summarized as follows: # AN interaction dataset including 55,022 toxin-channel interactions # Ion channel database (5,097 entries) # Ontology for ion channel classification (Ion Channel Ontology) # 3000 maps for toxins and ion channels interaction # More than 600 additional toxin entries # PDB view to visualize 3-D structure of molecule # More flexible option for data downloads. You may submit new toxins to the database.
Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.
PSORT: Prediction of Protein Sorting Signals and Localization Sites in Amino Acid Sequences
Portal to the PSORT family of computer programs for the prediction of protein localization sites in cells, as well as other datasets and resources relevant to localization prediction. The standalone versions are available for download for larger analyses.
SCOP: Structural Classification of Proteins
Structural Classification of Proteins database
The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of sequence and structural data allows more rigorous analysis and provides important information for understanding the protein world and its evolutionary repertoire. SCOP participates in a project that aims to rationalize and integrate the data on proteins held in several sequence and structure databases. As part of this project, starting with release 1.63, we have initiated a refinement of the SCOP classification, which introduces a number of changes mostly at the levels below superfamily. The pending SCOP reclassification will be carried out gradually through a number of future releases. In addition to the expanded set of static links to external resources, available at the level of domain entries, we have started modernization of the interface capabilities of SCOP allowing more dynamic links with other databases.
The goals of Antibiotic Resistance Genes Database (ARGB) are to provide a centralized compendium of information on antibiotic resistance, to facilitate the consistent annotation of resistance information in newly sequenced organisms, and also to facilitate the identification and characterization of new genes. ARGB contains six types of database groups: - Resistance Type: This database contains information, such as resistance profile, mechanism, requirement, epidemiology for each type. - Resistance Gene: This database contains information, such as resistance profile, resistance type, requirement, protein and DNA sequence for each gene.This database only includes NON-REDUNDANT, NON-VECTOR, COMPLETE genes. - Antibiotic: This database contains information, such as producer, action mechanism, resistance type, for each gene. - Resistance Gene(NonRD): This database contains the same information as Resistance Gene. It does NOT include NON-REDUNDANT, NON-VECTOR genes, but includes INCOMPLETE genes. - Resistance Gene(ALL): This database contains the same information as Resistance Gene. It includes all REDUNDANT, VECTOR AND INCOMPLETE genes. - Resistance Species: This database contains resistance profile and corresponding resistance genes for each species. Furthermore, ARDB also contians three types BLAST database: - Resistance Genes Complete: Contains only NON-REDUNDANT, NON-VECTOR, COMPLETE genes sequences. - Resistance Genes Non-redundant: Contains NON-REDUNDANT, NON-VECTOR, COMPLETE, INCOMPLETE genes sequences. - Resistance Genes All: Contains all REDUNDANT, VECTOR, COMPLETE, INCOMPLETE genes sequences. Lastly, ARDB provides four types of Analytical tools: - Normal BLAST: This function allows an user to input a DNA or protein sequence, and find similar DNA (Nucleotide BLAST) or protein (Protein BLAST) sequences using blastn, blastp, blastx, tblastn, tblastx - RPS BLAST: A web RPSBLAST (RPS BLAST) interface is provided to align a query sequence against the Position Specific Scoring Matrix (PSSM) for each type. Normally, this will give the same annotation information as using regular BLAST mentioned above. - Multiple Sequences BLAST (Genome Annotation): This function allows an user to annotate multiple (less than 5000) query sequences in FASTA format. - Mutation Resistance Identification: This function allows an user to identify mutations that will cause potential antibiotic resistance, for 12 genes (16S rRNA, 23S rRNA, gyrA, gyrB, parC, parE, rpoB, katG, pncA, embB, folP, dfr). ������ :Sponsors: ARDB is funded by Uniformed Services University of the Health Sciences, administered by the Henry Jackson Foundation. :
Database that provides comprehensive information about adverse effect targets of drugs described in the literature, including information about known drug adverse reaction targets, functions and properties. Moreover, proteins involved in adverse effect targets of chemicals not yet confirmed as adverse drug reaction (ADR) targets are also included as potential targets. Associated references are also included. This database gives physiological function of each target, binding drugs / agonists / antagonists / activators / inhibitors, IC(50) values of the inhibitors, corresponding adverse effects, and type of ADR induced by drug binding to a target. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3-dimensional structure, function, and nomenclature of each target along with drug/ligand binding properties, and related literature. Each entry can be retrieved through multiple search methods including target name, target physiological function, adverse effect, ligand name, and biological pathways. A special page is provided for contribution of new or additional information. Function for ADR-target prediction by SVMDART: Submit protein primary sequence for ADR-related protein prediction.
FASTLINK is significantly modified and improved version of main programs of LINKAGE that runs much faster sequentially, can run in parallel, allows the user to recover gracefully from a computer crash, and provides abundant new documentation.
An integrated genomic and functional genomic database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ' '''User Comments' ''' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate. TriTrypDB provides programmatic access to its searches, via REST Web Services. The result of a web service request is a list of records (genes, ESTs, etc) in either XML or JSON format. REST services can be executed in a browser by typing a specific URL. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).
AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid mutation matrix and AAindex3 for the statistical protein contact potentials. All data are derived from published literature. An amino acid index is a set of 20 numerical values representing any of the different physicochemical and biological properties of amino acids. The AAindex1 section of the Amino Acid Index Database is a collection of published indices together with the result of cluster analysis using the correlation coefficient as the distance between two indices. This section currently contains 544 indices. Another important feature of amino acids that can be represented numerically is the similarity between amino acids. Thus, a similarity matrix, also called a mutation matrix, is a set of 210 numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used for sequence alignments and similarity searches. The AAindex2 section of the Amino Acid Index Database is a collection of published amino acid mutation matrices together with the result of cluster analysis. This section currently contains 94 matrices. In the release 9.0, we added a collection of published protein pairwise contact potentials to AAindex as AAindex3. This section currently contains 47 contact potential matrices. Sponsors: This work was supported by grants and resources from the Ministry of Education, Culture, Sports, Science and Technology, and the Japan Science and Technology Agency, and the Bioinformatics Center, Institute for Chemical Research, Kyoto University and the Super Computer System, Human Genome Center, Institute of Medical Science, University of Tokyo.
CuticleDB - A relational database of Arthropod cuticular proteins
A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the five sequenced genomes where manual annotation has been applied to cuticular proteins: Anopheles gambiae, Apis mellifera, Bombyx mori, Drosophila melanogaster, and Nasonia vitripennis. Some sequences were confirmed as authentic cuticular proteins because protein sequencing revealed that they were present in cuticle; others were identified by sequence homology and other criteria. Entries provides information about whether sequences are putative or authentic cuticular proteins. CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin.
A curated collection of all the trapped ES cell clones. Gene-trapping is a valuable tool that uses random mutagenesis to create hypomorphic or null alleles by insertion of exogenous DNA. Since numerous public and private projects have been performing gene trapping over the last few years,it is natural that large overlaps exist and some vectors produce better knock-outs than others due to their insertion site. Considering the high need to develop a comprehensive database that would include both public and private data to provide public access to this essential biological resource, we developed UniTrap, a curated collection of all the trapped ES cell clones, collected from public and private databases. We have developed a bioinformatics pipeline to automate the identification and characterization of trapped genes starting from their transcriptional sequence tags.We process gene trap sequence tags from ES cell clones to generate ‘UniTraps’, i.e. distinct collections of unambiguous insertions at the same subgenic region of annotated genes (RefSeq and Ensembl genes). The UniTrap resource contains data relative to well-known trapped genes. We aim to provide the wet lab researchers with a comprehensive, regularly updated database and curated tools for(i) identifying and comparing the clones carrying a trap into the genes of interest,(ii) evaluating the severity of the mutation to the protein function in each independent trapping event, and(iii) supplying complete information to perform PCR, RT-PCR and restriction experiments to verify the clone and identify the exact point of vector insertion.
The Stanley Medical Research Institute (SMRI) is a nonprofit organization supporting research on the causes of, and treatments for, schizophrenia and bipolar disorder. Since it began in 1989, SMRI has supported more than $300 million in research in over 30 countries around the world. It is the largest nongovernmental source of funds for research on these diseases in the United States. Schizophrenia and bipolar disorder are the most important psychiatric disorders in the United States, affecting more than 4 million people at any given time. Until recent years, little research had been done on these diseases, and the treatment of them was unsatisfactory. The neuroscience revolution has brought with it great opportunities for increased understanding of brain diseases such as schizophrenia and bipolar disorder. SMRI is on the leading edge of this exciting research. Approximately 75 percent of SMRI expenditures goes towards the development of new treatments for schizophrenia and bipolar disorder. The remaining funds are used for research on the causes of these diseases. SMRI has a close relationship with and is the supporting organization for the Treatment Advocacy Center (TAC). The Treatment Advocacy Center is a nonprofit organization dedicated to eliminating barriers to the timely and effective treatment of severe psychiatric disorders. TAC promotes laws, policies, and practices for the delivery of psychiatric care and supports the development of innovative treatments for and research into the causes of severe and persistent psychiatric disorders, such as schizophrenia and bipolar disorder.
Hierarchically-organized annotated list of approximately 2,500 neuroscience-related web resources. Last update August 2009. Major Topics include: Anatomy: Non-primate Anatomy: Primate (including Atlases) Computing: CS, IT, AI Conditions: Affective Conditions: Agnosia, Aphasia, Dyslexia Conditions: Alzheimer Conditions: Autism Spectrum Conditions: Developmental, Learning, Attentional Conditions: Epilepsy Conditions: Miscellaneous Other Conditions: Multiple Sclerosis Conditions: Neuromuscular Conditions: Stroke, Trauma, Tumor General: Dictionaries, Glossaries, Encyclopedias General: Link Lists, Resource Lists, Organizations Mind: Cognitive Science Mind: Consciousness, Philosophy Physiology: Cardiovascular System Physiology: Cellular, Synapse Physiology: Muscle Physiology: Neurochemistry, Pharmacology Physiology: Sleep Physiology: Speech, Language Physiology: Systems Psychology: Behavior, General Psychology: Illusions, Sensory Phenomena, Synesthesia Psychology: Learning Theory Senses: Auditory, Vestibular Senses: Chemical Senses: Somatic, Proprioceptive, Pain Senses: Vision, Art Techniques: Assistive Technology, Rehabilitation Techniques: Data Mining, Data Visualization Techniques: Math Techniques: Microscopy Techniques: Neuroimaging Techniques: Scientific Method Techniques: Virtual Reality, 3D, SL, OS, VRML
HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism
The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version.
SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank and provides functional residue annotation based on data from the Catalytic Site Atlas and PDBsum. The web service is aimed to facilitate the use of the SAS tool when having a huge number of queries. Currently, the web service provides annotation for binding sites (to ligand, metal or nucleic acid), catalytic residues and amino acids related to protein-protein interactions.
MiCroKit - An Integrated Database of Midbody Centrosome and Kinetochore
MiCroKit - An Integrated Database of Midbody Centrosome Kinetochore
MiCroKit - Midbody Centrosome and Kinetochore
MiCroKit - Midbody Centrosome Kinetochore
MiCroKit database is the first integrative resource to pin point most of identified components and related scientific information of midbody, centrosome and kinetochore. In this work, we have collected all proteins identified to be localized on kinetochore, centrosome, and/or midbody from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musculus and H. sapiens. From the related literature of PubMed, numerous proteins have been manually curated to be localized on at least one of the sub-cellular localizations of kinetochore, centrosome and midbody. And to promise the quality of data, based on the rationale of Seeing is believing (Bloom K et al., 2005), these proteins have been unambiguously observed under fluorescent microscope as directly supportive evidences. Then an integrated and searchable database MiCroKit - Midbody, Centrosome and Kinetochore has been established. The version 1.0 of MiCroKit database was set up on Nov. 2nd, 2005, containing 1,065 unique proteins. The MiCroKit version 2.0 was released on Jun. 5th, 2006, with 1,120 entries. Currently, the MiCroKit 3.0 database was updated on July 9, 2009, containing 1,489 unique protein entries. The online service of MiCroKit 3.0 was implemented in PHP + MySQL + JavaScript. And the local packages of MiCroKit 3.0 were developed in JAVA 1.5 (J2SE). The database will be updated routinely as new microkit proteins are reported.
MRM NeAt (Neurological Atlas) Mouse Brain Database
Magnetic Resonance Microimaging Neurological Atlas Mouse Brain Database
MRM Neurological Atlas Mouse Brain Database
Comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. This database consists of: Individual MRI images of mouse brains; three types of atlases: individual atlases, minimum deformation atlases and probabilistic atlases; the associated quantitative structural information, such as structural volumes and surface areas. Quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, have been computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities. You must register First (Mandatory) and then you may Download Images and Data.
Part of zebrafish genome project. ZGC project to produce cDNA libraries, clones and sequences to provide complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All ZGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of ZGC project in September 2008, GenBank records of ZGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which we have ZGC clones will likely change in future, users planning to order ZGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).
Ontology that describes multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.
SysZNF: the C2H2 Zinc Finger Gene Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. SysZNF is an information resource for C2H2 Zinc Finger genes in humans and mice. C2H2 Zinc Finger genes (C2H2-ZNF) constitute the largest class of transcription factors in humans and mouse. C2H2 zinc finger proteins primarily bind to DNA. In most cases, they attach to regions near certain genes and turn the genes on and off as needed. The researches on these genes show light on the evolution of gene regulation systems and development. Therefore, we develop SysZNF (Systematical information resource of Zinc Finger genes) to collect the information related to C2H2 Zinc Finger genes. The aim of SysZNF was to provide a user-friendly interface for rendering the information (DNA, Expression, Protein, Reference and so on) of each C2H2-ZNF (e.g., ZNF10) and to enable a comprehensive analysis of C2H2-ZNF. This project was supported by the Proteome-Center at Rostock University (PCRU) who conceives the concept of the database and Key laboratory of Systems biology at the Shanghai Institute for Biological Sciences (SIBS) who implemented the database. It is maintained jointly by PCRU and SIBS.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Database of functional residues in alpha-helical and beta-barrel membrane proteins. Each protein is identified with its name and source alongwith the Uniprot code. The protein data bank (PDB) codes are also given for available proteins. Different methods and experimental parameters, for example, affinity, dissociation constant, IC50, activity etc. are given in the database. Further, the database provides the numerical experimental value for each residue (or mutant) in a protein. The experimental data are collected from the literature both by searching the journals as well as with the keyword search at PUBMED. In addition, complete reference is given with journal citation and PMID number. TNFunction is cross-linked with the sequence database, Uniprot, structural database, PDB, and literature database, PubMed. The WWW interface enables users to search data based on various terms with different display options for outputs.
Software application that is part of the LINKAGE auxiliary programs (entry from Genetic Analysis Software)
Digital Anatomist Interactive Atlases Project
Digital Anatomist Project Interactive Atlases
Atlases of human brain, thoracic viscera and knee designed for teaching gross anatomy. Also provides a neuroanatomy Interactive syllabus, suitable as a laboratory guide, with an instructive caption accompanying each image and interactive quizzes. The Digital Anatomist Project is motivated by the belief that anatomy is the basis of all the biomedical sciences (including clinical medicine). Manifestations of health and disease can be regarded as attributes of anatomical structures ranging in size from molecules to body parts. Therefore DAP''s goal is to represent anatomy in a comprehensive and consistent way, which should meet the needs of all biomedical applications that require anatomical knowledge. DAP has pursued two parallel tracks for representing anatomical information: 1. The generation of graphical models derived from cadaver and clinical imaging data; and 2. Symbolic modeling of the structures and relationships that constitute the human body. It''s initial work with graphical representations of anatomy provided the impetus and motivation for the National Library of Medicine to establish the Visible Human Project, and it''s symbolic modeling has enhanced NLM''s Unified Medical Language System in order to represent deep anatomical knowledge. In collaboration with the knowledge systems group at Stanford, it has now created a very large knowledge base which provides the foundation for the machine-based intelligence needed to remotely interact with biomedical image data.
A structured controlled vocabulary for the anatomy of Gramineae. Please note that this ontology has now been superseded by the Plant Ontology, http://bioportal.bioontology.org/ontologies/1587.
Stanley Brain Research Laboratory and Brain Collection
Stanley Brain Research Laboratory Brain Collection
It is a widely used resource for researchers trying to find the causes of, and better treatments for, schizophrenia, bipolar disorder and major depression. Brains were collected 1994 to 2005 with the permission of the families in a standardized manner, with half of each specimen being frozen and half fixed in formalin. Currently four cohorts are available for study; the Neuropathology Consortium consisting of 60 cases (15 each schizophrenia, bipolar disorder, depression, and controls), the Array Collection consisting of 105 cases (35 each schizophrenia, bipolar disorder, and controls), the Depression Collection consisting of 36 cases (12 each depression with psychosis, depression without psychosis, and controls), and the Parietal Collection of 48 cases (fixed inferior parietal sections from 24 each schizophrenia and controls). Since 1996, the Stanley Brain Collection has sent over 200,000 sections and 10,000 blocks of brain tissue to 240 research laboratories in 23 states and 20 foreign countries. All tissue has been provided to the researchers without charge. All costs for collecting, processing, and storing the brain tissue have been borne by The Stanley Medical Research Institute as a public service. All reasonable requests for brain tissue (over 90 percent of applications) have been honored. Researchers selected to receive tissue must sign an agreement that sets forth conditions for its use. Results received from researchers become part of the Stanley brain collection data set and will be used for integrative, multivariate analyses. In addition to overseeing the brain collection, the laboratory conducts research on the neuropathology of schizophrenia and bipolar disorder and on brain development. Many studies carried out at the Stanley Brain Research Laboratory are done in cooperation with studies at the Stanley Laboratory of Developmental Neurovirology.
gpDB - a database of GPCRs G-proteins Effectors and their interactions
gpDB: a database of GPCRs G-proteins Effectors and their interactions
A publicly accessible, relational database of G-proteins and their interactions with GPCRs and effector molecules. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature search. There is full sequence information with cross-references to publicly available databases, and the user may submit advanced queries for text search. Furthermore there is an interface for running BLAST against the database and a pattern search tool. The main innovation besides the classification of both G-proteins and GPCRs is the relational model of the database, describing the known coupling specificity of the GPCRs to their respective alpha subunit of G-proteins and also the interaction between G-protein subfamilies and specific effector types, a unique feature not available in any other database. The database will be very useful for the study of G-protein/GPCR and G-protein/effector interactions and for future development of algorithms predicting this interaction.
Kinetic Data of Bio-molecular Interaction
A collection of experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligandbinding or reaction events described in the literature. Currently, KDBI contains 63 pathway simulation parameter sets, 19,263 records (about 2.3 fold of 8,273 in year 2003) of 10,532 distinctive bio-molecular binding and 11,954 interaction events, which involve 2,635 proteins/protein complexes, 847 nucleic acids, 1603 small molecules and more than 100 pathways.
Ontology that contains terms describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels.
This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The name 4DXpress stands for expression database in 4D. The 4D (four dimensions) of 4DXpress can be interpreted either as: 3 spatial dimensions plus time, or as 1. species 2. gene 3. developmental stage 4. anatomical structure. The major focus of this database lies in cross species comparison. The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments. Data was integrated from several species specific expression pattern databases, such as ZFIN, BDGP, GXD, MEPD as well as directly submitted by researchers of the participating groups at EMBL. The 4DXpress database is a project within the Centre for Computational Biology at EMBL. It is developed by Yannick Haudry, Thorsten Henrich and Ivica Letunic and coordinated by Thorsten Henrich. Hugo Berube is developing the 4D ArrayExpress Data Warehouse at EBI for integrating in situ data with microarray data.
Ontology that represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was built reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clinical manifestations are semantically annotated with a domain phenotype ontology and registered with a time-stamped value.
The Molecular Toolkit is a group of programs for analysis and manipulation of nucleic acid and protein sequence data. The programs are written in Java (1.0) and require that your browser support this language. Also, it''s best if your monitor supports a screen resolution of at least 800x600. Nucleic Acid Analysis and Manipulation Programs: *Dot Plots - Examine the similarity of two DNA (or RNA) sequences by production of a similarity matrix displayed as a dot plot. *Manipulate and Display Sequences - Perform simple manipulations on a DNA sequence (inverse, complement, inverse-complement, double-stranded etc). *Restriction Maps - Generate graphical and text-based maps for restriction endonuclease cleavage of DNA. *Translate - Translate a DNA or RNA sequence and obtain graphical and text depictions of the resulting protein sequences. Protein Analysis Programs *Reverse Translate - Reverse translate a protein sequence into DNA. *Protein Composition - Obtain the amino acid composition of a protein. *Hydrophobicity Plots - Plot hydrophobic and hydrophilic domains of a protein.
It is a dual function database that associates an informatics database to a structural database of known and potential drug targets. PDTD is a comprehensive, web-accessible database of drug targets, and focuses on those drug targets with known 3D-structures. PDTD contains 1207 entries covering 841 known and potential drug targets with structures from the Protein Data Bank (PDB). Drug targets of PDTD were categorized into 15 and 13 types according to two criteria: therapeutic areas and biochemical criteria. The database supports extensive searching function using PDB ID, target name and category, related disease.
American Journal of Psychiatry Audio Downloads
The American Journal of Psychiatry Podcast
An audio summary of highlights and key articles from each issue of The American Journal of Psychiatry. Users may subscribe to the podcast to get automatic updates with each issue or download each issue''s audio file individually.
UniProt Chordata protein annotation program
Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms.
Data set of metabolic pathways for the malaria parasite based on the present knowledge of parasite biochemistry and on pathways known to occur in other unicellular eukaryotes. This site extracted the pertinent information from the universal sites and presented them in an educative and informative format. The site also includes, cell-cell interactions (cytoadherence and rosetting), invasion of the erythrocyte by the parasite and transport functions. It also contains an artistic impression of the ultrastructural morphology of the interaerythrocytic cycle stages and some details about the morphology of mitochondria and the apicoplast. Most pathways are relevant to the erythrocytic phase of the parasite cycle. All maps were checked for the presence of enzyme-coding genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). The site is constructed in a hierarchical pattern that permits logical deepening: * Grouped pathways of major chemical components or biological process ** Specific pathways or specific process *** Chemical structures of substrates and products or process **** Names of enzymes and their genes or components of process Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and to IUBMB reaction scheme. Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula. Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme''s coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database.
Biomedical and genomic research center located in Cambridge, Massachusetts, United States. Nonprofit research organization under the name Broad Institute Inc., and is partners with Massachusetts Institute of Technology, Harvard University, and the five Harvard teaching hospitals. Dedicated to advance understanding of biology and treatment of human disease to improve human health.
Database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites. A variety of bioinformatics tools for the prediction, analysis and visualization of regulons and gene reglulatory networks is included. The integrated approach provides information about molecular networks in prokaryotes with focus on pathogenic organisms. In detail this concerns: * transcriptional regulation (transcription factors and their DNA binding sites * signal transduction (two-component systems, phosphylation cascades) * protein interactions (complex formation, oligomerization) * biochemical pathways (chemical reactions) * other regulation events (e.g. codon usage, etc. ...) It aims to be a resource to model protein-host interactions and to be a suitable platform to analyze high-throughput data from proteomis and transcriptomics experiments (systems biology). Currently it mainly contains detailed information about operon and promoter structures including huge collections of transcription factor binding sites. If an appropriate number of regulatory binding sites is available, a position weight matrix (PWM) and a sequence logo is provided, which can be used to predict new binding sites. This data is collected manually by screening the original scientific literature. PRODORIC also handles protein-protein interactions and signal-transduction cascades that commonly occur in form of two-component systems in prokaryotes. Furthermore it contains metabolic network data imported from the KEGG database., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options.
National Cancer Institute Office of Biorepositories and Biospecimen Research
NCI Office of Biorepositories and Biospecimen Research
Office of Biorepositories and Biospecimen Research
The NCI Office of Biorepositories and Biospecimen Research (OBBR) was established in 2005 in recognition of the critical role that biospecimens play in cancer research. The OBBR is responsible for developing a common biorepository infrastructure that promotes resource sharing and team science, in order to facilitate multi-institutional, high throughput genomic and proteomic studies. OBBR is focused on the following objectives: * Establish biobanking as a new area of research, in order to determine the impact of various collection and processing protocols on the usefulness of biospecimens in genomic and proteomic studies * Disseminate first-generation Best Practices in order to harmonize policies and procedures of NCI-supported biorepositories * Develop future generations of biorepository best practices, based on the data generated in the biobanking research programs above * Promote professional oversight of biospecimen standards development by standards organizations * Develop new technologies for biorepository operations * Develop a biorepository accreditation program * Coordinate with the international biobanking community to harmonize policies and procedures to facilitate multi-national research
Low Resolution Electromagnetic Tomography
LORETA: low resolution brain electromagnetic tomography
Software package for functional imaging of human brain. Used to compute three dimensional distribution of electric neuronal activity from non-invasive measurements of scalp electric potential differences with high time resolution in millisecond range. Non-invasive intracranial time series are used for studying functional dynamic connectivity.. Current software version includes two new, improved variants of the original method: standardized (sLORETA) and exact (eLORETA). The new methods are characterized by exact localization when tested with point sources. Due to the fact that these methods are multivariate tomographies that are solutions to the inverse EEG problem, and that they are linear in nature, they will produce a low spatial resolution image for any distribution of activity. This property is not shared by naive one-at-a-time single dipole techniques.
University of Texas Health Science Center at San Antonio Department of Pharmacology
The Department of Pharmacology at the Health Science Center at San Antonio is uniquely positioned to carry out research into the most relevant areas in pharmacology as well as to deliver superior training in pharmacology. Our faculty use approaches that range from the molecular and cellular through electrophysiology and systems to behavior. The Department of Pharmacology at the University of Texas Health Science Center at San Antonio (UTHSCSA) has 18 tenure-track or tenured faculty, 11 research-track faculty, 15 graduate students, and 15 postdoctoral fellows. We are very excited about recent developments in pharmacology that allow new and challenging means of exploring the biological effects of drugs. Graduate studies leading to a Doctor of Philosophy degree in the basic biomedical sciences at UTHSCSA are offered in the Integrated Multidisciplinary Graduate Program (IMGP). The Department of Pharmacology administers two tracks within the IMGP: the pharmacology track and the neuroscience track. The Department of Pharmacology has a ten-week summer research program that offers participants a variety of experiences that will help prepare them for success in research-intensive doctoral programs. Participants will have research responsibilities, attend seminars, actively participate in a student journal club and take part in formal course work. Prior research experience is not necessary, and students of all undergraduate levels are encouraged to apply.
The initial objective of Genoscope was to compare the genomic sequences of this fish to that of humans to help in the annotation of human genes and to estimate their number. This strategy is based on the common genetic heritage of the vertebrates: from one species of vertebrate to another, even for those as far apart as a fish and a mammal, the same genes are present for the most part. In the case of the compact genome of Tetraodon, this common complement of genes is contained in a genome eight times smaller than that of humans. Although the length of the exons is similar in these two species, the size of the introns and the intergenic sequences is greatly reduced in this fish. Furthermore, these regions, in contrast to the exons, have diverged completely since the separation of the lineages leading to humans and Tetraodon. The Exofish method, developed at Genoscope, exploits this contrast such that the conserved regions which can be identified by comparing genomic sequences of the two species, correspond only to coding regions. Using preliminary sequencing results of the genome of Tetraodon in the year 2000, Genoscope evaluated the number of human genes at about 30,000, whereas much higher estimations were current. The progress of the annotation of the human genome has since supported the Genoscope hypothesis, with values as low as 22,000 genes and a consensus of around 25,000 genes. The sequencing of the Tetraodon genome at a depth of about 8X, carried out as a collaboration between Genoscope and the Whitehead Institute Center for Genome Research (now the Broad Institute), was finished in 2002, with the production of an assembly covering 90 of the euchromatic region of the genome of the fish. This has permitted the application of Exofish at a larger scale in comparisons with the genome of humans, but also with those of the two other vertebrates sequenced at the time (Takifugu, a fish closely related to Tetraodon, and the mouse). The conserved regions detected in this way have been integrated into the annotation procedure, along with other resources (cDNA sequences from Tetraodon and ab initio predictions). Of the 28,000 genes annotated, some families were examined in detail: selenoproteins, and Type 1 cytokines and their receptors. The comparison of the proteome of Tetraodon with those of mammals has revealed some interesting differences, such as a major diversification of some hormone systems and of the collagen molecules in the fish. A search for transposable elements in the genomic sequences of Tetraodon has also revealed a high diversity (75 types), which contrasts with their scarcity; the small size of the Tetraodon genome is due to the low abundance of these elements, of which some appear to still be active. Another factor in the compactness of the Tetraodon genome, which has been confirmed by annotation, is the reduction in intron size, which approaches a lower limit of 50-60 bp, and which preferentially affects certain genes. The availability of the sequences from the genomes of humans and mice on one hand, and Takifugu and Tetraodon on the other, provide new opportunities for the study of vertebrate evolution. We have shown that the level of neutral evolution is higher in fish than in mammals. The protein sequences of fish also diverge more quickly than those of mammals. A key mechanism in evolution is gene duplication, which we have studied by taking advantage of the anchoring of the majority of the sequences from the assembly on the chromosomes. The result of this study speaks strongly in favor of a whole genome duplication event, very early in the line of ray-finned fish (Actinopterygians). An even stronger evidence came from synteny studies between the genomes of humans and Tetraodon. Using a high-resolution synteny map, we have reconstituted the genome of the vertebrate which predates this duplication - that is, the last common ancestor to all bony vertebrates (most of the vertebrates apart from cartilaginous fish and agnaths like lamprey). This ancestral karyotype contains 12 chromosomes, and the 21 Tetraodon chromosomes derive from it by the whole genome duplication and a surprisingly small number of interchromosomal rearrangements. On the contrary, exchanges between chromosomes have been much more frequent in the lineage that leads to humans. Sponsors: The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute.
Database of Poplar Transcription Factors
Database of collected known and predicted transcription factors (TF) of the black cottonwood tree, Populus trichocarpa. They have made extensive annotations, including similarity searches against major databases (Uniprot, RefSeq, EMBL, TRANSFAC et al) and EST expression information extraction from UniGene clusters and microarray expression, to provide comprehensive information for the putative TFs. In addition, multiple alignment of the DNA-binding domain of each family, Neighbor-Joining phylogenetic tree of each family, the GO annotation, homolog with the Database of Arabidopsis Transcription Factors (DATF), the Database of Rice Transcription Factors (DRTF) are included.
A Matlab toolbox for the statistical analysis of univariate and multivariate surface data using linear mixed effects models and random field theory.
VBASE2: the integrative germ-line V gene database
Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences. Based on the properties of the source sequences, V genes are classified into 3 different classes: * Class 1: genomic and rearranged evidence * Class 2: genomic evidence only * Class 3: rearranged evidence only This allows careful sequence quality validation by the user. References to other immunological databases ( KABAT, IMGT/LIGM and VBASE ) are given to provide all public annotation data for each V gene. The VBASE2 database can be accessed either by the Direct Query interface or by the DNAPLOT Query interface. The Sequences given by the user are aligned with DNAPLOT against the VBASE2 database. Direct Query allows to enter sequence IDs and names (Field 1), choose species, locus, V gene family and class (Field 2) or search for 100% sequences (Field 3). At the DNAPLOT Query, the sequences given by the user are aligned with DNAPLOT against the VBASE2 database. The DNAPLOT program offers V gene nucleotide sequence alignment referring to the IMGT V gene unique numbering. The Quick Search can be used either for Direct Query to search for sequence IDs and V gene names or for DNAPLOT Query for up to 5 sequences. The new Fab Analysis allows you to align Fab, scFab, scAb or scFv sequences with DNAPLOT against the VBASE2 database, where both heavy and light chain are analyzed.
Open Biological and Biomedical Ontologies
Open Biological and Biomedical Ontology Foundry
A collaboration involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. In addition to a listing of OBO ontologies, this site provides a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development. Feedback is welcome and participation encouraged.
Database of Human Hemoglobin Variants and Thalassemias
HbVar is a relational database of information about hemoglobin variants and mutations that cause thalassemia. The initial data came from Syllabi authored by Prof. Titus H.J. Huisman, Mrs. Marianne F.H. Carver, Dr. Erol Baysal, and Prof. Georgi D. Efremov. This information was converted to a database, and now new entries are added and old entries are corrected by curators. HbVar results from a collaboration among several investigators at Penn State University (USA), INSERM Creteil (France), and Boston University Medical Center (USA). Visit our query page or summary page to see the types of information available.
An application ontology integrating knowledge about the eukaryotic cell cycle.
Los Alamos Hepatitis C Immunology Database
The HCV Immunology Database contains a curated inventory of immunological epitopes in HCV and their interaction with the immune system, with associated retrieval and analysis tools. The funding for the HCV database project has stopped, and this website and the HCV immunology database are no longer maintained. The site will stay up, but problems will not be fixed. The database was last updated in September 2007. The HIV immunology website contains the same tools, and may be usable for non-HCV-specific analyses. For new epitope information, users of this database can try the Immuno Epitope Database (http://www.immuneepitope.org).
Set of standards and practices for using XML to facilitate information exchange between user application software and neuroscience data repositories. It allows for common shared library routines to handle most of the data processing, but also supports use of structures specialized to the needs of particular neuroscience communities. This site also serves as a repository for BrainML models. (A BrainML model is an XML Schema and optional vocabulary files describing a data model for electronic representation of neuroscience data, including data types, formats, and controlled vocabulary. ) It focuses on layered definitions built over a common core in order to support community-driven extension. One such extension is provided by the new NIH-supported neuroinformatics initiative of the Society for Neuroscience, which supports the development of expert-derived terminology sets for several areas of neuroscience. Under a cooperative agreement, these term lists will be made available Open Source on this site. The repository function of this site includes the following features: * BrainML models are published in searchable, browsable form. * Registered users may submit new models or new versions of existing models to accommodate data of interest. * BrainML model schema and vocabulary files are made available at fixed URLs to allow software applications to reference them. * Users can check models and/or instance documents for correct format before submitting them using an online validation service. To complement the BrainML modeling language, a set of protocols have been developed for BrainML document exchange between repositories and clients, for indexing of repositories, and for data query.
A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.
Implementation of a database of ionic conductance models stored in simulator-independent NeuroML format, with a parser to convert the representation into GENESIS simulation scripts. It was developed as a means of sharing channel models between different neural simulators. It is also one of the first core components of the Modelers Workspace (MWS). At present, ChannelDB is implemented as a stand-alone module, with its own graphical user interface to the database, which is implemented with MySQL. After further development, the ChannelDB GUI will be merged into the MWS. The NeuroML development kit parser (from http://www.neuroml.org/ndk.html) is used to create Java objects from the NeuroML format XML files stored in the database. These are then accessed with Java software to create simulation scripts for the particular simulator. The first implementation of a parser to create simulation scripts is for GENESIS. The files in this package will let you * Search a small remote database of ion channel models to retrieve and view their descriptions and NeuroML representations, and generate simulator scripts from the model representation. * Set up your own database of ion channel models * Extend ChannelDB with the addition of parsers for other simulators, and with Java classes to cover other types of channels.
A searchable databases of diatom ESTs (expressed sequence tags) that can be used to explore diatom biology. Research has generated approximately 90,000 ESTs from P. tricornutum cells grown in a range of conditions. Here we present a database of these sequences, that can be used for digital gene expression studies to explore this organisms responses to a range of environmental conditions. Such studies should provide a foundation for interpreting the ecological success of diatoms.
neurodatabase.org Laboratory of Neuroinformatics Weill Medical College of Cornell University
Neurodatabase.org: Laboratory of Neuroinformatics Weill Medical College
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 09, 2015. A repository of neurophysiology data conforming to BrainML data models and protocols: BrainML-formatted experimental data submissions are published in searchable, browsable form. Registered users may submit new experiments. The site contains spike trains, voltage time series, and some derived histograms from single cell and multi-unit activity. The database focuses on in vivo somatosensory and visual activity during task performance. This resource contains only a few datasets, but they are of high quality and have been used for reanalysis by several parties. There are three primary interfaces for querying data from this repository: a web-based browse interface, a web-based HTML query form, and a Java web start desktop application. In addition, there is an XML interface useful for direct access by software clients. To download the source code, please read and acknowledge the license agreement.
Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in.
CLIVAR & Carbon Hydrographic Data Office
CLIVAR and Carbon Hydrographic Data Office
Supports oceanographic research by providing access to high quality, global, vessel-based CTD and hydrographic data from GO-SHIP, WOCE, CLIVAR and other repeat hydrography programs. These data are openly accessible and served in standardized community formats (WHP-Exchange, WOCE, and netCDF). CCHDO also manages public and non-public CTD data for use by the global Argo and OceanSITES programs.
The Eurofung project is a Coordination Action with the aim of developing a strategy to build up and maintain an integrated, sustainable European genomic database required for innovative genomics research of filamentous fungal model organisms of interest. This database will become a crystallization point for related systems and then could be integrated and conserved in a central European genomic database. The consortium counts 32 member laboratories, three of which have partner status. A Fungal Industrial Platform (FIP) of 13 members is also associated with the project. The project focuses on several filamentous fungi for different reasons. Aspergillus nidulans has a long record of use as a fungal model organism. Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum are important cell factories used for the production of enzymes and metabolites including compounds such as Beta-lactams with benefits to human health. The human pathogen Aspergillus fumigatus serves not only as a model pathogen, but becomes more and more a serious threat to human health. The project contributes to create the conditions and facilities within Europe to widely apply all genomics technologies in filamentous fungal research. This will greatly expand our knowledge about filamentous fungi. This new genomics information will thus be beneficial to European biotechnology industries and help to improve the prevention and treatment of fungal disease. Expected results: The main results expected from this project are: - The contribution of the community to the manual annotation of important fungal genomes through annotation jamborees. - The realization of an integrated sustainable fungal genomic database through collaboration with bioinformatics centers and incorporation of the community data. - The realization of a fungal genomics knowledge base for the Eurofungbase community and the European fungal biotech industry through meetings, workshops and web-based information. - Intensified collaboration between the members of the network including the participating industries, thus strengthening the infrastructure for high quality fungal genomics research in Europe and furthermore determining joint research targets for the future. -Individualized training of a next generation of young scientists in fungal genomics and biotechnological research.
LabTrove is a blogging tool for scientific researchers. Comes with features like version control, complex metadata framework to enable effective classification of content and an extensive plug in architecture. Sponsors: Blog, Scientific, Researcher, Metadata,
ontology for the formal representation of cell lines and their correspnding culture conditions.
The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Users can BLAST sequences, browse by protein name, or view by protein function and functional subclass.
Magnetics Information Consortium (MagIC)
Databases that accept and provide access to paleomagnetic and rock magnetic data. The paleomagnetic data range from individual measurements to specimen, sample or site level results, including a wide variety of derived parameters or associated rock magnetic measurements. The rock magnetic database includes data collected during rock magnetic experiments on remanence, anisotropy, hysteresis and susceptibility. The MagIC Console Software provides an effective environment in Microsoft Excel where users can collate and prepare their paleomagentic and rock magnetic data for uploading in the Online MagIC Database.
Biological Research Assistant for Text mining
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. An information extraction (IE) tool specifically designed to perform biomedical IE and which is able to locate and analyze both abstracts and full-length papers. BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE.
University at Buffalo Department of Behavioral Neuroscience Program
Buffalo Behavioral Neuroscience Doctoral Program
Goal of Behavioral Neuroscience Program is to provide student with broad and deep knowledge of physiological and biological factors that control and affect behavior. Through close and personalized student mentor relationship we try to instill in student appreciation for programmatic problem oriented, rather than technique oriented, research. Program provides training toward the PhD for approximately 20 students at time. All students are expected to master core of theoretical and research methods, as well as to become skilled in conduct of their own research. In addition, students tailor their education to fit their own interests and professional goals through selection of appropriate elective courses and research projects.
Database of Arabidopsis Transcription Factors
Database that collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families. It uses not only locus (gene), but also gene model (transcript, protein) and the detail information is for each gene model not for locus. It adds multiple alignment of the DNA-binding domain of each family, Neighbor-Joining phylogenetic tree of each family, the GO annotation, homolog with the Database of Rice Transcription Factors (DRTF). It also keeps old information items such as the unique cloned and sequenced information of about 1200 transcription factors, protein domains, 3D structure information with BLAST hits against PDB, predicted Nuclear Location Signals, UniGene information, as well as links to literature reference.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Rickettsia are obligate intracellular bacteria living in arthropods. They occasionally cause diseases in humans. To understand their pathogenicity, physiologies and evolutionary mechanisms, RicBase is sequencing different species of Rickettsia. Up to now we have determined the genome sequences of R. conorii, R. felis, R. bellii, R. africae, and R. massiliae. The RicBase aims to organize the genomic data to assist followup studies of Rickettsia. This website contains information on R. conorii and R. prowazekii. A R. conorii and R. prowazekii comparative genome map is also available. Images of genome maps, dendrogram, and sequence alignment allow users to gain a visualization of the diagrams.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 24, 2015. This package is no longer supported. The majority of the functionality for conditional haplotype tests in population-based samples has been implemented in PLINK, with a better interface and more robust, faster computation: please use that from now on. Software tool to perform haplotype-based association analysis, for quantitative and qualitative traits, in population and family samples, using single nucleotide polymorphism or multiallelic marker data. What whap can do: * Analyze quantitative and qualitative traits * Handle unrelated individuals and/or parent-offspring trio data * Perform a regression-based haplotype association test for SNP data * Perform a secondary test based on pairwise haplotype similarity * Phase genotype data using a standard E-M approach, and handle ambiguity in E-M inferred haplotypes * Include covariates and moderator variables * Flexibly constrain effects across haplotypes to tested nested models * Perform a robust within-family test when parental genotypes are present * Analyze multiallelic markers (new) * Use dominant or recessive (new) genetic models (new)
Software program that performs the auto-alignment and the composition of images to create the mosaic.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
RTPrimerDB- The Real-Time PCR and Probe Database
Database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridization Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimization, and to introduce a certain level of uniformity and standardization among different laboratories. Researchers are encouraged to submit their validated primer and probe sequence, so that other users can benefit from their expertise. The database can be queried using the official gene name or symbol, Entrez or Ensembl Gene identifier, SNP identifier, or oligonucleotide sequence. Different options make it possible to restrict a query to a particular application (Gene Expression Quantification/Detection, DNA Copy Number Quantification/Detection, SNP Detection, Mutation Analysis, Fusion Gene Quantification/Detection, Chromatin immunoprecipitation (ChIP)), organism (Human, Mouse, Rat, and others) or detection chemistry.
Software program to adjust the alignment of two adjacent images. Allows to correct for any misalignment that may occur during auto-alignment step. Serves as a bootstrap to get the images in approximately the right place.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that is intended to provide p-values for the hypothesis of association between evolutionary clades and continuous traits, using haplotype trees. (entry from Genetic Analysis Software)
Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution.
IBASPM: Individual Brain Atlases using Statistical Parametric Mapping Software
Individual Brain Atlases using Statistical Parametric Mapping Software
Individual Brain Atlases using Statistical Parametric Mapping Software (IBASPM)
The aim of this work is to present a toolbox for structure segmentation of structural MRI images. All programs were developed in MATLAB based on a widely used fMRI, MRI software package, SPM99, SPM2, SPM5 (Wellcome Department of Cognitive Neurology, London, UK). Other previous works have developed a similar strategy for obtaining the segmentation of individual MRI image into different anatomical structures using a standardized Atlas. Have to be mentioned the one introduced by Montreal Neurological Institute (MNI) that merges the information coming from ANIMAL (algorithm that deforms one image (nonlinear registration) to match previously labelled) and INSECT (Cerebral Tissue Classification) programs for obtaining a suitable gross cortical structure segmentation (Collins et al, 1999). Here both, nonlinear registration and gray matter segmentation processes have been performed through SPM99, SPM2, SPM5 subroutines. Three principal elements for the labeling process are used: gray matter segmentation, normalization transform matrix (that maps voxels from individual space to standardized one) and MaxPro MNI Atlas. All three are combined to yield a good performance in segmenting gross cortical structures. The programs here can be used in general for any standardized Atlas and any MRI image modality. System Requirements: 1. The IBASPM graphical user interface (GUI) runs only under MATLAB 7.0 or higher. The non-graphical version runs under MATLAB 6.5 or higher. 2. Statistical Parametrical Mapping Software SPM2, SPM5 Main Functions: * Atlasing: Main function ( This file contains spm_select script from SPM5 toolbox and uigetdir script from MATLAB 7.0 ). * Auto_Labeling : Computes individual atlas. * Create_SPAMs : Constructs Statistical Probability Anatomy Maps (SPAMs). * Create_MaxProb : Creates Maximum Probability Atlas (MaxPro) using the SPAMs previously computed. * All_Brain_Vol : Computes whole brain volume masking the brain using the segmentation files (if the segmentation files does not exist it segments). * Struct_Vol : Computes the volume for different structures based on individual Atlas previously obtained by the atlasing process. * Vols_Stats : Computes mean and standard deviation for each structure in a group of individual atlases.
Virus Database at University College London
VIDA contains a collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family, users can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures. * Search homologous protein families from particular virus families * Links to complete genome sequence: Arteriviridae, Coronaviridae, Herpesviridae, Poxviridae The Virus Database at University College London has been developed as a system to organize animal virus open reading frame sequences. All known and predicted protein sequences from complete and partial genomes of particular virus families are extracted from GenBank and filtered to remove 100% redundancy. On the basis of sequence similarity the sequences are then clustered into homologous protein families (HPFs). The families are enriched with annotations including function and functional classification, related protein structures, taxonomy, length of the proteins, boundaries of the conserved region/s, virus-specific gene name and links to EMBL entries and SWISSPROT., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
BLIMP: Biomedical LIterature Mining Publications
Biomedical LIterature (and text) Mining Publications
Bibliography covering all publications related to the fast-growing field of biomedical literature and text mining. This forum for collecting, compiling and sharing is a one-stop resource, letting researchers find out who-does-what in the area and where it is published, bridging across the many discipline-specific venues in which biomedical text-mining papers are published. If you know of a relevant paper that is missing from BLIMP, or have an accepted-for-publication paper, PhD/MSc thesis or a technical report, that you believe is relevant to biomedical text mining, fill in the submission form. The fast-growing field of biomedical literature mining is highly-interdisciplinary. Publications appear in forums ranging from the SIGIR conferences (the ACM Special Interest group on Information Retrieval) to journals such as Nature and Science, with the whole range of bioinformatics forums in-between. To substantially contribute, one must know what was/is being done in this diverse area, and place the work in context - both biologically and computationally. Instead of starting a journal fully dedicated to biomedical literature mining, thus creating yet another publication venue, this site offers an alternative: It holds in one place a compilation of references to relevant papers that have been published or accepted for publication.
A UNIX-style command-line program which quickly computes multifactorial ANOVAs for very large data sets with minimal memory use (without loading all of the data into memory). It has been used for fMRI analysis, e.g. CLEAVE adds the following to the standard ANOVA analyses: # Unlimited numbers of factors can be analyzed. # Factor Correlation and Unequal Variance Corrections # Treatment Magnitudes: omega^2, partial eta^2, and R^2 # A convenient Ranking of Factors based upon treatment magnitudes and significance levels. # Post-Hoc Significance Tests # Post-Hoc Power Table to gauge how many subjects will be needed to achieve significance. # Allows the use of Random Factors. # A Configuration File to make the program more tunable # A Histogram and Cell Line Diagrams: which help the user to detect outliers. # Associated MATLAB functions: port CLEAVE-style data sets in or out of MATLAB.
Sixty years of study have made Escherichia coli K-12 the most deeply understood organism at the molecular level. Much of what we know about cellular processes can be traced to fundamental discoveries in E. coli. In spite of its great importance as a model organism, information about E. coli is distributed among many online resources. EcoliHub uses web services that are being developed to make seamless bidirectional connections between E. coli resources, thereby enabling the full use of existing knowledge and supporting cutting-edge research into the molecular basis of life. :topical portal;
Boston Area Community Health (BACH) Survey
An epidemiologic study being conducted in the Boston metropolitan area to examine the prevalence of symptoms for health problems such as interstitial cystitis, urinary incontinence, benign prostatic hyperplasia, prostatitis, hypogonadism, and sexual function. Of interest to the survey are health disparities and inequalities. BACH is especially concerned with lack of adequate health insurance, lack of access to adequate medical care, and how these problems influence patterns of disease. The study also focuses on social determinants of disease that are over and above the contribution of individual characteristics and risk factors. To achieve a randomly sampled population, four neighborhoods were divided into 12 strata and from them investigators selected census blocks. Households were then randomly selected from the census blocks and sampled to identify eligible study participants. Investigators conduct a two-hour, in-home, bilingual field interview of all eligible participants, looking at symptoms and asking questions about lifestyle, physical activity, alcohol use, nutrition, demographics, and morbidity. They also conduct a detailed inventory of medications, both prescribed and over-the-counter, and take two non-fasting blood samples for hormone, cholesterol, and lipid levels that will be stored for future studies. By the time the study ends, approximately 6,000 men and women, ages 30 to 79, from four Boston area neighborhoods that have density levels proportionate with minority populations will have been interviewed in their homes. One third of the randomly sampled population will be African American; one third, Hispanic; and one third, Caucasian.
Probe Explorer is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query. Platform: Online tool
Neuroimaging Informatics Technology Initiative Data Format Working Group
The DFWG is charged with arriving at a technical solution to the problem of multiple data formats used in fMRI research. This was identified by many investigators as a fundamental obstacle to fMRI fulfilling the promise it has to elucidate brain function. The solution arrived at by the DFWG will not be imposed on the research community, but several groups that develop fMRI-related software have already indicated their willingness to adopt the solution. Suggestions for membership on the DFWG were broadly solicited from the research community.
Virtual NeuroMorphology Electronic Database
A database of virtually generated anatomically plausible neurons for several morphological classes, including cerebellar Purkinje cells, hippocampal pyramidal and granule cells, and spinal cord motoneurons. It presently contains 542 cells. In the trade neurons collection the database contains an amaral cell archive, neuron morpho reconstructions, and mouse alpha motoneurons. Their collection of generated neurons include motoneurons, Purkinje cells, and hippocampal pyramidal cells.
CNYETB: Central New York Eye and Tissue Bank
One of the country''s leading procurement organizations and is just one of eight nationwide to house organ, tissue, and eye donation in one location. With the addition of community blood banking services in the summer of 2007, Upstate New York Transplant Services became the only organization nationwide to offer such services in conjunction with organ, tissue, and eye donation. Licensed by the NY State Dept. of Health, FDA-Registered Accredited by the Eye Bank Association of America (EBAA) and American Association of Tissue Banks (AATB)
Helicobacter Pylori Database of Protein Interactomes
H.pylori Database of Protein Interactomes
Helicobacter Pylori Database of Protein-Protein Interactions
Database that provides users with information on protein-protein interactions, as well as experimental and inferring interactions, for the organism Helicobacter pylori. Searching the database provides users with the ORF, locus, similarity comparisons, and description for the object queried.
Genes to Cognition: Neuroscience Research Programme
Genes to Cognition - Neuroscience Research Programme
Genes to Cognition-Neuroscience Research Programme
Genes to Cognition: Neuroscience Research Program
A neuroscience research program that studies genes, the brain and behavior in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Central to G2C investigations is the NMDA receptor complex (NRC/MASC), that is found at the synapses in the central nervous system which constitute the functional connections between neurons. Changes in the receptor and associated components are thought to be in a large part responsible for the phenomenon of synaptic plasticity, that may underlie learning and memory. G2C is addressing the function of synapse proteins using large scale approaches combining genomics, proteomics and genetic methods with electrophysiological and behavioral studies. This is incorporated with computational models of the organization of molecular networks at the synapse. These combined approaches provide a powerful and unique opportunity to understand the mechanisms of disease genes in behavior and brain pathology as well as provide fundamental insights into the complexity of the human brain. Additionally, Genes to Cognition makes available its biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline. The resources are freely-available to interested researchers.
Bookshelf, the books division of the NLM Literature Archive, is an online collection of full-text books, reports, databases and other documents, providing free access to over 700 texts in life science and healthcare. A vital node in the data-rich resource network at NCBI, Bookshelf enables users to easily browse, retrieve, and read content, and spurs discovery of related information. Some Bookshelf contents have a corresponding entry in PubMed. The books we host have been given to us by the publishers (we do not pay them any kind of fee). Each book is viewed as a new candidate for Bookshelf. Whether the next edition of a book comes out on Bookshelf depends on whether we have a new agreement for that edition with the publisher. The publisher must contact us with this request. You may also contact the publisher directly to request that the next edition be placed on Bookshelf.
This database have been funded by the National Human Genome Research Institute (NHGRI) to produce shotgun sequence of the Tetraodon nigriviridis genome. The strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated. Whole genome shotgun libraries were prepared from Tetraodon genomic DNA obtained from the laboratory of Jean Weissenbach at Genoscope. Additional sequence data of approximately 2.5X coverage of Tetraodon has also been generated by Genoscope in plasmid and BAC end reads. Broad and Genoscope intend to pool their data and generate whole genome assemblies. Tetraodon nigroviridis is a freshwater pufferfish of the order Tetraodontiformes and lives in the rivers and estuaries of Indonesia, Malaysia and India. This species is 20-30 million years distant from Fugu rubripes, a marine pufferfish from the same family. The gene repertoire of T. nigroviridis is very similar to that of other vertebrates. However, its relatively small genome of 385 Mb is eight times more compact than that of human, mostly because intergenic and intronic sequences are reduced in size compared to other vertebrate genomes. These genome characteristics along with the large evolutionary distance between bony fish and mammals make Tetraodon a compact vertebrate reference genome - a powerful tool for comparative genetics and for quick and reliable identification of human genes.
Duke University Medical Center Neuropsychiatric Imaging Research Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Neuropsychiatric Imaging Research Laboratory (NIRL) analyze magnetic resonance images to research numerous psychiatric disorders including depression, bipolar disorder, and post traumatic stress disorder. NIRL also develop new methods for MR image processing to improve quality and reliability of research in the field of neuroimaging. The laboratory computer resources include Sun MicroSystems SPARC workstations, Windows PCs, over 3 terabytes of online hard disk space, and a web server system. The lab has a site filtered anonymous ftp server system for data transfer. There are individual offices for visiting fellows and analysts for image processing as well as shared work-study rooms and conference facilities.
Database of known enzyme structures that have been deposited in the Protein Data Bank (PDB). The enzyme structures are classified by their E.C. number of the ENZYME Data Bank. Browse the classification hierarchy or enter an EC number or search-string. There are currently 45,638 PDB-enzyme entries in the PDB (as at 23 February, 2013) involving 38,109 separate PDB files - some files having more than one E.C. number associated with them.
Minimally Invasive Surgical Therapies Treatment Consortium for Benign Prostatic Hyperplasia
Minimally Invasive Surgical Therapies (MIST) Treatment Consortium for Benign Prostatic Hyperplasia (BPH)
Minimally Invasive Surgical Therapy Consortium for Benign Prostatic Hyperplasia
Randomized clinical trial to determine the efficacy and safety of three treatments for benign prostatic hyperplasia (BPH): transurethral needle ablation (TUNA), transurethral microwave therapy (TUMT), and medical therapy with alfuzosin and finasteride. The study has been terminated. (Inability to recruit required sample size.)
High-resolution electronic atlases for mouse strains c57bl/6j, a/j, and dba/2j in either coronal or horizontal section. About this Atlas: The anterior-posterior coordinates are taken from an excellent print atlas of a C57BL/6J brain by K. Franklin and G. Paxinos (The Mouse Brain in Stereotaxic Coordinates, Academic Press, San Diego, 1997, ISBN Number 0-12-26607-6; Library of Congress: QL937.F72). The abbreviations we have used to label the sections conform to those in the Franklin-Paxinos atlas. A C57BL/6J mouse brain may contain as many as 75 million neurons, 23 million glial cells, 7 million endothelial cells associated with blood vessels, and 3 to 4 million miscellaneous pial, ependymal, and choroid plexus cells (see data analysis in Williams, 2000). We have not yet counted total cell number in DBA/2J mice, but the counts are probably appreciably lower.The brain and sections were all processed as described in our methods section. The enlarged images have a pixel count of 1865 x 1400 and the resolution is 4.5 microns/pixel for the processed sections.Plans: In the next several years we hope to add several additional atlases of the same sort for other strains of mice. A horizontal C57BL/6J atlas and a DBA/2J coronal atlas were completed by Tony Capra, summer 2000, and additional atlases may be made over the next several years. As describe in the MBL Procedures Section is not hard to make your own strain-specific atlas from the high resolution images in the MBL.
The Dinucleotide Property Database is designed to collect and analyse thermodynamic, structural and other dinucleotide properties. The table presenting all the dinucleotide properties can be pruned and rearranged by different criteria. The database contains different export and analysis functions.
A tool that can be used to predict caspase cleavage sites from human protein sequences.
Focal Segmental Glomerulosclerosis in Children and Young Adults Interventional Study
Focal Segmental Glomerulosclerosis (FSGS) Clinical Trial
Focal Segmental Glomerulosclerosis (FSGS) in Children and Young Adults Interventional Study
Focal Segmental Glomerulosclerosis Clinical Trial
Focal Segmental Glomerulosclerosis Clinical Trial (FSGS-CT)
FSGS in Children and Young Adults Interventional Study
Network of collaborative research centers that tested the effects of treatment with cyclosporine to treatment with mycophenalate mofetil combined with oral pulse dexamethasone in children and young adults with focal segemental glomerulosclerosis. Efficacy was assessed in terms of induction of remission of proteinuria after 52 weeks of treatment and sustained remission after 26 weeks off treatment. The clinical sites were State University of New York, Stony Brook; Montefiore Medical Center; Seattle Children' '''s Medical Center; Medical City Dallas Hospital; and the University of North Carolina. The Cleveland Clinic is the data-coordinating center, and NephCure will fund ancillary studies.
Complementary and Alternative Medicine for Urological Symptoms
Complementary and Alternative Medicine for Urological Symptoms (CAMUS)
Complementary and Alternative Medicine for Urological Symptoms (CAMUS) Clinical Trial
Complementary and Alternative Medicine for Urological Symptoms Clinical Trial
Randomized, multicenter, double blind, placebo controlled clinical trial of phytotherapy for benign prostate symptoms among men. The CAMUS trial will test Saw palmetto in about 369 men. Men who decide to be part of the CAMUS trial will be given one out of two possible treatments at random. One out of every two men would get an inactive placebo treatment. One out of every two men would get Saw palmetto pills. This kind of scientific study is the best way to find out if the plant extracts really work to prevent men with benign prostatic hyperplasia (BPH) from getting worse. During the study, men will not know which of the two treatments they are assigned to. They will be followed very closely by a study team every 12 weeks to see how they are doing. Men in the CAMUS trial will be studied over 72 weeks. Ten clinical centers will participate in the trial. They are located at: Columbia University, NY, NY; New York University, NY, NY; University of Texas Southwestern Medical Center, Dallas, Texas; University of Colorado, Denver, CO; Washington University, St. Louis, MO; Yale University, New Haven, CT; Queens University, Hamilton, Ontario, Canada; Northwestern University, Chicago, IL; University of Maryland, Baltimore, MD; University of California at San Francisco, San Francisco, CA.
HDBase - A Community Website for Huntington''s Disease Research
HDBase - A Community Website for Huntingtons Disease Research
A community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse models
Standard brain atlas of the honeybee presented as an interactive three-dimensional surface model with integrated neuron and neuronal tracts. The standard atlas was created as an average-shape atlas of 22 neuropils, calculated from 20 individual immunostained whole-mount bee brains. After correction for global size and positioning differences by repeatedly applying an intensity-based nonrigid registration algorithm, a sequence of average label images was created. The Honeybee, Apis mellifera has been studied extensively with respect to its sensory and neural capacities in navigation, communication, visual and olfactory learning and memory processing. The goal is to integrate the entirety of information into a Virtual Atlas of the Honeybee Brain. This common spatial reference map will potentiate the representation of structural and functional data obtained in different experiments and from different individuals.
Database containing the DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented; the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. The objective of this project is to generate a comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications. There are over 360 disease-associated genes or loci on chromosome 7. A major challenge ahead will be to represent chromosome alterations, variants, and polymorphisms and their related phenotypes (or lack thereof), in an accessible way. In addition to being a primary data source, this site serves as a weighing station for testing community ideas and information to produce highly curated data to be submitted to other databases such as NCBI, Ensembl, and UCSC. Therefore, any useful data submitted will be curated and shown in this database. All Chromosome 7 genomic clones (cosmids, BACs, YACs) listed in GBrowser and in other data tables are freely distributed.
University of Reading; Reading; United Kingdom
Public university in Reading, Berkshire, England. It was founded in 1892 as University College, Reading, a University of Oxford extension college.
Annotea is a W3C LEAD (Live Early Adoption and Demonstration) project under Semantic Web Advanced Development (SWAD). Annotea enhances collaboration via shared metadata based Web annotations, bookmarks, and their combinations. By annotations we mean comments, notes, explanations, or other types of external remarks that can be attached to any Web document or a selected part of the document without actually needing to touch the document. When the user gets the document he or she can also load the annotations attached to it from a selected annotation server or several servers and see what his peer group thinks. Similarly shared bookmarks can be attached to Web documents to help organize them under different topics, to easily find them later, to help find related material and to collaboratively filter bookmarked material. Annotea is part of the Semantic Web efforts. It provides a RDF metadata based extendible framework for rich communication about Web pages while offering a simple annotation and bookmark user interface. The annotation metadata can be stored locally or in one or more annotation servers and presented to the user by a client capable of understanding this metadata and capable of interacting with an annotation server with the HTTP service protocol.
The Yeast Microarray Global Viewer (yMGV) is an on-line database providing a synthetic view of the transcriptional expression profiles of yeast genes among most of the published expression datasets. yMGV displays a one-screen graphical representation of gene expression variations for each published genome-wide experiments, allowing a quick retrieval of experimental conditions having an effect upon expression of this gene. It can show expression data for orthologs of supported yeasts, and also provides tools to isolate groups of genes sharing similar transcription profiles in a defined subset of experiments. Additionally, yMGV provides a set of statistical tools allowing a critical assessment of the published data.
Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical representations from Geno Ontology (GO) annotated interaction data maintained by The Grid. The following list describes some of the important characteristics of the Osprey Network Visualization System: * Portability ( cross platform availability ) o Osprey is available on almost all Platforms that support the latest Java Plugin * Tools for Biological Analysis o Osprey provides many features such as network filters, connectivity filters, advanced layouts, and dataset superimposing which are extremely useful to biologists who are interested in analyzing their data * Powerful Support Database o Integrated with Osprey is a powerful database of interactions and annotation, see section 8. The GRID ( The General Repository of Interaction Datasets ). * Ease of use o Osprey provides an extremely user friendly interface for working with interaction data * Online Database Add-on Ability o Osprey can be incorporated as a standard visualization tool with online databases such as The GRID * Support for figures o Osprey networks can be saved in SVG, PNG and JPG format so they can be used with image programs Sponsors: Development of Osprey was funded by a grant from the Canadian Institutes of Health Research.
Clusters of Orthologous Groups of proteins
COGs - Clusters of Orthologous Groups of proteins
COGs - Phylogenetic classification of proteins encoded in complete genomes
A database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be.
DMAPS - A Database of Multiple Alignments for Protein Structures
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. DMAPS database contains pre-computed multiple structure alignments for protein chains in the Protein Data Bank (PDB). Automated structure alignments have been generated for classified protein families using CE-MC algorithm. Alignments have been built only for those families with at least three members. Currently, multiple structure alignments are available for 3050 SCOP-, 3087 CATH-, 664 ENZYME- and 1707 CE-based families. Users will be able to retrieve multiple alignments for a given PDB chain classified by one of these criteria.
BOA is an R/S-PLUS program for carrying out convergence diagnostics and statistical and graphical analysis of Monte Carlo sampling output. It can be used as an output processor for the BUGS software or for any other program which produces sampling output. BOA includes all of the analysis options found in CODA, plus a few others. It is designed to be faster, more efficient, and offer more flexible data management than CODA. BOA can be used at the command-line or with the supplied menu-driven interface. Either way, the program enables the user to focus on the analysis at hand rather than on the manipulation of data. Sponsors: This resource is supported by the University of Iowa. Keywords: Bayesian, Analysis, Program, Diagnostics, Statistical, Graphical, Software,
New York Brain Bank at Columbia University
A brain bank which collects postmortem human brains to meet the needs of neuroscientists investigating specific psychiatric and neurological disorders. NYBB disburses tissue samples to investigating clinicians or scientists whose research has been approved by their Institutional Review Board. The tasks of the NYBB include: collection and processing of human postmortem brain samples for research; neuropathological evaluation and diagnosis; storage and computerized inventory of brain samples; and distribution of brain samples to investigating clinicians and scientists. Brains from individuals without neurological or psychiatric disorders are used as normal controls.
Lyngby - A Toolbox for Functional Neuroimaging
Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files.
Database of information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Listed are known spliceosomal introns in the yeast genome and the splice sites actually used are documented. Through the use of microarrays designed to monitor splicing, they are beginning to identify and analyze splice site context in terms of the nature and activities of the trans-acting factors that mediate splice site recognition. In version 3.0, expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors is included. These data are displayed on each intron page for browsing and can be downloaded for other types of analysis.
Duke University NeuroAnatomy Web Resources
Duke University: NeuroAnatomy Web Resources
Comprehensive neuroanatomy resource created for course PTA 201 Practical Neuroanatomy, including animated images and hyperlinked descriptions with the following major categories: Blood supply, motor systems, cranial nerves, neurohistology, functional organization, sensory systems, and major coverings.
University of Arizona Biology 181 Honors Course
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. HIV ...and its Coreceptors is a University of Arizona Biology 181 Honors Course describing HIV, its mechanisms of action, and more. Topics covered include: * What is HIV? The Human Immune System, How HIV attacks the Body, and How does HIV get into cells and infect them? * Interpreting and Understanding: CC CKR5: A RANTES, MIP-1a, MIP-1B Receptor as a Fusion Cofactor for Macrophage-Tropic HIV-1 * Interpreting and Understanding: Coreceptors: Implications for HIV Pathogenesis and Therapy * Statistics * Treatment: Nucleoside Reverse Transcriptase Inhibitors, Non-Nucleoside Reverse Transcriptase Inhibitors, Protease Inhibitors, Effects on Antiviral Therapy on Viral Burden * Present Research * Glossary * Links
A mouse-related portal of genomic databases and tables of mouse brain data. Most files are intended for you to download and use on your own personal computer. Most files are available in generic text format or as FileMaker Pro databases. The server provides data extracted and compiled from: The 2000-2001 Mouse Chromosome Committee Reports, Release 15 of the MIT microsatellite map (Oct 1997), The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001), and the Map Manager and text format chromosome maps (Apr 2001). * LXS genotype (Excel file): Updated, revised positions for 330 markers genotyped using a panel of 77 LXS strain. * MIT SNP DATABASE ONLINE: Search and sort the MIT Single Nucleotide Polymorphism (SNP) database ONLINE. These data from the MIT-Whitehead SNP release of December 1999. * INTEGRATED MIT-ROCHE SNP DATABASE in EXCEL and TEXT FORMATS (1-3 MB): Original MIT SNPs merged with the new Roche SNPs. The Excel file has been formatted to illustrate SNP haplotypes and genetic contrasts. Both files are intended for statistical analyses of SNPs and can be used to test a method outlined in a paper by Andrew Grupe, Gary Peltz, and colleagues (Science 291: 1915-1918, 2001). The Excel file includes many useful equations and formatting that will help in navigating through this large database and in testing the in silico mapping method. * Use of inbred strains for the study of individual differences in pain related phenotypes in the mouse: Elissa J. Chesler''s 2002 dissertation, discussing issues relevant to the integration of genomic and phenomic data from standard inbred strains including genetic interactions with laboratory environmental conditions and the use of various in silico inbred strain haplotype based mapping algorithms for QTL analysis. * SNP QTL MAPPER in EXCEL format (572 KB, updated January 2002 by Elissa Chesler): This Excel workbook implements the Grupe et al. mapping method and outputs correlation plots. The main spreadsheet allows you to enter your own strain data and compares them to haplotypes. Be very cautious and skeptical when using this spreadsheet and the technique. Read all of the caveates. This excel version of the method was developed by Elissa Chesler. This updated version (Jan 2002) handles missing data. * MIT SNP Database (tab-delimited text format): This file is suitable for manipulation in statistics and spreadsheet programs (752 KB, Updated June 27, 2001). Data have been formatted in a way that allows rapid acquisition of the new data from the Roche Bioscience SNP database. * MIT SNP Database (FileMaker 5 Version): This is a reformatted version of the MIT Single Nucleotide Polymorphism (SNP) database in FileMaker 5 format. You will need a copy of this application to open the file (Mac and Windows; 992 KB. Updated July 13, 2001 by RW). * Gene Mapping and Map Manager Data Sets: Genetic maps of mouse chromosomes. Now includes a 10th generation advanced intercross consisting of 500 animals genetoyped at 340 markers. Lots of older files on recombinant inbred strains. * The Portable Dictionary of the Mouse Genome, 21,039 loci, 17,912,832 bytes. Includes all 1997-98 Chromosome Committee Reports and MIT Release 15. * FullDict.FMP.sit: The Portable Dictionary of the Mouse Genome. This large FileMaker Pro 3.0/4.0 database has been compressed with StuffIt. The Dictionary of the Mouse Genome contains data from the 1997-98 chromosome committee reports and MIT Whitehead SSLP databases (Release 15). The Dictionary contains information for 21,039 loci. File size = 4846 KB. Updated March 19, 1998. * MIT Microsatellite Database ONLINE: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. ONLINE. Updated July 12, 2001. * MIT Microsatellite Database: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. File size = 3.0 MB. Updated March 19, 1998. * OurPrimersDB: A small database of primers. Download this database if you are using numerous MIT primers to map genes in mice. This database should be used in combination with the MITDB as one part of a relational database. File size = 149 KB. Updated March 19, 1998. * Empty copy (clone) of the Portable Dictionary in FileMaker Pro 3.0 format. Download this file and import individual chromosome text files from the table into the database. File size = 231 KB. Updated March 19, 1998. * Chromosome Text Files from the Dictionary: The table lists data on gene loci for individual chromosomes.
Since 1839, B. Braun has delivered innovative healthcare products, services and educational programs that enhance the care and safety of patients and healthcare professionals in the fields of drug delivery, IV therapy, pain control, clinical nutrition, dialysis and vascular intervention. Their products and services are used in hospitals, outpatient surgery centers and in the home care setting. Keywords: Innovation, Healthcare, Product, Educational, Program, Hospital, Outpatient, Clinical, Nutrition, Dialysis, Vascular, Intervention,Surgery,
PerkinElmer designs, manufactures and delivers advanced technology solutions that address the world''s most critical health and safety concerns, including maternal and fetal health, clean water and air, and safe food and toys. It''s expertise combines science, innovation and a culture of operational excellence to offer our customers technology services and support that improve the quality of people''s lives worldwide.
Computational Neuroanatomy Group at the Krasnow Institute for Advanced Study
Multidisciplinary research team devoted to the study of basic neuroscience with a specific interest in the description and generation of dendritic morphology, and in its effect on neuronal electrophysiology. In the long term, they seek to create large-scale, anatomically plausible neural networks to model entire portions of a mammalian brain (such as a hippocampal slice, or a cortical column). Achievements by the CNG include the development of software for the quantitative analysis of dendritic morphology, the implementation of computational models to simulate neuronal structure, and the synthesis of anatomically accurate, large scale neuronal assemblies in virtual reality. Based on biologically plausible rules and biophysical determinants, they have designed stochastic models that can generate realistic virtual neurons. Quantitative morphological analysis indicates that virtual neurons are statistically compatible with the real data that the model parameters are measured from. Virtual neurons can be generated within an appropriate anatomical context if a system level description of the surrounding tissue is included in the model. In order to simulate anatomically realistic neural networks, axons must be grown as well as dendrites. They have developed a navigation strategy for virtual axons in a voxel substrate.
Graphical Overview of Linkage Disequilibrium
Software package that provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data.
Michael J. Fox Foundation for Parkinson's Research Funded Grants
The Foundation supports research that can lead to the creation of better Parkinson's treatments. Here you can search previously awarded grants by keyword, program name, researcher name, institution/organization name, or year.
Software package of programs for complex segregation analysis in animal pedigrees.
Association for the Scientific Study of Consciousness
An academic society that promotes rigorous research directed toward understanding the nature, function, and underlying mechanisms of consciousness. The ASSC includes members working in the fields of cognitive science, medicine, neuroscience, philosophy, and other relevant disciplines in the sciences and humanities. The ASSC web site has several main functions: * coordinating annual conferences on aspects of the scientific study of consciousness. * promotion of other activities in the field (smaller conferences, mailing lists, bibliographic resource, etc). * facilitate consciousness research with awards for new investigators. * publication of papers relevant to the scientific study of consciousness in the inter-disciplinary journal Psyche. The ASSC Students community''s aim is to foster greater involvement of graduate students within the Association for the Scientific Study of Consciousness (ASSC) and improve ways in which the ASSC serves the needs of its student members. Its primary goal is to promote research and debate about consciousness among new researchers. It organizes activities like the current essay contest, details of which are on the news page. It also manage the student pages of the ASSC website and conduct occasional surveys of the ASSC student members.
This automatic primer design service uses the Primer3 Software (through EMBOSS primer3 interface) to design two sets of primers for doing a nested PCR. The input can either be in Fasta format or in GENOTRACE output format. You will have to indicate with square brackets which region should be included in the amplicon. Primers for multiple amplicons (for example all exons) can be designed in a single run.
The AIDS.gov blog serves as a forum to foster public discussion on using new media effectively in response to HIV/AIDS, as well as HIV/AIDS research and policies. Along with weekly new media posts, the blog features other AIDS.gov-authored posts, guest posts, cross-posts from the White House Office of National AIDS Policy blog and the CDC Health Protection Perspectives blog, PEPFAR blog, and posts from the National Institute of Allergies and Infectious Diseases'' (NIAID) Division of AIDS. A large number of Federal agencies and programs are engaged in HIV/AIDS prevention, testing, treatment, policy, and research efforts in the United States. AIDS.gov serves as a gateway for information about these Federal efforts, with a focus on domestic programs. Since the launch of AIDS.gov on December 1, 2006 (World AIDS Day), there has been a growing interest in using new media tools to disseminate information about HIV/AIDS and improve prevention, testing, treatment, and research outcomes. AIDS.gov created this blog to address that interest, and has since expanded content areas to include key US Government HIV/AIDS-related research and policy posts, among other topics.
The CDU provides free access and support to the UK Census Aggregate Statistics, Experian Mosaic Public Sector data, postcode lookup data and other derived data to the UK academic sector. This is the start of the Census registration process to obtain free access to census data. Registration will provide online access to the 1971-2001 census data resources and will also entitle you to use the resources of the Economic and Social Data Service (ESDS) and the History Data Service (HDS). Each individual requiring access to data is required to register before access can be granted. Registration is only available to those carrying out academic and related work in UK higher and further education, some associated institutions and UK Research Council staff. Sponsors: This resource is provided by the University of Manchester. Keywords: Statistics, Mosaic, Data, Postcode, Census, Database,
Australian Government Bureau of Meteorology
The Bureau of Meteorology is Australia''s national weather, climate and water agency. Its expertise and services assist Australians in dealing with the harsh realities of their natural environment, including drought, floods, fires, storms, tsunami and tropical cyclones. Through regular forecasts, warnings, monitoring and advice spanning the Australian region and Antarctic territory, the Bureau provides one of the most fundamental and widely used services of government. The Bureau contributes to national social, economic, cultural and environmental goals by providing observational, meteorological, hydrological and oceanographic services and by undertaking research into science and environment related issues in support of its operations and services. The Bureau of Meteorology operates under the authority of the Meteorology Act 1955 and the Water Act 2007 which provide the legal basis for its activities, while its operation is continually assessed in accordance with the national need for climatic records, water information, scientific understanding of Australian weather and climate and effective service provision to the Australian community. The Bureau of Meteorology must also fulfill Australia''s international obligations under the Convention of the World Meteorological Organization (WMO) and related international meteorological treaties and agreements.
Rankprop - Protein Ranking by Network Propagation
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on May,18,2020. Ranking algorithm that exploits global network structure of similarity relationships among proteins in database by performing diffusion operation on protein similarity network with weighted edges. Source code and web server for searching non-redundant protein database. Web server ranks proteins found in NRDB40 (from PairsDB) against query sequence of amino acids using Rankprop algorithm.
A research forum portal for ALS-related resources targeted specifically towards academic and industry-based researchers. The aim of the ALS Forum is to identify existing research resources and build new tools to help veteran researchers accelerate their work and to help those new to the ALS field quickly get up to speed. It currently consists of content developed through a partnership with the Alzforum and filtered for its relevance to ALS, as well as links to ALS review articles, and a dynamic listing of current drug development efforts relevant to ALS.
Allows users to download Unigene or BAC information using a list of identifiers or complete datasets with FTP., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software that provides a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy.
The purpose of the Budapest Open Access Initiative was to accelerate progress in the international effort to make research articles in all academic fields freely available on the internet. The participants represented many points of view, many academic disciplines, and many nations, and had experience with many of the ongoing initiatives that make up the open access movement. In Budapest they explored how the separate initiatives could work together to achieve broader, deeper, and faster success. They explored the most effective and affordable strategies for serving the interests of research, researchers, and the institutions and societies that support research. Finally, they explored how OSI and other foundations could use their resources most productively to aid the transition to open access and to make open-access publishing economically self-sustaining. The result is the Budapest Open Access Initiative. It is at once a statement of principle, a statement of strategy, and a statement of commitment. The initiative has been signed by the Budapest participants and a growing number of individuals and organizations from around the world who represent researchers, universities, laboratories, libraries, foundations, journals, publishers, learned societies, and kindred open-access initiatives. We invite the signatures, support, and participation of the entire world scientific and scholarly community.
Supports researchers using Xenopus models. Researchers are encouraged to deposit Xenopus transgenic and mutant lines, Xenopus in situ hybridization probes, Xenopus specific antibodies and Xenopus expression clones with the Centre. EXRC staff perform quality assurance testing on these reagents and then make them available to researchers at cost. Supplies wild-type Xenopus, embryos, oocytes and Xenopus tropicalis fosmids.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. This server takes a multiple-alignment file in either GCG''s MSF-format or Clustals ALN-format. Sponsors: This resource was supported by the Swiss EMBnet Node Server. Keywords: Server, Multiple-alignment,, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Brandeis University Neuroscience Undergraduate Program
Students entering Neuroscience Program at Brandeis have opportunities to work in range of fields, from cognitive neuroscience to structure and function of ion channels. Undergraduate concentration in neuroscience is designed to provide interdisciplinary program of study of neural mechanisms involved in control of human or animal behavior. Program is especially appropriate for students wishing to pursue further study in medicine, experimental psychology, or neuroscience.
Life Extension: Laboratory and Blood Testing Services
Blood testing is the single most important preventive tool you can use to help head off health problems. Life Extension makes it possible to take advantage of that tool at a fraction of the cost commercial blood labs charge. Get a picture of your overall health. Identify potential disease risks. Test for specific problems with comprehensive blood test panels and individualized tests like these: * Male and Female Comprehensive Panels * Cardiac Risk Factors * Vitamin Deficiencies * Hormone and Thyroid Panels * Metabolic and Chemistry Profiles
Software program for automated construction of genetic maps (entry from Genetic Analysis Software)
The NIH Biowulf cluster is a GNU/Linux parallel processing system designed and built at the National Institutes of Health and managed by the Helix Systems Staff. The system is designed for large numbers of simultaneous jobs common in bioinformatics as well as large-scale distributed memory tasks such as molecular dynamics. Sponsor: This work was supported by the National Institutes of Health Intramural Research Program through the Center for Information Technology and the National Institute of Neurological Disorders and Stroke, and by the Internal National Institute of Standards and Technology Research Fund. Keywords: Software, Program, Processing, System, Simulatenous, Bioinformatics, Memory, Molecular, Dynamics,
DNAReplication: A Resource for Eukaryotic DNA Replication
The DNA replication website''s aim is to provide an up to date knowledge base for the eukaryotic DNA replication community. It also aims to provide a discussion forum for replication related topics and newly published papers on the blog boards.
The Neurocommons project is an Open Source knowledge management platform for biological research. It seeks to make all scientific research materials - research articles, annotations, data, physical materials - as available and as usable as they can be. We do this by both fostering practices that render information in a form that promotes uniform access by computational agents - sometimes called interoperability. We want knowledge sources to combine meaningfully, enabling semantically precise queries that span multiple information sources. Our work covers general data and knowledge sources used in computational biology as well as sources specific to neuroscience and neuromedicine. The practices that we develop and promote are designed to play well on the Semantic Web. We view our technical work not as creating a new service or content library, although we do both, but rather as helping to promote the growth of semantically linked scientific information.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 18,2025. Biosceen C is a system designed for automating routine microbiology work. It uses a unique micro-plate format (10x10 wells), so called Honeycomb format, which is especially well suited for highly accurate temperature control. It features two covered honeycomb plates making it possible to run 200 samples simultaneously. Its unique patented incubator system features temperature control maintaining the set temperature with a 0,1 degree centigrade accuracy, while avoiding condensation of liquid on the inside of the micro plate lid. It can cool down the samples 6 degrees centigrade below the ambient temperature and its working range is from 1 to 60 degrees in steps of 0,1 degree centigrade. Sponsors: Oy Growth Curves Ab Ltd is a privately held company established in 2002 by a former Labsystems executive. It aquired the Bioscreen product line from Thermo Labsystems and has continued to maintain the product excellence Bioscreen is known for. Today the company is controlled by a new generation of owner operators, dedicated to continue developing Bioscreen to meet the demands of today''s users Keywords: Microbiology, Automation, Honeycomb, Incubation, System, Temperature, Technology, Supplier,
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. It works along with the Open Bioinformatics Foundation, who generously host it''s website, bug tracker, and mailing lists. Sponsor: This resource is supported by the Open Bioinformatics Foundation. Keywords: Tool, Software, Python, Biological, Computation, Bioinformatics,
Cerrado concepts and plant community dynamics
Ontology of Cerrado wood plant dynamics to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate.
Harvard Medical School Biopolymers Core Facility
Harvard Medical School Biopolymers Facility
Provided core services include Sanger DNA Sequencing, Next Generation DNA Sequencing (Four Illumina MiSeqs, four Illumina NextSeq 500s and one Illumina NovaSeq 6000),Next Generation Automated Library Sample Prep (Perkin Elmer Sciclone Genomic, ChIP, RNAseq and other methods), Single Cell DNA and RNA-Seq (10X Genomics Chromium), Bioanalyzer Analysis DNA and RNA (Two Agilent 2100 BioAnalyzers and two Agilent 2200 TapeStations), Qiagen Qiacube Automated DNA / RNA Prep (single to multiple samples), Oligonucleotide Ordering (IDT Portal), Reagents and Supplies Ordering (multiple vendors / products). Facility web based Laboratory Information Management System provides users with access to order services and supplies as well as retrieve data and review and pay invoices all online.
This is portal takes you to the BioRobotics Laboratory website. Keywords: Laboratory, Software, Robot, Robotics, Biology,
The Modelling and Analysis of Biological Network Activity
This project encompasses development of novel biological network analysis methods and infrastructure for querying biological data in a semantically-enabled format, and aims to create a semantic interactome model. Research within the BioMANTA project will focus on computational modelling and analysis, primarily using Semantic Web technologies and Machine Learning methods, of large-scale protein-protein interaction and compound activity networks across a wide variety of species. A range of information such as kinetic activity, tissue expression, and subcellular localization and disease state attributes will be included in the resulting data model. Protein interactions are a fundamental component of biological processes. Many proteins are functional only in multimeric complexes, or require interaction partners to achieve their correct localisation or function. For this reason, the study of protein-protein interaction (PPI) networks has become an area of growing interest in computational biology. Through the use of Semantic Web technologies such as Resource Description Framework (RDF) and Web Ontology Language (OWL), interaction data is modelled to create a knowledge representation in which meaning is vested in the ontology rather than instances of data. Stochastic and computational intelligence methods are applied to this data to infer high coverage networks. Semantic inferencing is used to infer previously unknown and meaningful pathways. Major project components: - The BioMANTA Ontology:- An OWL DL ontology incorporating the PSI-MI Ontology, the NCBI Taxonomy, and elements of BioPax ontology and Gene Ontology (describing subcellular localisation). This allows us to re-use existing ontologies, thereby reducing overheads associated with knowledge acquisition in the ontology development process. We are able to integrate existing public data that contain annotation in these formats. - Data conversion & semantic protein integration:- A set of software components that convert protein-protein databases (DIP, MPact, IntAct, etc.) from PSI-MI XML to RDF compliant with the BioMANTA ontology. These software allow us to make these protein-protein interaction datasets (and more generally, any PSI-MI XML data) semantically available for querying and inference within BioMANTA. - A RDF triple store based on RDF Molecules and the MapReduce architecture:- A proof-of-concept RDF triple store using RDF molecules and Hadoop scale-out architectures. Regular RDF graphs are deconstructed into RDF molecules, which are distributed over distributed compute nodes in the MapReduce architecture, and are subsequently combined to form equivalent RDF graphs. Such an approach makes the distributed SPARQL querying and reasoning on RDF triple stores possible. - A quantitative framework to integrate networks extracted from independent data sources (gene expression, subcellular localization, and ortholog mapping):- The model is multi-layer, with a first layer based on Decision Trees where each Decision tree is built on each dataset independently. The tree nodes are cut using Shannon''s entropy (mutual information); the decision of these independent trees is integrated using logistic regression, and the parameters are optimised using maximum likelihood. Sponsors: This resource is supported by the Pfizer Global Research and Development, the Institute for Molecular Bioscience (IMB), and the University of Queensland, Australia.
Blog discussing preprints in population and evolutionary genetics.
BioLayout Express3D is a powerful new tool for the visualization and analysis of networks derived from biological systems. Network-based approaches are becoming increasing popular for the analysis of ''omics and other high dimensional data. Networks can be produced from a wide variety of biological relationships, such as interactions between individuals, disease transmission, sequence similarity, metabolic pathways, protein interactions, pathways, regulatory cascades, gene expression, etc. BioLayout Express3D has been specifically designed for visualization, clustering and analysis of large network graphs in two- and three-dimensional space derived primarily, but not exclusively, from biological data. Sponsors: This resource is supported by BBSRC (BB / F003722 / 1) and the Wellcome Trust (GR077040RP). Keywords: Biology, Tool, Software, visualization, Analysis, Network, Biological, System, Dimentional, Data, Disease, Transmission, Sequence, Metabolic, Pathway, Protein, Interaction, Gene, Expression, Clustering, Analysis,
Project dedicated to providing Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. Sponsor: BioJava is not formally funded by any grants. Through the OBF they have received sponsorship from Sun Microsystems, Apple Computers and NESCent. The initial development of the phylogenetics module was undertaken as a Google Summer of Code 2007 project in collaboration with NESCent.
This service offers a gateway to well-benchmarked protein structure and function prediction methods. Structural models collected from the prediction servers are assessed using the powerful 3D-jury consensus approach. The Structure Prediction Meta Server provides access to various fold recognition, function prediction and local structure prediction methods. The Server takes the amino acid sequence of the query protein, the reference name for the prediction job, and the E-mail address as input. The E-mail address is used only for notification about errors during the execution of the job. The query sequence and the reference name are placed in the process queue. The Meta Server accepts only sequences, which have not been submitted before. In case of duplicate sequences the second user will be notified with a link to the previous submission. Sequences longer than 800 amino acids are not accepted by some services. The internal SQL database offers the possibility to find any previous jobs processed by the Meta Server using regular expressions addressing field like E-mail, Job Name and the host name, from which the job was initiated. Each server has its own process queuing system managed by the Meta Server. All results of fold recognition servers are translated into uniform formats. The information extracted from the raw output of the servers includes the PDB codes of the hits, the alignments and the similarity (reliability) scores specific for every server. Mapping of the hits to the SCOP and FSSP classifications are made either using known PDB representatives or alignment of the template sequence with the databases of proteins in both classifications. The secondary structure assignments for all hits are taken from the mapped FSSP (red for helices and blue for strands). Underscored amino acids indicate the first residue after an insertion in the template sequence. The Meta server provides translation of the alignments in standard formats like FASTA, PDB or CASP. The Meta Server is coupled to consensus servers. They provide jury predictions based on the results collected from other services. Not all fold recognition servers are used by the jury system. The data stored on the meta server is available through http://meta.bioinfo.pl/data/JOBID/. Jobs older than 2 months are not shown. The Meta Server is only a set of programs aimed to process and manage biological data, while the predictive power of the service comes from (mostly) remote prediction providers. Sponsors: This resource is supported by The BioInfoBank Institute.
Bayesian Analysis of Common NMR Problems
Welcome to the Bayesian Analysis of Common NMR Problems software home page. This Bayesian analysis software is a series of programs with a Java interface that use Bayesian probability theory to solve common data analysis problems that occur in the sciences and in NMR in particular. Click here for a complete list of the applications addressed. The programs that run the various Bayesian analysis, the server software, were developed at Washington University by Dr. G. Larry Bretthorst and the Java language client interface was developed by Dr. Karen Marutyan. The combination of the server and client software is called the Bayesian Analysis of Common NMR Problems software. However, this name is slightly misleading because this software can analyze data from many different sources, not just NMR data. Additionally, unlike the previous interface to this software, this new interface does not require the user to have access to any specialized NMR software, i.e., this interface is completely independent of Varian''s VnmrJ, although the interface can load and process data from a Varian spectrometer. Sponsors: This resource is supported by the Washington University in St. Louis. Keywords: Analysis, Software, Java, Theory, Science, NMR, Server, Data, Spectrometer,
ProLysED - Prokaryotic Lysis Enzymes Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 14, 2014. Database on the subject of bacterial (prokaryotic) proteases. ProLysED is a freely browsable using the Demo account. Certain services will require user registration.
BIDS provided bibliographic database services to the academic community in the UK. Their mission is to provide, on a not-for-profit basis, the highest possible level of service to allow UK Academic institutions and their members access to bibliographic data, scholarly publications and research data. BIDS is believed to have been a world first - a national service providing widespread network access to commercially supplied bibliographic databases, free at the point of delivery. BIDS academic and scholarly journals services are now incorporated into IngentaConnect www.ingentaconnect.com If you are a student, researcher or member of staff at a UK higher or further education institution you can access any of the services to which your institution has subscribed. In addition, there are some services which can be searched without a subscription. These include ingentaJournals and Medline. You can discover which services are available to you by logging in to BIDS with your Athens username and password. All available services will be highlighted in the service selection page.
SNPSequer is hunting for susceptibility genes for Bipolar disorder using both positional cloning and candidate gene strategies. Statistics, genomics, informatics and molecular genetics technologies have been implemented to pursue the goal. Sponsors: This resource is supported by the University of Chicago. Keywords: Gene, Bipolar, Disorder, Clone, Cloning, Genomics, Genetic, Technology,
Bone Marrow Donors Worldwide (BMDW) is the continuing effort to collect the HLA phenotypes of volunteer stem cell donors and cord blood units, and is responsible for the co-ordination of their worldwide distribution. Participants are 63 stem cell donor registries from 44 countries, and 43 cord blood banks from 25 countries. The current number of donors and cord blood units in the BMDW database is: 14,605,618 (14,178,976 donors and 426,642 CBU''s The original goal to collect the HLA phenotypes of volunteer stem cell donors and cord blood units, and to co-ordinate their world-wide distribution remain their primary goals. But new initiatives have been added: - To maximise the chance of finding a stem cell donor or cord blood unit by providing access to all stem cell donors and cord blood units available in the world. - To minimise the effort required for stem cell donor or cord blood unit searches: only registries with potential stem cell donors or cord blood units need to be contacted. - To provide an estimate of the chance of finding a stem cell donor or cord blood unit for a given patient. - To provide advanced search programs to identify partially matched stem cell donors or cord blood units. - To facilitate search advice requests via the Internet. - To facilitate improvements in family search strategies. - To provide relevant general information for the benefit of the patient. - To provide statistics on the increase of different registries, the number of DNA typed donors, etc. Sponsors: Bone Marrow Donors Worldwide is an initiative of the Immunobiology Working Party of the European Group of Blood and Marrow Transplantation (EBMT) in 1988. Keyworss: Bone marrow, Donor, Cell, Phenotype, Stem cell, Cord blood unit,
COPE: Cytokines and Cells Online Pathfinder Encyclopaedia
Cytokines and Cells Online Pathfinder Encyclopedia
COPE is an encyclopedia of cytokines and has fully integrated subdictionaries on Angiogenesis, Apoptosis, Bacterial Modulins, CD Antigens, Cell lines, Eukaryotic cell types, Chemokines, CytokineTopics, Cytokine Concentrations in Body Fluids, Cytokine Inter-Species Reactivities, Dual identity proteins, Hematology, Innate Immunity Defense Proteins, Metalloproteinases, Protein domains, Regulatory peptide factors, Virokines, Viroceptors, and Virulence Factors. Most entries have a description as well as references.
The Biology WorkBench is a web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems. Register for a free account.
MADS+ - discovery of differential splicing events from Affymetrix exon junction array data
The Affymetrix Human Exon Junction Array is a newly designed high-density exon-sensitive microarray for global analysis of alternative splicing. Contrary to the Affymetrix exon 1.0 array, which only contains 4 probes per exon and no probes for exon-exon junctions, this new junction array averages 8 probes per probeset targeting all exons and exon-exon junctions observed in the human mRNA/EST transcripts, representing a significant increase in the probe density for alternative splicing events. Here, we present MADS+, a computational pipeline to detect differential splicing events from the Affymetrix exon junction array data. For each alternative splicing event, MADS+ evaluates the signals of probes targeting competing transcript isoforms to identify exons or splice sites with different levels of transcript inclusion between two sample groups. MADS+ is used routinely in our analysis of Affymetrix exon junction arrays and has a high accuracy in detecting differential splicing events. For example, in a study of a novel epithelial-specific splicing regulator ESRP1, MADS+ detects hundreds of exons whose inclusion levels are dependent on ESRP1, with a RT-PCR validation rate of 88.5% (153 exons validated out of 173 tested).
This is the portal to the BLAST Server provided by the WUSTL Genome Ceneter BLAST Server. The Genome Center is a world leader in the fast-paced, constantly changing field of genomics. A truly unique institution, The Genome Center is pushing the limits of academic research by creating, testing, and implementing new approaches to the study of biology with the goal of understanding human health and disease, as well as evolution and the biology of other organisms. The Genome Center is helping to lead the way in high-speed, comprehensive genomics. Since its inception in 1993, The Genome Center has played a vital role in the field of genome sequencing, receiving over 800 million in funding. The Genome Center began as a key player in the Human Genome Project an international effort to decode all 3 billion letters of our genetic blueprint ultimately contributing 25 percent of the finished sequence. Sponsors: This resource is supported by the NIH. Keywords: Genome, BLAST, SErver, Genomics, Academic, Research,
A Weblog on Bioinformatics, Genome Science and Next Generation Sequencing.
Gist contains software tools for support vector machine classification and for kernel principal components analysis. The SVM portion of Gist is available via an interactive web server. The Gist package contains the following programs: * gist-train-svm trains a support vector machine based upon a given set of labeled training examples, permitting feature selection and leave-one-out cross-validation, * gist-classify applies a trained support vector machine to unlabeled data to produce predicted binary classifications. * gist-fast-classify does the same thing as gist-classify, but uses less time and memory. However, this program only works in conjunction with a linear kernel function. * gist-kpca performs kernel principal components analysis on a given data set, and * gist-project projects a data set onto the components discovered by gist-kpca. In addition to the primary programs, the following auxiliary programs are included: * gist-fselect performs linear feature selection on a given data set, using binary classification labels, * gist-matrix performs basic manipulations of matrices, * gist-score-svm computes performance statistics from the outputs of gist-train-svm and gist-classify, * gist-rfe performs SVM recursive feature elimination on a given data set, * gist-sigmoid converts the discriminant values produced by gist-train-svm into probabilities, * gist2html converts an output file from one of the Gist programs into HTML format, and * gist-kernel computes a square kernel matrix from a given data file, using a user-specified list of kernel transformations. Gist is written in ANSI C. Source code, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded.
Belgian Co-Ordinated Collections Of Micro-Organisms: GeneCorner Plasmid Collection
The BCCM/GeneCorner Plasmid Collection accepts plasmids from and distributes plasmids to researchers worldwide. Funding by the Belgian Science Policy (Belspo) allowed BCCM/GeneCorner to evolve into a unique plasmid repository in Europe. The collection is part of Ghent University. Keywords: Bacteria, Plasmid, DNA, Library, Collection, Microbiology, Molecular biology, Biology,
CNVVdb - Copy Number Variations across Vertebrate genomes
Copy Number Variations across Vertebrate genomes
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A web interface for identification of potential inter-species CNV information by finding duplicated regions within a genome (paralogues) and between different genomes (orthologues). The paralogues/orthologues are inferred from pairwise sequence alignments between 16 vertebrate species. Note that the CNVs referred here are not equal to copy number polymorphisms of a population. Further experimental evidence is needed to support the polymorphism status of the inferred CNVs in this database.
The overall mission of the Comprehensive Neuroscience Center (CNC) is to promote and support interdisciplinary neuroscience research, clinical care and education at UAB. Despite significant advances over the last 15 years in understanding many basic neurological processes, development of more effective treatments for neurological and psychiatric diseases have been identified as the largest and fastest growing unmet medical need in this country. The institutions that can most rapidly and creatively establish the necessary neuroscience initiatives to facilitate the translation of basic research discoveries into effective therapies will be positioned to lead neurological and psychiatric disease research into the future. The Center integrates a variety of disciplines, including neurology, psychiatry, neurobiology, neurosurgery, psychology, vision science, and biomedical engineering. Faculty from the Schools of Medicine, Optometry, Social and Behavioral Sciences, Dentistry, Engineering, Health Professions, and Public Health are affiliated with the Center. The need to address neuroscience research is great: one in three Americans are affected by nervous system diseases including brain and spinal cord injury, dementing illnesses, schizophrenia, depression, movement disorders, multiple sclerosis, and autism. The burden of these diseases has an estimated economic cost of 500 billion per year in the United States. Center Research: The CNC serves as a vital center for neuroscience research at UAB and oversees six thematic programs of investigation: neurodevelopment and neurogenetics, neurodegeneration and experimental therapeutics, neuroregeneration and plasticity, behavioral and cognitive health, glial biology in medicine, and neuroimaging. The CNC helps coordinate the efforts of multiple neuroscience related centers at UAB, such as the Center for Glial Biology in Medicine, the Evelyn F. McKnight Brain Institute, the Civitan International Research Center, and the Alzheimers Disease Research Center. By interacting directly with these centers and establishing coalitions of centers and neuroscience subdisciplines, the CNC aids the UAB neuroscience community in meeting the challenges of modern neuroscience investigation. The CNC builds on other recent advances in neuroscience at UAB, including an 8.6 million grant from the National Institutes of Health to establish the Alabama Neuroscience Blueprint Core Center Facility awarded in September 2006. The Neuroscience Blueprint establishes research infrastructure on campus that is shared by investigators from institutions across Alabama and the Southeast. UAB has also added dynamic new leadership in the neuroscience fields including the following new chairs: Ray L. Watts, MD, Neurology (from Emory University); David Sweatt, PhD, Neurobiology (from Baylor College of Medicine); and James Meador-Woodruff, MD, Psychiatry (from the University of Michigan).
The Jackson Laboratory Hearing Research Program
The fairly common occurrence of hearing-loss or deafness in both humans and mice, and the anatomical and functional similarities of their inner ears, attest to the potential of mice as models to study hereditary hearing loss. Hundreds of standard inbred, recombinant inbred, and congenic strains are maintained at The Jackson Laboratory, as well as hundreds of inbred strains with spontaneous or induced mutations. To assess hearing impairment in inbred and mutant strains of mice we measure auditory-evoked brainstem response (ABR) thresholds.
neuroConstruct: Biophysical Neural Network Modeling Software
Software for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface.
Audacity: Free Audio Editor and Recorder
Audacity is free, open source software for recording and editing sounds. It is available for Mac OS X, Microsoft Windows, GNU/Linux, and other operating systems. The latest release of Audacity is 1.3.12 (Beta). This is their active work in progress version with their latest features. Documentation and translations into different languages are not quite complete. They recommend this version for more advanced users, and for everyone on Windows 7, Windows Vista and Mac OS X 10.6. See New Features in 1.3 for more information about the 1.3 Beta series. You can use Audacity to: Convert tapes and records into digital recordings or CDs. Edit Ogg Vorbis, MP3, WAV or AIFF sound files. Cut, copy, splice or mix sounds together. Change the speed or pitch of a recording. And more See the complete list of features. Sponsors: This resource is supported by UmixIt Technologies, LLC. Keywords: Software, Recording, Audio, Sound, Editor, Recorder,
Atlas of Genetics and Cytogenetics in Oncology and Haematology
Online journal and database devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. Its aim is to cover the entire field under study and it presents concise and updated reviews (cards) or longer texts (deep insights) concerning topics in cancer research and genomics.
This is a Research Community that is focused on reducing the threat of the Aspergillus flavus fungus and its toxin to human and animal health. Aspergillus flavus is a plant, animal, and human pathogen that produces the carcinogen, aflatoxin. An organized multidisciplinary team is coordinating research efforts to control this fungus and to prevent the formation of its toxin in food and feeds. Aspergillus flavus is a fungus. It grows by producing thread like branching filaments known as hyphae. Filamentous fungi such as A. flavus are sometimes called molds. A network of hyphae known as the mycelium secretes enzymes that break down complex food sources. The resulting small molecules are absorbed by the myceilium to fuel additional fungal growth. The unaided eye cannot see individual hyphae, but dense mats of mycelium with conidia (asexual spores) often can be seen. The ear of maize below shows the growth of the fungus covering four maize kernels. When young, the conidia of A. flavus appear yellow green in color. As the fungus ages the spores turn a darker green. Sponsors: This resource is supported by the Center for Integrated Fungal Research. Keywords: Aspergillus flavus, Research, Fungus, Toxin, Human, Animal, Health, Plant, Pathogen, Carcinogen, Aflatoxin, Food, Feed, Mold, Network, Enzyme,
Arizona Center for Education and Research on Therapeutics
Arizona CERT is an independent research and education center whose mission is to improve therapeutic outcomes and reduce adverse events caused by drug interactions and drugs that prolong the QT interval, especially those affecting women. The CERTs mission is to conduct research and provide education that will advance the optimal use of drugs, medical devices, and biological products The Arizona CERT is a program of the Critical Path Institute in collaboration with the Center for Health Outcomes and PharmacoEconomic Research at The University of Arizona College of Pharmacy. It is one of 14 national CERTs funded by the U.S. Agency for Healthcare Research and Quality (AHRQ).
Family Pairwise Search - Protein Family Classification
Family Pairwise Search (FPS) is a protein homology detection algorithm that combines sequence similarity scores from a pairwise alignment algorithm such as Smith-Waterman or BLAST. Source code and a web server are available. This is a method for scoring a query sequence against a family of sequences. (Note: the query sequence may alternatively be a sequence, a GCG profile or a BLAST checkpoint file.) FPS compares the query sequence individually (pairwise) to each sequence in the family and then combines the pairwise scores into an overall score for the match. This site provides access to * a web server to allow you to use FPS to search various protein family libraries for matches to a protein sequence, * an overview of the FPS algorithm, * a description of the inputs and outputs for the FPS server, * a sample output from the FPS server, and * a release notes for FPS, and * links to several papers about FPS, and * the FPS source code for non-comercial use. * COPYRIGHT information and how to license FPS for commercial use is described here.
Their primary focus is in the area of structural, evolutionary and functional genomics of crop plants. AGI is divided into 5 Centers each lead by a Center Leader and a senior Manager (BAC Library Construction Center, BAC/EST Resource Center, Sequencing & Physical Mapping Center (including: production sequencing and fingerprinting, and sequence finishing), Bioinformatics Center and the Evolutionary and Functional Genomics Center). AGI is housed in the state of the art Thomas W. Keating Bioresearch Building on the northeast part of campus near the Medical School. AGI currently employees about 30 scientists and is primarily funded through federal grants, private contracts, and the Bud Antle Endowed Chair in Plant Molecular Genetics. Sponsors: AGI is supported by Bio5, Plant Sciences, National Science Foundation, National Institues oh Health, and USDA.
Our research group develops and applies computational techniques for modeling and understanding biological processes at the molecular level. Our research emphasizes the application of statistical and machine learning techniques, such as hidden Markov models and support vector machines. We apply these techniques to various types of biological data, including DNA and protein sequence data, as well as gene expression data from microarray experiments. We are currently developing methods for analyzing shotgun proteomics data, for characterizing protein function, structure and interactions, and for understanding the structure and regulatory influence of chromatin.
This portal takes you to the website of Professor Anne Chao of the National Tsing Hua University, China. She studies birds. The portal offers Software, course information, publications and teaching. There are about 458 bird species in Taiwan. We have observed 155 species in our neighboring Ker-Yar estuary. We would estimate the total number of species in this area to be 180 including those unobserved. The more we discover about birds, the more we realize how intimately and closely our lives are entwined with those of birds. When the habitats of birds are destroyed and birds become extinct, we human beings are losing the land....
It provides quantitative information about phenotypes for the complete collection of deletion strains in yeast (Saccharomyces cerevisiae). PROPHECY evalutes the phenotype of a deletion strain on the basis of growth behaviour during micro-cultivation. PROPHECY quantifies growth aberrations by estimating the rate of growth, the efficiency of growth and the adaptation time.
The Power Atlas is a web-based resource to assist investigators in the planning and design of microarray and expression based experiments. This software is currently aimed at estimating the power and sample size for a two group comparison based upon pilot data. The methods underlying the web site are reported in Gadbury et al (2004) and the software is described in further detail at Page et al (2006). There are two ways to use the Power Atlas: 1. We have downloaded the datasets currently in the Gene Expression Omnibus (GEO) and processed each of them with our power analysis software. Investigators may search among the datasets for the experiment that most closely resembles their proposed project and get sample size and power estimates. 2. Investigators may upload their own preliminary data and the program will extrapolate power from this dataset.
GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms
As fascinating as diversity is, it''s not the sort of thing that computational scientists usually get excited about. Uncovering how diversity came to be has captured the attention of a team of researchers at Alliance partner University of New Mexico and the University of Texas, though. Using the 512-processor LosLobos Linux Pentium III supercomputing cluster at the Albuquerque High Performance Computing Center, the team has created a phylogeny reconstruction - or evolutionary history - of 12 bluebell species, predicting all of the steps that take these species back to a single common ancestor. To meet the challenge, they created a whole new piece of software known as GRAPPA. GRAPPA is is free software available as a gzipped tar file containing all source files needed to compile an executable version.
National Institutes of Neurological Disorders and Stroke Research Programs
The National Institute of Neurological Disorders and Stroke (NINDS) conducts and supports research on brain and nervous system disorders. Created by the U.S. Congress in 1950, NINDS is one of the more than two dozen research institutes and centers that comprise the National Institutes of Health (NIH). NINDS has occupied a central position in the world of neuroscience for more than 50 years. It provides access to different research programs both extramural and intramural. Research Topics: Epilepsy, Parkinson''s Disease, Traumatic Brain Injury, Anticonvulsant Screening, CounterACT, Bioengineering, Neural Interfaces, Stem Cell Research. Offices and Programs: *Channels, Synapses and Neural Circuits *Neural Environment *Neurodegeneration *Neurogenetics *Office of Clinical Research *Office of International Activities *Office of Minority Health and Research *Office of Translational Research *Office of Training and Career Development *Repair and Plasticity *Systems and Cognitive Neuroscience
The American Heart Association (AHA) publishes medical scientific statements on various cardiovascular disease and stroke topics. AHA volunteer scientists and healthcare professionals write the papers. The statements are supported by scientific studies published in recognized journals and have a rigorous review and approval process. Scientific statements generally include a review of data available on a specific subject, an evaluation on its relationship to overall cardiovascular disease science, and often an American Heart Association position on the basis of that evaluation. The American Heart Association sponsors accredited scientific conferences and professional development seminars to disseminate new and emerging scientific knowledge and stimulate discussion on future research and the application of knowledge. Keywords: Heart, Cardiovascular, Disease, Stroke, Volunteer, Scientist, Healthcare, Development, Knowledge,
Amblyomma Americanum (Lone Star Tick) cDNA Sequencing
Doris Kupfer, Sara Downard, and Laura Hern in our Genome Center at the University of Oklahoma, have sequenced the 3'' and/or 5'' ends of double stranded cDNAs constructed from the salivary glands of the lone star tick, Amblyomma americanum constructed by Richard Essenberg and Majd Aljamali, Department of Biochemistry and Molecular Biology at Oklahoma State University, Stillwater OK. Four libraries are included in this August 27, 2003 release. Lib1:TSG Lib1, female, salivary gland, 50-200 mg feeding adults Lib2:TSG Lib2, female, salivary gland, unfed adults, feeding adults, replete adults Lib3:TSG Lib3, female, salivary gland, 3 day feeding adults Lib4:TSG Lib4, female, salivary gland, 50-200 mg feeding adults, was constructed from TSG Lib1 by normalization following procedure of, Bonaldo et al (Genome Res. 1996 Sep;6(9):791-806). Amblyomma americanum lone star tick Latest Data Release - August 27, 2003 1757 total ESTs that were assembled into 810 entries and 608,477 nucleotides in the four separately libraries and combined into one searchable database. - The Amblyomma americanum lone star tick salivary gland cDNA libraries Lib1, Lib2 and Lib4 were constructed from multiple feeding stages in Clonetech pTriplEx2 vector by directionally cloning into the 5'' EcoRI and 3'' SfiIb sites. Lib3 was constructed from 3 day feeding adults by Stratagene, Inc. into pBlueScript SK- . - Ribosomal RNA, mitochondrial RNA, vector and small (less than 100bp) inserts, will be removed prior to assembly of a UniGene database using Phred (Phil Green, University of Washington) . All of our data is available from our ftp site, and we now have added the ability to perform blast searches on this data. A keyword search of a blastx search of GenBank with this data also is available. Sponsors: This resource is supported by University of Oklahoma. Keywords: CDNA, Dataset, Library, RNA, Mitochondrial, Ribosomal,
AltTox: Non-animal Methods for Toxicity Testing
A website dedicated to advancing non-animal methods of toxicity testing, both to better protect the health of humans, animals, and the environment and to reduce the numbers and suffering of animals used in current toxicology assessments. The website is designed to encourage the exchange of technical and policy information on in vitro and in silico methods for all types of toxicity tests. The AltTox Forum is a message board for the AltTox community to use for posting news, information, and perspectives as well as encouraging feedback and commentary. This online community is intended to foster progress internationally in the development, validation, and acceptance of in vitro methods, with the goal of decreasing our reliance on animal-based safety testing. The Forum is moderated by a group of internationally-recognized subject matter experts. The Way Forward invited commentaries, which are posted in the TTRC, are opinion pieces written by experts in each relevant subfield. These essays are meant to help chart the course for future developments by advancing opportunities to overcome challenges and barriers to progress. Stakeholders are invited to comment on these essays in The AltTox Forum. AltTox users are encouraged to contribute to the website and interact with other users in several ways, including: :- Participating in the online forum :- Providing invited expert commentaries :- Suggesting or submitting content, events, monthly features, data, and graphics :- Providing feedback through the Website Feedback surve To encourage objectivity, the website content is overseen by an editorial board of distinguished subject matter experts.
WAViS: Alignment Visualization Tools Server
WAViS generates pictures of your alignment files. These tools should help you with preparation of publication-quality pictures of your alignment. Sponsors: This resource is supported by Institute of Molecular Genetics. Keywords: Software, Server, Picture, Alignment,
Frontiers Community: A Network that Serves researchers
Frontiers community is a web portal for both open access Frontiers journals and a community portal for jobs, books, and scholarly events. Frontiers is more than just an open-access publisher of scholarly articles: it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed. The grand vision of Frontiers is a world where all people have an equal opportunity of seeking, sharing and generating knowledge. As a first active measure in this direction, Frontiers provides immediate and permanent online open access to all of its publications, but this alone is not enough to realize our grand goals. The Frontiers solution develops around two main concepts, mutually integrating each other within the innovative Frontiers'' platform: * the Frontiers Journal Series, and * the Frontiers Community. As an open-access Journal Series, Frontiers revolutionizes research publishing by freely delivering the most outstanding research, evaluated with no bias from both the academic and social point of view. As an interdisciplinary Community system, Frontiers is reshaping research management with a state-of-the-art platform, designed as a collaborative architecture and aimed at all research communities, whether academicians or research enthusiasts, investors or grantmakers. By applying the most advanced information technologies, Frontiers is catapulting scholarly publishing into a new 21st century generation.
ESTIMA - Expressed Sequence Tag Information Management and Annotation
ESTIMA: a Tool for EST Management in a Multi-Project Environment
A web application called Expressed Sequence Tag Information Management and Annotation (ESTIMA) has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against arbitrary reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http://titan.biotec.uiuc.edu/ESTIMA/download/. The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee.
Swami: The Next Generation Biology Workbench
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Next Generation Biology Workbench is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics. The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed. The NGBW is designed to be an organic tool that evolves with the needs of the Biomedical research and education communities. The Next Generation Biology Workbench (NGBW) is now available for public use, in its production release.
Boston University Department of Neuroscience
Neuroscience research at BU is coordinated through unified community of investigators from multiple research groups of Charles River and MED campuses.Neuroscience faculty support Undergraduate Program in Neuroscience and Graduate Program for Neuroscience. Students can get specialized training in additional disciplines while carrying out neuroscience thesis research (Anatomy & Neurobiology, Biology, and Pharmacology and Experimental Therapeutics).
A statistical framework for genomic data fusion
A statistical framework for genomic data fusion is a computational framework for integrating and drawing inferences from a collection of genome-wide measurements. Each dataset is represented via a kernel function, which defines generalized similarity relationships between pairs of entities, such as genes or proteins. The kernel representation is both flexible and efficient, and can be applied to many different types of data. Furthermore, kernel functions derived from different types of data can be combined in a straightforward fashion. Recent advances in the theory of kernel methods have provided efficient algorithms to perform such combinations in a way that minimizes a statistical loss function. These methods exploit semidefinite programming techniques to reduce the problem of finding optimizing kernel combinations to a convex optimization problem. Computational experiments performed using yeast genome-wide datasets, including amino acid sequences, hydropathy profiles, gene expression data and known protein-protein interactions, demonstrate the utility of this approach. A statistical learning algorithm trained from all of these data to recognize particular classes of proteins--membrane proteins and ribosomal proteins--performs significantly better than the same algorithm trained on any single type of data. Matlab code to center a kernel matrix and Matlab code for normalization are available.
Case Western Reserve University School of Medicine Department of Pharmacology
Case Western; SOM; Dept. of Pharmacology
Department of Pharmacology research mission is to discover specific mechanisms that control physiological processes at cellular and molecular levels. Department offers broad range of educational opportunities ranging from undergraduate research to classes leading toward Ph.D. and M.D.Training Programs include MOLECULAR THERAPEUTICS TRAINING PROGRAM, BIOMEDICAL SCIENCES TRAINING PROGRAM, MEDICAL SCIENTIST TRAINING PROGRAM, SUMMER UNDERGRADUATE RESEARCH PROGRAM, Cancer Pharmacology Training Program.
California Institute of Technology; Division of Biology
Caltech; Division of Biology; Division of Biology at Caltech
For more than 75 years, the division of biology has provided many of the major research advances that have made biology the premier science of the 21st century, and has trained many of the world''s most eminent biologists. The division at present has 38 professors of various ranks, who in their classes and laboratories have approximately 100 undergraduates, 100 graduate students, and 160 postdoctoral scholars, as well as more than 250 staff members. We occupy parts or all of seven buildings on the Caltech campus; we also operate a marine laboratory 50 miles from campus. Each building is devoted to state-of-the-art educational facilities and cutting-edge laboratories. We have three major research emphases: Structural, Molecular and Cell Biology; Developmental and Regulatory Biology; and Molecular, Cellular and Integrative Neuroscience. In each area we are trying to solve one of the great problems of modern biology: How do the proteins and other components of cells interact to provide a marvelous nanomachine of more than 100,000 integrated parts, a machine that has numerous extraordinary functions and can reproduce itself? How does a single cell become, by division and formation of new cell types, an entire multicellular organism, which in the case of humans has thousands of different cell types and more than 1 trillion different cells in specific places, communicating to form complex organs? How does the brain, the most complex organ of all, work to allow calculations beyond those of any computer, as well as to demonstrate amazing sensory capabilities, emotions, and consciousness?
Brown University Alpert Medical School Department of Molecular Pharmacology Physiology and Biotechnology
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 20, 2021. Department of Molecular Pharmacology, Physiology, and Biotechnology has closed, effective June 30, 2021. Department of Molecular Pharmacology, Physiology and Biotechnology is basic science department within Brown Medical School, and is full participant in undergraduate based Program in Biology within Division of Biology and Medicine at Brown University.
Brown University Department of Neuroscience
Brown Neuroscience; Neuroscience at Brown
Mission of Department of Neuroscience is to do teaching and research on basic functions and diseases of nervous system. Areas of interest include neural plasticity, information processing, and neuronal and synaptic functions, particularly as they relate to development, sensory perception, motor behavior, and cognition. Members of Department also participate in MRI Research Facility, Center for Vision Research, and several NIH and NIMH training grants for graduate and postdoctoral fellows studying neuroscience and vision sciences.Department is also major contributor to Brown''s Institute for Brain Science, multidisciplinary consortium that promotes collaborative theoretical and experimental studies of brain.
Baylor University Department of Psychology and Neuroscience
Baylor University Psychology & Neuroscience
Baylor University Psychology and Neuroscience
Goal of Department is creation and dissemination of knowledge in psychological sciences, fostering environment conducive to creative scholarship and learning among both students and faculty, and application of knowledge to betterment and service of society. Offers Bachelor of Science and Bachelor of Arts degree in Psychology as well as few undergraduate degree programs in Neuroscience.
Baylor College of Medicine Department of Neuroscience
Department offers graduate and postgraduate programs that provide students with intensive education and training in neuroscience, along with opportunity to excel in laboratory. Our program brings together researchers from diverse backgrounds to study brain and its function in health and disease. Educational experiences are provided by faculty members actively involved in research into function of central nervous system through experimentation in molecular neurobiology, neuroanatomy, neurodevelopment, neural systems analysis, biophysics, imaging, and computer-assisted neural system modeling.Ongoing studies in our department range from molecular biophysics of ion channels and receptors, to analysis of neuronal development, signal processing, brain circuitry, and animal behavior all the way to human brain function.
An ontology for describing clinical signs and symptoms.
Albany Medical College Center for Neuropharmacology and Neuroscience
Center for Neuropharmacology and Neuroscience; Albany Medical College
The Center for Neuropharmacology and Neuroscience; Albany Medical College
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 20,2021. Center for Neuropharmacology & Neuroscience (CNN) is composed of faculty and students with research interests that are focused on the nervous system. One major purpose of the CNN is to facilitate and strengthen collaborations in neuroscience research; it also provides a unique interface for interactions among clinical and basic scientists. Neuropharmacology and Neuroscience are large and diverse fields that encompass physiology, pharmacology, anatomy, behavior, development, neural disorders and diseases.
REGARDS - REasons for Geographic and Racial Differences in Stroke
REasons for Geographic and Racial Differences in Stroke
The REasons for Geographic and Racial Differences in Stroke (REGARDS) project, sponsored by the National Institutes of Health (NIH), is a national study focusing on learning more about the factors that increase a person''s risk of having a stroke. REGARDS is an observational study of risk factors for stroke in adults 45 years or older. 30,239 participants were recruited between January 2003 and October 2007. They completed a telephone interview followed by an in-home physical exam. Measurements included traditional risk factors such as blood pressure and cholesterol levels, and an echocardiogram of the heart. At six month intervals, participants are contacted by phone to ask about stroke symptoms, hospitalizations and general health status. The study is ongoing and will follow participants for many years. The purpose of the REGARDS project is to understand why people in some parts of the country develop more strokes than people in other parts of the country, and why blacks develop more strokes than whites. We hope to learn how to reduce the number of people having strokes.
It is a database of keys facts about proteins, families, and complexes involved in cell migration. This ongoing project provides a large amount of automated and curated data, collected from numerous online resources that are updated monthly. These data include names, synonyms, sequence information, summaries, CMC research data, reagents, structures, as well as protein family and complex details. CMKB''s ultimate goal is to create a database that will enable the cell migration community to conveniently access significant information about molecules of interest. This will also serve as a stepping stone to pathway analysis and demonstrate how these molecules coordinate with one another during cell adhesion and movement. Sponsors: This resource is supported by the Cell Migration Consortium.
SNPselector and High Quality SNP Database
This is the HQSNP DB (high-quality SNP database) developed by CHG bioinformatics group. The high-quality SNP is defined as a SNP having allele frequency or genotyping data. The majority of the HQSNPs come from HapMap, others come from JSNP (Japanese SNP database), TSC (The SNP Consortium), Affymetrix 120K SNP, and Perlegen SNP. There are four kinds of SNP search you can do: * Get SNPs by dbSNP rs#: Choose this search if you have already selected a list of SNPs and you just want to get the SNP information. The program will generate a Excel file containing the SNP flanking sequence, variation, quality, function, etc. In the Excel file, there are 10 highlighted fields. You can send only those highlighted information to Illumina to get SNP pre-score. (The same fields are presented in other types of searches as well.) * Get gene SNPs by gene names: Choose this search if you have a list of gene names and you want to get the SNP information in these genes. The gene name can be official gene symbol, Ensembl gene ID, RefSeq accession ID, LocusLink number, etc. * Get gene SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get all gene SNP information in these regions. The software will find all the Ensembl genes in the regions and find SNPs associated to each Ensembl gene. * Get genome scan SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get evenly spaced SNPs in these regions. A SNP selection tool (SNPselector) was built upon HQSNP. It took snp ID list, gene name list, or genome region list as input and searched SNPs for genome scan or gene assoctiation study. It could take an optional ABI SNP file (exported from ABI SNP search web page) as input for checking whether the candidate SNP is available from ABI. It could also take an optional Illumina SNP pre-score file as input to select SNP for Illumina SNP assay. It generated results sorted by tag SNP in LD block, SNP quality, SNP function, SNP regulatory potential, and SNP mutation risk. SNPselector is now retired from public use (as of September 30, 2010).
The Cancer Genome Project is using current high throughput techniques to characterise a series of approximately 800 cancer cell lines including those most frequently used in biological and pharmaceutical research and drug discovery. These screens include sequencing of known cancer genes, copy number and genotyping analysis using SNP arrays and identification of microsatellite instability. Pair-wise comparison of the SNP array data for the entire series of cell lines under study has been performed identifying those lines which, in our set, are either identical or derived from a parental line. These lines are termed synonymous cell lines. Sponsors: This study was supported by the Wellcome Trust and Glaxo Smith Kline. :K eywords: Cancer, Genome, Technique, Research, Pharmaceutical, Drug, Discovery, Gene, Number, Genotype, SNP, Array, Microsatellite, Instability, Biological, Cell line, SNP, Data,
Clusters of Orthologous Groups Analysis Ontology
Clusters of Orthologous Groups (COG) Analysis Ontology
Ontology designed for supporting the COG enrichment study by using Fisher''s exact test
Cerep offers a panel of over 630 validated in vitro pharmacological assays that cover a broad range of targets including receptors, ion channels, transporters, enzymes and second messengers. These assays are used to identify lead compounds, to define mechanism of action, and to identify off-target activities. All assays are available on an ad hoc basis. At any time, clients can select one or more assays to be tested against one or more compounds at one or more concentrations. In addition to ad hoc access, client specific and Cerep profiles are available. Client specific profiles can be adapted using any of the over 630 Cerep assays. Standard Profiles are designed by Cerep and available to all clients. The Standard Profiles are a rapid and cost effective way of prioritizing the most promising compounds in the lead selection process. Benefiting from increased efficiency generated from optimized processes, Cerep is happy to expand custom made profiles clients can design at set prices. While offering more flexibility, clients are able to select among predefined lists of functional GPCR, kinase and binding assays. Keywords: In vitro, Pharmacology, Assay, Target, Receptor, Ion channel, Transporter, Enzyme, Mechanism, Hoc, Compound, Kinase, GPCR, Secondary messenger,
Canadian Microelectronics Corporation Microsystems
CMC Microsystems enables and supports the creation and application of micro- and nano-system knowledge by providing a national infrastructure for excellence in research and a path to commercialization of related devices, components and systems. CMC Microsystems provides the tools, technologies and services that make microsystems research and development possible in universities across Canada. CMC delivers innovative and cost-effective services to a growing community of microsystems researchers that connect 43 universities and one college across Canada, and presently involves over 3,100 faculty and graduate students. A 4th Pillar organization stimulating synergistic collaboration among universities, companies and government agencies, CMC is a pioneer in developing creative solutions including Canada-wide Internet-based access to advanced microsystems testing facilities-at a fraction of the cost of conventional methods. Over the last five years, CMC delivered a value of 342 million to Canadian universities. Throughout the last 25 years CMC has successfully demonstrated the ability to specify, acquire and distribute all the necessary tools and technologies to design, make and test microsystems devices, components and systems and in the last five years has significantly expanded its skill base and partnerships. CMC has also developed a series of key relationships with suppliers which have enabled smooth and uninterrupted access to the latest tools and technologies. The governance structure is widely viewed as one of the soundest among organizations of this type and the management team of five people has a total experience of well over 100 years in the microsystems field.
Clinical Randomisation of an Antifibrinolytic in Significant Haemorrhage
This is a trial for a large randomised placebo controlled trial among trauma patients with, or at risk of, significant haemorrhage, of the effects of antifibrinolytic treatment on death and transfusion requirement. Sponsors: This resource is supported by UK NIHR Health Technology Assessment programme, Pfizer, BUPA Foundation, and J P Moulton Charitable Foundation. Keyowrds: Trial, Placebo, Drug, Trauma, Haemorrhage, Antifibrinolytic, Treatment, Death, Transfusion,
Conversion Software Registry (CSR) has been designed for collecting information about software packages that are capable of file format conversions. The work is motivated by a community need for finding file format conversions inaccessible via current search engines and by the specific need to support systems that could actually perform conversions, such as the NCSA Polyglot. In addition, the value of CSR is in complementing the existing file format registries and introducing software quality information obtained by content-based comparisons of files before and after conversions. The contribution of this work is in the CSR data model design that includes file format extension based conversion, as well as software scripts, software quality measures and test file specific information for evaluating software quality. The CSR system serves as the source of information and a test bed for the system that can execute the conversions automatically by using the third party software, for example, NCSA Polyglot. The CSR system is a database with a web-based interface that provides services related to a) finding a conversion path between formats b) uploading information about the 3rd party software packages and file extensions, c) uploading files for testing, and finally d) uploading scripts in operating system (OS) specific scripting languages (Windows AutoHotKey, AppleScript and Perl) for automated conversions according to the idea of imposed code reuse used by NCSA Polyglot. In order to provide file format conversion services, CSR have included the following components into CSR related to software capable of conversions: input and output file formats (extensions), scripts operating on the software, validated files to be used for information loss measurements, as well as quantitative measures of the information loss for conversions. The CSR focuses: on software and finding the format conversion paths described by a number of software packages and unique input and output formats. The formats themselves are represented by extensions. While not always unique, extensions are often the only accessible information when the 3rd party software is installed (often listed under the File/Open menu in most packages). The CSR also contains information about the software, operating system, software interface and scripts to execute the software. The scripts are important for the automating conversions with the 3rd party software and can be implemented using AutoHotkey scripts (Windows), AppleScript (Mac) or one of a variety of scripting languages for Unix. The information loss due to file format conversions is measured externally by different techniques within the NCSA object-to-object comparison framework called Versus. The comparison is relevant to the software domain, for example for 3D applications surface area or spin images are used and the loss (0-100 range with 100 representing no loss) for a particular software-conversion pair is stored in the database. The information loss also represents edge weights to Input/Output (I/O) Graph, a simple workflow used for finding the shortest conversion path. The CSR is written as a web service. It consists of three main components: Query, Add, Edit. In the Query mode users can a) view list of all software packages with their conversion options, b) select subsets of software in the I/O-Graph, c) search the database by conversions, software, extensions, MIME and PUID. The I/O-Graph contains all information about installed applications and the conversions they allow. The JAVA applet front end is part of the CSR web visualization interface. Section Add allows users to add new software packages with their conversion capabilities and upload the software scripts to automate them. The last section, Edit is designed for adding detailed information about the software, extensions and for uploading the test files. CSR requires users to login for adding and editing. The web fields are auto completed to help search. Sponsors: This research was partially supported by a National Archive and Records Administration (NARA) supplement to NSF PACI cooperative agreement CA #SCI-9619019. Keywords: Software, Registry, Information, Conversion, Database, Tool
This web site has been created to provide a centralized source for CS2 and related vector information. It will be updated (on an irregular basis) with additional information, including new vector designs. CS2 vector: pCS2 is a multipurpose expression vector. Although originally designed for expressing proteins in Xenopus embryos from either injected RNA or DNA, pCS2 is also useful for high-level transient expression in a wide variety of mammalian and avian cells. It is also functional in zebrafish embryos (as DNA or RNA), and it can be used for in vitro transcription/translation (using, for example, the Promega TnT system). A number of derivatives of CS2 have been constructed that allow fusions to epitope tags and other marker proteins, as well as nuclear localization signals or the gal4 DNA binding and activation domains. In almost all cases, the same reading frames are used for the fusion vectors, to facilitate moving genes between multiple CS2 derivatives. pCS2 features: pCS2 contains a strong enhancer/promoter (simian CMV IE94) followed by a polylinker and the SV40 late polyadenlyation site. An SP6 promoter is present in the 5'' untranslated region of the mRNA from the sCMV promoter, allowing in vitro RNA synthesis of sequences cloned into the polylinker. A T7 promoter in reverse orientation between the polylinker and the SV40 polyA site for probe synthesis, as well as a second polylinker after the SV40 polyA site to provide several possible sites to linearize the vector for SP6 RNA transcription. The vector backbone is from pBluescript II KS and includes the amp resistance gene and an f1 origin for producing single stranded DNA. :Sponsors: This resource is supported by the University of Michigan. : Keywords: Vector, Resource, Expression, Protein, Xenopus, Embryo, RNA, DNA, Transient, Zebrafish, Domain, mRNA, Synthesis, Promoter,
Calculator for Association with Two Stage design
power Calculator for Association with Two Stage design
Software tool for carrying out power calculations for large genetic association studies, including two stage genome wide association studies.
California Institute for Regenerative Medicine
The California Institute for Regenerative Medicine is accelerating the development of new therapies for chronic disease and injury by funding stem cell research programs throughout California. T he mission of CIRM is to support and advance stem cell research and regenerative medicine under the highest ethical and medical standards for the discovery and development of cures, therapies, diagnostics and research technologies to relieve human suffering from chronic disease and injury. CIRM was established in 2004 after Californians passed Proposition 71, the California Stem Cell Research and Cures Initiative. The statewide ballot measure, which provided 3 billion in funding for stem cell research at California universities and research institutions, called for the establishment of a new state agency to make grants and provide loans for stem cell research, research facilities and other vital research opportunities. CIRM funds stem cell research at for-profit and not-for-profit institutions throughout California. Grants are awarded as part of Requests for Applications (RFAs). Applications for these RFAs are reviewed by a panel of experts, which makes recommendations to the Governing Board. The board then votes on grants to fund for each RFA. Keywords: Regenerative, Medicine, Development, Therapy, Chronic, Disease, Ilness, Stem cell, Research, Meidcal, Discovery, Cure, Therapy, Diagnostic, Technology, Human, Grant, Funding,
Center for Biological and Compulational Learning Face Database
This is a database of faces and non-faces, that has been used extensively at the Center for Biological and Computational Learning at MIT. It is freely available for research use. CBCL FACE DATABASE #1: :- Includes complete Readme File :- 19 x 19 Grayscale PGM format images :- Training set: 2,429 faces, 4,548 non-faces :- Test set: 472 faces, 23,573 non-faces :- 27 Megabytes compressed : 110 Megabytes uncompressed :- tar / gz format compression Sponsors: This database is supported by the MIT Center for Biological and Compulational Learning. Keywords: Download, Database, Face, Non-face, Biological, Comuptaitonal, Research,
This portal shows you the current research projects happening with in the Cancer Genomics Project. Sponsors: This project is supported by Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agenecy. Keywords: Research, Cancer, Genomics, Genetic, Gne, Project,
This web site contains information relevant to nomenclature of the avian brain. Its current purpose is to serve as a communication means by which scientists can become more knowledgeable about the avian brain, exchange ideas, and formulate proposals for changing the existing nomenclature. Sponsors: This resource is supported by the Duke University Medical Center. Keywords: Avian, Brain, Rearch, Research, Nomenclature, Atlas,
COLELMS: Stata module to calculate Coles LMS values for growth data
COLELMS calculates LMS values, smoothed LMS, and growth reference centiles based in smoothed LMS values. df value is set to when calculating smoothed LMS values. You are responsible for setting an appropriate df for your data. This is version 0.2 of the software. Sponsors: This resource is supported by Boston College. Keywords: Software, LMS, Calculation, Growth, Data, Stata, Module,
A working guide to the rapidly developing world of Next-Generation DNA sequencing, with an emphasis on bioinformatics.
Candrive''s aim is to improve the health, safety and quality-of-life of Canada''s older drivers. Candrive''s vision is to establish a national multi-disciplinary collaborative approach to identify, analyze and examine the issues pertaining to the safe operation of vehicles by older persons. One of the goals of the Candrive research program is to find a way to extend the length of time that older drivers can drive. Candrive will examine both the effectiveness of retraining programs and the use of customized or restricted licensing for older drivers who might automatically have had their licence revoked. Unfortunately, even if such measures prove useful, there will still be a small minority of older drivers who are no longer safe to drive. By identifying this minority as early as possible, the program will help protect the reputation, public image and rights of the majority of older drivers who represent the safest and most experienced drivers on the road. Sponsors: This resource is supported by a Team Grant from the Canadian Institutes of Health Research (CIHR). Candrive also receives support from the Ottawa Hospital Research Institute. Keywords: Health, Safety, Analysis, Vehicle, Driver,
The primary goal of the CardioGenomics PGA is to begin to link genes to structure, function, dysfunction and structural abnormalities of the cardiovascular system caused by clinically relevant genetic and environmental stimuli. The principal biological theme to be pursued is how the transcriptional network of the cardiovascular system responds to genetic and environmental stresses to maintain normal function and structure, and how this network is altered in disease. This PGA will generate a high quality, comprehensive data set for the functional genomics of structural and functional adaptation of the cardiovascular system by integrating expression data from animal models and human tissue samples, mutation screening of candidate genes in patients, and DNA polymorphisms in a well characterized general population. Such a data set will serve as a benchmark for future basic, clinical, and pharmacogenomic studies. Training and education are also a key focus of the CardioGenomics PGA. In addition to ongoing journal clubs and seminars, the PGA will be sponsoring symposia at major conferences, and developing workshops related to the areas of focus of this PGA. Information regarding upcoming events can be found in the Events section of this site, and information about training and education opportunities sponsored by CardioGenomics can be found on the Teaching and Education page. The CardioGenomics project came to a close in 2005. This server, cardiogenomics.med.harvard.edu, remains online in order to continue to distribute data that was generated by investigators under the auspices of the CardioGenomics Program for Genomic Applications (PGA). :Sponsors: This resource is supported by The National Heart, Lung and Blood Institute (NHLBI) of the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
CASPLab: Comet Assay Software Project Laboratory
CASP is a tool to image analysis in comet assay. CASP has been developed to work with either color, or gray-scale images of fluorescence-stained comets saved in TIF format. In its present version CASP does not control a video or CCD camera. Comets stained with silver (dark cells on white background) must be converted into negative images in order to be analysed correctly. An unlimited number of images can be marked, CASP will load them successively into a image view window (see screenshot). Only comets oriented from left (head) to right (tail) can be analysed correctly. The user can adjust various thresholds of sensitivity and save the adjustments for future use. A measurement frame is drawn on the screen and its size adjusted. The adjustments are frozen to prevent accidental modification. The frame is moved onto a cell and measurement is activated. An intensity profile shows up on a profile window together with selected result values (right window on figure 1) and the result can be saved. In addition to such parameter as head radius, tail length etc, the program calculates the tail moment (TM) and the Olive tail moment (OTM). If several cells are present on the same picture, the user can proceed with the measurement of another cell on the same picture or can load a new picture. The saved results can be visualized during the working session in a spreadsheet in view results window. When measurements are terminated, the results can be exported into a text file and imported into a commercial spreadsheet calculation program. CASP is optimized for a 600x800 resolution. Sponsors: This work has been supported by the University of Wroclaw. Keywords: Comet, Assay, Software, Laboratory, Camera, Negative, Cell, Analysis, Image,
This form allows you to assemble a set of contiguous sequences (contigs) with the CAP3 program. The CAP3 program has a capability to clip 5'' and 3'' low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward-reverse constraints to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints. Sponsors: This project was supported by NIH Grant R01HG01502-02 from NHGRI. Keywords: CAP3, Program, Form, Computation, DNA, Dataset, Database, Program,, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The Brain Architecture Management System
Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions.
Company offers Data Curation, Data Governance and Models, Bioinformatics Analysis, Workflows and Pipelines, Knowledge Mining, Target Profiles, Building Databases with content, Business Analyst services to clients in Pharmaceutical and Biotech companies, Foundations, Government and Hospitals.
Welcome to CPAN, where you you will find All Things Perl. CPAN is the Comprehensive Perl Archive Network, a large collection of Perl software and documentation. You can begin exploring from either http://www.cpan.org/, http://www.perl.com/CPAN/ or any of the mirrors listed at http://www.cpan.org/SITES.html. Note that CPAN is also the name of a Perl module, CPAN.pm, which is used to download and install Perl software from the CPAN archive. This FAQ covers only a little about the CPAN module and you may find the documentation for it by using perldoc CPAN via the command line or on the web at http://search.cpan.org/dist/CPAN/lib/CPAN.pm. Sponsors: CPAN works with the generosity and cooperation of hundreds of developers, over 100 participating mirrors, funet.fi donating the network bandwidth, storage space and computing power, volunteers who help keep everything together and users whose interest in Perl keep the archive alive and growing. Keywords: Comprehension, Perl, Archive, Software, Documentation,
This portal allows for the detection of regions of genomic sequences that are rich in the CpG pattern is important because such regions are resistant to methylation and tend to be associated with genes which are frequently switched on. Regions rich in the CpG pattern are known as CpG islands. The function of the program cpgplot is to plot CpG rich areas, and cpgreport to report all CpG rich regions. The nuclear genomes of vertebrates are mosaics of isochores, very long stretches of DNA that are homogeneous in base composition and are compositionally correlated with the coding sequences that they embed. Isochores can be partitioned in a small number of families that cover a range of GC levels. Program isochore plots GC content over a sequence. Sponsors: This resource is supported by European Bioinformatics Institute. Keywords: Software, Plotting, Pattern, CpG, Gene, Function, Isochore, DNA, Genome, Homogeneous, Coding, Sequence, Family, Sequencing,
Collaborative Computational Project Number 4
The Collaborative Computational Project Number 4 in Protein Crystallography
Portal for Macromolecular X-Ray Crystallography to produce and support an integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. Used in the education and training of scientists in experimental structural biology for determination and analysis of protein structure.
It is a Company Limited by Guarantee comprising golf handicapping experts from all the Golf Unions and Associations that administer golf in Great Britain and Ireland. A golf handicap allows players of all levels of golfing ability to compete against each other on a fair and equal basis. Thus a handicap system is effectively essential to the popularity and prosperity of the game of Amateur Golf. The System developed and refined by the Council of National Golf Unions (CONGU) provides a player with a golf handicap that reflects their playing ability relative to that of all other players handicapped by the CONGU Handicapping System. In 2004 CONGU incorporated Ladies golf handicaps within the system and this effectively completed the objective of providing a golf handicap that allowed players of all levels of ability to compete on an equal basis at Club, District, Provincial, National and International levels. What CONGU does? Develop and maintain a Golf Handicapping System that provides CONGU Handicaps for all players of the Clubs affiliated to the National Unions and Associations. Also to assist and support these Organisations, and their Affiliated Clubs, in administering golf handicaps on a day-to-day basis. Why CONGU does it? To promote the development of golf at Affiliated Clubs by providing a Handicapping System which produces golf handicaps that allow amateur players, male and female, of significantly varying abilities to compete against each other on as equitable a basis as possible. Keywords: Golf, Handicap, Popularity, Player, Devlopment, Handicapping, Organization,
The Surf-Hippo neuron simulator is used to investigate morphologically and biophysically detailed compartmental models of single neurons and networks of neurons. Surf-Hippo allows ready construction of cells and networks using built-in functions and various anatomical file formats (Neurolucida, NTS and others). Surf-Hippo is a public domain package, written in Lisp, and runs under Unix and Linux.
Software application that treats the disease-associated markers and their interactions via a bayesian partitioning model and computes, via Markov chain Monte Carlo, the posterior probability that each marker set is associated with the disease. (entry from Genetic Analysis Software)
Allele Frequencies in Worldwide Populations
The main purpose of the allelefrequencies.net website is to provide one central source, freely available to all. For the storage of allele frequencies from different polymorphic areas in the HUMAN genome. Users can contribute the results of their work into one common database, and can perform database searches on information already available. They have currently collected data in allele, haplotype and genotype format. The success of this website will depend on you to contribute your data. Sponsors: This resource is supported Royal Liverpool University. Keywords: Allele, Polymorphic, Genome, Database, Data, Haplotype, Genotype,
Avon Longitudinal Study of Parents and Children
The Avon Longitudinal Study of Parents and Children
A long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally.
The roots of the American Thoracic Society reach back to 1905, when a small group of physicians decided that the best way to improve care for tuberculosis patients was to share their experiences and discoveries. Today, the ATS has grown into an international society with more than 15,000 members. In this introductory section, you will find information about the people and programs that make the ATS the world''s leading medical association dedicated to advancing our clinical and scientific understanding of pulmonary diseases, critical illnesses and sleep-related breathing disorders. It created a new program to enhance the Societys commitment to discovering new knowledge and advancing patient care. Over the last seven years, the ATS Research Program has grown tremendously, providing more than 7.5 million in grants to 76 young researchers investigating a wide spectrum of lung diseases, ranging from asthma and COPD to pulmonary fibrosis and alpha-1 antitrypsin. The program has also funded the career development of 24 pulmonary and critical care fellows. A main purpose of the American Thoracic Society is to foster the gathering, evaluating, and disseminating of scientific and clinical information. This part of the ATS Website contains clinical information arranged by topic. Most of the information is developed and contributed by the scientific assemblies of the American Thoracic Society.
The American Epilepsy Society promotes research and education for professionals dedicated to prevention, treatment and cure of epilepsy. American Epilepsy Society members work to improve the quality of life for people with epilepsy. In the support of its members, AES is committed to providing those engaged in research with information and assistance of potential benefit in advancing their work. AES also has formed alliances with other organizations that provide research funding, including the Grass Foundation, Epilepsy Foundation, and other funding sources. Keywords: American, Epilepsy, Society, Research, Education, Professional, Prevention, Treatment, Cure, Member, Benefit,
CellDesigner: A modeling tool of biochemical networks
CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface. Sponsors: ERATO-SORST program (JST); International Standard Development area of the International Joint Research Grant (NEDO); Strategic Japanese-Swedish Cooperative Program on Multidisciplinary BIO (JST-VINNOVA/SSF); Establishment of a Human Genome Network Platform (MEXT) and through the special coordination funds for promoting science and technology from the Japanese government''s Ministry of Education, Culture, Sports, Science and Technology (MEXT) Keywords: Cell, Designer, Gene, Biochemical, Network, Diagram, Biology, System, Gene, Biolohy, Database,
Johns Hopkins Bloomberg School of Public Health
It was created to serve as a gateway to alternatives news, information, and resources on the Internet and beyond. Altweb now is the U.S. home of the journal ALTEX: Alternatives to Animal Experimentation, which is the official publication of the Johns Hopkins Center for Alternatives to Animal Testing (CAAT). Altweb is intended to serve: *Biomedical researchers *Industry *The international alternatives community *The international regulatory community(ies) *IACUCs and other institutional groups that review animal protocols *The animal welfare community *Individuals and groups who work with laboratory animals (technicians, veterinarians, etc.) *Educators *Students *The general public Altweb has five practical goals: 1. To assist scientists and others seeking to conduct a search for alternatives methods. 2. To serve as a CRPcentral reference pointfor alternatives information, publications, databases, calendars, and other resources. 3. To support the creation and maintenance of new alternative resources as needed, when no other organization can/will do so. 4. To promote the use of alternatives resources by publicizing them on the site and through e-mail or other outreach. 5. To facilitate communication and collaboration among members of the alternatives community, in particular those who work in database or information management.
The Genetics of Learning Disability (GOLD) Study is aimed to identify the genes on the X chromosome that contribute to significant intellectual disability and to lead the way towards greater understanding of the mechanisms by which intellectual disability occurs. Ultimately the aim is to improve the services available to affected families. Sponsors: The work was supported by the European Community''s Seventh Framework Programme-the GEN2PHEN Project, the New South Wales Department of Health, the Australian NHMRC, the SMILE foundation, the WCH Foundation, D. Harwood, EU grant QLG3-CT- 2002-01810 (EURO-MRX), US National Institutes of Health (HD26202) to C.E.S., the South Carolina Department of Disabilities and Special Needs (SCDDSN), Action Medical Research and the Wellcome Trust.
This is the homepage of Dr. Cavalli''s Chromatin and Cell Biology Laboratory. Keywords: Chromatin, Cell, Biology, Scientific, Science, Research, Laboratory,
BOMP: beta-barrel Outer Membrane protein Predictor
BOMP is a tool for prediction of beta-barrel integral outer membrane proteins. The user may submit a list of proteins, and receive a list of predicted BOMPs. The program, called the beta-barrel Outer Membrane protein Predictor (BOMP), is based on two separate components to recognize integral beta-barrel proteins. The first component is a C-terminal pattern typical of many integral beta-barrel proteins. The second component calculates an integral beta-barrel score of the sequence based on the extent to which the sequence contains stretches of amino acids typical of transmembrane -strands. To use the BOMP tool simply paste your fasta-formatted sequences into the text area, or choose a file which contains sequences. Then hit the submit button. It is possible to perform a BLAST search parallel with the predictions, which may be suitable in some cases. Using the BLAST search will however increase the running time substantially. Sponsors: This work was supported in part by grants from the Norwegian Research Council [SUP 140785/420 (GABI); FUGE/CBU151899/ISO], and the Meltzer Foundation, University of Bergen. Keywords: Beta-barrel, Membrane, Protein, Program, Software, Beta strand, Bacteria,
PaperMaker delivers feedback on the use of terms and language in a biomedical manuscript. It does not store any submitted data. PaperMaker is a novel IT solution that receives a scientific manuscript via a Web interface, automatically analyses the publication, evaluates consistency parameters and interactively delivers feedback to the author. It analyses the proper use of acronyms and their definitions, and the use of specialized terminology. It provides Gene Ontology (GO) and Medline Subject Headings (MeSH) categorization of text passages, the retrieval of relevant publications from public scientific literature repositories, and the identification of missing or unused references. The end result is that the author receives a summary of findings, the manuscript in its corrected form and a digital abstract containing the GO and MeSH annotations in the NLM/PubMed format.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 22, 2016. A plugin for ImageJ, an NIH-sponsored image viewer and analysis tool, that allows the user to extract from neuronal images measurements of coordinates and diameters of sections of neurons together with other information that can be used to reconstruct the neuron morphology. It allows the user to measure the x, y and z coordinates of a selected point of a stack of confocal images and the radius of the corresponding section of the neuron together with other information that can be used to reconstruct the neuron morphology. The measurement output is in swc format. It is possible to transform it in a hoc file for the program neuron using the neuron morphology viewer cvapp.
Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions.
Neuroanatomy and Neuropathology on the Internet
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. A set of human neuroanatomical resources developed at the University of Hungary. Resources include an on-line brain atlas, a neuropathology atlas, functional neuroanatomy for neurologists and an extensive series of links to other neuroanatomy and neurological resources on the web. The original resources developed by this site include a set of neuropathological slides covering many neurological conditions, e.g., Alzheimer's disease, an atlas of normal human neuroanatomy based on unstained brain slices, along with histological images of brainstem and spinal cord. On-line quizzes are also provided. This is an excellent educational site and gateway to neurological resources on the web.
This web site provides browsers with images and information from one of the world''s largest collection of well-preserved, sectioned and stained brains of mammals. Viewers can see and download photographs of brains of over 100 different species of mammals (including humans) representing over 20 Mammalian Orders. Also available are examples of stained sections from a wide variety of brains of special interest, including Humans, Chimpanzees, Monkeys, various Rodents and Carnivores, California Sealion, Florida Manatee, Big Brown Bat, American Badger, American Raccoon, Yellow Mongoose, Zebra, Cow, and the Atlantic Bottlenose Dolphin. A complete list of all available specimens is available. How brain evolution has occurred is discussed. Viewers will learn why these collections are important, why and how they were assembled, and why it is important to protect, preserve and maintain them. Moreover, a variety of issues in brain science are discussed. For users who are interested in using any of our images for educational or research purposes, you have our permission to use them. But, they are not to be published and copyrighted since this would prohibit others from using the same images. At any rate, we request that you identify them as from the University of Wisconsin and Michigan State Comparative Mammalian Brain Collections, as well as from those at the National Museum of Health and Medicine. Also, we request that you refer to the Web Site where you obtained them, as well as the fact that preparation of all these images and specimens have been funded by the National Science Foundation, as well as by the National Institutes of Health.
An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children' '''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).
In this atlas you can view axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem. The creators of the site encourage the use of the data and it is available freely, but ask that they be contacted before any use. This site contains a series of axial sections stained for cell bodies or fibers at six rostro-caudal levels of the human brain stem. Sections are labeled for approximately 50 structures and are searchable through a web interface. For each level, a fiber and cell stain is provided. Labels may be turned on or off.
The SenseLab Project is a long-term effort to build integrated, multidisciplinary models of neurons and neural systems. It was founded in 1993 as part of the original Human Brain Project, which began the development of neuroinformatics tools in support of neuroscience research. It is now part of the Neuroscience Information Framework (NIF) and the International Neuroinformatics Coordinating Facility (INCF). The SenseLab project involves novel informatics approaches to constructing databases and database tools for collecting and analyzing neuroscience information, using the olfactory system as a model, with extension to other brain systems. SenseLab contains seven related databases that support experimental and theoretical research on the membrane properties: CellPropDB, NeuronDB, ModelDB, ORDB, OdorDB, OdorMapDB, BrainPharmA pilot Web portal that successfully integrates multidisciplinary neurocience data.
CoCoMac (Collations of Connectivity Data on the Macaque Brain)
Collations of Connectivity Data on the Macaque Brain
Online access (html or xml) to structural connectivity ("wiring") data on the Macaque brain. The database has become by far the largest of its kind, with data extracted from more than four hundred published tracing studies. The main database, contains data from tracing studies on anatomical connectivity in the macaque cerebral cortex. Also available are a variety of tools including a graphical simulation workbench, map displays and the CoCoMac-Paxinos-3D viewer. Submissions are welcome. To overcome the problem of divergent brain maps ORT (Objective Relational Transformation) was developed, an algorithmic method to convert data in a coordinate- independent way based on logical relations between areas in different brain maps. CoCoMac data is used to analyze the organization of the cerebral cortex, and to establish its structure- function relationships. This includes multi-variate statistics and computer simulation of models that take into account the real anatomy of the primate cerebral cortex. This site * Provides full, scriptable open access to the data in CoCoMac (you must adhere to the citation policy) * Powers the graphical interface to CoCoMac provided by the Scalable Brain Atlas * Sports an extensive search/browse wizard, which automatically constructs complex search queries and lets you further explore the database from the results page. * Allows you to get your hands dirty, by using the custom SQL query service. * Displays connectivity data in tabular form, through the axonal projections service. CoCoMac 2 was initiated at the Donders Institute for Brain, Cognition and Behaviour, and is currently supported by the German neuroinformatics node and the Computational and Systems Neuroscience group at the Juelich research institute.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community.
Portal used to coordinate activities of the German portion of the INCF group. The main focus is the development and free distribution of software tools for handling and analyzing neurophysiological data.
Portal to neurogenetic resources: the mouse brain library, digital atlases of the mouse brain, extensive brain microarray data in WebQTL, and internet access to microscopes and stereology tools.Mouse Brain Library. Mouse Brain Library is an expanding collection of high-resolution histological images, atlases, MRIs, and databases on brain structure of more than 120 different lines of mice. Nervenet also includes several useful genetics and gene mapping databases to download (SNP databases, Map Manager databases, and the Portable Dictionary of the Mouse Genome). The publications section includes revised, expanded, and annotated papers, tutorials, and reviews on neurogenetics, gene mapping, complex trait analysis, stereology, and the control of neuron number.
NIH Model Organisms for Biomedical Research
Information about national and international activities and major resources that are being developed to facilitate biomedical research using animal models Mammalian Models: * Mouse * Rat Non-Mammalian Models * S. cerevisiae (budding yeast) * S.pombe (Fission Yeast) * Neurospora (filamentous fungus) * D. discoideum (social amoebae) * C. elegans (round worm) * Daphnia * D. melanogaster (fruit fly) * D. rerio (zebrafish) * Xenopus (frog) * Gallus (chicken) Other Model Organisms: * Arabidopsis
Archive used for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MRI, PET, MRA, DTI and other imaging modalities.
DOQCS - Database of Quantitative Cellular Signaling
A repository of models of signaling pathways that includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions.
A repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells. The database is presently focused on neurons but will eventually include other cell types, such as glia, muscle, and gland cells. This resource is intended to: * Serve as a repository for data on gene products expressed in different brain regions * Support research on cellular properties in the nervous system * Provide a gateway for entering data into the cannonical neuron forms in NeuronDB * Identify receptors across neuron types to aid in drug development * Serve as a first step toward a functional genomics of nerve cells * Serve as a teaching aid
OdorDb is a database of odorant molecules, which can be searched in a few different ways. One can see odorant molecules in the OdorDB, and the olfactory receptors in ORDB that they experimentally shown to bind. You can search for odorant molecules based on their attributes or identities: Molecular Formula, Chemical Abstracts Service (CAS) Number and Chemical Class. Functional studies of olfactory receptors involve their interactions with odor molecules. OdorDB contains a list of odors that have been identified as binding to olfactory receptors.
Olfactory Bulb Odor Map DataBase (OdorMapDB)
OdorMapDB is designed to be a database to support the experimental analysis of the molecular and functional organization of the olfactory bulb and its basis for the perception of smell. It is primarily concerned with archiving, searching and analyzing maps of the olfactory bulb generated by different methods. The first aim is to facilitate comparison of activity patterns elicited by odor stimulation in the glomerular layer obtained by different methods in different species. It is further aimed at facilitating comparison of these maps with molecular maps of the projections of olfactory receptor neuron subsets to different glomeruli, especially for gene targeted animals and for antibody staining. The main maps archived here are based on original studies using 2-deoxyglucose and on current studies using high resolution fMRI in mouse and rat. Links are also provided to sites containing maps by other laboratories. OdorMapDB thus serves as a nodal point in a multilaboratory effort to construct consensus maps integrating data from different methodological approaches. OdorMapDB is integrated with two other databases in SenseLab: ORDB, a database of olfactory receptor genes and proteins, and OdorDB, a database of odor molecules that serve as ligands for the olfactory receptor proteins. The combined use of the three integrated databases allows the user to identify odor ligands that activate olfactory receptors that project to specific glomeruli that are involved in generating the odor activity maps.
Mammalian protein-protein interaction database focusing on synaptic proteins. The Protein-Protein Interaction Database was originally a single-person's attempt to integrate a gamut of biological/bibliographical/molecular data and build a framework which might help understanding how cells orchestrate their protein content in order to become what they are: machines with a purpose. This is based on the simple paradigm that functionality like signal cascades are held together in a close space, thereby allowing specific events to occur without the necessity of passive diffusion and random events. The PPID database arose from the need to interpret Proteomic datasets, which were generated analysing the NMDA-receptor complex (see H. Husi, M. A. Ward, J. S. Choudhary, W. P. Blackstock and S. G. Grant (2000). Proteomic analysis of NMDA receptor-adhesion protein signaling complexes. Nat Neurosci 3, 661-669.). To study these clusters of proteins requires unavoidably the handling of large datasets, which PPID is generally aimed and tailored for. This database is unifying molecular entries across three species, namely human, rat and mouse and is is footed on sequence databases such as SwissProt, EMBL, TrEMBL (translated EMBL sequences) and Unigene and the literature database PubMed. A typical entry in PPID holds up to three general entries for the three species, all protein and gene accession numbers associated with them (assembled from Blast2 searches of the databases) and the OMIM entry as maintained by Johns Hopkins University. Furthermore protein sequence information is also included, together with known and novel splice-variants of each molecule as found by ClustalW sequence alignments. Entry points also include protein-binding information together with the literature reference. The whole database is curated manually to insure accuracy and quality. Querying the database will be possible by online browsing and batch-submission for large datasets holding accession number information, as can be generated using software like Mascot for mass-spectrometry. Cluster-analysis of the submitted datasets in the form of a graphical output will be developed as well as an easy-to-use web-interface. An interface is currently being built in collaboration with the Department of Informatics (T. Theodosiou and D. Armstrong) and will be deployed soon The current team of people collating and deploying the database are H. Husi (database mining and information gathering) and T. Theodosiou (web-interface and deployment). Please note that this database is not funded financially, and cannot survive without sponsorship.
A controlled vocabulary of terms used in Computational Neurosciences to describe models of the nervous system. This first release of CNO is an alpha version and should be further aligned with other ontologies accessible on Bioportal and should be made compliant with the OBO foundry recommendations.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. It was established to develop, implement and support the information infrastructure necessary to achieve large-scale data sharing among the test bed participants (function, morphometry and mouse birn). The BIRN-CC consists of a unique and well-established partnership between computer scientists, neuroscientists and engineers. This partnership addresses a large array of technical, policy, and architectural issues to fundamentally enable a new suite of information technology supported database and analysis tools that allow scientists to analyze and interpret significantly larger sets of data than is possible in the traditional single-institution study paradigm.
The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source.
Interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. First developed on Matlab 5.3 under Linux, EEGLAB runs on Matlab v5 and higher under Linux, Unix, Windows, and Mac OS X (Matlab 7+ recommended). EEGLAB provides an interactive graphic user interface (GUI) allowing users to flexibly and interactively process their high-density EEG and other dynamic brain data using independent component analysis (ICA) and/or time/frequency analysis (TFA), as well as standard averaging methods. EEGLAB also incorporates extensive tutorial and help windows, plus a command history function that eases users'' transition from GUI-based data exploration to building and running batch or custom data analysis scripts. EEGLAB offers a wealth of methods for visualizing and modeling event-related brain dynamics, both at the level of individual EEGLAB ''datasets'' and/or across a collection of datasets brought together in an EEGLAB ''studyset.'' For experienced Matlab users, EEGLAB offers a structured programming environment for storing, accessing, measuring, manipulating and visualizing event-related EEG data. For creative research programmers and methods developers, EEGLAB offers an extensible, open-source platform through which they can share new methods with the world research community by publishing EEGLAB ''plug-in'' functions that appear automatically in the EEGLAB menu of users who download them. For example, novel EEGLAB plug-ins might be built and released to ''pick peaks'' in ERP or time/frequency results, or to perform specialized import/export, data visualization, or inverse source modeling of EEG, MEG, and/or ECOG data. EEGLAB Features * Graphic user interface * Multiformat data importing * High-density data scrolling * Defined EEG data structure * Open source plug-in facility * Interactive plotting functions * Semi-automated artifact removal * ICA & time/frequency transforms * Many advanced plug-in toolboxes * Event & channel location handling * Forward/inverse head/source modeling
Brain atlas in sagittal, coronal, and axial planes some from myelin stained sections, others from MRI. The structures are outlined and labeled on the zoomable images in the coronal series. The labels can also be used in quiz mode. Designed as part of of program for second year medical students studying neuroanatomy.
An integrated resource for genomics and bioinformatics in vision research including expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAST search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. To see the same region at the full UCSC site, cut and paste the location from the position window of the genome browser. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank.
HubMed provides an interface to PubMed. Quick access to searches with a Firefox search plugin or a HubMed bookmarklet (drag to your browser''s bookmarks toolbar). Export citations in RIS, BibTeX, RDF and MODS formats, or directly to RefWorks. Unzip HubMed''s import filter into Endnote''s Filters folder for direct import into Endnote, or install the RIS Export plugin for direct import into ProCite, RefMan and older versions of Endnote. Use the Citation Finder to convert reference lists from PDFs into search results. Create lists of closely related papers using Rank Relations, then visualise and browse clusters of related papers using TouchGraph (requires Java). Graph occurrences of keywords in published papers over time. Tag and store annotated metadata for articles of interest.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. Resource aimed at promoting awareness and facilitating access to online neuroscience databases.
Series of MRI slices from 3 male Japanese snow monkeys (Macaca fuscata). Images are provided of 2 mm MRI slices of male monkey brain in the coronal (N = 5), horizontal (N =1) and sagittal (N =1) planes. Slices are presented according to distance from interaural line. The slices are low resolution and no annotations are provided. Would be suitable for low resolution 3D reconstruction of monkey brain, however. Also, there are datasets provided for 5 monkeys total, 3 m.fuscata and 2 m. mulatta.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2011. This database contains gene expression data for various physiological and pathological processes in mouse brain. All the data have been obtained by adaptor-tagged competitive PCR, an advanced version of quantitative PCR. Brain Gene Expression Database (BGED) contains gene expression data for various physiological and pathological processes in mouse brain. All the data have been obtained by adaptor-tagged competitive PCR, an advanced version of quantitative PCR. Manual Download 1. Data retrieval Gene expression data can be retrieved either by ID numbers or by keywords representing functional annotations from this page. The ID numbers include GenBank, RefSeq, SwissProt, Gene Ontology, and BED (our own ID). The keyword search is based either on definition in GenBank, SwissProt and RefSeq, functional annotation of SwissProt database, or Gene Ontology terms. 2. Gene expression pattern display * Display of multiple gene expression patterns. Expression patterns of multiple genes selected by the keyword search can be displayed from the result page of the keyword search. * Gene expression pattern similarity search This function is available on the information page of each gene accessed through BED ID (in-house ID).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The 7 database (or a7db) provides physiological, pharmacological and structural data pertaining to the 7 subunit of the nicotinic acetylcholine receptor. As well as the simple boolean-based query, there are several other ways to help you interrogate the database; * One page query builder * Query builder based on the category of data * Upload a prebuilt/previous query * Browse the database To gain insight into what sort of data can be queried, the one page or categorized query builders are recommended. Or you can just browse the database. The best way to navigate is to use the links on the left. Please be aware that we are presenting the raw data and that it is up to the user on how best to interpret that data. You can read more about the database in the recent article in BMC Neuroscience
A web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborious preprocessing.
An open international project under the patronage of the Human Proteome Organisation (HUPO) that aims: To analyze the brain proteome of human as well as mouse models in healthy, neurodiseased and aged status with focus on Alzheimer's and Parkinson's Disease; To perform quantitative proteomics as well as complementary gene expression profiling on disease-related brain areas and bodily fluids; To advance knowledge of neurodiseases and aging in order to push new diagnostic approaches and medications; To exchange knowledge and data with other HUPO projects and national / international initiatives in the neuroproteomic field; To make neuroproteomic research and its results available in the scientific community and society. Recent work has shown that standards in proteomics and especially in bioinformatics are mandatory to allow comparable analyses, but still missing. To address this challenge, the HUPO BPP is closely working together with the HUPO Proteome Standards Initiative (HUPO PSI).
Imagebank consists of freely available images contributed by academics, researchers, Learned Societies, industry and individuals with rights cleared for educational purposes. :Users are able to search for images based on keywords or browse within a wide range of bioscience subject areas. Images are then downloadable along with informative descriptive text provided by the contributor. All images undergo a validation process by Centre for Bioscience staff with good subject knowledge. ImageBank also offers reviews of, and links to existing bioscience image databases.
FlexProt detects the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected.
Monte Carlo simulator of cellular microphysiology
Software modeling tool for realistic simulation of cellular signaling in complex 3-D subcellular microenvironment in and around living cells. Program that uses spatially realistic 3D cellular models and specialized Monte Carlo algorithms to simulate movements and reactions of molecules within and between cells.
NSL, Neural Simulation Language, is a simulation system for large-scale general neural networks. NSL provides a simulation environment simplifying the task of modeling neural networks. In particular, NSL supports neural models having as basic data structure neural layers with similar properties and similar connection patterns, where neurons are modeled as leaky integrators with connections subject to diverse learning rules. Development of NSL has gone hand in hand with modeling of neural mechanisms underlying visuomotor coordination, with special emphasis on the analysis of data from anurans, monkeys, and humans. NSL follows an object-oriented design, providing higher level programming abstraction corresponding to neural elements. NSL provides system development tools, such as visualization capabilities and a run-time interpreter, which give the user powerful tools in developing and analyzing models. NSL has been widely used throughout the world for both teaching and research. simulation; software
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The main site for the Medical Shool of Georgia's Alzheimer's research.
It records bibliographic, chemical and crystallographic information for organic molecules and metal-organic compounds whose 3D structures have been determined using X-ray diffraction and neutron diffraction. The CSD records results of single crystal studies and powder diffraction studies which yield 3D atomic coordinate data for at least all non-H atoms. In some cases the CCDC is unable to obtain coordinates, and incomplete entries are archived to the CSD. The CSD includes crystal structure data arising from: * publications in the open literature * Private Communications to the CSD (via direct data deposition) The Cambridge Structural Database System (CSDS) is a single product that comprises the following components: The Cambridge Structural Database (CSD); CSDS Software: search and information retrieval (ConQuest), structure visualization (Mercury), statistical analysis of retrieved data (VISTA), and software for database creation (PreQuest); Knowledge bases derived from the CSD: Mogul (intramolecular geometry) and IsoStar (intermolecular interactions, including data from the PDB). Cambridge Structural Database (CSD) is the world repository of small-molecule crystal structures. For example, the crystal structures supported by the National Institute on Drug Abuse are deposited here.
Focus is the generation of a reference expression database for the C57BL/6J mouse. The current dataset will consist of 90 samples, primarily from adult tissue, and was analyzed using a technique known as Massively Parallel Signature Sequencing (MPSS). The data are stored in the Gene Expression Omnibus (GEO).The focus of this project is the generation of a reference RNA transcriptome expression database for the C57BL/6J mouse. The current dataset will consist of 90 samples, primarily from adult tissue, and was analyzed using a technique known as Massively Parallel Signature Sequencing (MPSS)
Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource
NIH Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource
Repository of knockout mice that have been extensively characterized. For each mouse line, the contractors will provide not only the mouse line itself, but also detailed, objective data on the impact of the specific gene deletion on the mouse''s phenotype, which includes appearance, health, fitness, behavior, ability to reproduce, and radiological and microscopic data. Such comprehensive information on such a large group of mice has never been available to public sector researchers, and is expected to greatly accelerate efforts to explore gene functions in health and disease. This resource will give researchers unprecedented access to two private collections of knockout mice, providing valuable models for the study of human disease and laying the groundwork for a public, genome-wide library of knockout mice. The contracts also provide for the opportunity for NIH to obtain up to 1500 additional mouse lines and phenotypic data over the next three years, pending available funds. The new contracts provide NIH with irrevocable, perpetual, worldwide, royalty-free licenses to use and distribute to academic and non-profit researchers these lines of knockout mice. The mouse lines, which will be stored in the form of frozen embryos, frozen sperm and frozen embryonic stem (ES) cells, will be delivered to NIH-funded mouse repositories that supply mice to universities, medical schools and research labs all over the world. When researchers express interest in obtaining a certain knockout mouse line, the repositories will send them live mice, frozen embryos, sperm, and/or ES cells, so they can study the mice in their own labs. All data on the mice will be made available to researchers worldwide without restriction in publicly available databases on the Web. This resource will be available for a nominal fee which will be used to cover the cost of handling, shipping and replenishing the stock. Under the license agreements with Deltagen and Lexicon, researchers who receive the knockout mice lines through NIH are free to publish any results from research involving the line and also to seek patent or other intellectual property protection for any of the inventions or discoveries resulting from such research. List of Available Knockout Mice: http://www.informatics.jax.org/external/ko/
National Cell Repository for Alzheimer's Disease
Cell repository for Alzheimer's disease that collects and maintains biological specimens and associated data. Its data is derived from large numbers of genetically informative, phenotypically well-characterized families with multiple individuals affected with Alzheimer's disease, as well as individuals for case-control studies.
National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS)
Genetics of Alzheimer’s Disease Data Storage Site
NIA Genetics of Alzheimer's Disease Data Storage Site
National genetics data repository facilitating access to genotypic and phenotypic data for Alzheimer's disease (AD). Data include GWAS, whole genome (WGS) and whole exome (WES), expression, RNA Seq, and CHIP Seq analyses. Data for the Alzheimer’s Disease Sequencing Project (ADSP) are available through a partnership with dbGaP (ADSP at dbGaP). Repository for many types of data generated from NIA supported grants and/or NIA funded biological samples. Data are deposited at NIAGADS or NIA-approved sites. Genetic Data and associated Phenotypic Data are available to qualified investigators in scientific community for secondary analysis.
An R package that specifically focuses on statistical and population genetics methods. The motivation behind the package is to produce an easy to use interface to many of the commonly used methods and models used in statistical and population genetics and an alternative interface for some of the methodology produced by our group. (entry from Genetic Analysis Software)
A free software using a sliding-window approach to identify differentially methylated regions (DMR) from whole-genome bisulfite sequencing.
Colonies of barrier-raised, Specific Pathogen-Free (SPF) rodents under contractual arrangement with commercial vendors, specifically for use in aging research. They are not available for use as a general source of adult animals for unrelated areas of research. Animals from the NIA aged rodent colonies are available to investigators at academic and non-profit research institutions under the terms described on the Eligibility Criteria page. Orders must be submitted through the online rodent ordering system (ROS) (http://arc.niapublications.org/acb/stores/1/). Available strains: * Inbred Rats: Fischer 344 (F344), Brown Norway (BN) * Hybrid Rats: F344xBN F1 (F344BN); * Inbred Mice: BALB/cBy, CBA, C57BL/6, DBA/2 * Hybrid Mice: CB6F1 (BALB/cBy x C57BL/6), B6D2F1 (C57BL/6 x DBA/2) * Caloric Restricted Rats: F344 (males only), F344BN F1 (males only) * Caloric Restricted Mice: C57BL/6; B6D2F1 (males only)
UC Davis KOMP Repository Knockout Mouse Project
UCDavis KOMP Repository Knockout Mouse Project
Repository of mouse vectors, ES cells, mice, embryos, and sperm generated by NIH KOMP Mutagenesis Project. In addition, KOMP Repository offers services in support of KOMP products, including ES cell microinjection, vector cloning, post-insertional modification of cloned ES cells, cryopreservation, assisted reproduction techniques (IVF, ICSI) and mouse breeding, pathology services, phenotyping services, etc. KOMP Repository is final component of more than $50 million trans-NIH initiative to increase availability of genetically altered mice and related materials. The University of California, Davis (UC Davis) and Children''s Hospital Oakland Research Institute (CHORI) in Oakland, Calif., are collaborating to preserve, protect, and make available about 8,500 types of knockout mice and related products available to research community. Products are generated by two KOMP mutagenesis teams (CSD consortium and Regeneron Inc). All KOMP products generated by CSD consortium and Regeneron are available through KOMP Repository. Notice as of December 19, 2019: Materials from KOMP Repository have been deposited into MMRRC, including all mouse models and mouse embryonic stem cell lines. Eventually www.komp.org will be sunsetting, and IMSR will remove KOMP Repository listings, since they were double listed in MMRRC. MMRRC will contain the most accurate and up to date resource models.
NINDS/UCLA Repository for Parkinson's Disease Mouse Models
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Information for depositors Investigators who are willing to share mice with the PD research community through this resource should send an email to PDMice_at_ninds.nih.gov describing the mouse. The submission will be reviewed by the PD Models Repository Oversight Committee and, if accepted, a copy of the MTA will be sent by return email. NINDS is most interested in distributing mice that have been characterized in a peer-reviewed publication, but other models will certainly be considered. The email should describe the following: The protocol for identification from tail DNA. The health report of the mice to be shipped (the report has to be less than 2 months old). Information about the strain and any special needs for care and breeding. Information about any publications involving the mice Certification that mice are not encumbered by continuing intellectual property or other rights to any research, data or discovery utilizing the animals. Information for consumers Investigators desiring to study the mice available through the repository should send a request via email to PDMice_at_ninds.nih.gov. Requests will be reviewed by the PD Models Repository Oversight Committee and priority will be determined on a first come, first served basis; two breeding pairs will typically be shipped to any single requester. As detailed in the MTA, mice are not available for commercial research, including but not limited to drug screening. Neither the creator nor UCLA have a role in the governance of the Repository, and specifically, cannot impose conditions upon availability or distribution. It is anticipated that until the Repository is in a mode of steady state production, requests will be collected and mice distributed as supply allows. The email requesting mice should include: A brief description of the protocol Either a copy of the IACUC approval letter or numberNINDS/UCLA Repository for Parkinson's Disease Mouse Models: One of the most immediate and important benefits of discoveries regarding the genetic or environmental causes of Parkinson's disease (PD) is the subsequent development of animal models wherein therapeutic and/or preventative interventions may be studied. The widespread availability of such models is critically important to making progress against a disorder that affects more than 500,000 Americans at any given time. The National Institute of Neurological Disorders and Stroke (NINDS) fully recognizes the burden placed on investigators by the financial and logistical realities of distributing high demand research resources. Some investigators have deposited their mice with national distribution facilities but many mouse models are not available through such resources. Developing means to facilitate greater sharing of mouse models of PD is one of the goals developed by the PD research community at the July 2002 summit meeting convened by the NIH Director. Accordingly, as part of the effort to accelerate PD research, NINDS and the University of California at Los Angeles (UCLA) created a resource that will distribute transgenic mouse models of human PD that are not yet available through national commercial resources. Investigators who are willing to share mice with the PD research community can simply arrange with NINDS to have the mice deposited at UCLA and investigators desiring to study the mice may arrange with NINDS to obtain two breeding pairs. The process will use Material Transfer Agreements created specifically for this arrangement.
A cell repository containing cells and DNA for studies of aging and the degenerative processes associated with it. Scientists use the highly-characterized, viable, and contaminant-free cell cultures from this collection for research on such diseases as Alzheimer's disease, progeria, Parkinson's disease, Werner syndrome, and Cockayne syndrome. The collections of the Repository include DNA and cell cultures from individuals with premature aging disorders, as well as DNA from individuals of advanced age from the the Baltimore Longitudinal Study of Aging at the Gerontology Research Center and other Longevity Collections. The Repository also includes samples from an Adolescent Study of Obesity, Apparently Healthy Controls, Animal Models of Aging, and both human and animal differentiated cell types. The cells in this resource have been collected over the past three decades using strict diagnostic criteria and banked under the highest quality standards of cell culture. Scientists can use the highly-characterized, viable, and contaminant-free cell cultures from this collection for genetic and cell biology research.
Mouse Mutagenesis Center for Developmental Defects
NIH Mouse Mutagenesis Center for Developmental Defects
Mouse Mutagenesis for Developmental Defects
THIS RESOURCE IS NO LONGER IN SERVICE. For updated mutant information, please visit MMRRC or The Jackson Laboratory. Produces, characterizes, and distributes mutant mouse strains with defects in embryonic and postembryonic development. The goal of the ENU Mutagenesis project III is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval.
SEURAT: Visual analytics for the integrated analysis of microarray data
A software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data.
Collects, stores, and distributes samples of nervous tissue, cerebrospinal fluid, blood, and other tissue from HIV-infected individuals. The NNTC mission is to bolster research on the effects of HIV infection on human brain by providing high-quality, well-characterized tissue samples from patients who died with HIV, and for whom comprehensive neuromedical and neuropsychiatric data were gathered antemortem. Researchers can request tissues from patients who have been characterized by: * degree of neurobehavioral impairment * neurological and other clinical diagnoses * history of drug use * antiretroviral treatments * blood and CSF viral load * neuropathological diagnosis The NNTC encourages external researchers to submit tissue requests for ancillary studies. The Specimen Query Tool is a web-based utility that allows researchers to quickly sort and identify appropriate NNTC specimens to support their research projects. The results generated by the tool reflect the inventory at a previous time. Actual availability at the local repositories may vary as specimens are added or distributed to other investigators.
A repository of tissue collected from nonhuman primate (NHP) species under contractual arrangement with Wisconsin National Primate Research Center (WI NPRC). NIA' '''s Nonhuman Primate Tissue Bank collects and archives tissue from necropsies performed at primate centers nationwide. The goal is to collect various tissues from aged monkeys with smaller amounts of the same tissues from young and middle-aged monkeys. Tissue will be provided as: (1) fresh frozen, stored at ����?��������??80 degrees Celsius; (2) formalin fixed; or (3) fresh frozen tissue in OCT medium.Most frozen tissues are provided in approximately 1 gram of tissue per vial. Fixed tissue is available as slides (sections) from paraffin-embedded blocks. Slides can be stained if requested. Tissue from NIA' '''s Nonhuman Primate Tissue Bank is available to investigators at academic and nonprofit research institutions who are engaged in funded research on aging. The project name and funding source must accompany all orders. The NIA will not be able to ship non-human primate tissue outside of the United States or US territories. Investigators at for-profit entities are not eligible to purchase tissue from NIA' '''s Nonhuman Primate Tissue Bank unless it is for a Small Business Innovation Research grant from NIA. NIA provides the health information as given by the donor site and cannot guarantee other aspects of the health status not explicitly stated in the Vital Statistics Information Sheet. Concerns about the specific health status of donor animals should be indicated on the order form.
Website with multiple information including curent news and publications, clinical trials, and a mitochondria database. :clinical trials related to mitochondria; publications related to mitochondria, mitochondria database : :
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Lexicon that provides entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. These sources may include complex image databases, such as data from structural and functional magnetic resonance imaging (MRI) on human subjects involved in studies on Alzheimer''s disease or schizophrenia. The BIRNLex is a specialized vocabulary utilized by BIRN scientists in the context of their research, including common terms for neuroanatomy, molecular species, subject information, behavioral and cognitive processes, experimental practice and design, and the associated elements of primary data provenance required for large-scale data integration across disparate experimental studies.The BIRNLex offers well defined terms from several domains of importance to neuroimaging across scales.
National Alzheimer's Coordinating Center
A clinical research, neuropathological research and collaborative research database that uses data collected from 29 NIA-funded Alzheimer's Disease Centers (ADCs). The database consists of several datasets, and searches may be done on the entire database or on individual datasets. Any researcher, whether affiliated with an ADC or not, may request a data file for analysis or aggregate data tables. Requested aggregate data tables are produced and returned as soon as the queue allows (usually within 1-3 days depending on the complexity).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 09, 2013. Supply aged mutant and transgenic mice for NIH-supported research directly related to the biology of aging. The mice are raised by the NIA's contractor, Taconic Farms, in Specific Pathogen-Free (SPF) barrier facilities. The strains in the mutant mouse aging colony have been donated by the investigators who developed the models, and those investigators are still the legally recognized owners of the intellectual property. A Material Transfer Agreement (MTA) is required to purchase the mice (a one-time requirement per strain). There are restrictions to the use of this colony as described in the MTA. These restrictions include a prohibition against breeding the mice purchased from the NIA Mutant Mouse Aging Colony, agreement that the mice will not be used for commercial purposes, and agreement that the mice and all derivatives will not be transferred to third parties. The restrictions are further spelled out in the MTA. Animals are sold by age, not weight, and ages are stated in 1 month intervals only; all animals born within a calendar month are considered to be the same age, so date of birth (DOB) is given as month/year. All mice are virgins. The mutant mouse aging colony is slated to end in September 2013. Old mice will be available until September 2013 but the availability of young mice will end earlier. Entries of different strains into the mutant mouse aging colony will end at different times, dependent on the lifespan and pattern of use of the strain. Mouse models include: * Snell Dwarf (3623) ??????????????? last entry will be the November 2011 DOB (date of birth) * Ames Dwarf (324) ??????????????? last entry will be the October 2012 DOB * A53T ???????????????????????-synuclein Transgenic (322) ??????????????? last entry will be the December 2012 DOB * GFP Transgenic (317) ??????????????? last entry will be the January 2013 DOB
R package for quantifying variation in DNA methylation as a cancer biomarker.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. CATs Card Sort is a free, general purpose card sorting program which allows the user to design sorting tasks similar to those described by Vigotsky (1934), Weigel (1941), and Grant and Berg (1948). Card sorting tasks have been shown to be particularly sensitive to frontal lobe dysfunction, but have also shown sensitivity to motor disorders, schizophrenia, chronic alcoholism, aging, and attention deficit disorder. The CATs Card Sort package provides extensive flexibility in the development of stimulus cards, allowing the experimenter to define the relevant dimensions of cards in terms of figures, letters or words, figure/letter/word color, card color, figure/letter numerosity, and a user defined dimension. Considerable flexibility is also provided in designing lists of to be sorted cards, sort criteria, and the criteria for sort classification shift. The package also provides limited analysis capabilities as described by Grant and Berg (1948). However, as with all CATs packages raw data can be copied to the clipboard in a format acceptable for import into commonly available spreadsheets such as Excel allowing the user to design analysis routines appropriate to their needs.
Aged Rodent Tissue Bank Handbook - Tissue Arrays
NIH Aged Rodent Tissue Bank Handbook Tissue Arrays
Offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbers
JAX Developmental Biology Research: Neural Tube Defects
This Resource maintains and distributes mouse models for neural tube defects. Current Neural Tube Defect stains include: * Repository- Live: 129(Cg)-Foxg1<tm1(cre)Skm>/J, B6.129P2(Cg)-Foxg1<tm1(cre)Skm>/J, B6.129P2-Apob<tm1Unc>/J, B6.129S7-Twist1<tm1Bhr>/J, B6.129X1(Cg)-Shh<tm6Amc>/J, B6.Cg-Lootl/GrsrJ, B6.D2-Kitl<Sl-d>/J, B6;129-Pax3<tm1(cre)Joe>/J, B6;129-Shh<tm2Amc>/J, B6;SJL-Tg(Sox10-cre)507Mcln/J, C57BL/6J-Pax3<Sp>/J, STOCK Ptch1<tm1Mps>/J, STOCK Sec24b<Y613X>/J, STOCK Smo<tm2Amc>/J, STOCK Tgfb3<tm1(cre)Vk>/J, WCB6F1/J-Kitl<Sl>/Kitl<Sl-d>, * Cryopreserved - Ready for recovery: 129-Ski<tm1Cco>/J, 129-Tulp3<tm1Jng>/Pjn, 129/Sv-Csk<tm1Sor>/J, 129P4.Cg-Axin1<Fu>/J, 129S-Dvl2<tm1Awb>/J, 129S-Dvl3<tm1Awb>/J, 129S-Nog<tm1Amc>/J, 129S1/Sv-Sufu<tm1Aeb>/J, 129X1-Smo<tm1Amc>/J, A.129P-Ski<tm1Cco>/J, A/WySnJ-ctl/GrsrJ, B6-Pax3<Sp>.Cg-N/J, B6.129-Dll1<tm1Gos>/J, B6.129-Kif3a<tm1Gsn>/J, B6.129-Ski<tm1Cco>/J, B6.129-Tulp3<tm1Jng>/Pjn, B6.129S1-Twist1<Pde>/J, B6.129S2-Mgat1<tm1Jxm>/J, B6.129S4-Shroom3<Gt(ROSA53)Sor>/J, B6.129S4-Strap<Gt(ROSA)71Sor>/J, B6.129S6-Crebbp<tm1Dli>/Jm, B6.129S6-Dnmt3l<tm1Bes>/J, B6.C3 Pde6b<rd1>Hps4<le>/+ +-Lmx1a<dr-8J>/J, B6.C3-Gli3<Xt-J>/J, B6;129-Apob<tm2Sgy> Apoe<tm1Unc>/J, B6;129S-Ldlr<tm1Her> Apob<tm2Sgy>/J, B6;129S-Twist1<tm1Bhr>/J, B6;129S6-Apaf1<tm1Her>/J, B6;129S7-Apob<tm2Sgy>/J, B6C3Fe a/a-Lmx1a<dr-J>/J, B6C3Fe a/a-Wnt1<sw>/J, B6CBACa A<w-J>/A-we a Mafb<kr>/J, B6EiC3Sn a/A-Egfr<wa2> Wnt3a<vt>/J, BNT/LeJ, C3H/HeSn-Gpr161<vl>/J, C3HeB/FeJ x STX/Le-Mc1r<E-so> Gli3<Xt-J> Tw/J, C57BL/6J-Pax3<Sp-d>/J, FL/1Re-Kit<W>/J, FL/1ReJ, JE/LeJ, LPT/LeJ, STOCK Apaf1<fog>/J, STOCK Grhl3<ct>/J, STOCK Mttp<tm2Sgy> Ldlr<tm1Her> Apob<tm2Sgy> Tg(Mx1-cre)1Cgn/J, STOCK Pax3<Sp> Mlph<ln>/J, STOCK Shh<tm1Amc>/J, STOCK T<c>/J, STOCK a/a Egfr<wa2>/J, STOCK t<w82> tf/J, WB.Cg-f/J, WB.D2-Kitl<Sl-d>/J, 129S1.B6-Shroom3<m1Nisw>/J * Under Development - Now Accepting Orders: 129S1.B6-Shroom3<m1Nisw>/J, 129S1.B6-Zic2<m1Nisw>/J, STOCK Nog<tm1.1Rmh>/J, STOCK Tg(TCF/Lef1-cre/ERT2)1Dje/J First time users are required to fill out a request form for mice. Information on individual strains is also available through links on the Web site.
The Current Population Survey (CPS) is a monthly survey of about 50,000 households conducted by the U.S. Census Bureau for the Bureau of Labor Statistics for more than 50 years. It provides a comprehensive body of data on the labor force, employment, unemployment, and persons not in the labor force. The CPS is the primary source of information on the labor force characteristics of the U.S. population. The sample is scientifically selected to represent the civilian noninstitutional population. Respondents are interviewed to obtain information about the employment status of each member of the household 15 years of age and older. However, published data focus on those ages 16 and over. The sample provides estimates for the nation as a whole and serves as part of model-based estimates for individual states and other geographic areas. Estimates obtained from the CPS include employment, unemployment, earnings, hours of work, and other indicators. They are available by a variety of demographic characteristics including age, sex, race, marital status, and educational attainment. They are also available by occupation, industry, and class of worker. Supplemental questions to produce estimates on a variety of topics including school enrollment, income, previous work experience, health, employee benefits, and work schedules are also often added to the regular CPS questionnaire. CPS data are used by government policymakers and legislators as important indicators of our nations economic situation and for planning and evaluating many government programs. They are also used by the press, students, academics, and the general public.
University of Quebec in Montreal; Quebec; Canada
A French-language university with an international reputation. Firmly committed to research and creation, it offers more than 300 programs of study.
Vascular Therapies - Innovative Vascular Solutions
Commercial organization that offers vascular devices research and development services to the healthcare industry.Current development plan is focused on hemodialysis vascular access indication – investigating safety and usefulness of drug product to improve outcomes of Arterio-Venous Fistula (AVF).
CIDR - Center for Inherited Disease Research
Next generation sequencing and genotyping services provided to investigators working to discover genes that contribute to disease. On-site statistical geneticists provide insight into analysis issues as they relate to study design, data production and quality control. In addition, CIDR has a consulting agreement with the University of Washington Genetics Coordinating Center (GCC) to provide statistical and analytical support, most predominantly in the areas of GWAS data cleaning and methods development. Completed studies encompass over 175 phenotypes across 530 projects and 620,000 samples. The impact is evidenced by over 380 peer-reviewed papers published in 100 journals. Three pathways exist to access the CIDR genotyping facility: * NIH CIDR Program: The CIDR contract is funded by 14 NIH Institutes and provides genotyping and statistical genetic services to investigators approved for access through competitive peer review. An application is required for projects supported by the NIH CIDR Program. * The HTS Facility: The High Throughput Sequencing Facility, part of the Johns Hopkins Genetic Resources Core Facility, provides next generation sequencing services to internal JHU investigators and external scientists on a fee-for-service basis. * The JHU SNP Center: The SNP Center, part of the Johns Hopkins Genetic Resources Core Facility, provides genotyping to internal JHU investigators and external scientists on a fee-for-service basis. Data computation service is included to cover the statistical genetics services provided for investigators seeking to identify genes that contribute to human disease. Human Genotyping Services include SNP Genome Wide Association Studies, SNP Linkage Scans, Custom SNP Studies, Cancer Panel, MHC Panels, and Methylation Profiling. Mouse Genotyping Services include SNP Scans and Custom SNP Studies.
The National Eye Institute (NEI) created the VISION Public Information Network for the purpose of communicating with public information officers at NEI grantee institutions. The Network''s primary mission is to work with the NEI in disseminating research results to the national and local media. The Network also works to inform the public of the mission of the National Institutes of Health (NIH) to improve the health of America through medical research. The NEI is part of the NIH, U.S. Department of Health and Human Services (DHHS). General information portal for eye and vision related resources for the public. Sponsors: This resource is supported by the National Eye Institute.
Center that acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism. A searchable strain database, general information about C. elegans, and links to key Web sites of use to scientists, including WormBase, WormAtlas, and WormBook are available.
Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core
Tulane Stem Cell Research Regenerative Medicine Tissue Culture Core
The Stem Cell Research and Regenerative Medicine''s Tissue Culture Core provides cells for research use within the department, as well as for distribution to other facilities. The core obtains hMSCs from bone marrow donor samples and expands these cells for research use. The hMSC''s are also characterized for bone, fat and cartilage differentiation, and are stored on site for use. The Tissue Culture Core also handles the expansion and characterization of mouse and rat MSC''s. The animal cells are cultured in a separate area, and never interact with human derived cells. We also have a supply of hMSC''s marked with GFP+, Mito Red and Mito Blue available.
Salamons Neuroanatomy and Neurovasculature Web-Atlas Resource
Annotated images of human brain derived from CT, MRI, angiography and post-mortem sections and drawings. Brain vasculature: arteries, arterioles, veins. Pathological specimens. Quizzes and general information on brain structures and clinical syndromes. Extensive collection of images, many from pathological conditions.
DICOMscope is a free DICOM viewer which can display uncompressed, monochrome DICOM images from all modalities and which supports monitor calibration according to DICOM part 14 as well as presentation states. The application is rather a feasibility study for DICOM presentation states. DICOMscope offers a print client (DICOM Basic Grayscale Print Management) which also implements the optional Presentation LUT SOP Class.
PhysioNet: The Research Resource for Complex Physiologic Signals
Collection of dissemination and exchange recorded biomedical signals and open-source software for analyzing them. Provides facilities for cooperative analysis of data and evaluation of proposed new algorithm. Providies free electronic access to PhysioBank data and PhysioToolkit software. Offers service and training via on-line tutorials to assist users at entry and more advanced levels. In cooperation with annual Computing in Cardiology conference, PhysioNet hosts series of challenges, in which researchers and students address unsolved problems of clinical or basic scientific interest using data and software provided by PhysioNet. All data included in PhysioBank, and all software included in PhysioToolkit, are carefully reviewed. Researchers are further invited to contribute data and software for review and possible inclusion in PhysioBank and PhysioToolkit. Please review guidelines before submitting material.
Brain Computer Interface 2000 Software Package
BCI2000 is a general-purpose system for brain-computer interface (BCI) and adaptive neurotechnology research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. The mission of the BCI2000 project is to facilitate research and applications in the areas described. Their vision is that BCI2000 will become a widely used software tool for diverse areas of real-time biosignal processing. In order to achieve this vision, BCI2000 system is available for free for non-profit research and educational purposes. BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms. During operation, BCI2000 stores data in a common format (BCI2000 native or GDF), along with all relevant event markers and information about system configuration. BCI2000 also includes several tools for data import/conversion (e.g., a routine to load BCI2000 data files directly into Matlab) and export facilities into ASCII. BCI2000 also facilitates interactions with other software. For example, Matlab scripts can be executed in real-time from within BCI2000, or BCI2000 filters can be compiled to execute as stand-alone programs. Furthermore, a simple network-based interface allows for interactions with external programs written in any programming language. For example, a robotic arm application that is external to BCI2000 may be controlled in real time based on brain signals processed by BCI2000, or BCI2000 may use and store along with brain signals behavioral-based inputs such as eye-tracker coordinates. Because it is based on a framework whose services can support any BCI implementation, the use of BCI2000 provides maximum benefit to comprehensive research programs that operate multiple BCI2000 installations to collect data for a variety of studies. The most important benefits of the system in such situations are: - A Proven Solution - Facilitates Operation of Research Programs - Facilitates Deployment in Multiple Sites - Cross-Platform and Cross-Compiler Compatibility - Open Resource Sponsors: BCI2000 development is sponsored by NIH/NIBIB R01 and NIH/NINDS U24 grants. Keywords: General, Purpose, Systems, Brain, Computer, Interface, Research, Application, Brain, Diverse, Educational, Laboratory, Software, Network, Signals, Behavioral, Eye, Tracker,
Database and associated software tools providing access to clinical and research data on stroke, including deidentified patient data. Data types include imaging (e.g. CT, MRI, PET), clinical demographic data, genetic data, simulation perfusion data for verifying deconvolution algorithms used in bolus-tracking perfusion-weighted imaging (PWI). Also available are programs for performing deconvolution of bolus-tracking PWI, DTI tractography and an automated program for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke (CCS)
Diffusion tensor imaging (DTI) tractography: An automated system for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke DTI Task Card for Siemens systems, DTI Visualization platform independent tool kit, PWI analysis tools for bolus-tracking data
A plated array of approximately 450 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research. Similar collections of FDA approved drugs have proven to be rich sources of undiscovered bioactivity and therapeutic potential. The clinically tested compounds in the NCC are highly drug-like with known safety profiles. These compounds can provide excellent starting points for medicinal chemistry optimization and, for high-affinity targets, may even be appropriate for direct human use in new disease areas.
Gradient Non-linearity Distortion Correction
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool to correct gradient non-linearity distortions in MR structural images. This correction improves test-retest reproducibility crucial for multi-site studies.
Data-, machine-, and application- independent software system for the visualization and analysis of multidimensional images. This transportable, very inexpensive software system, has capabilities for visualizing, manipulating, and analyzing multidimensional, multimodality image information. It is designed to run on Unix machines under X-windows. It uses a data protocol that is a multidimensional generalization of the ACR-NEMA standards. We have tested it extensively on SGI and Sun workstations and PCs. Other recipients of 3DVIEWNIX have installed it on a variety of platforms including IBM RS6000s, HP700s, and Stardent, all from a single source code version. UNIQUE FEATURES OF 3DVIEWNIX * Transportable - based on UNIX, X-window, and C * Based on multidimensional generalization of ACR-NEMA standards of data representation * Application-independent * Image dimensionality independent * Can handle rigid, non-rigid, static, and dynamic objects and object assemblies * Can handle object information from multiple modalities and longitudinal acquisitions * Multitudes of visualization, manipulation, and analysis methods incorporated * Open software system distributed with source code
Data analysis software with the following main features: fMRI spatial and temporal pre-processing (gaussian filtering) with motion correction, time slicing and template co-registration ; fMRI multithreaded bloc processing with one or more conditions (up to 999), lateralization index, paradigm design (box-car style with HRF convolution), anatomic coregistration, multiplanar reconstructions, opengl 3D surfacic rendering. DPTools and Activ 2000 are now one single software: DPTools v 3.0 and above. All the features already included in DPTools are available for the fMRI processings (statistics, motion correction, time slicing, aso). DPTools 3.0 can read Siemens Mosaic and Philips REC/PAR files for diffusion / dynamic series, and can export files to SPM99 format. Features: * Images Conversion * Paradigm Creation * Images Pre-Processing * Images Processing * Statistics * Co-registration * 3D * Filming * Loading / Saving * Batch Script * PACS Integration * and more... Activ 2000 is freely downloadable (46 MB)
Advanced 3D Visualization and Volume Modeling
Software tool for visualizing, manipulating, and understanding data from tomography, microscopy, MRI and other imaging processes.Used to import and export options, to processes 3D image filtering and DTI based fiber tracking to visualization, volume and surface rendering, author tools for virtual reality navigation, video generation, and more.
BrainVISA is a modular an customizable software platform built to host heterogeneous tools dedicated to neuroimaging research. Many toolboxes have already been developed for BrainVISA (T1 MRI, sulcal identification and morphometry, cortical surface analysis, diffusion imaging and tractography, fMRI, nuclear imaging, EEG and MEG, TMS, histology and autoradiography, etc.). Anatomist is a software for interactive visualization of multimodal data and for manipulation of structured 3D objects. It allows to build scenes that merge or combine images, meshes, regions of interest, fibers, textures, color palettes, referential changes, etc. A user can interact in 3D and in real time with the objects of an Anatomist scene: change point of view, select objects, add/suppress objects, change colors, draw regions of interests, do manual registration, etc. BrainVISA main features are: * Harmonization of communications between different software. For instance, BrainVISA toolboxes are using home-made software but also third-party software such as FreeSurfer, FSL, SPM, nipy, R-project, Matlab, etc. * Ontology-based data organization allowing database sharing and automation of mass of data analysis. * Fusion and interactive visualization of multimodal data (using Anatomist software). * Automatic generation of graphical user interfaces. * Workflow monitoring and data quality checking. * Full customization possible. * Runs on Linux, Mac and Windows. * Programming Language: C++, Python * Supported Data Format: ANALYZE, DICOM, GIfTI, MINC, NIfTI-1, Other Format
Microtomy is a standard technique used for 2D microscopy, but it can also provide the foundation for 3D analysis using AutoAligner. AutoAligner reads a stack of serial sections and automatically aligns the single images, building up a 3D space that can be explored using Imaris. Each image is aligned in translation and rotation relative to its precursor image in the sequence. In addition to a fully automated mode, AutoAligner also provides manual control for neighboring images that are too different from each other for automatic alignment. The visual alignment tool uses fast display techniques for aligning images in real time.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19, 2015. Commercial brain atlases distributed by Theime Medical Publishers. It supports a complete electronic version of the Talairach Atlas, as well as gyral-level description of the human brain and atlases for cerebral vasculature, cranial nerves and a probabilistic functional atlas. In addition, this tool permits the incorporation of user image data, both structural and functional, into the viewer for direct co-visualization with the atlas. This CD-ROM provides numerous tools for the analysis of functional images: It contains the fully color-coded and labeled Talairach-Tournoux brain atlas in the axial, coronal and sagittal orientations, along with Brodmann''s areas and gyri in the axial orientation. -Allows anatomical and functional images to be loaded and registered. -Enables interactive placement of the Talairach landmarks in 3D Space. -Provides automatic data-to-atlas warping based on the Talairaich proportional grid system transformation. In addition, real-time interactive warping for fine tuning is available. -Allows the user to place marks on the activation loci in the warped functional images, display these marks with the atlas, and edit them simultaneously on the axial, cornal and sagittal orientations. Mark placement is assisted by a grey-value thresholding feature. -Provides simultaneous display of the atlas, anatomical image and functional image withing one interactively blended image. Atlas-data blending and anatomical-functional image blending are controlled independently. -Labels the data by means of the atlas. The atlas can be flipped left/right so that Brodmann''s areas areas and gyri can be labeled on both hemispheres. -Provides additional functions such as friendly navigation, simultaneous display of axial, coronal and sagittal atlas plates, cross-referenced display, image and atlas sequencing, readout of the Talairach coordinates and intensities, save, print, help.
Brain Research: Analysis of Images, Networks and Systems
A group of software packages for image analysis, mainly used in MRI image processing. BRAINS (Brain Research: Analysis of Images, Networks, and Systems) contains manual and automated tools for structural identification and methods for tissue classification and cortical surface generation. BRAINS2 is most commonly used to analyze magnetic resonance (MR) scans, but the package can also be used to analyze images acquired with positron emission tomography (PET), single photon emission computed tomography (SPECT), and functional magnetic resonance (fMR). It is implemented in an object-oriented, cross-platform compatible manner and includes a toolbar and command line interface, a graphical interface, and a computational kernel.
CellProfiler - cell image analysis software
Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types.
COMKAT: COmpartment Model Kinetic Analysis Tool
COMKAT is a software package for compartmental modeling oriented for biomedical image quantification. Free for academic research use, COMKAT has various functions for modeling and imaging analysis in both command-line function and GUIs. COMKAT is MATLAB software for compartmental modeling oriented to nuclear medicine applications (PET & SPECT). It supports models of a wide range complexity including multiple injection, receptor model with saturation. It supports many image formats, including DICOM images. Using either the command line interface or GUI, models are easily specified, solved or used to fit experimental data. Sensitivity equations are supported. No mathematical derivations are required on the part of the user.
Software collection of libraries and applications implementing large parts of DICOM standard for medical image communication.Includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over network connection, as well as demonstrative image storage and worklist servers.
Software tool as biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7 and sequence analysis program. Provides sequence manipulation and analysis options and links to external analysis programs to view and manipulate sequences with simple point and click operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
EM3D is a software application designed to facilitate the analysis and visualization of electron microscope (EM) tomography data by cellular and molecular biologists. Such data are collected as a tilt series, a sequence of 2D electron micrographs taken at many tilt angles with respect to the electron beam. EM3D features an integrated graphical user interface that automates most of the initial alignment and reconstruction of the tilt-series data to form a 3D volume. These functions seamlessly connect with segmentation and model-generation tools that permit the user to easily and reliably extract specific structural components from the reconstructed volume. The 3D models can then be visualized and manipulated using an extensive package of surface- and volume-rendering techniques. EM3D also provides a set of analysis tools to quantify structural information from the models, including their moments, proximity relationships, and spatial reliability. Altogether, EM3D facilitates the analysis of 3D cell structure at the full resolution of a reconstructed volume (2-3 nm)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Functional MRI Analysis and Clustering Tools
FACT (Functional MRI Analysis and Clustering Tools) is free software for analyzing time series data like fMRI and perfusion MRI. It provides correlation analysis, t-test and temporal clustering analysis -- Kohonen Clustering Network and Fuzzy Clustering. A set of analysis tools applicable to fMRI time-series data.
A cross-platform system for exploring diffusion tensor images and to reconstruct fiber tracts between two regions of interest, intended for tdoctors, medical technicians or medical researchers. The Fiber-Tracking tool allows the user to load data from MRIs or similar images (like a basic 3D image viewer), load DTI datasets (7 diffusion- weighted images), calculate the fractional anisotropy (FA) and the mean diffusivity (MD) images, and also load ROIs to reconstruct fibers.
An interactive, graphic, fiducial marking software for placing, editing and tracking fiducial marks on images in a tomography tilt series. You can also use this tool to view the tilt series as well as crop it.
A software application that automatically detects neurons (dendritic trees, axons and spines), microtubules, and other filament-like structures in 2D, 3D and 4D. Imaris FilamentTracer uses strategies that involve an optimal combination of automated analysis and operator decision. The choice of the best method is an essential element in optimizing efficiency. FilamentTracer allows the choice between four complementary tracing strategies ranging from manual to automatic and utilizes a creation wizard to easily guide the user through the creations steps. It has been specifically designed to deal with the complex problem of spine analysis over time.
A set of Java libraries for rapidly creating GUIs for software modules (C, C++, Fortan, PERL scripts, etc.), and graphically controlling process flow among them. This allows a GUI to be created for existing image processing and analysis routines, which provides: 1) graphic elements for setting parameters, arguments, etc. (i.e., text dialogs, file browsers, etc.); 2) links to web based documentation; 3) simple point-and-click interface for setting up a path for data flow from one module to another. The purpose of FisWidgets is to provide an integrated and user-friendly environment for using the disparate and growing array of image processing and analysis tools created by different laboratories.
Image-Pro Plus Morphometric Analysis Software
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data.
Imaris provides range of capabilities for working with three dimensional images. Uses flexible editing and processing functions, such as interactive surface rendering and object slicing capabilities. And output to standard TIFF, Quicktime and AVI formats. Imaris accepts virtually all image formats that are used in confocal microscopy and many of those used in wide-field image acquisition. Imaris version 10.1 for image analysis workflows using AI trainable object detection.
MIPAV: Medical Image Processing and Visualization
Medical Image Processing Analysis and Visualization
A Java-based application that enables quantitative analysis and visualization of medical images of numerous modalities such as DTI, PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders. MIPAV can be run on any Java-enabled platform such as Windows, UNIX, or Macintosh OS X. Functionality includes segmentation, inter- and intra multi-modality registration, surface rendering, volume rendering and reading and writing a large number of biomedical file formats including: DICOM 3.0, Analyze, NIFTI, SPM, MINC, Phillips, GE, Zeiss, Biorad, jpeg, png, tiff, mrc, fits, interfile, and many more.
An integrated environment for the analysis and visualization of functional neuroimages. It is intended to provide extremely fast and flexible image processing, via an intuitive user interface that encourages experimentation with analysis parameters and detailed inspection of both raw image data and processing results. All processing operations in NeuroLens are built around a Plugin architecture, making it easy to extend its functionality. NeuroLens runs on Apple computers based on the G4, G5, or Intel chipsets and running MacOSX 10.4 (Tiger) or later. It is available free for academic and non-profit research use. * Operating System: MacOS * Programming Language: Objective C * Supported Data Format: AFNI BRIK, ANALYZE, COR, DICOM, MGH/MGZ, MINC, Other Format
Booly: A Resource for Biological Data Integration
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A database tool that allows for any combination of the Boolean operations union/disjunction (OR), intersection/conjunction (AND), and subtraction/negation (NOT) to be performed on multiple datasets. Booly brings the power of biological data integration to the researcher by helping researchers analyze and integrate their data. Booly offers a simple contribution model, where users can simply cut and paste spreadsheet data to create new datasets that could thereafter be stored, shared, and compared. Users may also take advantage of publically available datasets created by other members such as Gene Ontology datasets and species-species BLAST datasets.
Informatics resources for mouse functional genomics
Over recent years, the European Commission has supported an increasing number of functional genomics projects focusing on the use of the laboratory mouse as a model of human disease. (see http://www.prime-eu.org/euromouseiiprojects.htm for a fuller listing of current and recent projects). CASIMIR (Coordination and Sustainability of International Mouse Informatics Resources: http://www.casimir.org.uk) is aimed at recommending standards to allow data sharing and integration between the different projects. CASIMIR spans a number of areas: data representation (in particular the use of shared ontologies), non-semantic, technical issues concerning database compatibility and interoperability, data acquisition, curation and ownership, integration of biological collections and material resources into the data network, and user interactions. As part of the CASIMIR initiative i-mouse.org was created as a common portal to CASIMIR and other resources we hope will be helpful for investigators using the mouse as a model system for humans or systems biologists and geneticists using the mouse as an experimental system. ontology; metadata;
An fMRI analysis software package with a GUI (Graphical User Interface) front end. Stimulate offers a comprehensive set of fMRI analysis tools integrated into a single package for convenient and flexible data processing. Users can point and click with the mouse to modify analysis or display variables. Activation maps can be calculated from the fMRI data and overlaid onto structural MRI image displays.
T-One weighted Perfusion imaging Parameter CAlculation Toolkit
TOPPCAT stands for T-One weighted Perfusion imaging Parameter CAlculation Toolkit. TOPPCAT creates quantitative maps of Ktrans (volume transfer constant between blood plasma and the extravascular extracellular space) and fPV (fractional plasma volume) from dynamic T1-weighted perfusion images. At the current time, analysis using the method of Patlak plots (most appropriate for first pass dynamic contrast-enhanced MR imaging) is supported. As a preliminary step for the parameter calculation, TOPPCAT also creates maps of T1 and S0 (equilibrium magnetization) from multi-flip angle T1-weighted SPGR (or FLASH) sequences.Daniel P. Barboriak, James R. MacFall, Anthony O. Padua,Gerald E. York, Benjamin L. Viglianti, and Mark W. Dewhirst. Standardized software for calculation of Ktrans and vp from dynamic T1-weighted MR images. Presented at the International Society for Magnetic Resonance in Medicine Workshop on MR in Drug Development: From Discovery to Clinical Therapeutic Trials, McLean VA, April 2004.
Xvoxtrace enables volume segmentation of tomographic data using manual tracing. This program allows the researcher to outline features on individual planes of the volume while being guided by simultaneous views of the tracing displayed on a volume rendering or tilt-series. Traced contours can be viewed using XDend or used to generate surfaces for viewing in Synu. Basic Requirements:OpenGL, X windows, and Linux platforms : :
A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
National Simulation Resource Physiome Project
Database of physiological, pharmacological, and pathological information on humans and other organisms and integration through computational modeling. Models include everything from diagrammatic schema, suggesting relationships among elements composing a system, to fully quantitative, computational models describing the behavior of physiological systems and an organism''s response to environmental change. Each mathematical model is an internally self-consistent summary of available information, and thereby defines a working hypothesis about how a system operates. Predictions from such models are subject to test, with new results leading to new models.BR /> A Tool developed for the NSR Physiome project is JSim, an open source, free software. JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim''s primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim''s model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats. All JSim models are open source. Goals of the Physiome Project: - To develop and database observations of physiological phenomenon and interpret these in terms of mechanism (a fundamentally reductionist goal). - To integrate experimental information into quantitative descriptions of the functioning of humans and other organisms (modern integrative biology glued together via modeling). - To disseminate experimental data and integrative models for teaching and research. - To foster collaboration amongst investigators worldwide, to speed up the discovery of how biological systems work. - To determine the most effective targets (molecules or systems) for therapy, either pharmaceutic or genomic. - To provide information for the design of tissue-engineered, biocompatible implants.
Portal covering the broad field of primatology, providing original content and links to resources about nonhuman primates in research, education and conservation. Through email lists and other resources, PIN also supports an informal primate information network comprised of thousands of individuals around the world working with nonhuman primates in a variety of roles. Services Provided: - Primate Info Net (PIN): A comprehensive Web site with links to research, conservation, and education resources related to nonhuman primates. - PrimateLit Database (1940 to date): PrimateLite is a free, bibliographic database of more than 200,000 citations to the nonhuman primate literature. Indexing for PrimateLit is provided by the Primate Information Center, Washington NPRC, Seattle. - International Directory of Primatology: The International Directory of Primatology is a searchable directory of the field of primatology with detailed information about organizations, field studies, population management groups, and contact information for more than 3,000 primatologists. - Primate-Science: Primate-Science is a professionally oriented, e-mail-based electronic discussion forum for people engaged in research with nonhuman primates. - Primate-News: Primate-News is an e-mailed-based news clipping service open to anyone interested in nonhuman primates. - Primate Enrichment Forum: Primate Enrichment Forum is a professionally oriented, e-mail-based electronic discussion forum for individuals interested in environmental enrichment for nonhuman primates. - AskPrimate: AskPrimate is a cooperative e-mail reference service available to the research community and the general public. - Primate-Jobs: Primate-Jobs is a job listing service that includes paid and volunteer positions, wanted and available. - Careers in Primatology: Careers in Primatology is a resource for people considering careers in primate research, education, conservation, or veterinary medicine. - Audiovisual Resources: Audiovisual Resources is a collection of primate-related videotapes, slides, and audiotapes available for research and educational uses. - The Callicam: The Callicam is a Webcam feature of the Wisconsin NPRC''s common marmoset site that allows students in the classroom to observe marmoset behavior and learn about their natural history, care, and management.
Software platform, general technologies and theoretical supports for computational biology with the grand aim to make precise whole cell simulation at the molecular level possible.Technologies include formalisms and techniques, including technologies to predict, obtain or estimate parameters such as reaction rates and concentrations of molecules in the cell. The E-Cell System is a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale system like the cell. The E-Cell Project is open to anyone who shares the view with u that development of cell simulation technology, and, even if such ultimate goal might not be within ten years of reach yet, solving various conceptual, computational and experimental problems that will continue to arise in the course of pursuing it, may have a multitude of eminent scientific, medical and engineering impacts on our society.
TMRPres2D: High quality visual representation of transmembrane protein models
TransMembrane protein Re-Presentation in 2 Dimensions tool
Software that automates the creation of uniform, two-dimensional, high analysis graphical images/models of alpha-helical or beta-barrel transmembrane proteins. Protein sequence data and structural information may be acquired from public protein knowledge bases, emanate from prediction algorithms, or even be defined by the user. Several important biological and physical sequence attributes can be embedded in the graphical representation. The application has been written using the platform independent Java language by Sun Microsystems. The implementation is likely to encapsulate the Applet and JavaBean technology. Consequently, the tool, apart from standalone application, may be used as an applet or even embedded in a web-server. Thus, it can serve to exhibit transmembrane protein schematic models in web pages. Requirements for the stand-alone application: Java Runtime Environment 1.4.x The source code is available to any interested party, upon request from the authors.
An academic genealogy platform that collects information about graduate students and posdoctoral research connections. The Neuroscience Academic Family Tree is a free, volunteer-run website designed to help you track your academic genealogy. Our goal is to collect information about the graduate student and postdoctoral connections between most researchers in the field. :How do I navigate the tree? :There are several ways to wander around Neurotree. The basics are summed up in the commands at the top of each page: :* Tree - Jump to a random node on the tree :* Search - Search for a specific person or people at a specific institution :* Recent additions - List the most recent additions :* Distance - Trace the connection between two people in the tree :* Add person - Add a new person to the tree (and be a good citizen!). You must sign up for an account to make additions. :* Analysis - Learn more amazing facts about neurogenealogy! ... and possibly something about the field of neuroscience.
Database of hundreds of thousands of products submitted by reagent provider partners, and millions of webpages selected from reagent suppliers. All are organized according to genes, species, and reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones, biochemicals, and others).
The Open Access Series of Imaging Studies
Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated.
Association of Neuroscience Departments and Programs
The mission of the Association for Neuroscience Departments and Programs is to advance education and research training in academic neuroscience. We serve member programs and their trainees by maintaining a searchable directory of neuroscience training programs in North America and around the globe. An important goal for the ANDP is disseminate information about neuroscience education and training, and this is achieved through Fall and Spring meetings as well as electronic resource development. We perform a biannual survey of neuroscience education and training that provides key information on current trends in trainees, faculty and programs. Outstanding neuroscience educators are recognized with an annual ANDP award. Active ANDP members create an advocacy group for neuroscience that informs policy makers about neuroscience research and workforce needs. We work to be the stewards of the discipline..
The Animal Welfare Information Center (AWIC) is part of the U.S. Department of Agriculture (USDA) National Agricultural Library (NAL) in Beltsville, Maryland. The Center was established in 1986 and is staffed by a coordinator, three program support assistants, three full-time and three part-time information specialists, and one webmaster. About AWIC - Mission Congress'' mission for the Center was clearly provided in the 1985 amendments to the Animal Welfare Act (AWA): The Secretary [of Agriculture] shall establish an information service at the National Agricultural Library. Such service shall, in cooperation with the National Library of Medicine, provide information-- (1) pertinent to employee training; (2) which could prevent unintended duplication of animal experimentation as determined by the needs of the research facility; and (3) on improved methods of animal experimentation, including methods which could-- (A) reduce or replace animal use; and (B) minimize pain and distress to animals, such as anesthetic and analgesic procedures. Not surprisingly, the focus of the Center''s information products, services, and activities is to help the regulated community with employee training and to promote the humane care and use of animals by providing information on alternatives (improved methods of animal experimentation which could reduce or replace animal use or minimize pain and distress to animals). AWIC also provides support to other USDA agencies such as the Animal and Plant Health Inspection Service, Animal Care and the Agricultural Research Service..
The UCSD-Nature Signaling Gateway Molecule Pages provide essential information on more than 3900 proteins involved in cellular signaling. Each Molecule Page contains regularly updated information derived from public data sources as well as sequence analysis, references and links to other databases. Published Molecule Pages contain an expert-authored review article that describes the biological activity, regulation and localization of the protein. This review is supplemented by highly structured data that illustrate protein-protein interactions, post-translational modifications, subcellular localization and biological function. :Prior to publication, Nature Publishing Group administers rigorous peer and editorial review of each Molecule Page. The published pages are citable by digital object identifiers (DOIs). All data in the Molecule Pages are freely available to the public. :proteins, cellular signaling, neurobiology, genetic and structural information, biophysical properties, 5-Hydroxytryptamine receptor 2A, 5-Hydroxytryptamine receptor 2B, 5-Hydroxytryptamine Receptor 6, Adrenergic receptor a1a, Adrenergic Receptor 1, Ags1, Ags3, Arg, Darpp32, DCLK1, Dopamine receptor D3, Galanin receptor 1, Galanin receptor 2, (Glutamate receptor, metabotropic, type 1), (Glutamate receptor, metabotropic, type 5), (Glutamate receptor, metabotropic, type 8), Homer 1a, Homer 1b, Homer 1c, Homer 2a, Homer 2b, Homer 3, Laminin 2, Mark1, Mlk3, Neurotensin receptor 1, Neurotensin receptor 2, Trpc3, Trpc6, Trpc7, Trpm1, Trpm3, Trpm6, Trpv4, sequence analysis, protein-protein interactions, post-translational modifications, subcellular localization, biological function, signaling molecules, transcription factors, membrane receptors, Lcmt2, HB-EGF, Pak1, Itpk1, Ubr5, Rab35, CAP1, Plasma membrane calcium transporting ATPase isoform 4, 5-Hydroxytryptamine receptor 2C, Vangl2, mTOR, Catenin, beta, Pak1, Ubr5, Adrenergic receptor alpha 2a, Plasma membrane calcium transporting ATPase isoform 4, PCAF lysine acetyltransferase, G protein alpha 13, Rab35, Cell signaling, molecules, signaling protein, protein-protein interactions, subcellular localizations, post-translational modifications, enzymatic functions, states (A state is a physiological condition of a molecule), functions, transitions, network map, protein class, protein function, regulation of activity, interactions with ligands and other proteins, regulation of concentration (both protein and mRNA), subcellular localization, major sites of expression, phenotypes, splice variants and antibodies, pathways, Domains and Motifs, Orthologs and Blast Data,
Cognitive and Emotional Health Project: The Healthy Brain
Cognitive and Emotional Health Project (CEHP)
Cognitive Emotional Health Project: The Healthy Brain
Trans-NIH project to assess the state of longitudinal and epidemiological research on demographic, social and biologic determinants of cognitive and emotional health in aging adults and the pathways by which cognitive and emotional health may reciprocally influence each other. A database of large scale longitudinal study relevant to healthy aging in 4 domains was created based on responses of investigators conducting these studies and is available for query. The four domains are: * Cognitive Health * Emotional Health * Demographic and Social Factors * Biomedical and Physiologic Factors
Ikaros is an open infrastructure for system level modeling of the brain including databases of experimental data, computational models and functional brain data. The system makes heavy use of the emerging standards for Internet based information and makes all information accessible through an open web-based interface. In addition, Ikaros can be used as a control architecture for robots which in the extension will lead to the development of a brain inspired robot architecture. The main components of the Ikaros systems are: a platform independent simulation kernel; a set of computational brain models; a set of I/O modules for interfacing with data files and peripheral such as robots or video cameras; tools for building systems of interconnected models; a plug-in architecture that allows new models to be easily added to the system; and a database with data from learning experiments that can be used for validation of the computational models.
Network-based Prediction of Human Tissue-specific Metabolism
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Network visualizations in which the expression and predicted flux data are projected over the global human network. These network visualizations are accessible through the supplemental website using the publicly available Cytoscape software (Cline, Smoot et al. 2007). Since many high degree nodes exist in the network, special layouts are required to produce network visualizations that are readily interpretable. To this end we produced network visualizations in which hub nodes are repeated multiple times and hence layouts with a small number of edge crossings can be generated. Contains entries for brain compartments and brain pathways.
Biological General Repository for Interaction Datasets (BioGRID)
Biological General Repository for Interaction Datasets
Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.
A funding agency for basic research in Finland and operates within the administrative sector of the Ministry of Education. Their mission is to finance high-quality scientific research, act as a science and science policy expert, and strengthen the position of science and research. The Academy works to contribute to the renewal, diversification and increasing internationalisation of Finnish research. Its operation covers the full spectrum of scientific disciplines.
A Java application developed to visualise distribution of genomic features in high resolution.
Software and hardware core facility supporting clinical investigators at VA Research Center at Case Western Rserve University. The APT Center is a VA Research Center of Excellence established January 2005 in partnership with Case Western Reserve University. Clinicians, investigators, and staff work together to bring the clinical needs of veterans to the attention of the engineers and scientists pursuing new and emerging technologies in order to apply them for the purposes of reducing disability, improving daily functions, and enhancing quality of life. We are a technical center that designs and builds prototype devices that are clinically meaningful. We support rehabilitation research by adapting cross-cutting foundational technical platforms to meet specific needs for advanced prosthetic systems, sensory aids, and other clinical applications. Most grant-supported research concentrates on system development, pre-clinical testing, and clinical studies. The APT Center focuses on other aspects of the device development cycle, specifically: 1 the identification of user needs, 2 the generation of new concepts (innovation), 3 the development of new technologies through prototype and intial fabrication stages By shifting our focus, we are able to provide support to other Centers of Excellence when they need novel technologies or reach the point of technology transfer. List of projects the APT Center is attempting to undertake: Clinical needs assessment, Novel technologies to accelerate wound healing, Subcutaneous myoelectric signal (EMG) telemeter for prosthetic control, Switchable polymer materials that match their properties to the body, MEMS based implantable pressure sensors, Integrated control and sensory feedback for powered limb prostheses, Networked neural prostheses grants, funding.
The Alzheimers Drug Discovery Foundation (ADDF) is the only public charity whose sole mission is to accelerate the discovery and development of drugs to prevent, treat and cure Alzheimers disease, related dementias and cognitive aging. Founded in 1998 by the Este Lauder family, the ADDF awards grants to leading scientists conducting breakthrough drug discovery research. We use a venture philanthropy model to bridge the worldwide funding gap between basic research and later-stage drug development, using any return on investment to support new research. We have granted more than 40 million to fund over 295 Alzheimers drug discovery programs in academic centers and biotechnology companies in 15 countries. Scientists funded by the ADDF have entered clinical trials with several new drugs. The ADDF has invested over 8 million in 40 biotechnology companies, which have received follow-on commitments of over 1 billion. Keywords: Research, Funding, Alzheimer''s, Drug, Discovery, Biotechnology, Biomedical, Development, Investment, Prevention, Treatment, Cure, Cognitive, Aging, Dementia, Disease,
A non profit organization dedicated to providing support for patients and families with Alzheimer's disease, to educating the public about the disease, to funding a wide range of Alzheimer's disease related research and to finding ways to treat and eventually to prevent Alzheimer's disease. Resources include: the Alzheimer's Association Green-Field Library, a research grants program, and the Journal of the Alzheimer's Association.
The American Health Assistance Foundation (AHAF) is a registered 501(c)(3) non-profit organization that funds research seeking cures for Alzheimers disease, age-related macular degeneration and glaucoma, and provides the public with information about risk factors, preventative lifestyles, available treatments and coping strategies. :AHAFs three programs are Alzheimers Disease Research, Macular Degeneration Research and National Glaucoma Research. :We disseminate vital information to the public, especially those affected by these age-related degenerative diseases, through our website, print publications, and TV and radio Public Service Announcements (PSAs). Our aim is to educate people about risk factors, the latest research, treatments, risk reduction through healthy lifestyles, and ways to cope with the effects of these diseases. :Through our toll-free phone number, 1-800-437-AHAF (2423), people can speak directly with a member of our information services staff, Monday through Friday from 9am to 5pm for answers to questions, support and referrals. :The AHAF website contains a wealth of information on treatment, symptoms, risk factors, medical and research news updates and valuable resources for all three of these diseases. :AHAF is one of America''s leading supporters of basic scientific investigations to better understand and find cures for Alzheimer''s disease, age-related macular degeneration and glaucoma. We have awarded more than 90.3 million in research grants to some of the most prominent scientists at universities, hospitals and medical centers around the world. AHAF is currently supporting a total of 110 research grants: 48 projects through Alzheimer''s Disease Research; 27 through National Glaucoma Research; 25 through Macular Degeneration Research; 10 through the National Heart Foundation grants, funding resource :The AHAF website includes information on risk factors, symptoms, screening, diagnosis and treatment of Alzheimers disease, age-related macular degeneration and glaucoma. The website also has expert answers to Real Life Questions, responses to Frequently Asked Questions (FAQs), and the latest research news. Medical illustrations and videos provide easily understood descriptions of the brain, the eyes and the progress of these diseases. :grants; funding resource :
Association for Research in Vision and Ophthalmology
An eye and vision research organization whose goal is to encourage and assist research, training, publication, and dissemination of knowledge in vision and ophthalmology. ARVO membership is comprised of more than 11,500 individuals. Some 42% of members reside in over 70 countries outside the U.S. The membership is multidisciplinary and consists of both clinical and basic researchers (approximately 44% MD/Ophthalmologists, 26% PhDs, and 30% Other, including optometrists, osteopaths, and veterinarians). ARVO is governed by a Board of Trustees, who are elected from candidates put forth by the 13 Scientific Sections.
ASA, the nations leading grassroots autism organization, exists to improve the lives of all affected by autism. We do this by increasing public awareness about the day-to-day issues faced by people on the spectrum, advocating for appropriate services for individuals across the lifespan, and providing the latest information regarding treatment, education, research and advocacy. :Founded in 1965 by Dr. Bernard Rimland, Dr. Ruth Sullivan and many other parents of children with autism, ASA is the leading source of trusted and reliable information about autism. Through its strong chapter network, ASA has spearheaded numerous pieces of state and local legislation, including the 2006 Combating Autism Act, the first federal autism-specific law. ASAs website is one of the most visited websites on autism in the world and its quarterly journal, Autism Advocate, has a broad national readership. ASA also hosts the most comprehensive national conference on autism, attended by 2000 people each year. Our information and referral team, our program staff, and our strong chapter presence serve thousands of families each year who are searching for help in their journey with autism. :ASAs national office is headquartered in Bethesda, Maryland. ASA is a member and chapter organization whos national Board of Directors is composed of democratically elected members and appointed members. We are proud to be one of the few organizations to have members with autism serving as active board directors. ASAs Panel of Professional Advisors sets the standards for our Options Policy that governs our practices, and we are proud to count the top professional experts in autism on our PPA. ASAs Panel of People on the Spectrum of Autism Advisors is a first-of-its-kind advisory panel comprised solely of individuals with autism, who help ASA staff create programs and services that will advocate for the rights of all people with autism to live fulfilling, interdependent lives. :Each year, people with autism, families and professionals volunteer thousands of hours to help ASA achieve its mission of serving all those affected by autism. To each and every one of you, thank you :
The British Neuroscience Association, formerly known as The Brain Research Association, was officially relaunched in 1997, continuing many of the traditions of the BRA but with a professional and revamped style. Membership has increased dramatically since this time, now standing at 2000, and the BNA has increasingly taken a leading role in major events, such as hosting the Second Forum of European Neuroscience in Brighton in June, 2000. The BNA is the largest body representing all aspects of neuroscience from ion channels to whole animal behaviour. The Aims and Objectives of the Association are as follows: 1. To promote on a multidisciplinary basis the study of the development structure and function of the nervous system in health and disease. 2. To promote the dissemination of information to all those interested in the neurosciences and related disciplines by means of lectures, discussions, meetings and reports from time to time obtained from such researchers. 3. To advise as far as possible on issues in neurosciences related to health and disease. 4. To endeavour to increase public awareness and understanding of neuroscience research in health and disease. 5. To assist in the training of neuroscientists and other professionals engaged in neuroscience teaching and research. The BNA achieves these aims as follows: 1. By hosting a national meeting biennially, by publishing the proceedings of that meeting and distributing them to the scientific community. 2. By organising a number of focussed ''One Day symposia'' during the year, contributing to training courses for young neuroscientists and organising public lectures and events . 3. By regularly distributing information by the BNA Newsletter or by the BNA News E-mail Alert facility that can inform members about other relevant events, publications and topical issues. 4. By encouraging attendance at its own national meeting and those to which it is affiliated by awarding bursaries to students and young postdoctoral workers, and facilitating participation in the Society for Neuroscience annual meeting by offering sponsored abstract forms. 5. By awarding graduate and undergraduate prizes, and special awards to senior neuroscientists and to lay people who have contributed significantly through their own charitable work to the success of our discipline. 6. By constantly negotiating special discount prices of relevant books and journals, and by offering free online access to the European Journal of Neuroscience.The BNA is the fastest growing learned society, now boasting more than 2000 members, a rise of more than 40% since its relaunch as the BNA in 1997 from the former Brain Research Association. In addition to discounted journals and books and other occasional ''special offers'', the benefits of membership now include the following: 1. Reduced registration fees (up to 50%) to the National Meeting, and FREE admission to many events throughout the year including ''One Day Symposia'' and The Christmas Symposium. 2. Regular mailing of BNA Bulletin and other relevant items. 3. Regular BNA and FENs Email Alert service. 4. Student prizes, and bursaries for attendance at BNA, FENS and IBRO meetings. 5. Free on-line access to European Journal of Neuroscience. 6. Concessionary (SFN membership rate) registration fees and sponsored abstract forms for Society for Neuroscience annual meeting. 7. Free advertising in the BNA Bulletin and on the BNA Website. 8. Free (automatic) membership of the Federation of European Neuroscience Societies (FENS), the International Brain Research Organisation (IBRO) and the Biosciences Federation (BSF). educational resource; jobs.
This is an umbrella site for the major neuroscience programs in Germany, including GTTINGEN: MSc/PhD/MD-PHD Neurosciences Program BOCHUM: International Graduate School of Neuroscience TBINGEN: Graduate Training Center of Neuroscience MNCHEN: MSc/PhD Neurosciences Program BERLIN: International Graduate Program Medical Neurosciences, International Graduate Program Computational Neurosciences, Bernstein Center for Computational Neuroscience, Berlin School of Mind and Brain, Helmholtz International Research School Molecular Neurobiology MAGDEBURG: Integrative Neuroscience.
Institute of Neurosciences Mental Health and Addiction
Canadian Institutes of Health Research Institute of Neurosciences, Mental Health and Addiction (INMHA) supports research on the functioning and disorders of the brain, the spinal cord, the sensory and motor systems, and the mind. The burden of disease in terms of the social, economic and health care costs associated with these disorders and related illnesses are staggering and there are indications that the number of people affected either directly or indirectly will continue to increase in the years to come. The INMHA is a unique institute because, based on recent discoveries, it has been designed to address all aspects of research dealing with Brain-Mind relationships inclusive of the four pillars of the CIHR, which are: * biomedical, * clinical, * health services and * population health research. It is a daunting endeavour, but the INMHA can transform this challenge into a unique opportunity for fostering innovation in our area of health research.
IA (CHIR, Canada) supports research that promotes healthy aging and addresses causes, prevention, screening, diagnosis, treatment, support systems, and palliation for a wide range of conditions associated with aging. :funding resource, grants :
International Brain Research Organization
l''Organisation internationale de recherche sur le cerveau
A central organization that develops, supports, co-ordinates and promotes scientific research in all fields concerning the brain; promotes international collaboration and interchange of scientific information on brain research throughout the world; and provides for and to assist in education and the dissemination of information relating to brain research by all available means. IBRO represents the interests of more than 50,000 neuroscientists around the globe. Over the years, IBRO has set up a number of program to stimulate international contacts in brain research. Symposia and workshops are sponsored on the basis of competitive applications. Under its Publications Programme, IBRO publishes the journal Neuroscience and the annual newsletter IBRO News. IBRO offers post-doctoral fellowships and travel grants to students from less-developed countries. It has run a Neuroscience Schools Programme, organized by the committees of IBROs six Regions, aimed at forming interactive networks among students and teachers during training courses in Africa, Asia, Central and Eastern Europe, Latin America, Western Europe, and the US and Canada. With just three schools in 1999, expansion has been rapid - in 2007 there were 22 schools around the world.
West Virginia University School of Pharmacy Graduate Programs
School of Pharmacy offers two graduate Doctor of Philosophy degree programs. Health Services and Outcomes Research program emphasizes research related to access, cost, quality and outcomes of pharmaceuticals and health services. Pharmaceutical and Pharmacological Sciences program emphasizes basic laboratory research and training in biomedical sciences.Graduate programs feature multidisciplinary coursework and seminars to provide students with diversified background in theories and techniques of contemporary research.
Queens University Canadian Institutes of Health Research Group in Sensory-Motor Integration
Group provides systematic and comprehensive study of sensory motor behavior that combines movements of eyes, head, arm and hand. Study of sensory motor coordination also include design of rigorous behavioral paradigms to detect and monitor treatment of diseases or injuries affecting sensory motor function. Other investigations include development of novel strategies that either promote recovery from injury or protect neurons from disease or injury.
CORE MISSION: The core mission of the IRSF is to fund research for treatments and a cure for Rett syndrome while enhancing the overall quality of life for those living with Rett syndrome by providing information, programs, and services. ELEMENTS OF MISSION RESEARCH: The IRSF will coordinate, cultivate, accelerate, and fund research that will produce a cure for Rett syndrome and reveal and develop treatments that will make the lives of people living with Rett syndrome richer and free of pain and discomfort. FAMILY SUPPORT: The IRSF will assist families of individuals living with Rett syndrome by providing them with connections to critical and useful information, programs, services, and support from diagnosis to day-to-day life. ADVOCACY AND AWARENESS: The IRSF will advocate for and raise awareness about individuals with Rett syndrome so the scientific and medical community, policy makers, educators, care givers, and the general public can more thoroughly know, understand, and be motivated to help the research efforts and individuals dealing with Rett syndrome on a daily basis. ACCOMPLISHING THE MISSION FUND DEVELOPMENT: To accomplish this core mission, the core priority of the IRSFs leadership will be effective, assertive, comprehensive, and strategic fundraising. FISCAL RESPONSIBILITY: The IRSF will operate in accordance with those generally accepted principles necessary to maintain a Four Star Charity Navigator rating. Keywords: grants, funding, research, advocacy, awareness, family support, education, fundraising,
The English web portal www.research-in-germany.de is an information platform and contact point for all looking to find out more about Germany''s research landscape and its latest research achievements. An interdisciplinary portal The portal not only informs researchers and scientists about what Germany has to offer them. It also covers the 17 future fields of the High-Tech Strategy and other fields of science and learning. In addition, it addresses a whole host of other players from politics and government, business and industry, or science and research, as well as our young researchers, of course. Editorial responsibility for the portal lies with the German Academic Exchange Service (DAAD), acting on behalf of the Federal Ministry of Education and Research (BMBF). The Research in Germany Land of Ideas Campaign The campaign to Promote Innovation and Research in Germany was launched in November 2006 to position German research in the international market. Since then, the campaign has been running worldwide under the brand Research in Germany Land of Ideas. Its declared goal is to highlight research in Germany and the advantages that it offers. This makes German research institutions more visible to our partners, customers and competitors. The campaign primarily aims to strengthen the networks that exist between German research institutions and our strategic partners worldwide. A further goal involves inspiring the world''s best minds in research and development to come to Germany to carry out their projects and then to make the most of the resulting opportunities that open up for both sides. Not to forget the goal of encouraging more international cooperation in science and research. job resource; funding resource; grants; training resource.
International Drug Abuse Research Society
IDARS is an international scientific organization that promotes and fosters the research and collaboration of scientists around the world in the area of substances of abuse and addiction. Our focus is to foster research in molecular, cellular and systems biology and includes neuropharmacological, neurobehavioral, neurochemical and neuroanatomical themes. The purposes of IDARS are scientific, educational and charitable. We strive to promote excellence in: advancing the understanding of drug abuse, substance abuse and addictions, including the part they play in behaviors of humans and in animal models bringing together scientists of varying backgrounds and disciplines within the field of drug abuse research integrating drug abuse research directed at all levels of biological organization and its translation to improvement in clinical prevention and treatment efforts promoting education in the addiction sciences informing the general public on the results and implications of current research in the addiction sciences promoting other activities that will contribute to the development of addiction sciences IDARS is a 501c3 nonprofit organization.
Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING
Dockground: Benchmarks Docoys Templates and other knowledge resources for DOCKING
Dockground: Benchmarks Docoys Templates other knowledge resources for DOCKING
Data sets, tools and computational techniques for modeling of protein interactions, including docking benchmarks, docking decoys and docking templates. Adequate computational techniques for modeling of protein interactions are important because of the growing number of known protein 3D structures, particularly in the context of structural genomics. The first release of the DOCKGROUND resource (Douguet et al., Bioinformatics 2006; 22:2612-2618) implemented a comprehensive database of cocrystallized (bound) protein-protein complexes in a relational database of annotated structures. Additional releases added features to the set of bound structures, such as regularly updated downloadable datasets: automatically generated nonredundant set, built according to most common criteria, and a manually curated set that includes only biological nonobligate complexes along with a number of additional useful characteristics. Also included are unbound (experimental and simulated) protein-protein complexes. Complexes from the bound dataset are used to identify crystallized unbound analogs. If such analogs do not exist, the unbound structures are simulated by rotamer library optimization. Thus, the database contains comprehensive sets of complexes suitable for large scale benchmarking of docking algorithms. Advanced methodologies for simulating unbound conformations are being explored for the next release. The Dockground project is developed by the Vakser lab at the Center for Bioinformatics at the University of Kansas. Parts of Dockground were co-developed by Dominique Douguet from the Center of Structural Biochemistry (INSERM U554 - CNRS UMR5048), Montpellier, France.
Bernstein Network Computational Neuroscience Germany
The Bernstein Network for Computational Neuroscience, Germany, is a funding initiative of the German Federal Ministry of Education and Research that supports the development of this field in Germany. Understanding the brain is the prerequisite for creating new methods for prevention and treatment of diseases of the nervous system. It may also help developing new strategies for learning and teaching. It may even be used for the design of new, ''intelligent'' technical devices, such as neuroprostheses or more powerful computer systems. For investigating the brain, the interdisciplinary approach of computational neuroscience, in which experts in biology, physics, psychology, medicine, mathematics and engineering join forces, holds especially promising perspectives. By combining experiment, data analysis, theoretical modelling and computer simulations, computational neuroscience allows translating basic research to targeted applications. The Bernstein Network currently comprises more than 200 research groups at over 20 locations all over Germany. It entertains partnerships with more than 20 companies. Besides its research activities, the network offers attractive teaching and training options for young researchers. A large number of open positions are available, ranging from PhD students positions up to professorships. Keywords: grant, funding, resource, training, job, research, Network, Scientist, Teaching, biology, physics, psychology, medicine, mathematics, engineering, Computational, Neuroscience, Computational Neuroscience, Germany,
SPECTRAL graph approach for GEnetic Matching
It is at the forefront of new ideas and developments in microscopy and imaging. The RMS is the only truly international microscopical society, drawing distinguished members from all over the world. It also serves the needs of its company members who represent all the major manufacturers and suppliers of microscopes, equipment and services. In addition to this, the Society is pursuing an initiative to encourage young microscope users who may go on to influence microscopy in years to come. The Society is dedicated to advancing science, developing careers and supporting wider understanding of science and microscopy through its Science and Society activities. In support of the above, it publishes The Journal of Microscopy and microscopy handbooks, as well as helping young scientists through bursaries. The Society is incorporated by Royal Charter. Its governing documents are its Charter and By-laws. The most recent AGM minutes, Trustees Report and Accounts are available below - 2007 AGM draft minutes Full 2007 Trustees Report and Accounts - as submitted to the Charity Commission The RMS is a member of: - the Foundation for Science and Technology - the Biosciences Federation - the International Federation of Societies for Microscopy - the European Microscopy Society training opportunities; jobs.
Allen Institute for Brain Science Human Cortex Study
Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with suite of visualization and mining tools to create open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is desktop software application for viewing human brain anatomy and gene expression data in 3D.
The National Eye Institute Research funding resource provides notifications of funding opportunities in eye and vision research. National Eye Institute supports the 28 grant mechanisms listed on the site and lists extramural funding data. The National Eye Institute (NEI) was established by Congress in 1968 to protect and prolong the vision of the American people. NEI research leads to sight-saving treatments reduces visual impairment and blindness and improves the quality of life for people of all ages. NEI-supported research has advanced our knowledge of how the visual system functions in health and disease. Vision research is supported by the NEI through approximately 1600 research grants and training awards made to scientists at more than 250 medical centers hospitals universities and other institutions across the country and around the world. The NEI also conducts laboratory and patient-oriented research at its own facilities located on the NIH campus in Bethesda Maryland.
Platform for exploring spinal cord at cellular and molecular levels. Map of gene expression for adult and juvenile mouse spinal cord. Provides map of normal mouse when used to compare gene expression in diseased or injury models. Interactive database of gene expression mapped across all anatomic segments of mouse spinal cord at postnatal days 4 and 56. Indexed set of images based on RNA in situ hybridization data, searchable and sortable by gene, age, expression, cervical, thoracic, lumbar, sacral, and coccygeal segments.
The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). :The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, t he system provides computationally derived data such as multiple sequence alignments, homology models, and a series of query and visualization tools. :The GPCRDB is designed to be a data storage medium, as well as a tool to aid biomedical scientists with answering questions by offering a single point of access to many types of data that are integrated and visualized in a user-friendly way. Although most parts of the GPCRDB are self-explanatory, if you have not used this resource before it is adviced that you to take a look at the usage page. Sponsors: This resource is supported by Organon and Unilever, and the NIH. Keywords: G protein, Coupled, receptor, Molecular, Heterogenous, Data, Sequence, Ligand, Mutation, Computational, Software, Alignment, Homology, Model, Visualization, Tool, Biomedical, Scientist, Integration,
Software application that is a stepwise approach to identifying recombination breakpoints in a sequence alignment (entry from Genetic Analysis Software)
Virtual Cell at the National Resource for Cell Analysis and Modeling
V-Cell is a remote user modeling and simulation environment utilizing Java''s Remote Method Invocation (RMI). The biologically oriented user interface allows experimentalists to create models, define cellular geometry, specify simulations and analyze the simulation results. The results are run and stored on a remote server and can be reviewed in the software and/or exported in a variety of popular formats. The design of the biological to mathematical mapping allows for separate use of biological and math components, and includes automatic mathematical simplification using pseudo-steady approximations and mass conservation relationships. This allows for direct specification of mathematical problems, performing simulations and analysis on those systems. The stand alone mathematics user interface is also a powerful tool for modeling reaction-diffusion systems. A transparent general purpose solver is used to translate the initial biological description into a set of concise mathematical problems. The solver is transparent to the average user, but is accessible to the theorist as the Math Editor component. The software is composed of three main components: 1. The modeling framework represents the physiological models of the Virtual Cell and allows for persistence and database support. 2. The mathematics framework transparently solves an important class of mathematical problems encountered in the cellular modeling. 3. The WWW accessible graphical user interface provides access to the technology mentioned above. The user interface has been developed using Java 2 Applets.
A computer-readable format for representing models of biochemical reaction networks in software. It''s applicable to models of metabolism, cell-signaling, and many others. This website is the portal for the global SBML development effort; you can find information about all aspects of SBML.
University of Regensburg; Bavaria; Germany
Public research university located in the medieval city of Regensburg, Bavaria, a city that is listed as a UNESCO World Heritage Site.
Translating Time across developing mammalian brains
Web tool for translating neurodevelopemental time across species and predicting neurodevelopemental events. This tool was created because clinicians and researchers rely on neurodevelopment data obtained from a variety of non-human species, it is essential to be able to relate studies across the different experimental animals, and ultimately to humans, in an easily accessible format. This web site is based on a mathematical model originally described by Finlay and Darlington (Science, 268:1578-84) that predicts post conception (PC) dates using log transformations. It integrates hundreds of empirically-derived neural events to translate neurodevelopmental time across hamsters, mice, rats, rabbits, spiny mice, guinea pigs, ferrets, cats, rhesus monkeys and humans.
A database of domain-domain and peptide-mediated interactions of known 3D structures. The database of 3D Interaction Domains (3did) is a collection of domain-domain and domain-peptide interactions for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how these interactions occur. It also offers an overview of how similar in structure are interactions between different members of the same protein family. The database also contains GO-based functional annotations and interactions between yeast proteins from large-scale interaction discovery studies. Sponsors: This resource is partially supported by the Spanish Ministerio de Educacin y Ciencia (PSE-010000-2007-1 and BIO2007-62426) and the 3D-Repertoire from the European Commission under FP6 contract LSHG-CT-2005-512028. Keywords: Database, Domain, Peptide, Protein, 3D structure, Interaction, Dimentional, Structure, Molecular, Functional, Annotation, Interaction, Yeast, Study, Research,
Collects and stores genetic (DNA) samples along with associated healthcare information from patients of Northwestern-affiliated hospitals and clinics. This resource is available to scientists to conduct groundbreaking genetic research. The information and blood samples provided will be used by researchers to examine the role genes play in the development and treatment of common diseases. The NUgene Project seeks to increase the understanding of genetic mechanisms underlying common diseases, assist in the development of DNA-based technology for diagnosis and treatment of disease, and aid physicians and other healthcare providers in the application of genetics to the practice of medicine. NUgene participants are recruited throughout the Northwestern-affiliated healthcare community in order to create an ethnically and medically diverse population for research. Participants must be 18 years of age or older and receive their medical care from a Northwestern-affiliated provider, regardless of health status. Consenting individuals complete all aspects of enrollment in a single meeting with a research coordinator. The enrollment process includes the donation of a single sample of blood and the completion of a self-administered questionnaire. Participants also sign a consent form during this encounter. The NUgene Project is an interdisciplinary project that relies on the expertise of individuals working in a variety of fields, including science, medicine, clinical research, statistics, epidemiology, and computational biology. NUgene''s multidisciplinary approach has spurred collaborations within Northwestern-affiliated institutions and with other outside institutions. This collaboration of ideas is the future of genetics and genomic research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
(at)neurIST - Integrated Biomedical Informatics for the Management of Cerebral Aneurysms
aneurIST - Integrated Biomedical Informatics for the Management of Cerebral Aneurysms
Project focused on cerebral aneurysms and provides integrated decision support system to assess risk of aneurysm rupture in patients and to optimize their treatments. IT infrastructure has been developeded for management and processing of vast amount of heterogeneous data acquired during diagnosis.
eMERGE Network: electronic Medical Records and Genomics
eMERGE Network: electronic Medical Records & Genomics
eMERGE Network: electronic Medical Records & Genomics - A consortium of biorepositories linked to electronic medical records data for conducting genomics studies
eMERGE Network: electronic Medical Records Genomics
The eMERGE Network: electronic Medical Records & Genomics
A national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. The consortium is composed of seven member sites exploring the ability and feasibility of using EMR systems to investigate gene-disease relationships. Themes of bioinformatics, genomic medicine, privacy and community engagement are of particular relevance to eMERGE. The consortium uses data from the EMR clinical systems that represent actual health care events and focuses on ethical issues such as privacy, confidentiality, and interactions with the broader community.
An Integrative small RNA Sequencing database for miRNA research and provides an integrative web interface for miRNA quantification, isomiR identification, arm switching discovery, and, most of all, novel miRNA predictions.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Database containing structural annotations for the proteomes of just under 100 organisms. Using data derived from public databases of translated genomic sequences, representatives from the major branches of Life are included: Prokaryota, Eukaryota and Archaea. The annotations stored in the database may be accessed in a number of ways. The help page provides information on how to access the database. 3D-GENOMICS is now part of a larger project, called e-Protein. The project brings together similar databases at three sites: Imperial College London , University College London and the European Bioinformatics Institute . e-Protein''s mission statement is To provide a fully automated distributed pipeline for large-scale structural and functional annotation of all major proteomes via the use of cutting-edge computer GRID technologies. The following databases are incorporated: NRprot, SCOP, ASTRAL, PFAM, Prosite, taxonomy, COG The following eukaryotic genomes are incorporated: Anopheles gambiae, protein sequences from the mosquito genome; Arabidopsis thaliana, protein sequences from the Arabidopsis genome; Caenorhabditis briggsae, protein sequences from the C.briggsae genome; Caenorhabditis elegans protein sequences from the worm genome; Ciona intestinalis protein sequences from the sea squirt genome; Danio rerio protein sequences from the zebrafish genome; Drosophila melanogaster protein sequences from the fruitfly genome; Encephalitozoon cuniculi protein sequences from the E.cuniculi genome; Fugu rubripes protein sequences from the pufferfish genome; Guillardia theta protein sequences from the G.theta genome; Homo sapiens protein sequences from the human genome; Mus musculus protein sequences from the mouse genome; Neurospora crassa protein sequences from the N.crassa genome; Oryza sativa protein sequences from the rice genome; Plasmodium falciparum protein sequences from the P.falciparum genome; Rattus norvegicus protein sequences from the rat genome; Saccharomyces cerevisiae protein sequences from the yeast genome; Schizosaccharomyces pombe protein sequences from the yeast genome
University of Massachusetts at Worcester Medical School Department of Biochemistry and Molecular Pharmacology
Department of Biochemistry and Molecular Pharmacology seeks to foster interactive, innovative environment in which faculty, students and postdoctoral fellows bring molecular perspective to problems in biology. By establishing interface between biology and disciplines of chemistry, mathematics and physics, this department encourages development and application of quantitative approaches to complex problems in life sciences. Department also serves to strengthen and, in turn, be strengthened by close interactions with other basic science and clinical departments at medical school.
The purpose of IMAG is to bring together program officers who have a shared interest in applying modeling and analysis methods to biomedical systems. The meetings are formatted to facilitate an open discussion of what is currently being supported, and for planning future directions in these areas. At each meeting, time is allotted to hear focused presentations from one or two participants to discuss issues relating to modeling and analysis across the government agencies. Discussions also occur online, and participants are informed of talks, conferences and other activities of interest to the group. The NIH BISTIC, (Biomedical Information Science and Technology Consortium), is very supportive of IMAG and serves as the larger body at NIH for disseminating IMAG activities. Associated agencies: NIH: Center for Scientific Review, National Cancer Institute, National Center for Research Resources, National Heart, Lung and Blood Institute, National Human Genome Research Institute, National Institute on Aging, National Institute of Allergy and Infectious Diseases, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute of Biomedical Imaging and Bioengineering, National Institute of Child Health and Human Development, National Institute on Deafness and Other Communication Disorders, National Institute on Drug Abuse, National Institute of Environmental Health Sciences, National Institute of General Medical Sciences, National Institute of Mental Health, National Institute of Neurological Disorders and Stroke, National Library of Medicine NSF (National Science Foundation): Directorate for Biological Sciences, Directorate for Computer and Information Science and Engineering, Directorate for Engineering, Directorate for Mathematical and Physical Sciences NASA (National Aeronautics and Space Administration): Human Research Program DOE (Department of Energy), Office of Advanced Scientific Computing Research, Office of Biological and Environmental Research DOD (Department of Defense): Air Force Office of Scientific Research (AFOSR), Army, Defense Advanced Research Projects Agency, Office of Naval Research, Telemedicine and Advanced Technology Research Center, USDA (United States Department of Agriculture), USDVA (Unites States Department of Veteran Affairs) Soliciting programs: Predictive Multiscale Models of the Physiome in Health and Disease (MSM Physiome) Initiative; and Multi-Scale Modeling (MSM) InitiativeKey words: MRI, Imaging, human.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.BOND, which requires registration of a free account, is a resource used to perform cross-database searches of available sequence, interaction, complex and pathway information. BOND integrates a range of component databases including GenBank and BIND, the Biomolecular Interaction Network Database. BOND contains 70+ million biological sequences, 33,000 structures, 38,000 GO terms, and over 200,000 human curated interactions contained in BIND, and is open access. BOND serves the interests of the developing global interactome effort encompassing the genomic, proteomic and metabolomic research communities. BOND is the first open access search resource to integrate sequence and interaction information. BOND integrates BLAST functionality, and contains a well-documented API. BOND also stores annotation links for sequences, including links to Genome Ontology descriptions, MedLine abstracts, taxon identifiers, associated structures, redundant sequences, sequence neighbors, conserved domains, data base cross-references, Online Mendalian Inheritance in Man identifiers, LocusLink identifiers and complete genomes. BIND on BOND The Biomolecular Interaction Network Database (BIND), a component database of BOND, is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature. BIND is an interaction database with three classifications for molecular associations: molecules that associate with each other to form interactions, molecular complexes that are formed from one or more interaction(s) and pathways that are defined by a specific sequence of two or more interactions.Interactions A BIND record represents an interaction between two or more objects that is believed to occur in a living organism. A biological object can be a protein, DNA, RNA, ligand, molecular complex, gene, photon or an unclassified biological entity. BIND records are created for interactions which have been shown experimentally and published in at least one peer-reviewed journal. A record also references any papers with experimental evidence that support or dispute the associated interaction. Interactions are the basic units of BIND and can be linked together to form molecular complexes or pathways. The BIND interaction viewer is a tool to visualize and analyze molecular interactions, complexes and pathways. The BIND interaction viewer uses Ontoglyphs to display information about a protein via attributes such as molecular function, biological process and sub-cellular localization. Ontoglyphs allow to graphically and interactively explore interaction networks, by visualizing interactions in the context of 34 functional, 25 binding specificity and 24 sub-cellular localization Ontoglyphs categories. We will continue to provide an open access version of BOND, providing its subscribers with free, unlimited access to a core content set. But we are confident you will soon want to upgrade to BONDplus.
Add Health (National Longitudinal Study of Adolescent Health)
National Longitudinal Study of Adolescent Health
Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.
University of North Carolina School of Pharmacy PhD Program
The PhD program in pharmaceutical sciences offers you the rigorous grounding in a broad range of disciplines that are critical to your success as a pharmaceutical scientist in academia and industry. We take an interdisciplinary approach to graduate research by combining the aspects of areas such as chemistry, biology, engineering, and economics that relate to pharmaceutical science. PhD students choose a concentration in one of the School's four academic divisions, each of which corresponds to a stage in the drug-development cycle.
National Institute of Mental Health (NIMH) Human Genetics Initiative
The Connectivity Map aims to generate a detailed map that links gene patterns associated with disease to corresponding patterns produced by drug candidates and a variety of genetic manipulations. The Connectivity Map is the most comprehensive effort yet for using genomics in a drug-discovery framework. It allows researchers to screen compounds against genome-wide disease signatures, rather than a pre-selected set of target genes. Drugs are paired with diseases using sophisticated pattern-matching methods with a high level of resolution and specificity. To build a Connectivity Map, the Broad Institute brings together molecular biologists, genomics specialists, computational scientists, pharmacologists, chemists and chemical biologists, as well as expertise from across the breadth and depth of medicine.Connectivity map is a large public database of signatures of drugs and genes, and pattern-matching tools to detect similarities among these signatures.The parent site for the Broad Institute at MIT has a software library of software applications developed for use in genetic analysis.
Neuroscience Mutagenesis Facility of the Jackson Laboratory
Produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The impetus for the program resulted from the recognition that: * The value of genomic data would remain limited unless more information about the functionality of its individual components became available. * The task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e.N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. The resulting mutant mouse lines have been available to the scientific community for the last five years and over 700 NMF mice have been sent to interested investigators for research; these mutant mouse lines will remain available as frozen embryos (which can be re-derived on request) and can be ordered through the JAX customer service at 1-800-422-6423 (or 207-288-5845). The results of the work of the Neuroscience Mutagenesis Facility and that of two other neurogenesis centers, i.e. The Neurogenomics Project at Northwestern University, and the Neuromutagenesis Project of the Tennessee Mouse Genome Consortium, can also be seen at Neuromice.org, a common web site of these three research centers; in addition, information about all mutants produced by these groups has been recorded in MGI.
Nature Precedings is a free online service from NPG that enables researchers in the life sciences to openly share preliminary findings, disseminate emerging results, solicit community feedback, and claim priority over discoveries by posting preprint manuscripts, white papers, technical reports, posters, and presentations. It is a permanent, citable archive for pre-publication research and preliminary findings.
Software program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. (entry from Genetic Analysis Software)
GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database
Gallus Expression in Situ Hybridization Analysis
GEISHA - Gallus Expression in Situ Hybridization Analysis
Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA.
SpBase - Strongylocentrotus purpuratus: the Sea Urchin Genome Database
SpBase is designed to present the results of the genome sequencing project for the purple sea urchin. The sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through National Center for Biotechnology Information and other large databases. Additionally, the unique information on that links gene identities and sequences to the plate and well location to the library filters from the Sea Urchin genome Resource will also be presented. The software used to organize and present the sea urchin genome comes from GMOD, a collection of open source software tools for creating and managing genome-scale biological databases. That sea urchins eggs and embryos have long remained a popular research subject for cell and developmental biologists is one rationale for sequencing the genome. In addition, studies of embryonic development in the California Purple Sea Urchin, Strongylocentrotus purpuratus , have paralleled the emergence of molecular techniques ranging from the characterization of genomic repeat sequences in the 1970''s to the elucidation of gene regulatory networks in recent times. The parent of this site, SUGP, was meant to provide a focal point for the exchange of genomic information as the genome of the Purple sea urchin was being sequenced. Over these past years it has served as a repository for small sequencing projects and a source of sequence information useful for gene discovery projects. Here one could find information on macro-array libraries of cDNAs from the purple sea urchin and genomic DNA from several species. In addition, a Sequence Tag Connector (STC) collection has been assembled from 5% of the genome sequence and a very extensive repeat sequence catalog prepared. All of the sequence data that we maintained at SUGP was incorporated into the new SPBase. Of course, it is all in public sequence databases such as the National Center for Biological Information as well. Some additional sequence information is available at the Resource Center of the German Human Genome Project. With the publication of The Genome of the Sea Urchin Strongylocentrotus purpuratus by The Sea Urchin Genome Sequencing Consortium a link to the first 9941 gene annotations are now publicly available. The effort to sequence the whole purple sea urchin genome was a cooperative one that included contributions from the Sea Urchin Genome Facility here at the Center for Computational Regulatory Genomics, Beckman Institute, Caltech, and support from the Human Genome Research Institute of the National Institutes of Health. The sequencing was done at the Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas. Funding was approved based on an initiative submitted by the Sea Urchin Genome Advisory Committee.
University of Illinois at Urbana-Champaign; Beckman Institute for Advanced Science and Technology
Beckman Institute for Advanced Science and Technology
The Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign is an interdisciplinary research institute devoted to leading-edge research in the physical sciences, computation, engineering, biology, behavior, cognition, and neuroscience. It offers senior, graduate, postdoctoral, and Carle-Beckman fellowships. The Beckman Institute Postdoctoral Fellows program is intended for recent Ph.D.s or students in their final year of doctoral study with research interests relevant to the Beckman Institute. A competition is held yearly and four fellows are selected for terms of up to three years. The Beckman Graduate Fellows Program, offers University of Illinois graduate students at the M.A., M.S., or Ph.D. level the opportunity to pursue interdisciplinary research at the Institute. The Senior Fellows Program gives established faculty from other universities the opportunity to do short-term, onsite, interdisciplinary research with other Beckman Institute researchers. Participation in the Senior Fellows Program is by invitation from the Beckman Institute. Usually Senior Fellows have previous ties to Beckman researchers and stay for a period of three to six months. Beckman Institute research is focused around four research themes: Biological Intelligence, Human-Computer Intelligent Interaction, Integrative Imaging, and Molecular and Electronic Nanostructures More than 600 researchers from 40 University of Illinois departments as far-ranging as psychology, computer science, and biochemistry, comprising 13 Beckman Institute groups, work within and across these overlapping areas. The building is magnificent and offers more than 200 offices; specialized, state-of-the-art laboratories and other facilities; and meeting areas. The Arnold and Mabel Beckman Foundation provides ongoing financial assistance for various Institute and campus programs. Daily operating expenses of the Institute are funded by the state and its research programs are mainly supported by external funding from the federal government, corporations, and foundations.
Boston University School of Medicine Department of Behavioral Neuroscience
Boston University School of Medicine; Behavioral Neuroscience
The Behavioral Neuroscience program''s focus is on the delineation and analysis of perceptual, cognitive, linguistic, affective, and behavioral disorders observed in neurologic disease, as these disorders contribute to an understanding of normal brain function and its modification by pathology. The subject matter derives chiefly, but not exclusively, from clinical populations with neurological disorders affecting higher processes, particularly from the study of syndromes involving selective impairment of functional systems such as memory, language, or purposeful movement. Current methods of clinical assessment, cognitive psychology, experimental design, and the neurosciences are integrated into a broad program of clinical and basic research. The Behavioral Neuroscience Ph.D. Program is administered through the Division of Graduate Medical Sciences, BUSM, by faculty members of the Department of Neurology, Division of Psychiatry, and Anatomy & Neurobiology, BUSM (holding joint appointments at the Department of Veterans Affairs [VA] Medical Centers in Boston or Bedford, MA). Only the doctoral program is offered (no master''s degree). The Program is not designed to meet requirements for accreditation as to clinical competence in psychology nor in any discipline which has a certification procedure. It does, however, accept students in the M.D./Ph.D. Program at Boston University School of Medicine, or other students enrolled elsewhere in related programs (including the Master of Arts in Medical Sciences Program), to take some or all of the offerings. Boston University School of Medicine is an accredited institution. Behavioral Neuroscience is a degree-granting Program having the same representation as other Ph.D.-granting Departments in the Division of Graduate Medical Sciences.
Brandeis University Neuroscience Graduate Program
Students entering the Neuroscience Program at Brandeis have opportunities to work in a range of fields, from cognitive neuroscience to the structure and function of ion channels. Brandeis University is an exciting place for Neuroscience research and study because we have an outstanding and highly interactive research community. The Neuroscience laboratories are housed within the Volen Center and adjoining buildings, and this close proximity facilitates the high degree of collaboration and exchange for which Brandeis has become famous. There are today over 45 Neuroscience Program Ph.D. students, who often work side-by-side with Ph.D. students in the other Life Sciences graduate programs at Brandeis. The Brandeis Life Sciences offers a M.S. program and a Ph.D. program in Neuroscience. Postdoctoral Training in Neuroscience There are numerous opportunities for postdoctoral training at Brandeis University. Funding for postdocs is available under the auspices of a NINDS training grant, as well as funding from the research grants of individual faculty members.
Columbia University Medical Center Department of Neuroscience
The Department of Neuroscience is a basic science department within the College of Physicians and Surgeons at the Columbia University Medical Center. The 35 faculty members in the department use a wide range of approaches to study fundamental aspects of neural circuit development, organization, and function. They share a common goal of relating the biology of such circuits to the control of behavior. A broad array of animal models, as well as human subjects, are examined using a wide range of approaches, including electrophysiology, biophysics, molecular and cell biology, systems neuroscience, imaging, behavior and theory. Interdisciplinary research is facilitated by widespread collaboration between different labs. Several research projects in the department are focused on animal models of nervous system disease. The department''s faculty has a distinguished record in neuroscience teaching and training. They are actively engaged in the training of medical students, Ph.D. and M.D./Ph.D. candidates, postdoctoral fellows and medical postgraduates. The faculty members of the Center play a major role in organizing and teaching the course Basic and Clinical Neuroscience, which is a Columbia Continuing Medical Education Course for students, fellows, residents, and practicing physicians. The outstanding research and training activities of the department are enhanced by the fact that it is embedded in a medical center with exceptional strength in many areas related to basic neuroscience, including Psychiatry and Neurology. In addition, the department sponsors the Graduate School of Arts & Sciences Ph.D. Program in Neurobiology and Behavior that includes over 100 faculty from the Medical Center and Morningside Campus.
Weill Cornell Medicine Department of Neurology
Weill Cornell Dept. of Neurology and Neuroscience
Weill Cornell Medical College Department of Neurology and Neuroscience
Weill Cornell Medical College Neurology & Neuroscience
Weill Cornell Medical College Neurology and Neuroscience
Weill Cornell Neurology and Neuroscience
The Department of Neurology and Neuroscience at NewYork-Presbyterian Hospital/Weill Cornell Medical Center is considered one of the premier academic neurology departments in the world. The department has over eighty faculty members focusing on the education of medical students, interns, residents and graduate students, on all aspects of the Neurological systems. The department also offers a two-year postdoctoral specialty training program and CME courses. The Department currently has several thousand square feet of research space, 25,000 square feet of clinical outpatient office space, a 30-bed dedicated inpatient unit and an 11-bed Neurological Intensive Care Unit. Last year, our clinical neurologists had over 23,000 patient care visits in our offices. In 2008, five of our faculty members were voted Best Doctors in New York Magazine and US News and World Report ranked NewYork-Presbyterian Hospital services in neurology and neurosurgery #1 in New York City and #5 in the United States. Our Department attracts the best and brightest graduates of medical schools from around the world to our residency training program, and many of our trainees go on to lead other academic departments. Our department continues to expand in all of its fundamental missions treating patients with neurologic disorders, performing research, and teaching medical students and residents in Neurology. One of the key missions of the department is to translate critical research advances discovered in our laboratories to benefit, treat and possibly cure a wide array of neurological diseases.
It is the beginning of an image database on Drosophila development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes).The concept of FlyView includes compatibility to FlyBase, the main Drosophila database. Our aim is to establish the possibilty to compare images on the computer screen and to search for special patterns at different developmental stages. Therefore, all images are accompanied by text descriptions that can be used for searching.
Cornell University College of Veterinary Medicine Program of Study
Pharmacology training program offers an intensive course of study and research emphasizing molecular, cellular, and systems pharmacology that prepares students for productive careers in biomedical research and teaching. The program accepts outstanding college graduates as well as physicians and veterinarians seeking advanced training in pharmacology.
The establishment of the Neuroscience Center at Dartmouth (NCD) in 2002 has produced a new and unique interdisciplinary group whose mission is to foster collaborative and interactive research and education in the neurosciences. Training opportunities in neuroscience include undergraduate minor/major in Neuroscience, graduate training toward a Ph.D., and postdoctoral training. The NCD draws from the strengths in three key areas: Clinical, Cognitive & Behavioral, and Molecular/Cellular/Systems Neuroscience. It is the vision of its researchers to produce and disseminate new knowledge, and in doing so train and educate the next generation of neuroscientists. Interactions among members of the neuroscience community are enhanced and foster a highly interactive atmosphere through the development of this integrated Center. By promoting multidisciplinary efforts in both basic and applied research, the Center''s scientists will contribute to human health and well being by increasing our understanding of the mechanisms underlying nervous system function, both in health and disease. This will lead to valuable discoveries that translate into novel pharmaceutical agents and therapeutic approaches for the treatment of a variety of central nervous system diseases and disorders. The research facilities are located in Hanover, NH, Lebanon, NH (Dartmouth-Hitchcock Medical Center) and the Veteran Affairs Medical Center in White River Junction, Vt. Research interests comprise a broad range of studies within the neurosciences and provide a wide range of research opportunities for students. In addition, the NCD augments the education of residents and fellow at the clinical level who have academic neuroscience interests.
Queens University at Kingston Department of Pharmacology and Toxicology Graduate Program
This program is now part of the new interdisciplinary program of Biomedical and Molecular Sciences.
Florida State University Program in Neuroscience
The Program in Neuroscience is an independent research and graduate training program at Florida State University, which is a Carnegie Research I university. The Program includes faculty from the departments of Biological Science, Biomedical Science, Mathematics, and Psychology. Its objective is to promote interdisciplinary basic research into neural processes, including the biological mechanisms underlying behavior, and to provide advanced graduate training leading to the Ph.D. degree in Neuroscience. The program maintains specialized research support services and personnel, and provides special courses and symposia on contemporary neuroscience issues. Each semester the program brings to Florida State prominent neuroscientists who give colloquia and hold informal discussions with graduate students and faculty. Neuroscience, the study of brain and nervous system function, encompasses many of the unanswered questions about the nature of humans and other species. It stakes out a territory along the frontier of human knowledge where research can make a real difference to understanding. Traditionally, the primary emphasis of the FSU program has been on sensory processes. This focus is now supplemented by research and instruction in the biophysics and electrophysiology of excitable cells, neurotransmitter and hormone action, neural development and plasticity, circadian rhythms, feeding and regulatory processes, and the genetic bases of neurobiology and behavior. Broad interdisciplinary training is emphasized in the early years so that students develop skills in approaching research problems with multiple levels of analysis, from molecular to behavioral.
Harvard Medical School Division of Medical Sciences
The Division of Medical Sciences was established at Harvard University in 1908. The Division was designed to provide students wishing to pursue careers in research and teaching with a broad education in basic biomedical science fields and specialization in one of them. Classroom and laboratory instruction are conducted primarily by the 450 faculty members of the basic sciences departments and affiliated hospital laboratories of the Harvard Medical School (HMS) in Boston. The Ph.D. degree is awarded by the Graduate School of Arts and Sciences (GSAS) of Harvard University. For 100 years, this fruitful collaboration has spawned research achievements across the spectrum from basic science to experimental medicine. Since 1909, over 2,000 Division graduates, including six Nobel Laureates, have gone on to distinguished careers in biomedical research, university teaching, and a number of increasingly diverse careers.
peakrots - Optimized procedure for ChIP-seq peak detection
Bioinformatics analysis software tool for optimized ChIP-seq peak detection written in R.
Howard University Washington D.C Department of Pharmacology
Howard University; College of Medicine; Department of Pharmacology
The Department of Pharmacology offers programs leading to the Master of Science and Doctor of Philosophy degrees. The primary objective of these programs is to prepare candidates for research and teaching careers. The first few semesters are devoted primarily to core course work designed to give the student a broad background in the fundamental theories and techniques of pharmacology.During this time, the student gains exposure to methods for the solution of research problems by working in the laboratories of various faculty members culminating in a selection of a thesis advisor. The department has spacious laboratories equipped with modern instruments that are used by both faculty and students in such research areas as biochemical, molecular, cardiovascular, autonomic, clinical, and neuropharmacology, drug metabolism, cancer research and toxicology.
Johns Hopkins University; Department of Neuroscience
Solomon H. Snyder Department of Neuroscience at Johns Hopkins University
The Neuroscience Training Program at The Johns Hopkins University School of Medicine addresses the broad areas encompassed by modern neuroscience. The purpose of the Program is to train doctoral students for independent research and teaching in neuroscience. It is the goal of the Program to ensure that candidates for the Ph.D. and M.D./Ph.D. degrees obtain a background covering molecular/cellular and systems/cognitive approaches to neuroscience, as well as receive training that brings them to the forefront of research in their particular area of interest. A series of core courses in neuroscience, along with advanced electives, seminar series, laboratory rotations and original independent dissertation research form the Neuroscience Graduate Training Program. The Neuroscience Training Program and the Neuroscience Department are among the oldest in the United States and date back to 1980. The faculty of the Neuroscience Training Program have trained about 250 Ph.D. and M.D./Ph.D. students and 500 postdoctoral fellows over the past ten years. All doctoral candidates receive full tuition remission and a stipend. Research within the department ranges from investigating the development of the nervous system, synaptic plasticity and the molecular and cellular mechanisms of learning and memory to the neural basis of higher brain function such as perception and decision-making. Our faculty are also at the forefront of research into the molecular mechanisms of neurological and psychiatric diseases, including Parkinson''s, Alzheimer''s'' disease, amyotrophic lateral sclerosis (ALS), schizophrenia, depression, drug addiction, mental retardation and autism.
Karolinska Institute Department of Clinical Neuroscience
Karolinska Institutet Department of Clinical Neuroscience
Karolinska Institutet; Department of Clinical Neuroscience
Department of Clinical Neuroscience at Karolinska Institutet conducts research and teaching regarding the function of the brain - from a molecular level to the effect on society. This activity is closely integrated with medical clinics within Stockholm.
Software program for drawing genetic maps (entry from Genetic Analysis Software)
Kent State University Department of Neuroscience
Kent State University; School of Biomedical Sciences; Neuroscience Program
Neuroscience is dedicated to understanding how the brain and nervous system function in health, disease and repair. Neuroscience research at Kent State University is supported by over 50 faculty members from numerous departments and disciplines. Our researchers have a wide range of expertise including behavioral neuroscience, sensory neuroscience, developmental neuroscience and neurodegenerative diseases.
University of Houston College of Pharmacy
University of Houston College of Pharmacy Bachelor of Science in the Pharmaceutical Sciences (B.S.PS) is a four-year undergraduate degree program for students interested in pursuing health-related careers. The purpose of the B.S.PS program is to provide undergraduate students with educational experiences and training in the pharmaceutical and related health sciences. The pharmaceutical sciences include medicinal chemistry, pharmaceutics, pharmacology, toxicology, health administration and pharmacokinetics. This program will also prepare students for professional and advanced degrees in healthcare.
Marshall University Medical Center Marshall Neuroscience
Marshall University JCESOM Department of Neuroscience
Purpose of Neuroscience department is to treat diseases of central and peripheral nervous systems and their supporting elements including skull and spine, as single system, utilizing expertise of variety of specialists, closely interacting with one another professionally with regard primarily for care of individual patient and their particular situation.Neuroscience department is committed to teaching and research in the fields of neurology and neruosurgery. Residents and medical students are welcome to rotate with us, or to join us for any of our scheduled lectures and conferences.
Mayo Graduate School; Neurobiology of Disease
A graduate training program that offers an M.D.-Ph.D. Program.
McGill University Department of Pharmacology and Therapeutics
McGill Dept. of Pharmacology and Therapeutics
Mcgill University Faculty of Medicine; Department of Pharmacology and Therapeutics
Mcgill University; Department of Pharmacology and Therapeutics
Department focuses on basic molecular interactions between drug molecules and target proteins that will lead to the discovery of more selective and effective therapeutic approaches for managing disease. Our research mission is to discover new biomedical knowledge and to apply basic science insights to translate studies that decipher mechanisms of diseases or discover novel diagnostic/therapeutic targets into improved health care. Our degree programs in pharmacology provide a solid foundation in biomedical sciences and prepare individuals for a wide range of career options in universities, hospitals, pharmaceutical and biotech industries, private and public research organizations, consulting companies, and government agencies.
Medical University of South Carolina Department of Cell and Molecular Pharmacology and Experimental Therapeutics
MUSC Department of Cell and Molecular Pharmacology
MUSC Department of Cell and Molecular Pharmacology and Experimental Therapeutics
There are tremendous opportunities for students and postdoctoral fellows interested in joining our department. Faculty members in our Department have new or renovated laboratory facilities, with access to core facilities that can serve as functional drivers for trainee research projects. The Department has major foci in redox and cell signaling (facilitated by an NIGMS funded COBRE grant; see the link to the COBRE program within the department website), proteomics and mass spectrometry (with an MUSC supported core facility) and mass spectrometry based imaging. Moreover, MUSC has committed to supporting a drug discovery program, which provides opportunities for early stage discovery and development of new drug entities. Present faculty research interests encompass new drug discovery/development, cancer therapeutics, cell signaling and stress responses, redox pathways, G protein signaling in aging and neurological disorders, kinase signaling, epigenetics and cancer, ALS and associated neurological pathologies, proteomics and mass spectrometry based imaging.
Mount Sinai School of Medicine Department of Neuroscience
The Mount Sinai Department of Neuroscience comprises the Fishberg Department of Neuroscience and the Kastor Neurobiology of Aging Laboratories. The department is dedicated to performing groundbreaking research, mentoring tomorrow''s investigators, and providing a critical basic science component of neuroscience education at Mount Sinai School of Medicine. Our department ranks fourth in the United States in National Institutes of Health funding. Department faculty conduct a major portion of the multidisciplinary training in neurosciences for the Graduate School of Biological Sciences. This program represents one of eight training areas that make up the PhD program and the PhD component of the MD/PhD program. Additionally, we collaborate with other academic departments to deliver comprehensive medical education through such initiatives as joint seminars, instruction at the residency level, and postdoctoral fellowships. The Department of Neuroscience investigates the nervous system at the molecular, cellular, systems, and behavioral levels. We are engaged in several translational research projects directed at the pathology of the nervous system as well as the molecular and cellular mechanisms of neuronal dysfunction. Our multidisciplinary collaborations with the Departments of Geriatrics and Adult Development, Psychiatry, and Neurology focus on the mechanisms of aging and on psychiatric and neurologic diseases, respectively.
New York University School of Medicine Department of Neuroscience and Physiology
NYU SOM Dept. of Physiology and Neuroscience
In affiliation with NYU Langone Health’s Neuroscience Institute, the Department of Neuroscience and Physiology is home to an interdisciplinary team of scientists working to enhance our knowledge of fundamental and emerging principles of neuroscience. By bringing together investigators from basic research, translational, and clinical laboratories, we facilitate partnerships that lead to innovative research projects.
Ohio State University Department of Neurology
Ohio State University Department of Neurology is enjoying tremendous growth. As a program prioritized by the university, we are well on our way to doubling our faculty, and we continue to expand an innovative and rigorous research portfolio. Dedicated to multidisciplinary collaboration, our goal is to accurately diagnose, treat and improve the lives of individuals with neurological diseases, while increasing our understanding of the causes of neurological disease and discovering more effective treatments. An equally important mission is to educate and foster the careers of the next generation of neurologists and translational neuroscientists.
Pomona College Department of Neuroscience
Provides opportunity to learn fundamentals of neuroscience, perform experimental techniques in state-of-the-art teaching laboratories, and discover how neuroscience provides insight into other liberal arts disciplines, including psychology, economics, computer science and philosophy. Areas of neuroscience include:cell and molecular neuroscience;systems-level neuroscience;nervous system disorders such as anxiety and depression;neuroscientific models of social behavior and interaction;and imaging the mind at work.Majors have the opportunity to assist faculty in research or conduct their own project through the Summer Undergraduate Research Program.
Purdue University School of Pharmacy and Pharmaceutical Sciences Department of Medicinal Chemistry and Molecular Pharmacology
The Department of Medicinal Chemistry and Molecular Pharmacology is one of the three departments comprising the School of Pharmacy and Pharmaceutical Sciences. There are currently over 80 graduate students enrolled in the Department, the vast majority of whom are engaged in studies leading to the Ph.D. degree. The presence of approximately 30 postdoctoral associates and other research staff professionals further enriches the intellectual atmosphere. Graduate students in the Department have the opportunity to interact with researchers in a wide variety of fields, including many who are associated with other departments at Purdue. Various research groups actively collaborate with groups from departments such as biochemistry, biological sciences, chemical engineering, chemistry, foods and nutrition, horticulture, and physics. In addition, approximately half of our faculty belong to the Purdue Cancer Center, the Neuroscience Program, the Graduate Program in Virology and/or the Purdue University Biochemistry and Molecular Biology Program (BMB), leading to extensive, formalized interactions campus-wide. Graduate students attend research seminars across campus, -affording the opportunity to observe firsthand many of the world's foremost researchers.
University of Massachusetts Amherst Department of Neuroscience and Behavior
Neuroscience and Behavior Program is an independent, graduate degree-granting academic unit that brings together faculty members from a number of different departments and colleges to provide cutting-edge interdisciplinary research training in Neuroscience and Behavior. Graduate students are recruited and admitted directly into the NSB Program and not through the home departments of participating faculty members, as is the case at many institutions.
Rutgers University Robert Wood Johnson Medical School Department of Pharmacology
Department of Pharmacology is committed to fulfilling its roles in education, research and service, both locally and on a broader scale. Our faculty contributes to the education of medical, graduate and undergraduate students in the classroom and in the laboratory; carries out research at the forefront of biomedical science while training the next generation of research scientists; and serves the medical school, university, national and international scientific communities.
An algorithm to identify transcription factor binding sites from ChIP-seq data.
Rutgers University Integrative Neuroscience Graduate Program
Neuroscience program offers a multidisciplinary curriculum and research opportunities to provide students with a comprehensive understanding of the basic tenets and underpinnings of this modern discipline. Emphasis is placed on early entrance into research laboratories, seminar programs and journal clubs. Students have the opportunity to experience the breadth of Neuroscience -- from Cellular and Molecular approaches to Translational and Clinical Neuroscience. Advanced students also have opportunity to assist in teaching Graduate and Medical students. The goal of the Graduate Program in Neuroscience is to couple broad educational opportunities with intense laboratory experiences so our graduates are prepared to excel as research scientists, academicians, and educators.
South Dakota State University College of Pharmacy, Department of Pharmaceutical Sciences
The Department of Pharmaceutical Sciences offers courses and research opportunities in pharmaceutical and biomedical sciences to fulfill the requirements for the Doctor of Philosophy (PhD) degree in Pharmaceutical Sciences. The Department also offers a curriculum and research opportunity for combination of Doctor of Pharmacy (PharmD)/PhD degrees in Pharmaceutical Sciences. The core courses, along with the concentration in a major area of research, provide a valuable broad background of preparation for an academic or industrial career. The major objective of the program is to provide the student an opportunity to gain high quality graduate and research experience. A Master of Science (MS) in Biological Sciences with specialization in Pharmaceutical Sciences is also available.
University of Texas Southwestern Medical Center Neuroscience
The mission of the Department of Neuroscience at the University of Texas Southwestern Medical Center at Dallas is to advance fundamental knowledge in this field by conducting cutting edge research and by providing training to the next generation of neuroscientists. The research activities within the Department of Neuroscience focus on cellular, molecular, genetic, and developmental mechanisms underlying behavior, neural circuits and related neurological disorders. Scientists within the Department of Neuroscience participate in a vibrant, interdisciplinary, interdepartmental, and highly collaborative research community within the University.
St. Louis University Medical School Pharmacology and Physiology
The Department of Pharmacological and Physiological Science is a major participant in the current excitement involving research in modern biomedical science. The faculty in the department have diversified backgrounds in the fields of biochemistry, medicine, molecular biology, neuroscience, pharmacology and physiology. A common theme involves the physiology, pathophysiology and pharmacology of intracellular and intercellular communication. Major areas of specialization include: neurotransmitter biochemistry, physiology and pharmacology; molecular biology, biochemistry and pharmacology of neurotransmitter, autacoid, neurohumoral and hormone receptors; intracellular signaling and transduction mechanisms; electrophysiology and ion channels; neurochemistry; cardiovascular and circulatory control mechanisms; regulation and function of the autonomic, somatic and central nervous systems; molecular, cellular and endocrine control mechanisms; respiratory physiology; neuropharmacology and drugs of abuse. Modern research in pharmacological and physiological science applies the experimental methods derived from disciplines that range from clinical medicine to biophysics, biochemistry and molecular biology to provide a detailed understanding of drug action and physiological function at many different levels of inquiry.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that uses Monte Carlo method for assessing significance of a case-control association study with multi-allelic marker. (entry from Genetic Analysis Software).
Software application that uses likelihood calculation and simulation to perform parentage studies with codominant, dominant, cytoplasmic markers or combinations of the different types (entry from Genetic Analysis Software)
Stanford University School of Medicine Neurology and Neurological Sciences
The Department of Neurology and Neurological Sciences offers comprehensive evaluation and treatment of adults and children with neurological disorders. Clinical programs include general neurology, epilepsy, stroke, movement disorders, memory disorders, multiple sclerosis, neuromuscular diseases, neuro-oncology, neurophysiology, and child neurology. Their educational programs offer outstanding residency training in adult and child neurology and post-residency fellowship training in many neurological subspecialties. Many current faculty members are international leaders in their field. Included among its former trainees and faculty are many department chairs and other leaders in American neurology. The Department provides care and consultative services to patients referred from throughout California and from throughout the nation. The combination of recent and current enhanced development of clinical facilities at Stanford and its allied medical centers along with continued robust population growth in Northern California and the Bay Area provides a remarkable breadth and depth of clinical neurology experience. Research in the Department of Neurology and Neurological Sciences covers a wide range of multidisciplinary programs ranging from basic neuroscience studies, preclinical studies and clinical trials. In addition, Stanford is well known for its outstanding neuroscience community. The outstanding academic milieu at Stanford along with cutting edge programs promoting multidisciplinary research makes possible an exceptional degree of research integration that links Department faculty members and trainees with those from multiple schools and departments, each with major national stature, across the Stanford campus. The Department has a particularly rich tradition of integrating cutting edge advances in basic science with novel clinical approaches.
SUNY Stony Brook Department of Neurology Stony Brook NY
The Department of Neurology has a commitment to teaching, clinical care, and research. They include divisions of Clinical Neurophysiology (with training in EEG and EMG, including inpatient and outpatient monitoring facilities, intraoperative monitoring, and access to a sleep laboratory), Neuropsychology (both adult and pediatrics), Child Neurology (including special interest groups in Epilepsy, Developmental Disabilities, Pediatric AIDS, and Autism), and Vascular Neurology (with an accredited training program, board certified faculty, close cooperation with Vascular Surgery, Interventional Radiology, and Cardiology, and an emphasis on clinical trials and neuroimaging research). They have a very strong program in Multiple Sclerosis/Neuroimmunology (including multiple clinical trials, Neuroimaging research, the only Pediatric MS Center in the country, and a focus on gender issues in MS). They also have strong programs in Neuromuscular Disease (with a particular interest in ALS, and nerve/muscle biopsies), Neurologic Infections (with a particular interest in emerging pathogens), Parkinson's Disease, Neurorehabilitation, and Behavioral Neurology.
SUNY Stony Brook, Pharmacological Sciences
The Department ofPharmacological Sciencesat Stony Brook offers a collegial atmosphere with one of the highest ratios of postdoctoral to predoctoral researchers of any Pharmacology Department in the country. Students in Molecular and Cellular Pharmacology work alongside students from several other graduate programs at Stony Brook, including Molecular and Cellular Biology, Neurobiology, Chemistry, Genetics, Microbiology, Structural Biology, and Physiology and Biophysics. Several students in Molecular and Cellular Pharmacology have been trainees in the NIH-funded MSTP (Medical Scientist Training Program).
SUNY Upstate Medical University, Pharmacology
Research in the Department of Pharmacology focuses on three major areas: 1) cardiovascular science 2) cell signaling 3) cancer biology and therapeutics. Within those areas, research ranges from basic biological problems to those with clinical orientations. The cardiovascular science research strives to understand the normal and abnormal functioning of the heart at the molecular, cellular and organ levels, and is exceptionally strong in cardiac electrophysiology and the mechanisms of cardiac arrhythmia. The cell signaling research concerns regulation of cell function by extracellular factors, the molecular biology of signaling pathways, cell communication, and intracellular proteolysis. The cancer biology and therapeutics research is focused on molecular mechanisms regulating cell death and survival in human malignancies, development and testing of novel cancer therapeutics, novel tumor markers, oncogenic transformation and apoptosis, regulation of tumor suppressors and molecular mechanisms of leukemogensis. The Pharmacology Department has multiple research grants for the next five years. Most of the funding comes from the National Institutes of Health (NIH), with additional funding from the Association for International Cancer Research, the American Society of Hematology, the Department of Defense and the American Heart Association.
Texas A and M Health Science Center College of Medicine Department of Neuroscience and Experimental Therapeutics
The Department of Neuroscience and Experimental Therapeutics (NExT) at the Texas A&M Health Science Center College of Medicine has 16 full-time faculty members and is one of four basic science departments within the College of Medicine. Program strengths within the department include brain development, cellular/molecular basis of drug addiction, circadian biology, ocular pharmacology and experimental therapeutics, neurobiology of aging, neurodegenerative diseases such as stroke and Alzheimer''s disease, neuro-oncology and neuroteratology of alcohol, nicotine and other drugs of abuse. The Department of Neuroscience and Experimental Therapeutics participates in an interdisciplinary graduate program in the Medical Sciences that leads primarily to the Ph.D. degree with special emphasis in interdisciplinary training in Neurosciences or Pharmaceutical Sciences. The Ph.D. program in Medical Science usually requires 4-5 years to complete. Graduates from our program are prepared for leadership roles in research and teaching in academic, industrial, or governmental positions. Faculty within the department are affiliated with university-wide interdisciplinary faculties including the TAMU Faculty of Neuroscience rand our clinical science partner, the Texas Brain and Spine Institute. The department is also home to the Women''s Health in Neuroscience Program, consisting of interdisciplinary research faculty and a clinical advisory group aimed at developing a cohesive preclinical approach to the impact of puberty, pregnancy and menopause on brain development, mental health and brain disease.
Texas Tech University Department of Pharmacology and Neuroscience
Texas Tech University Department of Pharmacology Neuroscience
TTU Department of Pharmacology and Neuroscience
The Department of Pharmacology and Neuroscience at Texas Tech University is committed to providing a strong education experience for all trainees. The department's primary areas of training emphasis are neuroscience/ neuropharmacology and cardiovascular/ autonomic pharmacology.Our objective is to prepare students for careers in research and teaching. We currently have 14 faculty and who conduct research in a broad variety of subjects ranging from environmental toxicology to molecular pharmacology. This allows a broad basis for a strong theoretical as well as 'hands-on' education in pharmacology. The faculty of the program work hard to foster a creative and productive research atmosphere, to provide encouragement and positive challenges, and to equip students with the intellectual tools they will need to be good teachers and investigators.
Rosalind Franklin University of Medicine and Science, Department of Cellular and Molecular Pharmacology, North Chicago, IL
Department of Cellular and Molecular Pharmacology carries out research in areas ofphysiology, anatomy, behavioral neuroscience, biochemistry and molecular biology. It is committed to preparing students for careers in pharmacological and medical research and service. They contribute to academic teaching by providing a solid foundation in pharmacology and therapeutics for medical, podiatry and physician's assistant students and also in neuropharmacology for graduate students.
The Department of Biology includes 30 tenured or tenure-track faculty who teach and lead research programs in the biological sciences. Research and teaching expertise/interests include Biochemistry, Cellular and molecular biology, Developmental biology, Ecology, Immunology, Microbiology, Neurobiology, Physiology, Plant hormones and gene expression, Virology.
UTHealth at Houston Neuroscience Research Center
University of Texas Health Science Center at Houston Neuroscience Research Center
The Neuroscience Research Center (NRC) is a university-wide center where diverse and multidisciplinary research is conducted to further the understanding of neural and behavioral disorders. Whether conducting cellular research in laboratories or clinical trials in patient care settings, the work of NRC researchers may someday contribute to preventing and treating such devastating disorders as: * Dementias resulting from Alzheimer''s disease and stroke * Mental retardation and other learning disabilities * Mental illnesses, including schizophrenia and manic-depressive illness * Alcoholism and other substance abuse problems * Inability to process knowledge due to factors such as aging and head trauma * Disabilities due to disorders of the developing nervous system More than 280 faculty hold NRC appointments, and are on the faculties of the Medical School, School of Public Health, School of Nursing, Dental Branch, and School of Biomedical Informatics. Departments with significant NRC research activities within the Medical School include Neurobiology and Anatomy; Neurology; Neurosurgery; Ophthalmology and Visual Science; Psychiatry and Behavioral Sciences and Radiology. NRC activities are guided by an executive committee appointed by the President of the Health Science Center. The Neuroscience Research Center (NRC) is affiliated with educational opportunities at the graduate and postdoctoral levels.
University of Toledo Department of Neurosciences
The Department of Neurosciences at the University of Toledo Health Sciences Campus is highly committed to advancing the state of knowledge of nervous system structure and function through a tripartite mission of innovative research, state-of-the-art teaching methods, and dedicated service to the broader academic and surrounding communities.
The Department of Neurology at Jefferson Medical College has a long tradition of excellence in clinical training and care. They are committed to providing an active and exciting research program, exemplified by the Farber Institute for the Neurosciences, established in the spring of 2002. Consolidation of our academic and research base with the neurology ambulatory care facility at the new Jefferson Hospital for the Neurosciences underscores the continuing evolution of the Neurology department, and of its many functions, including, our fully approved residency program.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A web application and database schema for storing and interactively displaying genetic map data.
Trinity College, Department of Neuroscience
Neuroscience at Trinity involves faculty from the Departments of Biology, Chemistry, Engineering, Philosophy, and Psychology. The major is designed to give students a fundamental grounding in the sciences, and the flexibility to direct their studies towards biological, behavioral, and cognitive aspects of neuroscience. A major in Neuroscience can lead to a career in scientific research, the health professions, education, business, law, or government. Neuroscience is a broad, multidisciplinary field concerned with the nervous system, its components, and functional activities, including behavior and consciousness. How do nerve cells function and develop, and how do they communicate? How do brains work, and how have they evolved? What is the nature of consciousness, and the neural basis for behaviors and for human brain dysfunction? These are among the many questions being answered by contemporary neuroscience.
Tufts University Department of Neuroscience
The Graduate Program in Neuroscience at Tufts University School of Medicine is a member of the Sackler School Integrated Studies Program (ISP). The research programs of the 20 faculty members incorporate a broad range of approaches - from molecular to systems analysis - to understand the form and function of the nervous system, with a particular emphasis on the synapse. The graduate course of study, likewise, strongly emphasizes multidisciplinary training to prepare students for research careers in the complex field of neuroscience. Such training is additionally promoted through the technical expertise and research facilities offered by the Tufts Center for Neuroscience Research (CNR).It is based in newly renovated space in the Neuroscience Department, occupying three floors of the Tufts Medical School research complex in downtown Boston.
Tulane University Medical Center Department of Pharmacology
Department to educate and train medical and graduate students in principles of pharmacology using modern techniques and to conduct state of art research in pharmacology related fields in order to expand frontiers of science and medicine.
The Department of Neurobiology offers students interested in the nervous system a program of study that leads to the Ph.D. in Neurobiology or a combined M.D./Ph.D. through The University of Alabama School of Medicine located at UAB. The graduate program has numerous faculty members with active research programs from a broad range of areas in contemporary neuroscience with a major focus on topics of biomedical importance. Molecular, cellular and biophysical approaches are emphasized to address fundamental problems of brain function, development and disease. All students take a series of graduate courses in biochemistry and molecular biology, cell biology, ion channel biophysics, synaptic function, developmental neurobiology and medical neurobiology. Evidence of the faculty's national and international impact in fundamental Neuroscience research includes: their substantial number of publications in high impact journals; appointments to editorial boards and editorships of leading neuroscience journals; appointments to NIH and NSF study sections and review boards; awards of over 28 million dollars in annual research grant funds; and numerous invitations to speak at national and international research symposia. Faculty members also have received numerous national and international awards recognizing excellence in research and training.
University of Arizona Graduate Interdisciplinary Program in Neuroscience
The University of Arizona offers a Ph.D. through the Graduate Interdisciplinary Program in Neuroscience. The Program, administered by the Committee on Neuroscience, is designed to provide students with the knowledge and tools that they will need to embark on careers as educators and researchers in the field of neuroscience. Students participate in designing their own individually tailored programs that provide a thorough base of knowledge in the many facets of neuroscience as well as depth in chosen areas of specialization, and that enhance their abilities to think creatively and express themselves clearly. Because of the breadth of expertise represented by the faculty, students have access to educational and research training opportunities in areas ranging through molecular, cellular, systems, behavioral, cognitive, theoretical, and clinical neuroscience. The program currently enrolls 27 students.
Software application that identifies likely genotyping errors and mutations for a sib pair in the context of multipoint mapping. (entry from Genetic Analysis Software)
University of Arkansas for Medical Sciences Department of Pharmacology and Toxicology
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 25,2022. Department of Pharmacology and Toxicology is the professional home to 18 faculty, 11 research faculty, 22 graduate students and 3 postdoctoral fellows. They offer graduate training leading to the Ph.D. degree in Pharmacology or Interdisciplinary Toxicology. Their faculty also participate in the Interdisciplinary Biological Sciences (IBS) training programs. Trainees receive a broad-based education to prepare for a career in translational research. An emphasis on therapeutic development, identification of drug targets and mechanisms of organ injury prepare our trainees for a career in drug discovery and medical toxicology. All of our students currently receive a $24,000 yearly stipend and we pay tuition! Their 'magnet areas' for research include behavioral and drug abuse pharmacology, drug discovery and antibody therapeutics, mechanisms and therapies of organ toxicology and neurodegenerative diseases, and CNS and vascular ion channels. Extramural research funding obtained by the faculty has increased to more than 5 million annually, and the Department ranks in the top quarter of all medical school pharmacology departments in the country in NIH funding.
University of California Santa Cruz, Department of Molecular, Cell and Developmental Biology
The Department of Molecular, Cell & Developmental Biology (MCD), with 20 faculty members, focuses on fundamental problems in the molecular, cell and developmental biology of animals and plants. The scope of research conducted in this group spans the broad range of modern biological research; from classical and molecular genetics to biochemistry and molecular biology. Research laboratories in the MCD Biology Department use both simple model organisms and vertebrate systems to study important biological processes, ranging from the mechanism of protein synthesis to the development and function of the nervous system.
University of California, Berkeley, Neuroscience Graduate Program
The Neuroscience Graduate Program at UC Berkeley is a unique, diverse Ph.D. training program that offers intensive, integrated training in multiple areas of neuroscience research. The program involves more than 50 faculty from different campus departments, with expertise ranging from molecular and cellular neuroscience, to developmental neuroscience, systems and computational neuroscience, and human cognitive neuroscience. They provide a highly interdisciplinary, intellectually dynamic training environment of coursework, research training, and mentoring, within a strong research program that produces fundamental advances in knowledge and cutting-edge techniques. They welcome highly qualified applicants to join us in better understanding the brain and its functions and disorders.
University of California, Los Angeles, Department of Molecular and Medical Pharmacolog
The Department of Molecular and Medical Pharmacology offers an opportunity for gifted students, basic and clinical scientists to fulfill a vision of exploring the molecular and biological mechanisms that regulate cellular and organ functions, of identifying and understanding the molecular errors of disease, and of developing the pharmacological means to correct these errors. Remarkable scientific discoveries and astonishing technological innovations are occurring as biological, physical, engineering and clinical sciences come together to explore both the mechanisms by which cells are programmed from the genome to construct protein based cell circuits and the functions they perform, as well as the inter-cellular networks that form organ systems and the whole organism. This combination of new perspectives, new technologies and new scientific discoveries is having a tremendous impact on the way we think about and perform science today, and will have an even greater impact on biology and medicine in the future.
University of California, Riverside, Department of Cell Biology and Neuroscience
Research in the Department of Cell Biology and Neuroscience uses multidisciplinary approaches to understanding basic cellular processes in various tissues, including the nervous system, as well as more integrative levels of analysis, including behavior. Areas of research represented in the department include biophysical properties of excitable membranes, DNA repair, transcriptional regulation, mechanisms of toxicity, insect development, membrane transport, mechanisms of mitotic chromosome transmission, telomere maintenance, synaptic structure and function, changes in nervous system with experience, interactions of nervous and endocrine systems, reproductive biology and fertilization, chemokine function in wound healing and tumor development, glia-neuron signaling, & brainstem and spinal cord control of locomotion.
University of Maryland, College Park, MD, Department of Neuroscience and Cognitive Sciences
The Program in Neuroscience and Cognitive Science at the University of Maryland offers research and training opportunities in neuroscience, cognitive neuroscience and computational neuroscience with internationally-renowned faculty who interact among three campuses: in Baltimore City, at Baltimore County and at College Park. Each campus offers graduate training leading to a Ph.D. degree.
University of Iowa College of Medicine Department of Pharmacology
UI College of Medicine Department of Pharmacology
The Department of Pharmacology is one of five basic science departments in the Roy J. and Lucille A. Carver College of Medicine at The University of Iowa. The Department currently consists of 25 faculty members, holding either primary or joint appointments in Pharmacology, many of whom are nationally and internationally recognized for their research. The Department occupies almost 32,000 square feet of newly renovated space in the Bowen Science Building, a component of the Health Sciences Complex on the west bank of the Iowa River. Departmental laboratories are well-equipped for the pursuit of research, and our faculty members use a wide variety of experimental methodologies to address contemporary issues in cellular and molecular pharmacology.
University of California, San Diego, Department of Pharmacology
The Department of Pharmacology is renowned for its strength in elucidating basic cellular and molecular mechanisms of signal transduction that lead to drug target identification and ultimately to drug discovery. Many of the department's research efforts impact directly on human health, supported by NIH grants on hypertension, cardiovascular regulation, cancer, and neurological and inflammatory diseases. The department's research directions include computational and molecular science, catalyzed by the department's close affiliation with the San Diego Supercomputer Center, and structure guided drug design and bioinformatics. Cross campus efforts in environmental health sciences and pharmacogenomics have been launched through major NIH funded project grants. Appointments of adjunct faculty from the local biotechnology and pharmaceutical industry create a natural bond for cross fertilization and communication, bridging the department's basic science efforts, and enhances endeavors in drug discovery.
University of California, Santa Barbara, Pharmacology Undergraduate Program
UCSB's Pharmacology major is designed for students with research interests in all areas of the health sciences and is not related to pharmacy training. Students planning to major in pharmacology enter as a biological sciences premajor and take a common core curriculum of introductory biology, general chemistry, mathematics, physics, and organic chemistry. Students should complete this preparatory coursework in their freshman and sophomore years. Following successful completion of seven of these courses, students may advance from biology premajor to full major status. The pharmacology major requires completion of upper division coursework in biochemistry, pharmacology, molecular biology, and genetics. Students round out their degree by selecting electives in molecular and cellular biology, neurobiology, biochemical pharmacology, physiology and developmental biology. Students should review the full requirement sheet for the major they intend to declare and plan their schedules accordingly.
University of Chicago Department of Neuroscience
The Integrative Neuroscience graduate program at the University of Chicago is designed to provide the training and research opportunities for the next generation of behavioral, cognitive, and social neuroscientists. Behavioral, cognitive, and social neuroscience represent three complementary and partially overlapping aspects of this integrative neuroscience of mind and behavior. Behavioral neuroscience places an emphasis on the biological mechanisms underlying basic behavioral processes; cognitive neuroscience places an emphasis on the biological mechanisms underlying cognition, with a specific focus on the neural substrates of mental processes and their behavioral manifestations; and social neuroscience places an emphasis on the biological mechanisms underlying social processes and behavior, including the ability to perceive and communicate mental states including the beliefs and desires of others and to form and maintain interpersonal and group relationships. The University of Chicago is optimally positioned to meet this challenge because its unique academic structure facilitates interactions across disciplinary perspectives.
University of Cincinnati, Neuroscience Graduate Program
The Graduate Program in Neuroscience at the University of Cincinnati was established in 1988 as an interdisciplinary program offering the Ph.D. degree. More than 80 faculty members from 22 departments the Colleges of Medicine, Pharmacy, the Arts and Sciences are members of the Neuroscience Program. Research interests of the faculty are diverse and reflect a variety of state of the art approaches toward understanding the brain. Many faculty have research programs with a clinical focus on brain diseases such as stroke, Alzheimer's Disease, brain tumors, substance abuse, schizophrenia, bipolar disorder and obesity.
University of Houston, Department of Psychology
The Department of Psychology bring the best of psychological theory, techniques and research methods to the solution of real world problems. Their goal is to solve important human problems and to use these problems as critical vehicles for dynamic teaching and the enhancement of psychological theory and practice. A major objective of our teaching is to empower our students to use psychological knowledge for the solution of scientific, social and business problems.
University of Kansas Medical Center Pharmacology
The Department of Pharmacology, Toxicology and Therapeutics at the University of Kansas Medical Center have faculty with diverse research interests. These three areas are essential for the development of new drugs and to determine the safety of all chemicals. Thus, students obtain a broad educational background in our department, which markedly increases their opportunities for employment. During the last three years, the Department has undergone a marked expansion. Seven new faculty have been hired. In addition, a number of new pieces of scientific equipment have been purchased: HPLC-MS/MS, nucleotide sequencer, robot, etc. In September of 2006 we plan to move into a new research building, as shown in the architects drawing. We also plan to hire six additional faculty the next three years. Thus, this department is an exciting place to be.
University of Kentucky Medical Center College of Pharmacy
The University of Kentucky College of Pharmacy is one of the top 5 pharmacy schools in the nation and continues to be a leader in pharmacy education, clinical care and pharmaceutical research. For more than a century, the College has attracted the best and brightest students from the Commonwealth, the United States and the world to train as pharmacists, pharmaceutical scientists and leaders in academia, health care, and industry.
University of Louisville, Department of Pharmacology
The Department of Pharmacology & Toxicology in the School of Medicine at the University of Louisville focuses upon the interaction of drugs and other chemicals with biological systems ranging from individual molecules, to cells, to tissues, to organ systems or individuals. The two disciplines are a continuum incorporating the therapeutic to toxic effect of every drug and chemical. Our departmental programs incorporate pharmacology and/or toxicology, and graduates are well trained to accept employment in either or both disciplines. Our research and curriculum incorporate molecular biology, genetics, neuroscience, biochemistry, physiology and other biomedical sciences, providing maximum flexibility for our graduates.
University of Manitoba, Faculty of Medicine, Department of Pharmacology
The Department of Pharmacology and Therapeutics at the University of Manitoba consists of 15 full time faculty, 21 joint faculty, and 1 senior scholar, with research interests including cardiovascular pharmacology, clinical pharmacology, hepatic pharmacology, neuropharmacology, and renal pharmacology, teaching in Medicine and Pharmacy, and offering courses of study leading to M.Sc. and Ph.D. degrees in Pharmacology. It is a modern well equipped facility with a thriving graduate program, based on the 2nd, 3rd, and 4th floors of the Chown Building on the Bannatyne Campus next to the Health Science Centre and at the Division of Neurodegenerative Disorders at St. Boniface General Hospital Research Centre in Winnipeg, Manitoba Canada.
University of Maryland Dental School, Organized Research Center on Persistant Pain
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 25,2022. Research unit in the University of Maryland School of Dentistry specializing in neural pain. The program includes a major Program Project on Plasticity and Modulation in Models of Persistent Pain and the University of Maryland, Baltimore Research Center for Neuroendocrine Influences on Pain.
University of Maryland School of Pharmacy, Pharmaceutical Sciences Graduate Program
The School of Pharmacys Department of Pharmaceutical Sciences has a rapidly expanding research program in the areas of cellular and molecular biology, chemistry, neuroscience and pharmacology, biopharmaceutics and drug delivery and clinical pharmaceutical sciences. Faculty and graduate students in the Department of Pharmaceutical Sciences are organized into Research Areas. The mission of the graduate program is to foster individual and collaborative research, faculty growth, and a graduate student education which provides a strong, broad background in the drug development process along with intensive expertise in a focal research area of the pharmaceutical sciences. The department also provides opportunities to conduct research in the area of Clinical Pharmaceutical Sciences. This is one of only 4 such programmatic themes of its kind in the U.S. This program is a collaborative effort between the departments of Pharmacy Practice and Science and Pharmaceutical Sciences in the School of Pharmacy. The clinical pharmaceutical research scientists trained by this program will be well-suited to meet the demand expressed by federal agencies (FDA, NIH), academia, and the pharmaceutical industry, with the potential to develop new therapeutic strategies to optimize patient care in Maryland, the U.S., and worldwide.
Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software)
University of Medicine and Dentistry of New Jersey Neuroscience Graduate Program
The Graduate Program in Neuroscience is committed to educating and training outstanding young scientists in the multidisciplinary concepts and contemporary techniques at the heart of modern Neuroscience. Students selected for this program generally have had exceptional undergraduate training in the physical, biological and social sciences. It offers students an outstanding opportunity for graduate training in a rapidly growing joint program of the Graduate School of Rutgers University and the Graduate School of Biomedical Sciences of the University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, both located in Piscataway/New Brunswick, New Jersey. A major goal of the Graduate Program in Neuroscience is to prepare students-in the classroom and in active research laboratories-for careers of independent research in universities, medical schools, governmental facilities and industry.
University of Minnesota Graduate Program in Neuroscience
The graduate program in neuroscience at the University of Minnesota is a large, multidisciplinary program consisting of over 100 faculty members from all parts of the University of Minnesota, over 25 departments from over 10 colleges. The multidisciplinary nature of the Ph.D. program is one of its most significant strengths.
University of Mississippi Department of Pharmacology
Department of Pharmacology reflect a flexible, research-oriented program designed to develop the interests, capabilities and potential of all participating students. Graduate students in this department have received B.S./B.A. degrees usually in biochemistry, biology, chemistry, psychology, toxicology, pharmacy, or related disciplines. The department is committed to maintaining an ethnic and gender-balanced student body. Furthermore, the faculty-student ratio is suitable to permit a maximum of personal and informal contact among members of the department and collaborating faculty, and the individual student. Course work and seminars are arranged to provide the student with a diversified background in the theories and techniques of contemporary research.
University of Missouri Department of Medical Pharmacology and Physiology
The Department of Medical Pharmacology and Physiology has been known for outstanding programs in exercise physiology and cardiovascular physiology. The Department offers both Master of Science (MS) and Doctor of Philosophy (PhD) degree programs that provide students with excellent preparation for a variety of challenging and rewarding careers. The degrees offered are programs in Pharmacology or Physiology. The Medical Pharmacology and Physiology Department and its modern research and teaching facilities are on campus in the School of Medicine. The research laboratories of the faculty have excellent equipment and maintenance support. The award-winning Health Sciences Library, containing a wide variety of current journals and resource books, is located in the School of Medicine. Modern student computer stations are also available. Animal quarters and animal care are under the direction of qualified veterinarians. Other important University facilities include a nuclear reactor for providing short-lived radioisotopes and a campus-wide computer network. The Center for Gender Physiology manages four core facilities that provide animal models, equipment and expertise required to explore gender differences in physiological function.
University of Nevada Reno Department of Pharmacology
Department is located within the Medical School at the north end of the University of Nevada, Reno campus which is in the foothills of the eastern Sierra. The Department is committed to excellence in both teaching and research. Major topics of research within the Pharmacology Department include: Cardiac and Smooth Muscle Electrophysiology, Biophysics and Molecular Biology of Ion Channels, Biochemistry and Biophysics of Skeletal and Cardiac Muscle Cells, Cellular and Molecular Neuropharmacology, Vascular Wall Cell Biology, Cell Physiology and Molecular Biology of Smooth Muscle Contraction and Motility.
University of New Mexico Sleep Disorders Clinic
University of New Mexico Health Sciences Center Program in Sleep Medicine Sleep Disorders Center was established in 1983 and was the first nationally accredited sleep disorders center in the State of New Mexico receiving accreditation in March of 1992 from the American Academy of Sleep Medicine. They provide comprehensive services to individuals having symptoms occurring during sleep or while awake due to unrefreshing sleep. The Program combines a state-of-the-art outpatient sleep laboratory, inpatient sleep laboratory, sleep medicine clinic, and trained medical and technical staff dedicated to the diagnosis and treatment of sleep/wake disorders in adults and children. The University of New Mexico Health Sciences Center Program in Sleep Medicine has the distinction of having a first and many onlys attached to it. The criteria for accreditation is very stringent and to date, there is only one other accredited center in the entire state. The Center is also accredited by the Joint Commission on the Accreditation of Health Care Organizations.
University of North Carolina Department of Pharmacology
Department of Pharmacology is to educate and train scientists and physicians in the discipline of pharmacology, to make discoveries in research that are relevant to medicine and the basic mechanisms underlying the causes of human disease, to work with other scientists and physicians in interdisciplinary approach to translate basic discovery into new treatments and cures of human disease.
University of North Dakota Department of Clinical Neuroscience
Multidisciplinary department which includes psychiatry-behavioral science, neurology, neurosurgery, neuropharmacology, and neuroradiology. Department philosophy is based on a comprehensive, integrated biopsychosocial model of brain functioning (mind, brain and behavior) in health and illness. The department provides undergraduate training in behavioral science, neuroscience, psychiatry, neurology and neurosurgery and operates a fully accredited psychiatry residency training program in Fargo.
University of North Dakota Department of Pharmacology Physiology and Therapeutics
Department of Pharmacology, Physiology and Therapeutics at the University of North Dakota School of Medicine and Health Sciences is strongly committed to providing their students and the people of North Dakota excellent programs in education, research and service and they are dedicated to the development of leadership, innovation, and scholarly excellence. The translation of fundamental knowledge in the basic sciences to medically relevant problems is a major goal of the department and they are capable of providing the individualized attention and training necessary for the development of the medical scientist of the future.
University of Oklahoma Health Sciences Center College of Pharmacy
University of Oklahoma Health Sciences Center College of Pharmacy Graduate Programs
Department of Graduate Pharmaceutical Sciences offers programs leading to the Master of Science (M.S.) and Doctor of Philosophy (Ph.D.) degrees. These programs are designed to prepare scientists, educators, and practitioners for careers in pharmaceutical education, research, industry, and related areas of pharmacy practice. The graduate programs do not prepare students for practice as a registered pharmacist, so applicants who are interested in a pharmacy career should apply to the Doctor of Pharmacy (Pharm.D.) program. However, students who have already completed one year in the Pharm.D. program may apply to the dual degree, Pharm.D./M.S. program and study concurrently for a graduate degree.
University of Pennsylvania Medical Center Pharmacology
Department of Systems Pharmacology and Translational Therapeutics at the University of Pennsylvania
Pharmacology involves the discovery of new drugs, the investigation of how drugs work and the use of drugs to probe mechanisms of disease. But pharmacology also involves the elucidation and manipulation of macromolecular structures, the analysis of regulatory mechanisms in cell biology and development, and the translation of this information into clinical research. Thus, the science of pharmacology spans the most fundamental aspects of basic research, through transgenic animal models, to clinical investigation.
University of Pittsburgh Department of Pharmacology
The Department of Pharmacology & Chemical Biology creates an intellectual and physical environment in which basic chemical principles are applied to the understanding of cell signaling events, with these new insights then used in the creation of new therapeutic strategies. The major responsibilities of the Department are to: (1) educate medical students and physicians in the rationale for drug selection; (2) train contemporary pharmacologists; (3) develop new knowledge in the biomedical sciences; and (4) provide information about existing and emerging drugs to members of the University of Pittsburgh Medical Center, the University of Pittsburgh and the general community.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A Java program for analyzing the pairwise linkage disequilibrium.
University of Puerto Rico Institute of Neurobiology
The Institute of Neurobiology is an interdisciplinary, interdepartmental research center of the Medical Sciences Campus of the University of Puerto Rico. Its members carry out basic research in Neuroscience, with particular emphasis on the use of simple systems to understand basic mechanisms of nervous system function and development. There are currently 14 full-time faculty members who carry out research and graduate teaching at the Institute. Their research interests range from the development of insect synapses to the anatomy of retinal projections in mammals. Graduate students carrying out research at the Institute are enrolled in Ph.D. and M.Sc. programs in the Medical Sciences Campus and in the Department of Biology, UPR. The Institute houses laboratories equipped for electrophysiology, biochemistry, molecular biology and histology, including confocal and electron microscopy.Located in Old San Juan, the Institute overlooks the Atlantic Ocean and El Morro, the fortress which guards San Juan bay.
University of Rhode Island College of Pharmacy Graduate Programs
The University of Rhode Island College of Pharmacy is a professional school, but it is also an integral part of University of Rhode Island. The College of Pharmacy fosters a learning-centered, research-oriented educational environment that encourages individuals to make positive life-long contributions to global health. We prepare professional degree students to provide compassionate pharmacist-delivered patient care, and inspire our students through innovative problem-based learning, rich experiential curricula and inter-professional collaboration. We foster a community of scholars who will further the body of knowledge in pharmaceutical, biomedical, and clinical sciences. We strive to improve quality of life: locally, nationally and globally.
University of Rochester Department of Neuroscience
Department that includes over 60 faculty members in ten different departments from both the School of Medicine and Dentistry and The College of Arts and Sciences. Several graduate and undergraduate degree programs exist on campus that are designed to meet the diverse needs and interests of students engaged in the study of the nervous system. The tight physical proximity of the medical and main campuses generates a highly collaborative and interactive Neuroscience community, and provides students with broad and flexible opportunities in their training.
University of South Alabama Department of Cell Biology and Neuroscience
Offers graduate program and training. Areas include mechanisms of DNA repair, oligodendrocyte development and maturation, functional neuroanatomy, neurophysiology, cellular responses to oxidative stress, kinesin motor proteins and motility, regulation of nuclear transcription, and hormonal regulation of fertility. Program emphasizes understanding of biological principles at the cellular level and training in the anatomical disciplines to ensure success during career development. To achieve these objectives the department participates extensively in the Interdisciplinary Graduate Curriculum which teaches fundamental biological principles during the first year. After the first year, students select a mentor and begin to focus on a significant research topic.
University of South Alabama Department of Pharmacology
The Department of Pharmacology is a program that combines an interdisciplinary core curriculum, advanced coursework and original research, and is designed to give students a broad interdisciplinary base and flexibility. Research training is offered in each of six formal advanced programs organized around traditional disciplines basic to medicine: Biochemistry and Molecular Biology, Cell Biology and Neuroscience, Microbiology and Immunology, Molecular and Cellular Pharmacology, or Physiology, and in the interdisciplinary Cancer Biology Program. There are also a number of research focus areas shared among the graduate faculty in the College of Medicine.
University of Virginia Charlottesville VA. Biomedical Sciences
University of Virginia's Biomedical Sciences Program provides students with the requisite knowledge and skills with which to pioneer major advances in our understanding of the complex biology of cells and tissues, and to lead efforts to cure and/or better treat human disease in the 21st Century. To help meet the challenges of modern biological/biomedical research training, the University of Virginia faculty have adopted an interdepartmental structure for graduate training that optimizes the research training opportunities available to you, and the flexibility to chose a mentor and advanced graduate specialty training area ideally suited for your professional interests and aspirations. To ensure personalized attention, entering students are asked to identify one of seven graduate program groups within the Biomedical Sciences Graduate Program that best suits their initial professional interests. However, students are free to change their program selection as their interests evolve during their first year, and have access to a plethora of research interests from over 200 biological/biomedical science faculty in the School of Medicine and College of Arts and Sciences on the main University of Virginia campus.
University of Southern California Department of Neuroscience
Neuroscience department portal characterized by collaborative interactions between faculty and students working at many different levels of analysis, including research on cell-molecular neurobiology, systems-level analysis of neural circuits, neural engineering, and cognitive and computational neuroscience. When combined with a varied curriculum, weekly seminars, an annual graduate student symposium, and an extremely active neuroscience graduate student forum, the USC Neuroscience Graduate Program provides a highly inter-disciplinary and supportive training experience designed to prepare students for a variety of successful careers. More than 60 USC Neuroscience faculty conduct externally funded research programs in areas ranging from the molecules that determine neuronal function to the principles of human cognition and emotion. Find out more about ongoing Neuroscience research at USC in each of the following major topic areas: - Behavioral, Systems, & Cognitive Neuroscience - Cellular & Molecular Neurobiology - Development, Plasticity & Repair - Computational Neuroscience & Neural Engineering - Aging, Neurobiology of Disease, & Translational Research Sponsors: Funded by the University of Southern California
University of Texas Medical Branch at Galveston Department of Pharmacology and Toxicology
The Graduate Program in Pharmacology and Toxicology has dual aims of (1) advancing scientific knowledge, and (2) preparing students to become independent future scientists. The Program is housed within the Department of Pharmacology and Toxicology, which has a full-time graduate program faculty of 19. An additional 5 faculty from other departments are active members of the Graduate Program, bringing the total number of graduate program faculty to 24. These faculty provide a wide range of research opportunities for addressing pharmacology research questions at a wide variety of experimental levels, ranging from whole animal responses to specific drugs and toxins, to the structural and molecular basis of gene expression of specific receptors.
University of Toronto Toronto Ontario Canada Pharmacology and Toxicology
The Department of Pharmacology is among the oldest and largest in North America, with its official foundations in 1887, at the same time that the Faculty of Medicine was re-established in the University of Toronto. We offer training in pharmacology and toxicology to both undergraduate and graduate students who may subsequently go on to exciting research, regulatory and administrative careers in academic, industrial and healthcare provision settings.Current areas of research investigation in the Department include Receptor Pharmacology, Signal Transduction Pathways, Neuropharmacology, Drug Addiction Studies, Drug Metabolism and Pharmacokinetics, Pharmacogenetics, Cardiovascular Pharmacology, Clinical Pharmacology, Behavioural Pharmacology, Immunopharmacology, Endocrine Pharmacology and Molecular Toxicology. Our research laboratories are located not only in the core Department situated in the Medical Sciences Building on the downtown St. George campus, but also within a number of nearby university Departments, Faculties, university-affiliated research institutes and teaching hospitals. This strategic positioning also enables a wealth of potential opportunities for interdisciplinary collaboration with internationally recognized investigators within one of the largest and densest existing concentrations of biomedical research expertise in North America.
University of Utah Salt Lake City Utah. Pharmacology & Toxicology
The Department of Pharmacology and Toxicology at the University of Utah is located in Salt Lake City at the foot of the beautiful Wasatch Range of the Rocky Mountains. Our Department focuses on research, graduate and professional training, and service. The faculty of this department place a high priority on the teaching and research training of graduate students for the Ph.D. degree. Our program features close working relationships between individual students and their faculty mentor, rich and diverse research opportunities, and individualized programs of study based on the needs of the students. Doctoral graduates of our program gain employment in research and teaching positions at colleges and universities, engage in research and development in the biotechnology and pharmaceutical industries, and have additional opportunities in research institutes, government agencies, environmental protection organizations, and many other arenas. Our Summer Undergraduate Research Fellowship (SURF) Program provides enriching research experiences for undergraduate students anticipating research careers in the biological sciences.
The Department of Pharmacology has designed a program of study that involves required and elective graduate courses, laboratory rotations introducing various approaches to the solution of pharmacological problems, journal clubs and seminars.The doctoral training program in Pharmacology exposes our students to the latest scientific thinking and technical developments in the biomedical sciences and to develop their critical thinking and problem solving skills. Upon completion of their graduate training, our students should be able to identify - and to design experiments to test - ideas at the limits of current knowledge in one of the major areas of pharmacology including cancer biology and neuroscience. Students should also learn to analyze, interpret and communicate effectively the results of their thoughts and their experiments to other scientists.
University of Washington Seattle WA. Pharmacology
The Department of Pharmacology are involved in diverse areas of research with special emphasis on molecular pharmacology, cellular regulation, neuropharmacology, and environmental toxicology. Active areas of research include evaluating the effects of drugs and chemicals on humans and animals; studying the actions of hormones, neurotransmitters, and other physiological regulators on individual cells; examining the detailed molecular structure of cellular constituents; and exploring how the cell regulates it's vital processes through transcriptional and post-transcriptional mechanisms. Through our research, we'd ultimately like to gain detailed insights into drug action and cellular regulation at many different levels of inquiry: the human patient, the experimental animal, the individual cell, its complement of proteins, and the genetic code.
A uniform core set of data elements (whose formal semantics are captured in OWL) for use in a Computer-Based Patient Record (CPR)
University of Western Ontario London Ontario Canada Physiology and Pharmacology
UWO Department of Physiology and Pharmacology
Research-based medical science department of physiology and pharmacology in the Schulich School of Medicine and Dentistry at the University of Western Ontario that focus on biological processes from the cellular-molecular level to the integrative-systemic level, and on the effects of drugs and environmental agents on these processes. Their areas of research excellence include the physiology and pharmacology of the cardiovascular, neural, reproductive, endocrine and musculoskeletal systems. Several faculty work in the area of developmental biology related to these organ systems. Faculty members in this Department are leaders in nationally-funded collaborative research programs studying skeletal / bone development and biology, heart and vascular biology, cell communication and gap junctions, neural control of vision and movement, and osteoarthritis and pain. Funding from several large infrastructure grants from both national and provincial governments has facilitated the development of state-of-the-art research laboratories and core facilities.
University of Wisconsin Madison WI. Molecular and Cellular Pharmacology
Modern molecular biology, protein biochemistry, immunology, cell biology, genetics, electrophysiology, and morphology are well represented in the Program in Molecular and Cellular Pharmacology. Students will be instructed thoroughly in these fields as well as in the unique principles of Pharmacology. One major objective of the Program is to teach the students a fundamental understanding of the molecular basis of signal transducing systems and their regulation. The Program brings together an outstanding group of dedicated trainers with a focus on cellular signal transduction. Graduates of the Program will be well prepared for a career in basic biomedical sciences. The Program provides a unique training experience for young scientists who want to elucidate basic principles of cellular signal pathways. Detailed knowledge of these pathways is the most important prerequisite for the discovery of new drugs and the treatment of diseases.
Washington State University Pullman WA. Pharmacology and Toxicology
The research-oriented program in pharmacology and toxicology prepares students for careers in independent research and teaching in pharmacology, toxicology and related areas.The research interests of the faculty are very broad and active areas of research include cancer biology, pharmacogenomics, pharmacokinetics, immuno-pharmacology and -toxicology and neuroscience. The diversity in faculty research interests provides students with a solid foundation in many areas of molecular and cellular pharmacology and toxicology and gives them a wide variety of research programs from which a dissertation proposal may be selected. The curriculum provides exposure of students to virtually all areas of current research in molecular and cellular biochemistry, immunology, molecular biology, pharmacology and toxicology and formal course requirements are flexible to tailor programs to individual needs.Our graduates have been successfully placed in careers in universities and colleges, the pharmaceutical and biotech industries, and in federal and state agencies. The program awards Ph.D. and M.S. degrees.
Washington University in St. Louis Neuroscience
The Neuroscience PhD Program at Washington University in St. Louis aims to train the next generation of leaders in neurobiology. The main objectives of the program are to: Provide students with the skills necessary to conduct research including the planning and implementation of a unique research project in the field of neuroscience. Teach students the fundamental concepts within neuroscience and how to apply those concepts in the critical analysis of scientific research. Promote the professional development of students in the areas of scientific writing and oral presentation. Promote interdisciplinary science by encouraging cooperation and collaboration among students in different programs and departments.
A database on nucleotide sequences of 5S rRNAs and their genes. The database contains 1985 primary structures of 5S rRNA and 5S rDNA, and was last updated in 2002, according to the website. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. The multiple sequence alignments of 5S ribosomal RNAs can be downloaded in TAB-delimited and FASTA formats.
ADDA - Automatic Domain Decomposition Algorithm
Automatic Domain Decomposition Algorithm
This is a web interface for ADDA, an automatic algorithm for domain decomposition and clustering of all protein domain families. We use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model. ADDA is downloadable. There are three ways in which you can retrieve a protein sequence and its domains from ADDA. Sequences can be located using sequence identifiers and/or accession numbers, using a identical fragment lookup, or by running BLAST against all sequences in ADDA. ADDA is a protein sequence clustering algorithm. It takes a set of sequences and returns domain families. ADDA has two steps corresponding to the two aspects of the protein sequence clustering domain. First, ADDA splits protein sequences into domains. The idea behind ADDA is in principle the application of Occam''s razor; the goal is to describe the diversity of protein sequences with a minimal set of protein domains. The algorithm behind ADDA approximates this minimal set. In practice ADDA works by looking at where BLAST alignments are located on the sequence and splits the sequences, so that as few as possible alignments are cut by domain boundaries and that as many alignments as possible stretch over complete domains. Secondly, ADDA takes all the domains and then arranges them in a minimum spanning tree, where the similarity between two domains is determined by their relative overlap given a BLAST alignment. Each link in the tree is then checked by a pairwise profile-profile comparison and links below a threshold are removed. The remaining connected components are then taken to represent protein domain families.
A curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase provides tools designed to assist with the analysis of proteomics data and tools to evaluate experimental datasets using the GO. Additional tools for sequence analysis are also provided. We use controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species. AgBase will also accept annotations from any interested party in the research communities. AgBase develops freely available tools for functional analysis, including tools for using GO. We appreciate any and all questions, comments, and suggestions. AgBase uses the NCBI Blast program for searches for similar sequences. And the Taxonomy Browser allows users to find the NCBI defined taxon ID for or taxon name for different organisms.
AGD is a genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from Ashbya gossypii and the model organism Saccharomyces cerevisiae. It also provides access to comparative genomics data from those two fungi as well as Schizosaccharomyces pombe and Neurospora crassa. Comparative DNA and protein-level data is available, including synteny information in fungi. Additionally, AGD now displays microarray expression data from A.gossypii and S.cerevisiae.
The Annozilla project was designed to view and create annotations associated with a web page, as defined by the W3C Annotea project. Annotations are stored as RDF on a server, using XPointer (or at least XPointer-like constructs) to identify the region of the document being annotated. Additionally, the Annozilla source code is available. The intention of Annozilla is to use Mozilla' '''s native facilities to manipulate annotation data - its built-in RDF handling to parse the annotations, and nsIXmlHttpRequest to submit data when creating annotations. To use Annozilla, you will need to install the packages, get set up with a user account with an annotation server (e.g., the W3C test server), and then you should be ready to start using the extension.
LAPlacian eigenfunctions learn population STRUCTure
Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software)
Comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. Data may be submitted directly to the database or reprints and notifications of new papers may be sent to database curation staff.
ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins
A database of putative membrane proteins of Thale Cress (Arabidopsis thaliana), Rice (Oryza sativa) and about some 6700 putative membrane proteins of ~300 other seed plants. The database stores data about: * protein, cDNA and genomic sequences * exon predictions (A.thaliana and O.sativa) * different cDNA/protein models of genes (A.thaliana and O.sativa) * ontology terms according to the Gene Ontology (GO) Consortium * protein sequence motifs as predictable by using the PFAM database * transporter classification as predictable by using the TC-system * bibliographic references * predictions for transmembrane spanning proteins (transmembrane alpha helices, beta barrels) * predictions for membrane-anchored proteins (GPI-attachment, prenylation, myristoylation) * prediction of the subcellular location * consensus predictions (transmembrane alpha helices, subcellular location) * isospecic homologs (''paralogs'') * heterospecic homologs (''orthologs'')
ARGONAUTE 2 - A database on mammalian microRNAs and their function in gene and pathway regulation
A database is a of mammalian miRNAs and their known or predicted regulatory targets. It provides information on origin of miRNAs, tissue specificity of their expressions and their known or proposed functions, their potential target genes as well as data on miRNA families based on their co-expression and proteins known to be involved in miRNA processing. This database also contains three other navigation tools that can be used to find information relating to miRNA: 1.) Gene Annotations is an information retrieval system for miRNA target genes. It provides comprehensive information from sequence databases and allows to simultaneously search PubMed with all synonyms of a given gene. 2.) miRNA Motif Finder - Argonaute predicts miRNA motifs binding to the gene sequence of the user. The miRNA mature sequences are taken from Agronaute 2 database. miRNA Motif Finder - Custom predicts miRNA motifs binding to the gene sequence, both the gene sequence and miRNA mature sequences provided by the user. 3.) miRNA Statistics provides statistics for the mature miRNA sequences from Argonaute 2 as well as for the miRNA sequences uploaded by the user. It provides statitics on the individual nucleotide as well as pattern of nucleotides apperaing in the sequence.
Alternate Splicing - induced ALteration of Protein Structure
This database, AS-ALPS (Alternative Splicing-induced ALteration of Protein Structure), is aimed at providing useful information to analyze effect of AS on protein interaction and network through alteration of protein structure. In AS-ALPS, regions of amino acid sequences changed by AS (AS regions) which are detected in human and mouse transcript sequences in H-InvDB, FANTOM and RefSeq, are linked to information extracted from PDB about residues forming hydrophobic cores and inter-molecular interaction sites. This makes it possible to directly infer whether protein structure and/or interaction are affected by each AS event. In addition, AS-ALPS provides links to a protein network database KEGG, making it easy to know which network and which node in the network can be influenced by AS. :Sponsors: This database was supported by a grant of the Genome Network Project from Ministry of Education, Culture, Sports, Science and Technology of Japan. :
It has been established with the intention of assembling in a central, publicly accessible site information about alternatively spliced genes, their products and expression patterns. Version 2.1 of ASDB consists of two divisions, ASDB(proteins) , which contains amino acid sequences, and ASDB(nucleotides) with genomic sequences. SWISS-PROT uses two formats for description of alternative splicing Thus the protein sequences were selected from SWISS-PROT using full text search for both the words alternative splicing (usually in the CC lines) and varsplic (in the FT lines). In order to group proteins that could arise by alternative splicing of the same gene, we developed the clustering procedure. Two proteins were linked if they had a common fragment of at least 20 amino acids, and clusters were initially defined as maximum connected groups of linked proteins. It turned out that some clusters were chimeric, in the sense that they contained members of multi-gene families, but not alternatively spliced variants of one gene. Therefore the multiple alignments were subject to additional analysis aimed at detection of chimeric clusters. Each cluster is represented by multiple alignment of its members constructed using CLUSTALW. The distribution of cluster size, representation of species and other relevant statistics of ASDB(proteins) can be accessed through the links below. This processing covers the cases when alternatively spliced variants are described in separate SWISS-PROT entries. The other kinds of ASDB records, originating from the SWISS-PROT entries with the varsplic field in the feature table, usually describe the proteins that are not part of any cluster. In these cases, the information on the variable fragments of the several proteins which result from the alternative splicing of a single gene is contained in the entry itself. ASDB(proteins) entries are marked with different symbols to allow for easy differentiation among the three types: those proteins which are part of the ASDB clusters and the corresponding multialignments, those which have the information on different variants in the associated SWISS-PROT entries, and those for which the information on the variants is not available at the present time. ASDB contains internal links between entries and/or clusters, as well as external links to Medline, GenBank and SWISS-PROT entries. The ASDB(nucleotides) division was generated by collecting all GenBank entries containing the words alternative splicing and further selection of those entries that contain complete gene sequences (all CDS fields are complete, i.e. they do not have continuation signs). Sponsors: This work was supported by the Director, Office of Energy Research, Office of Biological and Environmental Research, of the US Department of Energy under Contract No. DE-ACO3-76SF00098. Additional support came from grants from the Russian Fund of Basic Research (99-04-48347), the Russian State Scientific Program Human Genome (65/99), and the Merck Genome Research Institute (244).
Software application for non-parametric linkage analysis using allele sharing in sib pairs (entry from Genetic Analysis Software)
Artificial Selected Proteins/Peptides Database
Artificial Selected Proteins Peptides Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 04, 2014. Curated database on selected from randomized pools proteins and peptides designed for accumulation of experimental data on protein functionality obtained by in vitro directed evolution methods (phage display, ribosome display, SIP etc.) ASPD is integrated by means of hyperlinks with different databases (SWISS-PROT, PDB, PROSITE, etc). The database also contains modules for pairwise correlation analysis and BLAST search.
BANMOKI: Searchable database of BActerial Nucleoside MOnophosphate KInases
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 10, 2011. BANMOKI is a collection of models of 3D structures of all Bacterial Nucleoside Monophosphate Kinases (NMPK), their pre-computed properties and other relevant information. The web server provides information in regard to sequence identity, 3D structure, Enzyme Commission (EC) number, pKa, desolvation penalty, interaction energy with permanent dipoles and the net charge of folded and unfolded states as a function of pH. The database and datasets are searchable by: seq ID name of protein Enzyme commission number pKa desolvation penalty(in pk units) interaction energy with permanent dipoles(in pk units) No. of basic residues No. of acidic residues No. of titratable residues Total no. of residues The web server development and the corresponding scientific work was supported by NATO collaborative grant CBP.EAP.CLG 981749
Bcipep is collection of the peptides having the role in humoral immunity. The peptides in the database have varying measure of immunogenicity. This database can assist in the development of methods for predicting B cell epitopes, designing synthetic vaccines, and in disease diagnosis. These peptides lead to the generation of antibodies which combine with antigens and are responsible for the host defense, and can be very useful for subunit vaccine designing. The database has 3031 peptide entries. For each peptide, the user can find a plethora of information, including entry number, peptide sequence, pathogen group, protein source, antigen structure, antibody, etc.
Bacterial Carbohydrate Structure DataBase
The Bacterial Carbohydrate Structure DataBase is aimed at provision of structural, bibliographic, taxonomic and related information on bacterial carbohydrate structures. It currently requires Internet Explorer in order to function properly. Two key points of this service are: :* covering - is above 95% in the scope of bacterial carbohydrates. This means the negative search answer remains the valuable information too. :* consistence - we manually check the data, and aim at hight quality error-free content The source of data are Carbbank database (University of Georgia, Athens; structures published before 1995, approx. 4000 records) and manual data posting (structures published after 1995, approx. 3000 records). The scope is bacterial carbohydrates and covers nearly all structures of this class published before 2006. Bacterial means that a structure has been found in bacteria or obtained by modification of those found in bacteria. Carbohydrate means a structure composed of any residues linked by glycosidic, ester, amidic, ketal, phospho- or sulpho-diester bonds, in which at least one residue is a sugar or its derivative. Besides the structure itself, each record includes bibliography, abstract, keywords, biological source, methods used to elucidate the structure, bioactivity, NMR assignment tables and a lot of other information. More details, including a format of records, are available at data submission page. You can search the database by IDs, bibliographic data and keywords, biological source, the fragment of structure and NMR data. The substructure search implies either a query language (expert form) or a structure wizard. The database is cross-linked with GlycoSCIENCES DB, which includes all the data from Carbbank (not only bacterial). This means you can search the substructure you entered in GlycoSCIENCES DB, and each record, which contains a structure also present in Carbbank, has a cross-link to data from GlycoSCIENCES DB, including NMR spectra.
Protein Classification Benchmark Collection
It was created in order to create standard datasets on which the performance of machine learning methods can be compared. The collection contains datasets of sequences and structures, each subdivided into positive/negative training/test sets. Such a subdivision is called a classification task. Typical tasks include the classification of structural domains in the SCOP and CATH databases based on their sequences, as fell as various functional and taxonomic classification tasks. Running a performance evaluation test on an entire database can include many different classification tasks. These ensembles of classification tasks are encoded in a simple matrix format - called the cast matrix or membership table - that specifies the role of each sequence (or structure) in the different calculations. Each column of this matrix is a subdivision of the objects (rows) into positive/negative training/test sets. Typically, a database record contains such an ensemble of classification tasks, encoded in a single cast matrix. In addition, there is a collection of distance matrices that contain an all vs. all comparison of the datasets using methods as BLAST, Smith-Waterman, 3D-comparisons etc. Evaluation of a method on a given database consists of calculating a performance measure such as a receiver operating curve (ROC) AUC value. Results of evaluation are deposited along with the data, each dataset is evaluated at least by one classification method, such as 1NN (nearest neighbour) or SVM (support vector machines), ANN (artificial neural networks), RF (random forests) etc.. There are small datasets meant for program developers, as well as downloadable programs for various classification algorithms.
Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci.
The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite.
Biodefense Proteomics Resource Center presents information on Class A-C biodefense organisms. :This list includes Bacillus anthracis, Brucella abortus, Francisella tularensis, salmonella typhi, salmonella typhimurium, Virbio cholerae, Yersinia pestis, Cryptosporidium parvum, Toxoplasma gondii, Avian influenza, SARS, Monkeypox, Vaccinia, and Variola. For each organism, the page provides a general overview of the organism and the diseases it causes, protein (and protein interaction) data, reagents, and data from experiments performed with this organism. Users may also find links to the NCBI Taxonomy center.
Bionemo stores manually curated information about proteins and genes directly implicated in biodegradation metabolism. The database includes information on sequence, domains and structures for proteins; and sequence, regulatory elements and transcription units for genes. Bionemo complements other biodegradation databases such as the University of Minessota Biocatalysis/Biodegradation Database, or Metarouter, which focus on the biochemical aspects of biodegradation. Bionemo has been built by manually associating sequences databases entries to biodegradation reactions, using the information extracted from published articles. Information on transcription units and their regulation was also extracted from the literature for biodegradation genes, and linked to the underlying biochemical network.
BioThesaurus is a web-based system designed to map a comprehensive collection of protein and gene names to UniProt Knowledgebase protein entries. It covers all UniProtKB protein entries, and consists of several millions of names extracted from multiple resources based on database cross-references in iProClass. The web site allows the retrieval of synonymous names of given protein entries and the identification of ambiguous names shared by multiple proteins. Searches can be done on protein/gene name, organism, or unique identifier.
Blocks is a database of highly conserved regions of proteins, or Blocks. THe database is no longer maintained or updated and some of its tools are no longer functional. However, Blocks does provide Block Searcher, Get Blocks and Block Maker, aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks (current version), retrieve blocks, and create new blocks, respectively. Users can further view blocks by (keyword or number), search a sequence against the database of blocks, search blocks against each other, or make blocks of their own.
BPS- Database of RNA Base-pair Structures
BPS is a database of RNA base pairs with quantitative information on the spatial arrangements of interacting bases, including higher-order base associations, and the context of these interactions in high-resolution crystal structures. The structures are taken from the Nucleic Acid Database (NDB), and the base pairs are identified and characterized with the 3DNA software package. The interactions are classified in terms of residue identities, base-pair positioning, and hydrogen-bonding patterns and related to the structural context in which they occur. A user can browse the atlas of base-pair patterns and carry out searches for patterns of specific types or from specific structures.
CIPRO: Ciona intestinalis Protein Database
CIPRO is an integrated protein database of the ascidian Ciona intestinalis. It has been developed to provide widespread information of the proteins expressed in the ascidian Ciona intestinalis, especially for the researcher who wants to get advanced and useful information for starting biological and biomedical research. The protein information in CIPRO directly links to gene expression, a tool for peptide mass fingerprinting (PMF), intracellular localization, 3D image of early development, and transgenic resources.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.BSD is a database resource that provides information on strains of bacteria with biodegradative properties. The goal of the database is to consolidate and provide rapid access to comparative data on known biodegradative microorganisms and the hazardous substances they degrade as a readily accessible resource for researchers and field practitioners. The database also aims to: # facilitate comparative analyses and highlight deficiencies in our current knowledge base # provide corresponding microbiological data to complement and integrate with the chemical and metabolic data of the University of Minnesota Biocatalysis/ Biodegradation Database and the phylogenetic data of the Ribosome Database Project (RDP-II) # to organize strain data and analyze biocatalysis and biodegradation within a phylogenetic perspective # provide database users a forum for input and contribution and correction of data # serve as a model for the presentation of strain-level, microbial data on the internet To this end, it includes individual data and strain pages, search capabilities, and user input functionality., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Software application that tests for association between genetic marker and disease by examining the transmission of markers from parents to affected offspring. The main features which differ from other similar programs are: (1) It can deal with transmission of multi-locus haplotypes, even if phase is unknown, and (2) Parental genotypes may be unknown. (entry from Genetic Analysis Software)
BuchneraBase is a database designed to encapsulate and reference information obtained from the complete genome sequence of the gamma-proteobacterium Buchnera sp. APS. We have derived a high quality gene and functional annotation for Buchnera sp. APS. BuchneraBASE also provides for cross-referencing to the genomes of six further symbiotic bacteria for which full sequences are now available: Buchnera sp. SG from the aphid Schizaphis graminum, Buchnera sp. Bp from the aphid Baizongia pistacea, Wigglesworthia glossinidia brevipalpis from the tetse fly Glossina brevipalpis, Blochmannia floridanus from the carpenter ant Camponotus floridanus, Blochmannia pennsylvanicus from the carpenter ant, Camponotus pennsylvanicus, and Baumannia cicadellinicola from the glassy winged sharpshooter, Homalodisca coagulata. We also include Mycoplasma genitalium, with the smallest genome of an organism that can be grown in pure culture. We have constructed BuchneraBASE to facilitate the post-genomic analysis of these bacteria, especially the genomic correlates of co-operative intracellular lifestyles.
CADB - Conformational Angles DataBase of Proteins
Conformation Angles DataBase is a comprehensive, authoritative and timely knowledge base developed to facilitate retrieval of information related to the conformational angles (main-chain and side-chain) of the amino acid residues present in the non-redundant (both 25% and 90%) data set. The database includes the options of determining the dependency of the conformation angles of a particular residue upon the flanking residues in main-chain, doublet analysis, triplet analysis and analysis of a particular protein structure. It is worth mentioning that for all the options, a user-friendly and convenient Java Graphical User Interface (GUI) has been provided to display the output on the client machine.
Expression profiling and promoter identification software tool for transcriptional network analysis and transcriptome characterization. DeepCAGE, the combination of next-generation sequencing with next generation expression profiling provides unsurpassed solutions for expression profiling and genome annotation. CAGE will be the experimental approach at need to link gene expression and control regions in the genome. With the availability of next-generation sequencing methods, DNAFORM now offers DeepCAGE services. DeepCAGE libraries are prepared for direct analysis by an Illumina/Solexa Sequencer. One sequencing run using one channel on an Illumina/Solexa Sequencer can yield in over 4,000,000 reads per sample. CAGE is based on our full-length cDNA library technology, where an adaptor is ligated to the 5' '''-end of full-length cDNAs, which introduces a recognition site for a Class IIs restriction endonuclease adjacent to the 5' '''-end of the cDNA. The Class IIs restriction endonuclease, here MmeI, allows for the cloning of short tags as derived from the 5' '''-end of transcripts into concatemers for high-throughput sequencing. CAGE tags are further characterized by mapping to genomic sequences, which enables the identification of transcriptional start sites. As such CAGE can contribute to projects in Gene Discovery, Gene Expression, and Promoter Identification. After the genome sequencing projects have provided us with the genetic blueprints for many organisms, new questions have to be answered on how to correlate the observed genotypes with related phenotypes, and how to understand the regulation of genetic information in time and space. The dynamics of living systems and the functional behavior of cells in multicellular organisms has thus become the subject of the emerging field of system biology. Integration of experimental approaches and computer aided theories on a system level will be the fundamental principle to drive systems biology in order to understand the principles behind complex regulatory networks, which will be an ambitious goal requiring new approaches in life sciences. For ordering and additional information, please contact us under contact_at_dnaform.jp
Cancer Chromosomes is an integration of three databases, the NCI/NCBI SKY/M-FISH & CGH Database, the NCI Mitelman Database of Chromosome Aberrations in Cancer, and the NCI Recurrent Aberrations in Cancer, which all focus on various aspects of cancer and cancer genes. The goal of the SKY/M-FISH and CGH database is to provide a public platform for investigators to share and compare their molecular cytogenetic data. The database is open to everyone and all users can view an individual investigator''s public data or compare public cases from different investigators. The information in the Mitelman Database of Chromosome Aberrations in Cancer relates chromosomal aberrations to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature. Complete karyotypes, patient characteristics, and references are found in the Mitelman Database of Chromosome Aberrations in Cancer. Users can search all three databases for cytogenetic, clinical, and/or reference information.
extended transmission/disequilibrium test
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application for TDT test on markers with more than two alleles using a logistic regression analysis. (entry from Genetic Analysis Software).
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2015. The CancerGenes resource simplifies the process of gene selection and prioritization in large collaborative projects. CancerGenes combines gene lists annotated by experts with information from key public databases. Gene lists in the CancerGenes resource are from various sources and have been mapped to UCSC canonical gene IDs. Each gene is annotated with gene name(s), functional description, organism, chromosome number, location, Entrez Gene ID, GO terms, InterPro descriptions, gene structure, protein length, transcript count, and experimentally determined transcript control regions, as well as links to Entrez Gene, COSMIC, and iHOP gene pages and the UCSC and Ensembl genome browsers. The user-friendly interface provides for searching, sorting and intersection of gene lists. Users may view tabulated results through a web browser or may dynamically download them as a spreadsheet table.
CATMA - Complete Arabidopsis Transcriptome MicroArray
Complete Arabidopsis Transcriptome MicroArray
A database of Arabidopsis Gene-specific Sequence Tags (GSTs) designed and produced by the CATMA consortium. The aim of CATMA is the design and production of high quality GSTs covering most Arabidopsis genes. The GST repertoire is used by numerous groups for the production of DNA arrays for transcript profiling experiments.The database contains information about the GST probes, the PCR primers used for their amplification and the genes to which they hybridize, together with other information such as details of the groups involved and quality control results. CATMA microarrays constitute the foundation of the CAGE project aiming at the construction of a gene expression reference database for Arabidopsis. The CATMA GSTs are also the basic materials in the AGRIKOLA project focusing on the large-scale systematic RNAi silencing of Arabidopsis genes. CATMA is a consortium of research groups from eight European countries. All CATMA members are public laboratories, some with ties to private research institutions.
CandidaDB is a database dedicated to the analysis of the genome of the human fungal pathogen, Candida albicans. Its purpose is to collate and integrate various aspects of the genomic information from C. albicans, which is currently responsible for the vast majority of life-threatening fungal infections in immuno-compromized individuals. CandidaDB provides an almost complete dataset of DNA and protein sequences derived from C. albicans strain SC5314, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). Nucleotide sequence data for C. albicans were obtained from the Stanford Genome Technology Center website. Sequencing of C. albicans was accomplished with the support of the NIDR and the Burroughs Wellcome Fund. CandidaDB is supplemented with information from C. albicans entries present in the EMBL/GenBank/DDBJ databanks, as well as observations either published in international journals or communicated directly to us by individual researchers.
CarpeDB is a database focused on epilepsy genetics. It serves as a novel source for epilepsy researchers by featuring scores of epilepsy genes and associated publications in one locus. Furthermore, because multiple genes implicated in epilepsy are also implicated in other human disorders, the use of CarpeDB need not be limited to epilepsy researchers. Users can search the data in Carpe DB by chromosome, gene, species, or keyword. They can also browse genes by an alphabetical list. The website also provides links to other epilespy-related resources, and the ability for users to submit their own data or papers.
CASRDB- Calcium Sensing Receptor Database
CASRdb is a calcium-sensing receptor locus-specific database for mutations causing familial (benign) hypocalciuric hypercalcemia, neonatal severe hyperparathyroidism, and autosomal dominant hypocalcemia. The information can be searched by mutation, genotype-phenotype, clinical data, in vitro analyses, and authors of publications describing the mutations. CASRdb is regularly updated for new mutations and it also provides a mutation submission form to ensure up-to-date information. The home page of this database provides links to different web pages that are relevant to the CASR, as well as disease clinical pages, sequence of the CASR gene exons, and position of mutations in the CASR. The CASRdb will help researchers to better understand and analyze the mutations, and aid in structure-function analyses.
CATdb: a Complete Arabidopsis Transcriptome database
CATdb collects together all the information on transcriptome experiments done at URGV with CATMA micro arrays. All data in CATdb come from the URGV micro array platforms. Common procedures are used including any steps from the experiment design to the statistical analyses. Directed through a WEB interface, biologists enter the standard description of each experimental step (extraction, labelling, hybridization and scanning). Then, normalization and statistical analyses are done following a set of selected methods depending on the experimental design and array types.
CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis Users can search CATH by ID/Sequence/text. They can also browse CATH from the top of the hierarchy, or download CATH data.
An ontology that describes the Congenital Heart Defects data.
CE is a databases of alignments for all polypeptide chains. A representative set of proteins is available and kept current with the PDB, a method for calculating pairwise structure alignments. CE aligns two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. Matches are termed aligned fragment pairs (AFPs). Heuristics are used in defining a set of optimal paths joining AFPs with gaps as needed. The path with the best RMSD is subject to dynamic programming to achieve an optimal alignment. For specific families of proteins additional characteristics are used to weight the alignment. Complete details are described in the paper (PDF format). Databases of alignments for all polypeptide chains and a representative set of proteins is available and kept current with the PDB
CellCircuits is an open-access database of molecular network models. Its goal is to bridges the gap between databases of individual pair-wise molecular interactions and databases of validated pathways. It contains functional network hypotheses produced by algorithms that screen molecular interaction networks based on their correspondence with expression or phenotypic data, their internal structure, or their conservation across species. The database is searchable using protein/gene names and Gene Ontology terms. Models are available either as images or in machine-readable formats. Overall, this resource serves as a clearinghouse in which theorists may distribute or revise models in need of validation and experimentalists may search for models or specific hypotheses relevant to their interests. Funding provided by the National Science Foundation (NSF 0425926).
A database to provide cleansed EST sequences of classified dbEST libraries. All dbEST libraries were classified according to organism, sequencing center, and eVOC ontologies (for human libraries). For each dbEST library, we provide three different EST sequences: raw, pre-cleansed, and user-cleansed. pre-cleansed ESTs are obtained from major contamination databases and cleaned of contaminated sequences. User-cleansed ESTs, however, involve the use of an automatic user-cleansing pipeline, in which sequences in a user-selected library are cleansed on-the-fly according to user-input options. CleanEST contains 62,008,259 EST sequences (24,000 libraries) with contamination information.
Centrosome:db contains a set of human genes encoding proteins that are localized in the centrosome, either as centrosome constituents or as centrosome visitors. Genes have been considered as centrosomal on the basis of different kinds of evidences including high-throughput proteomics assays, annotations in public databases and orthology relationships to centrosomal genes in closely related species (e.g. mouse). For each of these human genes we have compiled information from various sources such as Ensembl, OMIM, HPRD, SNPs, GeneOntology or Compara, among others. Orthologs in other species, ranging from yeast to mammals, have been also included in centrosome:db. The domain structure of all the associated peptides has been characterized based on the domain profiles of the Pfam and Superfamily databases (scanned with the RPS-BLAST program) and on the coiled-coil predictions of the COILS program. You can browse the database by: :* Searching with a gene name, database identifier or submmiting full text queries (uniprot, ensembl, hgnc, entrez, ipi and refseq identifiers are supported) :* Searching for a given domain in a particular specie (or all species) :* Accesing the orthology information related to a gene :* Comparing your own sequence with those in centrosome:db :* Retrieve all the human centrosomal genes based on their evidences
CSRDB is a bioinformatics resource for cereal crops consisting of large-scale datasets of maize and rice and small RNA sequences. The sequences were generated by 454 Life Science sequencing. The small RNA sequences have been mapped to the rice genome and available maize genome sequence and are presented in two genome browser datasets using the Generic Genome Browser. Potential target sequences representing mature mRNA sequences have been predicted using the FASTH software from the Zuker lab. and access to the resulting small RNA target pair (SRTP) dataset has been made available through a mysql based relational database. Within the genome browser the small RNAs have links to the SRTP database that will return a list of potential targets. The SRTP database may also be searched independently using both small RNA and target transcript queries. Data linking and integration is the main focus of this interface and to this aim links are present in the SRTP results pages back to the browser and the SRTP database as well as external sites.
CGED (Cancer Gene Expression Database) is a database of gene expression profile and accompanying clinical information. The data of CGED were obtained through collaborative efforts to identify genes of clinical importance. This database offers graphical presentation of expression and clinical data with similarity search and sorting functions. CGED includes data on breast (prognosis and docetaxel data sets), colorectal, hepatocellular, esophageal, thyroid, and gastric cancers (updated in March 2007). Genes in CGED can be searched by: 1) gene names or identifiers, or 2) gene ontology terms or keywords in functional annotations in the SwissProt, or 3) cancer types and its clinical factors, or 4) gene expression differentials based on p value or q value.
Drug Interaction Knowledge Base Ontology
An evidence taxonomy for pharmacologic studies that, when combined with a set of inclusion criteria, enable drug experts to specify what their confidence in a drug mechanism assertion would be if it were supported by a specific set of evidence.
ChemBank is a public, web-based informatics environment that includes freely available data derived from small molecules and small-molecule screens, and resources for studying the data so that biological and medical insights can be gained. ChemBank is intended to guide chemists synthesizing novel compounds or libraries, to assist biologists searching for small molecules that perturb specific biological pathways, and to catalyze the process by which drug hunters discover new and effective medicines. ChemBank stores an increasingly varied set of cell measurements derived from, among other biological objects, cell lines treated with small molecules. Analysis tools are available and are being developed that allow the relationships between cell states, cell measurements and small molecules to be determined. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the ICG in collaborations involving biomedical researchers worldwide. These scientists have agreed to perform their experiments in an open data-sharing environment. The goals of ChemBank are to provide life scientists unfettered access to biomedically relevant data and tools heretofore available almost exclusively in the private sector. We intend for ChemBank to be a planning and discovery tool for chemists, biologists, and drug hunters anywhere, with the only necessities being a computer, access to the Internet, and a desire to extract knowledge from public experiments whose greatest value is likely to reside in their collective sum.
DOOR (Database of prOkaryotic OpeRons) is an operon database. The operons in the database are based on prediction. The database provides an organism view, gene search, operon search, and operon prediction tools. Currently DOOR has operons for 675 prokaryotic genomes.
A database of general chemical information. The datasets are comprised of various available chemical datasets annotated with interesting properties to train and test machine-learning prediction and searching methods. Tools provided include ChemicalSearch, Virtual Chemical Space, Reaction Explorer, Datasets, and supplemental material. ChemicalSearch is a tool that allows users to find a chemical by basic criteria like molecular weight and predicted logP, or by the more abstract notion of structural similarity. Virtual Chemical Space is a tool which lets users interactively deconstruct target compounds into component precursors and reconstruct similar building-blocks into combinatorial libraries representing the virtual chemical space near the target compound. Reaction Explorer is a synthesis explorer and mechanism explorer. It provides an interactive system for learning and practicing reactions, syntheses and mechanisms in organic chemistry, with advanced support for the automatic generation of random problems, curved-arrow mechanism diagrams, and inquiry-based learning.
ChickVD hosts high-quality sequence variation data, variation analysis in the context of chicken genes, cDNAs, chicken orthologs of human disease genes, genetic markers, quantitative trait loci (QTLs) etc . All data are uniquely mapped onto the RJF draft genome and graphically represented in MapView, an efficient visualization tool that allows users to browse sequence variations in the genomic and functional context. The sub-viewer TraceView assists users to view the vivid graphics of the original traces around the detected SNP. Users may query the data by the online search tool and define concrete limitations to extract records that are best suited to their research needs. For the convenience of data presentation in ChickVD, different types of sequence variations (substitutions, insertions or deletions) are all referred as ???SNPs''. ChickVD is updated constantly as more data generated and is under the continued improvement for its content and functionality
Knowledgebase of fusion transcripts collected from various public resources such as the Sanger CGP, OMIM, PubMed, and Mitelman's database. It is an alignment viewer to facilitate examining reliability of fusion transcripts and inferring functional significance., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
ChromDB is a chromatin database. Three types of sequences are included in the database: genomic-based (predominantly plant sequences); transcript-based (EST contigs or cDNAs for plants lacking a sequenced genome); and NCBI RefSeq sequences for a variety of model animal organisms. The Gene Record Page for any sequence indicates the type of sequence. The broad mission of ChromDB is display, annotate, and curate sequences of two broad functional classes of biologically important proteins: chromatin-associated proteins (CAPs) and RNA interference-associated proteins. Plant proteins are the major focus of the work support by The Plant Genome Research Program (PGRP) of the National Science Foundation. Our intent is to produce intensively curated sequence information and make it available to the research and teaching community in support of comparative analyses toward understanding the chromatin proteome in plants, especially in important crop species. In order to do a comparative analysis, it is necessary to include non-plant proteins in the database. Non-plant genes are not curated to the degree carried out for plants and to automate the process of data import, our non-plant genes are from the RefSeq database of NCBI. We reason that the inclusion of non-plant, model organisms will broaden the relevance and usefulness of ChromDB to the entire chromatin community and will provide a more complete data set for phylogenetic analyses in support of the evolution of the plant chromatin proteome. ChromDB is funded by a grant from the National Science Foundation Plant Genome Research Project(#DBI-0421679).
Healthcare Common Procedure Coding System
Ontology for the healthcare common procedure coding system.
IES-MDS DB is a database of macronuclear and micronuclear genes in spirotrichous ciliates. The database contains information on 440 MDS pairs (each pair composed of the MIC and the MAC version of a given MDS), 392 IES and 361 pointer triples (each pointer has two active copies in the MIC and one copy in the MAC) (7). Out of the 440 MDSs, 235 are scrambled, and 65 are in the opposite strand in the MIC. A total of 320 IESs and 202 pointers are scrambled. For each pair of genes in the database the user can see the micronuclear and macronuclear organization and has the option to see all the MDS, IES and pointer sequences. Another option is to download the MIC sequence with the MDSs and pointers in uppercase and the IESs in lowercase. It is also possible to graphically compare the organization of several genes.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented June 24, 2013 as per the Miriam database (http://www.ebi.ac.uk/miriam/main/collections/MIR:00000021). The CluSTr database offers an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMs, Gene3D, SUPERFAMILY, PIR Superfamily and PANTHER. To date (2011), CluSTr contains the following information: * 9,450,285 sequences from UniProt Knowledgebase release 15.6 * 308,281 sequences from IPI * 3,636,831,744 similarities, with pairwise alignments generated on-the-fly * 17,616,060 clusters * Clustering for 972 organisms with completely sequenced genomes. For the full list of the genomes see Integr8 * Putative homologues predictions for the above species. For more information see Homologue Selection at Integr8
CMGSDB- Computational Models for Gene Silencing
CMGSDB is a database whose objective is to investigate gene silencing from a computational perspective using tools of computational biology and bioinformatics. The database is C. elegans centric, although the schema is suitable for any organism and can be extended with minor changes to support multiple organisms. CMGSDB contains details of genome annotation data (chromosomes, genes, coding transcripts), protein structure data (secondary structure, physical properties), microarray expression data (genomewide gene expressions for over 500 microarray experiments), RNA interferance data (RNAi experiment details, phenotypes exhibited by genes in different experiments, phenotype hierarchy and associations between them), protein-protein interaction data, and gene-regulation data.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 26, 2016. CoC Central is a searchable database of residue conservation data covering the universe of known protein structures. CoC is useful for identifying functionally, kinetically, and thermodynamically important residues. Knowledge of universally conserved positions in protein folds may aid in identifying positions of kinetic or thermodynamic importance in protein folding, as well as those with a functional role.
DB-PABP: a database of polyanion binding proteins
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. DB-PABP is an attempt to document the publicly available experimentally determined polyanion binding proteins (PABPs). The purpose of the database is to provide life scientists who are interested in PA/PABP interactions with a comprehensive data repository, as well as computer scientists with a publicly available dataset to perform knowledge discovery and datamining studies. The database is manually curated. It uses protein annotations from NCBI protein database and literature information is retrieved from PubMed. Whenever applicable, links to NCBI protein database and PubMed are provided so users may access additional information available in these public databases.
COGEME Phytopathogenic Fungi and Oomycete EST Database
COGEME is an ongoing BBSRC-funded study to construct a relational database of genomic information from phytopathogenic fungi. This site also hosts microarray data for Blumeria graminis. Expressed sequence tags (ESTs) obtained from eighteen species of plant pathogenic fungi, two species of phytopathogenic oomycete and three species of saprophytic fungi are included here. Hierarchical clustering software was used to classify together ESTs representing the same gene and produce a single contig, or consensus sequence. The unisequence set for each pathogen therefore represents a set of unique gene sequences, each one consisting of either a single EST or a contig sequence made from a group of ESTs. Unisequences were annotated based on top hits against the NCBI non-redundant protein database using blastx.
coliBASE is a database for comparative genome analysis of Enterobactericaiae, e.g. Escherichia, Shigella etc. coliBASE covers a greater sequence diversity than most other online E. coli resources (which tend to be limited to the K12 genome sequence), and provides novel tools such as the alignment viewer and whole genome viewer that are not available elsewhere. It is supported by a 5 year BBSRC grant until Feburary 2012.
Database dedicated to the analysis of the genome of Escherichia coli. Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). The data contained in Colibri originates from two major sources of information, the reference genomic DNA sequence from the E. coli Genome Project and the feature annotations from the EcoGene data collection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
COMe is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif. COMe consists of three types of entities: Molecule (MOL), Bioinorganic Motif (BIM), and Bioinorganic Proteins (PRX). Both Molecule (MOL) and Bioinorganic Motif (BIM) entities consist of substructure elements. Substructure literally means that these elements can form parts of a bigger structure, i.e. complete protein. MOL is an entity representing small molecule (as opposed to macromolecule) which, in complex with polypeptide, forms a functional protein. Users can query by COMe ID or using a case sensitive or insensitive text search, use predefined queries, or look at the paths via the online ontology provided by COMe.
Comparasite is an integrated database of our original full-length cDNA sequence data. It consists of seven sub-databases of apicomplexa protozoa, Plasmodium falciparum, Plasmodium yoelii, Plasmodium vivax, Toxoplasma gondii, Cryptosporidium parvum, Echinococcus multilocularis. Homologous gene groups are clustered and comparative analysis of any combination of these seven species is implemented, such as interspecies comparisons as to cellular localization, motifs or transmembrane regions and so on. For submitted keywords and other search conditions, Comparasite retrieves orthologous gene groups containing a given protein motif/GO term etc in common or in a species-specific manner. By enabling multi-faceted comparative analyses of genes of apicomplexa protozoa, monophyletic organisms that have evolved to diversify to parasitize various hosts by adopting complex life cycles, Comparasite should help elucidate the mechanism behind parasitism.
CORG - A database for COmparative Regulatory Genomics
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Non-coding DNA segments that are conserved across multiple homologous genomic sequences are good indicators of putative regulatory elements. We use a systematic approach to delineate such conserved non-coding blocks from a collection of vertebrate species. Upstream regions of homologous gene pairs from man, rhesus monkey, mouse, rat, dog, cow, chicken, tetraodon, zebrafish and xenopus are considered for this purpose. Pairwise as well as Multiple alignments based on the pairwise ones are available. Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and provide the CORG-''COmparative Regulatory Genomics''-database. The data were computed based on statistically significant local suboptimal alignments of 15 kb regions upstream of the translation start sites of, currently, 10 793 pairs of orthologous genes. The resulting conserved non-coding blocks were annotated with EST matches for easier detection of non-coding mRNA and with hits to known transcription factor binding sites. CORG data are accessible from the ENSEMBL web site via a DAS service as well as a specially developed web service for query and interactive visualization of the conserved blocks and their annotation.
The FlyTF database contains information on the manual curation of FlyBase identifiers based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database. FlyBase identifiers are putative site-specific transcription factors. There are currently1052 of them in this database.
The Crop EST Database (CR-EST) is a public available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at the IPK. Summarized numbers about genomic data of species are listed in tables. The main database content is original sequence data and cDNA library information from different organisms as well as results from BlastX searches against major protein sequence databases contained in NRPEP. Additionally sequence alignments of stackPACK clustering projects are available. This web application allows to BLAST against CR-EST ESTs and to query and retrieve data from Gene Ontology and metabolic pathway annotations as well as sequence similarities from stored results of BLASTX searches against the NRPEP database. CR-EST also features interactive JAVA-based tools, such as open reading frame visualization and explorative analysis of Gene Ontology mappings to ESTs.
CREMOFAC: A web-database of Chromatin Remodeling Factors
CREMOFAC is a database for chromatin remodeling factors has been developed. The database harbors 64 types of remodeling factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. In addition, it also provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways, and phylogenetic relationships has also been covered.
A database of information about each Cancer-Testis (CT) gene, its gene products and the immune response induced in cancer patients by these proteins. CT antigens are proteins normally expressed only in the human germ line but that are also present in a significant subset of malignant tumors. The practical importance of these proteins is that due to their restricted expression pattern they are frequently recognized by the immune system of cancer patients. Moreover, this antigenicity has raised the possibility of their being used as vaccines to actively stimulate immune responses in order to combat tumor growth. As a result worldwide research into many aspects of CT antigens is rapidly growing prompting the construction of this database as a resource for investigators involved in this area.
CyanoBase provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. Users can view by data type, search using BLAST2, or search by species.
Cyclonet database is a database on cell cycle regulation in eukaryotes. The database contains information about cell cycle specific genes, proteins, protein complexes and their interactions, diagrams of cell cycle regulation for vertebrates, models of cell cycle and results of their analyses, microarray data, literature references and other related resources. The data are compiled from different databases and from literature annotation. Known cell-cycle models are imported from SBML and CellML model repositories and developed by ourselves.
The Cypriot National Genetic Database is an online repository of information about inherited disorders in the Cypriot population. The Cypriot National Genetic Database results from the fruitful collaboration among several investigators from Erasmus Medical Center (The Netherlands) and Kypriako Idryma Erevnon Gia Ti Myiki Distrofia (Cyprus) encouraged by the Human Genome Variation Society and financially supported in part by the European FP6 INCO grant MedGeNet and by Asclepion Genetics in Switzerland.
Database of Liver Protein Expression Profile- dbLEP
The Liver Expression Profile database aims to be an information center of liver protein expression profile. dbLEP contains two datasets, with plans to provide more datasets in the future. For each dataset, dbLEP provides all identification results including none-redundant identified protein, all possible identified proteins, peptides and their spectrums. The detailed annotation is also provided for each identified protein. Benefit from large number of intact data resources, abundant links and flexible search functions, researchers may get all the information for the proteins they are interested in by text query or similarity comparison. Besides of judging the quality of the identified proteins according to their identified peptides and spectrums, researchers could analysis these data using the annotation information. We hope dbLEP could help you step from data to knowledge finally.
dbPTM: An informational repository of proteins and post-translational modifications
dbPTM is a database that compiles information on protein post-translational modifications (PTM) such as the modified sites, solvent accessibility of surrounding amino acids, protein secondary and tertiary structures, protein domains, and protein variations. The version 2.0 of dbPTM integrates the experimentally validated PTM sites with referable literatures from Swiss-Prot, Phospho.ELM, O-GLYCBASE, and UbiProt. In all of the collected PTM information, about 25 types of PTM with enough experimentally validated sites are trained the profile hidden Markov models (HMMs) to detect the potential PTM sites with 100% specificity against Swiss-Prot proteins. To help users investigating more detail in each type of PTM, the substrate peptide specificity such as positional amino acid frequency, solvent accessibility and secondary structure surrounding the modified sites are also provided. Moreover, the information of orthologous protein clusters is provided to users for analyzing whether the PTM sites located in the evolutionary conserved regions or not., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
DBTGR provides information on tunicate gene regulation, such as the location of expression, or the identified regulatory elements present in promoter sequences. The database also contains the promoters of homologous genes in multiple species to allow identification of conserved cis elements.
Dragon Database for Exploration of Ovarian Cancer Genes
:DDOC provides a comprehensive compilation of the published research related to the genes associated with ovarian cancer. DDOC provides details of the cell line, tissue or cell type, expression status, disease stage, tumor grade, OC type and laboratory method provided in the literature. The links to the relevant sources of data used to extract information related to genes are also included. Many aspects of the information provided in the DDOC were curated by biologists, which increases its accuracy. DDOC is freely accessible for academic and non-profit users.
Decoys-R-Us is a database of decoys, computer-generated conformations of protein sequences that possess some characteristics of native proteins, but are not biologically real. The primary use of decoys is to test scoring, or energy, functions. All the decoys in the Decoys ''R'' Us database can be downloaded.
The defensins knowledgebase is a manually curated database and information source devoted to the defensin family of antimicrobial peptides. The current version of the database holds a comprehensive collection of 363 defensin records each containing sequence, structure and activity information. A web-based interface provides access to the information and allows for text-based searching on the data fields. With the rapidly increasing interest in defensins, we hope that the knowledgebase will prove to be a valuable resource in the field of antimicrobial peptide research.
A database of human, chimpanzee, mouse, and rat proteases and protease inhibitors, as well as as the growing number of hereditary diseases caused by mutations in protease genes. Analysis of the human and mouse genomes has allowed us to annotate 581 human, 580 chimpanzee, 667 mouse, and 655 rat protease genes. Proteases are classified in five different classes according to their mechanism of catalysis. Proteases are a diverse and important group of enzymes representing >2% of the human, chimpanzee, mouse and rat genomes. This group of enzymes is implicated in numerous physiological processes. The importance of proteases is illustrated by the existence of 99 different hereditary diseases due to mutations in protease genes. Furthermore, proteases have been implicated in multiple human pathologies, including vascular diseases, rheumatoid arthritis, neurodegenerative processes, and cancer. During the last ten years, our laboratory has identified and characterized more than 60 human protease genes. Due to the importance of proteolytic enzymes in human physiology and pathology, we have recently introduced the concept of Degradome, as the complete repertoire of proteases expressed by a tissue or organism. Thanks to the recent completion of the human, chimpanzee, mouse, and rat genome sequencing projects, we were able to analyze and compare for the first time the complete protease repertoire in those mammalian organisms, as well as the complement of protease inhibitor genes. This webpage also contains the Supplementary Material of Human and mouse proteases: a comparative genomic approach Nat Rev Genet (2003) 4: 544-558, Genome sequence of the brown Norway rat yields insights into mammalian evolution Nature (2004) 428: 493-521, A genomic analysis of rat proteases and protease inhibitors Genome Res. (2004) 14: 609-622, and Comparative genomic analysis of human and chimpanzee proteases Genomics (2005) 86: 638-647.
Software package for TDT with extended haplotypes in the R language. R is the public domain dialect of S. It should be possible to port this library to the commercial Splus product. The main problem would be translation of the help files. (entry from Genetic Analysis Software)
DoOP - Databases of Orthologous Promoters
DoOP is a database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species. Based on the Arabidopsis thaliana and Homo sapiens genome annotation, we collected the orthologous promoter sequences from Viridiplantae and Chordata species. You can search the database with sequences or text (annotation) to find promoter clusters of different genes. In addition to the sequence and annotation data, the positions of the conserved regions and transcription start sites can be viewed graphically.
DPInteract is a database of DNA-binding site matrices. This dataset is being collected with several purposes in mind: 1. Cataloging demonstrated sites and non-sites for E.coli DNA-binding proteins; 2. Aiding the annotation of such sites in other E.coli databases and sequence entries; 3. Interpreting the results of whole-genome in vivo methylation protection experiments; 4. Developing better computational tools for recognizing DNA binding proteins in sequence data.
A database of published cross-link data of the E. coli ribosome. The website provides information on rRNA-rRNA cross-links, rRNA-rProteins cross-links, cross-links between ribosomal proteins, tRNA-ribosome cross-links, growing peptide-ribosome cross-links, factors-ribosome cross-links, and mRNA-ribosome cross-links. All data are presented in tables.
Database providing a collection of all the existing polymorphic sequences in the Drosophila genus. It allows users to search for any polymorphic set according to different parameter values of nucleotide diversity. For data collection, diversity measures and updating they use PDA, a pipeline made of a set of Perl modules that automates the process of sequence retrieving, grouping, aligning and estimating diversity parameters from GenBank sequences. Diversity measures, including polymorphism estimates in synonymous and non-synonymous sites, linkage disequilibrium and codon bias, are calculated for each polymorphic set in different functional regions. The database also includes the primary information retrieved from different external sources: the Drosophila publicly available nucleotide sequences (excluding ESTs, STSs, GSSs, working draft and patents) with their annotations and references from GenBank (see the NCBI's Disclaimer and Copyright), additional information of genes and aberrations (from FlyBase), and the cross-references to the PopSet database (from NCBI). The database content is updated daily and records are assigned unique and permanent DPDB identification numbers to facilitate cross-database referencing.
DSD: a database of dehydrogenase stereospecificities
DSD is a database of dehydrogenase stereospecificities. It provides stereochemical data and BLASt capability, and also presents other tools to allow users to freely access enzyme stereochemistry data. Users can search using keywords, BLAST, or by enzyme, enzyme type, species, organ/tissue, coenzyme, method, or side.
DSMM - a Database of Simulated Molecular Motions
DSMM provides an easily-searchable source of information about movies showing biomolecular motions that have been generated by computer simulation. All of the movies are available through the internet. Molecules simulated include proteins, DNA, RNA, sugars and lipids. Simulation techniques include Molecular Dynamics, Brownian Dynamics and automated docking procedures.
The iProClass database provides value-added information reports for UniProtKB and unique UniParc proteins, with links to over 90 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genomes, ontologies, literature, and taxonomy. iProClass combines both data warehouse and hypertext navigation methods for integrating data, providing a comprehensive picture of protein properties that may lead to novel prediction and functional inference for previously uncharacterized hypothetical proteins and protein groups.
It presents an advanced online database for dynamic access to proteomes and two-dimensional (2D) gels. The database was designed to administer complete in silico proteomes and links them with experimental proteomic data in the manner of 2D electrophoresis gels (IPG-Dalt). The 2D gels serve as reference maps in 2D gel analysis as well as tools for navigation of the database to switch between experimental and predicted data. Therefore, all identified spots in the gels are clickable and linked with summarized protein information. The protein information tables contain calculated characteristics, which are often used in proteomics, such as the molecular weight, isoelectric point, codon adaptation index, grand average of hydropathicity, etc. The design of the database permits online extension of gel data and protein attributes without knowledge of any software language. Besides navigation via 2D gels, the clear graphical user interface permits quick and intuitive searching throughout complete proteomes and supports, e.g. the search for proteins with isoelectric points within pH ranges of interest or protein classes (e.g. ribosomal proteins or transporters). The first organism implemented in the database is Lactococcus lactis.
ECgene: Gene Modeling with Alternative Splicing
ECgene - Genome Annotation for Alternative Splicing
Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns.
The EcID database (E. coli Interaction Database) provides a common framework for exploring the sizeable amount of protein interaction-related data available for Escherichia coli. EcID integrates information related with functional interactions extracted from the following sources: EcoCyc (metabolic pathways, protein complexes and regulatory information) KEGG (metabolic pathways) and MINT (protein interactions). :It also contains information on protein complexes from the two published high throughput pull down experiments carried out in E. coli, and potential interactions directly extracted from the literature using the web-services associated to the iHOP text-mining system. Additionally, EcID incorporates results from two protein interaction prediction methods based on genomic information (Phylogenetic Profiles and Gene Neighborhoods) and three methods based on analysis of the potential co-evolution of the corresponding protein families (Mirror Tree, In Silico 2 Hybrid and Context Mirror). EcID associates to each predicted pair a confidence score that reflects the reliability of the functional interaction between those two proteins. :In order to provide a global score to combine the predictive power of the prediction methods described above we have integrated in EcID a Bayesian-based classifier. This method includes the scores of five different prediction methods (Phylogenetic Profiles, Gene Neighborhood, Gene Fusion, Mirror Tree and In Silico 2 Hybrid), together with information on a number of simple sequence features. The classifier was trained to predict the type of protein functional associations contained in EcID (derived from regulation data, biochemical pathways, protein complexes and protein physical interactions).
Encyclopedia of Hepatocellular Carcinoma Genes Online
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ECHO is a web resource of Hepatocellular Carcinoma genes. The fundamental part of EHCO2 is the collections of thirteen gene sets related to HCC. It also contains tools to search by homology, pathway, or phenotype.
EICO DB - Expression-based Imprint Candidate Organiser
EICO DB is an integrated database for discovery of novel imprinted genes. EICO DB provides candidate imprinted genes by cDNA microarray and single Nucleotide Polymorphisms between MSM and C57BL/6J within RIKEN mouse full-lenght cDNA for validation of imprinting. The tools provided by the website are candidate Imprinted Transcripts by Expression (CITE), MoUse SNP CATalog (MuSCAT), EICO DAS Server, and EICO Wiki.
EMGlib - Enhanced Microbial Genomes Library
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database devoted to the completely sequenced bacterial genomes and the yeast genome. Starting from the sequences available in the "genome" division of GenBank, we have improved and corrected their annotations and structured the flat files using the ACNUC database management system.
A database that provides information about endocrine networks. Using information about hormones' donor and acceptor cells a network is built that represents hormonal signaling pathways as a bipartite graph comprising hormones and tissues as node classes. The involved components, the intercellular information flow and the inhibition or activation effects are displayed. For each entity a detailed page is available. To represent some known pathways predefined sets are prepared. These sets can be used for quick overview or as starting point for a more complex query It is possible to search for hormones, receptors or tissues and combine several items from different searches in one complex set, from which the network is built.
Epitome is a database of structurally inferred antigenic epitopes in proteins. It includes all known antigenic residues and the antibodies that interact with them, including a detailed description of residues involved in the interaction and their sequence/structure environments. Additionally, Interactions can be visualized using an interface into Jmol. The website also contains specialized software, NLProt, to enable users to extract protein names and sequences from natural language text, and links to several other databases involved in antibody/antigen interactions. antibody/antigen interactions, antigen epitope
Database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites. This database is no longer maintained or updated.
The aim of the Ethanol-Related Gene Resource (ERGR) database is to provide a comprehensive and useful gene resource to the Ethanol/Alcohol research community. Currently, the ERGR database contains more than 30 large datasets from literature and 21 mouse QTLs from public database. These data are from 5 organisms (human, mouse, rat, fly and worm) and produced by multiple approaches (expression, association, linkage, QTL, literature search etc). Users can browse or search the database in different levels. Moreover, ERGR provides data integration (union and intersection) and candidate gene selection based on multiple datasets or organisms.
Enteropathogen Resource Integration Center
Enteropathogen Resource Integration Center (ERIC)
ERIC is a resource of annotated enterobacterial genomes. Information is available and accessed through a open web portal uniting biological data and analysis tools. ERIC contains information on Escherichia, Shigella, Salmonella, Yersinia, and other microorgansims. ERIC has recently been moved over to PATRIC: The PATRIC BRC is now responsible for all bacterial species in the NIAID Category A-C Priority Pathogen lists for biodefense research, and pathogens causing emerging/reemerging infectious diseases. For ERIC users, we understand that the resource was valuable to your work. As such, we will be doing our very best to create a useful PATRIC resource to continue supporting your work. We realize that the transition will cause disruptions. However, it is a priority for us to work with established BRC users and communities to identify and prioritize our transition efforts. We have concentrated on the transfer of genomic data for this initial release. We anticipate adding new data, tools, and website features over the next several months. We look forward to working with you during the next 5 years., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 23, 2016. The euHCVdb is oriented towards protein sequence, structure, function analysis and structural biology of the Hepatitis C Virus. It is monthly updated from the EMBL Nucleotide sequence database and maintained in a relational database management system (PostgreSQL). Programs for parsing the EMBL database flat files, annotating HCV entries, filling up and querying the database used SQL and Java programming languages. Great efforts have been made to develop a fully automatic annotation procedure thanks to a reference set of HCV complete annotated well-characterized genomes of various genotypes. This automatic procedure ensures standardization of nomenclature for all entries and provides genomic regions/proteins present in the entry, bibliographic reference, genotype, interesting sites (e.g. HVR1) or domains (e.g. NS3 helicase), source of the sequence (e.g. isolate) and structural data that are available as protein 3D models. The euHCVdb is funded as part of the HepCVax cluster (EC grant QLK2-CT-2002-01329) and viRgil network of excellence (EC grant LSHM-CT-2004-503359).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017. Software application (entry from Genetic Analysis Software)
Ontology for host pathogen interactions in farmed animals
The University of Rennes 1 is one of the two main universities in the city of Rennes, France. It is under the Academy of Rennes. It specializes in science, technology, law, economy, management and philosophy.
EVEREST - EVolutionary Ensembles of REcurrent SegmenTs
EVEREST is an automatic process of identifying and classifying of protein domains. Users can search for specific proteins using Protein ID or name, browse through protein families, and upload/download protein sequence data. EVEREST combines methodologies from the fields of finite metric spaces, machine learning and statistical modeling and achieves state of the art results. The process begins by constructing a database of protein segments that emerge in an all vs. all pairwise sequence comparison. It then proceeds to cluster these segments into putative domain families, choosing the best putative families using machine learning techniques, and creating a statistical model for each of the chosen families. This procedure is then iterated: The aforementioned statistical models are used to scan all protein sequences, to recreate a segment database and to cluster them again. Performance was evaluated by comparing with Pfam and SCOP.
Evola is a sub-database of H-InvDB, providing ortholog data as evolutionary annotation. Representative transcripts (one transcript per one gene locus) were analyzed as genes. Orthologs were first detected by computational analysis. Then, more reliable orthologs were determined by manual curation inspecting the phylogenetic trees., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
EXProt- database for EXPerimentally verified Protein functions
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. EXProt (database for EXPerimentally verified Protein functions) is a new non-redundant database containing protein sequences for which the function has been experimentally verified. EXProt is a selection of 6491 entries which are described to have an experimentally verified function. The entries in EXProt all have a unique ID number and provide information about organism, protein sequence, functional annotation, link to entry in original database, and if known, gene name and link to references in PubMed. The EXProt database can be searched with BLAST or FASTA with amino acid or nucleotide sequence as query sequence. Note that only the sequence goes into the field. EXProt database is also searchable in SRS6 at CMBI. In a near future entries from the genome project of Lactobacillus plantarum by Wageningen Centre for Food Sciences (WCFS) will be added to EXProt.
F-SNP: a collection of functional SNPs, specifically prioritized for disease association studies
F-SNP database provides integrated information about the functional effects of SNPs obtained from 16 bioinformatics tools and databases. The functional effects are predicted and indicated at the splicing, transcriptional, translational, and post-translational level. As such, the F-SNP database helps identify and focus on SNPs with potential pathological effect to human health. Users can find SNP's based on ID, associated disease, gene, or chromosomal region.
FCP is a publicly accessible web tool dedicated to analyzing the current state and trends of available proteome structures along the classification schemes of enzymes and nuclear receptors. It offers both graphical and quantitative data on the degree of functional coverage in that portion of the proteome by existing structures and on the bias observed in the distribution of those structures among proteins. Users can choose to search the website based on structures or ligands, and can also sort by enzyme or receptor. Users can also view data based on structural and population (species) filters.
A database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords. FireDB contains information on every chemical compound in the PDB, including their descriptions, the PDB structures in which the compounds are found and the amino acids that are in contact with the ligand.
University of Rhode Island; Rhode Island; USA
Evolutionary Tree - Transmission Disequilibrium Test
It is an automated system for human transcripts (mRNA & ESTs) annotation and elucidation of de-novo genes. GeneTIDE aims to integrate various data resources in order to create a comprehensive list of human genes. This is done by association between the set of over ~5.5 million human ESTs currently available from dbEST and mRNA sequences from GenBank to the set of ~35,000 human genes as defined in GeneCards. Heretofore transcripts (mRNA & EST) can be : :1. Proven to belong to an existing GeneCards gene :2. Used to define de-novo genes :3. Demonstrated to be an artifact or contaminated(genomic DNA, vector, etc.), and should therefore be discarded.
A database for the functional analysis of the Arabidopsis genome. The ultimate objective of this project is to develop a database and associated bioinformatics tools based on the integration of genomic data around a selection of plant complete genomes. This tool will help users to understand the biological role of plant genes by considering them in a wide context: a multigene family, a topological environment, and/or a functional network. The database and the associated user-friendly interface is developed with a conceptual effort for the graphical display and the hierarchical organization of the data. The running integration involves the structural and functional international annotations, EST from different plant species, novel gene predictions, mutant tags, gene families, protein motifs, transcriptome data, repeat sequences, primers and tags for genomic approaches (DNA chips, synteny studies, BAC library screening, RT-PCR, SNP discovery, ...), subcellular targeting, secondary structures, 3D models, MPSS tags, curated annotations and mutant phenotypes.
A database that has been designed to facilitate the integration of data from high-throughput experiments carried out in Drosophila cell culture. It includes phenotypic information from published cell-based RNAi screens, gene expression data from Drosophila cell lines, protein interaction data, together with novel tools to cross-correlate these diverse datasets, such as the phenotype clustering tool Shuffle. We believe it will complement existing Drosophila databases and will prove useful to researchers working in other organisms who are looking for a simple way to navigate their way through the fly genome.
MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous System
An interactive database of the Drosophila melanogaster nervous system. It is used by the drosophila neuroscience community and by other researchers studying arthropod brain structure. Flybrain contains neuroanatomical peer reviewed descriptions of the central and peripheral nervous system of Drosophila melanogaster. It also contains an introductory hypertext tour guide to the basic structure of the nervous system, as well as more specific information concerning different anatomical structures, developmental stages, and visualization techniques for the Drosophila nervous system. Additionally, The site contains schematic representations, a 3D project, immunocytology stains, a library of golgi impregnations, and enhancer-trap images.
FlyEx is a database that stores quantitative data on gene expression in segmentation genetic network in fruit fly Drosophila melanogaster. It includes images of gene expression patterns, quantitative and processed data, conceptual schemes, and integrated patterns constructed from available data. The design of the FlyEx database is supported by awards from the Center for Research Resources of the NIH, grant RR-07801. Drosophila melanogaster genome, Drosophila gene expression, Drosophila segmentation
This project aims to provide the information and technical resources to support high-throughput positional cloning in Drosophila melanogaster. These resources include a high-density genome-wide map of single nucleotide polymorphisms (SNPs), and inexpensive, high-throughput assays for SNP genotyping. The specific aims were as follows: 1. To establish a map of >2200 SNP marker loci in the Drosophila genome. These SNP markers have been identified in several commonly used genetic strains. The FlySNP project identified SNP markers within the sequenced, euchromatic regions of the X, 2nd and 3rd chromosomes. The average distance between SNPs is about 50 kb. 2. To establish robust, high-throughput assays for SNP genotyping. Assays have been established using PCR, microarray and mass-spectrometry methods. The tag-array mini-sequencing (TAMS) approach has proven to be an especially fast and reliable method for SNP genotyping.
fRNAdb is a database of comprehensive non-coding RNA (ncRNA) sequences including known (or previously reported) ncRNAs, which are acquired from other sequence databases, and ncRNA sequences reported by the joint research groups of the Functional RNA Project. It is funded by the New Energy and Industrial Technology Development Organization.
FATCAT Flexible Structural Neighborhood Database
Flexible Structural Neighborhood is a database of structural neighbors of proteins as seen by FATCAT - a flexible protein structure alignment program. The server accepts either a protein (PDB ID) or a domain (SCOP ID) as a query. For the former case, the server first displays the information of chains and domains of a given protein. Afterwards, users can retrieve similar structures for a domain (if domain information is available, i.e., the protein is collected by SCOP), or for a chain otherwise. The protein structure database we collected for similar structure search includes a representative set at 90% sequence identity of SCOP domains, and of up-to-date PDB entries that are not included in the latest release of SCOP.
Full-Length cDNA Database is a resource for cDNA libraries of arhtropods and parasites. The arthropod species covered are Anopheles stephensi, Glossina morsitans (Tsetse fly), and Dermatophagoides farinae (House dust mite), while the parasitic species included are Plasmodium falciparum (Malaria), Toxoplasma gondii, Cryptosporidium parvum, Babesia bovis (Babesia), and Echinococcus multilocularis. A specialized database of each species is available as a link from the home page. This database has been constructed and maintained since 2001 by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science. Anopheles stephensi, Glossina morsitans, Tsetse fly, Dermatophagoides farinae, House dust mite, Plasmodium falciparum, Malaria, Toxoplasma gondii, Cryptosporidium parvum, Babesia bovis, Babesia, Echinococcus multilocularis, cDNA, cDNA library, arthropod genome, parasite genome
FUNPEP: Information system for low complexity sequence regions
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. As a part of the FUNPEP project, we made a small collection of peptides, which are known to form these amyloid plaques (Known amyloidogenic peptides). Sequences, including respective animal analogues, were extracted from SWISSPROT, and aligned. These sequences and some words about the peptides can be found under the links in the table below. Some molecular modelling was also perfomed, to show some possible structures of amyloids. The peptides on these pages were not chosen because of some kind of sequence similarity, what is more, they hardly have any. Their common, and very starnge property is the ability to form amyloid plaques (or fibrils). The exact structure and the formation of these supermolacular structures are still subject of research, but there are lots of promising results.
GELBANK is a government project that provides an interactive interface for the comparison of 2DE patterns in the context of proteome sequence queries. Only proteomes of species with completed genomes (bacterial genomes, some eukaryotic genomes, human proteome) are presented in the database. The image database also contains not only scanned images, but also modeled gel patterns representing a collection of images (e.g. a master pattern for a sample). 2DE gel patterns are grouped by: tissue type, sample type, staining method used, separation technique used in the first dimension (by charge), the pH-range of the media used in first dimension, technique used in the second dimension (by size). Tools pertinent to the querying of two-dimensional gel-electrophoresis are implemented and integrated into database. When searching for sequences, tools that allow allow the discovery of sequences and alignment of multiple sequences are presented. Individual 2DE gel-patterns can be displayed or a collection of patterns can be animated.
GENATLAS contains relevant information with respect to gene mapping and genetic diseases. GENATLAS compiles the information relevant to the mapping efforts of the Human Genome Project. This information is collected from more than 48,000 articles in the literature, collected in more than 870 reviews. The articles are daily analyzed by annotators to update the GENATLAS database. Only the objects with a known cytogenetic location are retained. GENATLAS repertories three kinds of objects Genes database ( more than 21.000 entries) Phenotypes database ( 4104 entries , 2000 cloned) References database linked to the two previous ( more than 48000 entries)
Genomic Distribution of structural Superfamilies
Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases. GenDiS has been curated in direct correspondence with SCOP and represents 4001 highly resolved domains in 1194 structural superfamilies across protein sequence databases. Sequences showing reliable homology to entries in SCOP and PASS2 databases have been obtained from the non-redundant protein sequence database and aligned. Similar alignments of the superfamily members are provided in the genome level. GenDiS provides a platform for cross genome comparison at the superfamily level. GenDis relates proteins sequence information across all strata of taxonomy. One may navigate through the database to obtain structural homologues across different levels in taxonomic classification. The nomenclature of the various genomes and their hierarchy is in direct correspondence with the taxonomy database maintained at the NCBI. Sequence homologues for the various structural members are obtained from the non-redundant protein sequence database employing sensitive sequence search methods. Multiple approaches such as PSI-BLAST, HMMsearch of the HMMer suite and an interacting motif constrained PHI-BLAST have been employed to identify homologues in the sequence databases.
A database of gene expression in tooth. It includes expression information on the initiation, bud, cap, bell, differentiation, and secretory stages, as well as on root development. The website also examines epithelial layers, growth factors and receptors, signaling molecules and transcription factors.
A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match. Where such matches are not found, probe-sets are annotated by their relation to GenBank mRNA sequences and UniGene clusters. The results are integrated with the GeneCards, GeneLoc and GeneNote databases. HG-U95, HG-U133, HG-U133
GeneFarm is a database of structural and functional annotation of plant gene and protein families. The goal of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for plant nuclear genes and gene products and to enter them into added-value database. The improved annotation will allow better data mining of the plant genomes (mainly Arabidopsis thaliana), and more secure planning and design of experiments. It is also a necessary step for building knowledge management tools for integrating plant genomic data, either for plant breeding or to get a broader interactive view of plant biological processes, like gene interaction networks. This re-annotation project, launched is mainly focused on gene families. A complete annotation pipeline using the most efficient prediction tools has been defined. The involved partners, each contributing with genes from his/her field of expertise, have exhaustively annotated families of homologous genes. A database named GeneFarm (Gene Families for Arabidopsis Management) gathers all these expert-curated annotations of plant gene families. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. GeneTrees provides an interface to databases and analysis methods designed to explore the global phylogenetic patterns of gene homology groups within and across species. GeneTrees consists of several databases of pre-compiled alignments and gene phylogenies for a variety of taxonomic groups. Within each taxonomic group, genome-scale sequences have been globally searched for mutually consistent conserved homology groups.
GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources. The GeneLoc algorithm creates an integrated map of the human genome. GeneLoc unifies gene collections, eliminates redundancies, and assigns each gene a meaningful location-based identifier, which also serves as its GeneCards ID. GeneLoc currently uses gene sets from NCBI and Ensembl. It compares these collections, deciding which entries should be consolidated and which are discrete. Since the gene annotations use the same assembly and coordinate scheme, GeneLoc effects this gene integration by comparing genomic locations. The resulting GeneLoc 'gene territory' reflects the range of the unified genes, taking into account every exon. Additionally, DNA segments, classified by categories (such as STSs mapped by various methods and EST clusters) are presented, alongside the genes, on a Megabase-scale map, with further information and links to relevant databases. Coming soon: genomic clones and more EST clusters will be added to the GeneLoc map. GeneLoc includes data from numerous resources, including the Genome Database, Whitehead Institute/MIT Center for Genome Research, Genethon, NCBI and others.
GeneNest is a comprehensive visualization of gene indices of several organisms. The aim of GeneNest is to represent each gene by a single cluster of ESTs and/or mRNAs. Further subdivision of a cluster into contigs may be caused by alternative splicing, genomic sequences, or artifacts like chimeric sequences. Consensus sequence derived from GeneNest contigs are a basis for mapping genes onto the genome, and for analysis of splice isoforms. Organisms included are human, mouse, arabidopsis, zebrafish, drosophila, and sheep. human, mouse, arabidopsis, zebrafish, drosophila, sheep, EST, mRNA, alternative splicing, genomic sequences
Integrated system GeneNetWorks is designed for accumulation of experimental data, data navigation, data analysis, and analysis of dependencies in the field of gene expression regulation. It integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description. The unique property of above described system is that all the resources within the system GeneNetWorks are divided according to the natural hierarchy of molecular genetic systems and has the following levels: (1) DNA; (2) RNA; (3) proteins; and (4) gene networks. Each module contains: 1) experimental data represented as a database or some sample; 2) program for data analysis; 3) results of an automated data processing; 4) tools for the graphical representation of these data and the results of the data analyses.
THIS RESOURCE IS NO LONGER IN SERVICE, documented June 14, 2013. GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E. It offers: An expression profile (tissue vector) for each gene in the human genome Gene and tissue clustering based on expression profiles A full genome ranking procedure according to the gene''s tendency for tissue specificity, from tissue-specific to housekeeping genes.
A digital atlas of gene expression patterns in the mouse. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. An accompanying atlas based on maps of sagittal sections at embryonic day 14.5. E14.5 NMRI embryo was prepared, sectioned and imaged identically to the embryos used for in situ hybridization. Maps are accessed from the set viewer page using the appropriate button above the image directory. Both, the in situ hybridization section and the appropriate atlas section can be viewed side-by-side. Section thickness is 20 m and inter-section distance is 100 m. Tissue was stained with cresyl violet (Nissl-method). All sections were digitally scanned using a 5x objective. Structures annotated for gene expression are indicated in the maps with red pointers. Boundaries between brain regions are indicated with dashed yellow lines.
Genetics Home Reference provides consumer-friendly information about the effects of genetic variations on human health. Genetics Home Reference contains condition summaries (describing major features of genetic conditions), gene summaries (describing normal function, chromosomal location, etc), and gene family summaries.
A database of high-throughput data being collected to understand comprehensively the living E. coli K-12 model cell. GenoBase is a public repository for sequence information, proteome, transcription, and metabolome data. The GenoBase contains columns labeled Gene, Synonym, ECK, Genome, ID, Left, Right, Direction, Description, Comment, and Status. The table displays two rows for each gene: one row shows data for the E. coli K-12 MG1655 genome; the other shows data for the E. coli K-12 W3110 genome. Left, Right, and direction give the coordinates and orientation of the gene. Search/Clip allows the user to find information in GenoBase based on gene, position, or DNA sequence. References is currently not fully operational. Other search allows execution of an SQL query., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
GenoList is a resource for microbial genomes. It provides links to databases that give information on specific microbes. A link to the Genolist itself also incorporates many microbial genomes and search and analysis tools. Of the links provided on the GenoList homepage, species included are: Bacillus subtilis Escherichia coli Mycobacterium tuberculosis Mycobacterium leprae Mycobacterium bovis Mycobacterium ulcerans Listeria monocytogenes Legionella pneumophila Helicobacter pylori Mycoplasma pulmonis Synechocystis Anabaena Staphylococcus aureus Streptococcus pneumoniae Streptococcus agalactiae Photorhabdus luminescens Candida albicans Bacillus subtilis Escherichia coli Mycobacterium tuberculosis Mycobacterium leprae Mycobacterium bovis Mycobacterium ulcerans Listeria monocytogenes Legionella pneumophila Helicobacter pylori Mycoplasma pulmonis Synechocystis Anabaena Staphylococcus aureus Streptococcus pneumoniae Streptococcus agalactiae Photorhabdus luminescens Candida albicans
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2013. GIB is a comprehensive data repository of complete microbial genomes in the public domain. GIB will diffuse the genome sequence data and annotation in a day whenever the data is submitted to the International Nucleotide Sequence Databases (DDBJ, EMBL database and GenBank). You can explore any microbial genome by clone name, ORF name/number, function, gene name, product name, location, sequence (namely, homology search), and other features/qualifiers defined by INSD. The result of query is displayed either in graphics or in a table format.
THIS RESOURCE IS NO LONGER IN SERVICE, documented April 24, 2017. The Genome Reviews database provides an up-to-date, standardized and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota. Genome Reviews is available as a MySQL relational database, or a flat file format derived from that in the EMBL Nucleotide Sequence Database. An Ensembl-style browser is now available for Genome Reviews, providing a zoomable graphical view of all chromosomes and plasmids represented in the database. The location and structure of all genes is shown and the distribution of features throughout the sequence is displayed.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 29,2022. Whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
An R package for ranking ChIP-seq peaks with shape information.
The Genomic Threading Database (GTD)is a fast and powerful protein fold recognition method, whichcontains structural annotations of proteomes, translated from the genomes of key organisms. GenTHREADER can be applied to either whole, translated genomic sequences (proteomes), as in the case of the GTD, or individual protein sequences, as in the case of the PSIPRED server. Annotations are made using a modified version of our recently developed GenTHREADER software.
Collection of male germ cell transcriptiome information derived from Serial Analysis of Gene Expression (SAGE). It includes the three key germ cell stages in spermatogenesis, including mouse type A spermatogonia (Spga), pachytene spermatocytes (Spcy), and round spermatids (Sptd). A total of 452,095 SAGE tags are represented in all the libraries and is by far the most comprehensive resource available. Users can choose a global view of germ cell transcriptome data in the UCSC Genome browser. They can also search genes or specify searching criteria based on tag sequence, chromosomal location or tag counts.
GLIDA is a database developed for those who work in the field of GPCRs-related drug discovery and need information on both GPCRs and their known ligands. It has the following characteristics: 1) A complex information system covering biological information of GPCRs as well as chemical information of their known ligands. 2) Two starting points : Enterable either by GPCR search or ligand search. 3) Cross-searchable between GPCRs and their ligands. The pages of GLIDA are continuesly updated.
Gene Ontology Annotation (UniProtKB-GOA) Database
An annotation program which aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). It is a central dataset for other major multi-species databases, such as Ensembl and NCBI. Because of the multi-species nature of the UniProtKB, UniProtKB-GOA assists in the curation of 200,000 species. This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. Gene Association Files can be accessed from the Downloads section of the website.
A taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts It contains single reference whole-genome sequences for each species from which we have complete mitochondrial or chloroplast data. A new release of this database also includes 42,000 new mitochondrial sequences and 39,000 new chloroplast sequences.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The GO Partition Database was designed to feature ontology partitions with GO terms of similar specificity. The GO partitions comprise varying numbers of nodes and present relevant information theoretic statistics, so researchers can choose to analyze datasets at arbitrary levels of specificity. The GO Partition Database, featuring GO partition sets for functional analysis of genes from human and ten other commonly-studied organisms with a total of 131,972 genes.
A database for expression profiles of macrophages challenged with a a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults. The objectives of the database are: Provide access to quality assessed gene expression datasets Rapid access to gene expression profile macrophage treated with a variety of conditions Provide datasets for Systems biology
Software package aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3.
Grain Genes is a genome database for Triticeae and Avena. It contains tools that allow users to browse graingenes, search the MySQL database, and view maps, genetic markers, gene expression and sequences.
GRSDB2 is a second generation database of G-quadruplexes. Like its first version, GRSDB, it contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB2 is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. Computations were performed with the help of an indigenously developed and previously published software program QGRS Mapper. What is new in GRSDB2: The entire database has been built with a new and much improved version of QGRS Mapper program. It contains data from a large number of eukaryotic genes from several organisms in addition to human and mouse. The data model is different than the first version in that it is centered around Entrez Gene rather than solely GenBank/RefSeq nucleotide entries. The search module has been greatly enhanced. It is possible to search the database with Entrez Gene ID, Gene Name, Gene Symbols, Aliases, relevant Accession numbers and many other parameters like numbers of poly A signals and alternatively spliced products. Complex queries can also be performed. In addition, it is now possible to search the database with Gene Ontology terms. The list of genes matching the query can be sorted. The website also allows to manipulate the list to form sets of genes and perform further computations on these sets through a ''Workbench''. The Gene View, Data View and Graphic View for individual database entries have been significantly enhanced with several additional computational capabilities and links. The data can now be exported into Excel for further analysis. In addition, we have added a Sequence View which displays mapped G-quadruplexes in the context of pre-mRNA sequence. GRSDB2 replaces GRSDB at, http://bioinformatics.ramapo.edu/grsdb/index.php
GTOP is a database consists of data analyses of proteins identified by various genome projects. This database mainly uses sequence homology analyses and features extensive utilization of information on three-dimensional structures. GTOP is built by the Laboratory of Gene-Product Informatics at the National Institute of Genetics. This research is supported by the Japan Science and Technology Corporation and Grants-in-Aid for Scientific Research (Genomes in category C) from the Ministry of Education, Science, Sports and Culture of Japan. We use the following methods: Prediction of 3D structure Sequence homology search of PDB, using REVERSE PSI-BLAST. Functional predictions (family classifications) Sequence homology search of Swiss-Prot, a well-annotated sequence database, with the use of BLAST. Other analytical methods We are also carrying out the following analyses: Motif Analysis(PROSITE) Family classification(Pfam) Prediction of transmembrane helix domains(SOSUI) Prediction of coiled-coil regions(Multicoil) Repetitive sequence analysis(RepAlign)
It is a database of point mutations and short additions and deletions in the factor IX gene. The database attempts to offer a view of the spectrum of mutations causing haemophilia B that is as accurate as possible and this is helped by the fact that about 1/3 of all mutations have been detected as a result of full population studies. However, some bias cannot be completely avoided. Obviously there is an over-representation of severe haemophilia-causing mutations as these tend to be the first analysed and the most likely to come to notice. We also expect under-representation of double mutants as not all laboratories have done complete gene screens. Haemophilia B, Haemophilia B Mutation, IX, IX gene, IX gene mutation
Collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses. A major resource in HAGR is GenAge, which includes a curated database of genes related to human aging and a database of ageing- and longevity-associated genes in model organisms. Another major database in HAGR is AnAge. Featuring over 4,000 species, AnAge provides a compilation of data on aging, longevity, and life history that is ideal for the comparative biology of aging. GenDR is a database of genes associated with dietary restriction based on genetic manipulation experiments and gene expression profiling. Other projects include evolutionary studies, genome sequencing, cancer genomics, and gene expression analyses. The latter allowed them to identify a set of genes commonly altered during mammalian aging which represents a conserved molecular signature of aging. Software, namely in the form of scripts for Perl and SPSS, is made available for users to perform a variety of bioinformatic analyses potentially relevant for studying aging. The Perl toolkit, entitled the Ageing Research Computational Tools (ARCT), provides modules for parsing files, data-mining, searching and downloading data from the Internet, etc. Also available is an SPSS script that can be used to determine the demographic rate of aging for a given population. An extensive list of links regarding computational biology, genomics, gerontology, and comparative biology is also available.
High-quality Automated and Manual Annotation of microbial Proteomes
HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
Haptendb is a database of haptens which provide comprehensive information about the Hapten molecule, ways to raise antibodies against particular group of haptens, specificity and cross reactivity of raised antibody with related haptens, use of antibodies in constructing cost effective and simple detection kits. Major Features of the Database include: It covers wide array of haptens that includes; pesticides, herbicides, insecticides, drugs, vitamins, steroids, hormones, toxins, dyes, explosives, etc. The database contains 2021 entries for antibodies either raised against haptens or cross-reactivity of antibody raised against one Hapten with other related haptens. Every single record in the database contains detailed information about the Hapten, the carrier and the antibodies along with the assay methods and their sensitivity towards Hapten detection. The database provides information about 1087 haptens that includes: (i) common and chemical name of Hapten, (ii) molecular mass, physical and chemical properties, (iii) biological importance and the structure. Haptendb provides online web tools that allows users to retrieve and analyze the data that includes: (i) tools for searching database using keywords with many options and, (ii) browsing tool that allows the user to browse the database on Hapten name, carrier protein and antibody. The database has 2-D and 3-D structures of most of haptens in standard format based on information in literature. It also allows sketching structures online and searching of similar structures in database. One of the powerful tools in Haptendb is structure similarity search tool, which allows user to search similar structures.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The euHCVdb is a Hepatitis C Virus database oriented towards protein sequence, structure and function analyses and structural biology of HCV. In order to make the existing HCV databases as complementary as possible, the current developments are coordinated with the other databases (Japan and Los Alamos) as part of an international collaborative effort. It is monthly updated from the EMBL Nucleotide sequence database and maintained in a relational database management system. Programs for parsing the EMBL database flat files, annotating HCV entries, filling up and querying the database used SQL and Java programming languages. Great efforts have been made to develop a fully automatic annotation procedure thanks to a reference set of HCV complete annotated well-characterized genomes of various genotypes. This automatic procedure ensures standardization of nomenclature for all entries and provides genomic regions/proteins present in the entry, bibliographic reference, genotype, interesting sites or domains, source of the sequence and structural data that are available as protein 3D models. Hepatitis C, Hepatitis C Virus, Hepatitis C Virus protein .
Highly Expressed Genes Database (HEG-DB)
Genomic database that includes prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection.
HepSEQ is the International Repository for Hepatitis B Virus Strain Data. It is web-accessible, quality-based, molecular, clinical and epidemiological database for hepatitis B infection and provides a tool for the research community or for those involved in hepatitis B case management. This database currently has 1012 patient records and 1253 viral sequences. The quality of all submitted sequences is checked. The tools provided include: SeqMatch: search the database for matching sequences Genotyper: genotype HBV strains (based on HBV surface antigen genes) Gene Mutation: display the sequences that contain mutations in HBV coding regions Mutation Annotator: annotate sequences for mutation known to be associated with anti-viral resistance This web database development is funded by the UK Department of Health is curated and is hosted by the Health Protection Agency.
The Horizontal Gene Transfer DataBase (HGT-DB) is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer.
Kinomer is a multilevel HMM library that models these protein kinase groups. It allows accurate identification of protein kinases and classification to the appropriate kinase group. Profile hidden Markov models (HMMs) are statistical descriptions of sequence conservation from multiple sequence alignments, and have been shown to outperform standard pairwise sequence comparison methods, both in terms of sensitivity and specificity. HMMs form the basis of protein family and domain description libraries such as SUPERFAMILY and Pfam.
Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser.
Hetero-compound Information Centre- Uppsala
HIC-Up, the Hetero-compound Information Centre - Uppsala, a freely accessible resource for structural biologists who are dealing dealing with hetero-compounds ("small molecules"). This site contains information about hetero-compounds encountered in files from the Protein Data Bank (PDB). For every compound, a subset of the following information is available: Coordinate files (PDB and text files) Visualisation files (Chime and VRML) Dictionary files (X-PLOR/CNS, O, TNT) Links to off-site databases and servers (PDBsum, EDS, PRODRG, Relibase, MSDchem, ChemDB, Jena HCD, etc.) Miscellaneous files and information
Histone Database is a database of histones and their corresponding sequences. Sequence- and text-based searches were performed on NCBI's redundant and non-redundant (nr) peptide sequence databases. These databases are derived from GenBank, EMBL, and DDBJ translated DNA coding regions, plus protein sequences from the PDB (Protein Data Bank), SWISS-PROT, the PIR (Protein Information Resource), and the PRF (Protein Research Foundation). :Users can search by keyword, sequence fragment, category, organism, and redundancy of the set.
Curated collection of human metabolite and human metabolism data which contains records for endogenous metabolites, with each metabolite entry containing detailed chemical, physical, biochemical, concentration, and disease information. This is further supplemented with thousands of NMR and MS spectra collected on purified reference metabolites.
A human mitochondrial resource aimed at supporting population genetics and mitochondrial disease studies. It consists of a database of Human Mitochondrial Genomes annotated with population and variability data, the latter estimated through the application of a new approach based on site-specific nucleotidic and aminoacidic variability calculation (SiteVar and MitVarProt programs). The goals of HmtDB are: to collect and integrate the publicly available human mitochondrial genomes data; to produce and provide the scientific community with site-specific nucleotidic and aminoacidic variability data estimated on all the collected human mitochondrial genome sequences; to allow any researcher to analyse his own human mitochondrial sequences (both complete and partial mitochondrial genomes) in order to automatically detect the nucleotidic variants compared to the revised Cambridge Reference Sequence (rCRS) and to predict their haplogroup paternity. HmtDBs first release contains 1255 human mitochondrial genomes derived from public databases (GenBank and MitoKor). The genomes have been stored and analysed as a whole dataset and grouped in continent-specific subsets (AF: Africa, AM: America, AS: Asia, EU: Europe, OC: Oceania). :The multialignment and site-variability analysis tools included in HmtDB are clustered in two Work Flows: the Variability Generation Work Flow (VGWF) and the Classification Work Flow (CWF), which are applied both to human mitochondrial genomes stored in the database and to newly sequenced genomes submitted by the user, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Klotho: Biochemical Compounds Declarative Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of biochemical compound information. All files are available for download, and all entries are cataloged by accession number. Klotho is part of a larger attempt to model biological processes, beginning with biochemistry.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It provides access to the results of tests for positive selection in 14,000 human genes. Multiple alignments of protein-coding regions of genes from human and other mammals were extracted from whole-genome alignments available from UC-Santa Cruz. Each gene was analyzed using the maximum likelihood tests of selection using PAML. Branch, site, and branch+site tests were performed, each with at least one matching null model.
A database of homologous invertebrate genes, structured under ACNUC sequence database management system. It allows one to select sets of homologous genes among invertebrate species, and to visualize multiple alignments and phylogenetic trees. The database itself contains all invertebrate protein sequences from UniProt (SWISS-PROT+TrEMBL), with some data corrected, clarified or completed (notably to address the problem of redundancy and orthology/paralogy) and with some annotation modifications. It contains also all the corresponding nucleotide sequences in EMBL. Homologous proteins are classified into families and multiple alignments and phylogenetic trees are computed for each family. Sequences and related information have been structured in an ACNUC database. Thus, HOINVGEN is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOINVGEN gives an overall view of what is known about a peculiar gene family.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 23, 2013. Homophila utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase). Sequences are compared using NCBI's BLAST program. The database is updated weekly and can be searched by human disease, gene name, OMIM number, title, subtitle and/or allelic variant descriptions.
Hoppsigen is a nucleic database of homologous processed pseudogenes. It contains 5,823 human retroelements and 3,934 mouse retroelements. These retroelements were annotated and stored in the database HOPPSIGEN (Homologous processed pseudogenes). Sequences were grouped in families considering their homologies. The database contains 3,168 families of exclusively human (1,966) or mouse retroelements (1,202) and 323 families containing human and mouse retroelements. 5,206 human retroelements were annotated as processed pseudogenes (respectively 3,428 mouse retroelements). The database contains functional genes from ENSEMBL homologous to Hoppsigen retroelements.
HORDE - Human Olfactory Receptor Data Exploratorium
HORDE (The Human Olfactory Data Explorer) is a database of human Olfactory Receptors (ORs), the largest multigene family in multicellular organisms. You will find here information on the OR proteins, their gene structure and their genomic organization. Also available are OR repertoires of other mammalian species, along with a set of analysis tools. human olfactory receptor, :OR, OR proteins, olfactory receptor, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Computational Hot Spots of Protein Interfaces
It provides information about the evolutionary history of the residues on the interface and represents which residues are highly conserved on the interface. In this way, functionally and structurally important residues on the interface can be distinguished. Hotsprint contains overall properties of the interface such as number of computational hot spots on the interface, number of conserved residues on the interface, average conservation score of interface residues and buried ASA of the interface. Additionally, residues of the interface along with their position, name, conservation score, ASA in monomer, ASA in complex, type (contacting interface residue, neighboring interface residue or none) and whether the residue is computational hot spot or not information are presented.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A database system for retrieve human genome information in different data sources that are available to public. The information you could find here is automatically extracted from the genetic databases and shown with all data having the identifiers in common and linking to one another. HOWDY facilitates obtaining information of human genes by using official symbols and aliases approved by HGNC, GDB and Entrez Gene. It also provides a graphical view of the Human Genome maps for the finished contigs as well as radiation hybrid maps.
HumHot is a collection of human meiotic hot spots obtained from the literature along with interesting information on meiotic recombination and molecular features of meiotic hot spots. It is also updated as more hot spots get discovered in the human genome. The database can be queried by hot spot name or chromosome number.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 11th,2023. The database HOX Pro contains information about organization, functions and evolution of gene ensembles, key roles in which play homeobox-genes. It is aimed at: 1. analysis and classification of regulatory and coding regions in diverse homeobox and related genes; 2. describing mutations and knock-outs of hox-genes, as well as hereditary diseases related to these genes; 3. graphical representation, comparisons and classification of hox-genes expression patterns and profiles (sea urchin blastula, Drosophila blastoderm and imaginal discs, vertebrate limbs, mammalian brain, human EC cells); 4. comparative analysis of organization of hox-based genetic networks the nematode Caenorhabditis elegans the sea urchins Strongylocentrotus purpuratus and other echinids, the fruit flies Drosophila melanogaster and D.virilis, the vertebrates chicken and mouse; 5. analysis of phylogeny and evolution of homeobox genes and clusters.
HPID - Human Protein Interaction database
Database that provides human protein interaction information and integrated interaction and also finds proteins from databases that can potentially react with proteins submitted by users. The human protein interaction information was pre-computed by a statistical method from existing structural and experimental data, while the integrated human protein interactions are derived from BIND, DIP and HPRD. A score composed of three parts is assigned to the predicted interaction data, and those interactions with high scores were found reliable. HPID allows the user to use the protein IDs in EMBL, Ensembl, MIM, RefSeq, HPRD and NCBI to search protein interactions of interest. A set of web-based software tools has also been developed so that users can visualize and analyze protein interaction networks.
HPMR is a database of human plasma membrane ligands and receptors. Users can search for ligands or receptors to reveal their pairing partners and browse through ligand or receptor families to identify ligand-receptor relationships. Users can also submit their own microarray data to perform online genome-wide online searches for paracrine/autocrine signaling systems. Survey of transcriptomes based on liganded receptome allows the discovery of paracrine/autocrine signaling for known ligand-receptor pairs in previously uncharacterized tissues or developmental stages.
The Human Gene Expression Index (HuGE Index) aims to provide a comprehensive database to further our understanding of the expression of human genes in normal human tissues. mRNA expression levels of thousands of genes are obtained using high-density oligonucleotide array technology and used to create a public database. The website also provides interactive tools for researchers to query and visualize data over the Internet. To facilitate data analysis, genes are alsocross-referenced with their annotation in the LocusLink database at NCBI.
The Human BAC Ends Database is a database of sequences from the ends of bacterial artificial chromosome (BAC) clones. A whole genome sequencing approach has been described in a map-as-you-go strategy. The complete sequence of a seed BAC is searched against a BAC end database and the minimally overlapping clones in each direction are selected for sequencing. As coverage increases, BAC end sequences provide samples for whole genome survey. It currently contains 743,000 end sequences from 470,000 clones (20 X clone coverage and 12% sequence coverage), generated by TIGR, UofWashington and CalTech, providing a sequence marker every 5 kb across the genome. The coverage by paired-ends on chromosome 22 is over 5X. The project is funded by DOE.
Human Genome Segmental Duplication Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It contains information about segmental duplications in the human genome. The criteria used to identify regions of segmental duplication are: Sequence identity of at least 90, Sequence length of at least 5 kb, Not be entirely composed of repetitive elements. Background Previous studies have suggested that recent segmental duplications, which are often involved in chromosome rearrangements underlying genomic disease, account for some 5 of the human genome. We have developed rapid computational heuristics based on BLAST analysis to detect segmental duplications, as well as regions containing potential sequence misassignments in the human genome assemblies. Results Our analysis of the June 2002 public human genome assembly revealed that 107.4 of 3,043.1 megabases (Mb) (3.53) of sequence contained segmental duplications, each with size equal or more than 5 kb and 90 identity. We have also detected that 38.9 Mb (1.28) of sequence within this assembly is likely to be involved in sequence misassignment errors. Furthermore, we have identified a significant subset (199,965 of 2,327,473 or 8.6) of single-nucleotide polymorphisms (SNPs) in the public databases that are not true SNPs but are potential paralogous sequence variants. Conclusion Using two distinct computational approaches, we have identified most of the sequences in the human genome that have undergone recent segmental duplications. Near-identical segmental duplications present a major challenge to the completion of the human genome sequence. Potential sequence misassignments detected in this study would require additional efforts to resolve. The segmental duplication data and summary statistics are available for download. Data for Human Genome (based on the May 2004 Human Genome Assembly (hg17)) Visualize duplication relationships in GBrowse (GBrowse) Duplicon Pair relationships (GFF) Genes within duplication regions (HTML) Genome duplication content (MS Excel) The segmental duplication data can be visualized in a genome browser in the GBrowse section. Selected human genome annotation tracks (except the segmental duplication track) have also been obtained from UCSC and loaded into the genome browser. Detailed information (e.g. overlapping genes, overlapping clones, detailed alignment) can be obtained by clicking on a duplication cluster in GBrowse. Both keyword search and BLAT search are available. Analyses based on previous human genome assemblies can be found in the Previous Analyses section. Acknowledgments We thank The Centre for Applied Genomics at the Hospital for Sick Children (HSC) as well as collaborators worldwide. Supported by Genome Canada the Howard Hughes Medical Institute International Scholar Program (to S.W.S.) and the HSC Foundation.
A database that serves as a repository for both, sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments. It aims at supporting the setup and actual procedure of specific RNAi experiments in human cells.
Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE.
The IARC TP53 Mutation Database compiles all TP53 gene variations identified in human populations and tumor samples. Data are compiled from the peer-reviewed literature and from generalist databases. The following datasets are available: # TP53 somatic mutations in sporadic cancers # TP53 germline mutation in familial cancers # Common TP53 polymorphisms identified in human populations # Functional and structural properties of P53 mutant proteins # TP53 gene status in human cell-lines # Mouse-models with engineered TP53 The database includes various annotations on the predicted or experimentally assessed functional impact of mutations, clinicopathologic characteristics of tumors and demographic and life-style information on patients. The database is meant to be a source of information on TP53 mutations for a broad range of scientists and clinicians who work in different research areas: # Basic research, to study the structural and functional aspects of the p53 protein # Molecular pathology of cancer, to understand the clinical significance of mutations identified in cancer patients # Molecular epidemiology of cancer, to analyze the links between specific exposures and mutation patterns and to make inferences about possible causes of cancer # Molecular genetics, to analyze genotype/phenotype relationships
IL2Rgbase is a database of mutations in the X-linked gene IL2RG, leading to the autoimmune disease XSCID. Data on mutations in any of the eight exons may be retrieved and examined, as well as intervening sequences.
Datasets and tools for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context. Plasmids that are not part of a specific microbial genome sequencing project and phage genomes are also included in order to increase its genomic context for comparative analysis. The user interface (see User Interface Map) allows navigating the microbial genome data space along its three key dimensions (genes, genomes, and functions), and groups together the main comparative analysis tools. Microbial genome data analysis in IMG usually starts with the definition of an analysis context in terms of selected genomes, functional annotations, and/or genes, followed by the individual or comparative analysis of genomes, functional annotations, or genes.
A database of three-dimensional protein structures. It contains molecules, complexes, sequences, ligand/receptor pairings, and other useful tools. Currently, 1655 entries are managed , with 1602 IMGT/3Dstructure-DB cards (PDB) and 53 IMGT/2Dstructure-DB cards (INN).
Database of Spatially Interacting Motifs in Proteins
Comprehensive collection of spatially interacting motifs in proteins. Interacting motif database lists interacting motifs that are identified for all structural entries in PDB. Conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting common motifs shared among all superfamily members.
DriverDB: A database for cancer driver gene/mutation
A database for cancer driver gene/mutation that incorporates a huge amount of exome-seq data, annotation databases (such as dbSNP, 1000 Genome and Cosmic), and published bioinformatics algorithms dedicated to driver gene/mutation identification.
The Imprinted Gene Catalogue is a database of imprinted genes and related effects in humans and animals. Users can search the Imprinted genes and related effects database by taxon, chromosome, gene name, or a text word from the description. Users can also search the Catalogue of Parental Origin of de novo Mutations by type of mutation, disorder, chromosomal location, inheritance pattern, gene name, or author of publication. There are also many detailed entries which provide a cross-species summary of imprinted genes.
Registry for Familial Mediterranean Fever (FMF) and hereditary inflammatory disorders mutations. As of 2014, it includes twenty genes including: MEFV, MVK, TNFRSF1A, NLRP3, NOD2, PSTPIP1, LPIN2 and NLRP7, and contains over 1338 sequence variants. Confidential data, simple and complex alleles are accepted. For each gene, a menu offers: 1) a tabular list of the variants that can be sorted by several parameters; 2) a gene graph providing a schematic representation of the variants along the gene; 3) statistical analysis of the data according to the phenotype, alteration type, and location of the mutation in the gene; 4) the cDNA and gDNA sequences of each gene, showing the nucleotide changes along the sequence, with a color-based code highlighting the gene domains, the first ATG, and the termination codon; and 5) a download menu making all tables and figures available for the users, which, except for the gene graphs, are all automatically generated and updated upon submission of the variants. The entire database was curated to comply with the HUGO Gene Nomenclature Committee (HGNC) and HGVS nomenclature guidelines, and wherever necessary, an informative note was provided.
Database of microsatellite characteristics of five fully sequenced insect genomes (fruit-fly, honeybee, malarial mosquito, red-flour beetle and silkworm). InSatDb allows users to obtain microsatellites annotated with size (in bp and repeat units); genomic location (exon, intron, up-stream or transposon); nature (perfect or imperfect); and sequence composition (repeat motif and GC%). One can access microsatellite cluster (compound repeats) information, and a list of microsatellites with conserved flanking sequences (microsatellite family or paralogs). InSatDb is complete with insect information, web links to find details, methodology and a tutorial. A separate Analysis section illustrates the comparative genomic analysis that can be carried out using the InSatDb output.
Integr8 : Access to complete genomes and proteomes
The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny.
This database identifies and characterizes all inter-chain beta-sheet interactions within entries in the Protein Data Bank (PDB) and within the corresponding hypothetical quaternary structures that are automatically generated at the European Bioinformatics Institute (EBI), and that are currently available through the Protein Quaternary Structure (PQS) server, within the Macromolecular Structure Database. The data are stored in a relational database. The database can be accessed through the Web and queried through a simple form. Entries can be ranked according to the relative structural importance of their inter-chain -sheet interactions, or according to other criteria. The ICBS database is intended as a tool to: :* further the study of -sheet protein-protein interactions :* identify new ICBS interactions as new structures are deposited and as old structures are revised in the Protein Data Bank :* help select targets for drug design.
InterDom is a database of putative interacting protein domains derived from multiple sources, ranging from domain fusions (Rosetta Stone), protein interactions (DIP and BIND), protein complexes (PDB), to scientific literature (MEDLINE). Interdom focuses on providing supporting evidence for validating and annotating detected protein interactions and complexes based on putative protein domain interactions. InterDom enhances the quality of in silico derivations by adopting an integrative strategy, assigning higher confidence to domain interactions that are independently derived from different data sources and methods.
Interferome is a database that provides identification of interferon regulated gene signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It will also assist in identifying regulatory elements and enable comparison of tissue expression of IRGs in human and mouse. Availability of sequence information from more than 37 species, together with comprehensive annotation will enable comparative genomics and phylogenetic analysis to be performed on these IRGs. Within the database, Type I, II and III IFN regulated genes have been manually curated from more than 28 publicly available microarray datasets. Interferon Regulated Genes (IRGs) were identified from multiple microarray and proteomic experiments where cells were treated with IFNs. Genes that were up or down regulated more than 1.5 fold relative to control samples were defined as IRGs.
The Human Intermediate Filament Database is a continuously updated review of the intermediate filament field. It is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants. Suggestions on ways to improve the database are also welcome. The entire database can be searched through the Browse and Search options. A number of different parameters can be used to search the database including unique identifier, intermediate filament, disease DNA variations, amino acid variations, domain, date accepted, author and abstract. Output from the search is returned in a table containing all the pertinent cross referenced information. Multiple sequence alignment can also be performed via the CLUSTALW program to determine cDNA or protein sequence conservation. The database is linked to multiple other resources including NCBI RefSeq, PDB, OMIM, UCSC genome browser, NCBI Gene, HomoloGene, PubMed and HGNC. In the case of HGNC, reciprocal links are also available from HGNC that links to Human Intermediate Filament Database. Due to the protein centric nature of the Human Intermediate Filament Database and the gene centric nature of HGNC, a HGNC record will potentially link to multiple records in this database due to the presence of alternative splicing. In such an event, the Human Intermediate Filament Database will present to the user a list of all the protein records resulting from the HGNC gene record. The database uses Jalview and Jmol applets for the visualization of multiple sequence alignment and structure respectively. The database contains information on disease phenotypes of a variety of different intermediate filament related diseases.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A collection of tools for exploring the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing. It includes: Tracks Display- View splicing diagrams for any gene in the Sanger C. elegans database alongside cDNA and EST alignments. Retrieve DNA sequences with the exons in upper case. Search the literature. Alt Splicing Catalog - As defined by Chuck's altGraphX process. A frames based viewer linking to the genome browser. Alt-Splicing Catalog - A catalog of genes for which the cDNA and EST evidence indicates alternative splicing.
IPD-ESTDAB- The European Searchable Tumour Line Database
The European Searchable Tumour Line Database (ESTDAB) Database and Cell Bank provide a service enabling investigators to search online for HLA typed, immunologically characterised tumour cells as part of the European Commission Fifth Framework Infrastructures Program. The following tools and pages are available in ESTDAB: :* Search ESTDAB on primary search determinants :* Search ESTDAB on all search determinants :* Dictionary of markers and techniques used
A centralised repository for the data which define the human platelet antigens (HPA). Alloantibodies against human platelet antigens are involved in neonatal alloimmune thrombocytopenia, post-transfusion purpura and refractoriness to random donor platelets. The Human Platelet Antigen (HPA) nomenclature system was adopted in 1990 to overcome problems with the previous nomenclature. Since then more antigens have been described and meanwhile the molecular basis of many has been resolved, and the nomenclature was revised in 2003.
IPD-KIR - Killer-cell Immunoglobulin-like Receptors
The IPD-KIR database provides a centralized repository for human KIR sequences. Killer-cell Immunoglobulin-like Receptors (KIR) have been shown to be highly polymorphic at the allelic and haplotypic level. KIRs are members of the immunoglobulin superfamily (IgSF) formerly called Killer-cell Inhibitory Receptors. They are composed of two or three Ig-domains, a transmembrane region and cytoplasmic tail which can in turn be short (activatory) or long (inhibitory). The Leukocyte Receptor Complex (LRC) which encodes KIR genes has been shown to be polymorphic, polygenic and complex like the MHC.
IPD-MHC- Major Histocompatibility Complex
The IPD - MHC Database provides a centralized repository for sequences of the major histocompatibility complex from a number of different species. Through a number of international collaborations IPD is able to provide the MHC sequences of different species. The sequences provided by each group are curated by experts in the field and then submitted to the central database.
L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes: a) intact in the two ORFs, full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full length (>6000bp) non-intact L1s (FLnI-L1s) were also included in the database.
University of Rome Tor Vergata; Rome; Italy
iProLINK (integrated Protein Literature, INformation and Knowledge) has been developed as a resource to facilitate text mining in the area of literature-based database curation, named entity recognition, and protein ontology development. The collection of data sources can be utilized by computational and biological researchers to explore literature information on proteins and their features or properties. The data sources for bibliography mapping and feature evidence attribution include mapped citations (PubMed ID to protein entry and feature line mapping) and annotation-tagged literature corpora. The latter includes several hundred abstracts and full-text articles tagged with experimentally validated post-translational modifications (PTMs) annotated in the PIR protein sequence database.
IRESdb - the Internal Ribosome Entry Site database
Database of experimentally verified IRES structures. Presents information about experimentally studied Internal Ribosome Entry Site segments.
IRIS - International Rice Information System
IRIS is the rice implementation of the International Crop Information System (ICIS) which is a database system that provides integrated management of global information on genetic resources and crop cultivars. This includes germplasm pedigrees, field evaluations, structural and functional genomic data (including links to external plant databases) and environmental (GIS) data.
ISED- Influenza Sequence and Epitope Database
It catalogues the influenza sequence and epitope information obtained in Asia and currently hosts a total of 33388 influenza A and 4762 influenza B virus sequence data collected in 21 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea. ISED provides users with pre-built application tools to analyze sequence alignment and difference patterns and allows users to visualize epitope matching structures.
Non-synonymous Enriched Coding muTation Archive
A database and web application to annotate disease-related and functionally important amino acids in human proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. Islander is a comprehensive online database containing genomic islands discovered in completely sequenced bacterial genomes by the algorithm. Islands are transmitted between prokaryotic strains and therefore play a major role in genome evolution. An island often encodes an integrase gene that specifies the island''s position in the host genome. Usually integrases specify tRNA genes, and the island splits the the tRNA gene when it integrates. However the island also carries sequence that replaces the split-off portion, restoring an intact tRNA gene. Thus an island is often marked by a tRNA gene at one end, and a fragment of that gene at the other end. The islands in this database were identified using this principle through the following procedure: :1. Search for tRNA and tmRNA genes using tRNAscan-SE and BRUCE on whole prokaryotic genomes. :2. Search for significant hits to each tRNA and tmRNA gene using BLAST against the source genome. :3. Narrow down hits to those containing integrase genes (required for site-specific integration into the host genome). :4. Remove false positives (e.g., tRNA gene fragment not from end of gene, or in wrong orientation). :5. Enter into mysql database, display on website using Perl CGI pages., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
KinMutBase: A registry of disease-causing mutations in protein kinase domains
KinMutBase is a comprehensive database of disease-causing mutations in protein kinase domains. The current release of the database contains 582 mutations in 20 tyrosine kinase domains and 13 serine/threonine kinase domains. The database refers 1790 cases from 1322 families. KinMutBase is a registry of mutations in human protein kinases related to disorders. Kinases are essential cellular signaling molecules, in which mutations can lead to diseases, including immunodeficiencies, cancers and endocrine disorders. Mutations appear both in conserved hallmark residues of the kinases as well as in non-homologous sites. The KinMutBase WWW pages provide plenty of information, namely mutation statistics and display, clickable sequences with mutations and changes to restriction enzyme patterns.
LEGER: the post-genome Database for Listeria Research
Knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species.Provides information on gene functions (as annotated or supposed by literature from homologous organisms) , protein expression levels under defined experimental conditions ,subcellular localization of proteins (expected and/or experimentally validated) , biological meaning of genes and proteins based on KEGG, InterPro and Gene Ontology.
LIS is a publicly accessible legume resource that integrates genetic and molecular data from multiple legume species and enables cross-species genomic, transcript and map comparisons. The intent of the LIS is to help researchers leverage data-rich model plants to fill knowledge gaps across crop plant species and provide the ability to traverse between interrelated data types. LIS, a component of the Model Plant Initiative (MPI), is being developed as part of a cooperative research agreement between the National Center for Genome Resources (NCGR) and the USDA Agricultural Research Service (ARS).
Database that integrates information on sequence and structure of lipases and related proteins sharing the same a/b hydrolase fold to facilitate protein engineering. Users can browse the database by classification, organism, hierarchic tree, and structure. They can also perform homology searches against the lipase database, and query the Lipase Engineering Database using SQL.
LOCATE: subcellular localization database
LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications.
The lipoxygenases database (LOX-DB) aims to be a web accessible compendium of information in particular on the mammalian members of this multigene family. This resource includes molecular structures, reference data, tools for structural and computational analysis as well as links to related information maintained by others. The data can be retrieved by the use of various search options and analyzed applying publicly available visualization tools. Lipoxygenases are a family of enzymes involved in a variety of human diseases like inflammation, asthma, artherosclerosis and cancer.
LPFC is a database of structural alignments of protein families and computed average core structures for each family. The core structures can be divided into residues with low spatial variation and those with high spatial variation. Amino acids with low spatial variance occupy essentially the same relative position in all family members. This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
LumbriBASE is aa research tool for both Earthworm biology and environmental pollution monitoring.It provides a simple, easy-to-use access point to the publicly available Lumbricus rubellus sequence and functional data. It is a research tool for both Earthworm biology and environmental pollution monitoring. It is currently being developed by the Worm Consortium.
M3D is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains Affymetrix expression compendia for Escherichia coli, Saccharomyces cerevisiae, and Shewanella oneidensis. M3D (Many Microbe Microarrays) was developed by the Gardner Lab at Boston University to facilitate the exchange and analysis of high quality, curated, microbial gene expression data. Currently, the database only includes data obtained using Affymetrix GeneChip technology, because the high quality of the platform facilitates cross-laboratory integration of data sets. The database allows downloading of raw data (CEL files) or preprocessed data that has been uniformly normalized with RMA. M3D also enables convenient web-based expression data exploration and visualization - accessable via the Analysis page.
MAMEP - Molecular Anatomy of the Mouse Embryo Project
Database of gene expression in whole-mount mouse embryos derived from in situ hybridization on mid-gestation mouse embryos. A genome wide screening for genes showing a tissue restricted expression pattern in mid-gestation embryos is performed to identify genes that are likely to play an important role in the regulatory networks controlling pattern formation and organogenesis. The screening provides the basis for imaging the molecular anatomy of the mouse embryo, and for creating a gene resource for a directed functional analysis of developmental processes. The experimental protocol is available. Pattern genes in MAMEP: 1912 Images in MAMEP: 23994
Database providing a collection of all the existing polymorphic sequences in the Mammalia group. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity. For data collection, diversity measures and updating they use PDA, a pipeline made of a set of Perl modules that automates the process of sequence retrieving, grouping, aligning and estimating diversity parameters from GenBank sequences. Diversity measures, including polymorphism estimates in synonymous and non-synonymous sites, linkage disequilibrium and codon bias, are calculated for each polymorphic set in different functional regions. The database also includes the primary information retrieved from different external sources: the mammalian publicly available nucleotide sequences (excluding ESTs, STSs, GSSs, working draft and patents) with their annotations and references from GenBank, and the cross-references to the PopSet database. The database content is daily updated, and records are assigned unique and permanent MamPol identification numbers to facilitate cross-database referencing.
Thermodynamic Database for Nucleic Acids
NTDB is a database is a collection of thermodynamic and structural data, experimental methods, conditions and relevant literature citations on nucleic acids. This database is updated continuously. The thermodynamic data of interest can be searched by structural features, thermodynamic parameters, experimental methods and the use of citation. Tools relating to the thermodynamic properties of nucleic acids are also made available in this database and can be applied to predict thermal denaturation profiles, free energy, etc. Some related links are also available. Users are encouraged to deposit new thermodynamic data on nucleic acids to this database.
Database containing several body fluid proteomes, including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU datasets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools.
Mutation Database for Parkinsons Disease
The Mutation Database for Parkinson's Disease (MDPD) is designed to fulfill the need for information integration so that users can easily retrieve, inspect and enhance their knowledge on PD. The database contains 2391 entries on 202 genes extracted from 576 publications and manually examined by biomedical researchers. Each genetic substitution and the resulting impact are clearly labeled and linked to its primary reference. Every reported gene has a summary page that provides information on the variation impact, mutation type, the studied population, mutation position and reference collection. In addition, MDPD provides a unique functionality for users to compare the differences on the type of mutations among ethnic groups. As such, we hope that MDPD will serve as a valuable tool to bridge the gap between genetic analysis and clinical practice.
A database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis. MMDB contains experimentally determined biopolymer structures obtained from the Protein Data Bank. MMDB contains a subset of three-dimensional structures obtained from the Protein Data Bank (PDB), excluding theoretical models. MMDB is a database of ASN.1-formatted records. It was designed for flexibility, and as such, is capable of archiving conventional structural data as well as future descriptions of biomolecules, such as those generated by electron microscopy (surface models).
A catalog of known and/or predicted biochemical pathways from barrelclover (Medicago trunculata). It features more than 240 pathways with related genes, enzymes, and metabolites. MedicCyc was assembled based on over 225,000 Medicago truncatula ESTs and available genomic sequences. This is a mirror database kindly provided by the MedicCyc group from the SR Nobel Foundation. The initial compilation was manually annotated to remove non plant pathways, and several Medicago-specific pathways including isoflavonoid, lignin, and saponin biosyntheses were modified or added based on available literature. Predicted pathways and annotations in MedicCyc were then verified through comparison with AraCyc and RiceCyc database. MedicCyc can be used as a reference for the study of primary and secondary metabolism of Medicago truncatula as well as for other legume species.
A database of structural motifs for protein structures related at the family and-or superfamily level. Such motifs among structurally aligned proteins are recognized by the conservation of amino acid preference and solvent inaccessibility and are examined for the conservation of other important structural features like secondary structural content, hydrogen bonding pattern and residue packing. These motifs may form the common core by maintaining a particular spatial orientation pattern when compared across different proteins belonging to the same family or superfamily. Such motifs can also be employed to design and rationalize protein engineering and folding experiments. Therefore, the MegaMotifbase can be a useful resource to gain knowledge about structure and functional relationship of proteins. Alignments are available for download.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A database of metal ion binding sites in RNA. It provides information that allows the classification of and search for specific metal binding motifs (e.g., tandem G-U pairs, loop E motif, A-platform motif). The RNA binding sites of 23 different metal ions are described, the most common of these being Mg2+, Na+, Ca2+, Cd2+ and K+. The user can browse the database or search by PDB or NDB identifier, metal ion, binding motif, type of binding, distance cutoff criteria, experimental conditions (NMR, X-ray, etc.), resolution and R-values, and any combination of the aforementioned criteria or author(s) name. The design and development of the database of metal ion binding sites in RNA is part of a research program which focuses on classification and understanding of RNA motif structure, function, tertiary interactions and their relationships. Using the information contained in our database, we will explore approaches to predicting metal ion binding sites in RNA sequence and structure and to identifying new RNA metal ion binding motifs, which will eventually lead to the design of RNA structures with specific metal binding characteristics.
An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.
MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,200 pathways from more than 1,600 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes.
A free web-oriented database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats. MMsINC is provided by the Molecular Modeling Section in the Department of Pharmaceutical Sciences at the University of Padova, (Italy) in collaboration with the Software Support Services & Development Laboratory (S3D) at the Center for Advanced Studies, Research and Development (CRS4) in Sardinia.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. Database and Browser containing quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics, and answer questions such as: How many mononuclear zinc-containing sites are five coordinate with X-ray resolution better than 1.8 Angstroms?, and then be able to visualize and manipulate the matching sites. The database also includes enough information to answer questions involving type and number of ligands (e.g. "at least 2 His"), and include distance cutoff criteria (e.g. a metal-ligand distance no more than 3.0 Angstroms and no less than 2.2 Angstroms). This database is being developed as part of a project whose ultimate goal is metalloprotein design, allowing the interactive visualization of geometrical and functional information garnered from the MDB. The database is created by automatic recognition and extraction of metal-binding sites from metal-containing proteins. Quantitative information is extracted and organized into a searchable form, by iterating through all the entries in the latest PDB release (at the moment: September 2001). This is a comprehensive quantitative database, which exists in SQL format and contains information on about 5,500 proteins.
metaTIGER is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes. Phylogenomic information is provided by 2,257 large phylogenetic trees which can be interactively explored. High-throughput tree analysis can also be carried out to identify trees of interest, e.g. trees containing horizontal gene transfers. metaTIGER also provides novel facilities for viewing and comparing the metabolic profiles.
A database of information on nuclear receptors. Included in the database are sequence information, structural information, and mutation data. Users can BLAST sequences, view 2D structural data, see the chromosomal location of nuclear receptors genes, and utilize other tools found on the website.
MfunGD - MIPS Mouse Functional Genome Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019.Database for annotated mouse proteins and their occurrence in protein networks. It contains cDNA and protein sequences, annotation, gene models and mapping, FunCat, UCSC Genome Viewer, SIMAP, pseudogenes (Genome Viewer Track), InterPro, and splice variants. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme, which is a hierarchically structured classification system. To provide up-to-date similarity search results and InterPro domain analyses, the protein entries are interconnected with the SIMAP database. The gene models are based on the RefSeq mouse cDNAs. The work of our group is focussed on the annotation of biological systems. Therefore, results from the Mammalian Protein-Protein Interaction Database and the Comprehensive Resource of Mammalian Protein Complexes are linked to the MfunGD dataset. Links to external resources are also provided. MfunGD is implemented in GenRE, a J2EE based component oriented multi-tier architecture.
The MHC-Peptide Interaction Database version T (MPID-T) is a new generation database for sequence-structure-function information on T cell receptor/peptide/MHC interactions. It contains all structures of TcR/pMHC and pMHC complexes, with emphasis on the structural characterization of these complexes. MPID-T will facilitate the development of algorithms to predict whether a peptide sequence will bind to a specific MHC allele. The database has been populated with the data from the Protein Data Bank(PDB). The data from the PDB is manually verified and classified, after which each structure is analysed for atomic interactions relevant to MHC-Peptide complex.
MHCBN: A comprehensive database of MHC binding and non-binding peptides
The MHCBN is a curated database consisting of detailed information about Major Histocompatibility Complex (MHC) Binding,Non-binding peptides and T-cell epitopes. The version 4.0 of database provides information about peptides interacting with TAP and MHC linked autoimmune diseases.
This repository contains full data from MHCPEP database, and selected data including independent data sets of proteins and protein fragments, non-binding peptides, lists of T-cell epitopes, and recommendations for scaling and comparison of performance of prediction systems. It can be used in conjunction with IEDB data sets for the development of advanced machine learning and pattern recognition solutions.
In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers access to their tools. Programs that are available through this portal are: * AliBaba 2.1: AliBaba2 is a program for predicting binding sites of transcription factor binding sites in an unknown DNA sequence. Therefore it uses the binding sites collected in TRANSFAC. AliBaba2 is currently the most specific tool for predicting sites. * Boxshade 3.3.1: Pretty Printing and Shading of Multiple-Alignment files. * ClustalW 1.8: ClustalW Multiple Sequence Alignment Program. * Dialign2.0: Multiple Sequence Alignment Program. * F-Match 1.0: F-MATCH is a program for identifying statistically overrepresented Transcription Factor Binding Sites (TFBS) in a set of sequences compared against a control set, assuming a binomial distribution of TFBS frequency. The program reads MATCH output files for the query and control sets. F-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * Match 1.0 Public: Match is designed for searching potential binding sites for transcription factors (TF binding sites) nucleotide sequences. MatchTM uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * molwSearch 1.0: Search for transcription factors with a certain molecular weight. * P-Match 1.0: P-Match is a new tool for identifying transcription factor binding sites (TF binding sites) in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 along with the site alignments associated with these matrices. * Patch 1.0: Search for potential transcription factor binding sites in your own sequences with the pattern search program using TRANSFAC 6.0 public sites. * m2transfac 1.0: m2transfac is a PWM-PWM alignment interface for the TRANSFAC(R) database. For given user motifs, m2transfac reports all non-overlapping pairwise alignments to a TRANSFAC(R) matrix which satisfy a specified threshold. * MatrixCatch 2.7: The MatrixCatch tool is designed for searching potential composite elements (CEs) for transcription factors (TFs) in any DNA sequence, which may be of interest. MatrixCatch uses a library of CE matrix models, which were compiled on a basis of experimentally identified CEs collected in TRANSCOMPEL database and mononucleotide weight matrices for single TF-binding sites collected in TRANSFAC 6.0 public database. * Composite Module Analyst (CMA) 1.0: CMA reads output of Match program and applies a genetic algorithm in order to define promoter models based on the composition of transcription factor binding sites and their pairs. * PolyA Scan 0.000707: Scanning a Sequence for potential Polyadenylation Sites. * ReadSeq 2.0: ReadSeq reads and writes nucleic/protein sequences in various formats. * SignalScan: Analysis of DNA Sequences for known Eukaryotic Signals * SbBlast 1.0: Search Tool for Sequence Search in the S/MARt Binder Database. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000). * SnpFind 0.3: SNPFIND is a tool for searches in the Database of Single Nucleotide Polymorphisms. The search algorithm used for the database search is the BLAST algorithm. * TfBlast 0.1: Search Tool for Sequence Search in the TRANSFAC Factor Table. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000).
It analyzes protein queries for the presence of short functional motifs that, in at least one protein, has been demonstrated to be involved in posttranslational modifications (PTM), binding to other proteins, nucleic acids, or small molecules, or proteins trafficking. The low sequence complexity of motifs, suggest that "false positive" motifs may occur and any prediction made by MnM should be experimentally tested. To aid in the selection of motifs, MnM ranks motifs based on frequencies in proteomes, protein surface prediction, and evolutionary conservation. Using annotation of motifs in the Swiss-Prot database, we have found that higher scores are globally correlated with experimentally validated motifs when compared to a similar analysis using randomized motifs with the same amino acid composition. We suggest that the known biology of the protein of interest and of motifs be used in selecting motifs for experimental study.
OPD is a public database for storing and disseminating mass spectrometry based proteomics data. It covers Escherichia coli, Homo sapiens, Saccharomyces cerevisiae, Mycobacterium smegmatis, and Mus musculus. The database currently contains roughly 3,000,000 spectra representing experiments from these 5 different organisms. The mirror url is provided below as the OPD website is no longer functional (http://bioinformatics.icmb.utexas.edu/OPD/).
Health Research Funding is designed to bring researchers with peer-reviewed, worthwhile, unfunded projects together with patient advocacy organizations and other funding sources. Working together, we hope to foster the funding of new research that will provide hope to millions of people in this country with chronic diseases and disabilities. * We invite researchers with promising projects that have been scored but not funded by the NIH to submit their abstracts. By registering, you will be able to search for information about organizations that fund research and their requests for abstracts. * Researchers with proposals that have been peer-reviewed but not funded by a NHC member patient advocacy organization may also register. The National Health Council (NHC) developed this site with input from the National Institutes of Health (NIH), the nation''s medical research agency.
Munich Information Center for Protein Sequence
It aims to provide a data and information resource for individual plant species. In addition PlantsDB provides a platform for integrative and comparative plant genome research. It provides information on monocots and dicots, a comparative map viewer, and other specialized databases.
A manually curated database, aims at providing a comprehensive resource of miRNA deregulation in various human diseases. Each entry in the miR2Disease contains detailed information on a miRNA-disease relationship, including miRNA ID, disease name, a brief description of the miRNA-disease relationship, miRNA expression pattern in the disease state, detection method for miRNA expression, experimentally verified miRNA target gene(s), and literature reference . All entries can be retrieved by miRNA ID, disease name or target gene. miR2Disease will be updated bimonthly. miR2Disease sincerely looks forward to recently established relationship between miRNA and human diseases to be submitted.
miRGator: an integrated system for functional annotation of microRNAs
Database of compiled, public, deep sequencing miRNA data and several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data are of great utility for studying iso-miRs, miRNA editing and modifications. miRNA����??target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets.
A database of the molecular structure and functional network of the entirely sequenced, filamentous fungus Neurospora crassa. The underlying sequence is the release 7 of the high quality draft sequence of the Broad Institute. The goal is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The database contains the manually modelled gene set generated in the German Neurospora genome project and is combined with Broad calls from release 7 version 3.
A resource dedicated to the distribution of information about nucleotide variation found in the PHEX gene, the majority of which are found in patients with X-linked hypophosphatemia. Users can search by mutation, phenotype, or author, or submit their own mutations.
An integrated database of positional relationships between animal miRNAs and genomic annotation sets and animal miRNA targets according to combinations of widely used target prediction programs. miRGen has three connected interfaces which query this data. The Genomics interface allows the user to explore where whole-genome collections of miRNAs are located with respect to UCSC genome browser annotation sets such as Known Genes, Refseq Genes, Genscan predicted genes, CpG islands, and pseudogenes. The Targets interface provides access to unions and intersections of four widely used target prediction programs, and experimentally supported targets from TarBase. The Clusters interface provides predicted miRNA clusters at any given inter-miRNA distance, and provides specific functional information on the targets of miRNAs within each cluster.
miROrtho: the catalogue of animal microRNA genes
It contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. The current release of miROrtho covers 46 animal genomes. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A web site dedicated to providing links to mitochondrial data and databases, as well as links to other mitochondrial sites and relevant information. It provides links to databases, complete mitochondrial genomes, genome maps, and publications.
MitoDat - Mendelian Inheritance and the Mitochondrion
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It is dedicated to the nuclear genes specifying the enzymes, structural proteins, and other proteins, many still not identified, involved in mitochondrial biogenesis and function. MitoDat highlights predominantly human nuclear-encoded mitochondrial proteins, although it also includes proteins from other animals in addition to those currently known only from yeast and other fungal mitochondria, as well as from plant mitochondria. he database consolidates information from various biological databases, eg., GenBank, SwissPro, Genome Data Base (GDB), Online Mendelian Inheritance in Man (OMIM), et al. Because the mitochondrion has a central role in cellular metabolism, it is involved in many human diseases. This database should help us in studying these diseases. We are also hyperlinked to the Report of the committee on human mitochondrial DNA, maintained by the Wallace group at Emory. It can be accessed here and also from the results when searching mitoDat for mitochondrially encoded genes. The Report of the committee on human mitochondrial DNA is currently the most comprehensive source of information on mitochondrial DNA mutations, other defects, and disorders in which the mitochondrial DNA deficiencies have been associated.
A database for comparative analysis of mitochondrial genomes and arrangements within metazoan. A particular function of the database is the automatic reconstruction of phylogenetic relationships among metazoans selected by a user from a taxonomic tree menu based on nucleotide sequences, amino acid sequences or gene arrangement patterns. Mitome also enables us (i) easily to find the taxonomic positions of organisms of which complete mitochondrial genome sequences are publicly available; (ii) to acquire various metazoan mitochondrial genome characteristics through a graphical genome browser; (iii) to search for homology patterns in mitochondrial gene arrangements; (iv) to download nucleotide or amino acid sequences not only of an entire mitochondrial genome but also of each component; (v) to find interesting references easily through links with PubMed. In order to provide users with a dynamic, responsive, interactive and faster web database, Mitome is constructed using two recently highlighted techniques, Ajax (Asynchronous JavaScript and XML) and Web Services. Mitome has the potential to become very useful in the fields of molecular phylogenetics and evolution and comparative organelle genomics.
MolMovDB - Database of Macromolecular Movements
MolMovDB is a database that describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis. The morph server enables the automatic generation of 2D and 3D animations of a plausible or semi-plausible pathway between two static conformations of a protein subunit, such as those conventionally solved by x-ray crystallography. We believe these animations and associated interpolated pathways will become a valuable research and educational tool, allowing the researcher or educator to quickly visualize the chemical transformation of a protein subunit from one conformation into another. With the server, it is easy to determine quickly whether a valid chemical pathway exists between two protein conformations, as in a protein such as calmodulin, or whether, as is the case with diphtheria toxin, the two conformations have no clearly valid chemical pathway and therefore exist most likely as the result of other processes, such as domain swapping.
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Madison Metabolomics Consortium Database
Madison Metabolomics Consortium Database (MMCD)
A database which supports high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples. MMCD serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature. Each metabolite entry in the MMCD is supported by information in separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, calculated isotopomer masses, information on the presence of the metabolite in different biological species, and links to images, references, and other public databases. The MMCD search engine supports versatile data mining and allows users to make individual or bulk queries on the basis of experimental NMR and/or MS data plus other criteria.
A database of RNA modification pathways. The MODOMICS database contains the following types of items: * Modified Bases : Each modified base consists of a unique chemical structure. They are sorted by the regular RNA bases they originate from. The modified base queuosine is special, since it is synthesized first, and then attached to the ribose by a transglycosylation reaction. The letters in the small modification icons indicate what kingdoms of life the modifications occur in (Eukaryota, Archaea, EuBacteria, Mitochondria). In the download section, the .mol structure files for alare available. * Modification Pathways : Here, we present four pathway graphs showing what modifications emerge from the different bases. The letters in the small modification icons indicate what kingdoms of life the modifications occur in (Eukaryota, Archaea, EuBacteria, Mitochondria). All lines connecting two modifications are clickable, and show details on a particular reaction. * Enzymes : Lists enzymes that catalyse known reactions between modified bases. In the table, several alternatively used names for the enzymes are given, as well as a list of participating proteins. * Sequences : Shows sequences of RNAs with modifications highlighted. Currently, tRNAs and small and large subunit rRNAs are included in MODOMICS. * Publications : exactly that.
The database has been developed to structurally and functionally annotate, and where possible predict, the phenotypic consequences of mutations in protein kinases implicated in cancer. The 518 human protein kinases identified in KinBase, are listed alphabetically to facilitate browsing, and each gene is labelled with tumour type(s) in which mutations have been found. The list can also be sorted by selective pressure - the ratio of non-synonymous:synonymous mutations compared to that expected by chance, and by ''rank'' - the probability of the mutated gene containing at least 1 driver mutation. Both these measures can be used to predict which kinases contain driver mutations, i.e. those that are causal of the cancer, rather than passenger mutations that have arisen by chance but do not contribute to disease. Entries can be searched directly by gene name. Mutational data from the Cancer Genome Project have been mapped onto the crystal structures of the affected human protein domains where known, or onto the most closely related homologous structure if not known. Proteins are linked to functional annotation resources and are annotated with structural and functional features such as domains and phosphorylation sites, and protein interaction partners. This annotation is being expanded to include PROSITE patterns, which identify short peptide segments of functional consequence and sites of post-translation modifications, and Driver/Passenger assessment of the mutations.
A database dedicated to the comparative genomics of Mollicutes. Usual tools required to explore genomes have been infered in MolliGen. They include various ways to search for genes or groups of genes and to access to a wide range of related data. General information describing whole genome properties are also available as well as graphical representations. The genomic sequences deposited in MolliGen as well as related annotation data are inferred from the corresponding GenBank entries. The genomes implemented in MolliGen are all publicly accessible from general databases. Additionaly, some unpublished genomes can be deposited in MolliGen.
A resource for publicly available sequences of the rice genome(Specifically, Oryza sativa L.). Our goal at MOsDB is to provide all available data about rice genes and genomics, including (in the future) mutant information and expression profiles. At this moment, the MOsDB database includes current published sequences and gene annotation information of two Oryza sativa subspecies: japonica and indica. Rice is an experimental model for the cereal crops research and an agriculturally important plant, providing food for more than half of the world population. The estimated rice genome size is about 430 Mb, which is the smallest among all the cereal crops and about one seventh of human and 3.5 times of Arapdopsis genomes.
A database containing information on ca. 4300 synthetic oligonucleotides with a sequence of up to 100 nucleotides. Data are mainly taken from the literature and are encoded on the basis of controlled vocabularies. The probes target 821 different genes, of which 691 human and 112 viral. The probes can be used for genetic polymorphisms study (1944), human inherited disease diagnosis (834), cancer diagnosis (517), infectious disease diagnosis (517), neurologic disease diagnosis (72), autoimmune disease diagnosis (40). Oligonucleotides are described on the basis of: name, oligo type (primer, probe, antisense), nucleotide sequence, amino acid sequence (if part of a coding region), target gene and related infos (localization within the gene and recognized variants or specificities), applications, methods, technical notes, complementary primer (if used for PCR), primers for amplification (if probe), bibliographic references. At the moment MPDB is searchable through some SRS servers. MPDB can easily be retrieved from our FTP server, together with SRS syntax files. Typology * ca. 4300 oligonucleotides * 821 different genes, of which 691 human and 112 viral * ca. 3536 oligonucleotides are human gene specific * ca. 620 oligonucleotides are viral gene specific
MPIM - Mitochondrial Protein Import Machinery
Mitochondrial Protein Import Machinery of Plants
A database of Arabidopsis mitochondrial protein import components. Detailed information can be found in two main areas of the website, one of which contains a diagram detailing the plant mitochondrial import process which users can click on and interact with, and the other containing information about arabidopsis mitochondrial protein import components.
A database of sequence-tagged sites (STSs) and a user interface for mapping partial deletions in the male-specific region of the human Y chromosome (MSY). Naturally occurring partial deletions in the human Y chromosome are associated with diverse phenotypes including male infertility, sex reversal, Turner syndrome, and germ cell tumor formation. With the complete sequence of the euchromatic Y chromosome in hand, it is now possible to precisely demarcate each deletion and the repertoire of genes lost, and to propose mechanisms of deletion. Detailed DNA-sequence analysis of MSY deletions is most readily accomplished with Y-specific STS assays, which employ the polymerase chain reaction (PCR). Each such STS assay provides a straightforward means of determining the presence or absence, in a sample of human genomic DNA, of a specific point along the length of the Y chromosome. In the course of analyzing normal and aberrant Y chromosomes over the past two decades, we and our colleagues have generated robust, Y-specific STSs at an average spacing of less than 14 kilobases across the MSY euchromatin. MSY Breakpoint Mapper provides information about these STSs and is useful for efficiently and systematically defining the breakpoint(s) of virtually any Y chromosome deletion.
A database dedicated to the analysis of gene expression and regulation data in Mycobacterium tuberculosis. It is designed to contain most of the characterized transcription start sites and DNA binding sites cross-referenced with their respective transcription factor, along with some predicted regulatory motifs.
A database of multiple position specific scoring matrices of protein domain families with constant alignments. Representation of multiple sequence alignments of protein families in terms of position-specific scoring matrices (PSSMs) is commonly used in the detection of remote homologues. A PSSM is generated with respect to one of the sequences involved in the multiple sequence alignment as a reference. We have shown recently that the use of multiple PSSMs corresponding to an alignment, with several sequences in the family used as reference, improves the sensitivity of the remote homology detection dramatically. MulPSSM contains PSSMs for a large number of sequence and structural families of protein domains with multiple PSSMs for every family. The approach involves use of a clustering algorithm to identify most distinct sequences corresponding to a family. With each one of the distinct sequences as reference, multiple PSSMs have been generated. The current release of MulPSSM contains ~33 000 and ~38 000 PSSMs corresponding to 7868 sequence and 2625 structural families. A RPS_BLAST interface allows sequence search against PSSMs of sequence or structural families or both. An analysis interface allows display and convenient navigation of alignments and domain hits.
Narcisse is a comparative genome browser. The aim is to provide a simple and intuitive access to the results of comparison of genomes completely or partially sequenced. The principle of construction of conserved segments based on the idea that the concept of conservation depends on the level of resolution. The number of levels of conservation is fixed, more or less arbitrary for animals 5 and 2 for the other kingdoms. Narcisse software allows users to move between these levels of conservation.
A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal.
It is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Currently, the database includes over 30,000 individual sequences from 99 species of Bacteria, Archaea and Eukaryota. The primary source of sequences included in the database was the GenBank. Additional annotation information for mouse and human ncRNAs was derived from FANTOM3 database and H-inviational Integrated Database of Annotated Human Genes version 3.4, respectively. Genome mapping information was derived from tha data available at the UCSC Genome Browser site. The sequences and annotations of small cytoplasmic RNAs from bacteria, for which annotation is lacking in the genome sequences, were derived from the Rfam database. The microRNAs or snoRNAs which were available in previous editions, as well as other housekeeping (infrastructural) RNAs (e.g. rRNA, tRNA, snRNA, SRP RNA) are not included in our database to avoid redundancy with more specialized databases which emerged in recent years.
The home page of the parasitic nematode EST project at Washington University's Genome Sequencing Center, St. Louis. It was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum Nematoda."
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 17,2023. Affymetrix is a partially commercial resource that provides DNA Analysis Arrays, Expression Analysis Arrays, Gene Regulation Analysis, and Microarrays. It also provides reagents and assays, instruments, software, and services for a fee. Information is provided for Rats, Humans, and Mice.Affymetrix is now Applied Biosystems, brand of DNA microarray products sold by Thermo Fisher Scientific that originated with an American biotechnology research and development and manufacturing company of the same name.
A method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins. This website allows a user to browse/search and investigate predictions made using the NetworKIN algorithm. The site is powered by the latest phosphoproteome in Phospho.ELM. Alternatively users can submit their own protein sequences and phosphorylation sites and obtain new NetworKIN predictions.
NMPdb - Nuclear matrix associated proteins database
NMP-db is a database of nuclear matrix associated proteins. The NMP-db consists of two parts. The first part is the actual literature based NMP-db, containing all nuclear matrix proteins (NMPs) that were originally found in PubMed. The second part is a database of homologues to the NMP-db proteins. This database is called NMP-db(hom) and contains proteins which have at least an HSSP-value of 55 to one of the proteins in the NMP-db. The NMP-db holds informations about the protein names, their organism and the cell-type in which NM association was observed. Also links to the respective PubMed abstracts are given in each entry. Additionally, we provide information about predictions of secondary structure, solvent accessibility, coiled-coil regions and domain-architecture, as well as the sequence, links to PDB (database of 3D-structures), molecular weight, theoretical pI, links to SWISS-2DPAGE, OMIM, PEP and many other databases. If available, we also list regions in a protein sequence that are known to be cruicial for NM-targeting. Finally, links to the S/MARt DB allow users to find DNA-regions that bind to NMPdb proteins.
NRESTdb is an online resource which provides access to sequence, clustering, classification and annotation data of ESTs from rubber. The NRESTdb consists of EST sequences, BLASTX search results against the non-redundant protein database (NR), Pfam and InterPro, annotations based on KOG, Inparanoid and GO classifications, enhanced datasets related to rubber research topics of interest and search tools to facilitate user navigation. The NRESTdb resources and facilities are aimed at providing a genomic data resource to facilitate rubber biotechnology research. The development of NRESTdb is a collaborative project of the Malaysia Genome Institute EST database working group and the Malaysian Rubber Board genomics group.
National Microbial Pathogen Data Resource
NMPDR - National Microbial Pathogen Data Resource
The National Microbial Pathogen Data Resource provides curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma. This edition of the NMPDR includes 47 archaeal, 725 bacterial, and 29 eukaryal genomes with 3,257,100 genetic features, of which 1,338,895 are in FIGfams curated using 616 active subsystems. ' ''' ''Notice to NMPDR Users' ''' '' - The NMPDR BRC contract ended in December 2009. At that time we ceased maintenance of the NMPDR web resource and data. Bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois.
Collection of non-coding RNAs (excluding tRNAs and rRNAs) as an integrated knowledge database. Used to get text information such as class,name,location,related publication,mechanism through which it exerts its function, view figures which show their location in the genome or in a specific DNA fragment, and the regulation elements flanking the ncRNA gene sequences.
A platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides. The name Norine stands for Nonribosomal peptides, with "ine" as a typical ending of peptide names. For each peptide, the database stores its structure as well as various annotations such as the biological activity, producing organisms, bibliographical references and others. The database can be queried in order to search for peptides through their annotations as well as through their monomeric structure. In the latter case, the user can specify either the whole structure or a structural pattern (possibly including "undefined monomers") of the searched peptide.
A searchable database of information on proteins that are localised to the nucleus of vertebrate cells. The NPD contains information on >2000 vertebrate proteins (mainly those from mouse and human) that are thought to, or known to, be localised to the cell nucleus. Where known, the sub-nuclear compartment where the proteins have been found are reported. Also stored is information on the amino acid sequence, predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. Biological and molecular functions of the proteins are described using GO terms. Where appropriate, links to other databases are provided (e.g. Entrez, SWISS-PROT, OMIM, PubMed, PubMed Central).
A database covering eight category functional interactions between noncoding RNAs (except tRNAs and rRNAs) and proteins related biomacromolecules (proteins, mRNAs and genomic DNAs) in six model organisms. Functional interactions imply both physical interactions between the ncRNA and protein, and other forms of interaction where the combination of an ncRNA and an mRNA or a genomic DNA sequence elicits a cellular reaction. This database is distinguished from other biomolecular interaction database by: 1. The data of NPInter is novel, in the sense that no earlier database has especially cataloged this type of data (ncRNA-protein interactions). The database now contains more than 700 published functional interactions from the six organisms E. coli, yeast, worm, fly, mouse and human in which functional interactions experiments have been concentrated. The amount of data is not large, but the NPInter covers almost all experimentally verified ncRNA functional interaction data which had been published before the end of last year. 2. The ncRNA functional interaction data are entered into NPInter only following publication in books or peer-reviewed journals. Entry is done manually by a curator, and thereafter double-checked by a second curator. 3. We introduce a classification of the functional interaction data, which is based on the functional interaction process the ncRNA takes part in. 4. NPInter also provides an efficient search option, allowing recovery of interactions, related publications and other information., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A reference database on Nuclear Hormone Receptors. It is a bioinformatic database of nuclear receptors. NuReBase Version 4 is hosted on the PBIL server, contains protein and DNA sequences arranged according to the official nomenclature. In addition, for each group of homologous genes a phylogenetic tree and a protein alignment is provided. NuReBase also contains EMBL sequences and annotations for proteins and DNA, enriched with nuclear hormone receptor-specific information. The core of the NuReBase database is reviewed and this core is complemented by another database, NuReBase_DAILY, which is automatically updated every 24 hours. Recently, the NuReBase database has been expanded. It now includes data on alternative transcripts for each gene in the database and expression data for human and mouse nuclear receptors.
ODB (Operon DataBase) aims to collect known operons in multiple species and to offer a system to predict operons by user definitions. All the known operons are derived from the literature and from publicly available database including operon information. This system provides candidates of operons based on the conditions that users choice and also provide its prediction accuracy. This database integrates both known literature-based operons and as well as operon prediction, to provide a useful system for bioinformatics researchers and experimental biologists.
The Oomycete Genomics Database is a publicly accessible resource that includes functional assays and expression data, combined with transcript and genomic analysis and annotation. OGD builds upon data available from the Phytophthora Genome Consortium, Syngenta Phytophthora Consortium and the Phytophthora Functional Genomics Database. Data are analyzed and annotated using NCGR''s XGI System. The knowledge gained from these studies provide significant insight into key molecular processes regulating an economically important pathosystem and will provide novel tools for improvement of disease resistance in crop plants.
OGRe is a searchable relational database which currently contains the complete mitochondrial genome sequences of 1244 metazoan organisms. In addition to gene sequences, OGRe also contains information on gene order and codon usage., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Database of vertebrate olfactory receptors genes and proteins. It supports sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. The database also incorporates a broad range of chemosensory genes and proteins, including the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), and fungal pheromone receptors (FPRs). ORDB currently houses chemosensory receptors for more than 50 organisms. ORDB contains public and private sections which provide tools for investigators to analyze the functions of these very large gene families of G protein-coupled receptors. It also provides links to a local cluster of databases of related information in SenseLab, and to other relevant databases worldwide. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes: * It is a repository of olfactory receptor sequences. * It provides tools for sequence analysis. * It supports similarity searches (screens) which reduces duplicate work. * It provides links to other types of receptor information, e.g. 3D models. The database is accessible to two classes of users: * General public www users have full access to all the public sequences, models and resources in the database. * Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors.
Oncogenomic Database of Hepatocellular Carcinoma
OncoDB.HCC is the first comprehensive oncogenomic database for HCC. It effectively integrates three datasets from public references to provide multi-dimension view of current HCC studies. The three datasets included are Chromosome aberration studies, Gene expression studies, and HCC model organisms (rats and mice).
Ontology for Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.
University of Salamanca; Salamanca; Spain
Spanish higher education institution, located in the city of Salamanca, west of Madrid, in the autonomous community of Castile and León. It was founded in 1134 and given the Royal charter of foundation by King Alfonso IX in 1218.
Oncomine Research Platform is a partially-commercial suite of products for online cancer gene expression analysis dedicated to the academic and non-profit research community. Oncomine combines a rapidly growing compendium of 20,000+ cancer transcriptome profiles with a sophisticated analysis engine and a powerful web application for data-mining and visualization. Oncomine facilitates rapid and reliable biomarker and therapeutic target discovery, validation and prioritization. Oncomine was developed by physicians, scientists, and software engineers at the University of Michigan and is now fully supported for the academic and non-profit research community by Compendia Bioscience.
Open source, open access database and literature curation system for community based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. Automatically cross referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, eVOC: Cell type ontology, and Taxonomy database. Community driven resource for curated regulatory annotation.
ORENZA : a database of ORphan ENZyme Activities
ORENZA is a relational database of Orphan Enzyme Activities. ORENZA provides an accurate and up to date list of Enzyme Activities for which no sequences are available in the main sequence protein databases. Orphan enzyme activities correpond to the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), and which are not associated with any amino acid sequences in the major public databases.
Organelle DB: A Database of Organelles and Protein Complexes
Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light.
Curated sequence data and related information on organelles from NCBI Refseq for the community to use as a standard. The animal mitochondrial records are considered reviewed; that is, they have been manually curated by the NCBI staff. Other mitochondrial and chloroplast genome records are provisional and are presented with varying levels of review compared to the primary record used to build the RefSeq. Additionally, protein clusters for the metazoan and plastid genomes proteins can be reviewed with Entrez Protein Clusters.
OrthoMCL DB: Ortholog Groups of Protein Sequences
OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. OrthoMCL starts with reciprocal best hits within each genome as putative in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as putative ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org/mcl) is invoked to split mega-clusters. This process is analogous to the manual review in COG construction. MCL clustering is based on weights between each pair of proteins, so to correct for differences in evolutionary distance the weights are normalized before running MCL.
A comprehensive rice science database established in 2000 by rice researcher''s committee in Japan. The database is originally aimed to gather as much knowledge as possible ranging from classical rice genetics to recent genomics and from fundamental information to hot topics. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant images, and (5) fundamental knowledge of rice science. We are planning to do more extensive cross-referencing of Oryzabase to the major DNA sequence database, literature database and other plant databases in order to provide the wealth of information to rice researchers. We are calling for additional mutants and mapped gene information to incorporate into the Oryzabase. Newly identified mutants and mapped trait genes published in the scientific journals will be welcome to integrate into the Oryzabase maps.
It was established with an overall objective to provide a resource of protein phosphorylation data from multiple plants. P3DB was constructed with a dataset from oilseed rape. The data was obtained using a combination of data-dependent neutral loss and multistage activation mass spectrometry. The dataset includes 14,670 non-redundant phosphorylation sites from 8,894 phospho-peptides in 6,382 substrate proteins.
It has made an effort to collect known PAIs and to detect the potential PAI regions in the prokaryotic complete genomes. PAIDB was developed and maintained by Genome Encyclopedia of Microbes (GEM) at Korea Research Institute of Bioscience and Biotechnology (KRIBB) in Korea. Previously, we have developed a computational method for identifying PAIs in sequenced genomes by combining a homology-based method and detection of abnormalities in genomic composition.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A collection of protein sequences and the BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually, results can be retrieved from a database of pre-computed alignments. PairsDB is continually updated and we aim to be as comprehensive as possible.
PALI- Phylogeny and Alignment of homologous protein str
It provides structure based sequence alignments for homologous proteins of known 3-D structure. The alignments available include those of pairwise (two proteins at a time) and multiple (simultaneous superposition of all the structures in a family). The database also provides dendrograms depicting phylogentic relationships based on sequence and structural similarities. The present version of the database consists of 1922 protein families containing over 13,500 protein domains, more than 2,00,000 structural alignments and over 1400 orphansorphans (single member families). PALI (version 2.7) has been derived largely from SCOP 1.73 database. The pairwise superpositions were performed using DALI by Holm and Sander while superposition of multiple structures has been performed using MUSTANG ver.3 by Konagurthu et.al. and the structural similarities are assessed using the metrices defined by Johnson and Levitt & Gerstein.
It contains the genotype, phenotype, and polymorphism data produced by the NSF-funded project; Genetic Architecture of Maize and Teosinte. The PANZEA project will identify genes that control domestication traits and three key agronomic traits: flowering time, plant height, and kernel quality. Genetic linkage, association, and fine mapping analyses will be performed on the largest and most diverse set of mapping families publicly available for any species. A large series of isogenic lines will be used to characterize allelic series and epistatic interactions. The genetic architecture of each of the four trait groups will be compared and contrasted, and the influence of recombination and past domestication bottlenecks on the genomic distribution of functional diversity will be examined. Finally, the ability of genetic architecture-based models to predict phenotype will be evaluated in a broad range of germplasm, including elite US hybrids. This project will take a step toward the ultimate goal of predicting phenotype from genotype.
Growth, trait and development ontology for soybean
A publicly available database resource containing the assembled partial genomes for ~700 eukaryotic organisms. Partial genomes are generated from expressed sequence tag datasets containing more than 1000 sequences. PartiGeneDB allows users to view sets of genes and identify genes of interest in organisms for which a full genome is not currently available. PartiGeneDB is automatically updated to include new organism datasets as they are generated. PartiGeneDB provides four portals of entry into the database. It is hosted and supported by the Hospital for Sick Children, Toronto. In addition to providing a comprehensive resource facilitating comparative analyses, PartiGeneDB allows researchers to access the partial genomes of organisms that may not be available elsewhere. However, we recommend and encourage users interested in exploring datasets from a single organism in more depth, that you visit the specific web sites associated with the sequencing effort associated with that organism .
It contains pre-calculated structural and phylogenomic analyses of over 57,000 protein families and domains. The PhyloFacts resource includes "books" for protein families across the Tree of Life. Each book includes a multiple sequence alignment, one or more phylogenetic trees, predicted subfamilies, predicted 3D protein structures, active sites and other key residues, cellular localization, and Gene Ontology (GO) annotations and evidence codes. PhyloFacts includes hidden Markov models for classification of user-submitted (DNA or protein) sequences to protein families and subfamilies across the tree of life. Our primary current focus is on covering all the gene families represented in the human genome and all structural domains, but plan to expand the resource to include all proteins in all species. The protein families in this resource typically contain homologs from many species. The phylogenetic distribution of a protein family can vary from highly restricted (e.g., to hominidae or mammals) to throughout the tree of life. Gathering homologs from many divergent species enables us to take advantage of experimental investigations in different systems, and allows powerful inferences of function and structure that might not otherwise be possible.
Database for phylomes, that is, complete collections of phylogenetic trees for all proteins encoded in a given genome. It aims at providing a repository of high-quality phylogenies and alignments for proteins encoded in model species. To derive a phylome, each protein encoded in a given genome is used as a seed to retrieve its homologs in other complete genomes. These sequences are aligned and processed to derive reliable phylogenies using several phylogenetic methods. Besides providing the evolutionary history of the gene families, phylomeDB includes phylogeny based predictions of orthology and paralogy relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A database of phylogenetic patterns of evolution between 46 different species. PhyloPat uses the latest release of EnsMart (release 52), and their one-to-one, one-to-many and many-to-many orthologies. First, we stored all of the Ensembl IDs within the 46 species, and the orthologies between them. Second, we determined the evolutionary order of the studied species using the NCBI Taxonomy database. The phylogenetic tree of these species can be viewed here. Third, we used this phylogenetic tree as a starting point for building our phylogenetic lineages. For each gene in the first species (S. cerevisiae), we looked for orthologs in the other species. All orthologs were added to the phylogenetic lineage, and in the next round were checked for orthologs themselves, until no more orthologies were found for any of the genes. This process was repeated for all genes in all species that were not connected to any phylogenetic lineage yet. The complete phylogenetic lineage determination generated 329,998 phylogenetic lineages, consisting of 973,821 genes. These lineages can be queried here by phylogenetic patterns, MySQL regular expressions or simply a list of Ensembl/EMBL/EntrezGene/HGNC IDs. Output can be given in HTML, Excel or plain text format.
An online comparative genomics resource that is built upon publicly available sequence and map information from a diverse set of plant species, with a focus on the angiosperms, or flowering plants. It provides an interface to the results from a variety of phylogenomic analyses. Phytome is designed to facilitate functional genomics, molecular breeding and evolutionary studies in model and non-model plant species. Currently, Phytome contains phylogenetic and functional information for predicted protein sequences ("Unipeptides"). Future development will incorporate data and tools for analysis of sequence-based comparative maps.
Protein Inter-Atomic Distance Distribution Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A database for the study of protein inter-atomic distance distribution. Currently, the distances are extracted from the protein structures determined through X-ray Crystallography, but they could also be obtained from NMR structural models. The known structures with the resolution higher than 2A and less than 70% sequence similarities are selected. Each type of distances is specified in terms of the types of the atoms it involves, the types of the residues containing the atoms, and the types of the residues in between the two end residues in sequence. An automated system is built to generate and process the data dynamically. The system consists of two levels of databases. The first one stores the sequence and structure information for a large set of high-resolution protein structures, with a similar data structure as the structural data represented in the PDB Data Bank. The second one stores the information for the distance distributions, with each record corresponding to a distribution function. The second database is built dynamically from the first one. The database can provide structural information in terms of distance distributions to structural biologists. Such information can be valuable for the study of many fundamental biological problems including protein structure prediction and determination, protein dynamics simulation, molecular design, protein structural analysis and classification, etc.
A database dedicated to the study of host-pathogen protein-protein interactions (PPIs). PIG provides a number of user interfaces for searching available data and tools for predicting interactions between host and pathogen proteins.
Protein-protein Interactions Thermodynamic Database
A protein-protein interactions thermodynamic database which contains data of several thermodynamic parameters along with sequence and structural information experimental conditions and literature information. Each entry contains numerical data for features of the interacting proteins such as the free energy change, dissociation constant, association constant, enthalpy change, and heat capacity change. PINT includes: the name and source of the proteins involved in binding, SWISS-PROT and Protein Data Bank (PDB) codes, secondary structure and solvent accessibility of residues at mutant positions, measuring methods, and experimental conditions such as buffers, ions and additives, and literature information. PINT is cross-linked with other related databases such as PIR, SWISS-PROT, PDB and the NCBI PUBMED literature database.
PIPs- Human Protein-protein Interaction Prediction
A database of predicted human protein-protein interactions. The predictions have been made using a naïve Bayesian classifier to calculate a Score of interaction. There are 37606 interactions with a Score ≥1 indicating that the interaction is more likely to occur than not to occur.
A web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals. It compiles all the possible clusters of piRNAs and also depicts piRNAs along with the associated genomic elements like genes and repeats on a genome wide map. piRNABank mainly provides data onnamely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila.Search options have been designed to query and obtain useful data from this online resource. It also facilitates abstraction of sequences and structural features from piRNA data. piRNABank provides the following features: * Simple search * Search piRNA clusters * Search homologous piRNAs * piRNA visualization map * Analysis tools, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
PiSITE: Database of Protein interaction SITEs
A web-based database of protein interaction sites. PiSITE provides not only information of interaction sites of a protein from single PDB entry, but also information of interaction sites of a protein from multiple PDB entries including similar proteins. PiSite also provides a list of sociable proteins, proteins with multiple binding states and multiple binding partners.In PiSITE, the identification of the binding sites of protein chains is performed by searching the same proteins with different binding states in PDB at first, and then mapping those binding sites onto the query proteins. The database PiSITE provides real interaction sites of proteins using the complex structures in PDB. According to the progress of several structural genomic projects, we have a large amount of structural data in PDB. Consequently, we can observe different binding states of proteins in atomic resolutions, and can analyze actual interaction sites of proteins. It will lead better understandings of protein interaction sites in near future. Usual practice to identify the interaction site has been done using a representative complex in PDB. However, for the proteins with multiple partners, non-interaction sites identified by using a single complex structure is not enough, because some part of the non-binding sites may be involved in the interaction sites with another proteins. Therefore, the real interaction sites should be obtained by using all of the binding states in PDB. For the purpose, the identifications of the binding site in PiSITE are done by searching the same proteins with different binding sites in PDB at first, and then mapping the binding sites onto the query proteins. PiSITE also provides the lists of transient hub proteins, which we call sociable proteins to clarify the different of so-called hub proteins. The sociable proteins are identified as the proteins with multiple binding states and multiple binding partners. On the other hand, so-called hub proteins have been identified as the proteins at the hub position in protein-protein interaction networks obtained by large-scale experiments, but the definition of the hub proteins cannot differentiate transient hub proteins from stable ones, although the differentiation is critically important for the better understanding of protein interaction networks. In addition, the usual definition of hub proteins can contain supermolecules as hub proteins. The supermolecules can be identified as the proteins with a single binding state and multiple binding partners, which we call stable hub proteins.
A small ontology for anatomical spatial references, such as dorsal, ventral, axis, and so forth.
It provides access to a veriety of databases of plant genomics databases. These include: *Arabidopsis PARE Database *Arabidopsis SBS Database *Arabidopsis MPSS Plus Database *Rice MPSS Database *Legume SBS Database *Maize SBS Database *Gallus Gallus SBS Database *Magnaporthe MPSS Database *Grape MPSS Database These data have been generated by a series of different projects, mainly based at the University of Delaware and funded primarily by grants from the National Science Foundation and the United States Department of Agriculture. The database and the web pages that you see were produced by the Meyers lab, with data generated within our lab, by collaborating laboratories like the Green or Wang labs. Some data we've gathered from Genbank or other public sources. Much of the data was produced under contract by Illumina, Inc (Hayward, California), but some SBS libraries are now being sequenced at other sites.
Software tool that allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the rough shape and intensity of individual features.
It is an objective classification system for plan proteins based on cluster analyses of the inferred proteomes of the sequenced angiospermsArabidopsis thaliana v Columbia, Oryza sativa v. japonica (Rice), and Populus trichocarpa (poplar). Sequence data for Carica papaya and Medicago papaya are also included in the current version of Tribes. Results for these species are currently masked from view, but will be available when the genomes are publicly released. In addition to the genome-based tribe scaffold, unigenes from more than 200 plant and algal species TIGR Transcript Assemblies have been associated with each tribe (see documentation), resulting in a global classification of about 4 million putative plant protein sequences. PlantTribes 1.0 incorporates an extensive collection of microarray expression data from Arabidopsis microarray experiments. Expression data is linked to the individual genes in PlantTribes, and can be accessed through any result including Arabidopsis gene sequences. PlantTribes is based on the similarity-based clustering procedure TribeMCL (Enright et al, 2002,2003) to classify protein-coding genes into putative gene families. MCL classifications have been constructed using three clustering stringencies , allowing the user to explore the stability of the protein classification. A second round of MCL clustering identifies SuperTribes that approximate objective superfamilies. PlantTribes also includes information about domains, traditional gene family names, and a unified nomenclature based on common terms.
A plastid protein database. It integrates data from large scale proteome analyses of different plastid types.These include etioplasts, chloroplasts, chromoplasts and the undifferentiated proplastid-like organelles of tobacco BY2 cells. This comparison allows establishing a core proteome that is common to all plastid types and provides furthermore information about plastid type-specific functions.
A relational database that integrates data from rice, maize, and Arabidopsis by placing the complete Arabidopsis and rice proteomes, and the available maize sequences into "putative orthologous groups" (POGS). Annotation efforts are now beginning and will focus on predicted RNA binding proteins (e.g. those with known RNA binding domains or known to influence RNA function). Putative Orthologous Groups (POGs) form the heart of the database, and were assigned using a mutual best hit strategy after performing BLAST comparisons of the predicted Arabidopsis and rice proteomes. Each POG entry includes cross-referenced orthologs and paralogs in Arabidopsis and rice, annotated with domain organization, gene models, phylogenetic trees showing closely-related proteins, and intracellular targeting predictions. The database can be queried to identify POGs with specific domain combinations and predicted intracellular locations.
POINT is a protein-protein interaction database. It includes annotation of interologs and protein phsophorylation. This work analyzes the applicability of orthologs-based PPI prediction and provide the theoretical upper-bound of this approach.
A database of mRNA polyadenylation sites. PolyA_DB version 1 contains human and mouse poly(A) sites that are mapped by cDNA/EST sequences. PolyA_DB version 2 contains poly(A) sites in human, mouse, rat, chicken and zebrafish that are mapped by cDNA/EST and Trace sequences. Sequence alignments between orthologous sites are available. PolyA_SVM predicts poly(A) sites using 15 cis elements identified for human poly(A) sites.
A database of quadruplex motifs. It is composed of two parts (EuQuad and ProQuad). EuQuad gives information on quadruplex motifs present in human, chimpanzee, rat and mouse genes. ProQuad contains quadruplex information of 146 prokaryotes. Apart from gene-specific searches QuadBase has a number of other modules. ‘Orthologs Analysis' queries for conserved motifs across species in a user-defined manner; ‘Pattern Search' can be used to fetch specific motifs of interest and the ‘Pattern Finder' tool can search for motifs in any given sequence
An integrated database of human coding single nucleotide polymorphisms (SNPs) and their annotations. Unlike other databases of similar nature, apart from integrating several coding SNPs (cSNPs) and protein-related information resources, we predict the implications of the non-synonymous SNPs (nsSNPs) using two well known algorithms (SIFT and PolyPhen). The results are presented in an intuitive visualization that depicts the cSNPs mapped onto protein domains and highlights those nsSNPs that are potentially damaging/deleterious or have been reported as disease allelic variants (based on OMIM). The query interface also supports searching for a list of proteins associated with any gene ontology term, pathway, disease term or gene family. Results can also be downloaded as a spreadsheet. The visualization page also provides links to several other related sources and dynamic links to literature references.
A database of information on pox viruses. Goals of this project are to acquire and annotate data on poxviruses, and to develop and utilize new tools to facilitate the study of this group of organisms. This basic research is being undertaken with an eye toward the development of novel antiviral therapies, vaccines against human orthopoxvirus infections, new approaches for the environmental detection of virions, and methods to accomplish more rapid diagnosis of disease.
PPD: a database of protein ionization constants
A searchable database of pKa values of amino acid residues within proteins. These values have been measured experimentally using a variety of methods, including NMR and the linearized Poisson-Boltzmann equation. This database of protein ionization constants was sourced from the primary literature and contains in excess of 1400 entries. The database contains pKa values for amino acid side-chains, as well as the N and C termini, over 75% of which focus on Glutamate, Lysine, Histidine and Aspartate. These four residues are all key ionizable residues, and therefore the apparent bias is not driven by our selection, but by the available experimental data. Very little data is currently available for Arginine: its pKa value (~12) essentially precludes measurement by titration as proteins will denature at high basic pH.
A Plant Proteome DataBase for Arabidopsis thaliana and maize (Zea mays). The PPDB stores experimental data from in-house proteome and mass spectrometry analysis, curated information about protein function, protein properties and subcellular localization. Importantly, proteins are particularly curated for possible (intra) plastid location and their plastid function. Protein accessions identified in published Arabidopsis (and other Brassicacea) proteomics papers are cross-referenced to rapidly determine previous experimental identification by mass spectrometry. All protein-encoding gene models in the Arabidopsis nuclear and organellar genomes, as assembled by TAIR, as well as all maize EST assemblies (ZmGI) as assembled by DFCI Maize Gene Index project. These are all uploaded in PPDB and are linked to each other via a BLAST alignment. Thus every predicted protein in both species can be searched for experimental and other information (even if not experimentally identified).
PPNEMA is abioinformatic database of rRNA genes from plant-parasitic nematodes. It consists of a database of ribosomal cistron sequences from various species grouped according to nematode genera, and a search system allowing data to be extracted according to both text and pattern searching. PPNEMA offers to the scientific community a preprocessed archive of plant parasitic nematode sequences useful for nematologists. It is a tool to retrieve plant nematode multialigned sequences for phylogenetic studies or to recognize a nematode by comparing its rDNA sequence with the PPNEMA available genus specific multialignments.
Predicted and Consensus Interaction Sites in Enzymes
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of interactions between amino acid residues of enzyme and its ligands. Provides summary of interactions between amino acid residues of enzyme and its various ligands including substrate and transition state analogues, cofactors, inhibitors, and products., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A sister database to ProSite, is constituted of manually created rules that increase the discriminatory power of PROSITE motifs (generally profiles) by providing additional information about functionally and/or structurally critical amino acids and can automatically generate annotation based on PROSITE motifs in the UniProtKB/Swiss-Prot format. Each ProRule is defined in the UniRule format. In addition to these rules corresponding to a unique PROSITE motif, there are also rules triggered by a specific combination of PROSITE motifs called metamotifs. Metamotifs allow the definition of arrangements of domains separated by spacers of variable size, as well as the anchoring to the N- and/or C-termini and the exclusion of a PROSITE motif. ProRule uses the UniRule format that is common to all types of rules created to annotate UniProtKB/Swiss-Prot, including the HAMAP family rules. Each rule contains information used to provide template based annotation associated with the domain or family detected by the PROSITE motif. ProRule is used to create UniProtKB/Swiss-Prot lines with basic and complex annotation derived from the presence of the domain and of biologically critical amino acids: domain name and boundaries, EC number, function, keywords, associated PROSITE patterns, PTMs, active sites, disulfide bonds, etc.). ProRule contains notably the position of structurally and/or functionally critical amino acid(s), as well as the condition(s) they must fulfil to play their biological role(s). Part of these supplementary data are used by ScanProsite that not only provides the protein sequence matched by a profile, but also information about the relevance of biologically meaningful residues, like active sites, binding sites, post-translational modification sites or disulfide bonds, to help function determination
Protein Structure and Alternative Splicing
This database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database. Users can search based on Ensembl gene or Ensembl transcript ids, Gene descriptions, Uniprot gene names, Genes matching patterns, Swissprot/Uniprot identifiers or Affymetrix probeset ids.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures). The rest of entries are constructed from PDB files for multi-chain protein complexes by leaving only two interacting chains, (in the database nomenclature designators of those chains are appended to the name of the original PDB file). The homo-complexes in this database are the complexes with two monomers having more than 95 % sequence identity. Each entry consists of the X-ray structure taken from the PDB data bank (in the PDB/ folder), sequence file (in the SEQ/ folder) and the data file (in the INF/ folder) where all relevant information is stored. File names consist of PDB ID and extensions .pdb (X-ray structures), .seq (sequence files or .inf (data files). Current implementation of the database accommodates the following information for each entry, separately for larger (denoted as chain A*) and smaller (chain B) components: * Full sequence; * Number of residues; * Number of residues on the interface; * List of interfacial residues; * Number of helices and strands; * Absolute (in �2) and relative interface areas. The database is searchable with respect to majority of the above parameters. Additional search is possible with respect to the PDB ID and protein names. Downloads are possible for both individual entries (as plain text files) and for the whole content or search (checked) result list (as one gzipped file). Supplementary search and download is available for the subset of the database at 40% sequence identity level (the DPPC40 database).
It provides information on natural and artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, and each entry in the database corresponds to one article which may describe one, several or a number of protein mutants. Each database entry is identified by a serial number and is defined as either natural or artificial, depending on the type of the mutation. For each entry the following are recorded : JOURNAL, TITLE, CROSS-REFERENCE, PROTEIN, N-TERMINAL, CHANGE, FUNCTION, STRUCTURE, STABILITY, etc. CROSS-REFERENCE indicates the code names of the protein given in other databases such as Protein Identification Resources (2). N-TERMINAL shows the N-terminal sequence of five amino acids which may help to show the unambiguous numbering of th e sequence. CHANGE indicates the position and kind of mutations, such as amino acid substitution, insertion and deletion, denoted with a specific notation. Any functional or structural features (FUNCTION, STRUCTURE, STABILITY,etc) observed in the mutant are described immediately after ''CHANGE''. Relative differences in activity and/or stability, in comparison with the wild-type protein, are indicated with symbols (- -),(-),(=),(+) or (+ +). Complete loss of activity is denoted as (0). Data Submission A data submission system was newly prepared in the PMD. We welcome the authors of articles published in academic journals to submit their own mutant data to the PMD. After checking the contents, we will register the data with a unique accession number.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It provides information about primers and probes that can be used to quantitate human and mouse mRNA by reverse transcription polymerase chain reaction (RTx96PCR) assays. Users can search the QPPD to find: * Primer sets and probes for a given gene * Primer location * Amplicon size * Assay type * Positions of single nucleotide polymorphisms (SNPs) * Literature references * Available I.M.A.G.E. cDNA clones * The Primer Viewer, a graphical representation of the gene and primer sets, which includes hyperlinks to Gene Info from the Cancer Gene Anatomy Project (CGAP) and the CGAP SNP viewer.
SCMD - Saccharomyces cerevisiae Morphological Database
The Saccharomyces Cerevisiae Morphological Database(SCMD) is a collection of micrographs of budding yeast mutants. Micorgraphs of mutants with altered cell morphology from a set of the haploid MATa deleted strains obtained from EUROSCARF. From the micrographs, disruptant cells are automatically extracted by our novel cell-image processing software.
A database of comprehensive information about mutant phenotypes, reporter-gene expression patterns, flanking sequences of T-DNA insertional sites, seed availability, and others are collected in the database. RMD can be searched by keywords, nucleotide sequence or protein sequence. This database provides three classes of functions: (1) identifying novel genes, (2) identifying regulatory elements, and (3) identifying pattern lines for ectopic expression (misexpression) of target gene at specific tissue or at specific growth stage.
A new source of RESP or ESP atomic charge values for small structures or model systems. Its goals are multiple. R.E.DD.B. freely stores and distributes derived RESP or ESP charges of high quality and high reproduciblility within force field library(ies) in the scientific community. However, R.E.DD.B. can also be seen as a tool devoted to reproduce, compare, criticize and improve the different RESP and ESP models. As indicated by its name, R.E.DD.B. deals _only_ with RESP or ESP charges, and not with other types of atomic charges (Mulliken, Gasteiger or Bader analysis...). As previously said, many different procedures are used to derive such RESP or ESP charges, and the charge values are affected by many parameters (Quantum Mechanics programs, algorithms, molecular orientation, molecular conformation, human errors, etc..). Thus, R.E.DD.B. not only stores RESP or ESP charge values, but also the structures and information about the procedure used to derive the reported charge values. Two types of "projects" can be found in R.E.DD.B. - A WHOLE MOLECULE "project", which corresponds to an intact (un-broken) molecule. Examples are small organic or inorganic molecules such as solvent (DMSO, ethanol, cyclohexane etc...), and ligands of proteins or nucleic acids. - A MOLECULE FRAGMENT "project", which corresponds to a part (or fragment) of an organic or inorganic macro-molecule. This means that some atoms have to be removed from the structure(s) used in the charge derivation process to lead to the target fragment(s). Examples are amino-acid (AA) fragments 'NH-CH(R)-CO' where the atomic charges are generally derived using capped amino acids 'ACE-AA-NME', nucleotide fragments originating from the fusion between dimethylphosphate and the corresponding nucleosides, or monosaccharide fragments. These fragments are generally compatible with previously existing ones (available in force field topology databases), and used to construct macro-molecules such as proteins, nucleic acids or polysaccharides.
RARGE - RIKEN Arabidopsis Genome Encyclopedia
This database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, sequence homology or keyword, and rapid access to detailed information on the resources. We have isolated 245 946 RAFL cDNA clones and collected 11 933 transposon-tagged lines, which are available from the RIKEN Bioresource Center and are stored in RARGE.
THIS RESOURCE IS NO LONGER IN SERVICE, documented April 14, 2017. The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL's, etc. that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters.
Database of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Several tools are available including REBsites, BLAST against REBASE, NEBcutter and REBpredictor. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. Users may submit new enzyme and/or sequence information, recommend references, or send them corrections to existing data. The contents of REBASE may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email.,
RECODE- The database of the translational recoding events
A compilation of programmed; translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. The entries for each event include the sequences of the corresponding genes, their encoded proteins for both the normal and alternate decoding, the types of the recoding events involved, trans-factors and cis-elements that influence recoding.
University of Santiago de Compostela; Santiago de Compostela; Spain
It contains entries for refolding protocols for a wide range of proteins. REFOLD provides a means of dissminating refolding protocols and techniques to the scientific community. A large number of recombinant proteins expressed in bacteria are insoluble and thus require renaturation. Identifying optimal conditions and methodology for refolding can be time consuming and often rate-limiting. To this end, REFOLD was designed to assist in the design and implementation of methodologies for the in vitro refolding of proteins. The database contains heavily annotated entries for the refolding of a wide range of proteins which can be searched via multiple parameters using either simple or advanced search functions. The database can also be browsed by categories such as structural class, family, or refolding method. The web interface allows a detailed, sortable, spreadsheet-like list of results allowing quick visualisation of search results. Each entry contains detailed information regarding the protein of interest, methods and conditions employed, as well as reference and links to the relevant journal publication. Effective use of hyperlinks in results pages also allows useful browsing of entries for other proteins sharing similar properties or methods. REFOLD also provides analysis of the database through graphical representation of the data. The available graphs show the breakdown of refolding records in the database according to different parameters, such as refolding method, protein constructs and various refolding conditions. REFOLD graphs can be found here., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
This database provides some information and resources related to LTR-retrotransposons in rice genome. The availability of the pseudomolecules of the Asian cultivated rice (Oryza sativa ssp. japonica cv. Nipponbare) allowed the construction, for the first time, of a non-redundant database of LTR retrotransposon sequences for an agronomically important plant species. 242 distinct families are curated, of which 194 have not been described elsewhere. These newly identified sequences, representing mainly low copy number elements, were identified by in-silico approaches. Reference molecules of each LTR retrotransposon family were characterized, annotated and deposited in RetrOryza. Further analysis will be focused on the identification and the annotation of LTR retrotransposons of several species within the Oryza genus.
The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome
A contig-oriented database for high-quality manual annotation of RGP, which can present non-redundant contig analyses by merging the accumulated PAC/BAC clones. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results (30000 predicted genes.) The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. Note that the annotation data of chromosomes 1, 3, 4 and 10 are restored from flat files of the public database. These basically contain the predicted genes information but not contain their evidence information.
A public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Memorial Sloan-Kettering Cancer Center''s ontology of surgical secondary events (adverse events).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application for calculation of the restricted likelihood-ratio affected sib-pair test for linkage allowing for imprinting (entry from Genetic Analysis Software)
A rice genome automated annotation system. This system integrates programs for prediction and analysis of protein-coding gene structure. Integrated softwares are coding region prediction programs ( GENSCAN, RiceHMM, FGENESH, MZEF ), splice site prediction programs (SplicePredictor ), homology search analysis programs ( Blast, HMMER, ProfileScan, MOTIF ), tRNA gene prediction program ( tRNAscan-SE ), repetitive DNA analysis programs ( RepeatMasker, Printrepeats ), signal scan search program ( Signal Scan ), protein localization site prediction program ( PSORT ), and program of classification and secondary structure prediction of membrane proteins ( SOSUI ). Blast against full-length cDNA sequences of japonica rice is integrated. The full-length rice cDNA sequence is provided by KOME database. Interpretation of the coding region is fully automated and gene prediction is accomplished without manual evaluation and modification. Therefore some differences exist between the predicted genes by the system and the manually predicted genes included in the GenBank entries. Please see "comparison table of gene prediction", http://RiceGAAS.dna.affrc.go.jp/rga-bin/col_accur.pl in detail. Further, a unique function is automatically assigned for predicted gene by GFSelector based on the protein homology of the gene. Additionally, the keyword search from the functions predicted by GFSelector is provided.
Ridom - Ribosomal Differentiation of Medical Microorganisms
A partly-commercial resource that also supplies freeware to the general public. The freeware it supplies include a DNA trace viewer and editor (TraceEdit), MRSA strain/spa-typing software (SpaServer), and epidemiological typing software (EpiCompare). The SpaServer can be used to collate and harmonize data from various geographic regions. This WWW site is freely accessible to internet users and the spa-repeat sequences and the -types can be downloaded. Chromatograms of new spa-repeats and/or -types can be submitted online for inclusion into the reference database. Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. The program Ridom EpiCompare can calculate various criteria for data of different typing techniques. It combines easy calculation with ease of data handling. Ridom EpiCompare can calculate the following parameters: *Typability is the percentage of distinct microbial strains which can be assigned a positive typing marker. *Reproducibility is the percentage of strains that give the same result on repeated testing. *Discriminatory power of a typing method is its ability to distinguish between unrelated strains. the an important ability of typing systems. *Typing system concordance helps to compare different independent typing systems.
RISSC - Ribosomal Internal Spacer Sequence Collection
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 25, 2013. RISSC is a database of ribosomal 16S-23S spacer sequences intended mainly for molecular biology studies in typing, phylogeny and population genetics. Ribosomal spacers have proven to be extremely useful tools for typing and identifying closely related prokaryotes due to their high variability in size and/or sequence, much more so than the flanking 16S and 23S rRNA genes. These genes are commonly used to establish molecular relationships among microbes at a taxonomic level of species or higher (e.g genus, domain...). However their internal transcribed spacers (ITS) are much more useful to discriminate at the species or even strain level. Currently, many published papers are showing the growing importance of these regions of the ribosomal operon in these types of studies. A second, much shorter, ribosomal spacer can be found between rRNA genes 23S and 5S, also of phylogenetic interest. We intend to incorporate them into the database in the near future. By creating RISSC, our intention is to provide the scientific community with a comprehensive set of ribosomal spacer sequences, fully edited and characterized with a key feature as is the presence/absence of tRNA genes within them, ready to be used and compared with their own ITS sequences.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments (in species where more than one isolate has been fully sequenced) and contains translated genome sequences for all species. It has been created for two main purposes: to facilitate the comparative analysis of RNA viruses and to become a hub for other, more specialised virus Web sites.
It provides access to results from RNAi interference studies in C. elegans, including images, movies, phenotypes, and graphical maps. RNAiDB contains all published RNAi experiments in C. elegans that have been deposited in WormBase, including data from the literature and published large-scale RNAi studies. RNAi to gene mappings for all experiments have been re-analyzed using ePCR and/or a sliding n-mer window method to identify all genes in different genomic locations that may potentially be inhibited by each experiment. Gene maps showing canonical and putative alternate mappings are displayed graphically on RNAi Experiment and Gene/ORF card pages.
Welcome to the computational genomics laboratory''s home page. Main research interests: computational biology, bioinformatics and systems biology applied to the study of the mechanisms underlying gene expression regulation. They also develop bioinformatic software aiming at helping the research community solve some problems.
It is a tool developed for RNR research that gives you the opportunity to retrieve RNR protein sequences from any organism that have been either experimentally characterised or predicted from genome sequence data. The RNR database contains a compilation of all published 3D structures of different RNR proteins as well as a compilation of all mutant proteins constructed including links to the relevant publication(s). RNRs by organism gives an overview of the entire database. Users can also search the database for occurrence of ribonucleotide reductases in taxonomic groups. The BLAST server of the RNR database allows sequences to be BLASTed against our database that contains RNR sequence, genomic, and species data.
ROSPath- Reactive Oxygen Species Related Signaling Pathway
Reactive Oxygen Species Related Signaling Pathway
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. Database that offers information on molecules and interactions involving signaling pathways through literature-based curative explanation and laboratory results as well as basic information through links to other databases. Its major content consists of signaling entities and signaling interactions designed to describe various levels of signaling events. It is designed to convey chemical changes and logical information flow in detail through careful data modeling of complex signaling processes. ROSPath was developed for the purpose of aiding the research of ROS-mediated signaling pathways including growth factor-, stress- and cytokine-induced signaling that are main research interests of the Division of Molecular Life Sciences and Center for Cell Signaling Research in Ewha Womans University. ROSPath is designed to describe cellular signaling processes in molecular detail and to accumulate data and knowledge regarding signaling pathways with the organized database structure. It offers useful means to researchers by providing curative Information on the signaling pathways of interest and by providing means of managing data produced by high-throughput experiments such as proteomics and genomics tools. Furthermore, its goal is to provide effective and flexible tools for signaling pathway analysis and data mining by means of extensive data modeling and development of computer-aided tools.
It is a database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms. Users can search this database by gene name and organism. Each record includes sequences (genomic, cDNA, and amino acid sequences), intron/exon structures, genomic locations, and information about orthologs. In addition, users can view and compare the gene structures from different organisms and make multiple amino acid sequence alignments. RPG also provides information on small nucleolar RNAs (snoRNAs) that are encoded in the introns of RP genes.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a curated database that catalogs the numbers of genes that encode for 16S, 23S and 5S ribosomal RNAs in Bacteria and Archaea. Typically, a single copy of each of these genes is clustered into a rRNA operon, with as many as 15 rRNA operons present per genome. The genomic locus for any of the rRNA encoding genes is ?rrn? ? hence the name of this database. Because the number of genes encoding tRNAs is positively correlated with the number of rRNA-encoding genes (1), tRNA gene copy number is also cataloged in the rrnDB. Data are gathered both from sequenced genomes and from published articles that include estimates of the number of rRNA encoding genes.
It is a database that details the interactions of extruded, unpaired RNA nucleotide bases. It presents and classifies the protein binding pockets that accommodate them, and also allows the recognition of similar protein binding patters involved in interactions with different RNA molecules. Given an unbound structure of a target protein, it allows the prediction of its RNA nucleotide binding sites. The goal of this database is to describe, classify, and predict the interactions between protein binding sites and single-stranded RNA bases. Specifically, RsiteDB describes the protein binding pockets that accommodate extruded nucleotides not involved in RNA base pairing. RsiteDB has two modes of operation. Analysis and classification of protein-RNA interactions: Given a protein-RNA complex RsiteDB analyzes its nucleotide and dinucleotide binding sites. It details the properties of the protein binding pockets that accommodate these extruded nucleotides and presents a list of proteins with similar binding pockets. These proteins may have a totally different overall sequences and structural folds. RsiteDB details and visualizes the features shared by all the binding sites classified to the same cluster. Prediction of RNA dinucleotide binding sites: Given a target, potentially unbound, protein structure we search its surface for regions similar to the created 3-D consensus binding patterns of RNA dinucleotides. The recognized regions are predicted to serve as binding sites. Using leave-one-out tests, the success rate of these predictions was estimated to be about 80%. It must be noted that currently we do not aim to predict whether a protein can bind RNA; rather, given an unbound RNA binding protein, our goal is to predict its binding sites and their modes of interaction. In addition, due to a low number of single nucleotide clusters, currently, we do not use them for the prediction.
The Vertebrate Genome Annotation database (VEGA)
Central repository for high quality frequently updated manual annotation of vertebrate finished genome sequence. Human, mouse and zebrafish are in the process of being completely annotated, whereas for other species the annotation is only of specific genomic regions of particular biological interest. The majority of the annotation is from the HAVANA group at the Welcome Trust Sanger Institute. Users can BLAST, search for specific text, export, and download data. Genomes and details of the projects for each species are available through the homepages for human mouse and zebrafish. The website is built upon code from the EnsEMBL (http://www.ensembl.org) project. Some Ensembl features are not available in Vega. From the users point of view perhaps the most significant of these is MartView. However due to their inclusion in Ensembl, Vega human and mouse data can be queried using Ensembl MartView. Vega contains annotation of the human MHC region in eight haplotypes, and the LRC region in three haplotypes. Vega also contains annotation on the Insulin Dependent Diabetes (IDD) regions on non-reference assemblies for mouse.
RTCGD - Retroviral Tagged Cancer Gene Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of high throughput insertional mutagenesis screening projects of retroviral and transposon insertional mutagenesis in mouse tumors. Information in the RTCGD is obtained from sequence comparison by using public databases UCSC genome mm9 browser. Data based on previous genome assembly mm8 is also available at RTCGD mm8. MCGP has developed three web search tools including Easy Search to query proviral integration sites using mouse gene symbol of gene name; Model Search to obtain RIS information based on tumor models and/or tumor types; Interaction Search to find gene-to-gene interaction. It displays the list of genes which reside in the same tumor to your gene of interest.
RTKdb - Receptor Tyrosine Kinase database
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a database dedicated to Receptor Tyrosine Kinase. The RTKdb is the web-based interface of the RTKdb which is a database containing all the protein sequences of RTK, organized into families. It allows one to select sets of homologous genes from different species (only common species for the moment) and to visualize multiple alignments and phylogenetic trees. Thus the RTKdb is particularly useful for comparative genomics, phylogeny and molecular evolution studies. It contains a total of 159 proteins.
It collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. It covers the whole range from yeast to human. The SMAR table gives information on individual sequence elements of experimentally proven matrix binding activity. In release 2.3 it contains 500 entries. The sequences therein can be assigned to more than 150 genes from eukaryotic species ranging from yeast to human. The SMARbinder table contains 96 entries (release 2.3), but this figure does not reflect the number of independent S/MAR binding proteins. First of all, homologous factors from different species such as human and mouse SATB1 are given in different entries since they may differ in some aspects. Moreover, products of distinct but very similar genes or alternative splice products are included as separate entries. In some cases a more general term defining a S/MAR-binding activity may appear as one entry eventhough it might be composed of two or more subunits. The SMARbinder table will only contain those proteins of nuclear localization for which an interaction with a well defined S/MAR has been shown. Besides that the SMARbinder table will also include proteins that are proven components of the the salt-resitent (LIS-resistent) nuclear matrix. Gene entries, besides of giving the gene name in a long and a short (abbreviated) denomination, collect all links to individual S/MARs given in S/MARt DB and/or provide pointers to "S/MARbinders". The entries also contain links to transcription factor binding sites listed in TRANSFAC and give a link to the corresponding TRRD entry describing the regulatory features of the gene on different hierarchical levels.
S4: Structure-based Sequence Alignments of SCOP Superfamilies
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The S4 database contains sequence alignments of domains in SCOP superfamilies. The aligned domains are selected using ASTRAL so that no two domains in the alignment have more than 40 percent identity and, moreover, they align all domains identified by ASTRAL as having less than 40 percent sequence identity. The alignments are generated using information from pairwise structural alignments of all domains in a given superfamily. These structural alignments generate residue equivalences and distances between residues, as well as an overall similarity of the two domains being compared (RMSD). This information is used to score individual the equivalences between residues. The scores are then integrated using a multiple sequence alignment program to generate the finished alignment. This database allows alignments to be retrieved in clustal format, or viewed in a web browser, with either structural or sequence features annotated. In addition, the statistics of structural diversity for each superfamily can be seen. The pairwise structural alignments were performed using the SAP program. The output of SAP was converted to a T-Coffee library so that the multiple sequence alignment T-Coffee could be use to compute the sequence alignments.
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 9, 2014. SARS-CoV RNA SSS DATABASE is a database of the predicted RNA secondary structural sequences of six SARS coronaviruse complete genomes. These structures were sequenced and submitted to GenBank by the separate sequencing and research groups from countries and areas, including Beijing, Hong Kong, Taiwan, USA, Canada, and Germany. The database provides the detailed information of all the possible hairpin loops, interior loops, bulge loops, multi-branched loops, double-stranded stems, and free unpaired nucleotides of RNA secondary structural sequences of six SARS isolates, BJ01(Accession: AY278488), CUHK-AG01 (Accession: AY345986), TWY (Accession: AP006561), Urbani (Accession: AY278741), TOR2 (Accession: AY274119), and Frankurt 1 (Accession: AY291315). . The ORIGIN sequences in the database are from the NCBI's GenBank.
The graduate program in Neuroscience is a multidisciplinary, interdepartmental program divided into three main areas: Cell and Molecular Neuroscience, Development and Regeneration, and Systems Neuroscience. Their research relates to many human diseases and disorders including fetal alcohol syndrome, spinal cord injury, degenerative retinal disease, Alzheimer''s disease, multiple sclerosis, cerebral palsy, and amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig''s disease.
SBASE is a database of protein domain sequences collected from the literature, from protein sequence databases and from genomic databases. The protein domains are defined by their sequence boundaries given by the publishing authors or in one of the primary sequence databases (Swiss-Prot, PIR, TREMBL etc.). Domain groups are included if they have well defined sequence boundaries, and if they can be distinguished from other sequences using a similarity search technique. The SBASE database uses a set theoretical approach for representing similarities, which in practical terms is extremely simple. Sequences are considered similar if they are members of a similarity group in which all or most sequences are similar to each other and less similar to other members of the database. Sequences that have an above threshold BLAST similarity score to at least one member of the group is called the neighbourhood of the group. The below sketch shows such a neighborhood; the similarities within the group (self-similarities) and those pointing to non-member neighbours (non-self similarities) are shown in different colours., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
SCAdb: A CANDIDATE GENE DATABASE FOR SPINOCEREBELLAR ATAXIAS
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A candidate gene database for Spinocerebellar ataxia (SCA), which collected 3185 genes for 17 types of SCA. Those SCA subtypes that have known disease genes can be used as positive controls to optimize the parameters. The users may browse the candidate genes of a given SCA subtype by using the default parameters. The known disease genes were found to be the top three candidates using the default parameters. Alternatively, the users may score the candidate genes by changing the weight or the scores on the basis of their own working hypothesis.
SCOPPI: Structural Classification of Protein-Protein Interfaces
SCOPPI is a database of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions. Interfaces are classified according to the geometry of the domain associations and are annotated with various interaction characteristics. Screenshots of all interfaces are available. More than 4,000 distinct types of domain interfaces are collected from Protein Quaternary Structure Server and Protein Data Bank. Given a pair of interacting domains, we define face as the set of interacting residues in each single domain and the pair of interacting faces as an interface. We investigate how the geometry of interfaces relates to a network of interacting protein families, such as how many different binding orientations are possible between two families or whether a family uses distinct surfaces or the same surface when the family has diverse interaction partners from various families. We show there are, on average, 1.2-1.9 different types of interfaces between interacting domains and a significant number of family pairs associate in multiple orientations. In general, a family tends to use distinct faces for each partner when the family has diverse interaction partners. Each face is highly specific to its interaction partner and the binding orientation. The relative positions of interface residues are generally well conserved within the same type of interface even between remote homologs.
SDR: Specificity-Determining Residues in Protein Families
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of predicted specificity-determining residues in protein families. Predicted positions may have been used during evolution to change the function of proteins within a protein family. These positions are excellent targets for mutational studies and should lead to a better understading of protein function. SDR uses the PFAM database of protein domains for sequence alignments and domain definitions as well as the GPCR database for G-protein coupled receptors.
A database for the functional and evolutionary analysis of sex-biased genes. Sebida integrates data from multiple microarray studies comparing male versus female gene expression in D. melanogaster, D. simulans, and A. gambiae. In addition to the ratio of male to female (or testes to ovaries) expression for each gene, Sebida provides information useful for evolutionary studies, including measures of recombination, codon bias, and interspecific divergence.
A database of eukaryotic selenoprotein genes, proteins, SECIS elements and related molecules. Selenoproteins are routinely mispredicted by automatic annotation systems and, therefore, misannotated in most genomic databases. We aim to provide correct annotations for the growing number of known selenoprotein genes. Current efforts are directed towards the construction of an initial set of genomic annotations in selected sequenced organisms using ad hoc computational tools and manually curated predictions. Computational approaches include ab initio and comparative gene prediction together with RNA secondary structure predictions.
ResearchCrossroads Funding Opportunities Database
A database of funding opportunities from both public and private funding sources. Search by keyword and the funding opportunities matching your criteria are displayed. Click on the funding title to view the complete record. You may also add opportunities to the ResearchCrossroads database if you have registered.
A database for the accumulation of experimental data on selected affinity-enriched sequences from different combinatorial libraries. During the last ten years, the novel technologies have been designed for identification of high affinity DNA and RNA sequences (ligands) to a wide variety of different targets, including nucleic acid binding proteins, peptides, and small organic molecules. Among these technologies are the following: SELEX (Systematic Evolution of Ligands by Exponential enrichment), SAAB (Selected And Amplified Binding site imprint assay), REPSA (Restriction Endonuclease Protection Selection and Amplification), CASTing (Cyclical Amplification and Selection of Targets) and other binding site selection procedures. In general, genetic analysis in vitro of the structural and functional properties of many nucleic acids was enhanced by the availability of methods for the amplification of nucleic acid sequences. Given current advance in sequencing whole genomes, combinatorial methods will be important in the next generation of studies, thus making the bridge between raw sequence data and actual biological processes. At present, enormous starting libraries are used in different SELEX processes and contain up to 1014?1015 sequences. Naturally, this information needs to be collected into public databases available via the Internet. The site sequences listed within the SELEX_DB may be used as independent control data in developing both novel methods for functional site recognition within gene sequences and recognition under concrete experimental conditions documented in the database. Additionally, information on functional site sequences and experimental conditions for their determination is useful for planning novel experiments applying SELEX technology.
SENTRA: a database of prokaryotic signal transduction proteins
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A database of signal transduction proteins encoded in completely sequenced prokaryotic genomes. Sentra consists of two principal components, a manually curated list of signal transduction proteins in 202 completely sequenced prokaryotic genomes and an automatically generated listing of predicted signaling proteins in 235 sequenced genomes that are awaiting manual curation. In addition to two-component histidine kinases and response regulators, the database now lists manually curated Ser/Thr/Tyr protein kinases and protein phosphatases, as well as adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases, as defined in several recent reviews. All entries in Sentra are extensively annotated with relevant information from public databases (e.g. UniProt, KEGG, PDB and NCBI). Sentra's infrastructure was redesigned to support interactive cross-genome comparisons of signal transduction capabilities of prokaryotic organisms from a taxonomic and phenotypic perspective and in the framework of signal transduction pathways from KEGG. Sentra leverages the PUMA2 system to support interactive analysis and annotation of signal transduction proteins by the users.
The Shanghai Rapeseed Database contains genomic information about the Rapeseed plant. Resources available through the website include BLAST search functions, cDNA library construction, microarray hybridization, SAGE, and ethylmethanesulfonate (EMS) induced mutant population data. Multiple high-throughput genomic approaches were performed to study the gene expression profiles during Brassica napus (huyou-15) seed development and fatty acid (FA) metabolism, as well as the relevant regulation. Serial Analysis of Gene Expression (SAGE) using seed materials obtained a total of 68,716 tags, of which 23,895 were unique and 503 tags were functionally identified, and further revealed the transcriptome of approximately 35,000 transcripts in B. napus developing seeds. Further, ~22,000 independent ESTs were obtained by large-scale sequencing using immature embryos at different stages. 8462 uni-ESTs and 3526 full-length cDNAs were identified respectively, resulting in the systemic identification of B. napus FA biosynthesis-related genes. Gene expression profiles were further studied employing cDNA chip hybridization to reveal the global regulatory network of FA metabolism in developing seeds.
Stress Induced (DNA) Duplex Destabilization
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of stress induced DNA destabilizations. It currently incorporates prokaryotic and eukaryotic genomes only, with archea and viruses to follow. This research group has developed statistical mechanical methods to computationally analyze the occurrence of structural transitions in stressed DNA molecules. When these methods are used to analyze genomic DNA sequences, they make highly precise predictions of the locations at which the DNA duplex is destabilized, and the amount of destabilization experienced. Several experiments have been performed to date to assess stress-induced DNA destabilization in specific DNA sequences, both in vitro and in vivo. In all cases our methods correctly predicted the locations and extents of separated regions at single base pair resolution as functions of the level of imposed superhelical stress. This quantitatively close agreement enables our computational methods to be used with confidence to analyze other sequences, on which experiments have not been performed. We have analyzed a wide variety of genomic DNA sequences in this way, including the complete genomes of Escherichia coli and Saccharomyces cerevisciae. This work has shown that the susceptibility to stress-induced destabilization is closely associated with several classes of DNA regulatory regions, including promoters and terminators, replication origins, nuclear matrix attachment sites, DNase hypersensitive sites, and hotspots for translocation, retrotransposon integration or recombination. Working in collaboration with experimental groups, this approach is providing unprecedented new insights into the precise mechanisms governing numerous biologically important events, including eukaryotic nuclear scaffold attachment to c-myc oncogene regulation, activation of transcription from IHF-regulated genes in E. coli, transcription termination in yeast, and activation of replication of a mutant, encephalopathy-producing JC virus.
SIEGE- Smoking Induced Epithelial Gene Expression
Smoking Induced Epithelial Gene Expression
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A database that provides access to data from several gene expression profile analysis results of smokers and non-smokers. In the experiment, researchers first obtained brushings from intra-pulmonary airways (the right upper lobe carina) and scrapings from the buccal mucosa, from normal smoking and non-smoking volunteers. RNA was isolated from these samples and gene expression profiles from intra-pulmonary airway epithelial cells were analyzed using Affymetrix U133A human gene expression arrays. All microarray data from these experimentshave been stored, preprocessed and analyzed in a relational MySQL database that is accessible through this website.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 20,2019.A database of integrated genome resources for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biological information such as microarray expression data, ESTs and corresponding references. SilkDB will be useful for the silkworm research community as well as comparative genomics. Recently, an international collaboration has been launched to assemble a complete silkworm genome sequence, which is based on the 6� and 3� draft genome sequences created by Chinese group and Japanese group in 2004 (Mita et al., 2004; Xia et al., 2004), respectively. The genome assembly quality has been greatly improved. Base on a high density SNP genetic map, over 80% of genome sequence could be mapped on 28 chromosomes of the silkworm. The first version of SilkDB was released in 2004. Since that time, the silkworm has become a focus in insect research community and the study of silkworm has been greatly accelerated. Now, we are happy to announce the release of a new version of SilkDB, which updated all of the data, added new information of genome sequence and genes, and provides new tools to facilitate use of the genome database.
It provides a database based on a pre-computed similarity matrix covering the similarity space formed by >4 million amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and is updated incrementally. For sequence similarity searches and pairwise alignments, we implemented a grid-enabled software system, which is based on FASTA heuristics and the Smith Waterman algorithm. SimpleSIMAP and AdvancedSIMAP retrieve homologs for given protein sequences that need to be contained in the SIMAP database. While SimpleSIMAP provides only selected parameters and preconfigured search spaces, the AdvancedSIMAP allows the user to specify search space, filtering and sorting parameters in a flexible manner. Both types of queries result in lists of homologs that are linked in turn to their homologs. So the web interfaces allow users to explore quickly and interactively the protein world by homology. Sponsors: SIMAP is supported by the Department of Genome Oriented Bioinformatics of the Technische Universitt Mnchen and the Institute for Bioinformatics of the GSF-National Research Center for Environment and Health.
On this site, you can search siRNA records, design siRNAs, or submit siRNA records resulting from your own study (requires register/login). Small interfering RNAs (siRNAs) are a class of 20-25 nucleotide-long double-stranded RNAs, and they are widely used as gene knock-down tool in molecular genetics, functional genomics, and drug discovery studies. However, despite numerous efforts, the design of potent siRNA remains inadequate. Design rules resulting from different studies often disagree with each other, and are often unsatisfactory. Typically, only about 75-80% siRNAs designed based on current rules result in >50% knock-down efficacy. Observing these difficulties, we have established this database of experimentally validated mammalian siRNAs with efficacy ratings. As of August 18, 2008, 17,192 records of experimentally validated siRNAs, targeting 5,086 genes, originated from 6,122 independent studies are hosted in siRecords.
This is a site with links to several siRNA services, including siRNA base sequence searches, specificity searches, known siRNA molecule searches, and target sequences. One of the sites, called siSVM, allows users to predict efficacy of siRNAs given their base sequence using features derived from the siRNA sequence. siSVM is designed to allow common methods of siRNA design to be included in the search. This includes motif rules,energy conditions and specificity searching. The second site it links to, siRNA specificity prediction, allows users to perform a specificity search for siRNAs to avoid off-target effects. SpecificityServer is designed to help you identify potential non-specific matches to your siRNA. It incorporates the latest information about non-specific matches (sequence-specific only). The third site it links to, siRNAdb, is a database of known siRNA molecules. It provides a list of sirnaID, target, geneID, geneAcc, TargetStart, and targetEnd.Category: RNA sequence databases
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A collection of manually curated protein structural alignments and their interrelationships. Each multiple alignment within the SISYPHUS database consists of structurally similar regions common to a group of proteins. These regions range from oligomeric biological units, or individual domains to fragments of different size representing either internal structural repeats or motifs common to structurally distinct proteins. The SISYPHUS multiple alignments are displayed with SPICE, a browser that provides an integrated view of protein sequences, structures and their annotations.
Data analysis service to predict the functional consequences of known and unknown variants.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of known ligand binding sites within the PDB which is navigable by PDB identifier or ligand 3 letter code e.g. NAD. Each binding site has a frequently updated register of structurally similar binding sites sharing atomic similarity detected by geometric hashing. Multiple alignments, structural superpositions and links to other structural databases are also available enabling further analysis. The rapid expansion of structural information for protein-ligand binding sites is potentially an important source of information in structure-based drug design and in understanding ligand cross reactivity and toxicity. We have developed a large database of ligand binding sites extracted automatically from the Protein Data Bank. This has been combined with a method for calculating binding site similarity based on geometric hashing to create a relational database for the retrieval of site similarity and binding site superposition. It contains an all-against-all comparison of binding sites and holds known protein-ligand binding sites, which are made accessible to data mining. Here we demonstrate its utility in two structure-based applications: in determining site similarity and in aiding the derivation of a receptor-based pharmacophore model.
The SKY/M-FISH and CGH databases provide a public platform for investigators to share and compare their molecular cytogenetic data. The database is open to everyone and all users can view an individual investigator's public data or compare public cases from different investigators. Those wishing to contribute their own data must register and can choose to keep their data private for a period not to exceed two years. Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH) and Comparative Genomic Hybridization (CGH) are complementary fluorescent molecular cytogenetic techniques. SKY/M-FISH permits the simultaneous visualization of each human or mouse chromosome in a different color, facilitating the identification of chromosomal aberrations. CGH utilizes the hybridization of differentially labeled tumor and reference DNA to generate a map of DNA copy number changes in tumor genomes.
A database that integrates all available data associated with the planarian genome, including predicted and annotated genes, ESTs, protein homologies, gene expression patterns and RNAi phenotypes. It is GMOD compliant. The planarian Schmidtea mediterranea is rapidly emerging as a key model organism for the study of regeneration, tissue homeostasis and stem cell biology. Thus, SmedGD features a genome browser, BLAST capability, and other search options in order to facilitate the advancement of scientific knowledge of this organism.<
GenoTan - Genotyping of microsatellite loci
A free software tool to identify length variation of microsatellites from short sequence reads.
A sequence analysis tool providing a simple but detailed analysis of human genes and their variations. For each gene, a gene-gene relationship network can be generated based on protein-protein interaction data, metabolic pathway connections and extended through phylogenetic relations. Snap provides tools for designing sequence primers and evaluating RNA splicing effects of single SNPs - known from the databases or defined by you. Primers can be designed for the amplification or sequencing of cDNA, genomic DNA, introns only or exons only., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An object-oriented database of domain-domain interactions observed in structural data. SNAPPI-DB is a useful resource for any analysis of structures but has been opitmised for analysis on domain-domain interactions and domain-ligand interactions. The database has already been employed for 3 studies on the properties of domain-domain interactions and is currently being employed to train a protein-protein interaction predictor and a functional residue predictor. SNAPPI-DB has several features which are not available in other databases, including links to the MSD, speed, being object oriented, storage of multiple domain definitions, and storage of Protein Quaternary Structures (PQS).
A curated database for small nucleolar RNAs and small cajal body-specific RNAs. It presents sno/scaRNA-associated genetic and functional data and provides access to several other database sources via web-accessible search interfaces. Consisting of 1979 sno/scaRNA records obtained from 85 organisms, sno/scaRNAbase is a combination of systematic literature curation and annotation effort. small nucleolar RNA, small cajal body-specific RNA
snoRNABase- a comprehensive database of human H/ACA and C/D box snoRNAs.
This is a database of human C/D box and H/ACA modification guide RNAs. Information on a particular snoRNA can be accessed by three ways: 1- On the Search page, just type the name of the snoRNA (for example ACA17) in the Id window. 2- The Find guide RNA contains the sequences of the human ribosomal rRNAs 28S, 18S and 5.8S, and of the snRNAs U1, U2, U4, U5 and U6, with the positions of modified (2''O-ribose methylated or pseudo-uridinylated) nucleotides, and the identity of the corresponding modification guide RNAs. You can click on the name of the relevant snoRNA. 3- By utilizing the link to the UCSC Human Genome Browser.
SNP at Ethnos is a catalog of human SNPs and genes that contain human ethnic variation. The database contains the following results for detecting natural selection and population difference: * Neareast Shrunken Centroid Method Score for detecting ethnic difference * Fst * Hudson, Kreitman and Aguade (HKA) test (1987) * Tajima' '''s D test (1989) * Fu and Li D test (1993) It also contains copious links to dbSNP, Entrez Gene, GeneCards, OMIM, HGMD, International HapMap SNP at domain, and Haplotter (EHH). You can search by entering a gene symbol or an rs number in the text box at Data Search page. Search results provide above selection analysis data, rs lists corresponding a searched gene, and a genome viewer which contains functional annotation. The data underlying these analyses are from the Phase I HapMap Project.
A database for human SNPs (single nucleotide polymorphisms) that result in PTCs (premature termination codons) and trigger nonsense-mediated mRNA decay (NMD). The SNP2NMD interfaces provide extensive genetic information on and graphical views of the queried SNP, gene, and disease terms.
Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology.
It provides a central resource for sequence verification of SNPs. The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer. The site allows users to search for SNPs using SNP identifier, gene symbol, gene alias, chromosome location, or gene ontology pathway.
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. It is a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT.
A database containing compound microsatellite-SNP markers in human, dog, mouse, rat and chicken. SNPSTRs are a relatively new type of compound genetic marker which combines a STR marker with one or more tightly linked SNPs. This combination of co-inherited markers evolving at different rates may offer the possibility of gaining better resolved insights into population genetic processes compared to when these different marker types are used separately. SNPSTRs were first described by Mountain et al (2002) who developed experimental protocols for autosomal SNPSTRs which contain a SNP and a microsatellite within 500 base pairs apart. microsatellite-SNP, dog microsatellite-SNP, mouse microsatellite-SNP, rat microsatellite-SNP, chicken microsatellite-SNP
A web based graphical tool for exploring gene structure of the human genome, including alternative splicing. It is based on a mapping of the EST consensus sequences (contigs) from GeneNest to the complete human genome. SpliceNest is integrated with GeneNest and the SYSTERS protein sequence cluster set in one framework, permitting an overall exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA. Users can search for alignments by browsing, utilizing the graphical chromosome display feature, or performing a cluster, keyword or BLAST search.
Search Tool for Interactions of Chemicals
Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database.
StrainInfo.net connects users with information resources on different strains and taxa of microorganisms. The StrainInfo.net bioportal was established to stimulate movement towards the use of multi-perspective integrated information in a broadened biological and clinical context. It brings together the biological material kept at multiple biological resource centers into a single portal interface, with direct pointers to the relevant information at the collections'' websites, and provides both historical traces and geographic distribution of the strains they keep in culture. In addition, this information is automatically linked to related sequences in the public domain and refers to all known scientific publications that deal with the organism. To support taxonomic depth of the information provided by the StrainInfo.net bioportal, all taxonomic names appearing in the bioportal are fully integrated with and linked out to key taxonomic information sources. Predefined workflows allow further integration of additional information sources into the bioportal, resulting in direct access to all organisms involved in completed or ongoing whole-genome sequencing projects. As the bioportal further unfolds itself as a helpful add-on to the microbiologists'' toolbox, we hope to gather around it a growing community of users that might become active contributors to both its content and implementation.
highssr - Microsatellites prediction and analysis with next generation sequencing data
Software that predicts microsatellites with Tandem Repeats Finder (TRF).
Subtilist is a database dedicated to the analysis of the genome of Bacillus subtilis. It provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments. It also allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). The purpose of the website is to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. The data contained in SubtiList originated mainly from the worldwide collaborative B. subtilis genome sequencing project, supplemented with information from the B. subtilis entries present in the EMBL/GenBank/DDBJ databanks, as well as observations either published in international journals or communicated directly to us by individual researchers.
Software for identifying haplogroups from low coverage sequence data.
Superfamily - HMM library and genome assignments server
SUPERFAMILY is a database of structural and functional protein annotations for all completely sequenced organisms. The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 1,700 completely sequenced genomes against the hidden Markov models.
SURFACE: Surface Residues and Functions Annotated, Compared and Evaluated
A database containing the results of a large-scale protein annotation and local structural comparison project. A non-redundant set of protein chains is used to build a database of protein surface patches, defined as putative surface functional sites. Each patch is annotated with sequence and structure-derived information about function or interaction abilities. Users can search the annotations and the results of the surface patches comparisons stored in the DB based on PDB code, PROSITE pattern, or ligand. A new procedure for structure comparison is used to exert an all-versus-all patches comparison. Selection of the results obtained with stringent parameters offers a similarity score that can be used to associate different patches and may allow reliable annotation by similarity. protein, protein structure, structural comparison, protein ligand, protein surface, protein morphology
Systematic Platform for Identifying Mutated Proteins (SysPIMP)
Systematic Platform for Identifying Mutated Proteins
A database ofhuman disease-related mutated proteins identified by mass-spectrometry (MS). For achieving this goal, we collected human mutated sequences known to be related to diseases till now. After surveying mutated sequence sources: PMD, OMIM, SwissProt polymorphism, HGMD, etc, we found that currently HGMD contains the largest human gene mutation information. However, because, for academic users, HGMD does not provide with whole data download service, we decided to systematically extract and curate mutation information from PMD, OMIM, SwissProt, MSIPI database to form SysPIMP and provide it free for academic users.
SYSTERS is a database of protein sequences grouped into homologous families and superfamilies. The SYSTERS project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. A refined two-step algorithm assigns each protein to a family and a superfamily. The sequence data underlying SYSTERS release 4 now comprise several protein sequence databases derived from completely sequenced genomes (ENSEMBL, TAIR, SGD and GeneDB), in addition to the comprehensive Swiss-Prot/TrEMBL databases. To augment the automatically derived results, information from external databases like Pfam and Gene Ontology are added to the web server. Furthermore, users can retrieve pre-processed analyses of families like multiple alignments and phylogenetic trees. New query options comprise a batch retrieval tool for functional inference about families based on automatic keyword extraction from sequence annotations. A new access point, PhyloMatrix, allows the retrieval of phylogenetic profiles of SYSTERS families across organisms with completely sequenced genomes. Gene, Human, Vertebrate, Genome, Human ORFs
Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface.
The HIV Positive Selection Mutation Database
This is a dataset of clinical HIV sequences, including a method of decoding the evolutionary pathways by which HIV evolves drug resistance. "Fitness landscape" describing how HIV proteins can evolve, is shown as a kinetic network. Drug resistance is a major problem in the treatment of AIDS, due to the very high mutation rate of human immunodeficiency virus (HIV) and subsequent rapid development of resistance to new drugs. Identification of mutations associated with drug resistance is critical for both individualized treatment selection and new drug design. We have performed an automated mutation analysis of HIV Type 1 (HIV-1) protease and reverse transcriptase (RT) from approximately 50,000 AIDS patient plasma samples sequenced by Specialty Laboratories Inc. from 1999 to mid-2002. This dataset provides a nearly complete mutagenesis of HIV protease and enables the calculation of statistically significant Ka/Ks values for each individual amino acid mutation in protease and RT. Positive selection (i.e., Ka/Ks>1 indicating increased reproductive fitness) detected 19 of 23 known drug-resistant mutation positions in protease and 20 of 34 such positions in RT. We also discovered 163 new amino acid mutations in HIV protease and RT that are strong candidates for drug resistance or fitness. Our results match available independent data on protease mutations associated with specific drug treatments and mutations with positive reproductive fitness, with high statistical significance (the P values for the observed matches to occur by random chance are 1e-5.2 and 1e-16.6, respectively). Our data indicate that positive selection mapping is an analysis that can yield powerful insights from high-throughput sequencing of rapidly mutating pathogens. This database has been made possible by the generous contribution of HIV sequence chromatograms by Specialty Laboratories, Inc.
SYSTOMONAS: SYSTems biology of pseudOMONAS
SYSTOMONAS is a comprehensive database of molecular networks in Pseudomonas focusing on Pseudomonas aeruginosa. We use a systems biology approach to get a deeper understanding of all cellular processes of P. aeruginosa during infection. Our long term goal is the development of a dynamic model simulating P. aeruginosa during infection. The basis for such an approach is SYSTOMONAS, a comprehensive database that includes systems data from all levels of analysis as microarray and proteomics data, metabolite measurements, sequence data, gene-regulatory networks and enzyme data. Therefore, we started with metabolomics analysis and extended to transcriptomics, genomics, and proteomics aspects. Along with the wet lab results additional data is stored, which is extracted from literature or derived from other external databases. Major sources of SYSTOMONAS are KEGG, PRODORIC, BRENDA (see section ''Sources''), which are partly stored via the data warehouse system and partly dynamically connected via SOAP, a platform-independent data transfer protocol. Comparing a Pseudomonas protein of interest with other well-characterized proteins may deliver useful insights into the evolution, distribution, and species specific function. Therefore, we searched for all deduced proteins of the SYSTOMONAS database for orthologous proteins in other Pseudomonas species to obtain orthologous protein clusters. Pseudomonas aeruginosa, systems biology, transcriptomics, genomics, proteomics
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data.
TargetDB: Structural Genomics Target Search
TargetDB, a target registration database, provides information on the experimental progress and status of targets selected for structure determination. Search sequences from the PSI Structural Genomics Centers and other Structural Genomics projects.For more information about how these proteins were cloned, expressed, purified, or other experimental protocols please go to the Protein expression, purification, and crystallization DataBase.
TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. Currently, 114,554 tandem splice sites of eight species are contained in the database, 5,209 of which have EST/mRNA evidence for alternative splicing. Users can search by Transcript Accession Number and Gene Symbol, SQL Query, and Tandem Donor/Tandem Acceptor pairs.
The taxonomically broad EST database TBestDB serves as a repository for EST data from a wide range of eukaryotes, many of which have previously not been thoroughly investigated. Users can search by annotated name, EC#, and view datasets that contain classification hierarchies for pathways, for reactions (the enzyme nomenclature system), for compounds, and for genes. Most of the data contained in TBestDB has been generated by the labs of the Protist EST Program located in six universities across Canada.
This database functions both as a website where researchers can look for information on their targets of interest; and as a tool for prioritization of targets in whole genomes. Using the database as a tool, researchers can quickly prioritize a genome of interest by performing any number of individual queries on a species of interest, then assigning numerical weights to each query (in the history page) to finally obtain a ranked list of genes by combining the weighted queries. This site is part of a WHO/TDR project seeking to exploit the availability of diverse datasets to facilitate the identification and prioritization of drug targets in pathogens causing neglected diseases.
Topology Data Bank of Transmembrane Proteins
Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data.
TPMD - Taiwan polymorphic microsatellite marker database
Taiwan polymorphic microsatellite marker database
A marker database designed to provide experimental details and useful marker information allelotyped in Taiwanese populations accompanied by resources and technical supports. Our aims to construct TPMD are to share useful genotyping information including data of genotyped microsatellite markers, genotyping resources and laboratory supports for promoting genotyping and gene cloning of prevalent diseases. TPMD contains microsatellite markers with di-, tri-, and tetranucleotide repeats deposited by four qualified genotyping laboratories and presented with user-friendly web interfaces for researchers. The newly developed TPMD graphic displays with integration of markers into genetic, cytogenetic and physical maps not only show the comparison of marker&rsquo;s heterozygosities in Taiwanese, Japanese, and Caucasian but also facilitate the selection and download of commonly used microsatellite markers for refined mapping and positional candidate cloning of disease genes.
A database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signalling pathways.TRANSCompel was created by a commercial entity, but is usable by the academic community on a limited bases for free. Composite regulatory elements are found in many promoters and enhancers of eukaryotic genes. They consist of two binding sites of two different transcription factors, which through this combination form a module with new regulatory properties. Composite elements frequently serve as integration sites of two (or more) signaling pathways.TRANSCompel is equipped with our proprietary CATCH program, an analysis software for searching potential composite elements in DNA sequences. A sequence under study is scanned by this program using all composite elements collected in TRANSCompel as individual searching patterns. All found matches are directly linked to the TRANSCompel entries containing the corresponding composite elements.
TrSDB - A Proteome Database of Transcription Factors
A Biological Proteome KnowledgeBase linking IPI and SPTR-NR based Proteome analyses with TranScout, TransMem and ProtLoc and offering crosslinks with other relevant information from worldwide highly acknowledged biodatabases such as SWISS-PROT, NCBI Refseq, Ensembl, InterPro or Gene Ontology Annotation. TrSDB is a BioDB (Biological Relational DataBase) that through the same web interface joins several predictive analyses of protein motifs, domains, cellular localization and functional annotation around different compiled sequences, now IPI and SPTR Non-Redundant proteomes.TranScout, TransMem and ProtLoc predictions with crosslinks to InterPro, Gene Ontology Annotation, ENSEMBL, SWISS-PROT/TREMBL, REFSEQ and inter and intraspecies precomputed BLAST Analyses are provided when suitable for each proteome entry. By now, nine eukaryotic organisms proteomes (human, mouse, rat fruit fly, worm, Arabidopis, an alga and two yeasts) may be queried. Periodically compiled proteomes will be updated all at the same time to mantain temporal coherency and new analyses will be provided as well.When one organism has been selected, a funny icon in the upper-right part of the web screen may help you to remind your organism selection.Emphasis is placed upon Transcription Factor prediction supported by TranScout. Complex analyses are performed searching for Transcription Factor evidence from TranScout and InterPro matches as well as existing GO annotation. Mutual transcription factor evidence among homologues is also considered and compiled analyses files are available.
UgMicroSatdb : Database for mining microsatellites from Unigenes
This is a database of microsatellite sequences (short tandem repeats useful in gene comparison and kinship studies) present in 80 genomes. Users can search the database by microsatellite type, repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. They can also search by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. Microsatellites, also known as simple sequence repeats (SSRs) or simple tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications including genome characterization and mapping. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed UgMicroSatdb (Unigene MicroSatellite database), a web based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type simple (perfect) and compound (perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. Microsatellites can also be retrieved by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. The database also provides information about trinucleotide repeats encoding various amino acids. Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar) and their hydrophobic or hydrophilic nature. The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of any desired microsatellite.
VFDB - Virulence Factors of Bacterial Pathogens
Virulence Factors of Bacterial Pathogens
An integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma). VFDB is a platform for further study of comparative pathogenomics. Major features include tabular comparison of pathogenomic composition in terms of virulence, multiple alignments and statistic analysis of homologous virulence genes, and graphical comparison of pathogenomic organization of VFs. Category: Genomics Databases (non-vertebrate) Subcategory: Prokaryotic genome databases
A database containing predicted viral miRNA candidate hairpins. Users may query the putative miRNA hairpins of a specific viral species by the hierarchical menu or by search function using the GenBank Identifier or RefSeq accession number. In addition, users can also search for the putative target genes of a particular viral miRNA hairpins by a RNAhybrid service link. We have previously identified human intronic microRNA as well as zebrafish microRNA. The microRNA hairpin discovery pipeline was also applied to discover viral encoded microRNAs. All viral genomes were obtain from NCBI. The classification of virus is based on the taxonomy table of NCBI (Jun, 2006). Totally, the genomes of 2266 viruses were analyzed. The 3&rsquo;-UTR regions of human, mouse, rat, zebrafish, arabidopsis and rice genes are available for search.
University of New Mexico Department of Neurosciences
This interdisciplinary Neuroscience Program is one division of the Biomedical Sciences Graduate Program at the University of New Mexico. Participating faculty are affiliated with the Department of Neurosciences. Students complete a core curriculum in biomedical sciences and then an individualized program of courses and research in neuroscience. Students may choose among neuroscience research laboratories in the Neurosciences Department or at the Los Alamos National Laboratories. Neuroscience graduate students are part of an active neuroscience group that sponsors weekly seminars and journal clubs.
Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth.
GenePath is a web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks. GenePath uses abductive inference to elucidate network constraints and logic to derive consistent networks. Typically, it starts with a set of genetic experiments, uses a set of embedded rules (patterns) to infer relations between genes and outcome, and based on these relations constructs a genetic network.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2011. The VNTRDB is a database useful for searching common polymorphic tandem repeats or unique tandem repeats in selected bacteria. Additionally, a visualization tool is accompanied with this database to observe sequence differences between bacterial strains and to avoid false positive records result from misestimating copy number and locus length of tandem repeats. Variable number tandem repeats (VNTRs) are one kind of DNA markers that have been widely used in molecular typing of bacteria. For finding potentially polymorphic tandem repeats, more genome sequences of a bacterial species should be compared. Till now, however, only 357 bacterial genome sequences are fully sequenced. Many of these bacterial species merely one strain has been sequenced. Therefore, all fully sequenced bacteria of a same genus are usually compared together to find the polymorphic potency of tandem repeats. It means that the more bacteria or sequences are compared, the more polymorphic tandem repeats will be truly identified. Here, a variable number tandem repeat locus database (VNTRDB) was constructed to microbiologists to meet the requirements of epidemiological studies. All potentially polymorphic tandem repeats in this database are found by comparing homologous tandem repeat loci between different bacteria of a same genus or among different genera. Currently, we provide two kinds of tandem repeats for query in the VNTRDB, i.e., polymorphic TRs and putatively unique TRs. These two query pages contain their own setting parameters for searching common polymorphic tandem repeats or unique tandem repeats in selected bacteria. This VNTRDB is an open resource and can be freely accessed without any restriction. The data in it will be updated or added continuously when new bacterial genome sequences are fully sequenced. Category: Genomics Databases (non-vertebrate) Subcategory: Prokaryotic genome databases
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A relational database that contains all the eukaryotic protein-encoding DNA sequences in GenBank. It provides detailed and comprehensive features about both the intron containing and the intron-less genes. In addition to the information found in the GenBank records, which includes properties such as sequence, position, length and description about introns, exons and protein coding regions, Xpro provides annotations on the splice sites motifs and intron phases. Furthermore, Xpro validates intron positions using alignment information between the records sequence and EST sequences found in dbEST. The entries in the XPro are also cross-referenced to SWISS-PROT/TrEMBL and Pfam databases. Unprecedented growth data in GenBank, the primary repository of nucleotide sequences due to the ever increasing number of genome and EST sequencing projects and the poor annotation of exon/intron details required for molecular evolution studies in the primary nucleotide database have made development of Xpro database. It is a specialized database that contains details about genomic features specific to eukaryotic genes and provides various web tools for analyzing/visualizing these features., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
This database contains different yeast strains searchable by ORF and gene name, and serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The database is hyperlinked with other public databases. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. 5791 heterozygous diploid and 4706 homozygous diploid deletion strains were monitored in parallel using molecular barcodes on fermentable (YPD, YPDGE) and non-fermentable substrates (YPG, YPE, YPL). The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. Strains can be searched by ORF or Gene name to access growth measurements and data plots for each strain. Category: Genomics Databases (non-vertebrate) Subcategory: Fungal genome databases Category: Organelle databases Subcategory: Mitochondrial genes and proteins
University of Pennsylvania Medical Center Neuroscience
The Department of Neuroscience is located in the School of Medicine at the University of Pennsylvania. Founded in 1992 to recognize the growing importance of neuroscience as a scientific discipline, the Department laboratories pursue a wide variety of research interests reflecting the entire range of modern neuroscience. The Department lies at the heart of the campus-wide Mahoney Institute of Neurological Sciences, the first research organization to receive NIH funding for training in the neurosciences.
University of Sao Paulo; Sao Paulo; Brazil
Public university in the Brazilian state of São Paulo. It is the largest Brazilian public university.
A database of S. cerevisiae H/ACA and C/D box snoRNAs, useful for research on rRNA nucleotide modifications in the ribosome, especially those created by small nucleolar RNA:protein complexes (snoRNPs). The interactive service enables a user to visualize the positions of pseudouridines, 2'-O-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. The tools provide additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications. This package of tools is presented as a major enhancement of an existing but significantly upgraded yeast snoRNA database. The other key features of the enhanced database include details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms.
University of Arkansas for Medical Sciences Department of Neurobiology and Developmental Sciences
The Department of Neurobiology and Developmental Sciences is structured around three divisions originally intended as academic entities designed to facilitate and support the growth and development of faculty with common interests. Ideally, this will continue to foster the development of programmatic, interdisciplinary funding which would benefit both young and established faculty. The Divisions also provide leadership opportunities for Senior faculty, as they help the Chair with faculty development. In essence, the divisions are sites for mentoring of faculty who need training and skills in specific areas. Many faculty participate in multiple divisions, depending on their needs, interests, and expertise. The three divisions include the Division of Anatomical Education, the Division of Translational Neuroscience, and the Division of Cellular and Molecular Neuroscience.
University of California Los Angeles Department of Neurobiology
The Department of Neurobiologys doctoral program provides a strong theoretical and practical foundation in the area of cellular and systems neurobiology with the goal of developing a better understanding of nervous system function and behavior. The graduate program has three major aims to provide basic and advanced instruction in the fundamentals of neurobiology, advanced independent research training in the areas of cellular, structural and systems neurobiology, and teaching experience in undergraduate and professional (dental and medical) courses in neuroscience. The educational program consists of a core series of courses that provide fundamental training in neurobiology. Course subject matter is focused on molecular, cellular, structural, systems and regulatory neurobiology. Advanced topic seminar courses provide training in synaptic and neuronal communication, neuronal plasticity, neuroanatomy, learning and memory, neuroendocrinology, developmental neurobiology, sensory and motor systems, and integrative neurobiology. The educational program is also distinguished by the availability of seminars and journal clubs that provide students with the opportunity for discussion and presentation of contemporary neuroscience literature.
University of California San Diego Department of Neurosciences
The Department of Neurosciences is composed of 33 ladder-rank faculty members, 23 research and project scientists, and 27 faculty who hold adjunct and joint appointments. Additionally, there are 61 individuals outside the university who participate in our clinical teaching programs. We are proud that Neurosciences at UCSD ranks first out of 90 competitors in overall NIH grant funding. The Department of Neurosciences also supports adult and pediatric residency training programs in neurology utilizing clinical facilities at the UCSD Medical Centers in Hillcrest and La Jolla, VA San Diego Medical Center, and Rady Children''s Hospital of San Diego. Areas of particular interest include the diagnosis, management, and research of neurodegenerative diseases (in particular Alzheimer''s disease and Parkinson''s disease), stroke, epilepsy, neuromuscular disorders, metabolic disorders, and neuro-developmental disorders, including autism. The Department maintains close ties with its neighboring institutions, including the Salk Institute, Scripps Research Institute, and Burnham Institute. The La Jolla Mesa has the greatest concentration of neuroscientists of any single area in the United States .
University of Medicine and Dentistry of New Jersey Pharmacology
Pharmacology and Physiology are scientific fields directed toward understanding the molecular, cellular and organ systems that are essential to life itself as well as their alteration by the actions of exogenous agents. Our understanding of these systems is the essential basis for rational clinical diagnosis, treatment of disease and our knowledge of how drugs and toxic agents exert their effects in humans. The interests of the department faculty members cover a broad range of research topics and experimental approaches.
University of Pittsburgh Department of Neuroscience
The Department of Neuroscience in the School of Arts and Sciences at the University of Pittsburgh provides outstanding undergraduate and graduate education with innovative independent and collaborative research, a well-rounded curriculum, and a seminar series by the world''s most renowned leaders in the field of neuroscience. The Department has become successful and prominent based on the determination, energy, imagination, and skills of its faculty as investigators and as mentors, and on the support of the institution and the funding agencies. Consequently, morale is high and so is our optimism that we will continue to develop and maintain a world-class department.
University of Pittsburgh Center for Neuroscience
The Center for Neuroscience at the University of Pittsburgh oversees all neuroscience-related activities on the Pitt campus. CNUP is a multidisciplinary center with members whose primary appointments are in 16 different departments. Their research interests span the breadth of neuroscience, and a number of concentration areas involve diverse groups of scientists. CNUP has a sense of community highlighted by interactive and collaborative aspects in many of our research programs.
The UK Crop Plant Bioinformatics Network (UK CropNet) was established in 1996 as part of the BBSRC''s Plant and Animal Genome Analysis special initiative. Our focus is the development, management, and distribution of information relating to comparative mapping and genome research in crop plants. Find out more about our background or read our UK CropNet paper published in Nucleic Acids Research (pdf reader required).This site hosts a wide range of databases and software developed by UK CropNet, as well as hosting many other plant databases developed in the USA. You can perform a keyword text search across all of these databases or use our UK CropNet BLAST server to search against all of the sequences in these databases.
The Wisconsin Primate Research Center supports one of the largest colonies of common marmosets (Callithrix jacchus) in the United States. Through the Callicam, anyone with web access can observe one of the WPRC''s common marmoset families. The Callicam webcam allows site visitors to pan, zoom, and manipulate the camera themselves for two minutes at a time. Accompanying links to comprehensive information about the species along with sample exercises for use with the Callicam provide the opportunity to learn about this engaging primate while observing it live online.
Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. The EBI Gene Expression Atlas Blog discusses ideas, features and problems of creating a large scale meta-analytical atlas of gene expression from publicly available microarray data. Atlas REST API provides all the results available in the main web application in a pragmatic, easy to use form - simple HTTP GET queries as input and either JSON or XML formats as output. Gene Expression Atlas goals: 1. Provision of a statistically robust framework for integration of gene expression experiment results across different platforms at a meta-analytical level 2. A simple interface for identifying strong differential expression candidate genes in conditions of interest 3. Integration of ontologies for high quality annotation of gene and sample attributes 4. Construction of new gene expression summarized views, with a view to analysis of putative signaling pathway targets, discovery of correlated gene expression patterns and the identification of condition/tissue-specific patterns of gene expression.
GENIA Project: Mining literature for knowledge in molecular biology
Resources and tools from a project to automatically extract useful information from texts written by scientists to help overcome the problems caused by information overload. The primary annotated resource created is the GENIA corpus, a collection of biomedical literature which consists of multiple layers of annotation, encompassing both syntactic and semantic annotation. The project also created or coordinated the annotation of multiple other corpus resources. Additionally, a rich set of automatic tools are available for various annotation tasks, most trained on various parts of the GENIA corpus annotations. The GENIA corpus was developed to provide a reference material for the development of bio-TM systems. The corpus currently contains 1,999 Medline abstracts which were collected using the three MeSH terms, human, blood cells, and transcription factors. The corpus has been annotated with various levels of linguistic and semantic information. The GENIA corpus includes the following: * POS annotation * Treebank * Coreference Annotation * Term annotation * Event annotation * Relation annotation * Cellular localization * Disease-Gene association * Pathway corpus The GENIA Project initiated the BioNLP Shared Task series and has organized a number of tasks in three different shared task events, many using resources based on GENIA Corpus annotations. Tools include: * XConc suite: a collection of XML-based tools which are integrated to support the corpus development and annotation.
This is a blog about post genomic knowledge. The website''s goal is to make public datasets from the bioinformatics community available in RDF format via standard SPARQL endpoints.
A computational hosting resource which assissts with lab organization by splitting functions into four modules. “Order requests” is a module where users can view and track order requests. The module “Inventory” allows users to track commercial and lab-made products. “Documents” allows users to organize and share protocols and other documents. “Equipment sign-up” allows users to manage shared equipment. An active help system, video guides, and 1-on-1 demos are available for assistance when setting up.
A professional organization focused on advancing neurosurgery by providing members with the educational and career development opportunities. They have an annual meeting and offer CME opportunities. The Congress of Neurological Surgeons seeks to improve the quality of healthcare through: * The development of educational programs that convey knowledge, enhance self-directed learning and improve patient outcomes. * Advancing the science of medical education. * Promoting original inquiry and the exchange of clinical and scientific evidence. * Public advocacy for the enhancement of quality, safety and access to neurosurgical care. The Congress of Neurological Surgeons seeks to advance the profession of neurosurgery through: * Refining neurosurgical practice based on evidence. * Promoting volunteerism and leadership development within our specialty. * Development of programs to promote safety, quality and efficiency in practice for domestic and international members.
George Washington University Medical Center Pharmacogenomics Program
George Washington University is a pioneer in the field of pharmacogenomics offering the only Bachelor''s degree program in the country. Students are admitted into this full-time program in their Junior year. The program strives to educate a new generation of health science graduates who are acutely aware of the interface between human genetic variability and drug action. Our mission is to offer a world-class education to students and equip future pharmacists, scientists, physicians, policy makers and health care professionals with concrete knowledge and unparalleled experience in pharmacogenomics. Our graduates play integral roles in the resolution of the scientific, policy and ethical issues surrounding personalized medicine. The program will uniquely prepare individuals for a variety of positions in the biopharmaceutical industry and allied health professions as well as continued advanced education in health policy, medicine, pharmacological/genomic research and pharmacy.
Spatio- Spectro- Temporal Receptive Field
STRFPak is a Matlab toolbox for estimating the linear and nonlinear stimulus-response mapping function of sensory systems. This mapping function is commonly called the spatio- or spectro-temporal receptive field (STRF). A quantitative estimate of the STRF can be used in subsequent computational modeling studies or to predict future responses of the system. STRFPak implements several general STRF estimation techniques and can be used with any stimuli (including natural scenes and sounds). The theoretical basis for STRF estimation has been known for some time, but estimation software has not been widely available. This project aims to develop appropriate software and make it available to the wider community of sensory neuroscientists. Although STRFPak is based on established methods it incorporates two important innovations. First, STRFPak can be used to characterize a sensory system from its response to arbitrary stimuli including natural signals (e.g., vocalizations, natural scenes). Second, STRFPak incorporates several methods for estimating nonlinear STRFs. STRFPak also includes tutorial examples and documentation.
BrainWeb provides information and links to validated sites about brain diseases and disorders. These include outside resources reviewed by scientific advisers, as well as articles in Dana publications. Sites listed in BrainWeb detail common brain diseases and disorders, and include general neuroscience and health resources. They offer descriptions of conditions, frequently asked questions, organization contacts, and sources for more information. BrainWeb and its links are suitable for lay readers, including students and educators, as well as people with brain disorders, their families, and caregivers.
The CMTA is a 501(C)(3)nonprofit organization founded in 1983 whose goals are patient support, public education, promotion of research and ultimately the treatment and cure of CMT. Charcot-Marie-Tooth, or CMT, is the most commonly inherited neurological disorder and is found world-wide in all races and ethnic groups. Discovered in 1886 by three physicians, Jean-Martin-Charcot, Pierre Marie, and Howard Henry Tooth, CMT affects an estimated 2.6 million people. CMT patients slowly lose normal use of their feet/legs and hands/arms as nerves to the extremities degenerate and the muscles in the extremities become weakened because of the loss of stimulation by the affected nerves. Many patients also have some loss of sensory nerve function. CMT is one of the 40 diseases covered by the MDA, but unlike muscular dystrophy, in which the defect is in the muscles, CMT is a disorder in which the defect is in the nerves that control the muscles. CMT usually isnt life-threatening and almost never affects brain function. It is not contagious, but it is hereditary and can be passed down from one generation to the next. CMT... * ...is also known as peroneal muscular atrophy (PMA) and hereditary motor sensory neuropathy (HMSN). * ...is slowly progressive, causing deterioration of peripheral nerves which control sensory information and muscle function of the foot/lower leg and hand/forearm. * ...causes degeneration of peroneal muscles (located on the front of the leg below the knees). * ...causes foot-drop walking gait, foot bone abnormalities, high arches and hammertoes, problems with balance, problems with hand function, occasional lower leg and forearm muscle cramping, loss of some normal reflexes, scoliosis (curvature of the spine) and sometimes, breathing difficulties. * ...does not affect life expectancy, but can, in rare instances, cause severe disability. * ...has no cure, although physical therapy, occupational therapy and moderate physical activity are beneficial. * ...is sometimes surgically treated. * ...is usually inherited in an autosomal dominant pattern, which means if one parent has CMT there is a 50/50 chance of each child inheriting the disorder. * ...may become worse if certain neurotoxic drugs are taken. * ...can vary greatly in severity, even within the same family. * ...can now be diagnosed by a blood test (CMT types: 1A, 1B, 1C, 1D, 1E, 1F, 1X, 2A, 2B, 2E, 2F, 2I, 2J, 2K, 4A, 4C, 4E, 4F, 4J, HNPP, CHN, and DSN).
University of Saskatchewan; Saskatchewan; Canada
An integrated exploration of biomedical literature and data. An anatomy viewer can be accessed and searches of PubMed literature are visualized as to the anatomical regions that they effect. PubAnatomy takes advantage of the 25-micron voxel level mouse brain structure annotation generated by the Allen Brain Institute and integrates Allen Brain Atlas gene expression data, relationships between brain regions and diseases for more efficient exploration of Medline database and gene expression data.
EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation.<BR
Software application to create gene maps using either radiation hybrid data or linkage data (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented October 4, 2017. A sub-project of the Cell Centered Database (http://ccdb.ucsd.edu) providing a public repository for animal imaging data sets from MRI and related techniques. The public AIDB website provides the ability for browsing, visualizing and downloading the animal subjected MRI data. The AIDB is a pilot project to serve the current need for public imaging repositories for animal imaging data. The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy. The AIDB data model is modified from the basic model of the CCDB where microscopic images are combined to make 2D, 3D and 4D reconstructions. The CCDB has made available over 40 segmented datasets from high resolution magnetic resonance imaging of inbred mouse strains through the prototype AIDB. These data were acquired as part of the Mouse BIRN project by Drs. G. Allan Johnson and Robert Williams. More information about these data can be found in Badea et al. (2009) (Genetic dissection of the mouse CNS using magnetic resonance microscopy - Pubmed: 19542887)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19,2022. The BAMS Thesaurus is a part of the larger BAMS The Foundational Model of Connectivity (FMC). The principle of constructing the resource are: 1. Systematic attempts to produce internally consistent classifications and taxonomies require theoretical frameworks for deciding between alternatives. 2. Alternate classification and taxonomy schemes are always possible and must be accommodated. 3. The FMC is based on evidence, not authority. All components are justified by reference to the best observational or experimental evidence from the literature, combined with reference to priority when possible, not by undocumented statements from textbooks, the Web, or elsewhere. 4. The FMC is based on evolving evidence and concepts, revisions are based on enforced rules, and versioning is systematic and historical. The first version of FMC and the foundation of this online version was published in Swanson & Bota (2010). Please cite this reference whenever any part of the FMC is used in any way. This online version of FMC has the following main parts: 1. Thesaurus, which includes an alphabetical list of all concepts and terms used in FMC to date. The preferred terms are in bold. Clicking on each term of the Thesaurus will retrieve its definition, reference, list of synonyms, and a comment form that can be used by registered users. 2. References, which includes an alphabetical list of the literature used to construct FMC. Listed references are associated with the definitions included in the Thesaurus, and PubMed links. 3. Search form that can be used to search for terms defined in FMC, included in their definitions, their abbreviations, and references (search by authors). We strongly recommend to read FMC rules and notations before starting to use the online version.
Biological Expression Language Framework
A markup language and a set of technologies for capturing, storing and operationalizing structured biological knowledge. It also makes the knowledge available to other applications, such as the GTP, as a navigable network of biological facts. The BEL Framework assembles biological facts recorded using BEL syntax. BEL is a use-neutral format for unambiguously capturing biological entities and their inter-relationships and associating them with external vocabularies and ontologies. To facilitate context-based analysis, BEL syntax captures causal (e.g., AKT1 phosphorylates SKP2 at serine 72) and correlative relationships (e.g., increased LRG1 levels in serum are correlated with ovarian cancer) along with the experimental context in which the relationships were observed (e.g., AKT1 phosphorylates SKP2 at serine 72 in HeLa cells) and citations in which the peer reviewed knowledge has been reported (Pubmed ID 19270695 illustrates AKT1 phosphorylation of SKP2 and Pubmed ID 20831812 discusses the correlation between LRG1 and ovarian cancer). The BEL Framework provides an environment for managing and operationalizing biological facts stored in the BEL format (BEL document) and consists of the following components: * A user-friendly, web-based, knowledge-capture and knowledge-management application * A compiler that can assemble composite knowledge networks from multiple sources containing BEL statements from the BEL document store * A portable storage format for compiled BEL statements * Application Programming Interfaces (APIs) to allow applications such as the GTP to access and use the knowledge The BEL Framework is unique in that it is designed to deal with the fundamental contradictions and ambiguities associated with assimilating scientific findings from disparate biological experiments and quality issues associated with manual and algorithm-driven collation methods. Following eight years of development and proprietary use, BEL has proven to be an intuitive and effective language for scientists, supporting the creation of a large knowledgebase used in the interpretation of ''omics data sets via causal relationship-based analytics. BEL and supporting tools are now being made publicly available to the research community through the introduction of the BEL Web Portal. The BEL Web Portal provides public access to BEL language specifications, documentation, knowledge representation examples, and BEL software tools.
Center for Bio-Image Informatics: bioView3D
bioView3D is an open source and cross-platform application intended for biologists to visualize 3D stack (laser scanning confocal, etc.) imagery. It runs on Windows, MacOS X and Linux. Features include: - Cross-platform with binaries for Windows, Mac, Linux - Reads many bio image and video formats - Reads meta-data from BioRad PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III - Has two modes of rendering: textures and voxels - On-the-fly 3D visualization (mapping/enhancement) of multi-channel data - Export of fly-over video to several popular formats: QuickTime, WMV, AVI, Flash, MPEG1/2/4 - Visualization of graphical annotations: XML GObjects Sponsors: This work is supported in part by an NSF infrastructure award No. EIA-0080134 and IIS-0808772.
The objectives of Open Science Summit are to create an annual flagship event and news hub to build and maintain the identity of the international Open Science Movement as well as organize the various sub-communities into an effective, global, socio-technological force for rapid change in science/innovation policy. The Open Science Summit is the first and only event examining the full spectrum of the most crucial policy questions affecting the future of science. We consider the disruptive changes required to improve the functioning of 21st science, including institutional changes, new infrastructure for data driven science, and new practices. Scientists, Hackers, Students, Patients, and Activists, Entrepreneurs, Funders, Citizens should attend. Anyone who cares passionately about unleashing the full potential of Open Science to solve the big problems confronting humanity. Topics include: Synthetic Biology, Open Data, Open Access, Microfinance for Science, Citizen science, DIY Biology, Alternative Funding for Research, Open Source Drug Discovery, The Future of Patents, Accelerating Innovation, Open Genomics/Medicine, and More!
Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results.
www.thehumanbrain.info is a unique repository that provides the most detailed and accurate delineations of the brain structures available. It offers multiple, multifarious tools for educational training and scientific use. Free content of the website: Series of images from several heads depicting head and brain anatomy in detail Brain structures are presented in the standard stereotaxic space Consistent color coding uses the same color fr individual structures that can be followed from section to section but also identifying same structures in horizontal, coronal and sagittal planes through the complete head and isolated brain Multiple languages support Innovative navigations allowing effortless switch between the names and descriptions of anatomical structures Terminology organized into a hierarchy defined upon a partitive relationship Structure description Supplementary high resolution images (X-ray, cyto- and myeloarchitecture) Advanced search facilities for structures and abbreviations
A database, and associated atlas, that characterizes gene expression across genetic backgrounds and sex, expanding beyond the adult male C57BL/6J reference brain comprising the Allen Mouse Brain Atlas to include seven strains of male mice and female C57BL/6J mice. Gene expression was detected using colorimetric RNA in situ hybridization (ISH) that provides cellular level anatomic resolution. ISH data are searchable and organized by gene, strain, or sex.
BIRD''s mission is to aid the progress of bioinformatics and promote creation of new biology, which has computational, deductive, predictive, and theoretical features. (most of this site is in Japanese) To carry out its responsibilities, BIRD: * Promotes appropriate development of bioinformatics research and development, such as what kinds of databases and analysis software should be developed and what kind of computer facilities are needed for that development. * Maintains the computer environment and network and functions as a funding agency to further promotion plans. * Develops basic databases: genome sequence database, protein 3D structure database, gene expression profile database, molecular interaction database, etc. * Conducts and coordinates integration, enhancement, and standardization of the basic databases. * Develops computing tools for analyzing various kinds of biological and experimental data, data mining from databases, computer simulation of living systems and so on. * Develops ontologies necessary for data and knowledge description of databases storing biological functions and integration of the basic databases. * Conducts and coordinates research and development of innovative and creative technologies and theories which move toward understanding life as an information system, especially approaches by collaboration of computer scientists and experimental scientists. * Provides computer facilities for developing databases and software and making them publicly available. * Sets up training courses for teaching utilization of databases and tools for novices in bioinformatics and sponsors scientific meetings. * Provides community space with high performance computing facilities where innovative ideas are cultivated by free discussion and "trial and error" with the computer in order to promote development of young scientists who will create new biological discoveries based on bioinfomatics and become leaders in the field.
Institute of Medical Psychology and Behavioral Neurobiology, University of Tbingen
Institute of Medical Psychology and Behavioral Neurobiology
The Institute of Medical Psychology and Behavioral Neurobiology in Germany is an institutional portal established at the Faculty of Medicine of the University of Tbingen in 1993. With the assignment of the chair for Medical Psychology and Medical Sociology to Professor Birbaumer the educational task became the instruction of medical students in Medical Psychology and Medical Sociology. Christoph-Dornier-Center of Clinical Psychology at the University of Tobingen Medical Faculty In March 2001, a new institute of the Christoph Dornier Foundation was opened under the direction of Prof. Niels Birbaumer. The aim of this institute is to advance research in behavioral neurobiology and behavioral medicine. The results of the research should be directly translated into treatments. The emphasis in Tbingen is on the treatment of chronic pain and intractable epilepsy, using a combination of biofeedback training and behavioral therapy. Even though a positive effect of biofeedback has been proven in many controlled studies, the method is still far from being accepted in everyday clinical practice. The outpatient department in Tbingen intends to enable access to this treatment to a wider population of patients. Magnetoencephalography(MEG)-Center The MEG-Center (established 1997) is a central research facility at the University of Tbingen. The Center is operated by the Institute of medical psychology and behavioural Neurobiology and hosts a whole-head 151-channel system built by VSMMedtech (www.vsmmedtech.com). In early 2006 in addition to the wholehead MEG an additional special purpose MEG system will be installed in Tbingen (funded by the DFG and Land Baden Wrttemberg). This MEG is dedicated to the investigation of fetal brain signals in utero (fMEG) . The fMEG will be installed at the University Woman Clinic and operated by the staff of the MEG center. This is the first dedicated fMEG system in Europe. Some content on the website is only in German.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Data analysis software for complete multipoint analysis.
Medical Research Council Harwell: An International Centre for Mouse Genetics
UK’s national facility for mouse genetics and use of mouse models for preclinical study of human disease.Offers services to researchers around the world. Services include free archiving of mouse lines to protect them for future use, distribution of mouse lines from the Archive, breeding and phenotyping of genetically altered mice, and genome engineering services to generate new mouse models.Offers archiving and distribution of mouse lines to safeguard germplasm collected from unique strains and make it readily available to the scientific community.
A publisher of original scholarly work focused on psychiatric education and professional development in academic psychiatry. The journal features work that furthers knowledge in psychiatric education and stimulates improvements in academic psychiatry. Articles address teaching, research, and administration, as well as clinical, organizational, and economic issues relevant to the academic missions of departments of psychiatry. Overview articles present empirical research and critical analysis of important topics in academic psychiatry. Other features include a new ideas section, commentaries, and letters to the editor. Academic Psychiatry also publishes the best papers from meeting workshops, provides a forum for debates, and often presents theme issues that focus on a single area of psychiatric education.
Alzheimer's Australia: Living with Dementia
A website which provides in-depth fact sheets on aspects of dementia and dementia care. It provides information on member organizations in each state, support and respite services as well as counseling and education available through Alzheimer's Australia. This organization's vision is for a society committed to the prevention of dementia, while valuing and supporting people living with dementia. Alzheimer's Australia manages a wide range of innovative National Programs which provide information, support, counseling, training and education to people with dementia, their families and carers as well as to professionals working in the dementia field.
The Archives of General Psychiatry strives to publish original, state-of-the-art studies and commentaries of general interest to clinicians, scholars, and research scientists in psychiatry, mental health, behavioral science, and allied fields. The Archives seeks to inform and to educate its readers as well as to stimulate debate and further exploration into the nature, causes, treatment, and public health importance of mental illness. Archives of General Psychiatry is an international peer-reviewed journal published 12 times a year. The online version is published on the first Monday of the month. There is a Middle Eastern edition of Archives of Neurology/Psychiatry published quarterly. The editor is interested in publishing high-impact articles that cover the field broadly, from genetic mechanisms to psychotherapeutic intervention trials. The acceptance rate is 17%. The average time from submission to first decision is 32 days; from acceptance to publication, 5.4 months. Its 2008 impact factor is 14.27 (the impact factor is a measure of citation rate per article, and is calculated by dividing 1 year''s worth of citations to a journal''s articles published in the previous 2 years by the number of major articles (eg, research papers, reviews) published by that journal in those 2 years).
Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology
Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013.
Canadian Bioinformatics.ca Links Directory
Database of curated links to molecular resources, tools and databases selected on the basis of recommendations from bioinformatics experts in the field. This resource relies on input from its community of bioinformatics users for suggestions. Starting in 2003, it has also started listing all links contained in the NAR Webserver issue. The different types of information available in this portal: * Computer Related: This category contains links to resources relating to programming languages often used in bioinformatics. Other tools of the trade, such as web development and database resources, are also included here. * Sequence Comparison: Tools and resources for the comparison of sequences including sequence similarity searching, alignment tools, and general comparative genomics resources. * DNA: This category contains links to useful resources for DNA sequence analyses such as tools for comparative sequence analysis and sequence assembly. Links to programs for sequence manipulation, primer design, and sequence retrieval and submission are also listed here. * Education: Links to information about the techniques, materials, people, places, and events of the greater bioinformatics community. Included are current news headlines, literature sources, educational material and links to bioinformatics courses and workshops. * Expression: Links to tools for predicting the expression, alternative splicing, and regulation of a gene sequence are found here. This section also contains links to databases, methods, and analysis tools for protein expression, SAGE, EST, and microarray data. * Human Genome: This section contains links to draft annotations of the human genome in addition to resources for sequence polymorphisms and genomics. Also included are links related to ethical discussions surrounding the study of the human genome. * Literature: Links to resources related to published literature, including tools to search for articles and through literature abstracts. Additional text mining resources, open access resources, and literature goldmines are also listed. * Model Organisms: Included in this category are links to resources for various model organisms ranging from mammals to microbes. These include databases and tools for genome scale analyses. * Other Molecules: Bioinformatics tools related to molecules other than DNA, RNA, and protein. This category will include resources for the bioinformatics of small molecules as well as for other biopolymers including carbohydrates and metabolites. * Protein: This category contains links to useful resources for protein sequence and structure analyses. Resources for phylogenetic analyses, prediction of protein features, and analyses of interactions are also found here. * RNA: Resources include links to sequence retrieval programs, structure prediction and visualization tools, motif search programs, and information on various functional RNAs.
Lab interested in understanding how neuronal circuitries of the brain support its cognitive capacities. Its goal is to provide rational, mechanistic explanations of cognitive functions at a descriptive level. In the lab''s view, the most promising area of cognitive faculties for scientific inquiry is memory, since it is a well-circumscribed term, can be studied in animals and substantial knowledge has accumulated on the molecular mechanisms of synaptic plasticity. Available software: * NeuroScope: NeuroScope can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities. * Klusters: Klusters is a powerful and easy-to-use cluster cutting application designed to help neurophysiologists sort action potentials from multiple neurons on groups of electrodes (e.g., tetrodes or multisite silicon probes). * KlustaKwik: KlustaKwik is a program for automatic cluster analysis, specifically designed to run fast on large data sets. * MATLAB m-files: A selection of MATLAB files developed in the lab., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Cal-IT2: Immersive Visualization Laboratory
This resource is a Wiki page providing information about the Immersive Visualization Laboratory of Cal-IT2 at the UCSD. Sponsors: This resource is supported by Cal-IT2.
Cellular Open Resource is a Microsoft Windows environment for cellular modeling that is built around CellML (except for reactions and metadata which are not supported). It offers, through CellML, an ''out of the box'' access to a large database of single cell models. COR was among the early adopters of this standard, eventually forming the first publicly available CellML-based modeling and collaboration environment. From the onset, COR was designed to provide an environment that could not only be used by experienced modelers, but also by experimentalists, teachers and students. It therefore tries to combine a user-friendly interface with a computationally efficient numerical engine. In this paper, we introduce the philosophy behind COR, explain its user interface and current functionality, including the editing and running of CellML files, highlight lessons learned from user feedback and problems experienced during the development of COR and conclude by exploring future development potential. Sponsors: This study has been supported by a grant from the UK Biotechnology and Biological Sciences Research Council (BB/E024955/1). Keyword: Cell, Model, Cellular, Modeling, Open resource, Microsoft, Environment, Database, Experimentalist, Teacher, Student, Modeler, Computationally, Development,
University of Sciences in Philadelphia; Pennsylvania; USA
National Polytechnic Institute; Department of Physiology, Biophysics, and Neurosciences
The National Polytechnic Institute''s (Instituto Politecnico Nacional) department of Physiology, Biophysics, and Neurosciences (Departamento de Fisiologa, Biofsica y Neurociencias) is an institutional topical portal and offers a Masters and doctorate program. The web sites content is in Spanish. In forty years of life, this Department has maintained constant activity and has a well sustained scientific prestige within the national and international levels; in addition, the departments of the Center for Research and Advanced Studies (Centro de Investigacin y de Estudios Avanzados (CINVESTAV)) has had more recognition and support of external agencies. The achievements realized during this time yields the following results: 245 graduate students (140 Masters and doctorate 108), 272 directed theses, 190 research articles published in national journals and 831 in international journals with strict arbitration, 75 chapters in books published abroad, 210 chapters in national books, five complete books published outside the country, fourteen national books, and thousands of citations at the international level to the research work done by its members. Today, its teaching plant is composed of 31 teachers and there are 38 students enrolled in the doctorate program and 11 in the Masters program. The rigorous selection of students has allowed for the production of scientists concerned about the quality of their research. In the Department an atmosphere of cordiality exists and collective performance of the delivery of the work. Lines of inquiry Medication access and drugs across the epithelia and endothelium Accession, proliferation, differentiation and cancer Biophysics of Ionic Channels Endocrinology Sensorimotor integration in the spinal cord Environment and cellular injury Developmental neurobiology Neuropharmacology Nervous system pathologies Gene therapy
A tool for finding significant combinations of multisource annotations in gene lists.
The Centre d''Etude du Polymorphisme Humain (CEPH) is a research laboratory, the main activities of which are the setting up, storage, processing and distribution of DNA collections for the identification of genetic factors conferring susceptibility to complex disorders. These collections are established in partnership and full collaboration with external French or international research groups. The Foundation currently hosts the CEPH reference panel, the HGDP panel (Human genome Diversity Cell Line Panel) and several collections amounting mid-2008 to more than 250 000 samples. The goal of CEPH is to understand complex multifactorial disorders necessitates the establishment of structures facilitating access to large and integrated collection of individuals, characterized by a large number of variables emanating from different technologies and platforms. To achieve this goal, CEPH facilitates the setting up of integrated analyses combining clinical, genetic and environmental data, for the identification of susceptibility factors to complex multifactorial disorders Additionally, CEHP allows the reception, storage, processing and distribution of biological sample collections. At the same time, it promotes and participates in the design and setting up of genetic studies: - in partnership and full collaboration with external research groups - giving access to a large number of variables - in a sufficient number of subjects - allowing large scale integrated analyses
CRE Binding-protein Target Gene Database
CREB target gene database that uses a multi-layered approach to predict, validate and characterize CREB target genes. For each gene, the database tries to provide the following information: 1. CREB binding sites on the promoters 2. Promoter occupancy by CREB 3. Gene activation by cAMP in tissues CREB seems to occupy a large number of promoters in the genome (up to ~5000 in human), and the profiles for CREB promoter occupancy are very similar in different human tissues. However, only a small proportion of CREB occupied genes are induced by cAMP in any cell type, possibly reflecting the requirement of additional regulatory partners that assist in recruitment of the transcriptional apparatus. To use the database, choose the species, select the table you want to search, leave field (''All'') and type in the gene you want to search. A table listing the search results will be returned, followed by the description of the table. If no search result is returned, try the official gene symbol or gene ID (locuslink number) from NCBI Entrez Gene to search. Sponsors: This work was supported by National Institutes of Health Grants GM RO1-037828 (to M.M.) and DK068655 (to R.A.Y.).
DNA From The Beginning: AN Animated Primer on the Basics of DNA, Genes, and Heredity
An animated primer on the basics of DNA, genes, and heredity organized around three key concepts: Classical Genetics, Molecules of Genetics, and Genetic Organization and Control. The science behind each concept is explained by: animation, image gallery, video interviews, problem, biographies, and links.
biolab - Bioengineering and Bioimages Laboratory
The Bio-Lab is a Bioengineering and Bioimages laboratory and it''s part of DIST (Department of Computer Science, Control Systems and Telecommunications- University of Genoa). The main research activities of the Bioengineering Laboratory are related with the acquisition, processing and rendering of bioimages with the aim of exploring the links between structure and functionality of biological systems (images of cells in optical confocal microscopy) and for diagnostic and therapeutical processes (images of the human body in Magnetic Resonance, Computerized X-ray Tomography, ultrasounds and other modalities). The main research activities of the laboratory are related to: - Bioimages: medical/biological image analysis and visualization methods are investigated, with a deep attention to the applications development for the driven therapy. - Bioinformatics: in this field, advanced technologies and knowledge related to production and treatment of gene expression microarray distributed data have been implemented. - Tissue Engineering: this research activity is addressed to the development and testing of biomaterials, coupled with adult stem cells for the in vivo bone formation. - Neuroinformatics: the interaction between results of functional neuroimaging and brain computational models has been studied. Among the equipment of the Bioengineering Laboratory there are of particular interest: 2D-3D cell culture bioreactor systems and a virtual reality platform for the interaction person-bioimages, medical data and 3D models. The Bio-Lab also manages a GRID node belonging to the international GILDA network, which is built by 6 server, for a total amount of 12 CPU, 7 GB RAM and 500 GB Disk Space. Additionally, the confocal laser is a very essential tool in this lab; it is a scanning optical microscope with a hardware/software framework virtual reality-like for the interaction person-bioimages, with stereovision, and equipment for head tracking and pointing. The Bio-Lab collaborates with several research institutes and centers, such as the National Institute of Nuclear Physics, the National Research Council, and the Advanced Biotechnology Center (visit Research area or Project area in the web site). Promising collaborations are also on going with different technological companies in the national scenario. The laboratory has also been involved in several international and national projects funded by the European Commission and MUR. Specifically, it is involved in several projects funded by the European Commission projects related to the area of Health Care Telematics, with special reference to emergency telemedicine.
lobSTR - Profiling STRs in personal genomes
A software tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Multiscale Object Orientation Simulation Environment
MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. it is backwards-compatible with GENESIS, and forward compatible with Python and XML-based model definition standards like SBML and MorphML. MOOSE is coordinating with the GENESIS-3 project towards the goals of developing educational resources for modeling. MOOSE is open source software, licensed under the LGPL (Lesser GNU Public License). It has absolutely no warranty. Sponsors: - National Center of Biological Sciences (NCBS) - National Institutes of Health (NIH) Collaboration - EU-India grid - Department of Atomic Energy Science Research Council (DAE/SRC) - Department of Biotechnology (DBT)
Electroencephalogram Database: Prediction of Epileptic Seizures
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 29,2025. Electroencephalogram (EEG) data recorded from invasive and scalp electrodes. The EEG database contains invasive EEG recordings of 21 patients suffering from medically intractable focal epilepsy. The data were recorded during an invasive pre-surgical epilepsy monitoring at the Epilepsy Center of the University Hospital of Freiburg, Germany. In eleven patients, the epileptic focus was located in neocortical brain structures, in eight patients in the hippocampus, and in two patients in both. In order to obtain a high signal-to-noise ratio, fewer artifacts, and to record directly from focal areas, intracranial grid-, strip-, and depth-electrodes were utilized. The EEG data were acquired using a Neurofile NT digital video EEG system with 128 channels, 256 Hz sampling rate, and a 16 bit analogue-to-digital converter. Notch or band pass filters have not been applied. For each of the patients, there are datasets called ictal and interictal, the former containing files with epileptic seizures and at least 50 min pre-ictal data. the latter containing approximately 24 hours of EEG-recordings without seizure activity. At least 24 h of continuous interictal recordings are available for 13 patients. For the remaining patients interictal invasive EEG data consisting of less than 24 h were joined together, to end up with at least 24 h per patient. An interdisciplinary project between: * Epilepsy Center, University Hospital Freiburg * Bernstein Center for Computational Neuroscience (BCCN), Freiburg * Freiburg Center for Data Analysis and Modeling (FDM).
gene-regulation.com: Public Databases for Academic and Non-profit Organizations
In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers academic and non-profit organizations free access to reduced functionality versions of their products. TRANSFAC Professional provides gene regulation analysis solutions, offering the most comprehensive collection of eukaryotic gene regulation data. The professional paid subscription gives customers access to up-to-date data and tools not available in the free version. The public databases currently available for academic and non-profit organizations are: * TRANSFAC: contains data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. * TRANSPATH: provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signaling components.TRANSPATH focuses on signaling cascades that change the activities of transcription factors and thus alter the gene expression profile of a given cell. * PathoDB: is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. * S/MARt DB: presents data on scaffold or matrix attached regions (S/MARs) of eukaryotic genomes, as well as about the proteins that bind to them. S/MARs organize the chromatin in the form of functionally independent loop domains gained increasing support. Scaffold or Matrix Attached Regions (S/MARs) are genomic DNA sequences through which the chromatin is tightly attached to the proteinaceous scaffold of the nucleus. * TRANSCompel: is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signaling pathways. * PathoSign Public: is a database which collects information about defective cell signaling molecules causing human diseases. While constituting a useful data repository in itself, PathoSign is also aimed at being a foundational part of a platform for modeling human disease processes.
GeneNetWorks is designed for accumulation of experimental data, data navigation, data analysis, and analysis of dependencies in the field of gene expression regulation. It integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description. The unique property of above described system is that all the resources within the system GeneNetWorks are divided according to the natural hierarchy of molecular genetic systems and has the following levels: (1) DNA; (2) RNA; (3) proteins; and (4) gene networks. Each module contains: 1) experimental data represented as a database or some sample; 2) program for data analysis; 3) results of an automated data processing; 4) tools for the graphical representation of these data and the results of the data analyses.
GEneral NEural SImulation System: The Neurospaces Project
The GEneral NEural SImulation System (GENESIS) started as a very advanced software package in the late eighties, for biologically accurate neuronal modeling. Besides being used as a neuronal simulator, it was also applied to various domains outside computational neuroscience. The Neurospaces project is a departure from the monolithic software system design of the original GENESIS system. It is a development center for software components of computational neuroscience simulators. There are many advantages of developing independent software components: - Interfacing to an individual component is obviously more simple than interfacing to a do-all monolithic system. The compartmental solver developed for the Neurospaces project can be connected to Matlab fi. - It simplifies the individual components and encourages other developers to get involved. - It allows for separate testing of the components. More than 1000 use case tests been defined for these software components, including integration tests. - Integrating different component, gives different flavours of the same simulator, and enhances the user experienced consistency when doing multilevel simulations. - A component based software system avoids vendor-lockin. Its life-cycle is more smooth than that of a monolithic system, because software components can be upgraded one at a time. The Neurospaces project embodies many software components that all have been developed in full isolation. The core of the most important components is finished. The current development focus has shifted from component integration to the support of specific use case with an emphasis on single neuron modeling. This is a list of software components that have been developed or are under construction. Together, these tools give the core for the upcoming GENESIS 3 GUI. - GShell: a simple replacement for the Genesis 2 SLI. - Heccer: a fast compartmental solver, a backend. - Dash: a second compartmental solver faster than Heccer, for simpler models. - Neurospaces Model Container: provides a solver independent internal and external storage format for models. - Discrete event system: consists of a discrete event distributor and queuer. This is used for abstract modeling of an action potential traveling inside an axon as a ''discrete event''. - SSP: a flexible scheduler written in perl, to run simulations with the Neurospaces model container and Heccer. - The Neurospaces Studio: some tools for graphical browsing and command line usage. - The Genesis Script Language Interface: a scripting component that reads Genesis 2 scripts and feeds them to the Neurospaces model container. - The Geometry Library is a general purpose geometry library, with some essential geometrical operators, not commonly found in other geometrical libraries. - Using the Geometry Library, a Reconstruct Interface has been written. This interface supports the conversion of contours exported by the Reconstruct software to the Neurospaces declarative NDF format. - The Neurospaces project browser for browsing projects and inspecting simulation results. - The Installer package contains the Neurospaces installer and developer tools that have emerged from developing Neurospaces software components. - The Configurator package contains configuration utilities for the other tools. It is not needed for the other tools to work properly. Rather, it allows to set up model database and simulation servers in a convenient way. - There is also a Neurospaces blog and a wiki at googlecode for the Neurospaces project, with information for developers.
Genomatix Software: Understanding Gene Regulation
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 13,2026. Genomatix is a privately held company that offers software, databases, and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology. Its multilayer integrative approach is a working implementation of systems biology principles. Genomatix combines sequence analysis, functional promoter analysis, proprietary genome annotation, promoter sequence databases, comparative genomics, scientific literature data mining, pathway databases, biological network databases, pathway analysis, network analysis, and expression profiling into working solutions and pipelines. It also enables better understanding of biological mechanisms under different conditions and stimuli in the biological context of your data. Some of Genomatix'' most valuable assets are the strong scientific background and the years of experience in research & discovery as well as in development & application of scientific software. Their firsthand knowledge of all the complexities involved in the in-silico analysis of biological data makes them a first-rate partner for all scientific projects involving the evaluation of gene regulatory mechanisms. The Genomatix team has more than a decade of scientific expertise in the successful application of computer aided analysis of gene regulatory networks, which is reflected by more than 150 peer reviewed scientific publications from Genomatix'' scientists More than 35,000 researchers in industry and academia around the world use this technology. The software available in Genomatix are: - GenomatixSuite: GenomatixSuite is our comprehensive software bundle including ElDorado, Gene2Promoter, GEMS Launcher, MatInspector and MatBase. GenomatixSuite PE also includes BiblioSphere Pathway Edition. Chromatin IP Software - RegionMiner: Fast, extensive analysis of genomic regions. - ChipInspector: Discover the real power of your microarray data. Genome Annotation Software - ElDorado: Extended Genome Annotation. - Gene2Promoter: Retrieve & analyze promoters - GPD: The Genomatix Promoter Database, which is now included with Gene2Promoter. Knowledge Mining Software - BiblioSpere : The next level of pathway/genomics analysis. - LitInspector: Literature and pathway analysis for free. Sequence Analysis Software - GEMS Launcher: Our integrated collection of sequence analysis tools. - MalInspector: Search transcription factor binding sites - MatBase: The transcription factor knowledge base. Other (no registration required) Software - DiAlign: Multiple alignment of DNA/protein sequence. - Genomatix tools: Various small tools for sequence statistics, extraction, formatting, etc.
Harvard Medical School, Department of Systems Biology: The Megason Lab -GoFigure Software
GoFigure is a software platform for quantitating complex 4d in vivo microscopy based data in high-throughput at the level of the cell. A prime goal of GoFigure is the automatic segmentation of nuclei and cell membranes and in temporally tracking them across cell migration and division to create cell lineages. GoFigure v2.0 is a major new release of our software package for quantitative analysis of image data. The research focuses on analyzing cells in intact, whole zebrafish embryos using 4d (xyzt) imaging which tends to make automatic segmentation more difficult than with 2d or 2d+time imaging of cells in culture. This resource has developed an automatic segmentation pipeline that includes ICA based channel unmixing, membrane nuclear channel subtraction, Gaussian correlation, shape models, and level set based variational active contours. GoFigure was designed to meet the challenging requirements of in toto imaging. In toto imaging is a technology that we are developing in which we seek to track all the cell movements and divisions that form structures during embryonic development of zebrafish and to quantitate protein expression and localization on top of this digital lineage. For in toto imaging, GoFigure uses zebrafish embryos in which the nuclei and cell membranes have been marked with 2 different color fluorescent proteins to allow cells to be segmented and tracked. A transgenic line in a third color can be used to mark protein expression and localization using a genetic approach that this resource developed called FlipTraps or using traditional transgenic approaches. Embryos are imaged using confocal or 2-photon microscopy to capture high-resolution xyzt image sets used for cell tracking. The GoFigure GUI will provide many tools for visualization and analysis of bioimages. Since fully automatic segmentation of cells is never perfect, GoFigure will provide easy to use tools for semi-automatically and manually adding, deleting, and editing traces in 2d (figures-xy, xz, or yz), 3d (meshes- xyz), 4d (tracks- xyzt) and 4d+cell division (lineages). GoFigure will also provide a number of views into complex image data sets including 3d XYZ and XYT image views, tabular list views of traces, histograms, and scattergrams. Importantly, all these views will be linked together to allow the user to explore their data from multiple angles. Data will be easily sorted and color-coded in many ways to explore correlations in higher dimensional data. The GoFigure architecture is designed to allow additional segmentation, visualization, and analysis filters to be plugged in. Sponsors: GoFigure is developed by Harvard University., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University of Science and Technology of China; Hefei; China
Public research university in Hefei, Anhui, China, under direct leadership of Chinese Academy of Sciences. Member of elite C9 League. Chinese state Class A Double First Class University.
3D interactive atlas of two mouse brains, 129S1/SvImJ and C57Bl/6J. The aim of this resource is to enhance comparative morphometric analyses and stereotactic surgical procedures in mice. These representations of the murine brain and skull, in conjunction with the resource''s development of a new, more dynamic master coordinate system, provide improved accuracy with respect to targeting CNS structures during surgery compared with previous systems. The interactive three-dimensional nature of these atlases also provide users with stereotactic information necessary to perform accurate off-axis surgical procedures, as is commonly required for experiments such as in vivo micro-electroporation. In addition, three-dimensional analysis of the brain and skull shape in C57Bl, 129Sv, CD1, and additional murine strains, suggests that a stereotactic coordinate system based upon the lambda and rostral confluence of the sinuses at the sagittal midline, provides improved accuracy compared with the traditional lambdabregma landmark system. These findings demonstrate the utility of developing highly accurate and robust three-dimensional representations of the murine brain and skull, in which experimental outputs can be directly compared using a unified coordinate system.
Human Protein-Protein Interaction Mining Tool
Web-based tool used to mine human protein-protein interactions (PPIs) from PubMed abstracts based on their co-occurrences and interaction words, followed by evidencs in human PPI databases and shared terms in GO database.
Institute of Experimental Medicine of the Hungarian Academy of Sciences: Laboratory of Cerebral Cortext Reserach
The aim of this laboratory is to understand how information is encoded in specific spatiotemporal activity patterns and structural configurations at the circuit, cellular, and molecular levels in the hippocampus, thereby enabling the process of memory. A major task is to find the neuronal codes of internal representations of memory items and the mapping rules between the levels of gene expression/proteins synthesis and the level of cognitive processing. Novel combinations of approaches, including multiple single-cell recording technology, patch-clamp electrophysiology, neuroanatomy/neurochemistry at the cellular and subcellular levels, and computational models are employed to test specific hypotheses about that mapping process (such as local circuit anatomy and activity-dependent short-term and long-term synaptic plasticity). Collaborations within the Institute allows the group to also incorporate gene targeting methods and behavioral learning/memory tests in their methodological repertoire. The laboratory has been focusing on the normal and pathological (epileptic, ischemic) activity of cortical networks, with particular attention to the generation of behaviour-dependent population discharge patterns (theta and gamma oscillations, hippocampal sharp waves). Anatomical, in vitro and in vivo electrophysiological, pharmacological and molecular techniques and modeling are combined to elucidate the functional roles of inhibitory cell types in the control of population synchrony and synaptic plasticity in the hippocampus, their local and subcortical modulation via selective afferent pathways (GABAergic and cholinergic septal, as well as serotonergic raphe input) and pre- or postsynaptic receptors. An expanding new direction of research is related to the role of endocannabinoid signaling in the activity-dependent modulation of GABAergic and glutamatergic transmission, and its involvement in anxiety-like behavior.
Integrative Neuroscience Initiative on Alcoholism
Consortium set out to identify the molecular, cellular, and behavioral neuroadaptations that occur in the brain reward circuits associated with the extended amygdala and its connections. It is hypothesized that genetic differences and/or neuroadaptations in this circuitry are responsible for the individual differences in vulnerability to the excessive consumption of alcohol. Chronic exposure to alcohol results in neuroadaptive phenomena, including tolerance, sensitization, dependence, withdrawal, loss of control of drinking, and relapse that contribute to the development of excessive alcohol consumption. The INIA has the following goals: 1) To establish animal models to study specific neurobiological targets for vulnerability that lead to excessive consumption of alcohol at the molecular, cellular and neural circuit level of analysis, 2) To identify specific clusters of genes whose expression is regulated by alcohol and which are responsible for any given model of excessive alcohol consumption using gene expression arrays, differential display, mutagenesis directed at specific brain areas, and the development of new informatics tools to analyze and interpret gene expression, cellular circuitry and brain circuitry data with the use of transgenic and knockout approaches, and 3) To attract new and innovative investigators to the field of alcohol research by recruiting individuals for development of U01 grants and pilot projects and by developing online interactive capacity among INIA scientists and others, and by making the neuroinformatics integrated data sets accessible, searchable and interactive with other databases for all scientists interested in alcoholism research. The structure of INIA is envisioned as two domains, Dependence-induced drinking and Binge drinking, comprised of multiple U01 research grants. The flow of information within each domain moves from molecular, to cellular, to neurocircuitry levels of analysis. These U01s share information with the core facilities, which act as data depositories. The Administrative Core coordinates the flow of information among the Domains and Cores and disseminates the information back to the U01s. A Pilot Project program will identify exciting new areas for research and the continual recruitment of new investigators to the alcohol field. The INIA program is directed by an Administrative Core in close cooperation with the Animal Models, Gene Array and Neurocircuitry Cores via a Steering Committee and with the continual advice of the Scientific Advisory Committee.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 28, 2013. (URL is no longer valid) A platform for high-throughput proteomic analysis. Major objectives of IPP include the establishment of a broadly applicable platform of routine methods for the analysis of protein interaction networks in bio-medical research. A multidisciplinary approach will address; * their validation by cell biological, biochemical and biophysical methods. * their collection in a new type of public database. * their exploitation and use for in silico simulations of protein-interaction networks. The innovations generated in IPP will provide the basis for an efficient analysis and systems modeling of fundamental biological processes in health and disease. It will develop novel technology, including a high-end mass spectrometer with extremely large dynamic range, high-density peptide arrays, and improved visualization technology for light and electron microscopy. Additionally, the novel technologies will be validated with selected model systems of high relevance to medicine and biotechnology. Extensive bioinformatics support is a key element in the project to cope with the massive increase in experimental data on protein interactions obtained using the novel technologies. In particular, the efficient integration of disparate data sets represents a key challenge in proteomics and functional genomics. Therefore, the consortium includes the creator of the only European protein-interactions database, MINT. The multi-disciplinary efforts required in the scientific program of IPP are organized into four sub-projects (SP): * SP1: Tools for interaction analysis - SP1 is dedicated to the development of innovative proteomics technology to map protein-interaction networks and their cellular topology for the interaction analyses in SP2 and SP3. * SP2: Identification of interaction partners for protein domains - SP2 will generate (high throughput) data for important protein-protein interactions defined by bioinformatics and biomedical interest and by SP3, utilizing technology developed in SP1. * SP3: Functional analysis of interactions - SP3 focuses on the validation of technologies and tools developed in SP1. It will perform functional analyses of protein-interactions in medically and biochemically relevant prokaryotic and eukaryotic (mammalian) model systems. * SP4: Interactome database and modelling - SP4 provides the required bioinformatics infrastructure for the project, comprising the improvement of the public MINT database for the collection and dissemination of the interactome data; modelling and simulation of protein-interaction networks characterised in SP2 and SP3; and the dissemination of the technology developments to the scientific community.
University of Southern California Brain Project
The USC Brain Project is engaged in the effort to develop new tools and methodologies for neuroinformatics in modeling neural mechanisms of visuomotor coordination and exploring the evolution of the human language-ready brain, as well as conducting work in both neural modeling and database construction in relation to rehabilitation after stroke. Sponsors: USCBP is funded by the University of Southern California.
Software that currently allows to process an amount of bisulfite sequencing reads obtained in one or several bisulfite sequencing experiments.
Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki
Special interest group that brings together program officers who have a shared interest in applying modeling and analysis methods to biomedical systems. The meetings are formatted to facilitate an open discussion of what is currently being supported, and for planning future directions in these areas. At each meeting, time is allotted to hear focused presentations from one or two participants to discuss issues relating to modeling and analysis across the government agencies. Discussions also occur online, and participants are informed of talks, conferences and other activities of interest to the group. IMAG recognized that the modeling community is on the forefront of thinking across the biological continuum, rather than just focusing at one scale or level of resolution. In addition IMAG identified a strong desire among modelers to form multi-disciplinary partnerships across varied research communities. Overall Intent of IMAG through the MSM Consortium is: * To develop new methodologies that span across biological scales * To develop multiscale methodologies applicable to biomedical, biological and behavioral research * To develop methodologies within the local multidisciplinary team and within the larger Framework environment * To further promote multiscale modeling through model sharing This wiki contains information relevant to the IMAG (Interagency Modeling and Analysis Group) and the MSM (Multi-scale Modeling Consortium).
In-Vivo Cellular and Molecular Imaging Center, Brussels
Imaging core offering multiple small animal imaging modalities including MicroSPECT, Optical imaging, MicroCT and Ultrasound have been centralized together with a unit for probe development and a vivarium for the housing of animals in one laboratory.
Max Planck Institute for Biological Intelligence Circuits - Computation – Models
Max Planck Institute of Neurobiology Systems and Computational Neurobiology
Merger of the Max Planck Institute of Neurobiology and the Max Planck Institute of Ornithology and has been renamed to Circuits - Computation – Models. Department devoted to the study of how the brain computes to understand neural information processing at the level of individual neurons and small neural circuits.
Medical College of Georgia Animal Behavior Center
The Medical College of Georgia Animal Behavior Center has considerable experience testing the short-term memory and attention capabilities of non-human primates. Testing programs are available to MCG faculty on a collaborative basis, and they are available for contractual agreements with pharmaceutical companies and other external research programs. Delayed-response testing is a well-established means of examining neurochemical, neuroanatomical and therapeutic aspects of ATD, ADHD and schizophrenia. Behavioral paradigms at the Animal Behavior Center are designed around an automated delayed-response task assessing the function of mnemonic and attention processes. Particularly significant is the fact that each paradigm differs regarding the relative emphasis on these two different, yet interdependent, cognitive constructs. The Animal Behavior Center also is experienced in stereotaxic implantation of intracranial electrodes and cannulas in rodents and non-human primates. The basic approaches and procedures of the Animal Behavior Center include: - Delayed Matching-to-Sample (DMTS) - DMTS With a Distractor During the Delay Interval - DMTS With a Titrated Delay Interval
MDVU - Movement Disorder Virtual University
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The Movement Disorder Virtual University is the healthcare professional's source for movement disorder news, resources and educational activities. MDVU is brought to you by WE MOVE, a not-for-profit organization that has been educating and informing the movement disorder community for over a decade. WE MOVE believes that increased knowledge and understanding promote timely, accurate diagnosis and up-to-date treatment, resulting in a better quality of life for individuals affected by movement disorders. Educational Programs and Resources for Professionals WE MOVE's mission is to facilitate the communication of emerging clinical advances and therapeutic approaches to the management and treatment of movement disorders. Through its award-winning, HON-compliant Web site and as an accredited provider of continuing medical education (CME), WE MOVE strives to meet the educational needs of providers. WE MOVE develops up-to-date training programs and comprehensive, interactive teaching materials to assist professionals in deepening their understanding of neurologic movement disorders, their pathophysiology, etiology, differential diagnosis and state-of-the-art interventions. Case-based Learning (CBL) WE MOVE Case-based Learning (CBL) modules provide an environment that allows for participative learning a well-recognized tool to facilitate the adult learning experience. This self-paced, private learning environment encourages physicians to employ a problem-solving approach, walking step-by-step through the case history, family history, and symptomatology of the patient featured in the case. WE MOVE CBL modules illustrate the diagnostic process and varied approaches to treatment utilized by the thought leader who submitted the case, an invaluable experience for physicians looking to expand their expertise in the diagnosis and treatment of movement disorders. The depth of the WE MOVE CBL learning technology allows each case to highlight treatment of certain aspects of the condition or the efficacy of a given treatment regimen at different stages of disorder progression further enriching the physician's learning experience. For therapies requiring specific expertise in administration (e.g., injectable therapies), video footage of the therapeutic procedure itself enhances the depth of the experience. Co-location of WE MOVE CBL modules within the MDVU creates an unrivaled learning environment for physician education. WE MOVE CBL modules are available at no charge to physicians, 24 hours a day, seven days a week.
Sequenced Treatment Alternatives to Relieve Depression Study
NIMH Sequenced Treatment Alternatives to Relieve Depression (STAR*D) Study
NIMH Sequenced Treatment Alternatives to Relieve Depression Study
Sequenced Treatment Alternatives to Relieve Depression (STAR*D) Study
A nationwide public health clinical trial conducted to determine the effectiveness of different treatments for people with major depression, in both primary and specialty care settings, who have not responded to initial treatment with an antidepressant. This is the largest and longest study ever done to evaluate depression treatment. The study is completed and no longer recruiting participants. Each of the four levels of the study tested a different medication or medication combination. The primary goal of each level was to determine if the treatment used during that level could adequately treat participants����?? major depressive disorder (MDD). Those who did not become symptom-free could proceed to the next level of treatment. The design of the STAR*D study reflects what is done in clinical practice because it allowed study participants to choose certain treatment strategies most acceptable to them and limited the randomization of each participant only to his/her range of acceptable treatment strategies. No prior studies have evaluated the different treatment strategies in broadly defined participant groups treated in diverse care settings. Over a seven-year period, the study enrolled 4,041 outpatients, ages 18-75 years, from 41 clinical sites around the country, which included both specialty care settings and primary medical care settings. Participants represented a broad range of ethnic and socioeconomic groups. All participants were diagnosed with MDD, were already seeking care at one of these sites, and were referred to the trial by their doctors. * STAR*D Study Medications: Citalopram (Celexa), Sertraline (Zoloft), Bupropion SR (Wellbutrin SR), Venlafaxine XR (Effexor XR), Buspirone (BuSpar), Mirtazapine (Remeron), Triiodothyronine (T3) (Cytomel), Nortriptyline (Pamelor, Aventyl), Tranylcypromine (Parnate), Lithium (Eskalith, Lithobid) *STAR*D Talk Therapy:Cognitive Therapy
Database on Brain Map Transformations in Cerebellar Systems
This site contains the NeSys archive on structure and structure-function data about brain map transformations in the cerebellar system of the rat. This archive presents data not illustrated in the original publications, downloadable original data sets, interactive illustration sequences, including 3-D models. The repository is based on 5 original publications. The publications deal with: - organization of projections to the pontine nuclei from three cortical areas: primary and secondary somatosensory areas (SI and SII), and the primary motor cortex (MI) - organization of pontine neurons projecting to somatosensory representations in the posterior cerebellum The data are also included in the FACCS application, a relational database application with embedded analytical tools, available via the The Rodent Brain Workbench (www.rbwb.org). Sponsors: NeSys Research and Database development is supported by The Research Council of Norway, The European Community (grants QLRT-2000-02256 and QLG3-CT 1999-00763), The Norwegian Consortium for High Performance Computing, and The Jahre Foundation.
OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. OWW provides a place for labs, individuals, and groups to organize their own information and collaborate with others easily and efficiently. In the process, the hope is that OWW will not only lead to greater collaboration between member groups, but also provide a useful information portal to our colleagues, and ultimately the rest of the world. OWW''s approaches to achieve their goals: # Lower the technical barriers to sharing and dissemination of knowledge in biological research # Build a community of researchers in biology and biological engineering that values, practices, and innovates the open sharing of information # Integrate OpenWetWare into existing and future reward structures in research
H-Invitational Database: Protein-Protein Interaction Viewer
The PPI view displays H-InvDB human protein-protein interaction (PPI) information. It is constructed by assigning interaction data to H-InvDB proteins which were originally predicted from transcriptional products generated by the H-Invitational project. The PPI view is now providing 32,198 human PPIs comprised of 9,268 H-InvDB proteins. H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. Sponsors: This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program.
Salk Institute for Biological Studies: Jude Mitchells Neuron Exchange and Matlab Analysis
This resource contains to MATLAB code to make and show videos that can be acquired for free. Data for the movies came from a Macaque attention task. Data on this page came from the multiple-object tracking attention task in a Macaque: The monkeys fixated the white dot at the center of the computer monitor, and four striped stimuli appeared. Their eye position was monitored using an IR camera. The red cross shows where the eyes were pointing throughout each trial. The circle shows the location of the receptive field of the neuron under study during the recording. At the beginning of each trial, either one or two of the stimuli were highlighted, indicating to the monkey that they were the targets of attention. The stimuli then moved to new locations and paused, with one stimulus in the receptive field. After a brief pause, they moved to new locations and the fixation point disappeared. The monkey was rewarded with juice if it then looked at the cued targets. Attention Dask Demo (Avi File) contains Matlab code to make and show movies. Publication from this Dataset: * Differential attention-dependent response modulation across cell classes in macaque visual area V4. JF Mitchell, KA Sundberg, JH Reynolds. Neuron, 2007, 55. 131-141. * Supplemental Material, Neuron, 2007, 55. 131-141. :A Subset of data can be downloaded with analysis routines (easiest to download whole set with full subdirectory structure). Additionally, neuron data files can also be downloaded. :* Routines for Fano Factor, Autocorrelation, and Power Spectra (poster above): :o Plots Spike Waveform and Tests if Significant Visual Response: basic_info.m :o Firing Rate and Fano Factor Analysis (Mitchell et. al, 2007): rate_fano_psth.m :* Routines for Spike-LFP Coherence: :o Spike-LFP Coherence with Rate Normalization (attempting Womelsdorf & Fries, Cosyne, 2008): rate_normalized_coherence.m Sponsors: This work was supported by a grant from the National Eye Institute (EY016161, J.F.M. and J.H.R.), a National Institutes of Health Training Fellowship (J.F.M.), and a National Science Foundation Graduate Research Fellowship (K.A.S.).
University of Sheffield; South Yorkshire; United Kingdom
Founded in 1905, the University of Sheffield is one of the UK''s leading Russell Group universities with an outstanding record in both teaching and research.
An algorithm for detecting chimeric sequences.
A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console.
An open source framework for systems biology connecting heterogeneous software applications written in diverse programming languages and running on different platforms-to communicate and use each others'' capabilities via a fast binary encoded-message system. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. Many biological modeling and simulation tools are a part of SBW, including JDesigner and Jarnac.
Caltech, The Beckman Institute: The Biological Network Modeling Center
The Beckman Institute BNMC brings together researchers from many disciplines at Caltech to address problems in the mechanistic modeling of coupled genomic, intercellular and intracellular processes. It represents an attempt to encourage closer interaction and collaboration between groups in Biology, Control and Dynamical Systems, and the Center for Advanced Computing Research. The focus of BNMC is biochemical phenomena occurring within and between cells, in particular the mechanistic modeling of molecular networks of all kinds (e.g., transcriptional, regulatory, metabolic, signal transduction, mechanical, etc.) with and without spatial variation and intercellular communication. BNMC is formed as a coordinated effort aimed at (1) applying existing capabilities to collaboratively solve biological modeling problems that arise in answering scientific questions in Caltech laboratories, (2) exploring a diversity of novel approaches in order to achieve fundamental advances necessary to address the classes of modeling problems biologists want to solve, and (3) organizing projects to better share human experience as well as common infrastructure to avoid duplication and maximize solution interoperability.
The CellML language is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models; CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). The CellML team is committed to providing freely available tools for creating, editing, and using CellML models. We provide information regarding tools we are developing internally and links to external projects developing tools which utilize the CellML format. Please let us know if you have an open source CellML tool looking for a home on the internet, as we are able to offer limited hosting services on cellml.org.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A hardware and software package with which a scientist could trace the structure of neurons and other neuroscientific features directly from tissue sections or from a stack of their images into a computer. Then it also could edit, merge, filter, display in 3D, and make realistic plots of the structures. The NTS also includes a substantial statistical package that provided many, now standardized, mathematical and statistical summaries that described each neuron and compared one population to another. Additionally, NTS also provided an embryonic electrotonic modeler that simulates and displayes the electrical functioning of a cell. The NTS uses a special purpose graphics display processor called the VDP3 whose output is presented on a very high resolution CRT. During tracing, the VDP3 presents a variable-diameter cursor and other information directly in the microscope and enables tracing at a high spatial resolution and with measurement of process diameters limited only by the microscope''s optics. Control of tracing is done with a 3D joystick that allows easy control of five input variables: X,Y,Z position, cursor diameter, and a numeric tag. Finally, superb 3D interactive displays of completed cells are provided on the VDP3.
It is an interdisciplinary research group dedicated to tackling the ethical, legal, policy and social implications of frontier technological developments in the neurosciences. Our objective is to align innovations in the brain sciences with societal, cultural and individual human values through high impact research, education and outreach. The Core''s major research projects are focused on high impact, high visibility areas including the use of drugs and devices for neuroenhancement, ethics in neurodegenerative disease and regenerative medicine research, international and cross-cultural challenges in brain research, neuroimaging in the private sector, and the ethics of personalized medicine, among others. Members of the Core also lead initiatives aside from their research projects. Sponsors: This Core is supported by the University of Brititsh Columbia.
University of Texas at San Antonio Laboratory of Professor Brenda Claiborne
USTA Laboratory of Professor Brenda Claiborne
The long-term goals of my research are to understand the relationship between neuronal structure and function, and to elucidate the factors that affect neuronal morphology and function over the lifespan of the mammal. Currently we are examining 1) the effects of synaptic activity on neuronal development; 2) the effects of estrogen on neuronal morphology and on learning and memory; and, 3) the effects of aging on neuronal structure and function. We have focused our efforts on single neurons in the hippocampal formation, a region that is critical for certain forms of learning and memory in rodents and humans. From the portal, you may click on a cell in your region of interest to see the complete database of cells from that region. You may also explore the Neuron Database: * Comparative Electrotonic Analysis of Three Classes of Rat Hippocampal Neurons. (Raw data available) * Quantitative, three-dimensional analysis of granule cell dendrites in the rat dentate gyrus. * Dendritic Growth and Regression in Rat Dentate Granule Cells During Late Postnatal Development.(Raw data available) * A light and electron microscopic analysis of the mossy fibers of the rat dentate gyrus.
Voxelation Map of Gene Expression in a Coronal Section of the Mouse Brain
Two-dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 cubic mm gene expression patterns in the brain obtained through voxelation. Voxelation employs high-throughput analysis of spatially registered voxels (cubes) to produce multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems.
International Consortium of Brain Mapping DTI-81 Atlas
A stereotaxic probabilistic white matter atlas that fuses DTI-based white matter information with an anatomical template (ICBM-152). This atlas is based on probabilistic tensor maps obtained from 81 normal subjects acquired under an initiative of the International Consortium of Brain Mapping (ICBM). The subjects were normal right-handed adults ranging from 18 to 59 years of age. A hand-segmented white matter parcellation map was created from this averaged map. This map can be used for automated white matter parcellation. The precision of the affine-based image normalization and automated parcellation was measured for a group of normal subjects using manually defined anatomical landmarks. The raw diffusion-weighted images (DWIs) were first co-registered to one of the least diffusion-weighted images and corrected for subject motion with 6-mode rigid transformation with Automated Image Registgration (AIR). The average of all DWIs (aDWI) was calculated and used for a DTI-based anatomic image. For anatomical images to drive the normalization process, aDWIs were used. These images were normalized to the template (ICBM-152) using a 12-mode affine or 4th order polynomial non-linear transformation of AIR. The transformation matrix was then applied to the calculated diffusion tensor field. In the white matter parcellation map (WMPM), deep white matter regions were manually segmented into various anatomic structures based on fiber orientation information.
Department of Psychiatry, Turner Laboratory
Turner Laboratory Developmental Neurobiology Research
Dr. Eric Turner''s laboratory studies the mechanisms underlying the development of the nervous system. The vertebrate brain is comprised of a tremendous variety of neurons, each class exhibiting a unique phenotype characterized by the expression of specific neurotransmitter receptors, ion channels, patterns of axonal growth, and synapse formation. The research we conduct focuses on the critical role transcription factors play in the specification of neuronal cell type during development. We are particularly interested in transcription factors of the homeodomain family that bind to DNA and in doing so activate or repress gene expression. One area of study is the role of POU-domain transciption factor Brn3a in axon growth and survival. The primary research areas are: * Neuronal cell fate determination: The expression of regulatory genes is manipulated in living chick embryos using microsurgery and electroporation and the effects on neural marker genes studied. * Molecular mechanisms of gene regulation: Target DNA binding sites of neural transcription factors are biochemically characterized and findings coordinated with sequence data from the mouse and human genomes. * Targeted misexpression of regulatory genes: Transgenic and knockout mouse technology is used to misexpress genes of interest, and the effects on neural marker genes, axonal growth, and cell survival studied. * Global analysis of neural gene expression: Micro-arrays (GeneChips) are employed in conjunction with other areas of study to understand the coordinated regulation of gene expression in the nervous system. Dr. Turner is a member of the University of California, San Diego''s Graduate Program in Neuroscience and Biomedical Sciences Program and accepts students from these two programs. Interesting rotation projects are available using methods ranging from biochemistry and molecular biology to embryology. Additionally, Dr. Turner is also the Director of this NIMH-funded training program for research-oriented psychiatrists, psychologists, and basic neuroscientists working in areas relevant to psychiatry. Typically Fellows spend two years in the program, during which they develop a research project under the close supervision of one of the highly productive members of the UCSD Department of Psychiatry, or another investigator in the La Jolla (UCSD/Salk/Scripps) research community.
The Institute for Neural Computation (INC) is an organized research unit of the University of California at San Diego with 44 members representing 14 research disciplines, devoted to the research and development of a new generation of massively parallel computers through a coherent and cohesive plan of research spanning the areas of neuroscience, visual science, cognitive science, artificial intelligence, mathematics, economics and social science, and computer engineering. INC is a leading center in the field of neural computation, initiating joint research projects, providing special facilities for carrying out research, coordinating the training of young investigators, and offering special activities through its Industrial Affiliates Program. The INC also supports training programs for graduate students and postdoctoral fellows in Cognitive Neuroscience (NIH) and Computational Neurobiology (NFS).
National Center for Microscopy and Imaging Research: SAGE
NCMIR Scalable Adaptive Graphical Environment
A software resource which supports high-resolution, scalable, and collaborative scientific visual environments. Scalable Adaptive Graphical Environment is a graphics streaming architecture that allows users to treat high-resolution distributed displays as one contiguous desktop where users can move or resize application windows. It is designed specifically for Windows 32-bit environments and is network centric.
CHARTER - CNS HIV Antiretroviral Therapy Effects Research
CNS HIV Anti-Retroviral Therapy Effects Research
THIS RESOURCE IS NO LONGER IN SERVICE, documented April 14, 2017. Clinical trial designed to determine how central and peripheral nervous system complications of HIV are affected by different histories and regimens of antiretroviral therapy (ART). CHARTER is able to provide fluid specimens, pilot data, and analysis and interpretation expertise for qualified investigators.
An interdisciplinary group of scientists and clinicians who study the human brain using a variety of imaging, recording, and computational techniques. Their primary goal is to bridge non-invasive imaging technologies to the underlying neurophysiology of brain neuronal circuits for a better understanding of healthy human brain function, and mechanisms of disruption of this function in diseases such as Alzheimer's, epilepsy and stroke. The other goal of the MMIL is to develop and apply advanced imaging techniques to understanding the human brain and its disorders. In order to ground these methodological developments in their underlying neurobiology, invasive studies in humans and animals involving optical and micro physiological measures are also performed. These methodologies are applied to understanding normal function in sleep, memory and language, development and aging, and diseases such as dementia, epilepsy and autism.
Gladstone Institute of Neurological Disease
GIND provides a highly interactive academic environment and state-of-the-art research facilities that are ideal for training in neuroscience and biomedical research. GIND Investigators hold university appointments at UCSF and participate in educational activities, including the teaching and training of graduate students and postdoctoral fellows. Additionally, GIND is actively engaged in efforts to translate scientific discoveries into better treatments for major diseases of the nervous system. Sponsors: Support for GIND comes from the University of California at San Francisco.
Know Stroke. Know the Signs. Act in Time.
Campaign to help educate the public about the symptoms of stroke and the importance of getting to the hospital quickly, with a wide range of materials about stroke prevention, treatment, and rehabilitation available through the site. The campaign includes outreach to consumers and health care professionals using mass media, grassroots outreach, partnerships, and community education.
Center for Premature Infant Health and Developement
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. CPIHD is a novel Center that blends research and outreach targeting preterm infants and their families. Faculty of the Center work together to find solutions to the complex biomedical, psychological, and social problems associated with preterm delivery. The Center for Premature Infant Health and Development goals are to: discover the causes of health and developmental problems encountered by preterm infants; develop and disseminate optimal family-centered prevention, assessment, and intervention strategies to improve long-term outcomes for preterm infants and families; and eliminate racial disparities in adverse birth outcomes in our community. The missions of CPIHD are: conducting interdisciplinary, translational, and family-centered research; educating the next generation of researchers and practitioners serving preterm infants and their families; and providing community-based outreach to serve families of, and health care workers caring for, preterm infants.
University of Washington Integrated Brain Project
The UW Integrated Brain Project is one project within the national Human Brain Project, a national multi-agency effort to develop informatics tools for managing the exploding amount of information that is accumulating about the human brain. The objective of the UW Integrated Brain Project effort is to organize and integrate distributed functional information about the brain around the structural information framework that is the long term goal of our work. This application therefore extends the utility of the Digital Anatomist Project by using it to organize non-structural information. The initial driving neuroscience problem that is being addressed is the management, visualization and analysis of cortical language mapping data. In recent years, advances in imaging technology such as PET and functional MRI have allowed researchers to observe areas of the cortex that are activated when the subject performs language tasks. These advances have greatly accelerated the amount of data available about human language, but have also emphasized the need to organize and integrate the sometimes contradictory sources of data, in order to develop theories about language organization. The hypothesis is that neuroanatomy is the common substrate on which the diverse kinds of data can be integrated. A result of the work done by this project is a set of software tools for generating a 3-D reconstruction of the patient''s own brain from MRI, for mapping functional data to this reconstruction, for normalizing individual anatomy by warping to a canonical brain atlas and by annotating data with terms from an anatomy ontology, for managing individual lab data in local laboratory information systems, for integrating and querying data across separate data management systems, and for visualizing the integrated results. Sponsors: This Human Brain Project research is funded jointly by the National Institute on Deafness and Other Communication Disorders, the National Institute of Mental Health, and the National Institute on Aging.
Psychology Post-doctoral Training Program, US Department of Veterans affairs, Salt Lake City, UT
This web site is an overview of the post-doctoral psychology training program at the VA Salt Lake City Health Care System (VA SLC HCS). Its purpose is to help prospective psychology post-docs learn about the training and professional growth opportunities that are available. The VA Salt Lake City Health Care System postdoctoral fellowship is a full-time, 12-month continuous appointment focused on specialty training in the evaluation and treatment of veterans with Post-Traumatic Stress Disorder. Postdoctoral Fellows will be active members of two interdisciplinary treatment teams: - The PTSD Clinical Team through the Mental Health Department - The Polytrauma Team through the Physical Medicine and Rehabilitation Department. Fellows will also provide community outreach to returning veterans from Afghanistan and Iraq. Especially relevant to the VA Mental Health Strategic Plan, psychological services are provided within the complementary areas of emotional trauma (e.g., military combat, military sexual trauma), physical trauma (e.g., TBI, orthopedic injuries), substance abuse, and couples/family discord, primarily within the OEF/OIF veteran population. Sponsors: This work is funded by the US Department of Veterans Affairs, Salt Lake City.
Mid-Atlantic (VISN 6) Mental Illness Research, Education and Clinical Center
The VISN 6 MIRECC is organized as a translational medicine multi-site center focused on post deployment mental health issues. The overarching goals are improving clinical assessment and treatment and development of novel interventions through basic and clinical research. This MIRECC aims: (1) To determine whether early intervention in post-deployment mental health is effective in forestalling the development or decreasing the severity of post-deployment mental illness, (2) To determine what neuroimaging, genetic, neurocognitive, or other characteristics predict the development of post-deployment mental illness, and (3) To assess the longitudinal course of post-deployment mental illness.
A low-level specification for describing mathematics as a basis for machine to machine communication, developed by the W3C.
Genomic Object Net (GON) is a software platform for biological pathway modeling and simulation, based on two architectures hybrid functional Petri net (HFPN) and XML technology. This website provides pathway models of HFPN as well as the detailed explanation about these pathways.
BraInSitu: A homepage for molecular neuroanatomy
Database of detailed protocols for single and double in situ hybridization (ISH) method, probes used by Yamamori lab and others useful for studies of brain, and many photos of mammalian (mostly mouse and monkey) brains stained with various gene probes. Also includes a brain atlas of gene expression. Currently, the atlas comprises a series of un-annotated images showing the localization of a particular probe or molecule, e.g., AChE.
WE MOVE: Worldwide Education and Awareness for Movement Disorders
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 12, 2016. A not-for-profit organization that utilizes creativity, innovation, and collaborative approaches to improve awareness, diagnosis, and management of movement disorders among people living with these conditions and the professionals who care for them. WE MOVE's mission is to facilitate the communication of emerging clinical advances and therapeutic approaches to the management and treatment of movement disorders. WE MOVE develops up-to-date training programs and comprehensive, interactive teaching materials to assist professionals in deepening their understanding of neurologic movement disorders and their associated pathophysiology, etiology, differential diagnosis and interventions. It also provides research news information on the latest developments in movement disorder research, comprehensive listings of other existing supportive nonprofit organizations dedicated to helping those with movement disorders, and information on movement disorder-related events. For those unfamiliar with different movement disorders, a glossary of terms is provided. WE MOVE is based in New York, New York. :NIF thanks the Parkinson's Disease Foundation for their referral of this resource to us., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain)
BrainSpan - Atlas of the Developing Human Brain
BrainSpan: Atlas of the Developing Human Brain
NIMH Transcriptional Atlas of Human Brain Development
Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. Consists of RNA sequencing and exon microarray data profiling up to sixteen cortical and subcortical structures across full course of human brain development, high resolution neuroanatomical transcriptional profiles of about 300 distinct structures spanning entire brain for four midgestional prenatal specimens, in situ hybridization image data covering selected genes and brain regions in developing and adult human brain, reference atlas in full color with high resolution anatomic reference atlases of prenatal (two stages) and adult human brain along with supporting histology, magnetic resonance imaging (MRI) and diffusion weighted imaging (DWI) data.
University of Pittsburgh Alzheimer Disease Research Center
University of Pittsburgh Alzheimer's Disease Research Center
A research center associated with the University of Pittsburgh that specializes in the diagnosis of Alzheimer's disease and related disorders. The overall objective of the ADRC is to study the pathophysiology of Alzheimer's disease, with the aim of improving the reliability of diagnosis of Alzheimer's and developing effective treatment strategies. Current research foci emphasize neuropsychiatry and neuropsychology, molecular genetics and epidemiology, basic neuroscience, and structural and functional imaging that aid in the diagnosis and treatment of Alzheimer's disease. Specific services at the ADRC include: comprehensive diagnostic evaluation of patients with suspected Alzheimer's disease and other forms of dementia; evaluation of memory, language, judgment, and other cognitive abilities; and education and counseling for patients and families.
NIMH Interdisciplinary Behavioral Science Center
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. A framework for understanding human cognition, grounded in principles specifying the character of human cognitive processes, and constrained by properties, of the underlying neural mechanisms. The Center will exploit this framework to guide formulation of explicit, testable models of normal and disordered cognition, including models of the development of cognitive functions and of their disintegration as a result of brain damage or disease. This site is intended as a public service and as a focal point for exchange of ideas among the participants in the Interdisciplinary Behavioral Science Center (IBSC). Public areas of the site provide information about the Center as a whole and about the various projects in the Center, as well as web-accessible documents and tools that we are making available as a public service. A fundamental tenet is that cognition is an emergent phenomenon, arising from the interactions of cooperating processing elements organized into specialized populations. One aim of the center will be to investigate the utility of explicit models that are formulated in terms of this approach, addressing many aspects of cognition including semantic knowledge, language processing, cognitive control, perception, learning and memory. A second aim will also investigate the principles that are embodied in the models, including principles of learning, processing and representation. Learning will be a central focus, since it plays a crucial role in cognitive development, acquisition of skills, formation of memories, and remediation of cognitive functions. A third aim of the Center will be to incorporate constraints from neuroscience. Findings from neuroscience will guide the specification of the principles and the formulation of domain-specific details of particular models, and will provide target experimental observations against which to assess the adequacy of the models. In addition, the Center will make use of neurophysiological methods in animals and functional brain imaging in humans to test predictions and generate additional data needed to constrain and inform model development. The Center will provide training funds for interdisciplinary research fellowships, to train junior scientists in the convergent use of behavioral, computational, and neuroscience methodologies. The outcome of the Centers efforts will be a fuller characterization of the nature of human cognitive processes, a clearer formulation of the underlying principles, and a more complete understanding of normal and disordered functions across many domains of cognition. This Center includes eight projects dedicated to various aspects of cognition and various general issues that arise in the effort to build explicit models that capture different aspects of cognition, and also includes an administrative core to help foster integration and provide computing resources. * Project 1: Functional and Neural Organization of Semantic Memory * Project 2: Interactive Processes in Language: Lexical Processing * Project 3: Interactive Processes in Language: Sentence Processing * Project 4: Mechanisms of Cognitive Control * Project 5: Interactive Processes in Perception: Neurophysiology of Figure-Ground Organization * Project 6: Basic Mechanisms and Cooperating Systems in Learning Memory * Project 7: Age and Experience Dependent Processes in Learning * Project 8: Theoretical Foundations * Core: Integration, Computational Resources, and Administration
University of Southampton; Southampton; United Kingdom
HHsim: Graphical Hodgkin-Huxley Simulator
A graphical simulation of a section of excitable neuronal membrane using the Hodgkin-Huxley equations. It provides full access to the Hodgkin-Huxley parameters, membrane parameters, stimulus parameters, and ion concentrations. In contrast with NEURON or GENESIS, which are vastly more sophisticated research tools, HHsim is simple educational software designed specifically for graduate or undergraduate neurophysiology courses. The user interface can be mastered in a couple of minutes and provides many ways for the student to experiment. Also included are sample exercises that use the simulator. HHsim is available as a Windows, Mac, or Unix executable file that does not require a Matlab license. Source code is included. It is also available in source-only form if you have Matlab R2007a or later. The latest release of HHsim is version 3.1, released February 16, 2008.
Connectionist Models of Cognitive, Affective, Brain, and Behavioral Disorders
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site aims to provide a discussion and source list for connectionist and neural network models of disorders associated with mental or brain conditions. Recent connectionist and neural network models of behavior, information processing patterns, and brain activity present in people with cognitive, affective, brain, and behavioral disorders are reviewed on this web site. Ways that assumptions regarding normal and disordered behavior may be represented in connectionist models are discussed for features of various disorders. Similarities and differences between the models and criteria for their evaluation are presented, and suggestions for inclusion of information which may help to make these models more directly comparable in the future are considered. References to Connectionist Models of Cognitive, Affective, Brain, and Behavioral Disorders include: General Neural Network Information Reviews, General Introductions, and Calls for More Connectionist Models of Mental Disorders Models of Psychopathologies and Psychiatric Disorders Models of Cognitive, Affective, Brain, and Behavioral Disorders Not Associated with Psychopathology Additionally, Web Sites for Neural Network Modelers of Disorder are provided.
This website allows visitors to search for genes of interest based on their spatial expression patterns in the Postnatal Day 7 mouse brain. Geneatlas provides two searching tools: A graphical interface for customized spatial queries; A textual interface for querying annotated structures. Geneatlas is the product of a collaboration between researchers at Baylor College of Medicine, Rice University, and University of Houston.
Caltech micro MRI Atlas of Mouse Development
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on October, 01, 2019. 3D digital atlas of normal mouse development constructed from magnetic resonance image data. The download is a zipped file containing the six atlases Theiler Stages (ts) 13, 21,23, 24, 25 and 26 and MRI data for an unlabeled ts19 embryo. To view the atlases, download and install MBAT from: http://mbat.loni.ucla.edu Specimens were prepared in aqueous, isotonic solutions to avoid tissue shrinkage. Limited specimen handling minimized physical perturbation of the embryos to ensure accurate geometric representations of developing mouse anatomy. Currently, the atlas contains orthogonal sections through MRI volumes, three stages of embryos that have annotated anatomy, photographs of several stages of development, lineage trees for annotated embryos and a gallery of images and movies derived from the annotations. Anatomical annotations can be viewed by selecting a transverse section and selecting a pixel on the displayed slice.
Mouse Gene Expression at the BC Cancer Agency
A portal to the Mouse Atlas of Gene Expression Project and Dissecting Gene Expression Networks in Mammalian Organogenesis Project. This Atlas will define the normal state for many tissues by determining, in a comprehensive and quantitative fashion, the number and identity of genes expressed throughout development. The resource will be comprehensive, quantitative, and publicly accessible, containing data on essentially all genes expressed throughout select stages of mouse development. Serial Analysis of Gene Expression (SAGE) is the gene expression methodology of choice for this work. Unlike expressed sequence tags (ESTs) and gene chip data, SAGE data are independent of prior gene discovery and are quantitative. Furthermore, SAGE data are digital, easily exchanged between laboratories for comparison and can be added to by scientists for years to come. Thus, this Atlas will include a data structure and data curation strategy that will facilitate the ongoing collection of gene expression data, even after the completion of this project. The Mouse Atlas project compromises 202 SAGE Libraries from 198 tissues. The list of libraries is available in a number of different groupings, including groups of libraries taken from specific tissue locations and libraries taken from specific developmental stages. Furthermore, this atlas will assemble gene expression profiles for a few focused experiments that will test hypotheses related to the techniques employed, tumor models and models of abnormal development. This will test the resource and provide quality control, validation and demonstrate applicability. Additionally, The Mammalian Organogenesis - Regulation by Gene Expression Networks (MORGEN) project will provide a complete, permanent, and accurate picture of mouse gene expression in the heart (atrioventricular canal and outflow tract), pancreas, and liver; new techniques to understand the interplay of proteins governing the expression of genes key to the development of these organ systems; and the identification of the master regulatory switches that control development of the tissues.
Resells antibodies incorporating quality control metrics for antibody reagents. Antibodies-online is based in Germany and provides valuable content in terms of information about antibodies, recent research news and specific news about current antibodies. All these informations are generated by antibodies-online staff or external databases like Pubmed, EMBL Harvester or from Google Scholar.
University of Southern California; Los Angeles; USA
American private research university in Los Angeles, California. Founded in 1880, it is the oldest private research university in California. USC has historically educated a large number of the nation's business leaders and professionals.
Effects of CoEnzyme Q10 in Early Parkinson's Disease
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This site has a dataset from the QE2 Study: Effects of CoEnzyme Q10 in Early Parkinson's Disease, was an NINDS funded pilot study of 80 subjects with early untreated Parkinson's disease (PD). The PI was Clifford Shults, MD at UCSD. It was a randomized, double-blind, parallel group comparison of three doses of coenzyme Q10 (CoQ10) (300, 600 and 1200 mg/day) versus placebo in patients and do not yet require treatment with levodopa. The QE2 Study: Effects of CoEnzyme Q10 in Early Parkinson's Disease, was an NINDS funded pilot study of 80 subjects with early untreated Parkinson's disease (PD). The PI was Clifford Shults, MD at UCSD. It was a randomized, double-blind, parallel group comparison of three doses of coenzyme Q10 (300, 600 and 1200 mg/day) versus placebo in patients and do not yet require treatment with levodopa or any other antiparkinsonian medication. Enrollment period May 1999 Feb. 2000; study participation ended June 2001.
A patient led charity that funds research which will have an impact on the lives of people with Parkinson's, with the hope of an eventual cure for the condition. The Cure Parkinson's Trust has the clear goal of finding a cure for Parkinson's disease by investing in under resourced and underfunded projects that offer a possible cure in the future. This trust's primary role is identifying, funding and evaluating research projects, as well as hosting scientific forums to bring together relevant scientists within the field to discuss key areas of research and technology. Cure Parkinson's provides researchers with information on current research, research events, and the ability to apply for grants through the Cure Parkinson's Trust.
Parkinsons Center at Dartmouth-Hitchcock Medical Center
A Parkinson's disease portal that provides information, materials, and programs to help Parkinson's patients and their care partners manage their everyday lives. The Center aims to enhance the quality of life for people with Parkinson's and their care partners and increase public awareness and education on Parkinson's disease. It provides resources for regional support group meetings, referrals to regional physicians, allied health professionals, home care agencies, and other resources, and information on current therapies and research programa. It also provides materials such as informational pamphlets and booklets, videos, DVDs, newsletters, and educational materials.
Laboratory of Molecular Neuroscience, University of Oslo
A laboratory that investigates the molecular mechanisms involved in the development of acute and chronic neurodegenerative disease, with a focus on the role of glutamate excitotoxicity. It aims at unraveling the molecular basis for cell death and edema development in stroke, and explores the pathophysiology of Alzheimer's disease and temporal lobe epilepsy. The main objective of the LMN is to advance understanding of the role of glutamate, as a transmitter substance in the normal brain and as a mediator of excitotoxicity in pathological conditions such as stroke. To this end the LMN employs several vital and nonvital imaging techniques. Model systems includes organotypic slice cultures and transgenic animals. An important focus of the LMN is to explore the role of DNA damage and repair in the pathogenesis of neurodegenerative disease. LMN is also engaged in research on molecular mechanism underlying brain edema, epilepsy, and Alzheimer's disease.
Michael Stern Parkinsons Research Foundation
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 18th, 2016. A foundation that was founded in 2001, and sponsors academic centers throughout the US. The MIchael Stern Parkinson's Research Foundation focuses its efforts mainly on finding the causes of the disease, finding effective treatments, and discovering a cure for the disease. The foundation is notably looking into dopamine and its effects on neural connections, as well its possibility to be used for treatment. Dr. Greengard has assembled a close knit group of more than 25 outstanding scientists who are focused on translating the fundamental understandings about the dopamine system into new treatments for Parkinson's. The core team of researchers is based at the Stern Foundation laboratory on the campus of The Rockefeller University interacts continually with collaborators from the United Kingdom, France, Sweden, Italy, Japan and Korea. This global presence ensures that no promising research lead is overlooked, and that progress can be made on multiple fronts simultaneously. As the Foundation grew it was able to expand its support for critical neurological research to two other institutions, Harvard University's McLean Hospital, where we support the research of Dr. Ole Isacson whose research lab, The Stern Center for Neuroregeneration Research is using gene therapy to protect the most vulnerable neurons in PD models; and the Institute for Neurodegenerative Disorders, where Yale Professors Dr. Ken Marek and Dr. John Seibyl are developing novel tools for early detection and monitoring of Parkinson's disease by studying physiologic, biochemical and neuroimaging biomarkers for non-dominergic manifestations of Parkinsonism. :NIF thanks the Parkinson's Disease Foundation, http://www.pdf.org for their referral of this resource to us.
Parkinson's Disease Research, Education and Clinical Center
An organization involved in the clinical research of Parkinson's disease. They are involved in a variety of clinical research including: deep brain stimulation (DBS), drug therapies, gait and falling issues, depression and other psychiatric problems, non-motor fluctuations, basic science and olfactory function during Parkinson's disease.
Database of Domain Interactions and Bindings
DDIB collects information of domain-domain interactions and domain interactions with biological molecules such as RNA, DNA, peptides, inorganic ions, phospholipids and cholesterols. Most of the data were extracted automatically from publication abstracts in MEDLINE, and the rest were collected from other public databases, research laboratories and individual scientists. In addition, DDIB includes many putative domain-domain interactions inferred from documented protein-protein interactions. To provide comprehensive knowledge of a domain, DDIB also integrates relevant information from PFAM, InterPro, GO and KEGG databases.
A graphic, interactive program to map quantitative trait loci by regression methods; MAP MANAGER CLASSIC enhanced by quantitative trait mapping. (entry from Genetic Analysis Software)
American Parkinson's Disease Association National Young Onset Center
An organization that is centered around the education of younger Parkinson's disease patients as well as their families, friends and healthcare professionals. They primarily provide educational and support programs and services that are designed to help younger Parkinson's patients manage the disease and maintain a healthy lifestyle. The center provides information about treatment options, clinical trials, support groups, person to person chats, local chapters,regional referral information, and Parkinson's related events.
Minimaps are designed to supplement the Metabolic Pathways Charts by enlarging selected major individual pathways so as to illustrate additional aspects of metabolism such as Membranes, Compartmentation, Organs, Organelles, Shuttles and Regulation. The selection is designed to stimulate the exploration of the pathways and make metabolism more meaningful.
A statistical method for interpreting variations in protein sequence (e.g. coding SNPs in the population, SNVs in cancer genomes) in the context of protein post-translational signaling modifications.
A database of imaging probes useful for preclinical and clinical studies. The National Institute of Mental Health (NIMH) and the Society for Non-Invasive Imaging in Drug Development (SNIDD) are in the process of creating a centralized, searchable PET, SPECT, and MRI tracer database as a resource for the scientific community. The goal of this effort is to promote the use of imaging probes in preclinical and clinical research and in drug discovery to accelerate the identification and validation of novel targets for therapeutic intervention in human diseases, especially those with central nervous system components. NIMH will maintain the tracer database as part of the Psychoactive Drug Screening Program (PDSP). The database will contain records for each radiotracer with relevant information such as target, research uses, pharmacology, pharmacokinetics, synthesis protocols, toxicology and safety data, dosimetry, other clinical data, IND info, permission to cross-reference pharmacology, toxicology, or safety data in a drug master file (if an IND exists), contact information, patent, etc. with appropriate safeguards in place to protect the intellectual property of proprietary compounds.
NEI (neuro-endocrine-immune) Network Database
Version 1.0 database for neuro-endocrine-immune (dbNEI) is a web-based knowledge resource specific for the NEI systems. It provides a knowledge environment for understanding the main regulatory systems of NEI in a molecular level. dbNEI provides a knowledge environment for understanding the main regulatory systems of NEI in a molecular level. dbNEI collects 1,058 NEI related signal molecules, their 940 interactions and 72 affiliated tissues from the Cell Signaling Networks database and manually selects 982 NEI papers from PubMed. NEI related information, such as signal transductions, regulations and control subunits, are integrated. Especially, dbNEI represents as graphic visualization, by which control subunits can be automatically obtained according to the inquiring issues. Version 2.0: We updated the database in four aspects. 1. Recruiting new NEI genes and compounds. 2. Adding KEGG,HPRD,Transcription factor and microRNA target relations. 3. Collecting drug-gene and disease-gene relation. 4. Building multi-layer network for drug-NEI-disease.
Database of oligomerization domains from lambda experiments
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Doodle is a database that was developed to store and distribute information about the protein oligomerization domains that are encoded by various genomes. The protein oligomerization domains described here were found using the lambda repressor fusion system. Doodle uses a schema that is based on EnsEMBL, while also utilizing bioperl modules to both store and retrieve data. The frontend was developed entirely in perl, while the backend utilizes MySQL. GMOD was used to develop the genomic view.
Software application that map QTLs in F-2 intercross in model organisms (entry from Genetic Analysis Software)
Arabidopsis enzymes and biochemical pathways database
Curated species-specific database present at the Plant Metabolic Network. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.
Athena is a web-based application that warehouses disparate datatypes related to the control of gene expression. Athena provides several features to enable exploration of the regulatory mechanisms of Arabidopsis gene control. The first main tool we provide is visualization of promoter domains of selected genes. Database crossreference for these transcription factors is provided as well as a statistical test for enrichment of binding activity within the set of selected promoters. The data mining tools in Athena allow for selection of sets of genes based on two different factors. -Genes can be select by specifying a set of binding factors whose putative sites must be present within all of those genes'' promoter regions. -Alternatively, genes can be selected using Gene Ontology annotations. Both GO (Gene Ontology) Slim terms and Gene Ontology terms are available. One can select a set of genes by either choosing a union of the genes annotated by a selected set of Slim terms or Gene Ontology terms. The selected gene''s putative binding factors are listed, including enrichment data. Furthermore, enriched presence of Gene Ontology terms is given. The analysis suite provides both enhanced data mining tools for selecting genes as well as several data displays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A database of biochemical pathways that provides access to metabolic transformations and cellular regulations derived from the Roche Applied Science Biochemical Pathways wall chart.
University of Sherbrooke Hospital Centre; Quebec; Canada
Centre hospitalier universitaire de Sherbrooke
University of Sherbrooke Hospital Center
University of Sherbrooke Hospital Centre
Public healthcare network in Sherbrooke, Quebec, Canada, affiliated with the Université de Sherbrooke Faculty of Medecine.
Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource.
A database for facilitating the analysis of Drug Binding Competitiveness. It contains information about Computed Ligand-Receptor Interaction Energy and other attributes such as energy components; ligand classification, functions and properties. Ligand structure is also included. The database now contains 67,184 entries, in which there are 5,978 distinctive ligands and 2,258 distinctive receptors.
Human Cancer Protein Interaction Network
The Human Cancer Pathway Protein Interaction Network (HCPIN) was constructed as a step toward better integrating protein three-dimensional (3D) structural information in cancer systems biology. It was constructed by analysis of several classical cancer-associated signaling pathways and their physical protein-protein interactions. The HCPIN Website provides a comprehensive description of this biomedically important multipathway network together with experimental and homology models of HCPIN proteins useful for cancer biology research.
A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base .
Interaction Reference Index Web Interface
iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from nine different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. Integration is achieved through a rigorously documented procedure for mapping protein IDs across databases, enabling systematic backtracking of the links used to establish the identity of the interaction partners. The iRefWeb interface groups interaction records from the different databases into a single non-redundant view. In particular iRefWeb facilitates comparing interaction records as seen by the various source databases relative to the PubMeds they were annotated from. iRefWeb is one of several views of the iRefIndex resource. Data are also available in a tab-delimited plain-text format (PSI-MITAB) as well as planned releases of a PSI-XML formatted version and a Cytoscape plugin. Further details about the iRefIndex project as well as data downloads are available from here . The method used to build iRefIndex is described in a recent publication.
Intergrated Transcription Factor Platform
ITFP is an integrated transcription factor (TF) platform, which included abundant TFs and targets message of mammalian. Support vector machine (SVM) algorithm combined with error-correcting output coding (ECOC) algorithm was utilized to identify and classify transcription factor from protein sequence of Human, Mouse and Rat. For transcription factor targets, a reverse engineering method named ARACNE was used to derive potential interaction pairs between transcription factor and downstream regulated gene from Human, Mouse and Rat gene expression profile data. Detailed information of gene expression profile data can be found in help page. Moreover, all data provided by the platform is free for non-commercial users and can be downloaded through links on help page.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. LINNEA Pathways is a user-friendly comprehensive online resource for gene- or protein-based scientific research. It is based on a total of 248 signaling and metabolic human biological pathway maps created for Invitrogen by GeneGo. The current version of iPath features 225 maps displaying human regulatory and metabolic pathways established in experimental literature produced by MetaCore from GeneGo, Inc. The map objects (proteins, genes, EC functions, and compounds) are connected via metabolic transformations and physical protein interactions, which were assembled by the GeneGo team of experienced annotators, geneticists, and biochemists. The pathways are organized in a vertical fashion following the general signaling path from signaling molecules and membrane receptors, via signal transduction cascades, to transcription factors and their gene targets. Following the natural organization of cellular machinery with highly interconnected pathways and modules, many maps are linked together via hyperlinked box symbols. Such linkage allows the reconstruction of a big picture view of human cell biology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
This database currently holds E-MAP scores (individual interactions and correlation coefficients) for budding yeast genes involved in the early secretory pathway and chromosome function (including DNA damage and repair, transcriptional control, chromosome segregation and telomere regulation). E-MAPs (Epistatic Mini Array Profiles) are formed by creating and quantifying high-density genetic interaction maps. With this method, observed double mutant colony sizes are compared to those that would be expected from a distribution of typical double mutant colonies of each strain. Each interaction is assigned a score, which indicates the magnitude of the difference from the expected value and the certainty of the score. Negative (or aggravating) scores (< -2.5) correspond to synthetic sick/lethal interactions while positive (or alleviating) scores (> +2.5) corresponds to epistatic or suppressor interactions.
An algorithm that generates lists of genes associated with a gene or one or more disorders. The algorithm can be used in high-throughput screening experiments, can create disease-specific micro-arrays, and can sort the results of gene profiling data. Based on the co-citations of all Medline records, MedGene can retrieve the following relationships: 1. A list of human genes associated with a particular human disease in ranking order 2. A list of human genes associated with multiple human diseases in ranking order 3. A list of human diseases associated with a particular human gene in ranking order 4. A list of human genes associated with a particular human gene in ranking order 5. The sorted gene list from other disease related high-throughput experiments, such as micro-array 6. The sorted gene list from other gene related high-throughput experiments, such as micro-array
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2013. Resources for teaching biochemistry, including videos, animations and graphics. NetBiochem is intended to be a complete Medical Biochemistry center which can be accessed over a computer network. All of NetBiochem, including text, animations and graphics, can be captured to a local hard drive. There a user can modify it in any way they please. They can run the modified version locally for their own purposes as long as they do not charge anyone any fee for the use of the material. Further, one can use the animations and graphics to illustrate your lectures or other local presentations.
MetNet database contains information on networks of metabolic and regulatory and interactions in Arabidopsis. This information is based on input from biologists in their area of expertise. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another. Other fields describing the interactions are subcellular location, confidence, directionality, references, evidence, and synonyms. Data on entities (DNA, RNA, polypeptides, protein complexes, metabolites) are derived from web databases (gene related databases: TAIR, GO, MapMan/GabiPD; protein related databases: PPDB, AMPDB, AtNoPDB, AraPerox, PLprot, BRENDA; metabolite related databases: ChEBI, PubChem, KEGG, NCI compound library, NIST MS library), in some cases with additional annotation by experts. Network information from MetNetDB can be converted to an XML file by XML Builder. From this XML file, it can be transferred to exploRase, which uses the network in conjunction with statistical analysis of expression data; to Cytoscape/FCM, which finds cycles and pathways in the network, and visualizes and models it in combination with expression data; and to MetNetVR, where the network can be visualized in 3D.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. An integrated software suite for functional analysis of experimental data. The scope of data types includes microarray and SAGE gene expression, SNPs and CGH arrays, proteomics, metabolomics, pathway analysis, Y2H and other custom interactions. MetaCore is based on a proprietary manually curated database of human protein-protein, protein-DNA and protein compound interactions, metabolic and signaling pathways and the effects of bioactive molecules in gene expression.
NASCArrays: The Nottingham Arabidopsis Stock Centre Arrays
NASCArrays is the Nottingham Arabidopsis Stock Centre''s microarray database. Currently most of the data is for Arabidopsis thaliana experiments run by the NASC Affymetrix Facility. There are also experiments from other species, and experiments run by other centres too. NASCArrays is an Affymetrix microarray database. It contains free Affymetrix microarray data, and also features a series of tools allowing you to query that data in powerful ways. Most of the data currently comes from NASC''s Affymetrix Service. It also includes data from other sources, notably the AtGenExpress project. They currently distribute over 30,000 tubes of seed a year. There are currently the following data mining tools available. All of these tools allow you to type in a gene(s) of interest, and identify experiments or slides that you might be interested in: -Spot History: This tool allows you to see the pattern of gene expression over all slides in the database. Easily identify slides (and therefore experimental treatments) where genes are highly, lowly, or unusually expressed -Two gene scatter plot: This tool allows you to see the pattern of gene expression over all slides for two genes as a scatter plot. If you are interested in two genes, you can find out if they act in tandem, and highlight slides (and therefore experimental conditions) where these two genes behave in an unusual manner. -Gene Swinger: If you have a gene of interest, this tool will show you which experiment the gene expression varied most -Bulk Gene Download: This tool allows you to download the expression of a list of genes over all experiments. You can get all genes over all experiments (the entire database!) from the Super Bulk Gene Download Sponsors: This is a BBSRC funded consortium to provide services to the Arabidopsis community.
A systems biology tool for simulation of kinetic models from a curated model database. JWS Online is both a repository of curated biochemical pathway models and a simulation tool for these models. Users are able to view the models in the database, select a particular model, alter its parameters and perform a simulation on it. JWS Online aims to provide a service to the Systems Biology community by 1) giving access to a database of curated models of biological systems, and 2) allowing the users to run these models in a web browser via an easy to use interface, and 3) helping in reviewing of manuscripts containing kinetic models. In addition to this service role, JWS Online is an important component of an ambitious research initiative: The Silicon Cell. Whereas as a service JWS Online is a repository of published models, in the research activity models are not stored as published but are changed to reflect standardized notation of metabolites and enzymes, and a direct link between model and experimental data is provided.
HOVERGEN: Database of homologous vertebrate genes
HOVERGEN is a database of homologous vertebrate genes, structured under ACNUC sequence database management system. It allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. HOVERGEN is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generaly, HOVERGEN gives an overall view of what is known about a peculiar gene family.
Alternative splicing essentially increases the diversity of the transcriptome and has important implications for physiology, development and the genesis of diseases. This resource uses a different approach to investigate alternative splicing (instead of the conventional case-by case fashion) and integrates all transcripts derived from a gene into a single splicing graph. ASG is a database of splicing graphs for human genes, using transcript information from various major sources (Ensembl, RefSeq, STACK, TIGR and UniGene). Each transcript corresponds to a path in the graph, and alternative splicing is displayed by bifurcations. This representation preserves the relationships between different splicing variants and allows us to investigate systematically all possible putative transcripts. Web interface allows users to display the splicing graphs, to interactively assemble transcripts and to access their sequences as well as neighboring genomic regions. ASG also provide for each gene, an exhaustive pre-computed catalog of putative transcriptsin total more than 1.2 million sequences. It has found that ~65 of the investigated genes show evidence for alternative splicing, and in 5 of the cases, a single gene might produce over 100 transcripts.
Ancient conserved untranslated sequences
THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Database that identifies new regulatory elements in untranslated regions of protein-coding genes (5 prime flanks, 5 prime UTRs, introns, 3 prime UTRs and 3 prime flanks). The analyses is focused on genes from metazoan species (essentially vertebrates, insects and nematodes). Information on highly conserved regions (sequences, alignments, annotations, bibliographic references) are compiled. Currently 176 out of 326 detected highly conserved regions (HCRs) have been analyzed and incorporated in the database. You can also access the list of annotated conserved elements and the list of conserved elements that remain to be processed. Their approach is based on comparative sequence analysis, for the identification of phylogenetic footprints.
ARGH is an automated, accurate and scalable method by which acronym-definition pairs can be identified within text. Its primary advantage is in enabling information processing methods to resolve author-defined acronyms, however it also allows an automated creation of a reference work on acronym definitions. ARGH has several advantages over manual or semi-automated methods, besides time and effort saved, such as enabling identification of relative frequencies for alternate acronyms and definitions as well as spelling, phrasing and hyphenation variants for a unique acronym-definition pair. It also aids users in identifying acronym/definition variants present in the literature that may not necessarily be in biomedical databases. ARGH functions by a set of heuristics to accurately locate and identify the boundaries of acronym-definition pairs was developed and refined in terms of precision and recall on subsets of MEDLINE records. These training sets were gradually increased in size and heuristics re-evaluated to ensure scalability. ARGH can be tested on over 12 million MEDLINE records, and it can identify more than 174,000 unique acronyms and their 737,000 associated definitions. Currently, it is the world''s largest and most comprehensive catalog of biomedical acronyms and abbreviations, containing approximately 257,000 out of an estimated 277,000 unique acronyms within MEDLINE. Sponsors: ARGH is a service of UT Southwestern eTBLAST team.
Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms.
This resource contains an alphabetical listing of the various mice knockout genes according to name. Each of the listing contains the phenotypical information observed when a particular gene is knocked out. Other information, such as papers associated to a particular gene and methodology used to conduct the knockout may also be present. This resource contains 314 different knockout genes and provides various navigation tools for easy access. Sponsors: This resource portal is supported by FBS.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. A collection of cDNA, gene and protein records of cytokines deposited in public databases provides various information about the cytokine members of vertebrates in other databases including NCBI GenBank, Swiss-Prot, UniGene, TIGR (The Institute for Genomic Research) Gene Indices, Ensembl, Entrez Gene, Mouse Genome Informatics (MGI) and Rat Genome Database (RGD). It also provides orthologous relationship of cytokine members and includes novel members identified in the databases.
Glycoword presents up-to-the-minute glycoscience-related keywords, selected by researchers in various fields of the science and interpreted intelligibly by specialists with expertise on each of the fields in the hope of bringing about a better understanding of the rapidly growing modern glycoscience. The website contains information on the following: -lectin -proteoglycan -glycoprotein -glycolipid -saccharide -glycotechnology -glycopathology -glycogene -structural glycobiology -immunity & sugar chain -nervous system & sugar chain -comparative glycomics and life evolution -glycobiology in plant defense -infection & sugar chain -quality control, trafficking and sorting of glycoproteins -fertilization / development & sugar chain
The mission of the Arabidopsis Biological Resource Center (ABRC) is to acquire, preserve and distribute seed and DNA resources that are useful to the Arabidopsis research community. More than 100,000 stocks are shipped annually to researchers in more than 60 countries, and modest fees for stocks are charged. The ABRC database functions and ordering system are incorporated into The Arabidopsis Information Resource (TAIR). Researchers can obtain information about Arabidopsis, perform stock searches, order stocks, and view current and past orders. Sponsors: ABRC is supported by the National Science Foundation under Grant No. 0542034.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2022. Human Gut Microbiome Initiative (HGMI) seeks to provide simply annotated, deep draft genome sequences for 100 cultured representatives of the phylogenetic diversity documented by 16S rRNA surveys of the human gut microbiota. Humans are supra-organisms, composed of 10 times more microbial cells than human cells. Therefore, it seems appropriate to consider ourselves as a composite of many species - human, bacterial, and archaeal - and our genome as an amalgamation of human genes and the genes in ''our'' microbial genomes (''microbiome''). In the same sense, our metabolome can be considered to be a synthesis of co-evolved human and microbial traits. The total number of genes present in the human microbiome likely exceeds the number of our H. sapiens genes by orders of magnitude. Thus, without an understanding of our microbiota and microbiome, it not possible to obtain a complete picture of our genetic diversity and of our normal physiology. Our intestine is home to our largest collections of microbes: bacterial densities in the colon (up to 1 trillion cells/ml of luminal contents) are the highest recorded for any known ecosystem. The vast majority of phylogenetic types in the distal gut microbiota belong to just two divisions (phyla) of the domain Bacteria - the Bacteroidetes and the Firmicutes. Members of eight other divisions have also been identified using culture-independent 16S rRNA gene-based surveys. Metagenomic studies of complex microbial communities residing in our various body habitats are limited by the availability of suitable reference genomes for confident assignment of short sequence reads generated by highly parallel DNA sequencers, and by knowledge of the professions (niches) of community members. Therefore, HGMI, which represents a collaboration between Washington University''s Genome Center and its Center for Genome Sciences, seeks to provide simply annotated, deep draft genome sequences for 100 cultured representatives of the phylogenetic diversity documented by 16S rRNA surveys of the human gut microbiota.
NIDA Networking Project: Facilitating information exchange and research collaboration
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Provides opportunities for information sharing and research collaboration among NIDAs networks across the country. It gives researchers and clinicians access to networks locations, people, expertise, and resources to help synergize efforts, improve efficiency, and accelerate scientific discovery. It currently consists of 14 networks and more than 230 sites involved in research and data collection sponsored by NIDA around the nation. The NNP was developed to provide the opportunity for these organizations to learn about each other and potentially work together on research collaboration and data collection in the future. In December 2008, NIDA added the first in a series of Research Interest Groups to the NNP to encourage more interdisciplinary collaboration among network and non-network grantees.
The E. coli Genome Project has the goal of completely sequencing the E. coli and human genomes. They began isolation of an overlapping lambda clonebank of E. coli K-12 strain MG1655. Those clones served as the starting material in our initial efforts to sequence the whole genome. Improvements in sequencing technology have since reached the point where whole-genome sequencing of microbial genomes is routine, and the human genome has in fact been completed. They initiated additional sequencing efforts, concentrating on pathogenic members of the family Enterobacteriaceae -- to which E. coli belongs. They also began a systematic functional characterization of E. coli K-12 genes and their regulation, using the whole genome sequence to address how the over 4000 genes of this organism act together to enable its survival in a wide range of environments.
Through its Microbial Genome Program (MGP) and its Genomics:GTL (GTL) program, DOEs Office of Biological and Environmental Research (BER) has sequenced more than 485 microbial genomes and 30 microbial communities having specialized biological capabilities. Identifying these genes will help investigators discern how gene activities in whole living systems are orchestrated to solve myriad life challenges. The MGP was begun in 1994 as a spinoff from the Human Genome Program. The goal of the program was to sequence the genomes of a number of nonpathogenic microbes that would be useful in solving DOE''s mission challenges in environmental-waste cleanup, energy production, carbon cycling, and biotechnology. Past projects include microbial genome program, microbial cell project, and the Laboratory Science Program at the DOE Joint Genome Institute. The two ongoing projects are Genomics: GTL program and Community Sequencing Program at the DOE Joint Genome Institute. Sponsors: Site sponsored by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
This website includes a list of projects that the Sanger Institute is currently working on or completed. All projects consist of the genomic sequencing of different bacteria. Each description of the bacteria includes its classification, a description, and the types of diseases that the bacteria is likely to cause. The Sanger Institute bacterial sequencing effort is concentrated on pathogens and model organisms. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing users to search the sequences with their own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing you to search the sequences with your own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. The primary sequence viewer and annotation tool, Artemis is available for download. This is a portable Java program which is used extensively within the Microbial Genomes group for the analysis and annotation of sequence data from cosmids to whole genomes. The Artemis Comparison Tool (ACT) is also useful for interactive viewing of the comparisons between large and small sequences.
BoLA Nomenclature: International Society for Animal Genetics
International Society for Animal Genetics
This website is intended to be the definitive source of information on the bovine major histocompatibility complex - its genes, proteins and polymorphism. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The BoLA nomenclature committee is a standing committee of the International Society for Animal Genetics. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The information gathered here is based on the BoLA workshop reports, which are published in Animal Genetics and the European Journal of Immunogenetics. The workshop report data are reproduced with the permission of the publishers Blackwell Science, and other text on the site is used with the permission of CRC Press.
The Fungal Genetics Stock Center is a resource available to the Fungal Genetics research community and to educational and research organizations in general. While some fungi can cause disease in humans, most people have innate immunity against fungi. Some people with diseases of the immune system are at increased risk of infection by fungi. Drugs have been developed in the last 5 years that help with this. Fungal Genetics is the study of genes and genetic traits in fungi. In the past this has been important in the elucidation of what a gene is, what the genetic material is, how genes relate to enzymes, how enzymes relate to traits and how important traits change or evolve. In the present, Fungal Genetics is important to understanding how fungi are pathogens of plants and animals, how fungi can be used in industry for the production of enzymes, chemicals, food, and drugs. Fungi are also essential to processing bio-mass in the attempt to use ethanol as a fuel source. The FGSC is funded largely by a grant from the National Science Foundation (Award Number 0235887) of the United States of America. Sponsors: Supported by a grant from the National Science Foundation.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This website contains information about the mapping of the caprine genome. It contains loci list, phenes list, cartography, gene list, and other sequence information about goats. This website contains 731 loci, 271 genes, and 1909 homologue loci on 112 species. It also allows users to summit their own data for Goatmap. ARK-Genomics is not-for-profit and has collaborators from all over the world with an interest in farm animal genomics and genetics. ARK-Genomics was initially set up in 2000 with a grant awarded from the BBSRC IGF (Investigating Gene Function) initiative and from core resources of the Roslin Institute to provide a laboratory for automated analysis of gene expression using state-of-the-art genomic facilities. Since then, ARK-Genomics has expanded considerably, building up considerable expertise and resources.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The objective of the project is the standardization of micro-satellite markers used within participating laboratories, use of DNA markers to define genetic diversity and to enable monitoring of breeds to promote conservation programs where required, and the determination of diversity present in rare and local breeds across Europe. The blood typing laboratories are now beginning to use micro-satellite markers as an alternative to serology for parentage verification, and are selecting a common set to be used from the several hundred micro-satellite markers available that cover the bovine genome, produced as part of the Bovine genome mapping project (See BovMaP). Work with micro-satellite markers has shown that they are valuable tools for examining genetic diversity and phylogeny in many species. However, for work carried out in different laboratories to be comparable, it is essential that the same markers are used. To maintain the compatibility of data generated by the various typing labs, it is essential that all laboratories adopt the same markers and typing protocols. It is therefore of paramount importance that the blood typing laboratories and research labs that are examining the genetic structure of the cattle populations adopt a common panel of the best micro-satellite markers available. Some pilot comparative work has been undertaken through the International Society for Animal Genetics, but so far this has only involved the blood typing laboratories. One objective of this project is to facilitate the comparison of the micro-satellite markers currently in use in the different types of laboratory and determine the efficiency of the markers available in revealing genetic differences within and among breeds. It will also be important to compare the use of markers in different laboratories to determine how robust they are and how easily results can be compared. From comparison of the markers, those that are most suitable will be selected to form a panel which will be recommended for pedigree validation and genetic surveys. Cattle are an important source of food in Europe, and intense selection has resulted in the development of specialized breeds. Selection for high-producing dairy cattle has been successful, but one associated drawback is that the cattle population, both in Europe and North America, has been skewed dramatically towards one breed, the Holstein/Friesian. So there has been a decline in the number of individuals of other breeds, and hence a general erosion of the genetic base of the cattle population. The progressive move towards the North American-type Holstein animals has also resulted in the requirement for high input/high output farming and intensive management schemes. The impact of this on the environment has been significant, e.g. pollution problems arising from the need for high nitrogen fertilizers to produce sufficient high quality fodder, and disposal problems associated with slurry waste. Poorer areas of the community have been unable to compete with such farming systems, and are more suited to low input/low output farming using traditional stock. It is however the future perspective that is of greatest concern. It is impossible to predict requirements for cattle production - quality, production type, management systems, etc. The ability to switch rapidly to alternative production will be dependent on the genetic base of the population available to selection programs. It is therefore essential to maintain the greatest genetic diversity possible in the cattle population. Whilst current farming practices are perceived to be both efficient and acceptable, the breeds less favored by commercial farmers will dwindle. It is therefore important that on an European scale efficient management of these breeds maintains the widest genetic base possible. This project aims to carry out a survey of the current genetic base of the European cattle population and to provide the tools to assist breeding programs to maintain a broad base. The blood typing laboratories are now beginning to use micro-satellite markers as an alternative to serology for parentage verification, and are selecting a common set to be used from the several hundred micro-satellite markers available that cover the bovine genome, produced as part of the Bovine genome mapping project. Early work to measure genetic diversity used blood groups to show differences between breeds and the diversity present. Unfortunately, the number of loci available are limited, with only the B system being sufficiently polymorphic to be really useful. However, since there is a wealth of information available from such typing, this information can be used to estimate changes in the genetic structure of cattle populations across Europe over the past twenty years. More recently mini-satellite probes have been used to generate ''genetic fingerprints'' which have been used to show differences between individuals. Such fingerprints have been used to estimate genetic diversity - the greater the number of bands revealed by the fingerprint being equated with greater diversity. This is valid within limits. The main disadvantage of the fingerprint approach is that the chromosomal location and number of loci being sampled, and so the proportion of the genome examined, is unknown. The allelic bands on the gel cannot be easily identified, so allele inheritance cannot be addressed making it impossible to trace ancestry. Through the EC funded BovMaP project, large numbers of highly polymorphic micro-satellite markers have become available, which are being mapped on the bovine genome. These markers are particularly suited to measuring genetic diversity, and markers can be selected to cover the entire genome.
This website contains the mapping sequence of poultry. The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal species. In doing so, it aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data. It's supported, in part, by the USDA-CSREES National Animal Genome Research Program in order to serve the poultry genome mapping community. This system represents a complete rewrite of the original version with the code migrated to java and the underlying database targeted at postgres (although any standards-compliant database engine should suffice). The initial release records details of maps and the markers that they contain. There are alternative entry points that target either a chromosome or a specific mapping analysis as the starting point. Limited relationships between markers are recorded and displayed. As with the previous version, all maps are drawn using data extracted from the database on the fly.
The Daphnia Genomics Consortium (DGC) is an international network of investigators committed to mounting the freshwater crustacean Daphnia as a model system for ecology, evolution and the environmental sciences. Along with research activities, the DGC is: (1) coordinating efforts towards developing the Daphnia genomic toolbox, which will then be available for use by the general community; (2) facilitating collaborative cross-disciplinary investigations; (3) developing bioinformatic strategies for organizing the rapidly growing genome database; and (4) exploring emerging technologies to improve high throughput analyses of molecular and ecological samples. If we are to succeed in creating a new model system for modern life-sciences research, it will need to be a community-wide effort. Research activities of the DGC are primarily focused on creating genomic tools and information. When completed, the current projects will offer a first view of the Daphnia genome''s topography, including regions of high and low recombination, the distribution of transposable, repetitive and regulatory elements, the size and structure of genes and of their neighborhoods. This information is crucial in formulating testable hypotheses relating genetics and demographics to the evolutionary potential or constraints of natural populations. Projects aiming to compile identifiable genes with their function are also underway, together with robust methods to verify these findings. Finally, these tools are being tested, by exploring their uses in key ecological and toxicological investigations. Each project benefits from the leadership and expertise of many individuals. For further details, begin by contacting the project directors. The DGC consists of biologists from a broad spectrum of subdisciplines, including limnology, ecotoxicology, quantitative and population genetics, systematics, molecular biology and evolution, developmental biology, genomics and bioinformatics. In many regards, the rapid early success of the consortium results from its grass-roots origin promoting an international composition, under a cooperative model, with significant scientific breadth. We hold to this approach in building this network and encourage more people to participate. All the while, the DGC is structured to effectively reach specific goals. The consortium includes an advisory board (composed of experts of the various subdisciplines), whose responsibility is to act as the research community''s agent in guiding the development of Daphnia genomic resources. The advisors communicate directly to DGC members, who are either contributing genomic tools or actively seeking funds for this function. The consortium''s main body (given the widespread interest in applying genomic tools in environmental studies) are the affiliates, who make use of these tools for their research and who are soliciting support.
Parasite genome databases and genome research resources
This website contains information about the genomic sequence of parasites. It also contains multiple search engines to search six frame translations of parasite nucleotide databases for motifs, parasite protein databases for motifs, and parasite protein databases for keywords and text terms. * Guide to Internet Access to Parasite Genome Information * Guide to web-based analysis tools * Parasite Genome BLAST Server: Search a range of parasite specific nucleotide sequence databases with your own sequence. * Parasite Proteome Keyword Search Facility: Search parasite protein databases for keywords and text terms * Parasite Proteome Motif Search Facility: Search parasite protein databases for motifs * Parasite Six Frame Translation Motif Search Facility: Search six frame translations of parasite nucleotide databases for motifs * Genome computing resources: A list of ftp and gopher sites where genome computing applications and other resources can be found.
Database and resources on the pig genome.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This page contains a list of websites relating to sheep gene mapping. Users may chose from the list to view any desired webpage. The website also contains information on sheep maps, sheep markers, map comparisons, experiments, DNA tests, and other genome sites.
Comparative Saccharinae Genomics Resource
The objective of this project is to develop physical maps of the sorghum and rice genomes, based on BAC contigs that are cross-linked to each other and also to genetic maps and BAC islands for other large-genome crops and a library of ca. 50,000 expressed-sequence tags (EST''s) and corresponding cDNA clones, from diverse sorghum organs and developmental states. It also aims to improve understanding of genetic diversity and allelic richness that might be harbored ex situ (in gene banks) or in situ (in nature), and refine techniques for assesing allelic richness and Expedite data acquisition and utilization by a sound parnership between laboratory scientists and computational biologists. Specific goals of developing physical maps of sorghum and rice genomes include: -Enrich cross-links between sorghum and rice by mapping additional rice probes on sorghum. -Apply mapped DNA probes to macroarrays of sorghum, sugarcane, rice, and maize BACs. -Fingerprint 10x BAC libraries of Sorghum bicolor and S. propinquum. Libraries presently 3x and 6x respectively, to be expanded to 10x each. -Use fragment-matching (BAC-RF) method to determine locus-specificity in polyploids. - Contig assembly based on 1-3, plus rice BAC fingerprints generated under a separate Novartis project. -Evaluate methodology for rapid high-throughput assignment of new ESTs to BACs. -Conduct genomic sequencing in a region duplicated in both sorghum and arabidopsis. Selected BACs from sorghum(2), sugarcane, maize, rice, wheat. By improving the understanding of genetic diversity and allelic richness, the goal is to: -Sequence previously mapped sorghum DNA probes. -Discover & characterize 100 single nucleotide polymorphisms (SNPs) from cDNA markers. -Develop colorimetric high-throughput genotyping assays, and utilize to assess genetic diversity in geographically- and phenotypically-diverse sorghums. -Develop colorimetric high-throughput asssays for identifying phytochrome allelic variation, and apply these assays to a core collection representing a large set of genetic resources. -Support informatics group to streamline cataloging of DNA-level information relevant to large genetic resources collections. Lastly, the goals of expediting data acquisition and utilization include: -A new web-based resource for 3D-integration and visualization of structural and functional genomic data will be developed. -New sequence assembly and alignment software SABER (Sequence AssemBly in the presence of ERror), and PRIMAL(Practical RIgorous Multiple ALignment), will be evaluated with reference to existing standards (PHRED, PHRAP). -Specialized image processing and image analysis tools will be developed for acquistion and interpretation of qualitative and quantitative hybridization signals. To deal expeditiously with large volumes of data, parallel processing approaches will be investigated. Sponsors: * National Science Foundation (NSF) * National Sorghum Producers * University of Georgia Research Foundation (UGARF) * Georgia Research Alliance (GRA)
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 23, 2016. The Human Papillomaviruses Database collects, curates, analyzes, and publishes genetic sequences of papillomaviruses and related cellular proteins. It includes molecular biologists, sequence analysts, computer technicians, post-docs and graduate research assistants. This Web site has two main branches. The first contains our four annual data books of papillomavirus information, called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. and the second contains papillomavirus genetic sequence data. There is also a New Items location where we store the latest changes to the database or any other current news of interest. Besides the compendium, we also provide genetic sequence information for papilloma viruses and related cellular proteins. Each year they publish a compendium of papillomavirus information called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. which can now be downloaded from this Web site.
Caenorhabditis Genome Sequencing Projects
The Sanger Institute and the Genome Sequencing Center at the Washington University School of Medicine, St. Louis have collaborated to sequence the genomes of both C. elegans and C. briggsae. The completed C. elegans genome sequence is represented by over 3,000 individual clone sequences which can be accessed through this site (or through WormBase). These sequences are submitted to EMBL whenever the sequence or annotation changes (e.g. modification to gene structures) and these submissions are then mirrored to GenBank and DDBJ. These sequences (along with ESTs and proteins) can be searched on our C. elegans BLAST server. WormBase is the repository of mapping, sequencing and phenotypic information for C. elegans. The worm informatics group at the Sanger Institute play a key role in assembling the whole database. They also curate and develop some of the constituent databases that comprise WormBase.
University of Western Sydney; New South Wales; Australia
Western Sydney University is one of Australia's leading institutions. Ranked in the top 400 in the world.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. A manual generated database for alternative exons and their properties from numerous species - the data is gathered from literature where these exons have been experimentally verified. Most alternative exons are cassette exons and are expressed in more than two tissues. Of all exons whose expression was reported to be specific for a certain tissue, the majority were expressed in the brain. At the moment, AEdb products that are available are sequence (a database of alternative exons), function (a database of functions attributed to constitutive and alternative exon), regulatory sequence (a database of transcript regulatory motifs), minigenes (a table of minigenes and their associations to splicing events), and diseases (a table of diseases associated with splicing and their associations to AltSplice). Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. The continuation and upgrade of the ASD consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database of computationally delineated alternative splicing events. Its data include alternatively spliced introns/exons, events, isoform splicing patterns and isoform peptide sequences. AltSplice data are generated by examining gene-transcript alignments. The data are annotated for various biological features including splicing signals, expression states, (SNP)-mediated splicing and cross-species conservation. AEdb forms the manually curated component of ASD. It is a literature-based data set containing sequence and properties of alternatively spliced exons, functional enumeration of observed splicing events, characterization of observed splicing regulatory elements, and a collection of experimentally clarified minigene constructs.
National Agricultural Library Catalog (AGRICOLA)
National Agricultural Library Catalog AGRICultural OnLine Access
A database, catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. This database resource covers materials in all formats and periods, including printed works from as far back as the 15th century. AGRICOLA is a bibliographic database of citations to the agricultural literature created by the National Agricultural Library and its cooperators. The records describe publications and resources encompassing all aspects of agriculture and allied disciplines, including animal and veterinary sciences, entomology, plant sciences, forestry, aquaculture and fisheries, farming and farming systems, agricultural economics, extension and education, food and human nutrition, and earth and environmental sciences. Although the NAL Catalog (AGRICOLA) does not contain the text of the materials it cites, thousands of its records are linked to full-text documents online, with new links added daily. The NAL Catalog (AGRICOLA) is organized into two bibliographic data sets: *The NAL Online Public Access Catalog (AGRICOLA NAL) contains citations to books, audiovisuals, serials, and other materials, most of which are in the Library''s collection. (The Catalog does contain some records for items not held at NAL.) *The Article Citation Database (AGRICOLA IND) includes citations, many with abstracts, to journal articles (see Journals Indexed in AGRICOLA), book chapters, reports, and reprints, selected primarily from the materials found in the NAL Catalog.
All the Virology on the WWW is a site for virology information on the Internet. They have collected all the virology related web sites that might be of interest to virologists, and others interested in learning more about viruses. Additionally, they have created an index to virus pictures on the web, The Big Picture Book of Viruses, which also functions as a resource for viral taxonomy. A collection of some of the best Online Virology and Microbiology Course Notes available can also be found here. If users are interested in even more information, The Virology Bookshop, an on-line microbiology and virology bookstore with a significant discount for our users. It is their goal that this site will provide both the professional virologist and the general public with access to information about viruses. Over the past several years, these pages have grown to encompass something of interest for everyone. The lists of virology related sites are divided into multiple pages, all of which are accessible from this page and from the more descriptive Complete Table of Contents. There are also links to Virology Dictionaries if users are confused by some of this site''s more technical content. These sites are listed without bias and with much organization Categories: Metadatabases and Directories
Bibliography on Alternatives to the Use of Live Vertebrates in Biomedical Research and Testing
Bibliography to assist in identifying methods and procedures helpful in supporting the development, testing, application, and validation of alternatives to the use of vertebrates in biomedical research and toxicology testing. This bibliography is produced from MEDLINE database searches, performed and analyzed by subject experts from the Toxicology and Environmental Health Information Program (TEHIP) of the Specialized Information Services Division (SIS) of the National Library of Medicine (NLM). The purpose of these bibliographies on animal alternatives is to provide a survey of the literature in a format which facilitates easy scanning. This bibliography includes citations from published articles, books, book chapters, and technical reports. Citations to items in non-English languages are indicated with brackets around the title. The language is also indicated. Citations with abstracts or annotations relating to the method are organized under subject categories. This publication features citations which deal with methods, tests, assays or procedures which may prove useful in establishing alternatives to the use of intact vertebrates. Citations are selected and compiled through searching various computerized on-line bibliographic databases of the National Library of Medicine, National Institutes of Health. The focus of the bibliography is to assist in identifying methods and procedures helpful in supporting the development, testing, application, and validation of alternatives to the use of vertebrates in biomedical research and toxicology testing. Toxicology Databases
Center for Computational Mass Spectrometry
UCSD Center for Computational Mass Spectrometry
Biomedical technology research center that focuses on the computational bottlenecks that impair the interpretation of data, bringing modern algorithmic approaches to mass spectrometry and building a new generation of reliable, open-access software tools to support both new mass spectrometry instrumentation and emerging applications.
AltSplice Database of Alternative Spliced Events
AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations. This data is being integrated with other data that is generated by other members of the ASD consortium. The ASD project will provide the following in its three year duration: -human curated database of alternative spliced genes and their properties -a computer generated database of alternatively spliced genes and their properties -the integration of the above and newly found knowledge in a user-friendly interface and research workbench for both bioinformaticists and biologists -DNA chips that are based on the data in the above databases -the DNA chips will be used to test against predisposition for and diagnoses of human diseases ASD aims to analyse this mechanism on a genome-wide scale by creating a database that contains all alternatively spliced exons from human, and other model species. Disease causing mutations seem to induce aberrations in the process of splicing and its regulation. The ASD consortium will develop a DNA microarray (chip) that contains cDNAs of all the splicing regulatory proteins and their isoforms, as well as a chip that contains a number of disease relevant genes. We will concentrate on three models of disease (breast cancer, FTDP-17, male infertility) in which a connection between mis-splicing and a pathological state has been observed. Finally, these chips will be developed as demonstrative kits to detect predisposition for and diagnosis of such diseases. Categories: Nucleotide Sequences: Gene Structure, Introns and Exons, & Splice Sites Databases
Database of images on medical parasitology created to provide educational materials for medical students primarily, but professional workers in medical or paramedical fields may also refer to this site covering the significant parasites in the world. Each database of protozoans, nematodes, trematodes, cestodes and arthropods contains information on the morphology, life cycle, geographical distribution, symptoms, prevention, etc. Users who wish to contribute can send the editor unpublished images of human parasites (microscopical, clinical, radiological or epidemiological aspects of human parasitic infections) by mail or e-mail. Pathology specimens (slide, samples) are welcome too. The A.M.P. received the citation of reliable sources such as Parasitology today and The Lancet, and is now listed in the Internet Resources on Specific Infectious Diseases Topics of the Mandell, Douglas and Bennets Principles and Practice of Infectious Diseases Fifth Edition. This website was established with a great contribution of the PROJECT COLLABORATORS and many contributors of The Korean Society for Parasitology.
The Amphibian Species of the World database has two searching tools, a BROWSE table and a SEARCH table. It provides needed information for research and conservation needs and to help illuminate where geographical data or taxonomic information are woefully inadequate. In addition, all underlined author names, dates, and publications may be clicked through to see other records citing this author, date, or publication. The basic structure of a taxonomic record is (1) Current scientific name, author and year of publication; (2) original name, authorship, citation, and if relevant, location of primary types and type locality (direct quotation if possible). This is followed by a synonymy composed of all new names, their authorship, literature citation, and (if relevant) location of primary types, and type locality as well as all new combinations and the literature source of the synonymy or combination; (3) published English names; (4) known or inferred distribution of the taxon; (5) comments to controversies or relevant taxonomic literature. A synonymy follows the currently recognized name. The synonymy includes synonyms and relevant combinations (in the sense of the International Code of Zoological Nomenclature, 1999) as well as deposition of types, type localities, and the source of the synonymy. Users who are looking for the synonymy to provide unerringly and precisely the names by which a taxon have been mentioned will be disappointed, and will be misled if they approach synonymies this way.
Database of comparative gene mapping between species to assist the mapping of the genes related to phenotypic traits in livestock. The linkage maps, cytogenetic maps, polymerase chain reaction primers of pig, cattle, mouse and human, and their references have been included in the database, and the correspondence among species have been stipulated in the database. AGP is an animal genome database developed on a Unix workstation and maintained by a relational database management system. It is a joint project of National Institute of Agrobiological Sciences (NIAS) and Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF-Institute), under cooperation with other related research institutes. AGP also contains the Pig Expression Data Explorer (PEDE), a database of porcine EST collections derived from full-length cDNA libraries and full-length sequences of the cDNA clones picked from the EST collection. The EST sequences have been clustered and assembled, and their similarity to sequences in RefSeq, and UniGene determined. The PEDE database system was constructed to store sequences and similarity data of swine full-length cDNA libraries and to make them available to users. It provides interfaces for keyword and ID searches of BLAST results and enables users to obtain sequence data and names of clones of interest. Putative SNPs in EST assemblies have been classified according to breed specificity and their effect on coding amino acids, and the assemblies are equipped with an SNP search interface. The database contains porcine nucleotide sequences and cDNA clones that are ready for analyses such as expression in mammalian cells, because of their high likelihood of containing full-length CDS. PEDE will be useful for researchers who want to explore genes that may be responsible for traits such as disease susceptibility. The database also offers information regarding major and minor porcine-specific antigens, which might be investigated in regard to the use of pigs as models in various medical research applications.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 22, 2023. A database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world' '''s most important malaria vector. AnoBase is an integrated, relational database of basic biological and genetic data on anopheline species, with a particular emphasis on Anopheles gambiae. It has been designed as an information source and research support tool for the broad vector biology community. Although AnoBase is not a primary genomic database that develops and provides tools to access the genome of the malaria mosquito, it nevertheless contains several sections that offer data of genomic interest such as in situ hybridization images, an integrated gene tool and direct online access to AnoXcel, the proteomic database of An. gambiae. Moreover, AnoBase also contains information on non-gambiae mosquito species and a novel section on studies related to insecticide resistance.
Tulane National Biomedical Research Center
Center focused on understanding human health problems, including infectious diseases that require the use of nonhuman primates to develop diagnostics, therapeutics and preventive strategies. Primary research interests include developing vaccines, treatments and diagnostic tools for infectious diseases such as AIDS, tuberculosis, CMV, COVID-19, Lyme disease, and malaria. TNPRC has both biosafety level 2 and biosafety level 3 laboratories facilities to accommodate various research needs, and is the only National Primate Research Center with Regional Biosafety Laboratory.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The BayGenomics gene-trap resource provides researchers with access to thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes. The major goal of BayGenomics is to identify genes relevant to cardiovascular and pulmonary disease.
BELIT provides access to about 350.000 records from the integrated German, American and French databases. It is an extensive bibliographic directory of literature in the area of bioethics unique world wide, containing references to monographs, grey literature, legal documents, journal articles, newspaper articles and book contributions. It is an integrated online database developed by the German Reference Centre for Ethics in the Life Sciences. BELIT Search enables the retrieval of bibliographical data filtered by categories. Choose a category from the drop down lists in the top section of the main screen. Enter the query term(s) in the text field next to the search category chosen. Help texts are available by clicking on Help. Users can combine different search categories with and or or respectively as well as restrict their search by selecting further categories from the drop down lists in the lower section of the main screen. The default display of the search results is an abbreviated title list. Click on Full details to see the complete bibliographical record, including the short code of the source database in the top right hand corner of each record. Refer to the BELIT intro screen for an explanation of the short codes. Using the arrow keys users can navigate through the lists. Users may also carry out searches using the various indexes. An index is an alphabetically ordered register containing all query terms assigned to a search category. There is an index for each category.
Biological Information Browsing Environment
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A facility to help novices and experts find information about plants and animals in digital collections. The objectives of the Project are to facilitate access to online flora and fauna by both novices and experts through enhanced indexing, searching, and visualization techniques. Specific search facility and content will be added to help users with different levels of domain knowledge identify species based on the augmentation of professionally developed taxonomic treatments or species descriptions. This is a novel use of taxonomic descriptions.
International Database of Tetrahydrobiopterin Deficiencies
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The BIODEF database have tabulated the most common clinical and laboratory data related to hyperphenylalaninaemia and tetrahydrobiopterin deficiencies. Additionally, there are data regarding treatment, outcome, and DNA analysis. Approximately 2% of newborns with hyperphenylalaninaemia are deficient in tetrahydrobiopterin. Selective screening must be performed in all instances where hyperphenylalaninaemia is detected by neonatal screening. In the last 20 years, 308 patients with tetrahydrobiopterin deficiencies have been recognized as a result of screening carried out, worldwide, in Departments of Paediatrics. Of these 308 patients, 181 suffered from 6-pyruvoyltetrahydropterin synthase deficiency, 92 from dihydropteridine reductase deficiency, 13 from pterin-4a-carbinolamine dehydratase deficiency, 12 from GTP cyclohydrolase I deficiency, and 10 are still unclassified. The BIODEF database have tabulated the most common clinical and laboratory data related to hyperphenylalaninaemia and tetrahydrobiopterin deficiencies. Additionally, there are data regarding treatment, outcome, and DNA analysis. Preliminary evaluation reveals that the degree of hyperphenylalaninaemia can vary from normal to 2500 mumol/L. Analyses of pterins in urine and measurement of dihydropteridine reductase activity from Guthrie cards are absolutely essential tests for accurate diagnosis. There is a regional (demographic) variation in the frequency of tetrahydrobiopterin deficiencies indicating the highest incidence in Saudi Arabia, probably a consequence of the high consanguinity rate.
The Ligand Protein Database is designed to allow the selection of complexes based on various properties of receptors and ligands for the design and parametrization of new scoring functions or to assess and improve existing ones. Moreover, for each complex, a continuum of ligand positions ranging from the crystallographic position to points on the surface of the protein receptor allows an assessment of the energetic behavior of particular scoring functions. Access to the database is password protected. To obtain access to the LPDB, complete a form, available online, have it signed by your research advisor, and fax the completed form back to the attention of Professor Charles L. Brooks III, (858) 784-8688. There is no fee for academic use of the LPDB. We are currently working out details for licensing to our colleagues in industry. Please contact Professor Brooks to obtain current information on access to the LPDB.
Bioethics database comprises over 645 bioethics institutions (bioethics committees, commissions, training, research and documentation centres) in over 80 countries, including information on activities and publications. Information is based on replies obtained from a widely distributed questionnaire and has been gathered in cooperation with National Commissions and Permanent Delegations to UNESCO. The Program develops four main action areas: -Intellectual forum -Standard-setting action -Advisory role and capacity-building -Education and awareness raising The Bioethics Program is part of UNESCOs Division of the Ethics of Science and Technology in the Social and Human Sciences Sector. It is primarily responsible for the Secretariat of two advisory bodies: the International Bioethics Committee (IBC), composed of 36 independent experts, and the Intergovernmental Bioethics Committee (IGBC), composed of representatives of 36 Member States. These Committees cooperate to produce advice, recommendations and proposals that each submits to the Director-General for consideration by UNESCOs governing bodies.
BioMail is a small web-based application for medical researchers, biologists, and anyone who wants to know the latest information about a disease or a biological phenomenon. It is written to automate searching for recent scientific papers in the PubMed Medline database. BioMail is free and will stay free. What does BioMail do? Periodically BioMail does a user-customized Medline search and sends all matching articles recently added to Medline to the users'' e-mail address. HTML-formatted e-mails generated by BioMail can be used to view selected references in medline format (compatible with most reference manager programs). Why is BioMail helpful? If you use Medline, it may be hard to remember when you did your last search. Often you must scan titles you have already seen to be certain you didn''t miss an important reference. BioMail will perform routine searches for you. This program alerts users to all new papers in their fields automatically. It also helps the user to ''refine'' search patterns once and for all. There is no need to wonder: ''What was that great search pattern I used last Saturday?''. All patterns are safe in the database and can be accessed, tuned, or deleted any time. It is also useful for countries where access to the Internet is not yet widely available. If a person has a permanent e-mail address, but only sporadic www access, she/he only needs to fill out a BioMail form once and then will receive new references from Medline continually.
BITOLA: Biomedical Discovery Support System
An interactive literature-based biomedical discovery support system. The goal of this system is to discover new, potentially meaningful relations between a given starting concept of interest and other concepts, by mining the bibliographic database MEDLINE. To make the system more suitable for disease candidate-gene discovery and to decrease the number of candidate relations, we integrated background knowledge about the chromosomal location of the starting disease as well as the chromosomal location of the candidate genes from resources such as Entrez Gene, HUGO and OMIM. The BITOLA system can also be used as an alternative way of searching the Medline database. The system is available in two versions: closed discovery and open discovery. Closed discovery allows the input of two concepts (Example 1: a disorder and a gene. Example 2: a drug and a side effect) and generates potential explanations of the relationship between two entities. It does this by searching published literature to finds intermediate links. Open discovery allows the input of a single concept, then categories for first-order relatives of that concept, then categories for relatives of those first order concepts. Thus it can link from a disease to related drugs, then to genes related to those drugs and then test if those genes have been mentioned/tested in association with the disease. If the answer is no, then the gene is potentially related yet untested in the literature. Thus the open discovery tool is a nominator of new genes, drugs or neuroscience correlates to be investigated with diseases, disorders, physiological responses or any other phenotype.
The BNF aims to provide prescribers, pharmacists and other healthcare professionals with sound up-to-date information about the use of medicines. The BNF provides ready access to key information on the selection, prescribing, dispensing and administration of medicines. Medicines that are generally prescribed in the UK are covered and those considered less suitable for prescribing are clearly identified.
Computer-Assisted Information Retrieval Service System for Music
CAIRSS is a bibliographic database of older literature (prior to 1993) of music research literature in music education, music psychology, music therapy, and music medicine. Citations have been taken from 1,354 different journal titles; 18 of which are primary journals, meaning that every article ever to appear is included. The primary journals are: * Arts in Psychotherapy * Bulletin of the Council for Research in Music Education * Bulletin of the National Association for Music Therapy * Contributions to Music Education * Hospital Music Newsletter * International Journal of Arts Medicine * Journal of the Association for Music and Imagery * Journal of Music Teacher Education * Journal of Music Therapy * Journal of Research in Music Education * Medical Problems of Performing Artists * Music Perception * Music Therapy * Music Therapy Perspectives * Psychology of Music * Psychomusicology * The Quarterly * Applications of Research to Music Education
Chemical Carcinogenesis Research Information System
Toxicology data file of the National Library of Medicine''s (NLM) Toxicology Data Network (TOXNET). It is a scientifically evaluated and fully referenced data bank, developed and maintained by the National Cancer Institute (NCI). It contains over 9,000 chemical records with carcinogenicity, mutagenicity, tumor promotion, and tumor inhibition test results. Data are derived from studies cited in primary journals, current awareness tools, NCI reports, and other special sources. Test results have been reviewed by experts in carcinogenesis and mutagenesis. CCRIS is easily accessible and free of charge. Users can search by chemical or other name, chemical name fragment, Chemical Abstracts Service Registry Number (RN), and/or subject terms. Search results can easily be viewed, printed or downloaded. Search results are displayed in relevancy ranked order. Users may select to display any combination of data from the following broad groupings: (a) Carcinogenicity Studies (b) Tumor Promotion Studies (c) Mutagenicity Studies (d) Tumor Inhibition Studies Users can easily conduct their CCRIS search strategy against other databases: Hazardous Substances Data Bank, Integrated Risk Information System, GENE-TOX, TOXLINE, and ChemIDplus.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The CDKN2A Database presents the germline and somatic variants of the CDKN2A tumor suppressor gene recorded in human disease through June 2003, annotated with evolutionary, structural, and functional information, in a format that allows the user to either download it or manipulate it for their purposes online. The goal is to provide a database that can be used as a resource by researchers and geneticists and that aids in the interpretation of CDKN2A missense variants. Most online mutation databases present flat files that cannot be manipulated, are often incomplete, and have varying degrees of annotation that may or may not help to interpret the data. They hope to use CDKN2A as a prototype for integrating computational and laboratory data to help interpret variants in other cancer-related genes and other single nucleotide polymorphisms (SNPs) found throughout the genome. Another goal of the lab is to interpret the functional and disease significance of missense variants in cancer susceptibility genes. Eventually, these results will be relevant to the interpretation of single nucleotide polymorphisms (SNPs) in general. The CDKN2A locus is a valuable model for assessing relationships among variation, structure, function, and disease because: Variants of this gene are associated with hereditary cancer: Familial Melanoma (and related syndromes); somatic alterations play a role in carcinogenesis; allelic variants occur whose functional consequences are unknown; reliable functional assays exist; and crystal structure is known. All variants in the database are recorded according to the nomenclature guidelines as outlined by the Human Genome Variation Society. This database is currently designed for research purposes only and is not yet recommended as a clinical resource. Many of the mutations reported here have not been tested for disease association and may represent normal, non-disease causing polymorphisms.
THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. ChemBioFinder.com is an online chemistry and biology reference database. With more than 500,000 compounds indexed and linked to other web sites, it provides a wealth of chemical information for professional chemists and students alike. ChemBioFinder.com is the gateway to all databases available from CambridgeSoft. At ChemBioFinder.com, a subscriber can search for compounds by name, CAS Registry Number, molecular formula or weight, or by structure (exact and substructure). Successful searches return a basic profile of molecules indexed by this site. The profile contains the name, molecular formula and weight, CAS Registry Number, SMILES and InChI strings for each located compound, and lists the databases which contain entries for the located compound(s). Free trials to any of these databases are available, as are annual subscriptions for continuous use of the contents. Users of ChemBioFinder.com are allowed 5 free searches before we request them to register with us as a cambridgesoft.com website user. The CambridgeSoft user account is free and will give you access to a growing list of products and services which includes, our quarterly print publication Chem & Bio News, frequent webinars, white papers and articles on all our offerings. Set up is fast & easy. For ChemFinder.com users: ChemFinder.Com has become ChemBioFinder.Com and has a whole new look and layout. This is part of a gradual redesign of the entire CambridgeSoft website. Here are some of the changes that were made to improve the vital information presented here to the scientific community: 1. Search results show the ChemBioFinder databases which have entries for the compound(s), and indicate the databases to which the logged in user has active subscriptions. 2. There are hyperlinks to the detailed records in the databases with active subscriptions. 3. Search results provide the name, molecular formula and weight, CAS Registry Number, SMILES and InChI strings for the compound. 4. Physical properties are no longer provided unless the user has a subscription to ChemIndex or other CambridgeSoft online databases that provide this information. Many of our products come with one year subscriptions to ChemIndex as part of the package. So you may actually be entitled to a subscription and dont realize it.
ComBase: A Combined Database For Predictive Microbiology
A database of information about how microorganisms respond to different environments. The information in ComBase is referred to as quantitative microbiological data since it describes how levels of microorganisms, both spoilage organisms and pathogens, change over the course of time. The primary goal of the ComBase consortium is to improve efficiency in locating specific microbiological information, provide a more rapid means to compare data from different laboratories, and to reduce unnecessary redundancy in conducting microbiological studies. Cornbase was launched in 2003 The ComBase Initiative is a collaboration between the Food Standards Agency and the Institute of Food Research from the United Kingdom; the USDA Agricultural Research Service and its Eastern Regional Research Center from the United States; and the Food Safety Center in Australia. Its purpose is to make data and predictive tools on microbial responses to food environments freely available via web-based software. The ComBase Database (accessible via the ComBase Browser) consists of thousands of microbial growth and survival curves that have been collated in research establishments and from publications. They form the basis for numerous microbial models presented in ComBase Predictor, a useful tool for industry, academia and regulatory agencies. They can be used in developing new food technologies while maintaining food safety; in teaching and research; in assessing the microbial risk in foods or setting up new guidelines.
Integrated Tumor Transcriptome Array and Clinical data Analysis
THIS RESOURCE IS NO LONGER IN SERVICE, documented on 6/12/25. ITTACA is a database created for Integrated Tumor Transcriptome Array and Clinical data Analysis. ITTACA centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular interest to the Institut Curie: breast carcinoma, bladder carcinoma, and uveal melanoma. ITTACA is developed by the Institut Curie Bioinformatics group and the Molecular Oncology group of UMR144 CNRS/Institut Curie. A web interface allows users to carry out different class comparison analyses, including comparison of expression distribution profiles, tests for differential expression, patient survival analyses, and users can define their own patient groups according to clinical data or gene expression levels. The different functionalities implemented in ITTACA are: - To test if one or more gene, of your choice, is differentially expressed between two groups of samples exhibiting distinct phenotypes (Student and Wilcoxon tests). - The detection of genes differentially expressed (Significance Analysis of Microarrays) between two groups of samples. - The creation of histograms which represent the expression level according to a clinical parameter for each sample. - The computation of Kaplan Meier survival curves for each group. ITTACA has been developed to be a useful tool for comparing personal results to the existing results in the field of transcriptome studies with microarrays.
Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible
Software package that contains a collection of statistical tools for analysing RNA-seq expression data.
CSB.DB presents the results of bio-statistical analysis on gene expression data in association with additional biochemical and physiological knowledge. The main aim of this database platform is to provide tools that support insight into life''s complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. The main focus of the CSB project is the generation of new easily accessible knowledge about the relationship and the hierarchy of cellular components. Thus new progress towards understanding lifes complexity pyramid is made. For this aim statistical and computational algorithms are applied to organism specific data derived from publicly available multi-parallel technologies, currently such as expression profiles. The underlying data are derived from various research activities. Thus CSB project provides an integrated and centralized public resource allowing universal access on the generated knowledge CSB.DB: A Comprehensive Systems-Biology Database. The derived knowledge should support the formulation of new hypotheses about the respective functional involvement of genes beyond their (inter-) relationships. Another major goal of the CSB project is to supply the researchers with necessary information to formulate these new hypotheses without demanding any a-priori statistical knowledge of the user. The CSB project mainly focuses on application of required statistical tests as well as to assist the user during exploration of results with information / help files to support hypothesis generation
Extended Alternatively Spliced EST Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. An online available compendium of alternative splice forms for several organisms (Arabidopsis thaliana, Bos taurus, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Homo sapiens, Mus musculus, Rattus norvegicus, Xenopus laevis). Alternative splice forms are defined by comparing high-scoring ESTs to mRNA sequences (both from GenBank) with known exon-intron information (from ENSEMBL database) using BLAST. Repetitive sequences of all mRNAs have beforehand been masked by MaskerAid. Filtering programs with defined parameters compare the ends of each aligned sequence pair for deletions or insertions in the EST sequence, which suggest the existence of alternative splice forms. The database is accessible by typing in accession numbers (ACC) or keywords like description, gene names, organism or other keywords. (If more than one hit was found a list of all results is given.) And the result page is divided into 4 major parts. The first part (General Information About The Entry) summarizes the most important information as database ids, organism, and description. The so called alternative splice profile (ASP) of each human sequence is shown in the second part (Alternative Splice Frequency). The ASP indicates the number of alternatively spliced ESTs (NAE), the number of constitutively spliced ESTs (NCE) as well as the number of alternative splice sites (NSS) per mRNA. NAE and NCE corresponds to the EST coverage and can be used as a quality value for the predicted alternative splice variants. The NSS value specifies the splice propensity of a gene. Moreover the number of ESTs from cancerous tissues is shown. The histological source and the developmental stages are illustrated with several colors to enables the user to get an overview of the origins of the matching ESTs. Also, the Splice Site View shows graphically all alternative splice sites for the whole transcript.
EDGE: Environment, Drugs and Gene Expression
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. EDGE is a scientific resource for toxicology-related gene expression information. The site contains databases and analyses of gene expression studies following exposure to a variety of chemicals or physiological changes. The ultimate goal of the EDGE is to map transcriptional changes from chemical exposure that will someday be used as a diagnostic fingerprint to predict toxicity as well as provide valuable insights into the basic molecular changes responsible. EDGE gives you the ability to easily answer the following fundamental questions about your data 1. Can I compare transcriptional profiles across treatments? 2. What genes respond to my treatment? 3. What influences my favorite gene(s)? One of the major objectives of toxicology is to understand the adverse health effects that result from exposure to foreign chemicals. The traditional method for assessing the toxicity of a test chemical is very resource intensive; requiring the commitment of large amounts of money, time, and animals. According to the National Toxicology Program (NTP), each chemical study requires between 2 and 4 million dollars and several years to complete. Due to the cost and labor intensive nature of these studies, the number of chemicals currently tested by the NTP stands at less than 500. Given these statistics and the fact that there are approximately 70,000 chemicals in commerce today, it is increasingly apparent that alternative methods for assessing toxic potential must be explored if a significant portion of the remaining chemicals is to be tested. One potential solution is to develop a comprehensive database that describes alterations in gene expression resulting from chemical exposure. The pattern of transcriptional activity will not only be highly sensitive indicator of chemical exposure, but that this pattern will be diagnostic for mechanistically linked toxicants. In our laboratory, we have chosen to address this problem through a combination of high throughput sequencing of expressed sequence tags (ESTs) and construction of custom toxicology-related cDNA microarrays derived from the unique ESTs identified in the sequencing effort. By using this approach, we can simultaneously develop a quantitative gene expression profile using ESTs and the reagents for further analyzing these changes in a rapid, highly parallel manner. In addition, the expression profiles are not biased for preselected favorite genes. The resulting gene expression pattern can then be used as diagnostic fingerprint to predict toxicity and/or carcinogenicity as well as provide valuable insight into the basic biochemical and molecular changes responsible for toxicity. Submission of total RNA for Bradfield Lab Microarray Microarray comparisons are made between untreated, control animals and animals treated with ONE treatment. Please make sure the RNA submitted adheres to this experimental design. Necessary information is available on the site.
eTBLAST: a text-similarity based search engine
eTBLAST is a unique search engine for searching biomedical literature. Our service is very different from PubMed. While PubMed searches for keywords, our search engine lets you input an entire paragraph and returns MEDLINE abstracts that are similar to it. This is something like PubMed''s Related Articles feature, only better because it runs on your unique set of interests. For example, input the abstract of an unpublished paper or a grant proposal into our engine, and with the touch of a button you''ll be able to find every abstract in MEDLINE dealing with your topic. No more guessing whether your set of keywords has found all the right papers. No more sorting through hundreds of papers you don''t care about to find the handful you were looking for--our search engine does it for you. When most people use PubMed to search MEDLINE they pick one or two keywords to describe their topic, then browse through a long list of results. When they find a paper that looks interesting they click on its Related Articles, in hopes of finding more papers like that one. If they find another relevant paper, they explore it''s related articles--and so on. This process of culling long lists of documents by hand makes literature searching tedious and time consuming. We make it easier for you by providing better results the first time, and then allowing you to automatically combine the papers you care about for a second round. Our Iterate feature allows you to checkmark the abstracts you found interesting in the first round and combine them all to create a new query. It''s like rolling several Related Articles lists into one. * We sort our results by relevance, while PubMed sorts by date. * We save you the time and effort of creating a complicated query. * We let you iterate your search over several good papers to narrow your focus. * We provide you the full MEDLINE abstract in our results, and a link to the PubMed page. * We can send your results straight to your email so you never lose a reference or forget where you found it. * This absolutely free service is provided by the University of Texas Southwestern Medical Center. No registration necessary!
The Foundational Model Explorer (FME) is an internet based software application developed for viewing the content and organization of the Foundational Model of Anatomy Ontology (FMA). The initial purpose of the FME was to provide a simple and intuitive interface to the FMA for domain experts, in the field of anatomy, participating in the evaluation of the FMA. The FME also provides an easily available method of exploring the FMA to individuals or groups considering the adoption of the Foundational Model of Anatomy knowledge base. The FME display consists of two panes: a hierarchical tree may be opened up in the pane on the left side; if a class is selected in the hierarchical tree, the pane on the right side displays the information that has been entered in the FMA for that class. The information associated with a given class is organized in so-called slots. Each slot has a name (e.g., Definition, Parts) and some content, which is that particular slots value (e.g., the English definition and the names of parts of the selected class, respectively). For an explanation of the interactive features of the FME, see the Knowledge Navigation Section. For a guided tutorial check out the Conducted Tour. In the left pane, the default tree is a subclass hierarchy, based on the -is a- or -kind of- relationship; it is the instantiation of the Anatomy taxonomy (At) component in the high level scheme of the Foundational Model of Anatomy. Apart from the slots Preferred Name and Synonyms, other slots relate to the Anatomical Structural Abstraction (ASA) component in the FMAs high level scheme. Hierarchies based on various part-whole relationships can also be opened up in the left pane. Once a class has been highlighted in the subclass hierarchy, you can choose a relationship from a drop down list labeled Select navigation tree type. Some other transitive relationships (e.g., -branch of- and -tributary of-) are also available. The Search facility matches a search term to the preferred name, as well as to the Latin name, or synonym of an FMA class (if such exist). The tree is expanded to reveal the matching class and the information about this class is displayed. The wildcard * is allowed in the search term and will match to any sequence of characters. For example the search term h*d matches the class names Head and Hepatic cord (amongst others). The search function is not case sensitive. If more than one class name matches with the search term, a list of matching terms is presented for the user to choose between.
G2D - Candidate Genes to Inherited Diseases
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases.
JenPep is a database of quantitative binding data for immunological protein-peptide interactions. It is a system which allows speedy access to this binding data through simple on-line interfaces and effective search mechanisms.
A REST-based web application designed for visualizing deep sequencing data and other genome annotation data.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. It contains annotated structural elements characteristic for certain classes of structural and/or functional RNAs. These elements are described in a language specifically designed for this purpose. The language allows convenient specification of hybrid patterns, i.e. motifs consisting of sequence features and structural elements together with sequence similarity and thermodynamic constraints. A system that searches complex patterns (on nucleic-acid or protein level) in large biosequence-databases. As patterns, they allow hybrid patterns, which combine sequence similarity, structure similarity and arbitrary characteristics, like thermodynamic constraints. Applications are in the research of highly specific Protein/RNA-interactions or in the search of RNA-tertiary-structure-interactions. They developed a declarative pattern description language, which is implemented by known and new pattern-matching algorithms and an optimizing backtracking procedure. To achieve high efficiency when screening large data sets, the patterns are divided and queries are composed. The significance of patterns is estimated by a Monte-Carlo procedure. Complex results of queries are processed by a visualizing component. A library of biologically relevant patterns is developed and it is provided on the WWW together with the search-tool. The evaluation of the tool w.r.t. to the biosequence databases will in some cases mean to make laboratory-experiments, in order to check algorithmically developed functional hypothesis. Sponsors: This project is supported by a grant from the Deutsche Forschungsgemeinschaft. It is part of the special program on Computational Methods for the Analysis and Interpretation of large genomic data
INFOMINE: Scholarly Internet Resource Collections
INFOMINE is a virtual library of Internet resources relevant to faculty, students, and research staff at the university level. It contains useful Internet resources such as databases, electronic journals, electronic books, bulletin boards, mailing lists, online library card catalogs, articles, directories of researchers, and many other types of information. It is librarian built. Librarians from the University of California, Wake Forest University, California State University, the University of Detroit - Mercy, and other universities and colleges have contributed to building INFOMINE.INFOMINE is a unique Web resource featuring well organized access to important university level research and educational tools on the Internet. A virtual library, INFOMINE is notable for its collection of annotated and indexed links. Information in INFOMINE is easy to find given the multiplicity of access points provided (ways of finding the information contained). It contains over 100,000 links (26,000 librarian created links and 75,000 plus robot/crawler created links). Substantive databases, electronic journals, guides to the Internet for most disciplines, textbooks and conference proceedings are among the many types of resources included. The life sciences INFOMINE alone, for example, provides interactive access to several hundred databases. Separate virtual collections or INFOMINEs exist in most major areas of university level research and educational interests. Click here to see the Database Content Information. It began in January of 1994 as a project of the Library of the University of California, Riverside. It was one of the first Web resources of any type offered by a Library. It was also one of the first Web-based, academic virtual libraries as well as one of the first to develop a system combining the advantages of the hypertext and multi-media capabilities of the Web with those of the organizational and retrieval functions of a database manager. We now include focused, automatic Internet crawling as well as automatic text extraction and metadata creation functions to assist our experts in content creation and users in searching. Many of INFOMINE''s important features and services, described below, remain unique among Internet resource collections. INFOMINE, as mentioned, provides a great number of access points, BROWSE (What''s New, Title, Table of Contents, Subject -- LCSH, Subject - LCC, Search -- Research Discipline, Key Word, Megatopics - Keyword in context, Title, Author, hyperlinked indexing) and SEARCH (Title, Subject -- LCSH, Key Word, Author, Description, Full-text), and LIMIT search (Resource Type, Resource Origin and Access) modes. Searching in fielded and full-text mode allows the user to quickly find high quality resources on the chosen subject(s). Nested, boolean searching capabilities are featured as is exact searching. Search results come back in the form of dynamically created Web pages. Results within these can be ranked by relevance to the search or alphabetically by title. Displays available include title only, regular display, long display and full display. Many of the displays feature indexing terms that are viewable and in hyperlink form and, when clicked upon, allow further broadening or narrowing of the search as desired. Noteworthy as well is that INFOMINE is augmenting its content with a large, second-tier collection of automatically selected and described resources that should complement its first-tier collection of expert created records and allow the user more detail in searching and a greater number of useful results. Finally, on the Advanced Search page, we have browsing indexes which cover all topics and more. These include: * Subjects -- LCSH (Library of Congress Subject Headings), Table of Contents (LCSH with titles filing under each heading), LCC (Library of Congress Classifications) and Research Disciplines * Keywords -- MegaTopics (keyphrases drawn from our title, subject, keyword and annotation fields) and standard Keywords * Other Indexes: Authors, Titles, Resource Types and What''s New Among the contributions of INFOMINE is the essential enrichment or value added service, as mentioned, of providing concise descriptive information (e.g., an annotation as well as in-depth indexing terminology including Library of Congress Subject Headings) for each record. This greatly helps users to quickly retrieve a focused results set, examine the relevance of individual records and then choose among them immediately prior to accessing thus saving considerable time. Librarian collection expertise and concerns regarding resource comprehensiveness, quality and general usefulness from an academic perspective guide all INFOMINE resource selection activities. Also a crucial behind-the-scenes contribution from INFOMINE is that we are addressing the challenge of better subject portal scaling (keeping up with the growth of important resources on the Internet) by semi-automating or automating a number of collection building tasks (e.g., identification of significant resources for collecting and developing metadata descriptions of these resources). This will help us save crucial resources and redirect them into creating a better and larger collection. In-depth description and indexing, careful selection, a considerable number of options in browsing/searching, and ample help in usage mean that faculty, students and staff can find important, relevant Internet resources quickly and easily via INFOMINE. Sponsors: INFOMINE is supported by the University of California, Riverside.
International Toxicity Estimates for Risk
ITER is a toxicology data file on the National Library of Medicine''s (NLM) Toxicology Data Network. It contains data in support of human health risk assessments. It is compiled by Toxicology Excellence for Risk Assessment (TERA) and contains over 600 chemical records with key data from the Agency for Toxic Substances & Disease Registry (ATSDR), Health Canada, National Institute of Public Health & the Environment (RIVM) - The Netherlands, U.S. Environmental Protection Agency (EPA), and independent parties whose risk values have undergone peer review. ITER provides a comparison of international risk assessment information in a side-by-side format and explains differences in risk values derived by different organizations. ITER data, focusing on hazard identification and dose-response assessment, is extracted from each agencys assessment and contains links to the source documentation. Among the key data provided in ITER are ATSDRs minimal risk levels; Health Canadas tolerable intakes/concentrations and tumorigenic doses/concentrations; EPAs carcinogen classifications, unit risks, slope factors, oral reference doses, and inhalation reference concentrations; RIVMs maximum permissible risk levels; NSF International''s reference doses and carcinogen risk levels, IARC''s cancer classifications, and noncancer and/or cancer risk values (that have undergone peer review) derived by independent parties. Users can search by chemical or other name, chemical name fragment, or Chemical Abstracts Service Registry Number(RN), and/or subject terms. Search results can easily be viewed, printed or downloaded. Search results are displayed in relevancy ranked order. Users may select to display exact term matches, complete records, or any combination of data from the following broad groupings: -Noncancer Oral -Cancer Oral -Noncancer Inhalation -Cancer Inhalation
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. MAP-O-MAT is a web-based server for automated linkage mapping of human polymorphic DNA markers. The server uses publicly available genotype data for over 15,000 markers. It facilitates the verification of order and map distances for custom mapping sets using genotype data from the CEPH database, and from the Marshfield, SNP Consortium and Rutgers linkage maps. The CRI-MAP program is used for likelihood calculations and some mapping algorithms, and physical map positions are provided from the human genome assembly.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. International interdisciplinary Internet based unbiased forum for review of medical literature. Very much like an on-line journal club, we aim to provide a venue which will improve communication amongst physicians and lead to better understanding and interpretation of medical literature. In the academic world, Journal Clubs are a common way to discuss and critically question medical literature. The knowledge gained by this activity can be immeasurable, and often leads to ideas both relating to patient care and to future research. However, many clinicians are unable to participate in these academic activities. In addition, information shared within an individual journal club is seldom disseminated. Here you will find a free, user-friendly website where you can rate and discuss medical literature. It offers innovative and powerful search tools that will allow you to quickly query the medical literature and identify the information you need. In addition, their exclusive tools will help identify the most important and controversial articles. It is their hope to bring both insight and questions to the literature -- both of which will be used to shape future research. Clinicians will have a better understanding of the evidence, and ability to partake in a venue that fosters communication between peers.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. KinasePathwayDatabase is an integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface. The protein-protein interactions are extracted by natural language processing (NLP) from abstracts using basic word pattern and protein name dictionary GENA: developed by our group. In this system, pathways are easily compared among species using protein interactions data more than 47,000 and orthologous tables.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modeling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. It is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships. Key terms belonging to four different categories are used for the annotation process: -Genes: Names of genes and gene products. Gene name recognition is based on Ensembl . Synonyms and aliases are resolved. -Chemical Compounds: Names of chemical compounds and their respective aliases. -Diseases and Phenotypes: Names of diseases and phenotypes -Tissues and Organs: Names of tissues and organs LitMiner uses a database of disease and phenotype terms for literature annotation. Currently, there are 2225 diseases or phenotypes, 801 tissues and organs, and 10477 compounds in the database.
The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects. Its transcriptomic data provide invaluable information for molecular entomology study of the insect and pave a way for comparative studies of other medically, agronomically, and ecologically relevant insects. This first transcriptomic database of the locust (LocustDB) has been developed, building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. It currently hosts 45,474 high quality EST sequences from the locust, which were assembled into 12,161 unigenes. This database contains original sequence data, including homologous/orthologous sequences, functional annotations, pathway analysis, and codon usage, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. LocustDB also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. It starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporation of in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs.
University of West Bohemia; Pilsen; Czech Republic
The University of West Bohemia is a university in Pilsen, Czech Republic. It was founded in 1991 and consists of nine faculties.
Infers both the sample genotypes and error parameters that produced a metagenome data set.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. MILANO provides a useful tool for the automatic custom annotation of microarray results which is based on all the available literature. It has two major advances over similar tools: the ability to expand gene names to include all their informative synonyms while removing synonyms that are not informative and access to the GeneRIF database which provides short summaries of curated articles relevant to known genes. MILANO allows annotation of lists of genes derived from microarray results by user defined terms. The annotation strategy is based on counting the number of literature co-occurrences of each gene on the list with a user defined term. This strategy allows the customization of the annotation procedure and thus overcomes one of the major limitations of the functional annotations usually provided with microarray results. MILANO expands the gene names to include all their informative synonyms while filtering out gene symbols that are likely to be less informative as literature searching terms. It supports searching two literature databases: GeneRIF and Medline (through PubMed), allowing retrieval of both quick and comprehensive results. MILANO''s ability can improve microarray analysis by analyzing a list of 150 genes that were affected by p53 overproduction. This analysis reveals that it enables immediate identification of known p53 target genes on this list and assists in sorting the list into genes known to be involved in p53 related pathways, apoptosis and cell cycle arrest. This program performs automatic searches in PubMed or the GeneRIF collection for articles containing co-occurrences of search terms with a list of genes (e.g. from a microarray experiment). The program is used by pasting the list of Gene ID''s or symbols in the Primary Search Term field, and the list of cross-reference search terms in the Secondary Search Term field. The output is a table containing the number of hits for each pair of search terms. Sample input is provided in the fields, so you can just click submit and see what happens. If you want to run data of your own, delete the sample input first.
MIPS Mammalian Protein-Protein Interaction Database
The MIPS Mammalian Protein-Protein Interaction Database
The MIPS mammalian protein-protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published experimental evidence that has been processed by human expert curators. It is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions. To suit different users needs we provide a variety of interfaces to search the database: -Expert interface Simple but powerful boolean query language. -PPI search form Easy to use PPI search -Protein search Just find proteins of interest in the database Sponsors: This work is funded by a grant from the German Federal Ministry of Education and Research.
MitoRes, is a comprehensive and reliable resource for massive extraction of sequences and sub-sequences of nuclear genes and encoded products targeting mitochondria in metazoa. It has been developed for supporting high-throughput in-silico analyses aimed to studies of functional genomics related to mitochondrial biogenesis, metabolism and to their pathological dysfunctions. It integrates information from the most accredited world-wide databases to bring together gene, transcript and encoded protein sequences associated to annotations on species name and taxonomic classification, gene name, functional product, organelle localization, protein tissue specificity, Enzyme Classification (EC), Gene Ontology (GO) classification and links to other related public databases. The section Cluster, has been dedicated to the collection of data on protein clustering of the entire catalogue of MitoRes protein sequences based on all versus all global pair-wise alignments for assessing putative intra- and inter-species functional relationships. The current version of MitoRes is based on the UniProt release 4 and contains 64 different metazoan species. The incredible explosion of knowledge production in Biology in the past two decades has created a critical need for bioinformatic instruments able to manage data and facilitate their retrieval and analysis. Hundreds of biological databases have been produced and the integration of biological data from these different resources is very important when we want to focus our efforts towards the study of a particular layer of biological knowledge. MitoRes is a completely rebuilt edition of MitoNuc database, which has been extensively modified to deal successfully with the challenges of the post genomic era. Its goal is to represent a comprehensive and reliable resource supporting high-quality in-silico analyses aimed to the functional characterization of gene, transcript and amino acid sequences, encoded by the nuclear genome and involved in mitochondrial biogenesis, metabolism and pathological dysfunctions in metazoa. The central features of MitoRes are: # an integrated catalogue of protein, transcript and gene sequences and sub-sequences # a Web-based application composed of a wide spectrum of search/retrieval facilities # a sequence export manager allowing massive extraction of bio-sequences (genes, introns, exons, gene flanking regions, transcripts, UTRs, CDS, proteins and signal peptides) in FASTA, EMBL and GenBank formats. It is an interconnected knowledge management system based on a MySQL relational database, which ensures data consistency and integrity, and on a Web Graphical User Interface (GUI), built in Seagull PHP Framework, offering a wide range of search and sequence extraction facilities. The database is compiled extracting and integrating information from public resources and data generated by the MitoRes team. The MitoRes database consists of comprehensive sequence entries whose core data are protein, transcript and gene sequences and taxonomic information describing the biological source of the protein. Additional information include: bio-sequences structure and location, biological function of protein product and dynamic links to both, external public databases used as data resources and public databases reporting complementary information. The core entity of the MitoRes database is represented by the protein so that each MitoRes entry is generated for each protein reported in the UniProt database as a nuclear encoded protein involved in mitochondrial biogenesis and function. Sponsors: MitoRes has been supported by Ministero Universit e Ricerca Scientifica, Italy (PRIN, Programma Biotecnologie legge 95/95-MURST 5, Proiect MURST Cluster C03/2000, CEGBA). Currently it is supported by operating grants from the Ministero dellIstruzione, dellUniversit e della Ricerca (MIUR), Italy (PNR 2001-2003 (FIRB art.8) D.M. 199, Strategic Program: Post-genome, grant 31-063933 and Project n.2, Cluster C03 L. 488/929).
A database of manually annotated mammalian protein complexes. To obtain a high-quality dataset, information was extracted from individual experiments described in the scientific literature. Data from high-throughput experiments was not included.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on 6/24/13. A repository of information on commercially available phospho-specific antibodies to human phosphorylation sites. It provides a BLAST search for phosphorylation sites using as query the amino acid sequence surrounding the site. It also provides direct links to the relevant antibodies from many companies including BD Pharmingen, Biosource International, Cell Signaling Technology (CST), Santa Cruz Biotechnologies, Upstate Biotechnology.
National Cancer Institute 3D Structure Database
The NCI DIS 3D database is a collection of 3D structures for over 400,000 drugs. The database is an extension of the NCI Drug Information System. The structural information stored in the DIS is only the connection table for each drug. The connection table is just a list of which atoms are connected and how they are connected. It is essentially a searcheable database of three-dimensional structures has been developed from the chemistry database of the NCI Drug Information System (DIS), a file of about 450,000 primarily organic compounds which have been tested by NCI for anticancer activity. The DIS database is very similar in size and content to the proprietary databases used in the pharmaceutical industry; its development began in the 1950s; and this history led to a number of problems in the generation of 3D structures. This information can be searched to find drugs that share similar patterns of connections, which can correlate with similar biological activity. But the cellular targets for drug action, as well as the drugs themselves, are 3 dimensional objects and advances in computer hardware and software have reached the point where they can be represented as such. In many cases the important points of interaction between a drug and its target can be represented by a 3D arrangement of a small number of atoms. Such a group of atoms is called a pharmacophore. The pharmacophore can be used to search 3D databases and drugs that match the pharmacophore could have similar biological activity, but have very different patterns of atomic connections. Having a diverse set of lead compounds increases the chances of finding an active compound with acceptable properties for clinical development. Sponsor: The ICBG are supported by the Cooperative Agreement mechanism, with funds from nine components of the NIH, the National Science Foundation, and the Foreign Agricultural Service of the USDA.
Nh3D: A Reference Dataset of Structures of Non-homologous Proteins
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. It is a dataset of structurally dissimilar proteins. This dataset has been compiled by selecting well resolved representatives from the Topology level of the CATH database which hierarchically classifies all protein structures. These have been been pruned to remove: i) domains that may contain homologous elements (by pairwise sequence comparison and structural superposition of aligned residues) ii) internal duplications (by repeat detection) iii) regions with high B-Factor The statistical analysis of protein structures requires datasets in which structural features can be considered independently distributed, i.e. not related through common ancestry, and that fulfill minimal requirements regarding the experimental quality of the structures it contains. However, non-redundant datasets based on sequence similarity invariably contain distantly related homologues. Here a reference dataset of non-homologous protein domains is provided, assuming that structural dissimilarity at the topology level is incompatible with recognizable common ancestry. It contains the best refined representatives of each Topology level, validates structural dissimilarity and removes internally duplicated fragments. The compilation of Nh3D is fully scripted. The current Nh3D list contains 570 domains with a total of 90780 residues. It covers more than 70% of folds at the Topology level of the CATH database and represents more than 90% of the structures in the PDB that have been classified by CATH. Even though all protein pairs are structurally dissimilar, some pairwise sequence identities after global alignment are greater than 30%. Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB.
Generates data for use in developing and refining computational tools for comparing genomic sequence from multiple species. The NISC Comparative Sequencing Program's goal is to establish a data resource consisting of sequences for the same set of targeted genomic regions derived from multiple animal species. The broader program includes plans for a diverse set of analytical studies using the generated sequence and the publication of a series of papers describing the results of those analysis in peer-reviewed journals in a timely fashion. Experimentally, this project involves the shotgun sequencing of mapped BAC clones. For each BAC, an assembly is first performed when a sufficient number of sequence reads have been generated to provide full shotgun coverage of the clone. At that time, the assembled sequence is submitted to the HTGS division of GenBank. Subsequent refinements of the sequence, including the generation of higher-accuracy finished sequence, results in the updating of the sequence record in GenBank. By immediately submitting our BAC-derived sequences to GenBank, it makes their data available as a public service to allow colleagues to speed up their research, consistent with the now well-established routine of sequencing centers participating in the Human Genome Project. However, at the same time, it has made considerable investment in acquiring these mapping and sequence data, including sizable efforts of graduate students, postdoctoral fellows, and other trainees. Furthermore, in most cases, large data sets involving multiple BAC sequences from multiple species must first be generated, often taking many months to accumulate, before the planned analysis can be performed and the resulting papers written and submitted for publication.
Concise, clinically useful information for diagnosing, managing and treating infectious diseases in adults; however it does cover some pediatric topics including vaccines. It is designed for primary care providers and other non-infectious disease specialists as a tool that can be used at the point of care to assist in prescribing antibiotics.
NSDL: The National Science Digital Library
NSDL is a digital library of exemplary resource collections and services, organized in support of science education at all levels. Starting with a partnership of NSDL-funded projects, NSDL is emerging as a center of innovation in digital libraries as applied to education, and a community center for groups focused on digital-library-enabled science education. The National Science Digital Library (NSDL) was created by the National Science Foundation to provide organized access to high quality resources and tools that support innovations in teaching and learning at all levels of science, technology, engineering, and mathematics (STEM) education. As a national network of learning environments, resources, and partnerships, NSDL seeks to serve a vital role as STEM educational cyberlearning for the nation, meeting the informational and technological needs of educators and learners at all levels. Educators need efficient and reliable methods to discover and use science and math materials that help them meet the demands of instruction, assessment, and professional development in an increasingly complex technology-based world. NSDL provides an organized point of access to: -High-quality STEM content aggregated from a variety of other digital libraries, NSF-funded projects, and NSDL-reviewed web sites. -Services and tools that enhance the use of this content in a variety of contexts. NSDL is designed primarily for K-16 educators, but anyone can access NSDL.org and search the library at no cost. Access to most resources discovered through NSDL is free; however, some content providers may require a login, or a nominal fee or subscription to retrieve their specific resources. NSDL serves as a nexus for educators, researchers, policy makers and the public by building bridges: -Between private sector and public interests by providing access to resources such as publisher'' journal articles, teacher-created lesson plans and real-time data sets from scientists -Between the scientific, research and educational communities by applying advanced technologies to stimulate new ways for educators and learners to access and use scientific information -Between teachers and learners at all levels, in all locations by supplying content and tools in open-access, non-proprietary formats in an easily accessible online environment. Sponsors: This work supported by the National Science Foundation under Grant No. 0733600, Grant No. 0424671, Grant No. 0227648, Grant No. 0227656, and Grant No. 0227888.
CanPredict: A computational tool for predicting Cancer-associated mutations
Web application that uses a combination of computational methods to identify those changes most likely to be cancer-associated.
Efficient Mixed-Model Association (EMMA)
Statistical test for model organisms association mapping correcting for the confounding from population structure and genetic relatedness. EMMA takes advantage of the specific nature of the optimization problem in applying mixed models for association mapping, which substantially increases the computational speed and the reliability of the results. The current implementation of EMMA is available in an R package. The documentation is included in the installation package.
This website contains a list of elements from the periodic table. It provides information about the atomic mass, excess mass, binding energy, beta decay energy, half life, mode of decay, and possible parent nuclides for each isotope of the elements listed. Aside from the elements listed, the information for a neutron is also listed.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 18, 2013. 15 annotated electron micrographs of different parts of the nervous system. Different nerve tissues are depicted.
The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules. Macromolecular structures, as discovered by crystallographic or NMR methods, are scientific objects in much the same sense as fossil bones or dried specimens: they can be archived, studied, and displayed in aesthetically pleasing, educational exhibits. Hence, a museum seems an appropriate designation for the collection of displays that we are assembling. The OMM''s exhibits are interactive tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to illustrative renderings of the molecule at hand. Why devote a site to detailed visualizations of different macromolecules? In learning about the intricacies of life processes at the molecular level, it is important to understand how natural selection has fashioned the structure and chemistry of macromolecular machines to suit them for particular functions. This understanding is greatly facilitated by the visualization of 3-dimensional structure, when known. So, if static views of molecules (even in stereo) are worth a thousand words, then interactive animations of molecules should be worth much more. Indeed, we have found the types of displays represented here invaluable in gaining an appreciation for the details of key biochemical processes. Sponsors: This resource is federally-funded by the Protein Data Bank
OrthoDisease: A Database of Human Disease Orthologs
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. OrthoDisease is a comprehensive database of model organism genes that are orthologous to human disease genes. It was constructed by applying the Inparanoid ortholog detection algorithm to disease genes derived from the Online Mendelian Inheritance in Man database (OMIM). Over 1000 human genes have been associated with a disease phenotype to date and this number continues to rise on a daily basis. Studying their orthologous counterparts in model organisms assists in the understanding of the role these genes both in normal and pathological situations. A confounding factor in this process is that cross-species comparisons often identify genes which, although highly similar, do not represent a true ortholog and may in fact be functionally dissimilar. In order to resolve this we plan to identify truly orthologous genes in several model organisms, initially in the worm C. elegans, the fly D. melanogaster, the mustard weed A. thaliana and the yeast S. cerevisiae. They will collect and curate a set of genes that are associated with diseases by extracting and filtering excerpts from the Online Mendelian Inheritance in Man. The sequences of the resulting genes will then be analyzed and scored for orthology using methods previously developed at the Center for Genomics and Bioinformatics, primarily the Inparanoid algorithm. This will yield assignments of orthologs in model organisms, at different levels of confidence, forming the database OrthoDisease. Orthodisease is constructed primarily using Inparanoid analysis. Inparanoid is a program that automatically detects orthologs (or groups of orthologs) from 2 species. Pairwise comparisons between several model organisms are shown here. The species are derived mainly from the Ensembl resource as well as several submitted organism genomes. The program itself and accessory programs can be downloaded from the Inparanoid website.The algorithm is based on pairwise similarity scores which are by default calculated with NCBI BLAST program. Inparanoid detects best-best hits between sequences from 2 different species. These are the two seed ORTHOLOGS that form an orthologous group. Other sequences are added to this group if they are closely related to one of the main orthologs. These members of the orthologous group are called IN-PARALOGS. A confidence value is provided for each in-paralog that shows how closely related it is to the main ortholog. Genes/proteins are derived from the Online Inheritence In Man (OMIM) database, both from the Morbid map, which contains genes directly linked to specific diseases,and from the Genemap which contains genes with a know cytogenetic location that have been mentioned in OMIM (but not necessarily in morbidmap). Keyword: model, organism, gene, orthologous, human, disease, gene, Mendelian, man, phenotype, pathological, cross-species, C. elegans, D. melanogaster, mustard, weed, A. thaliana, yeast, S cerevisiae, genomic, bioinformatic, specie, Model Organisms and Comparative Genomics Databases
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. This is the official database of the environmental chlamydia genome project. This resource provides access to finished sequence for Parachlamydia-related symbiont UWE25 and to a wide range of manual annotations, automatical analyses and derived datasets. Functional classification and description has been manually annotated according to the Annotation guidelines. Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells. Environmental chlamydiae have recently been recognized as obligate endosymbionts of free-living amoebae and have been implicated as potential human pathogens. Environmental chlamydiae form a deep branching evolutionary lineage within the medically important order Chlamydiales. Despite their high diversity and ubiquitous distribution in clinical and environmental samples only limited information about genetics and ecology of these microorganisms is available. The Parachlamydia-related Acanthamoeba symbiont UWE25 was therefore selected as representative environmental chlamydia strain for whole genome sequencing. Comparative genome analysis was performed using PEDANT and simap. Sponsors: The environmental chlamydia genome project was funded by the bmb+f (German Federal Ministry of Education and Research) and is part of the Competence Network PathoGenoMiK.
Phylogenetic Clusters of Orthologous Groups Ranking
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 20,2019.The COG-database has become a powerful tool in the field of comparative genomics. The construction of this data-base is based on sequence homologies of proteins from different completely sequenced genomes. Highly homologous proteins are assigned to clusters of orthologous groups. The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies. The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Here is a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or approximately 54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of approximately 20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (approximately 1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes.
A database of binding affinities for the protein-ligand complexes in the Protein Data Bank (PDB). The PDBbind database is a collection of the experimentally measured binding affinities exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). It thus provides a link between energetic and structural information of those complexes and may be of great value to various molecular recognition studies. This site was last updated in 2007. The updated version of the resource is maintained by the Shanghai Institute of Organic Chemistry (http://www.pdbbind.org.cn).
Pacific Rim Applications and Grid Middleware Assembly
PRAGMA was formed to establish sustained collaborations and advance the use of grid technologies in applications among a community of investigators working with leading institutions around the Pacific Rim. Currently there are 35 institutions in PRAGMA, who meet twice a year at PRAGMA Workshops. In PRAGMA, applications are the key, integrating focus that bring together the necessary infrastructure and middleware to advance the applications goals. Sponsors: This resource is made possible by a grant from National Science Foundation Grant No. INT-0314015 and OCI-0627026.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. PDBfun is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. PDBfun is an integrated web tool for querying the PDB at the residue level and for local structural comparison. It integrates knowledge on single residues in protein structures coming from other databases or calculated with available or in-house developed instruments for structural analysis. Each set of different annotations represents a feature. Features are listed in PDBfun main page in orange. Features can be used for building residues selections.
Protein Data Bank (PDB) contains data on the spatial protein structures and their biologically active sites (i.e., ligand binding regions, enzyme catalytic centers, regions subjected to biochemical modifications, etc.). However, neither of the well known systems searching PDB does not provide the user with possibility to make the queries related with the active sites. A database PDBSITE storing the data on biologically active sites contained in the PDB database has been developed. PDBSITE accumulates amino acid content, structure features calculated by spatial protein structures, and physicochemical properties of sites and their spatial surroundings.
The Plasmid Genome Database aims to collate biological and genomic data for all bacterial plasmids in the hopes of enabling rapid, interrogation of both meta- and genomic data. Data maintained includes access to all plasmid genomes and information on core genomic features obtained from parsing the original EMBL/DDBJ/NCBI submission. In addition a suite of third party analyses has been performed for each genome to supplement the original annotation. This site also links to Genome Atlases provided by the Centre for Biological Sequence Analysis (CBS). The motivation behind the construction of this site derived from observations from genome sequencing projects: the abundance and inferred importance of the horizontal gene pool (HGP) in bacterial adaptation and evolution. In so far as plasmids are autonomously replicating, extrachromosomal elements they are a readily identifiable and accessible component of the HGP. Also plasmids have been identified in almost all bacterial divisions, ranging in size from less than 2 kbp to > 1.5 Mbp and as such represent a defined, yet diverse and complex sample of genes in the HGP.
Species 2000 is a federation of database organizations working closely with users, taxonomists and sponsoring agencies. The goal of the Species 2000 project is to create a validated checklist of all the world''s species (plants, animals, fungi and microbes). This is being achieved by bringing together an array of global species databases covering each of the major groups of organisms. Each database covers all known species in the group, using a consistent taxonomic system. The participating databases are widely distributed throughout the world and currently number 52. The existing global species databases presently account for some 60% of the total known species, so substantial investment in new databases will be needed for full coverage of all taxa to be achieved.
PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu.
The Protein Coil Library is a library of protein structure fragments derived from the Protein Data Bank (PDB). The fragments in this library are those fragments in the PDB that cannot be classified as either alpha-helix or beta-strand. Three-dimensional structures as well as side-chain and backbone torsion angles are stored in the database. The Protein Coil Library allows rapid and comprehensive access to non-alpha-helix and non-beta-strand fragments contained in the Protein Data Bank (PDB). The library contains both sequence and structure information together with calculated torsion angles for both the backbone and side chains. Several search options are implemented, including a query function that uses output from popular PDB-culling servers directly. Additionally, several popular searches are stored and updated for immediate access. The library is a useful tool for exploring conformational propensities, turn motifs, and a recent model of the unfolded state. The library stores the complete torsion angle descriptions for the fragments as well as the three dimensional structures of the fragments themselves. The goal of extracting and pre-calculating this data is to allow for more straightforward investigation of peptide structure without the background of secondary structure elements. In addition to searching by PDB ID, it is possible to download a particular size class, perform a batch search of PDB/chain ID''s, or download precompiled lists of PDB ID''s of interest (PDB Select, etc.). For users interested in browsing the entire database at once or maintaining their own locally-updated copy of the library, FTP access instructions are also provided. The files stored in the coil library FTP site or returned after a batch search are organized heirarchically by PDB ID. This is done to reduce filesystem access times and fascilitate searches using the UNIX find utility. At the lowest directory level in the heirarchy, files are further sorted by fragment length. As a result, the number of files in a particular directory is generally less then 50, yielding relatively fast access on UNIX/Linux filesystems. The heirarchical organization is based on the middle two letters of the PDB ID. For example, hen egg lysozyme, which has a PDB ID of 1HEL, will be located in the directory h/he/. At the final level, fragments of varying sizes are stored in directories that correspond to their fragment length. Again, using lysozyme as an example, any seven-residue fragments, if they exist, will reside in the directory h/he/7/. Similarly, seven-residue fragments from 2HEX and 1HE0 will also be in this location. Sponsors: The Protein Coil Library is funded by Johns Hopkins University.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 30, 2015. Refer to Proteome Analyst 3.0. Subcellular Localization and GO General Molecular Function predictions for many model organism proteomes using Protein Analyst, with a very high coverage rate. When users blast their proteins against the database of results, they will not only be shown blast homologs from the model organisms, but also the Subcellular Localization and GO General Molecular Function predictions as well.
PubCrawler is a free alerting service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases. PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests. The free PubCrawler web service has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. PubCrawler searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters (keywords, author names, etc.) specified by the user. There is no limit on the number of searches that can be carried out. Previous search hits are stored and only the newest PubMed or GenBank records are shown each day. The results are presented as an HTML Web page, similar to the results of an NCBI PubMed or Entrez query. This Web page can be located on our computer (the PubCrawler WWW-Service), on your computer (the stand-alone program), or you can receive it via e-mail (set this up using the PubCrawler WWW-Service). The Web page sorts the results into groups of PubMed/GenBank entries that are zero-days-old, 1-day-old, 2-days-old, etc., up to a user-specified age limit. Sponsors: Development of PubCrawler was supported by EMBnet
PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence. PubMatrix is a simple way to rapidly and systematically compare any list of terms against any other list of terms in PubMed. It reports back the frequency of co-occurrence between all pairwise comparisons between the two lists as a matrix table. Lists of terms can be anything; gene names, diseases, gene functions, authors, etc. The user can then quickly sort or browse the frequency matrix table to do individual searches independently. This allows the user to build up tables of word relationships in PubMed in the context of your experiments or your scientific interests. This is useful for analyzing combinatorial datasets, as found with multiplex experimental systems, such as cDNA microarrays, genomic, proteomic, or other multiplex comparisons. The PubMatrix database is an archive of previous searches on many topics. Sponsors: PubMatrix is supported by the National Institutes of Health.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26,2019. Portal that provides information about and links to immunostaining agents, protocols, discussion forums and an image gallery. Immunohistochemical Staining Immunohistochemistry (IHC) is a technique for identifying cellular or tissue constituents (antigens) by means of antigen-antibody interactions, the site of antibody binding being identified either by direct labelling of the antibody, or by use of a secondary labelling method. In Situ Hybridization (ISH) techniques allow the demonstration of specific nucleic acid sequences (genes) in their cellular environment.
Reciprocal Net - a distributed crystallography network for researchers students and the general public
Database of crystallographic information. Its membership includes crystallographic service facilities (that analyze crystals submitted by research chemists) located at major universities. These labs analyze anywhere from a few dozen to several hundred molecular structures each year and post the data online for the public to access. A distributed database engine takes care of shuttling this data across the Internet so that every structure can be located by the search engine. There may be a delay of a year or more between the time a structure is first analyzed and the time it finally becomes available for the public to see. This is due to intellectual property issues - the intervening time allows the chemists who first discovered the structure to publish it in a trade journal.
Literature database on disability and rehabilitation maintained by the National Rehabilitation Information Center. The database describes over 80,000 documents covering physical, mental, and psychiatric disabilities, independent living, vocational rehabilitation, special education, assistive technology, law, employment, and other issues as they relate to people with disabilities. The collection spans 1956 to the present. Full text search is supported.
The aim of the repairGenes site is to be a source of information about DNA repair genes and a useful resource for research on DNA repair. At the moment, the site contains information about a number of DNA repair genes from a set of selected species. The information is organized by organism and by biological process term as defined by the Gene Ontology (GO) project. The coverage of DNA repair genes is not complete, but hopefully it satisfies to demonstrate the concept and generate ideas for future versions of the system. At present, the raw data about DNA repair genes is extracted from the SWISS-PROT database, and categorized using the GO system. SWISS-PROT entries are being annotated by the Gene Ontology Annotation project at EBI. GOA is an ongoing project which will become more complete with time. As more data is released, this will be fed into repairGenes to keep it up-to-date. In future versions, the user will be able to search freely among organisms and categories of repair genes, enabling easy comparisons between species. For a taste of this, please have a look at the overview of repair genes from five major organisms. The amount of information in the system will be increased and the quality will be improved in the future. So will the features of the system.
Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level.
Silkbase''s objective is to build a foundation for the complete genome analysis of Bombyx mori.
It is divided to four categories based on extracellular signal molecules (Growth factor, Cytokine, and Hormone) and stress, that initiate the intracellular signaling pathway. SPAD is compiled in order to describe information on interaction between protein and protein, protein and DNA as well as information on sequences of DNA and proteins. There are multiple signal transduction pathways: cascade of information from plasma membrane to nucleus in response to an extracellular stimulus in living organisms. Extracellular signal molecule binds specific intracellular receptor, and initiates the signaling pathway. Now, there is a large amount of information about the signaling pathway which controls the gene expression and cellular proliferation. We have developed an integrated database SPAD to understand the overview of signaling transduction.
Database that provides access to mRNA sequences and associated regulatory elements that were processed from Genbank. These mRNA sequences include complete genomes, which are divided into 5-prime UTRs, 3-prime UTRs, initiation sequences, termination regions and full CDS sequences. This data can be searched for a range of properties including specific mRNA sequences, mRNA motifs, codon usage, RSCU values, information content, etc.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Toxics Release Inventory (TRI), a resource of the U.S. Environmental Protection Agency, is a set of publicly available databases containing information on releases of specific toxic chemicals and their management as waste, as reported annually by U.S. industrial and federal facilities. This inventory was established under the Emergency Planning and Community Right to Know Act of 1986 (EPCRA). TRI''s data, beginning with the 1987 reporting year, covers air, water, land, and underground injection releases, as well as transfers to waste sites. In agreement with the Pollution Prevention Act of 1990, source reduction and recycling data is also included in TRI. The Toxicology and Environmental Health Information Program (TEHIP) in the Division of Specialized Information Services (SIS) of the National Library of Medicine (NLM) provides access to TRI as part of its TOXNET (TOXicology Data NETwork) databases, which cover toxicology, hazardous chemicals, environmental health and related areas.
The Molecular Biology and Genetics Department at Bogazii University is one of the major reference laboratories in Turkey, specialized in molecular analysis of common genetic disorders. Over the years, the rapid accumulation of mutation data in connection with detailed clinical and laboratory information, has led to the idea of establishing a national database for storing, analysing and presenting it in a more efficient and systematic way. For this purpose, an interdisciplinary project was initiated in 1995. b-Thalassemia and Hemophilia-B Databases were selected as preliminary models, for they offer alternative design and implementation strategies due to different clinical and genetic characteristics. b-Thalassemia is an autosomal recessive disorder, characterized by microcytosis and hemolytic anemia, which is the result of reduced b-Globin chain synthesis. In Turkey, the disease is represented with a gene frequency of 2 and reflected by a wide spectrum of clinical manifestations with the presence of more than 40 different mutation. Currently, there is no database available for thalassemia mutations. Hemophilia B is an X-linked recessive disorder caused by heterogenous mutations, resulting in a marked deficit of coagulation factor IX (FIX); an essential component of the clotting mechanism. A hemophilia B database was first published in 1990 as a list of point mutations and short additions and deletions with 115 mutations comprising 216 entries Gene-, System-, or Disease- Specific Databases
Vivisimo''s mission is to help organizations maximize the business value of their information through innovations in search and discovery technology. Building on its other innovations, Vivisimo was first to offer enterprise social search, which lets enterprise users share their knowledge with coworkers by tagging, ranking, and annotating search results. Vivisimo''s founders first developed new ways to categorize search results as a research project at Carnegie Mellon University''s computer science department. After years of product development and further innovations, Vivisimo today offers Velocitya complete enterprise search platform that unifies access to secure business repositories, presents search results with an unmatched user experience, and enables knowledge sharing across an organization. Velocity is making single-search-box access to wide selections of corporate information a reality at organizations large and small. You can install Velocity in minutes, use its web console to configure access to diverse document, email, database, and web page repositories, and import their access rights so that searchers get just what they''re authorized to see and nothing more. Use the console to spotlight high-value information, package repositories into search tabs, enable clustered results by topic or meta-data, enliven the search results with embedded images, and more, all without custom programmingjust configuration.
Scripps Research Institute Florida Campus
Scripps Florida - The Scripps Research Institute
Research institute that focuses on basic biomedical science, drug discovery and technology development. The Scripps Florida research team focuses on the development of therapeutics in areas including neurology, cancer, the immune system, cardiovascular disease, metabolic disease, and infectious diseases. This institute has six departments: Cancer Biology, Molecular Therapeutics, Immunology and Microbial Science, Metabolism and Aging, Chemistry, and Molecular and Integrative Neurosciences. There is also the Translational Research Institute (TRI) which includes the following components: Discovery Biology, Drug Metabolism and Pharmacokinetics (DMPK), TRI-Informatics, Lead Identification and HTS, and Medicinal Chemistry. These groups collaborate in the discovery and development of new therapeutic agents. The Scripps Florida institute also offers a graduate program that emphasizes chemistry, chemical biology, biophysics and the biological sciences. This resource also provides a variety of programs for middle school, high school and college-age students to participate in research activities. These programs have a special emphasis on recruiting from historically underrepresented groups in the sciences.
Quantitative Insights Into Microbial Ecology
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.
World Health Organization Statistical Information System
WHOSIS, the WHO Statistical Information System, is an interactive database bringing together core health statistics for the 193 WHO Member States. It comprises more than 100 indicators, which can be accessed by way of a quick search, by major categories, or through user-defined tables. The data can be further filtered, tabulated, charted and downloaded. The data are also published annually in the World Health Statistics Report released in May. The WHO Statistical Information System is the guide to health and health-related epidemiological and statistical information available from the World Health Organization. Most WHO technical programs make statistical information available, and they will be linked from here. Sponsors: WHOSIS is supported by the World Health Organization. Note: The WHO Statistical Information System (WHOSIS) has been incorporated into the Global Health Observatory (GHO) to provide you with more data, more tools, more analysis and more reports.
The JCSG is a multi-institutional consortium that aims to explore the expanding protein universe to find new challenges and opportunities to significantly contribute to new biology, chemistry and medicine through development of HT approaches to structural genomics. The mission of JCSG is to to operate a robust HT protein structure determination pipeline as a large-scale production center for PSI-2. A major goal is to ensure that innovative high-throughput approaches are developed that advance not only structural genomics, but also structural biology in general, via investigation of large numbers of high-value structures that populate protein fold and family space and by increasing the efficiency of structure determination at substantially reduced cost. The JCSG centralizes each core activity into single dedicated sites, each handling distinct, but interconnected objectives. This unique approach allows each specialized group to focus on its own area of expertise and provides well-defined interfaces among the groups. In addition, this approach addresses the requirements for the scalability needed to process large numbers of targets at a greatly reduced cost per target. JCSG production groups are: - Administrative Core - Bioinformatics Core - Crystallomics Core - Structure Determination Core - NMR Core JCSG is deeply committed to the development of new technologies that facilitate high throughput structural genomics. The areas of development include hardware, software, new experimental methods, and adaptation of existing technologies to advance genome research. In the hardware arena, their commitment is to the development of technologies that accelerate structure solution by increasing throughput rates at every stage of the production pipeline. Therefore, one major area of hardware development has been the implementation of robotics. In the software arena, they have developed enterprise resource software that track success, failures, and sample histories from target selection to PDB deposition, annotation and target management tools, and helper applications aimed at facilitating and automating multiple steps in the pipeline. Sponsors: The Joint Center for Structural Genomics is funded by the National Institute of General Medical Sciences (NIGMS), as part of the second phase of the Protein Structure Initiative (PSI) of the National Institutes of Health (U54 GM074898).
Launched in 2004, the HIV Guide is a single disease resource, with two main parts: the HIV database, which is accessed by searching on diagnosis, drug name, pathogen, or management or by accessing the resistance tool, and there are also browsable areas of the site, which include news, features, continuing medical education programs and other types of additional readings and information. Guides are authored by academic clinicians and subject to rigorous peer review. You may browse the guide by: Diagnosis Covering opportunistic infections, malignancies, and complications of therapy. Drugs Includes indications, dosing, drug interactions, and author recommendations. Pathogen - Describes microbiology, clinical syndromes, and therapy. Management Including antiretroviral therapy guidelines and strategies. Resistance Tool Provides up-to-date interpretation of genotypic resistance test results. Whether searching for a drug, a pathogen, a diagnosis, or a management issue, your search results will be delivered in a concise and standard form designed to give you the most clinically useful information first, with the option to go deeper if you choose. If you search by diagnosis, you will receive a page listing points covering establishment of a diagnosis, related pathogens, treatment recommendations, issues to consider on follow up, references and more. At each step, we provide you immediately with the information you need to treat the diagnosis and give you the option to read more or more deeply if you choose. On the diagnosis page, you are also provided with links to the information sheet for each drug that may be prescribed, and if you indicate which drug you intend to use, you will be provided with relevant drug selected comments. If you search by drug, you will receive a page listing FDA indications, usual adult dosing, adverse drug reactions, drug interactions, spectrum, and forms. You are also able to access full pharmacological information (mechanism, absorption, Cmax, volume of distribution, protein binding, metabolism/excretion, t _, dosing for glomerular filtration of 50-80, dosing for glomerular filtration of 10-50, dosing for glomerular filtration of <10 ml/min, dosing in hemodialysis, dosing in peritoneal dialysis, dosing in cavh, dosing for decreased hepatic function, pregnancy risk, and breast feeding compatibility). If you search by pathogen, you will receive a page covering the microbiology, clinical relevance, sites of infection, drug selected comments, other information and references. You are also provided with links to information for each drug that may be prescribed, and if you indicate which drug you intend to use, you will be provided with the drug selected comments for that choice. If you search by management, you will receive a page listing definition, indications, and clinical recommendations and additional details, including references. If you click on more wherever it appears on a page, you will find more detailed material about the topic. In addition, the HIV Guide homepage contains a Features section and Literature Review that contain synopses and articles about pertinent topics. The Publications section also provides .pdf versions of the Hopkins HIV Report. Prices represent the cost per unit specified, reflecting the Average Wholesale Price (AWP). AWP prices are taken from the Red Book, manufacturer information, and the McKesson database. These prices are updated every six months. We have listed up to 10 FDA-approved indications for uses of drugs. Though in some cases more may exist, for brevity and formatting issues authors and editors have chosen what they deem the most important. Also listed are disease states for which a drug may be likely prescribed regardless of FDA approval status (see Non-FDA approved uses). The HIV Guide is primarily focused on adult care but does cover issues of perinatal transmission. The material presented on this site represents the considered opinion of the Hopkins expert listed as the author of the module as of the date indicated. The reference section contains an annotated list of the articles that the author considers to be most relevant to the topic. Where authoritative guidelines exist, such as CDC, IDSA or Medical Letter guidelines, they are referenced and discussed along with the author''s recommendations presented.
A human full-length cDNA sequence analysis database focused on mRNA varieties caused by variations of transcription start site (TSS) and splicing. Also available is ATGpr, a program for identifying the translational initiation codons in cDNA sequences. Data are derived from several full-length cDNA studies in Japan. Human gene number was estimated to be 20-25 thousand. However, the number of human mRNA varieties was predicted to be about 100 thousand. The varieties are thought to be caused by variations of TSS and splicing. In their previous human cDNA project, about 30 thousand of FLJ human full-length sequenced cDNAs were deposited to DDBJ/GenBank/EMBL, and they obtained about 1.4 million of 5''-end sequences (5''-EST) of FLJ full-length cDNAs from about 100 kinds of cDNA libraries consist of human tissues and cells constructed by oligo-capping method. The majority of the insert cDNA sizes were over 2 kb and the full-length rate of 5''-end was 90. And our FLJ cDNAs were covered about 80 of human genes. About 22 thousand of finished grades of full-length sequenced cDNAs were obtained in this project. The sequence analysis databases is focused on mRNA variations using human genome and cDNA sequences, FLJ full-length sequenced cDNAs, 5-ESTs of FLJ full-length cDNAs and other cDNA sequences described below. After those sequences were mapped onto the human genome sequences, clustering of the cDNA sequences were done based on the mapping results.
An initiative for Alzheimer's disease clinical studies that works to facilitate the discovery, development and testing of new drugs, and is a part of the Alzheimer's Disease Prevention Initiative. This resource has an emphasis on expanding the range of its patients, mainly by enhancing the recruitment of minority groups. There is a further emphasis placed on testing agents that cannot be patented, as well as developing novel compounds that had been developed by individuals, academic institutions and drug discovery units. This resource also helps in the development of Alzheimer's disease centers to carry out studies, as well as establish administrative, data, operations and medical cores in San Diego. This organization is specifically involved in studies demonstrating the lack of benefit associated, previously used treatments such as: the use of estrogen, non-steroidal anti-inflammatory drugs, B vitamins and a statin drug. The Alzheimer's Disease Cooperative Study also develops assessment instruments to be used in clinical trials. The most frequently used of these tools include: the Alzheimer's Disease Assessment Scale-Cognitive sub-scale (ADAS-cog), Activities of Daily Living (ADL), and the Clinical Global Impression of Change Scale (CGIC). There is also an associated tissue bank at UCSD that includes materials from the clinical trials including: human tissue, blood, plasma, DNA, urine and cerebrospinal fluid.
Fisher Center For Alzheimers Research Foundation: ALZinfo.org
A portal to educate, engage and create an online community. The Fisher Center for Alzheimer''s Research Foundation, founded in 1995, was created in answer to the recommendations of three U.S. Senate commissioned symposia held in the 1990s by the National Institutes of Health (NIH) to gather information on the cause, care and cure of Alzheimer''s disease. The Fisher Center was created following this design. The funding initiatives of the Foundation are appropriated accordingly to the three areas cited by the NIH task force cause, care and cure. The primary resources of the Foundation are directed toward scientific research into the cause and hopefully the cure of Alzheimer''s disease. To this end, the Foundation under the direction of its founder, Zachary Fisher, and in collaboration with David Rockefeller, constructed the Fisher Center for Alzheimer''s Disease Research at The Rockefeller University, headed by 2000 Nobel Prize winner, Paul Greengard, Ph.D. The 10,000 square foot laboratory is the most advanced facility of its kind in the country equipped with the latest in equipment necessary to undertake an interdisciplinary assault on this disease. The Fisher Center also has collaborative programs at the University of Genoa and supports the work of well over 60 scientists and researchers across the United States and in 17 foreign countries. The Foundation also funds projects for the care of people with Alzheimer''s disease and their caregivers. The Fisher Alzheimer''s Disease Education and Resources Program at the New York University School of Medicine was established under the direction of Barry Reisberg, M.D., internationally known expert in the care of Alzheimer''s patients. The Foundations Alzheimer''s Information Program was created in 2001 to answer the primary need of caregivers for comprehensive, easily accessible information. Our goals are to: Understand the Cause of Alzheimer''s To find a Cure for this devastating disease Improve the Care of people living with the disease to enhance their quality of life and that of their caregivers and families About Our Research Beating Back Beta Amyloid Improving the Quality of Life for Alzheimers Patients Reversing Nerve Cell Damage Using Hormones to Slow the Progress of Disease Curing Early-Onset Alzheimers The Science of Caregiving Scientific Studies
University of Freiburg Bioinformatics Group: Servers and Web-Applications
This resource takes you to the Server and Web-Applications of the University of Freiburg Bioinformatics Group. Sponsors: This resource is supported by University of Freiburg. Keywords: Server, Web application, Bioinformatics, Software,
National Institute on Aging, Division of Neuroscience
National Institute on Aging Division of Neuroscience
A funding resource that supports the research and training for understanding the structure and function of the aging nervous system, with an emphasis on studies involving Alzheimer's disease and age-related dementia. There is an emphasis on brain-behavior relationships. This program is composed of three branches: Neurobiology, Neuropsychology, and Dementias of Aging. The overall aim of this program is to understand the aging nervous system to minimize mental decline and improve the lives of older patients. This resource also includes links to sites for Alzheimer's disease (AD) studies that include: specimen repositories, genetic materials, bio-markers, data, policies on NIA and AD genetics sharing plans, and additional aging or other AD related links.
Core facility that provides the following services: Circulating Tumor Cell analysis, Circulating Tumor Cell Purification. The Circulating Tumor Cell Core Facility uses immunomagnetic technology developed by Veridex, LLC (Raritan, NJ) to isolate rare tumor cells from whole blood. Isolated tumor cells can then be counted or used for downstream analysis such as molecular studies or flow cytometry.
National Institute on Aging, Database of Longitudinal Studies
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 11, 2015. A searchable database for epidemiologic research on aging changes across the lifespan. In 2003, the National Institute on Aging (NIA) established the Longitudinal Data on Aging (LDA) working group to assist with the development of research initiatives for identifying the physiologic and other types of factors across the lifespan, affecting onset and progression of disease with advancing age, as well as elucidation of protective factors contributing to exceptionally healthy aging. This database was developed based on input from the LDA working group which indicated that establishing a database of existing sources of longitudinal data on aging (e.g., ongoing longitudinal cohorts, longitudinal data sets, biospecimen repositories) would be a valuable resource for facilitating future research on aging changes across the lifespan. The longitudinal studies, data sets and repositories included in this database encompass a wide range of age groups (childhood to old age), studies in minority populations, as well as sources of longitudinal data existing in the United States and abroad. Our primary purpose for establishing this database is to provide a resource for potential applicants for grants to the NIA. No part of this database can be used for commercial purposes.
Crustacean stomatogastric model neuron database
This page describes the contents of a database of 1.7 million model neurons. This database is available for interested researchers after contacting the creators, but is not web accessible. The construction and analysis of the database are described in detail in Prinz AA, Billimoria CP, Marder E (2003). Alternative to hand-tuning conductance-based models: construction and analysis of databases of model neurons. J Neurophysiol 90: 3998-4015. Because of its size (over 6 GB even in the zipped version), it is not practicable to download the database over the internet. Instead, we have made multiple copies of the database on sets of two DVDs each. We are happy to send a set of DVDs to anybody who is interested upon e-mail request to Astrid Prinz.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on Feb. 05, 2014, however, NIF holds the Research Crossroads data and makes it available through Integrated Grants. World of publicly funded research aggregated into a database providing funding, publication, clinical trial and grant data from government and private research agencies. Advanced reporting and analysis tools are then used to connect research to researchers, organizations and topic areas to uncover non-obvious associations. Use ResearchCrossroads for: Researchers * Make your research visible to funding organizations and collaborators. * Connect with peers to stay up to date on their research progress * Update your investigator profile, biography and publications so funding organizations can find you * Discover available funding from private foundations and government funding organizations * Annotate your previous research grants with outcomes * Create a research diary and participate in discussions with your peers Foundations Participating in ResearchCrossroads is free if you share your research data. Send us a spreadsheet with your grant and investigator information. * Create a community for your researchers to learn from each other * Locate potential investigators and collaborators * Post available funding and be matched with investigator profiles * Access to analytical reporting of funding and research statistics * Update your personalized organization profile page * Display your logo in search results * Link to your ResearchCrossroads grants and investigator profiles from your own website Corporations, Academia & Governments Contact us about subscriptions to funding trend analytics and marketing opportunities. * In-depth reporting of 15 years of funding data from government and private institutions * Subscriptions available to advanced analysis & reporting tools * Display your corporate logo in search results * Update your organization profile page * Highly targeted marketing & advertising by research areas, keywords and categories of investigator * Register for notifications of the newest grants in your area of interest
DIADEM Challenge: DIgital reconstruction of Axonal and DEndritic Morphology (DIADEM) Software Development Competition
A software development competition, the DIADEM Challenge,to benefit the scientific community by encouraging the development of better software for automating three-dimensional reconstructions of neuronal arbors. The intent of the Sponsors is to ensure that the best software submitted for the competition is made available to the scientific community within a reasonable time and on reasonable terms. No purchase is necessary to enter or win. The competition will have two rounds. As of April 10, 2009, individuals and teams may register to participate in the competition and may download sets of image stacks (Data Sets) of non-human animal brains along with three-dimensional reconstructions for some of these Data Sets for training purposes. Submissions of software, including executable programs, supporting documentation, and reconstruction files for the Data Sets, must be uploaded to the competition website no later than April 9, 2010. In order to be eligible to win the competition, the individuals and at least one member of any teams whose submissions are selected for the Final Round (Finalists) must participate in the Final Round and scientific conference. Personal participation in the Final Round and scientific conference is important for two main reasons: first, because the Finalists software will be tested at the Final Round against additional Data Sets so that the judges can select a winner or winners, and second, because the larger scientific conference, of which the Final Round will be a part, is intended to foster extensive scientific interaction among neuroscientists and computational scientists, including plenary and poster sessions to discuss challenges, solutions, and future directions. There are 5 datasets, all of which have to be reconstructed for the qualifier phase. Once you have registered your group, dataset download information will be sent to you via E-mail. The 5 datasets are: - Cerebellar Climbing Fibers - Hippocampal CA3 Interneuron - Neocortical Layer 6 Axons - Neuromuscular Projection Fibers - Olfactory Projection Fibers Sponsors: The sponsors of this competition are: Allen Institute for Brain Science, Seattle, Washington; Howard Hughes Medical Institute (HHMI), Chevy Chase, Maryland; and Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia.
A fast basecalling scheme for Illumina''s Next Generation sequencing machines, specifically designed for GAII.
MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyze MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms. Some features of MRIcro are: - Converts medical images to SPM friendly Analyze format. - View Analyze format images (big or little endian). - Create Analyze format headers (big or little endian). - Create 3D regions of interest (with computed volume & intensity). - Overlap multiple regions of interest. - Rotate images to match SPM template images. - Export images to BMP, JPEG, PNG or TIF format. - Yoked images: linked viewing of multiple images (e.g. view same coordinates of PET and MRI scans). Users familiar with other Windows programs will find that this software is fairly straightforward to use. Resting the mouse cursor over a button will cause a text hint to appear over the button. However, a tutorial with a step by step guide of how to use MRIcro with SPM is available.
University of Pennsylvania School of Medicine Penn Diabetes Research Center Pancreatic Islet Cell Biology Core Facility
Penn Diabetes Research Center Pancreatic Islet Cell Biology Core
Core that gives support including experimental design, islet isolation, and performance of and training in an expansive range of assays for physiological and morphometric assessment of pancreatic islet function and growth. It contributes to the basic and translational research activities of the Institute of Diabetes, Obesity and Metabolism (IDOM) at the Perelman School of Medicine of the University of Pennsylvania. Its services include perform individual islet and single cell fluorescence imaging, respirometry with islet batches using a Seahorse Extracellular Flux Analyzer, perifusion coupled with respirometry, and closed respirometry experiments for our investigators.
NIA''s ITP is a multi-institutional study investigating treatments with the potential to exte nd lifespan and delay disease and dysfunction in mice. Priority consideration will be given to the treatments that are easily obtainable, reasonably priced, and can be delivered in the diet (preferred) or water. Interventions that require labor intensive forms of administration, such as daily injections or gavage, are not feasible within the design of the ITP. Treatments currently under study include: - Pharmaceuticals - Nutraceuticals - Foods - Diets - Dietary supplements - Plant extracts - Hormones - Peptides - Amino acids - Chelators - Redox agents - Other agents or mixtures of agents Although the mice involved in this study will be housed at the University of Michigan, the Jackson Laboratories, and the University of Texas Health Sciences Center at San Antonio, the project is designed to involve collaborations with investigators at any university, institute, or other organization that has ideas about pharmacological interventions that might decelerate aging and wishes to test these in a lifespan study of mice. Sponsors: This program is supported by the National Institute of Aging.
A simple Java graphical user interface for running the program ISIM. ISIM is a package that simulates the thermodynamic ensemble of ions around a macromolecule using a grand canonical Monte Carlo scheme and simple hard sphere ion models. It is meant to provide an alternative mechanism to mean field approaches to allow the calculation of ion distributions around a highly charged molecule using a simple model that takes into account ion-ion correlations and steric interactions. The original source was created in the McCammon group at UCSD but is no longer available. The version of ISIM used is available in the ISIM project on simtk.org.
SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The other major component of SimTK is OpenMM which is packaged separately. This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions. SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering. Accessible High Performance Computing We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today''s practice, that means commodity multiprocessors and small clusters. The difference in performance between the best methods and the do-it-yourself techniques most people use can be astoundingeasily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as: Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present. The resulting pre-built binaries are available for download and immediate use. Audience: Biosimulation application programmers interested in including robust, high-performance physics-based simulation in their domain-specific applications.
NIA Non-Human Primate Centers and Tissue Banks
A resource that provides information on the vast number of resources available from the National Institute of Aging. NIA maintains approximately 150 primates (Macaca mulatta) at four regional primate centers where aging-related research is conducted. NIA also maintains colonies of aged rats and mice that are used for age-related disease research. This resource supports a multi-institutional study, the Interventions Testing Program (ITP), that investigates diets and dietary supplements that extend lifespan, delay disease and avoid dysfunction. NIA is also in charge of a microarray facility which provides filter arrays of 17,000 mouse cDNA clone sets that were developed at the NIA Intramural Research Program Laboratory of Genetics. NIA supports studies that provide biospecimens that can be shared for later research. This resource also helps the C. elegans Genetic Center at the University of Minnesota, which contains 1,000 strains of C. elegans that can be used for aging studies. This resource also provides a searchable database for epidemiological research on aging. There is access to social and behavioral research materials, including books on aging and health, from the research was conducted and supported by NIA. There are links to federal web sites that are further resources for aging research that were supported by NIA.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 16, 2016. The establishment of open access literature makes it possible for knowledge to be extracted from scholarly articles and included in other resources. BioLit aims to extract database identifiers and rich meta-data from open access articles in the life sciences and integrate that information with existing biological databases. We have begun prototyping this effort using a clone of the RCSB Protein Data Bank, a database of macromolecular structures. Cyberinfrastructure is integral to all aspects of conducting experimental research and distributing those results. However, it has yet to make a similar impact on the way we communicate that information. Peer-reviewed publications have long been the currency of scientific research as they are the fundamental unit through which scientists communicate with and evaluate each other. However, in striking contrast to the data, publications have yet to benefit from the opportunities offered by cyberinfrastructure. While the means of distributing publications has vastly improved, publishers have done little else to capitalize on the electronic medium. In particular, semantic information describing the content of these publications is sorely lacking, as is the integration of this information with data in public repositories. This is confounding considering that many basic tools for marking-up and integrating publication content in this manner already exist, such as a centralized literature database, relevant ontologies, and machine-readable document standards. We believe that the research community is ripe for a revolution in scientific communication and that the current generation of scientists will be the one to push it forward. These scientists, generally graduate students and new post-docs and have grown up with cyberinfrastructure as a part of their daily lives, not just a specialized aspect of their profession. They have a natural ability to do science in an electronic environment without the need for printed publications or static documents and, in fact, can feel quite limited by the traditional format of a publication. Perhaps most importantly, they appreciate that the sheer amount of data and the number of publications is prohibitive to the traditional methods of keeping current with the literature. Fink, L., Bourne, P. Reinventing Scholarly Communication for the Electronic Age, CTWatch Quarterly, Volume 3, Number 3, August 2007., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A biosimulation education and training resource for Neuromuscular Biomechanics, RNA folding, cardiovascular dynamics, and myosin dynamics. The repository contains educational, training, and teaching materials for physics-based simulation of biological structures.
Software tool for determining the statistically significant regions of activation in single or multi-subject human brain functional studies. It can be also applied to structural brain data for analyzing developmental, dementia and other changes of anatomy over time. This package was originally developed to work on Sun SPARC and SGI stations using the "C" language compiler provided by Sun/SGI as part of the standard system software.
Equipment access: All new users must be trained by the facility manager over two orientation sessions and be approved to use the equipment in the facility. All users must obtain the financial approval from their PI and financial manager. Please submit a PO number or the Harvard billing code prior to the first use of the facility.
A portable software framework for medical imaging research. jViewbox consists of a set of Java classes organized under a simple but extensive API that provides the core functionality of 2D image presentation needed by most imaging applications. It follows Java's Swing model closely to make it easy for application developers to build GUIs where end users can use various tools in a tool bar to manipulate the image displays. No optional add-ons or native code is used, which makes jViewBox compatible with any standard Java 2 Runtime Environment (version 1.3 or later).
A segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Its features include: segmentation of three-dimensional brain volumes into two or more regions (for example, regions could be WM, GM, and CSF), visualization of surfaces representing boundaries of different brain regions, and being written in Matlab with the ability to run on any platform with Matlab installed.
Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.The plugins use Java Image I/O interfaces to read and write metadata and image data and can read and write AFNI, ANALYZE 7.5, DICOM, ECAT 7.2, GE 5.0, INTERFILE (including hrrt), MINC, NIFTI, and UCLA PACS file formats. All source code is provided and usage examples are included.
The DualSurfaceMin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces. The method is developed for automatic surface extraction from noisy volumetric images. Its features include: global DSM, DSM-OS, and DSM-IS algorithms for automatic surface extraction from volumetric images using deformable simplex meshes; support for the VRML and OFF formats; output pf both triangulated and simplex meshes; and support for the raw and Analyze 7.5 image formats.
NIRC maintains and provides available research facilities accredited by the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International; a ready source of chimpanzees of mixed ages and sex for use in biomedical and behavioral sciences, and also provides professional staff necessary to support investigators with their research needs. Current Research: Vaccine development and testing; pharmacokinetic, pharmacodynamic, preclinical safety, and efficacy studies. Services Provided: The University of Louisiana at Lafayette-New Iberia Research Center (UL Lafayette-NIRC) is an AAALAC-International-accredited nonhuman primate research facility dedicated to the support of basic and applied biomedical and behavioral research. All proposed programs must be approved by the presenting institution and the UL Lafayette-NIRC animal care and use committees. State-of-the-art biomedical support facilities are available that include access to ultrasound, radiography with automatic processor and computer imagery for diagnostic enhancement, and endoscopy and laparoscopy with video monitors, camera and color photo imagery. Diagnostic Laboratory: A 12,000-square-foot laboratory is available for investigators'' research support requirements. Capabilities within the laboratory include but are not limited to hematology, chemistry, microbiology, urinalysis, parasitology, and histology. Among the investigator support procedures are Ficoll gradient isolation of peripheral blood mononuclear cells, platelet aggregation profiles, nonhuman primate lymphocyte proliferation assay, and flow cytometry (lymphocyte enumeration). Emergency generator power is accessible in each laboratory unit and for all major instrumentation and critical freezers. Animals: The center cares for approximately 360 chimpanzees and 5,500 New and Old World species of nonhuman primates. In addition to chimpanzees, the following species of nonhuman primates are being bred at the center: Vervet monkey (Chlorocebus aethiops), cynomolgus macaque (Macaca fascicularis), pigtailed macaque (M. nemestrina), rhesus macaque (M. mulatta).
Charged Fluid Model for Brain Image Segmentation
A computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model. It allows researchers to perform 2-D image segmentation in brain MR image data. Each interactive visualization element corresponding to the embedded function enables the end user to easily manipulate the image data. The visual environment of this tool provides an easy-to-use means of inspection and interpretation of image data using the LONI jViewbox library. CFMBIS uses the Java Image I/O plug-in architecture to read a wide variety of common medical image file formats.
University of Wisconsin-Madison; Wisconsin; USA
University of Wisconsin–Madison is a public research university in Madison, Wisconsin.UW–Madison is official state university of Wisconsin, and the flagship campus of the University of Wisconsin System. The UW is one of America's Public Ivy universities, which refers to top public universities in the United States capable of providing a collegiate experience comparable with the Ivy League.
Alcohol and Drug Abuse Institute, University of Washington
The Alcohol and Drug Abuse Institute is a multidisciplinary research center at the University of Washington. Its mission is to support and facilitate research and research dissemination in the field of alcohol and drug abuse. Recognizing the need to address the enormous problems caused by alcohol and drug abuse, the University of Washington established the Alcohol and Drug Abuse Institute in October of 1973 as an interdisciplinary research center in the Warren G. Magnuson Health Sciences Center. From its beginning, the mission of the Institute has been to conduct and support substance abuse research at the University of Washington, and disseminate research findings in substance abuse. The activities of the Institute may be described under three general headings: Intramural research by ADAI Research Scientists supported through federal, state, and other grants and contracts; Stimulation and support of research by ADAI Research Affiliates and faculty in departments throughout the University through a Small Grants Program. Since 1973, ADAI has awarded almost three million dollars to researchers in 40 University departments, for approximately 300 projects. Many of those funded projects led to outside funding for expanded research. Dissemination of research findings through its Library and Information Service, publications and presentations by ADAI scientists, web page, listservs, newsletters, and symposia. The Institute receives financial support from the State of Washington under state Initiative 171, which mandates that a portion of fees collected for state liquor licenses be allocated to the two state research universities for research on alcohol and drug abuse, and dissemination of research information. The University of Washington provides additional funding. Research studies are funded primarily through grants and contracts awarded by federal and state agencies and private foundations. The Alcohol and Drug Abuse Institute serves as a focal point for alcohol and drug abuse research at the University of Washington and in the region, benefiting the citizens of Washington State by expanding our knowledge and making information available to health and social service professionals and policy makers. The Institute''s multidisciplinary staff of clinical and social psychologists, sociologists, epidemiologists, public health experts, educators, and librarians plays a key role in working to understand and reduce the harm caused by alcohol and drug abuse. Dennis M. Donovan, Ph.D. has been the Director of the Alcohol and Drug Abuse Institute since 1993. Dr. Donovan is a Professor in the Department of Psychiatry and Behavioral Sciences and an Adjunct Professor in the Department of Psychology.
It is a very information rich protein structure database. Unfortunately, the PDB people are not very good at making their data available for search engines. There are several reasons why search engines often fail on the PDB: * The PDB has zillions of small administrative errors * The PDB-format is search-engine unfriendly * Many PDB files are incomplete The PDBFINDER project is a possible solution to these problems. The PDBFINDER holds for each PDB file a structured, search-engine-friendly-formatted entry that holds the data-items most likely needed for people search for certain types of PDB entries. The PDBFINDER is not useful to search in atomic coordinates; it is meant to ad searches in the administrative records of PDB files. Originally, the PDBFINDER was just for searching in PDB files. However, as all the time more people are using the PDBFINDER to aid modelling and database projects, they decided to also produce the so-called PDBFINDER2. The PDBFINDER2 also holds a lot of quality information about the PDB entries. Please only use the PDBFINDER2 if you really need that quality determination aspect because the PDBFINDER2 is five times bigger than the original PDBFINDER.
Washington University Basic Local Alignment Search Tool
It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterized genes.
Alzheimer Disease and Frontotemporal Dementia Mutation Database
A locus-specific database aimed at collecting known mutations and non-pathogenic coding variations in the genes related to Alzheimer disease (AD) and frontotemporal dementia (FTD), following the guidelines of the Human Genome Variation Society. Mutations can be retrieved based on the gene, phenotype and publication. The database contains mutations reported in the literature and at scientific meetings, and unpublished mutations directly submitted to the database. To date, AD&FTDMDB contains mutations in the genes encoding the Amyloid Beta Precursor Protein (APP), Presenilin 1 (PSEN1), Presenilin 2 (PSEN2), Chromatin Modifying Protein 2B (CHMP2B), fusion (involved in t(12;16) in malignant liposarcoma) (FUS), Granulin (GRN), Microtubule Associated Protein Tau (MAPT), TAR DNA binding protein (TARDBP) and Valosin-containing Protein (VCP) and holds 415 different mutations observed in 1027 patients or families. As of March 2013, the latest publications referenced were from 2008, indicating that this resource may not be up to date.
This resource contains news articles and commentaries on neuroscience, psychology, and cognitive science. Some articles are in English while most are in Italian. Please be aware that this portal is mostly in Italian.
A 501(c)(3) non-profit organization that gives out grants created to develop new therapies to control and reverse the causes of aging, as well as treat and prevent the diseases of aging. The goal is to eventually control the processes of aging, reverse their effects, and stay younger longer and ultimately create indefinite youthful, happy and productive lifespan using innovative scientific methods that are under development today in biotech companies and research labs around the world. The foundation also offers education on what we can do now to stay younger, live longer and be happier while new therapies are being developed.
THIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. A center that focuses on performing bio-medical research on nonhuman primates to aid in human health research. The center also focuses on training young scientists for professional careers in bio-medical research and primate biology. One of the New England Primate Research School's main accomplishments was the creation of an animal model for AIDS that first demonstrated that vaccine protection could be possible. Recent research has led to the development of novel agents for brain imaging that will aid in the diagnosis and treatment of Parkinson's disease.
Center that aims to develop biomedical technologies using nonhuman primate (NHP) models. Its goal is to uncover the root causes of various disease and disorders, unlock secrets of the brain, and unleash new methods of diagnostics and treatment.
Southwest National Primate Research Center
Center that supports studies of nonhuman primate models of human diseases, including common chronic diseases and infectious diseases and the effects that genetics and the environment have on physiological processes and disease susceptibility. SNPRC encourages the use of its resources by investigators from the national and international biomedical research communities.
Boston Area Diabetes Endocrinology Research Center Metabolic Physiology and Energy Balance Core Facility
Boston Area Diabetes Endocrinology Research Center Metabolic Physiology
Core in BADERC that provides services in consultation and teaching, use of DEXA scanner for determination of body fat and/or bone density, and use of Coulter Counter to measure cell number and cell size distribution.
University of California Davis Center for Comparative Medicine
The University of California Davis Center for Comparative Medicine (CCM) is a cooperative, interdisciplinary research and teaching center that is co-sponsored by the School of Medicine and the School of Veterinary Medicine. CCM Faculty members have academic appointments in one or both Schools. The CCM Research Mission is to investigate the pathogenesis of human and animal disease, using animal models or naturally occurring animal diseases. Areas of emphasis include host-agent interactions during infectious disease, intervention and prevention strategies for infectious diseases, cancer, and mouse biology. CCM faculty contribute a broad range of expertise to these areas, including the disciplines of immunology, genomics, pathology, biochemistry, physiology, microbiology, molecular virology, and informatics. Through its robust and interdisciplinary research programs, the CCM provides a rich academic environment for teaching at the professional, graduate, and post-graduate levels within the School of Medicine and School of Veterinary Medicine. Opportunities are available for professional students from both schools to gain research experience. PhD candidates can pursue training opportunities in the CCMs faculty-sponsored research laboratories, with support from a number of training grants. This diverse research environment is intended to attract and train high-quality candidates to the disciplines of comparative medicine, independent and collaborative research, and mouse biology. Sponsors: CCM is supported by UC Davis.
Open Library is a project of the non-profit Internet Archive, and is funded in part by a grant from the California State Library. They have a small team of fantastic programmers who have accomplished a lot, but we can''t do it alone! This is an Open project - the software is open, the data is open, the documentation is open, and the site is open. To build it, they need hundreds of millions of book records, a brand new database infrastructure for handling huge amounts of dynamic information, a wiki interface, multi-language support, and people who are willing to contribute their time, effort, and book data. To date, they have gathered about 30 million records (20 million are available through the site now), and more are on the way. They have built the database infrastructure and the wiki interface, and you can search millions of book records, narrow results by facet, and search across the full text of 1 million scanned books. Sponsors: Open Library is funded by a grant from the California State Library.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 27,2022.This program helps address the shortage of veterinarians who are trained for independent research. It supports veterinarians during the first 3 years of their PhD training. Trainees can participate in any graduate program involved in biomedical research at Stanford University: Biochemistry, Biological Sciences, Biophysics, Cancer Biology, Developmental Biology, Genetics, Immunology, Microbiology & Immunology, Molecular & Cellular Physiology, Molecular Pharmacology, Neurosciences, Structural Biology, Bioengineering, and Biomedical Informatics (graduate programs in biomedical research). All share common features: :1. Year 1 focuses on a limited group of courses and laboratory rotations. :2. Subsequent years focus on developing critical thinking via seminars and journal clubs and on independent research. :3. Annual retreats to present and learn about ongoing research in the graduate program. :4. Emphasis on mastering communications skills essential for success in science: oral presentation, writing manuscripts and grant proposals. :5. Developing an appreciation of the role of scientists in the context of society with emphasis on ethical and professional responsibility. Sponsors: It is funded by a T32 training grant from the NIH.
Johns Hopkins School of Medicine Department of Molecular and Comparative Pathobiology
Department of Molecular and Comparative Pathobiology
Provides leadership in biomedical research on animal and human diseases and assists with the health and humane care of research animals within the institution.
University of Missouri Comparative Medicine Program
Program provides advanced graduate training to veterinarians who wish to pursue careers in comparative medicine. Trainees may combine one year of residency training in clinical, administrative and diagnostic laboratory animal medicine with two or more years of research training. Alternatively, trainees with experience in laboratory animal medicine, comparative pathology or related disciplines may begin research training at the time of admission. Training is designed to prepare individuals for a variety of careers including comparative medicine research, clinical and administrative laboratory animal medicine and comparative and diagnostic laboratory animal pathology. Students may either pursue an MS or PhD. Research opportunities are available in several areas including infectious disease, pathology, molecular biology, mouse biology and cardiovascular physiology. Resources available include the University of Missouri Office of Animal Resources (OAR) and Research Animal Diagnostic Laboratory (RADIL) and Mutant Mouse and Rat Resource and Research Centers. The University of Missouri Comparative Medicine Program (CMP) is post Doctor of Veterinary Medicine training that combines graduate residency training, course work and research. Trainees with relevant experience in laboratory animal medicine or comparative pathology may pursue research training without residency training. In the residency year of training, two rotations are performed: diagnostic laboratory animal pathology in the Research Animal Diagnostic Laboratory (RADIL); clinical medicine and animal resource management in the Office of Animal Resources (OAR). The remaining two to four years focus on research training under an established investigator. After three years, trainees successfully fulfilling program requirements receive a certificate of residency training. MS students complete their program while PhD students continue to pursue research training. Sponsors: CMP is supported by the University of Missouri comparative, medicine, veterinarian, residency, training, clinical, administrative, diagnostic, laboratory, animal, pathology, cardiovascular, molecular, biology, mouse, physiology
Center for Comparative Medicine and Translational Research
The mission of the CCMTR is to promote scientific discovery and facilitate its clinical application to achieve the goal of improving the health of animals and humans. The needs of the patients direct the emphasis of basic research, patient samples provide the critical resource to investigate the basis of disease, and patient participation in clinical studies is required to generate the evidence needed to apply new drugs, vaccines and technology to the broader patient population. Initiatives at the Center are designed to develop the multidisciplinary teams necessary to bring an idea from the lab to the patient. The Center is home to service cores that provide advanced technology, collect and store clinical patient samples, and perform clinical trials to validate new medical interventions. North Carolina State University''s College of Veterinary Medicine (CVM) is a dynamic community whose members are dedicated to preparing veterinarians and veterinarian scientists while advancing animal and human health from the cellular level through entire ecosystems.
Laboratory animals are used in nearly half of all research projects supported by the National Institutes of Health. Significant needs exist at the national level for skilled scientists trained to work with and interpret the data generated from the use of rodent animal models. In response to this national need a research training program has been established through funding by the National Centers for Research Resources to provide an environment for veterinarians (D.V.M. or V.M.D.) and D.V.M./Ph.D.''s to effectively utilize mouse models of human disease. Specifically, veterinarian scientists are trained in state of-the-art molecular and cellular techniques to systematically evaluate the mechanistic pathobiology and phenotype of experimental mouse models of human disease. The training program is coordinated through an established graduate program in the College of Veterinary Medicine, Department of VeterinaryBiosciences and supported by a unified group of basic and clinical scientists with ongoing collaborative programs at The Ohio State University and Children''s Hospital. The scientists have expertise in endocrinology, infectious disease, genetics, oncology, molecular biology, immunology, physiology, biochemistry, and pathology. Trainees gain knowledge and skills to fully understand and evaluate pathophysiologic alterations of murine models of human disease through both didactic coursework and applied training in pathology and molecular biology. In addition, trainees interact with our multidisciplinary faculty to identify the range of research problems that use murine models. They acquaint themselves with the ongoing basic and clinical research studies in the laboratories and clinical sites of the participating faculty, and select a research problem that utilizes a murine model for endpoint evaluation. Following the selection of a preceptor and research problem, the trainee participates in the design and performance of experiments, as well as analysis and presentation of data regarding a murine model. Trainees develop skills in clinical, gross, and histologic pathology, molecular and immunologic techniques, and use transgenic and immunodeficient mouse models to identify and characterize alterations in embryonic and postnatal development. Therefore, trainees acquire a broad background in molecular biology, genetics, pathology, laboratory animal medicine, as well as research design methodology to fulfill national needs in the development of skilled scientists in mouse pathobiology. :Sponsors: Mouse Pathology Training Grant is funded by the National Centers for Research Resources.
The aim of the Summer Scholars Program is to provide veterinary medical students the opportunity to explore the world of biomedical research, develop and complete a biomedical research project during the summer. The intent is to engage students in a creative, problem-solving research activity and to provide a learning experience that will lead to the discovery of new knowledge in an area of their choosing and identify potential pathways to a career in biomedical research. Research plans will be developed by students with faculty mentor input, on any topic of interest to the student and likely to lead to the discovery of new information. Example topics are: immunology and infectious diseases, cancer biology, molecular epidemiology, experimental studies focused on nutrition and obesity, pharmacology, environmental toxicology, mechanisms of pathogenesis, zoonoses, biomechanics, cardiovascular pathophysiology, and others. The mentor and other advisors will provide guidance to students and an assessment of progress. Students will provide at completion of the study, an oral presentation of their results to their colleagues and all mentors and a presentation of results via posters at the annual Merial NIH National Veterinary Scholars Symposium, to be held in 2010 at the University of Georgia, and at the LSU Phi Zeta Research Emphasis Day. It is noteworthy that one Summer Scholar won an award at the 2008 LSU Phi Zeta Research Emphasis Day. LSU Students will receive elective credit in the curriculum (VMED 5010 or VMED 5463) for successful completion of the program. Students will be strongly encouraged to work with their mentors to publish their findings in peer-reviewed journals separately or as a smaller piece of work with their mentors. Sponsors: The program is funded by a Merial Foundation grant and an NIH T35 training grant.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software)
Post-DVM Training Program on Animal Model Research for Veterinarians
Virginia-Maryland College of Veterinary Medicine
An institutional training program to train veterinarians in conducting research. The program trains veterinarians in acquiring the skills of a researcher as they undergo a specific M.S. or Ph.D program. The program urges graduates to take part in research concerning animal models of infectious diseases, immunology, and nutrition, among other health topics.
Comparative Biomedical Sciences Graduate Program
The Comparative Biomedical Sciences Graduate Degree program provides exceptional graduate research training in core areas of animal and human health including genomics, immunology, molecular and cellular biology, physiology, infectious disease, neuroscience, pharmacology and toxicology, and oncology. Seventy-five faculty members in a diverse number of UW departments including Bacteriology, Biochemistry, Medical Microbiology and Immunology, Medicine, Oncology, Pathology, Radiology in addition to the 4 departments of the School of Veterinary Medicine are trainers in the program. These internationally recognized professors, as well as the integrative nature of our program, provide outstanding and unique research opportunities for our students. Because the University of Wisconsin is consistently ranked as one of the best 10 graduate institutions in the nation, the strength of our program is not only due to the superb research and teaching of our faculty but also due to the University as a whole. Approximately 55 students, most of whom are Ph.D. candidates, are currently enrolled in the program. Research strategies and academic curricula are tailored to the specific needs of each individual student. Graduates from our program are highly successful in the biotechnology industry and at top-ranked research institutions in the U.S. and abroad. The Comparative Biomedical Sciences Graduate Program offers a diverse number of research opportunities in multiple fields of study. A brief description of some of the major areas of research being performed by faculty affiliated with the Comparative Biomedical Sciences Graduate Program is provided below. Use the pull down menu above or click on the heading to find faculty members doing research in these areas. Sponsors: CBMS is supported by the University of Wisconsin
Basic Research Immersion Training Experience Veterinary Student Program
The BRITE Veterinary Student Program provides DVM students interested in research with a subsidized, in-depth mentored research experience. The opportunity can be used to gain research experience, to obtain an MS, or to jump-start a DVM/PhD program. The BRITE veterinary student program is designed to expose DVM students to hypothesis-driven research activities, methodologies involved in design and execution of laboratory experiments and ethical issues pertinent to biomedical research, at a formative stage of their veterinary education. BRITE veterinary students are given a unique opportunity to utilize the rigorous didactic basic science training obtained during the first two years of the professional curriculum in pursuit of a research problem relevant to human and animal health. Sponsors: The program is funded by Kansas State University.
Summer Fellowships - Comparative Medicine
The program seeks to help veterinary students become biomedical researchers. A secondary goal is to provide research experience to veterinary students interested in careers in laboratory animal medicine and/or pathology. Previous participants were veterinary students at Colorado State University, Cornell University, Kansas State University, Michigan State University, North Carolina State University, Ohio State University, Purdue University, Tufts University, Tuskegee University, University of California, University of Illinois, University of Tennessee, Washington State University, and Western University. The Program consists of workshops on research-related topics, a veterinary student journal club, sessions on research career development for veterinarians, an individual research project, and a veterinary student research symposium. The research project is the most important part of the Program. The goals of the research project are to have students address a significant experimental question, work independently and with other researchers, and produce and publish results. Students are matched with a preceptor (see list of faculty below) according to research interests. The preceptor outlines a focused project for the student to perform in their laboratory. Students become completely involved in their assigned laboratory participating in laboratory meetings and social events, attending seminars with other members of their laboratory, and working on their research project at least 40 hours/week.
Visionary: A Dictionary for the Study of Vision
It is a dictionary for terminology used in the study of human and animal vision. It includes terms from the areas of biological and machine vision, visual psychophysics, visual neuroscience and other related fields. Sponsors: Visionary is sponsored by Educational Software for Autism.
A cloud platform for next-generation sequencing analysis.
Summer Veterinary Student Research Fellows Program
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 28,2022. College of Veterinary Medicine Summer Veterinary Student Research Fellowship (SVSRF) Program provides stipends to first- and second-year professional veterinary students for a 12-week summer research experience. The purpose of the program is to introduce veterinary students to research in the hope that some will find this an attractive career option. The student fellows conduct full-time research during a 12-week period in the summer, with the advice and direction of a Faculty Mentor. An orientation to veterinary and biomedical research and the SVSRF program is provided at the beginning of the summer. Weekly lunch seminars and field trips to other research sites broaden and enrich the student''s exposure to veterinary research. The Program concludes with a Research Conference, during which the students present reports on their research activities, and a closing banquet. Student fellows are also strongly encouraged to participate in the Merck-Merial-NIH Veterinary Scholars Symposium with students from over 20 other colleges of veterinary medicine. Sponsor: The program is supported by Texas A&M University
This resource is geared towards providing educational video in various fields. All the videos are compiled from various sources and are freely accessible. Some of the topics covered are: - Business - Education - Engineering - Fine Arts & Design - Health & Medicine - History - Humanities - Journalism & Media - Law - Literature - Mathematics - Science - Social Science Sponsors: This resource is supported by YouTube, LLC.
Develops improved methods in analytical chemistry and bioinformatics to capture and utilize metabolomic data. These tools are employed to understand, which parts of larger biochemical networks respond to genetic perturbation or environmental stress.
ConnectomeViewer: Multi-Modal Multi-Level Network Visualization and Analysis
Extensible, scriptable, pythonic software tool for visualization and analysis in structural neuroimaging research on many spatial scales. Employing the Connectome File Format, diverse data such as networks, surfaces, volumes, tracks and metadata are handled and integrated. The field of Connectomics research benefits from recent advances in structural neuroimaging technologies on all spatial scales. The need for software tools to visualize and analyze the emerging data is urgent. The ConnectomeViewer application was developed to meet the needs of basic and clinical neuroscientists, as well as complex network scientists, providing an integrative, extensible platform to visualize and analyze Connectomics data. With the Connectome File Format, interlinking different datatypes such as hierarchical networks, surface data, volumetric data is easy and might provide new ways of analyzing and interacting with data. Furthermore, ConnectomeViewer readily integrates with: * ConnectomeWiki: a semantic knowledge base representing connectomics data at a mesoscale level across various species, allowing easy access to relevant literature and databases. * ConnectomeDatabase: a repository to store and disseminate Connectome files.
Information and human resource exchange services for academia and industries, professional and commercial societies from major industrial sectors and academic organizations. Events: Annual Drug Discovery Science & Technology (IDDST), World DNA and Genome Day celebrating the discovery of DNA double helix structure, Life science Forum, World AIDS Day, Pepcon Conference, iBio and World Cancer Congress.
IEEE is the worlds largest professional association advancing innovation and technological excellence for the benefit of humanity. IEEE and its members inspire a global community to innovate for a better tomorrow through its highly cited publications, conferences, technology standards, and professional and educational activities. IEEE is the trusted voice for engineering, computing and technology information around the globe. Through its global membership, IEEE is a leading authority on areas ranging from aerospace systems, computers and telecommunications to biomedical engineering, electric power and consumer electronics among others. Members rely on IEEE as a source of technical and professional information, resources and services. To foster an interest in the engineering profession, IEEE also serves student members in colleges and universities around the world. Other important constituencies include prospective members and organizations that purchase IEEE products and participate in conferences or other IEEE programs. IEEE has: -more than 375,000 members in more than 160 countries; 45 percent of whom are from outside the United States -more than 80,000 student members -329 sections in ten geographic regions worldwide -1,860 chapters that unite local members with similar technical interests -1,789 student branches in 80 countries -483 student branch chapters at colleges and universities -390 affinity groups -- IEEE Affinity Groups are non-technical sub-units of one or more Sections or a Council. The Affinity Group patent entities are Consultants'' Network, Graduates of the Last Decade (GOLD), Women in Engineering (WIE) and Life Members (LM) IEEE''s core purpose is to foster technological innovation and excellence for the benefit of humanity. It will be essential to the global technical community and to technical professionals everywhere, and be universally recognized for the contributions of technology and of technical professionals in improving global conditions., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An educational site providing accessible information about how the brain works and how people learn
The Computation and Neural Systems degree program is organized jointly by the Division of Biology, the Division of Engineering and Applied Science, and the Division of Physics, Mathematics and Astronomy. It is the program''s objective to provide a broad knowledge of this inherently multidisciplinary field, while at the same time requiring an appropriate depth of knowledge in the particular field of the thesis research. For example, a student working on cooperative circuits for early visual processing will also develop an in-depth knowledge of the anatomy and electrophysiology of early visual areas and a knowledge of visual psychophysics. A student working on olfactory cortex electrophysiology and its simulation would include the study of concurrent processing and the ethology of olfaction, and the relevant knowledge of dynamical and collective systems. A student working on the theory of complex systems could study collective and statistical properties of physics as well as the anatomical and algorithmic structure of biological and applied networks. Sponsors: The computational and neural systems is funded by the California Institute of Technology.
The general goal is to achieve a deeper understanding of natural image statistics because from this knowledge it should be possible to explain the behavior of the visual cortex and propose new alternatives in a number of applications in image processing and computer vision in which the basic problem is the choice of an appropriate signal representation. The range of basic and applied topics in which we are currently working include: * Mathematical models of human vision * Statistical image models * Image distortion metrics * Image coding * Motion estimation * Video coding * Image restoration * Color representation
Conical: The Computational Neuroscience Class Library
CONICAL is a C++ class library for building simulations common in computational neuroscience. Currently its focus is on compartmental modeling, with capabilities similar to GENESIS and NEURON. Future classes may support reaction-diffusion kinetics and more. A key feature of CONICAL is its cross-platform compatibility; it has been fully co-developed and tested under Unix, DOS, and Mac OS. Any C++ compiler which adheres to the emerging ANSI standard should be able to compile the CONICAL classes without modification. It is intended to encourage the rapid development of simulator software, especially on non-Unix systems where such software is sorely lacking. The present focus of the CONICAL library of C++ classes is compartmental modeling. A model neuron is built out of compartments, usually with a cylindrical shape. When small enough, these open-ended cylinders can approximate nearly any geometry, just as the stack of cylinders approximates a cone in the logo above. While any compartment has passive electrical properties (like a simple resistor-capacitor circuit), more interesting properties require the use of active ion channels whose conductance varies as a function of the time or membrane voltage. A standard Hodgkin-Huxley ion channel is included as one of the built-in CONICAL object types. Most of the voltage-gated ion channels in the literature can be directly implemented merely by setting the parameters of this class. For extensibility, this class is derived from several layers of more general classes. Connections between neurons can be implemented in several ways. For a gap junction (i.e., simple electrical connection), a passive current (or pair of currents, one in each direction) can be used. Synapses are more complex objects, but used in a similar fashion. The Alpha-function synapse is a very popular model of synaptic transmission, and is a basic CONICAL class. More complex (and realistic) synapses can be built using the Markov-model synapse. (A Markov model can be used on its own for other purposes as well.) In addition to classes directly related to neural modeling, CONICAL contains several other useful object types. These include a current injector, and a column-oriented output stream for storing data in table form.
CVonline: The Evolving, Distributed, Non-Proprietary Online Compendium of Computer Vision
The Compendium is a collection of hypertext summaries on the central topics in computer vision. We have organized an index of about 700 topics. (The top-level categories are listed at the bottom of this message.) Everyone will have written some notes on a few topics - we propose to set up the WWW links from the central index to your text. Thus, everyone can benefit from your efforts, and the computer vision community can advance by having a common set of widely read text materials available at virtually no expense to your library nor students. The Compendium is intended to be a clear summary of methods and applications of computer vision, organized into sections covering the main topics of practice and research. Each section will contain a number of topics, and each topic will be a hyperlink to a set of materials associated with that text. Sponsors: CVonline is a projected funded by the Edinburgh University.
Combines genetic and epigenetic data to facilitate SNP classification, prioritization and prediction of their functional effect.
Components And Tools for Accessible COmputer Modeling in (neuro)Biology
Catacomb consists of a set of frameworks for various types of models in neuroscience, user interfaces to facilitate building models within these frameworks, and numerical algorithms to compute their behavior. The available frameworks include reaction kinetics, reaction diffusion systems, kinetic scheme models of ion channels, small neuron models and integrate and fire networks. It is a library of models (data structures and algorithms) covering a range of problems in neuroscience together with a versatile graphical user interface for constructing and running specific instances of the models. Some features of Catacomb include: * Class models. There is a growing set of classes containing data structures and calculation methods for various problem domains in neuroscience - reaction schemes, stochastic channel models, integrate-and-fire networks, cell geometry et al. * Dynamic interface builder. Using Java''s reflection capabilities, individual user interfaces are constructed for each class model allowing new instances to be created and displaying the results of any calculation methods they may contain. * Parameter watching. Using Java threads, the calculations are rerun and results displayed whenever parameters upon which they depend are changed. * Session recording. Operations can be recorded and played back for illustrating how to use Catacomb or for preconfigured demonstrations of model behavior. * Compatible with JPython. Catacomb does not include its own interpreter except in the minimal sense required to parse its own saved files. But its objects and methods are accessible to JPython which can be used for command line access or scripting. * Applet building. The contents of windows in the display can be extracted and packaged together in a single panel for loading as an applet. The model is saved as a java source file which, once compiled, can be packaged with the original Catacomb archive for loading from a Web page. See the AppletConfigEditor.
University of Wollongong; New South Wales; Australia
Public research university in New South Wales, Australia which offers degree programs across a wide spectrum of disciplines, as well as providing research facilities to scientists
Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Vision Science is a large discipline at the ANU that is found in several teaching and research faculties and several large research institutes. About 85 research staff participate in all forms of vision science from machine vision, to neurophysiology, behaviour and cognition. The scale of analysis ranges from molecular to systems approaches and covers insect, vertebrate and human visual systems. Topics such as disease and development of the human visual system are also covered. CVS works to connect and sustain the component parts of the ANU vision science community.
This website contains a list of classic articles in visual perception. They are listed alphabetically by the last name if the article''s author.
Non profit, private research and education institution that performs molecular and genetic research used to generate methods for better diagnostics and treatments for cancer and neurological diseases. Research of cancer causing genes and their respective signaling pathways, mutations and structural variations of the human genome that could cause neurodevelopmental and neurodegenerative illnesses such as autism, schizophrenia, and Alzheimer's and Parkinson's diseases and also research in plant genetics and quantitative biology.
This page leads you to some screen shots from the Color Vision Demonstrations program CVD for IBM PCs and compatibles as described in this reference: Irtel, H. (1992). Color-vision demonstrations on an IBM PC/AT with VGA. Behavior Research Methods, Instruments, & Computers, 24, 88-89. Note that in order to display these images correctly you need a true color display with 8 bits resolution per color channel.
This web site focuses on neuroscience, the study of the nervous system. Links on this page are limited to those Dr. Chundler finds to be the most interesting and useful.
Human and Information Science Laboratory
This site provides information about the NTT Human and Information Science Laboratory. Technologies that enable users to get along well with information and technologies that can handle information properly on computers and networks are the keys to secure and high-quality information distribution services in a network society. In realizing those technologies, a comprehensive understanding of how human beings, the creators and the recipients of information, process information and novel principles for handling information are indispensable. From this viewpoint, the NTT Human and Information Science Laboratory has been pursuing scientific research in two areas: Sensory and Emotion Research, and Sensory and Motor Research. Sponsors: This resource is supported by NTT Communication Science Laboratories.
Collection of some common optical illusions
The mission of the Institute is to discover the key principles by which brains work and to implement these in artificial systems that interact intelligently with the real world. The Institute of Neuroinformatics is built of many people covering a wide range of disciplines and research areas. The major research projects and areas are listed below. - Behavior and Cognition: At the Institute of Neuroinformatics researchers investigate in Behavior and Cognition on various levels, ranging from neuronal circuit models of learning and adaptation over psychophysical experiments for color constancy up to modeling complex behavioral tasks such as exploration and goal-directed navigation. - Computation in Neural Circuits: By examining the brains of cats, rats and monkeys, and by making simulations of the cortex, INI hopes to learn how this circuit performs such widely different tasks. This knowledge might lead to advances in how computers are designed, and will certainly lead to advances in the subtlety and power of medical neuroscience. - Neurotechnologies: INI aims to harness the principles of biological computation, which can be expected to have a major impact on the technology market as autonomous intelligence pervades equipment, vehicles, buildings, utilities and clothing. Sponsors: INI is supported by European Union (EU), Gerbert Ruf Stiftung, Neuroscience Center (ZNZ), Swiss Confederation (KTI), Swiss Federal Institute of Technology Zurich (ETH), Swiss National Science Foundation (SNF), University of Zurich (UZH), and VW Stiftung
MaNIS is a database and infrastructure meant to facilitate open access to combined specimen data from a web browser, enhance the value of specimen collections, conserve curatorial resources, and use a design paradigm that can be easily adopted by other disciplines with similar needs. With support from the National Science Foundation, seventeen North American institutions and their collaborators developed the Mammal Networked Information System. The original objectives of MaNIS were to 1) facilitate open access to combined specimen data from a web browser, 2) enhance the value of specimen collections, 3) conserve curatorial resources, and 4) use a design paradigm that can be easily adopted by other disciplines with similar needs. As an NSF-funded initiative, MaNIS has achieved these objectives while avoiding the need for long-term, external maintenance of the network and centralized data management. As MaNIS faces the future, it is only through expansion of the network, both nationally and internationally, that the real impact of this collaborative effort will be maximized. Participation by other institutions is now welcome and those wishing to join have at their disposal the data standards, software and documentation that were developed for this project. All that is asked of future participants is that they make the same institutional commitment as the original collaborators to maintain their repositories of high-quality specimen collections and make the accompanying data available for the benefit of all. At the time of its inception, development of MaNIS addressed the urgent call for natural history museums to come together to build and support a biodiversity informatics infrastructure to facilitate and enhance research, education, conservation, and public health. That call has now been answered. It is hoped that continued expansion of the network will allow the preservation and sustainable use of biodiversity in all its complexity as we attempt to address the magnitude of human impacts on the Earth''s ecological systems during the 21st century. Supported by NSF
Center that conducts multidisciplinary studies on captive baboons and provides a resource of laboratory-born and laboratory-reared baboons for NIH-sponsored research programs.
Phenote: A Phenotype Annotation Tool using Ontologies
Phenote is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies. It provides an interface and infrastructure to record genotype-phenotype pairs, together with the provenance for the annotation. Typical users of Phenote include literature curators, laboratory researchers, and clinicians looking for a method to record data in a user-friendly and computable way. Features of Phenote include the use of any OBO-format ontology, ontology navigation and term information display, bulk sort, copy, edit, and delete of phenotype-genotype character entries, and a variety of export formats. Phenote is a project of the Berkeley Bioinformatics Open-Source Projects (BBOP).
Mayavi: 3D Scientific Data Visualization and Plotting Software Project
Software packages for 3D visualization: Mayavi2 for data visualization and TVTK for object manipulation.
A web catalog of over 1M antibodies from hundreds of different companies and other research supplies. Biocompare has made large quantities of data available to the antibodyregistry.org facilitating tagging important research reagents to literature and continues to work with the antibodyregistry.
This website provides summary collections written for a broad audience highlighting some of the significant advances in a particular field. These are not scientific articles although they may reference scientific work. Sponsors: This resource is supported by Nature.com
A database of 3D magnetic resonance (MRI) images of fish accessible to scientists, educators and the general public via the web. The Marine Vertebrate Collection at the Scripps Institution of Oceanography provides the majority of the DFL specimens.
Clinical and Translational Science Awards Consortium
Clinical and Translational Science Awards
National consortium of medical research institutions working together to transform the local, regional, and national environment to increase the efficiency and speed of clinical and translational research across the country. Consortium members share a common vision to reduce the time it takes for laboratory discoveries to become treatments for patients, to engage communities in clinical research efforts and to train clinical and translational researchers. This consortium includes 60 medical research institutions located throughout the nation, linking them together to energize the discipline of clinical and translational science. The CTSA consortium has five Strategic Goals: * National Clinical and Translational Research Capability * The Training and Career Development of Clinical and Translational Scientists * Consortium-Wide Collaborations * The Health of our Communities and the Nation * T1 Translational Research
Supplier of xiphophorus (platyfish or swordtails) from pedigreed parental lines, representing variety of species. In addition to supplying strains and providing consultation on husbandry and genetic questions, the XGSC produces custom interspecies hybrids (both first generation F1, and backcross hybrid generation BC1) for a variety of projects.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. An integrated packages of tools for microarray data analysis. GEPAS provides a web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-color microarray experiments and other preprocessing options), to the final step of the functional profiling of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), which include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management.
Isofinder: Isochore Computational Prediction
Isofinder is an algorithm running on the web able to predict isochores at the sequence level. Isochores are long genome segments homogeneous in G+C. The algorithm works by moving a sliding pointer from left to right along the DNA sequence and computing the mean G+C values to the left and to the right of the pointer at each point. Additionally, the program checks whether this significance exceeds a probability threshold. If so, the sequence is cut at this point into two subsequences; otherwise, the sequence remains undivided. The procedure continues recursively for each of the two resulting subsequences created by each cut. This leads to the decomposition of a chromosome sequence into long homogeneous genome regions (LHGRs) with well-defined mean G+C contents, each significantly different from the G+C contents of the adjacent LHGRs. Most LHGRs can be identified with Bernardi''s isochores, given their correlation with biological features such as gene density, SINE and LINE (short, long interspersed repetitive elements) densities, recombination rate or single nucleotide polymorphism variability. The resulting isochore maps are available at http://bioinfo2.ugr.es/isochores/, and also at the UCSC Genome Browser (http://genome.cse.ucsc.edu/). Sponsors: Isofinder is funded by Universidad de Granada, Spain.
G protein receptor interaction feature finding instrument
Griffin (G-protein-receptor interacting feature finding instrument) is a high-throughput system to predict GPCR - G-protein coupling selectively with the input of GPCR sequence and ligand molecular weight. This system consists of two parts: 1) HMM section using family specific multiple alignment of GPCRs, 2) SVM section using physico-chemical feature vectors in GPCR sequence. G-protein coupled receptors (GPCR), which is composed of seven transmembrane helices, play a role as interface of signal transduction. The external stimulation for GPCR, induce the coupling with G-protein (Gi/o, Gq/11, Gs, G12/13) followed by different kinds of signal transduction to inner cell. About half of distributed drugs are intending to control this GPCR - G-protein binding system, and therefore this system is important research target for the development of effective drug. For this purpose, it is necessary to monitor, effectively and comprehensively, of the activation of G-protein by identifying ligand combined with GPCR. Since, at present, it is difficult to construct such biochemical experiment system, if the answers for experimental results can be prepared beforehand by using bioinformatics techniques, large progress is brought to G-protein related drug design. Previous works for predicting GPCR-G protein coupling selectivity are using sequence pattern search, statistical models, and HMM representations showed high sensitivity of predictions. However, there are still no works that can predict with both high sensitivity and specificity. In this work we extracted comprehensively the physico-chemical parameters of each part of ligand, GPCR and G-protein, and choose the parameters which have strong correlation with the coupling selectivity of G-protein. These parameters were put as a feature vector, used for GPCR classification based on SVM.
Human Hereditary Diseases of Proteolysis
This resource has cataloged a total of 80 human hereditary diseases caused by mutations in protease-coding genes, which implies that more than 10% of the human protease genes are involved in human pathologies. They are classified in three groups: loss of function, gain of function, and an heterogeneous group including non-protease homologs (np), putative proteases, and hedgehog proteins with only autoprocessing activity. Type of inheritance is indicated by R (recessive) or D (dominant).
Caribbean Primate Research Center Program
Center for the study of non-human primates. Its mission is the study and use of non-human primates as models for studies of social and biological interactions and for the discovery of methods of prevention, diagnosis and treatment of diseases that afflict humans. Through the stewardship of three unique facilities—Cayo Santiago Field Station, Sabana Seca Field Station, and the Laboratory of Primate Morphology supports a diverse range of research programs that enhance understanding of primate biology and behavior, with direct applications in biomedical and translational research.
Fluorescent Allele-calling Software Toolkit: Microsatellite Automation Package
Fluorescent allele-calling software toolkit: a computer software for fully automated microsatellite genotyping. (entry from Genetic Analysis Software)
The GeneSeeker allows you to search across different databases simultaneously, given a known human genetic location and expression/phenotypic pattern. The GeneSeeker returns any found gene names which are located on the specified location and expressed in the specified tissue. To search for more expression location in one search, just enter them in the textbox for the expression location and separate them with logical operators (and, or, not). You can specify as many tissues as you want, the program starts 20 queries simultaneously, and then waits for a query to finish before starting another query, to keep server loads to a minimum. You can also search only for expression, just leave the cytogenetic location fields blank, and do the query. If you only want to look for one cytogenetic location, only fill in the first location field, and the GeneSeeker will search with only this one. Housekeeping genes , found in Swissprot can be excluded, or genes that are to be excluded can be specified. Human chromosome localizations are translated with an oxford-grid to mouse chromosome localizations, and then submitted to the Mgd. Sponsors: GeneSeeker is a service provided by the Centre for Molecular and Biomolecular Informatics (CMBI).
WebProAnalyst provides web-accessible analysis for scanning the quantitative structure-activity relationships in protein families. It searches for a sequence region, whose substitutions are correlated with variations in the activities of a homologous protein set, the so-called activity modulating sites. WebProAnalyst allows users to search for the key physicochemical characteristics of the sites that affect the changes in protein activities. It enables the building of multiple linear regression and neural networks models that relate these characteristics to protein activities. WebProAnalyst implements multiple linear regression analysis, back propagation neural networks and the Structure-Activity Correlation/Determination Coefficient (SACC/SADC). A back propagation neural network is implemented as a two-layered network, one layer as input, the other as output (Rumelhart et al, 1986). WebProAnalyst uses alignment of amino acid sequences and data on protein activity (pK, Km, ED50, among others). The input data are the numerical values for the physicochemical characteristics of a site in the multiple alignment given by a slide window. The output data are the predicted activity values. The current version of WebProAnalyst handles a single activity for a single protein. The SACC/SADC may be defined as an estimate of the strongest multiple correlation between the physicochemical characteristics of a site in a multiple alignment and protein activities. The SACC/SADC coefficient makes possible the calculation of the possible highest correlation achievable for the quantitative relationship between the physicochemical properties of sites and protein activities. The SACC/SADC is a convenient means for an arrangement of positions by their functional significance. WebProAnalyst outputs a list of multiple alignment positions, the respective correlation values, also regression analysis parameters for the relationships between the amino acid physicochemical characteristics at these positions and the protein activity values.
SVM based method for predicting beta hairpin structures in proteins
Bhairpred server is based on machine learning technique SVM using single sequence information, evolutionary profile, predicted and observed secondary structure (as obtained using Psipred and DSSP), predicted and observed accessibility values (as obtainned from Netasa and DSSP). The methods were trained and tested on dataset of 2880 proteins and their performance was evaluated on dataset of 534 proteins used by Thornton (PNAS, 2002). Best prediction results were obtained with hybrid approach that combined prediction results from evolutionary profile, predicted secondary structure and accessibility.
The Genetic Analysis Workshops (GAWs) are a collaborative effort among genetic epidemiologists to evaluate and compare statistical genetic methods. For each GAW, topics are chosen that are relevant to current analytical problems in genetic epidemiology, and sets of real or computer-simulated data are distributed to investigators worldwide. Results of analyses are discussed and compared at meetings held in even-numbered years. The GAWs began in 1982 were initially motivated by the development and publication of several new algorithms for statistical genetic analysis, as well as by reports in the literature in which different investigators, using different methods of analysis, had reached contradictory conclusions. The impetus was initially to determine the numerical accuracy of the algorithms, to examine the robustness of the methodologies to violations of assumptions, and finally, to compare the range of conclusions that could be drawn from a single set of data. The Workshops have evolved to include consideration of problems related to analyses of specific complex traits, but the focus has always been on analytical methods. The Workshops provide an opportunity for participants to interact in addressing methodological issues, to test novel methods on the same well-characterized data sets, to compare results and interpretations, and to discuss current problems in genetic analysis. The Workshop discussions are a forum for investigators who are evolving new methods of analysis as well as for those who wish to gain further experience with existing methods. The success of the Workshops is due at least in part to the focus on specific problems and data sets, the informality of sessions, and the requirement that everyone who attends must have made a contribution. Topics are chosen and a small group of organizers is selected by the GAW Advisory Committee. Data sets are assembled, and six or seven months before each GAW, a memo is sent to individuals on the GAW mailing list announcing the availability of the GAW data. Included with the memo is a short description of the data sets and a form for requesting data. The form contains a statement to be signed by any investigator requesting the data, acknowledging that the data are confidential and agreeing not to use them for any purpose other than the Genetic Analysis Workshop without written permission from the data provider(s). Data are distributed by the ftp or CD-ROM or, most recently, on the web, together with a more complete written description of the data sets. Investigators who wish to participate in GAW submit written contributions approximately 6-8 weeks before the Workshop. The GAW Advisory Committee reviews contributions for relevance to the GAW topics. Contributions are assembled and distributed to all participants approximately two weeks before the Workshop. Participation in the GAWs is limited to investigators who (1) submit results of their analyses for presentation at the Workshop, or (2) are data providers, invited speakers or discussants, or Workshop organizers. GAWs are held just before the meetings of the American Society of Human Genetics or the International Genetic Epidemiology Society, at a meeting site nearby. We choose a location that will encourage interaction among participants and permit an intense period of concentrated work. The proceedings of each GAW are published. Proceedings from GAW16 were published in part by Genetic Epidemiology 33(Suppl 1), S1-S110 (2009) and in part by Biomed Central (BMC Proceedings, Volume 3, Supplement 7, 2009). Sponsors: GAW is funded by the Southwest Foundation for Biomedical Research.
Structure modeling of 907 G protein coupled receptors in the human genome
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19,2019.Database of tertiary structural modeling results of threading assembly refinement (TASSER) method for all 907 G protein-coupled receptors (GPCRs) in human genome. All sequences were collected from GPCR database http://www.gpcr.org/7tm/ and http://www.expasy.org/cgi-bin/lists?7tmrlist.txt. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. G protein-coupled receptors (GPCRs), encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction of endogenous signal into a cellular response. Although tertiary structural information is crucial for function annotation and drug design, there are few experimentally determined GPCR structures. To address this issue, we employ the recently developed threading assembly refinement (TASSER) method to generate structure predictions for all 907 putative GPCRs in the human genome. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. These features are essential for the comprehensive modeling of all human GPCRs when close homologous templates are absent. Based on a benchmarked confidence score, approximately 820 predicted models should have the correct folds. The majority of GPCR models share the characteristic seven-transmembrane helix topology, but 45 ORFs are predicted to have different structures. This is due to GPCR fragments that are predominantly from extracellular or intracellular domains as well as database annotation errors. Our preliminary validation includes the automated modeling of bovine rhodopsin, the only solved GPCR in the Protein Data Bank. With homologous templates excluded, the final model built by TASSER has a global C(alpha) root-mean-squared deviation from native of 4.6 angstroms, with a root-mean-squared deviation in the transmembrane helix region of 2.1 angstroms. Models of several representative GPCRs are compared with mutagenesis and affinity labeling data, and consistent agreement is demonstrated. Structure clustering of the predicted models shows that GPCRs with similar structures tend to belong to a similar functional class even when their sequences are diverse. These results demonstrate the usefulness and robustness of the in silico models for GPCR functional analysis. Sponsors: GPCR is funded by the University at Buffalo, Buffalo, New York.
The aim of the PEROXISOME database (PeroxisomeDB) is to gather, organize and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders. PeroxisomeDB contains the complete peroxisomal proteome of Homo sapiens (encoded by 85 genes) and Saccharomyces cerevisiae (encoded by 61 genes). Now, we have included 34 new organism genomes with the acquisition of 2426 new peroxisomal homolog proteins. PeroxisomeDB 2.0 integrates the peroxisomal metabolome of whole microbody family by the new incorporation of the glycosome proteomes of trypanosomatids and the glyoxysome proteome of Arabidopsis thaliana. The site also provides a Peroxisome Metabolome of peroxisomal genes and proteins, their molecular interactions and metabolic pathways, tools for comparative genomics, predictive tools. Sponsors: Preoxisome Database is funded by Institut de Gntique et deBiologie Molculaire et Cellulaire.
The knot server allows the user to check PDB entries or uploaded structures for knots and to visualize them. The size of a knot is determined by deleting amino acids from both ends. This procedure is, however, not perfect and the resulting size should only be treated as a guideline. Mathematically, knots are only well defined in closed (circular) loops. However, both the N- and C-termini of open proteins are typically located close to the surface of the protein and can be connected unambiguously: We reduce the protein to its backbone and draw two lines outward starting at the termini in the direction of the connection line between the center of mass of the backbone and the respective ends. The two lines are joined by a big loop, and the structure is topologically classified by the determination of its Alexander polynomial. To determine an estimate for the size of the knotted core, we successively delete amino acids from the N-terminus until the protein becomes unknotted. The procedure is repeated at the C-terminus starting with the last N-terminal deletion structure that contained the original knot. For each deletion, the outward-pointing line through the new termini is parallel to the respective lines computed for the full structure. Unfortunately, the size of a knot is not always precisely determined by this procedure, so reported sizes should therefore only be treated as approximate. Sponsors: Knots is funded by MIT.
Paris School of Neuroscience PhD Program
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 31, 2022. The Paris School of Neuroscience (ENP) is a network of outstanding neuroscience laboratories in Paris area, within major universities and research institutes. ENP aims at facilitating graduate training of selected students in the Paris area. It covers all areas of Neuroscience and associated methodologies, from fundamental to clinical and from molecular to cognitive. It brings together a majority of the outstanding teams in Neuroscience in le-de-France region. ENP forms a network of research groups, scientific and technological facilities, and research centers, with recognized expertise in Neuroscience, which is original at the international level. Pre-PhD and PhD programs are open to highly talented and motivated students, who received their undergraduate training outside of France, irrespective of their original disciplines. Pre-PhD > Up to a year of rotations in participating laboratories. This can include a Masters degree. PhD > Three year program (with possible one year extension). Training and Courses > Courses in neuroscience and relate topics ? International Conferences and seminars ? French language courses ? Individual supervision by a tutor and a thesis committee ? Annual retreat with faculty members and guest scientists. Principal activities : -Coordinating the offers of the associated universities to organize an advanced international doctoral training program -Facilitating collaborative efforts and innovative research of the participating laboratories -Attracting outstanding scientists to the le-de-France region and facilitating their setting up in Paris area -Organizing joint activities, including seminars, conferences, summer schools, workshops, symposia, etc.
Homologous Sequences in Ensembl Animal Genomes
Database of homologous genes from Ensembl organisms, structured under ACNUC sequence database management system. It allows to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. It is possible to search for orthologous genes in a wide range of taxons. HOMOLENS is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOMOLENS gives an overall view of what is known about a peculiar gene family. Note that HOMOLENS is split into two databases on this server: HOMOLENS contains the protein sequences while HOMOLENSDNA contains the nucleotide sequences. Protein sequences of HOMOLENS have been generated by translating the CDS of HOMOLENSDNA and using associated cross-references to generate the annotations.
KCCMR Rhesus Monkey Breeding and Research
Keeling Center for Comparative Medicine and Research Rhesus Monkey Breeding and Research
This colony provides a national resource of rhesus monkeys and their tissues to carry out research benefiting the scientific community. The RMBRR maintains a colony of monkeys that have been derived to be specific pathogen free for members of both the herpes and retrovirus families. Over its history, the RMBRR has developed specialized management techniques, housing facilities and highly trained staff to avail these purposefully bred laboratory models, which are 93% genetically identical to humans, to researchers worldwide. Historically, this animal model has been instrumental in research involving blood classification, polio vaccine development, and drug safety and efficacy while currently they are the preferred model for studying the mechanisms of immunodeficiency diseases. Their susceptibility to Simian Immunodeficiency Virus and their homology to the human major histocompatibility complex (MHC) Class I, II and TCR genes make them valuable in HIV research. They are currently the models of choice for HIV/AIDS vaccine development and study. Other areas of research include atherosclerosis, myocarditis, alcoholism, diabetes, cancer and aging. The overall objectives of this resource are to improve the resources available at the RMBRR and to conduct resource-relevant research that improves both the health of the rhesus colony and its usefulness for studies of human disease. The Resource and Management Core is responsible for providing animal resources, tissues/biological fluids, cell lines, expert advice and research support to NIH extramural and intramural programs, other federal agencies and to private sponsors. The Resource-Related Research Core conducts research to improve the health of the animals maintained with special emphasis on studies that will enhance the usefulness of the rhesus as a model for studies of human disease.
Kyte-Doolittle hydropathy plots give you information about the possible structure of a protein. A hydropathy plot can indicate potential transmembrane or surface regions in proteins i did not find a parent or sponsor
National Institutes of Health Stem Cell Tables
Data tables providing an overview of information about stem cells that have been derived from mice and humans. The tables summarize published research that characterizes cells that are capable of developing into cells of multiple germ layers (i.e., multipotent or pluripotent) or that can generate the differentiated cell types of another tissue (i.e., plasticity) such as a bone marrow cell becoming a neuronal cell. The tables do not include information about cells considered progenitor or precursor cells or those that can proliferate without the demonstrated ability to generate cell types of other tissues. The tables list the tissue from which the cells were derived, the types of cells that developed, the conditions under which differentiation occurred, the methods by which the cells were characterized, and the primary references for the information.
A Comprehensive Resource Base for C. elegans K+ Channels
Resource Base for C. elegans K+ Channels
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Supplies potassium channel cDNA clones in vectors suitable for functional expression and stocks of gene knockout strains. Supporting this resource base are studies showing the basic biophysical properties of the channels, studies showing the phenotypes of mutants, and information on the cell-type expression patterns of potassium channels. Studies of potassium channel cell-type expression patterns and functional properties; studies of behavioral phenotypes; generation of knockout mutants. Full-length cDNAs encoding C. elegans potassium channels in a vector suitable for functional expression in Xenopus oocytes and mammalian cell lines are available on request. Information is also provided describing the cell-type expression patterns and basic biophysical properties of potassium channels. And data on behavioral phenotypes are also available. C. elegans strains carrying knockouts of potassium channels are also generated and deposited at the C. elegans stock center at the University of Minnesota.
Center where Aplysia californica are cultured and raised for research purposes. Aplysia from the facility serve in research on genomics, human brain function, toxicology for developmental studies, natural products, chemistry for isolation of novel anti-tumor and antibacterial compounds, in the study of transport by digestive tissues and have potential for use in studies of substance addiction and nerve senescence and regeneration.
Resource Center For Tetrahymena Thermophila
Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites.
Ancillary Domains Associated With Human and Mouse Proteases
Domains found in human and mouse proteases colour-coded according to the catalytic class in which they appear. Some of them appear in more than one catalytic group, and two-colours are used. Yellow, aspartyl proteases; blue, cysteine proteases; green, metalloproteases; and red, serine proteases.
Center dedicated to understanding and treatment of neurological diseases by creating and using imaging methods to study human nervous system. Dedicated to research imaging of human brain. Brain structure is imaged using anatomical Magnetic Resonance Imaging (aMRI) while brain physiology is imaged using Positron Emission Tomography (PET), Magnetic Resonance Spectroscopy (MRS), functional MRI (fMRI) and magnetoencephalography (MEG). BIC maintains linkages with clinical, clinical research and basic research communities within Montreal Neurological Institute (MNI), McGill University and has collaborations across Quebec, Canada, USA and internationally.
Secondary Structure Matching (SSM) is an interactive service for comparing protein structures in 3D. SSM compares to other protein matching services, see results here. It is used as a structure search engine in PISA service (Protein Interfaces, Surfaces and Assemblies). It queries may be launched from any web site, see instructions here and it is based on the CCP4 Coordinate Library, found here. The service provides for: -pairwise comparison and 3D alignment of protein structures -multiple comparison and 3D alignment of protein structures -examination of a protein structure for similarity with the whole PDB or SCOP archives -best Ca-alignment of compared structures -download and visualization of best-superposed structures using Rasmol (Unix/Linux platforms), Rastop (MS Windows machines) and Jmol (platform-independent server-side java viewer) -linking the results to other services - PDBe Motif, OCA, SCOP, GeneCensus, FSSP, 3Dee, CATH, PDBSum, SWISS-PROT and ProtoMap. Sponsors: The project is funded by the Collaborative Computational Project Number 4 in Protein Crystallography of the Biotechnology and Biological Sciences Research Council
THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2012. The function of the IMR is to select, import, cryopreserve, maintain, and distribute these important strains of mice to the research community. To improve their value for research, the IMR also undertakes genetic development of stocks, such as transferring mutant genes or transgenes to defined genetic backgrounds and combining transgenes and/or targeted mutations to create new mouse models for research. The function of the IMR is to: * select biomedically important stocks of transgenic, chemically induced, and targeted mutant mice * import these stocks into the Jackson Laboratory by rederivation procedures that rid them of any pathogens they might carry * cryopreserve embryos from these stocks to protect them against accidental loss and genetic contamination * backcross the mutation onto an inbred strain, if necessary * distribute them to the scientific community More than 1000 mutant stocks have been accepted by the IMR from 1992 through December 2006. Current holdings include models for research on cancer; breast cancer; immunological and inflammatory diseases; neurological diseases; behavioral, cardiovascular and heart diseases; developmental, metabolic and other diseases; reporter (e.g., GFP) and recombinase (e.g., cre/loxP) strains. About eight strains a month are being added to the IMR holdings. Research is being conducted on improved methods for assisted reproduction and speed congenic production. Most of the targeted mutants arrive on a mixed 129xC57BL/6 genetic background, and as many of these as possible are backcrossed onto an inbred strain (usually C57BL/6J). In addition, new mouse models are being created by intercrossing carriers of specific transgenes and/or targeted mutations. Simple sequence length polymorphism DNA markers are being used to characterize and evaluate differences between inbred strains, substrains, and embryonic stem cell lines.
Producer and supplier of a collection of mice bearing spontaneous mutations. These mice contribute to a better understanding of the genetic bases of neurological, neuromuscular, sensory, metabolic, skeletal/craniofacial and developmental disorders and conditions such as diabetes, obesity and heart disease.
Neuroptikon is a tool for visualizing and interacting with neural circuits. Sponsors: This resource is supported by Janelia Farms.
Downloadable files of the bos taurus genome. Draft assemblies available for download as contigs or linearized scaffolds of the genomic sequence of cow, Bos taurus, including the final draft assembly (7.1 coverage) and the two previous assemblies. The genome is sequenced to 6- to 8-fold sequence depth, with high-quality finished sequence in some areas. Accompanying EST and SNP analyses is also included. The bovine genome assembly and analysis and the study of cattle genetic history were published in April 24, 2009 issue of Science. The Human Genome Sequencing Center provides BLAST searches of the genome assemblies, either as contigs or as linearized chromosome sequences. The WGS sequence enriched BAC assemblies and the unassembled reads (sequencing reads that did not end up in the genome assembly) can also be searched by BLAST. Traces are available from the NCBI Trace Archive by using the link in the sidebar or by using NCBI MegaBLAST with a same species or cross species query.
This portal leads to the Chi-sq Hardy-Weinberg equilibrium test calculator for biallelic markers (SNPs, indels etc), including analysis for ascertainment bias for dominant/recessive models (due to biological or technical causes.) The purpose of this web program is for estimating possible missingness and an approach to evaluating missingness under different genetic models. Mendelian randomization (MR) permits causal inference between exposures and a disease. It can be compared with randomized controlled trials. Whereas in a randomized controlled trial the randomization occurs at entry into the trial, in MR the randomization occurs during gamete formation and conception. Several factors, including time since conception and sampling variation, are relevant to the interpretation of an MR test. Particularly important is consideration of the missingness of genotypes that can be originated by chance, genotyping errors, or clinical ascertainment. Testing for Hardy-Weinberg equilibrium (HWE) is a genetic approach that permits evaluation of missingness. Through this tool, the authors demonstrate evidence of nonconformity with HWE in real data. They also perform simulations to characterize the sensitivity of HWE tests to missingness. Unresolved missingness could lead to a false rejection of causality in an MR investigation of trait-disease association. These results indicate that large-scale studies, very high quality genotyping data, and detailed knowledge of the life-course genetics of the alleles/genotypes studied will largely mitigate this risk. Sponsors: This resource is supported by an Intermediate Fellowship (grant FS/05/065/19497) from the British Heart Foundation.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest.
Network Analysis, Visualization and Graphing TORonto
NAViGaTOR - Network Analysis Visualization & Graphing TORonto
NAViGaTOR - Network Analysis Visualization and Graphing TORonto
A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches.
HerpNET is a collaborative effort by natural history museums to establish a global network of herpetological collections data. Sixty-four institutions are participating in the HerpNET community, with an open ended invitation to institutions who would like to join. Currently 56 institutions are available on the specimen searching portal, with data from over 5.5 million specimens available for searching. VertNet: The Future HerpNET, ORNIS, MaNIS and FishNet2 are taxon-based web portals that now serve georeferenced data on vertebrates from over 90 global institutions. Together these comprise VertNET, a cooperative project working to maintain and expand these distributed database projects. Future plans include biodiversity informatics workshops, enhancement of the portal design, better searching capabilities, and a dynamic cache to expand performance and analytic features. Sponsors: This resource is supported by the National Science Foundation (NSF No. 0132303) and by a GBIF DIGIT .
Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It houses chimpanzees that have been used in biomedical research, but no active, invasive research is conducted on the site. The APF provides for the long-term care and husbandry of chimpanzees that have been used in biomedical research. Charles River Laboratories Inc. operates the facility under contract with the National Institutes of Health. To be used in continuing virological research, the animals must be transferred to active chimpanzee research settings. All chimpanzees at the APF have been exposed to various microorganisms, such as hepatitis C virus and HIV. For this reason, they may be candidates for studies related to these diseases. The National Center for Research Resources (NCRR) may remove infected animals from the APF to other accredited chimpanzee facilities for research purposes. Investigators interested in the chimpanzees at the APF should contact Dr. Harold Watson in NCRR''s Division of Comparative Medicine to discuss research requirements.
Center that supports long-term, cost-effective housing and maintenance at NCRR-supported facilities for chimpanzees. NCRR provides programmatic oversight of the facilities and ensures they comply with the Animal Welfare Act, and policies concerning laboratory animal care and use.
Blog about how leading-edge bio-science and technology is impacting individuals and society. This blog is an outgrowth of David Ewing Duncan''s new book, Experimental Man: What one mans body reveals about youy future, your health, and our toxic world. In the book he reports taking over 250 tests in the realms of genes, environment, brain and body and explore what these tests can tell us about one persons health, past, present, and future.
This program is an international Bioinformatics course at KMUTT designed for students who desire focused training in the elements of computer science, biology and biochemistry needed for a successful career in this exciting new discipline. Students in this program will receive comprehensive training in genomics, algorithms for sequence analysis, database design and management, software engineering and programming (including web-based development). Each student will apply their skills to a practical project, where they will design and implement a solution to a real-world problem under the guidance of an experienced mentor in industry or academia. In order to receive a Masters degree, students must demonstrate mastery of the core subject matter (expected to maintain a minimum grade of B in all core courses) and reach a minimum TOEFL test score of 500 (paper) or 173 (computer) or equivalent prior to or on completion of the course. In 24 monhs students gain the knowledge and skills necessary to enter a career with industry or a career in research as a bioinformatics or biocomputing specialist. The program offers fifteen scholarships each year include tuition and fees plus an additional to cover living expenses for 24 months. :Keywords: Bioinformatics, Computer Science, Biology, Biochemistry, Genomics, Algorithms, Sequence, Analysis, Database, Design, Management, Software, Engineering, Programing, Industry, Academia, Master''s, :
Chem Service, Inc. offers the convenience, cost savings and reliability of 1,000 Certified Standards Grade Organic Chemicals at your fingertips with our Organic Mini Stockroom Kit. Whether your lab is big or small, disposal fees are a concern. The Organic Mini-stockroom offers you the ability to have 1000 different chemicals at quantities ranging from 100mg to 10gm; thus, reducing disposal costs. Over 95% of their neat Standards Grade materials have a purity of 98.0% or greater, and have been analyzed by three or more (where feasible) independent methods of analysis. These do not require purity corrections when preparing a solution for use with EPA methods. Their more than 13,000 organic and inorganic standards, and solutions, support EPA Methods, ASTM Methods, State UST Methods, Air monitoring Methods, and International Methods. They offer explosive residue standards, PCB congeners, petroleum hydrocarbon standards for the petrochemical industry, pesticide standards, FAME, and vitamin standards for food analysis. Suited for identification of unknowns, product screening, optimal chemical selection and small scale chemical reactions, the O-1000A Organic Ministockroom Kit was designed for laboratories with broad chemical classification and indentification needs. Chem Service, Inc. is registered by ABS Quality Evaluations, Inc., to the internationally recognized requirements of ISO 9001 for design, development, production, distribution and servicing of organic neat and synthetic reference materials.
RJaCGH: Reversible Jump MCMC for the analysis of CGH arrays
Software for Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models.
A clinical study linking childhood maltreatment and later-life health and well-being. As a collaboration between the Centers for Disease Control and Prevention and Kaiser Permanente''s Health Appraisal Clinic in San Diego, Health Maintenance Organization (HMO) members undergoing a comprehensive physical examination provided detailed information about their childhood experience of abuse, neglect, and family dysfunction. Over 17,000 members chose to participate. To date, over 50 scientific articles have been published and over 100 conference and workshop presentations have been made. Future Directions: The ACE study is now in its 10th year and the prospective phase is currently underway. In this ongoing stage of the study, data are being gathered from various sources including outpatient medical records, pharmacy utilization records, and hospital discharge records to track the subsequent health outcomes and health care use of ACE Study participants. In addition, an examination of National Death Index records will be conducted to establish the relationship between ACE and mortality among the ACE Study population. The ACE Study findings suggest that these experiences are major risk factors for the leading causes of illness and death as well as poor quality of life in the United States. Progress in preventing and recovering from the nation''s worst health and social problems is likely to benefit from the understanding that many of these problems arise as a consequence of adverse childhood experiences. :Sponsors: This resource is supported by the Centers for Disease Control and Prevention and the Kaiser Permanente''s Health Appraisal Clinic in San Diego.
Australian Center For Plant Functional Genomics PTY LTD
At the Australian Centre for Plant Functional Genomics (ACPFG), scientists are improving wheat and barley''s tolerance to environmental stresses such as drought, heat, salinity and nutrient toxicities. These stresses known as abiotic stresses, are a major cause of yield and quality loss throughout the world and cause significant problems for cereal growers. These scientists are developing the technologies and resources needed to produce new cereal varieties that allow sustainable farming to generate economic, social and environmental benefits to Australia. ACPFG research is helping to ensure Australia maintains its competitive position in cereal production. - Identify the genetic mechanisms that control tolerance to specific stresses and compare these with those controlling broad range tolerance to abiotic stresses - Use genome-wide analyses to define key cellular processes that enable adapted plants to withstand abiotic stress, and to apply that understanding to the genetic improvement of crops such as wheat and barley - Unravel regulatory networks that control plant growth under abiotic stress - Identify ways of manipulating these networks, through existing genetic diversity or through functional genomics technologies, to deliver tangible industry outcomes, namely cereal varieties better tailored to hostile environments
Alizadehlab: MeeboChip and HeeboChip Open Source Project
This is an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and are in the process of building the human counterpart, HEEBOChip. The set of 70mers for MEEBOChip is already available from Illumina, Inc., with synthesis of HEEBOChip 70mers in progress. Both arrays are based on a novel selection of exonic long-oligonucleotides (70-mers) from a genomic annotation of the corresponding complete genome sequences, using a transcriptome-based annotation of exon structure for each genomic locus. Using a combination of existing and custom-tailored tools and datasets (including millions of mRNA and EST sequences), we built and performed a systematic examination of transcript-supported exon structure for each genomic locus at the base-pair level (i.e., exonic evidence). This strategy allowed them to select both constitutive and in many cases alternative exons for nearly every gene in the corresponding genome (e.g., protocadherin locus), allowing an unprecedented exploration of human and mouse biology. Furthermore, they used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, they applied and refined the ArrayOligoSelector algorithm from Joe DeRisis laboratory to select 70mers, considering not only their uniqueness (i.e., hybridization specificity) within the content of the entire genome, but also to overcome the known biases of labeling and hybridization methods (e.g., 3-biased reverse transcription and in vitro transcription reactions).
Australian Medical Bioinformatics Resource
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. AMBeR's aim is to bring together Australia's unique resources for genetic epidemiology and genomics with high level expertise in bioinformatics and statistical science, conduct advanced methodological research, develop new research capacity and competitiveness in cutting-edge techniques, bring them to bear on important medical research problems, train young Australians in bioinformatics and advanced biostatistics, and transfer this expertise to the medical research community.
Accurate Recognition of Transcription Starts in Human
ARTS are new methods for finding transcription start sites (TSS) of RNA Polymerase II binding genes in genomic DNA sequences. Employing Support Vector Machines with advanced sequence kernels, we achieve drastically higher prediction accuracies than state-of-the-art methods. While ARTS'' predictions are point-wise, resolution has been decreased to 1/50 and 1/500 respectively to reduce traffic. Also note that these scores are real-valued, i.e. no artificial cut-off value has been set. This has the advantage that one may choose the cut-off threshold based on ones own cost function and that the relative promoter activity is visible. Finally, note that non ACGT bases have been randomly substituted, therefore especially long N-sleds may completely screw up results on not yet reliably annotated chromosome parts. Sponsors: This resource is partially supported by the PASCAL Network of Excellence (EU #506778), DFG grants JA 379/13-2 and MU 987/2-1. :Keywords: Transcription, Human, RNA polymerase II, binding, Gene, Genomic, DNA, Sequence, :
APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. It also provides implicit solvent models of nonpolar solvation which accurately account for both repulsive and attractive solute-solvent interactions. APBS uses FEtk (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FEtk is a portable collection of finite element modeling class libraries written in an object-oriented version of C. It is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods.
The Australian Research Council (ARC) Centre of Excellence in Bioinformatics (ACB) is a multi-nodal interdisciplinary Center that uniquely brings together genomic and post-genomic bioinformatics, mathematics, statistics, systems analysis and experimental phenomics to produce a deep understanding of how information in the genome is transformed into structure and function in the mammalian cell. ACB is committed to: - Research excellence providing insights into genome-phenome biology. - An advanced education and training program that fosters excellence, exposes students from diverse disciplines to new perspectives in bioinformatics, and generates human capital. - Improved access to skills, tools and facilities at the interface among genomic and post-genomic biology, molecular cell biology, mathematics, statistics, and computing and information sciences. - Critical mass and a national focus for genome-phenome bioinformatics in Australia. Sponsors: This resource is supported by the following: Institute for Molecular Bioscience Newcastle Bioinformatics Initiative QosCosGrid University of Newcastle Centre for Bioinformatics, Biomarker Discovery and Information-based Medicine Keywords: Research, Bioinformatics, Multi-nodal, Interdisciplinary, Genomic, Mathematics, Statistics, System, Analysis, Experimental, Phenomics, Deep, Structure, Function, Mammalian, Cell, Biology, Education, Training, Program, Molecular, Cell biology, Mathematics, Statistics, Computation, Information, Science, Phenome,
ARC Centre of Excellence in Structural and Functional Microbial Genomics
Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics
ARC Centre of Excellence in Structural & Functional Microbial Genomics
A unique, academic, basic research institute elucidating the key aspects of microbial pathogens and the hosts they infect. Focusing on diseases of importance to Australian Primary Industry, the Centre is developing new veterinary vaccines and identifying novel antimicrobial targets. The ARC Centre of Excellence in Structural and Functional Microbial Genomics has brought together a team of leading Australian researchers in the fields of bacterial genomics, bioinformatics, microbial genetics, biochemistry, cell biology, proteomics, structural biology and vaccine immunology. Sponsors: The Centers based at Monash University, Clayton, Victoria and works in partnership with the veterinary faculties of The University of Sydney and The University of Queensland, the CSIRO through its Division of Livestock Industries, the Victorian Bioinformatics Consortium (VBC), the Victorian Partnership for Advanced Computing (VPAC), The State of Victoria through the Department of Primary Industries, the Australian Genome Research Facility (AGRF) and Pfizer Australia. The Centre commenced operations in 2006 and evolved from the ARC Centre for Structural and Functional Microbial Genomics- an earlier ARC initiative. The Centre is also supported by the Victorian State Government through The Department of Innovation, Industry and Regional Development.
Australian ResearCH Enabling enviRonment
The ARCHER project is built upon the prototype software developed by the DART (http://dart.edu.au) and ARROW (http://arrow.edu.au) projects to produce a robust set of software tools. These tools: - may be customised to suit the needs of diverse research areas - automate the collection and management of instrument generated data - enable the repository storage of research data and associated metadata - enable collection and tagging of research data in a collaborative environment, and - provide these capabilities in a secure end-to-end proces. :ARCHER developed a ''production-ready'' software tools, operating in a secure environment, to assist researchers to: - collect, capture and retain large data sets from a range of different sources including scientific instruments - deposit data files and data sets to eResearch storage repositories - populate these eResearch data repositories with associated metadata - permit data set annotation and discussion in a collaborative environment, and - support next-generation methods for research publication, dissemination and access.
The aim of this resource is to facilitate and promote, even through fund-raising, the scientific research for the treatment of Friederich''s Ataxia. The mission of this portal is to: - To distribute information to the people affected by the disease and to make the general population aware. - Promote, fund and support the diagnosis, research, cure and potential treatments. - Promote the cooperation with other voluntary associations both national and international. Sponsors: This resource is supported by the RUDI Committee. Keywords: Research, Diagnosis, Cure, Treatment, Disease, Scientific, Friederich''s Ataxia,
Company offering a broad range of instrument systems and diagnostic tests for hospitals, reference labs, blood banks, physician offices and clinics to aid in the diagnosis of a range of serious health issues such as infectious diseases, cancer, and diabetes, as well as monitor other important indicators of health.
Programming language for all operating systems that lets users work more quickly and integrate their systems more effectively. Often compared to Tcl, Perl, Ruby, Scheme or Java. Some of its key distinguishing features include very clear and readable syntax, strong introspection capabilities, intuitive object orientation, natural expression of procedural code, full modularity, exception-based error handling, high level dynamic data types, extensive standard libraries and third party modules for virtually every task, extensions and modules easily written in C, C (or Java for Python, or .NET languages for IronPython), and embeddable within applications as a scripting interface.
Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms.
Affymetrix Gene Expression Service Lab, AGESL was established by IPMB, IMB and IBS, Academia Sinica and opened for service in June 2004. The lab provides a full service from quality control of customer-provided RNA samples to raw data acquisition, including Affymetrix recommended QC procedures, cDNA synthesis, in vitro transcription, fragmentation, hybridization, washing, staining and scanning. Sponsors: This resource is supported by Affymetrix, Inc. Keywords: Gene, Expression, Service, Laboratory, RNA, Data, Synthesis, cDNA, In vitro, Transcription, Fragmentation, Hybrdization, Washing, Staining, Scanning,
TRACK-HD is a multi-centermulti-national prospective, observational biomarker study of premanifest and early stage HD with no experimental treatment. Objectives: - determine what combination of measures is the most sensitive for detecting change over the natural course of premanifest and early HD - to validate these as potential outcome measures for use in future therapeutic trials Design: - focused on intensive battery of novel assessments - extensive annual assessments - dynamic and fluid protocol - robust evidence-based measures TRACK-HD is a major new international study of Huntingtons disease. It aims to be the most comprehensive study of premanifest and early HD, and will define the best combination of assessments to be used in clinical trials of disease-modifying treatments in HD. TRACK-HD began in January 2008 and involves 360 subjects at 4 sites internationally. Sponsors: This resource is supported by The UK Medical Research Council (MRC), CHDI Foundation, Inc., The Euro-HD Network, The Wellcome Trust, The Department of Health, The Huntingtons Disease Association, and The Brain Research Trust. Keywords: Biomarker, Experimental, Treatment, Research, Therapeutic, Trail, Hunginton''s, Disease, Health,
A life science modeling and simulation suite of applications focused on optimizing the drug discovery process. Discovery Studio makes it easier to examine the properties of large and small molecules, study systems, identify leads and optimize candidates. Discovery Studio ADME Descriptors allow scientists to eliminate compounds with unfavorable ADME characteristics early in the discovery process and evaluate proposed structural refinements prior to synthesis. Applications of predictive ADME include pharmaceutical, cosmeceutical, and environmental sciences.
Commercial instrument supplier for human activity monitors. ActiGraph devices are used by researchers and clinicians in hundreds of universities and research organizations in more than 56 countries. ActiGraph activity monitors are the most validated and widely used devices of their kind. ActiGraph activity monitors use triaxial accelerometers and our validated proprietary filtering algorithms to accurately measure the amount and intensity of human activity. They are powered by rechargeable lithium ion batteries, and battery charging and communication are accomplished via a standard USB connection. All ActiGraph activity monitors can be worn at the waist or wrist and are suitable for subjects of all ages. ActiGraph devices have been used in hundreds of research studies in nearly 60 countries around the world since 1992. Leading research facilities including the U.S. National Institute of Health (NIH), the Institute of Child Health in the UK, and Karolinska Institutet in Sweden rely on our products to provide objective activity measurement in dozens of areas including obesity, diabetes, sleep, elderly behavior, and athletics. ActiGraph often works with scientific organizations to develop and implement software and hardware features that reflect the evolving needs of the research community. ActiGraph devices are well recognized as some of the most accurate activity measurement products on the market. Extensive research has confirmed our accuracy against the VO2 and doubly labeled water (DLW) methods of estimating energy expenditure. Keywords: Device, Researcher, Clinician, University, Research, Organization, Obesity, Diabetes, Sleep, Elderly, Behavior, Athletics, Scientific, Activity monitor, Physical, Measurement, Human, Activity,
The goal is to understand as completely as possible the relationships between sets of inputs and outputs in signaling cells that vary both temporally and spatially. The same goal, stated from a slightly different perspective, is to understand fully how cells interpret signals in a context-dependent manner. This will involve identification of all the proteins that comprise the various signaling systems, the assessment of time-dependent information flow through the systems in both normal and pathological states, and finally the reduction of the mass of detailed data into a set of interacting theoretical models that describe cellular signaling. Sponsors: The AfCS Project was conceived under the Glue Grant Initiative of the National Institute of General Medical Sciences. Support is received from the National Institute of General Medical Sciences and the National Institute of Allergy and Infectious Diseases. Keywords: Alliance, Cellular, Signaling, Temporally, Spatially, Cell, Model,
Affymetrix Power Tools (APT) are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChip arrays. APT programs are intended for power users who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality. APT provides platform for developing and deploying new algorithms without waiting for the GUI implementations. This resource is supported by Affymetrix, Inc.
A prediction algorithm based on the helix/coil transition theory. Agadir predicts the helical behaviour of monomeric peptides. It only considers short range interactions. Conditions such as pH, temperature and ionic strength are used in the calculation. Modifications of the termini are also allowed. To submit a job to Agadir, log in the calculation part using the login button in the right bottom. Then fill-in the input form and proceed to next page, etc. You will reach a final page that resumes all the input information and allows you to run the calculation. You can submit one or more peptide sequences in one-letter format. Sequences should be separated by one return character. Spaces and tabulations are automatically removed. Only standard amino acids are accepted. Agadir accepts two modifications at the N-terminus (acetylation or succynilation), and one at the C-terminus (amidation). Just choose the desired option in the input form. You can use only one set of parameters: temperature, ionic strength (calibrated for NaCl) and pH, or explore a particular range of conditions for one parameter. In the latter case the intervals between any two values are: Ionic strength 0.05 M Temperature 1 K pH 0.2 units When setting the conditions for these parameters please be aware that the allowed ranges are: Ionic strength between 0.001 and 1 M Temperature between 273 and 400 K pH between 1 and 14 Output of the prediction at the residue level is available only when submitting no more than ten peptide sequences, and without any screening of conditions. Hstaple is the Hydrophobic Staple motif, Schellman is the Shellman motif, CaH are the expecte chemical shifts of the Calpha proton, 13Ca are the alpha Carbon 13 chemical shifts, JaN is the Jalpha--nitrogen coupling.
Web-based tool for identifying hot spots of aggregation in polypeptides. Aggrescan uses an aggregation-propensity scale for natural amino acids derived from in vivo experiments and on the assumption that short and specific sequence stretches modulate protein aggregation. The algorithm is shown to identify a series of protein fragments involved in the aggregation of disease-related proteins and to predict the effect of genetic mutations on their deposition propensities. It also provides new insights into the differential aggregation properties displayed by globular proteins, natively unfolded polypeptides, amyloidogenic proteins and proteins found in bacterial inclusion bodies.
THIS RESOURCE IS NO LONGER IN SERVICE. A computer generated high quality dataset of human transcript-confirmed constitutive and alternative exons and introns. The alternative events have been delineated and annotated with various characterizations. AltExtron is the prototype database for the production version AltSplice. AltExtron is more geared towards investigating various aspects of the methodologies used, and focuses in general on the biology behind alternative splicing. The complete data used in this work is available for downloading in several flat files, containing human genes, introns, exons, isoform events, human-mouse comparisons, and additional information on GC-AG introns. Two versions of AltExtron data are available - one as prototype (for human) and another as latest build (for human, drosophila, mouse, and others) based on EMBL/GenBank (Feb 2003).
AmaZonia: Explore the Jungle of Microarrays Results
A web interface and associated tools for easy query of public human transcriptome data by keyword, through thematic pages with list annotations. Amazonia provides a thematic entry to public transcriptomes: users may for instance query a gene on a Stem Cells page, where they will see the expression of their favorite gene across selected microarray experiments related to stem cell biology. This selection of samples can be customized at will among the 6331 samples currently present in the database. Every transcriptome study results in the identification of lists of genes relevant to a given biological condition. In order to include this valuable information in any new query in the Amazonia database, they indicate for each gene in which lists it is included. This is a straightforward and efficient way to synthesize hundreds of microarray publications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Division of Applied Biosystems selling products for the isolation, detection, quantification, amplification, and characterization of RNA.
A commercial software company focusing on doctor patient communication.
An Open-Source MATLAB-to-Python Compiler
OMPC aims to enable reuse of the huge open and free code base of MATLAB on a free and faster growing Python platform. Running Python and MATLAB in a single interpreter avoids issues with running two separate applications. Python adds general purpose programming libraries to the convenient syntax of the language of technical computing. OMPC is not an interpreter, it lets Python to do the work. This means that if Python gets faster OMPC gets faster too. OMPC translates the m-files preserving the structure of the original programs as much as possible. Although OMPC comes with a library that emulates the features of numerical array of MATLAB there is nothing that will stop you from running the translated code the way you like it. This means that you could run the OMPC generated code on IronPython, Jython, PyPy or whatever else if you write your own numerical class. Sponsors: This resource is supported by RIKEN Brain Science Institute.
Invitrogen Antibodies & Secondary Detection
Invitrogen Antibodies and Secondary Detection
Invitrogen Antibodies Secondary Detection
Supports research in cellular analysis, genomics, proteomics, and drug discovery. It has merged with Thermo Fisher Scientific. One of several brands under Thermo Fisher Scientific corporation.
Apache Tomcat is an open source software implementation of the Java Servlet and JavaServer Pages technologies. The Java Servlet and JavaServer Pages specifications are developed under the Java Community Process. Apache Tomcat is developed in an open and participatory environment and released under the Apache License version 2. Apache Tomcat is intended to be a collaboration of the best-of-breed developers from around the world. We invite you to participate in this open development project. Apache Tomcat powers numerous large-scale, mission-critical web applications across a diverse range of industries and organizations. Some of these users and their stories are listed on the PoweredBy wiki page.
It presents beautifully. Even if youve never used Keynote before, youll find creating a presentation surprisingly simple. It all starts with an enhanced Theme Chooser that lets you preview an impressive collection of 44 Apple-designed themes. Drag across a theme to skim through its slide designs. Once youve chosen the perfect canvas for your presentation, simply substitute placeholder text and graphics with your own words and images. Thanks to the Slide Navigator, the progress of your presentation and its organization are always in view. Easy-to-use tools let you add elements such as tables, charts, media, and shapes to your slides. Add a table with a click. Just as easily add a 3D chart that you can animate. With the Media Browser, you can drag and drop photos from your iPhoto or Aperture libraries, movies from your Movies folder, and music from your iTunes library. Make each slide in your presentation look its absolute best, using the powerful graphics tools built into Keynote. Quickly and cleanly remove the background of an image using the Instant Alpha tool. Or mask it within a predrawn shape, such as a circle or a star. With alignment and spacing guides, you can easily find the center of the slide and see if objects are spaced evenly. So anything you add to your slides graphics, images, text boxes, or shapes is placed precisely where you want it. If youre adding a flowchart or a diagram to your slide, then youll appreciate the new connection lines feature. Connection lines between two objects remain anchored, no matter what changes you make. Move the objects around, and the lines move with them.
For the purposes of the Aquatic Code, spring viraemia of carp (SVC) means infection with the viral species SVC virus (SVCV) tentatively placed in the genus Vesiculovirus of the family Rhabdoviridae. Methods for surveillance and diagnosis are provided in the Aquatic Manual. The recommendations in this Chapter apply to: common carp (Cyprinus carpio carpio) and koi carp (Cyprinus carpio koi), crucian carp (Carassius carassius), sheatfish (also known as European catfish or wels) (Silurus glanis), silver carp (Hypophthalmichthys molitrix), bighead carp (Aristichthys nobilis), grass carp (white amur) (Ctenopharyngodon idellus), goldfish (Carassius auratus), orfe (Leuciscus idus), and tench (Tinca tinca). These recommendations also apply to any other susceptible species referred to in the Aquatic Manual when traded internationally. 1) Periodicals *Scientific and Technical Review (available on the Online Bookshop and Website); *Bulletin (available on the Online Bookshop and Website); *Disease Information (available on the WAHID interface); *World Animal Health (available on the Online Bookshop and on the WAHID interface); Health standards *Terrestrial Animal Health Code (available on the Online Bookshop and Website); *Aquatic Animal Health Code (available on the Online Bookshop and Website); *OIE Quality Standard and Guidelines for Veterinary Laboratories: Infectious Diseases (available on the Online Bookshop); *Manual of Diagnostic Tests and Vaccines for Terrestrial Animals (available on the Online Bookshop and Website); *Manual of Diagnostic Tests for Aquatic Animals (available on the Online Bookshop in English only (2009 version) and also on the Website).
A set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits. (entry from Genetic Analysis Software)
Biolog Inc. Bacterial Identification Microbial Identification Phenotype MicroArray
Service to identify a wide range and large number of microbial species (~ 2000) by simple phenotypic testing for dangerous pathogens and for filamentous fungi. The company produces and sells a variety of test kits and instruments. Keywords: Microbial, Microarray, Phenotype, Bacterial, Bacterium, Cell, Technology, Assay, Phenotypic, Testing, PAthogen, Bio terrorism, Fungus, Drug, Discovery, Development, Cellular, Research, Genomics, Toxicogenomics,
Information Technology Applied to Biodiversity Conservation - Atta
Atta is an information system that supports the core information process at the National Biodiversity Institute in Costa Rica (INBio). As such, Atta facilitates the processes of capturing, managing, generating and disseminating information on Costa Rican biodiversity. This system maintains a relational database with over two million records, each one corresponding to a single specimen. Through a unique bar code physically attached to each specimen, users of Atta have efficient and systematic access to the associated digital information. This information includes, but is not restricted to, the where, when, how, and who collected the specimen. When the taxonomic identification process is concluded, this information is supplemented with a complete taxonomic description of the specimen Atta is INBio''s second version of a comprehensive, efficient, scalable, multi-taxa information system that now exploits modern technologies such as multimedia, object-oriented development, GIS, and Internet. Sponsors: This resource is supported by Costa Rican Biodiversity. Keywors: Biodiversity, Database, Speciman, Biology, Technology, Taxonomy,, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.
A healthcare company that provides biomedical solutions and diagnostic and preclinical systems to life science professionals.
The goals of this sequencing effort are to produce and publicly release a whole-genome assembly and auto-annotation of the Aedes genome representing 8X sequence coverage. In collaboration, these centers have delivered the target 8X draft coverage of the disease vector genome. Assembly of the genome was performed using the Broad''s whole genome assembly package ARACHNE (Batzoglou et al., 2002 and Jaffe et al., 2003). The Aedes genome will be annotated in a collaborative effort involving both MSCs and Vectorbase, which is a bioinformatics resource center at the University of Notre Dame. Sponsor: This resource is supported by the National Institute of Allergy and Infectious Diseases. Keywords: Genome, BLAST, Similarity, Search, Engine, Sequence, Bioinformatics, Resource,
This portal takes you to the NCBI''s BLAST Assembled RefSeq Genomes. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Sponsors: This resource is supported by the National Institutes of Health. Keywords: BLAST, Genome, Search engine, Sequence, Biological, Local, Alignment, Nucleotide, Protein, Program, Database, Stastical, Functional, Evolutionaary, Gene,
A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The Bahler Laboratory: Genome Regulation
The laboratory studies global gene expression programs in fission yeast (S. pombe). They apply a wide range of integrated approaches to analyse regulatory networks during cell proliferation, differentiation and quiescence including genetic and environmental perturbations. They are also interested in genetic diversity, genome evolution, and the complex interactions between genotypes, phenotypes, and the environment. The relative simplicity of the yeast cell promises a deeply satisfying, systems-level understanding of its inner workings within our life time Sponsors: This research is mainly funded by Cancer Research UK and the EC FP7 PhenOxiGEn project. Keywords: Gene, Expression, S.pombe, Yeast, Cell, Proliferation, Differentiation, Environmental, Genetic, Diversity, Genome, Evolution, Genotype, Phenotype, Environment,
BiQ Analyzer: A Software Tool for DNA Methylation Analysis
BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data from bisulfite sequencing. Highlights: - End-to-end support of the analysis process: from raw sequence files to a comprehensive documentation and visualization. - Automatically generate publication-quality lollipop diagrams (show example.) - Integrated 1-click multiple sequence alignment. - Automated CpG highlighting- never spend your time highlighting CpGs by hand anymore. - Open electropherogram files to check for sequencing problems (requires an electropherogram viewer such as Chromas LITE.) - Generate MethDB-compatible DNA methylation files for database submission. - Factor 5 speedup of sequence analysis while at the same time achieving better data quality. Intended users: - Anyone who works with DNA methylation data from bisulfite sequencing. - Occasional users as well as experts (the former will benefit from the help that the program gives in order to achieve a good quality management whereas the latter will save hours and days of tedious work.) Sponsors: This resource is supported by the Max Planck Institute. Keywords: Software, Visualization, DNA, Methylation, Data, Bisulfite, Sequencing, Electropherogram, Analysis,
Systems used in areas such as pharmaceutical drug discovery, antibody characterization, proteomics, immunogenicity, biotherapeutic development and manufacture, and many life science research applications.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Map improvement server that returns a bias minimized, 6-fold averaged map generated from a model and diffraction data (with optional preceding Molecular Replacement). It does not build or repair the model for you (yet). For automated model building, you need to install a local copy of CCP4 and ARP/wARP (aka wARP&Trace), RESOLVE, MAID, or TEXTAL.
Commercial instrument and chemical vendor. Developer and manufacturer of specialized technological products for life science research and clinical diagnostics markets.
The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center.
BioSig: An Imaging Bioinformatics System for Phenotypic Analysis
Software library for processing of electroencephalogram (EEG) and other biomedical signals like electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Biosig contains tools for quality control, artifact processing, time series analysis, feature extraction, classification and machine learning, and tools for statistical analysis. Many tools are able to handle data with missing values (statistics, time series analysis, machine learning). Another feature is that more then 40 different data formats are supported, and a number of converters for EEG,, ECG and polysomnography are provided. Biosig has been widely used for scientific research on EEG-based BraiN-Computer Interfaces (BCI), sleep research, and ECG and HRV analysis. It provides software interfaces several programming languages (C, C++, Matlab/Octave, Python), and it provides also an interactive viewing and scoring software for adding, and editing of annotations, markers and events.
Software application that allows pedigree entry and retrieval from an internet browser into a distant MS ACCESS database. Includes IP access restriction, automatic numbering of families and individuals and database consistency checks. (entry from Genetic Analysis Software)
Bork Group's WU-BLAST2 Search Service at EMBL
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This portal let you search BLAST through the WU-BLAST2 Search Service provided by the Bork Group at EMBL. Sponsors: This resource is supported by EMBL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An Open Access On-Line Breast Cancer Mutation Data Base
When the BRCA1 gene was cloned, a Steering Committee was initiated to help coordinate the formation of a Breast Cancer Information Core (BIC) that could act as such a central repository. NHGRI has chosen as the most accessible format for the BIC this World Wide Web site. The recent identification of mutations in breast cancer susceptibility genes has provided the exciting opportunity to help identify women who are at high risk to develop breast cancer. One of the serious impediments to achieving clinical benefits from this information however, is finding and assessing the significance of mutations in these new susceptibility genes. It is imperative that the detection and interpretation of these mutations is coordinated and that this information is made available to as many qualified investigators as possible. There are many sites on the web that contain general as well as scientific information relevant to breast cancer. A partial list of these can be found here. Having participated in the poorly coordinated analysis of other cancer susceptibility genes, we consider it important to create and maintain a central repository for information regarding mutations and polymorphisms. NHGRI also think it critical to make available the reagents necessary to carry out many different techniques for the detection of such mutations. Sponsors: This resource is supported by the National Human Genome Research Institute (NHGRI). Keywords: Breast, Cancer, Mutation, Clincial, Polymorphism, Gene, Scientific,
A commercial software provider designed for legal, risk management, corporate, government, law enforcement, accounting, and academic markets. Sponsors: This resource is Reed Elsevier, Inc. Keywords: Workflow, Professional, Legal, Risk, Management, Corporate, Government, Law, Enforcement, Accounting, Academic, Technology, Information,
Critical Assessment of Techniques for Protein Structure Prediction
The main goal of CASP is to obtain an in-depth and objective assessment of our current abilities and inabilities in the area of protein structure prediction. To this end, participants will predict as much as possible about a set of soon to be known structures. These will be true predictions, not ''post-dictions'' made on already known structures. Sponsors: This resource is supported by the US National Library of Medicine (NIH/NLM), National Institute of General Medical Sciences (NIH/NIGMS), BioSapiens Network of Excellence, and HP Invent. Keywords: Clinical, Technique, Protein, Prediction, Structure,
UCSD Center for AIDS Research Molecular Biology Core
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 31, 2022. The UCSD CFAR/VMRF Molecular Biology Core (MBC) is a service core designed to facilitate and support HIV/AIDS research at the University of California San Diego (UCSD), the VA San Diego Healthcare System (VASDHCS), the Veterans Medical Research Foundation (VMRF), the UCSD Antiviral Research Center (AVRC), the Scripps Research Institute, and others in the San Diego HIV/AIDS research community. The MBC provides a variety of services, including DNA sequencing, viral DNA and RNA quantification, cDNA microarray analysis of herpesvirus expression, lentiviral vectors, RNAi design and synthesis, custom vector and plasmid design and construction, plasmids and other reagents of interest to HIV/AIDS research, shared access to computational biology software, and a variety of other services. The core is operated in association with the VMRF, the UCSD AIDS Research Institute (ARI), the VASDHCS, and the VA Research Center for AIDS and HIV Infection (RACHI). The VMRF/CFAR MBC is open to all UCSD, VA, and VMRF investigators as well as those from outside institutions. Keywords: Biology, Research, Medical, Molecular, DNA, Sequencing, Healthcare, RNA, DNA, cDNA, Microarray, Analysis, Herpesvirus, Expression, Lentiviral,
Software program that prepares pedigree data for calculation of Elston-Stewarts'' likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays (entry from Genetic Analysis Software)
Whether you are a senior executive looking for an industry overview, an experienced manager searching for the latest trends, or a new contingency planner in need of the basics, you will find the GUIDE to be the most comprehensive source for crisis/emergency management and business continuity information. The online DISASTER RESOURCE GUIDE is set up to help you find information, vendors, organizations and many resources to help you prepare for (mitigate) or recover from any type of natural or other type of disaster. The GUIDE is to help you keep your business running, your government agency operational, no matter what!
With remarkable advances in genomic technologies, the National Cancer Institute established the Core Genotyping Facility (CGF) to investigate the contribution of germline genetic variation to cancer susceptibility and outcomes. Working in concert with epidemiologists, biostatisticians and basic research scientists in the intramural research program, the CGF has developed the capacity to conduct genome-wide association studies and candidate gene approaches to identify the heritable determinants of various forms of cancer. In order to ensure the accuracy and timely completion of all CGF provided operations, the following Information Systems were developed. While the investigator does not have direct access to these systems, their availability to CGF staff members greatly aids in their querying and reporting capabilities. In turn this provides benefit to the investigator by providing the most up to date reporting possible. The Core Genotyping Facility (CGF) offers a wide variety of sample preparation and genotyping operations. All samples received must meet minimum requirements and are taken through the Sample Handling pipeline prior to completing any genotyping. The Sample Handling pipeline includes DNA quantification and genetic fingerprinting. Also offered are Whole Genome Amplification (WGA) assays, to get the most yield out of low quantity DNA samples. Theirr genotyping products cover a wide-range of assay sizes. The CGF operates the Illumina BeadLab system which supports Illumina assay technologies including the whole genome genotyping Infinium assays, custom GoldenGate OPA assays, and Custom Infinium (iSelect) assays. In addition, the CGF offers Affymetrix GeneChip arrays and uniplex TaqMan genotyping. Sponsors: CGF is supported by the SAIC-Frederick. :Keywords: Genomic, Technology, Cancer, Genotyping, Germline, Genetic, Epidemiologist, Biostatistician, Research, Gene, Assay, Genotype, Pipeline, Genome, DNA, :
Cyberinfrastructure for Phylogenetic Research
Cyberinfrastructure for Phylogenetic Research Science Gateway
This database is a public resource for inference of large phylogenetic trees. It is designed to provide all researchers with access to large computational resources of the NSF TeraGrid through a simple browser interface. The CIPRES Science Gateway provides new hybrid parallel versions of RAxML (7.2.7) and MrBayes (3.1.2), as well as parallel GARLI (1.0) code to insure the fastest possible run times for submitted jobs. Through a collaboration with Alexandros Stamatakis and Wayne Pfeiffer, they now offer the fastest hybrid versions of RAxML and MrBayes currently available. Sponsors: The CIPRES project is a multi-site collaboration funded by the NSF Information Technology Research (ITR) program grant entitled BUILDING THE TREE OF LIFE: A National Resource for Phyloinformatics and Computational Phylogenetics.
COILS: Prediction of Coiled Coil Regions in Proteins
COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.
Cytokines are a diverse group of cell intercellular messengers responsible for signaling variety of cell functions, such as immunity, hematopoiesis, chemotactic activities, cell maturation, proliferation, growth and differentiation through their interactions with respective receptors on cell membranes. Currently, a number of cytokines have been identified and classified
This database contains nearly 300 sequences known to bind calmodulin, published as of March 2003. Calmodulin is an intracellular calcium receptor found ubiquitously in eukaryotes. It is capable of regulating biological activities of many cellular proteins and transmembrane ion transporters mainly in a Ca2 -dependent manner. When the intracellular calcium level rises to 10-5 M, four Ca2 ions bind to calmodulin, and this Ca2 -calmodulin complex binds the target proteins, initiating various signalling cascades. Calmodulin has four EF-hand motifs that change conformation upon binding calcium ions. Each EF-hand motif contains two alpha helices connected by a 12-residue loop. The calcium ion binds to the loop region and changes the relative positions of the alpha helices (Yap et al, 1999). In absence of calcium, the alpha-helices in the EF-hand motif of calmodulin are positioned almost parallel to each other. This is known as the closed conformation. Sponsors: This resource is supported by the Ikura Lab, Ontario Cancer Institute. Keywords: Database, Sequence, Calmodulin, Intracellular, Calcium Receptor, Eukaryote, Transmembrane, Protein, Biological, Cellular, Target, Motif, Helix, Signaling,
Program DynaFit Analysis of (bio)chemical kinetics and equilibria Welcome to the DynaFit home page. Purpose Symbolic Notation Bibliographic Reference Numerical Methods Minimum System Requirements Purpose The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data. The experimental data can be either initial reaction velocities in dependence on the concentration of varied species (e.g., inhibitor concentration vs. velocity), or the reaction progress curves (e.g., time vs. absorbance). Symbolic Notation The main advantage in using the program DynaFit is in the ability to characterize the (bio)chemical reacting system in terms of symbolic, or stoichiometric, equations. For example, the ``slow, tight' ''' inhibition of a dissociative dimeric enzyme is described by the following text: Monomer Monomer <==> Enzyme : k1 k2 Enzyme Inhibitor <==> Complex : k3 k4 Enzyme Substrate <==> ReactiveX : k5 k6 ReactiveX --> Product Enzyme : k7 k8 The names of chemical species (Monomer, Enzyme, etc.) are entirely arbitrary and can be freely chosen by the investigator. Bibliographic Reference If you publish any results obtained by using DYNAFIT, plase cite the following reference: Kuzmic, P. (1996) Anal. Biochem. 237, 260-273. Program DYNAFIT for the Analysis of Enzyme Kinetic Data: Application to HIV Proteinase ABSTRACT A computer program with the code name DYNAFIT was developed for fitting either the initial velocities, or the time-course of enzyme reactions, to an arbitrary molecular mechanism represented symbolically by a set of chemical equations. Seven numerical tests and five graphical tests are applied to judge the goodness of fit. Experimental data on the inhibition of the dissociative dimeric proteinase from HIV were used in four test examples. A set of initial velocities was analyzed to see if a tight-binding inhibitor could bind to the HIV proteinase monomer. Three different sets of progress curves were analyzed (i) to determine the kinetic properties of an irreversible inhibitor; (ii) to investigate the dissociation and denaturation mechanism for the protease dimer; and (iii) to investigate the inhibition mechanism for a transient inhibitor. See a MEDLINE abstract with related references concerning the kinetics of HIV-1 protease. Numerical Methods The nonlinear regression module uses the Levenberg-Marquardt algorithm [1]. The time-course of (bio)chemical reactions is computed by the numerical integration of simultaous first-order ordinary differential equations, using the Livermore Solver of ODe Systems (LSODE, [2]). The composition of complex mixtures at equilibrium (e.g., in the concentration jump experiment where a complex mixture is incubated prior to the addition of a reagent) is computed by solving simultaneous nonlinear algebraic equations, namely, the mass balance equations for the component species, by using the multidimensional Newton-Raphson method [3]. References G. A. F. Seber and C. J. Wild (1989) Nonlinear Regression, Wiley, New York, p. 624. A. C. Hindmarsh (1983) ODEPACK: a systematized collection of ODE solvers; in Scientific Computing, ed. R. S. Stepleman et al., North Holland, Amsterdam, pp. 55--64. E. Kreyszig (1993) Advanced Engineering Mathematics; 7th ed., John Wiley, New York, p. 929. Minimum System Requirements DynaFit for Windows Intel Pentium III or Celeron class 800 MHz or faster processor Microsoft Windows XP (SP1) or 2000 (SP2) 128 MB RAM 20 MB Hard Disk Space Ethernet Network Interface Card required for license activation(1) CD/DVD-ROM drive required for software installation(2) (1) The Network Interface Card is used to compute a unique Computer ID, tied to a particular DynaFit license. Essentially the Computer ID required for license activation is an encrypted Media Access Control (MAC address) associated with the given Network Card. (2) CD/DVD-ROM is not required if the software is being installed by using the downloadable installer file dynafit-install.zip. Sponsor. This work has been supported by the NIH, grant No. R43 AI52587-02 and the U.S. Department of Defense, U.S. Army Medical Research and Materials Command, Ft. Detrick, MD, administered by the Pacific Telehealth & Technology Hui, Honolulu, HI, contract No. V549P-6073.
Cancer Genetic Markers of Susceptibility
The Cancer Genetic Markers of Susceptibility
The Cancer Genetic Markers of Susceptibility Project
The project began as a pilot study to identify inherited genetic susceptibility to prostate and breast cancer. CGEMS has developed into a robust research program involving genome-wide association studies (GWASs) for a number of cancers to identify common genetic variants that affect a person''s risk of developing cancer. In collaboration with extramural scientists, NCI''s Division of Cancer Epidemiology and Genetics (DCEG) has carried out genome-wide scans for breast, prostate, pancreatic, and lung cancers, while a GWAS of bladder cancer is currently underway. By making the data available to both intramural and extramural research scientists, as well as those in the private sector through rapid posting, NIH can leverage its resources to ensure that the dramatic advances in genomics are incorporated into rigorous population-based studies. Ultimately, findings from these studies may yield new preventive, diagnostic, and therapeutic interventions for cancer. Sponsors: This resource is supported by the U.S. National Institues Of Health.
GeneCluster 2: An Advanced Toolset for Bioarray Analysis
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A software package for analyzing gene expression and other bioarray data, giving users a variety of methods to build and evaluate class predictors, visualize marker lists, cluster data and validate results. GeneCluster 2.0 greatly expands the data analysis capabilities of GeneCluster 1.0 by adding supervised classification, gene selection, class discovery and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting (WV) and k-nearest neighbor (KNN) algorithms, a module for systematically finding and evaluating clustering via self-organizing maps, and modules for marker gene selection and heat map visualization that allow users to view and sort samples and genes by many criteria. It enhances the clustering capabilities of GeneCluster 1.0 by adding a module for batch SOM clustering, and also includes a marker gene finder based on a KNN analysis and a visualization module. GeneCluster 2.0 is a stand-alone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 31, 2022. Data services to support validation of economically relevant traits for the livestock industries. Sponsors: This resource is supported by Pfizer Animal Health. Keywords: Animal, Genetics, Health, World, Genetic, Information, Service, Industry, Livestock, DNA, Maker, Technology, Phenotypic, Productivity,
This website is designed for the Caulobacter cell cycle control model''s latest paper: Temporal Controls of the Asymmetric Cell Division Cycle in Caulobacter crescentus. Sponsors:This resource is supported by the OTKA (F 60414), the European Commission (COMBIO: LSHG-CT-2004-503568), and the OTKA (T043770). Keywords; Cell, Cell cycle, Modeling, Caulobacter, Asymmetry, Temporal,
This the homepage for the Flow Cytometers Facility in UC Berkeley. :Sponsors: This Research Facility is supported by the Cancer Research Laboratory and CIRM Human Embryonic Stem Cell Shared Research Facility at the UC Berkeley Campus. Keywords: Laboratory, Service, Testing, Assessment, Research, Flow cytometer,
Center for Eukaryotic Structural Genomics
The Center for Eukaryotic Structural Genomics
It is a specialized research center supported by the Protein Structure Initiative (PSI) of the National Institute of General Medical Sciences (NIGMS), one of the National Institutes of Health (NIH). PSI is a federal, university, and industry effort aimed at dramatically reducing the costs and lessening the time it takes to determine a three-dimensional protein structure. The long-range goal of PSI is to solve 10,000 protein structures in 10 years and to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences. CESG is located within the Department of Biochemistry at the University of Wisconsin-Madison (Madison, WI) and the Department of Biochemistry at the Medical College of Wisconsin (Milwaukee, WI). CESG develops new methods and technologies to address unique eukaryotic bottlenecks and disseminates its methodologies and experimental results to the scientific community worldwide through: :- Cell-Free Protein Production Workshops :- Plasmids at PSI Materials Repository :- Posters Presented at Scientific Meetings :- Publications in PubMed / PubMed Central :- Sesame (LIMS) Available for Researchers :- Solved Structures in the Protein Data Bank :- Technology Dissemination Reports They have welcomed requests by researchers to solve eukaryotic protein structures, particularly medically relevant proteins, through our Online Structure Request System for Researchers. They have solved many community-nominated targets and deposited information about these targets in public databases and published on our investigations and findings. Sponsors: CESG is supported by NIH / NIGMS Protein Structure Initiative grant numbers U54 GM074901 and P50 GM064598.
Commercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.
C-Maps project is an international collaboration between Discovery Informatics and Computing Laboratory in Indiana University Purdue University Indianapolis (IUPUI) and State Key Laboratory of Intelligent Technology and Systems (LITS) in Tsinghua University China. Connectivity Maps (C-Maps) is created to connect diseases with genes/proteins whose mutations cause them and drugs which treat them. Recent studies focus on developing systematic methods to build C-Maps using gene-expression data to connect small molecules, genes, and disease. Justin Lamb et. al. established a systematic approach to build C-Map using gene-expression profiling as the common vocabulary to connect small molecules, genes, and diseases. They created the first installment of a reference collection of gene-expression profiles from cultured human cell treated with bioactive small molecules, together with pattern-matching software to mine these data [1]. Atul J Butte et. al build a C-Maps using the UMLS (Unified Medical Language System) annotation of gene expression data to connect phenotypic, disease, environmental and experimental contexts as well as genes with differential expression associated with these concepts [2] Sponsor. We would like to thank the generous grant support from Indiana University - Purdue University Indianapolis, and National Basic Research Program of China (973 Program), National High Technology Research and Development Program of China (863 Program).
Consumers Union (CU) is an expert, independent, nonprofit organization whose mission is to work for a fair, just, and safe marketplace for all consumers and to empower consumers to protect themselves. The organization was founded in 1936 when advertising first flooded the mass media. Consumers lacked a reliable source of information they could depend on to help them distinguish hype from fact and good products from bad ones. Since then CU has filled that vacuum with a broad range of consumer information. To maintain its independence and impartiality, CU accepts no outside advertising and no free samples and employs several hundred mystery shoppers and technical experts to buy and test the products it evaluates. The organization generates more than $200 million in revenue, and a staff totaling more than 600 work at CU''s 50 state-of-the-art labs and offices in Yonkers, N.Y.; its 327-acre Auto Test Center in East Haddam, Conn.; and our three advocacy offices, in Washington, D.C., Austin, Texas, and San Francisco. Consumers Union is governed by a board of 18 directors who are elected by CU members and meet three times a year
Continua Health Alliance is a non-profit, open industry coalition of the finest healthcare and technology companies joining together in collaboration to improve the quality of personal healthcare. With more than 200 member companies around the world, Continua is dedicated to establishing a system of interoperable personal health solutions with the knowledge that extending those solutions into the home fosters independence, empowers individuals and provides the opportunity for truly personalized health and wellness management. Mission To establish a system of interoperable personal telehealth solutions that fosters independence and empowers people and organizations to better manage health and wellness Objectives The Continua Health Alliance is comprised of technology, medical device and health care industry leaders dedicated to making personal telehealth a reality. Our objectives include: Developing design guidelines that will enable vendors to build interoperable sensors, home networks, telehealth platforms, and health and wellness services. Establishing a product certification program with a consumer-recognizable logo signifying the promise of interoperability across certified products. Collaborating with government regulatory agencies to provide methods for safe and effective management of diverse vendor solutions. Working with leaders in the health care industries to develop new ways to address the costs of providing personal telehealth systems.
Software program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects (entry from Genetic Analysis Software)
PPD is a leading global contract research organization (CRO), celebrating 25 years of providing drug discovery, development and lifecycle management services. Our clients and partners include pharmaceutical, biotechnology, medical device, academic and government organizations. With offices in 41 countries and more than 10,500 professionals worldwide, PPD applies innovative technologies, therapeutic expertise and a commitment to quality to help clients and partners accelerate the delivery of safe and effective therapeutics and maximize the returns on their R&D investments. Discovery Services: BioDuro, A PPD Company A drug discovery services company focused on integrated drug discovery programs Nonclinical development Preclinical services partners. Compound Partnering PPD''s compound partnering business is now Furiex Pharmaceuticals, Inc., an independent, publicly traded company. Collaboration with Merck Our strategic collaboration with Merck enabled us to acquire its vaccines and biologics infrastructure, broaden our therapeutic expertise and expand our existing relationship. Alliance with WHISCON We have expanded our post-approval safety expertise and risk management through an alliance with World Health Information Science Consultants. Partnership with PUL To meet growing client demand in Southeast Asia, we partnered with Peking Union Lawke Biomedical Development Limited (PUL) to establish our central lab services in China. Our e-Newsletter is your source for what is happening at PPD and in the CRO industry.
DNA Direct was founded in 2005 to address the growing need for genetic expertise and guidance across the healthcare continuum. Genetic technology is rapidly advancing and new associations between common genes and disease are being discovered every day. With more than 2000 molecular diagnostic and genetic tests available today, the impact of genetics has never been greater and is becoming an integral part of medicine and patient care To bring the power of personalized medicine to patients, providers and payors reducing health risks, preventing disease, and better targeting therapies. DNA Direct''s Precision Health Services include: * Utilization Management * Clinical Decision Support Programs * Clinical Management * Online and Telephone Support Resources for Providers and Patients * Lab Network
Computational and Systems Neuroscience 2011
The annual Cosyne meeting provides an inclusive forum for the exchange of experimental and theoretical/computational approaches to problems in systems neuroscience. The first Cosyne meeting, held in 2004 at Cold Spring Harbor Laboratory, drew over 350 participants. Since 2005, the meeting has been held in Salt Lake City, Utah. It has attracted a growing number of participants, from nearly 400 in 2005 to over 500 in 2010. To encourage interdisciplinary interactions, the main meeting is arranged in a single track. A set of invited talks are selected by the Executive Committee, and additional talks and posters are selected by the Program Committee, based on submitted abstracts. Cosyne topics include but are not limited to: neural coding, natural scene statistics, dendritic computation, neural basis of persistent activity, nonlinear receptive field mapping, representations of time and sequence, reward systems, decision-making, synaptic plasticity, map formation and plasticity, population coding, attention, computation with spiking networks. Sponsor. Thanks to the generosity of The Gatsby Charitable Foundation, of Qualcomm Incorporated and of Brain Corporation, up to 40 travel grants will be available to support student and postdoc participation in the main Cosyne meeting.
Criterion Ventures is launching a new venture that will adapt existing financial services and connect them with consumers through affinity groups to address the needs of the cash market of healthcare. Currently, the healthcare industry is dominated by an insurance market. But sitting next to the insurance market is a $300 billion/year cash market for health care. This cash market lacks the rational pricing, products, services and intermediaries needed to deliver health care affordably and in a way that maximizes access. In the end, consumers are not getting the best value per dollar spent. By introducing and bringing to scale innovative products and services, and connecting them to consumers through existing affinity groups whose members are struggling with the impact of the cash portion of healthcare, we will be able to rationalize the market. By creating a rational market we will bring greater value to consumers for their healthcare dollars and increase access to care. The business will draw revenues from four sources: Charging transaction fees to consumers who use our products Charging interest to consumers who take advantage of our lines of credit offerings Interest earned on deposits that we or our partners will hold for consumers Charging management fees to affinity groups for setting up their customized set of products and services. Partners. Thomas H. Cochran, Managing Director, CivilCredit Advisors Catherine (Cathy) Dunham, Director, Access Project Richard Eskow, CEO, Health Knowledge Systems Tim Freundlich, Founder and Managing Principal, Good Capital; Director of Strategic Initiatives, Calvert Foundation Ben Geyerhahn, Principal, Hudson TG Kevin Jones, Founding Principal, Good Capital Claudia Machaver, Consultant Robert Mittman, Founder, Facilitation, Foresight, Strategy Sara Olsen, Founding Partner, SVT Group Mark Rukavina, Executive Director, Access Project Michael Tobman, Principal, Hudson TG Dana Wright, Founder, Take Action, Inc.
This Blast server offers searches against all D. rerio finished and unfinished clones in the Sanger sequencing pipeline. You can now also search the de novo assemblies generated from sequencing of one doubled haploid homozygous individual of each the AB and Tuebingen strain. Both fish were sequenced to ~40x coverage using Illumina GA sequencing technology and the sequences were assembled using Phusion2, resulting in a 1,33 Gb AB and a 1.48 Gb Tuebingen assembly. Due to the short reads and short inserts and no integration of physical or genetic map data, both assemblies are highly fragmented - with an N50 contig size of about 5kb. Mis-assembly errors may also be present in the contigs. Please note these assemblies are independent additions to the assemblies released by the zebrafish genome project and are intended to aid identification of polymorphisms between these two strains. Charity. Genome Research Limited is a charity registered in England with number 1021457
Cryptococcus neoformans is an encapsulated yeast that infects the human host via the respiratory tract where it usually causes an inapparent infection. In the susceptible host, it may disseminate, typically producing a chronic and life-threatening meningitis. The Cryptococcus neoformans serotypes A and D are responsible for the overwhelming majority of pulmonary infections in AIDS patients. Cryptococcus neoformans strain H99 Latest Data Release - May 19, 2004 To date, we have isolated ca. 3750 cDNA clones from Cryptococcus neoformans strain H99 in collaboration with Drs. Juneann Murphy and Dave Dyer at the University of Oklahoma Health Sciences Center''s Department of Microbiology and Immunology in Oklahoma City and Kent Buchanan at the Tulane University Medical School, New Orleans, LA. The Cryptococcus neoformans strain H99 EST''s have been generated by Doris Kupfer, Heather Bell, Sunkyoung So, Yuong Tang, and Jennifer Lewis at the University of Oklahoma''s Advanced Center for Genome Technology, in the Department of Chemistry and Biochemistry. We now have end sequenced all available templates (ca. 7500 reactions) from both ends of the directionally cloned inserts after excision into pBlueScript SK-. . All of our data is available from our ftp site, and we now have added the ability to perform blast searches on this data. A keyword search of a blastx search of GenBank with this data also is available but we have not yet linked this to a unigene database as the number of EST''s sequenced doesn''t warrent this yet.
In probability theory and statistics, the cumulative distribution function (CDF), or just distribution function, describes the probability that a real-valued random variable X with a given probability distribution will be found at a value less than x. Intuitively, it is the area so far function of the probability distribution. Cumulative distribution functions are also used to specify the distribution of multivariate
The Cystic Fibrosis Foundation has built a dynamic pipeline for the development of more new potential cystic fibrosis (CF) therapies than ever before. To treat a complex disease like CF, therapies must target problems in the airways and the digestive system. In the CF drug development pipeline, there also are promising new therapies designed to rectify the cause of CF a faulty gene and/or its faulty protein product. Cystic fibrosis is an inherited chronic disease that affects the lungs and digestive system of about 30,000 children and adults in the United States (70,000 worldwide). A defective gene and its protein product cause the body to produce unusually thick, sticky mucus that: clogs the lungs and leads to life-threatening lung infections; and obstructs the pancreas and stops natural enzymes from helping the body break down and absorb food. In the 1950s, few children with cystic fibrosis lived to attend elementary school. Today, advances in research and medical treatments have further enhanced and extended life for children and adults with CF. Many people with the disease can now expect to live into their 30s, 40s and beyond.
An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data.
Cython is a language that makes writing C extensions for the Python language as easy as Python itself. Cython is based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. The Cython language is very close to the Python language, but Cython additionally supports calling C functions and declaring C types on variables and class attributes. This allows the compiler to generate very efficient C code from Cython code. This makes Cython the ideal language for wrapping external C libraries, and for fast C modules that speed up the execution of Python code. Sponsor. Google and Enthought funded Dag Seljebotn to greatly improve Cython integration with NumPy. Kurt Smith and Danilo Freitas were funded through the Google Summer of Code program to work on improved Fortran and C support respectively.
Cytopathology Foundation is a non-profit organization dedicated to the health care for the advancement of art and science of Cytopathology dealing with study of cells for proper disease management especially cancer. Cytopathology is a well established diagnostic sub-specialty of pathology. Instead of using surgically removed tissue to arrive at a diagnosis it attempts to identify diagnostic and prognostic information from dispersed cells obtained by non-invasive or minimally invasive techniques. An example, and its greatest success story thus far, is the role it has played in the battle with cervical cancer. The introduction of the Pap smear has contributed immensely to the early diagnosis and significantly decreased mortality of cervical cancer. Activities of the foundation 1. Support the mission statement in general. 2. Support the editorial and publication expenses of CytoJournal. 3. Future activities may include publication and marketing of cytopathology related literature, to generate funds. 4. Support any other scholarly activities in Cytopathology and related areas.
The Lausanne Genomics Technologies Facility (GTF) is a genomic technologies core laboratory serving the Lausanne and Lemanic region research community. It is housed in and administered by the Center for Integrative Genomics. The GTF offers a range of microarrays services, including : providing access to the instrumentation and the consumables that are required for the use of the pre-printed oligonucleotide microarrays available from Affymetrix and Illumina as well as miRNA gene microarrays from Agilent Technologies providing access to and supporting applications using the Illumina Genome Analyzer 2 ultra high throughput DNA sequencing platform providing access to the instrumentation and the consumables that are required for performing quantitative real-time PCR analyses using the Applied Biosystems 7900HT Sequence Detection System. providing bioinformatics support and consultation services at the stages of experimental design, data collection and storage, image analysis and data analysis acting as a center of experience, expertise and training in microarray and quantitative PCR technologies and methodologies. Laboratory space and computer workstations are available to users wanting to perform the experiments and/or analyses in the facility. The GTF also acts as an information clearing house for the user community by providing a forum for the sharing of methods, protocols and experience generated by the GTF and community scientists using microarray and quantitative PCR technology investigating and implementing, when appropriate, microarray-based methods for applications other than gene expression monitoring (e.g. SNP detection) participating in the evaluation of new RNA expression profiling and nucleic hybridization detection technologies as they develop and incorporate the appropriate technologies into the services offered by the facility
Drosophila Genomics and Genetic Resources
Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request.
DNAWorks automates the design of oligonucleotides for gene synthesis by PCR-based methods. The availability of sequences of entire genomes has dramatically increased the number of protein targets, many of which will need to be overexpressed in cells other than the original source of DNA. Gene synthesis often provides a fast and economically efficient approach. The synthetic gene can be optimized for expression and constructed for easy mutational manipulation without regard to the parent genome. DNAWorks accesses a computer program that automates the design of oligonucleotides for gene synthesis. The website provides forms for simple input information, i.e. amino acid sequence of the target protein and melting temperature (needed for the gene assembly) of synthetic oligonucleotides. The program outputs a series of oligonucleotide sequences with codons optimized for expression in an organism of choice. Those oligonucleotides are characterized by highly homogeneous melting temperatures and a minimized tendency for hairpin formation. The approach presented here simplifies the production of proteins from a wide variety of organisms for genomics-based studies.
The Drugs for Neglected Diseases initiative
It is an independent, not-for-profit product development partnership working to research and develop new and improved treatments for neglected diseases such as leishmaniasis, human African trypanosomiasis, Chagas disease, and malaria. DNDi was founded in 2003 by the Oswaldo Cruz Foundation from Brazil, the Indian Council for Medical Research, the Kenya Medical Research Institute, the Ministry of Health of Malaysia, Frances Pasteur Institute, Mdecins sans Frontires (MSF) and WHO/TDR which acts as a permanent observer to the initiative.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 4,2025. These centers support existing and newly developed techniques for bioinformatic analysis aimed at obtaining a deeper understanding of the fundamental biology of a specific set of pathogenic organisms, and efforts to counter the threats posed by these pathogens. The mission of the PathogenPortal is to showcase the collective efforts of the BRCs, and to make the efforts of each BRC more accessible. The PathogenPortal''s content is organized by BRC in both the menus at the top of each page, and the categories in the left column of most pages.. As part of the Pathogen Portal, we have established a Scientific Working Group (SWG) comprised of members with deep expertise in a broad range of domains of relevance to the Pathogen Portal. The SWG provides advice about the management and performance of the resource, and about the needs of the scientific community in relation to the resource. Sponsor. Pathogen Portal is a repository linking to four Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) and maintained by The Virginia Bioinformatics Institute. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases
EH is a program to test and estimate linkage disequilibrium between different markers or between a disease locus and markers. This is an updated version in which the previous disease (case-control) option has been deleted (but see below how to work with case-control data). The program is written in Free Pascal, which is compatible with (but mch more flexible than) Turbo Pascal. Free Pascal is available for various platforms, e.g. Windows and Linux. The data are taken to consist of a number of individuals collected at random from a population. Based on these sample data, the EH program estimates allele frequencies for each marker. Haplotype frequencies are estimated with allelic association (H1) and without (H0). The EH program also provides log likelihood, chi-square and the number of degrees of freedom under hypotheses H0 and H1. For more information please refer to Terwilliger and Ott (1994). Notes: For sparse data (relatively few observations with large numbers of alleles), the chi-square approximation to the test statistics used by EH is unreliable. Then, more sophisticated programs are recommended. Another program for estimating haplotype frequencies is SNPHAP. It is very flexible although it is restricted to analyzing bi-allelic markers. Also, PHASE is very useful for estimating haplotype frequencies and for inferring haplotypes to individuals. See Marchini et al. (2006). Files in this package (Windows): EH.PAS: Source code of EH program. EH.EXE: Executable code of EH program, which is compiled with a maximum of 30 alleles per locus, 10 loci, 1000 haplotypes, and 3600 genotype patterns (product of numbers of genotypes at each locus). EH.DAT, EH.OUT, etc: Sample input and output files. Input file The EH program does not require additional programs although you need a Pascal compiler (Free Pascal) to recompile the program when you change program constants. There is one input file whose name the user can determine, for example, EH.DAT (this is the default name). It contains the numbers of alleles for each marker and the observations for each genotype. First line: Number of alleles at the first marker, number of alleles at the second marker, and so on. Assuming you have 2 markers, the first marker has 2 alleles and the second marker has 3, you write 2 3 in the first line. The order of markers in the remainder of the input file is determined by the order of markers you entered in the first line. Subsequent lines: Number of observations for given genotypes. These numbers must be arranged as follows: The number of columns is the number of the possible genotypes at the last locus. Let M be the number of alleles at the last locus, then the number of the possible genotypes equals M(M 1)/2. For example, if the last locus has two alleles, then there are 3 possible genotypes which are 1/1, 1/2 and 2/2. Therefore, in each row there are 3 columns corresponding to the genotypes 1/1, 1/2, 2/2. Similarly, if the last marker has three alleles, then there are 6 columns corresponding to 1/1, 1/2, 2/2, 1/3, 2/3, 3/3. The number of rows is the product of the number of the possible genotypes at the first (N - 1) markers, where N is the total number of markers. That is, no. of rows = L1(L1 1)/2 L2(L2 1)/2 ... Li(Li 1)/2 ..., where Li is the number of alleles at the i-th locus. For example, assume you have 3 loci and the first and the second locus each have 2 alleles, and the third locus has 3 alleles. Thus, there are 6 columns and 9 rows (see example 1 below). However, if the first locus has 3 alleles and the second and third have 2 alleles each, there are 18 rows and 3 columns. The output file from the EH program, EH.OUT by default, contains the estimated haplotype frequencies and their corresponding log likelihoods. Sponsor. supported by the Wellcome Trust, the National Institutes of Health (NIH), The SNP Consortium, the Wolfson Foundation, the Nuffield Trust, and the Engineering and Physical Sciences Research Council. M.S. is supported by NIH grant 1RO1HG/LM02585-01. N.P. is a recipient of a K-01 NIH career-transition award. G.R.A. is supported by NIH National Human Genome Research Institute grant HG02651. E.E. is supported by the California Institute for Telecommunications and Information Technology, Calit2. Computational resources for HAP were provided by Calit2 and National Biomedical Computational Resource grant P41 RR08605 (National Center for Research Resources, NIH).
Daylight provides enterprise-level cheminformatics software technologies to life science companies. Our superior chemistry, high performance, and open architecture have earned Daylight a reputation for delivering the state-of-the-art in chemical information processing since 1987. Daylight Chemical Information Systems, Inc. is a privately held company with corporate offices in Aliso Viejo, CA and research offices in Santa Fe, NM and Cambridge, England. Support At Daylight, support means a wide array of services that are designed to empower users to make the most of Daylight software. We offer detailed administration documentation and guides through this website. Our User Group Meetings allow in-depth exploration of our technology. And, of course, our support staff is available to assist you whenever the need occurs. Download - Downloading current releases as well as contributed code, system requirements, installation directions, and release information Reference Guides - List of available documentation such as programming guides and user manuals. Cheminformatics - List of additional general resources including introductory materials, theory manual, tutorials and user meeting archives. Sponsor. Daylight
His research interests cover many different questions in population genetics and molecular evolution. He considers himself an evolutionary geneticist, with strengths in computational biology and stochastic models. He has worked on frequency-dependent selection models, spatial genetic models, indel evolution models, sequence alignment, and phylogenetic models. His current research involves estimating indel rates and length distributions, applying population genetic models to phylogeny reconstruction, and finding de novo mutations and SNPs from next-gen sequencing of human genomes. In addition to running De Rerum Natura, Reed also manages the largest group blog on evolution, The Pandas Thumb. In addition he develops plugins and hacks for the Movable Type blogging software. He is an expert on dispatching MT under FastCGI and Lighttpd, as well as integrating it with jQuery. He was editor and designer of The Open Laboratory: The Best Science Writing on Blogs 2007. He is co-creator of Prof. Steve Steve. Partners. Movable Type Site Meter Melody Lulu
Harvard FAS Magnetic Resonance Laboratory
Core facility that provides the following services: Magnetic resonance spectrometer training service, Magnetic Resonance Instrument Access. Welcome to the Magnetic Resonance Facility of the Department of Chemistry and Chemical Biology, Harvard University, in the Laukien-Purcell Instrumentation Center.
This demonstration application illustrates how Hierarchical Temporal Memory (HTM) can be applied to video recognition. The HTM network in this demo has been trained to locate people in surveillance video footage. You can see how the HTM operates by experimenting with the sample videos that are bundled with this application. For each video, the application will process it in real time on your machine and track the locations of people and other moving objects, while correctly discriminating between the two. This demonstration application, called Vision4, gives a sense of how Hierarchical Temporal Memory (HTM) performs in recognizing objects in static images. Sponsor. Numenta has fewer than twenty employees and has been privately funded by its founders, board members, and close associates.
The Diabetes Genetics Initiative is a collaboration of the Broad Institute of MIT and Harvard, Lund University, and Novartis Institutes for BioMedical Research The Diabetes Genetics Initiative combines the resources and expertise of the Novartis Institutes for BioMedical Research, the Broad Institute of MIT and Harvard, and Lund University to identify the genetic determinants of type 2 diabetes. This unique collaboration aims to collect and analyze samples from type 2 diabetic patients from nations across the globe, performing whole genome scans to provide a comprehensive view of the DNA sequence variants associated with the disease. This partnership has been forged with the explicit goal of making this vast amount of crucial data available to researchers globally and free of cost, which should lead to a greater understanding of disease biology and speed the development of more effective therapies. Contribute Although the astounding generosity of Eli and Edythe L. Broad and several other venture philanthropists empowers our scientists to tackle many of the most important problems at the cutting edge of genomic medicine, there are many other critical challenges that they cannot yet pursue because of limited resources. We need additional visionary partners to join the Broads and the Broad Institute in transforming medicine with the power of genomics.
R package to identify differentially expressed genes from RNA-Seq data.
It was founded in 1985 by Professor Rury Holman, specialises in performing diabetes-related national and multinational mega trials in partnership with the NHS, NIH, MRC, BHF, DUK, academic institutions and industry. The DTU also undertakes major modelling and statistical programmes to utilise fully the data available from its many studies, with a particular emphasis on modelling diabetes and cardiovascular disease processes. Current studies include 4-T, ACE, TECOS and UKPDS~Post Study Monitoring. Sponsor. Funded by the UK National Institute for Health Research
Dialog provides critical information from the world''s most authoritative publishers, combined with the tools to search every bit of it with speed and precision. With direct operations in 27 countries, Dialog products and services are a combination of highly accurate online research tools offering access to unique and relevant databases designed to meet the specific needs of a wide range of users. Information professionals and end-users at business, professional, scientific, academic and government organizations in more than 100 countries prize Dialog services to meet their searching needs. As part of the Deep Web, which is estimated to be 500 times larger than the content accessible via Web search engines, Dialog products offer unparalleled depth and breadth of content coupled with the ability to search with precision and speed. Our collection of over 900 databases handles more than 700,000 searches and delivers over 17 million document page views per month. Searchable content on Dialog services includes articles and reports from thousands of real-time news feeds, newspapers, broadcast transcripts and trade publications, plus market research reports and analyst notes providing support for financial decision-making, as well as in-depth repositories of scientific and technical data, patents, trademarks and other intellectual property data. Additional content areas include government regulations, social sciences, food and agriculture, reference, energy and environment, chemicals, pharmaceuticals and medicine.
Metagenomes Used in The Statistical Analysis
his table shows the metadata and links to sources of the data and citations associated with the publicly available metagenome sequences used in the Dinsdale, Edwards, et al., analysis of 87 different metagenomes. The links will take you to the annotated sequences in the metagenomics SEED, CAMERA, and the NCBI Short Read Archve. Please note that all metagenomes are currently available to download via the ftp links, some are available in the meta-RAST, and other links will be added as soon as they become available. Citations for individual metagenomes will also be added as and when they become available. DNA sequences for all metagenomes are avaialble via anonymous FTP. Sponsor. This project was supported by the Gordon and Betty Moore Foundation Marine Microbial Initiative, National Science Foundation grants (F.R. and D.L.V.), a Department of Commerce ATP grant (F.R.), a National Research Initiative Competitive Grant from the USDA Cooperative State Research, Education and Extension Service (B.W.), the National Institute of Allergy and Infectious Diseases, the National Institutes of Health and the Department of Health and Human Services (R.S.).
This web site is your introduction to the world of Florida Aquaculture. It represents a compilation of information about a division in the Florida Department of Agriculture and Consumer Services-the Division of Aquaculture. The Division plays a key role in the regulation of aquaculture facilities and shellfish processing plants, is responsible for opening/closing of shellfish harvesting waters to protect human health, ensures the continued productivity of oyster reefs through a restoration program and issues leases of submerged state lands for aquaculture. The creation of this division is unprecedented for a state agriculture department. Florida''s Division of Aquaculture is one-of-a-kind and serves a unique industry like no other in the United States. Please browse this site and learn more about Florida Aquaculture. I welcome your comments on the topics contained in this web site.
Sustainability plan EpiData Software has since 2000 grown from securing the principles of Epi Info V6 to an independent and documentation based system with several translations and numerous downloads. To secure continued viability organisations and governments work is being done to secure for the future, see also the license principles - the ambition is to convert the programs to open-source within few years. Contributions are used for costs of development after version 1.5 (e.g. refining of programming, enhancing speed, maintenance of website, to pay for absence from paid work to do EpiData or other developmental and promotional efforts for EpiData). About the EpiData Association EpiData Software is from EpiData Entry version 2.0 and above released by the non-profit organisation The EpiData Association Odense, Denmark (In Danish: EpiData foreningen). The association receives NO baseline budget from anyone. The association has no employees Postal adress is: The EpiData Association, att. Jens Lauritsen, Enghavevej 34, DK5230 Odense M, Denmark, Europe The body of users of EpiData form the most important part of the basis of the EpiData Association. Those who choose to register as users will be asked when desicions are to made regarding additions to the program. Needs for documentation etc. Registration is done by adding your e-mail to the Information list. Supporting members or institutions adds to the foundation and development of EpiData by securing funding to pay for the associated costs. List of donors. The board of the association is made up of the core persons developing EpiData, currently Jens M.Lauritsen and Michael Bruus in collaboration with experienced users and the Friends Of EpiData group (FoED), comprising a group of international persons wishing to support the development of EpiData Sponsor. Without support from a number of NGO''s, Universities, Regional Health Authorities and other funding bodies EpiData development would have stopped
A Comprehensive Canine Genetics Resource Including Gene and Variation Annotation
The genome of the domesticated dog, a close evolutionary relation to human, is a powerful new tool for understanding the human genome. Comparison of the dog with human and other mammals reveals key information about the structure and evolution of genes and genomes. The unique breeding history of dogs, with their extraordinary behavioral and physical diversity, offers the opportunity to find important genes underlying diseases shared between dogs and humans, such as cancer, diabetes, and epilepsy. The Canine Genome Sequencing Project produced a high-quality draft sequence of a female boxer named Tasha. By comparing Tasha with many other breeds, the project also compiled a comprehensive set of SNPs (single nucleotide polymorphisms) useful in all dog breeds. These closely spaced genomic landmarks are critical for disease mapping. By comparing the dog, rodent, and human lineages, researchers at the Broad Institute uncovered exciting new information about human genes, their evolution, and the regulatory mechanisms governing their expression. Using SNPs, researchers describe the strikingly different haplotype structure in dog breeds compared with the entire dog population. In addition, they show that by understanding the patterns of variation in dog breeds, scientists can design powerful gene mapping experiments for complex diseases that are difficult to map in human populations. Contribute Although the astounding generosity of Eli and Edythe L. Broad and several other venture philanthropists empowers our scientists to tackle many of the most important problems at the cutting edge of genomic medicine, there are many other critical challenges that they cannot yet pursue because of limited resources. We need additional visionary partners to join the Broads and the Broad Institute in transforming medicine with the power of genomics.
This is the website of the Structural Brain Mapping Group at the Department of Psychiatry, University of Jena. Our principal research focuses on the development of methods for structural brain imaging and their application. Specific areas of interest include the investigation of structural brain plasticity and schizophrenia research. Regional structural brain changes are among the most robust biological findings in schizophrenia, yet the underlying pathophysiological changes remain poorly understood. Recent evidence suggests that abnormal neuronal/dendritic plasticity is related to alterations in membrane lipids. We examined whether serum activity of membrane lipid remodeling/repairing cytosolic phospholipase A2 (PLA2) were related to regional brain structure in magnetic resonance images (MRI). The study involved 24 schizophrenia patients, who were either drug-nave or off antipsychotic medication, and 25 healthy controls. Using voxel-based morphometry (VBM) analysis of T1-high-resolution MRI-images, we correlated both gray matter and white matter changes with serum PLA2-activity. PLA2 activity was increased in patients, consistent with previous findings. VBM group comparison of patients vs. controls showed abnormalities of frontal and medial temporal cortices/hippocampus, and left middle/superior temporal gyrus in first-episode patients. Group comparison of VBM/ PLA2-correlations revealed a distinct pattern of disease-related interactions between gray/white matter changes in patients and PLA2-activity: in first-episode patients (n = 13), PLA2-activity was associated with structural alterations in the left prefrontal cortex and the bilateral thalamus. Recurrent-episode patients (n = 11) showed a wide-spread pattern of associations between PLA2-activity and structural changes in the left (less right) prefrontal and inferior parietal cortex, the left (less right) thalamus and caudate nucleus, the left medial temporal and orbitofrontal cortex and anterior cingulum, and the cerebellum. Our findings demonstrate a potential association between membrane lipid biochemistry and focal brain structural abnormalities in schizophrenia. Differential patterns in first-episode vs. chronic patients might be related to PLA2-increase at disease-onset reflecting localized regenerative activity, whereas correlations in recurrent- episode patients might point to less specific neurodegenerative aspects of disease progression.
The ImageJ installations below correspond to the WCIF ImageJ manual. The manual is written for this particular installation of ImageJ. This ImageJ installation has, among other plugins, one that links to an online version of the manual. The online manual is more up-to-date than the PDF version. Windows users Download WCIF ImageJ bundle (~23Mb) v1.34i, 3rd March 2005 with J2SE 5.0 (formerly J2SE 1.5). For Windows: download and run program. Mac and Linux users Download your OS specific version of ImageJ from the ImageJ website then extract the following file to the plugins folder. Download WCIF ImageJ bundle plugins only (~2Mb) This contains only the plugins, IJ preferences, LUTs and plugin source code. Image Processing and Analysis Software ImageJ LSM Browser (*.lsm) Axiovision viewer (*.zvi) Manufacturers of our microscopes and related equipment Zeiss - Microscopes and imaging systems. P.A.L.M. Microlaser Technologies - Manufacturer of our laser capture system. Sutter Instruments - Micromanipulators. Uniblitz - Shutters. Ludl - Manufacturers of our motorised x-, y-stage Hamamatsu - Digital cameras. Molecular Probes - Dyes and reagents. Scanalytics - Image acquisition and processing software. MicroBrightField - Developers of the Neurolucida and Stereo Investigator software. DVC - Digital cameras. Bitplane - Developers of the Imaris suite of software. AutoQuant - Developers of the AutoDeblur deconvolution software
Drew Scientific manufactures and sells Analytical Instruments and Reagents world-wide : Cell Counters for Clinical Hematology Cell Counters for Veterinary Hematology and Research Hemoglobin Analyzers for Diabetes (HbA1c) Reagents and Controls You can place an order on us in a variety of ways : by post, by fax, or by email. See the Contact Us page for addresses and telephone numbers. This section is to enable you to send an order by email. We need the following information : Your Order Number Your Company or Organisation Your contact name (and phone number if we don''t already know it). Your full email address. This is essential so that we can reply to you. The Delivery details (As Normal is acceptable if you are a frequent customer.) Your requested delivery date. A list of the items you require, with Part Number and Quantity. We will acknowledge your order by email, confirming the availability of the items, the delivery date, the price and the delivery details. In many parts of the world our customers are supported by our local distributors. If appropriate, we will pass your order to the relevant distributor and put them in touch with you. You can fill in the email order form directly with the above information, or you may use the Frequent Items tab to add those items that are most frequently ordered. Please use the Spares or Consumables lists to find the Part Numbers of any other items you require. But please do this before you start to fill in the Order Form, because if you leave this Ordering section before submitting your order, you will lose any data you have entered, and will have to enter it again.
Engine for question-Answering in Genomics Literature
A software tool, text mining based, for annotating text with gene ontology terms. The tool combines knowledge-driven methods on top of a standard vector- space retrieval approach to identify pointers to ontology terms. Passage selection methods were tested based on vocabulary density estimation using several terminologies of the domain. The tool improves on standard retrieval approaches based on vector-space similarities by using a Boolean completion principle.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 11, 2013. Web-based tool to explore the relationship between population frequency and extended linkage disequilibrium measured as haplotype homozygosity of observed haplotypes within a specified candidate region. Haplotype homozygosity (HH) is an effective measure of linkage disequilibrium (LD) for more than 2 markers. If we want to see, how LD breaks down with increasing distance to a specified core region, we can calculate HH in a stepwise manner as extended HH (EHH, Sabeti et al. 2002). EHH is calculated between a distance x and the specified core region for a chromosome population carrying a single core haplotype. Distance x increases stepwise to the most outlying marker. The procedure is repeated for each core haplotype. HH is evaluated as HH = sum(pi2) - 1/n / 1 - 1/n with pi being the relative haplotype frequency and n the sample size. It corrects for sampling effects (Sabatti & Risch 2002). The variance of HH is estimated according to Nei (1975). EHH estimates the level of haplotype splitting due to recombination and mutation at extended regions on both sides of a specified core region. It may be used to explore haplotype-specific LD patterns, e.g. for disease associated haplotypes. In combination with the core haplotype frequency it may also serve as an indicator of recent positive selection. Frequent core haplotypes with an unusually high long-range LD are supposed to be positively selected. The various core haplotypes can serve as internal controls. Input file: A text file consisting of a haplotype (chromosome) population
ELDERMET Gut microbiota as an indicator and agent of nutritional health in elderly Irish subjects
Latest publications: ELDERMET research has recently been published in the Proceedings of the National Academy of Sciences (USA). This work focuses on the composition and stability of the intestinal bacteria in older Irish adults. Read the paper here. Would you like to be part of ELDERMET? We are currently looking for people, aged 65 years or older, living in the community. All we ask is that you live in the Cork area, or are willing to travel to Cork, and have recently (within the last two/three weeks) taken any kind of antibiotic. It doesnt matter if you are still taking the antibiotic, as long as the finishing date isnt more than four weeks before your first visit to ELDERMET. ELDERMET Objectives To assess the composition of the faecal microbiota of elderly volunteers in the Irish population, using state-of-the-art molecular techniques. To correlate diversity, composition, and metabolic potential of the faecal microbial metagenome with health, diet and lifestyle indices that are a) likely to be influenced by the microbiota or b) to influence the microbiota. To develop recommendations for specific dietary ingredients, foodstuffs, functional foods and/or dietary supplements, that will improve the health of elderly consumers. To provide evidence-based recommendations for prospective studies to determine the molecular mechanisms for health improvements promoted by specific food ingredients that modulate components of the microbiota. ELDERMET Rationale The human intestinal microbiota is made up of approximately 1000 genetically unique organisms (phylotypes ) [1]. The bacteria present in the intestine make an important contribution to: metabolism executed in the gut [2] health, in diverse activites from pain perception [3] to cognitive function [4]. There is an increasing body of evidence linking alterations in the human gut microbiota with Inflammatory Bowel Disease [5, 6] and Irritable Bowel Syndrome [7]. The changing pattern of the gut microbiota in elderly subjects [8, 9] may be linked to host changes such as immunosenescence, increased susceptibility to disease and potentially systemic effects. The composition of the intestinal microbiota may be modulated by dietary components including prebiotics [10]. ELDERMET will determine the baseline composition of the gut microbiota of several hundred elderly Irish subjects using a combination of traditional culutre and molecular (culture-independent) methodologies. ELDERMET will explore potential correlations between microbiota composition and a range of health indices; cross-referencing data to dietary intake. Data will be analyzed in the context of the related FHRI projects in Nutrigenomics, Food Consumption, Food Safety, and Diet-Health. ELDERMET will provide recommendations to all stakeholders (including health practitioners and the health service, the food industry and the general public) on how to improve health based on defined modifications to dietary intake. Sponsor. This work is supported by the Goverment of Ireland Department of Agriculture Fisheries and Food/Health Research Board Food for Health Research Initiative award to the ELDERMET project as well as by a Science Foundation Ireland award to the Alimentary Pharmabiotic Centre. M.J.C. is now funded by a fellowship from the Health Research Board of Ireland.
European Molecular Biology Open Software Suite
The European Molecular Biology Open Software Suite
Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication.
Welcome to the EMQN website. EMQN is a not-for-profit organisation promoting quality in molecular genetic testing through the provision of external quality assessment (proficiency testing schemes) and the organisation of best practice meetings and publication of guidelines. The European Molecular Genetics Quality Network (EMQN) started in October 1998 after a successful pilot trial. From January 1999 to March 2002, the network was supported by a grant from the European Commission under the Standards Measurement and Testing Programme (contract number SMT4-CT98-7515). From April 2002, the network is supported by subscriptions from it users. External Quality Assessment (EQA): There are 26 EQA schemes being offered in 2010. To participate you must be a registered member of the network. For more information on EQA schemes, click the link here. Best Practice: EMQN is actively promoting ''best practice'' meetings on individual diseases. To assist in this process, EMQN will be organising best practice meetings. To participate you must be a registered member of the network. Following the meeting, draft best practice guidelines are produced and publised on this and other related websites, for example, the web site of the UK Clinical Molecular Genetics Society (CMGS). To find out more about best practice click here. Administration: The EMQN is based at the National Genetics Reference Laboratory (Manchester), St Mary''s Hospital, Manchester, The United Kingdom. The Network is co-ordinated and administered by Dr''s Rob Elles and Simon Patton. A management group is responsible for the activities and direction of the network. National partners in different countries help to disseminate information about the network. Quality Policy The EMQN provides a comprehensive range of quality assurance programs for molecular genetics to laboratories and industry worldwide. The European Molecular Genetics Quality Network (EMQN) is committed to helping ensure diagnostic molecular genetic laboratory test results are accurate, reliable and comparable wherever they are produced. The EMQN will provide a high quality and timely service which takes into account the needs and requirements of its users. Objectives To help to raise and maintain the standards of diagnostic clinical molecular genetic testing. To undertake and promote educational activities. To be a leading authority in quality assurance . To design and provide the best possible materials and data management. To design and provide quality reports that are timely and valid. To provide professional support and consultation. To develop new programs as required. To participate in peer review. To strive for continual improvement of the quality system. Sponsor. the network was supported by a grant from the European Commission under the Standards Measurement and Testing Programme (contract number SMT4-CT98-7515
It ranks amino acid residues in a protein sequence by their relative evolutionary importance, and when a structure is available for that protein, it also can display a structural map of where top-ranked residues fall. This can be useful for rational function re-design and protein engineering because biologist can then efficiently target mutations to the most relevant parts of a protein. For example, one may selectively block, separate, rewire, or mimic functions. ET-based functional annotations may also be useful to suggest protein function (see the ET Annotation Server). ET rank essentially captures the extent of evolutionary pressure at a given sequence position. It is obtained by correlating the sequence variations in an alignment of a protein family with its evolutionary divergences. Top-ranked residues are associated with variations that correlate with large divergences near the root of the evolutionary tree, and presumably linked to significant functional changes. Poorly-ranked residues in contrast are associated with variations near the leaves of the tree, presumably linked to modest functional differences, if any at all. We provide two means of generating and visualizing the ET ranks of importance: the ET Viewer and the ET report_maker. 0. The ET Viewer runs real-value ET or integer ET and displays results. Its ET Wizard takes a PDB identifier, or file, for input, and it outputs ranks of evolutionary importance for every sequence position in the protein. All trace parameters may be adjusted; custom alignments and phylogenetic trees may be used. The ET Viewer then displays a color map of the structure showing which residues are ranked among the top nth percentile, where n is adjustable, and whether they cluster (a z-score indicates whether these top-ranked residues cluster in a statistically significant manner). A multiple sequence alignment viewer and phylogenetic tree viewer display the underlying data. 0. (06/19/2009)A special note for Mac users: 0. The latest Java update for Mac, Java for Mac OS X 10.5 Update 4, moves the Java Web Start application to a new location, causing problems launching ET viewer and other Java Web Start programs. In order to fix this, you need to show your computer where the new location is for Java Web Start. In Finder, select the ET_Viewer_2_pub.jnlp file (which is probably in your downloads folder). Under the File menu, select Get Info. In the resulting window, there''s a section called Open With: Click the drop-down menu and select Other.... A new window will open. Navigate to your hard drive, select System, then Library, then CoreServices, and then select Java Web Start.app. Then click the Change All... button in the Open With: section to make this change permanent. Sponsor. A.D.W., S.E. and R.M.W. were also supported by train- ing fellowships from the National Library of Medicine to the Keck Center for Interdisciplinary Bioscience Training of the Gulf Coast Consortia.
Specific short oligonucleotide sequences that enhance pre-mRNA splicing when present in exons, termed exonic splicing enhancers (ESEs), play important roles in constitutive and alternative splicing (ESE References). A hybrid computational/experimental method, RESCUE-ESE, was recently developed for identifying sequences with ESE activity. In this approach, specific hexanucleotide sequences are identified as candidate ESEs on the basis that they have both significantly higher frequency of occurrence in exons than in introns and also significantly higher frequency in exons with weak (non-consensus) splice sites than in exons with strong (consensus) splice sites. Representative hexamers from ten different classes of candidate ESEs, together with 6 or 7 bases of flanking sequence context on each side, were introduced into a weak (poorly spliced) exon in a splicing reporter construct. These reporter minigenes were then transfected into cultured cells, where they are transcribed and spliced, and the relative level of inclusion of the test exon was assayed by quantitative (radio-labeled) RT-PCR. Point mutants of these sequences were also analyzed to confirm the precise motifs responsible for ESE activity. The RESCUE-ESE approach identified 238 hexamers as candidate ESEs using a large database of human genes of known exon-intron structure containing over 30,000 nonredudant exons. In more recent analyses by Yeo et al., the RESCUE-ESE approach was utilized to predict hexamers as candidate ESEs in other vertebrate genes, namely, Fugu rubipes, Zebrafish and Mouse. This allows the identification of motifs that are conserved in vertebrates. This web server allows a sequence to be checked for presence of these candidate ESE hexamers.
A complete online Product Catalog of chemicals, supplies, accessories, and equipment for Electron and Light Microscopy, Histology, Cell Biology, Neuroscience, and all biological related research fields. At the site, you can find technical tips and recommended articles of interest, technical and product data sheets, Material Safety Data Sheets, and many revolutionary new products and exclusive items. A complete product catalog of the entire Diatome collection of Diamond knives, tools, and accessories for Electron and Light microscopy for Biological and Materials Science at room and cryo temperatures. Available on-line as well is information on our services, programs, specials, and policies. The complete handling and use technical manual as well as troubleshooting can also be found at our site. The Summers Optical on-line catalog including a complete line of optical cements and adhesives, decementing agents, hardness testers, ultrasonic baths and UV lights as well as technical and transmission data and problem solving can be found at this site. As well as, our unique bonding manual including troubleshooting and charts for how to choose a cement for specific applications and a complete set of MSDS on all of our products can be seen here. EMS Contract Packaging is a total service contract manufacturer, packager, and formulator with over 40 years experience in drug and cosmetic formulating and packaging. Negafile furniture quality wood filing systems and storage cases for grids, negatives, film and microscope glass slides. And a full line of shipping and packaging solutions for all your traditional or digital media.
You can begin your search immediately using the Quick form on the home page or you can access the other specialized search forms in Embase. You can choose any section from the options on the top menu bar: Search, Emtree, Journals, Authors, or Help. You can start to search without logging in but if you would like to set up an email alert or save a search, then you may Login or Register from the upper-right part of the screen. Note: if you are outside your institution IP range, you will first be directed to the info site before accessing the Embase Home page. For more information on remote access, please see Login section. Search Forms Search is at the core of Embase and all search forms are designed to allow you to look for biomedical and pharmaceutical clinical and research information easily and quickly, whether you are a new or experienced searcher. The Embase search engine allows Boolean searching with wildcard and truncation features, as well as many predefined search limits. Search is divided into five options: Quick, Advanced, Drug, Disease and Article. Quick lets you perform easy yet powerful searches without having to learn a complex search language. It is perfect if you are starting your research and looking for an overview of the literature or good terms to include in your search strategy. Autocomplete will help you to search using the bext terminology. Advanced incorporates options from Emtree term mapping including explosion searching for maximum precision in subject searching (see Emtree) and Drug and Disease provide access to specialized features useful to search these topics, such as ''Adverse Drug Reaction' '''Drug Combination''. Generally speaking, drug searches are best carried out in the Drug form, diseases in the Disease form and non-drug and disease searches in the Advanced form. Article allows you to pinpoint individual articles. Embase is owned and operated by Elsevier B.V., Radarweg 29, 1043 NX Amsterdam, The Netherlands, Reg. No. 33156677, BTW No. 002967455B65 (Elsevier).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. During the embryogenesis of human embryo, the development of each organ may be impaired during specific time periods. As illustrated, such impairment leads to congenital anomalies. After such critical periods, the environmental factors cause either minor congenital anomalies or lead to functional abnormalities. True beginning of gestation starts with the fertilization of the ovum which normally occurs one to several days after ovulation. By convention, however, due the fact that the day of the last menstrual period is easily defined, gestation starts on such day. During the first two weeks of pregnancy the embryo does not exist and endometrium is undergoing its normal menstrual and then proliferative phases. Stage one of the development starts with the fertilization of the ovum and stage 2 is initiated by the cleavage of the fertilized ovum. It is during the 4th and 5th stages of development that blastocyst starts its implantation process. By the end of the second week after fertilization, the stage 6 is initiated. During this stage, the primary chorionic villi and embryonic disc are formed.
Emergent Neural Network Simulation System
emergent is a comprehensive, full-featured neural network simulator that allows for the creation and analysis of complex, sophisticated models of the brain in the world. With an emphasis on qualitative analysis and teaching, it also supports the workflow of professional neural network researchers. Its high level drag-and-drop programming interface, built on top of a scripting language that has full introspective access to all aspects of networks and the software itself, allows one to write programs that seamlessly weave together the training of a network and evolution of its environment without ever typing out a line of code. Networks and all of their state variables are visually inspected in 3d, allowing for a quick visual regression of network dynamics and robot behavior. This same 3d world sports a highly accurate Newtonian physics simulation, allowing you to create rich robotics simulations (for example, a car). As a direct descendant of PDP (1986) and PDP (1999), emergent has been in development for decades. In the most recent versions available strive to distill it down to its essential elements. Those that take the time to learn the best practices will be rewarded with the ability to create and understand the most complicated neural models ever published.
Applied Math and Science Education Repository
AMSER is a portal of educational resources and services built specifically for use by those in Community and Technical Colleges but free for anyone to use. AMSER provides links to resources for faculty, staff, librarians, students and others for use in both educational settings or in their pursuit of life long learning. Sponsors: AMSER is funded by the National Science Foundation (NSF) as part of the National Science Digital Library, and is being created by a team of project partners led by Internet Scout.
Emphron Informatics provides full data management and statistical analysis services across the range of biological research. Our areas of expertise include: Biotechnology - especially drug and diagnostic discovery. We have world class expertise in the management and analysis of data from modern discovery platforms, including gene chips, next generation sequencing, and antibody arrays. Clinical Research - We are experienced in the management and statistical analysis of data from regulatory trials (across a range of theraputic areas and development phases), and we provide low-cost flexible solutions for investigator initiated trials. Environmental Studies. We provide data management, statistical design and statistical analysis services. Emphron Solutions We meet client needs in these areas through a number of solution types: Hosted data management and analysis services. We provide on-line web-enabled data management and analysis systems tailored to our clients needs across our interest areas. These include on-line 21CFR11 compliant clinical databases, gene chip data management and analysis systems, and environmental monitoring databases. These systems are hosted in our enterprise class data centre Full service data management and data analysis. We take over all of your data management and data analysis needs, and provide solutions based on our in-house tools and technologies. System development and integration. We build tailored data management and analysis systems, based on open-source components and install them on your premises. Emphron Professionals Emphron professionals are mostly qualified to Doctoral level, with many years experience of advanced informatics and statistics. They combine cutting-edge technology knowledge, with a sound grasp of business and practical realities.
Integration objectives Training and education Standardisation in technology Share of material Web based sharing of information and communication Translational research Spreading excellence objectives Coordinated by Treviso Courses on bone pathology and molecular biology Standard Operation Protocols Web-based discussion forums Research objectives Work packages on: Cartilaginous Tumours (Leiden) Osteogenic Tumours (Munster) Giant Cell Tumours (Oxford) Ewing Sarcoma (Bologna)
European Centre for the Validation of Alternative Methods
ECVAM was created by a Communication from the Commission to the Council and the Parliament in October 1991*, pointing to a requirement in Directive 86/609/EEC** on the protection of animals used for experimental and other scientific purposes, which requires that the Commission and the Member States should actively support the development, validation and acceptance of methods which could reduce, refine or replace the use of laboratory animals: Article 7.2: An experiment shall not be performed if another scientifically satisfactory method of obtaining the result sought, not entailing the use of an animal, is reasonably and practicably available. Article 23: The Commission and Member States should encourage research into the development and validation of alternative techniques which could provide the same level of information as that obtained in experiments using animals, but which involve fewer animals or which entail less painful procedures, and shall take such other steps as they consider appropriate to encourage research in this field. ECVAM has been established in 1992 as a unit of the Environment Institute, part of the Joint Research Centre, and has been transferred to, at that time, newly formed Institute for Health and Consumer Protection in Ispra, Italy in 1998 of which ECVAM is still part of. Duties of ECVAM As defined in the Communication of the European Commission to Council and the European Parliament in October 1991*: 1. To coordinate the validation of alternative test methods at the European Union level. 2. To act as a focal point for the exchange of information on the development of alternative test methods. 3. To set up, maintain and manage a data base on alternative procedures. 4. To promote dialogue between legislators, industries, biomedical scientists, consumer organisations and animal welfare groups, with a view to the development, validation and international recognition of alternative test methods. Moreover, ECVAM should help to expand the JRC''s role in prenormative research. ECVAM thus seeks to promote the scientific and regulatory acceptance of alternative methods which are of importance to the biosciences, through research, new test development and validation, and the establishment of specialised databases, with the aim of contributing to the replacement, reduction and refinement of laboratory animal precedures (in accordance with the 3Rs concept of Russell & Burch***) Due to the political sensitivity of its duties, ECVAM, uniquely at the JRC, has its own Scientific Advisory Committee (ESAC) with participation from all Member States, relevant industrial associations, academic toxicology, the animal welfare movement, as well as other Commission services with interest in the alternatives topic area. The Validation Process Validation is the process by which the reliability and relevance of a procedure are established for a specific purpose. In 1995, based upon experience gained during several recent large-scale validation studies, and in consultation with various international experts (including members of ERGATT), ECVAM published recommendations concerning the practical and logistical aspects of validating alternative test methods (ECVAM workshop report 5). Five main stages in the evolution of new test methods were identified: test development; prevalidation; validation (involving a formal interlaboratory study with the testing of coded chemicals); independent assessment; and progression toward regulatory acceptance. ECVAM has implemented a prevalidation scheme, which includes three main phases: protocol refinement, protocol transfer, and protocol performance. The objective of the prevalidation process is to ensure that any method included in a formal validation study adequately fulfills the criteria defined for inclusion in such a study, so that financial and human resources are used more efficiently, and so that there is a greater likelihood that the expectations of those in the scientific, regulatory and animal welfare communities, who seek the replacement of current animal tests by relevant and reliable alternative methods, will be met. In 2004, ECVAM has published the Modular Approach to the ECVAM Principles on Test Validity (select from the top-menu bar the sector Publications followed by ECVAM Selected Articles) that makes the validation process more flexible, by breaking down the various steps in validation into indipendent modules, and defining for each module the information needed for assessing test validity. Collaborations ECVAMs activities are undertaken in collaboration with numerous laboratories and organisations in the EU Member States, and all over the world. ECVAM also works in close collaboration with other Commission services, such as DG Environment, DG Enterprise, DG Research and DG Health and Consumer Protection. Sponsor. This is a Five years project funded by DG RTD that aims to develop a testing strategy to improve the prediction of oral acute toxicity using non-animals based systems.
The directing and coordinating authority responsible for public health within the United Nations system. The WHO Regional Office for Europe (WHO/Europe) is one of the six regional offices around the world. It serves the WHO European Region, which comprises 53 countries from the Atlantic to the Pacific oceans. WHO/Europe collaborates with a range of public health stakeholders in the Region and globally, to ensure that coordinated action is taken to develop and implement efficient health policies and to strengthen health systems. WHO/Europe is made up of public health, scientific, and technical experts.
Core facility that provides the following services: Flow cytometry equipment and software access, FACS machine training, FACS data analysis, FACS analysis and population isolation, FACS assay consultation. The goals of this Core Facility are to provide flow cytometry services for Howard University?s research investigators, and develop new applications.
This website is an invitation. an invitation to join scientists and stakeholders in an effort to review the scientific basis of traditional toxicological risk assessment, to provide the toxicological community with the tools it needs to efficiently and transparently judge risks of a diversifying nature and to make toxicology thus fit to meet the challenges of the 21st century. an invitation to participate in the inception and continuous implementation of a new movement in toxicology that aims at adopting an evidence-based approach. an invitation to help bridging the gap between modern toxicological science and risk assessment in order to exploit the wealth of information from new technologies in modern life sciences & toxicological research and to arrive at informed, transparent, judicious and conscientious decisions made on the basis of all evidence available. an invitation to develop a framework that allows combining precious expert insight grown over years of practical experience with structured approaches in basic science, in method assessment and in decision-making. Such evidence-based toxicology might help to make the best possible use of all sources of evidence in an efficient, productive, reliable, acceptable and transparent manner. Why do we need evidence-based toxicology (EBT)? Toxicology and the delivery of effective safety assessment critically relies on concepts and understanding generated by basic scientific research and must therefore adapt constantly to advances in knowledge. However, particularly from the perspective of regulatory toxicology, some of the assessment paradigms and methodologies were established decades ago and have changed little in response to scientific progress. At the same time, changes in our understanding of human disease, changes in the types of product now requiring safety assessment, and changes in the legislative landscape and public expectations pose significant challenges for industry, academia and regulators alike. It is necessary to challenge the status quo and ensure that as a matter of course best scientific practice and technical sophistication is reflected in safety assessment practices such that current and future challenges can be met. It is important therefore to ensure that structures are available that will encourage, facilitate and support a process of critical appraisal and renewal of the toxicological repertoire available for safety assessment. Part of this process is to embrace evidence-based toxicology such that the best possible scientific evidence is applied to judge product safety and likely risks to human health.
ExPASy Aldente Peptide Mass Fingerprinting tool
THIS RESOURCE IS NO LONGER IN SERVICE documented on June 4, 2013. Aldente is a tool to identify proteins from peptide mass fingerprinting data. This fast and powerful tool takes advantage of the Hough transform for spectra recalibration and outlier exclusion. The Aldente search form can be used in two modes: for a global view of all the search parameters on one page: click on the section tab All. This global view is useful to have a quick overview before sending the query. to have search parameters grouped into smaller logical sections: click on the corresponding section tab in the tabs banner. Note! Moving from one section to another keeps search parameter selections. For your convenience, you may view / hide the help during your search parameters selection. Use the Help or No help section tab accordingly.
Foundation for Informed Medical Decision Making
Mission The Foundation for Informed Medical Decision Making is a non-profit organization dedicated to assuring that people understand their choices and have the information they need to make sound decisions affecting their health and well being. To accomplish our mission: We promote understanding and adoption of informed medical decision-making. We organize and frame medical evidence in an unbiased manner to help people evaluate their options, particularly in instances where differences in individual preferences and perspectives are likely to affect personal choice. We sponsor research to expand knowledge of how to improve decision quality in health care. Medical Evidence The science of medical care is advancing at a rate that makes the delivery of quality patient-focused care an enormous challenge. New information about disease biology and genetics, rapid development of new tests and treatments, and the shift in disease from largely acute to largely chronic are all important contributing factors. Patient Perspective Medical research on practice variation indicates that patient perspectives are often less important in treatment decisions than factors having little to do with patients or their illnesses, such as geography, economics or supplier-induced demands. The Foundation brings the patient perspective into focus by interviewing real patients who can talk about the choices they made and why. Without the perspective of the patient, we cannot achieve a quality medical decision. Informed Medical Decisions The Foundation believes that it is the convergence of the two concepts: medical evidence and patient perspectives that create a truly informed decision in medical care. Funding The Foundation has worked in a unique partnership with Health Dialog since 1997. Health Dialog delivers patient support services to employers and health plans that are committed to providing excellence to their members or employees. As of July 2006, Health Dialog served seventeen million people through its contracts with healthcare insurers and corporations. Access to the Foundation''s decision support materials is a key benefit that Health Dialog''s clients receive. Health Dialog produces the Foundation''s new programs and distributes decision support materials and services to patients. A portion of Health Dialog''s revenue goes to the Foundation in the form of royalties to support the development of new decision support materials and research on how best to support patient decisions. The Foundation does not accept funding from any source that has a financial interest in any particular approach to medical testing or treatment. Foundation employees and clinical content experts do not accept support from companies that commercially market any kind of treatment or device that might be relevant to a program.
Solvers, or optimizers, are software tools that help users find the best way to allocate scarce resources. The resources may be raw materials, machine time or people time, money, or anything else in limited supply. The best or optimal solution may mean maximizing profits, minimizing costs, or achieving the best possible quality. An almost infinite variety of problems can be tackled this way, but here are some typical examples: Finance and Investment Working capital management involves allocating cash to different purposes (accounts receivable, inventory, etc.) across multiple time periods, to maximize interest earnings. Capital budgeting involves allocating funds to projects that initially consume cash but later generate cash, to maximize a firm''s return on capital. Portfolio optimization -- creating efficient portfolios -- involves allocating funds to stocks or bonds to maximize return for a given level of risk, or to minimize risk for a target rate of return. Manufacturing Job shop scheduling involves allocating time for work orders on different types of production equipment, to minimize delivery time or maximize equipment utilization. Blending (of petroleum products, ores, animal feed, etc.) involves allocating and combining raw materials of different types and grades, to meet demand while minimizing costs. Cutting stock (for lumber, paper, etc.) involves allocating space on large sheets or timbers to be cut into smaller pieces, to meet demand while minimizing waste. Distribution and Networks Routing (of goods, natural gas, electricity, digital data, etc.) involves allocating something to different paths through which it can move to various destinations, to minimize costs or maximize throughput. Loading (of trucks, rail cars, etc.) involves allocating space in vehicles to items of different sizes so as to minimize wasted or unused space. Scheduling of everything from workers to vehicles and meeting rooms involves allocating capacity to various tasks in order to meet demand while minimizing overall costs.
EyesWeb refers both to the research projects of InfoMus Lab on multimodal interactive systems and expressive gesture, and to the open software platform to support the development of real-time multimodal distributed interactive applications. The EyesWeb project started in 1997, as a natural evolution of the HARP Project (see www.infomus.org). The current release of the open software platform is EyesWeb XMI (eXtended Multimodal Interaction). The EyesWeb software platform has been developed in EU IST projects in the 5th (MEGA, www.megaproject.org) and 6th Framework Programme (TAI-CHI, Tangible Acoustic Interfaces for Computer Human Interaction). EyesWeb has been adopted in several other EU projects, has been licensed to more than 15,000 individual users, companies, and institutions. EyesWeb is also used in University courses and summer schools (e.g. the New York University Summer Program on Music, dance and new technologies). Software tools EyesWeb open software platform FreeFrame SDK Harp Petri Net Visual Editor and Simulation Software (Linux Version) Petri Net Visual Editor and Simulation Software (Win32 Version) Hardware tools Wireless On-Body-Sensors-to-Midi Box Long-distances MIDI tx/rx Video Multiplexer for connecting and synchronizing two videocameras to the same frame grabber Multimedia interfaces for robot-human interaction DanceWeb ultrasound sensor system
The database has now been updated to include ALL mutations found in HUS patients, including those in Factor I(FI) and Membrane (MCP). Homology models are available for the domains of FI and MCP and all analysis previously available for Factor H (FH) are now also available for FI and MCP. All SNP records for FH, FI and MCP are also now included in the database on the SNP pages. Only those SNPs within coding regions will be included in the full list of mutations and within the advanced search. For more information on the different versions of the database click here. We have also redesigned the site in order to display information more clearly. Please let us know what you think of the new design. Home Information Mutations Models References Links Submit Contact Us Help Collaborators NEWS !! SEP 2009 The database has now been recovered. Please report any bugs that you notice. NEWS !! MAY 2009 We have suffered from a complete server failure this month but these issues have been sorted out and work is being carried out to restore all the data within our FH-HUS database. Sorry for any inconvenience this may have caused. NEWS !! JAN 2007 Mutations within complement Factor B have also been associated with aHUS. (Goicoechea de Jorge et al., 2007) NEW !! Nov 2006 FH-HUS Database Version 2.1 The database has now been updated to include ALL mutations found in HUS patients, including those in Factor I(FI) and Membrane (MCP). Homology models are available for the domains of FI and MCP and all analysis previously available for Factor H (FH) are now also available for FI and MCP. All SNP records for FH, FI and MCP are also now included in the database on the SNP pages. Only those SNPs within coding regions will be included in the full list of mutations and within the advanced search. For more information on the different versions of the database click here. We have also redesigned the site in order to display information more clearly. Please let us know what you think of the new design. Quick Search Enter Codon No : Choose Protein : Advanced Search Have you or someone you know been diagnosed with aHUS? The information contained on this web site is provided for scientific research purposes only. We do not give medical advice or recommend any particular treatment for specific individuals. Here are several links for patient information on aHUS: http://renux.dmed.ed.ac.uk/ http://en.wikipedia.org/ http://kidney.niddk.nih.gov http://www.webmd.com HUS HUS (Haemolytic Uraemic Syndrome) is a disease associated with microangiopathic haemolytic anemia, thrombocytopenia and acute renal failure. A subgroup of the syndrome is strongly associated with abnormalities within the complement regulator factor H gene. To read information on HUS click here. To read information on Factor H (FH) click here. FH Mutations There are currently 74 Factor H mutations, 10 Factor I mutations and 25 MCP mutations linked with HUS patients within this database. There are also 5 mutations within FH that are associated with MPGN patients. . Following HGVS guidelines, mutations are numbered starting from the ATG initiation codon and include the 18-residue signal peptide. The number of the codon with respect to the mature FH protein and consistent with the RSCB PDB entry for secreted FH (1haq.pdb) is shown alongside in parenthesis. Type I and Type II Phenotype Type I indicates that the mutant protein is either absent from the plasma or present in lower amounts. This indicates the mutation has a structural effect on the mutant protein - ie reducing the stability Type II indicates that the mutant protein is present in normal amounts in plasma. This indicates that the mutation has a functional effect on the protein ie affecting substrate binding References There are three references you can use to reference this database Saunders et al, 2007. The interactive Factor H-atypical hemolytic uremic syndrome mutation database and website: update and integration of membrane cofactor protein and Factor I mutations with structural models. Hum Mutat. 2007 28:222-234. Saunders et al, 2006. An interactive web database of factor H-associated hemolytic uremic syndrome mutations: insights into the structural consequences of disease-associated mutations. Hum Mutat. 2006 27:21-30. Saunders & Perkins, 2006. A user''s guide to the interactive Web database of factor H-associated hemolytic uremic syndrome. Semin Thromb Hemost. 2006 32:160-8. Abstract. BACKGROUND: cblC disease is a cause of hemolytic uremic syndrome (HUS), which has been primarily described in neonates and infants with severe renal and neurological lesions. PATIENTS: Two sisters aged 6 and 8.5 years presented with a latent hemolytic process characterized by undetectable or low plasma haptoglobin, respectively, associated with renal failure and gross proteinuria. Renal biopsies performed in both patients found typical findings of thrombotic microangiopathy suggesting the diagnosis of HUS. Both patients were free of neurologic signs. RESULTS: Biochemical investigations found a cobalamin processing deficiency of the cblC type. Search for additional factors susceptible to worsen endothelial damage revealed homozygosity 677C--> T mutation in the methylenetetrahydrofolate reductase gene as well as heterozygosity for a 3254T--> C mutation in factor H in the patient with the most severe clinical presentation. Long-term subcutaneous administration of hydroxocobalamin in combination with oral betaine and folic acid resulted in clinical and biological improvement in both patients. CONCLUSION: cblC disease may be a cause of chronic HUS with delayed onset in childhood. Superimposed mutation of factor H gene might influence clinical severity.
Family members connect with our Family Tree application. We have over 178,385,793 relatives added and growing! Familybuilder, the top family destination on social networks, today announced that it has been chosen by AlwaysOn as one of the AlwaysOn East Top 100 winners. Inclusion in the AlwaysOn East 100 signifies leadership amongst its peers and game-changing approaches and technologies that are likely to disrupt existing markets and entrenched players. Familybuilder was specially selected by the AlwaysOn editorial team and industry experts spanning the globe based on a set of five criteria: innovation, market potential, commercialization, stakeholder value, and media buzz. Familybuilder and the AlwaysOn East Top 100 companies will be honored at AlwaysOn''s Venture Summit East event on June 21st, 2010, at Harvard Business School in Boston, MCA. This two-day executive event features CEO presentations and high-level debates that highlight the significant economic, political, and technology trends impacting the global growth investor on the East Coast. Now more than ever, staying abreast of market conditions and innovations is crucial to financial success. After examining the companies that are on the AOE100 list, it''s obvious that innovation is not only alive and well on the East Coast, it''s accelerating in economic power and scope. says Tony Perkins, founder and editor of AlwaysOn. The companies certainly represent some of the highest-growth opportunities in the private company marketplace. The AlwaysOn East 100 winners were selected from among hundreds of other technology companies nominated by investors, bankers, journalists, and industry insiders. The AlwaysOn editorial team conducted a rigorous three-month selection process to finalize the 2010 list. Familybuilder is the first company to offer applications for communicating and staying in touch with family members on social networks including Facebook, MySpace, and others. The Company, with over 26 million users and over 160 million family members added, is quickly becoming one of the most used family services online. The Company''s flagship application on Facebook, Family Tree, is one of the top 15 non-gaming applications on the platform. With its substantial base of customers, Familybuilder is now expanding into new lines of businesses including a newsletter http://familybuilder.com/newsletter as well as subscription functionality. About AlwaysOn AlwaysOn is the leading business media brand networking the Global Silicon Valley. AlwaysOn helped ignite the social media revolution in early 2003 when it launched the AlwaysOn network. In 2004, it became the first media brand to socially network its online readers and event attendees. AlwaysOn''s preeminent executive event series includes the Summit at Stanford, OnMedia, OnHollywood, Venture Summit Mid-Atlantic, OnDemand, Venture Summit Silicon Valley, Venture Summit East, GoingGreen Silicon Valley, GoingGreen East, and GoingGreen Europe. The AlwaysOn network and live event series continue to lead the industry by empowering its readers, event participants, sponsors, and advertisers like no other media brand.
This document defines the processes and standards that all FLTK developers must follow when developing and documenting FLTK, and how trouble reports are handled and releases are generated. The purpose of defining formal processes and standards is to organize and focus our development efforts, ensure that all developers communicate and develop software with a common vocabulary/style, and make it possible for us to generate and release a high-quality GUI toolkit which can be used with a high degree of confidence. Much of this file describes the existing practices that have been used up through FLTK 1.1.x, however I have also added some new processes/standards to use for future code and releases. The fltk-dev mailing list and fltk.development newsgroup are the primary means of communication between developers. All major design changes must be discussed prior to implementation. Specific Goals The specific goals of the FLTK are as follows: Develop a C++ GUI toolkit based upon sound object-oriented design principles and experience. (*) Minimize CPU usage (fast). (*) Minimize memory usage (light). (*) Support multiple operating systems and windowing environments, including UNIX/Linux, MacOS X, Microsoft Windows, and X11, using the native graphics interfaces. (*) Support OpenGL rendering in environments that provide it. (*) Provide a graphical development environment for designing GUI interfaces, classes, and simple programs. (*) Support UTF-8 text. Support printer rendering in environments that provide it. Support schemes, styles, themes, skinning, etc. to alter the appearance of widgets in the toolkit easily and efficiently. The purpose is to allow applications to tailor their appearance to the underlying OS or based upon personal/user preferences. Support newer C++ language features, such as templating via the Standard Template Library (STL), and certain Standard C++ library interfaces, such as streams. However, FLTK will not depend upon such features and interfaces to minimize portability issues. Support intelligent layout of widgets. Many of these goals are satisfied by FLTK 1.1.x (*), and many complex applications have been written using FLTK on a wide range of platforms and devices. Development of the remaining features is proceding for FLTK 2.0 with a new, namespace-based API. While 2.0 offers some limited 1.x source compatibility, the changes to the underlying widget classes are significant enough to prevent full compatibility. Software Development Practices Documentation All widgets are documented using the Doxygen software; Doxygen comments are placed in the header file for the class comments and any inline methods, while non-inline methods should have their comments placed in the corresponding source file. The purpose of this separation is to place the comments near the implementation to reduce the possibility of the documentation getting out of sync with the code. All widgets must have a corresponding test program which exercises all widget functionality and can be used to generate image(s) for the documentation. Complex widgets must have a written tutorial, either as full text or an outline for later publication The final manuals are formatted using the HTMLDOC software. Sponsor. Easy Software Products
A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST.
Flavornet is a compilation of aroma compounds found in human odor space. A seemingly infinite number of perceptions are invoked by less than 1000 odorants that make up this space. These chemicals with mass less than 300 Daltons bind to proteins on the olfactory receptor neurons (ORNs) at the surface of the olfactory epithelium. Excitation of ORNs generates a topographic map of sensory information in the brain that is a representation of the stimulating chemical features of the external world. The Flavornet lists only those odorants that have been found in a human odor space at supra-threshold levels i.e. at levels likely to stimulate ORNs. In Flavornet odorants are arranged by chromatographic and sensory properties. Except for indexing standards the data have been taken from published research using GCO. They are listed by retention indices both Kovats n-paraffin and ethyl ester on four different substrates. A link to a summary page containing chemical properties, sensory descriptors, bibliographies and pdb (protein data bank) files of MM2 minimized structures is provided for each ligand. To be included in Flavornet an odorant must have been detected in a natural product or real environment by some form of quantitative GCO method e.g. dilution analysis (Aroma Extraction Dilution Analysis or CharmAnalysis) perceived intensity analysis (e.g. Osme) or detection frequency analysis (e.g. SNIFF). Therefore, the Flavornet lists only those volatiles that humans use in their chemical ecology. Once on the list, missing data about an odorant was filled in with estimates (shown in square brackets). These estimates will be replaced with experimental measurements as they become available. In every case data from the first report of a GCO detection will be used unless a more accurate report is subsequently made, then, the new data will be included along with the original. The present data was collected from articles published since 1984 using GCO to detect odorants in natural products. In the summers of 2003 and 2004 Hannah E. Collins, Yale University, read over 100 of these articles and checked the chemical data for the odorants against the Chemical Abstract Service databases. Sponsor. Sponsored by DATU Inc.
DNA software and consultancy: The DNA Alignment software and Network software is used by biologists, anthropologists, medical researchers and students world wide. We carry out phylogeographic consultancy for US, UK and German clients, including legal medical work. We were involved in the tv projects The Real Eve (Discovery Channel) and Motherland (BBC). Our biotechnological director Dr Peter Forster is on the editorial board of the International Journal of Legal Medicine since 1999. Technology and sales consultancy: Clients include multinational corporations, research institutions, and medium to small businesses. Client quotes: Vorbildlicher Einsatz (Dr Stephan Hitzel, EADS, in CADplus 1/2003 journal, Cover Story). We have had an effective business relationship with Fluxus Technology since 1999, and their experience of the German market has proved to be invaluable as part of our operations supplying high end engineering software and consultancy services right across the engineering supply chain (Andy Chinn, Business Development Manager, ITI TranscenData, February 2006). Abstract. Indo-European is the largest and best-documented language family in the world, yet the reconstruction of the Indo-European tree, first proposed in 1863, has remained controversial. Complications may include ascertainment bias when choosing the linguistic data, and disregard for the wave model of 1872 when attempting to reconstruct the tree. Essentially analogous problems were solved in evolutionary genetics by DNA sequencing and phylogenetic network methods, respectively. We now adapt these tools to linguistics, and analyze Indo-European language data, focusing on Celtic and in particular on the ancient Celtic language of Gaul (modern France), by using bilingual GaulishLatin inscriptions. Our phylogenetic network reveals an early split of Celtic within Indo-European. Interestingly, the next branching event separates Gaulish (Continental Celtic) from the British (Insular Celtic) languages, with Insular Celtic subsequently splitting into Brythonic (Welsh, Breton) and Goidelic (Irish and Scottish Gaelic). Taken together, the network thus suggests that the Celtic language arrived in the British Isles as a single wave (and then differentiated locally), rather than in the traditional two-wave scenario (P-Celtic to Britain and Q-Celtic to Ireland). The phylogenetic network furthermore permits the estimation of time in analogy to genetics, and we obtain tentative dates for Indo-European at 8100 BC 1,900 years, and for the arrival of Celtic in Britain at 3200 BC 1,500 years. The phylogenetic method is easily executed by hand and promises to be an informative approach for many problems in historical linguistics.
Functional Genomics in Embryonic Stem Cells
This website is dedicated to the dissemination of information about the European research project FunGenES (Functional Genomics in Embryonic Stem Cells). FunGenES is a research programme carried out on mouse embryonic stem cells with the aim to improve our understanding of cellular self-renewal and differentiation processes into tissue-specific cells. The website contains general knowledge about stem cell research and related issues such as ethics in stem cell related research, and more detailed information about the specific scope and objectives of the FunGenES project. A brochure containing a general project description in PDF format is available for download in the section Publications. FunGenES - Functional Genomics in Embryonic Stem Cells brings together experts in stem cell research from 18 organisations from industry and academic research across Europe. This research initiative is set up as an Integrated Project with a budget of approximately 12 Million Euros, partially funded by the 6th Framework Programme of the European Union. Specialists from Germany, France, Italy, Portugal, Greece and the UK collaborate for a period of 3 years to investigate the functional genomics of mouse embryonic stem (ES) cells. FunGenES aims to achieve a detailed basic understanding of stem cell self-renewal and differentiation. FunGenES investigates the unique ability of mouse embryonic stem cells to develop into any cell of an organ (this ability is also known as pluripotency), creates new tools for functional genomic studies and will thus provide key knowledge to understand the commitment of cells to a particular cell type. This complex process occurs in several steps and controls the development of pluripotent cells into highly specialised cells of an organism. In particular, FunGenES aims to identify genes controlling the development of the pluripotent ES cells into heart cells (cardiomyocytes), nerve cells (neurons), smooth muscle cells, vascular endothelial cells, fat cells (adipocytes), liver cells (hepatocytes) and insulin-producing cells of the pancreas. FunGenES will deliver a gene expression atlas summarising the genetical pathways for cell differentiation. The project aims to contribute to future therapeutic strategies for degenerative diseases such as heart disease, diabetes and Parkinson''s. All these diseases are characterised by the irreversible loss of functional cells. FunGenES was selected from a large number of proposals to be funded as an advanced and promising project in the area of functional genomics in the Life-Science-Health Programme of the European Union. In addition to its ambitious scientific programme, FunGenES aims to inform the general public about stem cell research, its ethical aspects and future therapeutical applications The project is coordinated by Professor Jrgen Hescheler (University of Cologne) Jrgen Hescheler is excited about the potential of the project: By understanding how mammalian genomic information is selectively used in development, we will acquire an essential key to understanding ourselves and our health. Sponsor. The FunGenES Integrated Project was funded by a grant from the European Commission (6th Framework Programme, Thematic Priority: Life sciences, Genomics and Biotechnology for Health, Contract No. : FunGenES LSHG-CT-2003-503494; http://ec.europa.eu/grants/index_en.htm). H.B. and M.T. were also supported by the University Bordeaux 2 (http://www.u-bordeaux2.fr/index.jsp) and CNRS (http://www.cnrs.fr/); A.K.H. received NIH support, grant HL08395 (http://www.nih.gov/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Welcome to Flintbox, an application that revolutionizes the way the innovation community can share technologies, distribute new materials and software, and collaborate on research projects. Hundreds of research institutions are participating in the Flintbox open innovation network. Become a member to contribute and explore We are excited to present the Flintbox Application Programming Interface (API) to provide users with an easy way to upload data from any system to Flintbox. This freely available tool for synchronized information exchange will be a valuable resource to the open innovation community. The Flintbox API gives you the power to: Import existing technology postings directly into Flintbox Avoid duplicate data entry to market your technologies, ideas, and materials Create postings from any database Export project information to other websites For more information about using and implementing the Flintbox API, please see the About the Flintbox API page. Featured Project The New Flintbox offers expanded transactional capabilities: credit cards, purchase orders, purchase authorizations, donations, and much more The global Flintbox community is ideal for marketing new technologies, creative works, course materials, and innovative ideas. Flintbox enables universities to maximize their outreach to a broad spectrum of the innovation community. Plus, Wellspring provides expertise in assisting TTOs, inventors, and industrial liaison offices to promote their technologies, research programs, and partnering opportunities to Flintbox. Flintbox for Corporations Corporations turn to Flintbox to cultivate existing relationships and engage in new opportunities for collaborative research and solution sourcing from universities and other companies. For example, a pharmaceutical firm uses Flintbox to provide researchers and physicians software to assess patient outcomes. Flintbox for Technology Communities Flintbox empowers technology communities to connect effectively in a geographic region, building a Sphere of Innovation to truly recognize and capitalize on the valuable relationships and innovation assets in your community. For example, by creating or joining a community Group of members with common interests, say tissue engineering or artificial intelligence, you can link to other groups and explore common interests and complementary resources, for a dynamic collaborative effort and to efficiently share related technology projects. Flintbox is a registered trademark of Wellspring Worldwide, LLC
Software for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.
FlowingData explores how designers, statisticians, and computer scientists are using data to understand ourselves better - mainly through data visualization. Money spent, reps at the gym, time you waste, and personal information you enter online are all forms of data. How can we understand these data flows? Data visualization lets non-experts make sense of it all. About Nathan As for me, I''m a PhD candidate in statistics. I live and breathe data. I also have a background in computer science and design. I do some freelancing from time to time, but mostly I''m just trying to work on my dissertation. You can find more about me here. For the New Readers If you''re new here, welcome to FlowingData. A good place to start is the archives where you''ll find FlowingData''s most popular posts or take a look at the FlowingData beginner''s guide. If you like what you see, subscribe to the feed, follow on Twitter, or fan on Facebook More specifically, I''m most interested in Social data visualization Self-surveillance Data for non-professionals FlowingData readers are data-savvy people who are interested in visualization, statistics, design, analysis, and programming. If you have a product or service that is of interest to them, then FD sponsorship is a great way for you to connect with them. There are two exclusive ways for you or your group to connect with readers. The first is through a banner ad, which appears in the top right of every page. The second is via a bimonthly sponsorship of the FlowingData RSS feed. Both sponsorship types also include a mention in the monthly thank you post.
A computer algorithm that provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. The predictive power of FOLDEF has been tested on a very large set of point mutants (1088 mutants) spanning most of the structural environments found in proteins . FoldX uses a full atomic description of the structure of the proteins. The different energy terms taken into account in FoldX have been weighted using empirical data obtained from protein engineering experiments.
C. elegans Gene Knockout Project Containing information about the Gene Knockout consortium, an on-line version of targeted gene database, knockout submission form and oligo prediction software. C. elegans Gene Expression Project Members investigating C. elegans gene expression using promoter GFP fusions and serial analysis of gene expression (SAGE). Serial Analysis of Gene Expression View and download C. elegans SAGE data. Provided are tag to gene mappings, various filters (e.g. sequence quality, minimum tag count), and search by keyword or tag. Also available are supplemental data from publications. Microarray Data Download C. elegans expression data generated from the Affymetrix GeneChipTM or a NimbleGen custom array. These experiments were done in parallel with the SAGE experiments, and there is data available for the six major developmental stages. Expression Patterns for promoter GFP fusions View and search expression patterns of C. elegans promoter GFP fusions. Tools for automated PCR primer design PCR-based screening for deletions in C. elegans genes, including the ''poison primer'' strategy Construction of promoter GFP fusions using PCR stitching (fusion PCR) Fosmid Clone Search We have created a C. elegans fosmid library. Use this site to search for fosmid clones for your gene or region of interest, and request clones.
Fungal genomes available from the Sanger Institute. Data are accessible in a number of ways; for each organism there is a BLAST server, allowing search of the sequences. Sequences can also be down-loaded directly by FTP. In addition, for those organisms being sequenced using a cosmid approach, finished and annotated cosmids are submitted to EMBL and other public databases.
A tool for mapping transcriptome data and for creating a database with an overview of the entire pathway, a web-based resource consisting of a web-application for the visualization of complex omics data onto KEGG pathways to overview all entities in the context of cellular pathways, and databases created with the software to visualize a series of microarray data. The web-application accepts transcriptome, proteome, metabolome, or the combination of these data as input, and because of this scalability it is advantageous for the visualization of cell simulation results. Several databases of transcriptome data obtained at Mori Laboratory, Nara Institute of Science and Technology, Japan, are also presented.
The Institute for Advanced Biosciences, Keio University, is an academic research institute pioneering the new life science field of Systems Biology, using both experimental and computational biology. There are several groups working in collaboration, focusing mainly on genome biology and engineering, genome design and synthetic biology, metabolic engineering, proteomics, metabolomics, RNA biology, bioinformatics and computational biology. Using cutting-edge technologies, intracellular components can be analyzed comprehensively to construct computer simulation models that can find numerous applications in fields such as biomedical, environmental, and agricultural science. Experimental and computational facilities are located in Tsuruoka, Yamagata prefecture, in northern Japan while the SFC campus, in the Tokyo area, hosts the bioinformatics laboratory and most undergraduate curricular activities. IAB has successfully attracted very significant funding for multiple research projects from major funding organizations including the New Energy and Industrial Technology Development Organization (NEDO) (2002-2006), for bioprocesses and cell modeling, the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and its COE network, for biosimulation and systems biology (2003-2008), the Japan Science and Technology Agency (CREST, 2004-2009) for simulation and systems biology, the Ministry of Health, for cancer biology (2005), as well as from Yamagata prefecture and Tsuruoka city, 2001-2006 and 2006-2011). Over the past few years, IAB scientists have accumulated several awards including the 1st prize during the 5th Japan Biotechnology Business Competition (2005), the Minister of State for Science and Technology Policy award in recognition for industry-academia-government collaboration performance (2004), the IBM Shared University Research Award (2003), and the Nihon Kogyo Shimbunsha Award (2003) during the 17th Leading-edge Technology for Originality and Creativity. Sponsor. This study was supported by a grant from the Global COE Program entitled, Human Metabolomic Systems Biology and by a Grant-in-Aid for Scientific Research on Priority Areas Systems Genomes and on Lifesurveyor from the Ministry of Education, Culture, Sports, Science and Technology of Japan as well as research funds from the Yamagata prefectural government and the City of Tsuruoka.
VAMP: Visualization and Analysis of CGH arrays transcriptome and other Molecular Profiles
Visualization and Analysis of array-CGH transcriptome and other Molecular Profiles
Software for visualization and Analysis of CGH arrays, transcriptome and other Molecular Profiles.
Global Alliance for Vaccines and Immunisation
The Global Alliance for Vaccines and Immunisation
Although Haemophilus influenza type b (Hib) diseases and Hepatitis B (Hep B) infections are preventable with one combined life-saving vaccine, both continue to pose risks to the worlds most vulnerable populations, leading to life-long disabilities or even death. Vaccinating against Hib and Hepatitis B represents an essential step towards reaching Millennium Development Goal 4. The Hib bacterium causes meningitis and pneumonia and is considered the third vaccine-preventable cause of death in children aged under five. It is estimated that there are three million cases of serious Hib infection annually, of which 400,000 result in childhood death. The majority of survivors suffer paralysis, deafness, mental retardation and learning disabilities. Babies and young children are most at risk from Hep B, a viral disease, which attacks the liver and can cause both acute and chronic disease. This can lead to chronic liver disease and puts victims at high risk of death from cirrhosis of the liver and liver cancer in later life. More than two billion people are infected by Hep B worldwide of whom 360 million suffer from chronic Hep B infection; the latter is highly prevalent in all countries that GAVI supports. Children are most vulnerable to infection with 90 percent of infants infected in the first months of their lives developing chronic Hep B infection. Infections in the developing world are mostly from mother to child, or from child to child, mainly through cuts, bites, scrapes and scratches. Vaccinating against Hib and Hep B represents an essential step towards reaching Millennium Development Goal 4, which is to reduce the under-five mortality rate by two thirds by 2015. GAVI uses two mechanisms that draw heavily on private-sector thinking to help overcome historic limitations to development funding for immunisation. These mechanisms are the AMC and the IFFIm. The former reflects the need to meet disproportionately high costs in the early stages of implementing aid programmes; the latter developing countries'' need for sustainable predictable funding., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
GD library is an open source code library for the dynamic creation of images by programmers. GD is written in C, and wrappers are available for Perl, PHP and other languages. GD creates PNG, JPEG and GIF images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the fly. While not restricted to use on the web, the most common applications of GD involve website development. gd is a graphics library. It allows your code to quickly draw images complete with lines, arcs, text, multiple colors, cut and paste from other images, and flood fills, and write out the result as a PNG or JPEG file. This is particularly useful in World Wide Web applications, where PNG and JPEG are two of the formats accepted for inline images by most browsers. gd is not a paint program. If you are looking for a paint program, you are looking in the wrong place. If you are not a programmer, you are looking in the wrong place, unless you are installing a required library in order to run an application. gd does not provide for every possible desirable graphics operation. It is not necessary or desirable for gd to become a kitchen-sink graphics package, but version 2.0 does include most frequently requested features, including both truecolor and palette images, resampling (smooth resizing of truecolor images) and so forth. What if I want to use another programming language? Not all of these tools are necessarily up to date and fully compatible with 2.0.33. PHP A variant of gd 2.x is included in PHP 4.3.0. It is also possible to patch PHP 4.2.3 for use with gd 2.0.33; see the gd home page for a link to that information. It would be a Good Idea to merge all of the things that are better in mainstream gd and all of the things that are better in PHP gd at some point in the near future. Perl gd can also be used from Perl, courtesy of Lincoln Stein''s GD.pm library, which uses gd as the basis for a set of Perl 5.x classes. Highly recommended. OCaml gd can be used from OCaml, thanks to Matt Gushee''s GD4O project. Tcl gd can be used from Tcl with John Ellson''s Gdtclft dynamically loaded extension package. Pascal Pascal enthusiasts should look into the freepascal project, a free Pascal compiler that includes gd support. REXX A gd interface for the REXX language is available. Any Language The fly interpreter performs gd operations specified in a text file. You can output the desired commands to a simple text file from whatever scripting language you prefer to use, then invoke the interpreter.
A program that opens a new perspective to the analysis of microarray data (e.g., gene expression profiling). Unlike traditional gene clustering software, GEDI is primarily sample-oriented rather than gene-oriented. By treating each high-dimensional sample, such as one microarray experiment, as an object, it accentuates the genome-wide response of a tissue or a patient and treats it as an integrated biological entity. Hence, GEDI honors the new spirit of a system-level approach in biology. Yet, it also allows the researcher to quickly zoom-in from global patterns onto individual genes that exhibit interesting expression behavior and retrieve gene-specific information. Therefore, GEDI unites a novel holistic perspective with the traditional gene-centered approach in molecular biology. GEDI allows experimental biologists or clinicians with no bioinformatics background to efficiently and intuitively navigate through a large number of expression profiles, each with a memorizable face, and inspect, group and collect them, like managing a stack of baseball cards. DYNAMIC ANALYSIS: The unique strength of GEDI, for which GEDI was originally developed, is that it can display the results of parallel monitoring of multiple high-dimensional time courses, such as the comparison of expression profile time evolution in response to a series of drugs. GEDI creates animated graphics showing how 10,000s of genes change their expression over time in response to 100s of separately tested drugs. STATIC ANAYLSIS: The signature graphical output of GEDI, the GEDI-mosaics provide a unique, one-glance visual engram that gives each microarray or other high-dimensional dataset a face. A characteristic of GEDI''s analysis is that it does not prejudicate any particular structure in the data (such as clusters or hierarchical organization). Thus, it allows the researcher to use human pattern recognition to perform a global first-level analysis of the data. Sponsor. The project was supported by the Air Force Office of Scientific Research and the National Health Institutes. It is distributed for free academic use by the Childrens Hospital, Boston., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A suite of web-based open source software programs for clinical and genetic study. The aims of this software development in the Laboratory of Neurogenetics, NIA, NIH are * Build retrievable clinical data repository * Set up genetic data bank * Eliminate redundant data entries * Alleviate experimental error due to sample mix-up and genotyping error. * Facilitate clinical and genetic data integration. * Automate data analysis pipelines * Facilitate data mining for genetic as well as environmental factors associated with a disease * Provide an uniformed data acquisition framework, regardless the type of a given disease * Accommodate the heterogeneity of different studies * Manage data flow, storage and access * Ensure patient privacy and data confidentiality/security. The GERON suite consists of several self contained and yet extensible modules. Currently implemented modules are GERON Clinical, Genotyping, and Tracking. More modules are planned to be added into the suite, in order to keep up with the dynamics of the research field. Each module can be used separately or together with others into a seamless pipeline. With each module special attention has been given in order to remain free and open to the academic/government user., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 23, 2014. Consortium that generated a reference library of gene trap sequence tags (GTST) from insertional mutations generated in mouse embryonic stem (ES) cells. The gene trap database represents a repository of sequences produced in a large scale gene trap screen in mouse ES cells using various gene trapping vectors which are delivered either by electroporation or retroviral infections. A type of retroviral gene trap vector has been developed that can induce conditional mutations in most genes expressed in mouse embryonic stem (ES) cells. The vectors rely on directional site-specific recombination systems that can repair and re-induce gene trap mutations when activated in succession. After the gene traps are inserted into the mouse genome, genetic mutations can be produced at a particular time and place in somatic cells. In addition to their conditional features, the vectors create multipurpose alleles amenable to a wide range of post-insertional modifications. Here they have used these directional recombination vectors to assemble the largest library of ES cell lines with conditional mutations in single genes yet assembled, presently totaling 1,000 unique genes. The trapped ES cell lines, which can be ordered from the German Gene Trap Consortium, are freely available to the scientific community.
A computational biologist''s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery.
The Gregor Mendel Institute of Molecular Plant Biology (GMI) was founded by the Austrian Academy of Sciences in 2000 in the form of a company to promote research excellence within the field of plant molecular biology. It is the only international centre for basic plant research in Austria. The GMI is located at the Vienna Biocenter Campus within the purpose-built Austrian Academy of Sciences Life Sciences Center Vienna, completed in January 2006. The Vienna Biocenter Campus, which encompasses both independent and academic research institutes as well as biotechnology companies, provides an ideal environment for the GMI. Neighbouring institutes include the Research Institute of Molecular Pathology (IMP), the Institute of Molecular Biotechnology (IMBA), as well as the Max F. Perutz Laboratories of the University of Vienna and of the Medical University of Vienna. Research at the GMI is curiosity driven and covers many aspects of molecular genetics, from basic mechanisms of epigenetics to population genetics. Arabidopsis thaliana is used as the primary model organism, and research groups are evaluated annually by an international external Scientific Advisory Board. The working language of the GMI is English. Research at the GMI is carried out by independent research groups, led either by senior group leaders with contracts of unlimited duration, or junior group leaders with temporary (5 3 years) appointments. GMI''s research activities are supported by its administration and a platform consisting of the GMI''s own services, including state-of-the-art plant growth facilities, as well as joint services with the Research Institute of Molecular Pathology and the Institute of Molecular Biotechnology Funding Our employees are expected to apply for grants and additional financial support from various external national and international funding bodies. The list below provides an overview of the funding opportunities that could be relevant for GMI members. The Frderassistent of the FFG (in German) or the Frderkompass of the Federal Ministry of Transport, Innovation and Technology (in German) can also be used to find appropriate funding.
GOstat is a tool that allows you to find statistically overrepresented Gene Ontologies within a group of genes. The Gene-Ontology database (GO: http://www.geneontology.org) provides a useful tool to annotate and analyze the function of large numbers of genes. Modern experimental techniques, as e.g. DNA microarrays, often result in long lists of genes. To learn about the biology in this kind of data it is desirable to find functional annotation or Gene-Ontology groups which are highly represented in the data. This program (GOstat) should help in the analysis of such lists and will provide statistics about the GO terms contained in the data and sort the GO annotations giving the most representative GO terms first. Run GOstat: * Go to search form - Computes GO statistics of a list of genes selected from a microarray. * GOstat Display - You can store results from a previously run and view them here, either by uploading them as a file or putting them on a selected URL. * Upload Custom GO Annotations - This allows you to upload your own GO annotation database and use it with GOstat. Variants of GOstat: * Rank GOstat - Takes input from all genes on microarray instead of using a fixed cutoff and uses ranks using a Wilcoxon test or either ranks or pvalues to score GOs using Kolmogorov-Smirnov statistics. * Gene Abundance GOstats - Takes input from all genes on microarray and sums up the gene abundances for each GO to compute statistics. * Two list GOstat - Compares GO statistics in two independent lists of genes, not necessarily one of them being the complete list the other list is sampled from. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool for detecting epistatic interactions in genome-wide association studies (entry from Genetic Analysis Software)
Gene Relationships Across Implicated Loci
A tool to examine relationships between genes in different disease associated loci. Given several genomic regions or SNPs associated with a particular phenotype or disease, GRAIL looks for similarities in the published scientific text among the associated genes. As input, users can upload either (1) SNPs that have emerged from a genome-wide association study or (2) genomic regions that have emerged from a linkage scan or are associated common or rare copy number variants. SNPs should be listed according to their rs#''s and must be listed in HapMap. Genomic Regions are specified by a user-defined identifier, the chromosome that it is located on, and the start and end base-pair positions for the region. Grail can take two sets of inputs - Query regions and Seed regions. Seed regions are definitely associated SNPs or genomic regions, and Query regions are those regions that the user is attempting to evaluate agains them. In many applications the two sets are identical. Based on textual relationships between genes, GRAIL assigns a p-value to each region suggesting its degree of functional connectivity, and picks the best candidate gene. GRAIL is developed by Soumya Raychaudhuri in the labs of David Altshuler and Mark Daly at the Center for Human Genetic Research of Massachusetts General Hospital and Harvard Medical School, and the Broad Institute. GRAIL is described in manuscript, currently in preparation.
Features: * This software takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. A point-and-click interface is now available! * The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. * A short tutorial on q-values and false discovery rates is provided with the manual. * Various plots are automatically generated, allowing one to make sensible significance cut-offs. * Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. * The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. This research was supported in part by a National Science Foundation graduate research fellowship.
A commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis.
QTL Cartographer is a suite of programs to map quantitative traits using a map of molecular markers. The programs are available via an anonymous ftp server. See the README for more information. You will also want a copy of Gnuplot to display plots made by QTL Cartographer. Gnuplot is freely available on the web. Do a search to find the latest version for your operating system. Windows QTL Cartographer Windows QTL Cartographer is a user friendly version of QTL Cartographer. It has a GUI interface and runs under Microsoft Windows. Manual The manual for QTL Cartographer is written in LaTeX2e. An Adobe Portable document format (pdf) version is available with the distribution of the programs. Look in the doc/pdf folder for the manual.pdf file. This file can be printed or viewed using Acrobat Reader, available through the Adobe website. The manual has also been translated into html. It is available through the following link. Please note that the translator is not perfect: The pdf form of the manual is much more accurate. Specifically, latex2html failed to translate figure 2.4 and simply printed 2.3 twice. Man Pages In the UNIX world, it is comman to have man pages for programs. We have written such a set of man pages, and these are available with the UNIX distribution. The man pages are also a part of the manual.pdf file. Here is a list of the man pages. 1. Emap 2. Rmap 3. Rqtl 4. Rcross 5. Qstats 6. LRmapqtl 7. SRmapqtl 8. Zmapqtl 9. JZmapqtl 10. MImapqtl 11. MultiRegress 12. Prune 13. Preplot 14. Eqtl 15. QTLcart Perl scripts QTL Cartographer comes with some perl scripts to automate repetitive tasks and reformat output files. They are available in the doc/scripts subdirectory of the distribution. Here are the man pages that explain what the scripts can do. 1. Bootstrap.pl is a script for running a bootstrap analysis. 2. CWTupdate.pl is used with Permute.pl for the comparison-wise thresholds. 3. EWThreshold.pl is used with Permute.pl for the experiment-wise thresholds. 4. GetMaxLR.pl is used with Permute.pl for the experiment-wise thresholds. 5. Model8.pl iterates Zmapqtl to find a stable set of cofactors for composite interval mapping. 6. Permute.pl is a script for running a permutation test. 7. Prepraw.pl allows you to reformat and check a Mapmaker data file. 8. SRcompare.pl will compare the set of cofactors in two SRmapqtl output files. 9. SSupdate.pl is used with Bootstrap.pl to update the sum and sum of squares for the likelihoods and parameter estimates. 10. Vert.pl converts text file line endings between Unix, Macintosh and Windows. 11. Ztrim.pl redisplays Zmapqtl output so that it fits in a terminal window. Data We are now posting published data sets to our web site. A list of links to the ftp subdirectories follows. Each directory contains a set of text files of data. Please read the Readme file in the directory for information on the data. 1. Zeng et al provide data for their paper Genetic architecture of a morphological shape difference between two Drosophila species. If you have any data that you would like to make available via our server, contact Chris Basten. Presentations From time to time, Chris Basten gives presentations on how to use QTL Cartographer. These presentations are created in Microsoft Powerpoint. The source file for the presentation is available with the distribution of the programs. Look in the doc subdirectory. Binary Traits See this for more information on the BTmapqtl module. This is an add-on written in LaurenMcIntyre''s lab. BTmapqtl is in the binary directory of the distribution (and is created with a make for the UNIX version).
Rutgers University Quantitative Neuroscience Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The brain is made of billions of neurons, which together form the world''s most powerful information-processing machine. Despite decades of research, the fundamental principle by which these cells work together is still unknown. Many theories for brain function have been proposed over the last century. But only in the last few years has it become possible to record simultaneously from large enough numbers of neurons to put these theories to the test experimentally. This is an unprecedented opportunity, but it opens up a new question: how do we go from the gigabytes of experimental data that we now have, to concise conclusions about the function of the brain? The data processing methods traditionally used in neuroscience are not sophisticated enough to exploit this new flood of information. Fortunately, modern statistics and machine learning theory is making great strides in precisely the type of techniques needed to process these large multivariate databases. By applying these methods to neuronal data, we can now test long-standing hypotheses about brain function. The Cell Assembly The main focus of our research is an experimental search for cell assemblies. Before describing what a cell assembly is, it will be useful to describe what it is not. The brain is often thought of as a feed-forward system. In this scheme, sensory information is processed by successive levels of cortical analyzers, each of which transforms the results of previous levels, until sensory information is in a suitable form to guide the animals behavior. In support of this idea, the pattern of connections in the cortex does appear to respect a hierarchical organization, with the output of low-level areas corresponding to a single sensory modality being integrated into high-level multi-modal areas. Responses in higher-level sensory areas appear to have more complex responses to sensory stimuli, in agreement with increased abstraction as the hierarchy is traversed. However, there are several levels at which this feed-forward picture is incomplete. At the circuit diagram level, there more connections projecting across and down the hierarchy, than there are feed-forward projections. What''s more, if information were processed in a strictly feed-forward manner, one would expect a neuron to respond identically to repeated presentations of the same sensory stimulus. Although this is a fairly good approximation in primary sensory areas of cortex, in high-level structures responses are often more variable than expected from strict sensory control. Finally, although feed-forward processing can describe how an animal could perform simple stimulus-response behaviors, it cannot explain more complex top-down behaviors such as memory or thought. An alternative point of view, put forward over 50 years ago by Canadian psychologist Donald Hebb, holds that recurrent and feedback connections play an essential role in brain function. The principal actor in this view is the cell assembly, an anatomically distributed subset of neurons, amongst which mutually excitatory connections have been strengthened by repeated co-activation, allowing the assembly to later maintain its activity through reverberation without direct sensory stimulation. This theory allows for sensory-response behavior, and also behavior resulting purely from internally generated cognitive activity, by the sequential activation of a series of assemblies, leading in turn to the production of motion. In our research, we search for signatures of assembly activity in simultaneous recordings from multiple neurons, and aim to characterize the properties of assembly activity in ways not possible from theory alone. Software for Automatic Clustering KlustaKwik is a program developed in the lab for automatic cluster analysis, specifically designed to run fast on large data sets. In order facilitate open-source development, it is now located at klustakwik.sourceforge.net. This study was supported by NIH grants MH073245 and DC009947; NSF grant SBE-0542013 to the Temporal Dynamics of Learning Center, an NSF Science of Learning Center; a National Institute on Deafness and Other Communication Disorders, NIH, grant DC-005787-01A1; and a Spanish grant FIS 2006-09294. K.D.H. is an Alfred P. Sloan fellow. We would like to dedicate this work to the memory of D. J. Amit.
Quasi Opportunistic Supercomputing for Complex Systems
Complex systems are defined as systems with many interdependent parts which give rise to non-linear and emergent properties determining the high-level functioning and behavior of such systems. Due to the interdependence of their constituent elements and other characteristics of complex systems, it is difficult to predict system behavior based on the sum of their parts alone. Examples of complex systems include bee hives, bees themselves, human economies and societies, nervous systems, molecular interactions, cells and living things, ecosystems, as well as modern energy or telecommunication infrastructures. Arguably one of the most striking properties of complex systems is that conventional experimental and engineering approaches are inadequate to capture and predict the behavior of such systems. To complement the conventional experimental and engineering approaches, computer-based simulations of complex natural phenomena and complex man-made artifacts are increasingly employed across a wide range of sectors. Typically, such simulations require computing environments which meet very high specifications in terms of processing units, primary and secondary storage, and communication. Supercomputers constitute the de facto technology to deliver the required specifications. Acquiring, operating and maintaining supercomputers involve considerable costs, which many organizations cannot afford. The working assumption of the QosCosGrid project is that a grid could be enhanced by suitable middleware to provide features and performance characteristics that resemble those of a supercomputer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The abbreviated name, mfold web server, describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and energy dot plots, are available for the folding of single sequences. A variety of bulk servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as MFOLDROOT.
RANDOM.ORG is a true random number service that generates randomness via atmospheric noise. This page explains why it''s hard (and interesting) to get a computer to generate proper random numbers. Random numbers are useful for a variety of purposes, such as generating data encryption keys, simulating and modeling complex phenomena and for selecting random samples from larger data sets. They have also been used aesthetically, for example in literature and music, and are of course ever popular for games and gambling. When discussing single numbers, a random number is one that is drawn from a set of possible values, each of which is equally probable, i.e., a uniform distribution. When discussing a sequence of random numbers, each number drawn must be statistically independent of the others. With the advent of computers, programmers recognized the need for a means of introducing randomness into a computer program. However, surprising as it may seem, it is difficult to get a computer to do something by chance. A computer follows its instructions blindly and is therefore completely predictable. (A computer that doesn''t follow its instructions in this manner is broken.) There are two main approaches to generating random numbers using a computer: Pseudo-Random Number Generators (PRNGs) and True Random Number Generators (TRNGs). The approaches have quite different characteristics and each has its pros and cons.
Regulation of cell cycle by Retinoblastoma protein
The retinoblastoma tumor suppressor gene RB plays a major role in cell cycle entry: RB sequesters a family of transcription factors, E2Fs, responsible for the transcription of many genes involved in the cell cycle regulation, DNA replication and in the activation of the apoptotic pathway. RB functions as a brake in the cell cycle which is released when external signals (growth factors, ) inform the cell that it can proceed to S phase. The target of the external signals is the G1 cyclin/Cdk complex. Once active, the complex phosphorylates pRB which can then free E2F. E2F can then participate in the synthesis of many genes, among them, cyclin E, which immediately binds to the Cdc2 kinase Cdc2. The complex then fires DNA replication. The understanding of the pathway regulating the tumor suppressor RB and the transcription factors E2F might give insight in the regulation of many cancers. Constructing the pathway Based on the literature, a quasi-exhaustive pathway has been built around RB to relate the regulation around the phosphorylation of the tumor suppressor protein. Once validated, the pathway can be exploited by computers to analyze deregulations observed in some cancers and used by biologists as a reference of the signalling pathways leading to RB phosphorylation. The diagram allowed to integrate an important amount of information. However, the goal would also be to exploit these data in order to understand the pathway and anticipate the behaviour of any kind of mutations in the cell. For that purpose, different tools are available to manipulate this kind of diagrams (Cytoscape, BiNoM, ...). Click here to find the page you are interested in Modeling the pathway The diagram was divided in different modules, each module representing a subpart of the diagram that describes the mechanism of modification (acetylation, phosphorylation) of a major protein in the cell cycle. The simplified diagram can be analyzed qualitatively (Boolean or discrete approaches) or quantitatively (ODEs) to provide a first understanding of the network. What for? The final purpose of the construction of this diagram is to provide a map of the RB pathway that can become a reference when studying different cancers and mutations. This project was partly funded by the EC contract ESBIC-D (LSHG-CT-2005-518192), the PIC Retinoblastome from Institut Curie, the PIC Bioinformatique et Biostatistiques from Institut Curie and the Research Networks Program in Bioinformatics from the High Council for Scientific and Technological Cooperation between France and Israel (Ministere des Affaires Etrangeres, Ministere de l''Education Nationale, de l''Enseignement Superieur et de la Recherche).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A database containing all genomic human and mouse binding sites of the Repressor Element 1 Silencing Transcription factor (REST), identified by PSSM. The RE1 silencing transcription factor (REST; also known as the neuron-restrictive silencer factor), is a nine zinc-finger transcription factor, related to the Gli-Kruppel family. REST binds to a conserved 21-nucleotide element, known as repressor element 1 (RE1; also known as the neuron-restrictive silencer element). REST was proposed to be a ''master'' silencer of neuron specific gene expression in non-neuronal tissues and undifferentiated neuroepithelium (precursor of neuronal cells), preventing the default expression of the neuronal phenotype during embryogenesis. It has been shown to function independently of orientation and distance from a gene promoter. REST has an important role during embryonic development, as homozygous gene knockout mice (Rest-/-) die by embryonic day 11.5. The constitutive expression of REST has also been shown to disrupt neuronal gene expression and cause axon path finding errors in chicken embryos (Paquette et al. 2000). RE1 sequences that are known to bind REST have also been found near to non-neuronal genes, including keratin and cytochrome P450 genes.
Founded on the principle that strong science would lead to important new medicines, Regeneron has become an integrated biopharmaceutical company that discovers, develops, and commercializes medicines for the treatment of serious medical conditions. Regeneron currently markets ARCALYST (rilonacept) Injection for Subcutaneous Use for the treatment of a rare, inherited, inflammatory condition. Regeneron has therapeutic candidates in Phase 3 clinical trials for the potential treatment of gout, age-related macular degeneration, central retinal vein occlusion, and certain cancers. Additional therapeutic candidates are in earlier stage development programs in rheumatoid arthritis and other inflammatory conditions, pain, cholesterol reduction, allergic conditions, and cancer. The Company''s ability to develop product candidates is enhanced by the application of several proprietary technologies that Regeneron has incorporated into a comprehensive drug discovery and development process. This process is designed to thoroughly understand the biology of specific diseases, discover potential therapeutic candidates, and evaluate these candidates in clinical trials. One specific area of Regeneron expertise is the rapid development of fully-human monoclonal antibodies. In November 2007, Regeneron and sanofi-aventis entered into a global, strategic collaboration to discover, develop, and commercialize fully-human therapeutic antibodies utilizing Regeneron''s proprietary VelociSuite of technologies, and we expanded the collaboration in November 2009. Five human antibodies developed under the sanofi-aventis collaboration are in clinical development today, with a goal of advancing an average of four to five new antibodies into clinical development each year through 2017. In addition to the Company''s corporate headquarters and research laboratories in Tarrytown, New York, Regeneron has a large-scale biologics manufacturing facility in Rensselaer, New York, where it produces commercial and investigational products for its clinical trials, and a satellite office in Bridgewater, New Jersey.
A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.
RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R nor is it dependent on any component of the BioConductor project. If focuses on processing 3'' IVT expression arrays, exon and WT gene arrays. What is RMA? RMA is the Robust Multichip Average. It consists of three steps: a background adjustment, quantile normalization (see the Bolstad et al reference) and finally summarization. Some references (currently published) for the RMA methodology are: Bolstad, B.M., Irizarry R. A., Astrand, M., and Speed, T.P. (2003), A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2):185-193 Supplemental information Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15 Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2002) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Accepted for publication in Biostatistics. [Abstract, PDF, PS, Complementary Color Figures-PDF, Software] What do I need? You will need the appropriate CDF and CEL files for your dataset. For Exon and WT Gene arrays, the PGF and CLF should be used instead of the CDF file to build a CDFRME file. The process for doing this is explained in the user manual. Some pre-built CDFRME files are also available. CDFRME files HuEx_CDFRME.zip (95.9MB) HuGene_CDFRME.zip (5.5MB) MoEx_CDFRME.zip (79.6MB) MoGene_CDFRME.zip (6.3MB) RaEx_CDFRME.zip (48.4MB) RaGene_CDFRME.zip (5.7MB) Can I use affy/BioConductor instead? Of course. Hypothetically you will get the same results from both places, provided you have consistent settings in affy/BioConductor and RMAExpress. Some people prefer the power and flexibility of R and others like the point and click simplicity of a GUI. RMAExpress caters to the second option. Since RMAExpress outputs the computed expression values to a text file, you may of course load the expression measures into R and use features of Bioconductor for the analysis of your gene expression values. You can of course open the results file in any other application that supports importing plain text files. Will I get the same results as I would using affy/Bioconductor? Yes. The results from RMAExpress should be consistent. What are the machine requirements? A good rule of thumb is the more RAM you have the better. I would recommend at least 1GB, though 512MB will work in most situations. At this point the program has been tested using Windows 2000, Windows XP, Windows Vista and Linux. Most recently I have had a report of over 10,000 arrays processed in a single session. Can I do any quality assessment? Yes, store the residuals when you compute the expression values. Then you may examine chip pseudo-images of the residuals. Note that high positive residuals are colored increasingly read and low negative residuals are colored increasingly blue. To better interpret these images and gain a better feel for what is typical you may visit the PLM Image Gallery where images for a number of different datasets are shown. Access to the NUSE and RLE quality assessment metrics is also provided. How do I download and install it? Click here for the current release Windows version. Use the installer to install the program. The current release version number is 1.0 (released June 29, 2008). A pre-built linux version is not currently available, but you may build it using the source code. You can download pre-release versions from the following table (the release versions will be more stable, the development versions may have features that are incomplete or will be removed or altered before the next release was supported by the PGA U01 HL66583.
This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT
ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures that can be freely combined to create two-dimensional performance curves. Standard methods for investigating trade-offs between specific performance measures are available within a uniform framework, including receiver operating characteristic (ROC) graphs, precision/recall plots, lift charts and cost curves. ROCR integrates tightly with R''s powerful graphics capabilities, thus allowing for highly adjustable plots. Being equipped with only three commands and reasonable default values for optional parameters, ROCR combines flexibility with ease of usage. Performance measures that ROCR knows: Accuracy, error rate, true positive rate, false positive rate, true negative rate, false negative rate, sensitivity, specificity, recall, positive predictive value, negative predictive value, precision, fallout, miss, phi correlation coefficient, Matthews correlation coefficient, mutual information, chi square statistic, odds ratio, lift value, precision/recall F measure, ROC convex hull, area under the ROC curve, precision/recall break-even point, calibration error, mean cross-entropy, root mean squared error, SAR measure, expected cost, explicit cost. ROCR features: ROC curves, precision/recall plots, lift charts, cost curves, custom curves by freely selecting one performance measure for the x axis and one for the y axis, handling of data from cross-validation or bootstrapping, curve averaging (vertically, horizontally, or by threshold), standard error bars, box plots, curves that are color-coded by cutoff, printing threshold values on the curve, tight integration with Rs plotting facilities (making it easy to adjust plots or to combine multiple plots), fully customizable, easy to use (only 3 commands). ROCR can be used under the terms of the GNU General Public License. Running within R, it is platform-independent.
LOCI is a biophotonics instrumentation laboratory stemming from the research activities of Kevin Eliceiri, Dave Beebe, Bill Bement, Paul Campagnola, Patti Keely, Brenda Ogle, Justin Williams and other LOCI investigators. Our mission is to develop advanced optical and computational techniques for imaging and experimentally manipulating living specimens. New and improved imaging instrumentation and optical-based experimental techniques are being developed. These projects are driven by demands arising from the scientific studies of external collaborators and the principal investigators and opportunities that arise with the emergence of new technology. Instrumentation development is undertaken in a form that is both accessible and beneficial to the scientific community. LOCI is directed by Kevin Eliceiri, and all inquiries about LOCI collaborations or general imaging questions may be directed to him.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A business division of Sigma-Aldrich Corporation, focusing on providing custom manufactured products and specialized services used in the industrial development and manufacturing, including processes, that bring new drugs and new electronic products to market., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application for a fast exact Hardy-Weinberg Equilibrium test for SNPs (entry from Genetic Analysis Software)
Recombineering (recombination-mediated genetic engineering) is a powerful method for fast and efficient construction of vectors for subsequent manipulation of the mouse genome or for use in cell culture experiments. It is also an efficient way of manipulating the bacterial genome directly. Recombineering is a method based on homologous recombination in E. Coli using recombination proteins provided from ? phage. Our bacterial strains contain a defective ? prophage inserted into the bacterial genome. The phage genes of interest, exo, bet, and gam, are transcribed from the ?PL promoter. This promoter is repressed by the temperature-sensitive repressor cI857 at 32C and derepressed (the repressor is inactive) at 42C. When bacteria containing this prophage are kept at 32C no recombination proteins are produced. However, after a brief (15 minutes) heat-shock at 42C a sufficient amount of recombination proteins are produced. exo is a 5''-3'' exonuclease that creates single-stranded overhangs on introduced linear DNA. bet protects these overhangs and assists in the subsequent recombination process. gam prevents degradation of linear DNA by inhibiting E. Coli RecBCD protein. Linear DNA (PCR product, oligo, etc.) with sufficient homology in the 5'' and 3'' ends to a target DNA molecule already present in the bacteria (plasmid, BAC, or the bacterial genome itself) can be introduced into heat-shocked and electrocompetent bacteria using electroporation. The introduced DNA will now be modified by exo and bet and undergo homologous recombination with the target molecule. The method is so efficient that co-electroporation of a supercoiled plasmid and a linear piece of DNA into heat-shocked, electrocompetent bacteria will work as well.
Division of Nutrition, Physical Activity and Obesity
Our vision a world where regular physical activity, good nutrition, and healthy weight are part of everyone''s life. Our mission to lead strategic public health efforts to prevent and control obesity, chronic disease, and other health conditions though regular physical activity and good nutrition. Our goals: * Increase health-related physical activity through population-based approaches. * Improve those aspects of dietary quality most related to the population burden of chronic disease and unhealthy child development. * Decrease prevalence of obesity through preventing excess weight gain and maintenance of healthy weight loss. Our Work With fiscal year (FY) 2008 funding of 38 million, CDC''s DNPAO is working to reduce obesity and obesity-related diseases. This is done through state programs, research, surveillance, training, intervention development and evaluation, leadership, policy and environmental change, communication and social marketing, and partnership development. See At A Glance 2009 for more. Supporting State Programs The Nutrition, Physical Activity and Obesity Program (NPAO) is a cooperative agreement between the Centers for Disease Control and Prevention''s Division of Nutrition, Physical Activity and Obesity (DNPAO) and 23 state health departments. The program goal is to prevent and control obesity and other chronic diseases through healthful eating and physical activity. The state program will develop strategies to leverage resources and coordinate statewide efforts with multiple partners to address all of the following DNPAO principal target areas: 1. Increase physical activity. 2. Increase the consumption of fruits and vegetables. 3. Decrease the consumption of sugar sweetened beverages. 4. Increase breastfeeding initiation, duration and exclusivity. 5. Reduce the consumption of high energy dense foods. 6. Decrease television viewing. Our Research DNPAO supports research to enhance the effectiveness of physical activity and nutrition programs. Topics of these research activities include: * the effectiveness of parent-focused strategies to reduce the time children spend watching television * the influences of the home environment on sugar-sweetened beverage consumption * the use of policy interventions to promote physical activity * the effectiveness of breastfeeding interventions in various settings. Publications: http://www.cdc.gov/nccdphp/DNPAO/aboutus/manuscripts/index.html
About the LAGAN Toolkit The LAGAN Tookit consists of four components: CHAOS CHAOS is a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome. It uses both exact matching and degenerate seeds, and is able to find homology in the presence of gaps. LAGAN LAGAN is our highly parametrizable pairwise global alignment program. It takes local alignments generated by CHAOS as anchors, and limits the search area of the Needleman-Wunsch algorithm around these anchors; Multi-LAGAN Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment. M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic tree. Alignments are aligned to other alignments using the sum-of-pairs metric. Shuffle-LAGAN Shuffle-LAGAN is a novel glocal alignment algorithm that is able to find rearrangements (inversions, transpositions and some duplications) in a global alignment framework. It uses CHAOS local alignments to build a map of the rearrangements between the sequences, and LAGAN to align the regions of conserved synteny. The website uses scripts written by Alex Poliakov. The website was designed by Marina Sirota.
Cambridge, Massachusetts-based biotechnology company focused on cancer. Focus areas are blood cancers and solid tumors. Compounds: ponatinib, AP26113, ridaforolimus and AP1903., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools. AVAILABILITY: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum.
Rensselaer Mathematical Sciences Faculty Member
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 20, 2019. Development and implementation of algorithms to predict nucleic acid folding and hybridization by free energy minimization using empirically derived thermodynamic parameters. Modeling and algorithm development have been closely coupled with the derivation of nearest neighbor and related energy rules. Current work is focused on the computation of partition functions for systems containing two molecules in solution that can fold as well as hybridize with each other. Ensemble free energies, mole fractions of different monomer and dimer species and base pair probabilities are computed over a range of temperatures. These computations lead to the prediction of UV absorbance (optical density) and heat capacity (Cp) melting profiles that can be directly compared with experimental data. A related project is the development of an algorithm named FASTH that searches RNA or DNA sequence databases for optimal hybridization sites for nucleic acid query sequences. Unlike traditional search algorithms, such as BLASTN and FASTA, FASTH uses hybridization free energy as the criterion for selection
Welcome to the Department of Genome Sciences, which began in September 2001 by the fusion of the Departments of Genetics and Molecular Biotechnology. Our goal is to address leading edge questions in biology and medicine by developing and applying genetic, genomic and computational approaches that take advantage of genomic information now available for humans, model organisms and a host of other species. Our faculty study a broad range of topics, including the genetics of E. coli, yeast, C. elegans, Drosophila, and mouse; human and medical genetics; mathematical, statistical and computer methods for analyzing genomes, and theoretical and evolutionary genetics; and genome-wide studies by such approaches as sequencing, transcriptional and translational analysis, polymorphism detection and identification of protein interactions. Our chair, Dr. Robert Waterston, joined the department in January 2003. Our department includes both faculty with primary appointments in Genome Sciences, as well as adjuncts in other departments and Seattle institutions. Nine faculty are members of the National Academy of Sciences, including 2001 Nobel Prize winner Dr. Lee Hartwell, who conducted much of his groundbreaking work in the Department of Genetics. Five training faculty are Howard Hughes Medical Institute Investigators. Graduate research in the Department leads to a Ph.D. in Genome Sciences and students may also choose to participate in the Computational Molecular Biology or Molecular Medicine programs. Our department has around 55 - 60 graduate students at any given time and has moved into the new William H. Foege Building.
This site is designed for researchers and students who want a quick way to generate random numbers or assign participants to experimental conditions. Research Randomizer can be used in a wide variety of situations, including psychology experiments, medical trials, and survey research. The program uses a JavaScript random number generator to produce customized sets of random numbers. Since its release in 1997, Research Randomizer has been used to generate number sets over 10.7 million times. This service is part of Social Psychology Network and is fast, free, and runs with any recent web browser as long as JavaScript isn''t disabled. Research Randomizer is a free service offered to students and researchers interested in conducting random assignment and random sampling. By using this service, you agree to abide by the SPN User Policy and to hold Research Randomizer and its staff harmless in the event that you experience a problem with the program or its results. Although every effort has been made to develop a useful means of generating random numbers, Research Randomizer and its staff do not guarantee the quality or randomness of numbers generated. Any use to which these numbers are put remains the sole responsibility of the user who generated them. What are the system requirements needed to run Research Randomizer? This program works best with Firefox and other recent web browsers. If you''re using a browser that came with America Online, or older browsers made prior to 2003, you may experience some difficulties with Research Randomizer. You may also not be able to use Research Randomizer with some limited-function browsers that do not fully support JavaScript, such as the Opera broswer used on certain game consoles. We would suggest that you update to a fairly recent, fully- functional stand-alone browser. How do I know what browser I am using? The easiest way to find this out is to click Help on the pulldown menu at the top of the screen. One of the options should be About Mozilla Firefox, About Internet Explorer, About Netscape, or something similar. Selecting this option will open a window that displays the name, version number, and copyright date of your browser. How does Research Randomizer generate its numbers? Research Randomizer uses the Math.random method within the JavaScript programming language to generate its random numbers for all modern web browsers. If you are using an older version of Microsoft Internet Explorer or Netscape Navigator (that is prior to version 4.0 of either), Research Randomizer uses an adaptation of the Central Randomizer by Paul Houle. Note that Research Randomizer no longer supports much-older browsers by other vendors (e.g., Mosaic). Who designed Research Randomizer? The original idea and programming for Research Randomizer came from Geoffrey C. Urbaniak in 1997. Research Randomizer was then jointly developed with Scott Plous, webmaster of Social Psychology Network, and online tutorials were added to the main program. In 1999 the site was redesigned with the assistance of Mike Lestik, in 2003 Mike Lestik added the download function, and in 2007 Mike Lestik and Scott Plous redesigned the site and added new content.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Tools were developed by the Critical Appraisal Skills Programme (CASP) to help with the process of critically appraising articles of the following types of research. These are available and free to download for personal use.
Wheaton Industries Inc. is a leading marketer, manufacturer and re-packager of containers, laboratory ware, instrumentation and associated products and services sold principally to customers in the general laboratory, life sciences, and diagnostics and reagent / chemicals packaging markets. Our products and services are marketed and sold globally through two divisions. The laboratory research products are sold through Wheaton Science Products, and the packaging products are sold through Wheaton Science Packaging.
Headquartered in Redwood City California, WideTag is a pioneer in architecting computing systems that integrate sensors, positioning devices and memory with social, Web 2.0-style services in applications that revolutionize business and push consumer technology.
Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS.
3D Macromolecular Analysis and Kinemage Home Page
Resources for macromolecular X-ray crystallography from the Richardson Laboratory, including kinemages (a scientific illustration presented as an interactive computer display), databases, software, training materials and images
Organization that facilitates spinal cord injury research and care. By accelerating the translation of discoveries and best practices into improved treatments, it aims to improve the lives of people living with SCI.
Roche NimbleGen, Inc. is a leading innovator, manufacturer and supplier of a proprietary suite of DNA microarrays, consumables, instruments and services. Roche NimbleGen uniquely produces high-density arrays of long oligo probes that provide greater information content and higher data quality necessary for studying the full diversity of genomic and epigenomic variation. Roche NimbleGen is enabling a new era of High-Definition Genomics by providing scientists with cost-effective, high-throughput tools for extracting and integrating complex data on important forms of genomic and epigenomic variation not previously accessible on a genome-wide scale. Scientists can thus obtain a clearer understanding of genomic and epigenomic structure and function and how they impact biology and medicine. This improved performance is made possible by Roche NimbleGen''s proprietary Maskless Array Synthesis (MAS) technology, which uses digital light processing and rapid, high-yield photochemistry to synthesize long oligo, high-density DNA microarrays with extreme flexibility. NimbleGen Systems was established in 1999. The MAS technology is the result of research collaborations between the departments of biotechnology, genetics, physics, and semiconductor engineering at the University of Wisconsin - Madison. Roche NimbleGen has the exclusive worldwide license to the MAS technology from the Wisconsin Alumni Research Foundation (WARF).
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Rosetta Inpharmatics in Seattle, WA Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck & Co. Inc., develops and implements technologies that will improve drug discovery. The company''s leading-edge genomic research and data analysis efforts focus on how medical compounds affect biology, enabling more accurate selection of drug targets and more efficient drug development. Rosetta Inpharmatics was founded in 1996 to design and implement DNA microarray gene expression technologies.
The Centre for Automotive Safety Research at the University of Adelaide, is internationally recognised as a leading research organisation in its field. The Centre conducts high quality independent research that enables rational decision making, leading to a reduction in the human and economic losses from road crashes. The Centre is focused on: * Conducting multidisciplinary research to understand how road crashes and the resulting injuries are caused * Proposing and evaluating ways to prevent crashes and injuries * Providing independent professional advice on road safety matters to government and non-government organisations in Australia and overseas The Centre began life in 1973 as the Road Accident Research Unit (RARU) with the planning and undertaking of an in-depth study of road accidents in the Adelaide metropolitan area. From 1981 through 1998, the Unit''s work was supported by a grant from the National Health And Medical Research Council. During that grant period RARU''s research program was concentrated in two areas: the study of brain injury mechanisms in fatally injured road users and the epidemiology of drink driving and alcohol related crashes. Notably, an investigation of the influence of vehicle speed in fatal pedestrian accidents led on to case control studies of the relationship between a driver''s travelling speed and risk of involvement in a casualty crash in both urban and rural areas. RARU''s analysis of the occurrence of brain injury in road crashes called into question the then prevailing paradigm of brain injury mechanisms. This prompted the development of an experimental study of axonal injury that, in turn, led to the Japan Automobile Research Institute initiating a formal collaborative research agreement with RARU, and now with CASR, in the area of crash injury biomechanics. Also a part of our legacy is that over 40 years ago the Centre''s previous Director, Professor Jack McLean, co-authored the first paper in the world to show that car design played a major role in pedestrian protection, revealing that pedestrians are run under, not over, by the striking car.
The Royal Ontario Museum is among the worlds leading museums of natural history, and of world cultures. Indeed, in combining a universal museum of cultures with that of natural history, the ROM offers an unusual breadth of experience to visitors and scholars from around the world. We realize more acutely now that nature and humanity are intertwined, and the ROM offers many examples in its collections and programs of these fundamental relationships. It is the ROMs mission to engage the public in exploration of cultural change and to serve as an advocate for science in the study of nature. Our collections and research serve as the basis for programs ranging from formal student education courses to public debates, lectures, symposia, films, tours, publications, travel and family activities. The museum aims to host and produce programs of intellectual depth and social relevance on both sides of its mandate, including unique ROM exhibitions and works of a collaborative nature. Through the ROMs Institute for Contemporary Culture, the museum also explores current issues through works of art and programs in many media. The ROM is near completion of a major capital project (Renaissance ROM) that will see the building of 27 new galleries, the liberation of many stranded collections, the addition of valuable public amenities, and the creation of dramatic new architecture in the Michael Lee-Chin Crystal, designed by Daniel Libeskind. This is among the largest capital projects in the history of Canadian cultural institutions, and brings the assets of the museum fully to the public again even as the ROM prepares to celebrate its centenary in 2014. On this website, you have access to thousands of photographs and summaries from the ROMs collections, results of its research activities around the world, information on current programs and exhibitions, and means to download information, watch podcasts and purchase tickets to the museum and its events. You will also find information about its restaurants, the ROM Museum Store and rental services for ROM facilities after hours. The Royal Ontario Museum offers a unique platform to the engage the worlds of culture and the environment at the centre of one of North Americas great cities. We look forward to meeting you here, and to sharing the adventures of this place, with all its treasures.
Rules-Based Medicine (RBM) uses proprietary Multi-Analyte Profiling (MAP) technology to make life science research and drug and diagnostic development programs more efficient and effective. Whether measuring hundreds of biomarkers or simply a few, our approach provides reproducible, quantitative immunoassay data from a small sample volume at a cost-effective price. RBM is CLIA certified and supports GLP studies. * Quality: All immunoassays are validated to clinical laboratory standards. This means complete validation for the clinic, not fit for purpose validation which at RBM means inferior validation. Learn More * Content: We have the most comprehensive menu of biomarker immunoassays available. * Small Sample Volumes: Multiplexing provides you with more data using a smaller sample volume. * Cost Effective: Multiplexing and automation combine to deliver high quality data at reasonable prices. * Ease of use: Ship us your samples and get results within 2 weeks. Rules-Based Medicine (RBM), the worlds leading multiplexed biomarker testing laboratory, provides comprehensive protein biomarker products and services based on its Multi-Analyte Profiling (MAP) technology platform. RBMs biomarker testing service provides pre-clinical and clinical researchers with reproducible, quantitative, multiplexed immunoassay data for hundreds of proteins in a cost-effective manner, from a small sample volume and from multiple species. Our biomarker testing laboratory is CLIA certified and supports GLP studies. Most diseases and drug effects manifest themselves in abnormal levels of specific biomarkers found in the peripheral blood. By providing multiplexed, quantitative, and reproducible tests for hundreds of biomarkers, RBM enables research that historically was not available due to sample volume requirements and associated costs. Use of our testing services can identify the sources of both the positive and negative effects of drugs during pre-clinical research and clinical trials. Biomarker testing results identify patients most likely to respond to a given therapy and the biochemical reason for that response, making clinical trials more successful and effective. Through its wholly owned subsidiary EDI GmbH, RBM provides Human Organo-Typic (HOT) cell culture systems. These co-culture systems consist of multiple primary cell types grown in a 3-D architecture that closely mimic particular human organs and are an ideal platform for ex vivo studies of drug safety and efficacy. RBM combines EDIs cell culture systems with its HumanMAP biomarker testing services to provide researchers with an unprecedented view of the physiological and biochemical impact of a new drug compound or consumer product prior to testing in a human subject. RBM also performs custom assay development, participates in co-sponsored research programs, and pursues in-licensing of novel high-value assays.
Software products and services for behavioral and physiological research, including control software for experiments on primates and rodents, analysis of electrophysiological data, display of visual and auditory stimuli, and synchronization of experimental data from other measurement devices. The company offers a range of consulting services and provides product support services that assist customers in developing, deploying, and managing custom behavioral testing programs.
Western Australian State Agricultural Biotechnology Centre
The SABC is the collaborative university Centre for R&D in agricultural and veterinary biotechnology in Western Australia. It provides platform technologies and world class equipment and facilities for R&D in agricultural biotechnology to researchers from universities, state government and industry. More than 20 research groups and companies rent space and use the SABC facilities. It is based at Murdoch University in Perth. Our Vision To be an eminent, internationally recognized centre for research and development in agriculture and veterinary biotechnology Our Mission To provide state-of-the-art facilities and equipment enabling multi disciplinary research in biotechnology which under pins the agricultural and veterinary industry, for the benefit of the community. This will be achieved by being recognised as the centre for agricultural biotechnology in WA providing national and international research links and collaborations fostering establishment of national centres in leading edge technologies Characteristics of the SABC * The SABC is a multi-user centre with a research spend of about $9 million pa * There is a critical mass of more than 225 researchers * The SABC combines university, state government and industry researchers in one cost-effective centre * The SABC operates as a ''Research Hotel'' in which different groups rent common laboratory space and access to platform technologies * The SABC supports incubation and co-location of new ag biotech companies in WA * The SABC promotes collaborative research, undertakes contract research, and provides many local, national and international linkages * SABC researchers are members of eight agricultural Cooperative Centres (CRCs) Research Focus The research focus is on molecular activities that involve or promote primary production of commercial livestock, crop plants or microbes, or their subsequent processing for added value. The SABC also supports research in biomedical sciences, and environmental biotechnology. Deliverables and Outcomes SABC researchers have an outstanding track record of outputs and outcomes. These include the provision of co-located, state-of-the art, well run platform technologies for all WA researchers plant breeding support leading to improved crop varieties (molecular markers, yield, resistance to diseases and pests, better quality, variety ID, diagnostics), improved productivity and health of livestock, and biomedical diagnostics. Facilities and platform technologies The SABC provides the most comprehensive set of equipment and facilities for biotechnology R&D in WA, with full facilities for: cell and molecular biology, robotics, high throughput agricultural genetic analyses and diagnostics, structural, comparative and functional genomics, microarray technologies, proteomics and mass spectroscopy and bioinformatics support via the (CBBC). Training and Mentoring The SABC plays a major role in advanced training in ag biotech. There are about 100 Honours and PhD students in the research complement. The SABC also runs a series of hands on short courses in molecular biology, gene mapping, diagnostics, proteomics and bioinformatics. In 2005 new postgraduate certificate and diploma courses on Application of Molecular Technologies was established at Murdoch University, run by internationally qualified SABC researchers. These provide advanced education at the Postgraduate Certificate, Diploma and MSc levels, for local and international participants. click here for details The SABC runs the following hands-on training workshops: * Introduction to Molecular Biology * Molecular Mapping Techniques in Diagnostic Biotechnology * High Throughput Genetic Analysis * Introduction to Proteomics * Advanced Proteomics * Bioinformatics (with the CBBC) Competitive Advantages The SABC: * combines crop, veterinary and biomedical research in biotechnology in one centre * is multidisciplinary and inclusive * provides enabling facilities, platform technologies and common laboratories * is highly cost effective Researcher Groups Using the SABC * Division of Health Sciences (Murdoch)/Veterinary Sciences * Division of Science and Engineering (Murdoch)/Biological Sciences and Biotechnology * UWA (Natural Resources and Agriculture, Biochemistry) * Curtin University (Molecular Biotechnology, Horticulture) * Edith Cowan University (Human Genetics) * WA Dept of Agriculture (animal, plant, microbial) * Fisheries * Perth Zoo * Plant Biotechnology Research Group * Australian Centre for Necrotrophic Fungal Pathogens (ACNFP) * Rumen Biotechnology * Centre for High Throughput Agricultural Genetic Analysis (CHAGA) * Veterinary Virology, Parasitology, Microbiology * Saturn Biotech Pty Ltd * Grain Biotech Australia Pty Ltd * Proteomics International * Lighthouse Laboratories Pty Ltd * ID PLUS Pty Ltd * Royal Perth Hospital * Fremantle Hospital * Australian Neuromuscular Research Institute (ANRI) Partnering Opportunities The SABC can provide full facilities for contract R&D, start up companies or co-location of existing companies in agricultural, veterinary and biomedical sciences via its incubation program. Contact the Director for further information. Partnering Needs Investors interested in commercializing outputs of SABC researchers.
SABiosciences, as part of QIAGEN, offers nucleic acid (DNA, RNA, miRNA) and protein isolation, preparation and purification services, as well as assay,array, sequencing, NGS and biomarker services and lab essentials.Offers PCR services, assays, array systems, and expression vectors. Acquired by QIAGEN in 2009.
A large collection of tools for basic and advanced analyses of nucleotide and protein sequences. The tools are wrapped into a common user interface making handling, storage, retrieval and viewing the results easy and logical. A seqtools project can accommodate many thousand sequences making unattended batch analyses like database searching at NCBI painless with the robust search engine included in seqtools.
Retroelements constitute important evolutionary forces for the genome of higher organisms, yet their uncontrolled spread, whether from endogenous loci or within the context of viral infections, can cause diseases such as cancer, hepatitis and AIDS. Correspondingly, a variety of host-encoded activities limit this process, belonging to a line of defense commonly called intrinsic or innate immunity, which notably contributes to taming endogenous retroelements and to restricting the cross-species transmission of retroviruses. Our work aims at characterizing the relationship between retroelements and their hosts, which has recently led us to become more generally interested in epigenetic mechanisms regulating the expression of mammalian genomes.
The DeRisi Lab focuses on genomic approaches to the study of infectious disease. Specifically, we are studying Plasmodium falciparum, the causative agent of the most deadly form of human malaria. We are also involved in a major effort for the discovery of new viral pathogens associated with diseases of unknown etiology. Software tools developed in the lab include: HMMSplicer discovers splice sites in high throughput sequencing datasets without using gene models. HMMSplicer can also be used to find non-canonical junctions as well. HMMSplicer was benchmarked on publickly available A. thaliana, H. sapiens, and P. falciparum datasets and performs well on all genomes. Information about the datasets tested, including the exact command parameters and the final results, is provided. HMMSplicer is implemented in Python and is freely available for all. VersaCount is a simple application to assist with the counting of cells by microscopy. When used with a numeric keypad, it can significantly increase counting efficiency when compared with a traditional clicker. Although it was designed for malaria work, it can be customized for a wide variety of cell counting applications. VersaCount was written by Charlie Kim. ExpressionNet is a program written by Jingchun Zhu that uses Bayesian network learning algorithms to explore relationships among random variables to generate network models. The software has been used to study the transcriptional response to environmental perturbations in budding yeast. Details of the program and the study of yeast transcription using Bayesian Networks was published in PLoS ONE. DNA microarrays may be used to identify microbial species present in environmental and clinical samples. However, automated tools for reliable species identification based on observed microarray hybridization patterns are lacking. We present an algorithm, E-Predict, for microarray-based species identification. ArrayOligoSelector (AOS) is an open source program developed by Jingchun Zhu for the purpose of systematically designing gene-specific long oligonucleotide probes for entire genomes. For each open reading frame, the program optimizes oligo selection based upon several parameters, including uniqueness, complexity, secondary structure, GC content, and 3'' end proximity. AOS also is hosted at SourceForge. This site contains documentation and a user-friendly how-to. ArrayMaker 2 provides high performance robotic control of microarrayer robots with an incredibly intuitive, easy to use interface. ArrayMaker 2 is optimized for use with the new generation of ultra fast linear servo driven arrayers, yet it is backwards compatible with the original MGuide style of ball-screw driven arrayers.
Our principal research interest is the organization and the dynamics of the large-scale neuronal networks of the brain that characterize mental functions, and the understanding of disturbances of these networks in patients with brain dysfunctions. Electromagnetic imaging based on high-resolution EEG is our principal instrument to study these questions. It is combined with Transcranial Magnetic Stimulation (TMS), Functional Magnetic Resonance Imaging (fMRI), and multichannel intracranial recordings in patients. Sponsors: Swiss National Science Foundation Fondation Louis Jeantet de Mdecine Fondation Leenards
WDIN is a collaborative project working to develop a Web-based monitoring and reporting system to provide state and federal resource managers, animal disease specialists, veterinary diagnostic laboratories, physicians, public health workers, educators, and the general public with access to data on wildlife diseases, mortality events, and other critical related information. Data are contributed voluntarily, with partners deciding which data they choose to share.
CONsensus DELeteriousness score of missense SNVs
A method to assess the outcome of nonsynonymous SNVs using a consensus deleteriousness score that combines various tools (e.g. SIFT, Polyphen2, MutationAssessor).
This collection of Free Statistics Calculators offers a wide range of descriptive and explorative types of statistical measures and analysis: Central Tendency, Average, Mean, Median, Variability, Interquartile Range, Concentration, Lorenz Curve, Gini Coefficient, Skewness, Kurtosis, Quartiles, Percentiles, Notched Boxplot, Histogram, Correlation, Partial Correlation, Rank Correlation (Spearman and Kendall), Simple Regression, Kernel Density Estimation, Harrell-Davis Quantiles, Bivariate KDE, Correlation Matrix, Stem-and-leaf plot, Explorative Data Analysis
INB is a technological plattform of Genoma Espaa. A National Network for coordination, integration and development of Spanish Bioinformatics Resources in genomics and proteomics projects. The INB (Instituto Nacional de Bioinformtica) is a community-driven technology platform of Genoma Espana founded in 2003 with the mission to consolidate Bioinformatics as a scientific discipline and to generate and apply solutions for the development and execution of projects related to genomics and proteomics, providing technical support in Bioinformatics to laboratories, institutions and companies throughout the Spanish territory.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Following completion of the acquisition of Rosetta Biosoftware assets from Merck & Co., Inc. by Microsoft Corp. on June 26, 2009, Merck & Co., Inc. selected Ceiba Solutions, Inc (http://www.ceibasolutions.com) as the provider of product support for Rosetta Resolver, Elucidator and Syllego customers. Ceiba Solutions is a software and IT services company helping customers streamline and extend business processes through composite software development, application integration, and managed application services. Ceiba currently serves Life Science industry customers with outsourced managed services for R&D applications, as well as business software and integrated business processes. Ceiba Solutions is an active member of the Massachusetts Biotechnology Council and the BayBio Council. Ceiba Solutions has assumed complete responsibility for software maintenance and support associated with Rosetta Biosoftware product Licensees who are eligible for continued Technical Support and Software Upgrade Protection, and will retain that responsibility throughout the remainder of the 24 month Desupport Period.
Provides support for the Apache community of open-source software projects. The Apache projects are characterized by a collaborative, consensus based development process, open and pragmatic software license, and a desire to create high quality software that leads the way in its field.
Bioinformatics, statistical genetics, functional genomics, databases and scientific computing support and services for The Wellcome Trust Centre for Human Genetics to support the disease gene cloning projects within the centre and to maintain independent research in development of methods, algorithms and software for mapping multifactorial trait loci. The group has current research foci in the areas of sequence alignment statistics, comparative genomics, ancestral haplotype construction, LIMS database development, QTL linkage and association methods, variability in patterns of linkage disequilibrium and multivariate modelling of quantitative traits.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Jan 16th 2025. WinLTP is a stimulation, data acquisition and on-line analysis electrophysiological software for studying Long-Term Potentiation (LTP), Long-term Depression (LTD), and related phenomena. WinLTP is multitasking and simultaneously runs 1) LTP stimulus/acquisition/analyzing sweeps with protocol scripting, and 2) continuous acquisition saving Axon Binary Files (abf). WinLTP runs on Windows PCI bus computers and uses National Instruments PCI M-Series boards and Axon Instruments'' Digidata 1320A and 1322A data acquisition boards. Other software that can use the M-Series boards includes Axograph Scientific''s AxoGraph X, WaveMetrics'' IGOR, National Instruments'' LabView, John Dempster''s Strathclyde Electrophysiology Suite (WinWCP and WinEDR), Silver lab''s Nclamp, and QUB data acquisition., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A substantial biological challenge is to understand the regulation and execution of developmental decisions that lead from multipotential, undifferentiated precursor cells to their specialized differential products. In the World lab at the California Institute of Technology, we are interested in several interrelated aspects of this problem, and we also work to develop new methods for studying it. The particular cell lineage problem we study begins with the specification of mesoderm in early development and continues to the final differentiation of skeletal muscle or cardiac muscle in the fully developed animal. To study this process we use the mouse as our experimental system. Molecular-level analyses use cell culture model systems and transgenic mice. These projects include studies of in vitro and in vivo protein-DNA interactions and of factors that amplify or suppress expression activity. Computational approaches involve the development of algorithms for use in large-scale gene expression analysis and the construction of a simulator framework for regulation in muscle development.
An organization that promotes the highest possible standards of medical ethics. The WMA provides ethical guidance to physicians through its Declarations, Resolutions and Statements. These also help to guide National Medical Associations, governments and international organizations throughout the world. The Declarations, Resolutions and Statements cover a wide range of subjects, including an International Code of Medical Ethics, the rights of patients, research on human subjects, care of the sick and wounded in times of armed conflict, torture of prisoners, the use and abuse of drugs, family planning and pollution.
Provides equipment for TEER measurement, nitric oxide testing, and electro-physiology applications.
The YUI Library is a set of utilities and controls, written with JavaScript and CSS, for building richly interactive web applications using techniques such as DOM scripting, DHTML and AJAX. YUI is available under a BSD license and is free for all uses. YUI is proven, scalable, fast, and robust. Built by frontend engineers at Yahoo! and contributors from around the world, it''s an industrial-strength JavaScript library for professionals who love JavaScript.
Zebrafish Models for Human Development and Disease
ZF-MODELS - Zebrafish Models for Human Development and Disease is an Integrated Project funded by the European Commission as part of its Sixth Framework Programme (EC Contract LSHG-CT-2003-503496). The project started on January 1, 2004 and is scheduled to run over a period of five years. The aim of this project is to exploit the advantages of the zebrafish to produce knowledge, technology and materials in the form of disease models, drug targets and insight into pathways of gene regulation applicable to human development and disease.
Welcome to ZINC, a free database of commercially-available compounds for virtual screening. ZINC contains over 13 million purchasable compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). To cite ZINC, please reference: Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82 PDF, DOI. We thank NIGMS for financial support (GM71896). There are release notes for ZINC 10. - We have a survey where you can give us feedback.
Aquatic Habitats (AHAB) is the worlds largest manufacturer of housing systems for aquatic research animals. We are biologists first and engineers second, so we understand the complexity of aquatic life and how to sustain it. Our turnkey systems are secure, efficient and as fail-safe as possible.
This site provides several tools for selecting zinc finger protein (ZFP) target sites and for designing the proteins that will target them. These ZFPs can be fused with effector domains that confer transcriptional activation or repression activity as well as catalytic functions.
Computational tool developed to help identify cancer-associated ''driver'' mutations from ''passenger'' ones in a cancer genome.
A free web server for the analysis of short RNAs from high throughput sequencing data.
Zoomify makes high-quality images zoom-and-pan for fast, interactive viewing on the web. Zoomify''s image viewing solutions use just HTML, JPEGs, and Flash - no large downloads, no special installs, and no server-side setup is required. And Zoomify''s innovative features provided added value including support for slideshows, hotspots, annotation, side-by-side comparison, and much more. Zoomifys products meet the high-quality, high-resolution imaging needs of creative professionals and image-centric applications. Zoomify is revolutionizing digital imaging in medicine and the sciences, image archiving and museum exhibits, defense and security, education, entertainment, and more.
Founded in 1981, ZymoGenetics is a biopharmaceutical company focused on the development and commercialization of therapeutic proteins. ZymoGenetics is publicly traded (NASDAQ: ZGEN) and headquartered in Seattle, Washington in the historic Seattle City Light Steam Plant building. Our mission is to create novel protein drugs that will significantly help patients fight their diseases. We have contributed to the discovery or development of six recombinant protein products now marketed by other companies. Current programs target viral infection, cancer, inflammatory diseases and bleeding. Our first internally developed product, RECOTHROM Thrombin, topical (Recombinant), was approved by the U.S. Food and Drug Administration (FDA) on January 17, 2008 for use as a topical hemostat to control moderate bleeding during surgical procedures and is now marketed in the United States. We have a promising pipeline of novel therapeutics, which we are developing on our own or in collaboration with partners.
MMV, a not-for-profit public-private partnership, was established as a foundation in Switzerland in 1999. Our mission is to reduce the burden of malaria in disease-endemic countries by discovering, developing and facilitating delivery of new, effective and affordable antimalarial drugs. Our vision is a world in which these innovative medicines will cure and protect the vulnerable and under-served populations at risk of malaria, and help to ultimately eradicate this terrible disease. Sponsors/Donors: -Bill and Melinda Gates Foundation -CRIMALDDI -ExxonMobil -Irish Aid -National Institutes of Health -Netherlands Ministry of Foreign Affairs -Rockefeller Foundation (former donor) -Secretaria de Estado de Cooperacin Internacional (Spanish Agency for International Cooperation) -Swiss Agency for Development and Cooperation -UK Department for International Development -USAID -Wellcome Trust -World Bank -World Health Organization
Welcome to the Air Force Suicide Prevention Program (AFSPP) Website. This site is designed to provide information and tools to members of the Air Force community (Suicide Prevention Program Managers, commanders, gatekeepers, IDS members, etc.) in their efforts to help reduce Air Force suicides. Reducing suicide requires a community effort and we welcome your visit to our site.
Anopheles gambiae Gene Expression Database
Anopheles gambiae Gene Expression Profile
Welcome to the Anopheles gambiae Gene Expression Database at UC Irvine. Presented here is a relational database that combines data from microarray experiments, functional annotation, and the An. gambiae genome project to provide insight into gene expression and regulation in this mosquito vector of human malaria. Microarray analyses included in this site were based on the Affymetrix GeneChip Plasmodium/Anopheles Genome Array. Abundance of specific mRNAs represented in the array were determined for larvae (3rd and 4th instars), adult males (3 days post emergence), non-blood fed females (3 days post emergence) and females at 3, 24, 48, 72, and 96 hours following a blood meal, and females aged 18 days with or without a bloodmeal. Functional annotation integrated into the site for keyword searching combines keywords indexed in the ENSEMBL Mosquito Genome database, NCBI non-redundant databases and conserved motifs databases (GO, PFAM, SMART). Sequence data was captured from the ENSEMBL Mosquito Genome database.
Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License. Because of the overwhelming success of the first open movie project, Ton Roosendaal, the Blender Foundation''s chairman, has established the Blender Institute. This now is the permanent office and studio to more efficiently organize the Blender Foundation goals, but especially to coordinate and facilitate Open Projects related to 3D movies, games or visual effects.
The LVC64 accepts 64 microvolt-level buffered input signals from headstage preamps and serves as a 24-bit recording device. It is connected to a PC with an USB2.0 cable and provides a complete digital system to record broadband bioelectric signals. It has two parts such as a 64-channel ADC unit and a digital interface & power supply unit. Between these units there is a slip ring commutator and a DC motor. The main features of the LVC system include: Up to 128 Analog inputs per system; Each Analog input is sampled with an individual 24 bit delta-sigma A/D converter Analog inputs are simultaneously sampled at 1750 to 32000 samples per second In addition to multiple unit activity - the EEG, field potentials and behavioral marker signals are recorded simultaneously in the same file Full scale analog input range is 5 millivolts RMS (14 mV peak-to-peak) Analog inputs are differential inputs Extremely low input referred noise levels of max. 8 uV peak-to-peak Direct headstage tether and tether extension cable inputs Slip ring commutator for un-twisting the twisted tether cable Headstage power supplies Up to 24 bit TTL compatible Parallel Input Port for monitoring external signals and external Timestamp Clock input and output for multiple system synchronization Totally electrically isolated system from AC Power and Ground ''Microvolts-to-harddisk dumper'' data acquisition program running in host PC (32-bit MS Window XP) Online display of records during data acquisition in Host PC''s monitor Offline spike sorting by Cooperative Linux software of the Host PC
Purpose of the Myc Hubsite The emergence of complex DNA microarray data on gene expression creates vast new opportunities but also poses serious challenges for information and library sciences. This complexity becomes more challenging as certain genes, such as MYC that encodes a transcription factor, switch on other genes. The purpose of this website is to provide a hub for the integration of information on Myc target genes, the role of Myc in human cancers, and proteins that interact with the Myc transcription factors. Links are provided that connect to PUBMED citations, Unigene database, and in specific cases to original data. Sponsor: Funded by a grant from the National Library of Medicine
The CpG island searcher screens for CpG islands which meet the criteria selected below in submitted DNA sequences. Abstract The unique variability in the 5'' region of the GR gene, with 9 alternative first exons and 13 splice variants plays a critical role in transcriptional control maintaining homeostasis of the glucocorticoid receptor (GR). This 5''mRNA heterogeneity, common to all species investigated, remains untranslated since the alternative first exons are spliced to exon 2 immediately upstream of the translation initiation codon. These alternative first exons are located either immediately upstream of the coding exons in the CpG island (exons B-H and J), or further upstream (exons 1A and 1I). The mechanisms regulating the differential usage of these first exons in different tissues and individuals, and the role of the 5''UTR in the splicing of the coding exons are still poorly understood. Here we review some of the mechanisms that have so far been identified. Data from our laboratory and others have shown that the multiple first exons represent only a first layer of complexity orchestrated probably by tissue-specific transcription factors. Modulation of alternative first exon activity by epigenetic methylation of their promoters represents a second layer of complexity at least partially controlled by perinatal programming. The alternative promoter usage also appears to affect the 3'' splicing generating the different GR coding variants, GRalpha, GRbeta, and GR-P. Aberrant GR levels are associated with stress-related disorders such as depression, and affect social behaviour, mood, learning and memory. Dissecting how tissue-specific GR levels are regulated, in particular in the brain, is a first step to understand the significance of aberrant GR levels in disease and behaviour. Copyright 2010. Published by Elsevier Inc.
A database and analysis of the brainwaves of individuals with pronounced physical disabilities. BrainGate''s mission is to further the advancement of this life-changing technology to promote wider adoption to help impaired individuals communicate and interact with society. For instance, the Cyberkenetics BrainGate Neural Interface is currently the subject of a pilot clinical trial being conducted under an Investigational Device Exemption (IDE) from the FDA. The system is designed to restore functionality for a limited, immobile group of severely motor-impaired individuals. It is expected that people using the BrainGate System will employ a personal computer as the gateway to a range of self-directed activities. These activities may extend beyond typical computer functions (e.g., communication) to include the control of objects in the environment such as a telephone, a television and lights. BrainGate offers a systems approach which applies the language of neurons in both short and long-term settings. The platform technology is based on the results of several years of research and development at premier academic institutions such as Brown University, the Massachusetts Institute of Technology, Emory University, and the University of Utah.
It is a collaboration between owners, breeders and scientists with the goal of studying the genetics of the Portuguese Water Dog. The Georgie project sends out periodic reports of our findings. These reports are generally sent to the participants along with detailed information on their dogs. Here we have reproduce the public versions of the report for your reference.
A simple program for finding nearly matched primers Sponsor: This material is based upon work supported by the National Science Foundation under Grant No. 0114726.
Sponsor: support is NIH grant R01 GM077122 National Institutes of Health, Claudia Adams Barr Program, and Friends of DFCI. We are interested in how genomics changes promote cancer progression. Through collaboration with biomedical researchers, we analyze high-throughput microarray and sequencing data to study genomics, expression, and network changes in cancer cells. New methods are packaged into widely-used software such as dChip, which has been cited more than 1600 times.
DISABKIDS is a European project which aims at enhancing the quality of life and the independence of children with chronic health conditions and their families. The project proceeds according to three phases: 1. Development of an instrument (paper/pencil as well as a computer assisted version) to assess quality of life and patient needs in children/adolescents with chronic health conditions. 2. Psychometric testing of the developed instrument in the 7 pariticipating countries in a pilot study with 378 children/ adolescents and a subsequent field study with 1260 children/adolescents and their families (180 families in each country). 3. Implementation and Evaluation of the instrument in routine care The project expects to achieve progress in quality of life assessment in children and adolescents with disabilities a) by focussing on an European co-operation in construction of an assessment instrument for quality of life, in which the persons concerned (children/adolescents and their families) play a major role, b) by addressing needs for care as explicitly voiced by the persons concerned, c) by including psychosocial as well as clinical and socio-economic determinants of quality of life and d) by developing a mode of administration which is practicable for the patient group concerned, so that in using the instrument, current care can be evaluated and future care can be improved by corresponding to the patients'' needs. Sponsors: The DISABKIDS project funded by the European Commission within the Fifth Framework Programme (FP5)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A database which contains the information of heparin-binding proteins of E. coli K-12 MG1655 cells. Heparin affinity columns were applied to enrich and fractionate proteins. Identification of proteins was done via the collaboration with David Russell''s lab. Because heparin is negatively charged sulfated glucosaminoglycan, polyamion binding proteins, which contain nucleic acid-binding proteins, are expected to bind to heparin columns. Study of the expression pattern of heparin-binding proteins will help to study the nucleic acid-binding proteins, most of which are related to regulation. Moreover, heparin affinity columns will also erich low abundance proteins. Heparome database is constructed using MySQL. Website interface is built using HTML and PHP. Queries between MySQL database and website interface are executed using PHP. Besides including information of identified proteins, such as swiss accession number, gene name, molecular weight, isoelectric point, condon adaptation index (CAI), functional classification, et. al. , it also includes information of experiments, such as sample preparation, heparin-HPLC chromatography, SDS-PAGE gel separation and MALDI-MS.
Exponentially Modified Protein Abundance Index
emPAI (exponentially modified protein abundance index), developed by Ishihama et al., is a measure to describe the protein composition in sample solutions. When the total protein amount in the sample is available, emPAI can be converted to the absolute amount of each protein in the sample. emPAI is derived from PAI, which is defined as the number of the observed peptides divided by the number of the observable peptides per protein. We recently found that log (PAI) had linear relationship to the protein amounts, and that emPAI, 10^(PAI)-1, was proportional to the protein amounts for whole cell lysate digested by trypsin. The accuracy of this method was within factor 5, similar or better than determination of abundance by protein staining
Provides summary of gene and genomic information from eukaryotic organism databases. This includes gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information, links to extended gene information.
The DNA Alignment software and Network software is used by biologists, anthropologists, medical researchers and students world wide. We carry out phylogeographic consultancy for US, UK and German clients, including legal medical work. We were involved in the tv projects The Real Eve (Discovery Channel) and Motherland (BBC). Our biotechnological director Dr Peter Forster is on the editorial board of the International Journal of Legal Medicine since 1999.
Gnuplot is a portable command-line driven graphing utility for linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don''t have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986. Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines, points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types. Demos here. Gnuplot supports many different types of output: interactive screen terminals (with mouse and hotkey input), direct output to pen plotters or modern printers, and output to many file formats (eps, fig, jpeg, LaTeX, metafont, pbm, pdf, png, postscript, svg, ...). Gnuplot is easily extensible to include new output modes. Recent additions include an interactive terminal based on wxWidgets and the creation of mousable graphs for web display using the HTML5 canvas element.
An Extended and Parallel version of Clustal
This portal runs on a processor cluster and allows Biochemists to use our parallel implementation of Clustal W together with our parallel implementation of Minimum Vertex Cover.
Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD)
Single Nucleotide Polymorphism Spectral Decomposition
SNPSpD is a method of correcting for non-independance of single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of LD between SNP''s. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.
In many respects, this book will be an extension of many of the preoccupations Ive pursued here at Epidemix. Those handful of you who follow my magazine writing will no doubt recognize the theme as well. The premise is that we are at a new phase of health and medical care, where more decisions are being made by individuals on their own behalf, rather than by physicians, and that, furthermore, these decisions are being informed by new tools based on statistics, data, and predictions. This is a good thing it will let us, the general public, live better, happier, and even longer lives. But it will require us to be stewards of our health in ways we may not be prepared for. We will act on the basis of risk factors and predictive scores, rather than on conventional wisdom and doctors recommendations. We will act in collaboration with others, drawing on collective experience with health and disease, rather than in the isolation and ignorance that can come with privacy concerns. And we will act early, well before symptoms appear, opting to tap the science of genomics and proteomics in order to mitigate our risks down the road. Together, these tools will create a new opportunity and a new responsibility for people to act to make health decisions well before they become patients. This can be characterized as a decision tree, a series of informed choices we will make to minimize uncertainty and optimize our outcomes. Indeed, we will use decision trees to navigate most of our health decisions, sometimes in overt ways new decision support tools will both inform us and guide us, and theyll be steeped in statistics, predicition, and the power of collective experience.
Python 2D plotting library which produces publication quality figures in variety of hardcopy formats and interactive environments across platforms. Used in python scripts, web application servers, and six graphical user interface toolkits. Used to generate plots, histograms, power spectra, bar charts, error charts, scatter plots.
A commercial distributed memory object caching system, generic in nature, but originally intended for use in speeding up dynamic web applications by alleviating database load. memcached allows you to take memory from parts of your system where you have more than you need and make it accessible to areas where you have less than you need. With memcached, you can see that all of the servers are looking into the same virtual pool of memory. This means that a given item is always stored and always retrieved from the same location in your entire web cluster.
ADFS is a web server system that integrates a database of allergenic proteins for food safety. This allergen database for food safety was launched as a project of the Novel Foods and Immunochemistry of National Institute of Health Sciences, and this project was partly supported by a grant from the Ministry of Health, Labor and Welfare. To survey the sequence homology in assessing a potential of allergenicity of a protein in the food, the database has been constructed to include known allergens and B-cell epitope sequences. This database includes 13 (aero animal, aero fungi, aero insect, aero mite, aero plant, contact, food animal, food fungi, food plant, gliadin, protozoan, venom/salivary, and worm) categorized allergens based on allergen type in AllergenOnline, with their accession numbers, epitope information, 3D-structure information, and sugar-containing information . This site also provides sequence search tools for obtaining the sequence homology of a certain protein or peptide relating to allergens (BLAST, epitope(peptide) search). Furthermore, this site provides allergenicity prediction tools of a certain protein (FAO/WHO method, Motif-based method).
motif-x (short for motif extractor) is a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.
Grid Enabled Molecular Science Through Online Networked Environments
Integrated framework for accessing grid resources that supports scientific exploration, workflow capture and replay, and a dynamic services oriented architecture. This framework provides researchers in the molecular sciences with a tool to discover remote grid application services and compose them as appropriate to the chemical and physical nature of the problem at hand. The initial set of application services include molecular quantum and classical chemistries (GAMESS, APBS, Polyrate), along with supporting services for visualization (QMView), databases, auxillary chemistry services, and documentation and education materials. * Rich-client Desktop Interface - Gemstone is a Firefox extension that provides a dynamic user interface to backend computational, data and visualization services. * Workflow Integration - Gemstone supports a workflow component based on Informnet (see http://grid-devel.sdsc.edu/informnet). They are adapting the Informnet workflow engine to support workflow publication and discovery, brokering, and fault tolerance. They are also adding support for automatic generation of workflows based on user interaction. * Strongy Typed Data Schemas - They are working extensively with CML, integrating their data schemas into workflow systems and providing bridges to the GamesXML that they defined.
Database of long noncoding RNA expression that integrates annotated expression data from various sources in human and mouse. The database contains both microarray and in situ hybridization data, and supplies a rich tapestry of ancillary information for featured ncRNAs, including evolutionary conservation, secondary structure evidence, genomic context links and antisense relationships.
A software package for modelling large networks of neurons (typically hundreds or thousands), using spiking point-neuron models. Nengo is designed around the neural engineering framework (NEF). This is a mathematical framework that describes how neurons interact to represent information, perform computations, and behave dynamically. This framework has been used to develop sophisticated models of spatial working memory, probabilistic sound localization, and lamprey locomotion, among others. Nengo makes it easy for beginners to develop models using the NEF. If you accept defaults for spiking models, tuning curves, firing rates, etc. then you can have a rough approximation of a complex system assembled and running in minutes. Nengo also makes it easy for experts to do advanced work with the NEF. The design carefully encapsulates separable aspects of model behaviour, so that it is highly customizable and easy to extend.
NeuroProSight allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using the Top-Down Approach. This site has many tools and graphical features to facilitate analysis of single (recombinant) proteins, proteins in mixtures, and proteins fragmented in parallel. Sponsors: Dr. John Garavelli is assisting us by incorporating the RESID database of post-translational modifications. We gratefully acknowledge these sources of generous support: * Searle Scholars Program and The Chicago Community Trust * The Burroughs Wellcome Fund * The University of Illinois
NumPy is the fundamental package needed for scientific computing with Python. It contains among other things: * a powerful N-dimensional array object * sophisticated (broadcasting) functions * tools for integrating C/C and Fortran code * useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. Sponsored by ENTHOUGHT
We are principally interested in mechanisms of short-term synaptic plasticity and the impact of that plasticity on function in the nervous system. For our research we use two model vertebrate systems. A simple vertebrate model that affords us some fundamental advantages in this research is the lamprey central nervous system. The lamprey has a central nervous system that is very simple for a vertebrate and which may be kept alive, isolated but otherwise intact, for a number of days. Additionally, a group of axons in the spinal cord are very large and contain presynaptic structures that are exceptionally accessible to the experimentalist. This combination of features enables us to investigate synaptic plasticity at great detail and to determine its role in motor control. We have focused on the means by which G protein coupled receptors mediate enhancement and inhibition of glutamate release. We have identified a direct target for Gbg on the SNARE complex, the machinery for fusion of synaptic vesicles More recently we have utilized the rat hippocampus to determine whether similar mechanisms of synaptic plasticity are present in the mammalian brain. We have begun to focus on the role of kinase activation and short-term modification of transmitter release, in addition to how these modifications can alter the formation of memory during induction phases of long-term plasticity. Available software includes that for Electrophysiological Analysis, Image Analysis, and Confocal Software.
THIS RESOURCE IS NO LONGER IN SERVICE. Documetned on May 12,2023. Software application (entry from Genetic Analysis Software)
tRNAdb 2009 provides a powerful and fast search engine. Taxons can be identified by browsing the taxonomic tree or by using the search form. Queries can include DNA or RNA sequences, amino acid family, anticodon, references, Pubmed-ID of the reference, gene ID as well as comments. In addition, individual searches concerning sequence or structure characteristics are possible. The server accepts IDs of the new as well as the old tRNA database as queries and can perform BLAST searches. All sequences can be downloaded in several file- and alignment formats on the result list. This site is hosted and maintained in a cooperation between the universities of Leipzig (Germany), Marburg (Germany) and Strasbourg (France). Recent Visitors
Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file).
The Tropical Disease Initiative aims to provide a kernel for open source drug discovery. Such kernel should allow scientists from laboratories, universities, institutes, and corporations to work together for a common cause: find new drugs against tropical disieases such as Malaria or Tuberculosis. Computation plays an increasing role in biology. The convergence between computing and biology suggests that open source methods can be used to organize early phase drug discovery. We argue that a new approach, which we call open source drug discovery, would significantly reduce the cost of discovering, developing and manufacturing cures for tropical diseases. First, it would give hundreds of scientists a practical way to donate urgently needed manpower. Second, open source discoveries would not be patented, permitting sponsors to award development contracts to the company that offered the lowest bid. Finally, competition from generic drug makers would keep manufacturing prices at or near the cost of production, significantly accelerating drug development for the 500 million people who currently suffer from tropical diseases. The TDI was initiated by: Thomas Kepler - Duke University Marc A. Marti-Renom - Prince Felipe Research Center, Valencia, Spain Stephen Maurer - University of California, Berkeley Arti Rai - Duke University Andrej Sali- University of California, San Francisco
Our genes and lifestyle factors, such as calorie rich diets and a lack of exercise, contribute to the development of Type 2 diabetes. But what we dont know is the exact nature of the genetic risk and how this interacts with lifestyle factors to cause diabetes. The Diabetes UK Warren 2 Group was formed in 1992 to investigate the genetic basis of Type 2 diabetes. The Group, comprising of researchers from six UK diabetes research centres, began by recruiting families into the study enriched for Type 2 diabetes ie having two or more siblings with the condition. With over 2000 individuals from 843 families in the collection, it is now being used to search for the genes that make people susceptible to Type 2 diabetes. When identifying susceptibility genes it is important to know how the gene affects normal metabolism in relatives without diabetes. In 1999. the Warren 2 Extension study recruited first degree relatives (siblings and children) of the original Warren 2 families, who did not have diabetes, in the knowledge that they would also be enriched with the same susceptibility genes. This study recruited 811 relatives without diabetes (586 offspring and 225 siblings) all of whom have undergone detailed metabolic assessment. A similar study was undertaken in Oxford called the Diabetes In Families (DIF) Study. In 2001, the Warren 2 Trios and Duos Study recruited 500 families from around the country consisting of an individual with Type 2 diabetes and both their parents (trios) or an individual with diabetes, one of their parents and at least 2 siblings (duos). In addition to this, a further 1500 individuals with diabetes were recruited as part of the Warren 2 Cases study. This website is run by the Diabetes Research department and the Centre for Molecular Genetics at the Peninsula Medical School and Royal Devon and Exeter Hospital, Exeter, UK.
Berkeley Drosophila Transcription Network Project
The goal of this project is to decipher the transcriptional information contained in the extensive cis-acting DNA sequences that direct the patterns of gene expression that underlie animal development. Using the early embryo of the fruitfly Drosophila melanogaster as a model, these researchers are developing experimental and computational methods to systematically characterize and dissect the complex expression patterns and regulatory interactions already present prior to gastrulation. They have identified 37 principal regulatory factors within this network for initial analysis together with their target genes. Sponsors: This project is chiefly funded by a grant from NIGMS and NHGRI, R01 GM070444. Additional funding comes from grants to Michael Eisen, Sue Celniker, and Bernd Hamann.
The Transgenic Hydra Facility is a non-profit facility in the laboratory of Thomas Bosch at the University of Kiel that assists scientists to use and to develop transgenic Hydra polyps. Our mission is to provide investigators access to the latest technology for the efficient production of transgenic polyps. We particularly encourage scientists from laboratories lacking the infrastructure for transgenic Hydra technologies to use our services. Abstract: Understanding the evolution of development in large part relies on the study of phylogenetically old organisms. Cnidarians, such as Hydra, have become attractive model organisms for these studies. However, despite long-term efforts, stably transgenic animals could not be generated, severely limiting the functional analysis of genes. Here we report the efficient generation of transgenic Hydra lines by embryo microinjection. One of these transgenic lines expressing EGFP revealed remarkably high motility of individual endodermal epithelial cells during morphogenesis. We expect that transgenic Hydra will become important tools to dissect the molecular mechanisms of development at the base of the Metazoan tree. Sponsors: Financial support for this research was provided by the German Research Foundation [Deutsche Forschungsgemeinschaft Grants B0848/13 and SFB617.
A viewing program for Statistical Parametric Mapping (SPM2, SPM5 and SPM8). p-value slider, displays multiple images at a time and can be used to build Region of Interest (ROI) masks. For a given region you can find the anatomical name and search the selected region in online database (wiki, Google scholar and PubMed).
LAMHDI: The Initiative to Link Animal Models to Human DIsease
THIS RESOURCE IS NO LONGER IN SERVICE, it has been replaced by Monarch Initiative. LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal model for their research. LAMDHI is a free, Web-based, resource to help researchers bridge the gap between bench testing and human trials. It provides a free, unbiased resource that enables scientists to quickly find the best animal models for their research studies. LAMHDI includes mouse data from MGI, the Mouse Genome Informatics website; zebrafish data from ZFIN, the Zebrafish Model Organism Database; rat data from RGD, the Rat Genome Database; yeast data from SGD, the Saccharomyces Genome Database; and fly data from FlyBase. LAMHDI.org is operational today, and data is added regularly. Enhancements are planned to let researchers contribute their knowledge of the animal models available through LAMHDI. The LAMHDI goal is to allow researchers to share information about and access to animal models so they can refine research and testing, and reduce or replace the use of animal models where possible. LAMHDI Database Search: LAMHDI brings together scientifically validated information from various sources to create a composite multi-species database of animal models of human disease. To do this, the LAMHDI database is prepared from a variety of sources. The LAMHDI team takes publicly available data from OMIM, NCBI''s Entrez Gene database, Homologene, and WikiPathways, and builds a mathematical graph (think of it as a map or a web) that links these data together. OMIM is used to link human diseases with specific human genes, and Entrez provides universal identifiers for each of those genes. Human genes are linked to their counterpart genes in other species with Homologene, and those genes are linked to other genes tentatively or authoritatively using the data in WikiPathways. This preparatory work gives LAMHDI a web of human diseases linked to specific human genes, orthologous human genes, homologous genes in other species, and both human and non-human genes involved in specific metabolic pathways associated with those diseases. LAMHDI includes model data that partners provide directly from their data structures. For instance, MGI provides information about mouse models, including a disease for each model, as well as some genetic information (the ID of the model, in fact, identifies one or more genes). ZFIN provides genetic information for each zebrafish model, but no diseases, so zebrafish models are integrated by using the genes as the glue. For instance, a zebrafish model built to feature the zebrafish PKD2 gene would plug into the larger disease-gene map at the node representing the zebrafish PKD2 gene, which is connected to the node representing the human PKD2 gene, which in turn is connected to the node representing the human disease known as polycystic kidney disease. (Some of the partner data LAMHDI receives can even extend the base map. MGI provides a disease for every model, and in some cases this allows the creation of a disease-to-gene relationship in the LAMHDI database that might not already be documented in the OMIM dataset.) With curatorial and model information in hand, LAMHDI runs a lengthy automated process that exhaustively searches for every possible path between each model and each disease in the data, up to a set number of hops, producing for each disease-to-model pair a set of links from the disease to the model. The algorithm avoids circular paths and paths that include more than one disease anywhere in the middle of the path. At the end of this phase, LAMHDI has a comprehensive set of paths representing all the disease-to-model relationships in the data, varying in length from one hop to many hops. Each disease-to-model path is essentially a string of nodes in the data, where each node represents a disease, a gene, a linkage between genes (an orthologue, a homologue, or a pathway connection, referred to as a gene cluster or association), or a model. Each node has a human-friendly label, a set of terms and keywords, and - in most cases - a URL linking the node to the data source where it originated. When a researcher submits a search on the LAMHDI website, LAMHDI searches for the user''s search terms in its precomputed list of all known disease-to-model paths. It looks for the terms not only in the disease and model nodes, but also in every node along each path. The complete set of hits may include multiple paths between any given disease-to-model pair of endpoints. Each of these disease-to-model pair sets is ordered by the number of hops it involves, and the one involving the fewest hops is chosen to represent its respective disease-to-model pair in the search results presented to the user. Results are sorted by scores that represent their matches. The number of hops is one barometer of the strength of the evidence linking the model and the disease; fewer hops indicates the relationship is stronger, more hops indicates it may be weaker. This indicator works best for comparing models from a single partner dataset: MGI explicitly identifies a disease for each mouse model, so there can be disease-to-model hits for mice that involve just one hop. Because ZFIN does not explicitly identify a disease for each model, no zebrafish model will involve fewer than four hops to the nearest disease, from the zebrafish model to a zebrafish gene to a gene cluster to a human gene to a human disease.
The data for the smoking challenge consisted exclusively of discharge summaries from Partners HealthCare which were preprocessed and converted into XML format, and separated into training and test sets. I2B2 is a data warehouse containing clinical data on over 150k patients, including outpatient DX, lab results, medications, and inpatient procedures. ETL processes authored to pull data from EMR and finance systems Institutional review boards of Partners HealthCare approved the challenge and the data preparation process. The data were annotated by pulmonologists and classified patients into Past Smokers, Current Smokers, Smokers, Non-smokers, and unknown. Second-hand smokers were considered non-smokers. Other institutions involved include Massachusetts Institute of Technology, and the State University of New York at Albany. i2b2 is a passionate advocate for the potential of existing clinical information to yield insights that can directly impact healthcare improvement. In our many use cases (Driving Biology Projects) it has become increasingly obvious that the value locked in unstructured text is essential to the success of our mission. In order to enhance the ability of natural language processing (NLP) tools to prise increasingly fine grained information from clinical records, i2b2 has previously provided sets of fully deidentified notes from the Research Patient Data Repository at Partners HealthCare for a series of NLP Challenges organized by Dr. Ozlem Uzuner. We are pleased to now make those notes available to the community for general research purposes. At this time we are releasing the notes (~1,000) from the first i2b2 Challenge as i2b2 NLP Research Data Set #1. A similar set of notes from the Second i2b2 Challenge will be released on the one year anniversary of that Challenge (November, 2010).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. Web-based portal to connect all the constituencies in the global biobank community. The project seeks to increase the transparency and accessibility of the scientific research process by connecting researchers with an additional source of funding - microinvestments received from the broader online community. In exchange for these public investments, researchers will maintain research logs detailing the play-by-play progress made in their project, as well as publishing all of their data in a public database under a science commons license. These research projects, in turn, will serve to continually update a research-based neuroscience-based human brain & body curriculum. Biobanks are the meeting point of two major information trends in biomedical research: the generation of huge amounts of genomic and other laboratory data, and the electronic capture and integration of patient clinical records. They are comprised of large numbers of human biospecimens supplemented with clinical data. Biobanks when implemented effectively can harness the power of both genomic and clinical data and serve as a critical bridge between basic and applied research, linking laboratory to patient and getting to cures faster. As science and technology leaders work to address the many challenges facing U.S. biobanks logistical, technical, ethical, financial, intellectual property, and IT BioBank Central will serve as an accurate and timely source of knowledge and news about biorepositories and their role in research and drug development. The Web site also provides a working group venue, patient and public education programs, and a forum for international collaboration and harmonization of best practices.
V3D: A Swiss army knife for bioimage visualization & analysis
V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily.
Phenol Explorer: Database on Polyphenol Content in Foods
Phenol-Explorer is the first comprehensive web-based database on polyphenol content in foods. It contains more than 37 000 original data points collected from 638 scientific articles published in peer-reviewed journals. The quality of these data has been evaluated before they were aggregated to produce final representative mean content values for 502 polyphenols in 452 foods. The web interface allows making various queries on the aggregated data to identify foods containing a given polyphenol or polyphenols present in a given food. For each mean content value, it is possible to trace all original content values and their literature sources. Phenol-Explorer is a major step forward in the development of databases on food constituents and the food metabolome. It should help researchers to better understand the role of phytochemicals in the technical and nutritional quality of food, and food manufacturers to develop tailor-made healthy foods. Sponsors: The project has been supported by the NUTRIALIS program of the French Ministry of Research (2002-2004) and by Unilever, Danone and Nestl (2005-2009).
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An initiative to build connections among the many powerful resources across the region. Between colleges and universities, pharmaceutical and biotechnology companies, device developers, startups and service businesses, the Cure Corridor, Einsteins''s Alley, the Pharm Belt, or whatever you like to call the region, offers opportunities for discovery and development of new therapies that is unmatched. Sponsors: The NeuroScience Network is made possible, in part, through funding from Bio 1 WIRED.
This portal provides information about the neuroscience department at the University of Cambridge. Cambridge has a strong tradition in neuroscience having been host to the first analyses of neural signaling in the 1930s, determined the mechanisms of neuronal firing in the 1950s, and heralded some of the early theoretical approaches to the functions of neural circuitry in the 1960s. Neuroscience continues to grow at Cambridge, with an impressive record of achievement in multidisciplinary research.
Rhesus Macaque Atlases for Functional and Structural Imaging Studies
NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL.
GeneTraffic is a web-based microarray data analysis and management software developed by Iobion Informatics that allows users to log onto a server, upload their microarray data and perform analysis and project management remotely. GeneTraffic was made by Iobion Informatics (now under Stratagene) and can be accessed thorough Internet Explorer 6.0 or greater on Windows XP.
Many science fairs have a group of people called a Scientific Review Committee (or SRC) that reviews each project application to ensure that all safety and legal requirements will be met and that the appropriate forms have been completed. The committee also reviews the completed project displays. Typically, a Scientific Review Committee is composed of at least three people: a biomedical scientist, a physical scientist, and a science teacher. Some fairs also have an Institutional Review Board (IRB), which reviews all proposed projects that in any way involve human beings. An IRB''s purpose is to ensure that the project will not present undue risk to the subjects.
A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest.
Biological Concept Diagram Editor (BCDE) is a conceptual relationship diagramming tool specifically designed for biomedical researchers. It allows for efficient knowledge and data capture, fast diagram creation, easy data retrieval, and flexible exporting. The BCDE application is the main diagramming tool in the system. Through it, users can create, modify, load, and save BCDE diagrams. The diagrams created with BCDE application are network oriented. Each BCDE figure can be annotated using fields from the BioPAX level II format. In addition, a user can add URL links and attachments to a BCDE figure. Diagrams generated in BCDE are stored in the BCDE XML format for better database integration and better data extraction.
A network of protein-protein, protein-DNA and modulatory interactions in human B cells. The network contains known interactions (reported in public databases) and predicted interactions by a Bayesian evidence integration framework which integrates a variety of generic and context specific experimental clues about protein-protein and protein-DNA interactions with inferences from different reverse engineering algorithms, such as GeneWays and ARACNE. Modulatory interactions are predicted by the MINDY, an algorithm for the prediction of modulators of transcriptional interactions (please refer to the publication section for more information). The BCI can be downloaded as one tab delimited file containing the complete network (BCI.txt) with each type of interaction explicitly defined.
Company that provides healthcare and develops tools for the prevention, diagnosis, and treatment of disease. Its domains include radiology, cardiology, oncology, critical care, women's health, and other fields.
JIV: A 3D Image Data Visualization and Comparison Tool
JIV is a Java software for visualization and side-by-side comparison of multiple 3D image datasets. While it was originally designed for remote data access, it can be used as a traditional local application as well. It features include being highly portable and platform-independent, the ability to run with a common Web browser and to cope with slow network links, an independent 3D image data format, and a display of gray-level (intensity) image data with a user-controlled color-mapping, among other features.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 19, 2012. CTI is a technology company that is continuously learning, adapting, and adopting. CTI has a strong advantage in creative thinking in the use and development of technology. You will see CTI in your new homes with home automation, and smart home technology. CTI will continue to progress Internet in Central Illinois with faster Internet service. You will see CTI launching services such as CTI Remote Backup Service and CTI Vehicle Management Service. In short, by keeping up with technology, CTI will help their customers continue to use technology more efficiently.
Oracle''s complete, open, and integrated product strategy provides flexibility and choice to our customers across their IT infrastructure. Now, with Sun server, storage, operating-system, and virtualization technology, Oracle is the only vendor able to offer a complete technology stack in which every layer is integrated to work together as a single system. Oracle''s open architecture and multiple operating-system options gives our customers unmatched benefits, including excellent system availability, scalability, energy efficiency, powerful performance, and low total cost of ownership Starting more than 30 years ago with Oracle''s innovative relational database, the Oracle stack today includes Oracle Enterprise Linux, Oracle VM, Oracle Fusion Middleware, and the largest and most complete set of industry and business applications software on the market. The addition of Sun storage and systems technology makes the Oracle stack complete. Oracle integrates every layer of the IT stack to deliver compelling value, based on high system availability and security, stunning performance, and low TCO. Only Oracle can offer this stack advantage to its customers through deep and seamless integration between the tiers that our competitors cannot match.
Gene Interaction Extraction from the Literature
GIN-IE is a high precision system for extracting protein/gene interactions, interaction cue words, and directionality from the literature. Syntax-aware inferences about the roles of the entities are made by using the syntactic and dependency parse tree structures of the sentences. Negation and speculation are frequently occurring language phenomena that modify the factuality of the information contained in text. GIN-IE detects and distinguishes interactions that are extracted from negated or speculative sentences. GIN-IE has been integrated with the NCIBI PubMed daily update and processing pipeline. The extracted interactions are accessible through MimiWeb.
This project is the SimTK Core implementation of the extremely reliable, high speed linear algebra package LAPACK and the underlying BLAS library on which LAPACK is built. It uses ATLAS to generate hand tuned BLAS kernels for a variety of hardware platforms, including multiprocessors, using a variety of operating systems including Windows, Mac, and Red Hat Linux. These platforms are pre-built and make the binaries available as a single shared library which can be conveniently used by any program. This means that users who are not experts in high performance scientific computation can nonetheless use the fastest linear algebra methods available for their machines.
A commercial software for computerized physician order entry and electronic health record system (EHR) enhancements for data analysis, along with other software products and services.
Protein Subcellular Location Image Database
PSLID - Protein Subcellular Location Image Database
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. Annotated database of fluorescence microscope images depicting subcellular location proteins with two interfaces: a text and image content search interface, and a graphical interface for exploring location patterns grouped into Subcellular Location Trees. The annotations in PSLID provide a description of sample preparation and fluorescence microscope imaging.
Software application that is a faster version of SLINK (entry from Genetic Analysis Software)
Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package. It contains twelve individual programs, each with their own function.
QuadraMeds Computerized-Patient Record (QCPR) helps healthcare facilities achieve meaningful use and qualify for ARRA stimulus funds by providing a robust, EHR solution that integrates every aspect of patient care into a single, confidential, computer-based patient record. Benefits: -Streamlines administrative functions -Delivers CPOE with integrated, clinical-decision support -Supports the Six Rights with integrated medication management -Improves clinical workflow processes throughout the continuum of care
STRIDE Anonymous Biospecimen Search Tool
STRIDE J2EE-based biospecimen registration management tracking and distribution system
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7th, 2023. An online, searchable record of biospecimen attributes and storage location for the following three biobanks at Stanford: * The Bone Marrow Transplant (BMT) program * The Hematology biospecimen bank is a research sample repository focusing on blood, plasma and bone marrow, primarily from leukemia patients. * Cancer Center Pathology Core: The Stanford Comprehensive Cancer Center Tissue Bank stores research samples of both solid tumor and blood from cancer patients, with an emphasis on prostate. As of November 2009, the system contains data on 50,000 biospecimens stored in multiple banks at Stanford. An anonymous Biospecimen Locator allows Stanford researchers to search the STRIDE Virtual Biospecimen Bank for suitable samples without having to know, or expose, any protected patient-specific information. Having determined that suitable specimens exist in one of the constituent biospecimens banks, the researcher can generate a Web-based request form to obtain additional information from the appropriate bank operator(s). Access to specimens is restricted to Stanford Faculty and Staff or affiliates., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A commercial organization that suppplies software which creates separate HIPAA-compliant repositories of de-identified patient records and reports. This software allows clinicians, researchers, and administrative leadership to safely access, search, share, and analyze de-identified patient-level data. DE-ID can be acquired as stand-alone tool or integrated with data networks or clinical information systems.
DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast, accurate, and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions. DelPhi takes as input a coordinate file format of a molecule or equivalent data for geometrical objects and/or charge distributions and calculates the electrostatic potential in and around the system, using a finite difference solution to the Poisson-Boltzmann equation. DelPhi is a versatile electrostatics simulation program that can be used to investigate electrostatic fields in a variety of molecular systems. Features of DelPhi include solutions to mixtures of salts of different valence; solutions to different dielectric constants to different regions of space; and estimation of the best relaxation parameter at run time.
Designed to identify Driver Genes and Pathways in cancer genome sequencing studies.
A pipeline for ranking nonsynonymous single nucleotide variants given a specific phenotype.
A robust, secure, medical-grade, web application that lives in the cloud and has the ability to analyze and annotate entire human genomes in a rapid and cost-effective way.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Commercial software vendor.
PathoNet is a virtual meeting place for pathologists from all over the world. They can use it as a virtual pathology laboratory in which they can exchange their views on their cases. Join us and share your experience. Special or rare cases maybe very useful in the diagnostic practice. Everybody who would like to use digital microscopy in human, veterinary or forensic pathology; in laboratory medicine, in human anatomy; in experimental research, and when teaching can benefit from this resource. Additionally, practicing physicians, students, tutors, experts and researchers can all contribute and benefit from PathoNet. Sponsors: This resource is supported by 3DHISTECH Ltd.
The images in this collection are derived from high resolution scans of glass 3.25 X 4 inch lantern slides that were part of a large collection of slides covering his years at the Rockefeller University and Yale University School of Medicine. These selected images were scanned by James D. Jamieson, M.D., Ph.D., a student of Palade. The images also include some of the earliest electron micrographs taken by collaborators of George Palade both at the Rockefeller University (1945 - 1973) and at Yale (1973 - 1990). They include micrographs taken by Professor Marilyn Farquhar, Ph.D., whose studies elucidated the function of the glomerular basement membrane in renal filtration. There are 5 ways to find information in this collection: search for particular words that appear in the text by clicking the Search button; browse documents by Title by clicking the Titles button; browse documents by Subject by clicking the Subjects button; browse documents by Creator by clicking the Creators button, and browse documents by References by clicking the References button. Sponsors: This collection is the result of a collaboration between James D. Jamieson, M.D., Ph.D., Professor, Dept. of Cell Biology, and Arthur R. Belanger, OBE, Systems Manager, Harvey Cushing/John Hay Whitney Medical Library, both at the Yale University School of Medicine.
Quertle: Relationship-Driven Biomedical Search
Quertle is a biomedical search engine focused on delivering informative results to biomedical researchers using advanced linguistic technologies, along with an in-depth understanding of the biomedical field. Quertle''s friendly interface makes it simple to search and refine results. Using advanced semantics, Quertle finds quality results, not just long lists. And it hods: all of PubMed, a growing number of full-text documents, news, and more. Features: :- Find Relationships, not Just :- Focus on Core Concepts: Since Quertle searches for Relationships, all the terms in your query must be found together in a meaningful way. Thus, Quertle immediately gives you results with more relevance. :- Unleash the Strength of Power Terms: Use Power Terms to search for categories of objects. For instance, you can use Protein to search for any protein, rather than the occurrence of the term, protein. View all Power Terms. :- Search Full-text Documents: The Quertle search engine has been optimized to search full-text documents, including the Material and Methods section (but not the Bibliography). :- Use Real Biology & Chemistry Terms: Quertle recognizes capital TWIST as the transcription factor (not the verb), and capital NO as nitrous oxide(not a negative). So, use proper capitalization in your query, and you won''t be lost in a sea of irrelevant results. :- Look for the Quertle Difference on the Results Page : More relevant results : Easy filtering and breadcrumb tracking : Automatic identification of key concepts : Single-click access to PDFs of full-text documents :Keyword: Biomedical, Search engine, Database, Researcher, Linguistic, Technology, Semantic, Relationship, Protein, Biology, Chemistry, :
BrainU: The Neuroscience Teacher Institute
A neuroscience training program for Minnesota students and teachers. It provides teachers with three years of neuroscience training, materials, and staff support to bring brain science to their students. In these professional workshops, participants receive updates on the latest in neuroscience research -- discussion is complemented with hands-on activities and lab work. Teachers also receive curriculum materials to aid them in using neuroscience topics in support of Minnesota Intermediate and Middle Level standards. The program was expanded in 2008 to include high school teachers.
Stanford/VA Aging Clinical Research Center
Portal for gerontology research with a variety of clinical, research and educational programs, with the aim of improving the lives of those affected by Alzheimer's Disease and memory losses associated with normal aging. The Center investigates the nature of Alzheimer's Disease, its progression over time, its response to treatments, and problems patients and caregivers experience in dealing with the changes that occur. It also conducts studies that look at changes that occur over the course of normal aging and have a Normal Aging Brain Donor Program. The Aging Clinical Research Center puts out a newsletter that showcases various projects and includes informative articles on dementia.
The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Bacteria, which houses bacterial species. All bacterial collections in Ensembl Bacteria have been updated with the latest data from ENA and UniProtKB. New genomes have been added to Escherichia/Shigella (3 additional genomes) and Staphylococcus (3 additional genomes). The mapping of array probes has been expanded to all genomes in the Escherichia/Shigella and Staphylococcus collections. Ensembl Bacteria also now features improved interfaces for selecting regions of circular molecules a new visualisation allowing the large scale comparison of multiple genomes. In multi-synteny view, users can select multiple genomes and observe the syntenic relationships between them. Sponsors: EnsembBacteria is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute.
Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Plants, which houses plant species. Sponsors: EnsembPlants is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute.
The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Fungi, which houses fungal species. Sponsors: EnsembFungi is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute.
The Finite Element ToolKit (FETK) is a collaboratively developed, evolving collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE). The FETK libraries and tools are written in an object-oriented form of ANSI-C and in C , and include a common portability layer (MALOC) for all of FETK, a collection of standard numerical libraries (PUNC), a stand-alone high-quality surface and volume simplex mesh generator (GAMer), a stand-alone networked polygon display tool (SG), a general nonlinear finite element modeling kernel (MC), and a MATLAB toolkit (MCLite) for protyping finite element methods and examining simplex meshes using MATLAB. The entire FETK Suite of tools is highly portable (from iPhone to Blue Gene/L), thanks to use of a small abstraction layer (MALOC) and heavy use of the GNU Autoconf infrastructure. The primary FETK ANSI-C software libraries are: :- MALOC is a Minimal Abstraction Layer for Object-oriented C/C programs. :- PUNC is Portable Understructure for Numerical Computing (requires MALOC). :- GAMer is a Geometry-preserving Adaptive MeshER (requires MALOC). :- SG is a Socket Graphics tool for displaying polygons (requires MALOC). :- MC is a 2D/3D AFEM code for nonlinear geometric PDE (requires MALOC; optionally uses PUNC GAMER SG). Application-specific software designed for use with the FETK software libraries is: :- GPDE is a Geometric Partial Differential Equation solver (requires MALOC PUNC MC; optionally uses GAMER SG). :- APBS is an Adaptive Poisson-Boltzmann Equation Solver (requires MALOC PUNC MC; optionally uses GAMER SG). :- SMOL is a Smoluchowki Equation Solver solver (requires MALOC PUNC MC; optionally uses GAMER SG). MATLAB toolkits designed for use with MC and SG or as standalone packages: :- MCLite is a simple 2D MATLAB version of MC designed for teaching. :- FEtkLAB is a sophisticated 2D MATLAB adaptive PDE solver built on top of MCLite. Related packages developed and maintained by FETK developers (included in PUNC above): :- PMG is a Parallel Algebraic MultiGrid code for general semilinear elliptic equatons. :- CgCode is a package of Conjugate gradient Codes for large sparse linear systems. Sponsors: This resource is developed and supported by the MCP Research Group at the UCSD Center for Computational Mathematics.
Biomedical Search: Medical Research and Health Resources
BioMedSearch is a biomedical search engine that contains NIH/PubMed documents, plus a large collection of theses, dissertations, and other publications not found anywhere else for free, making it the most comprehensive free search on the web. :Besides free-form search, users can search based on Author, Journal Title, Publication Date, the Language in which the article was published (many non-English articles have English language abstracts), MeSH (Medical Subject Headings) and more. : The goal of BioMedSearch.com is to provide free access to a massive collection of authoritative documents relating to the biomedical field. Our mission is to make these important works available to the community in a way that is fast and easy, while still offering the advanced features demanded by power users such as portfolios, collaboration features, bibliographical citation export, alerts, and more. Whether you are doctor, scientist, or someone interested in researching a medical topic out of personal interest, BioMedSearch aggregates a vast number of authoritative documents in one place to make finding medical information easy, fast and free.
Service that allows you to process CEL files from Affymetrix, Inc. GeneChip Exon 1.0 ST Arrays to identify alternative splicing.
Rat Genome Database: Neurological Disease Portal
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools.
Tools for the integration of data from various sources (public and confidential), for the generation and validation of computer models for toxic effects, libraries for the development and seamless integration of new algorithms, and scientifically sound validation routines. The goal of OpenTox is to develop an interoperable predictive toxicology framework which may be used as an enabling platform for the creation of predictive toxicology applications. OpenTox is relevent for users from a variety of research areas: Toxicological and chemical experts (e.g. risk assessors, drug designers, researchers) computer model developers and algorithm developers non specialists requiring access to Predictive Toxicology models and data OpenTox applications can combine multiple web services providing users access to distributed toxicological resources including data, computer models, validation and reporting. Applications are based on use cases that satisfy user needs in predictive toxicology. OpenTox was initiated as a collaborative project involving a combination of different enterprise, university and government research groups to design and build the initial OpenTox framework. Additionally numerous organizations with industry, regulatory or expert interests are active in providing guidance and direction. The goal is to expand OpenTox as a community project enabling additional expert and user participants to be involved in developments in as timely a manner as possible. To this end, our mission is to carry out developments in an open and transparent manner from the early days of the project, and to open up discussions and development to the global community at large, who may either participate in developments or provide user perspectives. Cooperation on data standards, data integration, ontologies, integration of algorithm predictions from different methods, and testing and validation all have significant collaboration opportunities and benefits for the community. OpenTox is working to meet the requirements of the REACH legislation using alternative testing methods to contribute to the reduction of animal experiments for toxicity testing. Relevant international authorities (e.g., ECB, ECVAM, US EPA, US FDA) and industry organizations participate actively in the advisory board of the OpenTox project and provide input for the continuing development of requirement definitions and standards for data, knowledge and model exchange. OpenTox actively supports the development and validation of in silico models and algorithms by improving the interoperability between individual systems (common standards for data and model exchange), increasing the reproducibility of in silico models (by providing a quality source of structures, toxicity data and algorithms) and by providing scientifically sound and easy-to-use validation routines. OpenTox is committed to the support and integration of alternative testing methods using in vitro assay approaches, systems biology, stem cell technology, and the mining and analysis of human epidemiological data. Hence the framework design must take into account extensibility to satisfy a broad range of scientific developments and use cases.
The Disease Ontology group has developed a set of standard representations of phenotypes associated with diseases useful in bioinformatics applications. These are formalized into an ontological structure and are encoded in OWL. Neurodegenerative diseases have a wide and complex range of biological and clinical symptoms. While neurodegenerative diseases share many pathological features in common, they also contain unique signatures. Animal models of these disorders are key to translational research. However, animal models typically replicate only a subset of disease features or display features that are only indirectly related to a given disorder, whose relationship to the human condition may be across several diseases. Matching animal models to human diseases is therefore a significant informatics challenge. We have been working to develop ontologies that capture essential features of neurodegenerative diseases and associated animal models in a way that allows more flexible matching of animal models to human disorders and in a way that makes explicit commonalities and differences among animal models and human neurodegenerative disease. Creating ontologies for diseases and disorders is a very challenging task (Gupta et al., 2003) because of the complexity of the disorders and because of the limitations of current ontology formalisms. In order to simplify the approach and make it practical for use in information systems, we have focused on formal descriptions of phenotypes associated with diseases and animal models rather than on a formal model of the disease process itself. We employ the modular ontologies developed as part of the Neuroscience Information Framework (NIF: http://nif.nih.gov) and the Phenotype and Trait Ontology (PATO), an ontology of qualities associated with biological phenotypes, to create a flexible template for creating phenotypic statements at the class and instance levels. We show how these phenotypes can be used to look for commonalities across multiple neurodegenerative conditions and animal models.
ADAPT: A Database of Affymetrix Probesets and Transcripts
Library of many-to-many relationships between Affymetrix probesets transcripts and genes, by directly mapping every probe against publicly available mRNAs/cDNA sequences from RefSeq and Ensembl. You can search the database by AffymetrixProbeset ID, Transcript Accession, Gene Symbol or Gene Accession. Currently, the ADAPT database holds information on 23 Array Types containing 255771 unique Probesets, that themselves map onto 252788 entries in both RefSeq and Ensembl. ADAPT is clusterable, cross platform, runs on any Java Virtual machine after version 1.4, and utilises the following software: :- Apache Tomcat :- Apache Struts :- JBoss Application Server :- Postgresql Sponsors: ADAPT has been written with funding by Cancer Research UK. Keywords: Database, Gene, Transcript, Mapping, Probe, mRNA, cDNA, Sequence, Association, Array, Probeset,
Molecular Brain: Transcription Profiles of Mouse and Human Brains
MolecularBrain is an attempt to collect, collates, analyze and present the microarray derived gene expression data from various brain regions side by side. Transcription Profile of any gene in Mouse (online) and Human Brain (not yet) can be accessed as a histogram along with links to access various aspects of that gene. The expression levels were calculated from microarray data deposited at GEO (Gene expression omnibus). The molecular brain database could be searched using the built in search tool with the terms Entrez GeneID, gene symbol, synonym or description. Gene information along with their expression values can be also accessed from the alphabetical list of gene symbols on the footer. The protocol and GEO sample information is available.
International Observatory on Neuro-Information
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The International Observatory on Neuro-Information is the central source of knowledge, research and data on all skills and issues for Neuroscience applied in Information Sciences. It is an initiative of the Documentation Sciences Foundation, from Spain, which aims to gather information, express opinions, prepare documents, make comparative research, support and promote policy-making, evaluate trends, and take other appropriate action relating to the Neuroscience and its application to the Information Sciences (Libraries, Archives, Documentation centers), and how the traditional knowledge of Information Sciences can bring expertise in data visualization and retrieval techniques, records management, quality assurance and usability in Neuroscience. The Observatory may work together, or in agreement with other national or international organizations pursuing similar or compatible aims.
Database for Sharing Aging Research Models
Database for Sharing Aging Research Models (D-SARM)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 18, 2014. A networking site for investigators using animal models to study aging, developed to provide a venue for sharing information about research models for aging studies. If you have tissue or data from animal models relevant to aging research that you are willing to share with other investigators, D-SARM allows you to identify the model and provides a secure, blinded email contact for investigators who would like to contact you about acquiring tissue or related resources. Investigators looking for resources from a particular model enter search terms describing the model of interest and then use the provided link to send emails to the contacts (names blinded) listed in the search results to initiate dialog about tissue or resources available for sharing. The database is housed on a secure server and admission to the network is moderated by the NIA Project Officer and limited to investigators at academic, government and non-profit research institutions. The goal is to provide a secure environment for sharing information about models used in aging research, promoting the sharing of resources, facilitating new research on aging in model systems, and increasing the return on the investment in research models.
The BioInformatics Resource Inventory (B.I.R.I.) is a public online searchable index of bioinformatics resources developed at the Biomedical Informatics Group. Information describing the resources has been automatically extracted from the literature and indexed using Natural Language and Text Mining techniques. The index is automatically updated by analyzing new papers describing existing resources (databases, tools, services). Sponsors: BIRI is supported by the Biomedical Informatics Group, Spain. Keywords: Resource, Bioinformatics, Inventory, Searchable, Database, Index, Biomedical, Literature, Language, Mining, Analysis, Tool,
The purpose of this database is to make it easy for psychology students (and also researchers and journalists) to find and discuss: peer-reviewed articles on scientific psychology, that don''t require a paid subscription to access, and places on the web where these articles have been discussed/blogged about. There are other excellent sites which do a similar job (e.g., Research Blogging), but this one is aimed at psychology, and specifically at the curriculum covered by psychology students.
The aim of Psychology Page is to provide a concise introduction in a broad range of psychological topics. From Alzheimers disease to Z-scores, from cognitive dissonance to mirror neurons. It is an open resource for students, or for people who are just interested in psychology and science in general. If you click ARTICLES in the navigation bar at the top, you will get an overview of all the articles that have been written so far. For more information on a wide variety of themes in psychology, click LINKS. To get in touch with the webmaster, click CONTACT. Click HOME to return to the homepage. Every article consists of approximately 500 words, so it fits on one page (hence the name of the site). All of them are accompanied by a clarifying picture, a funny cartoon or an interesting video clip. Used references and date are added on the right, as well as related articles. Besides, every article is available for download in a convenient PDF-format. Keywords: Psychology, Alzheimer''s, Disease, Mirror, Neuron, Student, Science,
Genetic and Rare Diseases Information Center
Genetic Rare Diseases Information Center
Genetic and Rare Diseases Information Center (GARD) is a collaborative effort of two agencies of the National Institutes of Health, The Office of Rare Diseases Research (ORDR) and the National Human Genome Research Institute (NHGRI) to help people find useful information about genetic conditions and rare diseases. GARD provides timely access to experienced information specialists who can furnish current and accurate information about genetic and rare diseases. So far, GARD has responded to 27,635 inquiries on about 7,147 rare and genetic diseases. Requests come not only from patients and their families, but also from physicians, nurses and other health-care professionals. GARD also has proved useful to genetic counselors, occupational and physical therapists, social workers, and teachers who work with people with a genetic or rare disease. Even scientists who are studying a genetic or rare disease and who need information for their research have contacted GARD, as have people who are taking part in a clinical study. Community leaders looking to help people find resources for those with genetic or rare diseases and advocacy groups who want up-to-date disease information for their members have contacted GARD. And members of the media who are writing stories about genetic or rare diseases have found the information GARD has on hand useful, accurate and complete. GARD has information on: :- What is known about a genetic or rare disease. :- What research studies are being conducted. :- What genetic testing and genetic services are available. :- Which advocacy groups to contact for a specific genetic or rare disease. :- What has been written recently about a genetic or rare disease in medical journals. GARD information specialists get their information from: :- NIH resources. :- Medical textbooks. :- Journal articles. :- Web sites. :- Advocacy groups, and their literature and services. :- Medical databases.
Neuroscience Online: An Electronic Textbook for the Neurosciences
This is an online, interactive courseware for the study of neuroscience is provided by the Department of Neurobiology and Anatomy at The University of Texas Medical School at Houston. The project is being developed under the direction of the Department Chair and Editor, John H. Byrne. This content is intended to function as an online multimedia resource, and therefore is not supported as a downloadable or printable text.
Software tool for data sharing, incorporating blogs and spatial registration of data. Mainly used in geological data sets. A Virtual Research Environment (VRE) aims to combine the capabilities of two existing technologies that have already seen wide adoption among scientists: - The Godiva2 data visualization system provides a means for scientists to browse interactively in a ''Google Maps-like'' fashion through large environmental datasets, including numerical model outputs and high-resolution satellite imagery, using only a web browser. - The LabBlog is a web-based blogging tool specifically designed for the practising scientist to record, disseminate and evaluate their research. The Blog can also be used as a collaboration tool that allows secure discussion between colleagues. Although initially designed for the use of laboratory chemists, the LabBlog is being adapted in this project to meet the needs of environmental scientists. The BlogMyData VRE will allow scientists to explore data visually using Godiva2, then make comments about features in the data on a blog. Colleagues will discover these blog entries and offer further information, providing answers to research questions through comments. Through RSS and GeoRSS feeds, colleagues, investigators and other interested parties can be notified of research activity, and scientists can discover hitherto-unknown colleagues working with similar data in similar geographic regions. Sponsors: BlogMyData is a collaboration between the Reading e-Science Centre and the University of Southampton and is one of the JISC VRERI projects.
This is a multiscale network diagram of aging pathways, from molecules to organism. The many observable signs of human senescence have been hypothesized by various researchers to result from several primary causes. Close inspection of the biochemical and physiological pathways associated with age-related changes and with the hypothesized causes reveals several parallel cascades of events that involve several important interactions and feedback loops. This network diagram is presented to aid in conceptualizing the many processes and interactions among them, including promising intervention points for therapy development. Environmental effects and proposed interventions are highlighted around the margins of the network. This diagram is maintained on the Web as a reference for researchers and students. Content is updated as new information comes to light. Sponsors: This work has been supported by Legendary Pharmaceuticals. Keywords: Network, Diagram, Human, Cell, Aging, Senescence, Biochemical, Pathway, Physiological, Therapy, Environmental, Researcher, Student,
OpenII (pronounced open-eye-eye) is a freely downloadable, open source information integration (II) tool suite. It includes 1) an extensible, plug-and-play platform for II tools and 2) several tools that assist with common integration tasks, including fully- or semi-automated support in the following scenarios: :- An integration engineer building a data warehouse must determine how diverse component data schemas map to the schema of the warehouse. :- An XML document that conforms to one schema needs to be converted into an equivalent document that conforms to a second (different) schema. :- To support data exchanges, a community needs to create a shared data model based on the models of its members. When a new member joins, the community needs to identify promising data exchange partners, and to what extent its shared model needs to be extended. Similarly, a chief information officer must identify data integration opportunities and make level-of-effort estimates after an acquisition or merger. To support these scenarios, OpenII provides a schema repository into which diverse data models can easily be imported. It also provides tools that 1) assist with identifying semantic correspondences across data models (Harmony), 2) compare a set of data models against a common reference model (Proximity), 3) visually organize a set of data models into clusters of related data models (Affinity), and 4) establish a common data model for a set of inter-related data models (Unity). Why should You use OpenII? Here are some reasons: :- OpenII is the only open-source platform for information integration tools. OpenII and its source code are freely available using the Apache 2.0 license, so you are free to borrow, extend or resell any portions of OpenII. :- The OpenII schema and mapping repository is based on a neutral modeling language. Thus, all of the OpenII tools can be used regardless of the underlying modeling language. For example, Harmony can identify correspondences among an XML schema, a relational database, and an OWL ontology. By comparison, most commercial tools are tied to a particular modeling language. :- OpenII is based on the Eclipse framework. As a result, the environment is already familiar to many programmers. Non-programmers can choose, instead, to use OpenII off-the-shelf without needing to first install Eclipse. :- OpenII is fully extensible. If needed components do not exist, they can be readily added. For example, adding a new importer or exporter is a straightforward task that can be completed in only a few hours. Moreover, each of the tools supports the introduction of new algorithms. And, programmers familiar with the Eclipse environment can add new views with moderate effort. Sponsors: This resource is supported by the MITRE Corporation.
ORCID - Open Researcher and Contributor ID
ORCID: Open Researcher and Contributor ID
Non-profit organization dedicated to solving the author/contributor name ambiguity problem in scholarly communications by creating a central registry of unique identifiers for individual researchers and an open and transparent linking mechanism between ORCID and other current author ID schemes. These identifiers, and the relationships among them, can be linked to the researcher''s output to enhance the scientific discovery process and to improve the efficiency of research funding and collaboration within the research community. The ideal solution is to establish a registry that is adopted and embraced as the de facto standard by the whole of the community. A resolution to the systemic name ambiguity problem, by means of assigning unique identifiers linkable to an individual''s research output, will enhance the scientific discovery process and improve the efficiency of funding and collaboration. The organization brings together the leaders of the most influential universities, funding organizations, societies, publishers and corporations from around the globe and is managed by a fourteen member Board of Directors. A disambiguated set of authors will allow new services and benefits to be built for the research community by all stakeholders in scholarly communication: from commercial actors to non-profit organizations, from governments to universities.
Ask a Biologist is designed as an educational resource for students preK-12, and their teachers and parents. Anyone is welcome to use Ask A Biologist. Keep in mind that it is intended primarily to serve grades preK-12, and to be available as a resource for teachers and parents. They also find that life-long learners enjoy many of the content areas on their web site and encourage anyone interested in biology to make use of the web content. As always, ASU faculty and staff will be accessible through email to their students. Sponsors: Ask A Biologist funded in part by the National Science Foundation and NSDL.
Large-scale archive of normalized digital spatial and functional data with an analytical query mechanism. One of its many applications is the elucidation of brain structure-function relationships. BRAID stores spatially defined data from digital brain images which have been mapped into normalized Cartesian coordinates, allowing image data from large populations of patients to be combined and compared. The database also contains neurological data from each patient and a query mechanism that can perform statistical structure-function correlations. The project is developing database technology for the manipulation and analysis of 3-dimensional brain images derived from MRI, PET, CT, etc. BRAID is based on the PostgreSQL server, an object/relational DBMS, which allows a standard relational DBMS to be augmented with application-specific datatypes and operators. The BRAID project is adding operations and datatypes to support querying, manipulation and analysis of 3D medical images, including: * Image Datatypes: BRAID supports a family of 3D image datatypes, each having an abstract type and an implementation type. Abstract types include boolean (for regions of interest), integer, float, vector (for representing morphological changes), tensor (for representing derivatives and standard deviations of vector images) and color. Implementation types at present include line-segment format and voxel array. * Image Operators: BRAID supports addition of images, multiplication (which is interpreted as intersection for boolean images), coercion of an image''s abstract or implementation type to another value, and determination of volumes of regions of interest. * Statistical Operators: A chi-squared test has been added to SQL as an aggregate operator on pairs of boolean values. * Web Interface: A general-purpose Web gateway allows the results of queries that return computed images to be displayed. You can download the BRAID source code 2.0. This version is developed under postgreSQL 7.3.4., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Institute for Neuroinformatics: Cortex 3D
INI has developed a novel simulation tool, CX3D, for modeling the development of large realistic neural networks such as the neocortex, in a physical 3D space. The development of neural tissue is a complex organizing process, in which it is difficult to grasp how the various localized interactions between dividing cells leads relentlessly to global network organization. Simulation is a useful tool for exploring such complex processes because it permits rigorous analysis of observed global behavior in terms of the mechanistic axioms declared in the simulated model. In CX3D, as in biology, neurons arise by the replication and migration of precursors, which mature into cells able to extend axons and dendrites. Individual neurons are discretized into spherical soma and cylindrical neurite elements that have appropriate mechanical properties. The growth functions of each neuron are encapsulated in set of pre-defined modules that are automatically distributed across its segments during growth. The extracellular space is also discretized, and allows for the diffusion of extracellular signaling molecules, as well as the physical interactions of the many developing neurons. CX3D is a powerful tool for understanding neural development. Sponsors: CX3D has been developed with the support of the SECO EU Project (EU grant 216593). Keywords: Neuinformatics, Cortex, 3D, 3 Dimentional, Neocortex, Physicis, Neural, Tissue, Simulation, Neuron, Structure, Biology, Axon, Dentrite, Soma, Neurite, Development,
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 08, 2014. A multi-disciplinary institute providing specialized diagnostic evaluations, innovative treatments, education and research. It provides a collaborative, team-centered approach to provide innovative diagnostics to assist in developing cutting-edge brain based interventions and treatment strategies to best serve their patient's individual needs. Comprehensive Neuroscience Center is dedicated to working with children and adults who demonstrate neurodevelopmental disorders such as Autism Spectrum Disorders, Attention Deficits Hyperactivity Disorder, Learning Disabilities and Language-based deficits, as well as other neurological-based disorders including Traumatic brain injury, Disorders of Consciousness, Disorders of Aging, Alzheimer's and Dementia.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023.
Centro Nacional de Investigaciones Oncologicas Tumor Bank Network
Centro Nacional de Investigaciones Oncologicas Tumour Bank Network
Spanish National Cancer Center Tumor Bank Network
Spanish National Cancer Centre Tumour Bank Network
Spanish National Cancer Research Center Tumor Bank Network
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The need to use human neoplastic tissue under ideal conditions is currently of particular importance due to the development molecular pathology techniques that allow large-scale studies of genetic expression that are also of clinical significance. The Tumour Bank Network (TBN), instigated and coordinated by the Molecular Pathology Programme (MMP) aims to respond to this need by the promoting of Tumour Banks in Spanish hospitals. This will be achieved through the application of homogeneous procedures for the collection, processing and storage of neoplastic and normal tissue samples in such a way as to make molecular studies possible, avoiding that avoid the intrinsic bias of multi-centre studies possible. These Hospital Tumour Banks are based within the Pathology Departments of the collaborating Hospitals, that are interconnected through a computer-based network. In this way, each Centre''s tissue remains in the Hospital itself, thereby playing a key role in the development of the welfare, teaching and research activities within the Hospital. At the same time, it represents a tool to encourage of multi-hospital cancer research and of cooperation between basic and clinical researchers, constituting important collaboration between biomedical disciplines. The design does not correspond to a Central Tumour Bank, but that of a cooperative and coordinated Network of Hospital Banks, based on simple, homogeneous and optimal tissue treatment protocols. This Network is promoted by the Centro Nacional de Investigaciones Oncologicas (CNIO), which thereby undertakes the work of coordinating the network, using and maintaining the database, adhering to quality control. The aim of the CNIO's TBN is to acquire neoplastic and control non-neoplastic material of all types of malignant neoplasias, in the form of tissue fixed in formalin and paraffin embedded, of samples that are unfixed or frozen according to conventional methods as set out in Annexe 1 and even, exceptionally as fresh tissue. When other types of samples are required to carry out a specific project, the central office of the TBN will draw up a protocol with the group leading the project for the collection and maintenance of the tissue and clinicopathological data required for the proposed research. These protocols will be disseminated among the Associated Hospitals in order to gather the previously agreed number cases. Basic data surrounding the processing and preservation conditions for each case will be sent to the central office of the Bank, which under no circumstances will reveal the identity of the patient. Any Spanish cancer research team will be able to request tissue from the Tissue Bank Network. Absolute priority will be afforded to projects whose principal researcher belongs to one of the Associated Centres of the TNB, to other institutions with special agreements concerning the exchange of samples, and to the CNIO's researchers.
Patent data resources at the EBI contain patent abstracts, patent chemical compounds, patent sequences and patent equivalents. There are various ways of accessing and searching the patent data.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19, 2019. The Functional Catalogue is an annotation scheme for the functional description of proteins of prokaryotic and eukaryotic origin. Taking into account the broad and highly diverse spectrum of known protein functions, the FunCat consists of 28 main functional categories (or branches) that cover general fields like cellular transport, metabolism and cellular communication/signal transduction. The main branches exhibit a hierarchical, tree like structure with up to six levels of increasing specificity. In total, the FunCat version 2.1 includes 1362 functional categories. This general concept was retained since the annotation of the Saccharomyces cerevisiae genome with only 4 revisions and later on also proved to be well suited for the annotation of genomes from different domains of life (Ruepp et al. 2004). The present and previous versions as well as a version mapping file of the FunCat and annotation data of our core projects can be downloaded via FTP. The MIPS Functional Catalogue Database provides a search tool to browse and search the Functional Categories including the FunCat Number, description, EC number, GO number or keywords associated with the categories. All FunCat annotated proteins and the amount of Co-annotated-FunCats can be retrieved starting with a specific category in a selected organism. A statistical survey of the functional distribution of a given set of genes/entries, e. g. a set of genes with up-regulated expression under a certain condition can be retrieved.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Biobehavioral blog on research and medicine as a continuum from biological mechanisms to behavioural phenomena., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A suite of parallel bioinformatics applications based upon a popular open-source Java implementation of MapReduce, Hadoop.
Transcriptome database of acutely isolated purified astrocytes, neurons, and oligodendrocytes. Provides improved cell-type-specific markers for better understanding of neural development, function, and disease.
A biomaterial supply resource containing over 600,000 samples of human tissue, serum, DNA, and RNA. Samples are handled consistently according to validated protocols and each tissue sample comes with detailed demographic information, gold standard clinical diagnostic information, complete drug history, full pathology reports, and complete phenotypic data.
Cliniques Universitaires Saint-Luc Cancer Center Tumor Bank
Cliniques Universitaires Saint-Luc Cancer Centre Tumour Bank
When a patient suffering or thought to be suffering from cancer is cared for, samples are often taken to determine the precise diagnosis and to determine any treatment necessary. After this essential stage of the patient''s care, unused biological material is sometimes left over. This material is an essential and precious tool for research into cancer. For this reason, patients can decide to make the material available to researchers the world over who study either the development mechanism of cancer or the new treatments available. Residual samples are centralized and stored in the Tumor Bank at the Cliniques Universitaires Saint-Luc Cancer Centre. The research carried out on this material primarily benefits cancer patients. It can help improve existing treatments or discover new drugs, and also allows new diagnostic tools to be tested. Any financial profits obtained from assessing the results obtained are entirely reinvested in the work of the Cancer Centre''s Tumour Bank and in new research projects at the Catholic University of Louvain. Using and sharing material, and verification and retrospective analysis of clinical data, all comply with strict rules. As with donations of blood, marrow or organs, an Ethics Committee oversees the operations of the Tumour Bank and research projects. This committee is responsible for ensuring compliance with current Belgian and legal texts, especially those concerning the protection of patient privacy and rights.
Founded in 1997 with the mission to provide a new source of microbial extracts for drug discovery, agrochemical, enzyme, and specialty chemical research. Discovery company pursuing untapped sources of chemical diversity and identifying lead candidates derived from microorganisms for development of new chemical entities.
Virgin Health Bank was developed to meet the needs of families in the UK who are considering banking their baby''s cord blood stem cells and want the support of an ethically motivated cord blood bank committed to delivering high quality service. We provide an HTA licensed state-of-the-art processing and storage service for parents who would like to store the stem cells from their newborn baby''s umbilical cord blood. * Uniquely we offer you a choice of cord blood banking services; your family can choose from our Family Banking service or our Community Banking service. * We empower UK families to make informed decisions about storing their baby''s cord blood stem cells by providing them with accurate and honest information and do not pressure them into buying our services. * Stem cells from our cord blood bank have been used for transplantation by Doctors in the UK''s National Health Service and we''re proud to operate under a license issued to us by the Human Tissue Authority. If you choose our Family Banking service or our Community Banking you will be informed once your baby''s stem cells have been safely collected, tested and stored. If you have chosen our Community Banking service then we will separate the unit into two elements. Your family''s portion of the unit will be treated in exactly the same way as those in our Family Banking service. It is your family''s and nothing will be done to it or with it without your express written permission. We will test the cells to determine the HLA type. Information on the element of the stem cell unit that you have chosen to donate to the community will be included on an international registry alongside those of others. The registry provides real hope to families and individuals afflicted with diseases where cord blood stems cells are approved for treatment. Doctors use this registry as a resource from which they can request donated cord blood for treatments. These are used in circumstances where a tissue typed, donated unit is required rather than the patient''s own. By contributing to the development of this international registry you maximize the availability of stem cells for the treatment of your family and others. By helping others you also help yourself by helping to develop a community stem cell bank from which your own family may benefit.
Software to help selecting up to five oligo probes for each of the DNA sequences you provided for microarray spotting.
University of Miami Brain Endowment Bank
A biomaterial supply resource which collects and disseminates over 1500 brains and links tissue specimens to patient data. The Brain Endowment Bank distributes brain tissue specimens to scientists worldwide who are investigating neurodegenerative and neuropsychiatric diseases, as well as to scientists involved in ongoing studies on the affects of aging. Its overall objective is to support basic and clinical research activities by providing a systematic method for obtaining detailed pre-mortem clinical information, developing procedures for optimizing brain autopsies, cryopreserving neuropathological specimens, and obtaining neuropathological diagnoses after death.
The main goal of PROCURE is to provide science and humanity with means to help prevent and cure prostate cancer a disease which this year alone will be diagnosed in an estimated 25,500 Canadian men and one which will, on average, take the lives of 85 men every week. PROCURE strives to redefine the boundaries of research and knowledge by: * Initiating an on-going dialogue with the public and healthcare community to provide needed information and support through accessible means such as: ** A comprehensive website in French and English ** Lectures and special events ** Free book on prostate cancer * Funding and structuring over time a bank of biological materials and data on men with prostate cancer as well as those at risk of developing the disease. Such a Biobank, as it is known, will accelerate breakthrough scientific discovery. Join our alliance today by informing yourself and loved ones. Encourage the other men you care about to have an examination. Make a contribution to our cause. Help us keep information on this site up-to-date. In doing so you will become part of the force against prostate cancer!
A collection of tissue and related clinical data for breast cancer. The Bank stores three types of information on each case within a secure location in CancerCare Manitoba. This information relates to the tissue, clinical, and follow-up information. Tissue information includes the composition of the tissue, the size and type of tumor. Clinical information includes the patient age, clinical symptoms and the results of clinical tests such as x-rays. Follow-up information includes the type of treatment after surgery and the response to this treatment. The Bank provides an important resource both for breast cancer research at the University of Manitoba and for researchers across Canada and internationally. Researchers are charged to cover the costs of storage and release but no tissue or information is sold. The Bank has supported over 50 research studies on breast cancer across North America and Europe. Information is never released from the Bank with any label that might allow it to be traced to an individual. Information is only released as part of a set of anonymized cases, where each case is labeled by an anonymous tumor bank number and consists of a section of tissue with related information. Researchers can apply to study these cases only through a review process and if they obtain approval for their research project from an institutional ethics review board. If approved, researchers are provided with tissue sections and the related clinical information from a set of typically 100 or more ����??cases����??. These cases are carefully selected from the computer database on the basis of selection criteria such as size and type of tumor that are relevant to the research question under study. During the assessment of each breast biopsy specimen small tissue samples are taken by Pathologists to process and examine under a microscope and these samples are then stored as a ����??clinical archive����??. After all diagnosis has been completed the Bank organizes these tissues and related clinical data into ����??cases����?? for both future research and future clinical purposes and stores these ����??cases����?? in CancerCare Manitoba. All cases are distinguished by a Tumor Bank number but are anonymous due to the absence of any tag that might allow it to be traced to an individual patient.
Non profit organization and informational portal directed towards patients and families. AFA is an umbrella orgnization uniting over 1600 member organizations to collaborate on education, resources, best practices and advocacy. AFA provides several grant opportunities for AFA's nonprofit member organizations and to individuals in need.
USC Geriatric Studies Center/Alzheimer's Disease Research Center
The USC Geriatric Studies Center includes the State of California Alzheimer's Research Center of California and the National Institute of Aging funded clinical program of the USC Alzheimer's Disease Research Center. It is staffed by USC faculty and physicians with expertise in Alzheimer's disease and age related memory loss. The Center provides evaluation, diagnosis and treatment recommendations, referral to caregiver services and support groups, and the opportunity to participate in clinical drug trials for memory problems.
A collection of brain tissue from individuals suffering from schizophrenia, bipolar disorder, depression, anxiety disorders, and substance abuse, as well as healthy individuals. The research mission of the NIMH Brain Bank is to better understand the underlying biological mechanisms and pathways that contribute to schizophrenia and other neuropsychiatric disorders, as well as to study normal human brain development.
Mayo Alzheimer's Disease Research Center
Mayo Clinic Alzheimer's Disease Research Center
A clinical research department that specializes in the study of Alzheimer's disease. The Mayo Clinic Alzheimer's Disease Research Center conducts many types of research studies related to dementia, as well as normal or successful aging. The purpose of the center is to provide care for dementia patients and promote research and education on Alzheimer's Disease and related dementias.
NIMH Intramural Research Program Clinical Brain Disorders Branch
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. A multidisciplinary neuroscience laboratory in which basic and clinical scientists work side by side exploring neural mechanisms and models of mental and cognitive function and of neuropsychiatric illness. Experiments are performed at many levels of inquiry, from basic molecular biology of the gene to clinical examinations of patients. A major area of investigation of this laboratory is the genetic mechanisms implicated in the pathogenesis of schizophrenia and its treatment. The laboratory is organized as a multi-disciplinary team of investigators with a common mission: to identify and fully characterize basic genetic and neurobiological mechanisms of schizophrenia and related cognitive and emotional disorders. The various components of this effort are centered various different units or divisions represented by groups of investigators, at various levels of training and experience, working on related experiments. The Director of the Branch and of the Genes, Cognition and Psychosis Program (GCAP) is Daniel R. Weinberger, M.D. The CBDB is the principle research laboratory in the created (2003) Genes, Cognition, and Psychosis Program (GCAP) of the NIMH. After twelve years of residing on the pastoral grounds of St. Elizabeths Hospital, in Southeast Washington, CBDB moved back to the main NIH campus in Bethesda, Maryland in 1998. While the unique setting of St. Elizabeths is irreplaceable, we have occupied beautiful new laboratories and clinic spaces that were created for us, and we are in the mainstream of NIH life., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Established in 2002, Angioma Alliance is a patient-driven, non-profit patient advocacy organization. Our mission is to inform and support individuals affected by cerebral cavernous malformations while facilitating improved diagnosis and management of the illness through education and research. We are dedicated to improving the lives of those affected by cavernous angioma. There are many needs that we have been addressing together. First and foremost, people diagnosed with cavernous angiomas have needed more information and a way to talk to others who have the illness. Physicians are frequently unfamiliar with the disease. Internet information has been scarce and technical, and until Angioma Alliance there had been no active internet forums. Many of us have never known anyone else with the illness. Angioma Alliance''s website, peer support program, patient literature, family conferences, and medical convention exhibits have been providing vital information and opportunities for support to those of us affected by cavernous angioma and to the physicians who care for us. Second, we have needed to increase if the public awareness of cavernous angioma. Third, we have needed a way to connect with the research community. Angioma Alliance can be as active and effective as those who choose to volunteer. If you or a family member or friend is affected by cavernous angioma, please consider joining us in our effort.
H. Lee Moffitt Cancer Center & Research Institute
H. Lee Moffitt Cancer Center and Research Institute
H. Lee Moffitt Cancer Center & Research Institute has made a lasting commitment to the prevention and cure of cancer, working tirelessly in the areas of patient care, research and education to advance one step further in fighting this disease. As part of an elite group of National Cancer Institute (NCI) Comprehensive Cancer Centers, Moffitt focuses on the development of early stage translational research aimed at the rapid translation of scientific discoveries to benefit patient care. Since the first patient admission in October 1986, Moffitt physicians, scientists and staff members have worked together to establish a tradition of excellence offered in an atmosphere characterized by kindness, caring and hope. The Cancer Center''s future growth in clinical care and research rests firmly on this tradition and makes possible the changes ahead. The mission of Moffitt Cancer Center is to contribute to the prevention and cure of cancer. Moffitt''s vision is to be the leader in scientific discovery and translation into compassionate care, cures, and prevention of cancer for our community and the world. As it grows to fulfill its mission, the Cancer Center will continue to be distinguished by its compassionate and effective patient care. Moffitt Cancer Center is a not-for-profit institution. It includes private patient rooms, the Southeast''s largest Blood and Marrow Transplant Program, outpatient treatment programs that record more than 320,500 visits a year, the Moffitt Research Center, Moffitt Cancer Center at International Plaza and the Lifetime Cancer Screening & Prevention Center.
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. CarePath was founded for inducing change and delivering evidence based care in America that can lead to better medical outcomes for seriously ill and reduction in cost of care. The initial focus of CarePath is on traumatic brain injury CarePath is now working with several states and many of the leading trauma hospitals on the implementation of evidence-based treatment guidelines on behalf of traumatic brain injured patients in order to dramatically improve patient outcomes and reduce the need for long term care.
A cross-national data archive located in Luxembourg that contains two primary databases: the Luxembourg Income Study Database (LIS Database) includes income microdata from a large number of countries at multiple points in time. The newer Luxembourg Wealth Study Database(LWS Database) includes wealth microdata from a smaller selection of countries. Both databases include labor market and demographic data as well. Our mission is to enable, facilitate, promote, and conduct cross-national comparative research on socio-economic outcomes and on the institutional factors that shape those outcomes. Since its beginning in 1983, the LIS has grown into a cooperative research project with a membership that includes countries in Europe, North America, and Australia. The database now contains information for more than 30 countries with datasets that span up to three decades. The LIS databank has a total of over 140 datasets covering the period 1968 to 2005. The primary objectives of the LIS are as follows: * Test the feasibility for creating a database containing social and economic data collected in household surveys from different countries; * Provide a method which allows researchers to use the data under restrictions required by the countries providing the data; * Create a system that allows research requests to be received from and returned to users at remote locations; and * Promote comparative research on the social and economic status of various populations and subgroups in different countries. Data Availability: The dataset is accessed globally via electronic mail networks. Extensive documentation concerning technical aspects of the survey data, variables list, and the social institutions of income provision in member countries are also available to users through the project Website. * Dates of Study: 1968-present * Study Features: International * Sample Size: 30+ Countries Link: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00150
CTSpedia: A Knowledge Base for Clinical and Translational Research
CTSpedia is a national effort to collect wisdom, tools, educational materials, and other items useful for clinical and translational researchers and to provide timely and useful advice to clinical and translational researchers with specific problems. The CTSpedia is a collaborative vehicle for the CTSA''s Biostatistics/Epidemiology/Research/Design (BERD) Online Resources and Education taskforce to identify and share resources across the national consortium and community researchers world-wide. With the support of the national BERD consortia, the project obtained funding and support from the National Center for Research Resources (NCRR) to expand the original scope and content of CTSpedia and foster collaboration amongst CTSAs. The main goal of CTSpedia.org is to create a definable academic home on the internet for the discipline of clinical and translational sciences across the country and the world. * While the CTSA consortium serves the onsite physical level of the institutions involved, CTSpedia.org seeks to fill the gaps where the network is lacking, and to augment that network as the central hub for the peer to peer sharing of knowledge and resources. * While the CTSA national scope comes to fruition, the international scope of the consortia is more readily facilitated with an online resource like CTSpedia. * Utilizing the collaborative nature of the wiki-style website, CTSpedia.org allows for researchers anywhere in the world to ask questions and receive answers and related information in a timely and efficient manner, overcoming the logistical issues of distance and scheduling. * The streamlined availability of an online resource and knowledge repository will aid in addressing common issues that arise in clinical research, which will filter out consultation requests for minor questions, allowing for CTSA consultants to address more prevalent consultations.
A permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations.
INTRuST Posttraumatic Stress Disorder and Traumatic Brain Injury Clinical consortium
Post-traumatic Stress Disorder / Traumatic Brain Injury Clinical Consortium
The overarching goal of the Post-traumatic Stress Disorder / Traumatic Brain Injury (PTSD / TBI) Clinical Consortium is to combine efforts of the nation''s leading Investigators to bring to the market novel treatments or interventions that will ultimately decrease the impact of military-relevant psychological health problems and TBI. Working together we hope to improve the function, wellness, and overall quality of life for Service members, as well as their families, caregivers, and the American public. Our vision is to design and conduct a series of innovative coordinated clinical trials that are characterized by: * Scientific excellence * State-of-the-art methodology in prevention, detection and treatment * Advanced translational research that will inform future therapies * Dignity and respect for all stakeholders Funding Trials Coming Soon: We anticipate about 10 trials of novel approaches for the treatment of PTSD, TBI, and their combination. Current Trials: * A PILOT SAFETY and FEASABILITY STUDY of HIGH DOSE LEFT PREFRONTAL TRANSCRANIAL MAGNETIC STIMULATION (TMS) to RAPIDLY STABILIZE SUICIDAL PATIENTS with PTSD or TBI, or BOTH. * THE EFFECT of TELEPHONE FOLLOW-UP on OUTCOME for SERVICE MEMBERS with MILD TBI / PTSD * A PROOF-OF-CONCEPT, DOUBLE-BLIND, RANDOMIZED, PLACEBO-CONTROLLLED STUDY of GANAXOLONE in POSTTRAUMATIC STRESS DISORDER
A listing of grants and other funding types to support health research, programs and scholarship. Funding sources most frequently listed on ScanGrants include those of private foundations, corporations, businesses, and not-for profit organizations. Finding and listing less traditional funding opportunities is also a priority. Federal and state funding sources are typically not included on ScanGrants because they are readily available on other sites (e.g., www.grants.gov). The funding sources listed on ScanGrants may be of interest to virtually anyone associated with the health field medical researchers, social workers, nurses, students, community-based health educators, academics and others. They include grants, scholarships, fellowships, prizes for scientific achievement or distinguished service, travel awards to professional meetings, abstract, essay and poster awards among other sources of funding. ScanGrants is a free resource that lists funding opportunities for researchers and students at many stages of their research projects or careers. Examples include: poster awards for completed projects; travel grants that could help finance trips to meetings that would enable you to discuss with peers in your field projects you are contemplating undertaking or in the midst of; calls for nominations for science prizes you could nominate colleagues you admire for; and announcements of funding for programs for violence or disease prevention. We invite you to give ScanGrants a try. If you would like your grant or scholarship announcement reviewed for possible posting on ScanGrants, please fill out the form with your name, email address, link to the original online listing of the funding opportunity, the title of the grant or scholarship and as much additional detail as possible.
An information extracting and processing package for biological literature that can be used online or installed locally via a downloadable software package, http://www.textpresso.org/downloads.html Textpresso's two major elements are (1) access to full text, so that entire articles can be searched, and (2) introduction of categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., methods, etc). A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. The Textpresso project serves the biological and biomedical research community by providing: * Full text literature searches of model organism research and subject-specific articles at individual sites. Major elements of these search engines are (1) access to full text, so that the entire content of articles can be searched, and (2) search capabilities using categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or identify one (e.g., cell, gene, allele, etc). The search engines are flexible, enabling users to query the entire literature using keywords, one or more categories or a combination of keywords and categories. * Text classification and mining of biomedical literature for database curation. They help database curators to identify and extract biological entities and facts from the full text of research articles. Examples of entity identification and extraction include new allele and gene names and human disease gene orthologs; examples of fact identification and extraction include sentence retrieval for curating gene-gene regulation, Gene Ontology (GO) cellular components and GO molecular function annotations. In addition they classify papers according to curation needs. They employ a variety of methods such as hidden Markov models, support vector machines, conditional random fields and pattern matches. Our collaborators include WormBase, FlyBase, SGD, TAIR, dictyBase and the Neuroscience Information Framework. They are looking forward to collaborating with more model organism databases and projects. * Linking biological entities in PDF and online journal articles to online databases. They have established a journal article mark-up pipeline that links select content of Genetics journal articles to model organism databases such as WormBase and SGD. The entity markup pipeline links over nine classes of objects including genes, proteins, alleles, phenotypes, and anatomical terms to the appropriate page at each database. The first article published with online and PDF-embedded hyperlinks to WormBase appeared in the September 2009 issue of Genetics. As of January 2011, we have processed around 70 articles, to be continued indefinitely. Extension of this pipeline to other journals and model organism databases is planned. Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 24 different literatures, among them Neuroscience, and can readily be extended to other corpora of text.
University College London - Royal Free Hospital BioBank
A physical repository located in London, UK which banks all types of frozen samples. In particular, samples considered relevant material, such as tissues and cells, that are licensed by the Human Tissue Authority, can be stored long term. Existing holdings of tissues and cells where appropriate can be transferred to the Physical BioBank at the Royal Free. Samples can be stored at -80 or in Liquid nitrogen and will be stored in either 1.2ml or 2ml cryotubes. The UCL-Royal Free BioBank will set up service level agreements with all users which define the responsibilities of the user and the biobank in all aspects of biobanking from consent and collection through to disposal and transfer to third parties. Depositors will remain the owner of the tissues which they deposit (either physically or virtually). Samples are tracked using a specific database (BioVault) and all samples submitted are entered into a secure inter-relational database hosted by UCL. Patient-specific identifiers are removed and held on a separate database. In addition, all holders of samples held in other locations in UCL (including fixed tissues, plasma, sera, DNA and RNA) will be invited to add their holdings to the BioBank Research Database hosted by UCL. The biobank also provides logistical support to more conventional clinical trials and the capacity to store trial samples for additional or future testing.
A basic screening measure for depression in older adults. They have a FREE iPhone APP and a FREE ANDROID APP that allows you to do the 15-item GDS on your phone and automatically calculate the results. They provide no interpretation of results, but patients with scores higher than 5 should be interviewed carefully. These apps are also available through the Android Marketplace or iTunes stores on your phones. Note: This page is under continuous development but they will try to keep translations of the scale available. Anyone with their own translation can submit it and they''ll post it.
A gene set analysis algorithm for biomarker identification in the cloud.
Nature Publishing Group (NPG) is a publisher of high impact scientific and medical information in print and online. NPG publishes journals, online databases and services across the life, physical, chemical and applied sciences and clinical medicine. Focusing on the needs of scientists, Nature (founded in 1869) is the leading weekly, international scientific journal. In addition, for this audience, NPG publishes the Nature research journals and Nature Reviews journals, plus a range of prestigious academic journals including society-owned publications. Online, nature.com provides over 6 million visitors per month with access to NPG publications and online databases and services, including news and comment from Nature, NatureJobs plus access to Nature Network and Nature Education''s Scitable.com. Scientific American is at the heart of NPG''s newly-formed consumer media division, meeting the needs of the general public. Founded in 1845, Scientific American is the oldest continuously published magazine in the US and the leading authoritative publication for science in the general media. Together with scientificamerican.com and 16 local language editions around the world it reaches over 3 million consumers and scientists. Other titles include Scientific American Mind and Spektrum der Wissenschaft in Germany. Scientific American is available for site license access on the nature.com platform. Throughout all its businesses NPG is dedicated to serving the scientific and medical communities and the wider scientifically interested general public. Part of Macmillan Publishers Limited, NPG is a global company with principal offices in London, New York and Tokyo, and offices in cities worldwide including Boston, Buenos Aires, Delhi, Hong Kong, Madrid, Barcelona, Munich, Heidelberg, Basingstoke, Melbourne, Paris, San Francisco, Seoul and Washington DC. Read our history for a timeline of NPG and the scientific events which have helped shape the direction of the business.
STochastic Engine For Pathway Simulation
STEPS is a package for exact stochastic simulation of reaction-diffusion systems in realistic, complex 3D geometries. Our core simulation algorithm is an efficient implementation of a variation on Gillespie''s SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh. While it was mainly developed for simulating detailed models of neuronal signaling pathways in dendrites and around synapses, it is a general tool and can be used for studying any biochemical pathway in which spatial gradients and morphology are thought to play a role. We have implemented STEPS as a set of Python modules, which means STEPS users can use Python scripts to control all aspects of setting up the model, generating a mesh, controlling the simulation and generating and analyzing output. The core computational routines are still implemented as C/C++ extension modules for maximal speed of execution.
Database of negated biomedical sentences in literature consisting of more than 32 million negated sentences. Negated sentences were detected using the algorithm described in - Shashank Agarwal, Hong Yu Biomedical negation scope detection with Conditional Random Fields Journal of the American Medical Informatics Association (JAMIA), 2010; 17:696-701. After entering your query in the search box (for example MeCP2 autism), the search results with the negated sentence and the sentences preceding and following the negated sentences are displayed. A link to the source of the sentence is also provided, which links to the article from which the negated sentence was extracted. BioNOT is no longer updated. Documented 2013.
The WEB ATLAS contains photographs of dissected brains showing important structures. The diagrams folder contains drawings showing functionally important parts of the brain as well as drawings of dissections adapted from C.G. Smith. We are particularly pleased to make Nan Cheney''s medical illustrations of the brain and the head available. The STROKE MODEL portion of the website has syndromes associated with strokes of different vessels of the brain as well as extensive diagrams and tables about the vessels of the brain. The 3D RECONSTRUCTIONS featured on this website were made from MRI scans through the brain - where indicated the source material was from the NIH Visible Human Project. The website will also contain material important for the neuroanatomy labs for med students at UBC. Weekly quizzes will help you keep up with studying the material, the podcasts will help you review material presented in the labs, and the weekly wikis will help you share information with your peers.
Biospecimen repository that provides scientists with the opportunity to bank their pluripotent stem cell lines and develops in-house induced pluripotent stem cell (iPSC) lines for distribution. They have developed core capabilities to maintain, characterize, bank, and distribute important stem cell resources. The SCB performs extensive identification and characterization testing for all submitted human induced pluripotent stem cell (iPSC) and mouse embryonic stem cell (mES) lines. The identification and quality control measures include karyotype analysis, microsatellite analysis for parental cell line identity matching, sterility testing, and assessment of viability after cryopreservation. Pluripotency characterizations performed by SCB vary depending upon the distributing repository. * NIGMS iPSCs: Surface antigen expression, Embryoid body formation, Pluritest Gene Expression assay * NINDS iPSCs: Surface antigen expression, Embryoid body formation * NIA mES: Surface antigen expression, Embryoid body formation, Transgene induction Each characterized human iPSC line and mES line released for distribution is provided with a Certificate of Analysis, which includes information regarding characterization and quality of the line, images and links to original publications. The human iPSCs distributed by Coriell are strictly for research purposes and cannot be used in human subjects. All terms described in the Material Transfer Agreement (NIGMS and NINDS Repositories) or Assurance Form (NIA Repository) for the stem cell line must be agreed to prior to using stem cell lines from Coriell.
MassGeneral Institute for Neurodegenerative Disease
Massachusetts General Hospital Institute for Neurodegenerative Disease
Massachusetts General Institute for Neurodegenerative Disease
An institute whose mission is to translate laboratory discoveries into prevention, treatment and cures for Alzheimer's, ALS, Huntington's, Parkinson's and other neurodegenerative diseases. MIND seeks to accelerate therapies that lessen the toll of disease on patients and families. Researchers of the institute collaborate, strategize, and share technology to find treatment for these diseases. As promising leads are developed in one area, they are tested in the other neurodegenerative disorders.
Center for Theoretical Neuroscience; University of Waterloo
The Centre for Theoretical Neuroscience (CTN) was recently established at the University of Waterloo. The Centre is a growing research initiative of the University. The Centre consists of several labs focused on various areas of theoretical neuroscience (aka computational neuroscience). At present, the Centre consists of faculty members from Applied Mathematics, Biology, Psychology, Engineering, Philosophy, Statistics, Computer Science, and their students. The Centre has established a unique Graduate Program in theoretical neuroscience and hosts a regular academic colloquium series. The Centre also hosts the annual public Waterloo Brain Day lectures. The Centre is currently expanding, running searches for additional core faculty. The distinguished faculty of the Centre include two Canada Research Chairs and a fellow of the Royal Society of Canada. In addition, the Centre has a number of student researchers, both graduate and undergraduate, and hosts postdocs and visiting researchers. The Centre also hosts a graduate program for students wishing to obtain an officially recognized specialization in theoretical neuroscience. Faculty at the Centre pursue work on purely theoretical questions regarding the foundational principles guiding the function of neural systems, as well as constructing detailed neurobiological models of specific brain areas.
Central Brain Tumor Registry of the United States
Voluntary, non-profit organization dedicated to collecting and disseminating statistical data. Resource for gathering and disseminating epidemiologic data on all primary benign and malignant brain and other CNS tumors.
HUMAN CONNECTOME PROJECT WU-Minn Consortium
WU-Minn Consortium: Human Connectome Project
Consortium to comprehensively map long-distance brain connections and their variability. It is acquiring data and developing analysis pipelines for several modalities of neuroimaging data plus behavioral and genetic data from healthy adults.
Software brain visualization, analysis and discovery tool for fMRI and dMRI brain imaging data, including functional and structural connectivity data generated by the Human Connectome Project. Used to map brain imaging data. Allows for visualization of outputs from HCP pipelines from single subject, or average data from group of subjects and register that data onto standard brain atlas.
Software application that is a graphic way of organizing the mass of information gathered during a family assessment and finding patterns in the family system (entry from Genetic Analysis Software)
Signal Detection Software for Receiver Operator Characteristics
Software program designed to help the average clinician/researcher with a PC to evaluate clinical databases and discover the characteristics of patients, including genetics that best predict a binary outcome. That outcome may be any binary outcome such as: * Whether or not the patient has a certain disorder (medical test evaluation) * Whether or not the patient is likely to develop a certain disorder (risk factor evaluation) * Whether or not the patient is likely to respond to a certain treatment (evaluation of treatment moderators) When the predictors considered are themselves all binary (e.g., male/female; inpatient/outpatient; symptoms present/absent), the program identifies the optimal predictor. When one or more of the predictors are ordinal (e.g., age, severity of symptoms) it identifies the optimal cutpoint for each or the ordinal predictors, as well as the overall optimal predictor.
Mayo Clinic Jacksonville: Neuropathology and Microscopy
Mayo Clinic Florida: Neuropathology and Microscopy
Mayo Clinic Florida: Neuropathology and Microscopy - Dennis W. Dickson
Mayo Clinic Jacksonville: Neuropathology Microscopy
Neuropathology and Microscopy - Dennis W. Dickson
A brain bank and laboratory focused on memory and motor disorders. Brains are sent to the laboratory for diagnosis and research for the State of Florida Alzheimer Disease Initiative and for the Society for Progressive Supranuclear Palsy. As part of this brain banking function, fixed and frozen brain samples are obtained at autopsy and sent to the laboratory for diagnostic evaluation and for various types of research studies. The major types of analyses performed on the brain samples include neuro-histology, immunohistochemistry, confocal microscopy, electron microscopy and image analysis, as well as immunoassays. The latter are based upon Western blotting and enzyme linked immunoassays. The laboratory has a specific interest in the interface between normal aging and Alzheimer's disease, as well as in non-Alzheimer's degenerative disorders such as Lewy body dementia, corticobasal degeneration, progressive supranuclear palsy and frontotemporal dementia. The primary focus of research on aging is neuropathologic characterization of brains of individuals who had been prospectively and longitudinally evaluated during life. These studies aim to determine differences in a range of biologic parameters in brains of people with normal cognitive, mild cognitive impairment and dementia. Their focus on Parkinson's disease is to identify preclinical Parkinson's disease in order to develop means for early diagnosis.
New York University Alzheimer's Disease Center
The NYU Alzheimer's Disease Center is part of the Department of Psychiatry at New York University School of Medicine. The center's goals are to advance current knowledge and understanding of brain aging and Alzheimer's disease, to expand the numbers of scientists working in the field of aging and Alzheimer's research, to work toward better treatment options and care for patients, and to apply and share its findings with healthcare providers, researchers, and the general public. The ADC's programs and services extend to other research facilities and to healthcare professionals through the use of its core facilities. The NYU ADC is made up of seven core facilities: Administrative Core, Clinical Core, Neuropathology Core, Education Core, Data Management and Biostatistics Core, Neuroimaging Core, and Psychosocial Core.
Wien Center For Alzheimer's Disease and Memory Disorders
A joint program between Mount Sinai Medical Center and the University of Miami Department of Psychiatry that seeks an end to Alzheimer's disease and similar disorders through research, diagnosis, education and treatment. The goals are to improve memory and mental responsiveness of Alzheimer's patients, delay the onset of the disease and, ultimately, find a cure. The Wien Center typically conducts multidisciplinary initiatives utilizing clinical trials.
Brain Research Institute Biobank Resources
Brain Research Institute Research Resources
Brain bank resources which include postmortem human frozen brain tissue and matched cerebrospinal fluid (CSF) and blood available for scientists to search for etiopathogeneses of human disease. The National Neurological Research Specimen Bank and the Multiple Sclerosis Human Neurospecimen Bank maintains a collection of quick frozen and formalin fixed postmortem human brain tissue and frozen cerebrospinal fluid from patients with neurological diseases, including Alzheimer's Disease, amyotrophic lateral sclerosis, depressive disorder/suicide, and epilepsy, among others. Diagnoses are documented by clinical medical records and gross/microscopic neuropathology. The Neuropathology Laboratory at the UCLA Medical Center maintains a bank of frozen, formalin and paraformaldehyde-fixed and paraffin-embedded postmortem human brain tissues and frozen cerebrospinal fluid (CSF) from patients who die with Alzheimer's disease and other dementing and degenerative illnesses, as well as control materials removed in a similar fashion from patients who are neurologically normal.
Johns Hopkins Alzheimer's Disease Research Center
A Alzheimer's Disease Research Center (ADRC) whose goal is to conduct basic and clinical research aimed at understanding Alzheimer's disease. The Center enrolls a variety of individuals for clinical trials, evaluation and follow-up, including: normal control subjects, individuals with mild memory problems, and patients diagnosed with Alzheimer's Disease or related dementias. Researchers can request data and specimens obtained from ADRC subjects. These include blood or DNA, brain specimens, and cross-sectional or longitudinal clinical and cognitive data, all from ADRC subjects.
International Tissue Engineering Research Association Life - Sciences Forum
A forum for scientists specialized in stem cells, tissue engineering and regenerative medicine. The international board of the ITERA Life-Sciences Forum is composed of researchers and physicians from universities, university hospitals, stem cell and research institutes and biotechnological companies. The annual international ITERA Life-Sciences Forum workshop is dedicated to the latest developments in stem cell research. Cryo-Save, Europe' '''s leading provider of stem cell banks, is a founding member of ITERA and sponsors the yearly workshops with an unrestricted educational grant. Members of ITERA Life-Sciences are participating members in three EU-Framework projects: e.a. CRYSTAL and HEPADIP and were recently awarded the HYPERLAB project. The IWT (Agency for Innovation by Science and Technology) recently confirmed that ITERA members will be involved in the HEPSTEM project with participating groups from the Flemish Universities and one research group (KUL, UGENT, VUB and IMEC). ITERA Life Sciences Forum has created this networking to share the knowledge of the academic world with the knowledge of small and middle sized enterprises (SME' '''s), with the aim to participate in the Framework programs of the European Union. At the third Workshop in Maastricht (25-26 October 2007) we asked some opinion leaders who participated to explain their actual vision about stem cells of the cord, cord blood and placenta. The videos on what they had to say are available.
The data sets included in this resource are published in Kravitz et al, 2012 Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci). The data shows: optogenetic activation of dopamine D1 or D2 receptor-expressing striatal projection neurons influenced reinforcement learning in mice. Stimulating D1 receptor-expressing neurons induced persistent reinforcement, whereas stimulating D2 receptor-expressing neurons induced transient punishment. These 3 recording files contain data collected in 2010 and 2011 by Lex Kravitz in Anatol Kreitzer''s lab at the Gladstone Institutes. Each file contains ~ 1 hour of awake in vivo recording data, containing the spike times for ~30 minutes of spontaneous activity, preceeded or followed by 400 laser pulses (473nm laser light, 1 sec pulses, 3 seconds inter-pulse-interval). The laser pulses were presented at 4 intensities: 0.1mW, 0.3mW, 1.0mW, and 3.0mW, and pulse times at each intensity are given in separate columns in each data file. Finally, each data file contains the identification of ''light-modulated units'' as we identified them (see methods below). Methods: Viral expression of DIO-ChR2-YFP and DIO-YFP We used double-floxed inverted (DIO) constructs to express ChR2-YFP fusions and YFP alone in Cre-expressing neurons, which virtually eliminates recombination in cells that do not express Cre-recombinase (Sohal et al, Nature, 2009). The double-floxed reverse ChR2-YFP or YFP cassette was cloned into a modified version of the pAAV2-MCS vector (Stratagene, La Jolla, CA) carrying the EF-1a promoter and the Woodchuck hepatitis virus posttranscriptional regulatory element (WPRE) to enhance expression. The recombinant AAV vectors were serotyped with AAV1 coat proteins and packaged by the viral vector core at the University of North Carolina. The final viral concentration was 4 x 10^12 virus molecules/mL (by Dot Blot, UNC vector core). This viral construct can now be ordered in single aliquots directly from UNC Vector core as product AAV-EF1a-DIO-hChR2(H134R)-EYFP, at http://genetherapy.unc.edu/services.htm) Implantation of electrode arrays for awake recordings Anaesthesia was induced with a mixture of ketamine and xylazine (100mg ketamine plus 5mg xylazine per kilogram of body weight i.p.) and maintained with isoflurane through a nose cone mounted on a stereotaxic apparatus (Kopf Instruments). The scalp was opened and a hole was drilled in the skull (0.0 to +1.0mm AP, -1.0 to -2.0mm ML from bregma). Two skull screws were implanted in the opposing hemisphere. Dental adhesive (C&B Metabond, Parkell) was used to fix the skull screws in place and coat the surface of the skull. An array of 16 or 32 microwires (35-��m tungsten wires, 100-��m spacing between wires, 200-��m spacing between rows; Innovative Physiology) and one optical fiber in a ferrule was lowered into the striatum (3.0mm below the surface of the brain) and cemented in place with dental acrylic (Ortho-Jet, Lang Dental). After the cement dried, the scalp was sutured shut. Animals were allowed to recover for at least seven days before striatal recordings were made. In vivo electrophysiology Voltage signals from each recording site on the microwire array were band-pass-filtered, such that activity between 150 and 8,000Hz was analysed as spiking activity. This data was amplified, processed and digitally captured using commercial hardware and software (Plexon). Single units were discriminated with principal component analysis (OFFLINE SORTER, Plexon). Two criteria were used to ensure quality of recorded units: (1) recorded units smaller than 100��V (~3 times the noise band) were excluded from further analysis and (2) recorded units in which more than 1% of interspike intervals were shorter than 2ms were excluded from further analysis. Average waveforms were exported with OFFLINE SORTER. During the recording we coupled the array to a laser and pulsed the laser at four intensities (0.1mW, 0.3mW, 1mW, and 3mW). Laser stimulation was run in a cyclical fashion, on for 1 second, and off for 3 seconds. Each neuron received 100 pulses at each laser intensity. Identification of ChR2 expressing units in in vivo recordings For all neurons, peri-event histograms were generated for each laser intensity independently. Neurons were classified as ChR2-expressing if they exhibited a firing rate greater than 3x above the standard deviation of the 1-second preceding the laser pulse within 10msec of the laser onset. Each neuron was tested independently at each laser power, and neurons that satisfied this criteria at any one power were defined as ChR2-expression.
This software package provides the implementation of distance weighted discrimination (DWD) using an interior point method for the solution of second order cone programming problems.
Emory Alzheimer's Disease Research Center
An Alzheimer's research center which focuses on mild cognitive impairment and early diagnosis and treatment of memory disorders. The Center hosts clinical trials in which the public can participate. Its resources for scientists include a tissue and biospecimen banking facility, the Emory neurology database, and research seminars.
A list of information about key sources of funding in various countries worldwide, from the SfN. The listings below include notes about each funding agency''s area of research and type of funding, as well as information about special funding opportunities. Most funders have multifaceted programs and schemes, and more detailed information can be found by following the links provided. You can download a PDF version of the entire directory or browse the links below that will take you directly to the funders'' Web sites. SfN welcomes suggestions or changes to existing information; please contact globalaffairs @ sfn.org.
An Alzheimer's disease center which researches the cause, treatment and prevention of Alzheimer's disease with a focus on four main areas of research: risk factors for Alzheimer's and related disorders, the neurological basis of the disease, diagnosis, and treatment. Data includes a number of computed variables that are available for ROS, MAP and MARS cohorts. These variables are under categories such as affect and personality, chronic medical conditions, and clinical diagnosis. Specimens include ante-mortem and post-mortem samples obtained from subjects evaluated by ROS, MAP and clinical study cores. Specimen categories include: Brain tissue (Fixed and frozen), Spinal cord, Muscles (Post-mortem), and Nerve (Post-mortem), among other types of specimens. Data sharing policies and procedures apply to obtaining ante-mortem and post-mortem specimens from participants evaluated by the selected cohorts of the RADC.
Massachusetts Alzheimer's Disease Research Center
An Alzheimer's disease research center which supports new research and enhances ongoing research by providing core support to bringing together behavioral, biomedical, and clinical scientists. The Center conducts multidisciplinary research, trains scientists, and spreads information about Alzheimer's disease and related disorders to the general public. The principal goal of the Massachusetts ADRC is to support research in aging, Alzheimer's Disease and other related disorders. Researchers work with national and international multi-disciplinary teams to understand: normal aging, the transition from normal aging to mild forms of memory problems, and the later stages of dementia. The Massachusetts ADRC has an active brain donation program at the Massachusetts General Hospital (MGH) for patients as well as subjects enrolled in research studies.
A center which focuses on research dedicated to the aging process and age-related brain diseases, as well as education, outreach, and clinical programs that promote healthy brain aging. The major foci of the Center are basic and applied research in Alzheimer's disease and related neurodegenerative disorders. Its objectives include expanding translational neuroscience research and providing educational opportunities to the general public, as well as healthcare students and professionals., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University of Kentucky's Alzheimer's Disease Center
UK-Alzheimer's Disease Center Biospecimen Data or Clinical Request
University of Kentucky Alzheimer's Disease Center Biospecimen Data or Clinical Request
An organization which includes a tissue bank, a database, study design consultation, clinical resources, and a community registry database. The UK-ADC shares data with the NIA national database (NACC), as well as with independent, qualified investigators both within and outside the UK-ADC. This resource's associated tissue bank is comprised of anonymized brain tissue, blood, and cerebrospinal fluid samples from patients in the clinic, as well as frozen post-mortem brain tissue samples. This organization also shares research resources with the National Alzheimer's Coordinating Center (NACC), NACC collaborative initiatives, the Alzheimer's Disease Neuroimaging Initiative (ADNI), other Alzheimer Disease Centers (ADCs), and any qualified investigators from either the University of Kentucky or the general scientific community.
University of Kentucky Alzheimer's Disease Center
Alzheimer's Disease Center at the University of Kentucky
Alzheimer's Disease Center that serves as the focal point for all Alzheimer's disease-related activities at the University of Kentucky and the Commonwealth of Kentucky providing an environment and core resources that catalyze innovative research, outreach, education, and clinical programs. Their ADC plans to build on its historic strengths and capitalize on emerging opportunities to provide an infrastructure that supports research designed to translate knowledge into therapeutic strategies for AD. They focus on two interrelated themes: Transitions and Translation. Their overall emphasis is to more effectively bridge the gap between basic research and clinical studies by facilitating translational efforts. They also carefully characterize transitions across the spectrum of cognitive impairment (normal/ preclinical AD/ MCI/ dementia), with focus on definition of early disease, and continue to support neuropathology as the bedrock of our center. The Alzheimer Disease Center's 2006-2011 grant award from the National Institute on Aging consists of five cores: * Administrative Core * Clinical Core * Biostatistics and Data Management Core * Neuropathology Core * Education & Information Transfer Core
The Society for Neuroscience (SfN) is a nonprofit membership organization of scientists and physicians who study the brain and nervous system. Since its inception in 1969, the Society has grown from 500 members to over 40,000. Today, SfN is the world''s largest organization of scientists and physicians devoted to advancing understanding of the brain and nervous system. SfN''s mission is to: 1. Advance the understanding of the brain and the nervous system by bringing together scientists of diverse backgrounds, by facilitating the integration of research directed at all levels of biological organization, and by encouraging translational research and the application of new scientific knowledge to develop improved disease treatments and cures. 2. Provide professional development activities, information, and educational resources for neuroscientists at all stages of their careers, including undergraduates, graduates, and postdoctoral fellows, and increase participation of scientists from a diversity of cultural and ethnic backgrounds. 3. Promote public information and general education about the nature of scientific discovery and the results and implications of the latest neuroscience research. Support active and continuing discussions on ethical issues relating to the conduct and outcomes of neuroscience research. 4. Inform legislators and other policymakers about new scientific knowledge and recent developments in neuroscience research and their implications for public policy, societal benefit, and continued scientific progress..
brat rapid annotation tool - online environment for collaborative text annotation
brat is a free, open-source, web-based tool for text annotation, visualisation and editing. brat is designed in particular for structured annotation, where the notes are not freeform text but have a fixed form that can be automatically processed and interpreted by a computer. brat is built entirely on standard web technologies, and it is not necessary to install any local software or browser plugins to use it. An annotator can set up and start using brat simply by entering the address of the brat installation into the address bar of a browser. (Setting up an entirely new brat server does require some action, but can be done in just five minutes on any system running a web server.) brat is fully configurable and can support a wide variety of annotation tasks, including, for example: * entity mention (named entity) annotation * binary relation annotation * dependency syntactic annotation * structured, n-ary event annotation * attribute/meta-knowledge annotation (e.g. negation, speculation, etc.) The tool also provides annotation support features such as text and annotation search with detailed constraints, keyword-in-context concordancing, and integrated configurable checking of task-specific semantic constraints. Annotations created in brat can be exported with a few clicks from the interface in a simple standoff format that can be easily analyzed, processed, and converted into other formats. Visualizations can be similarly be exported in their native SVG format, rendered as a bitmap (PNG format), or converted into other vector formats for embedding into documents (PDF or EPS). brat is developed as a collaborative effort between several research groups as an open source project (MIT license), and we warmly welcome contributions and participation from the community, including feature requests. We hope this tool will prove valuable to the natural language processing community, and will gladly answer questions and welcome any feedback.
Patterned Alignments for Splicing and Transcriptome Analysis
A complete pipeline for the analysis of alternative splicing using RNA-Sequencing data.
McKnight Endowment Fund for Neuroscience
An endowment that offers funding for memory research. The McKnight Endowment Fund for Neuroscience is an independent charitable organization established by The McKnight Foundation to carry out the wishes of its founder, William L. McKnight (1887-1979). Currently, the Endowment Fund for Neuroscience administers four awards which support young and established neuroscientists and encourage interdisciplinary collaboration: * Memory and Cognitive Disorders Awards * Neuroscience of Brain Disorders Awards * Scholar Awards * Technological Innovations in Neuroscience Awards Mr. McKnight, who led the 3M company for three decades, had a personal interest in memory and its diseases. He chose to set aside part of his legacy to bring hope to those suffering from brain injury or disease and cognitive impairment.
isva: Independent Surrogate Variable Analysis
An algorithm for feature selection in the presence of potential confounding factors.
University of Michigan Health System Alzheimer's Disease Center
An Alzheimer's disease center which aims to conduct and promote research on Alzheimer's disease and enhance public and professional understanding of dementia through education and outreach efforts. The MADC promotes clinical research on memory and aging which involves the direct use of research volunteers, biomarkers, and other clinical data collected through the University of Michigan Memory and Aging Project.
Michigan Alzheimer's Disease Center Brain Bank
An organization that provides scientists with human tissue from Alzheimer's patients and patients with related brain disorders. Brain tissue is collected from research studies at the University of Michigan, as well as other research centers, and are donated by the families of the patients or the participants themselves. Tissues that are present in the Brain Bank are pre-characterized by pathologists and can be provided to researchers upon request.
Alzheimer's Association International Research Grant Program
An organization that funds research for Alzheimer's disease, provides information on new treatment strategies, provides information on caring for afflicted people, and generally increases public knowledge of disease prevention. This program financially supports new Alzheimer's studies. These research projects are selected by the Medical and Scientific Advisory Council. The council chooses which studies to address based on their potential uses in diagnostics, genetics, treatments, prevention, early detection and general enhancement of lifestyle.
An endowment that offers funding for neuroscience research, especially as it may apply to Minnesota, agriculture, or if the researchers are based in Minnesota. The McKnight Foundation, a Minnesota-based family foundation, seeks to improve the quality of life for present and future generations through grantmaking, collaboration, and strategic policy reform in the following areas: arts, education and learning, environment, the region and communities, agricultural research, and neuroscience research. The McKnight Foundation assists nonprofit organizations and public agencies to improve the quality of life for all people, particularly those in need. Through grantmaking, coalition-building, and encouragement of strategic policy reform, we aim to build and maintain vibrant communities; enrich people''s lives through the arts; encourage protection of the natural environment; and promote research in selected fields. The Foundation had assets of approximately $1.8 billion and gave about $98 million in grants in 2009. Generally speaking, McKnight supports nonprofit organizations in Minnesota, U.S., only. McKnight''s primary geographic focus in grantmaking is to nonprofit organizations located within the state of Minnesota. We do not provide funding outside Minnesota, with five important programmatic exceptions: * Collaborative Crop research: International. * East Africa: Tanzania and Uganda only. * Mississippi River: 10 states bordering or encompassing the Mississippi River. * Neuroscience research: National. * Southeast Asia: Cambodia, Laos, and Vietnam only. Each program is different. Please consult the specific guidelines appropriate to your project or organization for funding details. With very few exceptions, McKnight funds nonprofit organizations only. To be eligible for a grant, applicants must be classified by the Internal Revenue Service as tax-exempt, nonprofit organizations. We discourage the use of fiscal agents.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Software application with implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing (entry from Genetic Analysis Software)
Udall Center of Excellence in Parkinson's Disease Research
Center of Excellence in Parkinson's Disease Research
Mayo Parkinson's Disease Center of Excellence
A research program associated with bringing together researchers from various disciplines to study the genetic and molecular basis of Parkinson's disease. The program focuses on epidemiological and longitudinal studies of Parkinson's disease, dementia with Lewy bodies, and aging and dementia. It also provides clinical materials for other research projects. This program provides faculty research funds, invited speaker seminar series, sponsorship of movement disorder fellowships, pilot research grants, and support for faculty travel to promote intra-institutional collaborations.
Mount Sinai Alzheimer's Disease Research Center
Mount Sinai School of Medicine Alzheimer's Disease Research Center
A research facility and clinical program that is dedicated to the study and the treatment of both normal aging and Alzheimer's disease. This facility will accommodate requests for its resources (for example, data or tissue) from investigators that are not funded by the ADRC. Their team is composed of experts in geriatrics, geriatric psychiatry and psychology, neurology, pathology, and radiology. All team members work to provide services to those with memory disorders. This center sponsors educational programs for healthcare professionals and community groups. Data from the ADRC cores are available to all ADRC investigators after approval from the PI who collected the data. Data generated by the ADRC cores are communicated to the National Alzheimer's Coordinating Center (NACC) and can be available through them. Tissue can be distributed after approval of the Tissue Allocation Committee, and can be used for further research.
A set of Java programs for genetic epidemiology analysis (entry from Genetic Analysis Software)
A biweekly news feed that includes a sampling of new and updated award information from COS Funding Opportunities. COS Funding Opportunities is the most comprehensive source of funding information available on the Web, with more than 25,000 awards from around the world. For highlights of funding available for the health sciences and for the humanities, check out COS Health Science Funding News and COS Humanities and Social Sciences Funding News. Which funding opportunities are most popular? To find out, see last week''s Top Ten Funding Opportunities. COS Funding News is now available as an RSS feed.
Ontology that models research resources such as instruments, protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/) and consists of over 3451 classes of which over 1200 were created within the ERO namespace, while the rest come from existent ontologies such as the Ontology for Biomedical Investigation (OBI), the uber-anatomy ontology (Uberon), VIVO, the Ontology for Clinical Research (OCRe), the Sequence Ontology (SO), the Software Ontology (SWO) and we include terms from the NCBI Taxonomy as well. The main ontology can be browsed in OntoBee. All purls resolve to OntoBee.
COS mirrors grants.gov and several other funding resources. There may soon be some conditions for access the data. It also allows users to advertise their funding opportunities. COS is the leading global resource for hard-to-find information critical to scientific research and other projects across all disciplines. We aggregate valuable information so you spend less precious time and money searching for the information you need, leaving you more time and money for your projects. Find funding with COS Funding Opportunities: search the world''s most comprehensive funding resource, with more than 25,000 records worth over $33 billion. COS Expertise profiles and profile tools will no longer be available beginning January 18, 2012. Profiles will be available on COS Pivot, the new tool for connecting to funding and collaborators. The COS Funding Opportunities database includes announcements of grants, prizes and other funding available to researchers, educators and students, professionals, nonprofit organizations, and businesses such as faculty or medical staff spin-offs. * More than 25,000 records representing over $33 billion in funding. * Opportunities by sponsors throughout the world for recipients throughout the world. * Sponsors include private foundations, public agencies, national and local governments, corporations and more. * Monies available for work in all disciplines physical sciences, social sciences, life sciences, health & medicine, arts & humanities. * Funding for many purposes, such as research, collaborations, travel, curriculum development, conferences, fellowships, postdoctoral positions, equipment acquisitions, capital or operating expenses. * Updated daily, all information verified with sponsor, edited for consistency and optimized for accurate searching. If you would like to promote your institution''s funding opportunities, have them listed in our COS Funding Opportunities database.
Aggregator of blogs about new developments in science and other fields that allows readers to easily find blog posts about serious peer-reviewed research, instead of just news reports and press releases. If you''re a blogger who writes about serious research, Research Blogging offers you a way to distinguish your serious posts from news, politics, family, bagpipes, and so on. They can direct your regular readers - and new readers - to the posts you''ve worked the hardest to create. All you need to get started is a blog and a peer-reviewed research report that you''d like to discuss. How it works * Bloggers -- often experts in their field -- find exciting new peer-reviewed research they''d like to share. They write thoughtful posts about the research for their blogs. * Bloggers register and use a simple one-line form to create a snippet of code to place in their posts. This snippet not only notifies this site about their post, it also creates a properly formatted research citation for their blog. * Their software automatically scans registered blogs for posts containing their code snippet. When it finds them, it indexes them and displays them on their front page -- thousands of posts from hundreds of blogs, in one convenient place, organized by topic. * Their editors identify the notable posts in each major discipline, publishing the results on their news page. * Other services like PubGet index their database as well, so every time readers search for a journal article, they can also locate blog posts discussing the article. * The quality of the posts listed on their site is monitored by the member bloggers. If a post doesn''t follow their guidelines, it is removed from their database. Borderline cases may be discussed publicly on the blog as well. Bloggers are also provided with an icon they can use to show when they''re talking about a peer-reviewed work that they''ve read and analyzed closely. There are already over seven thousand blog posts using the icon, and now it''s easier than ever to find them.
Popular science magazine which includes news and blogs on topics including Health & Medicine, Mind & Brain, Technology, Space, Human origins, Living World, Environment, and Physics & Math. NIF Indexes include: The Brain: DISCOVER blogger, columnist, and contributing editor Carl Zimmer''s monthly column will make your brain happy. Discover Interview: The magazine''s signature in-depth discussion with the leading lights of the world of science Vital Signs: A medical mystery, as written by the doctor involved.
Brain Facts - A Primer on the Brain and Nervous System
Brain Facts is a 74-page primer on the brain and nervous system, published by SfN. Designed for a lay audience as an introduction to neuroscience, Brain Facts is also a valuable educational resource used by high school teachers and students who participate in Brain Awareness Week. The 2008 edition updates all sections and includes new information on brain development, learning and memory, language, neurological and psychiatric illnesses, potential therapies, and more. Download the full book (PDF) or download individual sections. All downloads are PDFs. Educators, request a copy of the Brain Facts book (paperback or CD) - contact BAW@SfN.org.
A blog concerning the relationships between genes, risk factors and immunity in Alzheimer's disease, autism, Bipolar disorder, multiple sclerosis, Parkinson's disease, schizophrenia and chronic fatigue.
McConnell Brain Imaging Center MNI Rhesus Macaque Atlas
A reference atlas of rhesus macaque monkey magnetic resonance images that offers a common stereotaxic reference frame. The atlas can be used to localize anatomical and functional information in an organized and reliable way for comparison across individual rhesus monkeys and studies. We have used MRI volumes from a group of 7 normal adult rhesus monkeys (Macaca mulatta) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous rhesus monkey brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the rhesus macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.
QPALMA: Optimal Spliced Alignments of Short Sequence Reads
An alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454.
A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
McConnell Brain Imaging Center MNI Cynomolgus Macaque Atlas
A reference atlas of cynomolgus macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual cynomolgus monkeys and studies. We have used MRI volumes from a group of 18 normal adult cynomulgus monkeys (Macaca fascicularis) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous cynomolgus monkey brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the cynomolgus macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.
BIC NIHPD Objective 1 atlases (4.518.5y)
McConnell Brain Imaging Center NIHPD Objective 1 atlases (4.518.5y)
An unbiased standard magnetic resonance imaging template brain volume for pediatric data from the 4.5 to 18.5y age range. These volumes were created using data from 324 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Tools for using these atlases can be found in the Software section. To view the atlases online, click on the appropriate JIV2 link in the Download section. You can download templates constructed for different age ranges. For each age range you will get an average T1w, T2w, PDw maps normalized between 0 and 100 and tissue probability maps, with values between 0 and 1. Also each age range includes a binary brain mask.
NIHPD Objective 2 atlases (birth - 4.5 years)
BIC NIHPD Objective 2 atlases (birth - 4.5 years)
McConnell Brain Imaging Center NIHPD Objective 2 atlases (birth - 4.5 years)
An unbiased magnetic resonance imaging template brain volume for pediatric data from birth to 4.5y age range. These volumes were created using 317 scans from 108 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Templates are constructed for different age ranges. Each age range includes an average T1w, T2w, PDw maps normalized between 0 and 100. Also each age range includes a binary brain mask. Tools for using these atlases can be found in the Software section.
BIC ICBM 152 Nonlinear atlases version 2009
Unbiased standard magnetic resonance imaging template brain volume for normal population. These volumes were created using data from ICBM project. 6 different templates are available: * ICBM 2009a Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, also T2 relaxometry (T2 values calculated for each subject using single dual echo PD/T2 scan), and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.10.1. * ICBM 2009a Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.10.1. Also included brain mask, eye mask and face mask. * ICBM 2009b Nonlinear Symmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009b Nonlinear Asymmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009c Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.11. Sampling is different from 2009a template. * ICBM 2009c Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.11 Also included brain mask, eye mask and face mask.Sampling is different from 2009a template. All templates are describing the same anatomy, but sampling is different. Also, different versions of N3 algorithm produces slightly different tissue probability maps. Tools for using these atlases can be found in the Software section. Viewing the multiple atlas volumes online requires Java browser support. You may also download the templates - see licensing information.
Probabilistic atlas of the human cerebellum
A probabilistic atlas of the cerebellar lobules in the space defined by the MNI152 template. The anatomical definitions are based on the fMRI atlas of an individual cerebellum by Schmahmann et al. (2000). To obtain a representative anatomical atlas, we separately masked the lobules on T1-weighted MRI scans (1mm isotropic resolution) of 20 healthy young participants (10 male, 10 female, average age 23.7 yrs). Using a different set of 23 participants, we also masked the deep cerebellar nucelei. These cerebella were then aligned using different commonly used normalization algorithms. The resultant probabilistic maps allow for the valid assignment of functional activations to specific cerebellar lobules and the nuclei, while providing a quantitative measure of the certainty of such assignments. Furthermore, maximum probability maps derived from these atlases can be used to define regions of interest (ROIs) in functional neuroimaging and neuroanatomical research. The atlas is included in the newer releases of FSL and the Anatomy toolbox. More version of the atlases for use with MRICroN are also available.
University of Pennsylvania Center for Neurodegenerative Disease Research
Penn Center for Neurodegenerative Disease Research
A research institution which conducts clinical research to understand brain dysfunction and degeneration in Alzheimer's disease (AD), Parkinson's disease (PD), Frontotemporal disease (FTD), Amyotrophic Lateral Sclerosis (ALS or Lou Gehrig's disease), and other age-related neurodegenerative disorders. This organization also houses a general training program that has a focus on drug discovery. This program teaches trainees in etiology, pathogenesis, and diagnosis and treatment of Alzheimer's disease, Parkinson's disease, frontotemporal dementias, motor neuron disease and related disorders. This program also trains Ph.D and M.D/Ph.D students, as well scientists, physicians, and veterinarians who have already completed their advanced degree and are looking for a postdoctoral research fellowship. The program is designed to give a solid background in basic and translational neuroscience, and related disciplines.
Community wiki for an open-content textbooks collection that anyone can improve or add to, start new books, and join project-related discussions in the reading rooms. Contributors maintain the property rights to their contributions, while the Creative Commons Attribution-ShareAlike License and the GNU Free Documentation License makes sure that the submitted version and its derivative works will always remain freely distributable and reproducible. Categories include: Computing, Engineering, Humanities, Languages, Mathematics, Miscellaneous, Science, Social sciences, All subjects. Wikibooks has two sub-projects; Wikijunior which is aimed at children and the Cookbook which is a collection of recipes and culinary topics. * 2,440 books with 40,746 pages (March 2012)
The Talairach brain atlas visualized via BrainVoyager (Commercial software) can be used to visualize Brodmann areas as they were defined for the Talairach brain (Talairach & Tournaux, 1988) and to compare regions of subjects with respect to the Brodmann areas. The demarcated areas are based on the Talairach demon, which is a digitized version of the Talairach atlas and which has been transferred into BrainVoyager VOI files by Matthias Ruf, Mannheim. Using the Brodman.voi file you may ask questions like the following: What is the signal time course of subject N in experiment A within Brodmann area X ?. Note, however, that the defined areal boundaries should be used only as a rough guideline for determining the location of activated regions: There is substantial variation of histologically defined areas between subjects. Since cytoarchitectonically defined Brodmann areas are not available in vivo, we advise to use the provided information with care. The TalairachBrain.vmr file is located in the same folder as your BrainVoyager executable file. It can be loaded as any VMR project by using the Open... item in the File menu (or the Open icon). The TalairachBrain.vmr file is also loaded automatically when using the glass brain visualization tool.
1000 Genomes Project and Amazon Web Services
A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow.
Taub Institute for Research on Alzheimers Disease and the Aging Brain
Taub Center for Alzheimer's Disease Research
Taub Institute Alzheimer's Disease Research Center
Taub Institute for Research on Alzheimer’s Disease
An institute which conducts research of Alzheimer's, Parkinson's and other age-related brain diseases. This organization also provides clinical evaluations to patients with memory problems, Alzheimer's disease or other types of dementia. Furthermore, the institute leads multi-center clinical trials for the treatment and prevention of Alzheimer's, Parkinson's and other age-related brain diseases. There is a brain donation program for enrolled/examined patients. The Education Core of the Taub Institute sponsors community events and Continuing Medical Education programs, as well as the distribution of periodic newsletters and brochures highlighting research developments and other Alzheimer's topics.
The moonlighting protein database is not yet available publicly. Stay tuned. Moonlighting proteins have multiple, seemingly unrelated functions not due to gene fusions or alternative splicing. Like PGI, which is a cytosolic enzyme and an extracellular cytokine, dozens of other proteins have been found to moonlight. Connie coined the term moonlighting proteins and has written several review articles that develop the idea of moonlighting proteins and describe additional moonlighting proteins from the literature, how they switch between functions, how they might have evolved, and how they might benefit the cell. She is currently writing two additional invited articles and planning computational studies of the sequences and structures of known moonlighting proteins.
Portal providing access to metagenomics projects, data and tools supported by the DOE Joint Genome Institute (JGI). A primary motivation for metagenomics is that most microbes found in nature exist in complex, interdependent communities and cannot readily be grown in isolation in the laboratory. One can, however, isolate DNA or RNA from the community as a whole, and studies of such communities have revealed a diversity of microbes far beyond those found in culture collections. It is suspected that these uncultivated organisms must harbor considerable as-yet undiscovered genomic, functional, and metabolic features and capabilities. Thus to fully explore microbial genomics, it is imperative that we access the genomes of these elusive players.
Interfaces to various state-of-art SVD and eigensolvers.
Institute for Basic Research in Developmental Disabilities
New York State Institute for Basic Research in Developmental Disabilities
NYS-OPWDD: Institute for Basic Research in Developmental Disabilities
A research arm of the New York State Office for People with Developmental Disabilities (OPWDD), which conducts basic and clinical research into the causes, treatment, and prevention of intellectual disabilities and other developmental disabilities. The goals of the IBR's research, services and education program are designed to provide prevention, earlier detection, and improved treatment of intellectual disabilities and other developmental disabilities. This research program has a total of 46 laboratories over 7 departments. These programs include the George A. Jervis Clinic (a tertiary-level diagnostic and research clinic), the Specialty Clinical Laboratories (conduct specialty testing for genetic, metabolic, neurodegenerative disorders), and the Comprehensive Genetic Disease Program at Richmond County (provides genetics and genetic counseling services). This institute provides educational activities in the graduate studies program, and the Programs in Developmental Neuroscience and Developmental Disabilities (PDNDD). The PDNDD collaborates with the faculty from the City University of New York and the State University of New York. The IBR staff regularly conducts public education workshops and professional seminars about developmental disabilities.
The Vietnam Era Twin (VET) Registry is a closed cohort composed of approximately 7,000 middle-aged male-male twin pairs both of whom served in the military during the time of the Vietnam conflict (1964-1975). The Registry is a United States Department of Veterans Affairs (VA) resource that was originally constructed from military records; the Registry has been in existence for almost 20 years. It is one of the largest national twin registries in the US and currently has members living in all 50 states. Initially formed to address questions about the long-term health effects of service in Vietnam, the Registry has evolved into a resource for genetic epidemiological studies of mental and physical health conditions. Several waves of mail and telephone surveys have collected a wealth of health-related information on Registry twins, referred to as members. In addition to twins, selected adult offspring of twins and the mothers of those offspring are also VET Registry members. More recent data collection efforts have focused on specific sets of twin pairs and have conducted detailed clinical or laboratory testing. Selected Vietnam Era Registry Research Studies: * Veteran Health Study * VETSA 2: A Longitudinal Study of Cognitive Aging * Alcoholism Course thought Midlife: A Twin Family Study and Offspring of Twins: G, E and GxE Risk for Alcoholism * GE: Offspring of Twins with Substance Use Disorder * Mechanisms Linking Depression to Cardiovascular Risk (Twins Heart Study 2) * Post-traumatic Stress Disorder and Cardiovascular Disease * Biological Markers for Post-traumatic Stress Disorder (T3) * Memory and the Hippocampus in Vietnam-era Twins with PTSD (Time 3)
Vietnam Era Twin Registry Biospecimen Repository
The Vietnam Era Twin (VET) Registry maintains a repository of biological specimens obtained from Registry members. The VET Registry Biospecimen Repository includes DNA, plasma, and serum samples obtained from selected VET Registry members. As the VET Registry is a national resource for studies investigating genetic and non-genetic influences on health and disease in middle age men, this enhances the value of the information collected from VET Registry members to the research community. The VET Registry has developed a general system of protocols for the collection and storage of biological specimens that assures confidentiality for all participants. The biological specimens currently in use are stored at the R&D Core Laboratory at the VA Puget Sound Health Care System (VAPSHCS) in Seattle, WA. The R&D Core Laboratory performs DNA extraction procedures and separates out DNA, plasma, and serum for testing and storage. It is important to note that Core Laboratory staff has absolutely no phenotypic (non-genetic) information about VET Registry members, as the lab is completely blinded to the identity, disease characteristics, and any other research data collected from VET Registry members. The Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) Core Laboratory is located at the VA Boston Health Care System in Boston, MA, and serves as the long-term storage site for the VET Registry Biospecimen Repository. Before a VET Registry member decides whether to participate in the Biospecimen Repository, the procedures, confidentiality safeguards, and potential risks are explained in great detail. To be able to accommodate the wishes of members, a so-called layered consent process is used which allows members to choose from several options with regard to how their biological specimen will be used in current or future research studies. Such options may include: 1) not having their samples used for any testing beyond the immediate goals of the study; 2) allowing for future testing of their samples restricted to the study for which they provided the sample; or 3) allowing unrestricted future research use of their samples. Members are informed that any future use of their samples would have to be approved by the VET Registry, in addition to an independent ethics committee that protects the rights and welfare of research subjects, this board is more commonly known as an Institutional Review Board or IRB. Confidentiality safeguards include assigning code numbers, as opposed to name or other personal information, on all biological specimens. Zygosity Testing The accuracy of DNA testing makes it the best method for determining zygosity, identical (monozygotic) versus fraternal (non-identical or dizygotic), in VET Registry twin members. The use of DNA for zygosity testing is only performed when both members of a twin pair agree to the testing. Other Genetic Testing for specific genes will not necessarily involve providing the participants with test results.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Is the Brain (Like) a Computer is an e-book written by Prof. Mark Dubin. It consists of the following: Introduction. Why do we consider the relationship of brains and computers and what does this have to do with consciousness? What's a Brain Made Of? A thought experiment. Test Drive a Turing Machine. A theoretical approach. Interim Summary. Many of the main pages have links to additional information. When you click on one of those links a NEW page will open ON TOP of the page you are clicking from. This convention is adopted so that you can look at the additional information and then easily return to the main page you got there from.
Study of Womens Health Across the Nation (SWAN) Repository
Study of Women''s Health Across the Nation (SWAN) Repository
Study of Women''s Health Across the Nation Repository
Study of Womens Health Across the Nation Repository
The SWAN Repository is the biologic specimen bank of the Study of Women''s Health Across the Nation (SWAN). SWAN is a National Institutes of Health funded, multi-site, longitudinal study of the natural history of the midlife including the menopausal transition. The overall goal of SWAN is to describe the chronology of the biological and psychosocial characteristics that occur during midlife and the menopausal transition. In addition, SWAN is describing the effect of the transition and its associated characteristics on subsequent health and risk factors for age related chronic diseases. SWAN was designed to collect and analyze information on demographics, health and social characteristics, reproductive history, pre-existing illness, physical activity, and health practices of mid-life women in multi-ethnic, community-based samples; elucidate factors that differentiate symptomatic from asymptomatic women during the menopausal transition; identify and utilize appropriate markers of the aging of the ovarian-hypothalamo-pituitary axis and relate these markers to alterations in menstrual cycle characteristics as women approach and traverse the menopause; and explain factors that differentiate women most susceptible to long-term pathophysiological consequences of ovarian hormone deficiency from those who are protected. The biological specimen bank can also be linked by identification number (not by participant name) to data collected in the Core SWAN protocol. The specimen bank can also be linked with data from the Daily Hormone Study as well as menstrual calendars. Types of data include: epidemiological data, psychosocial data, physical measures, as well as data from assays (endocrine and cardiovascular information). SWAN has seven clinical study sites located in six states, two in California, and one each in Chicago, Boston, Detroit area, northern New Jersey and Pittsburgh. The SWAN cohort was recruited in 1996/7 and consists of 3302 African American, Caucasian, Chinese American, Hispanic and Japanese American women. Cohort members complete an annual clinic visit. The Core Repository includes over 1.8 million samples from the first 11 years of specimen collection. This includes samples from annual visits and samples from the Daily Hormone Sub-study (DHS). During an Annual visit, participants provide materials for up to 24-28 aliquots to be incorporated into the Repository. During a DHS visit, a participant provides 6 serum samples and between ~30-50 urine samples depending upon the length of her menstrual cycle. DHS participants (887) provide urine samples collected throughout one menstrual cycle each year. A typical DHS collection consists of a blood draw plus collection of 10 ml of urine daily throughout the month-long menstrual cycle, up to 50 days. DHS Repository samples consist of 6 serum samples and 30 5 ml urine samples. Specimen collection occurs from the time of menstrual bleed to the subsequent menstrual bleed or up to 50 days, whichever come first. The current DHS collection consists of more than 200,000 specimens stored in 5 ml vials. The SWAN DNA Repository currently contains extracted diluted DNA from 1538 SWAN participants. B-lymphocytes were transformed with Epstein Barr virus, and the resulting transformed b-cells aliquoted. Information about using these transformed cells for genomic or proteomic studies is available. DNA has been extracted from one aliquot (per woman) of the immortalized cells using the Puregene system. There was an average DNA yield of 217.0 mg/mL and a A260/A280 average ratio of 1.86. This DNA, in turn, has been aliquoted into 20ng/1 ml units for release by the DNA Repository. Samples are free of personal identifiers and collected under consents that allow a broad range of activities related to women''s health. All of these samples are available to researchers who wish to study the midlife and menopausal transition. Scientists who use these specimens can also request data collected during a participant''s annual visit including medical and health history, psychosocial measures, biological measures and anthropometry.
Powerful database software with improvement tools for paternity testing, database searching (like CODIS) and NRC II recommendations based formulae for investigating likelyhood ratios in putative contributors to crime evidences. Additional genetic population parameters estimations are added in this version. Only spanish version available. (entry from Genetic Analysis Software)
QuasiRecomb - Probabilistic inference of viral Quasispecies
A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.
Dynamics of Health Aging and Body Composition (Health ABC)
Dynamics of Health Aging and Body Composition
Dynamics of Health Aging Body Composition
Health Aging and Body Composition (Health ABC) Study
A study that characterizes the extent of change in body composition in older men and women, identifies clinical conditions accelerating these changes, and examines the health impact of these changes on strength, endurance, disability, and weight-related diseases of old age. The study population consists of 3,075 persons age 70-79 at baseline with about equal numbers of men and women. Thirty-three percent of the men are African-Americans as are 46% of the women. All persons in the study were selected to be free of disability in activities of daily living and free of functional limitation (defined as any difficulty walking a quarter of a mile or any difficulty walking up 10 steps without resting) at baseline. The core yearly examination for HEALTH ABC includes measurement of body composition by dual energy x-ray absorptio��������metry (DXA), walking ability, strength, an interview that includes self-report of limitations, a medication survey, and weight (Measurements in the Health ABC Study). Provision has been made for banking of blood specimens and extracted DNA (HealthABC repository). Study investigators are open to collaboration especially for measures focused on obesity and associated weight-related health conditions including osteoporosis, osteoarthritis, pulmonary function, cardiovascular disease, vascular disease, diabetes and glucose intolerance, and depression. The principal goals of the HEALTH ABC are: # To assess the association of baseline body weight, lean body mass, body fat, and bone mineral content, in relation to weight history, with: incident functional limitation; incidence and change in severity of weight-related health conditions; recovery of physical function after an acute event; baseline measures of strength, fitness and physical performance; gender, ethnicity and socioeconomic status # To access the contribution of episodes of severe acute illness in healthier older persons to changes in body weight, bone mineral content, lean body mass and body fat, and the relationship of these episodes to risk of functional limitation and recovery. # To assess the impact of weight-related co-morbid illness on the risk of functional limitation and recovery. # To assess the ways in which physiologic mediators of change in body composition influence and are influenced by changes in health in older adults and contribute to change in body composition; to understand how changes in body composition affect weight-related cardiovascular disease risk factors such as lipids, blood pressure and glucose tolerance. # To assess the interdependency of behavioral factors, such as nutrition and physical activity, co-morbid health conditions, and their association with change in body composition in old age. # To provide a firm scientific basis for understanding issues related to weight recommendations in old age through increased knowledge of the potential trade-offs between weight and risk of functional limitation, disability, morbidity and death; to provide information critical for developing effective strategies for the maintenance of health in older persons.
University of Washington Alzheimers Disease Research Center
Alzheimer's Disease Research Center at University of Washington
Research center investigating the basic mechanisms underlying the development of Alzheimer's disease and related disorders, directing particular attention to biomarkers and experimental new treatments. They also continue to search for genetic risk factors underlying Alzheimer's disease (AD). Their main priorities are to find causes, effective treatments, and prevention strategies. Their investigators also are partnering with other Alzheimer's Centers across the country to evaluate promising new medications and other treatments for AD. The ultimate goal of their basic and clinical studies is to improve patient care and function, and improve the quality of life for both the patient and the caregiver. ADRC Cores: * Administration * Clinical Core * Satellite Core * Data Management & Biostatistics * Neuropathology Core * Education & Information Transfer * Genetics
Clinical Research Study Investigators Toolbox
Clinical Research Study Investigator''s Toolbox
NIA Clinical Research Study Investigator''s Toolbox
NIA Clinical Research Study Investigators Toolbox
The purpose of the NIA Clinical Research Toolbox is to provide a Web-based information repository for investigators and staff involved in clinical research. The Toolbox contains templates, sample forms, guidelines, regulations and information materials to assist investigators in the development and conduct of high quality clinical research studies.
An online game for mapping neuronal connections in the retina. The site provides microscopic retinal images and uses crowdsourcing to make sense of the images. EyeWire is where the general public can help make discoveries about the neural structure of the retina. The challenge is to map the neural connections of the retina by analyzing images that were acquired using serial electron microscopy at the Max Planck Institute for Medical Research in Heidelberg, Germany. A retinal volume of size 350��300��60 micrometer cubed was imaged, amounting to about one terabyte of data. Retinal Connectome * Game 1: Reconstructing Neurons * Game 2: Identifying Synapses Eyewire incorporates computational technologies developed by the laboratory of Prof. Sebastian Seung at MIT.
Vendor for life sciences products and services ranging from instruments to antibodies.
An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.
The HIV Brain Sequence Database (HIVBrainSeqDB) is a public database of HIV envelope sequences, directly sequenced from brain and other tissues from the same patients. For inclusion in the database, sequences must: (i) be deposited in Genbank; (ii) include some portion of the HIV env region; (iii) be clonal, amplified directly from tissue; and (iv) be sampled from the brain, or sampled from a patient for which the database already contains brain sequence. Sequences are annotated with clinical data including viral load, CD4 count, antiretroviral status, neurocognitive impairment, and neuropathological diagnosis, all curated from the original publication. Tissue source is coded using an anatomical ontology, the Foundational Model of Anatomy, to capture the maximum level of detail available, while maintaining ontological relationships between tissues and their subparts. 44 tissue types are represented within the database, grouped into 4 categories: (i) brain, brainstem, and spinal cord; (ii) meninges, choroid plexus, and CSF; (iii) blood and lymphoid; and (iv) other (bone marrow, colon, lung, liver, etc). Currently, the database contains 2517 envelope sequences from 90 patients, obtained from 22 published studies. 1272 sequences are from brain; the remaining 1245 are from blood, lymph node, spleen, bone marrow, colon, lung and other non-brain tissues. The database interface utilizes a faceted interface, allowing real-time combination of multiple search parameters to assemble a meta-dataset, which can be downloaded for further analysis. This online resource will greatly facilitate analysis of the genetic aspects of HIV macrophage tropism, HIV compartmentalization and evolution within the brain and other tissue reservoirs, and the relationship of these findings to HIV-associated neurological disorders and other clinical consequences of HIV infection.
A brain and tissue bank that contains human brain samples from patients with Alzheimer's disease (AD), Parkinson's disease (PD) and other related neurodegenerative dementias and movement disorders. This brain bank serves as a resource for scientists and researchers, providing access to tissue samples for further research. While priority is given to University of Pennsylvania researchers, this bank will provide requests to researchers not associated with the University of Pennsylvania. This tissue bank accepts donations from those seeing a University of Pennsylvania physician or collaborator.
OHSU Layton Aging and Alzheimer's Disease Center
C. Rex and Ruth H. Layton Aging and Alzheimer’s Disease Center
Layton Aging and Alzheimers Disease Center
An aging and Alzheimer's disease research center that conducts studies of treatments, technologies for patient support, genetics, neuroimaging, and pathology. The Center's clinical research focuses on understanding differing rates of progression and cognitive decline as compared to optimal cognitive health in the elderly and are currently studying methods of gauging the progression of Alzheimer’s disease through research in genetics, neuroimaging, and cerebrospinal fluid biomarkers. Clinical trials performed at the Center include drugs targeted to ameliorate the symptoms of memory failure and slow the progression of disease.
Layton Aging and Alzheimer's Disease Center Clinical Data Resources
A database housing longitudinal relational research data from over 4,000 research subjects. The database includes the following types of data: physical and neurological exam findings, neurocognitive test scores, personal and family history of dementia, personal demographic genotypes (APOE, HLA), age at service evaluations, age at onset, age at death, clinical diagnosis, neuropathology diagnosis, tissue inventory information (when available), health status, medications, laboratory tests, and MRI data.
Layton Aging & Alzheimer's Disease Center Neuro-Imaging Lab
Layton Aging Alzheimer's Disease Center Neuro-Imaging Lab
Layton Aging and Alzheimer's Center Neuro-Imaging Lab
Layton Aging and Alzheimer's Center NeuroImaging Laboratory
Layton Aging and Alzheimer's Disease Center Neuro-Imaging Lab
NeuroImaging laboratory focused on detecting early brain changes associated with cognitive decline and dementia that manages the neuroimaging component of all studies at the Layton Aging and Alzheimer's Center including acquisition and archival services, as well as volumetric analysis of anonymized MRI scans. Assistance with resulting data is also available, including statistical analysis, and preparation of materials for presentation and publication. The Layton Center also manages a library of thousands of digitized MRI scans, including what is believed to be the largest collection of longitudinal MRI scans of cognitively intact elderly subjects. The OADC Neuroimaging Lab conducts MRI studies on both 3 and 7T MRI systems using advanced sequences, employing a multimodal approach to brain imaging research.
Layton Aging and Alzheimers Disease Center Biomarkers and Genetics
A center that works with the Oregon Alzheimer's Disease Center's Data Core, and collects and stores tissue samples, family history and genotype data of various populations. These include samples and data from subjects from the following sources: OADC clinical studies, the Oregon Brain Aging Study, the Community Brain Donor Program, the Preventing Cognitive Decline with Alternative Therapies program (informally called the Dementia Prevention Study or DPS), the African American Dementia and Aging Project, and the Klamath Exceptional Aging Project. The collected data samples include genomic DNA, lymphoblast cell lines, genome-wide and candidate region SNP marker data, APOE, AD candidate gene markers.
Medical University of South Carolina Center on Aging
A center dedicated to research, service, and education concerning aging. MUSC primarily promotes the health, increased longevity, and improved quality of life of senior South Carolinians. This organization does such through the establishment of a national translational research program about aging, the development of a comprehensive/coordinated system of health care delivery for older individuals, and providing health education and outreach to students, faculty members, practicing health providers and the overall public. This center consists of several different research programs, including the Movement Disorder program, Stroke program, Alzheimer's program, Biology of Aging program, Outreach and Education program, and the Clinical Geriatric program.
MUSC Center on Aging Campbell Neuropathology Laboratory
Carroll A. Campbell Jr. Neuropathology Laboratory
Carroll A. Campbell Jr. Neuropathology Laboratory (Brain Bank)
Carroll A. Campbell Jr. Neuropathology Laboratory at MUSC
Medical University of South Carolina Center on Aging Carroll A. Campbell Jr. Neuropathology Laboratory
MUSC Center on Aging Carroll A. Campbell Jr. Neuropathology Laboratory
A brain bank and biospecimen repository that provides research materials to clinicians, scientists and pathologists in South Carolina. The bank provides both control and diseased biospecimens and brain tissue needed for research in Alzheimer's disease, Parkinson's disease and other related neurological disorders. The Campbell Laboratory coordinates the brain tissue donation program, provides post-mortem confirmation of a patient having neurological disorders, and leads research trials. Any South Carolina resident can choose to sign up as a tissue donor and have their brain tissue donated post-mortem to be used for neurological disorder research. The tissue bank will process and analyze these tissue samples and send the results to the deceased person's family.
The MUSChealth.com Podcast Library, featuring podcasts on a variety of topics related to your health and our services here at MUSC. These medical podcasts are hosted by MUSC faculty, physicians and special guests and are produced and directed by Linda Austin, M.D. Current topics include: * Academics and Education * Aging, Geriatrics and Caregiving * Alcohol and Drug Dependency * Allergies and Asthma * Ashley River Tower * Bones, Joints, Muscles and Spine * Cancer * Children''s Health * Cosmetic Surgery * Dental * Dermatology/Skin Problems * Diabetes, Endocrinology and Metabolism * Digestive Health * ENT: Ear, Nose and Throat * Executive Health * Eye Health * General Health and Wellness * Heart and Vascular Health * Hospice * Kohl''s Take a Minute for Kids * Lungs and Breathing * Men''s Health * Mental Health * MUSC News and Events * Neurological Health * Organ Transplant * Osteoporosis * Pregnancy - Week by Week * Pregnancy and Childbirth * Radiology * Research and Clinical Trials * SC Health, Leadership and Policy * Sports Medicine * Stroke * Urology * Weight Loss Surgery Follow-up * Weight Management * Women''s Health
International Neuroinformatics Coordinating Facility Job Board
International Neuroinformatics Coordinating Facility Jobs
Job offerings in the field of neuroinformatics. You may suggest a job.
A network that provides support and NIH funding for neuroscience research and drug development through access to contract research organizations for outsourcing and research consultation. Successful applicants will receive funding to conduct biological testing, access to a full range of industry-style drug development services and expertise, and control of the intellectual property for drug candidates. Funded projects include treatments for age-related macular degeneration, ALS, Alzheimer's disease, depression, hearing loss, optic neuropathy and stroke.
Functional Neurogenesis - New neurons in the adult brain. How they work and what they are good for.
A blog focusing on the function of adult neurogenesis in the dentate gyrus of the hippocampus, including discussion of scientific research papers, methods and protocols, and other trends or observations about the field.
Treatment of SSRI-resistant Depression in Adolescents (TORDIA)
Treatment of SSRI-resistant Depression in Adolescents
A multi-site, clinical research study examining treatment options for teens whose depression has not improved after one adequate trial of a selective serotonin reuptake inhibitor (SSRI), a type of antidepressant. The purpose of the study is to determine how best to treat adolescents with depression that is resistant to the first SSRI antidepressant they have tried. Participants receive one of three other antidepressant medications, either alone or in combination with cognitive behavioral therapy. The TORDIA study aims to develop useful clinical guidelines for the care and management of adolescent depression. Adolescents ages 12 to 18, currently taking a prescribed selective serotonin reuptake inhibitor (SSRI) and still experiencing depression, participate in a 12-week randomized treatment study that includes one of four conditions: (1) switching to an alternative SSRI, (2) switching to a different non-SSRI antidepressant, (3) switching to an alternative SSRI and receiving cognitive behavioral therapy (CBT), or (4) switching to a different non-SSRI antidepressant and receiving CBT. This is a double-blind study, which means that neither the participant nor the clinical staff will know which of the three possible medications has been assigned. Participants who respond to the assigned treatment will receive 12 additional weeks of the same treatment. Those who do not appear to be getting better will be offered 12 weeks of an alternative, individualized treatment plan based on each participant''s particular needs. All participants will receive follow-up psychiatric evaluations for 12 months after the 12-week continuation phase of the study, regardless of treatment adherence. For more information visit, http://www.clinicaltrials.gov/ct2/show/NCT00018902?term=clinical+trial+AND+treatment+of+ssri-resistant+AND+depression+AND+TORDIA+AND+study&rank=1
Provides relevant and curated health news and articles specifically tailored to individual interests. Content is curated from sources such as JAMA, BMJ, BMA and more that are archived in an easy-to-search manner. The portal contains video content that is created in partnership with Healthology, a network of holistic care clinics, to bring informative videos to the public on a regular basis. The site also provides a platform to interact with fellow readers through forums, weekly newsletters and notifications when relevant content is added to categories of interest.
Channelrhodopsin-2 enables optical activation of neurons
Laser tool that enables neurons to be optically silenced by pulses of yellow light, the light-activated chloride pump halorhodopsin (Halo), in a paper entitled Multiple-color optical activation, silencing, and desynchronization of neural activity, with single-spike temporal resolution. Temporally precise, noninvasive control of activity in well-defined neuronal populations is a long-sought goal of systems neuroscience. We adapted for this purpose the naturally occurring algal protein Channelrhodopsin-2, a rapidly gated light-sensitive cation channel, by using lentiviral gene delivery in combination with high-speed optical switching to photostimulate mammalian neurons. We demonstrate reliable, millisecond-timescale control of neuronal spiking, as well as control of excitatory and inhibitory synaptic transmission. This technology allows the use of light to alter neural processing at the level of single spikes and synaptic events, yielding a widely applicable tool for neuroscientists and biomedical engineers. The quest to determine how precise neural activity patterns mediate computation, behavior, and pathology would be greatly aided by a set of tools for reliably activating and inactivating genetically targeted neurons, in a temporally precise and rapidly reversible fashion. Having earlier adapted a light-activated cation channel, 1channelrhodopsin-2 (ChR2), for allowing neurons to be stimulated by blue light, we searched for a complementary tool that would enable optical neuronal inhibition, driven by light of a second color. Here we report that targeting the 1codon-optimized form of the light-driven chloride pump halorhodopsin from the archaebacterium Natronomas pharaonis (hereafter abbreviated Halo) to genetically-specified neurons enables them to be silenced reliably, and reversibly, by millisecond-timescale pulses of yellow light. We show that trains of yellow and blue light pulses can drive high-fidelity sequences of hyperpolarizations and depolarizations in neurons simultaneously expressing yellow light-driven Halo and blue light-driven ChR2, allowing for the first time manipulations of neural synchrony without perturbation of other parameters such as spiking rates. The Halo/ChR2 system thus constitutes a powerful toolbox for multichannel photoinhibition and photostimulation of virally or transgenically targeted neural circuits without need for exogenous chemicals, enabling systematic analysis and engineering of the brain, and quantitative bioengineering of excitable cells.
PROTOTYPE - Suspected Overlap Among OBO Foundry Candidate Ontologies
PROTOTYPE Suspected Overlap Among OBO Foundry Candidate Ontologies
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Service that determines the Suspected Overlap Among OBO Foundry Candidate Ontologies.
The Committee on Publication Ethics (COPE) was established in 1997 by a small group of medical journal editors in the UK but now has over 7000 members worldwide from all academic fields. Membership is open to editors of academic journals and others interested in publication ethics. Several major publishers (including Elsevier, WileyBlackwell, Springer, Taylor & Francis, Palgrave Macmillan and Wolters Kluwer) have signed up their journals as COPE members. COPE provides advice to editors and publishers on all aspects of publication ethics and, in particular, how to handle cases of research and publication misconduct. It also provides a forum for its members to discuss individual cases (meeting four times a year in the UK and once a year in North America). COPE does not investigate individual cases but encourages editors to ensure that cases are investigated by the appropriate authorities (usually a research institution or employer). All COPE members are expected to follow the Code of Conduct for Journal Editors. COPE will investigate complaints that members have not followed the Code. COPE also funds research on publication ethics, publishes a quarterly newsletter and organises annual seminars in the UK and the USA. COPE has also created an audit tool for members to measure compliance with its Code of Conduct and Best Practice Guidelines for Journal Editors. What guidance is available on this website (for members and non-members)? * COPE Code of Conduct and Best Practice Guidelines for Journal Editors * Flowcharts on how to handle common ethical problems * Other COPE guidelines (eg on retractions) * Sample letters (to adapt for use) * Database of all cases discussed at COPE Forum (including podcasts of the discussion (where available), the advice given and the outcome of cases) Benefits of COPE membership COPE members can: * receive advice on individual cases via the Forum * access the eLearning package (due Q2 2011) * use the ethical audit tool to see how well their journals match COPE''s guidelines * use the COPE logo in their journal * apply for COPE research grants * stand for election to COPE Council
University of Texas Southwestern Medical Center - Alzheimer's Disease Center
A center dedicated to discovering treatments and providing preventative measures for Alzheimer's Disease. Research is strongly focused on brain changes in regards to healthy aging, mild cognitive impairment and other disorders, such as dementia. It aims to improve diagnostic measures and care giving techniques, discover more effective medical interventions, and understand the etiology of the disease and find an eventual cure. The center provides diagnostic evaluations of adult memory problems, as well as the opportunity to participate in clinical research to aid in finding better Alzheimer's treatments.
UT Southwestern ADC Brain Tissue Donation Program
Brain tissue donation program at the UT Southwestern Memory Clinic that aims to utilize these contributions for research on Alzheimer's. Diagnosis of Alzheimer's disease or other dementias are made through autopsy, the results of which are available to family members.
Software programs that are extensions of the LINKAGE programs that allow the disease phenotype to be under the control of disease two loci. (entry from Genetic Analysis Software)
Dataset from an investigation of biochemical evidence of myocardial strain, oxidative stress, and cardiomyocyte injury in 55 acute KD subjects (30 with paired convalescent samples), 54 febrile control (FC), and 50 healthy control (HC) children by measuring concentrations of cardiovascular biomarkers. NT-proBNP and sST2 were elevated in acute KD subjects and correlated with impaired myocardial relaxation. These findings, combined with elevated levels of cTnI, suggest that both cardiomyocyte stress and cell death are associated with myocardial inflammation in acute KD.
The mission of the Spinal Muscular Atrophy Foundation is to accelerate the development of a treatment for SMA, the number one genetic killer of infants and toddlers. To help speed the realization of a treatment or cure, the SMA Foundation is committed to: Developing private sector involvement in SMA drug development by fostering alliances between academia, government, and pharmaceutical and biotechnology companies Increasing government funding and support through targeted efforts to increase Congressional and NIH awareness Raising awareness of SMA among government leaders, members of the pharmaceutical and biotechnology industries, and the public at large
National Institute of Mental Health Director's Blog
National Institute of Mental Health Directors Blog
Blog by the NIMH Director, Thomas R. Insel, M.D. Users may sort posts by topic and/or subsribe to the RSS Feed, http://www.nimh.nih.gov/site-info/feed-directors-blog.atom
Brain's Inner Workings: Activities for Grades 9 through 12
Brains Inner Workings: Activities for Grades 9 through 12
The Brain's Inner Workings: Activities for Grades 9 through 12
This comprehensive free collection of multimedia resources and inquiry-based activities tied to the National Science Education Standards help teachers and students learn about the structure, function and cognitive aspects of the human brain. The packet includes a teacher's manual, student manual, DVD of videos, and a CDROM of accompanying materials.
Neuroscience and Psychiatry Module 2: Fear/Safety Anxiety and Anxiety Disorders
Fear/Safety Anxiety and Anxiety Disorders
Neuroscience Psychiatry Module 2: Fear/Safety Anxiety Anxiety Disorders
This is the second in a series of modules on neuroscience and psychiatry. This module describes neuroscience research on animal models of fear that informed human studies of fear/safety, anxiety and anxiety disorders. This model helps shed light on the symptoms of PTSD and lead to the development of a novel treatment that has been successful in research studies for several anxiety disorders.
Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD)
Systematic Treatment Enhancement Program for Bipolar Disorder
A long-term outpatient study designed to find out which treatments, or combinations of treatments, are most effective for treating episodes of depression and mania and for preventing recurrent episodes in people with bipolar disorder. This study has been completed. (2005) STEP-BD is evaluating all the best-practice treatment options used for bipolar disorder: mood-stabilizing medications, antidepressants, atypical antipsychotics, and psychosocial interventions - or talk therapies - including Cognitive Behavioral Therapy, Family-focused Therapy, Interpersonal and Social Rhythm Therapy, and Collaborative Care (psychoeducation). There are two kinds of treatment pathways in STEP-BD, and participants may have the opportunity to take part in both. The medications and psychosocial interventions provided in these pathways are considered among the best choices of treatment for bipolar disorder in everyday clinical practice. In the Best Practice Pathway, participants are followed by a STEP-BD certified doctor and all treatment choices are individualized. Everyone enrolled in STEP-BD may participate in this pathway. Participants and their doctors work together to decide on the best treatment plans and to change these plans if needed. Also, anyone who wishes to stay on his or her current treatment upon entering STEP-BD may do so in this pathway. Adolescents and adults age 15 years and older may participate in the Best Practice Pathway. For adults age 18 and older, another way to participate is in the STEP-BD Randomized Care Pathways. Depending on their symptoms, participants may be offered treatment in one or more of these pathways during the course of the study. The participants remain on mood-stabilizing medication. However, because doctors are uncertain which of several treatment strategies work best for bipolar disorder, another medication and/or talk therapy may be added. Each Randomized Care Pathway involves a different set of these additional treatments. Unlike in the Best Practice Pathway, the participants in the Randomized Care Pathways are randomly assigned to treatments. Also, in some cases, neither the participant nor the doctor will be told which of the different medications is being added. This is called a double-blind study and is done so that the medication effects can be evaluated objectively, without any unintended bias that may come from knowing what has been assigned. Participants will not be assigned medications that they have had bad reactions to in the past, that they are strongly opposed to, or that the doctor feels are unsuitable for them. The medication(s) participants may be randomly assigned to in the Randomized Care Pathways are free of charge. There are other treatment options for participants if they do not respond well to the treatment assigned to them. Also, participants may return to the Best Practice Pathway at any time. About 1,500 individuals will be enrolled in at least one Randomized Care Pathway during their period of participation in STEP-BD. It is important to note that STEP-BD provides continuity of care. For example, if a participant starts out in the Best Practice Pathway and later chooses to enter one of the Randomized Care Pathways, he or she continues with the same STEP-BD doctor and treatment team. Then, after completing the Randomized Care Pathway, the participant may return to the Best Practice Pathway for ongoing, individually-tailored treatment. Follow the link to view study info at Clinicaltrials.gov, http://www.clinicaltrials.gov/ct/show/NCT00012558?order=1
Merging Two Gene Expression Studies via Cross Platform Normalization.
National Institute of Mental Health Publications
Publications put out by the National Institute of Mental Health. Publications are available by topic: Disorders: * Attention Deficit Hyperactivity Disorder (ADHD) * Anxiety Disorders * Autism * Bipolar Disorder * Borderline Personality Disorder * Depression * Eating Disorders * Generalized Anxiety Disorder * Obsessive-Compulsive Disorder (OCD) * Panic Disorder * Post-Traumatic Stress Disorder * Schizophrenia * Social Phobia Populations * Older Adults * Men''s Mental Health * Women''s Mental Health * Children and Adolescents Research * Basic Research * Clinical Research and Trials * Research Funding * Mental Health Services Research Other * Coping with Traumatic Events * Genetics * HIV/AIDS * Imaging * Medications * NIMH * Prevention * Statistics * Suicide Prevention * Treatments
High throughput screening services to identify small molecules that can be optimized as chemical probes to study the functions of genes, cells, and biochemical pathways, along with medicinal chemistry and informatics. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. The NIH Molecular Libraries Initiative NIH is designed to discover small molecules that interact with biologically important proteins and pathways and to provide open access to the bioassay and chemical data generated by its research centers. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. As these HTS Technologies were not previously available to the public sector, many investigators may not be familiar with the components and requirements of high throughput screening. A key challenge is to identify small molecules effective at modulating a given biological process or disease state. The Molecular Libraries Roadmap, through one of its components, the Molecular Libraries Probe Production Centers Network (MLPCN), offers biomedical researchers access to the large-scale screening capacity, along with medicinal chemistry and informatics necessary to identify chemical probes to study the functions of genes, cells, and biochemical pathways. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. There are two kinds of data that are available to the scientific community through a dedicated database: Chemical Compounds and Bioassay Results (NCBI). Various types of data, including informative records on substances, compound structures, and biologically active properties of small molecules are housed respectively within PubChem' '''s three primary databases: PCSubstance, PCCompound, and PCBioAssay. To date, PubChem contains over 11 million substance records, details about approximately 5.5 million unique compound structures with links to bioassay descriptions, relevant literature, references, and assay data points and over 250 bioassays, a good percentage of which were contributed by the pilot phase of the MLP. The deposition will continue during the current MLPCN phase. NIH anticipates that these projects will also facilitate the development of new drugs, by providing early stage chemical compounds that will enable researchers in the public and private sectors to validate new drug targets, which could then move into the drug-development pipeline. This is particularly true for rare diseases, which may not be attractive for development by the private sector. Funding opportunities are available through the site.
Map of neural connections in mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types. In addition to the connectivity data, information about the transgenic mouse lines and genetic tracers is available. Consists of high resolution 2-D projectivity image data that can be viewed side-by-side with the associated reference atlas and other reference datasets. Enables 3-D visualization and spatial/ontological search of connectivity models through a combination of manual and informatics analyses.
Open tools to support data management for biological light microscopy produced by a multi-site collaborative effort among academic laboratories and a number of commercial entities. Designed to interact with existing commercial software, all OME formats and software are free, and all OME source code is available under the GNU General public license or through commercial license from Glencoe Software. OME is developed as a joint project between research-active laboratories at the Dundee, NIA Baltimore, and Harvard Medical School and LOCI. In addition, OME has active collaborations with many imaging and informatics groups. While many other applications could use OME''s architecture and design, their specific implementation is focused on biological and biomedical imaging. Those interested in applying OME''s technology to other applications should contact the developers. OME work is divided into several different standards and software projects: * Bio-Formats: A Java-based library for reading and writing over 90 microscopy file formats. * OMERO Software: The Java-based OMERO software project, which currently includes tools for storing, visualizing, managing, and annotating microscopic images and metadata. * OME-XML & OME-TIFF: The OME-XML and OME-TIFF file format specifications, which are open file formats for sharing microscope image data. * OME Server: This was the original OME server project which has now ended and is a legacy product. It implements image-based analysis of cellular dynamics and image-based screening of cellular localization or phenotypes, and included a fully developed version of the 2003 version of OME-XML Schema language.
My laboratory has created a family of natural product-inspired anticancer agents. We have evaluated our compounds at the Yale Center for Chemical Genomics, and they are exhibiting IC50 values in the low nM range against K562, HeLa, LnCAP, and HCT-116 lines. Their mechanism of action is unknown, although the natural products have been shown to cleave DNA. An evaluation of the natural products at the NCI has shown that they have a toxicity profile that is distinct from other known DNA damaging agents. We can readily access gram-quantities of these agents for further studies. We are looking for researchers who might find these compounds useful in medicinal applications, for example, for treatment of a specific cancer. We are capable of synthesizing new analogs, such as those incorporating a specific recognition or targeting element, and would be excited to pursue this avenue of research.
Database of blood-brain barrier properties of peptides including structure, method, responses, physicochemical properties and related literature. The database is linked to a manuscript entitled Brainpeps: the blood-brain barrier peptide database, in which the BBB methods and responses are clarified and correlated to each other. Data may be submitted for addition to the database.
Trans-NIH Brain Molecular Anatomy Project
The Brain Molecular Anatomy Project is a trans-NIH project aimed at understanding gene expression and function in the nervous system. BMAP has two major scientific goals: # Gene discovery: to catalog of all the genes expressed in the nervous system, under both normal and abnormal conditions. # Gene expression analysis: to monitor gene expression patterns in the nervous system as a function of cell type, anatomical location, developmental stage, and physiological state, and thus gain insight into gene function. In pursuit of these goals, BMAP has launched several initiatives to provide resources and funding opportunities for the scientific community. These include several Requests for Applications and Requests for Proposals, descriptions of which can be found in this Web site. BMAP is also in the process of establishing physical and electronic resources for the community, including repositories of cDNA clones for nervous system genes, and databases of gene expression information for the nervous system. Most of the BMAP initiatives so far have focused on the mouse as a model species because of the ease of experimental and genetic manipulation of this organism, and because many models of human disease are available in the mouse. However, research in humans, other mammalian species, non-mammalian vertebrates, and invertebrates is also being funded through BMAP. For the convenience of interested investigators, we have established this Web site as a central information resource, focusing on major NIH-sponsored funding opportunities, initiatives, genomic resources available to the research community, courses and scientific meetings related to BMAP initiatives, and selected reports and publications. When appropriate, we will also post initiatives not directly sponsored by BMAP, but which are deemed relevant to its goals. Posting decisions are made by the Trans-NIH BMAP Committee
We aim to facilitate the pathway for access, storage, use and transfer of human organs, cells and tissue between clinical centers within UCL Partners, academic groups in UCL, other universities, hospitals, medical researcher and biotechnology companies, to enhance the ability for researchers to access the materials they need. Alongside this, researchers will be able to exchange information and access guides on regulatory, ethics and practical issues concerning access, transfer and use of this type of material. These guides will be video and documents format, based on talks at organized events given by experts in the relevant fields. All of this information will be accessible on a website that seeks to link groups within UCL and attract attention from the wider world through social media and expansion of existing contacts. Our vision is to develop a centralized human tissue provision and utilization service for academic and commercial researchers UCL has the highest concentration of biomedical researchers in Europe. As part of this, UCL has numerous licensed biobanks and is associated with many research intensive hospitals in North London. The role of a biobank is to prepare and hold human tissue samples in for use by medical researchers to help delivery new treatments. Hospitals can also provide human tissue for research by utilizing waste human tissue taken as part of surgery or diagnostic procedures, but is normally incinerated. The researchers using the human tissue could be working within academic laboratories in UK universities and institutions or as part of commercial companies. Researchers currently cannot easily access human tissue to meet the demands of their research, often due to the long ethical, regulatory and contractual processes. However, with the enormous UCL biobanking and research Hospital resources, UCL could be a leading academic institution in providing human tissue for medical research within the UK and internationally. Our vision is to develop a centralized human tissue provision and utilization service for academic and commercial researchers. This relies on creating an overarching infrastructure, to consolidate information on disparate human tissue resources around UCL, and (where possible) gain centralized ethical and regulatory and contractual approval for use of the tissue. Funding the infrastructure will rely on a cost recovery model for a per sample basis. As a result the time needed to obtain tissue for research will be dramatically reduced, whilst providing a simple costing model for obtaining human tissue. This will make human tissue procurement much more efficient for end users.
Onto-Express is a web-based tool in the Onto-Tools suite that performs automated function profiling for a list of differentially expressed genes. However, Onto-Express does not support functional profiling for the organisms that do not have annotations in public domain, or use of custom (i.e. user-defined) ontologies. This limitation is also true for most of the other existing tools for functional profiling, which means that researchers working with uncommon organisms and/or new annotations or ontologies may be forced to construct such profiles manually. Onto-Express To Go (OE2GO) is a new tool added to the Onto-Tools ensemble to address these issues. OE2GO is built on top of OE to leverage its existing functionality. In OE2GO, the users now have an option to use either the Onto-Tools database as a source of functional annotations or provide their own annotations in a separate file. Currently, OE2GO supports annotation file in the Gene Ontology format. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Tk-GO is a GUI wrapping the basic functions of the GO AppHandle library from BDGP. GO terms are presented in an explorer-like browser, and behavior can be configured by altering Perl scripts. All available documentation is included in the download. Tk-GO uses the GO database (connects directly to the BDGP database by default) but is user-configurable. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
EGAN: Exploratory Gene Association Networks
Exploratory Gene Association Networks (EGAN)
Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible
UCSF Helen Diller Family Comprehensive Cancer Center
The UCSF Helen Diller Family Comprehensive Cancer Center combines basic science, clinical research, epidemiology/cancer control, and patient care throughout the University of California, San Francisco. UCSF''s long tradition of excellence in cancer research includes, notably, the Nobel Prize-winning work of J. Michael Bishop and Harold Varmus, who discovered cancer-causing oncogenes. Their work opened new doors for exploring genetic mistakes that cause cancer, and formed the basis for some of the most important cancer research happening today. * Basic Scientific Research: From understanding normal cellular processes and replication to discovering the underlying molecular and genetic causes of cancer when these processes go awry, UCSF researchers are committed to moving scientific insights beyond model systems and pursuing their relevance for clinical oncology and cancer prevention. * Clinical Research: Clinical scientists explore how greater understanding of fundamental biological events can be transformed into clinically relevant tools. New forms of cancer treatment, as well as innovations in diagnosis and prognosis, undergo rigorous evaluation for safety and efficacytranslating into improved patient outcomes and hope for the future. * Patient Care: The Helen Diller Family Comprehensive Cancer Center provides superlative cancer patient care at four San Francisco medical centers: UCSF Medical Center at Mount Zion; UCSF Medical Center at Parnassus; San Francisco General Hospital; and the San Francisco Veterans Affairs Medical Center. * Population Science: Cancer population sciences at UCSF includes a broad range of research on the causes of new cancers and the sickness and death due to the disease in order to develop ways to improve the prevention and early detection of cancer as well as the quality of life following diagnosis and treatment for all of Northern California''s diverse populations.
Spotfire Gene Ontology Advantage Application
The Spotfire Gene Ontology Advantage Application integrates GO annotations with gene expression analysis in Spotfire DecisionSite for Functional Genomics. Researchers can select a subset of genes in DecisionSite visualizations and display their distribution in the Gene Ontology hierarchy. Similarly, selection of any process, function or cellular location in the Gene Ontology hierarchy automatically marks the corresponding genes in DecisionSite visualizations. Platform: Windows compatible
Frey Lab - Probabilistic and Statistical Inference Group University of Toronto
The Frey Lab develops techniques that use large scale datasets to derive predictive models of how genes and many other genomic features act in combination to produce genetic messages that control cellular activities. We have most recently focused on how organisms use alternative splicing to generate a tremendous level of biological complexity that cannot be explained by gene expression alone (Nature, 2010). Some of the tools, software and databases provided by the Frey Lab are affinity propagation, splicing prediction, PTMClust - A Post-translational Modification Refinement Algorithm, the ''epitome'': A new model of patterns, transformation invariant clustering and subspaces, learning flexible sprites from images and videos, phase unwrapping by loopy belief propagation, useful Matlab scripts, bioinformatics links, and SeedSearcher: A motif finder.
The Edwards lab conducts research in various aspects of computational biology and bioinformatics, particularly proteomics and mass spectrometry informatics and DNA and protein based signatures for pathogen detection. Some tools provided by Edwards Lab are the PepArML Meta-Search Engine, PeptideMapper Web-Service, Peptide Sequence Databases, Rapid Microorganism Identification Database (RMIDb), and GlycoPeptideSearch. Our primary area of research is the analysis of mass spectrometry experiments for proteomics. Proteomics, the qualitative and quantitative analysis of the expressed proteins of a cell, makes it possible to detect and compare the protein abundance profiles of different samples. Proteins observed to be under or over expressed in disease samples can lead to diagnostic markers or drug targets. The observation of mutated or alternatively spliced protein isoforms may provide domain experts with clues to the mechanisms by which a disease operates. The detection of proteins by mass spectrometry can even signal the presence of airborne microorganisms, such as anthrax, in the detect-to-protect time-frame. Recent research has focused on the discovery of novel peptides in proteomics datasets, improving the sensitivity and specificity of peptide identification using spectral matching with hidden Markov models, and unsupervised machine-learning based peptide identification result combining. Outside of proteomics, we work on computational tools for the design of highly specific oligonucleotides useful for pathogen signatures and PCR assay design. Recent research has focused on precomputing all human oligos of length 20 that are unique up to 4 string edits; and all bacterial 20-mer oligos that are species specific up to 4 string edits.
Neurostruct - Project: Image and object processing filters for the tracing and analysis of neuroanatomy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A built-in toolbox for the tracing and analysis of neuroanatomy from nanoscale (high-resolution) imaging. It is a project under ongoing development. The name is originating by merging the words Neuron + reconstruct. The working concept is organized in filters applied successively on the image stack to be processed (pipeline). Currently, the focus of the software is the extraction of detailed neuroanatomical profiles from nanoscale imaging techniques, such as the Serial Block-Face Scanning Electron Microscopy (SBFSEM). The techniques applied, however, may be used to analyze data from various imaging methods and neuronal versatility. The underlying idea of Neurostruct is the use of slim interfaces/filters allowing an efficient use of new libraries and data streaming. The image processing follows in voxel pipelines by using the CUDA programming model and all filters are programmed in a datasize-independent fashion. Thus Neurostruct exploits efficiency and datasize-independence in an optimal way. Neurostruct is based on the following main principles: * Image processing in voxel pipelines using the general purpose graphics processing units (GPGPU) programming model. * Efficient implementation of these interfaces. Programming model and image streaming that guarantees a minimal performance penalty. * Datasize-independent programming model enabling independence from the processed image stack. * Management of the filters and IO data through shell scripts. The executables (filters) are currently managed through shell scripts. The application focuses currently in the tracing of single-biocytin filled cells using SBFSEM imaging. : * Extraction of neuroanatomical profiles: 3D reconstrution and 1D skeletons of the imaged neuronal structure. * Complete tracing: Recognition of the full neuronal structure using envelope techniques, thereby remedying the problem of spines with thin necks of an internal diameter approaching the SBFSEM resolution. * Separation (Coloring) of subcellular structures: Algorithms for the separation of spines from their root dendritic stem. * Evaluation and analysis of the imaged neuroanatomy: Calculation of the dendritic and spine membrane''s surface, spine density and variation, models of dendrites and spines
CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher
CBioC - Collaboratively uncovering the nuggets of knowledge buried in millions of biomedical texts
A tool for extraction and collaboration for data curation related to biology. CBioC runs as a web browser extension and allows unobtrusive use of the system during the regular course of research in PubMed. It can also be accessed directly (without having to install a plug-in). Automated text extraction is used as a starting point to bootstrap the database, but then it is up to biologists improve upon the extracted data, ironing out inconsistencies by subsequent edits on a massive scale. * After install, it loads when you visit PubMed. * Gets interactions from PubMed abstracts. * Allows you to vote and modify extracted data. * Also shows data from BIND, DIP, MINT, GRID, IntAct.
Gene Ontology for Motifs (GOMO) is an alignment- and threshold-free comparative genomics approach for assigning functional roles to DNA regulatory motifs from DNA sequence. The algorithm detects associations between a user-specified DNA regulatory motif (expressed as a position weight matrix; PWM) and Gene Ontology terms. The original method for predicting the roles of transcription factors (TFs starts with a PWM motif describing the DNA-binding affinity of the TF. GOMO uses the PWM to score the promoter region of each gene in the genome for its likelihood to be bound by the TF. The resulting ' '''affinity' ''' scores are then used to test each term in the Gene Ontology for association with high-scoring genes. The algorithm was subsequently extended to leverage conserved signals using multiple, related species in a comparative approach, which greatly improves the resulting annotations. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
OrChem is an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today''s powerful database servers to provide fast response times in equally large data sets. OrChem is an Oracle chemistry plug-in using the Chemistry Development Kit (CDK). The CDK is an open source Java library for Chemoinformatics and Bioinformatics. OrChem is maintained by the chemoinformatics and metabolism team of the European Bioinformatics Institute. Oracle Data cartridges extend the capabilities of the Oracle server. For chemistry various commercial cartridges exist that facilitate searching and analyzing chemical data. OrChem also provides functionality like this, but is not a cartridge. It doesn''t need Oracle''s extensibility architecture because its Java components run as Java stored procedures inside the Oracle standard JVM (Aurora). OrChem is suitable for Oracle 11G and onwards. Starting with Oracle 11g release 1 (11.1) there is a just-in-time(JIT) compiler for Oracle JVM environment. A JIT compiler for Oracle JVM enables much faster execution because it manages the invalidation, recompilation, and storage of code without an external mechanism. This new Oracle feature makes Java classes perform better than before.
Twin Study of Environmental Factors in Parkinson's Disease
The primary purpose is to assess the importance of environmental factors for Parkinson's Disease (PD) in a population-based sample of Swedish twins. In PD discordant twin pairs, what are the environmental factors that contribute to the disease in the affected twin and or protect the unaffected twin? Second, we want to investigate whether the earlier reports of low heritability for elderly male twins can be confirmed for female pairs. All twins 55 years of age and older in the Swedish Twin Registry have been screened for most complex diseases. 626 twins have screened positive for PD and most pairs are discordant. To establish diagnosis, a physician will examine all potential cases and their co-twins and their medical records will be reviewed. Environmental factors will be studied through the use of discordant pairs, where genetic susceptibility to the disease can be controlled. Environmental exposures are being secured with telephone interviews and from a questionnaire collected 30 years ago. Recent results indicate that genetic factors play a very small role. A better understanding of the etiology of PD is important for the possibility of delaying onset or even preventing the disease, as well as for providing guidance for molecular biology studies. Types of samples * DNA Number of sample donors: 333 (sample collection completed)
An algorithm to estimate isoforms expression from RNA-seq data based on a model that doesn''t assume uniform distribution of count within transcripts.
GFINDer: Genome Function INtegrated Discoverer
Genome Function INtegrated Discoverer (GFINDer)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. Multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results.
American Society of Hematology Image Bank
Image library offers a collection of peer reviewed images relating to hematology available to the ASH members and the hematology community. Image Bank slides are downloadable and users may create unique collections called My Collections. The Image Bank contains over 2100 images, and new images will be added each month. ASH encourages new submissions that are subject to review by the Image Bank Editor.
The Generic GO Term Finder finds the significant GO terms shared among a list of genes from an organism, displaying the results in a table and as a graph (showing the terms and their ancestry). The user may optionally provide background information or a custom gene association file or filter evidence codes. This tool is capable of batch processing multiple queries at once. GO::TermFinder comprises a set of object-oriented Perl modules GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script. This implementation, developed at the Lewis-Sigler Institute at Princeton, depends on the GO-TermFinder software written by Gavin Sherlock and Shuai Weng at Stanford University and the GO:View module written by Shuai Weng. It is made publicly available through the GMOD project. The full source code and documentation for GO:TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Agile Protein Interactomes DataServer (APID)
APID (Agile Protein Interactomes DataServer)
APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.
genes2mind is a tool for rapid exploratory analysis of psychotropic drug-induced gene expression in the brain. We present here an open resource containing comparison of effects of various classes of psychotropic drugs on transcriptional alterations of ~20,000 genes in the mouse brain (C57BL/6J). Data stored in the database include raw gene expression values as well as results of drug comparison. * Genomic Signature Identification section allows for the identification of drug-specific genomic signatures. * Genomic Signature Analysis section allows for further inspection and visualization of the signatures using multidimensional data analysis (PCA), co-expression analysis and heatmaps. * Single Gene Inspection allows for brief review of expression of specific candidate genes using barplots.
Quick ASL Wrapper for preprocessing arterial spin labeled (ASL) Data and computing blood flow measurements using UPenn ASL toolbox.
Max Planck Institute for Biological Intelligence
The Max Planck Institute of Neurobiology was a research institute of the Max Planck Society located in Martinsried, a suburb of Munich in Germany. It existed between 1984 and 2022 and merged with the Max Planck Institute for Ornithology to the new, joint Max Planck Institute for Biological Intelligence in 2023. The institute is dedicated to basic research on topics in behavioral ecology, evolutionary biology and neuroscience.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The aim of EXT (extinction) is to investigate the relation between specific genetic variations and cognitive control process in fear. Blood samples will be collected from about 300 healthy, young individuals (age 18-35).
Integrated Manually Extracted Annotation
Integrated Manually Extracted Annotation View
NIF Integrated Manually Extracted Annotation
A virtual database of annotations made by 50 database providers (April 2014) - and growing (see below), that map data to publication information. All NIF Data Federation sources can be part of this virtual database as long as they indicate the publications that correspond to data records. The format that NIF accepts is the PubMed Identifier, category or type of data that is being linked to, and a data record identifier. A subset of this data is passed to NCBI, as LinkOuts (links at the bottom of PubMed abstracts), however due to NCBI policies the full data records are not currently associated with PubMed records. Database providers can use this mechanism to link to other NCBI databases including gene and protein, however these are not included in the current data set at this time. (To view databases available for linking see, http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Databases_Available_for_Linking ) The categories that NIF uses have been standardized to the following types: * Resource: Registry * Resource: Software * Reagent: Plasmid * Reagent: Antibodies * Data: Clinical Trials * Data: Gene Expression * Data: Drugs * Data: Taxonomy * Data: Images * Data: Animal Model * Data: Microarray * Data: Brain connectivity * Data: Volumetric observation * Data: Value observation * Data: Activation Foci * Data: Neuronal properties * Data: Neuronal reconstruction * Data: Chemosensory receptor * Data: Electrophysiology * Data: Computational model * Data: Brain anatomy * Data: Gene annotation * Data: Disease annotation * Data: Cell Model * Data: Chemical * Data: Pathways For more information refer to Create a LinkOut file, http://neuinfo.org/nif_components/disco/interoperation.shtm Participating resources ( http://disco.neuinfo.org/webportal/discoLinkoutServiceSummary.do?id=4 ): * Addgene http://www.addgene.org/pgvec1 * Animal Imaging Database http://aidb.crbs.ucsd.edu * Antibody Registry http://www.neuinfo.org/products/antibodyregistry/ * Avian Brain Circuitry Database http://www.behav.org/abcd/abcd.php * BAMS Connectivity http://brancusi.usc.edu/ * Beta Cell Biology Consortium http://www.betacell.org/ * bioDBcore http://biodbcore.org/ * BioGRID http://thebiogrid.org/ * BioNumbers http://bionumbers.hms.harvard.edu/ * Brain Architecture Management System http://brancusi.usc.edu/bkms/ * Brede Database http://hendrix.imm.dtu.dk/services/jerne/brede/ * Cell Centered Database http://ccdb.ucsd.edu * CellML Model Repository http://www.cellml.org/models * CHEBI http://www.ebi.ac.uk/chebi/ * Clinical Trials Network (CTN) Data Share http://www.ctndatashare.org/ * Comparative Toxicogenomics Database http://ctdbase.org/ * Coriell Cell Repositories http://ccr.coriell.org/ * CRCNS - Collaborative Research in Computational Neuroscience - Data sharing http://crcns.org * Drug Related Gene Database https://confluence.crbs.ucsd.edu/display/NIF/DRG * DrugBank http://www.drugbank.ca/ * FLYBASE http://flybase.org/ * Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ * Gene Ontology Tools http://www.geneontology.org/GO.tools.shtml * Gene Weaver http://www.GeneWeaver.org * GeneDB http://www.genedb.org/Homepage * Glomerular Activity Response Archive http://gara.bio.uci.edu * GO http://www.geneontology.org/ * Internet Brain Volume Database http://www.cma.mgh.harvard.edu/ibvd/ * ModelDB http://senselab.med.yale.edu/modeldb/ * Mouse Genome Informatics Transgenes ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt * NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html * NeuroMorpho.Org http://neuromorpho.org/neuroMorpho * NeuronDB http://senselab.med.yale.edu/neurondb * SciCrunch Registry http://neuinfo.org/nif/nifgwt.html?tab=registry * NIF Registry Automated Crawl Data http://lucene1.neuinfo.org/nif_resource/current/ * NITRC http://www.nitrc.org/ * Nuclear Receptor Signaling Atlas http://www.nursa.org * Olfactory Receptor DataBase http://senselab.med.yale.edu/ordb/ * OMIM http://omim.org * OpenfMRI http://openfmri.org * PeptideAtlas http://www.peptideatlas.org * RGD http://rgd.mcw.edu * SFARI Gene: AutDB https://gene.sfari.org/autdb/Welcome.do * SumsDB http://sumsdb.wustl.edu/sums/ * Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat http://www.temporal-lobe.com/ * The Cell: An Image Library http://www.cellimagelibrary.org/ * Visiome Platform http://platform.visiome.neuroinf.jp/ * WormBase http://www.wormbase.org * YPED http://medicine.yale.edu/keck/nida/yped.aspx * ZFIN http://zfin.org
Garrison Institute on Aging - Brain Bank Program
Garrison Institute on Aging Brain Bank Program
TTUHSC Garrison Institute on Aging Brain Bank Program
The Brain Bank was developed with two service-minded objectives: provide a free brain autopsy to confirm clinical diagnosis of dementia, and collect, bank and provide brain tissue to qualified scientific researchers studying diseases related to dementia. By working together, patients and researchers can help us understand the origins of neurodegenerative disease and eventually improve the treatment and care of dementia. The clinical diagnosis of Alzheimer's disease can only be confirmed by brain autopsy, or the examination of brain tissue after death. This examination will determine a patients's precise type of dementia. To confirm the diagnosis of Alzheimer's, for example, the brain tissue is examined for amyloid plaques and neurofibrillary tangles by a neuropathologist. The presence of these plaques and tangles will verify the clinical diagnosis of Alzheimer's disease. While it is important to us to enroll patients with dementia, it is equally important to enroll people with no dementia. These subjects are termed as controls and the brain tissue from controls will enable researchers to make comparisons to brain tissue from dementia patients. We are seeking donations from individuals who have had an age-related neurodegenerative disease like Alzheimer's, Parkinson's, Lewy Body or other related dementia.
Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research. Features of Google Scholar * Search diverse sources from one convenient place * Find articles, theses, books, abstracts or court opinions * Locate the complete document through your library or on the web * Learn about key scholarly literature in any area of research How are documents ranked? Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature. * Publishers - Include your publications in Google Scholar * Librarians - Help patrons discover your library''s resources
Cancer Registry of Norway: Institute of Population-based Cancer Research
Comprises 3 registries of cancer patients in Norway: the Incidence Registry, the Clinical Registry and Cancer Statistics. The Incidence Registry contains the basic data items collected from clinicians and pathologists, as well as from administrative discharge and mortality sources. It is updated continuously with information on both new cases, as well as cases diagnosed in previous years. All medical doctors in the country are instructed by law to notify new cancer cases. Clinical Registries: Registration of treatment and follow-up of Norwegian cancer patients. Clinical registries comprehensive registration schemes dedicated to specific cancers have been established to include detailed information on diagnostic measures, therapy, and follow-up. Cancer Statistics: Database of cancer statistics. The Cancer Registry of Norway is maintained by the Institute of Population-based Cancer Research and established in 1951. It is one of the oldest national cancer registries in the world. This, combined with the unique personal identification number used in Norway, makes the Cancer Registry''s data suitable, also internationally; by establishing new knowledge through research and spreading information on cancer.
Alcohol abuse among women: improved understanding of psychiatric co-morbidity and personality traits as a basis for better treatment.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of the study is to improve the understanding of psychiatric co-morbidity and personality traits as a means to improving prevention and treatment for women with hereditary vulnerability to develop alcohol and / or drug dependence. In depth phenotypic assessment through structured interviews with women with alcohol or drug abuse in order to assess history, psychiatric morbidity and personality traits potentially related to environmental and/or hereditary alcoholism. Association studies of polymorphic markers in candidate genes. Blood samples and interviews performs on 200 women with alcohol dependents to examine mental illness and specific personality characteristics associated to environment and/or hereditary form of alcoholism. Blood samples are also collected from 200 healthy women which functions as controls.
Express Yourself: microarray data processing platform
ExpressYourself: microarray data processing platform
A fully integrated platform for processing microarray data.
We''re bringing Web-based research into the Internet Era by empowering people to mark up web pages in the browser and manage and collaborate on them online. And that''s just the start... We''ve got much more planned in a variety of areas to help people manage the mounds of info they''re pulling off the Web everyday. Simply drag the scrible bookmarklet to your browser''s Bookmarks toolbar. Click it later to mark up, save or share web pages. Even though the world uses the Internet to research nearly everything for work, school and home (job postings, press releases, Wikipedia articles, medical info, etc.), most folks still use old-school ways of annotating, organizing and sharing online info (printing to mark by hand, copying/pasting into Word, etc.). It''s archaic, laborious and a waste of time. We''re changing that. A bookmarklet is a bookmarked link that, when clicked, adds functionality to your browser. When the scrible Bookmarklet is clicked, it loads the scrible Toolbar atop the current webpage you''re viewing. Adding the scrible Bookmarklet to your browser is a breeze. Simply drag it to your browser''s Bookmarks Toolbar.
The Swedish Registry was established in the 1960s to study how smoking affects our health. Then little was known about the dangers of smoking. There is, at present, information on approximately 85 000 twin pairs, both monozygotic and dizygotic. As described by Lichtenstein et al., 2002, Pedersen et al., 2002 and Lichtenstein et al., 2006, the Swedish Twin Registry (STR) is the largest and most comprehensive twin registry in the world. Founded in 1961, the registry covers all like-sexed twin births since 1886, and all twin births (like- and unlike-sexed) since 1906. There are currently 89,000 pairs of twins registered, of which both members of 65,000 pairs are alive, with regular updates concerning vital status, addresses, hospital discharges, tumors, and causes of death, through subscriptions to national registries. Furthermore, there is extensive epidemiological data (exposures, symptoms and disease through questionnaires or interviews) on all pairs born 1986 or earlier, for most individuals involving 30 year baseline to follow-up information. Furthermore, data from the cohort of twins born since 1991 have been or will be contacted with a telephone interview with the parents of twins as they turn 9 (CATSS). Because the STR is an (inter)national resource, we are receptive to collaboration academic and industry-based researchers. Regardless of the type of research all potential collaborations or data access agreements must be first reviewed Steering Committee of the STR.
A twin study characterizing the importance of genetic factors for dementia and using discordant twin pairs to study other putative risk factors which control for genetic propensity to develop the disease. Molecular genetic studies have identified a number of mutations and other markers associated with early age of onset Alzheimer' '''s disease. However, most cases of late age of onset dementia are considered sporadic, that is, without a clear genetic basis. Twin studies provide a unique opportunity to characterize the importance of genetic factors for dementia. Discordant twin pairs additionally provide the opportunity to study other putative risk factors which controlling for genetic propensity to develop the disease. In the first wave of the Study of Dementia in Swedish Twins, all SATSA twins born before 1935 have been screened for dementia symptoms. Over 190 suspects have been identified. This pilot study has been expanded to the entire registry in the study known as HARMONY. All twins aged 65 and older were invited to participate in a computer assisted telephone screening interview. A total of 13,519 individuals completed the interview (response rate = 75.9%). Dementia screening was based on the TELE, which includes the 10-item MSQ, other cognitive items (counting backwards, recalling three words, and similarities), and questions about health and daily functioning; or on Blessed scores obtained from a proxy interview. Among those screened, 1565 were positive for suspicion of dementia and were referred for complete clinical evaluation by a physician and a nurse. Once the preliminary in-person evaluation suggested that the suspected case was demented, the twin partner was also invited for an identical clinical work-up. Response rate for clinical evaluations is 71.4%. Approximately half of those visited for evaluation have been diagnosed as demented according to DSM-IV criteria, of which two-thirds have Alzheimer' '''s disease. An extensive assessment of probable risk exposure is also included. Longitudinal follow-up is yet another feature of the study. Association studies with candidate genes are also being performed. Types of samples * DNA Number of sample donors * 1154 (sample collection completed)
DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on diseases related to the assembled human proteins. Database is richly annotated in the systemic information on the nomenclature, chemistry and structure of the DNA damage and drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA metabolism pathway analysis. Database includes illustrations of pathway, damage, protein and drug. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines it has to be extensively linked to numerous external data sources. Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. DNAtraffic database is freely available and can be queried by the name of DNA network process, DNA damage, protein, disease, and drug.
A native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University).
Functional Analysis of Diffusion Tensor Tract Statistics
Pipeline developed for delineating the association between multiple diffusion properties along major white matter fiber bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these white matter tract properties in various diffusion tensor imaging studies. FADTTS can be used to facilitate understanding of normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. The advantages of FADTTS compared with the other existing approaches are that they are capable of modelling the structured inter-subject variability, testing the joint effects, and constructing their simultaneous confidence bands.
Alameda County Health and Ways of Living Study
Alameda County [California] Health and Ways of Living Study
Data set from a long-term population-based prospective study of non-institutionalized residents (aged 21 or older, or aged 16-21 and older if married) in Alameda County, California investigating social and behavioral risk factors for morbidity, mortality, functioning and health. Questions were asked on marital and life satisfaction, parenting, physical activities, employment, health status, and childhood experiences. Demographic information on age, race, height, weight, education, income, and religion was also collected. Included with this dataset is a separate file (part 2) containing mortality data. With the aging of this cohort, data are becoming increasingly valuable for examining the life-long cumulative effects of social and behavioral factors on a well-characterized population. The first wave collected information for 6,928 respondents (including approximately 500 women aged 65 years and older) on chronic health conditions, health behaviors, social involvements, and psychological characteristics. The 1974 questionnaire was sent to 6,246 living subjects who had responded in 1965, and were able to be located. The third wave provides a follow-up of 2,729 original 1965 and 1974 respondents and examines health behaviors such as alcohol consumption and smoking habits, along with social activities. Also included is information on health conditions such as diabetes, osteoporosis, hormone replacement, and mental illness. Another central topic investigated is activities of daily living (including self-care such as dressing, eating, and shopping), along with use of free time and level of involvement in social, recreational, religious, and environmental groups. The fourth wave is a follow-up to the 1994 panel and examines changes in functional abilities such as self-care activities, employment, involvement in community activities, visiting friends/family, and use of free time since 1994. * Dates of Study: 1965-1999 * Sample Size: 1965: 6,928; 1974: 4,864; 1994: 2,729; 1995: 2,569, 1999: 2,123 * Study Features: Longitudinal Links: * 1965 ICPSR, http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06688 * 1974 ICPSR, http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06838 * 1994 and 1995 ICPSR, http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03083 * 1999 ICPSR, http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04432#summary
Automatic Hippocampal Estimator using Atlas-based Delineation
Automatic Hippocampal Estimator using Atlas-based Delineation (AHEAD)
Open-source turnkey software for automatic hippocampus segmentation. Its primary use is for delineating hippocampus in T1-weighted MRI images. AHEAD is developed by Jung W. Suh, Hongzhi Wang, Sandhitsu Das, Brian Avants, Philip Cook, John Pluta and Paul Yushkevich, and colleagues at the Penn Image Computing and Science Laboratory (PICSL) at the University of Pennsylvania.
An R extension to ANTs that performs multivariate statistical parametric mapping of DTI, T1 and other datatypes for the purpose of both performing clinical studies and for tracking the performance of ANTs (and other) image processing methodologies. ANTsR depends upon the R statistical language, bash scripts and the ANTs toolkit. Some branches of ANTsR will also depend upon pipedream and specific datasets. Some of these datasets will be open access and, in that case, ANTsR will provide a 100% reproducible neuroimaging study on that data.
Second Malaysian Family Life Survey (MFLS-2)
A follow-up of the 1976-1977 MFLS-1 dataset covering the respondents'' and spouses'' marriage, fertility, employment, education and migration histories as well as extensive information on the household economy. The MFLS-2 contains a supplementary sample of persons age 50 or older. The data permit analysis of intergenerational transfers to the elderly and their covariates; the living arrangements of the elderly; the health of the elderly; labor supply, occupation and retirement status of the elderly; and their migration patterns. This supplement fills the gap left by many standard sources of demographic and economic information about Third World populations, such as fertility surveys and labor force surveys, which effectively exclude the elderly. Field work for MFLS-2 began in Aug. 1988 and was completed in Jan. 1989. The survey was fielded in four samples: * The Panel Sample Women who were the primary respondents to the MFLS-1, who at that time (1976) were ever-married women aged 50 or younger. There are 926 panel households in MFLS-2, a follow-up rate of 72%. * The Children Sample Children aged 18 or older in 1988 of the women interviewed as primary respondents for MFLS-1; i.e. adult children of the women eligible for the MFLS-2 Panel sample. There were interviews with one child, selected at random, inside the Panel household and two children, selected at random, living elsewhere in Peninsular Malaysia. There are 1,136 respondents in the Children sample. * The New Sample A sample of households with a woman aged 18-49 (regardless of her marital status) or an ever-married woman under age 18. There are 2,184 respondents in MFLS-2 New Sample. * The Senior Sample Selected households with a person age 50 or over. There are 1,357 respondents in the Senior Sample. Data Availability: The MFLS-2 (and MFLS-1) data files and documentation are available on-line or from NACDA at ICPSR as Study No. 9805. * Dates of Study: 1988-1989 * Study Features: International * Sample Size: Seniors (aged 50+): 1,357 Link: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/09805
G-node portal electrophysiology data sharing
Platform for sharing data, with very large storage capability for electrophysiological data, EEG data is included. This service is provided for neuroscientists to facilitate data access, data storage, data analysis and data sharing. This service is developed and maintained by the German Node of the International Neuroinformatics Coordinating Facility. The global scale of neuroinformatics offers unprecedented opportunities for scientific collaborations between and among experimental and theoretical neuroscientists. To fully harvest these possibilities, coordinated activities are required to improve key ingredients of neuroscience: data access, data storage, and data analysis, together with supporting activities for teaching and training. Focusing on the development and free distribution of tools for handling and analyzing neurophysiological data, G-Node aims at addressing these aspects as part of the International Neuroinformatics Coordination Facility (INCF) and the German Bernstein Network for Computational Neuroscience (NNCN). G-Node also serves as an international forum for Computational Neuroscientists that are interested in sharing experimental data and tools for data analysis and modeling. G-Node is funded through the German Federal Ministry of Education and Research and hosted by Ludwig-Maximilians-Universit-Munchen.
FishFace - An atlas of zebrafish craniofacial development
FishFace: An Atlas of zebrafish craniofacial development
ishFace is an atlas of zebrafish craniofacial development. How do the elements of the craniofacial skeleton arise, grow, and reshape? Answers to this question are coming from both molecular-genetic and cell-biological approaches, which rely, first of all, on precise description of the developmental events and processes that comprise skeletogenesis. Zebrafish, with a sophisticated knowledge of its genetics and genomics, with favorable attributes for phenotypic analyses of development, and with patterns of development conserved among all vertebrates, provides a powerful animal model for learning about craniofacial development. In particular, with current transgenic approaches one can examine craniofacial skeletal elements in exquisite cellular detail during an extended period of development within living, intact embryos and larvae an investigative method unsurpassed in accuracy and sensitivity. We constructed this developmental atlas of the craniofacial skeleton, FishFace, to serve as a guide for such study. We hope that the FishFace Atlas will be particularly useful in comparative and mutational analyses where there is interest in understanding the cellular basis of early skeletogenesis. The heart of the FishFace Atlas uses high magnification (generally a 40x objective) confocal image stacks showing transgenically-labelled chondrocytes or osteoblasts, along with mineralized bone matrix, which is visualized by vital staining with Alizarin red. We present these stacks in sequences that follow particular individual cartilages and bones of the first two pharyngeal arches as they develop during embryonic and larval stages. To do so, we build on the foundation set out in the gold standard reference for describing comprehensively skeletal elements in the zebrafish craniofacial complex, Cubbage and Mabee (1996), which used fixed preparations stained for cartilage and bone through adult stages. The FishFace Atlas element development section adds considerable detail to arch one and two early development, particularly at the cellular level, but also in description of element growth and shaping. Other sections of the FishFace Atlas, at lower magnification, provide anatomical context for the element development section, including an interactive tool made by optical projection tomography (OPT) for learning the anatomy of the entire larval skull. Hence, the FishFace Atlas provides the community with an interactive resource with which the user can understand not only the cellular details, but also complex 3D anatomical relationships, of developing elements in the craniofacial skeleton of the zebrafish.
The Charleston Heart Study (CHS) is a prospective cohort study of 2,283 subjects (1,394 whites, 889 blacks) in which risk factors of coronary disease have been examined for the past 43 years. The CHS began enrolling a random selection of community residents who in 1960 were 35 years of age and older ����?? including men and women, black and white. A unique feature of this cohort is the fact that 102 high socio-economic status (SES) black men were purposefully included. The primary hypothesis of the original study was to investigate racial differences in the manifestation and risk factors for coronary disease. Over the ensuing 40+ years, a variety of outcome measurements were incorporated into the re-examination of the participants, including psychosocial, behavioral, aging and functional measures. Subjects were initially interviewed and examined in 1960 and 1963. Subsequent interviews and examinations took place during the following time periods: 1974-1975, 1984-1985, 1987-1989, and 1990-1991. During the most recent questionnaire (1990-1991), the following topics were examined: general health, smoking, functional disability, physical disability, cardiovascular health, sexual dysfunction, cognitive disability, depression, coffee consumption, medication history, medical history, nutrition, and body image. In addition, serum samples and blood pressure measurements were taken, and a physical exam was performed by a physician. A search of the National Death Index was completed through the year 2000, matching individuals with date and cause of death. Vital status of the CHS study participants through 12-31-2000 is presented below. Dead * White Men 539 (82.5%) * White Women 500 (67.5%) * Black Men 281 (84.4%) * High SES Black Men 59 (57.8%) * Black Women 343 (75.6%) Data Availability: Datasets are stored in the National Archive of Computerized Data on Aging (NACDA) in the ICPSR as Study No. 4050. Data are also available from the Medical University of South Carolina Library; contact a PI, Paul J. Nietert, nieterpj (at) musc.edu for further information. * Dates of Study: 1960-2000 * Study Features: Longitudinal, Minority Oversamples, Anthropometric Measures * Sample Size: 1960: 2,283 (baseline) Link ICPSR, http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04050
Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML
Twin Study of Child and Adolescent Development - TCHAD
Twin Study of Child Adolescent Development - TCHAD
Twin Study of Child and Adolescent Development
Data and biomaterial from a longitudinal study of 1,500 Swedish twin pairs from age 8 to age 20. Twins, parents, and teachers responded to 4 waves of questionnaires (1994, 1999, 2002, 2006) and a clinical interview. In the last follow up (2006) 1325 biological samples for DNA-extraction were collected. A paper that describes the study was published (Lichtenstein, Tuvblad, Larsson, Carlstrom, 2007, Twin Research and Human Genetics). Twins were followed prospectively from childhood to emerging adulthood. The data include a broad spectrum of measures of environments as well as internalizing and externalizing problems behaviors from different informants (twins, parents, teachers, clinical assessments).
An Antibody supplier. Now called Bio-Rad Antibodies.
hiPathDB - human integrated Pathway DB with facile visualization
hiPathDB is an integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. In total, it includes 1661 pathways consisting of 8976 distinct physical entities. (2010.03.09) hiPathDB provides two different types of integration. The pathway-level integration, conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account and subsequently reformatting all pathways in accordance with our model. The entity-level integration creates a single unified pathway that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Another strong merit of hiPathDB is the built-in pathway visualization module that supports explorative studies of complex networks in an interactive fashion. The layout algorithm is optimized for virtually automatic visualization of the pathways.
ADEPT - Assessment of Doctor-Elderly Patient Encounters
Assessment of Doctor-Elderly Patient Encounters
Assessment of Doctor-Elderly Patient Encounters (ADEPT)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on Septemeber 02, 2014. Through a collaborative effort with experts in doctor-elderly patient interaction who participated in the development of ADEPT, a database of approximately 435 audio and video tapes of visits of patients age 65 and older (n=46) to their primary physician was established for testing ADEPT and for access by medical educators and researchers. Data associated with each tape include reason for visit, physician characteristics (age, race, gender), patient characteristics (age, race, gender), companion characteristics (age, race, gender), and length of doctor-patient relationship. Through a collaborative effort with experts in doctor-elderly patient interaction who participated in the development of ADEPT, a database of approximately 435 audio and video tapes of visits of patients age 65 and older (n=46) to their primary physician was established for testing ADEPT and for access by medical educators and researchers. Data associated with each tape include reason for visit, physician characteristics (age, race, gender), patient characteristics (age, race, gender), companion characteristics (age, race, gender), and length of doctor-patient relationship. Patient visits to their primary physician were videotaped at four sites: an academic medical center in the Midwest, an academic medical center in the Southwest, a suburban managed care medical group, and an urban group of physicians in independent practice. Repeat visits between the same doctor and patient were taped for 19 patients resulting in 48 tapes of multiple visits. Patients were recruited in the waiting room for a convenience sample. Before the visit, patients provided demographic data and completed a global satisfaction form. Following the visit, patients completed the SF-36, and the ABIM for patient satisfaction. Two weeks following the visit, patients were contacted by telephone and asked about their understanding, compliance and their utilization of health services over the past year. At twelve months, patients were contacted by telephone for administration of the SF-36, the global satisfaction form, and the utilization of health services survey. Data Availability: Archived at the Saint Louis University School of Medicine Library. Interested researchers and medical educators should contact the PI, Mary Ann Cook, JVCRadiology (at) sbcglobal.net * Dates of Study: 1998-2001 * Study Features: Longitudinal, Anthropometric Measures * Sample Size: 46
Dynamics of Population Aging in ECE Countries
Dynamics of Population Aging in Economic Commission for Europe Countries
Population Activities Unit Census Microdata Samples Project
Status of Older Persons in UNECE Countries
A data set of cross-nationally comparable microdata samples for 15 Economic Commission for Europe (ECE) countries (Bulgaria, Canada, Czech Republic, Estonia, Finland, Hungary, Italy, Latvia, Lithuania, Romania, Russia, Switzerland, Turkey, UK, USA) based on the 1990 national population and housing censuses in countries of Europe and North America to study the social and economic conditions of older persons. These samples have been designed to allow research on a wide range of issues related to aging, as well as on other social phenomena. A common set of nomenclatures and classifications, derived on the basis of a study of census data comparability in Europe and North America, was adopted as a standard for recoding. This series was formerly called Dynamics of Population Aging in ECE Countries. The recommendations regarding the design and size of the samples drawn from the 1990 round of censuses envisaged: (1) drawing individual-based samples of about one million persons; (2) progressive oversampling with age in order to ensure sufficient representation of various categories of older people; and (3) retaining information on all persons co-residing in the sampled individual' '''s dwelling unit. Estonia, Latvia and Lithuania provided the entire population over age 50, while Finland sampled it with progressive over-sampling. Canada, Italy, Russia, Turkey, UK, and the US provided samples that had not been drawn specially for this project, and cover the entire population without over-sampling. Given its wide user base, the US 1990 PUMS was not recoded. Instead, PAU offers mapping modules, which recode the PUMS variables into the project' '''s classifications, nomenclatures, and coding schemes. Because of the high sampling density, these data cover various small groups of older people; contain as much geographic detail as possible under each country' '''s confidentiality requirements; include more extensive information on housing conditions than many other data sources; and provide information for a number of countries whose data were not accessible until recently. Data Availability: Eight of the fifteen participating countries have signed the standard data release agreement making their data available through NACDA/ICPSR (see links below). Hungary and Switzerland require a clearance to be obtained from their national statistical offices for the use of microdata, however the documents signed between the PAU and these countries include clauses stipulating that, in general, all scholars interested in social research will be granted access. Russia requested that certain provisions for archiving the microdata samples be removed from its data release arrangement. The PAU has an agreement with several British scholars to facilitate access to the 1991 UK data through collaborative arrangements. Statistics Canada and the Italian Institute of statistics (ISTAT) provide access to data from Canada and Italy, respectively. * Dates of Study: 1989-1992 * Study Features: International, Minority Oversamples * Sample Size: Approx. 1 million/country Links: * Bulgaria (1992), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/02200 * Czech Republic (1991), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06857 * Estonia (1989), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06780 * Finland (1990), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06797 * Romania (1992), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06900 * Latvia (1989), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/02572 * Lithuania (1989), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03952 * Turkey (1990), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03292 * U.S. (1990), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06219
Cross-Sectional and Longitudinal Aging Study
Cross-Sectional and Longitudinal Aging Study (CALAS)
A data set designed to provide a cross-sectional description of health, mental, and social status of the oldest-old segment of the elderly population in Israel, and to serve as a baseline for a multiple-stage research program to correlate demographic, health, and functional status with subsequent mortality, selected morbidity, and institutionalization. Study data are based on a sample of Jewish subjects aged 75+, alive and living in Israel on January 1, 1989, randomly selected from the National Population Register (NPR), a complete listing of the Israeli population maintained by the Ministry of the Interior. The NPR is updated on a routine basis with births, deaths, and in and out migration, and corrected by linkage with census data. The sample was stratified by age (five 5-year age groups: 75-79, 80-84, 85-89, 90-94, 95+), sex, and place of birth (Israel, Asia-Africa, Europe-America). One hundred subjects were randomly selected in each of the 30 strata. However, there were less than 100 individuals of each sex aged 95+ born in Israel, so all were selected for the sample. The total group included 2,891 individuals living both in the community and in institutions. A total of 1,820 (76%) of the 75-94 age group were interviewed during 1989-1992. An additional cognitive exam (Folstein) and a 24-hour dietary recall interview were added in the second round. Kibbutz Residents Sample The kibbutz is a social and economic unit based on equality among members, common property and work, collaborative consumption, and democracy in decision making. There are 250 kibbutzim in Israel, and their population constitutes about 3% of the country''s total population. All kibbutz residents in the country aged 85+, both members and parents, were selected for interviewing, of whom 80.4% (n=652) were interviewed. A matched sample aged 75-84 was selected, and 85.9% (n=674) were successfully interviewed. The original interview took approximately two hours to administer, and collected extensive information concerning the socio-demographic, physical, health, functioning, life events (including Holocaust), depression, mental status, and social network characteristics of the sample. The questionnaire used for kibbutz residents in the follow-up interview is identical to that utilized in the national random sample. Data Availability: Mortality data for both the national and kibbutz samples are available for analysis as a result of the linkage to the NPR file updated as of June 2000. The fieldwork for first follow up was completed as of September 1994 and for the second follow up as of December 2002. The data file of the three phases of the study is ready for analysis. * Dates of Study: 1989-1992 * Study Features: Longitudinal, International * Sample Size: 2,891
Chinese Longitudinal Healthy Longevity Survey (CLHLS)
Chinese Longitudinal Healthy Longevity Survey
The project has been collecting detailed panel data about the health, disability, demographic, family, socioeconomic, and behavioral risk-factors for mortality and healthy longevity of the oldest old, with a comparative sub-sample of younger elders, to examine the factors in healthy longevity. The baseline survey was conducted in 1998 and the follow-up surveys with replacement to compensate for deceased elders were conducted in 2000, 2002, 2005, and 2008, For each centenarian, one near-by octogenarian (aged 80-89) and one near-by nonagenarian (aged 90-99) of pre-designated age and sex were interviewed. Near-by is loosely defined it could be in the same village or street if available, or in the same town or in the same county or city. The idea was to have comparable numbers of male and female octogenarians and nonagenarians at each age from 80 to 99. In 2002, the study added a refresher sub-sample of 4,845 interviewees aged 65-79, and a sub-sample of 4,478 adult children (aged 35-65) of the elderly interviewees aged 65-110 in eight provinces Comparative study of intergenerational relationships in the context of rapid aging and healthy longevity between Mainland China and Taiwan is possible. At each wave, the longitudinal survivors were re-interviewed, and the deceased interviewees were replaced by additional participants. Data on mortality and health status before dying for the 12,136 elders aged 65-112 who died between the waves were collected in interviews with a close family member of the deceased. The study also included interviews and follow-ups with 4,478 elderly interviewees' ''' children aged 35-65. * Dates of Study: 1998-2005 * Study Features: Longitudinal, International * Sample Size: ** 1998: 8,993 ** 2000: 11,199 ** 2002: 16,064 ** 2005: 14,923 Links * Data Archive, http://www.geri.duke.edu/china_study/CLHLS6.htm * ICPSR, http://www.icpsr.umich.edu/icpsrweb/NACDA/studies/03891
SHEEP - Stockholm Heart Epidemiology Program
DNA from a population-based case-control study designed to investigate causes of myocardial infarction. The study population comprised all Swedish citizens living in the county of Stockholm who were 45 to 70 years of age and free of previously clinically diagnosed MI. Sample types: * DNA Number of sample donors: 2831 (sample collection completed)
LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes
LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes
LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression.
miRNEST - a database of animal and plant microRNAs
A database of animal, plant and virus microRNA data maintained at the University of Poznan. The database provides: * 9980 miRNA candiates from 420 animal and plant species predicted in Expressed Sequence Tags * predicted targets for plant candidates * RNA-seq reads mapped to candidates from 29 species * external data from 12 databases that includes sequences, polymorphism, expression and regulation. miRNEST 1.0, it contains miRNA from 563 animals, plants and viruses plant species.
A foundation that offers grants for researchers in cardiology, lipid and organ transplant in Washington and Alaska. The Robert B McMillen Foundation is a non-profit charitable foundation established to; promote research in the areas of cardiology, lipid and organ transplant, support education at the university and college level in the states of Washington and Alaska and provide funding for social service organizations. What we fund: * MEDICAL: 50% of our annual giving is earmarked for medical research. We will consider making grants to non-profit organizations involved in researching cardiology, lipid and organ transplants. * EDUCATION: 25% of our annual giving is earmarked for Education at the University level in the states of Washington and Alaska. Funding will be provided to support the art departments of post secondary schools who offer a degree in the visual arts. * SOCIAL: 25% of our annual giving is earmarked for social areas including, but not limited to, Goodwill, Salvation Army & United Way. Preference is given to organizations and/or programs that use art as the vehicle to impact communities and change individual lives.
Established Populations for Epidemiologic Studies of the Elderly
A collection of data that describes and identifies predictors of mortality, hospitalization, and placement in long-term care facilities and investigates risk factors for chronic diseases and loss of functioning. The EPESE project consisted of baseline and annual follow-up surveys on approximately 14,000 noninstitutionalized persons aged 65 and older in four geographically-defined communities: East Boston, Massachusetts; Iowa and Washington counties, Iowa; New Haven, Connecticut (started in 1982-1983); and a five-county-wide region in north-central North Carolina (started in 1986). Half of the participants in the North Carolina EPESE are African-American. The baseline data cover demographic characteristics (age, sex, race, height, weight, income, education, marital status, number of children, employment, and religion); social and physical functioning; chronic conditions; related health problems; health habits; self-reported use of dental, hospital, and nursing home services. More detailed descriptions of the Iowa and North Carolina surveys follow in this document (Iowa 65+ Rural Health Study and PHSE Ten-Year Follow-up of North Carolina EPESE). Data Availability: Data from the baseline and the first 6 years of follow-up are available as ICPSR Study No. 9915. Information from death certificates obtained for deaths occurring in the first 6 years of follow-up is also available. * Dates of Study: 1981-1993 * Study Features: Longitudinal, Minority Oversamples, Anthropometric Measures * Sample Size: ** 1981: 14,458 (Baseline) ** 1982: 14,070 (First follow-up) ** 1983: 13,382 (Second follow-up) ** 1984: 12,381 (Third follow-up) ** 1985: 11,657 (Fourth follow-up) ** 1986: 10,998 (Fifth follow-up) ** 1987: 9,998 (Sixth follow-up) Link * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/09915
Functional Genomics Data Pipeline (FGDP)
A Java-based, Microarray or Genechip data analysis system.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2025. Human protein knowledge platform. Knowledge platform for human proteins selects and filters high throughput data pertinent to human proteins from UniProtKB. Extends UniProtKB/Swiss-Prot annotations for human proteins to include several new data types.
PDBj (Protein Data Bank Japan) maintains a centralized PDB archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU.
ELK is an ontology reasoner with the goal of supporting the OWL 2 EL profile. ELK is a specialized reasoner for the lightweight ontology language OWL EL. The practical utility of ELK is in its combination of high performance and comprehensive support for language features. At its core, ELK employs a consequence-based reasoning engine that can take advantage of multi-core and multi-processor systems. A modular architecture allows ELK to be used as a stand-alone application, Protege plug-in, or programming library (either with or without the OWL API).
Medical Image Analysis (MIA) Laboratory - Resting State Data
Medical Image Analysis Lab - Resting State Data
Medical Image Analysis Laboratory - Resting State Data
An MRI data set that demonstrates the utility of a mega-analytic approach by identifying the effects of age and gender on the resting-state networks (RSNs) of 603 healthy adolescents and adults (mean age: 23.4 years, range: 12-71 years). Data were collected on the same scanner, preprocessed using an automated analysis pipeline based in SPM, and studied using group independent component analysis. RSNs were identified and evaluated in terms of three primary outcome measures: time course spectral power, spatial map intensity, and functional network connectivity. Results revealed robust effects of age on all three outcome measures, largely indicating decreases in network coherence and connectivity with increasing age. Gender effects were of smaller magnitude but suggested stronger intra-network connectivity in females and more inter-network connectivity in males, particularly with regard to sensorimotor networks. These findings, along with the analysis approach and statistical framework described, provide a useful baseline for future investigations of brain networks in health and disease.
Neuroscience Gateway - A Portal for Computational Neuroscience
Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists.
Health Conditions of Elderly Puerto Ricans (PREHCO)
Puerto Rican Elderly: Health Conditions (PREHCO)
A dataset that provides researchers and policy makers information about issues affecting the elderly population in Puerto Rico: health status, housing arrangements, functional status, transfers, labor history, migration, income, childhood characteristics, health insurance, use of health services, marital history, mistreat, sexuality, etc. It investigates the characteristics of older adults (aged 60+) through an island-wide cross-sectional sample survey of target individuals and their surviving spouses. The sampling frame was constructed on the basis of an advance release of the 2000 US Census. The population for the study consists of the elderly population (60+) in households in Puerto Rico. The sample design used a multistage probabilistic sample by cluster. All elderly adults who lived in the selected households were eligible. If more than one person was in the target population, one 60+ adult was the target and one was the spouse. Respondents 80+ and males in couples who were both 80+ were oversampled. There were 4,293 targets aged 60+ and 1,444 spouses (all ages) in the first wave. Types of data include demographic; household composition; marital history; Cantrill Scale; mini-mental (designed to measure cognitive capacity of Spanish-speaking Latinos with low levels of education and to provide early indications of dementia); self-reported health status; diagnosed health conditions; childhood conditions; transfers; labor history; migration; housing; assets; Activities of Daily Living; Instrumental Activities of Daily Living; medicines; health insurance and use of health services; family structure; sexuality; anthropometric measures. Project innovations include: (1) the design and test of a new tool for assessing cognition among Spanish speaking elderly of low levels of education, (2) a symptoms section to assess the validity of selected self reported conditions, (3) a modification of the Cantrill''s Ladder Scale, (4) protocols for physical measurements to assess current, as well as past, conditions, and (5) the use of GIS and GPS in the fieldwork supervision and to geocoding the survey data. At this moment PREHCO has completed a second wave to become a longitudinal study. The questionnaire included questions regarding the changing conditions (health, residential, social and economic) of those individuals who responded the first questionnaire. The new questionnaire included novel components: vignettes for health status self-report, a new improved section on disability and dependency, and on labor force participation. We also expanded the section of anthropometry by adding a few measurements and physical efficiency tests. Those participants deceased or institutionalized were interviewed using a proxy. Data Availability: First and second wave data are available for public use through BADGIR, the online data archive at the University of Wisconsin-Madison, at: http://nesstar.ssc.wisc.edu/ * Dates of Study: 2002-2003, 2004-2006 * Study Features: Longitudinal, International, Minority Oversampling, Anthropometric measures * Sample Size: 5,336
Statistical Torsional Angles Potentials of NMR Refinement Database
STAP refinement of NMR Database is based the Statistical Torsion Angles Potentials to refine the NMR structure. It stored original solution NMR structures from the Protein Data Banks and our refined structures. Currently we carried out 2,405 refined NMR structure (until Sept 20, 2011). According to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. STAP of NMR Refinement Database is a public database of 2405 refined NMR solution structures from the Protein Data Bank (PDB). A simulated annealing protocol was employed to obtain refined structures with target potentials, including the newly developed STAP. The refined database was extensively analyzed using various quality indicators from several assessment programs to determine the nuclear Overhauser effect (NOE) completeness, Ramachandran appearance, (1)-(2) rotamer normality, various parameters for protein stability and other indicators. Most quality indicators are improved in our protocol mainly due to the inclusion of the newly developed knowledge-based potentials. This database can be used by the NMR structure community for further development of research and validation tools, structure-related studies and modelling in many fields of research.
Termini oriented protein Function Inferred Database
An integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases. It lists more than 120,000 N- and C-termini and almost 10,000 cleavages. TopFIND is a resource for comprehensive coverage of protein N- and C-termini discovered by all available in silico, in vitro as well as in vivo methodologies. It makes use of existing knowledge by seamless integration of data from UniProt and MEROPS and provides access to new data from community submission and manual literature curating. It renders modifications of protein termini, such as acetylation and citrulination, easily accessible and searchable and provides the means to identify and analyse extend and distribution of terminal modifications across a protein. The data is presented to the user with a strong emphasis on the relation to curated background information and underlying evidence that led to the observation of a terminus, its modification or proteolytic cleavage. In brief the protein information, its domain structure, protein termini, terminus modifications and proteolytic processing of and by other proteins is listed. All information is accompanied by metadata like its original source, method of identification, confidence measurement or related publication. A positional cross correlation evaluation matches termini and cleavage sites with protein features (such as amino acid variants) and domains to highlight potential effects and dependencies in a unique way. Also, a network view of all proteins showing their functional dependency as protease, substrate or protease inhibitor tied in with protein interactions is provided for the easy evaluation of network wide effects. A powerful yet user friendly filtering mechanism allows the presented data to be filtered based on parameters like methodology used, in vivo relevance, confidence or data source (e.g. limited to a single laboratory or publication). This provides means to assess physiological relevant data and to deduce functional information and hypotheses relevant to the bench scientist. TopFIND PROVIDES: * Integration of protein termini with proteolytic processing and protein features * Displays proteases and substrates within their protease web including detailed evidence information * Fully supports the Human Proteome Project through search by chromosome location CONTRIBUTE * Submit your N- or C-termini datasets * Contribute information on protein cleavages * Provide detailed experimental description, sample information and raw data
Database of helpful set of CreERT2 driver lines expressing in various regions of the developing and adult zebrafish. The lines have been generated via the insertion of a mCherry-T2A-CreERT2 in a gene trap approach or by using promoter fragments driving CreERT2. You can search the list of all transgenic lines or single entries by insertions (gene) or expression patterns (anatomy/region). In most cases the CreERT2 expression profile using in situ hybridization at 24 hpf and 48 hpf is shown, but also additional information (e.g. mCherry or CreERT2 expression at adult stages, transactivation of a Cre-dependent reporter line) is displayed. Currently, not all insertions have been mapped to a genomic location but the database will be regularly updated adding newly generated insertions and mapping information. Your help in improving and broadening the database by giving your opinion or knowledge of expression patterns is highly appreciated.
A database of all mouse strains developed and/or housed in the Alexander Fleming Biomedical Sciences Research Center (BSRC), Greece, available to both internal and external researchers. The animal house unit provides its services to the various research groups of the BSCR as well as to external contractors in Europe and U.S.A. (pharmaceutical and biotechnology companies, leading hospitals, and academic institutions). The information provided includes: general information (i.e. internal Fleming contact, original mouse creator, allelic composition and MTA details), availability (i.e. available genetic background and strain state), allele & mutations (i.e. allele name and symbol and mutation type), publications and handling & genotyping instructions.
Early Indicators of Later Work Levels Disease and Death (EI) - Union Army Samples Public Health and Ecological Datasets
Early Indicators of Later Work Levels Disease and Death ������?? Union Army Samples
Early Indicators of Later Work Levels Disease and Death
A dataset to advance the study of life-cycle interactions of biomedical and socioeconomic factors in the aging process. The EI project has assembled a variety of large datasets covering the life histories of approximately 39,616 white male volunteers (drawn from a random sample of 331 companies) who served in the Union Army (UA), and of about 6,000 African-American veterans from 51 randomly selected United States Colored Troops companies (USCT). Their military records were linked to pension and medical records that detailed the soldiers������?? health status and socioeconomic and family characteristics. Each soldier was searched for in the US decennial census for the years in which they were most likely to be found alive (1850, 1860, 1880, 1900, 1910). In addition, a sample consisting of 70,000 men examined for service in the Union Army between September 1864 and April 1865 has been assembled and linked only to census records. These records will be useful for life-cycle comparisons of those accepted and rejected for service. Military Data: The military service and wartime medical histories of the UA and USCT men were collected from the Union Army and United States Colored Troops military service records, carded medical records, and other wartime documents. Pension Data: Wherever possible, the UA and USCT samples have been linked to pension records, including surgeon' '''s certificates. About 70% of men in the Union Army sample have a pension. These records provide the bulk of the socioeconomic and demographic information on these men from the late 1800s through the early 1900s, including family structure and employment information. In addition, the surgeon' '''s certificates provide rich medical histories, with an average of 5 examinations per linked recruit for the UA, and about 2.5 exams per USCT recruit. Census Data: Both early and late-age familial and socioeconomic information is collected from the manuscript schedules of the federal censuses of 1850, 1860, 1870 (incomplete), 1880, 1900, and 1910. Data Availability: All of the datasets (Military Union Army; linked Census; Surgeon' '''s Certificates; Examination Records, and supporting ecological and environmental variables) are publicly available from ICPSR. In addition, copies on CD-ROM may be obtained from the CPE, which also maintains an interactive Internet Data Archive and Documentation Library, which can be accessed on the Project Website. * Dates of Study: 1850-1910 * Study Features: Longitudinal, Minority Oversamples * Sample Size: ** Union Army: 35,747 ** Colored Troops: 6,187 ** Examination Sample: 70,800 ICPSR Link: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06836
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Database of chemicals and reactions inside of US patents (2001 - 2011). SCRIPDB provides the full original patent text, reactions and relationships described within any individual patent, in addition to the molecular files common to structural databases. The patent literature is a rich catalog of biologically relevant chemicals; many public and commercial molecular databases contain the structures disclosed in patent claims. However, patents are an equally rich source of metadata about bioactive molecules, including mechanism of action, disease class, homologous experimental series, structural alternatives, or the synthetic pathways used to produce molecules of interest. Unfortunately, this metadata is discarded when chemical structures are deposited separately in databases. SCRIPDB is a chemical structure database designed to make this metadata accessible. The SCRIPDB information is valuable in medical text mining, chemical image analysis, reaction extraction and in silico pharmaceutical lead optimization. SCRIPDB may be searched by exact chemical structure, substructure or molecular similarity and the results may be restricted to patents describing synthetic routes.
Los Angeles Family and Neighborhood Survey
Los Angeles Family and Neighborhood Survey (L.A.FANS)
A dataset of a panel study of a representative sample of all neighborhoods and households in Los Angeles County, with poor neighborhoods and families with children oversampled, for investigating the social and economic determinants of health and race and ethnic disparities. The study follows neighborhoods over time, as well as children and families. Two waves have been conducted to date, in 2000-2001 (L.A.FANS 1) and again beginning in 2006 through early 2009 (L.A. FANS 2). L.A.FANS-2 will significantly enhance the utility of the L.A.FANS data for studies of adult health disparities by: 1) Replicating self-reported health measures from L.A.FANS-1 and collecting new self-reports on treatment, health behaviors, functional limitations, quality and quantity of sleep, anxiety, health status vignettes, and changes in health status since the first interview; 2) Collecting physiological markers of disease and health status, including diabetes, hypertension, obesity, lung function, immune function, and cardiovascular disease; and 3) Expanding the data collected on adults'' work conditions, stressful experiences, and social ties. Wherever possible, L.A.FANS uses well-tested questions or sections from national surveys, such as the Health and Retirement Study (HRS), Panel Study of Income Dynamics (PSID), National Longitudinal Surveys (NLS), and National Health Interview Survey (NHIS), and other urban surveys, such as the Project on Human Development in Chicago Neighborhoods, to facilitate comparisons. Data Availability: Public use data, study design, and questionnaire content from L.A.FANS are available for downloading. Researchers can also apply for a restricted use version of the L.A.FANS-1 data that contain considerable contextual and geographically-referenced information. Application procedures are described at the project Website. L.A.FANS-2 fieldwork was completed at the end of 2008. The PIs anticipate L.A.FANS-2 public use data will be released in summer 2009. * Dates of Study: 2000-2008 * Study Features: Longitudinal, Minority Oversamples, Anthropometric Measures, Biospecimens * Sample Size: ** 2000-1: 2,548 (L.A.FANS 1) ** 2006-8: ~3,600 (L.A.FANS 2) Link: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00172
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 11, 2022. Project for human epigenomic data from experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent normal counterparts of tissues and organ systems frequently involved in human disease. Consortium expects to deliver collection of normal epigenomes that will provide framework or reference for comparison and integration within broad array of future studies. Consortium is also committed to development, standardization and dissemination of protocols, reagents and analytical tools to enable research community to utilize, integrate and expand upon this body of data.
Digital Imaging and Communications in Medicine
Standards for communications between medical imaging devices, including handling, storing and transmitting information in medical imaging. It includes a file format definition and a network communication protocol.
Science Niblets - The Science Behind Everyday Topics
An online science magazine with short science articles about everyday life and popular science book reviews. We like science. Thus, we have created this popular science online magazine to describe and explain scientific topics that confront us in our everyday life. These topics can be about natural phenomena, physics of sports, biology and life science, or the physics behind standard devices or common technologies. Additionally, we present and review popular science books. We address the general public in our science articles. Thus, our articles are short and explanations are easy to understand. We use a simple language to explain the science behind everyday topics so that it is fun to read. The texts are suitable for all age groups and also for non native English speakers and ESL classes. Submissions are welcome and after a review process, we would be happy to publish your contribution under your name. We also included a section in which readers can post questions. These posts inspire future articles. Science articles can be used as authentic sources in content-based instruction to teach English Language Learners (ELLs). For this purpose, I have created materials for teaching English in a scientific context. Select Science Niblets articles have been supplemented with relevant activities and additional authentic materials that encourage intercultural discussion and the use of the four receptive and productive language skills: reading, listening, writing and speaking. The theoretical and pedagogical framework that underlie the materials are explained in the teachers'' guide. The materials themselves consist of a lesson plan for the teacher and a learner worksheet that are printable pdf files.
Archive of medical images of cancer accessible for public download. All images are stored in DICOM file format and organized as Collections, typically patients related by common disease (e.g. lung cancer), image modality (MRI, CT, etc) or research focus. Neuroimaging data sets include clinical outcomes, pathology, and genomics in addition to DICOM images. Submitting Data Proposals are welcomed.
University of Michigan Health and Retirement Study
University of Michigan Health and Retirement Study (HRS)
A data set of a longitudinal panel study of health, retirement, and aging that surveys a representative sample of more than 26,000 Americans over the age of 50 every two years. The HRS explores the changes in labor force participation and the health transitions that individuals undergo toward the end of their work lives and in the years that follow. The study captures a dynamic picture of an aging America''s physical and mental health, insurance coverage, financial status, family support systems, labor market status, and retirement planning. The sample in 2006 numbered over 22,000 persons in 13,100 households, with oversamples of Hispanics, Blacks and Florida residents. Beginning in 2006, half the sample received enhanced face-to-face follow-ups that included the collection of physical measures and biomarkers HRS provides a research data base that can simultaneously support continuous cross-sectional descriptions of the US population over the age of fifty-five, longitudinal studies of a given cohort over a substantial period of time (up to 18 years by 2010 for the original HRS cohort, following them from age 51-61 to age 69-79) and research on cross-cohort trends. By 2010 the HRS will be able to support cross-cohort comparisons of trajectories of health, labor supply, or wealth accumulation for persons who entered their 50s in 1992, 1998 and 2004. The HRS also has provided the sampling frame for targeted sub-studies. The Aging, Demographics, and Memory Study (ADAMS) supplement on dementia involved a field assessment of a sample of about 930 HRS panel members aged 75+ to clinically assess their dementia status and dementia severity. Special topics including consumption and time use, prescription drug use and the impact of Medicare Part D, parents'' human capital investments in children, and diabetes management by self-reported diabetics, have appeared on mail surveys that have used the HRS as a sampling frame. The HRS also can accommodate a number of experimental topics using Internet interviewing. The HRS is also characterized by links to a rich array of administrative data, including: Employer Pension Plans; National Death Index; Social Security Administration earnings and (projected) benefits data; W-2 self-employment data; and Medicare and Medicaid files. The HRS has actively collaborated with other longitudinal studies of aging in other countries (e.g., ELSA, SHARE, MHAS), providing both scientific and technical assistance. Data Availability: All publicly available data may be downloaded after registration. Early Release data files are typically available within three months of the end of each data collection, with the Final Release following at 24 months after the close of data collection activities. Files linked with administrative data are released only as restricted data through an application process, as outlined on the HRS website. * Dates of Study: 1992-present * Study Features: Longitudinal, Minority Oversamples, Anthropometric Measures, Biospecimens * Sample Size: 22,000+ Link * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06854
An open course site where you can take the World''s Best Courses, Online, For Free. We are a social entrepreneurship company that partners with the top universities in the world to offer courses online for anyone to take, for free. We envision a future where the top universities are educating not only thousands of students, but millions. Our technology enables the best professors to teach tens or hundreds of thousands of students. Through this, we hope to give everyone access to the world-class education that has so far been available only to a select few. We want to empower people with education that will improve their lives, the lives of their families, and the communities they live in. Our Courses Classes offered on Coursera are designed to help you master the material. When you take one of our classes, you will watch lectures taught by world-class professors, learn at your own pace, test your knowledge, and reinforce concepts through interactive exercises. When you join one of our classes, you''ll also join a global community of thousands of students learning alongside you. We know that your life is busy, and that you have many commitments on your time. Thus, our courses are designed based on sound pedagogical foundations, to help you master new concepts quickly and effectively. Key ideas include mastery learning, to make sure that you have multiple attempts to demonstrate your new knowledge; using interactivity, to ensure student engagement and to assist long-term retention; and providing frequent feedback, so that you can monitor your own progress, and know when you''ve really mastered the material. We offer courses in a wide range of topics, spanning the Humanities, Medicine, Biology, Social Sciences, Mathematics, Business, Computer Science, and many others. Whether you''re looking to improve your resume, advance your career, or just learn more and expand your knowledge, we hope there will be multiple courses that you find interesting.
Oregon Health and Science University Brain Institute
A clinical care and research center for neurological conditions such as Alzheimer's, dementia and seizure disorders. It provides a dynamic setting for training healthcare professionals and neuroscience researchers to develop and implement evidence-based treatment.
A database of over 300 Electron Microscopy (EM) images of centrioles and centriole related structures from almost 60 species, described by a controlled vocabulary allowing detailed description of the observed structures. This knowledge is supplemented by a manually curated list of proteins known to be involved in centriole assembly, their (putative) orthologs, and localization information. mtocDB aims to characterize the naturally occurring morphological variation observed in centrioles and centriole associated structure alongside molecular information on the proteins involved in their assembly. Examining these in an evolutionary context will allow the cell biology community to infer meaningful relationships between cellular assembly mechanisms and the structures they form. This community resource for cell biologists interested in the the evolution of centrioles and centriole related structures aims to bridge the gap between structural morphology and molecular function by examining naturally occurring structural variation in a phylogenomic context. Centrioles are cylindrical microtubule arrays required for stability and duplication of the centrosome in animal cells, and for the assembly of cilia and flagella in many eukaryotes. The presence of centrioles throughout most eukaryotic branches suggests that this structure was present in the last eukaryotic common ancestor. Although centrioles show a typically well conserved structure, they can perform several functions and display a diversity of accessory structures. However, this diversity is not properly classified beyond model organisms, and the information contained in decades of electronic microscopy of other organisms remains untapped.
A neuro blog that is no longer updated but has interesting archives. Categories: * Academia * Activism * Addiction * Aging/Gerontology * Basic Science Posts * Behavioral Neuro * Blog Carnivals * CNS Diseases and Disorders * Cognition * Creationism / Intelligent Design * Evil Journal Club * Evolution * Friday Weird Science * Health Care / Medicine * Menopause * Natural Sciences * Neuroanatomy * Neuroscience * Philosophy * Physiology / Pharmacology * Politics/Policy * Primatology * Religion * Rocket Surgery * Samsara * SchadenFriday * Synaptic Misfires
A dataset, 1970-2009, containing equivalently defined variables for the British Household Panel Study (BHPS), the Household Income and Labour Dynamics in Australia (HILDA), the Korea Labor and Income Panel Study (KLIPS) (new this year), the Panel Study of Income Dynamics (PSID), the Russia Longitudinal Monitoring Survey (RLMS-HSE) (new this year), the Swiss Household Panel (SHP), the Canadian Survey of Labour and Income Dynamics (SLID), and the German Socio-Economic Panel (SOEP). The data are designed to allow cross-national researchers not experienced in panel data analysis to access a simplified version of these panels, while providing experienced panel data users with guidelines for formulating equivalent variables across countries. The CNEF permit researchers to track yearly changes in the health and economic well-being of older people relative to younger people in the study countries. The equivalent file provides a set of constructed variables (for example pre- and post-government income and United States and international household equivalence weights) that are not directly available on the original surveys. Since the Cross-National Equivalent File 1970-2009 can be merged with the original surveys, PSID-CNEF users can easily incorporate these constructed variables into current analyses. The most recent release of the Equivalent File includes: * BHPS data from 1991 to 2005 on over 21,000 individuals and approximately 6,000 households. * GSOEP data from 1984 to 2007 on over 20,000 individuals and approximately 6,000 households in Germany. * HILDA data from 2001 to 2006 on over 19,000 individuals and 7,000 households. * PSID data from 1980 to 2005 on over 33,000 individuals and approximately 7,000 households. * SHP data from 1999 to 2006 on 12,900 individuals and 5,000 households. * SLID data from 1993 to 2006 on over 95,000 individuals and approximately 32,000 households. With one exception, the CNEF country data are available on CD-ROM from Cornell University for a fee. The Canadian SLID data are not distributed on the CD but are available to CNEF registered researchers through special arrangements with Statistics Canada. Complete instructions for obtaining CNEF data may be accessed on the project website. * Dates of Study: 1980-2007 * Study Features: International, Longitudinal * Sample Size: ** BHPS: 21,000+ ** PSID: 33,000+ ** SLID: 95,000+ ** GSOEP: 20,000+ ** HILDA: 19,000+ ** SHP: 12,900+ NACDA link: http://www.icpsr.umich.edu/icpsrweb/NACDA/studies/00145/detail
Kannisto-Thatcher Database on Old Age Mortality
Kannisto-Thatcher Database on Old Age Mortality at the Max Planck Institute for Demographic Research
A database that includes data on death counts and population counts classified by sex, age, year of birth, and calendar year for more than 30 countries. This database was established for estimating the death rates at the highest ages (above age 80). The core set of data in the database was assembled, tested for quality, and converted into cohort mortality histories by V��in�� Kannisto, the former United Nations advisor on demographic and social statistics. Comparable materials on England and Wales, was made available by A. Roger Thatcher, the former Director of the Office of Population Censuses and Surveys and Registrar-General of England and Wales (Kannisto, 1994). The Kannisto-Thatcher database was computerized under the supervision of James W. Vaupel at the Aging Research Unit of the Centre for Health and Social Policy at Odense University Medical School in 1993. Currently, the database is maintained by the Max Planck Institute for Demographic Research, Germany.
A data set and sister study to the Established Populations for Epidemiologic Study of the Elderly (EPESE). It complements the findings of the three other EPESE sites (East Boston, MA; New Haven, CT; and north-central North Carolina) and has common items and methods in many domains. The target population was all persons 65 years and older in two rural counties in east central Iowa: Iowa and Washington counties. In 1981 a census of older persons in the target area was conducted by the investigators, creating an ascertainment list having 99% of the persons identified in the previous year by the US Decennial Census. The baseline survey was conducted between December 1991 and August 1992. Overall, 3,673 persons, or 80% of the target population were interviewed: 65-69 (N = 986), 70-74 (N = 988), 75-79 (N = 815), 80-84 (N = 523), and 85+ (N = 361). The population is virtually entirely Caucasian. Subsequently, personal follow-up surveys were conducted 3, 6, and 10 years after the baseline survey. Telephone surveys were conducted 1, 2, 4, 5, and 7 years after the baseline survey. Data collected from respondents included information about demographics, major health conditions, health care utilization, hearing and vision, weight and height, elements of nutrition, sleep problems, depressive and anxiety symptoms, alcohol and tobacco use, cognitive performance and dementia screening, incontinence measures, life satisfaction index, social networks and support, worries, medication use, activities of daily living, dental problems, satisfaction with medical care, life events, brief economic status, automobile driving habits, multiple measures of physical and disability status, and blood pressure. At follow-up #6, there were a series of physical function performance tests, the so-called NIA-MacArthur Battery, and blood was drawn for biochemical tests and potentially other determinations. In addition, some datasets were linked to the EPESE dataset under appropriate restrictions, including Iowa state driving records and clinical diagnoses and medical care utilization from the Centers for Medicare and Medicaid Services. Data Availability: The dataset has been shared with several investigative teams under special arrangement with the Principal Investigator. Early surveys are available from ICPSR. A small storage of blood is available for exploratory analyses. * Dates of Study: 1991-2001 * Study Features: Longitudinal, Anthropometric Measures, Biomarkers * Sample Size: 1991-2: 3,673 (baseline) Link: EPESE 1981-93 ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/09915
An academic and industrial research consortium in Digital Human Modeling that will create an advanced data-driven biomechanical statistical anatomical model as a digital ergonomics and design tool to help users augment or accelerate human abilities. They believe that two key problems have fundamentally restricted progress on understanding human properties and responses: a lack of direct community collaboration and a focus on animal-based research. Due to the highly multi-disciplinary nature of our undertaking, sharing of data and algorithms between institutions will be critical to their success. However, this data must be strictly based on human anatomy and human tissue sources. The strategy is to provide strategic and technical leadership to the research community in the form of a collaborative modeling framework to encode human properties and processes. Within this framework: * determine morphological variation of human anatomy * determine material properties of all human tissues * model physiological and biomechanical human processes The strategy is also to enable academic, industrial and government applications leveraging a complete human model to develop a broad variety of solutions to serve humanity.
Longitudinal Study of Generations (LSOG)
A dataset of a survey of intergenerational relations among 2,044 adult members of some 300 three- (and later four-) generation California families: grandparents (then in their sixties), middle-aged parents (then in their early forties), grandchildren (then aged 16 to 26), and later the great-grandchildren as they turn age 16, and further surveys in 1985, 1988, 1991, 1994, 1997 and 2001. This first fully-elaborated generation-sequential design makes it possible to compare sets of parents and adult-children at the same age across different historical periods and addresses the following objectives: # To track life-course trajectories of family intergenerational solidarity and conflict over three decades of adulthood, and across successive generations of family members; # To identify how intergenerational solidarity, and conflict influence the well-being of family members throughout the adult life course and across successive generations; # To chart the effects of socio-historical change on families, intergenerational relationships, and individual life-course development during the past three decades; # To examine women''s roles and relationships in multigenerational families over 30 years of rapid change in the social trajectories of women''s lives. These data can extend understanding of the complex interplay among macro-social change, family functioning, and individual well-being over the adult life-course and across successive generations. Data Availability: Data from 1971-1997 are available through ICPSR as Study number 4076. * Dates of Study: 1971-2001 * Study Features: Longitudinal * Sample Size: ** 345 Three-generational families ** 2,044 Adults (1971 baseline) Link: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04076
An Organization portal, Material service resource, Antibody supplier, Instrument supplier
Longitudinal Study of Elderly Mexican American Health
Hispanic Established Populations for Epidemiologic Studies of the Elderly
Longitudinal Study of Mexican-American Elderly Health
Longitudinal Study of Mexican-American Elderly Health (The Hispanic EPESE)
A dataset of a longitudinal study of over 3,000 Mexican-Americans aged 65 or over living in five southwestern states. The objective is to describe the physical and mental health of the study group and link them to key social variables (e.g., social support, health behavior, acculturation, migration). To the extent possible, the study was modeled after the existing EPESE studies, especially the Duke EPESE, which included a large sample if African-Americans. Unlike the other EPESE studies that were restricted to small geographic areas, the Hispanic EPESE aimed at obtaining a representative sample of community-dwelling Mexican-American elderly residing in Texas, New Mexico, Arizona, Colorado, and California. Approximately 85% of Mexican-American elderly reside in these states and data were obtained that are generalizable to roughly 500,000 older people. The final sample of 3,050 subjects at baseline is comparable to those of the other EPESE studies. Data Availability: Waves I to IV are available through the National Archive of Computerized Data on Aging (NACDA), ICPSR. Also available through NACDA is the ����??Resource Book of the Hispanic Established Populations for the Epidemiologic Studies of the Elderly����?? which offers a thorough review of the data and its applications. All subjects aged 75 or older were interviewed for Wave V and 902 new subjects were added. Hemoglobin A1c test kits were provided to subjects who self-reported diabetes. Approximately 270 of the kits were returned for analyses. Wave V data are being validated and reviewed. A tentative timeline for the archiving of Wave V data is November 2006. Wave VI interviewing and data collection is scheduled to begin in Fall 2006. * Dates of Study: 1993-2006 * Study Features: Longitudinal, Minority oversamples, Anthropometric Measures * Sample Size: ** 1993-4: 3,050 (Wave I) ** 1995-6: 2,438 (Wave II) ** 1998-9: 1,980 (Wave III) ** 2000-1: 1,682 (Wave IV) ** 2004-5: 2,073 (Wave V) ** 2006-7: (Wave VI) Links: * ICPSR Wave 1: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/2851 * ICPSR Wave 2: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/3385 * ICPSR Wave 3: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/4102 * ICPSR Wave 4: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/4314 * ICPSR Wave 5: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/25041 * ICPSR Wave 6: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/29654
Matlab Health and Socio-Economic Survey (MHSS)
Matlab Health and Socioeconomic Survey (MHSS)
A data set of the health and socioeconomic factors that affect the elderly in Matlab, a region of rural Bangladesh. The survey captures measurements and statistics such as adult survival, health status, health care utilization, resource flows between generations and the impact of community services and infrastructure on adult health care. Data was collected through surveys that touch on four topics: household and individual information; determinants of natural fertility; migration out of the community; and community and provider survey of healthcare and education infrastructure.
A data set of a longitudinal survey designed to study changes in the health and functional status of older Americans (aged 65+). It also tracks health expenditures, Medicare service use, and the availability of personal, family, and community resources for caregiving. The survey began in 1982, and follow-up surveys were conducted in 1984, 1989, 1994, 1999, and 2004. The surveys are of the entire Medicare-enrolled aged population with a particular emphasis on the functionally impaired. As sample persons are followed through the Medicare record system, virtually 100% of cases can be longitudinally tracked so that declines, as well as increases, in disability may be identified as well as exact dates of death. NLTCS sample persons are followed until death and are permanently and continuously linked to the Medicare record system from which they are drawn. Linkage to the Medicare Part A and B service use records extends from 1982 to 2004, so that detailed Medicare expenditures and types of service use may be studied. Through the careful application of methods to reduce non-sampling error, the surveys provide nationally representative data on: * The prevalence and patterns of functional limitations, both physical and cognitive; * Longitudinal and cohort patterns of change in functional limitation and mortality over 22 years; * Medical conditions and recent medical problems; * Health care services used; * The kind and amount of formal and informal services received by impaired individuals and how it is paid for; * Demographic and economic characteristics like age, race, sex, marital status, education, and income and assets; * Out-of-pocket expenditures for health care services and other sources of payment; * Housing and neighborhood characteristics. In each of the six surveys, large samples (N~20,000) of the oldest-old population (i.e., those 85 and over) are obtained. The survey data (i.e., detailed community and institutional interviews. The linkage to Medicare enrollment files between 1982 and 2004 was 100%, i.e., there was complete follow-up of all cases (including survey non-respondents) for Medicare eligibility (and for most years, detailed Part A and B use), mortality, and date of death. Medicare mortality records (and dates of death) are available for 1982 to 2005. The number of deaths (i.e., about 32,000 from 1982 to 2005) is large enough that detailed mortality analyses can be done. Over the 22 years spanned by the six surveys, a total of 49,242 distinct individuals were followed from and linked to Medicare records. Data Availability: The data are available through ICPSR as Study No. 9681. The data are available only on CD-ROM and only upon completion of a signed Data Use Agreement. Continuously linked Medicare data (1982 through 2004) for the National Long Term Care Surveys are only available from CMS. * Dates of Study: 1982-2004 * Study Features: Longitudinal, Anthropometric Measures * Sample Size: ** 1982: 20,485 ** 1984: 25,401 ** 1989: 17,565 ** 1994: 19,171 ** 1999: 19,907 ** 2004: 20,474 Link: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/09681
National Longitudinal Mortality Study (NLMS)
A database based on a random sample of the noninstitutionalized population of the United States, developed for the purpose of studying the effects of demographic and socio-economic characteristics on differentials in mortality rates. It consists of data from 26 U.S. Current Population Surveys (CPS) cohorts, annual Social and Economic Supplements, and the 1980 Census cohort, combined with death certificate information to identify mortality status and cause of death covering the time interval, 1979 to 1998. The Current Population Surveys are March Supplements selected from the time period from March 1973 to March 1998. The NLMS routinely links geographical and demographic information from Census Bureau surveys and censuses to the NLMS database, and other available sources upon request. The Census Bureau and CMS have approved the linkage protocol and data acquisition is currently underway. The plan for the NLMS is to link information on mortality to the NLMS every two years from 1998 through 2006 with research on the resulting database to continue, at least, through 2009. The NLMS will continue to incorporate data from the yearly Annual Social and Economic Supplement into the study as the data become available. Based on the expected size of the Annual Social and Economic Supplements to be conducted, the expected number of deaths to be added to the NLMS through the updating process will increase the mortality content of the study to nearly 500,000 cases out of a total number of approximately 3.3 million records. This effort would also include expanding the NLMS population base by incorporating new March Supplement Current Population Survey data into the study as they become available. Linkages to the SEER and CMS datasets are also available. Data Availability: Due to the confidential nature of the data used in the NLMS, the public use dataset consists of a reduced number of CPS cohorts with a fixed follow-up period of five years. NIA does not make the data available directly. Research access to the entire NLMS database can be obtained through the NIA program contact listed. Interested investigators should email the NIA contact and send in a one page prospectus of the proposed project. NIA will approve projects based on their relevance to NIA/BSR''s areas of emphasis. Approved projects are then assigned to NLMS statisticians at the Census Bureau who work directly with the researcher to interface with the database. A modified version of the public use data files is available also through the Census restricted Data Centers. However, since the database is quite complex, many investigators have found that the most efficient way to access it is through the Census programmers. * Dates of Study: 1973-2009 * Study Features: Longitudinal * Sample Size: ~3.3 Million Link: *ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00134
National Longitudinal Survey of Older Men
National Longitudinal Survey: 1990 Resurvey of Older Males
National Longitudinal Survey: 1990 Resurvey of Older Males (NLS-Older Males)
National Longitudinal Surveys of Older Men
A dataset that permits examination of health, economic, work, and retirement trajectories for a representative national sample of men from middle to old age. The original sample of 5,020 men, first interviewed in 1966, was re-interviewed periodically until 1983 under a contract with the US Department of Labor. The study provided a detailed longitudinal record of their labor market activity, health, financial status, family structure, and attitudes toward and experience in retirement. The NIA grant made possible a re-interview in 1990 with the surviving men and the widows (or other next-of-kin) of the decedents. The merging of the 1990 data includes death certificate information for the decedents, Blacks were over-represented in the original sample in a ratio of about three or four to one, resulting in about 500 surviving black men in the sample. Information on labor market activity, income, and assets also is available for a sample of about 1,350 widows, 90 percent of whom are between 60 and 89 years of age. This information can be linked to earlier data on the women''s health and work activity that was reported by their late husbands. Due to the original sample selection, other NLS cohorts contain wives and daughters of the older men. These other surveys also hold a wealth of detailed information on aging and retirement issues, especially on income transfers. * Dates of Study: 1966-1990 * Study Features: Longitudinal, Minority Oversamples * Sample Size: ** 1966: 5,020 men (baseline) ** 1990: 2,092 surviving men, 1,341 widows, 865 other next-of-kin Links: * BLS Website on NLS: http://www.bls.gov/nls/ * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04675
National Nursing Home Survey Followup (NNHSF)
A longitudinal study which follows the cohort of current residents and discharged residents sampled from the 1985 National Nursing Home Survey (NNHS), thus permitting study of nursing home and hospital utilization over time. The study was conducted in three waves. To supplement the current and discharged resident components, the 1985 NNHS included a new component - the Next-of-Kin (NOK). The NOK, using a Computer Assisted Telephone Interviewing (CATI) system, was designed to collect information about current and former nursing home residents that is not generally available from patient records or other sources in the nursing home. The NNHSF obtains additional information on a portion of the residents for whom a Current Resident Questionnaire (CRQ) or a Discharged Resident Questionnaire (DRQ) was completed. In September 1994, the NNHSF Mortality Public Use Data Tape was released, covering the years 1984-1990. It contains the multiple cause-of-death information for 6,507 subjects from the NNHSF found to be deceased after linking and matching of files with the National Death Index. Information on the mortality tape includes the date of death, region of occurrence and residence, etc. All NNHSF tapes include a patient identification number common across files to allow linkage among them. Data Availability: Public Use data tapes for each wave and the mortality tape are available through the National Technical Information Office (NTIS), NACDA and the ICPSCR at the University of Michigan. The 1985 survey tape includes eight files: the facility questionnaire, nursing staff questionnaire, current resident questionnaire, discharged resident questionnaire, expense questionnaire, nursing staff sampling list, current resident sampling list, discharged resident sampling list. The next-of-kin questionnaire is available on a separate tape. * Dates of Study: 1987-1990 * Study Features: Longitudinal * Sample Size: ** 1987: 6,001 (Wave I) ** 1988: 3,868 (Wave II) ** 1990: 3,041 (Wave III) Links: * Wave I (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/09813 * Wave II (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/09838 * Wave III (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06142
Software application to simulate sequences drawn from a population under the Wright-Fisher neutral model. The purpose of this program is to simulate sequences on the whole genome scale within practical time. (entry from Genetic Analysis Software)
National Social Life Health and Aging Project (NSHAP)
National Social Life Health and Aging Project
A longitudinal, population-based study of health and social factors, aiming to understand the well-being of older, community-dwelling Americans by examining the interactions among physical health and illness, medication use, cognitive function, emotional health, sensory function, health behaviors, social connectedness, sexuality, and relationship quality. NSHAP provides policy makers, health providers, and individuals with useful information and insights into these factors, particularly on social and intimate relationships. The study contributes to finding new ways to improve health as people age. In 2005 and 2006, NORC and Principal Investigators at the University of Chicago conducted the first wave of NSHAP, completing more than 3,000 interviews with a nationally representative sample of adults aged 57 to 85. In 2010 and 2011, nearly 3,400 interviews were completed for Wave 2 with these Wave 1 Respondents, Wave 1 Non-Interviewed Respondents, and their spouses or cohabiting romantic partners. The second wave of NSHAP is essential to understanding how social and biological characteristics change. NSHAP, by eliciting a variety of information from respondents over time, provides data that will allow researchers in a number of fields to examine how specific factors may or may not affect each other across the life course. For both waves, data collection included three measurements: in-home interviews, biomeasures, and leave-behind respondent-administered questionnaires. The face-to-face interviews and biomeasure collection took place in respondents' ''' homes. NSHAP uses a national area probability sample of community residing adults born between 1920 and 1947 (aged 57 to 85 at the time of the Wave 1 interview), which includes an oversampling of African-Americans and Hispanics. The NSHAP sample is built on the foundation of the national household screening carried out by the Health and Retirement Study (HRS) in 2004. Through a collaborative agreement, HRS identified households for the NSHAP eligible population. A sample of 4,400 people was selected from the screened households. NSHAP made one selection per household. Ninety-two percent of the persons selected for the NSHAP interview were eligible. For Wave 2 in 2010 and 2011, NSHAP returned to Wave 1 Respondents and eligible non-interviewed respondents from Wave 1 (Wave 1 Non-Interviewed Respondents). NSHAP also extended the Wave 2 sample to include the cohabiting spouses and romantic partners of Wave 1 Respondents and Wave 1 Non-Interviewed Respondents. Partners were considered to be eligible to participate in NSHAP if they resided in the household with the Wave 1 Respondent/Wave 1 Non-Interviewed Respondent at the time of the Wave 2 interview and were at least 18 years of age. Wave I biomeasures: height; weight; waist circumference; blood pressure; smell; taste; vision; touch; respondent-administered vaginal swabs; oral mucosal transudate (OMT) for HIV-1 antibody screening; saliva; ����??get up and go����??; and blood spots. Technological advances in biomeasure collection methods have decreased respondent burden and increased ease of collection, storage, and yield of various biomeasures for the second wave of NSHAP. Wave II biomeasures: anthropometrics, including height, hip and waist circumference, and weight; cardiovascular function, including blood pressure, heart rate variability, and pulse; 2 of the 3 components of the short physical performance battery (SPPB) including chair stands and a timed walk; sensory function including smell; and actigraphy. In addition, we collect dried blood spots, microtainer blood, passive drool and salivettes, urine, and respondent-administered vaginal swabs, each of which are analyzed using multiple assays for a variety of measures and rationales. Furthermore, we assess respondents����?? cognition using the Montreal Cognitive Assessment (MoCA). Data Availability: NSHAP data made available to the public does not contain any identifiable respondent information and uses code numbers instead of names for all data. De-identified data from the 2005 and 2006 interviews are available to researchers through the National Archive of Computerized Data on Aging, located within Inter-University Consortium for Political and Social Research (ICPSR). Data from the Wave 2 interviews in 2010 and 2011 will be available in the summer of 2012. * Dates of Study: 2005-2006, 2010-2011 * Study Features: Biospecimens, Anthropometric Measures * Sample Size: ** Wave 1: 3,005 ** Wave 2: 3,377 Links: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/20541
A network to improve measurement of biological risk for late life health outcomes in large representative samples of populations. Activities of the network include designing and carrying out a series of focused meetings, interactive activities, workshops, and pilot projects to harmonize and develop measurement of biological risk in populations. This project will improve the methods of measuring health used in populations and improve comparability of results over time and across studies, which is important for monitoring population health. Biological risk represents objective measurement of major dimensions of population health. The level of risk can indicate the health of the population, need for health care treatment in a population, and the effectiveness of that treatment in controlling risk or delaying disease progression, and death. The measurement of biological risk in large populations often requires adoption of methods not used in laboratory settings. The overarching goal of the network is to promote interdisciplinary research that clarifies the biological paths to health outcomes that can be measured or monitored in population surveys. The network will address the following questions: * What array of biological markers can be included reliably and validly in population studies in order to better monitor health and predict health outcomes at the older ages? * What are the best methods of collecting biological risk information under a variety of circumstances? * What are the best methods for processing the biological risk information collected? * What methods of harmonization will allow us to compare biological risk across studies? * What are the best approaches to measurement of cumulative biological risk or dimensions of biological risk for a variety of health outcomes in a variety of settings? * What are the best approaches in including indicators of genetic risk for complex diseases and conditions into data from population-based surveys? * How do we best capture indicators of life-long social, psychological and economic conditions along with lifelong biological risk to explain later life health outcomes? * What particular ethical issues are posed by our linking of biological data to extensive social, psychological, and economic information? A dataset of descriptions of Selected Population Studies with Biomarkers is available.
Pediatric Imaging Neurocognition and Genetics
Pediatric Imaging Neurocognition and Genetics (PING)
A large multi-site pediatric MRI and genetics data resource to facilitate studies of the genomic landscape of the developing human brain. It includes information about the developing mental and emotional functions of the children to understand the genetic basis of individual differences in brain structure and connectivity, cognition, and personality. Investigators on the project are studying 1400 children between the ages of 3 and 20 years so that links between genetic variation and developing patterns of brain connectivity can be examined. Investigators interested in the effects of a particular gene will be able to search the database for any brain areas or connections between areas that differ as a function of variation in a particular gene, and also to determine if the genes appear to affect the course of brain development at some point during childhood. A data exploration tool has been created for mapping and analyzing MRI data sets collected for PING and related developmental studies. Approved investigators will be able to view raw image sets and derived 3D brain maps of MRI and DTI data, conduct hypothesis testing, and graph brain area measures as they change across the time course of development. PING Cores * Coordinating Core: Functions include project management, screening of participants and maintaining the database * Neuroimaging Core: applying a standardized high-resolution structural MRI protocol involving 3-D T1-weighted scans, a T2-weighted volume, and a set of diffusion-weighted scans with multiple b values and diffusion directions, scans to estimate MRI relaxation rates, and gradient echo EPI scans for resting state fMRI. Importantly, adaptive motion compensation, using ����??PROMO����??, a novel real-time motion correction algorithm will be used. Specific PING protocols for each scanner manufacturer: ** PING MRI Protocol - GE ** PING MRI Protocol - Philips ** PING MRI Protocol - Siemens * Assessment Core: Cognitive assessments for the PING project are conducted using the NIH Toolbox for Cognition. * Genomics Core: functions as a central repository for receipt of saliva samples collected for each study participant. Once received, samples are catalogued, maintained, and DNA is extracted using state-of-the-field laboratory techniques. Ultimately, genome-wide genotyping is performed on the extracted DNA using the Illumina Human660W-Quad BeadChip. PING involves 10 sites throughout the country including UCSD, University of Hawaii, Scripps Genomics, UCLA, UC Davis, Kennedy Krieger Institute/Johns Hopkins, Sacker Institute/Cornell University, University of Massachusetts, Massachusetts General Hospital/Harvard, and Yale. Families who may want to participate in the study, or others who want to know more about it, may email questions to ping (at) ucsd.edu.
An ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation. Two independent modalities exist: either XML-based projects, working directly with the file system, or database-based projects, working on top of a local or remote PostgreSQL database. What can you do with it? * Semantic segmentation editor: order segmentations in tree hierarchies, whose template is exportable for reuse in other, comparable projects. * Model, visualize and export 3D. * Work from your laptop on your huge, remote image storage. * Work with an endless number of images, limited only by the hard drive capacity. Dozens of formats supported thanks to LOCI Bioformats and ImageJ. * Import stacks and even entire grids (montages) of images, automatically stitch them together and homogenize their histograms for best montaging quality. * Add layers conveniently. A layer represents, for example, one 50 nm section (for TEM) or a confocal section. Each layer has its own Z coordinate and thickness, and contains images, labels, areas, nodes of 3d skeletons, profiles... * Insert layer sets into layers: so your electron microscopy serial sections can live inside your optical microscopy sections. * Run any ImageJ plugin on any image. * Measure everything: areas, volumes, pixel intensities, etc. using both built-in data structures and segmentation types, and standard ImageJ ROIs. And with double dissectors! * Visualize RGB color channels changing the opacity of each on the fly, non-destructively. * Annotate images non-destructively with floating text labels, which you can rotate/scale on the fly and display in any color. * Montage/register/stitch/blend images manually with transparencies, semiautomatically, or fully automatically within and across sections, with translation, rigid, similarity and affine models with automatically extracted SIFT features. * Correct the lens distortion present in the images, like those generated in transmission electron microscopy. * Add alpha masks to images using ROIs, for example to split images in two or more parts, or to remove the borders of an image or collection of images. * Model neuronal arbors with 3D skeletons (with areas or radiuses), and synapses with connectors. * Undo all steps. And much more...
Dataset of dendritic spine neck lengths and head sizes
Data set of spine morphology parameters assembled from published literature published in Stepanyants, A. and Escobar, G., Statistical traces of long-term memories stored in strengths and patterns of synaptic connections, J Neuroscience, 31(21): 75797590 (2011). Data set is available as a pdf under the Resources tab.
DELIMINATE: A fast and efficient method for loss-less compression of genomic sequences
A practical implementation of a novel compression approach that can rapidly compress FASTA files containing genomic sequence data in a loss-less fashion.
An ontology for neuroimaging or medical imaging studies based on DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering), as the foundational ontology. Detailed description from web: Our aim is the design of a common semantic model providing a unified view on all data and tools to be shared between NeuroLOG partners. For this purpose, we built a multi-layered and multi-components formal ontology. We chose a design framework that structures the ontology at different levels of abstraction while respecting common conceptualization choices. At the highest level is a top-level ontology that includes abstract concepts and relationships valid across domains. We adopted DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering), as the foundational ontology. We then added Core ontologies, which provide generic, basic and minimal concepts and relations in a specific domain. By minimal we mean that core ontologies should include only the most reusable and widely applicable categories. These kinds of ontologies are essential for sharing intended meaning between different domains. We adopted I& DA (Information and Discourse Acts), a core ontology initially built for classifying documents as a function of their content.We use it to model medical images, which we consider as types of documents. Participant Roles is the core ontology we use to describe the modes of image participation in data processing. I& DA and Participant Roles are built according to DOLCE ontological commitments. On the basis of these two layers, we constructed our Domain ontology dedicated to conceptualizing a specific domain, in this case neuroimaging. Obviously, large domains such as neuroimaging can be divided into sub-domains for the sake of modularization.
clearScience: Dragging Scientific Communication Into the Information Age
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 27, 2015. Infrastructure for more effective scientific communication by leveraging the open APIs of GitHub, Amazon Web Services, and Synapse, clearScience demonstrates how scientists can easily transition from exploring dataexecuting scienceand providing the scientific community all the resources and artifacts to recreate analyses. By capturing the complete lifecycle of a project, reproducibility becomes a byproduct rather than a burden of publication. Further, we provide for forking an analysis, allowing anyone to explore and elaborate on "published" work. If the goal of biomedical research is to deliver results that will ultimately alleviate suffering and minimize harm to patients, being able to transparently share, reproduce, and build off of one another's work is critical to scientific progress. clearScience represents one compelling model for facilitating this progress.
Brain and Body Genetic Resource Exchange
A database and associated tools for investigating the genetic basis of neurodisability. It combines phenotype information from patients with neurodevelopmental and behavioral problems with clinical genetic data, and displays this information on the human genome map. Basic access to genetic information (deletions, duplications) relating to participants with neurodevelopmental disorders is provided without an account; access to the full dataset requires an account. The genetic information that is available to view comprises potentially pathogenic copy number variation across the genome, detected by array comparative genome hybridization (aCGH) using a customized 44K oligonucleotide array.
Software application allowing to simulate population genetics datasets. It allows generating genetic data for haploid, diploid, and haplodiploid organisms under a variety of mating systems. It includes various migration and mutation models. Output can be generated for the FSTAT, GENEPOP, and ARLEQUIN genetic analysis packages. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A 20 year, 20,000 person, open longitudinal epidemiological study of a cohort town. GAZEL was not constructed to answer a specific question rather it was designed to help analyze a wide range of scientific problems and is accessible to the community of researchers specializing in epidemiology. Translation is not available for all pages. The GAZEL cohort, set up in 1989 by Inserm Unit 88 (subsequently Unit 687), in cooperation with several departments of ��lectricit�� de France-Gaz de France (EDF-GDF), was a public utility firm in France involved in production, transmission and distribution of energy. GAZEL initially included 20 624 volunteers working at EDF-GDF (15 010 men and 5614 women), aged from 35 to 50 years. In accordance with its purpose as a scientific research platform, the GAZEL cohort is permanently open to epidemiologic research teams. Today, more than 50 projects on very diversified themes have been set up in GAZEL by some 20 teams, French, belonging to different bodies, and foreign (Germany, Belgium, Canada, Great Britain, Sweden, Finland, and USA).
A longitudinal, epidemiologic study to identify the common risk factors or characteristics that contribute to cardiovascular disease by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms or suffered a heart attack or stroke. Since that time the FHS has studied three generations of participants resulting in biological specimens and data from nearly 15,000 participants. Since 1994, two groups from minority populations, including related individuals have been added to the FHS. FHS welcomes proposals from outside investigators for data and biospecimens. The researchers recruited 5,209 men and women between the ages of 30 and 62 from the town of Framingham, Massachusetts, and began the first round of extensive physical examinations and lifestyle interviews that they would later analyze for common patterns related to CVD development. Since 1948, the subjects have continued to return to the study every two years for a detailed medical history, physical examination, and laboratory tests, and in 1971, the Study enrolled a second generation - 5,124 of the original participants' ''' adult children and their spouses - to participate in similar examinations. In 1994, the need to establish a new study reflecting a more diverse community of Framingham was recognized, and the first Omni cohort of the Framingham Heart Study was enrolled. In April 2002 the Study entered a new phase, the enrollment of a third generation of participants, the grandchildren of the Original Cohort. In 2003, a second group of Omni participants was enrolled. Over the years, careful monitoring of the Framingham Study population has led to the identification of major CVD risk factors, as well as valuable information on the effects of these factors such as blood pressure, blood triglyceride and cholesterol levels, age, gender, and psychosocial issues. Risk factors for other physiological conditions such as dementia have been and continue to be investigated. In addition, the relationships between physical traits and genetic patterns are being studied. FHS clinical and research data is stored in the dbGaP and NHLBI Repository repositories and may be accessed by application. Please check the following repositories before applying for data through FHS. Investigators seeking data that is not available through dbGaP or BioLINCC or seeking biological specimens may submit a proposal through the FHS web-based research application. The FHS data repository may be accessed through this FHS website, under the For Researchers link, then Description of Data, in order to determine if and how the desired data is stored. Proposals may involve the use of existing data, the collection of new data, either directly from participants or from previously collected samples, images, or other materials (e.g., medical records). The FHS Repository also has biological specimens available for genetic and non-genetic research proposals. Specimens include urine, blood and blood products, as well as DNA.
Africa Centre for Health and Population Studies
Africa Center for Health and Population Studies
Africa Centre for Health and Population Studies Datasets
Longitudinal datasets of demographic, social, medical and economic information from a rural demographic in northern KwaZulu-Natal, South Africa where HIV prevalence is extremely high. The data may be filtered by demographics, years, or by individuals questionnaires. The datasets may be used by other researchers but the Africa Centre requests notification that anyone contact them when downloading their data. The datasets are provided in three formats: Stata11 .dta; tables in a MS-Access .accdb database; and worksheets in a MS-Excel .xlsx workbook. Datasets are generated approximately every six months containing information spanning the whole period of surveillance from 1/1/2000 to present.
Community built zebrafish RNAi platform that contains plasmids, successfully targeted genes and shRNA sequences, and a forum for discussion. This is a true community platform with users who add data, modify entiries, request features and share using the discussion board.
Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.BeeBase is an archive and will not be updated. The most up-to-date bee genome data is now available through the navigation bar on the HGD Home page.
An integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A commercial service organization that for DNA Methylation available for bisulfite treatment of DNA for methylation-specific analysis, histone, chromatin, and small RNA analysis and for the next era of DNA methylation detection and analysis.
Collection of legacy literature in biodiversity assembled by an international consortium of natural history and botanical libraries. It also serves as the foundational literature component of the Encyclopedia of Life. Browse by author, title, subject, collection, map, year, language, and contributor. Taxonomic search using UBio. Also supports data export and a variety of machine interfaces.
CAMARADES Protocols for Systematic Reviews of Animal Studies
Protocols for Systematic Reviews of Animal Studies
A site for sharing meta-analysis protocols for translational neuroscience research. Protocols for systematic review of in vivo data modelling human neurological disease. Making the protocol for your systematic review available to the community has a number of benefits; it provides evidence that prespecified analyses were indeed prespecified; allows others to comment on your approach; provides examples for others planning such reviews; and can help you identify if other reviews in similar areas are already in progress. This site was created to foster collaboration.
A panel data set for use in cross-cultural analyses of aging, health, and well-being between the U.S. and Japan. The questionnaires were designed to be partially comparable to many surveys of the aged, including Americans'' Changing Lives; 1984 National Health Interview Survey Supplement on Aging; Health and Retirement Study (HRS), and Well-Being Among the Aged: Personal Control and Self-Esteem (WBA). NSJE questionnaire topics include: * Demographics (age, sex, marital status, education, employment) * Social Integration (interpersonal contacts, social supports) * Health Limitations on daily life and activities * Health Conditions * Health Status (ratings of present health) * Level of physical activity * Subjective Well-Being and Mental Health Status (life satisfaction, morale), * Psychological Indicators (life events, locus of control, self-esteem) * Financial situation (financial status) * Memory (measures of cognitive functioning) * Interviewer observations (assessments of respondents) The NSJE was based on a national sample of 2,200 noninstitutionalized elderly aged 60+ in Japan. This cohort has been interviewed once every 3 years since 1987. To ensure that the data are representative of the 60+ population, the samples in 1990 and 1996 were refreshed to add individuals aged 60-62. In 1999, a new cohort of Japanese adults aged 70+ was added to the surviving members of previous cohorts to form a database of 3,990 respondents 63+, of which some 3,000 were 70+. Currently a 6-wave longitudinal database (1987, 1990, 1993, 1996, 1999, & 2002) is in place; wave 7 began in 2006. Data Availability: Data from the first three waves of the National Survey of the Japanese Elderly are currently in the public domain and can be obtained from ICPSR. Additional data are being prepared for future public release. * Dates of Study: 1987-2006 * Study Features: Longitudinal, International * Sample Size: ** 1987: 2,200 ** 1990: 2,780 ** 1993: 2,780 ** 1996: ** 1999: 3,990 ** 2002: ** 2006: Links: * 1987 (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06842 * 1990 (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03407 * 1993 (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04145 * 1996 (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/26621
National Survey of Midlife Development in the United States
Data set from a collaborative, interdisciplinary investigation of patterns, predictors, and consequences of midlife development in the areas of physical health, psychological well-being, and social responsibility. Respondents were asked to provide extensive information on their physical and mental health throughout their adult lives, and to assess the ways in which their lifestyles, including relationships and work-related demands, contributed to the conditions experienced. An additional series of questions focusing on childhood queried respondents regarding the presence/absence of their parents, religion, rules/punishments, love/affection, physical/verbal abuse, and the quality of their relationships with their parents and siblings. Respondents were drawn from a nationally representative random-digit-dial sample of non-institutionalized, English-speaking adults, aged 25-74, selected from working telephone banks in the coterminous United States. Those queried participated in an initial telephone interview and responded to a mail questionnaire. MIDUS 2 carried forward MIDUS 1 and enlisted a new sample of African Americans. MIDUS2 also expanded the focus by incorporating detailed neurophysiological assessments on a large subsample in three geographic regions. Data collection largely repeats T1 assessments (45 minute phone interview, 100 page self-administered questionnaire) plus additions in select areas (e.g., cognitive functioning, optimism and coping, life events, caregiving). In addition, MIDUS 2 is using diary techniques to assess daily stressors in a subsample of respondents; conducting cognitive testing through telephone interviews; collecting biological data on a subsample of respondents, including baseline biomarkers as well as laboratory challenge studies, with assessments of salivary cortisol, blood pressure, and heart rate variability; and collecting EEG measures to focus on the central circuitry of emotion, related to affect and depression. Siblings and Twins: Similar data were collected from a survey of 951 siblings of a respondent in the main survey. MIDUS also contains twins data, from a separate national survey unrelated to the main MIDUS survey. From this separate national survey, a total of 1,996 twins agreed to participate. The Twins respondents were given the same assessments as the Main and Siblings samples. Additionally, the Twins sample was asked a series of questions about their birth, shared physical characteristics, childhood and adult relationships with their twin, whether they were dressed alike as children, and whether others experienced difficulty identifying them correctly. Data and comprehensive documentation for MIDUS 1 and 2 are available via ICPSR. * Dates of Study: 1995-2008 * Study Features: Longitudinal, Minority Oversampling, Anthropometric Measures * Sample Size: ** 1995-6: 4,242 (MIDUS 1) ** 2004-6: 7,108 (MIDUS 2) Links: * ICPSR ����?? MIDUS 1: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/02760 * ICPSR ����?? MIDUS 2: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04652
Public use data set on new legal immigrants to the U.S. that can address scientific and policy questions about migration behavior and the impacts of migration. A survey pilot project, the NIS-P, was carried out in 1996 to inform the fielding and design of the full NIS. Baseline interviews were ultimately conducted with 1,127 adult immigrants. Sample members were interviewed at baseline, 6 months, and 12 months, with half of the sample also interviewed at three months. The first full cohort, NIS-2003, is based on a nationally representative sample of the electronic administrative records compiled for new immigrants by the US government. NIS-2003 sampled immigrants in the period May-November 2003. The geographic sampling design takes advantage of the natural clustering of immigrants. It includes all top 85 Metropolitan Statistical Areas (MSAs) and all top 38 counties, plus a random sample of other MSAs and counties. Interviews were conducted in respondents'' preferred languages. The baseline was multi-modal: 60% of adult interviews were administered by telephone; 40% were in-person. The baseline round was in the field from June 2003 to June 2004, and includes in the Adult Sample 8,573 respondents, 4,336 spouses, and 1,072 children aged 8-12. A follow-up was planned for 2007. Several modules of the NIS were designed to replicate sections of the continuing surveys of the US population that provide a natural comparison group. Questionnaire topics include Health (self-reports of conditions, symptoms, functional status, smoking and drinking history) and use/source/costs of health care services, depression, pain; background; (2) Background: Childhood history and living conditions, education, migration history, marital history, military history, fertility history, language skills, employment history in the US and foreign countries, social networks, religion; Family: Rosters of all children; for each, demographic attributes, education, current work status, migration, marital status and children; for some, summary indicators of childhood and current health, language ability; Economic: Sources and amounts of income, including wages, pensions, and government subsidies; type, value of assets and debts, financial assistance given/received to/from respondent from/to relatives, friends, employer, type of housing and ownership of consumable durables. * Dates of Study: 2003-2007 * Study Features: Longitudinal * Sample Size: 13,981
Nihon University Japanese Longitudinal Study of Aging
Longitudinal data set of a nationally representative sample of the population aged 65 and over in Japan, comparable to that collected in the US and other countries. The first two waves of data are now available to the international research community. The sample is refreshed with younger members at each wave so it remains representative of the population at each wave. The study was designed primarily to investigate health status of the Japanese elderly and changes in health status over time. An additional aim is to investigate the impact of long-term care insurance system on the use of services by the Japanese elderly and to investigate the relationship between co-residence and the use of long term care. While the focus of the survey is health and health service utilization, other topics relevant to the aging experience are included such as intergenerational exchange, living arrangements, caregiving, and labor force participation. The initial questionnaire was designed to be comparable to the (US) Longitudinal Study of Aging II (LSOAII), and to the Asset and Health Dynamics Among the Oldest Old (AHEAD, a pre-1924 birth cohort) sample of the Health and Retirement Study (HRS), which has now been merged with the HRS. The sample was selected using a multistage stratified sampling method to generate 340 primary sampling units (PSUs). The sample of individuals was selected for the most part by using the National Residents Registry System, considered to be universal and accurate because it is a legal requirement to report any move to local authorities within two weeks. From each of the 340 PSUs, 6-11 persons aged 65-74 were selected and 8-12 persons aged 75+ were sampled. The population 75+ was oversampled by a factor of 2. Weights have been developed for respondents to the first wave of the survey to reflect sampling probabilities. Weights for the second wave are under development. With these weights, the sample should be representative of the 65+ Japanese population. In fall 1999, 4,997 respondents aged 65+ were interviewed, 74.6 percent of the initial target. Twelve percent of responses were provided by proxies, because of physical or mental health problems. The second wave of data was collected in November 2001. The third wave was collected in November 2003. Questionnaire topics include family structure, and living arrangements; subjects' ''' parents/spouse' '''s parents/children; socioeconomic status; intergenerational exchange; health behaviors, chronic conditions, physical functioning; activities of daily living and instrumental activities of daily living; functioning in the community; mental health depression measures; vision and hearing; dental health; health care and other service utilization. A CD is available which include the codebook and data files for the first and second waves of the national sample. The third wave of data will be released at a later date. * Dates of Study: 1999-2003 * Study Features: Longitudinal, International * Sample Size: ** 4,997 Nov/Dec 1999 Wave 1 ** 3,992 Nov 2001 Wave 2 ** Nov 2003 Wave 3 Link: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00156
International project database indexing all formal names (scientific names) in the Fungi Kingdom. Index Fungorum provides Life Science Identifiers (LSIDs) for records in its database and indicates the status of a name. In the returns from the search page a currently correct name is indicated in green, while others are in blue (a few, aberrant usages of names are indicated in red). All names are linked to pages giving the correct name, with lists of synonyms. Index Fungorum provides a SOAP protocol web service for searching its database and retrieving records. A WSDL file describing the services is available. (adapted from Wikipedia)
PSID - A national survey of socioeconomics and health over lifetimes and across generations
Long-term longitudinal dataset with information on generational links and socioeconomic and health conditions of individuals over time. The central foci of the data are economic and demographic, with substantial detail on income sources and amounts, wealth, savings, employment, pensions, family composition changes, childbirth and marriage histories, and residential location. Over the life of the PSID, the NIA has funded supplements on wealth, health, parental health and long term care, housing, and the financial impact of illness, thus also making it possible to model retirement and residential mobility. Starting in 1999, much greater detail on specific health conditions and health care expenses is included for respondent and spouse. Other enhancements have included a question series about emotional distress (2001); the two stem questions from the Composite International Diagnostic Interview to assess symptoms of major depression (2003); a supplement on philanthropic giving and volunteering (2001-03); a question series on Internet and computer use (2003); linkage to the National Death Index with cause of death information for more than 4,000 individuals through the 1997 wave, updated for each subsequent wave; social and family history variables and GIS-linked environmental data; basic data on pension plans; event history calendar methodology to facilitate recall of employment spells (2001). The reporting unit is the family: single person living alone or sharing a household with other non-relatives; group of people related by blood, marriage, or adoption; unmarried couple living together in what appears to be a fairly permanent arrangement. Interviews were conducted annually from 1968 through 1997; biennial interviewing began in 1999. There is an oversample of Blacks (30%). Waves 1990 through 1995 included a 20% Hispanic oversample; within the Hispanic oversample, Cubans and Puerto Ricans were oversampled relative to Mexicans. All data from 1994 through 2001 are available as public release files; prior waves can be obtained in archive versions. The special files with weights for families are also available. Restricted files include the Geocode Match File with information for 1968 through 2001, the 1968-2001 Death File, and the 1991 Medicare Claims File. * Dates of Study: 1968-2003 * Study Features: Longitudinal, Minority Oversampling * Sample Size: 65,000+ Links * ICPSR Series: http://www.icpsr.umich.edu/icpsrweb/ICPSR/series/00131 * ICPSR 1968-1999: Annual Core Data: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/07439 * ICPSR 1968-1999: Supplemental Files: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03202 * ICPSR 1989-1990: Latino Sample: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03203
THIS RESOURCE IS NO LONGER IN SERVICE, documented April 28, 2017. Videos and presentations from the Summer Course Cellular biology of addiction.
Global Rare Diseases Patient Registry and Data Repository
Data repository of de-identified patient data, aggregated in a standardized manner, to enable analyses across many rare diseases and to facilitate various research projects, clinical studies, and clinical trials. The aim is to facilitate drug and therapeutics development, and to improve the quality of life for the many millions of people who are suffering from rare diseases. The goal of GRDR is to enable analyses of data across many rare diseases and to facilitate clinical trials and other studies. During the two-year pilot program, a web-based template will be developed to allow any patient organization to establish a rare disease patient registry. At the conclusion of the program, guidance will be available to patient groups to establish a registry and to contribute de-identified patient data to the GRDR repository. A Request for Information (RFI) was released on February 10, 2012 requesting information from patient groups about their interest in participating in a GRDR pilot project. ORDR selected 30 patient organizations to participate in this pilot program to test the different functionalities of the GRDR. Fifteen (15) organizations with established registries and 15 organizations that do not have patient registry. The 15 patient groups, each without a registry, were selected to assist in testing the implementation of the ORDR Common Data Elements (CDEs) in the newly developed registry infrastructure. These organizations will participate in the development and promotion of a new patient registry for their rare disease. The GRDR program will fund the development and hosting of the registry during the pilot program. Thereafter, the patient registry is expected to be self-sustaining.The 15 established patient registries were selected to integrate their de-identified data into the GRDR to evaluate the data mapping and data import/export processes. The GRDR team will assist these organizations in mapping their existing registry data to the CDEs. Participating registries must have a means to export their de-identified registry data into a specified data format that will facilitate loading the data into the GRDR repository on a regular basis. The GRDR will also develop the capability to link patients' ''' data and medical information to donated biospecimens by using a Voluntary Global Unique Patient Identifier (GUID). The identifier will enable the creation of an interface between the patient registries that are linked to biorepositories and the Rare Disease Human Biospecimens/Biorepositories (RD-HUB) http://biospecimens.ordr.info.nih.gov/.
Portal to resources, expertise, and best practices for investigators, study staff, participants and partners/affiliates to facilitate efficient, compliant and ethical study conduct and management. This collaborative effort across a number of organizations and administrative units was built to leverage existing resources and create new content where readily accessible resources currently don' '''t exist. The goals of the HUB are to: * Promote excellence in the quality of clinical research management through education. * Facilitate effective and timely clinical research initiation by improving institutional processes and providing clinical research protocol, regulatory, budget, and financial tools. * Increase awareness of clinical trials in the community through education and community participant recruitment outreach activities. * Interface with institutional/industry partners to support enhanced clinical research practice.
A tool for finding dbGaP studies containing phenotype variables of interest. Lack of standardization makes locating and categorizing previously measured variables difficult. This query tool for biomedical researchers is to identify studies and phenotype variables of interest.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 2nd, 2022. Antibody supplier.
An Organization portal, Antibody supplier, Service resource,
A research tool company focused on the creation of the largest commercial collection of full-length human cDNAs in a standard expression vector. The availability of the complete human genome sequence and the subsequent development of genome-based tools have enabled the identification of relevant drug targets through system biology approaches. OriGene''s vision is to prepare comprehensive, genome wide research tools and technology platforms to enable scientists to study complete biological pathways, thus enabling a better understanding of disease mechanisms including cancer and stem cell research. OriGene Technologies uses high-throughput, genome wide approach to develop products for pharmaceutical, biotechnology, and academic research. Their flagship product is the cDNA clone collection, a searchable gene bank of over 30,000 human full-length TrueClone cDNA collection and over 25,000 TrueORF cDNA clones. From their TrueORF cDNA clones, they have developed the largest offering of full length human proteins expressed in mammalian cells, ideal for functional studies. Their TrueMAB project develops mouse monoclonal antibodies against protein antigens with the goal to develop protein assays for every human protein. They also offer complete molecular biology services from codon optimization, gene synthesis, protein expression and assay development. In addition, they offer unique gene expression products such as TissueScan cancer tissue qPCR arrays and tissue biorepository for biomarker discovery and validation.
Proteintech Europe Ltd is an ISO 9001:2008 certified company
American chemical, life science and biotechnology company owned by Merck KGaA. Merger of Sigma Chemical Company and Aldrich Chemical Company. Provides organic and inorganic chemicals, building blocks, reagents, advanced materials and stable isotopes for chemical synthesis, medicinal chemistry and materials science, antibiotics, buffers, carbohydrates, enzymes, forensic tools, hematology and histology, nucleotides, proteins, peptides, amino acids and their derivatives.
Software application that is a forward-time population simulation method that can simulate realistic patterns of LD in both family-based and case-control datasets. (entry from Genetic Analysis Software)
Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing.
Java library and a web service for extracting metadata and content from scientific articles in born-digital form. The system analyses the entire content of a PDF file containing a publication and attempts to extract information such as: the title of the article, journal information (title, etc.), bibliographic information (volume, issue, page numbers, etc.), authors and affiliations, keywords, abstract, bibliographic references and structured sections hierarchy.
Neuroscience Information Framework Integrated Cell Lines
A virtual database currently indexing available cell lines from: Coriell Cell Repositories, International Mouse Strain Resource (IMSR), ATCC, NIH Human Pluripotent Stem Cell Registry, NIGMS Human Genetic Cell Repository, and Developmental Therapeutics Program.
experimental studies reporting connection probabilities and/or unitary PSP amplitudes
Data set of connection probabilities and PSP amplitudes from Chapeton, J., Fares, T., LaSota, D., and Stepanyants, A., Efficient associative memory storage in cortical circuits of inhibitory and excitatory neurons, PNAS, 109(51): E3614E3622 (2012). Available as a PDF under Resources tab.
Metalloprotein Ligand Interaction Database
A publicly accessible web-based database through which the interactions between a variety of chelating groups and various central metal ions in the active site of metalloproteins can be explored in detail. Additional information can also be retrieved including protein and inhibitor names, the amino acid residues coordinated to the central metal ion, and the binding affinity of the inhibitor for the target metalloprotein.
National Mouse Metabolic Phenotyping Centers
Center mission is to advance medical and biological research by providing the scientific community with standardized, high quality metabolic and physiologic phenotyping services for mouse models of diabetes, diabetic complications, obesity and related disorders.
Biomedical Technology Resource Center that develops image processing and analysis techniques for basic and clinical neurosciences. The NAC research approach emphasizes both specific core technologies and collaborative application projects. The core activity of the center is the development of algorithms and techniques for postprocessing of imaging data. New segmentation techniques aid identification of brain structures and disease. Registration methods are used for relating image data to specific patient anatomy or one set of images to another. Visualization tools allow the display of complex anatomical and quantitative information. High-performance computing hardware and associated software techniques further accelerate algorithms and methods. Digital anatomy atlases are developed for the support of both interactive and algorithmic computational tools. Although the emphasis of the NAC is on the dissemination of concepts and techniques, specific elements of the core software technologies have been made available to outside researchers or the community at large. The NAC's core technologies serve the following major collaborative projects: Alzheimer's disease and the aging brain, morphometric measures in schizophrenia and schizotypal disorder, quantitative analysis of multiple sclerosis, and interactive image-based planning and guidance in neurosurgery. One or more NAC researchers have been designated as responsible for each of the core technologies and the collaborative projects.
Northeastern Collaborative Access Team Undulator Resource for Structural Biology
Biomedical technology research center for macromolecular crystallography at Sector 24 of the Advanced Photon Source at Argonne National Laboratory. The macromolecules studied by resource users often involve large unit cells, small crystals, weakly diffracting crystals and crystals with weak anomalous scattering. Technological research includes use of silicon monochromators, focusing optics, methods of phase determination, radiation damage, X-ray detectors, automated sample mounting, microdiffraction and crystallographic software.
Stanford Synchrotron Radiation Lightsource Structural Molecular Biology
Synchrotron Radiation Structural Biology Resource
Biomedical technology research center that operates as a integrated center with three primary areas (or cores) of technological research and development and scientific focus: macromolecular crystallography (MC), X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering/diffraction (SAXS) . Central to the core technological developments in all three areas is the development and utilization of improved detectors and instrumentation, especially to be able to take maximum advantage of the high brightness of SSRL?s third-generation synchrotron X-ray storage ring (SPEAR3). A primary focus is the use of enhanced computing and data management tools to provide more user-friendly, real-time and on-line instrumentation control, including full remote access for crystallography, data reduction and analysis.
Gene Expression: Computation and Knowledge Organization
A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.
Software tool for determining a regression model of quantitative or binary trait variation when the number of possible genetic predictors is very large, considering only a moderate number of predictors at one time, using unrelated or family data. (entry from Genetic Analysis Software)
Integrated Technology Resource for Biomedical Glycomics
NCRR Integrated Technology Resource for Biomedical Glycomics
Biomedical technology research center that develops and implements new technologies to investigate the glycome of cells, including glycoproteomics and glycoconjugate analysis, transcript analysis and bioinformatics. It develops the tools and technology to analyze in detail the glycoprotein and glycolipid expression of mouse embryonic stem cells and the cells into which they differentiate. The technology developed in the Center will allow an understanding of how glycosylation is controlled during differentiation and will allow the development of tools to promote the use of stem cells to treat human disease. In addition, the technology developed will be applicable to the study of other cell types, including cancer cells that are progressing to a more invasive phenotype. The technology developed will also allow others in the scientific community to participate in glycomics research through dissemination of the new methods developed and through the analytical services provided by the resource to other scientists requesting assistance in glycomic analyses.
National Bio-Organic Biomedical Mass Spectrometry Resource Center
Provides high-performance tandem mass spectrometry and proteomics, including multiplexed quantitative comparative analysis of protein and post-translational modifications, and a suite of tools for the analysis of mass spectrometry proteomics data. It provides both scientific and technical expertise and state-of-the-art high-performance, tandem mass spectrometric instrumentation. The facility also provides a service for small molecule analysis. Significant instrumentation in the facility includes three QSTAR quadrupole orthogonal time of flight instruments, and both an LTQ-Orbitrap platform with electron transfer dissociation (ETD) and an LTQ-FT linear ion trap FT-ICR instrument equipped with the ability to perform electron capture dissociation (ECD). The Center also has a 4700 Proteomic Analyzer MALDI tandem time of flight instrument; as well as a QTRAP 5500 hybrid triple quadrupole linear ion trap instrument; and a Thermo Fisher LTQ Orbitrap Velos. Major research focuses within the Center are the analysis of post-translational modifications, including phosphorylation and O-GlcNAcylation and development of methods for quantitative comparative analysis of protein and post-translational modification levels. The program also continues to develop one of the leading suites of tools for analysis of mass spectrometry proteomics data, Protein Prospector. The current web-based release allows unrestricted searching of MS and MSMS data, as well as the ability to perform comparative quantitative analysis of samples using isotopic-labeling reagents. It is the only freely-available web-based resource that allows this type of analysis.
National Center for Multiscale Modeling of Biological Systems
MMBioS - National Center for Multiscale Modeling of Biological Systems
National Center for Multiscale Modeling of Biological Systems (MMBioS)
Biomedical technology research center that develops and makes available to the scientific community high performance computing algorithms, tools and software to leverage modeling efforts at disparate scales of structural biology, cellular microphysiology and large-scale bioimage processing and analysis, with the goal of advancing understanding of the molecular and cellular organization and functional mechanisms that underlie synaptic signaling and regulation.
National Resource for Biomedical Accelerator Mass Spectrometry
Biomedical technology research center that develops and refines accelerator mass spectrometry methods and instrumentation for the precise, quantitative and cost-effective measurement of the effects of drugs and toxicants on humans at safe doses. It facilitates the use of accelerator mass spectrometry in biomedical research and provides training and access for researchers.
National Resource for the Mass Spectrometric Analysis of Biological Macromolecules
Biomedical technology research center that develops cutting-edge mass spectrometric tools for analyzing peptides and proteins. It makes its software tools developed for data analysis freely available.
Biomedical technology research center that develops technologies to increase understanding of the molecular basis of the involvement of carbohydrates in protein-carbohydrate interactions in disease and to develop more powerful technologies necessary to achieve this goal. Complex carbohydrates play an important role in many biomedically important processes, including inflammatory response, hormone action, malignancy, viral and bacterial infections and cell differentiation. The resource combines complimentary technologies: synthetic chemistry, nuclear magnetic resonance, mass spectrometry, computational biology, protein expression and cell-based assays. As new technologies are developed, application to these processes will be pursued through collaborative and service projects.
NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis
Mass Spectrometry Resource at Washington University in St. Louis
Washington University Mass Spectrometry Resource
Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5, 2022. Endoscopic Reporting Software, aggregated and individual research data and tailor-made services aimed to advance the overall practice of endoscopy. It was developed to study outcomes of gastrointestinal (GI) endoscopic procedures in real life settings, using data obtained from the CORI Endoscopic Reporting Software or from other endoscopic reporting software. Practice sites include hospitals, ambulatory care centers, private practices, universities, and Veteran' '''s hospitals (VA' '''s). The CORI v4 Endoscopic Reporting Software is a specialty Electronic Health Record used to document endoscopic procedures and provide reporting services to your practice. Data from participating providers is also sent to a central data repository to become part of the National Endoscopic Database (NED), which now contains data from over 2.7 million GI procedures. The CORI v4 Endoscopic Reporting Software offers significant benefits for participating practices, providers and patients, as well as for everyone who benefits from CORI' '''s research efforts. You may actively participate in research with CORI. If you have ideas for research using the NED, their research team can help you evaluate those ideas, collect and analyze the data. In addition, you may choose to participate in one of the prospective research projects conducted by CORI research staff.
Computer Access to Research on Dietary Supplements
Computer Access to Research on Dietary Supplements Database
Database of federally funded research projects pertaining to dietary supplements. CARDS contains projects funded by the United States Department of Agriculture (USDA), the Department of Defense (DOD) and the Institutes and Centers (ICs) of the National Institutes of Health (NIH) beginning with fiscal year 1999, the first year that NIH ICs began reporting research related to dietary supplements. Projects funded by other Federal agencies will be added to CARDS as they become available. The Office of Dietary Supplements (ODS) will post notices on its website and listserv when CARDS updates are completed. Codes assigned to each research project allow the CARDS user to identify: * research related to specific dietary supplement ingredients; for example, vitamin E or St. John' '''s wort * the type of study; for example, a Phase III study or an animal study * health outcomes or biological effects; for example, osteoporosis or antioxidant function * whether the research is directly related or indirectly related to dietary supplements. For example, a clinical trial comparing bone density in women given a daily calcium supplement versus a placebo would be classified as directly related to dietary supplements. A study examining the activation of steroid hormone receptors by supplemental vitamin D in cell culture would be classified as indirectly related to dietary supplements because the direct physiological or health effects of vitamin D supplementation are not being studied. A search of the CARDS database can be used to sort and tabulate information for a variety of purposes. For example, a researcher may want to know which ICs at the NIH fund research on herbal supplement ingredients. A consumer may want to know if the Federal government is supporting research on a popular dietary supplement ingredient such as vitamin C.
Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations.
A genetic/radiation hybrid mapping software that looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms inspired from TSP (Traveling Salesman Problem) technology. It can handle large data sets made up of different populations (either F2 backcross, recombinant inbred lines, F2 intercross, phase known outbreds, haploid/diploid radiation hybrids). It can also exploit existing syntenic relationships between the organism mapped and a reference (sequenced) organism for accurate dense RH mapping. (entry from Genetic Analysis Software)
A repository database to achieve continuous and intensive management of GWAS data and variation data identified by next generation sequencing (NGS) and data-sharing among researchers. In this database, variations including short/long insertions / deletions and structural variations related to disease susceptibility, virus resistance, and drug response are registered along with statistical genetic results and simple clinical characteristics to clarify the locus specific characteristics. Currently this database contains information extracted from scientific papers and next generation sequencing results and other small scale experimental results of several research laboratories. Mutation data submission is greatly appreciated.
Action to Control Cardiovascular Disease Risk in Diabetes
Study testing whether strict glucose control lowers the risk of heart disease and stroke in adults with type 2 diabetes. In addition the study is exploring: 1) Whether in the context of good glycemic control the use of different lowering lipid drugs will further improve these outcomes and 2) If strict control of blood pressure will also have additional beneficial effects on reducing cardiovascular disease. The design was a randomized, multicenter, double 2 X 2 factorial trial in 10,251 patients with type 2 diabetes mellitus. It was designed to test the effects on major CVD events of intensive glycemia control, of fibrate treatment to increase HDL-cholesterol and lower triglycerides (in the context of good LDL-C and glycemia control), and of intensive blood pressure control (in the context of good glycemia control), each compared to an appropriate control. All 10,251 participants were in an overarching glycemia trial. In addition, one 2 X 2 trial addressed the lipid question in 5,518 of the participants and the other 2 X 2 trial addressed the blood pressure question in 4,733 of the participants. The glycemia trial was terminated early due to higher mortality in the intensive compared with the standard glycemia treatment strategies. The results were published in June 2008 (N Eng J Med 2008;358:2545-59). Study-delivered treatment for all ACCORD participants was stopped on June 30, 2009, and the participants were assisted as needed in transferring their care to a personal physician. The lipid and blood pressure results (as well as the microvascular outcomes and eye substudy results) were published in 2010. All participants are continuing to be followed in a non-treatment observational study.
Chronic Renal Insufficiency Cohort Study
Chronic Renal Insufficiency Cohort (CRIC) Study
A prospective observational national cohort study poised to make fundamental insights into the epidemiology, management, and outcomes of chronic kidney disease (CKD) in adults with intended long-term follow up. The major goals of the CRIC Study are to answer two important questions: * Why does kidney disease get worse in some people, but not in others? * Why do persons with kidney disease commonly experience heart disease and stroke? The CRIC Scientific and Data Coordinating Center at Penn receives data and provides ongoing support for a number of Ancillary Studies approved by the CRIC Cohort utilizing both data collected about CRIC study participants as well as their biological samples. The CRIC Study has enrolled over 3900 men and women with CKD from 13 recruitment sites throughout the country. Following this group of individuals over the past 10 years has contributed to the knowledge of kidney disease, its treatment, and preventing its complications. The NIDDKwill be extending the study for an additional 5 years, through 2018. An extensive set of study data is collected from CRIC Study participants. With varying frequency, data are collected in the domains of medical history, physical measures, psychometrics and behaviors, biomarkers, genomics/metabolomics, as well as renal, cardiovascular and other outcomes. Measurements include creatinine clearance and iothalamate measured glomerular filtration rate. Cardiovascular measures include blood pressure, ECG, ABI, ECHO, and EBCT. Clinical CV outcomes include MI, ischemic heart disease-related death, acute coronary syndromes, congestive heart failure, cerebrovascular disease, peripheral vascular disease, and composite outcomes. The CRIC Study has delivered in excess of 150,000 bio-samples and a dataset characterizing all 3939 CRIC participants at the time of study entry to the NIDDKnational repository. The CRIC Study will also be delivering a dataset to NCBI' '''s Database for Genotypes and Phenotypes.
Pharmacology is a wikibook covering topics within pharmacology and pharmaceutical sciences.
Program to Reduce Incontinence by Diet and Exercise
PRIDE (Program to Reduce Incontinence by Diet and Exercise)
Randomized controlled trial being conducted at two clinical centers in the United States to learn more about the effects of weight loss on urinary incontinence. About 330 overweight women aged 30 or older will participate and will be followed for 18 months. Efficacy of weight reduction as a treatment for urinary incontinence will be examined at 6 months following the intensive weight control program, and the sustained impact of the intervention will be examined at 18 months. To increase the maintenance of weight reduction and facilitate evaluation of the enduring impact of weight loss on urinary incontinence, they propose to study a motivation-based weight maintenance program. At the end of the intensive weight control program, women randomized to the weight loss program will be randomized to either a 12-month skill-based maintenance intervention or to a motivation-based maintenance intervention. The maintenance interventions maximize the potential for sustained weight loss and will allow them to determine if long-term weight reduction will produce continued improvement in urinary incontinence.
Diabetes research center which provides patient care and performs diabetes research. Its primary aim is to provide a facilitating framework for conducting multi-disciplinary basic and clinical research and to encourage the scientific development of young investigators.
Database of age-related changes covering different biological levels, including molecular, physiological, psychological and pathological age-related data, to create an interactive portal that serves as a centralized collection of human aging changes and pathologies. To facilitate integrative, system-level studies of aging, the DAA provides a centralized source for aging-related data as well as basic tools to query and visualize the data, including anatomical models. Data in the DAA is manually curated from the literature and retrieved from public databases. For more detailed analyses users are able to download the entire database. More information on how to use the DAA is available on the help page. The DAA primarily focuses on human aging, but also includes supplementary mouse data, in particular gene expression data, to enhance and expand the information on human aging. If you would like to contribute to the database yourself, for instance if you have new data on aging, please use the contribute page to submit your data.
Service that generates Ramachandran-like plots of carbohydrate linkage torsions in pdb-files. The Ramachandran Plot, where backbone torsion angles are plotted against each other, is a frequently used tool to evaluate the quality of a protein 3D structure. For carbohydrate structures, linkage torsions can be evaluated in a similar way. Preferred Phi/Psi values of the torsion angles of glycosidic bonds depend strongly on the types of monosaccharides involved in the linkage, the kind of linkage (1-3, 1-4, etc) as well as the degree of branching of the structure. CARP analyses carbohydrate data given in PDB files using the pdb2linucs algorithm. For each different linkage type a separate plot is generated. The user can choose between two sources for plot background information for comparison: data obtained from PDB provided by GlyTorsion or from GlycoMapsDB. GlycoMapsDB provides calculated conformational maps, which show energetically preferred regions for a specific linkage, while PDB data are based on experimentally solved structures. For seldom occuring linkages, however, PDB data are often rare, so maybe not sufficient background information for comparison will be available from this source., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 29, 2014. Data set of disaccharides accessible by selecting the families implied in the glycosidic bond and the type of carbons involved. For each disaccharide, conformations of lower energy are then visualized with the Ramachadran diagram, the three-dimensional structure and the values of the corresponding Phi and Psi angles.
A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions.
Multi-threaded, parallel and CUDA based application that provides an interface to the R statistical language, MATLAB, Accord and Aforge APIs, along with Neural Maestro to accomplish fMRI, EEG, speech signals, commodity price analysis, general machine learning, classification and time series analysis and forecasting. Because it unifies research development work in MATLAB, R and C++, it provides a mathematical canvas the permits researches to experiment with both pure and hybrid models that use the best of all software development languages.
Interactive laboratory of the mind composed of 4 themed sessions housing four short introductory movies and sixteen trials with those you can experience visual phenomena and illusions used for study in psychological experiments.
Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins.
A collection of content, including podcasts and blogs, to advance life science research, connecting people and ideas in the life sciences. Mendelspod creates a space for probing conversations and deep insight into the topics and trends which shape the industry''s future and therefore our future as a species. The podcasts are engaging, thoughtful thirty minute shows twice a week on highly relevant topics to those working around the life sciences. Their format enables them to go in depth with scientists who are leaders in their field, or CEOs of high growth companies to explore trends and the latest technologies. At Mendelspod, they offer a front row seat to the revolution going on in biology, putting a human face on some complicated, highly technical topics. Here you can tune in to hear Steve Burrill give his ''state of the industry'' overview, or listen to George Church talk about art and science, or find out how the latest developments in NGS are helping in the war on cancer. The blogs cover the latest trends and products, and can be entertaining. Guest bloggers featured and welcomed.
Blog written by Do Tromp and Samuel Hurley (University of Wisconsin, Madison) that intends to show what Diffusion Tensor Imaging (DTI) entails and give a comprehensive overview of available software, analyzing methods and research possibilities. Diffusion-imaging.com invites guest writers to contribute to this website.
50 question test devised by Javaid Sheikh, M.D., and Jerome A. Yesavage, M.D., of the Department of Psychiatry and Behavioral Sciences at Stanford University School of Medicine, to test one''s knowledge of certain aspects of geriatric psychiatry, including five broad areas: psychodynamics and psychotherapy, cognitive assessment, psychosocial and developmental aspects, psychopharmacology, and clinical syndromes.
An integrated resource for information on genes, QTLs and strains associated with a variety of kidney and renal system conditions such as Renal Hypertension, Polycystic Kidney Disease and Renal Insufficiency, as well as Kidney Neoplasms.
A list of snippets for databases in NIF data federation.
DNA sequence compression using a reference genome.
Software application that contains the following modules: ibd, calculates the proportion of gene shared identical by decent for a nuclear family; ibdn, (modified program of ERPA), which implements a method for assessing increased-allele sharing between all pairs of affected relatives within a pedigree; multic, multivariate analysis for complex traits; ml, estimation of variance components using maximum likelihood; ql, estimation of variance components using quasi likelihood; relcov, generates first degree relationship coefficients for extended families; sim2s, the simulation program that was used to test ACT; cage, Cohort Analysis for Genetic Epidemiology; gh: GeneHunter, heavily modified to assist multipoint calculation using multic; TDT: TDT programs written in SAS; gcc and f77 compilers are necessary. Executable programs are included for compatible operating systems, i.e., Solaris2.6. (entry from Genetic Analysis Software)
Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software)
General-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for constructing 2-d crossover-based map.
A Likelihood Based Estimation of Risk in Trios
Software application that estimates genotype relative risks, genotyping error rates and population risk allele frequencies from marker genotype data in case-parent trios. ALBERT uses the distribution of trio marker genotypes to compute maximum likelihood estimates for the parameters. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. An algorithm resource for scalable phasing method for trios and unrelated individuals.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application used to infer the age of a rare, selectively-neutral mutation.
Software application that allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families (entry from Genetic Analysis Software)
Web application to investigate gene-gene interactions in genetic association studies designed to: 1. Interface your SNP data with biological information from several online bioinformatics databases. 2. Generate biologically plausible hypotheses for testing gene-gene interactions. 3. Select a subset of SNPs and conduct SNP-SNP interaction tests. 4. Store analysis results. 5. Explore analysis results through interactive plots and summary tables. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application that integrates a broad spectrum of data mining, statistical analysis, interactive visualization and modeling tools that allow QTL analysis based on advanced and sophisticated methods for maximum extraction of the mapping information from data. (entry from Genetic Analysis Software)
Software application for analysis of segregation in single-sperm data (entry from Genetic Analysis Software)
Software application to reduce family members so the families can be used in GENEHUNTER program. FASTER eliminates the most redundant individuals according to the set of weights (preferences) (Age, Information about genetic Markers, etc.) The program has several features such as automatical reducement of branches without any affected individuals, etc. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application to calculate kinship coefficient or coefficient of coancestry (the probability that alleles at a given locus are identical by descent).
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for SNP data managing, import & export from linkage format, data validation, pairwise LD calculation and visualisation, case-control and TDT tests, visual comparison of two datasets, relationships testing. Suitable for large projects.
GRONingen university LOR score calculation
Conversion programs from LINKAGE files are available. The program uses peeling and can employ nested conditioning. There is an automatic peeling program that will unravel (multiple) loops. Alleles do not need to be recoded, so real allele sizes can be used. Genotype probabilities for a chosen person can be calculated for purposes of genetic risk calculation. Later versions include one for calculations using linked markers and mutations and mosaicism, made by Martin van der Meulen. A symbolic versions will generate the formula to compute the pedigree likelihood. (entry from Genetic Analysis Software)
Software application designed for the construction of highly saturated linkage maps, based on BC1, DH, Radiation Hybrid or CP (CrossPollinators) data sets. F2 is not supported. (entry from Genetic Analysis Software)
a character of the Italian Commedia dell''Arte. He has many aspects
but can switch among them very easily according to needs and necessities. Similarly
this software is about the study of genetic polymorphism.)
An exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data). (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software for segregation and pathway analysis.
An efficient tool for mining complex inbred genealogies that identify clusters of individuals sharing the same expected amount of relatedness is described. Additionally it allows for the reconstruction of sub-pedigrees suitable for genetic mapping in a systematic way. (entry from Genetic Analysis Software)
Software program for conducting combined association analysis of triads and unrelated subjects (entry from Genetic Analysis Software)
Software application for population-based haplotyping (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A suite of programs for association analysis of multilocus haplotypes from unphased genotype data. These include TDTPHASE for case-parent trios, COCAPHASE for case/control data, QTPHASE for quantitative traits in unrelateds, PDTPHASE for general pedigrees, and QPDTPHASE for quantitative traits in general pedigrees. Features include global and individual haplotype tests, main effects and conditional tests, grouping of rare haplotypes, pairwise comparisons of haplotype risk, flexible permutation procedures and calculation of LD measures.
Windows-based program for computation of sample size and power for binary outcome studies (case-control and cohort studies) based on a logistic-like regression model with one covariate or two covariates (e.g., gene-exposure interactions). (entry from Genetic Analysis Software)
Haplotyping with computation of conditional probabilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that assigns each person the haplotype with the highest conditional probability using Elston-Stewart algorithm (entry from Genetic Analysis Software)
Software application that estimates frequencies of multi-site haplotypes using the EM algorithm (entry from Genetic Analysis Software)
Software application that aims to speed up the preparation of linkage data files passed on to the Alohomora software for data from the Affymetrix or Illumina assays. Chip2Spell gathers the information necessary to supplement the genotype data (such as the genetic map of the markers and the population-specific allele frequencies) from publicly available annoation files from Affymetrix and Illumina. The program formats the genotype data for input into the Alohomora program. (entry from Genetic Analysis Software)
A graphic, interactive program to map quantitative trait loci using intercrosses, backcrosses or recombinant inbred strains in experimental plants or animals. A completely rewritten cross-platform version of Map Manager QT with enhanced analysis functions. (entry from Genetic Analysis Software)
Software tool for construction of genetic linkage maps and analyzing Mendelian phenotypes. (entry from Genetic Analysis Software)
A Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that uses multilocus genotypic data to allocate individuals to their most likely source population.
Software application employing multilocus genotypes to select or exclude populations as origins of individuals (Assignment and Migrants Detection). (entry from Genetic Analysis Software)
Software application that is a meiotic recombination rate estimation program. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Semiparametric Variance-Component for Censored data
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016.
Software application that is an extension of GENEHUNTER-IMPRINTING, based on the original GENEHUNTER version 2.1 release 6, that allows for a MOD-score analysis, in which parametric LOD scores are maximized over the parameters of the trait model, i.e., the penetrances and disease allele frequency. As of version 2.0, it is possible to use sex-specific recombination frequencies. The genetic positions of markers can be automatically read from a publicly available genetic map. (entry from Genetic Analysis Software)
Software application for haplotype association analysis of unphased genotype data. It can be used both for population data (case-control) and nuclear family data. The program is optimized for haplotype frequency estimation with the EM-algorithm for many markers. FAMHAP provides a method which searches for potential genotyping errors and several tests for haplotype-based association analysis. Particular emphasis is on Monte-Carlo simulations, which are necessary in the context of haplotype association, where asymptotic theory often fails, and in the context of multiple testing problems. (entry from Genetic Analysis Software)
Bayesian Analysis of Multilocus Association
Software application to select a trait-associated subset of markers among many candidates. The program is based on Bayesian modeling/estimation and it suits for both quantitative and qualitative traits. It can handle bi- and multiallelic markers as well as applied in situations where part of the marker genotypes may be missing. As an output of the program, one obtains posterior estimate of number and positions of trait-associated markers. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An interactive web site useful for exploring the genetic modulation of thousands of phenotypes gathered over a 30-year period by hundreds of investigators using reference panels of recombinant inbred strains of mice. WebQTL includes dense error-checked genetic maps, as well as extensive gene expression data sets (Affymetrix) acquired across more than 35 strains of mice. WebQTL accepts user-entered traits for BXD, AXB/BXA, CXB, BXH, AKXD recombinant inbred strains. (entry from Genetic Analysis Software)
Computerized Affected Sibling Pair Analyzer and Reporter
Software application who''s main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing. (entry from Genetic Analysis Software)
Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application using a method for combining SNP association and admixture association statistics to increase power in GWAS in admixed populations. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A user-friendly, graphical package for power evaluation and enhancement planning through variance component linkage analysis in a multipoint framework. (entry from Genetic Analysis Software)
Software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A tool designed to help visualize the joint effect of genes and continuous environmental covariates on complex human disease simulation models.
Software application for semiparametric family-based association (entry from Genetic Analysis Software)
Fragmented Exhaustive Seearch for TAgsnps
Software application for detecting recent effective population size reductions from allele data frequencies (entry from Genetic Analysis Software)
Software application that can (1) compute the likelihood of specified parameter values; (2) compute the probability of each genotype for pedigree members; (3) simulate phenotypes for output into files; (4) maximize the likelihood over specified parameters (with or without standard errors); (5) compute the standard errors of parameters for unknown estimates; (6) simulate phenotypes and estimate parameter values; (7) estimate expected lod score; (8) compute a grid of likelihood over one or two parameters. New additions to V5: assortative mating; TDT; additive multi-locus models (entry from Genetic Analysis Software)
Software program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs. Quanto is a 32-bit Windows application requiring Windows 95, 98, NT, 2000, ME or XP to run. The graphical user interface allows th e user to easily change the model and view the results without having to edit an input file and rerun the program for every model. The results of a session are stored to a log file. This log can be printed or saved to a file for reviewing at a later date. An option is included to create a text file of the log that can be imported into other documents. (entry from Genetic Analysis Software)
Software program for mapping quantitative trait loci in experimental crosses. (entry from Genetic Analysis Software)
Software application for EM algorithm estimations of SNP haplotypes (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that provides analysis tools for the detection of shifts in relative allele frequency between pooled genomic DNA from cases and controls using SNP-based genotyping microarrays. GenePool supports genotyping platforms from Affymetrix and Illumina.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that calculates likelihood on pedigrees (entry from Genetic Analysis Software)
Likelihood-based Estimation of Admixture
Software application (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application for inferring haplotypes composed of both CNV alleles and SNP alleles.
Software pipeline to detect SNPs and call their genotypes from a list of BAM files. UMAKE pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies. (entry from Genetic Analysis Software)
Transmission Disequilibrium Test Allowing for Errors
Software program that computes a likelihood-based transmission disequilibrium test. The data are genotypes on trios (father, mother, affected child) in which random genotyping errors leading to Mendelian inconsistencies may or may not have occurred. This program computes the TDT-AE statistic on all trios (whether Mendelianly consistent or not) and thereby maintains a correct type I error rate in the presence of random genotyping errors. (entry from Genetic Analysis Software)
STatistical Explanation for Positional Cloning
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Software application (entry from Genetic Analysis Software)
Software application that can be used for the ordering of loci on genetic linkage maps. The method is based on minimisation of the total number of recombination events. Since the criterion does not require intensive calculations, the algorithm rapidly produces an optimal ordering as well as a series of near-optimal ones. The latter provides insight into the local certainty of ordering along the map. RECORD can deal with the following types of mapping populations: BC1, F2, F3, RILs (in fact any generation obtained by repeated selfing of a hybrid between homozygous parents). Data files are .LOC JoinMap format. Mapping populations from non-inbreds should be split into BC1 or HAP data that represent the maternal and paternal gametes. (entry from Genetic Analysis Software)
Case-Control RAre Variant Analysis Tool CCRAVAT
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application for enabling the analysis of rare variants in large-scale case control and quantitative trait association studies. CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait) are software packages that enable efficient large-scale analysis of rare variants across specific regions or genome-wide. These programs implement a rare variant super-locus or collapsing method that investigates the accumulation of rare variant alleles in either a case-control or quantitative trait study design. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application to incorporate regressive models into the VITESSE likelihood engine.
Resource no longer in service. Documented on February 23,2021.Software tool as modification of GENEHUNTER software package . Allows for parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait.
Power calculation of family-Based Association Tests FBAT
An interactive software package that provides tools for the design and the data analysis of family-based association studies. (entry from Genetic Analysis Software)
Markov chain Monte Carlo program for association in two-dimensional contingency tables, and for testing Hardy-Weinberg equilibrium. (entry from Genetic Analysis Software)
Software application that is a companion program to STRUCTURE that is a structured association method, for use in association mapping, enabling valid case-control studies even in the presence of population structure. (entry from Genetic Analysis Software)
Free software tool for mapping complex trait loci. TreeLD performs a multipoint LD-analysis by inferring the ancestry of a genomic region and analyzing this ancestry for signals of disease mutations. The generated likelihoods can be used to test for the presence of a disease locus and to fine-map its location, providing a point estimate and a credible region. Furthermore, the package provides a novel way of visualizing the association signal in a sample. TreeLD is designed for high-density SNP haplotypes and can be applied to case-control data, TDT trio data and quantitative trait data. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 22, 2016. Free software package for estimating allele frequencies for all the SNPs available in a population reference panel (e.g. HapMap data base) based on genotype data from a subset of markers (e.g. the Illumina HumanHap300 BeadChip SNP set) in a group of subjects (e.g. the cases in a case-control sample)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that simulates either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scalable way. It is based on XML, completely written in C++ and published under the GNU General Public License.
Integrate Genotypes for genome-wide Genetic studies
Allelix - Paternity Linkage Analysis Online
THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 23, 2013. Software application / data analysis service where one can enter the alleles of commonly used STR by clicking the mouse. The algorithm calculates the paternity index and the Essen-Moeller probability of kinship for the deficiency- and the trio case. Everybody can use the network-software online after registering. The usage on the internet is free. Academic users can ask me to unlock an option to display the details (formulas/frequencies etc.) and to have an export-funktion to MS Word. The program is in German and (non-professional) English. An expansion to other languages is easy, if somebody helps us with the translation. For those who are interested to have the software running on their own intranet (for database security reasons) an individual agreement can be found. (entry from Genetic Analysis Software) (German version is: http://www.allelix.de)
Software application that is a faster version of GENEHUNTER and Allegro 1.2 (several degrees of increase of speed, can handle bigger families, up to 50 bits) (entry from Genetic Analysis Software)
Software application designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. (entry from Genetic Analysis Software)
Microsoft Windows application designed to analyze microsatellite DNA fragments separated on an Automated Laser Fluorescence sequencer. (entry from Genetic Analysis Software)
Allele Matching Empirical Locus-specific Integrated Association test
Software application that employs allele matching to analyse the effects of rare variants within a specific locus. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, AMELIA has been developed as an allele-matching approach that is robust to the presence of both directions of effect for variants within the locus analysed. (entry from Genetic Analysis Software)
A set of useful accessory programs to the LINKAGE package. It simplifies the performance of a large array of parametric and nonparametric tests for linkage and association on data entered in LINKAGE format pedigree and parameter files. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that provides an easy to use web-based user interface to compute individual ancestry estimates using the Maximum Likelihood Estimation method. This website also allows registered users to manage genotype and marker/allele frequency files. Registration is optional.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that extends partially observed genotype data to the whole pedigree. Can be used for generating starting points for MCMC samplers and for checking that the genotype data are consistent with the pedigree structure.
Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Association in the Presence of Linkage with Ordered Subset Analysis
Software application that in the presence of genetic heterogeneity, can identify a genetically homogenous subset of families based on a trait-related covariate. APL-OSA then tests the relationship between the association statistics (i.e., the APL statistics) calculated based on the subset and the family-specific covariate. APL-OSA is based on the OSA method for linkage and the family-based association test, APL. Thus, APL-OSA has similar properties with OSA and APL. Bi-alleleic markers such as SNPs are accepted by APL-OSA. APL-OSA is a single-marker test and considers one covariate each time. (entry from Genetic Analysis Software)
Accumulation of Rare variants Integrated and Extended Locus-specific test
Software application that explores the effects of rare variants within complex traits through locus-based analysis. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, ARIEL has been developed as a locus-wide regression-based collapsing approach that incorporates variant quality scores. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. A platform independent Java program for the analysis of genome wide association experiments. (entry from Genetic Analysis Software).
Software applications including ASP, a power calculator for gene mapping using a sibpair design (concordant or discordant) and ASPSHARE, which complements ASP in that it allows rapid calculation of the expected ibd sharing at the trait locus, based upon the model parameters, and the incidence corresponding to the respective parameters. (entry from Genetic Analysis Software)
Bayesian IMputation-Based Association Mapping
BIOmedical Integrated Discovery Environment
Collection of data analysis tools and interrelated biomedical information in a single easy-to-use software package that includes a component-based software/data integration platform that can quickly transform fragmented enterprise legacy data and software into an integrated suite of tools and knowledge base to achieve maximal usability, interoperability, scalability, and extensibility. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application that is a research bioinformatics system for inputting, validating, organizing, archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password protected BiolAD-DB SQL compliant server database. BiolAD-DB tools further provide functionalities for generating customized reports and views. (entry from Genetic Analysis Software)
Blocking Gibbs sampler for pedigree analysis
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that performs general pedigree analysis on a general pedigree with any number of loops. It also allows users to perform two-point linkage analysis on a general pedigree with an arbitrary number of alleles., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. A set of programs for calculations under different linkage disequilibrium (LD) distribution models (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Robust haploblock border reliability estimation tool implemented for LD based haploblock detection method. The most important new features are bootstrapping and overlapping block borders. (entry from Genetic Analysis Software)
Berkeley method for Perfect Phylogeney Haplotyping
Software application for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent). In population genetic terms, BPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. (entry from Genetic Analysis Software)
Bayesian Quantitative Trait Locus mapping
Software application for the mapping of genetic traits from line crosses and recombinant inbred lines. It performs (1) maximum likelihood estimation of multi-gene models; (2) Bayesian estimation of multi-gene models via Laplace Approximations; and (3) interval mapping and composite interval mapping of genetic loci (entry from Genetic Analysis Software)
Software tool for manual and automatic DNA sequence assembly, DNA sequence analysis, automatic sample processing, contig editing, metadata integration, file format conversion and mutation detection. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Case-Control Quasi-Likelihood Score test
Case-Control RAre Variant Analysis Tool QUTIE
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2026. Software application for enabling the analysis of rare variants in large-scale case control and quantitative trait association studies. CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait) are software packages that enable efficient large-scale analysis of rare variants across specific regions or genome-wide. These programs implement a rare variant super-locus or collapsing method that investigates the accumulation of rare variant alleles in either a case-control or quantitative trait study design. (entry from Genetic Analysis Software)
Case-Control association analysis with RELlated individuals
Software program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application to convert output from CEPH DBMS to CRIMAP format.
Software application developed from crimap v2.4 for use with the map suite of programs. (entry from Genetic Analysis Software)
A graphical tool for visualizing genotype intensity data in order to assess genotype calls as part of quality control procedures for genome-wide association studies. It provides a solution to the computational and storage problems related to being able to work with the huge volumes of data generated by such projects by implementing a compact, binary format that allows rapid access to data, even with hundreds of thousands of observations. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. General-purpose program for monitoring genetic diversity. CFC allows for several pedigree analyses such as: (1) computing inbreeding coefficients and relationships; (2) computing average relationships very quickly within and between specified groups of individuals; (3) computing average relatedness; (4) ancestral decomposition of the average or the individual inbreeding coefficient; (5) ancestral decomposition of the average coancestry; (6) optimizing matings to minimize the average inbreeding coefficients in the next generation; (7) computing founder equivalent, founder genome equivalent and effective number of non-founders; (8) computing numerator relationship matrix, its Cholesky decomposition and its inverse; (9) providing useful information on the structure of pedigrees.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application to detect genetically abnormal subjects in a case-control sample based on genotypes at multiple marker loci. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A MATLAB utility for estimating genetic linkage in exotic line-cross mating designs.
Software application that serves as a visualization tool to validate constructed genetic maps. CheckMatrix generates graphical genotypes and two-dimensional heat plots of pairwise scores. Visualization of regions with positive and negative linkage as well as of allele fraction per marker simplifies genetic map validation without applying statistical approaches. CheckMatrix works in conjunction with MadMapper and freely available at http://www.atgc.org/XLinkage/MadMapper/ (entry from Genetic Analysis Software)
Software application for calling genotypes from the Affymetrix 500K Mapping chip. The program allows for multiple cohorts which have potentially different intensity characteristics that can lead to elevated false-positive rates in genome-wide studies. The underlying model has a hierarchical structure that allows for correlation between the parameters of each cohort. The output files produced by CHIAMO feed directly into both the programs SNPTEST and IMPUTE. CHIAMO was used to call genotypes for the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC).
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that is an implementation of a genome-based scan statistic that detects genomic regions.
A simulation program that simulates and plots (in real time) ancestral recombination graphs. This is currently primarily a teaching/educational tool. (entry from Genetic Analysis Software)
COllaborative Pedigree drawing Environment
Software application that includes a Java program for drawing pedigrees and a standardized system for pedigree storage. Unlike other existing pedigree programs, this software is particularly intended for epidemiologists in the sense that it allows customized automatic drawing of large numbers of pedigrees and remote and distributed consultation of pedigrees. (entry from Genetic Analysis Software)
Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application that refines linkage analysis of affected sibpairs by considering attributes or environmental exposures thought to affect disease liability. This refinement utilizes a mixture model in which a disease mutation segregates in only a fraction of the sibships, with the rest of the sibships unlinked. Covariate information is used to predict membership within the two groups corresponding to the linked and unlinked sibships. The pre-clustering model uses covariate information to first form two probabilistic clusters and then tests for excess IBD-sharing in the clusters. The Cov-IBD model determines probabilistic group membership by joint consideration of covariate and IBD values. (entry from Genetic Analysis Software)
Software application that is a parallel version of CRIMAP (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for detecting and displaying well-characterized meiotic breakpoints in human family data.
THIS RESOURCE IS NO LOGER IN SERVICE. Documented on May 16,2023. A simple dBASE III program for the management of pedigree and locus data. It permits easy extraction of genetic data for use with MENDEL and FISHER. (entry from Genetic Analysis Software)
Decay of Haplotype Sharing MAPping software
Software application for fine-mapping of qualitative traits by linkage disequilibrium. Given a set of marker haplotypes or genotypes from affected individuals, haplotypes or genotypes from appropriately selected controls, and a genetic map of the markers at which both sets of individuals are typed, DHSMAP estimates the location of the trait-associated variant by maximum likelihood or maximum quasi-likelihood. (entry from Genetic Analysis Software)
Software application that is a visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers. (entry from Genetic Analysis Software)
Software application - part of the LINKAGE auxiliary programs (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that manage genetic data (entry from Genetic Analysis Software)
Direct method for Perfect Phylogeney Haplotyping
Software application that is similar to the BPPH program (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software program that allows students and scientists to explore potential manifestations of genetic models and stochastic processes. It also provides a means to evaluate the effectiveness of statistical procedures such as linkage analysis or QTL detection. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Efficient Analysis of Genetic Linkage: Testing and Estimation
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software package that provides a number of improved statistics for detecting linkage and estimating trait location. EAGLET uses multiple subsamples of dense SNP data to detect linkage with increased power, and to construct sharp 95% confidence intervals for the true trait location.
Software application that combines automated setup and performance of linkage analyses and simulation. The program package supports currently single-point linkage analyses, multi-point linkage analyses, and the simulation package SLink, and provides genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P values, and other parameters. The software can analyze STRPs as well as SNP chip data from Affymetrix, Illumina, or self-defined SNP data. The program performs single- and multi-point simulation studies.
Software application detecting association between haplotypes and phenotypes (entry from Genetic Analysis Software)
Estimation of Haplotype frequencies from Pooled DNA samples EH
Software application that provides variance estimates for haplotype frequency estimates, it allows several kinds of missing information in the genotype data, it also allows for combined genotype data of different pool sizes. This program can be used for testing haplotype-disease associations in case control studies by calculating the likelihood ratio test: 2 log(likelihood for cases) + 2 log(likelihood for controls) - 2 log(likelihood for case+controls). (entry from Genetic Analysis Software)
EM estimation of haplotype frequencies and LD calculation
Software application to calculate pair-wise linkage disequilibrium based on SNP genotype data from unrelated individuals. EM algorithm is used to estimate pair-wise haplotype frequencies. The output file is in the format of input file for GOLD program, thus it can be directly plug into GOLD to get LD plots. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that for detecting linkage/disequilibrium signals # between genetic markers and disease loci, particularly if only one # or a few large pedigrees are available. The strategy differs from # conventional approaches that require at least a moderate number of # families to attain adequate statistical power. The proposed testing # procedure is advantageous in that it provides high statistical power # coupled with reduced sample collection. Furthermore, the proposed # method avoids problems such as potential population stratification # and genetic heterogeneity, and is robust with respect to misspecification # of phenotype. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application for non-parametric analysis (entry from Genetic Analysis Software)
Software application that suggests individuals to be sequenced in a large pedigree. ExomePicks assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree. We are currently using it in the context of whole exome and whole genome sequencing studies to pick individuals to be sequenced from large family collections. (entry from Genetic Analysis Software)
Software application for fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 7, 2016.
(haplotype) Family Based Association Test PBAT
Software application that allows the user to test for association/linkage between disease phenotypes and haplotypes by utilizing family-based controls. The method extends the approach for testing described in Rabinowitz and Laird (2000) to handle multiple tightly linked markers. It is robust to population admixture, yet efficient in the sense that it utilizes data from families where phase cannot be completely resolved in all individuals by using weights, which are estimated from the sample. However, the method remains robust to population stratification and population admixture. The method can handle any type of phenotype, including multiple phenotypes and missing parents, marker data, and/or phase, and provides both bi-allelic and multi-allelic tests. PowerFBAT is a tool for power simulation of association analysis using FBAT with binary outcomes. XWXW is an extension to the Haseman-Elston method for non-parametric linkage test with quantitative traits. XDT is a software that performs classical TDT, SDT and Rabinowitz TDT for nuclear families (not supported anymore). (entry from Genetic Analysis Software)
Software application that tests for deviation from Hardy-Weinberg equilibrium and tests for association in case controls studies; Plot genotype frequencies graphically using a de Finetti diagram. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application for demonstration of method for preliminary ordering of loci based on two-point lod scores. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 1st, 2022. Software application for genetic analysis of classical biometric traits like blood pressure or height that are caused by a combination of polygenic inheritance and complex environmental forces. (entry from Genetic Analysis Software)
Genetic Association Interaction Analysis
Web-based application for testing for locus-locus interaction using genetic association. It is based upon the case-control study design and is designed so that non-specialists may routinely apply tests for interaction. GAIA allows simple testing of both additive and additive plus dominance interaction models and includes permutation testing to appropriately correct for multiple testing. The application is useful for both candidate gene based studies and genome-wide association studies. For large scale studies GAIA includes a screening approach which prioritizes loci for further interaction analysis. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software package for the management and analysis of pedigree data. it offers: 1. Powerful database management tools, specifically designed for family data; 2. Automatic pedigree drawing; 3. Segregation and linkage analysis, based on traditional maximum likelihood methods and newer, more powerful, Monte Carlo methods that can model both genetic and environmental factors. (entry from Genetic Analysis Software)
Software application for statistical analysis of genetic linkage data, sib-pair analysis, association studies (entry from Genetic Analysis Software)
SeqSaw - Short Spliced Sequence Mapping Tool
A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.
Gene Counting method for HAPlotype analysis. GENEPI.JAR
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals. By excluding haplotypes with zero MLE at an early stage, this implementation uses many orders of magnitude less space and time than naive implementations. A second program, ApproxGCHap, is provided to give alternate estimates for data sets with large numbers of loci or large amounts of missing genotypes.
Software application designed to accompany the second edition of Bruce Weir''s book Genetic Data Analysis (1996. Sinauer Associates) (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for fitting Genetic Epidemiology Models by running stochastic simulation in relation to disease dynamics.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software application that uses GEE method to estimate the location of the susceptibility gene based on the allele-sharing of affected sib pairs for multiple markers. GENEFINDER can further the analysis of GENEHUNTER by providing a more accurate gene location estimation and the corresponding confidence interval.
Software application for multipoint analysis of pedigree data including: non-parametric linkage analysis, LOD-score computation, information-content mapping, haplotype reconstruction (entry from Genetic Analysis Software)
Software application that is a modification of the GENEHUNTER software package (version 1.3)that allows users to perform parametric (LOD-score) analysis of traits caused by imprinted genes - that is, of traits showing a parent-of-origin effect. (entry from Genetic Analysis Software)
Software application that is a modification of the GENEHUNTER software package which produces output files containing the null and conditional distributions of the test statistic (in nullprobs.dat and probs.dat, respectively). These files can then be used as input to the ASM program which incorporates the allele sharing modeling for lodscores and likelihood ratio tests as developed by Kong and Cox (1997). (entry from Genetic Analysis Software)
Population genetic data analysis software package. Used to perform exact Hardy Weinberg Equilibrium test. Used for population differentiation and for genotypic disequilibrium among pairs of loci. Computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc. and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software)
A desktop analysis workbench for analyzing high-volume, high-density genotyping data. The software provides a comprehensive set of linkage and association algorithms that allow researchers to discover relationships between genotypes and phenotypes. Researchers can visually explore fully annotated SNPs and genes at varying levels of detail. Designed for biologists and statisticians, GeneSpring GT is capable of importing, visualizing, and analyzing hundreds of thousands of variation measurements simultaneously, for rapid localization of disease or phenotype markers. (entry from Genetic Analysis Software)
Software application that performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application for automated power analysis for variance components (VC) quantitative trait locis (QTL) linkage and association tests in sibships, and other common tests (entry from Genetic Analysis Software)
Software application that provides flexible simulations of family data within an easy-to-use, high-level programming language. GENETSIM has no limit on pedigree sizes or structures, or number of families, or number of marker, or number of chromosomes. Genetic transmission is modeled by first generating the locations of recombination events, and then performing gene dropping according to the given recombination pattern. Any pattern of missing data can be specified and genotyping errors can be simulated. GENETSIM can simulat multiple QTLs with pleiotropic effects, multivariate polygenic background and any number of environmental factors, age effects, epistasis and variable expression. Users can also select families based on ascertainment schemes by repeating simulations. (entry from Genetic Analysis Software)
GENetic Object Oriented Modeling in population genetics
Software application that implements a virtual computer world where biological entities are digital objects. In this world, each individual of a population is represented by a set of chromosomes with genetic elements (markers, genes, Quantitative Traits Loci, etc.) and attributes (phenotype, age, fertility, living status, exposure, etc.). It comes with a built-in model allowing basic genetic studies by simulations, performed according to parameter values such a penetrance matrix (phenotype probabilities for each genotype), exposure, between-relative mating probabilities, and a probability of migration in a two-dimensional migration process. The simulated populations could be analysed with different packages for statistical or genetical analysis (e.g., SAS, S-PLUS, Linkage, Mapmaker/sibs, Genehunter). Pedigrees can also be simulated according to a pedigree file at the LINKAGE format. (entry from Genetic Analysis Software)
A database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression in eQTL studies. Genevar allows researchers to investigate eQTL (expression quantitative trait loci) associations within a gene locus of interest in real time. The database and application can be installed on a standard computer in database mode and, in addition, on a server to share discoveries among affiliations or the broader community over the internet via web services protocols. (entry from Genetic Analysis Software)
Software application for charting family medical/health history (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application designed to identify genotypes that are likely to be errors. The statistical method was designed to identify typing error rather than pedigree errors, but is general enough to pinpoint any unlikely genotype still consistent with Mendelian inheritance. (entry from Genetic Analysis Software)
Software package for the analysis of multiplex PCR kits within the scope of paternity testing, kinship cases and population studies. GenoProof offers: (1) probably the most extensive existing population database for all supported markers of more than 50 ethnic groups, (2) individually configurable quality assurance options, (3) complex concept of user rights in order to guarantee data security, (4) languages German and English (entry from Genetic Analysis Software)
Software application for analysis and manipulation of genetic linkage data of genetic linkage data, including conversions of pedigree files between CRI-MAP and LINKAGE format. (entry from Genetic Analysis Software)
Gene-Environment interaction and STability
GEnotype Visualization and ALgorithmic Tool
Software application designed to simplify and expedite the process of genotype analysis and disease association tests by providing a common interface to several common tasks relating to such analyses. It is aimed for analysis of unrelated individuals as well as two-generation families. (entry from Genetic Analysis Software)
Software application that combines genetic map data and locus data to display Graphical Genotypes. Data can be viewed by individual or by linkage group, and sorted on markers. Statistics are calculated and simultaneous filtering/selection on multiple linkage groups is possible. Output of hi-res genotype drawings directly to printer or to emf/jpeg/bitmap image. A module for constructing GGT-datafiles from common mapmaker/joinmap style formatted data is available. (entry from Genetic Analysis Software)
Software package for family-based genomewide association (GWA) analysis, with the ability to infer missing genotypes using the Elston-Stewart algorithm. When SNPs from an association panel are less complete (i.e., having more missing genotypes) than markers from a linkage panel, many of the missing genotypes can be determined. GHOST can handle large pedigrees -- when pedigrees are small, Merlin is also recommended for this analysis. (entry from Genetic Analysis Software)
Genome-wide LInkage DisEquilibrium Repository and Search engine
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016.
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. A web interface to several commonly used statistical genetics programs, including Linkage, Genehunter, Merlin, Unphased, and Transmit. It simplifies their use through graphical selection of program options, automation of multiple analyses, and viewing of graphical output. GLUE is available to HGMP account holders; registration is free to all academic users., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure.
Software application that finds the posterior probabilities for data errors for genotypes and phenotypes in pedigree data (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 7,2025. Software application that is a rank-based meta-analysis method for analyzing results from genome-wide linkage searches. A software package is now available. The gsma software calculates the summed rank for any number of studies and bins, then obtains p-values for the Summed Rank and the Ordered Rank statistics, by simulation. Weighted and unweighted analyses are performed. A test data set is included. (entry from Genetic Analysis Software)
Software application for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. (entry from Genetic Analysis Software)
A R package for assessing the power of genome-wide association studies using commercially available genotyping chips. The package encapsulates extensive simulation results generated by our program HAPGEN. (entry from Genetic Analysis Software)
HAPlotype analysis of polymorphic markers
Software application to infer haplotype from genotype data. It uses the parsimony principle, i.e. try to find the minimum number of haplotypes that can reconstruct the input genotypes. (entry from Genetic Analysis Software)
a dynamical programming algorithm for haplotype block partitioning
Software application that simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region. The disease model is specified through the choice of a single SNP as the disease causing variant together with the relative risks of the genotypes at the disease SNP. The program is designed to work with publically available files that contain the haplotypes estimated as part of the HapMap project and the estimated fine-scale recombination map derived from that data. Hapgen is computationally tractable. On a modern desktop HAPGEN can simulate several thousand case and control data on a whole chromosome at Hapmap Phase 2 marker density within minutes. This program has been used to assess the power of several different commercially available genotyping chips, in the design stage of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC) and for evaluating the power of different methods for detecting association in genome-wide studies. (entry from Genetic Analysis Software)
Software package which provides an integrated approach to haplotype block identification, haplotype resolution and linkage disequilibrium mapping, suitable for high-density phased or unphased SNP data. (entry from Genetic Analysis Software)
Software application for constructing and testing haplotypes for SNPs in close physical proximity to one another but which are not necessarily contiguous. Furthermore, the number of SNPs contained in the haplotype is not restricted, thereby permitting the evaluation of complex haplotype structures. The analysis of large amounts of SNP data creates difficulties for the analysis of haplotypes and their association to traits of interest. Commonly fairly simple methods, such as two- or three-SNP sliding windows are used to create haplotypes across large regions, but these may be of limited value when adjacent SNPs are in strong LD and provide redundant information. This program alleviates these difficulties. (entry from Genetic Analysis Software)
Software program for estimating haplotype frequencies either from genotypes of individuals or from genotypes of pooled individuals. The genotypes must be for a block of bi-allelic SNPs (meaning that the SNPs should be in linkage disequilibrium with each other). The program assumes that it is given many genotypes of unrelated diploid individuals in Hardy-Weinberg equilibrium. If the genotypes are from pooled DNA, the program assumes that every pool contains the same number of individuals and the individuals were chosen at random when placed into the pools. For a reasonable running-time, the number of individuals in a pool needs to be between 2 and 4. (entry from Genetic Analysis Software)
Software application for haplotype reconstruction in general pedigree without recombination (entry from Genetic Analysis Software)
A suite of routines for the analysis of indirectly measured haplotypes. (entry from Genetic Analysis Software)
A simple software program for graphical presentation of haplotype block structures, tagSNP selection and SNP variation. (entry from Genetic Analysis Software)
A web application that has been developed to display the results of a scan for positive selection in the human genome using the HapMap data. It can be used as a resource to examine various population genetic measures in a genomic region. Measures that are currently displayed include iHS (a statistic developed to detect recent positive selection), Fay and Wu''s H, Tajima''s D and Fst. (entry from Genetic Analysis Software)
Software package for analyzing two-locus susceptibility gene models in affected sib-pair data (entry from Genetic Analysis Software)
Haplotype estimation service available in two variants: one for genetic data from unrelated probands (e.g., case/control studies) and one for core family data (entry from Genetic Analysis Software)
Software application for association mapping based on directly mining the haplotypes from case-control data via a density-based clustering algorithm. HapMiner can be applied to whole-genome screens, as well as candidate-gene studies in small genomic regions. (entry from Genetic Analysis Software)
Web application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be genotyped, along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans. (entry from Genetic Analysis Software)
Software platform that is based on real haplotype data from the HapMap ENCODE project that can simulate heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model. Moreover, both qualitative and quantitative traits can be simulated using additive genetic model with various genetic parameters designated by users. (entry from Genetic Analysis Software)
Software application that implements the PAC (Products of Approximate Conditional) model for estimating recombination rate (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An analysis tool for performing haplotype estimation on genetic markers such as SNPs and microsatellites. It is able to handle datasets that include case-control status as well as covariates and marker location variables (such as gene name, chromosome location, etc). (entry from Genetic Analysis Software)
Haplotype Sharing Transmission Disequilibrium Test
Software application for testing association using tightly linked markers in nuclear pedigrees (entry from Genetic Analysis Software)
Software application for haplotype association mapping using unrelated individuals; fixed and sliding window analysis; overall tests and tests for individual haplotype effects (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Java program for characterizing the haplotype block structure and selecting haplotype tagging SNP (entry from Genetic Analysis Software)
Multifactor Dimensionality Reduction and genotype Pedigree Disequilibrium Test
genome-wide association and INTERaction analysis of SNP
Software application for genome-wide interaction analysis (GWIA) of case-control SNP data. SNPs are selected for joint analysis using a priori information. Sources of information to define meaningful strategies can be statistical evidence (single marker association at a moderate level, computed from the own data) and genetic/biologic relevance (genomic location, function class or pathway information). (entry from Genetic Analysis Software)
Software application for estimating (imputing) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. (entry from Genetic Analysis Software)
Software application for non-parametric linkage and association tests primarily for a quantitative trait (entry from Genetic Analysis Software)
Java based LINkage disequilibrium plotter
Software application designed for customizable, intuitive visualisation of LD analysis across all common computing platforms. Customisation allows the researcher to choose particular visualisation, statistical measures and measurement ranges. JLIN also allows the researcher to export images of the LD visualisation in several common document formats. As there appears to be no single best measure of LD under all possible circumstances, JLIN allows the researcher to visually compare and contrast the results of a range of statistical measures on the input data set(s). These measures include the commonly used D'' and R2 statistics and empirical p-values. New additions include calculation of HWE, a completely revamped interface, and a numer of minor bug fixes. We have added a display measure to show marker distances visually, embedded fonts to improve image clarity and additional LD measures including d,OR,Pexcess and Q. (entry from Genetic Analysis Software)
Software for the calculation of genetic linkage maps
Software application for construction of genetic linkage maps for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, outbreeders full-sib family. Can combine (''join'') data derived from several sources into an integrated map. Further: linkage group determination, automatic phase determination for outbreeders full-sib family, several diagnostics, and map charts. Everything available in an intuitive MS-Windows user interface. (entry from Genetic Analysis Software)
Java Programs for Statistical Genetics and Computational Statistics GENEPI.JAR
Software application to address problems in statistical genetics; however, they include several programs and packages that may be more generally useful, for instance, programs to draw and manipulate graphs, simulation programs, and programs to estimate graphical models. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A Java GUI for the popular QTL data analysis software R/QTL that provides a flexible and powerful working environment for users to perform a variety of tasks. (entry from Genetic Analysis Software)
Software toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) for applications such as family relationship inference and population structure identification (entry from Genetic Analysis Software)
Likelihood Analysis with Metropolis Algorithm using Random Coalescence
Software application that estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data. (entry from Genetic Analysis Software)
Software application that is a parametric model-based approach to analyzing pedigree data for genomic imprinting. They have modified widely used LINKAGE program to incorporate imprinting. In addition, the LINKAGE-IMPRINT program allows for the use of sex-specific recombination in the analysis, which is of particular importance in a genome-wide analysis for imprinted genes. (entry from Genetic Analysis Software)
An easy and practical database-program made for researchers who want to connect the genotype data produced by automatic sequencers ( ABI Prism 377 (Perkin Elmer) and ALF (Pharmacia) ) to linkage and sib-pair programs. (entry from Genetic Analysis Software)
Software application for conversion of LINKAGE format data files to CRI-MAP format (entry from Genetic Analysis Software)
Software application designed to facilitate viewing of local association results together with useful information about a locus, such as the location and orientation of the genes it includes, linkage disequilibrium coefficients and local estimates of recombination rates. It was developed by popular demand, as a result of many questions we have had about How did you make the figures in your talk? or How did you make the figures for your GWAS paper? (entry from Genetic Analysis Software)
Software program using loss of heterozygosity data to enhance the power to detect linkage in cancer families. (entry from Genetic Analysis Software)
Software program for analyses a quantitative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis. The trait may be determined by multiple loci. (entry from Genetic Analysis Software)
Software application that detects population stratification in samples of unrelated individuals for whom a number of unlinked genotypes have been measured. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application that is part of the LINKAGE auxiliary program (entry from Genetic Analysis Software)
A compression tool recently proposed for compressing genome resequencing data using a reference genome sequence., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Likelihood Ratio Test Allowing for Errors
Software application to compute a likelihood ratio test statistic that increases power to detect genetic association in the presence of phenotype, genotype, and/or haplotype misclassification errors. In addition, the program produces asymptotically unbiased estimates of frequency parameters. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. A software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power. LTSOFT employs a liability threshold model approach that takes advantage of known epidemiological results to better model the covariates'' relationship to the phenotype of interest (entry from Genetic Analysis Software)
Suite of Python scripts for quality control of genetic markers, group analysis and inference of linear order of markers on linkage groups. MadMapper_RECBIT analyses raw marker scores for recombinant inbred lines. MadMapper_RECBIT generates pairwise distance scores for all markers, clusters based on pairwise distances, identifies genetic bins, assigns new markers to known linkage groups, validates allele calls, and assigns quality classes to each marker based on several criteria and cutoff values. MadMapper_XDELTA utilizes new algorithm, Minimum Entropy Approach and Best-Fit Extension, to infer linear order of markers. MadMapper_XDELTA analyzes two-dimensional matrices of all pairwise scores and finds best map that has minimal total sum of differences between adjacent cells (map with lowest entropy). MadMapper is freely available at http://www.atgc.org/XLinkage/MadMapper/ (entry from Genetic Analysis Software)
Marker And Gene Interpolation and Correlation
Software program to generate targeted marker sets for genome-wide association studies.
Software program for admixture mapping of complex trait loci, using case-control data. The samples should come from a recently-admixed population; additional ''learning'' samples from the parental populations are helpful. (entry from Genetic Analysis Software)
Multivariate Association Mapping Algorithms
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that tests for population structure through the use of Mantel tests (entry from Genetic Analysis Software)
(MAP+H is the radiation Hybrid module of MAP+)
Software application for multiple pairwise linkage analysis under interference (entry from Genetic Analysis Software)
Windows software for the graphical presentation of linkage maps and QTLs
Software application that produces charts of genetic linkage and QTL data. The charts are composed of a sequence of vertical bars representing the linkage groups or chromosomes. On these bars the positions of loci are indicated, and next to the bars QTL intervals and QTL graphs can be shown. MapChart reads the linkage information (i.e. the locus and QTL names and their positions) from text files. Many options to adapt the charts to different purposes. Can produce graphic files (enhanced windows metafile format) which can be enhanced with other MS-Windows software. (entry from Genetic Analysis Software)
Multiallelic Interallelic Disequilibrium Analysis Software
Software application for analysis and visualisation of interallelic disequilibrium between multiallelic markers (entry from Genetic Analysis Software)
Software program for mapping genetic markers in experimental segregating populations like backcross, doubled haploids, single-seed descent. Its specificity is to propose recombination fraction estimates in case of segregation distortion. It can (1) compute and draw genetic maps easily and quickly through a graphical interface; (2) facilitate the analysis of marker data showing segregation distortion due to differential viability of gametes or zygotes. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that draws genetic linkage maps on PC same as what MAPMAKER does on Mac. (entry from Genetic Analysis Software)
Software application that can be used to compare linkage maps obtained from different sources/populations/etc.. It will draw the linkage maps and look for common marker names, these are then connected in the drawing with dashed lines. All neighboring maps are compared in this way. Images can be printed and saved. Orders of the MAPs (ie which map is compared with which other map) can be changed and maps can be flipped (right mouse button). remark: MapComp bears close relationships with the GGT software package (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software programs that allow a user to get results on segregation ratio, linkage test, recombination value, grouping of markers, ordering of markers by metric multidimensional scaling, drawing map and graphical genotype. ALso QTL analysis by interval mapping and ANOVA are possible. (entry from Genetic Analysis Software)
Software application that infers genealogies from population genotype data and uses these to map disease loci. These genealogies take the form of the Ancestral Recombination Graph (ARG). The ARG defines a genealogical tree for each locus, and as one moves along the chromosome the topologies of consecutive trees shift according to the impact of historical recombination events. (entry from Genetic Analysis Software)
Minimum Description length method for haplotype BLOCKS
Software application using the mimimum description length model to delineate haplotype blocks (entry from Genetic Analysis Software)
Software application that calculates multipoint lod scores in pedigrees with inbreeding loops (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. Software application (entry from Genetic Analysis Software)
Software for the calculation of QTL positions on genetic maps
Software application for mapping of quantitative trait loci (QTLs) for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, full-sib family of outbreeders. Analyses: interval mapping, composite interval mapping, nonparametric mapping, automatic cofactor selection, permutation test for interval mapping. QTL charts. Everything available in an intuitive MS-Windows user interface. (entry from Genetic Analysis Software)
Software package to perform QTL mapping in multi-cross designs that allows the analysis of the usual populations derived from inbred lines and can link the families by assuming that the QTL locations are the same in all them. Moreover, a diallel modelling of the QTL genotypic effects is allowed in multiple related families. Obviously, the analysis of a single cross is also feasible. (entry from Genetic Analysis Software)
a Manipulation Environment for Genetic Analyses
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that uses as input a trio of files: 1) a LINKAGE-format locus file modified to contain locus name information; 2) a LINKAGE-format pedigree file; and 3) a map file. Mega2 then takes this trio of input files and, via a menu-driven interface, transforms them into various other file formats, thus greatly facilitating a variety of different analyses. In addition, for many of these options, it also sets up a C-shell script that then can automatically run these analyses (if you are using Mega2 in a Unix environment that supports C-shell scripts). (entry from Genetic Analysis Software)
Software application that takes case-control genotype data as input and produces a ranked list of multi-SNP interactions. In particular, the whole genome is first partitioned into multiple short subgenomes and a boosting tree classifier is built for each subgenomes based on multi-SNP interactions and then used to measure the importance of SNPs. The method keeps relatively more important SNPs from all subgenomes and let them compete with each other in the same way at the next level. The competition terminates when the number of selected SNPs is less than the size of a subgenome. (entry from Genetic Analysis Software)
Software application for genetic analysis of human pedigree data under models involving a small number of loci. MENDEL is useful for segregation analysis, linkage calculations, genetic counseling, allele frequency estimation, and related kinds of problems. (entry from Genetic Analysis Software)
Multipoint Engine for Rapid Likelihood INference
Software application that carries out single-point and multipoint analyses of pedigree data, including IBD and kinship calculations, nonparametric and variance component linkage analyses, error detection and information content mapping. For multipoint analyses in dense maps, Merlin allows the user to impose constraints on the number of recombinants between consecutive markers. Merlin estimates haplotypes by finding the most likely path of gene flow or by sampling paths of gene flow at all markers jointly. It can also list all possible nonrecombinant haplotypes within short regions. Finally, Merlin provides swap-file support for handling very large numbers of markers as well as gene-dropping simulations for estimating empirical significance levels. (entry from Genetic Analysis Software)
A compression utility designed to be a replacement for compress.
Software application that is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. (entry from Genetic Analysis Software)
Software application to calculate the sample size of genotypes minimally required to ensure that all alleles with a specified frequency at one locus are detected with a given confidence (entry from Genetic Analysis Software)
Software program for analysis of mitochondrial diseases (entry from Genetic Analysis Software)
ASPSHARE (rapid calculation of the expected ibd sharing at the trait locus
comparing specific types of simple hypotheses regarding the familial relationships involved)
EASYPAT (calculation of likelihood ratios for single locus data
FINDSIRE (identify mothers or sires by means of the comparison of a large number of potential parents
including ASP (power calculator for gene mapping using a sibpair design)
Michael Krawczak''s Genetics Software Tools
MUTPROF/MUTCOMP (comparison of mutation profiles)
PATERN (calculation of paternity probabilities from the multilocus DNA profiles of trios
with given infants or parent-infant duos)
Software application to draw chromosome maps from the output of MAPMAKER/EXP. The output format is a Enhanced Metafile, which can be imported into most Windows-based presentation or document editing programs. (entry from Genetic Analysis Software)
Maximum-Likelihood-Binomial analysis of affected sib-pair and sibship data extended from the GENEHUNTER program
Software application that is an extension of the GENEHUNTER program to perform sib-pair and sib-ship linkage analysis using the Maximum Likelihood Binomial (MLB) method. (entry from Genetic Analysis Software)
Software application performing a shuffling version of the exact conditional tests for different combinations of allelic and genotypic disequilibrium on haploid and diploid data, or their combination. (entry from Genetic Analysis Software)
Software application that can be used for tagging SNP selection and genotype prediction (entry from Genetic Analysis Software)
A compression tool for FASTA and multi-FASTA files.
Statistical Analysis for Genetic Epidemiology
Software application that provides researchers with the tools necessary for various types of statistical genetic analysis of human family data. (entry from Genetic Analysis Software)
A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software)
A multipoint linkage analysis software which allows Marker-Marker LD (entry from Genetic Analysis Software)
Bayesian QTL mapping software for analysing backcross, double haploid, and F2 data from designed crossing experiments of inbred lines (entry from Genetic Analysis Software)
Bayesian QTL mapping software for analysing backcross and F2 data from designed crossing experiments of outbred lines (entry from Genetic Analysis Software)
Software program that selects a near-minimal set of tagging single-nucleotide polymorphisms (tagSNPs) that account for all observed patterns of linkage disequilibrium (LD) in multiple populations. (entry from Genetic Analysis Software)
Software application to analyze the numbers of individuals that founded new populations following a bottleneck or founding event (entry from Genetic Analysis Software)
Software application that uses genome-wide genotype data to estimate disease susceptibility. Our system integrates three data sources: HapMap, whole-genome marker correlation data, and OMIM database. It accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete. (entry from Genetic Analysis Software)
Software application to estimate parameters for mixture of normal distributions (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that splits extended pedigrees into nuclear families, with the option of recoding all sibs as half-sibs with distinct mothers of fathers. (entry from Genetic Analysis Software)
Software tool for the retrieval of articles from MEDLINE related to the sequence variants reported for a human gene. The variations considered are single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (indel), microsatellite, and named variations (e.g. Alu sequences). (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
P-values: Adjustment for Correlated Tests
An R program that adjusts sets of up to 1000 p-values from association tests between correlated traits and SNPs for multiple testing, accounting for the correlation between tests. (entry from Genetic Analysis Software)
Software application to draw the most complex family trees in a matter of minutes instead of hours of work. The basis of this is an algorithm for automatically builing a family tree. Of course, manual adjustments in the family tree can be made for your specific requirements. PASS Pedigree meets all international conventions concerning the drawing of pedigrees. A converter can convert historical Cyrillic pedigrees automatically to PASS Pedigree. Unlike before, all your family trees are stored in one single database. PASS Pedigree can intelligently connect to many genetic centers (e.g. three genetic centers in the Netherlands) with the existing patient information, via the lab system HELIX based on HL7 techniques. (entry from Genetic Analysis Software)
Software application for power and sample size calculations for genetic case-control association studies allowing for errors (entry from Genetic Analysis Software)
Software tool for analyses of pooled DNA data (entry from Genetic Analysis Software)
Software application that is a Windows-based system designed for pedigree data management, providing a graphical interface for pedigree construction and output. (entry from Genetic Analysis Software)
Software analysis program to evaluate evidence of linkage disequilibrium (LD) in general pedigree data. All family data may be used without nullifying the validity of the association test, even when there is more than one affected in a family. The PDT program performs both allele-specific and genotype-specific LD analysis of individual markers. Version 5.1 adds the ability to perform genotype-specific analysis over marker sets. (entry from Genetic Analysis Software)
Powerful pedigree drawing program with two drawing modes: Input mode for fast and automatic drawing; edit mode for text annotations, legends, special symbols. Both input and edit mode provide auto numbering, auto resizing of symbols and fonts, and zooming. PED 4.2a complies with the Recommendations for standardized human pedigree nomenclature. Apart from fully sizeable printed output, pedigrees can be exported as metafiles to virtually any Windows word processor or drawing program. (entry from Genetic Analysis Software)
Software program for detecting autosomal marker Mendelian incompatibilities in pedigree data (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,20023. Software application for identifying all Mendelian inconsistencies in pedigree data. (entry from Genetic Analysis Software)
Software application for error checking and data summary of large or small data sets in QTDT, LINKAGE or MENDEL format. Checks for basic formatting errors, disconnected family groups, ancestor-descendant loops and can detect all Mendelian (including X-linked) inheritance errors in any pedigree without loops. Produces text and graphical (PDF) summaries of the family structure, trait and marker information of pedigree data and can break down summaries by sex, relative pair type or family. PEDSTATS also does Hardy-Weinberg testing using either a fast exact or asymptotic test and can summarize information in text or graphical PDF format. Additional features include a number of options for filtering data prior to summary and checks for inappropriate age or covariate values. Lastly, PEDSTATS can identify and trim uninformative individuals from a pedigree and rewrite the reorganized data to a new pedigree file. (entry from Genetic Analysis Software)
Full-scale database system developed as a specialized tool for management of genetic, pedigree and demographic data. (entry from Genetic Analysis Software)
A Java Api for the visual analysis of large and complex pedigrees that provides all the necessary functionality for the interactive exploration of extended genealogies. Available packages are mostly focused on a static representation or cannot be added to an existing application; the goal of this open-source library is to provide an application program interface that enables the efficient construction of visual analytic applications for the analysis of family based data. (entry from Genetic Analysis Software)
Software collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have * detected batch effects and experimental confounders * increased the number of expression QTL findings by threefold * allowed inference of intermediate cellular traits, such as transcription factor or pathway activations This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python.
Software program that implements a new statistical method for reconstructing haplotypes from population genotype data (entry from Genetic Analysis Software)
Partition-Ligation EM algorithm for haplotype inference with single nucleotide polymorphisms
Software application for complex segregation analysis with the mixed model (major locus and polygenes). (entry from Genetic Analysis Software)
POOLing alleles of Short Tandem Repeat markers
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A comprehensive set of statistical methods for genetic marker data analysis, designed especially for SSR/SNP data analysis. PowerMarker builds a powerful user interface around both new and traditional statistical methods for population genetic analysis. See analysis to check out the versatility of PowerMarker. PowerMarker is also a 2D Viewer - which was used intensively for visualizing linkage disequilibria results. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11,2023. Software application that automate the decision to remove objects from a pedigree with a minimum loss information (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Excel spreadsheet to calculate power of affected sibpairs and TDT analyses (entry from Genetic Analysis Software)
Software program that detects pedigree errors in general outbred pedigrees by use of genome-screen data. When a potential pedigree error is detected, our companion program, ALTERTEST, determines which relationships are compatible with the observed genotype data. Both programs are freely available on the web. (entry from Genetic Analysis Software)
Software application for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny (entry from Genetic Analysis Software)
Software application that is a user defined SAS procedure for mapping quantitative trait loci (QTL). Since this procedure is not a built-in SAS procedure, users need to obtain a copy of the executable file of PROC QTL and install the software in their personal computers before PROC QTL can be executed. Of course, users need a regular SAS license prior to the installation of PROC QTL. Once PROC QTL is installed, it can be called just like any other SAS procedures. Users will not notice the differences between this customized procedure and other built-in SAS procedures. (entry from Genetic Analysis Software)
A flexible software tool to generate the probability distribution of joint multilocus genotypes defined by sets of individuals within the pedigree and sets of markers within the framework map. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application for partition of single generation into sibling groups (entry from Genetic Analysis Software)
Population Stratification Association Test
A compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files.
Software application for summarizing marker properties (allele & genotype frequencies, tests for Hardy-Weinberg equilibrium, measures of marker informativeness), examining marker-marker relationships (tests and measures of linkage disequilibrium, and haplotype frequency estimation), and exploring marker-trait associations using case-control or family-based tests (entry from Genetic Analysis Software)
Software application that estimates genomewide empirical p-values for Kong and Cox tests of linkage using the replicate pool method, which for many data sets, improves upon the computational efficiency of conventional gene-dropping methods by several orders of magnitude. This allows Pseudo to handle data sets with large families and makes it particularly applicable to those situations where p-value estimation by standard methods is computationally prohibitive. Pseudo also estimates variance for reported p-values, produces graphical and text summaries of results, and is able to assess significance of multiple correlated outcomes. Pseudo is designed to work with the Merlin package and includes utilities for generating input files from standard Merlin output. (entry from Genetic Analysis Software)
A linkage analysis software for joint linkage and/or linkage disequilibrium analysis. PSEUDOMARKER can analyze different data structures jointly such as cases-controls, trios, sib-pairs, sib-ships, and extended families. (entry from Genetic Analysis Software)
A set of programs written in MATLAB for the analysis of QTL data from inbred line crosses. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software package designed to make as many as possible of the new statistics (e.g. score statistics) widely available. The software consists of a MEGA2-like interface for data analysis preparation and a library of R routines that computes linkage statistics. QTL-ALL reads in input data, creates re-formatted output data files, calls external IBD-generation software such as MERLIN or SIMWALK2, then computes statistics using our R library, and finally produces tables and plots of statistics and p-values. This entire sequence is highly automated, requiring minimal user-intervention. The initial release of the software computes a number of newer QTL-mapping statistics, including several score statistic variants, and can handle nuclear family data, including specialty designs such as discordant and concordant (affected) pairs. (entry from Genetic Analysis Software)
Software program to map quantitative traits sing a map of molecular markers. (entry from Genetic Analysis Software)
A web-based user-friendly package to map Quantitative Trait Loci in outbred populations. Population structures catered for are line crosses, halfsib families, nuclear families and sibpairs. Permutation tests to determine empirical significance levels and bootstrapping to estimate empirical confidence intervals of QTL locations are optional. Fixed effects/covariates can be fitted and models may include single or multiple QTL. Results are presented in tabular and graphical format. (entry from Genetic Analysis Software)
Software package for quantitative analysis of genetic models (entry from Genetic Analysis Software)
Windows program for risk calculation in families with Duchenne muscular dystrophy. It is based on an extended genetic model which includes germline mosaicism and different new mutation rates depending on sex and mutation type. Arbitrary family structures and additional diagnostic information like genotypes from intragenetic and flancing genetic markers of the dystrophin gene, creatin kinase values and female deletion test results can be taken into account. (entry from Genetic Analysis Software)
Reconstruction-Combined Transmission Disequilibrium Test
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application using a family-based association method that allows testing for linkage in the presence of linkage disequilibrium between an autosomal marker and a disease even if there is only incomplete parental-marker information. Recently, Horvath et al. (2000) described a similar procedure (XRC-TDT) for X-linked markers. The distribution contains SAS macros that calculate the RC-TDT and XRC-TDT test statistics, as well as their respective exact P values. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Tag SNP selection tool according to r2-bins method that is specifically designed for full genome scale deterministic tagging.
Software application for relationship estimation, in particular between putative sibs when parents are untyped (entry from Genetic Analysis Software)
Software program for checking relationships between pairs of individuals. There are many excellent programs that carry out similar tasks. Some of the unique features in relativeFinder are the batch mode options, that allow large jobs to be divided into many smaller jobs (suitable for deployment on a compute cluster environment), and the flexibility of the underlying Merlin engine, which allows relative finder to handle large pedigrees and consider a variety of alternate relationships -- including potential relationships specified by the user on the fly. (entry from Genetic Analysis Software)
Software program for verifying the relationships between all pairs of individuals in a linkage study, by use of (autosomal) genome scan data, with allowance for the presence of genotyping errors. (entry from Genetic Analysis Software)
Software program that infers the relationships of pairs of individuals based on genetic marker data, either within families or across an entire sample. (entry from Genetic Analysis Software)
Software program for determining biological relatedness between individuals based on allele sharing at microsatellite loci (entry from Genetic Analysis Software)
Regression of Offspring on Mid-Parent (REVised)
Software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data. (entry from Genetic Analysis Software)
Compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 2, 2014. A genetic data management and analysis system designed to advance your whole genome association, linkage, and eQTL studies, providing you with an easy-to-use project workspace so that you can organize, analyze, and share your genotype and phenotype data along with your analysis results. With the Syllego system, generating high quality analysis data and meaningful results becomes simple. The Syllego system automates all tedious data management and data formatting tasks so that you can streamline your genetic analysis workflows using your analysis methods of choice. Managing all your genetic data and reference information is straightforward. The Syllego system converts public and private genotype data sets and reference annotations, such as dbSNP and HapMap, as well as individual (sample) information into a single, consistent repository for fast, convenient access. (entry from Genetic Analysis Software)
An integrated software package for genetic data analysis of both population and family data. Currently it contains functions for sample size calculations of both population-based and family-based designs, classic twin ACE/ADE/AE/CE models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates (entry from Genetic Analysis Software)
Software application using a likelihood approach to inference of haplotype and nongenetic effects and their interactions in generalized linear models of disease penetrance, when haplotype phase is unknown for some subjects. Parameter estimates are obtained by use of an expectation-maximization (EM) algorithm and standard errors are calculated using Louis'' formula. (entry from Genetic Analysis Software)
An R package that uses an individual-based approach to simulate distributions of genotypes that result from arbitrary within and among population demographies (including extinction/recolonization). These distributions can be used to test new or existing population-genetics summary statistics or develop null distributions under various demographies. (entry from Genetic Analysis Software)
Software environment for constructing linkage maps in outcrossing plant species, using full-sib families derived from two outbreed (non-inbreeding) parent plants. (entry from Genetic Analysis Software)
Software library for QTL Bayesian Interval Mapping that provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits. (entry from Genetic Analysis Software)
An R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program for fast calculation of empirical and adjusted p-values for correlated and uncorrelated hypotheses in multiple testing experiments. It is based on the Free Step-Down Resampling Method for controlling the Family Wise Error Rate, originally proposed by Westfall and Young (1993), and implements a variation of the efficient algorithm of Ge et al. (2003), in which the originally necessary re-sampling effort was reduced considerably and the method made computationally more feasible. The program is independent of the underlying test statistic and works with provided observed and permutation test statistics. (entry from Genetic Analysis Software)
Software program which can simulate population genetic data in which a single site has experienced natural selection. When designing methods which provide the necessary power to detect regions of the genome which have experience historical selective pressures it is important to consider which patterns of genetic diversity are indicative of particular forms of natural selection. (entry from Genetic Analysis Software)
Software program that analyzes sequence data. It obtains an approximation to the likelihood of a summary of the data (as such it can be thought of as a marginal likelihood approach). It does not use all the information in the data, but computationally it can be substantially more efficient than the full-likelihood methods (and hence able to analyze larger data sets). (entry from Genetic Analysis Software)
Software application that identifies pedigree errors in sibship data. Examples include half siblings, unrelated individuals, identical twins, and parental exclusions. The test statistic is based on the summation of the number of alleles shared by a pair of relatives for a large number of markers and the number of alleles and allele frequencies for those markers. (entry from Genetic Analysis Software)
Software application that allows the user to perform multipoint linkage analysis based on estimated IBD sharing between affected sibpairs. IBD sharing is inferred from IBS status, given marker genotypes, frequencies, and locations. Resulting LOD scores are maximized across a grid of possible disease locations and IBD sharing vectors. (entry from Genetic Analysis Software)
Software program that performs a number of simple analyses of family data that tend to be nonparametric or robust in nature, includes IBD and IBS based APM, Haseman-Elston sib pair, TDT and association analyses. (entry from Genetic Analysis Software)
Software application to calculate nominal significance levels and critical LOD scores depending on the length of the investigated region, number of chromosomes, and the cross-over rate. The global significance level as well as the precision of the calculation have to be specified. (entry from Genetic Analysis Software)
Software application providing a comprehensive modelling framework and a multiple-imputation approach to haplotypic analysis of population-based data. It uses biallelic SNP genotype data to impute haplotype frequencies at the individual level. SimHap also tests for haplotype associations with outcomes of interest while incorporating the uncertainty around inferred haplotypes into the modelling procedure. SimHap allows epidemiological (ie, non-genetic) and both single SNP and haplotype association analyses of quantitative Normal, binary, longitudinal and right-censored outcomes under a range of genetic models. SimHap can accommodate large data sets, and can model genetic and environmental effects, including complex haplotype:environment interactions. SimHap features cross-platform functionality via Java, and a sophisticated graphical user interface (GUI). SimHap will also perform association analysis on more simple epidemiological models, with or without the inclusion of genetic covariates. (entry from Genetic Analysis Software)
SIMulation of pedigree data for Linkage and Association studies
SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages (entry from Genetic Analysis Software)
Software application to generate visual patterns that can be easily interpreted as a single specific Single Nucleotide Polymorphism (SNP) genotype, based on reiterative pattern recognition from validated SNP data (entry from Genetic Analysis Software)
Software program to estimate the probability (power) of detecting linkage given family history information on a set of identified pedigrees. (entry from Genetic Analysis Software)
Software program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies. (entry from Genetic Analysis Software)
Sequential Imputation for MultiPoint Linkage Estimation
Software application that calculates linkage statistics, such as lod scores and NPL statistics by Sequential Imputation. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Simulation program that generates data sets of families for use in linkage and association studies. SIMLA_3.2 is a major upgrade to versions 2.3 and 3.0 that provides the ability to simulate two disease loci and two environmental covariates. Gene-gene and gene-environment interactions may also be simulated which jointly determine the disease risk of all pedigree members.
Software program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package. (entry from Genetic Analysis Software)
A forward-based population genetics simulation program capable of simulating very complex evolution processes on large (think of millions) populations. Major features include variable population size; many built-in and hybrid (write in python) mutation, migration, selection models. simuPOP can be extended in Python so there is no limit on what you can do with it. (entry from Genetic Analysis Software)
Software programs for generating optimal haplotype configurations on general pedigrees using a likelihood-based approach to correctly take intermarker recombination fractions into account. simcross ignores untyped parts of the pedigree, and it uses simulated annealing. simwalk combines simulated annealing with random walk method. (entry from Genetic Analysis Software)
Software application that finds starting points for MCMC analysis performed on large, complex pedigrees and polymorphic markers. (entry from Genetic Analysis Software)
Computational Platform for analysis of Small RNA deep Sequencing data BioStaCs group., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
SNP-set (Sequence) Kernel Association Test
Software application that is a SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies. (entry from Genetic Analysis Software)
Software tool that recognises and removes the most unrealistic data pointsfor the construction of accurate linkage maps, which is not so much depending on the quality of the mapping software, but mostly on the marker data quality. Missing values and scoring errors can severely influence the calculated marker order. This software was used to construct the 10,000 marker potato map. The removal of improbable data point is a good medicine for linkage maps, that is not easily overdosed. One error is more harmfull than ten missing values. The software was never intended as user-friendly software. In these days it would be more useful to re-do the programming of the pascal source code into a perl script. Anyone who takes the initiative to generate such a script is welcomed to contact the authors. SMOOTH works best in close cooperation with mapping algorithm RECORD (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 29, 2016. A workbench tool to make existing population genetic software more accessible and to facilitate the integration of new tools for analyzing patterns of DNA sequence variation, within a phylogenetic context. Collectively, SNAP tools can serve as a bridge between theoretical and applied population genetic analysis. The exploration of DNA sequence variation for making inferences on evolutionary processes in populations requires the coordinated implementation of a Suite of Nucleotide Analysis Programs (SNAP), each bound by specific assumptions and limitations.
Simulation of sNp haplotype data And Phenotypic traits
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software program can be used to generate SNP haplotype sequence data of unrelated individuals and nuclear families with a fixed or random number of children.
Software library and API for manipulating large SNP datasets with associated meta-data, such as marker names, marker locations, individuals'' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPFile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols. (entry from Genetic Analysis Software)
Software application for multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. SNPLINK requires these other programs installed on the system: MERLIN (used for nonparametric analysis), ALLEGRO (used for parametric analysis), R and PERL, all are freely available. (entry from Genetic Analysis Software)
Single Nucleotide Polymorphism Processor
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. A dynamic general database management system to manage high-throughput SNP genotyping data. It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting. Furthermore, SNPP may generate files for repeat genotyping and transform them into files that can be executed by a liquid handling system.
Software program for the analysis of single SNP association in genome-wide studies. The tests implemented can cater for binary (case-control) and quantitative phenotypes, can condition upon an arbitrary set of covariates and properly account for the uncertainty in genotypes. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). (entry from Genetic Analysis Software)
Statistics Program for Analysing Mixtures
Software application that estimates the relative contributions of discrete populations to a mixture sample, solving what is commonly referred to in fisheries as the mixed stock analysis or genetic stock identification problem. (entry from Genetic Analysis Software)
Software application for analysis of sperm typing data. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application that simulate pedigrees and genetic data in age-structured populations (entry from Genetic Analysis Software)
Software application that can calculate virtually any linkage test statistic under several sib pair study designs: affected, discordant, unaffected, and pairs defined by threshold values for quantitative traits, such as extreme discordant sib pairs. It uses the EM algorithm to compute maximum likelihood estimates of sharing (subject to any user-specified domain restrictions or null hypotheses) and then plots lod scores versus chromosomal position. It includes a novel grid scanning capability that enables simultaneous visualization of multiple test statistics. Phenotype definitions can be modified without recalculating inheritance vectors, thereby providing considerable analytical flexibility. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The mission of the CCRTD Research Support Core Facilities is to provide the scientists of CCRTD, Clark Atlanta University, and Atlanta University Center with access to modern technology, resources, and instruments essential for cutting-edge research in molecular biology, genomics, proteomics, cell biology, and biological imaging.
Software tool to select, evaluate and visualize LD tag SNPs for single or multiple populations. The input files can be a set of dumped genotype files from International HapMap Project (http://www.hapmap.org/) (Hapmap format) or Seattle SNPs (http://pga.gs.washington.edu/) (Prettybase format). The ouput is a set of LD tag SNPs for single or multiple populations. (entry from Genetic Analysis Software)
Software application for linkage analysis using affected sib pairs (entry from Genetic Analysis Software)
Sequence Search and Alignment by Hashing Algorithm for SNP detection
A polymorphism detection tool that detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. For those less repetitive or non-repetitive reads, we place them uniquely on the reference genome sequence and find the best alignment according to the pair-wise alignment score if there are multiple seeded regions. From the best alignment, SNP candidates are screened, taking into account the quality value of the bases with variation as well as the quality values in the neighbouring bases, using neighbourhood quality standard (NQS). For insertions/deletions, we check if the same indel is mapped by more than one read, ensuring the detected indel with high confidence. (entry from Genetic Analysis Software)
Software application that assess the joint disease association of multiple unlinked SNPs via sums of SNP specific test statistics. Genome-wide significance levels are obtained by per mutation analysis. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,6th, 2021. Software application as extension to SLINK/FastSLINK to allow more marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with trait locus. entry from Genetic Analysis Software.
Software application that allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection. Primarily, it uses the Long Range Haplotype test to look for alleles of high frequency with long-range linkage disequilibrium, which suggest the haplotype rapidly rose to high frequency before recombination could break down associations with nearby markers. SWEEP takes phased genotype data as input, detects all haplotype blocks in that data, and then determines the frequency and long-range LD for each allele in each block. (entry from Genetic Analysis Software)
Relative Lempel-Ziv Compression of Genomes
Optimized relative Lempel-Ziv compression of genomes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 6th,2023. Software package for inferring natural selection from unusual population differentiation between closely related populations. (entry from Genetic Analysis Software)
Weighted Haplotype test And an Imputation-based Test.
National Data Center that accepts and makes available weather, climate, paleoclimate, meteorological data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29,2019. Sedimentary geologic and biostratigraphic data.
National Data Center that provides scientific stewardship, products, and services for geophysical data from sea floor and solid earth environments, including Earth observations from space. Please note that routine underway geophyiscal shipboard data collected with standard equipment aboard the UNOLS fleet (e.g. bathymetry, subbottom, magnetics, gravity) are routinely transmitted to NGDC via Rolling Deck to Repository (R2R).
Index to Marine and Lacustrine Geologic Samples
A repository of geologic material from sea floor and lakebed cores, grabs, and dredges archived by participating institutions.
This atlas takes advantage of ultra-high resolution 7T MRI to provide unprecedented levels of detail on structures of the basal ganglia in-vivo. The atlas includes probability maps of the Subthalamic Nucleus (STh) using T2*-imaging. For now it has been created on 13 young healthy participants with a mean age of 24.38 (range: 22-28, SD: 2.36). We recently also created atlas STh probability maps from 8 middle-aged participants with a mean age of 50.67 (range: 40-59, SD: 6.63), and 9 elderly participants with a mean age of 72.33 (range: 67-77, SD: 2.87). You can find more details about the creation of these maps in the following papers: Young: http://www.ncbi.nlm.nih.gov/pubmed/22227131 Middle-aged & Elderly: http://www.ncbi.nlm.nih.gov/pubmed/23486960 Participating institutions are the Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany, and the Cognitive Science Center Amsterdam, University of Amsterdam, the Netherlands.
ATID: Alternative Translational Initiation Database
Alternative Translational Initiation Database
A database of publicly available genes, alternatively translational isoforms and their detailed annotation. Alternative translational initiation is one of mechanisms to increase the complexity level of an organism by alternative gene expression pathways. The use of alternative translation initiation codons in a singe mRNA contributes to the generation of protein diversity. The genes produce two or more versions of the encoded proteins, and the shorter version, initiated from a downstream in-frame start codon, lacks the N-terminal amino acids fragment of the full-length isoform version. Since the first discovery of alternative translation initiation, a small, yet growing, number of mRNAs initiating translation from alternative start codons have been reported. Various studies began to emerge focusing on this new field in gene expression and revealed the biological significance of the use of alternative initiation. In response to the need for systematic studies on genes involving alternative translational initiation, Alternative Translational Initiation Database(ATID) is established to provide data of publicly available genes, alternatively translational isoforms and their detailed annotation.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Certified clinical laboratory (ISO15189). To clinicians in oncology we offer genetic and epigenetic analyses together with interpretation. iGen also provides professional genetic counseling ?????????????????? a healthcare service, which advises people who are at the risk of hereditary cancer. In the research field iGen performs assay development and genotyping services. Our customers are clinical laboratories, research groups and genetic tests distributors. To improve molecular diagnostics in cancer treatment iGen is continuously carrying out research and applied science projects. Currently, our main cooperation partners are the Competence Centre of Cancer Research and North Estonian Medical Centre. We are looking for other cooperation opportunities, and are interested in participating in national and international cooperative research projects, to which we can contribute with our expertise in molecular diagnostics. Our laboratory and office are situated in Tehnopol Tallinn Science Park territory, next to the campus of Tallinn University of Technology. Prices quoted are highly dependable on the number of samples and are given based on full plate/machine, please contact us for pricing for smaller projects.
A set of deformable modeling algorithms for shape analysis and structure-specific normalization. Applications of cm-reps include structure-specific fMRI analysis, DTI analysis, and structural brain mor
Nathan Kline Institute (NKI) / Rockland Sample
Nathan Kline Institute / Rockland Sample
A phenotypically rich neuroimaging sample, consisting of data obtained from individuals between the ages of 4 and 85 years-old. All individuals included in the sample undergo semi-structured diagnostic psychiatric interviews, and complete a battery of psychiatric, cognitive and behavioral assessments in order to provide comprehensive phenotypic information for the purpose of exploring brain / behavior relationships.
Portal for scientific dissemination, teaching and interdisciplinary research that includes the integration of the sciences of mind, brain and education in Brazil. The contents are in Portuguese. English version coming soon.
3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood
3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood
3D DTI anatomical rat brain atlases have been created by the UNC- Chapel Hill Department of Psychiatry and the CAMID research collaboration. There are three age groups, postnatal day 5, postnatal day 14, and postnatal day 72. The subjects were Sprague-Dawley rats that were controls in a study on cocaine abuse and development. The P5 and P14 templates were made from scans of twenty rats each (ten female, ten male); the P72, from six females. The individual cases have been resampled to isotropic resolution, manually skull-stripped, and deformably registered via an unbiased atlas building method to create a template for each age group. Each template was then manually segmented using itk-SNAP software. Each atlas is made up of 3 files, a template image, a segmentation, and a label file.
A novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation. AutoSeg is designed for use with human and non-human primate pediatric, adolescent and adult data. AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction, rigid registration to a common coordinate image, tissue segmentation, skull-stripping, intensity rescaling, atlas-based registration, subcortical segmentation and lobar parcellation, regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes.
A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts.
Software toolkit developed for the fbrain project that consists of several image processing tools: image reconstruction, image denoising, image segmentation, tractography etc., for a better understanding of fetal brain development.
Best Practices for Software Development in the Imaging Community: Users and Developers Unite
A tutorial that took place as part of MICCAI 2010 is the 13th International Conference on Medical Image Computing and Computer Assisted Intervention, September 20-24, 2010 in Beijing, China. See http://www.miccai2010.org/ This project supporedt community outreach and dialog between presenters and audience, both before and after the tutorial session, and is intended to engage the broader community in the deliberations on this important topic. ''Best Practices'' covered software engineering practices as well end-user installation and support practices.
High quality data, open and freely available to everyone to celebrate the diversity of the vertebrate brain. Do you have data that you would like to share? Do not hesitate to contact them! The Brain Catalogue is developed by Florencia Grisanti (Taxidermy Workshop of the Natural History Museum in Paris) and Roberto Toro (Neuroscience Department of the Institut Pasteur). Many of our specimens come from the Vertebrate Brain Collection of the Jardin des Plantes, curated by Marc Herbin, and are scanned at the Institut du Cerveau et de la Moelle (ICM) by Mathieu Santin and Alexandra Petiet, from the CENIR laboratory, with financial and methodological support kindly provided by Olivier Colliot, head of the Cogimage team at the ICM.
Commercial organization for hardware and software for neurophysiological research. Provides EEG and ERP amplifier systems, EEG recording caps, Data recording and analysis software, TMS Stimulator for combined EEG/TMS coregistrations and more.
Draw3D is a 3D rendering tool written entirely in VTK-TCL script. It is intended for fast command line rendering and visual inspection of datasets commonly found in medical imaging. It also allows the generation of images for reports or videos. As it is based on pure VTK, it can render whatever VTK can render, and runs wherever VTK can run. Meshinator is a simpler tool that uses VTKs isosurface functions to generate meshes from volumetric data. Please see the wiki for documentation
A free collection of MRI brain images for testing segmentation algorithms. It is available for download to assess the accuracy, reproducibility and sensitivity of MRI segmentation software. It includes data from infants and adults as well as patients with Alzheimer's disease.
Aa brain network visualization tool, which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick, easy, and flexible way.
A collection of tools for MRI T1 brain image segmentation in the Windows environment. It helps construct a complete pipeline with necessary preprocessing and postprocessing procedures besides brainparser, the core program of our fast brain segmentation. The execution of the whole pipeline can be completed in 2 hours with good segmentation results. Execution requires: FSL
An interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data (Damasio and Frank, 1991; Frank, Damasio and Grabowski, 1997).
A small, stand-alone MatLab toolbox that measures sagittal cross-section thickness and area of the human corpus callosum from high-resolution T1 in vivo MR images. C8 takes as input affine normalized white matter segmentations derived from high-resolution (in-plane) T1 images and outputs both regional callosal thicknesses in three different formats and geometrically-defined regional areas in three different configurations. It is a small package that is easily configurable and modifiable and it measures callosa at the rate of several per minute.
Software package that allows interoperability between CAMINO and TRACKVIS. CAMINO is a leading software package in DTI processing. The package is from University of College London. TRACKVIS is a tract visualizing utility with capability of visualizing up to and over a million white matter tracts seamlessly. The package is from Massachusetts General Hospital. With increasing efforts on brain connectivity analyses it becomes important to have tools that can allow increased interoperability among different tractography tools. The tools in this package allow conversion of tracts from one format to another in a very effective way with ability to handle over a million tracts.
CANDI Share: Schizophrenia Bulletin 2008
This project hosts data for CANDI Share Schizophrenia Bulletin 2008 (reference below) as part of the CANDI Neuroimaging Access Point. This set includes preprocessed MRI images and segmentation results of all 4 diagnostic groups (Healthy Controls, N=29; Schizophrenia Spectrum, N=20; Bipolar Disorder with Psychosis, N=19; and Bipolar Disorder without Psychosis, N=35). Frazier JA, Hodge SM, Breeze JL, Giuliano AJ, Terry JE, Moore CM, Kennedy DN, Lopez-Larson MP, Caviness VS, Seidman LJ, Zablotsky B, Makris N. Diagnostic and sex effects on limbic volumes in early-onset bipolar disorder and schizophrenia. Schizophr Bull. 2008 Jan;34(1):37-46.
A fully automated processing pipeline for cortical analysis of structural MR images at a resolution of up to 400������m, including skull stripping, whole brain segmentation, cortical extraction, surface inflation and mapping, as well as dedicated tools for profile estimation across the cortical thickness. The tools are released as a set of plug-ins for the MIPAV software package and the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats.
An open-source C++-based application that allows automatic as well as user-interactive segmentation of the Corpus Callosum. Via a Qt-based graphical user interface, CCSeg also performs semi-automatic segmentation.
Cerebral Blood Flow Database and Analysis Pipeline
A web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner.
This package is a set of three slicer modules which together are able to compute a DWI Atlas given a set of DWI''s. The modules included are: # A Groupwise Registration module -> compute''s a deformation field for each DWI, using, for example, FA maps as input # Warp DWI module -> used to warp each DWI using the deformation from (1) # DWI Averager -> used to average the set of warped DWI''s producing the final DWI Atlas
A suite of tools for efficient management of neuroimaging project data. Specifically, DFBIdb was designed to allow users to quickly perform routine management tasks of sorting, archiving, exploring, exporting and organising raw data. DFBIdb was implemented as a collection of Python scripts that maintain a project-based, centralised database that is based on the XCEDE 2 data model. Project data is imported from a filesystem hierarchy of raw files, which is an often-used convention of imaging devices, using a single script that catalogues meta-data into a modified XCEDE 2 data model. During the import process data are reversibly anonymised, archived and compressed. The import script was designed to support multiple file formats and features an extensible framework that can be adapted to novel file formats. Graphical user interfaces are provided for data exploration. DFBIdb includes facilities to export, convert and organise customisable subsets of project data according to user-specified criteria.
UC Davis IDeA Lab Applications for Management Of Neuroimaging Data
Software to: view dicom files and assemble them into 3D volumes. View and convert between Analyze, Nifti, and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans.
A Java tool that takes an unorganized collection of DICOM scans, sorts and categorizes them according to user-customizable rules, gathers metadata about the scans, and saves out this information to help facilitate data uploads. Batch pr
Diffusion-Oriented Tract Segmentation White Matter tract segmentation
A fast, scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging. With an atlas-based Markov Random Field representation, DOTS directly estimates the tract probabilities, bypassing tractography and associated issues. Overlapping and crossing fibers are modeled and DOTS can also handle white matter lesions. DOTS is released as a plug-in for the MIPAV software package and as a module for the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats.
This is a command line tool which allows the user to study the behavior of water diffusion (using DTI data) along the length of the white matter fiber-tracts. Various tract-oriented scalar diffusion measures obtained from DTI brain images, are treated as a continuous function of white matter fibers'' arc-length. To analyze the trend along a given fiber tract, a command line tool performs kernel regression on this data. The idea is to try out different noise models and maximum likelihood estimates within kernel windows (along the tract), such that they best represent the data and are robust to noise and Partial Volume effect. The package contains several command line based modules and an GUI based tool called DTIAtlasFiberAnalyzer to access most functions. The features available in the tool currently, its use and input / output formats and other relevant details are provided in the first draft of the documentation. (http://www.na-mic.org/Wiki/index.php/Projects:dtistatisticsfibers).
This code registers linearly and non-linearly Diffusion Weighted Magnetic Resonance Images (DW-MRIs) by extending FLIRT (linear registration of 3D scalar volumes) and FNIRT (non-linear registration of 3D scalar volumes) in the FMRIB Software Library (FSL) to work with 4D volumes. The basis for registering DW-MRIs is the concept of Angular Interpolation (Tao, X., Miller, J. V., 2006. A method forregistering diffusion weighted magnetic resonance images. In: MICCAI. Vol. 9. pp. 594?602), which is implemented and extended to non-linear registration, based on the FLIRT and FNIRT models in FSL. See http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2013.00041/abstract. The code does not overwrite FLIRT, FNIRT or any of the FSL C++ code. It is added as FLIRT4D, FNIRT4D and supporting cost functions. The makefiles will however be overwritten to compile the new code, without affecting any version of FSL.
Tool to assist site staff with curation of data dictionary, data item, and subject item files for preparation to uploading and sharing data with DbGaP resource.
Software package that provides 3D imaging resources such as multimodal imaging, volume and mesh processing or segmentation for Dental Research. DentalTools package intends to contribute to the free exchange of information and methods in the dentistry research community.
Diffusion MRI - In-vivo and Phantom Data
An open-data initiative for the distributation of common datasets for the evaluation and validation of diffusion MRI processing methods. http://www.dkfz.de/en/medphysrad/projectgroups/dwi/DTI_projects.html#inhalt3
This central project points to all open-source and open-data initiatives provided by the German Cancer Research Center in the field of diffusion MRI.
Software tools appropriate for the registration of diffusion tensor images to an average coordinate system. The tools include image registration methods and algorithms for the correct alignment of the diffusion tensor when applying the resulting transformation. The program uses the Slicer3 execution model framework to define the command line arguments, and can be fully integrated using the module discovery capabilities of Slicer3.
These are the scripts used for the analyses reported in: Craddock RC, Holtzheimer PE, 3rd, Hu XP, Mayberg HS. (2009): Disease state prediction from resting state functional connectivity. Magn Reson Med 62(6):1619-28. Specifically included are scripts for performing t-test filter, reliability filter, recursive feature elimination, and reliability recursive feature elimination feature selection methods. These make use of wrappers that perform .632 bootstrap and k-fold cross validation strategies. The scripts are written in matlab and require the Bioinformatics toolbox. If you do not have the bioinformatics toolbox, the scripts can be easily modified to run with other matlab SVM toolboxes (i.e., libsvm, svmlight, shogun, etc.).
A collection of 32-channel data from 14 subjects (7 males, 7 females) acquired using the Neuroscan software. Subjects are performing a go-nogo categorization task and a go-no recognition task on natural photographs presented very briefly (20 ms). Each subject responded to a total of 2500 trials. Data is CZ referenced and is sampled at 1000 Hz (total data size is 4Gb; more details are given later).
Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. R code is available from the corresponding author.
An efficient framework for building and analyzing graphs called epsilon radial networks (ERNs) using tractography data in a normalized space. Currently there is no agreed-upon method for constructing the brain anatomical connectivity graphs out of large number of white matter tracts. The key challenge in defining brain networks is node delineation and their method defines nodes in the graph using tract-end points clustered in a sphere of a given radius (epsilon). Using a kd-tree based search algorithm they can identify the nodes computationally efficiently and in a fully automatic way. These networks can be used not only to analyze topo-physical properties of the structural brain networks but also to perform classical region-of-interest (ROI) analyses in a very efficient way. Thus ERNs can be used as a novel image processing lens for statistical and machine learning based analyses.
A FSL package for the comprehensive management of large-scale multi-site fMRI projects, including data storage, retrieval, calibration, analysis, multi-modal integration, and quality control.
A reference for modifications, extensions, and utilities for the FMRIB Software Library (FSL).
Simple and efficient, this application performs the Weighted False Discovery Rate procedure of Benjamini and Hochberg (1997) to correct for multiple testing. The good think is that you can test virtually any number of p-values (even millions) obtained with any test-statistics for any data set. The bonus is that you can assign a-priori weights to give a better chance to those variables that you deem important. In practice, this procedure is powerful only with a relatively small number of p-values.
Used to analyze the fibers produced by ukf tractography
Fiber-tracking based on Finsler distance
Software provided as a sub-project in the Finsler-tractography module: http://www.nitrc.org/projects/finslertract
Light version of the existing tool Fiber Viewer. It includes every clustering methods of Fiber Viewer such as : Lenght, Gravity, Hausdorff, and Mean methods but also a Normalized Cut algorithm. As in the full version you can also display a plane on the fiber. This tool works faster than the full version due to simplified visualizations.
This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost. The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles (VTK required). The software can be built as either a stand-alone or a CLI plugin for 3D Slicer.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 05, 2013. It has been superseeded by the CALATK, available here http://www.calatk.org c++ libraries and applications for performing fluid registration based operations on 2D and 3D images. The registration method is based on the large displacement diffeomorphic mapping (LDDM) registration method and implements discretized fluid registration. This registration method is then applied to time series analysis, cross-sectional atlas building, and longitudinal atlas building. The individual tool components are: * LDDM: Fluid registration between two images. * TimeSeries: Time series analysis of longitudinal data for a single subject. * AtlasBuilder: Cross-sectional atlas building for a population of images. * LongitudinalAtlasBuilder: Longitudinal atlas building for a population of subjects, each with a longitudinal data set. * FRATUtils: A collection of utility functions for working with volumes and time series files
A standardized framework for communication and data exchange between medical imaging applications, with particular focus on neuroimaging technologies. FOPA is an attempt to design and implement a common protocol for network and command line communication with either file-system or imbedded data structures. Initial reference implementations will support interoperability between ITK, VTK, and Java platforms. Contributions are welcome from other neuroimaging development communities.
A community for the discussion of functional connectivity and all related topics. This includes discussion of related tools, data sets, methodological discussion, related websites and publications, etc.
An effort to provide a set of quasi-probabilistic atlases for established functional ROIs in the human neuroimaging literature. Many atlases exist for various anatomical parcellation schemes, such as the Brodmann areas, the structural atlases, tissue segmentation atlases, etc. To date, however, there is no atlas for so-called functional ROIs. Such fROIs are typically associated with an anatomical label of some kind (e.g. the _fusiform_ face area), but these labels are only approximate and can be misleading inasmuch as fROIs are not constrained by anatomical landmarks, whether cytoarchitectonic or based on sulcal and gyral landmarks. The goal of this project is to provide quasi-probabilistic atlases for fROIs that are based on published coordinates in the neuroimaging literature. This is an open-ended enterprise and the atlas can grow as needed. Members of the neuroscience and neuroimaging community interested in contributing to the project are encouraged to do so.
Functional and Structural Neuroimaging Journals Listing
Journals addressing functional and structural neuroimaging topics.
An end-to-end application allowing Group-wise Automatic Mesh-Based analysis of cortIcal Thickness as well as other surface area measurements. This cross-platform tool can be run within 3D Slicer as an external module, or directly as a command line.
GAMMA suite is an open-source cross-platform data mining software package designed to analyze neuroimaging data. A neuroimaging study often focuses on biomarker detection and classification. We designed and implemented a Bayesian, multivariate, nonparametric suite of algorithms for analyzing neuroimaging data. The GAMMA suite can be used for brain morphometric analysis, lesion-deficit analysis, and functional MR data analysis.
Tool to generate brain volume mask from input of T1 and T2-weighted images alongside a region of interest brain mask. This volume mask omits dura, skull, eyes, etc. The program is built upon ITK and uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.
This tool can be used as a command line module with 3D Slicer (version 3 and above) for the affine registration of image volumes. The registration toolbox has 2 options: 1) a Mutual Information based registration, 2) a Sum-of-Square differences registration method. The final output is in the same space as the fixed image. You do require to have CUDA v2.2 or greater installed on your system with atleast 256MB Nvidia GPU memmory card. All operating systems are supported, but take a look at the CMakeLists.txt file for how to compile for you system.
A graph theoretical network analysis toolbox which allows researchers to perform comprehensive analysis on the topology of brain connectome by integrating the most of network measures studied in current neuroscience field.
A platform for any Principal Component Analysis (PCA)-based analysis on functional neuroimaging data (PET and fMRI). Includes: * Ordinal Trend Canonical Variance Analysis for parametric designs (C. Habeck et al. A New Approach to Spatial Covariance Modeling of Functional Brain Imaging Data: Ordinal Trend Analysis. Neural Computation 2005; 17: 1602-1645) * Partial Least Squares for any design matrix * Subprofile Scaling Model for cross-sectional designs (JR. Moeller, Strother SC. A regional covariance approach to the analysis of functional patterns in positron emission tomographic data.J Cereb Blood Flow Metab. 1991 Mar;11(2):A121-35.)
Generalized Psychophysiological Interaction Toolbox
An automated toolbox for a generalized form of psychophysiological interactions for SPM and FSFAST. The automated toolbox can do the following: (a1) produce identical results to the current implementation in SPM (a2) use the current implementation of PPI in SPM but using the regional mean instead of the eigenvariate (a3) use a generalized form that allows a PPI for each task to be in the same model using either the regional mean of eigenvariate (b) create the model using the output of one of the (a) options and the first level design (c) estimate the model (/results directory) (d) compute the contrasts specified.
A set of MATLAB scripts for analysis of networks derived from neuroimaging data. Some of these scripts are entirely original, while some are adapted (or just copied) from the Brain Connectivity Toolbox (https://sites.google.com/a/brain-connectivity-toolbox.net/bct) The source code is available via git: git clone ssh://user
Software toolbox for group-information guided Independent Component Analysis (ICA). In GIG-ICA, group information captured by standard Independent Component Analysis (ICA) on the group level is used as guidance to compute individual subject specific Independent Components (ICs) using a multi-objective optimization strategy. For computing subject specific ICs, GIG-ICA is applicable to subjects that are involved or not involved in the computation of the group information. Besides the group ICs, group information captured from other imaging modalities and meta analysis could be used as the guidance in GIG-ICA too.
A method for group-wise image registration by pairwisely registering similar images identified using graph theoretic techniques. Particularly, they use sparse coding to estimate image similarity measures among images to be registered, yielding asymmetric, group-wise image similarity measures for each image to others in the group.
Huntington Disease Nueroimaging Initiative
An international effort to establish resources necessary to study the application of neuroimaging measures as (surrogate) biomarkers in Huntington''s Disease (HD). The primary aims are to develop and apply software tools, imaging protocols, quality control procedures, data archiving, data distribution, and participation guidelines that will accelerate existing and prospective imaging studies.
A Matlab script to convert the raw .csv Hitachi ETG4000 output file into a .nirs file for use with Homer2. The script also requires a .pos file. This is the output of the polhemus 3D digitiser that they use to record where the optodes are located spatially. I realize that not everyone uses a 3D digitiser so I have included three example .pos files - one for each of the possible optode arrangements of the Hitachi system (either two 3x3 arrays, one 3x5 array or one 4x4 array). If you use a different arrangement or have more probes than them, feel free to get in touch and they may be able to advise on how to create a model .pos file. There are two versions of the conversion script: 1. single - this will read in ONE .csv file and ONE .pos file and create ONE .nirs file 2. multi - this will read in a user-specified number of .csv files and ONE .pos file. It will then create one .nirs file for each .csv file that was read in and deposit it in the same directory as that .csv file.
Suite of tools for brain image analysis. Image manipulation, 2D visualization, linear alignment, BBSI, template-based bias correction, skullstrip. GUI Image analysis tools. Now modified to read/write single file nifti (.nii) format. Other packages to be added.
A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.
Program to develop generic standards and tools to facilitate the recording, sharing, and reporting of neuroimaging metadata. It is expected that these efforts will greatly improve upon current practices for archiving and sharing neuroscience data. Neuroscience data, particularly those in neuroinformatics related areas such as neuroimaging and electrophysiology, are associated with a rich set of descriptive information often called metadata. For data archive, storage, sharing and re-use, metadata are of equal importance to primary data, as they define the methods and conditions of data acquisition (such as device characteristics, study/experiment protocol and parameters, behavioral paradigms, and subject/patient information), and statistical procedures. A further challenge for datasharing is the rapidly evolving nature of investigative methods and scientific applications.
Primate brain atlas created from over 100 structural MR scans of 19 rhesus macaque animals. The atlas currently comprises high-resolution T1-weighted average MR images with and without skull stripping, tissue probability maps, and a detailed parcellation map based on the NeuroMaps atlas.
This project is used for students enrolled in courses using the JIST framework. Content in this CVS is freely available, but it is not intended for any specific purpose.
JIST Resources for Algorithm Development
This repository stores plugins, tutorial code, and examples demonstrating MRI manipulation within the MIPAV plugin environment. This project is separate from JIST so that we can provide WRITE access to any interested party without overly exposing the infrastructure to unplanned modification. Please contact the administrators if you would like to join this project - open use is encouraged.
Automatically creates a mask based on the "foreground" of an anatomical scan volume.
Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI
Joint Anisotropic LMMSE Filter for Stationary Rici
This module reduces Rician noise on nhdr/nrrd DWIs. Filters image in mean squared error sense using Rician noise model. All estimations are performed as sample estimates in a "shaped neighborhood" defined by the weights extracted from structural similarity of voxels following same idea as in Non-Local Means filter.
Project to provide long-term hosting and release for small tools related to medical image analysis. Source repository contains highly experimental code intended for collaborative development. However, any interested parties are welcome to browse/reuse code. Stable/evolved projects will be moved to independent projects.
Software using a novel local label learning strategy to estimate the target image?s segmentation label using statistical machine learning techniques. They used a support vector machine (SVM) with a K nearest neighbor (KNN) based training sample selection strategy to learn a classifier for each of the target image voxel based on a training dataset consisting of its neighboring voxels in the atlases. Validation experiments on hippocampus segmentation of 117 MR images demonstrated that the method can produce segmentation results consistently better than state-of-the-art label fusion methods.
Tool that provides a unified framework for testing and applying statistical and voting label fusion techniques. The project will include implementations of several different voting techniques including majority vote, weighted voting, and regionally weighted voting. Additionally, multiple statistical fusion methods will be included, notably, STAPLE, Spatial STAPLE, STAPLER and COLLATE. In addition to the fusion algorithms, code for running specialized simulations and various tools and utilities to test the efficacy of the algorithms will be provided.
This repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development. The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, they are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling.
An on-line tutorial on how to use MATLAB for Diffusion-Weighted MRI processing. The following subjects are covered in this tutorial: Generation of Synthetic Diffusion-Weighted MRI datasets, Diffusion Tensor (DTI) Estimation from DW-MRI, DTI Visualization as a field of ellipsoids, Higher-order Diffusion Tensor Estimation from DW-MRI, Computing of Tensor Orientation Distribution Functions (Tensor ODF), Computing of Fiber Orientations, Higher-order Diffusion Tensor Image Visualization as fields of spherical functions, Multi-fiber reconstruction etc. The tutorial contains numerous illustrations, figures and Matlab scripts embedded in the text. The reader/user can automatically generate Matlab script for a self-designed DW-MRI experiment by selecting which steps needs to be followed. The code that corresponds to the selected steps is then appropriately merged in the Matlab Script Generator, and the user can easily copy and paste the produced code directly to the Matlab command prompt.
Multi-Echo Independent Component Regression Group-Level Connectivity Dataset
Multi-Echo Independent Component Regression (ME-ICR) Group-Level Connectivity (GroupInCorr) Dataset
Data set of an AFNI GroupInCorr session for multi-echo independent component regression (ME-ICR) for a cohort of 52 subjects. This dataset provides a high-quality atlas of seed-based functional connectivity with strong statistical conditioning.
This program contains Python modules for modeling and reconstruction of diffusion weighted MRI data. It is a subset of the code internally used in the CVGMI lab at the University of Florida. Three different reconstruction methods are currently included in this program, namely, Mixture of Wisharts (MOW), Diffusion Orientation Transform (DOT) and Q-ball Imaging (QBI). This program is mainly developed and maintained by Bing Jian, as part of his Ph.D. research, supervised by Prof. Baba Vemuri. Please note that the source code of this program is hosted at Google Code, see the Source Code link on the left.
Bibliography of books related to neuroscience addressing the topic of functional and structural neuroimaging.
Tool that associates localized white matter (WM) lesions with disruptions in gray matter connectivity as a step toward understanding the lesions? functional implications. A Tractogram Reference Set (TRS), i.e. collections of white matter fibers, is constructed from 73 normal healthy individuals and coregistered to a common space (MNI). The NeMo Tool uses the TRS to assess structural network disruption due to a particular WM lesion mask on a region and network-wise level. This tool is an easy way for researchers and clinicians to investigate changes in the structural brain network without having to perform tractography on their own normal data or on diseased/injured brains where the results may not represent the underlying physiology.
An open source implementation of a non-rigid groupwise registration method. This project is implemented by Serdar K Balci (serdar at csail.mit.edu) and supervised by Polina Golland and William M. Wells All metrics are implementing in a multi-threaded fashion. The algorithm will run faster on computers with multiple CPU''s.
Script which points browser to Nathan Kline Institute (NKI) Rockland Sample.
While the traditional temporally concatenated Group ICA (TC-GICA) adopting three steps of PCA reduction, it could result in inconsistent and variable components when different subject orders were used, both for the group- and individual-level results. Such instability can further cause instable and thus unreliable statistical results. Subject Order-Independent Group ICA (SOI-GICA) aims to fix this problem by producing stable and reliable GICA results. For details please see the paper Subject Order-Independent Group ICA (SOI-GICA) for Functional MRI Data Analysis (Zhang et al., 2010, NeuroImage)(http://dx.doi.org/10.1016/j.neuroimage.2010.03.039). MICA is the toolbox inplemented SOI-GICA for convenience of usage.
Task Independent Fluctuations Discussion
The methodology and applications of task independent fluctuation measures including: connectivity maps of fMRI resting state scans, research using EEG/MEG/PET etc, methods to remove non-neural fluctuations, and applications to clinical populations.
Human DTI brain atlases have been generated at UNC-Chapel Hill for several age groups, by iterative joint deformable registration of training datasets into a single unbiased DTI average image. Atlases packages include an atlas DTI tensor image, atlas DTI property images (FA, MD, AD, RD), and single tensor tractography based fiber tracts of major tracts with related 3D planes for fiber profile information: genu, splenium, anterior and posterior limb of internal capsule, uncinate fasciculus.
About 1.2GB of anonymized imaging data of many different file formats used by the BRAINS suite of tools (BRAINSFit, GTRACT, BRAINS, BRAINSTracer... and others) as a common set of anonymized data for nightly regression testing.
A Matlab toolbox that allows computation of task-related functional connectivity between multiple pairs of regions. Task-related functional connectivity is computed using the correlational psychophysiological interaction (cPPI) methodology described in Fornito et al. (2012) PNAS, 109: 12788-12793. The toolbox assumes that first-level design matrices have been specified and estimated using SPM5 or later. It takes as input these design matrices as well as user-extracted regional time courses and returns a matrix of pair-wise, task-related functional connectivity for each participant. The method is scalable to large networks comprising hundreds of regions and is well-suited to graph theoretic analyses and functional connectomics. One modifiable script, cPPI_master.m, can be used to run the analysis for an entire sample of participants.
They demonstrate and provide R code that can classify between groups of fMRI scans based on functional network connectivity differences, requiring only 4 lines of code to be altered. In addition, they include a detailed article explaining the methods behind and motivations of this tool. This code can also be altered to perform connectivity analysis and classification using ROI based methods by reading in distance arrays previously created. They run Independent component analysis (ICA) on fMRI data to establish functional networks, measure the functional connectivity between these networks using the temporal cross-correlations between independent component to create a distance matrix and indicating the networking. Connectivity properties are used as a feature matrix for an SVM classifier. Collectively, this project provides and explains both methods and code to perform functional network connectivity and fMRI SVM classi?cation.
fMRI Constrained Principal Component Analysis
fMRI-Constrained Principal Component Analysis
Constrained Principal Component Analysis (CPCA) combines regression analysis and principal component analysis into a unified framework. This method derives images of functional neural networks from singular-value decomposition of BOLD signal time series, and allows derivation of images when the analyzed BOLD signal is constrained to the scans occurring in peristimulus time, using all other scans as baseline. CPCA provides allows (1) determination of multiple functional networks involved in a task, (2) estimation of the pattern of BOLD changes associated with each functional network over peristimulus time points, (3) quantification of the degree of interaction between these multiple functional networks, and (4) a statistical test of the degree to which experimental manipulations affect each functional network. fMRI CPCA provides all results in matlab.mat file format, as well as writing images in analyze format for all components, rotated and unrotated.
A web tool for the identification of microRNAs and their isomiRs, as well as differential expression from NGS datasets.
A data analysis environment for diffuse optical tomography (DOT) functional neuroimaging data. Developed to process data from steady-state time-series measurements, it allows for maximal flexibility in the number and positions of optodes. The central component is an application called NAVI. Features include: # An electronic ledger (records metadata for all data transformations). # Data conditioning (e.g., frequency-filtering, selection of data on the basis of signal-to-noise ratio.) # 2D or 3D image formation and display. # Interpretation: atlas-based mapping; automated anatomical labeling; GLM; data-driven methods (e.g., PCA, ICA); model-based (e.g., dynamic causal modeling) and data-driven (e.g., correlation) connectivity analysis. Another important component is the Brain Model Generator, which includes FEM meshes for all parts of the head accessible to DOT measurements. The user can input the numbers of optodes, and manually specify their locations or input tracking-system data.
Tools to make easier on using spm, pipedream, dti-tk, and other softwares to analyze t1 or dti images.
A command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library. This a an ITK based implementation of various forms of Thirion Demons based registration (including diffeomorphic demons registration originating from Tom Vercauteren at INRIA ).
An opensource software for image analysis, processing and visualization. It provides convenient visualization tools for 2D and 3D images and it is highly extensible through its own scripting language. At visualization level, AMILab includes a 2D/3D image viewer, a 3D polygon viewer based on OpenGL, a 2D Curve viewer to visualize 2D curves, histograms and color/opacity transfer functions, and a GPU-enabled raycasting script for Volume Rendering based on VTK. The software includes an automatic C++ wrapping system which permits fast development of new visualization tools and image processing algorithms. This wrapping system currently wraps about 200 classes from wxwidgets library and about 100 classes from VTK.
ADJUST: automatic algorithm for EEG artifact removal
A completely automatic algorithm for artifact identification and removal in EEG data. ADJUST is based on Independent Component Analysis (ICA), a successful but unsupervised method for isolating artifacts from EEG recordings. ADJUST identifies artifacted ICA components by combining stereotyped artifact-specific spatial and temporal features. Features are optimised to capture blinks, eye movements and generic discontinuities. Once artifacted IC are identified, they can be simply removed from the data while leaving the activity due to neural sources almost unaffected.
ALVIN - Automatic Lateral Ventricle delIneatioN
A fully automated algorithm which works within SPM8 to segment the lateral ventricles from structural MRI images. The algorithm has been validated in infants, adults and patients with Alzheimer's disease (ICC>0.95). ALVIN is insensitive to different scanner sequences (ICC>0.99, 8 different sequences 1.5T and 3T) and sensitive to changes in ventricular volume. Processing time is approx 10mins per subject.
Dataset of structural MR images of 70 subjects collected during 2008-2010 across a wide range of ages. The dataset also contains resting state fMRI for most subjects. The structural images are T1 weighted, T2 weighted-FLAIR, 25 direction DTI, and the T1 mapping DESPOT [1] sequence. Reconstructed T1 maps for each subject are also available. The aquisition protocol was designed to study structural differences between young and older adults including both shape and intensity changes. Anonymized DICOM image sessions and processed images for each subject are available. The data is licensed under the Creative Commons Attribution License. It may be used freely for commercial, academic, or other use, as long as the original source is properly cited. http://www.bsl.ece.vt.edu/index.php?page=ara-dataset
B0 and Eddy Current Correction Code for Diffusion MRI
Software tool (excecutable and source code in C and C++) to correct distortions in diffusion MR images that are generated by main magnetic field inhomogeneities and eddy current induced fields generated from the direction-dependent diffusion encoding
Software for source analysis and dipole localization in EEG and MEG research. BESA Research has been developed on the basis of 20 years experience in human brain research by Michael Scherg, University of Heidelberg, and Patrick Berg, University of Konstanz. BESA Research is a highly versatile and user-friendly Windows program with optimized tools and scripts to preprocess raw or averaged data for source analysis. All important aspects of source analysis are displayed in one window for immediate selection of a wide range of tools. BESA Research provides a variety of source analysis algorithms, a standardized realistic head model (FEM), and allows for fast and easy hypothesis testing and integration with MRI and fMRI.
Bayesian Spatial Model for Brain Activation and Connectivity
BSMac: Bayesian Spatial Model for Brain Activation and Connectivity
A statistical and graphical visualization MATLAB toolbox for the analysis of fMRI data, called the Bayesian Spatial Model for activation and connectivity (BSMac). BSMac simultaneously performs whole-brain activation analyses at the voxel and region of interest levels as well as task-related functional connectivity (FC) analyses using a flexible Bayesian modeling framework (Bowman et al., 2008). BSMac allows for inputting data in either Analyze or Nifti file formats. The user provides information pertaining to subgroup memberships, scanning sessions, and experimental tasks (stimuli), from which the design matrix is constructed. BSMac then performs parameter estimation based on MCMC methods and generates plots for activation and FC, such as interactive 2D maps of voxel and region-level task-related changes in neural activity and animated 3D graphics of the FC results.
A Matlab-based toolbox for the reading, writing, and processing of BrainVoyager (QX) files in Matlab. The toolbox is freely available.
Core facility that provides the following services: Laser confocal microscope access. Penn Dental Medicine houses a Radiance 2100 laser confocal microscope available for use by researchers throughout the School as well as others inside and outside the University.
A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh.
A web-enabled brain surface viewer that allows the user to explore in real time a 3D brain map expressed on a base surface. BrainBrowser has two modes of operation, exploring either a pre-calculated database of structural correlation maps or working with user-defined data. In this mode, the user may choose to explore the correlation structure for cortical thickness, cortical area or cortical volume, or any other pre-calculated metric. In the second mode, the user is prompted for the local filenames of the statistical map and the base surface. BrainBrowser can also be used to manipulate 3D fibre pathways derived from DTI, using the same simple file format (.obj) as for surface data. BrainBrowser on Youtube: http://www.youtube.com/watch?v=HlRTUYUf1Ew NOTE: BrainBrowser requires a WebGL-enabled browser such as Google Chrome to support its 3D graphics capability.
A JAVA application designed to create taxonomies or hierarchies in order to classify and organize information.
A free, professional viewer for SPM fMRI results. SPM (Statistical Parametric Mapping, UCL, London) is a powerful fMRI analysis software but its visualization capabilities are sometimes a limitation for the researchers. That's why Imagilys has decided to offer the neuroimaging community a free version of its commercial "BrainMagix" neuroimaging software, called "BrainMagix SPM viewer". BrainMagix SPM Viewer's Features - Professional viewer for your SPM-based fMRI activations - JAVA-programmed, cross-platform (Windows, MAC, Linux), without Matlab license, making it possible to share your results with colleagues who do not have SPM installed - Reads SPM.mat files and NIfTI images in an user-friendly way - Overlay the blobs with an atlas or any anatomical image - On the fly adjustment of threshold and cluster size - Localize your activations in an atlas - BOLD signal curves in ROIs (future feature) - Export your results as PNG images
Segmentation of the brain from three-dimensional MR images is a crucial pre-processing step in morphological and volumetric brain studies. BrainMask implements a fully automatic brain segmentation algorithm that uses advanced thresholding with morphology and 3D edge detection algorithms. BrainMask demonstrates high segmentation accuracy. For a representative 26 datasets, the segmentation error averaged 3.4% ������ 1.3% (Mikheev A et al. J Magn Reson Imag 27(6):1235-41;2008). BrainMask includes NNN - a tool based on the algorithm developed by John Sled for correcting the intensity non-uniformity in MR data (Sled JG et al. IEEE Trans Med Imag 17(1):87-97;1998). BrainMask also includes a versatile DICOM wiewer and allows to selectively load and organize DICOM images into 3D and 4D datasets.
Neuronavigation system for use in human cognitive neuroscience (TMS, EEG, NIRS) and for non-human neurosurgical applications.
Characterization of small-world networks constructed from wavelet analysis of resting fMRI. This package is currently available as an R library. Futrure development will take place within the CamBA software repository
Vanderbilt Free Radicals in Medicine Core
This core facility can assist with measurements of reactive oxygen species, nitric oxide, and assist in measurements of vascular reactivity for investigators in the Vanderbilt community. The FRIMCORE employs state of the art methods, including electron spin resonance, fluorescent techniques and HPLC (High-Performance Liquid Chromatography) for measurement of reactive oxygen species and nitric oxide in cells and tissues.
A series of structural brain images, as well as their anatomic segmentations, demographic and behavioral data and a set of related morphometric resources (static and dynamic atlases) made avaialble from the Child and Adolescent NeuroDevelopment Initiative (CANDI) at UMass Medical School. Schiz Bull 2008 data is now available on NITRC-IR. Please register for access: http://www.nitrc.org/project/request.php?group_id=377
Cerebral Blood Flow Biomedical Informatics Research Network
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. A web based central repository for individual and group analysis of Arterial Spin Labeling (ASL) data sets and ASL pulse sequences developed at CMFRI UCSD for MRI researchers. This resource currently hosts more 1300 ASL data sets from 22 projects and consists of mainly two main tools 1) The Cerebral Blood Flow Database and Analysis Pipeline (CBFDAP) is a web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner. 2) Pulse Sequence Distribution System (PSDS) for managing dissamination of ASL pulse sequences developed at the UCSD CFMRI. This resource also includes web and video tutorials for end users.
A Matlab demo for group wise point set registration using a novel CDF-based Havrda-Charvat Divergence, which is based on the paper: Ting Chen, Baba C. Vemuri, Anand Rangarajan and Stephan J. Eisenschenk, Group-wise Point-set registration using a novel CDF-based Havrda-Charvat Divergence. In IJCV : International Journal of Computer Vision, 86(1):111-124, January, 2010.
Graphical Interface for Medical Image Analysis and Simulation
A workflow-oriented environment focused on biomedical image computing and simulation. The open source framework is extensible through plug-ins and is focused on building research and clinical software prototypes. Gimias has been used to develop clinical prototypes in the fields of cardiac imaging and simulation, angiography imaging and simulation, and neurology.
Processing software for multimodal neuroimaging centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. They are now combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition, data analysis, source localization and source imaging package.
An open-source toolkit for cross-sectional and longitudinal atlas building. The CalaTK project develops innovative methods and tools for longitudinal atlases with a focus on neurodevelopment. The computational toolbox is developed with the objective to analyze the neural developmental patterns observed in human and non-human primate structural and diffusion tensor magnetic resonance (MR) images.
An interactive interface of macaque stereotaxic atlas with a connectivity database, allowing integrated data analysis and mapping between 3D structures with database vocabularies. These Java-based tools are capable of reading stacks of polygons described in svg vector format and arrange them in 3D space so that the corresponding structures can be viewed and manipulated individually. An additional excel (currently v. 1997-2003) file maintains the structure abbreviations and their mapping to the terminology of databases that provide supplementary information. Here in particular we have manually drawn the cortical, striatal, thalamic and amygdaloid structures of the 151 frontal sections from the Rhesus Monkey Brain in Stereotactic Coordinates authored by Paxinos and colleagues in 1999. After loading the excel file and a set of the svg files, the view can be rotated, zoomed and individual brain structures be selected for identification and simple geometric measures. A stereotaxic grid is a display option. The abbreviations of the brain structures are mapped to entities recorded in the CoCoMac database of primate brain connectivity. Thereby one can retrieve mapping and connectivity information for the selected structure as text or connecting arrows.
Informatics Visualization in Neuroimaging
A visualization environment that enables you, via your computer, to display and interact with hundreds of neuroimaging data sets at once ?bringing together brain image data from some of the world?s best neuroscience research teams. INVIZIAN empowers both researchers and students of neuroscience to explore and understand the human brain using a simple yet powerful user interface for neuroimaging data exploration and discovery. See a beautiful example of a cloud of individual brains tumbling around in the INVIZIAN interface in Vimeo (http://vimeo.com/67984681). Visit often to see how we are making continuing progress to make Invizian even more amazing.
Matlab based cross platform software package for computation, display, and analysis of functional connectivity in fMRI (fcMRI). Used for resting state data (rsfMRI) as well as task related designs. Covers pipeline from raw fMRI data to hypothesis testing.
A container format for multi-modal neuroimaging data. It comprises connectome objects of type: CMetadata, CNetwork, CVolume, CSurface, CTrack, CScript, CData, CTimeseries, CImagestack. The Python library cfflib provides read/write functionality.
A free, open source, cross-platform Python-based software application for visualization and analysis in connectome research. Features of the software include: Connectome File Format including metadata, networks, surfaces, volumes, track files; complex network analysis toolboxes; modular plugin architecture for extensibility; Mayavi2 for 3D Scientific Visualization and Plotting; interactive data manipulation and scripting capabilities; and Neuroimaging and Diffusion in Python libraries.
A tool for automatic segmentation of 3D biological datasets, with emphasis on 3D electron microscopy. It works best for 3D blob shaped objects like mitochondria, lysosomes, etc. The project is written in Python and uses the pythonxy platform (which includes scipy and ITK image processing tools).
Dense Individualized and Common Connectivity-based Cortical Landmarks predictor
A software toolbox to predict 358 DICCCOL landmarks (Dense Individualized and Common Connectivity-based Cortical landmarks (http://dicccol.cs.uga.edu) ) on a new brain given b0, brain surface data and DTI derived fiber data (vtk format). Each DICCCOL landmark is defined by group-wise consistent white-matter fiber connection patterns derived from diffusion tensor imaging (DTI) data. DICCCOL aims to provide large-scale cortical landmarks with finer granularity, better functional homogeneity, more accurate functional localization, and automatically-established cross-subjects correspondence.
Deformable Registration via Attribute Matching and Mutual-Saliency Weighting
DRAMMS: Deformable Registration via Attribute Matching and Mutual-Saliency Matching
A software designed for deformable 2D-to-2D and 3D-to-3D image registration. Some typical applications of DRAMMS include, ** Cross-subject registration of the same organ (can be brain, breast, cardiac, etc); ** Mono- and Multi-modality registration (MRI, CT, histology); Longitudinal registration (pediatric brain growth, cancer development, etc); ** Registration under partial missing correspondences (small lesions, tumors, histological cuts). DRAMMS is implemented as a Unix command-line tool. It is fully automatic and easy to use ? users input two images, and DRAMMS will output the registered image and deformation. No need for pre-segmentation of any structures, no need for any prior knowledge, and no need for human initialization or intervention.
Core facility that provides the following services: Stable isotope analysis service. The Alaska Stable Isotope Facility is a state-of-the-art laboratory conducting stable isotope analyses of wide range of sample types for researchers from all over Alaska, the USA and the globe. Sample types include organic samples (C, N, O and H isotopes), inorganic samples (e.g. carbonate for C and O) and water (O and H).
A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system.
Slicer3:Module:Level-Set Segmentation Framework
The modules in the framework support different tasks in the segmentation realization in 3DSlicer. A module called Level-set label map evolver was developed, which takes an initial label image and a feature image as input and performs a Geodesic Active Contours evolution on the label image according to the feature image and to a different terms in the level-set equation. The evolution takes place for a customizable number of iterations. The output is a label image that can be used to produce a model. Other modules were developed to accompany the main module as can be seen in http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Level-Set_Segmentation_Framework-Documentation
Software package for processing diffusion tensor imaging data. The following functions are included: 1. Converting imaging data in DICOME format to ANALYZE format 2. Extracting binary brain mask for quick scalp-removing 3. Correcting eddy-current induced distortion 4. Optimized tensor estimation based on noisy diffusion-weighted imaging (DWI) data 5. Scalp removal using a brain mask image 6. Corregistering imaging data and generating deformation field for mapping images from individual spaces to a template or target space 7. Spatial Normalization and Warping DTI 8. Fiber tracking 9. Clustering fiber tracts 10. Identifying brain ventricles and generating binary masks for the baseline and DW imaging data 11. Deriving diffusion anisotropy indices (DAIs) and principal directions (PD) and the corresponding color-coded PD-map.
An open-source C++ application that performs pair-wise DTI registration, using scalar FA map to drive the registration. Individual steps of the pair-wise registration pipeline are performed via external applications - some of them being 3D Slicer modules. Starting with two input DTI images, scalar FA maps are generated via dtiprocess. Registration is then performed between these FA maps, via BRAINSFit/BRAINSDemonWarp or ANTS -Advanced Normalization Tools-, which provide different registration schemes: rigid, affine, BSpline, diffeomorphic, logDemons. The final deformation is then applied to the source DTI image via ResampleDTI.
A DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include dtiestim, dtiprocess, dtiaverage, fibertrack, fiberprocess, et al..
DTIPrep performs a Study-specific Protocol based automatic pipeline for DWI/DTI quality control and preparation. This is both a GUI and command line tool. The configurable pipeline includes image/diffusion information check, padding/Cropping of data, slice-wise, interlace-wise and gradient-wise intensity and motion check, head motion and Eddy current artifact correction, and DTI computing.
A software tool for post-processing diffusional kurtosis imaging (DKI) datasets. DKE consists of a suite of command-line programs along with a graphical user interface (GUI). DKE is currently supported on 32- and 64-bit Windows platforms. Given a set of diffusion-weighted images acquired following a valid DKI protocol, DKE generates a set of kurtosis (axial, mean, radial) parametric maps. DKE also generates diffusivity (axial, mean, radial) and fractional anisotropy maps using both DKI and diffusion tensor imaging signal models. DKE features include: DICOM and NIfTI format support, interactive (GUI) as well as batch mode (command-line) processing, and rigid-body motion correction. DKE implements the methods described in the following paper: Tabesh A, Jensen JH, Ardekani BA, and Helpern JA. Estimation of tensors and tensor-derived measures in diffusional kurtosis imaging. Mag Reson Med. 2011 Mar;65(3):823-36. http://www.ncbi.nlm.nih.gov/pubmed/21337412
An open-source, open content-development project for exploring, discovering, navigating, learning, and computational utilization of diverse probability distributions.
An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A new volume rendering program developed by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility (as shown in the images). Scalability and interactivity for ImageVis3D mean that both on a notebook computer as well as on a high end graphics workstation, the user can interactively explore terabyte sized data sets. Finally, the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it, such as the rendering core. This rendering core, for instance, is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with their collaborators.
A suite of applications to fulfill all of your computerized experiment needs. Used by more than 15,000 professionals in the research community, E-Prime provides a truly easy-to-use environment for computerized experiment design, data collection, and analysis. E-Prime provides millisecond precision timing to ensure the accuracy of your data. E-Prime's flexibility to create simple to complex experiments is ideal for both novice and advanced users. The E-Prime suite of applications includes: * E-Studio ? Drag and drop graphical interface for experiment design * E-Basic ? Underlying scripting language of E-Prime * E-Run ? Once the experiment is generated with a single click, E-Run affords you the millisecond precision of stimulus presentation, synchronizations, and data collection. * E-Merge ? Merges your single session data files for group analysis * E-DataAid ? Data management utility * E-Recovery ? Recovers data files
Software designed to optimize E-Prime experiments for fMRI research. EEfMRI allows you to synchronize the start of your experiment with the first scanner trigger pulse along with several valuable features to enhance the control you have over your experiment. Implementing EEfMRI into your current experiments is achieved by simply dragging and dropping the correct EEfMRI package calls into the E-Prime experiment in the appropriate places. EEfMRI is designed to integrate with other PST hardware and software to increase usability for researchers while maintaining the millisecond accuracy of E-Prime.
A MATLAB toolbox for exploration of multi-channel EEG and other large array-based data sets using multi-scale drill-down techniques. The toolbox can be used directly in MATLAB at any stage in a user's processing pipeline, as a plug in for EEGLAB, or as a standalone precompiled application without MATLAB running. EEGVIS and its supporting packages are freely available under the GNU general public license. The toolbox also supplies a number of extensible base classes for users who wish to develop their own visualizations.
A complete software package for the study of event-related brain activity with high-resolution EEG/MEG. This package has been designed to suit the high standards of neuroscience research. The software has been developed originally at the Max Planck Institute for Cognitive Neuroscience in Leipzig, Germany, and is available for other institutions through ANT Neuro B.V., The Netherlands, enhanced with the EEProbe Databrowser. ERP investigations, both in psychophysiology research and clinical applications require a multitude of processing steps. Analysis of large data sets is made efficient through advanced scripting possibilities. All different aspects of data handling are efficiently available in the EEProbe Databrowser. Alternatively, external data can be imported from a multitude of formats. Processing in EEProbe makes use of open file formats (see LIBEEP) and is designed to integrate with ASA for advanced source analysis. EEProbe is available for Linux and Mac OS X.
A technically supported modular platform for space-time-frequency analyses of EEG/MEG/ECoG integrated (optionally) with structural MRI and functional hemodynamic measures (fMRI and NIRS). The Locator module uses Polhemus devices to acquire 3D sensor coordinates. Data Editor provides pipelines of spatial and temporal filters, and easy-to-use event pipelines for conditional binning of time, frequency, and time-frequency data across participants, with group results. Coherence, phase synchronication, and quasi-causal information assess connectivity. Source Estimator enables modeling of discrete overdetermined and distributed underdetermined sources, and spatial filtering for 3D brain regions of interest. Statistical nonparametric mapping (SnPM) may be performed for all measures. MR Viewer and Image Processor comprise tools for BEM and FEM volume conductor models, using cortical source space models. See http://www.sourcesignal.com/Features_EMSE_550.pdf for details and a supported free trial.
Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.
A Matlab-based software package developed for supporting researchers in performing studies on the prediction of epileptic seizures. It provides an intuitive and convenient graphical user interface. Fundamental concepts that are crucial for epileptic seizure prediction studies were implemented.This includes, for example, the development and statistical validation of prediction methodologies in long-term continuous recordings. Seizure prediction is usually based on electroencephalography (EEG) and electrocardiography (ECG) signals. EPILAB is able to process both EEG and ECG data stored in different formats. More than 35 time and frequency domain measures (features) can be extracted based on univariate and multivariate data analysis. These features can be post-processed and used for prediction purposes. The predictions may be conducted based on optimized thresholds or by applying classifications methods such as artificial neural networks, cellular neuronal networks, and support vector machines.
A set of open source, freely available Matlab routines for analyzing Event Related Potential (ERP) data. It is tightly integrated with the EEGLAB Toolbox. ERPLAB routines can be accessed from the Matlab command window and from Matlab scripts in addition to being accessed from the EEGLAB GUI. Consequently, ERPLAB provides the ease of learning of a GUI-based system but also provides the power and flexibility of a scripted system.The development of ERPLAB Toolbox is being coordinated by Steve Luck and Javier Lopez-Calderon at the UC-Davis Center for Mind & Brain, with financial support from NIMH.
A tool for visualizing functional and anatomic MRI data.
An easy to use matlab-based graphical user interface that calculates power for future studies based on older analyses or pilot data.
Instrument that accurately gathers participant responses and verifies signals. The Celeritas Series response units are assembled using high-impact, chemical resistant, medical grade plastic. The response units include a tactile indicator to ensure correct finger placement during experiments and comfortably attach to the participant?s wrists. The units communicate button presses through fiber optic cabling which connects to a Fiber Optic Interface Console located in the control room through an available wave guide. The interface console provides real-time feedback of participant responses via LED indicators and includes a set of switches which can be used to make responses for the participant as needed.
Free-D allows the reconstruction of 3D models from image stacks (segmentation, registration, surface reconstruction, 3D rendering). It is designed in the goal of non-linear spatial normalization and averaging of collections of individual 3D models (this module is currently in alpha version only and not included in the distributed version)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Geometry format under the Neuroimaging Informatics Technology Initiative (NIfTI). Basically, it is the surface-file format complement to the NIfTI volume-file format .nii. Programs which support the Gifti format, intended to allow exchange of each others surface files, include: Freesurfer, Caret, BrainVISA, Brain Voyager, CRkit, VisTrails and AFNI.
CDU Cancer Research and Training Core Facility
Core facility that provides the following services: Establishing primary cell line from human tissues, HLA genotyping, Immunohistochemical staining, Immortalization of primary cell lines, Testing RNA quality for mRNA array analysis. Molecular and Translational research in oncology
GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data
Granger Multivariate Autoregressive Connectivity
Open-source software toolbox implemented multivariate spectral Granger Causality Analysis for studying brain connectivity using fMRI data. Available features are: fMRI data importing, network nodes definition, time series preprocessing, multivariate autoregressive modeling, spectral Granger causality indexes estimation, statistical significance assessment using surrogate data, network analysis and visualization of connectivity results. All functions are integrated into a graphical user interface developed in Matlab environment. Dependencies: Matlab, BIOSIG, SPM, MarsBar.
The tool is a GUI for a complete processing pipeline of brain MR images. It provides functions on skull-stripping, cerebellum removal, tissue segmentation, and HAMMER registration.
HERramientas de MEdida de la Sincronizacion
A toolbox for the Matlab environment designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. This toolbox may be very helpful to all the researchers working in the emerging field of brain connectivity analysis.
HI-SPEED Software Packets contain # unconstrained and constrained nonlinear least squares diffusion tensor estimation techniques, # 2-dimensional and 3-dimensional analytical (Shepp-Logan) magnetic resonance imaging phantoms in both the Fourier and image domains, # techniques for reporting the underlying signal-to-noise ratio in magnetic resonance (MR) images, # Probabilistic Identification and EStimation of NOise (PIESNO)---a technique for identifying noise-only pixels and estimating the underlying noise standard deviation in MR images, and # a signal-transformational technique for breaking the noise floor in MR images. Many more computational tools will be shared with users and developers as they become available.
Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data.
Illinois Institute of Technology Human Brain Atlas
Atlas that contains new anatomical, DTI, HARDI templates and probabilistic gray matter labels of the adult human brain in ICBM-152 space. Artifact-free MRI data from 72 human subjects was used in the development of the atlas. All diffusion MRI data collection was conducted using Turboprop, and spatial normalization was accomplished in a population-based fashion. A description of the contents of the atlas can be found in the Downloads link. NOTE: The files of the older IIT2 DTI Brain Template are still available. However, the new DTI template of the IIT Human Brain Atlas (v.3) is of superior quality and allows more accurate registration across subjects.
Software toolkit for analysis of rodent and non-human primate fMRI data. The toolkit consists of binary executables, highly portable open-source c code, and image resources that enable 1) Automated registration based upon mutual information (affine, non-linear warps), with flexible control and visualization of each step; 2) visualization of 4-dimensional data using either mosaic or tri-planar display of the z/slice dimension, and integration of a general linear model for graphical display of time series analysis; 3) A simple and flexible 1st-order GLM for fMRI time series analysis, a 1st-order GLM analysis for PET data within the SRTM framework, plus a 2nd-order GLM analysis following the Worsley 2002 scheme, and 4) MRI templates to place your rodent and non-human primate data into standardized spaces.
A medical image display package that allows easy viewing and analysis of Magnetic Resonance, x-ray CT and other types of medical image. Jim is an up-to-the-minute design with a familiar user-interface.
Large Deformation Diffeomorphic Metric Mapping
Software application which aims to assign metric distances on the space of anatomical images in Computational Anatomy thereby allowing for the direct comparison and quantization of morphometric changes in shapes. As part of these efforts the Center for Imaging Science at Johns Hopkins University developed techniques to not only compare images, but also to visualize the changes and differences. For additional information please refer to: Faisal Beg, Michael Miller, Alain Trouve, and Laurent Younes. Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision, Volume 61, Issue 2; February 2005. M.I. Miller and A. Trouve and L. Younes, On the Metrics and Euler-Lagrange Equations of Computational Anatomy, Annual Review of biomedical Engineering, 4:375-405, 2002. Software developed with support from National Institutes of Health NCRR grant P41 RR15241.
Software library that deals with reading and writing RIFF-format CNT/AVR-files. This file format is also called EEProbe data format, and is used in the software packages EEProbe, ASA, ASA-Lab, Cognitrace, eemagine EEG, Visor, by ANT Neuro B.V., The Netherlands. The file format provides for storage of EEG/ERP/MEG data as 32-bit values, and includes a very efficient compression algorithm. Encoding/decoding from the compressed data is performed automatically through the LIBEEP interface functions.
A matlab toolbox (EEGlab compatible) allowing the processing of MEEG data using single trials and hierarchical linear models. Almost all statistical designs can be analyzed with the tool. Across subject analyses are performed using bootstrap offering robust inferences.
Software application for removing patient-identifying information from medical image files. Removing this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner.
Leipzig Image Processing and Statistical Inference Algorithms
Lipsia: Leipzig Image Processing and Statistical Inference Algorithms
Lipsia: Leipzig Image Processing and Statistical Inference Algorithms ? a tool for fMRI data analysis
Software tool for processing functional magnetic resonance imaging (fMRI) data.Software system for evaluation of functional magnetic resonance images of human brain.
A reliable patient response system designed specifically for use in an fMRI. Lumina was developed to satisfy the requirements of both the clinical and research fields.
MRI Dataset for Hippocampus Segmentation
This dataset contains T1-weighted MR images of 50 subjects, 40 of whom are patients with temporal lobe epilepsy and 10 are nonepileptic subjects. Hippocampus labels are provided for 25 subjects for training. The users may submit their segmentation outcomes for the remaining 25 testing images to get a table of segmentation metrics.
MaCH-Admix: Genotype Imputation Software
A genotype imputation software that is an extension to MaCH for faster and more flexible imputaiton, especially in admixed populations. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s). This reference selection method generates better imputation quality in shorter running time. MaCH-Admix also separates model parameter estimation from imputation. The separation allows users to perform imputation with standard reference panels + pre-calibrated parameters in a data independent fashion. Alternatively, if one works with study-specific reference panels, or isolated target population, one has the option to simultaneously estimate these model parameters while performing imputation. MaCH-Admix has included many other useful options and supports VCF input files. All existing MaCH documentation applies to MaCH-Admix.
Software that performs logistic regression, using imputed SNP dosage data and adjusting for covariates.
A variety of MEG- and fMRI-compatible hardware for research use including typical response collection devices such as joysticks, response pads, mice, as well as stimulation devices such as vibrotactile stimulators, olfactometers, and pressure/force generators. The company also offers custom design and production services for many different applications.
A complete line of non-invasive magnetic stimulation systems designed for clinical examinations and for research in the areas of neurophysiology, neurology, cognitive neuroscience, rehabilitation and psychiatry.
THIS RESOURCE IS NO LONGER AVAILABLE,documented on February 1st, 2022. Instrument supplier providing eye tracking capabilities for behavioral labs as well as for MRI, MEG, and EEG research environments.
A viewer for medical research images that provides analysis tools and a user interface to navigate image volumes. There are three versions of Mango, each geared for a different platform: * Mango ? Desktop ? Mac OS X, Windows, and Linux * webMango ? Browser ? Safari, Firefox, Chrome, and Internet Explorer * iMango ? Mobile ? Apple iPad Key Features: * Built-in support for DICOM, NIFTI, Analyze, and NEMA-DES formats * Customizable: Create plugins, custom filters, color tables, file formats, and atlases * ROI Editing: Threshold and component-based tools for painting and tracing ROIs * Surface Rendering: Interactive surface models supporting cut planes and overlays * Image Registration: Semi-automatic image coregistration and manual transform editing * Image Stacking: Threshold and transparency-based image overlay stacking * Analysis: Histogram, cross-section, time-series analysis, image and ROI statistics * Processing: Kernel and rank filtering, arithmetic/logic image and ROI calculators
Manually Labeled MRI Brain Scan Database
Collection of neuroanatomically labeled MRI brain scans, created by neuroanatomical experts. Regions of interest include the sub-cortical structures (thalamus, caudate, putamen, hippocampus, etc), along with ventricles, brain stem, cerebellum, and gray and white matter and sub-divided cortex into parcellation units that are defined by gyral and sulcal landmarks.
MarsBaR region of interest toolbox for SPM
A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery.
A complete set of tools that enables researchers to perform spatial and navigational behavior experiments within interactive, easy to create, and extendable (e.g., multiple rooms) 3D virtual environments. MazeSuite can be used to design/edit adapted 3D environments where subjects? behavioral performance can be tracked. Maze Suite consists of three main applications; an editing program to create and alter maps (MazeMaker), a visualization/rendering module (MazeWalker), and finally an analysis/mapping tool (MazeAnalyzer). Additionally, MazeSuite has the capabilities of sending signal pulses to physiological recording devices using standard computer ports. MazeSuite, with all 3 applications, is a unique and complete toolset for researchers who want to easily and rapidly deploy interactive 3D environments. Requirements Maze Suite is designed for Windows 7, Windows Vista and Windows XP. 3D rendering quality depends on available graphics card hardware; OpenGL 2.1 or above compliant is recommended. For Windows XP systems, .NET Framework Version 2.0 or above is required and can be downloaded from Microsoft's website.
Designed for use in an MRI simulator, MoTrak software uses Ascension Technology?s Flock of Birds. The sensor attaches to the subject?s head and determines the position of the head in space relative to the transmitter. The sensor records angular rotations as well as positional displacements from an initially calibrated position. This information is displayed and logged by the program in real-time, allowing observation of head motion in an MRI simulator. In the simulator, the participant can simultaneously be habituated to the MRI environment, while being trained to remain still via feedback from the MoTrak system.
Core facility that provides the following services: Ultrasound/sonography access service. Ultrasound, which is also known as sonography, is a painless, non-invasive imaging technique that lets us look inside your child''s body without the use of radiation. It uses high-frequency sound waves to create pictures of organs, bones, tissues and blood vessels.
National Center for Image-Guided Therapy Fast Imaging Library
This software provides algorithms for the reconstruction of raw MR data. In particular, it supports the reconstruction of accelerated data acquisitions where k-space is subsampled and the Fourier domain encoding is complemented by temporal encoding, spatial encoding, or and/or a constrained reconstruction. This library of functions provides a number of reconstruction algorithms that accurately employ advanced MR imaging methods including: UNFOLD; parallel imaging methods such as SENSE and GRAPPA; Homodyne processing of partial-Fourier data, and gradient field inhomogeneity correction (gradwarp); EPI Nyquist Ghost correction and ramp-sampling gridding. The target audience is research groups who may be interested in exploring or employing advanced MR reconstruction techniques, but don't have the necessary expertise in-house. Inquires may be directed to: ncigt-imaging-toolkit -at- bwh.harvard.edu
Infrastructure for data aggregation, processing, and management in multi-dimensional medical imaging research (i.e., MRI, CT, PET). NeuroWeb is designed for rapid deployment on a small/moderate scale with limited hardware.
Blog presenting some scripts that can be used to facilitate and automate processing and analysis of brain data. In addition, it could be helpful explaining non clear stages and steps of brain data processing using some software such as; Freesurfer, FSL, Brainvoyager QX... At the moment, there are more than 10 applescripts in the main website http://www.easyneuroimaging.com that control different tools and commands (aparcstats2table, asegstats2table, BET, dcm2nii, FIRST, fslsplit, fslswapdim, fslview, mri_convert, Qdec, Recon-all, SIENAX, tkmedit, tksurfer)
The Neurophysiological Biomarker Toolbox
An open source Matlab toolbox for the computation and integration of neurophysiological biomarkers. NBT offers a pipeline from data storage to statistics including artifact rejection, signal visualization, biomarker computation, and statistical testing. NBT allows for easy implementation of new biomarkers, and incorporates an online wiki that facilitates collaboration among NBT users including extensive help and tutorials. NBT is specialized in analyzing EEG data, however it allows the processing of any kind of signal. NBT can, e.g., be used to analyze ongoing oscillation between: * Eyes-closed rest of subject populations (e.g., healthy subjects and patients, males vs. females, young vs. old, etc.). * Two experimental condition (e.g., classical eyes-closed rest vs. meditation, or before vs. after consumption of a CNS-active substance (a drug, coffee, nicotine, alcohol, etc.)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software application that has been designed to facilitate rapid and flexible visualization from neuroanatomically segmented results.
Two Slicer3 modules removing rician noise in diffusion tensor MRI
UNC/Utah NAMIC DTI Fiber Analysis Framework
Project hosting binary packaged distributions, scripts, example datasets, and corresponding results of analysis using their UNC/Utah NAMIC DTI Fiber Analysis Framework. This project can be seens as a master project encompassing several current NITRC projects into a coherent set. Their workflow utilizes tools already available on NITRC including: * DTIPrep * DTIAtlasBuilder * FiberViewerLight * DTIAtlasFiberAnalyzer * FADTTS
Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells.
caGWAS (Cancer Genome-Wide Association Studies)
Too that allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes. SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously, enabling whole genome association studies. Within the Clinical Genomic Object Model (CGOM), the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a A semantically annotated domain model that captures associations between Study, Study Participant, Disease, SNP Association Analysis, SNP Population Frequency and SNP annotations. caGWAS APIs and web portal provide: * a semantically annotated domain model, database schema with sample data, seasoned middleware, APIs, and web portal for GWAS data; * platform and disease agnostic CGOM-caGWAS model and associated APIs; * the opportunity for developers to customize the look and feel of their GWAS portal; * a foundation of open source technologies; * a well-tested and performance-enhanced platform, as the same software is being used to house the CGEMS data portal; * accelerated analysis of results from various biomedical studies; and * a single application through which researchers and bioinformaticians can access and analyze clinical and experimental data from a variety of data types, as caGWAS objects are part of the CGOM, which includes microarray, genomic, immunohistochemistry, imaging, and clinical data.
An open-source MATLAB software package for imaging brain functional connectivity from electrophysiological signals. It provides interactive graphical interfaces for EEG/ECoG/MEG preprocessing, source estimation, connectivity analysis and visualization. Connectivity from EEG/ECoG/MEG can be mapped over sensor and source domains. This package is designed for use by researchers in neuroscience, psychology, cognitive science, clinical neurophysiology, neurology and other disciplines. The graphical interface-based platform requires little programming knowledge or experience with MATLAB. eConnectome is developed by the Biomedical Functional Imaging and Neuroengineering Laboratory at the University of Minnesota, directed by Dr. Bin He. The visualization module is jointly developed with Drs. Fabio Babiloni and Laura Astolfi at the University of Rome La Sapienza.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023. Software toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. A paper describing elastix contains more details: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, elastix: a toolbox for intensity based medical image registration,; IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
fMRI Artefact rejection and Sleep Scoring Toolbox
FASST - fMRI Artefact rejection and Sleep Scoring Toolbox
An EEG toolbox developed to help users with 3 specific types of data and problems: simulatenous EEG-fMRI recording, continuous EEG scoring (e.g. sleep) and handling (visualisation, cutting, power spectrum, etc.) multi-channel recording of spontaneous EEG. The toolbox is written in Matlab and is specifically compatible with the BrainAmp family of EEG recorders (from BrainProducts GmbH) Three other data formats are now also supported: the edf "European Data Format", exported raw-EGI data (from Electrical Geodesics, Inc.) and the BCI2000 format.The results are directly compatible with SPM8 and are saved with SPM8 EEG data format.
QTL analysis based on imputed dosages/posterior_probabilities.
Software toolbox containing many kinds of kits that you may be interested in during fMRI data analysis. This toolbox is a homebrew kits built during practical ASL(arterial spin labeling) based Cerebral Blood Flow (CBF) data analysis. Meanwhile, this toolbox is also compatible with BOLD data analysis. Everyone would find something useful for their own data analysis! This toolbox is run and tested on SPM8 with MATLAB 7.6.0(R2008a) under the Linux OS. Theoretically, most of the functions (except the menu1&2 which are specially designed for the Batch Editor of SPM8) of this toolbox should be compatible with SPM5 and should also work smoothly under the Windows OS. Feel free to give feedback to authors if you encounter any bugs or problems. Senhua Zhu Center for functional Neuroimaging, University of Pennsylvania 3 W.Gates Bldg, 3400, Philadelphia, PA (19104), United States Email: zshtom@gmail.com ; senhua@mail.med.upenn.edu QQ group number (QQ?): 60524357 Google group: https://groups.google.com/d/forum/fmri-grocer
fNIR Imager 1100 is a new generation portable functional near-infrared (fNIR) imaging research tool capable of monitoring brain?s hemodynamics and thereby the cognitive state of the subject in natural environments. Neuroimaging Solution for Natural Environments: * fNIR is the only stand-alone and field-deployable technology able to determine localized brain activity. * fNIR can be readily integrated with other physiological and neurobehavioral measures that assess human brain activity, including eye tracking, pupil reflex, respiration and electrodermal activity. fNIR can also complement other techniques. * Studies have shown a positive correlation between a participant's performance and fNIR responses as a function of task load. * It has also been shown that fNIR can effectively monitor attention and working memory in real-life situations.
fanDTasia Java Applet: DT-MRI Processing
A Java applet tool for DT-MRI processing. It opens Diffusion-Weighted MRI datasets from user's computer and performs very efficient tensor field estimation using parallel threaded processing on user's browser. No installation is required. It runs on any operating system that supports Java (Windows, Mac, Linux,...). The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in user's local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors, as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking (DTI-based) which is also shown using 3d graphics on the user's browser.
An interactive environment for multimodal biosignal data processing and analysis in the fields of clinical research and life sciences. It is the most comprehensive package to analyze non-invasive and invasive brain-, heart- and muscle-functions and dysfunctions. It includes many functions such as support vector machines, event-related ECG, support for P300 and SSVEP/SSSEP BCIs, zero class detection for BCIs, compressed spectral array, minimum energy, and more! g.BSanalyze consists of a base version for data import, visualization, transformation and pre-processing and has several dedicated toolboxes. The package comes with many sample biosignal data-sets, including P300, SSVEP, motor imagery, CSP BCIs, Tilt-Table, EPs, multi-unit activity, CFM, and ERD/ERS.
An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).
A non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include: * Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. * Includes stimulus presentation software ?Experiment Center? and is compatible with 3rd party products such as ?Presentation? by NeuroBS. * Utilizes mirror box customized for large field of view. * Includes powerful analysis software ?BeGaze2? for graphical and statistical analysis of eye movements. * Includes fixation, saccade and blink detection, and area-of-interest based statistics * Real-time data available via digital or analog output
A scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models such as high resolution EEG, MEG, and ECG.
A nice sign of bias field correction (nonuniformity) in medical images. This tool is fast and efficient. Technical details can be found at http://zheng.vision.googlepages.com/biasCorrection_miccai09_Zheng.pdf
A SPM and MATLAB-based software package for statistical analysis of near-infrared spectroscopy (NIRS) signals. Based on the general linear model (GLM), and Sun's tube formula / Lipschitz-Killing curvature (LKC) based expected Euler characteristics, NIRS-SPM not only provides activation maps of oxy-, deoxy-, and total-hemoglobin, but also allows for super-resolution activation localization. Additional features, including a wavelet-minimum description length detrending algorithm and cerebral metabolic rate of oxygen (CMRO2) estimation without hypercapnia, were implemented in the NIRS-SPM software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
NITRC-wide community facilities: Forums, Wiki, Tracker, and News.
From state of the art post-processing and visualization software for BOLD, Diffusion / DTI, and Perfusion / DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, they provide products and solutions that define the field of functional MR imaging. They are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. Through collaboration with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors they develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. Their products are used around the world by researchers and clinicians alike.
This package contains a software implementation for joint label fusion and corrective learning, which were applied in MICCAI 2012 Grand Challenge on Multi-Atlas Labeling and finished in the first place. Joint label fusion is for combining candidate segmentations produced by registering and warping multiple atlases for a target image. Corrective learning can be applied to further reduce systematic errors produced by joint label fusion. In general, corrective learning can be applied to correct systematic errors produced by other segmentation methods as well.
Software application for millisecond accurate experimental control for cognitive neuroscience, psychology and linguistics research. Presents text, images, sounds, movies, self-paced reading trials and rating scales. An integrated Python scripting API is available. Joystick and microphone response are available. Supports button boxes from PST, Cedrus, fORP and custom built response boxes. Paradigm can detect fMRI triggers through serial and parallel ports. Includes sample experiments that implement many of the most popular experiment designs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Pipeline Neuroimaging VirtualEnvironment
LONI Pipeline Neuroimaging Virtual Environment
A self-contained virtual machine that can be executed on a common laptop or desktop, enabling the Pipeline to run virtually anywhere. Neophytes to the Pipeline can have their own private server running in minutes, software engineers and workflow designers can use the PNVE as a sandbox, and those without access to grid computing facilities can now take full advantage of the Pipeline processing environment.
A pipeline for small RNA-seq data analysis.
A lightweight software library to manage complex multi-stage data processing. A pipeline is a collection of jobs, i.e. Matlab or Octave codes with a well identified set of options that are using files for inputs and outputs. To use PSOM, the only requirement is to generate a description of a pipeline in the form of a simple Matlab / Octave structure. PSOM then automatically offers the following services: * Run jobs in parallel using multiple CPUs or within a distributed computing environment. * Generate log files and keep track of the pipeline execution. These logs are detailed enough to fully reproduce the analysis. * Handle job failures : successful completion of jobs is checked and failed jobs can be restarted. * Handle updates of the pipeline : change options or add jobs and let PSOM figure out what to reprocess !
A multichannel capable tool for probabilistic inhomogeneity correction implemented as both a standalone command line tool and a Slicer3 module.
Program for optimal design of blocked fMRI experiments
Program for optimal design of blocked experiments
Computer program that provides a graphical user interface for fMRI researchers to easily and efficiently design their blocked experiments. The computer program POBE calculates the optimal number of subjects and the optimal scanning time for user specified experimental factors and model parameters so that the statistical efficiency is maximised for a given study budget. POBE can also be used to determine the minimum budget for a given power. Furthermore, a maximin design can be determined as efficient design for a possible range of values for the unknown model parameters.
Quadratically constrained quadratic programing
Quadratically constrained quadratic programing (QCQP) technique in medical image analysis. QCQP based tools are provided for classification, segmentation, and bias field correction.
REsting State fMRI Data analysis Toolkit
Resting-State fMRI Data Analysis Toolkit
A user-friendly convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, calculate your images, regress out covariates, extract Region of Interest (ROI) time courses, reslice images, and sort DICOM files.
To enable widespread application of the Biological parametric mapping (BPM) approach, they introduce robust regression and non-parametric regression in the neuroimaging context of application of the general linear model. Biological parametric mapping (BPM) has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities (both for regressors and regressands) along with scalar valued observations. This approach offers great promise for direct, voxelwise assessment of structural and functional relationships with multiple imaging modalities. However, as presented, the biological parametric mapping approach is not robust to outliers and may lead to invalid inferences (e.g., artifactual low p-values) due to slight mis-registration or variation in anatomy between subjects.
Penn Automated Claims and Medical Record Databases
A core facility in the Center for Pharmacoepidemiology Research and Training created to foster epidemiologic research into therapeutics, using large population-based automated claims databases (Medicaid/Medicare) and medical records databases (GPRD and THIN), and the FDA''s adverse event reporting system (FAERS) database. Goals: * Encourage investigators with diverse training to conduct studies focused on translational therapeutics and drug safety * Provide access to large databases that allow for rapid and cost-effective research on therapeutics and drug safety * Foster collaboration with CTSA sites outside of Penn who wish to use these databases for clinical research
SPM toolbox for subject-specific analyses
Spm-toolbox that performs region of interest (ROI)-level and voxel-level between-subjects analyses of functional MRI data, restricting the analyses to those areas identified using subject-specific functional localizers. Methods: The toolbox implements ROI-level and voxel-level analyses, and it implements an automatic cross-validation procedure when the localizers are not orthogonal to the effects-of-interest. ROI-level analyses allow manually defined parcels of interest, as well as automatically-defined ones (GcSS procedure, Fedorenko et al. 2010). General linear model second-level analyses are implemented, including ReML and OLS estimation of population level effects. Hypothesis testing includes standard univariate tests as well as multivariate tests for mixed within- and between-subject designs (T, F, and Wilks' lambda statistics) This toolbox requires Matlab and SPM5/SPM8.
Software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing. The goal of this project is to merge two important research directions in modern science, genetics and neuroimaging. This entails combining modern statistical genetic methods and quantitative phenotyping performed with high dimensional neuroimaging modalities. So far, however, standard imaging tools are unable to deal with large-scale genetics data, and standard genetics tools, in turn, are unable to accommodate large size and binary format of the image data. Their focus is to create imaging genetics tools for classical genetic and epigenetic epidemiological analyses such as heritability, pleiotropy, quantitative trait loci (QTL) and genome-wide association (GWAS), gene expression, and methylation analyses optimized for traits derived from structural and functional brain imaging data
VIEWPixx /3D (VPixx Technologies) is a 1920x1080 resolution, 120 Hz, calibrated research-grade LCD monitor. It is designed for stereoscopic (3D) stimulus presentation and other high-dynamic vision-science paradigms where deterministic timing and synchronized I/O are critical. It pairs fast-response industrial TN LCD glass with a custom VPixx panel/video controller and a scanning direct-RGB LED backlight engineered to reduce motion artifacts/ghosting/crosstalk, and to improve spatial uniformity, while bypassing consumer “enhancement” processing for predictable experimental output. For stereoscopic workflows, VIEWPixx /3D supports 120 Hz frame-sequential 3D (60 Hz/eye) when used with 3DPixx active shutter glasses (RF emitter + glasses kit), and it can provide a dual-link DVI console output to mirror the participant's view without adding GPU load. The system is also a synchronized display + acquisition toolbox: integrated button-box interface, 24-channel TTL triggers, stereo audio I/O, and a full analog I/O subsystem are implemented on the same board as video control to enable microsecond-precision synchronization to video refresh—useful for EEG triggers, reaction-time tasks, and other timing-sensitive paradigms.In terms of bit depth, the VIEWPixx /3D is native 8 bits per colour, with support fot 10-bit resolution per RGB channel via custom video modes.
resting-state pediatric imaging template
Group ICA (Independent Component Analysis) was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children, ages 9-15. They have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates.
Supplies a complete multi-function data and video processing USB peripheral for vision research. In addition to a dual-display video processor, the DATAPixx includes an array of peripherals which often need to be synchronized to video during an experiment, including a stereo audio stimulator, a button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and even a complete analog I/O subsystem. Because we implemented the video controller and peripheral control on the same circuit board, you can now successfully synchronize all of your subject I/O to video refresh with microsecond precision.
Arnold Arboretum of Harvard University: Weld Hill Growth Facilities
The Weld Hill Growth Facilities consist of 12 individually controlled greenhouses and several types of Conviron growth chambers for precise control of growing conditions.
A de novo splice junction discovery and alignment tool.
Guided Tensor Restore Anatomical Connectivity Tractography
A Diffusion Tensor fiber tracking software suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. This suite of programs is built using the NA-MIC toolkit and uses the Slicer3 execution model framework to define the command line arguments. These tools can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. NOTE: All new development is being managed in a github repository. Please visit, https://github.com/BRAINSia/BRAINSTools
Wisconsin White Matter Hyperintensities Segmentation Toolbox
WM Hyperintensities Segmentation Toolbox
An open source MATLAB toolbox designed for detecting and quantifying White Matter Hyperintensities(WMH) in Alzheimer?s and aging related neurological disorders.Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. WMHs arise as bright regions on T2-weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer?s disease (AD) with regard to its prognosis.
Citation-ranked antibody search engine that provides a simple way to find antibodies that work. They use the number of citations as a transparent method to rank antibodies. Nobody can pay to be ranked higher. They are always looking for more commercial and academic antibodies to make CiteAb better. There is no charge to list.
A face-to-face household survey of assessing the prevalence of mental health disorders in a probability sample of 3005 adolescents aged 12-17 years residing in the Mexico City metropolitan area during 2005. The prevalence of mental health disorders and the use of services were assessed with the computer-assisted adolescent version of the World Mental Health Composite International Diagnostic Interview.
Tablet annotation tool for reading, marking up, and sharing PDF documents, Word/PowerPoint files, and images.
Outline of a generic plan for analysis of a whole exome sequencing project.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. A national center for biospecimen science and standards to advance cancer research and treatment. It was created in response to the critical and growing need for high-quality, well-documented biospecimens for cancer research. The initiative builds on resources already developed by the NCI, including the Biospecimen Research Network and the NCI Best Practices for Biospecimen Resources, both of which were developed to address challenges around standardization of the collection and dissemination of quality biospecimens. caHUB will develop the infrastructure for collaborative biospecimen research and the production of evidence-based biospecimen standard operating procedures.
Boosting Sequence Compression Algorithms using Locally Consistent Encoding
A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.
BIDMC Berenson-Allen Center for Noninvasive Brain Stimulation
Provides education and training on the use of noninvasive brain stimulation for both clinical practice and research. Uses techniques like TMS and tDCS for diagnosing, treating, and researching neuropsychiatric conditions, aiding neurorehabilitation after brain injuries, and educating professionals, focusing on disorders like depression, schizophrenia, epilepsy, chronic pain, and stroke recovery to improve brain function and quality of life
BIDMC Biomedical Research Informatics Core Laboratory
The mission of the Biomedical Research Informatics Core (BRIC) is to utilize the expertise of BIDMC ''informaticians'' with backgrounds in medicine, biology, engineering, biostatistics, and computer science to facilitate research at our institution by (a) providing a high level of service and experience in informatics that is difficult for individual laboratories to achieve and maintain, (b) developing the infrastructure required to address common informatics needs of all researchers, and (c) identifying areas in which there can be closer collaboration among life scientists and quantitative scientists. View our portfolio for examples of BRIC projects. To arrange for a free consultation, please contact Griffin Weber. If you choose to use BRIC services, hourly fees vary depending on the types of services needed. You will be given an estimate of the number of hours before any work begins.
Core facility that provides the following services: Fluorescence activated cell sorting, Data analysis and interpretation. Cytometry and cell sorting core at the Center for Virology and Vaccine Research. The facility has a BD FACSAria II housed in a sterile biosafety cabinet in a BSL2+ facility, allowing sorting of unfixed, live cells into a variety of tubes and plates. Equipment, consultation, dedicated operator, and data analysis available to outside researchers. To schedule an appointment, please fill out and submit the Investigator Sort Form available on our website or contact us below.
BIDMC Cardiac Physiology Core Laboratory
Core facility that provides the following services: Adult cardiac myocyte isolation service, Adult rat cardiac myocyte cultures service, Animal maintenance service, Aortic banding surgery service, Echocardiography service, Hind limb ischemia surgery service, I/R surgery service, Invasive cardiac output measurement service, Laser Doppler service, MI surgery service, Special animal care maintenance service, Tail vein blood collection service, Telemetric BP monitoring service. The goal of Cardiac Physiology Core is to provide expertise in evaluation of cardiac pathology for non-cardiovascular and cardiovascular researchers who are not equipped for such analysis. The core provides non-invasive and invasive evaluation of cardiac physiology that may be difficult or time-consuming for those investigators without proper expertise, experience and equipments.
BIDMC Clinical Research Coordinator Core Laboratory
Partially funded through Harvard Catalyst, the Clinical Research Coordinator Core is available to support and collaborate with investigators and their research teams in all phases of clinical research, providing services that include assisting with the organization, implementation and completion of clinical research studies.
Core facility that provides the following services: DNA sequencing service. The BIDMC DNA Sequencing Facility is equipped with an ABI 3130xl Automated DNA Sequencer. Turn around time is 24 hours: drop off samples by 10am (at CLS-426E or SL-232) and obtain results by 11am of the following day. Some results can be posted the same day of sample submission. Sample pick up is available in Longwood Medical Area - please send requests by email. Also available through the BIDMC DNA sequencing core to the Harvard Research community is the newest model of the Arcturus Laser Capture Microdissection System!
Oregon Health and Science University; Oregon; USA
Oregon Health & Science University; Oregon; USA
As the state''s only health and research university, OHSU brings together patient care, research, education of the next generation of health care providers and scientists and community service to improve the health and well-being of all Oregonians.
Core facility that provides the following services: Cell sorting service. The Department of Pathology Flow Cytometry Facility provides flow cytometric analysis and cell sorting services to investigators in the Harvard Medical School and in the Harvard affiliated hospitals and institutions. The facility currently has a FACSCalibur for assisted as well as unassisted flow cytometric acquisition and analysis, and a FACSAria for cell sorting (performed by an expert technician).
Beth Israel Deaconess Medical Center Electron Microscopy Core Facility
Beth Israel Deaconess Medical Center BIDMC-Electron Microscopy Core
Core provides service for grossing, tissue processing, tissue embedding, thick and thin sectioning, staining grids, and taking images of samples in the electron microscope. Training is available to use the electron microscope independently. For tissue processing, we also have training or service for high pressure freezing, freeze substitution, and tissue embedding. The core also has the expertise to do Advanced 3-D Focused Ion Beam/Scanning Electron Microscopy and 3-D segmentation and analysis on cells or tissues.
Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center
Bioinformatics and Systems Biology Center
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics.
Beth Israel Deaconess Medical Center Histology Core Facility
Beth Israel Deaconess Medical Center BIDMC-Histology Core
Core does routine paraffin and frozen sectioning on tissues for research purposes. We offer consultation services, and fee-for-service tissue grossing, processing, embedding, sectioning and staining. Special stains are also done routinely. Paraffin-embedded or frozen sections can be passed-on to a partner core, the BIDMC-Confocal and Immunostaining core, for DAB or fluorescence staining and analysis. No training or independent usage of Histology core or its equipment is possible.
BIDMC Longwood Small Animal Imaging Core Facility
Core facility that provides the following services: In Vivo Magnetic Resonance Imaging (MRI), Quantitative Image Analysis: Standard Uptake Value (SUV), 3D Volume Measurements, Animal Handling Techniques: Blood Collection, Injections (IV, IP), Oral Gavage, Tumor Inoculation, Transcardiac Perfusion, etc., Whole-body and Tissue Cryosectioning, Ex Vivo Tissue Radioactivity Measurement. Our goal is to provide state-of-the-art small animal imaging services to researchers in the Longwood Medical Area of Harvard Medical School. These services include multi-modality imaging, advanced data analysis, image fusion resources, and a satellite animal facility for longitudinal studies. A detailed description of our instruments and services are provided on our website, and we welcome questions and comments.
Core facility that provides the following services: User-based microscopy service, Microscopy training service. The Imaging Core provides access to standard digital and laser scanning confocal microscopy, multiphoton microscopy, unbiased stereology, and automated confocal microscopy for large scale genome-wide screens. In addition, the Core has substantial capabilities in quantitative and three-dimensional volumetric image reconstruction.
BIDMC Mass Spectrometry (Proteomics / Metabolomics) Core
Core facility that provides the following services: Mapping of post-translational modifications by LC/MS/MS, Protein (complex) identification by LC/MS/MS, Relative quantification of peptides by LC/MS/MS, SILAC, iTRAQ, and Isotope-free ratio quantification service, Metabolomics profiling service. The Mass Spectrometry Core Facility has been serving the BIDMC community since 2004. We specialize in a targeted mass spectrometry based proteomics approach for isolated proteins and protein complexes, especially phosphorylation and other post-translational modifications involved in cellular signaling using cutting edge instrumentation. Our trained staff offers the highest quality and reliable service with meticulous attention to detail for each sample. We routinely provide services including protein identification, post-translational modification mapping, and relative peptide/protein quantification by stable isotope labeling and label free methods using highly sensitive microcapillary LC/MS/MS techniques at nanoliter flow rates. Several different types of mass spectrometry are utilized depending upon the needs of the researcher including a fast scanning and highly sensitive 2D linear ion trap and a high resolution/high mass accuracy LTQ-Oribitrap mass spectrometer acquired in 2007. In 2005, in agreement with Harvard Medical School''s Pathology Dept., the BIDMC Mass Spectrometry Core became part of the NRB Mass Spectrometry and Proteomics Core, expanding its services and became part of the Cancer Proteomics Core for the Dana Farber Harvard Cancer Center. We serve all institutions regardless of affiliation and have an interest in samples related to many diseases such as cancer and diabetes.
BIDMC Multi-Gene Transcriptional Profiling Core
Core facility that provides the following services: Multi-Gene transcriptional profiling (MGTP) service. Multi-Gene Transcriptional Profiling (MGTP) is a real-time PCR based technique, developed in our lab, for quantifying mRNA copy numbers per cell with high reproducibility and accuracy. Primary Goals of the MGTP Core: * To make MGTP services available to investigators, and assist them in advancing their research and obtaining grants; * To assist studies of molecular signaling mechanisms and pathways, discovery of biomarkers, and development of clinical assays; and * To share the resources of our primer library, which currently includes about 2400 pre-validated human, and mouse genes. The MGTP Core makes these unique and powerful capabilities available to biomedical researchers. Thousands of pre-validated primers are available for use, and others can be designed on demand.
Beth Israel Deaconess Medical Center Preclinical MRI Core Facility
Beth Israel Deaconess Medical Center BIDMC Preclinical MRI Core
Preclinical MRI Core at Beth Israel Deaconess Medical Center provides services including imaging of anatomy and function for small animals including mice, rats, and amphibians. Ex vivo samples from larger animals and patients can be imaged. Offers consultation on protocol design and pilot data for new projects. Analysis services are available as well.
BIDMC Preclinical Murine Pharmacogenetics Core
Core facility that provides the following services: Mouse breeding service, Mouse genotyping service, Tail vein injections service, Tissue service, Cancer mouse model service, Human tumor xenografts service.
Core facility that provides the following services: Real-Time PCR service, Real-time PCR training service. Performs Real-Time-PCR and provides quantitative data on levels of gene expression. The Core comprises an ABI 7700 Sequence Detector System, equipped with all an investigator needs for experimental design/run and data processing.
Core facility that provides the following services: DNA injection service, Embryonic stem cell injection service, Transgenic mouse line rescue service, Transgenic mouse embryo handling services, Mouse assisted reproductive services. The Beth Israel Deaconess Transgenic Core Facility opened in October of 1991.The Transgenic Core is a state-of-art facility that produces genetically altered animals.
Core facility that provides the following services: X-ray crystallography service, X-ray crystallography reference database access service, X-ray crystallographic data analysis and processing service, Access to x-ray crystallography using synchrotron radiation, X-ray crystallography advising and consultation service. The X-ray Crystallography Facility located at 99 Brookline Ave. (Research North) was recently established as a core to serve the needs of investigators in the BIDMC and Harvard Medical School community interested in using structural biology as a tool in their research.
Core facility that provides the following services: Data acquisition service, Data storage service. The Research Electronic Data Collection Core can help you capture research data by supporting all aspects of data acquisition, storage and retrieval. The core is designed to significantly improve the efficiency, cost structure and overall quality of research data collection. The Data Collection Core will provide expert services including: study forms design and implementation; training in all aspects of using TELEform software; database construction and exporting / preparing data for statistical applications such as SAS and SPSS; and technical assistance with scanners and computers running electronic form capture process.
Biostatistics support is available to investigators in the Brigham and Women''s and Harvard Medical research community for statistical consulting on issues such as study design and data analysis for manuscripts and grant applications. Resources are limited, so planning ahead is essential. The Biostatistics Consulting Service is part of the Biostatistics Core of the BWH Center for Clinical Investigation (CCI).
Core facility that provides the following services: Fluorescence in situ hybridization. The CytoGenomics Core provides an invaluable technical resource to the investigators of the BWH, MGH, and affiliated institutions. Services are also available to external academic and commercial laboratories; these should contact us via our website for sample submission and pricing. Cytogenetic studies can provide insight into regions of the genome that are pathogenetic in various neoplasms leading to an understanding of the molecular pathways participating in the biology of cancer. It is appropriate to consider cytogenetics as a fundamental adjunct to a variety of investigations underway, including basic and clinical research. For example, a rather simple cytogenetic analysis of mouse ES cells to determine ploidy prior to injections into blastulas leads to a greater success rate in establishing founders for knock-out and knock-in experiments. The primary chromosomal assignment of a gene by a FISH experiment may lead to correlation of a disease with that gene. Other cytogenetic studies may be important in establishing a diagnosis for correlation with clinical outcome. The advent of molecular probes for FISH analysis has facilitated cytogenetic studies in the mouse, and other model organisms and this Core aggressively implements such technologies. In addition to state-of-the-art analyses for human samples, the BWH CytoGenomics Core also performs routine mouse karyotyping and a variety of other molecular cytogenetic analyses, services not easily obtainable elsewhere.
Core facility that provides the following services: DNA sequencing, Multiplex ligation-dependent probe amplification analysis, Capillary electrophoresis. The DNA Sequencing Core mission is to provide a highly accurate, high quality DNA sequencing service to the BWH community and other users. Our turn-around-time is 36 to 72 hrs.
Core facility that provides the following services: Sorting or analysis with operator service, Calcium flux measurements service, DNA analysis service, Cell sorting service. This lab''s mission is to provide high standard cell sorting and analysis services to the research community at the Brigham and Women?s Hospital and the Longwood Medical area.
Core facility that provides the following services: PSG Procedures, PSG Data Archiving, PSG Training to Staff, PSG Data Processing and Analysis Support. The Sleep & EEG Core within the Division of Sleep Medicine (DSM) provides an integrated infrastructure and knowledge base in support of research projects that use polysomnography (PSG), quantitative EEG analysis and related methodologies. The Core consists of a team of specialists lead by the Core director and a chief PSG technologist. The Core provides support and services in different areas: # It provides basic training and certification in PSG and EEG instrumentation to technicians and investigators, particularly those conducting studies at the Center for Clinical Investigation (CCI) at Brigham and Women?s Hospital. # It acts as liaison between DSM investigators and CCI technical staff, and implements and monitors quality assurance measures. # It carries out standard vigilance state scoring of PSG recordings and different types of waking EEG and electrooculogram analyses. # It carries out spectral analysis of sleep and waking EEG. # It evaluates, acquires, and maintains PSG and EEG equipment used by investigators of the CCI. # It carries out PSG procedures such as sleep screens and multiple sleep latency tests. # It assists investigators in the analysis and interpretation of sleep and EEG data. Over the years, the Sleep & EEG Core has been a central part of many projects funded by NIH, the Air Force Office of Scientific Research (AFOSR), and the National Space Biomedical Research Institute (NSBRI) that had a main focus on the physiology of human sleep-wake regulation. Scientifically, the Core has contributed by providing investigators with important quantitative measures of homeostatic and circadian components of the human sleep-wake regulatory system.
Office of logistics and acquisition operations
BWH Specialty Assay Research Core Laboratory
Core facility that provides the following services: Immunoassay expertise for several methodologies, Specialty hormone analysis. The Specialty Assay Research Core Lab (CLIA certified laboratory) is an analytical research core designed to provide scientific and analytical services to the Partners and non-Partners research communities. The primary objective of the core is to provide sensitive, cost-effective, and reproducible clinical research assays to investigators for endocrine, diabetes, bone markers, inflammatory and sleep medicine related research in both human and animal clinical research protocols. The core hopes to collaborate with investigators in biomarkers discovery and to offer new tools to the scientific community. The core also serves as a central laboratory for multisite studies. The SARC facility offers tests for any investigators (local or national) or industry, but preference may be given to internal users. Different rates may apply.
We are equipped for proteomics research including Cell Fractionation on one floor and tabletop Ultracentrifuges (Beckman Coulter) , Fast Protein Liquid Chromatography (FPLC), Two-Dimensional Protein Electrophoresis (Protean II, Biorad), and Gel Documentation Systems (one Bio-Rad and one Fuji Medical). Protein quantification can be done using UV-Vis spectrophotometry ( DU650, Beckman Coulter) or multimode Plate Spectrophotometers in both 96-well and 384-well micro well plate formats. Protein gels can also be visualized, digitized, and documented on Multi-Mode Imager Typhoon 9410.
Core facility that provides the following services: ES cell transfection (electroporation), Thawing/expansion of targeted ES cells, Microinjection of ES cells into blastocysts, Microinjection of DNA constructs into egg pronuclei for generating transgenic mice, Microinjection of BAC DNAs, DNA injection and microdissection, Lentiviral transgenics service, Injection of induced pluripotent stem cells for testing totipotency, Tail biopsy service, Breeding services, Mouse manipulation consultation. The Brigham & Women''s Hospital Transgenic Core Facility provides services for generating transgenic and knockout mice. Established in 1992, the BWH Core Facility has been providing gene targeting and microinjection services using state-of-the-art facilities and equipment. Dr. Lina Du, formerly a plastic surgeon in Beijing and an expert in microvascular surgery, performs both blastocyst and pronuclear injections. She has over 15 years of experience in embryo manipulation and the generation transgenic mice. The Core Facility has all of the equipment necessary for generation of transgenic mice including a Nikon Diaphot microscope equipped with Nomarski Optics and Narishige micromanipulators for microinjections, Nikon surgical microscopes for egg isolation ad transfer, a sutter needle puller and a de Fonbrune microforge. The facility maintains mice necessary for egg donors, egg recipients, and vasectomized males. This is a non-profit facility and charges are based upon anticipated mouse costs, maintenance of mice and equipment, and purchase of necessary surgical supplies and chemicals. The ES cell culture service has been offered for 6 years. Our staff carries out electroporation of targeting vectors into ES cells and provides investigators with DNA to identify ES cells carrying the desired recombination events. Then they expand the appropriate ES Cells for microinjection into blastocysts by the BWH Transgenic Core.
The BWH-BRI Antibody Core Facility provides high quality, purified monoclonal antibodies to the BWH research community. Because the antibodies are made in-house and require no shipping, they are available at a cost substantially lower than that of commercial vendors. Antibodies are of standardized quality and are available in two convenient aliquots: 500ugs and 10mgs. The Core maintains an inventory of commonly used antibodies, which allows orders to be filled quickly.
Core facility that provides the following services: DNA analysis - Affymetrix GeneChip arrays service, DNA analysis - Illumina infinium whole genome genotyping service, DNA analysis - custom content genotyping service, RNA Analysis - Affymetrix gene expression service, RNA Analysis - Illumina Gene Expression service, RNA Analysis - Illumina whole-genome DASL service. The Genetic Analysis Platform collaborates with scientists at the Broad and across the world to identify and characterize patterns of genetic variation and gene expression. These patterns can yield a deeper understanding of how genetic factors influence disease risk and treatment outcomes in a wide range of human diseases, including type 2 diabetes, Crohn''s disease, schizophrenia, and cancer, among many others. Over the past several years, the platform has been a leading contributor to major projects such as the International Haplotype Map Project, The Cancer Genome Atlas, the 1,000 Genomes Project, the Genes and Environment Initiative, and served as a national genotyping center under a NIH/NCRR program. Genetic Analysis Platform (GAP) scientists are experts in a wide range of genomic technologies and technology platforms, including genotyping, gene expression and directed resequencing, and routinely apply these technologies to studies of both human and non-human samples. In addition, teams of platform researchers work to test out emerging genetic technologies, develop informatics tools and infrastructure to enhance scientific research, and coordinate large-scale projects involving collaborators both within and beyond the Broad.
In CCRTD, we provide excellent support for Cell Biology research and advanced cell visualization applications. We have complete facilities for cell growth, handling, and storage. Cell Culture Facility maintains Cell Storage Cryo Tanks with uninterruptable liquid nitrogen supply and two separate Cell Culture rooms fully equipped with eight temperature and CO2-controlled Cell Growth Incubators, two Biological Safety Cabinets, Fluorescence-Activated Cell Sorter (FACS), two late model Inverted Digitized Microscope (Zeiss), one of which is fluorescence-enabled and possesses Z-stacking and live cell imaging capabilities, automated Cell Counter (Nexcelom Bioscience), and refrigerated storage for media and cell culture reagents.
CCRTD Core Facilities house major equipment for DNA and RNA-based applications. We offer polymerase chain reaction ( PCR ) instruments including Real-Time PCR machine (I-Cycle, Bio-Rad), Liquid Scintillation Counter (Beckman Coulter), Lyophilizer and Freeze-Dryer for biological samples, Cell Porator, high-speed and ultra-high-speed Centrifuges, ultra-sensitive Balances, and other supporting equipment. DNA and RNA quantification can be carried out on Spectrophotometers, both single-cuvette (DU650, Beckman Coulter) and 96-well plate based. DNA and RNA can be visualized, digitized, and quantified using Gel Documentation system (Bio-Rad) or Multi-Mode Imager Typhoon 9410, in fluorescent, luminescent, UV, or visible wavelengths; time-resolved fluorescence option is available on BioTek Plate Imager. For X-Ray imaging, we maintain an Automated X-Ray processor and Dark Room; radioisotope imaging is also supported on Typhoon 9410.
Core facility that provides the following services: Mouse Long Bone Scans, Mouse Vertebrae Scans. The Harvard School of Dental Medicine under the direction of The Office of Research operates a core facility composed of two micro CT machines.
CCRTD houses several major instruments to support structural studies of biological molecules, cells, modern cell, and molecular visualization applications. We have an Inverted Digitized Microscope (Zeiss) of general use, plus an advanced Fluorescence-enabled Inverted Digitized Microscope with Z-stacking and Live Cell Imaging modules (Zeiss). For advanced applications including In Situ Hybridization (ISH) and Immunohistochemistry (IHC), in addition to Zeiss microscope above we offer Confocal Fluorescent Microscope (Nikon). The latter is currently undergoing a major upgrade of computer system, software, and optics including addition of lasers.
Clark Atlanta University Collaborative Center for Cancer Genomics and Bioinformatics Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core provides next generation sequencing service. Collaborative effort between the CCRTD and the Ovarian Cancer Institute at Georgia Tech University (OCIGT). CCRTD provides laboratory to prepare libraries and to operate the instrument, while OCIGT contributes bioinformatics support for processing the data and additional services to complement genomics data including hardware, software, and personnel. OCIGT contributes patients sample procurement and complementary technologies including Affymetrix microarray technology and mass spectroscopy analysis.
CCNY Fluorescence Activated Cell Sorting
LSR II A State-of-the-Art RCMI Flow Cytometry Core is located in MR613 with full time technical support, provided by the Flow Technician Mr. Jeffrey Walker. Mr. Walker is BD trained and certified in both analysis and sorting and has extensive experience in sorting both lymphocytes and larger epithelial cells, as well as with specialized applications including cell cycle analysis and calcium flux. Mr. Walker provides training for regular users wishing to perform independent analysis, and is responsible for all sorting.
The microscopy center is a shared central facility whose primary goal is to promote scientific research by providing training in basic operation of the scanning electron microscope (SEM), the transmission electron microscope (TEM) and the Confocal.RRRRR RRRRR New users of the facility are asked to submit an application then schedule an appointment with the manager to discuss the project or to begin training.
Basic research equipment for RCMI Faculty
CDU AXIS Biomedical Informatics function
The AXIS Biomedical Informatics function is dedicated to providing investigators at Charles Drew University (CDU) with state-of-the-art informatics solutions for their research projects. AXIS Biomedical Informatics comprises a multi-disciplinary team of researchers with backgrounds and interest in clinical medicine, biomedical informatics, medical geography and geographical information systems, computer science, sociotechnical theories and qualitative methods.
A 3,000 square foot Exercise Physiology Lab is located in the ERC Business Park approximately one mile from KDMC. It is fully equipped with Keiser pneumatic resistance training equipment, free weights, treadmills, stationary exercise cycles, as well as state-of-the-art, computerized equipment for measuring muscle performance, cardiopulmonary response, and body composition. These tools are available for utilization by investigators working the field of health disparities related to endocrine metabolism and exercise physiology.
A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome.
CDU Metabolic and Oxidative Stress Core Laboratory
Core facility that provides the following services: Assay analysis consulting services, Sandwich immunoassays, Competitive immunoassays, Hormone immunoassay service, Inflammation marker immunoassay service, Oxidative stress immunoassay service, Cancer marker immunoassay service, Kidney function immunoassay service, Cardiovascular immunoassay service, DNA damage/repair assay service, Metabolic profile assay service, Apoptosis/ survival pathways assay service. Since its inception fifteen years ago, the Technology Core Laboratory has surpassed its goals in new assay development and assay refinement. It has provided top-quality services, been innovative in developing new assays, and has encouraged collaborations between molecular biologists and clinical investigators. This core laboratory has an outstanding record of accomplishments and has supported many high-impact, peer-reviewed publications.
CDU Morphometry and Stereology Laboratory
Core facility that provides the following services: Morphometric study design, Tissue embedding and sectioning service, Tissue embedding, sectioning and microscopy training. The Morphometry and Stereology Laboratory is a service and training laboratory for the faculty, students, and staff of CDU and other interested researchers. The mission of the laboratory is to: 1) teach up-to-date stereology theory and practical morphometric techniques; 2) help design unbiased efficient morphometric studies; 3) train researchers to use the equipment and software available in the laboratory; 4) develop an outreach program for community students to visit a microscopy research laboratory; 5) organize stereology workshops for CDU personnel and other interested researchers.
The Vivarium is a facility dedicated to the humane care and use of laboratory animals.
Core facility that provides the following services: Advanced ultrasound imaging. The mission of the Advanced Fetal Care Center (AFCC) is to provide the finest diagnosis and care for a mother carrying a baby with a congenital anomaly. For these families, our center offers entry to a continuum of care and support that extends throughout childhood--from prenatal diagnosis and counseling, through treatment and long-term follow-up. On rare occasions, our team will recommend and perform intervention during fetal life. Our physicians, who represent all pediatric subspecialty areas, work with a wide range of babies with anomalies. Together, they have developed ground-breaking procedures in fetal medicine and surgery.
Core facility that provides the following services: Flow cytometry analysis service, Cell cycle analysis, Cell sorting service, Side population cell sorting, Zebrafish cell sorting and analysis. The Stem Cell Core Facility has been part of the IDDRC center for more than 30 years fostering collaboration and innovation among IDDRC investigators and members of the academic research community. It was used to develop chromosome sorting for human chromosome specific recombinant libraries and these techniques were utilized by others to generate large scale libraries for the early genome project. The facility was the first to develop cell sorting of fetal cells in the maternal circulation as a means to detect fetal genetic abnormalities. Throughout its history the Stem Cell Core has provided careful and accurate cell cycle analysis via DNA content analysis using Hoechst dye uptake. This service is still used today by investigators. The facility was among the first to take advantage of the ability to express GFP in cells transfected with vectors and induced to express GFP in transgenic animals conditionally expressing a specific gene promoter. This ability allowed IDDRC investigators to isolate neurons, muscle cells and other cell types which express GFP from those which do not. IDDRC investigators were among the first to subsequently culture sorted neurons. Based on the extensive experience of the core using Hoechst dye for cell cycle analysis, the core was able to help IDDRC investigators prepare side population cells (tissue derived potential multipotent progenitor cells) based on Hoechst dye efflux. These methods have allowed the isolation of different muscle side population cells and have facilitated experiments that aim to use the cells for treating muscle disease. The interactive and collaborative nature of the core has fostered these developments, and the interests of the core director, advisory committee, manager and IDDRC investigators will continue to make this core as innovative in the future as it has been in the past. The overall goal of the Stem Cell Core Facility is to provide both IDDRC and non-IDDRC researchers comprehensive analytical flow cytometry and cell sorting services in a timely, dependable and cost-effective manner., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Core facility that provides the following services: Gene targeting service, Transgenics service. The Transgenic Core centralizes the production of genetically altered mice for MRRC investigators in a cost-effective and efficient manner. The Core also provides expert assistance in the additional areas required for generating genetically altered mice, including transgene and targeting construct production, and transgenic mouse colony management. Core personnel are available to train investigators in all of the techniques required for the generation of genetically modified mice.
CHB Cellular Neuroscience Core Laboratory
Core facility that provides the following services: Rapid golgi staining service, Luxol fast blue service, Electron microscopy service, Electron microscopy embedding service, Electron microscopy sectioning service, H&E and cresyl violet staining service, Golgi Cox service, Cryostat, vibratome, and microtome usage service, Ultramicrotome usage service. The core allows investigators to perform diverse types of histological studies at several levels, including light and electron microscopy. Furthermore, since mental retardation may not be associated with structural abnormalities visible at the light microscopic level, analysis of protein expression by immunohistochemistry and gene expression by in situ hybridization are also facilitated by this Core.
Core facility that provides the following services: Imaging consultation service, Image analysis service. The CRL was formed with the mission of improving our understanding of the structure and function of the brain and other organs of the human body, in order to improve our capacity to diagnose and treat disease. Members of the CRL achieve this by developing novel technologies and computational modeling strategies for understanding and interpreting radiological images.
CHB Computed Tomography Core Imaging Facilities
Computed Tomography (CT) at Children''s Hospital Boston helps doctors quickly answer urgent questions about your child''s health. In just seconds or minutes, CT scans can produce incredibly detailed, three-dimensional images of your child''s bone, tissue and blood vessels. CT exams in our powerful multi-detector scanners are quick, painless and non-invasive. Located at two locations: Boston and Waltham. Should be contacted about scanner technology, image acquisition, etc., but not for actual access to the facility.
Within Children''s Hospital Boston''s Department of Radiology, Diagnostic Radiology offers standard radiography (conventional X-rays) and fluoroscopy, an imaging technique that uses X-rays to create real-time images of the body. We perform more than 135,000 exams each year in Boston and at our satellite locations, which makes us one of the country''s largest general diagnostic centers for children.
Core facility that provides the following services: Cell culture services, Cell line freezing, Transient transfection, FACS Analysis, n-Counter mRNA analysis. Provides technologies and resources required for studies on polarized epithelial cells that line mucosal surfaces. We provide specialized epithelial cell culture and gene manipulation services, customized materials and instrumentation, expert know-how, and training to facilitate structural and functional studies on polarized epithelial cell culture systems or mucosal intestinal tissue in situ.
Children's Hospital Boston Gnotobiotic and Microbiology Core
The Center promotes further understanding of host-microbiome interactions in health and disease, emphasizing a focus on function to define causative effects of the microbiota in vivo and to harness this knowledge in developing new therapies, diagnostics and further commercial applications.
Core facility that provides the following services: Magnetic resonance imaging (MRI) access. Magnetic Resonance Imaging (MR or MRI) at Children''s Hospital Boston performs pediatric MRIs in a friendly, child-centered environment designed to make your child''s experience as pleasant as possible. Our dedicated staff has years of experience imaging children and teens. Physicians order MRI studies to rule out or diagnose diseases. The technology produces incredibly detailed pictures of your child''s organs, bones and tissues without using ionizing radiation (X-rays). Instead, it uses strong magnets, radiofrequency waves and powerful computers to generate 2- and 3-dimensional images of a given organ or body part. We use protocols and procedures developed specifically for babies and children, which means age-appropriate care for your child and the best possible images for the radiologist.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 8,2024. Core facility that provides the following services: DNA sequencing (standard) service, Taqman gene expression service, Taqman SNP genotyping, Digital PCR service, Genomic mapping facility standard service, DNA purification from blood and saliva, RNA purification service, Master 96-well plate sample preparation, Gene expression service, SNP genotyping service, Bioanalysis of RNA and DNA, Next-generation sequencing service, Sequenom SNP genotyping, SNP and qPCR 7900HT instrument access. The Molecular Genetics Core Facility (MGCF) is a non-profit core laboratory in the Program in Genomics and Genetics Division of Children''s Hospital Boston offering genomics services for academic research institutions. The majority of MGCF users are investigators from Children''s Hospital Boston and the surrounding Harvard affiliates, but the MGCF also serves laboratories throughout the entire United States. The MGCF is comprised of a compilation of smaller cores partially supported by private and federal funds. Funding is provided in part through The Intellectual and Developmental Disabilities Research Center, The Manton Center for Orphan Disease Research, The Wellstone Center for Muscular Dystrophy, and The Neuromuscular Disease Project of the Program in Genomics at Children''s Hospital Boston. The overall objective of the MGCF is to provide a location where researchers can have access to high quality, low cost genomic technology services and expertise in a timely, affordable manner. The services offered include DNA sequencing, Next-Gen sequencing, Affymetrix and Illumina whole-genome expression and genotyping microarray technology, microsatellite genotyping, high-throughput qPCR and SNP services on the Fluidigm Biomark System, multiplex SNP genotyping on the Sequenom MassARRAY, and sample extraction and banking. The MGCF also assists investigators with project design and collaborates on linkage and association study analysis.
CHB Molecular and Cellular Biochemistry Core
Core facility that provides the following services: Lipoprotein analysis, Biliary lipid concentrations analysis, Biliary particle analysis, Quantitative real-time PCR, Sequential ultracentrifugation for lipoproteins, Radiolabeling of lipoproteins, Fluorescence labeling of lipoproteins, Purification of biliary lipid aggregatesfrom model biles, Preparation of recombinant proteins, Protein identification from gel bands, Protein Identification from complex mixtures. The Molecular and Cellular Biochemistry Core is dedicated to providing HDDC investigators and their trainees with access to a variety of methods to determine the compositions of tissues, as well as their cellular and subcellular specimens. The Core Scientists offer a broad range of analyses and preparatory services including Proteomics. Importantly, the Core also provides training in the application of state-of-the-art techniques in molecular analysis of proteins, lipids and nucleic acids. The main Core laboratory is located at Brigham and Women?s Hospital (BWH) and the satellite Core laboratory is located at Children?s Hospital Boston (CHB). We perform a broad array of biochemical and analytical assays that are not typically available within laboratories of HDDC members. These have generally been adapted so that they may be performed in large numbers on microplates. These include quantification of lipids, mRNA and protein and a full array of mass spectroscopy services for protein analysis (and soon to be expanded for lipidomics). We also offer both analytical and preparatory separations by a variety of methods.
CHB Nuclear Medicine and Molecular Imaging
Nuclear Medicine and Molecular Imaging performs non-invasive, painless imaging tests that can reveal important information about your child''s health. Nuclear medicine uses short-lived radiopharmaceuticals and specialized cameras to create images of the human body. The images show blood flow and functional and metabolic activity within organs and lesions. This technology allows early diagnosis and monitoring of disease and can often make invasive procedures unnecessary. It also complements information obtained from X-rays, computed tomography (CT), ultrasound, and magnetic resonance imaging (MRI). Some applications of nuclear medicine are used for treatment of certain specific diseases.
CHB Radiopharmaceutical Chemistry Laboratory
The radiopharmaceutical chemistry research program occupies two research laboratories in the Enders research building at Children''s: a radiopharmaceutical chemistry laboratory and a hot laboratory. A separate cell-culture laboratory is also available. The radiopharmaceutical chemistry laboratory contains four fume hoods, approximately 50 linear feet of bench space, and is set up to accommodate three postdoctoral researchers.
CHB Small Animal Imaging Core Laboratory
In recognition of the value of small animal imaging to the research community, Children''s Hospital Boston has committed to developing a state-of-the-art Small Animal Imaging Laboratory. The SAIL facility is located within the Department of Radiology''s Kresge Laboratory.
CHOP Biostatistics and Data Management Core
Core facility that provides the following services: Data management/information technology subcore services, Statistical analysis and database consulting service, Limited statistical analysis service. The Biostatistics and Data Management Core (BDMC) at The Children''s Hospital of Philadelphia (CHOP) supports investigators from virtually all subspecialties of pediatric medicine and supports studies ranging from small, narrowly defined basic science projects to large, multi-site clinical trials. The Biostatistics and Data Management Core currently supports more than 50 funded studies and collaborates with investigators on numerous grant applications each year. The BDMC is staffed by a Scientific Director, Deputy Director, and data management/information technology managers, as well as approximately 20 additional staff members representing the disciplines of biostatistics, data management, information technology and administration. The BDMC is located on the CHOP campus (3535 Market Street), and is operated and supported by Westat, a large health research organization with extensive biostatistics, data management and information technology capabilities.
Core facility that provides the following services: Development of assessment methods for pediatric psychological, neuropsychological, and psychiatric research, Intervention development and implementation. The Behavioral Neurosciences Core provides consultation and assistance to investigators regarding psychological, neuropsychological, and psychiatric components of research studies involving pediatric subjects. Together, the services provided by the Behavioral Neurosciences Core offer research infrastructure support across the entire process of research, from pre-design consultation to development and analysis of behavioral data, and across multiple domains of functioning and outcomes.
Core facility that provides the following services: Vascular laboratory services, Vascular laboratory service, Carotid intima medial thickness measurment (IMT), Vascular laboratory service, Brachial Artery Reactivity (BART), Echocardiographic laboratory services, Exercise physiology laboratory services, Vascular laboratory service, Continuous arterial spin-labeling perfusion magnetic resonance imaging. The Cardiovascular Core provides cardiac testing services for children. The Core provides the technical services and expertise to conduct the highest quality research, provides research tests in a cost-effective manner, and provides unparalleled training opportunities in clinical research for investigators, fellows, students and technicians.
CHOP CTRC Nutrition Core Nutrition Assessment
The Nutrition Assessment Unit of the Nutrition Core is a state-of-the-art facility for the assessment of growth and body dimensions, body composition (the amount of muscle, fat and bone in the body), energy expenditure, bone density, and muscle strength. The Unit has two locations and four experienced technicians for performing research assessments.
The Clinical and Translational Research Center (CTRC) offers ophthalmological testing services for children. The Ophthalmology Core at CHOP?s CTRC was established t**provide clinical and translational research services in ophthalmology for the assessment of visual function and structure. Services provided include: * Eye exams (includes visual, recognition and grating acuity; anterior segment, fundus exam, refraction) **Contrast sensitivity **Color vision testing * Optical coherence tomography (OCT) tests of the: **Anterior segment **Posterior segment ? optic nerve **Posterior segment ? retin A* Visual field measures: **Using Humphrey **Using Goldman * Full field sensitivity testing * Electroretinography * Visual evoked potential * Fundus photography * Ocular ultrasound * Professional interpretation of all tests is als**available
Core facility that provides the following services: Clinical trials consultation service, Document storage service, Investigational new drug or investigational device exemption application support service, Institutional Review Board submission service, Additional regulatory submissions support service, Protocol development service, Human subject recruitment support service, Study feasibility service, Study placement service. The Clinical Trials Office (CTO) at The Children''s Hospital of Philadelphia is a centralized office that provides resources and assistance to clinical research investigators, enabling them to carry out clinical research in a manner consistent with the Hospital''s goals ? excellent patient care, top-quality education, and innovative research. The CTO has expertise in implementing, conducting, and monitoring clinical trials and provides a variety of services that benefit both novice and experienced clinical researchers. The CTO is designed to ensure the excellence and compliance of an investigator''s clinical research trial. The Children''s Hospital of Philadelphia established the CTO in 1999 as part of the institution''s emphasis on clinical research. Since then, the CTO has experienced rapid growth. The CTO advances the quality and quantity of clinical research at Children''s Hospital and its associated network. Specifically, the CTO supports research at the Hospital by developing and completing submissions to the Hospital''s Institutional Review Board; assisting in the preparation of Investigational New Drug and Investigational Device exemption application submissions to the Federal Drug Administration; conducting clinical research studies under the guidance of principal investigators; and developing budgets and providing research training for investigators, study coordinators, and administrative staff. The CTO staff works in partnership with investigators to ensure the protection of human subjects in accordance with Good Clinical Practice, federal, state and/or local regulations and the requirements of the study sponsor.
Children's Hospital of Philadelphia Flow Cytometry Core Facility
Core provides access to instrumentation and technical expertise. Offers services, including sample preparation, advanced multi-color analysis, and high-speed cell sorting. Our experienced staff delivers personalized training and project-specific consultations.
CHOP Human Embryonic stem cell/induced pluripotent stem cell Core
Core facility that provides the following services: Stem cell differentiation, Stem cell line propagation. The human embryonic stem cell/induced pluripotent Stem Cell (hESC/iPSC) Core generates control and patient-specific iPSC lines by cellular reprogramming using current technologies. The core has a training course in cell maintenance and growth, specialized differentiation protocols for disease modeling and drug screening, and quality-control reagents for the Children?s Hospital and University of Pennsylvania academic communities. The facility maintains five NIH-approved human ESC lines and has generated more than 60 disease-specific iPSC lines.
Core facility that provides the following services: DNA sequencing service, Oligonucleotide synthesis portal to IDT service, Oligonucleotide purification service, DNA fragment analysis service. The Nucleic Acid/Protein Research Core Facility, located on the 9th floor of the Abramson Building, provides a centralized source for specialized services, technical expertise and reagents to support investigators'' molecular biology research needs. These services include DNA sequencing analysis, fluorescent fragment analysis (microsatellite genotyping), oligonucleotide synthesis, microarray services, denaturing high-performance liquid chromatography, Affymetrix GeneChip expression analysis, SNP analysis and RNA analysis.
Core facility that provides the following services: Tissue microarray construction service, Unstained slides preparation service, H&E staining (on unstained slide) service, Special stain (from slide) service, TUNEL labeling service, IHC stain from slide service, In situ hybridization RNAscope service, New antibody workup service, Decalcification service, Laser capture service, Histopathology-related techniques training, Histopathology technical consultation service, Basic imaging workstation access, Laser capture microdissection microscope access. The Pathology Core Laboratory at the Children''s Hospital of Philadelphia Research Institute provides basic histopathology, research immunohistochemistry, tissue microarray, and laser capture microdissection services to researchers at Children''s Hospital and within the surrounding academic community. We are located on the 7th Floor of the Leonard and Madlyn Abramson Pediatric Research Center in room 706. The Pathology Core Laboratory unites three core components in a single core facility: histopathology, tissue microarray and laser capture microdissection. The core offers a full range of histopathology services including tissue processing, embedding, and cutting, for both paraffin and frozen tissue. We also perform most standard stains as well as immunohistochemistry, antibody workup, fluorescence, in situ hybridization and TUNEL. Tissue microarrays can be constructed using a Beacher Arrayer. Sophisticated imaging instrumentation is available for virtual microscopy (ScanScope from Aperio) and image analysis (Image ProPlus, Volocity). Specialized software is available to image and analyze tissue microarrays, and to manage and store array data.
Core facility that provides the following services: Scientific computing for data analysis and scientific graphics, Advice and consultation regarding grant applications and management of clinical trials data, Training in study design, data collection, computerization, and statistical methods. The Biostatistics Core facility is a shared resource supporting consultation on biostatistics and epidemiology throughout the Dana-Farber/Harvard Cancer Center (DF/HCC). The mission of the core is to ensure that experimental designs, study monitoring and data analyses take advantage of robust, efficient methods that reflect ''best practices'' in biostatistics and epidemiology; to support NIH-funded peer reviewed grants that do not contain salary support for statisticians; and to enable pilot and small scale studies to become part of successful applications for peer-reviewed funding. These services are available to Dana-Farber / Harvard Cancer Center members only. The Biostatistics Core is located across several of the member institutions of the DF/HCC. To contact the Core, please email or call the statistician associated with your disease site.
Public research university in Corvallis, Oregon. The university currently offers more than 200 undergraduate-degree programs along with a variety of graduate and doctoral degrees.
Core facility that provides the following services: Metabolite identification service, PK data analysis and interpretation service. The Cancer Pharmacology Core provides DF/HCC investigators with the necessary expertise and resources to design and undertake pharmacokinetic studies in the context of phase I and phase II clinical trials, and preclinical investigations. The core has the ability to implement and validate previously developed analytical methods to quantify drugs and their metabolites in biological fluids as well as the capability to modify or develop entirely new assays when warranted. The core also offers comprehensive analysis of pharmacokinetic data as an additional service, including the estimation of pharmacokinetic parameters and identifying their relationship to pathophysiological variables and pharmacodynamic effects.
Dana Farber and Harvard Cancer Center Cancer Proteomics Center
Core provides all of the tools of modern functional proteomics. Equipped with technologies for proteomics; protein profiling, protein identification, protein and peptide fractionation, and quantization. Personalized experimental design consultation, comprehensive individualized bioinformatics support. The mission of the DF/HCC Cancer Proteomics Core is to develop a comprehensive and interdisciplinary proteomics core for High Sensitivity, High Resolution and High Throughput Proteomics with particular emphasis on in depth proteomic consultation, referral to the optimal proteomics facility and a strong focus on clinical sample analysis. The core combines consultation, service and education into a comprehensive, translationally and clinically oriented proteomics core.
Core facility that provides the following services: Hematopoietic progenitor cell (HPC) components processing, Tumor cell vaccine generation, Dendritic cell vaccine generation, Validation consultation. The (Connell and O''Reilly Families) Cell Manipulation Core Facility (CMCF), at Dana-Farber Cancer Institute (DFCI) was created in 1996 to be the manufacturing facility that produces safe and effective novel cellular component therapy that meets regulatory guidelines for clinical use and also facilitates research to be translated from the bench to the bedside. The goal of this facility is to assist DF/HCC investigators in developing new cell-based therapies for cancer and to support clinical research studies designed to evaluate the toxicity and efficacy of these novel treatments. In November 2004, CMCF moved to a newly constructed 6,700 square feet facility on the third floor and ground floor of the Jimmy Fund Building (JFB) at DFCI. The new facility is dedicated to the production of clinical grade cellular products for patients who participate in clinical trials conducted by DF/HCC investigators. All procedures are performed in environmentally controlled conditions according to current Good Manufacturing Practices (cGMP) for cell and tissue processing. The third floor accommodates all of the production areas while space on the ground floor is devoted to the long-term storage of cellular products, tissues and samples in liquid nitrogen and mechanical freezers. The CMCF is available to both clinical and laboratory investigators at all DF/HCC institutions and will provide services to patients at all DF/HCC affiliated hospitals. The staff of the CMCF are committed to working with DF/HCC investigators at all levels of clinical trial development and execution, including pre-clinical development, trial design, DF/HCC and FDA review, data management, quality control, internal and external audits as well as reports and publications. The Cell Manipulation Core Facility (CMCF) has been accredited by the Foundation for the Accreditation of Cellular Therapy (FACT). The CMCF services as a Regulatory Core for Center for Human Cell Therapy and is also a member of the Joint Program in Transfusion Medicine.
The Community Practice Research Core (CPRC) provides DF/HCC investigators access to a racially diverse population of over 11,000,000 patients within the community-based clinical practices of Harvard Vanguard Medical Associates (HVMA)/ Atrius Health, a Boston-based medical specialty group comprised of over 20 office locations across eastern Massachusetts providing care to more than 510,000 adult and pediatric patients; Harvard Pilgrim Health Care (HPHC), one of the largest health maintenance organizations in New England with close to 1,000,000 members and an extensive provider network that includes physicians who practice in a variety of settings; the Cancer Research Network is comprised of 9 health care systems and 6 affiliate sites across the nation with a total membership of 11,000,000 patients. The populations of HVMA/Atrius, HPHC, and the CRN are particularly ideal for studies: (1) involving basic, clinical, and population sciences; (2) addressing diverse communities; (3) investigating dissemination of proven technologies and interventions; (4) requiring large samples of patients and/or providers; (5) involving rare cancers; and (6) of cancer prevention.
DF/HCC High-Throughput Polymorphism Detection Core
Core facility that provides the following services: Whole genome amplification service, Genotyping service using Illumina GoldenGate and Infinium technologies, SNP Analysis using OpenArray Genotyping, SNP Analysis using Taqman, Custom Illumina GoldenGate genotyping, Illumina Infinium genotyping. The mission of the High-Throughput Polymorphism Detection Core is to provide services to investigators conducting molecular analyses of somatic DNA collected as part of a wide range of investigations. This Core provides high-throughput assays of specific gene mutations and polymorphisms (SNPs) in the many situations where previously defined specific nucleotide alterations are of interest.
A web based life sciences identifier (LSID) resolution service allows you to view the data and metadata of an LSID with a web browser. This service will display the metadata, formatted as a standard webpage, for any LSID.
Dartmouth Department of Physics: Apparatus Shop Core Laboratory
Core facility that provides the following services: Custom design and development of equipment, tools and instruments for scientific research.
Paul Sabatier University - Toulouse III; Toulouse; France
University of Toulouse III - Paul Sabatier
University of Toulouse III - Paul Sabatier; Toulouse; France
University of Toulouse III; Toulouse; France
Core facility that provides the following services: Protein development/cloning, Western blot service, ELISA service, Flow cytometry service. The mission of the DF/HCC Monoclonal Antibody Core (MAC) is to produce novel monoclonal antibodies that are directed against antigens of interest to Dana-Farber, the Harvard Cancer Center, and affiliated investigators. These monoclonal antibodies may be useful for basic research, drug discovery and clinical applications including diagnosis, surrogate markers for disease status, response to therapy or drug toxicity. Given the diverse research needs of investigators at DFCI and the Harvard Community, the MAC should strive to support a wide range of antibody requests. A key component of the DF/HCC MAC is the ability to explore and develop new technologies that facilitate generation of monoclonal antibodies. The DF/HCC MAC should be capable of supporting all basic functions of generating, screening, storing and producing monoclonal antibodies.
PSL is a consultative Core with components in each of the five DF/HCC hospitals. We have established a web-based network of autonomous, distributed, searchable databases, which contain de-identified, coded, pathologic information on post-diagnostic, excess human materials (including frozen or paraffin-embedded tissues and bodily fluids). Standardized specimen core dataset includes age, gender, anatomic location, tissue type, and diagnoses. Access to the PSL is through the password-protected Harvard eCommons. Two types of generic PSL uses are envisioned: (1) Center members with eCommons accounts can quickly retrieve aggregated tissue availability information to determine the feasibility of a proposed study. (2) Approved investigators can discover and review materials from suitable, de-identified and coded cases online and then request the samples they want.
DF/HCC Rodent Histopathology Core Facility
Core facility that provides the following services: Histopathology analysis service, Histopathologic diagnosis training service, Cryosectioning service, Rodent necropsy service, Paraffin sectioning service, Bacteria, fungi, and inclusion bodies histological staining service, Rodent tissue processing, Carbohydrate and mucoproteins histological staining service, Connective tissue and muscle histological staining service, Cytoplasmic granules histological staining service, Fats and lipids histological staining service, Hematologic and nuclear elements histological staining service, Nerve cells and fibers histological staining service, Equipment training service, Equipment access service. The Rodent Histopathology Core was founded in 1999 as one of the pathology cores within the Dana-Farber/Harvard Cancer Center. The Core was established to provide high quality professional, technical, and educational pathology services. The ultimate goal of the facility has been to support investigator research that leads to the identification of pathologic processes in mice and can be directly translatable to human disease. The core provides an essential and unique service to the many Center members and labs invested in mouse research. While many commercial and academic histology services are available, no other service is available that offers comparable high quality service with rapid turn around time and highly experienced professional supervision. The educational mission of the Core also adds an important dimension.
DF/HCC Tissue Microarray and Imaging Core Facility
Core facility that provides the following services: Construction of standard and custom TMA service, Nucleic acid isolation from paraffin embedded tissue service, Immunofluorescent staining service, Access to the Automated Quantitative Analysis (AQUA) system, Tissue microarray consultation service. The mission of the Tissue Microarray and Imaging Core is to generate tissue microarrays by allowing placement of up to 480 0.6 mm diameter tissue samples into a single standard tissue block, allowing hundreds of tumors and samples to be evaluated on a single slide. The DF/HCC Tissue Microarray & Imaging (TMI) Core is dedicated to the construction and evaluation of high quality TMAs for cancer research. In addition, the Core performs high-throughput isolation of DNA and RNA from formalin-fixed paraffin-embedded tissues. The Core also provides web-based digital pathology services using the Aperio system. These services include slide scanning, image viewing and storage, and quantitative image analysis, which facilitate tissue-based research. Finally, the Core provides access to the Automated Quantitative Analysis (AQUA) system.
DF/HCC Tumor Imaging Metrics Core Facility
Core facility that provides the following services: Reporting and database management service of radiological data for clinical trials, Radiologic exam quality control service. The mission of the Tumor Imaging Metrics Core (TIMC) is to provide standardized, consistent, longitudinal radiological measurements to evaluate therapeutic response for DF/HCC clinical trials. The TIMC - * Makes reliable, quantitative, longitudinal measurements (such as RECIST, WHO, SWOG, standardized uptake value (SUV) etc.) of lesions from serial MRI, CT, PET, and PET/CT scan images * Presents results of analyses on a password-protected secure web-based report * Provides an independent service, with verifiable measurement of treatment response for patients enrolled in cancer center trials * Serves as a centralized, computerized resource to facilitate efficient internal or external auditing Reliable tracking of changes in lesion size or metabolism is essential for clinical trials that use radiological measurements as surrogate endpoints. The Tumor Imaging Metrics Core provides a service for managing these images, making measurements in a routine, reliable, and centralized way, and making results available to investigators efficiently.
Core facility that provides the following services: Mouse breeding management, Mouse irradiation service, Technical services for laboratory animal experimentation, Veterinary care, Animal care training. The facility provides services and resources for investigators looking to accomplish animal research objectives. This includes housing mice and rats, purchasing animals, training researchers regarding proper animal care and use, and monitoring the safety of all personnel with laboratory animal contact in conjunction with Dana-Farber?s Environmental Health and Safety and Occupational Health Services. Dana-Farber has established an Institutional Care and Use Committee (IACUC) to oversee the Institute?s animal program, facilities, and projects involving the use of animals. The IACUC serves as the approval body for all protocols involving animal research, and assists faculty, students and staff in upholding Dana-Farber?s commitment to providing the finest care and most humane utilization of laboratory animals. In addition to basic husbandry services, the ARF staff provides technical and veterinary services, mouse breeding management and mouse irradiation.
DFCI Biohazard Containment Core Facility
The Biocontainment Core Facility supports researchers whose experiments require a Biosafety Level 2 enhanced (BL2+) containment level. The Biocontainment Core adheres to Biosafety Level 3 (BL3) practices. Protective apparel, equipment, and other materials are provided by the core. Two core facilities are available: one is located at the Jimmy Fund building at Dana Farber; the second at The Center for Life Science. Authorized core users may have access to both facilities. Use of the facility is limited to researchers who receive training in BL3 procedures and comply with authorized user requirements. Training is provided by the Biosafety Officer, Core Manager, and authorized users.
DFCI Biospecimen Repository Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core facility that provides the following services: Storage services for -80 degrees C and -190 degrees C in secure facility. The Biospecimen Repository provides long-term storage of clinical and research material in -80 degrees C and liquid nitrogen freezers located at Dana Farber''s Harbor Campus. Transportation of samples to and from Harbor Campus is provided by the facility for a small fee. Competitive prices are available on per box or per freezer basis in both segregated or non-segregated environments.
Core facility that provides the following services: Mass spectrometry service. The Blais Proteomics Center develops and applies state-of-the-art proteomics, informatics, and related technologies for direct interrogation of protein expression, modification, and function in response to biological perturbation in cell-based models of human cancer and primary tissues. The Blais Proteomics Center serves as a valuable resource to support individual research labs at the Dana-Farber and throughout the surrounding research community. As a key component of Dana-Farber?s Strategic Plan for Research, Blais Proteomics actively participates with other Dana-Farber Strategic Research Centers in large-scale studies, designed to leverage disparate capabilities in pursuit of novel, in-depth, and otherwise unattainable insights into human biology and disease. Consistent with our role as a world-class, center of excellence in proteomics science, members of the Blais Proteomics center contribute to the teaching mission at Harvard Medical School and participate in outreach activities designed to introduce and train young scientists and others who may not otherwise have access to these advanced technologies.
Core facility that provides the following services: Separation of plasma and serum from blood samples, Mononuclear cell counting and isolation, DNA isolation, 24 hour urine volume and aliquoting, Research specimen processing, Bone marrow aspiration and blood fixation, Research specimen storage. The Clinical Research Laboratory (CRL) utilizes protocol-driven standard operating procedures for the processing of pharmacokinetics, pharmacodynamic, and biomarker samples. This includes the processing, storage, and tracking of all research specimens to ensure the successful completion of clinical trials associated with patient treatment. The CRL is dedicated to the highest standards of specimen handling to maintain the integrity of data procurement and analysis for clinical trials.
Core facility that provides the following services: Data collection, data entry and analysis, Database design, data management and process tracking, Qualitative data collection, management and analysis. The Survey and Data Management Core (SDMC) provides efficient, high-quality survey data collection and management services and consultation to support the research needs of investigators and staff throughout the Harvard Medical research community. The Core, housed within the Center for Population Sciences at the Dana-Farber Cancer Institute, is dedicated to rigorous quantitative and qualitative survey data collection and management.
Core facility that provides the following services: Cell Sorting. The Flow Cytometry Core Facility provides sterile sorting and analysis of samples in support of research at DFCI. The core has 2 high-speed cell sorters, the BD FACSAria II SORP and BD FACSAria IIu with up to 12-color simultaneous detection utilizing multi-laser platforms. Sample populations can be sterile sorted into a variety of tubes or plates. The BD FACSAria II SORP and BD FACSAria IIu are both equipped with the Automated Cell Deposition Unit (ACDU) for sterile sinlge cell sorting into 96, 384 micro titer plates. The core presently has 2 analyzers, the BD LSRFortessa SORP and BD LSRII with up to 12-color simultaneous detection utilizing multi-laser platforms. The BD LSR II is also equipped with an HTS(high throughput sampler) for analyzing samples directly from 96 well micro titer plates as well as being able to run 5ml tubes. The Facility staff is available to assist researchers with their sorting and analysis needs. Researchers who would like to utilize the analyzers are trained so that they can analyze their experiments independently. The staff will assist with data acquisition and analysis as well as interpretation. They will also assist in experiment design and implementation as well as troubleshooting. Training sessions are available for researchers who would like to run their sorting experiments independently.
Core facility that provides the following services: Graphics services, All Research Related Photography. Medical Arts Core DFCI offers complete services for Publications, Presentations and Advertising as follows: Custom/Computer Graphics illustrations, Design and Consulting full productions services, Photoshop training. Posters Productions/Brochure Printing on best selection of paper, canvas material and Backlit poster films. Lamination, LCD announcements creation and posting. Research Related Photography Equipment: * iMAC and PC computers * Posters printer * LCD electronic announcements TV units * Backlit Display units * Laminator * Scanner * Digital camera
Core facility that provides the following services: Gene expression profiling service, Single nucleotide polymorphism analysis service, Tiling arrays service. The Microarray Core provides services for genome-wide analysis of gene expression, nucleotide variation, copy number variation, and chromatin protein binding sites. The core platforms include microarrays and next generation sequencing. Consultation on experimental design, and assistance with data analysis are also available. The Microarray Core carries out gene expression profiling on 3'' arrays and on Exon arrays; genotyping and comparative genomic hybridization both on single nucleotide polymorphism (SNP) arrays, and Chromatin ImmunoPrecipitation localization (ChIP-on-Chip). All services use oligonucleotide microarrays. Biostatistical support to assist in analyzing the data is available. The services of the Core are accessible to DFCI investigators and to investigators outside of DFCI.
Dana-Farber Cancer Institute Molecular Biology Core Facility
Dana-Farber Cancer Institute Molecular Biology Core Facilities
Core offers services for genomic next-generation sequencing library preparation, sequencing and analysis applications including RNAseq, ChIPseq, ATACseq, CRISPR screening, whole genome methylation profiling, targeted resequencing, single-cell RNAseq, exome sequencing, and more. Performs bioinformatics analysis such as integration of multi-omics datasets or specialized analyses. Genomics core technology platforms include Illumina NovaSeq6000, NextSeq500s, MiSeqs, MiniSeq. High throughput sample preparation is performed on Beckman Coulter Biomek FX and i7 systems. Low throughput samples are prepared by technical staff.
DFCI RNA Interference Screening Facility
Core facility that provides the following services: Genome-scale screening of lentiviral human and mouse shRNA libraries. The RNAi Screening Facility provides investigators with access to RNAi reagents and high-throughput screening technology. Lentiviral-based RNAi constructs against the human and mouse genomes are provided by the RNAi Consortium of the Broad Institute, and can be used to transduce a wide range of target cells, including primary and non-dividing cells. The Facility provides reagents, equipment, and technical expertise to design, optimize, and perform cell-based, arrayed lentiviral RNAi screens. Additionally, lentiviral RNAi constructs against individual genes can be requested.
DFCI Shannon McCormack Advanced Molecular Diagnostics Laboratory
The Molecular Diagnostics Laboratory provides such research services as microRNA expression profiling, human cell line identity verification, mutation detection for clinical research studies, and specimen processing for clinical research studies to investigators at the Dana Farber Cancer Institute, as well as to investigators at other institutions. Consultation on experimental design and assistance with data analysis are also available.
Core facility that provides the following services: Medium-density speed congenic backcross service, Medium-density genetic background check service, DNA extraction. DartMouse is a not-for-profit core facility funded by the National Institutes of Health''s National Center for Research Resources. The mission of DartMouse is to facilitate the development of congenic mice in support of pre-clinical projects across the United States. Use of DartMouse allows the generation of congenic mice in 5 generations (~1.5 years), versus the 10 generations (~3 years) required by conventional back-crossing. Facility staff provides expert advice on mouse speed congenic development, mouse genetic background analysis, and mouse genetic mapping. Investigators provide us with mouse tail clippings. From these, DartMouse isolates genomic DNA and performs and analyzes complete genome-wide scans. We return data in graphical and spreadsheet formats, and make specific recommendations on breeder selection. We operate an Illumina BeadStation 500. Chips use a 1449 SNP array covering the mouse genome with an average density of <5 cM.
Dartmouth-Hitchcock Bioinformatics Shared Resource
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 29,2022. Core to support the implementation of bioinformatics resources for cancer research at Dartmouth. Provides consultation and collaboration for research projects of NCCC members, regular workshops, seminars, services including applied bioinformatics and data mining, computer programming and software engineering, database development and programming and high performance computing and systems administration.
Dartmouth Biomedical NMR Research Center
Core facility that provides the following services: Animal in vivo MRI and MRS Service. The Biomedical NMR Research Center belongs to the Research Division of the Department of Diagnostic Radiology. Dr. Barjor Gimi is currently Director of the MR center. The Center houses a 7T horizontal bore Varian MR scanner in Vail and a 9.4T horizontal bore Varian MR scanner in Borwell. Research at the Biomedical NMR Research Center aims to advance applications of NMR techniques for tissue characterization in health and disease. We are developing non-invasive MR techniques to reveal unexplored details of anatomy, physiology and biochemistry in vivo. We use multinuclear MR technique both in imaging and spectroscopy modes and work with several animal models to achieve the goals above. Biomedical NMR Research Center provides a wide range of in vivo MR protocols for Dartmouth College and Dartmouth-Hitchcock Medical Center scientists. These include high resolution anatomical and functional MRI scanning procedures from rodents. Localized ��������H and ����������������P NMR spectroscopy can be acquired from several target organs to map, for instance metabolite concentrations, energy state, intracellular pH or tissue temperature.
The primary mission of the Biostatistics Shared Resource (BSR) is to improve the statistical aspects of cancer research at Dartmouth by providing expert statistical collaboration for research projects of Cancer Center members. Because every aspect of cancer research involves data, all research programs potentially may require the participation of the BSR. Areas of special faculty expertise include clinical trial design, longitudinal data, statistical methods for genomics and managing data, measurement error methods, nonlinear dose response modeling, quality of life data, decision sciences, cost effectiveness analysis, and diagnostic test assessment. Faculty and staff offices are located on the 8th floor of the Rubin building at Dartmouth-Hitchcock Medical Center (DHMC). The BSR maintains an extensive statistical software library providing access to all major statistical analysis platforms. Server and network access are provided through Cancer Center administration, DHMC, and Dartmouth College. The BSR collaborates closely with other shared resources for project development and monitoring through the Office of Clinical Research, and the Integrative Biology and Experimental and Translational Models Shared Resources.
Dartmouth Cigarette Smoke Exposure Analysis Laboratory
Core facility that provides the following services: Cigarette smoke exposure analysis service. Our lab is interested in the innate immune system at the mucosal surfaces of the female reproductive and respiratory tracts. A special focus of this work is to determine the effects of cigarette smoke on changes in immune protection. The relationship of cigarette smoke exposure to increased risk of infection is well established, however the mechanisms involved are not. Our research shows that cigarette smoke exposure reduces production of a key antimicrobial chemokine, CCL20. Ongoing research in the lab seeks to determine if similar responses to cigarette smoke exposure underlie increased rates of infection and how cigarette smoke exposure associated infection is linked to the development of cancer. Consulting; training; planning; experimental management assistance. Banked tissue samples available for preliminary studies. Small animal cigarette exposure.
Core facility that provides the following services: Electron micrscopy facility access. The EM Facility is an institutional resource to meet the electron microscopy needs of faculty, staff and students of the Dartmouth College community, including the College, Thayer School of Engineering, the Dartmouth Medical School, and the Dartmouth-Hitchcock Medical Center. The instruments are housed in the EM wing of Remsen. Because the facility is intended to provide service to all the campus, yet has limited personnel, a major effort is made to provide training in the use of appropriate instruments to enable users to do their own microscopy. In addition to this training, there will be service assistance available for those unable to spend time on the microscopes, and for processing of biopsy samples from DHMC.
Core facility that provides the following services: Illumina Bead Array service, Affymetrix Microarray service. The Genomics Shared Resource provides technologies to the Norris Cotton Cancer Center and Dartmouth community investigators that enable profiling of gene expression, miRNA, GpC Island, and CGH on a whole-genome scale. The long-term goal of the Genomics Shared Resource is to provide an efficient and affordable fee-for-service operation that will provide high quality genomics and microarray data for the growing number of Cancer Center investigators who require this service.
Dartmouth Institute for Health Policy and Clinical Practice: Data and Analytic Core
Core facility that provides the following services: Data and Analysis of large health care datasets. The Data and Analytic Core (DAC) includes research analysts and programmers, research assistants, a data librarian, and a Director who reports to the Director of the Center for Health Policy Research and the DAC Advisory Committee. The DACs responsibilities are to maintain an extremely secure environment for health care datasets provided to Principal Investigators by the U.S. Centers for Medicare and Medicaid Services, state governments, and other organizations under data use agreements and licenses. The DAC works under the direction of faculty investigators who have specific permission to use the data to conducted research. The DAC consists of 15 analysts (and an additional 5 staff) with a combined 150 years of healthcare claims analytic experience and a mastery of a broad range of programming and statistical methods. New analysts undergo a comprehensive training program lasting the better part of 6 months to assure a strong foundation in Medicare data analytics.
Dartmouth Media Research Lab Shared Resource
Core facility that provides the following services: Coding of data. The Dartmouth Media Research Lab (DMRL) specializes in the content coding of all types of media including movies, television programming and advertising. We have an extensive database of top box office hits from 1995 to the present. Past areas of research have included tobacco, alcohol, food, violence, and sexual activity. The team consists of two trained coders and a supervisor who ensures consistency and reliability.
Dartmouth Molecular Biology Shared Resource
Core facility that provides the following services: Genotyping service, DNA sequencing service, DNA fragment analysis. DNA Sequencing, DNA Fragment Analysis
Core facility that provides the following services: Multi-photon imaging. This SynergyT1 Shared Resource Core includes two microscopes sharing two femtosecond pulsed Ti:Sapphire lasers (tunable between 690 and 1080 nm) for imaging fluorescently-tagged molecules in tissues in vivo and in vitro.
Dartmouth SYNERGY: Recruitment and Retention Core
Core facility that provides the following services: Comprehensive, Expert Recruitment and Retention support. The Recruitment and Retention Core (RCC) helps investigators make their studies visible across Dartmouth and to the public to increase awareness of clinical study opportunities. RRC Director: Sheila B. Noone, PhD
Dartmouth SYNERGY: Research Design and Epidemiology Core
The Research Design and Epidemiology Core (RDE) provides consultation and guidance to investigators at the earliest stages of their study design.
Dartmouth Pathology Translational Research Core Facility
Dartmouth Pathology Translational Research
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2026.Core facility that provides the following services: Tissue collection, Histology services, Molecular pathology services, Pathologist consultation. The Pathology Shared Resource (PSR) provides four primary services for NCCC investigators: # it partners researchers with appropriate pathologists to provide specific expertise matched to the needs of the research project; # it coordinates the procurement, preservation, and distribution of human tissues and cells for funded and developmental NCCC basic and clinical research; # it performs histologic, immunohistologic, and molecular diagnostic procedures including DNA sequencing SNP genotyping and quantitative gene expression analysis for NCCC researchers; and # it provides a GMP cell processing laboratory for the isolation/purification, manipulation, expansion and/or storage of cells derived from a patient''s/subject''s peripheral blood intended for autologous reinfusion. The Pathology Shared Resource is closely integrated with the anatomic pathology laboratory of Mary Hitchcock Memorial Hospital and provides a cost-effective mechanism for NCCC investigators to take advantage of the economic efficiencies provided by that high-volume facility. The Core is managed by the Norris Cotton Cancer Center as a shared resource on behalf of the university and is available to all investigators within the greater Dartmouth research community. This Shared Resource is supported by funds from the Norris Cotton Cancer Center Core Grant and is overseen by the EMTG, an oversight and advisory committee of the Cancer Center.
Dartmouth SYNERGY: Biomedical Informatics Core
Core facility that provides the following services: Research Consulation: Informatics Research. The Biomedical Informatics Core (BIC) offers clinical and translational investigators support on informatics tools for cohort discovery, data integration, data management, text mining and visual analytics. In addition, the BIC provides consultative services on integration of data systems and on procedures for research data security.
Currently under development, the SYNERGY Bioregistry is a centralized virtual biorepository that will integrate information about samples from existing and future biorepositories. The Bioregistry will comprise: A standardized data warehouse of information on existing research biorepositories at Dartmouth eSample, a research tool to allow tracking of specimens and integration with the Bioregistry Access to the Dartmouth freezer farm of large freezer storage units to support archived materials The Bioregistry will enhance access to a diverse array of biologic samples, allowing investigators to manage sample collection and storage based on individual project needs and enabling researchers to learn about existing samples that can be used to pursue new clinical and translational studies. Bioregistry Director: Margaret Karagas, PhD
Dartmouth SYNERGY: Biostatistics Consultation Core
The BCC provides essential statistical and quantitative methods support to Dartmouth investigators, helping to remove impediments to initiating new clinical translational research programs for young physicians and other scientists. Specialized support for statistical genetics/genomics, decision sciences and comparative effectiveness research, health services research, mathematical demography, psychometrics, geographic information systems, and imaging applications. The BCC also provides statistical expertise related to critical data management, in cooperation with the SYNERGY Biomedical Informatics Core, and fully supports statistical education initiatives throughout SYNERGY
Dartmouth SYNERGY: Clinical Trials Office
Core facility that provides the following services: Study management service, Administrative and financial support, Regulatory support. The Clinical Trials Office (CTO) supports clinical research study initiation and conduct, including assurance of regulatory and financial compliance. The CTO works to enhance patient safety, promote high-quality research, and create increased standardization and consistency within the overall clinical research enterprise at Dartmouth. Current responsibilities of the CTO include: clinical trial contract review and negotiation; budget review in collaboration with PI and negotiation with sponsor; financial oversight of the trial with Medicare Coverage Analysis and management of the research billing activities of open trials; regulatory support for investigators, including study monitoring of investigator-initiated trials and registration of studies at clinicaltrials.gov; consistent registration of all new trials in Velos eResearch system prior to study initiation; and education and training for clinical research professional.
Dartmouth SYNERGY: Ethics Consultation Core
The Ethics Consultation Core (ECC) leverages current ethics activities across Dartmouth, and thus provides the capacity for real-time collaborative ethics advice for investigators throughout the translational research community.
Rotterdam Ophthalmic Institute; Rotterdam; Netherlands
The scientific research institute of the Rotterdam Eye Hospital that works with ophthalmologists and other specialists at the Rotterdam Eye Hospital as well as with national and international research centers.
Dartmouth Trace Element Analysis Core Facility
Dartmouth Trace Element Analysis Laboratory
Dartmouth Trace Element Analysis Core Laboratory
Analysis of elemental composition of biological tissues and fluids by Inductively Coupled Plasma Mass spectrometry. Analysis of Arsenic species in urine and blood by chromatography-ICP-MS. Laser ablation analysis of tissue sections for imaging of elemental distributions.
Dartmouth Translational Research Animal Core
TRAC is affiliated with the the Irradiation and Small Animal Imaging Shared Resource, which together provides irradiation services for basic and translational researchers and state-of-the-art non-invasive in vivo imaging of cultured cells and small animals. Services are used by Dartmouth investigators to irradiate cells in culture and small experimental animals. A separate set of irradiation devices is available through Norris Cotton Cancer Center for clinical and experimental irradiation of human patients.
Core facility that provides the following services: Animal handling training service, Animal surgery.
FAMU Molecular biology research laboratory
Core facility that provides the following services: HPLC service.
Core facility that provides the following services: Protein analysis, 2D gel electrophoresis service.
Forsyth Institute Bioinformatics Core Facility
Core specializes in oral microbial genomics, taxonomy, phylogenetics and the next generation sequence (NGS) data analysis with both in house and cloud high performance computational resource. In addition to supporting funded bioinformatics projects, Bioinformatics Core will also provide computational support to Forsyth and other researchers for processing, analyzing, and interpreting biological data.
The Biostatistics Core collaborates with clinical and laboratory investigators providing support for experimental design, statistical methods, data analysis and data management for epidemiologic studies, clinical trials and laboratory investigations. Collaborations have included Center grants, Program Projects and numerous individual investigator grants. These studies have largely focused on oral health research, particularly dental caries and periodontitis, with an emphasis on the microbial and immunologic aspects as well as diagnosis and treatment of these conditions and use of high throughput technologies in their evaluation.
Forsyth Institute Flow Cytometry Core Facility
Core offers consulting and support services for detection of different fluorescent parameters simultaneously, RBC contaminated samples, and high throughput analysis using 96 or 384-well plates. Cell sorter allows for collecting cells/particulates of interest, after screening for positively selected markers, downstream applications, and is capable of sorting four separate cell populations simultaneously.
Royal College of Surgeons in Ireland; Dublin; Ireland
Private university responsible for the medical speciality of surgery throughout Ireland.
Analysis of air pollution samples: including gravimetric determination of particle mass from filter samples; chemical analysis for passive and active samples of pollutant particles and gases; instrumental analysis of elemental and organic carbon collected on quartz fiber filters; trace elemental analysis of filter samples, and ; reflectance analysis of atmospheric black carbon.
Forsyth Human Microbe Identification Microarray Core
Core facility that provides the following services: DNA screening from clinical samples, Comparison of bacterial associations in health vs. disease by microarray, Human microbial identification microarray service. The Microbial Identification Microarray Core (MIM) at The Forsyth Institute is a one-of-a-kind core service that enables the rapid determination of bacterial profiles of human clinical samples. The first MIM offering focuses on the detection of bacterial profiles from clinical samples from the oral cavity. Drs. Bruce Paster and Floyd Dewhirst, have used molecular analyses based on 16S rRNA sequencing to identify about 600 oral bacterial species, of which over half have not yet been cultivated. Using this information, they have developed the Human Oral Microbe Identification Microarray, or HOMIM, which allows the simultaneous detection of about 300 of the most prevalent oral bacterial species, including those that cannot yet be grown in vitro. Microarrays targeting bacterial species of the human and mouse intestines are presently under development. In addition, exploratory and pilot studies to identify bacteria within any human clinical sample by 16S rRNA cloning and sequencing are available. This service is available to researchers from all academic institutions and to industry. Researchers submit DNA isolated from clinical samples and receive an online comprehensive data analysis and easy-to-interpret readout. Depending upon the number of samples to be analyzed and position in the queue, results can usually be obtained within days. Note that results are presently for research purposes only.
Out of service. Documented on May,04,2021. This record has been removed from eagle-i search; this page is an archival copy only. Imaging Services offers high-quality poster printing.
The Forsyth Institute established the micro computed tomography core in 2011. The Facility is located in the 4th floor of the Forsyth research building. The core now accepts samples from outside academic institutions and for-profit organizations.
Forsyth Mineralized Tissue Analysis Core Facility
Characterization of mineralized tissues, natural or synthetic, is a challenging task, since these materials are comprised of organic and mineral constituents, each with strikingly different physical and chemical properties. The function of the Forsyth Mineralized Tissue Analysis (MTA) Core is to provide a comprehensive structural, physical, and chemical analysis of wild type, mutant and engineered mineralized tissues, including teeth (enamel, dentin, cementum), cartilage and bone. The strengths of the MTA Core include a unique combination of specialized instrumentation, techniques, and expertise based on more than 30 years of experience in this field.
Core facility that provides the following services: Flow cytometer equipment access, Flow cytometry consultation, Immunofluorescence analysis, Cellular sorting, Measurement of intracellular calcium signaling, DNA cell cycle analysis, Apoptosis assay service. The purpose of this Immunology Flow Cytometry Core of the Boston Area Diabetes Endocrinology Research Center (BADERC) is to provide flow cytometric techniques in a cost effective manner to the diabetes research community. The core is committed to providing to investigators both training and a diversity of state-of-the-art flow cytometric techniques. The Core will assist investigators in applying a variety of tough and cumbersome immunologic techniques and offers in-depth training of new methods.
Harvard Medical School Electron Microscopy Core Facility
Harvard Medical School HMS Conventional Electron Microscopy Facility
Core provides electron microscopy services, instrumentation and training. Services include consultation and experimental design for wide variety of biological samples for both Transmission Electron Microscopy and Scanning Electron Microscopy.
Core facility that provides the following services: Drosophila genome-wide and focused cell-based RNAi libraries, Custom synthesis of double-stranded RNAs for Drosophila cell-based RNAi. The DRSC facilitates genome-wide and related cell-based screening at our state-of-the-art facility. Since our beginnings in 2003, we have successfully guided screeners through the process, including help with assay development and optimization, data and image analysis, and planning of follow-up assays. Screens performed at the DRSC have resulted in an impressive number of publications on a wide range of topics in high-profile journals.
Core facility that provides the following services: Small molecule and peptide NMR spectrometry service. Formerly the NERCE NMR Resource. Nuclear magnetic resonance spectroscopy is a powerful tool for studying structural and conformational parameters of molecules. This tool is vital for the chemical analysis of both small molecules (like those discovered in small-molecule screens) and large molecules, such as carbohydrates and proteins found to have potential biologic importance.
HMS Genetically Modified NOD Mouse Core Facility
Core facility that provides the following services: Maintainence and dissemination of transgenic and mutant mice. The Genetically Modified NOD Mouse Core provides Center investigators, as well as researchers elsewhere, with access to transgenic and mutant lines derived from the NOD mouse model: some will be generated within the Core; others are established lines of proven experimental value that are maintained in the Core. The Core will construct transgenic mice in strains that have a high susceptibility to diabetes (in particular in the NOD line). This includes trangenesis by conventional pronuclear injection or by delivery of RNAi cassettes on lentiviral vectors. The Core will also provide a panel of existing transgenic and mutant lines. These lines are chosen because of their established interest in allowing the dissection of immunological tolerance in Type 1 Diabetes, and in response to Center investigator needs.
HMS Human Sample Procurement Core Facility
Core facility that provides the following services: Autoantibody determination, HLA typing and Genotyping for the best recognized susceptibility loci (INS, PTPN22, CTLA4). The Human Sample Procurement Core will support translational research endeavors within the JDRF Center by providing the Center''s laboratories access to well-characterized blood samples from patients with diabetes at different stages of the disease. This availability will greatly facilitate the translational exploration of concepts and targets emerging from the basic research projects. Individuals with T1D (recent onset, long-standing Type-1 diabetes) and matched controls (healthy or T2D) will be recruited from the patient population at the Joslin Diabetes Center and neighboring institutions. The Core will perform and record a basic characterization of patients and their samples. This analysis will include a thorough evaluation of clinical characteristics from a diabetes and autoimmune standpoint, and an immunogenetic workup (outsourced to Joslin or other cores): autoantibody determination, HLA typing and genotyping for the best recognized susceptibility loci (INS, PTPN22, CTLA4). A relational database will be adapted to record all patient information, copies of which will be provided in a de-identified manner to the investigators.
Harvard Medical School ICCB-Longwood Screening Core Facility
Harvard Medical School ICCB-Longwood Screening Facility
ICCB-Longwood Screening Facility at Harvard Medical School
Facility is small molecule and functional genomics high-throughput screening laboratory. It is built around modular work stations and most assays are performed in 384-well plates. There are over 500,000 small molecules available for screening at ICCB-Longwood and compound collection is continuously growing. Whole human and mouse genome siRNA libraries, arrayed sgRNA libraries, lncRNA siRNA libraries, as well as miRNA mimic and inhibitor libraries, are also available for screening. These libraries can be screened at the genome level or in focused subsets.
Core facility that provides the following services: Computational image data analysis. IDAC provides image data analysis services to individual labs and core facilities at Harvard Medical School, including the ICCB-Longwood Screening Facility (ICCB-L), the Drosophila RNAi Screening Center (DRSC), and the Nikon Imaging Center (NIC).
HMS Microbiology and Immunobiology Biological Chemistry Mass Spec Facility
Core facility that provides the following services: Instrument operation and data analysis. Instrumentation for this facility includes an Agilent 6520 Accurate-Mass quadrupole time-of-flight (Q-TOF) LC/MS system with great mass accuracy, mass resolution, and sensitivity for small molecule mass identification/quantitation and metabolomics experiments. It is equipped with an Agilent 1200 series HPLC with DAD UV/V is detection for normal flow LC/MS and nitrogen CID for MS/MS. The Q-TOF LC/MS is located in laboratory of Dr. Suzanne Walker in the Department of Microbiology and Immunobiology.
Core facility that provides the following services: Soft-lithography service, Soft-lithography training and consultation. The HMS Microfluidics Facility aims to make the tools of Microfabrication and Microfluidics available to all HMS users.
HMS Molecular Electron Microscopy Facility
The molecular electron microscopy facility at Harvard Medical School is predominantly used for our own research and can therefore not be considered a service facility. We are, however, committed to make our technology available to as many research groups in the community as possible. If you are interested to use molecular electron microscopy, please contact us by phone or email.
Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.
HMS NERCE Biomolecule Production Core Laboratory
Core facility that provides the following services: Protein production, Bacterial fermentation for recombinant protein production, Baculovirus culture, Protein purification. The NERCE Biomolecule Production Core Laboratory is a core service laboratory with capability for expression and purification of recombinant proteins using bacterial and baculoviral expression systems, and preparation of bacterial carbohydrate components. It supports all New England investigators conducting research on NIAID priority pathogens that requires purified proteins or carbohydrates. Investigators are expected to provide data demonstrating efficacy of production and purification methods, as well as strains or purified recombinant plasmid preparations where applicable. See lab website for details. Please note that since the NERCE program will end in February 2014, our ability to support new requests for services is limited.
Core facility that provides the following services: Confocal microscopy. Confocal microscopy offers multiple benefits compared to conventional microscopy, particularly the ability to collect serial, high-resolution optical sections from thick specimens. Multicolor, three-dimensional images can be obtained, providing high-content information from single images. To assist NERCE investigators from throughout the region, NERCE has established a Confocal Microscope Facility at the University of Massachusetts Medical School. Funding through the NERCE has procured a state-of-the-art LEICA SP2 AOBS laser scanning confocal microscope, which combines spectrophotometric detection with confocal microscopy. The instrument is located at the BL2+ facility at the Lazare Research Building, at the University of Massachusetts Medical School, Worcester, MA. The use of live cell imaging combined with green fluorescent protein (GFP) technology is an exciting methodology with which to study the interactions between infectious agents and living cells. A variety of applications are amenable to confocal microscopy techniques and include: monitoring the localization of proteins in living or fixed cells, monitoring changes in the cellular distribution of proteins, and monitoring changes in the activation status and morphological changes in cells exposed to infectious agents.
Core facility that provides the following services: Imaging system training, Live cell imaging. Live-cell imaging is a powerful method that enables investigators to observe cellular trafficking events with a high degree of spatial and temporal resolution, including visualization of individual bacteria or viral particles engaged in the process of infecting eukaryotic cells. A quantitative description of bacterial and viral invasion mechanisms can be obtained through such approaches. NERCE has provided funding to support the use of live-cell imaging for any New England investigator studying NIAID priority pathogens and agents of emerging infectious disease. Investigators interested in working with the Live-Cell Imaging core laboratory should complete the Imaging Core Request Form and send it to Gerald Beltz. There are no fees for use of the live-cell imaging core for research related to NIAID priority pathogens and agents of emerging infectious disease. Please note that since the NERCE program will end in February 2014, our ability to support new requests for services is limited.
HMS NERCE Microbiology and Animal Resources Core
Core facility that provides the following services: Enzyme-linked immunosorbent spot assay service, Fluorescence microscopy service, Real-time PCR Service. The NERCE Microbiology and Animal Resources Core maintains two laboratories, a BSL-2 and a BSL-3 laboratory, to support the research efforts of all New England investigators conducting research on NIAID priority pathogens. Each laboratory provides the physical environment, equipment, and support personnel required for scientists to work with these agents. The BSL-3 laboratory is an isolated suite that includes individual laboratory rooms and rooms for housing experimental animals, all within a single containment facility. The BSL-3 lab provides the extensive security and administrative support structure required for possession of CDC select agents. The laboratory acquires strains of viruses and bacteria, prepares seed stocks, and characterizes these seed stocks using phenotypic and molecular methods to ensure a well-characterized, pure biological reagent. Laboratory staff members assist investigators with experiments involving pathogen culture, fractionation of biological material, animal challenge, and vaccine and drug administration. The laboratory is equipped for commonly used analytical methods, including fluorescence microscopy, PCR, EIA, and ELISPOT. A single suite with both laboratory and experimental animal capability eliminates the need to transport infectious material between laboratories. The BSL-2 laboratory provides support required by the BLS-3 facility, access to attenuated strains exempt from select agent registration, and laboratory space for visiting investigators. Investigators interested in working with the Microbiology and Animal Resources core laboratory should complete the Core A Request Form and send it to Christine Anderson. See lab website for details. There are no charges for projects focused on NIAID priority pathogens and agents of emerging infectious disease.
Harvard Medical School Neurobiology Imaging Core Facility
Harvard Medical School Neurobiology Imaging Facility
Open access light microscopy and tissue core located within Neurobiology Department. Provides services in optical imaging, tissue clearing, in situ hybridization as well as introduces new equipment and cutting technology to the basic science community. Provides expertise, equipment, services and learning opportunities to researchers in the greater Boston area.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on 4/1/14. Software providing a framework to find isomiRNAs, templated and non-templated modifications in microRNAs.
Core facility that provides the following services: User-based microscopy service, Live Specimen Imaging, Widefield Fluorescence, Spinning Disk Confocal Microscopy, Laser Scanning Confocal, Color Imaging, Image Analysis, Microinjection, Phase Contrast and Differential Interference Contrast (DIC), Photo-bleaching, Photo-activation, & Laser Ablation, Microfluidic Perfusion, Imaging and microscopy training. The mission of the NIC@HMS is to: enhance basic research by providing access to state-of-the-art microscopy and imaging equipment, provide training courses on basic and advanced light microscopy techniques for the benefit of HMS and the greater Boston research community, introduce the latest innovations in light microscopy and imaging to the HMS community, serve as a learning center for our corporate partners and contributions, and provide a dedicated NIC@HMS director for ongoing technical consultation and support.
The SBGrid Core team provides research computing sysadmin support to structural biology laboratories in the Boston area.
Core facility that provides the following services: Project Consultation, CADD Design, and Fabrication. We have many years of experience designing and manufacturing custom tools for medical research. This has allowed us to compile a large collection of different solutions to a wide range of problems. We work on a daily basis with researchers working in these areas of medical science: * Cell Biology * Genetics * Anesthesiology Research * Surgical Research * Pathology Research * Respiratory Biology * Environmental Sciences
HMS Taplin Mass Spectrometry Core Facility
Core facility that provides the following services: Protein identification from SDS-PAGE gel bands/spots (Coomassie stained level of protein), Protein phosphorylation service, TCA samples service. The Taplin Biological Mass Spectrometry Facility opened in February 2001 as a core facility for the analysis of proteins and peptides by mass spectrometry. The facility is focused on serving the needs of investigators at Harvard Medical School (HMS) and all the Harvard affiliated Institutions.
The West Quad Computing Group (WQCG) serves the research community of the BCMP and Cell Biology departments at Harvard Medical School. We provide support for your advanced computing needs, including design and maintenance of computational clusters, large data-set management, web and database backed applications, and workstation support, including workstations connected to research equipment. Please see Resources for more information, including a sample of some of our recent projects. We work in collaboration with the HMS Information Technology department. Please contact us using our support form for all of your computer support needs.
There is a growing need for animal models to carry out in vivo developmental and regenerative medicine studies of human cells, tissues and organs. The Humanized Neonatal Mouse Center (HNMC) was created to accelerate research in the stem cell field by providing humanized mouse models to study human stem cell engraftment and differentiation in regenerative medicine. We have over 4 years of experience in constructing different types of humanized mouse models, including neonatal heart, lung and kidney injury models. We have extensive experience in hematopoietic stem cell reconstruction. It is our goal at HNMC to facilitate collaborative research in human stem cell biology, where physiologically relevant microenvironments (niches) may be created in vivo to study human stem cell fate and function under experimental settings where disease, damage or degenerative conditions can be controlled. We can provide customized humanized mouse models to the HSCI research community, to collaborate on research studies of common interest, and to advance the general use of these models for a broad range of translational and preclinical studies.
HSCI and BIDMC Flow Cytometry Core Facility
Core facility that provides the following services: Cell sorting service, Cell analyzing service, Cell separation service, Cell cytometer service, Data services, Flow cytometry protocol development service, Benchtop flow cytometry analyzer training, Flow cytometry beta-testing service. Committed to meet all of the flow cytometry needs for the BIDMC and the external research community, the Flow Cytometry Core facility offers state of the art instrumentation for routine flow cytometry and cell sorting. It is continuously expanding with the newest software and machinery for both sort and analysis capabilities of up to 30 flourescent parameters. The Flow Cytometry Core facility is available to: answer technical questions; assist you in setting up flow cytometry experiments; assist you with acquiring, analyzing and interpreting your data; assist in data presentation and data storage; provide training on the four benchtop analyzers and on software. To schedule an appointment for regular flow cytometry (user operated), log onto our online web calendar at: http://bidflow.calendarhost.com/
HSPH Biological Analysis Service Facility
The Biological Analysis Service facility provides and/or facilitate access to digital imaging and biological analysis services in and out of Harvard campus. We aim to foster new research opportunity for HSPH investigator through providing initial support for pilot studies. Check out Bioanalysis Mini-Pilot Funding for description of the funding mechanism and an application form to request funds. Inside HSPH: * Biomedical Imaging * Flow Cytometry * Electron Microscopy * Proteomics Facility * Molecular Analysis Facility
All new users must be trained by the facility manager over two orientation sessions and be approved to use the equipment in the facility. All users must obtain the financial approval from their PI and financial manager. Please submit a PO number or the Harvard billing code prior to the first use of the facility.
Electron microscope access facility. All new users must be trained and approved by the facility manager to use the equipment in the facility and obtain the financial approval from their PI and financial manager. Please submit a PO number or the Harvard billing code prior to the first use of the facility. Approved users can sign up with the facility manager.
HSPH Environmental Genomics Service Facility
The aims of the EGS are: to assist Center investigators in preparing genomic DNA from blood/buccal swabs collected in their human population studies. This activity involves assistance in the proper collection, extraction, concentration, quality testing and hand or robotic plating for candidate gene and even Genome-Wide studies of gene-environment interaction; to assist Center investigators in creating a genomic DNA biorepository for DNA for genotyping and for epigenetics studies; to assist investigators in obtaining efficient genotyping and epigenetic services either in-house or through partner organizations in the Harvard system; and to assist Center investigators in selection of SNP''s, haplotypes, genotyping platforms and for environmental genetic and epigenetic studies of human populations.
The EM Lab supports study relating to aerobiology. The laboratory has the capability to generate, sample, and analyze fungal, bacterial, and viral microbes.
Harvard School of Public Health Environmental Statistics and Bioinformatics Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core provides intellectual guidance for quantitative aspects of the design and analysis of center studies and expertise in biostatistical methods, environmental risk assessment, Geographic Information System (GIS) , spatial statistics, molecular biology, bioinformatics and statistical genetics. Core runs a regular seminar series and often sponsors short courses on specialized topics of interest to the community.
Royal Liverpool University; Liverpool; United Kingdom
HSPH Exposure and Environmental Analysis Service
The Exposure and Environmental Analyzes Service provides exposure assessment equipment, design of experimental apparatus, laboratory analyzes of environmental and biological samples, support for methods development and pilot data, as well as training for researchers and students. The service maintains facilities such as clean rooms and exposure chambers. Specific services are provided by the four affiliated laboratories.
Flow cytometry access facility. All new users must be trained by the facility manager over two orientation sessions and be approved to use the equipment in the facility. All users must obtain the financial approval from their PI and financial manager. Please submit a PO number or the Harvard billing code prior to the first use of the facility.
An application for discovering potential splice junctions in high throughput sequencing (HTS) data.
Harvard Bioinformatics Core at Joslin Diabetes Center
Bioinformatics and Biostatistics Core at Joslin Diabetes Center
The Bioinformatics and Biostatistics Core at Joslin Diabetes Center
Core for data driven projects related to basic, clinical and translational research, with a particular emphasis on diabetes. Aims to ensure that researchers take advantage of the most modern and robust methods available in the field of Bioinformatics and Biostatistics.
Harvard CNS Imaging and Analysis Facility
Center for Nanoscale Systems facility dealing with SEM, TEM, ESEM, sample prep etc.
Harvard CNS NNIN/C Computational Facility
The National Nanotechnology Infrastructure Network?s computational activity (NNIN/C) is the computational counterpart of the NNIN experimental initiative. Like the NNIN experimental program, NNIN/C is a multi-university initiative, funded by the National Science Foundation (NSF). Harvard University serves as the coordinating hub of NNIN/C, the object of which is to establish a national computing resource that provides hardware resources and simulation tools dedicated to nanoscience research for the academic and industrial research communities. Strong technical and scientific support is provided by staff experts so that the tools and resources can benefit interdisciplinary research. The software tools include commercial software packages for design, characterization and analysis of nanometer scale devices as well as some of the latest academic advances in nanoscale modeling and simulation software. The goals and strategies of NNIN/C are: * Assemble and create a wide suite of robust software that addresses critical issues related to the physical, chemical, and biological properties of artificial and natural nanoscale structures. * Maintain and, where necessary, modify these simulations to address a broad range of research problems. * Provide strong technical support and thorough instruction on the software tools so that even novice users can rapidly develop solutions to their own unique research problems. * Provide web-based graphical user interfaces (GUIs) for user-friendly access to simulation tools as well as web-based resources for instruction and feedback to the community of researchers employing the same tools
Core facility that provides the following services: Access/training service. Lab performs services related to paleontology, paleopathology, and paleohistology. This core houses significant expertise in processing and analysis of mineralized tissues.
Core facility that provides the following services: Nanofabrication cleanroom and instrumentation access, instrument training, staff assistance. The Center for Nanoscale Systems'' Nanofabrication Facility (CNS-NF), offers resource and staff support for fabricating and characterizing nanoscale devices and structures. The facility currently operates the 10,000 sq.ft. LISE Cleanroom with leading-edge equipment capable of electron-beam and optical lithography, physical and chemical vapor deposition, dry and wet processing, metrology, and device characterization.
Center for Nanoscale Systems facility dealing with FIB, XPS, AFM, Optical Microscopy and Spectroscopy, Biomaterials, Soft Lithography, Microfluidics, Nano Particles, Chemical Nanotechnology, etc.
Harvard FAS Center for Biological Imaging
Core facility that provides the following services: Use of instruments service, Training service. The Harvard Center for Biological Imaging (HCBI) has been created to foster collaborative research in the most state-of-the-art facility available. To do this, we have set up a unique partnership with Carl Zeiss International in which our microscopy systems are continually replaced every 2-3 years ensuring we always have the most up-to-date equipment possible. The facility is open 24 hours/day, 7 days/week and access to the facility is open to all Harvard investigators as well as to affiliates and investigators from collaborating institutions.
Self-training Algorithm for Splice Junction Detection using RNA-seq.
Harvard Digestive Diseases Center Biomedical CORE B: Microscopy and Histopathology
Core facility that provides service for paraffin embedding, sectioning, staining, and frozen sectioning; shared equipment and service for confocal, widefield, photodocumentation, electron microscopy, and digital image processing; and an immunostaining service.
Harvard FAS Bauer Core: Mass Spectrometry and Proteomics Core Laboratory
Core facility that provides the following services: Complex protein mixture analysis service, Project consultation service, Data analysis service, Protein identification service, Posttranslational modification site determination service, N-terminal Edman Sequence Analysis Service, C-terminal sequence analysis service, De novo sequence analysis service, Quantitative proteomics service, Labeled quantitative proteomics - SILAC, Labeled quantitative proteomics - ICAT service, Labeled quantitative proteomics - iTRAQ service, Labeled quantitative proteomics - AQUA service, Intact molecular weight determination service, Low resolution GC/MS service, Low resolution GC/MS/MS service, Exact mass MS & MS/MS electrospray for structural elucidation service. The FAS Center for Systems Biology Mass Spectrometry and Proteomics Resource Laboratory provides mass spectrometry and strategic consulting in Proteomics and Small Molecule analysis for Life Science and Chemistry researchers as well as others worldwide. This resource brings together the state-of-the-art expertise and instrumentation of the Microchemistry and Proteomics, CCB Mass Spectrometry, and Bauer Center Core laboratories, leveraging our breadth of experience to provide the best possible support for your research.
Harvard FAS Center for Brain Science - Electron Microscopy Core Facility
CBS houses a core facility with a transmission electron microscope (TEM) and several scanning electron microscopes. The SEMs are part of ongoing research that will lead to a three-dimensional electron microscopy facility, to image neural circuits with the highest possible resolution.
Harvard PCMM Flow and Imaging Cytometry Resource
The Flow and Imaging Cytometry Resource provides research flow and imaging cytometry services to all investigators in the PCIMM at Children''s Hospital, Boston and Immune Disease Institute, HMS and the local scientific community on a case-by-case basis. With state of the art instrumentation, such as the standard configuration 3-lasers FACSAria located in BL2+-facility, 20-parameters 4-lasers FACSAria SORP and DIVA FACSVantage SE TurboSort?, the facility offers high speed cell sorting and complex analytical services, development of collaborative projects as well as consulting on design and development of new protocols and methods.
Harvard FAS Center for Brain Science - Imaging Core Facility
CBS hosts an optical imaging facility that houses advanced devices for widespread use by neuroscientists and is developing the next generation of optical techniques. The optical imaging is intended to be an extension of individual labs, housed in shared space. By pooling equipment, highly skilled technical management of the tools is available, allowing for routine technological upgrades, quicker troubleshooting, and expert advice. In addition, the joint space leads to camaraderie amongst users, and allows new technical advances in one lab to spread rapidly to other labs. This core facility also frees up space in individual labs that can be used in other ways. Finally, the shared equipment lowers barriers to adoption of the latest technology. This core facility provides: * Laser scanning microscopes with motorized stages for high throughput reconstructions of the nervous system * A histology suite for brain sectioning and tissue preparation * Stereo fluorescence macroscopes * The newest tools for high-resolution optical microscopy * Ultra-fast optical scanning microscopes
Harvard FAS Center for Brain Science - Neuroengineering Core Facility
Core facility that provides the following services: Access to fabrication lab. Technological advances hold a key to greater understanding of the structure and function of complex neural circuits. Neuroengineering is a core facility that provides customized engineering solutions to neuroscience problems faced by our members. Assistance with experimental design, electronics, machining, and software development, are all services provided.
Harvard FAS Center for Brain Science - Neuroimaging Core Facility
The Neuroimaging facility has a 3-Tesla magnetic resonance imaging scanner for non-invasive human brain imaging. Our aim is to: * Provide functional and anatomic magnetic resonance imaging (MRI) to scientists studying human cognition, brain development and aging, and individual differences * Provide training for undergraduate and graduate students destined to become the next generation of neuroscientists * Pioneer innovative ways of imaging the human brain and is a first adopter of new neuroimaging technology, tools and applications * Develop and make available the data processing and visualization tools demanded by advancing neuroimaging technologies.
Harvard FAS Center for Crystallographic Studies
Core facility that provides the following services: Macromolecular X-ray diffraction service, Charge density analysis, Single-Crystal service, Crystal mounting service, Cambridge structural database access, Inorganic crystal structure database access. The X-ray diffraction facility in Harvard University offers single crystal X-ray data collection, structure solution and refinement of small molecule structures.
Core facility that provides the following services: Progamming and sequencing classes and training. Research Computing (RC) facilitates the advancement of complex research by providing leading edge computing services across the Faculty of Arts & Sciences (FAS). RC staff maintain expertise in constantly changing computing technologies, while ''speaking the language'' of the FAS researchers, to help them use computing more effectively.
Harvard FAS Small Molecule Mass Spectrometry Facility
The Small Molecule Mass Spectrometry Facility at the FAS Center for Systems Biology offers support for the analysis of a wide variety of analytes using mass spectrometry based techniques. We are located in the second basement (B2) level of the Northwest Laboratory building at 52 Oxford Street, Cambridge, MA 02138. We provide services for molecular formula confirmation (accurate mass measurement), structural elucidation (MS/MS) and quantitation of small molecules. In addition, we can assist you in the mass analysis of a wide variety of non-proteomics samples including metabolites, medium sized proteins and oligonucleotides. Please contact us and tell us about your samples prior to submission or use of our Open Access laboratory.
Core facility that provides the following services: ABI Prism Taqman Allelic Discrimination Assay, OpenArray SNP genotyping, Illumina genotyping, Custom Illumina GoldenGate genotyping, Illumina Infinium genotyping analysis, Illumina methylation analysis. The Partners Genotyping Facility, part of the Partners HealthCare Center for Personalized Genetic Medicine (PCPGM), provides flexible, high quality, high-throughput SNP genotyping to the Harvard-Partners research community, including Harvard Medical School, hospitals in the Partners HealthCare network, investigators in the Dana-Farber-/ Harvard Cancer Center, and the Harvard School of Public Health. The portfolio of Genotyping methods at PCPGM now includes Illumina, TaqMan and TaqMan OpenArrays. Note: DF/HCC members will receive the DF/HCC discount on both genotyping and sequencing services from our facility
Harvard Forsyth Center for Clinical and Translational Research
The Forsyth Center for Clinical and Translational Research (CCTR) is a unique clinical facility with 6 fully-equipped dental units and associated laboratories that are specifically dedicated to conduct clinical research in oral and related systemic diseases. Clinical trials following FDA guidelines are performed at all levels, from early phase 1 trials to large, multicenter definitive clinical trials, with the goal of improving outcomes and the long-term health of patients. We routinely conduct studies in the oral environment, that include standard clinical measurement protocols for dental caries, dental calculus, gingivitis, periodontal diseases, intraoral local anesthetic evaluation, tooth restoration and tooth whitening evaluation. In addition, the clinic is equipped for obtaining and processing microbiological samples, gingival crevice fluid samples, blood and saliva samples for analysis of bacteria, inflammatory mediators, as well as for genomic and proteomic analyses. Under the new leadership of Dr. Thomas Van Dyke, Vice President of Clinical Research at The Forsyth Institute, the Center proposes new goals/efforts in discovering new techniques, testing new ideas and searching for valuable biomarkers for preventing and treating periodontal diseases and associated systemic inflammatory conditions. The CCTR is actively involved with the design and conduct of clinical research under Good Clinical Practices for submission to regulatory agencies. It has a published international reputation in evaluating intraoral local drug delivery devices, oral diagnostic systems, local anesthesia, restorative materials, tooth whitening systems and the association of oral diseases with systemic conditions. Forsyth''s Institutional Review Board is a member of the Harvard Catalyst Regulatory Group and meets on a monthly basis providing complete review of clinical protocols.
Core facility that provides the following services: MLV plasmid construction service, HIV plasmid construction service, Adenovirus plasmid construction service. The Harvard Gene Therapy Initiative was founded with the objective of promoting the use of gene therapy in both research and therapeutic applications and to conduct research developing new gene delivery vector technologies.
Harvard Genome Modification Facility Harvard University
Core facility that provides the following services: Transgene microinjection service, Embryonic stem cell gene targeting service, Blastocyst injection service, Cryopreservation of embryos and sperm, Genotyping service, Mouse consulting service. The Genome Modification Facility (GMF) provides transgenic, gene targeting, and other services to investigators of Harvard University and its affiliated institutions, as well as to investigators within the US and abroad. The GMF performs microinjections of DNA into fertilized embryos to generate transgenic mice, DNA transfection into ES cells for the creation of recombinant ES cell clones, injection of gene-targeted ES cells into host blastocysts to generate gene knock-out or knock-in mice, teratoma formation studies, and other related ES cell-based services. Other services include cryopreservation of mouse sperm and embryos, in vitro fertilization (IVF), recovery of cryopreserved mouse sperm and embryos, rederivation of pathogen free mouse lines, and derivation ES cell lines from wild type and mutant mice with a variety of genetic backgrounds. Our staff provides general consultations on experimental designs and vectors for gene modification-related projects, DNA preparation, recombinant ES clones, mouse genotyping, colony breeding and husbandry. We can also customize services as requested to support development of animal models of human diseases.
Harvard NeuroDiscovery Center - Biostatistics Consultation
High quality statistical support is important in the preparation of grant applications or study protocols for clinical trials. Such support typically is not readily available to investigators who are new to clinical trials. To address this weakness, the NeuroDiscovery Center provides consulting and collaborative services to its members who are engaged in clinical research applicable to neurodegenerative disease.
UCC Common Instrumentation Area and Services
Core facility that provides the following services: Equipment support, Research software design. Is a core area housing major equipment such as ultracentrifuges, freezers, spectrophotometers, gamma counters, etc, as well as the centralized cell culture facility. The unit fosters equipment sharing, centralizes maintenance of equipment and provides repair for the equipment of all the projects.
Harvard NeuroDiscovery Center - Cell-based Assays Core
Core facility that provides the following services: Introduction to the GE In Cell Analyzer 1000 for High Content Analysis (HCA). In collaboration with GE Healthcare Bio-sciences, the NeuroDiscovery Center has established a program centered around the IN Cell Analyzer 1000 - a flexible and easy to use sub-cellular analysis system suitable for medium-throughput screening, assay development and basic research. Based in the NeuroDiscovery Laboratory for Drug Discovery in Neurodegeneration, the IN Cell Analyzer 1000 is available for use by NeuroDiscovery members. (While priority is given to members investigating neurodegenerative diseases and the central nervous system, we welcome enquiries from all investigators.)
Royal Netherlands Academy of Arts and Sciences; Amsterdam; Netherlands
Core facility that provides the following services: Microscope access service, Microscope training service. Confocal and multiphoton are modern fluorescence techniques in microscopy for generating optical sections from live or fixed biological specimens. In general, both techniques employ a point scanning and point detecting design. The confocal microscope achieves point detection by using a confocal pinhole to block off out-of-focus emission from the specimen. The multiphoton microscope, on the other hand, generates intrinsic point emission directly from the in-focus spot, thereby eliminating the need for a confocal pinhole. Subsequent scanning of the entire field of view results in an optical section. Computer reconstruction of serial optical sections, collected at consecutive axial (z) positions, can reveal the spatial localization of cells and tissues (sometime subcellular molecules) in 3D. The ability to see biochemical processes in live cells, in real time, sheds light on the vastly complex molecular world of cells and may allow IDI scientists to identify new targets for drugs that will treat exposure to dangerous toxins and bacteria as well as fight a wide variety of diseases.
Harvard PCPGM Biorepository for Medical Discovery
The Partners Biorepository for Medical Discovery (PBMD), operated by the Partners HealthCare Center for Personalized Genetic Medicine, aims to foster collaborations among investigators, physicians and patients seen at Partners HealthCare institutions. This Partners-wide project is at the forefront of developing the tools needed to expedite the discovery and introduction of new ways to fight disease. As we advance the age of personalized medicine, it is critical that physicians and scientists work with large numbers of patients to advance the delivery of healthcare. The Biorepository provides an opportunity for patients to interact with investigative studies ? safely, securely and privately ? in ways that could have an enormous benefit for us all. The Biorepository continues in a development phase, and is actively working with a number of groups at BWH and MGH who are consenting patients for clinical and translational research studies. Samples are maintained in an institution-wide repository which is a growing resource available to Partners investigators and research groups.
Harvard PCPGM Biosample Services Facility
Core facility that provides the following services: DNA extraction from whole blood, saliva, isolated cell pellet, RNA extraction from whole blood with PaxGene tubes, Lymphoblast transformation, Isolation and cryo-preservation of white blood cells. The BioSample Services Facility (BSF) provides sample handling and preparation resources to investigators in the Partners research community. Our goal is to efficiently and effectively process specimens enabling the generation of high quality data via down stream processes. All projects containing subject samples and submitted to the BSF for handling must be IRB approved in advance. All specimens must be entered into our Laboratory Information Management System (GIGPAD) prior to delivery to the BSF. Our staff will work with you to design an implementation plan that would best fit your research needs.
Howard Imaging Core Facility: Molecular Imaging Laboratory
Core facility that provides the following services: Imaging training, Imaging equipment access. The Molecular Imaging Laboratory?s research focuses on small animal in vivo imaging using MRI, and optical fluorescent and bioluminescent imaging. In particular, we are interested in using molecular imaging techniques to study mechanisms of image contrast enhancement, improvement of sensitivity and specificity of tumor detection, and applications of diagnostics using small animal disease models.
Core facility that provides the following services: Clinical diagnosis services, Genomic sequencing service, ABI capillary sequencing service, Illumina next generation sequencing service, shRNA library sequencing service, High throughput genome sequencing, PCR to detection service, Plasmid sequencing service, Sequencing, Chip-Seq service, Digital Gene Expression Service, Nucleic acid library construction service, Next gen seq bioinformatics support service, Transcriptome and RNA-Seq service.
Executive department of the federal government concerned with promoting economic growth. Among its tasks are gathering economic and demographic data for business and government decision-making, and helping to set industrial standards.
Core facility that provides the following services: Illumina Gene Expression, Affymetrix gene expression. The Partners HealthCare Center for Personalized Genetic Medicine Microarray Facility is a full service facility dedicated to providing analysis for DNA or RNA samples. We provide support for high density microarrays to the Harvard Partners research community, including Harvard medical School, hospitals in the Partners Healthcare network, investigators in the Dana-Farber/Harvard Cancer Center, and the Harvard School of Public Health. Our services are open to both the PHS and non-PHS community.
Harvard Partners Research Computing Core
The Partners Research Computing Core was created by Enterprise Research Infrastructure & Services (ERIS) to offer dedicated services, consultation, and support within the teaching hospitals. Please check the service catalog as new services are added, or contact us if you need a consultation. Initial discussion is at no charge.
Core facility that provides the following services: Access to clinical physiology equipment. The Biobehavioral Core Laboratory houses the facilities for clinical exercise physiology and psycho-physiological research. The Clinical Exercise Physiology Research facility is equipped with a Cosmed Quark b2 metabolic cart and Cosmed electrocardiogram (ECG) equipment that is programmed into a Burdick Treadmill. This is used for performing graded exercise tests to assess risk for cardiovascular disease and functional work capacity training. An Ergoline 500 medical ergometer is used for exercise testing when a cycle ergometer is needed. In addition, the laboratory has 3 other treadmills that are used exercise intervention training programs. The Psychophysiology component consists of 3 computers (Dell Desktop Pentium 4, Gateway Pentium 4, and Toshiba Portege Tablet PC Pentium III). One desktop is used for data acquisition, one for data analysis and the third for internet usage. There is a surveillance camera (Security Labs) that is used to monitor participants as they take part in study tasks. To collect impedance cardiograph data, the HIC-2002 Impedance Cardiograph is used along with the COP ?Win 5.10 USB version cardiac output program for windows. This equipment is designed to measure a variety of cardiovascular measures (heart rate, stroke volume, cardiac output, pre-ejection period, left ventricular ejection time, total ejection period, and heather index). The Dinamap Vital Signs Monitor (Model 1846 SX) is used to assess systolic blood pressure and diastolic blood pressure. Lastly, a number of psychological tasks are also included in the lab such as the Automatic Mirror Tracer (Model 5403), the Peabody Picture Vocabulary Test (3 rd Edition Form IIIA and Form IIIB) and the Wisconsin Card Sorting Task for Windows.
The Biostatistics Core is a resource for Howard University Cancer Center (HUCC) that provides statistical and computer/data management support services to affiliated members. Members of the Biostatistics Core provide advice in matters of design, randomization, power analysis, data processing, quality control, database development and management and statistical analysis in clinical and population based studies. The Biostatistics Core aims at excellence in biostatistical and methodological issues related to cancer studies and to advocate proper use of statistics, data monitoring and data analysis.
Howard University Center for Computational Biology and Bioinformatics Core Facility
Laboratory of Molecular Computations and Bioinformatics
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core for bioinformatics consultation and software access. Laboratory of Molecular Computations and Bioinformatics (LMCB) is a resource facility dedicated to the support of computational biomedical research at Howard University. Provides molecular modeling, molecular dynamics, bioinformatics, and computational quantum chemistry capabilities and support to a variety of research projects at Howard University.
Core facility that provides the following services: SNP detection service, DNA sequencing service, EBV cell transformation service, DNA sequencer access. The molecular genetics research interests are in human population genetics, anthropological genetics, immunogenetics, and the genetics of complex diseases. Ultimate goals surround elucidating questions of human variation, the evolutionary history of genes within populations and how these gene histories are involved in the etiology of complex diseases. While the laboratory''s research goals have shared consequences for all humanity, specific interests focus on populations of African ancestry. Operational Objectives: 1. Develop a SNP database for mapping functional mutations linked to diseases common in African peoples. 2. Utilization of evolutionary history of candidate genes to identify polymorphisms that are associated with diseases. 3. Exploit the linkage disquilibrium generated by admixture in the African American population for gene mapping.
Penn/CHOP CTRC Informatics Services Core
Core facility that provides the following services: Informatics consultative support. The staff of this core gives guidance and/or coordinates data management, capture and analysis on behalf of the investigator within the Institute and assists more broadly with computing issues related to the approved protocol. This core provides services to investigators for their Clinical and Translational Research Center (CTRC)-approved studies that are utilizing other CTRC core services.
Howard Nanoscale Science and Engineering Facility
Howard Nanoscale Science and Engineering Facility (HNF) occupies a specially renovated wing on the first floor of the Engineering Building.The five large laboratories cover ~6000 sq. ft. of space and the HNF has about 2000 sq ft of contiguous office space. The HNF is an established centralized user facility containing over $17M of micro- and nano fabrication and characterization equipment, accessible by external and internal academic, government and industrial users. Currently, HNF has integrated facilities in the following categories: Lithography Facilities Nanofabrication Facilities Plasma Etching / Deposition Facilities CVD Deposition Facilities (SiC,GaN) Nanomembrane Facilities Characterization Facilities Computer Facilities Societal and Ethical Issues
Core facility that provides the following services: Equipment access, Training on proteomics equipment. Mission: To use mass spectrometry for studies of infectious and chronic diseases and to promote and facilitate biomedical and translational research at Howard University Objectives: To provide modern analytical instrumentation, technical expertise and essential services for biomolecular analysis To provide a broader training experience for students and faculty in biomolecular analysis through methodology- centered seminars, workshops, mini-courses, and internships To foster new multidisciplinary research collaborations using modern Proteomics technology The RCMI Proteomics Core Facility runs several research projects and provides collaborative consolidation of instrumentation, technical expertise, and support personnel to enhance the impact and availability of Mass Spectrometry and other analytical techniques for biological and biomedical science community at Howard University
Core facility that provides the following services: Bio-imaging instrumentation training, Bio-Imaging data analysis service. The Bio-Imaging facility currently provides optical and video microscopy services.The facility is equiped with two confocal microscopes, a Leica TCS SP2, and a Perkin Elmer UltraVIEW ERS Spinning Disc confocal . In addtion to confocal microscopy the facility is also equipped for bright field, phase contrast, modulation contrast and epi fluorescence microscopy. The facility has two separate wide field image analysis stations. A Nikon Optiphot microscope equipped with a color video system and Compix imaging software, and a Nikon Eclipse TE200 inverted scope. This inverted scope in specially configured to perform calcium ratio imaging is equipped with Molecular Devices Meta Fluor software The facility has recently expanded with the aquisition of a JEOL JEM-100C/CX Transmission Electron Microscope. The facility also is equiped with Typhoon 9410 scanner for the quantitation and localization of sub cellular fluorescent and radioactive molecules. In addition a Densitometer allows for the analysis of 1 and 2 D gels, Southern, northern and western blots and RFPL gels. The facility is also equipped with color and B&W laser printers for the production of publication quality graphics and presentation materials.
The Flow-Cytometry (FACS) facility is located on the ninth floor of the Hunter North building. This facility provides analyses of up to 7 parameters in eukaryotic cell populations and sorts cells under sterile conditions. These analyses can be used to identify and isolate rare cell populations, determine chromosome ploidy in individual cells, study apoptosis, and study cell-signaling among other applications.
RNASEQR-a streamlined and accurate RNA-seq sequence analysis program
A streamlined and accurate RNA-seq sequence analysis program.
Core facility that provides the following services: Single-crystal X-ray analysis. The mission of the CUNY X-ray Diffraction (X-ray) Facility is to perform single-crystal analyses for the structure determination of molecules, which make up a crystal. This technique is called single-crystal X-ray crystallography. It is the ultimate method for definitive determination of molecular structures at the atomic level for both organic and inorganic compounds. Its uses range from simple identification of compounds to various exotic configuration and conformational studies.
Joslin Diabetes Center Advanced Genomics and Genetics Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core that provides services for genetic and genomic analysis, including DNA extraction from blood, access to DNA collections from the Core?s repository, SNP genotyping, and support for gene expression studies based on both high-density oligonucleotide arrays and real-time quantitative PCR.
San Diego State University; California; USA
Public research university in San Diego, California. Founded in 1897 as San Diego Normal School, it is the third-oldest university in the 23-member California State University system.
Joslin Diabetes Center Advanced Microscopy Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core that provides services for performing specific morphological procedures, providing training and access to equipment, maintaining the specialized microscopes, and giving advice and interpretation.
Joslin Diabetes Center Animal Physiology Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core that provides technically advanced physiological evaluation of metabolism in diabetes, obesity, and their associated complications in rodents for DRC investigators and outside users. It also provides training of investigators and trainees in several physiological procedures.
Implements and maintains specialized computer facilities required by the DERC investigators. A major emphasis of JoslinResearch.org is to provide dynamic web applications that serve essential informational needs of the research community at the Joslin Diabetes Center. These applications provide such functions as automating media provisioning services to DERC laboratories, distributing DERC event schedule information, providing access to troubleshooting information, fully-searchable call schedules with contact information, text messaging services, and access to information about Section, Investigator and Fellow projects and affiliations. All applications adhere to the JoslinResearch.org paradigm of distributed administration without requiring knowledge of web design or web programming. For DERC use only.
Joslin Diabetes Center Flow Cytometry Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core that provides cell sorting and flow cytometry services. Specific services include cell analysis, large object sorting,magnetic cell enrichment, and automatic cell counting.
Core facility that provides the following services: Data management service, SNP genotyping service. The Genetics Core was established in 1991 with the aim of promoting and facilitating genetic studies of diabetes and its complications in humans at the Joslin Diabetes Center and collaborating institutions. More than 1,000 DNA samples from human subjects have been collected in these years and are available to researchers. The Genetics Core also provides services assisting investigators in the use of these samples. Investigators wishing to use the Core resources should contact Dr. Alessandro Doria by phone at x4340 or (617) 732-2406, or by e-mail. A detailed project description is required for the use of DNA samples. There is no restriction on the Core access.
A web-based application which predicts the impact of a SNP on putative microRNA targets.
The main objective of the Joslin''s Media Core is to reduce the cost and labor of making tissue culture media and other reagents required by the Joslin investigators. By centralizing preparation of these reagents, the Core provides high quality reagents at a significantly reduced cost to the investigators. In addition, the Core provides services to overcome labor intensive reagent needs, like plate pouring services and preparation of specialized buffers and reagents for cell and molecular studies. The Media Core makes and provides over 10 different mammalian tissue culture media to the Joslin investigators for their studies. In addition, the Core prepares and provides several buffers and solutions to the Joslin investigators. The core also makes a variety of broths and agars for growing bacterial cultures, and provides agar plates and plate pouring service to the investigators. Over the past five years (2006-2010), by preparing and providing over 6250 liters of media and 2850 agar plates per year to the Joslin investigators the Media Core serves an important function in the efforts of these investigator to find cure for diabetes and its complications.
Joslin Diabets Center Proteomics Core Facility
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 24, 2019. Core provides the following services: Trypsinization service. Core provides a full range of services to the Joslin research community spanning from consulting on proteomic experimental design to data acquisition and analysis. The core operates a high throughput nano liquid chromatography, nanospray ionization, LTQ 2D ion trap tandem mass spectrometer system. This system is used for two routine proteomic services, including Targeted Protein Analysis and Protein Inventory. Targeted Protein Analysis is used to identify and provide in depth characterization, including phosphorylation site mapping, of proteins isolate by SDS-PAGE. Protein Inventory is used to catalogue the protein composition in a sample separated by 1D SDS-PAGE. This service provides information on protein identification, molecular weight (gel mobility), and spectral/peptide counts, a semi-quantitative measure of protein abundance. In addition, the Core works with investigators on specialized analyses involving tandem mass spectrometry, including specialized enzymatic digests (peptide preparation), selective reaction monitoring (SRM), and targeted peptide detection. The Proteomic Core provides in house database resources and analysis tools and also coordinates with Joslin's Bioinformatics Core to provide further assistance with data organization and interpretation. The Core hosts seminars on proteomic topics and provides instruction on practical and theoretical aspects of mass spectrometry-based proteomics.
Core facility that provides the following services: Hematology/immunology assay service. The major objective of the Specialized Assay Core is to create greater efficiency by providing radioimmunoassays (RIAs), enzyme-linked immnosorbent assays (ELISA), bead based multiplex assays, and other basic biochemical assays to support human and animal studies performed by individual investigators at the Joslin Diabetes Center and external users who do not have access to Core Facilities. The Core allows more economic use of expensive or limited materials, provides for training of junior investigators, fosters interactions among research fellows and provides a basis for generating productive collaborative studies between institutions.
Core facility that provides the following services: Spectrofluorometry service, FTIR service, Atomic absorption spectrometry service, Raman spectrometry service, Gas chromatography service, GC/MS service, HPLC service, LC/MS/MS service, Capillary electrophoresis/mass spectrometry service, FPLC service. The Analytical Core Laboratory objectives are to: 1) provide spectroscopic and chromatographic equipment to investigators of pilot projects in the RCMI Program as well as investigators in other programs in the College of Science, Engineering and Technology for their research needs, 2) to acquire new analytical instruments as well as computers and printers to satisfy the needs of the user community, 3) to respond to the needs for obtaining analytical information in a timely manner, 4) To offer workshops for using major equipment including LC/MS/MS, CE/MS/MS, LC-ICP/MS, Raman microscope system, and FT-IR as well as other conventional instruments at least once each semester for each instrument.
Core facility that provides the following services: Animal husbandry service. The Animal Care Facility (ACF) is one of the essential units of support and service to the biomedical research at Jackson State University. Its long term goal is to develop a state-of-the-art infrastructure as well as to provide technical and logistic support to RCMI investigators and other JSU faculty and students to conduct a high quality of animal research, in compliance with the guidelines and policies set for by accrediting and regulatory agencies, especially as they relate to IACUC protocol development, animal husbandry, food and water supply, veterinary care, quarantine and euthanasia, sanitation procedures, environmental monitoring, and record keeping. ACF provides accommodation for long-term storage of animals and maintains them in accordance with and in compliance with the PHS Policy on the Humane Care and Use of Laboratory Animals and the Animal Welfare Act, as described in the 2002 Guide for the Care and Use of Laboratory Animals.
Core facility that provides the following services: Flow cytometric analysis and cell sorting. The cell sorting and analysis lab provides access to the most sophisticated flow cytometers presently available. The core is able to analyze and physically separate cells based upon features detectable with fluorescently labeled monoclonal antibodies. This facilities has two locations: the Simches site and the Charlestown Navy Yard (CNY) site.
JSU BSU-RCMI Biostatistics Core Laboratory
Core facility that provides the following services: Statistical design and analysis. Applied statistical methodologies and data analysis techniques are critical under-girding factors in research and knowledge advancement. Appropriate experimental design lays foundation of sound research plans; sample size determines the power of significance and efficient utilization of scarce resources; and adequate data analysis generate results that are valid and true representative of the population in question. The Biostatistical Support Unit (BSU) provides statistical services and research support to RCMI investigators, other faculty, as well as to graduate and undergraduate students.(http://www.jsums.edu/cset/rcmi/bsu.htm)
JSU Cellomics and Toxicogenomics Research Core Laboratory
Core facility that provides the following services: Flow cytometry and microarray training service. The Cellomics and Toxicogenomics Research Laboratory (CTRL) has been established to provide RCMI investigators and other JSU faculty and students with state-of-the art instrumentation that would allow them to perform laser-based flow cytometric analysis and cell sorting, as well as microarray analysis of gene expression in connection to human diseases. Hence, the application of flow cytometry and modern genomic DNA microarray-based technology is providing an excellent opportunity to CTRL users to examine alterations in gene expression patterns associated with environmental exposure, as well as to study the molecular mechanisms and biochemical effects associated with cellular responses to toxic exposures.(http://www.jsums.edu/cset/rcmi/ctrl.htm)
Jacksonville State University Center for Bioinformatics and Computational Biology
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 18, 2022. Goal of the center is to translatate high biological data into solutions for health, agriculture and the environment The objectives of the center are to conduct research in bioinformatics and computational biology with translational endpoints and train students to become leaders in bioinformatics and computational biology.
JSU Computational Modeling Core Laboratory
Core facility that provides the following services: Computational access service. The Computational Modeling Core is part of the CREST Interdisclipinary Center for Nanotoxicity, aka the Center for Applied Computational Sciences.
Core facility that provides the following services: Nanoindenter strain test service, UTM strain test service, Topography transmission electron microscopy service, Topography environmental scanning electron microscope service, Electron microscopy sample preparation service. The specific aims of the Electron Microscope Core Laboratory are: To provide investigators with access to microscopy instruments necessary for ultrastructural research in all the STEM areas; to train faculty, staff, and students on relevant methods in ultrastructural research; to help faculty, staff, and students on relevant approaches to address research questions involving morphological characterization; to improve JSU competitiveness in the innovative field of electron microscopy-based research.
JSU Molecular Magnetic Resonance Core Laboratory
Core facility that provides the following services: Electron paramagnetic resonance (EPR) spectroscopy service. The specific aims of the MMR are to: 1. Provide high field FT-NMR spectrometers for all RCMI investigators and other researchers who need structural determination tools in their research. High field NMR spectrometers are key instruments in organic chemistry including biomedical and environmental research. Two high field FT-NMR spectrometers in the MMR Core Facility are made available for JSU researchers and off-campus users. 2. To offer technical support to users who need to apply NMR technology in their research but lack expertise. The sophisticated technology in NMR spectroscopy will be available for organic chemists as well as novice users and researchers from the biomedical and environmental areas. The MMR Core facility will host numerous workshops for new users including faculty and new graduate students.
Core facility that provides the following services: Mass spectrometry services. The mission of Proteomics Core Facility is to help researchers advance their biomedical research programs. The Facility is equipped with gel electrophoresis units, image analyzers and digitizers, and robotics for mass spectrometry sample preparation. Currently, a Matrix-Assisted Laser Desorption/Ionization Mass Spectrometer instrument implements protein identification. The various applications include the studies of protein expression profile, posttranslational modifications, and partial sequencing of novel proteins. The staff also consult with researchers about their particular research interests and assist with the development of specific applications and solution to problems.
Core facility that provides the following services: Tissue procurement, Quality assurance/histopathologic review, Biospecimen storage. The Louisiana Cancer Research Consortium (LCRC) Tissue Procurement and Biospecimen Core Facility (TPBCF) is a part of the infrastructure to support the conduct of basic and clinical research for members of the LCRC. The goal of the repository is to support LCRC programmatic research in order to further improve our understanding of those molecular factors that contribute to cancer and that may lead to prevention, early detection, and cure. The mission of the Biospecimen Core is to collect high quality samples of normal and diseased human material (e.g., whole blood, cellular blood components, plasma, urine, body fluids, DNA, and tumor tissue and cells) with appropriate clinical data and to make this material available to qualified researchers at Louisiana Cancer Research Consortium while ensuring the informed consent, safety, donor anonymity, and all regulatory safeguards are in place.
JSU Molecular and Cellular Biology Core Laboratory
Core facility that provides the following services: Genomics service, Proteomics services, Functional assays service, Cell culture services, Stress enzyme analysis. The specific aims of the MCB Core Laboratory are: To provide a variety of services and technical support in molecular biology and DNA technology by offering equipment access, expert advice, demonstration of techniques, operation of equipment, participation in discussion and data interpretation, and hands-on-training in molecular biology and cell culture; to increase faculty training in recombinant DNA technology to strengthen faculty development and technology transfer; to provide a research environment and instrumentation for investigators to pursue biomedical research opportunities and enhance overall research productivity; to foster collaborative research relationships among RCMI investigators and other MCB core users at JSU and other research intensive institutions.
JSU RCMI Translational Research Data Coordinating Center
Core facility that provides the following services: Statistical design and analysis, Data collection and management service. The mission of the Research Centers in Minority Institutions Translational Research Network (RTRN) Data Coordinating Center (DCC)is to provide the technology infrastructure and data management resources to facilitate inter-institutional collaborations, including community engagement, information and data sharing, and dissemination across the diverse RCMI communities to improve health outcomes, especially for underserved populations.
The Visualization Core Laboratory / GIS Remote Core Laboratories were established to bond existing capabilities and talents in the areas of Geographic Information Systems (GIS), Remote Sensing (RS) and Scientific Visualization (Sci-Viz) and co-locate them in a centralized facility. This created an infrastructure of technology, data, people and institutional linkages that enables the discovery, evaluation and application of geospatial and visual data for adding value to research across various areas and disciplines. The GIS/RS laboratories support the development, enhancement and transfer of GIS/RS applications, make geospatial data available and accessible and promote research and development innovation among users. The Sci-Viz laboratory supports the need of scientists and researchers relative to modeling, program application development and production of high quality advanced visualizations for all fields or disciplines. The TLGVRC addresses human resource development to ensure a skilled workforce which is vital for sustenance of any high level technology activity.
Core facility that provides the following services: Equipment access. Jackson State University Visualization Laboratory is part of the Trent Lott Geospatial and Visualization Research Center (TLGVRC). It is a research laboratory specializing in virtual reality and real-time interactive computer graphics. The mission of the visualization laboratory is to ensure highly advanced technical and theoretical visualization support to scientific research. Our goal is to provide a well-integrated and diverse scientific visualization knowledge and tools to the students, staff, and faculty.
Core facility that provides the following services: DNA Synthesis Service. The DNA Synthesis Lab serves the research community with custom oligonucleotides. The lab is capable of high-throughput standard, degenerate and modified oligo synthesis.
Sapienza University of Rome; Rome; Italy
Research university that is located in Rome, Italy.
The JHS is the largest single-site longitudinal, population-based, cohort study of 5,302 persons initiated in the fall of 2000 to prospectively investigate the determinants of CVD among African Americans in the Jackson, MS metropolitan statistical area. The JHS investigates the various genotype and phenotype factors that affect high blood pressure, heart disease, strokes, diabetes and other important diseases in African Americans. The primary objective of the Jackson Heart Study is to investigate the causes of cardiovascular disease (CVD) in African Americans to learn how to best prevent this group of diseases in the future. More specific objectives include: 1. Identification of factors, which influence the development, and worsening of CVD in African Americans, with an emphasis on manifestations related to high blood pressure (such as remodeling of the left ventricle of the heart, coronary artery disease, heart failure, stroke and disorders affecting the blood vessels of the kidney). 2. Building research capabilities in minority institutions at the undergraduate and graduate level by developing partnerships between minority and majority institutions and enhancing participation of minority investigators in large-scale epidemiologic studies. 3. Attracting minority students to and preparing them for careers in health sciences.
Core facility that provides the following services: Colony Forming Unit (CFU) Assay, Differentiation assays. Core purpose: To propagate, expand and supply high quality samples of normal mesenchymal stem cells (MSCs) from in vitro cultures with appropriate quality control assurances for use by LCRC investigators who are studying any aspect of MSCs in relationship to cancer.
A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.
LCRC Cell Analysis and Immunology Core Facility
XULA Cell Analysis & Immunology Core Facility
Core facility that provides the following services: FACS service, Flow cytometry analysis service, Data archival. The Cell Analysis & Immunology Core Facility is a customer oriented service dedicated to supporting the research needs of the investigators of the Louisiana Cancer Research Consortium (LCRC). It provides state-of-art instrumentation and expertise for addressing experimental issues related to single cells, nuclei and chromosomes. In addition to instrumentation, the Facility intends to collaborate with the investigators and contribute to all aspects of the research process. This includes consultation in experimental design, technical assistance in the operation of instruments, trouble shooting, data analysis and storage, interpretation of results and preparation and production of presentation graphics. The Facility is also communicating with investigators in other institutions and is devoted to introducing and developing new applications on our flow cytometers. In this way, investigators are provided with unlimited possibilities to answer questions regarding nature and function of cells by flow cytometry.
Core facility that provides the following services: Automated DNA sequencing, Quantitative real-time PCR, Genotyping service, Liquid handling service. The Genomics Core Facility is a core resource of LSU Health Science Center, sponsored jointly by the Cancer Center and Genetics Center. The Facility is committed to providing quality service by fulfilling the needs of the research community in a consistently rapid, dependable, and economical fashion. Services include automated DNA sequencing, using state-of-the-art instrumentation (ABI PRISM 3130XL Genetic Analyzers) and the latest protocols to ensure high quality results at reseasonable prices. The Facility also houses an ABI Prism 7900 HT (a high through-put real-time PCR system) and a Biomek2000 liquid handling robot.
Core facility that provides the following services: Probe hybridization, Microarray data analysis. In December 2000, the LSUHSC Program in Gene Therapy in conjunction with the Louisiana Gene Therapy Research Consortium created the Microarray Core to cater to the growing needs of investigators who wanted to perform expression studies. Since that time, our core has helped researchers from around the world process over 3000 samples, resulting in numerous peer-reviewed scientific publications.
Core facility that provides the following services: Microscopy, Imaging, and Analysis, Routine Histopathology, Specialized Histopathology. The purpose of this core laboratory is to assist investigators requiring detection, imaging, and morphometric analysis of gene and protein expression in any type of cell and tissue. Services, expertise and state-of -the-art biomedical imaging services will be provided with the hope of broadening and streamlining all morphological research.
Layton Aging and Alzheimers Disease Center Education Core
Layton Aging & Alzheimer''s Disease Center Education Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5th,2022. The Education and Information Core of the Layton Aging & Alzheimer?s Disease Center develops and carries out a wide range of educational programs to: * Increase public awareness and understanding of Alzheimer''s Disease research, * Aid in the recruitment of subjects for research studies, and * Improve care and quality of life for persons with dementia and support their family caregivers. Our educational activities include: * Training for health care professionals which include seminars and lectures and we also provide ?hands-on? experiences for medical students, * Community education on Alzheimer''s disease and related dementia disorders, * Workshops on doctor ? patient communication for families and caregivers, * Collaboration with community organizations and groups to promote awareness of the disease and publicize research activities, a particular focus is underserved populations including rural communities and minority groups, * Collaboration with other organizations that serve patients and families, e.g., the Alzheimer?s Association and other state and local agencies that serve the elderly and the loved ones who care for them, and * Distribution of printed material that provides topical information on a variety of subjects related to Alzheimer?s disease and dementia and how best to provide quality of life to those with the disease. * A newsletter, Aging & Alzheimer''s Update, which is published twice per year. The Education Core administers the Oregon Income Tax Check-off Alzheimer''s Research Fund in collaboration with The Oregon Partnership for Alzheimer''s Research, a community advisory committee.
Msbind - Accessibility of microRNA binding sites in meta-stable RNA secondary structures in the presence of SNPs
Software tool that calculates features of meta-stable RNA secondary structure target sites.
Layton Alzheimers Disease Center Biomarkers and Genetics Core Lab
Layton Alzheimer''s Disease Center Biomarkers & Genetics Core Lab
In cooperation with the Data and Clinical Cores at the Layton Center, the Biomarkers and Genetics Core generates and maintains biomarker data for select biomarkers which have established roles in the characterization of subjects with or at risk of dementia. Biological markers of brain aging, dementia risk, and neurodegeneration have the potential to accelerate the identification of disease mechanisms and treatment strategies. Biomarkers may include genes, proteins, or other metabolites, and may be identified in DNA, cerebrospinal fluid (CSF), or plasma. Apolipoprotein E (APOE) genotype is generated for all research subjects. Sub-groups of subjects have other types of biomarker data. Many subjects have had genome-wide SNP data generated. In order to foster collaborative research as well as expand resources and expertise, samples (DNA, CSF, and plasma) and data are distributed to qualified investigators worldwide. Most of these researchers are pursuing the causes and modifiers of dementia. Data and samples are collected from well characterized research subjects including the healthy elderly and dementia patients.
Layton Alzheimers Disease Center Clinical Core
Layton Alzheimer''s Disease Center Clinical Core
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on December 6th,2022. The Oregon Alzheimer?s Disease Center?s (OADC) Clinical Core program, directed by Dr. Jeffrey Kaye, performs longitudinal studies of the natural history of brain aging and Alzheimer''s disease in patients and healthy control volunteers. These studies which are performed through standardized neurological, neuro-psychological, and brain-imaging assessments are carried out in the Alzheimer''s Disease and Memory Assessment Clinics as well as through community-based assessments conducted in the homes of study volunteers. The Layton Center Neuroimaging Lab conducts brain-imaging MRI brain scans to assist in diagnosis of brain disease. Typically, MRI images are taken from three different planes. These planes are known as the coronal plane, sagittal plane and the axial plane. Each series of MRI images is named after the plane from which they were obtained. The Clinical Core?s research is focused on preclinical and early Alzheimer?s disease (AD) yet is also poised to participate in other relevant new research as it arises. The OADC Clinical Core recruits, assesses and follows individuals from population groups at high risk for dementia such as: the healthy ?oldest old?, subjects with family history of AD, and subjects with Mild Cognitive Impairment (MCI). Research with underserved populations The Oregon Alzheimer?s Disease Center also maintains two Satellite programs to enhance understanding of underserved populations: The Klamath Exceptional Aging Project (KEAP) is a community-based study of brain aging being conducted in Klamath Falls. The African American Dementia and Aging Project (AADAPt) s a Portland-based cohort of 100 African American seniors.
The Biostatistics Center provides support to MGH investigators, as well as serving as a Coordinating Center for several NIH-supported projects. The Center''s staff includes biostatisticians, physicians, research nurses, data managers, project managers, research assistants, and computing staff.
Core facility that provides the following services: 96-well plasmid preparation service. The Center for Computational and Integrative Biology (CCIB) Automation Core provides the greater Partners research community with high-throughput automation services as well as special automation project design and implementation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Core facility that provides the following services: DNA sequencing service, High volume DNA sequencing, Plasmid verification and primer walking service, PCR purification service, Microsatellite analysis. The DNA Sequencing Core at the Massachusetts General Hospital functions both as a small-scale sequencing facility and a high-throughput center for large-scale sequencing projects.
MGH CHGR Chromosome Substitution Strain Resource
Core facility that provides the following services: Breeding pair service, Mouse Phenotyping Services. This resource provides to MGH investigators a local source of breeding pairs of the 22 chromosome substitution strains (CSS)* of mice and access to basic phenotyping equipment for mapping of simple or complex traits, to promote the use of genetic mouse-based strategies in basic and clinical research. The CSS Resource comprises 22 mouse lines, each homozygous for a single A/J chromosome (Chr 1-19, X or Y and mitochondria) on a genetic background that is otherwise C57BL/J that were generated by Dr. Joseph Nadeau (Case Western Reserve University) and his colleagues. The CSS mice are available from The Jackson Laboratories. However, to save time and money, the MGH CSS Resource maintains CSS breeding colonies that are housed in the Simches-8 barrier facility, adjacent to a procedure room that will have equipment for basic standardized phenotyping, including behavioral and metabolic measurements.
MGH CHGR Clinical Genetic Research Facility
The Clinical Genetic Research Facility (CGRF) offers clinical investigators a convenient, modern research-dedicated facility for outpatient studies involving genetics. Our outpatient exam rooms and phlebotomy rooms are fully equipped and offer investigators an experienced medical assistant to facilitate the visit. Since the CGRF?s primary mission is to support and promote genetic clinical research, the facility?s investigators performing genetic studies supported by non-commercial sponsors are given priority. The CGRF also considers genetic studies sponsored by industry, as well as studies without a genetic component, on a space-available basis.
MGH CHGR DNA and Tissue Culture Resource
Core facility that provides the following services: DNA extraction from blood and cell lines. This facility provides processing of cell lines, human blood and tissue samples for DNA, plasma and buffy coat storage and for initiation of lymphoblast and fibroblast cell lines in furtherance of the CHGR mission to promote the use of genetic strategies in basic and clinical research.
Core facility that provides the following services: Custom mutation detection and DNA sequencing services, Custom genotyping service. This resource provides custom genotyping (microsatellite, SNP, other) in human and mouse, mutation detection/DNA sequencing, dosage analysis and related services to further the CHGR mission of promoting the use of genetic strategies in basic and clinical research.
Core facility that provides the following services: Fresh hepatocytes in suspension, Plated hepatocytes, Cryopreserved hepatocytes, Custom hepatocyte isolations, Decellularized whole rat livers. The mission of the Cell Resource Core (CRC) is to provide high quality primary cells and tissues to researchers reliably and affordably. Leveraging a new MGH technology that significantly increases the viable yield of high quality hepatocytes from human and animal donor livers, we are initially offering hepatocytes to the research community.
Core facility that provides the following services: Double- and triple-labeling experiments, Acquisition of high-resolution images: 2048 x 2048 pixels, Single molecule visualization, allowing dynamic observation and functional analyses of both in vivo and living cells, Total internal reflection fluorescence experiments (TIRF). This Core consists of a Zeiss LSM 5 Pascal laser confocal microscope with a Zeiss RGB vario laser module and Nikon C1 Confocal/TIRF System with 3 PMT. A Zeiss Axiovert 200 fully motorized light microscope is available with fluorescence, bright-field, phase-contrast and Nomarski (DIC) capabilities. Image acquisition and analyses are performed using Zeiss LSM 5 Pascal Confocal Microscopy Software (Release 3.2) on 2 workstations. Zeiss Physiology software is available also. Live cell imaging is available using a Zeiss temperature controller with custom chamber and heating stage. The Nikon C1 Confocal/TIRF System fully motorized Nikon Eclipse Ti microscope is available with fluorescence, bright-field and TIRF capabilities. Imaging acquisition and analyses are performed using EZ-C1 and NIC-Elements Software.
Puerto Rico Clinical and Translational Research Consortium Core Laboratory
The core laboratory facility has the necessary equipment to provide each study with the initial specimen processing and handling required for shipping to a reference laboratory and for storage and maintenance at a sample repository. Laboratory procedures provided by the core laboratory are intended for research use only,and not for diagnostic; it may provide other specialized services for specific protocols on a case by case basis.
MGH HSCI-CRM Flow Cytometry Core Facility
HSCI-CRM Flow Cytometry Core Facility at MGH
Core facility that provides the following services: Offline assisted or self-performed analysis. The HSCI-CRM Flow Cytometry Core Facility seeks to provide high quality, accessible cytometry sorting and analysis services to laboratories in the Center for Regenerative Medicine, Harvard Stem Cell Institute, and MGH research communities at an affordable rate. The Core''s equipment and highly trained operators provide an advanced level of sorting and analysis services to its investigators. Additionally, the Core is dedicated to training users on all aspects of flow cytometry, including practical issues, information about specific applications, and critical interpretation of sorting results. The Core''s three full-time staff members strive to ensure that each investigator''s visit benefits their individual experiments to the greatest extent possible. To ensure the best availability to all users, the Core offers an online scheduling system, and provides extended sorting hours until late evening. HSCI faculty have reduced pricing for use of the Core''s services.
MGH High Resolution Peripheral Quantitative Computed Tomography Core Facility
Core facility that provides the following services: 3D Imaging, Normative data comparison, Scan review. The High Resolution Peripheral Quantitative Computed Tomography (HR-pQCT) Core Facility offers measurements of the microscopic internal structure of cortical and trabecular bone in the distal radius and tibia. Additionally, the HR-pQCT Core Facility offers Finite Element Analysis to estimate key biomechanical properties of the bone including failure load and stiffness. By scanning the distal radius and tibia, the HR-pQCT Core can measure a variety of important parameters reflecting the integrity or cortical and trabecular bone. This information cannot be determined using standard clinical imaging techniques such as dual-energy x-ray absorptiometry (DXA). A scanning appointment is a 30 minute addition to a clinical research visit and involves less radiation exposure than traditional bone densitometry. With applications for both cross-sectional and longitudinal research, investigators have employed our facilities and expertise to study a variety of bone-related diseases with participants ranging in age from children to the elderly. The goal of the HR-pQCT Core is to provide facilities and personnel on a per study basis, allowing investigators access to important information about bone structure and function without requiring special expertise and equipment. Getting Started: To begin organizing a cohort for HR-pQCT studies or to inquire further, please contact the Core Director, Dr. Joel Finkelstein.
Core facility that provides the following services: 4.7T/7T MRI, PET-CT, SPECT, FMT, BLI, Animal housing service, Multimodality imaging and image fusion, Quantitative image analysis and processing, Animal surgical services, Radiochemistry, Histopathology, Data Management, In vivo confocal microscopy. The Mouse Imaging Program (MIP) at the Center for Systems Biology is a uniquely integrated imaging resource providing the larger Harvard/MIT research community with access to state-of-the-art in vivo imaging technologies. The program offers magnetic resonance imaging (MRI), positron emission tomography (PET-CT), single photon emission computed tomography (SPECT-CT), computed tomography (CT), bioluminescence (BLI), fluorescence mediated tomography (FMT), and various other fluorescence imaging technologies. The fully integrated program also provides mouse holding facilities for serial imaging, surgery, anesthesia and veterinary care. Image reconstruction, 3D display, fusion, quantitative image analysis and online data access are also available. The program performs its own research, aimed at continuously improving existing imaging technologies and has deep knowledge of cardiovascular, oncology and neurological mouse models of disease. A list of publications made possible by utilizing MIP resources is available on the Program web site. Imaging requests may be submitted through the MIP website.
MGH Musculoskeletal Imaging Research Core
Core facility that provides the following services: Magnetic Resonance Spectroscopy Service, Magnetic Resonance Imaging Service. The Musculoskeletal Imaging Research Core (MIRC) offers specialized imaging techniques including quantitative computed tomography (QCT), magnetic resonance (MR) spectroscopy of muscle and high-resolution soft tissue MR imaging. QCT is a technique widely employed for studies evaluating body composition and bone mineral density. MR spectroscopy is a technique that allows non-invasive quantification of metabolites in human tissues.
Core facility that provides the following services: Synthesis of Radiopharmaceuticals for PET, PET scanning/imaging service. The PET Core Laboratory provides a full range of technical and professional services for the design and execution of programs using Positron Emission Tomography (PET). The PET Core Facility provides the required facilities and personnel on a per study basis to allow investigators to use PET without requiring them to acquire the needed special expertise and equipment.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 30, 2023. Core facility that provides the following services: Microscopy consultation services, Technical microscopy service, Microscopy training services, Conventional immunofluorescence microscopy service, Confocal microscopy service, Live-cell imaging service, Conventional electron microscopy service, EM immunogold labeling service, Tissue sectioning service, Tissue fixation, Computer based image analysis and quantification.
Core facility that provides the following services: Fragment (microsatellite) analysis service, Enumeration of polymorphisms (SNPs), DNA sequencing. The DNA Sequencing Lab is the longest-established lab in the Gene Profiling Core, providing DNA sequence analysis to investigators involved in research utilizing molecular biology techniques. The lab uses capillary electrophoresis sequencing technology and is built around the ABI 3130xl Gene Analyzer (16-capillary) and associated software for DNA sequence analysis.
Core facility that provides the following services: Gene variations analysis, Genotyping service. The Human Genotyping Lab assists investigators to apply the genomic technologies to population-based research. The strategic plan is to create a link between basic science, clinical investigation and population-based research by integrating genomic sciences into our research program. The central hypothesis is that health disparities are related in part to ethnicity-specific DNA variants in critical genes that influence the susceptibility to common diseases. Morehouse School of Medicine has a longstanding interest on the studies of ethnic disparities and a longstanding strength on community outreach to underserved minority populations. Accordingly, the major objective of the MSM Human Genome Core Laboratory is to enhance the research capacity on these sample cohorts and upgrade our research to the molecular genetic level based on cutting-edge genomic technologies.
MGH Recombinant Protein Expression and Purification Core
Core facility that provides the following services: Recombinant protein expression and purification in yeast Pichia pastoris, Large-scale production of immunotoxins for cell depletion studies, Large scale production of recombinant cytokines, Cost effective small-scale production using E.coli system. The Recombinant Protein Expression and Purification (RPrEP) Core was established in 2009 to provide a cost-effective resource to the MGH and DF/ HCC community for expression and purification of recombinant proteins necessary for pre-clinical studies as well as for basic mechanistic studies by immunologists and cancer biologists. Recombinant Proteins can be manufactured by this Core for a variety of applications according to MGH-DF/ HCC investigator needs. In addition to large-scale production of recombinant proteins in yeast Pichia pastoris, a cost effective small-scale production service will be provided using E.coli or yeast Pichia pastoris expression system (e.g. for small animal studies, use as immunogens, ELISAs, or high throughput microarray platforms).
MGH Transgenic and Gene Targeting Facility
Core facility that provides the following services: Sperm Cryoperservation - Standard Mouse Backgrounds; including quality test (QC), 129 or Hybrid ES Cell transfection package for conventional or BAC vector (from DNA transfection to DNA preparation) ~200 colonies, C57BL/6 (JM8A) ES Cell transfection package for conventional or BAC vector (from DNA transfection to DNA preparation) ~200 colonies, Microinjection of one targeted 129, JM8A, or hybrid ES Cell clone, Microinjection of one targeted C57BL/6 (JM8 & others) ES Cell clone, Transgenic / DNA pronuclear Microinjection, Transgenic/ BAC DNA pronuclear Microinjection to hybrid mouse strain, Mice colony breeding, Mice ID tag & tail biopsy, Mice tail DNA preparation, Sperm Cryoperservation - Non-Standard Mouse Backgrounds; including quality test(QC), Recovery live born pups for testing following QC, IVF recovery of one mouse line from cryopreserved sperm for most strains (~10 pups provided), Recovery of cryopreserved mice embryos (up to 80 embryos), Special DNA Prep. The MGH Transgenic and Gene Targeting Facility generates transgenic and knockout or knock-in mice to study gene function in embryonic stem cell and somatic cell systems. Services include: microinjection of DNA into fertilized embryos for the creation of transgenic mice, transfection of DNA into ES cells for the generation of recombinant ES cell clones, injection of gene-targeted ES cell clones into host blastocysts for the generation of gene knockout or knock-in mice, and other related ES cell based services. The facility is also equipped to perform in vitro fertilization projects, cryopreservation of mouse sperm and embryos, recovery of cryopreserved mouse sperm and embryos, and derivation of ES cell lines from a variety of genetic backgrounds. The facility provides consultation within reason on experimental design and vectors for gene targeting-related projects. The facility can also provide advice for the preparation of DNA, recombinant ES clones, mouse genotyping, handling and husbandry. The facility supports innovative and experimental approaches involving transgenic and knockout or knock-in mice to better help investigators study gene regulation and function, and develop appropriate animal models to study human genetic disorders.
MSM Analytical Chemistry and Protein Profiling Core
MSM Analytical Chemistry & Protein Profiling Core
The Analytical Chemistry and Protein Profiling Core is comprised of three primary labs: * Analytical Chemistry * Protein Profiling/2D Gel * 2D Gel Electrophoresis Lab
Morehouse School of Medicine Biomedical Informatics Unit
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 25, 2019. Core focuses on integration of MSM and affiliated health information systems into an interoperable repository. The long-term goal is to establish an integrated standards-based informatics platform to support MSM clinical and translational research investigators in their own work and in sharing research information with collaborators and other investigators in parallel fields.
MSM Center of Laboratory Animal Resources
Core facility that provides the following services: Basic animal care service, Clinical and health monitoring service, Humane euthanasia service, Animal disposal service, Animal quarantine service, Necropsy and diagnostics service, Animal vaccination service, Animal use consultation service, Breeding service, Animal sample collection service, Assistance with minor surgery, Animal tattooing service. Access to CLAR facilities is restricted to authorized investigators with CLAR and IACUC approval. No individuals may enter the facilities without this CLAR/IACUC authorization. Since its inception, the Center for Laboratory Animal Resources (CLAR) has centralized most research and teaching animal care for the Atlanta University Center consortium. Our purpose is to provide total animal care services as needed to all academic and/or research faculty and staff affiliated with any one of the member institutions of the Atlanta University Center (AUC).
Core facility that provides the following services: Lab animal technician services, Animal husbandry service. The Mission of the Animal Resources Center is to provide healthy animals for use in IACUC-approved research, educational and testing protocols at Montana State University,ensure that University research animals are cared for in a humane and appropriate manner by the provision of modern, well maintained facilities, trained personnel, technical support, veterinary care and monitoring of animal care and use, provide resources, technical assistance, and information for University researchers and educators in meeting the requirements of animal-related protocols, and ensure observance of ethical standards and federal regulations pertaining to the care and use of animals for research, education and testing at Montana State University.
Montana State University Bioinformatics Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research.
Core facility that provides the following services: Assisted support, Equipment access, Cell sorting. Laboratory performs fluorescence cytometry services related to Immunology, Infectious Disease, and Immunostimulatory Compounds.
Montana State University Functional Genomics Core Facility
Core provides instrumentation and support for academic investigators throughout Montana and Rocky Mountain west. For most instrumentation, facility provides instruction and supervision followed by independent user access. For those doing Affymetrix microarrays, facility can also accept RNA samples and provides full service processing. Assists with experimental planning and grantmanship phases.
MSU Imaging and Chemical Analysis Core Laboratory
Core facility that provides the following services: ToF-SIMS service, X-ray photoelectron spectroscopy, Field emission scanning electron microscopy, Scanning electron microscopy, Epifluorescence microscopy. Laboratory performs services related to Nanoscale Imaging, Microbial Adhesion, Force Spectroscopy, Nano Elasticity, Bioprobe Development Surface Functionalization, Laser-Activated Atom Migration, Nano Lithography. Biosafety Level-2 Certified.
Core facility that provides the following services: Tissue harvest, Inoculation, Surgery, Large research animal husbandry. The MSU Large Animal BSL-2 is a specially designed facility providing research space to house larger research animals (<400 lbs) with BSL-2 containment for immunology and infectious disease experiments.
Core facility that provides the following services: NMR-based metabolite profiling, MS-based metabolite profiling service. Lab performs services related to Metabolomics and Metabolite Profiling.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 22, 2025. Core facility that provides the following services: Microscopy facility training and access. The Center for Biofilm Engineering Microscopy Facility is a research-only facility on the MSU campus, located on the third floor of the EPS building. The Microscopy Facilities Manager trains and assists faculty, research staff and students with capturing images of samples via optical microscopy and fluorescent confocal microscopy. The microscopy facilities include three separate laboratories - the Optical Microscopy Lab, the Confocal Microscopy Lab, and the Microscope Resource Room and Digital Imaging Lab. Large inventory of fluorescent stains. Inquire for availability, applications and collaborations.
Core facility that provides the following services: MicrOTOF (access), GCMS (access), MALDI (access), XCT ion trap (access), MicrOTOF high resolution (facility run), MicrOTOF low res (facility run), MALDI (facility run), GCMS (facility run), HPLC-micrOTOF (facility run), 2-D gel (access), 2-D gel (facility run). The mission of the Mass Spectrometry and Proteomics Facility is to seed mass spectrometry and proteomics technology to research labs at Montana State University and affiliated programs.
Core facility that provides the following services: Data management solutions, Managed server hosting, Storage and computation, Software development, IT consulting and training. Researchers face increasing challenges managing IT infrastructure. From software and servers, to data storage and back-ups, the Research Computing Group (RCG) is here to help you with all your IT needs as a researcher at MSU. We have the expertise to provide infrastructure for projects ranging from large-scale computation and storage to small-scale hosting. Contact us to find out how we can help you.
MSU Transmission Electron Microscopy Core Laboratory
Core facility that provides the following services: Training and access, Elemental spectroscopic imaging, Thin section imaging, Shadow casting, Negative staining, Electron diffraction, Brightfield imaging. This facility is a resource center for transmission electron microscopy, providing investigators with consultation, training, access to equipment and other services.
MSU X-ray Crystallography Core Laboratory
Core facility that provides the following services: Macromolecular crystal structure analysis, Macromolecular crystallization. The Montana State University Macromolecular Crystallography Facility provides modern facilities for macromolecular crystallization and structural analysis.
Core facility that provides the following services: 9.4T Facility rodent, nonhuman primate, and small animal proton spectroscopy. The McLean Hospital Translational Imaging Laboratory aims to provide cutting edge magnetic resonance imaging, functional imaging, chemical imaging (spectroscopy), and multimodal imaging services to the Harvard Catalyst Community. We have 3 magnetic resonance (MR) scanners, an ultra high magnetic field (9.4 Tesla) dedicated animal scanner and 3.0 and 4.0 Tesla large bore human systems available for large animal scans. Our scanners are capable of conducting scans in animals ranging in size from mice to large dogs, and we have experience imaging mice, rats, rabbits, nonhuman primates, and several canine species. All 3 scanners have dedicated animal prep areas. We offer high level biophysics, engineering, and data analytic expertise, along with veterinary technologist anesthesia support.
The Endocrine Core Laboratory is a fully accredited, CLIA approved, endocrine testing facility funded by the Meharry Medical College Clinical Research Center, U54 Reproductive Health Grants, and institutional resources. The Endocrine Core Lab performs a comprehensive list of routine and specialized endocrine tests on blood samples for government funded investigators... A full staff of board certified clinical endocrinologists and clinical scientists are available for consultation and interpretation of test results.
Core facility that provides the following services: Flow cytometry service. The FACS Core provides a state-of-the-art multi parameter flow cytometry and biosafty level 3 facility on the Meharry Medical College campus. The facility performs flow cytometry analysis, provides expertise in implementing and developing technologies for cell analysis, and provides training to investigators in the use of the instrumentation and in the interpretation of data analysis
OHSU Investigator Support and Integration Services
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. The mission of the Investigator Support and Integration Services (ISIS) program is to facilitate clinical and translational research at OHSU and the Portland VA Medical Center. ISIS works with these institutional partners to streamline study start-up and management processes and related administrative and compliance processes and provide pre-award and regulatory services to investigators. ISIS administers the Human Subjects Protection Program of the Clinical and Translational Research Center (CTRC) to maximize the protection of human subjects involved in OCTRI projects. The OHSU Clinical Trials Office, a unit within ISIS, provides study start-up services and negotiation of contracts for OHSU industry-sponsored clinical trials.
Meharry Human Tissue Acquistion and Pathology Core
Core facility that provides the following services: Immunohistochemistry service, Routine histology service, Tissue procurement service. The Human Tissue & Pathology Core provides tissue collection and storage services and access to human tissue, histology services, and specialized equipment. The Core collects human tissues prospectively from routine surgical resections and autopsies for use in basic, translational, and clinical research. Only remnant tissue samples not needed for diagnostic purposes are collected. Tissues are available fresh, snap frozen, or in a variety of fixatives, and normal, neoplastic, and other diseased tissues are available. Histology services include paraffin embedding, paraffin sectioning, automated Hematoxylin and Eosin staining, frozen sectioning, special stains, immunohistochemistry and other specialized processing and sectioning services.
The Molecular Biology Core Facility at Meharry Medical College is a multi-functional facility that provides to faculty, students, and staff of the college the primary service of DNA sequencing but also provides access to shared equipment housed in a centralized location and facilitates convenient and rapid access to frequently used molecular biological reagents.RRRRR RRRRR The Molecular Biology Core houses a number of shared items of research instrumentation. The core also maintains an Invitrogen Supply Center that stocks many routinely used reagents for molecular biological research. RRRRR RRRRR The major service activities of the Molecular Biology Core are to provide training and technical assistance with the use of shared equipment housed in the core and provide convenient access to molecular biological reagents. Training in the proper use of equipment is provided by the Laboratory Coordinator and also as needed by vendor technical personnel. The core maintains in-house freezers and supply cabinets stocked with many commonly used molecular biological reagents from Invitrogen. In-house reagents are ordered online from Invitrogen and picked up from stocks housed in the core. Invitrogen items not stocked in the core can be ordered online without shipping charges.
Core facility that provides the following services: Confocal and wide-field microscopy services, Confocal and wide-field microscopy training. It is the mission of the Meharry Medical College Morphology Core to provide the expertise and state-of-the-art instrumentation necessary to facilitate and enhance the productivity of Meharry?s investigators and trainees in the areas of fluorescence and bright-field microscopy and immunohistochemistry. This core strives to accomplish this by offering consultation on instrumentation and experimental design, training on instrumentation, and collaboration opportunities. We do our utmost to stay on the cutting edge of technology, skills, and knowledge in the field.
Monell Behavioral and Physiological Phenotyping Core
Monell''s Behavioral and Physiological Phenotyping Core provides training and research support in the behavioral and physiological phenotyping of rodents, including surgical and electrophysiological techniques utilized in rodent models. Core personnel offer expertise, instruction and equipment needed for methodologies common to research in the chemical senses, including preference tests, gustometers, olfactometers, LabMaster systems and metabolic cages.
Monell Chemosensory Receptor Signaling Core
The Chemosensory Receptor Signaling Core will provide training, advice and research support in molecular biological techniques used to analyze gene expression in cell culture and manipulate the genomes of rodent model organisms. The Core will centralize labor-intensive construct generation common to multiple users and provide users with technical expertise in molecular biological manipulations both in vitro and in vivo. The Core facility has all equipment, reagents, and expertise needed to carry out the following manipulations of RNA, DNA, and protein: RNA isolation, cDNA production, antisense RNA amplification, cloning, subcloning, recombineering, gel electrophoresis, transfection and tissue culture.
Monell Genotyping and DNA/RNA Analysis Core
This Research Core provides training and research support in genotyping and quantification of nucleic acids. The Core facility has equipment needed to genotype DNA samples and to measure nucleic acid concentrations in isolation or in tissue samples.
Monell Histology and Cellular Localization Core
The Histology and Cellular Localization Core provides training and research support in microscopy, anatomy and histology of chemosensory systems. Core personnel work with Monell researchers to develop and optimize in-house procedures and to establish cutting-edge techniques in histology and cell anatomy. The Core provides centralized services such as tissue sectioning and in situ probe preparation. The Core facility is equipped with cryostats, fluorescence microscopes, confocal microscopes, and a two-photon microscope.
OHSU Advanced Computing Center Core Facility
Provides technology solutions to meet non enterprise IT needs across OHSU for healthcare including limited clinical research project support, academic, and research missions. ACC is also home to Exacloud HPC cluster.
OHSU Advanced Imaging Research Center Core Facility
Provides magnetic resonance instruments including Siemens 3 Tesla Prisma, Siemens Magnetom 7 Tesla, and Bruker 11.75 Tesla to support research investigating normal physiology, brain development and aging, and disease pathophysiology with high performance non invasive imaging capabilities.
OHSU Advanced Light Microscopy Core Facility
Provides confocal image analysis and presentation training, microscope training, microscope access service, deconvolution training, super resolution imaging and training service. Offers research scientists access to high-end instrumentation for fluorescence microscopy. Offers support with image acquisition, processing, analysis and presentation.
OHSU Assisted Reproductive Technologies and Embryonic Stem Cell Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6, 2022. Core facility that provides the following services: Embyro stem cell tissue culture service. The Assisted Reproductive Technologies (ART) and Embryonic Stem Cell (ESC) Laboratory provides researchers with nonhuman primate gametes, embryos, follicular cells, embryonic stem cells, and other ART/ESC-related services in support of studies on gamete and follicular development, fertilization and contraception, early embryogenesis, pregnancy initiation, fetal development, stem cell biology, cell-based therapy of human disease, and the creation of disease models in non-human primates. The Core conducts research projects to investigate new areas of technology for creating or propagating valuable founder animals, including genetically modified and genetically identical monkeys and derivation, characterization, and transplantation of autologous, immunocompatible, pluripotent cells. In addition, the ART/ESC laboratory provides expertise and training in all aspects of the nonhuman primate ARTs and ESCs to scientists around the world.
OHSU Bioanalytical Shared Resource Pharmacokinetics Core Facility
OHSU Bioanalytical Shared Resource Pharmacokinetics Core Laboratory
OHSU Bioanalytical Shared Resource/Pharmacokinetics Core Laboratory
Core for analysis of drugs and their metabolites and bio-molecules such as simple peptides, oligonucleotides, carbohydrates, lipids, fatty acids and steroids. Provides open access to laboratory where users prepare and analyze their own samples by HPLC, GC/MS or LC/MS on equipment maintained by core personnel. Provides analysis of samples including development of analytical methods, sample preparation, and data analysis for clinical trials as well as basic science investigations.
Core facility that provides the following services: Amino acid analyses, Quantitative glycine analysis, Phytanic acid analysis, plasma, Succinylacetone with organic acids analysis, urine, Tay-Sachs carrier screening, serum, Very long chain fatty acid analysis, plasma, Quantitative alanine analysis, Aspartylglucosamine analysis, urine, Carnitine analysis, plasma, Cystathionine analysis, urine, Quantitiative cystine analysis, urine, Hexosaminidase A & B analysis, serum, Homocystine analysis, urine, Ketolytic enzyme testing, Leukocyte preparation, Mucopolysaccharide analysis, urine, Qualitative analysis of oligosaccharides, urine, Organic acids analysis, Quantitative analysis of phenylalanine, plasma, Phosphoethanoloamine analysis, urine. The OHSU Biochemical Genetics Laboratory is dedicated to providing specialized laboratory testing and comprehensive diagnostic evaluation of rare and unusual inherited metabolic diseases. Our expertise includes interpretation of results which requires detailed knowledge of the field by individuals specializing in clinical biochemical genetics.
Oregon Clinical and Translational Research Institute Biomedical Informatics Program
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility provides the following services: Data Management Consultation, Research Databases: REDCap & Customized Databases, Functional Genomics Consultation: Microarray Proteomics. The Biomedical Informatics Program (BMIP) provides investigators with informatics tools and methodologies to support translational researchers. Using a hybrid of collaborative and service approaches, BMIP is continually developing and deploying an array of informatics tools for bench research (bioinformatics), bedside research (clinical research informatics), and translation to practice (medical informatics). BMIP also provides a platform for collaborative and multidisciplinary informatics education and research. The Biomedical Informatics Program includes two major areas of emphasis: Translational Bioinformatics - Novel methodology development, Statistical Genetics, Functional Genomics, Clinical Research Informatics, Research Data Warehouse - Using Epic and other clinical data for research, Clinical research data management software, Epic as an interventional tool for research
OHSU Biomedical Informatics Shared Resource
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6, 2022. Core facility that provides the following services: Data storage planning, Database design and development, Website development. The BMISR provides expertise in data collection and management to clinical researchers. Through effective trial management and innovative data collection, clinical trial efficiency can be improved and high quality data collected for analysis. This automated data collection, storage and reporting reduce data errors and save time and effort during collection and analysis. Consultation and services are available during every stage of the research process--from grant proposal writing through research data collection, management and analysis. We can provide custom applications for data collection, management and dissemination using a broad array of technologies and tools. We can help with standalone database applications (such as Access), using scannable paper forms, developing web applications, designing database applications, just to name a few.
THIS RESOURCE IS NO LONGER IN SERVICE.December 6,2022. Core facility that provides the following services: Abortus, stillbirth, and neonatal death specimen chromosomal analysis, Amniotic fluid chromosomal analysis, Angelman genetic diagnostic testing, Blood chromosomal analysis, Blood chromosomal analysis, high resolution, Bone marrow chromosomal analysis, Chorionic villus sample chromosomal analysis, Chromosome breakage study, Cystic hygroma fluid chromosomal analysis, DiGeorge/velocardiofacial syndrome screening, Fibroblast chromosomal analysis, Fibroblast culture and storage, Fibroblast retrieval from storage, Fluorescent in-situ hybridization (FISH), HER2 testing by FISH, Kallman Syndrome (X-linked) testing, Microarray comparative genomic hybridization, Miller-Dieker lissencephaly syndrome testing, Neoplastic tissue chromosomal analysis, Pleural fluid chromosomal analysis, Prader-Willi diagnostic testing, Tissue culture for biochemical/DNA testing, Unstimulated peripheral blood chromosomal analysis, Williams syndrome screening, BCR-ABL RNA Quantitative PCR, Lymphoma complete surface marker panel. The OHSU Clinical Cytogenetics Laboratory specializes in high-resolution chromosome analysis. Emphasis has consistently focused on the highest quality preparations in order to provide the patient with the most accurate diagnosis. Certifications: CLIA; CAP; American Board of Medical Genetics; Clinical Cytogenetics; Medical Genetics
Oregon Health & Science University DNA Services Core
Oregon Health and Science University DNA Services Core
Services offered include Human cell line authentication: Accurate validation of human cell lines using STR analysis and meeting the ANSI/ATCC requirements; Fragment analysis: Detection of changes in length of specific DNA sequence to indicate presence or absence of genetic marker; Oligo synthesis: Creation of custom primers and probes for oligo and siRNA synthesis through Integrated DNA Technologies (IDT); DNA quantification: Quantification, size and quality assessment of DNA samples; Consulting: For project design and sample preparation assistance.
Oregon Health and Science University Multiscale Microscopy Core Facility
Oregon Health & Science University Multiscale Microscopy Core
Oregon Health and Science University Multiscale Microscopy Core
Multiscale Microscopy Core at OHSU is electron microscopy core that provides services and training to academic and corporate users.
Puerto Rico Clinical and Translational Research Consortium Nursing Services
These facilities contain three examination/study rooms, two gynecological examination rooms, two infusion rooms, one dental room, and one record room.
OHSU Electronics and Instrumentation Design Core Resource
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: Equipment design and fabrication service, Computer interfacing service, Embedded processor design service, Circuit board design service, Research equipment consulting. The Electronics & Instrument Design Core Resource provides hands-on design and fabrication of specialized equipment for research projects. Projects involve analog and digital electronics design, microcontroller, software development and optical and embedded processor design. The core director, John Hunt, MSEE, is a senior research engineer and instructor in the Department of Biomedical Engineering, OHSU School of Medicine. OHSU School of Medicine. He has worked as a research engineer at OGI/OHSU since 1980 and has developed equipment for many research projects and departments.
An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.
OHSU Endocrine Technology Support Core Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on December 6, 2022.Core facility that provides the following services: 17-hydroxyprogesterone (17a-P)-RIA, Androstenedioine (A4)-Ext-Chrom-RIA, b-Endorphin (bEP)-Iodination-RIA, Cholecystokinin (CCK)-Iodination-RIA, Corticosterone-Ext-RIA, Corticotropin-releasing factor (CRF)-Iodination-RIA, Dehydrocorticosterone (DOC)-Ext-RIA, Dihydrotestosterone (DHT)-Ext-Chrom-RIA, Estradiol-17b (E2)-Ext-RIA, Estradiol-17b (E2)-Ext-Chrom-RIA, Follicle-stimulating hormone (FSH)-Iodination-RIA, Gonadotropin-releasing hormone (GnRH)-Iodination-RIA, Growth hormone-releasing hormone (GHRH)-Iodination-RIA, Luteinizing hormone (LH)-Iodination-RIA, Neuropeptide Y (NPY)-Iodination-RIA, Progesterone (P4)-Ext-RIA, Progesterone (P4)-Ext-Chrom-RIA, 17-hydroxyprogesterone (17a-P)-Ext-Chrom-RIA, Testosterone (T)-Ext-RIA, Testosterone (T)-Ext-Chrom-RIA, Aldosterone-Active-RIA, Androstenedioine (A4)-CTC-RIA, Androstenedioine (A4)-Double-Antibody RIA, Corticosterone-RIA, Cortisol (17a-hydroxycorticosterone)-RIA, Cortisol (17a-hydroxycorticosterone)-ELISA, Dehydroepiandrosterone (DHEA)-ELISA, Dehydroepiandrosterone (DHEA)-RIA, Dexamethasone-ELISA, Dihydrotestosterone (DHT)-RIA, Estradiol-17b (E2)-Double-Antibody RIA, Estradiol-17b (E2)-Ultra-sensitive RIA, Estradiol-17b (E2)-Coat-the-Count RIA, Estradiol-17b (E2)-ELISA, Estrone (E1)-ELISA, Estrone (E1)-RIA, Free Testosterone (Free T)-Coat-the-count RIA, Free Testosteroine (Free T)-RIA, Glucagon-RIA, Insulin-RIA, Insulin-ELISA, Insulin (human)-RIA, Insulin (rat)-RIA, Insulin (sensitive rat)-RIA, Pregnenolone-EIA, Progesterone (P4)-RIA, Progesterone (P4) (17alpha-OH)-ELISA, Progesterone (P4)-EIA, Testosterone (T)-RIA, Testosterone (T)-EIA, Testosterone (T)-ELISA, Adiponectin (Rat)-ELISA, Adrenocorticotropins (ACTH)-RIA, Anti-Mullerian hormone-Active-ELISA, C-Peptide-RIA, Cotinine-ELISA, Cotinine (rat)-ELISA, C-reactive protein (CRP)-Ultra-sensitive ELISA, Cytokines, individual-ELISA, Dehydroepiandrosterone sulfate (DHEAS)-RIA, Delta-like 1 (DLK-1)-ELISA, Ethinyl estradiol (EE2)-Ext-RIA, Follicle-stimulating hormone (FSH)-RIA, Ghrelin (human)-RIA, Growth hormone (GH)-ELISA, Growth hormone (GH) (rat)-RIA, 5-Hydroxyindoleacetic acid (5-HIAA)-ELISA, Inhibin-a-ELISA, Inhibin-b-Active-ELISA, Insulin-like growth factor (IGF-1)-ELISA, Insulin-like growth factor (IGF-1) (mouse/rat)-ELISA, Leptin (mouse)-RIA, Leptin (primate)-RIA, Leptin (rat)-RIA, Levonorgestrel (LNG)-Ext-RIA, Low-density Lipoprotein (LDL)-EIA, Prolactin (rat)-ELISA, Prostate-specific antigen (PSA)-ELISA, Quantikine HS-High sensitivity ELISA, Serotonin (5-HT)-RIA, Serotonin (5-HT)-ELISA, Vasopressin-EIA-Extraction. The Endocrine Technology Support Core Lab (ETSL) has provided intra- and extramural investigators with analysis of protein and steroid content in blood, as well as in biological tissues and fluids for more than 3 decades. Principal support functions include provision of routine assays (for most naturally occurring steroid and protein hormones involved in the regulation of reproduction, metabolism, and the central nervous system) and development of new assays (e.g., Multiplex platforms for cytokines and signaling molecules).
OHSU Flow Cytometry and Monoclonal Antibody Shared Resource Core Facility
OHSU Flow Cytometry and Monoclonal Antibody Shared Resource
Core facility that provides the following services: Analytical flow cytometry service, Cell sorting service, Flow cytometry data analysis service, Grant preparation support service, Flow cytometry instrument training, Flow cytometry consultation service. The OHSU Flow Cytometry Shared Resource (FCSR) has operated as a core resource for OHSU Knight Cancer Institute members since 1996 and provides advanced flow cytometry instrumentation, technical expertise and technical services. The FCSR also provides training in data interpretation, experiment design and routine operation to researchers, offering an additional cost-saving option of doing some of the work themselves. Finally, this resource saves valuable investigator time by analyzing specimens and preparing them, if needed.
OHSU Gene Profiling Shared Resource Core Facility
OHSU Gene Profiling Shared Resource Core Laboratory
Full service genomics facility providing research scientists and clinicians with services for RNA expression profiling, DNA variation analysis, and nucleic acid extraction.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: Sterols assay, Mevalonic acid assay. The OHSU Lipid Lab offers precise determination of lipids and specialized lipid metabolites not routinely available in general hospital clinical labs or elsewhere in Oregon. Currently, the OHSU Lipid Lab is the only laboratory on the West Coast that does sterols.
OHSU Histopathology Shared Resource Core Facility
Provides routine and customized histology and immunohistochemistry services critical for progress of biomedical research.
OHSU Imaging and Morphology Support Core Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: Confocal and epi-fluorescence imaging, Image processing and analysis, Stereology measurement service, Laser Capture Microdissection service, Live cell imaging service. The Imaging and Morphology Support Core of the ONPRC is designed to meet the imaging needs of ONPRC scientists and of the OHSU scientific community by providing state-of-the-art facilities, expertise, assistance and training in the use of advanced light microscopy, image analysis, processing and printing, and laser capture microdissection. Special emphasis is placed on quantitative evaluation of imaging experiments using both stereology and automated image analysis.
THIS CORE IS NO LONGER IN SERVICE.Documented on December 6,2022. Core facility that provides the following services: Transmission electron microscopy. Imaging center has an excellent physical facility for handling samples for light or electron microscopy. We have a unique Multi-suite dissection, sectioning, and embedding area. This area is equipped with fume hood, two refrigerators, -80 freezer, tissue processors, and surgical instruments. Tissues of interest may be prepared ranging from fresh frozen for fluorescence microscopy to embedding in plastic for electron microscopy. We have or have access to; cryostats, paraffin microtomes, vibratomes, and ultramicrotomes. The EM core is experienced in many specialized electron microcopy techniques. These include immunogold labeling, negative staining. We have two FEI transmission electron microscopes, a Morgagni, and a Techni 12, both with AMT digital cameras for micrograph production.
OHSU Immunology Support Core Cellular Immunology Unit
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on December 6,2022. Core facility that provides the following services: Immunological study design and implementation, Flow cytometry assays service, High-throughput analysis service, Economies-of-scale reagent purchasing, Flow cytometry sorting service. The CIU offers all the study organization and technical expertise developed at the (Louis) Picker Lab to researchers whose questions require obtaining and processing monkey immunological samples, and/or utilizing cytometry to assay phenotype of CFC/ICS information. The CIU was originally developed as part of the Bill & Melinda Gates foundation CAVD (Collaboration for AIDS Vaccine Discovery) consortium.
OHSU Immunology Support Core Flow Cytometry Unit
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: Flow cytometry training service, Cell sorting service, Specialized flow cytometric assays. The mission of the Immunology Support Core (ISC) is to develop and provide a wide range of state-of-the-art services, assays, and training in support of NIH-sponsored immunology research involving nonhuman primates (NHP).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: Use of IOIC facility, In vivo optical imaging training service. The IOIC is located in Cardiac Imaging Laboratory on the first floor of the Biomedical Research Building (BRB). The laboratory was established through a Shared Instrument Grant (PI: Michael Deininger) but is maintained through user fees. The core facility includes the IVIS Spectrum optical imaging camera housed in a light-tight housing, rat and mouse imaging platforms for multi-subject simultaneous acquisition, an integrated inhaled anesthesia system, and advanced analysis software. A key component of the IOIC is the ability to operate either independently or under the guidance and supervision of core personnel. Independent use of the system requires that investigators undergo training that is offered every 2 months or on an ad hoc basis. All analysis will be charged on an hourly basis and is graduated according to the level of service (independent or supervised).
U.S. Department of Health and Human Services
U.S. Department of Health & Human Services
United States Department of Health & Human Services
United States epartment of Health and Human Services
OHSU Massively Parallel Sequencing Shared Resource Core Facility
OHSU Massively Parallel Sequencing Shared Resource
As of January 1, 2024, the Integrated Genomics Laboratory is one shared resource comprising the former Massively Parallel Sequencing Shared Resource, the Gene Profiling Shared Resource, and the DNA Services Core. Please be aware that the reorganization is an ongoing process, particularly regarding our iLab integration.Provides RNA-sequencing for gene expression analysis, DNA resequencing for single nucleotide polymorphism discovery, DNA resequencing for copy number variation discovery, ChiP-sequencing for promoter analysis, DNA methylation analysis, De novo sequencing for unique genomes, Sequence capture service. Offers sequencing including genome resequencing, transcriptome analysis, miRNA analysis, and prometer analysis via ChIP-seq.
OHSU Methamphetamine Abuse Research Center Animal Core Component
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on December 6,2022. Core facility that provides the following services: Mouse breeding service, Behavioral testing procedures service, Mouse breeding. Three of the MARC''s research components (5, 6, and 8) include experiments with lines of mice bred to have special genetic traits. The animal core supports these components by purchasing, testing, breeding, maintaining, and distributing these animals within the center. The core will breed special mouse lines F1 and F2 that are descendents of C57BL/6J (B6) and DBA/2J (D2) inbred strains. For Components 5 and 6, the animal core will also produce independent sets of replicated mouse lines selected for high and low tendencies toward methamphetamine drinking and for high and low methamphetamine-induced sensitization. In addition, the core is developing new behavioral-testing procedures and maintaining a database that will track individual animals and post their trait data for all MARC investigators to utilize.
OHSU Molecular and Cellular Biology Core Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: Automated DNA sequencing, Realtime PCR analysis and SNP analysis, Automated DNA and RNA preps using robotics, Lentiviral vector preparation for cDNA and shRNA transduction and infection, Semi-automated large-scale genomic DNA preparations., Freezing, thawing, and amplification of cell lines, Preparation of both routine and exotic cell culture medium. The Molecular and Cellular Biology Core provides services, reagents and training for all aspects of molecular biology and cell culture. Services include DNA sequencing, real-time PCR, genotyping, robotic RNA and DNA purification, monkey-specific cDNAs, and customized media and buffers for cell culture. The core also produces lentiviral vectors for cDNA and shRNA delivery. Core personnel assist researchers in maintaining and storing cell lines. The core makes available state-of-the-art equipment, including a 969capillary DNA sequencer, realtime qRT-PCR platforms, and fluorometers for cell-based kinetic analyses..
OHSU Monoclonal Antibody Core Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: Monoclonal antibody generation, Scaleup production and purification of antibody from existing cell lines. The VGTI Monoclonal Core offers two basic services: the generation of new monoclonal antibodies and the scaleup production and purification of antibody from existing cell lines (a stand -alone phase IV).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. The Neuropathology Core of the Layton Center for Aging and Alzheimer?s Disease Center is dedicated to studying, through autopsy, the brains of individuals who have been followed longitudinally in the Oregon Alzheimer?s Disease Center Clinical Core. Requests for tissue from the Oregon Brain Bank should be directed to Dr. Randall Woltjer. Dr. Woltjer will be glad to communicate with investigators regarding their tissue needs and to assist them in identifying suitable materials for their studies. Material Transfer Agreements between the requesting and sending institutions are needed before shipment.
OHSU Nuclear Magnetic Resonance Core Facility
Core facility that provides the following services: NMR instrument training. A facility that uses a state-of-the-art NMR spectrometer to verify or determine the structure of organic molecules. Housed in the Department of Physiology and Pharmacology, it is designed to exploit the power of designed small molecules as probes of protein and cellular function and to provide the foundation for the development of prototypic therapeutic agents.
Penn Mass Spectrometry Molecular Profiling Core
Core facility that provides the following services: Metabolomics profiling service. This core provides sophisticated analytical services based on liquid chromatography-mass spectrometry.
OHSU Proteomics Shared Resource Core Facility
OHSU Proteomics Shared Resource Core Laboratory
Core facility that provides the following services: Protein identification and partial sequencing, Determination of whole protein mass, Targeted SRM analysis of known proteins, Protein quantitation assay, Gel electrophoresis. The OHSU Protemics Shared Resource facility was established to make state-of-the-art mass spectrometry based protein analysis analytical capabilities available to the biomedical research community at OHSU.
OHSU Research Cytogenetics Core Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: G-banded karyotyping, Sister chromatid exchange service, Fluorescent in situ hybridization, Chromosome breakage and radial formation analysis, Ploidy/Aneuploidy Assessment, Mitotic index service. A fee-for-service cytogentics laboratory available to genetics researchers to assist in development and execution of cytogenetics experiments for research purposes. Through rigorous standardization of protocols and customized experiment development, the OHSU Research Cytogenetics Core Laboratory provides high quality metaphase and interphase cytogenetic data to the OHSU research community. Services are also available to non-profit and commercial investigators located in Oregon and elsewhere.
Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.
OHSU Transgenic Mouse Model Shared Resource
OHSU Transgenic Mouse Models Core Laboratory
Oregon Health & Science University Transgenic Mouse Models
Oregon Health and Science University Transgenic Mouse Models
Core assists investigators with developing genetically engineered rodent models of human diseases for studying mutant genes and investigating molecular mechanisms underlying pathological processes.
Oregon Clinical and Translational Research Institute Bionutrition Unit
Oregon Clinical & Translational Research Institute Bionutrition Unit
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6, 2022. Core facility that provides the following services: Consultation on protocol development and design process, Exercise testing service, Dual energy x-ray absorptiometry service. The Bionutrition Unit provides nutrition, body composition, and energy expenditure services. Bionutritionist and research kitchen staff are highly experienced and trained to assist investigators with the design and implementation of research meals, feeding studies, and related research. The Bionutrition Unit also provides a variety of energy expenditure and body composition measurement services using a range of equipment.
OHSU Oregon Clinical and Translational Research Center Core Facility
OHSU Clinical and Translational Research Center
OHSU Oregon Clinical and Translational Research Institute Core Laboratory
Oregon Clinical & Translational Research Institute Core Laboratory
Provides nursing, bionutrition, study coordination, and laboratory services and support. Laboratory is designed and equipped to perform both basic and specialized research assays and sample processing in support of translational research studies and trials. Laboratory staff have extensive experience in performance of wide variety of analytical and genetic based assays and procedures.
Oregon Stem Cell Center Monoclonal Antibody Core
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on December 6,2022. Core facility that provides the following services: Monoclonal antibody development. The Oregon Stem Cell Center Monoclonal Antibody Core is focused on developing monoclonal antibodies that aid investigators in the identification and isolation of novel stem and progenitor cell populations. To enable isolation of live stem cells, personnel within the Monoclonal Antibody Core develop monoclonal antibodies directed against cell surface antigens. Personnel within the laboratory are highly skilled in all aspects of monoclonal antibody generation and characterization, and work closely with investigators throughout the entire immunization, fusion, and screening process. The monoclonal antibody core offers a full complement of services related to the development of monoclonal antibodies.
Core facility that provides the following services: Hydrogel consultation service, ECM-coated acrylamide hydrogels, Hands-on guidance for cell lysis and molecular/cellular analysis, Preparation of acrylamide-based hydrogel training, Second harmonic generation microscopy, Atomic force microscopy. The Biomechanics Core works with ITMAT faculty from Penn, ITMAT partner institutions, and members of the ITMAT Program in Translational Biomechanics. Consultation and initial pilot experiments performed with the Biomechanics Core are free-of-charge to ITMAT faculty from Penn, ITMAT partner institutions, and members of the ITMAT Program in Translational Biomechanics.
Penn Biological Chemistry Resource Center
Core facility that provides the following services: Custom peptide synthesis service. The Biological Chemistry Resource Center (BCRC) at the Department of Chemistry has been established to provide an open access user facility for state-of-art biophysical analytical instrumentation. The goal of the center is not only to provide access to instrumentation, but also supply the graduate student and post-doc user community with a firm understanding of the scientific principles behind the techniques and on-site expertise to ensure successful experimentation. Instrumentation access will be available to the entire University of Pennsylvania research community.
International Epilepsy Electrophysiology Portal
Repository for EEG data. The International Epilepsy Electrophysiology Portal is a collaborative initiative funded by the National Institutes of Neurological Disease and Stroke. This initiative seeks to advance research towards the understanding of epilepsy by providing a platform for sharing data, tools and expertise between researchers. The portal includes a large database of scientific data and tools to analyze these datasets.
Core facility that provides the following services: Tissue processing and paraffin embedding, Cell processing and paraffin embedding, Cryosectioning service, Paraffin-embedded sectioning, Hematoxylin and eosin staining, Immuno-staining (IHC) of tissue sections, Histological staining service. The Cancer Histology Core is a non-profit, research-oriented resource core supported by the Abramson Cancer Center. It offers all histology-related services to all members of the Abramson Cancer Center with high quality, low cost, fast turnout, and easy interaction. Service will be open to all life sciences investigators at Penn, but priority will be given to full members of the Abramson Cancer Center.
Core facility that provides the following services: Antibody screening by ELISA, Cell Culture Training, Production and Purification of Antibodies from Hybridoma Lines, Endotoxin Testing, EBV Transformation, Special media production, Liquid N2 storage, Freezing Cells. Cell Center Services Facility is the service component of the Cell Center, provides training and services in various cell culture and associated procedures including Mycoplasma and Endotoxin testing. The cell culture service includes cell culture at various scales, large scale growth of hybridoma and other cell lines followed by antibody purification by protein G column and the generation of lymphoblastoid cell lines by EBV induced transformation of lymphocytes. In addition, the facility prepares specialized cell culture media, drosophila media, and various molecular biological reagents. Recently cell transfection and selection service has been introduced at the facility.
The Cell Center Stockroom is a division of the Genetics Core Facilities (GCF). The GCF is a University service center, established in 1973 to provide consultation, training, and services in the areas of cell culture and hybridomas. Also, the GCF to provides a full range of cell culture media and molecular biology reagents needed by investigators to perform cell culture techniques in their own laboratories. The DNA Sequencing Facility, Genetic Diagnostic Laboratory and Transgenic/Chimeric Animal Facility are the remaining three divisions of the GCF. The Stockroom serves University of Pennsylvania investigators and affiliate institutions (Cancer Center, Chidren''s Hospital of Philadelphia, Hospital of the Unviersity of Pennsylvania, The Wistar Institute, Monell Chemical Senses Center, and Presbyterian Hospital) by coordinating relations with various suppliers of molecular biological research materials. This involves not only bulk purchasing of these products, but the negotiation of discounts and convenient delivery arrangements. There are over 1,400 products on-site for immediate delivery in the Stockroom. Special ordering of non-regularly stocked products is available from 24 bioreagent vendors with discounted pricing and overnight delivery. List of Stockroom Vendors: * Accutek Laboratories * Amaxa Biosystems * Ambion, Inc. * Applied Biosystems * Atlanta Biologicals * Bio-Rad Laboratories * Biowhittaker * Cell Center Services * Cell Signaling Technologies * Clontech Laboratories * Collaborative * Denville Scientific * Difco Laboratories * EMD Chemicals * Fermentas * Fisher (Thermo) Scientific * Fuji Film * GE/Amersham Bioscience * Gemini Bio-Products�� * Hyclone Laboratories * Integrated DNA Technologies * Invitrogen * ISC Bioexpress * Kodak * KPL, Inc. * Life Technologies * Lonz A* MediaTech * Millipore * New England Biolabs * Open Biosystems * Perkin Elmer Life Sciences * Promeg A* Qiagen * Rainin Instruments * Roche�� * Sigma-Aldrich * Stratagene/Agilent Technologies * TruMark Scientific * USB Corporation/Affymetrix * VWR International * Zen-Bio, Inc.
Penn Cell and Developmental Biology Microscopy Core
Core facility that provides the following services: Microscope access service, Imaging experimental design consultation service, Confocal microscopy service, Microscopy training service, Scanning electron microscopy sample preparation service, Sputter coating access service, Scanning electron microscope access service. The Cell & Developmental Biology (CDB) Microscopy Core is a full-service facility serving the entire University of Pennsylvania community. Our aim is to provide personalized assistance on all aspects of imaging, from tips on sample preparation to training on one of our microscopes to processing and analysis of image data. Our facility currently houses five confocal and three widefield light microscopes, a scanning electron microscope, and several computers dedicated to image processing and analysis.
Core facility that provides the following services: NMR spectrometer access, NMR spectrometer training, NMR spectroscopy service, Consultation service for NMR experimental design. Penn Chemistry NMR Facility provides researchers in the Chemistry and Materials Science and Engineering department access to state-of-the-art instrumentation for high resolution NMR spectroscopy. The Facility provides users extensive training to use spectrometers without supervision and expert advice/consultation on advanced applications of NMR spectroscopy to solve research problems. At present, the Facility operates ten high resolution NMR spectrometers (300-600 MHz) of varying capabilities located in the Chemistry building at the corner of 34th and Spruce street, Philadelphia, PA. Penn Chemistry NMR Facility provides limited solution NMR services (data acquisition and spectrum/structure analysis) to other departments/centers of University of Pennsylvania based on hourly charges. However, these services will be limited to the availability of instrument time and personnel. NMR Facility accepts service samples from outside academic and industrial customers based on per hour charges.
Autism Spectrum Disorder Phenotype Ontology
Ontology that encapsulates the Autism Spectrum Disorder behavioral phenotype, informed by the standard ASD assessment instruments and the currently known characteristics of this disorder.
Penn Clinical Cell and Vaccine Production Facility
Core facility that provides the following services: Cryopreservation, Clinical Cell and Vaccine Production Facility quality control and quality assurance services, Clinical Cell and Vaccine Production Facility quality control training, Conjugation of proteins or antibodies to magnetic beads and quality control, Clinical Cell and Vaccine Production Facility vaccine preparation service, Enrichment of lymphocytes or monocytes from apheresis collection, WBC, lymphocyte and monocyte count, Conversion of patient/donor plasma to serum, Depletion of cell subpopulation from apheresis or lymphocytes, Clinical Cell and Vaccine Production Facility quality control testing. The Clinical Cell and Vaccine Production Facility (CVPF) is a GMP facility accredited by the Foundation for the Accreditation of Cellular Therapy (FACT) and a Department of Pathology/Lab Medicine and NCI approved Abramson Cancer Center Shared Resource. The CVPF provides focused scientific, technical and regulatory support for investigator initiated investigational new drug applications (INDs) in cell and gene therapy. Under compliance of FDA 21 CFR Parts 210 and 211, the CVPF performs cell processing on a range of different cell types, to include bone marrow derived CD4+ and CD8+ T lymphocytes, dendritic cells, and marrow stromal cells (aka mesenchymal stem cells). In each of these cases, cells are expanded ex vivo with or without genetic modification to the cells before being reintroduced back into the patient, either alone or in combination with other therapies such as vaccines. The overall mission of the Clinical Cell and Vaccine Production Facility is to help translate insights into novel cellular therapies.
Penn Community Engagement and Research Core
Core facility that provides the following services: Community engagement and research consultation services. Mission: The purpose of the Community Engagement and Research Core in the Penn CTSA is to facilitate community-based research and community engagement, especially community-based participatory research, and enhance the translation of research and technological developments to key public health and community stakeholders. Goals: 1. Foster community-based participatory research projects through developing training programs and integrating lectures into existing academic programs 2. Determine community health needs and priorities 3. Promote community-based research within the area of health disparities through seminar series 4. Continue the involvement in community outreach and education events to engage the community 5. Fund the conduct of CEAR Core pilot studies 6. Facilitate the use of academic-community partnerships to aid in the recruitment of subjects
Penn/CHOP CTRC Bionutrition Research Core Dietary Assessment
Core facility that provides the following services: Body composition measurements, Resting energy expenditure analysis. Nutrition plays a vital role in health at all ages. The Clinical and Translational Research Center offers a Bionutrition Research Unit (BRU) to facilitate and implement clinical and translational research services. Research dietitians assist investigators with research design, implementation, data collection and analysis in study protocols. The Dietary Assessment Unit of the Nutrition Core provides a broad range of nutrition-related research services to investigators at the Children''s Hospital of Philadelphia, the Hospital of the University of Pennsylvania (HUP) and Penn Presbyterian Medical Center (PMC).
Penn Electron Microscopy Resource Laboratory
Core facility that provides the following services: Biological specimen sample preparation for transmission electron microscopy, Phenotypic characterization and ultrastructural analysis of biological specimens, Consultation for transmission electron microscopy experiments, usage, and data presentation, Transmission electron microscopy image construction tomography service, Training in transmission electron microscope operation, Scanning electron microscopy service, Transmission electron microscope access. Structural organization is underlies nearly all cellular, molecular and biochemical processes in biological systems. The Electron Microscopy Resource Laboratory (EMRL) at Penn is dedicated to analysis of biological samples by electron microscopy (EM). The primary goal of the EMRL is to promote biomedical research by offering high quality EM imaging services at a low cost. With a team of experienced professional staff and state-of-the-art imaging equipment, the EMRL offers users a full spectrum of both transmission EM and scanning EM services. These services include: specimen preparation (including fixation, embedding, and sectioning of cells and tissues or preparation of non-cellular materials), operation of equipment, data acquisition, data interpretation, and free instruction on all aspects of EM analysis. We also offer free assistance on the preparation of manuscript and grant applications that incorporate various forms of EM analysis. For most users, the Core will perform a complete analysis from sample preparation through collection of data, most often with the user present during data collection. More experienced users can perform the work themselves, with the Core providing guidance and assistance as needed. The Core staff and affiliated Scientific Advisory Committee members are always available for consulting on the morphological aspects of a project, and the Core staff is willing to custom-design services to fit any investigator''s needs.
Penn Flow Cytometry and Cell Sorting Resource Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Core facility that provides the following services: Flow cytometry analysis service, Cell sorting and analysis service, Flow cytometer analyzer access, Introductory flow cytometry training, Advanced and customized flow cytometry training, Flow cytometry consultation service, FACSAria training, Flow cytometry data analysis, BSL2+ biohazardous human cell sorting, BSL2+ murine biohazardous cell sorting, BSL2+ murine cell sorting access, Non-infectious cell sorting access. The Flow Cytometry and Cell Sorting Resource Laboratory is currently recognized as one of the largest and most comprehensive flow cytometry laboratories in the US. In 2010 it was designated a laboratory of exceptional merit by the National Cancer Institute. Using state-of-the-art technology, the resource provides a broad array of, instrumentation, support, education and consultation to the research community at the University of Pennsylvania. A wide variety of cell sorting applications are supported, from high-speed multicolor (up to 14 colors) cell sorting to low-speed, large nozzle, improved viability sorting. Additionally, a wide variety of cell analysis services (up to 20 parameters) are offered, from traditional analog, easier to use tabletop analyzers to many-laser, many-color, high-speed, fully-digital modern instrumentation. Currently the facility offers 6 cell sorters and 19 analytical instruments. A very active training and consultation program is in place to support these activities. The Scientific Director, Dr. Jonni Moore, and the Technical Director, each have over 25 years experience in the field of cytomics. Researchers at the University of Pennsylvania are increasingly engaged in research projects that require 8-plus-parameter cell sorting of infectious cells and primary human tissues. Investigators using the Flow Cytometry and Cell Sorting Shared Resource have access to virtually any type of cytometric services required for a vast array of applications.
Core facility that provides the following services: Investigational drug services, Clinical trial support services. The IDS is charged with safe and responsible handling of investigational drugs. The purpose of the IDS is to maintain control and accountability of investigational drug use in the Medical Center to promote maximum benefit and safety for patients enrolled in studies. Investigational drugs are procured, stored, inventoried, dispensed and used through the IDS in compliance with regulations or guidelines of the FDA, JCAHO, ASHP, Code of Federal Regulations, Pennsylvania State Board of Pharmacy, other applicable organizations and in accordance with Hospital, Medical Center and University policies and guidelines.
The Penn Gene Targeting Service (PGT) is run by the Penn Gene Targeting Core and Laboratory in collaboration with two other Penn Cores (DNA Sequencing Facility and the Transgenic and Chimeric Mouse Facility) and has the capability to generate from scratch almost any type of genetically modified mouse. This includes complete knockout of any gene, tissue-specific and/or drug-inducible knockout of any gene, targeted mutagenesis of any region of any gene (knockin), tissue-specific activation of an endogenous gene using loxP flanked stop cassettes, and tissue-specific and/or drug-inducible transgene expression from defined loci. For details regarding services and prices please consult the PGT home page of the Department of Genetics and/or directly contact Dr. Tobias Raabe. The Client lab does not need to be involved in any experimental step and only needs to breed the resulting mice. However, if desired, participation of the client lab in almost any experimental step is possible. PGT has an outstanding record of germ line transmission and so far over 32 targeted mice - more than 12 in the desirable C57BL6 background - have been made, starting either with molecular design and construction of the targeting vector or with electroporation of an existing targeting vector into ES cells.
University of Pennsylvania Molecular Profiling Facility
Core provides full service whole genome and targeted molecular profiling of DNA and RNA on multiple platforms. The Facility offers a range of cost and performance options suitable for a variety of experimental projects. While the Facility staff performs most of the assays, investigator-performed studies are actively encouraged through the sharing of Facility procedures, individualized training of investigators or their technical staff, and use of core equipment.
Penn High-Throughput Sequencing Facility
Core facility that provides the following services: Illumina sequencing service, 5500xl sequencing service. The recent boon in high-throughput sequencing technologies has offered enormous potential to applications in genome sequencing, transcriptome profiling, epigenetics, metagenomics, discovery of non-coding RNAs and protein binding sites. A primary mission of PGFI is to lead the development of new genomics technologies at the University of Pennsylvania. In response to the ever growing demand for high-throughput sequencing at Penn, PGFI?s HTS facility was established. In this facility, investigators have access to different types of HTS technology: Illumina?s HiSeq and Applied Biosystem?s SOLiD4 and 5500xl. With two HiSeqs, the facility can provide the latest innovation from Illumina featuring up to 3 billion paired-end reads (up to 100x100 bp reads) per flow cell, 8 lanes per flow cell and 2 flow cells per machine. With the SOLiD4, the facility can provide up to 1.4 billion reads per slide, 50 x 25 bp paired-end reads, up to 8 sectors per slide and 2 flow cells per machine. With the 5500xl, the facility can provide up to 180 Gb or more than 2.8 B reads per run. The 5500xl offers 75 bp fragment runs, 75x35 bp paired-end runs and up to 60 bp x 60 bp mate paired runs with the added bonus of pay-as-you-go sequencing. All platforms offer multiplexing capability. Currently Illumina offers 48 barcodes and Life Technologies offers 96 barcodes. The SOLiD 4 system provides greater than 99.94% accuracy due to 2-base encoding. The 5500xl offers up to 99.99% accuracy utilizing 2-base encoding and Exact Call Chemistry.
University of Pennsylvania High-performance Computing
The High-Performance Computing (HPC) Facility provides the hardware and staff to support bioinformatics and biocomputational research. The central component of this facility is a large cluster of 64 high-speed compute nodes, along with approximately 900 terabyte of shared disk storage and nearly 1.8 petabytes of archival storage.
Core facility that provides the following services: Immunohistochemistry (IHC) staining service, Tissue processing and sectioning service, Staining service. The Histology and Gene Expression Core Facility provides expert professional services for members of the Cardiovascular Institute. Services for non- Institute investigators are available on a fee-for-service basis as time permits. The Histology and Gene Expression Core offers all histology-related services include tissue processing, embedding, sectioning, staining, immunocytochemistry and InSitu Hybridization.
Core facility that provides the following services: ELISA AND ELISpot assays, Multi-color flow cytometry immunophenotyping and proliferation assays, Luminex multiplex and Cytometric Bead immunological assays, Peripheral blood mononuclear cell isolation, Intraepithelial lymphocyte isolation from intestinal biopsy, Cryopreservation, Immunological assay training. The Human Immunology Core will provide expertise and instrumentation for the analysis of immune function in patients during treatment with anticancer drugs and immunotherapy. The Core will serve as a central facility for incorporating the newest technologies and performing validated immunology assays for phase I/II clinical studies, while also offering expert scientific and technical consultations to users interested in conducting this kind of innovative research.
Penn Interventional Radiology Animal Catheter Lab
In the Interventional Radiology Catheter Lab minimally invasive procedures are performed via fluoroscopy, ultrasound and endoscopy. Percutaneous vein and arterial access is performed via ultrasound-guided technique. Surgeons are then able to guide catheters, ballon dilation, and other small instrumentation through the blood vessels. Procedures that have been performed in the lab are: * Angiography * Aneurysm creation * Balloon angioplasty * Embolization (coil, glue, embospheres) * Inferior vena Cava (IVC) filter placement & retrieval * Selective arterial catheterization * Stent placement (renal, gastric, iliac) * Peroral gastroenteric anastomosis This lab has capabilities for full surgical and anesthesia protocols and full fluoroscopy imaging. Included in the lab are a small office space, an LCD monitor and computer for the fluoroscopy unit, eye wash station and a surgeon scrub sink.
We share commentaries, news and announcement that advance our goal of helping clinical labs to adopt next generation sequencing for the analysis of diagnostic gene targets.
Core facility that provides the following services: Mass spectrometer access. The Mass Spectrometry Facility is part of the Shared Instrument Facilities of the Department of Chemistry. It provides low and high resolution mass spectra to Penn Chemistry and to other research groups throughout the university community for the determination of elemental composition and purity of a wide variety of compounds. Investigators interested in using the facility are encouraged to call and discuss their project. Usage fees will be quoted at this time. Fees depend upon the instrument involved in the analysis, complexity of the project, training, etc.
University of Pennsylvania Molecular Profiling Facility Bioinformatics
Core facility that provides the following services: Desktop sequence analysis tools subscription, Database and web applications support, Genomic-scale sequencing analysis, Sequence analysis application support, Transcript profiling consultation service, Transcript profiling application support, Transcript profiling data analysis, Automating large or repetitive tasks, Web space for biological databases, Bioinformatics/genomics resource identification, and Data storage. The bioinformatics staff of the Penn Molecular Profiling Facility is available to provide experimental design and analytical services to users of the Facility and the basic and biomedical research community. Additional services are provided, including grant support, data management and custom computational projects. This facility provides one-on-one training and hosts instructional workshops. Their goal is to ensure that scientists across the University are able to exploit existing and emerging computational technologies, especially related to their genomics scale datasets.
Core facility that provides the following services: NBIC instrumentation training, Scanning probe measurement service. The NBIC serves as an incubator for new probes of nanostructure behavior and associated instrumentation development. It is equipped with a suite of scanning probes, opto-electronic/transport tools, and optical probes that are so recently developed as not to be available on commercial instruments. The environment facilitates the development and refinement of new probe-based techniques.
Core facility that provides the following services: Behavioral testing training, Behavioral testing consultation service, Neurobehavior Testing Core access, Evaluation of anxiety behavior, Evaluation of circadian activity and rest/activity patterns, Measurement of sleep/wake patterns, Video image analysis of behavioral assays, Tissue harvest and histology prep service, Customized behavior batteries. The Neurobehavior Testing Core provides core facilities and services to test mice in state of the art assays of simple and complex behaviors, including the assessment of circadian rhythms and sleep, learning and memory, motor and sensory function, as well as behavioral assays relevant to translational studies of neurological, neurodevelopmental and psychiatric disorders. The core offers comprehensive behavior phenotyping of your mice or can train your lab personnel to perform the tests in the facility. In addition, we provide consultation on study design including appropriate tests, mouse line/strain, numbers of animals, control groups and breeding strategies. The core will also provide consultation regarding ULAR, IACUC and other regulatory issues. Assistance with data analysis is also available. The behavior apparatus available in the core includes: running wheels and beam splitters to measure circadian activity and rest/activity patterns as well as EEG/EMG recording chambers to measure sleep/wake states. Motor function is assessed using open field activity monitors and Rotarod. Apparatus to measure anxiety-like behavior including zero maze, light/dark chamber, passive/active avoidance chambers and hole poke arenas are also available. Extensive assessment of cognition, learning and memory is conducted with Morris water maze, radial arm maze, 5 choice serial reaction time test and object recognition tests. Tests of behaviors associated with depression (forced swim), schizophrenia (startle/PPI), social interaction (choice and social memory), and drug addiction (conditioned place preference) are also available. Tests of general health and responsiveness are also performed, as these are critical for the evaluation of complex behavior. Support for the core is provided by the Comprehensive Neuroscience Center, the Institute for Translational Medicine and Therapeutics, the Center for Sleep and Circadian Neurobiology and the Perelman School of Medicine.
Blog presenting news and information, and spur discussion about topics related to RNA-Seq.
Core facility that provides the following services: Sequencing sample preparation service, Illumina sequencing service, Initial analysis of sequencing data, Next-generation sequencing data delivery. The NGSC offers ultra high throughput sequencing services for the Perelman School of Medicine research community. We offer library quality assessments, sequencing, and optional preliminary data analysis for a wide variety of experimental protocols including ChIP-seq, RNA-Seq, HITS-CLIP, miR-Seq, exome capture, and BIS-seq. We offer limited library preparation services, but can advise on library preparation techniques. We have two Illumina hiSeq2000s for large-scale sequencing and a MiSeq for sample evaluation or library testing. To get started, visit our website, create an account for yourself, then create a new experiment and we will contact you.
Penn Proteomics and Systems Biology Core
Core facility that provides the following services: 2D-DIGE equipment access, Trypsin digestion, Metabolite profiling by mass spectrometry, Biomarker quantification by mass spectrometry, Proteomics analysis service. The Proteomics Core Facility in the Penn Genomics Institute is a service and collaborative research resource that balances applied proteomics research with the development of new and improved methods for protein identification, characterization, and quantification. The facility encourages collaborations that apply the tools of proteomics to cutting edge biomedical research. The Proteomics Core Facility is a center not only for services but also for basic and collaborative research and development of two-dimensional gel electrophoretic - and mass spectrometric-based techniques. Prospective users are encouraged to make their inquiries either by e-mail (ian@spirit.gcrc.upenn.edu), or stop by our facility on the eighth floor of BRB II/III.
Penn Diabetes Research Center Radioimmunoassay and Biomarkers Core Facility
Penn Diabetes Research Center Radioimmunoassay and Biomarkers Core
Core which offers high quality immunoassay services to basic, translational, and clinical investigators performing diabetes and related metabolic disease research. The core also provides consultation and training and education services.
The Penn Regional Nanotechnology Facility (PRN) is a full-service center equipped with a wide range of state-of-the-art instrumentation for materials analysis. Nanoscale characterization of polymers, ceramics, composites, metals, electronics, and thin films is conducted using scanning, transmission, and scanning-transmission electron microscopes, atomic force microscopes, and ion scattering techniques. A wide range of specimen preparation equipment is used including cryo-ultramicrotomy, jet electrolytic polishing, mechanical dimpling, ion beam thinning, tripod polishing, vacuum evaporation, sputter-coating and replication. Both analog and digital output are produced and in-house hardware and software are available for a wide range of image and spectrum processing tasks and for the calculation/simulation of electron-beam specimen interactions and microscope performance. The Nanotech Facility is setup to accommodate both academic and corporate users. Users have the option of working with a staff member or they may take advantage of our comprehensive user training in order to work independently on the instrument of their choice. Please feel free to contact us for any questions or comments about our facility.
The Small Animal Imaging Facility (SAIF) of the University of Pennsylvania provides multi-modality radiological imaging and image analysis for cells, tissues, and small animals. The SAIF combines state-of-the-art instrumentation and a nationally recognized staff to assist investigators with a wide range of imaging based experimental approaches. The SAIF currently provides a comprehensive suite of imaging modalities including: magnetic resonance imaging (MRI) and spectroscopy (MRS), optical imaging (including bioluminescence, fluorescence, and near-infrared imaging), computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), and ultrasound (US). In addition, dedicated housing is available for mice and rats undergoing longitudinal imaging studies. Ancillary facilities and resources of the SAIF are devoted to chemistry, radiochemistry, image analysis and animal tumor models, including assistance with animal handling.
BRENDA Tissue and Enzyme Source Ontology
A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
Penn Small Animal Imaging Facility: MRI/MRS Sub-Core
The MR Sub-Core of the SAIF provides the instrumentation and expertise necessary to perform a broad spectrum of magnetic resonance imaging and spectroscopy studies on a wide range of biological samples including small animals (cats, rabbits, rats, mice), tissue specimens, cultured cells and tissue extracts. This facility includes a conveniently located, well equipped surgery room used for preparing the animals for MR exams and a wide assortment of supporting equipment, i.e. anesthesia machines, MR compatible vital signs monitors (SA Instruments), infusion pumps (Harvard), heating pads, etc. A variety of perishable supplies used in animal preparation are provided by the facility.
Penn Small Animal Imaging Facility: Optical/Bioluminescence Sub-Core
Core facility that provides the following services: Optical/bioluminescence in vivo imaging, Small animal bioluminescence/fluorescence imaging support services. The Optical/Bioluminescence Sub-Core of the SAIF provides the capability to perform cellular and molecular non-invasive in-vivo bioluminescence, fluorescence or near-infrared imaging. The instrumentation allows sensitive, non-invasive molecular imaging for a variety of applications including detection and quantification of various bioluminescent or fluorescent reporter-expressing cells or tissues (in culture or in small animals). The facility currently houses a Perkin Elmer IVIS Lumina II, two LI-COR Pearl Impulse Imagers and a Perkin Elmer IVIS Spectrum. The Facility offers assistance with experimental design, regulatory approval, troubleshooting, data management, analysis and display.
Penn Small Animal Imaging Facility: Ultrasound Sub-Core
Core facility that provides the following services: Contrast enhanced sonography, Quantitative analysis of images, Small animal ultrasound imaging, Blood flow velocity measurement, Tissue motion measurement. The Ultrasound Sub-Core of the SAIF offers an array of research services for pre-clinical research including quantitative image analysis and consultation. Our state-of-the-art ultrasound scanners are available as a resource for conducting your research studies. This rich resource for ultrasound imaging is available at nominal hourly fees for various categories of study. Ultrasound Research Services provides services to a host of groups working on diverse projects such as the measurement of angiogenesis, vascularity, tissue elasticity, the effects of various pharmaceuticals on these measures and more. Such research encompasses a variety of clinical areas including radiology, oncology, cardiology, gynecology, and hematology, among others.
Pennsylvania University Perelman School of Medicine Stem Cell and Xenograft Core Facility
Penn Stem Cell and Xenograft Core (SCXC)
Pennsylvania University Perelman School of Medicine SCXC
Offers in vivo services specializing in immunodeficient and xenograft models (PDX, humanized immune system). Facility has dedicated BSL2 barrier space equipped with optical imaging, for applications ranging from immunotherapy, cancer biology, infectious diseases and regenerative medicine. Offers services centered around repository of live and fully annotated cells from adult patients with hematologic malignancies (AML, ALL, MPN, MDS), and hematopoietic stem/progenitor cells from healthy donors (BM, CB, and FL).
Penn Diabetes Research Center Transgenic and Chimeric Mouse Core Facility
Penn Diabetes Research Center Transgenic and Chimeric Mouse Core
Mouse core which generates transgenic and gene-targeted mouse lines for diabetes research.
UH Manoa RCMI Magnetic Resonance Image Processing Core
Core facility that provides the following services: Brain MRI service. Researchers in the Neuroscience and Magnetic Resonance Research Program are using a research dedicated 3-Tesla scanner to study the human brain and brain diseases. Facilities: The Magnetic Resonance (MR) Processing Core serves the needs of researchers in the MR Research Facility at Queen''s Hospital. Specifically, the MR Image Processing Core provides image processing support, infrastructure development, methodological development and training; expertise is available.
University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Vector Core Facility
University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Vector Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core whose main aim is to provide vector technology for preclinical studies and other basic research applications. Its services include rovision of AAV, adenoviral and lentiviral based vectors, consultation and advice in the design of custom vectors and in vector serotype/pseudotype selection, and design, cloning and production of plasmid DNA for the production of custom vectors.
A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. It can furthermore serve as top-level model for creating new ontologies for more specific domains or as aid for aligning or improving existing ones.
Core facility that provides the following services: Outpatient study facility access, iDXA scan service, Research specimen processing, Research specimen storage, NIH/Industry clinical trial support, Pharmacy laboratory access, Adipose biopsy, Patient assessment and monitoring, Metabolic testing service, Phlebotomy, Support for bone marrow biopsies. The Clinical and Translational Research Center (CTRC) has two main locations as well as satellite locations. The protocols cover a wide variety of research areas including: HIV, sleep disorders, cholesterol, obesity, diabetes, various cancers, arthritis, hypertension, renal disease, short bowel syndrome, and neonatal and surgical studies as well as new treatments for various diseases. The CTRCs service over 1200 inpatients and over 6000 outpatients a year. Research subjects range from premature infants to the elderly, with the majority of adults being seen at HUP. HUP Unit - Dulles Building: * 8 bed inpatient * 8 chair and 2 bed outpatient unit * metabolic kitchen * Scatterbed nursing services throughout hospital units including the ICUs, ED and operating rooms UPPMC Unit ? 1st Fl Mutch Building: * 18 outpatient treatment beds * metabolic kitchen CHOP Units: * 4 bed inpatient unit - 5 West Main * outpatient unit with 2 treatment rooms, 4 treatment chairs and a consultation room - Main 7 * Scatterbed nursing services in Newborn Nursery - Ravdin Building The nurse manager should be contacted prior to submitting a new protocol submission to the CTRC and discussions should continue throughout the start-up process.
The CTRC Sleep Core provides services in support of clinical sleep research. It is based at two sites: the CHOP Sleep Laboratory, convenient to the CTRC Outpatient Facility on the 7th Floor of Main Hospital and the University of Pennsylvania?s Sleep Laboratory, located on the 11th Floor of the Gates Building which is part of the medical complex of the Hospital of the University of Pennsylvania. The Sleep Core contains a total of six designated research beds, dedicated staff, and state-of-the-art equipment that provides support for a variety of sleep-related research initiatives. Studies performed in the Sleep Core include overnight polysomnography, multiple sleep latency testing, neurobehavioral testing and actigraphy. The Sleep Core��s goals include providing highest-quality sleep studies, extending sleep research to disciplines not traditionally involved in this area, further developing extant multidisciplinary programs, and offering training opportunities for medical students, residents, fellows, and junior faculty in clinical sleep research. The Sleep Core is associated with CHOP?s and UPHS? American Academy of Sleep Medicine-accredited Sleep Center Laboratories. Services for pediatric and adult subjects: * Study Design * Overnight Polysomnography ** Polysomnography Interpretation * Multiple Sleep Latency Testing * Actigraphy * Neurobehavioral testing * Sleep Core Library
Core facility that provides the following services: Gene expression analysis service, SNP analysis service, Genotyping service. We conduct microarray-related experiments, including developing chips for pathogen discovery, evaluating RNA quality and test chips, processing RNA specimens, hybridizing microarray chips, scanning microarray chips and providing raw data for analysis.
Penn/CHOP CTRC Study Design and Biostatistics Core
Core facility that provides the following services: Data management assistance, Biostatistical analysis assistance. The Study Design and Biostatistics (SDAB) Core works closely with existing resources to provide targeted study design and biostatistics support to ITMAT/CTSA investigators. The Core serves as a direct provider of services, including protocol review, study design, proposal development, and performance of simple to potentially substantial complex analyses. SDAB integrates the support available with the HUP and CHOP Clinical and Translational Research Centers (CTRCs), the expertise and resources of faculty in the Center for Clinical Epidemiology and Biostatistics / Department of Biostatistics and Epidemiology (CCEB/DBE), the Biostatistics Analysis Center (BAC), and the Biostatistics and Data Management Core (BDMC) at CHOP.
Penn/CHOP CTRC Translational Core Laboratories
Core facility that provides the following services: Cell culture and tissue services, DNA isolation service, Cell culture and tissue services, Epstein Barr Virus (EBV) lymphocyte transformation service, Cell culture and tissue services, Fibroblast culture and cryopreservation service, Cell culture and tissue services, Specialized cell isolation service, Molecular biology services, microsatellite haplotyping service, Molecular biology services, mutation analysis service, Molecular biology services, Restriction fragment analysis service, Molecular biology services, RNA services, Molecular biology services, SNP genotyping service, Specimen Collection, Processing, and Point-of-Care services, Bedside tests by Bayer Rapid Point 400, Specimen Collection, Processing, and Point-of-Care services; Collection, processing and storage of specimens, Specimen Collection, Processing, and Point-of-Care services, Packaging and shipping of samples. The Translational Core Laboratory consists of the Specimen Collection, Processing and Point of Care, Biochemistry, Cell Culture/DNA Isolation, and Molecular Biology core laboratories. Laboratory testing is integrated across Penn and CHOP, and TCL services are provided at multiple physical locations at both Penn and CHOP. Penn location: first floor Smilow Center for Translational Research CHOP location: 804 Abramson Research Center (ARC)
Puerto Rico Clinical and Translational Research Consortium Patients Coordinator Services
Patient Coordinator Services is responsible for scheduling the subjects for the research-related appointments; her goal is to facilitate the participation of the subjects in the clinical studies in collaboration with the research staff and the investigators.
Penn/CHOP Office of Human Subject Recruitment and Protection
Core facility that provides the following services: Clinical study support services. The Office of Human Subject Recruitment and Protection (OHSRP) provides consultation and guidance to the Penn research community on all issues related to adult and pediatric human subjects being seen through the CTRC facilities, including recruitment and protection. The role of the OHSRP is to champion the mission of the feasible, safe and ethical conduct of human subject research within the CTRC. The original Research Subject Advocate (RSA) was a position mandated by the National Center for Research Resources under the NIH and was defined in order to ensure that research was being conducted in ways that did not increase the risk associated with conducting studies. In April 2008, the CTSA Consortium Steering Committee approved and endorsed best practices, which serve to define the mission, scope, and model for research advocacy within the CTSA consortium. The OHSRP has advanced the role of the Research Subject Advocate (RSA) by adopting the 2008 best practices defined by the CTSA Consortium. The OHSRP operations are complementary to and integrative with existing entities at the institution to promote and facilitate safe and ethical conduct of human research. The OHSRA complements the University of Pennsylvania Office of Human Research (OHR) and Institutional Review Board (IRB) in support of ensuring the safety of individuals participating in health research. The OHSRP serves as a resource to the research community and to participants; has a voice in policy regarding research ethics, participants? rights, and research safety; and plays a role in the protection of human subjects and responsible conduct of research educational programs of the institution. The OHSRP has direct access to, an authority that can temporarily suspend a research activity based on ethical and safety concerns so that problems can be explored or resolved through proper procedures. This capacity enables preliminary intervention into problems that might not necessarily invoke an institutional review board (IRB) suspension. The OHSRP has a reporting pathway to institutional officials of appropriate authority and is free of conflict of interest.
Ponce School of Medicine and Health Sciences AIDS Research Infrastructure Core
Core facility that provides the following services: HIV viral load test, Immunoprofile assay, HIV genotype by sequencing assay, Virtual phenotyping assay, RNA and DNA tropism, HCV genotyping, HCV qualitative and quantitative test, HIV ELISA. The Ponce School of Medicine (PSM) RCMI AIDS Research Infrastructure Program (ARIP) proposes to further upgrade its core laboratory units in order to best meet the needs of current and prospective ARIP faculty members. It also proposes to facilitate the institution of career development programs specifically designed to meet the identified requirements of the ARIP faculty members; the current mentoring and partnership program will be strengthened to support their careers. The proposed ARIP Phase V activities will revolve around three specific aims. Specific Aim #1: To further improve and expand the research capabilities of the AIDS research core laboratories in viral genetics, immunology, and drugs of abuse. ARIP cores will be made accessible to the AIDS/HIV investigators from other institutions and countries in order to facilitate the development of high caliber collaborative research that will share the same technologies. The advanced technologies and instrumentation offered by ARIP will enable investigators to study the characteristics of the AIDS/HIV infection in the Caribbean region. Sophisticated instruments and equipment will be made available in real time to investigators from other institutions (via an Internet-2 connection) in an ongoing effort to foster collaboration. By accessing the institution website (www.psm.edu), interested investigators can take part in online training sessions as well as reserve instruments. Specific Aim #2: To implement a career development program (tailor-made for individual ARIP faculty members) that will include research & career mentoring, research consultation, and partnership development. A concerted effort will be made to develop a viable institutional faculty retention plan, which will include faculty incentives through research enterprise activities; in the past, lack of effective faculty development and retention programs has caused the loss of key members. Critical self-analyses were performed to identify the needs of current faculty members so that specific plans might be designed around the requirements of each individual. Specific Aim #3: To implement additional AIDS/HIV-related research programs at PSM as well as at the island?s other three RCMI-sponsored institutions. PSM currently has eight faculty members with actively funded AIDS-related independent research projects (representing the greatest number among the PR RCMI institutions). ARIP members have been active in pursuing the possibility of developing CFAR and CTSA proposals via the program?s ongoing partnership with the consortium of U-FL, USF, FCU, and FSU.
Ponce School of Medicine and Health Sciences Behavioral Core Facility
Core facility that provides the following services: Pavlovian fear conditioning, Freezing response analysis, Insertion of cannula. The goals of this core are to enhance the neuroscience-related projects currently being undertaken by PSM investigators and to stimulate further neuroscience research through enhanced scientific interactions between basic scientists at PSM. In addition, this neuroscience core facility will also serve as a tool for attracting strong new recruits.
Ponce School of Medicine and Health Sciences Molecular Biology Core Laboratory
Molecular biology is a field with a tremendous capacity for advancing our scientific understanding of disease and human health. Our Core facility provides its users with a centralized source of expertise as well as access to sophisticated instrumentation. This strong combination of knowledge and equipment helps to increase the productivity of the scientists at PSM so that they may more quickly make discoveries that can be translated to the clinical level and thus have a measureable impact on improving health in the US and worldwide.
The Microscopy and Imaging Core at the University of Hawaii Cancer Center (CC) provides access to a wide range of imaging instruments to UHCC member, and will soon extend the service to non-members. The facility also offers access to a licensed MetaMorph software package for the processing and analysis of microscopy images. Currently, the core houses four major instruments and three microscopes for routine fluorescence and brightfield use. The core is also in charge of maintenance and service of an IVIS Lumina (Caliper Life Sciences). This is a highly sensitive system to image fluorescent and/or bioluminescent reporters both in vivo and in vitro.
Proteomics Center at Childrens Hospital Boston
Proteomics Center at Children''s Hospital Boston
Core facility that provides the following services: Protein identification from Coommassie stained gel, Protein identification from silver stained gel, Protein identification from complex mixtures (in solution) service, Running SDS-PAGE service, SILAC (Data Acquisition and Analysis), ICAT (Data Acquisition and Analysis), ITRAQ (Data Acquisition and Analysis). The Proteomics Center at Children''s Hospital Boston offers the most up-to-date proteomics equipment currently available. This includes the latest equipment for protein separation and several state-of-the-art mass spectrometers, which detect and quantify proteins in a sample and measure them to determine their structure and characteristics.
Puerto Rico Clinical and Translational Research Consortium Biostatistic Core Laboratory
The goal of the Biostatistical Support Service is to provide investigators expert advice on proper study design and data analysis. The support includes consults with the center biostatistician, faculty consultants from the School of Public Health, Department of Biostatistics and Epidemiology, Medical Sciences Campus, University of Puerto Rico, and use of statistical software.
Free online tools to find the best Sequencing Service provider for your project.
Puerto Rico Clinical and Translational Research Consortium Research Subject Advocate
The Research Subject Advocate''s main responsibility is to assure that all steps are taken throughout any clinical research activity to protect the participating subjects and to ensure that their safety is given the highest priority. Also it is her responsibility to assure that all investigators/collaborators and CRC personnel are managing patient health information according to the Health Information Portability and Accountability Act.
The Biostatistics Core serves the needs of the HIV/AIDS researchers within the Ragon Institute and its affiliates. In particular, members of the Biostatistics Core provide expertise in the planning, conduct and analysis of research with the goal of enhancing the scientific quality of HIV-related research at the institute. The primary objective of the core is to ensure that studies are well designed, correctly analyzed, clearly presented, and correctly interpreted.
Ragon Institute Imaging Core Flow Cytometry
Core facility that provides the following services: Flow Cytometric Cell Sorting. The mission of Ragon Institute Imaging Core, Flow Cytometry Division is to provide training and access to flow cytometers with up to 18 parameters, as well as cell sorting of biohazardous samples. As an MGH Core Facility, the Ragon Institute Imaging Core serves the greater MGH community. Since the Ragon Institute is also a collaboration between MGH, Harvard, and MIT, so too does the facility welcome members of the MIT and Harvard communities. The facility is equipped with three LSR2?s, an LSR Fortessa, a FACSCalibur, and a FACSAria IIu cell sorter in a biosafety cabinet. The core also serves as a resource for addressing a variety of flow cytometry needs including consultation on topics related to experimental design and sample preparation.
Core facility that provides the following services: Research equipment design and fabrication service, Sample collection service, Animal transporting/shipping service, Animal handling and husbandry service, Breeding colony management service. Animal Quarters (AQ) provides safe and sanitary facilities for animal research projects in accordance with the Animal Welfare Act, Public Health Service Policy, National Institutes of Health Guidelines for the Care and Use of Laboratory Animals and the UAF Institutional Animal Care and Use Committee. Housed animals include arctic ground squirrels, laboratory mice, red-backed voles, syrian hamsters, American widgeon, northern shovelers, lesser scaup, greater scaup, northern pintail, green-winged teal, zebrafish, sticklebacks, bettas, and black bears.
Core facility that provides the following services: Microscopy Instrumentation Access, Training in Microscopy/Imaging, Assisted Microscopy. The mission of Ragon Institute Imaging Core, Microscopy Division is to bring the latest imaging modalities and technology to bear on fundamental molecular and cell biological questions pertaining to infectious diseases. As an MGH Core Facility, the Ragon Institute Imaging Core also serves the MGH greater MGH community. Since the Ragon Institute is also a collaboration between MGH, Harvard, and MIT, so too does the facility welcome members of the MIT and Harvard communities as we are now located in Cambridge at MIT. The facility encompasses five imaging systems, including a Zeiss LSM510 laser scanning confocal microscope and a fully automated Zeiss Axio Observer microscope, both housed in BL2+ compliant facilities. These imaging systems are therefore fully equipped for both fixed and live cell imaging. In addition, the facility has two slide scanning systems (MIRAX MIDI and TissueFAXS) for high speed automated imaging and cellular screening of tissue sections and cultured cells on glass slides. In the Flow Cytometry section of the Imaging Core, we also have an ImageStream X Mark II by Amnis. The core also serves as a resource for addressing a variety of imaging needs including consultation on a topics related to imaging applications, experimental design, and sample preparation.
Core facility that provides the following services: Coulter XL flow analysis, Cytomation MoFlo cell sorting, LaserScan Cytometry, BD Biosciences LSR II flow cytometry analysis, Flow cytometry data analysis. The Flow Cytometry Facility is a core facility of Schepens Eye Research Institute that provides fluorescent-based cell analysis and sorting to Boston area biomedical researchers.
TSU Biosensor Biomarker and Environmental Toxicology Core Facility
The Biosensor and Biomarker Technology (BBT) Core Facility is a research support facility at Texas Southern University (TSU) that provides technical and resources support as well as hands-on training in molecular and biochemical techniques for environmental and biomedical research investigators. The main objective of the BBT is to provide essential research infrastructure to improve and facilitate the research capabilities of faculty investigators and graduate students at TSU. To accomplish this goal, the BBT core facility provides assistance to research investigators in the following molecular, environmental and toxicological techniques through RCMI-sponsored research resources.
TSU Environmental Research and Technology Transfer Center
The goal of the center is to address training, research problems, and technology transfer issues as they relate to the environment; by increasing the number of under-represented minority graduates in science, mathematics, engineering, and technology. ERT2C projects focus on analysis of toxic elements and compounds in a closed environment, trace metals in soil, soil sediments, air and wastewater processes, wastewater contaminants, and environmental policy and law. The Core Analytical Facility is an important component of the center. The Core?s mission is to achieve regional, community, and national recognition as a quality environmental analytical laboratory and environmental research program. This Mission will be achieved through the characterization of environmental toxicants in the ambient environment (air, soil, and/or water) and the investigation of the mechanisms involved in the toxicity effect.
Core facility that provides the following services: Analysis of gene function by RNA interference, MicroRNA profiling, Chromatin immunoprecipitation (ChIP) assay, Flow cytometry, Conventional and real time PCR assays.
Tuskegee Center for Biomedical Research - Digital Imaging
CBR/RCMI provides digital imaging facilities at three locations on the TU campus. The locations are Williams-Bowie Hall, The Carver Research Foundation, and the TU Animal Facility. The equipment within the facilities allows for numerous microscopy techniques, including the use of fluorescence, bright field, dark field, confocal, wide-field and long-term viewing of living cells. Additionally, an in vivo imager is available for non-invasive rodent studies.
Tuskegee Center for Biomedical Research Shared Instrumentation Core
TU Center for Biomedical Research Shared Instrumentation Core
THIS RESOURCE IS NO LONGER IN SERVICE, documented January 23, 2019. Core Facility enhances multidisciplinary research infrastructure by providing resources, services and technical support. Solely for Tuskegee University. Primary goal is achieved by providing instrumentation and personnel in two Cores. Core One addresses the need for lab instrumentation and Core Two provides resources in the areas of bioinformatics, computational biology and information technology.
Tuskegee University Computational Biology and Bioinformatics - Biomedical Information Management Services
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core provides services and training in computational biology, bioinformatics, experimental design and statistical analysis to the RCMI researchers and the biomedical research community at Tuskegee University.
UAF Community Engagement and Clinical Support Core
Core facility that provides the following services: Biological sample processing service, Research subject private information management service. The Community Engagement and Clinical Support Core facilitates and supports community-based participatory research by drawing on local community knowledge and scientific expertise to implement and evaluate culturally valid and effective approaches to research in Alaska Native communities. The functions of the core include: * Facilitating and sustaining community/CANHR partnerships by engaging the community in all phases of the research process. * Supporting researchers in the development and implementation of linguistically and culturally appropriate research protocols. * Providing technical capacity to collect clinical measures and biological samples. * Processing all biological specimens collected in the field and maintaining a secure biological storage facility for CANHR investigators and Alaska Native participants. The CECS Core supports CANHR''s central theme of community-based participatory research through strong and sustaining community partnerships with Alaska Native people.
Core facility that provides the following services: Sample sequencing service, Sequencing service, Fragment analysis service, Real-time PCR training service. A staffed facility intended to keep UAF at the cutting edge of nucleic acid analysis in evolutionary biology, molecular biology, and wildlife and fisheries management. The Core Facility provides nucleic acid sample analysis, and maintenance and support for molecular instruments (some of which may be too expensive for individual labs to own) for both UAF and outside users.
Ontology that facilitates representing the family health histories of persons related by biological and/or social family relationships (e.g. step, adoptive) who share genetic, behavioral, and/or environmental risk factors for disease. SWRL rules are included to compute 3 generations of biological relationships based on parentage and family history findings based on personal health findings.
UAF Epidemiology and Biostatistics Core Laboratory
Core facility that provides the following services: Data storage service, Confidentiality assistance service, Data entry service, Data importing service, Data extraction and monitoring service, ID linkage and tracking service, Quality control services, Database development and maintenance service. The EBC staff provide support for CANHR research projects in all data-related activities, including data entry, the development and management of databases, and generation of data related to field visits, analyses, and research proposals. It provides expertise in statistical and epidemiologic issues and is responsible for training seminars on the preparation of grants and publications.
UAF Nutrition and Physical Activity Core
Core facility that provides the following services: Data quality control and management service. The Nutrition and Physical Activity Core supports multidisciplinary research requiring dietary and/or physical activity assessment, as well as provide nutritional sciences expertise. The NPA Core offers a range of services including high-quality dietary assessment, active collaboration in the design, implementation, and analysis of nutrition-related research. In addition to supporting the needs of CAHNR projects, the NPA Core will also actively promote and foster new research programs investigating the diet of Alaska Natives.
The primary research of the laboratory aims at understanding the role of Rho-subfamily small GTPases, in particular Rac1A, as pivotal regulators of actin filament dynamics and redox homeostasis in central nervous system (CNS) neurons. A second project addresses neuronal stem cells and their generation, functional integration, and elimination in the adult male wild songbird Junco hyemalis.
Core facility that provides the following services: Free movement behavioral testing data acquisition and analysis service, Small animal vital sign evaluation. The Behavioral Testing Facility was created to facilitate the development of neuroscience research at the Universidad Central del Caribe recognizing the importance of behavioral testing. The facility has two mayor components: A) the equipment infrastructure and B) the technical support division. The facility offers equipment for remote behavior visualization (RBV).
Core facility that provides the following services: Protein separation service, 2D gel production, Analysis of protein distribution of 2D gel, Standardized imaging of 2D gel, Mass spectrometry analysis service, Desalting, Trypsin Digestion. The mission of the UCC Biomedical Proteomic Facility is to accelerate discovery by giving UCC investigators access to cutting edge mass spectrometry are rapidly advancing and requires considerable technical expertise and expensive equipments. To keep UCC scientists competitive, new technologies will be incorporated into the facility as soon as possible to meet the needs. The facility is open to all investigators on collaboration or a fee-for-service basis. User fees will be adjusted depending on demand and to keep costs competitive.
UCC Data Management and Statistical Research Support Unit
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 26,2026. Core facility that provides the following services: Research support, Research Training. The DMSRSU provides study design, data management, quality assurance, and statistical analysis support for UCC researchers. The DMSRSU has a strong infrastructure which includes the following subunits: Data Abstraction and Management; Data Entry; Quality Control; Data Analysis and Consultant; and Administrative and Computer Systems. Each of these subunits consists of experienced professionals readily available to assist researchers and to provide data management and statistical research support to investigators. In addition, the DMSRSU counts on a highly experienced and reliable consulting team.
UH Manoa COBRE Molecular and Cellular Immunology Core
UH Manoa COBRE Molecular & Cellular Immunology Core
Core facility that provides the following services: Cell cycle analysis with live or dead cells, Apoptosis analysis service, Calcium flux analysis service, Cell population isolation service. The of the goal of the Immunology Core of MCI, which functions as a fee-for-service facility, is to provide the Hawaii community with a service-oriented facility to meet the needs in the FACS research areas. We are equipped with BD FACSAria, BD FACSCalibur, GuavaEAsyCytePlus, Luminex 200, Beckman-Coulter ViCell, CTL-ImmunoSpot�� S5 Core Analyzer, Bio-Rad and BioTek ELx808 ELISA readers and washers, Faxitron compact 43855D x-ray irradiation system, and Faxitron x-ray CP160 for in vivo animal work.
UCC HIV and Substance of Abuse Laboratory Core
Core facility that provides the following services: HIV and HCV viral load extraction, Amplification and detection of HCV and HIV viral load, HIV-1 and HCV drug resistance genotyping, Neurotoxicity and neuroprotection assays, PBMC antiviral assay, MAGI antiviral assay, HIV-1 Tat inhibition assay, HIV p24 measurement service, Cytokine/Chemokine measurement, Hormone measurement, NF-kB expression induction assay, Detection of TH1, TH2, Treg, and TH17 cytokine profiles in T lymphocytes subsets, Immunophenotyping, intracellular cytokines/chemokines and apoptosis assay service, B and T cell immune activation, function, proliferation and differentiation assays, Macrophage function assay, Cell viability, cell proliferation and cytotoxicity, Cell cycle analysis, Inflammation and oxidative stress Calcium mobilization, kinase activation, and signal transduction, Gene expression service, Apoptosis test, In vivo/in vitro cytotoxicity measurement, Plaque and colony formation counting, Inflammation antibody array service, Apoptosis antibody array service, Angiogenesis antibody array, Protein and gene expression study, Standardized imaging of 2D gel. The laboratory supports research in the areas of HIV/AIDS and substances of abuse. Specialized facilities are made available to researchers for scientific studies in fields of immunology, drugs of abuse, HIV/AIDS and related infectious diseases. The core lab provides researchers with assays for nucleic acids detection, virus genotyping, flow cytometric phenotyping, lymphocyte proliferation, cytotoxic and non-cytotoxic activity, cytokine and chemokine determinations, and drugs of abuse quantification.
Core facility that provides the following services: Immunocytochemistry service. The immunocytochemistry laboratory specializes in the qualitative identification and localization of cells bearing selective markers by employing specific antibodies to these molecules.
Core facility that provides the following services: Qualitative measure of neuronal death, Computerized image analysis. The goal of the facility is to assist UCC investigators in the use of cultured neurons, glias and organotypic cultures. The cultures are used for patch clamping after in vitro treatments with drugs of addiction or inhibitors and for in vitro models of neurodegenerative diseases. The core facility consists of a coordinator and a technician. Neuronal cultures are prepared from fetal cortex, hippocampus or astrocytes from cerebral cortex.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 26,2026. The facility offers microscope-based systems that allow the assessment of cellular responses, such as calcium signaling with fast temporal resolution. The facility offers 1) Confocal imaging services; 2) Brightfield, darkfield, phase contrast, Nomarski and epi-fluorescence imaging; 3) High spatial and temporal resolution imaging, 4) Collection of serial sections (Deconvolution capabilities) and 5) Morphometric analysis.
UCC Protein and Nucleic Acid Core Facility
Core facility that provides the following services: Nucleic acid sequencing service, Real-Time PCR services, Cell culture service, Protein quantitation assay, Nucleic acid estimation service, Fusion protein purification and expression service, Transfection service, Site-directed mutagenesis service, Primer design service, Gel electrophoresis service, Polymerase chain reaction service. The Protein and Nucleic Acid Core Facility (PNACF) aids in the transition from classical to molecular analysis of the problems being addressed by faculty members. PNACF focuses on faculty training, seminars, training on specialized molecular biology techniques, protein expression and protein purification and characterization.
UCC Transmission Electron Microscopy Laboratory
Core facility that provides the following services: Image acquisition training. The TEM laboratory provides access to ultrastructural analysis of biological specimens via a Jeol 100 CX transmission electron microscope. The TEM is equipped with AMT 4 MP digital camera to facilitate image acquisition and 3D reconstruction from serial sections. In addition, to conventional EM procedures of in situ and cell culture specimens the laboratory also offers imunnogold labeling and the visualization of fluorescent dyes after photoconversion.
Core facility that provides the following services: Solid state studies service.
UH Manoa Hawaii Center for AIDS Imaging Analysis Core
Core facility that provides the following services: MRI image analysis service, MRI image processing service.
Swiss Commission for Technology and Innovation
Commission for Technology and Innovation
Commission for Technology and Innovation CTI
Swiss Commission for Technology and Innovation CTI
Swiss Commission for Technology Innovation
UH Manoa Analytical Biochemistry Shared Resource
Core facility that provides the following services: ELISA-based assay service, Luminex based ELISA assay service, Coenzyme Q10 in plasma analysis by HPLC/ECD (oxidized, reduced and total Q10), DNA analysis by HPLC, Phenolic agents from plasma, urine, breast milk, foods analysis by LC/MSMS, Lipid-phase micronutrients in plasma or foods analysis by HPLC/PDA/FD (12 carotenoids, 2 retinoids, 3 tocopherols), Metabolomics analysis by LCMS, Vitamin A and pro-vitamin A in plasma analysis by HPLC/PDA, Vitamin C in plasma, food analysis by HPLC/ECD or PDA, Vitamin D in plasma analysis by LC/MSMS, Vitamin E in plasma analysis by NP-HPLC/PDA/FD (all tocopherols), Vitamin K analysis by LC/MSMS. The Analytical Biochemistry resource was established to support and facilitate collaborative cancer research between the various disciplines at the Center by providing chemical analyses which contribute to understanding chronic diseases in our population. It also assists in the determination of the nature or structure of biological molecules as well as the quantification of those compounds. The facility is equipped with essential instruments needed to perform analytical chemistry, and modern, state-of-the-art technology for difficult-to-measure and ultra-low concentrated compounds.
A 2000 square foot BSL-3 facility located at the University of Hawaii, JABSOM.
UH Manoa Biological Electron Microscope Facility
Core facility that provides the following services: Scanning electron microscopy service, Conventional and energy-filtering transmission electron microscopy service, Laser scanning confocal microscopy service, Fluorescence microscopy service, Laser microdissection and laser tweezing service. The Biological Electron Microscope Facility (BEMF) at the University of Hawai''i is a multi-user/service facility, administered by the Pacific Biosciences Research Center (PBRC). The mission of the BEMF is to provide biological-biomedical researchers with state-of-the-art instrumentation, training and services for high-resolution scanning electron microscopy, conventional and energy-filtering transmission electron microscopy, optical, fluorescence, and laser scanning confocal microscopy, and image analysis on a recharge basis. The facility receives partial support from the Pacific Biosciences Research Center and the UH Manoa Chancellor''s Office. Includes the Richard Allen Image Collection, a unique set of images taken with electron microscopes (http://www5.pbrc.hawaii.edu/allen/).
The Biostatistics Shared Resource (BSR) provides statistical consultation and support to the research enterprise of the University of Hawai?i Cancer Center. The primary goal of the resource is to improve the quality of the research through sound statistical principles. The resource was established in 1995 and provides access to statistical support to all Center members on all aspects of research. The BSR provides short-term as well as long-term support for research projects. Support is provided to scientists in epidemiology, health behavior and quality of life research, and molecular and clinical oncology. The members of the Shared Resource often serve as co-investigators on epidemiology and cancer prevention and control projects. Consultation is available in the following areas: design, data collection, data analysis, statistical programming, interpretation and dissemination of results, and protocol review. The members of the resource have contributed to the publication of many peer-reviewed manuscripts from Center research projects. In addition, the statisticians work on methodological issues important to the research ongoing at UH Cancer Center. One area of interest is measurement error models that correct for bias in model parameter estimates when the exposure variable is measured with error. The role of dietary intake and sunlight exposure in cancer etiology are of interest at the Center, and these variables are measured with error. Another interest is in how susceptibility genes affect cancer risk, in combination with exposure data. Therefore, statistical techniques for the investigation of genes and lifestyle-gene interactions in cancer models are also studied.
University of Hawaii at Manoa Centers of Biomedical Research Excellence Bioinformatics Core Facility
Centers of Biomedical Research Excellence
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core provides access to high speed computer hardware and bioinformatics consultation. Research at the facility includes studying of evolutionary change in emergent dengue viruses associated with increasingly severe epidemics and confirm the impact of these changes in experimental models.
Core facility that provides the following services: Real-time/quantitative PCR service, Long read (900bp) sequencing service, Microarray sample labeling service, Automated liquid handling service, DNA/RNA sample concentration service, Spectrophotometry service, Microarray scanning service. Offers services in the areas of qPCR, Microarray, Sequencing, and Other Genomic Services. May expand or remove services depending on need or interest. If you have recurring processes that you would like to automate or have us take over, we would be glad to sit down and talk with you to discuss how we can help you acheive your goals. We are aiming to be a self-sustaining entity consisting solely on a chargeback system. Our prices reflect the costs of equipment service contracts, potential and actual maintenence costs, as well as direct and indirect labor costs and administration. Our costs are kept low by being able to provide services in bulk with high throughput, it is therefore sometimes necessary to have minimum orders or fees in order to maintain a positive cost structure.
Core facility that provides the following services: Fluorescent microscopy consultation service.
Core facility that provides the following services: Aortic banding service, Echocardiogram service, Blood pressure measurement service, Osmotic pump implantation service, LAD ligation service, Mini pump insertion service, Isolated perfused heart assay service, Cryoablation service, Cardiac output measurement service, Small animal surgery service, Transverse aortic constriction service, Invasive hemodynamic measurement service, Tail vein injection service, Training and advice for general mouse surgery techniques. The Center for Cardiovascular Research provides a Mouse Phenotyping Core for the use of investigators at the University, and by special arrangement, for investigators anywhere in Hawaii. We can provide murine echocardiography, blood pressure determinations, surgical procedures and phlebotomy, as well as assistance with mouse husbandry and genotyping.(http://www2.jabsom.hawaii.edu/mousecore/)
Core facility that provides the following services: Transgenic mouse generation, In vitro fertilization (IVF) service, Embryo culture service, Embryo freezing service. The Transgenic and Embryonic Stem Cell Gene Targeting Core is a state-of-the-art facility with the expertise in the production of genetically altered subjects. Transgenic subjects carrying new or novel genes are created by microinjection of DNA into the pronuclei of fertilized eggs. Knock-out lacking specific genes of interest are created by homologous recombination in embryonic stem cells followed by injection into blastocysts to create chimeric subjects. Highly experienced personnel produce transgenic and knock-out subjects for UH investigators at very reasonable cost and with very short lead times. (http://www.ibr.hawaii.edu/tc.html)
UH Manoa Clinical Protocol and Data Management Shared Resource
UH Manoa Clinical Protocol & Data Management Shared Resource
The Clinical Protocol and Data Management Shared Resource (CPDM) is a component of the Center?s Clinical Trials Unit that provides central management and oversight of all clinical trials activities of the Center. The Shared Resource provides a range of management and quality control functions that are essential for conducting clinical trials research in Hawaii?s decentralized community practice setting. It includes a central location for all cancer protocols, a centralized database of protocol-specific data, an updated list of currently active protocols for the use of Center investigators, and status reports of protocols. It provides a centralized organization for activating and monitoring protocols throughout Hawaii?s multiple community offices and medical centers involving several Institutional Review Boards (IRBs). Quality control functions include: insuring subject safety and compliance with federal requirements through the Data and Safety Monitoring plan, insuring staff competency through training for research nurses, CRAs, clinical trials assistants and community office, clinic, and hospital staff engaged in Hawaii?s cancer clinical trials enterprise, and insuring recruitment of underserved minorities through focused outreach activities.
UH Manoa Evolutionary Genetics Core Facility
The Evolutionary Genetics Core Facility (EGCF) at the Hawaii Institute of Marine Biology (HIMB) is located on Coconut Island in Kaneohe Bay, Oahu. The NSF EPSCoR-supported Core Facility provides technical services and support for the faculty and students doing research at HIMB and the University of Hawaii system, as well as other institutions worldwide. The EGCF provides access to various instrumentation and equipment and offers fee-based genomic services including sequence and fragment analysis. The EGCF manager is available to provide services and assist with questions regarding lab instrumentation or protocols.
UH Manoa Genomics Shared Resource Core Facility
Core facility that provides the following services: DNA and RNA quantification service, DNA quality analysis service, RNA quality analysis service, Genotyping service, Gene expression analysis and DNA copy number analysis service, Pyrosequencing service. The purpose of the Genomics Shared Resource (GSR) laboratory is to provide expertise in the fast developing area of genomic analysis. In response to a growing need for genotyping services by a number of UH Cancer Center investigators, this laboratory was converted into a UH Cancer Center Shared Resource in 1999. Its current mission is to provide nucleic acid extraction, genotyping and expression profiling services in support of the peer-reviewed and IRB-approved research conducted by UH Cancer Center members.
HURL''s facilities include two deep-diving (2000 m) submersibles Pisces V and Pisces IV, a remotely operated vehicle RCV-150, and the support ship R/V Ka''imikai-o-Kanaloa. The two submersibles are housed and maintained at Makai Pier. HURL Data Archive: HURL provides a data package for each Pisces IV, Pisces V or RCV-150 dive. This package includes voice transcripts (Pisces IV & V only), graphs of environmental data (Pisces IV & V only), copies of videotapes with videologs, and copies of up to 250 slides with a photolog. The Data Archive is the custodian of the original data which remain the property of HURL. Databases of organisms and substrates observed on the dives are available for use by the principal investigator. Use of dive data by other scientists is subject to principal investigator approval for 2 years. HURL and NOAA-NURP reserve the right to use slides and video from dives for program promotion.
HSFL was established in May 2007 within the School of Ocean and Earth Science and Technology (SOEST) and the College of Engineering (CoE) at the University of Hawaii. As a multidisciplinary research and education center HSFL brings together individuals from diverse areas to work on the exploration and understanding of the space environment. The mission of HSFL is to: * Promote innovative engineering and science research for terrestrial and planetary space missions. * Develop, launch, and operate small spacecraft from the Hawaiian Islands to accelerate the validation of new space technologies. * Provide workforce training in all aspects of unmanned space missions. * Build synergistic collaborations among educational, governmental, and corporate institutions interested in space exploration. Hawaii is located in a unique position to become a low-cost gateway to space and to place the University of Hawaii as the only university in the world to have both satellite fabrication capabilities and unique, direct access to orbital space. This will enable diverse missions that study Earth''s oceans and continents from low-Earth orbit, as well as the testing of engineering experiments in the hostile environment of space.
University of Hawaii at Manoa INBRE Bioinformatics Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core to provide bioinformatics analysis and consulting service, to increase the research capacity in bioinformatics in the State of Hawaii, to provides software applications, hardware, access, and support to researchers who utilize genomic and proteomic data. Undertake collaborative project with INBRE researchers to develop novel tools or applications that address specific needs. Develop an academic program in bioinformatics with the John A. Burns School of Medicine (JABSOM). Recruit a full-time junior faculty member to lead the academic program. Conduct training workshops and courses, and run a user support help desk.
University of Hawaii at Manoa Informatics Shared Resource
THIS RESOURCE IS NO LONGER IN SERVICE, documented January 24, 2019. Core aims to promote multidisciplinary collaboration, and enhance the research excellence and productivity of CRCH by providing access to biomedical informatics expertise and computational support to all members of the Center. The prime objective of the ISR is to facilitate the management, sharing, and integration of diverse data types in cancer research, as well as the synthesis and analysis of more focused data sets from the basic, clinical, genomics and population sciences. The bioinformatics group of the ISR supports a dedicated scientific computing network for computational cancer biology, and leads the development and application of advanced algorithms and software tools that enable Center investigators to take a more integrative approach to cancer research for the purpose of accelerating the translation of basic research results into the clinic.
UH Manoa Laboratory Support Shared Resources
Laboratory Support supplies support services for laboratory-based programs at the University of Hawai?i Cancer Center. This resource is operated in order to streamline and make more centralized common laboratory needs.
The Harold L. Lyon Arboretum is a leader in the fields of conservation biology, Hawaiian ethnobotany and horticulture. On its 194 acres, Lyon Arboretum maintains a world renowned collection of more than 5,000 tropical plant species; supports Hawaii''s horticultural and agriculture industries; and works to preserve and restore Hawaii''s tropical forests. It is an active research facility and academic resource offering a wide range of programs to local and international communities including an innovative and ground-breaking tissue culture program for propagation of endangered native Hawaiian plants. With an abundant average rainfall of 165 inches, this tropical rainforest setting is an ideal location for growing an enormous diversity of plants. The plant collection features heliconias, gingers, aroids, bromeliads, native Hawaiian plants, and one of the largest palm collections found in a botanical garden.
UH Manoa Nutrition Support Shared Resource
Nutrition Support Staff at CRCH provides dietary assessment information that will support diet-related cancer research studies. The staff of the resource perform several services: * Maintain a food composition table with information on up to 174 nutrients and food components for over 2300 foods. * Maintain a supplement composition table for up to 217 nutrients and food components in over 3300 dietary supplements. * Develop quantitative scannable food frequency questionnaires for use in epidemiologic studies and provide the nutrient composition data needed for the analysis of questionnaire responses. * Review the accuracy of food records, dietary recalls, and dietary supplement questionnaires, and assist with data entry procedures. * Provide training for project staff in appropriate dietary data collection methods. * Assist with the design, analysis, and interpretation of dietary data for studies of diet and cancer.
International Classification of Diseases Version 9 - Clinical Modification
Ontology of the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use.
UH Manoa PBRC Computer Network Support Facility
The Computer Network Support Facility delivers services, information and tools to enhance the scientific productivity of biomedical and bioscience investigators at the University of Hawaii at Manoa; Hawaii; USA. Our clients include researchers, administrators and staff in the Pacific Biosciences Research Center and those associated with NIH center grants in the John A. Burns School of Medicine and other departments. Because the majority of our funding comes from the University of Hawaii Research Centers in Minority Institutions Program, we emphasize the development of computer and network tools that are useful to RCMI investigators.(http://www5.pbrc.hawaii.edu/cnsf/index.html)
Core facility that provides the following services: Tissue embedding service, Tissue sectioning service, Immunohistochemistry service, In situ hybridization service, DNA extraction service, Tissue microarray slides service, Tissue microarrays service, Genotyping service. The Pathology Shared resource capitalizes on the existing infrastructure of the Center''s tissue repository. The Repository currently consists of fixed, paraffin-embedded tissue specimens from hospitals and laboratories statewide. The purpose of the repository is to provide tissue specimens to Center members and other investigators for research purposes. A priority is placed on the provision of specimens for population-based research and peer-reviewed, extramurally funded projects. The repository is a part of the Residual Tissue Repository Program of the NCI SEER program (http://seer.cancer.gov/biospecimen/).
UH Manoa RCMI Biostatistics and Data Management Facility
UH Manoa RCMI Biostatistics & Data Management Facility
The Biostatistics and Data Management Facility (BDMF) was established with a primary mission to provide a range of customized statistical and database management services for RCMI researchers. Realizing a need for a consolidated and integrated statistical resources for biomedical researchers and clinicians at the John A. Burns School of Medicine, the BDMF has rapidly extended services to other programs and groups, including the Asia-Pacific Institute of Tropical Medicine and Infectious Diseases (APITMID), Pacific Biosciences Research Center (PBRC), Excellence in Partnerships for Community Outreach, Research on Health Disparities, and Training (EXPORT), Specialized Neuroscience Research Program (SNRP-I/II), Center of Biomedical Research Excellence (COBRE), Centers of Clinical Research Excellence (CCRE), Clinical Research Education and Career Development (CRECD), RCMI clinical Research Infrastructure Initiative (RCRII), and IDeA Networks of Biomedical Research Excellence (INBRE). The overall mission of the BDMF is to provide quantitative resources essential for investigators to conduct methodologically rigorous medical research in a timely, cost-effective manner. (http://www5.pbrc.hawaii.edu/bdmf/index.html)
University of Hawaii at Manoa Greenwood Molecular Biology Facility
School of ocean and earth science and technology
Core facility provides the following services: DNA sequencing service, DNA fragment sizing and genotyping service, Real-time PCR analysis, DNA microarray analysis service, Protein sequencing service. The Greenwood Molecular Biology Facility is a primary research infrastructure operated by the Biotechnology Program of the Pacific Biosciences Research Center. Core serves the biomedical and molecular biology research and educational programs of the University and its associated institutions.
UH Manoa RCMI Histology and Imaging Core Facility
UH Manoa RCMI Histology & Imaging Core Facility
Core facility that provides the following services: Training and advice for general imaging techniques, Histology processing service, Hematoxylin and eosin staining service, Training and advice for general histology techniques. This lab provides routine histology processing, specialized histochemical and immunohistological techniques, and access to several microscopic platforms. The core also provides technical assistance, training, and consultation in histological and imaging techniques to investigators throughout the University on a cost-recovery basis.
UH Manoa RCMI Pathogen Reference and Reagent Core
UH Manoa RCMI Pathogen Reference & Reagent Core
Our core provides a standardized library of pathogens and reagent materials.
Core facility that provides the following services: Necropsy and tissue collection, Blood chemistries service, Bronchoalveolar lavage service, Cerebro-spinal tap service. The Animal Resources Center (ARC) is a part of the Unit of Comparative Medicine at the Medical Sciences Campus (MSC) of the University of Puerto Rico (UPR), committed to offer quality services to the university community and private entities, which through an accredited and properly regulated facility, and highly qualified personnel, provides care and maintenance of animals to be used in research.
UH Manoa SOEST Engineering Support Facility
ESF project support comes under four categories: # New Funded Grants: The ESF supports researchers in planning proposals that will utilize ESF capabilities. For funded grants, the support should ideally begin at the early proposal stage. In consultation with the researcher, ESF can suggest practical and creative ways of obtaining and recording the desired data. # Support for Ongoing Funded Programs: The Engineering Support Facility has personnel and experience to repair and maintain laboratory instruments and equipment. In some cases, the existing laboratory instruments need some custom enhancements or adaptations for the particular science in view. ESF has experience going back over 35 years in custom modifications and enhancements to existing instruments. # Machine Shop: The ESF has a well-equipped machine shop and an expert instrument maker. # Pressure Test Facilities: The ESF operates a hydraulic pressure test vessel that can test pressure cases from 15 to 10,000 psia, with electronic feed-thru capability. The test vessel can accommodate objects up to 30 inches in outside diameter by 13 feet length.
Core facility that provides the following services: Cell cycle analysis with live or dead cells, Cell cycle analysis service, Fluorescent cell (particle) analysis, Fluorescent cell (particle) sorting service. The Flow Cytometry Facility, operated out of the School for Ocean, Earth Sciences and Technology at the University of Hawaii, provides state of the art instrumentation for analyzing and sorting particles. Flow cytometers detect particles based on their size (scatter) and fluorescence (auto or imparted by a dye). These particles can be enumerated or simply characterized as to their scatter and fluorescence characteristics. Multiple populations can be separated visually and if desired, physically, based on these properties. Flow cytometers work ideally with cells in the 0.2 - 200 ��m diameter size range and cell concentrations as low as 1000 cells/ml.
Core facility that provides the following services: Construction and validation of random-sheared DNA fragment libraries, DNA sequencing (Sanger) service, 96-well plasmid preparation service, Genotyping/fragment analysis, BAC end sequencing, Plasmid library construction service, Genome sequencing project. The ASGPB genome infrastructure currently consists of several state-of-the-art capillary-based DNA sequencers and accessory equipment to deal with large sample volumes. The facility can process up to 9000 samples per day with a projected sequence output of 6.75 Million bases. Several prokaryotic and one eukaryotic genome project are currently in progress. The facility offers DNA sequencing services for a wide range of templates including plasmid DNA, PCR fragments, cosmid DNA, and Bacterial Artificial Chromosomes (BACs). Sequencing reactions are performed using Applied Biosystems BigDye terminator chemistry and are run on ABI 3730XL capillary-based DNA sequencers.
UPR AABRE Program: Functional Genomics Research Center
Core facility that provides the following services: Molecular biology services. The FGRc of the UPR is the only facility of its kind in Puerto Rico and the Caribbean. The unique infrastructure of the FGRc positions it to be the provider of expertise and services related to functional genomics research to academia, government and industry in Puerto Rico and abroad, all within one unique center.
UPR AABRE Program: Human Genetics Center
Core facility that provides the following services: Genotyping analysis service, Microarray service. The lab has the following general goals: 1. To strengthen the scientific interactions between basic scientists and clinicians from the MSC and to enhance collaborations with international scientists working in molecular biology, human genetics, and infectious diseases; 2. To provide training, education, and support for the development of young scientists as well as established basic and clinical researchers with participation of internationally recognized leaders in the field; 3. To establish a centralized DNA, plasma and cell banking facility for storage of clinical samples from human blood or skin biopsies; 4. To provide basic services in molecular biology and human genetics; and 5. To initiate webcasting of training sessions in specialized areas in collaboration with the Center for Information Architecture in Research.
UPR AABRE Program: Protein Mass Spectrometry Facility
Core facility that provides the following services: Training opportunities for protein analysis. The lab consists of materials and equipment for the identification and/or analysis of protein samples by electrospray LC/MS/MS.
UPR AABRE Program: Sequencing and Genotyping Facility
Core facility that provides the following services: Sequencing service, Genotyping service. We are a low cost, fee-for-service facility designed to provide students and researchers in Puerto Rico with access to state-of-the-art equipment for collecting sequence and genotype data. We offer full service sequencing (reaction set-up, clean up, run and delivery) and fragment analysis data generation and offer personalized support to our users.
University of Puerto Rico Biomedical Informatics Research Core
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 24, 2019. Core aims to enhance biomedical research in Puerto Rico by providing resources for research, education and training. These resources will work to advance these specific aims: 1. enhance biomedical research in PR by providing researchers with the bioinformatics tools and technical support they require to perform cutting-edge biomedical research; 2. enhance the computational biology research environment in Puerto Rico by establishing research collaborations with biomedical, computational and mathematics researchers; 3. enhance multidisciplinary research by developing new courses and educational materials in computational biology, statistics and bioinformatics in collaboration with research faculty and the Science and Technology Competency Enhancement (STCE) Core; 4. enhance research by promoting advanced networking between PRAABRE member institutions, to enable collaborative research on and off the island; 5. enhance biomedical research by promoting effective access to scientific literature and databases for the biomedical researchers in PRAABRE; and 6. enhance biomedical research by enabling effective management of bibliographic information by fostering the use of bibliographic software and applying it to literature searches, articles and references management and manuscript writing.
UPR Cayo Santiago Caribbean Primate Research Center
Cayo Santiago is one of the world''s most renowned field sites for short term and longitudinal non-human primate studies. Its unique research value consists of:a stable and minimally disrupted long-term population management policy which allows investigators to plan and conduct longitudinal studies, an extensive and detailed computerized demographic database on the colony that provides information on individuals dating back to 1957, and DNA fingerprinting which is applied to confirm maternal and paternal relatedness of individuals.
UPR Center for Drug Information and Research
The CDIR serves as the focal point for drug information, research, education, and service within the University of Puerto Rico - School of Pharmacy. The CDIR is the first academic-based research center in Puerto Rico solely dedicated to provide answers to drug related information inquires, health service research support consultations, and the development, implementation and evaluation of pharmacy educational programs. The mission of the CDIR is to improve drug therapy in Puerto Rico through drug information services, and educational, clinical and novel research initiatives.
UPR Center for Genomics in Health Disparities and Rare Disorders
Center for Genomics in Health Disparities & Rare Disorder
Center for Genomics in Health Disparities and Rare Disorder
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 26,2026. Core facility that provides the following services: Oligonucleotide synthesis service, Automated DNA sequencing, Genotyping analysis service, Analysis of DNA, RNA or proteins, Microarray service. The long-term goal of the Center for Genomics in Health Disparities and Rare Diseases (CGHDRD) is to provide the critical environment that will enable high quality translational and biomedical research in pharmacogenomics, human genetics and genomics, molecular biology. We aim to develop and strengthen a collaborative research environment by providing research infrastructure that supports the focal areas of research at the University of Puerto Rico Medical Sciences Campus (UPR-MSC), which encompass common diseases such as cancer, neurological and cardiovascular disorders as well as rare disorders, by improving the human and physical resources. The Center focuses these initiatives on externally funded, interdisciplinary, collaborative projects which enhance the quality of translational, biomedical and clinical research at the Medical Sciences Campus linked to health disparities and rare disorders in Puerto Rico and nationally. Collaborations with researchers at institutions outside of Puerto Rico or other RCMI institutions, as well as other academic units in the island and in the UPR system are encouraged. The Center provides the necessary expertise to apply high throughput genotyping, expression profiling and sequencing technologies at the UPR-MSC. Specialized technical staff trains researchers at different levels of their scientific careers in supported technologies. Novel DNA and RNA isolation methodologies are applied to a diverse group of organisms and biological samples for nucleic acids sequence analysis in general.
UPR Center for Information Technologies and Telecommunications
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 26,2026. The overall goal of the Center for Information Technologies and Telecommunications (CentIT2) is to provide specialized information technology services to support research, professional development and global interactions at the University of Puerto Rico Medical Sciences Campus. Collaboration from other information technology units from the University of Puerto Rico Medical Sciences Campus (MSC) and from the University of Puerto Rico (UPR) System has been secured to provide access to their unique assets when necessary, avoiding duplication of resources.
Core facility that provides the following services: Training in STEM, Consulting service, Training in TEM, TEM and SEM service, Assistance with immunogold labeling, Maintenance of SEM, Training in SEM. This lab maintains and operates electron microscope facilities for the faculty, investigators and students of the Medical Sciences Campus for research, training and diagnosis. Service charges apply. Contact lab for details.
OWL Representation of the models in the BioModels repository.
Core facility that provides the following services: Training in the use of FACSort instrumentation, Flow cytometry consulting service. The specific objectives of this unit are to provide access to flow cytometry technology resources to investigators, students, and technical personnel; to train users in the utilization of flow cytometry; instrumentation and in its multiple applications in biological research; to provide basic technical support in flow cytometry methodology to interested users of the facility, and to encourage the development of new methodology and applications in the area of flow cytometry. Provides specialized seminars in flow cytometry basic and clinical applications.
UPR Infectious and Global Diseases Program
The long-range objective of the MBRS SCORE Program at the University of Puerto Rico Medical Sciences Campus (UPR-MSC) is to develop productive health-related research programs among faculty, contribute to a supportive campus research environment, and stimulate under-represented minority students to enter careers in biomedical research. MBRS SCORE Program funding provides faculty an opportunity to generate sufficient data to present research results at national and international research forums, publish in peer-review journals, and apply for independent research support. The Program encourages the participation of developing investigators from throughout the Medical Sciences Campus with the expectation that this support will empower them to compete on a more equal basis with researchers from more gifted institutions.
UPR Macromolecular X-ray Crystallography Core Facility
Core facility that provides the following services: Macromolecular x-ray crystallography service. Facility is located at University of Puerto Rico, R��o Piedras Campus.
The center is dedicated to scientific research, training of health professionals and service to women who live with AIDS. The program offers patients with a multidisciplinary team that provides medical, gynecologic-obstetrics, psychiatric, psychological and social work services. Also we provide research clinics with new medicines related with HIV.
UPR Pharmaceutical Science Research Support Unit
The Pharmaceutical Sciences Research Support Unit responds directly to the Chair of the Pharmaceutical Sciences Department. Its mission is to promote research by making available to offering our investigators instruments such as HPLCs, GC-MSs, NMR, among others and facilitating physical complementary spaces.
UPR RCMI Program Shared Instrumentation Laboratories
These laboratories house large, relatively expensive research instruments, which are shared among the faculty, students and staff on campus.
UPR RCMI Translational Proteomics Center
The Translational Proteomics Center provides training, resources, and tools for new and established investigators seeking to use innovative approaches of proteomics to their research, as well as to undergraduate and graduate students in the biomedical field. The Center fosters collaborations and partnerships among researchers aiming to reduce health disparities, including infectious diseases, cancer, and neurological/neurodegenerative diseases. Currently located at the second floor of the Comprehensive Cancer Center, Laboratory # 5.
UPR Sabana Seca Field Station Caribbean Primate Research Center
University of Puerto Rico Caribbean Primate Research Center
Core facility that provides the following services: Necropsy. The Sabana Seca Field Station (SSFS) is the administrative headquarters for the Caribbean Primate Research Center, or CPRC. This area contains offices, a clinic, and laboratories for reproductive biology and bone densitometry, necropsy and maintenance buildings. It houses rhesus monkeys from the CS colony or from the CS genetic line.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 26,2026. The goal of this Unit is to establish a shared facility to assist investigators associated with the Institute of Neurobiology in the application of molecular biology techniques in studies of the regulation of gene expression in neurobiological systems. The Unit provides advisory, technical and instrumentation support to faculty, postdoctoral associates, students and laboratory technicians.
Core facility that provides the following services: RNA extraction, Immunofluoresence assay, Dendritic cell immunophenotyping, ELISA, Polymerase chain reaction service, Florescence activated cell sorting service, Western blot analysis service. Research interests include: immunogenicity and protective efficacy of multi-clade consensus ENV SHIV virus-like particle vaccine, cellular innate activation as a tactic to prevent HIV-1 transmission, molecular changes after serial DV infections in macaques, and immunization of rhesus macaques with a dengue vaccine candidate based on a Venezuelan Equine Encephalitis (VEE) replicon vector.
University of Texas El Paso Analytical Cytology Core Facility
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 23, 2019. Core facility that provides the following services: Zeiss LD-5 Pascal Scanning Confocal Microscope/Assisted access, Zeiss Axioskop Epifluorescence Microscope/Assisted access, Zeiss EM-10 Transmission Electron Microscope/Assisted access, Microscopy sample preparation, Observation and photography service. The Analytical Cytology Core Facility provides assistance in the designing of protocols and the use of sophisticated, well maintained and supervised equipment. Each microscope is equipped with software for image analysis, image processing and printing of digital images. Service contracts are maintained on each of the microscopes. Computers and software are regularly upgraded. Confocal workshops are held regularly to familiarize users with new techniques and new protocols. The specific aims of the Analytical Cytology Core Facility (ACCF) are: 1. to train users in the design of protocols, the fixations, sectioning, cryofixations, immunolocalizations, the use of the Zeiss EM-10, the Zeiss Axioskop epifluorescence microscope and the Zeiss Pascal scanning confocal microscope with image analysis and image processing, 2. to support new faculty in realizing their research objectives that utilize microscopy, 3. to support the productivity of the Infectious Diseases and Immunology unit, the Toxicology unit, the Neuroscience/Metabolic Disorders unit, the Statistical Consulting Laboratory and the Bioinformatics unit by assisting faculty, undergraduate, masters, doctoral and postdoctoral students in advancing biomedical research, 4. to maintain and upgrade equipment and expertise and; 5. to provide core services anticipating self-sustaining maintenance of the core facility.
University of Texas El Paso Bioinformatics Computing Laboratory
Core facility provides the following services: General Bioinformatics Computing Support, Software Development and Computational Modeling. The Bioinformatics Computing Laboratory (BCL) serves as a core facility for the Border Biomedical Research Center (BBRC). Core specializes in developing databases and software for: genomics and proteomics data analysis; biomolecular sequence analysis and structure prediction; and glycosylation site prediction. Core aids researchers in the use of these advanced bioinformatics software tools by building user-friendly, customized, web-based interfaces for them.
Core facility that provides the following services: Mass spectrometry analysis, Trypsin Digestion. The Biomolecule Analysis Core Facility (BACF) specializes in the separation and characterization of biomolecules. The facility possesses state-of-the-art equipment for proteomic analysis and the characterization of molecular binding interactions. These resources promote new insight into the mechanism of infectious agents, cancer, and other diseases that affect the population of the Paseo del Norte region. BACF services are available to external collaborators for a small fee.
UTEP Cell Culture and High Throughput Screening Core Facility
Core facility that provides the following services: Confocal microscope access, Flow cytometry analyzer access, FACS Cell Sorting, Cell culture technique training, Cryopreservation of cultured cells, Cell culture analysis assistance, Preparation of high titer viral stock, Flow cytometry for cytotoxicity assay, Viral plaque assay, Real-time imaging of cell cultures, Mycoplasma testing, Treatment of cell lines contaminated with mycoplasma, Provide SF-9 cell suspension, Establishment of seed stocks, AnnexinV-FITC/PI assay. The Cell Culture and High Throughput Screening (HTS) Core Facility is a comprehensive research cell-culturing and cytometry facility established in 2007, as part of the Border Biomedical Research Center (BBRC). This facility was conceived to provide investigators, students and other researchers access to state-of-the-art technology for conducting experiments related to cellular, immune and physiological responses to stress, infectious agents, and toxicants. The laboratory also provides assistance and training related to cell culture techniques and equipment operation . The 1,756 sq ft core facility includes 6 individual cell culture suites that are available 24/7 to any researchers that have completed in-house training. The core also provides customized project support for experimental design and data analysis. The integration of the Cell Culture and HTS Core Laboratories has allowed investigators to screen a large number of compounds for their therapeutic potential against pathogens, cancer, and other diseases.
Core facility that provides the following services: DNA Sequencing Service, DNA/protein microarray printing. The DNA Analysis Core Facility supports researchers in their nucleic acid-based research studies on a 24/7 basis. The facility provides access to a wide range of genomic research tools including: DNA sequencing; microsatellite and fragment length polymorphism analysis; quantitative and real-time PCR; microarray analysis; and sophisticated nucleic acid analysis software. The DNA Analysis Core Facility services are available to external researchers from the RCMI program and other institutions for a nominal fee.
The long-term goal of the Statistical Consulting Laboratory (SCL) is to be a regional resource for the statistical support of basic science research, clinical or population based research, and evaluation of interventions designed to address issues of health and health disparities in the region''s population. As a major component of the Border Biomedical Research Center (BBRC), the Statistical Consulting Lab will continue to serve as a focal point from which all BBRC participants may obtain statistical and computing support for both their research and for the education of students in the graduate programs of the Biological Sciences Department. Statistical support is provided by a Ph.D. level staff statistician and five resource statisticians (counting the SCL core director) in the Department of Mathematical Sciences.
The new Biophysics facility is committed towards providing computational biology tools and software designed to study the physical phenomena underlying the behavior of biological systems. Shortly, this facility will be furnished with a 6-quadcore server and 4 workstations with high resolution graphics capabilities and support for many simultaneous remote users. All these computing resources will be linked via 10GB optical wires. On the other hand, the Departmental network provides high speed access to the University Computer Center main-ports and Internet. As an extension of its functionality and performance, this facility will also share resources with the Computational Biology innovative at the Biology Department. A major goal is devoted to establishing the connection between this facility and the supercomputers at the Texas Advanced Computing Center (TACC) at 10GB data rate. This facility is currently used by the computational and theoretical biophysics researchers at the Department of Physics to study the properties of biomolecules that are strongly affected by their surrounding aqueous and ionic environment.
UTSA Cellular and Tissue Engineering Laboratory
UTSA Cellular & Tissue Engineering Laboratory
These laboratories are dedicated to ''Cellular and Tissue Engineering'' research activities which focus on in vitro studies of mammalian cell and protein interactions with material substrates, biomaterials (including nanostructured ones), biocompatibility, and the effect of select biochemical and biophysical (specifically, sustained and cyclic pressure and electrical) stimuli on mammalian cell function pertinent to new tissue formation and regeneration.
The High Performance Computing Center/Computational Biology Initiative (HPC/CBI) is a new interdisciplinary initiative at the University of Texas Health Science Center at San Antonio (UTHSCSA) and the University of Texas at San Antonio (UTSA) which was launched in January 2005. The overall goal of the initiative is to build infrastructure to significantly advance collaborative interdisciplinary bioscience research in San Antonio.
UTSA Kleberg Advanced Microscopy Laboratory
This laboratory houses an impressive collection of high-end microscopes including one of the most powerful transmission electron microscopes in the world. The microscope is kept in a specially designed space that inhibits intrusive vibrations. Its atomic resolution is propelling world-class research in nanotechnology, biology, chemistry, geology, engineering and medicine. The laboratory''s microscopes are accessible to trained collaborators from other institutions.
University of Texas San Antonio Cell Analysis Core Facility
Core provides access to instrumentation in flow cytometry, confocal microscopy, and consultative scientific services. Offers comprehensive training in cross-translational cytometry and imaging, including experimental design, sample preparation, instrument operation, and data analysis.
UTSA RCMI Computational Systems Biology Core
Core facility that provides the following services: Computational systems biology data analysis assistance, Biological computational software installation service. The objective of the Computational Systems Biology Core facility (CSBC) is to provide computational support for basic and translational health research at UTSA with the following specific aims: - Build the computational infrastructure to support modeling and simulation of biological systems - Live cell imaging - Protein Biomarker research
A bilingual (English-French) domain ontology for modeling knowledge about Alzheimer's Disease and Related Syndromes.
UTSA RCMI Nanotechnology and Human Health Core
The Nanotechnology and Human Health Core is part of the RCMI program at UT San Antonio. It focuses on the synthesis and characterization of nanomaterials for imaging, labels for bioassays, and active targeting for in vivo or in vitro diagnostics. The Core studies the interaction of nanoparticles with living cells for application in the targeted delivery of drugs, genes, and proteins; tissue engineering scaffolds; artificial organs and implants; and bioimaging and cell labeling. Additionally, the Core supports development of new advanced characterization methods to study biological tissue using nanoparticles and advanced electron microscopy techniques to produce three-dimensional structural information for imaging cell membranes, organelles, and other subcellular structures.
University of Texas San Antonio Mass Spectrometry and Proteomics Core Facility
USTA RCMI Proteomics & Protein Biomarkers Core
UTSA Mass Spectrometry & Proteomics Core
Core provides routine and custom mass spectrometry-based support. Services include High-resolution, high mass accuracy mass analysis (HRMS), Liquid chromatography-mass spectrometry (LC-MS), Proteomics-based analyses.
The Image Analysis Core provides state-of-the-art techniques and software for making use of 3-dimensional images acquired via the RCMI Advanced Imaging Center. Our existing facility, like other centers of its kind, offers investigators the capability to acquire large, high resolution, three dimensional data sets, often as time series. The Core assists investigators in establishing methods for reducing these complex data sets to a form suitable for statistical analysis. The Core draws on the computational resources of The Computational Biology Initiative (CBI) at UTSA to implement standard best practices in image analysis and deliver state of the art image storage, visualization, and quantification to users of the image center, or to users obtaining similar images from equipment in their own laboratories.
The mission of The Neurostatistics Core is to promote the use of the most effective and current biostatistical methods among Neuroscience faculty and students, and to make these methods more generally available. It is designed to overcome the communication gap between experimental neuroscientists and statisticians by integrating statistical experts, in the form of Applied Biostatistics PhD students, directly into the laboratories of SNRP Project Investigators.
Core facility that provides the following services: Single crystal growth service, Cambridge Structural Database access. The X-ray diffraction facility, under the supervision and care of Dr. Hadi Arman, offers the chemistry department with the means of X-ray diffraction analysis which is the most reliable route for ascertaining the structure of crystalline materials. The facility maintains a state of the art Rigaku diffractometer. This sealed tube system is equipped with a CCD area detector and can analyze samples at various temperatures. Data processing and analysis are executed on PCs running Microsoft Windows. In addition to the diffractometer, the facility also has access to the electronic Cambridge Structural Database.
Vanderbilt Technologies for Advanced Genomics
VANTAGE (Vanderbilt Technologies for Advanced Genomics) is a genomics core laboratory consolidation initiated by an $8.6 million ARRA funded NIH grant award to Vanderbilt University Medical Center, with an overall goal of creating a new collaborative shared resource that accelerates discovery in genome sciences and personalized medicine, providing state-of-the art research shared resource facilities and technology.
The Informatics Shared Resource catalyzes the research productivity of VICC investigators by providing a flexible physical and electronic infrastructure for acquiring, storing, communicating and analyzing data arising from wet bench, translational, and clinical cancer research as well as senior staff and faculty level assistance in the interpretation of research datasets using state-of-the-art analysis.
Fosters, promotes, and develops the welfare of the wage earners, job seekers, and retirees of the United States; improves working conditions; advances opportunities for profitable employment; and assures work-related benefits and rights.
Vanderbilt Antibody and Protein Resource
Core facility that provides the following services: Custom Polyclonal Antibody Services, Monoclonal antibody isotyping, Hybridoma Services, Antigen production and purification, Peptide Synthesis, Peptide conjugation to protein carriers (ex. KLH, BSA), Recombinant Protein Expression and Purification Services, Kinetic Analyses for Protein:Protein and Protein:Small Molecule Interactions, Sample Lysis and Preparation. The Vanderbilt Antibody and Protein Resource (VAPR) partners both with scientists locally and from across the country to design and develop reagents for research, diagnostics, and large-molecule therapeutics.
Vanderbilt Automation and Informatics Core
The Automation and Informatics Core is responsible for integrating automation and instrumentation with downstream data handling and reporting. Duties of the group include: a) maintaining the laboratory computer network and technology infrastructure, including maintaining network security, performing data backups, managing data access, and trouble-shooting b) database management and information processing, including management of the Laboratory Information Management System (LIMS) c) performing systems analysis and programming as needed for instrument interfaces and integration, as well as extracting, reformatting, uploading, aggregating and/or analyzing data gathered in the course of HTS experiments d) maintaining the automation and robotics, including configuration, calibration, implementation, and trouble-shooting, to ensure maximum uptime/availability and utmost precision and accuracy e) assisting laboratory and scientific personnel with all their informatics needs, including overseeing data exchanges with our collaborators.
Core facility that provides the following services: Experiment design assistance. The principal mission of the Biomolecular NMR Center is to provide instrumentation for, and aid in obtaining data on the structure and dynamics of biological macromolecules. The Facility offers state-of-the-art instrumentation, training, software and assistance in designing experiments
Vanderbilt Biophysical Instrumentation Core Facility
The CSB maintains a variety of instruments for studying the conformation and stability of macromolecules and for measuring the affinity and thermodynamics of biomolecular interactions.
Core facility that provides the following services: Biospecimen processing and analysis, DNA/RNA extraction and banking, Genotyping. The Molecular Epidemiology Laboratory provides genotyping and other lab services for large-scale studies to Vanderbilt investigators related to biological specimen collection and storage, as well as biomarker and genetic marker assays.
Vanderbilt Biostatistics Collaboration Center
The Biostatistics Collaboration Center at Vanderbilt (BCC) is a university sponsored core resource whose goal is to provide for, enhance, and/or facilitate statistical collaborations involving the design, conduct, analysis or publication of biomedical research at the university.
Vanderbilt Cardiovascular Translational and Clinical Research Core
The primary focus of the Core Lab is to build and properly maintain biospecimen collections in the repository.
Vanderbilt Diabetes Research and Training Center Cell Imaging Shared Resource Core Facility
Vanderbilt Diabetes Research and Training Center Cell Imaging Shared Resource
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility that provides any Vanderbilt researcher with access to imaging equipment and expert technical support for microscopy and analysis of tissue and cellular physiology.
Vanderbilt Center for Molecular Neuroscience Cores
The Center for Molecular Neuroscience (CMN) at the Vanderbilt University School of Medicine supports interdisciplinary research and training in cellular and molecular neurobiology. Internationally recognized faculty approach the intricacies of neurogenesis, neural signaling and synaptic plasticity using leading-edge techniques in state-of-the-art research facilities.
Ontology that represents the structure that BioPortal uses to represent all of its metadata (ontology details, mappings, notes, reviews, views)
Scientific agency of the United States government. The scientists of the USGS study the landscape of the United States, its natural resources, and the natural hazards that threaten it. The organization's work spans the disciplines of biology, geography, geology, and hydrology.
Vanderbilt Chemical Synthesis Core Laboratory
The Chemical Synthesis Core was established within the Vanderbilt Institute of Chemical Biology with the goal of supporting the organic and medicinal chemistry needs of investigators. The primary focus of the core is to facilitate biology-orientated projects within the medical center and the university by assisting with the chemistry aspect of the project. The core works independently or in collaboration with the VICB High Throughput Screening Center on the synthesis of literature-cited compounds (including patented ones) as well as full scale lead optimization of a compound.
The purpose of the Vanderbilt Clinical Research Center is to provide the resources needed by clinical and translational investigators to carry out their research in an environment optimized for safety, comfort and convenience of the patient or volunteer, with the facilities and expertise to provide the most advantageous milieu in which to address the investigator''s experimental requirements. This includes outpatient space, inpatient beds, laboratories, equipment and supplies for clinical research by the faculty of Vanderbilt University, Meharry Medical College, and their collaborating investigators. The use of the center is justified on the basis of the quality and significance of the research and the special need for the Center''s facilities.
Vanderbilt Clinical Trials Shared Resource
The primary mission of the Clinical Trials Shared Resource (CTSR), as identified in the Cancer Center Support Grant (CCSG), is to assist Cancer Center investigators develop, activate and complete scientifically-meritorious clinical trials in an efficient, cost-effective and technically-sound manner.
Vanderbilt University Center for Human Genetics Research Computational Genomics Core
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 25, 2019. Core provides software and hardware support for computing activities related to genetics and biology, as well as statistical analysis for human genetics data generated from both microsatellite markers and SNPs. Bioinformatics support, resources, and expertise are available in storing and managing demographic, clinical, genotypic, microarray, proteomic and biospecimen data.
Vanderbilt Cooperative Human Tissue Network
Core facility that provides the following services: Biospecimen acquisition. The Cooperative Human Tissue Network- Western Division at Vanderbilt University Medical Center is one of six institutions throughout the country funded by the National Cancer Institutes to procure and distribute remnant human tissues to biomedical researchers throughout the United States and Canada. CHTN operates through a shared networking system which allows investigators greater access to available research specimens. CHTN offers a variety of preparation and preservation techniques to ensure investigators are receiving the quality specimens needed for research. Remnant tissues are obtained from surgical resections and autopsies and are procured to the specifications of the investigator.
BioVU is a research resource providing a View into biology at the level of DNA and other important macromolecules. BioVU has two major components. The first is a repository of DNA samples (extracted from discarded blood samples) that are coded solely by a Research Unique Identifier (RUI) derived from the Medical Record Number (MRN) using a one-way hash function. This is a computer algorithm that creates a transformation of each MRN such that the resulting RUI (which is in this instance is a 512 byte identifier) is unique, and has the property that it is not possible to infer or compute the MRN that generated it. As of early 2009, over 50,000 DNA samples were in the biobank, with new samples being added at the rate of approximately 700 per week.
This core has several components. The DNA bank receives specimens from various studies, extracts DNA, and provides storage. Quality control, organization, and efficiency are critical. Genotyping services provide the necessary speed, efficiency, and accuracy to perform genomic screens (with standard markers) in as little time as possible.
The Eicosanoid Core Laboratory facility employs mass spectrometry to quantify lipid oxidation products produced in a variety of vascular (and other) disorders including prostaglandins, leukotrienes, isoprostanes, and their urinary metabolites.
University of Lyon, located in Lyon and Saint-Étienne, France, is a center for higher education and research comprising 11 members and 24 associated institutions.
Vanderbilt Genetic Studies Ascertainment Core
Ascertainment for genetic studies is a crucial and labor-intensive effort. The Genetic Studies Ascertainment Core offers a variety of services to Vanderbilt clinical and basic researchers interested in or currently conducting research involving genetic analysis of complex disorders. We can aid in the development and coordination of individual and family based genetic studies. The faculty and staff have expertise in the issues that need to be considered when setting up a genetic study and are qualified to discuss with individuals issues that might be raised by participation in a genetic study. We can provide services for you or assist you in developing your own program. Study consultations are available to determine cost, time, and personnel needs as well as the best method of ascertainment for your project.
Vanderbilt High Throughput Screening Facility
Core facility that provides the following services: Assay Design and Development, High Throughput Screening and automated data analysis. The biology and screening team is responsible for developing, adapting, and automating the HTS assay from the benchtop assay provided by the collaborator. We work closely with the providing researcher to insure that the assay is rapidly moved into high-throughput screening. Once the assay has been validated, the screening of the small molecule library begins. Generally, the screen is expanded to accommodate the full compound library; however, structure-specific searches can be made if the required reagents are limited or costly.
Vanderbilt Diabetes Research and Training Center Hormone Assay and Analytical Services Core Facility
Vanderbilt Diabetes Research and Training Center Hormone Assay and Analytical Services Core
Vanderbilt Hormone Assay & Analytical Services Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility that supports diabetes, endocrine, and metabolic research across a range of species. Its objective is to provide sensitive, reproducible, and inexpensive analyses of hormones, amino acids, and other relevant chemicals.
Vanderbilt Human Immunology Core Laboratory
Core facility that provides the following services: Cytometric Bead Array, Meso Scale Discovery''s Multi-Array��, Cytometry protein measurements, Elispot Assays, Phenotypic analysis with flow cytometry, Multifunctional/Polychromatic flow cytometry (7-14 color), Cell proliferation assays, Tetramer/pentamer staininng, Influenza hemagglutination inhibition assay, Bordetella pertussis ELISA IgG / IgA, Commercial ELISA. The Immunology Core provides assistance to investigators with sample processing, storage, shipping, documentation, assay design, assay development and evaluation of immune responses. It is the goal of the core to monitor immune responses during clinical trials using the latest advances in technology and provide practical applications of this technology to evaluating immune responses. We continue to develop new immune monitoring technology with industry and academic collaborators. The Immunology Core has extensive experience in assay development and optimization, and will assist in the selection of appropriate assays and antigens during the protocol/developmental phase of a study or trial.
Vanderbilt Innovative Translational Research Shared Resource
The mission of the Innovative Translational Research Shared Resource (ITR) is to advance the translation of basic and clinical research into improved clinical therapies by facilitating clinical discoveries and managing laboratory and clinical data exchange between researchers. The ITR has partnered with the Personalized Cancer Medicine Initiative (PCMI) and the Vanderbilt-Ingram Cancer Center (VICC) to characterize the molecular changes present in tumors. With a focus in clinical sample preparation and tumor genetic analyses, the ITR uses the most advanced laboratory techniques to uncover the genetic uniqueness of each patient''s tumor for research. This knowledge will lead to improved clinical therapies and a more personalized cancer care that will save lives and improve patient outcomes. The ITR gives scientific and technical assistance to clinical and laboratory researchers interested in experimentation using human tumor tissues or cell lines. In addition to our expertise in genetic analyses, the ITR is also interested in partnering with clinical investigators to study clinical phenotypes in a research laboratory. These studies are tailored to the needs of the clinical investigator.
Vanderbilt Institute for Integrative Biosystems Research and Education Automated Biosystems Core Laboratory
VIIBRE''s Automated Biosystems Core (VIIBRE-ABC) provides a powerful technical foundation for the study of dynamic cellular metabolism, signaling, and control, with more than $4.7 million received from the Defense Threat Reduction Agency (DTRA), the National Institute on Drug Abuse (NIDA), the NIH Shared Instrumentation Program, and Vanderbilt University. An important focus of this effort is to explore dynamic host responses to chemical agents, toxins, and microbial pathogens. The ABC comprises two major instruments: a custom Omni-Omics system built around a Waters Synapt G2 UPLC/GC/ESI/nESI Ion Mobility-Mass Spectrometer, and a microfluidics-enabled high-content screening system built around a Perkin Elmer Opera QEHS Automated Confocal Microscopy System.
Vanderbilt Institute for Integrative Biosystems Research and Education Microfabrication Core
Core facility that provides the following services: Photolithography Laboratory, Device Fabrication Laboratory, VIIBRE Machine Shop, VIIBRE Electronics Shop. The VIIBRE Microfabrication Core offers facilities and expertise for the design, manufacture, and implementation of micro- and small-scale electronic, mechanical and fluidic devices. Typical products include fluidic networks,pumps and valves, arrays of microfabricated traps for cellular study, implantable devices for in vivo imaging, liquid and gas control systems, biological habitats, environments and microbioreactors, and more.
Vanderbilt Institute of Nanoscale Science and Engineering
The Vanderbilt Institute of Nanoscale Science and Engineering (VINSE) is a University institute focused on new science and technology based on nanoscale materials. We carry out frontier science and technology by teaming locally and globally, and providing an environment where physicists, chemists, biologists, and all engineers may collaboratively solve forefront problems and create new scientific understanding.
Mass spectrometry is used to analyze the complex array of lipids in cellular membranes in an effort to dissect precursor-product relationships in lipid signaling networks.
Our mission is to provide cost effective, state-of-the-art instrumentation to students, fellows and faculty for identification and structural analysis of biological molecules and for qualitative and quantitative assays of drugs and metabolites in physiologic fluids. Our aim is to provide a collegial and cooperative environment in which to do research.
Vanderbilt Mass Spectrometry Research Center Proteomics Laboratory
Core facility that provides the following services: Simple Protein Identification, Multidimensional Protein Identification Technology, 2D Difference Gel Electrophoresis (2D-DIGE). The Proteomics Laboratory provides state-of the-art MS instrumentation and analytical methods to analyze proteins and proteomes.
Vanderbilt Diabetes Research and Training Center Vanderbilt Diet Body Composition and Metabolism Core Facility
Vanderbilt Diabetes Research and Training Center Vanderbilt Diet Body Composition and Metabolism Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility that provides training and expertise in nutrition/diet methodology to obtain valid and reliable assessment and analyses of dietary intakes, nutritional status, body composition and metabolism.
Vanderbilt Mouse Kidney Histology and Morphometry Core
The overall goal of the Histology and Morphometry Core is 1) to provide a common facility and expertise for the broad spectrum of morphologic studies that may be required for interpretation of studies of various models of kidney disease and their response to interventions; 2) to provide tissue samples from existing archival specimens from various mouse and rat kidney disease models that may be used for exploration and characterization of expression patterns of various novel target molecules; and 3) to develop and enhance existing morphologic techniques to improve the ability of center investigators to localize specific molecules and tissue sections, and to interpret their significance based on the spatial localization and relationship to patterns of injury.
Vanderbilt Mouse Kidney Physiology Core Lab
The objectives of the physiology core are to establish average values and normal ranges for physiologic parameters of renal function in mice, and to develop novel assays of mouse kidney structure and function. Our goal is to provide valuable institutional and national shared resources to facilitate better understanding of kidney diseases and treatments.
Vanderbilt Neurochemistry Core Laboratory
The Neurochemistry Core Lab performs assays of neurotransmitter concentrations in brain tissue, designs custom assays as well as provides training in HPLC methods.
Core facility that provides the following services: Immunophenotyping, Fluorescent protein expression analysis, Cell-cycle analysis, Functional assay service, Non-infectious cell sorting, BSL2+ biohazardous cell sorting, Flow cytometry consultation service, Flow cytometry training and ongoing advice, Flow cytometry data management service, Flow cytometry collaboration facilitation, Flow cytometer access. The Wistar Institute Flow Cytometry Shared Resource provides flow cytometric services, training, advice, and support for the use of flow cytometric techniques by Wistar Cancer Center investigators, as well as the greater basic research community.
Vanderbilt Rat Neurobehavioral Laboratory
The Rat Neurobehavioral Core provides equipment, training and consulting for Vanderbilt personnel who are interested in studying rat models of both neurological and psychiatric disorders. Examples of assays available for research in rats include models of anxiety, depression, drug abuse, learning and memory, cognition, attention, social interaction, pain, motor activity and coordination. Investigators can employ the latest technology in video capture and software-based analysis of behavior. Additionally, the facility offers a 24 hr/day home cage monitoring system that includes measurement of sleep EEG and core body temperature. A surgical suite is available, outfitted with a wide variety of equipment such as standard rat stereotaxic frames and a stereo-microscope, as well as various perfusion tables. Housing takes place inside the facility?s vivarium, which is Virus-Antibody free.
Core facility that provides the following services: Polysomnography, Titrations with continuous positive airway pressure, Multiple sleep latency testing, Wrist actigraphy, Video polysomnography. The Vanderbilt Sleep Research Core offers two hard-wired sleep systems with synchronized video-polysomnography and 21 channels of EEG, with dedicated registered sleep technologists. A sleep core/sleep reading center manager and the core director (Dr. Beth Malow) assist investigators with protocol development. It offers polysomnography, titrations with continuous positive airway pressure, multiple sleep latency testing, and wrist actigraphy (wireless devices that measure sleep-wake patterns non-intrusively based on accelerometers that measure activity vs. rest). The core provides for centralized scoring of polysomnography and actigraphy data for multicenter trials. In addition to the scoring component, emphasis is placed on the quality of the sleep recordings at the individual sites with close communication among the individual site technologists and the sleep core manager.
Vanderbilt Survey Research Shared Resource
Provides support for phone interview-based collection of information from study subjects. The Survey Research Shared Resource provides services to investigators related to development and implementation of mail, telephone, web and mixed mode surveys.
The Tissue Core laboratory provides direct proteome profiling and protein imaging of intact tissues by MALDI-MS. The Core also provides proteome profiling of biofluids by MALDI-MS as they pertain to a specific disease.
Vanderbilt Transgenic Mouse/Embryonic Stem Cell Shared Resource
Vanderbilt Transgenic Mouse/Embryonic Stem Cell Shared Resource (TMESCSR) provides services that facilitate the generation, storage and regeneration of genetically altered mice.
Vanderbilt Translational Pathology Shared Resource
Core facility that provides the following services: Hematology Services, Parasitology Services, Chemistry Analysis Services, Cell Line Testing, Customizable Chemistry Analysis, Phenotyping Services, Infertility evaluation in male mice, Veterinary Pathologist Consultation. Access to consented and de-identified human tissue specimens; Comprehensive, state of the art diagnostic, necropsy and comparative pathology services for animal model systems with specific expertise and focus on mouse models; Research histology including advanced techniques, immunohistochemistry, immunofluorescence, laser capture micro-dissection and tissue micro-array preparation; Access to experts in veterinary and human pathology.
The current zebrafish facility is composed of approximately 100 research tanks available for short and long-term studies, and a significant expansion project is underway. The facility enables investigator access to the unique advantages of the zebrafish model, which provides hundreds of mutant and transgenic zebrafish with unique properties suited for specific experiments. This core?s essential mission is to provide a reliable mechanism for incorporation and propagation of new and existing zebrafish lines into the core.
Core provides High Throughput Data Analysis, Customized Bioinformatics Services, Custom Programming, High Performance Computing, Data management. Located in the Center for Systems and Computational Biology. Provides Cancer Center investigators with database management, software application support, expertise in statistical analyses and computational modeling of biomedical research data.
Core facility that provides the following services: Microarray services, RNA amplification service, ABI 7900 Real-time qPCR service, Capillary DNA sequencing and microsatellite analysis, Illumina HiSeq 2000 sequencing service, Illumina Genome Analyzer services. The Wistar Genomics Facility serves as a hub for consultation and scientific interactions relating to nucleic-acid based methods and provides expertise and support to insure the best possible use of emerging nucleic-acid technologies. In addition to consultation and collaboration with Wistar Cancer Center members, the Facility provides services to the greater scientific community. The establishment of this facility was supported in part by an NCI Cancer Center Support Grant and equipment grants from the Commonwealth of Pennsylvania, The Pew Charitable Trusts and the National Cancer Institute.
Core facility that provides the following services: Paraffin sectioning service, Frozen sectioning service, Histology staining services. This facility provides basic histology services. These include fixing, processing and paraffin embedding of all types of tissues for light microscopy (i.e. routine stains, immunohistochemistry or in situ hybridization). Routine hematoxylin and eosin staining as well as special staining is done in the lab. Slides are prepared for immunohistochemistry and in situ and immunohistochemistry. Frozen sectioning is also available. It is advisable to contact the facility about freezing techniques so the best sections can be obtained.
Core facility that provides the following services: Live-cell time-lapse microscopy, Low magnification and photomacrography? service, Confocal microscopy service, Two-photon microscopy, Small animal whole body luminescence and fluorescence imaging?, 2, 3, 4, and 5D image analysis, Imaging consultation service, Imaging equipment, image processing, and image analysis training, In-lab microscopy assistance and maintenance service, Imaging Facility instrument access. The Imaging Facility is a shared resource with the primary goal of providing exceptional microscopy and imaging services, as well as individual access to a variety of state-of-the-art imaging resources for members of the Wistar research community. The imaging systems have been designed to be extremely flexible to reflect a broad range of challenging scientific questions and specimens. Each system provides a combination of illumination, optics and image capture options. Diverse subjects ranging from fluorescently tagged live cell cultures and stained tissue sections, to 3D tumor spheroids and low magnification explanted tissues, can be accommodated with available systems. Current equipment includes standard upright and inverted fluorescence microscopes, a customized live-cell time lapse microscope capable of 6D imaging, a laser scanning confocal microscope, a 2-photon microscope designed for in vivo imaging, a small animal, whole body luminescence and fluorescence imager, special low magnification (photomacrography) systems as well as a variety of traditional photographic cameras, lenses and lighting equipment. Users of the facility may be trained for unassisted use of all core assets, or they may elect assisted service with the facility staff performing the imaging. The Imaging staff also provides assistance to researchers with additional aspects of their imaging requirements. Ideal approaches to specimen documentation are often unique to the experiment and the staff can help design the most effective imaging protocols to answer a particular question. On-site assistance is available to help investigators get the most out of their own systems. Image analysis and specialized Photoshop training, creative imaging for journal covers, and guidance on digital imaging ethics help to round out the services available from the facility.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22,2024.Core facility that provides the following services: Tissue culture suite access, Biological assay development for screening experiments, High-throughput-screening service, Post-screening studies. The Wistar Molecular Screening Facility is a shared resource facility open to Wistar and non-Wistar scientists. The laboratory operates on a fee-for-service basis, providing expertise in bridging automated technology with the development of innovative, robust biochemical or cell-based assays for high-throughput chemical and functional genomic screens. The laboratory strives to possess the flexibility to accommodate diverse biological systems and a variety of investigator-developed assay types. While service is the primary role of the laboratory, the staff will also develop and implement new technology as needed to fulfill the needs of its users. Education and training is also part of the laboratory''s mission, as trainees apply high-throughput screening experiments to their investigations. The ultimate goal of the laboratory is to enable scientists to apply cutting edge technology and unique resources to discover agents (i.e. small molecules, siRNA) to further study the functions of poorly understood proteins, signaling pathways, and cells in complex biological process relevant to human physiology and disease. The combinations of these activities will provide scientists opportunities to develop new innovative basic and translational research, preliminary data for hypothesis driven research grant applications, and public-private partnerships. The Wistar Molecular Screening Facility was developed with support from the Lankenau Institute for Medical Research, the Commonwealth of Pennsylvania Department of Community and Economic Development Keystone Innovation Zone initiative, The F. M. Kirby Foundation, The CLAWS Foundation, The Florence & Daniel Green Foundation, The McClean Contributionship, From The Heart Foundation, and the Noreen O?Neill Foundation for Melanoma Research.
The Major Instrumentation Core has been established to provide technical services and consumable supplies necessary for the operation and maintenance of a variety of major instruments that support biomedical research at Xavier University. The long term goal of the Major Instrumentation Core is to enhance the overall biomedical research capabilities at Xavier University by making available essential instrument-based platforms for various research projects. To achieve this goal the Major Instrumentation Core has set the following specific aims: 1). support biomedical research projects on campus by providing essential analytical instrumentation, 2). maintain and operate existing instruments, 3). acquire new instruments, and 4). provide technical support for user community of the core.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22,2024.Core facility that provides the following services: Recombinant plasmid DNA engineering, Recombinant protein production via Baculovirus expression systems (BVES), Recombinant protein production in prokaryotic systems, Recombinant protein purification, Retrovirus production service. The Protein Expression Facility is a shared resource laboratory that provides Wistar Cancer Center Members and non-Wistar scientists technical assistance with viral vector preparation and the expression and purification of recombinant proteins. The Facility has greater than 20 years of experience in recombinant protein expression with special expertise in the use of baculovirus expression systems (BVES). The Facility offers the following services: 1. Recombinant plasmid DNA engineering 2. Viral vector production (i.e. baculovirus and retrovirus) 3. Analytical and preparative scale expression of nascent or epitope-tagged recombinant proteins 4. Protein purification These goals are accomplished by a centralized laboratory with dedicated, experienced staff, which enables high-throughput, economy of scale, virus preparation and protein expression services, including quality assurance and control procedures to ensure efficient, consistent production and purification of recombinant proteins and viral vectors. Many recombinant proteins produced by the facility have been used for crystallization efforts, analytical biochemistry studies designed to investigate enzymatic properties, structure-function relationships between protein-protein, protein-nucleic-acid, and protein-small molecule interactions, custom antibody production, experimental cancer vaccines, and development of miniaturized assays for small molecule screening. The facility is supported in part by an NCI Cancer Center Support Grant and a grant from the NIH National Institute of Aging (PO1 AG031862).
Wistar Proteomics and Metabolomics Core Facility
Core facility that provides the following services: In-gel protease digestion service, LC-MS/MS protein identification service, Gel/LC-MS/MS Comprehensive analysis of a subproteome or proteome, MudPIT (LC/LC-MS/MS) analyis?comprehensive analysis of a subproteome or proteome, Reverse phase microbore HPLC peptide mapping service, MALDI mass spectrometry, ESI of intact proteins, Post-translational modification identifications, Custom proteomics database creation, Custom proteomics data analysis, Proteomics methods development. The Wistar Proteomics Facility provides mass spectrometry (MS) and sequence analysis of proteins and peptides at maximum sensitivity using state-of-the-art instruments and methods. The most commonly used services are identifications of either purified proteins or complex protein mixtures, such as sub-proteomes or complete proteomes, using electrospray ionization tandem mass spectrometry (ESI MS/MS). Typically, either individual bands are excised from 1-D SDS gels, or the entire gel lane is analyzed by slicing it into uniform fractions followed by trypsin digestion and nanocapillary HPLC interfaced directly with hybrid ion trap mass spectrometry (Gel/LC-MS/MS). Data is analyzed and filtered to produce low false-positive rates. Several options are available for quantitatively comparing protein changes in related samples, and additional options will be implemented in the future. Complementary services include reverse-phase microbore HPLC peptide mapping with UV detection and mass measurements of intact peptides and proteins using MALDI MS or ESI MS. Posttranslational modification (PTM) analyses including identifications of specific modified residues also are provided, although investigators should recognize that in most cases these studies are quite complex and require substantial effort. These studies, as well as analyses of complex protein mixtures, usually require preparation of custom sequence databases and/or custom data analyses, which can be provided by the facility as needed.
Wyss Institute Machine Shop / 3D Prototyping Core
The Core''s capabilities include six Computer Numerical Control (CNC) milling centers (one of which is a five-axis micro-milling machine), two 3D printers, a waterjet cutter, a laser cutter, and a sinker Electrical Discharge Machining (EDM) tool. The Core has three full time machinists with experience in both industrial and academic machine shops, creating prototypes for varied applications. In addition to fabrication, these experts help researchers during the design phase, enabling development from a simple concept into real prototypes.
Wyss Institute Materials Characterization Core
The Wyss Institute Materials Characterization Core is dedicated to promoting leading edge biologically inspired research by providing users with a wide range of state-of-the-art materials characterization equipment and analysis software. These tools help support the characterization of a material?s unique physical, chemical, and mechanical properties. The Materials Characterization Core team provides exceptional hands on training, method development, and technical expertise. We also proactively stride to introduce the latest innovations in materials characterization to the Wyss Institute community and our affiliated partners. Our current techniques include chromatography, mass spectrometry, UV-Vis spectroscopy, particle sizing, quartz crystal microbalance, electrochemical testing, rheology, and nanoindentation.
Core facility that provides the following services: Animal husbandry. To provide the best husbandry and environment for housing, maintaining, and caring for research and laboratory animals used at Xavier University, with in all applicable guidelines, and to assist users by providing information and support for handling and care of animals.
XULA Center for Nanomedicine and Drug Delivery
XULA Center for Nanomedicine & Drug Delivery
Core facility that provides the following services: Drug Dosage Form Development. The center is focused on understanding and overcoming barriers to efficient oral, colonic, parenteral, pulmonary and vaginal delivery of drugs in the hopes of developing new treatments for chronic diseases such as cancer. Numerous new technologies are coming out of the Center as relationships have been formed with small, advanced technology businesses.
Innovatie door Wetenschap en Technologie
Government agency for Innovation by Science and Technology that helps Flemish companies and research centers in realizing their research and development projects by offering them financial funding, advice and a network of potential partners in Flanders and abroad. They also support the Flemish Government in its innovation policy.
A resource center that distributes important resources to the biogerontological community and facilitates interactions and collaborative efforts amongst researchers to aid biogerontologists and enhance research into the basic biology of aging. They aim to make SAGEWEB the premier aging-related website containing a variety of different content types including: * Databases related to the basic biology of aging * Software and bioinformatic tools for aging-related science * Educational tools for teachers and students interested in aging biology * Primers on important topics in aging-related science * Videos and podcasts of aging-related topics * Aging-related discussion forums and blogs * Links to additional aging-related labs, conferences, and resources
XULA RCMI Cell and Molecular Biology Core
Core facility that provides the following services: Bioassays service, Functional studies service, Gene expression service, Molecular biology service, Mass spectrometry based global scale protein profiling, 2D Gel Electrophoresis, Data analysis services. The RCMI Cell and Molecular Biology Core (CMB Core) provides focused services using cell and molecular biological techniques. It also provides access, upkeep and training on ?state of the art? equipment. Funding by the RMCI allows these services to be offered at minimal cost to users of the core. Technical services and necessary consumable supplies are provided to support cancer research projects at Xavier University. The long term goal of the Cell and Molecular Biology Core is to enhance the overall biomedical research capabilities at Xavier University.
XULA RCMI Molecular Structure and Modeling Core
Core facility that provides the following services: X-ray crystallography service. A Molecular Structure and Modeling Core laboratory has been established to provide technical services to support faculty researchers involved in cancer research and drug design at Xavier University. Drug design methods use molecular structure information and modeling methods to determine structure patterns among active and inactive compounds, identify and compare potential active sites, and screen databases to identify new leads. X-ray crystallography provides structure coordinates for druglike, organic compounds and small peptides. The goal of this core laboratory is to provide small molecule X-ray crystallographic services as well as to support ligand-based and structure-based drug design projects at any stage. The long term goal is to develop resources in order to enhance cancer related biomedical research capability at Xavier University. To achieve this goal, the Molecular Structure and Modeling Core Laboratory has set the following specific aims: 1. To provide salary support for a Core Scientist to provide molecular modeling services and training in support of Xavier faculty research projects 2. To establish new collaborations with faculty at other local and RCMI institutions who might benefit from molecular modeling services 3. To provide small molecule x-ray crystallography services 4. To provide support and maintenance costs for equipment in the MSM Core
Radiation Oncology is a featured book on Wikibooks because it contains substantial content, it is well-formatted, and the Wikibooks community has decided to feature it. This wiki project is an open source, free access reference book. Anyone is welcome and encouraged to contribute anytime, anything (as long as it relates to Radiation Oncology). Feel free to edit it, update it, correct it, and otherwise increase its teaching potential. Full Table of Contents *Preface *Clinical Radiation Oncology *Treatment Toxicity and Supportive Care *Treatment Approaches *Cancer Biology *Appendices
A discovery interface of digital objects, including documents, photographs, audio, video, and data sets, which reflect a range of materials collected, managed, and preserved by the UCSD Library to support teaching, learning and research. Content has been drawn from across the Library collections with strengths in the areas of Baja California, Melanesia, Oceanography, and UC San Diego history. Access to more content will increase over time. Items have been digitized from the original primary sources in our collections, and recently the Library began to partner with UC San Diego researchers on campus to make research data more readily available. The Digital Collections website gathers data into two broad categories of content: Library Digital Collections contains digitized versions of selected collections covering topics such as art, film, music, history and anthropology.
Johns Hopkins Bloomberg School of Public Health; Maryland; USA
Collection of annotated and manually curated data of genes related to aging divided into genes related to longevity and/or aging in model organisms (yeast, worms, flies, mice, etc.) and aging related human genes.
Database that contains gene sets and microRNA-regulated protein-protein interaction networks for longevity, age-related diseases and aging-associated processes.
MitoInteractome - Mitochondrial Protein Interactome Database
Database that gathers data on interactions in the mitochondrial proteome that has been used to construct a network for the aging process in humans and to identify interactions that influence this process, since mitochondria is a major source of cellular reactive oxygen species that accumulate during aging. It will: # aid in increasing our understanding of the molecular functions and interaction networks of mitochondrial proteins, # help in identifying new target proteins for experimental research using predicted protein-protein interaction information, and # help in identifying biomarkers for diagnosis and new molecular targets for drug development related to mitochondria. How is MitoInteractome different? * Provides protein-protein interaction information with graphical display. * Applies newly added new mitochondrial protein information by using BLAST incorporated in Mitointeractome * Shows correlation of mutation with their impact * Provides specific pathway information to aid study of their impact * Contains SNP Information
A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR' '''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26, 2019. Database of leaf senescence to collect SAGs, mutants, phenotypes and literature references. Leaf senescence has been recognized as the last phase of plant development, a highly ordered process regulated by genes called SAGs. By integrating the data from mutant studies and transgenic analysis, they collected many SAGs related to regulation of the leaf senescence in various species. Additionally, they have categorized SAGs according to their functions in regulation of leaf senescence and used standard criteria to describe senescence associated phenotypes for mutants. Users are welcome to submit the new SAGs.
A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
A website aimed at recruiting and assessing subjects for all types of neuroscience studies with the internet. The hope is to accelerate various types of observational studies and clinical trials, and also reduce costs. They are interested in having people, including healthy subjects of all ages, join the registry. Joining only takes a few minutes. The web-based project is designed to speed up cures for Alzheimer's, Parkinson's and other brain disorders. It uses online questionnaires and online neuropsychological tests (which are very much like online brain games).
Contract Research Organization focusing on medial diagnosis.
American company incorporated that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California.
A register of clinical trials for the Netherlands, that is mandatory prior to publication of NL sponsored research.
A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator.
An online database mainly about the order Hymenoptera. It contains some 115,000 species and literally millions of specimens in collections around the world. Some parts of this database have extensive information available (e.g., Proctotrupoidea, Platygastroidea, Ceraphronoidea, Apoidea), even to the level of specimens (see Platygastridae, Pelecinidae, Monomachidae, Stephanidae). These data have been gathered with the collaboration of a number of colleagues. Other taxa still need work. Hymenoptera Online (HOL) is no longer solely dedicated to Hymenoptera as recent acquisitions have expanded the taxonomic scope of this resource to include Hemiptera, Coleoptera, Mites, Fishes, and others with the help of a number of tireless collaborators. If you would like to contribute to the further development and enhancement of this resource or need technical assistance related to Hymenoptera Online services, please contact HOL Help, Norman F. Johnson, or the HOL Google+ Page. Search for taxa, collections, authors, collectors and specimens by typing your simple query in the text box below. Taxon name searches are case-sensitive and a wildcard (%) will automatically be appended to the end of your query (e.g. Telenomus); the same applies to collectors and authors (e.g. Johnson), collections (e.g. CNC), places (e.g. Bahia), journals (e.g. Memoirs), and specimen searches by specimen ID (e.g. ANIC DB 32).
Web addresses that act as permanent identifiers in the face of a dynamic and changing Web infrastructure. Instead of resolving directly to Web resources, PURLs provide a level of indirection that allows the underlying Web addresses of resources to change over time without negatively affecting systems that depend on them. This capability provides continuity of references to network resources that may migrate from machine to machine for business, social or technical reasons.
International Classification of Functioning Disability and Health
A classification of health and health-related domains. These domains are classified from body, individual and societal perspectives by means of two lists: a list of body functions and structure, and a list of domains of activity and participation. Since an individual''s functioning and disability occurs in a context, the ICF also includes a list of environmental factors.
Computational Biology and Functional Genomics Laboratory at Harvard
A computational biology laboratory that builds and redistributes genetic software tools.
International Commission on Zoological Nomenclature
An organization that acts as adviser and arbiter for the zoological community by generating and disseminating information on the correct use of the scientific names of animals. The ICZN is responsible for producing the International Code of Zoological Nomenclature - a set of rules for the naming of animals and the resolution of nomenclatural problems.
ABMapper: A suffix-array based spliced alignment tool
A portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping. The core module was written in C++ and wrapped in PERL scripts.
LIBSVM -- A Library for Support Vector Machines
An integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM) from the laboratory of Chih-Chung Chang and Chih-Jen Lin. It supports multi-class classification.
A set of global climate layers (climate grids) with a spatial resolution of about 1 square kilometer. The data can be used for mapping and spatial modeling in a GIS or with other computer programs. If you are not familiar with such programs, you can try DIVA-GIS or the R raster package.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. The aim of MLST is to provide a portable, accurate, and highly discriminating typing system that can be used for most bacteria and some other organisms. It is envisaged that this approach will be particularly helpful for the typing of bacterial pathogens. To achieve this aim we have taken the proven concepts of multilocus enzyme electrophoresis (MLEE) and have adapted them so that alleles at each locus are defined directly, by nucleotide sequencing, rather than indirectly from the electrophoretic moblity of their gene products. MLST was developed in the laboratories of Martin Maiden, Dominique Caugant, Ian Feavers, Mark Achtman and Brian Spratt. This site is hosted at Imperial College with funding from the Wellcome Trust. The location of the subsites for the individual species are shown on their respective front pages.
PSIPRED Protein Sequence Analysis Workbench
Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences.
Johns Hopkins University is private research university in Baltimore, Maryland. Founded in 1876, university was named for its first benefactor, American entrepreneur, abolitionist, and philanthropist Johns Hopkins.
Group headed by Professor David Jones, and was originally founded as the Joint Research Council funded Bioinformatics Unit within the Department of Computer Science at University College London. Supports the following tools: Protein Structure Prediction Threading (THREADER) Ab initio folding simulations Secondary structure prediction (PSIPRED) Protein disorder prediction (DISOPRED) Protein domain prediction (DomPred) Database of protein disorder (DisoDB) Protein Sequence Analysis Protein function prediction (ffpred) Metsite: Metal binding residue prediction HSPred : Protein-protein interaction characterisation Amino acid substitution matrices Hidden Markov Models (collaboration with N. Goldman, Cambridge, & J. Thorne, NCSU) Genome Analysis Genomic fold recognition (GenTHREADER) Genome annotation using software agents Protein Structure Classification CATH (collaboration with J. Thornton & C. Orengo, UCL Biochemistry) Transmembrane Protein Modelling MEMSAT & MEMSATSVM Folding In Lipid Membranes (FILM) MEMPACK Biological Applications of Data-mining and Machine Learning Techniques Information extraction for biological research (BioRat) Microarray Analysis Data integration for microarray analysis Data visualization Systems Biology Systems biology applied to stem cells Legacy Services (to be retired shortly) Comparison of structure classifications (CATH/SCOP/FSSP) Genomic Threading Database (GTD)
Nomenclature for innovative activity of biology and anatomo-pathology performed especially in the Centres Hospitalo-Universitaires is usually called activity off nomenclature (BHN for nomenclature and PHN biology for the anatomo-pathology off nomenclature). This character of nomenclature means that health insurance has not yet incorporated these acts in the Nomenclature of acts of biology medical (NABM) or the General Nomenclature of professional acts (NGAP).
Whole genome sequencing data for 454 unrelated Scripps Wellderly Study participants with European ancestry from a project that is studying the genetic architecture of exceptional healthspan from a cohort comprised of more than 1300 healthy individuals over the age of 80 years. SWGR_v1.0 includes chromosome-specific VCF4.1 bgzipped and tabix indexed files. Annotations for each variant can be found at Scripps Genome ADVISER (SG-ADVISER, http://genomics.scripps.edu/) Additional data releases are expected.
Bioinformatics and Evolutionary Genomics group
Bioinformatics and Systems Biology Group
A University of Ghent center of excellence in the fields of gene prediction and genome annotation, comparative and evolutionary genomics, and systems biology. The team is involved in many international genome projects and has a particular interest in genome evolution and gene and genome duplication events.
Laboratory of Phil Green at Univeristy of Washington
Lab portal that contains software including Phred, Phrap, Consed. Our broad research goal is to help provide the computational methods necessary to achieve a complete, quantitative understanding of how cells function at the molecular level. Such an understanding will require three things: a parts list, or catalogue of all cellular molecules; a wiring diagram that specifies the interactions that occur between those molecules; and, finally, quantitative models of systems of interacting molecules. The advent of large-scale genome sequencing is bringing the possibility of completing the parts list within view, although substantial work remains to be done. Most current research in molecular biology is directed at filling the wiring diagram (which may be taken as specifying molecular function). The modeling of molecular systems, still in its infancy, will become increasingly important as the wiring diagram approaches completion and our ability to accurately quantitate cellular molecules improve.
European Commission''s primary public repository and portal to disseminate information on all EU-funded research projects and their results in the broadest sense.
A free version of the Unreal Engine 2.0, a powerful and flexible game engine and toolset to create games that run on previous generation hardware configurations and platforms, for non-commercial use. Epic have also released a non-free version of the Runtime that gives licenses access to the native code headers and some limited commercial distribution rights.
Database that contains information about FDA-approved brand name and generic prescription and over-the-counter human drugs and biological therapeutic products. Drugs@FDA includes most of the drug products approved since 1939. The majority of patient information, labels, approval letters, reviews, and other information are available for drug products approved since 1998. Dates of Coverage: 1939-present Update frequency: Daily. Data imported from the Orange Book depends on its update frequency.
Search Orphan Drug Designations and Approvals
Database of Orphan Drug Product designations. Searches may be run by entering the product name, orphan designation, and dates. Results can be displayed as a condensed list, detailed list, or an Excel spreadsheet.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of approved veterinary drugs run by the FDA.
SIGnAL Salk Institute Genomic Analysis Laboratory
A biology and bioinformatics laboratory at the Salk containing the following databases: SIGnAL T-DNA Express Arabidopsis Tiling Array Transcriptome Salk Insertion Sequence Database Arabidopsis Gene ORFeome Collection Salk Homozygote T-DNA Collection High Resolution Arabidopsis Methylome Perlegen Arabidopsis Resequencing Arabidopsis GMUCT Uncapped & Cleaved Transcripts Single Feature Polvmorphism Database High Resolution Arabidopsis Exosome Arabidopsis Interactome Single-base Resolution Epigenome Maps Transgenerational Inheritance of Methylation Variants Arabidopsis Cyclome Rice Functional Genomics Database Salk Arabidopsis 1,001 Genomes Arabidopsis Population Epigenomic Diversity Arabidopsis Biotic Stress Epigenome EIN3 -Ethylene Chip-seq/RNA-seq browser Soybean Epigenome Browser Human Human DNA Methylomes Human Pluripotent Cell Methylomes Human/Mouse Brain Methylomes Mouse Circadian Epigenome
Genome Institue at Washington University
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. Genome databases housed at the Genome Institute at Washington University. Included are genome databases from Humans/Primates, other vertebrates, microorganisms, plants and invertebrates.
Program for Monitoring Emerging Diseases - is an Internet-based reporting system dedicated to rapid global dissemination of information on outbreaks of infectious diseases and acute exposures to toxins that affect human health, including those in animals and in plants grown for food or animal feed. Electronic communications enable ProMED-mail to provide up-to-date and reliable news about threats to human, animal, and food plant health around the world, seven days a week. By providing early warning of outbreaks of emerging and re-emerging diseases, public health precautions at all levels can be taken in a timely manner to prevent epidemic transmission and to save lives. ProMED-mail is open to all sources and free of political constraints. Sources of information include media reports, official reports, online summaries, local observers, and others. Reports are often contributed by ProMED-mail subscribers. A team of expert human, plant, and animal disease moderators screen, review, and investigate reports before posting to the network. Reports are distributed by email to direct subscribers and posted immediately on the ProMED-mail web site. ProMED-mail currently reaches over 60,000 subscribers in at least 185 countries. ProMED collaborates closely with HealthMap at Children''s Hospital Boston. We also gratefully acknowledge HealthMap for providing Website and hosting services to ProMED.
Nomenclature for the description of sequence variants
International Classification of Primary Care
Ontology of the international classification of primary care (ICPC). Denmark: World Organisation of Family Doctors, 1993.
VassarStats: Website for Statistical Computation
Tools for performing statistical computation including: Clinical Research Calculators Probabilities Distributions Frequency Data Proportions Ordinal Data Correlation & Regression t-Tests & Procedures ANOVA ANCOVA
Environmental Assessment Reports from the EPA
The environmental assessment web site provides guidance and risk assessments aimed at protecting human health and the environment.
Biomedical Research Integrated Domain Group Model
An instance of a Domain Analysis Model (DAM) with the goal of producing a shared view of the dynamic and static semantics for the domain of protocol-driven research and its associated regulatory artifacts. This domain of interest is further defined as: Protocol-driven research and its associated regulatory artifacts: i.e. the data, organization, resources, rules, and processes involved in the formal assessment of the utility, impact, or other pharmacological, physiological, or psychological effects of a drug, procedure, process, or device on a human, animal, or other subject or substance plus all associated regulatory artifacts required for or derived from this effort, including data specifically associated with post-marketing adverse event reporting. The Biomedical Research Integrated Domain Group (BRIDG) Model is a collaborative effort engaging stakeholders from the Clinical Data Interchange Standards Consortium (CDISC), the HL7 Regulated Clinical Research Information Management Technical Committee (RCRIM TC), the National Cancer Institute (NCI) and its Cancer Biomedical Informatics Grid (caBIG??), and the US Food and Drug Administration (FDA). Source repository: https://ncisvn.nci.nih.gov/WebSVN/listing.php?repname=bridg-model&path=%2Ftrunk%2FModel+-+OWL%2F&
A free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences.
University of York Centre for Reviews and Dissemination
A research department of the University of York provides research-based information about the effects of health and social care interventions via their databases. The institute undertakes systematic reviews evaluating research evidence on health and public health questions of national and international importance.
Ontology of the AURA + Inquire project at SRI International, Menlo Park.
The Li Lab in the Department of Urology and Helen Diller Family Comprehensive Cancer Center
Laboratory portal that houses the following databases. MethPrimer is a program for designing bisulfite-conversion-based Methylation PCR Primers. Currently, it can design primers for two types of bisulfite PCR: 1) Methylation-Specific PCR (MSP) and 2) Bisulfite-Sequencing PCR (BSP) or Bisulfite-Restriction PCR. CpG Island Prediction MethPrimer can also analyze input sequences for the existence of CpG islands. Human Prostate Gene Database (PGDB) is a curated and integrated database of human genes related to the prostate and prostatic diseases. Human Kidney Gene Database (KGDB) is a curated and integrated database of human genes related to the kidney and renal diseases. The Li Lab is interested in understanding how small RNA regulates gene expression at the transcriptional level by targeting gene promoter sequences, particularly how small RNA activates gene transcription, a phenomenon termed RNA activation (RNAa).
Protein Homology/Anology Recognition Engine
A structure prediction system to reliably detect remote homologies.
THIS RESOURCE IS OUT OF SERVICE, documented on February 1st,2022. BIOBASE offers academic and non-profit organizations free access to TRANSFAC?? non-professional version with much reduced functionality and content compared to our professional database.
Ontology that relates concepts and terminologies used for human nutrition in a clinical and biomedical setting.
The major British society representing scientists, clinicians and nurses who work with hormones.
Artificial Intelligence Rheumatology Consultant System Ontology
Ontology used for the diagnosis of rheumatologic diseases. AI/RHEUM contains findings, such as clinical signs, symptoms, laboratory test results, radiologic observations, tissue biopsy results, and intermediate diagnosis hypotheses. Findings and hypotheses, which include definitions, are used to reach diagnostic conclusions with definite, probable, or possible certainty. AI/RHEUM is used by clinicians and informatics researchers.
An ontology of CD markers for lymphocyte classification in the cell ontology, and other categories of surface and secreted proteins useful for discriminating between lymphocyte subsets by flow cytometry, ELISPOT, ELISA and other assays typically used for phenotypic identification of individual lymphocytes or lymphocyte populations have been included.
Homology detection & structure prediction by HMM-HMM comparison
The primary aim in developing HHpred was to provide biologists with a method for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs. In fact, HHpred''s sensitivity is competitive with the most powerful servers for structure prediction currently available. HHpred is the first server that is based on the pairwise comparison of profile hidden Markov models (HMMs). Whereas most conventional sequence search methods search sequence databases such as UniProt or the NR, HHpred searches alignment databases, like Pfam or SMART. This greatly simplifies the list of hits to a number of sequence families instead of a clutter of single sequences. All major publicly available profile and alignment databases are available through HHpred.
A platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. Most frequently used tools HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHblits software is part of the open source package HHsuite. HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite. Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2. Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation. PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive. PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated.
Web-based suite of phylogenetic analysis tools for use in evolutionary biology. Web application for comparative analysis of sequence alignments using statistical models. Used for analyzing evolutionary signatures in sequence data. Datamonkey 2.0 provides curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application.
Vector graphics software to create digital graphics, illustrations, and typography for several types of media: print, web, interactive, video, and mobile.
DA&TO - The Atlas of biology databases and tools
A biological database and software tool catalog based on text mined and human annotated url mentions in PubMed abstracts. Data are annotated as to the author' '''s country of origin and url status is checked.
A comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.
A species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is an application ontology developed in OWL that contains precomposed phenotypes descriptions that are defined using the Gene Ontology (GO) and the Phenotype Trait Ontology (PATO).
An ontology that represents neuropsychological assessments such as the Folstein Mini-Mental State Examination (MMSE), the Trail-Making Test, the Hopkins Verbal Learning Test, and the Wechsler Memory Scale. NPT is designed to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning and provides a set of classes for the annotation of neuropsychological testing data. Neuropsychological testing is an important component in developing the clinical pictures used in the diagnosis of patients with a range of neurological diseases such as Alzheimer''s disease, multiple sclerosis, and following stroke or traumatic brain injury. An initial goal of the NPT project is to test hypotheses about the diagnosis of Alzheimer''s disease based on the results of neuropsychological assessments. NPT is being built in accordance with the OBO Foundry principles. It is as an extension of the Ontology for Biomedical Investigations (OBI), which utilizes both the Information Artifact Ontology (IAO) and the Basic Formal Ontology (BFO). NPT is a corollary project of the Neurological Disease Ontology (ND) and is being developed in collaboration with the developers of the Mental Functioning Ontology (MF).
An ontology for the representation of the range of clinical and basic science aspects of neurological diseases. ND has a broad scope that includes neurological diseases as well as their associated signs, symptoms, diagnoses, pathologies, etiologies, processes, treatments, and any other aspect of a neurological disease that is or can be encountered in the course of clinical practice or medical research. ND is being built in accordance with the OBO Foundry principles. It is an extension of the Ontology for General Medical Science (OGMS) as well as the Basic Formal Ontology (BFO). ND aims to develop classes utilizing both textual and axiomatized definitions to describe and formalize relations between instances of classes both within the ontology itself as well as between ND and external ontologies such as the: Gene Ontology (GO), Cell Ontology (CL), Protein Ontology (PRO), Chemical Entities of Biological Interest (ChEBI), and Ontology for Biomedical Investigations (OBI).
Software tool for data graphing and analysis by Systat Software, Inc.
Allen Brain Atlas (ABA) Adult Mouse Brain Ontology
Allen Brain Atlas Adult Mouse Brain Ontology
An ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 200 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type. The ontology should be useful in increasing the amount of knowledge in anatomy ontologies, facilitating annotation and enabling interoperability across anatomy ontologies
Ontology that describes the actors'' function (healer, fetishist or soothsayer); the different types of proposed process treatment, the symptom''s roles and the disease consideration.
An open, public ontology representing relevant knowledge on Alzheimer's disease.
An ontology of amino acids and their properties. Inferred version.
A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.
Animal Natural History and Life History Ontology
An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.
University of Alabama at Birmingham School of Medicine; Alabama; USA
University of Alabama at Birmingham School of Medicine
Coding Symbols for a Thesaurus of Adverse Reaction Terms
Ontology for coding, filing, and retrieving post-marketing adverse drug and biologic experience reports. It is organized in body system and pathophysiology hierarchies, as well as a separate fetal/neonatal category of less than 20 terms. COSTART has been superseded by the Medical Dictionary for Regulatory Activities (MedDRA) Terminology. For more information about MedDRA in the Metathesaurus, see the MedDRA source synopsis. COSTART was last updated in the Metathesaurus in 1999.
Ontology that characterizes the state of current thought in cognitive science. It defines a set of mental concepts along with a set of mental tasks, and the measurement relations between those classes.
Common Terminology Criteria for Adverse Events
A coding system for reporting adverse events that occur in the course of cancer therapy. It was derived from the Common Toxicity Criteria (CTC) v2.0 and is maintained by the Cancer Therapy Evaluation Program (CTEP) at the National Cancer Institution (NCI).
A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science
Content Archive Resource Exchange Lexicon
Categories and terms used to classify content (documents, images, etc) in electronic content repositories for life science / BioPharma. Initial version contains content model for use with clinical trial electronic Trial Master Files or eTMF archives. A Content model contains content classification categories (classes) and metadata properties (data properties). Data properties should be assigned to each Content Type. Recent changes include: addition of electronic signature support, medical imaging classifications.
Ontology that includes crop-specific trait ontologies for several economically important plants like rice, wheat, maize, potato, musa, chickpea and sorghum along with other important domains for crop research such as germplasm, passport, trait measurement scales, experimental design factors etc.
Current Procedural Terminalogy Hierarchy
Metathesaurus of current procedural terminalogy (CPT).
Ontology of current procedural terminology.
DICOM Controlled Terminology (PS3.16 2013 Annex D)
Ontology that is a module of the OntoNeuroLOG ontology, that covers the domain of Datasets and the processing of datasets developed in the context of the NeuroLOG project, a french project aiming at integrating distributed heterogeous resources in neuroimaging. It includes a detailed taxonomy of datasets in the area of neuroimaging (and especially MR imaging) as well as a taxonomy of medical image processing.
A standardized terminology of dermatologic diagnoses, therapies, procedures, and laboratory tests.
Diagnosis Ontology of Clinical Care Classification
A computational diagnostic ontology containing 91 elements, including classes and sub-classes, which are required to conduct SR-MA (Systematic Review - Meta Analysis) for diagnostic studies, that will assist in standardized reporting of diagnostic articles. They also report high percentage of agreement among five observers as a result of the inter-observer agreement that they conducted among them to tag 13 articles using the diagnostic ontology. Moreover, they extend their existing repository CERR-N (Center of Excellence in Research Reporting in Neurosurgery) to include diagnostic studies.
Disease core ontology applied to Rare Diseases
A core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). </ br> Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr). Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database.
Ontology that is a schema for information brokering and knowledge management in the complex field of rare diseases. On the one hand, the Dispedia schema uses semantic technologies to describe patients affected by rare diseases, and on the other hand, to record expertise concerning these particular diseases in machine-processable form. In addition to the differentiated attribution of facts to the individual need for information, Dispedia enables information brokering which adjusts to the type of recipient, its character as well as its personal attitude. The schema was initially geared to an exemplified disease, Amyotrophe Lateralsclerose (ALS).
A structured controlled vocabulary of the development of Drosophila melanogaster.
A structured controlled vocabulary of the anatomy of Drosophila melanogaster.
Evidence in Documents Discovery and Analysis Study Design Terminology
Ontology terms useful for machine learning experiments. The terminology appearing in JMLA has been enriched with terms from MeSH and Emtree, the controlled vocabularies for MEDLINE and Embase, respectively. Synonyms include American and British variants and some inverted terms.
Ontology for describing electrocardiograms, their capture method(s) and their waveforms.
A set of 1,437 eligibility features that were organized into a feature hierarchy using 80 breast cancer trials.
Ontology to describe the active components of the enzyme''s reactions (cofactors, amino acid residues and cognate ligands) and their roles in the reaction. EMO builds upon this by formalizing key concepts, and the relationships between them, necessary to define enzymes and their functions. This describes not only the general features of an enzyme, including the EC number (catalytic activity), 3D structure and cellular locations, but also allows for the detailed annotation of the mechanism. This mechanistic detail can be either at a gross level (overall reaction only), or the more detailed granularity of the steps and components required to effect the overall chemical transformation.
Enzyme Reaction Ontology for partial chemical perspectives
An enzyme ontology that deals with partial reactions (transformations)
Ontology about the epilepsy domain and epileptic seizures. Based on the diagnosis proposed by the International League Against Epilepsy (ILAE).
An ontology for Loggerhead sea turtle (Caretta caretta) nesting behavior, based on the published ethogram of Hailman and Elowson. A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms.
An application ontology devoted to the standardized recording of data related to Fanconi Anemia (FA). This ontology was created using an OWL file provided by Dr. Ada Hamish (and Francois Schiettecatte) at the Centers for Mendelian Genetics, with their permission. Their original ontology can be found at: http://phenodb.net/help/features. Modifications were made using HPO, OMIM, NCI, and SNOMED. Novel classes pertaining to FA were added and defined as appropriate.
Ontology to represent the set of concepts about the fire occurring in natural vegetation, its characteristics, causes and effects, with focus on Cerrado vegetation domain. The fire plays a determinant role on the structure and composition of Cerrado physiognomies.
Ontology generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kew''s African Floras. Every class in the ontology has at least one taxon annotation. This is the pre-classified version of the ontology; the original OWL file is at http://jagannath.pdn.cam.ac.uk/plant/flopo-unclassified.owl
A structured controlled vocabulary for the anatomy of fungi.
Human Developmental Anatomy Ontology abstract version 1
A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just ''heart'' really means ''heart (CS 9-20)''. Timing details will be added to the abstract version of the ontology in a future release.
G Protein-Coupled Receptor BioAssays Ontology
Ontology (http://www.bioassayontology.org/bao_gpcr) that describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of academic and pharmaceutical research targets. Incorporation and comparison of various small molecule screening data sets, such as those deposited in PubChem, ChEMBL, KEGG, PDSP, and/or IUPHAR databases, requires a formalized electronic organization system. In order to bridge the gap between the overflow of HTS data and the bottleneck of integrated analysis tools, herein, we provide the first comprehensive GPCR ontology. The development and utility of GPCR ontology was based on previously developed BioAssay Ontology (BAO). The GPCR ontology contains information about biochemical, pharmacological, and functional properties of individual GPCRs as well as GPCR-selective ligands inclusive of their HTS screening results and other records. This provides the first all-inclusive GPCR ontology with all available data to model the relationship between the GPCR binding sites and their physiologic and pharmacologic role in physiology via small molecule chemical structures. We developed this system using emerging semantic technologies, by leveraging existing and descriptive domain level ontologies.
A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.
An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.
A top-level ontology integrating objects and processes.
A biological core ontology built on the General Formal Ontology.
Ontology to define the abstract division of the total genetic information of an organism by its physical separation into different components, thereby providing a high level reference point to which more specific descriptions of the characteristics of these components can be linked.
Genomic Clinical Decision Support Ontology
Ontology to unify several functionalities in a single resource, being: * A knowledge base for clinical pharmacogenomics/pharmacogenetics that can be used for question-answering (e.g., which SNPs are associated with this drug?) * A rule base for clinical decision support (e.g., inferring that a patient with a specific set of SNPs requires a lowered dose of warfarin and generating a CDS message that can be viewed by clinicians) * A tool for checking data consistency (e.g., highlighting which allele definitions in PharmGKB are overlapping, or which clinical decision support rules are matching the same group of patients)
Ontology to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information. See also Taxonconcept.org
Ontology that provides an up-to-date knowledge base of experimentally verified glycan structures. Glycan (oligosaccharide or polysaccharide) structures are represented as trees of monosaccharide residues. Linkage to proteins and lipids is supported as well. Insertion of a new glycan is controlled by curation process that includes matching the new glycan against a canonical glyco-tree (a highly branched representation for a family of glycans).
An ontology for courtship behavior of the spider Habronattus californicus. A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms.
Ontology for standardized health outcome and health determinant indicators as maintained by the CDC National Center for Health Statistics.
Health Level Seven Reference Implementation Model Version 3
Ontology for the data types used in the creation of HL7 (Health Level Seven International) V3 specifications. This version is the first update to Normative RIM, Release 3. It is based on changes approved in Harmonization in November 2010. This release of the RIM is bound to HL7 Abstract Data Types Release 2. https://www.hl7.org/implement/standards/product_brief.cfm?product_id=264
Human Developmental Anatomy Ontology abstract version 2
Human Developmental Anatomy Ontology timed version
A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.
An Interaction Network Ontology (INO) extension for the domain of human interaction networks. It has currently incoporated Reactome reactions and pathways. Like INO, HINO aligns with BFO. HINO is developed by following the OBO Foundry principles.
Ontology as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles.
Logical Observation Identifier Names and Codes
Ontology of logical observation identifier names and codes (LOINC); Version 2.26; January 2, 2009
Ontology for immunogenetics and immunoinformatics. Provides semantic specification of terms to be used in immunogenetics and immunoinformatics and manages related knowledge, thus allowing standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. Manages the knowledge through diverse facets relying on seven axioms, IDENTIFICATION, CLASSIFICATION, DESCRIPTION, NUMEROTATION, LOCALIZATION, ORIENTATION and OBTENTION. These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized. The axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels. IMGT, the international ImMunoGeneTics information system, has been built on IMGT-ONTOLOGY. The version 1.0.2 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and the concepts of CLASSIFICATION.
Image and Data Quality Assessment Ontology
Ontology for Image and Data Quality Assessment for scientific data management.
Ontology generated as part of the Bioinformatics Integration Support Contract (BISC) that is based on the National Library of Medicine (NLM) Medical Subject Headings; National Cancer Institute Thesaurus; International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM); ICD-10; and other open source public databases. Specific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc.
Ontologies designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases. Please note: The ontology metrics displayed by BioPortal do not distinguish IDO-developed terms from terms imported from other ontologies.
A custom-built terminology to describe the nanomanufacturing enterprise.
An ontology in the domain of interaction network that aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It is aimed to represent general interactions (e.g., molecular interactions) and interaction networks (e.g., Bayesian network). INO was initiated by supporting literature mining related to interactions and interaction networks. INO aligns with BFO. INO is a community-based ontology, and its development follows the OBO Foundry principles.
International Classification of External Causes of Injuries
A system of classifications to enable systematic description of how injuries occur. It is designed especially to assist injury prevention. It was originally designed for use in settings in which information is recorded in a way that allows statistical reporting--for example, injury surveillance based on collection of information about cases attending a sample of hospital emergency departments. It has also been found useful for other purposes. For example, it has been used as a reference classification during revision of another classification, to record risk-factor exposure of children in a cohort study, as the basis for special-purpose classifications and in a growing number of other ways.
International Classification of Diseases Version 10
Ontology of the International Statistical Classification of Diseases and Related Health Problems (ICD-10). 10th rev. Geneva, a medical classification list by the World Health Organization (WHO).
International Classification of Diseases Version 10 - Clinical Modification
Ontology of the International Classification of Diseases, 10th Edition, Clinical Modification, 2011_01
International Classification of Diseases Version 10 - Procedure Coding System
Ontology of the International Classification of Diseases Version 10, ICD-10-PCS (Procedure Coding System), 2009.
Ontology that is a module of the OntoNeuroLOG ontology, that covers the domain of Magnetic Resonance Imaging (MRI) dataset acquisition, i.e. MRI protocols, and MRI sequence parameters, developed in the context of the NeuroLOG project, a french project aiming at integrating distributed heterogeneous resources in neuroimaging. In particular, it includes a multi-axial classification of MR sequences.
Major Histocompatibility Complex Ontology
Ontology that contains terms necessary for describing and categorizing concepts related to Major Histocompatibility Complex, in general, for a number of model species, and also for humans.
Ontology that describes the content of the models used in medical image simulation developed in the context of the Virtual Imaging Platform project (VIP), a french project aiming at sharing medical image simulation resources. This ontology can be used to annotate such models in order to highlight the different entities that are present in the 3D scene to be imaged, i.e. anatomical structures, pathological structures, foreign bodies, contrast agents etc. The model allows also to associate to these entities information about their physical qualities, which are used in the medical image simulation process (to mimick physical phenomena involved in CT, MR, US and PET imaging). This ontology partly relies on the OntoNeuroLOG ontology (ONL-DP ONL-MR-DA), as well as PATO, RadLex, FMA and ChEBI.
Ontology to (i) Provide better account of and better access to medical information through natural languages in order to help physicians in their daily practice, and to (ii) Enhance European cooperation by multilingual access to standardised medical nomenclatures. The major achievements of MENELAS are the realization of its two functional systems: (i) The Document Indexing System encodes free text PDSs into both an internal representation (a set of Conceptual Graphs) and international nomenclature codes (ICD-9-CM). Instances of the Document Indexing System have been realised for French, English and Dutch ; (ii) The Consultation System allows users to access the information contained in PDSs previously indexed by the Document Indexing System. The test domain for the project was coronary diseases. The existing prototype shows promising results for information retrieval from natural language PDSs and for automatically encoding PDSs into an existing classification such as ICD-9-CM. A set of components, tools, knowledge bases and methods has also been produced by the project. These include language-independent ontology and models for the domain of coronary diseases; conceptual description of the relevant ICD-9-CM codes. This ontology includes a top-ontology, a top-domain ontology and a domain ontology (Coronay diseases surgery). The menelas-top ontology here is the part of the whole ontology without any reference to medical domain.
Ontology that is a module of the OntoNeuroLOG ontology that covers the field of mental state assessments, i.e. instruments, instrument variables, assessments, and resulting scores, developed in the context of the NeuroLOG project, a french project aiming at integrating distributed heterogeous resources in neuroimaging. It includes a generic domain core ontology, that provides a general model of such entities and a general taxonomy of behavioural, neurosychological and neuroclinical instruments, that can be easily extended to model any particular kind of instrument. It also includes such extensions for 8 relatively standard instruments, namely: (1) the Beck-depression-inventory-(BDI-II), (2) the Expanded-Disability-Status-Scale, (3) the Controlled-oral-word-association-test, (4) the Free-and-Cued-Selective-Reminding-Test-with-Immediate-Recall-16-item-version-(The-Grober-and-Buschke-test), (5) the Mini-Mental-State, (6) the Stroop-color-and-word-test, (7) the Trail-making-test-(TMT), (8) the Wechsler-Adult-Intelligence-Scale-third-edition, (9) the Clinical-Dementia-Rating-scale, (10) the Category-verbal-fluency, (11) the Rey-Osterrieth-Complex-Figure-Test-(CFT).
An ontology for metagenome sample metadata that mainly defines predicates.
Metagenome and Microbes Environmental Ontology
Ontology for organismal habitats (especially focused on microbes)
Structured controlled vocabulary for describing meta information of microbial calture collection maintained in biological research centers
Ontology that provides a comprehensive description of the existing microbial typing methods for the identification of bacterial Isolates and their classification. Such a description constitutes an universal format for the exchange of information on the microbial typing field, providing a vehicle for the integration of the numerous disparate online databases. In its current version, TyPon describes most used microbial typing methods but it is, and always will be, a work in progress given the constant advances in the microbial typing field.
Minimal Information about any Sequence Controlled Vocabularies
Minimal Information about any Sequence (MIxS) Controlled Vocabularies
Controlled vocabularies for the MIxS (Minimal Information about any Sequence) family of metadata checklists. See http://gensc.org/gc_wiki/index.php/MIxS for details on the MIxS checklists.
Minimal Information about any Sequence Ontology
Ontology providing an RDF representation of the MIxS (Minimal Information about any Sequence) family of checklists.
Neuroscience Information Framework (NIF) Dysfunction Ontlogy
Neuroscience Information Framework Dysfunction Ontlogy
Ontology that contains the former BIRNLex-Disease, version 1.3.2. -- The BIRN Project lexicon provided entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. It was built using the organizational framework provided by the foundational Basic Formal Ontology (BFO). It used an abstract biomedical layer on top of that - OBO-UBO which was constructed as a proposal to the OBO Foundry. This was meant to support creating a sharable view of core biomedical objects such as biomaterial_entity, and organismal_entity that all biomedical ontologies are likely to need and want to use with the same intended meaning. The BIRNLex biomaterial entities have already been factored to separately maintained ontology - BIRNLexBiomaterialEntity.owl which this BIRNLex-Main.owl file imports. The Ontology of Biomedical Investigation (OBI) is also imported and forms the foundation for the formal description of all experiment-related artifacts. The BIRNLex will serve as the basis for construction of a formal ontology for the multiscale investigation of neurological disease.
Neuroscience Information Framework (NIF) Subcellular Ontology
Neuroscience Information Framework Subcellular Ontology
Ontology that contains cell parts and subcellular structures from SAO-CORE and Gene Ontology Cellular Component (GO-CC). http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl
NMR-Instrument Component of Metabolomics Investigations Ontology
Metabolomics Standards Initiative-sanctioned ontology, created within the COSMOS EU project, to support the nmrML data standard for nuclear magnetic resonance data in metabolomics with meaningful raw data descriptors.
Ontology that connects organic name reactions such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles in an organic synthesis.
An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.
A vocabulary for clinical care, translational and basic research, and public information and administrative activities.
Ontology of the National Drug Data File plus source vocabulary
National Drug File - Reference Terminology
Ontology of National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11
An ontology for describing biological activities of natural products.
Ontology that aims at representing classes and relations to a specific set of diseases which persist in exactly the physical, psychosocial and economic situation of the poorest, most marginalized populations of the developing world, the Neglected Tropical Diseases (NTD). The current focus of NTDO is related to the transmission of vector-borne diseases and how they are related to the death. NTDO is based on BioTop (main classes and relations) and GFO (Time Representation) and represented in Description Logics (DL). NTDO includes information about the proper disease, its causative agent (when available), dispositions, and the geographic location the disease happens. In addition, NTDO includes a generic attempt to identify the process which leads a person to death, due to NTDs or other diseases. NTDO was built with a rich set of axioms and the intended usage is related to Health Surveillance of NTD-related morbidity and mortality cases.
Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.
Ontology of neural functional motor recovery.
Species ontology that adopts and integrates relevant portions of available taxonomies as needed based on the species and strain terms represented in the current release of NeuroMorpho.Org (72 terms as of the 5.7 release) and any future additions. When a NeuroMorpho.Org term is mapped with an external resource, its entire lineage (ancestors and descendants) is added to the NeuroMorpho.Org species ontology. The resulting 1,340 terms of this initial version of the ontology come for 65% from the NCBI taxonomy (24 NeuroMorpho.Org species/strain terms mapped), 30% from the Rat Gene Database (1 term mapped), and altogether 5% from NIFSTD (7 terms mapped), MeSH (2 terms mapped), ITIS (1 term mapped), and custom-added concepts (41 terms mapped, largely mouse strains from Jackson Labs).
Species taxonomy for the data curated in NeuroMorpho.Org. The existing ontologies are re-used as needed as the new metadata information for species and strains is deposited in NeuroMorpho.Org database. This species hierarchy consists of 56% of NCBI taxonomy and 39% of Rat strain ontology. The remaining 5% mostly consists of new concepts and few others from NIFSTD and MESH.
Non-Randomized Controlled Trials Ontology
Ontology to help the systematic review and meta-analysis process of non randomized clinical trials.
Ontology that contains activities that nurses use while coordinating care among patients.
Ontological Knowledge Base Model for Cystic Fibrosis
An ontological knowledge base model for cystic fibrosis. There are molecular genetic information (i.e. gene mutations) and health information included in OntoKBCF. The purposes of OntoKBCF include management of molecular genetic information and health information and embedding OntoKBCF into EHR settings.
Ontology for Drug Discovery Investigations
Ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI).
An ontology based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop (Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.
Ontology for Genetic Disease Investigations
Ontology used to model the scientific investigation, especially Genome-Wide Association Study (GWAS), to find out genetic susceptibility factor to disease, such as Diabetes. It models the genetic varaints, polymorphisms, statistical measurement, populations and other elements that are essential to determine a genetic susceptibility factor in GWAS study. It must be used with other two ontologies, in the case of Diabetes, :Ontology of Geographical Region (OGR) and Ontology of Glucose Metabolism Disorder (OGMD) .
Ontology for Genetic Susceptibility Factor
Application ontology to model / represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO2.0''s framwork. The ontology is under the domain of genetic epidemiology.
Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans'' various diseases and biological processes (usually through miRs'' respective target genes). OMIT has reused and extended a set of well-established concepts from existing bio-ontologies, e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy, Human Disease Ontology, Foundational Model of Anatomy, and so forth.
Ontology designed around the guiding concept of a symptom being: A perceived change in function, sensation or appearance reported by a patient indicative of a disease. Understanding the close relationship of Signs and Symptoms, where Signs are the objective observation of an illness, the Symptom Ontology will work to broaden it''s scope to capture and document in a more robust manor these two sets of terms. Understanding that at times, the same term may be both a Sign and a Symptom
Ontology for Newborn Screening Follow-up and Translational Research
Application ontology covering the domain of newborn screening, follow-up and translational research pertaining to patients diagnosed with inheritable and congenital diseases mainly identified through newborn dried blood spot screening. ONSTR is a central component of the project Newborn Screening Follow-up Data Integration Collaborative (NBSDC), https://nbsdc.org. ONSTR uses the Basic Formal Ontology v2 (BFO2, v2012-07-20) as top-level ontology and extends the classes imported from OBO Foundry ontologies and candidate ontologies.
Ontology of Alternative Medicine - French
Ontology for common concepts for communication between traditional medicine and western medicine. (In French)
Ontology of Biological and Clinical Statistics
A biomedical ontology in the domain of biological and clinical statistics that is primarily targeted for statistical representation in the fields in biological, biomedical, and clinical domains. It uses the Basic Formal Ontology (BFO) as the upper level ontology. OBCS imports all biostatistics related terms in the Ontology for Biomedical Investigations (OBI) including all logical axioms.
Ontology to support systematic description of, and interoperable queries on, human studies and study elements.
Generic ontology for the domain of data mining that includes the information processing processes that occur in the domain of data mining, participants in the processes and their specifications. OntoDM is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. The generality in scope allows wide number of applications of the ontology, such as semantic annotation of data mining scenarios, ontology based support for QSARs, etc.
Ontology for representing data mining investigations. Its goal is to allow the representation of knowledge discovery processes and be general enough to represent the data mining investigations. The ontology is based on the CRISP-DM process methodology.
Terms associated with pediatrics, representing information related to child health and development from pre-birth through 21 years of age; contributed by the National Institute of Child Health and Human Development.
Ontology of Experimental Variables and Values
Ontology that provides a lightweight representation of the variables used to measure experimental properties and the measurement scales that form the complex data types supporting that data. Many different variables measure the same thing, here they use a lightweight representation driven by a small number of classes and a large number of variables to focus only on providing a vocabulary of variables that may be extended for consolidation to standardized variables for specific things and functions to map between values from different measurements scales. They use the base ontology description to provide a very lightweight representation of the basic elements of an experimental design and they use views to instantiate it for specific domains.
Ontology that contains entities such as: datatype, datatype generator, datatype quality and others giving the possibility to represent arbitrary complex datatypes. This is an important fact for a general data mining ontology that wants to represent and query over modelling algorithms for mining structured data. The ontology was first developed under the OntoDM (Ontology of Data Mining, http://kt.ijs.si/panovp/OntoDM) ontology, but for generality and reuse purpose it was decided to export it as a separate ontology. Additionaly, the OntoDT ontology is based on and ISO/IEC 11404 (http://www.iso.org/iso/catalogue_detail.htm?csnumber=39479) standard and can be reused used independently by any domain ontology that requires representation and reasoning about general purpose datatypes.
Ontology that is used with other ontologies to represent the genetic susceptibility factors of diabetes. This OWL ontology classified the geograhical regions related vocabularies extracted from UMLS.
Ontology including the disease names, phenotypes and their classifications involved in Glucose Metabolism Disorder, Diabetes. (OBO and OWL format are available in sourceforge.)
Ontology of Homology and Related Concepts in Biology
Ontology that represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.
Ontology of language terms used in the domain of autism available for consultation and sharing. The language terms were obtained via text mining and automatic retrieval of terms from the corpus of PubMed abstracts.
Ontology to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (http://www.orpha.net) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, SNOMED CT, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). The ontology will be maintained by Orphanet and further populated with new data. Orphanet classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology is updated monthly and follows the OBO guidelines on deprecation of terms. It constitutes the official ontology of rare diseases produced and maintained by Orphanet (INSERM, US14).
Ontology that models provenance metadata associated with experiment protocols used in parasite research. The PEO extends the upper-level Provenir ontology (http://knoesis.wright.edu/provenir/provenir.owl) to represent parasite domain-specific provenance terms. The PEO (v 1.0) includes Proteome, Microarray, Gene Knockout, and Strain Creation experiment terms along with other terms that are used in pathway.
Vocabulary that describes a process that is the means of how a pathogen is transmitted from one host, reservoir, or source to another host. This transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.
An ontology for describing both human infectious disease caused by bacteria and the disease that is related to bacterial infection.
Ontology that proposes concepts and roles to represent relationships of pharmacogenomics interest.
Two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties.
THIS RESOURCES IS NO LONGER IN SERVICE, documented on April 23, 2014. REPLACED BY: Plant Ontology (PO). A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization. Note that this has been subsumed into the PO. This file is created by filtering plant_ontology_assert.obo to contain only terms from the plant anatomical entity branch of the PO. For more information, please see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/
Ontology that encodes agreement among experts about how Emergency Department (ED) chief complaints are grouped into syndromes of public health importance (consensus definitions).
A controlled vocabulary of growth and developmental stages in various plants. Note that this has been subsumed into the Plant Ontology (PO). This file is created by filtering plant_ontology_assert.obo to contain only terms from the plant structure development stage branch of the PO. For more information, please see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/
Ontology of a system for tracking grants and producing reports - Users can access grant data through a query interface and a variety of pre-defined forms and reports.
Ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified.
A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.
Proteomics Data and Process Provenance Ontology
A comprehensive proteomics data and process provenance ontology.
Ontology that expresses the PROV Data Model using the OWL2 Web Ontology Language (OWL2) providing a set of classes, properties, and restrictions that can be used to represent and interchange provenance information generated in different systems and under different contexts. It can also be specialized to create new classes and properties to model provenance information for different applications and domains.
Quantities Units Dimensions and Types Ontology
QUDT - Quantities Units Dimensions and Data Types Ontologies
Collection of ontologies that define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units.
An ontology that describes various concepts in quantitative imaging biomarkers.
A controlled terminology for radiology-a single unified source of radiology terms for radiology practice, education, and research. For license information see : http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/radlex_public_license_version_1-0-1.pdf Converted to use OWL format submissions
Ontology of a modified version of Medical Subjects Headings Thesaurus 2014, that is an OWL representation of MeSH so that it can be integrated with other ontologies represented in OWL. It contains all terms that are in MeSH and in the MeSH concept tree, including the pharmacological actions (represented as subclass relations). Concepts in the MeSH concept tree are merged with MeSH term ids. Note that, while this ontology is composed of MeSH terms, it does not correspond directly to UMLS MeSH. In particular, a single term in UMLS MeSH often results in multiple classes in this ontology. For example, in MeSH there is a single term with the label Heart. The internal code (unique identifier) for this term is A07.541. In this ontology there are two entirely different terms, both of which have the label Heart. The codes for these terms are A07.541 and D006321.
Ontology in the domain of role classification that aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.
A general-purpose STATistics Ontology to provide coverage for processes such as statistical tests, their conditions of applications, and information needed or resulting from statistical methods, such as probability distributions, variable, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results.
Controlled vocabulary used for various entity properties in the Synapse platform.
Sample Processing and Separation Techniques Ontology
A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative.
Santa Barbara Coastal Observation Ontology
Extensible Observation Ontology for the Santa Barbara Coastal Long Term Ecological Research project (SBC-LTER). It extends core concepts defined in the OBOE suite that are particular to the Santa Barbara Coastal Long Term Ecological Research project''s data collection activities. These include specific measurement protocols, sites, etc. This is meant as a case study ontology for the Semtools project.
Semantic Web for Earth and Environment Technology Ontology
A mature foundational ontology developed at the NASA Jet Propulsion Laboratory, currently containing over 6000 concepts organized in 200 ontologies represented in OWL, whose top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). SWEET is now officially under the governance of the ESIP foundation.
Ontology that provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.
Single-Nucleotide Polymorphism (SNP) Ontology
A domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name it is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. SNP-Ontology is general enough to enable the representation of variations observed in genome of various species. Latest versions of SNP-Ontology include the representation of haplotype and of CNV. The unambiguous representation of genomic variations provided by SNP-Ontology enables to integrate heterogeneous data related to genomic variations. To achieve this goal SNP-Ontology enables (1) to represent one variation in accordance with various ways that exist for describing it, (2) to represent the equivalence between two distinct descriptions of one variation, and (3) to represent correspondence between a genomic variation and its outcome at the transcriptome and proteome levels.
Ontology of context-based healthcare access-control policies.
A vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Cross references to appearances of each term in each source are provided. Consistent with its intended use as a vocabulary of labels, there is no relation specifying an ordering of the rank terms.
Taxonomy for Rehabilitation of Knee Conditions
Ontology that formally models information relevant for the rehabilitation of knee conditions. It provides the framework that can be used to collect coded data in sufficient detail to support epidemiologic studies so that the most effective treatment components can be identified, new interventions developed and the quality of future randomized control trials improved to incorporate a control intervention that is well defined and reflects clinical practice.
Terminological and Ontological Knowledge Resources Ontology
An Ontology describing Resources having different formats. This Ontology can be used to annotate and describe Terminological, Ontological Knowledge resources.
Anatomy Ontology of the Tick, Families: Ixodidae, Argassidae
An OWL schema that expands upon the Tissue microarray (TMA) data exchange specification to assist in data sharing and integration.
Traditional Medicine Constitution Value Set
Ontology of the value set for the constitution property of the International Classification of Traditional Medicine (ICTM).
Traditional Medicine Meridian Value Sets
Ontology of the meridian value set used in the International Classification of Traditional Medicine.
Traditional Medicine Other Factors Value Set
Ontology of the value set for the Other Factors property of the International Classification of Traditional Medicine (ICTM).
Traditional Medicine Signs and Symptoms Value Set
Ontology of the value set for the Signs and Symptoms property of the International Classification of Traditional Medicine (ICTM).
A high level patient-centric ontology for the pharmaceutical industry. The ontology should enable silos in discovery research, hypothesis management, experimental studies, compounds, formulation, drug development, market size, competitive data, population data, etc. to be brought together. This would enable scientists to answer new questions, and to answer existing scientific questions more quickly. This will help pharmaceutical companies to model patient-centric information, which is essential for the tailoring of drugs, and for early detection of compounds that may have sub-optimal safety profiles. The ontology should link to existing publicly available domain ontologies.
Ontology about the anatomical structures of the red flour beetle Tribolium castaneum in the developmental stages larva, pupa and adult.
A small ontology for the units of measurement developed during the development of the Sleep Domain Ontology (SDO). It supports the use of SDO within the PhysioMIMI application.
Metrical units ontology for use in conjunction with PATO
Vertebrate Homologous Organ Group Ontology
A multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 historical homology. Each mapping has been manually reviewed, and theye provide confidence codes and references when available.
Veterans Health Administration National Drug File
Ontology that includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.
An extension of the Ontology for General Medical Science (OGMS) that covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.
World Health Organization (WHO) Adverse Reaction Terminology
World Health Organization Adverse Reaction Terminology
Ontology of the WHO adverse reaction terminology, 1997.
Ontology that enables automated interaction with more complex Web services that are typical for example within life sciences. WSIO is however independent of the application domain and relevant for both SOAP and REST Web services, and for batch execution engines in general. If the interaction scenario with a Web service is nontrivial (and incorporates session handling), annotation with WSIO concepts will enable automatic generation of client programs, scripts, or interactive applications with a graphical user interface. WSIO also enables automation of different ways of data transfer and data un-/compression or en-/decoding. They strongly discourage providers from developing complex interaction and data-transfer/compression scenarios, however when needed, WSIO may enable smooth automated interaction with them. Future versions will support more interaction scenarios. WSIO aims to serve also as a means to standardise the complex interaction scenarios primarily within both SOAP and REST Web services, and secondarily to apply also to batch execution infrastructure in general.
Ontology that defines traits of the International Wheat Information System (IWIS) database and wheat descriptor.
Ontology to help plant scientists in documenting and sharing metadata describing the abiotic environment.
Ontology for pseudogenes including biological feature, classified type, Evidence code, and subcellular origin.
Terminology for the Description of Dynamics
Ontology for dynamical behaviors, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.
A commercial software tool for statistical analysis.
researchobject.org is a community web page that presents the ongoing activities of the open Research Object community and gathers knowledge about related developments and adoptions. The community is composed of representatives from science domains, research infrastructure development, publishing and policy making. The vision of the community is to facilitate knowledge interchange and reproducible computational research through the definition and promotion of Research Object principles, i.e. identification, annotation, and aggregation of scientific artefacts. The focus is not on replacing any solutions that are already in place, but on ''engaging'' with existing solutions.
treestoolbox - A Matlab toolbox to generate edit visualize and analyze neuronal structure
Software package, written in Matlab (Mathworks, Natick, MA), providing tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. It provides the basic tools to edit, visualize and analyze dendritic and axonal trees, methods for quantitatively comparing branching structures between neurons, and tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance.
NYU Institute for Pediatric Neuroscience Sample
NYU Phyllis Green and Randolph Cwen Institute for Pediatric Neuroscience Sample
Datasets including a collection of scans from 49 psychiatrically evaluated neurotypical adults, ranging in age from 6 to 55 years old, with age, gender and intelligence quotient (IQ) information provided. Future releases will include more comprehensive phenotypic information, and child and adolescent datasets, as well as individuals from clinical populations. The following data are released for every participant: * At least one 6-minute resting state fMRI scan (R-fMRI) * * One high-resolution T1-weighted mprage, defaced to protect patient confidentiality * Two 64-direction diffusion tensor imaging scans * Demographic information (age, gender) and IQ-measures (Verbal, Performance, and Composite; Weschler Abbreviated Scale of Intelligence - WASI) * Most participants have 2 R-fMRI scans, collected less than 1 hour apart in the same scanning session. Rest_1 is always collected first.
Virginia Tech Carilion Research Institute Sample
Dataset including a T1 weighted anatomical image as well as two 10-minute resting state scans acquired during the same session from 25 psychiatrically screened healthy adults (community sample) ranging in age from 18 to 65 years old, with age, sex, education level, and ethnicity provided. Some subjects also returned several weeks after the first scan for a second scanning session. The number of days between scan sessions, for subjects that had two sessions, is indicated in the demographics spreadsheet. The study scanning protocol included: # 13 sec localizer # 4 minute 38 second T1 weighted anatomical # Subject given instructions for resting state scan #1 # 10 minute 4 second resting state scan #1 # Subject given instructions for resting state scan #2 # 10 minute 4 second resting state scan #2 Scanning was performed on one of three different 3T Siemens TIM TRIOs at the Human Neuroimaging Lab at Baylor College of Medicine in Houston, Texas. All scans were acquired using the standard Siemen''s TIM 12-channel head matrix. The resting state scans were acquired with a custom sequence that is a slight modification to the standard Siemen''s EPI sequence that supports real-time fMRI. Images were acquired slightly oblique to minimize dephasing in the orbito-frontal cortex. Detailed scanning parameters are included in separate .pdf files.
NKI-RS Multiband Imaging Test-Retest Pilot Dataset
Enhanced Nathan Kline Institute-Rockland Sample (NKI-RS) Multiband Imaging Test-Retest Pilot Dataset
Enhanced Nathan Kline Institute-Rockland Sample Multiband Imaging Test-Retest Pilot Dataset
NKI-RS Multiband Test-Retest Pilot Dataset
A test-retest dataset to assess the reliability of multiband resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI) scans prior to launch of the Enhanced Nathan Kline Institute - Rockland Sample (NKI-RS). The dataset is primarily composed of individuals from the initial NKI-RS - for these individuals psychiatric assessment information is available and included (participants were not excluded due to history of illness. In addition to R-fMRI and DTI, they included: 1) simple visual checkerboard stimulation fMRI scans to allow for assessment of traditional fMRI data quality metrics (e.g., contrast-to-noise ratio), 2) breath holding data to enable assessment of regional differences in vascular responsiveness, and 3) eye movement calibration scans to enable the assessment of eye-movement related artifacts which may be particularly troublesome for multiband sequences since several slices are acquired simultaneously.
Enhanced Nathan Kline Institute - Rockland Sample
Dataset of 1000 characterized community-ascertained participants using state-of-the-art multiband imaging-based resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI), genetics, and a deep phenotyping protocol from a large cross-sectional sample of brain development, maturation and aging (ages 6 - 85 yrs). The Center for Magnetic Resonance Research (CMRR), University of Minnesota, provided the NKI-RS effort with the latest version of the Multiband EPI sequence (Xu et al. 2012) and associated image reconstruction algorithms, enabling the acquisition of state-of-the-art imaging datasets for this large-scale imaging effort. The enhanced NKI-RS expands upon the phenotypic protocol of the original NKI-RS and captures a broad range of behavioral and cognitive phenomenology relevant to psychiatric health and illness. The validity and value of assessments were evaluated by consulting leaders in the field of psychiatric phenotyping.
A data repository and analysis framework for spontaneous neural activity recordings in developing retina
A subset of the CARMEN repository, a curated set of data and code of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 29, 2014. The orbit project was a registry of biomedical resources.
An open source commercial platform for genomic analysis. Included is a home brewed workflow engine and code provenance tracking, no data provenance tracking. Multiple tools like HMMR and Blast are included in the platform with an architecture that allows others to be plugged in and the code to be modified. Data storage is handled by hadoop clusters.
Dementia-specific FDG PET Template for SPM analyses
Dementia-specific [18F]-FDG-PET Template for SPM analyses
This is a place holder for this tool. The documentation is not yet available (documented 5/30/2014).
Signaling Pathway Integrated Knowledge Engine
Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 1st, 2022. Commercial antibody vendor.
Position Orientation Adaptive Smoothing for SPM
Software toolbox for SPM to denoise diffusion MRI data. Used for diffusion weighted magnetic resonance imaging data enhancement based on structural adaptive smoothing in both voxel space and diffusion-gradient space.Part of the ACID-toolbox.
ACID - Artefact correction in diffusion MRI
Academic software toolkit for pre-processing of diffusion MRI data, estimation of DTI indices and spatially normalisation of DTI index maps, which fully integrates into the batch system of SPM8. These tools are made for users familiar with the underlying statistical, mathematical and image processing concepts. The ACID toolbox provides the option to write the estimated diffusion tensor in the format of the DTI and Fibertools Software Package.
Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data.
Resource for Genetic Epidemiology Research on Adult Health and Aging
Human genetics data from an immense (78,000) and ethnically diverse population available for secondary analysis to qualified researchers through the database of Genotypes and Phenotypes (dbGaP). It offers the opportunity to identify potential genetic risks and influences on a broad range of health conditions, particularly those related to aging. The GERA cohort is part of the Research Program on Genes, Environment, and Health (RPGEH), which includes more than 430,000 adult members of the Kaiser Permanente Northern California system. Data from this larger cohort include electronic medical records, behavioral and demographic information from surveys, and saliva samples from 200,000 participants obtained with informed consent for genomic and other analyses. The RPGEH database was made possible largely through early support from the Robert Wood Johnson Foundation to accelerate such health research. The genetic information in the GERA cohort translates into more than 55 billion bits of genetic data. Using newly developed techniques, the researchers conducted genome-wide scans to rapidly identify single nucleotide polymorphisms (SNPs) in the genomes of the people in the GERA cohort. These data will form the basis of genome-wide association studies (GWAS) that can look at hundreds of thousands to millions of SNPs at the same time. The RPGEH then combined the genetic data with information derived from Kaiser Permanente''s comprehensive longitudinal electronic medical records, as well as extensive survey data on participants'' health habits and backgrounds, providing researchers with an unparalleled research resource. As information is added to the Kaiser-UCSF database, the dbGaP database will also be updated.
ACADIS Gateway - An Arctic Data Repository
Advanced Cooperative Arctic Data and Information Service (ACADIS) Gateway
Advanced Cooperative Arctic Data and Information Service Gateway
A repository and data management services for Arctic research data. Data include long-term observational timeseries, local, regional, and system-scale research from many diverse domains.
ACEpepDB: Peptide Database of Central Food Technological Research Institute
Database of ~ 865 peptides where each record provides information on the food source, preparation, purification, reference(s) and any other additional information. The database provides a search and browsing option for a more personalized research experience.
Australian Institute of Marine Science Data Centre
Data catalogue, gathered by the Australian Institute of Marine Science (AIMS), a tropical marine research center, on marine science topics including reef weather, sea temperature, cyclones, and water quality.
ALADDIN (A Labelled Atomic Data INterface)
Numerical database of atomic and molecular processes and particle-surface interactions. It has formatted data on atomic structure and spectra (energy levels,wave lengths, and transition probabilities); electron and heavy particle collisions with atoms, ions, and molecules (cross sections and/or rate coefficients, including, in most cases, analytic fit to the data); sputtering of surfaces by impact of main plasma constituents and self sputtering; particle reflection from surfaces; thermophysical and thermomechanical properties of beryllium and pyrolytic graphites.
An American pharmaceuticals and health care products company that since splitting into Abbott and AbbVie, focuses on diversified medical products. (AbbVie focuses on research-based pharmaceuticals) It has 90,000 employees and operates in over 130 countries. The company headquarters are in Abbott Park, North Chicago, Illinois. (adapted from Wikipedia)
Advanced Spaceborne Thermal Emission and Reflection Radiometer
Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER)
ASTER - Advanced Spaceborne Thermal Emission and Reflection Radiometer
An imaging instrument onboard Terra, the flagship satellite of NASA''s Earth Observing System (EOS) that collects and archives data to create detailed maps of land surface temperature, reflectance, and elevation. The ASTER project is a collaboration between NASA and the Japanese government to develop a scientific understanding of the Earth.
Database of the U.S. National Archives and Records Administration that allows users to search by keyword or category. Specific topics in personal history, private sectors, places, wars or time periods can be chosen to help filter your research findings of the 85 million electronic records that have been made available.
AidData - Open Data for International Development
Portal of information about international economic development assistance, dating back to 1947, that includes a database of nearly one million past and present aid activities around the world, aid information management services and tools, data visualization technologies, and research designed to increase understanding of development finance. AidData is searchable by topic such as disaster prevention, energy supply, water supply or reconstruction relief. You may also search by specific regions including Africa, Europe, America, Asia, or Oceania.
Portal for ocean and coastal observations data. They address regional and national needs for ocean information, gather specific data on key coastal and ocean variables, and ensure timely and sustained dissemination and availability of these data. . AOOS programmatic focus areas are: * Safe marine operations * Coastal hazard mitigation * Tracking ecosystem and climate trends * Monitoring water quality
Center for Biomedical Research Excellence
Center for Biomedical Research Excellence (COBRE)
Data set of raw anatomical and functional MR data from 72 patients with Schizophrenia and 75 healthy controls (ages ranging from 18 to 65 in each group). All subjects were screened and excluded if they had: history of neurological disorder, history of mental retardation, history of severe head trauma with more than 5 minutes loss of consciousness, history of substance abuse or dependence within the last 12 months. Diagnostic information was collected using the Structured Clinical Interview used for DSM Disorders (SCID). A multi-echo MPRAGE (MEMPR) sequence was used with the following parameters: TR/TE/TI = 2530/(1.64, 3.5, 5.36, 7.22, 9.08)/900 ms, flip angle = 7��, FOV = 256x256 mm, Slab thickness = 176 mm, Matrix = 256x256x176, Voxel size =1x1x1 mm, Number of echos = 5, Pixel bandwidth =650 Hz, Total scan time = 6 min. With 5 echoes, the TR, TI and time to encode partitions for the MEMPR are similar to that of a conventional MPRAGE, resulting in similar GM/WM/CSF contrast. Rest data was collected with single-shot full k-space echo-planar imaging (EPI) with ramp sampling correction using the intercomissural line (AC-PC) as a reference (TR: 2 s, TE: 29 ms, matrix size: 64x64, 32 slices, voxel size: 3x3x4 mm3). Slice Acquisition Order: Rest scan - collected in the Axial plane - series ascending - multi slice mode - interleaved MPRAGE - collected in the Sag plane - series interleaved - multi slice mode - single shot The following data are released for every participant: * Resting fMRI * Anatomical MRI * Phenotypic data for every participant including: gender, age, handedness and diagnostic information.
Precursors of Premature Disease and Death
Data set of annual questionnaires of a long-term prospective study of 1,337 former Johns Hopkins University medical students to identify precursors of premature cardiovascular disease and hypertension. The purpose of the study has broadened, however, as the cohort has aged. The study has been funded for 15 years. Participants were an average of 22 years of age at entry and have been followed to an average age of 69 years. Data are collected through annual questionnaires, supplemented with phone calls and substudies. Self-reports of diseases and risk factors have been validated. Every year from 1988 to 2003, anywhere from 2 to 6 questionnaires have been administered, in categories such as the following, which repeat periodically: Morbidity, Supplemental Illness, Health Behavior, Family and Career, Retirement, Job Satisfaction, Blood Pressure and Weight, Medications, Work Environment, Social Network, Diabetes, Osteoarthritis, Health Locus of Control, Preventive Health Services, General Health, Functional Limitations, Memory Functioning, Smoking, Religious Beliefs and Practices, Links with Administrative Data, National Death Index searches for all nonrespondents * Dates of Study: 1946-2003 * Study Features: Longitudinal * Sample Size: 1,337 (1946)
A research-based biopharmaceutical company that develops advanced therapies to address global health problems.
Assembly package that contains a suite of software programs for correcting errors in short reads and assembling them. The assembler may take as input classical Sanger reads, 454 sequences, and Illumina reads.
A biorepository of human biological material from healthy and diseased populations with a special focus on subjects with Alzheimer's disease, multiple sclerosis, Parkinson's disease and other neurological disorders. Data is collected longitudinally. PrecisionMed aims to facilitate research in genetics, drug discovery, biomarker research and molecular diagnostics. Materials collected include DNA, RNA, plasma and cerebrospinal fluid, among others.
Public Use Microdata Sample for the Older Population
Public Use Microdata Sample: 3-Percent Elderly Sample
Public Use Microdata Sample: Elderly Households Extract
A public-use microdata sample focusing on the older population created from the 1990 census. This sample consists of 3 percent of households with at least one member aged 60 or older. Although, the highest age presented is age 90, this allows analysis of data on the very old for most states with a reasonable degree of reliability. Since data for all members in households containing a person 60 years and over will be on the file, users will be able to analyze patterns such as living arrangements and sources of household income from which older members may benefit. Additionally, users will be able to augment the PUMS-O sample with a PUMS file. The Census Bureau has issued two regular PUMS files for the entire population. One PUMS file will contain 1 percent of all households; the other PUMS file will contain 5 percent of all households. Both files have most sample data items, and differ only in geographical composition. The 1-percent file contains geographic areas that reflect metropolitan vs. non-metropolitan areas. The 5-percent file shows counties or groups of counties as well as large sub-county areas such as places of 100,000 or more. The geography on the 5-percent PUMS file matches that of the PUMS-O file. Since data for different households are present on the two files, users can merge the PUMS-O file with the 5-percent PUMS to construct an 8-percent sample. However, weighted averages must be constructed for any estimates created because each sample yields state-level estimates. Thus, it is possible to analyze substate areas even for the very old. In states where the geographic areas identified on the PUMS-O and the 5-percent PUMS are coterminous with State Planning and Service Areas (used by service providers in relation to the Older Americans Act), the Planning and Service Areas are identified. * Dates of Study: 1990-2000 Links: 1980: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/08101 2000: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04204
A commercial antibody vendor, specializing in secondary antibodies.
Database to advance the availability and use of public health data for science and policy making that includes data from all weekly notifiable disease reports for the United States dating back to 1888. Additional U.S. and international data will be released twice yearly.
A commercial protocol sharing tool, which allows scientists to check in protocols the way that computer scientists check in code.
Unbiased BIOmarkers in PREDiction of respiratory disease outcomes
A research project using information and samples from adults and children to learn more about different types of asthma to ensure better diagnosis and treatment for each person.
RA MAP is a public-private collaborative project into early Rheumatoid Arthritis (RA). Our goal is to: identify the key predictors of clinical response and remission in RA patients, and identify those individuals at high risk of developing RA. By understanding the human immune system in RA through the study of biological samples from RA patients we plan to develop an ''immunological toolkit'' measuring the immune status of healthy individuals and patients.
An ambitious project to develop an IT infrastructure for translational research that aims to facilitate the collection, storage, analysis, archiving, sharing and securing of data.
Portal for dataset discovery across a heterogeneous, distributed group of transcriptomics, genomics, proteomics and metabolomics data resources. These resources span eight repositories in three continents and six organisations, including both open and controlled access data resources.
A project that aims to improve access to human health data by developing a common information framework (EMIF-Platform) that allows for efficient re-use of existing health data, opening up new avenues of research for scientists. To ensure immediate applicability, the project includes two specific therapeutic research topics: the onset of Alzheimer's Disease (EMIF-AD) and metabolic complications of obesity (EMIF-Metabolics). The AD Topic aims to discover and validate biomarkers of AD onset in the preclinical and prodromal phase as well as for disease progression and identify high-risk individuals for therapeutic trials for prevention. The Metabolic Topic aims to discover and evaluate biomarkers for the risk of metabolic complications in obesity and to identify high-risk populations for intervention purposes. Collaboration between the 3 topics will ensure the development and delivery of an efficient Information Framework. This initiative has combined several data sets for neuroimaging including ADNI and several others, curating them into transmart.
A context-based approach to identify the most likely mapping for RNA-seq experiments.
A biopharmaceutical company that focuses on central nervous system (CNS) diseases. The company is the result of a merger between Alkermes, Inc. and Elan Drug Technologies (EDT), the former drug formulation and manufacturing division of Elan Corporation, plc. The company is headquartered in Dublin, and has an R&D center in Waltham, Massachusetts and manufacturing facilities in Athlone, Ireland; Gainesville, Georgia; and Wilmington, Ohio. Alkermes has more than 20 commercial drug products and candidates that address serious and chronic diseases such as addiction, schizophrenia, diabetes and depression. Among these, five products are primary to the company: risperidone Long-Acting Injection (Risperdal Consta) for schizophrenia and bipolar 1 disorder, paliperidone palmitate (Invega Sustenna in the U.S., Xeplion in Europe) for schizophrenia, 4-aminopyridine (Ampyra in the U.S., Fampyra in Europe) to improve walking in patients with multiple sclerosis, naltrexone for extended-release injectable suspension (Vivitrol) for alcohol and opioid dependence, and exenatide extended-release for injectable suspension (Bydureon) for the treatment of type 2 diabetes. Bydureon is a once-weekly, long-acting form of the drug exenatide (Byetta) and was developed through a partnership between Amylin, Alkermes and Eli Lilly. It is approved in Europe and the U.S. (Wikipedia)
Crop science company with products in crop protection and nonagricultural pest control. It also has activities in seeds and plant traits. (Adapted from Wikipedia)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017. A virtual database of annotations between databases.
Metabolite and Tandem MS Database (METLIN)
A public repository of metabolite information as well as tandem mass spectrometry data is provided to facilitate metabolomics experiments. It contains structures and represents a data management system designed to assist in a broad array of metabolite research and metabolite identification. An annotated list of known metabolites and their mass, chemical formula, and structure are available. Each metabolite is linked to outside resources for further reference and inquiry. MS/MS data is also available on many of the metabolites.
DPABI: a toolbox for Data Processing & Analysis of Brain Imaging
toolbox for Data Processing and Analysis of Brain Imaging
Software toolbox for data processing and analysis of brain imaging, evolved from DPARSF (Data Processing Assistant for Resting-State fMRI).
The project will focus on patients with a rare disease and their families and patients with cancer. The first samples for sequencing are being taken from patients living in England with discussions taking place with Scotland, Wales and Northern Ireland about potential future involvement. Genomics England, a company wholly owned and funded by the Department of Health, was set up to deliver this flagship project which will sequence 100,000 whole genomes from NHS patients by 2017. Its four main aims are; to create an ethical and transparent programme based on consent; to bring benefit to patients and set up a genomic medicine service for the NHS; to enable new scientific discovery and medical insights; and to kick start the development of a UK genomics industry.
A virtual database cataloging numerous data set resources, including: BrainMaps.org, Cell Centered Database, Clinical Trials Network (CTN) Data Share, ClinicalTrials.gov, CRCNS, Gene Expression Omnibus, ArrayExpress, MPD - Mouse Phenome Database, BioSharing, Gene Weaver, XNAT Central, 1000 Functional Connectomes Project, Health.Data.gov, SciCrunch Registry, NIF Registry Automated Crawl Data, NeuroVault, OpenfMRI, Physiobank, RanchoBiosciences, YPED, Data.gov Science, and Research Data Catalog.
BrainSlices is a repository of annotated high-resolution images of brain tissue.
A Python library for analysis of mouse behavior. The library can be used for loading and analyzing of data obtained from IntelliCage system in an intuitive way in Python programming language. The library provides users with an object oriented application programming interface (API) and a data abstraction layer. It also comes with auxiliary tools supporting development of analysis workflows. Any published research making use of PyMICE must provide the PyMICE resource identifier (RRID:nlx_158570).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017. Funding opportunities provided by projects or organizations other than government funding opportunities such as those from NIH or NSF.
A consortium of university groups to characterize human immune populations. The Human Immunology Project Consortium (HIPC) program, established in 2010 by the NIAID Division of Allergy, Immunology, and Transplantation, is a major collaborative effort that is generating large amounts of cross-center and cross-assay data including high-dimensional data to characterize the status of the immune system in diverse populations under both normal conditions and in response to stimuli. This large data problem has given birth to ImmuneSpace, a powerful data management and analysis engine where datasets can be easily explored and analyzed using state-of-the-art computational tools.
EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature.
bNAber is the Broadly Neutralizing Antibody E-Resource Database, analysis, visualization, and data discovery tool for broadly neutralizing HIV-1 antibodies (bNAbs). bNAber seeks to be a vital tool in the search for an AIDS vaccine.
Science in the Open: This blog contains the thoughts of Cameron Neylon on the technical and social issues involved with ''Open Research''. Most people would agree Open Research includes freely accessible literature or perhaps making raw data available. Others might think it also involves people working on collaborative documents such as Wikis or the freedom to re-use the published literature or data. At its logical extreme Open Research includes making all the details of what we do freely available as it happens. Many people find this scarey. Some, perhaps a growing number, find it tremendously exciting.
The web portal provides comprehensive local database of human genome variants with a user-friendly web page that provides a one-stop annotating and funtonal prediction service which is both convenient and up-to-date. A query can be accepted as either a dbSNP Id or a chromosomal location and our system will instantly provide all the annotation information in an interactive LD panel. The system can also simultaneously prioritize this variant based on additive effect mode by corresponding annotation information and evaluate the variant effect that is then displayed in a prioritization tree. Furthermore, cohort sequencing continuously produces lots of un-annotated variants such as rare variants or de novo variants, and our system can even fit this data by accepting genomic coordinates (hg19) to offer maximal annotations. Main Functions Over 40 up-to-date annotation items for human single nucleotide variations; Functional prediction for different types of variants; Dynamic LD panel for both HapMap and 1000 Genomes Project populations; Prioritization score and tree viewer based on variant functional model.
UniPathway: a metabolic door to UniProtKB/Swiss-Prot
UniPathway: a resource for the exploration of metabolic pathways
A manually curated database of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. Users may do a quick search, browse pathway, browse compound, or browse organism.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. An umbilical cord blood bank located in Seoul, South Korea.
A contract research service to the pharmaceutical industry, focusing on the use of fresh human tissues to predict drug activity prior to clinical trials. Biopta''s expertise in all areas of human tissue research including sourcing, handling and experimenting on human tissue allows us to act as your Human Tissue Research Department. Biopta has developed an extensive network of tissue collaborators and is accredited as a Research Tissue Bank. It manages procurement, ethics and logistics for human tissue research projects.
The FlyWeb Project is linking research image data from FlyTED with related data from the Berkeley Drosophila Genome Project, FlyBase, FlyAtlas and other sources. This project builds on the findings of the data web requirements analysis project Defining Image Access.
A Wiki devoted to topics in clinical informatics. Contents: 1 Health Information Technology Regional Extension Centers 2 Free and Open Source Software (FOSS) licensing in medicine 3 Electronic Healthcare Communication 4 Electronic Medical Record (EMR) Systems 5 Computer-based Provider Order Entry -- CPOE 6 Clinical Decision Support -- CDS 7 Books on Topics in Clinical Informatics 8 Medical Devices, Computerized -- SmartDevices 9 Personal Health Records -- PHRs 10 Personal Health Applications -- PHAs 11 Informatics Students'' Contributions 12 Blueprint for a Comprehensive HIT System 13 Biobanking -- a.k.a. Biorepositories or Tissue Banks 14 Organizational issues 15 Regional Health Information Organizations -- RHIOs 16 Evidence-Based Medicine -- EBM 17 Evaluation Methods in Informatics 18 Unintended Consequences of Health Information Technology 19 Quality & Quality Informatics 20 Public Health Informatics 21 U.S. Federal Health Information Technology Initiatives 22 The E-Patient-Provider Relationship 23 Interface Terminology 24 New CIS-related Technologies 25 Workflow 26 Terminology and Coding 27 Interface/Usability Testing 28 International views 29 Blogposium, April 2006 30 Departments / Schools of Biomedical or Medical Informatics 31 Endowed Professorships and Chairs in Health / Medical / Nursing / Biomedical Informatics 32 Leading Health Informatics and Medical Informatics Journals o 32.1 Ranking of ISI/SCI listed e-Health and Medical Informatics Journals o 32.2 Not listed / ranked in ISI/SCI 33 External Links 34 External Medical Reference Links 35 External Informatics Organizations Links
Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.
Biorepository of tissues and fluids relevant for the neurologic, neuropsychologic, psychiatric and neuropathologic manifestations of HIV infection, linked to medical records and an on-going clinical trial for research use by the scientific community. The MHBB conducts a longitudinal, observational study that follows a group of HIV-infected individuals who have agreed to be fluid and organ donors for the purposes of AIDS research. They are currently the largest, multidisciplinary neuroAIDS cohort in New York City, the epicenter of the US HIV epidemic. Research participants undergo regular neurologic, neuropsychologic, and psychiatric evaluations, and provide body fluid samples that are linked to clinical information. Upon their demise, study participants become organ donors. This program has supplied clinical information, tissue, and fluid samples to over 70 qualified AIDS researchers across America, Europe and Australia. In fulfilling its resource mission, the MHBB functions as part of the National NeuroAIDS Tissue Consortium (NNTC). MHBB provides a means by which people living with HIV can be engaged in the struggle to improve our knowledge about HIV infection and the damage it causes to the body.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Its Not Rocket Stats G. Tendayi Viki Academic, Multicultural Innovation Researcher and consultant. I write, blog and tweet about how to make social science research more fun and enjoyable!
The PRABI is the Rhone-Alpes Bioinformatics Center, a IBISA platform member of the RENABI (the French network of bioinformatic platforms). It gathers 11 research teams spread on 4 different sites. The PRABI has research, service and training activities in a large number of bioinformatics and biostatistics fields.
Biotechnology company dedicated to enhancing quality of patient care through development and manufacture of safe, high quality allograft solutions for healthcare professionals.
Swedish study to get a better understanding of how genes, environment and way of life affect health that will enable access to the longitudinal data on 500,000 participants after ethical approval. Half a million people in Sweden between the ages of 0 and 45 will be recruited as volunteers for 6 to 8 years. People between 18 and 45 will be invited and they may, in turn, bring children and other people that they live with into the project. Participants will be followed for many years with regular online surveys and health checks. Their blood and urine samples will also be stored in a biobank. All the data will form a very large information base, where researchers can follow what happens with people' '''s health. The LifeGene test center will measure height, hip, waist and chest measurements. A so-called spirometry test will be conducted which measures lung function, a hearing test and bioimpedance measurement (includes weight, BMI and distribution of body fat and muscle mass). They also take blood and urine samples and measure blood pressure and pulse. LifeGene foresees a lot of different research cooperation. Everything from simple withdrawal of longitudinal data, leverage of LifeGene infrastructure and cooperation between LifeGene and complementing scientific projects covering specific areas in more depth. LifeGene will enable access to unique longitudinal data on 500,000 participants available for researchers after ethical approval. LifeGene is also an infrastructure with Test Centers covering most of Sweden, logistics for sample management from arm-to-freezer and state-of-the-art large scale automatic biobanking enabling low cost, high quality, fast withdrawal of biological samples.
For computational modeling to become more widely used in biological research, researchers must be able to exchange and share their results. The development and broad acceptance of common model representation formats such as SBML is a crucial step in that direction, allowing researchers to exchange and build upon each other''s work with greater ease and accuracy. The BioModels.net project is another step: an international effort to: 1. define agreed-upon standards for model curation 2. define agreed-upon vocabularies for annotating models with connections to biological data resources 3. provide a free, centralized, publicly-accessible database of annotated, computational models in SBML and other structured formats To facilitate assembling useful collections of quantitative models of biological phenomena, it is crucial to establish standards for the vocabularies used in model annotations as well as criteria for minimum quality levels of those models. The BioModels.net project aims to bring together a community of interested researchers to address these issues. We are working towards defining these standards through white papers and process definitions. All of the products of our efforts are open and freely available through this site.
At Puget Sound Blood Center, when we talk about the work of our Research Institute, what we are really talking about is saving lives. Many recognize the lifesaving work of the Blood Center for its role in maintaining the blood supply for Western Washington. But that is only the beginning of how the Blood Center touches the lives of people all over the world. The Blood Center is widely considered the premier knowledge source on blood research and transfusion medicine and has been developing cutting-edge technologies and establishing best practices in this field for over sixty-six years. Medical institutions worldwide rely on the Blood Center''s research work. Scientific equipment manufacturers, as well as pharmaceutical companies turn to the Blood Center for help in developing effective equipment and successful therapies that are saving lives around the world every day.
Biological material management services provider including biospecimen storage, biobanking services, specimen collection kits, sample processing, DNA /RNA extraction and amplification, sample storage, distribution, and clinical trial support. They also offer transport and storage of active pharmaceutical ingredient(s) (API and bio-API), including cryogenic. They can assist with public health research, phase I???????????????IV studies, prospective and retrospective studies, IND/NDA submissions to the FDA, and entry of biotherapeutics into the commercial marketplace.
THIS RESOURCE IS NO LONGER IN SERVICE This is the website for a weekly social event called Dangerous Ideas, to promote more cross talk and cross pollination of ideas. There is a list of links to interesting new tools and technologies in the realm of computation and science. We'll be experimenting with webcasting this so others who can't physically join us can share in seeing what we think is cool. Its a completely open event-- anyone is welcome to join in, but should be prepared to present!
MTBBASE - Collection and Refinement of Physiological Data on Mycobacterium tuberculosis
MTBBASE is a database about the physiology of the tuberculosis bacterium, in widely-used formats, and publicly accessible. Available already is MTB-GOA, paper-centric Gene Ontology (GO) annotations. Pathway data on reactome is in progress. This is a private effort because I am not affiliated with a university nor a company. Nevertheless, I am putting a constant part of the day into the work. The annotations were checked by the UniProt-GOA group at the EBI (after passing my own checks) and pathways are checked by a reactome editor. This work would not have been possible without NCBI''s Entrez service, the german national licence, UniProt, and tuberculist at epfl.ch.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The NIEHS Genetic Alterations in Cancer (GAC) knowledgebase is a comprehensive collection of data compiled from studies reported in the published literature on genetic alterations in tumors associated with exposure to specific chemical, physical, or biological agents that can be linked to genes implicated in the development of cancers. GAC provides access to data from peer reviewed journals for hundreds of studies of gene mutations, loss of heterozygosity, and/or chromosome changes in tumors from humans, mice, or rats. Results are summarized in tables and graphic profiles that show the incidence (percent) of tumors with alterations in each gene that has been studied. Detailed data tables display results for each subject studied in the cited reference and the reference ID is hyperlinked to its PubMed abstract for more information. A mutation spectrum for individual genes and links to gene information from The Cancer Genome Anatomy Project and the Rat Genome Database are also provided.
Brains Lab: Synapses Somata and Systems Neuroscience
I''m studying how the brain works on various levels; this blog chronicles some of my informal notes along the way. I previously went to Vassar College, majoring in Neuroscience and Behavior with a minor in Math. Now I work at a biology lab in Maryland. I appreciate any feedback that you may have, good or bad. You can email me at amckenz at g mail dot com. What I write on here is obviously my opinion. Everything on the site is filed under a Creative Commons License v. 3.0. That means that you can copy and re-publish this stuff anywhere without my permission. Thanks for reading. Essay titles include: * A Loss of Agency Following Use of ADHD Medications in College Aged Adults * An Evolutionary Account of the Environmentally Programmed Stress Response * Changes in protein structure of myelin sheaths throughout vertebrate evolution * Effect of Glucocorticoids on the Attenuation in Neurogenesis due to Sleep Deprivation * Insulin sensitivity and age-related memory changes due to caloric restriction * Is Neurogenesis in the Hippocampus Linked to Depression? * Novelty-Seeking and Associative Learning of Chemotaxis in C. Elegans * The Effects of D2 Receptors on the Inverted U-Shape Response Curve to Psychostimulants * Three Applications of Optogenetics The author has included some tricks and illusions from around the web that reveal fascinating facets of our thought processes including: The Checker, Sensory Homonculus Picture, A Blindspot Demonstration, A Ball in a Box, Iterated Choices, The Max Plank Institute for Biological Cybernetics, The Motion Aftereffect Illusion, The Phi Phenomenon, The Common Fate Phenomenon, A Double Face, The Troxler Effect
Files of the full release and daily updates of the GenBank database are available for anonymous FTP. The full release in flat-file format is available as compressed files in the directory genbank. It is created every two months. Individual files for each day''s new or updated sequence entries processed since close of data for the latest release are located in the sub-directory daily-nc. ASN.1 formatted data is in the directory ncbi-asn1. Lists of all nucleotide and protein accession numbers, generated each Sunday evening, are available in the Live lists directory.
FTP site to access Schizosaccharomyces pombe protein data.
National Psoriasis Victor Henschel BioBank
The National Psoriasis Victor Henschel BioBank is a collection of biological samples and clinical information used by qualified scientists to further the field of psoriasis genetics. Once completed, the National Psoriasis BioBank will be the largest collection of psoriasis DNA samples in the world, moving us closer to understanding the causes of psoriatic diseases, discovering more and better treatments and finding a cure. The BioBank is currently collecting DNA from people with and without psoriasis and/or psoriatic arthritis. Simply by donating your DNA����??a blood sample and a swab of your cheek cells����??and providing us with your medical history, you can help us find a cure. Samples will be processed and stored at a private laboratory and not at the National Psoriasis Foundation. The National Psoriasis BioBank is part of the Genetic Alliance BioBank (GA BioBank), a centralized repository for the collection, storage and distribution of biological samples (including DNA, serum, cells and tissues) and clinical data for genetic researchers.
Stunning scientific discoveries have opened the possibilities for us to preserve our unaltered youth and healthy genome almost indefinitely. To do this, we propose to our clients to allow us to isolate and cryopreserve a small piece of tissue from their body in our unique tissue bank via a simple skin biopsy procedure. Our methods provide 100% assurance that the tissues we preserve will remain viable, healthy and young. We guarantee that these tissues will correspond to the age and physical status from the time when they were collected and can be preserved for many decades to come. In that way we strive to accomplish mankind''s most important dream ������?? to stop the hands of time and reduce the effects of aging. We will bring to a standstill the genetic program that is encoded in our cells that cause us to age and grow older. What is unique about this procedure, from a biological perspective, is that even as a person continues to live longer and get older, at the same time, part of his body remains invariably young. This well-preserved critical piece of tissue contains all the vitally important genetic material that harnesses the potential for invigorating one''s health. It will play an essential role in the rehabilitation and rejuvenation of human beings in the future. Recent studies have shown that certain parts of our skin are the most optimal material to be used for our program. For this purpose we utilize fibroblasts, the cells of the connective tissues located at the bottom side of our epidermis. In order to properly extract fibroblasts from our skin we have to perform a basic skin biopsy procedure. If you decide to participate in our program, StemCure will send to you the standard Tissue Collection Kit. This Kit contains detailed instructions for how your doctor should perform the biopsy procedure, as well as all the necessary components for the collection and transportation of a biopsy sample. StemCure will immediately start processing your biopsy samples once they arrive by overnight shipment to one of our laboratory facilities. We perform this very elaborate procedure because we understand perfectly well that our ultimate goal is not just the preservation of your tissue samples, but rather their subsequent utilization for the production of embryonic stem cells, which is the next stage of our program. Before subjecting the samples of your tissue to freezing, we will use the skin tissue to initiate the growth of the cell culture. After initial testing of the cell culture for viability and physiological activity, we will start its preparation for cyropreservation. StemCure will do everything in its power to ensure that the ������??Youth Genome������?? of our clients is safely protected and will remain a viable source for their healthy disease-free future.
A company which specializes in producing calcium-based products, particularly hydroxyapatite and tricalcium phosphate. Their activities are focussed on synthetic bone graft substitutes, sustained-release drug delivery devices, and applications of HAP for protein purification.
New York University Specialty Tissue Banks
Creighton University School of Pharmacy and Health Professions
If Occupational Therapy, Pharmacy, or Physical Therapy is not just a career choice for you - if it''s a calling - then you may belong at Creighton University. For our students, it''s about more than career training. It''s about serving patients. Restoring health. Changing lives. Health care is a serious career, perhaps a lifelong calling. Creighton seeks the cream of the crop for these programs - men and women who feel a genuine calling to serve patients, restore health, and save lives. There''s more for you in Omaha than a vibrant university community. It''s true that U.S. News & World Report lists us as among the best colleges in the Midwest. And that we''ve been educating health professionals for more than a century. We''re also home to one of the world''s leading medical communities. That means training in leading edge facilities and in one of the nation''s best teaching hospitals. Perhaps our greatest distinction, however, is our university-wide commitment to creating an ever better and more just world. You''ll find our PT doctoral students staffing a free clinic for the underserved our pharmacy students conducting drug and alcohol education seminars ... and our OT students volunteering for the Special Olympics. It''s all tied to the values we strive toward as a Jesuit institution.
As the integral bridge between researcher and patient, ProMedDx helps the world''s leading in-vitro diagnostic and research organizations fulfill the promise of disease eradication and healthier living. From a constantly evolving, high-grade Specimen Bank to a complete range of customized Clinical Services to a secure, state-of-the-art BioStorage, ProMedDx delivers the industry''s most trusted and comprehensive human biological solutions from collection to handling, storage, and transportation. Human biologics such as blood, plasma, urine, and tissue specimens possess crucial clues that can unlock the mystery of disease and lead to life altering treatments. As one of the most respected suppliers of human clinical specimens and patient samples, we are entrusted with a vital role in the advancement of medical research. ProMedDx is proud to further the scientific quest for discovery. That''s why we maintain an inventory of more than 1.8 million high quality healthy, and diseased human clinical specimens collected under IRB, ICH, and GCP guidelines and in adherence with HIPAA privacy regulations. Although our extensive Specimen Bank offers a wide ranging inventory, ProMedDx experts are also poised to help clients with clinical trial services or custom sample collections. ProMedDx has created one of the industry''s most secure, cost-efficient, and state-of-the-art specimen and tissue banks for for the storage of biological specimens. Strategically located between Boston, Massachusetts and Providence, Rhode Island, our on-site facility offers uncompromised Safety & Security. Best-in-class Technology runs our BioStorage facility and our centralized Logistics procedures have set new industry standards in packaging and shipping.
Throughout its history, the Royal Botanic Gardens, Kew has made important contributions to increasing the understanding of the plant kingdom with many benefits for mankind. Today it is still first and foremost a scientific institution. With its collections of living and preserved plants, of plant products and botanical information, it forms an encyclopaedia of knowledge about the plant kingdom.
Alfresco - FRont-End for Sequence COmparison
The aim is to develop a new visualization tool that allows effective comparative genome sequence analysis. The program will compare multiple sequences from putitatively homologous regions in different species. Results from various different existing analysis programs, such as gene prediction, protein homology and regulatory sequence prediction programs shall be visualized and used to find corresponding sequence domains. The program functions as an stand-alone application and also over the World Wide Web. With this in mind it is being developed using the Java programming language. A key feature of the program is to use available analysis programs relevant to comparative genome sequence analysis, combine the results of these, and graphically present them in an intuitive way, thereby facilitating the analysis of large genomic regions. We''ve decided to call this program Alfresco. We originally wanted to call it Fresco (FRont-End for Sequence COmparison) but that name was already taken. To run Alfresco you need to have jdk1.1 installed. Alfresco has only been tested on Solaris 2.5, Dec OSF 4.0D and Linux, but should run on any machine with jdk1.1. New: Alfresco now runs on Mac and Windows as well.
Autism Genetic Database: A comprehensive database for autism susceptibility gene-CNVs integrated with known noncoding RNAs and fragile sites
The Autism Genetic Database currently contains the full list of autism susceptibility genes as well as all Copy Number Variations (CNVs) found to have a relationship to autism. Additionally, all noncoding RNA molecules (snoRNA, miRNA, and piRNA) and chemically induced fragile sites are stored as well. This information is currently accessible via an in-house human genome browser focusing specifically on the chromosomal features associated with autism, and in a tabular format broken down by chromosome. Genome Browser:A genome browser that displays the genes, CNVs, ncRNAs and fragile sites in an easily accessible graphical visualization tool Tabular Data Display:A tabular data display that allows the user to observe the chromosomal spatial relationship between the genes, CNVs, ncRNAs and fragile sites. This also provides links to Entrez and pubmed for each gene, as well as miRBase for miRNAs, snoRNA-LBME-db for snoRNAs, and piRNABank for piRNAs.
St. Vincents University Hospital / University College Dublin Sleep Apnea Database
St. Vincent''s University Hospital / University College Dublin Sleep Apnea Database
St. Vincents University Hospital / University College Dublin Sleep Apnea Database: This database contains 25 full overnight polysomnograms with simultaneous three-channel Holter ECG, from adult subjects with suspected sleep-disordered breathing.
MIRIAM: Minimal Information Required In the Annotation of Models
MIRIAM is an effort to standardise the Minimal Information Required In the Annotation of Models, so that different groups can collaborate on annotating and curating computational models in biology. The goal of the project, initiated by the BioModels.net effort is to produce a set of guidelines suitable for use with any structured format for computational models. MIRIAM is a registered project of the MIBBI (Minimum Information for Biological and Biomedical Investigations). If you are looking for the online resources providing support to MIRIAM Standard, please go to: MIRIAM Resources.
Biological Resource Centre - National Institute for Cancer Research
Centro di Risorse Biologiche - istituto nazionale per la ricerca sul cancro
The Centro di Risorse Biologiche (CRB-IST), institutional facility of IST, has been recently established by the General Director (Deliberation number 624 July 11, 2008). It aims at co-ordinating already existing biobanking activities, and participating in the European Infrastructure of Biobanks and Biomolecular Resources (BBMRI), in preparation in the frame of the 7th FP of the European Community. Aims: * to facilitate high quality translational research dependent on biological material and data * to address ethical issues on biobanking * to promote the project at the population level * to co-ordinate the IST biobanks and cell banks * to harmonize technical and management SOPs, according to international best practices * to help reduce costs for collection and storage of biological material * to favor institutional recognition at a regional, national and international level - to sustain the role of the Institute in the European infrastructure.
National MagLab headquartered in Florida State University in Tallahassee. The lab also includes sites at Los Alamos National Laboratory in New Mexico and University of Florida in Gainesville. It serves as user facility. Major center for condensed matter physics and materials science, often collaborating with university researchers for scientific discovery.
A weekly podcast which features highlighted content from the week''s edition of Nature including interviews with the people behind the science, and in-depth commentary and analysis from journalists covering science around the world.
UC San Diego School of Medicine / WebMD - Medscape Videoblogs
Medscape Today: University of California San Diego School of Medicine
UC San Diego School of Medicine and Medscape, in association with WebMD, are proud partners in the production of timely video blogs that highlight cutting-edge, clinical information of relevance to physicians and other health care providers worldwide. The video blogs feature UC San Diego expert contributors covering topics in their areas of excellence. Log in required. Our FREE membership provides UNLIMITED ACCESS to all of our resources including: * In-depth medical news - updated daily * Coverage of most medical conferences around the globe * Continuing Medical Education programs (CME/CE) * Disease & condition clinical reference * Drug reference and drug interaction checker tools * Commentary from physician experts * Full-text journal articles, and much more Your free membership includes specialty-focused clinical newsletters and email alerts on breaking news, plus selected information from industry tailored to your area of clinical practice from our WebMD Professional service.
A commercial organization in regenerative medicine, focused in the areas of bio-active wound healing and soft tissue regeneration.
The Barth Syndrome Foundation, together with our affiliates, is a community of families, physicians, scientists, donors and volunteers around the world. As our mission statement says, we are dedicated to saving lives through education, advances in treatment, and finding a cure for Barth syndrome - a sometimes fatal, oftentimes debilitating genetic disease. Our work includes: * Raising awareness among physicians, scientists, and the general public; * Supporting relevant research through an international grant research program; * Providing a caring and educational community for affected families; and * Hosting a unique information resource. Working together we are making a difference in the lives of children and their families. One day there will be a cure; we hope you will help us make that day come sooner. We are the only world-wide volunteer organization dedicated to saving lives through education, advances in treatment and pursuit of a cure for Barth syndrome (BTHS). We started in 2000, after the first international conference held in Baltimore, MD (USA) where families from around the world met to discuss BTHS. As a result, we made a unanimous decision to work together to find a cure for this multi-system disorder. Our Foundation strives to accelerate progress through collaboration between families and scientists. We encourage family participation in research. Also, we provide several ways to keep up-to-date about advances in science and medicine. Our principal education event is our biennial international scientific, medical and family conference, which brings together the largest number of individuals interested in Barth syndrome. Our Family Services team is continually developing new informational resources in response to the needs of families, individuals, and professionals working with those affected by Barth syndrome.
Taiwan Biobank intends to conduct large-scale cohort studies and case-control studies on local diseases. The cohort study will call for 200,000 volunteers, while the case-control study will invite 100,000 patients with the 10 to 15 most common diseases. These studies will enable Taiwan Biobank to identify the disease-causing factors and mechanisms of common diseases to facilitate the development of better treatment and prevention, reduce the cost of medical treatment and make it possible to achieve the goal of improving the island nation’s health.
Atlas of gene expression in the developing rhesus macaque brain. This atlas is a free online resource with a unique set of data and tools aimed to create a developmental neuroanatomical framework for exploring the cellular and molecular architecture of the developing postnatal primate brain with direct relevance for human brain development. The atlas includes: * Microarray ** Microdissection: Fine structure transcriptional profiling across postnatal development for fine nuclear subdivisions of the prefrontal cortex, primary visual cortex, hippocampus, amygdala and ventral striatum ** Macrodissection: Gross structure transcriptional profiling across postnatal development for the same structures * ISH: ** Cellular resolution in situ hybridization image data of five major brain regions during postnatal developmental periods for genes clinically important for a variety of human neurodevelopmental disorders, including prefrontal cortex, primary visual cortex, hippocampus, amygdala and ventral striatum. ** Serial analysis of selected genes across the entire adult brain, focusing on cellular marker genes, genes with cortical area specificity and gene families important to neural function. * ISH Anatomic Search: Detailed gene expression search on the ISH data based on expert annotation * Reference Data: Developmental stage-specific reference series, consisting of magnetic resonance imaging (MRI) and Nissl histology to provide a neuroanatomical context for the gene expression data. These data and tools are designed to provide a valuable public resource for researchers and educators to explore neurodevelopment in non-human primates, and a key evolutionary link between other Web-based gene expression atlases for adult and developing mouse and human brain.
FuncBase: Yeast Gene Predictive Functional Annotation Browser
Yeast Gene Predictive Functional Annotation Browser
YeastFunc is a public database for browsing of quantitative S. cerevisiae gene function predictions, gene function linkage predictions, and the evidence behind the predictions, overlayed upon the experimentally verified annotations as taken from the SGD, MGI and Ensembl Gene databases, respectively. Three aspects of gene function predictions are displayed: * First, for a particular gene, users can view all functions ranked by certainty that the corresponding gene-function pair is a true annotation. * Second, for a particular function, users can view all genes ranked by certainty. * The third aspect is functional linkage predictions, displayed alongside the first two aspects as gene-centered and function-centered images, respectively, and editable via Cytoscape. These functional linkage graphs are independently informative, though they are also used as a step in one of the gene function prediction techniques whose certainty scores are displaying on this site, so they can be treated as evidence. Evidence leading to all gene function predictions in the first two aspects as well as all experimentally verified gene function annotation is displayed alongside each of the first two aspects, allowing the user to understand the basis for the certainty score. To get started type a Gene Ontology ID, an SGD ID, an ORF ID, an Ensembl gene id, an Entrez gene id, a Uniprot id, a standard gene name, or a general search term in the text box. The results of your search will appear below the search box. These results are solely Gene Ontology terms and genes for the species that you selected. Click the result that you would like to investigate further. Note the paging toolbar at the bottom of the results list. If you are interested in performing your own analyses upon all prediction scores displayed on this site you may download the file. Of the 15,633,440 scored yeast gene-function pairs, 6,368 genes have scores and 4,877 genes have at least one experimentally verified function.
Dr. Lewis Coriell''s pioneering techniques for characterizing, freezing, and storing cell cultures in liquid nitrogen constitute one of the greatest contributions to modern human research. Today, the Coriell Biobank is regarded as the most diverse collection of cell lines and DNA available to the international research community. In addition to these high-quality biospecimens, Coriell also maintains tissue, plasma, serum, urine, and cerebrospinal fluid. Few organizations have the history of innovations in repository science that have been developed and implemented at Coriell. For nearly 60 years, Coriell has set the standard in biobanking services, including the experimental design, collection, processing, distribution, cryogenic preservation, and information management of human biomaterials used in research. By developing and maintaining biorepositories as national and international resources for the study of human diseases, aging, and neurological disease, Coriell is committed to providing the scientific community with well-characterized, cell cultures and DNA preparations, annotated with rich phenotypic data. The Coriell Biobank has allowed both Coriell scientists, and research investigators around the world, to advance research programs in genetics and cell biology. Since the first repository ����?����������?? a National Institutes of Health collection ����?����������?? was established at Coriell in 1964, hundreds of thousands of cell lines and DNA samples have been distributed to researchers in 64 countries; more than 7,000 peer-reviewed papers have been published citing almost 12,000 biospecimens from the Coriell Biobank. Coriell''s repositories provided support to the Human Genome Project, a worldwide program to map the entire human genome, and to the International HapMap Project, a project providing an efficient tool to identify disease-causing genes. Coriell offers almost 60 years of experience in the banking, cryopreservation, and fail-safe storage of cell lines, DNA, and other biomaterials. The renowned Coriell biobank is ISO9001:2008 certified. Our highly-trained technicians, supported by on-staff scientists with expertise with genomics, provide proficient, individualized care for your biospecimens. From specimen collection, processing, quality control, enterprise level data, and inventory management, through rapid retrieval of specimens and secure shipment, Coriell offers full-service biorepository services.
Not for profit, precompetitive alliance of life science companies, vendors, publishers, and academic groups that aims to lower barriers to innovation by improving interoperability of R and D business processes.
Commercial medical device company focused on developing minimally disruptive surgical products and procedures for spine.
MethCGI is a tool to predict the methylation status of CpG islands in the human brain, developed on the data from human brain DNA using support vector machine (SVM).
A company which provides nonhuman primate products and bio-research services for the global scientific community. They provide serum, plasma, whole blood, and tissue samples from primates such as the Cynomolgus macaque, the Rhesus macaque, and the African Green. Products based on others species are available upon request.
Common Knowledge: I''m John Wilbanks. I run the Science Commons project at Creative Commons.
Leading contract research and manufacturing services company in the area of drug discovery and development.
An online tool to identify homologous miRNA genes. This tool can search for new miRNA candidates by requiring structural similarity and sequence conservations between new candidates and experimentally identified miRNAs. Simply Input your sequence and parameters.
A robust tool for microRNA target prediction with systematic identification of negative examples.
Established in 1980, the Life Extension Foundation is a nonprofit organization, whose long-range goal is to radically extend the healthy human lifespan by discovering scientific methods to control aging and eradicate disease. The largest organization of its kind in the world, the Life Extension Foundation has always been at the forefront of discovering new scientific breakthroughs for use in developing novel disease prevention and treatment protocols to improve the quality and length of human life. Through its private funding of research programs aimed at identifying and developing new therapies to slow and even reverse the aging process, the Life Extension Foundation seeks to reduce, and ultimately eliminate, such age-related killers as heart disease, stroke, cancer and Alzheimer''s disease. Long-time members are keenly aware of the scientific research that Life Extension Foundation funds to develop validated methods to slow and reverse the aging process. Less known is Life Extension''s multi-prong program to develop safer and more effective cancer therapies. One reason we focus so heavily on cancer research is that this dreaded disease represents a roadblock in our ability to develop effective means to combat aging.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017. Not yet vetted by NIF curator
One of three primary databases of PubChem (Pcsubstance, Pccompound, and PCBioAssay), PubChem Compound Database contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. Additionally, calculated properties and descriptors are available for searching and filtering of chemical structures. A PubChem FTP and structure download are available. New data are accepted into the repository.
An Antibody supplier. Now called Xtant Medical.
Bovine Gene Atlas: An Extensive Compendium of Bovine Transcript Profiles
A compendium of over 7.2 million unique 20 base transcript tags profiled from 81 tissues acquired from the cow L1 Dominette 01449 , her male fetus, her 255 day old heifer calf, and her father. The BGA tags were generated on Illumina''s GA1 sequencing platform. L1D''s genome (build: 3.1) was sequenced at the Baylor College of Medicine and Genome Canada sequenced EST and full-length transcripts from the same tissues used for the BGA. Tissues were chosen as a source of total RNA to minimize sequence differences between cDNA tags and genomic or expressed sequence and increase the probability of unequivocally mapping tags to build 3.1. The BGA is comprised of cardiovascular, digestive, endocrine, lymphatic, muscular, nervous system, reproductive and urinary tissues sampled from animals in the fetal, juvenile, and adult stages of development. This cover is a portal to view the tags positioned on the 3.1 build using GBrowse, and a new database schema for positional and functional queries.
Makes DNA sequencing services, Real Time PCR access and custom DNA products available to scientists. It provides automated fluorescent sequencing and oligonucleotides to the Hopkins Community. Using the JHU Finch Server facility staff capture orders, to distribute and store data indefinitely. Data produced using the Applied Biosystems 3730xl DNA Analyzer is then made available for download, for online or offline viewing, and for editing through the conveniences of the web-based JHU Finch Server. The facility also offers oligonucleotides through Sigma-Genosys.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The NeuroLOG consortium is addressing: *Management and access of partly structured data, heterogeneous and distributed in an open environment. *Access control and protection of private medical data. *Control of workflows implied in complex computing process on grid infrastructures. *Extraction and quantification of relevant parameters for different pathologies: Multiple sclerosis, Brain Vascular Stroke, Brain tumors Four application pipelines have been proposed in the context of the project. The pipelines are formalized using the Scufl data flow language. *Multiple Sclerosis image analysis pipelines *Brain Stroke application pipeline (from GIN) *Stroke / tumours Anacom application pipeline (from IFR49) Different softwares developed and/or used in this project are presented., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Stem Cell Banking stores non-embryonic stem cells from wisdom or baby teeth Dental Stem Cells are also known as DSC, DASC, DPSC, or SHED cells and are classified as a type of adult stem cells.
Mouse finder is a beta product that uses the phenotype ontology to search for the best mouse models for a particular OMIM disease. The phenotype ontology gives a score function for the similarity of two phenotypes based on ontology distance.
Pathema is one of the eight Bioinformatics Resource Centers designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms. The Pathema BRC contract ends in December 2009. At that time JCVI will cease maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania will support all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource.
International Cognition and Culture Institute
An open community platform for bioimage informatics providing the software resources to visualize, annotate and quantify bioimaging data. To bridge the gap between developers and users, it combines: a) an open-source image analysis software, offering a powerful and flexible environment for developers such as applied mathematicians to write algorithms fast and efficiently; b) a common set of tools to view and manipulate data, and a set of plugins to perform specific quantification or analysis on images; c) a community-based website centralizing all plugins and resources to facilitate their management and maximize their visibility towards users. Workspaces are virtual groups of plugins dedicated to a specific application or image processing domain. By downloading a workspace, ICY automatically installs all corresponding plugins. The workspaces are enabled, but the editing section is not ready yet. If you want to publish a plugin on this website, its code has to be GPL. Source code is available and provided in each application download.
SNPinfo Web Server is a set of freely available web-based SNP selection tools where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself. The program can also identify and choose tag SNPs for SNPs not in high LD with any GWAS SNP. We incorporate functional predictions of protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles of a SNP are likely to have differential effects on function. Users can assign weights for different functional categories of SNPs to further tailor SNP selection. The program accounts for LD structure of different populations so that a GWAS study from one ethnic group can be used to choose SNPs for one or more other ethnic groups. SNP Selection and Functional Information *Candidate Gene SNP Selection (GenePipe):SNP selection for candidate genes based on Genome Wide Association Study (GWAS) results, functional SNP prediction and Linkage Disequilibrium (LD) information. *GWAS Functional SNP Selection (GenomePipe):Functional SNP selection from SNPs that are in high LD with GWAS SNPs *GWAS SNP Selection in Linkage Loci (LinkagePipe):GWAS SNP selection in candidate genomic regions (such as linkage loci) *LD TAG SNP Selection (TagSNP):LD tag SNP selection and visualization for single or multiple populations. Finalization of SNP list from various queries. *SNP Function Prediction (FuncPred): Querying SNP function predictions and ethnic-specific allele frequencies. *SNP Information in DNA Sequence (SNPseq):Visualization of SNP related information in the context of DNA sequence. Preparing DNA Sequence for PCR Primer Design considering SNP information. Detailed information of CpG region.
Gene Regulation Ontology - Ontological resource from the BOOTStrep project for the representation of gene regulation events
Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of).
Clinical Psychology and Psychiatry: A Closer Look
Clinical Psychology and Psychiatry: A Closer Look Psychiatric medications, science, marketing, psychiatry in general, and occasionally clinical psychology. Questioning the role of key opinion leaders and the use of science to promote commercial ends rather than the needs of people with mental health concerns.
Psychology wiki is an up-to-date, authoritative statement of knowledge, theory, and practice in the whole field of psychology reflecting generally accepted academic standards. Its intended audience includes health workers, psychologists, and students and has 60,995 pages and 28,303 articles - and growing. You can access articles by following the links in the Foundations and Applied psychology sections, search for a term by entering it into the search box, or simply browse through various categories and subcategories. This centrally consolidated information resource aims to provide a conduit for authoritative information for academic and applied training, and continuing professional development, as well as provide a vehicle for informing the general public about our discipline. We also aim to be a forum for ideas, so on each discussion page we encourage alternative opinion, proposals for hypotheses requiring verification, practitioner reports, user views, etc. We hope to win the support of the national psychology societies, and through them to develop a mechanism of appropriate peer review of all articles and to restrict contributors to those with professional qualifications. This will allow articles to achieve academic status for referencing purpose and eventually ground the content solidly in the knowledge base of the discipline.
The Department of Pharmacology at Yale University offers integrated and interdisciplinary opportunities for graduate study under the newly organized Program in Biological and Biomedical Sciences (BBS). Students entering the BBS program can take courses, participate in laboratory rotations, and perform thesis research with any of the more than 200 faculty members in the biological sciences at Yale located at the closely situated School of Medicine and Science Hill ends of campus. The faculty and students of the BBS program are organized into moderately-sized, interest-based Tracks to ensure individualized attention and maximize scientific interactions. Prospective students apply to the Track that best matches their interests, although there is complete freedom to work with faculty members in any Track or to switch Tracks after arrival at Yale.
Museum of Vertebrate Zoology at Berkeley
The Museum of Vertebrate Zoology (MVZ) at the University of California, Berkeley, is a center for research and education in the biology of amphibians, reptiles, birds, and mammals. Founded in 1908, the Museum''s mission is to document and increase understanding of the diversity of terrestrial vertebrates, with particular emphasis on western North America. An MVZ Video Gallery is also available. The superb collections are at the heart of the MVZ program, where methods of field biology are combined with modern laboratory techniques and analytical methods in a comprehensive, synthetic approach. Our goals are to remain at the forefront of international research on evolutionary biology from the perspectives of systematics, ecology, behavior, functional and developmental morphology, population biology, and evolutionary genomics, and to lead the way in developing and using major natural history collections for research, education, and solving problems in biodiversity conservation. Because the MVZ was founded upon a philosophy that organisms should be studied in relationship to their natural environments, its collections are supplemented by extensive ancillary information (e.g., field notes, habitat photographs, tape-recorded vocalizations) that is connected to specimens and/or tissues and enhances their value to researchers. This concept was pioneered at the MVZ and continues to be the primary focus of current research efforts. To this end, there are strong research links between the Museum and the 2,000 acre MVZ/UC field station at Hastings Natural History Reservation. In addition, the MVZ is actively engaged in developing concepts and tools for Biodiversity Informatics through collaborations across the Berkeley Natural History Museums and international consortia.
SCREEM - Site Creation and Editing Environment
SCREEM is a web development environment. It''s purpose is to increase productivity when constructing a site, by providing quick access to commonly used features. While it is written for use with the GNOME desktop environment in mind it does not specifically require you to be running it, just have the libraries installed. Unlike most other web site / HTML editors SCREEM does not provide a WYSIWYG display of pages. Instead you are presented with the raw html source in its editor window. In general WYSIWYG editors do not produce good clean valid HTML, and can also slow you down if they do not support an element that you wish to insert. By utilising a text based editing system you can use the markup you want rather than what the application thinks you need, and also provide quick access to commonly used elements via toolbar buttons which insert the markup at the current cursor position. In addition to excelling as an HTML editor, SCREEM also lends itself to being a versatile XML editing package, perfect for use as a general purpose structured data editing environment.
A biomaterial supply resource that collects and distributes human brain tissue samples. The Dublin Brain Bank is a collaboration between the Neuropathology Department of Beaumont Hospital and the Royal College of Surgeons in Ireland. Investigators interested in applying for tissue samples need to complete tissue requisition forms and provide a record of the research groups'' ethical approval.
Mayo Clinic Mitochondrial Disease Biobank
A biobank of blood and tissue samples from patients with known and suspected mitochondrial diseases along with data from their families. Samples are used in research to understand the family of mitochondrial disorders such as Alpers' syndrome, encephalopathy, and Friedrieich's ataxia, among many others. The goal of the biobank is to advance the understanding of mitochondrial disease and improve patient care.
University of Florida Molecular Tissue Bank
The American Society for Cell Biology (ASCB) was founded in 1960 to bring the varied facets of cell biology together. The Society''s purpose is to promote and develop the field of cell biology. Its objectives are achieved through the scholarly dissemination of research at its Annual Meeting and Summer Meetings and in its publications. The ASCB strives to ensure the future of basic scientific research by providing training and development opportunities for students and young investigators, and also by keeping Congress and the American public informed about the importance of biological research. Since its founding, the ASCB has grown to approximately 10,000 members in the United States and more than 65 countries around the world. About 25% of ASCB members are international. Current members come from universities, colleges, professional schools, government, industry, and public and private research institutions. Membership in the ASCB is open to all research scientists, students, educators (high school, undergraduate, and graduate level), and technicians who have education or research experience in cell biology or an allied field.
FightSMA, known legally as Andrew''s Buddies Corporation, was created to strategically accelerate the search for a treatment and cure for spinal muscular atrophy (SMA), the number-one inherited cause of infant death. The organization pursues this objective by raising awareness and funding for SMA research.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Institute for Formal Ontology and Medical Information Science
The Institute for Formal Ontology and Medical Information Science (IFOMIS) comprehends an interdisciplinary research group, with members from Philosophy, Computer and Information Science, Logic, Medicine, and Medical Informatics, focusing on theoretically grounded research in both formal and applied ontology. Its goal is to develop a formal ontology that will be applied and tested in the domain of medical and biomedical information science.
University of California at San Francisco; California; USA
University of California at San Francisco
Public research university in San Francisco, California. Part of University of California system. Dedicated entirely to health sciences. Major center of medical and biological research and teaching. Ranked as one of top universities in biomedical field in USA and around world.
Evidence-Based Health Care Search Strategies
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. This wiki focuses on the process, techniques and tools of high quality searching in the context of evidence-based health care. Information collected in the wiki is primarily intended for medical librarians, but may be of interest to others. Please keep in mind that search strategies and tools here are intended for use by trained professionals in the course of their professional duties, and are not intended for use by the general public. If they are helpful or useful to others that is a plus, but not the primary purpose of the site.
NIA Aged Rodent Tissue Bank at the University of Washington
NIA Aged Rodent Tissue Bank (ARTB) is a repository of tissue collected from mice and rats maintained in the NIA Aged Rodent Colonies. Biospecimens are collected, archived, and distributed under a contractual arrangement with the University of Washington, Seattle. The NIA supports the three R’s of research (Replacement, Reduction, and Refinement) through maximizing the use of existing banked samples from mice and rats and providing tissues for research on aging. Researchers can select frozen tissues, unstained slides from formalin-fixed and paraffin-embedded (FFPE) tissues, or tissue microarrays (TMAs).
Museum of Vertebrate Zoology Collections
A collection of over 640,000 specimens of amphibians, reptiles, birds, bird eggs or nests, and mammals, as well as over 50,000 tissue samples from these vertebrate groups. These research collections are ranked as one of the largest in the United States, and the largest of any university museum. In addition, the Museum has numerous special collections that include archived field notes and photographs, historical annotated maps and correspondence, avian sound recordings, chromosome and histology preparations, Milton Hildebrand anatomical and film collections, artwork related to terrestrial vertebrate natural history, and a library of books, reprints, and journals for curation and research activities. Specimen data are accessible online, and the Museum is working to improve data access to the other collections. Museum Collections * Mammal Collection * Herpetological Collection * Bird Collection * Egg & Nest Collection * Tissue Collection * Fieldnotes, Photos, & Map Collection * Other Collections The Museum of Vertebrate Zoology (MVZ) welcomes donations of amphibians, reptiles, birds, bird eggs and nests, mammals and related materials. Acceptance of a donation is at the discretion of MVZ Curators. * Specimens -- May include preserved specimens and/or parts (e.g., tissue samples) as well as unpreserved material (e.g., frozen carcasses, live animals) that will be prepared by Museum Curators, curatorial staff, or students. * Related Materials -- Donations of images (digital or printed photographs or slides), sound recordings, field notes, and other natural history archival material. Materials must be connected to specimens or research projects. Donated material and associated data will be made available for research, education, or public exhibit according to the mission and policies of the Museum and Regents, except by prior signed agreement between the donor and the Museum.
The Ontario Institute for Cancer Research (OICR) is a centre of excellence in cancer research with a focus on prevention, early detection, diagnosis and treatment of cancer. The Institute is an independent, not-for-profit corporation bringing together multi-disciplinary, multi-institutional collaborations, which will allow complex questions to be pursued. It is translating research findings into programs, technologies and therapies. Established in December, 2005, the Institute will support more than 50 internationally recognized principal investigators; there will be a strong core of scientists at the MaRS Centre with the remainder in nodes of excellence around the province. The Institute is leveraging the current research excellence at universities, research hospitals and health research institutes across Ontario, leading to greater integration of cancer research efforts across institutions. The Ontario Cancer Research Network, established in 2002, has been incorporated into the Institute. Its initiatives will continue under the umbrella of the Institute and will include: Cancer Research Fund, Clinical Trials Infrastructure Fund, Clinical Trials Network, OntarioCancerTrials.ca, Ontario Cancer Research Ethics Board, and Ontario Tumour Bank.
Free medical app for comprising a drug reference, drug interaction checker, disease and condition reference, procedures and protocols and specialty-focused Medical News * Drug Reference: Search prescribing and safety information for over 8,000 brand, generic and OTC drugs, herbals and supplements * Drug Interaction Checker: Check mild interactions to serious contraindications for any combination of drugs, herbals and supplements * Disease & Condition Reference: Review the latest in-depth clinical information for 4,000+ diseases and conditions (enhanced with images and videos) *Procedures & Protocols: Follow detailed stepbystep instructions for 600+ clinical procedures, including 80+ widely used Tables & Protocols * Specialty-focused Medical News: Read in-depth medical news articles daily in 30 specialty areas
The University Memory and Aging Center (formerly known as University Alzheimer Center) is a partnership of Case Western Reserve University and University Hospitals of Cleveland promoting the best possible care for persons with memory problems, and assisting their families, through an integrated program of clinical services, research, and education. Our staff includes a wide range of professionals dedicating their time and efforts to understand and work for the betterment of those affected by any disorder which affects cognitive abilities. We include Neuroscientists, Neurologists, Psychologists, Sociologists, Social Workers, Nurses, Clinical trials coordinators, Research Assistants, Data Managers and Administrative staff. We work with researchers in Cleveland, throughout the US and around the globe.
Gossamer: A Space-Efficient Genome Assembler
A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability.
University of California Davis Alzheimer's Disease Center
We developed this Web site for researchers, primary care physicians, caregivers, students and those with a general interest in Alzheimer's Disease. Utilizing the many resources and web links, we think you will find this a useful portal to understanding the many facets of Dementia. The center is part of nationwide and statewide programs. The ADC has several important goals: * Educate health professionals and the public about Alzheimer's disease and related dementias * Conduct research in clinical and community populations into the causes and potential treatments for dementia * Advocate changes in health policy and practice that will enhance the recognition, treatment and management of dementia * Serve as an expert referral center for the diagnosis of dementia
As both the public health survey of Quebec, and the Quebec resource for scientists interested in personalized medicine, genomics and public health, this public resource operates under a governance framework and consists of a databank and a biobank. The database contains environmental, demographic and health data. The biobank contains DNA, blood and urine samples. Access to CARTaGENE will be granted to researchers who are seeking to better understand how genes interact with other genes, with the environment and with lifestyle factors. They have collected in-depth information on over 20 000 Quebecers, including 446 sociodemographic, life-style and health data, 190 physiological parameters, 22 types of biochemical analyses and 41 types of haematological analyses. They have also collected 11 types of blood, plasma, serum and urine samples from most participants. Genealogical reconstruction of recruited participants, in collaboration with BALSAC Project, is also possible. CARTaGENE data and samples include the following: Health Questionnaire, Physical measures, Biochemical and hematological analysis, Biological samples stored in the Biobank. CARTagene is currently contacting participants (who have agreed to be recontacted) to collect additional data on environmental exposure. Data on dietary habits will be collected during the second phase of this component which will begin soon. Any scientific researcher working in a public or private organization at the national or international level may apply for access to CARTaGENE samples or data.
AutoCSA (Automatic Comparative Sequence Analysis)
AutoCSA (Automatic Comparative Sequence Analysis) is a mutation detection program designed to detect small mutations (1-50 bases) in sequence traces. The software is capable of detecting both homozygous and heterozygous base substitutions, as well as small insertions and deletions, to a high sensitivity. It has specifically been written with high throughput environments in mind, so it is easy to automate the analysis of large amounts of data with little manual intervention. AutoCSA is written in java and will run under java 1.4 or later versions which must be downloaded and installed on your computer. It should be emphasised that AutoCSA uses the raw sequence channels from the trace files generated by the ABI sequencers (.ab1 file extension). Traces which have been processed and the raw channels removed are not suitable for use with the software. The software has been tested successfully under Linux, MS windows XP, and Mac OS X 10.
ECACC: European Collection of Cell Cultures
A cell culture collection to service the research community and provide an International Depository Authority recognized patent depository for Europe. The collections currently hold over 40,000 cell lines representing 45 different species, 50 tissue types, 300 HLA types, 450 monoclonal antibodies and at least 800 genetic disorders. ECACC has developed a comprehensive range of cell culture services and diversified into new product areas such as high quality genomic DNA extracted from cell lines. ECACC is one of the four collections which constitute the Health Protection Agency Culture Collections (HPA Culture Collections). Its products include: General Cell Collection, Hybridoma Collection, Primary Cells, Neuron Culture Kits, HepaRG Cells, GPCR Cell Lines, HLA-Typed Collection, Human Random Control Collection, Human Genetic Collection, and DNA Products. Its services include: Assay Ready Cells, Cell Culture Management Services, Contract Cell Culture, Cell Line Identity Verification, Genetic Support Services, Mycoplasma Testing and Eradication, Patent Deposits, Safe Deposits, Sterility Testing, and Training.
Families of Spinal Muscular Atrophy is dedicated to creating a treatment and cure by: - Funding and advancing a comprehensive research program; - Supporting SMA families through networking, information and services; - Improving care for all SMA patients; - Educating health professionals and the public about SMA; - Enlisting government support for SMA; - Embracing all touched by SMA in a caring community. Our vision is a world where Spinal Muscular Atrophy is treatable and curable.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 6, 2011. A project to collect, store and study DNA samples from tens of thousands of healthy volunteers and patients with diseases of major public importance. It aims to identify genes that are risk factors for the conditions. The network consists of 13 collections led by different clinicians throughout the UK. At its heart is an archive infrastructure which manages the DNA and the information associated with it. The European Collection of Cell Cultures in Porton Down handles the blood, peripheral blood lymphocytes and EBV-transformed cell lines, while the Centre for Integrated Genomic Medical Research at Manchester University manages the DNA. These banked samples are available to UK and international researchers, who can examine data and set up collaborative work by registering at the DNA Network's website. The conditions for which samples are currently collected and stored are: Acute leukemia, Asthma and eczema, Late onset Alzheimer's disease, Breast cancer, Colorectal cancer, Coronary artery disease, Glomerulonephritis, Hypertension, Age-related macular degeneration, Multiple sclerosis, Parkinson's disease, Type 2 diabetes, Unipolar depression.
Access service resource which connects labs needing and offering experimental services. Users can search for academic and government labs and experimental services, request and compare service quotes, and directly communicate with labs to arrange orders.
Project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.
BioBancUSA is a leading biotechnology company specializing in white blood cell collection, processing, cryopreservation and storage service. BioBancUSA, a private company headquartered in Monterey, California, is the exclusive licensee of the original patent for the collection, processing and cryopreservation technology of white blood cells, giving you the assurance of both technical integrity and legal legitimacy that you can count on. BioBancUSA is dedicated to providing our clients with the highest quality immune cell preservation for their future medical use. We are committed to the most advanced technology, exceptional, personalized service and leading-edge innovation to benefit our customers, health care providers, shareholders and employees.
The Molecular Modeling DataBase (MMDB), also known as Entrez Structure, is a database of experimentally determined structures obtained from the RCSB Protein Data Bank (PDB). MMDB is developed by the Structure Group of the NCBI Computational Biology Branch. The data processing procedure at NCBI results in the addition of a number of useful features that facilitate computation on the data and link them to many other data types in the Entrez system. The structure database is considerably smaller than Entrez''s Protein or Nucleotide databases, but a large fraction of all known protein sequences have homologs in this set, and one may often learn more about a protein by examining 3-D structures of its homologs. These are accessible as Related Structures in the Links menu of Entrez Protein sequence records (illustrated example). It is then possible to align the query protein to the structure-based sequence, as shown in the illustration on this page. Additional resources can be used along with MMDB to interactively view the structures, find similar 3D structures, learn about the types of interactions and bound chemicals that have been found to exist among the similar 3D structures, and more.
RUCDR is a biobank and a service organization that maintains human blood, serum, saliva, tissue and the genetic products derived from those. Services include technical consultation and logistical support for biobanking. Researchers can order biomaterials and apply for phenotypic / genotypic data.
Genetic Alliance Registry and BioBank is a centralized, clinical data registry and sample repository (including DNA, serum, cells and tissues) that enables translational research. It is a nonprofit organization established by seven patient advocacy organizations. These organizations share resources for their BioBanks, such as the contract to the independent lab that processes the samples, but each organization will maintain ownership, control and costs associated with their sample collection. Founded in 2003, this cooperative venture provides shared infrastructure and customized solutions for disease advocacy organizations to lead sophisticated research initiatives. Genetic Alliance Registry and BioBank is an advocacy owned repository for biological samples and clinical data. It provides: * Centralized, standardized collection and archiving * Highest biorepository and participant protection standards * Open access for all organization approved researchers * Advocacy organization control
Nord-Tr��������ndelag health study Biobank
International biobank storing whole blood and DNA from 200,000 individuals, serum and plasma samples from more than 100,000 individuals as well as urine, RNA tubes, cells, buffy coat and Na-heparin tubes for environmental analysis for as many as 50,000 individuals. All bio-specimens from the HUNT surveys are collected, processed and stored at the HUNT Biobank in Levanger. The National CONOR Biobank is located on the same site, where it serves as a central research repository for DNA samples from all the largest Norwegian health surveys. These make up the Cohorts of Norway (CONOR), which include samples from more than 200,000 individuals. * HUNT 1 was carried out in 1984-1986 to establish the health history of 75,000 people. * HUNT 2, carried out in 1995-1997, focused on the evolution of the health history of 74,000 people. This included blood sample collection from 65,000 people. The data that accompany biospecimens in the biobank are stored in secured computer systems that run complex database management and analysis software. * HUNT 3 was completed in June 2008. 93,210 people were invited to participate in the study, and as of the 6th of June, 2008, 48,289 people participated (52% participation rate). The data, collected by means of questionnaires, interviews, clinical examinations and collection of blood and urine samples, will be ready for analysis in January 2009. * Young-HUNT is the adolescent part of HUNT including participants aged 13-19 years. Young-HUNT1 (1995-97) was conducted as part of HUNT2, 9141 adolescents participated (90% response rate). Young-HUNT2 (2000-01) was a follow-up study of Young-HUNT1, 2400 students participated in both studies (77% of the invited). Young-HUNT3 (2006-08) was a new cross-sectional study as part of HUNT3. This time 8677 adolescents participated (87% response rate). Data collection included self-reported questionnaires, structured interviews, clinical measurements and, in Young-HUNT3, buccal smears. All institutions with research expertise can apply for access to analyze HUNT data. Projects must have recommendations from The Regional Committee for Medical Research in Norway (REK) and be registered with The Norwegian Social Science Data Services (NSD).
Down Syndrome Center for Research and Treatment
The Down Syndrome Center for Research and Treatment (DSCRT) is one of the first programs in the country to connect academic research with treatment of adults and children with Down syndrome. Our goal is to apply cutting edge basic research to develop treatments that will help people with Down syndrome improve their cognition and forestall the onset of Alzheimer''s disease. Members of this special population continue to live fuller, healthier lives. We hope to build on this progress and advance their potential even further. About 400,000 people with Down syndrome live in the U.S. today, and one in every 733 babies is born with the condition. Children with Down syndrome are at risk for congenital heart defects, respiratory and hearing problems, childhood leukemia, and thyroid conditions. They typically also have mild to moderate cognitive impairment that affects learning, memory and speech. This is an important topic for research. With increased health care, education, and societal support, people with Down syndrome are living longer, fuller lives. But as they age we are discovering an increased occurrence of the symptoms associated with Alzheimer''s disease. In fact, about 25 percent of individuals with Down syndrome over age 35 increasingly show clinical signs and symptoms of Alzheimer''s type dementia. By age 60, more than half show cognitive decline.
Molecular Biology Gateway is the gateway to Web resources for molecular biology, genomics, PCR, protocols, microbiology, and biochemistry. Major categories include: Current Molecular Biology News, Microbiology, Virology, Genomics and Bioinformatics, PCR, Journals, Books, and other Publications, Protocols, Technology, Books, and Recommended Reading.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 2nd, 2022. Manufacturer of Dermagraft, a bio-engineered skin substitute that assists in restoring damaged tissue and supports the body's natural healing process.
A commercial orthobiologics company whose main goal is to improve patient quality of life using the science of human biology to advance solutions for spine, orthopedics, and sports medicine.
University of California San Diego School of Medicine; California; USA
Graduate medical school of University of California, San Diego. It was the third medical school in the University of California system, after those established at UCSF and UCLA, and is the only medical school in the San Diego metropolitan area.
National Centers for Biomedical Computing
NIH Roadmap National Centers for Biomedical Computing
The NCBCs are a set of networked computation core facilities for biomedical infrastructure funded under the NIH Common Fund, the National Program of Excellence in Biomedical Computing (NPEBC). There are seven funded Centers that cover systems biology, image processing, biophysical modeling, biomedical ontologies, information integration, and tools for gene-phenotype and disease analysis. The centers will create innovative software programs and other tools that enable the biomedical community to integrate, analyze, model, simulate, and share data on human health and disease. Each Center has Cores that are focused on (1) computational science, (2) biomedical computational science and (3) driving biological projects whose intent is to drive the interaction between computational and biomedical computational science. In addition to the Centers, the NIH has a number of active program announcements to develop collaborations with the biomedical research community��this includes announcements from the Biomedical Information Science and Technology Initiative (BISTI) and the Program for Collaborations with National Centers for Biomedical Computing. There are numerous efforts in education and training that emanate from the Centers and there is an annual all hands meeting.
PrabiG is the Grenoble portal of the Prabi (Rhone-Alpes Bioinformatics Center) platform. It aims at providing the scientific community with tools and data related to proteomics and metabolomics. PrabiG is currently hosting the following projects : * UniPathway * ProteHome * OBIWarehouse * AT_Chloro
A commercial organization which provides construction, architecture, engineering, and ecological services to private and public sector clients in Malaysia and overseas. The main focus of the Renexus Group is to incorporate sustainability in the projects they service. The Group provides services for both small and large scale projects, from project inception and development to commissioning and support services.
The Museum of Comparative Anthropogeny (MOCA) is a collection of comparative information regarding humans and our closest evolutionary cousins (chimpanzees, bonobos, gorillas and orangutans i.e, great apes), with an emphasis on uniquely human features. MOCA is organized by Domains, each grouping Topics by areas of interest and scientific discipline. Each topic entry will eventually cover existing information about a particular difference (alleged or documented) between humans and non-human hominids. Comparisons of these non-human hominids with humans are difficult, as so little is known about their phenotypic features (phenomes), in contrast to humans. Ethical, fiscal and practical issues also limit collection of further information about great apes. MOCA attempts to collect existing information about human-specific differences from great apes, currently scattered in the literature. Having such information in one location could lead to new insights and multi-disciplinary interactions, and to ethically-sound studies to explain differences, and uniquely human specializations. MOCA is not targeted at experts in specific disciplines, but rather aims to communicate basic information to a broad audience of scientists from many backgrounds, and to the interested lay public. MOCA includes not only aspects wherein there are known or apparent differences between humans and great apes, but additionally, topics for which popular wisdom about claimed or assumed differences is not entirely correct. It is for all these reasons that MOCA is called a Museum, and not an Encyclopedia or Database.
THIS RESOURCE IS NO LONGER IN SERVICE documented June 6, 2013 Database of all S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs. Curation of new and existing literature is ongoing and changes are incorporated weekly. User feedback is welcome. The genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824, has been sequenced and annotated. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.
Microbiology Blog: The weblog for microbiologists
Microbiology news and views to help the busy scientist keep up-to-date on current research, forthcoming conferences, hot research topics, high impact publications, and much more.
Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health.
linked life data - a semantic data integration platform for the biomedical domain
A platform for semantic data integration through RDF warehousing and efficient reasoning that helps to resolve conflicts in the data. Search and explore over 5 billion RDF statements from various sources including UniProt, PubMed, EntrezGene and 20 more... Perform complex SPARQL queries and retrieve more than one billion RDF resources. One of the major problems that biotechnology and pharmaceutical industries face today is how to combine data from multiple sources and make their research more productive. Data integration takes much time and often leads to errors and redundancies that require more time and resources to resolve. LinkedLifeData is a data warehouse that syndicates tons of heterogeneous biomedical knowledge in a common data model. The platform uses an extension of the RDF model that is able to track the provenance of each individual fact in the repository and thus update the information. Data Sources include: Disease Ontology, LinkedCT, Reactome, HPRD, DBPedia, UniProt, CellMap, NCBI Entrez-Gene, UMLS, IMID, MINT, DrugBank, LHGDN, Gene Ontology, HumanCYC, PubMed, NCI Nature, Human Phenotype Ontology, BioGRID, IntAct, HapMap, Symptom Ontology, DailyMed, ChEBI, Diseasome, Freebase, SIDER
Harvard Medical School; Department of Neurobiology; Born Lab
In the Born Lab the goal is to seek to understand the circuitry of the mammalian cerebral cortex and how it endows us with the ability to see . . . and hear and think and talk. The approach is to study visual cortex of alert monkeys trained to report specific aspects of their visual experience. This allows us to define the neural correlates of specific percepts and then study their underlying mechanisms by activating or inactivating components of the circuit. Our primary tools are extracellular electrophysiologyboth with single electrodes and multi-electrode arraysand psychophysics. They are complemented by techniques that allow us to dissect and probe cortical circuitry: �� circuit tracing with genetically modified rabies viruses �� microstimulation to insert specific signals into cortical circuits �� cortical cooling (cryoloops) to reversibly inactivate circuit elements �� microarrays to identify molecular markers of neuronal subtypes �� optogenetics to improve the spatial and temporal specificity with which we can manipulate circuits Current Projects: *Dissecting parallel pathways. *Probing cortico-cortical feedback.
Corn Fungal Resistance Associated Sequences Database
A relational database with dynamic querying and data integration that can be used by researchers to identify genetic sequences with a high probability of being associated with aflatoxin accumulation resistance, according to multiple lines of evidence. CFRAS-DB integrates genomic, proteomic, and genetic data from multiple studies in maize dealing with aflatoxin accumulation or Aspergillus flavus resistance., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Biomarker Commons aggregates news and research on disease biomarkers, and includes links to biomarker journals, resources and commercial services. There are a number of biomarkers in use today, not only in experimental research but in the clinical setting. * Translation biomarkers are used in both a preclinical (i.e. animal models) and clinical setting * Early detection biomarkers are used to identify the earliest stages of disease onset * Diagnostic biomarkers are used to identify the presence or absence of a specific disease state * Staging biomarkers are used to distinguish between different stages of a chronic disorder * Prognostic biomarkers are used to determine patient survival probability * Disease biomarkers are related to a clinical outcome or measure of disease * Predictive or efficacy biomarkers are used to predict the efficacy of a specific drug therapy * Target biomarkers are used to determine the interaction of a drug or small molecule with its target * Mechanism biomarkers are used to report on the downstream effects of a drug * Toxicity biomarkers are used to determine the toxicological effects of drugs on an in vitro or in vivo system * Surrogate biomarkers are regarded as valid substitutes for measuring clinical outcomes Users may search biomarker news (search by tags, news archive. or insights), sign up for biomarker news email alerts, follow biomarker commons and view biomarker news top tags
Databases which provide clustered sets of sequences from UniProt Knowledgebase and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences from view. The UniRef100 database combines identical sequences and sub-fragments with 11 or more residues (from any organism) into a single UniRef entry. The sequence of a representative protein, the accession numbers of all the merged entries, and links to the corresponding UniProtKB and UniParc records are all displayed in the entry. UniRef90 and UniRef50 are built by clustering UniRef100 sequences with 11 or more residues such that each cluster is composed of sequences that have at least 90% (UniRef90) or 50% (UniRef50) sequence identity to the longest sequence (UniRef seed sequence). All the sequences in each cluster are ranked to facilitate the selection of a representative sequence for the cluster.
GenExpress: an intellectual system for analysis of genomic regulatory sequences of humans and higher eukaryotes
The intellectual system GenExpress designed for analysis of genomic regulatory sequences of higher eukaryotes comprises the following major units: (1) the database of transcription regulatory regions of eukaryotic genes TRRD that contains the description of regulatory regions of 427 eukaryotic genes, including 2133 transcription factor binding sites, 78 composite regulatory elements, 593 enhancers, and other types of transcription-regulating elements; (2) the database Activity that comprises the available data on the activity of the sites involved in the regulation of gene expression as well as the physico-chemical, conformational, and statistical DNA/RNA properties significant for the activity of these sites; (3) the database for gene networks GeneNet that contains the information on groups of the genes functioning coordinately to provide expression of genetic information; (4) a set of programs for detecting functional sites and predicting their activity; (5) programs for visualization of the information contained in the listed databases and the results of analysis; (6) semantic means to provide user''s navigation in the system. SRS (Sequence Retrieval System) query language was chosen for the system GenExpress, as it is widespread and Internet-compatible. GenExpress is available at /mgs/systems/geneexpress/. Applications of the system to analysis of the structure-function organization of human genomic nucleotide sequences are considered.
Crux tandem mass spectrometry analysis software
A software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. This software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification is provided as a single executable. Crux is implemented in C and is distributed with source code freely to noncommercial users. Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification.
The purpose of these three Banks (SUDDEN DEATH BRAIN AND TISSUE BANK, HIV BRAIN AND TISSUE BANK, and CJD BRAIN AND TISSUE BANK) is to collect donated samples from the brain and other organs of the body during post mortem examination, and to make these available for medical research. All the samples stored in the Edinburgh Banks are fully authorized for research by families and ethically approved for research use in accordance with the terms of current UK Human Tissue legislation. During the last 100 years or so, much of our knowledge of brain disorders has come from the study of post mortem tissues, based on identifying the differences between diseased and control (normal) brains. Advances in the diagnosis and treatment, as well as understanding the genetic background, of disorders such as Alzheimer''s disease, dementia with Lewy bodies, Parkinson''s disease and the effects of head injury have all depended on research using Brain Bank resources in different countries. Brain Banking in Edinburgh commenced in 1990, focusing specifically on HIV infection of the brain and on Creutzfeldt-Jakob disease (CJD). Significant progress in understanding these two brain infections has resulted both from the research in Edinburgh and from the work of scientists worldwide who have used tissue samples from the Edinburgh Brain Banks. These resources proved vital in establishing variant CJD as a new disease, different from the classic sporadic form and in demonstrating the brain changes in pre-AIDS and AIDS, particularly in drug abusers. In 2005 a third brain bank was established in Edinburgh with the specific aim of collecting donated normal brain tissue samples from the forensic post mortem service since there is a worldwide shortage of such material. This Bank also collects samples donated from individuals with psychiatric disorders or a history of head injury or of drug and alcohol addiction.
It is a prospective cohort study designed to investigate the relationship between sleep disordered breathing and cardiovascular disease. Participants were recruited from nine existing epidemiological studies in which data on cardiovascular risk factors had been collected previously.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The Microbe Division in RIKEN-BRC has been collecting, preserving, and distributing cultured microbial strains as one of the leading culture collections in the world since established as Japan Collection of Microorganisms (JCM) in 1981. JCM aims to contribute to scientific communities by maintaining and serving high-quality microbial resources useful for general microbial studies and various research fields particularly in health and environmental science. JCM has participated in the National BioResource Project supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan as the core facility for General Microbes. JCM maintains approximately 19,900 strains as of Sept. 2010, and the approximate numbers of the available strains from JCM are: 7,400 strains of aerobic and anaerobic bacteria including actinomycetes, 300 strains of archaea, and 4,100 strains of fungi including yeasts (in total ca. 12,000 strains). Strains held at JCM are limited to those classified in Risk Group 1 or 2. Information of the available strains is opened to the public through the JCM On-line Catalogue Database. Genomic DNA samples of some strains are also distributed in cooperation with RIKEN BRC-DNA Bank. More than 3,500 strains are annually distributed to domestic and overseas researchers. JCM welcomes a deposit of microbial strains published or designed to be published in scientific papers as well as an order for microbial cultures.
Computational Biology Research Center Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core performs research activities to create a wide array of industrial technologies using genomes and the other biological information to fulfill their mission. CBRC hosts research staff experts in diverse fields spanning computer science, mathematics, physics, chemistry, and biology and scientists affiliated with other institutions, with whom they work closely on joint, collaborative projects. Core offers internally developed and maintained software applications and databases, with corresponding external resources.
VAST is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. Related structures for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search page also allows you to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors. Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one. From the MMDB Structure summary pages, retrieved via Entrez, structure neighbors are available for protein chains and individual structural domains. If you already know a PDB/MMDB-Id you can try this at once, using the input form in the right column. VAST Search is a service that allows searching for structural neighbors starting with a set of 3D-coordinates specified by the user. This service is meant to be used with newly determined protein structures that are not yet part of MMDB. Structure neighbors for proteins already in MMDB have been pre-computed and can simply be looked up from MMDB''s Structure summary pages!
A component of EcoliHub, EcoliWiki is a wiki-based system for finding, editing, and adding information about E. coli K-12 and other model organism strains of E. coli. EcoliWiki is being constructed to include information about bacteriophage, plasmids, and mobile genetic elements. Information should be easily accessible and correct, and users have the right to edit any information they feel is incorrect. Most of the E. coli information was initially seeded with a subset of information from parsing EcoCyc data dumps. For phage gamma and the F plasmid, Genbank accessions were converted to GFF, which was parsed into the appropriate tables. Other sources of content include: * user additions * monthly addition of annotations from EcoCyc * structural data from the PDB * domains and motif information from InterPro * various databases including EcoGene, RegulonDB, Genbank, GenoBase, ASAP * many many scientific papers EcoliWiki participates in the RefGenome project. EcoliWiki provides REST web services as part of the EcoliHub Web Services infrastructure project.
Scirus - for scientific information only
Science-specific search engine with over 575 million scientific items indexed at last count (May 2013), it allows researchers to search for not only journal content but also scientists'' homepages, courseware, pre-print server material, patents and institutional repository and website information. Scirus helps you quickly locate scientific information on the Web: * Filters out non-scientific sites. For example, if you search on REM, Google finds the rock group - Scirus finds information on sleep, among other things * Finds peer-reviewed articles such as PDF and PostScript files, which are often invisible to other search engines. * Searches the most comprehensive combination of web information, preprint servers, digital archives, repositories and patent and journal databases. Scirus goes deeper than the first two levels of a Web site, thereby revealing much more relevant information. Scirus has proved so successful at locating science-specific results on the Web that the Search Engine Watch Awards voted Scirus ''Best Specialty Search Engine'' in 2001 and 2002 and ''Best Directory or Search Engine Website'' WebAward from Web Marketing Association in 2004, 2005, 2006 and 2007. Give your Web site greater functionality and enhance the experience of your users, by adding Scirus to your home page for free. Scirus uses the latest in search engine technology to pinpoint precise scientific information that other search engines can not reach, including pdf files and peer reviewed articles. Make your Web site more visible to the scientific community, by submitting it for inclusion on Scirus. You will increase the chance of scientists finding your site when looking for information and you could increase your visitor rate.
A biobank of human biological material and genetic information. It provides samples and information to researchers in order to identify new genes and clarify pathogenic mechanisms of diseases. The biobank offers biochemical and molecular diagnoses of genetic dystonias, Parkinson's disease and NBIA disorders, as well as storage of biological samples for external institutions.
Surgical Biologics - a MiMedx Group Company
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 2nd, 2022. Tissue bank and service organization for bioimplants.
The CTB (Chernobyl Tissue Bank) is an international cooperation that collects, stores and disseminates biological samples from tumors and normal tissues from patients for whom the aetiology of their disease is known - exposure to radioiodine in childhood following the accident at the Chernobyl power plant. The main objective of this project is to provide a research resource for both ongoing and future studies of the health consequences of the Chernobyl accident. It seeks to maximize the amount of information obtained from small pieces of tumor by providing multiple aliquots of RNA and DNA extracted from well documented pathological specimens to a number of researchers world-wide and to conserve this valuable material for future generations of scientists. It exists to promote collaborative, rather than competitive, research on a limited biological resource. Tissue is collected to an approved standard operating procedure (SOP) and is snap frozen; the presence or absence of tumor is verified by frozen section. A representative paraffin block is also obtained for each case. Where appropriate, we also collect fresh and paraffin-embedded tissue from loco-regional metastases. Currently we do not issue tissue but provide extracted nucleic acid, paraffin sections and sections from tissue microarrays from this material. The project is coordinated from Imperial College, London and works with Institutes in the Russian Federation (the Medical Radiological Research Centre in Obninsk) and Ukraine (the Institute of Endocrinology and Metabolism in Kiev) to support local scientists and clinicians to manage and run a tissue bank for those patients who have developed thyroid tumors following exposure to radiation from the Chernobyl accident. Belarus was also initially included in the project, but is currently suspended for political reasons.
Action for Autism: Supporting Autistic People Blog
This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and submit. Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. NEBcutter produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://rebase.neb.com/rebase/rebase.html). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini.
A wiki all about medical imaging. Anyone may contribute who registers. Popular pages include Optical Imaging, Imaging brain function with optical topography, Optical mammography, Introduction to optical imaging, Comparison of time domain and frequency domain systems, Forward problem in diffuse optical imaging, Optical molecular imaging.
The Tfsitescan tool is for promoter sequence analysis and works best with sequences of ~500 nt. Simply enter the nucleic acid sequence in one of the common sequence formats (IG, Genbank, EMBL, GCG, DNAStrider, or Fasta).
An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human.
An open visualization tool for the display of matrix data. It is available for download or interactive web use. It is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. Our group has found it useful for imaging all kinds of matrix-based data, not just microarray data.
HMMSeg is a program for the scale-specific segmention of continuous genomic data using hidden Markov models (HMMs). It can segment multiple datasets simultaneously. Scale-specificity is achieved via an optional smoothing step using wavelets. HMMSeg is written in Java and may be downloaded for unrestricted use. It has been tested on Windows and several Unix-type operating systems.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software genome database management system.
Tissue Solutions offers you a single point to access the entire range of human biological materials for all your research and development needs. This includes diseased and normal tissues in fresh, frozen and FFPE formats. Using our large network of ethical sources we find the tissues you require, to your specifications and will deliver them to your door. Our goal is to provide high quality and well characterized samples to biotech companies, the pharmaceutical community and contract research organizations worldwide. We also organize customized and prospective tissue acquisition projects and give specialized advice relating to all aspects of the acquisition process, including intellectual input on project design. We appreciate that you would rather spend your time finding new biomarkers and developing, testing and validating novel drugs to cure human disease than spend your time sourcing material to help you do your work, so let our dedicated Tissue Acquisitionists lessen your workload and become a virtual part of your team.
ICA (Independent Component Analysis) for dummies
ICA is a quite powerful technique and is able (in principle) to separate independent sources linearly mixed in several sensors. For instance, when recording electroencephalograms (EEG) on the scalp, ICA can separate out artifacts embeded in the data (since they are usually independent of each other). This page intends to explain ICA to researchers that want to understand it but only have a weak background both in matrix computation and information theory. Arnaud Delorme''s explanations are as intuitive as possible and based on practical examples from Matlab. He would value your feedback on this page.
Radiopaedia is a rapidly growing open-edit radiology resource which has been primarily complied by radiologists and radiology residents / registrars / fellows from across the globe. Our mission is to create the best radiology reference available, and to make it available for free, forever, for all. It is designed to facilitate a meaningful collaboration between contributing users from across the globe, as well as allow non-contributors to browse through thousands of articles and interesting and illustrative cases as well as get involved in editing or adding content. Radiopaedia.org has two major components: 1. articles and 2. cases. Articles are entirely collaborative and cover any and all topics relevant to the practice of radiology. Cases belong to the contributing user, and are shared with the site, allowing them to be included in articles, as well as used in tutorials or quiz mode. While the primary aim of Radiopaedia.org is to allow the creation of an up to date resource for the radiology community, it is also about creating a community. It is focused on bringing together like-minded folk who can collaborate on Radiopaedia.org content as well as on other projects.
Tissue bank that specifically provides human tissue and cell samples for research purposes. It offers PBMCs, whole blood, solid tumor tissues, circulating tumor cells, and a variety of other bio-specimens.
CiteXplore combines literature search with text mining tools for biology. Search results are cross referenced to EBI applications based on publication identifiers. Links to full text versions are provided where available. The underlying database is populated with data from Medline, Patents, C.B.A. and Citeseer. The site offers a quick search as well as an advanced search. Results of queries can be saved in formats compatible with commonly-used bibliographic management software and exported. We provide a Simple Object Access Protocol (SOAP) based service to retrieve data from the Citation database. Text mining is provided internally by Whatizit and externally by iHOP.
National Laboratory for the Genetics of Israeli Populations
Narayana Hrudayalaya Tissue Bank and Stem Cell Research Center
Narayana Hrudayalaya Tissue Bank and Stem Cell Research Center (NHTB-SCRC) is a joint venture between Rotary Bangalore Health City (RBHC) and Narayana Hrudayalaya. Our mission is to create awareness on Cord Blood Banking among the masses. Our vision is to make sure that every pregnant mother in India is able to afford to bank her child''s cord blood and cord tissue in a novel form of ������??Biological Insurance������??. The center would also assist in research and development of newer stem cell therapies. These goals are met while ensuring patient safety and well being by maintaining compliance with ICMR guidelines, Good Manufacturing Practice (GMP) guidelines, strict confidentiality and adherence to ethical standards. The private cord blood bank would store cord-blood and cord tissue derived stem cells for the exclusive use of clients who would pay for the cryo-storage, for a period of 21 years. These samples would be used for the child or its siblings anytime in the future, for therapy of various medical conditions. The public cord blood bank would enable us to collect cord blood from delivery and birthing centers, process these specimens, type their HLA signature and store them in ultra-low temperature conditions for use on prospective recipients. These recipients would have to be matched against their HLA signature with the stored stem cell concentrate. Patients with a disease treatable by stem cell therapy would have to have their HLA type known and they approach us for treatment. Such patients would be matched against our library of samples to identify a suitable match which would then be issued at a nominal cost. The cost of therapy would however be separate and informed to the patient before embarking on the treatment.
An assembler for the de novo assembly of large genomes using short sequence reads via jumping extension and read remapping.
University of Cambridge School of Clinical Medicine; Cambridge; United Kingdom
University of Cambridge School of Clinical Medicine
School of Clinical Medicine is medical school of University of Cambridge in England.
AlloSource is a non-profit organization founded in 1994 on a promise to honor and respect the gift of donation by responsibly developing, processing and distributing life-saving and life-enhancing allografts for our communities. Today, each of our 300 employees continues to fulfill this promise through multi-shift, 360-day processing to the highest quality and service standards. We strive to be the tissue network patients and the world''s most respected transplant teams ask for by name. This is accomplished by understanding the needs of our doctors and by providing the best tissue for our recipients. We offer more than 200 standard and customized precision allograft products, and act as a trusted and knowledgeable partner to the medical community, all with the intention of maximizing medical impact. In 1995, Allosource evolved from a local tissue bank in Denver, Colorado into a national organization serving communities around the country. Today, AlloSource is one of the largest, most respected tissue banks in the United States. Through our growth we''ve remained committed to the wishes of donor families, the needs of our surgeon customers, and the hopes of our patient recipients. Our promise of doing more with life reflects our unwavering focus on integrity, quality, safety, and respect today, and into the future.
Asia Pacific Association of Tissue Banking
A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.
SpikeNET is a program designed for simulating very large networks of asynchronous spiking neurons. Neurons are simulated with a limited number of parameters that includes classic properties like the post-synaptic potential and threshold, but also more novel features like dendritic sensitivity. SpikeNET can be used to simulate networks with millions of neurons and hundreds of millions of synaptic weights. Optimization of computation time and the aim of real time computation has been one of the driving forces behind the development of SpikeNET. It works on Unix. What SpikeNET can do * Perform image processing using biologically plausible network of neurons. * Simulate millions of integrate-and-fire neurons organized in retinotopical maps. * Connect these neuronal maps using projection files, and regroup common synaptic weights to save memory in order to be able to declare several hundreds of billions of synaptic connections. * Convert gray level images into lists of spikes (also SpikeNET can perform a variety of preprocessing on the input images). * Implement a complex mechanism for projection between neuronal maps of different sizes. * Implement supervised learning. * Implement the efficient neuronal Rank-Order-Coding scheme (optional)
MaxSprout Tool for Reconstruction of 3D coordinates from C(alpha) trace
A database algorithm for generating protein backbone and side chain coordinates from a C(alpha) trace. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimized in rotamer space using a rough potential energy function to avoid clashes.
Commercial tissue bank focused on human tissues.
The MITRE Corporation is a not-for-profit organization chartered to work in the public interest. As a national resource, we apply our expertise in systems engineering, information technology, operational concepts, and enterprise modernization to address our sponsors'' critical needs. MITRE manages Federally Funded Research and Development Centers (FFRDCs): one for the Department of Defense (known as the DoD Command, Control, Communications and Intelligence FFRDC), one for the Federal Aviation Administration (the Center for Advanced Aviation System Development), one for the Internal Revenue Service and U.S. Department of Veterans Affairs (the Center for Enterprise Modernization), and one for the Department of Homeland Security (the Homeland Security Systems Engineering and Development Institute). We believe that each FFRDC benefits from being part of an independent, not-for-profit company managing multiple FFRDCs. MITRE also has its own independent research and development program that explores new technologies and new uses of technologies to solve our sponsors'' problems in the near-term and in the future. MITRE has 7,000 scientists, engineers and support specialists65 percent of whom have Masters or Ph.D. degrees. Staff members work on hundreds of different projects across the company, demanding a high level of technical, operational, and domain knowledge. The MITRE Corporation has two principal locations: Bedford, Massachusetts, and McLean, Virginia. MITRE also has additional sites across the country and around the world.
A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Boston University Alzheimer's Disease Center
The goal of the Alzheimers Disease Center is to help reduce the human and economic costs associated with Alzheimers disease through the advancement of knowledge. The primary missions of the Center are to: conduct and facilitate cutting-edge Alzheimers disease research; enhance clinical care for Alzheimers disease patients and their families; and provide education regarding Alzheimers disease to both professional and lay audiences. The Center is made up of a multidisciplinary group of professionals dedicated to research, clinical care, and education.
A federally designated, non-profit organ procurement organization that coordinates organ and tissue donation in the six New England states and Bermuda.
PathServe Autopsy And Human Tissue Bank is a tissue supplier for bioresearch and educational institutions. It was established in 1990 in order to better satisfy the needs of Bay Area hospitals using inexpensive and reliable postmortem examinations. Today we''ve grown into a multidepartmental organization; serving nationwide as a human tissue supplier to biotech and neuropathological research institutions as well as a centralized autopsy provider to private citizens and local hospitals.
OKCAM: Ontology-based Knowledgebase for Cell Adhesion Molecules
OKCAM: Ontology-based Knowledgebase for Human Cell Adhesion Molecules
OKCAM (Ontology-based Knowledgebase for Cell Adhesion Molecules) is an online resource for human genes known or predicted to be related to the processes of cell adhesion. These genes include members of the cadherin, immunoglobulin/FibronectinIII (IgFn), integrin, neurexin, neuroligin, and catenin families. Totally 496 human CAM genes were compiled and annotated. We have mapped these genes onto a novel cell adhesion molecule ontology (CAMO) that provides a hierarchical description of cell adhesion molecules and their functions. It is intended to provide a means to facilitate better and better understanding of the global and specific properties of CAMs through their genomic features, regulatory modes, expression patterns and disease associations become clearer. You may browse by CAM ontology, Chromosomes and Full Gene list.
UC Davis Alzheimers Disease Center - Resources
University of California Davis Alzheimer's Disease Center - Resources
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Support research in Alzheimer's disease (AD) offering pilot grants, recruitment of research subjects, access to database, tissue samples, and statistical and research study design consultation for investigators. The scientific effort of the program seeks to: promote research directed at understanding factors that influence the expression and progression of Alzheimer's disease; develop and maintain cohorts of carefully diagnosed and well characterized research subjects available for research studies on Alzheimer's disease and dementia; provide support to investigators in subject recruitment, clinical research, experimental design, and statistical analysis of data; and maintain a variety of samples (brain, DNA, serum) and an extensive electronic database suitable for developing new research and supporting existing programs.
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
An algorithm for de novo genome assembly with short paired-end reads.
dictyBase - Teaching Tools Using Dictyostelium discoideum
Teaching Tools Using Dictyostelium discoideum
Dictyostelium discoideum is a great organism to use to teach cellular biology. It exhibits very interesting behaviors, such as chemotaxis and phagocytosis, that can readily be studied in standard laboratories without the need for expensive equipment. Lists of labs being used in real courses settings and all necessary information for performing those experiments are provided. Major headings: * Dictyostelium cell biology course, by Dr. David Knecht, University of Connecticut * Dictyostelium cell biology, by Dr. Derrick Brazill, Hunter College, New York * Report on the number of cells in a slug, contributed by John Bonner * Practical on chemotaxis, by Dr. Thierry Soldati, University of Geneva * Comments from Researchers * References suggested by contributors
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. A commercial tissue bank focusing on human tissue.
Asterand: Partners in Human Tissue Research
Provides human tissue for drug discovery scientists. * Human Biospecimens: Frozen & Fixed Human Tissues; Human RNA/DNA; Human Primary Cells / Cell lines; Custom Procurement; Oncology tissue, biofluid and RNA sets at special prices * Human Tissue-Based Services: Gene Expression, Molecular Pathology, Biochemical Pharmacology, Metabolism and Toxicity * Predictive Human Disease Models
eVOC (Expressed Sequence Annotation for Humans)
Expressed Sequence Annotation for Humans
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.
Molecular Biology news and views for research scientists and advanced students. Keep up-to-date on current research, forthcoming conferences, hot research topics, high impact publications, and much more.
Secure seed bank on the Norwegian island of Spitsbergen in remote Arctic Svalbard archipelago to preserve wide variety of plant seeds that are duplicate samples, or "spare" copies, of seeds held in gene banks worldwide. The seed vault is attempt to ensure against loss of seeds in other genebanks during large-scale regional or global crises.
The Human Proteome Organisation (HUPO) is an international scientific organization representing and promoting proteomics through international cooperation and collaborations by fostering the development of new technologies, techniques and training.
A portal that allows users to track specific words, phrases or nearby relationships from social media sources including Twitter, Digg and others. Datasift aggregates, filters, records, and analyzes real-time data from a variety of social sources using our Curation Stream Definition Language (CSDL) allowing customers to curate their own news.
Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements.
Proteomic Standard Initiative for Molecular Interaction
Proteomics Standards Initiative Molecular Interaction XML Format Documentation
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. As a first step, the PSI is developing standards for two key areas of proteomics: mass spectrometry and protein-protein interaction data. The document describes the molecular interaction data exchange format. PSI is following a leveled approach to building this specification. Level 1 will describe protein interactions at a basic level that covers a large amount of currently available data. Subsequent levels will add capability to represent new molecular interaction information that the community wishes to exchange. The scope of PSI MI is currently limited to protein-protein interactions. Other molecules, such as small molecules, DNA and RNA maybe taken into account in the future. The PSI MI format is a data exchange format for protein-protein interactions. It is not a proposed database structure. The purpose of the document is to describe the general structure of the PSI MI XML specification in a more user-friendly manner than the specification does itself. PSI MI was designed by a group of people including representatives from database providers and users in both academia and industry. PSI MI is supported by the DIP, MINT, IntAct, BIND and HPRD databases.
Austrailasian Leukemia and Lymphoma Tissue Bank
CARTA is developing two virtual libraries of books relevant to Anthropogeny * Library of Anthropogeny: A collection of book titles on human origins and human evolution, arranged chronologically. * Library of Primatology: A collection of book titles on non-human primate evolution, including basic biology, ecology and behavior. A listing of the book titles are made available for public interest.
The new NTNU Systems Biology website showcases the different systems biology efforts at NTNU. Regular updates on new initiatives and advertisements for new PhD and Postdoc vacancies in systems biology will be posted.
A web server interface of BioMart software and provides a unified view over disparate data sources that enable bioscientists to retrieve data from one or multiple sources in a simple and efficient way. This MartView web server features seamless data federation making cross querying of data sources in a user friendly and unified way. Data sources include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase, etc. The web server not only provides access through a web interface, it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web services.
T-REX: Software for the processing and analysis of T-RFLP data
T-REX is a free, platform-independent online tool that allows for an integrated, rapid, and more robust analysis of T-RFLP data. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model.
Boyce Thompson Institute for Plant Research
BTI is unique in being a private, not-for-profit research institute dedicated to plant biology, and located on a major university campus. Its mission is to advance and communicate scientific knowledge in plant biology to improve agriculture, protect the environment, and enhance human health. The institute was founded in Yonkers, New York, next to the home of its benefactor, William Boyce Thompson. In the mid-1970''s, however, it was recognized that a physical presence on a university campus would catapult the institute to a higher level of research, and the Cornell affiliation was born. BTI hires its own faculty, postdoctoral scholars and technicians, but also hosts undergraduate and graduate researchers from Cornell. BTI faculty generally have adjunct appointments at Cornell, and participate in graduate training and other university affairs. As envisioned in the Agreement of Affiliation, the partnership is advantageous for both parties, and contributes to a singularly strong environment for fundamental plant research on the campus. William Boyce Thompson founded BTI in 1924 on the premise that basic plant research leads to real benefits for people. Many potential applications of BTI research are to improve crops by increasing yield or nutritional content, or decreasing the need for harmful fertilizers and pesticides. Other research could lead to inexpensive plant-made vaccines, or even shed light on the human immune system. With aims like these in mind, scientists at BTI study life at the scale of genes and proteins to learn about processes such as how plants detect light, or how they respond when aphids bite into them. Along with research, BTI''s mission includes environmental responsibility and outreach to teachers, students, and community members. Though it remains an independent, non-profit institution, BTI is affiliated with Cornell University and is located on its Ithaca, New York campus.
Tissue bank that provides samples and associated clinical information to associated researchers.
University of Foggia, located in Foggia, Italy, was founded in 1991 and was fully recognized in 1999.
Textensor Limited specializes in software development and consulting related to interactive web based information management systems, web services, data modeling, and scientific computing. Our flagship product, a.nnotate.com, was launched in January 2008. It allows on-line review, annotation and discussion of web pages and a wide range of document types, including PDF and DOC, via a web browser. In April 2007 we launched PublicationsList.org to facilitate access to scientific research papers. It allows researchers to easily keep complete and reliable records of their research output on the web and gained more than 3000 users in the first 8 months. In 2005, Textensor won a SMART:Scotland award for a pilot study into techniques for authoring structured content from text. The first commercial product developed from this technology is a.nnotate.com. Recent consultancy clients include the University of Edinburgh for the development of PSICS, the Parallel Stochastic Ion Channel Simulator, the Okinawa Institute of Science and Technology for prototype code for stochastic diffusion, Memosyne Ltd for development of on-line memory tests for children, and Pearson Assessment for implementation of the Automated Working Memory Assessment.
Registry to assist individuals conceived as a result of sperm, egg or embryo donation that are seeking to make mutually desired contact with others with whom they share genetic ties. They are all about educating, connecting, and supporting donor families. Without any outside support, the DSR has single-handedly pioneered a national discussion about the donor conception industry and families, with it''s many media appearances and interviews. DSR advocates for the right to honesty and transparency for donor kids, and for social acceptance, legal rights and valuing the diversity of all families. The DSR''s core value is honesty, with the conviction that people have the fundamental right to information about their biological origins and identities. The donor conception industry is largely a for-profit enterprise, and after the product has been purchased, most doctors, clinics, egg donation agencies and cryobanks do not engage in discussions and activities which acknowledge the humanity and rights of the donor-conceived. It is our mission to bring these concepts to the public arena for discussion, as has been done in many European countries, as well as New Zealand and parts of Australia. Although you do not need to make a posting to browse the database, it is strongly recommended. Creating a posting in our database is the first step to ensuring the best possible chances of connecting with your biological relatives. If two users with the same donor number browse, but neither post, the connection cannot be made. Many folks are out there waiting to see someone else post for their donor number first! The DSR hope that this will be the first step in connecting with your donor relatives, but please always exercise sensible caution when making contact with those you meet through any internet website, including the DSR.
Provides sterile biologic implants of human bone and tissues used in spine, sports medicine, orthopedic, dental and other specialty surgeries.
Cognitive Daily: A new cognitive psychology article nearly every day
A collection of blood samples and health information donated by volunteers, not focusing on any specific disease. Unlike many biobanks already in existence at Mayo Clinic and elsewhere, the Mayo Clinic Biobank is NOT focused on any particular disease. Rather, this biobank will collect samples and health information on patients and volunteers regardless of their health history. The only requirement is that they be 18 years of age or older, have a Mayo Clinic number, and be able to give informed consent. Once a participant becomes a part of the Biobank, they will be a part of ongoing health research conducted at Mayo Clinic indefinitely. The Biobank was established at Mayo Clinic, Rochester, and recruitment began in April of 2009. The goal of this project is to enroll 20,000 Mayo Clinic patients over the course of a three-year period in an effort to support a wide array of health-related research studies throughout the Institution.
WebHealth Wiki is a medical encyclopedia anyone can edit. Major topics include: * Abdominal Pain * Anemia * Arteriosclerosis * Arthritis * Cancer * Chromosomal Abnormalities * Dentistry * Dermatology * Dieting * Digestive System * Drug Addiction * Ear, Nose, Throat * Eye Disease * Fitness * Heart Attack * Heart Disease * Hormones * Hypertension * Infectious Diseases * Lung Disease * Lyme Disease * Men''s Health * Mental Illness * Neurological Disorders * Women''s Health
GeneTests: Clinical Genetic Information Resource
The GeneTests Web site, a publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers, is available at no cost to all interested persons. By providing current, authoritative information on genetic testing and its use in diagnosis, management, and genetic counseling, GeneTests promotes the appropriate use of genetic services in patient care and personal decision making. At This Site: * GeneReviews: Expert-authored peer-reviewed disease descriptions * Laboratory Directory: International directory of genetic testing laboratories * Clinic Directory: International directory of genetics and prenatal diagnosis clinics * Educational Materials: Illustrated glossary, information on genetic services, PowerPoint presentations, annotated Internet resources We comply with the HONcode standard for trustworthy health information.
The mission of the Cystic Fibrosis Foundation, a nonprofit donor-supported organization, is to assure the development of the means to cure and control cystic fibrosis and to improve the quality of life for those with the disease. The Foundation is the leading organization in the United States devoted to cystic fibrosis. It funds and accredits more than 115 CF care centers, 95 adult care programs and 50 affiliate programs, and more than 75 chapters and branch offices nationwide. The Cystic Fibrosis Foundation is one of the most efficient organizations of its kind and is an accredited charity of the Better Business Bureau''s Wise Giving Alliance. Until we conquer this disease, our team will work tirelessly to extend and enhance life for those with cystic fibrosis by functioning as: * Scientific pioneers, blazing new trails in CF research; * Fund-raisers, securing the money needed to support our efforts; * Advocates, keeping CF a top priority in government, industry and research; * Investors, funding drug discovery and development; * Caregivers, linking patients and families to specialized CF care; and * Family, offering support, information and resources.
OBIWarehouse (Open Biological Warehouse) aims at integrating several biological data sources into a unified database. Content includes 3D structural data, Protein-related data, Metabolic-related data, Genomic-related data, and Biological classification.
Overall aim of the LifeLines Study is to unravel the interaction between genetic and environmental factors in the development of multifactorial diseases, their concurrent development in individuals and their complications as a complex trait. The LifeLines database contains questionnaire data, physical measurements and biological samples from different health examinations. Collaboration is encouraged as it helps to maximize the scientific value of the wealth of epidemiologic data made possible by the participation of more than 165,000 individuals in the LifeLines Cohort Study. Primary objectives of the LifeLines Cohort Study are: a. Which are the disease overriding risk factors which predict the development of a multifactorial disease during lifetime? b. How are these universal risk factors modified, or what determines the effect of a universal risk factor in an individual? Specific research questions will focus on risk factors and modifiers (genetic, environmental and combined or complex factors) for single and multiple diseases. In addition to co-morbidity, LifeLines focuses on co-determinants. The primary endpoints include measures of aging, metabolic and endocrine diseases, cardiovascular and renal diseases, pulmonary and musculoskeletal diseases, and psychopathology. Secondary aims include the assessment of the prevalence and incidence of multifactorial diseases, their risk factors and their treatment in individuals as well as in families. The burden of disease for the society will be quantified in terms of care needed, and total costs of care. Until November 3, 2011, almost 68,000 subjects have been included in the study. The 60,000th participant was screened in the beginning of September 2011. Recruitment rate at present is between 700 and 800 subjects per week. The laboratory measurements which are performed has changed. As of October 2011, LifeLines will continue to measure: hematologic parameters, including hemoglobin, white blood cells, platelets, WBC differentiation, blood glucose, cholesterol, HDL-cholesterol, triglycerides, serum creatinin and sodium/potassium. Liver enzymes, thyroid hormones, calcium, phosphate, albumin, uric acid and microalbuminuria will not be measured routinely. The samples that are available for almost all participants, are: # serum (taken either with or without gel separator) # EDTA plasma # citrate plasma # DNA # early morning urine sample # urine samples of 24-hour urine collection Any researcher who is member of an internationally recognized academic institution and who is interested in utilizing the research possibilities, data and materials of LifeLines may apply for access. The applicant who is acting as Principal Investigator must be connected to a department or institution with the competence to carry out the research project to term. A contract will give the right to use the data for a pre-determined period of time. This contract also comprises the costs for the LifeLines Biobank which the investigator needs to reimburse. To apply for access, refer to the electronic application process.
Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.
Software providing a method that eschews the traditional graph-based approach in favor of a simple 3'' extension approach that has potential to be massively parallelized.
A quality-value guided de novo short read assembler.
Data and information collection and repository for biological activities of small molecules and small interfering RNAs (siRNAs) hosted by the US National Institutes of Health (NIH). Used to select and summarize the bioactivities of tested substances.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. Features include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in ''Nice views'', SRSQuickSearch bookmarklets. Quick Searches allow users to make a number of searches without needing to learn how to use SRS in depth. The searches query some of the common databanks without having to go and select them explicitly and without the need to understand the SRS Query Forms. Quick Searches can be performed from either the Start page (when you first open SRS) or the SRS Quick Search page (when you are already in a project). SRS also has the ability to search for links between your current results and related information in other databanks. Additionally, it is able to analyze the results of your search using many bioinformatics analysis tools or applications. This enables you to seek out further information that may be relevant to your initial search.
A database of 250 recordings of 3-lead ECGs, ABP, PAP, CVP, respiration, and airway CO2 signals from patients in critical care units; some recordings include intra-cranial, left atrial, ventricular and intra-aortic pressure waveforms.
Developmental FunctionaL Annotation at Tufts
We are an interdisciplinary team dedicated to annotating gene function related to human fetal development. We are contributing new functional annotation to the Gene Ontology, curating and mining gene sets suitable for the interpretation of developmental genomic data, and creating the computational tools needed to apply genomics for better understanding the molecular mechanisms of human development. Our GO annotation is in the process of being incorporated into the GOA public release. The GONE (Gene Ontology Non-Eligible) database is where we store annotations relevant to our research but that don''t quite meet GOA''s standards. Usually an annotation falls into this category because either the gene/protein described is a family of genes/proteins rather than a specific one, there is no UniProt ID to identify the gene/protein in the system, a GO term does not yet exist to describe the particular function, process, or location of the gene/protein, the species is not clearly identifiable in the paper, or the evidence is not as reliable (GO evidence codes TAS and NAS). As individual annotations these are more suspect than current GO annotation. However, for functional analysis of expression data, these gene sets can be valuable even with a certain amount of noise. We also include here a link to the supplementary data from our forthcoming PSB 2011 paper on gene set mining.
TESS: Transcription Element Search System
TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest. Search for CRMs Genome-wide: TESS now has the ability to search whole genomes for user defined CRMs. Try a search in the AnGEL CRM Searches section of the navigation bar.. You can search for combinations of consensus site sequences and/or PWMs from TRANSFAC or JASPAR. Search DNA for Binding Sites: TESS also lets you search through your own sequence for TFBS. You can include your own site or consensus strings and/or weight matrices in the search. Use the Combined Search under ''Site Searches'' in the menu or use the box for a quick search. TESS assigns a TESS job number to all sequence search jobs. The job results are stored on our server for a period of time specified in the search submit form. During this time you may recall the search results using the form on this page. TESS can also email results to you as a tab-delimited file suitable for loading into a spreadsheet program. Query for Transcription Factor Info: TESS also has data browsing and querying capabilities to help you learn about the factors that were predicted to bind to your sequence. Use the Query TRANSFAC or Query Matrices links above or use the search interface provided from the home page.
Adverse reaction/vaccine damage database
Database of case reports of adverse reactions to vaccinations. There are 806 reports (May 2013). If you would like to report a case, please go to report your own vaccine reaction. The user may search by keywords or sort by vaccine, country, age, outcome, gender and hospital admission.
Commercial tissue bank for human tissues.
Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers.
Microarray Experiment Functional Integration Technology
MEFIT is a Microarray Experiment Functional Integration Technology. Given any amount of microarray data, it predicts the probability of pairwise functional relationship for any gene pair within individual biological functions. This web site makes the results of this evaluation available for download and provides an online view of the test set predictions based on hierarchical clustering. As a framework, MEFIT uses the results of many microarray experiments in combination with known biological process annotations (drawn from the Gene Ontology, KEGG, MIPS, or a biologist''s own pathways of interest) to predict new gene pair functional relationships within the given biological functions. Or in other words, MEFIT is a system that takes microarray results and known functional annotations as inputs and produces predicted gene pair functional relationships as output. To make these predictions, MEFIT uses a Bayesian network that consumes microarray data as input observations and produces predicted functional relationships through a single unobserved (except during training) node. Furthermore, to make predictions within the context of individual biological functions, a single Bayesian network structure is replicated once per function of interest. These networks with identical structure are then trained using known functional annotations such that each function''s network learns its own set of conditional probabilities. These probabilities encode how predictive each microarray experiment is of a particular function; for example, a sporulation time course might be very predictive of meiosis, but not much help in determining which genes perform ATP synthesis. We''ve evaluated this system using a collection of 40 microarray data sets and 200 biological processes. Select a biological function from the menu to view the results of clustering the S. cerevisiae genome using MEFIT''s test set predictions within that function as a similarity metric. Alternatively, enter a gene name or ORF identifier to list only functions in which that gene is predicted to be active. We are currently able to offer for download: The MEFIT README file, a Windows version and Linux version.
Mayo Validation Support Services Biobank
Mayo Validation Support Services Quality Biospecimens
Mayo Validation Support Services Biospecimens
A core laboratory facility provides high-volume, high-quality tissue and biospecimen preparation and processing in support of Mayo research. Mayo Validation Support Services utilizes these resources to deliver extensive validation capabilities specific to individualized Sponsor requirements. Medical scientific expertise at Mayo Clinic allows for unique collaborations combining quality biospecimens linked to comprehensive clinical outcomes. Biospecimens can be accessed via archives or prospectively collected via individualized standard operating procedures. Patient information for all biospecimens is protected through oversight by an Institutional Review Board (IRB). Specimens may be collected and/or processed in a variety of customized formats for individual collaborations. Typical formats include: * Specimen Processing: Tissue RNA/DNA extraction capabilities, Paraffin and frozen sectioning, Immunostaining, Digital imaging, Laser capture microdissection, Tissue microarray construction, Preparation of protocol-collected tissue (FFPE, OCT, Snap-frozen, PBS) * Blood: Circulating tumor cells, Serum, Plasma, PBMC, Whole blood for FACS analysis, Blood smears * Other: Induced sputum, Saliva, Buccal swabs, Lip biopsies, Colonoscopy biopsies, Synovium, Stool, Urine Biospecimens located within archives are well-characterized and associated with phenotypic information. Multiple types and formats of biospecimens are available for customized validation purposes.
A provider of bio-implants and organs for transplantation and tissue banking services.
Multiple Sclerosis Research Australia Brain Bank
Biomaterial supply resource which provides high quality and well-chracaterized brain tissue samples for MS research. Registered MS brain donors and their families are kept up to date on the latest progress in MS research.
A biobank created from a cross-sectional population of a town in Sweden. The Medical Biobank is mainly based on three cohorts: The V��sterbotten intervention cohort, the MONICA-cohort, and the Mammary screening cohort. These sub-cohorts together are named Northern Sweden Health and Disease Study Cohort (North Health). These sub-cohorts together is named Northern Sweden Health and Disease Study Cohort (North Health). Originally, the V��sterbotten Intervention program (VIP) is a long-term project intended for health promotion of the population of V��sterbotten. All individuals 40, 50 and 60 years of age in the population of the county are invited for screening (approx. 254.000 inhabitants). They are asked to complete a questionnaire concerning various lifestyle factors including diet. They are also asked to donate a separate blood sample to the Medical Biobank for freeze storage for later research purposes. The project started in 1985 and the cohort covered in December 2002, 74,000 individuals, of whom 67,000 had donated blood samples. The material is supplemented with population based samples from a local mammary screening (44,000 sampling occasions, 25,700 unique individuals) and from the Northern Sweden MONICA Project (11,500 sampling occasions, 7,500 unique individuals). The total cohort contains at the moment 85.000 unique individuals with 130.000 sampling occasions. The VIP and MONICA cohorts are population based and the mammary screening cohort are nearly population based. Follow-up: * For the VIP-cohort a second sample (and questionnaire) is collected with a 10-year interval of the individuals within the cohort. * Repeated sampling was performed in the MONICA project in 1999 on individuals participating in 1986, 1990, and 1994. * From 1997 repeated screening has started within the mammary screening program with sampling every second year, in the age group 50-69 years within the county. Biobank content: * Life-Style Questionnaire: Every attending subject is asked to answer a questionnaire, which in the VIP and MONICA-projects includes questions about education, occupation/working conditions, daily habits including smoking, diet, etc and in the mammary screening cohort on reproductive conditions. The dietary questionnaire has been validated twice. The data from the questionnaires, as well as from results from the biobank, are kept in a database for future research purposes. The questionnaires in the VIP and the MONICA project are optically read. * Measurements: Blood Pressure, Anthropometry, Glucose Tolerance Test, Blood Lipids * Blood Samples: The attendants are asked for their willingness to donate a sample of 20-ml whole blood for future analyses. The sample is taken after 4 hours of fasting or in the morning after an over night fasting (most samples) in the VIP and MONICA cohorts. The 20-ml sample is divided into 10 subsamples consisting of 6 plasma, 2 leukocyte (buffy coat) and 2 erythrocyte samples. All material is frozen at -80 degrees C. The organization of the bank is elaborated with specially trained staff and an organization of transport-, storage- and security facilities. For DNA handling a specialized laboratory has been built up. * End-points: Mortality, Cancer events, Cardiovascular events, Other morbidity, Other registry-based follow-up * Registries: At regular intervals the cohort is scanned for incident myocardial infarctions (MI) and stroke utilizing the Northern Sweden MONICA registry and for cancer using the regional cancer registry. In the future the same procedure will be applied also on other registries e.g. diabetes, osteoporosis, dementia.
Data analysis service for the standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. It identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. New functionalities were added through a complete rewrite in Java. IMGT/V-QUEST analyses batches of sequences (up to 50) in a single run. IMGT/V-QUEST describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST can detect insertions and deletions in the submitted sequences by reference to the IMGT unique numbering. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions, and IMGT/Automat for a full V-J- and V-D-J-REGION annotation. IMGT/V-QUEST displays, in ''Detailed view'', the results and alignments for each submitted sequence individually and, in ''Synthesis view'', the alignments of the sequences that, in a given run, express the same V gene and allele.
A de novo whole-genome shotgun (WGS) DNA sequence assembler.
A De Novo Next Generation Genomic Sequence Assembler Based on String Graph and MapReduce Cloud Computing Framework.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.
A new De Novo DNA sequence assembler based on global search-methods in order to contain the complexity of the assembly problem.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data.
A software package designed for the downstream analysis of short read mapping data produced by the ABI SOLiD and Illumina sequencing platforms.
A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes.
A software program to detect SNPs and short indels from pooled sequencing data generated using next-generation sequencing instruments.
A computational tool for calculating probability of variants in family-based sequencing data.
A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.
Software that identifies and annotates mutations in next-generation sequencing projects.
A GLF-based variant caller for next-generation sequencing data.
MoDIL: Detecting INDEL Variation with Clone-end Sequencing
Software for a novel method for finding medium sized indels from high throughput sequencing datasets.
MISA - MIcroSAtellite identification tool
Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.
SSR Locator - Simple Sequence Repeat Locator
A software tool for detection and characterization of micro- and minisatellites in DNA sequences.
SSR_pipeline: Computer Software for the Identification of Microsatellite Sequences from Paired-End Illumina High-Throughput DNA Sequence Data
Software for the Identification of Microsatellite Sequences from Paired-End Illumina High-Throughput DNA Sequence Data
An algorithm for de novo detection and alignment of repeats in sequences based on K-means algorithm.
Trhist - a tandem repeat profiler in personal genomes
A software tool for finding significant tandem repeats using short reads.
AgileVariantMapper - Autozygosity mapping using Next generation sequence data
Software that visualises sequence variant data from whole exome data, so that it is possible to identify autozygous regions in consanguineous individuals.
Homozygous Stretch Identifier from next-generation sequencing data
HomSI - Homozygous Stretch Identifier from next-generation sequencing data
A software tool that identifies homozygous regions using deep sequence data.
A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral.
Cologne University Protein Stability Analysis Tool
CUPSAT: Cologne University Protein Stability Analysis Tool
A tool to predict changes in protein stability upon point mutations.
A web tool for genome-wide annotation of human SNPs.
Multivariate Analysis of Protein Polymorphism
Multivariate Analysis of Protein Polymorphism:MAPP
Java program that predicts the impact of all possible amino acid substitutions on the function of the protein., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
mCSM: predicting the effect of mutations in proteins using graph-based signatures
Data analysis service to the study of missense mutations which relies on graph-based signatures.
Evaluates disease-causing potential of sequence alterations.
Web application tool developed to classify an amino acid substitution as disease-associated or neutral in human.
Software that analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.
nsSNPAnalyzer: predicting disease-associated nonsynonymous single nucleotide polymorphisms
A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect.
An approach to uncover driver genes or gene modules.
Predictor of human Deleterious Single Nucleotide Polymorphisms
A software aimed at the annotation and prediction of pathological mutations.
A toolkit for prioritizing SNVs and indels from next-generation sequencing data.
Offers the researchers an automatic pipeline to predict the disease-association of SAPs.
SNAP - Effects of Single Amino Acid Substitutions on Protein Function
A method for evaluating effects of single amino acid substitutions on protein function.
A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis.
TRANSformed Functional Impact for Cancer
A method to transform Functional Impact scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to different functional classes.
A fully automated software tool which is available for Linux to investigate associations between a diplotype group and a phenotype in linear or logistic regression.
Expectation-Maximized INtegreative Imputation
Expectation-Maximized INtegreative IMputation (EMINIM)
A software tool for imputation of unobserved genotypes using a set of reference haplotype panel at a higher-density SNP set such as HapMap, and lower-density genotypes of a target individual using such as genotyping arrays.
A max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual.
HAplotype inference using Reference and Sequencing tecHnology
Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data.
HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data
Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data.
Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals.
A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees.
392 phylogeny software packages and 54 free web servers describing all known software for inferring phylogenies (evolutionary trees). Submissions are welcome. Programs are listed by methods available, by computer systems on which they work, cross-referenced by method and by computer system, by ones which analyze particular kinds of data, to show the most recent listings, or to show ones most recently changed.
NHLBI Grand Opportunity Exome Sequencing Project
NHLBI Grand Opportunity Exome Sequencing Project (ESP)
Project focused on understanding the contribution of rare genetic variation to heart, lung and blood disorders through the sequencing of well-phenotyped populations.
PhenCode: Paving the Path between Phenotype and Genome
A collaborative project to better understand the relationship between genotype and phenotype in humans that connects human phenotype and clinical data in various locus-specific mutation databases (LSDBs) with data on genome sequences, evolutionary history, and function in the UCSC Genome Browser. PhenCode is a collaboration among researchers at Penn State, UC Santa Cruz, and locus experts at other institutions.
A comprehensive SNP and indel imputability database.
Analysis Workflow and Quality Metric Management for DNA-Seq Experiments.
An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent.
An automated pipeline for detecting genetic variants from High-throUghput GEnome SEQuencing.
It streamlines the next generation sequencing data analysis using BFAST for aligner, SAMTOOLS for SNP caller, and ANNOVAR for annotation.
The product line encompasses distinct products for the specific needs of clinical research, saving time and money while allowing customers to focus on the answers they need most.
A Toolkit for analyzing next-generation DNA Re-Sequencing data.
Cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. Targeted RE-sequencing Annotation Tool that offers a comprehensive, open framework, end-to-end solution for analyzing and interpreting targeted re-sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A complete whole-exome sequencing pipeline and provides easy access through interface to intermediate and final results.
breseq - Determine mutations in evolved microbes from next-generation sequencing data
A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data intended for haploid microbial genomes.
Lille 2 University of Health and Law; Lille; France
Lille 2 University of Health and Law is located in Lille, Nord-Pas-de-Calais, France. University was established in 1562. It is accredited by Ministère de l'Enseignement supérieur et de la Recherche, France.
SVDetect: a tool to detect genomic structural variations from paired-end and mate-pair sequencing data
Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.
Comparative Exome Quantification analyzer
A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads.
A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
A statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies from mapped short sequence reads in exome sequencing data.
A Bioconductor package to estimate Copy Number Aberrations (CNA) in cancer samples.
A novel framework for the identification of CNA events that uses flowcell-to-flowcell variability to estimate the false positive rate and the depth of coverage to finalize copy number calls.
A program to detect copy number variants from short read sequence data.
cnvalidator - a package for identification of high quality copy-number variations
Identifies high quality CNVs based on the density of homozygous SNPs and the ratio of heterozygous SNP reads.
A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation.
An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
Prediction of copy number alterations and loss of heterozygosity using deep-sequencing data.
Copy number estimation from read depth information.
This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome.
Designed to identify CNVs between two genomes.
An algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data.
Japanese national research university located in Chikusa-ku, Nagoya. It was the seventh Imperial University in Japan, one of the first five Designated National University and selected as a Top Type university of Top Global University Project by the Japanese government.
CoRAL - Classification of RNAs by Analysis of Length
Classification of RNAs by Analysis of Length
A machine learning software package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are most important for discriminating different populations of small non-coding RNAs.
Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data.
A web tool for simple microRNA prediction in genome sequences.
A stand-alone software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes.
miRNA sequence profiling (miRspring) document
Pipeline scripts for creating a miRspring (miRNA sequence profiling) document, a new way of sharing and analysing sequencing data for small RNA.
A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions.
ShortStack : Comprehensive annotation and quantification of small RNA genes
A software tool developed to process and analyze small RNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes. ShortStack discovers small RNA ''clusters'' de novo, based on user-set thresholds, and annotates clusters with respect to small RNA size, orientation, and repetitiveness. ShortStack also discovers and annotates MIRNA genes, and other Hairpin-associated small RNA genes. In addition, ShortStack includes a robust method to detect genes producing small RNAs in a phased manner. It outputs a descriptive table of all results, useful genome browser tracks, a table describing the results of the hairpin / MIRNA analysis for each cluster, and detailed text-based alignments of all MIRNAs and hairpin-associated clusters. It can also be run in ''count'' mode, to quantify a set of input loci with genomic coordinates determined a priori by the user. ShortStack is a perl program. Besides perl, ShortStack also requires samtools and the RNALfold and RNAeval programs from the Vienna RNA Package to execute. When used to control the alignment of small RNA data to a reference genome, ShortStack also requires bowtie and bowtie-build. Finally, for optimal results, ShortStack uses a file of inverted repeats produced by the EMBOSS application einverted.
National Institute of Genetics; Shizuoka; Japan
Institute for genetics, through National BioResource Project, collects, preserves, and provides bio-resources (strains, populations, tissues, cells, genes of animals, plants and microorganisms, and information on these materials for R&D use) that are essential for life science research.
RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure
Software / Web Server to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package.
A Bayesian decision fusion algorithm for microRNA target prediction that combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT. Users enter a Ref_seq ID for a query target gene and select a miRNA, which BCmicrO will use in its predictive algorithm. The prediction results can then be downloaded.
C-mii (A software for Computational miRNA identificaion)
C-mii: A software for Computational miRNA identificaion
A software tool for plant miRNA and target identification. C-mii pipelines are based on combined steps and criteria from previous studies and also incorporated with several tools such as standalone BLAST and UNAFold and pre-installed databases including miRBase, UniProt, and Rfam. C-mii provides following distinguished features. First, it comes with graphical user interfaces of well-defined pipelines for both miRNA and target identifications with reliable results. Second, it provides a set of filters allowing users to reduce the number of results corresponding to the recently proposed constraints in plant miRNA and target biogenesis. Third, it extends the standard computational steps of miRNA target identification with miRNA-target folding module and GO annotation. Fourth, it supplies the bird eye views of the identification results with info-graphics and grouping information. Fifth, it provides helper functions for database update and auto-recovery to ease system usage and maintenance. Finally, it supports the multi-project and multi-thread management to improve the computational speed.
Database that hosts elaborated information for both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus.
Manually curated database of experimentally supported animal microRNA targets. Collection of experimentally supported miRNA gene interactions.
Database serving as a tool for microRNA target prediction. The HOCTAR procedure is based on the integration of expression profiling and sequence-based miRNA target recognition softwares. HOCTAR database (db) is the first and unique database to use transcriptomic data to score putative miRNA targets looking at the expression behaviour of their host genes, and it includes and re-analyzes all miRNA target predictions generated by softwares such as miRanda, TargetScan and PicTar. The HOCTARdb contains the prediction target lists for 290 human intragenic miRNAs and also provides tentative assignments of miRNA function based on Gene Ontology analyses of their predicted targets. There are two ways to interrogate HOCTARdb: (i) by selecting a miRNA using either an alphabetically sorted pull-down menu in the microRNA query, or (ii) by typing a target gene symbol (HUGO Gene Name-approved) in the Target Gene Name query.
SICER: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
A clustering software package for identification of enriched domains from histone modification ChIP-Seq data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery.
Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.
Database of computationally predicted targets for microRNAs across many species.
Software for a specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data.
An online database for miRNA target prediction and functional annotations.
Data set of 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs.
A web-based tool used for homologous miRNA gene search in several species. The code is available on request.
An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts.
COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets
Software for detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets.
Catalogs of predicted microRNA targets in worm (based on ce6 genome assembly), fly (dm3), mouse (mm9) and human (hg18). We follow standard seed parameter settings and consider seeds of length 6-8 bases, beginning at position 2 of the microRNA. No mismatches or loops are allowed, but a single G:U wobble is allowed in 7- or 8-mers. In genes missing a 3' UTR annotation, 500 bp (fly), 800 bp (human and mouse) or 300 bp (worm) downstream of the annotated end of the coding sequence were used as the predicted UTR. For each organism, a catalog with zero flank and with a flank of 3 and 15 bases upstream and downstream.
Plant MicroRNA Target Expression Database
A Plant MicroRNA Target Expression Database to study the microRNA (miRNA) functions by inferring their target gene expression profiles among the large amount of existing microarray data. You may also predict your miRNA targets and retrieve their microarray expression data.
dPeak: High Resolution TFBS Identification using ChIP-exo PET and SET ChIP-Seq Data
A high resolution transcription factor binding site (TFBS) identification (deconvolution) algorithm. dPeak implements a probabilistic model that accurately describes ChIP-exo and ChIP-Seq data generation process for both the SET and PET assays.
A Python package for doing RNA-seq and ChIP-seq (hence the dual-use).
Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis).
A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data.
HPeak: An HMM-based algorithm for defining read-enriched regions from massive parallel sequencing data
A Hidden Markov Model-based algorithm for the purpose of defining genome-wide ChIP-enriched peaks in the human genome using short sequence reads.
MICSA: Motif Identification for ChIP-Seq Analysis
Motif Identification for ChIP-Seq Analysis
A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris).
MOdel-based one and two Sample Analysis and inference for ChIP-Seq Data
Software developed as a flexible mixture modeling approach for detecting peaks of one-sample (ChIP sample) or two-sample (ChIP sample and matched control sample) ChIP-seq data.
A software program to call peaks from ChIP-seq data for transcription factor binding sites.
Software for a multi-purpose ChIP Seq peak caller.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A specifically designed version of BSMAP for reduced representation bisulfite sequencing (RRBS).
SIPeS - Site Identification from Paired-end Sequencing
Site Identification from Paired-end Sequencing
An algorithm that allows researchers to identify transcript factor binding sites from paired-end sequencing reads. SIPeS uses a dynamic baseline directly through the piling up of fragments to effectively find peaks, overcoming the disadvantage of estimating the average length of DNA fragments from singled-end sequencing achieving more powerful prediction binding sites with high sensitivity and specificity.
Site Identification from Short Sequence Reads
Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.
A software for determining DNA/protein binding sites from a ChIP-Seq experiment.
Zero Inflated Negative Binomial Algorithm
zinba - Zero Inflated Negative Binomial Algorithm
Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts.
Manorm - a robust model for quantitative comparison of ChIP-Seq data sets
A robust software package for quantitative comparison of ChIP-Seq data sets.
R package for comparative analysis of RNA Polymerase II ChIP-Seq profiles by non-linear normalization.
Provides a solution for the identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries (L1 and L2).
Detects differential binding of transcription factors with ChIP-seq.
Finding differential chromatin modification sites from ChIP-seq data.
R-package for identifying differential ChIP-seq based on an ensemble of mixture models.
A software program which finds sequence elements conserved in a set of DNA sequences.
Arpeggio - Harmonic analysis of ChIP-seq experiments
Software for harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.
ChIPModule: Systematic discovery of transcription factors and their cofactors from ChIP-seq data
A software tool for systematic discovery of transcription factors and their cofactors from ChIP-seq data.
Data analysis service providing a motif discovery platform developed to help biologists to find novel as well as known motifs in their peak datasets from transcription factor (TF) binding experiments such as ChIP-seq and ChIP-chip.
diChIPMunk - motif discovery using dinucleotide PWMs
Software for motif discovery using dinucleotide position weight matrices (PWMs).
A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.
Hypergeometric Optimization of Motif EnRichment
Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.
A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations.
LASAGNA-Search 2.0: Searching for transcription factor binding sites (TFBSs)
LASAGNA-Search: Searching for transcription factor binding sites
Length-Aware Site Alignment Guided by Nucleotide Association Search
An integrated web tool for transcription factor binding site search and visualization. Both the Python Scripts for Offline Scanning and the Python implementation of the LASAGNA algorithm are available., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.
Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria.
Software tool that predicts motifs in full-size peak sets. It performs all steps from motif discovery to visualization of the predicted sites in genome browsers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
TFBSGroup: A Program for Predicting Transcription Factor Binding Sites
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A Software program for Predicting Transcription Factor Binding Sites.
Software for Transcription Factor Flexible Models (TFFMs) that represent Transcription Factor Binding Sites (TFBSs) and are based on hidden Markov models (HMM). They are flexible and are able to model both position interdependence within TFBSs and variable length motifs within a single dedicated framework.
NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model
A command line software tool for accurate placing of the nucleosomes using a Modified Gaussian Mixture Model. It was designed to resolve overlapping nucleosomes and extract extra information (fuzziness, probability, etc.) of nucleosome placement. To achieve this goal the tool clusters the input tags according to Nucleosome Model (see the paper for detailed description) using EM learning process. The tool is written in C++. There are no special requirements except for g++ compiler and *nix environment to compile and use the tool. It was checked to compile using g++ compiler under Ubuntu 11.04 and Mac OS X 10.6
NPS (Nucleosome Positioning from Sequencing)
A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.
A multithreaded Java application for finding positioned nucleosomes from sequencing data.
An R package mapping nucleosome-linker boundaries from both MNase-Chip and MNase-Seq data using a non-homogeneous hidden-state model based on first order differences of experimental data along genomic coordinates.
Software for inferring nucleosome positions with their histone mark annotation from ChIP data. It is a versatile tool that can be used to predict positioned nucleosomes from one or multiple ChIP-seq bam files and it can be also used in conjunction with a control experiment.
A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.
A public database that provides predicted transcription factor (TF) encoding genes annotated in genome sequences of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula.
A phylogeny-based comprehensive database of plant transcription associated proteins.
PlantTFcat: An Online Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool
A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family.
SoyDB: A Knowledge Database of Soybean Transcription Factors
A Knowledge Database of Soybean Transcription Factors. PSI-BLAST is available to find hits from the database.
A public database that provides the complete transcription factor (TF) repertoires of 6 genome sequenced tree species: papaya (Carica papaya), jatoropha (Jatropha curcas), cassava (Manihot esculenta), poplar (Populus trichocarpa), castor bean (Ricinus communis) and grape vine (Vitis vinifera). from annotated genes on each genome.
A hidden Markov model (HMM)-based software to predict clusters RNA motif sites.
Piranha -- CLIP- and RIP-Seq peak caller
A peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample.
An approach for the analysis of two-base encoding bisulfite sequencing data.
Improved mapper for bisulfite sequencing reads on DNA methylation.
QUantification tool for Methylation Analysis
You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis.
Tool that facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization. Download MethMarker or start it directly from within your web browser.
A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets.
Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.
A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
PPSEQ: Parallel Processing for Next-Generation Sequencing (NGS) Analysis
A software suite including a scalable hierarchical multitasking parallel infrastructure and the classical sequencing algorithms.
A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments.
A software tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs.
A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/
Software for a complete CGH and CGH+SNP microarray data analysis and data reporting solution to streamline the day-to-day cytogenetic sample analysis research workflow.
A comprehensive design and analysis tool for setting up and interpreting your microarray experiments.
An R package for analyzing large Affymetrix data sets.
An easy-to-use software tool for analyzing two color copy number alteration arrays from multiple platforms, including Agilent Technologies, Illumina, AffyMetrix, NimbleGen and others.
A software for the analysis and visualization of array CGH data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Software R package dedicated to the analysis of CGH profiles using segmentation models.
Data analysis service enabling users to analyse their array-CGH data with multiple algorithms simultaneously.
A software for detection of DNA copy number alterations (CNAs) from array comparative genomic hybridization (aCGH) data.
Software that estimates copy number and annotates regions with copy number variants(CNV).
A powerful and easy-to-use software package for the analysis of aCGH data, offering an impressive combination of features.
A web-based software tool for the integrative analysis of cancer genomics data. It stores different kinds of downstream processed data from multiple samples in a single database. A powerful search interface allows to dynamically filter the data to be displayed with respect to different criteria. The combination of AJAX technology and a fast visualization engine facilitates a highly dynamic visualization for large amounts of data. FISH Oracle 2 is able to simultaneously display different data sets, thus simplifying their comparison. Filter and display options can be changed on the fly. High quality image export enables the life scientist to easily communicate the results, e.g. in presentations or publications. A comprehensive data administration assures to keep track of the data stored in the database.
A genotyping algorithm for the Illumina Infinium SNP genotyping assay.
Software that integrates single nucleotide polymorphism (SNP) genotyping, copy number polymorphism (CNP) genotyping, rare copy number variation (CNV) identification, and cytogenetic analyses into one application.
A Detection and Visualization software tool for Genomic Variants.
Ginkgo: CGH and Expression Microarray Statistical Analysis and Normalization Platform
A spotted microarray data pre-processing platform featuring analysis functionalities for CGH and expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Tools for microarray quality control and pre-processing.
arrayMagic - two-colour cDNA array quality control and preprocessing
Software providing a collection of utilities for quality control and processing of two-colour cDNA microarray data
A flexible tool for visualizing and analyzing your two-colour microarray slides.
ArrayQuest - An On-line DNA Microarray Analysis System
A web-accessible program for the analysis of DNA microarray data. ArrayQuest is designed to apply any type of DNA microarray analysis program executable on a Linux system (i.e., Bioconductor statistical and graphical methods written in R as well as BioPerl and C++ based scripts) to DNA microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or in a password protected private database uploaded to the center point server. ArrayQuest analyses are performed on a computer cluster.
A set of web-based applications for the analysis of genomic and proteomic data. Asterias combines Python with R and C/C++, using MPI for parallelization, and aspires to become a standard for high-performance, distributed, web-based bioinformatics and biostatistics applications.
A comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software.
An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A user-friendly analysis software for high-throughput data.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 17, 2017. A MAGE-compliant software platform for the collaborative analysis and integration of microarray data.
A drawing software application designed for drawing and analyzing chemical structures and reactions.
Linnaeus Centre for Bioinformatics Data Warehouse
A microarray-experiment oriented warehouse for collections of expression data, integrated with gene annotation profiling and used to support genomic data mining processes. It provides means to access and extract valuable information from a Laboratory Information Management System (LIMS) and makes use of several plug-ins to process and analyze the data. The system consists of two parts: MIAME compliant data storage is handled by the LIMS while data analysis is performed in the DWH. The core of the system is BASE. Accessing LIMS and DWH is accomplished through secure connections.
Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.
Multi-Conditional Hybridization Intensity Processing System
A microarray data warehouse integrated with a software platform for microarray data analysis. It can be used as a LIMS for DNA chip experiments, also. Unlike other microarray data repositories, it entirely dispenses with free-text format, instead holding all the information in a format ready for statistical analysis.
Software providing a workbench for visualization, analysis and storage of microarray data. It features a graphical user interface and supports the development and integration of existing and new analysis methods. Besides the infrastructural core functionality, Mayday offers a variety of plug-ins, such as various interactive viewers, a connection to the R statistical environment, a connection to SQL-based databases, and different clustering methods, including phylogenetic methods. In addition, so-called meta information objects are provided for annotation of the microarray data allowing integration of data from different sources. This meta information can be used to enhance visualizations, such as in the enhanced heatmap visualization. Written in the Java programming language, Mayday is extremely portable and runs on all platforms supporting the Java runtime environment 1.6.
Integrates many useful tools to simplify ChIP-chip analysis for biologists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2021.A computational tool that allows the user to search, visualise and store different data associated with gene expression.
Data analysis server / software designed to test statistical significance of gene microarray data, visualize the results, and provide links to clone information and gene index. Several public datasets are also available.
Remote Analysis Computation for gene Expression data
A collection of web tools designed to assist with the analysis of DNA microarray data and results. RACE performs probe level data preprocessing, quality checks, normalization, and visualization for Affymetrix GeneChips. In addition, it performs clustering and differential analysis of normalized expression levels or ratios for arbitrary platforms, and estimates the false discovery rates in lists of potentially regulated genes. A Gene Ontology (GO)-term analysis assists in the biological interpretation of gene lists. The user can customize each analysis request; upon submission the analysis is executed in a fully automated way., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
SAM: Significance Analysis of Microarrays
Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments.
miRCURY LNA microRNA Array Analysis Software
Software for fast and accurate analysis of miRCURY LNA microRNA Array data.
A Perl based tool for the identification of differentially enriched regions in tiling microarray data.
A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing.
A software package designed to automate the pipeline for analyzing site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray.
A combined database and R package that allows you to investigate the methylation state of regions of interest across the genome.
A GUI software package for analysis of DNA methylation microarray data.
An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite sequencing protocols, but also MeDIP-seq and MBD-seq., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
RPPanalyzer: Reads annotates and normalizes reverse phase protein array data
A statistical tool developed to read reverse-phase protein array data, to perform the basic data analysis and to visualize the resulting biological information.
Oligo and cDNA Microarray Design Software that designs thousands of primers and probes for oligo and cDNA microarrays in seconds.
OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
OligoArray 2.1: Genome-scale oligonucleotide design for microarrays
A free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction.
A free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more��
Picky: Optimal Oligonucleotide Design and Analysis
A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize.
A Java software aimed at providing a framework for design and analysis of sets of oligonucleotide probes for use in multiplex assays for nucleic acid analyses and other purposes.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 1, 2014, A web-based software tool that enables selecting optimal oligos for PCR applications and multiplex detection.
Webserver that can be used to find oligonucleotide probe sets for microarray slides. The probes can be for individual sequences or for clusters of genes. This webserver accepts files up to 200 kb in size in order to minimize the running time. For larger files please download the program.
Recherche et Optimisation de Sondes Oligonucleotidiques
Recherche et Optimisation de Sondes Oligonucl��otidiques
A software to design optimized oligonucleotide probes (size over 25 nucleotides) for microarrays.
balony - Software for the analysis of high-throughput solid media-based screens
Image analysis and data inspection software for agar plates generated in high-throughput yeast genetics and genomics experiments.
Industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and intuitive workflows.
Software package which provides statistics and visualization for analysis of high dimensional quantification data including microarray or RTPCR data or Taqman data, genotype data including SNP or Copy Number data and Next Generation Sequencing data. Provides integrated environment for analyzing and visualizing high dimensional data.
A web-based microarray data management and microarray analysis system for researchers who need to organize microarray data efficiently and get microarray data analyzed instantly.
Powerful, accessible statistical tools for fast visualization and analysis of microarrays - expression arrays, miRNA, exon arrays and genomics copy number data.
Visualize and analyze data generated by all of Illumina''s platforms.
Adjusting batch effects in microarray expression data using Empirical Bayes methods.
A microarray platform that uses the Illumina and Affymetrix GeneChip microarray technology for genome and transcriptome analyses and a web-based database that consists exclusively of high quality Affymetrix data from immunological experiments hosted by a public, non-profit consortium of three scientific public institutions aimed to develop, integrate and disseminate Functional Genomics.
MicroGen - a Web Server for Microarray Experiments
Software application package for a Minimum Information About Microarray Experiments (MIAME) compliant web-based information system for managing all the information completely characterizing spotted microarray experiments and the produced data.
Medical University of South Carolina DNA Microarray Database
Medical University of South Carolina DNA Microarray Project Management System and the MUSC DNA Microarray Database
MUSC DNA Microarray Database and Project Management System
MUSC DNA Microarray Project Management System and MUSC DNA Microarray Database
Database that is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community.
Software for an Active Server Page web interface to a relational SQL database that automates recording scores and linking them with clinical data for future interpretation.
Database for microarray data storage, retrieval, analysis, and visualization.
An interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data.
An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors.
New York University Langone Medical Center Rodent Behavior Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 24,2024. Rodent Behavior Core, located in Berg, is slated to open to the NYULMC research community in September, 2012. The Rodent Behavior Core will provide facilities and equipment for: -Spatial Learning and Memory (Morris Water Maze, Place Preference) -Associative Memory Formation (Fear Conditioning) -Anxiety and Depression (Elevated Plus, Forced Swim, Tail Suspension, Sucrose Preference) -Sensory Motor Gating (Prepulse Inhibition, Acoustic Startle) -Drug Addiction and Withdrawal (Conditioned Place Preference, Locomotor Hyperactivity) -Social Learning (Three Chambered Arena) -Novelty Detection (Objection Recognition) -Motor Learning (Rotating Rod test) -Perseverative Learning (Y-Maze) -Working Memory (Radial Arm Maze) -Real time video tracking to adapt user designed paradigms
The Australian Synchrotron is a source of highly intense light ranging from infrared to hard x-rays used for a wide variety of research purposes. Officially opened in July 2007, the Australian Synchrotron is one of fewer than 40 similar facilities around the world. It is the largest stand-alone piece of scientific infrastructure in the southern hemisphere.
University of Southern California Flow Cytometry Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. USC Flow Cytometry Core Facility offers our extended research community with the technology to selectively analyze and sort specific populations of cells up to Biosafety Level 2 (BSL-2). The USC Flow Core maintains the following devices: Two analytic cytometers (LSR II, CyAn) Two cell sorting cytometers (Aria I, Aria II) One plate imaging system (Cellomics) Available laser lines include: UV (355nm) Violet (405nm) Blue (488nm) Red (633nm) *Both Aria I/II cell sorters are contained in state of the art BioSero Class II Type B Biosafety Cabinets. The USC Flow Cytometry Core has been used by prominent scientists in Southern California to address questions in adult and embryonic stem cell research, regenerative medicine, cellular immunology, cell biology, chemical carcinogenesis, radiology, human tumor cell cycle kinetics, drug efficacy trials, and in characterizing the differences between blood samples between patients and healthy donors. Cell Sorting & Analysis: Monday through Friday 10am - 8pm Consultations: Monday through Friday 11am - 4pm
Provider of in vivo pharmacology services.Pioneer of in vivo phenotypic screening and leader in area of drug repositioning. Its proprietary theraTRACE platform enables identification of new therapeutic potential by systematically screening candidates in diverse array of validated in vivo disease models.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd, 2022. KSF Labs is the virtual/real workshop(s).
An algorithm to inference isoform expression., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Founded in 1995 with intention of making DNA sequencing and genotyping laboratory to provide DNA sequencing and genotyping services for academic institutions or for private companies.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd, 2022.
Full service DNA sequencing and DNA prep provider founded in 2011, located at 85 Bolton Street in Cambridge, MA.
Located in Southern California, USA, Stamford Bioprocess Technologies provides bioprocess and related services for recombinant protein production.
Harvard NeuroDiscovery Center - Enhanced Neuroimaging Core
Harvard NeuroDiscovery Center Enhanced NeuroImaging Core
Core facility that provides access to advanced confocal, multi-photon and wide field microscopy and provides the following services: ImageJ Image Analysis Service. The facility specializes in various forms of fluorescence, brightfield, DIC (Differential Interference Contrast) and live cell imaging. They offer users comprehensive training (data acquisition and image analysis), assistance in the design of experimental protocols and imaging analysis service. Questions regarding cell and tissue fixation techniques, fluorophore selection and immunostaining principles are always welcome, as are requests for instruction in live cell and tissue imaging. They offer flexible and customized training and support to both established and new users throughout the NeuroDiscovery community.
Georgia Genomics and Bioinformatics Core at the University of Georgia
Georgia Genomics and Bioinformatics Core
Georgia Genomics and Bioinformatics Core at UGA
Core laboratory for nucleic acid sequencing and bioinformatics. Used for research support, education, and training. Services include genomic techniques and applications, sequencing technologies, and bioinformatics analyses, writting letters of support for grant applications submitted to funding agencies. GGBC operates multiple platforms for short-, long-, and single-molecule sequencing reads (i.e., Illumina MiSeq and NextSeq, PacBio Sequel, and Oxford Nanopore MinIon).
UC Irvine Transgenic Mouse Facility (TMF)
University of California Irvine Transgenic Mouse Facility
University of California Irvine Transgenic Mouse Facility (TMF)
The Transgenic Mouse Facility (TMF) is a core facility that provides services on a recharge basis for making, breeding, genotyping, importing, and preserving genetically-modified mice and embryonic stem cells. Advice is currently provided at no charge.
Number of core facilities and shared resources developed at University of Miami are available to researchers and trainees. These resources allow centralized access to specialized equipment and services, providing cutting edge technologies, reagents, and special products needed to conduct high quality, interdisciplinary research in cost effective way.
Cornell University Survey Research Institute
Provides survey research, data collection, and analysis services to academic, non-profit, governmental, and corporate clientele. With facility located at Cornell University, SRI possesses extensive capabilities for telephone, mail and web survey data collection. Conducts national and state studies on subjects as the long-term effects of the New York City school-based intervention study on risky behavior among young adults, assessment of prevalence of elder abuse in New York State, the effects of retirement on drinking behavior, health and safety issues of New York City firefighters, business climate assessment for the Division of the Budget of New York State, major trends in the telecommunication industry, rising tuition at universities, how people cope with aging and careers, and topical issues such as support for civil liberties and the war in Iraq. SRI has conducted over 1000 projects to date.
University of Georgia Comparative Pathology Laboratory
The Comparative Pathology Laboratory (CPL) is a service laboratory dedicated to serve the biomedical research community by providing preclinical, R&D, and discovery pathology services. The laboratory is headed by an ACVP (American College of Veterinary Pathologists) board-certified laboratory animal pathologist and its staff has expertise in both small and large laboratory animal pathology.
Indiana University School of Medicine Proteomics Core
Indiana University School of Medicine Proteomics Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. Indiana University School of Medicine Proteomics Core Facility provides protein and proteomic analysis services for protein identification, characterization, and quantification. The Core encourages collaborations that apply the tools of proteomics to cutting-edge biomedical research. Established in 2001, the Core has become a center not only for services but also for collaborative research and development of new technological platforms for proteomic research. The Core is available to Indiana Universities and the wider research community. Over the years, our facility has worked with many pharmaceutical and biotech companies, and developed a number of SOPs for biomarker discovery, mass spec-based protein assays, and biomarker candidate validation. Our major platforms are label-free protein quantification for biomarker discovery and multiple-reaction-monitoring (MRM) for protein assays and biomarker validation. Our goal is to deliver value to our investigators and our community as a world-class proteomics core lab providing services to meet the critical needs of biomedical researchers in life science industries and academia.
IUSM Angiogenesis Endothelial and Pro-Angiogenic Cell Core
Indiana University School of Medicine Angiogenesis Endothelial and Pro-Angiogenic Cell Core
Indiana University School of Medicine Angiogenesis Endothelial and Pro-Angiogenic Cell Core (AEPCC)
IUSM Angiogenesis Endothelial and Pro-Angiogenic Cell Core (AEPCC)
The Angiogenesis, Endothelial & Pro-Angiogenic Cell Core (AEPCC) is a state-of-the-art facility that has been established through the Indiana University Melvin and Bren Simon Cancer Center, a National Cancer Institute-designated cancer center, to conduct validated and highly reproducible in vitro and in vivo angiogenesis, endothelial, hematopoietic and multi-parametric flow cytometry assays and their role in normal and patient-related hematologic and cardiovascular disorders. In addition to possessing the in vitro and in vivo assays that define the endothelial progenitor outgrowth cells that possess in vivo vessel forming ability, the AEPCC recently stringently defined a population of pro-angiogenic and anti-angiogenic circulating hematopoietic stem and progenitor cells (CHSPCs) that has been shown to regulate angiogenesis. Discovery of these novel CHSPC subsets demonstrates the uniqueness and strength of the approach by the AEPCC that requires both phenotypic and functional data to validate specific circulating cells that participate in new blood vessel formation. The specific assays offered by the AEPCC function as quantitative analytical tools, potential biomarkers of several hematopoietic diseases, and as experimental platforms for understanding the basic mechanisms of angiogenesis and the interplay between the endothelial and hematopoietic systems. For example, not only are CHSPCs critical for normal and abnormal angiogenesis, but we and others have reported that certain endothelial cells are critical for CHSPC expansion ex vivo and that endothelial cells promote CHSPC engraftment post-ablation. The AEPCC serves to directly perform all of the assays required to analyze research samples, and as a consultation, education, and new assay development site for scientists within and outside the IU School of Medicine and Indiana University. Furthermore, the AEPCC is one of only five nationally recognized Core Centers of Excellence in Molecular Hematology by the National Institutes of Health and is a certified core of the Indiana Clinical and Translational Sciences Institute (CTSI).
NETZSCH Thermal Analysis Applications Laboratory
NETZSCH Thermal Analysis Applications Laboratories
Develops and manufactures complete high precision instrument line for thermal analysis and thermophysical properties measurement, as well as offering world class commercial testing services in our laboratories. Our instrumentation is employed for research and quality control in polymer sector, chemical industry, areas of inorganic and building materials, and environmental analysis.Customers of our laboratory services stem from wide range of large companies in industries such as chemical, automotive, electronics, air/space travel, racing, and polymer and ceramics.
Louisiana State University Genomics Core Facility
Louisiana State University Pennington Biomedical Research Center Genomics Core Facility
The Genomics Core Facility seeks to achieve high quality research data production through education of core facility users, optimal use of qPCR and RNA/DNA quality and quantity instrumentation, and quality Sanger sequencing, next-generation sequencing, robotics, and microarray services. Services are provided to internal and external researchers.
Indiana University School of Medicine Physiological Proteomics Core Facility
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 23, 2019. Facility enables researchers to identify and quantify proteins in simple or complex samples and characterize protein post-translational modifications or conjugates. PPCF provides the following mass spectrometry-based proteomics services: Protein Identification Protein Quantification Differential Protein Expression Analysis Protein Post-translational Modification Analysis Bioinformatics and Pathway Analysis Biomarker Discovery Please note, a set up fee is applied when the number of samples is less than 10.
Macquarie University Biomolecular Frontiers Research Centre
Macquarie Biomolecular Frontiers Research Centre
Macquarie University Department of Chemistry and Biomolecular Sciences Biomolecular Frontiers Research Centre
MQ Biomolecular Frontiers Research Centre
The Biomolecular Frontiers Research Centre brings together national and international researchers in the molecular and cellular analysis of living systems.
Provides real time gene expression data. Custom designs experiments according to individual needs and specifications. Offers custom designed gene panels.
University of Nevada Reno Labs and Facilities
University of Nevada Reno Labs & Facilities
Nevada Center for Applied Research coordinates access to Shared Research Facilities extensive resource of labs with cutting edge research and development equipment available to internal University community and external clients from industry, government, research organizations and other institutions.In addition to services and instrumentation, we offer support from highly experienced staff with expertise in designing and conducting experiments and analyzing data. Many facilities can also provide training and education upon request.
DDC Medical, division of DNA Diagnostics Center (DDC), provides STR DNA testing, supports Prostate Cancer Foundation (PCF) Cell Line Authentication Initiative (CLAI), by offering free Human Cell Line Authentication and Mycoplasma Detection testing to the PCF’s grant recipients. Provides private DNA paternity and other DNA tests for human and animal testing services accessible to clients all over the world.
Biotechnology company focused on developing robust gene delivery products, by using its proprietary technologies. Since 2004, we have worked with over 300 research labs in 20 different countries to provide gene delivery products and services using many viral platforms including recombinant adenoviruses, adeno-associated virus (AAV) and lentivirus.
University of Nebraska Lincoln Spectroscopy and Biophysics Core Facility
University of Nebraska Lincoln Spectroscopy and Biophysics Core
Core provides instrumentation, training and support for any type of experimental work involving biophysical and spectroscopic measurements. The services that our core provides can be extended to partially purified proteins, whole cell assays and analysis of tissues.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd,2022. Company specialized in industrial applications of electromagnetic radiation produced at synchrotron facilities.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd, 2022. Provides mouse genetic services. PTL develops proprietary technologies for the production of transgenic and genetically modified mice. One of PTL''s key technologies increases gene targeting frequency from 0%-5% to 30%-60% in mouse ES cells. Improvement in gene targeting frequency speeds up the production process of genetically modified mouse models. This translates into less production cost and faster delivery of our products. Genetically modified mouse models are guaranteed for delivery within 12 months or less with PTL''s full gene targeting services.
University of Iowa Magnetic Resonance Research Facility
University of Iowa Carver College of Medicine Magnetic Resonance Research Facility (MRRF)
The University of Iowa MR Research Facility was established in August of 2004 with the acquisition of a Siemens Trio 3T scanner, shared between research and clinical usage. While the Center is within the Department of Radiology, it is run as a Core University facility. The facility is managed on a daily basis by Vincent Magnotta, PhD, Alan Stolpen, MD, PhD, and Dan Thedens, PhD. Oversight is provided by a Research Advisory committee that reviews new project proposals and equipment acquisitions. Since its inception, the equipment managed by the Research Center has expanded. In 2006, a research dedicated Siemens Avanto 1.5T scanner was loaned to the University by Siemens Medical Solutions to support research studies. Then, in 2007 an NIH/NCRR High End Instrumentation grant supported the acquisition of a research dedicated Siemens TIM Trio 3T scanner. Standard operating hours for the research-dedicated 3T TIM Trio scanner are from 8:00 a.m. to 6:00 p.m., Monday through Friday. During this time, a technologist is provided to run the scanner. The shared research 3T TIM Trio scanner is available all day Tuesdays (8:00 a.m. - 4:30 p.m.), and Thursday afternoons (12:00 p.m. - 4:30 p.m.) for research studies. The shared Avanto 1.5T scanner is available Mondays, Wednesdays and Fridays from 2:00 p.m. to 4:00 p.m. The scanners are also available after-hours if technologist coverage is available, or if the user is certified to conduct MR studies on their own. The current rate for scanner usage is $600 per hour and can be scheduled in half hour increments.
Colorado State University EcoCore Analytical Services
EcoCore is one of the Specialized Facilities at Colorado State University (CSU), providing analytical, training and educational services related to ecology and ecosystem research to clients across several colleges at CSU, as well as local federal agencies and other universities and institutes. Our analytical facility is a campus-wide, common-use facility for a broad suite of elemental, molecular, microbial, and isotopic analysis of soil, plant, water and other environmental samples. We provide training and hands-on experience to students, post-docs and scientists on all our instruments while also operating as a service laboratory, offering a variety of analyses on a fee basis. The facility has also a dedicated area designed for teaching, research seminars and small workshops. EcoCore is housed and managed by the Natural Resource Ecology Laboratory (NREL), based in the Warner College of Natural Resources. Our mission is to provide and expand high-quality and cutting-edge capabilities, facilities, and expertise to our scientific community and to facilitate new and emerging research.
Trudeau Institute Contract Research Organization
Trudeau Institute Contract Research Organization (TICRO)
Full-service contract research organization providing high-quality research project execution to both academic scientists and the biopharmaceutical industry. For nearly 50 years, the Trudeau Institute has been a world-renowned research center with a focus towards understanding the immunological, biological and molecular basis of infectious diseases and immune disorders, particularly in the respiratory tract. TICRO works closely with clients to create the comprehensive study design, management, and execution strategies needed to achieve project objectives with exceptional efficiency. Our highly skilled experts are able to anticipate the challenges of infectious disease research and offer clients creative and personalized project design, while maintaining consistent performance with quality-focused SOPs throughout project execution. Our risk assessment experience, project management insights, established processes, and specialized infrastructure enable us to provide clients with high-quality, cost-effective research project design and execution. TICRO offers specialized expertise and facilities for: Immunophenotyping using models of infection and host defense, including murine models of influenza, tuberculosis and pneumonia Immunogenicity and immunotoxicology evaluation of candidate therapeutics, vaccines and adjuvants Preclinical efficacy testing of antibacterials, antivirals and vaccines with microbiological and clinical endpoints KEY CAPABILITIES Mouse models of infection with a broad range of pathogens, including many that target the respiratory tract Animal facilities and technical services, including bio-safety level 2 and 3 suites with select agent capabilities, surgery, rederivation, cryopreservation, breeding and aging Flow cytometry services, including design and execution of multi-parameter phenotyping of low frequency cells and isolation of specific cell populations from infected samples Microscopy and imaging services including advanced histology, immunohistochemistry, immunofluorescence, and imaging Molecular biology services, including investigations of the impact of candidate therapeutics, infectious disease, vaccines, and adjuvants on immune cell function at the molecular and gene expression levels
Contract manufacturing services company, specializing in plasmid DNA manufacturing, protein services and antibody development.Producesg high quality plasmid DNA, proteins, enzymes, antibodies, and other biologicals in support of clients objectives.
The Medical Research Council is a publicly-funded organization dedicated to improving human health. We support research across the entire spectrum of medical sciences, in universities and hospitals, in our own units, centers and institutes in the UK, and in our units in Africa.
U.S. based consulting firm with wet-lab facilities and access to world-class analytic equipment. Areas of expertise include petroleum chemistry, alternative fuels, polymer chemistry, materials chemistry, high throughput reactions screening analytics.
Indiana University School of Medicine Histology Core Facility
Indiana University School of Medicine Department of Anatomy and Cell Biology Histology Core
Indiana University School of Medicine Department of Anatomy and Cell Biology Histology Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 30,2024. The Histology Core of the Department of Anatomy and Cell Biology at the Indiana University School of Medicine provides histological services for basic science (non-clinical) research. Both mineralized (plastic embedded) and soft tissue (paraffin embedded) specimens can be prepared.
Mouse Clinical Institute; Alsace; France
Institut Clinique de la Souris; Alsace; France
Research infrastructure for generation of new mouse models,being therefore the most important transgenic mouse production unit in France.
BIDMC Transcranial Magnetic Stimulation Core
Beth Israel Deaconess Medical Center Transcranial Magnetic Stimulation Core
At the Berenson-Allen Center for Noninvasive Brain Stimulation (CNBS) at Beth Israel Deaconess Medical Center and Harvard Medical School we have three distinct missions: Research, Education and Patient Care. Our research explores brain-behavior relations, brain plasticity and its modulation, employing different noninvasive brain stimulation techniques combined with careful task design, electroencephalography, and functional brain imaging. Educational efforts feature several Continuing Medical Education Courses including a week long intensive course in noninvasive brain stimulation offered 3 times per year. Our clinical program offers noninvasive brain stimulation for treatment of neuropsychiatric disorders such as depression and schizophrenia, epilepsy, and chronic pain. Clinical work also includes studies of central motor conduction time, cortical excitability, and noninvasive cortical mapping.
WFU Center for Nanotechnology and Molecular Materials
Wake Forest University Center for Nanotechnology and Molecular Materials
The Center for Nanotechnology and Molecular Materials at Wake Forest University was founded in 2004 and serves scientists and engineers from both public and private interests in the Piedmont Triad and surrounding communities.
University of Missouri Nanotechnology Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2024. Center for Micro/Nano Systems and Nanotechnology is led by Professor Shubhra Gangopadhyay in electrical and computer engineering. This center is a multidisciplinary research facility that houses Nano Mems Semiconductor Lab (NMS) with state of art equipment to support research in the field of micro/nano-fabrication and nanotechnology. The mission of the Nano Mems Semiconductor Lab (NMS) is to serve and facilitate advanced research in processing and developing nanotechnology for academic and industrial users. NMS promotes the commercialization of nanomaterials research to meet the market needs in the commercial and defense sectors. Entrepreneurs, academic researchers, small and large companies can use our facility to turn their innovative ideas into novel product. NMS lab has 10,000 sq. feet facility housed at the University of Missouri. Top down microfabrication is performed in a class 100 clean room facility. The lab features additional 1100 sq.ft of class 10,000 cleanroom space equipped with various semiconductor processing equipment including metal and dielectric deposition systems, glove box, rapid thermal annealing system, fumehoods for chemical processing and thermal oxidation systems. Main activities of this center includes thin film process development for different applications, development of nano porous silicon films, functionalization of nanopours silicon films for biomedical application, development of SiCON films with high breakdown strength, diamond like carbon films based high through put cell ,microchip-based shock wave generator etc. This center is also working on synthesizing nanostructured materials such as quantum dots, nanoparticles, nanorods, and nanowires for life sciences, energy and defense applications.
WCMC Abby and Howard P. Milstein Chemistry Core Facility
WCMC Milstein Synthetic Chemistry Core Facility
Weill Cornell Medical College Abby and Howard P. Milstein Chemistry Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 11,2025. The Milstein Synthetic Chemistry Core Facility was created through the generosity of Weill Cornell Overseer Howard P. Milstein. The facility provides the equipment and expertise to assist investigators in several areas. Utilizing a newly renovated organic synthesis laboratory, we have the capacity to design and execute efficient and economical chemical syntheses. Additionally, assistance in the purification and identification of unknown metabolites can be provided. The facility primarily serves Weill Cornell Medical College, but can occasionally extend its services to include the tri-institutional academic community.
Medical University Innsbruck; Innsbruck; Austria
Medical University of Innsbruck is university in Innsbruck, Austria. Used to be one of four historical faculties of Leopold-Franzens-Universität Innsbruck and became an independent university in 2004.
Medical University of Graz; Graz; Austria
ISU Macromolecular X-ray Crystallography Facility
Idaho State University Macromolecular X-ray Crystallography Facility
The Macromolecular X-ray Crystallography Facility at Iowa State University provides a Rigaku/MSC rotating anode generator for single crystal X-ray diffraction studies, training in crystallography techniques, and a computer lab equipped with crystallography software. Facility services are provided on a fee basis and include consultation on protein purification, crystallization, and crystal optimization, as well as assistance with crystal screening, data collection, data processing, and structure determination and analysis. The following outline is used for general planning of a crystallography project: Protein purification: concentrated protein > 95% pure Crystallization: 3D, mountable crystals Crystal screening: search for high quality, high resolution crystals Data collection: using facility or synchrotron equipment Structure determination: processing, phasing, refinement, modeling, analysis, deposition
Private Baptist research university in Waco, Texas. Baylor was chartered in 1845 by the last Congress of the Republic of Texas.
Scientific research, development and consulting company. Developes noninvasive glucose detection system to be used for people with Diabetes. BioSciTech has scientific expertise in biopolymers and is developing several relationships with other companies for development of biopolymers and new magnetic resonance characterization techniques. Developes amorphous pharmaceutical materials.
THIS RESOURCE IS NO LONGER IN SERVICE,documented on February 3rd,2022.
University of Arkansas Stable Isotope Lab Core Facility
University of Arkansas Stable Isotope Lab
Facility provides high quality stable isotope analysis. Equipment includes Picarro G2201-I Cavity ring-down spectrometer for concentration and carbon isotope measurements of CH4 and CO2 gases, EA IsoLink CN analyzer and Delta V Plus Isotope Ratio Mass spectrometer for Carbon, Nitrogen and Sulphur analysis of solids, Delta V Advantage Isotope Ratio Mass with dual Gas Bench II peripherals, Delta V Advantage Isotope Ratio Mass with dual Gas Bench II peripherals, Shimadzu 2010 Quadrapole GC/MS with FID and liquid and headspace autosampler, Delta V Plus IRMS with TCEA and GC-IsoLink and Triplus RSH autosampler,
University of Georgia Labs and Facilities
University of Georgia Core Facilities provide equipment and services to researchers at UGA, other universities, government agencies, nonprofit organizations and industry. These facilities make use of highly specialized scientific equipment, diagnostic tools, adaptable prototyping processes and mechanical production shops.
Australian Microscopy and Microanalysis Research Facility
Australian Microscopy & Microanalysis Research Facility
The Australian Microscopy & Microanalysis Research Facility (AMMRF) is Australia''s leading facility for the characterisation of matter on a fine scale. We specialise in instrumentation, methodologies and applications for characterising samples in the physical, biological and environmental sciences using ion and electron beams, scanned probes, X-rays as well as light and laser optics. The six AMMRF nodes are located at the host universities in Adelaide, Brisbane, Canberra, Perth and Sydney. More information is available at www.ammrf.org.au and at http://www.ammrf.org.au/techniquefinder.
University of Southern California School of Pharmacy Lentiviral Laboratory Core Facility
University of Southern California School of Pharmacy Lentiviral Laboratory
USC School of Pharmacy Lentiviral Laboratory
USC School of Pharmacy Lentiviral Laboratory, located on the second floor of the Pharmaceutical Sciences Center, provides services for production of small-scale lentiviral stocks containing the gene of interest, lentiviral titrations, concentrations and transductions of cells of interest. We also construct individual lentiviral vectors including sub-cloning of the gene of interest into a pLVX-puro lentiviral vector.
Public university in Perth, Western Australia, with campuses also in Singapore and Dubai. It began operations as the state's second university on 25 July 1973, and accepted its first undergraduate students in 1975.
Myongji University; Gyeonggi-do; South Korea
Myongji University is private, Christian university founded in 1948 in South Korea. Provides higher education in fields of engineering, sciences and humanities.
Sanford-Burnham Medical Research Institute Stem Cell Research Center
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2024. Institutional Stem Cell Core has been discontinued, with the functions of the former Core now split into two separate operations. iPSCs: The generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators. Shared Laboratory: A well-equipped shared laboratory dedicated to the culture and analysis of stem cells is available to SBP investigators.
MQ Australian Proteome Analysis Facility
Macquarie Australian Proteome Analysis Facility
Macquarie University Australian Proteome Analysis Facility
APAF Ltd - Australian Proteome Analysis Facility, was the birthplace of the term proteomics in 1995 and was the world' '''s first dedicated high throughput proteomics laboratory. APAF has over 15 years of experience in providing proteomic services, and combined with our leading edge infrastructure and expertise we provide total solutions for all your proteomic research needs. APAF' '''s mission is to assist the scientific community address their protein analysis needs.
University of Texas Medical Branch at Galveston Mass Spectrometry Core
The Mass Spectrometry Core is dedicated to providing a wide range of mass spectral analyses. As an integral component of the BRF Proteomics Section, it is a vital proteomics resource, providing high quality data in a timely manner and engaging investigators in the interpretation of the results.
Rutgers University Waksman Institute of Microbiology Genomics Core Facility
Equipped with NextSeq500, MiSeq, and Ion Proton performs de novo genome sequencing, genome resequencing, ChIP-Seq and RNA-seq. Performs library construction, template preparation and sequencing of libraries or provides training in library preparation methods.Performs procedures to enrich or remove polyadenylated RNA, rRNA and/or tRNA as needed. Provides bioinformatics support for projects,data management and analysis plan before selecting samples and initiating data collection.
West Virginia University Genomics Core Facility
Performs and runs sequencing reactions and fragment analysis on an ABI model 3130XL genetic analyzer, as well as microarray analysis using the Affymetrix GeneChip system. They also have equipment available for self-service use.
Johns Hopkins University Deep Sequencing and Microarray Core
Our aim is to provide cost-effective and time-efficient access to cutting-edge genomic technologies and expert assistance with experimental design and data analysis.
University of Salerno Laboratory of Molecular Medicine and Genomics
Laboratory of Molecular Medicine and Genomics
UNISA Laboratory of Molecular Medicine and Genomics
Core equipped for structural and functional studies of genomes, includes equipment for next generation sequencing applications (Illumina HiSeq 1500, GAIIx and MiSeq, Life Technologies Ion Torrent PGM), RNA and microRNA expression profiling, array-based DNA methylation analyses and SNP genotyping (Illumina HiScan and Agilent High Resolution microarray scanners), informatics and bioinformatics (a server farm for genomics data computation and a high capacity data storage unit), fluorescence and confocal microscopy, long-term sample storage, cell culture, including a facility for generation and handling of viral vectors for gene transfer and gene therapy, access to a small animal facility for ''in vivo'' experimentations. Trained biotechnologists, molecular biologists and bioinformaticians handle all aspects related to experimental design, technical implementation and data analysis and storage.
Core facility which provides assistance in statistical analyses as well as in organization. Core facility offers two main analysis programs titled Spiral Genetics' BioGraph and Structural Variant Analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
ASU CLAS Goldwater Environmental Laboratory
Arizona State University CLAS Goldwater Environmental Laboratory
Arizona State University CLAS Goldwater Environmental Laboratory (GEL)
ASU CLAS Goldwater Environmental Laboratory (GEL)
A shared-use facility available to all research staff, faculty, and students of all disciplines. The facility encompasses seven laboratories and is part of the College of Liberal Arts and Sciences Research Technical Services group. GEL staff are committed to providing the tools necessary to meet the analytical needs of researchers while creating a valuable educational experience for users. Although most users perfer to receive individualized hands-on training enabling them to perform their own analyses, complete analytical services are also available.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Portal, Core facility.
Babraham Technology Development Laboratory
Babraham Institute Technology Development Laboratory
Babraham Institute Technology Development Laboratory Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024. Core facility at the Babraham Research campus offering biotechnology services, molecular biology services and chemistry. In addition to the scientific facilities and services available through the Babraham Institute, a unique offering of the Babraham Research Campus is BBT' '''s Technology Development Laboratory (TDL), which is accessible by companies both on and off site. Established to support innovation in biotechnology and biomedical fields, the TDL is a fully-equipped biology and chemistry laboratory. Companies, entrepreneurs and academics can hire bench space and equipment in the TDL ona flexible basis. Key equipment available for rent includes: Biacore T200 Equipped molecular biology and biochemistry laboratory Equipment for assay and screen development: - Protein expression (bacterial, mammalian and insect cell culture) - Protein concentration and purification (liquid chromatography) - Protein trafficking, expression and interaction (microscopy and imaging) - Protein array (array spotter) - HTRF (Homogeneous Time Resolved Fluorescence) assay platform
Iowa State University Labs and Facilities
Private Contract Research Organization providing pharmacological assays based on electrophysiological recordings of acute brain slices, spinal cord slices, cultured neurons, human brain slices and iPSC-derived neurons. These assays are performed with two complementary techniques: Multi-Electrode Array (MEA) and Patch-Clamp.
University of California Davis Mouse Biology Program
University of California Davis Mouse Biology Program (MBP)
UCD Mouse Biology Program (MBP) is a coordinated, campus-supported teaching, research, and service resource of infrastructure and fundamental expertise directed at developing, promoting, and enhancing the use of mouse model systems for understanding and resolving biological problems. Established in 1997, the goal of the MBP is to meet the needs of investigators utilizing genetically-altered mice for basic, clinical, and translational research. The mission of the MBP is to strive for excellence by focusing on hypothesis-driven research that advances health, well-being, and performance, and to educate and train the next generation of faculty, residents, graduate students, and veterinary students in the application of genetically-altered mice.
University of California San Francisco Nikon Imaging Center
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 19,2024. Nikon Imaging Center at UCSF/QB3 is a core facility for light microscopy established in partnership with Nikon Instruments, Inc. and a number of other microscopy vendors to provide access to cutting-edge microscopy tools for both UCSF researchers and outside researchers. We have six microscopes available for use: two widefield systems (one with temperature and CO2 control for mammalian cell time lapse imaging); a spinning disk confocal; a laser-scanning confocal; and structured illumination and STORM super-resolution systems.
THIS RESOURCE IS OUT OF SERVICE, documented on February 3rd,2022. Experiments generate millions of datapoints, hours of video, or terabytes of images. Manually coding or classifying large datasets can require thousands of hours of time that are better spent elsewhere. MobileWorks uses a crowd of thousands of trained individuals worldwide to carry out accurate data classification, labeling, and coding on demand. We can process images, audio and video data reliably according to your criteria. We use strict filtering and testing algorithms to verify that your labeling processes are followed precisely. Each label is produced through agreement by two or more individuals working in parallel and algorithmically verified.
USF Lisa Muma Weitz Laboratory for Advanced Microscopy and Cell Imaging
University of South Florida Lisa Muma Weitz Laboratory for Advanced Microscopy and Cell Imaging
This Imaging Core Facility provides the USF Health community with access to state-of-the-art instrumentation for biological imaging. The facility is a focal point for research involving microscopy and cell imaging at USF and a broad range of research applications are supported. A dedicated facility staff is available to provide training in instrument use, sample preparation, software applications and data analysis.
UMass Medical School Genomics Core Facility
University of Massachusetts Medical School Genomics Core Facility
A Resource for UMass Medical School and the entire UMass system, UMass Memorial Medical Center, and the research community.
Contract research organization that offers non-GLP and GLP contract flow cytometry services for all drug development stages from the research and development phase to nonclinical testing and finally into the clinic.
Macquarie University Centre for Analytical Biotechnology
Macquarie University Department of Chemistry and Biomolecular Sciences Centre for Analytical Biotechnology
The Centre manages substantial instrumentation resources appropriate for the contemporary study of biomolecules and natural products.
University of Pennsylvania Genomics Analysis Core
Core facility that provides the following services: Large sequencing project support, Sanger sequencing service, High throughput DNA sequencing, Ion Torrent Personal Genome Machine sequencing, Template preparation and purification, Roche 454 sequencing, Sequence analysis and database search support, Construction of targeting vector for gene targeting, Genotyping and Fragment Analysis service, Molecular biology services, Mouse genotyping, and Ion Personal Genome Machine sequencing data analysis. The DNA Sequencing Facility provides long read, automated Sanger sequencing; microsatellite-based genotyping and fragment analysis; plasmid and BAC DNA preparation and purification; and related molecular biological services including PCR, cloning, sub-cloning, site-directed mutagenesis, and preparation of targeting vectors for gene targeting in mice. Core also provides services and support for analysis and interpretation of sequence data as well as the design of approaches to complex sequencing projects. For the last four years the facility has been providing Roche 454 sequencing service that includes library preparation, emulsion PCR and pyrosequencing for both genomic DNA and amplicons.
Argonne National Laboratory Labs and Facilities
Argonne National Laboratory Labs & Facilities
Argonne National Laboratory, located just outside of Chicago, is one of the U.S. Department of Energy''s largest national laboratories for scientific and engineering research to solve most important challenges in energy, environment and national security. Programmatic activities cover all aspects of innovation ecology including basic research, technology development and prototype development and testing. We regularly work with industry through exclusive licensing, joint research and variety of other mechanisms to transfer our inventions to marketplace.
UChicago IGSB Next Generation Sequencing Core
Institute for Genomics & Systems Biology Next Generation Sequencing (NGS) Core
Institute for Genomics and Systems Biology Next Generation Sequencing Core
UChicago IGSB Next Generation Sequencing (NGS) Core
University of Chicago Institute for Genomics & Systems Biology Next Generation Sequencing (NGS) Core
University of Chicago Institute for Genomics and Systems Biology Next Generation Sequencing (NGS) Core
University of Chicago Institute for Genomics and Systems Biology Next Generation Sequencing Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15,2024. Laboratory: The Institute for Genomics and Systems Biology' '''s Next Generation Sequencing Core (IGSB-NGS) is a state-of-the-art facility for ultra-high throughput sequencing. The core was established in 2007 at Argonne National Laboratory and is housed in Argonne' '''s Computing, Environment and Life Sciences (CELS) directorate, providing world class computation power, software, and expertise critical to the acquisition, analysis, and interpretation of the unprecedented volume of genetic information being generated on next generation DNA sequencing platforms. The core provides resources and services to Argonne National Laboratory users, University of Chicago users, and to the broader scientific community. NGS is involved in a broad range of scientific research from the sequencing of metagenomic samples to both 16S and 18S rRNA amplicon sequencing for microbial community analysis using next generation sequencing. The NGS laboratory space at Argonne is approximately 1,200 square feet and is supplemented by 140 square feet of office space for the technical director, Ms. Sarah Owens, as well as two additional 140 square foot spaces for technicians. Equipment: The NGS maintains the following workflows: Illumina HiSeq2000 and MiSeq next generation DNA sequencing. The Illumina HiSeq2000 generates over 6 billion reads at 150 bp in length per read resulting in over 600 Gb worth of data across sixteen lanes available per run. The Illumina MiSeq generates over 24 million reads at 150 bp in length per read resulting in over 4.5 Gb worth of data available per run (over a single lane). Applications on both the Illumina HiSeq2000 and MiSeq include: shotgun metagenome sequencing; rRNA-based amplicon library sequencing; and genome sequencing and resequencing. All major equipment is housed within the main laboratory space including three 96-well PCR machines (Applied Biosystems), water baths, analytical balances, refrigerator/freezers (including a large-capacity -80 degree C freezer), incubators, and high and low speed centrifuges (table-top and floor models). Basic equipment and supplies for all advanced molecular techniques (deionized water (Millipore Milli-Q Advantage A10 system), multiple electrophoresis units and digital photographic documentation system) are housed here including equipment for high precision quantitation of nucleic acids (Agilent Bioanalyzer, NanoDrop, and Invitrogen Qubit). The facility also has a Covaris for sample shearing. Any additional equipment needed is located in or near by the NGS laboratory space including a real-time PCR machine (Roche LightCycler 480 with capabilities for both 96-well and 384-well plates) and a liquid handler, the Eppendorf epMotion 5075 robot. Some equipment (autoclaves, ice machine) is located in a common equipment room. Various instruments and methods have been implemented in the NGS' '''s standard procedures to maximize quality. These include the use of the Roche Lightcycler 480 II, Agilent Bioanalyzer 2100, Invitrogen Qubit Fluorometer, and barcoding of libraries destined for sequencing. (The latter allows for a test sequencing run of each library to be performed to optimize sequencing lane loading density prior to each library' '''s final sequencing run). Personnel overview. NGS operations are managed by Technical Director Sarah Owens. Ms. Owens has a Masters in Molecular Biology and Genetics, and 2 years experience working in high throughput facilities, with over 6 years of molecular biology experience. Ms. Owens was instrumental in trouble-shooting the application of rRNA-based amplicon sequencing for the Illumina HiSeq2000 and MiSeq, developing reproducible protocols in collaboration with Illumina. Under the guidance of the Technical Director, the NGS team helps users to determine the most efficient and cost effective approach to meet their research needs.
Memorial Sloan-Kettering Cancer Center Organic Synthesis Core Facility
Memorial Sloan-Kettering Cancer Center Organic Synthesis Core Facility (OSCF)
MSKCC Organic Synthesis Core Facility (OSCF)
GMP compliant Organic Synthesis Core Facility (OSCF) mission is to provide chemical synthesis work.
Idaho State University Labs and Facilities
Idaho State University Labs & Facilities
ISU has many facilities that are available for educational and research use. These include Idaho Accelerator Center in Physics Department and Nuclear Science research laboratory in Nuclear Engineering and Health Physics Department.
Company mission is to consistently deliver quality, scientifically based, GMP compliant early drug development services. With our top-tier pharmaceutical industry talent, we will treat your compound as if it were our own.
Macquarie University Animal Behaviour Laboratory
Exploring the mechanisms responsible for behaviour of clear functional importance.
Macquarie University Photonics Research Centre
Macquarie University Department of Chemistry and Biomolecular Sciences Photonics Research Centre
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2,2024. We undertake fundamental and applied research in the general area of lasers and photonics, with particular focus on the following seven frontiers of optical science: astrophotonics; biophotonics; microphotonic optical systems; nano-optics and nanophotonics; photonic sources; optical sensing and imaging; ultrafast laser applications.
MQ Ramaciotti Centre for Gene Function Analysis
Macquarie University Ramaciotti Centre for Gene Function Analysis
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024. Ramaciotti Centre for Gene Function Analysis was established in August 2000 as a focus for the development and application of Functional Genomics in New South Wales. The Centre is consortium of five universities and five medical research centres in the Sydney-Newcastle region.
Macquarie University BioFocus Research Centre
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2024. We develop and apply new analytical, microscopic, molecular, multiplexed, cellular, tomographic and related technologies for biomedical diagnosis, suitable for live cells or tissues or whole body. These will enable significantly increased sensitivity, resolution, speed, accuracy, penetration, and photostability , combined with reduced toxicity and risks to health.
MQ ARC Centre of Excellence for Engineered Quantum Systems
Macquarie University ARC Centre of Excellence for Engineered Quantum Systems
Macquarie University ARC Centre of Excellence for Engineered Quantum Systems (EQuS)
The ARC Centre of Excellence for Engineered Quantum Systems seeks to engineer complex, multi-component, quantum systems for new science and new applications. Cross-disciplinary scientific advances will link quantum physics with engineering, chemistry, and biology; and sophisticated technologies will be developed for 21st Century Australian industries. The EQuS collaboration possesses experimental capabilities in all major successful quantum technologies including spins in semiconductors, superconducting circuits, opto- and nano-mechanics, trapped atoms, and quantum photonics.
Macquarie University Seawater Core Facility
Macquarie University Department of Biological Sciences Seawater Facility
Operating since August 2004, Seawater Facility supports academic research and undergraduate teaching in Division of Environmental Life Sciences. Facility is used by marine scientists at Macquarie and their collaborative partners, to conduct controlled experiments and to temporarily house marine specimens.
Macquarie University Department of Biological Sciences Fauna Park
Situated on the corner of Culloden Rd and Tallavera Rd, Marsfield and originally farmed as market gardens, the Macquarie University Fauna Park stretches over 11Ha; 3.5Ha of which is protected Sydney Turpentine Ironbark Forest. The area is committed to non-intrusive research, e.g. learning to avoid predation, and other natural animal behaviours. Vertebrates (birds, fish, reptiles) or invertebrates (bees, flies, spiders) are observed in natural settings with minimal disruption to their normal environment. This allows the researchers to verify findings they have documented in the field. Other areas of investigation are water ecology and the competitive abilities of native trees.
Macquarie University Wireless Communications and Networking Laboratory
Macquarie University Department of Engineering Wireless Communications and Networking Laboratory
Macquarie University Wireless Communications and Networking Laboratory (WCNL)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. The Wireless Communications and Networking Laboratory (WCNL) at Macquarie University conducts research into emerging wireless communications and networking technologies.
Macquarie University Guided Wave Optics and Photonics Research group
Macquarie University Department of Engineering Guided Wave Optics and Photonics Research group
Macquarie University Guided Wave Optics and Photonics Research group (GWOPR)
The Guided Wave Optics and Photonics Research group (GWOPR) undertakes teaching, research, and development in the area of guided-wave optics, including integrated optics and optical fibres, specialising in microstructured and nanostructured materials. The group''s research capabilities are broad, but mainly target applications in telecommunications and sensing.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2,2024. Core facility
Beijing Normal University; Beijing; China
Colloquially known as Beishida, is a public research university located in Beijing, China, with a strong emphasis on basic disciplines of the humanities and sciences.
Macquarie University Automatic Weather Station
Macquarie University Department of Environment and Geography Automatic Weather Station
The Automatic Weather Station is located within the sports grounds of Macquarie University at North Ryde, Sydney, Australia. Its latitude, longitude and elevation are 33 degrees 45 minutes and 55.1 seconds South and 151 degrees 7 minutes and 3.2 seconds East and 66.8 m above mean sea level (accurate to 4.4 m). Access to both real-time and archived data is available and information is provided on what is measured and the instrumentation used. The data recorded at our weather station are archived at 1 minute intervals over the last 7 days, and at 15 minute intervals going back to April 1992.
Geographical information system software produced by Esri.
ImmunoSpot Software for Analyzing ELISPOT Assays
ImmunoSpot Software for ELISPOT Analysis
Stroke Registry in Chang Gung Healthcare System
Stroke patient registry containing thousands of patient CT scans, primarily as well as follow up medical information.
Adam Mickiewicz University in Poznan; Poznan; Poland
Research university in Poznań, Poland. It traces its origins to 1611, when under the Royal Charter granted by King Sigismund III Vasa, the Jesuit College became the first university in Poznań.
Agency for Science Technology and Research
Agency drives mission oriented research that advances scientific discovery and technological innovation. We play a key role in nurturing and developing talent and leaders for our Research Institutes, the wider research community, and industry.Our research creates economic growth and jobs for Singapore. As Science and Technology Organisation, we bridge gap between academia and industry in terms of research and development.
Agricultural University of Athens; Athens; Greece
Aix-Marseille University; Provence-Alpes-Cote d'Azur; France
Aix-Marseille University; Provence-Alpes-C�te d'Azur; France
University of the Mediterranean Aix-Marseille II
Universit� de la M�diterran�e - Aix-Marseille II
Universit� de la M�diterran�e Aix-Marseille II
Albany College of Pharmacy and Health Sciences; New York; USA
Albany College of Pharmacy and Health Sciences is committed to the advancement of health, with an array of degree programs designed to help students succeed in pharmacy and other health related fields. There are nearly 1,600 students enrolled at ACPHS and more than 100 full- and part-time faculty. The College''s main campus is located in Albany, New York; its satellite campus is in Colchester, Vermont. The College offers a Doctor of Pharmacy (Pharm.D.) program; four-year bachelor''s degrees in Pharmaceutical Sciences, Health and Human Sciences and Biomedical Technology; and a certificate program in Cytotechnology. Opportunities exist for students within each of these programs to work side-by-side with faculty on groundbreaking research in areas such as cancer, infectious disease and obesity. These experiences, along with access to resources such as the cutting edge Pharmaceutical Research Institute, are rarely afforded to undergraduates at most schools and are part of what distinguishes ACPHS from other colleges and universities. ACPHS also offers master''s degree programs in Pharmaceutical Sciences, Health Outcomes Research and Pharmacy Administration. In addition, students may pursue joint degrees in the fields of medicine, law and business through cooperative agreements with area institutions. Graduates of the College are prepared for a range of careers such as: biochemist, clinical laboratory scientist, consumer safety officer, drug information specialist, environmental toxicologist, health policy analyst, hospital administrator, pharmacist, physician, physician assistant and research scientist. The College is not only focused on the success of its own students, but also students throughout the region. ACPHS operates several programs for underserved youth in the area, each of which is designed to help them improve self confidence, develop new interests and skills, and inspire them to one day attend college themselves.
Albany Medical College; Albany; New York
One of the nation''s oldest private medical schools, prides itself in offering intimate, collegial environment which fosters humane values and genuine learning.Institution was founded in 1839. College still maintains policy of limiting enrollment to small group of carefully selected students.Trains doctors, scientists and other healthcare professionals.
Albert Einstein College of Medicine; New York; USA
Albert Einstein College of Medicine of Yeshiva University; New York; USA
Private medical school located in the Morris Park neighborhood of the Bronx in New York City. Einstein currently operates as an independent degree-granting institute under the Montefiore Medical Center. It was part of Yeshiva University until 2016.
All India Institute of Medical Sciences; New Delhi; India
All India Institute of Medical Sciences Delhi
An autonomous institution established through an Act of Parliament to serve as a nucleus for nurturing excellence in all aspects of health care. The object was to develop patterns of teaching in Undergraduate and Post-graduate Medical Education in all its branches so as to demonstrate a high standard of Medical Education in India; to bring together in one place educational facilities of the highest order for the training of personnel in all important branches of health activity; and to attain self-sufficiency in Post-graduate Medical Education. The Institute has comprehensive facilities for teaching, research and patient-care. As provided in the Act, AIIMS conducts teaching programs in medical and para-medical courses both at undergraduate and postgraduate levels and awards its own degrees. Teaching and research are conducted in 42 disciplines. In the field of medical research AIIMS is the lead, having more than 600 research publications by its faculty and researchers in a year. AIIMS also runs a College of Nursing and trains students for B.Sc.(Hons.) Nursing post-certificate) degrees. Twenty-five clinical departments including four super specialty centers manage practically all types of disease conditions with support from pre- and Para-clinical departments. However, burn cases, dog-bite cases and patients suffering from infectious diseases are not entertained in the AIIMS Hospital. AIIMS also manages a 60-bed hospital in the Comprehensive Rural Health Centre at Ballabgarh in Haryana and provides health cover to about 2.5 lakh population through the Centre for Community Medicine.
American University; Washington D.C.; USA
Private research university in Washington, D.C. Its main campus spans 90 acres on Ward Circle, in the Spring Valley neighborhood of Northwest D.C. Affiliated with the United Methodist Church but religious affiliation is not a criterion for admission.
Public university in San Angelo, Texas. It was founded in 1928 as San Angelo College. It gained university status and awarded its first baccalaureate degrees in 1967 and graduate degrees in 1969, the same year it took on its current name.
The Anthony Nolan Research Institute is fully dedicated to improving the outcome of bone marrow transplantation (BMT). The three main problems in BMT are graft versus host disease (GvHD) which is caused by differences in human leucocyte antigens (HLA), viral infection and the separation of GvHD from the graft versus leukaemia effect (GvL). Therefore, the five main aims of our Research Institute are the: # Investigation of the significance of HLA disparities between donor and patient at the molecular level and to analyze their influence on the outcome of bone marrow transplantation (BMT). # Maintenance and development of the HLA and KIR Sequence Databases. # Isolation and characterization of antigenic peptides from cytomegalovirus that act as targets for cytotoxic T-cell mediated responses. # Identification of target peptides and effector cells involved in graft versus leukemia (GvL). # Identification of target peptides and effector cells which initiate, maintain or perpetuate graft versus host disease (GvHD). During the past ten years our research team has made significant progress in many areas. For example, we have developed a new method that allows us to detect molecular differences that might be responsible for graft rejection and have identified CMV virus peptides that might be relevant in the future use of vaccinations. We are also studying the mechanisms of differentiation of the immune response after transplant and in this way we might be able to treat early stage GvHD. One of the most important activities of the Research Institute is orientated to academic teaching and training. We have established a structured research organization where a senior scientist is in charge of an individual research area and has under their supervision a team consisting of postdoctoral research fellows; PhD students and technicians. The teams interact with one another, as many of the projects overlap and this enables the sharing of experience and facilities.
For six decades, the U.S. Department of Energy''s (DOE''s) Argonne National Laboratory has excelled in conducting scientific research in support of a secure future for the nation. From Argonne''s inception, the University of Chicago has managed and operated the laboratorya laboratory that has become a scientific leader for DOE and the country. Achievements and honors earned by Argonne researchers include three Nobel Prizes, 90 R&D 100 awards, 700 national and international awards and honors, 750 patents and the start of over 30 small businesses. Argonne National Laboratory, one of the U.S. Department of Energy''s oldest and largest national laboratories for science and engineering research, employs roughly 3,200 employees, including about 1,000 scientists and engineers, three-quarters of whom hold doctoral degrees. Argonne''s mission is to apply a unique mix of world-class science, engineering and user facilities to deliver innovative research and technologies. We create new knowledge that addresses the most important scientific and societal needs of our nation. Research at Argonne centers around three principal areas: *Energy ** Energy Storage: Argonne develops transformational energy storage systems that enable and enhance electric-drive vehicles and a green-energy grid through electrical energy storage development, prototype and manufacturing process engineering, stationary storage and grid management, and electric transportation systems. ** Alternative Energy and Efficiency: Argonne is developing the next generation of alternative energy sources to promote energy independence through improved chemical fuels, advanced biofuels, and solar energy systems, as well as through the optimization of fuel and engine dynamics. ** Nuclear Energy: Argonne develops advanced reactor and fuel cycle systems including fast reactor and fuel cycle technologies, advanced modeling and simulation methods, and innovative nuclear energy systems to enable the safe and sustainable generation of nuclear energy. * Biological and Environmental Systems: Argonne produces integrated molecular-scale, hydrological, economic and social computational models to enable regionally focused ecological and climate assessments through metagenome analysis, protein discovery, regional climate prediction and integrated climate, energy and economic discovery. * National Security: Argonne provides critical security technologies that prevent and mitigate events with potential for mass disruption or destruction through the nonproliferation and forensics of weapons of mass destruction, decision sciences, new sensors and materials, and cyber security.
Aristotle University of Thessaloniki; Thessaloniki; Greece
Aston University; Birmingham; United Kingdom
Public research university situated in the city centre of Birmingham, England. Aston began as the Birmingham Municipal Technical School in 1895, evolving into the UK's first College of Advanced Technology in 1956
Public research and land grant university in Auburn, Alabama. It is one of the state's two public flagship universities.
Boston University School of Medicine; Massachusetts; USA
Boston University School of Medicine (BUSM) is a major research institution, providing an exceptional environment for students interested in basic science, clinical investigation, or public health and health services oriented research. BUSM has 660 medical students, and a similar number of graduate students in the medical school actively engaged in the study of medicine and the biomedical sciences.
Auburn University; Harrison School of Pharmacy
The James I. Harrison, Sr. School of Pharmacy, established in 1885, is the oldest professional school at Auburn University. It is the only public pharmacy school in Alabama and is also the only institution in the State that offers a graduate program in Pharmaceutical Sciences. Post-graduate education and continuing education are provided to practitioners across Alabama. Each year, the School receives two to three applications for every admission seat in the professional program. The Harrison School of Pharmacy faculty is a highly qualified group of educators who are nationally recognized for teaching, research and scholarship. The three departments of faculty within the Harrison School of Pharmacy are specialized for Pharmaceutical Sciences, Pharmacy Care Systems, and Pharmacy Practice.
Advanced Telecommunications Research Institute International
ATR - Advanced Telecommunications Research Institute International
ATR: Advanced Telecommunications Research Institute International
ATR is a unique private Company established in Kansai region March 1986through the broad support of industrygovernment and academiawith the aim of promoting fundamental and innovative RD activities as well as contributing to society in a wide range of telecommunication fields For the last quarter century since our foundation outstanding research outcomes have been steadily achieved in such fields as neuro/knowledge science intelligent roboticslanguage translation and wireless communication through original and innovative research activities and collaboration work with various universities research institutesand companies within and outside of Japan. Research and development for information and communication technology is indispensable to the formation of safe and secure society as well as a true communication societywhich will provide people with a more satisfying living environment by facilitating human communicationIn addition to continuous efforts in highquality advanced research and developmentwe are determined to focus on the feasibility of broadly applying our research results in society and making them more useful and accessible to a variety of people New Mission * To promote pioneering and innovative research on information and communication-related fields with global collaboration among industry, academia and government * To contribute to a wide variety of welfare of society and humanity by outstanding achievements, and to develop highly-professional human resources * To lead growth of Kansai Science City as a center of excellence in the world
Australian National Fabrication Facility
Established under the National Collaborative Research Infrastructure Strategy, the Australian National Fabrication Facility (ANFF) links 8 university-based nodes to provide researchers and industry with access to state-of-the-art fabrication facilities. The capability provided by ANFF enables users to process hard materials (metals, composites and ceramics) and soft materials (polymers and polymer-biological moieties) and transform these into structures that have application in sensors, medical devices, nanophotonics and nanoelectronics. The nodes, which are located across Australia, draw on existing infrastructure and expertise. Each offers a specific area of expertise including advanced materials, nanoelectronics & photonics and bio nano applications. Our commitment to providing a world-class user facility is underpinned by the sharing of best practice in service provision across the nodes.
Autonomous University of Barcelona; Barcelona; Spain
Autonomous University of Barcelona, is a public university mostly located in Cerdanyola del Vallès, near the city of Barcelona in Catalonia, Spain. As of 2012, the university consists of 57 departments in the experimental, life, social and human sciences, spread among 13 faculties/schools.
Autonomous University of Madrid; Madrid; Spain
The Babraham Institute - Life Sciences Research for Lifelong Health
Life sciences Institute within University of Cambridge, England. Focuses on the BBSRC strategic objective of research into healthy ageing by understanding basic molecular processes. Benefits from provision of core facilities like imaging, flow cytometry, next generation sequencing, mass spectrometry and small animal facilities. Has tradition of sustained innovation in areas of lipid and calcium signalling, in immunology and in genetics.
Banner Alzheimer's Institute; Arizona; USA
A leading destination for Alzheimer's disease care and treatment through research.
Bowling Green State University; Ohio; USA
Public research university in Bowling Green, Ohio with nationally recognized programs and research facilities in the natural and social sciences, education, arts, business, health and wellness, humanities and applied technologies.
Founded by Lydia Moss Bradley in 1897, Bradley University is a private, independent university offering undergraduate, graduate, and continuing education programs in the liberal and fine arts, the sciences, business administration, communications, education, engineering, and the health sciences. Our residential campus of 6,000 students blends large school opportunities with a small school personality where there is a commitment to excellent teaching and personal attention to students. Bradley''s comprehensive programs offer an effective integration of liberal education, professional preparation, and personal and social development.
Research institute for basic and translational research, clinical care, prevention and education in age-related conditions such as Alzheimer's and Parkinson's diseases, arthritis and cancer. Founded as a private, nonprofit biomedical research center, they now have nearly 100 international scientists and research staff. Their research programs have had significant impact on how physicians diagnose and treat diseases such as Alzheimer's, Parkinson's and arthritis. Sun Health is also internationally recognized for research on inflammation damage to brain tissue and how that affects Alzheimer's disease. They are one of just 31 national Alzheimer's Disease Core Centers in the nation. The Institute maintains collaborations with nationally-recognized institutions such as Johns Hopkins, Boston University and the University of Washington. In 2007, the institute opened a new research facility that allowed them to expand into areas such as orthopedics and fibromyalgia.
Public research university in the city of Ramat Gan the Tel Aviv District, Israel. Established in 1955, Bar Ilan is Israel's second-largest academic institution.
A private nonprofit applied science and technology development company that conducts research and development, designs and manufactures products, and delivers critical services for government and commercial customers. It serves the national security, health and life sciences, and energy and environmental industries.
Citizen-managed, non-profit research institution that uses genomics to benefit the human race. BGI (which includes both private non-profit research institutes and sequencing application commercial units) and its affiliated offshoots, BGI Americas and BGI Europe, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, to support a variety of healthcare, agricultural, environmental and related applications. BGI currently comprises of 4 regions: BGI China (Mainland), BGI Asia Pacific, BGI Americas (North and South America) and BGI Europe (Europe and Africa). Relying on advanced high-throughput sequencing technology, a highly efficient data analysis capability, uniquely rich biological resources, and a multidisciplinary scientific research system, BGI can provide innovative support for global communities, novel opportunities for researchers, and a regionally tailored application services in the fields of healthcare, agriculture and the environment.
Biotechnology High Performance Computing Software Applications Institute
DoD Biotechnology High Performance Computing Software Applications Institute
United States Department of Defense Biotechnology High Performance Computing Software Applications Institute
Bielefeld University; North Rhine-Westphalia; Germany
Bioinformatics Institute; Singapore; Singapore
The Bioinformatics Institute (BII) was set up by the Agency for Science and Technology Research (A*STAR) in July 2001; it was re-launched with a strong scientific program in the autumn months of 2007. Located in the Biopolis, BII is conceived as the computational biology research and postgraduate training institute as well as a national resource centre in bioinformatics within the Biomedical Research Council (BMRC) of A*STAR. The BII focuses on theoretical approaches aimed at understanding biomolecular mechanisms that underlie biological phenomena, the development of computational methods to support this discovery process, and experimental verification of predicted molecular and cellular functions of genes and proteins with biochemical methods. Together with the BMRC, A*STAR research institutes and multinational R&D organizations in the Biopolis, the BII is situated in a conducive environment for exchange of scientific knowledge and friendly interaction that will prompt greater collaborations, and position the Biopolis as a notable biomedical R&D hub in Asia and in the world.
Biotechnology and Biological Sciences Research Council
The UK''s leading funding agency for academic research and training in the non-clinical life sciences.
Birkbeck University of London; London; United Kingdom
Public research university located in Bloomsbury London, England, and constituent college of federal University of London. Research and teaching institution, provider of evening higher education in London.
Blaise Pascal University; Clermont-Ferrand; France
Universite Blaise Pascal Clermont-Ferrand II
Université Blaise Pascal Clermont-Ferrand II
Blaise Pascal University, also known as Université Blaise Pascal, Clermont-Ferrand II or just Clermont-Ferrand II, was a public university with its main campus on 53 acres in Clermont-Ferrand, France, with satellite locations in other parts of the region of Auvergne, including Vichy, Moulins, Montluçon, and Aubière.
Bordeaux Segalen University; Bordeaux; France
University of Bordeaux was founded in 1441 in France. The university is part of the Community of universities and higher education institutions of Aquitaine. It is one of the two universities in Bordeaux, with Bordeaux Montaigne University.
Biomedical Sciences Research Center Alexander Fleming
BSRC Alexander Fleming is a governmental, non-profit research institution. The Center became operational in 1998 and grew on the competency of its people into a model research center comprising of 5 research institutes, three of which are currently operational: * The Institute of Immunology (Operational) * The Institute of Molecular Biology and Genetics (Operational) * The Institute of Molecular Oncology (Operational) * The Institute of Microbiology-Virology * The Institute of Cellular & Developmental Biology The Center''s main research areas include: * Functional genetics and functional genomics * Molecular and cellular immunology * Animal models of human disease * Transgenesis, targeted gene knockout and high throughout mutagenesis * Transcriptional and post transcriptional mechanisms of gene regulation * Stem Cell differentiation
Brookhaven National Laboratories; New York; USA
One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. Brookhaven is operated and managed for DOE''s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization. Id=nlx_56211
Brown Alpert Medical School; Rhode Island; USA
Brown University Medical School; Rhode Island; USA
Warren Alpert Medical School of Brown University
Warren Alpert Medical School; Rhode Island; USA
Warren Alpert Medical School is the medical school of Brown University, located in Providence, Rhode Island. Established in 1811, the school is the third oldest medical school in New England.
The Buck Institute is the nation''s first and only independent research facility focused solely on understanding the connection between aging and chronic disease. Our mission is to increase the healthy years of life. At the Buck Institute, world-class scientists work in a uniquely collaborative environment to understand how normal aging contributes to the development of conditions specifically associated with getting older such as Alzheimer''s and Parkinson''s disease, cancer, stroke and diabetes. Our interdisciplinary approach brings scientists from disparate fields together to develop diagnostic tests and treatments to prevent or delay these maladies. Unlike traditional universities, which have departmental boundaries and large bureaucracies, the Buck Institute is designed for the free flow of information. Discoveries quickly result in new studies. Scientists studying breast cancer are collaborating with researchers examining aging and nutrition. Parkinson''s disease is being studied in three different model organisms. A unique inquiry into stem cells and aging is underway. It''s an exciting place for science that has the potential to change the way we live.
Butler University; College of Pharmacy & Health Sciences
Butler University; College of Pharmacy and Health Sciences
The College of Pharmacy and Health Sciences strives to provide effective educational experiences in the health sciences. By so doing, the College facilitates the development of life-long learners with a liberal arts foundation who are able to serve society as dedicated, competent health professionals and community leaders. The Butler University College of Pharmacy and Health Sciences is a member of the American Association of Colleges of Pharmacy and is accredited by the Accreditation Council for Pharmacy Education. By completion of the doctor of pharmacy curriculum of the College of Pharmacy and Health Sciences, its graduates fulfill the educational requirements for examination and licensure as pharmacists in every state in the nation. Degrees offered: -Doctor of Pharmacy -Master of Physician Assistant Studies -Master of Science in Pharmaceutical Sciences -Doctor of Pharmacy/Master of Business Administration Dual Degree Curriculum
Private university in Indianapolis, Indiana. Founded in 1855 and named after founder Ovid Butler, the university has over 60 major academic fields of study in six colleges.
California Polytechnic State University; California; USA
Nationally ranked, four-year, comprehensive public university located in San Luis Obispo, California.
California State University Channel Islands; California; USA
California State University Channel Islands
Public university in Ventura County, California. CSUCI opened in 2002 as the 23rd campus in the California State University system.
Center for Genomic Regulation; Barcelona; Spain
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. The CRG is a pioneering centre in Spain, based on a non-bureaucratic organisation research model, devoted to promoting basic research about fundamental life science issues. Particularly, it is focused on genomics, proteomics and biomedical research, and on attracting and producing top scientists at all levels. The CRG is in the unique position of being a top-level institute not belonging to a large corporation. Instead, the CRG is a compact and versatile research centre, well-funded and featuring cutting-edge technology and first-rate scientists from all over the world who are keen on pushing the frontiers of science forward.
Cornell University College of Veterinary Medicine
Cornell University''s College of Veterinary Medicine''s strength as a leader in veterinary medical education, animal medicine, biomedical research and public health springs from the aggregate strengths of its departments and programs; the achievements of its faculty, alumni, and students; and its commitment to diversity and inclusiveness. At the Cornell College of Veterinary Medicine, basic scientific research meets the clinical and research demands of human and animal health. Consistently ranked among the top veterinary colleges in the country, the College is also a leader in biomedical research. The Biological & Biomedical Sciences Graduate Program fosters an atmosphere of collaboration, focusing on the interface between scientific research and clinical practice as well as a commitment to animal and human health. Graduate students contribute to this pursuit through their PhD research projects and continue to impact the world in their post graduate careers in academia, government and business.
The California Academy of Sciences is a multifaceted scientific institution committed to leading-edge research, to educational outreach, and to finding new and innovative ways to engage and inspire the public. This world-class scientific and cultural institution is based in San Francisco and recently opened a new facility in Golden Gate Park that houses an aquarium, a planetarium a natural history museum and a 4-story rainforest all under one roof. The new facility is also home to the Academy''s staff of world-class scientists, an education department that provides a wide range of student and teacher services, and an extensive science library with over 26 million specimens and artifacts. The Academy is an international center for scientific education and research and is at the forefront of efforts to understand and protect the diversity of Earth''s living things. The Academy has a staff of over 50 professional educators and Ph.D.-level scientists, supported by more than 100 Research and Field Associates and over 300 Fellows. It hosts 11 fields of research, including anthropology, aquatic biology, botany, comparative genomics, entomology, geology, herpetology, ichthyology, invertebrate zoology,mammalogy and ornithology. The Academy''s research collections, which are among the world''s largest, include more than 26 million specimensessential tools for comparative studies on the history and future of the natural world.
California Environmental Protection Agency
State cabinet level agency within the government of California. The mission of CalEPA is to restore, protect and enhance the environment, to ensure public health, environmental quality and economic vitality.
Cardiff University; Wales; United Kingdom
Public research university in Cardiff, Wales. Founded in 1883 as the University College of South Wales and Monmouthshire, it became a founding college of the University of Wales in 1893.
Public comprehensive university in Ottawa, Ontario, Canada. Founded in 1942 as Carleton College, a private, non-denominational evening college to serve returning World War II.
Andrew Carnegie founded the Carnegie Institution of Washington in 1902 as an organization for scientific discovery. His intention was for institution to be home to exceptional individualsmen and women with imagination and extraordinary dedication capable of working at the cutting edge of their fields. Today, Carnegie scientists work in six scientific departments on the West and East Coasts. Carnegie investigators are leaders in the fields of plant biology, developmental biology, Earth and planetary sciences, astronomy, and global ecology. They seek answers to questions about the structure of the universe, the formation of our solar system and other planetary systems, the behavior and transformation of matter when subjected to extreme conditions, the origin of life, the function of genes, and the development of organisms from single-celled egg to adult. The Carnegie Institution for Science is headquartered in Washington, D.C. It is an endowed, independent, nonprofit institution. Significant additional support comes from federal grants and private donations. A board of trustees, consisting of leaders in business, the sciences, education, and public service, oversees Carnegie''s operations. Each of the six departments has its own scientific director who manages day-to-day operations under the leadership of Richard A. Meserve, Carnegie president. In addition to the scientists on staff, there is a constantly changing roster of pre- and postdoctoral fellows and associates, as well as visiting investigators, at each facility. Each of the six departments is independently managed by a director, who is aided by support staff. Carnegie is also involved in education at the lower levels.
Carnegie Mellon University; Pennsylvania; USA
Carnegie Mellon University is a private nonprofit research university based in Pittsburgh, Pennsylvania. Founded in 1900 by Andrew Carnegie as the Carnegie Technical Schools, the university became the Carnegie Institute of Technology in 1912 and began granting four-year degrees.
Case Western Reserve University; Ohio; USA
Private research university in Cleveland, Ohio.
Generalitat de Catalunya Departament de Salut
Catholic University of Louvain; Louvain-la-Neuve; Belgium
Belgium's largest French speaking university.
Private nonprofit university located in Lima, Peru. It was named in honor of Cayetano Heredia, one of the eminent Peruvian physicians of the 19th century. The university is overseen by a board of trustees and is not owned by any private or state entity.
The Center for Information Technology''s (CIT) mission is to provide, coordinate, and manage information technology and to advance computational science. CIT incorporates the power of modern computers into the biomedical programs and administrative procedures of the NIH by focusing on three primary activities: conducting computational biosciences research, developing computer systems, and providing computer facilities. CIT supports NIH''s research and management programs with efficient, cost-effective administrative and high-powered scientific computing, software development, networking, and telecommunications services. CIT also provides bioinformatics support through its scientists, engineers, and mathematicians. Among its activities, the CIT: * engages in collaborative research and provides collaborative support to NIH investigators in the area of computational bioscience * provides efficient, cost-effective information systems and networking services * provides state-of-the-art scientific and administrative computing facilities * identifies new computing technologies with innovative applications to biomedical research * creates, purchases, and distributes software applications * provides NIH staff with computing information, expertise, and training * provides data-processing and high-performance computing facilities, integrated telecommunications data networks, and services to the U.S. Department of Health and Human Service (HHS) and other Federal agencies * serves as a data center to HHS and other Federal agencies * develops, administers, and manages NIH systems and provides consulting services to NIH Institutes and Centers in support of administrative and business applications
Central Institute of Mental Health; Mannheim; Germany
Central Institute of Mental Health Mannheim
Zentralinstitut für Seelische Gesundheit
An independent public foundation of the State of Baden-Wuerttemberg associated with the University of Heidelberg, that is one of Europe''s premier research institutions dedicated to mental health. The CIMH combines a clinical inpatient (300 beds) and outpatient program in adult psychiatry, addiction, childhood and adolescent psychiatry and psychotherapy with outstanding research facilities, including two dedicated research fMRI scanners (currently 1.5 Ts and 3 Ts, from next summer 2 3 Ts magnets), an 9.4 Ts animal fMRI scanner, high-throughput facilities for genotyping and molecular biology, neuropsychology and an extensive transgenic animal (both mice and rats) and animal behavior assessment facility.
Central University of the Caribbean; Puerto Rico; USA
Private university in Bayamón, Puerto Rico that focuses on graduate studies and professional certifications in the health sciences.
Centre for Cellular and Molecular Biology; Hyderabad; India
Centre for Cellular and Molecular Biology
The Centre for Cellular and Molecular Biology (CCMB) is one of the constituent national laboratories of the Council of Scientific and Industrial Research (CSIR), the premier multidisciplinary Research & Development organisation of the Government of India. It was set up as a semi-autonomous Centre in 1977 in Hyderabad, the capital city of Andhra Pradesh, became a full-fledged national laboratory during 1981-82, and was dedicated to the nation on 26 November, 1987 by the then Prime Minister of India late Shri Rajiv Gandhi. The ongoing research programmes at the CCMB are in three major categories - high quality basic research in the frontier areas of modern biology, research relevant to societal needs, and application oriented research towards commercialisation. These include the areas of biomedicine & diagnostics, evolution & development, gene regulation in prokaryotes and eukaryotes, host-parasite interactions, membrane biology, protein structure, bioinformatics, functional genomics, theoretical biology, etc. CCMB has also taken lead in the dissemination of modern biological information through popularisation of science, science education in schools, and has been a meeting point for art and science. In recognition of its contribution to modern biology, CCMB has been chosen as a Centre of Excellence by UNESCO Global Network for Molecular and Cell Biology (MCBN) and has been designated as a South Centre for Excellence for Research and Training by the Third World Academy of Sciences (TWAS), Italy. Many prestigious international and national awards have come to CCMB including the CSIR Technology Award (twice) and FICCI Award for outstanding achievements in Science & Technology.
Centre for Genomic Regulation; Barcelona; Spain
International biomedical research institute created in December 2000 to discover and advance knowledge for benefit of society, public health and economic prosperity. Non profit foundation. Group leaders are recruited internationally and receive support from centre to set up and run their groups. External Scientific Advisory Board, made up of 15 world leaders in different areas, evaluates them.
Chalmers University of Technology; Gothenburg; Sweden
Swedish university located in Gothenburg that focuses on research and education in technology, natural sciences, architecture, mathematics, maritime and other management areas
Chang Gung University is a private university in Guishan District, Taoyuan City, Taiwan.
Chang Gung University College of Medicine; Taoyuan; Taiwan
Chang Gung University College of Medicine
Private university in Guishan District, Taoyuan City, Taiwan.
Charite - Universitatsmedizin Berlin; Berlin; Germany
Charite - University Medicine Berlin; Berlin; Germany
One of Europe's largest university hospitals, affiliated with Humboldt University and Free University Berlin. With numerous Collaborative Research Centres of the German Research Foundation it is one of Germany's most research-intensive medical institutions.
Charles III University of Madrid; Madrid; Spain
University Carlos III of Madrid is a public university in the Community of Madrid, Spain. Established in 1989, UC3M is an institution with a distinctly international profile.
Centre de Cooperation Internationale en Research Agronomique pour le Development
Centre de coopération internationale en recherche agronomique pour le dévelopement
French Agricultural Research Centre for International Development
A French research center working with developing countries to tackle international agricultural and development issues. They are a public industrial and commercial enterprise (EPIC) under the joint authority of the Ministry of Higher Education and Research and the Ministry of Foreign Affairs. CIRAD works with the whole range of developing countries to generate and pass on new knowledge, support agricultural development and fuel the debate on the main global issues concerning agriculture. They are a targeted research organization, and base their operations on development needs, from field to laboratory and from a local to a global scale. CIRAD' '''s activities involve the life sciences, social sciences and engineering sciences, applied to agriculture, food and rural territories. They work hand-in-hand with local people and the local environment, on complex, ever-changing issues: food security, ecological intensification, emerging diseases, the future of agriculture in developing countries, etc.
Public college in NYC offering undergraduate and graduate degrees in liberal arts and sciences, architecture, engineering, education and biomedical education.
Clarkson University is a private research university with its main campus in Potsdam, New York, and additional graduate program and research facilities in the New York Capital Region and Beacon, New York.
Private Methodist historically black research university in Atlanta, Georgia. Clark Atlanta University is the first HBCU in the Southern United States. Founded September 19, 1865, as Atlanta University; consolidated with Clark College to form Clark Atlanta University in 1988.
Private research university in Worcester, Massachusetts. Founded in 1887 with a large endowment from its namesake Jonas Gilman Clark, a prominent businessman, Clark was one of the first modern research universities in the United States.
Claude Bernard University Lyon 1; Lyon; France
Public university in Villeurbanne, France.
Public, land-grant research university in Clemson, South Carolina. Founded in 1889, Clemson is the second-largest university in student population in South Carolina.
Cleveland Clinic Lerner College of Medicine; Ohio; USA
Cleveland Clinic Lerner College of Medicine
Cleveland Clinic Lerner College of Medicine of Case Western Reserve University
Also known as the Latin Quarter, the 5th arrondissement is home to the Sorbonne university and student-filled cafes. It's also known for its bookshops, including the famed Shakespeare & Company. Family-friendly attractions include the Jardin des Plantes botanical gardens and the National Museum of Natural History. The stately Panthéon building holds the remains of notables like Voltaire and Marie Curie.
Colorado College seeks to provide a broad liberal arts education. During the second year at the college, a student chooses a major field in which to take concentrated work. Minors, double majors, and self-designed majors are possible.
Colorado State University; Colorado; USA
Public land-grant research university in Fort Collins, Colorado. It is the flagship university of the Colorado State University System.
Private Ivy League research university in New York City. Established in 1754 on the grounds of Trinity Church in Manhattan, Columbia is the oldest institution of higher education in New York and the fifth-oldest institution of higher learning in the United States.
Columbia University College of Physicians and Surgeons
Columbia University College of Physicians & Surgeons
P&S provides international leadership in educating physicians, physician-scientists, and research scientists; in caring for patients ranging from those who can select any physician in the world to our neighborhood''s most vulnerable residents; and in conducting basic, translational, and population-based research to improve human health.
Complutense University of Madrid; Madrid; Spain
Commonwealth Scientific and Industrial Research Organisation
Commonwealth Scientific and Industrial Research Organisation of Australia
Commonwealth Scientific and Industrial Research Organization
CSIRO - Commonwealth Scientific and Industrial Research Organisation
CSIRO, the Commonwealth Scientific and Industrial Research Organisation, is Australia''s national science agency and one of the largest and most diverse research agencies in the world. National Research Flagships: Large-scale, long-term, multidisciplinary science to address Australia''s major national challenges and opportunities. Divisions: CSIRO expertise is organised into 14 research areas: * Animal, Food and Health Sciences * Astronomy and Space Science * Earth Science and Resource Engineering * Ecosystem Sciences * Energy Technology * Food & Nutritional Sciences * ICT Centre * Land and Water * Livestock Industries * Marine and Atmospheric Research * Materials Science & Engineering * Mathematics, Informatics and Statistics * Plant Industry * Process Science and Engineering National Facilities: CSIRO manages national facilities and collections that are opened to researchers around Australia and overseas.
Consejo Nacional de Investigaciones Científicas y Técnicas
National Council of Scientific and Technical Research
National Council of Scientific and Technical Research (Argentina)
The CONICET is the leading organization dedicated to the promotion of science and technology in Argentina. It operates in four major areas * agricultural sciences, engineering and materials * life sciences and health * natural sciences * Social Sciences and Humanities The National Scientific and Technical Research Council (Spanish: Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET) is an Argentine government agency which directs and co-ordinates most of the scientific and technical research done in universities and institutes. It was established on 5 February 1958 by a decree of the national government. Its first director was Medicine Nobel Prize Bernardo A. Houssay. Nowadays, it is governed by a board completely independent from the federal government. It funds scientific research in three basic ways. First, CONICET gives grants for collective work to research teams of well-recognized scientists of every discipline (including social sciences and humanities). Secondly, it has a roll of 6,500 researches and 2,500 technicians as employees in different categories, from investigador asistente to investigador principal. And thirdly, it grants scolarships for doctoral and post-doctoral studies to 8,500 young researches from Argentina and other countries. (Wikipedia)
Meharry Medical College School of Graduate Studies and Research; Tennessee; USA
Private Jesuit research university in Omaha, Nebraska bridging health, law, business and arts and sciences for more just world.
In the Jesuit, Catholic tradition of caring for the whole person - mind, body and spirit - the School of Medicine and Creighton Medical Associates (CMA) are committed to providing excellent patient care and preparing future doctors for the medical challenges and opportunities that lie ahead in patient care, teaching and research, and service. The university provides Graduate Medical Education (GME) through a variety of ACGME approved residency training programs and specialty fellowships, as well as undergraduate and continuing medical education. The School of Medicine boasts a national presence in medicine. Our graduates practice in all 50 states. Surveys of our graduates and their residency doctors show that Creighton-educated physicians are nationally recognized for their extraordinary clinical skills, communication, empathy and cultural competence. A strong desire to make a difference in patients'' lives drives the research efforts at Creighton University''s School of Medicine. Researchers are making discoveries that can positively affect patients'' lives in the areas of bacterial resistance, cancer, hearing loss and the conditions that affect bone health and loss. Part of the mission at Creighton University''s School of Medicine is to develop new therapies to contribute to the health and well-being of patients. Research is essential to learning about the mechanism of diseases and new ways to prevent and treat disease.
An independent, non-profit organization dedicated to bringing scientists from the FDA, industry and academia all together to collaborate and improve the drug development and regulatory process for medical products.
CSIR-Central Food Technological Research Institute; Karnataka; India
Central Food Technological Research Institute
Central Food Technological Research Institute; Karnataka; India
CSIR-Central Food Technological Research Institute
Institute to pursue research and development in areas of food science and technology. Research focus in areas of Engineering Sciences,Technology Development,Translational Research,Food Protection and Safety.
CSIR-Institute of Genomics and Integrative Biology; Delhi; India
CSIR Institute of Genomics and Integrative Biology
CSIR-Institute of Genomics and Integrative Biology
Federal government agency for cancer research and training established in 1937. National Cancer Program is responsibility of NCI to coordinate, conduct and support research, training, health information dissemination with respect to cause, diagnosis, prevention, and treatment of cancer, rehabilitation from cancer, and continuing care of cancer patients and families of cancer patients. Supports construction of laboratories, clinics, and related facilities necessary for cancer research through award of grants.
CSIR - Indian Institute of Chemical Biology; Kolkata; India
Indian Institute of Chemical Biology; Kolkata; India
Institute for the advancement of the state of human knowledge related to the basic aspect of the causation and prevention of diseases of special concern for the country especially tropical diseases and also nutritional biochemistry and physiology. In 1956 the institute came under the umbrella of the CSIR. Today, by its mandate IICB is engaged in research on diseases and certain biological problems of global interest. IICB is putting emphasis on quality basic research, on projects having applied potential and is looking forward to a successful Industry-Institute liason towards closer partnership.
Curtin University; Western Australia; Australia
Australian public research university based in Bentley, Perth, Western Australia. It is named after John Curtin, Prime Minister of Australia from 1941 to 1945, and is the largest university in Western Australia.
Cyprus Institute of Neurology and Genetics; Nicosia; Cyprus
Cyprus Institute of Neurology & Genetics
Cyprus Institute of Neurology and Genetics
A bi-communal, non-profit, private, academic, medical center with a vision to function as an International Centre of Excellence and a Regional Referral Centre in the areas of Neurology, Genetics, Biomedical, Medical and other similar and related Sciences. They aim to develop and provide high level medical and clinical laboratory services, develop and pursue advanced research and provide education in the areas of Neurology, Genetics, Biomedical, Medical and other similar and related Sciences. Its ultimate scopes are to improve and upgrade the quality of life of all Cypriot citizens, irrespective of religion or national origin, and strengthen its international role in the areas of its specialty.
Private Ivy League research university in Hanover, New Hampshire, United States. Established in 1769 by Eleazar Wheelock, Dartmouth is one of the nine colonial colleges chartered before the American Revolution.
Dalian University of Technology; Dalian; China
Danish Agency for Science Technology and Innovation
Danish Agency for Science Technology Innovation
Established by the Danish Parliament, this independent foundation, aims at strengthening Danish basic research (frontier research) within the natural sciences, the technical sciences, the health sciences, the social sciences, and the humanities. The Foundation''s primary strategy is to set up and fund Centres of Excellence and has committed itself to support the Danish research environments. The funding goes to university research groups in Denmark active in basic science. A total of 77 Centers of Excellence have been established, and a new generation of centers will be up and running by 1 January 2012. Normally these centers receive funding for ten years. It is important to mention the Niels Bohr Visiting Professorship programme in this context. This initiative is designed to further the internationalization of the Danish research establishments by attracting foreign top-level researchers to Denmark for longer periods of time. There is a new call for proposals in 2011 and the Foundation is going to fund six to eight new professorships.
Dartmouth Medical School; New Hampshire; USA
The nation''s fourth-oldest medical school, draws on the world-class resources of Dartmouth College and Dartmouth-Hitchcock Medical Center for broad interdisciplinary programs in biomedical research, education, patient care and service. Educational Programs include: MD Program, MD-PhD Program, MD/MBA Program, MPH, MS Programs, PhD - Biomedical Science, Continuing Medical Education, Graduate Medical Education We are committed to updating our curriculum every year, and to finding ways to improve each course and clerkship. Students and faculty often work together to plan these modifications and improvements. These stimulating changes, combined with their traditions of close mentoring relationships between faculty and students, and cooperation between students while learning, make DMS a wonderful place to learn medicine.
David Geffen School of Medicine at UCLA; California; USA
Delft University of Technology; Delft; Netherlands
Dutch public technical university, located in Delft, Netherlands.
Division of cancer biology and diagnosis
Division of cancer control and population science
Drexel University was founded in 1891 as the Drexel Institute of Art, Science and Industry by Philadelphia financier and philanthropist Anthony J. Drexel to provide educational opportunities in the ''practical arts and sciences'' for women and men of all backgrounds. Undergraduate majors/minors, certificate programs, graduate & professional, and Interdisciplinary programs are offered. Drexel''s array of programs, concentrations, courses and curricula are designed to prepare students for critical issues in science, technology, health sciences, information science, media arts, the humanities, and business to shape the next generation workforce and professoriate, and provide them the basic skills to be effective practitioners, communicators, and leaders. Drexel''s programs are complemented by co-operative education experiences for many of our students, where theory and practice converge. Drexel has more than 87 majors and over 100 minors to choose from so that your academic experience can be exactly what you want. With nationally recognized programs and countless choices, selecting a major can be daunting.
Drexel University College of Medicine; Pennsylvania; USA
Drexel University College of Medicine is the consolidation of two venerable medical schools with rich and intertwined histories: Hahnemann Medical College and Woman''s Medical College of Pennsylvania. Established in 1848 and 1850, respectively, they were two of the earliest medical colleges in the United States, and Woman''s was the very first medical school for women in the nation. Academic programs include: M.D. program, Biomedical Graduate Studies, Postdoctoral Studies, Professional Studies in the Health Sciences and Continuing Medical Education. Today, with over 1,000 medical students, Drexel University College of Medicine (DUCOM) has the largest medical student enrollment of any private medical school in the nation. Graduate students number more than 500, and the College is the academic partner in the education of some 550 medical residents. There are more than 700 clinical and basic science faculty, and more than 1,700 affiliate and volunteer faculty. The College has established one of the largest centers for spinal cord research in the Mid-Atlantic Region, and founded one of the leading centers for malaria study in the nation. Collaborative projects leveraging Drexel University''s technological expertise push the frontiers of nanomedicine and neuroengineering. Drexel University College of Medicine houses one of just 21 National Centers of Excellence in Women''s Health designated by the Department of Health & Human Services. The College''s HIV/AIDS primary care practice is the largest on the East Coast and in the top 5 nationwide. Faculty clinicians are highly respected in numerous other specialties, including pain management, sports medicine and toxicology.
Private research university in Durham, North Carolina. Founded by Methodists and Quakers in 1838. Home of Blue Devils, Duke University has undergraduate and graduate students and world class faculty.
Duke University School of Medicine; North Carolina; USA
Center for medical education, clinical care and biomedical research. Medical education includes programs that train medical students, residents and fellows, research scientists and post-doctoral fellows, physical therapists, physician assistants and pathologist assistants.
German Research Center for Artificial Intelligence; Berlin; Germany
Deutsches Forschungszentrum fur Kunstliche Intelligenz
Deutsches Forschungszentrum für Künstliche Intelligenz
German Research Center for Artificial Intelligence
German research institute in the field of innovative software technology. In the international scientific community, it ranks among the most recognized Centers of Excellence and currently is the biggest research center worldwide in the area of Artificial Intelligence and its application in terms of number of employees and the volume of external funds.
Duquesne University is a private, coeducational university located on a bluff above downtown Pittsburgh, Pennsylvania. Duquesne has a 14:1 student/faculty ratio, and 87 percent of incoming freshman are drawn from the top half of their high school class. Duquesne offers undergraduate and graduate degree programs in natural and environmental sciences, leadership, business, nursing, health sciences, pharmacy, law, education, music, and the liberal arts. Founded in 1878 as a Catholic college by the Order of the Holy Spirit, Duquesne is the largest and most comprehensive Catholic university in Pennsylvania, and the only Spiritan institution of higher education in the world. Duquesne is consistently ranked among America's top Catholic universities for its award-winning faculty and a tradition of academic excellence. A coeducational university on a self-contained campus with dramatic views of Pittsburgh's skyline and rivers, the university has students representing nearly every state in the union and 80 nations. In keeping with our Catholic-Spiritan vision, the University Core Curriculum emphasizes the students' intellectual and ethical development through the liberal arts. Using the modes of inquiry particular to the humanities and the social and natural sciences, students expand their self-understanding and their knowledge of the world. Pittsburgh area corporations, high-tech businesses, health systems and non-profit organizations recognize the quality of a Duquesne education, seeking our students for cooperative projects, internships and jobs.
Duquesne University Mylan, School of Pharmacy
Duquesne University Mylan School of Pharmacy and the Graduate School of Pharmaceutical Sciences
The Mylan School of Pharmacy is one of the most respected schools of pharmacy in the country. For more than 80 years, the School has been at the forefront of growth and change in professional education and practice. We have maintained and strengthened our leadership position, by introducing new and innovative degree programs in the pharmaceutical sciences, pharmacy administration, and the nation''s first and only weekend Pharm.D. program and Health Care Supply Chain Management program to meet the ever-changing healthcare needs of the world. Our Academic Research Centers keep the School on the cutting edge-integrating research, teaching and practice to ensure that Duquesne University retains its traditional influence on the exciting future of pharmacy, and that our graduates are fully prepared for leadership as they face the challenges and opportunities that lie ahead. The School offers Doctor of Pharmacy, Master of Sciences, Doctor of Philosophy degree programs as well as Health Care Supply Chain Management and Fellowship and Residency Programs.
East Carolina University continues to supply the nation with some of its best educators, and now it has been joined by programs of high distinction in health care and the fine and performing arts. The university is no longer a small school but an engine of economic development and a hotbed of discovery. Today, East Carolina is a constituent institution of the University of North Carolina and offers 104 bachelor''s degree programs, 74 master''s degree programs, 4 specialist degree programs, 1 first-professional MD program, and 17 doctoral programs in our professional colleges and schools, Thomas Harriot College of Arts and Sciences, and the Brody School of Medicine. With a mission of teaching, research, and service, East Carolina University is a dynamic institution connecting people and ideas, finding solutions to problems, and seeking the challenges of the future.
East Tennessee State University; Tennessee; USA
Ecole Nationale Sup�rieure des Mines d'Al�s
French technology and engineering university.
East Tennessee State University Quillen College of Medicine
The primary mission of the Quillen College of Medicine is to educate future physicians, especially those with an interest in primary care, to practice in underserved rural communities. In addition, the College is committed to excellence in biomedical research and is dedicated to the improvement of health care in Northeast Tennessee and the surrounding Appalachian Region. Degrees of Study include Doctor of Medicine, Master of Science, and Doctor of Philosophy; CME''s are also offered in many forms including videos and podcasts. The Quillen College of Medicine endeavors to meet community and regional health needs by identification, creation, and execution of the necessary programs through utilization of its diverse resources. The college is a major health care provider for East Tennessee. In view of this responsibility, the college emphasizes primary care as the focus of medical practice and training programs. The primary care physician is defined as the physician of first and continuing contact, coordinating the entire care of the patient. Primary medical care is a function rather than a discipline. This care is provided by family physicians, general internists, general pediatricians, and obstetricians / gynecologists. In addition to meeting the clinical and service responsibilities, the college also supports a significant research endeavor. The Quillen College of Medicine has an experienced and qualified faculty in the biological, behavioral, and clinical sciences. In addition to the full-time faculty, a number of practicing physicians in the community participate in the educational process as both part-time and volunteer faculty. Average Class Size: 60 (medical class) Significant Accolades: U.S.News & World Report - 2010 American''s Best Graduate Schools: 7th in nation for rural medicine 17th in nation for family medicine education Major Educational Emphasis: Primary Care, Rural Medicine Major Research Programs: Cardiovascular Disease, Primary Care, Immunology, Infectious Diseases
National Institute for Research in Computer Science and Control; Brittany; France
French Institute for Research in Computer Science and Automation
French national research institution focusing on computer science and applied mathematics.
We fund research and training in social and economic issues. We invested more than £211 million in 2009-2010, funding over 2,500 world-leading social science researchers and supporting more than 3,000 postgraduate students. We are a non-departmental public body established by Royal Charter in 1965 and receive most of our funding through the Department for Business, Innovation and Skills. Our research is vigorous and authoritative, as we support independent, high-quality, relevant social science.
Emory University, a top 20 research university located in Atlanta, Georgia, is an inquiry-driven, ethically engaged and diverse community whose members work collaboratively for positive transformation in the world through courageous leadership in teaching, research, scholarship, health care and social action. The university offers academic degrees and programs ( undergraduate, graduate and professional) through nine schools, with particular strengths in the arts and sciences, business, law, theology and the health professions. The university is recognized internationally for its outstanding liberal arts college, superb professional schools and one of the Southeast''s leading health care systems. Emory maintains an uncommon balance for an institution of its standing: it generates more research funding than any other Georgia university, while maintaining its traditional emphasis on teaching. The university is enriched by the legacy and energy of Atlanta, and by collaboration among its schools, units and centers, as well as with affiliated institutions.
Emory University School of Medicine; Atlanta; Georgia; USA
Emory University School of Medicine is graduate medical school of Emory University and component of Emory’s Robert W. Woodruff Health Sciences Center.
The mission of EPA is to protect human health and the environment. Develops and enforces regulations.Nearly half of budget goes into grants to state environmental programs, non-profits, educational institutions, and others.
Eotvos Lorand University; Budapest; Hungary
Eötvös Loránd University; Budapest; Hungary
Erasmus University Rotterdam; Rotterdam; Netherlands
Public university located in Rotterdam, Netherlands. The university is named after Desiderius Erasmus Roterodamus, a 15th-century humanist and theologian.
Estonian University of Life Sciences; Tartu; Estonia
The Estonian University of Life Sciences (Estonian: Eesti Maaülikool, EMÜ), located in Tartu, Estonia, is the former Estonian Agricultural University, which was established in 1951 and renamed and restructured in November 2005. Eesti Maaülikool is, by its own claim, the only university in Estonia whose priorities in academic and research activities provide the sustainable development of natural resources necessary for the existence of Man as well as the preservation of heritage and habitat. The EMÜ is a centre of research and development in such fields as agriculture, forestry, animal science, veterinary science, rural life and economy, food science and environmentally friendly technologies. The university is a member of the BOVA university network. Teaching and research is carried out in five institutes: * Institute of Agricultural and Environmental Sciences * Institute of Veterinary Medicine and Animal Sciences * Institute of Forestry and Rural Engineering * Institute of Technology * Institute of Economics and Social Sciences. In 2009, there were 4704 students at EMU. There were 983 employees, among them 228 lecturers and 159 researchers and senior researchers. (Wikipedia)
One of the main institutions of the European Union, its job is to represent and uphold the interests of the EU as a whole. It drafts proposals for new European laws. It manages the day-to-day business of implementing EU policies and spending EU funds. The 28 Commissioners, one from each EU member country, provide the Commission''s political leadership during their 5-year term. Each Commissioner is assigned responsibility for specific policy areas by the President. The Commission oversees and implements EU policies by: * proposing new laws to Parliament and the Council * managing the EU''s budget and allocating funding * enforcing EU law (together with the Court of Justice) * representing the EU internationally, for example, by negotiating agreements between the EU and other countries. The Commission is based in Brussels and Luxembourg and has offices (representations) in every EU country and delegations in capital cities around the world.
An independent medical research institute dedicated to improving global health that conducts high impact research that targets preventable illnesses and injuries that are the leading causes of death and disability worldwide, including heart and kidney disease, stroke, diabetes, mental illness, falls and traffic crashes. (Adapted from Wikipedia)
George Washington University; Washington D.C.; USA
Private research university in Washington, D.C. It was chartered in 1821 by an act of the United States Congress.
An agency responsible for the evaluation and supervision of medicines developed by pharmaceutical companies for use in the European Union. Its main responsibility is the protection and promotion of public and animal health through the evaluation and supervision of medicines for human and veterinary use. The Agency also plays a role in stimulating innovation and research in the pharmaceutical sector. The Agency gives scientific advice and other assistance to companies for the development of new medicines. It publishes guidelines on quality-, safety- and efficacy-testing requirements. A dedicated SME Office provides special assistance to small and medium-sized enterprises.
Independent body that funds investigator-driven frontier research in the European Union (EU). It is part of the Seventh Research Framework Programme (FP7).
National university in the city of Gifu, Gifu Prefecture, Japan. It is sometimes abbreviated as Gidai or Gifudai. The Tokai National Higher Education and Research System established by integrating with Nagoya University in April 2020, both are major universities in Central Japan.
The establishment of the European Science Foundation (ESF) in Strasbourg in 1974 was one of the earliest milestones on the road to achieving real cooperation in European research. The ESF began life with a membership of 42 academies and research councils in 15 countries; in 2011 it counts 78 Member Organizations (MOs), including research funding organizations, research performing organizations, academies and learned societies, in 30 countries. As an independent, non-governmental organization dedicated to pan-European scientific networking and collaboration, the ESF has had a key role to play in mediating between a multitude of heterogeneous research cultures and agencies. The ESF hosts an array of instruments to accommodate various types and levels of international collaboration, within Europe and beyond. The ESF''s unique characteristic in this area is its responsiveness to the scientific community, in contrast with the more targeted approaches taken by the European Commission. Many of the instruments operated by the ESF, e.g. Exploratory Workshops, EUROCORES (European Collaborative Research scheme), Research Networking Programmes (RNPs) and ESF Research Conferences, are designed to respond to needs articulated by the research community. Open calls for proposals are published on an annual basis, so that the themes for programmes, networks and workshops are gathered from the research community, in line with the ESF''s bottom-up principles. This is particularly welcome in research areas which might not otherwise be prioritized for funding on an international level. In recent years, the ESF''s profile has shifted from being mainly a facilitator of collaborative research and networking to also providing a platform for Member Organizations to develop joint strategic operations and synergy among themselves. By influencing the strategic agendas of MOs in this way, greater leverage over a much larger European budget and agenda is achieved. In other words, the ESF maximizes the impact of its support to the research community by combining bottom-up and topdown approaches to scientific cooperation.
The European Union is a unique economic and political partnership between 27 European countries. It has delivered half a century of peace, stability, and prosperity, helped raise living standards, launched a single European currency, and is progressively building a single Europe-wide market in which people, goods, services, and capital move among Member States as freely as within one country. The EU provides funding and grants for a broad range of projects and programs. The EU was created in the aftermath of the second world war. The first steps were to foster economic cooperation: countries that trade with one another are economically interdependent and will thus avoid conflict. Since then, the union has developed into a huge single market with the euro as its common currency. What began as a purely economic union has evolved into an organization spanning all areas, from development aid to environmental policy.
Ewha Womans University; Seoul; South Korea
Federal University of Rio de Janeiro; Rio de Janeiro; Brazil
University of Brazil is a public university in the state of Rio de Janeiro, Brazil. UFRJ is the largest federal university in the country and is one of the Brazilian centers of excellence in teaching and research.
Federal University of Rio Grande do Sul; Rio Grande do Sul; Brazil
Universidade Federal do Rio Grande do Sul
Brazilian federal university based in Porto Alegre, Rio Grande do Sul. UFRGS is among the largest and highest-rated universities in Brazil, having one of the largest number of scientific publications.
Finnish Ministry of Employment and the Economy
Florey Institute of Neuroscience and Mental Health; Victoria; Australia
Florey Institute of Neuroscience and Mental Health
One of the world''s top 10 brain research centres. Their scientists comprise the largest neuroscience research team in Australia.
Georgia Institute of Technology; Georgia; USA
Georgia Institute of Technology, commonly referred to as Georgia Tech or, in the state of Georgia, as Tech, is a public research university and institute of technology in Atlanta, Georgia.
Florida Agricultural and Mechanical University, School of Pharmacy
FAMU College of Pharmacy and Pharmaceutical Sciences
Florida Agricultural and Mechanical University College of Pharmacy and Pharmaceutical Sciences
The College of Pharmacy and Pharmaceutical Sciences at FAMU strive to develop progressive leaders in pharmaceutical care, research and public health who enhance the quality of life for the people of Florida. In less than six decades since our founding, the College has emerged as a nationally recognized leader in pharmacy practice, research and public health. The successes that we have achieved have been built upon a solid foundation of attracting the most academically talented students from across the country; providing faculty who are on the cutting edge of research and practice in their respective disciplines; and new state-of-the-art facilities that provide the environment for outstanding intellectual growth and development. The College of Pharmacy and Pharmaceutical Sciences is a professional college with limited enrollment and selective admissions. The mission of the College is to produce highly qualified pharmacy practitioners who take an active role and responsibility in the delivery and outcomes of pharmaceutical care.
Florida Agricultural and Mechanical University; Florida; USA
Florida Agricultural and Mechanical University (FAMU) is an 1890 land-grant institution dedicated to the advancement of knowledge, resolution of complex issues and the empowerment of citizens and communities. The University provides a student-centered environment consistent with its core values. The faculty is committed to educating students at the undergraduate, graduate, doctoral and professional levels, preparing graduates to apply their knowledge, critical thinking skills and creativity in their service to society. FAMU''s distinction as a doctoral/research institution will continue to provide mechanisms to address emerging issues through local and global partnerships. Expanding upon the University''s land-grant status, it will enhance the lives of constituents through innovative research, engaging cooperative extension, and public service. While the University continues its historic mission of educating African Americans, FAMU embraces persons of all races, ethnic origins and nationalities as life-long members of the university community. Florida A&M University (FAMU) offers 62 bachelor''s degrees in 94 majors/tracks, and 37 master''s degrees with 50 majors/tracks and one specialist degree program. The university has 13 schools and colleges and one institute. FAMU offers three professional degrees: the JD, PharmD, and the doctor of physical therapy. FAMU also has 11 doctoral degree programs including 10 Ph.D. degrees and one doctor of public health. The Ph.D. degrees are offered in the following areas: biomedical engineering; chemical engineering; civil engineering; electrical engineering; mechanical engineering; industrial engineering; pharmaceutical sciences; physics; educational leadership; and environmental science.
Florida State University is a public research university in Tallahassee, Florida, United States. It is a senior member of the State University System of Florida and a preeminent university in the state. Chartered in 1851, it is located on Florida's oldest continuous site of higher education.
Fogarty International Center for Advanced Study in the Health Sciences
John E. Fogarty International Center for Advanced Study in the Health Sciences
The Fogarty International Center is dedicated to advancing the mission of the National Institutes of Health by supporting and facilitating global health research conducted by U.S. and international investigators, building partnerships between health research institutions in the U.S. and abroad, and training the next generation of scientists to address global health needs. Fogarty International Center''s programs provide funding to perform research and to train researcher in a variety of global health topics. Through these extensive programs, Fogarty and its partners throughout the National Institutes of Health (NIH) are working to build sustainable research capacity in low- and middle-income countries. Current Programs Research and Research Training Programs * Biodiversity (ICBG) * Bioethics * Brain Disorders * Chronic Diseases: Chronic, Non-communicable Diseases and Disorders Across the Lifespan (NCD-Lifespan); Millennium Promise Awards: Non-communicable Chronic Diseases Research Training (NCoD); Clinical, Operational and Health Services (ICOHRTA) * Ecology and Evolution of Infectious Diseases (EEID) * Environmental and Occupational Health (ITREOH) * Framework * Framework Innovations * Framework Signature Innovations * Global Environmental and Occupational Health (GEOHealth) * Global Infectious Diseases (GID) * HIV: Fogarty HIV Research Training; AIDS International Training and Research (AITRP); Clinical, Operational and Health Services AIDS/TB (IICOHRTA-AIDS/TB) * Informatics (ITGH) * Medical Education Partnership Initiative (MEPI) * New Foreign Investigators (GRIP) * Research Collaboration (FIRCA) * Tobacco * Trauma and Injury * Womens and Girls Health Administrative Grant Supplements Career Development Opportunities for Individuals * Fellows and Scholars Programs: Global Health Fellows and Scholars; Scholars and Fellows (FICRS-F) * Fulbright-Fogarty Fellowships in Public Health * Independent Scientist in Global Health (ISGHA) * Japanese Researcher Fellowships (JSPS) * Junior Research Scientists (IRSDA) Other Programs * American Reinvestment and Recovery Act (ARRA) * Genetics * Population * Stigma
Foundation for Research and Technology-Hellas; Heraklion; Greece
Foundation for Research and Technology-Hellas
Research center in Greece, supervised by the Ministry for Education through its General Secretariat for Research and Technology.
Fraunhofer Society for the advancement of applied research
Fraunhofer-Gesellschaft zur F�rderung der angewandten Forschung e. V.
Applied research organization with its focus on developing key technologies that are vital for the future and enabling the commercial exploitation of this work by business and industry, Fraunhofer plays a central role in the innovation process.
Fraunhofer Institute for Algorithms and Scientific Computing SCAI; North Rhine-Westphalia; Germany
Fraunhofer Institute for Algorithms and Scientific Computing SCAI
Fraunhofer-Institut fur Algorithmen und Wissenschaftliches Rechnen SCAI
Fraunhofer-Institut f�r Algorithmen und Wissenschaftliches Rechnen SCAI
Institute that develops innovative methods in Computational Science and actively supports their take-up in industrial practice. The Institute combines mathematical and computational knowledge with a focus on algorithms bringing benefits to customers and partners.
Georgia Health Sciences University; Georgia; USA
Augusta State University and Georgia Health Sciences University have consolidated to become Augusta University.
Public research university in downtown Atlanta, Georgia, United States. Founded in 1913. One of the University System of Georgia's four research universities.
German Federal Ministry of Economics and Technology
Fraunhofer Institute for Biomedical Engineering
Fraunhofer-Institut fur Biomedizinische Technik
Fraunhofer-Institut fur Biomedizinische Technik (IBMT)
Fraunhofer-Institut f�r Biomedizinische Technik
Fraunhofer-Institut f�r Biomedizinische Technik (IBMT)
Institute that acts as device and technology developer when it comes to the solution of individual research and development projects and tasks from the areas of biomedical / medical engineering, molecular and cellular biotechnology, biohybrid technology, cryo(bio)technology and nano(bio)technology, ultrasound technology, neuroprosthetics / implants, (mobile) laboratory technology, sensor and measurement technology, health telematics, environmental control systems, material testing, home systems, air quality control and security systems as well as laboratory automation including in-line / on-line process control. The institute works in the field of stem cell research and hosts extensive cell line stocks in industrial and clinically structured biobanks for low temperature storage of valuable samples (fluids, cells, tissue fragments).
Fraunhofer Institute for Toxicology and Experimental Medicine
Institute that offers contract research in the area of human health with a focus on airway research. The institute has pooled its competences to form six business units: Toxicology Testing; Pre-clinical Pharmacology; Early-Phase Clinical Trials; Registration and Risk Assessment; Environmental, Occupational and Consumer Protection; and Manufacturing of Biopharmaceuticals for Clinical Trials. Due to their broad spectrum of expertise, they are able to offer complete solutions from the idea to the product.
An independent public scientific authority responsible for promoting the quality and safety of patient care and to guarantee equity within the healthcare system. HAS activities are diverse ranging from assessment of drugs, medical devices, and procedures to publication of guidelines to accreditation of healthcare organisations and certification of doctors. All are based on rigorously acquired scientific expertise. Training in quality issues and information provision are also key components of its work program.
Goethe University Frankfurt am Main; Hessen; Germany
Johann Wolfgang Goethe-Universitat Frankfurt am Main
Johann Wolfgang Goethe-Universität Frankfurt am Main
Public university located in Oxford, Ohio.
Michigan State University; Michigan; USA
Public research university in East Lansing, Michigan.
Nonprofit, nonpartisan think tank that helps people build meaningful lives. Center for Regional Economics and California Center.
Mainz Institute of Molecular Biology Bioinformatics Core Facility
Fraunhofer Institute for Molecular Biology and Applied Ecology
Fraunhofer Institute for Molecular Biology and Applied Ecology IME
Fraunhofer-Institut fur Molekularbiologie und Angewandte Oekologie IME
Fraunhofer-Institut f�r Molekularbiologie und Angewandte Oekologie IME
Provides assistance with consulting on experimental design, training on bioinformatics tools and databases, data quality assessment, data processing, data visualization, data interpretation, data mining of published datasets, and assistance with preparation of manuscripts and grant proposals.
Free University of Berlin; Berlin; Germany
Public research university in Berlin, Germany. The Free University of Berlin is one of eleven elite German research universities in the German Universities Excellence Initiative.
French National Center for Scientific Research
Centre National de la Recherche Scientifique
A government-funded research organization with the following missions: * To evaluate and carry out all research capable of advancing knowledge and bringing social, cultural, and economic benefits for society. * To contribute to the application and promotion of research results. * To develop scientific information. * To support research training. * To participate in the analysis of the national and international scientific climate and its potential for evolution in order to develop a national policy. As the largest fundamental research organization in Europe, CNRS carried out research in all fields of knowledge, through its seven institutes: * Institute of Biological Sciences (INSB) * Institute of Chemistry (INC) * Institute of Ecology and Environment (INEE) * Institute for Humanities and Social Sciences (INSHS) * Institute for Computer Sciences (INS2I) * Institute for Engineering and Systems Sciences (INSIS) * Institute of Physics (INP) and three national institutes: * National Institute for Mathematical Sciences (INSMI) * National Institute of Nuclear and Particle Physics (IN2P3) * National Institute for Earth Sciences and Astronomy (INSU) CNRS''s annual budget represents a quarter of French public spending on civilian research. This funding comes from various sources: * Government and public funding; * CNRS funds, primarily from industrial and EU research contracts and royalties on patents, licenses, and services provided.
The ANR is a research funding organization. It was established by the French government in 2005 to fund research projects, based on competitive schemes giving researchers the best opportunities to realize their projects and paving the way for ground-breaking new knowledge. The role of the Agency is to bring more flexibility to the French research system, foster new dynamics and devise cutting edge-strategies for acquiring new knowledge. By identifying priority areas and fostering private-public collaborations, it also aims at enhancing the general level of competitiveness of both the French research system and the French economy. *The ANR supports the public and private-sector research community *Scientific departments
Friedrich Schiller University Jena; Thuringia; Germany
Leibniz Institute for Age Research - Fritz Lipmann Institute
The Leibniz Institute for Aging Research - Fritz Lipmann Institute (FLI) is the first national research institute in Germany that deals with biomedical research into human aging. Aging is a multifactorial process that is influenced by the environment and genetic factors.
Ministry of Agriculture of the Peoples Republic of China
Ministry of Agriculture of the People''s Republic of China
Ministry of Agriculture and Rural Affairs of the People's Republic of China is the cabinet-level executive department of the State Council which is responsible for agriculture and rural affairs in the country. The ministry is headquartered in Beijing.
Ministry of the Government of Singapore that directs the formulation and implementation of policies related to Education in Singapore.
The FRQS (Fonds de recherche du Québec - Santé) is a non-profit funding agency created under the Act Respecting the Ministère du Développement économique, de l'Innovation et de l'Exportation (L.R.Q., c. M-30.01). We report to the Minister in charge of Québec's department for economic development, innovation and export trade (ministère du Développement économique, de l'Innovation et de l'Exportation) and our mandate is to implement government strategy with respect to human health research as presented in the Québec Research and Innovation Strategy. The FRQS was established in 1964 by Québec's health department under the name Conseil de recherches médicales. A pioneer in both Québec and Canada, the FRQS advised the health minister in matters of medical research. Forty years later, the FRQS plays a leading role in planning and coordinating the development of health research in Québec. The FRQS allocates $100 million annually in awards and grants for public-sector research into human health carried out today in universities and hospital-based research centers. We fund projects using any of the recognized methodologies (basic, clinical, epidemiological, public health, health services and the social determinants of health). To fulfill our mission and maximize the economic and health benefits of scientific investigation, we invest in: *top-performing research investigators and students *research centers, groups and networks *excellence, innovation and the dissemination of knowledge *social responsibility and ethical practices *synergy and partnership, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Fujian Agriculture and Forestry University; Fujian; China
Fujian Agriculture and Forestry University
Fujian Agriculture and Forestry University is a leading higher education institution in Fujian Province, jointly supported by the Ministry of Agriculture, the State Forestry Administration and the Fujian Provincial Government in China.
Gachon University; Seongnam; South Korea
Academic institute located in South Korea. The current structure of Gachon university is the result of a merger between four existing universities.
Gachon University of Medicine and Science; Incheon; South Korea
Gachon University of Medicine and Science
Graduate School of Arts and Sciences at Columbia University Medical Center
CUMC Graduate School of Arts and Sciences
The Columbia University Medical Center is home to over 2,000 basic and clinical faculty and 3,000 students. In addition to the graduate school, this intellectual powerhouse incorporates schools of medicine, dentistry, nursing and public health. The campus also includes the New York Presbyterian Hospital, ranked within the top 10 in the nation. Columbia''s diverse academic resources, as well as its proximity to other scientific institutions offers endless opportunities to attend data clubs, lectures and symposia as well as to pursue research collaborations or learn new techniques. We offer a range of nationally top-ranked Ph.D. Programs grouped in five divisions. Regardless of program affiliation, students have access to all training faculty when selecting their research direction, ensuring that each student receives optimal training and research experience.
Greek Ministry of National Education and Religious Affairs
Guru Gobind Singh Indraprastha University; Delhi; India
Guru Gobind Singh Indraprastha University
Hadassah Medical Center; Jerusalem; Israel
Hadassah Medical Center is an Israeli medical organization established in 1934 that operates two university hospitals at Ein Kerem and Mount Scopus in West Jerusalem as well as schools of medicine, dentistry, nursing, and pharmacology affiliated with the Hebrew University of Jerusalem.
Hagedorn Research Institute; Gentofte; Denmark
A diabetes research facility that focuses its research efforts on early applied research. This approach will be based on translational biology-based innovations in five main specialty areas: * Insulin & Incretins * Beta-cell Reconstitution * Stem-cell Therapy * Diabetes Inflammation * diabetes genetics The expanded research focus will aim to identify new biology-based targets for potential drugs to supply Novo Nordisk''s pipeline within the key areas of diabetes pathogenesis, treatment and cure. The discovery primarily takes place through in vitro assays with proteins and peptides. They serve as an early applied research center for Novo Nordisk''s Diabetes Research Unit (DRU) and as a strategic hub for DRU''s early discovery research.
Harbin Institute of Technology; Harbin; China
Research university and a member of China's elite C9 League. HIT is a Chinese Ministry of Education Class A Double First Class University.
Harbin Medical University; Heilongjiang; China
Hamner Institutes for Health Sciences; North Carolina; USA
The Hamner Institutes for Health Sciences
An independent, nonprofit organization that offers an open, collaborative and cross-disciplinary approach to translational biomedical research. Based in Research Triangle Park, North Carolina, The Hamner strives to act as a catalyst with global academic institutions, industries, and government to support innovative research and rapid technology development. Hamner scientists have been recognized world-wide for their research contributions and training programs in environmental health sciences and chemical risk assessment. The Hamner has since broadened its mission to include translational research in biopharmaceutical safety, oncology, and nanosafety. Advances from Hamner research have contributed significantly to our understanding of human health concerns that include exposure to environmental chemicals, adverse events from prescription drugs, cancer prevention, and lung disease. The Hamner is poised for continued growth and exploration of new opportunities to protect public health and prevent human disease.
Hannover Medical School; Lower Saxony; Germany
One of the world''s leading university medical centres. Our research and patient care set national and international standards. We are also part of an excellent regional medical network. Our outstanding success in interdisciplinary collaboration both within the MHH and with extramural scientific institutions is reflected in the fact that the MHH is the German medical university with the greatest volume of grant funding.
Harvard Medical School; Massachusetts; USA
Graduate medical school of Harvard University and is located in the Longwood Medical Area of Boston, Massachusetts.
Harvard T.H. Chan School of Public Health
founded in 1913, Harvard T.H. Chan School of Public Health has provided graduate training in public health.
A large multidisciplinary world leader in genomic research with locations in Rockville, Maryland and San Diego, California. It was formed through the merger of several affiliated and legacy organizations - The Institute for Genomic Research (TIGR) and The Center for the Advancement of Genomics (TCAG), The J. Craig Venter Science Foundation, The Joint Technology Center, and the Institute for Biological Energy Alternatives (IBEA).
Idaho State University, College of Pharmacy
The College of Pharmacy consists of two departments: Biomedical and Pharmaceutical Sciences and Pharmacy Practice and Administrative Sciences. The Department of Biomedical and Pharmaceutical Sciences provides basic science instruction in the profession pharmacy curriculum, graduate training in the pharmaceutical sciences, and offers an undergraduate minor in pharmaceutical sciences. The department is also devoted to basic research in the biomedical sciences. The Department of Pharmacy Practice and Administrative Sciences provides instruction on therapeutics and clinical sciences to the professional pharmacy students and other health science students at ISU. In addition, the department is devoted to clinical research and scholarship. If you would like to know more about an individual faculty member, please see our biographical profiles.
Public research university in Pocatello, Idaho. Founded in 1901 as the Academy of Idaho, ISU offers more than 280 programs at its main campus and at locations in Meridian, Idaho Falls, and Twin Falls. It is the state's designated lead institution in health professions and medical education.
As the largest collaborative of its kind, the Harvard Stem Cell Institute is a truly unique scientific enterprise -- a gathering place for a whole community of scientists and clinical experts in stem cell science seeking to bring new treatments to the clinic, and new life to patients with a wide range of chronic illnesses. The Harvard community, consisting of the university, medical school and 11 teaching hospitals and research institutions, already represents one of the largest concentrations of biomedical researchers in the world. But stem cell research is a challenge that involves areas of expertise not encompassed in any one discipline, department or school. Most importantly, basic biology must interface with medical expertise if the promise of this field is to be fully realized. The Harvard Stem Cell Institute (HSCI) was founded in 2004 to draw Harvard''s resources together by establishing a cooperative community of scientists and practitioners, by developing new ways to fund and support research, and by promoting opportunities for open communication and education. Addressing the many societal issues, including legal, political and economic questions, raised by stem cell research requires an interdisciplinary approach, and HSCI draws in faculty not only from the biomedical sciences but also from Harvard''s professional schools, including Harvard Law School, the Harvard Kennedy School, the Harvard School of Public Health, the Harvard Business School and the Harvard Divinity School.
Harvard University; Cambridge; United States
Institution of higher education in the United States. Private Ivy League research university in Cambridge, Massachusetts.
Department of the Government of Canada responsible for the country's federal health policy. It is overseen by the minister of health as part of the minister's health portfolio.
An organization that provides healthcare services or that is involved in the provision of health care activities. Groupings or subdivisions of an organization, such as departments, may also be considered as organizations where there is a need to identify them.
Health Resources and Services Administration
Hebrew University Hadassah Medical School; Jerusalem; Israel
Hebrew University Hadassah Medical School
Hebrew University-Hadassah Medical School
Hebrew University of Jerusalem; Jerusalem; Israel
Heidelberg Institute for Theoretical Studies; Heidelberg; Germany
Heidelberg Institute for Theoretical Studies
Heidelberg University; Baden-Wurttemberg; Germany
Public research university in Heidelberg, Baden-Württemberg, Germany. Founded in 1386 on instruction of Pope Urban VI, is the oldest university in Germany.
Nonprofit medical research organization that ranks as one of the nation's largest philanthropies for advancing biomedical research and science education in the United States. Known for its scientific research and modern architecture.
Helmholtz Zentrum Munchen German Research Center for Environmental Health
Helmholtz Zentrum Munchen-German Research Center for Environmental Health
Lead research institution of Federal Republic of Germany and Free State of Bavaria with research mission of increasing understanding of disease mechanisms which affect human beings and essential parts of their environment. Center is divided into 28 research institutes and independent research units, which are interlinked and cooperate on various topics and in various research programs to develop new approaches to combat respiratory, metabolic and neurological diseases.The institute offers diabetes and lung information services, among others, and higher education training programs.
Illinois Institute of Technology; Illinois; USA
Chicago''s premier engineering, science, and technology based university.
Kirksville College of Osteopathic Medicine
The namesake of A.T. Still University, Andrew Taylor Still, M.D., D.O., founded the Kirksville College of Osteopathic Medicine in 1892. KCOM was the first institution of osteopathic education in the world and continues to provide leadership for comprehensive medical education, research, and healthcare. Consistent with the college''s mission, KCOM is consistently ranked in U.S. News & World Report as one of the best medical schools in the country for rural and family medicine training. KCOM graduates represent a diverse group of osteopathic physicians practicing in every state and several other countries. They span all medical specialties and sub-specialties and comprise approximately a quarter of all practicing osteopathic physicians.
Helmholtz Center Munich Institute of Epidemiology
Helmholtz Zentrum Munchen German Research Center for Environmental Health Institute of Epidemiology
Helmholtz Zentrum Munchen Institute of Epidemiology
The main aim of Epidemiology at the Helmholtz Zentrum Munchen is to examine the role of environmental factors and genetic predisposition on human health by the use of epidemiological methods. Research is conducted in cooperation with the Institute of Medical Information Processing, Biometrics and Epidemiology at Ludwig Maximilians University of Munich. The institute is organized in five research units: * Environmental Epidemiology * Epidemiology of Air Pollution Health Effects * Epidemiology of Chronic Diseases * Genetic Epidemiology * Epidemiology Biological Samples Genomics The institute runs several cohort studies with adult, school children and new-born study populations, as well as time series analyses, case control studies and family studies. Another goal is to provide infrastructure for epidemiological research. As a resource for future studies a collection of serum, plasma, DNA and an archive of EBV immortalized B-Lymphocytes is being established. International co-operation and qualification of our members is highly emphasized in this institute, there are co-operations with about 70 scientific institutes and universities in Germany and abroad. We would like to point to the co-operation with the Harvard School of Public Health (MPH-training of institute members, exchange of scientists) and with the US-Environmental Protection Agency (EPA) in Chapel Hill. Two thirds of the personnel is financed through external grants, which are provided by state ministries, federal institutions, the European Union and grant giving institutions in the United States of America.
Helmholtz Center Munich Institute of Experimental Genetics
Helmholtz Zentrum Munchen Institute of Experimental Genetics
The aim of the Institute of Experimental Genetics (IEG) is to further the basic understanding of mechanisms that underlie the etiology of human diseases. Metabolic diseases with focus on diabetes and bone/cartilage disorders are the new key areas of research. Experimental set-ups are centered on the mouse as pre-clinical model organism. Besides studying the effects of genotypes, the institute has recently started to identify and characterize environmental factors and the mechanisms by which these act on the etiology of diseases. The systemic phenotyping of models and the exploration of envirotypes as a source of important disease factors are integral to the German Mouse Clinic (GMC).
Hessian Ministry of Higher Education Research and the Arts
Hessisches Ministerium für Wissenschaft und Kunst
Hong Kong Baptist University; Hong Kong; China
Hong Kong Polytechnic University; Hong Kong; China
Public research university in Hong Kong. Founded in 1911, its origins trace back to the Hong Kong College of Medicine for Chinese, which was founded in 1887. It is the oldest tertiary institution in Hong Kong.
Howard University College of Medicine; Washington D.C.; USA
Health and Environmental Sciences Institute (HESI)
Health and Environmental Sciences Institute
A non-profit institution that engages scientists from academia, government and industry to identify and resolve global health and environmental issues. As a neutral third party organization, it acts as an objective forum for initiating dialogue among scientists with different perspectives and expertise, in the attempt to create a pathway that can resolve issues identified by its multi-sector membership and the external scientific community. HESI's bylaws require that all HESI activities are directed and carried out in an objective manner for the benefit of the public health. HESI conducts, organizes, and/or supports, original laboratory research; workshops; conferences; literature reviews; the development and analysis of databases; and many other scientific activities. HESI makes the outcomes of these activities available to the scientific community and the public through peer-reviewed journals; monographs; scientific symposia and posters; and other print- and web-based publications.
Imperial College London; London; United Kingdom
Imperial College of Science Technology and Medicine
Consistently rated amongst the world''s best universities, Imperial College London is a science-based institution with a reputation for excellence in teaching and research.
Public research university in Indiana. Has 8 statewide campuses known for innovation, creativity, and academic freedom.
Indiana University Bloomington; Indiana; USA
Founded in 1820, IU Bloomington is the flagship campus of Indiana University''s eight campuses statewide. Innovation, creativity, and academic freedom are hallmarks of IU Bloomington and its world-class contributions in research and the arts. For our traditions like the world-famous Little 500 bicycle race and our commitment to emerging technologies, IU was named the Hottest Big State School in 2005 by Newsweek, America''s Hot Colleges. We nurture bright minds with an exceptional support network and breadth of programs. For technology infrastructure and support, our campus was named most wired among public universities by PC Magazine in 2006. U.S. News & World Report has recognized IU for outstanding freshman programs and residential learning communities, and Time magazine praised our commitment to freshmen when it named IU College of the Year in 2001.
Indian Institute of Technology Kanpur; Uttar Pradesh; India
Indian Institute of Technology Kanpur is a public technical and research university located in Kanpur, Uttar Pradesh. It was declared to be an Institute of National Importance by the Government of India under the Institutes of Technology Act.
INRA - French National Institute for Agricultural Research; Paris; France
French National Institute for Agricultural Research
Institut National de la Recherche Agronomique
Institut National de la Recherche Agronomique Rennes
Institute for Research in Biomedicine; Barcelona; Spain
Fundacio Privada Institut de Recerca Biomedica
IRB Fundacio Privada Institut de Recerca Biomedica
Institute for biomedical research in Barcelona, Spain.
Instituto Superior de Psicologia Aplicada; Lisbon; Portugal
Instituto Superior de Psicologia Aplicada
University Institute of Psychological Social and Life Sciences
Institute for Scientific and Technical Information
Institut de l''Information Scientifique et Technique
For over a decade, the Institute for Scientific and Technical Information (INstitut de l''Information Scientifique et Technique - Inist) of the French National Center for Scientific Research (Cnrs) has been designing and developing services to facilitate access to and valorization of scientific information produced by international basic and applied research communities. The INIST has skilled expertise in the field of biocuration of digital resources and bibliographic databases. With the advent of the Internet, while continuing with its traditional document delivery and bibliographic activities, INIST''s role has evolved towards providing public sector researchers with the direct and permanent access to the scientific information they need. Nowadays, INIST is actively involved in activities concerning electronic resources negociations and electronic resource sharing, electronic publishing, electronic archiving, science monitoring, and information analysis and processing.
Jacobs University Bremen; Bremen; Germany
Institute for Systems Biology; Washington; USA
The Institute for Systems Biology (ISB) was established to address the greatest challenge of 21st-century science understanding biological complexity. Since its founding in 2000, ISB has been a pioneering source of new knowledge, innovative technologies and computational tools, and creative ways of understanding, conducting and communicating science. An independent, non-profit organization poised between academia and industry, ISB is deeply committed to discovering knowledge and translating its benefits to society. ISB commercializes its discoveries; advances science education; helps society better understand the impacts of science and technology; and creates exciting new organizations that facilitate these transfers. ISB is catalyzing fundamental paradigm changes in how the life sciences and medicine are practiced globally. Researchers at ISB are generating results that can be applied to some of society''s most perplexing problems in medicine, global health and the environment. They are creating productive strategic partnerships with universities, companies and governments around the world, which are essential to attacking these challenges in a trans-disciplinary manner.
Institute of Bioinformatics; Bangalore; India
The Institute of Bioinformatics and Applied Biotechnology (IBAB) is a non-profit autonomous institute set up by the Department of IT, BT and S and T, Government of Karnataka. It is located in a 20-acre campus in the southern part of the City of Bengaluru and is a part of Biotech Park.
Institute of Bioinformatics and Systems Biology; Neuherberg; Germany
Institute for Bioinformatics and Systems Biology
Hosts the Munich Information Center for Protein Sequences (MIPS) and its main focus is the genome-oriented bioinformatics, in particular the systematic analysis of genome information including the development and application of bioinformatics methods in genome annotation, expression analysis and proteomics. MIPS supports and maintains a set of generic databases as well as the systematic comparative analysis of microbial, fungal, and plant genomes.
The Institute of Biological Sciences (INSB) is a CNRS institute that develops and coordinates research in biological sciences with the overall aim to better understand life in all its complexity, starting at the level of atoms and biomolecules, extending to cells and through to organisms and populations. Scientific fields: structural biology, bioinformatics, pharmacology, neuroscience, cognitive science, immunology, genetics, cell biology, microbiology, physiology, plant biology, systems biology, biodiversity...
Institute of Biology and Chemistry of Proteins; Lyon; France
IBCP : Institute of Biology and Chemistry of Proteins - FR3302
Institut de Biologie et de Chimie des Proteines
Institut de Biologie et de Chimie des Prot�ines
Institute of Biology and Chemistry of Proteins
Institute of Biology and Chemistry of Proteins of Lyon University.
Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia
Institute of Cytology and Genetics of the Siberian Branch of the RAS
Institute of Cytology and Genetics SB RAS
Institute of Experimental Biology and Technology; Oeiras; Portugal
iBET - Instituto de Biologia Experimental Tecnol�gica
Institute of Experimental Biology and Technology
Instituto de Biologia Experimental e Technologica
Instituto de Biologia Experimental Tecnol�gica
A private not for profit research organization in the area of biotechnology and life sciences. They bridge university and industry research, by establishing partnerships particularly in the areas of health-pharma, agro-industry, forestry, agriculture and the environment. iBET has two satellite laboratories with Bayer and Merck Serono. Their network of collaborations is broad, ranging from national and international companies, research institutes, foundations and public institutions. At iBET they serve also as an incubation platform for start-up/spin-off companies. iBET is a certified service provider. Their Analytical Service Unit is certified with Good Manufacturing Practices (GMP), and their pilot plant unit (2.400m2) provides process development technology and manufacturing services. Their partner GenIbet (45% owned by iBET) follows current Good Manufacturing Practices, in early stage biopharmaceuticals production for phase I and Phase II clinical trials. iBET belongs to the Associated Laboratory of Oeiras (Laboratório Associado de Oeiras, LAO) along with Instituto de Tecnologia Química e Biológica (ITQB), Instituto Gulbenkian de Ciência (IGC) and the Chronic Diseases Research Center (CEDOC).
The main Public Research Entity funding, managing and carrying out biomedical research in Spain. Its key mission is to support the development of scientific knowledge in the health sciences and to contribute to innovation in healthcare and the prevention of disease. It reports directly to the Ministry of Economy and Competitiveness (Royal Decree 345/2012) and in operational terms to both this Ministry and to the Ministry of Health, Social Services and Equality (Royal Decree 200/2012). The Institute has been conducting research and providing key services in the life and health sciences for over 20 years. It is also the body responsible for managing Spain''s Health Research and Development Strategy within the framework of the National R+D+I Plan. Putting patients and the public at the heart of all its activities and objectives, the Institute promotes and coordinates biomedical research and provides scientific and technical services of the highest quality in partnership with all the organisations forming part of the Spanish System of Science, Technology and Innovation.
Jackson State University; Mississippi; USA
JSU covers 4 campus locations and offers more than 90 different bachelor's, master's, and doctoral degree programs. Jackson State is the 4th largest institution of higher learning in Mississippi.
Institute of Microbial Technology; Chandigarh; India
Established in 1984, the Institute of Microbial Technology (IMTECH) is one amongst the 38 national laboratories of the Council of Scientific & Industrial Research (CSIR) and is its youngest laboratory. Set-up to be a fore-runner in the area of Biotechnology, the Institute occupies an area of about 47 acres, of which the labs cover 22 acres and the residential campus, 25 acres. The Institute has a built up area of about 3.60 lakh sq. ft., is spread over five main buildings, the main R&D block (~2.00 lakhs sq. ft.), Fermentation block (~0.50 lakhs sq. Ft.), Animal House (~0.30 lakhs sq. ft.), Workshop, Stores and Services area (~0.50 lakhs sq. ft.), and Cafeteria (~0.10 lakhs sq. ft.). The Institute''s primary asset is a team of 50 highly motivated young scientists, more than two thirds of whom are Ph.D.s with many having several years of training in world-renowned laboratories. Supported by more than 300 well-trained technicians and graduate students, these scientists are engaged in basic and application-oriented research.
Institute of Molecular Biology and Biotechnology; Heraklion; Greece
FORTH Institute of Molecular Biology and Biotechnology
Institute of Molecular Biology and Biotechnology
Institute of Molecular Biology and Biotechnology-FORTH
Institute of Museum and Library Services
The primary source of federal support for the nation''s 123,000 libraries and 17,500 museums.
Instituto Gulbenkian de Ciencia; Oeiras; Portugal
Gulbenkian Institute of Science; Oeiras; Portugal
Instituto Gulbenkian de Ciência Oeiras; Portugal
Instituto Gulbenkian de Ciência, IGC, is a leading life science research institute in Portugal, founded by Fundação Calouste Gulbenkian
A nonprofit, worldwide organization whose mission is to provide science that improves human health and well-being and safeguards the environment. It achieves this mission by fostering collaboration among experts from academia, government, and industry on conducting, gathering, summarizing, and disseminating science. Their activities focus on nutrition and health promotion; food and water safety; risk science and toxicology; and sustainable agriculture and nutrition security.
International Prevention Research Institute
International Prevention Research Institute SAS
An independent, non-profit, research institute with experience in epidemiological research and macro health planning with a record of delivering real health and economic value to a range of public and private sources including governments, universities, research institutes, non-governmental organizations and large multi-national concerns. iPRI is conducting a broad range of research projects with emphasis on prevention of chronic diseases and conditions. All iPRI projects have an international dimension, and their results are expected to impact on clinical and preventive practices. Projects may include authoritative reviews and meta-analyses, secondary analyses of existing data and samples and collection of new data and biological samples in the field. All iPRI projects result in publications in leading scientific journals. Projects may be funded by public or private sources, as well as by iPRI itself. In all cases, sponsors have no influence in the planning, conduct, analysis or reporting of the projects. iPRI is also engaged in several research projects with partners from low- and medium-income countries.
IST National Institute for Cancer Research; Genoa; Italy
IST - National Institute for Cancer Research
IST Istituto Nazionale per la Ricerca sul Cancro
IST National Institute for Cancer Research
IST National Institute for Cancer Research - Genoa
National Institute for Cancer Research; Genova; Italy
Italian Ministry of Education Universities and Research
Italian Ministry of Education University and Research
A public organization whose duty is to carry out, promote, spread, transfer and improve research activities in the main sectors of knowledge growth and of its applications for the scientific, technological, economic and social development of the Country. To this end, the activities of the organization are divided into macro areas of interdisciplinary scientific and technological research, concerning several sectors: biotechnology, medicine, materials, environment and land, information and communications, advanced systems of production, judicial and socio-economic sciences, classical studies and arts. CNR is distributed all over Italy through a network of institutes aiming at promoting a wide diffusion of its competences throughout the national territory and at facilitating contacts and cooperation with local firms and organizations. From the financial point of view, the main resources come from the State, but also from the market: even 30% of its balance sheet, an extraordinary result, is the result of revenues coming from external job orders for studies and activities of technical advice as well as from agreements with firms, contracts with the European Union and with the other international organizations. One of CNR institutional duties is the carrying out of research activities in pursuit of excellence and strategic relevance within the national and international ambit, through its network of research institutes. The network of CNR research institutes, which are distributed all over the national territory, is multidisciplinary: it has competences in the field of health and biology, of computer science, of environment and climate, of chemistry and physics, of behavioral, economic and social sciences.
Axon™pCLAMP™ 10 Electrophysiology Data Acquisition and Analysis Software
Software suite for electrophysiology data acquisition and analysis by Molecular Devices. Used for the control and recording of voltage clamp, current clamp, and patch clamp experiments. The software suite consists of Clampex 11 Software for data acquisition, AxoScope 11 Software for background recording, Clampfit 11 Software for data analysis, and optional Clampfit Advanced Analysis Module for sophisticated and streamlined analysis.
James Hutton Institute; Scotland; United Kingdom
Multi-disciplinary research organization with strengths in crops, soils, land & environmental research, studying food, energy & environmental sustainability in Aberdeen and Dundee, UK. The James Hutton Institute brings together the Macaulay Land Use Research Institute and SCRI (Scottish Crop Research Institute) both of which have illustrious histories. The new institute was created on 1 April 2011. The new organization will make major, new contributions to the understanding of key global issues, such as food, energy and environmental security, and developing and promoting effective technological and management solutions to these. The James Hutton Institute is an internationally networked organization and operates from multiple sites, including two main ones in Scotland at Aberdeen and Dundee. It employs more than 600 scientists and support staff, making it one of the biggest research centers in the UK and the first of its type in Europe. The institute is one of the Scottish Government''s main research providers in environmental, crop and food science and will have a major role in the Scottish knowledge economy. James Hutton (1726 1797) was a leading figure of the Scottish Enlightenment, an eighteenth century golden age of intellectual and scientific achievements centered on Edinburgh. He is internationally regarded as the founder of modern geology and one of the first scientists to describe the Earth as a living system. His thinking on natural selection influenced Charles Darwin in developing his theory of evolution.
Japanese Ministry of Education Culture Sports Science and Technology (MEXT)
Japanese Ministry of Education Culture Sports Science Technology (MEXT)
Ministry of Education Culture Sports Science & Technology
Ministry of Education Culture Sports Science & Technology in Japan
Ministry of Education Culture Sports Science and Technology in Japan
Ministry of Education Culture Sports Science and Technology of Japan
Ministry of Education Culture Sports Science Technology in Japan
One of the eleven Ministries of Japan that composes part of the executive branch of the Government of Japan. Their goal is to improve the development of Japan in relation with the international community.
Japanese Ministry of Health Labor and Welfare
Japanese Ministry of Health Labour and Welfare
Ministry of Health Labour and Welfare - Japan
Cabinet level ministry of the Japanese government. It is commonly known as Kōrō-shō in Japan. The ministry provides services on health, labour and welfare.
Japanese government agency which aims to build infrastructure that supports knowledge creation and dissemination in Japan.
Jawaharlal Nehru University; New Delhi; India
Public central university located in New Delhi, India. It was established in 1969 and named after Jawaharlal Nehru, India's first Prime Minister. The university is known for leading faculties and research emphasis on liberal arts and applied sciences.
Sir Mortimer B. Davis Jewish General Hospital
Hospital known officially as the Sir Mortimer B. Davis Jewish General Hospital since 1978, is an acute-care teaching hospital in Montreal, Quebec, Canada. The hospital is affiliated with McGill University
John Innes Centre; Norwich; United Kingdom
An independent, international center of excellence in plant science and microbiology. Their mission is: * To generate knowledge of plants and microbes through innovative research * To apply their knowledge of nature''s diversity to benefit agriculture, the environment, human health and well-being * To train scientists for the future * To engage with policy makers and the public
Joint Information Systems Committee (JISC) is the UK''s expert on information and digital technologies for education and research. JISC inspires UK colleges and universities in the innovative use of digital technologies, helping to maintain the UK''s position as a global leader in education. JISC helps institutions make best use of technology to manage all aspects of their business. JISC provides access to the world-class Janet (UK) network, quality digital resources and a range of specialist advisory services. JISC provides: * A world-class network - JANET * Access to electronic resources * New environments for learning, teaching and research * Guidance on institutional change * Advisory and consultancy services * Regional support - JISC RSCs Partnerships JISC develops partnerships to enable the UK education and research communities to engage in national and global collaborations to overcome the challenges of delivering world-class ICT solutions and services. Funding Opportunities JISC funds a wide range of infrastructure, services, innovative projects and studies. A large number of these originate from a successful response to a grant funding call (previously known as a JISC Circular), inviting eligible HE and FE institutions to bid for project funding. JISC also procures other activities (usually studies such as an evaluation or market research), through invitations to tender which are available to other organizations to bid against. JISC is the name of our organization. Historically, it stood for Joint Information Systems Committee.
Johannes Gutenberg University Mainz; Rhineland-Palatinate; Germany
Public research university in Mainz, Rhineland Palatinate, Germany, named after the printer Johannes Gutenberg since 1946. With approximately 32,000 students in about 100 schools and clinics, it is among the largest universities in Germany.
Johannes Kepler University of Linz; Linz; Austria
A public institution of higher education in Linz, the capital of Upper Austria, that offers bachelor''s, master''s, diploma and doctoral degrees in business, engineering, law, science, and the social sciences.
Latvian Institute of Organic Synthesis; Riga; Latvia
Institute established to perform research in organic chemistry, molecular biology and bioorganic chemistry that has a experience in drug design and technology development; namely 17 original drugs were discovered and introduced into the market and more than 70 original preparation methods of known medicines were invented. Presently IOS has on-going projects with 11 pharmaceutical companies. Together with business partners more than 270 patents have been filed in the last 5 years. Services include: Process chemistry, Medicinal chemistry, Pharmacology and biological studies, Analytical chemistry, and Custom synthesis.
Public research university in Quebec City, Quebec, Canada founded by royal charter issued by Queen Victoria in 1852.The oldest centre of higher education in Canada and the first North American institution to offer higher education in French.
Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (UC) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 200-acre site in the hills above the UC Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 4,200 scientists, engineers, support staff and students. Its budget for 2010 is $707 million, with an additional $104 million in funding from the American Recovery and Reinvestment Act, for a total of $811 million.
Federal research facility in Livermore, California, United States, founded by the University of California, Berkeley in 1952.
Loyola University Chicago; Illinois; USA
Private Catholic research university in Chicago, Illinois. Founded in 1870 by the Jesuits, Loyola is one of the largest Catholic universities in the United States.
La Trobe University; Victoria; Australia
Public research university based in Melbourne, Victoria, Australia. Its flagship campus is located in the Melbourne suburb of Bundoora. The university was established in 1964, becoming the third university in the state of Victoria and the twelfth university in Australia.
Institute whose mission is to understand the molecular mechanisms that underlie the aging process and that lead to age-related diseases. They hope that eventually this knowledge can contribute to a more healthy aging of people. The central question they are aiming at answering is, What are the molecular mechanisms and genetic factors contributing to the evolution of cellular and organismal dysfunction during human aging?
Leibniz Institute of Plant Genetics and Crop Plant Research; Saxony-Anhalt; Germany
Leibniz Institute of Plant Genetics and Crop Plant Research
Leibniz-Institut fur Pflanzengenetik und Kulturpflanzenforschung
Leibniz-Institut fur Pflanzengenetik und Kulturpflanzenforschung (IPK)
Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung
Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
Public research university in Leiden, Netherlands. Founded in 1575 by William, Prince of Orange as a reward to the town of Leiden for its defense against Spanish attacks during the Eighty Years' War, it is the oldest institution of higher education in the Netherlands.
The Library of Congress is the nation''s oldest federal cultural institution and serves as the research arm of Congress. It is also the largest library in the world, with millions of books, recordings, photographs, maps and manuscripts in its collections. The Library''s mission is to support the Congress in fulfilling its constitutional duties and to further the progress of knowledge and creativity for the benefit of the American people. Thousands of dedicated staff acquire, catalog, preserve, and make available library collections within our three buildings on Capitol Hill and over the Internet.
Life Science Foundation; Santiago; Chile
Fundacion Ciencia para la Vida; Santiago; Chile
Fundación Ciencia para la Vida is playing a key role in researching and developing new biotechnology tools and processes that would enhance Chile's competitive position. To accomplish this goal, Fundación acts as an interphase between the productive and academic sectors, and collaborates with scientists all over the world, both in the public and private sectors. Founded in 1997 as a non-profit organization, Fundación has the mission of promoting the adoption and use of science-based innovations by Chilean and International companies. Fundación has specialized on building value by developing products and technologies that serve the needs of the Agriculture, Mining, Forestry, Aquaculture and Healthcare industries. It is actively building human resources capacities through the training of undergraduate and PhD students in collaboration with different local universities. It also, promotes and participates in a number of global networks of scientific collaboration with local and international centers of academic excellence. Fundación acts as a bridge between the productive and academic sectors in Chile and with international partners abroad. Fundación's Research and Development programs enjoy a leading position in the biotechnology sector both, in Chile and abroad. Its world-class research, its commitment to effective training of human resources in science and its productive connections with international research groups, has allowed Fundación Ciencia para la Vida to become one of Chile's most innovative research center in the life sciences arena.
Liverpool School of Tropical Medicine; Liverpool; United Kingdom
Liverpool School of Tropical Medicine (LSTM)
Institution dedicated to research and teaching in the field of tropical medicine. As a registered charity, they work in over 60 countries worldwide, often in very difficult circumstances, to fulfill their mission of reducing the burden of sickness and mortality in disease endemic countries through the delivery of effective interventions which improve human health and are relevant to the poorest communities. Their new Centre for Tropical and Infectious Diseases is a state of the art facility for developing new drugs, vaccines and pesticides which puts us at the forefront of infectious disease research. As a teaching institution, they attract more than 600 students from 68 countries, from PhD research and Masters programs to a range of short courses, and work in partnership with health ministries, universities and research institutions worldwide to train the next generation of doctors, scientists, researchers and health professionals. The provision of technical assistance is a major component of LSTM''s mission of promoting the improved health of the poor and disadvantaged peoples. LSTM consultancy improves health systems in developing countries whilst helping to inform their teaching and research agendas.
London School of Hygiene and Tropical Medicine; London; United Kingdom
London School of Hygiene & Tropical Medicine
London School of Hygiene and Tropical Medicine
Public research university in Bloomsbury, Camden, and a constituent college of the University of London that specialises in public health and tropical medicine.
Long Island University; Arnold & Marie Schwartz College of Pharmacy & Health Sciences
Arnold & Marie Schwartz College of Pharmacy and Health Sciences
Arnold and Marie Schwartz College of Pharmacy and Health Sciences
The Arnold and Marie Schwartz College of Pharmacy and Health Sciences is a student-centered institution that also serves its other stakeholders including faculty and staff, alumni, the pharmaceutical community and industry, and the public, in a variety of ways. Established in 1886 as the Brooklyn College of Pharmacy, it is one of the oldest and largest institutions of its kind in the nation. The Arnold & Marie Schwartz College of Pharmacy and Health Sciences is a student-centered institution. Our mission is to provide access and academic excellence to those who are interested in pursuing a career in pharmacy and related areas. An extraordinary faculty and state-of-the-art laboratories and facilities are integrated with the most prestigious and comprehensive array of clinical affiliations in the United States. Participating in our network are over thirty major medical centers and long-term care facilities, hundreds of community pharmacies, our own International Drug Information Center, and nearly 1,000 preceptors. In addition to our Doctor of Pharmacy (Pharm.D) program, the College offers M.S. and Ph.D degrees in a variety of pharmacy and related administrative and scientific disciplines of particular interest to the pharmaceutical industry. These programs provide graduate students with outstanding research opportunities and with the skills for career growth. On our website, prospective students can learn more about our academic programs, financial aid and the application process. For our alumni, the website will keep you abreast of various alumni events as well as our extensive continuing education offerings for practicing pharmacists.
Private university in Brooklyn, New York City. It is the original unit and first of two main campuses of the private Long Island University system.
Los Alamos National Laboratory is a premier national security research institution, delivering scientific and engineering solutions for the nation''s most crucial and complex problems. Our primary responsibility is ensuring the safety, security, and reliability of the nation''s nuclear deterrent. The Los Alamos of today emphasizes worker safety, effective operational safeguards & security, and environmental stewardship, while outstanding science remains the foundation of the Laboratory. In addition to supporting the Lab''s core national security mission, our work advances bioscience, chemistry, computer science, earth and environmental sciences, materials science, and physics disciplines.
Loughborough University; Loughborough; United Kingdom
Public research university in the market town of Loughborough, Leicestershire, in the East Midlands of England.
Louisiana State University; Louisiana; USA
Officially Louisiana State University and Agricultural and Mechanical College, commonly referred to as LSU is a public land-grant research university in Baton Rouge, Louisiana.The university was founded in 1853 in what is now known as Pineville, Louisiana, under the name Louisiana State Seminary of Learning and Military Academy.
Louisiana State University Health Sciences Center Shreveport; Louisiana; USA
The primary mission of Louisiana State University Health Sciences Center Shreveport (LSUHSCS) is to provide education, patient care services, research, and community outreach. LSUHSCS encompasses the Schools of Medicine, Graduate Studies, and Allied Health Professions in Shreveport, the LSU Hospital in Shreveport, E. A. Conway Medical Center in Monroe, and Huey P. Long Medical Center in Pineville. In implementing its mission, LSUHSCS is committed to: * Educating physicians, basic scientists, residents, fellows and allied health professionals based on state-of-the-art curricula, methods, and facilities, preparing students for careers in health care service, teaching or research. * Providing state-of-the-art clinical care, including a range of tertiary special services, to an enlarging and diverse regional base of patients. * Achieving distinction and international recognition for basic science and clinical research programs that contribute to the body of knowledge and practice in science and medicine. * Supporting the region and the State in economic growth and prosperity by utilizing research and knowledge to engage in productive partnerships with the private sector.
Ministry of Health and Welfare - Republic of Korea
Ministry of Health & Welfare - Republic of Korea
Ministry of Health Welfare - Republic of Korea
Louisiana State University School of Medicine; Louisiana; USA
Louisiana State University Health Sciences Center School of Medicine at New Orleans
Louisiana State University School of Medicine; Health Sciences Center
LSU Health Sciences Center School of Medicine at New Orleans
LSUHSC School of Medicine at New Orleans
The Louisiana State University School of Medicine in New Orleans is a place where you will find a conclave of distinguished scientists, outstanding healthcare professionals, their skilled staffs and our motivated students, all united in the vigorous pursuit of excellence in education, patient care, research and service to the community. Through systematic self-assessment, LSUHSC has made comprehensive modifications to their curriculum as exemplified by their state-of-the-art Student Learning Center. Here students learn in small groups and from the beginning are taught the connections between the basic sciences and clinical practice. Through advanced simulation technologies, their learners practice difficult procedures before they perform them on patients. With distance learning and telemedicine technologies they network with their students and residents in outlying hospitals as they benefit from the multiplicity of experiences that come with serving a broad geographic area. The school of medicine has maintained a deep commitment to serving all patients, particularly the under-served. It is aligned with the LSUHSC Health Care Services Division which consists of nine hospitals throughout the state. Through this important relationship, it''s faculty and house staff provide quality medical care to the residents of Louisiana regardless of income or insurance coverage. Simultaneously, it''s partnerships with the LSU Healthcare Network and local private hospitals supply outstanding care to a growing population of private patients. Here at the LSU School of Medicine, the researchers continually push at the edges of medical knowledge. We are continuing an active recruitment of both clinical and basic science faculty with a resultant increase in extramural grant funding. Through our many Centers of Excellence we collaborate across specialties by bringing the finest scientific minds to bear on creative and exciting new methods for improving the delivery of patient care and the quality of life for all people.
University is located in the city of Lund in the province of Scania, Sweden. It arguably traces its roots back to 1425, when a Franciscan studium generale was founded in Lund.
Loyola University Chicago Stritch School of Medicine; Illinois; USA
Ludwig-Maximilians-University; Munich; Germany
Ludwig-Maximilian-University Munich; Munich; Germany
Ludwig-Maximilians-University; Bavaria; Germany
Public research university located in Munich, Germany.
Maastricht University; Maastricht; Netherlands
The most international university in the Netherlands that stands out for its innovative approach to learning and international outlook. With 14,500 students and 3,500 staff, UM offers a wide choice of academic programs, all of which are designed to bring out the best in its students. Maastricht University has used Problem-Based Learning (PBL) ever since it was founded and has been an expert in this field for over 35 years. PBL is more than just acquiring knowledge; it''s about exchanging knowledge in a challenging and effective way. Maastricht University makes the difference. With unique Europe-focused and international-oriented programs. After all, UM is Leading in Learning.
Maisonneuve-Rosemont Hospital; Quebec; Canada
Mario Negri Institute for Pharmacological Research; Milan; Italy
Istituto di Ricerche Farmacologiche Mario Negri
Mario Negri Institute for Pharmacological Research
Mario Negri Istituto di Ricerche Farmacologiche
A not-for-profit biomedical research institute whose main aim is to help defend human health and life. Research programs span from the molecular level to the whole human being, and the findings help build up the basis for developing new drugs, and making existing ones more effective. The main research headings are the battle against cancer, nervous and mental illnesses, cardiovascular and kidney diseases, rare diseases and the toxic effects of environmental contaminants, mother and child' '''s health. The Institute is also involved in research on pain relief and drug addiction. Parallel to its biomedical investigations, the Mario Negri Institute runs training schemes for laboratory technicians and graduate researchers. It takes part in a range of initiatives to communicate information in biomedicine, on a general level and with the specific aims of improving health care practice, and encouraging more rational use of drugs. There are also research units in Bergamo, at Ranica - near Bergamo - and at Santa Maria Imbaro, near Chieti.
Private Jesuit research university in Milwaukee, Wisconsin.
Marquette University College of Health Sciences; Wisconsin; USA
Marshall University Joan C. Edwards School of Medicine; West Virginia; USA
At Marshall University, the Joan C. Edwards School of Medicine blends high-quality medical education and graduate education with a distinctive hands-on approach to meeting the health care needs of West Virginians and others who live in the nation''s rural areas. Marshall produces skilled, confident graduates who are successful in generalist and subspecialty medicine.
Nagahama Institute of Bio-Science and Technology; Nagahama; Japan
Nagahama Institute of Bio-Science and Technology
Private university in Nagahama, Shiga, Japan, established in 2003.
Max Planck Gesellschaft zur Förderung der Wissenschaften E.V.
Max Planck Society for the Advancement of Science
Max Planck Society for the Advancement of Science e.V.
Max-Planck Society for the Advancement of Science
Max-Planck-Gesellschaft zur Forderung der Wissenschaften
Max-Planck-Gesellschaft zur Forderung der Wissenschaften eV
Max-Planck-Gesellschaft zur Förderung der Wissenschaften
Max-Planck-Gesellschaft zur Förderung der Wissenschaften e. V.
Max-Planck-Gesellschaft zur Förderung der Wissenschaften eV
Society of prestigious German research institutions that conduct basic research in the service of the general public in the natural sciences, life sciences, social sciences, and the humanities. Max Planck Institutes focus on research fields that are particularly innovative, or that are especially demanding in terms of funding or time requirements. And their research spectrum is continually evolving: new institutes are established to find answers to seminal, forward-looking scientific questions, while others are closed when, for example, their research field has been widely established at universities. This continuous renewal preserves the scope the Max Planck Society needs to react quickly to pioneering scientific developments.
Max-Planck-Institute for Informatics; Saarbrucken; Germany
The Max-Planck Institute for Informatics is devoted to cutting-edge research in informatics with a focus on algorithms and their applications in a broad sense. Our research ranges from foundations (algorithms and complexity, programming logics) to a variety of application domains (computer graphics, geometric computation, constraint solving, program verification, databases and information systems, and computational biology/bioinformatics). * On the fundamental research side, this involves first-class research on new algorithms. * The algorithmic work for applications encompasses the integration of new algorithms into full-fledged systems and concrete application scenarios that are of high practical relevance. This involves the implementation of comprehensive software platforms and their experimental evaluation in application settings. * We provide a stimulating environment for junior researchers. Our goal is to have impact through publications, software and people alike. We test the value of our ideas by integrating new algorithms into systems and assessing their utility in realistic settings. This experience is useful in the short term in refining our designs and invaluable in the long term in advancing our knowledge. Most of the major advances in informatics and algorithms research have come through this combination of new theoretical insights and experimental validation.
Max Planck Institute of Molecular Plant Physiology; Golm; Germany
Max Planck Institute for Molecular Plant Physiology
Max Planck Institute of Molecular Plant Physiology
Max-Planck-Instituts für Molekulare Pflanzenphysiologie
German research institute for molecular plant physiology, based in the Golm district of Potsdam, Brandenburg.
Max Delbruck Center for Molecular Medicine; Berlin; Germany
Max Delbruck Center for Molecular Medicine
Max Delbrück Center for Molecular Medicine
A major biomedical research institute located in the northeastern corner of Berlin, Germany, with a mission of translating discoveries from molecular research into applications to improve the prevention, diagnosis, and treatment of major human diseases. The work of the MDC''s 57 research groups centers around three classes of disease which have an enormous impact on society: * Cardiovascular and metabolic diseases * Cancer * Nervous system disorders
Max Planck Institute for Biological Cybernetics; Tubingen; Germany
Max Planck Institute for Biological Cybernetics
Max Planck Institute for Biological Cybernetics; Tübingen; Germany
MMax-Planck-Institut für biologische Kybernetik
Max Planck Institute for Biophysical Chemistry; Gottingen; Germany
Max Planck Institute of Biophysical Chemistry
Max Planck Institute of Biophysical Chemistry; Göttingen; Germany
Max-Planck-Institut fur biophysikalische Chemie
Max-Planck-Institut für biophysikalische Chemie
Max-Planck-Institute of Biophysical Chemistry
Max Planck Institute for Biophysical Chemistry in Göttingen is a research institute of the Max Planck Society. Currently, 850 people work at the institute, about half of them are scientists.
Max Planck Institute for Demographic Research; Mecklenburg-Vorpommern; Germany
Max Planck Institute for Demographic Research
Max-Planck-Institut fur demografische Forschung
Max-Planck-Institut für demografische Forschung
Max Planck Institute for Demographic Research is located in Rostock, Germany. It was founded in 1996 by James Vaupel and moved into new buildings in Rostock in 2002. It is one of approximately 80 institutes of the Max Planck Society.
Max Planck Institute for Developmental Biology; Tubingen; Germany
Max Planck Institute for Developmental Biology
Max Planck Institute for Developmental Biology; Tübingen; Germany
Max-Planck-Institut fur Entwicklungsbiologie
Max Planck Institute for Developmental Biology is located in Tübingen, Germany; it was founded in 1954 as an offshoot of the Tübingen-based Max Planck Institute for Biology.
Max Planck Institute for Heart and Lung Research; Bad Nauheim; Germany
Max Planck Institute for Heart and Lung Research
Max Planck Institute for Human Cognitive and Brain Sciences; Leipzig; Germany
Max Planck Institute for Human Cognitive and Brain Sciences
MPI for Human Cognitive and Brain Sciences
Nanyang Technological University; Singapore; Singapore
Max Planck Institute for Infection Biology; Berlin; Germany
Max Planck Institute for Infection Biology
Max-Planck-Institut für Infektionsbiologie
The Max Planck Institute for Infection Biology was founded in 1993. The Institute commenced its operation in a provisional laboratory facility and a small group of scientists that has greatly expanded over the years, and relocated to an especially built facility in summer 2000. The new facility is located in the heart of Berlin on the historical Charite medical campus, where Robert Koch and Emil Behring had made their important discoveries paving the field of infection research, in close proximity to the Parliament house and the newly constructed government offices. The choice of the location was to support the goal of the Institute to research infectious diseases in close collaboration with universities and clinical units.
Max Planck Institute for Medical Research; Heidelberg; Germany
Max Planck Institute for Medical Research
Max-Planck-Institut fur medizinische Forschung
Max-Planck-Institut für medizinische Forschung
Max Planck Institute for Molecular Genetics; Berlin; Germany
Max Planck Institute for Molecular Genetics
Max-Planck-Institute for Molecular Genetics
Max Planck Institute of Biochemistry; Martinsried; Germany
Proteins are the molecular building blocks and engines of the cell, and are involved in almost all processes of life. The scientists at the Max Planck Institute of Biochemistry (MPIB) investigate the structure of proteins and how they function from individual molecules up to whole organisms. With about 850 employees coming from 45 nations, the MPIB is one of the largest institutes within the Max Planck Society. In currently seven departments and about 25 research groups, scientists contribute to the newest findings in the areas of biochemistry, cell biology, structural biology, biophysics and molecular science. They are supported by several scientific, administrative and technical service facilities.
Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany
Max Planck Institute of Molecular Cell Biology and Genetics
Biology research institute located in Dresden, Germany. Research includes molecular, cellular, and developmental biology and biophysics with topics in molecular motors, neural development, cell division, lipid rafts, endocytosis, embryogenesis, regeneration.
Max Planck Institute of Molecular Physiology; Dortmund; Germany
Max Planck Institute of Molecular Physiology
Max Planck Institute of Molecular Physiology is located in Dortmund, next to the Dortmund University of Technology. It is one of 80 institutes in the Max Planck Society.
Nonprofit academic medical center focused on integrated clinical practice, education, and research with three major campuses: Rochester, Minnesota; Jacksonville, Florida; and Phoenix/Scottsdale, Arizona. Practice specializes in treating difficult cases through tertiary care and destination medicine.
College offering a broad range of programs to train and provide continuing education for medical and biomedical research professionals. The college consists of five schools: * Mayo Medical School * Mayo Graduate School * Mayo School of Graduate Medical Education * Mayo School of Health Sciences * Mayo School of Continuous Professional Development
Mayo Clinic Florida is a comprehensive medical center belonging to the Mayo Clinic in Jacksonville, Florida. It is one of three Mayo campuses along with Phoenix/Scottsdale, Arizona and Rochester, Minnesota.
Nonprofit academic medical center based in Rochester, Minnesota, focused on integrated clinical practice, education, and research. Highly specialized in cardiovascular diseases and surgery. Practice specializes in treating difficult cases through tertiary care and destination medicine.
Mayo Graduate School has a distinguished history of achieving its mission to prepare students for careers as competitive, independent research investigators. The distinctive character of Mayo Clinic''s program stems from a core curriculum of courses covering many basic science disciplines. The Ph.D. Program places heavier emphasis on research training than coursework -- a natural outgrowth of Mayo''s role as a leading center for investigation in the life sciences. Mayo Graduate School offers a Ph.D. degree in biomedical sciences with an emphasis in one of seven areas of specialization: * Biochemistry and Molecular Biology * Biomedical Engineering * Immunology * Neurobiology of Disease * Molecular Pharmacology and Experimental Therapeutics * Virology and Gene Therapy * Clinical and Translational Science
Public research university in Montreal, Quebec, Canada. Founded in 1821 by royal charter granted by King George IV, the university bears the name of James McGill, a Scottish merchant whose bequest in 1813 formed the university's precursor, University of McGill College. Name was officially changed to McGill University in 1885.
Public research university in Hamilton, Ontario, Canada. The main McMaster campus is on 121 hectares of land near the residential neighbourhoods of Ainslie Wood and Westdale, adjacent to the Royal Botanical Gardens.
Medical College of Georgia; Georgia; USA
Georgia Health Sciences University Medical College of Georgia
Georgia Health Sciences University Medical College of Georgia; Georgia; USA
Medical Products Agency; Uppsala; Sweden
The Swedish national authority responsible for regulation and surveillance of the development, manufacturing and marketing of drugs and other medicinal products. Their task is to ensure that both the individual patient and healthcare professionals have access to safe and effective medicinal products and that these are used in a rational and cost-effective manner.
Ministry of Higher Education Research and Science of Quebec
Enseignement Supérieur Recherche et Science - Québec
Enseignement Supérieur Recherche et Science du Québec
Enseignement Supérieur Recherche et Science Québec
Ministere de l''Enseignement Superieur de la Recherche de la Science et de la Technologie du Quebec
Ministry of Higher Education Research and Science
Ministry of Higher Education Research Science and Technology - Quebec
Ministry of Higher Education Research Science and Technology of Quebec
Ministère de l''Enseignement Supérieur de la Recherche de la Science et de la Technologie du Québec
Ministry of Higher Education Scientific Research - Tunisia
Ministry of Higher Education Scientific Research (MHESR) - Tunisia
Republic of Tunisia - Ministry of Higher Education Scientific Research and Technology
Ministry of Information and Communication of Korea
Korean Ministry of Information and Communication
MIC (Ministry of Information and Communication of Korea)
Ministry of Information and Communication
The Ministry of Information and Communication, the government organ which in charge of the Telecommunications Policies, radiomanagement, broadcasting, postal service, and postalbanking servics, has Planned integrated and systematic policy to facilitate the information society and to develop the information and communications industry.
Ministry of Science and Technology of China
Ministry of Science and Technology of China of the People''s Republic of China
Ministry of Science and Technology of China of the Peoples Republic of China
Formerly the State Science and Technology Commission, is the central government ministry which coordinates science and technology activities in the country. It succeeded the State Science and Technology Commission in 1998.
Missouri University of Science and Technology
Missouri University of Science Technology
Ministry of Knowledge Economy - Republic of Korea
Montclair State University; New Jersey; USA
Public research university in Montclair, New Jersey, with parts of the campus extending into Little Falls, New Jersey. It is the second largest university in New Jersey.
Montpellier 2 University; Montpellier; France
Université Montpellier 2 Sciences et Techniques
University of Montpellier 2 is one of the three universities that were formed with the split of the original University of Montpellier in 1970.
Morehouse School of Medicine; Georgia; USA
Morehouse School of Medicine (MSM), located in Atlanta, Georgia, became an independently chartered institution and the first medical school established at a Historically Black College and University in the 20th century in 1981. MSM is among the nation''s leading educators of primary care physicians and was recently recognized as the top institution among U.S. medical schools for our social mission. Our faculty and alumni are noted in their fields for excellence in teaching, research, and public policy, and are known in the community for exceptional, culturally appropriate patient care. MSM has seven residency programs: Family Medicine (1981), Preventive Medicine (1986), Internal Medicine (1991), Psychiatry (1991), Surgery (1993), Obstetrics and Gynecology (1997), and Pediatrics (2000). The majority of MSM patient care and clinical training occurs at Grady Memorial Hospital, one of the largest public hospitals in the Southeast. The school''s research stature and reputation have grown exponentially over the past decade. In 2008, MSM ranked number three among the nation''s community-based medical schools in research funding from the National Institutes of Health and among Georgia''s four medical schools, MSM ranks number two. Moreover, MSM ranks in the top five of U.S. medical school with five or more Institute of Medicine (IOM) members, based on the ratio of the IOM members faculty size.
Coeducational and public research university located in Moscow, Russia. It was founded on 23 January 1755 by Mikhail Lomonosov. During the Soviet period, MSU was renamed after Lomonosov in 1940 and was then known as Lomonosov University.
Mount Allison University; New Brunswick; Canada
A public institution with a scientific and technical vocation under the dual auspices of the Ministry of Health and the Ministry of Research. It was created as a successor to the French National Institute of Health. INSERM consists of 339 research units, run by 6500 permanent staff members. Eighty percent of INSERM research units are embedded in research hospitals of French universities.
National Center for Complementary and Alternative Medicine
National Center for Complementary Alternative Medicine
The National Center for Complementary and Alternative Medicine (NCCAM) is the Federal Government''s lead agency for scientific research on the diverse medical and health care systems, practices, and products that are not generally considered part of conventional medicine. The mission of NCCAM is to define, through rigorous scientific investigation, the usefulness and safety of complementary and alternative medicine interventions and their roles in improving health and health care. NCCAM sponsors and conducts research using scientific methods and advanced technologies to study CAM. CAM is defined simply as a group of diverse medical and health care interventions, practices, products, or disciplines that are not generally considered part of conventional medicine. NCCAM has four primary areas of focus: # Advancing scientific research: We fund research projects at scientific institutions across the United States and around the world. # Training CAM researchers: We support training for new researchers as well as encourage experienced researchers to study CAM. # Sharing news and information: We provide timely and accurate information about CAM research in many ways, such as through our Web site, Twitter, Facebook, and other social media tools, our information clearinghouse, fact sheets, Lecture Series, and continuing medical education programs. # Supporting integration of proven CAM therapies: Our research helps the public and health professionals understand which CAM therapies have been proven to be safe and effective. We are 1 of the 27 institutes and centers that make up the National Institutes of Health (NIH) within the U.S. Department of Health and Human Services.
National center for immunization and respiratory diseases
National center for injury prevention and control
A former institute of the NIH that, for 50 years, provided laboratory scientists and clinical researchers with the tools and training they needed to understand, detect, treat, and prevent a wide range of diseases. They supported all aspects of clinical and translational research, connecting researchers, patients, and communities across the nation. This support enabled discoveries made at a molecular and cellular level to move to animal-based studies, and then to patient-oriented clinical research, ultimately leading to improved patient care. Through programs such as the Clinical and Translational Science Awards, they brought together innovative research teams and equiped them with essential tools and critical resources needed to tackle the nations complex health problems. NCRR, through all of its programs, sparked innovation and leveraged shared resources to: * Establish clinical research infrastructure, including specialized research staff, informatics support, and laboratories that enable studies of the full range of human disorders. * Fund career development programs that attract talented medical students, physicians, and dentists to the challenge of clinical research careers. * Enhance development programs for underserved states and institutions, focusing on health disparities that negatively impact racial and ethnic minority populations. * Stimulate basic research to develop versatile new technologies and methods that help researchers to study virtually every human disease. * Provide access to state-of-the art technologies and instruments that enable both basic biomedical research and clinical investigations of a multitude of health issues, from cancer to infectious diseases. * Develop and provide access to critical animal models, which offer essential clues to a broad range of human disorders such as Parkinson''s disease, multiple sclerosis, and AIDS. * Train veterinarians in translational research in order to respond to deadly human diseases, such SARS, influenza, and hepatitis. * Provide funding to expand, remodel, and renovate or alter existing research facilities or construct new research facilities. * Improve the public understanding of medical research and provide adults and children with information about healthy living and science career opportunities.
National Centre for Research and Development (Poland)
National Center for Research and Development
National Centre for Research and Development
The implementing agency of the Minister of Science and Higher Education, it is the entity in charge of the performance of the tasks within the area of national science, science and technology and innovation policies.
National Chiao Tung University; Hsinchu; Taiwan
Institute conducts and supports research, training, health information dissemination, and other programs with respect to blinding eye diseases, visual disorders, mechanisms of visual function, preservation of sight, and special health problems of individuals who are visually impaired or blind. Supports vision research through grants and training awards. Conducts laboratory and patient oriented research at its own facilities located on NIH campus in Bethesda, Maryland. NEI has established National Eye Health Education Program.
National Genotyping Center; Ile-de-France; France
National Genotyping Center; Île-de-France; France
National genotyping center to advance research of the genetics of human diseases through internal and collaborative research programs. To this end they have developed a number of state-of-the-art genomics technology platforms and laboratories. Technology available at CNG ranges from a fully integrated high-throughput genotyping facility to a next generation sequencing platform. Activities include whole genome association studies (GWAS), pan-genomic expression profiling, epigenetic studies (DNA methylation, chromatin structure studies) and whole genome sequencing. All platforms, tools and know-how developed at CNG are open to outside groups for through collaborative research programs, and also applied by the Centre for its own research into the genetic basis of hereditary diseases.
NHLBI provides leadership for a national program in diseases of the heart, blood vessels, lung, and blood; blood resources; and sleep disorders. Since October 1997, the NHLBI has also had administrative responsibility for the NIH Woman''s Health Initiative. The Institute plans, conducts, fosters, and supports an integrated and coordinated program of basic research, clinical investigations and trials, observational studies, and demonstration and education projects. The National Heart, Lung, and Blood Institute (NHLBI) provides global leadership for a research, training, and education program to promote the prevention and treatment of heart, lung, and blood diseases and enhance the health of all individuals so that they can live longer and more fulfilling lives. The NHLBI stimulates basic discoveries about the causes of disease, enables the translation of basic discoveries into clinical practice, fosters training and mentoring of emerging scientists and physicians, and communicates research advances to the public. It creates and supports a robust, collaborative research infrastructure in partnership with private and public organizations, including academic institutions, industry, and other government agencies. The Institute collaborates with patients, families, health care professionals, scientists, professional societies, patient advocacy groups, community organizations, and the media to promote the application of research results and leverage resources to address public health needs. The NHLBI also collaborates with international organizations to help reduce the burden of heart, lung, and blood diseases worldwide.
National Heart Lung and Blood Institute Office of the Director
National Heart Lung and Blood Institute: Office of the Director
Office of the Director (OD) of the National Heart Lung and Blood Institute
Office of the Director of the National Heart Lung and Blood Institute
Provides overall planning, direction, coordination, and evaluation of the Institute''s programs, and coordinates all related Federal health programs. The OD collects, develops, and disseminates information on the diseases of the heart, lung, and blood, on sleep disorders, and on transfusion medicine, with an emphasis disease prevention; and conducts and fosters educational programs for scientists and clinicians. It provides leadership in the transfer and assessment of information for the scientific community and the lay public, and establishes internal Institute policy for program and administrative operations, maintaining surveillance over their implementation.
National Historical Publications and Records Commission
National Historical Publications & Records Commission
Statutory body affiliated with the National Archives and Records Administration (NARA) that supports a wide range of activities to preserve, publish, and encourage the use of documentary sources, created in every medium ranging from quill pen to computer, relating to the history of the United States.
National Human Genome Research Institute
National Center for Human Genome Research
One of 27 institutes and centers that make up the NIH, National Human Genome Research Institute (NHGRI) is devoted to advancing health through genome research. The Institute led NIH''s contribution to the Human Genome Project, which was successfully completed in 2003 ahead of schedule and under budget. Building on the foundation laid by the sequencing of the human genome, NHGRI''s work now encompasses a broad range of research aimed at expanding understanding of human biology and improving human health. The NHGRI''s mission has expanded to encompass a broad range of studies aimed at understanding the structure and function of the human genome and its role in health and disease. To that end NHGRI supports the development of resources and technology that will accelerate genome research and its application to human health. A critical part of the NHGRI mission continues to be the study of the ethical, legal and social implications (ELSI) of genome research. NHGRI also supports the training of investigators and the dissemination of genome information to the public and to health professionals.
NIH is the nations medical research agency - making important medical discoveries that improve health and save lives. The National Institutes of Health (NIH), a part of the U.S. Department of Health and Human Services, is the primary Federal agency for conducting and supporting medical research. Helping to lead the way toward important medical discoveries that improve peoples health and save lives, NIH scientists investigate ways to prevent disease as well as the causes, treatments, and even cures for common and rare diseases. NIH research impacts: * child and teen health, * men's health, * minority health, * seniors' health, * women's health, and * wellness and lifestyle issues. Composed of 27 Institutes and Centers, the NIH provides leadership and financial support to researchers in every state and throughout the world.
National Institute for Health and Welfare; Helsinki; Finland
National Institute for Health and Welfare
The National Institute for Health and Welfare (THL) is a research and development institute under the Finnish Ministry of Social Affairs and Health. THL seeks to serve the broader society in addition to the scientific community, actors in the field and decision-makers in central government and municipalities. The aim is to promote health and welfare in Finland.
National Institute of Advanced Industrial Science and Technology
Advanced Industrial Science and Technology
The National Institute of Advanced Industrial Science and Technology (AIST), led by President Nomakuchi, is a public research institution funded by the Japanese government to a large extent. The present AIST is a rather new research organization established in 2001. However, AIST and its predecessor organizations have been contributing to society through continuous advancement in technologies and support of Japanese industries since 1882. Headquarters of AIST are located in Tsukuba and Tokyo. AIST has over 40 autonomous research units in various innovative research fields, and the units are located at nine research bases and several sites (smaller than research bases) of AIST all over Japan. About 2400 researchers (about 2100 with tenure: about 80 from abroad) and thousands of visiting scientists, post-doctoral fellows, and students from home and abroad are working at AIST. About 700 permanent administrative personnel and many temporary staff support research works of AIST.
National Institute of Agrobiological Sciences; Ibaraki; Japan
The largest agricultural research institute in Japan for basic life sciences focusing on understanding the biological phenomena of agriculturally important plants, insects, microbes and animals to create innovative technologies, and eventually contribute to the solution of global issues such as food shortage due to rapid population growth and environmental problems due to climate change. Research activities are pursued in a 5-year cycle to intensify all efforts towards a common goal and to forge the way for new breakthroughs with direct impact to agricultural productivity.
National Institute of Animal Science; Gyeonggi-do; South Korea
National Institute of Biomedical Imaging and Bioengineering
National institute to improve health by leading the development and accelerating the application of biomedical technologies. The Institute is committed to integrating the physical and engineering sciences with the life sciences to advance basic research and medical care. This is achieved through: research and development of new biomedical imaging and bioengineering techniques and devices to fundamentally improve the detection, treatment, and prevention of disease; enhancing existing imaging and bioengineering modalities; supporting related research in the physical and mathematical sciences; encouraging research and development in multidisciplinary areas; supporting studies to assess the effectiveness and outcomes of new biologics, materials, processes, devices, and procedures; developing technologies for early disease detection and assessment of health status; and developing advanced imaging and engineering techniques for conducting biomedical research at multiple scales.
National Institute of Biomedical Innovation; Osaka; Japan
National Institute of Biomedical Innovation
National Institute of Informatics; Tokyo; Japan
National Institute of Medical Statistics; New Delhi; India
National Institute of Medical Statistics
National Oceanic and Atmospheric Administration
NOAA provides science, service and stewardship to protect life and property, and conserve/protect the Earth''s natural resources.
National Polytechnic Institute; Mexico City; Mexico
One of the largest public universities in Mexico.
Ohio Northern University College of Pharmacy
Founded 1884, the Ohio Northern University''s College of Pharmacy has had the privilege to graduate over 7,000 pharmacists during its 125-year history. The R. H. Raabe College of Pharmacy is distinctive among other colleges of pharmacy as it integrates a comprehensive foundation in the pharmaceutical sciences and the practice of pharmacy along with a strong liberal arts curriculum. Our graduates are particularly active in local, state, and national health-related organizations. The College is committed to assuring that all students receive the finest education possible. Our faculty members are dedicated scholars with a desire to assist student learning. Our outstanding clinical facilities and preceptors illustrate the application of knowledge to actual therapeutic decisions. The Doctor of Pharmacy program is designed to provide the student with the preparation and background for a successful career in a vital health profession.
National Institute of Child Health and Human Development
Eunice Kennedy Shriver National Institute of Child Health and Human Development
A national institute that investigates human development throughout the entire life process, focusing on understanding developmental disabilities, including intellectual and developmental disabilities, and illuminating important events that occur during pregnancy. The NICHD conducts and supports laboratory research, clinical trials, and epidemiological studies that explore health processes; examines the impact of disabilities, diseases, and defects on the lives of individuals; and sponsors training programs for scientists, doctors, and researchers to ensure that NICHD research can continue. The Institute also supports research training across all its programs. In addition, an overarching responsibility of the NICHD is to disseminate information that emanates from Institute research programs to researchers, practitioners, other health care professionals, and the public.
National Institute of Environmental Health Sciences
National institute that reduces the burden of human illness and dysfunction from environmental causes by, defining how environmental exposures, genetic susceptibility, and age interact to affect an individual''s health. Its mission is to discover how the environment affects people in order to promote healthier lives. Achieving this mission depends on a set of core values that apply to all activities of the Institute: * Research excellence (innovation; discovery of new scientific knowledge and technology); * Management excellence; and * Community outreach, education, and involvement. At NIEHS and the National Toxicology Program, they engage in a special form of public service - producing scientific knowledge that promotes individual and public health. The Institute is uniquely positioned to help prevent disease and transform new scientific knowledge into improvements in human health. There are many opportunities before us to build and expand the contributions of the NIEHS: * Foster research on environmental triggers of disease; * Communicate advances in environmental health sciences to the public; * Foster training and development of emerging young environmental health scientists and practitioners; * Enhance translation of knowledge from research to disease prevention; and * Foster safety assessment research on chemicals and other environmental factors. The fulfillment of this mission requires the partnership and effort of everyone in the environmental health sciences communities.
National institute that is the largest scientific organization in the world dedicated to research focused on the understanding, treatment, and prevention of mental disorders and the promotion of mental health. NIMH envisions a world in which mental illnesses are prevented and cured. The mission of NIMH is to transform the understanding and treatment of mental illnesses through basic and clinical research, paving the way for prevention, recovery and cure. For the Institute to continue fulfilling this vital public health mission, it must foster innovative thinking and ensure that a full array of novel scientific perspectives are used to further discovery in the evolving science of brain, behavior, and experience. In this way, breakthroughs in science can become breakthroughs for all people with mental illnesses. In support of this mission, NIMH will generate research and promote research training to fulfill the following four objectives: * Promote discovery in the brain and behavioral sciences to fuel research on the causes of mental disorders * Chart mental illness trajectories to determine when, where, and how to intervene * Develop new and better interventions that incorporate the diverse needs and circumstances of people with mental illnesses * Strengthen the public health impact of NIMH-supported research To reach these goals, the NIMH divisions and programs are designed to emphasize translational research spanning bench, to bedside, to practice. For targeted priorities and funding initiatives, please visit our division websites
National Institute of Mental Health and Neuro Sciences; Bangalore; India
National Institute of Mental Health and Neuro Sciences
Institute of mental health and neuroscience in Bangalore, India.
National Research Foundation - Republic of Singapore
The mission of the National Institute of Nursing Research (NINR) is to promote and improve the health of individuals, families, communities, and populations. NINR supports and conducts clinical and basic research and research training on health and illness across the lifespan to build the scientific foundation for clinical practice, prevent disease and disability, manage and eliminate symptoms caused by illness, and improve palliative and end-of-life care. NINR''s research programs, both extramural and intramural, incorporate a broad range of interdisciplinary approaches designed to promote scientific exploration that will lead to better health outcomes and health services. Such approaches include: clinical intervention studies; translational and implementation research; comparative effectiveness research; and analyses of cost, outcomes, and quality of care. As part of its commitment to advancing the health of all populations, NINR funds research that promotes health equity and eliminates health disparities by investigating the interplay of behavioral, biological, and environmental determinants of health and wellness, with a special emphasis on underserved and resource-limited communities. NINR also maintains a focus on basic research, seeking to improve knowledge of underlying biological systems, including the genetic and genomic contributions to symptoms and health conditions. NINR also places great emphasis on research training to cultivate the next generation of nurse scientists, as well as other biobehavioral researchers whose work advances nursing science. NINR-supported opportunities for research training are available for students beginning their research careers, as well as for scientists seeking to expand their research expertise. Among these opportunities, NINR provides support for trainees from underrepresented and disadvantaged backgrounds. NINR fosters collaborations with many other disciplines in areas of mutual interest such as long-term care for older adults, the special needs of women across the lifespan, genetic testing and counseling, biobehavioral aspects of the prevention and treatment of infectious diseases, and the impact of environmental influences on risk factors for chronic illnesses, among many others.
Public research university in Columbus, Ohio. Originally known as Ohio Agricultural and Mechanical College. Home to Wexner Medical Center.
Public research university in Athens, Ohio. The first university chartered by an Act of Congress and the first to be chartered in Ohio, it was chartered in 1787 by the Congress of the Confederation and subsequently approved for the territory in 1802 and state in 1804, opening for students in 1809.
National institute that leads the federal government in conducting and supporting research on aging and the health and well-being of older people. The Institute seeks to understand the nature of aging and the aging process, and diseases and conditions associated with growing older, in order to extend the healthy, active years of life. In 1974, Congress granted authority to form NIA to provide leadership in aging research, training, health information dissemination, and other programs relevant to aging and older people. Subsequent amendments to this legislation designated NIA as the primary Federal agency on Alzheimer's disease research. Mission The Institute's mission is to: * Support and conduct genetic, biological, clinical, behavioral, social, and economic research on aging. * Foster the development of research and clinician scientists in aging. * Provide research resources. * Disseminate information about aging and advances in research to the public, health care professionals, and the scientific community,among a variety of audiences. Programs NIA sponsors research on aging through extramural and intramural programs. The extramural program funds research and training at universities, hospitals, medical centers, and other public and private organizations nationwide. The intramural program conducts basic and clinical research in Baltimore, MD, and on the NIH campus in Bethesda, MD.
National Institute on Alcohol Abuse and Alcoholism
Leadership in the national effort to reduce alcohol-related problems. It does this by by: * Conducting and supporting research in a wide range of scientific areas including genetics, neuroscience, epidemiology, health risks and benefits of alcohol consumption, prevention, and treatment; * Coordinating and collaborating with other research institutes and Federal Programs on alcohol-related issues; * Collaborating with international, national, state, and local institutions, organizations, agencies, and programs engaged in alcohol-related work; and * Translating and disseminating research findings to health care providers, researchers, policymakers, and the public. The Institute''s efforts to fulfill its mission are guided by the NIAAA vision to support and promote, through research and education, the best science on alcohol and health for the benefit of all by: * Increasing the understanding of normal and abnormal biological functions and behavior relating to alcohol use; * Improving the diagnosis, prevention, and treatment of alcohol use disorders; and * Enhancing quality health care. Research opportunities to increase our understanding of why, how, and when people drink, and why and how some people develop alcohol use disorders, are set forth in the NIAAA Strategic Plan for Research
National Institute on Drug Abuse: The Science of Drug Abuse & Addiction
National Institute on Drug Abuse: The Science of Drug Abuse Addiction
National Institute on Drug Abuse: The Science of Drug Abuse and Addiction
NIDA''s mission is to lead the Nation in bringing the power of science to bear on drug abuse and addiction. Its two main components include the strategic support and conduct of research across a broad range of disciplines and ensuring the rapid and effective dissemination and use of the results of that research to significantly improve prevention, treatment and policy as it relates to drug abuse and addiction. NIDA is the largest supporter of the worlds research on drug abuse and addiction. NIDA-funded scientific research addresses the most fundamental and essential questions about drug abuse, including tracking emerging drug use trends, understanding how drugs work in the brain and body, developing and testing new drug treatment and prevention approaches, and disseminating findings to the general public and special populations. NIDA funds meritorious and innovative scientific research on all aspects of drug abuse and addiction. NIDA and other agencies monitor what drugs are being abused by tracking trends in drug abuse through many different surveys and data collection systems. NIDA''s Publication Series: * Research Reports * InfoFacts (fact sheets) * NIDA Notes (newsletter) * Addiction Science & Clinical Practice (journal for researchers & health care providers) * Mind Over Matter: Drug info for grades 5-9 * Topics in Brief
National Institute on Minority Health and Health Disparities
National Center on Minority Health and Health Disparities
National Institute on Minority Health Health Disparities
The National Institute on Minority Health and Health Disparities (NIMHD) leads scientific research to improve minority health and eliminate health disparities. To achieve its mission, the NIMHD: * Plans, reviews, coordinates, and evaluates all minority health and health disparities research and activities of the NIH; * Conducts and supports research on health disparities; * Promotes and supports the training of a diverse research workforce; * Translates and disseminates research information; and * Fosters innovative collaborations and partnerships. The NIMHD envisions an America in which all populations will have an equal opportunity to live long, healthy and productive lives.
Ontario Ministry of Agriculture Food and Rural Affairs
Ontario Ministry of Agriculture and Food
An Ontario government ministry responsible for the food, agriculture and rural sectors of the Canadian province of Ontario.
Ontario Ministry of Economic Development Employment and Infrastructure
Ministry of Economic Development and Innovation
Ministry of Economic Development Employment and Infrastructure
Ontario Ministry of Economic Development and Innovation
NLM collects, organizes, and makes available biomedical science information to scientists, health professionals, and the public. The Library's Web-based databases, including PubMed/Medline and MedlinePlus, are used extensively around the world. NLM conducts and supports research in biomedical communications; creates information resources for molecular biology, biotechnology, toxicology, and environmental health; and provides grant and contract support for training, medical library resources, and biomedical informatics and communications research. Celebrating its 175th anniversary in 2011, the National Library of Medicine (NLM), in Bethesda, Maryland, is a part of the National Institutes of Health, U.S. Department of Health and Human Services (HHS). Since its founding in 1836 as the library of the U.S. Army Surgeon General, NLM has played a pivotal role in translating biomedical research into practice. It is the world's largest biomedical library and the developer of electronic information services that deliver trillions of bytes of data to millions of users every day. Scientists, health professionals, and the public in the United States and around the globe search the Library's online information resources more than 1 billion times each year. The Library is open to all and has many services and resources for scientists, health professionals, historians, and the general public. NLM has over 17 million books, journals, manuscripts, audiovisuals, and other forms of medical information on its shelves, making it the largest health-science library in the world. In today's increasingly digital world, NLM carries out its mission of enabling biomedical research, supporting health care and public health, and promoting healthy behavior by: * Acquiring, organizing, and preserving the world's scholarly biomedical literature; * Providing access to biomedical and health information across the country in partnership with the 5,800-member National Network of Libraries of Medicine (NN/LM); * Serving as a leading global resource for building, curating and providing sophisticated access to molecular biology and genomic information, including those from the Human Genome Project and NIH Common Fund; * Creating high-quality information services relevant to toxicology and environmental health, health services research, and public health; * Conducting research and development on biomedical communications systems, methods, technologies, and networks and information dissemination and utilization among health professionals, patients, and the general public; * Funding advanced biomedical informatics research and serving as the primary supporter of pre- and post-doctoral research training in biomedical informatics at 18 U.S. universities.
National Medicines Institute; Warsaw; Poland
Polish National Institute of Public Health
Government institution participating in the health care system fulfilling governmental health policy and European Union recommendations that is responsible for the quality, safety and efficacy of medicinal products and medical devices available on the Polish market. It carries out research connected with quality of medicinal products and with application of new analytical methods. Microbiological examinations concerning presence of bacterial virulence factors, estimation of specific antibodies levels as well as determination of drug resistance of clinical microorganisms are performed as well. All departments of the Institute offer services concerning complex evaluation of medicinal products and medical devices. Microbiological expert''s opinions and genetic analyses are offered as well.
National Natural Science Foundation of China
National Natural Science Foundation of China (NSFC)
The National Natural Science Foundation of China (NSFC) is an organization directly affiliated to the State Council for the management of the National Natural Science Fund. # In accordance with the guiding principles, policies and plans for the development of science and technology in China and by adopting the operating mechanisms for the National Natural Science Fund which conform to the socialism market economic system, NSFC supports basic research and some of applied research, identifies and fosters talented researchers in the realm of science and technology, accelerates the progress of science and technology, and promotes the socioeconomic development in China by giving full play the guidance and coordinating role of the National Natural Science Fund from the central government. # NSFC is in charge of the management of the National Natural Science Fund. It compiles and promulgates the annual Guide to Programs for basic research and some of applied research, handles applications of research projects, and organizes peer review and select the best projects to support. It endeavors to create an academic environment conducive to innovation. # NSFC cooperates with the Ministry of Science and Technology to formulate the principles, policies and plans for the development of basic research in China. When entrusted, it provides consultation and undertakes related assignments on major issues for the development of high technology and applied research in China. # NSFC gives help and support to other Chinese foundations in natural sciences. # NSFC establishes contacts with governmental departments in charge of science and technology, science foundations and related academic organizations in other countries and carries out international cooperation and exchange. # NSFC is responsible for the administration, supervision and guidance of the subordinated bodies. # NSFC undertakes other tasks entrusted by the State Council and the State Leading Group for Science and Technology and Education.
NCIRE - The Veterans Health Research Institute
Northern California Institute for Research and Education
Public, nonprofit research institute in the United States focused on advancing veterans health research.
Nencki Institute of Experimental Biology; Warsaw; Poland
Polish scientific research organization and part of Polish Academy of Sciences headquartered in Warsaw, Poland. Leading institution in country in field of neurobiology, molecular biology, and biochemistry. Member institution of Global Network for Molecular and Cell Biology within UNESCO.
Netherlands Ministry of Economic Affairs
Networks of Centres of Excellence of Canada
The Networks of Centres of Excellence (NCE) fosters multi-disciplinary, multi-sectoral partnerships between academia, industry, government and not-for-profit organizations. It supports academic research, the commercialization of products and ideas, and the development of significant Canadian business advantages. The partnerships that this initiative cultivates result in ideas that are transformed into economic and social benefits for all Canadians.
NEDO actively undertakes the development of new energy and energy-conservation technologies, verification of technical results, and introduction/dissemination of new technologies (e.g., support for introduction). Through these efforts, NEDO promotes greater utilization of new energy and improved energy conservation. NEDO also contributes to a stable energy supply and resolution of new energy and improved energy conservation. NEDO also contributes to a stable energy supply and resolution of global environmental problems by promoting the demonstration of new energy, energy conservation and environmental technologies abroad based on knowledge obtained from domestic projects. Enhancement of Japan''s industrial competitiveness NEDO pursues research and development of industrial technology, which is the foundation for Japan''s industrial competitiveness, with the goal of commercialization of advanced new technology. Drawing on the combined efforts of industry, academia and government as well as its sophisticated management know-how, NEDO carries out projects to explore future technology seeds as well as mid- to long-term national projects that form the basis of industrial competitiveness. It also supports research related to practical application.
New Jersey Institute of Technology; New Jersey; USA
Public research university in Newark, New Jersey. Founded in 1881 with the support of local industrialists and inventors especially Edward Weston
Medical university that specializes in health sciences, medical arts, public advocacy, and allied health profession training.
Private research university based in New York City with historical campus in Greenwich Village.
New York University School of Medicine; New York; USA
NHLBI Division of Blood Diseases and Resources
Division of Blood Diseases and Resources
DBDR supports research on the causes, prevention, and treatment of nonmalignant blood diseases, including anemias, sickle cell disease, and thalassemia; premalignant processes such as myelodysplasia and myeloproliferative disorders; hemophilia and other abnormalities of hemostasis and thrombosis; and immune dysfunction. Funding encompasses a broad spectrum of research ranging from basic biology to medical management of blood diseases. The Division has a major responsibility for research to assure the adequacy and safety of the Nation''s blood supply. The Division also has a leading role in applying scientific advances in transfusion medicine and stem cell biology to the development of new cell-based therapies to repair and regenerate human tissues and organs. DBDR has three branches: the Blood Diseases Branch, the Thrombosis and Hemostasis Branch, and the Transfusion Medicine and Cellular Therapeutics Branch.
NHLBI Division of Cardiovascular Sciences
NHLBI Division of Heart and Vascular Diseases
DCVS provides leadership and supports basic, clinical, population, and health services research on the causes, prevention, and treatment of cardiovascular diseases. DCVS represents the union of two previously existing divisions, the Division of Cardiovascular Disease (DCVD) and the Division of Prevention and Population Sciences (DPPS). The Division fosters research in disease areas, such as atherothrombosis, heart attack and heart failure, high blood pressure, stroke, atrial and ventricular arrhythmias, sudden cardiac death, adult and pediatric congenital heart disease, cardiovascular complications of diabetes and obesity, and other cardiovascular disorders. Technology development for the diagnosis and treatment of cardiovascular disorders is also supported. Research also includes a number of well-known epidemiological cohort studies that describe disease and risk factor patterns in populations; clinical trials of interventions to prevent disease and to prevent or modulate risk factors; studies of genetic, behavioral, sociocultural, health systems, and environmental influences on disease risk and outcomes; and studies of the application of prevention and treatment strategies to determine how to improve clinical care and public health. The Division supports training and career development for these areas of research. In addition to the Office of the Director, the Division is organized operationally as 3 Offices and 3 Programs that oversee 8 Branches.
Perform robusts scientific and clinical research leading to a better understanding of biology and clinical pathology. We have built a strong basic science foundation and coupled it closely with innovative technology development and outstanding clinical research both at the NIH Clinical Center and in partnership with local hospitals. The purview of our research is broad, encompassing investigations into the basic principles of molecular, cellular, and organ-level biology and their relationship to disease. Some current areas of fundamental interest include single molecule structure; protein assembly; molecular and cell biology; cell signaling and motility; membrane trafficking; physiology; systems biology; engineering and technology development. Insights into disease mechanisms derived from basic studies form the basis for translational research into new diagnostic and therapeutic approaches. DIR investigators also conduct concept-based clinical studies in the areas of interventional and surgical cardiology; pulmonary medicine; sickle cell anemia; bone marrow transplant; and hematologic disorders. The Center for Population Studies located in Framingham Massachusetts and associated with the Framingham Heart Study focuses on Epidemiology of cardiovascular disease. Providing state-of-the-art training in basic, translational, and clinical research for the next generation of scientific and clinical leaders is a high priority. This program provides opportunities for scientists and trainees to work together towards a better understanding of molecular machines, the cell, the body, and ultimately the treatment of human diseases.
NHLBI Division of Prevention and Population Sciences
Division of Prevention and Population Sciences
NHLBI Division of Epidemiology and Clinical Applications
Supports and provides leadership for population- and clinic-based research on the causes, prevention, and clinical care of cardiovascular, lung, and blood diseases and sleep disorders. Research includes a broad array of epidemiological studies to describe disease and risk factor patterns in populations and to identify risk factors for disease; clinical trials of interventions to prevent disease; studies of genetic, behavioral, sociocultural, and environmental influences on disease risk and outcomes; and studies of the application of prevention and treatment strategies to determine how to improve clinical care and public health. The Division also supports training and career development for these areas of research. The Division is organized into four major components: the Epidemiology Branch, the Clinical Applications and Prevention Branch, the Women''s Health Initiative Branch, and the Office of Biostatistics Research.
The NIH Clinical Center is the nation's largest hospital devoted entirely to clinical research. Clinician-investigators translate scientific observations and laboratory discoveries into new approaches to diagnosing, treating, and preventing disease. The Clinical Center was recognized with the 2011 Lasker~Bloomberg Public Service Award for serving as a model research hospital—providing innovative therapy and high-quality patient care, treating rare and severe diseases, and producing outstanding clinician-scientists whose collective work has set a standard of excellence in biomedical research. About 1,500 clinical research studies are in progress at the Clinical Center. Half are studies of the natural pathogenesis of disease, especially rare diseases, which often are not studied anywhere else. What researchers learn by studying rare diseases adds to the basic understanding of common diseases. Most other studies are clinical trials, the first tests of new drugs and therapies in people. The clinical trials at the Clinical Center are predominantly Phase I and Phase II—first-in-human to test safety and efficacy. Clinical and laboratory research is conducted shoulder-to-shoulder, and this tandem approach drives all aspects of the Clinical Center's operations. More than 400,000 research volunteers have participated in clinical research studies at the Clinical Center since the hospital opened in 1953. Each year, the center sees 10,000 new research participants, of which there are two types: patient volunteers and healthy volunteers. Patient volunteers are people with specific diseases or conditions who help medical investigators learn more about their condition or test new medications, procedures, or treatments. A healthy volunteer is a person with no known significant health problems who plays a vital role in research to test a new drug, device, or intervention. At the Clinical Center, clinical research participants are active partners in medical discovery, a partnership that has resulted in a long list of medical milestones, including the first cure of a solid tumor with chemotherapy, gene therapy, use of AZT to treat AIDS, and successful replacement of a mitral valve.
NIH roadmap initiative office of the director
Collection of far reaching initiatives designed to transform research capabilities and improve translation of research into practice. Program consists of three major themes: new pathways to discovery, research teams of future, and reengineering clinical research enterprise.
Computes both spliced and unspliced alignments at high accuracy while taking advantage of base quality information and splice site predictions.
Northeastern University, Bouve College of Health Sciences
Northeastern University Bouve College of Health Sciences
Northeastern University Bouvé College of Health Sciences
College of Health Sciences offering six majors in three schools - health professions, nursing, and pharmacy, with an interdisciplinary emphasis that reflects today''s team approach to health care. The mission of the Bouve College of Health Sciences is to be a center of excellence in health professional education, research, and service. The structure of the college fosters cross-disciplinary interaction among faculty and students, encourages innovation in the education of both entry level and advanced practice health professionals, and recognizes the autonomy of each profession. The College strives to educate individuals to develop skills to be effective health care providers and to instill in our graduates a commitment to life-long learning. The College builds partnerships with health care delivery systems and the community in order to assure that Bouve students and faculty have access to practice sites that prepare our graduates to meet the health care needs of our urban neighbors and society, provides access to health professional education for a diverse student body and strives to have a faculty that reflects varied backgrounds and a worldwide perspective, and is committed to the generation and advancement of knowledge to improve the health and health care services of individuals and communities through basic and applied research.
Northeastern University; Massachusetts; USA
Private research university in Boston, Massachusetts. Established in 1898, the university offers undergraduate and graduate programs.
Northeast Forest University; Harbin; China
Private research university in Evanston, Illinois, United States. Established in 1851 to serve the historic Northwest Territory, it is the oldest chartered university in Illinois. The university has its main campus along the shores of Lake Michigan in the Chicago metropolitan area.
North Carolina State University; North Carolina; USA
Public land-grant research university in Raleigh, North Carolina, United States. Founded in 1887 and part of the University of North Carolina system, it is the largest university in the Carolinas.
North East Cyberinfrastructure Consortium
Consortium of five states that are collaborating on building cyberinfrastructure in the NE region. The consortium is not formally affiliated with NSF EPSCoR or the NIH IDeA.
Norwegian Institute of Water Research; Oslo; Norway
An environmental research organisation committed to research, monitoring, assessment and studies on freshwater, coastal and marine environments in addition to environmental technology. Their key areas of work include environmental contaminants, biodiversity and climate related issues.
Norwegian University of Science and Technology; Trondheim; Norway
Norges teknisk-naturvitenskapelige universitet
Norwegian University of Science and Technology
With 20,000 students studying a range of disciplines in seven different faculties, NTNU is alive with the intellectual energy of people pursuing their dreams. Whether your passion is ship design or medical research , virtual reality or urban renewal in China , NTNU has something for you. NTNU is Norway''s second largest university, with an annual budget of about US $800 million. Its 53 departments are spread out over seven major campuses, and graduate about 3,300 students every year, two-thirds of which are master''s or PhD candidates. The university has more than 100 laboratory facilities distributed among the different faculties and departments. These are central elements in NTNU''s education and research work.
A multiprogram science and technology laboratory managed for the U.S. Department of Energy by UT-Battelle, LLC, to deliver scientific discoveries and technical breakthroughs that will accelerate the development and deployment of solutions in clean energy and global security, and in doing so create economic opportunity for the nation. Scientists and engineers at ORNL conduct basic and applied research and development to create scientific knowledge and technological solutions that increase the availability of clean, abundant energy and restore and protect the environment; and contribute to national security. ORNL also performs other work for the Department of Energy, including isotope production, information management, and technical program management, and provides research and technical assistance to other organizations.
Office of genomics and disease prevention
Osaka Medical Center for Cancer and Cardiovascular Diseases; Osaka; Japan
Center for cancer and cardiovascular diseases with a focus on advanced cancer therapy in the Kansai area. It consists of the Hospital, the Research Institute, and the Department of Cancer Control and Statistics. The Research Institute is responsible for acquiring and applying knowledge of the molecular and genetic aspects of human cancer. The mission of the Research Institute is to perform basic and applied cancer research through collaboration with the Hospital and the Department of Cancer Control and Statistics. The large tumor tissue collection is the major focus of their research efforts. The Research Institute includes seven official departments: Biology, Biochemistry, Pathology, Molecular Medicine & Pathophysiology, Molecular Biology, Molecular Genetics, and Immunology. In addition, a group conducted by the Director (Director''s Unit) and Laboratory of Genome Informatics. The research objectives are as follows. # Clinical research. ## Prognosis predictor of gliomas based on gene expression profiling ## Targeted oncolytic virus # Technical developments for cancer research ## A new method for storing cancer cells taken from human tumor tissues (cancer tissue-originated spheroid) ## Bioinformatics for personalized genomics # Basic research ## Mechanism of metastasis ## Low oxygen environment and cancer ## Structure analysis of oligosaccharide on human cancer cells ## Proof-of-principle study of artificial adjuvants
OTKA - Hungarian Scientific Research Fund
The Hungarian Scientific Research Fund (Hungarian abbreviation: OTKA) has been the major funding agency of basic science and scholarship since 1986 when the transition to competitive research funding started in Hungary. Its founding fathers modelled the principles of operation on the practice of German (Deutsche Forschungsgemeinschaft) and American research funds (National Science Foundation, National Institutes of Health). Upon a government decree, OTKA has been operating as an independent non-profit organisation since 1991. Its legal status and rules of operation were established in an act in 1993 and reinforced in 1997 by the Hungarian parliament in order to provide independent support to scientific research activities and infrastructure, to promote scientific achievements of international standards, and to provide assistance to young researchers. As an independent institution, OTKA reports to the parliament and the government of Hungary. With regards to the funds provided within the annual budget of the Republic of Hungary, the appropriations of OTKA are administered via the budget of the Hungarian Academy of Sciences. The administrative and financial tasks related to its operation are performed by the OTKA Office in Budapest.
Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany
Otto von Guericke University of Magdeburg
The Otto von Guericke University of Magdeburg was founded in 1993 and is one of the youngest German universities. It was formed in a merger of the existing Technical University, the Teacher Training College and the Medical School. The University now comprises 9 faculties and almost 13,800 students and is becoming increasingly important as a center of education and research. It plays an important role in the regional capital Magdeburg which is developing into a center of business, scholarship and culture. The University is a member of many organization and committees. The University is named after Otto von Guericke (1602-1686), Magdeburg''s famous son,whose pioneering research into the vacuum made him well-known beyond Germany. The University aspires to teach and research in the tradition of this great scientist, philosopher and engineer and to continue with his humanist work. At the University of Magdeburg students can choose from 72 degree courses in various areas of study and specialization. There are also many possibilities to combine different subjects across the faculties. Students find ideal study conditions: modern laboratories, experimental workshops and clinics with high-performance computer technology as well as an excellent ratio between staff and students. The offer of a sound, thorough education combining a high level of theoretical expertise with practical experience makes Magdeburg an attractive alternative. Magdeburg also attracts students because it can offer single and twin-bedded accommodation in its halls of residence. In the past few years research at the University has gone through a decisive change from applied to innovative pure research. Among the many areas represented the neurosciences, immunology, non-linear systems, new materials, processes and products, computational visualistics, social transformation as well as communication and culture deserve a special mention. With its research the University hopes to make a significant contribution to economic and social development in Magdeburg and the surrounding area. The recent acquisitions of the arts and social sciences together with economics and management have already made their decisive mark on our research profile. Affiliated institutes and the University''s Technology Transfer Centre act as links between academia and industry. They facilitate businesses'' access to the University''s research resources while simultaneously promoting innovation. The University''s Medical School, located in the south of Magdeburg is the second of the University''s sites. It provides the base for 1.300 trainee medics as well as health care for the citizens of Saxony Anhalt. The Medical School can provide treatment for a broad range of serious and complex complaints. It has 1.100 beds and is the largest hospital in the Magdeburg area. It handles as many as 45,000 in-patients annually as well as countless out-patients. In the past few years the Medical Schools'' various clinics and centers have focused increasingly on specialized patient care. A special emphasis is laid on the close cooperation between teaching staff and students.
Oxford Brookes University; Oxford; United Kingdom
Public, research university. Includes undergraduate, graduate, professional and continuing education offered through resident instruction and online.
Institute that contributes to the prevention and treatment of infectious diseases through research, teaching and public health initiatives. The Institut Pasteur enjoys an independent status and has numerous other assets, with its research laboratories, technological platforms, teaching center and medical center all located on one campus in the heart of Paris. It also has an international network which currently counts 30 members spread over the five continents. With its unique setup and prestigious history, the Institut Pasteur has always stood at the forefront of innovation, adapting to the rapidly developing world of biological research and its applications, in particular in the field of biotechnology. Nowadays, the Institut Pasteur has four priorities to carry out its activities successfully : * to target its scientific strategy towards infectious diseases, microbiology, virology and immunology; * to adopt an outward-looking attitude, both within France, through agreements and collaborations with its partners : CNRS (French National Scientific Research Centre), Inserm (French National Institute for Health and Medical Research), universities, hospitals, industrial partners, etc., and at international level with the development of the Réseau International des Instituts Pasteur (International Network of the Institut Pasteur or RIIP), which counts 30 institutes; * to implement transversal research programs on ambitious themes and led by young researchers; * to preserve the foundation''s independence, in particular through increased resources from sponsorship and donations. These priorities, upholding the traditional tasks and values of the Institut Pasteur, place it at the cutting edge of the 21st century''s scientific and human challenges.
A United States Federal Executive Department to develop and execute policy on farming, agriculture, and food. It aims to meet the needs of farmers and ranchers, promote agricultural trade and production, work to assure food safety, protect natural resources, foster rural communities and end hunger, in America and abroad. USDA also participates in overseas aid programs, by providing surplus foods to developing countries to support development programs with other organizations. (http://en.wikipedia.org/wiki/USDA)
Queensland Institute of Medical Research
Established in 1945 by the Queensland Government, the Queensland Institute of Medical Research (QIMR) is one of the largest and most successful medical research institutes in Australia, and is recognised worldwide for the quality of its research. Originally established to further the study of tropical diseases in North Queensland, QIMR has broadened the scope of research to include the genetic and environmental influences of a range of diseases including cancer, asthma, HIV, malaria, endometriosis and dengue fever. QIMR is home to more than 700 scientists, students and support staff in six research departments (in 50 separate laboratories) and a corporate division. Because of its close proximity to major teaching hospitals and The University of Queensland Medical School, the Institute is ideally placed for clinical research collaborations and as a centre for research seminars and symposia.
Queen Mary University of London; London; United Kingdom
Public research university in London, England, and constituent college of federal University of London.
Radboud University; Nijmegen; The Netherlands
The Radboud University is a public university with a strong focus on research located in Nijmegen, the Netherlands.
Public liberal arts college in Mahwah, New Jersey. It is part of New Jersey's public system of higher education.
Rene Rachou Research Center - FIOCRUZ; Belo Horizonte; Brazil
Centro de Pesquisas Rene Rachou - FIOCRUZ
Centro de Pesquisas Rene Rachou - FIOCRUZ; Belo Horizonte; Brazil
Rene Rachou Research Center Oswaldo Cruz Foundation
Rensselaer Polytechnic Institute; New York; USA
National Basic Research Program of China
A Chinese-based national program for furthering basic scientific research. The program has three main aims, which include: supporting research on issues concerning national socioeconnomic development, creating a highly-skilled cohort of scientists, and improving program management to encourage innovation.
Private Catholic university in New York City. The school was founded in 1870 by the Congregation of the Mission with a mission to provide a growing immigrant population with quality higher education.
RIKEN Yokohama Institute; Kanagawa; Japan
National Health and Medical Research Council
A funding agency of the Australian government which supports research across the full spectrum of health and medical research, from basic science through to clinical, public health and health services research.
Private university in Kyoto, Japan, that traces its origin to 1869. With the Kinugasa Campus in Kyoto, and Kyoto Prefecture, the university also has a satellite called Biwako-Kusatsu Campus and Osaka-Ibaraki Campus.
A Danish public university founded in 1972 and located in Trekroner in the Eastern part of Roskilde. The university awards bachelor, master''s degrees and Ph.D. degrees in a wide variety of subjects. (Wikipedia)
Private graduate university in New York City. It focuses primarily on the biological and medical sciences and provides doctoral and postdoctoral education.
Agricultural research station whose mission is to deliver the knowledge and new practices to increase crop productivity and quality and to develop environmentally sustainable solutions for food and energy production. Rothamsted integrates biotechnology with other areas of science such as agronomy and agro-ecology so both existing and new knowledge can be implemented through agricultural practice. Their strength lies in their integrated, multidisciplinary approach to research in plant and soil science.
Research Triangle Institute International
An independent, nonprofit institute that provides research, development, and technical services to government and commercial clients worldwide. Their mission is to improve the human condition by turning knowledge into practice through cutting-edge study and analysis in health and pharmaceuticals, education and training, surveys and statistics, advanced technology, international development, economic and social policy, energy and the environment, and laboratory and chemistry services.
Rudjer Boskovic Institute; Zagreb; Croatia
Ruhr University Bochum; North Rhine-Westphalia; Germany
Public university located in the southern hills of the central Ruhr area in Bochum. It was founded in 1962 as the first new public university in Germany after World War II.
Russian Academy of Sciences; Moscow; Russia
The Saint Petersburg Academy of Sciences
The Russian Academy of Sciences consists of the national academy of Russia and a network of scientific research institutes from across the Russian Federation as well as auxiliary scientific and social units like libraries, publishers and hospitals. Headquartered in Moscow, the Academy is incorporated as a civil, self-governed, non-commercial organization chartered by the Government of Russia. It combines members of RAS and scientists employed by institutions. The RAS consists of eleven specialized scientific branches, three territorial branches and 14 regional scientific centres. The Academy has numerous councils, committees and commissions, organized for different purposes. Territorial branches include the Siberian Branch of Russian Academy of Sciences (SB RAS), Ural Branch of Russian Academy of Sciences (URAN), and Far East Branch of Russian Academy of Sciences (FEB RAS). The Russian Academy of Sciences consists of many regional centers and a large number of research institutions.
Rutgers New Jersey Medical School; New Jersey; USA
Rutgers University New Jersey Medical School
Rutgers, The State University of New Jersey, commonly referred to as Rutgers University, Rutgers, or RU, is public research university in New Jersey.
Rheinisch-Westfalische Technische Hochschule
Rheinisch-Westfälische Technische Hochschule
Rheinisch-Westfälische Technische Hochschule Aachen
Saarland University; Saarbrucken; Germany
Research university located in Saarbrücken, capital of German state of Saarland. It was founded in 1948 in Homburg in co-operation with France and is organized in six faculties that cover all major fields of science.
Sacred Heart Hospital of Montreal; Quebec; Canada
Globally recognized for certain specialities and ultra-specialities such as severe trauma, serious heart and pulmonary problems, and important mental illnesses.
Saint Louis University School of Medicine; Missouri; USA
Saint Louis University School of Medicine
Saint Petersburg Academic University; Saint Petersburg; Russia
Saint Petersburg Academic University - Nanotechnology Research and Education Center of the Russian Academy of Sciences
Saint Petersburg Academic University of the Russian Academy of Sciences
St Petersburg Academic University - Nanotechnology Research and Education Center of the Russian Academy of Sciences
St Petersburg Academic University; St Petersburg; Russia
Alferov Federal State Budgetary Institution of Higher Education and Science Saint Petersburg National Research Academic University of the Russian Academy of Sciences was founded in 1997 originally as the Research and Education Center of the Ioffe Institute to integrate science and education in the field of physics and information technologies.
Sanford Burnham Prebys Medical Discovery Institute
Conducts world class collaborative research dedicated to finding cures for human disease, improving quality of life, and thus creating a legacy for its employees, partners, donors, and community. SBP is dedicated to discovering the fundamental molecular causes of disease and devising the innovative therapies of tomorrow. Has established major research programs in cancer, neurodegeneration, diabetes, and infectious, inflammatory, and childhood diseases. SBP is a U.S.-based, non-profit public benefit corporation, with operations in San Diego (La Jolla) and Orlando (Lake Nona) in Florida.
Science Foundation Ireland (SFI) is the national foundation for research in Ireland. SFI invests in academic researchers and research teams who are most likely to generate new knowledge, leading edge technologies and competitive enterprises in the fields of science and engineering underpinning three areas: Biotechnology; Information & Communications Technology (ICT) and Sustainable Energy & Energy Efficient Technologies (Energy). SFI also advances co-operative efforts among education, government and industry that support its fields of emphasis and promotes Ireland''s reputation for science and engineering research. SFI uses an international merit review process to choose far-reaching, high-impact research for support in its target areas and to fund excellent scientists and engineers on the dynamic intellectual frontiers of Biotechnology, Information Communications Technology (ICT) and Sustainable Energy & Energy Efficient Technologies (Energy)
Private liberal arts women's college in Claremont, California.
Seattle Childrens Research Institute; Washington; USA
A top five pediatric research center in the nation that brings together the best minds in pediatric research to set new standards of pediatric care and find new cures for childhood diseases. Their goal is that every patient at Seattle Children''s has the opportunity to participate in, or benefit from, their groundbreaking research. The research institute is organized into nine centers, each one specializing in areas like cancer immunotherapy, neuroscience and child health and behavior. The centers are supported by faculty from the Treuman Katz Center for Pediatric Bioethics , the nation''s first pediatric bioethics center.
Seoul National University; Seoul; South Korea
National research university located in Seoul, South Korea. Most prestigious university in North Korea. University comprises sixteen colleges, one graduate school and nine professional schools.
Seoul National University College of Medicine; Seoul; South Korea
Seoul National University College of Medicine
Shanghai Institutes for Biological Sciences; Shanghai; China
Shanghai Institutes for Biological Sciences
Research institute of the Chinese Academy of Sciences, in Shanghai, established on July 3, 1999. When it was created, it was one of four basic science research institutions of China.
Shanghai Jiao Tong University; Shanghai; China
Shanghai Jiaotong University; Shanghai; China
Major research university in Shanghai. Established on April 8, 1896, as Nanyang Public School by an imperial edict issued by the Guangxu Emperor, it is one of China's oldest universities.
Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia
Siberian Branch of the Russian Academy of Sciences
Silesian University of Technology; Silesia; Poland
Simon Fraser University; British Columbia; Canada
Public research university in British Columbia, Canada, with three campuses: Burnaby, Surrey, and Vancouver.
First modern university in Korea, dating its history back to 1897. It was founded under the Christian missionary William M. Baird.
Private university in Georgetown, Texas. Formed in 1873 from a revival of collegiate charters granted in 1840, Southwestern is the oldest university in Texas.
Spanish Ministry of Science and Innovation
Ministry of Science and Innovation - Spain
Spanish National Research Council; Madrid; Spain
Agencia Estatal Consejo Superior de Investigaciones Cientificas
Agencia Estatal Consejo Superior de Investigaciones Científicas
Consejo Superior de Investigaciones Cientificas
Consejo Superior de Investigaciones Científicas
Teaching hospital in Dublin, Ireland. Its academic partner is Trinity College Dublin. It is managed by Dublin Midlands Hospital Group.
SP Process Development; Sodermanland; Sweden
SP Process Development; Södermanland; Sweden
A national research institute focusing on chemical, biochemical and pharmaceutical process development. Their main task is to build, use and provide expertise to increase success rates for academic and industrial actors with the development of new products and production processes. The institute forms an important resource and competence platform for knowledge generation, knowledge transfer, concept testing and risk sharing. Via SP Process Development, researchers and small and medium- sized enterprises (SMEs ) are provided access to tools, technology, equipment and complementing specialist knowledge. Sections that constitute the institute: * Analysis and Solid State * Catalysis * Process Development and Crystallization * Substance and Formulation What they do * Bringing together academia and industry to solve challenges within chemical, biochemical, technical and medical applications * Helping SMEs and academic research groups to drive ideas from the laboratory to commercial application * Enabling companies from different industries to increase collaboration regarding mutual challenges * Communicating challenges and requirements from industry to academic research groups
St. Marianna University School of Medicine; Kawasaki; Japan
St. Marianna University School of Medicine
Stanford University; Stanford; California
Private, non profit university in Stanford, California, USA for research and undergraduate and graduate studies. Known for its academic strength, wealth, proximity to Silicon Valley, and ranking as one of the world's top universities. Particularly noted for its entrepreneurship and is one of the most successful universities in attracting funding for start-ups.
Stanford University School of Medicine; California; USA
Medical school of Stanford University and is located in Stanford, California. It traces its roots to the Medical Department of the University of the Pacific, founded in San Francisco in 1858.
State University of New York; New York; USA
Stellenbosch University; Western Cape; South Africa
Public research university situated in Stellenbosch, a town in the Western Cape province of South Africa.
The County Council is responsible for all publicly-financed healthcare and public transport in Stockholm County. The County Council is also responsible for other overall issues within the county, such as regional planning and cultural subsidies. Sweden''s political system has three democratically elected levels. At national level there is Parliament and the Government, at regional level there are county councils/regions, and at local level there are municipalities. The state decides on the laws and regulations that govern the work of county councils/regions and municipalities. healthcare, public transport and regional development the County Council''s broad responsibility
Public university in Stockholm, Sweden. One of the largest universities in Scandinavia.
Stony Brook School of Medicine; New York; USA
Stony Brook University School of Medicine
The State University of New York at Stony Brook
Public sea grant and space grant research university in Stony Brook, New York. It is one of four university centers of the State University of New York system.
Biomedical research organization that conducts basic research on genes and proteins that control fundamental processes in living cells to analyze diseases and find keys to their causes, treatment, and prevention.
St Georges University of London; London; United Kingdom
A specialist medical and health sciences college and part of the University of London.
Tulane University of Louisiana is a private research university in New Orleans, Louisiana, United States. Founded as the Medical College of Louisiana in 1834 by a cohort of medical doctors, it became a comprehensive public university in the University of Louisiana in 1847
SUNY Upstate Medical University; New York; USA
Upstate Medical University State University of New York
Public medical school in Syracuse, New York. It is part of the State University of New York system.
Sun Yat-sen University; Guangdong; China
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Swansea University; Swansea; United Kingdom
Public research university located in Swansea, Wales, United Kingdom. It was chartered as University College of Swansea in 1920, as the fourth college of the University of Wales.
Government agency in Sweden established in 2001, with the responsibility to support and develop basic scientific research. Its objective is for Sweden to be a leading nation in scientific research.
University of Missouri-St. Louis; Missouri; USA
University of Missouri-Saint Louis; Missouri; USA
Public research university in St. Louis County, Missouri.
The Swiss National Science Foundation (SNSF) is Switzerland''s leading provider of scientific research funding. The SNSF annually supports some 7200 researchers, almost 80 percent of whom are aged 35 years or younger. With its federal mandate, it supports basic research in all disciplines, from philosophy and biology to the nanosciences and medicine. It also invests in applied research in various scientific fields. The focus of its activities is the scientific endorsement of projects submitted by researchers. The best applicants are funded by the SNSF with an annual total amount equalling approximately CHF 700 million. Established in 1952 as a foundation under private law, the SNSF has the autonomy it needs to promote independent scientific research. The SNSF is committed to promoting young scientists and works to ensure that scientific research in Switzerland has the most favourable conditions for developing internationally. It also encourages dialogue between scientists and representatives in society, politics and the economy.
Szent Istvan University; Godollo; Hungary
Szent Istvan University Faculty of Veterinary Science; Budapest; Hungary
The Faculty of Veterinary Science Budapest, is the only veterinary school in Hungary. It is a state institution supervised and financed by the Ministry of Education and Culture and is accredited to issue the diplomas of Doctor of Veterinary Medicine (D.V.M.), Bachelor of Science (BSc) in Biology and the postgraduate degree of Philosophiae Doctor (Ph.D.) in veterinary sciences. The Faculty has a fundamental role in teaching in the course of Master of Science (MSc) in biology, too. The Faculty has an uninterrupted teaching record for more than two centuries, making it thus one of the oldest veterinary schools in the world.
Tata Institute of Fundamental Research; Mumbai; India
In the Tata Institute of Fundamental Research we do basic research in physics, chemistry, biology, mathematics and computer science. We have campuses in Mumbai, Pune and Bangalore and research facilities in various other places in India. We have master''s and doctoral programs in our fields of work. TIFR is an autonomous Institute under the umbrella of the Department of Atomic Energy of the Government of India.
Technical University of Braunschweig; Braunschweig; Germany
Technical University of Denmark; Lyngby; Denmark
Engineering institution in Kongens Lyngby, north of Copenhagen, Denmark. It was founded in 1829 as first polytechnic in Denmark.
Technical University of Munich; Bavaria; Germany
Research university focused on natural sciences, engineering, medicine and social sciences concerning technology issues. It holds campuses in Munich, Garching, Freising-Weihenstephan, Heilbronn and Dover, Singapore.
Ecole nationale superieure des telecommunications
École nationale supérieure des télécommunications
French public institution of higher education and research of engineering in France. Located in Paris, it is also a member of the ParisTech Group and the Institut Telecom.
Telemedicine and Advanced Technology Research Center
Telemedicine & Advanced Technology Research Center
U.S. Army Telemedicine and Advanced Technology Research Center
Telethon Institute of Genetics and Medicine; Naples; Italy
Telethon Institute of Genetics and Medicine
The graduate program inPharmaceutical Sciences at Temple University offers thesis and non-thesis degrees that cover the areas of concentration/study in: Medicinal Chemistry Pharmaceutics Pharmacodynamics After completion, graduates with expertise in the Pharmaceutical Sciences have a multitude of career opportunities and will be able to compete for prestigious post-doctoral positions in academia, the pharmaceutical industry and government agencies. They can also obtain positions as Research Scientists in the pharmaceutical and biotechnology industries or government agencies and academic positions in Schools of Pharmacy, Universities in Departments of Pharmacology, Neuroscience, Engineering, Biology, Chemistry, Neuroscience, or Psychology.
Temple University School of Medicine; Pennsylvania; USA
United States Department of Veterans Affairs
Launched in October 2007, TFRI is the brainchild of the Terry Fox Foundation. TFRI involves collaboration between cancer hospitals and research organizations across Canada, and will occur initially in British Columbia, Alberta, Ontario and Quebec. TFRI will support translational cancer research projects with the potential to significantly improve the health of cancer patients. TFRI is organized into functionally integrated yet geographically dispersed nodes. Regional cancer hospitals and research organizations participate in each node by providing space for researchers and by arranging for the participation of cancer patients in research projects. At each node, two node co-ordinators provide leadership, and bring together local scientific and clinical research teams to propose and manage specific projects. The TFRI headquarters team liaises with the TFRI nodes and provides direction, co-ordination and facilitates communication across the entire organization. The Terry Fox Foundation has committed a minimum of $50 million (CAN) over five years from donations obtained during the 25th anniversary of the Terry Fox Marathon of Hope and from new funds anticipated and those raised since 2005. Other partners sharing the same vision are being sought who will be asked to commit additional resources to support the ongoing work of the TFRI.
Texas Biomedical Research Institute; Texas; USA
An independent biomedical research institution specializing in genetics and in virology and immunology. Texas Biomed is funded by government and corporate grants and contracts, and donations from the public. (Wikipedia)
Texas A and M Health Science Center College of Medicine; Texas; USA
Texas A and M University-Kingsville; Texas; USA
Texas A M University-Kingsville; Texas; USA
Texas A&M University-Kingsville; Texas; USA
Texas AM University-Kingsville; Texas; USA
Public research university in Kingsville, Texas. It is part of the Texas A&M University System. The university has programs in engineering, agriculture, wildlife, music, and the sciences. It also developed the nation's first doctoral degree in bilingual education.
Texas Southern University, College Pharmacy and Health Sciences
TSU College of Pharmacy and Health Sciences
The College of Pharmacy and Health Sciences strives to produce quality health care professionals, especially African-Americans and other ethnic minorities, who are competent in health care delivery, including the provision of pharmaceutical care and other health care services and programs. In fulfilling its mission and purpose, the College is committed to an innovative, productive, and receptive learning environment for research, scholarly activities and service; and to infusing new technology into its infrastructure and academic programs. The College serves approximately 800 students in its pre-professional and professional programs. Through the efforts of dedicated faculty and administrators, the College has produced competent graduates who excel in all career paths in Pharmacy and Health Sciences.
Texas Tech University Health Sciences Center; Texas; USA
Texas Tech University Health Sciences Center
Texas Tech University System; Texas; USA
Public research university in Lubbock, Texas, United States. Established on February 10, 1923, and called until 1969 Texas Technological College, it is the main institution of the four-institution Texas Tech University System.
The Genome Analysis Centre; Norwich; United Kingdom
A research institute focused on the application of state of the art genomics and bioinformatics to advance plant, animal and microbial research to promote a sustainable bioeconomy. TGAC is a hub for innovative bioinformatics founded on research, analysis and interpretation of multiple, complex data sets. We host one of the largest computing hardware facilities dedicated to life science research in Europe.
Thomas Jefferson University; Pennsylvania; USA
Private university in Philadelphia, Pennsylvania. Established in its earliest form in 1824, the university officially combined with Philadelphia University in 2017.
Nederlandse Organisatie voor Toegepast Natuurwetenschappelijk Onderzoek
Netherlands Organisation for Applied Scientific Research
Netherlands Organisation for Applied Scientific Research (TNO)
Netherlands Organization for Applied Scientific Research TNO
TNO: Netherlands Organisation for Applied Scientific Research TNO
Toegepast Natuurwetenschappelijk Onderzoek
An independent, non-profit statutory research organization that is a knowledge organization for companies, government bodies and public organizations focusing on applied science. Their expertise and research make an important contribution to the competitiveness of companies and organizations, to the economy and to the quality of society as a whole. The organization also conducts contract research, offers specialist consulting services, and grants licences for patents and specialist software. TNO tests and certifies products and services, and issues an independent evaluation of quality. Moreover, TNO sets up new companies to market innovations. (Adapted from Wikipedia)
Tongji University is one of the leading universities directly under the State Ministry of Education in China. It offers degree programs both at undergraduate and postgraduate levels. The university has School of Sciences, School of Architecture and Urban Planning, School of Civil Engineering , Mechanical School, School of Environmental Science and Engineering, School of Material Science and Engineering, School of Electronics and Information Engineering, School of Traffic and Transportation, Medical School, School of Liberal Arts and Law, School of Foreign LanguagesSchool of Economics and ManagementSchool of Software Engineeringschool of Ocean and Earth Science. In addition, there are Institute of Further Education, Institute of Higher Technology, Institute of Vocational and Technical Education, Institute of E-Education, Women''s College, Institute of Automobile Marketing and Sino-German Institute which is authorized by Chinese and German governments to run postgraduate courses. There are also six university hospitals located in different campuses. The university now registers over 50,000 students at all levels from certificate and diploma courses to Bachelors Degrees, Masters, PhD programs and post doctoral attachments. There are over 4200 academic staff for teaching and/or research, among whom there are 6 Members of Chinese Academy of Science, 7 Members of Chinese Academy of Engineering, over 710 professors and 1500 associate professors. The university offers diverse courses in its 82 Bachelors Degrees, 218 Masters, 94 PhD programs and 16 post doctoral mobile stations. As one of the state leading centers for scientific research, the university has 22 state key laboratories and engineering research centers. Tongji University, formerly Tongji German Medical School, was established in 1907. It was given its present name and became a state university in 1927. It was one of the oldest and most prestigious institutions of higher education in China. The university has developed rapidly in all respects over the fifty years since the founding of China, especially since the country''s opening-up policy.
Translational Genomics Research Institute
Translational Genomics Research Institute (TGen)
The Translational Genomics Research Institute (TGen) is a non-profit 501(c)(3) organization focused on developing earlier diagnostics and smarter treatments. Translational genomics research is a relatively new field employing innovative advances arising from the Human Genome Project and applying them to the development of diagnostics, prognostics and therapies for cancer, neurological disorders, diabetes and other complex diseases. For the first time in history, we now have the knowledge to unravel the genetic components of common and complex diseases. The increased understanding of molecular medicine is shifting clinical practice from treatment based on symptoms to treatment based on the underlying causes of disease. Physicians will be prescribing drugs that are designed more intelligently, work more effectively, and have fewer toxic side effects. The mapping of the human genome was only the first step. Researchers are now working to translate variations in human genes to discover the underlying cause of disease progression and resistance to therapy and why some individuals encounter debilitating diseases and others live healthy lives. Although all the puzzle pieces of our genetic make-up have been identified, scientists and clinicians now have the formidable task of interpreting how they fit together in order to apply the genome map to patient care. TGen is on the cutting edge of translational research where investigators are able to unravel the genetic components of common and complex diseases. Working with collaborators in the scientific and medical communities, TGen believes it can make a substantial contribution to the efficiency and effectiveness of the translational process. TGen''s vision is of a world where an understanding of genomic variation can be rapidly translated to the diagnosis and treatment of disease in a manner tailored to individual patients. TGen is dedicated to the next revolution in health care. With the patient at its helm, TGen is guided by three core principles: integrate, translate and accelerate.
An independent, not-for-profit biomedical research organization with a scientific mission to make breakthrough discoveries that lead to improved human health. Trudeau researchers are identifying the basic mechanisms used by the immune system to combat cancer and infectious diseases, such as influenza and tuberculosis, so that better vaccines and therapies can be developed. The research is supported by government grants and philanthropic contributions.
Tulane University School of Medicine; Louisiana; USA
Land service branch of the United States Armed Forces. It is one of the eight U.S. uniformed services, and is designated as the Army of the United States in the U.S. Constitution.
U.S. Army Medical Research and Materiel Command
Medical Research and Materiel Command - U.S. Army Medical Department
Medical Research and Materiel Command U.S. Army Medical Department
U.S. Army Medical Department Medical Research and Materiel Command
US Army Medical Research and Materiel Command
United States Army's medical materiel developer, with responsibility for medical research, development, and acquisition and medical logistics management.
Government agency responsible for the United States Census that also gathers other national demographic and economic data. As a part of the United States Department of Commerce, it serves as a leading source of data about America' '''s people and economy. Its most visible role is to perform the official decennial (every 10 years) count of people living in the U.S. The most important result is the reallocation of the number of seats each state is allowed in the House of Representatives, but the results also affect a range of government programs received by each state. The agency director is a political appointee selected by the President of the United States.
United States Consumer Product Safety Commission
Consumer product safety commission charged with protecting the public from unreasonable risks of injury or death associated with the use of the thousands of types of consumer products under the agency''s jurisdiction - such as toys, cribs, power tools, cigarette lighters, and household chemicals. CPSC is committed to protecting consumers and families from products that pose a fire, electrical, chemical, or mechanical hazard.
UCSF School of Medicine; California; USA
University of California at San Francisco School of Medicine
University of California San Francisco School of Medicine
University of California San Francisco School of Medicine; California; USA
The UCSF School of Medicine strives to advance human health through a fourfold mission of education, research, patient care and public service. Consistently ranked among the nation''s top medical schools, the UCSF School of Medicine earns its greatest distinction from its outstanding faculty among them are three Nobel laureates, 70 Institute of Medicine members, 59 American Academy of Arts and Sciences members, 41 National Academy of Sciences members, and 16 Howard Hughes Medical Institute investigators. Founded in 1864 as Toland Medical College, the school became part of the University of California in 1873. In 1898, the school moved to its present Parnassus Heights campus, on land donated by San Francisco mayor Adolph Sutro. The first UC hospital opened here in 1907, growing into Moffitt-Long Hospitals and Children''s Hospital. These facilities, together with Mount Zion Hospital, now comprise the UCSF Medical Center. UCSF faculty have also treated patients and trained students at San Francisco General Hospital since 1873.
UC Davis School of Medicine; California; USA
UC Davis School of Veterinary Medicine; California; USA
Ulm University; Baden-Wurttemberg; Germany
Ulm University; Baden-Württemberg; Germany
Uniformed Services University of the Health Sciences; Maryland; USA
Uniformed Services University of the Health Services
Department of Health and Social Care is a department of Her Majesty's Government, responsible for government policy on health and adult social care matters in England.
United States Department of Health and Human Services granting agency
United States Department of Health and Human Services granting institution
University Medicine Berlin; Berlin; Germany
University of Alabama at Birmingham; Alabama; USA
Public research university in Birmingham, Alabama. Developed from an academic extension center established in 1936, the institution became a four-year campus in 1966 and a fully autonomous university in the University of Alabama System in 1969.
University at Albany - State University of New York
University at Albany State University of New York
University at Albany State University of New York; New York; USA
Strategically located in the state capital of New York, the University at Albany is an internationally recognized public research institution that brings The World Within Reach to nearly 18,000 students at the graduate and undergraduate levels. The varied perspectives and life experiences of a student body and faculty that represent more than 100 nations provide a diversity that enriches learning at UAlbany.
University at Buffalo The State University of New York
University College Dublin; Dublin; Ireland
Research university in Dublin, Ireland, and a member institution of the National University of Ireland.
University College London; London; United Kingdom
Public research university located in London, England.
University Hospital Erlangen; Bavaria; Germany
University hospital in Erlangen, Germany.
University Lille 1 - Sciences and Technologies; Lille; France
LILLE 1 University - Science and Technology
Lille University of Science and Technology
University Lille 1 - Sciences and Technologies
University Lille 1: Sciences and Technologies
University of Bath; North East Somerset; United Kingdom
The University of Bath ranks highly in the league tables of UK universities published by a number of national newspapers, including the Times, Independent and Guardian. Its research is internationally respected, and its students are in demand by employers because of the high quality of the teaching offered here. The University has had close connections with industry and the public and voluntary sectors since its inception in 1966. It has developed strong links with universities abroad. The University''s buildings are set in an attractive campus about a mile from the center of Bath, a World Heritage City. It is a safe and friendly campus with strong student services and good social opportunities. Its sports facilities are first-class.
Public research university in Bergen, Norway.
University in the Swiss capital of Bern and was founded in 1834. It is regulated and financed by the Canton of Bern.
University of Birmingham; Birmingham; United Kingdom
Research university in Bologna, Italy. Oldest university in the world, as well as one of the leading academic institutions in Italy and Europe.
Rheinische Friedrich-Wilhelms-Universitat Bonn
Rheinische Friedrich-Wilhelms-Universität Bonn
University of Bristol; Bristol; United Kingdom
University of British Columbia; British Columbia; Canada
Public research university with campuses in Vancouver and Kelowna, British Columbia.
UCalgary offers diverse educational and research experiences for Canadian and International students, with top undergraduate and graduate programs.
University of California; California; USA
Public research university system in the U.S. state of California with campuses at Berkeley, Davis, Irvine, Los Angeles, Merced, Riverside, San Diego, San Francisco, Santa Barbara, and Santa Cruz, along with numerous research centers and academic abroad centers.
University of California at Berkeley; Berkeley; USA
University of California at Berkeley; USA
Public research university in the United States. Located in the city of Berkeley, it was founded in 1868 and serves as the flagship institution of the ten research universities affiliated with the University of California system. Berkeley ranks 5th internationally in the Academic Ranking of World Universities.
University of California at Irvine; California; USA
One of the ten campuses of the University of California system, UCI offers 87 undergraduate degrees and 129 graduate and professional degrees.
University of California at Los Angeles; California; USA
University of California Los Angeles; California; USA
Public research university in Los Angeles. It became Southern Branch of University of California in 1919, making it fourth-oldest of 10-campus University of California system and oldest of campuses in Southern California.
University of California at Merced; California; USA
UC Merced is the 10th campus of the University of California system and the first American research university built in the 21st century.
University of California at Riverside; California; USA
Public research university in Riverside, California. It is one of the 10 campuses of the University of California system.
University of California at Santa Barbara; California; USA
University of California at Santa Barbara
Public research university in Santa Barbara, California, and one of the ten campuses of the University of California system.
University of California at Santa Cruz; California; USA
Public research university in Santa Cruz, California. It is one of 10 campuses in the University of California system.
University of California at San Diego; California; USA
University of California San Diego; California; USA
The University of California, San Diego, also known as UC San Diego, is public research university located in the La Jolla neighborhood of San Diego, California, in the United States. Established in 1960, UCSD has 6 different campuses.
University of Connecticut School of Pharmacy
The University of Connecticut School of Pharmacy offers challenging programs of study in pharmacy practice and the pharmaceutical sciences. Our exceptional faculty, groundbreaking research, and innovative graduate and professional programs position the School of Pharmacy as one of the top choices for pharmacy education in the United States. Our professional program, which leads to the Doctor of Pharmacy (Pharm.D.) and our research-intensive graduate programs in medicinal chemistry, pharmaceutics, and pharmacology/toxicology attract the best and brightest national and international students. The School of Pharmacy''s outstanding academic ranking is one of the reasons why U.S. News and World Reports named UConn the top public University in New England.
University of Copenhagen; Copenhagen; Denmark
University and research institution in Denmark founded in 1479. Member of the International Alliance of Research Universities, along with University of Cambridge, Yale University, The Australian National University, and UC Berkeley.
University of Debrecen; Debrecen; Hungary
Private-public research university located in Newark, Delaware.
Academic life at the University of Denver provides enriching intellectual and cultural experiences that will help you sharpen your mind, explore your values and deepen your commitments. Known for its excellence in undergraduate and graduate research and academics, DU offers more than 200 challenging programs, including traditional bachelor''s, master''s and doctorate degrees, innovative dual degrees, and online degrees and certificates for working professionals. With DU''s outstanding student-to-faculty ratio (10:1 in undergraduate courses and 12:1 overall), you will have the unique opportunity to forge collaborative, meaningful partnerships with internationally recognized faculty. These inspiring relationships stimulate intellectual and personal discovery-and inform your life''s direction. 61 percent of DU students study and live abroad for at least one quarter. A fundamental part of academic life, study abroad helps you develop cross-cultural connections-and the new perspectives that come with them-so that you can understand and appreciate the interdependencies that characterize our world.
University of Duisburg-Essen; North Rhine-Westphalia; Germany
Public university in Duisburg and Essen, North Rhine-Westphalia, Germany.
University of Luxembourg; Luxembourg; Luxembourg
Public research university with international, multilingual and interdisciplinary character, situated on Belval Campus and in Luxembourg City, Luxembourg. Founded in 2003.
University of Dundee College of Life Sciences; Scotland; United Kingdom
College of Life Sciences University of Dundee
University of Dundee College of Life Sciences
University of Dundee School of Medicine; Scotland; United Kingdom
University of Eastern Finland; Eastern Finland; Finland
University of East Anglia; Norwich; United Kingdom
University of East Anglia; Norwich; England
University of Edinburgh; Scotland; United Kingdom
Research university in Edinburgh, Scotland, founded in 1582. Has five main campuses. Known for arts, humanities and computer science.
University of Edinburgh College of Medicine and Veterinary Medicine; Scotland; United Kingdom
University of Edinburgh College of Medicine and Veterinary Medicine
University of Erlangen-Nuremberg; Bavaria; Germany
Friedrich-Alexander-Universitat Erlangen-Nurnberg
Friedrich-Alexander-Universität Erlangen-Nürnberg
University of Evry-Val d'Essonne; Ile-de-France; France
University of Exeter; Exeter; United Kingdom
Public research university in Exeter, Devon, South West England, United Kingdom.
University of Georgia College of Pharmacy; Georgia; USA
University of Georgia College of Pharmacy
The University of Georgia College of Pharmacy offers the Doctor of Pharmacy professional degree. Based in Athens, Georgia and affiliated with the Georgia Health Sciences University (formerly Medical College of Georgia) in Augusta, the college admits about 145 students a year. The four-year professional program integrates classroom, laboratory and experiential training in a curriculum organized around both human physiology and disease states. The college also offers graduate studies in disciplines associated with pharmacotherapeutic research, clinical work, and administration.
University of Glamorgan; South Wales; United Kingdom
University of Glasgow; Glasgow; United Kingdom
University of Glasgow; Glasgow; Scotland
University of Glasgow; Scotland; United Kingdom
Founded in 1451, the University of Glasgow is the fourth oldest university in the English-speaking world. Today we are a broad-based, research intensive institution with a global reach.
University of Gothenburg; Gothenburg; Sweden
University in Sweden in Gothenburg. Third oldest of university in country. Home of most comprehensive offerings of courses and programmes in Sweden.
University of Greifswald; Mecklenburg-Vorpommern; Germany
Ernst Moritz Arndt University Greifswald
Ernst Moritz Arndt University of Greifswald
Ernst-Moritz-Arndt-Universitat Greifswald
Ernst-Moritz-Arndt-Universit�t Greifswald
Public research university located in Greifswald, Germany, in the state of Mecklenburg-Vorpommern. Founded in 1456, it is one of the oldest universities in Europe, with generations of notable alumni and staff having studied or worked in Greifswald.
University of Groningen; Groningen; Netherlands
Founded in 1614, the University of Groningen enjoys an international reputation as one of the oldest and leading research universities in Europe. We offer degree programmes at Bachelor''s, Master''s and PhD levels in virtually every field, many of them completely taught in English. Located in the north of the Netherlands, Groningen is an ideal, safe student city with a flourishing student life.
Public research university in Guelph, Ontario, Canada.
Established in 1907, the university of Hawaii at Manoa is the largest and oldest of the 10 UH campuses. UH Manoa provides degrees in subjects including: tropical agriculture, tropical medicine, oceanography, astronomy, electrical engineering, volcanology, evolutionary biology, comparative philosophy, comparative religion, Hawaiian studies, Pacific Islands studies, Asian studies and Pacific and Asian regional public health.
University of Helsinki; Helsinki; Finland
Public university in Helsinki, Finland. Bilingual with teaching in Finnish and Swedish.
University of Hohenheim; Baden-Wurttemberg; Germany
University of Hohenheim; Baden-W�rttemberg; Germany
Campus university located in the south of Stuttgart, Germany. Founded in 1818, it is Stuttgart's oldest university. Its primary areas of specialisation had traditionally been agricultural and natural sciences.
Public research university in Houston, Texas, and the main institution of the University of Houston System.
University of Iceland; Reykjavik; Iceland
Public research university in Reykjavík, Iceland and the country's oldest and largest institution of higher education.
Public university located in Moscow, Idaho. Popular majors include Psychology, Mechanical Engineering, Liberal Arts and Humanities.
University of Illinois at Chicago; Illinois; USA
Public research university in Chicago, Illinois. Its campus is in the Near West Side community area, adjacent to the Chicago Loop.
University of Illinois at Urbana-Champaign; Illinois; USA
University of Illinois at Urbana-Champaign
Public research university in Illinois and flagship institution of University of Illinois System. Founded in 1867 its campus is located in twin cities of Champaign and Urbana.
Public research university in College Park, Maryland. Founded in 1856, UMD is the flagship institution of the University System of Maryland.
University of Massachusetts Lowell; Massachusetts; USA
UMass Lowell is a comprehensive University with a national reputation in science, engineering and technology, and committed to educating students for lifelong success in a diverse world and conducting research and outreach activities that sustain the economic, environmental and social health of the region. We offer more than 14,000 students more than 120 degree choices, internships, bachelor''s to master''s programs and doctoral studies in the colleges of Fine Arts, Humanities and Social Sciences, Sciences, Engineering and Management, the School of Health and Environment, and the Graduate School of Education.
University of Massachusetts Medical School; Massachusetts; USA
University of Massachusetts Medical School
University of Massachusetts Medical School - Worcester
University of Medicine and Dentistry of New Jersey; New Jersey; USA
Private research university in Coral Gables, Florida.
University of Miami Miller School of Medicine; Florida; USA
University of Miami Leonard M. Miller School of Medicine
University of Miami Miller School of Medicine
Public research university in Ann Arbor, Michigan. One of foremost research universities in United States.
University of Michigan Medical School; Michigan; USA
University of Michigan Medicine (branded as Michigan Medicine) is the academic medical center of the University of Michigan, a public research university.
University of Michigan Rackham Graduate School; Michigan; USA
A public, multidisciplinary teaching and research institution that offers 8 Faculties, 2 Schools, 136 study courses, 31 Doctoral Programmes and 63 Specialization Schools. Their 2000 professors represent the highest concentration of scientific expertise in the region and their research is ranked among the best in Italy and Europe.
University of Minnesota Medical School; Minnesota; USA
Medical school of the University of Minnesota. It is a combination of two campuses situated in Minneapolis and Duluth, Minnesota. The University of Minnesota Medical School is also part of one of the largest Academic Health Centers in the United States.
University of Minnesota Twin Cities; Minnesota; USA
Public research university in Minneapolis and Saint Paul, Minnesota.
University of Mississippi; Mississippi; USA
Public research university in Oxford, Mississippi. Including the University of Mississippi Medical Center in Jackson, it is the state's largest university by enrollment and promotes itself as the state’s flagship university.
University of Mississippi Medical Center; Mississippi; USA
University of Mississippi Medical Center
University of Missouri, Kansas City School of Pharmacy
University of Missouri-Kansas City School of Pharmacy
The UMKC School of Pharmacy will be a globally respected learning community, which creates higher standards in education, practice, and research to improve health and quality of life. The UMKC School of Pharmacy actively increases the level of patient care by its leadership in: educating students, health care practitioners, scientists, and the public; partnering with the community and the entire health care team; and conducting innovative research.
University of Wisconsin System; Wisconsin; USA
Institution in Wisconsin consisting of 13 four-year universities and 13 freshman-sophomore UW Colleges campuses.
University of Missouri-Kansas City; Missouri; USA
Public research university in Kansas City, Missouri. UMKC is part of the University of Missouri System and one of only two member universities with a medical school.
University of Missouri-Kansas City School of Medicine; Missouri; USA
University of Missouri-Kansas City School of Medicine
University of Missouri-Columbia; Missouri; USA
Founded in 1839 as the first public university west of the Mississippi River and the first state university in Thomas Jefferson''s Louisiana Purchase territory. MU provides all the benefits of two universities in one it''s a major land-grant institution and Missouri''s largest public research university. Considered one of the nation''s top-tier institutions, Mizzou has a reputation of excellence in teaching and research, and is the flagship campus of the four-campus University of Missouri System. It is one of only 34 public universities, and the only public institution in Missouri, to be selected for membership in the Association of American Universities. MU offers more than 280 degree programs including more than 75 online degree options and is designated as comprehensive doctoral with medical/veterinary by the Carnegie Foundation for the Advancement of Teaching. Students in academic regalia receive honors at the Tap Day event. Mizzou is recognized nationally and receives top rankings for its programs in many areas, including journalism, dispute resolution, family and community medicine, campus writing program and Freshman Interest Groups. As one of only six public universities in the country with medicine, veterinary medicine and law all on one campus, MU provides Missouri with an educated work force of doctors, veterinarians and lawyers.
University of Missouri School of Medicine; Missouri; USA
University of Missouri School of Medicine
University of Missouri-Columbia School of Medicine
University of Missouri-Columbia School of Medicine; Missouri; USA
University of Missouri System; Missouri; USA
Public land-grant research university in Columbia, Missouri. It is Missouri's largest university and the flagship of the four-campus University of Missouri System. Founded in 1839, it was the first public university west of the Mississippi River.
Public research university in Missoula, Montana. UM is a flagship institution of the Montana University System and its second largest campus.
A top university in the French-speaking world is the largest university in Quebec and the second largest in Canada with two affiliated schools, the École Polytechnique and the HEC Montréal. With over 60,000 students from around the world, the Université de Montréal awards more than 11,000 diplomas every year. With its 13 faculties and 80 departments and schools, the Université de Montréal offers programs in almost all academic fields. UdeM is the only Quebec university that teaches the full range of disciplines in health sciences, boasts the province's only faculty of veterinary medicine and houses one of Canada's largest faculty of arts and sciences. Whether you have a passion for international politics, cyberspace law, Asian social history or nanotechnologies, you'll find a department that best suits your needs. The Université de Montréal is one of Canada's major research centres. With its two affiliated schools-the École Polytechnique and the HEC Montréal-and its network of affiliated hospitals, it brings together 2,500 professors and researchers from all the fundamental disciplines, some 300 research units, and one of Canada's largest student bodies at the master's and doctoral levels.
University of Montreal Hospital Centre; Quebec; Canada
Centre hospitalier de l''Universite de Montreal
Centre hospitalier de l''Universit� de Montr�al
Hôpital Saint-Luc was a hospital in Montreal, Quebec, Canada, at the intersection of Saint Denis Street and René Lévesque Boulevard in the borough of Ville-Marie. It was named in honor of Luke the Evangelist, who is the patron saint of doctors in the Roman Catholic religion.
University of Munster; North Rhine-Westphalia; Germany
The University of Murcia is the third oldest university in Spain, after the University of Salamanca and the University of Valladolid, and the thirteenth in the world.
University of Natural Resources and Life Sciences
BOKU University (University of Natural Resources and Life Sciences, Vienna), founded in 1872, is a leading Austrian public university specializing in sustainability, life sciences, and natural resources. Located in Vienna, BOKU combines expertise in natural sciences, engineering, and social and economic sciences to address key societal challenges, including climate change, sustainable agriculture, and food security.
Public land-grant research university in Lincoln, Nebraska. It is the state's oldest university and the largest in the University of Nebraska system.
University of Nebraska College of Medicine; Nebraska; USA
University of Nebraska Medical Center College of Medicine
University of Southern California School of Pharmacy Graduate Programs
The USC School of Pharmacy is home to four nationally recognized graduate programs. Within the Department of Pharmacology and Pharmaceutical Sciences, degrees are offered in Molecular Pharmacology and Toxicology, as well as Pharmaceutical Sciences. Within the Titus Family Department of Clinical Pharmacy and Pharmaceutical Economics & Policy, degrees are offered in Pharmaceutical Economics and Policy, as well as Regulatory Science. The School offers a multidisciplinary educational experience that prepares students for successful careers in academia, the pharmaceutical industry, managed care organizations, and state and federal government.
University of Southern Denmark; Odense; Denmark
University in Denmark that has campuses located in Southern Denmark and on Zealand. The university offers a number of joint programmes in co-operation with the University of Flensburg and the University of Kiel.
University of Southern Mississippi; Mississippi; USA
University of South Australia; Adelaide; Australia
University of South Carolina; South Carolina; USA
Public research university in Columbia, South Carolina. It has seven satellite campuses throughout the state.
University of South Carolina School of Medicine; South Carolina; USA
University of South Carolina School of Medicine
University of South Dakota; South Dakota; USA
Public research university in Vermillion, South Dakota.
University of South Florida; Florida; USA
Public research university in Tampa, Florida. It is part of the State University System of Florida.
University of South Florida College of Medicine; Florida; USA
University of South Florida College of Medicine
University of Strasbourg; Strasbourg; France
University of Strathclyde; Glasgow; United Kingdom
Public research university located in Glasgow, Scotland.
University of St Andrews; Scotland; United Kingdom
Public university in St Andrews, Fife, Scotland. It is the oldest of the four ancient universities of Scotland and, following Oxford and Cambridge universities, the third-oldest university in the United Kingdom and English-speaking world.
University of Sussex; Brighton; United Kingdom
A leading research-intensive university close to Brighton in the UK.
University of Tartu is classical university in city of Tartu, Estonia. National university of Estonia.
University of Technology at Sydney; New South Wales; Australia
Public research university located in Sydney, Australia.
University of Tennessee System is comprised of campuses at Knoxville, Chattanooga, Pulaski and Martin; Health Science Center at Memphis; Space Institute at Tullahoma; and statewide Institute of Agriculture and Institute for Public Service.
University of Tennessee Health Science Center; Tennessee; USA
The University of Tennessee Health Science Center
University of Tennessee Health Science Center
University of Tennessee Knoxville; Tennessee; USA
Public research university in Knoxville, Tennessee.
Public university system in Texas, established by the Texas Constitution in 1876, comprising nine academic and six health institutions.
University of Texas at Arlington; Texas; USA
Public research university in Arlington, Texas, midway between Dallas and Fort Worth.
University of Texas at Austin College of Pharmacy
The College of Pharmacy at The University of Texas at Austin is one of the premier institutions of pharmaceutical education and research in the country. Our college is a national leader in pharmacy education with a curriculum designed to prepare pharmacy graduates for lifelong learning and leadership capabilities as drug therapy managers in the nation's healthcare system. The pharmacist of the 21st century has significant responsibility for managing drug therapy, counseling patients on proper use of medications, and monitoring drug therapy outcomes.
UTEP officially opened in the fall of 1914 and is the second oldest institution in The University of Texas System.
University of Texas at San Antonio; Texas; USA
Public research university in San Antonio, Texas.
University of Texas at Tyler; Texas; USA
Public university in Tyler, Texas. Founded in 1971, it is a part of the University of Texas System.
University of Texas Health Science Center at Houston; Texas; USA
The University of Texas Health Science Center at Houston
University of Texas Health Science Center at Houston
University of Texas Health Science Center at San Antonio; Texas; USA
University of Texas Health Science Center at San Antonio
University of Texas Health Science Center San Antonio
The University of Texas Health Science Center at San Antonio serves San Antonio and the 50,000 square-mile area of South Texas. It extends to campuses in the metropolitan border communities of Laredo and the Rio Grande Valley. More than 3,000 students a year train in an environment that involves more than 100 affiliated hospitals, clinics and health care facilities in South Texas.
University of Texas Health Science Center Graduate School of Biomedical Sciences at Houston
At theGraduate School of Biomedical Sciences, graduate training in Pharmacology is available in the following programs: Cell and Regulatory Biology Environmental and Molecular Carcinogenesis Genes and Development Each program has specific research opportunities in the area of Pharmacology as well as the research interests of the Program Faculty. A wide variety of factors (including its faculty, programmatic and curricular flexibility, financial aid package, facilities, and location) have led to a high ranking of GSBS in several surveys of graduate programs and research funding.
University of Texas Southwestern Medical Center; Texas; USA
University of Texas Southwestern Medical Center
Public academic health science center in Dallas, Texas.
University of Thessaly; Thessaly; Greece
University of the Pacific School of Pharmacy and Health Sciences
UOP School of Pharmacy and Health Science
Proud to be a premier California school for pharmacy and health sciences, The Thomas J. Long School was founded in 1955 and offers professional and graduate degrees in pharmacy, physical therapy and speech-language pathology. Located on the campus of the University of the Pacific in Stockton, California, our school's pharmacy and health science programs are accredited by the respective national accreditation entities. We provide an outstanding academic environment that combines didactic and experiential learning as a focal point for our students. We hold academic affiliations with major medical centers, teaching hospitals, and related practice settings in support of our educational programs. We prepare our students for lifelong success in health careers by providing an excellent student-centered learning environment. Our students develop leadership skills and a strong commitment to their professions and to society. We support outstanding professional and graduate teaching, research and other scholarly activities, and services as a means of achieving our mission.
University of the Sciences in Philadelphia College of Pharmacy
Pharmaceutical education began at Philadelphia College of Pharmacy (PCP), the first such institution in North America. With nearly two centuries of experience in pharmacy and science and thousands of alumni working in the healthcare industry, the world turns to PCP graduates for advice. From undergraduate majors to graduate degrees to our esteemed PharmD program, you can learn where the founders (alumni such as McNeil, Lilly, Rorer, Wyeth, Warner, Burroughs, and Wellcome) of six of the top pharmaceutical companies in the world got their education. Since 1821, they have been preparing professionals in pharmacy practice, science, and health care. There is no better place than PCP to prepare you for a lifelong career in the healthcare industry.
University of the Western Cape; Bellville; South Africa
University of the West Indies; Kingston; Jamaica
Originally University College of the West Indies, is a public university system.
Public research university in Toronto, Ontario, Canada, located on the grounds that surround Queen's Park.
Italian university located in Trento and nearby Rovereto. It has been able to achieve considerable results in didactics, research, and international relations according to CENSIS and the Italian Ministry of Education.
University of Tubingen; Tubingen; Germany
Public university located in city of Tübingen, Baden-Württemberg, Germany known as centre for study of medicine, law, theology and religion. Alumni include numerous presidents, ministers, EU Commissioners and judges of the Federal Constitutional Court, Nobel laureates, especially in fields of medicine and chemistry.
University of Tunis El Manar; Tunis; Tunisia
University of Twente; Overijssel; Netherlands
Public technical university located in Enschede, the Netherlands.
University of Veterinary Medicine Vienna; Vienna; Austria
University of Veterinary Medicine Vienna
University of Victoria; British Columbia; Canada
Public research university in Greater Victoria, British Columbia, Canada, located in the municipalities of Oak Bay and Saanich. The university traces its roots to Victoria College, the first post-secondary institution established in the province.
Public university located in Vienna, Austria. It was founded in 1365 and is the oldest university in the German-speaking world.
The university of Virginia opened in 1819.
University of Virginia School of Medicine; Virginia; USA
University of Virginia School of Medicine
University of Waikato; Hamilton; New Zealand
Waikato University, is a comprehensive university in Hamilton, New Zealand. The university was established in 1964, and has an additional campus located in Tauranga.
University of Wales; Wales; United Kingdom
Confederal university based in Cardiff, Wales. Founded by Royal Charter in 1893 as a federal university with three constituent colleges – Aberystwyth, Bangor and Cardiff – the university was the first and oldest university in Wales, one of the four countries in the United Kingdom.
University was established in 1816 and is the largest university in Poland. One of the top Polish universities.
University of Warwick; Coventry; United Kingdom
Public research university on the outskirts of Coventry between the West Midlands and Warwickshire, England. It was founded in 1965 as part of a government initiative to expand higher education.
University of Washington is public research university in Seattle, Washington. Has university campuses in Seattle, Tacoma and Bothell, academic medical center and professional and continuing education programs.
University of Wyoming School of Pharmacy
The University of Wyoming School of Pharmacy was founded in 1946. The school aims to help improve the quality of health care in Wyoming by graduating students who can provide primary pharmaceutical care in a rural and frontier environment, as well as in cities. Students receive a strong background in the pharmaceutical sciences on which to build clinical expertise. Complementing this, early in the curriculum students are exposed to pharmacy practice environments and seminars focusing on contemporary issues. Throughout the curriculum, faculty members integrate the teaching and application of critical-thinking skills, decision-making skills, and professional communication techniques as applied to pharmacy practice. This culminates in the final year with a series of rotations in diverse settings throughout Wyoming, Colorado, and beyond.
U.S. Department of Agriculture Agricultural Research Service
United States Department of Agriculture Agricultural Research Service
Utrecht University; Utrecht; Netherlands
Utrecht University is located in Utrecht in Netherlands and is one of the oldest universities in the country. International research university. Consists of seven faculties including humanities, social and behavioural sciences, law, economics and governance, geosciences, medicine, veterinary medicine and science.
UT Health Science Center San Antonio School of Medicine; Texas; USA
University of Texas Health Science Center at San Antonio School of Medicine
University of Texas Health Science Center San Antonio School of Medicine
University of Texas School of Medicine at San Antonio
UT Health Science Center San Antonio School of Medicine
Vall d'Hebron Institute of Oncology; Barcelona; Spain
A center of biomedical research with scientists and physicians working together at the nexus of basic science and clinical research related to oncological diseases. They also pursue to make contributions to the development of new and better therapies for the treatment of cancer. * Scientific practice into the clinic for the benefit of oncology patients * Scientific research excellence in the areas of basic, translational and clinical research * Scientific cooperation among national and international oncology research institutions * Promotion of all oncology research-related activities, thereby contributing towards improving the quality of life of people
Private research university in Nashville, Tennessee.
Vanderbilt University School of Medicine; Tennessee; USA
Vanderbilt University School of Medicine
Vanderbilt University School of Medicine trains leaders in medicine by providing the best faculty and physicians in the best learning environment for the best students in the world. We are known for our personal attention and our customized medical education. Our research program is the fastest growing in the U.S. But our ranking among the top medical schools comes not just from an innovative curriculum and state-of-the-art facilities. It comes from our commitment to people.
Private, coeducational, liberal arts college in Poughkeepsie, New York.
Vestische Children and Youth Clinic Dates; North Rhine-Westphalia; Germany
Vestische Children and Youth Clinic Dates
Vestische Kinder- und Jugendklinik Datteln
Flanders Interuniversity Institute for Biotechnology
Vlaams Interuniversitair Instituut voor Biotechnologie
A life sciences research institute that performs basic research with a strong focus on translating scientific results into pharmaceutical, agricultural and industrial applications. VIB works in close partnership with four universities UGent, KU Leuven, University of Antwerp and Vrije Universiteit Brussel and is funded by the Flemish government.
Victor Chang Cardiac Research Institute; New South Wales; Australia
Australian nonprofit medical research facility that is dedicated to finding cures for cardiovascular disease.
Vienna University of Technology; Vienna; Austria
A tool for visualizing and manually annotating whole genomes that can be run as Applet or Webstart application as well as standalone application.
Vilnius University is the oldest and largest Lithuanian higher education institution. Since its establishment in the 16th century, Vilnius University, as integral part of European science and culture has embodied the concept of a classical university and the unity of studies and research. Vilnius University is an active participant in international scientific and academic activities and boasts many prominent scientists, professors and graduates. Scientific development and the expanding relations with global research centres have contributed to the variety of research and studies at Vilnius University. With the support of social partners, the university educates globallyminded specialists who successfully integrate in the modern European community.
Swedish agency whose mission is to promote sustainable growth by improving the conditions for innovation, as well as funding needs-driven research. They promote collaborations between companies, universities, research institutes and the public sector by stimulating a greater use of research, by making long-term investment in strong research and innovation environments and by developing catalytic meeting places. Their activities also focus on strengthening international cooperation.
Virginia-Maryland Regional College of Veterinary Medicine; Virginia; USA
Virginia-Maryland Regional College of Veterinary Medicine
State supported college of two states, Virginia and Maryland, filling the need for veterinary medicine education in both states. Students from both states are considered "in-state" students for admissions purposes.
Virginia Commonwealth University; Virginia; USA
Public research university in Richmond, Virginia. MCV was founded in 1838 as the medical department of Hampden–Sydney College, becoming the Medical College of Virginia in 1854.
Virginia Polytechnic Institute and State University; Virginia; USA
Virginia Polytechnic Institute and State University
Virginia Polytechnic Institute and State University, commonly referred to as Virginia Tech, is a public land-grant research university with its main campus in Blacksburg, Virginia, United States. It was founded as the Virginia Agricultural and Mechanical College in 1872.
Vrije Universiteit Brussel; Brussels; Belgium
Dutch and English speaking research university located in Brussels, Belgium. It has four campuses: Brussels Humanities, Science and Engineering Campus, Brussels Health Campus, Brussels Technology Campus and Brussels Photonics Campus.
Wageningen University and Research Centre; Gelderland; Netherlands
Wageningen Universiteit en Researchcentrum
Wageningen University and Research Centre
Wake Forest University; North Carolina; USA
Private research university in Winston-Salem, North Carolina.
Walter and Eliza Hall Institute of Medical Research; Victoria; Australia
Walter and Eliza Hall Institute of Medical Research
Medical research institute in Australia that researches and develops treatments for cancer, infectious diseases and chronic inflammatory diseases.
Washington State University; Washington; USA
Washington University School of Medicine in St. Louis; Missouri; USA
Washington University in St. Louis School of Medicine
Washington University School of Medicine
Washington University School of Medicine in St. Louis
Wayne State University School of Medicine; Michigan; USA
Wayne State University School of Medicine
University of Western Ontario, corporately branded as Western University as of 2012 and commonly shortened to Western, is public research university in London, Ontario, Canada.
A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An open source software tool for visualizing high-density data plotted against coordinates on the genome.
Weill Cornell Medical College; New York; USA
Founded in 1898, and affiliated with what is now NewYork-Presbyterian Hospital since 1927, Weill Medical College of Cornell University is among the top-ranked clinical and medical research centers in the country. In addition to offering degrees in medicine, Weill Cornell also has PhD programs in biomedical research and education at the Weill Graduate School of Medical Sciences, and with neighboring Rockefeller University and the Sloan-Kettering Institute, has established a joint MD-PhD program for students to intensify their pursuit of Weill Cornell''s triple mission of education, research, and patient care. The Medical College is divided into 20 academic departments: seven focus on the sciences underlying clinical medicine; and thirteen encompass the study, treatment, and prevention of human diseases, and maternity care. In addition to its affiliation with NewYork-Presbyterian Hospital, Weill Medical College and Graduate School maintains major affiliations with Memorial Sloan-Kettering Cancer Center, Hospital for Special Surgery, as well as with the metropolitan-area institutions that constitute NewYork-Presbyterian Healthcare Network. The Joan and Sanford I. Weill Medical College and Graduate School of Medical Sciences of Cornell University are accredited by the Liaison Committee for Medical Education of the American Medical Association and the Association of American Medical Colleges.
A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser.
Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Wellcome Trust Sanger Institute Genome Research Limited
Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.
Wenzhou Medical University; Zhejiang; China
Wenzhou Medical College; Zhejiang; China
West Virginia University; West Virginia; USA
The Windber Research Institute (WRI) is the combination of: Biomedical Research Programs, the Center for Health Promotion and Disease and strategic partnerships. By embracing these three entities as one, WRI is in a prominent position to impact health, as the world knows it today. Through pioneering research and programs that focus on breast cancer, gynecological disease, cardiovascular disease, health promotion and disease prevention, WRI is in a position to play a fundamental role in the future health and well-being of people all over the world. Windber Research Institute and its Center for Health Promotion and Disease Prevention and strategic regional, national, and international research and clinical partnerships is committed to discovering personal molecular diagnostic and prognostic biomarkers and developing innovative advanced disease prevention measures that will lead to decreased disease, early diagnosis, and individualized approaches to treatments and education for patients and their families in the world community. Windber Research Institute is built on the foundation of professional ethics and strong moral values which foster an environment of cooperation, open communication, integrity, dedication, self motivation, teamwork, excellence, and mutual respect. WRI''s welcoming and culturally diverse environment excels through interdisciplinary collaborations. Our pursuit of excellence is driven by the recognition of our patients and their valuable contributions to the research.
Witten/Herdecke University; North Rhine-Westphalia; Germany
Private, state-recognized, nonprofit university in Witten, North Rhine-Westphalia, Germany.
A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.
A genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more.
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
An integrated application for viewing and analyzing sequence data.
ngsplot - Quick mining and visualization of next-generation sequencing data by integrating genomic databases
A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.
A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.
An open-source software for developing personalized genome browsers that work in web browsers.
A software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage.
A graphical interface for comparative genomics.
Alignment visualization based on SuperGenome coordinates.
An interactive, web-based tool for comparative genomic visualization.
Software that allows users to upload files which contain synteny regions between two or more genomes and interactively visualize the synteny between them.
A multiscale synteny browser for exploring conservation relationships in comparative genomics data.
A Genomic Laboratory Information Management System (LIMS) and Data repository that can function as an experiment tracking and workflow management system for Core Facilities as well as an advanced data repository for storing and sharing genomic data sets.
PipMaker computes alignments of similar regions in two DNA sequences. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.
A generic sequence comparison tool for visualizing genome alignments both within and between species.
Software tools for comparative genomics.Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.
Software for searching DNA sequence databases for RNA structure and sequence similarities.
A fast and accurate multiple sequence alignment algorithm.
Multiple Alignment using Fast Fourier Transform
Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
MUltiple Sequence Comparison by Log- Expectation
Multiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation.
ProbCons: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.
PSAR-Align: improving multiple sequence alignment using probabilistic sampling
Software for improving multiple sequence alignment using probabilistic sampling.
Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics
Software for a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes.
SABmark - Sequence and structure Alignment Benchmark
Sequence and structure Alignment Benchmark
Downloadable data set designed to assess the performance of both multiple and pairwise (protein) sequence alignment algorithms, and is extremely easy to use. Currently, the database contains 2 sets, each consisting of a number of subsets with related sequences. It''s main features are: * Covers the entire known fold space (SCOP classification), with subsets provided by the ASTRAL compendium * All structures have high quality, with 100% resolved residues * Structure alignments have been derived carefully, using both SOFI and CE, and Relaxed Transitive Alignment * At most 25 sequences in each subset to avoid overrepresentation of large folds* Automated running, archiving and scoring of programs through a few Perl scripts The Twilight Zone set is divided into sequence groups that each represent a SCOP fold. All sequences within a group share a pairwise Blast e-value of at least 1, for a theoretical database size of 100 million residues. Sequence similarity is thus very low, between 0-25% identity, and a (traceable) common evolutionary origin cannot be established between most pairs even though their structures are (distantly) similar. This set therefore represents the worst case scenario for sequence alignment, which unfortunately is also the most frequent one, as most related sequences share less than 25% identity. The Superfamilies set consists of groups that each represent a SCOP superfamily, and therefore contain sequences with a (putative) common evolutionary origin. However, they share at most 50% identity, which is still challenging for any sequence alignment algorithm. Frequently, alignments are performed to establish whether or not sequences are related. To benchmark this, a second version of both the Twilight Zone and the Superfamilies set is provided, in which to each alignment problem a number of false positives, i.e. sequences not related to the original set, are added. Database specifications: * Current version: 1.65 (concurrent with PDB, SCOP and ASTRAL) * Twilight Zone set (with false positives): 209 groups, 1740 (3280) sequences, 10667 (44056) related pairs * Superfamilies set (with false positives): 425 groups, 3280 (6526) sequences, 19092 (79095) related pairs
T-Coffee: Aligns DNA RNA or Proteins using the default T-Coffee
A multiple sequence alignment server which can align Protein, DNA and RNA sequences.
Software package for DNA and protein sequence alignment to find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.
Software for an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). It s nearly four times faster, while producing identical results. GPU-BLAST supports: protein alignment according to blastp (it does not support psiblast), multiple CPU threads working in parallel with a single GPU, and input files with multiple protein queries.
PatMaN - A DNA pattern matcher for short sequences
Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Tool to search translated nucleotide databases using a protein query.
A web-based tool used to search translated nucleotide databases using a translated nucleotide query.
Tool to find regions of sequence similarity within selected protein databases quickly, with minimum loss of sensitivity.
Hammer: error correction with non-uniform coverage
A tool for error correction of short read datasets with non-uniform coverage, such as single-cell data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Accurate error correction in high-throughput sequencing data.
An open infrastructure for managing projects and data in life sciences that allows to store and access experimental data together with its scientific context. The platform connects the data from scientific instruments with data analysis tools, including workflow, annotation, and data visualization support. All public data can be searched and used to carry out inter-experiment analyses. For a fee, B-Fabric Order allows you to order the following analytical services at the FGCZ independent of a User Lab research project: Mass spectrometry, Protein sequencing, peptide sequencing, Amino acid analysis, Chromatography, Electrophoresis.
Open Source laboratory information management systems.
A laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform.
Systems Biology Experiment Analysis Management System
Software providing a framework for collecting, storing, and accessing data produced by a wide variety of experiments.
Web based Laboratory Information Management System (LIMS) system which can be used to track samples and distribute results within small sequencing facility. Provides simple way to track samples within facility and return sequencing, mapping and QC results to users.
Discovering Context-Specific Sequencing Errors
Software for discovering motifs that induce sequencing errors.
A software package for building accurate ConSeqs from tagged reads.
Software program to remove residual adapter sequences from next generation sequencing reads. Used for cleaning of next-generation sequencing reads. AdapterRemoval v2 introduces improvements in throughput, through use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support; handles datasets containing reads or read-pairs with different adapters or adapter pairs; provides simultaneous demultiplexing and adapter trimming; has ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets; provides native gzip and bzip2 support.
Allows detecting and removing multiple alien sequences in both ends of sequence reads.
A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines.
A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.
Software tool as content dependent read trimmer for Illumina data. Content dependent read trimming software for Illumina/Solexa sequencing data.
A software package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.
Software tool as error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently.
Software tool that removes adapter sequences from DNA sequencing reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A next generation sequence quality trimming tool.
Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data.
Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads.
A customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data.The old version for Sanger sequences, Seqtrim, has been discontinued.
A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets.
Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.
Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
An error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer.
ECHO: A reference-free short-read error correction algorithm
Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.
A software program for correcting errors in sequencing data.
Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program.
Software for next-gen sequence assembly and analysis in a single, integrated package.
With their unique combination of proprietary algorithms and comprehensive data background, all our solutions do more than enable you to efficiently and effectively analyze and interpret biological data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An integrated collection of user-friendly, yet powerful analytic tools for managing, analyzing, and visualizing multifaceted genomic and phenotypic data.
Provides the tools you need to analyze rare and common variants, detect differential expression patterns, discover reliable biomarker profiles, and incorporate pathway information into your analysis workflows.
Automates the primary analysis of massive parallel sequencing data.
Software tool for Next Generation sequence analysis. Analytical partner for analysis of desktop sequencing data produced by Illumina iSeq, Miniseq, MiSeq, NextSeq, HiSeq, and NovaSeq systems, Ion Torrent Ion GeneStudio S5, PGM, and Proton systems as well as other platforms. Software runs on Windows Operating System, which provides biologist friendly interface. It does not require scripting or other bioinformatics support.
A comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data.
An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc.
A command line-based pipeline framework for bioinformatics research.
A mapping and analysis pipeline for short read data produced on the Illumina platform.
Service where users are able to upload and store data, access bioinformatics tools, and perform analyses.
An accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads.
An efficient model-based base-calling algorithm for high-throughput sequencing.
Script distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features.
Service that retrieves disease relevant information from Twitter tweets and shows current hotspots of disease outbreaks on an interactive map. It is an ontology-driven system for detecting global health events
A literature search tool providing gene and signal transduction pathway mining within NCBI' '''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite.
RefMED: Relevance Feedback Search Engine for PubMed
Relevance Feedback Search Engine for PubMed. When a user enters a keyword in the search box, the PubMed search results will be returned. The user then specifies on a sample of results how much they are relevant to what she intends to find, for example, by specifying whether each article is high relevant, somewhat relevant, or not relevant. Once the user clicks Push Feedback button, the system learns a relevance function from the feedback and returns the top articles ranked highly according to the relevance function. The user can repeat the process until she gets satisfying results.
Elastic Utility Computing Architecture for Linking Your Programs to Useful Systems
Open source software for building AWS-compatible private and hybrid clouds for IT organizations in enterprises and technology businesses.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2019. Delivers public cloud infrastructure that''s business grade, open source-based, and developer focused., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
High-performance cloud infrastructure and big data analytics company, offering organizations of any size the best public and hybrid cloud infrastructure for today''s demanding real-time web and mobile applications.
An open cloud company with performance Cloud Servers that offer 100% SSD storage & 10Gb Ethernet networking for your demanding applications.
A general-purpose full virtualizer for x86 and AMD64/Intel64 hardware, targeted at server, desktop and embedded use.
A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.
Software that virtualizes computing, from the data center to the cloud to mobile devices, to help customers be more agile, responsive, and profitable.
Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets.
An open and flexible cloud platform that enables you to quickly build, deploy and manage applications across a global network of Microsoft-managed datacenters.
Cloud platform to be directly integrated in to the industry?s leading sequencing platforms, with no cumbersome and time consuming data transfer steps.
Cloud Computing and a graphical workflow composer that uses distributed computing resources on demand.' '''
Offers genome analysis resources for cloud computing platforms such as Amazon EC2.
A cloud-based platform to support genomics at your organization.
A universal collaborative platform for bioinformatics application development that allows users to store and share large data sets securely within and across organizations, with free access to public data from major databases. The platform includes open-source and proprietary genomics applications, working together independent of file formats. For developers an SDK, APIs and a marketplace are provided.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29, 2019. A cloud platform for next-generation sequencing analysis and storage. Services include: * g-Analysis: Automated genome analysis pipelines at your fingertips * g-Cluster: Easy-of-use and cost-effective genome research infrastructure * g-Storage: A simple way to store, share and protect data * g-Insight: Accurate analysis and interpretation of biological meaning of genome data
Software-as-a-service for big data management offering fast, reliable, secure file transfer and sharing services to non-profit researchers. It combines state-of-the-art algorithms, data management tools, a graphical workflow environment, and an elastic computing infrastructure making it easy to manipulate, store, and share your data, no matter how big it gets.
Scotty - Power Analysis for RNA Seq Experiments
A tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims.
Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.
An iterative De Bruijn Graph De Novo short read assembler for transcriptome.
A C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information.
Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events.
FusionHunter: identifying fusion transcripts using paired-end RNA-seq
A perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data.
Software for identifying fusion transcripts using paired-end RNA-seq.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
Software designed to assemble Illumina single or paired-end reads.
A de novo transcriptome assembly from next-generation sequencing data.
TopHat-Fusion: An algorithm for Discovery of Novel Fusion Transcripts
An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.
Software to visualize the various data from the RNA-Seq analyzing process, for single or multiple samples.
A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.
A user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing.
Guide: Application for gene expression analysis
A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules, integrates data from multiple sources, and enables editing of R commands., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells.
Online Quantitative Transcriptome Analysis
It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis.
Pipeline for RNA-Sequencing Data Analysis
A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.
An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets.
Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure.
RseqFlow - An RNA-Seq analysis pipeline for Quality Control Expression Level Estimation Differentially Expressed Gene
An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets.
GeneStitch: Network Matching Algorithm to Gene Assembly
Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes.
Software for a novel de novo sequence assembler that discovers likely sequence reconstructions under the model.
Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.
Software for an iterative De Bruijn Graph De Novo short read assembler specially designed for de novo metagenomic assembly. (Please note that MetaIDBA is out of maintainance now, we recommend using IDBA-UD instead which generally performs better.)
A modular and open source metagenomic assembly and analysis pipeline.
MetaVelvet: a short read assember for metagenomics
Software for a short read de novo metagenome assembly created by modifying and extending a single-genome and de Bruijn-graph based assembler, Velvet.
A software package for de novo DNA sequence assembly.
A software program for assembling shotgun DNA sequence data.
Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers.
Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
Software that uses the greedy algorithm for nucleotide sequence alignment search.
Algorithm that divides a set of sequences into clusters
eXPatGen - An On-line Gene Expression Pattern Generator
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A simulator of gene expression patterns in order to evaluate different analysis methods, such as clustering and principle component analysis (PCA).
Web Server for Taxonomic Assignment of Metagenome Sequences that is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments.
CoMet - a web-server for fast comparative functional profiling of metagenomes
A web-server for fast comparative functional profiling of metagenomes.
A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels.
Rapid analysis of Multiple Metagenomes with Clustering and Annotation Pipeline
Metagenomic software pipeline for analysis and comparison of very large metagenomes with fast clustering and functional annotation.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains).
A software application for finding fragmented genes in short reads and may be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.
A family of gene prediction programs developed at Georgia Institute of Technology.
A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
Gene Locator and Interpolated Markov ModelER - MetaGenomics
Glimmer-MG: Metagenomics Gene-Finding System
A software system for finding genes in environmental shotgun DNA sequences.
Data analysis service for prediction of vertebrate and C. elegans genes.
A gene-finding software program for prokaryote and phage., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software application for finding complete and incomplete genes in metagenomic reads.
PROkaryotic DYnamic programming Gene-finding ALgorithm
Prokaryotic Dynamic Programming Genefinding Algorithm
Software tool for protein coding gene prediction for prokaryotic genomes.
Graphical user interface software for metadata-driven management, analysis, and visualization of microbiome data.
An online toolbox for metagenomic data visualization.
An interactive multi-view genome browser for next-generation comparative microorganism genomics.
A Sequencing Simulator for Genomics and Metagenomics.
A Next-Generation Sequencing Simulator for Metagenomics.
Software package for analyzing metagenomics datasets.
A clustering algorithm focusing on noise injection for subsequent cluster validation.
Comprehensive database of cancer relevant proteins and compound interactions supported by experimental knowledge.Knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data.
Auto Regressive TIme VArying regulatory models
Algorithm available in a R package that is a statistical framework to infer time-varying structures of gene-regulation networks.
An open-source software package for describing and comparing microbial communities. It incorporates the functionality of a number of computational tools, calculators, and visualization tools.
Delivers comprehensive shotgun metagenomics sequence analysis for accurate species frequency composition and protein searching.
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
A customizable web server for fast metagenomic analysis.
PTP - a Poisson Tree Processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree
A tool for delimiting species on phylogenies and evolutionary placements.
GeneTack: tools for frameshift prediction
Tools for frameshift prediction and a frameshift database.
Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species.
A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data.
A genomics database project is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs.
Database that contains about 1,170 drugs, 2,785 Cytochrome-Drug interactions and about 1,200 alleles.
An open-source program for doing molecular docking.
A database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations.
Potassium Channel Database - Structures and Simulations
A Database of Potassium Ion Channel Homology Models & Molecular Dynamics Simulations.
Orientations of Proteins in Membranes database
Orientations of Proteins in Membranes (OPM) database
Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal.
Protein Data Bank of Transmembrane Proteins
Comprehensive and continuously updated transmembrane protein database of the Protein Data Bank (PDB) created by scanning all PDB entries with the TMDET algorithm. Resource for transmembrane proteins and their structures., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
PREDDIMER - Prediction tool for an ensemble of transmembrane ?-helical dimer conformations
Prediction tool to reconstruct putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal alpha-helices.
Web server for the detection of the transmembrane regions of membrane proteins using their 3D structure only.
A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.
Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in different organisms
A package of web-servers for predicting subcellular localization of proteins in different organisms.
International Nucleotide Sequence Database Collaboration
International collaboration of the International Nucleotide Sequence Databases (INSD), DDBJ, ENA, and GenBank, maintained for over 18 years. Individuals submitting data to the international sequence databases should be aware of INSDC policy.
CELLO: subCELlular LOcalization predictor
A subCELlular LOcalization predictor based on a multi-class support vector machine (SVM) classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. They combine votes from these classifiers and use the jury votes to determine the final assignment.
Data analysis service for cluster-based Subcellular localization prediction.
A comprehensive database that gathers all prediction outputs concerning complete prokaryotic proteomes. It is a client-server application, with the server installed and staying at Biogenouest bioinformatics platform, keeping all needed pre-computed genomic data, while the CoBaltDB Client or GUI is a Java application which communicates with the server via web-services. The CoBaltDB Client needs to be downloaded on your computer.
Euk-mPLoc 2.0: Predicting subcellular localization of eukaryotic proteins including those with multiple sites
Data analysis service for predicting subcellular localization of eukaryotic proteins including those with multiple sites. Euk-mPLoc covers 22 eukaryotic subcellular locations.
HSLPred - A SVM-based Method for Subcellular Localization of Human Proteins
A support vector machine (SVM)-based method for the prediction of 4 major subcellular localization (cytoplasm, mitochondrial, nuclear and plasma membrane) of human proteins using various features such as i) amino acid composition, ii) dipeptide composition and iii) evolutionary information of proteins.
iLoc-Plant: Predicting subcellular localization of plant proteins with single and multiple sites
Data analysis service for predicting subcellular localization of plant proteins with single and multiple sites.
KnowPredsite: A general protein subcellular localization predictor for eukaryotes and prokaryotes
KnowPredsite: A web server for predicting single and multiple subcellular localization sites
A knowledge-based data analysis service to predict the localization site(s) of both single-localized and multi-localized proteins.
University of Pittsburgh, Health Sciences Library System
Database access to information services, educational opportunities, and resources in print and electronic format to faculty, students, and researchers in the schools of the health sciences.
Calpain for Modulatory Proteolysis Database
Calpain cleavage prediction using multiple kernel learning.
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection
Trustful Inference of Gene REgulation using Stability Selection
Software providing a scoring technique for stability selection, which improves the performance of feature selection with LARS. TIGRESS can be run online through the GenePattern platform (GP-DREAM, http://dream.broadinstitute.org).
A database that identifies orthologs among publicly available, complete genomes. It offers a comprehensive search and numerous display options for 4.7 million proteins from 1000 species. The main features are the orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed.
orthAgogue: a tool for high speed estimation of homology relations within and between species in massive data sets.
A software tool for high speed estimation of homology relations within and between species in massive data sets.
OrthoDB - The Hierarchical Catalog of Orthologs
Database of orthologous protein coding genes across vertebrates, arthropods, fungi, basal metazoans, and bacteria.
A large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. Contnet includes orthology predictions among 1621 complete genomes (1365 bacterial, 92 archaeal, and 164 eukaryotic), covering >7 million proteins and 4 million pairwise orthologs; Orthologous groups, comprising >300000 groups of orthologous proteins and >236000 corresponding gene trees; and inparalog groups, comprising >500000 groups of inparalogs.
A community created to advance the use and value of next-generation sequencing through knowledge sharing.
A subreddit dedicated to bioinformatics, computational genomics and systems biology.
A question and answer site for professional and enthusiast programmers.
This blog focusses on next-generation sequencing and microarray technologies.
A leading source of news on technology and innovation in life sciences IT, informatics, genomics, next-gen, drug discovery, development, and clinical trials.
A web magazine helping bioinformatician or scientists find jobs, conferences, courses, companies and more stuff related to Bioinformatics.
Open Access Bioinformatics resource portal.
Blog about getting Things Done in Genetics & Bioinformatics Research.
SIOMICS -Systematic Identification Of Motifs In ChIP-Seq data .
SIOMICS--Systematic Identification Of Motifs In ChIP-Seq data
A software to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments.
Data set providing an up-to-date compendium of HTS mappers initially provided in the article Tools for mapping high-throughput sequencing data. Please let fill out the provided form if you are a developer and your mapper is not listed or you want to update the data for your mapper.
A public source for microarray protocols and software.
The Need for an Up-To-Date Synthesis of Next Generation Sequencing Know-How.
A registry which provides links and reviews for material resources such as reagents, equipment, digital tools, and providers, as well as the companies that sell them. Users can search for specific materials or search by vendor, product, or service type.
Serves as a gateway that provides visible access to a large number of reagents and accompanying characterization data to the research and industrial community.
The aim of this site is to collect and to share experimental results on antibodies that would otherwise remain in laboratories, thus aiding researchers in selection and validation of antibodies.
Search Tool that lets researchers search over 1 million antibodies from hundreds of antibody suppliers quickly and easily.
American Association for Clinical Chemistry
An international society comprised of medical professionals with an interest in clinical chemistry, clinical laboratory science, and laboratory medicine.
The oldest and most diverse organization of public health professionals in the world and has been working to improve public health since 1872.
Association of Public Health Laboratories
Works to strengthen laboratories serving the public''s health in the US and globally.
Factor Analysis for Bicluster Acquisition
A model-based technique for biclustering that is clustering rows and columns simultaneously.
A Python library designed to simplify biclustering tasks.
ExpressionView - Visualize biclusters identified in gene expression data
An R package that provides an interactive environment to explore biclusters identified in gene expression data.
Combinatorial Algorithm for Expression and Sequence-based Cluster Extraction
Software that can use large collections of genomic data and Bayesian integration to predict coregulated gene modules, the conditions of regulation, and the consensus binding motifs for regulation.
Gene ARMADA (Automated Robust MicroArray Data Analysis)
Gene ARMADA: MATLAB software for the analysis of microarray data
Gene ARMADA: robust automated pipelines for the analysis of microarray data
Gene Automated Robust MicroArray Data Analysis
Software for the analysis of microarray data with a MATLAB implemented platform with a GUI that integrates all steps of microarray data analysis including automated data import, noise correction, filtering, normalization, statistical testing, clustering, classification and annotation.
GenoREAD - Sequencing Verification Pipeline
A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence.
Organization that serves the scientific and educational needs of bioinformatic practitioners and the general public. They develop and maintain computational resources to facilitate world-wide communications and collaborations between people of all educational and professional levels. They provide and promote open access to the materials and methods required for, and derived from, research, development and education.
International Society for Computational Biology
Community building portal that serves over 3,000 members from more than 70 countries by addressing scientific policies, providing access to high quality publications, organizing meetings, and serving as a portal to information about training, education, employment, etc.
Online community for industry news and careers for life science professionals.
A blog about genetics, genomics, and medical research.
This blog reflects the workings of a group of scientists working at the intersection of public health microbiology and bioinformatics.
Datbase and web-based system for visualization and analysis of genome-wide methylation data of human cancers.
A database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells.
A database for histone mutations and their phenotypes.
Genome Alteration Print (GAP): Mining complex cancer genomic profiles
Software for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.
methPrimerDB - DNA Methylation analysis PCR Primer Database
A public database holding PCR primers for popular DNA methylation analysis methods to prevent time-consuming primer design and experimental optimisation.
Classification of Human Transcription Factors
Database that classifies human transcription factors based on the characteristics of their DNA-binding domains. It comprises six levels (superclasses, classes, families, subfamilies, genera and factor species), two of which are optional (subfamilies and factor species). The full classification can also be obtained as html document and as ontology in obo-format., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
APPRIS - A system for annotating alternative splice isoforms
A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript.
easyRNASeq - Count summarization and normalization for RNA-Seq data
Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package.
Software using a statistical approach, based on a two-stage Poisson model, for modeling RNA sequencing data and testing for biologically important changes in gene expression.
Software for detecting differential features across the entire spectrum, including the lower counts.
A platform and application suite for bringing together omics and clinical data.
Software to generate a visual representation of sRNAs and user-imported genomic features. The tool may be run on its own or from other tools, e.g. miRCat.
Software for decoding error-correcting barcodes.
A genome browser specialized in next-generation sequencing data.
Software that combines digital gene expression (DGE) tags, RNA-Seq, tiling array expression data and species-comparison to explore new transcriptional regions and their specific biological features, particularly tissue expression or conservation.
A software package for predicting genome-wide co-binding between biological regulators such as Transcription factors (TFs).
Optimized GPU-based software to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples.
Source code providing a cost-effectiveness metric for guiding the design of large-scale RNA-seq differentially expressed (DE) studies.
Software to make Approximate Bayesian Computation inferences about population history using Single Nucleotide Polymorphism, DNA sequence and microsatellite data.
An automated variant annotation pipeline designed for facilitating target discovery for family-based sequencing studies.
Gene Annotation Relationship NEtwork Tools
An integrative platform for diverse types of gene set analysis with annotation network navigation. It includes tools for statistical analysis, visualization of annotation relationships, retrieval of genes from annotation database, and set operation for gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, they have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations.
Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest.
A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks.
A C software implementation of SAM, BAM and CRAM file I/O.
FiGS - Filter-based Gene Selection workbench for microarray analysis
A web-based workbench to conveniently compare the classification performances of many different filter-based gene selection procedures. In addition to the commonly used filter metric-classifier combinations, user can test various additive methodological options by specification of only up- or down-regulated genes to select, applying feature discretization and adding feature vectors to make a new feature. Throughout the comprehensive comparisons, user can identify the best performing gene selection procedure and subsequent classification performance measured by .632+ bootstrap error estimation for the given binary (two-class) microarray data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
PerlPrimer - open-source PCR primer design
A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing.
Software that performs retention time alignment on the given set of peaks.
Software for mass-spectrometry data processing, with the main focus on LC-MS data.
Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function.
An algorithm to align LC-MS samples and to match corresponding ion species across samples.
Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on May 23rd,2023. Software that provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows.
Software for pipelined analysis of mass spectrometry data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23rd,2023. Software that combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yen''s k shortest paths algorithm.
A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments.
A software tool for scientists working with stable isotopic labelling and high resolution liquid chromatography mass spectrometry.
Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).
A collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML.
PRoteomics IDEntification (PRIDE) Converter 2
Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra.
An open source software application and library written in Java that provides a uniform annotation of identified spectra stored in the PRIDE database.
A Java library to parse the msf files that constitute the output of Proteome Discoverer.
Software providing a user-friendly, lightweight and open-source graphical user interface for configuring and running the freely available OMSSA and X!Tandem search engines simultaneously.
An open-source Java library that parses X!Tandem XML result files into an easily accessible and fully functional object model.
Software that enables rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations.
Modular Application Toolkit for Chromatography Mass-Spectrometry
An application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics.
An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI.
A software tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.
A highly flexible software toolbox for processing 1D and 2D NMR and EPR spectra under MATLAB, creating high-quality 1D, 2D or 3D plots from the spectra and printing them in every type of format that is supported by MATLAB.
Free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.
Software that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy.
A software tool to locate all copies of sequences in a reference sequence using read-pairs.
Frequency-based Insilico Genome Generator
A large-scale whole genome simulation tool which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations.
A software tool to predict the conformational epitopes from 3D structures.
A modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.
A software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix.
A utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods.
Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway.
MOdel based Analysis of Bisulfite Sequencing data
Software providing a complete, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing.
Software that provides one-to-many alignments of reactions in a pair of metabolic pathways.
A software library containing code shared by many research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. This library can be of use to other research groups doing computational proteomics.
Software providing a user-friendly and lightweight graphical user interface for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics.
A Java-based proteomics cloud computing pipeline system for peptide and protein identifications.
An algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at once.
A metabolite identification software using tandem mass spectrometry and kernel methods.
probabilistic TRacking and Analysis of Clusters
A software which detects and analyses piRNA clusters based on quantifiable deviations from a hypothetical uniform distribution regarding the decisive piRNA cluster characteristics.
Software using a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements.
Algorithm for the problem of globally aligning a pair of protein-protein interaction (PPI) networks.
A connected-components based fast algorithm for network alignment.
An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application.
A software that facilitates and improves the design of chemical combinatorial libraries.
A small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation.
Fast motif detection algorithm for subgraph size no more than 6.
A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach.
A software tool to facilitate chemical similarity calculations.
Software providing a graphical front end for computational chemistry programs.
Open source (GPL) software providing an interactive, high quality molecular visualization system.
Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads.
Software that automates the finishing process using long sequence reads in a reference-guided assembly process.
A generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.
A flexible open source protein similarity search software tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss.
A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.
A Matlab package extending the scope of established COBRA metabolic modelling.
An open source annotation tool for the distributed creation of a large corpus.
A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system.
A GUI-based text annotation tool for creating and visualizing annotations.
A text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries.
An efficient software tool to connect overlapping pair-end reads using k-mer frequencies.
Software application that manages many PDF files of articles, whose information can be obtained by PubMed.
A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization.
A user-friendly plant miRNA prediction tool.
Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt.
A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).
A targeted gene assembly software program which aims to recover gene families of particular interest to biologists.
Software that implements a HMM Model to detect copy number variants in exome sequence data.
An editing and visualization software tool for pathway models represented by the BioPAX format, using SBGN Process Description Language, based on Chisio.
Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences.
Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data.
Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci.
A user-friendly software tool to estimate allele-specific gene expression.
Software tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures.
Software for a low frequency Virus Variant detection pipeline for Illumina data.
A web application creating Venn diagrams from two or three gene lists.
Software that annotates biologically functional gene fusion candidates.
An adaptive imaging cytometry software environment.
An open source Java application that provides a clear and concise analysis workbench for large amounts of cell motion data.
Software for the conversion of data acquired with the FlashQuant (MALDI version of ABSciex 4000) into MS images.
A software package for automated recognition of glycans from LC/MS data.
An intuitive and flexible software tool for building and displaying glycan structures.
Ministry of Health and Family Welfare - Government of India
Ministry of Health & Family Welfare (Government of India)
Ministry of Health and Family Welfare (Government of India)
Software that implements a computational model for predicting immunosuppressive domains (ISDs). The software could be used to identify typical ISDs in retroviruses including HERV, HTLV, HIV, STLV, SIV and MLV.
Software for accurate and sensitive CNV discovery and genotyping in long-range targeted resequencing.
A perl-based package to perform comparative analysis of metabolic pathways between two organisms.
Software that implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments.
Inferring Haplotype frequencies from Pooled sequencing
Software tool for inferring haplotypes from pooled sequencing. Enables to infer strain numbers and haplotype frequencies in silico from sequences of pooled samples.
Software that uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD).
A computational software tool for estimating linkage disequilibrium (LD) from pooled resequencing data.
PLEK: predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme
An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data.
A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data.
A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.
A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs.
A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit.
Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol.
A computational software tool to predict leucine-rich nuclear export signals (NESs) by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. It is a multiplatform command-line Perl application with activity-based NES profiles.
Dynamical Hierarchical Agglomerative Clustering
Software for clustering time-evolving networks.
Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing.
A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites.
A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.
Universite de Sherbrooke Najmanovich Research Group Core Facility
Universite de Sherbrooke Najmanovich Research Group
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility provides consultancy services as well as contract work in all areas of bioinformatics, chemoinformatics and systems biology.
A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.
Maximum Pseudo-likelihood Estimate of the Species Tree (MP-EST)
Maximum Pseudo-likelihood for Estimating Species Trees
Software that can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset. In addition, increasing the number of genes does not increase the computational time substantially. The MP-EST method is fast for analyzing datasets that involve a large number of genes but a moderate number of species.
Software that predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bow tie, although any alignment tool can be used to generate SAM alignments for use as input to HLAforest.
A fast and scalable local network alignment software tool for the identification of functionally conserved modules in multiple networks. LocalAli outperforms all existing algorithms in terms of coverage, consistency and scalability, meanwhile retains a high precision in the identification of functionally coherent subnetworks.
Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming.
National Climatic Data Center Paleoclimatology Data
Data sets derived from paleo proxy evidence, including ice cores, tree rings, ocean and lake sediments, corals, cave deposits, loess, climate models. Includes raw data and reconstructions of past climate and environment.
fMRI Joystick that is completely RF radiation free. It responds just like any other PC compatible joystick. The joystick is capable of standard X and Y axis but the Z-axis (swivel) is also available. The operation of the joystick is based on unique fiberoptic technology that allows for high resolution tracking. The joystick interfaces with the PC via the fMRI Joystick module. User can use the operating systems standard Joystick software utility to calibrate the joystick to their needs. Two standard buttons, the thumb button and the trigger button, but more can be added depending on customers specifications.
Extech | EA15: EasyView Dual Input Temperature Datalogger
EasyView Dual Input Temperature Datalogger
Temperature datalogger compatible with 7 types of thermocouples. This dual input thermometer accepts Types J, K, E, T, R, S, and N thermocouples. RS-232 port to transfer data to PC for analysis (PC software and cable included)
IITC Life Sciences | Plantar Test Apparatus
Plantar Test Apparatus (Hargreaves Method) for Mice and Rats
Plantar Test Apparatus for Mice and Rats
The IITC Plantar Analgesia Meter for thermal paw can be used on 12 mice, 6 rats and other animals (cats, rabbits) unrestrained when testing for narcotic drugs. Experiments are easy to perform, simply slide the test head under test subject, align the heat source via our exclusive guide light (idle state) by the attached, adjustable, angled mirror on test head to test subject and perform tests.
Mimics - Medical Image Segmentation for Engineering on Anatomy
Software for medical image processing. Use Mimics for the segmentation of 3D medical images (coming from CT, MRI, microCT, CBCT, Ultrasound, Confocal Microscopy) and the result will be highly accurate 3D models of your patient''s anatomy. You can then use these patient-specific models for a variety of engineering applications directly in Mimics or 3-matic, or export the 3D models and anatomical landmark points to 3rd party software, like statistical, CAD, or FEA packages.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 11, 2024. Light cycler software for analysis of quatitative real time PCR, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Customizable software program for behavioral testing. Users logically order simple text commands to direct experimental work flow and data collection, providing control of chamber components, stimuli, reinforcement mechanisms, data variables, and arrays. Standard pre-written procedures and custom coding solutions are available for purchase.
A tool for functional connectivity analysis of fcMRI data that maps functional data from individual sessions onto a priori spatial components from group level parcellations.
A software package for performing 2D microscope image processing and integrating and controlling a diverse array of instrumentation in a laboratory environment. The software suite has four basic areas of operation acquisition, image presentation, and storage, analysis, and automation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Macquarie University MQ Research Centre in Quantum Science and Technology
Macquarie University Research Centre in Quantum Science and Technology
Macquarie University Research Centre in Quantum Science and Technology (QSciTech)
Macquarie University has established a new multidisciplinary research centre combining physics, mathematics, computer science, engineering and biochemistry to engage in novel research towards deeping our understanding in quantum science and technology.
MQ Research Centre for Astronomy Astrophysics and Astrophotnics
Macquarie University Research Centre for Astronomy Astrophysics and Astrophotnics
Macquarie University Research Centre for Astronomy Astrophysics and Astrophotnics (MQAAAstro)
MQ Research Centre for Astronomy Astrophysics and Astrophotnics (MQAAAstro)
Macquarie University Research Centre for Astronomy, Astrophysics, and Astrophotnics (MQAAAstro) grew out of our Concentration of Research Excellence (CORE) and is now one of the largest and fastest growing astronomy groups in Australia. We are a highly active centre of astronomical research excellence. We have close ties to the Australian Astronomical Observatory (AAO) and CSIRO Astronomy & Space Science (CASS), both of which are close to campus. These strong links offer valuable synergies and opportunities for collaborations in observational astronomy, theoretical astrophysics, astrophotonics, science education, and Aboriginal astronomy.
Trenzyme is a privately owned German contract research organization offering highly individualized scientific services. As your life science service partner, we offer more than 11 years of experience and a continuously growing staff of highly skilled employees. Connected with our outstanding collection of state-of-the-art laboratory equipment this guarantees a flexible high-quality service to accommodate your needs. From the very first beginning of Trenzyme in 2000, we offered molecular biology services. In this field, we provide you with every service from gene to plasmid. Custom cloning, gene synthesis, mutagenesis and plasmid purification are only the main services in our baseline business domain. Whether expressed in microbials or mammalian cells, our protein services department delivers the exact proteins for your downstream applications. To keep your budget in balance, we offer standardized Fixed-Price-Protein-Manufactures. Cell culture is one of the most time-consuming and challenging life science branch of the last years. We understand the importance of your work and take pride in freeing you of valuable time, always keeping track of our mission: accelerating your innovation!
VCU Nanomaterials Characterization Center
Virginia Commonwealth University Nanomaterials Characterization Center
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Nanomaterials Characterization Center at Virginia Commonwealth University is a state of the art 4000 sq. ft. facility located within the new Health and Life Science Engineering Facility. The Center provides an academic structure for students in natural sciences, mathematics, engineering, and medicine to participate in nanoscience and nanotechnology research to acquire the skills necessary to pursue such careers. In the past year, VCU received two National Science Foundation major research instrumentation grants totaling more than $1.6 million to expand its capabilities for research in materials science. Combining these federal awards with state instrumentation grants and private donations, the facility has been able to build a state of the art facility with over $5 million in new equipment. This new equipment will allow faculty and student researchers from both VCU campuses, as well as other universities.
Preclinical contract research company performing CLIA-certified DNA Next Gen Sequencing Services.
Contract research organization for gene therapy product development. Services include adenoviral vectors, AAV vectors and lentiviral vectors and range from cell line optimization and vector development to process development and cGMP manufacturing through product release testing.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. ICCE certified instructors with 20 years experience in flow cytometry and assay development can deliver basic, intermediate, and advanced training tailored to your needs. We can ensure rapid assay development and implementation, using theoretical and hands-on training conducted at your site, using your assays and your instruments.
University of Utah Microarray and Genomic Analysis Core Facility
Utah Microarray and Genomic Analysis Core Facility
UUtah Microarray and Genomic Analysis Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22,2024. Microarray and Genomic Analysis Core Facility provides access to an Illumina Genome Analyzer, which enables massively parallel DNA sequencing. The resource is operated as a full service facility that provides experimental handling of all aspects of the Illumina sequencing processes.
UNC School of Medicine Animal Models Core
University of North Carolina at Chapel Hill School of Medicine Animal Models Core
The UNC Animal Models Core Facility provides the full range of mouse genetic modification services, reagents and related technologies. The Core''s services are available to both UNC and Non-UNC clients. Transgenic (pronuclear injection) animals can be generated in C57BL/6, FVB or C57BL/6 X DBA2 hybrid strains. Services for creating transgenic mice include transgene design, construct generation, isolation of the transgene fragment, pronuclear microinjection, founder genotyping and breeding. The core also offers the full suite of services for BAC (bacterial artificial chromosome) recombineering and microinjection of BAC transgenes. Gene targeting services are available in ES cells from C57BL/6 or 129P2/Ola strains. Other strains available upon request. Gene targeting services include design and cloning of targeting vectors, creating gene-targeted ES cells, blastocyst microinjection of the ES cells to create transmitting chimeras and chimera breeding for germline transmission. The core can also provide Southern blot validation and blastocyst microinjection of ES cells from EUCOMM, KOMP or other consortia. Additional services include Cre- or Flp-mediated excision in ES cells or in vivo, chromosome counting, PCR screening and Southern blotting. Rat model production is also available.
Moffitt Cancer Center Proteomics and Metabolomics Core Facility
H. Lee Moffitt Cancer Center and Research Institute Proteomics and Metabolomics Core Facility
Provides instrumentation for proteomics and metabolomics studies, including protein, peptide and metabolite separations, MS instrumentation for protein, peptide and metabolite analysis, and data systems, software, and bioinformatics tools for data archiving and analysis. Proteomics Core performs routine analytical proteomics services, including target discovery, identification and quantitation, and also provides platforms for functional proteomics using variety of strategies for protein separation, sub-proteome enrichment, post-translational modification analysis, and quantitation.
University of Toledo Instrumentation Center Core Facility
University of Toledo Instrumentation Center
Provides advice, technical assistance and access to advanced scientific equipment.Provides education and training for graduate students. Supports research activities of other Universities and assists local business ventures in solving scientific problems.
Monash University Micromon Core Facility
Provides complete sequencing and data analysis service based around second generation Illumina Genome Analyzer (GAIIx) and Illumina MiSeq sequencing platform. They also offer Agilent Bioanalyzer RNA and DNA analysis, Covaris focussed acoustic shearing of nucleic acids and tissues, qPCR assay design, execution and analysis, oligonucleotide synthesis and capillary electrophoresis (CE/Sanger) sequencing. Offers expertise in advanced DNA and RNA technologies.
Texas University Health Science Center at San Antonio Long School of Medicine Department of Cell Systems and Anatomy Optical Imaging Core Facility
University of Texas Health Science Center at San Antonio Optical Imaging Facility
University of Texas Health Science Center at San Antonio Optical Imaging Facility (OIF)
Service resource which makes imaging technology available to investigators on UTHSCSA campus and neighboring scientific community. Core Optical Imaging Facility offers access to technology for imaging of living cells, tissues, and animals, consultation, education and assistance regarding theory and application of optical imaging techniques, technical advice on specimen preparation techniques and probe selection.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Our contract antibody service is designed to be highly flexible to ensure we meet the individual needs of our customers. Whether you are looking for a complete start to finish service or simply one aspect such as clone yield optimisation, then SCIPAC can meet your needs. Our service caters for both monoclonal antibodies as well as recombinant antibodies.
NCSU Analytical Instrumentation Facility
NC State University Analytical Instrumentation Facility
NCSU Analytical Instrumentation Facility (AIF)
North Carolina State University Analytical Instrumentation Facility
The NCSU Analytical Instrumentation Facility (AIF) is a North Carolina State University resource for materials characterization. AIF operates a number of major analytical instruments providing quality analyses for all who require it. These instruments are operated and maintained by a professional staff who are experienced in the design and implementation of materials characterization experiments. For those who desire hands on involvement in their analyses, AIF staff trains users to operate analytical instrumentation, design efficient analytical experiments, and properly interpret the resulting data. In addition, AIF staff is involved in the development and/or enhancement of analytical techniques in a continuing effort to provide the level of capabilities required by the ever evolving needs of the NCSU research community. AIF provides short courses as well as formal classroom instruction to insure that NCSU' '''s future engineers and scientists can, upon graduation, take with them an understanding of modern analytical techniques and an understanding of the instrumentation required to implement them.
Beckman Research Institute Chemical GMP Synthesis Facility
City of Hope Beckman Research Institute Chemical GMP Synthesis Facility
City of Hope Chemical GMP Synthesis Facility
The Chemical GMP Synthesis Facility is a state-of-the-art manufacturing facility for small and large molecule therapeutics for clinical trials. The CGSF provides services for drug discovery, process research, development and early clinical manufacturing of pharmaceutical drug substances (APIs) that meet FDA requirements. www.cityofhope.org/chemicalgmp
University of Colorado Denver Labs and Facilities
University of Colorado Denver Labs & Facilities
University of Colorado Denver Induced Pluripotent Stem Cell Core
The new iPSC Core generates custom-designed iPSCs from mouse and human cells, including disease-specific human iPSCs. iPSCs from other species are currently under development. The Core is currently using both lentiviral- and sendai viral vector systems to deliver reprogramming factors to cells. Both systems are efficient, with the latter system having the advantage to generate iPSCs with a non-DNA-integrating vector system.
CU Denver Transgenic and Gene Targeting Core
University of Colorado Denver Transgenic and Gene Targeting Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22,2024. Transgenic and Gene Targeting Core is a full-service facility designed to assist you in generating genetically engineered mouse models for biomedical research. Our services include gene targeting in embryonic stem cells, the generation of ES cell-derived knockout and knockin mice, transgenic mice (conventional and BAC transgenic mice) and the cryo-preservation of mouse lines. The latter service is of particular importance for investigators that have long-term projects with non-commercial mouse lines. Changes in the genetic make-up of your mouse lines that occur spontaneously over time (gene drift) and disease outbreaks can significantly affect the outcome of your research. It is therefore advisable to preserve your mouse lines, providing you with a backup of your valuable research tools. We currently offer both embryo cryopreservation as well as sperm cryopreservation for this purpose.
University of Chicago Labs and Facilities
Core facility that aids investigators and trainees with high performance computation in proteomics, as well as other omics type applications needing efficient analysis of large-scale biological data sets. The ability to incorporate proteomics into translational and clinical biomedical research is critical for the discovery of therapeutic interventions and high fidelity biomarkers of disease and response to therapy. The Core provides state-of-the-art services, training, and bioinformatics-driven data analysis to the Meharry translational research community.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30, 2023. AKESOgen is a biomarker, genomics and pharmacogenomics contract research organization that services the academic, pharmaceutical, biotechnology and agricultural sectors. AKESOgen performs biomarker profiling and genomics services utilizing different types of markers (e.g. DNA, RNA, methylation) for the R&D market. AKESOgen establishes and validates biomarkers in the Clinical Trials arena. AKESOgen provides expertise in biobanking. AKESOgen is CLIA certified.
University of Oxford Central Proteomics Facility
The Central Proteomics Facility (CPF) of Oxford University offers proteomics mass spectrometry services and expertise to academic and commercial organisations. The facility is quipped with state-of-the-art Orbitrap and Q Exactive Orbitrap mass spectrometers. The facility routinely perfroms idenitification, post-translational modification and protein quantitation work using SILAC.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Molecule serves the needs of your businesses, both large and small. We are based in Silicon Valley with local and international labs. We are a team of experts who have worked for world-class companies over 2 decades and provide service in a wide range of chemistry, formulation and new technology development areas of medical device and drug control release products. We provide both contract work and consulting service in wet chemistries (customer design and synthesis) and formulation development. We have spent so much time to accumulate experience so your work can be developed in the shortest amount of time.
Richman Chemical offers a full range of custom synthesis and manufacturing services to life science and chemical industries. Our technical capabilities include: complex multi-step organic synthesis, emulsion or solution polymerization, inorganic custom synthesis (including organometallics), electronic chemicals, stereochemically pure compounds For our pharmaceutical clients, we also provide drug product formulation, compounding, and packaging.
University of Montana Magnetic Resonance Facility
The Department of Chemistry''s Magnetic Resonance Facility underwent a major upgrade in 2006 and in 2011 with the addition of three NSF funded spectrometers: Varian Direct Drive 500 MHz and 600 MHz NMR''s and a Bruker EMX PLUS EPR.
Arizona State University DNASU Core Facility
DNA Storage and University plasmid repository
DNASU Core Facility at Arizona State University
Core Facility within the Center For Personalized Diagnostics offers both Sanger DNA sequencing and Illumina NGS services (HiSeq 2000). DNASU is also a central repository for plasmid clones and collections. We currently store and distribute over 191,000 plasmids including over 75,000 human and mouse plasmids, full genome collections from numerous organisms, the protein expression plasmids from the Protein Structure Initiative as the PSI:Biology-Materials Repository (PSI:Biology-MR), and both small and large collections from individual researchers.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. We will design and produce DNA constructs for any purpose: Mutations/Deletions Knockout/Transgenic constructs Epitope tags & Fusion proteins Protein expression constructs Viral gene delivery constructs RNAi & related constructs Cost is generally about $300 per construct Turnaround time usually 5 business days
We are an academic Core Facility that supports the applications of DNA Sequencing and Fragment Analysis of Microsatellites and AFLP' '''s. Our Facility was founded in 2003 and expanded in 2005 with funds from NSF Instrumentation Development Grant (#0500993). In 2008 a generous gift from the Yale Provost allowed us to upgrade our Applied Biosystems Genetic Analyzer from a 48 to a 96-capillary. In 2010, with funds from NIH Equipment Grant (1S10RR025478-01) we upgraded additional equipment to ensure that we are a an efficient throughput Core. We are housed in the Yale Institute for Biospheric Studies Molecular Systematics and Conservation Genetics Center both under the Direction of Dr. Adalgisa Caccone. The presence of our Core within this setting enhances training within the MSCG Center by allowing students to obtain genetic information from large data sets in a time frame that is appropriate to their academic schedules, and to do so within the budget available for training. Our services are utilized by over 600 users from Yale, other academic institutions and private companies from across the United States and around the world. By promoting access to our equipment we enhance cost effectiveness, reducing idle time and avoid wasting consumables. This in turn allows us to reduce rates and have our services available to users that could otherwise not afford it. While our user base continues to expand our focus remains the same: to offer high quality services at prices affordable to small and medium sized laboratories.
Centre for Cellular and Molecular Platforms
Centre for Cellular and Molecular Platforms (C-CAMP), is a Dept. of Biotechnology (Govt. of India) initiative and a not for profit organisation, that also forms an important part of the Bangalore Bio-cluster. We are acting as an enabler of bioscience research and entrepreneurship by providing research, development, training and service in state of the art technology platforms.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Since 1988, Frontier Scientific Services, Inc. (FSSI) has functioned as a specialty CRO, working to enable dramatic cost reductions via outsourced compound management, reformatting, sample procurement, liquid handling, and compound library management. Our infrastructure and distribution capabilities empower smaller groups with logistics capabilities that would often not be available in-house, as well as offering the same services to larger groups, which maximizes their capital efficiency.
Dartmouth Genomics and Microarray Laboratory
Dartmouth College Geisel School of Medicine Genomics and Microarray Laboratory
The Genomics and Microarray Laboratory (DGML) is supported by the Norris Cotton Cancer Center. DGML is a core facility for investigators at Dartmouth College and Dartmouth Hitchcock Medical Center to provide genomics products and services at or below cost.
Specializes in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Their technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine.
University of Louisville Labs and Facilities
University of Louisville Labs & Facilities
SeqMatic provides comprehensive next generation sequencing services for DNA, RNA, and miRNA sequencing. We are proud to offer high quality sequencing with very fast turnaround time. We also offer customized experiment solutions including library generation, sequencing, and data analysis tailored to each customer''s needs.
Research organization offering R&D services to identify and develop vaccines and therapeutics for infectious diseases.
University of Illinois at Chicago Labs and Facilities
University of Illinois at Chicago Labs & Facilities
University of Virginia Genomics Core Facility
The GCF provides second generation genome sequencing service to all members of the scientific community. Using the 454 Life Sciences/Roche Genome Sequencer FLX, we facilitate data collection and analysis.
Peter Mac Translational Research Laboratory
Peter MacCallum Cancer Centre Translational Research Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 19,2024. Translational Research Laboratory at the Peter MacCallum Cancer Centre offers oncology focused, small animal PET imaging services to both academic and commercial investigators. Using the wide range of mouse models of cancer available at Peter Mac, experiments are tailored to investigators needs and performed in state of the art facilities. Infrastructure available includes 2 Philips Mosaic PET scanners, on-site radiotracer production, fully trained imaging staff and a dedicated animal facility. Digital autoradiography using the Biospace BetaImager and MicroImager allows high resolution ex-vivo imaging of labelled compounds in whole animal or tissue sections. The VisualSonics Vevo 770 small animal ultrasound is available for detection and monitoring of in vivo tumor growth. Ex-vivo correlative biomarker studies are also available.
Provides biomarker service activity for both large pharma and biotech.
Acellera is company focused on developing high-throughput molecular dynamics techniques that deliver solutions for estimating common physico-chemical properties such as binding affinities, kinetics, poses and pathways with validated accuracy.Company mission is to accelerate transition to rational, computerized drug discovery via simulations and machine learning.
University of California at Los Angeles Translational Pathology Core Facility
UCLA Translational Pathology Core Laboratory
Facility in the UCLA Department of Pathology and Laboratory Medicine and UCLA Jonsson Comprehensive Cancer Center Shared Facility. Provids pathology related services in support of basic, translational and clinical research at UCLA. Provides consultative services to investigators in pathology-related study design, tissue selection, microscopic interpretation, immunohistochemistry, laser capture microdissection, digital image analysis, and IRB-related tissue questions.
UCLA Clinical and Translational Research Laboratory
UCLA Clinical & Translational Research Laboratory
University of California Los Angeles Clinical & Translational Research Laboratory
University of California Los Angeles Clinical and Translational Research Laboratory
The Clinical & Translational Research Laboratory (CTRL) offers a full range of cost-effective laboratory testing to support your research efforts. The laboratory performs routine chemistry tests (basic metabolic panel, comprehensive metabolic group, electrolyte panel, hepatic panel, lipid panel and individual tests), thyroid function tests, fertility tests, tumor marker tests, basic coagulation testing and routine urinalysis testing. These tests are performed in the CTRL lab; however, referral tests can be sent to the UCLA Clinical Laboratory or outside reference laboratories. New assays not on the test menu can be validated and performed to meet the needs of individual research investigators. The laboratory is California-licensed, CLIA-certified, and CAP-accredited. A copy of each certificate can be issued upon request. The lab is staffed by ten research scientists, two hospital laboratory technicians, and two clinical laboratory scientists. It occupies approximately 5,000 square feet of space located on the A-level of the Center for Health Sciences (CHS) building. The facility works with investigators both inside and outside the UCLA enterprise on a collaborative and fee-for-service basis.
Northwestern University Keck Biophysics Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 31,2025. The award-wining Keck Biophysics Facility at Northwestern University has a comprehensive set of state of the art instruments for biophysical and biochemical characterization of macromolecules and their interactions. We provide staff-service, technical expertise and assistance to investigators and companies in the continental US and Canada. The Facility has 15 years of experience with a broad array of biophysical techniques and has generated over 500 publications in top-tier journals.
University of California Los Angeles Technology Center for Genomics and Bioinformatics Core Facility
University of California Los Angeles Technology Center for Genomics & Bioinformatics
Core is a fully automated, high-throughput genomic Center equipped with next generation sequencing and microarray platforms. TCGB provides genomics technologies, comprehensive services, specialized expertise and a wide range of trainings, enabling these services to serve basic science and translational/clinical research. In addition, TCGB provides pre-experiment consultation and post-experiment support, including preparation of grant applications, publications, and strategic planning for additional research steps. TCGB also provides educational training to faculty, staff, and students to raise awareness of new directions and major discoveries in the areas of genomics and bioinformatics.
UCLA High-Throughput Clinical Proteomics Core
University of California Los Angeles High-Throughput Clinical Proteomics Core
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. The High-Throughput Clinical Proteomics (HTCP) core laboratory is a mass spectrometry core facility designed to profile large numbers of clinical samples for changes in protein content. We use small amounts (micrograms) of protein from samples such as urine, plasma, CSF, and cell lysates and incubate them with magnetic beads that bind different subsets of the total proteome. We then examine the different subsets of small proteins and peptides by high-resolution MALDI-TOF mass spectrometry. We measure the amounts and intact masses of the proteins in the samples and determine which have the greatest statistical relevance in defining clinical groupings before moving to physically isolate those peptides/proteins and identify them. The method works best for peptides and small proteins below 25 kDa and is an excellent complement to gel-based methods such as DIGE.
University of California Los Angeles Immunogenetics Center
The UCLA Immunogenetics Center (UIC) provides comprehensive testing for organ and tissue transplantation. Transplant testing has a long history at UCLA. HLA typing was pioneered here in the 1960' '''s. The development of the microcytoxicity test in 1964 marked the beginning of international testing and standardization of HLA typing. The UCLA Immunogenetics Center has retained its leadership position in HLA research, and in the development of accompanying diagnostic testing. In the intervening years, laboratory and scientific personnel, from the US and abroad, have learned HLA typing through courses and workshops at the UCLA Immunogenetics laboratory. The center provides immunogenetics and histocompatibility testing services to a wide range of physicians, patients, pharmaceutical companies and other medical facilities. The laboratory is a World Health Organization reference laboratory for HLA, and is licensed by the State of California, New York, Maryland, Pennsylvania and Rhode Island, is CMS certified and accredited by the American Society for Histocompatibility and Immunogenetics.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Affina Biotechnologies is dedicated to excellence in helping our customers develop measurements of activities, kinetics and affinities of interactions and concentrations of biomolecules. We offer a unique mix of label-free and label-dependent assay technologies supported by scientific and technical expertise and a wide range of instrumentation.
Sanford-Burnham Applied Bioinformatics Core Facility
Sanford-Burnham Applied Bioinformatics Core
THIS RESOURCE IS NO LONGER IN SERVICE, documented January 23, 2019. Core supports SBMRI investigators in exploring, understanding and analyzing complex biological data. Core is equipped with cutting-edge computational infrastructure and a selective collection of bioinformatics software. Core's services include consultation, data analysis and management, software development, and accessing to large computing resources. To meet various demands from the investigators, we provide services at multiple levels, from full service to cost-effective limited service as well as collaborative projects requiring longer-term commitment of time and effort.
USF Center for Drug Discovery and Innovation Labs and Facilities
University of South Florida Center for Drug Discovery and Innovation Labs & Facilities
University of South Florida Center for Drug Discovery and Innovation Labs and Facilities
USF Center for Drug Discovery and Innovation Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. The Center for Drug Discovery and Innovation (CDDI) is a Florida Center of Excellence serving the research community at USF and south Florida. From concept to clinical trials there are significant challenges in the successful development of new pharmaceuticals. It is the mission of CDDI to assist research groups at USF in overcoming some of the critical bottlenecks in early phase drug discovery.
University of Utah Flow Cytometry Core Facility
Serving 120+ investigators with a 5 laser high speed sorter and 3 benchtop analyzers with 13+ color capabilities, the Utah Flow Cytometry Core Facility has developed a paradigm to balance productivity with quality to minimize the cost per research project, keep overall costs contained, and provide the necessary scientific support. Central to this paradigm is a close working relationship with investigators to define their projects in the early stages of development to make optimal and efficient use of flow cytometry. In addition to high quality and well maintained instrumentation, success of this approach requires focused efforts in three major areas: 1) education of ALL users (faculty and staff) in the science and technology of flow cytometry, 2) active involvement in the scientific development of the project, 3) continuing education for core staff.
Indiana University School of Medicine Therapeutic Validation Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22,2024. Therapeutic Validation core (TVC) assists clinical investigators to develop and perform correlative biological assays needed to validate mechanism(s) of action of candidate drugs/therapies and to develop and test new hypotheses. The TVC also provides technical and intellectual support in the development, implementation, and validation of predictive and pharmacodynamic biomarkers for novel, molecularly-targeted anticancer agents.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. GeneWake GmbH is a pharmacogenomics company with a sound scientific background in biomarker analysis in the field of oncology. Our mission is to realize a personalized and tailor-made cancer treatment by targeted analysis of relevant gene expression levels in tumour tissue and in circulating tumour cells in blood. By employing bioinformatical algorithms based on our knowledge in pathway structure and microarray data from public sources, biomarker screening can be limited to a low-density scale. The output of 10-20 potential genes can be used for ptient stratification or therapy tracking. In addition, GeneWake offers contract research like DNA and RNA sequencing and annotation, SNP genotyping, mutation detection, multiplex PCR, kit development, immune histology and genotyping for clinical studies.
Champalimaud Neuroscience Program Labs and Facilities
Champalimaud Neuroscience Program Labs & Facilities
UW-Madison Cardiovascular Physiology Core Facility
University of Wisconsin - Madison Cardiovascular Physiology Core Facility
The Cardiovascular Physiology Core Facility provides University of Wisconsin (UW) and non-UW researchers with a central resource for creating and studying animal models of disease on a fee-for-service basis. While the central focus of the facility is cardiovascular research, the techniques employed are often useful to investigators in other fields. Currently, the facility is conducting studies into diabetes, bone growth, drug toxicology, and gene therapy in liver and skeletal muscle, as well as cardiovascular disease. One of the most popular services provided by the facility is evaluation of the cardiovascular phenotype of transgenic mice.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22,2024. Microbe Inotech Laboratories, Inc. (The MiL, Inc.) is your direct source for answers to all of your microbiological inquiries. We are a full-service laboratory that can provide microbial and biochemical analyses for your specific industry. Whether you are concerned about food safety or you need microbiological testing for your field, Microbe Inotech Laboratories has the expertise and advanced technologies to provide solid answers. We have more than 18 years of experience in helping our customers find practical solutions to their microbiological needs. We offer our broad range of services to manufacturers, retailers, processors, and many other industries. Our laboratory divisions are environmental, food safety, industrial, pharmaceutical and governmental.
Kansas State University AFM Imaging Group
Kansas State University Atomic Force Microscopy Imaging Group
We specialize in atomic force microscopy (AFM). We offer: 1. Various AFM imaging assays in air, water, and biological buffers. 2. Single molecule force spectroscopy (FX-AFM and FC-AFM) on proteins and other biomolecules. 3. Hot-tip AFM surface modifications and imaging.
Provides genomics and proteomics equipment to researchers at Brown University and to entire Rhode Island research community, as well as assistance with experimental design, trouble shooting, and data analysis. Offers Affymetrix microarray and Illumina NextGeneration services to academic community and external customers.
CU Denver High Throughput and High Content Screening Core Facility
University of Colorado Denver High Throughput and High Content Screening Core Facility
The High Throughput and High Content Screening (HTS/HCS) Core Facility specializes in chemical biology as it relates to drug discovery, biological probe discovery, and phenotypic characterization of small-molecule effects on cellular systems. In addition to housing the instrumentation and robotics required for traditional HTS, the Core houses a cutting-edge High Content image-based system for next-generation small-molecule discovery research and analysis in fixed or live cells and cellular systems.
Brown Proteomics Shared Resource Facility
Brown University Proteomics Shared Resource Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. Proteomics Shared Resource Facility's mission is to provide well-maintained, state-of-the-art instrumentation and fundamental proteomics expertise to the Brown University and Rhode Island-EPSCoR scientific communities. It aims to be a focal point of intellectual activity in proteomics by enabling nationally recognized proteomics research within Rhode Island. As an NSF EPSCoR funded laboratory, the Proteomics Facility has a broadly-inclusive philosophy to ensure rapid and equal access to the facility's services for the entire Rhode Island research community. In addition to the acquisition of instrumentation, the Proteomics Core Facility will undertake the training of research in emerging proteomic techniques, a component that is essential to maintaining a productive and professional level of service. The Proteomics Facility has a strong commitment to be at the leading edge of current and developing technologies and provides consultation on their application.
University of Connecticut Labs and Facilities
University of Connecticut Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 16,2024. Portal, Core facility
Penn State Drug Discovery Development and Delivery Core
Pennsylvania State University Drug Discovery Development and Delivery Core
The Drug Discovery, Development and Delivery (D4) Core provides investigators with access to technological expertise enabling biochemical (100,000+ compounds) and siRNA library screening. We have expertise in development and screening, in both biochemical and cell-based assays. Our mission is to work with investigators to unlock the potential to discover chemical agents that affect cellular targets involved in human diseases.
WCMC Electron Microscopy and Histology Core Facility
Weill Cornell Medical College Electron Microscopy and Histology Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. The EM & H Core Facility functions as a merger of the facility at WCMC and the Analytical Microscopy Facility at HSS. The microscopes are located at WCMC in the Department of Cell & Developmental Biology. The HSS facility staff performs the TEM specimen preparation for their clients and then comes to WCMC to use the TEM. SEM sample preps for both client groups may be performed in the facility at WCMC.
North Dakota State University Center for Protease Research
We specialize in the synthesis of small molecules for biological applications and variety of analytical services. The facility works primarily with investigators from Center for Protease Research (CPR). However, we have always extended our services to neighboring institutions and other places all across US when possible. The facility enjoys a successful track record of achievements through service, collaborations, and interdisciplinary interactions.
BioSeek is a drug discovery services company that applies human primary cell assays and predictive disease models to the discovery and development of human therapeutics and safer chemicals. BioSeek improves the success rate of drug discovery and development by integrating human biology from the earliest stages of drug discovery onward through its unique BioMAP??????? platform. Our mission is to accelerate drug compound validation and enable our clients to take safer and more effective products into the market.
Scripps Florida Mass Spectrometry and Proteomics Laboratory
The Scripps Research Institute Scripps Florida Mass Spectrometry and Proteomics Laboratory
Scripps FL Mass Spectrometry and Proteomics Laboratory
The Scripps Florida Mass Spectrometry and Proteomics laboratory provides mass spectrometry support to the faculty and staff of The Scripps Research Institute, Scripps Florida. The laboratory also performs fee-for-service analyses for external academic and industrial researchers.
Washington University in St. Louis Hybridoma Center
Washington University in St. Louis Hybridoma Center / Monoclonal Antibody Development Core
WUSTL Hybridoma Center / Monoclonal Antibody Development Core
The Hybridoma Center / Monoclonal Antibody Development Core is a specialized cell culture facility that assists investigators in the generation of monoclonal antibody producing B cell hybridomas. Mouse and Armenian hamster models are utilized to generate antigen reactive monoclonal antibodies.
Penn State Center of Excellence in Nutrigenomics
Penn State University Center of Excellence in Nutrigenomics
Pennsylvania State University Center of Excellence in Nutrigenomics
The Center of Excellence in Nutrigenomics (CEN) is striving to be the focal point of molecular nutrition studies. The Center is a conduit to the Huck Institute of the Life Sciences and their genomics initiatives as well as the General Clinical Research Center and their expertise in human nutrition studies. Thus, PSU Nutrigenomics can fulfill our goal to understand nutrition from the table to the gene and back again.
University of Southern California School of Pharmacy Histology Laboratory Core Facility
University of Southern California School of Pharmacy Histology Laboratory
USC School of Pharmacy Histology Laboratory
Core is located on the fourth floor of the Pharmaceutical Sciences Center, is ready to help you with your histology and pathology research. Open to any USC researcher and has everything you will need to make microscope slides from tissue samples. Tissues can be paraffin embedded, sectioned and stained in the laboratory. Sectioning can involve making microtome, vibratome and cryostat thin slices. You can also make color photographs of your microscopic images for publication. Expert advice is available concerning staining techniques and the interpretation of microscopic images.
Meharry Microarray and Bioinformatics Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22,2024. Core facility that provides the following services: RNA quality analysis service, qRT-PCR service, Microarray service, Bioinformatics data analysis service. The Core provides state of the art training, instrumentation, services and bioinformatics-driven data analysis to the Meharry Community in microarray experimental design, manipulation, and gene expression analysis. They also aid investigators and trainees in validation of microarray results using RNA QA/QC and real time PCR results. Finally, this Core Resource aids Meharry investigators and trainees with high performance computation in proteomics as well as genomics. Gene and protein pathways analysis and shotgun proteomics (mass spectrometry) analysis are just two more of the services that we provide. It is their aim to keep this facility up to date computationally and intellectually with state of the art Omics services to support education and research in microarray, genomics and proteomics data analysis, computational biology, and systems biology.
University of Delaware Sequencing and Genotyping Center Core Facility
Delaware University Sequencing and Genotyping Center Core Facility
University of Delaware DNA Sequencing & Genotyping Center
University of Delaware DNA Sequencing and Genotyping Center
Provides genomics and molecular biology services for University of Delaware research groups and outside users.Supports genomic research through established expertise with genomics technologies.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 24,2024. Portal, Core facility
Vala is a fast-growing San Diego-based biotechnology company serving academic, pharmaceutical and biotechnology scientists. Vala Sciences's Hardware, CyteSeer Automated Cell Image Analysis Software and Reagents enable information-rich measurements for making fundamentally new insights into the cell functions critical to progress in the biological sciences.
University of Texas Health Science Center at San Antonio Biomolecular NMR Core Facility
The mission of the UTHSCSA Biomolecular NMR Core Facility is to provide UTHSCSA faculty and staff with access to modern high-field high-resolution NMR instrumentation for analysis of molecular structure. The instrumentation is available on an hourly basis for routine analyses, such as analysis of small molecule structures, or on a collaborative basis for non-routine analyses, such as structural analysis of biological macromolecules.
UTHSCSA Center for Macromolecular Interactions
University of Texas Health Science Center at San Antonio Center for Macromolecular Interactions
The facility helps to produce highly purified recombinant proteins for functional and structural studies and to provide researchers with state-of-the art capabilities for the characterization of protein-protein, protein-lipid, protein-nucleic acid and protein-small ligand interactions.
UTHSCSA Core for Advanced Translational Technologies
University of Texas Health Science Center at San Antonio Core for Advanced Translational Technologies
Provides standardized, high-quality services to support translational research, including pre-analytical biospecimen management, sample preparation, and analytical technologies that deliver a systems-oriented perspective on the composition of a sample. Services include automated DNA/RNA extraction, bisulfite conversion, cryostorage, miSeq-based sequencing, Illumina microarrays, pyrosequencing, microfluidic PCR, Luminex FlexMap 3D bead arrays, Ingenuity Pathway Analysis access and services.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. OYAGEN is a biotechnology company formed on September 5, 2003, for the purpose of discovering, developing, and commercializing novel pharmaceutical therapies that seek to exploit RNA editing and DNA editing enzymes. OyaGen holds exclusive rights to important technologies originating from the University of Rochester Medical Center (URMC), the Thomas Jefferson University (TJU), and Oregon Health Science Center.
University of Texas Health Science Center at San Antonio Genome Sequencing Facility
University of Texas Health Science Center at San Antonio Genome Sequencing Facility (GSF)
UTHSCSA Genome Sequencing Facility (GSF)
Core performs all protocols necessary for preparing a sample to be sequenced on the Illumina HiSeq2000 system. Core is also a research group with experience in customizing experiments and developing new applications. Core provides: Complete project consultation for optimal experimental design and setup, Super saver pricing for entire UT Health Science Center research community, especially research focusing on cancer genomics, Complete quality control analysis during library preparation and data generation, Secure website to download the sequencing data with quality information, Full project report, Bioinformatics analysis option available, NCBI GenBank submission option available
University of Texas Health Science Center at San Antonio Flow Cytometry Core Facility
The UTHSCSA Flow Cytometry Core Facility operates at two locations; at the Long (main) campus and Greehey (north) campus in the newly-built South Texas Research Facility (STRF). The facility at the Long campus is located in room 5.044V and occupies 800 sq. ft. The STRF site is located in room 251 and occupies a total of 1306 sq. ft. The FCF is administered through the Office of the Vice President for Research in coordination with the Executive Director of the Cancer Center. Access to the flow labs is available to all UTHSCSA and external investigators with priority given to NIH-funded investigators. FCF services are based on the presence of a flow cytometry cell sorter and an analyzer at each of its two locations. The main campus site houses a Becton Dickinson Biosciences (BD) FACSAria and a BD SORP LSRII. The FACSAria cell sorter is equipped with 5-lasers enabling the analysis of up to 13 parameters and concurrent sorting of 4 different cell populations. The LSRII is equipped with 3 lasers and allows for detection of up to 8 colors at a time. The STRF site houses a MoFlow Astrios and a FACSCalibur. The MoFlow Astrios cell sorter is equipped with 4 lasers that enables analysis of up to 14 colors and concurrent sorting of 6 different cell populations. The FACSCalibur analyzer is equipped with 2-lasers and allows for the parallel detection of up to 4 colors.
University of Texas Health Science Center at San Antonio Genomics Core
The mission of the Genomics Core is to provide state-of-the-art genomic services including genotyping and cell banking to investigators from UTHSCSA, CTRC and the local scientific community in an economical and timely manner.
University of Texas Health Science Center at San Antonio Mass Spectrometry Laboratory
The UTHSCSA Mass Spectrometry Laboratory provides state-of-the-art expertise and services in mass spectrometry and gel electrophoresis for identification, characterization and/or quantification of molecules of biomedical importance. The Mass Spectrometry Laboratory assists faculty members in their research endeavors and by promoting interdisciplinary and inter-institutional research. The activities of the Mass Spectrometry Laboratory continue to benefit the institution by enhancing ongoing research, by facilitating the acquisition of new research funding and by assisting with recruitment of new faculty members.
University of Texas Health Science Center at San Antonio MicroCT Core Laboratory
UTHSCSA Orthopaedics Bone and Mineral High-Resolution 3D Imaging Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22, 2024. UTHSCSA Orthopaedics Bone and Mineral High-Resolution 3D Imaging Facility is a NIH-funded imaging facility equipped with two ex-vivo desktop microCT systems, a reference point indenter and a furnace. The non-destructive nature of microCT imaging allows the researcher to strengthen his/her research by using the same sample for histology or biomechanical testing after microCT imaging. Advantages of Micro-CT - Micro-CT allows for extremely high-resolution, non-destructive, 3D imaging. - No staining, sectioning, or sample preparation needed - Samples can be frozen or fixed - Since Micro-CT is non-destructive, other assays may be carried out after, thereby increasing the amount of data per sample - Data acquisition is a rapid process, allowing for a speedy return of samples
UTHSCSA X-ray Crystallography Core Laboratory
University of Texas Health Science Center at San Antonio X-ray Crystallography Core Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15, 2024. The mission of the X-ray Crystallography Core Laboratory is to provide state-of-the-art resources to researchers at the University of Texas Health Science Center at San Antonio, and to external users, enabling the detailed 3-D analyses of biological macromolecules that play important roles in human health. This is a full service core in that it not only offers access to sophisticated equipment and technologies but also offers advice and technical assistance in sample preparation. Services are also provided to investigators without funding to facilitate the development of pilot data for new potentially fundable projects, as core resources permit. If priority of usage becomes an issue, this will be decided by the Core Director in consultation with the other principal scientists based on the feasibility of the projects, their scientific merits and their relevance to human health.
DIYgenomics provides crowdsourced health research study protocol design and operation in pre-clinical and disease cohorts. Founded in 2010, the mission of DIYgenomics is the realization of preventive medicine through the integrated study of multiple health data streams. The generalized hypothesis for DIYgenomics studies is that one or more genetic polymorphisms (mutations) may result in out-of-bounds phenotypic biomarker conditions (for example, low Vitamin B blood levels), that may be ameliorated through personalized intervention.
Cancer specific CNV caller for Next Generation sequence.
UTHSCSA Metabolomics Core Laboratory Mass Spectrometry
Metabolomics Core Laboratory Mass Spectrometry (UTHSCSA)
University of Texas Health Science Center at San Antonio Metabolomics Core Laboratory Mass Spectrometry
University of Texas Health Science Center at San Antonio Metabolomics Core Laboratory Mass Spectrometry (UTHSCSA)
Cutting-edge mass spectrometers deliver extremely high mass accuracy and resolution to elucidate the identity and quantity of small molecules. Metabolomics Laboratory Services: Qualitative and quantitative analysis of small molecules - Molecular mass determination - Structural elucidation - Quantification Targeted and discovery modes of analysis - Quantitative analysis of targeted metabolites - Metabolite profiling for differential comparisons between experimental groups - High-throughput sample analysis The Metabolomics Laboratory is supported by awards from the National Institutes of Health, including a Shared Instrumentation grant (1S10RR031586-01) and a supplement to the Clinical and Translational Sciences Award (3UL1RR025767-03S1).
UC Berkeley Marvell Nanofabrication Laboratory
University of California Berkeley Marvell Nanofabrication Laboratory
The Marvell Nanofabrication Laboratory at the University of California, Berkeley is a multidisciplinary facility that serves research and education in the areas of integrated circuits (ICs) and systems, micro/nanofabrication technologies, micro/nanoelectromechanical (MEMS/NEMS) systems, advanced materials and interdisciplinary applications of microelectronics. This facility offers processing for both 4 inch and 6 inch substrates (wafers).
Columbia Chemical Probe Synthesis Facility
Columbia University Chemical Probe Synthesis Facility
Located in the new Northwest Corner building on the Morningside campus of Columbia University in New York City, the Columbia University Chemical Probe Synthesis Facility (CPS facility) is a shared resource that assists researchers in designing and synthesizing small molecule probes for stem cell research projects. The CPS facility offers expertise, advice and services in the following areas: 1. Virtual screening and computational design of small molecules 2. Organic synthesis of individual compounds, building blocks or libraries of compounds 3. Drug metabolism/pharmacokinetics (DMPK) and metabolic profiling of small molecules
Gene By Gene offers a full suite of genetic services, including clinical gene tests, exome sequencing, genome sequencing. In addition, the recent acquisition of bioinformatics experts, Arpeggi Inc., core also offers a full end-to-end solution for sequencing projects and bioinformatics.
University of Kansas Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 16,2024. Portal and core facility.
Japan Bioinformatics KK is a Tokyo based biotechnology company specializing in bioinformatic software and data analysis. Products: Simbiot: Secure, easy-to-use, web and cloud-enabled software for management and analysis NGS data. SimGene: Free iOS and Android app for access to gene annotation information. SimAlign: Free iOS and Android app interfacing to NCBI BLAST+ service. Services include RNA-Seq, ChIP-Seq, miRNA-Seq, CAGE-Seq, mutation detection for amplicons, exomes and whole genomes as well as de-novo assembly and annotation of small genomes and transcriptomes. Project management services are also offered.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2024. Shipley Consulting, LLC is a private company specializing in advising customers on how to optimize their standard qPCR runs or focused mRNA and miRNA arrays, new qPCR assay design and post-design validation, tips on complying with the MIQE Guidelines, and how to apply automation to qPCR successfully.
Michigan State University Labs and Facilities
Michigan State University Labs & Facilities
University of Southern California School of Pharmacy Translational Research Laboratory
Core is equipped with a wide variety of technologically advanced instruments essential for cutting edge biomedical discovery and therapeutic development research. TRLab is composed of two major units. The Computational Bioinformatics Unit houses graphic workstations and modeling programs that enable in silico virtual screening and rational drug design applications. The Therapeutic Screening Unit houses a number of specialized instruments that enable a broad range of automated and multiplexed biological analyses in a throughput manner. The core mission of the TRLab has been to provide investigators with a state-of-the-art technological platform and technical expertise to advance translational research endeavors in the School of Pharmacy and at USC.
UT Southwestern Protein Chemistry Technology Core
University of Texas Southwestern Medical Center at Dallas Protein Chemistry Technology Core
University of Texas Southwestern Medical Center Protein Chemistry Technology Core
UT Southwestern Medical Center Protein Chemistry Technology Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. Protein Chemistry Technology Core was established to provide efficient, high quality services to researchers in the academic community. The services presently offered include peptide synthesis and Edman protein sequencing. Our facility, its state-of-the-art instrumentation, and computer software is constantly upgraded to ensure the highest possible level of support. It is our aim to provide quality performance and offer experienced support, both through our products and people.
CSU Proteomics and Metabolomics Facility
Colorado State University Proteomics and Metabolomics Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. The mission of the Proteomics and Metabolomics Facility is to serve as an enabling resource for research and development programs at Colorado State University. We strive to build instrumental capabilities that exceed the normal resources of individual research programs, and make those technologies available as a shared resource. We also aim to provide an environment rich in expertise and educational resources, and to foster collaboration across the CSU community and beyond.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Compound screening facility that has several drug-like compound collections available that amount to a total of about 74,000 compounds and a human siRNA library that targets almost 8,000 genes. State-of-the-art liquid handling systems and detection technologies are available for screening in-house or custom collections in 96- or 384-well plate format. The platform is compatible with biochemical assays, cell-based assays in a broad range of cellular systems and assays in the model plant Arabidopsis thaliana. Its core activities consist of managing the VIB screening collections, assisting researchers in assay development / automation and performing high-throughput screenings. After hit clustering and selection, the VIB-CSF team can contribute in structure-activity analysis, IC50 measurements, cytotoxicity analysis, secondary screening for hit validation and counter screening for specificity analysis.
Expert Glyco-Analytics Services by Procognia
Provides ICH-guidelines-compliant glycosylation analysis services. EGC is the analytical services branch of Procognia Ltd. Services include: N-link glycan Analysis by HPLC and Mass spectrometry O-link glycan Analysis by HPLC and Mass spectrometry Profiling and quantitative analysis of sialic acid Quantitative Monosaccharide Analysis High Throughput Analysis Using GlycoScope
Kansas State University Labs and Facilities
Kansas State University Labs & Facilities
UTHealth Laboratory for Developmental Biology
University of Texas Health Science Center at Houston Laboratory for Developmental Biology
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024. Laboratory for Developmental Biology was established to help scientists at the Institute of Molecular Medicine and the University of Texas conduct research that requires the production of transgenic and knock-out animal models of human diseases.
University of South Florida Center for Drug Discovery and Innovation NMR Laboratory
USF Center for Drug Discovery and Innovation NMR Laboratory
NMR facility provides state-of-the-art ultra-high field (14 and 18 Tesla) instruments that enable researchers to characterize protein structure at atomic resolution (along with the characterization of small molecules). Technical support and training are available for all aspects of project development. Experiments include structure elucidation of small molecules (e.g. synthetic molecules, natural products, and small peptides etc.) to studying advanced protein-ligand interactions.
USF Mass Spectrometry Biological Applications and High-Throughput Proteomics Facility
University of South Florida Center for Drug Discovery and Innovation Mass Spectrometry Biological Applications and High-Throughput Proteomics Facility
USF CDDI Mass Spectrometry Biological Applications and High-Throughput Proteomics Facility
USF Center for Drug Discovery and Innovation Mass Spectrometry Biological Applications and High-Throughput Proteomics Facility
The Mass Spectrometry, Biological Applications and High-Throughput Proteomics Facility is dedicated to the identification and quantification of components associated with complex biological matrices. The main goal of our lab is to produce high quality data related to any biological or environmental sample, i.e. cancer, Alzheimer_������_s, diabetes, cardiovascular disease, and parasitology, to name a few. To see a full list of facility activity, please visit our listed website.
University of South Florida Center for Drug Discovery and Innovation Chemodiversity Laboratory
USF Center for Drug Discovery and Innovation Chemodiversity Laboratory
The chemodiversity core facility offers a library of natural product-derived crude extracts, fractions and pure compounds for screening. Gas chromatography high-resolution mass spectrometry (MS) analysis, liquid chromatography MS targeted separation and high throughput screening (targeting solid tumor cell lines, anti-microbial activity, permeability and drug solubility determination) are provided. The services also include general chromatography (MPLC, HPLC) and spectrometric characterization (UV, IR) as well as microbiology workspace (biosafety cabinets), synthesis activities and training. Our facility offers advanced instrumentation (GC/MS Q-TOF, IR, UV, MPLCs, HPLCs, liquid handling robots, biosafety cabinets, and other essential lab equipment), consultation and services for sample isolation and analysis, derivatization and scale-up. Sample preparation and safety training are also available for commercial and USF clients using our chromatographic and analytical instrumentation.
USF Protein Production and Cell Biology Laboratory
University of South Florida Center for Drug Discovery and Innovation Protein Production and Cell Biology Laboratory
USF CDDI Protein Production and Cell Biology Laboratory
USF Center for Drug Discovery and Innovation Protein Production and Cell Biology Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. Protein production can be a significant bottleneck during early phase drug discovery. Our production facilities are fully equipped and staffed to help researchers produce proteins in bacteria, yeast or insect cells. Whether the protein is hopelessly insoluble or difficult to produce in quantity, the core staff is ready to work with individuals to turn failure into success. The Cell Biology facility provides researchers access to cell sorting and analysis for target characterization and validation. The BD FACS Aria II sorter is BSL2 capable permitting levels of safety in cell sorting not available in most flow cores. A second BD Canto II flow cytometer provides automated sampling for analytical flow cytometry. Fully automated Zeiss Axiovert 100 deconvolution and Lecia DM 6000 (laser microcapture) microscopes provide tools for cell imaging and content analyses.
Douglas Mental Health University Institute Douglas Cerebral Imaging Centre Core Facility
Douglas Cerebral Imaging Centre Core Facility
Douglas Mental Health University Institute Brain Imaging Centre
Douglas Research Centre Brain Imaging Core Facility
McGill University Douglas Mental Health University Institute Brain Imaging Centre
The Douglas Research Centre: Brain Imaging Center
Facility is dedicated to conducting preclinical and clinical brain imaging research in the field of mental health. Researchers at the Douglas CIC use several brain imaging methods, including MRI scanners, to non-invasively understand the brain structure and functions that are altered by mental illnesses. Provides platform to analyse brain imaging data from functional and structural neuroimaging techniques.
McGill University Surface Plasmon Resonance Facility
For applications including proteomics, drug discovery, immunogenicity, and food analysis, state-of-the-art Surface Plasmon Resonance (SPR) technology allows for label-free, real-time biomolecular interaction analysis. Using purified preparations or complex mixtures, binding interactions between proteins, lipids, carbohydrates, nucleic acids, small molecules, and cells/viruses can be examined quantitatively in their native state with low sample consumption. In a typical experiment, the ligand (_������������bait_������_) is immobilized to a gold-plated sensor chip and repeated injections of analyte (binding partner _������������target_������_) are then flowed overtop.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024.
UTS Chemical Technologies Research Facility
University of Technology Sydney Chemical Technologies Research Facility
The research facility in Chemical Technologies pulls together the resources of several well equipped laboratories specialising in chemistry and materials science. The facility is particularly focused on chemical, forensic, material and biochemical analysis, and materials technology, and is set up to serve the needs of Australian industry and academia in these areas. Specialties of the facility include the physical and mechanical characterization of engineering materials, and the chemical and physical characterisation of forensic and pharmaceutical samples. The facility is equipped to produce and characterise a diverse range of organic and inorganic materials, and is backed by a team of experienced researchers.
University of Technology Sydney Microstructural Analysis Unit
The MAU is comprised of five separate characterisation nodes: (1) Electron microscopy and microanalysis (2) Scanning probe microscopy (3) X-ray characterisation (4) Electrical measurement and characterisation (5)Optical characterisation. As well as a materials fabrication and processing equipment suite. This research infrastructure is supported by an academic Director, a Research Laboratory Manager and three highly experienced and highly skilled Professional Officers.
University of Technology at Sydney Biosciences and Proteomics Technologies
University of Technology Sydney Biosciences and Proteomics Technologies
UTS Biosciences and Proteomics Technologies
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 25, 2019. Core brings together leading technologies for sample preparation, protein separations, identification and characterization. Through collaboration with the Computational Research Support Unit, Biosciences and Proteomics Technologies is developing new systems for electronic laboratory information management and bioinformatics. The research facility offers services and training in proteomics discovery technologies to Australian and international researchers from academia and industry. Core has expertise in experimental design, custom method development, sample preparation, complex mixture fractionation and protein separations. Sydney Biosciences and Proteomics Technologies also manages the core infrastructure and operations for the Faculty of Science's extensive Biomedical and Bioscience research facilities.
Microbiology and Quality Associates Inc.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22, 2024. Microbiology & Quality Associates, Inc., located in the San Francisco Bay Area, is a service organization providing a variety of services to life sciences companies. Our services include: contract biotech development services, testing services, consulting, validation services, calibration services, training, and scientific resources. MQA is FDA registered. Our Quality System comply with GXP regulations and ISO 17025/9001. We provide services to a wide variety of companies in biotechnology, pharmaceutical, medical devices, nutritional products, dialysis centers, semiconductors, and other industries. MQA staff has many years of hands-on experience at pharmaceutical, biotechnology and medical device companies.
Bowling Green State University Electron Microscopy Core Facility
The Microscopy Core Facility at BGSU offers a range of services, including Scanning electron microscopy (SEM) and Transmission electron microscopy (TEM).
Sanford-Burnham Protein Production and Analysis Core
Sanford-Burnham Medical Research Institute Protein Production & Analysis Core
Sanford-Burnham Medical Research Institute Protein Production and Analysis Core
Sanford-Burnham Protein Production & Analysis Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. Sanford-Burnham''s Protein Production Core offers state-of-the-art resources with advanced biochemical engineering and bioprocessing capabilities. Specialized protein production scale-up services (65L bacterial or 25-50L insect/mammalian cell production) include optimization of production runs. Analytical services include measurement of protein-protein and protein-small molecule interactions using a variety of approaches such as surface plasmon resonance and isothermal titration calorimetry. Assistance in experimental design and technical support are also provided by the Core''s knowledgeable staff.
Creative Bioarray is a well-recognized service provider propelled by integrity, expertise and the desire to contribute to simplify, improve, and accelerate research speed of the scientists by providing the highest standard quality research products and services. Since it founded, Creative Bioarray had recognized that an important obstacle to make development of basic bioscience and preclinical researches using human specimens is the lack of access to reference materials. Consequently, Creative Bioarray was determined to be the first commercial entity specialized in building up the largest tissue-sharing platform by integrating the detailed clinical information of all the tissue samples. http://www.creative-bioarray.com/home.asp
Princeton University Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. Portal, Core facility
Applied Biosciences is a small miority owned LLC. We specialize in hormone assays from the very small (30 g to the 5000 kg elephant) to the very large. We have a vast experience of knowledge in the endocrine field. Our experts are board certified in animal pharmacology as well as theriogenology. Combined with our Endocrinologist, there is over 75 years of experience with animal medicine and more specficially endocrinology of many animal species.
A genomics data service provider offering genomic project management, data analysis, and bio-IT consulting services.
MEG (Magnetoencephalography) is a neuroimaging technology for cognitive and clinical brain research. In a nutshell, MEG measures non-invasively the tiny magnetic fields generated by neuronal currents. A unique asset of MEG imaging is its unrivaled temporal resolution, reaching the millisecond time scale across the entire brain volume. On the clinical side, MEG has been typically indicated for the pre-surgical work-up of severe, drug-resistant epilepsy and the functional pre-surgical mapping of brain tumors. There is however great potential to use MEG as an instrument of choice to investigate other neurological syndromes and neuropsychiatric disorders (e.g., stroke, dementia, movement disorders, depression, etc.). Overall, MEG has strong value in revealing the dynamics of brain activity involved in subject' '''s perception, cognition and responses: it has provided unique insight on the time-resolved processes ruling brain functions (resting-state dynamics, language, motor control, visual and auditory perception, etc.) and dysfunctions (movement disorders, tinnitus, chronic pain, dementia, etc.). MEG(at)McGill provides a full-suite of services related to MEG and MEG/EEG studies. This includes a variety of training programs for use of the MEG and related data acquisition and analysis software, Brainstorm.
UW Medicine High Throughput Genomics Center
University of Washington School of Medicine High Throughput Genomics Center
UW School of Medicine High Throughput Genomics Center
Provides high-throughput genomics data for government, biotechnology, and pharmaceutical industry customers worldwide. Created next-gen sequencing data sets including DNA sequencing, RNA-seq, ChIP-seq, DNase-seq, and Bisulfite-seq spanning a variety of organisms ranging from humans to plants. On-site bioinformaticians and biologists are available.
Center for Public Health Research Labs and Facilities
Center for Public Health Research (CSISP) Labs & Facilities
Center for Public Health Research (CSISP) Labs and Facilities
Center for Public Health Research Labs & Facilities
A portal and core facility. Contains the FISABIO sequencing and bioinformatics service.
Massachusetts General Hospital CCIB DNA Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 2025.Welcome to the CCIB DNA Core at Massachusetts General Hospital! The mission of the DNA Core is to accelerate fundamental scientific discoveries that will improve human health. Our professional team is committed to help investigators solve highly diverse biological and biomedical research questions by providing a portfolio of state-of-the-art molecular biology services, specialized expertise, detailed advice and support. We are constantly striving to advance research productivity by reliably generating the highest quality data with rapid turn-around time and competitive pricing, and by working with our clients on an individual basis to address and satisfy their specific research needs. Realizing the constant changes of our customers_������������_ demands, we make every effort to continuously improve our services and to offer new and innovative solutions. The DNA Core, founded in 1996, is a non-profit research core laboratory within the Center for Computational and Integrative Biology of Massachusetts General Hospital Boston providing high-quality genomics technology services and expertise for academic research institutions and for business (for-profit) organizations. The majority of the core' '''s clients are investigators from Massachusetts General Hospital and the greater Partners research community. The core also serves researchers from external academic institutions and biotech companies in Massachusetts as well as other states in the United States. Our facility provides high-quality molecular biology services in three major areas: Our DNA Sequencing group functions both as a small-scale sequencing facility and a center for large-scale sequencing projects. It is offering various genomics technologies, including ABI Sanger DNA sequencing, Microsatellite analysis, plasmid validation and primer walking. Currently, we are exploring new opportunities and are planning to expand our service portfolio soon. Our DNA Synthesis lab serves the research community with custom oligonucleotides (standard, degenerate, and modified). To diversify our current service options, we are in the process of exploring potential partnerships with third party vendors. Our Research Laboratory Automation group has been designed as a flexible entity within the DNA Core to extend the benefits of laboratory automation to a diverse user group and to assist in the execution of a variety of molecular biology projects that require large-scale robotics support. The group offers standard and custom high-throughput sample processing services, including protocol development, for various molecular biology and genomics applications. Current services include Mouse genotyping, cDNA and siRNA library screening, bacterial colony picking, library replication and archiving, 96-well plasmid DNA purification, large-scale PCR purification, and custom qPCR assays. In addition to providing the currently existing services for the research community, all three groups of the DNA Core are continuously engaged in the evaluation and/or development of new service options and in the optimization of current and new technologies and services.
University of Oklahoma Labs and Facilities
University of Oklahoma Labs & Facilities
Meharry Medical College Molecular Biology Core Facility
Meharry Medical College Molecular Biology Core
Multi-functional facility that provides primary service of DNA sequencing, access to shared equipment housed in a centralized location, access to frequently used molecular biological reagents. The Core also maintains an Invitrogen Supply Center that stocks many routinely used reagents for molecular biological research. Core staff facilitate through the Meharry-Vanderbilt Alliance the ordering of reagents and supplies.
Provides research data management cyberinfrastructure and is developed and operated as not-for-profit service by the University of Chicago. Researchers can move, share, and discover data across multiple storage system platforms – from supercomputer to lab cluster, tape archive, public cloud or laptop. Globus provides services to design and execute secure, reliable automated task orchestration, across systems and at scale. Remote function execution services enable researchers to execute functions on diverse compute systems.
UC Berkeley Molecular Imaging Center Core Facility
University of California Berkeley Molecular Imaging Center
Core microscopy facility managed by Cancer Research Laboratory. Provides campus community with training and access to state-of-the-art light microscopy equipment. Now in two locations: Life Sciences Addition Building (LSA) and the new Li Ka-Shing Center for Biomedical and Health Sciences (LKS). The MIC specializes in live cell imaging, confocal, multi-photon, fluorescent lifetime imaging (FLIM), and equipment for optogenetic research.
University of Colorado Denver Advanced Histology Services
The objective of the Morphology and Phenotyping Core - Advanced Histology Services, is to provide Investigators/clients with the tools and expertise to process and analyze tissue samples. The Core is able to process any type of animal and/or human tissue for research purposes. Our technicians are also highly trained in dermatology and delicate specimen handling. We consistently maintain the highest-quality results by utilizing state-of-the-art equipment and employing nationally-certified technicians. Our aim is to always provide excellent customer service by fulfilling each Investigators/clients' ''' specific needs and wants. Core services include recommendations for tissue harvesting and storage, preparation of paraffin blocks, sectioning of paraffin and frozen blocks, standard H&E histology, special staining procedures, and control slide preparation.
Centro Superior de Investigacion en Salud Publica
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 24, 2019. Core provides advisory services in study planning and data mining (debugging, analysis and interpretation of results) resulting from the sequencing of DNA and RNA. Core's goal is to help extract all possible information from sequencing data which will be useful for projects. Applications: Sequence trimming and quality control (quality index, length of sequences, etc...). Taxonomic assignment of prokaryotic 16S rDNA sequences. Comparative ecological analysis of environmental and/or clinical microbial communities based on 16S rDNA taxonomy. Assembly and/or annotation of genomes and metagenomes. Transcriptome annotation. Determination of SNPs in resequencing studies in bacterial systems. Sending Data. Sequences can be submitted in any of the usual formats (FASTA, SFF, FASTQ, etc) along with a description of the experimental design (including sufficient details) and the relevant information associated with each sample in order to perform the necessary analyses (factors associated with the samples, sub-samples, etc.).
Champalimaud Neuroscience Program Vector Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Main goal of the Vector facility is development and implementation of viral vectors and viral vector-based techniques, which allow manipulating neural circuits and characterizing neural populations in laboratory animals. We also see the Vector facility as a pole of shared resources and expertise. Many systems of recombinant viruses have been used in a wide number of applications, namely as gene delivery tools. Recombinant adeno-associated virus (rAAV) is very frequently a gene delivery vector of choice, especially in the field of gene therapy.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 19,2024. We provide 16S sequencing to allow you to learn about the microbiome, using similar technology and protocols to the Human Microbiome Project, a $173 million project by the National Institutes of Health, concluded in 2012. Compare human and non-human microbiomes, examine the effect of disease on the microbiome (and vice versa), examine the effect of clinical trials on the microbiome, or simply do citizen science. We''re hear to help! Also, contact us to join our research consortium at consortium(at)ubiome.com.
Yale University School of Medicine Pathology Tissue Services
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Mission- Developmental Histology The mission of the Developmental Histology unit is to provide 1. Timely high quality histology services to the Yale community 2. Access to tissue services from Yale Pathology archives 3. To maximize the value of the resources in the Yale Pathology Tissue Archive. 4. To provide Tissue Microarrays to assess multiple tissue samples Mission- Yale Pathology Tissue Services To provide the maximum amount and quality of human tissue for research at Yale University without impacting diagnostic quality, accuracy and safety in anatomic pathology.
Chiral Polyamines is a discovery-driven product and service oriented life science company offering chirally pure discovery chemicals, custom synthesis and technology services for the research, biotechnology and pharmaceutical market. Chiral Polyamines produces a broad product line of over 75,000 fully customizable chiral polyamines for research and drug discovery. We commit ourselves to provide researchers with novel high quality chiral products in a variety of formats.Chiral Polyamines also focuses on custom research and development. Our highly skilled scientists are experts in combinatorial chemistry techniques as well as biochemical and synthetic organic chemistry.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15, 2024. Xeno Diagnostics is a Contract Research Organization specializing in cell-based assays. Models include Non-human Primates, Porcine, Bovine, and Human. Services can be run under GLP, non-GLP, or CLIA regulations.
UTHealth Fluorescence Microscopy and Imaging Core Laboratory
University of Texas Health Science Center at Houston Fluorescence Microscopy and Imaging Core Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 22, 2024. The Fluorescence Microscopy and Imaging Core Laboratory is a multi-user facility located in the Department of Pathology and Laboratory Medicine at The University of Texas Medical School Houston, within the Texas Medical Center. Its purpose is to allow research scientists access to state of the art Fluorescence Microscopes and Imaging equipment, to foster experimentation for the further understanding of scientific phenomena in many diverse areas of clinical and basic research.
Massachusetts General Hospital NextGen Sequencing Core
Core facility that provides the following services: NextGen sequencing, Data Analysis. The NextGen Core is a collaboration between the Department of Molecular Biology, the Center for Human Genetics Research, the Center for Computational Biology, and the Executive Committee on Research (ECOR). Currently, the Core operates using a single Ilumina HiSeq instrument, accompanied by Illumina' '''s cBot for cluster generation. This upgrade from our Genome Analyzer II doubled our capacity and greatly increased the data amount, quality, and stability over extra-long reads. The Core is located in the state-of-the-art Richard Simches Research Center on Cambridge St. as part of the MGH main campus in Boston. The many multi-investigator groups in the building - including those that study human genetics, stem cells, genomics, and more - make it the perfect location for the Core to service the researchers in those groups. The majority of customers come from MGH, but they also service customers at other academic medical centers and industry.
Harvard Medical School East Quad NMR Facility
Formerly the NERCE NMR Resource. Nuclear magnetic resonance spectroscopy is a powerful tool for studying structural and conformational parameters of molecules. This tool is vital for the chemical analysis of both small molecules (like those discovered in small-molecule screens) and large molecules, such as carbohydrates and proteins found to have potential biologic importance. This is a user-based NMR facility; users run their own experiments on the NMR spectrometer.
Virginia Commonwealth University Labs and Facilities
Virginia Commonwealth University Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Portal, Core facility
Newcastle University Bioinformatics Support Unit
Core provides support to life science researchers with data analysis and experimental design from sequence analysis, microarrays, proteomics and beyond.
Harvard Tumor Imaging Metrics Core Facility
Harvard University Tumor Imaging Metrics Core
Core provides centralized, standardized, accurate, consistent, and timely longitudinal, multimodality anatomic, volumetric and functional tumor metrics including CT, MR, PET/CT and other nuclear medicine imaging studies to evaluate therapeutic response for patients enrolled in DF/HCC oncologic clinical trials. TIMC supports more than 30 tumor response assessment criteria including but not limited to RECIST 1.1, iRECIST, Lugano, LYRIC, IWCLL and RANO. Results of tumor metric analyses are offered on password-protected secure web-based report.
Joslin Diabetes Center Islet Isolation Core
Harvard University Islet Isolation Core (JDC)
Harvard University Joslin Diabetes Center Islet Isolation Core
Core facility that provides the following services: Rodent and Porcine Islet Isolation Services, Training Services. The main objective of the Islet Isolation Core is to provide Islets of Langerhans to investigators in the Boston area and beyond. By receiving islets from the Core one is assured of consistent high quality and purity of islets for experiments. The Core can isolate rodent and neonatal porcine islets. This leaves the investigator to concentrate on experiments rather than the complexity of islet isolation. The Core can buy the animals or the investigator can provide their own, such as special transgenic mice. Over the last five years the Core has isolated more than 10 million islets. They also provide training and advice. The Core can provide training not only for the isolation procedure but islet viability, islet size measurement, GSIS (Glucose Stimulated Insulin Secretion), STZ-induced diabetes, transplantation under the kidney capsule, and islet graft retrieval.
New York University Center for Health Informatics and Bioinformatics
Center for Health Informatics and Bioinformatics
MGH Psychiatric and Neurodevelopmental Genetics Unit Core Lab
Massachusetts General Hospital Psychiatric and Neurodevelopmental Genetics Unit Core Lab
MGH Psychiatric & Neurodevelopmental Genetics Unit
MGH Psychiatric & Neurodevelopmental Genetics Unit (PNGU)
MGH Psychiatric and Neurodevelopmental Genetics Unit
MGH Psychiatric and Neurodevelopmental Genetics Unit (PNGU)
Psychiatric and Neurodevelopmental Genetics Unit Core Lab (MGH)
Core facility that provides the following services: SNP genotyping, qPCR for CNV detection / confirmation, Genetic analysis services, DNA extraction, quantification, sample preparation, tracking, and storage. This resource provides custom genotyping (SNP, other), qPCR for CNV detection/confirmation, DNA extraction, quantification, sample preparation, tracking, and storage, and related services to further the PNGU mission of identifying and characterizing the genetic basis of psychiatric, behavioral, and neurodevelopmental disorders and to translate these discoveries to improvements in clinical care and public health.
Harvard Medical School Research Imaging Solutions
Core facility that positions digital imaging resources right where the research is being done: in Harvard Medical School''s quad-based basic science departments. The convenience of these locations makes it easy for researchers to access digital imaging expertise when faced with research imaging questions. This accessibility and convenience is supplemented by substantial web-based assistance, making Research Imaging Solutions a 24/7 resource. Seminars, Workshops and printed training materials guide faculty, students, post-docs and lab personnel on supported imaging hardware and software products. Supported hardware and software packages includes: Adobe products including Acrobat, Photoshop, and Illustrator; ACD Canvas; Microsoft Office applications including Word, PowerPoint and Excel; film recorders, slide and flatbed scanners, and color output devices such as color laser printers, poster printers and photo quality printers.
HSPH NIEHS Center for Environmental Health Flow Cytometry Core Facility
Harvard School of Public Health NIEHS Center for Environmental Health Flow Cytometry Facility
HSPH NIEHS Center for Environmental Health Flow Cytometry Facility
Self use flow cytometry facility. All new users must be trained by the facility manager over two orientation sessions and be approved to use the equipment in the facility.
Software tool as data transformation algorithm that restructures data in such a way that the transformed message is more compressible. Used for large scale compression of genomic sequence databases.
Beth Israel Deaconess Medical Center Flow Cytometry Core Facility
Beth Israel Deaconess Medical Center BIDMC-Flow Cytometry Core
Beth Israel Deaconess Medical Center Flow Cytometry Core
Core facility offers instrumentation for routine flow cytometry and cell sorting. Offers expertise and services including assisting in setting up flow cytometry experiments, acquiring, analyzing and interpreting data, data presentation and data storage, providing training with analyzers and software usage.
McGill Experimental Therapeutics Program
McGill University Experimental Therapeutics Program
The Experimental Therapeutics Program (ETP) is a program established within the unique MNI environment to pursue a mission of bridging basic research in neurobiology and immunology with human studies of neurological and immune-mediated diseases. The ETP accomplishes this mission through the establishment of core laboratory platforms that integrate fundamental research activities with rigorous studies on human biological samples derived from well-characterized patient populations. The goal of the program is to expedite the development and formal evaluation of emerging therapies aimed at halting and ultimately reversing disability caused by neurological disease.
Comprehensive Integrated Life Science Informatics solutions provider with service offerings that span Sample and Data Management (LIMS, Biologics Data Management), Genomics Data Analysis Services such as Gene Expression, Genotyping, and Next Gen Sequencing, Bioinformatics and Genomics Databases (BioExpress, ToxExpress) and Bio-IT consulting services.
Center for Public Health Research Next Generation Sequencing
Centro Superior de Investigacion en Salud Publica Next Generation Sequencing
The Center for Public Health Research (CSISP) provides next generation sequencing services via the GS FLX+ System. The Genome Sequencer FLX+ System, with long-read GS FLX Titanium chemistry, is the flagship 454 Sequencing platform. Offering more than 1 million high-quality reads per run and read lengths up to 700 bases, the system is ideally suited for de novo sequencing of whole genomes and transcriptomes of any size, metagenomic characterization of complex samples, resequencing studies and more. The GS FLX+ System is at the heart of breakthrough scientific discoveries and hundreds of peer-reviewed publications to date. Applications The Genome Sequencer FLX+ System provides the power to address a broad range of applications in diverse fields of biology. The tremendous versatility of the system is based on the unique combination of read length, throughput, and read accuracy. The technology platform has enabled groundbreaking research in various fields. Next we mention some of the most usual applications: _���� Eukaryote and prokaryote whole genome sequencing _���� Metagenomics & Microbial Diversity _���� Transcriptome sequencing _���� HIV sequencing
Harvard University Graphic Services Core
Harvard University Graphic Services Core (SERI)
Harvard University Schepens Eye Research Institute Graphic Services Core
Schepens Eye Research Institute Graphic Services Core
Core facility that provides the following services: Web and graphic services, Web design and content management service, Photography service. Peter Mallen is a designer and illustrator who manages a full-service web and graphics studio in a moderately sized scientific research facility, Schepens Eye Research Institute. He provides a full range of graphic design, scientific illustration, web design and development, content management, and general design and production services. His products are utilized by: faculty and scientific staff (books, scientific publications, slide shows, grant applications); professional staff (Administration, Development & Public Affairs; brochures, books, pamphlets); the general public (Institute websites) as well as clients of our 250-seat state-of-the-art conference center, Starr Center for Scientific Communications.
UW-Madison Mass Spectrometry/Proteomics Facility
University of Wisconsin - Madison Mass Spectrometry/Proteomics Facility
University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility has several mass spectrometers for the analysis of biomolecules, including proteins, peptides, oligonucleotides, oligosaccharides and other small organic and inorganic molecules.
Beth Israel Deaconess Medical Center Confocal Imaging Core Facility
Beth Israel Deaconess Medical Center Confocal Imaging Core
BIDMC Immunostaining and Microscopy Core
Core facility that provides immunostaining (frozen and paraffin embedded tissues) and image processing services in confocal microscopy, light microscopy and immunostaining for cells and tissues including confocal microscopy, brightfield and fluorescence microscopy, and immunoperoxidase and immunofluorescence staining. BIDMC Immunostaining and Microscopy Core offers consultation and service for tissue immunostaining with paraffin or frozen sections, and for training to use confocal and widefield microscopes.
DFCI Confocal and Light Microscopy Core Facility
Confocal and Light Microscopy core facility (DFCI)
Dana-Farber Cancer Institute Confocal and Light Microscopy Core Facility
Core facility that provides state-of-the-art imaging microscopy technology for fixed and live cells, tissues and multi-photon animal imaging along with scientific and technical expertise to assist in experimental design and optimal image collection. Imaging techniques available include Standard fluorescence, Live-cell long term imaging, Confocal, Deconvolution, Fluorescence spectral detection, TIRF, FRET, Calcium imaging, Multi-photon, and Fluorescence lifetime imaging. Available equipment includes: Yokogawa spinning disk confocal microscope (Andor), Leica SP5 laser scanning confocal with a white light laser, Zeiss 710 confocal/multi-photon, Nikon inverted widefield fluorescence microscope. Other services include training on all equipment, consultation about various imaging techniques and assistance with image analysis. In addition, staff are available to assist with troubleshooting regarding microscopes in individual research labs. All services are available on a fee basis, and equipment is available for either assisted use or unassisted use after training by core staff. NEW: The core has established a collaboration with Rockland Immunochemicals to provide free, trial-size samples of primary and secondary antibodies that may be useful in your experiments.
University of Massachusetts Amherst Labs and Facilities
University of Massachusetts Amherst Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented in August 16,2024. Portal, Core facility
Brigham and Women''''s Hospital Specimen Bank
Core facility that provides the following services: Open repositories service, Sample processing service, Medical/pathology informatics support service, BWH tissue repository service. The Specimen Bank provides materials to investigators with IRB-approved protocols. Staff are available to assist with selection of samples appropriate for downstream applications, development of processing protocols or preparation of derivatives from clinical materials. IT Staff are also available to assist researchers with creation of queries for prospective sample collection or queries to select samples from specific cohorts. Their goal is to drive quality research in an efficient and cost-effective manner. Each year they provide tens of thousands of samples to area researchers. Getting started: Partners investigators and study staff may request a Crimson user account to help manage studies and collected materials.
Fountainbridge is a chemical company that helps its customers to acheive the maximum level of success when purchasing chemicals from China. Our services are provided by Fountainbridge''s expert staff based in China and Europe and through close relationship with our partners based in China. Our aim is to give our customers direct access to services and products provided from China, allowing them to reduce costs, increase security and decrease the time it takes to bring chemicals to market.
PrimBio Research Institute uses the Ion Torrent gene sequencing platform to provide genomic sequencing services. We are also researching and developing targeted gene panels for diseases diagnosis, prevention and treatment. Provides customized analysis.
Harvard Digestive Diseases Center Biomedical CORE D: Gnotobiotic Mice, Microbiology and Metagenomics
Harvard Digestive Disease Center Gnotobiotics and Microbiology Core
Harvard Gnotobiotic and Microbiology Core (CHB)
Harvard University Gnotobiotic and Microbiology Core
Harvard University Gnotobiotic and Microbiology Core (CHB)
Harvard Gnotobiotic and Microbiology Core
Core facility that assists investigators evaluating host microbiota and its role in normal physiology and disease. It includes a number of resources for groups studying the role of the microbiota in human health and disease.
Firefly BioWorks, Inc. (Cambridge, MA) provides FirePlex????????????? miRSelect, a platform for targeted microRNA profiling of diverse biological samples. The FirePlex????????????? advantage lies in its streamlined, high-throughput protocol, affordable customization, and low capital cost. FirePlex????????????? readout is performed on standard flow cytometers, and FirePlex????????????? is offered as a service for users with limited access to flow instruments.
CU Boulder Electron Microprobe Laboratory
University of Colorado at Boulder Electron Microprobe Laboratory
University of Colorado Boulder Electron Microprobe Laboratory
CU-Boulder Electron Microprobe Laboratory
An electron microprobe is an electron microscope designed for the non-destructive x-ray microanalysis and imaging of solid materials. It is capable of high spatial resolution (1 micron beam size) and relatively high analytical sensitivity. The analytical facilities' ''' JEOL JXA-8600 can acquire digital secondary-electron and backscattered-electron images as well as elemental x-ray maps. It is equipped with 4 wavelength-dispersive spectrometers and an energy-dispersive spectrometer. Most of the periodic table can in principle be analyzed (Be through U), subject to several important considerations. The quality of analyses performed depends essentially on the quality of sample preparation, character of the sample material, and availability of appropriate primary and secondary calibration standards for the desired elements. A precision usually less than 0.5% relative depending on element abundance, and accuracy as good as 1-2% can be obtained with this instrument. The analytical sensitivity ranges from a low of ~50 parts per million for optimum cases, to a typical detection limit of several hundred ppm, but can be as high as several weight percent for problem elements. The volume sampled is typically a few cubic microns, corresponding to a weight of a few picograms.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2,2024. PharmaSages is a consulting company servicing pharma, biotech and CROs. It was created to help companies in focusing on their core business and becoming globally competitive. We help pharma and biotech companies in identifying the right CROs for their drug discovery and clinical trial projects, acquisition of expertise and execution of their projects, and reducing their costs through innovative ideas. We have lots of consultants ready to help with their expertise in basic and clinical science. In addition, we provide clinical document service to help with FDA filings including IND and NDA filings, study start up, SOPs, quality management, SAEs reporting, HIPPA compliance, protocol writing and management, contract negotiations and preparation, budget preparation, electronic filings, and clinical trainings.
Massachusetts General Hospital Ragon Institute Biostatistics Core Facility
Massachusetts General Hospital Ragon Institute Biostatistics Core
Biostatistics core serves the needs of the HIV/AIDS researchers within the Ragon Institute and its affiliates at Harvard, MGH, MIT and University of Kwazulu Natal, South Africa. Provides expertise in planning, conduct and analysis of research with goal of enhancing scientific quality of HIV-related research at the institute. Primary objective is to ensure that studies are well designed, correctly analyzed, clearly presented, and correctly interpreted.
MGH Martinos Center for Biomedical Imaging Core Facility
Massachusetts General Hospital Martinos Center for Biomedical Imaging Core Facility
Core facility that provides the following services: Positron emission tomography service. The Martinos Center' '''s dual mission includes translational research and technology development. The core technologies being developed and used at the center are magnetic resonance imaging (MRI) and spectroscopy (MRS), magnetoencephalography (MEG) and electroencephalograpy (EEG), near infra-red spectroscopy (NIRS) and diffuse optical tomography (DOT), Positron Emission Tomography (PET), electrophysiology, molecular imaging, and computational image analysis. A particular area of innovation at the Center is Multimodal Functional Neuroimaging which involves the integration of imaging technologies. They are also world leaders in the development of primate neuroimaging techniques. Major areas of research at the center include, psychiatric, neurologic and neurovascular disorders, basic and cognitive neuroscience, cardiovascular disease, cancer and more. With an extensive and expanding inventory of state-of-the-art imaging facilities, a world class team of investigators and collaborators, and important government, industry and private supporters, the Martinos Center is leading the way to new advances and applications in biomedical imaging.
University of Alberta Cell Imaging Centre
The Cell Imaging Centre is primarily equipped to benefit research scientists within the faculty of medicine and dentistry at the University of Alberta, and is also available to accommodate users from other academic institutes and commercial companies.
Georgia Tech Magnetic Resonance Laboratory
Georgia Institute of Technology Magnetic Resonance Laboratory
The Nanomedicine Research Institute Magnetic Resonance Laboratory at Georgia Tech operates a Bruker Pharmascan 7T with a magnet bore of 160 mm. We have a large expertise in the use of MRI as a tool in Biomedical and Chemical Engineering. Previous research projects were concerned with: MRI of anatomical preparations; evaluation of tumor growth; bio-compatibility of implants; cardiac MRI; Diffusion Tensor Imaging; pharmacokinetics; fluid ingress and distribution in complex substrates; flow MRI; 1H, 19F and 13P in vivo spectroscopy and relaxometry; development of MRI contrast agents; solid-state MRI.
UNC School of Medicine Macromolecular X-Ray Crystallography Core Facility
University of North Carolina at Chapel Hill School of Medicine Macromolecular X-Ray Crystallography Core Facility
X-ray crystallography is the principal technique used to determine three-dimensional structures of biological macromolecules. The central goal of the UNC Crystallography Core Facility is to provide the support and infrastructure necessary to enable individual investigators of any experience level to initiate and successfully complete a structural biology project. The facility is state of the art, offering a variety of services in these three areas: crystallization, x-ray diffraction, structure determination. The primary mission of the MX Facility is to work with researchers here at UNC, however, we are also able to work with researchers at non-UNC academic institutions and commercial companies.
University of North Carolina at Chapel Hill School of Medicine Protein Expression and Purification Core Facility
UNC School of Medicine PEP Core Facility
UNC School of Medicine Protein Expression and Purification Core Facility
Core specializes in production of pure, functional proteins for structural, biophysical, and biochemical studies. Has ability to produce and purify milligram amount of protein.
Department of Environment and Resource Management
Queensland Government Department of Environment and Resource Management
The department handles some of the most complex issues facing Queensland, including securing water for the future, managing land use, meeting the challenges of climate change, and conserving the states natural and cultural heritage. We promote sustainable living and resource use, and employ the latest science to underpin decision making. We are responsible for developing initiatives which ensure Queensland reduces its carbon footprint while also making sure the State is well-placed to meet the impacts of climate change. The Queensland Centre for Climate Change Excellence (QCCCE) provides specific climate science and research on climate change impacts and addresses issues that are specifically relevant to Queensland. A suite of ClimateSmart programs encourages householders and business to contribute to minimising the impacts of climate change by reducing their carbon emissions. This will help achieve the Queensland Governments Toward Q2 Green target: cut by one-third Queenslanders carbon footprint with reduced car and electricity use while also conserving water at home, work and in their communities. grants/funding Natural Resources Awareness Grants 2010 recipients announced The successful applicants for the Natural Resources Awareness Grants for 2010 have been announced. More than 100 000 has been allocated to 17 community projects to help promote the importance of natural resource management and reduce our carbon footprint. Koala disease research fund The Koala Disease Research Fund is offering grants to support high quality research that will guide DERM management actions to mitigate the effects of disease on wild populations of koalas. Indigenous cultural heritage grants Two cultural heritage grant programs administered by DERM offer funding formanaging and protecting Indigenous cultural heritage sites and helping registered Indigenous cultural heritage bodies fulfil their legislative role. Incentives for natural resource management Visit the Natural Resource Management Incentives database for information on grants offered by industry and federal, state, and local governments for natural resource management activities. Queensland Sustainable Energy Innovation Fund The Queensland Sustainable Energy Innovation Fund helps Queensland-based organisations to develop innovative technologies for reducing consumption of fossil fuels, water or greenhouse gas emissions. Great Artesian Basin Sustainability Initiative The Great Artesian Basin Sustainability Initiative provides financial assistance to landholders to rehabilitate bores and replace bore drains with piped systems, which help preserve water and restore artesian pressure. Other grants Visit Queensland GovernmentGrants, or call Smart Service Queensland on 13 13 04* for information on current funding and grants for all Queensland Government departments. * Local call costs apply Closed Low Carbon Diet Community Funding Program The Low Carbon Diet Community Funding Program assists with administration and delivery costs to help Queensland groups and organisations implement the diet. Applications for Round 4 close 7 December 2009. Lifestyle Waterwise Grants program The 10 million Lifestyle Waterwise Grants program was launched in December 2006 to encourage community-based not-for-profit organisations to reduce their water consumption.
UNC School of Medicine Antibody Core Facility
University of North Carolina at Chapel Hill School of Medicine Antibody Core Facility
The primary objective of our facility is to produce monoclonal antibody-producing hybridoma cell lines for UNC investigators. The core develops monoclonal antibodies in mice, rats and hamsters. The core can assist in the screening of hybridomas of interest by ELISA or flow cytometry. The facility can also produce large amounts of crude antibody in vitro for investigators as well as purify both polyclonal and monoclonal antibodies from tissue culture media or ascites.
Duke IGSP Genome Sequencing and Analysis Core
Duke University IGSP Genome Sequencing & Analysis Core
Duke University IGSP Genome Sequencing and Analysis Core
Duke IGSP Genome Sequencing & Analysis Core
The mission of the Genome Sequencing & Analysis Core Resource is to promote advance in biology by providing to researchers complete genomic solutions with the latest and most complementary technologies readily available. We provide services for traditional capillary sequencing, high-throughput next-generation sequencing, and various data analyses, both across Duke University campus and across the world. We offer services on seven sequencers at the moment.
Moffitt Cancer Center Molecular Genomics Core Facility
H. Lee Moffitt Cancer Center and Research Institute Molecular Genomics Core Facility
Molecular Genomics Core Facility at Moffitt Cancer Center in Tampa, FL offers services to assess gene expression, epigenetic modification and sequence variation. Performs bulk and single cell RNA and DNA sequencing on Illumina platform, NanoString nCounter, GeneChip and Illumina array services.Offers services to discuss your project and timeline for your project.
UC Davis Host-Microbe Systems Biology Core
University of California Davis Host-Microbe Systems Biology Core
The UC Davis Host-Microbe Systems Biology Core offers NGS analytical services which will utilize state-of-the-art open source software platforms and other customized scripts developed by the HMSB Core co-Director Jonathan Eisen, Ph.D. The HMSB Core is designed to provide researchers with easily accessible, customized, and cost-effective resources for integrating analyses of microbial community structure and host-microbe interactions in health and disease.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2, 2024. Parabase Genomics is a molecular diagnostic company offering whole exome sequencing services to physicians and researchers with a specialty in the identification of rare variants associated with Mendelian Disorders. Our sample processing and variant analysis pipelines are highly optimized for calling rare variants that are normally missed by less optimized workflows. At Parabase Genomics, we have combined a team of innovators and experts in genomics, pediatrics and targeted sequencing that are not available at other service organizations. Our team is also unique in that we can deliver both research and well as CLIA/CAP certified exomes with insurance reimbursement.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 19,2024. Core facility
Genetik Ink creates art from your own DNA. From a simple cheek swab, we collect your DNA, process it, and create an art piece on canvas or aluminum. Once you order, a DNA collection kit will be sent in the mail to you. Once you have collected your DNA, send it back to our lab with the mailer sleeve we provided in the kit. We take care of the rest. Typically, you can expect to have your art piece within 1-2 weeks. Since we are in beta phase of our business, development could take longer. If you are not happy with your final product, we have a 100% money back guarantee
University of Virginia Labs and Facilities
University of Virginia Labs & Facilities
UConn Analytical Ultracentrifugation Facility
UConn Biotechnology - Bioservices Center Analytical Ultracentrifugation Facility
University of Connecticut Analytical Ultracentrifugation Facility
The Analytical Ultracentrifugation Facility located at the University of Connecticut engages in collaborative research as well as training scientists, technicians, and students. The Facility has three Beckman XL-I ultracentrifuges along with associated instruments, hardware and computers. In addition, University scientists are on hand to provide user support and advice.
University of Connecticut Flow Cytometry Core Facility
University of Connecticut UCONN-Storrs Flow Cytometry Facility
Facility provides advanced analytical and cell‑sorting services to support research in immunology, cancer biology, stem cell biology, oceanography, microbiology, and translational medicine. Combines high‑parameter cytometry, precision cell sorting, and expert scientific support to enable deep single‑cell characterization across a wide range of experimental systems.
University of Western Australia; Perth; Australia
Public research university in the Australian state of Western Australia. The university's main campus is in Perth, the state capital, with a secondary campus in Albany and various other facilities elsewhere.
UConn High-Throughput Screening Facility
UConn Biotechnology - Bioservices Center High-Throughput Screening Facility
University of Connecticut Biotechnology - Bioservices Center High-Throughput Screening Facility
University of Connecticut High-Throughput Screening Facility
The University of Connecticut High-Throughput Screening Facility (HTS Facility) was established in 2011 with funding awarded through the University''s Major Equipment Competition. Over the last 20 years, high-throughput screening has become an integral tool utilized by both pharmaceutical industry and academic institutions to identify new lead compounds for drug development. The HTS Facility is comprised of integrated instrumentation dedicated to aiding researchers in the small molecule screening and drug discovery process.
UConn Biotechnology - Bioservices Center Microcalorimetry Facility
University of Connecticut Biotechnology - Bioservices Center Microcalorimetry Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22,2024. Microcalorimetry Facility was established in 2011 as the result of the acquisition of nano-ITC (Isothermal Titration) and nano-DSC (Differential Scanning) Calorimeters from TA Instruments, which was made possible with funding awarded through the VPR''s Major Equipment Competition in October 2010.
UConn Biotechnology - Bioservices Center Nanofabrication Facility
University of Connecticut Biotechnology - Bioservices Center Nanofabrication Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16, 20224. Nanofabrication Facility houses three instruments for patterning of flat surfaces and selective etching of materials. Researchers fabricate devices and structures to demonstrate novel device concepts and to characterize new materials. To carry out these functions this new facility consists of three instruments: a Tescan Electron-Beam Lithography Tool, an OAI high resolution Mask Aligner and Advanced Vacuum/Plasma Therm Reactive Ion Etcher.
UConn Nuclear Magnetic Resonance Facility
UConn Biotechnology - Bioservices Center Nuclear Magnetic Resonance Facility
University of Connecticut Biotechnology - Bioservices Center Nuclear Magnetic Resonance Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15,2024. Nuclear Magnetic Resonance Facility (NMR) was established in 2004. The Facility recognizes the important role that NMR plays in molecular structure determination, drug design, protein and nucleic acid characterization, and conformational analysis. The instrumentation serves the high-resolution research needs for investigators from the Departments of Molecular and Cell Biology, Chemistry, and Pharmacy at the University of Connecticut.
UConn Protein X-Ray Crystallography Facility
UConn Biotechnology - Bioservices Center Protein X-Ray Crystallography Facility
University of Connecticut Biotechnology - Bioservices Center Protein X-Ray Crystallography Facility
University of Connecticut Protein X-Ray Crystallography Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. Protein X-ray Crystallography Facility became operational in October 2010 following the acquisition of a Rigaku HighFlux HomeLab system with funding awarded by the VPR''s Major Equipment Competition in November 2009.
Bindley Biosciences Center Biophysical Analysis Lab
Purdue University Bindley Biosciences Center Biophysical Analysis Lab
The purpose of the Biophysical Analysis Lab (BAL) at the Bindley Biosciences Center is to provide complete biophysical analysis of macromolecules. In the lab, there are two analytical ultracentrifuges: Beckman-Coulter XLI and XLA, a Biacore 3000, an ITC, and a SEC-MALS platform. With these instruments we can determine kinetic parameters, stoichiometry of binding, size distribution, shape, oligomerization state and other biophysical measurements. Complementing these traditional biophysical methods, the BAL also provides mass spectrometric analyses at both the protein and peptide levels. The lab strives to establish long-term collaborations and deliver professional quality data that can be used for publications and grant proposals.
NYU Anti-Infectives Screening and Insectary Core Facilities
New York University Langone Medical Center Anti-Infectives Screening and Insectary Core Facilities
Our insectary produces five rodent malaria strains weekly and will ship live sporozoite infected Anopheles stephensi to investigators for research use (Plasmodium berghei GFP, luciferase or red-star and P. yoelii-GFP) Anti-infective testing including in vitro EC50, in vivo mice infection are available against for major parasitic diseases: Malaria, Leishmaniasis, Chagas and African Trypanosomiasis.
Purdue University Proteomics Core Facility
Provides LCMS/MS analysis of proteins in clinical, environmental and other biological samples. As a shared facility of the Bindley Bioscience Center (BBC) in Discovery Park of Purdue University, the facility enables both targeted and global analysis of proteins, their post-translational modifications and analysis of protein complexes and protein-protein interactions. Coupled with different chromatographic separation techniques, modern mass spectrometric instrumentation, and advanced scientific and bioinformatics expertise, the facility provides unique opportunities for researchers at Purdue and beyond to perform quantitative analysis of proteins in complex biological samples using both global, as well as, targeted proteomic approaches.
Bindley Bioscience Metabolite Profiling Facility
Bindley Bioscience Center Metabolite Profiling Facility
The Metabolite Profiling Facility (MPF) provides state-of-the-art technologies that enable both qualitative (defining all components of a metabolome) and quantitative (determining differential concentrations of metabolites) metabolomics in complex biological systems. This facility employs highly sensitive mass spectrometry coupled with liquid chromatography and multi-dimensional gas chromatography for precise sample analysis. Metabolite profiling is an integral component of systems biology, an exciting field that combines genomics, transcriptomics and proteomics to define cellular functionality. Our elite scientists will empower researchers with new technologies, methods development, expert training and consultation.
Bindley Bioscience Flow Cytometry and Cell Separation Facility
Bindley Bioscience Center Flow Cytometry and Cell Separation Facility
Bindley Bioscience Flow Cytometry & Cell Separation Facility
The Bindley Bioscience Flow Cytometry and Cell Separation Facility provides advanced cell and particle analysis and sorting using flow cytometry based technology. The facility also provides training in flow cytometry analysis and sorting techniques. The facility also provides expert consultation for assay and protocol development for flow cytometry analysis and cell separation.
Purdue Translational Pharmacology Core Facility
Purdue Translational Pharmacology Facility
Purdue Translational Pharmacology Facility at Bindley Bioscience Center
Purdue Translational Pharmacology (PTP) facility provides in vivo pharmacological evaluation using porcine models. The facility is situated in the Purdue University School of Veterinary Medicine complex, which provides constant care and monitoring of the animals. The PTP uses unique penning systems to automate blood sampling and maintain a humane and stress free environment for test subjects. The PTP synergizes with the Metabolite Profiling Facility in the Bindley Bioscience Center, which facilitates the pharmacological analysis of blood samples collected.
Purdue University Bioscience Imaging Core Facility
Purdue Bindley Bioscience Center Bioscience Imaging Facility
Purdue University Bindley Bioscience Center Bioscience Imaging Facility
Provides instruments and expertise needed to visualize molecules in preparations ranging from single cells to entire animals. All facility users receive individualized instrument training as well as project specific advice for optimal data acquisition. Consultation on sample preparation, image rendering, and data analysis are also available as our knowledge base permits.
Purdue University X-Ray Crystallography Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. The laboratory at Purdue is equipped with advanced instrumentation for small molecule crystallography. The main diffractometer is equipped with a micro-focus x-ray source to allow very small crystals (less than 0.1 mm) to be studied. Low temperature data collection is available to a temperature of 95K. The crystallographer has been at Purdue for over 26 years and is widely respected.
Vanderbilt University Eicosanoid Core Laboratory
Vanderbilt University School of Medicine Eicosanoid Core Laboratory
Eicosanoid is an umbrella term used to describe any oxidized derivative of arachidonic acid, a ubiquitous polyunsaturated fatty acid (PUFA) in humans. Arachidonic acid can be oxidized in vivo via both enzymatic and non-enzymatic mechanisms to yield bioactive lipid mediators that are of central importance to human physiology and pathophysiology. The Eicosanoid Core Laboratory at Vanderbilt University was established in 1988 in order to provide investigators at the university with a central location for analysis of prostaglandins, leukotrienes, and isoprostanes. Today the Eicosanoid Core Laboratory serves investigators not only at Vanderbilt but indeed around the world.
Centrillion offers a portfolio of genomic services to academic, clinical and industrial researchers. Core provides experimental design consultation, data production services, and bioinformatics analyses for a wide variety of genomic applications. Core offers access to next-gen sequencing, genotyping and bioinformatics analysis.
University of Rochester Genomics Research Center Core Facility
University of Rochester Medical Center Genomics Research Center
Provides core laboratory support, technical consultation, assistance with experimental design and data analysis for investigators using high throughput genomic sequencing, genotyping and gene expression in their research programs.Provides support for RNA-Seq, ATAC-seq, ChIP-Seq, Single Cell RNA-seq, Spatial Transcriptomics, Exome/Genome sequencing, Whole Genome and Reduced Representation Bisulfite Sequencing (WGBS, RRBS), 16S rRNA Sequencing, Small RNA-Seq, Metatranscriptomics, qRT-PCR, processing of RNA/DNA, as well as custom applications and approaches. Bioinformatic analysis support is also available.
University of Rochester Medical Center Flow Cytometry Core Facility
University of Rochester Medical Center Flow Cytometry Core
Provides investigators with instrumentation along with expertise. Core instrumentation includes traditional analytical cytometers, full spectrum cytometer, cell sorters, imaging cytometers, small(nano) particle detection system, metabolomics instrument, and mass cytometer.
University of Rochester Medical Center Proteomics Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. Offers state-of-the-art Mass Spectrometry and Biomarker Separation and Analysis Services.
University of Rochester Medical Center Multiphoton Microscopy Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2024.The mission of the URSMD Multiphoton Core Facility is to provide state-of-the-art multiphoton imaging capabilities to further the biomedical and bio-optical research at the URSMD and the University of Rochester with emphasis on intravital imaging and systems physiology. The Multiphoton Core Facility provides access to an Olympus Fluoview 1000 AOM-MPM imaging system and a Spectra-Physics MaiTai HP DeepSee Ti:Sa laser system with dispersion compensation. Further capabilities include engineering applications for opto-electronics and spectroscopy. Initial meeting with the director regarding the design of the experiments begins the process. Imaging will be initially performed by highly skilled staff to make sure all features of software are added for the study, thereafter, the investigator is trained until they are able to operate the microscope independently. Also offered is a blood gas analysis machine and supporting equipment.
Provider of services for generation and analysis of genetically modified rodents and cell lines. Offers services for transgenic and knockout mice and rats.
Moffitt Cancer Center Tissue Core Facility
H. Lee Moffitt Cancer Center and Research Institute Tissue Core Facility
Biorepository resource with mission of proper collection, handling, processing and storage of irreplaceable biological specimens to support spectrum of related basic science, translational and clinical research. Provides expertise in nucleic acid extractions, quantification, aliquoting and quality assurance; liquid specimen centrifugation, processing and aliquoting; histological tissue processing, immunohistochemistry and tissue microarray microtomy; pathologist consultation services. Tissue Core operations are divided into four distinct pillars of service that work collaboratively to ensure specimen quality is maintained from procurement to preservation.
URMC Confocal and Conventional Microscopy Core
University of Rochester Medical Center Confocal and Conventional Microscopy Core
The Confocal and Conventional Microscopy Core provides Medical Center researchers access to high-end confocal microscopy as well as more conventional brightfield and fluorescence microscopy. The Core provides assistance with all imaging procedures as needed by the investigators. Aid in customizing staining protocols to optimize obtainment of high quality data using Core instruments is also provided. The CCMC provides Medical Center researchers the ability and expertise to obtain high quality imaging-based data from tissue, culture, and materials-based research studies. Core instrumentation includes a new Olympus FV1000 laser scanning confocal microscope, an accompanying workstation containing full Olympus FV1000 software, an Olympus VanoxAH-2 microscope for brightfield and fluorescence imaging, and an imaging stand for large specimen imaging. The core also offers a PalmBeam Laser Capture Microdissection Instrument for microdissection of tissue.
University of Rochester Medical Center Electron Microscopy Core Facility
University of Rochester Medical Center Electron Microscope Research Core Facility
University of Rochester Medical Center Electron Microscopy Core
Electron Microscopy Resource supports ultra-structural interrogation of tissues, biologic solutions and nanomaterials for investigators utilizing transmission electron microscopy (TEM), scanning electron microscopy (SEM) and cryo-TEM.
University of Rochester Medical Center Gene Targeting and Transgenic Core
Currently, the Gene Targeting and Transgenic Core''s services include the production of mouse models using DNA microinjection and embryonic stem cell injection (from gene targeting in mouse ES cells to production of chimeric mice) methodologies. Additional services have included: various analytical techniques, embryo cryopreservation, rederivation of pathogen-free rodents, and assisted reproduction techniques (e.g., in vitro fertilization (IVF), superovulation, and embryo transfer). Specific strains, and alternative species and methods are considered when appropriate for individual research applications.
Axeq Technologies, a sister company to Macrogen, based in Rockville, Maryland focuses on providing high quality data at an affordable cost to researchers around the world. We pride ourselves with our publication grade data, fast turnaround time and very competitive prices. Axeq specializes in Exome, Transcriptome and Whole Genome Sequencing and can provide targeted DNA and RNA arrays. We help researchers from library preparation all the way to data analysis. Axeq your data today!
Bay Materials was founded in 1999 by Dr. Ray Stewart and Jim Reed to fulfill a need for applied polymer research and product development services in Silicon Valley. Bay Materials has the capability to address fundamental polymer development needs, from concept through to commercialization. We strive to be the most efficient solution to resolve our customer''s polymer problems. Over our history we have contributed to a broad array of developments from new orthodontics methods, to advancements in coronary catheter technology, to new light bulbs, and for customers ranging from Silicon Valley Start-Ups to Fortune 500 companies.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22, 2023. Microtech Lab is a laboratory open to all researchers involved in the development of genomics projects of basic, translational, and clinical research. Our lab provides the support and tools for microarray experiments for the following applications: 1) Analysis of gene expression profiles 2) Analysis of the expression profiles of microRNA (miRNA)
MSU Skobeltsyn Institute of Nuclear Physics Laboratory of Ion Beam Nanotechnologies
Laboratory of Ion Beam Nanotechnologies Skobeltsyn Institute of Nuclear Physics MSU
MSU SINP Laboratory of Ion Beam Nanotechnologies
UAMS Experimental Pathology Core Laboratory
University of Arkansas for Medical Sciences Experimental Pathology Core Laboratory
The Experimental Pathology Shared Resource Laboratory is a non-profit laboratory that provides investigators with centralized, comprehensive histological services. The laboratory currently works with over 70 investigators at the University of Arkansas, regionally, and nationally. By providing a centralized laboratory, we offer convenient access to all services within one facility, save costs for investigators and the institution, increase efficiency of sample processing, eliminate duplication of services and equipment, and maintain stringent quality control standards. The laboratory director, consultants, and technicians have extensive experience in routine histology and immunohistochemistry involving both human and animal tissues.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 24,2024. Reniguard Life Sciences Inc is a biotech company specialized in the construction, production, purification and analysis of biomolecules (DNA, RNA, protein) and cells, using conventional molecular, cellular, biochemical and immunological tools as well as proprietary technologies. We function as a contract research organization (CRO) assisting our clients in their clinical biomarker studies and drug discovery & development activities. We also develop clinical diagnostic tests. Our mission is to improve clinical management of various diseases through our scientific research and innovations.
Johns Hopkins University Labs and Facilities
Johns Hopkins University Labs & Facilities
Agile DiscoveryPartners is a Seattle-based chemistry provider, founded by experienced scientists with a track record of problem-solving and achievement in drug discovery. We aim to provide services to the life science community and focus on the needs of virtual companies, biotechs and academic and research institutions. ????????????? Our core expertise includes medicinal chemistry, synthetic chemistry, and design and synthesis of drug conjugates. www.agilediscoverypartners.com
CHEM-X-INFINITY specializes in the synthesis and development of original compound libraries for High-Throughput Screening (HTS) activities and Hit validations. All our compund are designed around original scaffolds which have not or barely been described in the literature. We use different QSAR model which allow us to provide the best selection of compounds for your needs.
Provides surface analysis and materials characterization services, including composition and contamination measurement, trace elemental analysis and microscopy.
HB Custom Media Inc. (HBCM) is a supplier of custom tissue culture media, reagents, supplements and mouse embryo culture media to the Research Use Only (RUO) market for cell culture and the culturing of embryonic stem (ES) cells, both human and mouse. The company was started with one simple idea; provide the research scientist with the ability to obtain high quality, custom tissue culture media and reagents for a lower cost with faster turnaround times and personalized service. H.B. Custom Media Inc. incorporates the flexible manufacturing expertise that made Specialty Media unique. This enables the company to modify schedules to deliver products faster than their competitors
Develops and commercializes recombinant proteins and custom monoclonal antibodies through integration of bioinformatics, gene cloning, protein expression and purification, and immunology, using high-throughput technologies. ProMab applies its proteins and antibodies to deliver diagnostic products as well as services targeting the global biomedical market through collaborations with other biotechnology and bio-reagent companies.
Wayne State University Labs and Facilities
Wayne State University Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. An Portal, Core facility
Tsinghua University Center of Biomedical Analysis
The center of biomedical analysis (CBA) is a multiple discipline platform. CBA is bound to provide the best services and support to our investigators in all research fields. We welcome any suggestions and recommendations. In consultation with the Advisory Committee for each facility, the facility manager sets up the fee structures and makes decision on equipment purchase and upgrade.
We are unique in the genomics market place with respect to our position both as a laboratory services provider and a developer of proprietary chemistries and instrumentation to drive cost efficient genomics solutions driven by our KASP technology. Sample preparation and nucleic acid extraction DNA sequencing , Genotyping , Biobanking. Our business operates from 3 laboratory centres in Berlin-Germany, Boston-USA and London-UK.
Pennsylvania State University Materials Characterization Lab Core Facility
Penn State Materials Characterization Lab
Pennsylvania State University Materials Characterization Lab
Fully-staffed, open access, analytical research facility at Penn State's Materials Research Institute. Provided services include Surface Analysis (XPS, AFM, AES), Electron Microscopy (TEM, SEM, FIB, EPMA), X-ray Scattering (XRD and SAXS), Molecular Spectroscopy (FTIR, Raman, UV-VIs-NIR), Electrical Testing, Optical Microscopy, Thermal Analysis, Mechanical Testing, and Sample Preparation.
PuriSpec, LLC laboratories are located are located in the newly renovated 50,000 sq/ft Innovation Center at Eagleview in Exton, PA (Previously Johnson and Johnson research). Analytical capabilities for project support include: JASCO SFC, Agilent GC and HPLC, Agilent HPLC/MS and Bruker NMR. Purispec, LLC specializes in chromatographic method development, separation and isolation of chiral and achiral molecules using Supercritical Fluid Chromatography (SFC). Wecurrently use state-of-the-art JASCO SFC equipment for chiral and achiral method development and small molecule isolations. Our capabilitites currently include SFC, GC, LC, LC/MS and NMR, with isolations ranging from 1 mg to multigram quantities. We offer synthetic chemistry, chromatographic and spectroscopic problem-solving and consulting services for non-GMP applications. Our company currently provides solutions to clients in the flavors, fragrances, beverages, foods, fine chemical and petrochemical industries. Contact us for your method development and analytical chemistry needs. Price quotes are available on request.
Roswell Park Cancer Institute Pathology Resource Network
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2,2024. New York State Department of Health Provisional License for Tissue Bank Operation issued in accordance with and pursuant to section 4364 Public Health Law of New York State. Tissue Bank ID No.: NA002 Approved for the following categories of Service: Cancer tissue and associated non-cancer tissue for use in medical research and/or education
Stony Brook Medicine Genomics Core Facility
Stony Brook School of Medicine Genomics Core Facility
The facility aims to provide scientists at Stony Brook with the tools required to maximize their research. In the longer term, it is hoped that this facility will pave the way for Stony Brook to become a center of excellence in translational medicine, with particular emphasis on human genetics.
Data for Solutions, Inc. is a small scientific consulting firm offering Comprehensive Services in Study Design, Data Analysis, Organizational and Systems Analysis and Evaluation, International Health Issues, and Scientific Writing. We specialize in research design and data analysis, with expertise in research methodology, grant development, program evaluation, quality assessment, data collection techniques, mathematical and statistical analysis, writing results for professional and peer-reviewed outlets, and creating data-driven business reports and presentations. We strive to be responsive to clients'' needs and constraints, creative in our solutions to statistical and data management challenges, and determined in our attention to detail. Our mission is to increase the productive use of scientifically sound and ethical methodological, numerical, and statistical research techniques by research, instructional, and administrative professionals. To accomplish this mission, we are engaged in research, consulting, and training activities, including: ?? Providing effective client/consultant interchange through in-person appointments, telephone appointments, and e-mail. ?? Offering indirect education and consulting through Web-based tutorials, documentation, and training program development. ?? Developing and delivering training through short courses and class tutorials. ?? Providing contractual grant development and data analysis services for University faculty and graduate students. ?? Engaging in continual professional development in order to maintain technical leadership in statistical and mathematical applications. Data for Solutions, Inc. can also design individualized training for your statistical and data analytic need.
Hospital for Special Surgery Labs and Facilities
Hospital for Special Surgery Labs & Facilities
Draconis Pharma offers scientific and technological services to pharmaceutical, biotechnology, fine chemical and food companies within research projects. With a strong know-how in research areas such as inflammation, allergy, immunology and neuroscience, the range of services covers: design, synthesis and analysis of chemicals; in vitro assays development for primary screening or diagnostic tools; cell-based assays and animal models focused on immune-based inflammatory diseases and studies for the characterization of compounds (ADME-PK, toxicity and safety).
CaresBio Laboratory (CBL) is a contract research organization, serving as a translational link with the one stop service approach to close the gaps between basic and clinical sciences for biomedical science community. We are serving academic laboratories, CROs, biotechnology and pharmaceutical companies and research organizations by providing high quality and cost effective pre-clinical and clinical research services. If you are doing biomarker and or drug discovery and development; therapeutics and translational research along with the applications of genomics and proteomics study; data validation and analysis; histopathology, immunohistochemistry, pathology or other immunostaining, imaging; histomorphometry, image analysis; small animal imaging; screening, efficacy and toxicity testing of your candidate compounds. We also provide biostatistics analysis of pre-clinical and or clinical data, data base developments or any subcategories of these fields. We do assay developments and provide customized assays to match your needs.
Vancouver Prostate Centre Laboratory for Advanced Genome Analysis
Core offers sequencing and microarray services, solutions for the profiling of FFPE tissues, and complete, project-tailored downstream bioinformatics analysis. The core's structure enables the management of research projects from experimental design to analysis and interpretation of data as well as support for grant applications and publications. The LAGA provides open fee-for-service access as a core facility (intra-institutional services to its researchers) and as regional, national and international facility (inter-institutional services).
We offer fast, reliable protein purification services. Our expertise includes bench scale purification, process development, scale-up, and validation. We have modern GE chromatography systems for bench and pilot scale. We are a terrific team of scientists from industry and academia that delivers only the highest quality results.
Harvard NeuroDiscovery Center - NeuroBehavior Laboratory
Harvard NeuroDiscovery Center NeuroBehavior Laboratory Core
Core facility that provides the following services: Surgery/necropsy service. Mouse models have become a popular and successful approach to elucidating the physiological and pathological roles of individual genes and are truly crucial to accelerate the development of effective treatments and cures for Alzheimer' '''s, Parkinson' '''s, ALS, MS and other neurodegenerative diseases. The increasing demand for mouse behavioral studies within the neuroscience community has led the Harvard NeuroDiscovery Center to develop a major new, state of the art mouse behavior laboratory, located in the Longwood medical area and carefully designed to meet the exacting standards required for this type of work. The NeuroBehavior Laboratory (NBL) will provide the Harvard community and other investigators access to a broad range of reliable behavioral/cognitive tests necessary to analyze and interpret the impact of a genetic, surgical or pharmacologic manipulation on specific behaviors. They can provide: * Assistance with experimental design. * Support for grant applications that have a significant component of mouse neurobehavioral research. * Full, fee-for-service, mouse behavioral testing services. * Training in all aspects of mouse neurobehavioral testing. * Assistance with data analysis and interpretation.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 19,2024. Specializes in de novo Synthetic Chemistry, Medicinal Chemistry, Targeted Library Synthesis, and Chemical Method Development. Our team of Ph.D. chemists has more than 100 years combined academic and pharmaceutical experience with multistep achiral and chiral synthesis. Capabilities currently include solution phase and solid phase chemistry ranging from mg to kilogram scale quantities. We provide separation and isolation of chiral and achiral molecules using Supercritical Fluid Chromatography (SFC). Our current analytical capabilities available for chemistry support include SFC, GC, LC, LC/MS, and NMR. We currently use state-of-the-art JASCO SFC equipment for chiral and achiral separation method development and small molecule isolations. We offer Synthetic Chemistry, Medicinal Chemistry, Pharmaceutical Intellectual Property Consulting, Chromatography Consulting, and Spectroscopic Consulting services for non-GMP applications. Our company currently provides solutions to clients in the flavors, fragrances, beverages, foods, fine chemical, and petrochemical industries. Contact us for your synthetic chemistry and medicinal chemistry needs. Price quotes are available on request.
University of California Berkeley Brain Imaging Center
University of California Berkeley Henry H. Wheeler Jr. Brain Imaging Center
The Henry H. Wheeler, Jr., Brain Imaging Center is one of four Technology Centers under the auspices of the Helen Wills Neuroscience Institute. It is a campus-wide resource that supports advanced brain imaging technologies dedicated solely to basic brain research.
University of Minnesota - Twin Cities Labs and Facilities
University of Minnesota - Twin Cities Labs & Facilities
Moffitt Cancer Center Small Animal Imaging Laboratory Core Facility
H. Lee Moffitt Cancer Center and Research Institute Small Animal Imaging Laboratory
H. Lee Moffitt Cancer Center and Research Institute Small Animal Imaging Laboratory (SAIL)
Moffitt Cancer Center Small Animal Imaging Laboratory (SAIL)
Small Animal Imaging Laboratory (SAIL) Core
Core provides advanced and affordable multi-modality imaging services including consultation, imaging and image analysis for both basic and translational research. Offers instrumentation including 7T MRI, multimodal PET/SPECT/CT, ultrasound and optical modalities. Used to evaluate tumor development, progression, metastasis and therapy response in rodent models of cancer including development of imaging biomarkers, contrast agents and tumor targeting agents, evaluating tumor metabolism and microenvironment, and high-resolution anatomical imaging of human specimens.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024.
Welcome! HTL Biosolutions, Inc. is a California based biotech service company, and was founded by former Amgen director and scientist. Our company founders have extensive experience in the development of protein therapeutics in biotech industry. Our Mission At HTL Biosolutions, Inc., our mission is to provide high quality contract research services to our clients who are engaged in developing protein therapeutics by employing innovative biotechnologies. We specialize in the areas of molecular biology including customized preparation of plasmid DNAs, bio-analytical such as amino acid and vitamin analysis, and protein stability analysis, structural characterizations.
LaboSpace is a laboratory service provider with branches in UK and Italy operating in the area of Immunology, Cancer Research, Neuroscience, Cardiovascular Disease, Endocrinology and Target Therapy application. LaboSpace services for the research market cover IHC validation, Multiplex IHC, Luminex and Elisa assays platform, DNA/RNA large HTS extraction. In May 2011 LaboSpace was granted by the Local Government of the accreditation as Diagnostic laboratory. Currently applying for ISO9001:2008 and ISO13485
ProGen - Protein & Gene Engineering specializes in custom molecular biology services including DNA cloning, sub-cloning, codon optimized artificial gene synthesis, site-directed mutagenesis and large scale custom projects such as DNA isolation and purification. The custom products of the company are used for gene engineering to study gene expression regulatory mechanisms, protein engineering, and analysis of gene and protein function. Customers of the company include research laboratories in academia, clinical researchers in medical institutes and biotechnology companies. In addition to our custom cloning services, as an authorized Israeli representative of SBS Genetech Co., we market molecular biology products of SBS at competitive prices. SBS is one of the largest sources of synthetic oligonucleotides. The range of the products cover biochemicals, enzymes and PCR products. As a young company we are highly motivated to deliver high quality services and products at lowest prices with a rapid schedule of delivery. We guarantee full customer satisfaction on all products and services.
Michigan State University RTSF Genomics Core Facility
Michigan State University Research Technology Support Facility Genomics Core
Michigan State University RTSF Genomics Core
RTSF Genomics Core offers services for investigators looking to utilize gene expression for their research. Our range of applications includes solutions for quantifying gene expression levels in nearly any species regardless of sample size. Services include Next Generation Sequencing using Illumina instruments, qPCR using the ABI QuantStudio 7 Flex Real-Time PCR System, and gene expression using NanoString nCounter system.
We provide custom synthesis of peptides and peptide conjugates.
University of Texas Southwestern Electron Microscopy Core Facility
University of Texas Southwestern Medical Center at Dallas Electron Microscopy Core
University of Texas Southwestern Medical Center Electron Microscopy Core
UT Southwestern Electron Microscopy Core
UT Southwestern Medical Center Electron Microscopy Core
Provides transmission and scanning electron microscopy, as well as other services, including correlative light and electron microscopy and immunogold labeling. Offers TEM of cells and tissues, negative staining, whole-mount SEM, correlative LM and EM, and immunogold labeling.
New York University Langone Medical Center Histopathology Core
Both animal model and clinical research require the production of high quality tissue samples for morphological and molecular analyses. The NYU Histopathology Core, one component of the Experimental Pathology Shared Resources provides?_services, instrumentation and training to facilitate the generation of these critical materials. Services offered by the Histopathology Core include: tissue preparation, processing, embedding, sectioning, histochemical staining, digital whole slide scanning, and laser capture microdissection of both animal and fixed human tissues. The Histopathology Core also makes available several instruments for investigator use on a self-serve basis. This option is valuable for researchers who wish to direct certain stages of specimen preparation and is more cost-effective in some cases. Available instrumentation includes a state-of the-art Laser Dissection Microscope, a microtome, a cryostat and a microscope fitted with a digital camera. Training is provided by Core staff. The components of pricing for each service include the cost of consumables, the cost for technician time for each service, and a small percentage of any associated service contracts. As with many of our services, the incremental cost of each procedure is affected by overall volume; as volume increases, we pass the resulting savings on to users in the form of reduced prices.
Independent Contractor - Computational and Mathematical Modeling
Independent Contractor - Computational & Mathematical Modeling
As our expertise is in computational/mathematical modeling, all deliverables should be sent through email (baf702(at)gmail.com) or cloud-based storage such as Dropbox. This will be discussed with each client on an individual basis to fit their needs.
University of California Los Angeles GenoSeq Core Facility
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 23, 2019. Core is involved in a broad range of scientific research. Medical research performed at the GenoSeq Core includes studies of human neurological disorders, such as: autism, bipolar disorder, and epilepsy; cancers of breast, colon, lung, and prostate; cardiac disease; and digestive disorders. Core also carries out studies of the genetics of non-human organisms. The GenoSeq Core is closely linked to the UCLA Bioinformatics Core in Gonda Center, which provides the computing power and sophisticated software needed to analyze and interpret the unprecedented volume of genetic data being generated with modern laboratory automation.
University of Pittsburgh Department of Ophthalmology Tissue Culture and Histology Module Core Facility
University of Pittsburgh School of Medicine Tissue Culture and Histology Module
University of Pittsburgh Tissue Culture & Histology Module
Core offers Tissue Culture Services including Basic Cell Culture, Specialized Culture Services, Virus Services; Histology Services including Paraffin Histology, Frozen Histology, Monolayers,Personnel Training and more.
University of Minnesota Genomics Center Core Facility
University of Minnesota Biomedical Genomics Center
Provides genomic technologies and services to researchers and clinicians. Services include Next Generation Sequencing, Epigenomics, SARS-CoV-2 services, GBS, Third Generation Sequencing, NGS Library Creation, Sanger Sequencing, DNA and RNA Extraction, Gene Expression.
Childrens Hospital Boston Intellectual And Developmental Disabilities Research Center - Molecular Genetics Core
Children''s Hospital Boston IDDRC - Molecular Genetics Core
Children''s Hospital Boston Intellectual And Developmental Disabilities Research Center - Molecular Genetics Core
Children?s Hospital Boston Intellectual and Developmental Disabilities Research Center - Molecular Genetics Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 8,2024. An Core facility
University of Delaware Animal and Food Sciences Department
We offer a wide range of disciplines including virology, physiology, nutrition, microbiology, immunology, molecular biology, engineering, and genomics. Our research addresses contemporary and future scientific challenges by using cutting edge technologies with the goal of assisting stakeholders in the poultry, livestock, and food industries.
Core is a nonprofit research institute that applies bioinformatics, software engineering and next-generation sequencing. Equipped with Illumina and PacBio instrumentation, our sequencing capabilities include genome, transcriptome, methylome, ChIP, small RNA, and exome sequencing, with corresponding analytical capabilities. NCGR provides researchers with experimental design assistance, custom data analysis, and data visualization.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2024. We are an innovation company reducing the risk in technology development and commercialization. We promote growth by research and development. Our team has 100 man years of experience and 50 issued US patents. We work with technology intensive businesses to help them take their idea to the next level. We partner with our clients to develop new products, manage innovation pipeline, build prototypes from patent portfolios and develop proof-of-concept of an idea. At Nayam Innovations, we strive to greatly reduce development time, cut down cost for productization while enabling enrichment of our client''s IP.
After more than a decade of experience in the sale and marketing of research products for Life Science Research, Werner Hassler, Switzerland and Gunther Jaeger, Germany founded the Cologne based BIOTREND Chemikalien GmbH in May 1988. BIOTREND was instigated in order to meet the growing demand from customers for an independent and technologically orientated distribution facility offering high quality, yet cost-effective products for biochemical, immunochemical and pharmaceutical research. Through our innovative strength we are not only providing our customers a vast product range, but also a high quality, first-class service package. At present we offer more than 90.000 products that have successfully been implemented not only in the drug discovery market, but also in cancer research as well as other scientific fields.
German research awards.Central self governing research funding organisation in Germany. Serves sciences and humanities and promotes research at universities and non-university research institutions. The focus is on funding projects developed by academic community.
University of Georgia Bioexpression and Fermentation Core Facility
UGA Bioexpression and Fermentation Facility
UGA Bioexpression and Fermentation Facility (BFF)
University of Georgia Bioexpression and Fermentation Facility
University of Georgia Bioexpression and Fermentation Facility (BFF)
BFF consists of Fermentation Research Facility, Protein Purification Facility, Monoclonal Antibody Facility and Cell Culture Facility. Provides services covering wide range of biomanufacturing areas, protein expression, purification and antibody discovery.Provides equipment and expertise in biotechnological applications to academic and industry clients.
UT Southwestern CRI Flow Cytometry Shared Facility
University of Texas Southwestern Medical Center at Dallas CRI Flow Cytometry Shared Facility
University of Texas Southwestern Medical Center CRI Flow Cytometry Shared Facility
UT Southwestern Medical Center CRI Flow Cytometry Shared Facility
The UT Southwestern CRI Flow Cytometry Shared Facility is a GLP certified lab.
Contract research organization that performs IHC detection of antigens in tissue and cell samples. Some target antigens are difficult-to-detect because of various reasons. We offer the following quality IHC services with the primary antibodies provided by customers: -Primary antibody selections -Formalin fixed paraffin embedded (FFPE) tissue sample sectioning -Processing condition optimizations -IHC single or double staining (colorimetric or fluorescent) FFPE slides TMA slides -IHC data analysis
Penn State Cancer Institute Organic Synthesis Core Facility
Penn State Organic Synthesis Core Facility - Hershey Cancer Center
Core to advance scientific impact of Penn State Cancer Institute investigators by synthesizing and providing chemical agents that are either not commercially available or cost-prohibitive, to facilitate ongoing cancer research. Assists in efforts towards discovering novel agents for treatment and prevention of cancer. Supports activities of development and synthesis of anticancer agents, chemical carcinogens, their detoxification products, reactive species of metabolic activation and DNA adducts formed with such species. Services also include identification and synthesis of biomarkers of uptake and activation of environmental carcinogens that require deuterated, tritiated, and 14C-labeled isotopes.
Massachusetts General Hospital Microscopy Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22, 2024. Core facility
UMD Sequencing Core - Institute of Bioscience and Biotechnology Research
UMD Sequencing Core - Institute of Bioscience & Biotechnology Research
University of Maryland Institute of Bioscience & Biotechnology Research Sequencing Core
University of Maryland Institute of Bioscience and Biotechnology Research Sequencing Core
University of Maryland Sequencing Core - Institute of Bioscience & Biotechnology Research
University of Maryland Sequencing Core - Institute of Bioscience and Biotechnology Research
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 24,2024. IBBR DNA Sequencing Facility currently offers its customers NextGen sequencing.
Core provides molecular biotechnology services and current molecular genetic methods. Services include DNA and RNA Extraction, transgenic mouse genotyping, Human Cell line Authentication, Sanger DNA Sequencing, Next-Generation sequencing platforms, Microsatellite DNA Typing, Agena multiplex SNP Genotyping, Real-time PCR, NanoString Gene Expression Analysis. Specializes in custom workflows that couple services with specific research needs.
UNC School of Medicine Center for Structural Biology
University of North Carolina at Chapel Hill School of Medicine Center for Structural Biology
The CSB provides an integrated platform of expertise, infrastructure and education to foster a wider use of structural biology by the UNC community. The CSB mission is to make structural biology available as a general tool to any researcher. Structures of macromolecules at atomic resolution have helped to revolutionize modern biology. Structural insight is often crucial for understanding the functions of biological macromolecules, including their interactions with small ligands (such as substrates, inhibitors, drugs) and other macromolecules (nucleic acids and/or proteins). Consequently, structural biology represents one of the pillars of basic biomedical research; it is indispensable for deciphering the details of life processes and for understanding the differences between natural and diseased states. Building on such insights, structural biology can assist in devising novel therapies, e.g., through structure-based or structure-aided drug design. The enormous information content available in high-resolution, three-dimensional structures has sparked the desire of non-structural biologists to examine the structures of the macromolecules that they study. Structural biology is technically demanding, and it requires highly specialized expertise. The CSB removes or reduces these barriers that usually prevent general researchers from engaging in structural biology-based projects by themselves.
University of Texas Southwestern Genomics and Microarray Core
Core provides access to next generation sequencing (NGS) to investigators at UT Southwestern, at other institutions in the UT System, and at additional cost to investigators outside of the UT system. Core can receive flow cell ready samples (sequencing libraries that are prepared by the user) or perform sequencing library production for genomic libraries, RNA-SEQ applications, and small RNA (microRNA) applications. Data output routinely will provide de-multiplexing and alignment to the genome of choice using a variety of assembly and analysis programs, including CLC-Biosystems workbench, a BWA-GATK-Genotyper pipeline, a BowTie-Top Hat analysis pathway, and the Illumina ELAND DNA sequence aligner. Limited access to post sequence data analysis software is also available through the core, including both CLC-Biosystems (2 floating licenses available for on campus users) and the Genome Studio software packages.
University of North Carolina Lineberger Comprehensive Cancer Center Tissue Culture Core Facility
UNC School of Medicine Tissue Culture Facility
University of North Carolina at Chapel Hill School of Medicine Tissue Culture Facility
Supply center and provides UNC Lineberger members and UNC colleagues with tissue culture products including stocks media, media supplements, serum, salt solutions, antibiotics, cell culture flasks and dishes, and many other in vitro cell culture and molecular biology-related items, kits and cell lines. Cell lines include normal and transformed mammalian, avian, insect, amphibian/reptile, and hybridoma cells. Services include checking Fetal Bovine Serum for quality and efficacy. TCF partners with Genetica Cell Line Services to offer qPCR-based Mycoplasma contamination testing for cell or DNA samples. Utilizes Genetica Cell Line Services for STR profiling of cell lines.
Core provides services to its partners in deploying genomic capabilities to bring critical solutions to both agriculture and industrial biotech operations. Core facility also provides assistance to research, biotech/pharma and government facilities. In addition to being an Agilent Certified Service Provider MOgene is also a CLIA certified genomics service facility offering one stop service and solution from Tissue/Cells to Analysis. Core offers RNA/DNA isolation, Microarrays, NextGen sequencing, Real time PCR and bioinformatics services.
Stellenbosch University Labs and Facilities
Stellenbosch University Labs & Facilities
Department of Animal Sciences houses well-equipped laboratories, and has access to animal facilities and two experimental farms that are used for both undergraduate training and postgraduate research. Collaboration with the Western Cape Department of Agriculture, other tertiary institutions, non-governmental organisations and the private sector is maintained by the Department of Animal Sciences to ensure that research is current and relevant to the various animal production industries.
Core aims to empower research institutes and private companies in the fields of bioinformatics, biostatistics, biotechnologies, data management and R&D. Core is organized into four specialized divisions: Sequentia Green, Sequentia Health, Sequentia Research, and Sequentia Training.
University of Texas at Arlington Genomics Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 17,2024. Independent contract laboratory. Its services include deformulation and reverse engineering, contaminant identification, purification, and component isolation from complex matrices.
Sanford-Burnham Histology Core Facility at Lake Nona
Sanford Burnham Medical Research Institute Histology Core Facility at Lake Nona
Sanford-Burnham Medical Research Institute Histology Core Facility at Lake Nona
Sanford-Burnham Histology Core at Lake Nona
The Histology Core at Lake Nona is a full-service shared resource facility that provides histological services to Sanford-Burnham researchers and investigators throughout the scientific community. The Core offers technical support, consultative, and interpretive pathology to all investigators. Tissue samples are processed with the highest industry quality standards, using state-of-the-art instrumentation. The Core also assists with experiment design as well as the development and interpretation of tests and their results. Sanford-Burnham' '''s Histology Core at Lake Nona is committed to collaborating with investigators and advancing research by carrying out critical tissue specimen validation and evaluation. Equipment and Resources: - Thermo Excelsior ES Tissue Processor - Thermo Histocentre_������������������������ 3 Embedding Unit - Thermo Cytospin 4 - Thermo Microm HM355S Microtome - Thermo Printmate 450 Cassette Printer - Thermo Microm HM550 Cryostat - Thermo Microm HM650 V Vibratome with cooling unit - Thermo Microm HM450 Sliding Microtome with freezing unit - Leica IP S Slide Printer - Leica RM2235 Microtome - Leica 1900UV Cryostat - Nikon Eclipse 80i Microscope with AR Elements imaging software - Ventana Discovery XT - Tissue-Tek?? Prisma Automated Slide Stainer and Glas_������������������������ g2 Coverslipper - Aperio ScanScope XT-Brightfield - Aperio ScanScope FL-Fluorescence
Evaluations at the tissue level are critical to musculoskeletal research. The Bone Histomorphometry Lab in the Department of Orthopedics has a rich history of conducting such in situ evaluations in both human and animal tissue. The primary expertise of the Bone Histo Lab is the processing of skeletal tissue in its calcified state for the preparation of histology slides.
A commercial contract research organization that mentions embryo culture media for IVF procedures and cell therapy on their website.
WUSTL School of Medicine Embryonic Stem Cell Core
WUSTL School of Medicine Murine Embryonic Stem Cell Core
The Murine Embryonic Stem Cell Core has been created to help you create mutations in murine embryonic stem cells. The core has several missions including development of state-of-the-art reagents for the production of targeted mutations in embryonic stem cells, the creation of quality-controlled embryonic stem cell lines, and the teaching of methods for embryonic stem cell culture and manipulation. The core utilizes quality-controlled cells developed here at Washington University.
University of Mississippi Medical Center Labs and Facilities
University of Mississippi Medical Center Labs & Facilities
Dartmouth Transgenics and Genetic Constructs Shared Resource
Dartmouth Transgenics and Genetic Constructs Shared Resource (TGCSR)
Dartmouth-Hitchcock ransgenics and Genetic Constructs Shared Resource
NCCC Transgenics & Genetic Constructs Shared Resource
NCCC Transgenics and Genetic Constructs Shared Resource
Norris Cotton Cancer Center Transgenics & Genetic Constructs Shared Resource
Norris Cotton Cancer Center Transgenics and Genetic Constructs Shared Resource
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2026.Core facility that provides the following services: Cigarette smoke exposure analysis service, Oocyte injection for transgenic animal production, Transgenic mice consultation, Generation of chimeric mice from ES cells, Transgenic lines establishment, Genotyping service, Tail biopsies and other services, Humanized mice production. The mission of the TGCSR is to support the generation and utilization of genetically modified mice by members of the Dartmouth research community. The support starts with intellectual support in planning and designing transgenic experiments provided by consultation with the TGCSR director. The TGCSR is now able to offer not only assistance with design of genetic constructs but also the production of genetic constructs for use in transgenic animal production through recombineering in either yeast or E. coli. TGCSR provides a full range of ES cell manipulation services. The tasks of manipulating the mouse embryo are fully provided by the TGCSR either in house or through an established relationship with the University of Vermont. Jackson labs is now providing cryopreservation services to protect and preserve valuable transgenic mouse lines. The TGCSR can also provide genotyping and mouse husbandry services. As currently organized, the TGCSR can provide the full range of services required to design, generate and maintain transgenic mouse lines. TGCSR currently maintains two specialized transgenic lines that express Cre or Flp in the germline for genetic manipulation of transgene/knockouts in vivo. TGCSR has a fully equipped embryo manipulation laboratory in the Borwell animal facility and an adjoining 4 room suite of mouse husbandry rooms.
Montana State University Labs and Facilities
Montana State University Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2024. Portal, Core facility
PHSA Centre for Translational and Applied Genomics
PHSA Centre for Translational and Applied Genomics (CTAG)
Provincial Health Services Authority Centre for Translational and Applied Genomics
Provincial Health Services Authority Centre for Translational and Applied Genomics (CTAG)
PHSA Laboratories' ''' Centre for Translational and Applied Genomics (CTAG) is a a CAP Accredited genomics and molecular pathology core facility supported by a world class team of molecular pathologists with diverse clinical and research interests and technical skills. CTAG operates at PHSA agencies including the BC Cancer Agency, BC Centre for Disease Control, BC Children' '''s Hospital and BC Women' '''s Hospital & Health Centre. CTAG offers a broad range of analytical services to the public and private sectors. As a division of PHSA Laboratories, CTAG' '''s mission is to develop novel laboratory tests to improve the management of a diverse spectrum of disorders including cancer, infectious diseases, and inherited syndromes.
University of North Carolina at Chapel Hill Labs and Facilities
University of North Carolina at Chapel Hill Labs & Facilities
Wake Forest University Labs and Facilities
Wake Forest University Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 19,2024. Trevigen Cell Assays (TCA), a division of Trevigen, Inc., was established in 2008 to conduct contract research work for the pharmaceutical, biotechnology, government and academic segments of the medical research market. TCA specializes in designing and conducting assays for lead compounds and genotoxic screening based on DNA damage and repair as well as cancer cell behavior.
North Dakota State University Labs and Facilities
North Dakota State University Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15,2024. Portal, Core facility
University of Nebraska Medical Center Labs and Facilities
University of Nebraska Medical Center Labs & Facilities
University of Nebraska Lincoln Labs and Facilities
University of Nebraska Lincoln Labs & Facilities
Montclair University Microscopy and Microanalysis Research Laboratory Core Facility
Montclair Microscopy and Microanalysis Research Laboratory
Montclair State University Microscopy and Microanalysis Research Laboratory
MSU Microscopy and Microanalysis Research Laboratory
Interdisciplinary research, teaching and service facility equipped with scanning and transmission electron microscopes, an atomic force microscope, and the ancillary instruments. Provides microscopic imaging, X-ray analysis, and specimen preparation services for biological, pharmaceutical, and materials scientific research. The MMRL consist of four individual microscope rooms, the Histology laboratory, and sample preparation and chemical storage areas.Graduate- and upper-undergraduate-level training is offered in the operation of electron microscopes, sample preparation, and thick/thin sectioning. Currently, MMRL houses transmission electron, scanning electron microscopes, and atomic force microscope. The microscopes available for use include: - Hitachi H-7500 transmission electron microscope - Hitachi S-3400N variable pressure scanning electron microscope with x-ray analysis and digital imaging - Hitachi S-2460N scanning electron microscope with x-ray analysis In addition, the following items are also available for MMRL users: - Three Leica 2030 rotary paraffin microtome - Two LKB ultramicrotomes - A LKB 7800 glass knife maker - Leica Reichert Ultratrim - Denton critical point dryer - Denton sputter coaters (Desk II and Desk IV) - Denton Vacuum evaporators (DV-502A) - Liquid nitrogen dewars (various sizes) - A Leica stereo dissecting microscope - A Tissue-TeK VIP Tissue Processor - A Tissue-TeK II Embedding Center
University of Rochester Labs and Facilities
University of Rochester Labs & Facilities
Stony Brook University Labs & Facilities
Stony Brook University Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2024. Portal, Core facility
CWRU Athymic Animal and Xenograft Core Facility
Case Western Athymic Animal and Xenograft Core Facility
Case Western Reserve University Athymic Animal and Xenograft Core Facility
The Athymic Animal and Xenograft Core Facility provides facilities for breeding and housing of athymic nude mice (NCRnu/nu) and rats, and other immunodeficient mice. The core provides pathogen-free facilities for experimentation using immunodeficient animal hosts and normal human cells and human tumor cell xenografts. Core staff maintain and monitor animals housed in the facility, and provide users with a variety of services, including transportation, health reports, animal handling, and experimental procedures. The staff will also train users in animal handling and experimental procedures. Entry to the animal facilities is controlled by key card access and is limited to employees who are listed on an IACUC-approved protocol, have enrolled in an animal contact Occupational Health program, and have completed access training. Experimental procedures, listed below, are provided either at the Case facility or in the Animal Tumor Core (ATC) at the Cleveland Clinic Taussig Cancer Institute. The Taussig Cancer Institute ATC was established in 2002 to help principal investigators at the Cleveland Clinic and CWRU perform tumor experiments, angiogenesis studies, and pharmacokinetic studies in mice. The ATC conducts syngeneic murine tumor experiments, and human xenograft (athymic nude mouse) tumor experiments. In addition, the ATC has developed several orthotopic human carcinoma models: HT-29 colon, HCT-116 colon, SW480 colon (all metastasize to liver), ACHN renal, A549 lung, multiple prostate, bladder, melanoma and ovarian tumors. ATC services utilize murine models to facilitate in vivo cancer drug screening, drug evaluation, and drug development. The core' '''s goal is to help in evaluation of new pharmacologic agents by providing data on tumor growth, metastasis, angiogenesis, and gene expression. The facility also provides consultation services to assist the investigator in all aspects of animal tumor model development.
Case Western Reserve University Labs and Facilities
Case Western Reserve University Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 14,2024. Portal, Core facility
Ohio State University Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024. Portal, Core facility
University of Texas Medical Branch at Galveston Labs and Facilities
University of Texas Medical Branch at Galveston Labs & Facilities
Virginia Polytechnic Institute and State University Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Portal, Core facility. Unfortunately, Virginia Polytechnic Institute and State University haven't yet shared their available services. Please, try again later.
University of Nebraska Medical Center Tissue Sciences Core Facility
University of Nebraska Medical Center Tissue Sciences Facility
Core provides basic and specialized histology and immunohistochemistry support to the research community for studies on animal and human tissues. Offers full range of services including tissue preparation and fixation, processing, embedding, sectioning, and routine and special stains for paraffin and frozen samples.
University of Pittsburgh Labs and Facilities
University of Pittsburgh Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 16, 2024. Portal, Core facility
University of Pennsylvania Labs and Facilities
University of Pennsylvania Labs & Facilities
Pennsylvania State University Labs and Facilities
Pennsylvania State University Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2,2024. Portal, Core facility
University of Minnesota Bionet - Academic Health Center
University of Minnesota - Twin Cities Bionet - Academic Health Center (AHC)
University of Minnesota Bionet - Academic Health Center (AHC)
BioNet serves the University of Minnesota' '''s Academic Health Center (AHC) as a centralized biorepository and bioregistry for patient consent and for the collection, processing, and distribution of de-identified tissue samples, blood and body fluids, purified DNA and specimen-matched clinical data for research. BioNet is becoming a major translational research resource linking clinical medicine, pathology, and basic and applied research to facilitate high quality and cost-conscious clinical and translational research. BioNet leverages the strengths of the Cancer Center' '''s Tissue Procurement Facility (TPF), which has become part of BioNet. BioNet currently provides: * an optimized consenting process, * collection of tissue, blood, and fluid samples, * computerized specimen tracking systems that link -specimens to clinical data and other databases, * addition of core pathologist-supported facilities for histologic interpretation, immunohistochemistry, laser capture microdissection, and slide digitalization.
Meharry Medical College Labs and Facilities
Meharry Medical College Labs & Facilities
A portal and core facility. Contains the Meharry Proteomics core, the Meharry Bioinformatics Core, and the Molecular Biology Core.
University of Texas at Austin Labs and Facilities
University of Texas at Austin Labs & Facilities
University of Texas at San Antonio Labs and Facilities
University of Texas at San Antonio Labs & Facilities
University of Texas Southwestern Medical Center at Dallas Labs and Facilities
University of Texas Southwestern Medical Center at Dallas Labs & Facilities
University of Wisconsin - Madison Labs and Facilities
University of Wisconsin - Madison Labs & Facilities
University of Southern California Epigenome Center Data Production Facility
Core conducts genome-scale epigenetic and genetic data production and analysis, technology development, and epigenomic and population-based genomic research.
West Virginia University Labs and Facilities
West Virginia University Labs & Facilities
University of Angers Plateforme SNP Transcriptome and Epigenomics
UA Plateforme SNP Transcriptome and Epigenomics
THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 02, 2014. Core facility that plays an active role in the Loire Valley Region''s officially-accredited fields of competitive excellence: plant sciences, medicine and pharmacy, child-oriented research.
UC Davis Genome Center Labs and Facilities
UC Davis Genome Center Labs & Facilities
University of California Davis Genome Center Labs & Facilities
University of California Davis Genome Center Labs and Facilities
Genome Center uses technologies to understand how heritable genetic information of diverse organisms functions in health and disease. Provides research facilities, service cores, and staff for genomics research and training. Core facilities for Bioinformatics,DNA Technologies and Expression Analysis, Metabolomics, Proteomics,TILLING Core,Yeast One Hybrid Services Core.
A molecular pathology company that sells tissue-based diagnostic tests for personalized medicine.
Montana State University Mass Spectrometry Core Facility
Metabolomics and Mass Spectrometry Facility
Montana State University Mass Spectrometry Facility
Provides access to mass spectrometers and mass spectrometry expertise. The facility currently maintains the following equipment Waters Synapt-XS Q-IMS-TOF with Waters I-Class UHPLC; Agilent 6538 Q-TOF with Agilent 1290 UHPLC;Agilent 7800 Inductively Coupled Plasma with Laser Ablation (193 nm);Bruker micrOTOF with Agilent 1290 UHPLC; Agilent 6490 Triple Quadrupole Mass Spectrometer; Bruker MALDI Autoflex; Agilent GC-MS; Waters Synapt G2S-i Q-TOF with Ion Mobility.
University Health Network Labs and Facilities
University Health Network Labs & Facilities
University of Kansas Protein Production Group Core Facility
University of Kansas Protein Production Group
COBRE Protein Production Group focuses on the cloning, expression and purification of prokaryotic and eukaryotic proteins for COBRE and other investigators in Kansas and the region. The laboratory maintains a variety of equipment to support the production of properly folded proteins in quantities suitable for structural studies (X-ray and NMR), functional studies (catalytic or biological), label-free binding studies (SPR) and/or high throughput (HTP) screening studies.
University of Edinburgh GenePool Next Generation Sequencing and Bioinformatics
The GenePool is a next-generation genomics and bioinformatics facility based within the School of Biological Sciences, The University of Edinburgh. Which offers collaborative access to DNA sequencing, genotyping and bioinformatics capabilities, using ABI 3730 Sanger, Illumina and Roche 454 technology platforms.
University of California Davis Crocker Nuclear Laboratory
Crocker Nuclear Laboratory hosts a diverse group of research programs, nearly all of which are related to applied science programs. Constructed in the mid-sixties, CNL, houses a low energy particle accelerator. The accelerator, an isochronous cyclotron, is one of the few of this design remaining in productive operation. The Crocker Nuclear Labortory' '''s Isochronous Cyclotron began operating in 1965, accelerating protons, alpha particles, and other light ions into various targets to study nuclear structure. Instead of the uniform magnetic fields used in the earlier cyclotrons, the isochronous design employed tailored sectors with a varying magnetic field. This design compensated for increases in the mass of ions as they accelerated, both focusing their paths and keeping them in resonance at high energies. In its day, this design was considered a major technological breakthrough.
Facility offers Next-Generation Sequencing services, Sanger sequencing, Fragment Analysis, qPCR, data analysis. Provided services include DNA sequencing, fragment analysis, RNA, DNA, protein and cell cytometry through various equipment.
Southwestern University Labs and Facilities
Southwestern University Labs & Facilities
Georgetown Histopathology and Tissue Shared Resource
Histopathology and Tissue Shared Resource at Georgetown Lombardi Comprehensive Cancer Center (Georgetown University)
The HTSR offers a full complement of histology services through our combined Human Tissue Bank, histology, and IHC departments. The Human Tissue Bank supports tissue procurement and the retrieval of fresh frozen and archival paraffin blocks. The Histology laboratory provides processing, embedding and microtomy services both for fresh frozen and fixed tissues. The Histology lab also provides numerous routine and non-routine histological stains. The Immunohistochemistry (IHC) laboratory supports colorimetric and fluorescent IHC staining for established antibodies as well as the development of protocols for new antibodies. The IHC lab also supports TUNEL labeling and novel labeling techniques.
University of Edinburgh Labs and Facilities
University of Edinburgh Labs & Facilities
Boston University Microarray Resource Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22,2024. Microarray Resource Core offers the full line of microarray products available from Affymetrix. This includes expression profiling, miRNA, exon, genotyping, resequencing, and tiling arrays. As part of our standard service, the resource provides assistance with experimental design and data analysis. Arrays for other organisms are available; please contact us for with specific requests.
UM Miller School of Medicine Division of Comparative Pathology
University of Miami Leonard M. Miller School of Medicine Division of Comparative Pathology
University of Miami Miller School of Medicine Division of Comparative Pathology
The Division of Comparative Pathology is a full service veterinary pathology laboratory with both clinical pathology and histology services. Routine hematology and serum biochemistry testing is available for multiple species; we work well with low volume samples. Specialized testing is available or can be implemented as needed. Routine histology services including processing, embedding, and sectioning are available with many routine and special staining options.
University of Toledo Labs and Facilities
University of Mississippi Medical Center Animal Behavior Core Facility
UMMC Center for Psychiatric Neuroscience Rodent Behavior Core
University of Mississippi Medical Center Animal Behavior Core
University of Mississippi Medical Center Center for Psychiatric Neuroscience Rodent Behavior Core
University of Mississippi Medical Center Rodent Behavior Core
Provides tools and assistance to identify and monitor behavior in rodents. Supports basic and translational research by providing assistance with project development, technical assistance to identify and monitor behavior in rats and mice, training in techniques for analysis of animal behaviors, assisting with interpretation and presentation of data and results relating to animal behaviors.
CU Boulder Institute for Behavioral Genetics
University of Colorado at Boulder Institute for Behavioral Genetics
University of Colorado Boulder Institute for Behavioral Genetics
The Institute for Behavioral Genetics (IBG) is an organized research unit of the University of Colorado Graduate School dedicated to conducting and facilitating research on the genetic and environmental bases of individual differences in behavior. Founded in 1967, IBG is one of the top research facilities in the world for genetic research on behavior. Data collection and analysis is ongoing for several internationally renowned studies including the Colorado Adoption Project, the Colorado Twin Registry, the National Youth Survey Family Study, the Colorado Learning Disabilities Research Center, and the National Longitudinal Study of Adolescent Health. IBG is home to one of the nation' '''s largest DNA repositories for research on human behavior, as well as housing a wide array of behaviorally and genetically defined lines of selected, recombinant inbred, transgenic, and knockout-gene mice. Current research includes studies of aging ( The Johnson Lab, The Link Lab), psychopathology, reading disability, cognition, substance abuse, behavioral development, and evolution. In addition to our research, we provide training opportunities for graduate students in affiliated programs at the University of Colorado campuses in Boulder and Denver. IBG receives funding from several federal agencies, principally through the National Institutes of Health, as well as a broad spectrum of Associations, Foundations and Programs. Welcome to our site, please feel free to contact us with any questions about our research or programs.
Duke University Neurotransgenic Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15,2024. Neurotransgenic Laboratory (NTL) at Duke University conducts technology development research and provides services, tools, and training towards the genetic analysis of the nervous system. Such tools include viruses for the precise stereotactical application of transgenes, plasmids and BACs for the generation of transgenic animals, genetically modified embryonic and induced pluripotent stem cells for differentiation and transplantation studies as well as for the generation of genetically modified animals.
Core provides whole genome to focused set gene expression and genotyping assays along with DNA sequencings services, sequence enrichment technologies and bioinformatics support. Platforms utilized include Affymetrix GeneChip, Agilent Sure Select, Fluidigm Access Arrays, Illumina BeadChip, iScan, Genome Analyzer and Hi-Seq, RainDance Technologies RDT 1000 and, the Pacific Biosciences PacBio RS. Expression Analysis offers solutions for challenging specimens such as whole blood and FFPE tissues, as well as nucleic acid isolation and data analysis services.
Georgetown Genomics and Epigenomics Shared Resource
Georgetown Genomics & Epigenomics Shared Resource (GESR)
Georgetown Genomics and Epigenomics Shared Resource (GESR)
Georgetown University Georgetown Lombardi Comprehensive Cancer Center Genomics and Epigenomics Shared Resource
The Genomics & Epigenomics Shared Resource (GESR) provides services for various high throughput experiments including gene expression profiling, SNP genotyping, CNV analysis, DNA methylation, microRNA expression profiling, siRNA screening, DNA/RNA isolation, RNA quality assessment, DNA plating and assay preparation, DNA sequencing, and fragment analysis. GESR uses state-of-the-art instruments and assays to provide these services. These include Affymetrix Microarray System, Agilent Microarray System, Applied Biosystems TaqMan assays, Illumina BeadXpress, Qiagen PyromarkMD, Qiagen Qiacube, Agilent Bioanalyzer, Beckman Multimek NXP Robotic Liquid Handling System, and Applied Biosystems Sequence Analyzer. In addition, GESR houses several user-operated specialized instruments for which the shared resource personnel provide technical support and training.
Emory University School of Medicine Rodent Behavioral Core
One of the Emory Integrated Core Facilities (EICF), is supported by Emory University School of Medicine and the Georgia Clinical and Translational Science Alliance. We plan, execute, and analyze behavioral experiments examining activity, arousal, coordinated movement, learning and memory, anxiety, depression, seizure susceptibility, reward/reinforcement, and aggression in mice and rats.
UMMS Proteomics and Mass Spectrometry Facility
UMass Medical School Proteomics and Mass Spectrometry Facility
University of Massachusetts Medical School Proteomics and Mass Spectrometry Facility
The University of Massachusetts Medical School Proteomics and Mass Spectrometry Facility is an analytical laboratory resource offering state-of-the-art proteomic, lipid, and small molecule mass spectrometric analyses to both the academic and external scientific community. This includes resources for study design, sample preparation and cleanup, sample fractionation, instrumentation, informatics, data interpretation, and publication assistance.
Tufts University offers a wide range of facilities, tools, and services available to researchers at Tufts and beyond. A core facility is a facility that performs specific technical services, primarily for the internal research operations of the University and affiliated Medical Centers, and charges users for its services, or are free to investigators as they are paid for by another funding source.
University at Albany Center for Functional Genomics DNA Microarray Core Facility
University at Albany DNA Microarray Core Facility
UAlbany CFG DNA Microarray Core Facility
Core provides microarray services for Affymetrix GeneChip arrays, Agilent microarrays, NimbleGen microarrays and custom-produced spotted cDNA microarrays. Projects developed through DNA Microarray Center have made use of arrays from variety of genomes, eukaryotic, prokaryotic, and plant. Core services includes RNA/DNA isolation, gene expression, miRNA, Chip-chip, Rip-chip and DNA methylation services. Provides bioinformatics tools for further analysis of results of expression experiments.
DKFZ Genomics and Proteomics Core Facility
German Cancer Research Center (DKFZ) Genomics and Proteomics Core Facility
German Cancer Research Center Genomics and Proteomics Core Facility
The core facilities at DKFZ are undergoing a restructuring and consolidating phase to adopt the new requirements and to provide high quality, up-to-date service. The focus is upon steadily improving service offers and the establishment of novel technologies to enable investigators to address the scientific questions in cancer.
Dana-Farber Cancer Institute Monoclonal Antibody Core Facility
Monoclonal Antibody Core Facility (DFCI)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2024. Monoclonal Antibody Core at Dana-Farber Cancer Institute produces novel monoclonal antibodies for use in basic research, drug discovery, and clinical applications including diagnosis, surrogate markers for disease status, response to therapy, and drug toxicity. Services include cloning and scale-up of immunization antigens to purification of the resulting antibodies. Researchers can choose to have all phases of antibody production conducted by the core or perform particular steps in their own lab. Services -Consultation on design of antigens and screening strategies -Production of vectors and protein with appropriate tags for immunization and screening -Immunization of animals including mice, rats and hamsters -Generation of monoclonal antibodies -Customized screening by WB, ELISA, flow cytometry -Antibody isotyping, titering, and specificity evaluation -Small, medium, and large-scale antibody production -Purification of antibodies -Antibody productivity assessment -Cryopreservation and recovery of hybridomas from liquid nitrogen -Hybridoma banking -Adaptation of hybridomas to serum-free media -Mycoplasma testing for hybridomas and other cell lines
University of Vermont Center of Biomedical Research Excellence (COBRE) in Neuroscience Cellular and Molecular Biology Core
University of Vermont Center of Biomedical Research Excellence in Neuroscience Cellular and Molecular Biology Core
UVM COBRE in Neuroscience Cellular and Molecular Biology Core
This is a free facility for everyone at the University of Vermont; however, preference will be given to the principle investigators listed on the COBRE grant, followed by members of the neuroscience community and finally, the university as a whole. Check in advance when planning experiments to determine space and equipment availability.
ArtforScience helps faculty and scientists communicate their research data for grants, talks, publications, posters, or websites. The illustrations and schematics of biological data have appeared in many of the widely-used textbooks and scientific journals. Our work has been featured on the covers of Cell, Science, and Nature, among others.
University of Chicago Flow Cytometry Core Facility
Flow Cytometry Facility at the University of Chicago is committed to providing the highest quality services to all its investigators.
UAB Center for Biophysical Sciences and Engineering
UAB Center for Biophysical Sciences and Engineering (CBSE). University of Alabama at Birmingham Center for Biophysical Sciences and Engineering
University of Alabama at Birmingham Center for Biophysical Sciences and Engineering (CBSE)
Since 1986, The Center for Biophysical Sciences and Engineering (CBSE) has integrated our strengths to become a leading structural biology center capable of embracing the _������������_genes to drug_���� paradigm. We are one of the world' '''s largest Structure Based Drug Discovery facilities with over 110 employees, including 15 Ph.D. level crystallographers. The CBSE is centered on a suite of integrated high throughput laboratories allowing us to offer a cost-effective platform of discovery services designed to increase the efficiency and success for drug discovery projects with industry, academic and government partners.
University of Kansas Nuclear Magnetic Resonance Laboratory Core Facility
KU Nuclear Magnetic Resonance Laboratory
University of Kansas Nuclear Magnetic Resonance Laboratory
Nuclear Magnetic Resonance Laboratory is responsible for maintaining the high field NMR spectrometers, training users, providing spectra on a service basis, and assisting users with design, execution, and interpretation of NMR experiments. Our capabilities extend from small molecules to isotopically enriched proteins, semisolids, and flow samples. We are part of the Molecular Structures Group (MSG) at KU, a campuswide facility encompassing NMR, MS, X-ray Crystallography, Biochemical Service, and Molecular Graphics and Modeling Laboratories.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15, 2024. Molecular physio-chemical processes in metabolism and medicine. Development of novel spectroscopic and chemometric tools for investigating human disease and toxicological mechanisms. Metabolism-driven top-down systems biology and modelling of complex system failure. Personalised healthcare through metabolic phenotyping. Surgical metabonomics, real-time diagnostics and integrative patient modelling.
Oregon Health & Science University Gene Microarray Shared Resource
Oregon Health & Science University Gene Microarray Shared Resource (GMSR)
Oregon Health and Science University Gene Microarray Shared Resource
Oregon Health and Science University Gene Microarray Shared Resource (GMSR)
OSHU Gene Microarray Shared Resource (GMSR)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. The OHSU Gene Microarray Shared Resource (GMSR) functions as a full-service genomics facility serving research scientists and clinicians with DNA microarray services for RNA expression profiling and DNA variation analysis on two microarray platforms, Affymetrix and Illumina. Support for RNA isolation and RNA/DNA quality assessment also available
University of Queensland Facility for Advanced Bioinformatics
University of Queensland QFAB Bioinformatics
University of Queensland Queensland Facility for Advanced Bioinformatics
Core facility providing support in bioinformatics, biostatistics and biodata to life sciences and health researchers across Queensland and beyond. Services include microarrays, next generation sequencing and proteomics profiling, biostatistical support from design of experiments, to analysis and interpretation, help High Degree Research students and Early Career Researchers in management, mining and visualization of small and big data, leveraging the cloud and hpc research infrastructure powered by the Queensland Cyber Infrastructure Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University of California Berkeley Labs and Facilities
University of California Berkeley Labs & Facilities
Tulane University School of Medicine Labs and Facilities
Tulane University School of Medicine Labs & Facilities
Tulane School of Medicine Labs & Facilities
Tulane School of Medicine Labs and Facilities
Oregon Health and Science University Labs and Facilities
Oregon Health & Science University Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5, 2022. An Portal, Core facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2024. Whether you need to analyze large data sets or deploy a cloud, building big infrastructure is a big job. StackIQ makes the job easier by offering a comprehensive software suite that automates the deployment and management of big infrastructure.
Wayne State University Applied Genomics Technology Center
Wayne State University Applied Genomics Technology Center (AGTC)
WSU Applied Genomics Technology Center (AGTC)
The Applied Genomics Technology Center (AGTC), a part of Wayne State University School of Medicine' '''s Department of Obstetrics and Gynecology, is an exceptional research support core facility located on campus. Housed on the ground floor of the C.S. Mott Center for Human Growth and Development, the AGTC is a state-of-the-art, fee-for-service genomics center that provides a wide range of genomic technologies to the medical research community. In addition to instrumentation, AGTC personnel are available to work with investigators to optimize experiments to meet their scientific goals.
SUNY Upstate Medical University Labs and Facilities
SUNY Upstate Medical University Labs & Facilities
School of Medicine at Stony Brook University Medical Center Labs and Facilities
School of Medicine at Stony Brook University Medical Center Labs & Facilities
School of Medicine at SBU Medical Center Labs & Facilities
School of Medicine at SBU Medical Center Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22,2024. Portal, Core facility
Newcastle University Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15,2024. Portal and core facility. Contains the Bioinformatics Support Unit.
Imperial College London Labs and Facilities
Imperial College London Labs & Facilities
Vancouver Prostate Centre Labs and Facilities
Vancouver Prostate Centre Labs & Facilities
Provincial Health Services Authority Labs and Facilities
Provincial Health Services Authority Labs & Facilities
Our mission is to provide our clients with the highest possible level of professional service in helping them design cloning and molecular biology solutions. Use our services to generate: -Constructs for bacterial and mammalian protein expression as well as in vitro transcription and translation -Chimeras, epitope tags, protease restriction sites, and other protein and vector modifications -Constructs for transgenic animals -Viral expression constructs -Promoter-luciferase constructs -siRNA constructs -Primer design -Project consultation
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 24,2024. Since 1998, RiNA GmbH is engaged in the field of biotechnology and has strengthened its position on the market in research, product development and production.
Base Pair Biotechnologies offers its customers a total solution for developing novel aptamer-based technologies. In addition to our numerous institutional customers, we support companies developing products ranging from: basic research detection, to clinical diagnostics, to therapeutic lead development. Our platform technology is a patent pending, multiplexed approach to aptamer discovery. This allows us to offer de novo aptamer discovery services at unprecedented speed and throughput. Our expertise in aptamer and related assay development allows us to support our customers in a wide range of novel applications.
University of Texas at Austin Texas Advanced Computing Center
University of Texas at Austin Texas Advanced Computing Center (TACC)
UT Austin Texas Advanced Computing Center
UT Austin Texas Advanced Computing Center (TACC)
Texas Advanced Computing Center (TACC) at The University of Texas at Austin is one of the leading centers of computational excellence in the United States. Located on the J.J. Pickle Research Campus, the center' '''s mission is to enable discoveries that advance science and society through the application of advanced computing technologies. To fulfill this mission, TACC identifies, evaluates, deploys, and supports powerful computing, visualization, and storage systems and software. TACC staff help researchers and educators use these technologies effectively, and conduct research and development to make these technologies more powerful, more reliable, and easier to use. TACC staff also help encourage, educate, and train the next generation of researchers, empowering them to make discoveries that change the world.
We are a not-for-profit scientific research corporation founded in 2010. The mission of the Baker Mountain Research Corporation has three complementary aspects: to advance scientific knowledge, to develop science-based solutions to local and global challenges, and to foster scientific education. A particular challenge we seek to address is the lack of scientific career and educational opportunities in our region. We work to build an interdisciplinary community that facilitates synthetic and analytic exploration, mentorship, sharing of experiences and which provides fair financial support.
Our project team is made of molecular biology scientists from both academia and industry. We have been working on basic research projects as well as product development and commercialization for more than twenty years. Over the years, we have been developing know-hows in the art of molecular biology technologies besides mastering basic techniques, which significantly improve the efficiency and success rate of the projects.
BioinfoTools is an independent consultancy built on a joint background in computer science and biology. Customers are assisted in developing a bioinformatics strategy through consulting, software development and data analysis services, working from their biological aims. Work can be carried out at the customers site, whether local or international. Studies on all types of biological data are invited. Specialist computational and biological background is available for studies of epigenetics and chromatin structure, protein-DNA (or protein-RNA) interactions, as well as protein sequence, structure and function studies and genomics. Original methods can be developed to exploit your particular dataset or solve your particular problem. Lines of work can include all of (but need not be limited to): Data analysis, Software development, including original algorithms, Training, advice, assessment, reviews & documentation, Web site development and hosting scientific databases.
Lifewizz is creating solutions that facilitate discovery in Life Sciences. Our strong partnerships with experimental groups provide us a 360??????? view on the current challenges and an early perception of arising demands. By keeping collaboration intrinsic to the whole product lifecycle we leverage the pragmatic and innovative aspects of our solutions. It was not by chance that we developed the first web-based collaborative environment for reconstructing metabolic networks.
Advanced Peptides, Inc. is an experienced global manufacturer of custom peptides and PNA''s. Our scientists have synthesized products for the scientific community for over 25 years and have met the highest standards of quality, service, and technical expertise. Advanced Peptides specializes in both Custom Peptide Synthesis and Custom Peptide Nucleic Acid (PNA) synthesis using Solid Phase Peptide Chemistry to manufacture Peptides and PNAs. Our services include a wide spectrum of peptide related chemistry: -Synthesis -Purification -Modification -Analysis & Characterization Our manufacturing facilities are state-of-the-art, implementing proven technologies to produce peptides and PNA''s with reliability, integrity, and value. We give the highest attention to quality, which in turn gives researchers the tools they need to succeed in their work.
Louisiana State University AgCenter Biotechnology Laboratory
LSU AgCenter Biotechnology Laboratory (ABL)
The LSU AgCenter Biotechnology Laboratory (ABL) is a core facility that provides basic and applied research expertise to support researchers in the LSU system as well as those in other academic institutions and industry. The ABL was formed in 1998 to provide support to faculty in performing biomolecular research. In 2010, the ABL was merged with the Protein Facility in LSU' '''s College of Basic Sciences. Today, the ABL consists of three units: the Protein Facility, the Plant Transformation Facility and the Animal Cell Culture Facility.
LSU Pennington Biomedical Research Center Labs and Facilities
Louisiana State University Pennington Biomedical Research Center Labs & Facilities
Louisiana State University Pennington Biomedical Research Center Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2,2024. Opened in 1988, the Pennington Center now houses 53 laboratories that span the Center' '''s three programs - Basic Research, Clinical Research, and Population Science - nineteen Core Service laboratories, inpatient and outpatient clinics, a research kitchen, an administrative area, and more than $20 million in technologically advanced equipment. The Center was expanded in 1993 to include the C.B. Pennington Jr. Conference Center, now the C.B. Pennington Jr. Building, residence apartments, and an exercise and fitness facility. More than 80 faculty members and over 600 physicians, scientists, and support personnel focus their research efforts on 10 research program areas: Epidemiology and Prevention, Physical Activity and Health, Cancer, Diabetes, Obesity, Neurodegeneration, Genomics and Molecular Genetics, Stem Cell and Developmental Biology, Neurobiology, and Nutrient Sensing and Signaling. The Pennington Center is led by Dr. Steven B. Heymsfield, formerly of Merck Pharmaceuticals, who specializes in clincal research. The Center' '''s funding is broad-based. The foundation is provided by an annual appropriation from the State of Louisiana. Additional funding is provided by grants and contracts from the National Institutes of Health, the U.S. Department of Agriculture, the U.S. Department of Defense, and private sector organizations and companies. The Pennington Medical Foundation and Pennington Biomedical Research Foundation are also major financial resources. The Pennington Medical Foundation is charged with administering the original donation and subsequent gifts from the C.B. Pennington family and establishing guidelines for investments and expenditures.
University of Edinburgh Roslin Institute Labs & Facilities
University of Edinburgh Roslin Institute Labs and Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024. Labs & core facilities at the Roslin Institute
University of Nebraska Medical Center Mass Spectrometry and Proteomics Core Facility
UNMC Mass Spectrometry and Proteomics Core Facility
MSPCF maintains and uses equipment for protein separation and imaging, as well as for sample preparation for mass spectrometry analysis. Offers range of bioinformatics tools for data mining and evaluation. Services include Protein Identification, Protein Interactome Analysis, Protein Post-translational Modifications, Quantitative Mass Spectrometry, Molecular Weight determination.
Iowa State University SIPERG Stable Isotope Lab Core Facility
Iowa State University SIPERG Stable Isotope Lab
Core performes continuous flow isotopic and elemental analyses of carbon, nitrogen, oxygen and hydrogen in organic and inorganic substrates (solids, liquids, and gases). Supports research in oceanography, paleoclimatology, geology, ecology, agronomy, and chemistry. Laboratory consists of ThermoFinnigan Delta Plus XL mass spectrometer coupled with several sample introduction systems, including GasBench II with CombiPal autosampler, Costech elemental analyzer and TC/EA with Conflo III interface. Additionally, the SIL operates Picarro L2130-i Isotopic Liquid Water Analyzer with autosampler for rapid measurements of deuterium and oxygen.
GVK Biosciences has expertise in small molecule synthesis from milligrams to kilo gram scale. Our Chemistry team serves diverse customer requirements from custom synthesis to scale-up through discovery chemistry. Customers can avail these services on a stand-alone or integrated services basis. Advantages of working with GVK Biosciences include: * No Conflict model: GVK BIO has no internal programs. * The IP /Confidentiality of Customers is well protected * Proven ability to Scale from mg to kg level at one location * On-line project tracking * E-Note book reporting (Optional) * Chemistry complemented by expert services in Biology and Computational Chemistry * The largest SAR manually curated database with 4 million compounds available * Multiple research sites across India * Comprehensive technical team with relevant Pharmaceutical, Biopharmaceutical, and Academic experiences. Highly qualified and experienced team * State of the art Analytical instrumentation with experienced analytical research scientists
Core provides outsourced bioinformatics solutions. Core combines cloud computing and Next Generation Sequencing (NGS) expertise with a track record in building scalable, efficient genomics analysis workflows using both commercial and open source software. Core has provided services to big pharma, crop science, personal hygiene and animal health.
Massachusetts General Hospital Labs and Facilities
Massachusetts General Hospital Labs & Facilities
Enzymatics is an independent, ISO 13485:2003 certified OEM manufacturer of enzymes that brings to the marketplace a unique, quality oriented, and customer focused approach to protein production. The company was founded in 2006 to specifically address the needs of commercial entities engaged in the development, manufacture, and distribution of platforms dedicated to nucleic acid identification. Enzymes are critical to the performance of these applications and the industry''s relentless pursuit of higher performance emphasizes the need for analytical reagent purity and absolute production consistency. Operating from the perspective that we are a manufacturing division of our customer, Enzymatics consistently delivers the highest quality and value enzymes, leveraging them to drive customer success via a partnership business model; and our tremendous success confirms the need in the marketplace for a dedicated partner in the realm of enzyme technologies.
Cureline, Inc., is a human biospecimen CRO specializing in human tissue research projects including study design, regulatory affairs, clinical network management, specimen collection and analysis, and complete logistics. We collaborate with major clinical centers in Europe, Asia, and the USA and maintain an extensive biorepository of human biospecimens in South San Francisco (CA, USA). Our expertise is biomarker research and diagnostic specimen collection for solid tumors, hematology, inflammation, cardiovascular conditions, sepsis/infectious diseases, and other indications. Our translational histology division is a CLIA, GLP laboratory that provides high-end tissue research services to the biomedical research community including IHC protocol development, clinical specimens processing and diagnostics, digital pathology, etc. Our managers have advanced degrees in medicine and/or science, and worked before in clinical trial operations, research laboratories, healthcare management and international business development areas.
Provides consultant and laboratory services to biotech and pharmaceutical industries as well as academic research laboratories.
Dana-Farber Cancer Institute Labs and Facilities
Dana-Farber Cancer Institute Labs & Facilities
University of Angers Labs and Facilities
ACRObiosystems is aiming to be one of the leading bulk proteins/mAb products and biologics research service providers. we offer exceptional speed without compromising product quality.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2024. Provides range of high-quality genomics services, including next generation sequencing (whole exome, pre-designed panels, custom panels, RNA-Seq) and microarray processing (aCGH-CNV, miRNA, gene expression).
Core is a systems proteomics/bioinformatics company that conducts in-house signal transduction research. Core services also enable for identification and validation of biomarkers, drug targets and therapeutic compounds.
MSU Comprehensive Phytopathogen Genomics Resource
Michigan State University Comprehensive Phytopathogen Genomics Resource
Michigan State University Comprehensive Phytopathogen Genomics Resource (CPGR)
MSU Comprehensive Phytopathogen Genomics Resource (CPGR)
The Comprehensive Phytopathogen Genomics Resource (CPGR) aims to provide a comprehensive plant pathogen genomics and annotation resource. A major part of the CPGR is the development of diagnostic molecular markers and robust diagnostic protocols for plant pathogens
Our Bioanalytical Group develops and validates proprietary and non-proprietary analytical methods to identify, quantify and characterize small molecules, new chemical entities, and biologics from many different matrices. Mass spectrometry methods characterize batches of protein biologics throughout the stages of discovery, production and lot release. Our Bioassay Group develops and validates custom assays to evaluate the therapeutic potential of biological macromolecules. Our bioassays are developed using the latest technologies and employed for all phases of drug development, as well as GMP-lot release testing of biologics destined for the clinic. Custom Biologics????????????? maintains a controlled storage facility that can accommodate sample and reagent storage at 2-8???????C, -40???????C, -80???????C, and under liquid nitrogen conditions.
Arista Solutions LLC can accelerate your cleantech R&D. We bring mechanical design to the world of material science.
Biotechnology company specializing in developing and production of antibodies and service provider for customized products and relevant services. Committed to changing traditional antibody model and establishing new service platform. Specialized in providing custom biotechnology and pharmaceutical services that cover full scope of biotechnology needs of early drug discovery and drug development.
Genetica DNA Laboratories is a full service DNA testing laboratory providing a wide range of DNA testing services for over two decades worldwide. Genetica has been accreadited by AABB for DNA parentage testing for almost 20 years.
Memorial Sloan-Kettering Cancer Center Labs and Facilities
Memorial Sloan-Kettering Cancer Center Labs & Facilities
Memorial Sloan Kettering Cancer Center is committed to exceptional patient care, leading edge research, and superb educational programs. Close collaboration between our physicians and scientists provides patients with care available to discover more effective strategies to prevent, control, and ultimately cure cancer. Provides researchers with Organic Synthesis Core Facility, High-Throughput Drug Screening Facility and Antibody and Bioresource Core Facility.
Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.
Neuro-Zone srl supports drug discovery and development by providing physiologically relevant cell systems and multiparametric cell based assays for preclinical projects. Primary cells Customized assays Multiparametric screening Drug development is time consuming, costly and inefficient. By increasing the quality of cell-based assays NeuroZone enables more efficient and informative drug screening programs.
Core which has adopted and incorporated a multidisciplinary, integrated approach that includes: genomics, analytical sciences, cellular sciences, and bioinformatics.
UA Department of Chemistry and Biochemistry Labs and Facilities
University of Arizona Department of Chemistry and Biochemistry Labs & Facilities
University of Arizona Department of Chemistry and Biochemistry Labs and Facilities
UA Department of Chemistry and Biochemistry Labs & Facilities
In the Chemistry and Biochemistry Department at the University of Arizona, a vibrant community of scholars conduct innovative research programs in the chemical and biochemical sciences that lead to fundamental advances in knowledge, ultimately producing technological advances that benefit society. Our faculty is multidisciplinary and highly collaborative, with ties to many other world-renowned campus units, including astronomy and planetary sciences, the life sciences, engineering, optics, and physics. Our research facilities are extensive and state-of-the-art, and feature multi-user capabilities in NMR, EPR, surface analysis, photoelectron spectroscopy, X-ray diffraction, mass spectrometry, computational chemistry, proteomics, and nanoscale materials characterization. Our Department is dedicated to expanding the boundaries of the molecular sciences and to educating the next generation of research and teaching professionals. We invite you to become an integral member of our community and work with us to solve important problems in the molecular sciences.
Maccine is an established preclinical contract research organization providing innovative discovery support and regulatory safety assessment services. Operating on a collaborative partnering model, Maccine has developed a portfolio of in vivo assays in key therapeutic areas including Neurology, Psychiatry, Metabolic Disorders, Pain & Inflammation, Oncology, Musculoskeletal Disorders and Women''s Health. Naturalistic models, clinical biomarkers and clinical technology platforms are employed to better represent the clinical disease state. The team is supported by significant investment in high-end technology and access to a world class scientific community. The main Contract Research Facility is located within Singapore Science Park II, a premier address in Asia for technology and at the heart of the bioscience district. The facility is fully AAALAC-accredited and GLP/GMP compliant and is monitored with a networked building management system. In addition to vivarium space the facility houses suites for: Clinical Pathology, Analytical Chemistry Test Article Control and Storage Tissue Culture and In Vitro Laboratory PET/CT/MRI Large Mammal Imaging Behavioural and Abuse Liability Laboratory Histology Surgery Archiving QC Testing and Release
Our mission at Brains On-Line is to provide preclinical research services to facilitate the development of new drugs that target the central nervous system. Brains On-Line benefits from its intimate connections with academia, as well as with several associated contract research organizations (CRO). Using our expertise, we aim to give full insight in the possibilities of your compound.
Babraham Commercialisation Services Limited
Babraham Institute Enterprise Limited (BIE) is the wholly-owned trading arm of the Babraham Institute. The Babraham Institute undertakes innovative life-sciences research to discover the molecular mechanisms that underlie normal cellular processes and functions, with the aim of improving lifelong wellbeing and healthy ageing.
Provides oligonucleotides. Synthesizes custom DNA/RNA oligonucleotides for scientific and therapeutic communities.
AM Biotechnologies develops DNA-based affinity agents called thioaptamers using unique chemistries and a proprietary bead-based selection process. Antibodies are currently the most widely-used affinity agents but they are produced in animals; are easily degraded; are expensive to produce; and suffer from batch-to-batch variability. In contrast, thioaptamers are chemically synthesized; they are stable in ambient environments with very long shelf life; and are rapidly produced in large quantities with easy quality control. We solve the problems associated with antibodies while delivering the same functionality. Thioaptamers can be substituted for antibodies in virtually any application. We can develop thioaptamer affinity agents for your targets using our bead-based development service. AM also offers DNA thiophosphoramidite reagents via a strategic partnership with Glen Research Corporation and the RNA thiophosphoramidites are near market introduction. These unique reagents are used to synthesize thioaptamers and are also highly useful for providing in vivo stability and increased potency in RNAi applications. The company was founded in 2006 and is primarily owned by two corporations. It has been awarded numerous SBIR grants and has also benefited from over $10M of prior university research into its technologies. Importantly, all of our technologies have freedom to operate.
Core develops and writes curriculum and interactive web-based materials in the following subjects: bioinformatics, genetics, molecular biology, microbiology, immunology Digital World Biology also offers on-site, hands-on, professional development workshops for college instructors and high school teachers.
CSIRO High Resolution Plant Phenomics Centre
Commonwealth Scientific and Industrial Research Organisation High Resolution Plant Phenomics Centre
The High Resolution Plant Phenomics Centre (HRPPC) is the Canberra node of the Australian Plant Phenomics Facility and is located in Canberra at CSIRO Plant Industry and the Australian National University. This centre focuses on _������_deep phenotyping_���� (delving into metabolism and physiological processes within the plant) and _������_reverse phenomics_���� (dissecting traits to discover their mechanistic basis). Next generation research tools are applied to probe plant function and performance, under controlled conditions and in the field. Recent advances in robotics, imaging and computing are used in applying these technologies and scaling them from the single plant to the ecosystem level. Two levels of service are provided in the HRPPC. First, projects can be housed in the _������_Research Hotel_���� environment where screening systems can be developed using facility staff and resources then deployed in the facility and in the user' '''s home institution. Second, users_������_ material can be screened for specific attributes using one or more of the modules housed at CSIRO or the ANU. The HRPPC' '''s focus is on flexibility from cereals to dicots and woody perennials at all stages of development.
Metabolic Solutions provides comprehensive support services for researchers interested in using stable isotope tracers. Since 1990, nearly 1,000 investigators from around the world representing the pharmaceutical industry, government and academia have benefited from our services. Our experienced, accessible and responsive staff coupled with our GLP compliant mass spectrometry service ensures that your study goals are realized in a timely and cost effective manner. If you are interested in employing stable isotope techniques to measure glucose metabolism, assess total body water, determine free-living energy expenditure, monitor gastric motility, evaluate breath samples or utilize another tracer application, Metabolic Solutions can help!
University of Edinburgh Immunodetection and Imaging
University of Edinburgh Small University Research Facilities Immunodetection and Imaging
University of Edinburgh SuRF Immunodetection and Imaging
Delivering high quality immunohistochemical and immunofluorescent staining on cells and tissue sections, specialising in multi immunoflourescent colocalisation staining technologies. Equipped with three Vision Biosystems Bond staining robots Mike offers high throughput or custom antibody optimisation services. Time consuming multi colocalisation including same species primaries, are automated saving time and money. A large range of imaging platforms including three confocals, widefield, stereology, image analysis, digital photograpy and PALM laser capture microscopy are available. A full range of secondary antibodies and detection systems are available for purchase in ul quantities. There are currently 1900 antibodies recorded on our database.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. A Contract research organization offering pre-clinical drug evaluation service specialising in models of cardiovascular and inflammatory diseases such as myocardial ischemia, haemorrhagic shock, endotoxaemia also inflammatory bowel disease (IBD), neutrophil migration, pulmonary fibrosis, systemic lupus erthematosus (SLE), adjuvant arthritis, collagen II arthritis, EAE and many more.
Commonwealth Scientific and Industrial Research Organisation Labs and Facilities
Commonwealth Scientific and Industrial Research Organisation Labs & Facilities
Advanced BioScience Laboratories, Inc (ABL) is a leading contract research and manufacturing organization, partnering with our clients to advance their vaccine and therapeutic development programs. Our unique combination of preclinical and clinical services provide the tools to address the scientific challenges encountered during any stage of product development. For preclinical studies, we utilize immunological, molecular, and cell-based assay platforms for candidate selection. We offer proof-of-concept in vivo studies with preclinical immunomonitoring and efficacy and potency testing. Once a clinical candidate is identified, ABL''s in-house cGMP suites are designed for single-use technologies accommodating a wide range of products, including mammalian- and microbial-based protein therapeutics as well as viral vectors and vaccines.
Meridian Life Science is a leading manufacturer and supplier of antibodies, viral antigens and critical assay reagents. We provide contract biologic R&D and manufacturing services to the diagnostic manufacturers along with cGMP biologics manufacturing for the biopharmaceutical market. We have been providing innovative life science solutions and building trusted partnerships for over 25 years. Our focus is to offer products and services that help to advance the diagnosis and treatment of disease. Contract manufacturing of proteins and other biologicals for biopharmaceutical and biotechnology companies engaged in research for new drugs and vaccines is an example of significant new product applications built from Meridian Life Science''s existing expertise in manufacturing bulk antigens and reagents using cell culture techniques. This business focuses on cGMP contract manufacturing of materials that will be used in Phase I and II clinical trials.
Vivalis contract manufacturing services offers a full suite of services that include GMP cell banking, GMP antibody production, and GMP virus production. Our manufacturing facility has been approved by the French Medicines Agency for GMP production up to Phase II clinical trials. A rigorous Quality Management System (QMS) maintains GMP compliance and further ensures adherence to these quality requirements.
Australian National Fabrication Facility Labs and Facilities
Australian National Fabrication Facility Labs & Facilities
The ANFF provides leading-edge research capability and supports excellence in science. The capability provided by ANFF enables users to process hard materials (metals, composites and ceramics) and soft materials (polymers and polymer-biological moieties) and transform these into structures that have application in sensors, medical devices, nanophotonics and nanoelectronics. It has a strong emphasis on service provision to the research community. ANFF seeks to enhance national and international collaborations and enable world-class-research.
Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
TG Labs Company, located in Colorado, has two divisions Technical division and Industrial division. Technical Division operates scientific, medical and chemical discovery laboratory in Englewood, Colorado. This division also develops special devices, equipment and processes for the medical, chemical and environmental industries. We offer proven solutions from concept through full scale production, including regulatory standards.
Located at Beijing Economic and Technological Development Area, Beijing, China, was founded by former employees from Invitrogen/Biosource and BD PharMingen and researchers at US universities in September 2009. QuantoBio focuses on developing and manufacturing high quality reagents on the research on immunology, cell biology, cancer, inflammation and related diseases for the market in the World as well as China. The product portfolios include immunoassays, recombinant bioactive proteins, antibodies on various applications including flow cytometry, Western blotting and Immunohistochemistry, microRNA profiling and assay kits and other cutting-edge research reagents. The vigorous product development combines internal product development, technology licensing, and collaborations with research laboratories worldwide. With rich experience and knowledge in product development, we offer the ranges of custom services on immunoassay and antibody developments, recombinant protein expression and bioassays, microRNA profiling, microRNA overexpression and knock-down.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. With broad and comprehensive capabilities, Waisman Biomanufacturing is uniquely situated and highly qualified to lead clients through the complex process of bringing a novel therapeutic into the clinic. Integral to any product campaign is a well thought-out product development plan. You can rely on our business manager and team of project leaders to work closely with you to maintain an on-going flow of communication and develop a time and cost effective plan that meets your needs. Utilizing our expertise in both Quality Assurance/Control and Process Development/Manufacture we can translate your bench top process to a large scale manufacturing process. Using this strategy Waisman routinely produces cGMP grade material qualified for clinical trials for a wide variety of applications.
California State University Channel Islands Labs & Facilities
California State University Channel Islands Labs and Facilities
Donald Danforth Plant Science Center Labs and Facilities
Donald Danforth Plant Science Center Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 21,2025. An Portal, Core facility.
UMass Amherst Laboratory of Medical Zoology
University of Massachusetts Amherst Laboratory of Medical Zoology
We offer expanded tick testing services for a variety of tick-borne pathogens, including Babesia, Anaplasma, Rickettsia, Bartonella, and others.
QMUL Blizard Institute of Cell and Molecular Science Pathology Core Facility
Queen Mary University of London Blizard Institute of Cell and Molecular Science Pathology Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2,2024. Core Pathology is a self funding, CPA accredited department and therefore is a fee-for-service facility providing Histopathology services to members of Queen Mary University and other academic institutes, as well as providing a diagnostic service to the private sector. Our remit is to advise, support or carry out work for research groups.
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Diet and Physical Activity Core
UNC Nutrition Obesity Research Center - Diet Physical Activity and Body Composition Core
UNC-Chapel Hill NORC - Diet Physical Activity and Body Composition Core
University of North Carolina at Chapel Hill NORC - Diet Physical Activity and Body Composition Core
University of North Carolina at Chapel Hill Nutrition Obesity Research Center - Diet Physical Activity and Body Composition Core
UNC NORC - Diet Physical Activity and Body Composition Core
Core that provides diet, physical activity, or statistical analysis consultation, as well as consultation for the design and development of diet and physical activity data collection protocols.
UVa W.M. Keck Biomedical Mass Spectrometry Laboratory
University of Virginia School of Medicine W.M. Keck Biomedical Mass Spectrometry Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. W.M. Keck Biomedical Mass Spectrometry Laboratory within the Biomolecular Research Facility identifies and analyzes proteins from gels and solution using current mass spectrometry techniques. There are techniques to compare samples which have different amounts of the same proteins. Analyses available: - Protein identification and sequencing from gel or solution by either peptide mass fingerprinting or ESI-LC/MS/MS at the low femtomole level. - Analysis of protein mixtures such as tissue and media analysis of tissue samples prepared by Laser Capture Microdissection - Proteomics, comparison of proteins in tissue samples using chemical/isotopic labels or label free analysis - Absolute quantitation of proteins using labeled peptides and selective reaction monitoring - Identification of phosphorylation sites using titanium dioxide enrichment - Identification of post-translational modifications (deamination, ubiquitination, etc) - De Novo (manual) sequence analysis of novel proteins to obtain sufficient sequence data for cloning - High resolution, high mass accuracy measurements of peptides and small proteins - Confirmation of peptide identity by MALDI mass measurements - Identification of binding partners Equipment Our current mass spectrometers: - Thermo Scientific LTQ Orbitrap Velos for high accuracy, high sensitivity analysis - Bruker Microflex for mass analysis by MALDI - Thermo Scientific TSQ Quantum Access MAX triple quadrupole instrument Sample types analyzed: - gel bands, stained with Coomassie, silver, fluorescent stains - proteins in solution - tissue samples - media - Laser Capture Microdissection tissue samples.
University of Western Sydney Labs and Facilities
University of Western Sydney Labs & Facilities
UAlberta Institute for Biomolecular Design
University of Alberta Institute for Biomolecular Design
The IBD provides a range of mass spectrometry and proteomic services such as protein identification and molecular weight determination. Additionally we also perform Amino Acid Analysis and Peptide Synthesis.
Alliance Protein Laboratories is a contract research and consulting firm specializing in biophysical analysis. We offer a broad and unique range of biophysical characterization services, as well as contract purification services (research scale) A.P.L. is a spin-off from the Protein Chemistry department at Amgen. It was founded in 1998 by Drs. Tsutomu Arakawa and John Philo. Our laboratory is located in San Diego, CA. Our clients include over 250 companies in North America, Europe, Asia, and Australia as well as major universities and non-profit institutes.
Founded in 1973, AltaBioscience* is recognised world-wide as a leading manufacturing laboratory providing analysis and synthesis of DNA, proteins and other biochemical molecules to researchers in academia, pharmaceutica and the food industry. *An ISO 9001: 2008 certified UK based laboratory offering CD analysis.
University of Maryland BioAnalytical Service Laboratory
The BioAnalytical Service Laboratory at the Institute of Marine and Environmental Technology assists researchers by providing state-of-the-art instrumentation and training to conduct routine analytical, synthetic and separation projects.
University of Kansas Molecular Graphics and Modeling Laboratory Core Facility
KU Molecular Graphics and Modeling Laboratory
University of Kansas Molecular Graphics and Modeling Laboratory
Provides or assists with docking and virtual screening of small molecule ligands against protein targets of interest, molecular dynamics simulation and modeling of small/macro molecules, proteins, and biomolecular systems, analysis of structure-activity relationships, visualization and graphics of biomolecules and biomolecular systems, and custom algorithm/software development along with databases and web applications.
Kansas State University - INBRE Bioinformatics Core Facility
The K-INBRE Bioinformatics Core collaborates with Kansas researchers to perform research on cell and developmental biology. Core aims to serve the needs of investigators engaged in computationally intensive biomedical research, and to promote education in bioinformatics to students and researchers across the state of Kansas.
Columbia University Protein Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. Columbia University Protein Core Facility provides a range of services to all Columbia researchers and to outside users, including mass spectrometry, protein sequencing, and DNA sequencing. Mass Spectrometry: Services available include protein identification from gel bands or spots by MALDI-TOF and ESI-LC-MS/MS, post-translational modification identification, and mass analysis of intact proteins. Mass spectrometry is used to identify interacting partners in protein complexes that have been purified by immunoprecipitation and other methods. The Core also routinely provides structural confirmation of expressed proteins and protein fragments for structural biology studies. Protein Sequencing: N-terminal sequencing of proteins in solution or blotted to PVDF membranes is available. DNA Sequencing: The core offers high quality, fast turnaround DNA sequencing of various types DNA - plasmids, PCR products, GC-rich templates, cosmids, and BACs. DNA sequencing results are distributed through a secure network server with automated email notification.
Idaho State University Molecular Research Core Facility
Core facility aides ISU investigators in the areas of molecular genetics, microbiology, developmental biology, physiology, anatomy, neurobiology, molecular evolution and systematics, phylogenetics, population genetics, bioinformatics, comparative and computational genetics, and pharmaceutical sciences. In addition the MRCF also serves the DNA sequencing and genotyping needs of an increasing number of investigators at other institutions throughout the state and the nation. Routine activities in the MRCF include automated DNA sequencing and microsatellite analysis (Genotyping), PCR, electrophoresis, and gel documentation and analysis.
Cleveland Clinic Molecular Biotechnology Core Facility
Cleveland Clinic Lerner Research Institute MBT Core
Cleveland Clinic Lerner Research Institute Molecular Biotechnology Core
Cleveland Clinic Molecular Biotechnology Core
Core offers services in areas of peptide synthesis, peptide modification, purification and quality analysis, N-terminal protein sequencing by Edman degradation, and biomolecular interaction analysis and equilibrium and kinetic measurements.
Ottawa Hospital Research Institute StemCore Laboratories Core Facility
Ottawa Hospital Research Institute StemCore Laboratories
StemCore Laboratories is a high-throughput genomics facility within the Ottawa Hospital Research Institute (OHRI). Core is capable of facilitating large-scale scientific research and biotechnology projects.Provides infrastructure for genomics, bioinformatics, and proteomics.
motifRG - A package for discriminative motif discovery designed for high throughput sequencing dataset
Software tools for discriminative motif discovery using regression methods.
University of Minnesota Clinical Pharmacology Analytical Services
University of Minnesota - College of Pharmacy Clinical Pharmacology Analytical Services
University of Minnesota - College of Pharmacy Clinical Pharmacology Analytical Services (CPAS)
University of Minnesota Clinical Pharmacology Analytical Services (CPAS)
The Clinical Pharmacology Analytical Services laboratory (CPAS) resides in the Department of Experimental and Clinical Pharmacology (ECP) in the University of Minnesota College of Pharmacy. CPAS offers quantification services of drug concentrations in biological samples. The CLIA-certified lab and its team of researchers and clinicians the resources to measure drug concentrations in blood and tissue samples of human and animal origin, including animals as patients and animals serving as research models. The lab which opened in October 2003 uses state-of-the-art equipment to facilitate analysis of drugs, xenobiotics, endogenous compounds and biological samples. Capabilities of the core lab include LC-MS/MS, LC-MS, GC-MS, HPLC-UV and HPLC-FLD. Additional, UV and fluorescent plate readers and liquid scintillation counters are available for conducting ELISA, RIA and other assays in a 96-well plate format. Because of its flexible structure, customers can purchase only the services they need, including assay consultation, assay development and validation, conduct of assays and application. Lab services are made available to researchers from within and outside the University of Minnesota community.
Core facility provides resources to researches in the bioinformatics field. Core also provides assistance in generating omics data, data analysis, biological interpretations, and infrastructure.
We provide high quality Drosophila transgenic service to both research institutions and companies. We offer you partial to full service ranging from DNA preparation, embryo microinjection, screening for white+, yellow+, and/or GFP/RFP phenotypes, to balancing crosses. Most importantly, the cost of our Drosophila embryo injection services is more reasonable compared to that of others. With a large number of facilities and the highly experienced staff, we are able to initiate the process immediately upon receiving your sample. Our friendly web-based database allows you to track your sample status, service history and more.
American Peptide Company, Inc. (APC) offers comprehensive selections of pre-manufactured catalog peptides, custom synthesis, and GMP peptide Active Pharmaceutical Ingredients. Our California based manufacturing facilities offer synthesis services under Non GMP (Sunnyvale, California) and cGMP (Vista, California) conditions. Our cGMP manufacturing is performed under strict adherence to FDA Regulations 21 CFR parts 210, 211 and ICH Guidance Q7A. Our Total Peptide Management services support clients in the drug development process from pre-clinical through commercial stage. Our value added services include process development, scale up production, analytical/process validation, stability studies, CMC, DMF, and regulatory support.
Supplier of aptamers, RNA or DNA that binds with high affinity and specificity to targets such as small organics, peptides, proteins, cells, and tissues. Unlike antibodies, some aptamers exhibit stereoselectivity. In addition, aptamers have been generated that exhibit greater than 10,000-fold binding affinity for theophylline over caffeine, which differ from one another in structure by only a single methyl group.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10th,2023. NanoRacks provides microgravity research facilities and currently includes NanoLab Platforms, NanoRacks Plate Reader, NanoRacks Microscope and NanoRacks MixStix.
University of Nebraska Medical Center Protein Structure Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 25,2024. Protein Structure Core Facility operates in the department of Biochemistry and Molecular Biology, on the UNMC campus. The facility performs protein sequencing, amino acid analysis and peptide mapping on a fee-for-service basis. It is located on the first floor of the Durham Research Center
Perelman School of Medicine Microarray Core Facility
University of Pennsylvania Perelman School of Medicine Microarray Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2,2024. Penn Microarray Facility provides instrumentation and expertise for RNA transcript profiling. DNA microarrays provide a highly parallel means of measuring the abundance of RNA for targeted genes in a biological sample. The Facility supports two microarray formats: oligonucleotide arrays synthesized by Affymetrix Inc. and arrays of probes printed in-house on glass slides. This reflects our goal of offering a range of cost and performance options suitable for a variety of experimental questions.
Offers Next Generation Sequencing (NGS) services and standard bioinformatics analysis. Their team of scientists is committed to returning quality data and analysis.
Provide editing of scientific-, technical, and other scholarly papers. Non-native-speakers of English are welcome.
UAlberta Mass Spectrometry Facility - Department of Chemistry
University of Alberta Department of Chemistry Mass Spectrometry Facility
University of Alberta Mass Spectrometry Facility - Department of Chemistry
There are currently eleven mass spectrometers housed in the mass spectrometry laboratory covering most ionisation techniques from electron impact to MALDI. 8 or more samples submitted at the same time and run under identical conditions qualify for a 25% discount for GC-coupled, LC-coupled and in-gel digest LC/MS/MS experiments Variable rate for high molecular weight samples (i.e., more than 3000 u), depending on the instrument and operator time required for the analysis. There will be a 50% surcharge for all RUSH orders (queue jumping).
University of Texas Health Science Center at San Antonio Nucleic Acids Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15,2024. Nucleic Acids Core Facility offers automated DNA sequencing with data analysis, custom DNA synthesis, genome project services, gene amplification services, and robotic application custom projects. These services are provided to researchers at the HSC and others in the surrounding scientific community. Our mission is to offer high quality synthesis and sequencing services to researchers through cutting edge instrumentation and a service-oriented and knowledgeable staff.
Group of microscopy scientists and technicians providing high-quality, full-service microscopy for life sciences and health technologies, offering expertise, performance, and technical solutions using advanced equipment.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 14,2024. OCBN is a not-for-profit corporation that was established in 2005 with a grant from the Ontario Institute for Cancer Research and the Ontario Ministry of Research and Innovation for the purpose of advancing biomarker research. The OCBN is designed to enable the co-ordination and amplification of the proteomic and genomic biomarker research efforts throughout the province of Ontario to better service academia and industry, whether provincially, nationally or internationally. As such, OCBN is much more than simply an academic research consortium. Residing at the core of the network is the OCBN Central Facility, located at the MaRS Incubator www.marsdd.com in the heart of the biomedical research community in Toronto, one of the most vibrant research hubs in the world. The Central Facility functions as the nexus for the network and its academic and industry partners by providing numerous support services for their clinical and basic research scientists in the conduct of their research.
University of Canterbury Biomolecular Interaction Centre
The Biomolecular Interaction Centre (BIC) is a multi-disciplinary centre dedicated to the study of molecular interactions critical to biological function. Understanding biomolecular interactions is central to a range of fundamental sciences, new treatments for disease, and a wide range of highly functional products. The Institute includes University of Canterbury researchers from the Colleges of Science and Engineering, as well as Education and Arts and partners with several New Zealand CRIs and Universities. The Centre was founded in 2007 after being awarded funding from the Innovation and Development Fund from the Tertiary Education Commission (TEC). The primary investment of $1.85 million was used to purchase of a suite of state-of-the-art equipment that was supplied by Bio-Rad Laboratories. BIC has recently received a multi-million dollar investment from the University of Canterbury to become one of two new premier research institutes on campus. BIC researchers seek to understand the molecular interactions vital to biology and harness them in a wide range of applications. BIC has a number of Principal, Partner, Associate and Affliated Investigators, together with Post Doctoral Fellows, Postgraduate students and technicians from the University of Canterbury, as well as, other national and international institutions. Many these investigators directly support the research themes of the Centre while others have related research projects that benefit from BIC support.
Princeton High Throughput Sequencing and Microarray Facility
High Throughput Sequencing and Microarray Facility
Core facility provides researchers with access to high-throughput sequencing technologies. The staff provide consultation on experimental design, library preparation, and data analysis. The Sequencing Core Facility works closely with Bioinformatics staff in the Center for Quantitative Biology to provide researchers with computing power and consulting services to analyze sequencing data.
UMass Medical School Small Animal Imaging Core
University of Massachusetts Medical School Small Animal Imaging Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2024. UMMS Small Animal Imaging Core was established in early 2008 to serve the UMMS and extramural research community by providing state-of-the-art small animal imaging.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Page listing Core facilities at Yale.
UHN Advanced Optical Microscopy Facility
University Health Network Advanced Optical Microscopy Facility
The Advanced Optical Microscopy Facility (AOMF) is centrally located in the Discovery District in Toronto, Ontario, serving University Health Network as well as external academic and industrial users. It is the largest microscopy facility in Canada with instruments at Princess Margaret Hospital and Toronto General Hospital. With over 30 instruments and 4 staff members, the AOMF is equipped to help you with nearly any optical microscopy application including: confocal, multiphoton, FRAP, FRET, live-cell, timelapse, spectral unmixing, in-vivo bioluminescence and fluorescence, whole-slide scanning, 3D rendering, colocalization and more. We offer: Free consultations to determine which microscopes would best suit your application Comprehensive training and support on our various instruments Full-service image capture and analysis (a great way to get started quickly) High-resolution whole slide scanning service for histology slides Practical courses on microscopy, including one-on-one hands-on sessions (eg: Fundamentals of Microscopy) and larger workshops tailored to your group' '''s applications Software and training for image processing and quantification
McGill Cell Imaging and Analysis Network Core Facility
McGill Cell Imaging and Analysis Network (CIAN)
McGill University Cell Imaging and Analysis Network
McGill University Cell Imaging and Analysis Network (CIAN)
Core facility at Biology Department in McGill Faculty of Science. Expertise in Light Microscopy and Image Analysis. Provides light microscopes, ranging from Point Scanning and Spinning Disc Confocals to Multi-Photon, TIRF, Light Sheet and Super-Resolution microscopes. Provides services in Automation/High throughput screening (liquid handler, pinning robot), Protein expression and antibody production. Users get training.
EpigenDx is a genomic and epigenomic research company specializing in disease biomarker discovery and molecular diagnosis. The company provides products related to DNA methylation analysis research. Currently available products include DNA methylation controls and validated DNA methylation assays for human, mouse, and rat. EpigenDx also provides products and laboratory services for scientific researchers from academic, government and industrial communities. Our commitment to quality comes from our desire and dedication to provide the best products and services to our customers. EpigenDx has knowledge and expertise in Pyrosequencing and its many applications. CpG methylation and allele quantification analysis are conducted using Qiagen-Pyrosequencing PSQ MD system, while short-read sequence analysis is carried out using Qiagen-Pyrosequencing PSQ ID system.
Core offers a repository from which researchers can drag and drop genetic sequence data into another application. Core offers a feature-surface to surface interoperation-that enables the system to be the hub for a network of applications researchers need to perform their work; LIMS, analytic tools, content management, workflow engines, visualization, etc. The core's system is optimized for cloud-based operations, and doesn't require users to re-download data.
LifeTein LLC, located in South Plainfield, New Jersey, was founded for its global custom peptide synthesis services, antibody production services and chemical services. LifeTein offers a wide range of custom research services and a staff of scientists with the first-hand campus-core-facility experience necessary to understanding the role of peptide and protein services in large research projects. LifeTein is the only peptide synthesis manufacturer to have developed its own line of PeptideSyn platform for peptide synthesis and AdjuBooster for antibody production.
Tubingen Ageing and Tumour Immunology Group
Tubingen Ageing and Tumour Immunology Group (TATI)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 19,2024. TATI is located at the Center for Medical Research (Zentrum fuer Medizinische Forschung, ZMF) within the University of Tuebingen Clinical School (Universitaetsklinikum Tuebingen) . We are engaged in immune monitoring (cancer immunotherapy, vaccination of elderly, Alzheimer) using 14-colour flow cytometry.
University of Southern California Stem Cell Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 16,2024. USC Stem Cell Core facility is a CIRM funded comprehensive support center and central hub for the provision of knowledge, resources and state of the art technology to researchers working with stem cells. Our primary aims are to facilitate stem cell and biomedical research at USC and the LA area and to develop new technologies for working with pluripotent stem cells. We offer a wide range of services in the following areas: Cells and Reagents Reproducibility in experimental science is dependent on homogeneity and consistency. One of the primary aims of the USC Stem Cell Core is to standardize stem cell research by providing quality controlled cells and reagents. Equipment The USC Stem Cell Core is a shared laboratory space housing communal cell culture workstations, a state of the art imaging core, spectral karyotyping facilities, a Q-PCR machine, fully equipped molecular biology work stations and a variety of equipment for performing histological analysis. Flow cytometry and high content screening equipment are made available through the FACS core. Laboratory Space As a shared research facility we offer communal laboratory space for investigators to conduct collaborative or start up research involving stem cells. Our goal is to expand stem cell research in the LA area and to encourage collaboration between novice and seasoned researchers. Technical Assistance The USC Stem Cell Core is staffed with a team of highly experienced technicians, boasting a combined technical expertise of over 60 years. We provide comprehensive assistance, which includes a biobanking and histology service. Training and Education Training and education are pivotal to the advancement of Stem Cell Research. The USC Stem Cell Core offers a broad range of educational services including technical protocols, one on one customized training and a week long course covering human pluripotent stem cell culture techniques. Research and Development The USC Stem Cell Core Research and Development program was established with two main aims: 1) to develop and centralize new technologies for working with human pluripotent stem cells, 2) to support researchers embarking on collaborative and pilot projects.
Duke University DNA Microarray Core Facility
The Duke Microarray Facility provides services for the analysis of gene expression. The facility is operated jointly with the Duke Cancer Institute and provides: Affymetrix Microarrays Agilent Microarrays Real-Time PCR RNA Quality Check with Agilent Bioanalyzer The Microarray Facility also maintains a comprehensive database server to manage the massive amounts of data generated by microarray analysis. The facility provides data analysis support through various software packages as well as gene annotation support.
UMass Medical School Flow Cytometry Core Lab
University of Massachusetts Medical School Flow Cytometry Core Lab
The Flow Cytometry Facility, located at UMass Medical School in Worcester, provides a wide variety of cytometry services for internal and external investigators with state-of-the-art sorting and analyzing capabilities. For analysis we currently have three 4-color FACSCaliburs, a 2 laser LSR II, a 4 laser LSRII and a 5 laser LSRII. Our cell sorters include a 3 laser Beckman Coulter MoFlo XDP hi-speed cell sorter, an all digital 3 laser 11 color FACSVantage DE DiVa sorter, a 19 parameter, 5 laser FACSAria, and a 14 parameter, 4 laser FACSAria dedicated to BSL3 cell sorting. Two LSR II''s and one Calibur are dedicated for investigator self use, after training is completed. We encourage all investigators to come to the main lab at S5-322 and learn how flow cytometry can be applied to your research. Rates are based per hour and billed in 15 minute increments. Training rates are based per person, per hour. Sorting includes a 1 hour setup fee unless there is a second sort on that instument that day, in which case each sort is billed 30 minutes for setup. BSL3 Sorting is billed 30 minutes for setup in all cases
UMass Medical School High Throughput Gene Expression/Biomarker Core Laboratory
University of Massachusetts Medical School High Throughput Gene Expression/Biomarker Core Laboratory
UMMS High Throughput Gene Expression/Biomarker Core Laboratory
The High Throughput Gene Expression/Biomarker Core Laboratory run by Drs. Tanriverdi and Freedman provides High Throughput/Rapid Gene Expression and Complete miRNA profiling analysis by using gold standard qRT-PCR with the combination of custom Integrated Fluidic Circuit (IFC) technology from Fluidigm (South San Francisco, CA). Also, high-throughput SNP and multi-plate immunoassay services are available. The core lab is located in a modular class 10,000 clean room.
University of Massachusetts Medical School Small Molecule Screening Core Facility
UMass Medical School Small Molecule Screening Facility
UMass Medical School Small Molecule Screening Facility (SMSF)
University of Massachusetts Medical School Small Molecule Screening Facility
University of Massachusetts Medical School Small Molecule Screening Facility (SMSF)
Screening facility assists researchers in developing high-throughput screening assays, performs HT screens of chemical libraries to identify new small molecules that can be used to probe biological processes of interest. Facility coordinates screening efforts of UMass Chan researchers, providing access to diverse chemical libraries and state-of-the art instruments including robotic compound transfer, liquid-handling equipment, imagers and plate readers.
University of Massachusetts Medical School Machine Shop
The UMMS Machine Shop is a support service dedicated to assisting research in a technical/mechanical manner. Although all types of basic laboratory apparatus are manufactured and repaired on a regular basis, we specialize in design and fabrication of equipment that is not commercially available. No job too big or too small, too simple or too complex. Our staff is experienced and knowledgeable in working with all plastics and composites, all metals and alloys. We have over 35 years combined of experience in biomedical design and machining experience and are always available to discuss projects either at the shop or at your location. The Machine Shop is located at the Shrewsbury Campus. Pick-up and delivery of jobs can be arranged at your convenience.
UMass Medical School Electron Microscopy Core Facility
University of Massachusetts Medical School Electron Microscopy Core Facility
The electron microscopy core facility provides services and expertise in all aspects of transmission and scanning electron microscopy. Services include conventional fixation and sectioning of cells and tissues, negative staining of organelles and macromolecular assemblies, shadowing of isolated protein molecules, freeze-fracture, immunolabeling, etc. Cryo-sectioning and cryo-electron microscopy are also available. Expert consultation on all aspects of experimental planning and micrograph interpretation is provided by the facility manager, Greg Hendricks.
Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV).
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 23, 2019. Core functions as a multi-user resource dedicated to the development and application of various high-throughput technologies to aid in the discovery of biological macromolecules. Core provides analysis platforms for DNA (sequencing and genotyping), RNA (gene expression analysis) and proteins (proteomics). They also offer a selection of molecular biology applications (colony picking, cloning, DNA/RNA isolations).
ANFF Micro Nano and Semiconductor Patterning
Australian National Fabrication Facility Micro Nano and Semiconductor Patterning
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. VBI trains and educates members of the laboratory animal science community on surgical refinements, biomethodologies, anesthesia and analgesia as well as a variety of other topics. VBI utilizes a global network of world-renowned experts to harmonize education and incorporate best practices into all training protocols. Though training, VBI improves the quality of research data, promotes animal welfare and enforcesrefinement, reduction, and replacement in animal research. VBI has validated competency and proficiency assessment tools that are an integral part of training and knowledge transfer. Our on-line courses have been validated to show that their use before hands-on training improves the knowledge transfer and competency of the end user.
Columbia University Radiological Research Accelerator Core Facility
Columbia Radiological Research Accelerator Facility
RARAF is dedicated to providing user-friendly radiation sources and bio-labs for research in biology, radiation biology, and radiation physics.
Columbia Transgenic Mouse Shared Resource
Columbia University Transgenic Mouse Shared Resource
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024. Core facility that specializes in the generation and analysis of genetically modified mice, including transgenic and knockout animals, is an essential technology for biomedical research. Our services include: Production of transgenic mice by pronuclear DNA microinjection and embryo transfer. Production of chimeric mice by blastocyst injection of genetically modified ES cells and embryo transfer, which is part of the procedure of producing knockout or knockin mice. Gene targeting, which involves the electroporation of a targeting vector into pluripotent mouse embryonic stem (ES) cells and the selection of gene-targeted clones. Education of investigators and advice on vector and experimental design for experiments using transgenic and knockout mice. Bioimaging: The Animal Imaging Service provides investigators the opportunity for non-invasive detection, localization, and longitudinal monitoring of primary and metastatic cancer cells in vivo, in allograft, zenograft, transgenic and knock-out mouse models. The IVIS Spectrum (Caliper Life Sciences, Hopkinton MA) uses optical imaging technology to detect bioluminescent and fluorescent reporters across the blue to near infrared wavelength region. DNA samples and ES cell lines are injected in the order in which the signed service request forms are received. Currently, the average time from receipt of the service request to injection is approximately 2 weeks. For ES Cell electroporation and expansion, success in gene targeting cannot be guaranteed due to inherent variability in the frequency of targeting different loci, and the possibility of mistakes or mutations in the targeting vector.
University of California at Davis Real Time PCR Research and Diagnostics Core Facility
Real Time PCR Research and Diagnostics Laboratory
UC Davis Real Time PCR Research and Diagnostics Core Facility
Real-time PCR Research and Diagnostics Core Facility accepts research projects from both academic and private sector. The Core Facility can accommodate projects involving laser microdissection, RNA and DNA extractions through semi-automated nucleic acid extractions systems, cDNA synthesis and complete Real-time PCR analysis using a laser 7900 HTA FAST platform.
Penn Electron Microscopy Core Laboratory
Perelman School of Medicine Electron Microscopy Core Laboratory
University of Pennsylvania Perelman School of Medicine Electron Microscopy Core Laboratory
The Electron Microscopy Resource Laboratory (EMRL ) at Penn is a research facility dedicated to ultrastructure analysis of biological samples by electron microscopy (EM). We offer high quality EM imaging services at low cost. With a team of experienced professional staff and state-of-the-art sample preparation and imaging equipment, the EMRL offers users a full spectrum of both transmission EM and scanning EM services.
Ohio State University Nucleic Acid Shared Resource
Ohio State University Nucleic Acid Shared Resource (NASR)
The Nucleic Acid Shared Resource (NASR) provides genomic and epigenomic support for cancer research at OSUCCC-James including: Sanger-based DNA Sequencing, Next-Generation Sequencing, Genotyping, DNA Methylation analysis and Gene Expression Analysis. Additionally, the NASR provides consultation and assistance in experimental design, troubleshooting, training, development of novel methodologies and applications, and publication preparation.
University of North Carolina Center for Gastrointestinal Biology and Disease Microbiome Core
University of North Carolina at Chapel Hill School of Medicine Microbiome Core Facility
UNC School of Medicine Microbiome Core Facility
Core facility that provides the research community with the facilities and the expertise to characterize complex microbial communities from different environments.Services offered by the Core include metagenomics methods to determine the composition and function of microbial communities using amplicon, Whole Genome Shotgun (WGS) and RNA sequencing, and traditional and high-throughput quantitative (q)PCR.
University of Arkansas Labs and Facilities
University of Arkansas Labs & Facilities
University of Arizona Labs and Facilities
UC Davis Respiratory Disease Immunology Core Laboratory
UC Davis Respiratory Disease Immunology Core Laboratory (RDICL)
University of California Davis Respiratory Disease Immunology Core Laboratory
University of California Davis Respiratory Disease Immunology Core Laboratory (RDICL)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 24,2024. Respiratory Disease Immunology Core Laboratory is to provide technical expertise and resources to investigators interested in the immunological evaluation of rhesus macaque models for lung disease. Studies are primarily carried out in conjunction with the Inhalation Exposure Core and the Computational Imaging Core at UCDavis, in order to provide a comprehensive evaluation of pathophysiological responses in the lung. Services provided by the RDICL include assistance with experimental design, allergen characterization and preparation (through Resource Services), evaluation of allergen-specific IgE and IgG, and quantitation of histamine. We also provide technical support for sample processing, including bronchoalveolar lavage, lung tissue, and blood. Flow cytometry and molecular analysis of lung and blood samples are coordinated with the Flow Cytometry Core Laboratory and the Infectious Disease Immunology Core Laboratory. In addition to immunological evaluation, the Respiratory Disease Immunology Core Laboratory can provide investigators with primary cell isolates and in vitro culture of rhesus lung epithelial cells and fibroblasts. The Core does not conduct studies with human lung cultures. Please inquire for additional assays that are in development. In the future, immunohistochemistry of lung samples will be offered in conjunction with the Computational Imaging Core at UCDavis.
University of Pittsburgh Research Histology Services Core Facility
University of Pittsburgh Research Histology Services
Research Histology Services is located in the Thomas E. Starzl Biomedical Science Tower at the University of Pittsburgh. RHS lab serves as the Core Liver and Kidney Laboratory for the Immune Tolerance Network (ITN) and the Core Heart Lab for the Clinical Trials in Organ Transplantation in Children (CTOTC04), providing histology services for ongoing clinical patient research studies throughout the United States and Canada. Provides range of histological research techniques that include decalcification, standard tissue processing, biopsy processing, paraffin embedding, OCT embedding of frozen tissues, serial sectioning, step/level sectioning, and cryostat sectioning. A wide spectrum of assays is available in addition to the routine hematoxylin and eosin (H&E) stain. Special histochemical stains routinely provided include; Masson Trichrome, PAS (periodic acid Schiff), Prussian Blue (Iron), Verhoff' '''s Elastin Stain, Cresyl Violet, Toluidine Blue, and Luxol Fast Blue; additional histochemical staining is done upon request. Wide arrays of Immunoperoxidase and Immunofluorescent staining and apoptosis/ tunel stains are also available. Our goal is to return quality work in the shortest time possible.
Software for a general workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules.
Core sells sequencing data and bioinformatic analytics services to the scientific community. Core aims to permit the development of research on sequencing protocols and encourage collaboration with clinicians to develop the next generation genomic DNA testing.
University of Pittsburgh Cell Culture and Cytogenetics Facility
Pitt Cell Culture and Cytogenetics Facility
The Cell Culture and Cytogenetics Facility carries out classical and molecular cytogenetic analyses. These studies include karyotyping, special staining and banding procedures, and fluorescence in situ hybridization (FISH). This analysis can be performed on cells from blood or tissue specimens from humans or experimental animals, cultured cells, and/or fresh, frozen, or paraffin-embedded tumor biopsies. This approach can be used to characterize the karyotype of cells; map the location of new genes, virus, or transgene insertions; monitor established cell lines to rule out interspecies cell culture contamination or other changes during cell culture; ensure the fidelity of embryonic stem cells prior to production of knockout mice; determine the pattern of chromosomal gains and losses; and enumerate copy numbers of chromosomes or cancer-related genes. The Cell Culture and Cytogenetics Facility provides comprehensive state-of-the-art cytogenetics services ranging from assisting investigators with study design, performing cell culture, preparing probes, carrying out and interpreting classical and molecular cytogenetic analyses, and assisting in manuscript preparation. The laboratory includes equipment for cell culture, cryopreservation, cytogenetic harvests, cytogenetic analysis of human and other mammalian cells, FISH, molecular genetic procedures requisite for FISH, including polymerase chain reaction (PCR) amplification, fluorescence and light microscopy, darkroom for standard photomicrography and printing as well as digital imaging and printing to laser or dye sublimation printers.
University of Alabama at Birmingham Labs and Facilities
University of Alabama at Birmingham Labs & Facilities
Proteomics involves analysis and identification of protein structure and function. Through Proteomics Core, investigators at Mayo Clinic and elsewhere have access to a broad range of proteomics services, technologies and guidance to help them answer scientific questions. Toward a goal of improving patient care, the core offers services and conducts research in the areas of mass spectrometry-based differential proteomics, peptide synthesis, protein and peptide purification, and protein identification, characterization and expression.
The Scripps Research Institute Labs and Facilities
The Scripps Research Institute Labs & Facilities
Harvard School of Public Health Bioinformatics Core
Core facility that offers consultations on basic questions in research computing, bioinformatics and computational biology during the initial stages of study design and grant proposals as well as for ongoing, funded studies requiring external expertise. Core has experience in large-scale data management, database design and software development. Staff members can provide assistance in quality assurance and analysis of gene expression arrays, genome-wide SNP arrays, CNV studies and different aspects of second-generation sequencing technologies such as ChIP-seq, RNA-Seq or resequencing efforts. Services also include provision of external information generated from public database, data curation and assistance on choosing the right data format and annotation standard to ensure best practices in data management and submission are being maintained.
University of California Santa Cruz Labs and Facilities
University of California Santa Cruz Labs & Facilities
University of California Los Angeles Labs and Facilities
University of California Los Angeles Labs & Facilities
University of California Irvine Labs and Facilities
University of California Irvine Labs & Facilities
University of Southern California Labs and Facilities
University of Southern California Labs & Facilities
UM Miller School of Medicine Farooq Laboratory of Macromolecular Biophysics
University of Miami Leonard M. Miller School of Medicine Farooq Laboratory of Macromolecular Biophysics
University of Miami Miller School of Medicine Farooq Laboratory of Macromolecular Biophysics
Our laboratory applies a diverse array of biophysical techniques to study macromolecular interactions at hydrodynamic, thermodynamic, kinetic and structural level in the context of key signaling circuitry pertinent to cell growth and differentiation, cell survival and motility, cell cycle regulation, apoptosis and cancer. Our laboratory provides services in regards to the study of proteins, protein-protein and protein-ligand interactions using the following tools: - Isothermal Titration Calorimetry - Differential Scanning Calorimetry - Pressure Perturbation Calorimetry - Static Light Scattering - Dynamic Light Scattering - Stop-Flow Spectroscopy - Circular Dichroism - Molecular Modeling - Molecular Dynamics Please contact us for pricing and quotation.
University of Alberta Labs and Facilities
The Gene Expression Core (GEC), part of the Advanced Genomics Technology Center at Mayo Clinic, provides comprehensive services and technical support for the measurement of gene expression in clinical and nonclinical samples. The GEC serves customers from both inside and outside Mayo Clinic. The GEC utilizes multiple state-of-the-art platforms _������������ including microarray-based technologies from Affymetrix, Illumina and Agilent, and quantitative polymerase chain reaction (qPCR) instrumentation from Fluidigm and Applied Biosystems _������������ for a variety of gene expression analyses. Services are also available for sample preparation for whole-genome messenger RNA (mRNA) and microRNA (miRNA) profiling by next-generation sequencing. The GEC currently provides whole-transcriptome and miRNA expression analyses of RNA derived from fresh-frozen tissues; formalin-fixed, paraffin-embedded tissues; laser-capture microdissected cells; and cell lines.
Queens Medical Research Institute Labs and Facilities
Queen''''s Medical Research Institute Labs & Facilities
Queens Medical Research Institute Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024. Queen' '''s Medical Research Institute houses over 600 researchers and aims to tackle a wide range of diseases at the most fundamental cellular level.
University of California at Davis Genome Center Proteomics Core Facility
University of California Davis Genome Center Proteomics Core Facility
Core provides LC-MS/MS analysis including Protein ID, Proteomics Profiling, Targeted Proteomics and Post Translational Modification analysis. Analytical proteomic services are provided with emphasis on label free quantitative proteomic profiling, analysis of macromolecular complexes, post-translational modification of their constituents and standard protein identification from complex protein mixtures.
Colorado State University Labs and Facilities
Colorado State University Labs & Facilities
University of Miami Stable Isotope Laboratory Core Facillity
University of Miami Stable Isotope Facillity
Laboratory facility has two Isoprime Isotope Ratio mass spectrometers. One capable of measuring oxygen and hydrogen isotope ratios of water and the other capable of measuring carbon and nitrogen isotope ratios of organic matter.
Baylor College of Medicine Analyte Center
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024. Analyte Center provides analytical services to the research community within Baylor College of Medicine and to investigators at other institutions. We provide access to state-of-the-art gas chromatography/mass spectroscopy, tandem mass spectroscopy, and high pressure liquid chromatography for the purpose of quantitative analysis of small organic molecules. In addition to a broad spectrum of routinely offered services we can also provide specialty services on demand provided our instrumentation will provide the sensitivity and specificity required for the investigator.
Harvard NeuroDiscovery Center - Advanced Tissue Resource Center
Harvard NeuroDiscovery Center Advanced Tissue Resource Center
NeuroDiscovery Advanced Tissue Resource Center
NeuroDiscovery Advanced Tissue Resource Center (ATRC)
Core facility that provides provides state-of-the-art molecular pathology resources to the Harvard community including laser capture microscopy, DNA/RNA/miRNA quality/expression analysis, Luminex FlexMap 3D multiplex bead cytometry, and real-time PCR. The ATRC is a fee-for-use facility. For NeuroDiscovery members, the first 10 hours of training, consultation and instrument use is free. This initial period is intended to provide a first time user with preliminary data/proof of concept regarding their project, and is generally sufficient when investigators work under the aegis of ATRC staff. Thereafter, the base fee varies depending on activity and the extent of your proposed work. Project-based charge-back agreements for large projects can be negotiated with the ATRC Director, Dr. Charles Vanderburg. Although priority is given to NeuroDiscovery members investigating neurodegenerative diseases and the CNS, the facility is also available to any academic investigators within the Harvard medical community and the greater-Boston research community. Under special arrangements the facility may also be made available to the commercial sector. Please contact ATRC Director, Dr. Charles Vanderburg, for details.
University of Arizona Infectious Disease Resource Core
IDRC aims to improve the detection and prevention of infectious diseases, by developing new diagnostic laboratory methods for use in evidence-based research and clinical practice
University of Southern California Norris Comprehensive Cancer Center Immune Monitoring Core Facility
USC Norris Comprehensive Cancer Center Immune Monitoring Core Facility
The mission of the USC Arnold and Mabel Beckman Center for Immune Monitoring is to provide the USC community and external customers with the highest quality support for clinical trials for immunotherapy of human cancers; facilitate basic, translational, and clinical research with an immunological monitoring component; and provide immunological assay training and education. The IM core provides quality assessments of immunological function necessary for the study of pathogenesis, treatment, and prevention of cancer and other human diseases. Supporting clinical trials for immunotherapy of human cancer: For physicians involved in clinical trials for immunotherapy of human cancer, the Beckman Center for Immune Monitoring Core offers several assays to assess patient immune responses. Such assays provide a highly sensitive and quantitative means of measuring the efficacy of an experimental treatment as a surrogate endpoint or as a correlative to clinical responses. It can help establish proof of principle that a treatment works, and suggest changes to adapt a standard treatment protocol to individual patient needs. Besides the Gold Standard of Immune monitoring: the ELISPOT assay for detection of cytokines released by activated T cells, we also perform intracellular cytokine staining and can detect tumor specific T cells by MHC tetramer analysis. Helper and killer T cells can be separated, and proliferative and cytotoxic responses are quantified in radioactive assays. The monitoring protocol of choice is tailor made to fit the needs and the possibilities of each treatment protocol. The core offers freezing and storage capacity for clinical samples and full analytical support for monitoring assays. It is also possible to send in samples for post-assay analysis using our state-of-the-art ELISPOT reader. Facilitating research with an immune monitoring component: For researchers within travel distance of our facility, we offer equipment and technical assistance for performance and/or analysis of ELISPOT assays, flow cytometry-based assays, radioisotope-based proliferation and cytotoxicity assays, multiplexing ELISA assays, and molecular-based quantitative PCR assays. Our lab has equipment for controlled rate freezing and storage of cryopreserved peripheral blood cells, tissue culture facilities and an ELISPOT reader to analyze your 96 well plates. Assays and technical support are also available to support translational projects that utilize in-vitro systems and in vivo animal models.
WUSTL Mouse Cardiovascular Phenotyping Core
Washington University in St. Louis Mouse Cardiovascular Phenotyping Core
Washington University Mouse Cardiovascular Phenotyping Core
Core that was established in 1998 and currently provides approximately 3,000 surgical, imaging and functional cardiovascular physiology services annually to its academic and industry partners throughout the world. With an experienced staff of 4 dedicated investigators, each with over 10 years of animal physiology experience, the MCPC provides a focused, systematic approach to the study of the basal physiology and pathophysiology of the mouse cardiovascular system.
Washington University in St. Louis National Nanotechnology Infrastructure Network - Nano Research Facility
Washington University in St. Louis NNIN - Nano Research Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15,2024. Nano Research Facility (NRF) at Washington University in St. Louis is a NNIN nodal facility supported by the National Science Foundation. It cultivates an open, shared research, and education environment that brings researchers across disciplines together, particularly in the emerging area of nanomaterials with applications in the energy, environment, and biomedical fields. The mission is to be a resource to the scientific and technical community for the advancement of nanoscience and nanotechnology in a safe and environmentally benign manner. NRF includes a micro- and nano-fabrication lab (clean room), surface characterization lab, particle technology lab, and imaging lab with a focus on bio-imaging. NRF provides unique technical expertise in: Knowledge-based synthesis of nanostructured materials Particle instrumentation tools for toxicity studies Non-invasive imaging modalities for biological applications Clean Energy Applications Energy and Environmental nanotechology Environmental Health and Safety As a member of the National Nanotechnology Infrastructure Network (NNIN), supported by the National Science Foundation, NRF is available to both academic and industrial users nation-wide and across the globe.
Bio Basic Inc. is a privately owned dynamic biotechnology company. The company was founded in 1990 in Toronto, Canada. From 1990 to 1995, Bio Basic Inc.''s primary focus has been in the field of biochemicals. Starting in 1995, Bio Basic Inc. has begun manufacturing various Life Science Products. Throughout the past years, the company has developed rapidly and served as a one-stop-shop to our customers in the life sciences field. To date, Bio Basic Inc. has approximately 600 employees, seven laboratories, three factory buildings, 40 international distributors and over 10,000 customers worldwide. Bio Basic Inc. is committed to innovation and excellence. In an effort to achieve this, Bio Basic Inc. has continuously directed efforts in R & D and improving the quality of our products. Bio Basic Inc. is proud to offer a breath of products and services to customers worldwide. Several of our product lines such as, Molecular Biology Kits, Biochemicals, Synthetic Genes and Synthetic Oligos have already shown dominant market presence and have been widely recognized by customers worldwide.
Dana-Farber/Harvard Cancer Center DNA Resource Core
A centralized laboratory that provides DNA sequencing and plasmid clone storage and distribution services to researchers in the DF/HCC community and around the world. It provides the following services: Large-scale DNA sequencing service, Small-scale DNA sequencing service, Same-day sequencing service, Automated, high-throughput plasmid DNA preparations, Chain termination sequencing service, DNA extraction service. The DNA Resource Core was started to meet a growing need for DNA sequencing services at a cost that is affordable for academic labs. Our services now include DNA sequencing for large- and small-scale projects and a plasmid repository & distribution service. Our highest priorities are quality assurance, user support and timely request fulfillment. Questions about the plasmid repository can also be directed to plasmidhelp(at)hms.harvard.edu.
The Duke Clinical Research Unit is a state-of-the-art research facility located within the Duke University Medical Center campus that provides infrastructure support to sponsors and investigators who are: - Testing new drug candidates and other cutting-edge therapies - Seeking to identify and validate novel biomarkers Building on the strength of Duke''s thought leadership, therapeutic expertise, patient base, and access to the latest technologies, the DCRU is a critical component of the Duke Translational Medicine Institute''s efforts to speedily translate new laboratory discoveries into treatments for patients DCRU is a Duke resource available to investigators for the conduct of clinical trials in either adult or pediatric populations. For non-commercial clinical trials funded by the NIH, foundations, investigators������������������������ departments, and similar funding mechanisms, the DCRU provides: - Space - Nursing support - Core laboratory support - Statistical support for study design and analysis - Metabolic kitchen support DCRU can also be your partner for industry-sponsored studies, offering either full-service execution of your studies or fee for service in the above areas.
Massachusetts General Hospital Flow Cytometry Core
The cell sorting and analysis lab provides access to the most sophisticated flow cytometers presently available. The core is able to analyze and physically separate cells based upon features detectable with fluorescently labeled monoclonal antibodies. The Simches site is located in the newly constructed space located in room 3.434 in the Simches Building. Major Equipment (Simches): Analytic Seven Laser LSR configured with 355 nm, 407 nm, 488 nm, 532 nm, 594 nm, 633 nm, and 780 nm air cooled lasers providing a wide range of excitation possibilities. Modified Digital Vantage cell sorter with 2 water-cooled argon, 2 krypton and one air cooled 633 nm laser. The CNY site is located in the newly constructed space located in room 6.307 in Building 149, 13th Street, Charlestown Navy Yard. Major Equipment (CNY): Analytic three Laser LSR II configured with 405 nm, 488 nm, and 633 nm air cooled lasers providing a wide range of excitation possibilities. A four laser FACS Aria II cell sorter configured with 405 nm, 488 nm, 594 nm and 633 nm air cooled lasers providing a wide range of excitation and sorting possibilities.
Brigham and Women''''s Hospital Confocal Microscopy Core Facility
Our facility provides equipment and training for researchers interested in using widefield & confocal microscopy, photobleaching, and live cell imaging studies.
HNDC Drug Discovery in Neurodegeneration
Harvard NeuroDiscovery Center - Laboratory for Drug Discovery in Neurodegeneration
Harvard NeuroDiscovery Center Drug Discovery in Neurodegeneration
Harvard NeuroDiscovery Center Laboratory for Drug Discovery in Neurodegeneration
Harvard University Drug Discovery in Neurodegeneration
NeuroDiscovery Center Laboratory for Drug Discovery in Neurodegeneration
Core facility that provides the following services: Assay design and development service. The NeuroDiscovery Center' '''s Laboratory for Drug Discovery in Neurodegeneration (LDDN) was established to discover chemical agents from which we and others will develop a new generation of drugs to treat neurodegenerative diseases (including degenerative diseases of the eye and ear). To accomplish this goal, LDDN has recruited a permanent staff of industry-seasoned scientists with expertise in assay development, laboratory automation, informatics, and medicinal chemistry, to work in close collaboration with principal investigators from the academic neuroscience community. In this way, LDDN helps transform discoveries in the basic biology of neurodegeneration into opportunities for drug discovery. (While priority is given to members investigating neurodegenerative diseases and the central nervous system, we welcome inquiries from all investigators.)
Gnarus Systems is pleased to offer cat-SAR; a peer-reviewed in silico toxicity prediction expert system. The cat-SAR system associates 2-dimensional chemical fragments with active or inactive compounds in a learning set. Unlike many other approaches, cat-SAR is transparent and model parameter selection is controlled by the user. As such, the approach is sharable and allows unrestricted user scrutiny, intervention and model optimization throughout the SAR modeling process. This rationale negates any a priori requirements that a given set of data must fit the attributes of a predefined and often proprietary modeling process. The cat-SAR system essentially ??????????????????learns???????????? about the biological activity of chemicals by analyzing ??????????????????learning sets???????????? of data. These are endpoint specific databases of toxicological or pharmacological chemical activity (e.g., carcinogens and developmental toxicants) that are assembled by us or others. Currently, we have validated and usable learning sets for a variety of health endpoints including cancer, anticancer, genotoxicity, developmental toxicity, and chemical allergy. Currently, cat????????????SAR models are available for: Rats, mice, and rodents carcinogenesis including gender-specific submodels Mammary Cancer in Rodents Tissue/organ specific carcinogenesis for 12 tumor types Salmonella mutagenicity (i.e. the Ames Assay) Developmental Toxicity Allergic Contact Dermatitis Respiratory Hypersensitivity Mouse Local Lymph Node Assay Ocular toxicity Estrogen mimics based on the E-SCREEN assay Anticancer activity to several different breast cancer cell lines
The main objective of the Joslin Diabetes Center Genomics Core is to facilitate research by laboratories by providing equipment, expertise, and services in nucleic acid analysis that would be too specialized or costly for individual laboratories to provide independently. Instruments include: ������������ Fluidics Station 400 ������������ GeneChip?������ Scanner 3000 ������������ Hybridization Oven 640 ������������ NanoDrop ND-1000 ������������ NanoDrop ND-3300
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Contract research organization that provides an architecture for text mining and semantic annotation. It provides facilities to link texts data to concepts of the Linked Open Data network through various sources like DBpedia, Geonames, CIA World Factbook or directly to Wikipedia or a search engine when there is no available resource.
WUSTL School of Medicine Center for Clinical Imaging Research
Washington University School of Medicine in St. Louis Center for Clinical Imaging Research
WUSTL School of Medicine Center for Clinical Imaging Research (CCIR)
The CCIR provides a full range of biomedical imaging services to support clinical research projects. These services include: (1) Pre-study services that help investigators design, set up, and kick off the study; (2) Coordinating services, including Scanning, that provide assistance in executing, monitoring and evaluating the study; and, (3) Information Technology management services to handle, track, and process imaging data.
3Scan uses the cutting edge technology of the KESM (Knife Edge Scanning Microscope) to automatically section and image samples. Knife-edge scanning, introduced in the KESM instrument, not only preserves image registration throughout the depth of the specimen block but also isolates the tissue above the knife from that below to eliminate undesirable events (back-scattering of light and bleaching of fluorescent-stained tissue below the knife). Using the KESM, 3Scan is able to scan a one cc^3 block of tissue (for example, a whole mouse brain) at submicron resolution in under 100 hours. With this resolution (a voxel size of 0.6 um x 0.7 um x 1.0 um) 3Scan is able to show cell scale phenomena in the context of a compete organ. In the example of a whole mouse brain this means that 3Scan is able to accurately model every neuron in the mouse brain sample.
WUSTL Biology Department Imaging Facility
Washington University in St. Louis Biology Department Imaging Facility
Dedicated imaging facility for many aspects of brightfield and fluorescence microscopy, including low-light imaging, scanning confocal imaging, imaging of fixed and living tissues, deconvolution, multi-channel imaging, FRAP, FRET, time-lapse and z stack (3D and 4D) acquisition, and spectral analysis.
Australian National Fabrication Facility Characterisation
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Network of laboratories which provides leading-edge research capability and supports excellence in science. The capability provided by ANFF enables users to process hard materials (metals, composites and ceramics) and soft materials (polymers and polymer-biological materials) and transform these into structures that have various applications.
DFCI Center for Cancer Computational Biology
Dana-Farber Cancer Institute Center for Cancer Computational Biology
DFCI Center for Cancer Computational Biology (CCCB)
Core facility that provides the following services: Microarray and other genomic data analysis, MiSeq. The Center provides broad-based support for the generation, analysis, and interpretation of genomic and other large-scale data in the context of basic, clinical and translational research. The CCCB has three primary elements. * The CCCB sequencing facility offers a wide range of services to assist in the design and execution of next-generation sequencing projects. Utilizing the Illumina (Solexa) sequencing technology, they currently support a number of applications inlcuding ChIP-Seq, RNA-Seq, whole genome, whole exome, and targeted re-sequencing. * The analytical services and support platform aims to provide state-of-the-art assistance in the collection, management, analysis, and interpretation of large-scale data with a focus on data generated using ' '''omic technologies. In addition, they offer software, services, and training designed to assist investigators in advancing their research. * The CCCB research program is focused on development of new methods for improving analysis and interpretation of genomic data through integration of diverse data types with the goal of creating open-source software tools to be made freely-available to the research community.
Australian National Fabrication Facility Specialist Device Fabrication
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. The ANFF provides leading-edge research capability and supports excellence in science. The capability provided by ANFF enables users to process hard materials (metals, composites and ceramics) and soft materials (polymers and polymer-biological moieties) and transform these into structures that have application in sensors, medical devices, nanophotonics and nanoelectronics. It has a strong emphasis on service provision to the research community. ANFF seeks to enhance national and international collaborations and enable world-class-research.
ANFF Materials Synthesis and Macro Fabrication
Australian National Fabrication Facility Materials Synthesis and Macro Fabrication
Australian National Fabrication Facility Bio Fabrication
MMDiff - Statistical Testing for ChIP-Seq data sets
Software package that detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples.
Australian National Fabrication Facility Photonics
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2,2024. ANFF provides leading-edge research capability and supports excellence in science. The capability provided by ANFF enables users to process hard materials (metals, composites and ceramics) and soft materials (polymers and polymer-biological moieties) and transform these into structures that have application in sensors, medical devices, nanophotonics and nanoelectronics. It has a strong emphasis on service provision to the research community. ANFF seeks to enhance national and international collaborations and enable world-class-research.
Georgetown University Labs and Facilities
Harvard NeuroDiscovery Center Labs and Facilities
Harvard Medical School NeuroDiscovery Center Labs & Facilities
Harvard Medical School NeuroDiscovery Center Labs and Facilities
Established in 2001 by Dr. Joseph Martin (Dean of Harvard Medical School, 1997-2007), the Harvard NeuroDiscovery Center is a pioneering biomedical research group focused on ending suffering from neurodegenerative diseases. By drawing on the intellectual strength and proven capability of the Harvard medical community and colleagues throughout the world, the NeuroDiscovery Center has developed a unique approach to understanding and treating these devastating diseases.
HMS Systems Biology Flow Cytometry Facility
Harvard Medical School Systems Biology Flow Cytometry Facility
Core facility that provides the following services: Sorting and analysis services. The facility houses two state-of-the-art BD analyzers with high-throughput capability, a Stratedigm benchtop analyzer, a high-speed BD cell sorter, and both Mac and PC workstations for data analysis. Sorting services are offered through the facility, as well as instrument and software training.
University of Southern California Norris Comprehensive Cancer Center Cancer Research Informatics Core
USC Cancer Research Informatics Core (CRIC)
USC Norris Comprehensive Cancer Center Cancer Research Informatics Core
USC Norris Comprehensive Cancer Center CRIC
Over the last 10 years the CRIC team has developed a set of software tools and applications to support the research activities of USC investigators. CRIC provides tools for data collection, migration, reporting, customized survey creation, and web-based data capture & reporting. CRIC has also developed and supported databases for laboratory data management, multi-center clinical trials coordination, epidemiologic & prevention studies as well as disease specific studies.
BCM Circulating Tumor Cells Core Facility
Baylor College of Medicine Circulating Tumor Cells (CTC) Core Facility
Baylor College of Medicine Circulating Tumor Cells Core Facility
The CTC Core is devoted to the biology and enumeration of CTC in metastatic cancers. The Veridex CellSearch?? CTC Test is used to measure Circulating Tumor Cells (CTC) cells in blood samples from cancer patients. The technology can also be used to measure Circulating Endothelial Cells (CEC) in blood, as indicators of other vascular damage-associated diseases such as diabetes.
exeResearch is an independent research company providing computational chemistry and biochemistry research assistance to those in academia and industry. We help scientists without the resources, time, or knowledge to complete the needed computational aspects of their research projects.
Washington University in St. Louis Histology Core
The Histology Core has all the requisite equipment and reagents to enable a variety of tissue processing, embedding and sectioning protocols, including epon/araldite, glycol and methyl methacrylate, polyethylene glycol (PEG), paraffin and cryosectioning. Users of the Histology Core can choose to submit full service jobs and allow core personnel to embed, section and counterstain fixed tissue samples or they can sign up to use a microtome and cut the tissue themselves. Training on any aspect of the histologic process is available on request. All core services are equally available to core members and non-members on a first-come first-served basis.
OSU Nutrient and Phytochemical Analytics Shared Resource
Ohio State University Nutrient and Phytochemical Analytics Shared Resource
Ohio State University Nutrient and Phytochemical Analytics Shared Resource (NPASR)
OSU Nutrient and Phytochemical Analytics Shared Resource (NPASR)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented in May 14,2024. Nutrient and Phytochemical Analytic Shared Resource (NPASR) provides expert bioanalytical method development and quantitative analysis. The NPASR will support development of methods and techniques to quantitatively determine nutrients and phytochemicals in foodstuffs as well as identification of these compounds and respective metabolites in biological samples from both human clinical trials and animal model investigations. The NPASR personnel are specialists in the field of analytical chemistry, concentrating their expertise in examining the bioavailability, metabolism and physiological significance of carotenoids, isothiocyanates, isoflavones and other phytochemicals. NPASR is capable of developing analytical methods for a Good Laboratory Practice (GLP) environment. Primary goals of NPASR are to provide investigators with expert, leading-edge bioanalytical method development and quantitative analysis of nutrients and phytochemicals in foodstuffs and their metabolites in biological samples and an enhanced understanding of the role of dietary compounds in cancer prevention and control.
Georgia Tech Center for Organic Photonics and Electronics
Georgia Institute of Technology Georgia Tech Center for Organic Photonics and Electronics
Georgia Institute of Technology Georgia Tech Center for Organic Photonics and Electronics (COPE)
Georgia Tech Center for Organic Photonics and Electronics (COPE)
The Georgia Tech Center for Organic Photonics and Electronics (COPE) is a premier national research and educational resource center that creates flexible organic photonic and electronic materials and devices that serve the information technology, telecommunications, energy, and defense sectors. COPE creates the opportunity for disruptive technologies by developing new materials with emergent properties and by providing new paradigms for device design and fabrication. This helps enable a new generation of devices and systems that meet the challenges that these sectors and our ever-changing society face in this decade and the future.
University of Maryland Bioprocess Scale-Up Facility
The Bioprocess Scale-Up Facility (BSF) is the Biotechnology Research and Education Program' '''s modern bioprocessing laboratory dedicated to the development and scale-up of biotechnology products and processes. With over 1000 fermentations conducted since 1998 alone, the BSF has accelerated the R&D of local biotechnology leaders such as Human Genome Sciences, NIH and MedImmune, as well as growing Maryland start-ups such as Martek Biosciences and Digene Corporation. The BSF' '''s capabilities include fermentation, purification, product analysis and solving challenging problems such as biopolymers, turbulence and multiphase fluid dynamics, biosensors, process analysis and control, and both metabolic and biochemical engineering. BSF is a unique facility in Maryland not restricted by current good manufacturing practices (cGMP) requirements, and production processes are directly transferable to partners operating under cGMPs (required for FDA-approved clinical trials), such as Cambrex Inc. and the Walter Reed Army Institute of Research. The BSF enables small manufacturing companies to offer extended capabilities to major pharmaceutical (Big Pharma) companies out-of-state. The Biopharmaceutical Advancement Facility (BAF) specializes in the development of cell culture-based biopharmaceutical products. BAF is part of the Biotechnology Research and Education Program and a companion to the Bioprocess Scale-Up Facility in the Maryland Technology Enterprise Institute (Mtech) at the University of Maryland. The facility' '''s staff members offer extensive expertise in addressing challenging problems with the advancement of anchorage-dependent or suspension-adapted cell lines. The facility is not restricted by current good manufacturing practices (cGMPs); however, production processes are directly transferable to partners operating under cGMPs.
University of Chicago Advanced Imaging Core
University of Chicago Advanced Imaging Core (AIC)
The Center' '''s Advanced Imaging Core (AIC) features state-of-the-art core technologies available on a fee for service basis.
University of Rochester Medical Center Neurobiology and Anatomy
The Department of Neurobiology and Anatomy is strongly committed to its major academic missions of research and education. Teaching and leadership roles in both graduate and medical education remain enduring commitments today, as they have been since the inception of the medical campus in the 1920s. This is matched by our commitment to research on the structure and function of the nervous system.
North Carolina State University Plant Transformation Laboratory Core Facility
NC State University Plant Transformation Laboratory
North Carolina State University Plant Transformation Laboratory
Provides innovative solutions, technologies, expertise, training, and services for research and applications related to plant transformation. The PTL staff and facilities are available for research collaborations; core resources are available for user-driven projects with cost recovery; fee-based plant transformation services can be provided for the NCSU community and external partners.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15, 2024. Commercial neuroimaging organization that provides services for compound profiling, biostatistics, computed tomography, and data modeling.
German Cancer Research Center Labs and Facilities
German Cancer Research Center (DKFZ) Labs & Facilities
German Cancer Research Center (DKFZ) Labs and Facilities
German Cancer Research Center Labs & Facilities
To perform research into cancer is the task of the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ). DKFZ is the largest biomedical research institute in Germany and a member of the Helmholtz Association of National Research Centers. In over 70 divisions and research groups, our more than 2,500 employees, of which more than 1,000 are scientists, are investigating the mechanisms of cancer, are identifying cancer risk factors and are trying to find strategies to prevent people from getting cancer.They are developing novel approaches to make tumor diagnosis more precise and treatment of cancer patients more successful.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Preclinical CRO for drug development services including a wide variety of disease model studies as well as PK and toxicity services. Major service areas are: - Preclinical In Vivo Efficacy Testing of compounds in many disease models including inflammatory diseases, cancer and bacterial infection. - Vaccine testing services including vaccine efficacy testing in disease model studies such as arthritis. - Bacterial efficacy studies in mice and rats to determine antibiotic efficacy. - Pharmacokinetics and related in vivo tests. - Our technical staff has a combined 70+ years of experience in drug and vaccine development services for efficacy and safety.
Barts and The London School of Medicine and Dentistry Labs and Facilities
Barts and The London School of Medicine and Dentistry Labs & Facilities
Barts and The London offers international levels of excellence in research and teaching while serving a population of unrivalled diversity. Through partnership with our linked trusts, notably Barts and The London NHS Trust, and our associated University Hospital Trusts _������������_ Homerton, Newham, Whipps Cross and Queen' '''s (Romford) the School' '''s research and teaching is informed by an exceptionally wide ranging and stimulating clinical environment.
Blizard Institute of Cell and Molecular Science Labs and Facilities
Blizard Institute of Cell and Molecular Science Labs & Facilities
The Blizard Institute is the largest institute of Barts and the London School of Medicine and Dentistry and aims to deliver excellence in all aspects of research, teaching and clinical service
Executive branch department of the federal government charged with coordinating and supervising all agencies and functions of the government directly related to national security and the United States Armed Forces.
University of California at Davis; California; USA
Louisiana State University Pennington Biomedical Research Center Cell Biology and Bioimaging Core
Louisiana State University Pennington Biomedical Research Center Cell Biology and Bioimaging Core (CBBC)
LSU Cell Biology and Bioimaging Core (CBBC)
LSU PBRC Cell Biology and Bioimaging Core
LSU Pennington Biomedical Research Center Cell Biology and Bioimaging Core
The Cell Biology and Bioimaging Core (CBBC) provides access to state of the art imaging, analytical, and histological equipment as well as technical expertise and assistance to researchers at the PBRC, LSU''s main campus, and outside the LSU university system.
National Institute of Arthritis and Musculoskeletal and Skin Diseases
Established in 1986, the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) was established in 1986. The mission of the NIAMS is to support research into the causes, treatment, and prevention of arthritis and musculoskeletal and skin diseases; the training of basic and clinical scientists to carry out this research; and the dissemination of information on research progress in these diseases. The Institute also conducts and supports basic research on the normal structure and function of bones, joints, muscles, and skin. Basic research involves a wide variety of scientific disciplines, including immunology, genetics, molecular biology, structural biology, biochemistry, physiology, virology, and pharmacology. Clinical research includes rheumatology, orthopaedics, dermatology, metabolic bone diseases, heritable disorders of bone and cartilage, inherited and inflammatory muscle diseases, and sports and rehabilitation medicine.
University of Arizona Nuclear Magnetic Resonance Core Facility
University of Arizona Nuclear Magnetic Resonance Facility
Interdisciplinary NMR spectroscopy research facility for structural elucidation and study of conformation and dynamics of organic compounds, peptides, oligonucleotides and other small biopolymers.
UVM Center of Biomedical Research Excellence in Neuroscience Labs and Facilities
University of Vermont Center of Biomedical Research Excellence (COBRE) in Neuroscience Labs & Facilities
University of Vermont Center of Biomedical Research Excellence (COBRE) in Neuroscience Labs and Facilities
University of Vermont Center of Biomedical Research Excellence in Neuroscience Labs & Facilities
University of Vermont Center of Biomedical Research Excellence in Neuroscience Labs and Facilities
UVM Center of Biomedical Research Excellence (COBRE) in Neuroscience Labs & Facilities
UVM Center of Biomedical Research Excellence (COBRE) in Neuroscience Labs and Facilities
UVM Center of Biomedical Research Excellence in Neuroscience Labs & Facilities
UVM COBRE in Neuroscience Labs & Facilities
UVM COBRE in Neuroscience Labs and Facilities
The Center of Biomedical Research Excellence (COBRE) in Neuroscience at the University of Vermont (UVM), which was established in 2001 with funding from the National Center for Research Resources of the National Institutes of Health, was created to integrate and expand neuroscience research and training at UVM by building a collaborative intellectual infrastructure, developing cutting-edge shared core facilities, and by providing research funding for neuroscience faculty, especially junior faculty, in multiple colleges. The Neuroscience COBRE supported formation of the university-wide Neuroscience Graduate Program, expanded interdisciplinary neuroscience research, and promoted translational research by increasing the interaction between basic and clinical neuroscientists at UVM.
University of Virginia Bioinformatics Core
Core serves as a centralized resource for providing expert and timely bioinformatics consulting and data analysis solutions. The core offers services to investigators both within and outside UVA on both grant-funded and chargeback-based projects for management and analysis of large-scale biological datasets produced by high-throughput genomics experiments. The Core's mission is to build and maintain an infrastructure that enables the application of strong bioinformatics analysis with a measurable impact on the ability of UVa investigators to both publish their work and obtain new funding.
University at Albany Center for Functional Genomics
University at Albany Center for Functional Genomics Labs and Facilities
CFG maintains core competencies in genomics, proteomics, bioinformatics, transgenesis and cell and tissue culture. Provides lab space, technological infrastructure, and staff. Provides basic laboratory services to bioscience researchers at companies, universities, and government agencies around world for fee. Works with Commonwealth Biotechnologies, Inc. for projects that need to meet FDA requirements for submission of data in support of new drug applications.
UM Sylvester Comprehensive Cancer Center Labs and Facilities
University of Miami Sylvester Comprehensive Cancer Center Labs & Facilities
University of Miami Sylvester Comprehensive Cancer Center Labs and Facilities
UM Sylvester Comprehensive Cancer Center Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2024. With more than 250 physicians and scientists dedicated to cancer care and research, Sylvester is leading the search for a cancer cure. Every day, our physicians and scientists within the cancer center' '''s site disease groups and multidisciplinary research programs, are discovering exciting new breakthroughs that are quickly transforming the way cancer patients are diagnosed and treated.
New York University Langone Medical Center Immunohistochemistry (IHC) Core
New York University Langone Medical Center Immunohistochemistry Core
The Immunohistochemistry Core, a component of the Experimental Pathology Shared Resource, is located in Bellevue Hospital within the NYULMC Department of Pathology''s Anatomic Pathology clinical space. The laboratory serves as an immunohistochemical antibody repository with a catalog of over 900 antibodies. Antibodies are in stock and available for use in the core laboratory for the collection of experimental immunohistochemistry data. The laboratory develops immunohistochemical protocols for new antibodies (commercial or proprietary) that have not been tested in fresh, frozen, fixed human or animal tissues and cells. In addition to performing manual labeling, the laboratory is equipped with two Ventana NEXES and one Discovery automated immunohistochemical staining instruments. The laboratory uses human and animal tissue micro-arrays for validation and employs a wide variety of antigen retrieval methods for protocol development. The core offers tyramide and polymer amplification methods (manual) and single or two color chromogenic immunohistochemistry. The laboratory has also commenced developing protocols and validating antibodies for immunoflorescence in frozen and FFPE tissue samples. The laboratory faculty and staff are available to provide hands-on informal training, as well as guidance and support for the design and execution of experiments involving histopathology and immunohistochemistry of human and animal cells and tissues. In conjunction with the Histopathology Core Laboratory, the Immunohistochemistry Laboratory can also assist investigators with routine and advanced histopathologic services for tissue and cell specimens (including guidance on initial processing steps: grossing/tissue preparation, processing, embedding, paraffin/frozen microtomy) for samples destined for histopathological interpretation and analysis. In addition, we offer extensive options for special and routine histochemical and immunohistochemical labeling of both human and animal model cells and tissues.
University of Delaware Labs and Facilities
University of Delaware Labs & Facilities
Advanced Analytical Testing Service (A.A.T.S.)
Advanced Analytical Testing Service (AATS)
Advanced Analytical Testing Service (AATS) is dedicated to providing premium testing services for food, dietary supplement, biotechnology and cosmetic industries. AATS is established on our clients'' greatest satisfaction with our sample processing, testing method development and post-testing consultation. Our goal is to report authentic and accurate testing results with optimal quality and minimum turnover time. AATS is FDA registered independent analytical testing provider that is familiar with cGMP, USP and ISO standards. AATS has established full quality system on personnel, training, sample receipt and handling, testing, quality control and documentation. We provide testing results of high quality, because we have a strong quality system built in our testing facilities.
Preclinical organization offers advanced services and collaborative projects in pharmacology, neurochemistry and tissue metabolism in experimental models of human diseases. Bioanalytical services include chromatographic and mass spectrometry techniques, as well as, immunoassays and enzymatic assays for quantification of neurotransmitters and other signaling molecules, metabolites, and drug levels in microdialysis samples, plasma, CSF, urine, culture media, cell lysates and tissue extracts.
UC Irvine High Throughput Screening Service
University of California Irvine High Throughput Screening Service
With the completion of the genome sequence, that offers us a variety of new genes to study, and advances in combinatorial chemistry, that delivers large numbers of synthetic compounds to test, high__������throughput screening (HTS) is becoming a necessary research endeavor. We specialize in HTS of G protein__������coupled receptors (GPCRs). Ligand recognition is quantified in binding experiments or monitored by second messenger responses. One technology that we use is the FLIPR technology that allows for real__������time fluorescent measurements.
University of Southern California Keck School of Medicine; California; USA
Keck School of Medicine of University of Southern California
University of Southern California Keck School of Medicine
Scripps Florida Macromolecular X-ray Crystallography Core Facility
The Scripps Research Institute Scripps Florida Macromolecular X-ray Crystallography Core Facility
Scripps FL Macromolecular X-ray Crystallography Core Facility
The Macromolecular X-ray Crystallography Core Facility of Scripps FL offers state-of-the-art equipment and resources to scientists inside and outside of the Scripps FL campus by providing crystallographic analysis of their chosen biological macromolecules. The core facility offers and operates as a full service core by performing protein crystallization, X-ray diffraction data collection (both in-house and at Argonne National Laboratory) and processing, phasing, crystallographic refinement, model building, and visualization. The structural data obtained by the core will provide scientists with a wealth of information including but not limited to biological functions, 3D-folding, ligand binding (small molecule or protein), or mutational effect of target macromolecules of their interests.
Rutgers Waksman Institute of Microbiology Labs and Facilities
Rutgers University Waksman Institute of Microbiology Labs & Facilities
Rutgers University Waksman Institute of Microbiology Labs and Facilities
Rutgers Waksman Institute of Microbiology Labs & Facilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 10, 2023. Our mission is to conduct research in microbial molecular genetics, developmental molecular genetics, plant molecular genetics, and structural and computational biology. We also provide a catalyst for general university initiatives, a life science infrastructure, undergraduate and graduate education, and a public service function for the State of New Jersey. The Institute employs faculty teams that concentrate on certain classes of organisms amenable to genetic analysis such as bacteria and fungi (E. coli and yeast), animal systems (e.g., Drosophila), and plants (Arabidopsis, tobacco, and maize). Although the Institute focuses on basic questions in microbial, animal, and plant research, it continues to engage in extensive technology transfer of its basic discoveries.
Rutgers Cell and Cell Products Fermentation Facility
Rutgers University Waksman Institute of Microbiology Cell and Cell Products Fermentation Facility
Since its inception in 1951, the fermentation facility''s goal has been to provide affordable fermentation services to a highly diverse client base. Completely renovated in 2011 the fermentation facility, which meets BL2-LS containment requirements, is comprised of four contiguous operation units: -Material Preparation Laboratory -Fermentation In-Process -Computer Control -Product Recovery Room Bio-reactor working capacities range from 10 to 800 liters. All systems are computer controlled with algorithm-based cascade-capable PID programming. In the recovery room, downstream processing includes: -Centrifugation -Filtration -Micro and Ultra-filtration -Cell Disruption With the advantage of having the world''s pharmaceutical industry in its backyard, a productive climate of industrial liaison has been the historical legacy of the facility. Many former facility students and graduates hold positions within the industry. www.waksman.rutgers.edu/fermentation/home
OHSU Molecular Virology Support Core (MVSC)
Oregon Health & Science University Molecular Virology Support Core
Oregon Health & Science University Molecular Virology Support Core (MVSC)
Oregon Health and Science University Molecular Virology Support Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5, 2022. Core facility that provides the following services: DNA isolation service, RNA isolation service, Cloning and endotoxin-free plasmid preparation service, Virus plaque assay, SIV p27 protein ELISA, HIV p24 protein ELISA with sample prep, Real time PCR titer of lentivirus prep with sample prep, Coculture of animal tissues/fluids service, Virus plaque purification service, Virus growth curve service, Protein determination, Bradford method, Crude viral DNA prep service, Gradient purified viral DNA prep service, Southern blot for viral DNA, Viral Real-time PCR, RhCMV Real-time PCR, HSV 1/2 B virus antibody ELISA, single dilution service, RhRRV antibody ELISA, single dilution, RhSFV antibody ELISA, single dilution, SIV antibody ELISA, single dilution, Virus antibody ELISA, RhCMV antibody ELISA, Virus neutralization service, Polyclonal IgG preparation, SIV in vitro susceptibility, p27 ELISA, Vaccinia (MVA) virus plaque assays, Antiviral antibody determination by ELISA, SIV in vitro infectivity (leukocytes) service, Viral load quantification with qPCR, Virus detection using nested PCR, Virus stock production, Cytomegalovirus plaque assays and purification, Cytomegalovirus stock and vector production, Western blot service for viral protein, Cell sample processing and banking, Nucleic acid isolation and purification service, Virus cloning and plasmid preparation service, Vaccinia (MVA) virus stock and vector production. The Core' '''s overall goal is to advance the efforts of the Oregon National Primate Research Center (ONPRC), the Vaccine and Gene Therapy Institute (VGTI), and collaborative research programs focused on nonhuman primate (NHP) infectious disease models and those using viral vectors as tools to modify genes or deliver macromolecules through provision of expertise, reagents, standardized assays, and training in the use of infectious viral agents in their research programs. The MVSC provides specialized expertise and infrastructure in five essential areas: * Virus identification and quantification in clinical specimens * Production of virus stocks, virus vectors, and viral antigen preparations * Serologic assays to assess host antiviral immune responses * Maintenance of cell stocks and sample processing * Development of new reagents and standardized assays The MVSC has considerable experience and expertise in both viral diagnostics and production, particularly for AIDS and CMV pathogenesis and vaccine studies, and in adenoviral vector production.
Supplies laboratory automation systems, reagent kits, stock solutions, proteins, and accessories for protein researchers. Tools to automate protein purification, liquid handling, and protein crystallization. Our reagents and stock solutions are available individually, in convenient screens, and as custom products. As the demands of protein research continue to grow, we now provide high purity proteins.
University of New South Wales School of Psychology
The School of Psychology at UNSW is located in the Faculty of Science and has approximately 30 academic staff, 1600 undergraduate students and 150 postgraduate students. Members of the School study a diverse range of topics such as children''s development of language and knowledge, how mood affects our social behavior, teamwork in organizations, bias in eyewitness testimony, the brain mechanisms underlying pleasure and pain, the effect of aging and brain damage on memory, how the visual system perceives a three-dimensional world, and the causes and treatment of psychological disorders ranging from psychopathy to depression and post-traumatic stress. We offer a broad range of undergraduate courses in the major areas of psychology that not only communicate contemporary knowledge but also train general skills in research design, critical thinking, statistical analysis and written and oral communication. Our postgraduate programs in clinical, organisational and forensic psychology provide intensive professional training, and our PhD program offers the opportunity for advanced study in a range of specialised research fields. What makes our School distinctive is the quality of our academic staff. We earn more competitive research funding and publish more Tier 1 journal articles per academic than any other School in Australia. Our academics are very well connected within Australia and internationally. Historically, the School has played a leadership role in research, teaching and professional issues. The School has an academically rigorous but supportive culture, excellent research facilities, and offers great opportunities for students, visitors and collaborators.
RetNet provides tables of genes and loci causing inherited retinal diseases, such as retinitis pigmentosa, macular degeneration and Usher syndrome, and related information. This information is provided to the research community and other interested individuals for research purposes only. The information should not be used for medical or commercial purposes. Although we strive for accuracy and completeness, we cannot guarantee that all information is correct and complete. We welcome comments and suggestions!
Intramural Research Program in the National Institute on Aging
Intramural Research Program of the National Institute on Aging
National Institute on Aging Intramural Research Program
A research program of the NIA which focuses on neuroscience, aging biology, and translational gerontology. The central focus of the program's research is understanding age-related changes in physiology and the ability to adapt to environmental stress, and using that understanding to develop insight about the pathophysiology of age-related diseases. The IRP webpage provides access to other NIH resources such as the Biological Biochemical Image Database, the Bioinformatics Portal, and the Baltimore Longitudinal Study of Aging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Database compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences. Sequences are provided in aligned format. Alignment takes into account secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure modles and nucleotide variability maps, is also available.
ExDom is a unique database developed for the comparative visualization and analysis of exon-intron structure of protein domains in seven eukaryotic genomes (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). The ExDom database integrates 3744 protein domains annotated in the Pfam database to their corresponding exon-intron structures in 40,390 genes annotated in the RefSeq database and provides a unique platform for integrated comparative analysis of exon-domain relationships. The comparative graphical viewer in ExDom, implemented in Flash MX 6, allows users to query for a domain of interest, retrieve all proteins across different organisms which have this common domain, and then, visualize and compare the exon-intron structures of the domain in these proteins. Homo sapien genome, Mus musculus genome, Bos taurus genome, Rattus norvegicus genome, Danio rerio genome, Gallus gallus genome, Arabidopsis thaliana genome
Software package that contains functions for inference of target gene regulation by miRNA, based on only target gene expression profile.
An international professional association of 24,000 neurologists and neuroscience professionals dedicated to promoting the highest quality patient-centered neurologic care. They provide guidance and inspiration through education, information, policy development and advocacy for our members and their patients. The Academy''s professional website is only one of the domains associated with the AAN: * TheBrainMatters.org, public & patient education website * m.AAN.com, mobile AAN.com for members * Neurology journal * Neurology Now, patient magazine * Neurology Today, magazine for neurology professionals The AAN is committed to bringing its members the highest quality continuing medical education and professional education opportunities. The Academy''s Education programs cover the spectrum of neurological disorders, from the most prevalent to newly emerging issues. The AAN also provides a wide range of program formats, including in-depth print, convenient online, and hands-on workshop options. The AAN Annual Meeting brings together more than 10,000 neuroscience professionals for one of the world''s largest neurology gatherings. It has long been a leading showcase for the latest developments in scientific research, and the place to honor peers at the forefront of the work. The AAN offers a variety of publications, news, blogs, jobs, and practice guidelines.
National Institute of Allergy and Infectious Diseases
NIAID research strives to understand, treat, and ultimately prevent the myriad infectious, immunologic, and allergic diseases that threaten millions of human lives. Major areas of investigation: * Acquired Immunodeficiency Syndrome (AIDS) * Asthma and Allergic Diseases * Biodefense * Emerging and Re-emerging Infectious Diseases * Enteric Diseases * Fundamental Immunology * Genetics and Transplantation * Immune-Mediated Diseases * Influenza * Pathogen Genomics * Sexually Transmitted Infections (STIs) * Vaccine Development * Drug Research and Development * Antimicrobial Resistance * Minority and Women''s Health
North Dakota State University School of Pharmacy; North Dakota; USA
School of Pharmacy at North Dakota State University with mission of educating future pharmacists and researchers.
An analytical tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from whole genome sequencing data.
DGIL Porcine Immunology and Nutrition Datebase
Performs studies demonstrating the nutritional and biochemical effects of trace elements with special emphasis on chromium. Performs studies to elucidate the role of natural products in the improvement of the function of insulin with emphasis on polyphenols from tea and cinnamon. Performs studies on the role of dietary polyphenols on neuropathological changes including those associated with Alzheimers disease. The ultimate goal of the research is to prevent or alleviate early signs and symptoms of the metabolic syndrome which is important in the prevention of type 2 diabetes, cardiovascular, Alzheimers and related diseases. Our database is focused on immunologically-related genes classified under the following categories: Apoptosis CD markers Chemokines Chemokine receptors Cytokines Cytokine receptors Dendritic cell associated genes Type 1 IFN induced proteins Inflammation NFKB signaling pathway Toll receptor signaling pathway T cell activation TH1 cell development TH2 cell development Partners. Partnering with the Diet, Genomics, and Immunology Laboratory
FINDbase Worldwide is an online repository of information about the frequency of different mutations leading to inherited disorders in various populations around the globe. Frequency data about 32 disorders, 25 genes within 98 populations covering 1226 mutations is now available. 28 curators worldwide contributed to this database containing data from 37 submissions.
GWAS: Catalog of Published Genome-Wide Association Studies
A Catalog of Published Genome-Wide Association Studies
Catalog of Published Genome-Wide Association Studies
Catalog of published genome-wide association studies. Genome-wide set of genetic variants in different individuals to see if any variant is associated with trait and disease. Database of genome-wide association study (GWAS) publications including only those attempting to assay single nucleotide polymorphisms (SNPs). Publications are organized from most to least recent date of publication. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasional comparisons with an existing database of GWAS literature (HuGE Navigator). Works with HANCESTRO ancestry representation.
Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids.
Northwestern University Cognitive Neurology and Alzheimers Disease Center
Cognitive Neurology and Alzheimers Disease Center
Northwestern University Cognitive Neurology and Alzheimer's Disease Center
The Cognitive Neurology and Alzheimer's Disease Center (CNADC) is a multidisciplinary organization dedicated to conducting research to discover how the brain coordinates mental functions such as memory, language, attention, and emotion; transferring the benefits of this research to patients with brain diseases that impair cognitive function; and training researchers and clinicians who want to work in this field. The CNADC's mission is to investigate the neurological basis of cognitive function, to elucidate causes of dementia, and to ensure that the patients and their families are the beneficiaries of resultant discoveries. * Clinical Services: Neurobehavior and Memory Health Clinical Services * Annual Grant Opportunities: Annual Core Pilot Project Funding Opportunities * Research Areas & Faculty: Alzheimer's Disease / Primary Progressive Aphasia / Frontal Dementia, Brain Endowment (Brains are permanently stored, and requests for tissue for research purposes are submitted to Dr. Bigio for review by the Northwestern Alzheimer's Disease Center); Cognitive Brain Mapping Group, Volunteer For A Study * Fellowships: Neuropathology Fellowship, Behavioral Neurology & Neuropsychiatry Fellowship * Training Programs: Mechanisms of Aging and Dementia (M.A.D.) Training Program; Training Program in the Neuroscience of Human Cognition
National Institutes of Health Office of the Director
Office of the Director at National Institutes of Health
The NIH is comprised of the Office of the Director and 27 Institutes and Centers. The Office of the Director is the central office at NIH. The OD is responsible for setting policy for NIH and for planning, managing, and coordinating the programs and activities of all the NIH components. The NIH Director provides overall leadership to NIH activities in both scientific and administrative matters. Although each institute within the NIH has a separate mission, the NIH Director plays an active role in shaping the agency''s research agenda and outlook. With a unique and critical perspective on the mission of the entire NIH, the Director is responsible for providing leadership to the institutes for identifying needs and opportunities, especially for efforts that involve several institutes. The NIH Director is assisted by the Principal Deputy Director, who shares in the overall direction of the agency''s activities. In carrying out these responsibilities, the NIH Director stays informed about program priorities and accomplishments through regular staff meetings, discussions, and briefing sessions with OD and institute staff. The Director also receives input from: * the extramural scientific community, including both individual researchers and scientific organizations * patient advocacy and voluntary health groups that deal directly with NIH or indirectly through Congress and the media * the Congress and the Administration the Council of Public Representatives, which brings public views to NIH. Ongoing discussions with these groups and others provides the basis for an established framework within which priorities for the agency are identified, reviewed, and justified. Dr. Francis Collins, the NIH Director, has outlined five key themes for NIH: * Applying high throughput technologies to understand fundamental biology, and to uncover the causes of specific diseases * Translating basic science discoveries into new and better treatments * Putting science to work for the benefit of health care reform * Encouraging a greater focus on global health * Reinvigorating and empowering the biomedical research community Program offices in the Office of the Director are responsible for stimulating specific areas of research throughout NIH and for planning and supporting research and related activities. Current program areas are: minority health, women''s health, AIDS research, disease prevention, and behavioral and social sciences research. Program offices within the Office of the Director fund research through the institutes.
VIOLIN: Vaccine Investigation and Online Information Network
Vaccine Investigation and Online Information Network
A web-based central resource that integrates vaccine literature data mining, vaccine research data curation and storage, and curated vaccine data analysis for vaccines and vaccine candidates developed against various pathogens of high priority in public health and biological safety. The vaccine data includes research data from vaccine studies using humans, natural and laboratory animals.VIOLIN extracts and stores vaccine-related, peer-reviewed papers from PubMed. Several powerful literature searching and data mining programs have been developed. These include an advanced keywords search program, a natural languagae processing (NLP) based literature retrieval program, a MeSH-based literature browser, and a literature alert program. Registered users can subscribe to our email alert service and will be notified of any newly published vaccine papers in the areas of interest. These literature mining programs are designed to help the user and VIOLIN database curators to find efficiently needed vaccine articles and sentences within full-text articles that contain searched keywords or categories.A web-based literature mining and curation system (Limix) is available for registered users/curators to search, curate, and submit structured vaccine data into the VIOLIN database. The curated vaccine-related information contains many categories such as general pathogenesis, protective immunity, vaccine preparation and characteristics, host responses including vaccination protocol and efficacy against virulent pathogen infections. All data within the database is edited manually and is derived primarily from peer-reviewed publications. The curated data is stored in a relational database and can be queried using various VIOLIN search programs. Vaccine-related pathogen and host genes are annotated and available for searchs based on a customized BLAST program. All VIOLIN data are available for download into an XML-based data exchange format.VIOLIN is designed to be a vital source of vaccine information and will provide researchers in basic and clinical sciences with curated data and bioinformatics tools to facilitate understanding and development of vaccines to fight infectious diseases. Category: Other Molecular Biology Databases Subcategory: Drugs and drug design
The aim of the project is to provide contemporary estimates of the incidence of, mortality and prevalence from major types of cancer, at national level, for 184 countries of the world. The GLOBOCAN estimates are presented for 2012, separately for each sex. 1-, 3- and 5-year prevalence data are available for the adult population only (ages 15 and over). Please note that: These estimates are based on the most recent data available at IARC and on information publically available on the Internet, but more recent figures may be available directly from local sources. Because the sources of data are continuously improving in quality and extent, estimates may not be truly comparable overtime and care should be taken when comparing these estimates with those published earlier. The observed differences may be the result of a change in the methodology and should not be interpreted as a time trend effect.
GABI-Kat is a database of flanking sequence tags (FSTs) from T-DNA mutagenised A. thaliana plants. Over time, an increasing number of lines will become available from NASC. The "show sequence" page of SimpleSearch will display if a GABI-Kat line for a given FST has already been donated to NASC. Lines that have so far not been regrown and confirmed are only available from GABI-Kat directly. We have used four vectors: pAC106 (GenBank:AJ537513), pAC161 (GenBank:AJ537514), pGABI1 (GenBank:AY529716) and pADIS1 (GenBank:AY529717). Sequence and overview map data of all vectors are available from the download page. Features of interest which are not included in the map should be deduced from the sequence. For a specified line, the vector is displayed in the "Show Sequence" page of SimpleSearch.
Software for normalization of Agilent miRNA arrays.
R functions for the normalization of Exiqon miRNA array data.
IFPMA - International Federation of Pharmaceutical Manufacturers and Associations
International Federation of Pharmaceutical Manufacturers and Associations
The International Federation of Pharmaceutical Manufacturers & Associations (IFPMA) facilitates dialogue and mutual understanding between the research-based pharmaceutical industry and other global health stakeholders. Our objective is to build trust and help to find broadly supported solutions to the huge and complex issues facing society in the arena of human health. The IFPMA was founded in 1968 as a global, non-profit, non-governmental organization. With members across the world and a secretariat based in Geneva, Switzerland, the IFPMA represents the research-based pharmaceutical industry, including the biotechnology and vaccine sectors. Our members comprise leading international companies as well as national and regional industry associations, in both developed and developing countries, across all five continents. Our primary role is to represent our members'' views in dialogue with global intergovernmental organizations, the diplomatic missions of national governments and specialized non-governmental organizations. The IFPMA advocates policies that encourage discovery of and access to life-saving and life-enhancing new medicines to improve the health of patients everywhere. To fulfill its mission, the IFPMA has established a number of key guiding principles: * To encourage a global policy environment that is conducive to innovation in medicine, both therapeutic and preventive, for the benefit of patients around the world; * To promote and support principles of ethical conduct and practices voluntarily agreed upon, as exemplified by the IFPMA Code of Pharmaceutical Marketing Practices; * To promote and support the adoption of high standards of manufacturing practices and quality assurance for pharmaceutical products; * To contribute industry expertise and foster collaborative relationships and partnerships with international organizations that are dedicated to the improvement of public health, especially in developing and emerging countries; and * To assure regular contact and experience-sharing and coordinate the efforts of its members towards achieving these objectives.
Blog where you will find a genomics resources news portal with daily postings about genomics resources, genomics news and research, science and more.
GDR is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, annotated EST databases of apple, peach, almond, cherry, rose, raspberry and strawberry, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, ORFs, Gene Ontology and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. We continue to add Rosaceae map data to CMap, a web-based tool that allows users to view comparisons of genetic and physical maps. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm, search their sequences for microsatellites using the SSR server or assemble their ESTs using the CAP3 Server.
International Committee of Medical Journal Editors
International Commitee of general medical journal editors and representatives of selected related organizations working together to improve quality of medical science and its reporting.
A global evaluation of the conservation status of plant and animal species. The IUCN Red List plays a prominent role in guiding conservation activities of governments, NGOs and scientific institutions. The introduction in 1994 of a scientifically rigorous approach to determine risks of extinction that is applicable to all species, has become a world standard. In order to produce The IUCN Red List of Threatened Species, the IUCN Global Species Programme working with the IUCN Survival Commission (SSC) and with members of IUCN draws on and mobilizes a network of scientists and partner organizations working in almost every country in the world, who collectively hold what is likely the most complete scientific knowledge base on the biology and conservation status of species. The IUCN Red List is underpinned by information management tools (the Species Information Service) which facilitate the collection, management and processing of species data from workshop to publication on The IUCN Red List.
The OIE is the intergovernmental organization responsible for improving animal health worldwide. The need to fight animal diseases at global level led to the creation of the Office International des Epizooties through the international Agreement signed on January 25th 1924. In May 2003 the Office became the World Organisation for Animal Health but kept its historical acronym OIE. It is recognised as a reference organisation by the World Trade Organization (WTO) and in 2013 had a total of 178 Member Countries. The OIE maintains permanent relations with 45 other international and regional organisations and has Regional and sub-regional Offices on every continent.
University of Cape Town; Western Cape; South Africa
Public research university located in Cape Town in the Western Cape province of South Africa. UCT was founded in 1829 as the South African College making it the oldest higher education institute in South Africa.
The goal of the project is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders. The groups participating and collaborating in the NHLBI GO ESP include: Seattle GO - University of Washington, Seattle, WA Broad GO - Broad Institute of MIT and Harvard, Cambridge, MA WHISP GO - Ohio State University Medical Center, Columbus, OH Lung GO - University of Washington, Seattle, WA WashU GO - Washington University, St. Louis, MO Heart GO - University of Virginia Health System, Charlottesville, VA ChargeS GO - University of Texas Health Sciences Center at Houston
GIRI is a private, non-profit research institution founded in 1994. Our mission is to understand biological processes which alter the genetic makeup of different organisms, as a basis for potential gene therapy and genome engineering techniques. We pursue and promote original peer-reviewed, public domain research on genetic information (DNA sequence data), as well as dissemination of databases and computer software related to this research. Our research is heavily based on computer power and human skills different from those applied in classical molecular biology and genetics.
Software package for statistical analysis and presentation of graphics. Statistical software for data science.
Unix-like operating system that is free software. GNU (more precisely, GNU/Linux systems) are entirely free software. The GNU Project was launched in 1984 to develop the GNU system. A Unix-like operating system is a software collection of applications, libraries, and developer tools, plus a program to allocate resources and talk to the hardware, known as a kernel. The Hurd, GNU''s own kernel, is some way from being ready for daily use. Thus, GNU is typically used today with a kernel called Linux. This combination is the GNU/Linux operating system. GNU/Linux is used by millions, though many call it Linux by mistake.
BCube A Broker Framework for Next Generation Geoscience
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 17,2023. Project that brings together an internationally recognized team of geo- and social-scientists, cyberinfrastructure experts and educators to explore how expert systems can mediate interactions and improve access between scientific fields. To address complex Earth system issues such as climate change and water resources, geoscientists must work across disciplinary boundaries, which requires them to access data outside of their fields. The initial focus is on hydrology, oceans, polar and weather, with the intent to make the technology applicable and available to all the geosciences. The team''s social scientists and educators will research how technology can improve knowledge exchange between scientific communities.
EXCAVATOR-tool: Tool for detecting CNVs from whole-exome sequencing data
A software package for the detection of copy number variants (CNVs) from whole-exome sequencing data.
Free and open access to data about development in countries around the globe.
RPA: Robust Probabilistic Averaging for probe-level analysis
A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.
CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
Software for strand specific peak-pair calling in ChIP-exo replicates.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on April 14,2022. Database of comprehensive information on the approximately 600 prokaryote species that are present in the human oral cavity. The majority of these species are uncultivated and unnamed, recognized primarily by their 16S rRNA sequences. The HOMD presents a provisional naming scheme for the currently unnamed species so that strain, clone, and probe data from any laboratory can be directly linked to a stably named reference entity. The HOMD links sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Full and partial oral bacterial genome sequences determined as part of this project and the Human Microbiome Project, are being added to the HOMD as they become available. HOMD offers easy to use tools for viewing all publicly available oral bacterial genomes. Data is also downloadable.
Smith-Waterman database searches with inter-sequence SIMD parallelisation
A software tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases.
Whole genome secondary analysis on Illumina sequencing platforms.
KEGG - Kyoto Encyclopedia of Genes and Genomes
Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
National Bio Resource Project for the Rat.
NBRP-Rat was established to overcome limitations associated with properly utilizing existing rat resources. The collection of existing strains and genetic sub strains, phenotypic and genotypic characterization, cryopreservation of embryos, distribution of the collected rat strains, and a publicly accessible database of all assembled data are the major goals of this project. Once achieved, this unique database including the unique rat strains will become a powerful tool for biomedical research. A catalog of comparable, standardized and well characterized rat strains will lead to new and more precise research topics as well as it will facilitate biomedical sciences, drug discovery, advanced chemical research, and contributes to life sciences worldwide. As mentioned before, the major goals of NBRP-Rat are the collection, preservation and supply of rat strains. The repository includes strains from Japan and abroad, spontaneous mutants, congenic and recombinant strains as well as transgenic and mutagenized rats. Deposited rat strains are not only conserved as cryopreserved embryos and sperm. Many reference and frequently used rat strains are also maintained as living animals under SPF conditions. Furthermore, NBRP-rat provides a unique database on various rat strain phenotypes accompanied with basic genetic information. This allows scientists the selection of standardized and research specific strains. The animals themselves are provided free of charge to the research community (except for shipping costs). Sponsors: This project is one part of the National BioResource Projects (NBRP) in Japan for more than 20 species including animals, plants, microbes, tissues and DNAs. It is founded by the Japanese Ministry of Education, Culture, Sports, Science and Technology (Monkasho) and started in 2002.
Institute of Molecular and Cell Biology; Singapore; Singapore
The Institute of Molecular and Cell Biology (IMCB) was established in 1987 at the National University of Singapore (NUS) before becoming an autonomous research institute (RI) of A*STAR. Its mission is to develop and foster a vibrant research culture for cutting-edge basic biomedical sciences and for training high-quality Ph.D. students for the flourishing biotechnology and pharmaceutical industries in Singapore. Funded primarily by the Biomedical Research Council (BMRC) of A*STAR, IMCB now boasts about 30 core research labs and 8 core facility units consisting of over 300 research scientists in total. IMCB''s research activities focus on six major fields: Cell Biology, Developmental Biology, Structural Biology, Infectious Diseases, Cancer Biology and Translational Research with core strengths in cell cycling, cell signalling, cell death, cell motility and protein trafficking. IMCB continues to strive for excellence in biomedical R&D to see the vision of Singapore being a world class hub for the Biomedical Sciences in Asia and beyond. IMCB''s achievements include being part of the international consortium that successfully sequenced the entire pufferfish (Fugu rubripes) in 2002. IMCB was awarded the Nikkei Prize 2000 for Technological Innovation in recognition of its growth into a leading international research centre and its collaboration with industry and research institutes worldwide. IMCB continues to publish in renowned international journals, with more than 1300 publications to its credit since 1987.
cancer-related analysis of variants toolkit
A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis.
An independent, not-for-profit organization, The Joint Commission accredits and certifies more than 19,000 health care organizations and programs in the United States. Joint Commission accreditation and certification is recognized nationwide as a symbol of quality that reflects an organization''s commitment to meeting certain performance standards. The Joint Commission is the nation''s oldest and largest standards-setting and accrediting body in health care. To earn and maintain The Joint Commission''s Gold Seal of Approval, an organization must undergo an on-site survey by a Joint Commission survey team at least every three years. (Laboratories must be surveyed every two years.) Our Mission: To continuously improve health care for the public, in collaboration with other stakeholders, by evaluating health care organizations and inspiring them to excel in providing safe and effective care of the highest quality and value. Vision Statement: All people always experience the safest, highest quality, best-value health care across all settings.
For each developmental stage (using the staging system defined by Theiler), the Mouse Anatomical Dictionary organizes the terms hierarchically from body region or system to tissue to tissue substructure. Modeling the anatomy hierarchically makes it possible to record expression results from assays with differing spatial resolution in a consistent and integrated manner. The Mouse Anatomical Dictionary Browser lets you navigate the extensive dictionary hierarchies for the different developmental stages, locate specific anatomical structures within those hierarchies, and see the expression results associated with those structures. Stages 1 through 26 (embryonic development) are being developed at the Department of Biomedical Sciences, University of Edinburgh, Scotland and the MRC Human Genetics Unit, Edinburgh, as part of The Mouse Atlas and 3D Graphical Gene Expression Database Project. Stage 28 (postnatal mouse) is being developed by the Gene Expression Database Project at The Jackson Laboratory.
A software package to do meta-analysis which works in a spreadsheet interface and also provides forest plots, which are useful for visualizing between-study heterogeneity.
IMGT - the international ImMunoGeneTics information system
A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.
Software that provides an integrated solution for the Illumina microarray data analysis.
Open-access database of antibodies against human proteins developed through collaboration between Antibodypedia AB and the Nature Publishing Group. It aims to provide the scientific community and antibody distributors alike with information on the effectiveness of specific antibodies in specific applications--to help scientists select the right antibody for the right application. Antibodypedia's mission is to promote the functional understanding of the human proteome and expedite analysis of potential biomarkers discovered through clinical efforts. To this end, they have developed an open-access, curated, searchable database containing annotated and scored affinity reagents to aid users in selecting antibodies tailored to specific biological and biomedical assays. They envisage Antibodypedia as a virtual repository of validated antibodies against all human, and ultimately most model-organism, proteins. Such a tool will be exploitable to identify affinity reagents to document protein expression patterns in normal and pathological states and to purify proteins alone and in complex for structural and functional analyses. They hope to promote characterization of the roles and interplay of proteins and complexes in human health and disease. They encourage commercial providers to submit information regarding their inventory of antibodies with links to quality control data. Independent users can submit their own application-specific experimental data using standard validation criteria (supportive or non-supportive) developed with the assistance of an international advisory board recruited from academic research institutions. Users can also comment on specific antibodies without submitting validation data.
SUNY Downstate Medical Center School of Graduate Studies
Founded in 1966, the School of Graduate Studies is one of four colleges comprising the State University of New York Health Science Center at Brooklyn, and is accredited by the Middle States Association of Colleges and Secondary Schools. The School of Graduate Studies grants the degree of Doctor of Philosophy in three programs: Neural & Behavioral Science, Molecular & Cellular Biology and Biomedical Engineering.
Interactive Fly: A cyberspace guide to Drosophila development and metazoan evolution
The InterActive Fly is an online database of Drosophilia development and metazoan evolution. It contains information on biochemical pathways, organs, images, a cis-decoder, and EvoPrinter, a machine that allows users to identify Evolutionarily Resilient DNA Sequences.
Software that allows hierarchical data to be explored with zoomable pie charts.
The mission of The Progeria Research Foundation is to discover treatments and the cure for Progeria, and its aging related disorders. Progeria is a rare and fatal genetic disease characterized by an appearance of accelerated aging in children. Without the discovery of new treatments, all children with Progeria will die of heart disease at an average age of 13 years. The Progeria Research Foundation (PRF) was founded in 1999 in response to the complete lack of progress being made to help children with Progeria. We have filled a void, taking these children out of the background where they had been for over 100 years and putting them and Progeria at the forefront of scientific efforts. In just 11.5 years, we have achieved extraordinary progress towards our mission: the Progeria gene discovery in 2003, first-ever clinical drug trials initiated in 2007, extensive global awareness of the disease and PRF''s work, and discovery of critical biological links between Progeria, heart disease and aging we all experience.
Alzheimer's Disease Education and Referral Center
Portal for Alzheimer's disease that compiles, archives and disseminates information about current treatments, diagnostic tools and ongoing research for health professions, people with AD, their families and the public. The Center provides informational services and referrals for AD symptoms, diagnosis and treatment for patients; clinical trial information and literature searches for researchers; training materials and guidelines for caregivers; and Spanish language resources.
Supports cross-cutting, trans-NIH programs that require participation by at least two NIH Institutes or Centers (ICs) or would otherwise benefit from strategic planning and coordination. The requirements for the Common Fund encourage collaboration across the ICs while providing the NIH with flexibility to determine priorities for Common Fund support. To date, the Common Fund has been used to support a series of short term, exceptionally high impact, trans-NIH programs known collectively as the NIH Roadmap for Medical Research. The Common Fund is coordinated by the Office of Strategic Coordination, one of the six offices of the Division of Program Coordination, Planning, and Strategic Initiatives (DPCPSI) within the Office of the Director. The intent of NIH Common Fund programs is to provide a strategic and nimble approach to address key roadblocks in biomedical research that impede basic scientific discovery and its translation into improved human health. In addition, these programs capitalize on emerging opportunities to catalyze the rate of progress across multiple biomedical fields. Common Fund programs are expected to transform the way a broad spectrum of health research is conducted. Initiatives that comprise Common Fund programs are intended to be catalytic in nature by providing limited term investments in strategic areas to stimulate further research through IC-funded mechanisms.
Health News Review Blog: Gary Schwitzer Blog on recent biomedical studies
University of California, San Francisco School of Pharmacy
The School of Pharmacy at the University of California, San Francisco is dedicated to improving human health worldwide and advancing scientific discovery. The School conducts exceptional pharmaceutical research, including basic science, translational science, clinical science, health policy, and health services research delivers world-class education to our Doctor of Pharmacy, graduate, postdoctoral students and others educates PharmD students to be leaders and effective team members in health care and to be lifelong experts in the safe and effective use of medicines educates graduate students to be outstanding researchers across the spectrum from the basic to the health sciences. provide strong postdoctoral training develops and delivers outstanding and innovative pharmaceutical care serves the community by sharing our expertise with the public, industry leaders, and policy makers
This site is intended to increase the nation''s ability to prepare for and respond to public health emergencies. Emergency preparedness requires attention not just to specific types of hazards but also to steps that increase preparedness for any type of hazard. The resources in this website are intended to help professionals take an all-hazards approach to preparedness. People prepared for emerging health threats-people in all communities will be protected from infectious, occupational, environmental, and terrorist threats, is one of CDC''s four health protection goals. CDC plays a key role in preparing the nation for all types of public health threats, including natural, biological, chemical, radiological, and nuclear incidents. When a disaster occurs, CDC is prepared to respond and support national, state, and local partners to save lives and reduce suffering. CDC also helps these partners recover and restore public health functions after the initial response. National emergency preparedness requires a coordinated effort involving every level of government as well as the private sector, non-governmental organizations, and individual citizens. CDC''s work in preparedness supports the Department of Homeland Security, which has overall authority for emergency response activities as laid out in the National Response Framework. Protecting the public from health threats involves public health preparedness as well as medical preparedness. Both are essential for national health security and, hence, to the overall preparedness of the nation. Sponsors: This resource is supported by the Center for Disease Control and Prevention. Keywords: Public, Health, Emergency, Disease, Prevention, Biological, Natural, Chemical, Radiological, Nuclear, Disaster,
The Samuel Roberts Noble Foundation is an independent, nonprofit institute headquartered in Ardmore, Okla. Founded in 1945, the Noble Foundation conducts direct operations, including assisting farmers and ranchers, and conducting plant science research and agricultural programs, to enhance agricultural productivity regionally, nationally and internationally. Employing more than 360 persons, the Noble Foundation conducts its operations through the activities of three operating divisions: * Agricultural Division: Serving a 47-county area within a 100-mile radius of the Noble Foundation''s headquarters in Ardmore, Okla., the Agricultural Division assists more than 1,700 regional farmers and ranchers in achieving their individual financial, production, stewardship and quality-of life goals. * Plant Biology Division: The Plant Biology Division conducts basic biochemical, genetic and genomic plant research for the purpose of improving crop productivity and value, and enhancing animal and human health. * Forage Improvement Division: The Forage Improvement Division translates basic plant science research into tangible plant varieties. Within the institution, the Forage Improvement Division serves as a link between the discoveries in the laboratory and the field, where such discoveries are intended to enhance agricultural outcomes in Oklahoma and around the world. The coordinated efforts of these operating divisions enable the Noble Foundation agricultural specialists and scientists to move science and innovation from the laboratory to the field, giving life to discovery and improving agriculture in Oklahoma, in the United States and around the world.
Software package that identifies differential expression in high-throughput ''count'' data, such as that derived from next-generation sequencing machines.
Chinese Academy of Sciences; Beijing; China
Public university for graduate education, under the direct leadership of the Chinese Academy of Sciences.
Southern Illinois University School of Medicine; Illinois; USA
Southern Illinois University School of Medicine
Medical school located in Springfield, the capital of the U.S. state of Illinois. It is part of the Southern Illinois University system, which includes a campus in Edwardsville as well as the flagship in Carbondale.
Listing of FDA-approved medications. In includes only drugs that have been the subject of a Healthcare Professional Information sheet, an Early Communication About an Ongoing Safety Review, or other important information. For every drug on the list there is information for healthcare professionals, including information regarding the proscribing of the specified drug, as well as other information that can include patient information sheets (current and previous), public health advisories (if applicable), and drug analysis and recommendations to patients and healthcare providers.
Human Genome Organisation (HUGO) is the international organization of scientists involved in human genetics. HUGO was conceived in 1988, at the first meeting on genome mapping and sequencing at Cold Spring Harbor. From a 42 scientists of 17 countries membership association, HUGO has increased its membership base to over 1,200 members, both established and aspiring of 69 countries after two decades. HUGO has, over the years, played an essential role behind the scenes of the human genome project. With its mission to promote international collaborative effort to study the human genome and the myriad issues raised by knowledge of the genome, HUGO has had noteworthy successes in some of the less glamorous, but nonetheless vital, aspects of the human genome project. As a truly international organization, HUGO is entering its 20th year of its history by making an inflection in its direction seeking the biological meaning of its information content. To this end, HUGO is focusing on the medical implications of genomic knowledge. Moving forward, HUGO is also working to enhance the genomic capabilities in the emerging countries of the world. The excitement and interest in genomic sciences in Asia, Middle East, South America and Africa are palpable and the hope is that these technologies will help in national development and health.
Empirical analysis of Digital Gene Expression data in R
Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
TGD Wiki is a user-updatable database of information about the Tetrahymena thermophila genome sequence determined at The Institute for Genomic Research (TIGR). TGD Wiki provides information on the genome, genes, and proteins of Tetrahymena collected from the scientific literature, research community and many other resources. In order to keep the information in our database as current as possible, we will soon be inviting the members of the Tetrahymena community to add and update these annotations to reflect published research. TGD Wiki currently offers the following features: * Free, unrestricted read access to all available data * Sequence and annotation data for 24,725 genes (TIGR v.2008) * GBrowse genome browser with links to and from each gene page (TIGR v.2006) * BLAST searching of the TIGR gene models and genome sequence (TIGR v.2006) Tetrahymena Genome Database (TGD) Wiki began in 2004 at Stanford University using the schema and programs of its parent project, Saccharomyces Genome Database. TGD Wiki is now a collaboration between Bradley University, Stanford University, and Cornell University. As we begin TGD Wiki at its new home at Bradley University, the TGD Wiki database contains the following data from TGD: * Gene Names and Aliases * Gene Descriptions * Gene Ontology (GO) Annotations * Homologs (similar genes in selected organisms) * Protein Domains * Associated Literature * Paragraphs (longer, free-text descriptions of gene function, structure, and significance) * Coding and Protein Sequences We have updated the following fields to match the newest gene model sequences (TIGR v.2008): Coding and Protein Sequences, Protein Domains and Gene Descriptions. We will also be recalculating the GO Annotations (IEA evidence code) and Homologs as part of our effort to keep the annotations in TGD Wiki as current as possible. We will be relying on members of the Tetrahymena community to maintain high-quality, updated annotations in the remainder of the fields using our annotation interface. Also setting up new database superdb - for unpublished data Look at Ciliate.org for news on this and other new databases
The Immunology Database and Analysis Portal (ImmPort)
Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology.
AngioCalc Cerebral and Peripheral Aneurysm Calculator
Providing quality resources for the management of cerebral aneurysms and features an online calculator that calculates cerebral aneurysm volume and percent packing volume after coil embolization. The site also host an imaging Library with neuroanatomy and neurovascular images.
SDAP: Structural Database of Allergenic Proteins
Structural Database of Allergenic Proteins
A database of allergenic proteins. It contains various computational tools that can assist structural biology studies related to allergens. SDAP is an important tool in the investigation of the cross-reactivity between known allergens, in testing the FAO/WHO allergenicity rules for new proteins, and in predicting the IgE-binding potential of genetically modified food proteins. Using this Internet service through a browser, it is possible to retrieve information related to an allergen from the most common protein sequence and structure databases (SwissProt, PIR, NCBI, PDB), to find sequence and structural neighbors for an allergen, and to search for the presence of an epitope other the whole collection of allergens.
The ALS Therapy Development Institute is a nonprofit biotechnology company discovering treatments for patients alive today. Our approach combines the power of a nonprofit mission with the best practices of a for-profit biotechnology company: rigorous, open-minded research and proven drug development techniques. ALS TDI combines the passion and dedication of a nonprofit organization with the entrepreneurial and scientific spirit of a biotechnology company * Our laboratory, the leading drug discovery program for ALS, bridges a critical research gap * Our in-house expertise translates research into potential drug candidates by screening drugs in the SOD1 mouse model of ALS. * Our scientific collaborations are designed to bring the most promising leads closer to patient use. * We share emerging knowledge on the disease with patients, physicians, and researchers as quickly and comprehensively as possible. * Every decision is made in the interest of finding effective treatments for people living with ALS. * Our unique approach accelerates drug development for ALS.
RNA FRABASE - RNA FRAgments search engine and dataBASE
RNA FRABASE - RNA FRAgments search engine dataBASE
RNA FRAgments search engine and dataBASE
Engine and database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation. The database contains RNA sequences and secondary structures, described in the dot-bracket notation, derived from PDB-deposited RNA structures and their complexes. It also contains atom coordinates of the unmodified and modified nucleotide and nucleoside residues extracted from the PDB-deposited RNA structures, as well as torsion and pseudotorsion angle values, sugar pucker parameters and classification of base pair types given for the PBD-deposited RNA structures. Knowledge of the three dimensional RNA structure is crucial for all fields of biomolecular research. In contrast to the protein field, only about 1.300 experimentally derived structures of RNAs are deposited in the Protein Data Bank (PDB). To complement the results of experimental studies, new approaches based on bioinformatics and calculation are pursued in several laboratories to make tertiary RNA structure prediction possible. RNA FRABASE version 2.0 should greatly facilitate various RNA structure modelling approaches, RNA structure analysis and motif searching. If one compares the three dimensional RNA structure to a spatial puzzle, the RNA FRABASE allows to pull out a defined piece of this puzzle - the 3D RNA fragment. The architecture of the web-accessible RNA FRABASE engine and database is based on the following information path: PDB-deposited RNA structures �� RNA sequences and secondary structures described in the dot-bracket notation �� secondary structures of RNA fragments �� 3D RNA fragments. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide on the spot structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided.
UCLA Multimodal Connectivity Database: Web-based brain network analysis and data sharing
Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately.
tRanslatome - Comparison between multiple levels of gene expression
Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR.
The mission of the Indiana Alzheimer Disease Center is to serve as a shared research resource in order to facilitate research in Alzheimer disease and related disorders and to distinguish them from normal aging. Within this mission, one objective is to provide an environment and core resources to enhance ongoing research and foster new lines by bringing together basic and clinical scientists to study the etiology, pathogenesis, diagnosis, and treatment of Alzheimer disease and related dementias, with an emphasis on hereditary dementias. The Center is composed of 6 cores: Administrative, Clinical, Neuropathology, Data Management, Education and Information Transfer, and Imaging. The Neuropathology Core functions as brain-bank facility, which stores samples from hundreds of autopsied cases and supplies them to research investigators around the world. The focus of the IADC is on behavioral neurology, clinicopathological correlations, biochemistry, and genetics of AD, frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17), Gerstmann-Str��������ussler-Scheinker disease (GSS), Parkinson disease and other hereditary diseases associated with abnormal protein accumulation. The Neuropathology Core carries out state-of-the-art neuropathological examination of brain, spinal cord and other tissue samples obtained from individuals affected by neurodegenerative dementia and/or other related neurodegenerative diseases. The Core is composed of five different laboratories: histology and immunohistochemistry, electron microscopy, molecular biology, biochemistry, as well as a small-animal laboratory dedicated to the study of murine models of human diseases. In the past 15 years, we have been among the first to discover mutations in genes implicated in the etiology and pathogenesis of early-onset dementia. Specifically we have identified novel mutations in the Amyloid Precursor Protein gene (APP) and Presenilin 1 (PSEN1) that are responsible for hereditary forms of early-onset AD. We have also found several novel mutations responsible for Gerstmann-Str��������ussler-Scheinker (GSS) disease, a hereditary degenerative disease causing ataxia, parkinsonism and dementia secondary to the accumulation of mutated prion protein (PrP). We have reported mutations in the MAPT gene in FTDP-17, a tauopathy which causes personality changes, cognitive dysfunction, rigidity and dementia. Other areas of research in neurodegeneration are related to the study of genetic mutations of Neuroserpin (SCNA) and Light Ferritin Polypeptide genes.
Blog intended for grantees of the National Institute on Aging (NIA) at the NIH, as well as applicants for funding, those with an application in mind, application reviewers, and students pursuing careers in research on aging and Alzheimer's disease.
Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.
Okinawa Institute of Science and Technology
Okinawa Institute of Science and Technology Promotion Corporation
The Okinawa Institute of Science and Technology Promotion Corporation (OIST PC) was established in September 2005 to conduct best in the world research and education in science and technology, and to prepare the ground for the creation of a new graduate University in Okinawa. Our concept was to grow the project out of interdisciplinary research in areas that integrate components from biology, physics, chemistry, mathematics and computation science. We have done so by recruiting researchers in Neurosciences, Molecular Sciences and Mathematical and Computational Biology, and we have recently added Environmental Science as a new focus. OIST P.C. is unique in that we are a Japanese government-funded agency, but maintain independence in developing and conducting our research and academic programs. We drive towards excellence, and we are committed to developing programs to enable outstanding researchers to be given the opportunity to conduct independent research and to excel in their chosen research topics, as well as extending to talented students the chance to access a world-class education program in Okinawa. At a time when worldwide support for research is increasingly risk-averse and obtaining funding places an ever-growing burden on faculty, OIST promotes innovative research in a highly facilitating and supportive environment. In addition to seminars and workshops, Okinawa Institute of Science and Technology Promotion Corporation (OIST) provides students from Japanese and overseas universities with education and research opportunities through a system of collaborative graduate programs and placements. Prior to the opening of the graduate university in FY 2012, these allow students to receive research guidance in a broad range of topics from Principal Investigators of research laboratories at OIST (units) through two different student research assistantships.
Biobank provides data collected at Assessment Center and via online questionnaires on participants aged 40-69 years recruited throughout United Kingdom and provides summary information to improve prevention, diagnosis and treatment of serious and life threatening illnesses.
An academic, non-profit foundation recognized of public utility that coordinates research and education in bioinformatics throughout Switzerland and provides high quality bioinformatics services to the national and international research community. * The first and primary SIB mission consists of providing services, i.e. the bioinformatics research infrastructure for life science research. It is carried through in a top-down approach, with objectives set by the SIB Board of Directors and an implementation plan agreed with the concerned groups. Federal funds are almost exclusively used to fulfill this mission. * Within the second mission the SIB plays a federating role, linking the Swiss bioinformatics community and promoting and coordinating research and education. This activity is mainly performed in a bottom-up way with funding from the universities and other partners and from research grants.
Neuroscience for Kids has been created for all students and teachers who would like to learn about the nervous system. Discover the exciting world of the brain, spinal cord, neurons and the senses. Use the experiments, activities and games to help you learn about the nervous system. There are plenty of links to other web sites for you to explore. Can''t find what you are looking for? Search the web site and the questions/answers page. Keep up-to-date on new discoveries in brain research with Neuroscience in the News, request the Neuroscience for Kids Newsletter or watch BrainWorks, a 30-minute TV show about the brain hosted by Dr. Eric H. Chudler. Portions of Neuroscience for Kids are available in Spanish, Slovene, Chinese, Portuguese, Italian, Korean, Dutch, Japanese and Turkish. Neuroscience for Kids is maintained by Eric H. Chudler, Ph.D. and was supported by a Science Education Partnership Award (R25 RR12312) from the National Center for Research Resources (NCRR). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of NCRR or NIH. Support: NCRR
RAPID- Resource of Asian Primary Immunodeficiency Diseases
Resource of Asian Primary Immunodeficiency Diseases
A web-based compendium of molecular alterations in primary immunodeficiency diseases. Detailed information about genes and proteins that are affected in primary deficiency diseases is presented along with other pertinent information about protein-protein interactions, microarray gene expression profiles in various organs and cells of the immune system and mouse studies. RAPID also hosts a tool, the mutation viewer, to predict deleterious and novel mutations and also to visualize the mutation positions on the DNA sequence, protein sequence and three-dimensional structure for PID genes. The information in this database should be useful to researchers as well as clinicians.
DNaseR: DNase I footprinting analysis of DNase-seq data
A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data.
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
Research Collaboratory for Structural Bioinformatics Protein Data Bank
Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.
ANNOVAR: Functional annotation of genetic variants
functional ANNOtation of genetic VARiants
An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)
MATCONT and CL MATCONT: Continuation Software in Matlab
MATCONT is a graphical MATLAB package for the interactive numerical study of parameterized dynamical systems. It is developed in parallel with the command line continuation toolbox CL_MATCONT and with the command line continuation toolbox CL_MATCONTM for the interactive numerical study of parameterized maps and iterates of maps. MATCONT and CL_MATCONT allow the numerical continuation of equilibria, limit cycles and homoclinic orbits, detection of codimension 1 and 2 bifurcations, continuation of the codimension 1 bifurcations and computation of their normal forms. For equilibria normal form coefficients of codimension 2 bifurcations are also computed, as well as switching to the codimension 1 curves in codimension 2 points. CL_MATCONTM provides similar facilities for maps and iterates of maps, including normal form coefficients of codimension 2 bifurcations and continuation of homoclinic and heteroclinic connections and tangencies of such connections.
Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
MBGD is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison. The heart of MBGD function is to create orthologous or homologous gene cluster table. For this purpose, similarities between all genes are precomputed and stored into the database, in addition to the annotations of genes such as function categories that were assigned by the original authors and motifs that were found in the translated sequence. Using these homology data, MBGD dynamically creates orthologous gene cluster table. Users can change a set of organisms or cutoff parameters to create their own orthologous grouping. Based on this cluster table, users can further analyze multiple genomes from various points of view with the functions such as global map comparison, local map comparison, multiple sequence alignment and phylogenetic tree construction.
The NASC International Affymetrix Service is a commercial website that provides transcripomics services for a fee. This data is available for any available species, any consortium chip, and any kind of experiment. The website also provides open source and free Xspecies software and techniques that can be (examples) used to perform GeneChip transcriptomics experiments on species for which no current Affymetrix chip exists.
NCL Resource - A gateway for Batten disease
It serves as a gateway for clinicians, families and researchers who have an interest in or are affected by Batten disease or who wish to find out more. Information can be accessed via four main routes - Clinicians, Families, Researchers, Professional Support. The Clinical route describes Batten disease and includes details on diagnosis and diagnostic services. The Family route also describes Batten disease and lists support groups. The Research route includes the NCL Mutation Database, established in 1998, and other useful information. The Professional Support route includes details of coordinated initiatives to support those affected by Batten disease. A fifth route, Research Consortia, serves to meet research needs and currently act as a focus for collaborative efforts to identify the remaining human and animal NCL genes and facilitate functional approaches. An additional route, Creativity, has been launched to display creative items from families with Batten disease, and to celebrate life, in both its fullness and fragility.
Next Generation Sequencing Eclipse Plugin
Next Generation Sequencing Experience Platform
Software whose main functionality is the variants detector, which allows to make simultaneous discovery of SNVs, small indels, and CNVs.Accurate variant calling across species and sequencing protocols.Used for analysis of DNA high throughput sequencing data.
Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.
Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies.
Software tools for analyzing and visualizing Illumina''s 450k array data.
Software package that provides classes for holding and manipulating Illumina methylation data.
National Environmental Public Health Tracking Program
The goal of environmental public health tracking is to protect communities by providing information to federal, state, and local agencies. These agencies, in turn, will use this information to plan, apply, and evaluate public health actions to prevent and control environmentally related diseases. Environmental public health tracking is the ongoing collection, integration, analysis, and interpretation of data about the following factors: :- Environmental hazards :- Exposure to environmental hazards :- Health effects potentially related to exposure to environmental hazards CDC''s goal is to develop a tracking system that integrates data about environmental hazards and exposures with data about diseases that are possibly linked to the environment. This system will allow federal, state, and local agencies, and others to do the following: :- monitor and distribute information about environmental hazards and disease trends :- advance research on possible linkages between environmental hazards and disease :- develop, implement, and evaluate regulatory and public health actions to prevent or control environment-related diseases. Planning for an environmental public health tracking network is an important priority for CDC because of the opportunity it provides to address some of the most challenging problems facing local, state, and national public health leaders. From the outset, this activity has involved substantial collaboration between CDC and its public health and environmental partners (e.g., see the memorandum of understanding between HHS/CDC and the Environmental Protection Agency). Sponsors: This resource is supported by the Center for Disease Control and Prevention. Keywords: Environment, Public, Health, Disease, Analysis, Integration, Data, Hazard, Health, Prevention,
Software package that provides pathway enrichment techniques for miRNA expression data.
This NINDS website is designed to facilitate research efforts on Parkinsons disease, as well as to provide researchers, patients and caregivers with related information and resources. Because the interests of the research and patient communities are overlapping yet distinct, the site contains separate web pages directed toward these two communities. For example, regarding funding for PD research, researchers will find information on relevant research funding opportunities, and people with PD can access information on currently funded NINDS and NIH projects. As part of their mission to decrease the burden of neurological disease, and building upon a strong foundation of research discovery, the NINDS is committed to the rapid translation of basic research findings into clinical practice. The NINDS supports a broad spectrum of basic, translational and clinical research on Parkinsons disease (PD), a chronic, progressive movement disorder that affects the lives of at least one million patients across the United States. The average onset of characteristic motor symptoms, which are initially subtle and impact purposeful movement, occurs in the sixth decade. People with PD also experience significant non-motor symptoms including changes in cognition and mood, sleep disturbances, and autonomic dysfunction. Currently available pharmacological and surgical treatments provide relief from some motor symptoms, but do not halt the ultimate progression of the disease. Although significant research advances have been made, including the recent identification of possible environmental and genetic risk factors, a clear cause and a definitive cure for PD have remained elusive. Through a constellation of funding mechanisms, representing over 86 million in fiscal year 2008, the NINDS promotes the advancement of research directed to the understanding, treatment and eventual cure of PD. Sponsors: This resource is supported by the National Institute of Neurological Disorders and Stroke. Keywords: Stroke, Neurological, Disorder, Research, Disease, Researcher, Clinical, Parkinson''s Disease, PD, Chronic, Treatment, Cure, Motor, Genetic, Environmental,
analysis of Affymetrix GeneChip data at the probe level
Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.
Contains functions for removing batch effects and other unwanted variation in high-throughput experiment.
Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software)
Instituts de recherche en sante du Canada
The Canadian Institutes of Health Research (CIHR) is the Government of Canada''s agency responsible for funding health research in Canada. CIHR was created in 2000 under the authority of the CIHR Act and reports to Parliament through the Minister of Health. CIHR''s budget for 2008-09 is $928.6 million, of which $132 million is allocated to administering the Networks of Centres of Excellence and Canada Research Chair programs. CIHR was created to transform health research in Canada by: * funding more research on targeted priority areas; * building research capacity in under-developed areas such as population health and health services research; * training the next generation of health researchers; and * focusing on knowledge translation, so that the results of research are transformed into policies, practices, procedures, products and services. CIHR consists of 13 virtual institutes, a structure that is unique in the world. These innovative institutes bring together all partners in the research process - the people who fund research, those who carry it out and those who use its results - to share ideas and focus on what Canadians need: good health and the means to prevent disease and fight it when it happens. Each institute supports a broad spectrum of research in its topic areas and, in consultation with its stakeholders, sets priorities for research in those areas.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data.
The Wistar Institute is the nation''s first independent institution devoted to medical research and training. The Wistar Institute has evolved from its beginnings as an anatomical teaching museum to its present-day status as an international leader in basic biomedical research. In 1972, The Wistar Institute was designated a National Cancer Institute Cancer Center in basic researcha distinction it holds to this day. Wistar discoveries have led to the development of vaccines for rabies, rubella, and rotavirus, the identification of genes associated with breast, lung, and prostate cancer, and the development of monoclonal antibodies and other significant research technologies and tools.
The mission of the Department of Energy is to ensure America''s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. Goal 1: Transform our Energy Systems - Catalyze the timely, material, and efficient transformation of the nation''s energy system and secure U.S. leadership in clean energy technologies. Goal 2: The Science and Engineering Enterprise - Maintain a vibrant U.S. effort in science and engineering as a cornerstone of our economic prosperity, with clear leadership in strategic areas. Goal 3: Secure Our Nation - Enhance nuclear security through defense, nonproliferation, and environmental efforts. Goal 4: Management and Operational Excellence - Establish an operational and adaptable framework that combines the best wisdom of all Department stakeholders to maximize mission success.
Department of Energy Office of Science national laboratory
National laboratory to perform research supporting missions of several U.S. federal agency sponsors including Department of Energy, National Nuclear Security Administration, Department of Homeland Security, National Institutes of Health, Department of Defense, Nuclear Regulatory Commission, and Environmental Protection Agency. National lab with Pacific Northwest roots and global reach to create world that is safer, cleaner, more prosperous, and more secure.
Centers of Disease Control and Prevention
Division for Heart Disease and Stroke Prevention
It funded programs in 32 states and the District of Columbia in 2006 to promote cardiovascular health and to prevent morbidity and mortality due to heart disease and stroke. The Heart Disease and Stroke Prevention (HDSP) Policy Project was conducted to support the states in policy development and implementation. Through a contract with Mathematica Policy Research, Inc. (MPR), the following resources were developed: An annotated bibliography of state HDSP policy and activity sources A centralized database for state HDSP policies A guide to the fundamentals of HDSP policymaking A handbook for evaluating HDSP policies using an adaptation of the RE-AIM framework Sponsor. The HDSP Policy Project was supported by the Division for Heart Disease and Stroke Prevention, National Center for Chronic Disease Prevention and Health Promotion, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention.
This website contains is a list of software applications which currently support NeuroML (last updated: 28th May 2010). Note that not all tools support all parts of NeuroML. The level of support is generally higher for applications closer to the top of the list. Sponsors: This resource is supported by NeuroML. Keywordsl Software, Application, Neuron, Support,
University of Edinburgh Royal (Dick) School of Veterinary Studies; Scotland; United Kingdom
Royal (Dick) School of Veterinary Studies
University of Edinburgh Royal (Dick) School of Veterinary Studies
At the vanguard of veterinary education since William Dick founded the School in 1823, the Royal (Dick) School of Veterinary Studies is one of the world''s most innovative and influential centers for clinical care and student education. Using outstanding clinical facilities, we provide veterinary services of the highest standards and a stimulating educational experience for our students, within an environment rich in high quality interdisciplinary research. Affectionately known as the ''Dick Vet'', the School is part of the College of Medicine and Veterinary Medicine at the University of Edinburgh, one of the top 15 centers of biomedical research in the world with annual research awards in excess of 100 million pounds. Our research spans all aspects of veterinary medicine, from molecules and genes through to animal and human populations. Our partnership with the Medical School is summed up in the ethos - One Health. Our vision is simple yet ambitious: we want to take the School''s work to a new level as a world leader in veterinary research and training. By 2011 we will have invested over 100 million pounds in building state-of-the-art teaching facilities, clinics and laboratories. We attract, and actively recruit, the world''s leading veterinary teachers, clinicians and researchers to maintain our customary high ranking in the UK league tables for international excellence in our teaching and research.
U.S. Agency for International Development
NGSmethDB - A database for NGS single-cytosine-resolution DNA methylation data
A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes.
Michigan State University College of Veterinary Medicine
The college includes four biomedical science departments -- microbiology and molecular genetics, pathobiology and diagnostic investigation, pharmacology and toxicology, and physiology; two clinical departments -- large-animal clinical sciences and small-animal clinical sciences; two service units -- the Veterinary Teaching Hospital and the Diagnostic Center for Population and Animal Health; and several research centers. In addition to the Doctor of Veterinary Medicine degree program, the college also offers certificate and bachelors degree programs in veterinary technology, as well as advanced degree (masters and doctor of philosophy) programs. The mission of the College of Veterinary Medicine is to develop a diverse academic community that fosters scholarly activity and encourages exemplary human qualities in order that the art and science of veterinary medicine may be imparted to students, expanded by research, and extended to the public for the benefit of animal and human health to meet the changing needs of Michigan, the nation, and the world. The College of Veterinary Medicine is fortunate to have an outstanding faculty, all of whom hold the doctor of veterinary medicine degree and/or the doctor of philosophy degree. Nearly all of the specialty boards recognized by the American Veterinary Medical Association are represented on the faculty. Many of these faculty members are leaders in their fields, both nationally and internationally. Michigan State has a long-standing commitment to equal opportunity, affirmative action, and multiculturalism. The College of Veterinary Medicine has attained national recognition for its leadership in programs for the encouragement of underrepresented groups at the preprofessional, professional, and advanced studies levels, as well as for increased diversity in its faculty. Special opportunities for preveterinary and professional students to participate in international veterinary activities further expand appreciation of different cultures. Indeed, international experience and opportunities abound in the college for both faculty and students. Nearly 300 individuals associated with the college have been involved in activities in 36 countries. A special endowment provides funds to support student travel abroad. The abundance and variety of animal agriculture and companion animals in Michigan provides the college with one of the largest clinical and diagnostic caseloads in the country. Educational and research opportunities are considerably enhanced by this large caseload. The college also takes seriously its obligation to meet the needs of society in addition to clinical services and education. The college has expertise in public health, biomedical and comparative medical research, ecosystem and environmental management, and the multiple facets that compose our complex global food system. CVM also supports key animal health programs conducted by both the Michigan Department of Agriculture and the U.S. Department of Agriculture.
NERC is the UK''s main agency for funding and managing research, training and knowledge exchange in the environmental sciences. It funds world-class science in universities and our own research centres that increases knowledge and understanding of the natural world. We are tackling the 21st century''s major environmental issues such as climate change, biodiversity and natural hazards. We lead in providing independent research and training in the environmental sciences. NERC is a non-departmental public body. We receive funding from the Department for Business, Innovation and Skills (BIS). Working internationally, we have bases in the most hostile parts of the planet. We run a fleet of research ships and aircraft and invest in satellite technology to monitor gradual environmental change on a global scale. We provide knowledge, forewarning and solutions to the key global environmental challenges facing society.
NEALS - The Northeast Amyotrophic Lateral Sclerosis Consortium
Northeast Amyotrophic Lateral Sclerosis Consortium
The Northeast ALS Consortium (NEALS) is an independent, non-profit consortium of clinical and scientific investigators who conduct research in Amyotrophic Lateral Sclerosis (ALS) and Upper Motor Neuron Disease (UMND) research at their affiliated institutions. The mission of NEALS is to take advances in ALS and UMND research from the lab and rapidly translate them into treatments for people. Databases and samples are available for researchers studying these diseases.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software as system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
Function for differentially methylated regions (DMR) detection that is a part of the charm package in R/Bioconductor.
IT infrastructure services for businesses in the form of web services, now commonly known as cloud computing. This highly reliable, scalable, low-cost infrastructure platform in the cloud powers hundreds of thousands of businesses. With data center locations in the U.S., Europe, Singapore, and Japan, customers across all industries are taking advantage of the following benefits: * Low cost * Agility and Instant Elasticity * Open and Flexible * Secure
Django is a high-level Python Web framework that encourages rapid development and clean, pragmatic design. Developed four years ago by a fast-moving online-news operation, Django was designed to handle two challenges: the intensive deadlines of a newsroom and the stringent requirements of the experienced Web developers who wrote it. It lets you build high-performing, elegant Web applications quickly. Django focuses on automating as much as possible and adhering to the DRY principle.
This program will find the mid-sagittal plane, the AC, PC, and mpj points in an image, and create an AC/PC aligned data set with the AC point at the center of the voxel lattice (la beled at the origin of the image physical space.) This work is an extention of the algorithms originally described by Dr. Babak A. Ardekani, Alvin H. Bachman, Model-based automatic detection of the anterior and posterior commissures on MRI scans, N euroImage, Volume 46, Issue 3, 1 July 2009, Pages 677-682, ISSN 1053-8119, DOI: 10.1016/j.neuroimage.2009.02.030. (http://www.sciencedirect.com/science/article/B6WNP-4VRP25C-4/2/8207b962a38aa83c822c6379bc43fe4c)
National Center for Advancing Translational Sciences
The National Institutes of Health (NIH) has established a new center, called the National Center for Advancing Translational Sciences (NCATS). Currently, many costly, time-consuming bottlenecks exist in the translational pipeline. Working in partnership with the public and private sectors, the Center will develop innovative ways to reduce, remove or bypass these bottlenecks. This will speed the delivery of new drugs, diagnostics and medical devices to patients. The mission of the National Center for Advancing Translational Sciences is to catalyze the generation of innovative methods and technologies that will enhance the development, testing, and implementation of diagnostics and therapeutics across a wide range of human diseases and conditions. NCATS is formed primarily by uniting and realigning existing NIH programs that play key roles in translational science. The Center will not be a drug development company, but will focus on using science to create powerful new tools and technologies that can be adopted widely by translational researchers in all sectors.
National Institute on Disability and Rehabilitation Research
Created in 1978, The National Institute on Disability and Rehabilitation Research (NIDRR) is a national leader in sponsoring research. We provide leadership and support for a comprehensive program of research related to the rehabilitation of individuals with disabilities. All of our programmatic efforts are aimed at improving the lives of individuals with disabilities from birth through adulthood. NIDRR is located in Washington, D.C., and is one of three components of the Office of Special Education and Rehabilitative Services (OSERS) at the U.S. Department of Education. NIDRR operates in concert with the Rehabilitation Services Administration (RSA) and the Office of Special Education Programs (OSEP). The mission of NIDRR is to generate new knowledge and promote its effective use to improve the abilities of people with disabilities to perform activities of their choice in the community, and also to expand society''s capacity to provide full opportunities and accommodations for its citizens with disabilities. Toward this end, NIDRR conducts comprehensive and coordinated programs of research and related activities to maximize the full inclusion, social integration, employment and independent living of individuals of all ages with disabilities. NIDRR''s focus includes research in areas such as employment; health and function; technology for access and function; independent living and community integration; and other associated disability research areas. Balanced between the scientific and consumer communities, NIDRR plays a unique role in federally-funded research activities. As part of the scientific community, NIDRR makes an important contribution to the overall knowledge in rehabilitation medicine, engineering, psychosocial rehabilitation, integration, vocational outcomes and the virtual and built environments. In addition, NIDRR''s work helps to integrate disability research into our nation''s policies regarding science and technology, health care, and economics.
National Institute on Deafness and Other Communication Disorders
National Institute on Deafness Other Communication Disorders
The National Institute on Deafness and Other Communication Disorders (NIDCD) is one of the Institutes that comprise the National Institutes of Health (NIH). Established in 1988, NIDCD is mandated to conduct and support biomedical and behavioral research and research training in the normal and disordered processes of hearing, balance, smell, taste, voice, speech, and language. The Institute also conducts and supports research and research training related to disease prevention and health promotion; addresses special biomedical and behavioral problems associated with people who have communication impairments or disorders; and supports efforts to create devices which substitute for lost and impaired sensory and communication function. It is estimated that more than 46 million people in the United States suffer some form of disordered communication. NIDCD has focused national attention on disorders of human communication and has contributed to advances in biomedical and behavioral research that will improve the lives of millions of individuals with communication disorders. NIDCD has made important contributions to the body of knowledge needed to help those who experience communication disorders and to advance research in all aspects of human communication. NIDCD accomplishes its mandate through the Division of Intramural Research, which conducts research in laboratories at the NIH, and the Extramural Research Program, a program of research grants, career development awards, individual and institutional research training awards, center grants, and contracts to public and private research institutions and organizations. As a whole, the Institute supports and conducts approximately 600 research projects. The Institute also conducts and supports research and research training in disease prevention and health promotion and the special biomedical and behavioral problems associated with people having communication impairments and disorders. NIDCD''s extramural grant portfolio demonstrates a balance of basic and clinical research. The intramural research program spans a variety of topics, including, but not limited to, the development of a vaccine against otitis media, the identification and characterization of genes responsible for hereditary hearing impairment, genes associated with neoplasms affecting human communication, and treatment of voice disorders.
The European Partnership for Alternative Approaches to Animal Testing
It is an unprecedented voluntary collaboration between the European Commission, European trade associations, and companies from seven industry sectors. The partners are committed to pooling knowledge and resources to accelerate the development, validation and acceptance of alternative approaches to further the reduction, refinement and replacement (3Rs) of animal use in regulatory testing. Three platforms organise the work on different projects and ensure their consistency. EPAA in a nutshell The European Partnership for Alternative Approaches to Animal Testing (EPAA) is a joint initiative from the European Commission, European trade associations from seven industry sectors and individual companies (see partners here). It was launched in November 2005 with the purpose to promote the development and implementation of new 3Rs methods (replace, reduce, refine) and modern alternative approaches in the field of safety testing. Main areas of activity The Partnership activities cover: Mapping and dissemination of information about in house methods and research programmes Support to development of new alternative approaches and testing strategies Removing barriers to validation and regulatory acceptance of 3Rs Dialogue with regulators on 3Rs & testing requirements Since 2009, three platforms Science, 3Rs in Regulation and Communication & Dissemination organise the work on different projects and secure their consistency: Science: new perspectives on safety Read more > 3Rs in Regulation: acute tox, consistency approach in vaccines testing, post-validation review Read more > Communication & Dissemination: 3Rs'' market place, thematic reviews Read more >
The EQUATOR Network is an international initiative that seeks to enhance reliability and value of medical research literature by promoting transparent and accurate reporting of research studies. This goal will be achieved through: raising awareness of the crucial importance of good reporting of research becoming the recognised global centre providing resources, education and training relating to the reporting of health research and use of reporting guidelines assisting in the development, dissemination and implementation of reporting guidelines monitoring the status of the quality of reporting across health research literature conducting research relating to the quality of reporting The EQUATOR Network Resource Centre provides up-to-date resources related to health research reporting mainly for: authors of research articles journal editors and peer reviewers reporting guideline developers Other users that benefit from the knowledge of principles of good research reporting include representatives of research funders, research ethics committee members, individuals and organisations involved in research education. The resources on our website are regularly updated (see the date of the last update at the foot of each page). Sponsor. Core programme funding for 2007 - 2013 NHS National Library for Health NHS National Institute for Health Research NHS National Knowledge Service UK Medical Research Council Canadian Institutes of Health Research Scottish Chief Scientist Office Pan American Health Organization
An automatic pipeline based on an algorithm that identifies new resources in publications every month to assist the efficiency of NIF curators. The pipeline is also able to find the last time the resource's webpage was updated and whether the URL is still valid. This can assist the curator in knowing which resources need attention. Additionally, the pipeline identifies publications that reference existing NIF Registry resources as this is also of interest. These mentions are available through the Data Federation version of the NIF Registry, http://neuinfo.org/nif/nifgwt.html?query=nlx_144509 The RDF is based on an algorithm on how related it is to neuroscience. (hits of neuroscience related terms). Each potential resource gets assigned a score (based on how related it is to neuroscience) and the resources are then ranked and a list is generated.
Founded in 1876, Meharry is a non-profit university in Tennessee. Meharry includes a medical school, dental school, and a graduate school.
Office of research facilities development and operations
BEDOPS: high-performance genomic feature operations
A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets.
Ohio State University College of Medicine; Ohio; USA
Ohio State University College of Medicine
This is an exciting time at The Ohio State University Medical Center. By every measure, we''re an organization on the move -- a rise that is reflected in our national rankings. Currently ranked 27th in the 2010 U.S. News & World Report''s America''s Best Graduate Schools, the OSU College of Medicine has made one of the greatest leaps in rankings history, gaining 17 positions since 2003 among public and private medical colleges and schools of osteopathic medicine. Great as that is, rankings alone do not tell the whole story. More than 170 of our faculty are listed in Best Doctors in America, and Ohio State has led the nation three years in a row in the number of faculty elected to the American Association for the Advancement of Science. We''ve embarked on a massive 15-year construction program that will set the standard for academic medical centers of the future, creating dramatic and dynamic research, clinical and learning environments. And we''re becoming a world leader in advancing personalized health care, a revolutionary new brand of healthcare delivery based on each person''s unique biological, behavioral and environmental characteristics. We invite you to take some time to explore our Web site to learn more about the great things happening here at The Ohio State College of Medicine.
A highly flexible EEG/ERP and MEG analysis package with a variety of source reconstruction, signal analysis and MRI processing features. ASA combines functional brain imaging with the visualization and incorporation of morphological information obtained from MRI or CT. ASA is a highly interactive and flexible software tool that can be applied to neuro-physiological and clinical brain research. ASA gives a realistic impression of your experimental configuration together with topographical mapping of EEG and MEG and the results of your analysis. ASA is developed for and by people dedicated to brain research. The concept of flexibility and openness covers even most complex analysis demands. The ASA environment is particularly attractive for those that wish to develop their own methods in third party packages like Matlab and use ASA for pre-processing and visualization purposes.
University of North Texas Health Science Center Department of Pharmacology & Neuroscience
The Department of Pharmacology & Neuroscience is dedicated to quality biomedical research and graduate education. Research Assistantships are provided for all doctoral students. The Graduate Biomedical Science Program at the University of North Texas Health Science Center is a recipient of the residential Award for Science Mentoring from the National Science Foundation.
rqubic - Qualitative biclustering algorithm for expression data analysis in R
This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data.
Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool
Department for International Development
Department for International Development - UK
Biomphalaria glabrata Genomic Initiative
An international consortium has successfully pursued the development of an internationally supported a molluscan genome project, one that is focused mainly on the freshwater gastropod Biomphalaria glabrata. This site provides information on design, management and progress of this initiative. Currently, the consortium encourages investigators to pursue external funding available at the national level, towards hypothesis-driven research projects that include a gene discovery component. Individual research groups may combine efforts in national and international settings to apply for large scale resources such as funding for exchange of information and investigators, production of BAC libraries, and sequencing capacity. The sequences generated as part of the consortium effort will be released to public databases in a timely fashion Data: - NCBI databases : 55767 nucleotide (54309 ESTs)/1 genome/650 protein entries. - Genome Project 12879: 265,481 records (WGS/EST/454/BES) in the trace archives. - Short Read Archive (SRA): 454 data projects: 23Gbases gDNA. Sponsors: This resource is supported by the University of New Mexico. Keywords: Gastropod, Biomphalaria glabrata, Genomic, Data, Nucleotide, Genome,
Southern Illinois University; Illinois; USA
Public research university in Carbondale, Illinois. Founded in 1869, SIU is the oldest campus of the Southern Illinois University system.
National Institutes of Neurological Disorders and Stroke: Research Funding
Research funding for basic and clinical neuroscience trials to help train investigators and better understand diagnosis, treatment, and prevention of neurological disorders. Funds are allocated by Congress on a yearly basis.
The European Society for Paediatric Urology is a non-profit society whose main purpose is to promote paediatric urology, appropriate practice, education as well as exchanges between practitioners involved in the treatment of genito urinary disorders in children. Philosophy and aims To share knowledge and experience between nurses and other paramedical staff interested in pediatric urology and continence, increase the quality of the caring for children suffering from these problems as well as to support nurses in their profession and research. Objectives To develop and maintain an international net-working group in pediatric urology nursing in association with ESPU. To raise the profile of this group by promoting educational activities such as annual conferences with papers presented by the members. In the future, make up standards for training in pediatric urology nursing. To support exchange visits between the members. To promote research activities and publications. To establish a universal approach to clinical practice through suggested guide lines. To collate and review new information and research. To improve and validate our clinical practice by communication and co-operation.
A central hub of content collected from bloggers who write about R (in English).
Mitelman Database of Chromosome Aberrations in Cancer
The web site includes genomic data for humans and mice, including transcript sequence, gene expression patterns, single-nucleotide polymorphisms, clone resources, and cytogenetic information. Descriptions of the methods and reagents used in deriving the CGAP datasets are also provided. An extensive suite of informatics tools facilitates queries and analysis of the CGAP data by the community. One of the newest features of the CGAP web site is an electronic version of the Mitelman Database of Chromosome Aberrations in Cancer. The data in the Mitelman Database is manually culled from the literature and subsequently organized into three distinct sub-databases, as follows: -The sub-database of cases contains the data that relates chromosomal aberrations to specific tumor characteristics in individual patient cases. It can be searched using either the Cases Quick Searcher or the Cases Full Searcher. -The sub-database of molecular biology and clinical associations contains no data from individual patient cases. Instead, the data is pulled from studies with distinct information about: -Molecular biology associations that relate chromosomal aberrations and tumor histologies to genomic sequence data, typically genes rearranged as a consequence of structural chromosome changes. -Clinical associations that relate chromosomal aberrations and/or gene rearrangements and tumor histologies to clinical variables, such as prognosis, tumor grade, and patient characteristics. It can be searched using the Molecular Biology and Clinical (MBC) Associations Searcher -The reference sub-database contains all the references culled from the literature i.e., the sum of the references from the cases and the molecular biology and clinical associations. It can be searched using the Reference Searcher. CGAP has developed six web search tools to help you analyze the information within the Mitelman Database: -The Cases Quick Searcher allows you to query the individual patient cases using the four major fields: aberration, breakpoint, morphology, and topography. -The Cases Full Searcher permits a more detailed search of the same individual patient cases as above, by including more cytogenetic field choices and adding search fields for patient characteristics and references. -The Molecular Biology Associations Searcher does not search any of the individual patient cases. It searches studies pertaining to gene rearrangements as a consequence of cytogenetic aberrations. -The Clinical Associations Searcher does not search any of the individual patient cases. It searches studies pertaining to clinical associations of cytogenetic aberrations and/or gene rearrangements. -The Recurrent Chromosome Aberrations Searcher provides a way to search for structural and numerical abnormalities that are recurrent, i.e., present in two or more cases with the same morphology and topography. -The Reference Searcher queries only the references themselves, i.e., the references from the individual cases and the molecular biology and clinical associations. Sponsors: This database is sponsored by the University of Lund, Sweden and have support from the Swedish Cancer Society and the Swedish Children''s Cancer Foundation
Stichting Netherlands Bioinformatics Center
Stichting Netherlands Bioinformatics Centre
A collaborative institute of the bioinformatics groups in the Netherlands that perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. They aim to build and maintain a strong bioinformatics and e-bioscience community that meets the (growing) demand for bioinformatics expertise, infrastructure and personnel in the Dutch life sciences field and provides a stimulating force for advanced research in biology. The NBIC grants aim to support the NBIC projects and (the visibility of) the NBIC community. Therefore, only people working in NBIC partner organizations can apply for sponsoring by NBIC. Positions for postdocs and others are available and there is a yearly conference.
Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. It contains resources from many different SIB groups as well as external institutions.
Biclustering Analysis and Results Exploration.
Iterative Binary Biclustering of Genesets
A bi-clustering algorithm which is optimizes for binary data analysis.
eisa - Expression data analysis via the Iterative Signature Algorithm
A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data.
Map of identifyied genes controlling traits of economic and welfare significance in the pig. The project objectives were to produce a genetic map with markers spaced at approximately 20 centiMorgan intervals over at least 90% of the pig genome; to produce a physical map with at least one distal and one proximal landmark locus mapped on each porcine chromosome arm and also genetically mapped; to develop a flow karyotype for the pig based on FACS sorted chromosomes; to develop PCR based techniques to enable rapid genotyping for polymorphic markers; to evaluate synteny conservation between pigs, man, mice and cattle; to develop and evaluate the statistical techniques required to analyze data from QTL mapping experiments and to plan and initiate the mapping of QTLs in the pig; to map loci affecting traits of economic and biological significance in the pig; and to develop the molecular tools to allow the future identification and cloning of mapped loci. Animal breeders currently assume that economically important traits such as growth, carcass composition and reproductive performance are controlled by an infinite number of genes each of infinitessimal effect. Although this model is known to be unrealistic, it has successfully underpinned the genetic improvement of livestock, including pigs, over recent decades. A map of the pig genome would allow the development of more realistic models of the genetic control of economic traits and the ultimately the identification of the major trait genes. This would allow the development of more efficient marker assisted selection which may be of particular value for traits such as disease resistance and meat quality.
About FamilySearch FamilySearch is the largest genealogy organization in the world. Millions of people use FamilySearch records, resources, and services to learn more about their family history. For over 100 years, FamilySearch has been actively gathering, preserving, and sharing genealogical records worldwide. Patrons may freely access our resources and service online at FamilySearch.org, or through over 4,500 family history centers in 70 countries, including the renowned Family History Library in Salt Lake City, Utah. Family Connection Families are meant to be central to our livesFamilySearch is a service provided by The Church of Jesus Christ of Latter-day Saints. Our commitment to helping people connect with their ancestors is rooted in our beliefs. We believe that families are meant to be central to our lives and that family relationships are intended to continue beyond this life. We therefore believe that all family membersthose living, those past, and those futureshare an enduring bond that reaches across the generations. All Are Welcome We encourage all people to seek out their ancestors and preserve their family histories. Because interest in family history is not limited by culture, ethnicity, or religious faith, we welcome all who wish to discover more about their family and their heritage.
USDA National Institute of Food and Agriculture
Cooperative State Research Education and Extension Service
National Institute of Food and Agriculture
U.S. Department of Agriculture Cooperative State Research Education and Extension Service
U.S. Department of Agriculture National Institute of Food and Agriculture
United States Department of Agriculture Cooperative State Research Education and Extension Service
United States Department of Agriculture National Institute of Food and Agriculture
USDA Cooperative State Research Education and Extension Service
National Institute of General Medical Sciences
NIGMS supports basic biomedical research that is not targeted to specific diseases. NIGMS funds studies on genes, proteins, and cells, as well as on fundamental processes like communication within and between cells, how our bodies use energy, and how we respond to medicines. The results of this research increase our understanding of life and lay the foundation for advances in disease diagnosis, treatment, and prevention. NIGMS also supports research training programs that produce the next generation of biomedical scientists, and it has special programs to encourage underrepresented minorities to pursue biomedical research careers. The National Institute of General Medical Sciences (NIGMS) primarily supports research that lays the foundation for advances in disease diagnosis, treatment, and prevention. The Institute's research training programs help provide the next generation of scientists. Each year, NIGMS-supported scientists make many advances in understanding fundamental life processes. In the course of answering basic research questions, these investigators increase our knowledge about the mechanisms and pathways involved in certain diseases. Institute grantees also develop important new tools and techniques, some of which have medical applications. In recognition of the significance of their work, a number of NIGMS grantees have received the Nobel Prize and other high scientific honors. At any given time, NIGMS supports approximately 4,700 research grants—approximately 11 percent of the grants funded by NIH as a whole. NIGMS also supports approximately 26 percent of the trainees who receive assistance from NIH. NIGMS also supports approximately 25% of the trainees who receive assistance from NIH. The Institute places great emphasis on supporting investigator-initiated research grants. It funds a limited number of research center grants in selected fields, including structural genomics, trauma and burn research, and systems biology. In addition, NIGMS supports several important scientific resources, including the NIGMS Human Genetic Cell Repository and the Protein Data Bank.
McGill University Faculty of Medicine; Montreal; Canada
University of Cincinnati College of Medicine; Ohio; USA
University of Cincinnati College of Medicine
Trowel - Error Correction Module for Illumina Sequencing Reads
An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.
ChAMP - Chip Analysis Methylation Pipeline for Illumina HumanMethylation450
Software package that includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations.
Public research university located in Ghent, Belgium. One of the biggest Flemish universities.
THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. The objectives of the BBSRC IGF funding that started FlyChip were to establish a genomics infrastructure that would provide UK Drosophila researchers access to these emerging technologies, thereby maintaining the internationally recognised research profile the UK fly community enjoys. Via the IGF initiative, and with other funding, we have developed core genomics resources for the UK Drosophila community and we continue to develop these resources in a national and international context. As the facility has developed we are providing access to genomics technologies for researchers working with other organisms. Our Specific objective are: To drive the development of genomics resources and techniques and make these widely available to the broader research community. It is our aim to implement new omics techniques and make them available to the community, both through our facility and also through transfer of expertise to other UK research groups. Provide access to state-of-the-art microarray platforms for expression profiling and other genomics applications. Develop methodologies, especially in terms of quality control, normalisation, quantification and data analysis, that will be broadly applicable to the design and implementation of genomics experiments in metazoans. As a complex eukaryote with a compact genome, the Drosophila model is ideally suited to such a role. To expand the scope of the genomics resources to enable the community to encompass the use of whole genome arrays for expression profiling, transcription factor binding studies and chromatin structure studies. To develop a more cohesive interaction with members of the community who require access to genomics tools. We wish offer a flexible and interactive service for UK researchers, accommodating those who need access to reagents to perform their own genomics studies or hosting researchers within the facility for more complex studies. Utilise Drosophila as a model for establishing an effective metazoan systems biology platform. To form multidisciplinary collaborations aimed at developing new genomics techniques and informatics methods. Take a proactive role in the creation of international public genomics resources that benefit not only the UK research community, but also, through the development of international standards and resources, the world wide fly community. Overview This microarray format is no longer available. Each microarray contains 18,240 elements (or ''spots''). This array is composed of transcript-specific oligonucleotides and controls developed by the International Drosophila Array Consortium (INDAC). These controls include spikes, i.e., probes complementatary to targets in A. thaliana, spotting buffer, and probe degradation. Empty wells in the INDAC set are also printed. The spot layout is randomised to facilitate correction of systematic biases. The spots have an estimated mean diameter of 90-120 m. Gene Expression Omnibus (GEO) accession: GPL5016 Materials and Equipment FL002 microarrays were printed using the Genetix Qarray2 contact-printing instrument and 48 Genetix aQu75 split-pins on FMB PowerMatrix slides. Probe DNA was dissolved in 150 mM NaPO4. The printed oligo-set consisted of: A gene-specific Drosophila melanogaster 70mer long oligonucleotide set prepared in conjunction with INDAC (INDAC) Gene-specific Arabidopsis thaliana 70mer long oligonucleotide spike controls developed by FlyChip (protocols) and prepared in conjunction with INDAC (INDAC) 70mer probe degradation long oligonucleotide set prepared in conjunction with INDAC (INDAC) Sponsor. DH is funded by a Grand Challenges in Global Health grant to a consortium led by Austin Burt.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme.
NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
National Institute of Diabetes and Digestive and Kidney Diseases
Center with mission to conduct and support medical research and research training and to disseminate science-based information on diabetes and other endocrine and metabolic diseases. The NIDDK supports a wide range of medical research through grants to universities and other medical research institutions across the country.
Accurate error-correction of amplicon pyrosequences.
The Department of Health is committed to improving the quality and convenience of care provided by the NHS and social services. Its work includes setting national standards, shaping the direction of health and social care services and promoting healthier living. Funding. The Association of Medical Research Charities (AMRC) was founded to further medical research in the United Kingdom, and develop the effectiveness of those charities for which medical research is a major activity. There are currently 114 charities including the world''s largest charity, the Wellcome Trust, within the Association of Medical Research Charities, covering a wide range of diseases. Their combined expenditure on medical research is approximatelly 800m per annum
Software package that provides functions to identify genomic regions of interest based on segmented copy number data from multiple samples.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 12,2025. The AIDSinfo Drug Database provides fact sheets on HIV/AIDS related drugs. The fact sheets describe the drug''s use, pharmacology, side effects, and other information. The database includes: -Approved and investigational HIV/AIDS related drugs -Three versions of each fact sheet: patient, health professional, and Spanish. AIDSinfo is a 100% federally funded U.S. Department of Health and Human Services (DHHS) project that offers the latest federally approved information on HIV/AIDS clinical research, treatment and prevention, and medical practice guidelines for people living with HIV/AIDS, their families and friends, health care providers, scientists, and researchers. Sponsors: -National Institutes of Health (NIH) Office of AIDS Research National Institute of Allergy and Infectious Diseases (NIAID) National Library of Medicine (NLM) -Health Resources and Services Administration (HRSA) -Centers for Disease Control and Prevention (CDC) -Centers for Medicare and Medicaid Services (CMS)
AASLD - American Association for the Study of Liver Diseases
American Association for the Study of Liver Diseases
A non-profit organization of scientists and healthcare professionals committed to preventing and curing liver disease, which runs three journals and an annual meeting. Its mission is to Advance the Science and Practice of Hepatology, Liver Transplantation and Hepatobiliary Surgery, Thereby Promoting Liver Health and Optimal Care of Patients with Liver and Biliary Tract Diseases. AASLD was founded in 1950 by a small group of leading liver specialists (including Hans Popper, Leon Schiff, Fred Hoffbauer, Cecil Watson, Jesse Bollman, and Sheila Sherlock, to name a few) to bring together those who had contributed to the field of hepatology. AASLD has grown to an international society responsible for all aspects of hepatology, and our annual meeting, The Liver Meeting, has grown in attendance from 12 to over 7,000 physicians, surgeons, researchers, and allied health professionals from around the world. AASLD sponsors two to four Single Topic Conferences each year in clinical, basic, hepatitis, or pediatric hepatology. Our two monthly journals, HEPATOLOGY and Liver Transplantation, provide the latest research findings for hepatology and surgery of the liver. AASLD''s membership includes ALL professionals dedicated to hepatobiliary discoveries and patient care. Mentoring, the sharing of knowledge, and dedication to professional growth and development are among the core values of AASLD and its members.
Genetic Engineering & Biotechnology News
Genetic Engineering and Biotechnology News
News source including the entire bioproduct life cycle from early-stage R&D, to applied research including omics, biomarkers, as well as diagnostics, to bioprocessing and commercialization.
Resource out of service. Documented on February 24,2021.
A plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses, imports, and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLAB's event structure, allowing easy saccade- and fixation-related EEG analysis (e.g., fixation-related potentials, FRPs). Alternatively, EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior (e.g. pupil size, microsaccades) in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLAB's GUI or called from the command line.
National Institute of Dental and Craniofacial Research
The mission of the National Institute of Dental and Craniofacial Research (NIDCR) is to improve oral, dental and craniofacial health through research, research training, and the dissemination of health information. We accomplish our mission by: * Performing and supporting basic and clinical research; * Conducting and funding research training and career development programs to ensure an adequate number of talented, well-prepared and diverse investigators; * Coordinating and assisting relevant research and research-related activities among all sectors of the research community; * Promoting the timely transfer of knowledge gained from research and its implications for health to the public, health professionals, researchers, and policy-makers.
Independent agency of the U.S. federal government that administers Social Security, a social insurance program consisting of retirement, disability, and survivor benefits.
University of Rochester Medical Center Pharmacology and Physiology
The Department of Pharmacology and Physiology consists of faculty, fellows and students who are dedicated to cutting-edge scientific research, in order to work towards a better understanding of how the human body functions and to alleviate human diseases. The faculty is composed of distinguished scientists who are international leaders in the fields of cell signaling and signal transduction, neurodegenerative diseases and mechanisms of cell death, cardiovascular diseases and ion channels, drugs of abuse and mechanisms of addiction, and integrative biomedical sciences. The department promotes a strong training program for both graduate students and post-doctoral fellows, and many of our graduates have gone on to become leaders in academia, industry and government. The University of Rochester Medical Center is now in the process of unprecedented growth, which includes the opening of two new research buildings and the establishment of over fifty new research laboratories. The Department is enthusiastic about being a part of that growth in the research enterprise, as we aim to be one of the finest medical centers in the world.
A bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences.
Wright State University Dayton OH. Pharmacology and Toxicology
The programs of study in the Department of Pharmacology and Toxicology are the Master of Science in Pharmacology and Toxicology and the Ph.D. programs in Biomedical Sciences and Environmental Sciences. The master's program is a research-based program that recruits students from universities as well as the military and industrial sectors. Faculty also participate in the summer research training program for minorities and persons with disabilities (STREAMS) as well as the Biomedical Science Exchange (BSE) a research and education with universities in Brazil.
Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site.
The CFGP (Comparative Fungal Genomics Platform) was designed for comparative genomics projects with diverse fungal genomes. The CFGP provides important bioinformatic tools, such as BLAST search, ClustalW analysis, InterPro Scan, SignalP, and PSORT2, which are very common tools for the researchers in the field of genomics. Many of them have been executed in the unix environment, so some specific computing knowledge is required. In the CFGP, users can use these tools simply by clicking their mouse button. In addition, all of the results of the analysis will be stored in the CFGP, so you can easily share those results with other members.
CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons. To achieve this goal, each single gene expression experiment is regularly mapped on a permanent target identifier consisting of a physical description of the targeted RNA. There is one entry per gene. To have a complete view of the transcript and its product, we also link each entry to the corresponding protein. We further provide the genomic position of the transcription start site from EPD, when available. Otherwise we give the annotated start site position in Ensembl.
American Parkinson Disease Association Inc.
The American Parkinson Disease Association, Inc. was founded in 1961 to ease the burden and find a cure for Parkinson''s disease. The organization focuses its energies on research, patient support, education and raising public awareness of the disease. It offers Parkinson Disease news and updates, as well as connecting users to other Parkinson-related resources, such as referral centers, Parkinson events, and research grant information for the scientific community. It also offers access to Parkinson-related publications, as well as Young Onset Parkinson-related resources. American Parkinson Disease Association Inc. is headquartered in Staten Island, New York. :NIF thanks the : :Parkinson''s Disease Foundation : : :for their referral of this resource to us.
This blog will appeal to those dealing with the practical day to day work of biological data analysis and presentation.
This mailing list is for announcements about Bioconductor and the availability of new code and questions and answers about problems and solutions using Bioconductor.
Indiana University School of Medicine; Indiana; USA
Medical school and medical research center connected to Indiana University. Its principal research and medical center is on Indiana University – Purdue University Indianapolis campus in Indianapolis.
Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ).
Differential Binding Analysis of ChIP-Seq peak data
Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
featureCounts: a universal read summarization program
A read summarization program, which counts mapped reads for the genomic features such as genes and exons.
The Comparative Genometrics website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarily focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles. The genometric analyses are available via phylogenetic tree or alphabetical list. It also offers small genome information, for mitochondria, chloroplasts, viruses, bacteriophages, and plasmids.
An open organization engaged in the development of interoperable online metadata standards that support a broad range of purposes and business models. DCMI''s activities include work on architecture and modeling, discussions and collaborative work in DCMI Communities and DCMI Task Groups, annual conferences and workshops, standards liaison, and educational efforts to promote widespread acceptance of metadata standards and practices. The Dublin Core Metadata Initiative provides simple standards to facilitate the finding, sharing and management of information. DCMI does this by: * Developing and maintaining international standards for describing resources * Supporting a worldwide community of users and developers * Promoting widespread use of Dublin Core solutions The major characteristics of DCMI as an organization are (the three Is): * Independent: DCMI is not controlled by specific commercial or other interests and is not biased towards specific domains nor does it mandate specific technical solutions * International: DCMI encourages participation from organizations anywhere in the world, respecting linguistic and cultural differences * Influenceable: DCMI is an open organization aiming at building consensus among the participating organizations; there are no prerequisites for participation The development and maintenance of a core set of metadata terms (the DCMI Metadata Terms) continues to be one of the main activities of DCMI. In addition, DCMI is developing guidelines and procedures to help implementers define and describe their usage of Dublin Core metadata in the form of Application Profiles. This work is done in a work structure that provides discussion and cooperation platforms for specific communities (e.g. education, government information, corporate knowledge management) or specific interests (e.g. technical architecture, accessibility). Anyone wishing to participate may do so by simply joining the appropriate mailing list for the activity of interest. The DC-General mailing list is the general forum for community participation and announcements.
Public research and education university in Northern Germany with main campus located in central district of Rotherbaum, with affiliated institutes and research centres spread around city state.
Newcastle University; Newcastle upon Tyne; United Kingdom
Newcastle University; Newcastle-upon-Tyne; United Kingdom
Newcastle University; Newcastle; United Kingdom
UK public research university based in Newcastle upon Tyne, North East England with overseas campuses in Singapore and Malaysia. The university is a red brick university and a member of the Russell Group, an association of research-intensive UK universities.
NarrowPeaks: Analysis of Variation in ChIP-seq using Functional PCA Statistics
Software package for post-processing of peaks and differential binding in ChIP-seq based on standard wiggle visualization files. The double aim of the package is to apply a functional version of principal component analysis (FPCA) to: (1) Process data in wiggle track format (WIG) commonly produced by ChIP-seq peak finders by applying FPCA over a set of selected candidate enriched regions. This is done in order to shorten the genomic locations accounting for a given proportion of variation among the enrichment-score profiles. The function ''narrowpeaks'' allows the user to discriminate between binding regions in close proximity to each other and to narrow down the length of the putative transcription factor binding sites while preserving the information present in the variability of the dataset and capturing major sources of variation. (2) Analyze differential variation when multiple ChIP-seq samples need to compared. The function ''narrowpeaksDiff'' quantifies differences between the tag-enrichment, and uses non-parametric tests on the FPC scores for testing differences between conditions.
Cybase is dedicated to the study of a fascinating new class of proteins that possess a cyclic backbone in which the N and C termini have been joined with a conventional amide bond. These recently characterized molecules have now been found in organisms from all kingdoms of life and given the current rate of discovery the number of sequences could soon number in the hundreds. Research in our lab is aimed at further characterizing cyclic proteins and adapting them for commercial and medicinal use. In particular we work on a class of cyclic protein named the cyclotides. These proteins are found in the plants of the Rubiaceae and Violaceae and our specific goals include: determining the role that cyclotides play in plants, discovering the mechanism of action of the wide range of biological activities displayed by the cyclotides (including anti-HIV, anti-bacterial and insecticidal activity), characterising the genetics of the cyclotides and further discovery of novel cyclotides.
The American Neurological Association is a professional society of academic neurologists and neuroscientists devoted to advancing the goals of academic neurology; to training and educating neurologists and other physicians in the neurologic sciences; and to expanding both our understanding of diseases of the nervous system and our ability to treat them. Our Goals 1. To disseminate knowledge about the nervous system and its diseases by: Presenting new scientific basic and clinical information at an annual meeting Publishing a scientific journal Formulating and promoting high standards of neurologic practice 2. To promote research into the causes and treatment of diseases of the nervous system by: Attracting promising physicians into academic neurology and supporting their development Advocating financial support from government, industry and individuals for research on the nervous system and its disorders 3. To formulate and promote policies and actions which will support the goals of academic neurology by: Providing a unified voice for academic neurology Setting guidelines and assuring excellence in programs that train and educate physicians in neurology Raising the standard of neurologic training of all physicians A few highlights within the portal: Clinical Neuroscience Pathway Startling breakthroughs in molecular biology and basic neuroscience have defined the cause of many diseases of the nervous system and are transforming the practice of neurology, neurosurgery and psychiatry. Basic research is giving new information on how the brain works and how brain injury occurs-and how it can be prevented or improved. Recognizing the exciting opportunities now available to better understand nervous system function and to design new treatments for neurological diseases, we''ve developed an interdepartmental program: The Clinical Neuroscience Pathway to provide an enhanced exposure to the neurosciences while pursuing the Doctor of Medicine degree. Program goal: The Clinical Neuroscience Pathway provides medical students with an enriched experience in the neurosciences throughout their four years in medical school. This program will provide students interested in Neurology, Neurosurgery, Ophthalmology, Pathology, or Psychiatry with access to a number of stimulating clinical and research activities. In addition, students will have the opportunity to participate in activities specifically designed for medical students in the program. Pathway students will be eligible for special summer research and year-out opportunities for clinical and basic neuroscience study. John N. Whitaker Visiting Professorships About the Program The ANA offers up to five 5,000 awards annually to fund visits of several days duration by persons who will interact with medical students and by both formal and informal contacts, stimulate them to consider academic neurology careers. The ideal visitor will be a role model of an accomplished academician who is enthusiastic and will effectively illustrate the applications between basic science and clinical neurology. The ANAs Education Committee must approve the visitor. The inviting institution should have acceptance from the visitor prior to submitting the name. The ANA suggests that an honorarium in the amount of 2,000 be given to the visitor. Special consideration will be given to institutions with small departments, but this is not a requirement. The Whitaker Professorships are intended to honor the life and contributions of John N. Whitaker M.D. (1940 - 2001) whose life and career exemplified high achievement as a person, neurological physician, teacher, investigator, mentor and citizen.
A database of curated, integrated and reusable high-throughput genomics experiments and a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; Next-Generation Sequencing or NGS). Algorithm developers and computer programmers can develop their own modules and extend the functionality of GeneProf. Existing software can be easily wrapped and integrated in the GeneProf framework and data from GeneProf may be used externally.
DROMPA - Peak-calling and Visualization Tool for Multiple ChIP-seq Data
A software program for peak-calling and visualization for ChIP-seq analysis.
THIS RESOURCE IS NO LONGER IN SEVICE. Documented on August 19,2019.It hosts records of currently available essential genes among a wide range of organisms. For prokaryotes, DEG contains essential genes in more than 10 bacteria, such as E. coli, B. subtilis, H. pylori, S. pneumoniae, M. genitalium and H. influenzae, whereas for eukaryotes, DEG contains those in yeast, humans, mice, worms, fruit flies, zebra fish and the plant A. thaliana. Users can Blast query sequences against DEG, and can also search for essential genes by their functions and names. Essential gene products comprise excellent targets for antibacterial drugs. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.
Statistical tools for the analysis of ChIP-seq data.
A commercial antibody supplier which supplies primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits.
Software for power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.
TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
Software to infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores.
Louisiana State University School of Medicine, Health Sciences Center: Department of Neurology
Louisiana State University Health Sciences Center School of Medicine at New Orleans; Department of Neurology
LSU Health Sciences Center School of Medicine at New Orleans; Department of Neurology
The Department of Neurology at Louisiana State University Health Sciences Center in New Orleans provides state-of the-art clinical evaluation and care for patients with neurological diseases. Its educational and research programs share the common goals of enhancing the knowledge of neuroscience and improving the diagnosis and care of patients. One of their primary missions is to educate and train medical students, physicians and other health care providers. Their residency and fellowship programs provide physicians with comprehensive training and experience in general and subspecialty neurology. Furthermore, their research programs encompass diverse areas and expertise in neurology and neuroscience. And additionally, many of the department''s faculty have established collaborative multi-disciplinary research projects, especially with members of the LSU Neuroscience Center of Excellence. The Neurology Residency Program at LSU Health Sciences Center is fully accredited by the ACGME. The Department of Neurology is a component of the nationally respected LSU Health Sciences Center, which is the major medical training institution for the State of Louisiana. The LSU Health Sciences has many components, one of which is the Neuroscience Center of Excellence, a state of the art research center for the neurosciences. The LSU Health Sciences Center not only sponsors medical education, but also has a School of Nursing, Dentistry, Physical and Occupational Therapy. This allows for the flourishing of multidisciplinary research and innovative thinking. It accepts three residents per year; residents must complete one year of internal medicine prior to entering into our program. Additionally, LSUHSC Neurology has fellowship available in: - Child Neurology - Pain Management - Neurophysiology
Flinders University; Adelaide; Australia
Public university founded in 1966, which is based in Adelaide, South Australia. Its main campus is located at Bedford Park in Adelaide's inner south, with sites at Victoria Square in the centre of the city,Tonsley,regional South Australia, south-west Victoria and throughout the Northern Territory.
Wake Forest School of Medicine; North Carolina; USA
Wake Forest University School of Medicine
Wake Forest School of Medicine (WFSM) occupies a firm position among the best medical schools in the United States. The desire to teach excellence in clinical medicine, promote strong clinical and basic research, render exemplary patient care, and stress service to the community has continued as an integral part of Wake Forest Baptist Medical Center, a leading research and teaching hospital. Wake Forest Baptist Medical Center is a preeminent, internationally recognized academic medical center of the highest quality primary care physicians with balanced excellence in patient care, research and education. Wake Forest Baptist Medical Center Teaching Hospital''s mission is to improve the health of our region, state and nation by: * Generating and translating knowledge to prevent, diagnose and treat disease. * Training leaders in health care and biomedical science. * Serving as the premier health system in our region, with specific centers of excellence recognized as national and international care destinations.
An independent federal agency created by Congress to promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense They are the funding source for approximately 20 percent of all federally supported basic research conducted by America''s colleges and universities. In many fields such as mathematics, computer science and the social sciences, NSF is the major source of federal backing. NSF leadership has two major components: a director who oversees NSF staff and management responsible for program creation and administration, merit review, planning, budget and day-to-day operations; and a 24-member National Science Board (NSB) of eminent individuals that meets six times a year to establish the overall policies of the foundation.The director and all Board members serve six year terms. Each of them, as well as the NSF deputy director, is appointed by the President of the United States and confirmed by the U.S. Senate. At present, NSF has a total workforce of about 2,100 at its Arlington, Va., headquarters, including approximately 1,400 career employees, 200 scientists from research institutions on temporary duty, 450 contract workers and the staff of the NSB office and the Office of the Inspector General. NSF is the only federal agency whose mission includes support for all fields of fundamental science and engineering, except for medical sciences. They are tasked with keeping the United States at the leading edge of discovery in areas from astronomy to geology to zoology. So, in addition to funding research in the traditional academic areas, the agency also supports high-risk, high pay-off ideas, novel collaborations and numerous projects that may seem like science fiction today, but which the public will take for granted tomorrow. And in every case, they ensure that research is fully integrated with education so that today''s revolutionary work will also be training tomorrow''s top scientists and engineers NSF''s task of identifying and funding work at the frontiers of science and engineering is not a top-down process.
eF-site - Electrostatic surface of Functional site
It is a database for molecular surfaces of proteins'' functional sites. It displays the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, for analysis of the molecular recognition mechanisms. The Connolly surfaces were made by using the MSP program and the electrostatic potentials were calculated by solving Poisson-Boltzmann equations with the self-consistent boundary method.
Louisiana State University School of Medicine, Health Sciences Center: Department of Psychiatry
LSU Health Sciences Center School of Medicine at New Orleans; Department of Psychiatry
LSUHSC School of Medicine at New Orleans; Department of Psychiatry
LSUHSC School of Medicine; Department of Psychiatry
The LSU Department of Psychiatry is committed to the finest quality medical student education, post-medical school training for residents and fellows in all aspects of psychiatry: general psychiatry, infant, child and adolescent psychiatry, emergency and administrative psychiatry, and consultation liaison psychiatry. This department also provides excellent graduate and post-graduate training in social work and psychology. The department provides major leadership in research spanning our field and makes important advances in the understanding of psychopharmacology and neuroscience, developmental disorders, psychodynamic psychiatry, and treatment of children and families exposed to community and family violence. It plays key roles related to transmission and treatment of HIV infection, prevention of school failure and incarceration among high risk youth and maintaining mental health in our senior citizens, to name but a few areas. Their nationally recognized Harris Infant Mental Health Center trains professionals in several states to understand and treat the most vulnerable of our children and their families during the first three years of life. The Harris Center for Infant Mental Health of the LSUHSC Department of Psychiatry is devoted to the study and treatment of infants and young children. The goals of the Center are: - To develop a crucial number of mental health professionals locally, nationally, and internationally trained to evaluate and treat infants. - To develop networks to provide support for individuals working with infants. - To bring together individuals from different mental health disciplines who will have a core set of skills and knowledge to assess and treat infants. - To develop expertise in evaluation and treatment for high-risk infants. - To educate the judges, lawyers and court personnel on the effects of violence on young children.
ReplicationDomain is an online database resource for storing, sharing and visualizing DNA replication timing and transcription data, as well as other numerical epigenetic data types. Data is typically obtained from DNA microarrays or DNA sequencing. Our site has a user registration system that allows registered users to upload their own data sets. While non-registered users may freely view and download public data sets, registered users may upload their own data sets and view them privately, share them with other registered users, or make published data sets publicly available. In addition we have implemented additional mechanisms that allow users to restrict sharing of data sets to a user designated group of registered users. Further details on the database usage are in the User Guide Page, while data set details are in the Documentation Page. Replication timing data were obtained by hybridizing early and late replication intermediates to Nimblegen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early and late stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. After unbiased amplification of recovered DNA, the samples are differentially labeled with Cy3 and Cy5 and hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 5.8 kb across the mouse genome (Nimblegen, 2006-07-26_MM8_WG_CGH). Raw data from two independent biological replicates in which the early and late replicating DNA were labeled reciprocally with Cy3 and Cy 5 (dye switch) are loess-normalized and scaled to have the same median-absolute deviation using the limma package (R/Bioconductor) and then averaged. Finally, the data are smoothed with a weighted moving average (loess: local polynomial smoothing).
Biomedical research institute in Germany that investigates the mechanisms of cancer and works to identify cancer risk factors. They provide the foundations for developing novel approaches in the prevention, diagnosis, and treatment of cancer and are a member of the Helmholtz Association of National Research Centers. Professor Harald zur Hausen was awarded the Nobel Prize for Medicine for his outstanding scientific contribution to the study of human papillomaviruses (HPV). In addition, the staff of the Cancer Information Service (KID) offers information about the widespread disease of cancer for patients, their families, and the general public. The Center is funded by the German Federal Ministry of Education and Research (90%) and the State of Baden-Württemberg (10%).
Oregon Health and Science University School of Medicine; Oregon; USA
Oregon Health & Science University School of Medicine
Oregon Health & Science University School of Medicine; Oregon; USA
Oregon Health and Science University School of Medicine
We are a vibrant community of educators, students, scientists, clinicians and others working side-by-side to heal, teach, discover and serve. We support 1,750 faculty, 1,200 students and 750 residents and fellows in 27 departments and 17 centers and institutes. We offer doctorates in medicine and philosophy, masters in science, public health and physician assistant studies and combined degrees. Our faculty is dedicated to preparing physicians for the medical, ethical and humanistic responsibilities of their calling, while also providing outstanding care to patients from Oregon and elsewhere. Along with the art of teaching and healing comes the responsibility for discovery. The School of Medicine faculty is widely recognized nationally and internationally for the pursuit of new knowledge in a breadth of investigative areas ranging from molecular biology and cancer to heart disease, behavioral science and issues of public health.
Physiome.jp has been established to provide building blocks useful to develop in silico human. The blocks will include mathematical models and experimental data representing physiological functions. Physiome.jp is a part of the Worldwide Integrative Biomedical Research Cooperation to promote Physiome and Systems Biology. The building blocks (modules, models, biological data) representing biological functions and structure are databased and served as elements in the catalogue of human knowledge. They can be reused for deeper understanding of human physiology, eventually contributing to establishment of in silico medicine and predictive medicine. The databases (insilicoDB) at www.physiome.jp currently include a Model Database and a Morphology Database. The Model Database stores a number of modules representing biological/physiological functions. Those models are formulated by mathematical equations to describe dynamic changes of states, i.e., specific biological functions. All models in the database are written in an XML format called insilicoML. The Morphology Database provides datasets representing morphometric models of biological organs. The morphometric data are provided in several data-types including surface data such as STL and VRML and volume/voxel data. The database contents are in the public domain and aim to provide valuable models to the scientific community for model sharing/reuse, simulation, model validation, visualization of biological structure, and morphology-based dynamic simulation of biological functions. These can be accomplished by combining insilicoML models with appropriate morphology datasets. Models and related data in the insilicoDB may be freely downloaded and reused for non-profit scientific purposes. When using the models in the Model Database, we ask the users to respect the effort spent in arranging/serving the mathematical models as well as the original model construction. For any reuse of the morphology data, we also ask the users to respect the intellectual property of those who provided the original data. This should be done by acknowledging insilicoDB@physiome.jp for model reuse and by including appropriate attribution information for any reuse of the morphology data. The insilicoDB owners will not be held responsible for misuse of the Morphology Database and/or Model Database, or damage caused by use of the data and models contained therein.
United States Food and Drug Administration
An agency of the United States Department of Health and Human Services, one of the United States federal executive departments that is responsible for protecting and promoting public health through the regulation and supervision of food safety, tobacco products, dietary supplements, prescription and over-the-counter pharmaceutical drugs (medications), vaccines, biopharmaceuticals, blood transfusions, medical devices, electromagnetic radiation emitting devices (ERED), cosmetics and veterinary products. The FDA also enforces other laws, notably Section 361 of the Public Health Service Act and associated regulations, many of which are not directly related to food or drugs. These include sanitation requirements on interstate travel and control of disease on products ranging from certain household pets to sperm donation for assisted reproduction. (Wikipedia)
Software providing methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.
A phylogenetic tree of global human mitochondrial DNA variation, based on both coding- and control-region mutations, and including haplogroup nomenclature.
Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.
A list of major inbred mouse strains from the Jackson laboratories. This list is not being actively maintained (found on Nov 27, 2013).
Neuropathology of CTE and Delayed Effects of TBI: Toward In-Vivo Diagnostics
Neuropathology of Chronic Traumatic Encephalopathy (CTE) and Late Effects of Traumatic Brain Injury (TBI): Toward In-Vivo Diagnostics
Neuropathology of CTE and Late Effects of TBI: Toward In-Vivo Diagnostics
A multi-center and multi-disciplinary study designed to dramatically increase understanding of chronic traumatic encephalopathy (CTE) and other late effects of traumatic brain injury (TBI). Overlapping clinical features, postmortem pathologies and patterns of involvement exist in TBI, CTE, and Alzheimer''s disease pose challenges to accurate diagnosis. Premortem diagnosis of CTE is currently impossible. The neuropathological consequences of single mild or moderate-severe TBI and its relationship with CTE and known dementias are unclear. The proposed project will leverage extensive resources from an ongoing population-based prospective cohort study of brain aging (Adult Changes in Thought; ACT, n=2,305) which includes excellent medical, behavioral, and genetic characterization of a cohort (20% of whom have a history of mild-moderate TBI) in addition to state-of-the-art neuropathology workup upon death. Neuropathological study of TBI effects can begin immediately in the existing ACT autopsy sample (n=489, 20% with TBI exposure). Additional cohorts of TBI- exposed individuals will come from the Brain Injury Research Center at Mount Sinai (n=150 individuals with moderate-severe TBI), the University of Texas Southwestern (n=50 retired boxers with repetitive TBI exposure), and the National Football League (n=76 retired players with repetitive TBI exposure). All participants in the proposed study (ACT and other sites) will undergo uniform harmonized neurobehavioral assessment (chosen to maximize correspondence with existing large-scale TBI and dementia studies), MRI scan, and genomic analysis. Those individuals who expire during the course of the study will undergo ex-vivo neuroimaging and extensive neuropathological exam using state-of-the-art techniques (such as Histelide) designed to quantify tau and A�� in whole brain specimens. Only by examining postmortem pathology in a sample of individuals with varying levels of TBI exposure who are well characterized during life (as proposed herein) can postmortem pathology facilitate identification of in-vivo biomarkers that can act as diagnostic tools. This project represents the most systematic and scientifically rigorous effort to date to develop a more complete understanding of the long-term clinical and neuropathological sequelae of single and multiple TBI.
New Castle University, The Institute of Neuroscience: Major Research Themes
This resource provides detailed information about the major research themes in the Institute of Neuroscience at the New Castle University. The major research themes of this department include: * Behavior, Psychology and Cognitive Neurosciences * Developmental Neuroscience, Aging and Neurodegeneration * Neural Circuits and Neuroimaging * Neurology, Neurosurgery, and Motor Control * Neuropharmacology and Neurotechnology * Psychiatric Neurosciences * Visual, Auditory and Sensory Neuroscience
Mouse Genome Informatics: Mouse Genome Database
Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology.
Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).
Database for molecular typing and microbial genome diversity.
NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016.
National Institute for Health and Care Excellence
An international team that works on a fee-for-service basis with policy makers and clinicians around the world to promote evidence-based decision making in healthcare.
Software package that uses hidden Ising models to identify enriched genomic regions in ChIP-chip data.
A not-for-profit alliance of 23 cancer centers devoted to patient care, research, and education, is dedicated to improving the quality, effectiveness, and efficiency of cancer care so that patients can live better lives. Through the leadership and expertise of clinical professionals at NCCN Member Institutions, NCCN develops resources that present valuable information to the numerous stakeholders in the health care delivery system. As the arbiter of cancer care, NCCN promotes the importance of continuous quality improvement and recognizes the significance of creating clinical practice guidelines appropriate for use by patients, clinicians, and other health care decision-makers.
An integrated application software tool for miRNA identification from RNA sequencing data.
University of Queensland; Brisbane; Australia
Public research university located primarily in Brisbane, the capital city of the Australian state of Queensland. Founded in 1909 by the Queensland parliament, UQ is one of the six sandstone universities, an informal designation of the oldest university in each state.
A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.
Software providing a fast scatterplot smoother suitable for microarray normalization based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5,2023. Integrated analysis of cross-platform microarray and pathway data.
ProbeSelect - Selecting probes in heterogenous transcriptional sets
Software for selecting probes in heterogenous transcriptional sets.
Software and server that performs intelligent design of oligonucleotides for DNA microarrays.
The FDA''s national strategy for transforming the way FDA-regulated products--human drugs, biological products, medical devices, veterinary drugs, foods, and cosmetics--are developed, evaluated, manufactured, and used. Specific key areas of focus identified by FDA experts and the public: * Developing better evaluation tools like biomarkers and new assays * Streamlining clinical trials by modernizing the clinical trial sciences to make trials safe and efficient * Harnessing bioinformatics (e.g., moving from a paper-based to electronic environment for exchanging information and overseeing the safety of FDA-regulated products) * Moving manufacturing into the 21st Century, using tools such as process analytic technology and nanotechnology * Developing products to address urgent public health needs, including, improved antimicrobial testing, new animal models to test bioterrorism countermeasures and vaccine testing * Focusing on at-risk populations, such as pediatrics
A next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute.
Center for Cancer Research: Schiller Laboratory
This is the lab portal of Dr. Schiller at the National Cancer Institue in Frederick, Germany. Keyowrds: Cancer, REsearch, Institute, Laboratory,
Mini cross-platform local genome browser software designed for visualizing next-generation sequencing data.
A GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species.
Allows the user to conveniently compare data from many loci., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software package that facilitates the primary analysis of ChIP-chip data.
Behavioral Risk Factor Surveillance System
The Behavioral Risk Factor Surveillance System (BRFSS) is a state-based system of health surveys that collects information on health risk behaviors, preventive health practices, and health care access primarily related to chronic disease and injury. For many states, the BRFSS is the only available source of timely, accurate data on health-related behaviors. BRFSS was established in 1984 by the Centers for Disease Control and Prevention (CDC); currently data are collected monthly in all 50 states, the District of Columbia, Puerto Rico, the U.S. Virgin Islands, and Guam. More than 350,000 adults are interviewed each year, making the BRFSS the largest telephone health survey in the world. States use BRFSS data to identify emerging health problems, establish and track health objectives, and develop and evaluate public health policies and programs. Many states also use BRFSS data to support health-related legislative efforts. Sponsors: This resource is supported by the Center for Disease Control. Keywords: Behavioral, Risk, Factor, Surveillance, System, Health, Disease, Chronic, Injury, Health, Behavior, Health,
A framework technology comprising file format and toolkit in which we combine highly efficient and tunable reference-based compression of sequence data with a data format that is directly available for computational use.
This website provides information about the American Spinal Injury Association. The mission of ASIA is to: (a) to promote and establish standards of excellence for all aspects of health care of individuals with spinal cord injury from onset throughout life. (b) to educate members, other healthcare professionals, patients and their families as well as the public on all aspects of spinal cord injury and its consequences in order to prevent injury, improve care, increase availability of services and maximize the injured individual''s potential for full participation in all areas of community life. (c) to foster research which aims at preventing spinal cord injury, improving care, reducing consequent disability, and finding a cure for both acute and chronic SCI. (d) to facilitate communication between members and other physicians, allied health care professionals, researchers and consumers.
AU-RICH ELEMENT-CONTAINING mRNA DATABASE
The ARE-mRNA database (ARED) reveals that ARE-mRNAs encode a wide repertoire of functionally diverse proteins belonging to different biological processes and important in several disease states. Cluster analysis was performed using the ARE sequences to demonstrate potential relationships between the type and number of ARE motifs, and the functional characteristics of the proteins. Sponsors: This database is supported by The King Faisal Specialist Hospital and Research Center. Keywords: mRNA, Database, Au-rich, Element, Biological, Disease, State, Cluster, Analysis, Motif, Functional, Characterstic, Protein,
Tool that compresses and decompresses fastq files.
An encoding and decoding tool for Sequence Alignment/Map (SAM) files.
EDNA - Energy Based Multiple Sequence Alignment (MSA) for Binding Sites
Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment.
An open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks.
Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research.
A Genotype Calling Algorithm for Affymetrix SNP Arrays.
An analytical software tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data.
Center that facilitates the optimal use of nonhuman primate models in biomedical research by identifying, developing, characterizing and producing reagents for monitoring or modulating immune responses. They distribute non-human primate-specific antibodies for in vitro diagnostics, as well as develop and produce primate recombinant antibodies for in vivo cell depletion or modulating immune responses.
Wisconsin National Primate Research Center
Research center aimed towards increasing understanding of basic primate biology and improving human health and quality of life. Its goals include helping discover treatments, preventative measures and cures for human disease; gathering knowledge of primate biology and ecosystems; providing resources to scientists world wide; and collecting and disseminating research to the larger scientific community and public.
Expression atlas of in situ hybridization images from large collection of genes expressed in brain of adult male zebra finches. Goal of ZEBrA project is to develop publicly available on-line digital atlas that documents expression of large collection of genes within brain of adult male zebra finches.
The Society aims to foster discovery and characterization of genomic variations including population distribution and phenotypic associations. We promote collection, documentation and free distribution of genomic variation information and associated clinical variations and endeavor to foster the development of the necessary methodology and informatics. Mission Statement To enhance human health through identification and characterization of changes in the genome that lead to susceptibility to illness. To this end, to collate the genomic information necessary for molecular diagnosis, research on basic mechanisms and design of treatments of human ailments. Society Journal Human Mutation is the Society journal. Members will receive a reduced subscription to the journal if they choose to subscribe. Meetings The Society holds two scientific meetings per year. One as a satellite to either the HUGO (Human Genome Organization) annual meeting or the ESHG (European Society of Human Genetics) annual meeting and one meeting is a satellite to the ASHG (American Society of Human Genetics annual meeting. The meetings are a forum for scientists to exchange ideas and form collaborations. Prominent speakers in the field are invited as well as a call for abstracts at large. The meetings are designed to update and increase knowledge of human genome variation and generally attract a stimulating and interesting collection of abstracts in all fields of human genome variation making it an ideal forum to share information and results. Past themes include: copy number variation, pathogenic or not?, pharmacogenomics, new DNA sequencing technologies, and genotype to pheontype relationships. We invite members and non-members alike to attend these meetings. The Society holds the Annual General Meeting of the members after the scientific meeting that is a satellite of the ASHG. Exhibitor''s booths The Society usually takes out an Exhibitor''s booth at the American & European Societies of Human Genetics annual meetings and sometimes the HUGO HGM meeting. GUIDELINES & RECOMMENDATIONS Members of the Society have formulated Guidelines & Recommendations on a number of topics, but especially for nomenclature of gene variations and guidelines on variation databases.
Onco-STS - A web-based Laboratory Information Management System
Software for a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments.
A peak-finding algorithm used to analyze ChIP-chip microarray data.
Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.
Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data.
A virtual software pipeline that contains several PERL modules for processing next generation sequencing data.
Software that allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments.
Software developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq).
A single program that takes of bisulfite-treated reads and outputs per-base methylation data.
Sequence mapper for bisulfite sequencing reads for DNA methylation studies.
A public resource composed of a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a one-stop resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes.
Contains data to inform healthcare decision-making from Cochrane and other systematic reviews, clinical trials, and more. Cochrane reviews bring you the combined results of the worlds best medical research studies, and are recognized as the gold standard in evidence-based health care. Consists of a regularly updated collection of evidence-based medicine databases, including The Cochrane Database of Systematic Reviews. This database includes systematic reviews of healthcare interventions that are produced and disseminated by The Cochrane Collaboration. It is published on a monthly basis and made available both on CD-ROM and the Internet. The review abstracts are available to browse and search free of charge on this website. The Cochrane Library Users'' Group (CLUG) provides a forum for discussion of usability, readability, searchability, and formatting issues related to the use of The Cochrane Library. The Cochrane Collaboration is an international not-for-profit and independent organization, dedicated to making up-to-date, accurate information about the effects of healthcare readily available worldwide. Funded by John Wiley and Sons Limited. The individual entities of The Cochrane Collaboration are funded by a large variety of governmental, institutional and private funding sources, and are bound by organisation-wide policy limiting uses of funds from corporate sponsors.
Flexible barcode and adapter removal for sequencing platforms.
Provides an efficient tool for trimming adapter sequences and low quality sequences, in raw reads generated by the high throughput sequencing platforms.
Material Safety Data Sheets for Infectious Substances of Canada
Material Safety Data Sheets for chemical products are available to laboratory workers for most chemicals and reagents. However because many laboratory workers, whether in research, public health, teaching, etc., are exposed to not only chemicals but infectious substances as well, there was a large gap in the readily available safety literature for employees. These MSDS are produced for personnel working in the life sciences as quick safety reference material relating to infectious micro-organisms. The MSDS are organized to contain health hazard information such as infectious dose, viability (including decontamination), medical information, laboratory hazard, recommended precautions, handling information and spill procedures. The intent of these documents is to provide a safety resource for laboratory personnel working with these infectious substances. Because these workers are usually working in a scientific setting and are potentially exposed to much higher concentrations of these human pathogens than the general public, the terminology in these MSDS is technical and detailed, containing information that is relevant specifically to the laboratory setting. It is hoped along with good laboratory practices, these MSDS will help provide a safer, healthier environment for everyone working with infectious substances. The MSDS is ran by the Public Health Agency of Canada. The Public Health Agency of Canada (PHAC) is the main Government of Canada agency responsible for public health in Canada. PHACs primary goal is to strengthen Canadas capacity to protect and improve the health of Canadians and to help reduce pressures on the health-care system. To do this, the Agency is working to build an effective public health system that enables Canadians to achieve better health and well-being in their daily lives by promoting good health, helping prevent and control chronic diseases and injury, and protecting Canadians from infectious diseases and other threats to their health. PHAC is also committed to reducing health disparities between the most advantaged and disadvantaged Canadians. Because public health is a shared responsibility, the Public Health Agency of Canada works in close collaboration with all levels of government (provincial, territorial and municipal) to build on each others skills and strengths. The Agency also works closely with non-government organizations, including civil society and business, and other countries and international organizations like the World Health Organization (WHO) to share knowledge, expertise and experiences.
SeqPrep - Tool for stripping adaptors and/or merging paired reads with overlap into single reads
A program to merge paired end Illumina reads that are overlapping into a single longer read.
IRIS is a toxicology data file on the National Library of Medicine''s (NLM) Toxicology Data Network. It contains data in support of human health risk assessment. It is compiled by the U.S. Environmental Protection Agency (EPA) and contains over 500 chemical records. It is a compilation of electronic reports on specific substances found in the environment and their potential to cause human health effects. IRIS was initially developed for EPA staff in response to a growing demand for consistent information on substances for use in risk assessments, decision-making and regulatory activities. The information in IRIS is intended for those without extensive training in toxicology, but with some knowledge of health sciences. The Integrated Risk Information System (IRIS) is an electronic database containing information on human health effects that may result from exposure to various substances in the environment. IRIS is prepared and maintained by the EPAs National Center for Environmental Assessment (NCEA) within the Office of Research and Development (ORD). The heart of the IRIS system is its collection of searchable documents that describe the health effects of individual substances and that contain descriptive and quantitative information in the following categories: -Noncancer effects: Oral reference doses and inhalation reference concentrations (RfDs and RfCs, respectively) for effects known or assumed to be produced through a nonlinear (possibly threshold) mode of action. In most instances, RfDs and RfCs are developed for the noncarcinogenic effects of substances. -Cancer effects: Descriptors that characterize the weight of evidence for human carcinogenicity, oral slope factors, and oral and inhalation unit risks for carcinogenic effects. Where a nonlinear mode of action is established, RfD and RfC values may be used.
A database of ingredients in brand-name household products linked to health information from Material Safety Data Sheets (MSDS) provided by manufacturers. The database is designed to help answer the following typical questions: *What are the chemical ingredients and their percentage in specific brands? *Which products contain specific chemical ingredients? *Who manufactures a specific brand? How do I contact this manufacturer? *What are the acute and chronic effects of chemical ingredients in a specific brand? *What other information is available about chemicals in the toxicology-related databases of the National Library of Medicine? NLM and its Contractor (the Database Providers) do not test products nor investigate to determine if this information is complete or accurate.
HECTOR: Parallel error corrector for 454 datasets
A parallel multistage k-hopo spectrum based homopolymer-length error corrector for 454 sequencing data.
Database of International Rehabilitation Research
The CIRRIE Database of International Rehabilitation Research currently contains almost 90,000 citations of international rehabilitation research published between 1990 and the present. The CIRRIE Database collects citations from all areas of rehabilitation and compiles them into one central source. In addition to indexing from mainstream journals and internet sites, CIRRIE also includes citations to resources not readily available to U.S. researchers. Over 5000 journals are represented in the Database and abstracts are available for most citations. A list of journals is now available. There are almost 90,000 citations currently indexed with citations added monthly. The database includes citations from 1990 to the present. It was created to facilitate the sharing of information and expertise in rehabilitation and disability research between the U.S. and other countries.
A bioinformatics tool for error correction of HTS read data.
This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.
BayesPeak - Bayesian Analysis of ChIP-seq Data
Software package that is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.
FishMicrosat - Fish and Shellfish Microsatellite Database
A microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent.
The information in this manual is presented to assist health care professionals caring for cancer patients undergoing treatment with cytotoxics, hormones or biological response modifiers. It is designed primarily for pharmacists and nurses in general practice, and may also be of interest to the family physician who is treating a patient in consultation with an oncologist. Efforts have been made to include information specific to the use of these drugs in the child with cancer. Because of the nature of individual drug monographs, this manual does not deal with therapeutics. For treatment decisions, the reader is referred to the protocol by which the patient is being treated, to the British Columbia Cancer Agency''s Cancer Management Manual and to the most current literature. The Cancer Drug Manual also provides a drug index for physicians and patients. The BC Cancer Agency, an agency of the Provincial Health Services Authority, provides a province-wide, population-based cancer control program for the residents of British Columbia and the Yukon. The BC Cancer Agencys mandate covers the spectrum of cancer care, from prevention and screening, to diagnosis, treatment, and through to rehabilitation. The BC Cancer Agencys mandate is driven by a three-fold mission: -To reduce the incidence of cancer -To reduce the mortality rate of people with cancer -To improve the quality of life of people living with cancer
THIS RESOURCE IS NO LONGER IN SERVICE,documented on August 16, 2019. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable reference genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. This site presents version 4 of the Fugu genome, released in October 2004 by the International Fugu Genome Consortium. Fugu rubripes has a very compact genome, with less than 15 consisting of dispersed repetitive sequence, which makes it ideal for gene discovery. A draft sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the ''whole-genome shotgun'' sequencing strategy. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs.
Washington University in St. Louis School of Medicine Division of Biology and Biomedical Sciences
The Division of Biology and Biomedical Sciences at Washington University in St. Louis offers exceptional doctoral training at one of the nations preeminent biomedical research centers. The Division consists of 12 doctoral training programs, 10 of which are ranked among the nations top 10.* :A collaborative, interdisciplinary approach to research and education is a hallmark of Washington University and the Division. As a university-wide consortium, the Division transcends departmental lines and removes traditional boundaries of scientific fields. Faculty and graduate students regularly cross disciplines, devising novel questions and approaches that might otherwise go unexplored. The Division currently consists of 685 graduate students and 410 faculty members from 32 university-wide departments..
Software that identifies protein binding sites from ChIP-seq and nucleosome positioning experiments.
Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data.
An open source package for primary data analysis on next-gen sequence data from images to basecalls. Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed to be platform agnostic.
TraceTuner - DNA sequencing quality values base calling and trace processing
Software tool for base and quality calling of trace files from DNA sequencing instruments.
Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq).
A resource for animal miRNA-target interactions consisting of the Validated Targets component, a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation, and the Predicted Targets component, an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs. April 27, 2013, the Validated Targets component of miRecords hosts 2705 records of interactions between 644 miRNAs and 1901 target genes in 9 animal species. Among these records, 2028 were curated from low throughput experiments. The Predicted Targets component of mIRecords integrates the predicted targets of the following miRNA target prediction tools: DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid, and TargetScan/TargertScanS. We would be glad to include your experimentally validated miRNA target data (published or unpublished) into miRecords., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Atlas of the brain and the disorders affecting it, aimed at general practitioners and specialists in training. It consists of three main parts: a description of the different parts of the normal brain and their functions, a description of the process of neurological control, and a description of 14 different brain disorders in psychiatry and neurology - as well as their cause, symptoms, and treatment.
ComiR - Combinatorial miRNA target prediction tool
ComiR: Combinatorial miRNA target prediction tool
Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.
A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.
A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.
A computational tool for analyzing the microRNA (miRNA) transcriptome in plants.
This resource gives information about the U.S. Human Genome Project, which was was a 13-year effort to to discover all the estimated 20,000-25,000 human genes and make them accessible for further biological study. The primary project goals were to: - identify all the approximately 20,000-25,000 genes in human DNA, - determine the sequences of the 3 billion chemical base pairs that make up human DNA, - store this information in databases, - improve tools for data analysis, - transfer related technologies to the private sector, and - address the ethical, legal, and social issues (ELSI) that may arise from the project. To help achieve these goals, researchers also studied the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse. These parallel studies helped to develop technology and interpret human gene function. Sponsors: The DOE Human Genome Program and the NIH National Human Genome Research Institute (NHGRI) together sponsored the U.S. Human Genome Project.
Center for Disease Control and Prevention: Genetic Testing Reference Materials Coordination Program
The goal of the Genetic Testing Reference Materials Coordination Program (GeT-RM) is to coordinate a self-sustaining community process to improve the availability of appropriate and characterized reference materials for: Quality control (QC), Proficiency testing (PT), Test development & validation, Research. The purpose of this program is: - To help the genetic testing community obtain appropriate and characterized reference materials - To facilitate and coordinate information exchange between users and providers of QC and reference materials - To coordinate efforts for contribution, development, characterization and distribution of reference materials for genetic testing Get-RM provides information about cell lines, DNA, and other kinds of materials that could be used as reference materials for molecular genetic testing. Some of these materials have been characterized by the GeT-RM program and can be divided into three categories: - Genetic Inherited Disease & Pharmacogenetics This section includes information about cell lines, DNA, and other samples that can be used as reference materials for various inherited diseases (including cystic fibrosis, fragile X, Huntington disease, and Ashkenazi Jewish-related diseases), pharmacogenetic loci, and biochemical genetics. The GeT-RM program has confirmed the genotype of many of the genomic DNA samples through testing in multiple clinical genetic laboratories. - Molecular Oncology This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various types of cancers, including leukemia/lymphoma and solid tumors. - Infectious Disease This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various infectious disease pathogens including viruses, bacteria, and protozoa.
Ascidian Network for InSitu Expression and Embryological Data
Database of ascidian embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, four organism models are described in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata. This version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. Users can explore their expression profiles during normal or manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories. ANISEED is a community tool, and the direct involvement of external contributors is important to optimize the quality of the submitted data. Virtual embryo: The 3D Virtual embryo is available to download in the download section of the website.
ncPRO-seq - A tool for annotation and profiling of ncRNAs from small RNA sequencing data
Software that aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions.
Database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.
AUTOmated server for predicting functional consequences of amino acid MUTations in protEins.
vcf2MSAT - Find Microsatellites in a .vcf report
A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files.
Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.
Copy Number estimation by a Mixture Of PoissonS
A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.
An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.
FishingCNV - CNV detection in exome sequencing data
FishingCNV - Copy number variation (CNV) detection in exome sequencing data
FishingCNV - Copy number variation detection in exome sequencing data
A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data.
ABACUS: an entropy based cumulative bivariate statistic robust to rare variants and different direction of genotype effect
An Algorithm based on a BivAriate CUmulative Statistic to identify SNPs significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions.
A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation.
Bamformatics - Toolkit and GUI for sequencing data analysis
Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data.
Project to study human gene expression and regulation in multiple tissues, providing valuable insights into mechanisms of gene regulation and its disease related perturbations. Genetic variation between individuals will be examined for correlation with differences in gene expression level to identify regions of the genome that influence whether and how much a gene is expressed. Includes initiatives: Novel Statistical Methods for Human Gene Expression Quantitative Trait Loci (eQTL) Analysis ,Laboratory, Data Analysis, and Coordinating Center (LDACC), caHUB Acquisition of Normal Tissues in Support of GTEx Project.
A C++ software program for multipoint IBD estimation based on high density SNP genotype data.
Haplotype Amplification in Tumor Sequences
A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.
A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.
Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp).
It consists of two modules - a database of regulatory interactions based on literature and an expertly curated database of transcription factor binding sites. The literature based information in RegTransBase is a manually curated database of regulatory interactions in prokaryotes, captures the knowledge in published scientific literature using a controlled vocabulary. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains various types of experimental data, in particular: * the activation or repression of transcription by an identified direct regulator * determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA * mapping or prediction of binding sites for a regulatory protein * characterization of regulatory mutations The analysis section of RegtransBase is based on a set of manually curated alignments of transcription factor binding sites and allows you to search for new binding sites and verify conservation of bindings sites across multiple species through the use of web based analysis tools.
Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Multivariate Analysis of Transcript Splicing
Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.
Software designed to detect single nucleotide variants from next generation sequencing data.
PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indices (NCBI Gene) and orthologs (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously. PhenomicDB contains data from publicly available primary databases: FlyBase, Flyrnai.org, WormBase, Phenobank, CYGD, MatDB, OMIM, MGI, ZFIN, SGD, DictyBase, NCBI Gene, and HomoloGene. We brought this wealth of data into a single integrated resource by coarse-grained semantic mapping of the phenotypic data fields, by including common gene indexes (NCBI Gene), and by the use of associated orthology relationships (HomoloGene). PhenomicDB is thought as a first step towards comparative phenomics and will improve the understanding of the gene functions by combining the knowledge about phenotypes from several organisms. It is not intended to compete with the much more dedicated primary source databases but tries to compensate its partial loss of depth by linking back to the primary sources. The basic functional concept of PhenomicDB is an integrated meta-search-engine for phenotypes. Users should be aware that comparison of genotypes or even phenotypes between organisms as different as yeast and man can have serious scientific hurdles. Nevertheless finding that the phenotype of a given mouse gene is described as ��similar to psoriasis�� and at the same time that the human ortholog has been described as a gene causing skin defects can lead to novelty and interesting hypotheses. Similarly, a gene involved in cancer in mammalian organisms could show a proliferation phenotype in a lower organism such as yeast and thus, give further insights to a researcher.
A suite of software tools that enables integrative SNP analysis in next generation sequencing data with large cohorts.
MendelScan - Variant scoring and linkage mapping for family exome sequencing
A software tool for prioritizing candidate variants in family-based studies of inherited disease.
LoFreq - Sensitive variant-calling from sequencing data
A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.
A computer program for phasing observed genotypes and imputing missing genotypes.
A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.
Commercial neuroimaging software package for multi-modal data analysis and management. It has been programmed in C++ with efficient statistical, numerical, and image processing routines. It supports parallelized basic math routines on all platforms and uses modern multi-core, multi-processor hardware for demanding computational routines.
A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences.
Software for a probabilistic framework for the discovery of single nucleotide variants in WGSS data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error.
National Institute on Drug Abuse Center for Genetic Studies
National Institute of Drug Abuse (NIDA) Human Genetics Initiative
Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website.
Monte Carlo Likelihood Estimation of Effective Population Size PANGAEA
Software for a de novo genome assembler implemented in C++.
A software to assemble short reads of next generation sequencing technologies at low coverage.
Software providing a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization.
A Hadoop based genome assembler for assembling large genomes in the clouds.
A collection of tools and class interfaces for the assembly of DNA reads.
A pipeline for assembling DNA sequence data generated on the Illumina sequencing platform.
Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.
PhosphoNET - Human Phospho-Site KnowledgeBase
PhosphoNET is an open-access, online knowledgebase developed by Kinexus Bioinformatics Corporation to foster the study of cell signaling systems to advance biomedical research in academia and industry. PhosphoNET is the world''s largest repository of known and predicted information on human phosphorylation sites, their evolutionary conservation and the identities of protein kinases that may target these sites. Search by protein name, UniProt number, IPI number, or 15 AA P-site sequence. PhosphoNET presently holds data on over 650,000 known and putative phosphorylation sites (P-sites) in over 23,000 human proteins that have been collected from the scientific literature and other reputable websites. Over 14% of these phospho-sites have been experimentally validated. The rest have been predicted with a novel P-Site Predictor algorithm developed at Kinexus with academic partners at the University of British Columbia and Simon Fraser University. With the PhosphoNET Evolution module, this website also provides information about cognate proteins in over 20 other species that may share these human phospho-sites. This helps to define the most functionally important phospho-sites as these are expected to be highly conserved in nature. With the Kinase Predictor module, listings are provided for the top 50 human protein kinases that are likely to phosphorylate each of these phospho-sites using another proprietary kinase substrate prediction algorithm developed at Kinexus. Our kinase substrate predictions are based on deduced consensus phosphorylation site amino acid frequency scoring matrices that we have determined for each of ~500 different human protein kinases. The specificity matrices are generated directly from the primary amino acid sequences of the catalytic domains of these kinases, and when available, have proven to correlate strongly with substrate prediction matrices based on alignment of known substrates of these kinases. The higher the score, the better the prospect that a kinase will phosphorylate a given site. Over 30 million kinase-substrate phospho-site pairs are quantified in PhosphoNET. Kinexus Bioinformatics Corporation has the capability to test most of these putative interactions in vitro for our clients.
The Node: a community site for development biologists
UBC HealthLib-Wiki - A Knowledge-Base for Health Librarians
HLWIKI Canada is an open, freely-accessible wiki with entries about health librarianship, social media, and current information technology topics. The intended audience is for information professionals, librarians, health professionals, social media experts.
Supports research on the causes, diagnosis, prevention, and treatment of lung diseases and sleep disorders. Research is funded through investigator-initiated and Institute-initiated grant programs and through contract programs in areas including asthma, bronchopulmonary dysplasia, chronic obstructive pulmonary disease, cystic fibrosis, respiratory neurobiology, sleep-disordered breathing, critical care and acute lung injury, developmental biology and pediatric pulmonary diseases, immunologic and fibrotic pulmonary disease, rare lung disorders, pulmonary vascular disease, and pulmonary complications of AIDS and tuberculosis. The Division is responsible for monitoring the latest research developments in the extramural scientific community as well as identifying research gaps and needs, obtaining advice from experts in the field, and implementing programs to address new opportunities. The DLD has three branches, the Airway Biology and Disease Branch, the Lung Biology and Disease Branch, and the National Center on Sleep Disorders Research.
A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.
Japanese Single Nucleotide Polymorphisms
JSNP is a database of Japanese Single Nucleotide Polymorphisms. It includes BLAST capability, keyword search, mapping information, and other tools that allow users to gather information on SNP's. SNPs are the most common form of DNA sequence variation. They are useful polymorphic markers to investigate genes susceptible to diseases or those related to drug responsiveness. Furthermore, a small subset of SNPs directly influences to the quality and/or quantity of the gene product, and increase a risk to certain diseases and to severe side effect by drugs. Through a discovery of a large number of SNPs, we would like to contribute to identification of disease-related genes and also to establish a diagnostic method to avoid drug side-effect.
International Union of Basic and Clinical Pharmacology Database
International Union of Pharmacology Database
Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target.
MIT-BIH Polysomnographic Database is a collection of recordings of multiple physiologic signals during sleep. Subjects were monitored in Boston''s Beth Israel Hospital Sleep Laboratory for evaluation of chronic obstructive sleep apnea syndrome, and to test the effects of constant positive airway pressure (CPAP), a standard therapeutic intervention that usually prevents or substantially reduces airway obstruction in these subjects. The database contains over 80 hours'' worth of four-, six-, and seven-channel polysomnographic recordings, each with an ECG signal annotated beat-by-beat, and EEG and respiration signals annotated with respect to sleep stages and apnea
The Chordoma Foundation is an international nonprofit organization working to improve the lives of chordoma patients by accelerating the development of effective treatments, and by helping patients to get the best care possible. Guided by a comprehensive research roadmap, the Foundation initiates and funds research, facilitates information exchange and collaboration among researchers, and provides scientific resources needed for research. Chordoma is a relentless and difficult to treat bone cancer that occurs in the head and spine in people of all ages. No drugs are approved to treat chordoma and the average survival after diagnosis is 7 years; a statistic we are determined to improve. Our Approach: * Fund results-oriented research: We proactively fund research projects identified by our Scientific Advisory Board as strategic priorities for advancing the development of new treatments for chordoma. * Provide scientific resources: We create, collect, store, and distribute the information and biological materials that researchers need in order to study chordoma and develop new treatments. * Facilitate communication and collaboration: We connect physicians, scientists and companies from across the world to share information and collaborate on projects they can only achieve together. * Guide patients to obtain quality care: We provide accurate information about treatment options and clinical trials, refer patients to experienced doctors, and match patients with trained peer-support mentors.
Software for handling and analysis of high-throughput microbiome census data.
The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic, and functional information on the homeodomain family. A description of each of the major sections of the database can be found below, and users can navigate through the site using the links found in the menu that appears on the left-hand side of every page within the site. The website provides lists of Homeodomain proteins, solved three-dimensional structures of homeodomain proteins and protein-DNA complexes, lists of protein-protein interactions involving homeodomain proteins, DNA binding sites, and human genetic and genomic disorders linked to homeodomain proteins. Preexisting Description: homeodomain, protein, protein-DNA complex,
PhyloPhlAn: microbial Tree of Life using 400 universal proteins
Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program for gene segregation and linkage analysis in breeding population (entry from Genetic Analysis Software)
Oregon Brain Bank: Human tissue repository for neurodegenerative research studies
Brain bank that harvests, banks and disperses postmortem tissue for use in brain and medical research. It also provides neuropathologic diagnoses of organic dementia in a cohort of NIH sponsored research subjects. The bank includes tissue primarily from patients with Alzheimer's but also includes Huntington's, Parkinson's, and other disorders.
Collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world. Distributes, throughout Australia and New Zealand, cell lines from the European Collection of Authenticated Cell Cultures (ECACC) at Public Health England, a major international cell line repository based in the UK and from the Japanese Collection of Research Bioresources (JCRB), both collections also include many ATCC cell lines.
GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome
A portal for bioinformatics analyses, including the following: alignment assembly database display genetics hmm information nucleic phylogeny protein sequence structure
CFR - Code of Federal Regulations Title 21
This database includes a codification of the general and permanent rules published in the Federal Register by the Executive departments and agencies of the Federal Government. Title 21 of the CFR is reserved for rules of the Food and Drug Administration. This database contains content that is current as of April 1, 2013. For a daily compilation of CFR and Federal Register amendments, see the Electronic Code of Federal Regulations.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Software to detect rare or de novo copy number alterations in normal DNA samples. Please note that QuantiSNP is no longer under active development.
Genetic Codes is a summary resource of the taxonomy of each record and assignment of the correct genetic code for every entry in the GenBank database. GenBank format by historical convention displays mRNA sequences using the DNA alphabet. Thus, for the convenience of people reading GenBank records, the genetic code tables shown here use T instead of U. The following genetic codes are described here: The Standard Code The Vertebrate Mitochondrial Code The Yeast Mitochondrial Code The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code The Invertebrate Mitochondrial Code The Ciliate, Dasycladacean and Hexamita Nuclear Code The Echinoderm and Flatworm Mitochondrial Code The Euplotid Nuclear Code The Bacterial, Archaeal and Plant Plastid Code The Alternative Yeast Nuclear Code The Ascidian Mitochondrial Code The Alternative Flatworm Mitochondrial Code Blepharisma Nuclear Code Chlorophycean Mitochondrial Code Trematode Mitochondrial Code Scenedesmus Obliquus Mitochondrial Code Thraustochytrium Mitochondrial Code
Software developed at Celera Genomics as part of Celera''s sequencing and annotation of the human genome, and released as open source in 2006.
Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs.
A tool for structural biology and drug design.
Cerebellar Development Transcriptome Database
Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains.
The EzCatDB database analyzes and classifies enzyme catalytic mechanisms on the basis of information from literature and data that are derived from entries in the Protein Data Bank (PDB). Each data set contains corresponding enzyme information, such as E.C. number, PDB entries with their annotated ligand information and active site residues, information on catalytic mechanisms, and links to other databases, such as Swiss-prot, CATH, KEGG, PDBsum, and PubMed.
Data analysis service for the prediction of multi-label protein subcellular localization based on gene ontology and support vector machines. Web services are also available.
The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalyzed by an enzyme. The CSA contains 2 types of entry: 1. Original hand-annotated entries, derived from the primary literature. References for these entries are given. 2. Homologous entries, found by PSI-BLAST alignment (using an e value cut-off of 0.00005) to one of the original entries. The equivalent residues, which align in sequence to the catalytic residues found in the original entry are documented. Access to the CSA is via PDB code, SWISS-PROT entry or E.C. number. Accessing via PDB code takes you straight to the CSA entry for that PDB, while accessing via SWISS-PROT or E.C. number gives a list of all PDB codes for structures assigned that particular SWISS-PROT identifier or E.C. number. Structures with entries in the CSA are given as hyperlinks. Each CSA entry lists the catalytic residues found in that entry, using PDB residue numbering. Each site is also marked with an evidence tag, which is either Literature reference or PSI-BLAST hit. If the entry is a PSI-BLAST hit you can follow the link to the original entry. You may download the CSA. JESS, an algorithm for constraint-based structural template matching and its application to 3D templates used by the CSA, is available for download.
ColiSNP: Database of Single Nucleotide Polymorphism
ColiSNP is a website made up of two databases focused on SNPS. The first database is a database of Single Nucleotide Polymorphism (SNP) located in the protein coding region, and the second is a database of Single Nucleotide Polymorphism (SNP) located in the gene regulation region. The database of Single Nucleotide Polymorphism (SNP) located in the protein coding region is a database of Single Nucleotide Polymorphism (SNP) mapped on protein structure. Users can search the data of SNP on this web site and display the structure of protein with SNP by RasMol. The database of Single Nucleotide Polymorphism (SNP) located in the gene regulation region is a database of Single Nucleotide Polymorphism (SNP) mapped on regulation region. Users can search genes mapped snp on regulation region.
A mutation registry for X-linked agammaglobulinemia (XLA). BTKbase lists mutation entries of 1,111 patients from 973 unrelated families showing 602 unique molecular events. Agammaglobulinemia is characterized by failure to produce mature B lymphocyte cells and is associated with a failure of Ig heavy chain rearrangement. Two thirds of cases are familial, and one third of cases are believed to arise from new mutations. Mutations of the BTK gene are found in approximately 80% of patients with agammaglobulinemia. The localization of the mutations on the gene and protein for BTK can be analyzed by clicking sequences on the web pages. It includes a mutation browser, which gives users access to mutations in Bruton tyrosine kinase (BTK) protein sequences, and XLA fact file, and forms for users to submit mutation to the dataset.
Blog that examines the intersection of traditional genealogical techniques and modern genetic research.
This software can be used to analyze EEG data either using a graphical interface (GUI) or using Matlab scripts, which make use of the functions provided by the MeanMachine. As compared to other libraries, MeanMachine can handle even very large data sets like, for example, 256 channels recorded at 2KHz.
U.S. Public Health Service Commissioned Corps
US Public Health Service Commissioned Corps
Commissioned Corps of the United States Public Health Service, is the federal uniformed service of the U.S. Public Health Service, and is one of the eight uniformed services of the United States.
This Matlab toolkit is a general purpose tool for editing, visualizing, and analyzing EEG data (both Event Related Potential - ERP and spectral) whose most recent version has been downloaded over 1000 times. Its three chief highlights are: 1) an optimized automatic artifact correction function that includes ICA correction for eye blinks and saccades. 2) Extensive support for easily conducting PCA and ICA through all stages of the procedure, including inspection of reconstituted waveforms and batch ANOVAs. 3) Implementation of robust ANOVAs, including McCarthy-Wood vector test. It has a graphical user interface for point and click usage and comes with an extensive illustrated tutorial. A description of the toolkit was published in Dien (2010) in Journal of Neuroscience Methods. It relies on both internal functions as well as borrowed functions from both EEGlab and FieldTrip.
Adenylate Uridylate-rich-Rich Element-Containing mRNA Database
Adenylate Uridylate-Rich Element-mRNA database
Database that contains the complete entries of human ARE-containing full-length mRNAs. ARED is further clustered into five groups depending on the number of motifs in the ARE stretch. Groups 1-4 contain five, four, three and two pentameric (AUUUA) repeats, respectively, while Group 5 contains only one repeat within the 13-bp pattern. Clustering was performed in such a way that, for example, Group 1 included not only exact five or more continuous ARE pentamers but also those with 10% ambiguity, so that a stretch of NUUUAUUUAUUUAUUUAUUUN would fall in this category. This process was verified by a phylogenic tree relationship using Clustal-W alignment of ARE stretches and their variations. As could be expected, this analysis showed that the lower the number of ARE motifs in a group, the higher the number of sequences that were included, and apparently the more functionally diverse the corresponding ARE-genes.
Software tools for the processing of liver images. These tools consist of a level set based variational approach that incorporates shape priors and appearance models. It uses ITK-SNAP 1.4 as interface. The tools are capable of automatic liver segmentation and semi-automatic injury segmentation.
A tool for the gene-set (or pathway) analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology, KEGG pathways, or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version.
General-purpose unsupervised data-analysis tool, most often used for brain imaging data.
The pursuit of the Department of Physiology & Pharmacology at Wake Forest University School of Medicine is excellence in research and education. Graduate education and training includes quality introductory and advanced courses in physiology, pharmacology and neuroscience, as well as seminars and journal clubs in several major research areas. Laboratory rotations encourage the graduate student to explore various experimental approaches and provide a diverse training experience. The department and Medical Center are frequented by distinguished visitors from other universities who further enrich the stimulating academic environment. Departmental faculty are active in the medical education as well as in residency training programs in Neurology, Psychiatry, Urology, and Surgery.
This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps : - Affine Registration with BRAINSFit - Non Linear Registration with GreedyAtlas A final step will apply the transformations to the original DTI images so that the final average can be computed. The main function writes a python script that will be executed to compute the Atlas. By running DTIAtlasBuilder, you will need to fill in informations in a Graphical User Interface, and then compute the Atlas. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a parameter file. The tool needs these other tools to work, so be sure to have these installed on your computer: - ImageMath - ResampleDTIlogEuclidean - CropDTI - dtiprocess - BRAINSFit - GreedyAtlas - dtiaverage - DTI-Reg - unu - MriWatcher If you download the package, be sure to have the glut library installed.
University of Maryland Department of Neuroscience
The Graduate Program in Neuroscience at the University of Maryland, Baltimore is one of eight programs in the Graduate Program in Life Sciences (GPILS). The Program in Neuroscience offers research and training opportunities with internationally-renowned faculty. Our Neuroscience Graduate Program is an interdisciplinary program of study leading to a Ph.D. degree in Neuroscience. This graduate program in neuroscience offers research training in a wide range of brain sciences and a flexible program of study.
Pipeline for small genome assembly using SOLiD sequencing technology.
University of Wisconsin School of Pharmacy
The University of Wisconsin - Madison School of Pharmacy is a world-class leader in pharmacy education, research, and service in the pharmaceutical, social, and clinical sciences. We educate future pharmacists and scientists and provide professional development opportunities globally to practicing pharmacists and the pharmaceutical industry. All of our programs are driven by our mission to enhance the quality of life for the people of Wisconsin and the global community through improved health.
National Institute of Neurological Disorders and Stroke
National institute whose mission is to reduce the burden of neurological disease - a burden borne by every age group, by every segment of society, by people all over the world. To accomplish this goal the NINDS supports and conducts basic, translational, and clinical research on the normal and diseased nervous system. The Institute also fosters the training of investigators in the basic and clinical neurosciences, and seeks better understanding, diagnosis, treatment, and prevention of neurological disorders. NINDS: * Conducts, fosters, coordinates, and guides research on the causes, prevention, diagnosis, and treatment of neurological disorders and stroke, and supports basic research in related scientific areas. * Provides grants-in-aid to public and private institutions and individuals in fields related to its areas of interest, including research project, program project, and research center grants. * Operates a program of contracts for the funding of research and research support efforts in selected areas of institute need. * Provides individual and institutional fellowships to increase scientific expertise in neurological fields. * Conducts a diversified program of intramural and collaborative research in its own laboratories, branches, and clinics. * Collects and disseminates research information related to neurological disorders.
Human Genome Epidemiology Network, or HuGENet, is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. Its goals include: establishing an information exchange that promotes global collaboration in developing peer-reviewed information on the relationship between human genomic variation and health and on the quality of genetic tests for screening and prevention; providing training and technical assistance to researchers and practitioners interested in assessing the role of human genomic variation on population health and how such information can be used in practice; developing an updated and accessible knowledge base on the World Wide Web; and promoting the use of this knowledge base by health care providers, researchers, industry, government, and the public for making decisions involving the use of genetic information for disease prevention and health promotion. HuGENet collaborators come from multiple disciplines such as epidemiology, genetics, clinical medicine, policy, public health, education, and biomedical sciences. Currently, there are 4 HuGENet Coordinating Centers for the implementation of HuGENet activities: CDC''s Office of Public Health Genomics, Atlanta, Georgia; HuGENet UK Coordinating Center, Cambridge, UK; University of Ioannina, Greece; University of Ottawa , Ottawa, Canada. HuGENet includes: HuGE e-Journal Club: The HuGE e-Journal Club is an electronic discussion forum where new human genome epidemiologic (HuGE) findings, published in the scientific literature in the CDC''s Office of Public Health Genomics Weekly Update, will be abstracted, summarized, presented, and discussed via a newly created HuGENet listserv. HuGE Reviews: A HuGE Review identifies human genetic variations at one or more loci, and describes what is known about the frequency of these variants in different populations, identifies diseases that these variants are associated with and summarizes the magnitude of risks and associated risk factors, and evaluates associated genetic tests. Reviews point to gaps in existing epidemiologic and clinical knowledge, thus stimulating further research in these areas. HuGE Fact Sheets: HuGE Fact Sheets summarize information about a particular gene, its variants, and associated diseases. HuGE Case Studies: An on-line presentation designed to sharpen your epidemiological skills and enhance your knowledge on genomic variation and human diseases. Its purpose is to train health professionals in the practical application of human genome epidemiology (HuGE), which translates gene discoveries to disease prevention by integrating population-based data on gene-disease relationships and interventions. Students will acquire conceptual and practical tools for critically evaluating the growing scientific literature in specific disease areas. HUGENet Publications: Articles related to the HuGENet movement written by our HuGENet collaborators. HuGE Navigator: An integrated, searchable knowledge base of genetic associations and human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. HuGE Workshops: HuGENet has sponsored meetings and workshops with national and international partners since 2001. Available are detailed summaries, agendas or the ability to download speaker slides. HuGE Book: Human Genome Epidemiology: A Scientific Foundation for Using Genetic Information to Improve Health and Prevent Disease. (The findings and conclusions in this book are those of the author(s) and do not necessarily represent the views of the funding agency.) HuGENet Collaborators: HuGENet is interested in establishing collaborations with individuals and organizations working on population based research involving genetic information. HuGE Funding: Funding opportunities for specific population-based genetic epidemiology research projects are available. Research initiatives whose aims include assessing the prevalence of human genetic variation, the association between genetic variants and human diseases, the measurement of gene-gene or gene-environment interaction, and the evaluation of genetic tests for screening and prevention are compiled to create a posted listing. Additional information and application details can be found by clicking on the respective links.
Ohio State University College of Pharmacy; Ohio; USA
Ohio State University College of Pharmacy
The overall mission of the College of Pharmacy is to advance pharmaceutical care for the people of Ohio and the global community through our teaching, through our research, and through our service. The College will provide high quality education in the pharmaceutical sciences and pharmacy practice to professional, undergraduate, graduate, and postgraduate students through teaching, research, practice, and related service activities including outreach and engagement.
Pedigree ANalysis for Genetics (And Epidemiological Attributes)
Collection of nine software packages for genetic analysis: BOREL, HARDY, MORGAN (now 2 and 3), Pedpack, InSegT, Loki, MCLEEPS, Pedfiddler, and Eclipse.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May24,2023. Software program that implements the Mantel statistics as proposed by Beckmann et al. (2005) to test for association between genetic markers and phenotypes in case-control studies using haplotype information. The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take into account linkage disequilibrium information between multiple markers, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for space time clustering, which we developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease. The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. Alternative measures for the phenotypic similarity were implemented. (entry from Genetic Analysis Software)
SCORE-type tests for detecting disease associations with rare variants in SEQuencing Studies
A command-line program for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software)
Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software)
Power of Indirect Association Studies of Gene-Environment Interactions
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program that performs estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects (Kraft P et al., 2007). Power and sample size estimations are based on Gauderman''s (2002) asymptotic approach for power and sample size estimations in direct studies of GxE. Hardy-Weinberg equilibrium and independence of genotypes and environmental exposures in the population are assumed. The estimates are based on genotypic codes (G=1 (G=0) for individuals who carry a (non-) risk genotype), which depend on the mode of inheritance (dominant, recessive, or multiplicative). A conditional logistic regression approach is used, which employs a likelihood-ratio test with respect to a biallelic candidate SNP, a binary environmental factor (E=1 (E=0) in (un)exposed individuals), and the interaction between these components. (entry from Genetic Analysis Software)
Software programs for pedigree analysis, including segregation analysis, gene extinction, and pedigree graphics. (entry from Genetic Analysis Software)
Software application that constructs feasible haplotype configurations and the corresponding segregation types on pedigrees. the haplotype configuration minimizes recombinations on the pedigree. (entry from Genetic Analysis Software)
Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software)
Software application that is a GLF-based variant caller for next-generation sequencing data. It takes one/three/multiple GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output. (entry from Genetic Analysis Software)
Web-based, relational database driven data management software package for the management of large scale genetic studies. (entry from Genetic Analysis Software)
Error Correcting Likelihoods In Pedigree Structure Estimation. PANGAEA
A set of three programs, preproc, eclipse2 and eclipse3 which analyze genetic marker data for genotypic errors and pedigree errors. Using a single preprocessing program (preproc), eclipse2 analyzes data on pairs of individuals, and eclise3 analyzes data jointly on trios. (entry from Genetic Analysis Software)
A statistical based program for association mapping of disease genes. It utilises the Malecot model and the linkage disequilibrium (LD) map for the candidate region to analyse the genotypes derive from large sample of matched cases and controls. (entry from Genetic Analysis Software)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application to compute composite measures of linkage disequilibrium, their variances and covariances, and statistical tests, for all pairs of alleles from two loci when linkage phase is unkown. An extension of Weir and Cockerham (1989) to apply to multi-allelic loci. (entry from Genetic Analysis Software)
BOolean Operation based Screening and Testing
Software application (entry from Genetic Analysis Software) for a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that simultaneously estimates a trait-locus position and its genetic effects for affected relative pairs (ARP) by one of two methods. Either allow a different trait-locus effect for each ARP type, or constrain the trait-locus effects according to the marginal effect of a single susceptibility locus. We include a goodness of fit statistic for the constrained model. (entry from Genetic Analysis Software)
Software application for inference of genealogical relationships from genetic data, including sibship inference.
Genetic ASSOCiation analysis software for cases and parent
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application for statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms. (entry from Genetic Analysis Software)
Research forum portal to address brain status by acquiring comprehensive, multimodal data from healthy humans across the lifespan to characterize brain status, assess its change over time, and associate composite descriptors of brain status. Specifically, the measurements are acquired noninvasively by existing neuroimaging technologies (structural MRI, functional MRI, magnetic resonance spectroscopy, diffusion MRI, and magnetoencephalography); in addition, genetic, cognitive, language, and lifestyle data are acquired. Goals: * Derive the Brain Health Index- An integrative assessment of brain status derived from multimodal measurements of brain structure, function, and chemistry. * Continue acquiring data to construct the first-ever databank on brain, cognitive, language and genetic measurements for healthy people across the lifespan. * Provide a novel and unique dataset by which to: characterize brain status, assess its change over time, and associate it with genetic makeup, cognitive function, and language abilities. * Forecast future brain health and disease based on current measurements and guide physicians towards new interventions and evaluate interventions as they develop. * Extend to siblings and other family members to further assess the genetic influences and inheritability.
iPhone and iPad app that provides a good overview of the brain and its structures allowing you to rotate and zoom around 29 interactive structures with your touch screen. Discover how each brain region functions, what happens when it is injured, and how it is involved in mental illness. Each detailed structure comes with information on functions, disorders, brain damage, case studies, and links to modern research. Compatible with iPhone, iPod touch and iPad. Requires iOS 3.0 or later.
A computerized data set of demographic, economic and social data for 227 countries of the world. Information presented includes population, health, nutrition, mortality, fertility, family planning and contraceptive use, literacy, housing, and economic activity data. Tabular data are broken down by such variables as age, sex, and urban/rural residence. Data are organized as a series of statistical tables identified by country and table number. Each record consists of the data values associated with a single row of a given table. There are 105 tables with data for 208 countries. The second file is a note file, containing text of notes associated with various tables. These notes provide information such as definitions of categories (i.e. urban/rural) and how various values were calculated. The IDB was created in the U.S. Census Bureau''s International Programs Center (IPC) to help IPC staff meet the needs of organizations that sponsor IPC research. The IDB provides quick access to specialized information, with emphasis on demographic measures, for individual countries or groups of countries. The IDB combines data from country sources (typically censuses and surveys) with IPC estimates and projections to provide information dating back as far as 1950 and as far ahead as 2050. Because the IDB is maintained as a research tool for IPC sponsor requirements, the amount of information available may vary by country. As funding and research activity permit, the IPC updates and expands the data base content. Types of data include: * Population by age and sex * Vital rates, infant mortality, and life tables * Fertility and child survivorship * Migration * Marital status * Family planning Data characteristics: * Temporal: Selected years, 1950present, projected demographic data to 2050. * Spatial: 227 countries and areas. * Resolution: National population, selected data by urban/rural * residence, selected data by age and sex. Sources of data include: * U.S. Census Bureau * International projects (e.g., the Demographic and Health Survey) * United Nations agencies Links: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/08490
A wide-ranging representative longitudinal study of private households that permits researchers to track yearly changes in the health and economic well-being of older people relative to younger people in Germany from 1984 to the present. Every year, there were nearly 11,000 households, and more than 20,000 persons sampled by the fieldwork organization TNS Infratest Sozialforschung. The data provide information on all household members, consisting of Germans living in the Old and New German States, Foreigners, and recent Immigrants to Germany. The Panel was started in 1984. Some of the many topics include household composition, occupational biographies, employment, earnings, health and satisfaction indicators. In addition to standard demographic information, the GSOEP questionnaire also contains objective measuresuse of time, use of earnings, income, benefit payments, health, etc. and subjective measures - level of satisfaction with various aspects of life, hopes and fears, political involvement, etc. of the German population. The first wave, collected in 1984 in the western states of Germany, contains 5,921 households in two randomly sampled sub-groups: 1) German Sub-Sample: people in private households where the head of household was not of Turkish, Greek, Yugoslavian, Spanish, or Italian nationality; 2) Foreign Sub-Sample: people in private households where the head of household was of Turkish, Greek, Yugoslavian, Spanish, or Italian nationality. In each year since 1984, the GSOEP has attempted to re-interview original sample members unless they leave the country. A major expansion of the GSOEP was necessitated by German reunification. In June 1990, the GSOEP fielded a first wave of the eastern states of Germany. This sub-sample includes individuals in private households where the head of household was a citizen of the German Democratic Republic. The first wave contains 2,179 households. In 1994 and 1995, the GSOEP added a sample of immigrants to the western states of Germany from 522 households who arrived after 1984, which in 2006 included 360 households and 684 respondents. In 1998 a new refreshment sample of 1,067 households was selected from the population of private households. In 2000 a sample was drawn using essentially similar selection rules as the original German sub-sample and the 1998 refreshment sample with some modifications. The 2000 sample includes 6,052 households covering 10,890 individuals. Finally, in 2002, an overrepresentation of high-income households was added with 2,671 respondents from 1,224 households, of which 1,801 individuals (689 households) were still included in the year 2006. Data Availability: The data are available to researchers in Germany and abroad in SPSS, SAS, TDA, STATA, and ASCII format for immediate use. Extensive documentation in English and German is available online. The SOEP data are available in German and English, alone or in combination with data from other international panel surveys (e.g., the Cross-National Equivalent Files which contain panel data from Canada, Germany, and the United States). The public use file of the SOEP with anonymous microdata is provided free of charge (plus shipping costs) to universities and research centers. The individual SOEP datasets cannot be downloaded from the DIW Web site due to data protection regulations. Use of the data is subject to special regulations, and data privacy laws necessitate the signing of a data transfer contract with the DIW. The English Language Public Use Version of the GSOEP is distributed and administered by the Department of Policy Analysis and Management, Cornell University. The data are available on CD-ROM from Cornell for a fee. Full instructions for accessing GSOEP data may be accessed on the project website, http://www.human.cornell.edu/che/PAM/Research/Centers-Programs/German-Panel/cnef.cfm * Dates of Study: 1984-present * Study Features: Longitudinal, International * Sample Size: ** 1984: 12,290 (GSOEP West) ** 1990: 4,453 (GSOEP East) ** 2000: 20,000+ Links: * Cornell Project Website: http://www.human.cornell.edu/che/PAM/Research/Centers-Programs/German-Panel/cnef.cfm * GSOEP ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00131
Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration.
Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC)
Repository that serves to coordinate searches across data and biospecimen collections from participants in numerous clinical trials and epidemiologic studies and to provide an electronic means for requests for additional information and the submission of requests for collections. The collections, comprising data from more than 80 trials or studies and millions of biospecimens, are available to qualified investigators under specific terms and conditions consistent with the informed consents provided by the individual study participants. Some datasets are presented with studies and supporting materials to facilitate their use in reuse and teaching. Datasets support basic research, clinical studies, observational studies, and demonstrations. Researchers wishing to apply to submit biospecimen collections to the NHLBI Biorepository for sharing with qualified investigators may also use this website to initiate that process.
A publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains experimental information about the topology of 2143 transmembrane proteins. This information was collected from studies in the literature that reported the use of biochemical methods for the determination of the topology of transmembrane proteins. Each record contains unique information about the given protein, such as its sequence, cross-references to many publicly available databases worldwide, the protein''s name and organism source. The web interface of the database offers the user the ability to submit advanced queries for text search within ExTopoDB''s protein entries and there is also an interface for running BLAST against the database. Furthermore, the results of topology prediction using the HMM-TM algorithm are included for each protein in the database (unconstrained prediction) and we also incorporated the experimental information about the topology of the proteins in the HMM-TM prediction procedure, producing more reliable topology models (constrained prediction).
GWASrap - SNPs Representing Annotating and Prioritizing Tool for Genome Wide Association Study
GWASrap is a comprehensive web-based bioinformatics tool to systematically support variant representation, annotation and prioritization for data generated from genome-wide association studies (GWAS) and Next Generation Sequencing (NGS). Our web-based framework utilizes state-of-the-art web technologies to maximize user interaction and visualization of the results. For a given SNP dataset with its P-values, GWASrap will first provide a Circos-style plot to visualize any genetic variants at either the genome or chromosome level. The tool then combines different genomic features (SNP/CNV density, disease susceptibility loci, etc.) with comprehensive annotations that give the researcher an intuitive view of the functional significance of the different genomic regions. The detailed statistics of the underlying study are also displayed on the web page, including variant distribution in different functional categories, classic Manhattan plot and QQ plot. Users can perform interactive operations in the Manhattan panel, such as zooming in and out to search regions or markers of interest. The system can also display a comprehensive range of relevant information from variant genetic attributes to nearby genomic elements, such as enhancers or non-coding RNAs. Furthermore, researchers can obtain extensive functional predictions for various features including transcription factor-binding sites, miRNA and miRNA target sites, and their predicted changes caused by the genetic variants. Our system can re-prioritize genetic variants by combining the original statistical value and variant prioritization score based on a simple additive effect equation. Researchers can also re-evaluate the significance of a trait/disease-associated SNP (TAS) using the dynamic linkage disequilibrium (LD) panel or the tree-like network panel. The GWASrap supports input variants in different formats, not only common variants with a dbSNP rs ID but also rare variants from NGS data, which are represented by chromosome and locations. GWASrap provides a range of web services for data retrieving about the annotation information and effect prediction of each variant in dbSNP using the SOAP interface. The WSDL for each service is available in the API tab. Each service returns JSON string including all related information with key/value. GWASrap provides running results about some current published GWAS as well as a category view for each hot disease / trait. The dataset is brought from published database GWAS or curated from literature.
MINAS - A Database of Metal Ions in Nucleic AcidS
Database compiling the detailed information on innersphere, outersphere and larger coordination environment of >70,000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. The results of each search can be saved individually for later use with so-called miniPDB files containing the respective metal ion together with the coordination environment within a 15 A radius. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids.
ALSA - The Australian Longitudinal Study of Ageing
ALSA - The Australian Longitudinal Study of Aging
Australian Longitudinal Study of Ageing (ALSA)
Australian Longitudinal Study of Aging (ALSA)
The general purpose of ALSA is to examine how social, biomedical, psychological, economic, and environmental factors are associated with age-related changes in the health and wellbeing of persons aged 70 years and older. The aim is to analyze the complex relationships between individual and social factors and changes in health status, health care needs and service utilization dimensions, with emphasis given to the effects of social and economic factors on morbidity, disability, acute and long-term care service use, and mortality. The study was designed to have common instrumentation with US studies. ALSA collected data from a random, stratified sample of all persons (both community and institution-dwelling) aged 70 years and older living in the metropolitan area of Adelaide, South Australia, using the State Electoral Database as the sampling frame. Spouses aged 65 and older and other household members aged 70 years and older also were invited to participate. The initial baseline data collection for ALSA began in September 1992 and was completed in March 1993. In the first wave, personal interviews were carried out for 2,087 participants, including 566 couples (that is, persons 70 years of age and over and their spouse, if 65 and over). Clinical assessments were obtained for 1,620 of the participants. Respondents were recontacted by telephone a year after initial interview (wave 2). The third wave of the study began in September 1994 and involved a complete reassessment, with a total of 1,679 interviews and 1,423 clinical assessments. To date, eleven waves of data have been collected, with the latest collection in May 2010, from 168 participants. Six of these waves were conducted via face-to-face interviews and clinical assessments, and five were telephone interviews. Future waves are planned, however are dependent on grant funding. Ancillary data collection has been ongoing since the initiation of the study, e.g., from secondary providers. Lists of ALSA participants are compared biannually with the agencies'' lists to determine the prevalence and incidence of receipt of services from these organizations. Another source of information has been the collection of data from the participants'' general practitioners about the respondent''s health status, history of services received, medication use, referrals to specialists, and current services provided. Baseline Sample Size: 2087 Dates of Study: 1992����������2010 (potentially ongoing) Study Features: * Longitudinal * International * Anthropometric Measures * Biospecimens Waves 1-5 (ICPSR), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06707 Wave 6 (ICPSR), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03679
Tripod Development - Cheminformatics proving ground
Tripod is a user-friendly chemical genomics browser that is currently being developed by the informatics group at the NIH Chemical Genomics Center. The main goal of Tripod is to facilitate easy access to chemical and biological data in an intuitive, user-friendly tool. To this end, the development of Tripod is inspired by the ubiquitous iTunes software, whereby browsing and managing of media contents are being adapted to chemical and biological data.
Baltimore Longitudinal Study of Aging (BLSA)
America''s longest-running scientific study of human aging, begun in 1958. BLSA scientists are learning what happens as people age and how to sort out changes due to aging from those due to disease or other causes. More than 1,400 men and women are study volunteers. They range in age from their 20s to their 90s. This study is currently recruiting healthy seniors over 70.
Djavad Mowafaghian Centre for Brain Health
Research facility for research on neurological and psychiatric disorders on the learning brain and the aging brain. The Centre utilizes a multidisciplinary approach to explore the causes and potential treatments of disorders like Alzheimer's disease, mental health and addiction, stroke and neurotrauma. The Centre focuses on translating research into patient care and therapies.
Software that performs ?decoding? of brain activity, by learning the difference between brain activity patterns among conditions and then classifying the brain activity based on the learning results. BDTB is a set of Matlab functions. BDTB is OS-independent.
NIH electronic Research Materials catalogue
eRMa: Electronic Research Materials Catalogue
Database and tool for finding and licensing unpatented research materials to for-profit entities. eRMa was developed by the NIH Office of Technology Transfer to expedite the process for transferring unpatented research materials to for-profit entities. NIH researchers make unpatented materials available to companies through internal use licenses executed by the OTT to support the continued advancement of scientific research. Examples of materials include mouse models used to develop new cancer therapies and cell lines used to test new therapies for chronic diseases, such as high blood pressure. An NIH internal use license is a contract that governs the transfer of tangible research materials from NIH to a company for commercial research use.
TRActs Constrained by UnderLying Anatomy
TRACULA - TRActs Constrained by UnderLying Anatomy
TRACULA: TRActs Constrained by UnderLying Anatomy
Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user' '''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons.
Web application to discover resources available at participating networked universities. This distributed platform for creating and sharing semantically rich data is built around semantic web technologies and follows linked open data principles.
The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Protists, which houses protists species. Sponsors: EnsembProtists is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute.
An Alphabetic List of Genetic Analysis Software
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Listing of computer software for the gene mapping community on the following topics: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. The inclusion of a program should not be interpreted as an endorsement to that program from us. In the last few years, new technology produces new types of genetic data, and the scope of genetic analyses change dramatically. It is no longer obvious whether a program should be included or excluded from this list. Topics such as next-generation-sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study, yet be specialized topics by themselves. Though programs on variance calling from NSG can be in, those can sequence alignment might be out; programs on eQTL can be in, those on differential expression might be out. This page was created by Dr. Wentian Li, when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002), and now takes its new home at North Shore LIJ Research Institute (2002-now). The present copy is maintained by Jurg Ott as a single file. More than 240 programs have been listed by December 2004, more than 350 programs by August 2005, close to 400 programs by December 2006, and close to 480 programs by November 2008, and over 600 programs by October 2012. A version of the searchable database was developed by Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of Harbin Medical School. Some earlier software can be downloaded from EBI: ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/ (Linkage and Mapping Software Repository), and http://genamics.com/software/index.htm may contain archived copy of some programs.
StemCore Laboratories is a high-throughput genomics facility within the Ottawa Hospital Research Institute (OHRI). StemCore Laboratories is developing a world-class infrastructure for genomics, bioinformatics, and proteomics, and is capable of facilitating large-scale scientific research and biotechnology projects. Stemcore Laboratories seeks out projects that are challenging, cutting-edge, extend the boundaries of biological knowledge, and will positively impact the state of human health. Funded: Genome Canada, The Ontario Genomics Institute, The Canadian Foundation for Innovation, The Government of Ontario, The Stem Cell Network, Stantive Solutions
To explore the elephant shark genome, we have conducted a survey-sequencing and comparative analysis of the elephant shark genome in collaboration with J. Craig Venter Institute. The elephant shark sequences generated under this project have been deposited at GenBank under the project accession number AAVX01000000. The sequences can also be searched using BLAST and retrieved here. Cartilaginous fishes (Chondrichthyes) represented by sharks, rays, skates and chimaeras, are phylogenetically the oldest group of living jawed vertebrates. They constitute an important group for our understanding of the origins of the complex developmental and physiological systems of jawed vertebrates. They are also an useful outgroup for bony vertebrates such as tetrapods and teleost fishes and help in identifying specialized features that have led to the evolution of diverse groups of bony vertebrates. The elephant shark (Callorhinchus milii), also known as the elephant fish and ghost shark, is a chimaera belonging to the Order Chimaeriformes and Family Callorhynchidae. It has the smallest genome among the known cartilaginous fish genomes. Thus, it was proposed as a model cartilaginous fish genome for whole-genome sequencing and comparative analysis (Venkatesh et al. 2005. Curr. Biol. 15: R82-R83). The following resources of the elephant shark are available for the scientific community: *Elephant Shark 1.4x assembly fasta sequences zipped 227 megabytes *Genomic DNA *~8x coverage BAC library (average insert size, ~150 kb) *cDNA libraries (under construction) *cDNA (dated 11 April 2008) with orthologs in 5 vertebrates (human, opossum, chicken, frog, fugu)
BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer.
cnvHiTSeq - A set of tools for detecting CNVs using sequencing data
A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 32,2023.
It is an international research infrastructure for investigators interested in conducting population and clinic-based interdisciplinary studies on the genetic and molecular epidemiology of colon cancer and its behavioral implications. A central goal of the C-CFR is the translation of this research to the clinical and prevention setting for the benefit of Registry participants and the general public. The C-CFR has information and biospecimens contributed by greater than 11,300 families across the spectrum of risk for colon cancers and from population-based or relative controls. Of particular interest are: identification and characterization of cancer susceptibility genes definition of gene-gene and gene-environment interactions in cancer etiology translational, preventive, and behavioral implications of research findings Special features include: population-based and clinic-based ascertainment systematic collection of validated family history epidemiologic risk factor data clinical and follow-up data biospecimens (including tumor blocks and EBV transformed cell lines) ongoing molecular characterization of the participating families Goals: to contribute to the development of public health measures for the general population by increasing knowledge on genetic factors affecting cancer susceptibility and modification by environmental and lifestyle factors to protect those with increased susceptibility from developing cancer to provide life-prolonging treatment to genetically susceptible individuals Objectives: to establish a comprehensive research resource infrastructure to assist with the implementation of collaborative, interdisciplinary research protocols in the genetic epidemiology of cancer to identify, characterize, and follow-up a cohort of individuals and their family members, spanning the spectrum of cancer risk to identify diverse genetically susceptible populations that could benefit from enrollment in preventive and therapeutic interventions to develop an adaptive and evolving informatics model to support ongoing and future research consortia Sponsor. This study was supported by National Cancer Institute Grants R01 CA47147, R01 CA47305, and R01 CA69664.
Cancer and many other human diseases arise from gene defects, which are either inherited or occur - as in most cancers spontaneously in somatic cells. These defects cause aberrant activities of gene products and malfunctioning of molecular and cellular interactions, thereby inducing tumors and accompanying cancer progression. The central objective of our division is to understand the complex molecular processes of human health and disease. In particular, we are working on tools for improving diagnosis of malfunctioning and prognosis for patients as well as the identification and validation of novel targets for therapies. Main interest of the division is on cellular signaling networks and their roles in cancer drug resistance and metastasis. To this end, we apply high-throughput functional genomics and proteomics technologies, and analyze candidate genes using in vitro and in vivo systems. The division organizes the conference Systems Genomics 2010 (September 29 - October 1, 2010 at the DKFZ Heidelbeg) and aims at advancing the integration of high-throughput genomics, quantitative proteomics, computational biology, and clinics. Internationally outstanding speakers will discuss their latest results in molecular and translational disease research Sponsor. This work was supported in part by the National Genome Research Network (Contract No. 01GS0864) of the Federal Ministry of Education and Research (BMBF) and by Wilhelm-Sander Stiftung (Contract No. 2009.051.1). JDZ is supported by the DKFZ International PhD Program. We thank Moritz Kblbeck, Christian Schmidt and Ute Ernst for their excellent technical assistance.
The HTPSELEX database contains sets of in vitro selected transcription factor binding site sequences obtained via a high-throughput SELEX (HTPSELEX) method. In addition, the database also contains binding sites obtained with conventional SELEX method. The database hosts 12 individual Selex libraries for the transcription factors CTF/NF1 and LEF/TCF families totaling more than 40,000 sites. In addition we also have manually curated SELEX datasets from the literature for 25 different transcription factors.
Traumatic Brain Injury Clinical Trials Network
Traumatic Brain Injury (TBI) Clinical Trials Network
The National Center for Medical Rehabilitation Research (NCMRR) established a multi-center network of sites that are working together to design clinical intervention protocols and measures of outcome for TBI. Through rigorous patient evaluation, using common protocols and interventions designed for multiple points of care����??including the accident scene, emergency room, intensive care unit, rehabilitation and long-term follow-up����??the NCMRR TBI Clinical Trials Network can study the required numbers of patients to provide answers more rapidly than individual centers acting alone. This interdisciplinary research Network is designed to evaluate the relationship among acute care practice, rehabilitation strategies, and the long-term functional outcome of TBI patients����??that is, to identify which intervention variables result in improvements in long-term outcomes. Taking advantage of the network model structure has allowed TBI research to progress toward a number of clinical research goals. Specifically, the NCMRR wants to highlight two major achievements to date. First, the TBI Network created a profile of its typical patient to determine the number of patients with different clinical features who might be eligible for future studies and to help estimate recruitment times necessary. Second, Network researchers are developing clinical treatment guidelines and procedures for all points in the continuum of care, including TBI Clinical Trials Network Guidelines for surgical care, systems-based protocol for severe and moderate TBI patients, deep-vein thrombosis prophylaxis procedures, and rehabilitation guidelines for physical therapy, speech-language pathology, occupational therapy, and neuropsychology.
Software tools and databases for plant genomics.
High Performance Computing and Collaboration
The Research Computing System is a vision for a user controlled collection of applications, tools, and services integrated through a uniform understanding of user identity and the communities (groups) to which the user belongs. This environment enables seamless access to shared resources and facilitates collaborations within departments, across campus and around the globe. The RCS development project is a collaborative effort to build a private cloud to support the construction and operation of research applications. RCS is the collection of these resources and the communities surrounding their development. RCS is an open development effort that welcomes participation of those interested in the construction, use, or operation of this platform.
We provide plasmid cloning services. Our procedures allow cloning not only by using restriction enzymes but also in restriction-enzymes-independent ways. This allows sequence modification in areas where no suitable restriction sites are present. Examples for services offered: - Amplification of insert from one plasmid and cloning in another plasmid. - Addition of sequence to an existing plasmid, for example adding FLAG+myc tags, restriction sites, linkers, shRNA coding sequences, can add up to 100 bp in one cloning operation. - Introducing site directed mutations, can modify multiple bases within a 50 bp sequence in one cloning operation. - Deletion of sequences of any length from a plasmid. - Insertion of one gene fragment in to another gene, for example for making a chimeric protein. - Cloning an insert in to a plasmid while adding a tag at the 5'' or 3'' ends of the insert. - Cloning an insert while adding a polyglycine spacer to prevent structural effects of tags on your protein. - Any other sequence modifications by request.
A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).
A nucleotide sequence similiary search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity.
bisReadMapper - Software for dealing with DNA methylation sequencing data
Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform.
A gold-standard dataset of biologically relevant binding sites in protein structures. It consists of proteins with one unbound structure and at least one structure of the protein-ligand complex. Both a redundant and a non-redundant (sequence identity lower than 25) version is available. Quaternary structures proposed by PQS (2) are used for all structures in the dataset. The availability of both unbound and bound structures for each protein guarantees that our dataset can be used to benchmark binding site prediction methods, in conditions that mimic cases where the binding site is truly unknown. In cases where several different bound structures are available for a given protein, all are used to define the binding sites.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. It provides annotated sequence data and classifications for the genomes of eighteen species of hemiascomycete yeasts, including nine complete genomes. The Gnolevures web resources provides genetic element pages, orthologs defined by syntenic homology, protein families, a genome browser for interspecies comparison, and data sets for downloading. An advanced search facility permits a number of criterion-based and full text queries. Classification data, including protein families and orthologs, and the most up-to-date genome annotations, are for the most part not available in general-purpose sequence data bases such as EMBL/GenBank/DDBJ.
A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads.
Software package to explore high-throughput ''C'' data such as 5C or Hi-C.
An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
Software application for identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes. (entry from Genetic Analysis Software)
Northwestern CNADC Tissue Bank / Neuropathology Core
Northwestern CNADC Tissue / Neuropathology Core
Northwestern Cognitive Neurology Alzheimer's Disease Center Tissue/Neuropathology Core
Northwestern Cognitive Neurology and Alzheimer's Disease Center Tissue/Neuropathology Core
Northwestern Neuropathology Core of CNADC
Northwestern University CNADC Tissue / Neuropathology Core
Northwestern University CNADC Tissue/Neuropathology Core
Northwestern University Cognitive Neurology and Alzheimer's Disease Center Tissue/Neuropathology Core
Northwestern's Cognitive Neurology and Alzheimers Disease Center Tissue/Neuropathology Core
Tissue bank for collecting, cataloging and storing postmortem brain tissue samples from subjects with and without neurological disorders. Specimens are available for research on cognitive impairment, Alzheimer's, dementia and other disorders along with clinical data such as demographic information, health and family history and neuropsychological test scores. The bank provides services to distribute postmortem brain tissue and other samples to investigators for use in research that will provide qualitative and quantitative diagnostic information to physicians, families, and researchers.
A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.
National Institute for Occupational Safety and Health
Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer.
SYFPEITHI: A Database for MHC Ligands and Peptide Motifs
SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database is based on previous publications on T-cell epitopes and MHC ligands. It contains information on: -Peptide sequences -anchor positions -MHC specificity -source proteins, source organisms -publication references Since the number of motifs continuously increases, it was necessary to set up a database which facilitates the search for peptides and allows the prediction of T-cell epitopes. The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between -1 and -3. Sponsors: SYFPEITHI is supported by DFG-Sonderforschungsbereich 685 and theEuropean Union: EU BIOMED CT95-1627, BIOTECH CT95-0263, and EU QLQ-CT-1999-00713.
National Creutzfeldt-Jakob Disease Surveillance Unit
The National Creutzfeldt-Jakob Disease Surveillance Unit
The incidence of Creutzfeldt-Jakob disease (CJD) is monitored in the UK by the National CJD Surveillance Unit (NCJDSU) based at the Western General Hospital in Edinburgh, Scotland. The Unit brings together a team of clinical neurologists, neuropathologists and scientists specialising in the investigation of this disease. This document is intended to summarise the research in progress at the NCJDSU and also provide some background information about CJD and other human spongiform encephalopathies. We have also provided some links to other resources and contrary points of view available on the Web.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. An online database containing information aboutMyxococcus xanthus. It provides a genome browser, microarray data, and BLAST functions. MyxoPedia is an online, community driven encyclopedia for information about ''anything Myxo''. Registered community members are welcome to add and edit articles on any aspect of Myxococcus xanthus here. Myxopedia faciliates M.xanthus and other myxobacterial researchers to contribute directly towards the ongoing genome annotation.
Set of different illusions, including color illusions, motion illusions, and optic illusions. Most illusions are from Professor Akiyoshi Kitaoka of the Ritsumeikan University in Kyoto, Japan.
This portal describes Professor Kitaoka Akiyoshi''s research in the science of visual illusions. Working as an associate professor at the Ritsumeiken University, Department of Psychology, he is one of the few researchers in Japan to be actively researching in this field of study. Professor Kitaoka defines an illusion as a misperception of a real object, adding that defining what is real is a difficult task that depends on recognition and epistemology. An illusion is formed when the perceived characteristics of the object differ from the physical characteristics. Professor Kitaoka first started studying visual illusions when working at the Tokyo Metropolitan Institute for Neuroscience, before coming to RU. He currently researches geometrical, color, lightness, and motion illusions and visual completion, and has become a prominent expert in the field, publishing a wide range of articles on the subject as well as the popular books Trick Eyes, Trick Eyes 2, Trick Eyes Graphics, and the Handbook of the Science of Illusion. To create his illusions, Professor Kitaoka uses graphic design software such as CorelDRAW, Adobe Illustrator, and the drawing software included in Microsoft Word in addition to making use of programming languages like Borland Delphi (Pascal). All of the images set out to test hypotheses that serve to advance his study of illusions and their applications for other visual functions. The goal of his research is to test visual mechanisms through visual illusions.
muliAlignFree: Multiple Alignment-free Sequence Comparison
R package intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data.
Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.
A de novo assembly algorithm for Next-Generation Sequencing technology.
FishNet is a collaborative effort by natural history museums and other biodiversity institutions to establish a global network of Ichthyology collections. There is an open invitation for any institution with a fish collection to join. The current portal is an outgrowth of the original FishNet project with improvements in network stability, georeferencing capabilities, and technical support. Users are provided access to searchable, mappable and downloadable data that are cached on a regular basis from participating institutions who have published their data via the DiGIR or TAPIR protocols with a Darwin Core schema. FishNet is also one of four (along with MaNIS, HerpNET, and ORNIS) vertebrate network portals that provide access to specimen collection records from around the world. These web portals, together, comprise VertNet and serve georeferenced, taxon-based data from 72 global institutions. VertNet is a cooperative project working to maintain and expand these distributed database projects. Future plans for VertNet include biodiversity informatics workshops, enhancement of the portal design, better searching capabilities, and a dynamic cache to expand performance and analytic features. :Sponsors: This resource is supported by the National Science Foundation :.
CallSim - Low-volume read processing base corrector
A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data.
An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software)
Tuxedo: Automated RNA-sequencing Pipeline Script
Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically.
An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE.
John Hopkins University, In-Vivo Cellular Molecular Imaging Center
The vision of the JHU ICMIC is to combine state-of-the-art imaging capabilities with powerful molecular biology techniques to define strategies with intent to cure. It has drawn upon its human resources at JHU to create a center consisting of a multidisciplinary group of premier individuals with diverse skills focused on translating molecular capabilities into imaging possibilities with the single purpose of understanding and curing cancer. Nearly all of the investigators participating in this ICMIC have interactive collaborative projects with one or more of the other investigators. The synergism generated by the collective skills of this unique group of individuals will lead to significant advances in the understanding of cancer and its treatment. The JHU ICMIC structure consists of four interactive and closely related research components focused on hypoxia, HIF-1, and exploiting the hypoxia response element to target cancer cells through choline kinase inhibition. These research components are anchored by the participation of world renowned expertise in HIF-1. The research components utilize MR, PET and Optical Imaging technology to understand cancer vascularization, invasion and metastasis, to achieve effective cancer therapy. The center has selected developmental projects which are highly relevant to the goals of the ICMIC and interactive with the research components. Five resources devoted to adminstration, molecular biology, imaging, probes, and translational application provide the infrastructure to support the research activities of the ICMIC. Research Components in the JHU ICMIC: - Combining Anti-angiogenic therapy with siRNA targeting of choline kinase. - Imaging the Role of HIF-1 in Breast Cancer Progression - Imaging and Targeting Hypoxia in Solid Tumors - Molecular and Functional Imaging of the HER-2/neu Receptor The following are developmental projects currently taking place in ICMIC 1. Receptor imaging using nonparamagnetic MRI contrast agents (2003) 2. New imaging agents for prostate cancer (2003) 3. Non-invasive monitoring of therapeutic effect of siRNA-mediated radiation sensitization in human prostate cancer xenografts (2003) 4. Imaging of the endothelin receptor in cancer (2003) 5. Imaging studies of c-myc regulation of tumor metabolism (2003) 6. Imaging studies of anti-tumorigenic effects of anti-oxidants in vivo (2005) 7. Molecular Imaging with Magnetic Resonance Microsystems (2005) 8. Endogenous angiogenesis inhibitors (2005) 9. MR imaging and spectroscopy in detection and localization of prostate cancer: a prospective trial in patients undergoing cystoprostatectomy and radical prostatectomy. (2005) 10. A versatile visualization system for the analysis of multi-modality and multidimensional cancer imaging (2007) 11. Non-invasive imaging of CXCR4 expression in breast cancer (2007)
SIU Center for Alzheimer's Disease and Related Disorders
SIU School of Medicine Center for Alzheimer's Disease and Related Disorders
Resource center that provides assistance for patients and families affected by Alzheimer's disease and related conditions. The Center provides patient care through the Memory and Aging Clinic as well as through research, education and service to the community. Additionally the Center provides training in dementia care, maintains centralized data collection, and sponsors programs of research that qualify for federal financial participation.
Program of studies designed to assess the health and nutritional status of adults and children in the United States. The survey is unique in that it combines interviews and physical examinations.
A Matlab / Octave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary, segmented or gray-scale images, such as those from MRI or CT scans, making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling.
Commercial software company offering on-demand cloud, hybrid hosting, hosted private cloud, and dedicated infrastructure for complex needs.
This database lists the G protein coupled receptors expressed endogenously in various cell lines. In so far as possible, we have tried to follow the receptor nomenclature recommended by IUPHAR. Please refer to the following web sites for additional information on receptor nomenclature: Official database of the IUPHAR committee on receptor nomenclature :http://www.iuphar-db.org/index.jsp British Journal of Pharmacology Volume 150 Issue S1 (February 2007) Guide to Receptors and channels. :http://www.nature.com/bjp/journal/vgrac/ncurrent/index.html The Endogenous GPCR List has been available in various forms since 1994 and seems to have enduring utility. We intend to continue to maintain, and when possible, improve this list. Suggestions for future enhancements are welcome. Information to be added to the database (e.g. additional endogenous receptors) is extremely welcome!
An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework.
RegRNA2.0 ? an integrated web server for identifying functional RNA motifs and sites
An integrated web server for identifying functional RNA motifs in an input RNA sequence.
A web server and DataBase for automated Carbohydrate-active enzyme ANnotation, funded by the BioEnergy Science Center of the DOE., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
American Association of Neurological Surgeons
The American Association of Neurological Surgeons is dedicated to advancing the specialty of neurological surgery and serving as the spokes organization for all practitioners of the specialty of neurosurgery, in order to provide the highest quality of care to our patients. :Founded in 1931 as the Harvey Cushing Society, the American Association of Neurological Surgeons (AANS) is a scientific and educational association with over 7,400 members worldwide. The AANS is dedicated to advancing the specialty of neurological surgery in order to provide the highest quality of neurosurgical care to the public. All Active members of the AANS are board certified by the American Board of Neurological Surgery, the Royal College of Physicians and Surgeons of Canada, or the Mexican Council of Neurological Surgery, A.C. Neurosurgery is the medical specialty concerned with the prevention, diagnosis, treatment and rehabilitation of disorders that affect the spinal column, spinal cord, brain, nervous system and peripheral nerves. For more information on what neurosurgeons do, visit our public pages at : :www.NeurosurgeryToday.org : : :. Visitors to our Web site can find Member Counts under membership including demographic details.
dbRIP is a database of human Retrotransposon Insertion Polymorphisms (RIPs), in which RIPs are highly integrated into the human genome annotation data provided by UCSC Genome Browser. dbRIP contains all currently known Alu, L1, and SVA polymorphic insertion loci in the human genome. dbRIP can be used for Querying Retrotransposon Insertion Polymorphisms (RIPs), Identifying RIPs associated with particular genes, Genome-wide browsing of RIPs, Verifying newly identified retrotransposon insertions, and viewing a genome-wide view of all RIPs from one selected class or all classes (Genome plots).
The Center for Scientific Review (CSR) is the portal for NIH grant applications and their review for scientific merit. We receive all research grant applications sent to NIH and handle the review of more than 70% of those by organizing peer review groups (study sections) to evaluate research grant applications. Our mission is to see that NIH grant applications receive fair, independent, expert, and timely reviews — free from inappropriate influences — so NIH can fund the most promising research. The Center specifically: * Serves as the central receipt point for all research and training grant applications submitted to NIH. Also receives some of the applications submitted to other components of the U.S. Department of Health and Human Services (HHS) and refers them to these components; * Assigns all NIH applications to the appropriate NIH institutes or centers for consideration for funding and also to the scientific review groups within CSR or other institutes or centers for review; * Provides the scientific merit review of most research grant and fellowship applications submitted to NIH; * Provides staff support to the Office of the Director, NIH, in the formulation of grant and award policies and procedures; and * Assists other NIH components in providing information on the NIH peer review system and information about the research grant and fellowship application process and procedures to the scientific community, Congress, other NIH staff, and the general public.
heurAA - NGS multiplexed amplicon aligner
Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.
HIV-1, Human Protein Interaction Database
The Division of Acquired Immunodeficiency Syndrome (DAIDS) of the National Institute of Allergy and Infectious Diseases (NIAID) has initiated a project, in collaboration with Southern Research Institute and the National Center for Biotechnology Information (NCBI), designed to compile a comprehensive database of the described interactions between HIV-1 and cellular proteins. The goal of this project is to provide scientists in the field of HIV/AIDS research a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. This database has been designed to track the following information for each protein-protein interaction identified in the literature: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * National Library of Medicine (NLM) PubMed identification numbers (PMIDs) for all journal articles describing the interaction.
The Genome-Wide Detection of Differential Splicing Events with RNA-seq.
This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms.
Blog including established profound know-how and proprietary protocols to cover a broad range of applications.
Public research university in San Marcos, Texas. Established in 1899 as the Southwest Texas State Normal School, it opened in 1903 to 303 students.
gencat - Gene''s Comprehensive Annotation Tool
Software designed as an open platform that allows users to incorporate as many datasets (concepts) as possible to annotate the input gene list, as long as these datasets are prepared in bigwig, BED, BAM/SAM formats.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 31,2023.
In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions.
Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences.
CUDA accelerated spherical model forward solution for EEG/MEG
A CUDA C based toolkit which provides a GPU based implementation of the spherical model forward solution for the 306 channel Elekta Neuromag MEG system and the EEG. The 1-Sphere forward solution for the MEG and the 4-Sphere forward solution for the EEG is implemented in CUDA C and an accelerated solution is obtained using the NVIDIA GPU when the solution is calculated for a large number of dipoles (on the order of 15000 and above) and sensor location. Speedup by a factor of 22 and 32 is obtained for the EEG and MEG solution respectively when compared to the fastest CPU implementation available in the public domain. The complete source code and pre-compiled binaries are also made available via an open source license (GPL Version 3). A CUDA enabled NVIDIA graphics card is required to use the software.
The Oryza sativa database displays sequence information resulting from the research of the Centre de cooperation internationale en recherche agronomique pour le developpement. It also includes related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data, etc.). Genome Browser (Gbrowse), a Web-based application for displaying genomic annotations and other features, is the core of our database. The reference annotation layer consists in the 12 rice pseudomolecules released by the TIGR (Version 5.0, January 2007). All the data are superposed as annotations layers and positioned with respect to these pseudomolecules. We developed a set of tools around GBrowse to retrieve as exhaustively as possible information related to queries with several starting points. These tools allow a molecular geneticist to readily find insertion lines (T-DNA, Tos17, Ds) in genes of interest and to retrieve all the associated annotations related to these sequences.
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 13, 2016. A searchable biotechnology database e-books with information on more than 9000 monoclonal antibodies. This database has antibodies produced for the diagnosis and therapy of human cancer, Alzheimer's disease, AIDS, and other diseases as well as for biomarker and proteomics research. Information such as antibody name, species, type, characteristics, antigen characteristics, and developer or distributor of antibody as well as mentions in journals, patents, abstracts and reports up until 2012 are included.
EMS is a freely available suite of Matlab functions and subroutines (with some externally compiled C routines) for fully-automated multi-spectral classification of brain tissues in Magnetic Resonance (MR) images. It uses a model based approach (including an explicit model for MR bias fields) in which all the model parameters are automatically estimated for each individual scan. This enables it to process large amounts of data from normal subjects and subjects suffering from Multiple Sclerosis without need for user intervention or preceeding manual training phase.
BEADS: Bias Elimination Algorithm for Deep Sequencing
Bias Elimination Algorithm for Deep Sequencing
Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.
Death Domain database: A manually curated database of protein-protein interactions for Death Domain Superfamily
A manually curated database of protein-protein interactions for Death Domain Superfamily. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The DD superfamily currently comprises four subfamilies: * Death domain (DD) subfamily * Death effector domain (DED) subfamily * Caspase recruitment domain (CARD) subfamily * Pyrin domain (PYD) subfamily
Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.
Cube-DB: Detection of Functional Divergence in Human Protein Families
Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera).
Genomic Analysis Software designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC).
Software that determines genotypes for microsatellite repeats in high-throughput sequencing data.
The purpose of this document is to give the exact definitions of the MORGAM cohorts and to describe their basic characteristics and data collection procedures, such as the follow-up procedures, the disease end-points recorded and diagnostic procedures. The definition and selection criteria for MORGAM cohort are described in section Definition and selection of cohorts of the MORGAM Manual. For convention, each cohort is assigned appropriate name and code number which is given in Table 1. The baseline characteristics of the MORGAM Cohorts are summarized in Table 2. An overall summary of MORGAM Cohorts along with the objectives of the Project has been published elsewhere [1]. Sponsor. The research was supported by the GenomEUtwin Project grant from the European Commission under the programme `Quality of Life and Management of the Living Resources'' of 5th Framework Programme (no. QLG2-CT-2002-01254) and by the Academy of Finland via its grant number 53646.
Multiparameter Intelligent Monitoring in Intensive Care
MIMIC II (Multiparameter Intelligent Monitoring in Intensive Care) Database contains comprehensive clinical data from tens of thousands of Intensive Care Unit (ICU) patients. Data were collected between 2001 and 2008 from a variety of ICUs (medical, surgical, coronary care, and neonatal) in a single tertiary teaching hospital. The database contains clinical data from bedside workstations as well as hospital archives. The database also includes thousands of records of continuous high-resolution physiologic waveforms and minute-by-minute numeric time series (trends) of physiologic measurements.
ZFIN Protocol Wiki is where zebrafish researchers can share experimental protocols and tips with the rest of the research community. Protocols are organized into sections corresponding to the chapters of The Zebrafish Book, 5th edition (4th edition on-line). Feel free to add new protocols to the appropriate section or add comments to any existing protocol. Sections * General Methods for Zebrafish Care * Breeding * Embryonic and Larval Culture * Imaging * Cellular Methods * Dissociated Cell Culture * Genetic Methods * Antisense Methods * Histological Methods * in situ Hybridization Techniques * Mapping * Transgenesis * Gene Cloning * DNA Analysis * RNA Analysis * Protein Analysis * Microarray * Recipes
QccPack provides an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack has been written to provide very flexible and general implementations of procedures commonly used in coding and compression applications. QccPack is intended for use in the development of prototypes of coding and compression systems, and in academic research. QccPack includes routines for entropy coding, scalar quantization, vector quantization, and wavelet transforms. Additonally, an open-source implementation of SPIHT is available as an optional module. QccPack provides an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack has been written to provide very flexible and general implementations of procedures commonly used in coding and compression applications. The essential component of the QccPack collection is a library (a static library, libQccPack.a, and, if supported on your system, a dynamic library, libQccPack.so) of procedures implementing a large variety of compression and coding algorithms. Application programs may make use of the QccPack library routines by linking the application against the library during compilation. Each library function is very general in its implementation so to be useful in a large variety of applications. Additionally, much of the functionality of the library routines has been provided in the form of stand-alone executable programs. Probably the prime importance of these utility programs is that they provide examples of how to interface with many of the QccPack library routines. The utility programs could also be called from scripts to simulate the operation of complex coding and compression systems before implementing all the system functionality into one stand-alone program. Currently, QccPack consists of over 55,000 lines of C code implementing over 500 library routines and over 50 stand-alone utility programs. The major functionalities currently implemented include: * Entropy coding o Arithmetic coding including multiple-context adaptive and nonadaptive models o Huffman coding o Golomb and adaptive Golomb coding * Scalar Quantization (SQ) o Uniform SQ o Dead-zone SQ o -law and A-law SQ o Lloyd algorithm for optimal SQ design * Vector quantization (VQ) o Generalized Lloyd algorithm (GLA) for VQ-codebook design o Full-search VQ encoding and decoding o Entropy-constrained-VQ (ECVQ) training, encoding, and decoding o Multistage VQ (MSVQ) (also called residual VQ (RVQ)) training, encoding, and decoding * Adaptive vector quantization (AVQ) o The generalized-threshold-replenishment (GTR) algorithm o The Paul algorithm o Gersho-Yano algorithm o Coding of side information * Wavelet transforms, wavelet-based subband coding o Discrete wavelet transform (DWT) using first-generation filter banks and popular orthonormal and biorthogonal wavelets o Lifting implementations of DWT for popular wavelets o Two-dimensional DWT in the form of dyadic subband pyramids o Three-dimensional DWT in the form of dyadic subband pyramids as well as a packet transform o Shape-adaptive DWT (SA-DWT) for 1D and 2D signals o Redundant DWT (RDWT), aka, the algorithme trous o The SR algorithm for wavelet-based image coding o The SFQ algorithm for wavelet-based image coding o The WDR algorithm for wavelet-based image coding o The 3D-WDR algorithm for wavelet-based image-cube coding o The tarp-filter algorithm for wavelet-based image coding o The 3D-tarp algorithm for wavelet-based image-cube coding o The TCE algorithm for wavelet-based image coding o The BISK algorithm for wavelet-based shape-adaptive image coding o The 3D-BISK algorithm for wavelet-based image-cube coding * Error-correcting codes o Field arithmetic, including Gaussian-elimination matrix inversion o Reed-Solomon encoding and decoding o CRC codes o Trellis codes o Hard and soft Viterbi decoding * Image processing o Routines for reading and writing gray and color still images and sequences of images (via PGM and PPM formats) o Routines for reading and writing 3D image-cube volumes o Image and image-sequence deinterlacing o Image differential-pulse-code modulation (DPCM) o Color-space conversions: RGB, YUV, CIE XYZ, CIE UCS, CIE modified UCS o Block-based DCT and inverse DCT * Video coding o The spatial-block algorithm for image-sequence coding o The RDWT-block algorithm for image-sequence coding o The RWMH algorithm for image-sequence coding o Block-based motion estimation and motion compensation o Motion estimation and motion compensation using regular triangle meshes o Encoding and decoding of motion-vector fields * General routines o Vector math (up/down sampling, sorting, dot product, addition/subtraction, etc.) o Matrix math (addition/subtraction, vector-matrix multiplication, etc.) o Linked lists and associated operations o Entropy estimation (first and second order) o General file input and output, including automatic detection and reading/writing of gzip-compressed files o Character bit-packing for binary bitstream input/output o Memory-based fifo for binary bitstreams o Conversion between various file formats used by library routines o Error-message tracking, formatting, and output o Automatic command-line parameter parsing In addition to the standard functionalities listed above, there exist optional modules that can be added to the QccPack library. Usually, these modules are available under licensing terms different from the GPL/LGPL licenses of QccPack and may contain patented algorithms; refer to the documentation included with each module for specific details. These modules are downloaded separately from QccPack and are not enabled by default during the building of QccPack. The currently available optional modules and their functionalities are: * QccPackSPIHT o The Set Partitioning in Hierarchical Trees (SPIHT) algorithm for wavelet-based image coding * QccPackSPECK o The Set-Partitioning Embedded Block (SPECK) algorithm for wavelet-based image coding Abstract: We describe the QccPack software package, an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack is being written to expedite data-compression research and development by providing general and reliable implementations of common compression techniques. Functionality of the current release includes entropy coding, scalar quantization, vector quantization, adaptive vector quantization, wavelet transforms and subband coding, error-correcting codes, image-processing support, and general vector-math, matrix-math, file-I/O, and error-message routines. All QccPack functionality is accessible via library calls; additionally, many utility programs provide command-line access. The QccPack software package, downloadable free of charge from the QccPack Web page, is published under the terms of the GNU General Public License and the GNU Library General Public License which guarantee source-code access and as well as allow redistribution and modification. Additionally, there exist optional modules that implement certain patented algorithms. These modules are downloadable separately and are typically issued under licenses that permit only non-commercial use. This material is based upon work supported in part by the National Science Foundation under Grant No. INT-9600260.
CEM: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads
Software tools for the analysis of enrichment-based epigenomic data.
SeqSite: ChIP-Seq Binding Site Identification
Software for detecting transcription factor binding sites from ChIP-seq data.
A tool for analysis of Magnetic Resonance Spectroscopy (MRS) data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images.
A stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies.
The EIB provides assessment tests for substance disorder related clinical instruments that are freely available. Details regarding copyright and/or possible use restrictions are specified for each instrument. Instruments are generally classed according to the intervention field they are designed to be used in (treatment, prevention, or harm reduction), though some instruments may be usable in more than one field.
Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.
An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa
Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment. Additional information is available in the NCBI Bookshelf Short Courses Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils) and the NCBI PowerScripting course. User Requirements: Please read for important information on scripting NCBI servers. EInfo: Provides field index term counts, last update, and available links for each database. ESearch: Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user''s environment. EPost: Posts a file containing a list of primary IDs for future use in the user''s environment to use with subsequent search strategies. ESummary: Retrieves document summaries from a list of primary IDs or from the user''s environment. EFetch: Retrieves records in the requested format from a list of one or more primary IDs or from the user''s environment. ELink: Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs. EGQuery: Provides Entrez database counts in XML for a single search using Global Query. ESpell: Retrieves spelling suggestions. SOAP Interface for Entrez Utilities PMID to PMC ID Converter Entrez DTDs Demonstration Program Announcement Mailing List Leasing Data from the National Library of Medicine Help Desk User Requirements Do not overload NCBI''s systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following: Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests. Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov, not the standard NCBI Web address. Make no more than 3 requests every 1 second. Use the URL parameter email, and tool for distributed software, so that we can track your project and contact you if there is a problem. NCBI''s Disclaimer and Copyright notice must be evident to users of your service. NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may. NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel.
A software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An antibody information database where antibodies are organized by the target protein UniProt id.
Located in Baltimore, MD., Kennedy Krieger Institute is an internationally recognized institution dedicated to improving the lives of children and adolescents with pediatric developmental disabilities and disorders of the brain, spinal cord and musculoskeletal system, through patient care, special education, research, and professional training. Patient Care--Specialists from various fields and disciplines work together to evaluate, diagnose, and create individualized treatment plans to guide patients and families through all stages of care. Research and Professional Training--Our innovative research and professional training programs are leading the way in the understanding, prevention, and treatment of a wide range of developmental disabilities. Special Education--We offer a number of school-based, hospital-based, and recreational programs designed to unlock the promise inside our students through innovative and customized educational approaches. Community--We are committed to helping people with developmental disabilities achieve their potential and enjoy success in community life by providing access to resources, services, and model programs.
A tool for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA.
Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the G&eacute;noplante rice insertion line library. To display the sequence information (Flanking Sequence Tags) resulting from the molecular characterization of the mutagen insertion sites in the collection, Oryza Tag Line is linked to OryGenesDB a GGB-derived interface or FLAGDB++ a Java based interface. Aside from generic data ( production record and seed stock ) Oryza Tag Line includes textual and pictorial information resulting from the following observations: (i.) GUS/GFP expression assays conducted on the primary transformants (T0) and/or T1 progenies (ii.) morpho-physiological alterations detected during the growth of the T1 progenies either in phytotron -up to the 5-6 leaf stage- or under agronomical conditions in the field (collaboration with CIAT, Cali, Colombia).
R package intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene.
A database of plant protein kinases and phosphatases as well as genomic information for these enzymes. Because protein kinases and phosphatases control so many processes in plants, and occur in networks that unite different cellular processes, a genome wide approach is needed to make significant advances in discovering the roles of these enzymes in the regulation of plant function.
An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.
Long-term Recordings of Gait Dynamics: Unconstrained and Metronomic Walking
Stride interval fluctuations were studied in ten young, healthy men. Participants had no history of any neuromuscular, respiratory or cardiovascular disorders, and were taking no medications. Mean age was 21.7 years (range: 18-29 years). Height was 1.77 ���� 0.08 meters (mean ���� S.D.) and weight was 71.8 ���� 10.7 kg. All subjects provided informed written consent. Subjects walked continuously on level ground around an obstacle free, long (either 225 or 400 meters), approximately oval path and the stride interval was measured using ultra-thin, force sensitive switches taped inside one shoe. For more details, please see the accompanying publication. Each subject was given an arbitrary id (si01, si02, ... si10). For each subject, there are six data files: normal (.norm), slow (.slow) and fast (.fast) walking for 1 hour each as well as walking in time to a metronome at normal (.metnrm), slow (.metslw) and fast (.metfst) paces.
Japanese Research Center of Genetic Resources NARO Genebank project
Japanese Research Center of Genetic Resources National Agriculture and Food Research Organization Genebank project
Research Center of Genetic Resources is central coordinating institute in Japan for conservation of plants, microorganisms, and animals related to agriculture. NARO Genebank coordinates this activity in collaboration with network of institutes throughout Japan. Conducts exploration, collection, characterization, preservation, and distribution service of microorganism genetic resources, animal genetic resources raised in Japan, and plant genetic resources.
Kennedy Krieger Institute: Diagnoses/Disorders
Kennedy Krieger Institute is an institution dedicated to improving the lives of children and adolescents with pediatric developmental disabilities through patient care, special education, research, and professional training. Kennedy Kriegers clinical programs offer an interdisciplinary approach in treatment tailored to the individual needs of each child. Services include over 40 outpatient clinics; neurobehavioral, rehabilitation, and pediatric feeding disorders inpatient units; plus several home and community programs providing services to assist families. At Kennedy Krieger, there is no shortage of clinical programs to meet the specialized needs of children and adolescents with developmental disabilities. More than 35 different outpatient clinics, three inpatient units, several home and community programs and clinical laboratories all address the specific conditions of children with a wide range of disorders. Kennedy Krieger is recognized for its range of services in areas including autism, cerebral palsy, spina bifida, neurorehabilitation and feeding disorders. Kennedy Krieger school, is a nationally recognized Blue Ribbon School of Excellence, and is a leader in providing model programs of innovative education for children, adolescents and young adults with a wide range of learning, emotional, physical, neurological, and developmental disabilities. Faculty at Kennedy Krieger are among some of the worlds leading experts in this field and are attuned to the special needs of this population. These faculty have made crucial medical discoveries leading to innovative treatments and have improved the lives of individuals with disabilities. In addition to providing evaluation, rehabilitation, educational services and cutting edge research on behalf of children with brain related disabilities, Kennedy Krieger also provides professional training by renowned experts dedicated to increasing the number of qualified specialists in the United States and abroad. Children treated at Kennedy Krieger are seen by a variety of health care professionals working together in one or more of the Institutes clinical disciplines or departments. These highly trained professionals work directly with the Institutes medical staff to provide coordinated, interdisciplinary care tailored to the special needs of each child. This interdisciplinary approach puts Kennedy Krieger at the forefront in providing patient care for individuals with multiple developmental disabilities. Additionally, Kennedy Krieger Institutes Department of Special Education includes a number of programs that offer service to children with disabilities in a variety of settings. Kennedy Krieger School programs offer special education and related services to students aged 3-21 in three day-school settings and in partnership settings within public schools. For your convenience, a list of diagnoses/disorders treated at Kennedy Krieger Institute has been compiled to provide helpful related information for each diagnosis/disorder and include definitions, symptoms, treatment programs available at Kennedy Krieger, research being conducted at Kennedy Krieger, press releases, Potential articles and links to other helpful additional resources and websites outside the Institute.
Software program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results. SPREG implements valid and efficient statistical methods. (entry from Genetic Analysis Software)
A population genetics computer program that conducts several genetic analyses on multilocus information in a user-friendly environment. Primary functions carried out by MOLKIN are the computation of the between individuals (and populations) molecular coancestry coefficients, the Kinship distance at individual and population levels. Additionally, users can compute with MOLKIN a set of among populations, genetic distances and F statistics from multilocus information. The program will help researchers or those responsible for population management to assess genetic variability and population structure at reduced costs with respect to dataset preparation (entry from Genetic Analysis Software)
The KNOTTIN database provides standardized data on the knottin structural family (also referred to as the Inhibitor Cystine Knot (ICK) motif/family/fold). Knottins are intriguing miniproteins with strong potential in drug design. This knot is achieved when one disulfide bridge crosses the macrocycle formed by the two other disulfides and the interconnecting backbone.
The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature. The data is from published scientific papers. Study data is recorded in the context of official human gene nomenclature with additional molecular reference numbers and links. It is gene centered. That is, each record is a record of a gene or marker. If a study investigated 6 genes for a particular disorder, there will be 6 records. Anyone may view this database and anyone may submit records. You do not have to be an author on the original study to submit a record. All submitted records will be reviewed before inclusion in the archive. Both genetic and environmental factors contribute to human diseases. Most common diseases are influenced by a large number of genetic and environmental factors, most of which individually have only a modest effect on the disease. Though genetic contributions are relatively well characterized for some monogenetic diseases, there has been no effort at curating the extensive list of environmental etiological factors. From a comprehensive search of the MeSH annotation of MEDLINE articles, they identified 3,342 environmental etiological factors associated with 3,159 diseases. They also identified 1,100 genes associated with 1,034 complex diseases from the NIH Genetic Association Database (GAD), a database of genetic association studies. 863 diseases have both genetic and environmental etiological factors available. Integrating genetic and environmental factors results in the etiome, which they define as the comprehensive compendium of disease etiology.
H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups. This database is produced by the Genome Information Integration Project (2005-) based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs.
A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome.
A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A small tool for simulating sequence reads from a reference genome.
Research-grade, CRT-replacement LCD display system for vision science and psychophysics. It combines a 22.5″ 1920×1200 industrial LCD (wide 176°/176° viewing angles) with a custom panel/video controller engineered for deterministic stimulus timing and synchronized acquisition. The display supports 12-bit intensity resolution per RGB channel via custom video modes. It uses a scanning RGB LED backlight to improve temporal precision (e.g., crisp frame transitions and reduced motion artifacts) while bypassing consumer “enhancement” processing to keep output predictable for experiments. VIEWPixx also integrates microsecond-synchronized peripherals commonly needed in timing-sensitive paradigms—24-channel TTL I/O (triggers), stereo audio I/O, analog I/O, and a button-box interface—implemented on the same board as the video pipeline for tight hardware-to-video synchronization.
Ranking Tables of NIH Funding to US Medical Schools in 2010
Excel files available for download of ranking tables of NIH Funding to US Medical Schools in 2010, school and Principal Investigator (PI) rankings by Medical School Department, direct plus indirect costs (excluding both R & D contracts and American Recovery and Reinvestment Act (ARRA) Awards), etc. Categories under the Basic Science Department and Clinical Science Department are available as well as the rank of each School of Medicine from 2001-2010. The data in the 2010 Award files was obtained from the Research Portfolio Online Reporting Tool (RePORT) from the National Institutes of Health at http://report.nih.gov/award/trends/AggregateData.cfm. The Award Data correspond to the US Government fiscal year. Awards for 2010 correspond to those granted from 1 October 2009-30 September 2010. There is considerable variation on how universities credit awards and how the NIH deals with these variations.
A MATLAB toolbox which uses three dimensional probabilistic cytoarchitechtonic maps to correlate microscopic, anatomic and functional data of the cerebral cortex. Correlating the activation foci identified in functional imaging studies of the human brain with structural (e.g., cytoarchitectonic) information on the activated areas is a major methodological challenge for neuroscience research. We here present a new approach to make use of three-dimensional probabilistic cytoarchitectonic maps, as obtained from the analysis of human post-mortem brains, for correlating microscopical, anatomical and functional imaging data of the cerebral cortex. We introduce a new, MATLAB based toolbox for the SPM2 software package which enables the integration of probabilistic cytoarchitectonic maps and results of functional imaging studies. The toolbox includes the functionality for the construction of summary maps combining probability of several cortical areas by finding the most probable assignment of each voxel to one of these areas. Its main feature is to provide several measures defining the degree of correspondence between architectonic areas and functional foci. The software, together with the presently available probability maps, is available as open source software to the neuroimaging community. This new toolbox provides an easy-to-use tool for the integrated analysis of functional and anatomical data in a common reference space.
GLOM MAP is a toolbox written for the MATLAB development enviroment
:GLOM MAP was written for MATLAB, it works equally as well on the PC as on the MAC. GLOM MAP consists of two components: 1. OBS can be used to map the location of glomeruli in transverse sections of the olfactory bulb. 2. GDB can be used to transform the OBS data and to analyze the collected glomerular activity data. This data can be scored and mapped in the radial and anterio-posterior dimensions as discussed in Salcedo et al, 2005. :
GeneSigDB - Curated Gene Signatures Database
Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service.
Informatics for Integrating Biology and the Bedside
Informatics for Integrating Biology and the Bedside Research Data Warehouse
A data warehouse that integrates information on patients from multiple sources and consists of patient information from all the visits to Cincinnati Children' '''s between 2003 and 2007. This information includes demographics (age, gender, race), diagnoses (ICD-9), procedures, medications and lab results. They have included extracts from Epic, DocSite, and the new Cerner laboratory system and will eventually load public data sources, data from the different divisions or research cores (such as images or genetic data), as well as the research databases from individual groups or investigators. This information is aggregated, cleaned and de-identified. Once this process is complete, it is presented to the user, who will then be able to query the data. The warehouse is best suited for tasks like cohort identification, hypothesis generation and retrospective data analysis. Automated software tools will facilitate some of these functions, while others will require more of a manual process. The initial software tools will be focused around cohort identification. They have developed a set of web-based tools that allow the user to query the warehouse after logging in. The only people able to see your data are those to whom you grant authorization. If the information can be provided to the general research community, they will add it to the warehouse. If it cannot, they will mark it so that only you (or others in your group with proper approval) can access it.
Loyola University Medical Center / Hines VA Brain Bank
Loyola University Medical Center/Hines VA Brain Bank
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. A medical center with a neuropathology research program focused on the normal and abnormal aging process of the central nervous system and a funding source for research. The center serves as a collection site for brains in order to study normal aging and neurodegenerative diseases like Alzheimer's.
PlantNATsDB - Plant Natural Antisense Transcripts DataBase
Plant Natural Antisense Transcripts DataBase
Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ' '''Gene Set Analysis' ''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs.
The Trinity Biobank was established in 2005 to serve the needs of researchers in the area of genetic epidemiology, population genetics and pharmacogenomics. Its services are available to researchers not only in Trinity College but to other institutions at home and abroad. We provide an automated DNA extraction service purifying large volumes blood (up to 10mL whole blood) and tissue DNA for archival and other purposes. In addition it makes available purified DNA and associated GWAS data from 2000 healthy donors for research use. A key requirement for reliable downstream use of DNA is purity and strand size. The quality of DNA in blood and tissue deteriorates upon storage without purification even at -80 degrees C. We ensure rapid turnaround of biological samples through automated extraction using the Qiagen Autopure system based on optimized ''salting out'' chemistry. The purified DNA sample may then be stored safely at -20 degrees C without deterioration thus freeing up valuable -80 degree C freezer space and the associated capital and maintenance cost as well as security and lab space provision. Automated DNA extraction is particularly suitable for high-throughput sample processing called for in epidemiological studies or simply for clearing sample inventory backlogs. The Trinity Biobank distributes control DNA to researchers as part of its remit to enhance the level of research activity and to synergize molecular medicine research nationally and internationally. The buffy coat collection has been made possible with the cooperation of the Irish Blood Transfusion Service (IBTS). An important requirement to access the collection is that the use of the samples relates only to ethically-approved research and to specifically-nominated research projects. The DNA collection consists of high quality human genomic DNA. Each of the available 2,000 samples is from a single individual and each sample comes with the age and gender data of the donor. The buffy coat sample is derived from the total white cell compliment (50mL buffy coat) of a blood donation (c 400mL). We will endeavor to fulfill samples number requests based on age and gender as best as possible. This collection has also been genotyped using the Affymetrix Genome-Wide Human SNP Array 6.0, featuring 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation (CNV). The DNA comes available as a 100ng/uL in 100uL of TE Buffer, ie in 10ug amounts in a separate screw-cap ampoule. The ampoules are shipped in 100-tube boxes (Sarstedt). Corresponding plasma (ACD) is also available on request. Genotype data is supplied in PLINK binary PED files format (http://pngu.mgh.harvard.edu/~purcell/plink/ ).
Kyushu University Definitive Haplotype Database
D-HaploDB genome-wide definitive haplotypes, determined using a collection of 100 Japanese complete hydatidiform moles (CHMs), each carrying a genome derived from a single sperm. The haplotypes incorporate 281 k (D-Haplo Phase I: D1), 581k (D-Haplo Phase II: D2), or 1M (D-Haplo Phase III: D3) SNPs, genotyped with high throughput array-based oligonucleotide hybridization techniques. The Definitive Haplotype Browser can be used to view various information, such as SNP alleles, haplotype blocks, LD-bins and extended shared haplotypes (ESHs) in our study.
An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework.
GpetView is light-weight image viewer based on Gtk+ library. The supported image format is ANALYZE(TM) format (Mayo Foundation ). GpetView can run on Unix-systems, such as Linux, Solaris, IRIX, Mac OS-X etc. From Version 2.0, GpetView can also run on Win32 system, if you have installed Glib and Gtk+(2.x). Glib andGtk+ can be found at http://www.gtk.org. For Windows users, you can find Gtk+ libraries at http://gladewin32.sourceforge.net/modules/news/ GpetView has the following features: * very light-weight * view images as transverse, coronal, or sagittal * change color-map (support Analyze lkup file) * zoom images * ROI (Region-Of-Interest) with shapes of circle, ellipse, rectangle, polygon and automatic edge detection * Image histogram and profile Sponsors: This resource is supported by Osaka University. Keywords: Image, Viewer, Software, Transverse, Coronal, Sagittal, Map, Histogram,
A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
Table providing information about integral membrane proteins whose crystallographic, or sometimes NMR, structures have been determined to a resolution sufficient to identify TM helices of helix-bundle membrane proteins (typically 4 - 4.5 angstroms). It is based upon Preusch et al. (1998) as revised by White & Wimley (1999). Reference is made to all of the protein types whose structures have been determined. They have attempted to make the database as inclusive as possible.
PRESTO: Genetic Association Analysis Software
Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data.
Effect of Deep Brain Stimulation on Parkinsonian Tremor
Effect of Deep Brain Stimulation on Parkinsonian Tremor: The recordings of this database are of rest tremor velocity in the index finger of 16 subjects with Parkinson''s disease (PD) who receive chronic high frequency electrical deep brain stimulation (DBS) either uni- or bi-laterally within one of three targets: Vim = the ventro-intermediate nucleus of the thalamus (n=3),GPi = the internal Globus pallidus (n=7), or STN = the subthalamic nucleus (n=6).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software)
A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.
MACS - Model-based Analysis for ChIP-Seq
Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
A free web-based application for the processing of high-throughput RNA-Seq data from next generation sequencing (NGS) platforms, such as Genome Analyzer of Illumina Inc. (Solexa) and SOLiD of Applied Biosystems (SOLiD).
Diogenes is a pan-European Programme targeting the obesity problem from a dietary perspective: seeking new insights and new routes to prevention. An Integrated Project of the EU Sixth Framework Programme for Research and Technological Development (2005-2009). A new methodology has been developed for consistent assignment of GI values to foods across the five European databases used in the Diogenes intervention study. GI values have been assigned according to five decreasing levels of confidence: (1) Measured values for specific foods; (2) Published values from published sources; (3) Equivalent values where published values for similar foods existed; (4) Estimated values three values selected representing low/medium/high GI ranges; (5) Nominal values assigned as 70, where no other value could be assigned with sufficient confidence. Sponsor. A a r h u s K a r l s h a m n D e n m a r k A / S Products: Vegetable Oils (Maize and Rapeseed) click here for the link to the website of AarhusKarlshamn Denmark B a r i l l a Products: Pasta click here for the link to the website of Barilla B e a u v a i s Products: Canned fish products, jam, soups & convenience foods click here for the link to the website of Beauvais C a m p i n a I n s t i t u t e At the Campina Institute dairy products and science come together. The Campina brands include among others: Optimel/ Optiwel, Vifit, Milner, Valess Click here for the link to the website of Campina Institute C o c a - C o l a S e r v i c e s S . A . Products: beverages click here for the link to the website of Coca-Cola Services S.A. D a l o o n Products: Spring rolls and other convenience foods click here for the link to the website of Daloon D a n g S / A Products: egg products click here for the link to the website of Dang A/S D a n i s c o Products: Sugar (different types) click here for the link to the website of Danisco D a n i s h D a i r y B o a r d Products: Dairy products (milk, yoghurt, cheese) click here for the link to the website of the Danish Dairy Board D a n s k e S l a g t e r i e r Products: Pig Meat Products (various types) click here for the link to the website of Danske Slagterier D r . O e t k e r Products: Ready meals click here for the link to the website of Dr. Oetker E u r o g r a n A / S Products: Instant chocolate, cappuccino, soup and mashed poptatoes click here for the link to the website of Eurogran A/S F r i g o d a n Products: Frozen vegetables click here for the link to the website of Frigodan F r i s k o Products: Ice cream click here for the link to the website of Frisko G a m b a F o o d Products: Frozen fish (different types of European and Asian origin) G i l d e N o r g e B A Products: meat click here for the link to the website of Gilde Norge BA H a t t i n g Products: Bread products (different types) click here for the link to the website of Hatting H e i n z Products: ketchup and a broad range of products under HONIG, Konininklijke de Ruijter, VENZ, Carvan Cevitan, Roosvicee click here for the link to the website of Heinz H j e r t i n g L a k s Products: salmon products click here for the link to the website of Hjerting Laks K e l l o g g '' s D e n m a r k Products: different types of Breakfast Cereals Click here for the link to the website of Kellogg''s Denmark K e l l o g g '' s E u r o p e Products: Ready-To-Eat Cereals and Cereal Bars Click here for the link to the website of Kellogg''s K d b r a n c h e n s F l l e s r d Products: meat: beaf and veal click here for the link to the website of Kdbranchens Fllesrd K r a f t Products: chocolate, Philadelphia cream cheese, pasta, Estrella chips & nuts, mayonaise, salad dressings click here for the link to the website of Kraft L a n t m n n e n M i l l s A / S Products: various grains and flour L U , G e n e r a l B i s c u i t s N e d e r l a n d B . V . Products: biscuits click here for the link to the website of LU L y k k e b e r g A / S Products: Fish (marinated herring) click here for the link to the website of Lykkeberg A/S M a s t e r f o o d s Products: Rice and confectionery click here for the different websites of Masterfoods: Uncle Bens, Mars, Twix, Snickers, M&M''s, Masterfoods N u t r i t i o n e t S a n t / M o d i f a s t Products: Modifast (Low Calorie Diet) click here for the link to the website of Nutrition et Sant click here for the link to the website of Modifast P a r t n e r s h i p f o r D a n i s h P o t a t o e s Products: potatoes (different varieties) click here for the link to the website of the Partnership for Danish Potatoes P a s t a l i f e Products: pasta (with high protein content) click here for the link to the website of Pastalife R a h b e k Products: Frozen, ready-made fish dishes click here for the link to the website of Rahbek R i e b e r & S n D a n m a r k A / S Products: mustard, ketchup, mayonnaise, sanwich filling, spreads and other dressings click on the following links for the different websites of Rieber and Sn Danmark A/S: Rieberson, Bahncke, K-Salat R o y a l G r e e n l a n d A / S Products: cold-water prawns click here for the link to the website of Royal Greenlands A/S S c h u l s t a d Products: Rye bread and wheat bread, including high- and low GI varieties click here for the link to the website of Schulstad S n d e r j y d s k K l Products: Frozen kale, spinach and cabbage. click here for the link to the website of Snderjydsk Kl S u i k e r U n i e Products: different types of sugar click here for the link to the website of Suiker Unie T u l i p F o o d C o m p a n y Products: Meat products (cold cuts, cooked meat, bacon, meat balls, ready-meals, soups etc.) Click here for the link to the website of Tulip Food Company U n i l e v e r Products: a broad range of products under Becel, Bertolli, Calv, Knorr, Iglo, Mora, Conimex, Unox click here for the link to the website of Unilever W a s a b r d A / S Products: Crisp bread click on the following links for the different websites of Wasabrd A/S: Wasa Denmark or Wasa International
SeqTRACS: LIMS for sequencing core facilities
Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility.
First of all, and most importantly, PC and Mac versions have been resynchronized. Support for direct login modelling submissions and result retrieval to/from the SwissModel Workspace Enhanced Import Menu Enhanced user interface with taxonomy support, and new sequence alignment features. New 3D Motif Searching feature Easy access to external user defined scripts directly from the interface Revised Help files accessible from the interface Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modeling tools are integrated and command files for popular energy minimization packages can be generated. Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images.
Annotation and Classification in Enzymes
MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a collaborative project on enzyme reaction mechanisms. MACiE currently contains 223 fully annotated enzyme reaction mechanisms, which comprise 218 EC numbers (161 EC sub-subclasses) and 310 distinct CATH codes. It is a joint effortbetween the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute.
Apnea-ECG Database has been assembled for the PhysioNet/Computers in Cardiology Challenge 2000. It consists of 70 ECG recordings, each typically 8 hours long, with accompanying sleep apnea annotations obtained from study of simultaneously recorded respiration signals, which are included for 8 of the recordings.
Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data.
Unique DLP LED projector which has been designed to be the most flexible display solution for vision research and neuroscience research. The PROPixx features a native resolution of 1920 x 1080, and can be driven with refresh rate up to 500Hz with deterministic timing. The PROPixx uses high brightness LEDs as a light source, giving a wide colour gamut and much longer lifetime than halogen light sources. It features high-bit depth, up to 12-bit per color for high-frequency full colour stimulation. For stereo vision applications, our high-speed ferro-electric circular polarizer can project stereoscopic stimuli with the use of passive glasses at up to 400Hz. In addition the PROPixx includes an array of peripherals which often need to be synchronized to video during an experiment, and with perfect microsecond precision.
Supplies chemicals and research probes that are either unavailable, difficult to obtain, or very expensive to buy to researchers. In addition, this program also provides analytical services for the analysis of researchers experimental samples. The NIDA Drug Supply Program is administered by the Chemistry & Physiological Systems Research Branch.
Software package for simultaneous genotype calling and haplotype phasing for unrelated individuals. BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes. BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes. BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation. (entry from Genetic Analysis Software)
University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA
Raymond & Ruth Perelman School of Medicine
University of Pennsylvania Perelman School of Medicine
University of Pennsylvania School of Medicine
Medical school of the University of Pennsylvania. It is located in the University City section of Philadelphia.
Software application that implements a novel variable selection method for GWAS data and is able to handle more than half million SNPs. Extensive simulation studies and real data analysis show that this method enjoys high power and low false discovery rate compared to existing variable selection methods. The variables selected by GWASelect can be readily placed into a logistic regression model for disease prediction. The current release is designed for binary outcome under the additive mode of inheritance. (entry from Genetic Analysis Software)
HEterogeneity and GEnome Search Meta Analysis
Software application for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels. (entry from Genetic Analysis Software)
Human Transcriptome Database for Alternative Splicing
H-DBAS - Human-transcriptome DataBase for Alternative Splicing
A specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis. It contains: * Genome-wide representative alternative splicing variants (RASVs) identified from following datasets * H-Inv full-length cDNAs (resource summary): H-Invitational cDNA dataset * H-Inv all transcripts (resource summary): Published human mRNA dataset * Mouse full-length cDNAs (resource summary): Mouse cDNA dataset * RASVs affecting protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain * Conserved RASVs compared with mouse genome and the full-length cDNAs (H-Inv full-length cDNAs only)
A scalable software pipeline for whole genome resequencing analysis.
Software application that is an interactive graphic interface to visualise results from whole genome genotyping. It allows one to visualise single subjects and groups of subjects, and provides a direct connection with the UCSC Genome Browser. (entry from Genetic Analysis Software)
An authoritative and comprehensive list of names of marine organisms, including information on synonymy. While highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature. The content of WoRMS is controlled by taxonomic experts, not by database managers. WoRMS has an editorial management system where each taxonomic group is represented by an expert who has the authority over the content, and is responsible for controlling the quality of the information. Each of these main taxonomic editors can invite several specialists of smaller groups within their area of responsibility to join them. This register of marine species grew out of the European Register of Marine Species (ERMS), and its combination with several other species registers maintained at the Flanders Marine Institute (VLIZ). Rather than building separate registers for all projects, and to make sure taxonomy used in these different projects is consistent, VLIZ developed a consolidated database called ''Aphia''. A list of marine species registers included in Aphia is available below. MarineSpecies.org is the web interface for this database. The WoRMS is an idea that is being developed, and will combine information from Aphia with other authoritative marine species lists which are maintained by others (e.g. AlgaeBase, FishBase, Hexacorallia, NeMys). Resources to build MarineSpecies.org and Aphia were provided mainly by the EU Network of Excellence ''Marine Biodiversity and Ecosystem Functioning'' (MarBEF), and also by the EU funded Species 2000 Europe and ERMS projects. Intellectual property rights of the European part of the register is managed through the Society for the Management of Electronic Biodiversity Data (SMEBD). Similar solutions are now being investigated for the other parts of the register.
Francisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. rancisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. Please visit the following sections of the website for more details about the tools currently available and those to be available in the near future. News 04/17/2008 F. novicida transposon mutant orders are now being handled by BEI Resources. 03/25/2008 New features have been added to the PSAT synteny analysis tool including a printer friendly version of the genomic neighborhood graphic, a text output of homologs in a region in spreadsheet format, and an option for displaying multiple alignments for a gene against a single comparison genome. 02/07/2008 Proteomics experimental data for F. novicida are now integrated into our genome browser. 02/05/2008 Updated genome annotations can now be submitted using the Panda tool. Your participation is encouraged. Please see the Panda page for more information. 02/04/2008 F. holarctica FTA is now available from Genbank (NC_009749) and has been added to our genome browser Tools Name Description Get surrounding sequence Given a gene, other genome feature, or genome coordinate, displays in FASTA format the surrounding sequence a specified number of nucleotides upstream and downstream Synteny Tool Analyze potential regions of local synteny between the Francisella genomes and any other published bacterial genome
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. FusionDB is a database of bacterial and archaeal gene fusion events - also known as Rosetta stones. Gene-fusion events are not the only resource to determine functional links between two proteins. Similar phylogenetic profiles and conserved chromosomal co-localization can also be used as an indicator for such interactions.
An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets.
A software tool optimized for mapping short RNAs onto a reference genome.
Computational Neurobiology and Imaging Center
Center to advance research and training in mathematical, computational and modern imaging approaches to understanding the brain and its functions. Software tools and associated reconstruction data produced in the center are available. Researchers study the relationships between neural function and structure at levels ranging from the molecular and cellular, through network organization of the brain. This involves the development of new computational and analytic tools for imaging and visualization of 3-D neural morphology, from the gross topologic characteristics of the dendritic arbor to the fine structure of spines and their synapses. Numerical simulations of neural mechanisms based on these structural data are compared with in-vivo and in-vitro electrophysiological recordings. The group also develops new theoretical and analytic approaches to exploring the function of neural models of working memory. The goal of this analytic work is to combine biophysically realistic models and simulations with reduced mathematical models that capture essential dynamical behaviors while reproducing the functionally important features of experimental data. Research areas include: Imaging Studies, Volume Integration, Visualization Techniques, Medial Axis Extraction, Spine Detection and Classification, Applications of Rayburst, Analysis of Spatially Complex Structures, Computational Modeling, Mathematical and Analytic Studies
An Antibody supplier and subset of ThermoFisher Scientific which provides fluorescence reagents for various experiments and methods.
Data set of extensive information on the changing circumstances of aged and disabled beneficiaries - Living, noninstitutionalized population of the continental United States from the Social Security Administration' '''s Master Benefit Record who were new recipients of Social Security benefits (first payment in mid-1980 through mid-1981) or who had established entitlement to Medicare and were eligible for, but had not received, Social Security benefits as of July 1982. Based initially on a national cross-sectional survey of new beneficiaries in 1982, the original data base was expanded with information from administrative records and a second round of interviews in 1991. Variables measured in the original New Beneficiary Survey (NBS) include demographic characteristics; employment, marital, and childbearing histories; household composition; health; income and assets; program knowledge; and information about the spouses of married respondents. The 1991 New Beneficiary Follow-up (NBF) updated marital status, household composition, and the economic profile and contains additional sections on family contacts, postretirement employment, effects of widowhood and divorce, major reasons for changes in economic status, a more extensive section on health, and information on household moves and reasons for moving. Disabled-worker beneficiaries were also asked about their efforts to return to work, experiences with rehabilitation services, and knowledge of SSA work incentive provisions. The NBDS also links to administrative files of yearly covered earnings from 1951 to 1992, Medicare expenditures from 1984 to 1999, whether an SSI application has ever been made and payment status at five points in time, and dates of death as of spring 2001. For studies of health, the Medicare expenditure variables include inpatient hospital costs, outpatient hospital costs, home health care costs, and physicians' ''' charges. The survey data cover functional capacity including ADLs and IADLs. For studies of work in retirement, the survey includes yearly information on extent of work, characteristics of the current or last job, and reasons for working or not working. No other data set has such detailed baseline survey data of a population immediately after retirement or disability, enhanced with subsequent measures over an extended period of time. The data are publicly available through NACDA and the Social Security Administration Website. * Dates of Study: 1982-1991 * Study Features: Longitudinal * Sample Size: ** 18,136 (NBS 1981) ** 12,677 (NBF 1991) Links: * 1982 (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/08510 * 1991 (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06118
psRNATarget: A Plant Small RNA Target Analysis Server
A plant small RNA target analysis server which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to ?open? secondary structure around miRNA?s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. PsRNATarget is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded miRNAs and transcript sequences; and outputs a comprehensive list of miRNA / target pairs along with the online tools for batch downloading, key word searching and results sorting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
A database of genes that give a seed phenotype when disrupted by mutation. The long-term goal of this project is to establish a comprehensive dataset of essential genes. The updated project database (December, 2007) presents information on 358 genes and 605 mutants. More than 60% of these mutants have been analyzed in the Meinke laboratory (Stillwater, OK).
Normalization by Expected Uniquely Mappable Area
Software for estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (''consistency coefficient'') for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data.
A blog on transcriptomics, bioinformatics and computational biology.
A catalog of antibodies important for zebrafish research, maintained by ZFIN. ZFIN Antibody Wiki is where zebrafish researchers can help each other by sharing antibody information - new antibodies, protocols, tips - anything that might be helpful.
Natural Sciences and Engineering Research Council of Canada
Conseil de recherches en sciences naturelles et en genie du Canada
NSERC aims to make Canada a country of discoverers and innovators for the benefit of all Canadians. The agency supports university students in their advanced studies, promotes and supports discovery research, and fosters innovation by encouraging Canadian companies to participate and invest in postsecondary research projects. NSERC researchers are on the vanguard of science, building on Canada''s long tradition of scientific excellence.
Operon DB is a method to detect and analyze conserved gene pairs - pairs of genes that are located close on the same DNA strand in two or more bacterial genomes. For each conserved gene pair, we calculate an estimate of probability that the genes belong to the same operon. The algorithm takes into account several alternative possibilities. One is that functionally unrelated genes may have the same order due simply because they were adjacent in a common ancestor. Other possibilities are that genes may be adjacent in two genomes by chance alone, or due to horizontal transfer of the gene pair.
A modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data.
It presents accurate pig gene annotations in all sequenced genomic regions. It integrates various available pig sequence data, including 3.84 million whole-genome-shortgun (WGS) reads and 0.7 million Expressed Sequence Tags (ESTs) generated by Sino-Danish Pig Genome Project, and 1 million miscellaneous GenBank records. The Pig Analysis Database has covered nearly 50% of the whole pig genome and over 70% of the coding sequences (CDS), and aims to provide the most complete pig gene set to date. In addition to gene annotations, the PigGIS also presents expressional information from 98 EST libraries, SNPs detected from both WGS reads and ESTs, oligos that can be used in microarray design and relevant evolutionary data. SIFT analysis of deleterious mutations will come in future.
Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene.
Probalign: multiple sequence alignment using partition function posterior probabilities
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software that uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. Computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.Produces accurate alignments on long and heterogeneous length datasets containing protein repeats.
The Center for New Technology Enterprise
It is an independent nonprofit organization established to provide meaningful trans-disciplinary experiential education to students by making the most cutting-edge instructional methods and technologies available to them to bring new inventions to the marketplace and to encourage knowledge sharing and collaboration among its numerous constituencies. The Center provides a comprehensive program in which its students learn and acquire real-world experience by assisting universities, private and public research institutions, companies, and entrepreneurs to evaluate new technologies and facilitate the creation and development of new ventures. By offering a virtual venue for students and other constituencies worldwide, our stakeholders and collaborators can connect and share knowledge, expertise, resources, best practices, and other important information. Employers, investors and others searching for talent place a premium on relevant experience. However, students, individuals seeking a change in their careers, and prospective entrepreneurs often find it difficult to obtain positions that can provide needed experience, even if they are willing to work without compensation. This conundrum often leads to people taking or staying in positions for which they have no passion and which do not make the best use of their abilities. The Centers program is designed to provide extensive, intensive and relevant experience to its participants, with particular emphasis on teaching them to adapt to and thrive in our lightning fast, rapidly changing and increasingly flat world. As an independent organization, the Centers program and activities are not restricted to any particular institution or jurisdiction. Thus the Center can attract students, clients, professionals and other stakeholders, establish collaborations, and pursue other opportunities appropriate to its mission almost anywhere. eductional resource.
CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians. In turn, CnidBase will help to illuminate the role of specific genes in shaping cnidarian biodiversity in the present day and in the distant past. CnidBase highlights evolutionary changes between species within the phylum Cnidaria and structures genomic and expression data to facilitate comparisons to non-cnidarian metazoans. CnidBase aims to further the progress that has already been made in the realm of cnidarian evolutionary genomics by creating a central community resource which will help drive future research and facilitate more accurate classification and comparison of new experimental data with existing data.
Blue Ridge Institute for Medical Research; North Carolina; USA
Blue Ridge Institute for Medical Research
The goal of the Institute is to explore the interfaces of fundamental biological science, clinical science, and clinical care with a special emphasis on targeted cancer therapy. The current focus centers on signaling by protein kinases. These enzymes (protein kinases) play a key regulatory role in nearly every aspect of cell biology. Owing to the myriad actions of protein kinases, it is imperative that they be stringently regulated because aberrant activity of these enzymes can lead to a variety of diseases including, inter alia, cancer, diabetes and autoimmune, cardiovascular, degenerative, inflammatory, and nervous disorders. Because mutations and dysregulation of protein kinases play causal roles in human disease, these enzymes represent attractive drug targets. Our research focuses on the epidermal growth factor receptor protein-tyrosine kinase, Raf/Mek/Erk protein kinases, and on the regulation of tyrosine hydroxylase activity by protein phosphorylation. The Blue Ridge Institute for Medical Research is a Federal tax exempt 501(c)(3) non-profit organization incorporated in the State of North Carolina on 24 March 2006 (EIN 20-4665742; DLN 17053144012016).
Alcohol and Drug Abuse Institute (ADAI) Library: Alcohol, Drugs and Tobacco Web Links
This database contains links to 600+ Alcohol, Tobacco, and Other Drugs (ATOD) organizations and resources on the web. It can be viewed by name in the A-to-Z list, by category or you can type any keyword or phrase into the search box to find links that match your search term. The categorical list includes ATOD Research Centers, Information Resources, Treatment, Training, U.S. Gov''t Agencies, Internat''l Gov''t Agencies, Recovery, Washington State, Organizations/Advocacy, Professional Societies, Journals/Newsletters, Other Sites
This Gateway is a collaboration between the Consortium for Functional Glycomics (CFG) and Nature Publishing Group (NPG), providing a comprehensive resource for functional glycomics research. Use this site to stay up-to-date on glycomics news, request CFG resources, and search databases of glycan-binding proteins, glycan structures, and glycosyltransferases. The Functional Glycomics Update provides a one-stop overview of the latest research in glycobiology for specialists and non-specialists alike. It is updated monthly to bring you the latest news and selected highlights from Nature journals. In addition, it will provide two featured articles a month on the most relevant advances in the field published in NPG and other top journals. By collating new articles into a key worded research library, we hope to provide a continuously updated and broad overview of the field. Sponsor. The CFG is a large international research initiative funded by NIGMS to elucidate the roles of carbohydrate-protein interactions in cell communication at the cell surface.
A command-line program for the imputation of untyped SNPs. tagIMPUTE is based on a few flanking SNPs that can optimally predict the SNP under imputation. (entry from Genetic Analysis Software)
A command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to estimate or test SNP effects and SNP-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty, study design and gene-environment dependence. For SNPs without missing data, the program performs the standard association analysis. For typed SNPs with missing data or untyped SNPs, the program performs the maximum-likelihood analysis. (entry from Genetic Analysis Software)
SNP HIgh-Throughput LINKage analysis system
Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (entry from Genetic Analysis Software)
Maximum Entropy Conditional Probability Moldeling
A unification tool which dynamically collects and compiles data from scientific databases in National Institute of Agrobiological Sciences (NIAS), and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Oryza sativa into easy to navigate. The mission of Rice PIPELINE is to provide a unique scientific resource of rice that pools publicly available data commonly sought after for any clone sequence, clone name, GenBank accession number, or keyword.
Coordination and sustainability of international mouse informatics resources
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2022. Much of the current effort in functional genomics, and our understanding of the biology of human disease, is underpinned by informatics infrastructures served by the scattered collection of relevant databases which exists in Europe. This infrastructure is essential for the support of a European Research Area in mouse functional genomics. CASIMIR, a coordination action of the 6th Framework Programme of the European Commission, will focus on co-ordination and integration of databases set up in support of FP5 and FP6 projects containing experimental data, including sequences, and material resources such as biological collections, relevant to the use of the mouse as a model organism for human disease. Interoperability of disseminated databases potentially provides enormous synergy in the provision, integration and analysis of a wide range of data with concomitant added value for research projects. Having set standards and benchmarks the proposed action will then reach out to co-ordinate other European and International databases and consult with the Community. EU FlagThe CASIMIR project is funded by the European Commission within its FP6 Programme, under the thematic area Life sciences, genomics and biotechnology for health, contract number LSHG-CT-2006-037811
A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned.
An R package for simulations and likelihood calculations of pair-wise family relationships using DNA marker data. (entry from Genetic Analysis Software)
A database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam. The database contains an assignment of PDB ligands to the domains of structures as classified by the CATH, SCOP and Pfam databases. Cognate ligands have been identified using data from the ENZYME and KEGG databases and compared to the PDB ligand using graph matching to assess chemical similarity. Cognate ligands from the known reactions in ENZYME and KEGG for a particular enzyme are then assigned to enzymes structures which have EC numbers.
Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A resource that allows users to identify cis-NATs in eleven eukaryotic species, screening eight of these species for the first time and bringing the number of candidate SA pairs in human to 7,246. We construct this free and publicly accessible database that allows researchers to query the dataset.
Software application that implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance. Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. (entry from Genetic Analysis Software)
A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
On line database of alu pairs. This map file is a subfile of repbase (Genetic Information Research Institute(GIRI)), derived by comparing genomic sequences in the GenBank database (release 112.0, National center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD) with the Alu consensus sequence, was made in April 1999 and is maintained at the GIRI), Sunnyvale, CA). The Alu map includes the following information in columnar form: locus, beginning sequence position, ending sequence position, fragment start relative to repeat consensus, type of Alu sequence, the fragment start relative to repeat consensus, the fragment end relative to repeat consensus, the orientation of the sequence (D, denoting direct, versus C, denoting complementary), the percent similarity to the Alu consensus sequence, the ratio of mismatches to matches, and the alignment score. The database is available for download. An Alu element is a short stretch of DNA originally characterized by the action of the Alu (Arthrobacter luteus) restriction endonuclease. Alu elements of different kinds occur in large numbers in primate genomes. In fact, Alu elements are the most abundant Transposable elements in the human genome. They are derived from the small cytoplasmic 7SL RNA, a component of the signal recognition particle. The event, when a copy of the 7SL RNA became a precursor of the Alu elements, took place in the genome of an ancestor of Supraprimates. (from Wikipedia).
The FlyTrap database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. Expression is under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns. Drosophila proteins tagged with Green Fluorescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion.
A data set of a multicohort study of persons 70 years of age and over designed primarily to measure changes in the health, functional status, living arrangements, and health services utilization of two cohorts of Americans as they move into and through the oldest ages. The project is comprised of four surveys: * The 1984 Supplement on Aging (SOA) * The 1984-1990 Longitudinal Study of Aging (LSOA) * The 1994 Second Supplement on Aging (SOA II) * The 1994-2000 Second Longitudinal Study of Aging (LSOA II) The surveys, administered by the U.S. Census Bureau, provide a mechanism for monitoring the impact of proposed changes in Medicare and Medicaid and the accelerating shift toward managed care on the health status of the elderly and their patterns of health care utilization. SOA and SOA II were conducted as part of the in-person National Health Interview Survey (NHIS) of noninstitutionalized elderly people aged 55 years and over living in the United States in 1984, and at least 70 years of age in 1994, respectively. The 1984 SOA served as the baseline for the LSOA, which followed all persons who were 70 years of age and over in 1984 through three follow-up waves, conducted by telephone in 1986, 1988, and 1990. The SOA covered housing characteristics, family structure and living arrangements, relationships and social contracts, use of community services, occupation and retirement (income sources), health conditions and impairments, functional status, assistance with basic activities, utilization of health services, nursing home stays, and health opinions. Most of the questions from the SOA were repeated in the SOA II. Topics new to the SOA II included use of assistive devices and medical implants; health conditions and impairments; health behaviors; transportation; functional status, assistance with basic activities, unmet needs; utilization of health services; and nursing home stays. The major focus of the LSOA follow-up interviews was on functional status and changes that had occurred between interviews. Information was also collected on housing and living arrangements, contact with children, utilization of health services and nursing home stays, health insurance coverage, and income. LSOA II also included items on cognitive functioning, income and assets, family and childhood health, and more extensive health insurance information. The interview data are augmented by linkage to Medicare enrollment and utilization records, the National Death Index, and multiple cause-of-death records. Data Availability: Copies of the LSOA CD-ROMs are available through the NCHS or through ICPSR as Study number 8719. * Dates of Study: 1984-2000 * Study Features: Longitudinal * Sample Size: ** 1984: 16,148 (55+, SOA) ** 1984: 7,541(70+, LSOA) ** 1986: 5,151 (LSOA followup 1) ** 1988: 6,921 (LSOA followup 2) ** 1990: 5,978 (LSOA followup 3) ** 1994-6: 9,447 (LSOA II baseline) ** 1997-8: 7,998 (LSOA II wave 2) ** 1999-0: 6,465 (LSOA II wave 3) Link: * LSOA 1984-1990 ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/08719
THIS RESOURCE IS NO LONGER IN SERVCE, documented June, 2019.Comparative Genomic Visualization with Adobe Flash.
A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The Mouse Brain Image/Atlas Visualizer (MBIV) is a Java-based 2D visualization tool, available both as a web-based applet or downloadable application, for browsing high resolution 3D MRI mouse brain images and their associated atlases. A user can dynamically access images and atlases in our mouse brain database through the interface provided by MBIV and then select from the database the datasets they wish to upload and browse on their local machine.
The operational criteria OPCRIT checklist for psychotic and affective illness has been designed to facilitate a polydiagnostic approach to mental illness. The package is specifically for the needs of the researcher and is intended to be used by clinicians or investigators trained in clinical research. It is not recommended for use by raters without previous experience in psychopathology and psychiatric diagnosis. Click the Download link below to download Opcrit. This download is compressed zip file which will yield the actual installer files. Open WinopInstallerFiles.zip and when prompted extract the contents to a temporary location. One of the files extracted is Setup.exe. Run this setup file and follow the instructions to install the Opcrit. Depending on your system type and version of Windows, you may need to reboot your system once installation is complete. After installation, you will also need to download and run the installer for the october 2009 update (see below).
Software program that performs exact linkage analysis with the same input-output relationships as in standard genetic linkage programs such as LINKAGE, FASTLINK, VITESSE, but can run larger files than previous programs. (entry from Genetic Analysis Software)
EASE: the Expression Analysis Systematic Explorer
Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible
Web server for identification of complete gene structures in genomic DNA.Tool for predicting locations and exon-intron structures of genes in genomic sequences from variety of organisms. Used for prediction of complete gene structures in human genomic DNA.
The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans. The GPCR NaVa database includes: 1) rare mutations (frequency < 1%); 2) polymorphisms (frequency > 1%), including Single Nucleotide Polymorphisms (SNPs); 3) variants without estimates of allele frequency. The GPCR NaVa database aids GPCR research by categorising and integrating information on variants from databases and scientific papers. Moreover, the GPCR NaVa database is linked with the reputable GPCRDB. In case of missing NaVas, please help our users by sending a completed Excel-file to Jeroen Kazius. human G Protein-Coupled Receptors, human G Protein, human G-protein
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. EPGD isfocused on the paralogs and the duplication events in the evolution. It is gene-centered and organized by paralog family. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website in plain text files. The database will be very useful for both experimentalists and bioinformaticians for the study of duplication events or paralog families.
Linkage Disequilibrium Analyses for Quantitative and Discrete Traits
How is association mapping going to help me find genes? During the past decade, the genes for a large number of rare mendelian traits have been identified. However, traditional linkage analyses lack power and precision when applied to complex disease. Association mapping, which compares the effects of different chromosomal variants, may be more successful at identifying genes of small effect. How does QTDT help association mapping? Association mapping can produce misleading results when the study population is not homogeneous, but includes individuals with different genetic backgrounds. Family based association tests, commonly referred to as TDTs (Transmission Disequilibrium Tests), do not produce misleading results in these circumstances. QTDT can use all the information in a pedigree to construct powerful tests of association that are robust in the presence of stratification. What does the Q stant for ? Q stands for Quantitative. Quantitative traits provide effective descriptions of many complex diseases, including asthma. For many of these conditions, all or nothing definitions of disease are arbitrary and unsatisfactory. QTDT incorporates variance components methodology in the analysis of family data and includes exact estimation of p-values for analysis of small samples and non-normal data. The QTDT abbreviation (for Quantitative Transmission Disequilibrium Tests) was first used by David Allison in his 1997 paper. This research was supported in part by the intramural program of the National Eye Institute and by National Institutes of Health Grants EY016862, EY007758, EY09859, EY012118, P30-EY014801, EY-014458, EY014467, HL084729, and HG002651, by the Foundation Fighting Blindness, the Macula Vision Research Foundation, the American Health Assistance Foundation, Research to Prevent Blindness, the Pew Charitable Trusts, the Mayo Clinic Foundation, the Casey Macular Degeneration Center Fund, the Marion W. and Edward F. Knight AMD Fund, the Harold and Pauline Price Foundation, National Genotyping Centre of Spain, and the Elmer and Sylvia Sramek Foundation. The Center for Inherited Disease Research, fully funded through a federal contract (HHSN268200782096C) from National Institutes of Health to
JAIL is a database that classifies the interfaces between domain architectures and those between protein chains and between proteins and nucleic acids. Interacting proteins are difficult to crystallize and rarely present within the Protein Data Base. Nevertheless, it is essential to analyze the interacting parts of the proteins to understand the process of protein-protein docking. To overcome this problem we have built up the JAIL database. Since interacting domains exhibit similar structural features than proteins, all known interfaces between interacting domains of the SCOP database were extracted and classified in JAIL. Only a part of all protein structures are included in SCOP. Particularly, new PDB entries are not yet annotated. To overcome this problem additionally all interfaces between protein chains were calculated and included in the database. This type of interface also comprises the interacting parts of the assumed biological units. The last important type of interfaces provided here is composed of the interacting parts between proteins and nucleic acids. Overall the data set consists of about 180,000 interfaces. JAIL is a comfortable tool to browse through the interface library and to analyze single interfaces. However, more general questions require large-scale analysis. For this purpose, a detailed form enables the compiling of comprehensive non redundant data sets for download.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website).
This site provides online servers for algorithms such as normal mode calculation, structural refinement, solvation, and mutation. The primary application is for biological macromolecules like proteins or DNA, but they can certainly be used for general structures.
Biological Interaction database for Protein-nucleic Acid
A database for protein-nucleic acid interaction that provides various features of protein-nucleic acid interfaces. There are 2333 protein-nucleic acid PDB complexes, 9547 SCOP domains, and 9633 domain-nucleic acid interfaces in BIPA. BIPA also provides a multiple structural alignment of representative structures at the SCOP family level using the program SALIGN, and the structural alignments were further annotated using the program JOY to detect local environments of amino acids.
International Gene Trap Consortium Pathways
IGTC uses GenMapp to provide maps of public gene trap data from members of the International Gene Trap Consortium (IGTC) to map sets of biological pathways and gene groupings. Users can browse the pathway diagrams and view which genes within the pathway have been trapped. Genes with gene trap insertions are colored on the pahtway diagram depending upon the number of traps of the gene. Clicking on a gene of interest will bring up a backpage of annotation data and detailed information about the gene trap cell lines.
An Illumina Genome-Analyzer (Solexa) base caller.
The Kidney Development Database was created to collect in one place the data from a large number of developmental studies that have a bearing on the study of kidney development. With its oldest parts dating back to 1993/4, it is, as far as we know, the earliest computer database in the field of vertebrate organogenesis. Data are displayed in tables, arranged according to a standard scheme of kidney development explained in the key. Many of the entries are derived from low-power in situs or published text-only descriptions, and should therefore be interpreted with mild caution.
American Parkinson's Disease Association Information and Referral Center
A patient resource to provide Parkinson's disease patients and their families with information and resources to help understand and manage Parkinson's disease and improve the quality of life for both patient and caregiver, while increasing public awareness about the disease. The website also connects users with resources, such as therapy groups, physical exercise classes, and patient care resources. It gives users access to mailing lists, support group information, and other Parkinson's-related event information for Parkinson's patients and their families. Based at Stanford University Medical Center, it is a partnership between the American Parkinson Disease Association, Inc. and Stanford University.
Software suite of six programs that can be used as a stand-alone extension of the pedigree drawing facilities found in the publicly available version of PEDPACK. (entry from Genetic Analysis Software)
GiardiaDB is a resource for information on Giardia lamblia. It contains gene information, including genomic attributes, protein expression patterns, evolution, and EST sequence information. The website provides tools for BLASTing, sequence retrieval, graphic visualization, and PubMed information.
Software program that presents complete raw datasets of individuals'' genotype data using a display format with samples as rows and polymorphisms as columns. The color code is: (1) blue: homozygous genotype for the common allele; (2) red: heterozygous genotype; (3) yellow: homozygous genotype for the rare allele; and (4) grey: missing data (entry from Genetic Analysis Software)
Mediagnost Gesellschaft für Forschung und Herstellung von Diagnostika GmbH
MALISAM: Manual ALIgnments of Structurally Analogous Motifs
MALISAM is a database of pairwise, structure-based alignments for structurally analogous motifs in proteins. Homology and analogy are two alternative scenarios to explain structural similarities among proteins. Homologs inherit similar features from their common ancestor, while analogs converge to similar structures due to a limited number of energetically favorable ways to pack secondary structural elements. Analogous pairs in this database are in three categories: a hybrid motif and a core motif, an interface motif and a core motif, an artificial protein and a natural protein. During evolution, a protein family usually preserves a common core while accumulating insertions and deletions in the periphery. A core motif is composed entirely of secondary structure elements belonging to the evolutionary core. A hybrid motif consists of both core elements and peripheral insertions that are not present in the majority of the family members. An interface motif uses secondary structural elements from two or more domains or subunits contacting along that interface.
Phenylalanine Hydroxylase Locus Knowledgebase
A database of centralized mutation data on the PAH gene. Searchable fields of the database available to users are: mutation name, polymorphic haplotype, population, geographic location, gene region, codon number, mutation type, substitution, phenotype, author's name and many more. The complete information provided for each mutation is regularly updated from both published data and personal communications.
Software interface for the statistical analysis of haplotype-disease association. HAPSTAT allows the user to estimate or test haplotype effects and haplotype-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty and study design. The current version considers cross-sectional, case-control and cohort studies. (entry from Genetic Analysis Software)
Children and Adults with Attention Deficit/Hyperactivity Disorder
Non-profit organization serving individuals with attention deficit-hyperactivity disorder (AD/HD) and their families. CHADD has over 16,000 members in 200 local chapters throughout the U.S. Chapters offer support for individuals, parents, teachers, professionals, and others. CHADD''s primary objectives are: to provide a support network for parents and caregivers; to provide a forum for continuing education; to be a community resource and disseminate accurate, evidence-based information about AD/HD to parents, educators, adults, professionals, and the media; to promote ongoing research; and to be an advocate on behalf of the AD/HD community. In general, CHADD works to improve the lives of people affected by AD/HD through: Collaborative Leadership, Advocacy, Research Education and, Support CHADD has three current priority objectives: (1) to serve as a clearinghouse for evidence-based information on AD/HD, (2) to serve as a local face-to-face family support group for families and individuals affected by AD/HD, and (3) to serve as an advocate for appropriate public policies and public recognition in response to needs faced by families and individuals with AD/HD. CHADD is a membership organization, produces the bi-monthly Attention! magazine (for members), and sponsors an annual conference. The National Resource Center on AD/HD (NRC) is the CDC-funded national clearinghouse for evidence-based information about AD/HD.
Renin Angiotensin System Blockage-DN (RASS)
Renin Angiotensin System Study (RASS/B-RASS)
Randomized, multicenter, double-blind study to determine if renin angiotensin medications, either losartan (angiotensin II blocker) or enalapril (converting enzyme inhibitor), can prevent or delay the onset of diabetic kidney disease in patients with type 1 diabetic patients who do not have hypertension, diabetic nephropathy, or predictive levels of microalbuminuria. Two hundred eight five patients ages 16-61 with 2-20 yrs of Type 1 Diabetes Mellitus and no renal functional abnormalities were randomized into a parallel, double-blind, placebo-controlled study involving 3 groups (95 patients/group). Each group received an angiotensin-converting enzyme inhibitor (ACEI) (enalapril), or an angiotensin II receptor blocker (Losartan), or placebo. All patients had their usual Diabetes Mellitus (DM) management. Baseline studies included measures of glomerular filtration rate (GFR), urinary albumin excretion rate (UAE), blood pressure (BP), and a percutaneous renal biopsy. Patients were followed by quarterly measures of BP, HbA1C, UAE, and drug compliance. There were annual measures of GFR and a repeat renal biopsy after 5 yrs in the study. The main endpoint is kidney structural changes over time, especially mesangial fractional volume (v(Mes/glom)). Secondary endpoints will be other DN structural measures and measures of kidney function (UAE, GFR). These studies will determine whether rennin angiotensin system blockage in the early stages of DN can prevent the early kidney structural changes in this important disorder. Ancillary studies will evaluate the effects of treatment group on the development and progression of diabetic retinopathy and will develop predictors of study participants' ''' compliance. Baseline, 2.5 and 5 year retinal fundus photographs in the RASS patients were obtained.
The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next. The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. Sponsors: Funding was provided by Genome Prairie and Genome Alberta A Bioinformatics Platform for Genome Canada''; Canadian Institutes for Health Research; The Natural Sciences and Engineering Research Council of Canada; The Heart and Stroke Foundation for BC and Yukon; The EPSRC through the myGrid (GR/R67743/01, EP/C536444/1, EP/D044324/1, GR/T17457/01) e-Science projects; The Spanish National Institute for Bioinformatics (INB) through Fundacin Genoma Espaa; The Generation Challenge Programme (GCP; http://www.generationcp.org) of the Consultative Group for International Agricultural Research. :Keywords: Ontology, Messaging, Standard, Client, Automatically, Discovery, Biological, Data, ANalytical, Service, Model, Organism, Database, Java, Platform, Semantic, Bioinformatics,
Cortical Box Method: Quantitative analysis for gene expressions in rodent cortex
The Cortical box method is an analytical method that standardizes the serial coronal sections of rodent cortex for quantitative analysis (details are written in the manual document). There are several tools necessary for this analysis. Currently, a program CxStand which is a core program of Cortical Box method is available for download. It standardizes a set of serial sections of rat cortex into standard rectangulars. Cortical box method was developed by Dr. Junya Hirokawa in the Yamamori Lab to map c-fos immunoreactivity in the rat cortex. This method was now applied to analyze the in situ data. From the original image, the cortical region is taken out and transformed, then normalized. You do this to a set of coronal sections of a rat cortex. Then, the cortex becomes a box. You can now slice the cortical box at desired lamina positions for layer maps. For more information, please refer to, http://www.nibb.ac.jp/brish/Gallery/corticalboxE.html. Requirements Cortical Box Method software is written in Labview and requires Labview version 7.0 (or later) and Vision development version 7.0 (or later). Labview and Vision are products of National Instruments (http://www.ni.com/ ). I confirmed (*) the Cortical box software works in the latest versions of Labview (ver.8.6) and Vision development (ver. 8.6), which can be downloaded without charge in the National Instruments web site (http://www.ni.com/ ) and can be used as evaluation softwares for 30 days. I tested the programs on PCs running the Windows family of operating systems. *A VI called image to image does not exist in Labview 8.6, please replace it into image to image 2. Programs CxStand ver 1.01 - (English, 680KB, Latest Version (2008/09/25 Update)) Standardization of a part of cortex into a rectangular. CBanalysis - construct 3D cortical box and create specific layer maps. DensityMap - Creating denisty map of staining signals. Copyright (c) 2008 Junya Hirokawa. All rights reserved. This program is free software; you can redistribute it and/or modify it.
National Survey of Families and Households
National Survey of Families and Households (NSFH)
A national sample survey dataset covering a wide variety of issues on American family life beginning in 1987-88 and at two subsequent timepoints1992-93 and 2001-03. Topics covered included detailed household composition, family background, adult family transitions, couple interactions, parent-child interactions, education and work, health, economic and psychological well-being, and family attitudes. The first wave interviewed 13,017 respondents, including a main cross-section sample of 9,643 persons aged 19 and over plus an oversample of minorities and households containing single-parent families, step-families, recently married couples, and cohabiting couples. In each household, a randomly selected adult was interviewed. In addition, a shorter, self-administered questionnaire was filled out by the spouse or cohabiting partner of the primary respondent. Interviews averaged about 100 minutes, although interview length varied considerably with the complexity of the respondent''s family history. In 1992-94, an in-person interview was conducted of all surviving members of the original sample, the current spouse or cohabiting partner, and with the baseline spouse or partner in cases where the relationship had ended. Telephone interviews were conducted with focal children who were aged 5-12 and 13-18 at baseline. Short proxy interviews were conducted with a surviving spouse or other relative in cases where the original respondent died or was too ill to interview. A telephone interview was conducted with one randomly selected parent of the main respondent. In 2001-03, telephone interviews were conducted with: Surviving members of the original respondents who had a focal child age 5 or over at baseline; the baseline spouse/partner of these original respondents, whether or not the couple was still together; the focal children who were in the household and aged 5-18 at baselinemost of whom were interviewed at wave 2; and all other original respondents age 45 or older in 2000, and their baseline spouse/partner. Oversamples: Blacks, 9.2%; Mexican-Americans, 2.4%; Puerto Ricans, 0.7% * Dates of Study: 1987-2003 * Study Features: Longitudinal, Minority Oversampling * Sample Size (original respondents): ** Wave I (1987-88): 13,017 ** Wave II (1992-93): 10,007 ** Wave III (2001-03): 8,990 Links: * Wave I (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06041 * Wave II (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06906 * Wave III (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00171
Quantitative (Trait) Transmission/Disequilibrium Test
Software application that performs linkage disequilibrium (TDT) and association analysis for quantitative traits. Includes support for the methods of Abecasis et al. (2000), Fulker et al. (1999), Monks et al. (1998), Allison (TDTQ5, 1997) and Rabinowitz (1997). Supports families of any size, with or without parental information. Includes simple variance components modelling. Interfaces with SimWalk2 for IBD estimation. (entry from Genetic Analysis Software)
It aims to provide correct information on introns, particularly in bacteria. Information in the web site includes: (1) introductory information on group II introns; (2) detailed information on subfamilies of intron RNA structures and intron-encoded proteins; (3) a listing of identified introns with correct boundaries, RNA secondary structures and other detailed information; and (4) phylogenetic and evolutionary information. The comparative data should facilitate study of the function, spread and evolution of group II introns.
Predicts the structure of a protein-protein complex from the individual structures of the monomer components.
Database for ESTs (Expressed Sequence Tags), consensus sequences, bacterial artificial chromosome (BAC) clones, BES (BAC End Sequences). They have generated 69,545 ESTs from 6 full-length cDNA libraries (Porcine Abdominal Fat, Porcine Fat Cell, Porcine Loin Muscle, Liver and Pituitary gland). They have also identified a total of 182 BAC contigs from chromosome 6. It is very valuable resources to study porcine quantitative trait loci (QTL) mapping and genome study. Users can explore genomic alignment of various data types, including expressed sequence tags (ESTs), consensus sequences, singletons, QTL, Marker, UniGene and BAC clones by several options. To estimate the genomic location of sequence dataset, their data aligned BES (BAC End Sequences) instead of genomic sequence because Pig Genome has low-coverage sequencing data. Sus scrofa Genome Database mainly provide comparative map of four species (pig, cattle, dog and mouse) in chromosome 6.
Collaborative Study on the Genetics of Alcoholism
A multi-site, multi-disciplinary undertaking with the overall goals of characterizing the familial transmission of alcoholism and related phenotypes and identifying susceptibility genes using genetic linkage. The study is being coordinated by the SUNY Health Science Center at Brooklyn (HSCB) under the leadership of Henri Begleiter. The study was initially funded by the National Institute of Alcohol Abuse and Alcoholism (NIAAA) in 1989. Additional useful information at http://www.niaaa.nih.gov/ResearchInformation/ExtramuralResearch/SharedResources/projcoga.htm
TCMGeneDIT is a database system providing association information about traditional Chinese medicines (TCMs), genes, diseases, TCM effects and TCM ingredients automatically mined from vast amount of biomedical literature. Integrated protein-protein interaction and biological pathways information collected from public databases are also available. In addition, the transitive relationships among genes, TCMs and diseases could be inferred through the shared intermediates. Furthermore, TCMGeneDIT is useful in deducing possible synergistic or antagonistic contributions of the prescription components to the overall therapeutic effects. TCMGeneDIT is a unique database of various association information about TCMs. The database integrating TCMs with life sciences and biomedical studies would facilitate the modern clinical research and the understanding of therapeutic mechanisms of TCMs and gene regulations.
Publicly available Web-based application that can perform QTL mapping on a variety of population types. GridQTL will extend the functionality of QTLExpress by adding new and advanced approaches for modelling QTL analysis in simple and complex populations. These new methods will be available on a Grid system that will offer flexible workflow management, resource allocation, data persistence, detached execution of simulations and the scalability required for the increase in data volume, data sources and complexity required by the new models. (entry from Genetic Analysis Software)
database of human DNA Methylation and Cancer
Database to study interplay of DNA methylation, gene expression and cancer that hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing. Interconnections between different data types were analyzed and presented. Search tool and graphical MethyView are developed to help users access all the data and data connections and view DNA methylation in context of genomics and genetics data. The search tool and graphical MethyView are developed to help users access all the data and data connections and view DNA methylation in context of genomics and genetics data. As part of the Cancer Epigenomics Project in China, MethyCancer serves as a platform for sharing data and analytical results from the Cancer Genome/Epigenome Project in China with colleagues all over the world.
A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007
A database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex phylogenies. TreeFam-A families are manually curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families. phylogenetic tree, animal, vertebrate, invertebrate, gene, ortholog, paralog, evolutionary history, gene families, single-metazoan animals, outgroup genes like yeast (S. cerevisiae and S. pombe), plant (A. thaliana), historical duplications, speciations, losses, Human, Genome, comparative genomics
Software application for displaying estimated haplotype data (entry from Genetic Analysis Software)
A non-supervised gene prediction algorithm for prokaryotic genomes with multivariate entropy distance method.
IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. For the convenience of efficient data utilization, our Q-Filter system classifies and ranks all nucleotide sequences into 7 categories according to sequence content and integrity. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively. A searching system is developed for users to retrieve a combination of different data types by setting various search options. To facilitate analysis of the global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) is developed to display worldwide geographic distribution of the viral genotypes and to couple genomic data with epidemiological data. The BLAST, multiple sequence alignment tools and phylogenetic analysis tools were integrated for online data analysis. Furthermore, IVDB offers instant access to the pre-computed alignments and polymorphism analysis of influenza virus genes and proteins and presents the results by SNP distribution plots and minor allele distributions. IVDB aims to be a powerful information resource and an analysis workbench for scientists working on IV genetics, evolution, diagnostics, vaccine development, and drug design.
Organization which manufactures bacteria for research and clinical investigations. List Biological Laboratories cultivates native and recombinant microorganisms and purifies, formulates, and lyopholizes enzyme products, virulence factors, and microbial cell wall components. Products include antibodies, microbial toxins, peptides, and virulence factors. Services include live biotherapeutics for clinical trials, contracting research capabilities, GMP regulatory support, lyopholization services and support, and toxin compliance.
A database listing potential G-quadruplex regulated genes. G-rich DNA sequences can form G-quadruplexes, a four-stranded structure that is stabilized by planar arrays of four guanines associated with hydrogen bonds. Promoter G-quadruplexes have emerged as a new way to regulate gene transcription, such as in c-MYC expression. Further, G-quadruplex motifs are highly enriched in gene promoter regions in humans and other mammals. Greglist contains genes whose promoter regions have G-quadruplex motifs, and these genes are highly likely to be regulated by G-quadruplexes.
It is part of the Institute for Advanced Studies at The Australian National University (ANU). CBiS forms a bridge between two areas of major strength at ANU, mathematics and biological sciences. CBiS brings together researchers with backgrounds in mathematics, statistics and quantitative biology with the goal of developing a conceptual architecture for an information-based, integrative approach to complex biological systems. Software available for download or use is: * Pozitiv * GE Bi-Plot * Chip Stability * PyEvolve * Vestige Most software is freely available under the GPL or similar licenses. For details, see each individual package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers
A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs.
This is a searchable database of U12-type introns. U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. Investigations into the evolution and mechanism of U12-depending splicing would be facilitated by access to a catalog of such introns. However, due to their relatively recent discovery and a systematic bias against recognition of non-canonical splice sites in general, the introns defined by U12-type splice sites are under-represented in genome annotations. Such under-representation compounds the already difficult problem of determining gene structures. It also impedes attempts to study these introns genome-wide or phylum-wide. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12 introns of completely sequenced eukaryotic genomes and associate orthologous introns with each other.Two pathways for the removal of eukaryotic spliceosomal introns exist: a major pathway that is dependent on the main U2 snRNA-containing spliceosome and a minor pathway that is dependent on the low abundance U12 snRNA-containing spliceosome. The two spliceosomes share only one snRNA, U5, but have many of the same protein components in common. They are distinguished mainly by the splice signal sequences in the pre-mRNA to which they bind. U12 consensus sequences for the donor site, RTATCCTTT, and branch point, TTCCTTRAY, are highly conserved and distinct from the U2 consensi. The two spliceosomes also differ in the order of spliceosomal assembly. U11 and U12 form a dimer which then recognizes the donor site and branch point simultaneously, whereas U1 and U2 recognize these sites independently before associating.Computational scans for U12 introns have previously been performed for human (Levine and Durbin, 2001) and Arabidopsis (Zhu and Brendel, 2003). Both scans used similar methodology, essentially predicting introns and confirming them using alignment to expressed sequence. We extended this approach to 20 genomes using spliced alignment of sequence flanking known introns or transcript-confirmed intron predictions to the genomic sequence of orthologous genes. Details can be found in forthcoming article in the Nucleic Acids Research database issue.
The MIPS Fusarium graminearum Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Fusarium graminearum (Anamorph of Gibberella zeae). The goal is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The underlying sequence is the initial release of the high quality draft sequence of the Whitehead Center for Genome Research.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics.
Life Sciences Advanced Technologies inc.
Swiss study on Air Pollution and Lung Disease in adults
SAPALDIA (Swiss study on Air Pollution and Lung Disease in adults) is a multi-center study in eight geographic areas representing the range of environmental, meteorological and socio-demographic conditions of Switzerland, which studies the effects of air pollution on the respiratory and cardiovascular health in adults. Local centers are: Aarau, Basel, Davos, Geneva, Lugano, Montana, Payerne, and Wald. It was initiated in 1991 (SAPALDIA 1) with a follow-up assessment in 2002 (SAPALDIA 2). This study has allowed to assess 1) prevalence and development of major respiratory and allergic symptoms and diseases and the age-related decline in lung function, 2) the distribution of heart rate variability in the general population over age 50, 3) the association of these health indicators with individual long term exposure to air pollution, other toxic inhalants, life style and molecular factors. Another follow-up examination (SAPALDIA 3) started in January 2010. This study is well positioned to address crucial questions of air pollution epidemiology and important environmental health policy-related questions in the coming years. When SAPALDIA was initiated in 1991, 9' '''651 subjects, aged 18 to 60 years, were recruited for a detailed computer-based interview and more than 90% of them underwent lung function and atopy testing. More than 7' '''000 of the subjects had bronchial reactivity tested by a methacholine challenge. SAPALDIA shares parts of its study protocol with the European Community Respiratory Health Survey (ECRHS) with which it is linked through the study center of Basel. Since 1991 SAPALDIA has been carefully following address histories of its participants. In the 2002 follow-up, 8' '''047 (83%) provided health information, 6' '''528 persons underwent physical re-examination, and 6' '''345 provided blood samples to establish an extensive blood, plasma, serum and DNA bank. In addition, 1' '''813 subjects aged 50 or older participated in 24h-ECG Holter monitoring to provide detailed data on parameters of heart rate variability. With the inclusion of cardiovascular endpoints, SAPALDIA is one of the first studies examining effects from long-term exposure to air pollution on cardiovascular health parameters as well as mutual influence between the respiratory and the cardiovascular system. The SAPALDIA bio-bank has allowed scientific publications on the association between some genetic profiles (gene polymorphism) and the propensity to develop asthma, allergic diseases, or accelerated lung function decline with age. Ongoing studies are focusing on gene-environment interactions a crucial question to understand why some persons suffer more from the effect of air pollution than others.
DomIns: A Web Resource for Domain Insertions in Known Protein Structures
DomIns is a web resource aimed at providing comprehensive information on domain insertions in proteins of known structure. We have followed the definition of protein domains as in the SCOP (Structural Classification of Proteins) database in order to identify insertions. We have considered only the major five classes (All-alpha, All-beta, alpha/beta, alpha+beta and Small Proteins), the fold and the superfamily level of SCOP hierarchy for identifying insertions. Apart from browsing insertions in whole PDB, we also provide an option to browse insertions in a pre-computed list of non-redundant PDB chains provided by PDB_Select with a sequence identity threshold of 90%.
DBAli. A Database of Structure Alignments.
DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. It is not currently being updated; however, updates should resume in the near future. All pairwise structural comparisons in DBAli have been obtained using the MAMMOTH program developed in the group of Prof. Angel R. Ortiz. All multiple structure alignments in DBAli have been obtained using the SALIGN command in MODELLER developed in the group of Prof. Andrej Sali.
The database of germline p53 mutations is a comprehensive database covering all published cases of germline p53 mutations. The current version lists 580 tumors in 448 individuals belonging to 122 independent pedigrees. The database describes each p53 mutation (type of the mutation, exon and codon affected by the mutation, nucleotide and amino acid change), each family (family history of cancer, diagnosis of Li-Fraumeni syndrome), each affected individual (sex, generation, p53 status, from which parent the mutation was inherited) and each tumour (type, age of onset, p53 status-loss of heterozygosity, immunostaining). Each entry contains the original reference(s).
The CutDB focuses on the annotation of individual proteolytic events, both actual and predicted. Its offers searchable lists of proteases, Merops code, substrate, and diseases from which users can specify their desired queries in order to obtain more specific information. CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and cleavage site. Currently, CutDB integrates 3070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications. CutDB supports various types of data searches and displays, including clickable network diagrams. Most importantly, CutDB is a community annotation resource based on a Wikipedia approach, providing a convenient user interface to input new data online. A recent contribution of 568 proteolytic events by several experts in the field of matrix metallopeptidases suggests that this approach will significantly accelerate the development of CutDB content.
The Chloroplast Genome Database contains annotated chloroplast/plastid genomes from the NCBI Organelle Genomes section at NCBI. Users can search for genes by their annotated names, conduct flexible BLAST searches, download protein and nucleotide sequences extracted from a selected chloroplast genome, and browse the putative protein families (tribes) created using TribeMCL.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Cardviews is a CARDinal plane VIEWing System developed at the Center for Morphometric Analysis at the Massachusetts General Hospital. It is a tool for brain morphometry (including volumetric analysis using xvol) and this program emerged as a product of our methodological development. While some of its functionality is specifically tailored for our general segmentation and neocortical parcellation routines, the imaging interface, segmentation tools, and localization capacity have utility extending beyond the specific aims motivating its initial conception. :
The CyberCell database (CCDB) is a comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655). It is intended to provide sufficient information and querying capacity for biologists and computer scientists to use computers or detailed mathematical models to simulate all or part of a bacterial cell at a nanoscopic (10-9 m), mesoscopic (10-8 m) and microscopic (10-6 m) level. The CCDB database is actually several databases: CCDB contains quantitative proteomic, genomic and metabolic information about E. coli. CC3D contains 3D structural data for E. coli structural proteomics work CCRD contains detailed information on E. coli RNA molecules CCMD database contains quantitative information on E. coli metabolites. Each database is presented as a re-formattable synoptic table which allows users to casually browse the databases. Detailed information about each gene, protein, RNA, structure or metabolite may be obtained by clicking on the *Card button on the left column. Each card contains more than 60 fields concerning all aspects of the sequence, function or structure of a given molecule. CCDB users may also perform text searches (using the Search button), BLAST sequence searches (using the BLAST button) or conduct more detailed data extraction or relational data searches (using the Extract button).
Software application to help plan quantitative trait locus (QTL) experiments. (entry from Genetic Analysis Software)
Software application based on the Ant Colony Optimization to solve the special case of the traveling salesman problem of ordering markers when the number of loci is large. ANYMAP performs segregation test, linkage grouping and locus ordering, and constructs a linkage map rapidly. (entry from Genetic Analysis Software)
Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software)
PLACE- A Database of Plant Cis-acting Regulatory DNA Elements
A database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included. Note: As of January 2007, PLACE is no longer updated or maintained.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A relational database in which all editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored and maintained in ad hoc designed textual flat files. Individual genes of interest can be searched by appropriate query strings containing the gene name or the intracellular location or the molecular type (as tRNA, rRNA, intron) or the organism or a combination of the previous terms. Moreover, each record of the REDIdb database can be also retrieved according to its specific accession number (more help on how to perform a REDIdb search is available at the ?help? page). To make easier the browsing of each REDIdb entry and quicker the identification of editing sites, two alternative but complementary facilities have been provided either to graphically display genomic and cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are shown by mousing over.
These programs have been written over the last 20 years for analysis of our own results. They all do some things that are still not available in any commercial program. The programs are written in protected-mode 32-bit Fortran 90, with some assembler subroutines for fast graphics, and the Gino graphics library. Thus they are essentially DOS programs, though they are usually run from Windows, either via a desktop icon (the .ico files) or in the DOS box. The manuals (now in pdf format), have now all been collected into a single document, DCMANUALS.PDF, which should be downloaded, and the bits that you need can then be printed. Note that some sections are common to many or all programs, e.g. the notes on the graph and histogram drawing subroutines, and it is important to read this before using any of the programs (though there is a lot of online help (hit F1) for the graphics, and also in SCAN. Sponsor. Our work was supported by the Wellcome Trust (project grant 074491) and the Medical Research Council (programme grant G0400869).
It is a database of RNA Junction and Kissing Loop Structures. RNA is versatile in both its structure and function. Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each. If you are interested in RNA as a building block for nano-scale design or if you are analyzing the properties of specific RNA motifs you should find utility in this site. The junctions in this database were extracted using a junction scanning algorithm from a number of structures from the Protein Data Bank. Coming from parent structures, both NMR and crystal, these junctions may be under contextual constraints. It is possible that these constraints play a critical role in the junction's conformation and stability.
Network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. Requests can also be submitted by e-mail to dali-server at helsinki dot fi. The body of the e-mail message must contain atomic coordinates in PDB format. If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database. If you want to superimpose two particular structures, you can do it in the pairwise DaliLite server. Academic users may download the DaliLite program for local use.
The DNA amount in the unreplicated gametic nucleus of an organism is referred to as its C-value, irrespective of the ploidy level of the taxon. The Plant DNA C-values Database currently contains data for 7058 plant species. It combines data from the Angiosperm DNA C-values Database, Gymnosperm DNA C-values Database, the Pteridophyte DNA C-values Database, the Bryophyte DNA C-values Database, together with the addition of the Algae DNA C-values database.
Diabetes / Endocrine Diseases Biorepository
Ohio University Diabetes / Endocrine Diseases Biorepository
Ohio University Diabetes/Endocrine Diseases Biorepository
Plasma and cell fractions obtained from patients with Diabetes and endocrine diseases and their first degree relatives who agreed to participate in the development of the biorepository. Plasma is aliquoted into multiple specimen containers and stored at -80C. Cell fractions are subjected to DNA and RNA fractionation, aliquoted into multiple specimen containers, and frozen at -70 to -80 degrees centigrade. Anyone who would like to obtain samples from the Biorepository must provide evidence that they have adequate training in the use of bloodborne pathogens, as outlined by OSHA. The investigator must agree to indemnify and hold harmless the Ohio University Diabetes/Endocrine Diseases Biorepository, the Appalachian Rural health Institute, and the Ohio University College of Osteopathic Medicine from any claims, liability, costs, and damages.
The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects.
DroSpeGe provides a preview of newly sequenced Drosophila genomes, with genome maps and BLAST sequence search. Genome maps include D. melanogaster genome homology, homologies to nine eukaryote proteomes, marker gene locations, and Drosophila microsatellites. Current genome assemblies can be BLASTed, with links to genome maps of your BLAST matches. Annotation data are available in Gene Finding Format (GFF) for these whole genome comparisons.
Software program for creating montages from multiphoton microscopy.
L2L Microarray Analysis Tool: A simple tool for discovering the hidden biological significance in microarray expression data
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019. Database of published microarray gene expression data, and a software tool for comparing that published data to a user' '''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don' '''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
DEDB - Drosophila melanogaster Exon Database
DEDB : Drosophila melanogaster Exon Database
Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers.
BGI-RISe - Beijing Genomics Institute Rice Information System
Integrated information resource for rice genomes as well as a workbench for comparative genomic analysis among cereal crops. Sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. The rice genomes have been annotated for gene content, repetitive elements, and SNPs. Sequence polymorphisms between different rice subspecies have also been identified. Designed as a basic platform for rice study, the sequenced genomes and related information is presented in systematic and graphical ways for the convenience of in-depth comparative studies. In addition to the comprehensive data of Oryza sativa L. ssp. indica sequenced, BGI-RIS will host carefully curated genome information of Oryza sativa L. ssp. japonica.
GenGen: Genetic Genomics Analysis of Complex Data
A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated.
A collection of secreted proteins from Human, Mouse and Rat proteomes, which includes sequences from SwissProt, Trembl, Ensembl and Refseq. The 18,152 entries are classified into fourteen functional categories, including "apolipoprotein", "cytokine", "protease", "toxin", etc. To make the dataset more comprehensive, nine related datasets were also collected, such as SPDI, Riken mouse secretome, SwissProt vertebrate secreted proteins, SubLoc etc.
Testing Haplotype EffectS In Association Studies
Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software)
It collects three dimensional protein models obtained by structure prediction methods. Users can both contribute new models and search for existing ones. The database currently stores all models submitted to the last four editions of the CASP experiment.
BSORF - Bacillus Subtilis Genome Database
This website provides a resource for the Bacillus subtilis genome. It provides a list of mutants, DNA array data, and search features against both the whole genome and coding sequences. It also contains Kegarrays and access to the KEGG Expression Database.
A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info
Disease Mapping using Linkage disEquilibrium
Software application for high-resolution mapping of the position of a disease mutation relative to a set of genetic markers using population linkage disequilibrium (LD). (entry from Genetic Analysis Software)
An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data
Data set on the prevalence of self-care behaviors by non-institutionalized older adults. Personal interviews were conducted with 3,485 individuals 65 years of age and older, with oversampling of the oldest old. Questions were asked about the type and extent of self-care behaviors for activities of daily living, management of chronic conditions (through self-care activities, equipment use, and environmental modifications), medical self-care for acute conditions, health promotion/disease preventions, social support, health service utilization, and socio-demographic/economic status. A follow-up study by telephone was conducted in 1994 to continue examination of subjects. Many of the same questions from the baseline were asked, along with questions regarding change in health status since baseline and nursing home visits. For subjects who had been institutionalized since baseline (Part 2), information was gathered (by proxy) regarding demographic status, living arrangements prior to institutionalization, and reasons for institutionalization. For subjects who had died since baseline (Part 3), information was again gathered through interviews with proxies. Questions covered nursing home admissions and date and place of death. In both waves, a proxy was substituted if the subject was hospitalized (or institutionalized since baseline), too ill, cognitively not able to respond, or deceased. Survey data were linked to Medicare/Medicaid health utilization records. The baseline data are archived at NACDA as ICPSR Study No. 6718, and the followup data are archived as ICPSR Study No. 2592 and linkable to the baseline data. * Dates of Study: 1990-1994 * Study Features: Longitudinal * Sample Size: ** 1990-1: 3,485 (Baseline) ** 1994: 2,601 (Followup) Links: * 1990-1991 Baseline ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06718 * 1994 Follow-up ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/02592
RARTF: RIKEN Arabidopsis Transcription Factor database
RIKEN Arabidopsis Transcription Factor database
Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available.
pTARGET: Prediction server for protein subcellular localization
pTARGET is a computational method to predict the subcellular localization of only eukaryotic proteins from animal species that include fungi and metazoans. Predictions are carried out based on the occurrence patterns of protein functional domains and the amino acid compositional differences in proteins from different subcellular locations. This method can predict proteins targeted to nine distinct subcellular locations that include cytoplasm, endoplasmic reticulum, extracellular/secreted, Golgi, lysosomes, mitochondria, nucleus, peroxysomes and plasma membrane. Current predictions are based on Pfam database version 19.0. Datasets used for developing pTarget method are available., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
It archives data on more than 700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene its domain structures and relevant protein homologues across species as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of 500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints highlighted by visualization means in the NOPdb provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/ uncharacterized proteins. The NOPdb is searchable by either gene names protein sequences Gene Ontology terms or motifs or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink OMIM and PubMed).
Although hundreds of miRNAs have been discovered in mammalian genomes, the function of less than a handful of miRNAs is known. This viewer allows access to the predicted protein coding gene targets that are conserved between human and mouse/rat. Searching by miRNA will display a ranked list of gene targets and allow you to analyze each conserved target gene/sites in detail. Similarly, searching by gene name/identifier will display the sequence of the three prime UTR and the positions of the miRNA sites along the sequence, allowing you to analyze the target sites in detail. * View miRNA target sites for any target gene * View target genes and sites for any miRNA
It provides the mapping of relationships between soybean genomic features in a way that is presentable in GBrowse. It combines Perl MySQL database programming with Gbrowse to provide an integrated way of presenting soybean genomic features. The database is also searchable for listings of these relationships.
BioIE: Extracting Informative Sentences From the Biomedical Literature
BioIE is a rule-based system that extracts informative sentences relating to protein families, their structures, functions and diseases from the biomedical literature. Based on manual definition of templates and rules, it aims at precise sentence extraction rather than wide recall. After uploading source text or retrieving abstracts from MEDLINE, users can extract sentences based on predefined or user-defined template categories. BioIE also provides a brief insight into the syntactic and semantic context of the source-text by looking at word, N-gram and MeSH-term distributions. Important Applications of BioIE are in, for example, annotation of microarray data and of protein databases.
A database of information on short tandem repeat systems. It contains facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes.
Epidemiology of Chronic Disease in the Oldest Old
Kaiser Permanente Study of the Oldest Old
A collection of data of an epidemiological study of chronic disease in the oldest old based on information collected from Kaiser Permanente facilities in Northern California (KPNC). The initial sample was drawn from the Kaiser''s active membership lists for the years 1971 and 1980. The sample was restricted to members that had a Multiphasic Health Checkup examination (MHC) within 7 years of the baseline date. The sample was stratified to attain equal numbers of observations (1,000 in each) in three sex-age cells for each cohort: 65-69, 70-79, and 80+. Each cohort was followed for 9 years through existing medical records and computerized hospitalization tapes. Mortality data was collected by matching the sampled data with state Vital Statistics data for an additional 3 years for a total follow-up time of 12 years. Part 1 of the data collections consists of Master Records, which includes information from the morbidity review, in which over 35 chronic conditions or diagnoses were abstracted from the member charts, as well as detailed diagnostic criteria for the major conditions. A prevalence review was done, which included the 4 years prior to the baseline date for these same conditions. Recurrent disease is included for the following conditions: cancers, myocardial infarction, and various forms of strokes. A detailed account of outpatient health services use, and data from the multiphasic health checkup, which was administered to each participant during the nine yearly follow-ups, are also included in the Master Records file. The labs and procedures included: chemistry, hematology, urinalysis, bacteriology, chest x-ray, GI x-ray, ultrasound, CT/MRI, mammogram, resting ECG, treadmill ECG, echocardiograms, nuclear scans, outpatient breast biopsy, cystoscopy, and cataract surgery. Inpatient utilization includes all hospitalizations, procedures done during a hospital stay, length of stay, admitting/discharge diagnosis. Part 2, Hospitalization, contains records of causes and dates of hospitalizations and discharges and nursing home admissions. There is also a section on incomplete reviews and the reasons for them. Demographic information and some lifestyle information from the multiphasic health checkup (e.g., smoking, alcohol, and Body Mass Index) are also in this file. Data Availability: These datasets have been documented extensively and are available from the ICPSR (Study No. 4219). * Dates of Study: 1971-1992 * Study Features: Longitudinal, Anthropometric Measures * Sample Size: ** 1971 cohort: 2,877 (baseline) ** 1980 cohort: 3,113 (baseline) ** 1971 & 1980: 5,990 ** Hospitalization: 14,730 Links: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04219 * HSRR: http://wwwcf.nlm.nih.gov/hsrr_search/view_hsrr_record_table.cfm?TITLE_ID=381&PROGRAM_CAME=toc_with_source2.cfm
Provides access to large scale cell culture at reasonable cost. The Cell Culture Center has experience with the production of over 1700 cell lines. Numerous common cell lines, such as HeLa, CHO, 293, BHK, and hybridomas are routinely produced at the Center. We will adapt your cell line or custom protocol to large scale production then deliver the cells in the quantity and frequency you need. Large Scale Production Services: Mammalian cells: Suspension culture (1 to 400 liters per day), Anchorage dependent culture (1 to 200 roller bottles per batch), Purified monoclonal antibodies (10 mg to 100 grams), Non-hybridoma cell secreted proteins, Conditioned media Secreted proteins from suspension cultures can be produced in automated hollow fiber bioreactor systems. These systems may be considered after initial static culture production yields are determined. Upon determining the quantities requested by the investigator, the appropriate automated system will be used. For more information on the automated instrumentation available for the use of secreted protein production, please refer to the Biovest International web page (www.biovest.com). Working with our experienced personnel and quality controlled, state-of-the-art facilities also permits access to large quantities of cells or protein so you aren''t limited by the cell culture capacities of your own laboratory. The Center fulfills the needs of small research laboratories as well as those of larger institutions. Customers from all sectors of the research and industrial community are welcome to inquire about our services. If you''d like to inquire about using our services, use the contact infromation below. Key words: Cell, cells, culture, monoclonal, antibodies, antibody.
A database of the genomes of representative strains of the four Shigella species and comparative genomic hybridization (CGH) of 43 different serotypes of Shigella strains by microarray. The intra-species comparison of Shigella genomes are presented at several different levels in the database, including not only basic genome features, structure of genomes and orthologs ordering, but also metabolic pathways and virulence factors. Moreover, the CGH results on 43 different serotypes of Shigella strains were also integrated into ShiBASE. The newly developed online sequence comparison visualization service, Shi-align, offers an easy way for biologists to perform comparative analysis on their own data.
A collection of Active protein Sequences, or protein fragments or subsequences, collected in the form of function-oriented databases. Since its first release, ASC has extended its topics to other specific functions as well as by including databases with structural peculiarities. The current release (Spring 2005) includes seven databases: - AIRS: a database of Auto Immune Related Sequences. The collected information comes from the literature and each entry reports the peptide sequence, information about its biological activity, the reference (with hyperlink to Medline or other similar service). - BAC: a database of Bio ACtive peptides. The collected information comes from the literature and each entry reports the peptide sequence, its biological activity, the reference (with hyperlink to Medline or other similar service). - CHAMSE: a database of CHAMeleon SEquences. This name indicates the structural feature of some segments which have been observed to assume both alpha helix and beta strand structure in 3D models of proteins. - DORRS: a Database Of RGD Related Sequences which collects active linear and cyclized short peptide sequences taken from literature. - DVP: a database of Delivery Vector Peptides. The collected information comes from the literature and each entry reports the peptide sequence and the reference (with hyperlink to Medline or other similar service). - SSP: a Database of Structures of Solved Peptides. - TRANSIT: a database of TRANsglutamination SITes which collects information from literature about protein amino acids substrates of the transglutaminase enzyme (E.C. 2.3.2.13 - click the number for the ENZYME database link at the ExPASy Molecular Biology Server).
A software tool that allows users to input a DNA (or RNA) sequence and obtain its inverse, complement or inverse complement. The program can also be used to display a DNA sequence and its complement in double-stranded format. Functions after users paste a DNA sequence into the upper text box, then click the appropriate button to place a manipulated form of the sequence in the lower text box.
Therapeutically Relevant Multiple Pathways Database
The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic targets described in the literatures, the targeted disease conditions, and the corresponding drugs/ligands directed at each of these targets. This database currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions along with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. Additional information provided include protein name, synonyms, Swissprot AC number, species, gene name and location, protein sequence (AASEQ) and gene sequence (NTSEQ) as well as potential therapeutic implications while applicable. Cross-links to other databases are provided which include Genecard, GDB, Locuslink, NCBI, KEGG, OMIM, SwissProt to facilitate the access of more detailed information about various aspects of the particular target or non-target protein. Queries can be submitted by entering or selecting the required information in any one or combination of the fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field. Sponsors: TRMP is supported by the National University of Singapore.
ArchDB - Biological Database of Protein Loops
ArchDB is a compilation of structural classifications of loops extracted from known protein structures. ArchDB includes 4 classifications: * ArchDB40 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 40% sequence identity. * ArchDB95 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 95% sequence identity. * ArchDB-EC is a classification of loops extracted from proteins with known enzymatic function * ArchDB-KI is a curated classification database of kinase loops EC number 2.7.X.X with functional information of residues. Futhermore, the functional annotation of residues in this database are further classified in four categories: 1. ATP interaction: for residues involved on ATP binding/interaction. 2. Substrate binding: for residues involved in substrate interaction/binding with the exception of ATP 3. Ion interaction: for residues involved in ion interaction/binding of ions needed for the catalytic mechanism 4. Catalytic: involved in reaction, the stabilization of a transition state or the activation of substrates. Additionally, three different approaches were applied to identify functional residues of the loops of the sub-classes: 1. Residues found within a cut-off distance of 6���� from an heteroatom, ligand, inhibitor, cofactor or complex partner molecule (protein or DNA), with the exception of D2O or crystallization buffer molecules. 2. Residues identified by functional information from ACTSITE and SITE records in the RCSB protein data bank. 3. Residues identified by the functional annotation collected from the literature and assigned to specific motifs of kinases. Lastly, the multiple ways to browse and query in ArchDB are: * Search by sequence: Users can search for classified loop(s) with sequence similarity to a query sequence. * Search by structure: Users can upload protein coordinates in PDB format and its loops will be extracted and compared with those from the classification. First: structural class is assigned comparing loop geometry and, second: the loop conformation is compared among the subclasses within the assigned class. * Search subclasses and/or Search Loops: A range of options are offered for subclass or loop searches. Users can query ArchDB asking for subclasses or loops with specific flanking secondary structures, length of loops or phi/psi loop conformation. Also, users can retrieve all subclasses or loops with PDB SITE annotations and contacts with co-crystallized ligands. Finally, users can search for subclasses that have SCOP, GO or EC annotations conserved at different percentage levels. * Search structures: Users can search for classified PDB structures in ArchDB with specific Sprot. Annotation/Keyword, GO annotation, SCOP and EC codes. * Specific queries for ArchDB-KI: Users can list functional subclasses or loops classified in ArchKI. :Sponsors: ArchDB is funded by grants from Fundacin Areces (Spain), Ministerio de Ciencia y Tecnologa Spain (MCYT; BIO2002-03609, BIO2001-246 and BIO2001-264), Centre de Referncia en Biotecnologia Generalitat de Catalunya (CERBA), and the Generalitat de Catalunya : :Enzyme-specific classification, :Kinase proteins, ligand, Protein residue, Protein motif, Protein loop,
It has been developed with the aim to annotate the complete set of Drosophila melanogaster nuclear genes encoding for mitochondrial proteins in order to contribute to their functional characterization. The data collected in MitoDrome derive from the comparison of Human mitochondrial proteins available in SWISSPROT vs. the Drosophila genome, ESTs and cDNA sequences available in the FlyBase database. According to the results, each Drosophila gene sharing significant homology with a human mitochondrial protein was classified as a putative Drosophila mitochondrial gene and annotated in MitoDrome.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database aiming to guide experimental studies and in silico simulation studies on the culture conditions of obligate parasitic bacteria. Now we are gathering biological data relevant to the improvement of culture conditions of different obligate parasitic bacteria, and organizing a database named Metagrowth. The data were collected from literature, genomic sequence information, metabolic databases and transporter databases. Each database entry is composed of evidences and derived hypotheses. The hypotheses are physical conditions or supplementation of molecules in culture media, that may lead to the improvement of the bacterial growth. Currently about 200 entries are available for six different bacteria.
The Essential Genes in E. Coli website provides links to data on essential genes in E. coli, and shows a short list of E. coli essential genes identified from the Neidhardt E. coli books. Essential genes are defined as those genes which are required in WT strain MG1655 for the formation of colonies on solid rich medium within 24 hours of incubation at 37 degrees C.
A database of protein domains shared by different sequence clusters. These were assembled by performing an "all-by-all" comparison of (putative) protein sequences with the BIOFACET software, building clusters of sequences based on their similarity and finally displaying &agrave; la Prodom the domains shared by the sequences in each cluster.
Software application for Bayesian estimation of the coancestry coefficient FST (entry from Genetic Analysis Software)
Software application for Bayesian estimation of the population inbreeding coefficient f (entry from Genetic Analysis Software)
VirOligo: Virus Oligonucleotide Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of virus-specific oligonucloetides and their primers. It allows users to search based on virus name, PMID, VirOligoID, or taxonomy ID. The VirOligo database is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place. To this end, researchers are also exploring Virus Signature Hybridization (ViSH) and Virus Signature Amplification (ViSA), microarray-based methods for hybridization and PCR amplification. The site employs Universal PCR techniques, a PCR that amplifies DNA fragments from more than one viral species, such as family- or genus-specific PCR.
HUGE - Human Unidentified Gene-Encoded large proteins
The HUGE protein database has been created to publicize the Human cDNA project at the Kazusa DNA Research Institute. This project will sequence and analyze long (>4 kb) human cDNAs and establish methods by using the sequence data how to predict the primary structure of proteins of various biological activities. Currently, it focuses on the analysis of cDNA clones encoding particularly large proteins (>50 kDa). The HUGE protein database contains various types of information derived from the predicted primary structure data of newly identified human proteins. The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on.
Software package providing an interactive graphical interface for computations in dynamical systems and visualization of resulting geometric structures, designed for researchers and educators studying dynamical systems (both differential equations and discrete time systems). DsTool readily produces nice pictures for both discrete and continuous systems.
A pathway-based graphical interface for navigating the glycoenzyme database. The goal of the project is to define the paradigms by which carbohydrate binding proteins function in cellular communication. These pages are divided into six categories: -Glycosphingolipid: Sub-categories are Isogloboseries, Globoseries, Neo-lactoseries, Lactoseries and Ganglioseries - N-linked: Sub-categories are High-mannose, Hybrid and Complex -Mucin -Terminal Core 1 -Other O-linked -Terminal All: Includes all potential terminal structures for each glycan category
DOLOP: A Database of Bacterial Lipoproteins
DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins.
A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
VKCDB - Voltage-gated K Channel Database
Voltage-gated potassium channel database (VKCDB) is designed to serve as a resource for research on voltage-gated potassium channels. Protein sequences, references, functional data and many other relevant data are included in this database. Mysql is used as the underlying database management system to meet the requirements of future development plans. VKCDB will allow you to browse and search using different annotation criteria, and search against the sequences in VKCDB with VKCBLAST. Displayed entries can be selected to download as multiple sequences in FASTA format for further analyses, such as ClustalW alignment. Several computational tools are being developed to help guide structure function analysis of voltage-gated potassium channels and other protein families in general. VKCDB currently stores 346 voltage-gated potassium channel entries, including some "unknown proteins" annotated by automatic genome annotation projects which share a high degree of sequence similarity with voltage-gated potassium channels. VKCDB was populated using automatic parsing of BLASTP search output. Entries were checked manually for redundancy, sequence conflicts, and isoforms, and they are hyperlinked to their variant entries as well as to entries with sequence conflicts. All entries contain GenBank annotations and Swissprot annotations if available. Current annotations were updated with Swissprot release 43.1 (Apr 2004) and GenBank as of Apr 2004. The snapshot version 3 of VKCDB in XML format as of Apr 2004 can be downloaded here. We collected available electrophysiological data and pharmacological data from over 200 journal articals and stored them in VKCDB. VKCDB is updated regularly from BLAST searches of new entries in GenBank and Swissprot. VKCBLAST are updated to include new sequences within a few days after new entries are added into VKCDB. Sequences of all VKCDB entries were sent to TMHMM and PHD for membrane domain prediction. Both results were parsed and linked to each VKCDB entry page. Multiple alignment of T1 and six transmembrane domains of Kv1-4 and KCNQ (Kv7) family are also presented here. VKCDB is a part of an ongoing high throughput voltage-gated potassium channel sequencing project in the laboratories of Dr. Warren J. Gallin and Dr. Andy N. Spencer at the University of Alberta, Canada.
Software application that selects high resolution mapping subsamples and performs bin mapping (entry from Genetic Analysis Software)
It is a comprehensive database of Gene Expression Profiles, which enable to compare the transcriptome of various tissues, organs and experiments. mRNA expression levels of thousands of genes are measured with oligo-nucleotide DNA microarray "GeneChip". All gene expression data in this database is produced by LSBM (Laboratory for Systems Biology and Medicine) and the collaborators. SBM DB provides two different databases: A reference database for fur expression analysis (RefEXA) and LSMB GeNet, a database of various organisms, tissues, and experiences. RefEXA provides a comprehensive gene expression database of Human normal tissues, normal cultured cells and cancer cell lines with GeneChip HG-U133A, can help investigation of Human disease. LSMB provides
Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene.
Engineering and Physical Sciences Research Council
EPSRC is the main UK government agency for funding research and training in engineering and the physical sciences, investing more than £850 million a year in a broad range of subjects from mathematics to materials science, and from information technology to structural engineering. We support research into engineering, mathematics, physics, chemistry, materials science, information and communications technologies. EPSRC is a non-departmental public body funded by the UK government through the Department for Universities, Innovation and Skills. We employ around 300 staff in Swindon. We manage our portfolio through programmes. Research base programmes focus on investigator-led research and training. Business innovation programmes deliver our priority research themes and maximise the economic and social impact of the research and training we fund.
Graphical Representation of Relationships
A graphical tool designed for detection of errors in relationship specification in general pedigrees by use of genome scan marker data. (entry from Genetic Analysis Software)
DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. Supported architectures are Linux-i586 and Mac OSX. Versions for IRIX, OSF1 and SunOS are made available sporadically, usually upon request. DINO is distributed in binary form only, the current DINO version is 0.9.1. Structural Biology is a multidisciplinary research area, including x-ray crystallography, structural NMR, electron microscopy, atomic-force microscopy and bioinformatics (molecular dynamics, structure predictions, surface calculations etc). The data produced by these different research areas is very diverse: atomic coordinates (models and predictions), electron density maps, surface topographs, trajectories, molecular surfaces, electrostatic potentials, sequence alignements etc... DINO aims to visualize all this structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines). The number and size of the data the program can handle is only limited by the amount of RAM present in the system. No artifical limits are set. Supported input file formats are PDB (coordinates), X-PLOR/CNS (coordinates, electron densities and trajectories), CHARMM (coordinates, trajectories and scalar fields), CCP4 (electron densities), UHBD (el, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The AARSs database is the collection of amino acid sequences of all published AARSs. Currently it contains 1047 primary structures of cytoplasmic and organellar AARSs from various organisms. The entries are grouped according to AARS amino acid specificity. They are based on EMBL/SWISS-PROT format. Each includes the AARS amino acid sequence, its SWISS-PROT name and the accession number, a short description of the sequence, its source (organism name with taxonomic classification) and bibliographic information. For the enzymes whose sequences were determined at the nucleotide level, the appropriate EMBL/GenBank or TIGR entries are included, and for those with already known 3D structure, the cross-references to the Brookhaven Protein Data Base are indicated. The partial sequences of AARSs are also included in the database. According to the original SWISS-PROT description, some of the entries have been marked as putative or probable.
Extensible MATLAB Medical image Analysis
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. EMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files, viewing images, performing ROI operations, and performing several popular analyses. Also, there are toolkits for performing kinetic analysis of dynamic PET rCBF (regional cerebral blood flow) and FDG data. The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools that are of use to the general community.
Aging Status and Sense of Control (ASOC)
A dataset generated longitudinal study that aims to explain the relationship between age and changes in the sense of control over one' '''s life, over two follow-up periods. The main hypotheses are (a) over a period of time, the sense of control declines by an amount that increases with age; (b) the change in sense of control reflects an underlying change in biosocial function, which accelerates with age; (c) higher social status slows the decline in the sense of control, possibly by preserving biosocial function; and (d) changes in biosocial function and in the sense of control have deviation-amplifying reciprocal effects that accelerate age-dependent changes in the sense of control. This was a three-wave panel survey with fixed 3-year intervals and repeated assessments of the same variables. Questionnaire topics focused on: physical health (subjective health; activities of daily living; height and weight; health conditions; expected personal longevity); health behavior (exercise, smoking, diet, alcohol use); use of medical services (medical insurance coverage, prescription drug use); work status (current employment status; title of current job or occupation and job description; types of work, tasks, or activities; description of work or daily activity and interactions; supervisory status; management position and level; work history); sense of controlextent of agreement or disagreement with planning and responsibility versus luck and bad breaks; sense of victimhood versus control; social support and participation; personal and household demographics; marital and family relations; socioeconomic status; history of adversity. * Dates of Study: 1994-2001 * Sample Size: 2,593 (Waves 1-2); 1.144 (Wave 3) * Study Features: Longitudinal Data Archives: http://www.sscnet.ucla.edu/issr/da/da_catalog/da_catalog_titleRecord.php?studynumber=I3334V1
A database for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion (ADME) associated proteins. It contains information about known drug ADME associated proteins, functions, similarities, substrates / ligands, tissue distributions, and other properties of the targets. Associated references are also included. Drug absorption, distribution, metabolism and excretion (ADME) often involve interaction of a drug with specific proteins. Knowledge about these ADME-associated proteins is important in facilitating the study of the molecular mechanism of disposition and individual response as well as therapeutic action of drugs. It is also useful in the development and testing of pharmacokinetics prediction tools. Several databases describing specific classes of ADME-associated proteins have appeared. A new database, ADME-associated proteins (ADME-AP), is introduced to provide comprehensive information about all classes of ADME-associated proteins described in the literature including physiological function of each protein, pharmacokinetic effect, ADME classification, direction and driving force of disposition, location and tissue distribution, substrates, synonyms, gene name and protein availability in other species. Cross-links to other databases are also provided to facilitate the access of information about the sequence, 3D structure, function, polymorphisms, genetic disorders, nomenclature, ligand binding properties and related literatures of each protein. ADME-AP currently contains entries for 321 proteins and 964 substrates. ADME Class Based on their respective role of pharmacokinetics, ADME-associated proteins can be classified into four categories: A: This Category includes proteins involved in the absorption or re-absorption of drugs into systemic system. D: This category includes proteins responsible for facilitating the distribution of drugs from the systemic system to the target sites or away from the target sites back to the systemic system. Certain plasma proteins and intracellular binding proteins may alter free drug concentration by acting as drug storage depot. These proteins thus play a regulatory role in drug distribution and they are thus included in Category D. Based on their role in drug distribution, proteins in this category can be further divided into three groups D1, D2, and D3. The first group D1 includes transporters capable of transporting chemicals across membranes of various tissue barriers from the systemic system into the target sites. Blood-brain barrier and placenta barrier are examples of tissue barrier. Proteins in the second group D2 are responsible for transporting drugs back into the systemic system. Proteins in the third group D3 mainly function as drug storage depot. These include ligand binding proteins in plasma and intracellular proteins. M: Proteins in category M are drug-metabolizing enzymes. These enzymes can be further divided into two separate groups M1 and M2, according to whether the corresponding enzymatic reaction is phase I or phase II. E: This category E includes proteins that enable the excretion or presystemic elimination of drugs. Some proteins belong to more than one category: e.g. P-glycoprotein both limits intestinal absorption and excludes drugs from the brain back to the blood. It thus belongs to both Category E and D. For those proteins capable of transporting natural substrates without literature report of interaction with a drug, a postfix potential is attached to their respective classification to indicate that their specific role in ADME is yet to be confirmed. Use of ADME-AP for commercial purposes is not allowed.
Software to graphically browse results of clustering and other analyses from Cluster.
dChip Software: Analysis and visualization of gene expression and SNP microarrays
Software for analysis and visualization of gene expression and SNP microarrays.
Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets.
Software to process fluorescent images of microarrays.
Welcome to Michael Eisens lab in the Howard Hughes Medical Institute (HHMI) at University of California at Berkeley (UCB) and the Lawrence Berkeley National Lab (LBNL). We are part of the Department of Molecular and Cell Biology of UCB and the Genomics Division of LBNL, and the. We are located in Stanley Hall on the Berkeley campus.Our lab applies computational and experimental genomic approaches to study how genome sequences specify organismal form and function. We are particularly interested in the regulation of gene expression, and focus on how the information that specifies when and where genes are expressed is encoded in genome sequences, the role that regulated gene expression plays in animal development and the response of microbes to their environments, and how variation in and evolution of gene expression contributes to phenotypic variation and the remarkable diversity of life on Earth. This site contains a more detailed description of our research projects, an introduction to members of the lab, reprints of all of our publications, free downloadable and web-based software. Sponsor. Experimental work described here was supported by a Howard Hughes Medical Institute Investigator award to MBE and by National Institutes of Health (NIH) grant GM704403 to MBE and MDB. Computational analyses were supported in by NIH grant HG002779 to MBE. Work at Lawrence Berkeley National Laboratory was conducted under Department of Energy contract DE-AC02-05CH11231. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
THe dQSNP database accumulates and presents experimental data of sequences and allele frequencies of SNPs in promoter regions. The regions studied here were mainly 1.0 kb upstream and 0.2 kb downstream of transcriptional start regions (TSS), which have been defined as the 5'' end of full length cDNA, obtained from the database of transcription start sites. Users can search dbQSNP records by Blast-search against STS sequences in this database, by key word or by chromosomal location.
A helper program to automate the tedious process of the creation of input files from genotype data of genome-wide scans (entry from Genetic Analysis Software)
This site has been developed by Kazusa DNA Research Institute for the purpose of offering the science community the analyzed sequence data produced by a multi-national Arabidopsis genome sequencing project coordinated by the Arabidopsis Genome Initiatives (AGI). The aim of this service is to enable users to browse the annotated sequence data produced by all the sequencing teams of AGI through an user-friendly graphic display system and search engines. Gene structures proposed on the annotated sequences as well as those predicted by computer programs are presented and each graphic item has a hyperlink to detailed information of the corresponding area. The nucleotide sequence data deposited in GenBank by AGI was downloaded, re-computer-analyzed at Kazusa and parsed results are displayed graphically.
TRIMmed-HAPlotype (previously named HAL: Haplotype ALgorithm)
Software application for linkage disequilibrium mapping based on ancestral founder haplotypes. Method uses haplotype data from general pedigrees. (entry from Genetic Analysis Software)
Fast error free and transparent compression (>2x) of image data on disk with NKI private or JPEG compression. A database browser and slice viewer integrated in the PACS system with options for: viewing DICOM header, creating BMP files (ideal for slides), sending selected images, printing, database fix tools such as changing patient IDs, deleting and anonymizing studies and series, and splitting and merging series. Uses drag and drop to load DICOM and HL7 files. A simple query/move user interface for diagnostic purposes, to improve your knowledge of DICOM, and to grab missing data from another server. Elementary DICOM print server and client - prints to the default printer. Correct display of JPEG and RLE compressed images in browser. Flexible configuration of JPEG and NKI private compression with optional (de)compression of incoming, dropped, transmitted and archived files. The JPEG compression is done using executables from the OFFIS DICOM toolkit (DCMTK version 3.5.4), developed by Kuratorium OFFIS e.V. A simple DICOM Modality Worklist implementation with HL7 import with configurable translation. A CGI WEB interface with several possible viewers (especially important for the Linux version without a GUI). The server can act as an advanced scriptable DICOM image forwarder and/or DICOM image cache. The server integrates an advanced DICOM viewer based on K-PAC DICOM training and testing Demonstration and research image archives Image format conversion from a scanner with DICOM network access DICOM image viewing and slide making DICOM image selection, (limited) editing, and splitting and merging of series Advanced scriptable image modification, filtering, forwarding and conversion DICOM caching and archive merging DICOM web access for viewing and data management (scriptable)
A compilation of E. coli mRNA promoter sequences. It includes documentation on the location of experimentally identified mRNA transcriptional start sites on the E. coli chromosome, as well as the actual sequences in the promoter region. The database is currently updated as of July 2000 and includes 471 entries.
Heart and Calcium Functional Network Database
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A specialized database for mouse heart and calcium signaling toolkit genes. It contains the functional gene modules pre-calculated from the microarray data compendium using various algorithms for genetic network analyses. The Heart and Calcium functional Network (HCNet) database is a collection of functional gene clusters calculated from microarray data compendium obtained from the Korea Systems Biology Initiative and from the publicly available GEO database. It was designed to assist experimentalists especially in the field of cardiac and calcium signaling research to detect potential network motifs and gene clusters that are functionally related or co-regulated by common transcription factors. Genes of defined numbers are classified into two categories, 1) heart-specific genes and 2) heart-specific genes plus calcium signaling toolkit-genes.
Original provider of rabbit monoclonal antibodies. Important Note for Epitomics Customers in the U.S.: As of Jan. 28, 2013, orders for Epitomics products will now be handled directly by Abcam.
Congressionally Directed Medical Research Program Grants Database
This is a database of awards granted by the Department of Defense congressionally directed research program. Vision: Find and fund the best research to eradicate diseases and support the warfighter for the benefit of the American public. :Mission: We provide hope by promoting innovative research, recognizing untapped opportunities, creating partnerships, and guarding the public trust. :Grants; funding :
Merge Healthcare Incorporated develops solutions that automate healthcare data and diagnostic workflow to enable a better electronic record of the patient experience, and to enhance product development for health IT, device and pharmaceutical companies. Merge products, ranging from standards-based development toolkits to sophisticated clinical applications, have been used by healthcare providers, vendors and researchers worldwide for over 20 years. Merge Healthcare utilizes decades of technology, expertise, intellectual property, innovative software development and expert services to build IT solutions for healthcare and biopharmaceutical customers worldwide. Merge Healthcares OEM applications and toolkits improve the process of transferring diagnostic data and images, and support integration of data from imaging procedures into broader health IT applications. These solutions provide an advanced start to software development, and are quietly inside many of today''s health IT systems. Merge Healthcares Medical Imaging Solutions bring mission-critical improvements for imaging workflow, from scheduling to billing through disaster recovery. Our Perioperative Solutions provide enhanced workflow for the entire surgery experience. Our customers, from the largest outpatient center chains to rural hospitals, have relied on Merge to bring them the solutions and services needed to run clinically and financially successful businesses. Merge Healthcares eClinical business unit, recently added through the acquisition of etrials Worldwide Inc., provides adaptive web-based tools that coordinate to transform data into intelligence and speed the path to an actionable study endpoint for clinical trials. Pharmaceutical, biotechnology, medical device and contract research organizations use integrated trial, site and patient solutions for real-time access to the high quality data they need to make informed decisions.
An Antibody supplier. Is part of Beckman Coulter.
Developmental Studies Hybridoma Bank at the University of Iowa
An antibody supplier which banks and distributes hybridomas and monoclonal antibodies for use in research. The bank includes antibodies against targets such as GFP, transcription factors, stem cells, and human.
An Antibody supplier; Dako was purchased by Agilent in 2012 and several years later the websites began to reflect the Dako products as part of the Agilent catalog.
Clinical Trial Management Application (CTMA)
THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 11, 2012. The Clinical Trials Management Tools are Java-based suite (accessed via a secure intranet) for managing various aspects of a clinical trial, research protocols, outcomes initiatives, statistical research analysis, as well as CTEP/CDUS reporting. Developed in collaboration with the Clinical Research Services (CRS) Office at the UPCI, this research-based application provides an integrated tool for managing administrative (e.g. IRB submissions and approvals) and clinical (e.g. tumor measurements, registrations/ screenings) functions for the collection and analysis of data generated from a clinical trial. More information can be found here, http://www.upci.upmc.edu/spore/skin/coreD.cfm
Established in 1981, the Foundation for Biomedical Research (FBR) is the nation''s oldest and largest organization dedicated to improving human and veterinary health by promoting public understanding and support for humane and responsible animal research. FBR is the leading voice of scientific reason and medical progress in the ongoing, sometimes violent debate that surrounds animal research. Their mission is to educate the public about the essential role of humane animal research in the quest for medical advancements, treatments and cures for both humans and animals. And through its innovative educational programs, FBR works to inform the news media, teachers, students and parents, pet owners and other groups about the essential need for lab animals in medical and scientific research and discovery. It serves as an accessible, reliable resource for the news media and works to bring American journalists and scientists together to promote exceptional and ongoing news coverage that contributes to public appreciation and respect for responsible animal research.
FUN is an international organization that is focused on neuroscience education and research at the undergraduate level. FUNs members and supporters include businesses and organizations; private liberal arts colleges, state and research university departments and programs; and individual faculty and students, all sharing a common interest in undergraduate neuroscience.
This foundation is dedicated to curing spinal cord injury by funding innovative research, and improving the quality of life for people living with paralysis through grants, information and advocacy.
Ontology-based Knowledgebase for Human Cell Adhesion Molecules
OKCAM (Ontology-based Knowledgebase for Cell Adhesion Molecules) is an online resource for human genes known or predicted to be related to the processes of cell adhesion. These genes include members of the cadherin, immunoglobulin/FibronectinIII (IgFn), integrin, neurexin, neuroligin, and catenin families. :We have mapped these genes onto a novel cell adhesion molecule ontology (CAMO) that provides a hierarchical description of cell adhesion molecules and their functions. It is intended to provide a means to facilitate better and better understanding of the global and specific properties of CAMs through their genomic features, regulatory modes, expression patterns and disease associations become clearer. :Cadherins, IgCAMs, Integrins, Neurexins, Neuroligins, Catenins :
NIH Pain Research Pain Information Index:The National Institutes of Health consists of many different institutes and centers. This site is an index to various NIH publications about pain symptoms, conditions and treatments of pain. :General Pain, Acupuncture, AIDS/HIV, Arachnoiditis, Arthritis, Avascular Necrosis, Back Pain, Behavioral and Relaxation Approaches, Behet''s Disease, Cancer Pain, Carpal Tunnel Syndrome, Central Pain Syndrome, Chiropractic Use, Chronic Pain, Complex Regional Pain Syndrome, Diabetic Neuropathy, Epidermolysis Bullosa, Fibromyalgia, Glossopharyngeal Neuralgia, Gout, Headache, Heritable Disorders of Connective Tissue, HIV/AIDS, Herpes Zoster Oticus, Hip Replacement, Juvenile Rheumatoid Arthritis, Knee Problems, Lichen Sclerosus, Lupus, Magnets, Manipulative and Body-Based Practices, Marfan Syndrome, Medicines by Design, Meralgia Paresthetica, Migrane, Omega-3 Fatty Acids, Osteoarthritis, Paresthesia, Peripheral Neuropathy, Pelvic Pain, Pinched Nerve, Piriformis Syndrome, Polymyalgia Rheumatica and Giant Cell Arteritis, Prescription Drugs and Pain Medications, Progressive Locomotor Ataxia, Prostate Problems, Psoriasis, Raynaud''s Phenomenon, Reflex Sympathetic Dystrophy, Repetitive Motions Disorders, Rheumatoid Arthritis, Scleroderma, Scoliosis, Shingles, Shoulder Pain, Sjogren''s Syndrome, Spinal Stenosis, Sports Injuries, Sprains and Strains, Tarlov Cysts, Temporomandibular Joint Disorders, Tethered Spinal Cord Syndrome, Third Molar (Wisdom Tooth) Removal, Thunder God Vine, Trigeminal Neuralgia Information Page, Whiplash, Wisdom Tooth Removal :
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2015. TranscriptionDetector is a tool for finding probes measuring significantly expressed loci in a genomic array experiment. TranscriptionDetector was originally created to analyze the transcriptome of Drosophila melanogaster. The study, a collaboration with Kevin White's Lab at Yale, is described in our 2004 Science paper. Later on, it has been elaborated and more recently presented in Gabor Halasz et al. in Genome Biol. 2006 July 19; 7(7):R59 The TranscriptionDetector algorithm requires that a set of negative control probes (NCPs) be included on each microarray used in the study. The significance of a data probe is evaluated relative to these NCPs, which represent non-specific binding.
Jambalaya is a plug-in created for Protg which uses Shrimp to visualize the knowledge bases the user has created. Protg is an ontology editor and a knowledge-base editor which allows domain experts to build knowledge-based systems by creating and modifying reusable ontologies and problem-solving methods.
Barrow Neurological Institute of St. Joseph''s Hospital and Medical Center in Phoenix, Arizona, is internationally recognized as a leader in neurological research and patient care. :Established in 1962 under the auspices of Dr. John Green, Barrow has been brought into the twenty-first century under the guiding influence of Dr. Robert Spetzler. :Barrow treats patients with a wide range of neurological conditions, including brain and spinal tumors, cerebrovascular conditions, and neuromuscular disorders. Barrow''s clinicians and researchers are devoted to providing excellent patient care and finding better ways to treat neurological disorders. :Barrow Neurological Institute of St. Joseph''s Hospital and Medical Center, Phoenix, Arizona :department portal :
We are interested on the mechanisms by which environmental factors affect neuronal health. We have found that trophic factors endogenous to the brain and spinal cord can be induced by the practice of select behaviors. We have recently reported that physical activity, learning, and nutritional factors control neurotrophins in the brain. These findings opened the exciting possibility that regulation of trophic factors by behavior can be a pivotal mechanism by which specific experiences can impact the structure and function of the CNS. It may account for the improvement of CNS function after trauma provided by rehabilitative therapies. On the contrary, it may explain the decay in function in aging or degenerative diseases following a lack of stimulation. These two avenues provide direction for my research program: 1) How trophic factors induced by activity can help functional recovery following brain and spinal cord trauma. We are using several exercise models to boost the production of trophic factors in the brain and spinal cord. Our goal is to provide critical information to guide the design of behavioral therapies for the reduction of the severity of insult or disease, and to increase CNS function. 2) We are evaluating the effects of lifestyle on trophic factor production, with resulting effects on circuit remodeling, synaptic function, and cognition. We believe that changes in trophic factor as a result of select experiences can affect neuronal health with profound consequences for cognitive function. :lab :
Company provides laboratories worldwide with analytical instruments and supplies, clinical and diagnostic testing services, consumables, applications and expertise in life sciences and applied chemical markets.
Edgewarp3D is a sophisticated workstation package for manipulation of 2D and 3D biomedical images and related data structures by a combination of landmark location, thin-plate spline, and image unwarping and averaging. Utilizes NLM Visible Human data set
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. An interactive program for resectioning and deriving measurements from contoured structures. It creates structural measurements obtaining lengths, surfaces, and volumes from volume data. Investigation of 3D structures and communication to others are greatly facilitated by this computer-based visualization.
A global health company contributing to the systemic improvement of health care delivery and the health of communities. We are transforming health care by eliminating error, variance and waste for health care providers and consumers around the world. Our solutions optimize processes for health care organizations ranging from single-doctor practices to entire countries, for the pharmaceutical and medical device industries, and for the field of health care as a whole. Our solutions are licensed by more than 9,000 facilities worldwide. We invite you to join us in our quest to make health care become all it should be. Since our company began, we have been committed to transformational change in the vital task of keeping people well. Now more than ever, our focus is on developing the innovations that will help improve the entire health care system. Ultimately, as our CEO Neal Patterson has said, health care is personal. Because in the end, nothing matters more than our health and our families. We''re changing the way people: * Use and share information ** We empower providers to base decisions on best clinical evidence. ** We coordinate care across traditionally fragmented health care systems. ** We provide clinical organizations with the reliability, flexibility and continuous innovation available through cloud-based intelligence. ** We provide contextually relevant information to the right people at the right time. * Pay for health and care ** We believe IT investment must be matched with innovative payment models that are much easier to navigate. ** We are replacing the current, claims-based system with streamlined electronic payments. ** We develop ways to reward people and their providers for proactively achieving positive health goals. * Think about health ** We empower people to actively engage in their health by providing them with a standards-based, lifetime Personal Health Record. ** We are replacing the reactive sick care model with a proactive, personalized plan for health.
International Behavioral Neuroscience Society
The International Behavioral Neuroscience Society (IBNS) was formed to encourage research and education in the field of behavioral neuroscience. Founded in 1992, the IBNS has approximately 719 members which derive from 36 different countries and consist of scientists, clinicians, teachers, and others with a background and interest in the relationship between brain and behavior. :
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The diffusion TENSOR Visualizer (dTV) is an analysis tool for diffusion MRI including diffusion tensor images. Several basic functions are available in dTV: fiber tracking and 3D display; diffusion profile visualization as ellipsoid, etc.; compute grey/color-coded FA map, ADC map, etc.; analysis DT-related values within ROI; ans customizing MPG data Current version is dTV.II SR (Second Release). The dTV works as an extension software, i.e. plugin, for a volume data viewer software VOLUME-ONE, which is also in this database.
Open clinical report and annotation repository
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Repository of de-identified clinical reports available for NLP researchers has been designed. Work with the AMIA NLP working group in designing annotation schemas and obtaining annotations, design a repository for shareable annotations, help design and execute a shared task in IE from clinical reports. The University of Pittsburgh NLP Repository contains clinical reports that are available to the community for NLP research purposes and comprises: # Report Repository - one month of de-identified clinical reports from multiple hospitals and # Annotation Repository - annotations performed on reports from the Report Repository. Anyone performing annotations on reports from the NLP Repository is required to deposit their annotations. The Repository contains reports of the following types generated from multiple hospitals during a single month: * History and Physicals * Progress Notes * Consultation Reports * Radiology Reports * Surgical Pathology Reports * Emergency Department Reports * Discharge Summaries * Operative Reports * Cardiology Reports
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. A database built up with software and services that maintains multiple versions of terminologies, map sets, and values sets concurrently. HDD Access has superseded Concept Hub.
Spike Train Computational Neuroscience Portal
This database contains hundreds of links to functional neuroscience databases, software, books, articles, research labs and institutions :link aggregation site; portal; :
DementiaNet is a Community on the Internet where people affected by dementia and their relatives have the opportunity to meet and exchange experiences as well as finding information and help. :Danish, English, Dementia, Dementia Diseases, Diagnosis, Treatment, Dementia-like Conditions, psychosocial aspects, pharmacological treatment, non-pharmacological treatment, Acetylcholinesterase inhibitors, NMDA receptor antagonists, Pharmaceutical Benefits Scheme (PBS), Alzheimer''s disease, beta-amyloid deposits, Secretory inhibitors, protein deposit inhibitors, beta-amyloid, Ginkgo Biloba, Alzheimer''s Medication, Medication Subsidies, Dementia-like Conditions, Social Perceptions :
XooNIps - Neuroinformatics Base Platform System
Neuroinformatics (NI) is a new discipline that challenges the understanding of the structure and mechanism of the brain by combining neuroscience and information technology. The global collaborations in this field have been actively started with the support of the International Neuroinformatics Coordinating Facility (INCF) launched in November 2005. The Laboratory for Neuroinformatics at RIKEN Brain Science Institute (BSI) is involved in developing various cutting-edge technologies related to NI such as XooNIps. XooNIps succeeded the concept and basic feature of the vision science platform; Visiome, constructed by the NRV (i.e., Neuroinformatics Research in Vision) Project and has been developed based on a content management system (CMS); XOOPS, as infrastructure for NI databases to share different types of data on the Internet. :XooNIps has three features: :The first is the flexibility of developing databases. CMS-based XooNIps makes it easy to change the design or to extend the functions of databases by combining the different modules available on XOOPS. Therefore, even those who are not expert in computer system can develop their database on XooNIps. :The second is the diversity and extensibility of the data which can be handled by XooNIps. In order to handle different types of actual data, it provides not only the various data forms per se, but also the extension method to handle a new data form, which enables to deal easily with even a non-standardized data form. :The third is the facility to distribute metadata. XooNIps implements OAI-PMH (i.e., Open Archive Initiative-Protocol for Metadata Harvesting) which is one of the standard protocols to distribute metadata. This enables to collect information on other databases which are developed on XooNIps or to coordinate databases by exchanging metadata with other databases which implement OAI-PMH than those on XooNIps. :Since April 2007, Neuroinformatics Japan Center (NIJC) at RIKEN BSI takes charge of extending and maintaining XooNIps, and is committed to manage the documentation hereafter. :NIJC, as a national node of INCF, is developing and operating various NI platforms in neuroscience based on XooNIps to establish and facilitate NI research in Japan. XooNIps is also being applied to databases or organizational repositories in several institutions and universities, and laboratory groupware in various fields. We hope XooNIps will be of universal use in and out of Japan. :database; binary executable; software development tool; metadata; data set; :
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. It analyzes and graphs time-lapse imaging data as acquired by a Bio-Rad confocal microscope, for experiments using nonratiometric fluorescent indicator dyes. Btrack can accommodate changes in the positions of imaged cells/tissue regions and can be used for analyzing an unlimited number of areas (cells/tissue regions) in an imaged field.
Samurai Graph: A highly functional and user-friendly graph plotter
Samurai Graph is a highly functional and user-friendly graph plotter. It can plot the graphs from the scalar to vector type 2-dimensional data. Samurai Graph is an open source development project, released under the GNU Lesser General Public License (LGPL). Samurai Graph is Java-based and platform-independent application. It runs on most major operating systems including MS-Windows, Linux, MacOS X, FreeBSD., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A database project for the neuroimaging community NeuroGenerator is a database project funded by the European Commission. The overall purpose is to make databases with data in comparable and compatible formats suited for meta research and for making models of the cerebral cortex of the human brain. Researchers can submit their own raw PET-data and fMRI data to NeuroGenerator. The data are analyzed with the statistical software package FSL. In this way databases are produced of PET and fMRI data in standard anatomical format Data as statistical parametric images in standard anatomical format immediately comparable due to the uniform processing Cytoarchitectural data (from post mortem brains) in standard anatomical format.
Neuromantic is a freeware reconstruction tool for Windows-based machines. It is designed to allow the efficient creation of 3D neuronal reconstructions from serial stacks of images. :Neuron, Morphological Reconstruction, Morphology, Freeware, Software, Dendritic Morphology : :May be used as a freeware alternative to Neurolucida or Neuron_Morpho for the 3D reconstruction of neurons from serial image stacks.
Theoretical and Computational Biophysics Group (TCBG)
The Theoretical and Computational Biophysics Group (TCBG), an NIH Resource for Macromolecular Modeling and Bioinformatics, was founded by Professor Klaus Schulten in 1989 and is located at the Beckman Institute of the University of Illinois at Urbana-Champaign (UIUC). The group is led by Professor Klaus Schulten (Physics, Biophysics, Chemistry) with Professors Laxmikant Kale (Computer Science), Zaida Luthey-Schulten (Chemistry) and Alek Aksimentiev (Physics), and with the Resource''s assistant director Dr. Emad Tajkhorshid (Biophysics). Research and development activities of the TCBG center on the structure and function of supramolecular systems in the living cell, and on the development of new algorithms and efficient computing tools for structural biology. :The TCBG brings the most advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance. We extend, refine and deliver these technologies in response to experimental progress and emerging needs of the wide biomedical research community. We magnify the impact of our work through direct collaboration with experimental researchers, the distribution of cutting-edge and user-friendly software, and via extensive training, service, and dissemination efforts. :cell, algorithm, simulation software, membrane potential, genome, molecule, ion channel, chromatin, Image Processing software, data Data visualization software, simulation software; Membrane Biophysics, Mechanobiology, Nanoengineering, Bioenergetics, Neurobiology, Molecular Dynamics, cellular membrane, osmotic pressure, proteins (use protein), Gatekeeper Protein, membrane, mechanosensitive channel of small conductance (MscS), Visual Molecular Dynamics (VMD), Quantum Biology, quantum chemistry, Molecular Dynamics Simulator, Nanoscale Imaging, cellular membrane tension, bacterial cell, electron paramagnetic measurements, computer modeling, atomic detail, computational microscope, Lipoproteins [high density lipoproteins (HDL)], Petascale Computing, Macromolecular Modeling, Bioinformatics, supramolecular systems, living cell, algorithms (use algorithm), computing tools, structural biology, molecular modeling, computational technologies, membrane proteins, structural information, molecular visualization, Molecular modeling tools, structural information, bioinformatics databases, molecular dynamics simulations, interactive modeling, collaborations, theoretical, experimental researchers, light energy, electrical membrane potentials (use membrane potential, add term as syn), synthesis of ATP, photosynthetic systems, storage and control of genetic information, classical and quantum dynamical motion of biopolymers, numerical experiments, non-equilibrium statistical mechanics, elasticity theory, theory of disordered systems, collaborative environment, Software Development, cells (use cell), molecular graphics viewer, static and dynamic structures, DNA sequencing, genomes (use genome), direct manipulation and observation, single molecules (use molecule), bioenergetic proteins, nanotechnology, steered/interactive molecular dynamics, dissemination, coarse-graining methods, residue-based and shape-based coarse graining, CG, polymeric systems, Computational Environment, Training, Workshops, Tutorials, Case Studies, Classes, research, Highly Cited, compute power, visualization equipment, desktop workstations, lipid bilayers, allow passage of ions across the membrane (use ion channel), mechanotransduction, membrane tension, 3-D graphics, built-in scripting, animating, analyzing, ideal DNA interbasepair helical parameters, plugin, nucleosomes, antialiasing, depthcueing, Molecular Representations, analysis and Data visualization software (use Image Processing software, and data Data visualization software, add terms as syn.), computer simulations (use simulation software), photosynthetic systems, computational clusters :
geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data. Example use cases include: * loading data from local or remote data sources. * visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways. * providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory networks reconstruction, BLAST searches, pattern/motif discovery, etc. * validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks (one of the 7 National Centers for Biomedial Computing funded through the NIH Roadmap). Additionally, geWorkbench is supported by caBIG, NCI''s cancer Biomedical Informatics Grid initiative.
The Lundbeck Institute is pleased to present Psychotropics Online, a comprehensive guide to CNS compounds and products. A database of psychotropic and neurological drugs. Generic name, Trade name, Description, Code numbers, Monographies, Tranquilizers - Anxiolytics, Anxiolytics / Antipsychotics, Neuroleptics and Antipsychotics, Monoamine Oxidase Inhibitors, Antidepressants, Antidementia drugs, Sympathomimetics, Antiparkinsonians, Anticonvulsants, Hallucinogenic Agents, Additional Group, Biochemical profiles, Side-effects, Antipsychotics, Tranquilizers - anxiolytics, Tricyclic Antidepressants (TCAs), Selective Serotonin Reuptake Inhibitors (SSRIs), Selective Serotonin and Noradrenaline Reuptake Inhibitors (SNRIs), Selective Noradrenaline Reuptake Inhibitors (NARIs), MAO inhibitors (MAOIs), Sympathomimetics, Anticonvulsants, Lithium, Barbiturates, Street names, Terminal plasma half-lives, Orphan drugs
Alzforum Antibody Directory for Neuroscience Research
The Alzheimer Research Forum is the web''s most dynamic scientific community dedicated to understanding Alzheimer''s disease and related disorders. It also contains a database of providers of antibodies directed against several hundred molecules and proteins of relevant to research on Alzheimer and other neurodegenerative diseases. The web site reports on the latest scientific findings, from basic research to clinical trials; creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across the numerous disciplines that can contribute to the global effort to cure Alzheimer''s disease. The ARF team of professional science writers and editors, information technology experts, web developers and producers all work closely with our distinguished and diverse Advisory Board to ensure a high-quality of information and services. We very much welcome our readers'' participation in all aspects of the web site. Sponsors: The Alzheimer Research Forum is an independent nonprofit organization. It is supported by grants and individual donations.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This software package provides two voxel-based image registration algorithms that are based on maximising Normalised Mutual Information (NMI). They are incorporated in a user-friendly command-line and graphical interface that includes a visualisation tool for 3D image pairs to permit analysis of registration results. These algorithms have been demonstrated on range of medical applications including brain, breast, liver, and cardiac data and results have been published.
Last update 2004. :VOLUME-ONE is a general-purpose software for viewing volumetric image data. :
THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 09, 2013. This tool is a program that allows you to calculate the head circumference based on MRI data. Using Fourier harmonics to parameterize the contour of the head this tool gives the length of the contour. This embedded tutorial software can automatically store the results in a Excel spreadsheet.
Baylor College of Medicine Human Genome Sequencing Center
Center for high-throughput DNA sequence generation and the accompanying analysis. The sequence data generated by the center's machines are analyzed in a complex bioinformatics pipeline, and the data are deposited regularly in the public databases at the National Center for Biotechnology Information (NCBI).
A peer-reviewed encyclopedia written by the leading experts in their respective fields. It does not publish research or position papers, but rather living reviews that will be maintained by the future generation of experts via the process of curatorship. :Computational neuroscience, Neuroscience, Electrophysiology, Neuron, Network Dynamics , Brain Models, Synapse, Memory, Conditioning, Consciousness, Vision, Olfaction, Neuroimaging, Dynamical Systems, Oscillators, Synchronization, Pattern Formation, Chaos, Bifurcations, Simulation Environment, Artificial Neural Networks, Models of Neurons, Spiking Networks, Brain Theory, Recurrent Networks, Feedforwar, Networks, Graph Theory, Reinforcement Learning, Evolutionary Computation, Information Theory, Statistics, Signal Analysis, Pattern Recognition, Navigation and Control, Robotics :
VideoScribbler is a program that makes it possible to trace directly onto live video. It was developed to provide a way to outline and count cells in a video image. The program displays the live video image in a 640x480 window. Userrs can click and drag the mouse to outline cells, while releasing the mouse button will complete the outline and increment the "Object Count" display at the bottom of the window.
Unys is a Java Web Start application for viewing Synu polygonal and MicroBrightField Neurolucida datasets. Other formats, such as OBJ and COLLADA will be added shortly. Unys is still in a state of being actively developed. This software has replaced the previously existing Synuview application. Requirements: Java 1.5 or more recent. No software installation is required but Java Web Start must be pre-installed. Most modern computers will have this installed. Sponsors: this software is supported by the National Center for Microscopy and Imaging Research. Keywords: Dataset, Neurolucida, Software, Java, Application, Synu polygonal, Viewing,
MRI structural/functional Visualization and Analysis
A tool for visualization of structural and functional MRI volumes. Features include structural and functional overlay display of volume sections, volume annotation, ROI analysis, interfacing with FSL''s brain extraction, and 3D rendering. mri3dX should run on most unix workstations, but requires Motif and OpenGL/Mesa graphics libraries.
MRIVIEW - An Interactive Tool for Brain Imaging
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. MRIVIEW is a software tool for viewing and manipulating volumetric MRI head data, and for using this data as an anatomical reference in studies of brain function. MRIVIEW supplies methods for reading in raw MRI data, segmenting structures in the data, reconciling coordinate systems between multiple imaging modalities, viewing combinations of anatomical and functional information, and building models of structures within the head. Recent extensions to MRIVIEW include an MEG/EEG forward simulator, and a parallelized multi-start multi-dipole MEG/EEG inverse procedure.
Stroketool-CT is a user friendly MS-Windows based software system for calculation and visualization of enhanced CT perfusion imaging data sets of the brain. It contains features such as quantitative perfusion using SVD algorithms; DICOM compatibility; rapid calculations of rCBF, MTT, rCBV, TTP,Tmax; and interactive and automatic AIF-detection.
:iiV is an interactive brain imaging data display tool written in Java. It displays 3-D data set as slices perpendicular to the 3 major axis. Individual slice voxels are mapped thru a linear scaling, threshold and color table to displayable pixel values. Any number of slices from any number of data files may be arranged, annotated, overlaid, cropped, zoomed and rotated. iiV maintains the original data internally for mouse selection and display of original voxel values. If input locations map to a real world valued coordinates that mapping may be applied to display selected voxel locations in real coordinates. Slices may also include tracking crosshairs and automatically update to display the same region of the brain as selected in another slice. iiV includes a fairly complete set of editing commands including selection, drag, group, delete, and undo/redo commands. It also includes a script language for saving and reloading of the interactive display and creating animated demos. iiV supports reading ANALYZE, ECAT, ECAT7, DICOM, GIF, JPEG, PPM, Stimulate SDT, and raw data formats and saving what is displayed as scripts, GIF and PPM files. :
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2015. PV-Wave is a interactive programming language designed for data analysis. We have several programs written for creating, viewing, and measuring MRI images of brains. PV-Wave is a very powerful programming language with a very simple syntax. We reuse code from one program to write a new program that does something slightly different. This only takes us a few hours. If we used another language, like C++, our program turn around time would be days instead of hours.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A Java-based tool for managing and sharing MRI/DTI datasets, and related subject and protocol metadata. Data entry, data access, general query, reporting, analysis, and administrative operations occur through browser-based forms. NeuroServ works with a webserver (Tomcat) and a backend database (e.g., Postgres); a schema and over 40 forms are provided in the distribution. Support for DTI includes entry of multi-orientation raw DWI files, semi-automated normalization to the B0 image and quality filtering. Planned extensions include full DTI processing through image production and data sharing using the SSC incremental visiblity model.
:OsiriX is an image processing software dedicated to DICOM images (.dcm / .DCM extension) produced by medical equipment (MRI, CT, PET, PET-CT, ...) and confocal microscopy (LSM and BioRAD-PIC format). It can also read many other file formats: TIFF (8,16, 32 bits), JPEG, PDF, AVI, MPEG and Quicktime. It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or medical imaging modality (STORE SCP - Service Class Provider, STORE SCU - Service Class User, and Query/Retrieve) . OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D Viewer, 3D Viewer, 4D Viewer (3D series with temporal dimension, for example: Cardiac-CT) and 5D Viewer (3D series with temporal and functional dimensions, for example: Cardiac-PET-CT). The 3D Viewer offers all modern rendering modes: Multiplanar reconstruction (MPR), Surface Rendering, Volume Rendering and Maximum Intensity Projection (MIP). All these modes support 4D data and are able to produce image fusion between two different series (for example: PET-CT). Osirix is at the same time a DICOM PACS workstation for medical imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D imaging, confocal microscopy and molecular imaging. :
Nonparametric Prediction Activation Influence Reproducibility re-Sampling
The NPAIRS (Nonparametric, Prediction, Activation, Influence, Reproducibility, re-Sampling) package provides a statistical resampling framework with GLM, PCA and CVA data analysis options forming the basic building blocks for benchmarking and comparing data processing choices and preprocessing pipelines using prediction and reproducibility performance metrics. The distribution package also includes flexible visualization and plotting tools for displaying the results of NPAIRS analyses. :
SigPath is a prototype of an information system for cell signaling pathways and networks. A primary emphasis of SigPath is that biochemical information can be stored both at the qualitative and quantitative levels. When information is stored quantitatively, SigPath can assist users in generating quantitative models that can be used to simulate how the concentrations of the molecules involved in a model change over time. For background, design goals, tutorials, and contact information, visit the SigPath Project Pages :Gs pathway, LSD_binds_serotonin 2AR, MAPK cascade, EGFR signaling and MAP kinase cascade, EGF receptors, mGluR activation :
Web site last updated August 26, 1998 Automatic method for comparing different MRI datasets by visual inspection of equivalent anatomical planes. Implementation is based on multi-scale, three dimensional (3D) cross-correlation, to register a given volumetric data set to an average MRI brain (n > 300) aligned with the Talairach stereotaxic coordinate system. :
THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. The NEMO ERP Analysis Toolkit includes tools for EEG/ERP and MEG data decomposition, and ontology-based mark-up, annotation, and labeling of patterns in EEG and MEG data. These tools have been implemented in MATLAB by Robert Frank, a mathematician and data analyst for NEMO. The current NEMO analysis pipeline has been designed with the aim to support cross-lab, cross-experiment meta-analysis of EEG and MEG data. The current proposed processing pipeline consists of the following steps: * Step 1: Decomposing ERP data (continuous data are transformed into discrete patterns for analysis) o PCA/ ICA/Microstate * Step 2: Marking up the analysis results o Each pattern is annotated with labels that relate pattern attributes to NEMO ontology concepts * Step 3: Clustering the observed patterns within and across experimental groups * Step 4: Labeling the cross-experiment clusters Each item in the above list is a step/phase in the processing pipeline and is associated with a set of matlab scripts in our NEMO ERP Analysis Toolkit, which is implemented by a collection of MATLAB scripts.
XV is an interactive image manipulation program for the X Window System. It can operate on images in the GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, and PM formats on all known types of X displays. It can generate PostScript files, and if you have ghostscript (version 2.6 or above) installed on your machine, it can also display them. XV allows users to: display an image on the root window, in a variety of styles; grab any rectangular portion of the screen and turn it into an image; arbitrarily stretch, compress, rotate or flip the image; view files as ASCII text or hexadecimal data; determine pixel values and x,y coordinates in the image; apply different gamma functions to the Red, Green, and Blue color components, to correct for non-linear color response; and run a number of image-processing algorithms on any rectangular portion of the image, among other functions.
Welcome to the Syracuse Biomaterials Institute! We are a new, interdisciplinary institute focused on research in biomaterials, smart medical devices, and biological/tissue-engineered constructs. Biomaterials are natural and synthetic substances designed to treat, augment, or replace tissues and organs of the human body as treatments to disease or injury. An outgrowth of the long-standing Biomaterials Group in the Biomedical and Chemical Engineering Department, the Syracuse Biomaterials Institute (SBI) was launched in Fall, 2007, through strategic investments by Syracuse University, New York State Foundation for Science, Technology and Innovation (NYSTAR), and private donations. SBI is a cohesive collection of highly collaborative faculty spanning eight (8) academic units, including faculty from SUNY Upstate Medical University and SUNY College of Environmental Science and Forestry. Our researchers are engaged in a wide spectrum of problems, ranging from fundamental studies of the biochemical and physical processes controlling cell functions to the development of new technologies for biomedical applications. In addition to our collaborative research and teaching activities, we are excited to be designing our future SBI home, planned for Fall 2009, that will collocate our research groups and central laboratory facilities. :jobs board, postdoctoral training program, graduate training program, portal :
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Collection of Unix-based programs for pre-processing and analyzing neuroimaging datasets. This includes tools for mean-normalization of images, image registration, ANOVA, post-hoc contrast analysis, region-of-interest identification and examination (including time series). Includes a test data set.
The Section for Biomedical Image Analysis
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher.
i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origin. For some resources (e.g. software) the use of the resource requires accepting a specific (e.g. OpenSource) license.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 10, 2012. With Cloverleaf Integration Services from Quovadx, Inc., the FDOH now provides managers and policy makers with access to critical data residing in various counties across the state. The Cloverleaf engine is used to map legacy electronic billing formats for Medicaid to HIPAA compliant formats for three of the largest patient care systems in the state without the need to make programming changes to the existing systems that bill Medicaid. The Cloverleaf solution also guarantees the delivery of messages, enables rapid development and deployment of application interfaces between systems and provides a means of maintaining compliance with any new HIPAA format changes. While making the data available to a larger audience, the privacy and security of sensitive health data is also maintained by the solution''s ability to manage security and business rules for each system.
Hasenwinkel Research Group is interested in creating absorbable biopolymeric gels for the prevention of post-surgical tissue adhesions, novel two-solution bone cements fro fixation of total join replacements, nerve and soft tissue regeneration, surface modification of materials to enhanve and promote biological function and biocompatibility, studying effects of chemical, mechanical, and electrical environments on the development of three-dimensional tissue scaffolds in culture. :datum, lab web page :
Stroke Trials Registry is a continuously updated registry of randomized clinical trials in stroke and cerebrovascular disease. This project is a free public service from the Internet Stroke Center at Washington University School of Medicine; with support from the American Stroke Association and the National Institute of Neurological Disorders and Stroke. This registry will meet technical standards for inclusion in the International Clinical Trials Registry Platform of the World Health Organization. The information on this site is intended for health professionals. SPOTRIAS is an NIH-funded network of stroke research centers that perform early phase clinical projects, share data, and promote new approaches to therapy for acute stroke. clinical data, human, homo sapien, stroke, translational medicine
Neurology Image Library from The Internet Stroke Center
The Internet Stroke Center at Washington University is pleased to offer this module for viewing CT, MR, and angiogram images of cerebrovascular and neurological diseases. While this project is still being perfected -- and many more cases have yet to be added -- we hope that you will find this collection useful in your education and practice. The images presented here are for educational use only. This information may not be used for diagnosis or treatment. All images are protected property of the Internet Stroke Center at Washington University and may not be reproduced without permission. Permission may be granted to students and professionals to borrow images from this site for educational purposes and/or presentations; we just ask that an email be sent detailing both the desired material and the intended use. Please direct all comments, questions, and requests to the Site Editor of the Internet Stroke Center.
Northern Eclipse 6.0 software is a Windows based full Image Analysis and Archiving System with a full suite of Image Processing techniques, Morphological and Densitometry measuring routines, digital and analogue camera control, SDK for custom camera driver solutions, 3D-Reconstruction, De-Convolution and programmable via 3 levels of automation plus access to hundreds of OLE applications and thousands of scripts.
G-Protein Coupled Receptor Oligomerization Knowledge Base (GPCR-OKB) ontology project
G-Protein Coupled Receptor Oligomerization Knowledge Base (GPCR-OKB) ontology project offers an ontology that can be downloaded. :G Protein-Coupled Receptors (GPCRs) are a large and diverse family of membrane proteins whose members participate in the regulation of most cellular and physiological processes and therefore represent key pharmacological targets. Although several bioinformatics resources support research on GPCRs, most of them have been designed based on the traditional assumption that monomeric GPCRs constitute the functional receptor unit (Figure 1 below). The increase in the frequency and number of reports about GPCR dimerization/oligomerization and the implication of oligomerization in receptor function makes necessary the ability to store and access information about GPCR dimers/oligomers electronically. :We present here the design blueprint for an information system that can manage the elements of information required to describe comprehensively the phenomena of both homo- and hetero-oligomerization of GPCRs. Specifically, we present the ontology (Figures 2-4 below) that we plan to use for the development of an intuitive and user-friendly GPCR-Oligomerization Knowledge Base (GPCR-OKB). This information system is being designed in close collaboration with experimental colleagues working on GPCR oligomerization, and adopts the list of recommendations recently stipulated by the NC-IUPHAR subcommittee for the recognition and nomenclature of GPCR multimers. :Our long term goal is to disseminate to the scientific community organized, curated, and detailed information about GPCR dimerization/oligomerization, and its related structural context. :Skrabanek L, Murcia M, Bouvier M, Devi L, George SR, Lohse MJ, Milligan G, Neubig R, Palczewski K, Parmentier M, Pin JP, Vriend G, Javitch JA, Campagne F, Filizola M. Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base. BMC Bioinformatics. 2007 May 30;8:177. PMID 17537266 :The ontology files (developed in Protege) can be downloaded. :
Clinicians can get a simultaneous consult about their patient''s diagnosis using SimulConsult''s diagnostic decision support software. After some patient findings are entered into the software, it provides an initial differential diagnosis and suggests other useful findings, including tests. The database used by the software has > 2,300 diagnoses, focused on genetic neurological and metabolic diseases, but is expanding with increasing content on non-neurological genetics and non-genetic neurology. The information about diseases is entered by clinicians, referenced to the literature and peer-reviewed by experts. The information includes many types of information ignored in other diagnostic approaches, allowing the software to take into account pertinent negatives, temporal information, and cost of tests. The approach is also flexible enough allow rapid addition of newly recognized diseases. SimulConsult enables both generalists and specialists to transform medical diagnosis, by lowering costs, reducing errors and eliminating the medical diagnostic odysseys experienced by far too many patients and their families. SimulConsult also enables researchers to find diseases with clinical presentations that are similar to other diseases or individual patients, assisting in identifying mechanisms of diseases. The software may be used only by medical professionals (doctors, nurse practitioners, genetic counselors, medical librarians and supervised trainees in these professions), who may register on the site or use the software through institutional access of their medical center. Keywords: diagnosis, diagnostic, software, neurology, genetic, neurological, metabolic, metabolism, human
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2015. Simbiome is a curated, online electronic resource that organizes and presents relevant resources for physics-based simulation of biomedical structures and related entities in biology and life sciences.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This website endeavors to provide information on the Chronic Fatigue Syndrome Working Group (CFSWG) and its programs that is helpful to researchers, health care providers, people with CFS and their families, and the general public. :The mission of the Trans-NIH Working Group for Research on Chronic Fatigue Syndrome is to: :* Stimulate and support research on CFS within the context of the missions of all Institutes, Centers and Offices. :* Collaborate and coordinate the research agendas of all Institutes, Centers and Offices to issue on a regular basis joint Program Announcements or theme related Request for Applications to further interdisciplinary research in CFS. :* Present new knowledge to and facilitate novel theoretical approaches to CFS among NIH scientists. :* Plan and sponsor scientific symposia to foster awareness, provoke new scientific interest, and generate interdisciplinary collaboration on CFS among both the NIH and Academic medical community.
The goal of the mouse genome project is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval. On this site one can obtain a list of mutations on chromosome 11.
Phenotype Context Database for Gene Ontology Annotations
PhenoGO is a computed database designed for high throughput mining that provides phenotypic and experimental context - such as the cell type, disease, tissue, and organ - to existing annotations between gene products and Gene Ontology (GO) terms, as specified in the Gene Ontology Annotations (GOA) for multiple model organisms. Phenotypic and Experimental (P&E) contexts to identifiers are computationally mapped to general biological ontologies, including: the Cell Ontology (CO), phenotypes from the Unified Medical Language System (UMLS), species from Taxonomy of the National Center for Biotechnology Information (NCBI) taxonomy, and specialized ontologies such as Mammalian Phenotype Ontology (MP) and Mouse Anatomy (MA).
This web resource allows the user to search and rank 23,517 programs at 2,356 universities based on the users priorities. Data come from the National Science Foundation, the National Research Council, and the National Center for Education Statistics. The graduate school guide has been made possible by generous support from: :* The Alfred P. Sloan Foundation :* The Burroughs Wellcome Fund :The Center for Science and the Media served as the fiscal sponsor for the project. :Jobs board, Career development, Graduate training program list :
Centre for Scientific Investigations and Training
The Centre for Scientific Investigations and Training
It fosters Interdisciplinary research, teaching, and service activities linked to health and development in Nigeria and resource limited settings of the developing world. :OBJECTIVES OF THE CENTRE: The Institute helps strengthen and sustain the interests and activities of the science community by: :Facilitation of international contacts for program development and training. :* Advocacy for better equity in global health investments. :* Assistance in securing resources for international activities. :* Standardization and facilitation of overseas administrative approaches. :* Improved communication through grand rounds, seminars, and discussion forums. :* Taking up public enlightenment campaigns and public health education :* Active partnerships with institutions in Nigeria and abroad that share the Institute''s goals and wish to partner with CSIT faculty, staff, and students. :* Publishes the JEN Biomedicine, an international journal that gives unfettered access to research from Nigeria and other parts of Africa and the world. :* It''s CSIT Service Centre that helps with works and writing of scientists to make them acceptable for publication. The centre is equipped with research aids and staff that can help out with planning, executing, writing, graphic works including black and white and colour photos, editing research papers to make them acceptable by journals of interest. You can also undertake statistical analyses. In particular preparing journal figures, peer-review before publication, and statistical analyses. :* It''s Teaching Aids Centre that provides teaching aids to institutions and for workshops and conferences. Has in store models for studying behaviour including Elevated plus, Y, T, Radial-arm, Light/Dark Box, Open Box mazes. Available also are projectors, image analysers, computers, scanners, microscopes, microscope slides, animal skeletons, fixed animal tissues for biology and anatomy, patch clamping, stereotaxic equipment and methods, etc. The Centre can also teach you how to use any of the above. :
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 16, 2013. The resource redirects to its parent, OSSP. Project seeking to increase the transparency and accessibility of the scientific research process by connecting researchers with an additional source of funding - microinvestments received from the broader online community. In exchange for these public investments, researchers will maintain research logs detailing the play-by-play progress made in their project, as well as publishing all of their data in a public database under a science commons license. These research projects, in turn, will serve to continually update a research-based neuroscience-based human brain & body curriculum.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 26,2023. CCAM is one of five National Technology Centers for Networks and Pathways, NTCNP, funded throught the NIH Technology Center for Networks and Pathways, TCNP. CCAM integrates new microscope technologies for making quantitative in vivo live cell measurements with new physical formulations and computational tools that will produce spatially realistic quantitative models of intracellular dynamics. :The overarching rationale for CCAMs research as a TCNP is that polarity in networks and pathways is determined by the spatial organization, subcellular distribution, dynamic behavior, interactions and functions of specific molecules within the cell. To investigate these relationships, we use a tripartite approach described as: :1) Measure - develop new tools for measuring spatially resolved dynamic behavior of molecules in cells, :2) Model - develop new methods for spatial modeling of biological systems. :3) Manipulate - develop new techniques for manipulating the spatial distribution of molecules in living cells. :Microscopy contrast enhancement protocol, biophotonics, subcellular :
Cure PSP: Society for Progressive Supernuclear Palsy
Progressive Supranuculear Palsy (PSP) is a little known but fatal degenerative brain disease that is often misdiagnosed as Alzheimers or Parkinsons disease. Only by becoming more aware of PSP and the devastating effects on its victims and their families can we begin to work toward more effective treatments and eventually a cure. :CurePSP has always believed that truly effective clinical interventions will follow good, solid basic scientific research. For this reason, CurePSP promotes research that helps generate an integrated picture of PSP and CBD at the molecular and cellular levels. CurePSP believes that in the long term, research of this nature will prove indispensable in developing a prevention or cure for PSP and CBD. :CurePSP has carefully structured its research program and has identified the programs that have been the most successful and those that need strengthening. With an increased research budget made possible through improved donor support, CurePSP will be able to markedly intensify the efforts to cure the disease in a way that promises relief for those afflicted today as well as hope for those who may be afflicted tomorrow. :grant :
Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology at the University of Michigan :Animal Diversity Web Has: Thousands of species accounts about individual animal species. These may include text, pictures of living animals, photographs and movies of specimens, and/or recordings of sounds. Students write the text of these accounts and we cannot guarantee their accuracy. Descriptions of levels of organization above the species level, especially phyla, classes, and in some cases, orders and families. Hundreds of hyperlinked pages and images illustrate the traits and general biology of these groups. Professional biologists prepare this part. :Animal Diversity Web Is An Online Encyclopedia: ADW is a large searchable encyclopedia of the natural history of animals. Every day, thousands of classroom students and informal visitors use it to answer animal questions. Other sites specialize in local, endangered, or particular kinds of animals. We aim to be as comprehensive as possible. :A Science Learning Tool: ADW facilitates inquiry-driven learning, that is, teaching about science by leading students to use the methods of science. Our large database is structured, providing consistent information for all species to foster comparisons. An advanced search tool allows a user to call up species accounts fitting any combination of descriptors. Students can explore for patterns and relationships, learn how to frame and answer scientific questions and, with the help of a good teacher, experience the excitement and satisfaction of doing science. Our long-term goal is to create a database rich enough that students can discover for themselves basic concepts in ecology and conservation biology. :A Virtual Museum: ADW provides a way to make the contents of research museums available globally for teaching and research. So far, our efforts have been directed mainly at mammals. Photographs of scientific specimens are available for representative species from most mammal families. We''ve also included several hundred Quick Time Virtual Reality Movies of skulls. These allow the user to rotate the specimen, providing an excellent impression of its 3-dimensional structure. We''ve written in depth about and illustrated many of the characteristics of interest to students of mammals. An important goal for the future is to expand to cover other groups of animals and include other media such as animal behavior video. :Wiki features, database, teaching tool :
American Association for the Advancement of Science
The American Association for the Advancement of Science
It is an international non-profit organization dedicated to advancing science around the world by serving as an educator, leader, spokesperson and professional association. In addition to organizing membership activities, AAAS publishes the journal Science, as well as many scientific newsletters, books and reports, and spearheads programs that raise the bar of understanding for science worldwide. :AAAS History: Founded in 1848, AAAS serves some 262 affiliated societies and academies of science, serving 10 million individuals. Science has the largest paid circulation of any peer-reviewed general science journal in the world, with an estimated total readership of one million. The non-profit AAAS is open to all and fulfills its mission to advance science and serve society through initiatives in science policy; international programs; science education; and more. For the latest research news, log onto EurekAlert!, the premier science-news Web site, a service of AAAS. :Membership and Programs: Open to all, AAAS membership includes a subscription to Science. Four primary program areas fulfill the AAAS mission: * Science and Policy * International Activities * Education and Human Resources * Project 2061 :AAAS Mission: AAAS seeks to advance science, engineering, and innovation throughout the world for the benefit of all people. To fulfill this mission, the AAAS Board has set these broad goals: * Enhance communication among scientists, engineers, and the public; * Promote and defend the integrity of science and its use; * Strengthen support for the science and technology enterprise; * Provide a voice for science on societal issues; * Promote the responsible use of science in public policy; * Strengthen and diversify the science and technology workforce; * Foster education in science and technology for everyone; * Increase public engagement with science and technology; and * Advance international cooperation in science. :
A networking tool for European researchers abroad. It provides information about research in Europe, European research policy, opportunities for research funding, for international collaboration and for trans-national mobility. Membership is free. :The objective of EURAXESS Links is a flourishing network of European researchers, scientists and scholars abroad. The network is already running in the USA since 2005 and has been launched in Japan in June 2008. The members of the network are informed about European Union research policies and made aware of career opportunities in Europe as well as opportunities for collaboration with Europe. The multidisciplinary network involves researchers at all stages of their careers and allows them to become well connected amongst themselves and in Europe, ensuring that they are recognised as an important resource for the European Research Area, whether they remain abroad or choose to return. :Through the success of the network, EURAXESS Links is intended to contribute to the improvement of Europe''s position in the global competition for talent, and the reinforcement of research collaboration. :EURAXESS Links focuses on three types of activity: networking of researchers, information dissemination and helping expatriate researchers to collaborate with colleagues in Europe or to return to rewarding careers in Europe. Membership of EURAXESS Links is free. :social networking; people resource :
NeuGen is a tool for the efficient generation and description of dendritic and axonal morphology of realistic neurons and neural networks in 3D. :NeuGen builds real neural network geometries and is based on experimental data. The ''in silico'' neurons are based on cells of cortical columns in the neocortex. :L4 spiny stellate neurons, L2/3 pyramidal cells, L5A and L5B pyramidal cells, L4 star pyramidal cells, measuring of morphological paprameters (This is misspelled so not sure we can use), .hoc files, .dx resp. .net files, Via .net files, Data visualization software, OpenDX DataExplorer, simulation software, NEURON, Anatomical Fingerprints, stochastic model, Electromagnetic Simulation Software :
Small-world Network Analysis and Partitioning
SNAP (Small-world Network Analysis and Partitioning) is an extensible parallel framework for exploratory analysis and partitioning of large-scale networks. SNAP is implemented in C, uses OpenMP primitives for parallelization, and targets sequential, multicore, and symmetric multiprocessor platforms. Our intent with SNAP is to provide a simple and intuitive interface for network analysis and application design, hiding the parallel programming complexity from the user. In addition to path-based, centrality, and community identification queries on large-scale graphs, we support commonly-used preprocessing kernels and quantitative measures that help understand the global network topology. The latest version of SNAP (0.4) was released in August 2010. Sponsors: This work was supported in part by NSF Grants CAREER CCF-0611589, NSF DBI-0420513, ITR EF/BIO 03-31654, IBM Faculty Fellowship and Microsoft Research grants, NASA grant NP-2005-07-375-HQ, and DARPA Contract NBCH30390004. Keywords: network, analysis, software, graph, traversal, betweenness centrality, community, identification, multicore,
Volume Visualization and Navigation Tool
Volume Visualization and Naviagtion Tool (VVNT) is a platform to visualize, navigate, process and analyze the multi-modality multi-dimensional medical images. Image processing functions from the Insight Registration and Segmentation tool kit (ITK), Volume visualization functionality from the Visualization tool kit (VTK) are seamlessly integrated into this application. It is built as a Multi-Document Interface (MDI) application, so that several windows can be opened, several operations compared.Some of the current features include * Opens all formats of the DICOM files. * Performs basic image processing functions, contrast brightness adjustments, zooming, panning and other operations. * Surface rendering and Maximum Intensity Projections. * Rotate the rendered volume by specified direction and angle * Automatic segmentation / object extraction * Voxel counts and statisticsSeveral volume measurements and processing functions are currently being added.
The Northwestern University Neuroimaging Data Archive
A resource for managing study data collected by the Northwestern University neuroimaging community. It includes a secure database, automated pipelines for processing managed data, and tools for exploring and accessing the data. Access to data in the NUNDA is restricted to users authorized by the specific study's investigators. The NUNDA is hosted by the Neuroimaging & Applied Computational Anatomy Lab, and it is modeled after the Washington University's Central Neuroimaging Data Archive (CNDA). The NUNDA is powered by XNAT, an open source software package for managing neuroimaging and related data.
Mass spectrometry Interactive Virtual Environment (MassIVE)
Mass spectrometry Interactive Virtual Environment
Mass spectrometry Interactive Virtual Environment (MassIVE) is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. Data repository for proteomics data.
Scientific Transparency (SciTran) is a software project that has grown out of the Project on Scientific Transparency at Stanford University. At the heart of SciTran is a scientific data management system – SDM – designed to enable and foster reproducible research. SciTran SDM delivers efficient and robust archiving, organization, and sharing of scientific data. We have developed the system around neuroimaging data, but our goal is to build a system that is flexible enough to accomodate all types of scientific data – from paper-and-pencil tests to genomics data. SDM will also allow for the sharing of data and computations between remote sites. SciTran is open-source software, released under the MIT license. Our code is hosted on GitHub. Feel free to try it out or to contribute. Commercial support for SciTran SDM is available through our partners at Flywheel. Check out their demo, if you''d like to give SDM a quick try.
Collection of specification documents that define extensions the the W3C PROV standard for the domain of human brain mapping. NIDM uses provenance information as a means to link components from different stages of the scientific research process from dataset descriptors and computational workflow, to derived data and publication.
FP-CIT SPECT brain template in MNI space
The FP-CIT SPECT brain template has been created using a fully automatic procedure involving posterization of the source image to three levels: background, brain and striatum. We performed a spatial affine registration of these 40 posterized source images to a posterized reference image in the MNI space. The intensity values of the transformed images is normalized linearly, assuming that the histogram of the intensity values follows an alpha-stable distribution. Lastly, we built the [123I]FP-CIT SPECT template by the mean of the transformed and normalized images. More info: 1) Salas-Gonzalez et al. Building a FP-CIT SPECT brain template using a posterization approach. Accepted in Neuroinformatics. 2) Salas-Gonzalez et al. Linear intensity normalization of FP-CIT SPECT brain images using the alpha-stable distribution. NeuroImage, Volume 65, 2013, pp. 449-455. http://dx.doi.org/10.1016/j.neuroimage.2...
A project''s launch partners are three research studies that have an established record crowd-sourcing health data for research studies. One initiatives is the Personal Genome Project, established at geneticist George Church''s Harvard lab, which creates a freely available scientific resource that brings together genomic, environmental and human trait data. These data are donated by volunteers enrolled in a PGP study from our global network. A second partner is the GoViral project, started by researchers at Harvard University and New York University, which enables volunteers to provide easy-to-collect specimens when sick with a respiratory infection, and get confirmation of what type of viral illness they have. By testing samples when symptoms occur, participants can validate symptomatic reports as well as enable a better understanding of the representativeness of self-reported data and symptom profiles for different acute respiratory illnesses. Third on the list is the American Gut project, based at the University of California-San Diego and the University of Chicago, which is studying the vast microbial flora that inhabit the human digestive system from crowd-sourced (and properly sealed) samples of feces or skin swabs.
The Cancer Genomics of the Kidney (CAGEKID) consortium brings together expertise in clinical care and epidemiology with genomic expertise. This consortium is an effort of the larger International Cancer Genome Consortium (ICGC), which has the goal of obtaining a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumour types and/or subtypes with the aim of elucidating the genomic changes present in the many forms of cancers that contribute to the burden of disease throughout the world.
The Care Connectivity Consortium (CCC) is working to address and overcome the most critical and key challenges to effective health information exchange (HIE), to make HIE technologies more versatile and valuable for patients, caregivers, and health care organizations. By developing improved technologies for comprehensive, secure, reliable and innovative HIE, the CCC aims to enable health care provider organizations nationwide to deliver better, timelier, and more informed patient care.
ZEN Digital Imaging for Light Microscopy
User interface software for Carl Zeiss light microscopy imaging systems. ZEN is the universal user interface you will see on every imaging system from ZEISS. After selecting fluorophore, ZEN applies the necessary settings to collect and organize data.
Leica LAS X Life Science Microscope Software
Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes.
Software package for editing and preparation of bitmap and vector graphics
Somatostatin Receptor SSTR2A Peptide Fragment
This is the synthetic antigen sequence from which Biotrend anti-SST2A antibodies are raised.
The BioMedical Materials (BMM) consortium focuses on advancing the use of new materials to biomedical research. As a public-private partnership, the consortium includes the participation of over 50 leading institutions, corporations, and health foundations, with support from the government of the Netherlands. The activities of this consortium have ended. The website and materials will be available until 12-31-2015.
The Cell4Cure consortium aims to advance the cGMP production of therapeutic cell therapies. The consortium is led by Cellectis, a biotech focused in the development of adoptive immunotherapies and CELLforCURE, the largest commercial industrial facility for the production of therapeutic cell therapies in Europe. The consortium also includes seven public-sector organizations and university medical centers, who collaborate with the private sector companies.
Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB)
The Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) aims to advance the safe and reliable production of biopharmaceuticals by mitigating the risk of cell culture contamination through agents such as viruses or mycoplasma, by creating a central database of accumulated industry knowledge. Currently, industrial knowledge about contaminating adventitious agents and successful approaches to combat these specific agents is largely limited to each company''s individual experience. The collection, analysis and dissemination of the full body of industry experience would enhance the reliable manufacture and supply of such safe and effective medications. This consortium operates under the umbrella of MIT Center for Biomedical Innovation (CBI).
Collaboratory of AIDS Researchers for Eradciation (CARE)
The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV.
Consortia Advancing Standards in Research Administration Information
The Consortia Advancing Standards in Research Administration Information (CASRAI) is dedicated to reducing the administrative burden on researchers and improving business intelligence capacity of research institutions and funders.The Consortia Advancing Standards in Research Administration Information (CASRAI) aim is to improve the flow of information within and between research stakeholders by developing and maintaining a common and extensible dictionary of terms and exchangeable business objects to advance collaboration. The members include research-performing and research-funding organizations, as well as the service providers that support them. CASRAI goal is to create a central and standardized method for research teams to quickly produce any documents needed by funders and institutions. CASRAI aims to have the following outcomes: save time for researchers in applying & reporting to their funding agencies; Improve access to quality data for institutions and funders; Simplify the measurement of research impacts on society; Provide peer networking opportunities for teams tackling administrative data issues
Centre for Commercialization of Regenerative Medicine (CCRM)
The Centre for Commercialization of Regenerative Medicine''s (CCRM) is an industry consortium that aims to accelerate the application of regenerative medicine to clinical practice. Stakeholder in the consortium include the pharmaceutical, devices, reagents, tools, biomaterials and cell therapeutic companies.
Centre for Drug Research and Developement (CDRD)
The Centre for Drug Research and Development (CDRD) is a Canadian consortium that serves as an integrated national drug development and commercialization center. CDRD''s mandate is to de-risk discoveries stemming from publicly-funded health research and transform them into viable investment opportunities for the private sector.
The Clinical Decision Support (CDS) Consortium aims to enable the use of electronic health records (EHRs) to improve the safety and quality of medical care by pairing these data resources with clinical decision support systems to effectively influence physician behavior. CDS aims to advance a variety of techniques designed to facilitate and guide doctors'' decision making toward evidence‐based practice.
The Centre for Drug Safety Science (CDSS) aims to coordinate the fundamental clinical and basic research into the causes, characteristics and consequences of adverse drug reactions (ADRs). It was established as a joint venture between the Universities of Liverpool and Manchester to bring together a critical mass of knowledge and technologies in order to advance our understanding of Adverse Drug Reactions.
Global CEO Initiative on Alzheimer's Disease
The Global CEO Initiative on Alzheimer's Disease is a public- private partnership that aims to stop Alzheimer's disease and dementia. The consortium brings together international public authorities with the private sector to serve as the leading business voice on Alzheimer's disease.
Consortium for Functional Glycomics (CFG)
The Consortium for Functional Glycomics (CFG) serves to combine the expertise and glycomics resources to reveal functions of glycans and glycan-binding proteins (GBPs) that impact human health and disease. The CFG offers resources to the community free of charge, including glycan array screening services, a reagent bank, and access to a large glycomics database and data analysis tools.
Colon Therapy Research Consortium (COLTHERES)
The Colon Therapy Research (COLTHERES) consortium brings together clinical centers and translational researchers funded in the European Union to define and perform biomarker driven clinical trials to improve cancer therapy outcomes. This 4-year consortium will use comprehensively molecularly-annotated colon cancers as a "test-bed" to define specific biomarkers of response or resistance to signaling pathway agents.
European Clinical Research Infrastructures Network (ERCRIN)
The European Clinical Research Infrastructures Network (ECRIN) is focused on synergizing and connecting the clinical research capabilities within the European continent.
European Management Platform for Emerging and Re-Emerging Infectious Disease Entities (EMPERIE)
The European Management Platform for Emerging and Re-emerging Infectious Disease Entities (EMPERIE) consortium brings together international experts of different disciplines in an efficient and decisive collaborative network, to coordinate the response and control of an emerging new disease.
European Network for Genetic and Genomic Epidemiology (ENGAGE)
The European Network for Genetic and Genomic Epidemiology (ENGAGE) consortium aims to translate data emerging from large-scale research efforts in molecular epidemiology into information of direct relevance to future advances in clinical medicine. The ENGAGE consortium will integrate and analyze one of the largest ever human genetics dataset (more than 80,000 genome-wide association scans and DNAs and serum/plasma samples from over 600,000 individuals). One goal is to demonstrate that the findings from ENGAGE can be used as diagnostic indicators for common diseases that will help us to understand better risk factors, disease progression and why people differ in responses to treatment.
MicroRNAs in the Pathogenesis Treatment and Prevention of Epilepsy (EpimiRNA) Consortium
The MicroRNAs in the Pathogenesis, Treatment and Prevention of Epilepsy (EpimiRNA) consortium aims to understand molecular mechanisms, diagnostics and develop novel therapeutics for epilepsy. The consortium aims to apply recent scientific breakthroughs that identified a new family of molecules that affect brain cell structure and function called microRNAs, to better understand medical products targeted to epilepsy.
Markers for Sub-Clinical Cardiovascular Risk Assessment (EU-MASCARA)
The Markers for Sub-Clinical Cardiovascular Risk Assessment (EU-MASCARA) consortium aims to improve diagnosis of cardiovascular diseases and prediction of cardiovascular risk by analyzing a panel of biomarkers. EU-MASCARA aims to validate biomarkers that have been proposed to be associated with cardiovascular disease and risk across different disease entities and also in independent general population samples. The most robust biomarkers will be implemented in novel biochip based assays for clinical use.
European large-scale functional genomics in the rat for translational research (EURATRANS)
The European large-scale functional genomics in the rat for translational research (EURATRANS) consortium brings together investigators who will use next-generation sequencing technologies to generate genomic, transcriptomic and epigenomic datasets. The goal is to create quantitative metabonomic and proteomic datasets to give significant depth of coverage, at multiple levels, across pathophysiological phenotypes. The aim is to enable insights into disease mechanisms, through an integrative, cross-disciplinary approach to understanding large-scale functional genomic datasets in rats and humans.
Central data repository that supplies organisms and reagents to the broad community of microbiology and infectious diseases researchers.
Immune tolerance data management and visualization portal for studies sponsored by Immune Tolerance Network (ITN) and collaborating investigators. Data from published studies are accessible to any user; data from current in-progress studies are accessible to study investigators and collaborators. Includes links to published Figures, tools for visualization and analysis of data, and ability to query study data by subject, group, or any other study parameter.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 9,2023. Registry that archives curated nanomaterial research data and their biological and environmental implications. The Registry provides data management plans for researchers, and accepts users' public-ready data, archive them, integrate them into the registry, allowing for the data to be shared publicly. Users can request more information on specific nanomaterial records, compare multiple nanomaterials, and export data to their desktop.
European Network for Translational Research in Atrial Fibrillation (EUTRAF)
The European Network for Translational Research in Atrial Fibrillation (EUTRAF) consortium brings together investigators aiming to accelerate knowledge in the pathophysiology and treatment of Atrial Fibrillation. By integrating the mutually complementary strengths and expertise from molecular and cellular electrophysiology to the study of large cohort of patients, EUTRAF aims to develop approaches for increasing knowledge of the arrhythmogenic substrate, with the ultimate goal of developing novel treatments and diagnostic tools.
Fatty Liver Inhibition of Progression (FLIP)
The Fatty Liver: Inhibition of Progression consortium (FLIP) aims to study the mechanisms of progression of liver disease in NAFLD to provide strategies for prevention and therapy. The project is based on the largest European cohort of patients with histologically diagnosed NAFLD, assembled with clinical and epidemiological data, and with biobanks of DNA, frozen liver tissue and serum. The consortium''s efforts span all the steps of the disease for studying cellular mechanisms of progression, with a goal of answering key issues dealing with the interplay of metabolic, inflammatory and fibrotic factors in the initiation and perpetuation of liver injury.
Genetic Association Information Network (GAIN)
The Genetic Association Information Network (GAIN) supports a series of Genome-Wide Association Studies (GWAS) designed to identify specific points of DNA variation associated with the occurrence of a particular common disease. Initially focusing on six major common diseases, GAIN focused on combining the results with clinical data to create a significant new resource for genetic researchers.
The NeuroML database is a curated relational database that provides for the storage and retrieval of computational neuroscience models expressed in NeuroML, which is an extensible XML-based language for describing complex mathematical models of neurons and neuronal networks. NeuroML models are unique in their modular and multi-scale structure, where subcomponents of models can correspond to neuroscience models. In particular, the NeuroML database allows for efficient searches over the components of models and metadata that are associated with a hierarchical NeuroML model description.
The Global Research in Paediatrics (GRiP) consortium focuses on the lack of appropriate testing of pediatric drugs. In particular, most pediatric medications having inadequate information about dosing regimen, dose adjustment and administration. GRiP partners are working to build and maintain an infrastructure matrix, which has the core aim of reducing the current fragmentation of the efforts to study and develop the use of medicine in children. By linking the existing pediatric research networks, GRIP will involve more than 1000 institutions worldwide.
Glycomics by High-throughput Integrated Technologies (GLYCOHIT)
The Glycomics by High-throughput Integrated Technologies (GlycoHIT) consortium aims to advance the development of reliable and fast diagnostic tests for the early detection of cancer. By creating high-throughput technologies to analyze altered sugars, or glycobiomarkers, the consortium aims to allow scientists to diagnose different forms of cancer from a simple blood test without the need for biopsy. GlycoHIT will also further develop sugar testing technologies to allow this rapid form of diagnosis to be used in a clinical setting.
Imaging of Neuroinflammation in Neurodegenerative Diseases (INMiND)
The goal of the Imaging of Neuroinflammation in Neurodegenerative Diseases (INMiND) consortium is to identify novel biological targets of neuroinflammation for both diagnostic and therapeutic purposes, and to translate this knowledge into clinical application and patient benefit. The consortium supports collaborative research on molecular mechanisms that link neuroinflammation with neurodegeneration.
Inflammatory Bowel Disease Biomarkers Consortium (IBD BIOM)
The Inflammatory Bowel Disease Biomarkers Consortium (IBD-BIOM) addresses the need to improve our understanding of inflammatory bowel disease (IBD) through new biomarkers into molecular dysfunctions that give rise to IBD. The biomarkers targeted by the consortium will be translated into early-detection clinical diagnostic tests for IBD patients.
Mendelian Forms of Parkinson's Disease (MEFOPA)
The Collaborative Project on Mendelian Forms of Parkinson's Disease (MEFOPA) is a consortium that advances the basic and clinical research on rare Mendelian forms of Parkinson's disease (PD) by identifying and validating relevant disease-related molecular pathways, drug-targets and biomarkers for disease susceptibility and progression.
Multiple Sclerosis Outcome Assessments Consortium (MSOAC)
The Multiple Sclerosis Outcome Assessments Consortium (MSOAC) is a public-private partnership which aims to accelerate the development of new therapies for MS by generating new tools for measuring outcomes in clinical trials. It is collecting, standardizing, and analyzing data about MS with the goal of qualifying new measures of disability for the disease. MSOAC is the newest of the eight consortia of Critical Path Institute (C-Path), a nonprofit organization that is dedicated to accelerating drug development by delivering on the mission outlined by FDA' '''s critical path initiative.
The OPTObacteria consortium aims to develop a multianalyte and automatic laboratory detector (ALD) for antibiotic resistant infections. The goal is to detect these analytes within 4-6 hours from the sample collection, providing a report with the actual patient status, and predicting emerging drug resistance through the companion epidemiology software. The platform technology for this consortium is an opto electronic device, in which the appropriate ligand-probe, linked onto an opto electronic surface, will be able of specifically recognize biomolecules of the resistant infections.
Osteoarthritis Biomarkers Project (OABP)
The Osteoarthritis Biomarkers Project (OABP) is a consortium designed to identify and classify biological markers of progression of knee osteoarthritis. Their goal is to advance the ability to predict the individual risk of developing severe OA and to monitor progression of OA.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2023. Software application which can analyze basic Western blot data and export them for use in spreadsheet programs. Users can create standardized or custom lab reports and can share them with colleagues. Image Studio Lite has been discontinued and replaced with Empiria Studio Software.
An image repository that provides access to published, peer-reviewed medical images from biomedical journals.
Cancer Nanotechnology Laboratory (caNanoLab)
Data sharing portal designed to facilitate information sharing across international biomedical nanotechnology research community to expedite and validate use of nanotechnology in biomedicine.
Database that contains information on adverse event and medication error reports submitted to FDA. The database is designed to support the FDA's post-marketing safety surveillance program for drug and therapeutic biologic products.
InterNano Resources for Nano Manufacturing
Database and knowledge base of techniques for processing nanoscale materials, devices, and structures that includes step-by-step descriptions, images, notes on methodology and environmental variables, and associated references and patent information. The purpose of the Process Database is to facilitate the sharing of appropriate process knowledge across laboratories.The processes included here have been previously published or patented
The GenDR Database of Dietary Restriction-Related Genes
Database of genes associated with dietary restriction. It includes genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of dietary restriction and genes robustly altered due to dietary restriction, derived from a meta-analysis of microarray studies in mammals.
Drug database published by the Food and Drug Administration of unique universal product identifiers for all drugs manufactured, prepared, propagated, compounded, or processed by it for commercial distribution.
Online higher education which offers vocational and professional courses to adults.
Imaging system for detection of chemiluminescent, colorimetric and UV fluorescent gels and blots.
Digitizer software which can convert graph images to useful (x,y) data by turning a scanner into an automatic graph digitizer. UN‑SCAN‑IT works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source to digitize plots, instrumental output, published graphs, etc. Its features include: automatically digitizing strip chart and xy recorder output, digitizing graphs that are on different scales to compare results, comparing data with published graphs of other investigators, digitizing old plots and charts for comparison with new data, and re‑scaling and appending existing printed graphs.
G*Power - Statistical Power Analyses for Windows and Mac
Data analytics software to compute statistical power analyses for many commonly used statistical tests in social and behavioral research. It can also be used to compute effect sizes and to graphically display the results of power analyses.
Approved Drug Products with Therapeutic Equivalence Evaluations
Database that contains drug products approved on the basis of safety and effectiveness by the Food and Drug Administration.
Avidin is a tetrameric or dimeric biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs.5 It consists of four high affinity binding sites for biotin. ExtrAvidin is prepared from egg white avidin. It is a modified form of affinity purified avidin and combines high specific activity of avidin with the low background staining of streptavidin. It is a biotin binding protein produced by the bacteria Streptomyces avidinii.6 ExtrAvidin has been conjugated to fluorescein isothiocyanate (FITC) and is used for various techniques.
dkNET Community Pilot Funding Opportunities
A list of community-based funding opportunities provided by projects or organizations other than government funding opportunities. They are available via various NIDDK-supported centers, e.g., pilot projects, training opportunities, etc.
National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics).
Gene Library Resource for the Sea Urchin Strongylocentrotus purpuratus
Database that provide a genomic information and comparative genomics platform on sea urchins and related echinoderms. It provide collection of information to directly support experimental work on these useful research models in cell and developmental biology.
Global Understanding in Dynamic Embryonic Systems
A worm atlas that provides an interactive 4D atlas of nuclear positions, from zygote until hatching which can be used to guide cell identification. The tools enable examination of the connectome during development from integrate knowledge of C. elegans embryogenesis to widely used resources, such as WormAtlas and WormBase.
This web service provides volcano and earthquake information. It also has tsunami events and tsunami tide gauges, and plate boundaries. BPR and DART stations. Also volcanic eruptions.
Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.
A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants.
Database of resources receiving federal financial assistance of more than $25,000. The Federal Funding Accountability and Transparency Act of 2006 was mandated to provide the public access to information regarding organizations and other entities receiving federal funding.
Database of summary statistics of resources receiving funding from the National Institutes of Health. The resources listed includes extramural grants and contract awards, grant applications, NIH supported organizations, trainees, and fellows, and the national biomedical workforce.
Open Access Infrastructure for Research in Europe
A research portal to share and obtain research data and journal articles openly accessible to all disciplines. Established to support the Open Access Policy, as set out by the ERC Scientific Council Guidelines for Open Access and the Open Access pilot launched by the European Commission.
Full text database of all patents granted in the United States since 1976, and the patent number, issue date, and current US classification for all patents granted from 1790 through 1975.
A data repository containing transcriptome and associated metadata for the developing and adult human brain. It provides genome-wide, exon-level transcriptome data from both sexes and multiple ethnicities.
Spatio-temporal transcriptome of the human brain
A research paper with supplementary materials reporting the generation and analysis of exon-level transcriptome and associated genotyping data. The experiment represented both males and females of multiple ethnicities and examines gene regulation and expression in different areas of the brain. A data set on the human brain transcriptome as well as insights into the transcriptional foundations of human neurodevelopment is provided.
A museum whose three main focuses are its specimen collection, academic research, and the popularization paleontology, zoology, botany, and anthropology.
Windows Multiple Document Interface for Flow Cytometry
Windows Multiple Document Interface software
Software to analyze flow cytometry listmode data files.
A database of tissue specific nuclear receptor transcriptomes based on annotated published genome wide transcriptional profiling experiments in the field of nuclear receptor signaling. Queries can include single and multiple genes, Gene Ontology terms, disease terms, and uploaded custom gene lists.
A non-governmental wildlife research institution involved in the conservation of nature, primarily biological diversity and threatened species through action based on research, education and public awareness. Contains publications, collections, and educational materials as well as information on current research.
Biotechnology Culture Collection Institution Pusat Penelitian dan Pengembangan Bioteknologi-LIPI
Biotechnology Culture Collection Institution
Pusat Penelitian dan Pengembangan Bioteknologi-LIPI
An institutional resource focusing on research in biotechnology. Their goals include becoming a reliable reference in the biotechnological field and improving the performance and professionalism of research institutes.
University of South Florida Center for Biological Defense
An institutional resource focusing on biological defense and infectious disease research. The institution teaches preparation and response to catastrophes, especially bioterrorism preparedness, to local communities and conducts research in detecting and fighting biological agents and infectious diseases.
National Bank for Industrial Microorganisms and Cell Cultures
Bulgarian national collection for microorganisms and cell culture
An institutional and material resource housing over 7400 strains of bacteria, yeasts, fungi, plant and animal viruses, and animal cell cultures. Certified for preservation, supply, import, and export of strains. An international depository which applies their collected strains in research, education, health services, industry, and agriculture.
A software registry containing digital research tools ranging from content management systems to statistical analysis packages and mind mapping software. The site contains detailed descriptions, license information, and links to software developer websites and downloads.
A software registry providing links to software programs designed to aid researchers. Connected Researchers actively adds new resources to its registry along with descriptions and links to the software developer's site.
Software tool for reformatting abstracts from original submission formats into a text encoding format for publishing on-line and book abstracts.
Multi-Disciplinary Approach to the Study of Chronic Pelvic Pain
Multidisciplinary Approach to the Study of Chronic Pelvic Pain Research Network
Collaborative research network specializing in urological chronic pelvic pain disorders. Project involves conducting research primarily on interstitial cystitis/painful bladder syndrome and chronic prostatitis/chronic pelvic pain syndrome and involves researchers from multiple disciplines. MAPP Network includes researchers with clinical, epidemiological, and basic research expertise.
Database that allows for the exploration of cancer on somatic missense mutations from the Cancer Genome Atlas and Cancer Cell Line Encyclopedia. The site maps proteins and mutations using 3D models and is an interface to the algorithms e-Driver and e-Drug allowing for the prediction of novel cancer drivers or drug biomarkers.
A software application which assists in managing and sharing scientific literature. Users can collect and share publications, collaborate with other researchers, and find new resources and publications for research.
A software application which contains a collection of biomedical resources and assist in the management resources. Resources consist of clinical trials, publications, abstracts, patents, news and events. Users can search, save, and make notes on publications.
A web application which stores and organizes scholarly papers and references. Papers of interest identified from the web can be added to the users' personal library and the associated references will be automatically extracted.
A reference manager software tool which manages references and journal articles. Individual users can search for and save references or share a library of resources with identified group members who can annotate and comment on the references
A web application which provides public access to scientific literature through text and data mining.
A web-based information resource providing current news and resources relevant to data science. Users can subscribe to the weekly newsletter by providing an email address or visit the site. The site displays the current week's news and houses an archive of their past newsletters.
A web application which enables users to access fee based scientific journals and articles. Users can rent peer-reviewed journals and articles from the website, regardless of their academic institution or library affiliations.
A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched.
A web-based collaboration tool specializing in sharing and promoting research. Users can share their research and collaborate with others or search the site for publications. Relevant scientific news is also available for users to view.
A web application that allows users to track new biomedical papers from the PubMed database. Users can search for articles concerning genes, species, disease, techniques, and other related topics and create a personalized Newsfeed related to bookmarked papers. New articles are also displayed in Newsfeed format.
A web application containing Open Access journals and papers from multiple disciplines. Relevant resources are collected from all fields of research, from the natural and physical sciences to the social sciences and humanities. Users can search for journals and papers or expose their papers to a wider audience.
A web application tool which visualizes papers collected in arXiv. Users can search for papers and create an interactive graph to organize their resources. The graph shows the relationships between papers, the dates they were published, and other relevant information. Papers can be tagged and graphs can be shared with colleagues.
A web application that recommends biomedical scientific articles based on articles saved to the users' ''' library. Users can search the National Library of Medicine databases and store articles of interest in a cloud library, which can be accessed on a computer or mobile device and can be shared with colleagues.
A web application which allows users to access life science research articles in PDF format. Users can search across all affiliated institution's subscriptions. Tools are provided to manage papers, which include downloading citations and creating email alerts for new, relevant articles.
A software application that enables users to peer review published research articles. Users must have a previous publication and an email address at an academic or research institution. Comments can be made in any article published with a digital object identifier, PubMed identifier or a preprint in arXiv. Authors are notified of any comments their paper has received and may respond to comments.
Culture Collection of Algae at the University of Cologne
An institution and biomaterial supply resource which houses more than 3500 strains of algae. The majority of the strains are derived from freshwater/terrestrial habitats while 15% are representative of marine and brackish water strains. 15% of the strains are axenic. 50% of the strains are currently available to the public and can be ordered from the CCAC's main site.
Universidade Federal do Ceara, Centro Ciencias Agrarias
Federal University of Ceará Center for Agricultural Sciences
An institution focused on furthering research and higher education in the field of agriculture.
An institution located in Bangalore focused on higher education. The university has established Gandhi Bhavan, Dr. B.R. Ambedkar Study and Research Centre, and Centre for Study of Social Exclusion and Inclusive policy as well as schools of biological sciences, social sciences, and business studies.
An institution which serves as a deposit of saprotrophic ascomycete and zygomycete strains. 3400 isolates are contained, 2400 of which are available to the public. The collection also provides atlases of each. While some strains are provided for free, other services, such as providing strains for teaching or research or identifying cultures, are provided for a charge.
An institution which records the natural history of Ekalaka county, Montana. The museum contains artifacts from 80 million years ago to the present, including fossils, arrowheads, and early pioneer artifacts. Another focus of the museum are vertebrates and invertebrates found in the area. Items are available to research by appointment.
A software resource application which organizes research literature. Users can import PDF articles into the application and create a searchable library. ReadCube enables users to perform keyword searches and provides references as well as note-taking tools. ReadCube also recommends articles to users based on library contents. For publishers, ReadCube enables interactive PDF versions of articles with tools for readers to make notes or perform author and keyword searches.
A software application that provides visual representations and organization for systematic literature searches. Users can observe trends in scientific literature through graphic visualizations while using keyword searches to find related articles or compare trends within a given graphic. SciCurve also allows users to locate journals which publish literature in users' fields of interest.
A database of flow cytometry experiments where users can query and download data collected and annotated according to the MIFlowCyt data standard.
A web application which organizes current scientific literature by fields, people, institutes, labs, places, and historical sets they are a part of. Sciencscape allows users to subscribe to topics to receive new material, as well as provides visual representations to organize recent and most cited papers.
A web application which finds new and relevant scientific literature based on keyword searches and filters. Users can also share, organize, and collaborate on papers using tools within Scizzle.
A web application which organizes and recommends new scientific literature to users' news feeds based on keyword searches and user preferences. The site contains materials such as articles, posters, patents, grants, videos, and events.
A database which holds summaries of landmark clinical trials. The topics of contributed articles range across various biomedical fields and disciplines such as immunology, nephrology, and urology.
A software application that allows users to add and store research content directly from the web. Users can use the tool to add research content and bibliographic references directly to their Zotero library from their browser. The application stores PDFs, images, audio and video files, and snapshots of web pages on a single searchable interface.
A web application which provides tools to share references and generate bibliographies with colleagues, organize and access references, and track metrics for ACS articles. Articles are automatically synced to user libraries and are accessible from multiple devices.
A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks.
A data set of defined genomic sequences used as reference standards for well-characterized genes. These standard nucleotide sequences serve as foundations for locating mutations, establishing conventions for numbering exons and introns, and defining the coordinates of other variations. Sequences are aligned to reference chromosomes. RefSeqGene is a subset of NCBI RefSeq.
An online repository which houses sequencing data from gel and capillary platforms (such as Applied Biosystems ABI 3730®). Most sequences are derived from Whole Genome Shotgun sequencing. Large data sets as well as only a few sequences can be obtained.
A database which provides viral and viroid genome sequence data and resource tools. Al viral genomes are downloadable and a complete RefSeq release of viral and viroid genome sequences are available.
A repository which supports the search, retrieval, and display of large virus sequence data sets concerning the viruses of Dengue, West Nile, and Influenza. Users can search sequences based on a number of biological and clinical criteria and selected sequences can be downloaded or analyzed using a variety of web-based tools and displays. Virus Variation is an extension of NCBI's Influenza Virus Resource.
A database which integrates information about genomic clones and libraries, including sequence data, map positions and distributor information. A clone's standardized name in Clone DB is comprised of its microtiter plate address with plate number row and column, prefixed by the standard library abbreviation, to provide a unique clone name. Libraries with records may be accessed via the genomic or cell-based library browsers.
Biospecimen Repository and Processing Core
A biomaterial supply and access service resource which provides a shared resource for coordinated tissue processing and biorepository services. Services include patient identification and informed consent, specimen collection, processing and banking, and annotation of banked specimens and specimen distribution. They provide biospecimen inventory management, services, and equipment. It is a shared resource of Duke University.
Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops.
National Database for Clinical Trials related to Mental Illness
A database which houses human subjects clinical trial data. NDCT currently contains data on 13,409 subjects and has access to data on 100,500 subjects from the NIMH Data Archive. Users can also sign up for news updates and watch video tutorials.
A database that houses human subjects data related to mental health research. Data from 691 subjects are shared in RDoCdb and data from 100,500 subjects are shared in the NIMH Data Archive. Users can plan for data submission, share data, query data, or share their results related to a publication or finding.
Thermo Fisher: Sartorius | Ambr 15 Cell Culture Generation 2
Automated, high throughput microscale bioreactor system that replicates laboratory scale bioreactor performance., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software application which allows reconstruction of neuronal structures from confocal and multi-photon images. NeuronStudio provides tools for manual, semi-manual, and automatic tracing of the dendritic arbor, as well as manual and automatic detection and classification of dendritic spines. Advanced 2D and 3D visualization techniques facilitate the verification of the reconstruction, as well as allowing accurate manual editing. The most current version is Version 0.9.92 which was last updated on November 19, 2009.
A software application which provides the source code for the Rayburst Algorithm. The fully automated algorithm casts rays in a 2D/3D dataset without the use of pre-generated ray tables. It is implemented in ANSI C as a single module. The most current version is Version 1.1, last updated on Aug. 15, 2006.
A software application designed to allow multiple stacks of tiled optical sections obtained from Laser Scanning Microscopy to be integrated into a single volumetric dataset. VIAS allows the user to select the individual image stacks from disk and to adjust their relative position on the screen interactively. By using a global 3D coordinate system, users can manipulate stacks and execute the integration of the data after all the stacks of images have been correctly positioned. VIAS was designed with large datasets in mind. The current version of VIAS is Version 2.4, last updated on January 26, 2009.
Volume Integration and Alignment System Source Code
Volume Integration and Alignment System (VIAS) Source Code
The source code for VIAS software Version 2.4. The code is written in the C programming language and uses Win32 for the graphical user interface.
A software application which enables the visualization of datasets obtained from Confocal Laser Scanning Microscopy (CLSM). P-View allows users to interact with a pre-computed model using a flight simulator type interface. The program makes use of several optimizations to allow visualization of large objects using standard PC workstation hardware, including the speed up techniques Level of Detail and Frustum Culling. The current version of this software is Version 1.2.1, last updated on October 1, 2002.
A software application which is used to create navigable visuals of neural structures. The current version of the program accepts NeuroZoom ASCII files as input. Users can visit CNIC's online repository for a full list of free, available models. The current version of the software available is Version 1.2, last updated on July 13, 2004.
A software application which reduces the number of voxels used to represent a volumetric dataset by means of subsampling, i.e., computes a smaller version of a given dataset. Stacks can be selected from the disk by point and click and users are free to specify the new dimensions as actual pixels or as a percent of the original dimensions. The current version is Version 1.0, last updated on February 10, 2003.
Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Web-based tool that predicts subcellular localization and GO molecular function of proteins. Proteome Analyst has the ability to explain its predictions and gives users the ability to run a large set of tools on their proteins.
An international consortium whose goals are to enable faster comparative studies and develop tools that make analysis accessible to the wider scientific community. InterMOD is an open source data warehouse where users can query and input their own data, access analysis tools, and create their own InterMine. Five core mines make make up InterMOD: RGD, SGD ZFIN, MGI, and WormBase.
A web application which modifies the online use of scientific articles published in eLife. eLife Lens is a tool created by eLife that enables users to explore figures, figure descriptions, and references while keeping their place in the article text. Users can search for papers by subject, organism, article type, and/or top authors.
A publishing company which aims to produce intellectual content as well as research platforms and intelligence solutions. Elsevier publishes works related to science, health, and technology in physical copies and online. The company also provides integrated technology and analytics which allows users to to interact with, manipulate, share, and extract informant from various resources.
A web application which provides interactive and in depth reading of online scientific articles published in Elsevier. While reading an article, users can access interactive data sources such as Protein Viewer and Google Maps as well as links to references and databases. Prototypes for seven different scientific areas are currently available for more specific research, but all scientific disciplines are represented within Article of the Future.
A software application which allows for interactive viewing and publishing of a wide range of 2D and 3D image data formats. Users can use the tool to build custom views of image data that can be saved, integrated with peer-reviewed articles, and shared with readers through the Optical Society's journals. ISP supports DICOM, TIFF, and JPEG image formats.
A web application which serves as an alternate way to read scientific literature in PubMed Central and Bookshelf. PubReader features an easy-to-read multi-column display, a figure strip for access to figures, and a search function. It is designed especially to support reading on tablets and other smaller devices but is available for reading on laptops and desktops.
A database which houses publisher policies regarding the self- archiving of journal articles on the web and in Open Access repositories. RoMEO contains publishers' general policies on self-archiving of journal articles and certain conference series. Each entry provides a summary of the publisher's policy, including what version of an article can be deposited, where it can be deposited, and any conditions that are attached to that deposit.
A web application which enhances online reading of articles from the Wiley Online Library. Wiley Anywhere Article is an alternate HTML version of articles found on the Wiley Online Library that is supported on all desktop, tablet, and mobile devices. Readers have access to sidebar and tray functions which display references, figures, and other important information while keeping their place in the article.
A web application which provides article tools specifically for the chemistry journals Applied Organometallic Chemistry, Chemistry – An Asian Journal, Chirality, Journal of Heterocyclic Chemistry, and Journal of Physical Organic Chemistry. The addition of Smart Article to these journals allows researchers to search across all five journals and to index and browse facilities for detailed information on compounds.
A collaboration tool which allows users to upload and share presentations, infographics, documents, videos, PDFs, and webinars. Individual slideshows are available for download and are easily uploaded to other websites and blogs.
A collaboration tool designed specifically for scientists as a place to collaborate and engage in activities with others. Users can create and manage a professional profile, meet new people and build their professional network, find the latest news and updates in science, participate in online conversations, upload and manage documents, and host a journal club, a live chat-based Q&A, or a presentation series.
A collaboration tool that aims to spread the stories and advice of researchers in the sciences, engineering, and the humanities. Researchers can share and collaborate on ideas, find resources and tools, and read the stories of other researchers.
A web application containing access to research services and products. Users can create custom services, find research services and compare them, request price quotes, exchange files and upload reports, place orders, and track studies. Assay Depot regularly updates its page with new services.
A database providing information about compounds under investigation for therapeutic use. There are currently 44 compounds on record with 100 compounds in the process of being uploaded to the database.
A database which provides a comprehensive and regularly updated collection of genetic association studies performed on multiple sclerosis phenotypes. Eligible publications are identified following systematic searches of scientific literature databases as well as the table of contents of journals in genetics, neurology, and immunology.
A set of many statistics calculators, including a confidence interval calculator.
Standard Low Resolution Brain Electromagnetic Tomography
Standardized low-resolution brain electromagnetic tomography
A software application which computes images of electric neuronal activity from EEG and MEG. Standard Low Resolution Brain Electromagnetic Tomography, or sLORETA, localizes “test point sources” exactly (under ideal conditions) when estimating electric neuronal generators. This property can be generalized to any source distribution, based on the principles of linearity and superposition. However, it would be noted that sLORETA has very low spatial resolution.
exact Low Resolution Electromagnetic Tomography
Exact Low Resolution Brain Electromagnetic Tomography
Software application which computes cortical three-dimensional distribution of current density of the brain based on the scalp-recorded electric potential distribution. The exact low resolution brain electromagnetic tomography method has the property of exact localization to test point sources, yielding images of current density with exact localization, albeit with low spatial resolution. eLORETA has no localization bias even in the presence of structured noise. Deep structures, such as the anterior cingulate cortex and mesial temporal lobes, can be correctly localized with these methods.
A neuronal simulation software application used to study spinal cord neuronal network systems for muscle control. Users can investigate phenomena at several levels of organization, such as the neuronal membrane level or the whole muscle behavior level. ReMoto can be used to interpret results, validate experimental protocols, and teach neurophysiology.
An on-going atlas project of the Virtual Insect Brain Project with the goal of reconstructing and standardizing Gal4 expression patterns in Drosophila brains. Neurofly will be a web-based tool that will enable the online comparison of mutations and Gal4 expression patterns in the Drosophila brain. To this end, a database of reconstructed and standardized Gal4 expression patterns - on the basis of the existing Drosophila StandardBrain - was developed along with tools for 3D image data set processing. Users will be able to evaluate the expression patterns intersections of various Gal4 driver lines and/or mutations.
A software registry which offers links to various free statistical software programs for stand-alone computing. The software programs are split into different categories: General Packages, Subset Packages, Curve Fitting and Modeling, Biostatistics and Epidemiology, Surveys, Testing and Measurement, Excel Spreadsheets and Add-ins, Programming Languages and Subroutine Libraries, Scripts and Macros, Miscellaneous, and Other Collections.
A collaborative project between the Broad Institute and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation, with the goal of conducting a detailed genetic and pharmacologic characterization of a large panel of human cancer models. The CCLE also works to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.
A biomaterial resource which stores and distributes dissected human brain samples and topographically oriented tissue blocks. Most brains were removed from the skull and frozen within 2-6 hours after death. The microdissection of 260 different brain nuclei is performed on frozen brains and the samples are kept in -70ºC. Materials must be studied in the course of an approved research project, which has scientific aims and is devoid of any commercial profit for the researches involved and for their respective institutions.
A biomaterial supply resource which supplies brain tissue for researchers studying dementia and other neurodegenerative diseases. The Maritime Brain Tissue Bank archives tissues related to Alzheimer's Disease, mixed dementias, Lewy Body Disease, and Huntington's Disease, among others.
MRC London Neurodegenerative Diseases Brain Bank
A biomaterial supply resource which provides high quality, clinically and neuropathologically well-characterised human brain and spinal cord tissue. The Brain Bank focuses on neurodegenerative diseases such as Alzheimer’s Disease (AD), Frontotemperal dementias (FTD) and Motor Neurone Disease (MND). However, it also contains tissues for the study of HIV, Autism and Schizophrenia, and movement disorders.
A biomaterial supply resource which collects, stores, and disseminates diseased and healthy brain tissue. The Netherlands Brain Bank currently contains more than 3600 samples, and each sample includes a neuropathological report and donor medical history. The samples can additionally be matched with ante-mortem parameters and post-mortem parameters upon request. Sample types include cortex, spinal cord, cerebrospinal fluid, plasma, and DNA, among others. Database mining is available with a financial contribution.
A biomaterial supply resource which collects, stores, and disseminates biomaterial and clinical data relating to neurological disorders, psychiatric disorders, cardiology pathologies, and pneumology pathologies. NeuroBioTec has 18 collections with a total of 100,000 samples of serum, plasma, cerebrospinal fluid, PBMC, urine, tissue, DNA and RNA. Some samples can be made available to external researchers under certain conditions.
A biomaterial supply resource which archives and disseminates brain tissue for the study of normal brain aging and brain disorders. Researchers must create an account in order to browse the database of available tissue. Samples are distributed to researchers in such a way that the identity and personal information of donors is protected.
Commercial biomaterial supply resource which provides an extensive biorepository as well as an exclusive human tissue-based research service. The biobank contains defined and categorized clinical samples of tissues, blood, serum, bone marrow, and tissue microarrays. ProteoGenex collects biomaterials for a variety fields, including oncology, neurology, and immunology. Normal tissues are collected, as well. All samples are supported by pathology information and patient clinical history documentation. ProteoGenex also offers custom collection design.
A biomaterial supply resource which provides human and animal biological matrices and services. Human biomaterials and tools include hepatocytes, clinical samples, normal samples, subcellular fractions, immunology products, renal cells, cell cultures, and diagnostic tools. Animal biomaterials include hepatocytes, blood, fluid, and tissue samples, subcellular fractions, and cell cultures. Custom cells and clinical samples are available for purchase, as are hepatocyte and renal media.
A software application which tracks EPBs. EPBscore tool uses maximal intensity for the following reasons: 1) the integrated intensity is affected by the sampling density and it is not clear how large an area one should integrate over. This is often determined by ad- hoc criteria with no theoretical justification. 2) The integrated intensity is susceptible to movement artifacts. 3) As shown in (Grillo et al. 2013), the maximal intensity scales over the whole range of EPB intensities is considered. Importantly, the tool successfully minimizes human input by automating the EPB scoring and measurement steps., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Residual Variation Intolerance Score (RVIS)
A gene-based score intended to help in the interpretation of human sequence data. The score is designed to rank genes in terms of whether they have more or less common functional genetic variation relative to the genome wide expectation given the amount of apparently neutral variation the gene has. A gene with a positive score has more common functional variation, and a gene with a negative score has less and is referred to as intolerant.
A global network group resource which provides crowdsourcing services for “innovation solutions.” InnoCentive utilizes an innovation framework, called Challenge Drive Innovation, which is based on leveraging open innovation and crowdsourcing. Software tools are available for idea management, innovation management, and external crowdsourcing programs and competitions.
A group resource which connects organizations to data scientists who produce accurate predictive models. Kaggle uses competition to incentivize data scientists to create the most accurate and precise predictive models for an organization’s sets of data. The data scientist or team of data scientists who creates the best model is awarded a prize and the organization receives the predictive model.
A funding resource which allows researchers to receive funding from citizen and organizational donors. Benefunder encourages relationships between the donor(s) and researcher(s) as well as wealth management which facilitates long-term funding and low overhead.
A for-profit funding resource which funds research through the contributions of donors and backers. Scientists can create project profiles which include stated funding goals that must be reached before the end of the campaign. Projects which do not achieve their funding goals will be dropped and no funding from Experiment backers will be received. Three basic criteria must be met before an experiment can receive consideration for funding: The experiment seeks to answer a specific research question, the process and results can be shared openly and transparently, and the researchers have the expertise needed to meet the goals. Additional criteria must be met for academic scientists, individual scientists, and corporate scientists, respectively. Experiments are reviewed by Experiment staff before they are accepted.
A non-profit funding resource that allows academic medical researchers to receive funding from donors. Researchers set a fixed amount for donor funding which must be reached within two months to ensure the continuation of the campaign. Consano allows quarterly communication between donors and researchers throughout the term of the project. Some non-academic research is approved to be funded through Consano.
A computational hosting resource designed to replace email as the primary means of team communication by allowing teams to manage, plan, and organize on the same interface. Asana provides an interface with different panels that organize team members’ tasks, meetings, projects, comments, and inboxes. It is compatible with a variety of software and web tools such as DropBox, GitHub, Evernote, WordPress, and JIRA.
A computational hosting resource which organizes lab inventories, including communal stocks, samples, and chemicals. Users can organize by predefined or custom sample types and store information for each type using specific fields. Samples can be stored in defined custom storage units and can be added to or searched within those storage units. ELabInventory supports 2D barcoding to identify samples.
A registry for reviewed material resources such as lab equipment, consumables, and services. LabCritics provides comparison charts, location of distributors, and distributor ratings along with extensive material reviews.
A computational hosting resource which provides lab management and collaboration in one location. When users create a new experiment, they can take note of the experimental design in LabGuru by searching for and adding protocols and reagents to the project main page. Information for reagents such as batch number and concentration are retained in the records. Users can also track the progress of experiments and receive results using a variety of tools provided by LabGuru.
A computational hosting resource used for keeping track of reagents and materials in wet-labs. Users can store and manage strains, cell-lines, proteins, plasmids, oligos, chemicals, inventories, and more, as well as search StrainControl for other such reagents and materials. Users can also customize text, columns, and modules to match their lab needs. Data is stored on a secure database on a user’s computer or computer network.
An web-based computational hosting resource which allows users to document scientific research and collaborate with others. Users can store experiments and protocols, organize and manage projects, share and collaborate with colleagues, and publish findings within their Docollab account.
Database of all cell lines used in biomedical research which include immortalized cell lines, naturally immortal cell lines (stem cells), widely used and distributed finite life cell lines, vertebrate cell lines (majority being human, mouse, and rat), and invertebrate (insects and ticks) cell lines, as well as cell line synonyms. Each cell line is provided with the following information: the recommended name (the name which appears in the original publication), a list of synonyms, a unique accession number, comments on a number of topics including misspellings and gene transfection, information on the tissue/organ origin with the UBERON code, the NCI Thesaurus or Orphanet ORDO code for the disease(s) the individual suffered from (for cancer and human genetic disease lines only), the species of origin, the parent cell line, cross-references of sister cell lines, the sex of the individual, the category in which the cell line belongs (Adult stem cell; Cancer cell line; Embryonic stem cell; Factor-dependent cell line; Finite cell line; Hybrid cell line; Hybridoma; Induced pluripotent stem cell; Spontaneously immortalized cell line; Stromal cell line; Telomerase immortalized cell line; Transformed cell line; Undefined cell line type), web links, publication references, and/or cross-references to cell line catalogs/collections, ontologies, cell lines databases/resources, and to databases that list cell lines as samples.
An online resource which helps researchers manage and organize labs and experimental results by supplying molecular biology software tools for experimental design and data analysis. Benchling provides tools for functions such as primer design and colony counting as well as CRISPR guide design and automated Gibson and Golden Gate cloning. Users can take notes in line with data, link data across entries, keep files and data in one place, and manage and keep track of team progress. An enterprise version of Benchling is available for scientists working within an organization with additional administrative, compliance, and security protocols.
An access service resource which serves as a global open access hub for the sharing and licensing of Biological Research Materials and related technologies with researchers. Biomedical researchers from research institutions and industry can connect with Technology Transfer Offices owning proprietary Biological Research Materials or rights to relevant technologies. Users can also search BioMedUSA's aggregated resources, such as biorepositotires and biologicals to share/license, for materials and technologies.
A collaboration tool and job resource which connects academic and industrial researchers and scientific professionals across various fields and discipines. Users can create their own profile and be matched with other users, follow news and events, search for jobs, Ph.D, and career opportunities, and use PubAdvanced, an app which searches PubMed with added features.
Distributed Interoperable Research Experts Collaboration Tool
An on-going project and collaboration tool where biomedical researchers can access to expertise and related resources across institutions, regardless of local platforms and tools. Users can work with participating institutions in order to connect to their existing research networking tools. Biomedical institutions that wish to participate must have a mature, deployed research networking tool and can commit resources to assessments.
A portal that connects users to reserch expertise and resources within Florida's universities. Users can search for experts (principal investigators), funded research projects, centers and institutes, technology licensing opportunities, speakers, and instructional programs.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March, 4, 2021. A meeting resource which lists current and up-coming scientific and medical events by discipline, location, and date.
A video resource which provides access to webinars and educational materials in various scientific fields. Users can also create communities in which to share materials and news.
A portal for malaria researchers and professionals. The site provides links to articles, news, discussion forums, the MalariaWorld journal, weblogs, events, and job listings.
A portal which provides simulation programs for nanoscale phenomena, online presentations, courses, learning modules, podcasts, animations, and teaching materials. Researchers can also collaborate with others and publish content.
A database and collaboration tool which allows researchers to make contacts or find collaborators within their field or from a different discipline. Users can create a profile detailing their collaboration interests, research areas, and methodologies as well as add links to external sites such as LinkedIn and Academia.edu. Piirus takes the information from users' profiles to suggest researchers with whom they may be interested in collaborating with. Users can also search for users with particular interests, expertise, or techniques.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented June 21, 2018. A service resource and collaboration tool which connects academically affiliated researchers to undergraduate and graduate students. Researchers can advertise their lab and open positions as well as organize and manage applicants. Students can browse labs based on university and field(s) of interest and apply directly for lab positions or jobs. Universities must officially partner with ResearchConnection to advertise labs.
A production service resource which transforms scientific articles into infographics. In order to make an infograph, users must submit a package to DrawScience containing a scholarly article(s) to base the infographic on, a summary of the rationale and conclusions of the research, and definitions for 5 or less terms necessary to understand the research. Users may also make an infographic which will be attributed to them.
A collection of concise summaries of scientific articles that link back to the physical article. Users can contribute resources to the site and may choose to provide a summary; if they do not, Useful Science will do so. Summaries are then tagged with the appropriate topic. Topics that relate to everday life such as health, fitness, nutrition, and sleep are the main focus of the site.
A production service resource which allows researchers to enlist the help of volunteers in projects. Researchers can build web-based projects where volunteers can assist in identification, classification, and/or characterization of specific "items" in images. An example of a project is having volunteers mark the instances when nematode worms lay eggs as part of a larger project concerning genes and behavior.
Life Technologies Instrument Management Tool
A web application which allows users to record, organize, and manage lab equipment online. Instrument Management provides tools to view service history and field service reports, request service or service quotes online, monitor warranty or contract statuses, and view instrument details.
An open access electronic lab notebook which helps users design and organize lab experiments. Users can upload files and embed images of any type into the ELN, as well as export in PDF or zip archive into the electronic notebook. The database stores reagents, protocols, and other lab and experiment necessities for different kinds of labs. It is a PHP + MySQL application that users install on a server. After it is installed, the ELN is located in the browser.
An ELN (electronic lab notebook) software application that allows researchers to organize and manage experiment tasks, protocols, and results. Users can divide experiments into tasks spread across weeks and keep track of multiple experiments and protocols using a variety of apps, such as timestamps and completion markers. Files can be stored in the Findings library and opened in a given application.
An ELN (electronic lab notebook) software application where researchers can record and organize their data in lieu of a paper notebook. Users can store and edit texts, PDFs, spreadsheets, images, sample collections, and other types of data. LabArchives automatically backs up data and data can be accessed anywhere. Users can choose to use the professional edition of LabArhives, the classroom edition, or to purchase an enterprise license.
An ELN (electronic lab notebook) software application where researchers can record and organize their data by recording, dragging, and dropping elements. Users can utilize tools and features such as image annotation, search and filter, protocol templates, and team communication. The format of the ELN is customizable and can be rearranged at any point.
An ELN (electronic lab notebook) software application which can be used to document neuroscience projects and store metadata. LabLog is meant to constitute a laboratory's long term memory for project related information. To do this, project information is stored in a central laboratory database and can be easily retrieved by searching and filtering.
A production service resource which allows researchers to conduct experimental procedures through the cloud. Researchers can ship samples for an experiment to Emerald, then design the experiment(s) over the web using ECL software. Emerald then conducts the experiment(s) in an automated lab as specified, organizing the data into a database in the cloud. Samples are then shipped back to the lab (within a metter of days) and results can be analyze ECL's data analysis suite. Standard experiment types include but are not limited to: analytical balance readings, light microscopy, solid phase extraction, flourescence thermodynamics, RNA extraction/cDNA prep, and Western blot. Additional experiment types may be contributed.
A software provider which supplies researchers with software that enables remote monitoring and management of experiments. TetraScience provides software for managing lab cameras, sensors, electrical switches, adapters, and timers. Users are notified by text or email of lab proceedings and alerts.
A web-based production service resource which provides access to remote life science research labs powered by custom robotic automation. The typical Transcriptic deployment happens in three stages. Transcriptic first executes a proof-of-concept (POC) to gather important reliability and sensitivity data that will inform the handling of the project and generate validation data for the customer. Once a POC has been successfully completed, w a four-to-six week pilot study is run where the customer provides real samples at small scale. Once the process is stable, scale up occurs and a larger number of samples can be processed. Users can access results, environmental monitoring data, and all workcell actions, as well as remotely monitor all environmental parameters taking place inside the enclosed, sterile automated lab (temperature, humidity and atmospheric composition).
Biorepositories and Biospecimens Research Branch
Biorepositories and Biospecimen Research Branch of the Cancer Diagnosis Program
Biorepositories and Biospecimen Research Branch of the CDP
A portal to numerous programs and databases associated with the BBRB, a department of the NCI which aims to improve the collection and dissemination of high-quality biosecimens used in cancer research. The BBRB hopes to do this by improving the quality and consistency of human biospecimens and developing biorepository standards and facilitating Biospecimen Science studies that form the basis of evidence-based practices. The site provides acces to the Biospecimen Research Database, which contains peer-reviewed primary and review articles as well as standard operating procedures in human biospecimen science. The BBRB also directs programs such as the Biospecimen Pre-Analytical Variables Program and the Cancer Human Biobank (caHUB).
A biomaterial supply resource which collects and disseminates human heart tissue. Samples include both failing and non-failing hearts, RNA/DNA analysis, tissue staining and immunofluorescence samples.The tissue that has been flash frozen and stored at -80˚C is acquired from distinct regions of the heart such as the LV free wall, septum, and valve leaflets. Individual sample sizes are typically 100-300mg for flash frozen tissues. The DHHR also serves as a resource for assay development, target identification, and sponsored research, capable of isolating cardiomyocytes from hearts and using them for in-vitro assays such as calcium handling, enzyme activity, signalling pathways and other biochemical research activities
A software application which automatically packages up the code, data, and environment required to deploy and run Linux programs on other machines without any installation or configuration. Users can prepend any set of Linux commands with the "cde" binary, and CDE will run them and automatically package up all files accessed during execution. A package is a directory that can be compressed and delivered to any x86-Linux machine and contains all the files and environment variables required to run the original commands. After receiving the package, the user can run those same commands from within the package on any modern x86-Linux distro., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A multi-purpose project automation tool written in Python which helps create technical documents. Dexy is a free-form literate documentation tool for writing any kind of technical document incorporating code. It provides a consistent interface to tools and scripts and keeps track of what to run, in which order, and with what parameters.
A software application which provides Git repository management with fine grained access controls, code reviews, issue tracking, activity feeds, wikis, and continuous integration. Four different versions are available, each with different packaging pricing: Community edition, Enterprise edition, Continuous integration, and GitLab.com.
A web application and interactive computational environment where users can combine code execution, rich text, mathematics, plots, and rich media. IPython Notebook consists of two parts, the web application and plain texts. The Ipython Notebook web application is used for interactive authoring of literate computations, in which explanatory text, mathematics, computations, and rich media output may be combined. Input and output are stored in persistent cells that may be edited in-place. The plain text documents, called notebooks, record and distribute the results of the rich computations. Saved files in the notebook can be put under version control and shared with colleagues.
A software application which provides distributed source control management for projects. Using Mercurial, each developer has a local copy of the project development history. Mercurialhas a user friendly interface, is written mostly in Python, and works independently of network access or a central server. Functionality can be increased using extensions, either by downloading them or writing new ones.
A software repository which provides and builds open source tools for open science. rOpenSci provides packages that allow access to data repositories through the R statistical programming environment. R packages are grouped by what the tools do: acquire data, full-text of journal articles, altmetrics, data-publication, reproducibility, and data visualization.
NO LONGER AVAILABLE. Documented on May 19, 2020. Software R tool for creating dynamic reports and reproducible research using LaTeX. Enables embedding of R code within LaTeX documents to generate PDF file that includes narrative and analysis, graphics, code, and results of computations. Software tool for complete data analyses in LaTex documents.
A software platform which enables users to conduct genetic engineering with genomic manipulation tools (provided in the platform). Genome Compiler includes multiple DNA synthesis providers, lab facility services, and advanced bioinformatics tools and genetic repositories. Data can be imported from VectorNTI, SnapGene, ApE, Clone Manager, and others. The Gibson Assembly and Restriction Ligation methods are supported by Genome Compiler.
A software repository which provides open source software and technology for visualization, computer vision, medical imaging, data publishing, and quality software process solutions. Kitware also provides services such as creating customized applications for clients, porting their open-source tools to specialized computing platforms, and supporting their open-source software tools with documentation, professional consulting services, and software training.
A software repository which provides open source software for machine learning. Software entries include information such as author, license, data format, and programming language. The ultimate goal of mloss.org is to create a comprehensive open source machine learning environment where open source machine learning software can compete with comercial closed source solutions.
Web application to collaboratively create interactive graphs and share them with others. JavaScript toolbox plotly.js enables users with little to no web development skills to make scientific charts.
A web application which allows users to collect data, perform complex analyses, and generate results. Users can upload data sets from their computer or from the internet for data analysis and graph creation which can be saved, printed, and downloaded. More than 15,000 statistical data sets are available.
THIS RESOURCE IS NO LONGER IN SERVICE, documented July 21, 2015. Web based software which allows users to navigate through RDF relations. Its features include: a light weight client side JavaScript solution using HTML5 and CSS3; the ability to hide and show detailed information of the center object; being tested in IE6+, Firefox 2+, Safari 2+, Chrome 3+; a "More Info" button which can be configured to be handled by the server, to allow specific page rendering options; the ability to run as a sandbox in memory: no conflicts with JQuery; and the option for the history manager to be switched off to enable the existing history manager of a website to take over.
A software application which utilizes drag-and-drop to create data visualizations of various formats. Users can collaborate on and discuss data and graphs that can be created from spreadsheets, databases, and big data sources. Three versions of Tableau Desktop are available: Tableau Server, Tableau Online, and Tableau Reader.
A web application which performs Python data analysis. Users can create IPython notebooks to hold uploaded data and use various tools to describe, analyze, and visualize the data. Notebooks, data, and Anaconda environments can be shared as "bundles" with other users, who can edit and download them.
Web based tool to extract data from plots, images, and maps. HTML5 based online tool to extract numerical data from plot images. Used to reverse engineer images of data visualizations to extract underlying numerical data.
Workflow Instance Generation and Specialization
A software application which assists scientists with designing computational experiments. WINGS is a semantic workflow system which incorporates semantic constraints about datasets and workflow components into its workflow representations. The workflow system has an open modular design and can be easily integrated with other existing workflow systems and execution frameworks to extend them with semantic reasoning capabilities. WINGS also allows users to express high-level descriptions of their analysis goals, and assists them by automatically and systematically generating possible workflows that are consistent with that request. In cases where privacy or off-line use are important, WINGS can submit workflows in a scripted format for execution in the local host. It uses Pegasus or OODT as the execution engine for large-scale distributed workflow execution.
A database of searchable grants and other funding opportunities for researchers and institutions. Grant Forward's Database contains more than 19,000 opportunities including 8,000+ federal and foundation opportunities each.
A database of funding opportunities for research administrators, research development professionals, and institutions. Researcher profiles are matched to current funding opportunities in the COS database using a proprietary algorithm. Users may also find funding opportunities by searching the database., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A database that contains different CSL citation styles. Styles can be searched by name, journal title, or by example and then viewed or installed. Users can also edit current styles and save them.
A software application which helps users build a bibliography as they write formatted papers, manuscripts and other research-rich documents. Users can search multiple databases and collect PDFs as references for papers, then organize them within EndNote. Bibliographies and citations can be compiled within Microsoft Word using built-in tools. Papers are stored within an EndNote library and can be shared with colleagues.
A web application which allows users to find reference papers and cite them during the authoring process. Paperpile utilizes Google and Chrome apps in order to directly download PDFs from various databases to Google Drive. If writing in Google Docs, users can search for certain reference papers and insert them into their draft as citations using the Google Drive Paperpile tool. Users can also collaborate on papers and add different citations.
A software application which translates plain text written in AsciiDoc syntax to HTML5, DocBook 5, and other backends. Asciidoctor reads and parses text written in the AsciiDoc syntax, then feeds the parse tree into a set of built-in templates to produce HTML5. Users can write their own converter or provide Tilt-supported templates to customize the generated output or produce alternative formats. Asciidoctor also recognizes additional markup and formatting options, such as font-based icons and UI elements.
A web application which allows users to collaboratively write documents and books with version control and revision history. Users can write in plain text or with Markdown and invite others to collaborate on their work. Math equations can be written with LaTeX or MathML with MathJax. eBooks can be downloaded and compiled into forms such as PDF, ePub, Word, and HTML . Works can be made public or kept private.
A web-based authoring platform for Wordpress which allows users to write, edit, and track changes and revisions. Users can see all revisions and edits to an artcle and decide which ones may be kept or reverted. After creating an article, users can upload it directly to WordPress.
A software application which provides feedback on writing, wording, and frequency of text by checking against databases of correct language. Users can highlight a chunk of text and use Writefull to see how often the specific text appears in different language databases. Writefull can also offer synonyms and suggestions for wording. Writefull is supported by numerous writing tools which include MS Word and Gmail.
A peer review service resource which allows researchers to dictate the time constraints in which their manuscripts are peer reviewed. Authors submit their manuscript to Peerage of Science before submitting to any journal and decide the deadlines for the four stages of the process (which are "Submission and Reviews," "Peer-review-of-peer-review," "Manuscript revision upload or withdrawal for re-submission," and "Final evaluation of the revised manuscript"). Once submitted, any qualified, non-affiliated Peer can choose to review the manuscript. The peer reviews are peer reviewed and are also available to all subscribing journals with automated event tracking. Authors may accept a direct publishing offer from a subscribing journal, or choose to export the peer reviews to any journal of their choice.
Collage Authoring Environment for Executable Publications
A web application which provides the framework for collaborative preparation and publication of computational experiments that can back executable papers. The Collage environment enables researchers to embed chunks of executable code and data into scientific publications and facilitate repeated execution of such codes on underlying computing and data storage resources. Executable papers made with Collage can be embedded into a web site.
A database and storage service resource that allows researchers to create a companion website, a website which allows people to run the computer codes associated with a scientific publication. Users upload or paste data, choose the value of the parameters, and click on the Exec&Share button. All calculations are done on a dedicated cloud computer and are automatically displayed to the user. It is also possible to only make the code downloadable, but not executable. In that case, users can download the code and run it on their own computer. Companion websites can currently be made from a code written in R, MATLAB©, C++, Fortran, and Rats.
A web application which allows users to create data visualizations using JavaScript that can be embedded in a web page. Users can load some Google Chart libraries, list the data to be charted, select options to customize their chart, and create a chart object with a personally chosen id. Then, in the web page, users create a with that id to display the Google Chart. Charts are customizable and interactive, and since they are rendered using HTML5/SVG technology, charts are cross-browser compatibility and cross platform portability to iPhones, iPads and Android.
A database and storage service resource which allows users to create, view, share, and download information from companion websites. RunMyCode allows users to create companion websites for their scientific publications. Users can share and download computer code and data from companion websites made with RunMyCode. Any software and data format is compatible with RunMyCode.
A training service which offers publishing advice and editorial support for scientific researchers. Cofactor Science offers workshops and editorial services on multiple levels of completeness and depth. Their Journal Selector tool selects journals from the Cofactor Science database that best fits a user's publishing criteria. Journals include Nature, PLOS One, PeerJ, and Genome Medicine.
A training service which offers English editorial support for primarily non-native English speaking scientific researchers. Users answer a questionairre concerning their progress with their manuscript and Edanz suggests which of its services users should utilize. Services include Journal Advisor, English Editing, Expert Scientific Review, Cover Letter Development, Review Editing, Abstract Development, Response Letter Edit and Manuscript Check, Author-guided Rewriting, and Reviewer Recommendation. Edanz also offers training workshops and seminars for non-native English speakers.
A database which allows researchers to view and comment on the logistics of scientific journals' review processes. JournalReviewer collects and aggregates feedback from users who have submitted manuscripts to journals in order to provide information for others considering journal submissions. Statistics such as turnaround rate, review length and quality, journal recommendations, and desk reject plausabilities are compiled from commentors' ratings.
A database where researchers can read and post reviews of publishing experiences with scientific journals. When writing comments, reviewers are adivsed to provide facts where possible, be specific, be honest, check the review, and offer constructive criticism when writing a negative report. Journalysis collates submitted reviews and data for each journal and provides useful summary information (metrics). Authors wanting to find out more about specific journals can search its databases and find the best journal for their next manuscript submission. Journals can use these reviews and metrics to demonstrate high publishing standards, or to improve standards where reviews may be negative.
A database where researchers and editors can read and post reviews and ratings of scientific journals and their publishing processes. Efficient journals get credits for their efforts to improve their review process and the way they handle manuscripts, while less efficient journals are stimulated to put energy in better organization. Researchers can search for a journal with a speedy review procedure and have their papers published earlier. Editors get the opportunity to compare their journal's performance with that of others and to provide information about their journal at our website.
A peer review management system which encourages timely and high quality peer review by using a credit system. Reviewers complete reviews using a general webform on academickarma.org, and if that review is submited to an editor within ten days, the reviewer is awarded a certain amount of points (karma credits). The author and editor both receive the review. Editors can use Academic Karma to identify specialized reviewers for future reference. A reviewer's personal profile, which includes the amount of karma credits they've received, is connected to their ORCID account and publication record for an overview of the reviewer's work.
A repository which hosts and archives original and edited scientific papers. Scientists can post their academic manuscripts on Libre, where they can find reviewers who will formally evaluate the manuscripts. Evaluated works are posted alongside the original manuscript with reviewers' identities disclosed and the work they edit given its own DOI. Users can post additional updated versions of their work to Libre or send their papers to journals. Papers and reviews are rated by other scientists, and from these Libre creates holistic indeces listing the best rated writers and reviewers.
A database that archives publications and allows users to review and critique them. Users can write comments for and rate submitted publications for references, originality, argumentation, and reliability. Papercritic also collects tweets and blog posts about published papers to add as reviews and comments. Researchers who submit their published work to PaperCritic can keep track of multiple types of feedback. All reviews must be submitted with full identity disclosure.
A service resource which allows peer reviewers to record and showcase the peer reviews they have completed, both those that led to publication and to rejection. Peer reviews can be recorded on Publons by forwarding review receipts from journals to the site. The merit of reviewers is accrued by pre- and post-publication peer review, discussion papers in Publons, and comments on or endorsment of the contributions of other reviewers. Reviewers may publish their own reviews so long as the reviewed manuscript is published and the review policies of the journal allow for it. Users can choose what personal information is displayed and easily export their profile in a format suitable for inclusion in promotion and funding applications.
A forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate comments.
A portal which provides access to article level metrics, PLOS news, and videos and presentations. PLOS ALMs provides altmetrics for every article published in PLOS. Researchers can stay up-to-date with their published work and share information about the impact of their publications with collaborators, funders, institutions, and the research community at large.
A service resource which provides researchers with metrics around usage, captures, social media, citations, and mentions from various online research outlets. Plum Analytics pulls information from reserch outlets such as journal articles, books, videos, presentations, conference proceedings, datasets, and source code. Plum Analytics also collects metrics for labs, departments, and other research groups. PlumX is a product of Plum Analytics.
Software tool that compares two gene expression signatures. Each signature is processed as a ranked list based on expression differences between two classes of samples. The signatures can be input either as raw expression data and sample and class labels, or as a preranked gene list.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Partec uses FloMax software on most cytometers, which produces FCS 3.0 compliant files. FloMax rescales the fluorescent data on the acquisition display without changing the stored values.
Réseau National des plates-formes Bioinformatiques
THIS RESOURCE IS NO LONGER IN SERVCE, documented August 11, 2015. It has been replaced by the Institut Fran�ais de Bioinformatic (IFB). A network built upon different bioinformatics platforms located within France to support the structuration of bioinformatics.The network provides access to resources such as databases, proteomics, transcriptomics, and structural bioinformatics for the life science and bioinformatics communities.
Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database.
A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow.
A simulation software package which hosts a collection of algorithms used to run bioelectric field simulations inside of SCIRun. The software provided in the package may be used for geometric modeling, simulation, and visualization for solving bioelectric field problems.
A server-based software wiki package written in PHP. It is a powerful, scalable software deigned for high-traffic websites. MediaWiki uses PHP to process and display data stored in a database such as MySQL. When a user submits an edit to a page, MediaWiki writes it to the database without deleting the previous versions, allowing easy reversions. MediaWiki is able to manage image and multimedia files, as well, which are stored in the filesystem.
Vanderbilt University Medical Center; Tennessee; USA
A public health center and research institution affiliated with Vanderbilt University.
Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery
A consortium whose goal is to further HIV research and accelerate the development of a preventative HIV vaccine. Its main research target is to define immunogens and immunization regimens that induce sustained HIV cross-protective B cell and CD4+ T cell responses.
McGill University Health Centre; Quebec; Canada
A public health center and research institution affiliated with McGill University.
Penn State Milton S. Hershey Medical Center; Pennsylvania; USA
Penn State Milton S. Hershey Medical Center
A public health center and research institution affiliated with Penn State.
Montefiore Medical Center; New York; USA
A public health center and research institution affiliated with the Albert Einstein College of Medicine.
University of Kansas Medical Center; Kansas; USA
A public health center and research institution affiliated with the University Kansas.
University of Rochester School of Medicine and Dentistry; New York; USA
University of Rochester School of Medicine and Dentistry
A public health center and research institution affiliated with the University of Rochester.
Public research university located in Tempe, Arizona, USA.
Centro Nacional de Investigaciones Oncologicos
A cancer research center whose goal is to offer innovative technoligies to spur the develpment of new methods of diagnosing and treating cancer. CNIO contains a variety of programs of investigation, including a biotechnology program, a clinical research program, and a molecular oncology program. CNIO also provides services that allow researchers to access and use technologies and tools such as cytogenetics and monoclonal antibodies, and hosts a biomedical biobank.
THIS RESOURCE IS NO LONGER IN SERVICE, docmented August 17, 2015. A web-based system for individuals or communities to publish and contest ideas and arguments. ClaiMaker provides tools for constructing argument maps, and a server on which they can then be published, navigated, filtered, and visualized.
A commercial organization which offers consultation services and performs research in the fields of global health and infectious disease epidemiology. Sage Analytica provides services to help design research or project programs, interpret data, and communicate reults. Ad hoc assistance is also offered.
A funding resource which promotes and supports high-level research and higher education in agricultural sciences and sustainable development research. The scientific work supported by the Foundation covers all aspects of the plant, from its genes to its environments, and concerns temperate, Mediterranean, and tropical climates. It supports research initiatives in: genetics and genomics, plant breeding, eco-physiology; integrated crop protection, plant pests and diseases, symbiotes, population ecology; agro-ecosystems, agri-environmental innovations, and resource management; agri-food systems, processing, and quality of food and non-food material; and innovation processes and social management of innovation.
An interactive software tool that predicts hair and eye color based on genetics. The website includes both the IrisPlex system and the HIrisPlex system.
A biorepository which collects and distributes human breast milk samples to the research community, as well as a research initiative which aims to learn more about the benefits of human milk, how it influences infant and child health and development, and the extent to which medications and other substances can be found in human milk. Nursing mothers who choose to donate are asked to provide around 2 ounces of breast milk to be used for future research projects. Breast milk, which include disease-specific and normal breast milk samples, is stored in the research bank for approved projects.
An online rental equipment marketplace which connects renters to instrument suppliers from various industries. Renters can rent directly from suppliers or request quotes from different suppliers.
A reagent manufacturer which provides custom peptide APIs and custom peptide synthesis services. These products and services include high throughput peptide library/array synthesis, high quality bulk API peptides, bioactive catalog peptides, and cosmetic peptides.
A custom genome browser which provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains of mice (both classical and wild-derived). Users can select a region of the genome and a set of laboratory strains and/or wild caught mice. The region is selected by specifying the start (e.g. 31200000 or 31200K or 31.2M), and end of the interval and the chromosome (i.e, autosome number and X chromosome). Samples can be selected by name or by entire set. Data sets include information on subspecific origin, heterozygosity regions, and haplotype coloring, among others.
MUGA genotypes for 458 samples from the developing CC lines described in the February 2012 issue of Genetics. Genotypes for 168 reference strains that include biological and technical replicates for the the 8 CC founder strains and their F1 crosses are also provided. Genotype calls are those reported by Illumina. All results are provided as comma separated files with one row per marker. Each marker is identified by a probe name and its genomic position in NCBI Build 37.
Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging.
A software application that calculates and runs a GLM on graph theory properties derived from brain networks. The GLM accepts continuous and categorical between-participant predictors and categorical within-participant predictors. Significance is determined via non-parametric permutation tests. Both fully connected and thresholded networks are tested. The toolbox also provides a data processing path for resting state and (block design) task fMRI data. Options for partialing nuisance signals include local and total white matter signal and PCA of white matter/ventricular signal. For task fMRI, connectivity matrices are computed for each condition by dividing up the timeseries. To compensate for HDR-related delay, the timeseries is deconvolved, allowing for division at the actual onset/offset times.
Software which predicts topology and other features of membrane proteins through hydropathy plots based on thermodynamic and biological principles. This version of MPEx uses two types of hydropathy scales: Experiment-based whole-residue partitioning scales and experiment-based biological partitioning scales. The whole-residue partitioning scales predict the transmembrane (TM) segments of membrane proteins of known structure. The biological scale utilizes current knowledge of the code the Sec61 translocon to identify TM segments. MPEx is a Java program (not a Java applet) deployed using Java Web Start, which is part of the Java Runtime Environment.
A Swedish national center of research for molecular biosciences with a focus on health and environmental research. Researchers from Sweden can use both the technology and the expertise provided by SciLifeLab. Swedish researchers typically pay only for reagents and other consumables. Users from commercial companies pay the actual costs of the analyses performed. SciLifeLab also provides educational courses, seminars, and programs for PhD students, postdocs, investigators and other employees within all Swedish universities.
A comprehensive index for locating and compiling bioinformatics and online science tools. Users can browse, rate, share and save various tools listed in the LabWorm repository. Resources contain a short description, a list of related sites, comments, a list of users who have shared and rated the resource, and the main site URL. Resources may be saved to a personal toolbox collection. User news feeds can be customized to include new scientific literature from journals of choice. Users who want to utilize LabWorm tools to improve their own website can access the alternate Developer site.
Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences.
Analysis of Patterns in Electrophysiological Recordings Toolbox with Utilities for REsearch
A MATLAB-based toolbox for analysis of EEG, MEG, and ECoG data. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity and supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large, high-dimensional datasets is made simple through data visualization tools, including advanced plotting routines and generation of PDF reports with many figures.
A command-line program and plugin for AFNI built around SVM-Light. It performs support vector machine (SVM) analysis on fMRI data and runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X.
Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases.
Atlases of amygdala and hippocampus for pediatric populations
Anatomical atlases constructed by Computational Anatomy of Johns Hopkins University for analysis of shape vectors. The atlases were generated from segmented hippocampal and amygdala structures in acquired populations of children, adolescents and young adults in neuroimaging studies of major depression disorder (MDD) at Washington University at St Louis.
A software tool (with GUI) for investigating inter-regional functional connectivity in event-related fMRI data and allows the user to assess the modulation of functional connectivity by an experimental condition.
Anatomical brain template library which includes models from ICBM 2009 template.Number of unbiased non-linear averages of MNI152 database have been generated that combines attractions of both high-spatial resolution and signal-to-noise while not being subject to vagaries of any single brain. Procedure involved multiple iterations of process where, at each iteration, individual native MRIs were non-linearly fitted to the average template from previous iteration, beginning with MNI152 linear template.
A semi-automated software tool for dental plaque biofilm quantification in quantitative light-induced fluorescence (QLF) images.
THIS RESOURCE IS NO LONGER IN SERVICE, documented December 11, 2015. A discussion group for those actively involved in research into, or applications of, biomagnetism and magnetoencephalography (MEG).
A toolbox that implements several EEG/MEG source localization techniques within the Maximum Entropy on the Mean (MEM) framework. These methods are particularly dedicated to estimate accurately the source of EEG/MEG generators together with their spatial extent along the cortical surface.
Brainnetome Atlas Viewer shows the anatomical connectivity-based parcellation results, including the maximum probabilistic maps, probabilistic maps and both the anatomical and functional connectivity patterns, which have been developed in Brainnetome Center, CASIA. The atlas is based on the analysis of connectional architecture with in vivo multi-modal MRI data.
An fMRI toolkit which contains a large selection of complex network measures in Matlab GUI. These measures are increasingly used to characterize structural and functional brain connectivity datasets.
A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations.
A database that contains brain imaging data collected on 3T MRI scanners from over 200 normally developing healthy children from birth to 18 years. The imaging data stored in the C-MIND database are DTI, HARDI, 3DT1W, 3DT2W, concurrent ASL-BOLD scans during two language tasks (Stories and Sentence-Picture Matching), Resting State fMRI and Baseline ASL scans.
CARLsim: a GPU-accelerated SNN Simulator
A GPU-accelerated library for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. CARLsim allows execution of networks of Izhikevich spiking neurons with realistic synaptic dynamics on both generic x86 CPUs and standard off-the-shelf GPUs. The simulator provides a PyNN-like programming interface in C/C++, which allows for details and parameters to be specified at the synapse, neuron, and network level.
A clinical toolbox useful for normalizing data from individuals with brain injury and/or modalities popular in the clinical environment (CT). It supports either enantiomorphic or lesion-masked normalization. It can be either scripted or used with SPM's simple graphical interface.
A python toolbox for analysis of MRI images. It relies on calls to a number of widely tested algorithms from the FMRIB software library (FSL) and the advanced normalization tools (ANTS) to provide analysis of simultaneously acquired ASL/BOLD fMRI data. It was developed for analyzing the datasets collected as part of the Cincinnati MR Imaging of NeuroDevelopment (C-MIND) project.
Connectivity Orientation Spherical distribution Tool
A tool that implements a graph-based connectivity assessment method. This method uses a multi-directional graph propagation method applied to sampled orientation distribution function (ODF), which can be computed directly from the original diffusion imaging data.
A tool for converting images from the complicated formats used by scanner manufacturers (DICOM, PAR/REC) to the NIfTI format used by various scientific tools. dcm2nii works for all modalities (CT, MRI, PET, SPECT) and sequence types.
A DICOM image converter based on the ITK IO mechanism for reading and writing images. The formats currently supported by the converter are DICOM to: Analyze (*.hdr); MetaImage (*.mhd); Nrrd (*.nhdr, *.nrrd).
A tool for visualizing displacement fields estimated in association with image registration. Based on the displacement vector field, a mesh is generated for visualization. The mesh can be color mapped with the jacobian determinant at each point for better localization of regions that undergo compression or expansion. Other key features include: view synchronization, adjustable mesh resolution, and conversion from deformation and HAMMER displacement fields.
A Matlab package which contains six denoising filters and a noise estimation method for 4D DWI. The package includes nonlocal means, local PCA and Oracle DCT methods. Based on image redundancy and/or sparsity, the proposed filters provide efficient denoising while preserving fine structures.
Efficient Longitudinal Upload of Depression in the Elderly (ELUDE)
Efficient Longitudinal Upload of Depression in the Elderly
A longitudinal study of late-life depression at Duke University. There are 281 depressed subjects and 154 controls included. An MR scan of each subject was obtained every 2 years for up to 8 years (total of 1093 scans). Clinical assessments occurred more frequently and consists of a battery of psychiatric tests, including several depression-specific tests.
Speeding Up Permutation Testing in Neuroimaging
A Matlab implementation for efficient permutation testing by using matrix completion.
A toolbox developed for multi-channel time-frequency analysis of event related activity of EEG and MEG data. It provides tools for data analysis and visualization of the most commonly used measures of time-frequency transformed event related data as well as data decomposition through non-negative matrix and multi-way (tensor) factorization. The decompositions provided can accommodate additional dimensions like subjects, conditions or repeats and as such they are perfected for group analysis. The toolbox enables tracking of phase locked activity from one channel-time-frequency instance to another as well as tools for artifact rejection in the time-frequency domain.
An R package for descriptive (i.e., fixed-effects) multivariate analysis with singular value decomposition.
Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation
A tool which offers a fast algorithm for computing myelin maps from multiecho T2 relaxation data using parallel computation with multicore CPUs and graphics processing units (GPUs). The tool also provides non-local spatial regularization to produce more accurate and reliable myelin maps for noisy T2 relaxation data.
Forward: Accurate finite element electromagnetic head models
A project which aims to simplify the preparation of accurate electromagnetic head models for EEG forward modeling. It builds off of the seminal SimNIBS tool for electromagnetic field modelling of transcranial magnetic stimulation and transcranial direct current stimulation. Human skin, skull, cerebrospinal fluid, and brain meshing pipelines have been rewritten with Nipype to ease access parallel processing and to allow users to start/stop the workflows. Conductivity tensor mapping from diffusion-weighted imaging is also included.
A software package which contains tools for doing group analysis of FreeSurfer surface data using the general linear model in R (lm). Results can be rendered in FreeSurfer freeview or AFNI SUMA. Plots for selected vertices can be rendered in R with ggplot2.
Functional Connectivity Analysis Tool for near-infrared spectroscopy data
A functional connectivity analysis tool for near-infrared spectroscopy data. Its functions include preprocessing, quality control, FC calculation and network analysis.
A toolbox for a point-process derived GLM analysis of eye tracking data in Matlab. Data loading, model specification, fitting and review are organized into a sequence of events, each of which is handled by a separate module in the toolbox. The graphical interface was created using the Matlab graphical user interface development environment.
A multivariate method for fMRI data analysis based on generalized canonical correlation analysis (gCCA) to maximize SPM reproducibility without adopting any model for the hemodynamic response or other temporal brain responses. For multiple subjects, gCCA explores a broad range of temporal responses in fMRI time-series space while maximizing the mean of correlation coefficients between the pair-wise spatial maps of the subjects.
An MRI resource which provides age-appropriate images of children. It includes an average, age-appropriate T1-weighted image, constructed from 130 typically developing children ages 6-to-10 and a set of 32 resting-state ICA components. These components were generated from 494 typically developing children, ages 6-to-10 years old, using the MELODIC ICA tool, bootstrapped with 1000 resamples. Both of these resources are described in detail in a manuscript submitted for publication.
Group Iterative Multiple Model Estimation
Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels.
GLMdenoise: a fast, automated technique for denoising task-based fMRI data
A MATLAB toolbox for denoising task-based fMRI data. It derives noise regressors from voxels unrelated to the experimental paradigm and uses these regressors in a general linear model (GLM) analysis of the data. The technique only requires a design matrix indicating the experimental design and an fMRI dataset.
GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity
A user-friendly graphical-user-interface (GUI)-based toolbox (MATLAB) for comprehensive graph-theoretical analyses of brain connectivity, including network construction and characterization, statistical analysis on network topological measures, and interactive exploration of results.
A software package which performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements.
A multi-day event hosted by the Organization for Human Brain Mapping which features collaborative and open neuroscience projects in data analysis and methods development. Locations change annually.
High Dimensional Brain Imaging Genomics Toolkit
A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association.
High-quality diffusion-weighted imaging of Parkinsons disease
A project which contains data and analysis pipelines for a set of 53 subjects in a cross-sectional Parkinsons disease (PD) study. The dataset contains diffusion-weighted images (DWI) of 27 PD patients and 26 age, sex, and education-matched control subjects. The DWIs were acquired with 120 unique gradient directions, b=1000 and b=2500 s/mm2, and isotropic 2.4 mm3 voxels. The acquisition used a twice-refocused spin echo sequence in order to avoid distortions induced by eddy currents.
An MRI preprocessing pipeline built with HOF (Heterogeneous Optimization Framework) methodology. MGA prepares neuro-oncology clinical imaging studies for scientific analysis in both longitudinal and cross-sectional studies. It works on DICOM images from a single MRI study and includes perfusion (DSC sequence based) analysis and DTI analysis. MGA spatially co-registers all study images to an atlas template and to a template image within the study.
A collection of software tools developed for medical image synthesis of typically magnetic resonance (MR) brain images. The approaches have been used to create computed tomography (CT) images from MR input. The goal of image synthesis is to recover MR images with a desired optimal contrast for further processing by either registration or segmentation.
A diffusion MRI service that handles the processing of diffusion data from raw data to structural connectivity. They provide high angular resolution (HARDI) reconstruction from DTI data with at least 20 gradient directions acquisitions.
International Imaging Genetics Conference
An international symposium held initially to assess the new technology and innovation in the various established fields of genetics and imaging, and to facilitate the transdisciplinary fusion needed to optimize the development of the emerging field of Imaging Genetics. This annual conference features presentations from investigators world-wide and places emphasis on facilitating in-depth discussions among the participants and presenters.
Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0
Intrinsic Unscented Kalman Filter Tractography Software
Intrinsic Unscented Kalman Filter Tractography Software v1.0
A tractography algorithm for HARDI which provides a relatively accurate and efficient fiber tracking mechanism by reconstructing a bi-tensor model for underlying signals and exploiting intrinsic operations on the space of diffusion tensors. Given HARDI data sets, IUKF is capable of tracking in the presence of complex local geometries, such as crossing and kissing fibers. Reconstruction is only performed at the voxels along estimated fibers.
Iterative dual-regression with sparse prior
Software which aims to better estimate the neuronal activation of an individual using the results of an independent component analysis (ICA) method applied to a temporally concatenated group of functional magnetic resonance imaging (fMRI) data (i.e., Tc-GICA method). This approach employs iterative LS solutions to refine both the individual SPs and TCs with an additional a priori assumption of sparseness in the SPs (i.e., minimally overlapping SPs) based on L(1)-norm minimization.
KWScene: MRML-based Atlas and Scene Builder/Reader/Writer
KWScene: MRML-based Atlas and Scene Builder/Reader/Writer collaboration with Kitware
ITK-based processing and 3D Slicer scene management in ParaView. It is meant to broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The effort is focused on developing ParaView plug-ins for managing VTK structures from 3D Slicer MRML scenes and encapsulating ITK filters for deployment in ParaView.
A program which creates anatomically realistic virtual neurons using the formalism of the Lyndenmayer systems to implement sets of neuroanatomical rules discovered by several research groups. The program algorithms read in experimental data - in the form of statistical distributions - to generate virtual structures. L-Neuron samples the values of the parameters within these statistical distributions in a stochastic (random) fashion during dendritic growth.
Laplace Beltrami Filter on QuadEdge Meshes
Laplace-Beltrami Filter on QuadEdge Meshes
A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface.
Library for Systems Biology Markup Language
A programming library to help users read, write, manipulate, translate, and validate SBML files and data streams. Specifically, it is a library that users may embed into their own applications.
A lightweight framework for setting up dependency-driven processing pipelines. The tool is essentially a configurable shell script (sh/bash), which can be included in other scripts and primarily provides a small number of utility functions for dependency checking and NFS-safe file locking for cluster processing.
Longitudinal MS Lesion Segmentation Challenge
The Longitudinal MS Lesion Imaging Archive provides Training data consisting of longitudinal images from five patients and Testing data consisting of 15 patients. Each longitudinal dataset includes T1-weighted, T2-weighted, PD-weighted, and T2-weighted FLAIR MRI with 3-5 time points acquired on a 3T MR scanner. T1-weighted images have approximately a 1mm cubic voxel resolution, while the other scans are 1mm in plane with 3mm sections. Accounting for the multiple time points, this constitutes approximately 80 individual data sets. The Training data contains manual segmentations of the MS lesions from two different raters for each of the time points provided.
Software which provides the automatic solutions for efficent segmentation/labeling anatomcial structures from medical images. It has integrated several multi-atlas based segmentation methods such as majority voting, local weighted voting, and non-local patch based segmentation methods.
A set of MINC-based image processing tools packaged together. It includes MINC, N3, BICPL, EBKTS, ANIMAL, INSECT, BEaST, Register, Display, and xdisp.
Sample data in MINC format and collection of scripts to verify correct installation of minc-toolkit.
MISST - Microstructure Imaging Sequence Simulation ToolBox
Microstructure Imaging Sequence Simulation Toolbox
A practical diffusion MRI simulator for development, testing, and optimisation of novel MR pulse sequences for microstructure imaging. MISST is based on a matrix method approach and simulates the signal for a large variety of pulse sequences and tissue models. It is designed for diffusion MRI researchers who are interested in understanding and developing diffusion pulse sequences for imaging microstructure.
A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap.
Multivariate General Linear Models (MGLM) on Riemannian Manifolds
Multivariate General Linear Models on Riemannian Manifolds
A statistical analysis tool for manifold-valued data. The SPD manifold for diffusion tensor images (DTI) and the Hilbert unit sphere for square root representation of orientation distribution functions (ODF) can be used.
A tool which computes an automatic segmentation of neonatal brain MRI. It uses a registered probabilistic brain atlas to select training samples and to be used as a spatial prior.
This tool allows segmenting neonate brain MRI using a subject-specific atlas. It generates a subject-specific atlas based on an atlas population and some diffusion images of the subject to segment. Then a single atlas method is run with this atlas to obtain results.
A set of ImageJ plugins for fully automated measurement of neurite outgrowth in fluorescence microscopy images of cultured neurons. The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length. NeuriteTracer accurately measures neurite outgrowth from cerebellar, DRG and hippocampal neurons.
A Matlab-based toolbox initially created for reading, writing, and processing of BrainVoyager (QX) files in Matlab.
A simulation language for modeling biophysically realistic neural circuits (1 to 10,000 neurons) and simulating physiology experiments on it. Programs for plotting and displaying data are included.
NIH MRI Study of Normal Brain Development Pediatric MRI Data Repository
A database which contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult.
A segmentation tool for the segmentation of a lung from CT images. The sofware can be run in two modes: fully automatic and semi-automatic with manual seeding by the user. The software also allows the user to perform basic filtering operations and manual correction to the segmentation. The VTK-based rendering implementation, along with option to view in axial, coronal, and sagittal, provides the user with better visualization of the segmented lung.
NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering
A MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. It imports a PET image and allows the user to draw region of interests (ROIs) in 2D or 3D to roughly separate the object of interest from the background. The areas are then segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification, the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax, SUVmean, and Volume (mm^3) and can be exported into an excel sheet.
A set of Matlab scripts for analyzing neuroimaging data from clinical populations. The NiiStat tools are designed to correlate behavioral data (task performance) with brain imaging data.
Northwestern University Schizophrenia Data and Software Tool (NUSDAST)
Northwestern University Schizophrenia Data and Software Tool
A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data.
Standalone software designed to be used by radiology researchers for storage and anonymization of research images.
NTU-DSI-122: a DSI template in ICBM-152 space
A diffusion spectrum imaging (DSI) template constructed in the standard ICBM-152 space from 122 healthy adults. The template was built through incorporating the macroscopic anatomical information using high-resolution T1-weighted images and the microscopic structural information obtained from DSI datasets, rendering it to achieve a high anatomical matching to the ICBM-152 space. This template can serve as a representative DSI dataset for a healthy adult population. It is released in its original DWI format.
A multi-platform software dedicated to designing, testing and using brain-computer interfaces (BCI). OpenViBE is a software for real-time neurosciences that can be used to acquire, filter, process, classify and visualize brain signals in real time.
Open source tool for multi-modal medical and brain data visualization. It is a tool for the scientific user and a powerful framework for the visualization researcher. It is written in Standard C++ and uses a number of portable libraries (e.g. Qt, Boost and OpenSceneGraph). It runs on common GNU/Linux operating systems, Mac OSX and Windows.
Orientation Distribution Function in Constant Solid Angle (CSA-ODF)
Orientation Distribution Function in Constant Solid Angle
A Matlab toolbox that computes the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) for diffusion-weighted MRI.
Parallel Stochastic Ion Channel Simulator
Software for efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. It computes the behavior of neurons taking account of the stochastic nature of ion channel gating and the detailed positions of the channels themselves. It is designed as a complement for existing tools.
THIS RESOURCE IS NO LONGER IN SERVICE, documented Jan. 5, 2016. Tools will be available for biomedical data mining and visualization as well as linkages to Google Maps and other online resources.
Prediction and Diagnosis for Depression and Schizophrenia
A topical portal for the UAIS Lab of Lanzhou University which researches predicting depression and schizophrenia based on demographics and physiological information (EEG, ERPs, Genetics, MRI, fMRI, etc.). It also researches wearable bio-signal sensors and antennas, bio-signal processing, speech analysis, pervasive mental health, psycho-physiological computing, bioinformatics and multimodal data fusion and modeling.
A project which systematically preprocess the data from the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI) and openly share the results. Data is currently hosted in an Amazon Web Services Public S3 Bucket and at NITRC.
Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data
An implementation of standard PCA algorithms for use on scalar or vector data sets. Kernel PCA is implemented in this class, where the data sets are scalar or vector valued functions assigned at each of the points in a PointSet. A Gaussian Distance Kernel class is provided with the PCA class.
A library for handling NIfTI data in the Ruby programming language. Ruby NIfTI supports basic read and write access to NIfTI files, including basic and extended header information and image information. It doesn't attempt to touch the image data but it does provide access to qform and sform orientation matrices. It also provides a nice interface to get at NIfTI info from within Ruby.
A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard.
Structure from motion algorithms repository. Common interface for various sfm algorithms.
Software that allows users to dynamically interact with multiple surfaces simultaneously. It is very useful for visualisation and comparison of 3D surfaces by also displaying their scalars or vectors attributes stored in the points, and allowing the user to simply modify the colormap. ShapePopulationViewer is available as an extension of 3D Slicer.
Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of Estimated Fiber Orientations
This resource provides simulated DW-MRI brain images and quantitative tools for evaluating the performance of diffusion analysis methods in terms of fiber orientation estimation and false-positive/-negative fiber rates, which are of fundamental importance to tractography based studies. DW data was generated using a multi-tensor model at SNRs of 9, 18 and 36, for sets of 20, 30, 40, 60, 90 and 120 gradient directions. For each combination of SNR and gradient direction set, 10 realizations of data are provided. All data is simulated with a diffusion-weighting of b=1000, as is common for clinical acquisitions.
SPIKECOR: fMRI tool for automated correction of head motion spikes
This algorithm corrects for spikes in fMRI data, typically caused by abrupt head motion during scanning. It identifies outliers using Principal Component Analysis (PCA) in a sliding time-window; it is sensitive to global motion artifact, and stable against non-stationary signal changes.
A comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord. The toolbox includes a template and several atlases, along with state-of-the-art methods to register any data to the template. It also includes useful scripts for data preprocessing: extraction of centerline, automatic segmentation, slice-wise motion correction, etc.
Behavioral and imaging data from about 120 participants aged 18-89. Data were collected as part of a grant to use high-resolution imaging and advanced behavioral tasks to understand how aging affects the hippocampus and how this is related to age-related cognitive decline. The full dataset includes traditional neuropsycholgical measures, hippocampal-specific behavioral measures, whole-brain DTI, high-resolution DTI of the medial temporal lobes, and structural MRI including segmentation of grey/white/CSF, of cortical regions and of hippocampal subfields.
The Brain Coactivation Map describes all the coactivation networks in the human brain based on the meta-analysis of more than 5,400 neuroimaging articles (from NeuroSynth) containing more than 16,000 individual experiments. The map can be browsed interactively (CoactivationMap.app on GitHub) or queried from a shell using a command line tool (cmtool on GitHub).
An atlas intended to provide accurate data in terms of specific uptake location to make the BP quantitation. The VOIs were manually drawn with software Analyze 9.0 (Mayo Clinic) in 18F-DOPA brain image after spatial normalization with a 18F-DOPA Template. Each striatum was divided into 6 sub-regions: ventral caudate, anterior dorsal caudate, posterior dorsal caudate, ventral putamen, anterior dorsal putamen and posterior dorsal putamen.
A software package for computational modeling of neural maps developed as part of the NIMH Human Brain Project. Topographica focuses on the large-scale structure and function that is visible only when many thousands of such neurons are connected into topographic maps containing millions of connections. The software package provides a general-purpose framework for building models at this level, at an appropriate level of detail and complexity, as determined by the available computing power, phenomena of interest, and amount of biological data available for validation. It is intended to complement low-level neuron simulators that are available, such as General Neural Simulation System and NEURON.
A software package for the real-time analysis and dynamic visualization of functional magnetic resonance imaging data sets. It allows users to observe the working brain "online" by incrementally computing statistical maps as contrasts of a General Linear Model (GLM). The program also performs real-time pre-processing, including 3D motion correction, spatial Gaussian smoothing and temporal filtering (drift removal).
CRL Unbiased and Deformable Spatiotemporal Atlas of the Fetal Brain
Computational Radiology Laboratory Unbiased and Deformable Spatiotemporal Atlas of the Fetal Brain
An atlas of of the fetal brain from MRI of normal fetuses scanned prenatally generated using a mathematical framework. The atlas shows the inter-subject anatomic variability of the fetal brain over the fetal brain growth period and is currently available between 27 weeks gestational age to 35 weeks. It has been constructed following an unbiased minimum distance template estimation approach which utilizes symmetric diffeomorphic deformation and the cross-correlation (CC) similarity metric integrated with kernel regression in age.
UNC-Wisconsin Neurodevelopment Rhesus MRI Database
A macaque brain MRI database characterizing the normal postnatal macaque brain development. This longitudinal primate database was acquired from a cohort of healthy macaque monkeys ranging from a few week olds up to 3-year-old adolescents. Each scan consists of structural (both T1 and T2) and diffusion MRI.
Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX)
Virtual Electrode Recording Tool for EXtracellular potentials
A Matlab tool for simulating extracellular potential recordings in spiking neural network (SNN) models. VERTEX is designed to facilitate the simulation of extracellular potentials generated by activity in SNNs; in particular, spatially-organised networks containing thousands or hundreds of thousands of neurons. It has a limited scope but has a simpler user interface so that a simulation can be specified simply by setting some parameters and run using a few function calls.
Wisconsin Cortical Thickness Analysis (CTA) Toolbox
A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR).
A set of many useful automation scripts to facilitate the neuroimaging data analysis process. It contains BASH scripts for MRI data management, FSL automation and web application.
A full featured and extensible application which simulates biological neural networks using graphic tools which edit neurons and networks, run the simulation and analyze results. It is written in C and runs on Unix and Windows. It is specifically targeted for neuroscientists who are less experienced with computer programming.
YMDTI: Diffusion Tensor Images of Healthy Young Males
Diffusion Tensor Images of Healthy Young Males
A dataset which contains diffusion tensor images of 93 healthy, young male subjects.
Segmentation software for multimodal image analysis of brain tumor studies. It performs volumetric segmentation of healthy and tumor tissues by employing multispectral MRI sequences. Segmented tissues include Gray Matter, White Matter, Cerebrospinal Fluid, necrotic core, edema, non-enhancing tumor and enhancing tumor.
A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit.
Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND)
A GUI-based software for real-time fMRI processing, multivoxel pattern decoding and neurofeedback. The package integrates routines for image preprocessing in real-time, ROI-based feedback and brain decoding-based feedback using the FSL and libSVM libraries. Users can create or employ pre-specified visual stimuli for neurofeedback experiments. FRIEND can be used as Windows standalone software or as a multiplatform toolbox (called FRIEND Engine).
A tool which implements a functional analysis pipeline for the joint analysis of longitudinally measured functional data and clinical data (for example age, gender and disease status). FMPM consists of a functional mixed effects model for characterizing the association of functional response with covariates of interest by incorporating complex spatial–temporal correlation structure, an efficient method for spatially smoothing varying coefficient functions, an estimation method for estimating the spatial– temporal correlation structure, a test procedure with local and global test statistics for testing hypotheses of interest associated with functional response, and a simultaneous confidence band for quantifying the uncertainty in the estimated coefficient functions.
A pure JavaScript medical research image viewer, compatible across a range of popular web browsers. The orthogonal viewer supports NIFTI and DICOM files, overlays and atlas labels. It requires Firefox (7+), Chrome (7+), Safari (6+), MobileSafari (iOS 6+), or IE (10+).
Sperm Stem Cell Libraries for Biological Research
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 18,2023. Stock center of Knockout and Transgenic Rats at UT Southwestern in Dallas.
BioXpress is a gene expression and cancer association database in which the expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas, International Cancer Genome Consortium, Expression Atlas and publications. BioXpress can be searched by gene name or cancer type. To search the database by gene name, select the appropriate identifier type from the dropdown menu and type in the corresponding identifier in the adjacent text box. The results are computed and presented to the user with information such as variable expression levels and tumor expression. To search by cancer type, select the desired type from the dropdown menu, such as "Cancer Type", "Significant", "Expression", "Adjusted p-value" and "p-value". Results are shown in a graph displaying the top 10 differentially expressed genes for the specified cancer type in terms of the frequency of significant altered expression between the tumor and normal pairs.
Primary Antibodies - Creative Diagnostics
An antibody manufacture service from the commercial organization Creative Diagnostics which provides monoclonal and polyclonal matched antibody pairs, tag antibodies, phospho-specific antibodies, anti-idiotypic antibodies, cardiac markers antibodies, and blood group antibodies.
A database that provides a comprehensive and quantitative assay of ion channel models currently available in the neuroscientific modeling community. Specifically, it contains analyses of the ion channel models from NEURON. The database quantifies the similarity in kinetics between models using a series of standardized voltage clamp simulation protocols and subsequent cluster analysis. Citation links and duplications of channels, along with similarity of kinetics between channel models, are combined into genealogical trees and dendrograms that are searchable through the ICG web interface. ICG also experimentally recorded current traces and provides tools for uploading new channel models.
Advanced Connectivity Analysis (ACA): a large scale functional connectivity data mining environment
A large scale functional connectivity data mining software package which enables large-scale seed-based analysis and brain-behavior analysis. It can examine a large number of seed regions with minimal user input. ACA has a brain-behavior analysis component to delineate associations among imaging biomarkers and one or more behavioral variables.
Software for image processing, analysis, and editing. The software includes features such as touch capabilities, a customizable toolbar, 2D and 3D image merging, and Cloud access and options.
A Javascript library that aims to deliver a starting point for interactive health data visualization. Examples and demos are available on the site. hFigures was built with d3.js and a copy of the library is included in this repository. All rights and license terms apply to the d3.js library accordingly.
Cincinnati Childrens Hospital Image Processing Software
Research software used for post-processing of functional MRI, diffusion MRI, spectroscopy, and perfusion MRI data. It is written in Interactive Data Language.
Case Western Reserve University In Vivo Animal Core Facilities
A set of core facilities of Case Western Reserve University School of Medicine which allows users to create and analyze in vivo animal models. The various facilities provide animal care, transgenic models, imaging, irradiation, and phenotyping for research concerning such topics as cancer, metabolic processes, and behavior. In vivo animals provided include mice, zebrafish, and rodents.
Imaging software used to acquire and analyze images from specific Bio-Rad imaging systems. Users can analyze gel or blot features, capture optimized image data, and generate a report of the data. Image Lab software exclusively runs on the Gel Doc EZ imager, Gel Doc XR+ imaging system, ChemiDo MP, ChemiDoc XRS+ imaging systems, Criterion Stain Free imager, and the GS-900calibrated densitometer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing.
Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures.
Human Thalamus in 3D Stereotactic Coordinates
A research tool for clinical and experimental neuroscience, which provides images of human thalamus in the stereotactic planes of the coordinate system based on intercommissural line. Images include histological sagittal sections, sagittal maps, coronal maps, horizontal maps, and MRI images all from the same brain. The website also provides materials and methods section, references to the articles and presentations describing research data (on which the maps are based), and a bibliography on the synaptic relationships of subcortical and cortical afferents with projection and local circuit neurons in the motor thalamus.
Image processing software used to modify and clarify sample images for FluoView FV1000 range of confocal laser scanning microscopes and Fluoview FV1000MPE multiphoton excitation systems. The software incorporates high-dynamic-range imaging, minimized signal-to-noise ratios, partial stitching with multiarea time-lapse imaging, and channel unmixing. The software also allows users to select specific areas of the whole sample, which can stitched together.
Software which processes diffraction data/images and produces an MTZ file of reflection indices with their intensities, standard deviations, and other parameters. The MTZ file is passed onto other programs of the CCP4 program suite for further data reduction. iMosflm processes data from CCD and pixel detectors. It is available for Windows, Mac OSX and Linux platforms. Tutorials are available at the website.
Pointless scores all the possible Laue groups consistent with the crystal class, which is based on cell dimension restraints, by matching potential symmetry equivalent reflections. For chiral systems, the Laue group uniquely implies the point group then checks sets of reflections which may be systematically absent to suggest a possible spacegroup. There is also a check for lattice centering, i.e., a check for whole classes of reflections having essentially zero intensity, including a check for obverse/inverse twinning in rhombohedral systems. Pointless is also capable of converting XDS, Scalepack, SHELX or SAINT formats to MTZ.
Crystallographic software which solves structures using algorithms and automated rapid search calculations to perform molecular replacement and experimental phasing methods.
A set of software programs that utilizes dual spaces algorithms for the determination of small and macromolecular crystal structures by single crystal X-ray and neutron diffraction. Libraries, extra files and environment variables are not required for the executables. SHELX is intended to be run on a command prompt but may be called from GUIs such as shelXle, Olex2, Oscail or WinGX, or hkl2map., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
buccaneer - Statistical protein chain tracing
Software which performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target. The target distributions are generated by a simulation calculation using a known reference structure for which calculated phases are available. The success of the method is dependent on the features of the reference structure matching those of the unsolved work structure. For almost all cases, a single reference structure can be used, with modifications automatically applied to the reference structure to match its features to the work structure.
Crystallographic Object-Oriented Toolkit
Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.
Software designed to provide a multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Features include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. Modules, libraries, utility programs, tutorials, and a syntax manual are available on the website.
Python-based Hierarchical ENvironment for Integrated Xtallography
A Python-based software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Phenix includes programs for assessing data quality, experimental phasing, molecular replacement, model building, structure refinement, and validation. It also includes tools for reflection data and creating maps and models. Phenix can also be used for neutron crystallography. Tutorials and examples are available in the documentation tab.
A molecular refinement program with two main modes: REVIEW, which checks and updates the input model to establish that the geometric restraints can be properly set up, and REFINE mode, which is the standard mode and documented in keywords. In REVIEW users can: check model coordinates and write an extended output set of coordinates, find disulphide bonds and other covalent links, cis-peptides, output the sequence and REMARK records. In REFINEMENT mode users can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. Also in REFINEMENT mode, Refmac produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps. The program is supported by CCP4.
A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot.
Software package for NMR spectra acquisition, processing, and data analysis. Features include: deconvolution/spectrum simulation/iteration; comprehensive functionalities for processing, displaying and analyzing one and multi-dimensional spectra; and user customization. A full list of features is available on the website.
A graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. Sparky displays NMR spectra, the peaks of which users may pick, assign, and integrate using a graphical interface. Users can work with any number of 2, 3 or 4 dimensional spectra simultaneously. Spectra for input to Sparky can be produced with processing programs NMRPipe, Felix, VNMR, XWinNMR or UXNMR. Output consists of text peak lists showing assignments, chemical shifts, volumes, line widths, etc.
Software for automated structure calculation of biological macromolecules on basis of conformational constraints from nuclear magnetic resonance. Program for automated NMR protein structure calculation. CYANA requires a sufficient list of assigned chemical shifts and lists of cross-peak positions and columns from 2D, 3D, or4D NOESY spectra in order to calculate the assignment of the NOESY cross-peaks and the 3D structure of the protein in solution.
Assisted Model Building with Energy Refinement (AMBER)
Assisted Model Building with Energy Refinement
Software package of molecular simulation programs. It is distributed into AmberTools15 and Amber14. AmberTools15 is a software package which can carry out complete molecular dynamics simulations with either explicit water or generalized Born solvent models. It is distributed in source code format and must be compiled in order to be used. Amber14 builds on AmberTools15 by adding the pmemd program, which provides better performance on multiple CPUs and dramatic speed improvements on GPUs compared to sander (molecular dynamics). GPU info, manuals, and tutorials are available on the website.
Software used to create presentation quality charts, graphs and slides for technical presentations, publications and reports. It can create complex drawings and 2D and 3D graphs with advanced scientific features.
Graphic design software which can be used for vector illustration and page layout, web design, and photo editing. Features include: search, preview, application and transformation capabilities for both vector pattern and bitmap pattern fills; a fill engine with complete control over fountain, bitmap pattern and vector pattern fills; templates for website design; and vector shaping and page layout tools.
A set of fluorescence microscope image processing packages which perform image restoration, interactive analysis, and volume visualization of 2D and 3D multi channel microscopy images or time series. The restoration is based on different deconvolution algorithms, that permit the recovery of objects from images that are degraded by blurring and noise. Tutorials and documentation are available on the website.
Heinrich Heine University Dusseldorf; North Rhine-Westphalia; Germany
Software which utilizes the properties of both light scattering and Brownian motion to obtain the particle size distribution of samples in liquid suspension. The Nanoparticle Tracking Analysis software tracks many particles individually and calculates their hydrodynamic diameters using the Stokes Einstein equation.
SoftMax Pro Data Acquisition and Analysis Software
A software package for microplate reader control and microplate data analysis. It includes analysis templates for a variety of assays run on Molecular Devices microplate readers.
Software which controls all operations in the experimental setup, data acquisition and monitoring, and data analysis stages of the Bio-Rad Opticon 2 system. In the experimental setup stage, setup and programming operations are accessed from the Master File window. The master file consists of a plate file, which specifies the parameters of the plate, and a protocol file, which specifies the experimental conditions. After a plate and a protocol setup have been created or selected, a run can be initiated, which begins the data acquisition and monitoring stage. Data collection can be monitored during the run by viewing a plot of fluorescence intensity vs. cycle number. In the data analysis stage, data can be analyzed using the Quantitation, Melting Curve, and/or Analysis windows. The window used depends on the type of data being collected.
Statistical software that uses dynamic graphics rather than tables or graphs to visualize raw data. More specific versions of JMP are available for statistical analyses, clinical work, and genomics. Features include statistical modeling, data cleanup, automation and scripting, and experimental design.
A spatial statistics program which provides tools for crime mapping and analyzing crime incident locations. CrimeStat is organized into five sections: data setup, which arranges and organizes the location data; spatial description, which performs analyses such spatial distribution, spatial autocorrelation, and distance and hot spot analysis; spatial modeling, which performs a number of analyses such as Bayesian journey to crime analysis and space-time analysis; crime travel demand modeling, which detects crime patterns and correlations over time and space; and CrimeStat libraries, which are component objects that include all of the routines that were developed through version 2.0 of the regular CrimeStat program.
Software that processes neural data at run-time to control the implant's electrical stimulation functionality for the Braincon brain-computer interface (BCI). Braincon Platform Software is a general, flexible and verifiable BCI software architecture with a filter pipeline for low-latency multi-threaded processing of neuronal signals.
Software designed to automatically realign brain images for easier cross patient examination regardless of age, disease or head position. It positions and aligns anatomy-related sagittal, coronal and axial slices using anatomical landmarks.
Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
In vivo imaging software which facilitates workflow for in vivo optical, X-ray and microCT image acquisition, analysis and data organization., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software program used to control G:BOX hardware, specifically to capture and process images. While viewing images in real time, GeneSnap controls the illumination and exposure length of the lens, as well as the focussing, zooming and iris setting of a motorized lens.
3D modeling, animation, and rendering software which allows users to create custom tools and share design projects. 3ds Max contains various tools and templates for rendering and and editing, including tools for graph construction, project collaboration, and complex topography creation.
A software tool that combines biomechanical simulation and biologically realistic neural networks to create realistic models of, and perform tests on, biomechanical workings. AnimatLab was primarily designed to model and test the operation of neural circuits that might produce behavior patterns observed in an intact animal. Users can create an animalistic or robotic body and place it in a virtual environment with physics that are accurate and realistic. Users can then design a nervous system that controls the behavior of the body within the physically realistic environment. Various models for different types of actions, builds, and movements are available.
Software used for automatic high throughput analysis of unconstrained rodent behaviors in a home cage. HomeCageScan is ideal for longitudinal studies where several animals are studied and tested over long periods. Its features include twenty-four-hour recording capabilities, statistical analysis, automatic adaptation to environmental changes (including day and night changes), and a batch‐mode which allows user to run multiple videos successively without human intervention. The software can detect various behaviors ranging from feeding and urination to jumping and foraging.
A video tracking system designed for high-throughput behavioral experiments. LimeLight can track up to 4 arenas at once and can collect images at up to 30 frames per second for one animal or up to 8 frames per second when tracking 4 arenas at once. The tracking system has 2 different hardware configurations: the 1-camera system can be used to record 1 to 4 animals at once, while for multiple animals, each one is placed in a separate arena in one quadrant of the image. The software contains productivity features such as flexible arena setup, user-defined behavior scoring, stimulus control, and various analytical functions for quantifying behavior. The program is designed for experiments such as Open Field, Plus Maze, Radial Arm Maze, Zero Maze, Novel Object Recognition, Conditioned Place Preference, and Barnes Maze.
Software toolbox able to perform electrophysiological experiments using simple stimulation protocols and more complex paradigms, such as dynamic clamp or hybrid networks.
Software tool for simulating heterogeneous networks composed of different model neurons and synapses. CSIM simulates networks containing up to a few thousand neurons and up to the order of 1.000.000 synapses. It is capable of supporting different levels of modeling and has an object oriented design. A user manual is available on the site.
A neural simulator which models integrate-and-fire neurons with conductance-based synapses. NCS supports simulations for larger models and also supports real-time neurorobotics applications. Two versions of NCS are available: NCS 5, which is based on CPU cluster; and NCS 6, a multi-box, multi-GPU version. NCS 5 models integrate-and-fire neurons with conductance-based synapses using two clusters: four SUN 4600 machines and 208 Opteron cores. NCS 6 is a neural simulator for heterogeneous clusters of both CPUs and GPUS.
A software package for numerical computation providing a powerful computing environment for engineering and scientific applications. It includes hundreds of mathematical functions and has a high level programming language allowing access to advanced data structures, 2D and 3D graphical functions.
A modeling tool for simulating intracellular calcium diffusion and buffering. CalC solves continuous reaction-diffusion PDEs describing the entry of calcium into a volume through point-like channels, and its diffusion, buffering and binding to calcium receptors. Its features include: being platform-independent; being operated by simple script; combinable with MATLAB; and providing real-time views. Demos and manuals are provided on the website.
Software application for simulation and analysis of biochemical network models and their dynamics. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespies stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. Models in COPASI are based on reactions that convert a set of species into another set of species. Simulation can be performed either with stochastic kinetics or with differential equations. COPASI also includes various methods of analysis and data visualization.
EDLUT: Event-Driven simulator based on Look-Up-Tables
Event-Driven simulator based on Look-Up-Tables
Simulation software which creates spiking cell models using either a time-driven strategy or an event-driven strategy based on look-up tables. EDLUT serves as a tool for studying the computational principles of neural systems to reveal how different functionalities of the brain and central nervous system are based on cell and topology properties.
ERNST: Event Related Neuronal Simulation Tool
An event-based neuronal network simulator designed to handle large, complicated neuronal networks. The software is capable of creating realistic and accurate neuronal models in terms of neuronal dynamics and spike timing. ERNST is written in Java.
KInNeSS: KDE Integrated NeuroSimulation Software
Neurosimulation software that links sophisticated model development with behavior. The software package provides a framework that can be expanded using standard KDE (K Desktop Environment) parts and plugins to incorporate a variety of different projects, like visual system, auditory system or memory system. KInNeSS contains two fully developed project environments: one for generic input and another for spatial navigation tasks. The option of creating a new project environment is provided for advanced users. A user manual and tutorials/examples are provided as part of documentation.
Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs.
Software suite of sequence analysis and design tools that help manage, view, analyze, transform, share, and publicize various types of molecular biology data within one analysis environment. Users can analyze and compare sequences, design cloning and other vector related experiments, and curate and organize data and collections. Different classes for different user and experimental focuses are available.
Software tool for plasmid and sequence editing, annotating and drawing plasmid sequences. Used to view circular or linear maps of DNA sequences. Users can perform virtual digests whereby they select predefined DNA ladder, or specify their own, and visualize theoretical DNA fragments. Used to highlight restriction sites in editing window, accurately reflect Dam/Dcm blocking of enzyme sites, highlighting and drawing graphic maps using feature annotations from genbank and embl files, highlighting text using pre-defined and custom feature libraries, and directly BLASTing selected sequence at NCBI or Wormbase. Runs across Windows, OS X, and Linux/Unix.
A software toolbox which provides MATLAB functions, apps, and a Simulink block for analyzing, designing, and simulating fuzzy logic systems. Fuzzy Logic Toolbox allows users to model complex system behaviors using simple logic rules, and then implement these rules in a user-designed fuzzy inference system. Functions are provided for many common methods, including fuzzy clustering and adaptive neurofuzzy learning. The toolbox can be used as a stand-alone fuzzy inference engine or in connection with Simulink. Different versions of the software are available for specific fuzzy inference systems.
An ImageJ plugin used for analyzing 2D time-lapse images or stacks. The plugin can be used to add a predefined ROI (Auto ROI) through mouse clicks. After selecting the object to be defined, an ROI is added on the image and in ROI Manager.
A suite of programs for recording and analyzing signals from intracellular electrophysiology experiments. A list of the latest software is available from the website. The programs work with common electrophysiological laboratory interface units, including: Cambridge Electronic Design 1401 / 1401plus / Micro1401 / Power 1401; Axon Instruments Digidata 1200 or 1320/22, 1440, 1550, 1550A; Instrutech ITC16 or ITC-18; National Instruments multifunction interface cards; Biologic VP500; Tecella patch clamps; and Heka EPC-9, EPC-10.
Software which can acquire, analyze, manage, and share mass spectrometry data. MassLynx controls any Waters mass spectrometry system, from sample and solvent management components to mass spectrometer and auxiliary detectors. The software can acquire nominal mass, exact mass, MS/MS and exact mass MS/MS data. The software system also maintains and consolidates all user sample data. Optional Application Manager programs provide additional information for specific MS analyses and data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software to calculate molecular descriptors and fingerprints. The descriptors and fingerprints are calculated using The Chemistry Development Kit with additional descriptors and fingerprints such as atom type electrotopological state descriptors, Crippen's logP and MR, extended topochemical atom (ETA) descriptors, and McGowan volume.
Software toolkit containing tools to render and canonicalize SMILES and manipulate MOL file and related formats, as well as structure fingerprinting.
RDKit: Open-Source Cheminformatics Software
RDKit Open-Source Cheminformatics and Machine Learning
An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website.
Software which can automatically detect descriptor classes defined in the CDK QSAR descriptor dictionary. Groups of descriptors and individual descriptors can be selected for evaluation. Input can be SDF or SMI formats, while output can be a variety of delimited text formats, annotated SDF or ARFF. The software can also evaluate fingerprints. A summary overview of the available descriptors and their names are available on the website.
A sweep-based data acquisition and analysis software package. Its uses range from a simple storage oscilloscope to complex applications requiring stimulus generation, data capture, control of external equipment and custom analysis. A built-in script language automates tasks and provides additional tools for custom analyses and applications. Signal includes functions for specific application areas, including dynamic clamp, whole cell and patch clamp electrophysiology, and evoked response including control of magnetic and other stimulus devices. Video tutorials and a demo version of Signal is available on the main page.
Software for browsing the image data acquired by Nikon C1 and a Nikon C1si system.
Software designed to provide an image analysis software solution for offline analysis of images, ideally for the analysis of images where image capture is not required. Available applications for MCID Analysis include gel/blot analysis, fluorescence microscopy, and stereology.
A software program that allows the user to perform data acquistion, stimulation and analyses. Users do not need to know the programming language or a new protocol view. AcqKnowledge Software is compatible with MP150 Research Systems, MP36R Research Systems, and MRI and fMRI Setups. A variety of offline and online analysis tools allows users to customize data recordings and targeted analyses. The software can perform automated analysis routines, output a range of stimulus paradigms, and allows users to record from multiple hardware devices simultaneously.
Software used for Bio-Rad imaging systems to acquire, quantitate, and analyze a variety of data. The software allows automatic configuration of imaging systems with appropriate filters, lasers, LEDs, and other illumination sources. It also contains tools for automated analysis of tests and assays such as 1-D electrophoretic gels, western blots, and colony counts.
A software program for the Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems. StepOne software allows the user to open and analyze experiments generated from either the StepOne or the StepOnePlus system. Users can set up experiments, send experiments to the instrument, control the instrument settings, and collect and analyze data.
Software tool for automated analysis of monolayer wound healing assays. Available as a stand alone application for Macintosh and Windows and as a source code. Offers a graphical user interface for inspection of analysis results and manual modification of analysis parameters., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation.
A software tool which provides a means to acquire and analyze time-series data, as well as a direct route to publication quality graphics. It provides a variety of graph styles and automated, extended, and/or customizable analyses.
A graphical source code file used for an automated motion detection and reward system for animal training (see comment for full paper title). It was designed on the LabVIEW programming system. Running the program requires the appropriate LabVIEW runtime software from National Instruments Corporation.
A protein family specific platform that works closely with the GPCR community to determine the high resolution structure and function of GPCRs. Structures are available in the glutamate, secretin, frizzled/TAS2, adhesion, and rhodopsin branches of the protein phylogenetic tree. Users can access a list of protein structure targets and completed protein structures.
Software used for modeling, simulation, and rendering of 3-D models. The tool is designed to provide a starting point to model, animate, work with lighting, and create VFX.
Illustration and communication software for engineers and technical graphics professionals that combines the ability to make 3D images while also applying filters and duatone images. The software has minimum precision levels and object illustration and image editing tools to keep data accurate throughout the authoring process. Users can accelerate and streamline the technical illustration workflow from initial import and design to final presentation, facilitate collaboration, and improve the overall productivity. Tutorials and technical documents are available on the website.
Video tracking system used to automate testing in a variety of behavioral apparatus. ANY-maze can automatically track the tail, head, or body of a test animal in up to 16 pieces of apparatus. The software can record live images or digital files with different camera types and save the data in multiple formats. ANY-maze contains built in statistical tests and standard measures for distance, speed, mobility, duration, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment.
Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server.
Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008.
A desktop application used to create and manage 2D and 3D animation and video and audio assets. SAP Visual Enterprise Author can be used to render visual content into common desktop documents, file formats, and business applications for secure downstream use. A variety of tools allows users to view, transform, optimize, animate, and publish in different formats.
MetaFluor Fluorescence Ratio Imaging Software
Software designed for single or multi-wavelength intracellular ion measurements. It provides simultaneous display of raw data, ratio image, graphs of intensities, ratios, ion concentrations, and a non-ratiometric image such as a brightfield or phase-contrast image. Two different ratiometric indicators can be imaged and measured simultaneously to provide greater insight to ion exchange and intracellular function regardless of dye loading concentrations, conditions, or emission intensities.
A suite of MATLAB/C and C++ tools for computing standard and extended versions of transfer entropy (as recorded by Thomas Schreiber) on sparse, binary time series. Delay 1, delayed, and higher-order transfer entropy are available in the toolbox. The speed of the program is dependent upon the number of delays, the length of the data set, the number of neurons, and the message length/order. Documentation and examples are provided on the website.
MED Associates Activity Monitor software
Software designed to record and organize data. All experiments and subject data are entered into a database, with all subject data linked together allowing the software to track everything, and save it based on the assigned Subject ID. All standard data is displayed in real time along with a cumulative plot of the subject’s activity for all chambers. Users may choose the specific chamber size allowing for distance traveled to be measured in real units instead of beams broken. A rotational analysis option allows examination of large or small rotations, allowing for rotational measures to be obtained on staggering, ataxic, lesioned, or other loco-motor impaired mice or rats. Zonal analysis allows the user to change boundaries around the animal in post analysis. Up to eight systems can be connected to one computer.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software used for a variety of functions including image automation frameworks and advanced 3D data quantification, and simulation technologies.
A software application for one-dimensional electrophoretic analysis of multi-labeled fluorophores. It was designed to analyze multi-channel fluorescence data from Fujifilm FLA-5000 and FLA-8000 scanning systems. The software also works with other scanners in the BAS/FLA series and with the LAS series.
Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton.
Software package for multi-parametric model-fitting of 4D Magnetic Resonance Imaging data. Software library to facilitate voxel wise fitting on a number of datatypes including T1 and T2 relaxometry, Arterial Spin Labeled MRI, Diffusion Weighted Imaging and Dynamic Contrast Enhanced MRI. T
A discovery platform used to analyze and annotate imagery for individual projects, while assembling shared data resources. It was originally applied to Drosophila neuronal anatomy and neuroblast lineage analysis and is currently being extended to support mouse whole-brain projection tracing. The Workstation is both a pipeline management system that extracts entities from 3D imagery and a suite of tools that enable scientists to annotate large imagery datasets. A Entity-Attribute-Value (EAV) graph permits any element to be annotated by users with custom ontologies. By allowing any entity to have multiple parents, the graph can be re-arranged by each user without copying the underlying image data.
Interactive rendering tool for confocal microscopy data visualization. Combines rendering of multi-channel volume data and polygon mesh data, where properties of each dataset can be adjusted independently and quickly. Designed for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. Features include feature tracking, 3D measurement tools, multiple render modes for multi-channel confocal data, and volume paint selection and segmentation.
THIS RESOURCE IS NO LONGER IN SERVICE, documented March 14, 2016. Research Integrative Query (ResearchIQ) tool, a semantically anchored resource discovery platform that facilitates semantic discovery of local and publicly available data through a single web portal designed for researchers in the biomedical informatics domain within The Ohio State University.
Data set about mapping information provided as text files. The text files contain 3D representations of neuronal morphologies reconstructed using Neurolucida.
Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features.
An ImageJ plugin for the automatic alignment of a source image (or a stack) to a target image. Manual, automatic, and batch alignment modes are available. Users may specify some landmarks to establish the initial correspondence between images. In automatic and batch modes, the landmarks are automatically refined to match the landmarks of the target image. After registration, the plugin creates a warped image using the final position of the source image and the target landmarks. The plugin can be called by a macro or by another plugin. Technical guidance is available on the website.
Point and click program used to quickly analyse circadian activity data using algorithms and embedded controls to make every graph interactive and useful for data analysis. The analysis program has been used for a variety of species including mice, hamsters, rats, sheep, Drosophila, and humans. This program has three separate applications: one for data collection, one for analysis, and a chamber control program.
A general stastical software for Windows which can perform basic statistical analysis, statistical modeling, multivariate analysis, and produce of graphs. InfoStat also has facilities that could be useful in teaching statistics. It can connect to R through the interpreter, which can run R scripts without leaving the InfoStat working environment, and through the implemented menu-driven procedures, which make use of the R calculation engine.
Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Image capture software which creates publication quality images. SPOT allows users to view the live image and a preview of the captured image side by side, enabling image editing before capture. Enhancements such as calibration marks and measurements can be applied after image capture. An advanced version is also available.
A dataset of brain region connectivity statements mined from neuroscientific literature. Users can search for brain regions and explore region connectivity.
Software used to analyze cellular image data obtained from BD Pathway bioimaging systems. Its features include object splitting for small spots or objects, band segmentation outputs, image preprocessing, and segmentation filters.
Software used to design, clone, and validate genetic sequences de novo. Users can remove or add sequence motifs, recode open reading frames, design oligonucleotides for sequencing primers, and more. Once the gene is designed, users can order the synthetic DNA fragments with Gene Designer files. Sequences can be imported and exported in GeneDesigner, Genbank, and FASTA formats. Demos and support are available on the main site.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Visualize and validate complex MS/MS proteomics experiments
A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters.
A nanoparticle research collaborative which engineers nanoparticle products in order to find cures for cancer and other diseases. The gold labels produced are uncharged molecules which are cross-linked to specific sites on biomolecules. Labels can be attached to any molecule with a reactive group (proteins, peptides, oligonucleotides, small molecules and lipids) for detection and localization. New probes can be engineered based on any fragment of a naturally occurring biomolecule, and the label can be positioned away from the binding site so it does not interfere with binding.
A development environment for engineers and scientists to visualize, create, and code engineering systems. The system design software is integrated with all measurement hardware and contains signal processing IP. Other features include multithreaded execution, software deployment to hardware, and program integration into a single environment.
Software that allows users to manually or automatically design custom primers and probes for gene quantitation and allelic discrimination (SNP) real-time PCR applications. It supports assays based on TaqMan and SYBR Green I dye chemistries.
Software for professional vector graphics and rich photo-editing tool. Used for digital drawing.
Microscope imaging software suite used with Nikon products. NIS-Elements includes software applications for advanced and standard research, documentation, confocal microscopy, and high-content analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software for Bio-Plex systems which automates data optimization, operates Bio-Plex instruments, and analyzes data.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software designed to take single or multi-wavelength intracellular ion measurements an provide simultaneous display of the raw data, ratio image, graphs of intensities, ratios, ion concentrations, and a non-ratiometric image for microscope techniques such as a brightfield or phase-contrast image. Two different ratiometric indicators can be imaged and measured simultaneously to provide greater insight to ion exchange and intracellular function regardless of dye loading concentrations, conditions, or emission intensities.
Software used with Illumina sequencing instruments to control PC acivity and perform base call and quality scoring. The primary analysis is performed during the chemistry and imaging cycles of a sequencing run, giving users the option to view data and decide how to proceed in the run.
AMT camera system software that performs digital image acquisition, processing, and storage. An operations manual and software specifications are available on the main site.
A video tracking system that takes automated recordings and analyzes animal activity through various arena and maze systems. It can track multiple arenas using one camera, and an unlimited number of zones of interest can be generated for performing spatial analyses or controlling data acquisition. Features include 3-point detection, 3D measurements, access to raw data, and reanalysis of tracking data.
Software designed for use in tandem with the Startle Monitor system. It is Windows NT based software with a single input screen for all processes. The user can input session parameters, order a trial list, input subject information, edit trials, and edit sessions.
iDigBio is the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public.
Software that provides subject tracking with body axis alignment and angle of view, which is then used to track body, nose and tail movements without marking the animal. Users may create the scoring system used by the software, as well as zones to observe, quantify, and compare the behavior of an animal in one or more areas. The software features several data acquisition and analysis tools to gather and interpret the data.
A commercial provider of imaging software that works in tandem with Pixera camera and imaging systems.
3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. The LSM Image Browser comes with many functions from the Zeiss LSM software package, however, it is not used only for the Zeiss image database. This browser is an ideal tool for general image archiving, handling and interactive measurement in labs and workgroups. Features include orthogonal sectioning, 3D cut function, 3D view with calculation of single projections, interactive measurement functions in the overlay dialog, such as scale bar, distance, area etc.
Biomarker detection and evaluation software which provides an advanced basis for mining unknown potential biomarkers in complex protein profiles. Visualization tools such as stack plots and box-and-whiskers plots can be used to interactively inspect and compare large data sets originating from samples that contain different clinical diagnoses. ClinProTools also supplies sophisticated mathematical algorithms for the discovery of complex biomarker pattern models. Besides validation, class-prediction tools are also integrated to allow the implementation of the whole biomarker detection and evaluation process.
A collection of 7 individual software packages that all control the Olympus Imaging systems while also providing different individual features including (but not limited to): basic measurement functions, process automation, ratio analysis, and real time image acquisition.
Software used to compile images obtained from the Zeiss LSM 510 confocal microscope. The browser can be used for general image archiving and handling and interactive measurement in labs and workgroups. Features include orthogonal sectioning, 3D cut function, 3D view with calculation of single projections, and interactive measurement functions in the overlay dialog, such as scale bar, distance, and area.
Software for MS/MS proteomic experiments to compare samples, identify biological relevance, and identify isoforms and protein PTMs. These proteins can be classified based on molecular function or organelle. Users can investigate spectrum details and counts, as well as use high through-put batch processing. Tutorials and a free trial are available through the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Visualizing Continuous Health Usability Test Results Dataset
Health Visualization Dashboard Usability Results
A dataset containing the results of three usability studies conducted on a modeled patient using a software tool that visualized the health situation of the patient over time. The modeled patient was diagnosed with Type 2 Diabetes and had begun a coaching program. The study followed the progress of the patient as he/she progressed through the coaching program. An after scenario questionnaire, computer system usability questionnaire, and Nielsens Heuristic Evaluation were used to evaluate the patient. Separate CSV files, available on the website, contain the answers to the questionnaires and the laboratory details.
Open source simulation software for thyroid homeostasis, based on published nonlinear model of pituitary thyroid feedback control. Simulates pituitary thyroid feedback control, which allows users to study relationship between structure and behaviour of thyroid homeostasis.
Structure Parameter Inference Approach Thyroid
Software tool to deliver estimated structure parameters of endocrine feedback control systems in vivo from serum or plasma hormone levels. Used for evaluation of thyroid function. Allows for calculating thyroid maximum secretory capacity (GT or SPINA-GT) and sum activity of peripheral 5'-deiodinases (GD or SPINA-GD) from levels of TSH, (F)T4 and (F)T3 that have been determined once only (SPINA Thyr). Binaries are available for Mac OS, Mac OS X, Palm OS, Garnet OS and Windows. For other operating systems, including Linux, Solaris and BSD, SPINA Thyr is available as sourcecode. Building from source requires THINK Pascal (for Mac OS Classic), winsoft PocketStudio (for Palm OS / Garnet OS) or Lazarus/Free Pascal (for Mac OS X, Windows, Linux, BSD and Solaris). Special version of calculation engine is available for modern S implementation, e.g. R.
A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations.
Xenopus laevis Research Resource for Immunobiology (XLRR)
Xenopus laevis Research Resource for Immunobiology
A comprehensive resource specializing in the use of the amphibian Xenopus laevis (the African clawed frog) for biomedical and immunological research. Several genetically-defined inbred strains and clones are available for study. The facility also maintains and develops research tools such as transgenic animals, monoclonal antibodies, cell lines, DNA libraries, and molecular probes. XLRR includes a satellite facility devoted to study infectious diseases caused by iridovirus. Technical assistance, education, and training are also provided.
A web application immune repertoire management, analysis, and archiving. Users can collaborate and share data either privately or publicly. Users can perform a variety of tasks, such as create and share projects with other users, conduct pre-processing tasks on single end reads, run IgBlast, and obtain basic repertoire characterization results for B cell receptor and T cell receptor repertoires.
A commercial geospatial tool typically used for orthorectification and mosaicking of aerial and satellite imagery; however, it can also be used for biomedical imaging and modeling purposes. The developer software contains image processing tools and functions to edit images and design custom applications.
A cross-platform class library for development of high-performance life science computer simulations. It supports modelling for biomedical cybernetics and systems biology with Object Pascal. It contains a set of Pascal units for rapid programming of high-performance computer simulations called the Brick collection.
Ion Channel ElectroPhysiology Ontology (ICEPO)
An ontology distributed in OWL format which contains comprehensive terms describing ion channel electrophysiology. Terms from related ontologies, such as Cell Physiology Ontology (CPO), Cardiac Electrophysiology Ontology (CEPO), and Unit Ontology, were integrated into ICEPO.
Free Pascal is a 32, 64 and 16 bit professional Object Pascal compiler targeting multiple processor architectures and operating systems. Documentation, including guides and manuals, are available on the website.
monoclonal antibody-based chemiluminescence immunoassay for 3,5-diiodothyronine (3,5-T2)
Specific, sensitive, precise and accurate CLIA for 3,5-T2 detection in human serum.
Lazarus integrated development environment
A cross-platform integrated development environment (IDE) for Free Pascal. It contains a class library (LCL) that supports rapid application development for native code on numerous platforms, processor architectures and operating systems.
Software tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be.
An application which provides an environment to explore and organize scholarly data. Rexplore leverages solutions in large-scale data mining, semantic technologies and visual analytics, which allows users to detect and follow research trends, identify and map relationships between authors, perform expert searches, and analyze research performance.
Isolectin GS-IB4 From Griffonia simplicifolia, Alexa Fluor 647 Conjugate
A conjugated form of isolectin B4 for fluorescence identification of non-peptidergic nociceptors in mouse dorsal root ganglia and spinal cord.
Lysosome Enrichment Kit for Tissues and Cultured Cells
A kit which enables isolation and enrichment for intact lysosomes from crude cell and tissue extracts. The kit provides sufficient reagents for preparing 25 extracts and uses OptiPrep Cell Separation Media for the density-based separation of lysosomes from contaminating cell structures.
A registry of cytokines, chemokines, and receptors generated for the purpose of collecting, integrating, and mapping between entity names and synonyms from several resources. These resources include MeSH, the Protein Ontology, EntrezGene, HGNC, MGI, UniProt and others.
National Institute of Diabetes and Digestive and Kidney Diseases Research Resources
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Registry listing NIDDK resources, such as reagents, data, and protocols. They are derived from publicly available information provided by NIDDK-funded investigators, projects, and publications.
Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study (ACCORDION)
Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study
A prospective, observational follow-up study of at least 8000 participants who were treated and followed in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) Trial. Treatment in ACCORD ended in 2009 and ACCORDION is designed to further elucidate the long-term effects of the ACCORD treatment strategies and provide additional data on the relationships among various cardiovascular and diabetic risk factors.
Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT)
Predicting Response to Standardized Pediatric Colitis Therapy
A study of how children newly diagnosed with ulcerative colitis (UC) respond to mesalamine and prednisone (corticosteroid), the standard initial therapies used to treat this disorder. Over a period of 5 years PROTECT will prospectively study the course of 430 children newly diagnosed with UC who are treated with standardized care. Biospecimens (blood, stool, colonic biopsy tissue) will be obtained and used to better understand the effects of genetics, mechanisms of inflammation, Vitamin D, and the bacteria contained in the stool (microbiome) on clinical outcomes.
Lifestyle Interventions for Expectant Moms (LIFE-Moms)
Lifestyle Interventions for Expectant Moms
A consortium whose overall goal is to identify effective behavioral and lifestyle interventions that will improve weight, glycemic control and other pregnancy-related outcomes in obese and overweight pregnant women, and determine whether these interventions reduce obesity and metabolic abnormalities in their children. The study/consortium is comprised of seven clinical centers, with each clinical center conducting its own trial. Additional information on the consortium and individual trials is located in the Consortium Summaries tab.
Hyperglycemia and Pregnancy Outcomes Follow-Up Study Consortium (HAPO-FUS)
Hyperglycemia and Pregnancy Outcomes Follow-Up Study Consortium
The goal of this follow-up study of mothers who participated in the Hyperglycemia and Adverse Pregnancy Outcomes (HAPO) study is to determine the levels of blood sugar during pregnancy that are linked to increased body fat in the child, as well as to determine the chances of a mother developing diabetes 8-12 years after the pregnancy. The original study examined 23,316 mother-child pairs, and researchers determined that the hyperglycemia of a mother was linked to newborn birth weight and body fat. HAPO-FUS will enroll 7,000 or the original HAPO mother-child pairs for one follow-up visit to assess body composition, blucose metabolism, medical history, and other metabolic parameters.
Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN)
Symptoms of Lower Urinary Tract Dysfunction Research Network
A research consortium with the long term goal of developing and testing measurement tools to describe symptoms of lower urinary tract dysfunction (LUTD) in women and men. The group plans to study targeted populations of patients with LUTD in order to expand our understanding of the causes of symptoms and common ways that symptoms change over time. The researchers will also collect biosamples from patients for current and future study of LUTD.
A consortium which includes five of the leading porphyria centers in the United States that provide expertise and experience in the diagnosis and treatment of patients with porphyria. The staff in each Center includes porphyria physicians, researchers, research coordinators, and technical/laboratory staff. Together with the American Porphyria Foundation, the Porphyrias Consortium enables a large scale collaborative effort to develop strategies and methods for diagnosis, treatment, and prevention of illness and disability resulting from these rare disorders.
Nephrotic Syndrome Study Network (NEPTUNE)
A consortium of researchers conducting a cohort study that investigates the underlying disease mechanisms of pro non-inflammatory glomerular diseases. The aim is to elucidate pathogenesis and identify therapeutic targets for clinical trials. The study participants will be classified according to the kidney biopsy results into one of three subcohorts, including Minimal change disease/Focal segmental glomerulosclerosis; Membranous nephropathy; and other conditions.
A consortium which aims to promote the discovery and validation of biomarkers to advance the field of CKD research. The NIDDK CKD Biomarkers Consortium brings together investigators whose expertise includes clinical nephrology, epidemiology, molecular biology, genomics, proteomics, metabolomics, systems biology, laboratory medicine, biostatistics, and laboratory test verification and qualification.
Vitamin D to Prevent Type 2 Diabetes (D2d)
A study to determine whether vitamin D supplementation is safe and effective in delaying the onset of type 2 diabetes in people at risk for the disease and to gain a better understanding of how vitamin D affects glucose metabolism.
Restoring Insulin Secretion Consortium (RISE)
Consortium which includes 3 studies, each assessing the hypothesis that aggressive glucose lowering will lead to recovery of beta-cell function that will be sustained after treatment in those with prediabetes and early type 2 diabetes.
Glycemic Reduction Approaches in Diabetes: A Comparative Effectiveness Study (GRADE)
Glycemic Reduction Approaches in Diabetes: A Comparative Effectiveness Study
A comparative study that aims to determine which combination of two medications is best for glycemic control in Type 2 Diabetes, has the fewest side effects, and is the most beneficial for overall health. GRADE is a randomized clinical trial of participants diagnosed with type 2 diabetes within the past 10 years who are already on metformin. Participants will be randomly assigned to 1 of 4 commonly-used glucose-lowering drugs (glimepiride, sitagliptin, liraglutide, and basal insulin glargine), plus metformin, and will be followed for up to 7 years.
Clinical Islet Transplantation Consortium (CITC)
Clinical Islet Transplantation Consortium
Network of clinical centers and a data coordinating center established to conduct studies of islet transplantation in patients with type 1 diabetes.
Assessment Serial Evaluation and Subsequent Sequelae in Acute Kidney Injury (ASSESS-AKI)
Assessment Serial Evaluation and Subsequent Sequelae in Acute Kidney Injury
A study which recruits patients with and without an episode of acute kidney injury during a hospitalization, and follows them longitudinally for major cardiac, renal and mortality events. An important aspect of the study is the prospective evaluation of potential biomarkers for renal and cardiac outcomes.
Integrated Islet Distribution Program (IIDP)
The goal of the Integrated Islet Distribution Program (IIDP) is to work with the leading islet isolation centers in the U.S. to distribute high quality human islets to the diabetes research community, in order to advance scientific discoveries and translational medicine.
A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like.
A database of domain-centric ontologies on functions, phenotypes, diseases and more. As a biomedical ontology resource, dcGO integrates functional, phenotypic, disease, and drug information. As a protein domain resource, it includes annotations to both the individual domains and supra-domains. Domain classifications and ontologies are organized in hierarchies, and dcGO includes the facility to browse the hierarchies: SCOP Hierarchy for browsing domains, GO Hierarchy for browsing GO terms, and BO Hierarchy for browsing other terms (mostly phenotypes). Users can mine and browse through resources.
Network helps to organize and support collaborative research related to loss of functional beta cell mass in Type 1 Diabetes (T1D). Project consists of four independent research initiatives: Consortium on Beta Cell Death and Survival (CBDS), Consortium on Human Islet Biomimetics (CHIB), Consortium on Modeling Autoimmune Interactions (CMAI), Consortium on Targeting and Regeneration (CTAR), and Human Pancreas Analysis Program (HPAP).
GDAL - Geospatial Data Abstraction Library
GDAL: Geospatial Data Abstraction Library
A translator library for raster and vector geospatial data formats that presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It includes formats such as GeoTIFF, Erdas Imagine, Arc/Info Binary, CEOS, DTED, GXF, and SDTS. It is intended to provide efficient access suitable for use in viewer applications, and also attempts to preserve coordinate systems and metadata. Python, C, and C++ interfaces are available.
A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.
A high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments. It may also be used as a batch-oriented language. Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, functions written in the Octave language, or by using dynamically loaded modules written in C, C++, Fortran, or other languages., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software library written to perform vectorized scientific computing and oriented to ease complex modelling tasks such as those typically needed within environmental models, even when involving irregular and heterogeneous data series. The Mastrave project attempts to allow a more effective, quick interoperability between GNU Octave and Matlab users by using a well documented wrap around the main incompatibilities between those computing environments and by promoting a general idiom based on their common, stable syntagms.
Eutherian comparative genomic analysis protocol
Eutherian comparative genomic analysis protocol as one framework of eutherian gene data set revisions. Protocol integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis with 3 new tests including test of reliability of public eutherian genomic sequences using genomic sequence redundancies, test of contiguity of public eutherian genomic sequences using multiple pairwise genomic sequence alignments and test of protein molecular evolution using relative synonymous codon usage statistics. Public eutherian reference genomic sequence data sets.
Sequence analysis software for filtering, mapping and OTU-picking NGS reads. SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
High Specific Oligonucleotide Design (HiSpOD)
A software dedicated to microbial ecology and environmental studies which uses individual nucleic sequences or consensus sequences produced by multiple alignments to design degenerate probes in order to target gene families covering many sequence variants. Probe specificity is assessed by similarity search against an exhaustive formatted database dedicated to microbial ecology containing coding sequences (CDS) and their putative 5-prime and 3-prime unstranslated regions (UTR). Potential cross-hybridizations identified by the program are clustered and results are organized in order to simplify user interpretation.
A database of carbohydrate antigens and matching antibodies. Epitopes and antibodies are listed within the database. Users may also search for epitopes and antibodies by keyword, epitope ID, tissue, receptor, enzyme, and other fields.
A database of experimentally-validate transcription factor binding sites (TFBS) in the Bacteria domain. CollecTF places special emphasis on providing a curation process that captures the experimental support for sites as reported by authors in peer-reviewed publications. Reported binding sites are mapped to NCBI RefSeq complete genome records. The database can be browsed by transcription factor families, NCBI taxonomy or experimental support, or through customized searches integrating these three elements.
Psychiatric disorders Gene association NETwork
Knowledge platform on psychiatric disorders and their genes. Resource for exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of database and set of analysis tools and is the result of the integration of information from DisGeNET and data extracted from the literature by text mining, followed by curation by domain experts.
UniCarb-DB structural- MS spectral library database
An experimental glycomic MS database initially created to meet the in-house need to store structural and MS-glycomic data. Users can search by taxonomy and tissue, mass and composition, and MS/MS.
Software used for detection of lesions in patients with multiple sclerosis. It provides an automated method for segmenting incident lesion voxels and allows for sensitive and specific detection of lesion incidence that can be applied to large collections of images. Using the explicit form of the statistical model, SuBLIME can be adapted to cases when more or fewer imaging sequences are available.
International effort which has created a glycomics knowledgebase with access to a database of information on the glycan structures of glycoproteins. It serves as and promotes an online information storage and search platform for glycomics and glycobiology research. Open access knowledgebase offers resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data.
An international collaborative effort to develop and enrich new and existing reference ontologies for plants, improve ontology use and cross-references, and to develop data annotation standards. Users can search for ontology terms and bioentities and submit the ontology-related term requests by visiting the following GitHub request trackers.
AML is a lightweight ontology matching system specialized on the biomedical domain but applicable to any ontology. It can be used to generate alignments automatically, as a platform for reviewing alignments, or as an alignment repair system (both automatically and interactively).
An organization of various participants and independent efforts representing four major diseases of hereditary nephrolithiasis. The Consortium facilitates cooperative exchange of information and resources among investigators, clinicians, patients, and researchers in order to improve care and outcomes for patients with rare stone diseases. The consortium promotes ready availability of diagnostic testing, pooling of clinical experiences, and availability of tissue banks in order to advance the science.
International Cell Line Authentication Committee
International Cell Line Authentication Committee (ICLAC)
An independent committee established to improve visibility of cell lines and promote awareness and authentication testing to combat false or misidentified cell lines. It contains a databases of cross-contaminated or otherwise misidentified cell lines, as well as resources to familiarize users of cell lines and the problem of misidentification. Their Terms of Reference defines false or misidentified cell lines and other commonly used terms, as well as sets out the committee goals and ground rules.
A network of clinical sites and core laboratories to accelerate discovery and innovate the way medical professionals diagnose and treat patients with previously undiagnosed diseases. It will serve to test whether this type of cross-disciplinary approach to disease diagnosis is feasible to implement in academic medical centers. It also provides clinical training of contemporary genomic approaches in diagnosing disease.
A protein database which connects multiple disparate bioinformatics tools and systems text mining, data mining, analysis and visualization tools, and databases and ontologies.
A standardized database for childrens disease classification and annotation. It is also an information exchange platform.
Muse | Portable Scalp EEG Device (Muse S Athena)
It is a portable scalp electroencephalography (EEG) system that can be used to measure brain activity. It is battery powered and has four active electrodes located at 10-20 coordinates TP9, AF7, AF8, and TP10, a common mode reference, and a driven right leg. It includes an accelerometer and gyroscope, and works with desktop and mobile EEG acquisition and visualization software. Muse 2 expands upon the first model with increasingly robust hardware.
A complete imaging software that accepts image files in various formats and serves as a host for phosphor imagers, laser scanners, scanning densitometers and similar devices. Camera support is via compatible digital cameras such as the CoolSNAP or Qimaging range. MCID Core is available as an off the shelf software solution or as part of a number of software/hardware packages optimized for specific applications.
Transformation software designed to help model and change Oracle account charts. This can be used to reorganize Oracle accounts due to events such as mergers, acquisitions, regulatory requirements and the need for more ranges when the data outgrows the range of the current chart of accounts. FlexField transforms an existing accounting flexfield segment structure, values, code combinations, and CCIDs according to user mappings, and applies the new code combinations and CCIDs. It propagates the change throughout an existing E-Business Suite data, everywhere the accounting flexfield is used. It removes the old code combinations and CCIDs, and aligns the new Chart of Accounts (COA) so that all balances belonging to a single CCID are summarized into a single line.
Used in tandem with the Navios Flow Cytometer in order to acquire data for use in analyzing cellular characteristics.
Software used for collecting and analyzing flow cytometry data. Files can be exported in FCS 3.1 format for import into other flow cytometry analysis programs such as FCS Express™ software and FlowJo™ software.
Software tool as a digital virtual microscope for viewing and moving scanned histological slides and for making annotations and measurements on them. Used in digital pathology. Helps to simplify the areas of the pathology workflow where imaging, slide digitization, storage, archivation, visualization and analysis are performed.
Imaging software for monochrome and color image acquisition and processing. It is fully integrated with Olympus microscopes, as well as third party stages and other devices, and supports various CCD and video cameras and TWAIN devices.
Statistical software for visualization, analysis and interpretation of MALDI imaging data. Its features are tailored to mining MALDI imaging data and include univariate analysis, unsupervised and supervised multivariate analysis, and preprocessing of data. Tutorials, software trainings, and example data sets can be accessed from the website.
A MATLAB toolbox for processing the functional areas of the brain using multi-modal fMRI data for pre-surgical mapping. It is composed of three types of individual-level ICA analyses for user use. Traditional ICA (task) can be used for task fMRI. Either Traditional ICA (rest) or ICA with DICI (rest) can be used for rs-fMRI. Traditional ICA (rest) is designed for users who already have a hypothesis of the pattern of the target component and want to have manually set components by themselves. ICA with DICI (rest) is completely automatic, given that the user provides a template (provided). The software utilizes an automatic component identification method that is based on the discriminatory-index. All the components from multiple ICA runs with multiple component settings are ranked and compiled.
A video-based system to detect animal movement in fear conditioning experiments, as well as movements in learned helplessness experiments. FreezeFrame can detect animal movements (as small as 1mm) and actions, including grooming, sniffing, turning, and rearing. It can also collect and process data for learned helplessness experiments, such as Tail Suspension and the Porsolt Forced Swim Test. This software can monitor animals for up to 15 times per second.
Image analysis software designed to process, measure, and analyze images on a personal computer. It is used with either an Olympus brand microscope or an Olympus brand digital camera. The AnalySiS FIVE software can be used to directly control an Olympus brand microscope or camera, take measurements, store results, and analyze the resulting images up to the particle level.
A 3D analysis software for scientific and industrial data. Avizo is used for image data processing, exploration, and analysis. This software is designed to mainly be used commercially in industries including but not limited to: material sciences, life sciences, geo-sciences, and engineering.
A microscopic image capturing software that is meant to be used in conjunction with Q-imaging cameras. Image workflow is managed using a multiple document interface (MDI). There is also a publish image feature to capture high quality images of what is on the screen, including the overlay, the region of interest, and capture of single frames in time lapses or movies.
Automated scanning software used in conjunction with the Leica DM6000B microscope to obtain whole-slide image mosaics of histological slides. When performing a scan, Turboscan or the standard scan may be used.
Software used to create phylogenetic trees through neighbor-joining, parsimony, maximum likelihood methods and bootstrap confidence tests. Specific taxonomic species groups as well as conserved regions can be defined using a mouse standard and then stored into sequence files. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria.
Software used to control and calibrate the Palm Robo Microbeam microscope according to user specified parameters. Processes such as system calibrations and correct laser settings are fully automated.
A multi-channel triggering hard-disk recording system designed specifically for bio-acoustics, although it can be used for other audio signals. This software uses real-time spectrographic and spectrum display and posesses a customizable metadata input tool for embedding user-defined data directly into the resulting .wav files. The maximum sampling rate for real-time display and streaming to disk depends on the type of acquisition board and computer performance. These embedded records can later be accessed from SASLab Pro and integrated into another metadata base.
Software for acquisition and analysis of flow cytometry data. FloMax data analysis works with data from flow cytometers that support the flow cytometry file standard (FCS). FloMax operates on computers with Windows 95, 98, and 2000., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Sound analysis software used to process and analyze animal acoustic communications. Its features include digital filtering, real-time spectrogram display, and advanced metadata management. Avisoft SASLabPro is designed to accommodate large numbers of sound files and includes organizational features, including labeling options for single point data and time section labels.
Audio recording and editing software. ProTools LE software allows sound mixing, batch fades, and other audio mixing techniques.
Bioimaging analysis software used to acquire quantitative and qualitative data from various types of biological samples. The software provides a variety of image modification features, including contrast optimizing, image printing, 1-dimensional densitometry, fragment length and molecular weight determination, and 2-D densitometry.
A consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. Their goal is to coordinate and integrate research to support the development and implementation of strategies such as de novo repair of nephrons, the re-generation of nephrons, and the in vitro engineering of a biological kidney to enhance renal repair and promote the generation of new nephrons in the postnatal organ. Investigators may apply for funding of a kidney-related project through the RBK Partnership Project. Funded projects would join the consortium.
A fully customizable program that uses a graphical user interface to locate transcription factor-binding sites in genomic sequences. xFITOM scans DNA or RNA sequences for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format, or a combination of the two.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 12,2024. A digital slide image software that is used with the VENTANA iScan Coreo Au slide scanner. This software helps facilitate viewing high quality images with little latency. The image view software can also support the viewing of multiple images simultaneously.
An image analysis software that can process spectra and other multi-dimensional data-sets. The software package is aimed at processing large data sets from (cryo-) electron microscopy, especially in the field of single particle analyses. This software can be used with light and raster-tunneling microscopes, computer tomographs, FT-IR spectrometers and other signal collecting devices. This resource provides three-dimensional data processing and angular reconstitution modules that allow the three-dimensional reconstruction with point-group symmetry from the two dimensional electron microscopy projections. These models aid in the analysis of the macromolecules.
A technical computing software and computing environment that provides users with algorithms and mathematical functions for various projects and purposes. The resource incorporates other Wolfram products such as Wolfram Algorithmbase, Wolfram Language, and Wolfram Knowledgebase.
Mathematical software that can compute both numeric and symbolic solutions. It can be used to analyze, explore, visualize, and solve mathematical problems.
Online Application for Survival Analysis (OASIS)
Online Application for Survival Analysis
A tool for various statistical tasks involved in analyzing survival data which provides a uniform platform to facilitate efficient statistical analyses of survival data in the aging field. The statistical features of OASIS include the calculation of Kaplan-Meier estimates, mean/median lifespan, mortality rate, Mantel-Cox Log-Rank test, Fishers exact test, weighted Log-Rank test, Kolmogorov-Smirnov test and Neymans smooth test. Moreover, OASIS generates survival and mortality curves that can be easily exported and modified by using common graphic softwares.
A company that provides a variety of next generation sequencing services. The company provides researchers with whole genome resequencing, exome sequencing, targeted sequencing, transcriptomics, and epigenome sequencing.
Software for automatic quantification of in vivo proton MR spectra. Though it is mainly used for brain analysis, it can be used for a variety of analyses in different areas of the body. It receives time-domain data as input and gives a one page summary output. It is fully automatic, non-interactive, and operator-independent., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A method to automatically extract the neurite centerline and compute orientation properties at multiple scales using source code. Code is dependent on standard Python-based scientific packages and presegmentation of images.
Cerebellar Development Transcriptome Database CDT-DB
A platform that allow users to visualize and analyze transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain. Users can search for cerebellar development genes by name, ID, keyword, expression, and tissue specificity. Search results include general information, links, temporal, spatial, and tissue information, and gene category.
A live cell imaging software that allows for control of iXon EMCCD and sCMOS cameras in synchronized combination with a number of additional imaging hardware devices. iQ can be used to run experiments to investigate dynamic processes in both single cells and multicellular systems, image fixed samples, and generate 3 dimensional image volumes for analysis.
A software designed to aid in macro or micro photography using the focus-stacking technique. It takes multiple shots at many different focus distances and combines the images to a fully focused image.
A technical graphing software that can be used to create various graph types including 2D or 3D plots, statistical graphs, pie charts, contour plots, and surface plots. The user can customize the graph, axes, legend, and plots.
A software for managing, testing, and drawing primers. The software can locate primers for target sequences, calculate the quality score, predict amplified fragments and dimers, and create graphic representations of the primers.
A software for analyzing digital assay data. The software performs RNA quality control, comparison between multiple chips, smear analysis, and data export in multiple formats.
FunRich: Functional Enrichment analysis tool
A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts.
A software for performing fast scan cyclic voltammetry recordings in brain tissue for detection of neurotransmitters. It was written in the LabView programming language and can be used to provide command voltage to equipment and record the resulting waveforms. The analysis portion of the software can view and export data, apply noise filters, perform chemometric and waveform kinetic analysis, and create figures.
An imaging software for collecting and analyzing astronomical image data. This software includes observatory integration, and control of astronomical equipment to integrate the researcher's camera, autoguider, filter wheels, focuser, camera rotator, telescope mount, observatory webcam, remote switches, weather station and dome.
A toolkit for mapping brain entropy using fMRI. It uses several functions from ASLtbx. At its core, the toolkit is a collection of batch scripts that implement a pipeline for processing fMRI data in order to get Sample entropy for each voxel.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. A full service viral vector core facility located at the University of Pennsylvania. This facility provides technological resources for investigators in their use of viral based vectors for gene transfer. The main objective of this core is to provide investigators with state-of-the-art vector technology for preclinical studies and other basic research applications, that will then increase understanding of gene function and the further development of therapeutic vectors.
Software for identifying, characterizing, and quantifying proteins in biological samples. Can be used for range of proteomics workflows such as protein and peptide identification, PTM analysis, and isobaric mass tagging for quantification. Supports multiple database search algorithms and multiple dissociation techniques., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software for spike waveform-to-cell classification which can be used both online and offline. The user can identify and isolate clusters/cells using 3D manipulation, as well as calculate waveform parameters like peak, valley, area, and energy.
A vector graphics software which runs on Windows, Mac OS X and GNU/Linux. It can import and export various file formats, including SVG, AI, EPS, PDF, PS and PNG. Features include object creation, object manipulation, color editing, and text editing.
A program for cluster analysis by fitting a mixture of Gaussians. KlustaKwik works by implementing a hard EM algorithm with unconstrained covariance matrices. It was designed for the specific problem of spike sorting of multi-electrode arrays, but can be used for any application.
A software tool for automated analysis and quantification of fluorescent microscopy images of nerve cells in vivo and in vitro. The tool also can be used for analysis of cell morphology, neurite length analysis for sections with no cell body, and ganglion explant analysis.
A software for analyzing animal movement on videos and images. The user can define the animal's joints so the software can analyze using a tracking algorithm.
A statistical software package that allows the user to import data, create graphs, and perform statistical analysis. It can perform basic statistical tests like descriptive statistics, hypothesis tests, confidence intervals, and normality tests as well as regression and ANOVA and quality assessment.
An application for extracting numerical data from pictures. It can be used to view the original data values (x,y) from printed graphs. The user can perform basic operations like cut, copy, paste as well as select axes colors, zoom in or out, remove noise, re-calibrate the y-axis, and insert, edit or move points. It offers support for GIF, JPEG, and PNG files.
A quantitative proteomics software package for analyzing large-scale mass-spectrometric data sets. It is a set of algorithms that include peak detection and scoring of peptides, mass calibration, database searches for protein identification, protein quantification, and provides summary statistics.
A software for analyzing real-time PCR data and quantifying DNA targets. It can perform copy number analysis, report confidence in copy number, display data in table and graphic format, change analysis parameters, and view data analysis information for multiple experiments at once.
A computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. It incorporates earlier programs including Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a discrete number of states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, ancestral states and correlations among pairs of traits., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A bioinformatics software for editing, annotating, and analyzing DNA, RNA, and amino acid sequences. It includes analytical tools and can be expanded with homology search, multiple alignment and base calling, and sequence assembly (Phred/Phrap) modules.
A software for acquiring and analyzing flow cytometry data. The user can create plots with elements like regions, gates, statistics, markers, and annotated text. The software can also be used for batch analysis or quality control of analysis. Results can be exported and saved., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software for primer design. The user can choose the target sequence or gene and design primers for the real-time PCR. After, the user can examine the results and choose from the recommended probes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software suite for creating, editing, composing, and converting bitmap images. It can read and write images in over 200 formats including PNG, JPEG, JPEG-2000, GIF, TIFF, DPX, EXR, WebP, Postscript, PDF, and SVG. The user can use this software to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.
A software for (scanning) transmission electron microscope experimental control and analysis.
A software package for quantification of histological sections. This software performs functions including: management and analysis of regions of interest, annotations, statistical analysis, and 3D visualization. These results are edited in an Excel-compatible spreadsheet.
A single point video tracking system. It uses the center of the mass of the animal and tracks it over the course of the experiment to determine location, distance traveled, velocity etc. Examples of applications include: Open Field, Novel Object Recognition, Maze Analysis, Morris Water Maze, Barnes Maze, Place Preference, etc.
Software for detecting the onset and completion of freezing behavior of a rodent. It outputs the freezing behaviors as a sequential list, allowing for further statistical analysis. Freezescan detects freezing behaviors, random intervals, interval freezing, and activity levels. It also detects animal activity during the experiment and can output in quantitative and graphical form.
A statistical process control (SPC) add-in for Microsoft Excel. The user can select their data and the program will draw the desired chart or run the desired statistical test.
A data acquisition and analysis software program. The program collects data from sensors and receivers and displays graphical data analysis as well as descriptive statistics.
Predicting Language Outcome and Recovery After Stroke (PLORAS)
A research project investigating the difficulties of recovering language after stroke (aphasia). The overall aim of the study is to give future stroke survivors accurate predictions of their aphasia recovery by creating clinical tools and discerning why some patients recover from aphasia better than others.
A toolkit for EEG-fMRI multimodal fusion and fMRI data preprocessing and analysis. NIT allows users to perform batch processing of fMRI data analysis and data preprocessing based on SPM8, as well as parallel computing for data preprocessing, nuisance signals removal, and FCD and FOCA calculating. Users can also use NIT to calculate functional connectivity density and four dimensional (spatio-temporal) consistency of local neural activities.
cell line identification testing; cell authentication
Genetica DNA Laboratories Cell Line Authentication
A material analysis service of the commercial organization Genetica DNA Laboratories which provides authentication of human cancer cell lines, stem cell lines and xenografts utilizing STR DNA technology.
A persistent unique identifier for samples and specimens collected from the natural environment. IGSNs are created by the user and are case sensitive. They should be concise, machine readable, and non-derivable to ensure originality. IGSNs were created and are organized by the IGSN e.V., whose goal is to implement and promote standard methods for locating, identifying, and citing physical samples with confidence by operating an international IGSN registration service with a distributed infrastructure for use by and benefit to its members.
A commercial biomaterial analysis service dedicated to developing antibody protein sequencing and characterization technologies. The main service it offers is antibody de novo sequencing. Both heavy and light chains are directly sequenced using multiple enzyme digestion and high resolution LC-MS/MS. The sequencing process does not require hybridoma, mRNA, or other sequence information. Rapid Novor also offers to make recombinant versions of antibody proteins sent in for sequencing.
A database which provides results of comprehensive immunogenomic analyses of next generation sequencing data for 19 solid cancers from The Cancer Genome Atlas and other datasources. The database can be queried for the gene expression of specific immune-related gene sets, cellular composition of immune infiltrates (characterized using gene set enrichment analyses and deconvolution), neoantigens and cancer-germline antigens, HLA types, and tumor heterogeneity (estimated from cancer cell fractions). It also provides survival analyses for different types immunological parameters.
A set of software tools used for morphometric analysis and visualization of the 3D structure of neurons. Py3DN works exclusively with data collected with the commercial system Neurolucida.
A database which indexes preprints from arXiv q-bio, PeerJ Preprints, Figshare, bioRxiv, F1000Research, and The Winnower.
Molecular biology software for DNA cloning and analysis and construct preparation. Serial Cloner provides tools for analyzing and manipulating sequences and assists in setting up new sub-cloning projects and in preparing electronic versions of these constructs. The software reads and writes DNA Strider-compatible files and imports and exports files in the universal FASTA format.
Genomic Data Commons Data Portal (GDC Data Portal)
A unified data repository of the National Cancer Institute (NCI)'s Genomic Data Commons (GDC) that enables data sharing across cancer genomic studies in support of precision medicine. The GDC supports several cancer genome programs at the NCI Center for Cancer Genomics (CCG), including The Cancer Genome Atlas (TCGA), Therapeutically Applicable Research to Generate Effective Treatments (TARGET), and the Cancer Genome Characterization Initiative (CGCI). The GDC Data Portal provides a platform for efficiently querying and downloading high quality and complete data. The GDC also provides a GDC Data Transfer Tool and a GDC API for programmatic access.
A web-interface that enables users to access and download the processed ChIP chip/seq data of nuclear receptors, co-regulators and histone modifications. The web resources also includes processed differential expression data under ligand induction in conditions matched to ChIP_chip/seq data whenever possible. All the ChIP chip/seq peak regions are annotated with enriched HRE and co-regulator motifs. A list of predicted hormone response genes from integration of nuclear receptor ChIP chip/seq data and differential expression data is also readily available to the users.
A European organization primarily concerned with the study of renal disorders. The organization is working towards discovering the genes responsible for renal development, renal disease and the related proteins and their actions. EuReGene consists of a consortium of scientists, clinicians, and SME partners that study functional genomics and their application in kidney research.
SCGAP Urologic Epithelial Stem Cells Project
A research organization which aims to conduct a variety of stem cell research projects. These projects include: to CD phenotype the human prostate and bladder using a confocal microscopy, to CD the phenotype of the mouse prostate and bladder, to profile samples of basal and stromal cells using uncultured cells, to confirm cell-type specific expression of genes that were identified by array analysis, and to create a database with the resulting database.
A database which can be used to search for genes critical for a variety of Genito-Urinary system functions and diseases.
A multi-modal multivariate pattern analysis of neuroimaging data in Matlab / GNU Octave. Links to examples, exercises, and information for developers are available on the main page.
Software for interfacing with Tucker-Davis System 3 hardware. It is a Python wrapper around Tucker-Davis Technologies ActiveX library. Along with standard operations, the software can conduct type conversions between analog and digital units, handle robust errors, and has a remote procedure call server that allows multiple processes and/or programs to communicate with the hardware across the same connection.
A software system to assist with cloning simulation, enzyme operations, and graphic map drawing. Clone Manager can also be used as a way to view or edit sequence files, find open reading frames, translate genes, or find genes or text in files. Clone Manager Professional is an upgraded version of Clone Manager Basic., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Cornell Heart Lung Blood Resource for Optogenetic Mouse Signaling (CHROMus)
Cornell Heart Lung Blood Resource for Optogenetic Mouse Signaling
A transgenic mouse supplier which develops mouse lines expressing genetically encoded calcium indicators (GECIs) and optogenetic effectors in lineages relevant to cardiac, vascular, lung and blood diseases. The mouse strains created are designed to allow for inter crossing resulting in co-expression of sensors with discrete emission wavelengths in interacting lineages (e.g. endothelial and smooth muscle cells), as well as optically compatible effector/detector pairs.
A Python package for doing linear mixed model associations in genome wide association studies (GWAS). The software corrects for population structure using EMMA.
Software to manage Seahorse XFe24 Analyzer, which measures OCR and ECAR of live cells in a 24-well plate format. Users can create and modify assay templates and analyze and manage data.
A startup research, development and innovation company based in The Grand Duchy of Luxembourg working on four major areas: Open Research, as Information Hub; Information Technology, as The Common Brain; Collective Awareness, as Manifesto; and Biophysics, as Human Extensibility. The Information Hub researches a methodology to conduct open research using a collaborative approach designed for multi-disciplinary interventions, multi-scope goal alignment, advanced analytics and a unified research experience for international cooperation. The Common Brain researches an open source intelligent architecture for future internet, one that is deeply sustainable over a highly distributed hybrid network, self-governed, heterogenous, and logical. Manifesto researches a methodology for a collaborative approach for policy making, open standardization, accreditation, verification and compliance. Human Extensibility researches the establishment of the scientific ground for a field of science concerned with the study of the physics and physiology of the human being, to provide techniques and genetic algorithms for human extensibility.
A test-driven framework for formally validating scientific models against data.
Stanford Center for Cognitive and Neurobiological Imaging
Stanford Center for Cognitive and Neurobiological Imaging (CNI)
A shared facility at Stanford University dedicated to research and teaching for researchers and students in cognitive and neurobiological sciences. The core instrumentation provided by the CNI is a research-dedicated 3T MRI scanner, a GE Discovery MR750. The CNI has an array of MRI Coils, including Nova Medical 32-channel and 16-channel head coils and a GE 8-channel head coil. For stimulus delivery they provide a custom large-screen flat-panel display as well as a goggle system with eye tracker and audio. Other equipment includes an MR-compatible 256-channel EEG system, a Polhemus 3D digitizer used for EEG electrode localization, Fiber Optic Response Devices (FORP), as well as a MRI Simulator (Mock Scanner).
A customized software application that generates a Global Unique Identifier for each study participant. The GUID is a universal subject ID that allows researchers to share data specific to a study participant without exposing personally identifiable information (PII). The GUID has been approved by the NIH Office of General Counsel.
A google drive interface for scientific big data. CyVerse cyberinfrastructure is applicable to all life sciences disciplines and works equally well on data from plants, animals, or microbes. It provides life scientists with computational infrastructure to handle large datasets and complex analyses. Its extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, and APIs.
Provides access to resources T1D researchers need to conduct clinical studies. Data sets from their clinic registry is openly available, as are new study results. They also offer use of T1D Discovery Tool, which allows users to search different fields from registry data, and T1D Exchange Biobank, which offers specimen types such as serum, plasma, white blood cells, DNA, and RNA.
A repository of human tissue samples collected during the LANDMark study (Longitudinal Assessment of Neuropathy in Diabetes using novel ophthalmic markers). The LANDMark Biobank longitudinal dataset contains blood and tissue (skin) samples and matching detailed phenotypic data of three microvascluar complications of type 1 diabetes: neuropathy, nephropathy and retinopathy.
Diabetes Research Centers (DRC) is an integrated program of diabetes, endocrinology and metabolism research.
A collection of big data analytics tools. FlashX performs data analytics in the form of graphs and matrices and utilize solid-state drives (SSDs) to scale to large datasets in a single machine. It has three main components: FlashGraph, FlashMatrix, and FlashR. FlashGraph is a general-purpose programming framework with a vertex-centric programming interface for large-scale graph analysis. FlashMatrix is a matrix computation engine that provides a small set of generalized matrix operations to express varieties of data mining and machine learning algorithms. FlashR is an extension of the R programming framework to process datasets at a scale of terabytes with the speed of optimized parallel C code.
A program that searches PubMed to generate a heat map using a user's search terms. It also allows you to see over the years how many publications there are with the user's search term(s).
A community encyclopaedia that links brain research concepts with data, models and literature from around the world. It is an open project where users can participate and contribute to the global research community.
NIRStar - NIRS Acquisition Software by NIRx
Commercial software tool designed to function as a multiplatform instrument controlling environment for NIRx products. Its features include the ability to run full or partial sensing configurations, montage views and viewing options, and a real-time system status reporting display.
A commercial cap product that records fNIR signals from the participant. NIRSport integrates for concurrent measurements with EEG, fMRI, eye-tracking, cochlear implants, TMS, tDCS, EMG, pulse oximetry, and other modalities for concurrent measurements. Researchers can conduct tandem studies with two separate systems synchronized to operate simultaneously.
A database of protein disorder and mobility annotations. The database features three levels of annotation: manually curated data (which are extracted from the DisProt database), indirect data, and predicted data. Additional annotations are included from external sources, including UniProt, Pfam, PDB, and STRING.
DataJoint: Data management for science labs
MATLAB and Python 3 high-level programming interface for MySQL databases to support data processing chains in science labs. Specifically designed to provide robust and intuitive data model for scientific data processing chains.Used for scientific data pipelines and workflow management.
A tool that allows users to search for appropriate, commercially available antibodies for research purposes, and to match each antibody to its respective genomic identifiers. The antibodies are screened by Western blot and the results are listed on AbMiner. AbMiner also includes the diluitons used and vendor information for all antibodies. Users can conduct general or advanced searches and browse antibodies by gene.
European College of Neuropsychopharmacology - Preclinical Data Forum Network
Preclinical Data Forum Network of the ECNP
Preclinical Data Forum Network of the European College of Neuropsychopharmacology
A forum for preclinical data sharing and interpretation to enhance its utility for clinical research and development. The forum allows researchers to communicate and collaborate on modern preclinical issues and data sharing.
A framework for generating Tract Profiles of tissue properties for major fiber tracts in healthy and diseased brains. Online documentation can be found at: https://github.com/yeatmanlab/AFQ/wiki. AFQ has been tested for MATLAB r2009b through MATLAB r2014b. It requires functions from the MATLAB stats toolbox, vistasoft and SPM.
A software to apply modeling techniques directly to individual pixels within an image and create a parametric map from it. The resulting outcomes show the values within the model parameter in each image pixel. This is used to make quantitative tissue properties easier to visualize and compare with information from other sources. Furthermore, the quantitative maps can then be statistically analyzed within the software using a step-by step method. This tool is designed to be used with the PKIN tool.
A software used for quantitative Western blot imaging and analysis. This software is compatible with several dyes and kits, providing extra flexibility for application. This software is designed to be able to look at multiple proteins simultaneously on a single assay. This software is sensitive enough to distinguish co-migrating proteins, such as phosphorylated and unphosphorylated isoforms.
An imaging system that can be used in lieu of conventional light microscopy. The specimen, rather than being viewed through the eyepiece of the microscope, is displayed a monitor after the system has scanned it at the desired resolution. This is done by a series of scans of single images acquired through the scanning process being automatically stitched together to make the ultimate seamless overview image through the "virtual slide". The digital images can be saved to a web-based database so that it can be accessible for online conferences.
Software suite for image acquisition and analysis. The software can be paired with high-quality cameras to maximize output quality and export it for sharing and research applications.
A non-profit organization that awards grants to a broad spectrum of charities, including those that benefit spinal cord injury efforts. The Foundation is primarily dedicated to funding extensive research, education and quality of life programs for improving the lives of people affected by spinal cord injury.
Aging Dementia and Traumatic Brain Injury Study
The Aging, Dementia and Traumatic Brain Injury Study is a detailed neuropathologic, molecular and transcriptomic characterization of brains of control and TBI exposure cases from a unique aged population-based cohort from the Adult Changes in Thought (ACT) study. The study contains six data sets: histology and immunohistochemistry, in situ hybridization, rna-seq, protein quantification by luminex, isoprostane quantification, and specimen metadata.
A portal that provides visualization, analysis and download of large-scale cancer genomics data sets.
European Infrastructure for Biological Information Tools
Elixir Interoperability Platform to help people and machines to discover, access, integrate and analyse biological data. Encourages life science community to adopt standardized file formats, metadata, vocabularies and identifiers and works internationally to achieve its goals. Bioinformatics resource registry that provides scientific and technical information about analytical tools and data services for bioinformatics. Gateway to databases and tools for life science data analysis.Provides comprehensive and up-to-date catalogue of resources that are interactive and downloadable, and that offer programmatic access. The registry also allows the community to upload their own resources to the registry following a simple log in procedure.
A Python library which provides Python access to and interaction with Galaxy's API and CloudMan. The library allows users to create a CloudMan compute cluster via an API and directly from a local machine, reconnect to an existing CloudMan instance and manipulate it, and interact with Galaxy via a straightforward API and an object-oriented API. The library itself can be used with either service irrespective of the other.
A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass.
An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Transgenic Huntington's Disease Monkey Resources
Transgenic Huntington's Disease Monkey Resources (THDMR)
Center for resources to facilitate basic and preclinical applications of the transgenic Huntington's disease (HD) monkey model to advance scientific knowledge and the discovery of a cure for HD. Their resources include longitudinal biomaterials and MRI data, postmortem biomaterials, and research proposal assistance.
A structural folding computational tool. The method is based on the assembly of supersecondary structural fragments taken from highly resolved protein structures using a simulated annealing algorithm.
linkRbrain: online tool for neuroscience
An online tool for managing and viewing datasets. Data can be viewed in 2D or 3D with activation points as points clouds or projections on the cortex surface. Data can be imported as a NIfTI file or a list of activation peaks and results can be exported as a PDF file.
Extensible Simulation Package for Research on Soft matter (ESPResSo)
Extensible Simulation Package for Research on Soft matter
A highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems like DNA and lipid membranes.
Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers.
A software that is used to analyze image stacks of biofilms that were recorded by confocal microscopes. While this program does not have any statistical calculation methods, it can extract a number of quantitative parameters from the images. This software was initially developed by Arne Heydorn and Bjarne Ersboll as a MatLab script until it was expanded into an independent software in 2008.
A software used to process stacks of digital images. All of the resulting images are processed to have the same dimensions and then are consolidated into a single image.
Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions.
A software for volume visualization that can be used by researchers to explore and analyze medical and scientific data. This software uses a variety of tools to load and visualize the data on either a 2D or 3D display. Theses tools include volume rendering, maximum intensity projections and oblique reformatting. Visualizations can be saved mid-session and be reopened at a later time.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 18, 2018; A software which provides unbiased stereological estimates of numbers, lengths, areas, and volumes present in images that were captured by microscopes or virtual slides. This software is intended to estimate structural information in a 3D format from 2D tissue sections. There are other software tools at this company, but they have either changed names or are simply different software tools.
Swedish Information Centre for Rare Diseases
Swedish Information Center for Rare Diseases
A database which contains detailed information rare diseases. The information is produced in collaboration with leading medical specialists and patient associations. New disease descriptions are added continuously and the texts are updated on a regular basis. Both the common names and the technical names for diseases are provided.
National Organization for Rare Disorders (NORD)
National Organization for Rare Disorders
An organization which supports those with rare diseases and those researching rare diseases.
A database which provides brief introductions of rare diseases. New topics and diseases are added with the help of rare disease medical experts. This is mainly targeted at patients and their families but has useful information for professionals.
Automation software used to analyze fear behavior in rodents. Freezing is represented in the data file in several different ways, including the total time the subject spends motionless during the session, the percent of time motionless, the number of freezing episodes or occurrences, or as an average index of motion.
Software designed to perform high-speed molecular dynamic simulations of biological systems on conventional commodity clusters, supercomputers and GPUs. This code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms with a large number of processors. It can be used with a single computer.
Brain Images of Normal Subjects (BRAINS) Imagebank
Brain Images of Normal Subjects Imagebank
A searchable collection of anonymised images and associated clinical data. It includes normal individuals at all ages (from prenatal to old age). The image bank contains integrated data sets already collected as part of research studies which include control subjects. New data is added as they become available.
A database for storing and efficiently retrieving realistic computational models of brain microcircuits and networks. The focus is on microcircuits that are based on experimentally demonstrated properties of neurons and their connectivity.
A repository of the results of the efforts of the scientific community in computationally elucidating the structure of the olfactory receptor with a view to establishing a mechanistic basis for OR-odorant binding.
A data analysis software developed to simplify and record data from fluorescent related assays such as Western Blots, EMSAs, and Western Assays. This software will consolidate all of the resulting data into one easy-to-track image, and thus removes the need for multiple exposures, as well as standardizing the resulting fluorescent bands without image saturation, blowout, or removed sensitivity. Odyssey CLx is capable of scanning multiple mini-blots, microplates, or slides at the same time.
An add-on tool used to export data retrieved with the MC_Rack program. This software is used to convert MC_Rack data files into other file formats.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Database built up with software and services that maintains multiple versions of terminologies, map sets, and values sets concurrently. HDD Access has superseded Concept Hub.
A software which is used to acquire physiological data from the HEKA Patch Clamp Amplifiers and HEKA interfaces.
Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis.
A software which is used to control the LAS-1000plus luminescent image analyzer. This software adjusts the focus, exposure time, sensitivity, and cooling temperature, and will record the data after the sample is scanned.
Software tool which deletes non-brain tissue from image of the whole head and estimates both internal and external skull surfaces.
THIS RESOURCE IS NO LONGER IN SERVCE, documented January 19, 2022. Software used to control the Zeiss Axioskop microscope.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. A software which collects, displays, and analyzes chromatographic signals. This software doesn't require any programming, and collects signals from one or two detectors. PowerChrom is supplied as part of the PowerChrom system, or separately for use with e-corder recording systems.
A programming library that uses standard graphics cards to produce 2D and 3D visual stimuli for vision research experiments.
Software used to automate the process of presenting stimulus signals and acquiring signal data. The software is designed to work with System 3 hardware and files generated by TDT's signal design software SigGenRP.
A software which tracks the number of occurrences and duration of up to 16 defined events. The user can group events together so that turning on one event in a group will automatically turn off other active events in the group. Sessions can end after a fixed length of time, or the sessions can be ended manually, At the end of the session, the data can be saved in a comma-delimited file which can be easily imported into a spreadsheet application.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 24, 2016. A software which is used with gel electrophoresis analysis and is used with the Ettan DIGE system. This system allows the option of reference to the internal standard for each spot, which ultimately eliminates gel-to-gel variation, and gives quantitation. This gel comparison method introduces nearly zero statistical error.
A software which acquires and processes data sets, primarily through the Xcalibur system.
A a configurable software package for peptide and protein mass spectrometry analyses. It includes the SEQUEST search algorithm to identify separate proteins in complex mixtures, interactive navigation tools to filter and sort protein summaries, customized spectral plots, and chromatograms using the PEPMATCH and PEPMAP tools. This software also has batch processing capabilities to improve throughput by queuing up several files, and custom-build proprietary databases, index databases, and retrieve databases through a public server.
A statistical software which can be used for basic statistics, experimental design, sample size calculations, and analysis of linear mixed models, time series, and spatial analysis.
Applied Biosystems 7500 Real-Time PCR Software
A software used to control and operate the Applied Biosystems 7500 Real-Time PCR system.
Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.
Gel analysis software which can be used on a PC with TWAIN-compatible scanners without specialty equipment. Users scan or load an image which can then be calibrated. SigmaGel allows users to make lane measurements, spot measurements, and molecular weight measurements. After data analysis was completed, users can print or copy and paste data and images.
An interactome of protein-protein interactions related to schizophrenia, it contains novel PPIs predicted with the HiPPIP model. Schizophrenia associated genes are gathered from GWAS genes, historical candidates, and OMIM. Members of the scientific community can also suggest genes to add to the interactome.
National Animal Germplasm Program (NAGP)
A national germplasm database where users can donate or request germplasms from a variety of non-human animals, including fish, invertebrates, bison, elk, pig, turkey, and yak. Germ plasm types include white blood cells, embryo, heart, larvae, liver, muscle, oocyte, ovarian tissue, DNA, red blood cells, semen, skin, sperm, spleen, testicular tissue, and blood.
Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables.
A tool used to screen for core gene sets as an indicator of completeness of draft genomes. The download includes a Perl script and required archaeal and bacterial core genes fasta and cluster files.
Rapid Annotation using Subsystem Technology
Rapid Annotation using Subsystem Technology Server
A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.
A GUI software package to help non-expert statisticians conduct multivariate analysis methods. Various multivariate analysis methods are available, including correspondance analysis, aglomerative hierarchical clustering, related multidimensional scaling, and discriminant analysis (linear, quadratic or distance-based).
An API and software suite for large scale data visualization and analysis.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A statistical software package for comparing metagenomic datasets and clinical data sets comprised of two treatment populations, with each treatment population being made up of multiple samples. It relies on a non-parametric t-test.
Microbiome Utilities Portal of the Broad Institute
A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.
Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP
An R-package which uses Dirichlet-Multinomial distribution to perform formal hypothesis testing on the species abundance distribution of human microbiome data, and to calculate power and sample size requirements for human microbiome experiments.
HMPTrees - Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data
Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data
An R-package which uses Object Oriented Data Analysis (OODA) methods to analyze taxonomic trees directly, providing tools to model, compare, and visualize populations of taxonomic tree objects.
A rapid and sensitive general-purpose k-mer search tool.
A software package for speciation of 16S sequence data.
THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample.
THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. Provides a suite of tools for the comparison of microbial communities using phylogenetic information.
An interactive data visualization tool which allows users to create and upload pictures of their study site, load diversity analyses, and display both diversity and taxonomy results in a spatial context.
A tool that discriminates between human reads and microbial reads without performing an alignment of all reads to the human genome.
HMP Unified Metabolic Analysis Network (HUMAnN)
A pipeline which takes short DNA/RNA reads as inputs and produces gene and pathway summaries as outputs. The pipeline converts sequence reads into coverage and abundance tables summarizing the gene families and pathways in one or more microbial communities.
A statistical package for comparing metagenomic data-sets at the pathway level. It relies on a combination of metagenomic sequence data and prior metabolic pathway knowledge, which is pulled from KEGG.
Center for Therapeutic Target Validation
Centre for Therapeutic Target Validation
A public–private initiative that supports research that provides evidence on the biological validity of therapeutic targets and that gain insight into the effectiveness of pharmacological intervention. It aims to provide a research and development framework that applies human disease. It shares its information openly.
A BioJS viewer for protein sequence features.
Software package with tools which assemble, identify, and provide access to subsets of data in a large and complex data collection workflow. The software utilities work primarily with BagIt packages that conform the BDDS Bagit and BDDS Bagit/RO profiles. JSON-LD is used to provide a standard way for linking metadata with existing ontologies and vocabularies.
International Human Epigenome Consortium Data Portal
International Human Epigenome Consortium (IHEC) Data Portal
A data portal of the International Human Epigenome Consortium which provides access to comprehensive data sets of reference epigenomes relevant to health and disease. The IHEC Data Portal can be used to view, search and download data already released by different IHEC-associated projects. Data are organized by consortium, by tissue, and by assay category. Users can visualize data sets using the data grid provided or the UCSC Genome Browser.
clValid - Validation of Clustering Results
clValid: Validation of Clustering Results
An R package which contains functions for validating the results of a clustering analysis.
Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation.
Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Web phylogeny server based on the maximum-likelihood principle.
Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output.
(Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists
(Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT)
Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Prediction of Intrinsically Unstructured Proteins
Prediction of Intrinsically Unstructured Proteins (IUPRED)
A web server which recognizes tertiary structures from an amino acid sequence based on estimated pairwise energy content. Users can input SWISS-PROT/TrEMBL identifier or accession number, or paste the amino acid sequence.
Metabolomics Workbench Metabolite Database
UCSD Metabolomics Workbench Metabolite Database
A database which contains structures and annotations of biologically relevant metabolites from public repositories such as LIPID MAPS, ChEBI, HMDB, PubChem, and KEGG. Users can search for molecular structure based on substructure, text, or mass.
National Institutes of Health (NIH) Common Fund Metabolomics
A US national program which supoorts the development of technologies in order to enhance the metabolomics field. It specifically increases the national metabolomics research capacity by supporting five core programs: Training in Metabolomics, Metabolomics Technology Development, Metabolomics Reference Standard Synthesis, Metabolomics Data Sharing and International Collaboration, and Comprehensive Metabolomics Resource Cores.
A statistical data analysis tool that works with Microsoft Excel and is designed especially for use in IOS systems. Tutorials and examples are provided within the program.
Software used to compute truncation thresholds, pair of spike detection thresholds that are used for separating extracellular neural recordings into two segments consisting of signal and noise, using truncated probability distributions.
A library of open source teaching and educational resources for professors and students. It includes resources such as textbooks, lesson plans, multimedia, and lectures from participating universities and institutions. Subject areas include the life sciences, the arts and humanities, law, social and behavioral sciences, medicine and health, engineering, education, the physical sciences, and mathematics. Users can share their own work and adopt others' on the platform.
Interactive software application used for manual image registration (e.g., aligning, scaling, warping) of ssLM and ssTEM images. Users place control points in one image, and these points' locations are predicted on a moving or warped second image. Transform parameters are updated once the user adjusts and corrects the predicted points on the second image.
Network for Pancreatic Organ Donors with Diabetes
Network for Pancreatic Organ Donors with Diabetes (nPOD)
The Network for Pancreatic Organ Donors with Diabetes
A collaborative research project that supports nPOD approved diabetes investigators by freely providing rare and difficult-to-obtain tissues from type 1 and type 2 diabetes donors. Interested researchers are encouraged to apply to obtain nPOD tissues, or to request access to analyze cases in the nPOD Online Pathology site. Interested donors can contact nPOD directly for more information.
Web based resource focused on the genetics and genomics of immunologically related human diseases. Their mission is to provide a curated and integrated set of datasets and tools to support and promote research in this area. The current focus of the site is to integrate and curate summary case/control association statistics from the consortium of 12 diseases originally targeted by the ImmunoChip consortium.
Scientific Data Analysis and Visualization (SciDAVis)
Interactive application for data analysis and visualization in the form of plots. Its main feature is its usability and its simple graphical user interface. SciDAVis runs on GNU/Linux, Windows and MacOS X.
KLayout - High Performance Layout Viewer And Editor
A GDS and OASIS file viewer editor that has file overlay and file creation capabilities. It features include: layer grouping, flexible rulers, image overlay, partial editing functions, and external library support.
Core facility that utilizes a ThermoFisher Cellomics ArrayScan VTI instruments and associated automated cellular analysis software. The High Content Screening (HCS) Core provides a multiplexed functional screening and imaging platform to perform multi-well cell-based assays.
A machine usable dictionary containing thousands of words, each with linguistic and psycholinguistic attributes (psychological measures are recorded for a small percentage of words). The dictionary may be of use to researchers in psychology or linguistics to develop sets of experimental stimuli, or those in artificial intelligence and computer science who require psychological and linguistic descriptions of words.
An open source library built to reduce technical friction and help modelers share their work. Models within SSM can be used for inference of time-series analysis.
NIH network designed to follow and help conduct clinical trials and research studies investigating acute stroke treatment, stroke prevention, and stroke recovery and rehabilitation. Clinical trials are listed once they are reviewed, approved, and ready for volunteer recruitment.
Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols.
3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders.
Human Integrated Protein Protein Interaction Reference
Human Integrated Protein-Protein Interaction rEference
Human Integrated Protein-Protein Interaction rEference (HIPPIE)
Web tool used to generate confidence scored and functionally annotated human protein-protein interaction networks. Users can run a protein query using a UniProt identifier (ID or accession), gene symbol or Entrez gene id, or a network query using set fields.
Spike detection algorithm that is improvement to native spike detection algorithm of Wave_clus spike sorting software. Software patch that incorporates Taller Peaks algorithm into Wave_clus as optional spike detection algorithm for single wire data.
Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Tool for the classification of known transposable elements in eukaryotic genomes. It can be combined with ab initio repeat finding in order to recover contrasting transposable element landscapes between species.
Genome sequence classification tool based on kmer. The code allows users to build nucleotide databases and protein databases, classify reads, construct binner databases, and create taxonomic relationship files. The website provides information on how to perform these actions with code, though users can access a web-based Taxonomer if they need/want to.
Program to Assemble Spliced Alignments (PASA)
Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute.
Reconfigurable eukaryotic gene finder based on the Generalized Hidden Markov Model framework. The run time and memory requirements are linear in the sequence length. Genezilla utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, and CAP sites.
Analysis and Annotation Tool (AAT) Package
Genome tool for analyzing and annotating large genomic sequences containing introns. It includes a program for comparing the query sequence with a protein database and another for comparing the query with a cDNA database. The database search program identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence, as well as reports the coordinates of exons in the query sequence. Pairwise alignments of the query sequence with protein and cDNA database sequences are combined into multiple sequence alignments, which provide a view of all protein and cDNA sequences matching a query region.
Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format).
Zero Mode Waveguide Imaging and Analysis package tools
MATLAB software tool collection for data acquisition and image analysis from zero mode waveguides.
Statistical analysis toolbox for MEG and EEG. There are three primary data-objects: Factor for categorical variables, Var for scalar variables, and NDVar for multidimensional data. Factor is a container for one-dimensional, categorial data – each case is described by a string label. Var is a container to associate one-dimensional numpy.ndarray objects with a name. NDVars offer numpy functionality that takes into account the dimensions. There is also a Dataset class which acts as a vessel for variable objects (Factor, Var and NDVar) describing the same cases.
Coordination of Standards in Metabolomics
COordination of Standards in MetabOlomicS (COSMOS)
A group which aims to create open standards for metabolomics data shsaring and analysis.
A cross-species, cross-technique database for metabolomics experiments, data, and derived information. It includes metabolite structures and their reference spectra, their biological roles, locations and concentrations, and experimental data from metabolic experiments.
International effort whose objective is to improve and encourage the exchange of Metabolomics data. Datasets are stored in external data repositories independent of MetabolomeXchange; however, MetabolomeXchange allows users to browse datasets directly then proceed to the external repository for more information.
An independent, non-profit organization whose main goal is to promote the growth and development of the field of metabolomics internationally. They also aim to provide collaborative opportunities among scientists in metabolomics, create connections between academia, government and industry in the field of metabolomics, provide opportunities for presentation of research achievements and creation of workshops, and promote the publication of meritorious research in the field.
A collection of experimental 1D and 2D J-resolved NMR spectra of 208 metabolite standards.
A multistage tandem mass spectral database using a variety of structurally defined glycans. It provides tools for glycomics research that enable users to identify glycans by spectral matching. The database stores MS2, MS3, and MS4 spectra of N-and O-linked glycans, and glycolipid glycans as well as the partial structures of these glycans.
A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals.
mzCloud - Advanced Mass Spectral Database
A mass spectral database that assists in identifying compunds in life sciences, matabolomics, pharmaceutical research, toxicology, forensic investigations, environemnta analysis, food control, and industry.
A metabolomics database which contains GC/MS metabolomics datasets. General users can search a curated annotated metabolite database, a metabolite response statistics database, experimental datasets, and uncurated repositories. Registered users can use Metabolome Express for data processing and management.
A mass spectral database for organic compounds. The spectra included in the database are: electron impact Mass spectrum (EI-MS), Fourier transform infrared spectrum (FT-IR), 1H nuclear magnetic resonance (NMR) spectrum, 13C NMR spectrum, laser Raman spectrum, and electron spin resonance (ESR) spectrum.
R interface to Chemical Translation Service which provides translation between chemical and biological database identifiers.
R documentation for hierarchical cluster analysis on a set of dissimilarities for n objects. Each object is assigned to its own cluster, which an algorithm proceeds through iteratively. Two of the most similar clusters are joined at each stage until there is a single cluster. Distances between clusters are recomputed at each stage by the Lance–Williams dissimilarity update formula according to the particular clustering method being used. Clustering methods include: Ward's minimum variance method, complete linkage method, and single linkage method.
Interactive modules for Data Exploration and Visualization
Interactive modules for Data Exploration and Visualization (imDEV)
A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data.
R documentation for a function to perform linear discriminant analysis; specifically, to detect if the within-class covariance matrix is singular.
R documentation for a function that performs a principal components analysis on a given data matrix and returns the results as an object of class prcomp.
R Package for downloading and parsing mwTab files from the Metabolomics Workbench
An R package that downloads and parses mwtab data from Metabolomics Workbench studies. Downloaded files are converted into R lists.
THIS RESOURCE IS NO LONGER IN SERVICE, documented October 19, 2016. A web tool for visualizing and integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data. 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for transcripts, proteins and metabolites.
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 27, 2016. A software package that provides 1D and 2D NMR tools as well as processing and interpretation for all other major analytical techniques (LC/MS, IR, Raman, and more) in one package. It also has support for structure verification and multiplet reports.
A data center that develops evaluated mass spectral libraries and provides related software tools that assist compound identification by providing reference mass spectra for GC/MS (by electron ionization) and LC-MS/MS (by tandem mass spectrometry). It also provides gas phase retention indices for GC. Resources include the mass spectral library, the peptide library, and a standard refernece material guide.
A translation service which contains a registry of pubicly available chemical information such as structures, chemical names, chemical synonyms, database identifiers, molecular masses, XlogP and proton-donor/acceptor data for compound-specific, structure-based cross references. It offers single ID conversion, batch ID conversion, InChI code conversion, and other services.
A software suite for identifying and quanitfying compounds in NMR spectra. Features include a compound profiler, tools to process data, a compound builder, spin simulator and library manager. More information can be requested, and installation instructions are available on the website.
A software suite for data wrangling, creating interactive data visualization, performing statistical analyses, cluster analyses, exploratory data analysis and visualization (such as principal component analysis), predictive modeling and biochemical pathway analysis.
Software program for overrepresentation (enrichment) analysis of categorical annotations for a set of compounds. These categorical annotations correspond to biological and chemical information found in public databases and software. Annotations can be biological (pathways, enzyme interactions, pharmacological action) or chemical (taxonomy and chemical groups).
An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 5,2023. Software tool for processing in metabolomics experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.
A company that provides data analysis software with features such as multivariate tools, data mining, process modeling and interactive graphics.
A portal and resource for tutorials on a variety of data analysis techniques, the use of tools such as MetaMapR, workshops on data visualization, and R code manuals.
Cutoff Linked to Interaction Knowledge (CLIK)
Statistical method that uses previously annotated interaction data to automatically determine biologically informed statistical significance cutoffs for genome-wide screens.
Intelligence BRain Analysis through Images and Networks
Intelligence BRain Analysis through Images and Networks (iBRAIN)
Brain research group affiliated with the Nanjing University of Aeronautics and Astronautics (NUAA) in China. The main research interests of iBRAIN include developing methods in machine learning, data mining, neural computation, and related areas for decoding brain functions or recognizing brain disease. Research related code and datasets can be found on the main site.
Software for magnetic resonance image reconstruction and computed tomography reconstruction. Its main application geared towards rapid prototyping, teaching, forensics, and medicine. Its features include the ability to import DICOM or Analyze files, to export files to the STL, OBJ, and PLY formats, volume rendering, and manual or semiautomatic image segmentation.
Ultimate Rough Aggregation of Metabolic Map
An Ultimate Rough Aggregation of Metabolic Map
Metabolic pathway map that collects metabolic data gathered from multiple public databases and organizes them in one central location.
Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.
Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
An online platform for open source data/datasets created, collected or annotated for scientific research of all fields and disciplines. Registered users can share data relating to their research project and view data from other projects. Groups can combine datasets into collections associated with the group, in contrast to individual members of the group hosting their own data.
An article repository which archives peer-reviewed papers and non-peer-reviewed preprints in PeerJ. It includes papers and preprints from the biological and medical sciences PeerJ journal and from the computer science PeerJ journal.
Publishing company which provides access to its four journals SYNTHESIS, SYNLETT, SynOpen, and SYNFACTS; their reference works Science of Synthesis and Pharmaceutical Substances; and the paired encyclopedia ROEMPP.
Software used to simulate tumor progression in various stages of growth in order to study the process' dynamics. The input can be fitness landscape, mutation rate, and cell division time. The output is growth dynamics and other relevant statistics, such as expected tumor detection time and expected appearance time of surviving mutants. The tool is implemented in Java and runs on all operating systems which run a Java Virtual Machine (JVM) of version 1.7 or above.
Data collection and self-expression/-discovery/-management software tool that separates conscious cognition, subconscious emotion, and unconscious motivation. Tests are given depending on the topic chosen and results are analyzed to give the user information concerning their subconscious motivators.
An object-oriented language for modeling large-scale neural systems, along with an IDE for writing and simulating models. N2A represents neural systems in a parts-relations framework combined with dynamics where each part has as set of equations that define its state variables and how they evolve over time. Each part is a pattern for a population of instances, and each instance has its own unique copy of the state variables.
Matlab statistics toolbox allowing the computation of a wide range of measures of effect size. Four main toolbox functions cover common analysis designs, including two-sample-, oneway- and twoway- data sets as well as categorical data. Data may be repeated-measures.
A consortium of leading national Australian universities which collects and preserves digital research data and makes these data available for secondary analysis. The consortium provides a data catalogue comprised of seven sub-archives: Social Science, HIstorical, Indigenous, Longitudinal, Qualitative, Crime and Justice, and International. All users can browse and search the catalogue, view study and variable documentation, and download related material. Registered users can also analyze and visualize most data online and users who have completed the relevant undertaking form(s) can download entire studies or subsets of variables. Deposited data are processed, reviewed, and published for research use.
Cambridge Crystallographic Data Centre (CCDC)
Institution which compiles and distributes small molecule crystallography data from the Cambridge Structural Database (CSD), a repository of experimentally determined organic and metal-organic crystal structures. CCDC also produces associated knowledge-based application software for structural chemists. Structures deposited with CCDC are made publically available for download at the point of publication or at consent from the depositor.
Organization which acquires, curates, and provides access to a collection of digital data in the social sciences and humanities in the United Kingdom.
Commercial organization which combines high-throughput sequencing and bioinformatics to profile T-cell and B-cell receptors.
MIT Laboratory for Computational Physiology
A group which conducts research on improving health care through new and refined approaches to interpreting data. LCP research incorporates physiology, computer science, engineering, and applied mathematics.
UCSF Clinical and Translational Science Institute
UCSF Clinical and Translational Science Institute (CTSI)
An institute which provides infrastructure, services, and training to support clinical and translational research. It develops broad coalitions and partnerships at the local and national levels to enable a transformation of the research environment.
Mobile software application for behavioral social science experiments on an online platform. It can be used on computers, tablets, and smartphones. It is hardware independent, does not require online connectivity to perform a test, and has the option of interfacing with outside sensors, such as heart rate or weighting scales.
Windows software program for recording and analyzing signals from whole cell voltage and current clamp experiments. Its features include automatic waveform measurement, quantal content analysis, command voltage pulse generation, and spontaneous event detection.
Research Data Centre of the German Centre of Gerontology
Forschungsdatenzentrum Deutsches Zentrum fur Altersfragen
Research Data Center of the German Center of Gerontology
A facility for data housing and research on gerontology in Germany. It focuses on making data of the German Ageing Survey DEAS and the German Survey on Volunteering (FWS) accessible to researchers by providing user-friendly Scientific Use Files (SUF), documentation of the contents and instruments as well support for scholars using the data.
A portal for online journals, meetings and research reports. It offers open access to scientific articles to scientists from the field of medicine along with the option to publish their research results online.
Association of the Scientific Medical Societies in Germany
Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften
An association of various medical entities in Germany. The organization advises on matters and tasks of fundamental and interdisciplinary interest in medicine, develops recommendations and resolutions and represents them at the institutions occupied with such tasks, such as research strategies, education, and postgraduate training.
Coherent X-Ray Imaging Data Bank (CXIDB)
Database of Coherent X-ray Imaging (CXI) experiments. This data is widely accessible to researchers worldwide.
Bioinformatics Infrastructure for Life Sciences
Bioinformatics Infrastructure for Life Sciences (BILS)
A national research infrastructure that provides bioinformatics support to life science researchers in Sweden. Their work is supported by the Swedish Research Council.
University of Essex; England; United Kingdom
A public research university in Colchester, Essex, England. The institution has degree programs that span the humanities, social sciences, and health.
Open access repository for Johns Hopkins University researchers to share their research data. Data repository is administered by professional curators at JHU Data Services, who will work with depositors to enable future discovery and reuse of your data, and ensure your data is Findable, Accessible, Interoperable and Reusable (FAIR). Each dataset has citation and DOI, facilitating attribution, and connection to research publications.
Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Nucleotide sequence alignment and alignment cleaning based on amino acid information. Users can paste nt-sequences into the application and select the desired protein alignment method and the genetic code, and the option for alignment cleaning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Application that uses molecular sequence data to compute unrooted phylogenetic networks. Given an alignment of sequences, a distance matrix, or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
MATLAB-based tool for use with NEURON network models. It supports the modeler with model design, organization, execution (including on supercomputers), analysis, and reproducibility.
Software used to automatically trace single neurons. It supports VTK 3D visualization.
A webserver for the prediction of prokaryote promoter elements and regulons. DNA in FASTA or plain format serve as input. A gene table can be included with the run.
Symbolic Circuit Analysis in Matlab (SCAM)
Software toolbox for deriving and solving circuit equations symbolically in MATLAB.
A software toolbox containing a symbolic linear circuit analysis program. It is a MATLAB application that helps set up and solve design equations of electronic circuits.
Analog circuit analyzer and approximator used as a pre-processor to find design formulas or as a post-processor to approximate design formulas. The program performs the .AC analysis in SPICE symbolically with optional numeric evaluation and user selected threshold approximation.
Block diagram environment that contains a graphical editor, customizable block libraries, and solvers for multidomain simulation and model-based design in MATLAB. It supports simulation, automatic code generation, and continuous test and verification of embedded systems.
Commercial software company that offers simulation technology for both simulation and PCB design. PSpice has integrated analog and event-driven digital circuit simulation and a focus on bringing the tools needed for simulation that will help bring customer products to market. The website contains resources, libraries, and a user forum to support use of PSpice technology.
A software add-on that builds upon GENESIS by adding a library to installed versions of GENESIS. It is useful for simulations that must be run many times independently and for large-scale network models.
Web application used to visualise and annotate collaboratively high resolution histology data. In short, it uses public ontologies to create collaborative, community-curated atlases. Annotations are vectorial, and users can use boolean operations to combine, subtract and split regions.
Web framework for collaborative applications for neuroimaging. It hosts various web applications for curation, editing, and analysis in conjunction with neuroimaging data available publicly online.
Web application which allows users to visualise and collaboratively segment and annotate any brain MRI dataset available online via URL. A list of brains are available for use on the main site. Segmentations are automatically saved and can be downloaded as Nifti files or triangular meshes. Users can point BrainBox to their own Nifti data, or try data catalogues created by the community.
Web application search tool intended to help users find MRI data shared publicly on the Web, particularly from projects organized under the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI). Users can perform queries visually to select a cohort of participants with brain imaging data based on their demographics and phenotypic information and then link out to imaging measures.
Stereotactic atlases with probabilistic values describing the location of the main cerebral arteries. The data collected are from the COBRA study as described in "COBRA: A prospective multimodal imaging study of dopamine, brain structure and function, and cognition" by Nevalainen et al.
Blue Brain Python Optimisation Library (BluePyOpt)
An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms.
Database of bacteriophage gene regulation elements, genes, and genomes. Data are collected from scientific papers and cross-referenced with other database resources. The database can be searched using keywords or browsed by phage genome. Sets of regulatory sequences can browsed and exported in various formats.
Neuron education application for smart phones which provides an introduction to neural simulations at a low entry point.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Atlas of functional ROIs (fROIs) containing 499 regions, with extensive gray matter coverage. Atlases are available for download directly from the website.
Atlas of functional ROI's, including individual networks (auditory network, sensorimotor network, etc.). Atlases of individual networks and combined networks are available for download directly from the website.
Network development Python package for NEURON
Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks.
Software which provides an interface for MindWave Mobile hardware, allowing users to view and listen to brainwave output of different "mind states". Users can: view any or all brainwaves, specify a combination of brainwaves via a formula, compare a base line session to a performance session, and create a log and run it through the application to view different graphical outputs. NeuroExperimenter only runs on Windows
Tool for modeling and simulating large, complex biological neural networks, particularly pulse-coupled, spiking neural networks. Its main features include modular or hierarchical modeling strategy of networks, phase-coded neurons, event-driven simulation, and integration of standard file formats.
Neuronal network model simulator for both individual neurons and networks of neurons. It uses NeuroML for network description. Various neuron and synapse model types are supported. CNN features include: an integration cycle which uses a Runge–Kutta 6-5-order method, extensive scripting capabilities, individual unit state introspection from scripts, and neuroplastic processes identified by label or regexp.
Software for kinetic modeling of ion channels which operates on Windows XP or Windows Vista.
Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support.
Environment for carrying out deterministic simulation Systems Biology Markup Language models. It relies on libraries for SBML support, conservation analysis, integration and steady state analysis and a .NET core.
A function which allows users to generate two biological conditions synthetic microarray datasets. The user provides a subset of parameters, but default parameter settings can be modified.
Simulation software which computes activity numerically in 2-dimensional neural fields by solving integral-differential equations involving transmission delays and visualizes the spatio-temporal activity. Installation and simulation documentation are provided on the homepage.
General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating.
Client/server application that makes parameter maps for neural simulations written in NEURON.
Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways.
Parallel Neural Circuit Simulator (PCSIM)
Software tool for simulating heterogeneous networks composed of different model neurons and synapses. It is intended to simulate networks containing up to millions of neurons and on the order of billions of synapses by distributing the network over different nodes of a computing cluster by using MPI.
Integrated simulation and analysis environment for dynamic systems models of physical systems. It supports symbolic math, optimization, phase plane analysis, continuation and bifurcation analysis, data analysis, and other tools for modeling. It is written in Python with some underlying C and Fortran legacy code.
Commercial organizations which develops, manufactures, and sells solutions and equipment for blood sampling, blood gas analysis, transcutaneous monitoring, and IT management systems under certain brand names.
Supplier and servicer of products for expression studies in Xenopus laevis oocytes. Products include overnight delivery of freshly prepared Xenopus laevis oocytes, Cell & Tissue Media necessary during preparation, maintenance, and recording of Xenopus oocytes and lab chemicals. Services for pharmacological studies include heterologous expression and in vitro electrophysiology.
Manufacturer and supplier of the DMZ Universal electrode pullers which produce pipettes and electrodes with a tip diameter down to 0.2 micrometers.
American manufacturer of premium specialty glass tubing products that meet the needs of hermetic seal production, electronics assembly, commercial applications, medical device manufacture, and various research fields. Products include hermetic seal glass, capillary tubing, glass spacers, insulator beads, and custom-made tubing.
Software tool which provides implementation of the continuous bag-of-words and skip-gram architectures for computing vector representations of words. These representations can be used in many natural language processing applications and for further research. It takes a text corpus as input and produces the word vectors as output. It first constructs a vocabulary from the training text data and then learns vector representation of words. The resulting word vector file can be used as features in natural language processing and machine learning applications.
An interchange format to represent, store and exchange data and annotations in a standardized manner.
A Java suite of core natural language analysis tools. It can take raw human language text input and give multiple outputs, including the base forms of words, their parts of speech, and marked up structure of sentences in terms of phrases or word dependencies. Supported languages include English, Arabic, Chinese, French, German, and Spanish.
BioC Experimental Molecular Interaction Detection
A manually annotated data set of full text articles and a tool for identifying passages describing experimental methods for physical protein-protein interactions.
Precision oncology knowledge base which contains information about the effects and treatment implications of specific cancer gene alterations. OncoKB contains detailed information about specific alterations in 418 cancer genes. Each variant entry contains biological effect, prevalence, prognostic information, and treatment implications. Information is curated from various sources, such as guidelines from the FDA, ClinicalTrials.gov, and scientific literature by a network of clinical fellows, research fellows, and faculty members at Memorial Sloan Kettering Cancer Center.
Image analysis software package that allows precise manual measurements and automatic object detection with measurements of object characteristics. Pictures may be X-rays, micrographs, and the like. Supported file formats include JPG, GIF, TIFF, BMP, PNG, WMF, EMF and DICOM files. Image rotation and light can be edited.
Commercial supplier of dental and medical laboratory equipment.
Optogenetics and Transgenic Technology Core
Core facility and data repository which creates and characterizes transgenic rats for use in models of neurological diseases, such as addiction and neurodegeneration. Researchers can request strain(s) from RRRC or go to the Transgenic Rat Request page.
Microscopy imaging software for image acquisition, processing, measurement, and analysis. iVision‐Mac directly supports the acquisition of images and time-lapse series.
Software repository containing code for measuring brain networks from structural and functional MRI data. Several programs require MATLAB to run.
Software that configures and controls the measurement protocols and actions performed by the FilterMax Multi-Mode Microplate Readers and the SpectraMax Paradigm Multi-Mode Detection Platform, which are commercially available microplate readers from Molecular Devices.
Desktop software application for bacterial identification, pathogen detection, or species identification. It can be used for cross-species identification for microarrays and real time PCR primers. It uses ClustalW to align sequences then analyzes conserved and species specific regions within those sequences.
R package for regularized supervised learning on high-dimensional data from an oscillatory system. Zeitzeiger can quantify rhythmic behavior, make accurate predictions, identify major patterns and important features, and detect when the oscillator is perturbed.
Software used to configure and control up to 32 neMESYS syringe pumps. Its features include automatic detection of connected dosing units, graphical display of syringe size, syringe level and valve position, configurable SI units for volumes and flow rates, and real-time display of all current values like flow rate, syringe fill level or dispensed volume.
Psychology Experiment Building Language (PEBL)
A programming language made for creating and conducting standard psychology experiments. The site also serves as a portal for experimental software, design, and exchange.
Simultaneous Multichannel Immunofluorescence Analysis
Simultaneous Multichannel Immunofluorescence Digital Imaging Analyzer
Software used to analyze and quantify images stained with multiple fluorophores in vitro or in vivo. It can output both image and value outputs.
Software used to automatically characterize the orientation and isotropy properties of a region of interest in an image based on the evaluation of the structure tensor in a local neighborhood. OrientationJ has four functionalities: visual representation of the orientation, quantitative orientation measurement, making distribution of orientations, and corner detection.
Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Database for published, indexed resources pertaining to psychological, psychiatric and other behavioral and social science research. Users can search for resources by document type, research methodology, and funding source.
Philips DVT2700 Voice Tracer Digital Recorder with Dragon NaturallySpeaking software
Software and accompanying hardware for transcription and voice recording. Software is Windows-compatible only and comes in a physical CD.
Software suite for qualitative data analysis for text-based data and higher-order forms of data. Various packages are available and are dependent on the system used and the type of data analysis needed.
Neural data acquisition software for signal visualization in neuron recordings along with spike wave-form classification methods. It is made up of the PlexControl software program and the OmniPlex Server.
GUI created by the Taub Institute in order to create an end-user friendly batch processing solution to complement Axona's new command line modification of TINT. This GUI allows the user to define a directory. Within this directory it will be continuously (unless closed) searching for new files to analyze via TINT.
Python package for calculation of extracellular potentials from multicompartment neuron models. LFPy can be used to set up a model, run simulations, and calculate the extracellular potentials arising from activity in the given model neuron. It relies on the Python interface provided by the NEURON simulator.
Database of neuronal cell types based on multimodal characterization of single cells to enable data-driven approaches to classification. It includes data such as electrophysiology recordings, imaging data, morphological reconstructions, and RNA and DNA sequencing data.
Commercial provider of equipment and resources for epigenetics research, biological sample preparation, and diagnostic assays. The products Diagenode provides include automation and semi-automation software, antibodies, reagents, kits, and shearing technologies.
Biotechnology company that develops products for genomics research and molecular diagnostics, such as systems for DNA and protein analysis, DNA and protein fractionation technologies, and other sequencing equipment.
HBio: Multichallel Systems | MEA2100 System
In vitro recording system for electrophysiology research with integrated amplifier and stimulus generator, temperature control, and the option for real-time signal detection and feedback. The system can record up to 4 MEAs in parallel at a sampling rate of 50 kHz per channel.
Public archive of neural signals recorded from various types of cells and sites in neural systems. Any data can be publicly accessed and downloaded, and users can submit their data.
Database of interactive neural computation computer models at levels ranging from simple linear filters to large-scale networks of spiking units. Interface tools are provided while browsing and exploring models.
Software for automated optical tracking for freely moving and head-fixed animals. It provides real-time and post-hoc tracking methods.
Graphical user interface that has been implemented as a 3D Slicer plugin (scripted module). It serves to display a corresponding set of cortical regions from functional connectivity matrix in an explorable 3D scene that represents brain anatomical environment. In addition to grey matter regions, MultiXplore automatically finds and extracts deterministic fiber bundles which exist between selected region(s) and adds them to the 3D environment. This feature helps in generating region-based fiber bundles given a desired whole-brain tractography data.
Automatic Tractography-based Parcellation Pipeline
Automatic Tractography-based Parcellation Pipeline (ATPP)
Integrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region. " ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) (https://www.nitrc.org/projects/atpp). Its source codes are hosted in GitHub9 (https://github.com/haililihai/ATPP_CLI; https://github.com/haililihai/ATPP_GUI), under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi: https://doi.org/10.5281/zenodo.239702; ATPP GUI v2.0.0, doi: https://doi.org/10.5281/zenodo.239705). "
Single-Cell RNA-Seq Portal for Brain Research
Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes.
Full featured, excitation and emission, FRET and ratio-imaging software module which allows users to view and change setup parameters as images are being acquired. It is a standard component of ISee Analytical Imaging Software.
Software tool designed for mapping short reads onto a reference genome generated from Illumina, Ion Torrent, and 454 NGS platforms. Its features include paired end alignment, methylation status analysis, automatic base quality calibration, and in built adapter trimming and base quality trimming.
GEMINI - a flexible framework for exploring genome variation
Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.
RZ6 processor tool designed for rapid animal screening. It automates the process of presenting stimulus signals and averaging response signal data. It automates the process of presenting stimulus signals and averaging response signal data by giving users control over the stimulus signal parameters used to generate stimuli that vary across successive presentations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Data acquisition and analysis software used for xCELLigence Real Time Cell Analysis SP, DP and MP instruments. The software is used to program and execute experiments and analyze data.
Image analysis software for cells and stained areas in samples stained with immunofluorescent markers.
Brightfield image analysis software for the FACS-like analysis of samples stained with immunohistochemical or other stains.
Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.
Server used to create spreadsheets with ontology based data validations. Webulous can process populated templates and transform them into OWL/RDF using design patterns expressed in OPPL. It also has an add-on with Google spreadsheets which supports loading templates from a Webulous server and allows users to submit populated spreadsheets back to the Webulous server for transformation into OWL.
Database and repository of tissues relating to mouse models of breast cancer. Users can search and share models, and members can enter details of available material to share on a collaborative basis.
Computing platform for biomolecular NMR available to not-for-profit or government users. It consists of a virtual machine (VM) provisioned with dozens of widely-used NMR software packages, and is available as a cloud-based Platform-as-a-Service (PaaS) or as a downloadable VM for local execution.
Image analysis software that learns modular models of things such as cell shape, nuclear shape, vesicular organelle distribution and microtubule distribution directly from 2D or 3D images and can produce specific instances of cell geometries without the need to create them by hand or to segment microscope images. These geometries can be combined with biochemical models to perform spatially realistic cell simulations if used in conjunction with MCell.
Commercial organization which provides hardware and software products for life science research and teaching.
Standalone solution dedicated to Visual Psychophysics running on Mac OS X. Psykinematix runs standard psychophysical protocols, presents complex stimuli, collects subject's responses, and analyzes results on the fly. It consists of a unique OpenGL-based software package that does not require any programming skill to create and run complex experiments.
La Jolla Institute for Immunology Bioinformatics Core Facility
La Jolla Institute; La Jolla Institute for Allergy and Immunology Bioinformatics Core;La Jolla Institute for Allergy and Immunology Bioinformatics Core Facility
Core Facility provides support for short or long-term projects requiring expertise the analysis of biological datasets. The services provided include the analysis of large-scale datasets (e.g. next-gen sequencing data, microarrays, etc.), the development of customized databases and reusable analysis pipelines, guidance on experimental design, support with technical sections of manuscripts and grants, and training on analysis software packages. All services are charged at our hourly rate.
La Jolla Institute for Immunology Flow Cytometry Core Facility
La Jolla Institute for Allergy and Immunology Flow Cytometry Core Facility
Flow cytometry core which offers a wide range of routine and custom flow cytometry, mass cytometry, cell sorting services, data analysis, strategic planning for novel assays, user training, and full scale research collaborations.
La Jolla Institute for Immunology Clinical Studies Core Facility
La Jolla Institute for Allergy and Immunology Clinical Studies Core
La Jolla Institute for Allergy and Immunology Clinical Studies Core Facility
Core facility for clinical studies carried out by the La Jolla Institute of Allergy and Immunology. It is also a non-profit research organization that focuses on studying topics lthat include pollen allergies, HIV, food allergies and tuberculosis.
La Jolla Institute for Allergy and Immunology Department of Laboratory Animal Care
La Jolla Institute for Allergy and Immunology Department of Laboratory Animal Care (DLAC)
La Jolla Institute for Allergy and Immunology DLAC
The department of laboratory animal care at the La Jolla Institute for Allergy and Immunology.
La Jolla Institute for Immunology Microscopy and Histology Core Facility
Core facility dedicated to providing a static or dynamic (in vitro/in vivo) imaging services by offering histology and microscopy services and providing support and training to interested researchers. The facility offers a range of light microscopes, related imaging systems and image analysis resources for assisted or independent use (upon training). It also can provide advice on proper sample fixation, processing, embedding of tissues with attention to desired orientation, decalcification of bone tissue, cutting of paraffin blocks, cryosectioning, routine and special stains as well as training in histological techniques.
La Jolla Institute for Allergy and Immunology Functional Genomics Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5, 2024. Core facility that combines large-scale automation and high-throughput capabilities with gene disruption techniques to pinpoint the function of individual genes and find new ways to disrupt genetic triggers of disease. The research capabilities are aimed towards finding new treatments for immune-related diseases.
La Jolla Institute for Allergy and Immunology
Non profit collaborative research organization located in La Jolla, California, UCSD Research Park. Institute researches immunology and immune system diseases to pinpoint specific genes involved, accelerate progress toward development of new treatments and vaccines to prevent and cure type 1 diabetes, cancer and infectious disease. Developer of Immune Epitope Database (IEDB). Provides core facilities with access to equipment, technologies, training and expertise to support innovative research.
Salk Institute Biophotonics Core Facility
Core facility equipped with commercial imaging and data analysis technologies. The facility will provide technical assistance to the Salk Institute faculty through access to confocal microscopy (both fixed and live cell), TIRF microscopy, two-photon microscopy, electron microscopy and super-resolution microscopy as well as in vivo imaging modalities.
Salk Institute Flow Cytometry Core Facility
Salk Institute Flow Cytometry Core Facility (FACS)
Core facility dedicated to advancing research projects requiring cell sorting and/or analysis of cell populations by flow cytometry. The core offers training on and access to shared use instrumentation for analytical flow cytometry, services for fluorescence activated cell sorting (FACS) as well as technical consultation and support on experimental design, execution, and data analysis.
Salk Institute Behavior Testing Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2024. Core facility that provides the resources to investigate sensory, motor and complex behavioral testing in rat and mouse models. The facility offers standard neurobehavioral tests, customized test batteries, training for independent use of the equipment, data interpretation and anlaysis.
Salk Institute Functional Genomics Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5,2024.Core facility that provides Salk researchers access to gene expression analysis services such as whole-genome expression and genotyping using Affymetrix GeneChip technology, high-throughput qPCR and SNP services using Fluidigm Biomark System and Applied Biosystems 7900HT System, and DNA miniprep extraction using Qiagen BioRobot.
Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC)
Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications.
Salk Institute Mass Spectrometry Core Facility
Salk Institute Mass Spectrometry Core (MASS)
Core facilty that provides access and services for analyzing targeted and complex mixtures of protein and small molecules, like metabolites. By utilizing these tools, research on disease states can be augmented by proteomic and metabolomic study.
Salk Institute Media Preparation Core Facility (MPRP)
Salk Institute Media Preparation Core Facility
Core facility that provides media, plates, and commonly used buffers for molecular biology applications and culturing mammalian cells, C. elegans, yeast, and bacteria. The Media Preparation Core Facility is equipped with 3 automatic plate pourers supported by 2 programmable media kettles capable of producing up to 9 liters of agar or nutrient media per run under gentle and reproducible conditions. Plates are available in 6 cm or 10 cm formats.
Institute dedicated to research in immunology by utilizing the academic and research communities in the La Jolla area as well as technological advances in biomedical research, imaging and analysis. Specific topics include autoimmune disease, cancer, allergies, infectious diseases and inflammation.
Salk Institute Next Generation Sequencing Core (NGS)
Salk Institute Next Generation Sequencing Core
Core houses state-of-the-art equipment in sequencing and genomics, including high-throughput sequencing systems such as Illumina NovaSeq 6000, NextSeq 2000, MiniSeq, and PacBio Sequel IIe system (long-read sequencing), as well as 10x Genomics Chromium Controller single-cell solution, NanoString nCounter MAX Analyzer, and GeoMx Digital Spatial Profiler instrument, along with QuantStudio Real-Time PCR instruments.
Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility
Salk Institute Gene Transfer Targeting and Therapeutics Core
Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core (GT3)
Core facility that provides consultation on the use of viral vector technologies as well as custom design and production services for multiple vector types. The GT3 facilitates the use of these research tools by Salk researchers and others across diverse fields of study such as systems neuroscience, stem cell biology, metabolism, ageing, cancer biology and gene therapy. The GT3 core is a designated Cancer Center Council (C3) core facility. Cancer Center members from participating C3 institutes have preferential rates.
Salk Institute Peptide Synthesis Core Facility
Core facility that provides services such as peptide synthesis, incorporation of non-conventional and/or modified amino acids, HPCL characterization and purification, and Mass spec analysis.
Sanford Burnham Prebys Medical Discovery Institute Animal Facility
SBP Medical Discovery Institute Animal Facility
Animal facility that provides housing for specific pathogen free rodents, frogs, and zebrafish. The facility also has trained animal care technicians provide expertise in animal husbandry, transgenic and knockout mouse breeding colony maintenance and assistance with routine technical procedures.
Salk Institute Stem Cell Core; STEM Core
Core facility that provides services to support stem cell research for Salk Institute researchers and their direct collaborators. The STEM Core provides well-characterized human embryonic stem (hES) cell lines and human induced pluripotent stem (iPS) cell lines, space and equipment for research, as well as training and consultation.
Sanford Burnham Prebys Medical Discovery Institute Animal Imaging and Analysis
SBP Medical Discovery Institute Animal Imaging and Analysis
Animal imaging and analysis lab that provides imaging and analytical services for SBP investigators. The facility can perform in vivo non-invasive luminescence and fluorescence imaging for xenograft tumor growth and metastasis studies. Analytical equipment supports complete blood cell counts (CBC) and analysis of serum components revealing metabolic or organ stress from small samples of mouse blood.
Salk Institute Scientific Core Facilities Senior Director's Office
The central leadership office of the Salk Institute's scientific core facilities. This office provides general management and oversight for administrative, scientific, budgetary and personnel matters for all the scientific core research facilities at the Salk Institute.
Sanford Burnham Prebys Medical Discovery Institute Model Organisms
SBP Medical Discovery Institute Model Organisms
Facility that provides Drosophila melanogaster and Caenorhabditis elegans as model systems. It also provides training in how to manipulate the organisms and use equipment and provides technician assistance.
Sanford Burnham Prebys Medical Discovery Institute Flow Cytometry Core Facility
SBP Medical Discovery Institute Flow Cytometry Facility
Facility that provides access to high-speed cell sorting and analytical flow cytometry. Core allows investigators to have 24-hr/day access to variety of analytical flow cytometers available for independent use. Core staff provide technical expertise and hardware and software training, operate the facility cell sorters, and are available to assist with analysis experiments for those who prefer to have their samples run by an expert cytometrist.
Sanford Burnham Prebys Medical Discovery Institute Cellular Imaging Facillity
SBP Medical Discovery Institute Cellular Imaging Facillity
Medical research facility that supports research programs by providing access to sophisticated microscopes for digital imaging, as well as training, assistance and guidance. The core facility offers expertise, training and assistance in advanced biological microscopic imaging techniques and use of complex image processing software, use of well-maintained, aligned, and calibrated microscopic equipment, and troubleshooting of equipment and experimental problems.
Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core
SBP Medical Discovery Institute Stem Cell Core
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators.
Sanford Burnham Prebys Medical Discovery Institute Histology Core Facility
SBP Medical Discovery Institute Histology Core Facility
Facility that provides standard and customized research specific histology services including tissue processing, fixed and frozen sectioning. It also offers routine and special histological stains as well as immunohistochemistry and immunofluorescence. Other services include training for several pieces of common use equipment, such as, paraffin microtome, cryostat, and a cytospin. Training is also provided for basic histological techniques such as perfusion and tissue collection. The tissue acquisition service assists investigators with regulatory/legal compliance, as well as obtains and stores human tissue samples and associated clinical data.
Sanford Burnham Prebys Medical Discovery Institute Tumor Analysis
SBP Medical Discovery Institute Tumor Analysis
Facility that provides analysis of animal models of human cancer and other diseases. It provides investigators access to a wide variety of human cancer cell lines for xenograft studies, some primary human xenograft models and additional transgenic mouse solid tumors and leukemia models. The core also offers serial passaging of tumors and derivation of 2D and 3D cultures from xenograft tumors, including patient-derived xenograft (PDX) models. These short-term cell cultures established from PDXs enable in vitro analysis including high throughput screening with compounds or RNAi for functional characterization.
Sanford Burnham Prebys Medical Discovery Institute Functional Genomics Core Facility
SBP Medical Discovery Institute Functional Genomics Core Facility
Facility that provides infrastructure for RNAi-based Target Discovery services, from initial feasibility assessment to verification of identified targets. It also serves as a repository for reagents and assays, expertise and other technical information, and works towards technical improvements when necessary. Other available services include consultation, libraries for cloning and screening, and access to equipment such as High-Throughput Microscopes and Plate Readers.
Sanford Burnham Prebys Medical Discovery Institute X-ray Crystallography Facility
SBP Medical Discovery Institute X-ray Crystallography Facility
Facility equipped with X-ray crystallography equipment, such as the Rigaku FR-E SuperBright Ultra high-intensity rotating anode generator. The instrument is inteded for self-usage by trained users. It utilizes both ports with two independent diffraction stations that can run simultaneously. Each station is equipped with an X-stream cryogenic system for standard low temperature (~100 K) data collection. The system is used to collect high resolution diffraction data from native and inhibitor-bound crystals or to test and optimize diffraction quality (cryo-protectant conditions, etc.) and screen for further data collection at synchrotron sources.
Sanford Burnham Prebys Medical Discovery Institute NMR Facility
SBP Medical Discovery Institute NMR Facility
Facility that acts as a centralized shared resource for NMR studies on proteins, peptides, small molecules, and carbohydrates in solution or in solid state. It provides instrumentation and expertise for NMR data collection. It also provides consultation with investigators on the feasibility of NMR for structural studies of protein candidates, as well as the optimal method to obtain solution structures and binding information by multi-dimensional NMR techniques. It can also train users in basic spectrometer operations, trouble-shoot for instrumental and operational problems, and set up NMR experiments for users as requested.
Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core
SBP Medical Discovery Institute Protein Analysis Core
Facility that provides a variety of analytical services focused on biophysical characterization of structural and functional properties of proteins in solution, under native, non-denaturing conditions. Examples of services include quality control of protein samples (folding, stability, aggregation); measuring molecular weight of proteins, protein complexes, oligomers and assemblies; charcaterizing protein conformation and shape in solution; determining oligomeric state of protein (including stoichiometry and Kd for self-association) and measuring protein binding to proteins, peptides, small molecules, compounds, metals, nucleotides and other ligands (including determination of equilibrium (Kd) and kinetic rate (kon, koff) constants, stoichiometry, binding enthalpy and entropy).
Sanford Burnham Prebys Medical Discovery Institute Genomics Microarray/Q-PCR Facility
SBP Medical Discovery Institute Genomics Microarray/Q-PCR Facility
Facility that provides full-service microarray-based global analysis of gene expression in RNA samples from humans or mice using an Illumina platform. Services include RNA sample quality and quantity analysis, microarray analysis, and Q-PCR service and analysis, as well as special services such as RNA purification and Copy Number Variation analysis.
Sanford Burnham Prebys Medical Discovery Institute Viral Vector Core Facility
SBP Medical Discovery Institute Viral Vector Core Facility
Facility that provides cost-effective production of high-quality, high-titer lentiviral, retroviral and adenoviral vectors. Services include production of ready-to-transduce lentiviral and adenoviral particles, custom lentiviral, retroviral, and adenoviral production and titrations. Other activities of the facility include packaging, concentrating, and titration of user-supplied lentiviral constructs. Specialized services include custom lentiviral vector construction for constitutive or inducible cDNA/shRNA expression as well as promoter/enhancer reporter, viral packaging, and titration (ready-to-transduce control particles provided).
Sanford Burnham Prebys Medical Discovery Institute Proteomics Facility
SBP Medical Discovery Institute Proteomics Facility
Facility that provides mass spectrometry-based proteomics services with methods tailored to the needs of scientific investigators for routine mass spectrometric analysis of peptides and proteins, identification of novel proteins, characterization of post-translational modifications, and quantitative proteomics analysis of simple to complex biological samples. The facility identifies, validates and develops new methods designed for the characterization and identification of biologically important proteins. It also supports users with software applications and development, data analysis and experimental design of proteomics studies.
Sanford Burnham Prebys Medical Discovery Institute Genomics DNA Analysis Facility
Core facility that provides sequencing services, access to equipment and consultation on experimental design and data analysis. Available instruments include the Life Technologies Ion Torrent PGM and Ion Proton sequencers. Core also provides amplification-free analysis of RNA expression using the NanoString nCounter, and additionally provides sequencing and analysis services to investigators outside of SBP. Included in the cost of sequencing is basic bioinformatic analysis (SNP/InDel calling, transcript abundance). Lastly, the core also provides advice on experimental design, and guidance on the capabilities of next-generation sequencing.
Sanford Burnham Prebys Medical Discovery Institute Assay Development Core Facility
SBP Medical Discovery Institute Assay Development Core Facility
Core facility that performs design, development, validation and pilot screening of biological high-throughput assays. It provides services such as designing and developing de-novo assays, converting low-throughput lab protocols (e.g. cuvette- or gel-based) into plate-based HTS assays, and access to major robotic equipment and resources. The facility also provides direct assistance with preparing screening-related grants, guidance through assay development stages, help in designing testing funnels, and generation of preliminary data.
Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility
SBP MDI Bioinformatics and Data Management Facility
SBP Medical Discovery Institute Bioinformatics and Data Management Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician.
Sanford Burnham Prebys Medical Discovery Institute High-content Screening Core Facility
SBP High-content Screening Core Facility
SBP Medical Discovery Institute High-content Screening Core Facility
Core facility that provides access to the HTS plate and liquid handling infrastructure of the screening center, as well as the screening center�s cell culture facility. Other services include assay development, screening, and data analysis/mining expertise and services for high content screens. Consultation from the team is available for high content image-based screens including sample preparation, image acquisition, image analysis, image data management, and algorithm development.
Sanford Burnham Prebys Medical Discovery Institute Cell-based Disease Modeling and Screening Core
SBP Cell-based Disease Modeling and Screening Core
SBP Medical Discovery Institute Cell-based Disease Modeling and Screening Core
Core facility that aims to develop cell based disease models for screening and testing small molecules and drugs, and specializes in culture, scaling, and directed differentiation of human embryonic and induced pluripotent stem cells. It provides resources and expertise to researchers at the Institute and to their external partners to facilitate development of stem cell based assays and patient-specific disease models in screenable formats.
Sanford Burnham Prebys Medical Discovery Institute High-Throughput Screening Facility
SBP Medical Discovery Institute High-Throughput Screening Facility
Core facility that provides diverse screening instrumentation, compound libraries and expertise on high throughput screens and automation in support of collaborative, and user- or facility-driven screening projects. The facility collaborates with a number of partners to develop molecular therapies. Services available include consultation for high throughput screening approaches, conversion of assays to automation compatible formats and data analysis.
Sanford Burnham Prebys Medical Discovery Institute Medicinal Chemistry Facility
SBP Medical Discovery Institute Medicinal Chemistry Facility
Core facility that provides general synthetic and medicinal chemistry resources and expertise to the biomedical research community. Services include chemistry consulting for projects, grant applications, synthetic chemistry, medicinal chemistry, and analytical chemistry, as well as access to equipment for synthesis, purification, and analysis.
Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core Facility
Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core
SBP Medical Discovery Institute Cancer Metabolism Core
Facility that aims to investigate role of metabolism in cancer on cellular and organismal level, combining in vitro and in vivo analysis. Comprehensive metabolic facility, including stable isotope tracing and flux analysis. Provides analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All instruments and approaches are available on fee-for-service basis to Cancer Center scientists, but alsoto outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis.
Scripps Research Institute Center for Antibody Development and Production
TSRI Center for Antibody Development and Production
Producer of antibodies for investigators to use as diagnostic tools and therapeutic reagents in their research studies. The center works in conjunction with the Department of Animal Resources, and is able to assist in all stages of both polyclonal and monoclonal antibody development.
Sanford Burnham Prebys Medical Discovery Institute Cheminformatics Core
SBP Medical Discovery Institute Cheminformatics Core
Core facility that supports assay development, high throughput (HTS), ultra-high throughput (uHTS), and high-content screening (HCS) activities performed at the Conrad Prebys Center for Chemical Genomics by providing databases and tools for compound registration and inventory, HTS plate formatting and tracking, HTS and HCS bioassay data processing as well as related data and information handling. Data mining and reporting are also facilitated with a user-friendly database interface. The Cheminformatics core also supports the design and obtaining of appropriate compound collections, as well as SAR follow-up of hits, hit-to-lead optimization and in silico screening through docking and other molecular modeling approaches.
Non-profit dedicated to conducting collaborative research to find cures for human disease, improve quality of life, and educate and train the next-generation of scientists. It is the overarching organization of more than a dozen core facilities that provide various resources in biomedical research.
Scripps Research Institute Florida Cell Based High Throughput Screening Core Facility
Cell-Based High-Throughput Screening Core
Scripps Research Institute Cell-Based Screening Core
The Scripps Research Institute (CBS) Core
The Scripps Research Institute Cell-Based Screening (CBS) Core
Core facility that provides access to genome-wide collections of cDNAs and siRNAs that can be used to interrogate cellular models of signal transduction pathways and phenotypes. Services include cell lines, hit-picking clones and various screening sets, and access to equipment.Provides instruments:Analyst Molecular Devices,Embla Molecular Devices, Envision Perkin Elmer, Platemate Matrix, Tecan M200, Wellmate Matrix.
Molecular graphics environment which provides biologists and chemists with representations of proteins, DNA, RNA, and multiple sequence alignments. Users can build, annotate, and edit interactive views and slides of molecules. Users can also superimpose protein structures, search PDB, measure distanaces and angles, and view and make high resolution images of alignments.
Commercial ogranization which provides molecular and drug discovery software and services to researchers. American software company that develops chemical simulation software for use in pharmaceutical, biotechnology, and materials science research. Provides products ranging from general molecular modeling programs to a full suite of chemical simulation and drug design software, including ligand- and structure-based methods.
Commercial organization which provides molecular modelling and cheminformatics software to the pharmaceutical industry.
Drug discovery platform for medicinal and computational researchers. Users can assess the binding affinity and contributions to binding of a complex, find new scaffolds, grow molecules towards pharmacophore points, link fragments, and investigate possible dock binding conformations.
Drug discovery software package which can be used in structure-based design, fragment-based design, pharmacophore discovery, medicinal chemistry, protein and antibody modelling, and molecular modeling and simulations. Each aspect of the software package has its own unique features: for example, features for structure-based design include active site detection, scaffold replacement, multi fragment search, and solvent analysis.
Drug and molecular design environment with tools for molecular modeling. It includes tools for small molecule and macromolecular modeling and simulation, cheminformatics, lead identification and lead optimization. Users can: perform multi-criteria drug design; predict safety issues and/or off-target pharmacology; identify leads using ligand-based or structure-based virtual screening, and chemical library design; and perform lead optimization using various QSAR methods.
Pharmacophore modeling software to create 3D structure activity relationships, screen databases, and generate hits through establishing a chemical space occupied by active ligands. Used in drug design.
Complementary OEDocking tool for virtual screening, it performs a systematic and non-stochastic examination of all possible protein-ligand poses. The software also filters for shape complementarity and chemical feature alignment before selecting and optimizing protein-ligand poses.
Public web server that provides structures, data, tools, programs and other useful information to the public for computer-aided drug design. It is the official database of the Computer-Aided Drug Design (CADD) Group.
Software package that uses homology modeling and fold recognition to make protein structure predictions.
Software that takes a macromolecular structure containing a bound ligand and identifies the key features on the ligand which are interacting with points on a protein. Its features include: automatic interpretation of PDB ligands using geometry, dictionaries and rule; advanced handling of co-factors, ions, water molecules and covalently bound ligands; pharmacophore export to Catalyst(tm), MOE(tm) and PHASE(tm) for virtual screening; and the ability to treat co-factors and water molecules as part of the ligand or part of the macromolecule.
Database of commercially accessible screening compounds from international chemistry suppliers. iResearchLibrary is updated on a weeky basis and offers support for creating internal screening libraries containing commercially accessible compounds, developing exploratory and targeted libraries, selecting commercially accessible compounds for SAR, lead expansion, and hit follow-up projects, and using structures for pharmacophore searching, virtual screening and other computational work.
Database of marketed and developed drugs indexed with internationally-recognized drug names, synonyms, trade names, trivial names and trial preparation codes in one source, plus compound structures and activity data. Each record has chemical structure and is classified by drug activity, mechanism of action, treatment, manufacturer, synonyms, medical nformation and literature references.
Software program that simulates molecular interactions. It has features that allow broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques, and a range of implicit solvent models. It also primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM can also be applied to inorganic materials with applications in materials design and has a comprehensive set of analysis and model builiding tools.
Collection of databases with standalone databases, which gives opportunity for customers to integrate the data into their internal tools and databases, as well as online databases, that are available to the customers from a dedicated website where an individual can query and export the data in the selected format. The standalone database topics include medicinal chemistry, drugs and target class based compounds. The online databases are comprised of three major compilations: GVK BIO Online Structure Activity Relation Database (GOSTAR), GVK BIO Biomarker Database (GOBIOM), and Clinical Trial Outcome Database (CTOD).
Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.
Ab initio molecular modeling software program that computes an array of molecular properties such as multipole moments, polarizabilities, and electrostatic potential. It can also map reaction coordinates between reactants, products, and transition states.
The General Atomic and Molecular Electronic Structure System
Software program for ab initio molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Capabilities include using nuclear gradients for automatic geometry optimization, modeling of solvent effects, computation of the energy hessian for prediction of vibrational frequencies, as well as computation of nuclear wavefunctions. The program can also compute variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities.
Software program for electronic structure modeling that enables researchers to study and predict the properties of molecules and reactions under a wide range of conditions, especially those that are difficult or impossible to observe experimentally.
Software program for semiempirical quantum chemistry for handling of biomolecules.
Molecular modelling software package with 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). It contains geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms.
Software toolkit of computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software is designed to work with biomolecules, nanostructures, and solid-state, from quantum to classical, and all combinations, ground and excited-states, Gaussian basis functions or plane-waves, scaling from one to thousands of processors, and the properties and relativistic effects of computational chemistry problems.
Software program for determining molecular structure and calculating chemical properties. It has a graphical interface and accurate computational models that are compatible with the iPad, iPhone and iPod Touch. When combined with the Spartan'16 Parallel Suite, this enables the first fully-functional open-ended molecular modeling environment on popular mobile technology.
Software toolkit for drug design and discovery, including plugins for in silico compound optimization, compound selection and integration into other databases.
Software program for advanced predictive modeling of Absorption, Distribution, Metabolism, Elimination, and Toxicity (ADMET) properties of chemical substances in the human body. ADMET Predictor can estimate a number of vital ADMET properties (listed below) from molecular structures and build predictive models of new properties from user's data.
Commercial developer of database and predictive model software tools used in chemical toxicity assessment.
Software program for high-speed virtual screening intended for simultaneous evaluation of ADMET properties of compounds. ADMEWORKS Predictor employs a number of models to predict ADMET properties using models based on values of topological, geometric, physicochemical and substructure descriptors derived from the molecular structures.
Software program for ADME property prediction for drug development. The program uses properties such as octanol/water and water/gas log Ps and 3D molecular structure. It is capable of screening compound libraries using computed properties to filter out unlikely drug candidates.
Software tool for high-throughput toxicity prediction; it assists in the early and quick identification of toxic drug candidates. ToxAlert provides probability percentages for different toxicity endpoints such as oncogenicity, mutagenicity, teratogenicity, neurotoxicity or cell toxicity.
Software tool for initial estimation of the structural formula of metabolites, which might be formed by a substance in humans, animals or in plants. MetabolExpert is also capable of predicting the most common metabolic pathways in animals, exporting results to SDF and RDF format and graphical highlighting that empasizes the essence of metabolic reactions that occurred.
Software tool for initial estimation of toxic symptoms of organic compounds in humans and in animals and estimating the bioavailability of the compounds by a simple but powerful model. HazardExpert Pro is capable of bioaccumulation calculation, histogram representation of the results including toxicity classification, graphical interface for editing toxic fragments and has open knowledge bases in which a user can add their own fragments.
Software tool for quick and sensitive prediction of the common first-pass metabolic routes. It supports high throughput screening, a graphical interface for editing transformation rules and open knowledge bases where users can add own rules.
Software package for molecular descriptors, ADME prediction and membrane permeability prediction. These can then be used with provided chemometric tools to build statistical models.
Software for accurate toxicity predictions in silico to identify potentially toxic chemicals during the drug development process.
Software design tool in retro-metabolic drug design that considers a variety of conepts such as prodrugs, soft drugs, and chemical drug-delivery systems. RetroMex predicts the structure of the retro-metabolites, collects them in compound databases, and presents the results in tree format.
Open source downloadable application which contains a framework for managing and analyzing chemical compounds, as well as supports editing in 2D, processing large collections of molecules in tables, calculate various types of properties, and more cheminformatics functionality. This software also is used for the management and analysis of biological sequences (DNA, RNA, and protein), and relates the chemical structures and a target and then describes them using mathematical descriptors and models them using statistical methods. Bioclipse is equipped with a scripting language (Bioclipse Scripting Language or BSL) which can be used to automate tasks or create reusable snippets that can be shared with others,
Software which predicts metabolic transformations related to cytochrome and flavin-containing monooxygenase mediated reactions in phase I metabolism. MetaSite uses both enzyme-substrate recognition and the chemical transformations induced by the enzyme. MetaSite provides the structure of the metabolites formed with rankings derived from the site of metabolism predictions. This software is not training set dependent, and can predict �hot spots� as well as suggest the regions that contribute most towards each one.
Software program to predict metabolic and degradation products of chemicals. METAPC has dictionaries on mammalian metabolism, aerobic microbial degredation, anerobic microbial degredation, and photo degredation.
Software used to automate the process of accessing, analyzing and reporting scientific data. This software can be used by a person with little or no software development experience can create scientific protocols that can be executed through a variety of interfaces including: BIOVIA Web Port, other BIOVIA solutions such as BIOVIA Electronic Lab Notebook, Isentris, Chemical Registration and third-party applications such as Microsoft SharePoint. The protocols aggregate and provide immediate access to volumes of research data, they automate the scientific analysis of data and allow researchers to explore, visualize and report results.
Heuristic algorithm used to generate plausible metabolic maps from a comprehensive library of biotransformations and abiotic reactions, and prioritizes the transformations based on estimated system-specific probabilities occurrence of the transformations. The reliability of generated pathways, metabolites and maps can be assessed according to the extent that they have been supported by observed metabolic data.
Computational chemistry related-software used for the computation management, analysis and visualisation of chemical information of any defined type. This software uses a worldwide network of databases with property descriptions, computational modules, data analysis tools, visualization servers, data type handlers and I/O modules to increase the software�s capacity extensibility.
Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats.
Software available from brainmap.org to perform meta-analyses via the activation likelihood estimation (ALE) method. It also includes the transforms for icbm2tal conversions.
Pennsylvania State University Social Life and Engineering Imaging Center
Imaging center dedicated to fostering research in the social, behavioral, biological, engineering, and materials sciences where imaging methodologies play a central role. The SLEIC provides the Penn State research community with instrumentation, technological and substantive expertise, educational opportunities, and financial support for conducting magnetic resonance imaging (MRI) and electrophysiology (EEG, ERP) experiments.
Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns.
Database of Xenopus gene expression patterns, queryable by specific location or region in the embryo. Each entry includes information such as images, species, and gene name.
Epilepsy T1 and Hippocampal Segmentation Datasets
Shared dataset which consists of skull-stripped T1 MRI images and segmented hippocampi of 163 Temporal Lobe Epilepsy (TLE) patients. The T1 and hippocampal segmentation data of TLE patients are uploaded in three separate datasets which can be accessed from the main site.
Accelerating Medicines Partnership (AMP)
Partnership between the National Institutes of Health (NIH), the U.S. Food and Drug Administration (FDA), and multiple biopharmaceutical companies and non-profit organizations whose goal is to increase the number of new diagnostics and therapies for patients and reduce the time and cost of developing them. The group explores three major areas of disease: diabetes, Alzheimer's disease, and rheumatoid arthritis and lupus.
Commercial organization which offers a catalog of building blocks, reagents, catalysts, reference materials, and research chemicals for various applications. Analytical services and laboratory services are also provided.
National Association of Science Writers (NASW)
Association whose goal is to foster the spread of accurate scientific information.
Open data repository fully dedicated to MEG data in raw and processed form. The archive also contains anatomical MRI volumes and demographic and questionnaire information. Organized and stored as the Brain Imaging Data Structure (BIDS) with the integration of multimodal electrophysiology data. Directly readable by data-analysis software with Brainstorm. OMEGA will continue to expand, with contributions from the scientific community.
Software which creates phylogenetic trees from molecular, morphological and/or behavioral data through high speed computer analysis.
Phylogenetic Analysis by Maximum Likelihood
Phylogenetic Analysis by Maximum Likelihood (PAML)
Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Web application for the analysis and detection of APOBEC-induced hypermutations. The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence.
Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.
Web application for the prediction of transmembrane helices in proteins using Hidden Markov Models. FASTA formatted sequences can be uploaded via file or copy-paste, and output can be formatted as extensive with graphics, extensive without graphics, or one line per protein. Submissions are limited to 10,000 sequences and 4,000,000 amino acids - each sequence is limited to no more than 8,000 amino acids.
Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.
Model based Bayesian method for eliminating physiological noise from fMRI data. This algorithm uses image voxel analysis to isolate the cardiac and respiratory noise from the relevant data.
Python script which calculates gene expression for RNA-Sequencing data. It analyzes files in formats such as BED, BAM, and SAM to output data about RNA.
Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies.
Capture HiC Analysis of Genomic Organisation
Capture HiC Analysis of Genomic Organization
CHiCAGO: Capture HiC Analysis of Genomic Organisation
Statistical pipeline for detecting significant chromosomal interactions in Capture Hi-C data. CHiCAGO uses a convolution background model accounting for both random Brownian collisions between chromatin fragments and technical noise. CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges, with scores representing soft-thresholded -log weighted p-values., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Supplier of algae strains that aims to be a resource to both the HAB research community and biotechnological applications. Researchers can order and deposit strains with the ARC.
Producer and supplier of organic medicinal mushrooms and medicinal mushroom products. Its product line includes raw materials and private label products for pharmaceutical and nutraceutical use, as well as its own branded line of "Condition Specific" dietary supplements available to the public.
Supplier of live porcine models and post mortem tissues, organs, glands, and glandular secretions.
Northern Spalting - Applied Mycology Lab
Supplier of non-toxic, pure-culture fungi through Oregon State University which are kept active in the lab. All organisms arrive in an aggressive, pigmenting state. It's website also features scientific information on spalting, DIY guides, lists of upcoming spalting events, and a menagerie of other spalting resources.
Supplier of laboratory-reared and field-collected freshwater, marine, and estuarine organisms. Invertebrates and vertebrates are available, and seasonal and unlisted organisms can be requested. Its test organisms are available for environmental and biomedical research.
Company developing spawning techniques to allow increased reproduction of tropical fish for the research industry.
Producer and supplier of swine and sheep for research purposes. Archer Farms delivers its specimens directly to research facilities throughout the East Coast.
Supplier of Ciona (C. robusta and C. savignyi) adults and stable transgenic animals expressing tissue-specific fluorescent proteins for research laboratories. This ascidian culturing facility is located at the marine laboratory of the University of California at Santa Barbara (UCSB).
Supplier of genetically characterized strains, cloning vectors, and bacteriophages for the genus Bacillus and related organisms. The BGSC can distribute these materials to qualified scientists and educators throughout the world.
Developer of specialized and appropriate hamster models for research on human diseases. These specialized hamsters have features similar to those seen in certain human diseases. Bio Breeders provides these specialized hamsters to the biomedical community worldwide.
Botanic Gardens Conservation International PlantSearch Database
Botanic Gardens Conservation International (BGCI) PlantSearch database
Global database of living plant, seed, and tissue collections. Users can search by genus, species, infraspecific epithet, and conservation status.
Research facility and licensed commercial research animal breeder that specializes in custom polyclonal antibody production, contract research, animal models for research, and animal tissue procurement. Brown Family Enterprises can make and distribute custom polyclonal antibodies using rabbits, goats, sheep, and horses.
C.M. Rick Tomato Genetic Resources Center
C.M. Rick Tomato Genetic Resources Center (TGRC)
Genebank of wild relatives, monogenic mutants and miscellaneous genetic stocks of tomato. TGRC offers seed samples for free to researchers worldwide.
Commercial data acquisition and analysis software that forms a data acquisition system for measuring extracellular activities of excitable cells in vitro and in vivo. It has been developed especially for use with the data acquisition systems from Multi Channel Systems MCS, but the software can also be used with other experimental setups.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for the analysis of cross-linking/mass spectrometry datasets using MS-cleavable cross-linkers. MeroX is specialized for MS/MS-cleavable cross linking reagents and identifies the specific fragmentation products of the cleavable cross links.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for analyzing cross-linking/mass spectrometry datasets using any bifunctional cross-linker. It can be used to identify cross links of peptides – such as DSS, BS3, Disulfides, and zero-length – in complex mixtures.
Caenorhabditis elegans Natural Diversity Resource (CeNDR)
Caenorhabditis elegans Natural Diversity Resource
Supplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery.
Center for Forest Mycology Research Culture Collection
The Center for Forest Mycology Research (CFMR)
Climate-controlled mycological herbarium housing preserved specimens of forest fungi. CFMR scientists and other researchers use the CFMR collections to test hypotheses of distribution, relatedness, and biological activity of forest fungi.
Central repository that receives, catalogs, preserves, and distributes wild type and mutant cultures of the green alga Chlamydomonas reinhardtii, as well as useful molecular reagents and kits for education and research.
Database and project to reveal open reading frames (ORFs) in the yeast genome in order to discover their functions. A PCR-based gene deletion strategy is used to assign functions through phenotypic analysis of mutants.
Software program that can illustrate the output of SEDFIT and SEDPHAT programs and can perform simple calculations with the data. It is designed to work with sedimentation velocity, sedimentation equilibrium, ITC, DLS, and isotherm data.
Software that automatically reads and processes up to 100 raw microarray image files. The software finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences.
Database that aggregates exome and genome sequencing data from large-scale sequencing projects. The gnomAD data set contains individuals sequenced using multiple exome capture methods and sequencing chemistries. Raw data from the projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects.
Jackson Laboratory Clinical Knowledgebase
Semi-automated and manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and oncology clinical trials. Users can search CKB via gene, gene variants, drug, drug class, indication, and clinical trials.
Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.
Interoperability framework which supports integrative genomics analysis via access to various bioinformatics tools. Rather than performing analyses itself, GenomeSpace acts as a hub for data from supported bioinformatics tools and reformats data and results when necessary.
Genomics knowledgebase for clinical relevance of genes and variants for use in research. ClinGen's primary function is to store and share information for the benefit of the scientific community. Laboratory scientists, clinicians, and patients can share and access data.
Data analysis tool that utilizes the Comparative CT (ddCT) method to rapidly and accurately quantitate relative gene expression across a large number of genes and samples. Raw input from plates or arrays can be analyzed according to user-determined settings.
Modeling and simulation environment for study of multi scale and multicellular systems. Users can construct and simulate models of gene regulation, signaling pathways, tissue patterning and morphogenesis and explore the effects of multiscale feedbacks between these processes. Morpheus can render 2D and 3D models using graphical user interface.
Website resource for researchers to order and send Drosophilia specimens to each other. This community-driven supplier also works with the FlyBase Drosophilia database to search for synonyms for fly species.
Group Sparse Canonical Correlation Analysis
Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data.
Commercial antibody supplier which provides a web-accessible database of reference and applications data with their reagents.
Elsevier Pathway Studio Software Package
Elsevier Pathway Studio software package version 10.0
Elsevier's Pathway Studio software package version 10.0
Text mining software that searches curated molecular pathway and cell interaction libraries.
Data analysis, graphing, and management application that allows users to import, manipulate, analyze data, and create customized plots. Plots include x-y probability, histogram, box, percentile, horizontal bar, stack bar, column, stack column, polar, and pie. Binned data can be exported to a histogram, step plot, or spike plot. KaleidaGraph works with Windows and Macintosh systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software implementing a method for assessing both the algorithmic and statistical reliability of estimated independent components developed by Himburg et al in their 2004 paper. The method is based on running the ICA algorithm many times with slightly different conditions and visualizing the clustering structure of the obtained components in the signal space. In experiments with magnetoencephalographic (MEG) and functional magnetic resonance imaging (fMRI) data, the method was able to show that expected components are reliable; furthermore, it pointed out components whose interpretation was not obvious but whose reliability should incite the experimenter to investigate the underlying technical or physical phenomena.
Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python.
High-throughput sequencing machine which enables sequencing of exomes, whole genomes, and transcriptomes. It also provides flow cell types, real-time analysis, and integration with Illumina's BaseSpace computing environment.
Integrated platform that serves as a central resource for rare disease research databases, registries, biobanks and clinical bioinformatics. The RD-CONNECT project utilizes researcher cooperation and data sharing to improve research methods and further scientific understanding of rare diseases.
Lancelet Genome Sequence and Annotation Project Database
Database project to document the genome sequence of the Lancelet, a basal extant chordate. Information provided includes reference haploid genome sequence and annotation data, gene models and function, and integrated information from diploid genome sequence and annotation data.
Online database documenting the genome of the Japanese lamprey. The project uses the genome to gain insight into the evolution of vertebrate organisms.
Online Resource for Community Annotation of Eukaryotes
Online Resource for Community Annotation of Eukaryotes (OrcAE)
Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community.
Fluorescence Image Evaluation Software for Tracking and Analysis
Fluorescence Image Evaluation Software for Tracking and Analysis (FIESTA)
Fully automated software program which can detect point-like and elongated objects with nanometer precision. Also included are analysis tools such as drift correction, color offset calculation, path statistics and mean-square-calculation.
Software for analyzing sedimentation equilibrium (SE) data from analytical ultracentrifugation experiments. It uses a model-dependent simulation of data for matching data in order to determine when equilibrium has been achieved.
LTQ-Orbitrap Fusion Tribrid Mass Spectrometer
Orbitrap Fusion Tribrid Mass Spectrometer
Mass spectrometer that combines quadrupole, ion trap, and Orbitrap mass analysis.
Thermo Fisher | EASY-nLC 1000 Liquid Chromatograph
THIS RESOURCE IS NO LONGER IN SERVICE, documented April 10, 2017. It has been succeeded by the Thermo Scientific EASY-nLC 1200 Liquid Chromatography system.
Hardware system which automates RNA, DNA, and protein sample QC, including sample loading, separation, and imaging.
Fixed-stage microscope for electrophysiological research. Features include open design, noise reduction, 16x objective lens, and water dipping objective with depth induced aberration correction.
Puerto Rico Open Data Interconnection Portal
Portal for datasets relating to all aspects of Puerto Rican life, including health, education, economy, and environment among others. The datasets available range in quality and amount of information provided, and some offer only limited information. Several of the health ones relate to methadone and methadone clinic usage.
NYC Health and Nutrition Examination Survey
New York City Health and Nutrition Examination Survey
NYC Health and Nutrition Examination Survey (NYC HANES)
Large scale, population-based, cross-sectional study containing interviews, physical exams, and biological samples. Data is prepared for analysis with SAS and SUDAAN, and is weighted in order to be representative of the New York population.
Economic Commission for Latin America and the Caribbean
Comision Economica para America Latina y el Caribe
Economic Commission for Latin America and the Caribbean (ECLAC)
Regional commission of the United Nations with the purpose of contributing to the economic development of Latin America, coordinating actions directed towards this end, reinforcing economic ties among countries and with other nations, and promoting social development.
CEPALSTAT - Bases de Datos y Publicaciones Estadisticas
Data repository for statistical information of Latin America and the Caribbean countries collected, systematized and published by CEPAL. CEPALSTAT provides access to statistics and indicators produced by separate ECLAC Divisions which can be used for socio-economic and environmental analysis, as well as various decision-making processes related to Central and South America. Users can export data and cross-tabulate indicators to produce tables combining data from different series, countries and/or periods.
CDC Laboratory Quality Assurance and Standardization Programs
Standardization program which helps assure the quality of laboratory test data and results so patients, healthcare providers, researchers, and public health officials can be confident that laboratory test results they receive are accurate. CDC services include reference materials, proficiency testing, training, guideline creation, and consultations. Quality assurance and standardization programs can be can be customized by and for users and laboratories.
Data capture software for use with Vicon motion capture system. Its features include MATLAB integration, Python pre-installed, customized workflow, and automated quality assessment.
Software package for modeling body biomechanics for use with the Vicon motion capture system. Bodybuilder allows users to, among other things, edit and modify trajectories and interpolate broken trajectories, model body segments and joints, create kinematic and kinetic models, and output results to text or file.
Collection of analysis scripts for pCASL (pseudo-Continuous ASL) data.
Genome Resources for Yeast Chromosomes (GRYC)
Database which provides annotated sequence data for the genomes of basidio and ascomycete yeasts. The resources provided include genetic element pages, data sets for downloading, quick and advanced searches, facilities for BLAST comparisons, and a genome browser powered by JBrowse from GMOD.
International non-profit organization for patients, relatives, and physicians with pituitary tumors and disorders.
Foundation to support research in and diagnosis of adrenal diseases. The portal provides basic information about adrenal diseases as well as a community for patients.
Benchmarking Universal Single-Copy Orthologs
Benchmarking Universal Single-Copy Orthologs (BUSCO)
Software tool to quantitatively measure genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.
Database for marine genomics data. Users can access genomics datasets from various organisms as well as carry out BLAST and submit genomics information of their own. Data sets include coral, aiptasia, sponges, and sybiodinium.
Organization studying thyroid biology and the prevention and treatment of thyroid disease and cancer. It offers professionals access to thyroid research resources and offers patients general thyroid information, clinical trial information, and patient support links.
Information portal for practicing endocrinology physicians, trainees, fellows, and other health professionals. Essentially a regularly updated web textbook, it contains endocrinological information written by physicians for other practicing endocrinologists.
Framework for creating 3D neuronal morphologies from point/diameter descriptions.
Cross-platform visualization software system for 3D computer graphics, image processing, and data visualization. Various visualization algorithms and advanced modeling techniques are supported within VTK, as well as parallel processing and interoperability with select databases.
Text mining consortium and hub for code and resources. Its ultimate goal is to create an infrastructure that encourages the use, incorporation, and interoperability of existing text mining technologies in scientific publications.
Text mining tool from Europe PMC that allows biological terms or concepts to be highlighted for readers on full text articles. These terms and concepts are identified by text mining algorithms, which are developed by a variety of text mining groups. However, it is up to the reader to control which selection of highlighted concepts they see. Once concepts of interest have been identified within the text, they are formatted according to the W3C Web Annotation Data Model and stored in a triple store via the EMBL-EBI RDF Platform. As a reader views an article in a web browser, any annotations in the triple store associated with the article are made available in a menu alongside the article.
Text mining tool that finds similarity between documents based on sentences and tokens such as ontology terms, instead of simple similarity based on lexical terms.
Search engine that mines life sciences papers using Natural Language Processing and Machine Learning to clean, tag and structure the data. Insights focus on experimentation and include objective recommendations, ratings and insights for reagents, lab equipment, assays, protocols and researchers.
Software semantic platform for curating and searching figures. Allows to share scientific figures and underlying data in way that is machine readable and findable. Platform for researchers and publishers to make their papers discoverable based on their data content. Used to make scientific papers discoverable based on data content, to enable researchers to find specific data, to test or generate new hypotheses, and to share and connect data. Openly accessible and easily applicable data discovery tool as initiative by EMBO.
Text mining tool for publishers and researchers. UNSILO modules possess functions such as searching, recommending articles with similar topics, mapping article relationships, and providing insights into article trends and metrics.
Question answering platform for integration of various Natural Language Processing tasks for the biomedical domain. It is built on top of the SAP HANA database and uses MeSH to navigate sentences extracted from papers. Olelo processes three types of questions based on the type of answer a user desires. Answers can be returned as MeSH ontological terms, short answers or facts, and summaries. Document abstracts associated with the search topic are also available for reference.
Server that contains a registry of text mining tools primarily within the biomedical field. It includes resources for biomedical text annotation visualization, biomedical text annotation prediction, and benchmarking biomedical entity recognition between independent automatic prediction systems.
Web based data analysis tool for microbiome statistical analysis, visual explortation, and data integration. It supports compositional profiling, functional profiling, comparative analysis, and meta analysis of microbiome datasets.
Semi-automatic crystallographic data collection software that integrates data collection, data reduction, phasing and model building in a single software package.
Multi-threaded software for rapid quality control and preprocessing of high throughput sequencing data specified for different experiments. It consists of four modules that speed up the report on statistics graphs of raw datasets, preprocessed datasets and preprocessing status.
Module of SOAPdenovo2 commonly used independently to close gaps in genome assemblies.
Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Biomedical Research Informatics Computing System
Biomedical Research Informatics Computing System (BRICS)
Modular, web-based bioinformatics system for research studies and clinical trials data collection. Tools include a data dictionary, data repository, meta study, global unique identifiers for studies, protocol management and data capture, and query and exportation of data.
International Image Interoperability Framework
International Image Interoperability Framework (IIIF)
Set of shared application programming interface specifications for interoperable functionality in digital image repositories. It utilizes JSON-LD, linked data, and standard W3C web protocols to parse and share digital image data, migrate across technology systems, and provide enhanced image access.
Group that provides open source, college-level textbooks to instructors and their students. Educators can use the textbooks in class and access faculty-specific resources and content online.
Program to map biomedical text to the UMLS Metathesaurus and to discover Metathesaurus concepts referred to in text based on symbolic, natural-language processing and computational-linguistic techniques.
Database containing information about RNA-sequencing and astrocyte reactivity. Searching a gene through this engine provides differential expression data for various experimental conditions.
Osteogenesis Imperfecta Foundation (OIF)
Foundation for improving the quality of life for people affected by OI through treatment and cure research, education, awareness, and mutual support. OIF lists personal resources for individuals affected by osteogenesis imperfecta as well as professional and clinical resources for researchers.
Group whose goal is to improve health outcomes for individuals with X-linked adrenoleukodystrophy by raising disease awareness, improving education, providing support for and information to patients, and performing clinical ALD research.
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses (EGSEA)
Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets.
Baylor College of Medicine; Houston; Texas
Health sciences university located in Texas Medical Center in Houston, Texas, US. It includes medical school, Baylor College of Medicine, graduate school of Biomedical Sciences, School of Allied Health Sciences, and National School of Tropical Medicine.
Database and encyclopaedic resource of macromolecular complexes found in key model organisms from scientific literature. Data includes protein-only complexes, protein-small molecules, and protein-nucleic acid complexes. The information within the portal is manually curated and available for download.
Web application which allows users to create interactive molecular network portraits using high-throughput datasets.
Agilent Masshunter Quantitative Analysis software
This resource is not available. Documented on October 6, 2020.Software for the analysis of mass spectrometry data. MassHunter also works with software-specific packages to do more specialized analysis tasks.
HCImage Image Acquisition and Analysis Software
Image acquisition and analysis software suite for Hamamatsu imaging devices. Hamamatsu Photonics imaging system for microscopy.
Software for empirical gramians for model reduction of (nonlinear) input-output systems.
Statistical software for ROC curve analysis. MedCalc performs several statistical tests such as method comparison, method evaluation, reference intervals, and meta-analysis.
Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging.
University of Massachusetts Boston; Massachusetts; USA
Public university located in Boston, Massachusetts that offers degree programs in the social sciences, humanities, and sciences.
Private organization that offers resources and serves as a community for those recovering from addiction and to help patients find the highest quality care for a successful recovery.
CMEIAS Microscopy Image Analysis Software
Collection of image analysis software developed for microbial ecology.
Molecular biology software for visualizing and documenting gene constructs for InFusion cloning, Gibson assembly, restriction cloning, PCR, and mutagenesis.
Visualization software that allows users to create, browse, and share annotated DNA sequence files from SnapGene.
Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Tool to annotate core genes in eukaryotic genomes (that was replaced by BUSCO). Its resulting core gene dataset can be used to train a gene finder or to assess the completeness of the genome or annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Method for mitochondrial baiting and iterative mapping. MITObim assembles novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software toolkit for the processing of ancient and modern HTS data. PALEOMIX also aids in metagenomic analysis of the extracts from the HTS processing.
Conversion software that both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees.
Dual Organellar GenoMe Annotator (DOGMA)
Web-based annotation tool for plant chloroplasts and animal mitochondrial genomes. DOGMA allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
Rice Functional Genomic Express Database
Gene database for Japonica rice. RiceGE is associated with SIGnAL at the Salk Institute.
Program that estimates the historical effective population size of a homogenous population. The input for the IBDNe program is the set of identity-by-descent (IBD) segments detected by the IBDseq program.
Einstein-Mount Sinai Diabetes Research Center Human Islet and Adenovirus Core Facility
Einstein-Mount Sinai Diabetes Research Center Human Islet and Adenovirus Core
Core which provides methodologies, technology and infrastructure to support investigators in the use of human islets for research studies for the Einstein-Mount Sinai Diabetes Research Center. It isolates and prepares human and rodent islets/beta cells and cell lines for investigator-initiated research and generates specific viral vectors (adenovirus and lentivirus) for gene delivery of cDNAs and shRNAs of interest to beta cells and other islet cell types.
Einstein-Mount Sinai Diabetes Research Center Biomarker Analytic Research Core Facility
Einstein-Mount Sinai Diabetes Research Center Biomarker Analytic Research Core
Einstein-Mount Sinai Diabetes Research Center Biomarker and Analytical Research Core
Core provides information and tools for Einstein and Montefiore investigators from initial study planning stage through analysis and data output. Facility services include: mass spectrometry analysis, including stable isotopes, as well as research-grade determination of lipids, and metabolic markers for human subjects and animal model projects; High-throughput robotics for semi-automated high-quality sample preparation and analysis by immunoassay and liquid chromatography–mass spectrometry (LC/MS); Support for novel developmental projects featuring applications of LC/MS and two-site bead-based assays; Research quality analysis of metabolites for human and animal samples using Olympus AU400 autoanalyzer; Advanced training in analytical chemistry.
Einstein-Mount Sinai Diabetes Research Center Translational Research Core Facility
Einstein-Mount Sinai Diabetes Research Center Translational Research Core
Core services include consultation, technical support and training and mentoring in clinical and translational research methods that are specifically applicable to diabetes, its complications and related metabolic disorders. Personel provides expertise in first-in-human and mechanistic studies in integrative physiology, in clinical trials of diabetes and obesity, and in application of new technologies.
Boston Area Diabetes Endocrinology Research Center Cell Biology and Morphology Core Facility
Boston Area Diabetes Endocrinology Research Center Cell Biology and Morphology
Services provided include tissue preparation, embedding and sectioning for electron microscopy, use of electron microscope and photography of thin sections, immunogold staining for electron microscopy, preparation and incubation of samples (cells and tissues) for immunofluorescence microscopy, confocal microscopy and digital imaging.
Einstein-Mount Sinai Diabetes Research Center
Research center that facilitates the research of diabetes and related studies in obesity, metabolism and endocrinology
Einstein-Mount Sinai Diabetes Research Center Stable Isotope and Metabolomics Core Facility
Einstein-Mount Sinai Diabetes Research Center Stable Isotope and Metabolomics Core
Core which uses stable isotope flux and metabolite profiling to help formulate and test hypotheses about the metabolic consequences of various changes in gene expression and protein function, in order to guide further integrative systems biology analyses of the underlying mechanisms in diabetes, insulin resistance, obesity, and diabetic complications.
Boston Area Diabetes Endocrinology Research Center
Consortium of laboratory-based and clinical investigators who research etiology, pathogenesis, treatment and cure of type 1 and type 2 diabetes, and their associated microvascular and atherosclerotic complications.
Boston Area Diabetes Endocrinology Research Center Pancreatic Islet
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 23,2024.Core which provides islets to the local diabetes research community in the Boston area. They collaborate with researchers nationally to provide nonhuman primate (NHP) islets for research.
Boston Area Diabetes Endocrinology Research Center Transgenic
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 23,2024.Transgenic core which generates transgenic and gene knockout mouse models relevant to obesity, diabetes and nutrition research. It also provides consultation on all aspects of making transgenic and gene knockout mice.
Research center which provides research support for investigators pursuing research on diabetes and metabolic disorders.
Einstein-Mount Sinai Diabetes Research Center Animal Physiology Core Facility
Einstein-Mount Sinai Diabetes Research Center Animal Physiology Core
Core which assists with the in vivo assessment of glucose and fatty acid metabolism, insulin sensitivity and energy homeostasis in mice and rats. It provides tools to understand the behavior and physiology mediating the relationships among diabetes, nutrient sensing, obesity and diabetic cardiovascular complications in rodents.
Columbia Diabetes Research Center Translational Biomarker Analytical Core Facility
Columbia Diabetes Research Center Translational Biomarker Analytical Core
Translational Biomarker Analytical Core (TBAC)
Core makes available to Diabetes Research Center investigators variety of high quality radio-immunoassay, ELISA, and other analytical methods, and facilitates access of DRC investigators to measurement of small molecules by targeted and untargeted metabolomics/lipidomics with the Irving Institute Biomarkers Core. TBAC also provides consultations and services for in vivo methods to measure insulin secretion and sensitivity.
Columbia Diabetes Research Center Flow Cytometry and Cell Sorting Core Facility
Columbia Diabetes Research Center Flow Cytometry and Cell Sorting Core
Core which assists investigators to quantify and phenotypically characterize cell populations that contribute to the metabolic, immunologic and developmental programs of diabetes and its complications; and to purify populations of cells of relevance to diabetes and its complications.
Boston Area Diabetes Endocrinology Research Center Molecular Biology
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 24,2024. Core that provides services for DNA sequencing and oligonucleotide synthesis, as well as support for projects that require research laboratory automation, such as siRNA screens and transcript abundance profiling. It also offers experimental design and advice for automation and high throughput screening of siRNA collections based on the Ambion siRNA collection.
Center that includes over seventy investigators engaged in basic and translational research in diabetes and related metabolic disorders, and their complications. It contains four Research Cores that serve for innovative and translational research.
Indiana University School of Medicine Center for Diabetes and Metabolic Diseases Islet and Physiology Core Facility
Indiana Diabetes Research Center Islet and Physiology Core
Indiana Diabetes Research Center Islet and Physiology Core Facility
Indiana University School of Medicine Center for Diabetes and Metabolic Diseases Islet and Physiology Core
Services include islet isolation services from mice and rats and access to porcine and human islets. The core is equipped with BioRep Perifusion Apparatus for measurement of insulin secretion and offers services for islet and beta cell calcium imaging. Provides services for islet transplantation and assists investigators who wish to perform immunohistochemistry, immunofluorescence and/or analysis of endocrine or beta cell mass on whole pancreata from mouse and rat models.Offers services for rodent metabolic characterization, including performance of insulin and glucose tolerance testing, analysis of body composition, and metabolic cage analysis using the TSE System cages. Recently added services include zebrafish characterization to screen genes and small molecules for their effects on islet development and function.
Columbia Diabetes Research Center Mouse Metabolic Function and Phenotyping Core Facility
Columbia Diabetes Research Center Mouse Metabolic Function and Phenotyping Core
Mouse Metabolic Function and Phenotyping Core
Core that provides services that facilitate the efficient characterization of mouse models of diabetes and its complications: NMR Body Composition Analysis, Whole Body Metabolic Assessment (chamber calorimetry with motion detection), Metabolic Clamps, Gastric Infusion/Feeding and Thermogenic Phenotyping.
Indiana Diabetes Research Center Microscopy Core Facility
Indiana Diabetes Research Center Microscopy Core
Core that provides consultation and specialized services for intravital microscopy of pancreas and transplanted islets, FRET assays, and fluorescent biosensors for analysis of intracellular signaling cascades to serve the area diabetes investigators.
Indiana Diabetes Research Center Translation Core Facility
Indiana Diabetes Research Center Translation Core
Core within Indiana Center for Diabetes and Metabolic Diseases that offers services that facilitate conduct of research involving human subjects, including providing low-cost, high quality analyte measurements for variety of hormones, cytokines, lipids and other analytes. Its human studies services include metabolic phenotyping (e.g. GTT, clamp studies, tracer studies), and access to a biobank of human tissues and serum.
Columbia Diabetes Research Center Advanced Tissue Pathology and Imaging Core Facility
Advanced Tissue Pathology and Imaging Core
Columbia Diabetes Research Center Advanced Tissue Pathology and Imaging Core
Core that provides spectrum of advanced cellular and tissue pathology and imaging services for diabetes researchers at Columbia University. It also has microscopy equipment and services such as confocal, live 2-photon and scanning and transmission electron microscopy.
Johns Hopkins University - University of Maryland Diabetes Research Center
Center whose goal is to understand the causes of both type 1 and 2 diabetes and promotes translational research that is aimed at reducing the burden of these diseases in the U.S. It has a specific focus on childhood diabetes and diabetes that affects minority populations.
Johns Hopkins University - University of Maryland Diabetes Research Center Administrative Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 24,2024. Core that typically organizes a meeting with the investigator/user and relevant core directors to discuss the different services and tests that the Diabetes Research Center would recommend to the investigator. It also provides support letters for grant proposals submitted by investigators.
Johns Hopkins University - University of Maryland Diabetes Research Center Integrated Physiology Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 24,2024. Core consisting of several subcores: Ligand Assay and Biomarker Subcore (offers services in Multiplex Assay Detection Systems, Comprehensive Laboratory Animal Monitoring System (CLAMS), and Body Composition), Rodent Physiology and Behavioral Analysis Subcore, and Glucose Metabolism Analysis Subcore (provides services in Dynamic Physiologic Testing).
Indiana Diabetes Research Center Swine Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 14,2024. Core which utilizes a breeding colony of Ossabaw swine with metabolic syndrome and long-term complications, most notably cardiovascular disease. It provides swine maintenance (glucose tolerance tests, body composition, glucose clamp studies, and imaging studies), characterization of cardiovascular disease (intravascular ultrasound, blood flow velocity, microvascular studies), and tissues (both banked and fresh) for analysis ex vivo.
Johns Hopkins University - University of Maryland Diabetes Research Center Cell Biology Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 9,2024. Core that provides services in tissue analysis and imaging, islet biology, liver biology, and adipocyte biology. It includes the indepedent cores Derivation of IPSC and Bioenergetics as well as the Specialty Animal Surgery Subcore and Bone Biology Subcore.
Johns Hopkins University - University of Maryland Diabetes Research Center Gene Editing Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 9,2024. Core that provides services in Gene Editing Expertise Using CRISPR/CAS9, Conventional Transgenic Mouse Generation, Conventional Knockout, Knock-In Mouse Generation, and Cryopereservation of Sperm, Oocytes and Embryos.
Joslin Diabetes Center Bioinformatics and Biostatistics Core
Core that offers support for data-driven projects related to basic, clinical and translational research, with a particular emphasis on diabetes. The core aims to ensure that researchers take advantage of the most modern and robust methods available in the field of Bioinformatics and Biostatistics.
Johns Hopkins University - University of Maryland Diabetes Research Center Health and Populations Science Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 9,2024. Contains description of and contact information for multiple health and social science departments.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 9,2024. Six component core which facilitates the exchange of research information and discussions among investigators, fellows and students within the Joslin Diabetes Center, as well as between Joslin Staff and outside researchers with similar interests.
University of California San Diego - University of California Los Angeles Diabetes Research Center Metabolic and Molecular Physiology Core Facility
UCSD UCLA DRC Metabolic and Molecular Physiology
University of California San Diego - University of California Los Angeles Diabetes Research Center Metabolic and Molecular Physiology Core
Provides DRC investigators with thorough scientific consultation and timely, accurate, and easily accessible mouse, tissue, and cellular phenotyping. Services include whole animal, tissue and cellular metabolism, insulin action, and inflammatory signaling as well as cardiac, vascular and renal phenotyping associated with diabetes complications research. It also administers drugs and other substances to mice by different routes in a well-controlled setting.
University of California San Diego - University of California Los Angeles Diabetes Research Center Transgenic and Knockout Mouse Core Facility
UCSD UCLA DRC Transgenic and Knockout Mouse Core
University of California San Diego - University of California Los Angeles Diabetes Research Center Transgenic and Knockout Mouse Core
Core that provides and produces transgenic mice. Services and methodologies include pronuclear microinjection and blastocyst microinjection for creation of new mouse cell lines as well as archival services like embryo and sperm freezing.
University of California San Diego - University of California Los Angeles Diabetes Research Center Genomics and Epigenetics Core Facility
UCSD UCLA DRC Genomics and Epigenetics Core
University of California San Diego - University of California Los Angeles Diabetes Research Center Genomics and Epigenetics Core
Core which provides Diabetes Research Center investigators access to high-throughput sequencing, data acquisition and analysis. Its main services include Sample QC and Processing, Illumina Platform Library Preparation and Sequencing, and Expression microarrays (RNA, microRNA).
University of California San Diego - University of California Los Angeles Diabetes Research Center Targeted Pathway Analysis Core Facility
UCSD-UCLA DRC Targeted Pathway Analysis Core
University of California San Diego - University of California Los Angeles Diabetes Research Center Targeted Pathway Analysis Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 8, 2024. Core with main goal to steer investigators through introductory discovery lipidomics and proteomics experiments toward statistically powered, targeted experiments aimed at measuring biological pathways relevant to diabetes and metabolism.
University of California San Diego - University of California Los Angeles Diabetes Research Center Human Genetics Core Facility
Core provides services such as assistance in the development and successful completion of well-designed genetic studies, establishment and storage of EBV-transformed lymphoblastoid cell lines (LCLs), as well as PAXgene tubes, and specialized (e.g., the exome chip) single nucleotide polymorphism (SNP) testing, candidate gene sequencing, whole exome sequencing (WES), whole genome sequencing (WGS), and large-scale gene methylation analysis.
University of California San Diego - University of California Los Angeles Diabetes Research Center
Research center across five institutions for clinical research in diabetes. Collaborators include UC San Diego's School of Medicine, Salk Institute, Cedars-Sinai Medical Center, UC Los Angeles' School of Medicine, and LA Biomedical Research Center.
University of California San Francisco Diabetes Research Center Mouse Metabolism Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 10,2024. Core which provides technical support for UCSF investigators to conduct metabolic studies using a 12-chambered Comprehensive Lab Animal Monitoring System (CLAMS), an EchoMRI, and Dual energy X-ray absorptiometry, which together allow measurement of food intake, water intake, motor activities, core temperature, and body composition in live mice. It also helps to identify emerging technologies that will enhance multiple research programs and coordinates the acquisition and maintenance of those facilities.
University of California San Francisco Diabetes Research Center
One of sixteen research centers established by the National Institute of Diabetes and Digestive and Kidney Diseases that fosters research and training in the areas of diabetes and related endocrine and metabolic disorders.
University of California San Francisco Diabetes Research Center Microscopy Core Facility
Core that consolidates, enhances and disseminates Diabetes Center resources and expertise in tissue and cell imaging technologies. Confocal fluorescence, widefield fluorescence, high throughput fluorescence and brightfield microscopes are available directly within the DRC Microscopy Core. Image quantification and analysis is performed at dedicated workstations.
University of California San Francisco Diabetes Research Center Lentiviral RNAi Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 5,2024. Core that provides reagents, equipment, training, supervision, and monitoring of investigators wishing to ensure the proper compliance with biosafety containment required for lentiviral-based research, lentiviral preparation services for investigators, and education on RNAi experimentation, through the lentiviral core website, and through protocols available at the facility.
University of California San Francisco Diabetes Research Center Islet Production Core Facility
Core that enables clinical and basic research that analyzes the function of isolated pancreatic islets. It coordinates and delivers purified human islets to investigators when research need matches the availability of a human pancreas.
University of Alabama at Birmingham Diabetes Research Center
Research center which operates in collaboration with the University of Alabama Birmingham Comprehensive Diabetes Center to promote excellence in diabetes research and patient care. The DRC supports the areas of animal physiology, human biology and intervention and translational research. It focuses on developing new methods to treat, prevent, and ultimately cure diabetes and its complications.
University of Alabama at Birmingham Diabetes Research Center Administrative Core Facility
Core responsible for the scientific, education/enrichment, and fiscal operations of the DRC. Their goal is to assure the growing vitality of an intellectual community and a highly productive research program in diabetes by effective deployment of DRC resources for the benefit of our investigators, patients, and trainees.
University of California San Francisco Diabetes Research Center Mouse Genetics Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 5,2024. Core that provides a shared resource for the establishment of mutant mouse models for DRC research. It coordinates DRC members with contacts to a number of UCSF-wide facilities for knock-out/knock-in and transgenic mouse generation.
University of Alabama at Birmingham Diabetes Research Center Animal Physiology Core Facility
Core that provides diabetes researches with diabetes related phenotyping in small animal models. Their services offered include the assessment of body composition, energy balance, glucose homeostasis, cardiovascular assessment, imaging, and transgenic animals models.
University of Alabama at Birmingham Diabetes Research Center Human Physiology Core Facility
Core which incorporates and combines expertise and technology for assessment of hormones and other analytes in both humans and animal models; body composition and fat distribution; insulin sensitivity and substrate metabolism; energy expenditure; and cardiovascular function.
Michigan Diabetes Research Center (MDRC)
Multidisciplinary unit of the University of Michigan funded by the National Institute of Diabetes and Digestive and Kidney Diseases/National Institute of Health. Promotes new discoveries and enhance scientific progress through the support of basic and clinical research related to diabetes, its complications, and related disorders. Creates environment that supports innovative research; attracts and retains early stage investigators and investigators new to diabetes research; provides core services that leverage funding and unique expertise; fosters interdisciplinary collaborations; raises awareness and interest in fundamental and clinical diabetes research at their institutions, as well as locally, regionally, and nationally.
University of Alabama at Birmingham Diabetes Research Center Bioanalytical REDOX Biology Core Facility
Bio-Analytical Redox Biology (BARB) Core
Core which promotes redox biology in diabetes-related research. It promotes research in areas common to the metabolic and vascular aspects of diabetes and cardiovascular disease. The core provides services in mitochondrial damage, function, proteomics, and oxidative stress assessment support for investigators carrying out diabetes mellitus (DM) and cardiometabolic disease (CMD) research at UAB.
University of Chicago Diabetes Research and Training Center
Center which promotes multidisciplinary research in diabetes through raising awareness and interest in fundamental and clinical research, enhancing diabetes research, education and training opportunities, and providing core services that leverage funding and unique expertise.
Michigan Diabetes Research Center Administrative Core Facility
Michigan Diabetes Research Center Administrative Core
Administration Core of the Michigan Diabetes Research Center (MDRC) provides leadership, infrastructure, and resources to support and enhance diabetes research, including the translation of scientific discoveries from bench to bedside. Establishes, promotes, and enhances multidisciplinary and collaborative basic biomedical and clinical research among member investigators studying diabetes, its complications, and related endocrine and metabolic disorders.
Johns Hopkins University - University of Maryland Diabetes Research Center Molecular and Translational Genomics Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Core that provides services in genotyping, sequencing, biobanks, and genetic epidemiology. It also offers access to the Amish exome variant database, basic molecular services, and viral vector construction and development.
Michigan Diabetes Research Center OMICS Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Core that supports the use of the OMICS technologies by MDRC members (specifically on projects relevant to diabetes and related endocrine and metabolic disorders, including their complications) by supporting pilot studies that utilize these technologies.
Michigan Diabetes Research Center Microscopy and Image Analysis Core Facility
Michigan Diabetes Research Center Microscopy and Image Analysis Core
Provides MDRC researchers with expert consultation, training and support for routine and advanced microscopy and image analysis techniques. Services include Consultation and Advice on Microscopy and Immunohistochemistry, Cryosection Service, Confocal Microscopy, Image Analysis, Widefield Light Microscopy,Live Cell Microscopy,Training and Education.
Michigan Diabetes Research Center Molecular Genetics Core Facility
Core that provides services related to the application of genetic methodologies to research related to diabetes. Services include generation of targeted genetic mouse models, using CRISPR/Cas9 system in mouse or rat embryos, generation of specialty viral vectors, specialty viral reagents, and specialty mouse models.
Joslin Diabetes Center Induced Pluripotent Stem Cell Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Core that maintains a centralized facility for the generation and propagation of reprogrammed iPS cells for use in molecular and cellular pathologies underlying diabetes and its complications.
Penn Diabetes Research Center Functional Genomics Core
Core which offers experiment planning, sample preparation, quality assessment, library construction, DNA sequencing, and data analysis services to DRC members. Its services also include RNAseq, microRNAseq, GroSeq, CLIP-seq, nucleosome mapping, ATAC-Seq, ChIPseq, Exome sequencing, whole genome and targeted methylome analysis, hydroxymethyl DIP, and single cell RNAseq.
Penn Diabetes Research Center Metabolomics Core
Core which aims to develop and validate metabolomic methods and data analysis software and provide high quality routine metabolomic services. Its services include quantitation of selected water-soluble metabolites, fatty acids, and lipids, quantitation of metabolic fluxes using stable isotope tracers, and identification of novel metabolites involved in diabetes pathophysoiology.
Diabetes research center created to address the prevalence of diabetes and obesity. The goal of the center is to support and develop successful approaches to the prevention, treatment, and cure of diabetes mellitus and obesity.
University of Washington Diabetes Research Center Administrative Core
Core facility that supports the Diabetes Research Center in its primary mission to enhance research, education and training in diabetes, obesity and related disorders at the University of Washington and in the Greater Seattle area. The Core coordinates and manages programs, evaluates Center activities, and performs other duties.
University of Washington Diabetes Research Center Cellular and Molecular Imaging Core
Core facility that provides Diabetes Research Center affiliates with access to specialized expertise and equipment required for high quality histochemical and morphological analyses in a cost-effective manner.
University of Washington Diabetes Research Center
University-affiliated center to support both basic and clinical research in diabetes and related metabolic disorders with the ultimate purpose of translating findings into opportunities to prevent these diseases and to improve clinical care and outcomes.
University of Washington Diabetes Research Center Human Studies Core Facility
University of Washington Diabetes Research Center Human Studies Core
Core facility that provides specialized technical resources and expertise to enhance the efficiency, productivity and multidisciplinary nature of clinical research performed by Diabetes Research Center (DRC)-affiliated investigators.
University of Washington Diabetes Research Center Cell Function Analysis Core Facility
University of Washington Diabetes Research Center Cell Function Analysis Core
Core facility that supports the Diabetes Research Center affiliates by offering precise real time functional analysis of intact cells and primary tissue. The Cell Function Analysis Core also provides an islet isolation service, which gives affiliates easy access to primary tissue/cells ex vivo.
University of Chicago Diabetes Research and Training Center Molecular Biology and Genetics Core Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Molecular biology and genetics core which helps independently funded investigators with an interest in diabetes mellitus and other metabolic disorders to clone, sequence and characterize cDNAs and genes of interest. It also provides research tools and expertise to enable investigators to discover how genetic variation in diabetes genes leads to hyperglycemia.
University of Washington Diabetes Research Center Vector and Transgenic Mouse Core
Core facility that provides Diabetes Research Center affiliates with vectors necessary to overexpress, knockdown, knockout, or alter expression of RNAs and proteins of interest in cultured cells, isolated tissues, and animals.
University of Washington Diabetes Research Center Quantitative and Functional Proteomics Core Facility
University of Washington Diabetes Research Center Quantitative and Functional Proteomics Core
Core facility that provides the powerful tools of modern mass spectrometry and complex data set analysis to Diabetes Research Center investigators to permit structural identification and quantitation of proteins involved in diabetes and its complications.
University of Chicago Diabetes Research and Training Center Islet Cell Biology Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core which provides services and hands-on training in the isolation and functional characterization of pancreatic islets from normal and diabetic humans and mice. It also maintains a repository of insulinoma cell lines for distribution. It puts emphasis on facilitating studies of primary islet cells and it has developed many unique tools and techniques for carrying such studies including novel animals models, biophysical methods and a library of adenovirus-based expression constructs for studying beta-cell function.
Michigan Diabetes Research Center Animal Studies Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Fee-for-service laboratory that provides consultation and utilizes specialized skills and equipment to assess the metabolic state and related endocrine and behavioral phenotypes of rats and mice. The labs include Rat Metabolic Phenotyping Lab, Optogenetics and Behavioral Phenotyping Lab, Islet Laboratory, and Continuous Glucose Monitoring Lab.
University of Chicago Diabetes Research and Training Center Animal Models and Physiology Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core whose goal is to facilitate the use of model organisms in diabetes and metabolism-related research. The Core provides access to resources, technology, equipment and services for the generation and study of genetically modified mice and other model organisms; consultation on experimental design and analysis; technology development; and opportunities for collaboration and training.
University of Alabama at Birmingham Diabetes Research Center Interventions and Translation Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core which provides expertise and services that range from methods of intervention development, basic study design and data analysis, and cutting-edge methodologies in measurement, to subject recruitment and retention strategies with an emphasis on increasing minority participation.
Washington University School of Medicine Diabetes Research Center Morphology and Metabolic Analysis Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core facility with the goal of assisting Diabetes Research Core investigators in obtaining metabolic tissues and conducting functional and metabolic analysis of cells and tissues relevant to the pathogenesis of diabetes.
Washington University School of Medicine Diabetes Research Center Mass Spectrometry Core
Core facility which provides mass spectrometry analyses to Diabetes Research Center investigators that includes quantification as well as structural characterization of diabetes-related biomolecules.
Washington University School of Medicine Diabetes Research Center
University-affiliated center established to support and enhance research in diabetes and related metabolic diseases. Its long-term goal is the development of new preventive strategies and therapies aimed at improving the lives of Americans with or at risk for diabetes.
Michigan Diabetes Research Center Clinical Core Facility
Michigan Diabetes Research Center Clinical Core
Clinical Core of the Michigan Diabetes Research Center (MDRC) provides expertise and services to support basic biomedical research, research focused on the translation of basic science findings into early phase clinical trials, and the testing of treatments related to diabetes in human subjects.
Washington University School of Medicine Diabetes Research Center Cell and Tissue Imaging Core
Core facility which provides researchers access to and technological support for advanced cellular microscopy and tools.
Washington University School of Medicine Diabetes Research Center Transgenic and ES Cell Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core facility that provides services for efficient and cost-effective development of genetically altered mouse models to elucidate the pathogenesis of diabetes and related metabolic disorders.
University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Yale University.
Washington University School of Medicine Diabetes Research Center Immunology of Type 1 Diabetes Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core facility that provides logistic support to investigators examining autoimmune or type 1 diabetes mellitus (T1DM) or other endocrine autoimmunities. Its main purpose is to foster fundamental studies on T1DM through support for acquisition and use of diabetogenic strains of mice, islet isolation, and distribution of cells and antibodies relevant for immunological studies of T1DM.
University of Chicago Diabetes Research and Training Center Administrative Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core which coordinates and directs the research and training efforts in diabetes conducted at the University of Chicago. It administrates the Pilot and Feasibility Program that supports new investigators in diabetes research as well as established investigators in other fields to conduct novel research related to diabetes.
Yale Diabetes Research Center Molecular Genetics Core
Core facility which provides genetically modified mice and rodents, mainly transgenic and knockout mice and rodents in the NOD system. It also provides transgenic mice in F2 (usually B6/C3H) and rats on Sprague-Dawley, and chimeric mice using the 129 strain ES cells. It also provides training and management
Center for American Indian and Alaska Native Diabetes Translational Research
Center dedicated to extending prevention and management research of proven efficacy to both clinical and community settings, with the goal of improving the diabetes-related health of Native Americans. The CAIANDTR provides core services and consultation locally, regionally, and nationally in areas relevant to NIDDK's translational research agenda.
Yale Diabetes Research Center Physiology Core Facility
Yale Diabetes Research Center Physiology Core
Fee-for-service core facility for DRC members to facilitate in vivo diabetes-related research dealing with biological outcomes in normal, diabetic, and genetically manipulated rodents and mice. Physiology Core is divided into two Sub-cores: the Animal Surgery and Experimental Procedure Sub-core, which provides assistance with in vivo rodent studies the Analytical Sub-core, which assists with measurement of various analytes in rat and mouse samples.
Center for American Indian and Alaska Native Diabetes Translational Research Administrative Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Administrative Core of the Center for American Indian and Alaska Native Diabetes Translational Research. The CAIANDTR is dedicated to extending prevention and management research of proven efficacy to both clinical and community settings, with the goal of improving the diabetes-related health of Native Americans.
Centers for Diabetes Translation Research
Centers that are part of an integrated program whose cores support and enhance diabetes type II translation research. The CDTRs aim to enhance the efficiency, productivity, effectiveness and multidisciplinary nature of diabetes translation research.
Vanderbilt Diabetes Research and Training Center Metabolic Physiology Shared Resource
Human Metabolic Physiology and Genomics Core
Core facility that provides a range of animal model systems to investigators working in the areas of diabetes and metabolism. It also offers surgical and experimental services, with limited analytical capacity in blood glucose and serology. The Human Metabolic Physiology and Genomics Core evolved from the Metabolic Physiology Shared Resource.
Center for American Indian and Alaska Native Diabetes Translational Research National Resource
Purpose is to assemble, focus, mobilize, provide, monitor, and evaluate resources necessary to stimulate, carry out, and translate the outcomes of diabetes prevention and management research.
Center for American Indian and Alaska Native Diabetes Translational Research Resource
Provides access to the CAIANDTR engagement core, technology core, sustainability core, and implementation, dissemination, and diffusion core.
Vanderbilt Diabetes Research and Training Center
University-affiliated center that facilitates the discovery, application, and translation of scientific knowledge to improve the lives of people with diabetes.
Vanderbilt Diabetes Research and Training Center Transgenic Mouse and ES Cell Shared Resource
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025.Core facility that provides services, consultation and collaboration to enable the generation, storage and regeneration of genetically altered mice at Vanderbilt.
Georgia Center for Diabetes Translation Research Engagement and Behavior Change Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Core which works to create more equitable health promotion and educational programs.
Washington University School of Medicine Diabetes Research Center Diabetes Models Phenotyping Core Facility
Diabetes Research Center Diabetes Models Phenotyping Core
Washington University School of Medicine Diabetes Research Center Diabetes Models Phenotyping Core
Core facility that provides services to multiple funded research projects in the area of diabetes and its complications so that rigorous experiments performed in model systems have the potential to yield compelling results that can be translated to a clinical context.
Georgia Center for Diabetes Translation Research Disparities Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Core which facilitate combined diabetes-disparities translation research that can identify ways to improve engagement in evidence-based diabetes prevention and management interventions among vulnerable populations. Their services include methodological expertise, sociocultural competencies, access to populations in community, and clinical settings, and relevant databases, tools, and technologies that help diabetes investigators.
New York Regional Center for Diabetes Translation Research Population Health and Health Systems Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Core facility that supports research that promotes the health of populations with or at risk for diabetes. The Core addresses how to improve the uptake of type 2 diabetes research findings into practice and disseminate effective interventions across health care and community settings.
Health Delivery Systems Center for Diabetes Translational Research Diabetes and Obesity Prevention Core
Research core for the prevention of diabetes and obesity in young women and children. The core works to collaborate on issues of translational interventions for diabetes and obesity prevention by research, evaluation and implementation studies.
Health Delivery Systems Center for Diabetes Translational Research
Research center for translation research on diabetes within the health care delivery systems affiliated with the HMO Research Network, University of California San Francisco, and the State of California. Their aims include improving health care disparities, diabetes and obesity prevention, and health information technology interventions.
Washington University School of Medicine Diabetes Research Center Translational Diagnostics Core
Core provides range of assays for human and animal hormones, peptides, and metabolites related to metabolic disorders.
Yale Diabetes Research Center Clinical Metabolism Core Facility
Yale Diabetes Research Center Clinical Metabolism Core
Core facility which provides personnel, methodology, and instrumentation for the centralized analysis of stable isotopic enrichment of biochemical compounds using Gas Chromatographic-Mass Spectrometric (GC-MS), Liquid Chromatographic-Mass Spectrometric-Mass Spectrometric (LC-MS-MS) and nuclear magnetic resonance spectroscopy (NMR) spectroscopic methods.
Yale Diabetes Research Center Molecular Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30, 2025. Core facility whose goal is to facilitate the introduction and use of molecular genetic methods by potential DERC investigators at Yale. It provides services, training, consultation, and equipment and resources dedicated to support essential molecular techniques.
Georgia Center for Diabetes Translation Research Design and Evaluation Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Core which provides services such as translation research and data, especially in the areas of health services research, design, and evaluation, and uptaking of prevention programs to reduce morbidity, and by generating policy- and practice-oriented data to inform investments in diabetes interventions.
Health Delivery Systems Center for Diabetes Translational Research Health Disparities Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Research core dedicated to translational research for diabetes with a focus on interventions for closing the gap in health disparities among various underserved populations. The core works to increase awareness of and techniques to survey populations equitably and effectively, evaluate the implementation of various interventions, and identify mediators for health disparities.
Yale Diabetes Research Center Administrative Core Facility
Yale Diabetes Research Center Administrative Core
Core which is designed to provide centralized offices for the coordination of the Diabetes Research Center's research activities. The core manages grant and financial management, supervises other cores and programs, and provides informataional services.
Yale Diabetes Research Center Cell Biology Core Facility
Yale Diabetes Research Center Cell Biology Core
Core whose goal is to provide instrumentation, technical personnel, and expertise for the analysis of cell function to Yale Diabetes Research Center investigators. The Core focuses on molecular and cellular imaging techniques and on analysis of islet cell function. Imaging methods include light and electron microscopy, and quantitative infra-red imaging of gels and multiwell plates.
Yale Diabetes Research Center Diabetes Translational Core Facility
Yale Diabetes Research Center Diabetes Translational Core
Core facility whose goal is to provide training and education for the development of clinical researchers in diabetes.
Michigan Center for Diabetes Translational Research Leveraging Community, Peer, and Family Support Core Facility
Michigan Center for Diabetes Translational Research MCDTR and UNC-Chapel Hill Peer Support Core
Core is outgrowth of Michigan-UNC Peer Support Core, funded through Michigan Center for Diabetes Translational Research, 2016-21. It continues the Peer Support Core’s emphasis on the variety of peers and peer support approaches and the processes that undergird them, while expanding on these to include families and communities. Services include individual consultation to researchers and on research projects, national outreach, and facilitation such as through webinars and annual research workshops of national Special Interest Group of researchers interested in contributions of and interactions among community, peer, and family supports for reducing inequity in diabetes prevention and management.
Michigan Center for Diabetes Translational Research Intervention and Technology Research Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Core that provides assistance to the Michigan Center for Diabetes Translational Research. Its three main services are consultation on content development and technologies, consultation about evidence for translatable diabetes interventions, and providing access to patient-centered health platforms.
Vanderbilt Center for Diabetes Translation Research Translation Methods Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30, 2025. Core which provides support for translational research methodological issues such as health literacy, risk communication, patient centered communication, and cultural communication.
Vanderbilt Center for Diabetes Translation Research
Research center dedicated to providing services to investigators with externally funded, diabetes-related translational research in areas such as innovations in care, community engagement, and clinical trials.
Vanderbilt Center for Diabetes Translation Research Community Engagement Core
Core facility which offers services such as consultation of study design for community-based research, development of IRB protocols, usage of community resources for recruitment efforts, and access to community charcateristics data and geographic information on the community.
New York Regional Center for Diabetes Translation Research
Center designed to increase collaboration and enhance communication among diabetes researchers from multiple institutions and diverse disciplines
Vanderbilt Center for Diabetes Translation Research Community Outreach and Heath Disparities Core
Core facility whose goal is to encourage and facilitate effective diabetes translation research among vulnerable minority populations, especially African and Hispanic Americans. They have three sub-units which include the Community-Based Participatory Research Unit/Planning Unit, the Behavioral Intervention Unit, and the Assessment, Design, and Analysis Unit. Services include a variety of assessments (psychological, dietary, community health surveys, physical activity) as well as research and implementation.
New York Regional Center for Diabetes Translation Research Life Course Methodology Core
Core facility that supports type II translational research in diabetes prevention and control. The life course perspective focuses on biopsychosocial and behavioral processes that individuals experience during particular periods in their life, and examines the interplay between these exposures in shaping disease risk.
Vanderbilt Center for Diabetes Translation Research Behavioral Intervention Technologies and Services Core
Core facility whose goal is to incorporate and implement diabetes research outcomes into clinical settings. Services include data processing management and a software toolset and workflow methodology for electronic collection and management of research and clinical trial data.
Chicago Center for Diabetes Translation Research Health Disparities and Community-Based Participatory Research Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 30,2023. Core facility that provide support for diabetes translation research aiming to reduce health disparities and support translation research in the community.
Chicago Center for Diabetes Translation Research
Center to improve the lives of people with diabetes and people at risk for diabetes through prevention, improved diabetes care, and community empowerment.
New York Regional Center for Diabetes Translation Research Translational Intervention Methodology Core
Core facility that supports research that addresses the prevention and control of diabetes using a social-ecological approach to address the dynamic interrelations of biological, psychological and social factor at a personal and environmental level.
Marion Bessin Liver Research Center Animal Models Stem Cells and Cell Therapy
Core that provides resources, technologies and scientific expertise to advance translational applications of animal and human liver cells. It also provides bred animals for research, isolation and culture of animal and human liver cells, as well as provision of cell culture additives and materials.
Marion Bessin Liver Research Center Imaging and Cell Structure
Core that supports and assists with use of specialized instrumentation, including laser scanning confocal microscopy, deconvolution microscopy, multi-photon microscopy, cryo-electron microscopy (cryo-EM) and correlative light electron microscopy (CLEM). It also provides expertise in and assistance with specialized imaging techniques such as correlative microscopy, vesicle tracking, volumetric measurements, ultrastructural sample preparation, super resolution fluorescence microscopy (STORM/SIM), Fluorescence Recovery After Photobleaching (FRAP), Fluorescence Resonance Energy Transfer (FRET) and Total Internal Reflection Microscopy (TIRF).
Washington University Center for Diabetes Translation Research Research Partnerships with American Indian/Alaskan Native Communities Core
Core facility whose services include consultation for community engagement strategies, communication with Native and non-Native American policy experts, and technical assitance in developing culturally appropriate study paradigms.
Molecular Biology and Next Generation Technology
Core that provides services ranging from classical qPCR and RT-qPCR plus specialized preparation of miRNA and development of targeted genotyping assays.
Georgia Center for Diabetes Translation Research
Research center for translational research on type 2 diabetes with a strong emphasis on translation into real world health care settings and communities.
Marion Bessin Liver Research Center Genetic Engineering and Gene Therapy
Core that provides Liver Research Center investigators an extensive array of customized viral and non-viral vectors, viral and non-viral vectors for reprogramming somatic cells, generating special non-viral vectors, consultation for study design and, if appropriate, data analysis.
Michigan Center for Diabetes Translational Research
Multidisciplinary unit of the University of Michigan funded by National Institute of Diabetes and Digestive and Kidney Diseases/National Institutes of Health. MCDTR is one of seven NIH Centers funded to focus on type 2 translational research in diabetes with mission to establish, promote, and enhance multidisciplinary collaboration among researchers directed at prevention and control of diabetes, its complications, and comorbidities, by providing access to specialized expertise and resources.
Michigan Center for Diabetes Translational Research Methods and Measurements Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Research core that works to assist investigators in designing studies, collecting data, and analyzing data to examine questions related to the causes, prevention, and control of diabetes, its complications, and comorbidities.
New York Regional Center for Diabetes Translation Research Latino Network for Diabetes Translational Research
Research network dedicated to supporting translation research in diabetes prevention and control. The core has a strong emphasis on sociocultural adaption for Latinos in the U.S and can provide expertise in Latino biopsychosocial research.
Center that conducts scientific investigation to understand fundamental mechanisms of normal liver function, alterations in these functions resulting from metabolic disorders, genetic diseases, acute and chronic liver injury, hepatitis virus infection, hepatic fibrosis and liver cancer, and ways to overcome these abnormalities through methods of genetic engineering, gene therapy and liver cell transplantation.
Texas Medical Center Digestive Diseases Center
Center designed to serve basic and clinical scientists at institutions within the Texas Medical Center, including Baylor College of Medicine, The University of Texas Health Science Center at Houston and the MD Anderson Cancer Center. It facilitates digestive diseases research, promotes translational collaborative research between basic and clinical areas, develops new projects, nurtures new investigators, and provides GI educational activities.
Health Delivery Systems Center for Diabetes Translational Research California State Resource Program
Program and partnership for supporting the California Diabetes Program. This partnership engages in various supportive activtes, including diabetes surveillance; the design, implementation, and evaluation of prevention and care strategies for diabetes; understanding the implications of policy change on diabetes care and prevention; and dissemination of new findings to diabetes stakeholders throughout the state.
Health Delivery Systems Center for Diabetes Translational Research Health Information Technology Core
Core dedicated to promoting and integrating health information technology into every day health care settings. These technologies include data networks, surveillance of patterns of diabetes care, and management tools for diabetic populations.
Michigan Center for Diabetes Translational Research Administrative Core Facility
Administrative core for the Michigan Center for Diabetes Translational Research. It works to raise awareness of and interest in type 2 diabetes research, manage its grant program, and support investigators working on both clinical and implementationl diabetes research.
Cincinnati Children's Hospital Digestive Health Center
Core that provides Digestive Health Center (DHC) investigators technologies for gene and protein expression. The services provided by the Core are grouped into five types of technologies: Gene Expression Service, DNA Sequencing and Genotyping Core, Bioinformatics Service, Protein Expression-Research Flow Cytometry Core, and Protein Multiplexing-Luminex Assay.
Center that is located within Cincinnati Children's Hospital Medical Center, that serves as a University of Cincinnati Academic Health Center resource to foster pediatric digestive disease research and make discoveries to restore digestive health.
Cincinnati Digestive Health Center Integrative Morphology
Core that provides pathology research service, live microscopy service, and confocal imaging to facilitate morphologic studies in digestive diseases.
Washington University Center for Diabetes Translation Research Health Communication and Health Literacy Core
Core facility whose services include assisting with outreach and recruitment to various populations, developing strategic community partnerships, and developing materials and methods for effective health education within the community.
Cincinnati Digestive Health Center Pluripotent Stem Cell and Organoid Core
Core whose services include generation of human induced pluripotent stem cells (iPSCs) from DHC-relevant patient cells and directed differentiation of human pluripotent stem cells (hPSCs) to human intestinal organoids (HIOs).
Cincinnati Digestive Health Center Clinical Component-Data Analysis and Management
Core that is meant to provide members with biostatistical support and the infrastructure to execute disease-based clinical research. Its services include advising on research designs, including project implementation and data collection methods, guidance on appropriate statistical methods based on study design, training and access to REDCap (Research Electronic Data Capture) for research studies, and reviewing REDCap Data Base Structure.
Center for the Study of Inflammatory Bowel Disease Genetics Genomics and Molecular Biology Core
Core that provides services in the utilization of advanced genetics and molecular biological techniques and facilitates the implementation of advances in genomics and molecular biology to IBD research. It provides access to capital or resource-intensive methodologies, such as laboratory automation cDNA and siRNA libraries, and BAC-centered recombinant DNA techniques.
Center for the Study of Inflammatory Bowel Disease
Multidisciplinary program which aims to define fundamental mechanisms underlying Crohn?s disease and ulcerative colitis. It actively promotes clinical and translational research efforts to apply insights gained in studying various disease mechanisms through its five biomedical cores: the Human Genetics and Microbiome Core, the Morphology Core, the Immunology Core, the Genetic Animal Models Core and the Clinical Core.
Washington University Center for Diabetes Translation Research Policy and Systems Science Analysis in Diabetes Research Core
Core facility whose services include policy consultation and research design advice, workshops on systems science analysis, and management of a resource library of policy and system science tools and datasets.
Washington University Center for Diabetes Translation Research
Research center for diabetes that offers regional and national resources to investigators for translation interventions into healthcare settings, communities, and populations at-risk. The CDTR supports studies investigating the root causes of diabetes and disparities as well as the prevention of obesity as a major contributing cause of Type 2 diabetes.
Vanderbilt Center for Diabetes Translation Research Administrative Core
Management core which oversees the Vanderbilt University Medical Center Pilot and Feasability Program and promotes education, training, and outreach to the research community.
Washington University Center for Diabetes Translation Research Health Informatics in Diabetes Research Core
Core facility whose services include consultation for management of complex datasets and literature resources, as well as promoting education of data analysis tools for researchers.
CURE - Digestive Diseases Research Center Human Studies Core
Core facility whose services include secretory tests, motility and pH tests, videoendoscopy, biopsy and histology, serum bank of patients with ulcer hemorrhage, and visceral sensitivity and autonomic function tests.
Chicago Center for Diabetes Translation Research Quantitative Analysis Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 30,2023. Core facility that provides analytic support for a wide range of projects in diabetes translation research ranging from program evaluation to cost-effectiveness analysis.
CURE - Digestive Diseases Research Center Morphology and Imaging Core
Core facility which provides services through centralized resources and facilities, as well as training and assistance for the application of morphological, imaging and stem cell biology technologies and promoting collaborations among CURE:DDRCC investigators with independently-funded research projects.
Cleveland Digestive Diseases Research Core Center
Center that is focused on what produces the digestive diseases that affect millions of people in the U.S., such as inflammatory bowel disease, hepatitis, metabolic syndromes and obesity.
Mayo Clinic Center for Cell Signaling in Gastroenterology Optical Microscopy Core
Core provides essential optical technologies and applications expertise to support faculty research by providing microscopic technology to all faculty members that facilitates their study of GI cellular signaling cascades, educating and training faculty members in the use of both basic and sophisticated cellular imaging methods, and developing and applying optical imaging technologies to GI tissues and cells based on faculty needs.
Center of collaborating research centers working on the research of digestive and liver-related diseases. Each center focuses on etiology, treatment, and prevention of digestive and/or liver diseases.
CURE - Digestive Diseases Research Center Molecular Biology and Peptidomics Core
Core whose aim is to promote and facilitate basic and translational GI research. Its services include consultation and troubleshooting in techniques for efficient gene delivery, as well as cloning and functional protein expression in mammalian cells in vitro and in vivo and consultation and to perform customized gene expression profiling, cytological phenotype profiling, and high-throughput molecular screening studies by utilizing high-throughput and highly automated robotic systems.
Texas Medical Center Digestive Diseases Center Functional Genomics and Microbiome
Core whose services include consultation in the choice of genomics methodologies to be applied to research problems being addressed by Digestive Diseases Center members, training in the conduct of functional genomics and metagenomics relevant to GI research, providing mammalian gene expression, cytokine/transcription factor/signaling pathway arrays, and gut microbial profiling/metagenomics to DDC members at discounted prices, and conducting periodic workshops and disseminating information about new technologies available in the Core and to obtain feedback on needed technologies / services.
Washington University Center for Diabetes Translation Research Solutions to Diabetes in Black Americans Core
Core facility whose services include consultation about the challenges that Black Americans face regarding diet and food advertising, study design and implementation assistance, and positing relevant questions to the larger core for relevant research questions.
Cleveland Digestive Diseases Research Core Facilities
Collection of four cores: the biorepository core, for clinical specimen storage; the Histology/Imaging Core, for tissue preparation and sectioning; the Mouse Models Core, for education and training on various mouse modeling techniques; and the Clinical Component of the Administrative Core, for clinical study design consultation.
CURE - Digestive Diseases Research Center Animal Models Core
Core that provides in vivo characterization of normal and pathophysiological mechanisms of hormonal and neural regulation of gastrointestinal (GI) function and brain-gut interactions in rodents to members and associate members of the CURE: DDRCC.
Texas Medical Center Digestive Diseases Center Study Design and Clinical Research Core Services
Core that provides epidemiological and biostatistical support for design and analysis, and also provides investigators with access to the clinical specimens required for their basic and translational research activities. It offers assistance as well as didactic training in issues involving local and foreign IRB?s, HIPPA regulations, and importing or exporting clinical specimens.
Texas Medical Center Digestive Diseases Center Cellular and Molecular Morphology Core
Core facility whose services include histology, immunohistochemistry, RNA in situ hybridization, mRNA probe generation, frozen sections for enzyme histochemistry, immunofluorescent antibody studies, live and fixed cell confocal, deconvolution microscopy and super resolution microscopy (SIM and STORM), and transmission electron microscopy, quantitative morphometric analysis, high throughput microscopy and high content analysis, laser capture microdissection for molecular genetic analyses, and digital images for internet communication and publication.
Texas Medical Center Digestive Diseases Center Integrative Biology Core
Core that aims to provide turnkey access to organoids/enteroid technologies to TMC-DDC researchers. These include samples (enteroids, organoids), reagents (specialized growth media, etc.), training, and consultative expertise. The core also provides access to gnotobiotic facilities and animals, training and consultative expertise.
Chicago Center for Diabetes Translation Research Outcomes Improvement Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 30,2023. Core facility that provides support to investigators in designing and carrying out translational studies assessing outcomes for patients with diabetes, or populations at risk.
Texas Medical Center Digestive Diseases Center Administrative Core
Core that provides governance, financial and operational management, and strategic planning functions for the DDC. This core is also responsible for coordinating the annual Pilot Feasibility Awards program, as well as the weekly GI Research Forum and the annual Frontiers in Digestive Medicine Symposium.
Vanderbilt Digestive Disease Research Center Bioanalytical Mass Spectrometry and Proteomics Core
Core that aims to further digestive disease research by providing services including identification of oxidized lipids by GC/MS and HR-LC/MS, proteomics for identification and characterization of proteins by MudPIT and LC-MS/MS techniques, quantification of protein expression by LC-MS/MS, interpretation and analysis of mass spectrometry data, and quantification of trace elements in physiologic fluids by ICP-MS.
Mayo Clinic Center for Cell Signaling in Gastroenterology
Center whose mission is to improve understanding of the signaling pathways that control the function of gastrointestinal cells in health and disease. It serves as a hub that provides access to research resources and expertise to multidisciplinary groups of basic scientists and clinical researchers.
Vanderbilt Digestive Disease Research Center
Center whose objectives include promoting digestive diseases-related research in an integrative, collaborative and multidisciplinary manner, developing and implementing programs for attracting, training, and retaining young investigators in digestive disease-related research, and facilitating the transfer of basic research discoveries to improvements in prevention and/or clinical care.
Mayo Clinic Center for Cell Signaling in Gastroenterology Gene Editing and Cell Engineering Core
Core whose services include designing, constructing and validating custom plasmids and other DNA vectors, making custom genome engineering reagents, including TALENs, transposons, bacterial artificial chromosomes and CRISPRs, and providing consults and training on a variety of topics, including rodent and zebrafish transgenic and knockout model development support.
Center for the Study of Inflammatory Bowel Disease Clinical Core
Core whose objective is to provide an infrastructure that facilitates the translation of basic research findings into the clinic. Its services include consultation, training, and education, biospecimen services, and facilitating data collection and analysis.
Center for the Study of Inflammatory Bowel Disease Morphology Core
Core that provides CSIBD investigators with the technical support, expertise and access to instrumentation necessary for their morphological and cell biological studies related to IBD. These services include routine tissue fixation and processing for light microscopy, imaging flow cytometry, perfusion-fixation of organs, conventional electron microscopy, low temperature embedding in Lowicryl HM20, and immunocytochemistry.
Mayo Clinic Center for Cell Signaling in Gastroenterology Clinical Core
Core facility which supports faculty research by facilitating access to human biospecimens. Its services include centralized access to participating Mayo Clinic GI biobanks and other institutional biospecimen resources, de-identified, phenotypic and demographic data, and coordination of fresh tissue acquisition from surgical pathology.
Washington University Center for Diabetes Translation Research Dissemination and Implementation in Diabetes Research Core
Core facility whose services include consultion for further dissemination of diabetes research and assistance with design methods for early dissemination of results.
CURE - Digestive Diseases Research Center Administrative Core
Management core that develops mission, goals, and strategies relating to the functioning of the CURE:DDRCC.
USC Liver Transplant Program and Center for Liver Disease Analytical Metabolic Instrumentation Core
Core that maintains and provides access and training in the use of a large base of major and expensive equipment, including thermocyclers, plate readers, centrifuges, a wide range of customized HPLC services, and Seahorse metabolic applications.
USC Liver Transplant Program and Center for Liver Disease Cell Separation and Culture Core
Core facility which provides primary hepatocytes cultures of normal and diseased mice and rats and various cell lines to investigators. The cell separation subcore plays a role in translational research in DILI and alcoholic hepatitis, supporting funded studies of the role of innate and adaptive immune systems in elucidating pathophysiology, identifying biomarkers, and predicting response to treatments.
USC Liver Transplant Program and Center for Liver Disease Cell and Tissue Imaging Core
Core that provides instrumentation (confocal and fluorescence microscopy) and technical support for cell biology and pathophysiology studies.
Washington University Center for Diabetes Translation Research Administrative Core in Diabetes Research Core
Management core whose main functions include organizing and managing membership committees, coordinating communication with the NIH and other research bases, and overseeing the use of funds.
USC Liver Transplant Program and Center for Liver Disease Liver Histology Core
Core that provides standard and customized slide preparation, liver histochemistry and immunohistochemistry as well as laser-capture microscopy.
USC Liver Transplant Program and Center for Liver Disease
Center whose goal is the facilitation and fostering of interdisciplinary collaborative research in the field of pathobiology of diseases of the liver and digestive tract and the development of new treatments for these diseases.
Center for the Study of Inflammatory Bowel Disease Genetic Animal Models Core
Core whose services include breeding and maintenance of mutant mouse stocks, characterization of murine models, bone marrow transfers and adoptive T cell transfers, in vivo tracking of fluorescently labeled bacteria and cells, and whole body imaging of bioluminescent and fluorescent signals.
Center for the Study of Inflammatory Bowel Disease Immunology Core
Core whose focus is on modern approaches to the study of the human immune system and their application to the study of IBD and related disorders. Its services include routine immunology tools, specialized immunology services, and education and training services.
Mobile simulation app for visualizing molecular interactions in liquids, solids and gases. The simulations are performed with the molecular dynamics code LAMMPS.
Simulator to help students understand basic properties of excitable membranes, particularly ion flow across an excitable membrane. The simulator is based on the equations developed by Alan Hodgkin and Andrew Huxley following their research on the excitability properties of the squid giant axon.
Neurodata Without Borders - Neurophysiology
Interactive web visualization tool for populations of bacterial genomes linked by a phylogeny.
Software tool used to carry out statistical selection of best-fit models of nucleotide substitution without the aid of PAUP*. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests, Akaike and Bayesian information criteria, and a decision theory method. It also provides estimates of model selection uncertainty, parameter importances, and model-averaged parameter estimates.
Software suite that provides an efficient way for scientist with minimal knowledge of computers to create anatomical maps and integrate this information with behavioral and physiological data for sharing on the web. It uses R for data analysis and graphical plotting and uses OpenCV for image analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Interactive Learning And Segmentation Toolkit
Interactive Learning And Segmentation Toolkit (Ilastik)
Tool for interactive image classification, segmentation and analysis, built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection.
Web software capable of scanning large-scale sequences for full-length LTR retrotranspsons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Data analysis and visualization software with features that include a R interface, demographic maps, bivariate density estimation, multiple time series visualization, repeated ANOVA measures, and a multivariate visualizers.
Software toolkit for data aquisition and analysis. Its features include remote control of Abberior Instruments microscopes via a Python/MATLAB script, third-party compatibility with other data-analysis softwares/methods, and the easyCommander graphical user interface for experimental set up.
Vanderbilt Digestive Disease Research Center Cellular Imaging Core
Core facility whose goals include furnishing professional guidance in experimental design and data interpretation and providing access to optical and electron microscopy. Its services include confocal microscopy, wide-field microscopy, transmission electron microscopy, and processing and embedment of tissue or cells for EM.
Vanderbilt Digestive Disease Research Center Flow Cytometry Core
Core facility whose services include training, acquisition and analysis on cytometers for experiments that include different fluorochromes, imaging cytometry, and mass cytometry.
Washington University Digestive Diseases Research Core Center
Research center whose purpose is to advance research in digestive disease with a focus on interactions between host and environment. It provides research resources to basic and translational investigators through various core facilities.
Washington University Digestive Diseases Research Core Center Administrative and Resource Access Core
Core facility which provides DDRCC members facilitated access to technology and assistance for genetic profiling of clinical and experimental samples.
Washington University Digestive Diseases Research Core Center Advanced Imaging and Tissue Analysis Core
Core facility which provides comprehensive histologic and immunohistochemical support, advanced microscopic imaging and image analysis services to digestive disease researchers. The Tissue Analysis Component performs animal and human tissue embedding, sectioning, routine and special staining, and immunohistochemical analyses, and provides training in all services while the Advanced Image Analysis Component provides access to and training in routine light, fluorescent and inverted fluorescent microscopy and quantitative image analysis.
Research center which supports investigation of liver structure, function and disease through access to its four core facilities (Administrative, Physiology, Clinical and Translational, and Morphology cores) and Pilot Feasability Projects.
Washington University Digestive Diseases Research Core Center Biobank Core
Core facility that collects and provides specimens and longitudinal clinical data from patients with digestive diseases. Specimens collected and processed by the core currently include blood, surgical resections, endoscopic biopsies, and stool. Clinical information is stored in a database and linked to specimens and data obtained from these specimens.
Core facility which acts as the administrative structure of the Liver Research Center. The activities it oversees include all scientific and administrative supervisory functions of the Center and its administrative leadership, including the organization and supervision of Core facilities, the planning and scheduling of the enrichment program and the review and oversight of individual pilot feasibility projects.
Yale Liver Center Cellular and Molecular Physiology Core
Core facility that provides technical expertise, equipment and personnel to Liver Center Investigators who wish to work with animal models of liver disease, isolated liver cells, or gene expression in liver tissue. The Cell Isolation sub-core isolates hepatocytes and non-parenchymal liver cells primarily from rat and mouse, while the Molecular Biology sub-core provides equipment and expertise to Liver Center members in a centralized facility.
Yale Liver Center Clinical and Translational Core
Core facility which aims to develop an infrastructure for patient-oriented research by streamlining regulatory and compliance processes, obtaining and storing high-quality samples linked to clinical information, offering consultation in the design and implementation of clinical trials, and supplying statistical expertise for interpreting clinical and translational data.
Washington University Digestive Diseases Research Core Center Murine Models and Gnotobiotics Core
Core facility that provides advice and technical services to DDRCC investigators that include production of transgenic and chimeric mice, derivation of speed congenics and assisted reproduction services for maintaining pedigrees via the Mouse Genetics Core, as well as gnotobiotic mouse provision, colonization and rederivation.
Research center which investigates the interaction between microbes and mucosal tissues in humans. It provides three core facilities for research: the Genetically-Defined Microbe Core, the Molecular Pathology and Human Cell/Tissue Core, and the Gnotobiotic and Genetically-Engineered Mouse Core.
Mucosal HIV and Immunobiology Center Genetically-Defined Microbe Core
Core composed of the Viral Unit, which provides labeled andn unlabeled viral components, and Bacterial Unit, which provides bacteria and bacterial proteins for research. The retroviral unit focues on the viral components of the retrovirus HIV-1.
Mucosal HIV and Immunobiology Center Gnotobiotic and Genetically-Engineered Mouse Core
Core facility which generates and provides gnotobiotic and genetically engineered mice to research projects. It also provides specialized breeding, marker-assisted genotyping, and histopathologic evaluation services for studies using these mice.
Core facility that provides instrumentation and technical expertise for the preparation, acquisition and analysis of images of cells and tissues at the light microscopic level. Its services include confocal and super-resolution microscopy, epifluorescent microscopy with quantitative and ratio imaging, timelapse microscopy with image processing and analysis, multiphoton microscopy, and cryosectioning.
Mucosal HIV and Immunobiology Center Molecular Pathology and Human Cell and Tissue Core
Core that provides both morphological analysis of mucosal tissues and instructs investigators in the techniques used to prepare tissue sections and analyze the morphology and cellular components of the mucosa and primary human gut (intestinal and rectal) cells, gastric mononuclear cells and genital (cervical and vaginal) cells and instruction on how to construct mucosal tissue explants in a transwell chamber system.
George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center Physiology Core
Core that provides measurement of serum and or urine Creatinine by Capillary Electrophoresis, measurement of serum and urine citrate by capillary electrophoresis, Microanalysis of serum and urine electrolytes by: Flame photometry, Atomic absorption or Ion-Selective Electrode, and Klotho IP-IB Assay.
Duke O'Brien Center for Kidney Research Animal Models Core
Core facility that provides access to a range of experimental models of kidney, heart and vascular diseases. It also provides comprehensive phenotyping services for kidney functions, blood pressure and other cardiovascular functions.
Research center which investigates the mechanisms underlying the impact kidney disease has on cardiovascular morbidity and mortality using genetic and basic science approaches.
Duke O'Brien Center for Kidney Research Renal Genomics Core
Core facility that provides resources for investigators researching the genetic mechanisms of chronic kidney disease, cardiovascular disease, and hypertension. Its services include pre-study consultation, standardized services for DNA isolation and storage, and assisstance in carrying out molecular genetic studies.
Research program whose aim is to make state-of-the art technologies and resources accessible to a broad spectrum of investigators pursuing studies in kidney research areas.
Indiana O'Brien Center for Advanced Microscopic Analysis
Imaging center which provides renal and urological researchers access to intravital optical microscopy and 3-dimensional quantitative digital image analysis.
Duke O'Brien Center for Kidney Research Clinical and Translational Core
Core facility which investigates the connections between chronic kidney disease, cardiovascular disease, and hypertension. It focuses specifically on investigating the pathophysiology, epidemiology, and therapeutic response in on-going studies or existing datasets of one of the three diseases with the aim of relating data from individual diseases to each other.
Indiana O'Brien Center for Advanced Microscopic Analysis Intravital Microscopy Core
Core facility which primarily provides service, animal models, consultation training and intravital optical microscopy customized to kidney and urologic research. It also develops and characterizes novel biosensor probes and in vivo delivery methods for these probes, as well as intravital multiphoton microscopy technologies.
Indiana O'Brien Center for Advanced Microscopic Analysis Probe Delivery Core
Core facility which develops and characterizes methods for expressing fluorescent biosensors in the rodent kidney to be paried with intravital microscopy.
Indiana O'Brien Center for Advanced Microscopic Analysis Education Core
Core faciltiy which provides instructional workshops, a visiting speakers program, and a web resource for the dissemination of methods, educational materials and software relating to imaging technologies.
Indiana O'Brien Center for Advanced Microscopic Analysis Digital Image Analysis Core
Core facility which develops and implements software and methods of image segmentation for fluorescence microscopy data.
Indiana O'Brien Center for Advanced Microscopic Analysis Administration Core
Core facility which manages and directs the activities of the O'Brien Center, facilitates interactions and collaborations among the research base, ensures quality control of the core services and promotes scientific development and enrichment on the IU SOM campus.
UAB-UCSD Core Center for Acute Kidney Injury Research Pre-Clinical Studies of AKI
Core that provides services such as expertise in development and training in the use of rodent models of AKI, specifically in the setting of ischemia/reperfusion (I/R) injury, sepsis and renal transplantation, gamma-ray imaging (gamma camera, microSPECT/CT, microPET/CT), metabolic assessments of kidney O2 consumption, and technical expertise in isolation of primary renal and vascular cell in culture.
UAB-UCSD Core Center for Acute Kidney Injury Research Administrative Core
Core facility which coordinates the various activities of the center. Its various duties include facilitating interactions and collaboration among the researchers of the center, promoting scientific development through education and Pilot funding, organizing and supporting seminars, journal clubs and symposia, and maintaining communication with members.
UAB-UCSD Core Center for Acute Kidney Injury Research Bioanalytical Core
Core that provides bioenergetics, oxidative stress analysis and metabolite analysis support for AKI research. It includes protocols and technology for bioanalytical analysis of oxidative stress and cellular bioenergetics as well as post-translational modifications.
Indiana O'Brien Center for Advanced Microscopic Analysis Biosensor Development Core
Core facility which develops, characterizes and validates fluorescence protein biosensors for intravital multiphoton microscopy.
UAB-UCSD Core Center for Acute Kidney Injury Research
Research center for kidney research, specifically acute kidney injury. It supports shared core facilities, encourages collaboration between investigators from different backgrounds and disciplines whose shared interest is in kidney research, and provides intellectual resources and infrastructure.
University of Alabama at Birmingham-University of California San Diego O'Brien Center for Acute Kidney Injury Research Biostatistical Core
Core Center for Acute Kidney Injury Research
Core provides statistical expertise in the conceptualization and design of projects, expertise in data management for the resulting clinical and bioinformatics data, and assistance with the preparation of project reports, presentations and manuscripts.
Pittsburgh Center for Kidney Research Cellular Physiology
Core that provides investigators with in vitro systems for the study of transport processes at the molecular, cell, and epithelial levels.
Pittsburgh Center for Kidney Research Single Nephron and Metabolomics
Core that offers functional (in vitro microperfusion of isolated segments, measurements of transepithelial ion/solute fluxes, fluorescence functional imaging of single tubular cells), biochemical (microassays of enzyme/transporter activity), molecular (quantitation and analysis of RNA and protein), and analytical (targeted renal metabolomics of interrelated networks of small molecules) strategies applied to microdissected tubules, single cells, and urinary exosomes to address relevant questions proposed by users. It also provides analytical services for determining concentrations of exogenous pharmacological agents and molecular probes achieved within the tissue of interest.
Center whose focus is to advance knowledge of normal kidney function, cellular mechanisms that contribute to kidney disease, and the myriad altered cellular functions that occur in the setting of renal insufficiency.
UAB-UCSD Core Center for Acute Kidney Injury Research Clinical Studies of AKI
Core facility which provides investigators access to patients with AKI through an established international network of collaborating investigators. It also provides core resources to support the design and conduct of clinical research in AKI and genomics resources to perform systematic genomic analyses and allow correlation with clinical phenotypic information.
Pittsburgh Center for Kidney Research Model Organisms
Core that uses the yeast S. cerevisiae and the zebrafish D. rerio to dissect fundamental aspects of kidney development and protein structure and function.
Pittsburgh Center for Kidney Research Kidney Imaging
Core that provides qualitative and quantitative image analysis of the kidney and lower urinary tract through performing light and electron microscopic analysis of epithelial cells and tissues, quantifying and reconstructing kidney and lower urinary tract-associated tissues and organs in 3D, and visualizing and quantifying molecular and cellular dynamics in living animals.
Pittsburgh Center for Kidney Research Biostatistical Analysis Services
THIS RESOURCE IS NO LONGER IN SERVICE, documented on Feb 16, 2022. Core that offers biostatistical analysis to users of the Pittsburgh Center for Kidney Research. Available to the Pittsburgh Center for Kidney Research community.
Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Clinical and Translational Core Resource
Core facility that provides clinical applications and methods to make kidney research translational and applicable to care settings.
George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center Animal Models Core
Core that generates and distributes several kidney-specific Cre recombinase and tetracycline-inducible activator and repressor lines to be crossed to floxed or tet responder lines provided by co-investigators.
George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center
Center whose goal is to generate new animal models to study the pathogenesis and treatment of human kidney diseases and their cardiovascular complications, accelerate the clinical application of discoveries made in renal basic science laboratories, and provide investigators with specialized tools and expertise to study kidney development, physiology, and pathophysiology.
Center that facilitates translational and clinical research that will advance the prevention and treatment of kidney diseases.
George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center Clinical and Translational Core
Core whose aim is to translate basic science research into effective diagnostic and therapeutic strategies that will improve the lives of patients by interrupting the pathogenesis of chronic kidney disease and its attendant high risk of cardiovascular disability and death. It combines comprehensive human genetics with phenotyping of subjects.
George M. O'Brien Kidney Center at Yale Renal Physiology Core
Core provides specialized services and training for assessing renal function in small animals at the level of single tubules in vitro and in vivo (e.g. micropuncture, microperfusion, and tubule-specific microdissection), the whole kidney (e.g. clearance studies in anesthetized animals, perfusion fixation for histology studies), and the intact organism (e.g. balance studies in metabolic cages, acute and chronic BP measurements).
George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center Cell Biology and Imaging Core
Core that provides services such as imaging of rodent kidney and heart including functional MRI, processing of tissues for routine paraffin embedding, and single tubule isolation and immunocytochemistry.
George M. O'Brien Kidney Center at Yale Human Genetics and Clinical Research Core
Core that provides infrastructure support for several key steps in translational research, including development of HIC protocols, patient recruitment, patient DNA extraction and archiving, tools for high throughput SNP genotyping and DNA sequencing, and analysis of genetic linkage and linkage disequilibrium.
George M. O'Brien Kidney Center at Yale Mouse Genetics and Cell Line Core
Core provides services to generate unique in vivo mouse models and kidney specific cell lines.
Pediatric Centers of Excellence in Nephrology at Cincinnati Children's Hospital Medical Center Biomarker Core
Core whose goals are to provide high throughput Clinical Biofluid Profiling Services (including initial web-based and in-person consultation, study design, sample preparation and processing, data acquisition, data analysis, protein purification, target identification, and specific assay development and validation) and services pertaining to Biomarker measurement and validation (including design of ELISA and Western Blots, measurement of known and emerging markers of acute and chronic kidney diseases, as well as consultation for biomarker statistics and clinical trials design).
Pediatric Centers of Excellence in Nephrology at Cincinnati Children's Hospital Medical Center Gene Expression Core
Core aims include to empower the Nephrology Center of Excellence investigators by providing access to integrated state of the art gene expression technologies with which to apply genomics methods to accelerate molecular nephrology research, educate, assist, and improve the use of global genomics approaches, infrastructure and specialized tools for the enhancement of research productivity and discovery by the Nephrology Center of Excellence investigators, and develop and disseminate specialized data sets and the use of advanced analytic techniques and/or protocols to facilitate translation of research data to accelerate basic and applied research and its translation to improved clinical care.
Pediatric Centers of Excellence in Nephrology at Cincinnati Children's Hospital Medical Center
Center whose goal is to support basic, translational, and clinical research on critical pediatric kidney diseases by focusing on Acute Kidney Injury, Nephrotic Syndrome, and Lupus Nephritis.
Pediatric Centers of Excellence in Nephrology at Duke Division of Pediatric Nephrology
Center that emphasizes diagnosis, treatment and management of all types of nephrologic and hypertensive disorders in infants, children, and adolescents. Therapies range from medical management to renal replacement therapy.
Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester Human Imaging Core
Core provides semiautomated MRI and computed tomography (CT) image and volumetric analyses of polycystic kidneys and liver as well as functional assessment of the kidney and heart, including measurements of renal blood flow. It also facilitates the transmission, collection and storage of anonymized imaging data used in translational PKD research and provides a system that enables PKD researchers to exchange images.
Polycystic Kidney Disease Research and Translation Centers
A portal with detailed information about various research centers that focus on kidney disease and translational research funded by NIDDK.
Cincinnati Children's Hospital Pediatric Center of Excellence
Core that provides quantitation and identification of protein changes by 2D gel-based methods and isotope tagging and nanoLC-MS/MS, identification of protein biomarkers detected from biofluids in the Biomarker Core, and provision of dedicated and expert Biostatistical and Bioinformatic support for data analysis.
Pediatric Centers of Excellence in Nephrology at University of Virginia
Center for the study of the development of the kidney during embryonic, fetal and postnatal life. As a collaboration between the University of Virginia and Tulane University, they use an interdisciplinary and inter-institutional approach for their research.
Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester Molecular Genetics and Biomarker Core
Core services include mutation screening of cell lines derived from ADPKD patients, mutation screening of large, typical ADPKD populations, genetic screening of atypical PKD families, cystic Kidney and Liver Disease Biobank (CKLBB) from ADPKD patients, and urine collection and fractionation.
UAB Hepatorenal Fibrocystic Diseases Core Center Hepato-Renal Fibrocystic Diseases Translational Resource
Core whose goals are to establish a national resource for clinical data, DNA, and tissue biopsies from human patients with HRFDs, develop algorithms to identify causative genetic mutations in HRFD patients and utilize a suite of new tools to assess the pathogenicity of sequence variants, and expand the portfolio of educational information and tools to encompass the HRFD spectrum of disorders.
UAB Hepatorenal Fibrocystic Diseases Core Center Engineered Models Resource
Core whose goals include Generation of New Animal and Cell Models of HRFDs, to establish In Vivo Biosensors to Study Signaling Pathways Involved in HRFD Ciliopathies, and to generate and distribute HRFD Related Biologicals to the Center?s Investigator Base.
UAB Hepatorenal Fibrocystic Diseases Core Center
Center that focuses on understanding the causes of Cystic Kidney Disease and other related disorder and the development of new therapeutic strategies.
Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester Model Systems Core
Core that makes available PKD model systems and technologies to PKD researchers at Mayo and at other institutions. Its services include C. elegans PKD-targeted services, Zebrafish PKD-targeted services, and Rodent PKD-targeted services.
Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester
Center that concentrates on the common, adult form of the disease, autosomal dominant PKD (ADPKD). The services provided focus on understanding the genetic basis of disease, more accurately monitoring disease progression and improving prognostics, and employing model systems to explore pathogenesis and conduct preclinical testing.
UAB Hepatorenal Fibrocystic Diseases Core Center Therapeutic Screening and Drug Development Resource
Core goals include to develop in vitro predictive assays to identify and characterize HRFD lead compounds, develop in vivo predictive translational HRFD models to enhance efficacy assessment in preclinical testing, and develop advanced HRFD-specific toxicology and safety screens.
Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center
Center for research in polycystic kidney disease (PKD) with collaboration by international investigators. The center has several cores, including biomedical cores for antibody validation and cell cultures, educationa programs, and pilot programs for new projects.
UAB Hepatorenal Fibrocystic Diseases Core Center Cellular Physiology Resource
Core whose goals include to characterize mouse models of HRFD in vivo, establish mTERT and hTERT immortalized cell lines, and the physiological and molecular characterization of HFRD cell lines.
Yale Cooperative Center of Excellence in Hematology Cell Preparation and Analysis Core
Core facility which provides emerging technologies in hematology and relevant training for junior investigators. Its services include in vitro hematopoiesis assays services, automated complete blood counts, morpholoigcal analyses, CRISPR based genomic editing, and FACsorting and analysis.
Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Antibody Validation and Vector Core
Core which supports the work of the Baltimore Polycystic Kidney Disease research center by providing antibody validation services and vectors to researchers.
Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Mouse Models and Biobank
Core facility which provides mouse models and a biobank of tissues and other materials for research.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July,27,2022. Core facility that provides scientific and budgetary oversight for all CCEH activities. This includes training programs, high school summer internships, and and pilot and feasibility program for new projects.
Online portal with thorough information about hematology research centers and cores. Each entry details the center's research aims, its activities and core services, and links to pilot programs.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Antibody Technology
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides custom designed monoclonal antibodies made in mice, rats and rabbits. Services include design of antigens, immunization and screening strategies; hybridoma cell line production and optimization; and custom designed antibodies for biomarker discovery.
Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Cell Culture and Engineering
Core faiclity that provides researchers with cell culturing and engineering services.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource
Co-operative Center for Excellence in Hematology
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core provides bioinformatics specialists available to assist researchers with processing, exploring, and understanding genomics data.
Yale Cooperative Center of Excellence in Hematology Imaging Core
Core facility which provides access to and training and consultation for imaging technology and platforms for hematology research.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Comparative Medicine
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides a variety of animal housing, veterinary and research support services.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Genomics Shared Resource
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides expertise and support for generating genomics-based data. Services for DNA arrays, genetic analysis, and high-throughput screening are provided through three specialized laboratories.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Arnold Library
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27, 2022. Library that provides physical and digital research resources for Fred Hutchinson's Center in Cancer Research. Physical resources include a library with high-speed internet and computer lab resources as well as access to digital research journals, databases and web services.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Experimental Histopathology Shared Resource
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2022. Core facility which provides various histology, histochemistry, immunochemistry, and pathology services. They also provide technical training for histopathological methods and tools.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Electron Microscopy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2022. Core facility that provides transmission electron microscopy and scanning electron microscopy for Fred Hutch, Cancer Consortium and Seattle area researchers. Services include immunogold labeling, negative staining, and a variety of sample preparations including cryo techniques, high pressure freezing (HPF) and automatic freeze substitution (AFS).
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Glassware Services
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides cleaning and sterilization of reusable laboratory glassware. Services include washing, drying and sterilization of glassware, pipette plugging and autoclaving of laboratory liquids. The core also provides support for operation of media services and biohazardous waste processing.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Specimen Processing/Research Cell Bank
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. A specimen processing/research cell bank that provides a broad range of services including processing of blood, urine, buccal, peripheral blood mononuclear cells (PBMC); DNA extractions; mycoplasma testing; and DNA fingerprinting for cell line verification. The facility also offers specimen storage options and tissue culture of B cells.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Flow Cytometry
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility which offers various options for instrumentation, from single-laser benchtop analyzers to complex multi-laser cell sorts for cell analysis and sorting. Technical assistance is available for the evaluation and interpretation of data as well as assistance in experimental design.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Research Freezers and Sample Storage Resource
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2022. Core facility that provides space for freezers used to store research samples, offers assistance with evaluating the space and power needs for new freezers, provides information on best practices, and provides access and allocates space in the shared freezer facility.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Proteomics Resource
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides support for characterizing proteins and peptides by mass spectrometry and high-performance liquid chromatography.
Center for Iron and Heme Disorders at the University of Utah Iron and Heme Core
Core facility that provides analysis of metals, precursor porphyrins and heme for cell pellets, tissue, whole blood, urine, feces and other complex biological materials. It also provides measurements of activity of the enzymes responsible for heme biosynthesis for cell pellets, tissue and blood.
Center for Iron and Heme Disorders at the University of Utah Metabolomics Core
Core facility which provides metabolite profiling analysis through three chemical analysis platforms, GC-MS, LC-MS and NMR.
Center for Iron and Heme Disorders at the University of Utah Administrative Core
Core facility which oversees the operational and financial functioning of the CIHD. It aims include periodically reviewing current membership and selecting new members, monitoring administrative and scientific activities of the CIHD, and selecting projects to be funded through the Pilot and Feasibility Program.
Center for Iron and Heme Disorders at the University of Utah Mutation Generation and Detection Core
Core facility which provides custom TALEN and Crispr-Cas9 DNA nucleases to induce targeted mutations in a genomic region of interest. It also provides hardware, reagents, and expertise for optimizing and performing HRMA for genes of interest.
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Scientific Imaging
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Scientific imaging service that serves as a centralized facility for imaging and visualization. The core facility provides access to time lapse and 3-D microscopy and quantitative autoradiography.
Center for Iron and Heme Disorders at the University of Utah
Research center for iron and hematology research. It hosts cores that provide services for mutation generation and detection, metabolomics, and iron and heme experiments and research. In addition to these cores, it has an Enrichment Program, and Internal and External Advisory Committees, and a Pilot and Feasibility program.
Indiana University Cooperative Center of Excellence in Hematology Experimental Mouse Resources Core
Core facility which maintains on-site breeding colonies of mouse strains essential for study of murine and human hematopoietic cells in vivo. It also provides specialized core services and consultation to CHSCC investigators and serves as an educational resource for CHSCC laboratories.
Indiana University Cooperative Center of Excellence in Hematology
Research center for hematology research. It provides services through four scientific core facilities: the Experimental Mouse Resources Core, the Optical Microscopy Services Core, the Angiogenesis Core, and the Flow Cytometry Core in addition to the Enrichment Program of the Center.
MMPC-University of Michigan Medical School Animal Care and Germ-Free Mouse Core
Core that provides services to the University of Michigan community and can also ship germ-free mice to locations worldwide. Its projects include studies investigating inflammatory bowel disease and cancer, host microbiome interactions, infectious disease pathogenesis, and mammalian and bacterial metabolism.
Indiana University Cooperative Center of Excellence in Hematology Angiogenesis Core
Core facility which conducts validated and reproducible in vitro and in vivo angiogenesis, endothelial, hematopoietic and multi-parametric flow cytometry assays and their role in normal and patient-related hematologic and cardiovascular disorders.
Indiana University School of Medicine Flow Cytometry Core Facility
Indiana University Cooperative Center of Excellence in Hematology Flow Cytometry Core
Indiana University School of Medicine Flow Cytometry Core
Core facility which provides flow cytometry consultation, technical advice, flow cytometric analysis and cell sorting services as well as flow cytometric image analysis.
Indiana University Cooperative Center of Excellence in Hematology Optical Microscopy Core
Core facility which provides access to and training on optical microscopy instruments to Indiana University researchers.
Boston Children's Hospital Center of Excellence in Molecular Hematology
Research center investigating molecular hematology through mouse and zebrafish models.
Yale Cooperative Center of Excellence in Hematology Animal Modeling Core
Core facility which provides expertise, technical assistance, and mice for human-into-mouse xenotransplantation studies. Mouse models include MITRG-SKI (KnockIn) mice that express human cytokines and huSIRPa from the endogenous murine loci in the Rag-/- IL-2Ry -/- background. It also offers training and technical assistance in the study of hematopoiesis and benign hematologic questions in mice.
Boston Children's Hospital Center of Excellence in Molecular Hematology Mouse Embryonic Stem(ES) Cell and Gene Targeting Core
Core facility which generates genetically modified mice with gene knockout/knockin lines for analysis gene function in hematopoiesis.
Yale Cooperative Center of Excellence in Hematology
Research center that provides access to and training in hematology technologies via three technology cores, Pilot and Feasibility funding, and an Enrichment Program.
Boston Children's Hospital Center of Excellence in Molecular Hematology Stem Cell Engineering and Analysis Core
Core facility for basic and translational stem cell research. The core's areas of expertise include human pluripotent stem cell biology, cGMP cell manufacturing, reprogramming, genome editing, genotyping, laboratory automation, chemical screening, and imaging/image analysis.
MMPC-Vanderbilt University School of Medicine Cardiovascular Pathophysiology Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 6th,2023. Core whose objective is to provide investigators at Vanderbilt and outside institutions a means to accurately assess cardiovascular phenotypes in mouse models of diabetes and metabolic disease. The CPC uses validated approaches and state-of-the-art instrumentation that allow for sensitive screening of phenotypic variations.
MMPC-University of Michigan Medical School Metabolism Bariatric Surgery and Behavior Core
Core whose services include in vivo physiological assessments encompassing glucose homeostasis (glucose tolerance, insulin tolerance, hyperinsulinemic/euglycemic clamps), energy homeostasis (indirect calorimetry by CLAMS, dietary challenge), ultradian hormone secretion (Culex platform for serial biological fluid sampling from unrestrained mice), behavioral measurements (locomotor activity, meal pattern analysis, operant conditioning) and generation of bariatric surgery models.
Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core
Zebrafish core facility which generates and maintains transgenic and mutant fish lines for hematology research. It also provides expertise and training in model production, study design, and fish production for research.
MMPC-University of California Davis Animal Care Surgery and Pathology Core
Core that provides importation/exportation, colony management, customized mouse models, rederivation and creation of genetically-modified mutant mice (e.g. CRISPR), and re-animation of a variety of models cryopreserved within the KOMP or MMRRC repositories. It also provides ancillary services and procedures, including blood sampling for in vivo testing for glucose tolerance tests and insulin tolerance tests.
Center that provides the scientific community with metabolic and physiologic phenotyping tests, services, and procedures for mouse models of diabetes, diabetic complications, obesity and related disorders in order to advance medical and biological research.
MMPC-University of California Davis Endocrinology and Metabolism Core
Core that provides phenotyping services for the assessment of endocrine function and metabolic pathways in mouse models of obesity, diabetes, and related metabolic diseases including dyslipidemia and fatty liver disease.
MMPC-University of Cincinnati Medical Center Cardiovascular and Renal Function Core
Core that offers services in testing animal physiological variables such as blood pressure, heart rate, pulse pressure and activity after inserting a PA-C10 telemetry device in them.
MMPC-University of California Davis Microbiome and Host Response Core
Core that offers measurement of gut permeability, plasma lipopolysaccharide binding protein (LBP) assay, and inflammatory profiling.
MMPC-University of California Davis Administrative Core
Core responsible for oversight and coordination of all aspects of the scientific and administrative operations of the MMPC-UCD. This includes providing full customer support services, overseeing management and operation of the Center, and foster interactions and synergism among cores and research projects. The ultimate goal of the Core is to ensure that the Center effectively and efficiently delivers services to its users.
MMPC-University of Cincinnati Medical Center Lipid Lipoprotein and Glucose Metabolism Core
Core that provides services based on the testing and analysis of fat lipids, intestinal lipid absorption, and cholesterol in tissues.
MMPC-University of California Davis Energy Balance Exercise and Behavior Core
Core that provides investigators with services to accurately measure the major components of energy balance in their mouse models and tests that allow investigators to examine physiological factors that may influence food intake or energy expenditure.
MMPC-University of Massachusetts Medical School Analytical Core
Core that provides analysis of hormones, cytokines, chemokines, metabolites, and electrolytes across multiple platforms (serum, tissues, homogenates, and cells) as well as liver function analysis through instrumentation.
MMPC-University of Cincinnati Medical Center
Research center that provides metabolic and physiologic phenotyping services for mouse models of diabetes, diabetic complications, obesity and related disorders. It specializes in the immunological aspects of Type I diabetes, measurement of various glucose and lipid metabolism parameters relevant to Type II diabetes as well as diabetic complications such as heart disease and obesity.
MMPC-University of Massachusetts Medical School Animal Care Core
Core which provides services and facilities for stable, biocontainment housing, husbandry, and health care of mice. The Core manages transfer of mice from the user's institution and testing of mice for the quarantine process.
MMPC-University of Massachusetts Medical School Metabolism Core
Core that conducts specialized and non-invasive metabolic experiments to measure insulin sensitivity, glucose/lipid/protein metabolism, pancreatic beta-cell function, body composition and energy balance. Its services include access to hyperglycemic clamps to assess insulin secretion and pancreatic beta cell function in awake mice and exercise studiesl with acute, chronic endurance, and exhaustive exercise protocols and using in-house cage wheels.
MMPC-University of Massachusetts Medical School Islet Core
Core which provides comprehensive in vivo, ex vivo, and in vitro analysis of pancreatic function and islet structure. Its services include mouse pancreas preparation for histological experiments, surgical isolation of mouse islets, and islet structural analysis.
MMPC-University of Cincinnati Medical Center Energy Metabolism Food Intake and Body Weight Regulation Core
Core that specializes in total body/carcass analysis, measurement of oxygen consumption and carbon dioxide production, meal pattern analysis, and feeding mass/bouts, drinking volume, VO2 and VCO2.
MMPC-University of Massachusetts Medical School Humanized Mouse Cell Transplantation and Assessment Core
Core which provides humanized mice that enable clinically relevant in vivo studies of human cells, tissues, and immune system without putting patients at risk and expert in vivo functional analysis of transplanted human islets and stem cell-derived b-cells in immunodeficient mice that are highly valuable to the mouse research community.
MMPC-University of Michigan Medical School
Research center which aims to contribute to a national database of metabolic phenotyping data in wild-type mouse strains and a broad range of mouse models relevant to the pathogenesis and treatment of diabetes, obesity and associated metabolic disorders. It also aims to foster continued technical development, refinement of assay sensitivity and specificity, data reproducibility, and transmission of best research practices within the areas of fundamental and applied diabetes and obesity research.
MMPC-Vanderbilt University School of Medicine
Research center whose mission is to advance research in the area of diabetes by providing experimental tools to the scientific community for phenotyping mouse transgenic models of diabetes and related disorders.
MMPC-University of Massachusetts Medical School Cardiovascular Core
Core that provides phenotyping of cardiovascular system in mouse models of metabolic disease and an easily accessible cardiovascular disease model pipeline. It services include 2D and M-mode echocardiography in lightly-anesthetized mice to non-invasively assess cardiac structure and function using state-of-the-art high-frequency, high-resolution in vivo digital imaging platform as well as Transverse Aortic Constriction (TAC) model to investigate pressure-overload hypertrophy, congestive heart failure, and aortic stenosis.
MMPC-University of Michigan Medical School Microvascular Complications Core
Core which provides a complete range of microvascular phenotyping of murine models of diabetes, obesity and metabolic disease, including validated, reproducible and standardized phenotyping of the three major microvascular complications: diabetic polyneuropathy, nephropathy and retinopathy.
MMPC-Vanderbilt University School of Medicine Metabolic Regulation Core
Core whose services include determining the components of energy balance with high precision and time resolution, providing robust imaging technology to monitor the dynamics of cellular process, and providing innovative mouse bariatric surgery models with application to basic and translational research.
MMPC-University of Michigan Medical School Microbiome Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 16,2025. Core whose mission is to provide analytical tools to investigators to permit determination of the structure of the microbiome in mouse models of disease and assistance in the cultivation of microbes that will permit hypothesis testing in murine models including the germfree animals that are available in the Animal Care Core.
MMPC-Vanderbilt University School of Medicine Analytical Resources Core
Core that consists of three subcores: Hormone Assay and Analytical Services, Lipids, Lipoproteins, and Atherosclerosis, and Mouse Pathology. The Hormone Assay and Analytical Services provides analyses that facilitate research in diabetic, cardiovascular, and obese animal models. Lipids and Lipoproteins Subcore provides quantitative and qualitative measurements of plasma and tissue lipids and lipoproteins to researchers who use mice to study atherosclerosis, dyslipidemia, diabetes, obesity, hypertension, and other metabolic diseases. Mouse Pathology services include standard pathology testing in hematology, clinical chemistry, parasitology, microbiology, serology, molecular diagnostics, necropsy, and research histology and pathology expertise and counseling.
MMPC-Vanderbilt University School of Medicine Animal Health and Welfare Core
Core that ensures the health and welfare of mouse models by assuring that mice admitted to the MMPC meet defined health criteria and that post-quarantine protocol assignment. It diagnoses disease and identifies unique metabolic or cardiovascular phenotypes of mice through interaction with the Comparative Pathology Subcore.
Software that fits s-shaped psychometric functions to psychophysical data using a maximum-likelihood technique. The psychometric functions available are logistic, Weibull, Gaussian integral, cumulative Poisson and step. PsychoFit produces, among other things, files with graphic information suitable for importing in a graphic program for plotting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Microscope that can visualize multiple nuclear, cytoplasmic and membrane markers in the same tissue section and with intact morphology. Its features include detection and measurement of weakly expressed and overlapping biomarkers in fixed tissue sections, autofluorescence removal technology, and the ability to work with both fluorescence and brightfield samples.
Cystic Fibrosis Research and Translation Centers
Research centers that provide support for basic, preclinical, and clinical research efforts to advance scientific knowledge and new therapies for cystic fibrosis.
Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Molecular Biology Core
Core facility that provides expertise, equipment, training, and reagents to serve the molecular biology needs for cystic fibrosis research.
Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Histology Core
Core that provides light microscopy services like prosection, tissue fixation, processing, embedding, sectioning, staining and cover slipping of paraffin, frozen and soft plastic tissue sections, as well as specialized and routine fixation, tissues processing, ultramicrotomy, staining, photomicrograph production, and analysis.
Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Functional Analysis Core
Core that analyzes ion channel properties and correction efficiency of human bronchial epithelial (HBE) cells from harvested CF lungs to provide a full characterization report to investigators, measures ion transport function of CFTR and ENaC in HBE and human nasal epithelial (HNE) cultures by bioelectric and organoid assays to asses efficacy of candidate therapies, evaluates CFTR expression and processing by biochemical analyses to assess efficacy of CFTR modulation strategies, and validates the suitability of reagents, supplies, and techniques for optimizing HBE and HNE cell integrity.
Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Pre-Clinical Core
Core whose objectives include evaluation of pre-clinical drug candidates in vitro, pre-clinical drug candidates ex vivo, and pre-clinical drug candidates in vivo.
Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center
Research team dedicated to finding a cure for cystic fibrosis lung disease. This team utilizes ion transport physiology, transgenic and gene-targeted mouse models, Phase I clinical trials, and more to research this cause.
Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Mouse Models Core
Core that provides support and expertise for mouse colony maintenance, breeding strategies, mouse lung phenotyping protocols, and submission of live-animal applications to maintain compliance with IACUC guidelines.
Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Michael Hooker Microscopy Core Facility
The Michael Hooker Microscopy Core Facility
Core that provides advanced digital light microscopy, image processing and analysis resources for users from the UNC Chapel Hill campus. It also offers instrumentation and instruction to enable users to acquire, process and analyze images from a wide variety of sample types.
Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Clinical Translational Core
Core whose services include biospecimen collection and storage, development of lung imaging outcomes, imaging training, and biostatical analysis.
Gregory Fleming James Cystic Fibrosis Research Center
Research center that maintains core facilities available for studies of cell biology, ion transport, and translational aspects of cystic fibrosis research.
Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Mucus and Mucin Biochemistry and Biophysics Core
Core that provides a service to quantify the concentration of given mucus samples for both total mucus concentration and the absolute relative contributions of each secreted mucin. It also provides quantitation of extracellular DNA. The mucus biphysics subcore component, provides core users with information on the biophysical properties of the mucus layer and its interaction with the cell surface.
Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Tissue Procurement and Cell Culture Core
Core that provides standardized cell cultures for cystic fibrosis research, notably normal, cystic fibrosis and disease control cells, tissues and fluids. Its functions include tissue procurement, airway epithelial cell isolation and culture, collecting airway surface liquid from in vivo and in vitro samples, genetic manipulation of cell cultures, creating and characterizing novel cell lines, and translation of technology and reagents to the greater cystic fibrosis research community.
Gregory Fleming James Cystic Fibrosis Research Center Cell Model and Evaluation Core
Core that assists with patch clamp and single channel analysis relevant to ion channel gating. The core also provides primary murine airway epithelial cells.
Gregory Fleming James Cystic Fibrosis Research Center Cystic Fibrosis Animal Models Core
Core that assists in mouse line generation by both oocyte micro-injection and by embryonic stem cell gene targeting technologies. It also establishes breeding colonies of cystic fibrosis mice, and genotypes and provides these to UAB investigators and furnishes electrophysiology tests of CFTR activation, including murine nasal potential difference assays and intestinal short circuit current measurements.
Gregory Fleming James Cystic Fibrosis Research Center Cystic Fibrosis Transmembrane Conductance Regulator Expression Core
Core that maintains a repository of reagents for studying CFTR and assists with expression technologies using vaccinia, adenovirus and other methodologies and antibody based detection of cystic fibrosis related gene products.
Cystic Fibrosis Center - University of California San Francisco
Research center that focuses on developing novel therapies for cystic fibrosis, enhancing research projects examining the mechanisms of the disease, and developing new small-molecule therapies that can be translated into the clinic.
Gregory Fleming James Cystic Fibrosis Research Center Cystic Fibrosis Clinical and Translational Core
Core that provides human primary nasal airway epithelial cells and bronchial airway epithelial cells, expertise in the nasal potential difference measurement, and a means to understand pathogenesis of cystic fibrosis and other metabolic diseases.
Cystic Fibrosis Center University of Pittsburgh
Research center whose goal is to understand and translate the basic mechanisms of cystic fibrosis. It uses the molecular and cell biology of CFTR, CFTR mutants, infection, and inflammation with the overall theme of translating preclinical science into clinical investigations.
Cystic Fibrosis Center - University of Washington
Research center that aims to provide resources and expertise to expedite development of potential new therapeutic approaches to correct dysfunctional CFTR and its secondary consequences, enhance understanding of evolving bacterial ecosystems and resultant host response in CF gastrointestinal and respiratory tracts, and how these interactions impact health. It also aims to develop improved assays, new drug screening assays, biomarkers and improved clinical outcome measures, as well as to better understand the metabolic and inflammatory consequences of CFTR dysfunction.
Cystic Fibrosis Center - University of Washington Clinical Core
Core that aims to provide preclinical support for novel therapeutics, work with other biomedical cores to enhance and support bacterial and human specimen repositories, and support developmental research and training.
Cystic Fibrosis Center - University of Washington Microbiology Core
Core facility which provides tools, reagents, and training for microbiological researchers investigating cystic fibrosis. They specifically provide resources for research in anti-bacterial therapies,
University of Washington Genomics Core Cystic Fibrosis Research Translation Center and Research Development Program
Cystic Fibrosis Research Translation Center
CF Research Translation Center and Research Development Program
Core provides genomics-based tools, data management and analysis tools, and creates platforms that integrate data from the Clinical and Immunology Cores for human samples and bacterial isolates. Services include consultation and experimental design assistance for using new-generation sequencing technology, data analysis, bioinformatic support, data access and storage, high throughput and new-generation whole-genome sequencing, and RNA-seq analysis of transcriptomes.
Cystic Fibrosis Center - University of Washington Host Response Core
Core whose objective is to obtain information on relevant parameters of the host response that is unique to cystic fibrosis using a variety of techniques, including in vivo and in vitro imaging, immunohistochemistry, imaging and image analysis, cells and bacteria in tissues, and quantification of chemokines, cytokines, and other factors with ELISA.
University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis
Research center whose focus is on developing effective gene vectors derived from recombinant viruses. Much of their research is in the development of new adeno-associated virus (AAV) vectors, although some of their research involves both adenoviruses and lentiviruses.
Gregory Fleming James Cystic Fibrosis Research Center Assay Core
Core that provides Ussing chamber capabilities and expertise for testing vectoral anion transport in polarized airway epithelial monolayers, and florescent dye-based methods for evaluating CFTR activity in cells grown on coverslips. The core also performs immunolocalization for proteins relevant to cystic fibrosis pathogenesis.
Cystic Fibrosis Center - University of Washington Administrative and Enrichment Core
Core that manages and oversees the UW CFRTC and its cores and pilot and feasibility programs.
University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Immunology Core
Core facility which provides a variety of assay services to evaluate cell-mediated and humoral responses to in animal models of gene therapies.
University of Iowa Center for Gene Therapy Cell Tissue Core
Core that provides centralized access to non-cystic fibrosis and cystic fibrosis tissue specimens and airway cells used for model systems to assess gene transfer to the airway and pathophysiology in cystic fibrosis.
University of Iowa Center for Gene Therapy Comparative Pathology Core
Core facility which provides comprehensive necropsy, histology, and pathology services for animal models in order to facilitate translational research in animal models of cystic fibrosis. It also houses instrumentation which allows for high-throughput optimization of immunostaining protocols and has access to morphologic equipment that allow for the scanning of large tissue areas and morphometric quantification of histologic endpoints.
University of Iowa Center for Gene Therapy
Research center which provides access to core facilities and services to aid gene therapy researchers.
University of Iowa Center for Gene Therapy Animal Model Core
Core that provides support to investigators who use animal models to study the pathogenesis of cystic fibrosis and who develop gene and other molecular therapies for cystic fibrosis. Specifically, it provides centralized production, care, breeding, genotyping, and quality control of cystic fibrosis mouse and ferret models used by investigators in the Center.
New York Obesity Nutrition Research Center Animal Phenotyping Core
Core that allows investigators to efficiently and cost effectively define the phenotypes of small rodents in ways that are relevant to the study of obesity, nutrition, and metabolism. Its services range from whole animal measurements of body composition and energy utilization, to ex vivo measurements of substrate fluxes, to histological analyses of adipose tissue.
University of Iowa Center for Gene Therapy Clinical Core
Core facility which aims to provide cystic fibrosis researchers with a biobank of archived biosamples collected during routine clinical visits and research-related visits. Biospecimens include normal and CF specimens including DNA, bronchoalveolar lavage fluid, whole blood, plasma, feces, urine, and bacterial isolates. It also aims to facilitate patient recruitment and enrollment in clinical trials.
University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Cell Morphology Core
Core facility which provides a range of technologies for morphologically based studies and technically more complex support in the detection of transgenes and transgene products using techniques of in situ hybridization and immunohistochemistry.
University of Iowa Center for Gene Therapy Vectore Core
Core facility which provides support to cystic fibrosis investigators in gene transfer technologies through consultation, development of novel vectors, collaborative testing of vectors for function and purity, and routine vector preparations.
University of Alabama at Birmingham Nutrition and Obesity Research Center
Research center that aims to understand the causal factors underlying nutrition and obesity-related health problems and the generation and evaluation of evidence on their consequences, prevention, and alleviation.
Boston Nutrition and Obesity Research Centers Adipose Biology and Nutrient Metabolism Core
Core that facilitates and fosters research on mechanisms regulating white, brite or beige and brown adipose tissue mass, distribution, nutrient signaling and depot-specific metabolic and endocrine functions in health and disease.
Boston Nutrition and Obesity Research Centers
Center that is organized to address cross-cutting themes that represent gaps in understanding the relationship between nutrition and health, and the pathogenesis of obesity and its associated metabolic diseases.
Boston Nutrition and Obesity Research Centers Epidemiology and Genetics Core
Core that provides a central focus to translate the findings from clinical and cellular studies to applications in ongoing epidemiologic studies.
Nutrition and Obesity Research Centers at Harvard
Research center at Harvard University that seeks to establish a research environment which encourages the approach to defining common clinical nutrition research problems. It aims to promote, facilitate and enhance research relating to nutrition and health within the Boston area.
Boston Nutrition and Obesity Research Centers Functional Genomics and Bioinformatics Core
Boston Nutrition and Obesity Research Center
Core provides services to investigators within BNORC and the Boston area looking to expand their research using state-of-the-art genomic applications. This core utilizes technologies and sequencing platforms to help identify the complex molecular mechanisms underlying human disease.
Nutrition and Obesity Research Centers at Harvard Administrative Core
Core that supports and coordinates the NORCH and all the components of the center. It provides insight into the processes that govern the center, to recruit and vet new members, and to communicate with all our members about center happenings.
Boston Nutrition and Obesity Research Centers Administrative Core
Core that provides administrative support and direction to all of the participating institutions and BNORC members. These services include financial management, payment requests, policy development and data management.
Nutrition and Obesity Research Centers at Harvard Metabolic Imaging Core
Core that links a variety of imaging facilities providing services to NORCH investigators who currently require or plan to conduct human studies using imaging research instrumentation and expertise. Its goal is to provide users with access to imaging technology for in-vivo phenotyping of human tissues for nutrition, obesity and metabolism studies.
Nutrition and Obesity Research Centers at Harvard Genomics and Cell Biology Core
Core that facilitates the application of genomics, bioinformatics, cell biology, and immunology techniques to nutrition and metabolic research.
Nutrition and Obesity Research Centers at Harvard Statistical Consultation
Core that provides consultations for study design and analysis, preparation of grant applications, preparation of statistical methods and results for manuscripts on completed studies, responses to reviewer comments for manuscript resubmissions, identification of possible long term statistical collaborators for grants.
Nutrition and Obesity Research Centers at Harvard Metabolic Phenotyping Core
Core that provides NORCH investigators with access to model creation and detailed metabolic phenotyping. Its services include: model generation, including genomic targeting and production of metabolically relevant cell types; metabolic characterization of patient-derived, user-provided, or model generated samples; consultation on model development and metabolic characterization projects; and training for Core techniques in model generation and detailed metabolic characterization.
Mid-Atlantic Nutrition Obesity Research Center
Center that fosters multidisciplinary research approaches to understanding the impact of nutrition on risk for chronic disease and aims to translate this knowledge into effective clinical treatments and prevention efforts.
Mid-Atlantic Nutrition Obesity Research Center Clinical and Translational Research Core
Core that facilitates the conduct of clinical nutrition and obesity research. Its team of experts in nutrition, exercise physiology, body composition, metabolism and behavioral therapy aim to assist and train NORCH investigators in the skills necessary to conduct clinical nutrition and obesity research.
Mid-Atlantic Nutrition Obesity Research Center Biological Mechanisms and Functional Genomics Core
Core that provides investigators with access to adipose tissue samples from well-characterized subjects. It also assists investigators with analysis of adipose tissue morphology and metabolism, specialized cell and organ culture methods, and analysis of gene and protein expression.
Boston Nutrition and Obesity Research Centers Transgenic Core
Core that utilizes investigator-derived DNA constructs or investigator derived (or obtained) genetically modified embryonic stem cells to create founder transgenic organisms that can be used to address questions relevant to obesity, diabetes and nutrition, including questions related to brain control of feeding, metabolism and reward.
Mid-Atlantic Nutrition Obesity Research Center Biostatistics and Medical Informatics Subcore
Core that provides biostatistical consultation to other investigators who are doing research in the fields of obesity and nutrition at University of Maryland and the Baltimore VA Medical Center. It aims to develop new methods for data collection data from older subjects.
Louisiana State University Pennington Biomedical Nutrition Obesity Research Center Core Facility
Pennington Biomedical Research Center Nutrition and Obesity Research Center Administrative Core
Provides scientific cores including Molecular Mechanisms Core (genomics and cellular), Human Phenotyping Core (characterization of phenotypes predisposing to obesity and metabolic syndrome and behavioral interventions to counteract those) and Animal Models and Phenotyping Core. Includes organizing administrative process to announce, collect, review and award Pilot and Feasibility grants, setting criteria for use of core facilities, and maintaining access to data management services.
New York Obesity Nutrition Research Center Molecular Biology and Molecular Genetics Core
Core whose goal is to assist investigators in applying the tools and technologies of molecular genetics and genomics to elucidate the molecular-genetic bases of obesity and its comorbidities. Its services include consultation on study design, analysis, and applicable molecular biological techniques and developing and making research tools and reagents.
New York Obesity Nutrition Research Center Human Phenotyping Core
Core which provides obesity and other medical eating disorder researchers with specialized measurements in body composition, energy expenditure, imaging analysis, and adipose tissue analysis in human subjects.
Pennington Biomedical Research Center Nutrition and Obesity Research Center
Research center that supports clinical investigation addressing the etiology of nutritionally induced chronic diseases across the entire age span, from gestational and perinatal development through childhood and adolescence. It provides core services to promote the investigations around the theme of molecular mechanisms of nutritional programming induced by environmental factors.
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Administrative Core
Core facility that is responsible for managing and organizing the activities of the internal governance committee and the external advisory board, promoting the techniques, methodologies, instrumentation, and resources offered by the core facilities, and supporting the integration of bioinformatics, biostatistics, clinical research, and metabolomics into clinical and translational research.
Pennington Biomedical Research Center Nutrition and Obesity Research Center Human Phenotyping Core
Core that provides users with expertise and phenotyping services for different stages in life. It specifically provides services for obesity research, unique populations (pregnant women, children, infants, etc.), and clinical and translational studies through their Energy Balance subcore and Behavioral subcore.
Pennington Biomedical Research Center Nutrition and Obesity Research Center Molecular Mechanisms Core
Core that includes a genomics subcore that provides services in genomics such as Sanger DNA sequencing and fragment analysis service, microarray analysis service, quantitative PCR, robotic pipetting for quantitative PCR and custom pipetting projects, and software analysis solutions. The Cell Biology &and Bioimaging subcore provides histology and specipmen preparation, imaging, and flow cytometry/cell sorting.
New York Obesity Nutrition Research Center
Obesity research center which provides access to core facilities, seminars, and collaborations for researchers.
Pennington Biomedical Research Center Nutrition and Obesity Research Center Animal Models and Phenotyping Core
Core that is comprised of the Animal Models Subcore and Animal Phenotyping Subcore. The former provides expertise and services for design and construction of transgenes, ES cell transfection and screening, pronuclear injection, and cryopreservation. The latter provides expertise and services for metabolism, physical activity, body composition, and behavioral research.
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Clinical Nutrition Research Facilitation Program
Core for nutrition researchers that consists of two subcores: the Human Research Core and the Nutrition Research Kitchen and Metabolism Core. The Human Research Core provides human metabolism and body composition assessments, clinical laboratory and support services, and preparation and delivery of precisely designed meals for study participants. The Nutrition Research Kitchen and Metabolism Core offers nutrition research assistance to complement clinical studies.
University of Alabama at Birmingham Nutrition and Obesity Research Center Metabolism Core
Core whose services include energy expenditure, substrate metabolism and body composition analysis to provide assessments of human energy expenditure, substrate metabolism, body composition, body fat distribution, and bone quality.
University of California San Francisco Nutrition and Obesity Research Center
Research center whose goal is to define the underlying mechanisms of disease and to contribute to the prevention and treatment of obesity and its complications. It provides collective research facilities, a lecture program that fosters interactions amongst laboratories conducting cellular, animal, translational, clinical and epidemiologic research, pilot funding for new and interdisciplinary research directions plus administrative infrastructure that promotes these integrative goals.
University of California San Francisco Nutrition and Obesity Research Center Genetics and Genomics Core
Core that provides services for genetic and genomic research, including DNA extraction, SNP genotyping, and gene expression, ES cell services with a high probability of germline transmission, microinjection of DNA for producing transgenic mice, microinjection of ES cells for producing gene knock-out mice, and 8 cell microinjection, and collection in vitro maturation and embryo transplant.
University of California San Francisco Nutrition and Obesity Research Center Human Metabolism Core
Core that renders services that provide consulting with study design, subject recruitment, and statistical analyses, conducting clinical research, and an array of specialized NORC-focused methods, instruments, and facilities for human body composition/metabolism, radiologic imaging and biobehavioral measurements for human nutrition, obesity and metabolism research.
University of Alabama at Birmingham Nutrition and Obesity Research Center Biostatistics Core
Core which provides services and expertise in the design, management and analysis of nutrition-related research projects. Its services include coordination and management of statistical activities within the Core, statistical consultation on study design, research proposal development and manuscript submission, and statistical analysis.
University of California San Francisco Nutrition and Obesity Research Center Mouse Metabolism and Imaging Core
Core that provides access to instrumentation used in metabolic studies. Instruments include a 12-chambered Comprehensive Lab Animal Monitoring System (CLAMS), an EchoMRI, and dual energy X-ray absorptiometry.
University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center
Research center that aims to provide an infrastructure to support ongoing nutrition and obesity research by providing measurements and expertise. It also aims to promote interdisciplinary collaborative, vertically integrated research among members of the Colorado research community, as well as translate basic and clinical research into programs to improve health and wellness and reduce obesity in the community.
Mayo Clinic O'Brien Urology Center Biostatistics and Epidemiology Core
Core that is responsible for all statistical, data management and epidemiological aspects of studies in the Mayo Clinic O'Brien Urology Research Center. Its services include consultation to project investigators regarding study design, data analysis and interpretation of results, maintanence of the Olmsted County kidney stone database, and development of additional linkable databases and quality control procedures.
Core that aims to define the pathogenesis of nephrolithiasis in order to improve patient care and treatment and prevention strategies
Mayo Clinic O'Brien Urology Center Imaging Core
Core that provides renal stone imaging and analysis techniques, including dual energy CT data acquisition and analyses, dual energy material decomposition analysis, high-resolution image reconstruction and analysis, and coordination of micro-CT scanning and data analysis.
Mayo Clinic O'Brien Urology Center Urine Phenotyping Core
Core that aims to increase understanding of the factors that modulate the interface of urinary proteins and crystals, and hence their subsequent interaction with other crystals or cells. Its services include quantification of urinary components of the supersaturation profile, quantification of urinary inhibitor activity, quantification of known urinary macromolecular inhibitors, and application of differential proteomics to urine samples of stone forming and control populations.
University of Michigan Nutrition and Obesity Research Center Molecular Phenotyping Core
Core that provides analytical tools to MMOC investigators to permit structural identification and quantification of metabolites as well as perform metabolic studies in in vitro systems. It also provides consultation and collaboration to apply metabolomics platforms in nutrition and obesity research.
University of Michigan Nutrition and Obesity Research Center
Research center for obesity investigators which aims to provide researchers with infrastructure, expertise, and training to facilitate improved data integration, analysis and modeling from properly designed basic, clinical, and population-based studies in obesity and metabolism-related diseases.
University of Michigan Nutrition and Obesity Research Center Animal Phenotyping Core
Core whose services include infrastructure to perform advanced, standardized, metabolic phenotyping of animal models of obesity or metabolic diseases that arise from dietary, genetic, pharmacologic or other perturbations. It also provides centralized equipment and services and aims to develop new techniques and acquire new technologies for rodent phenotyping.
Mid-Atlantic Nutrition Obesity Research Center Molecular Genetics and Nutrigenomics Core
Core that aims to discover genes and gene-nutrient interactions associated with risk of obesity, diabetes, hypertension, atherogenesis and longevity. Its goal is to understand the molecular, cellular and physiological roles of genes in the etiology of obesity, diabetes, and associated metabolic abnormalities.
University of Michigan Nutrition and Obesity Research Center Human Phenotyping Core
Core that aims to enhance and expand the research capabilities of investigators performing clinical and translational studies related to nutritional interventions, obesity, or obesity-related disorders in humans. Its services include standardized nutritional assessments and physiological testing of human subjects, researcher assistance in conducting dietary, behavioral, and/or exercise intervention in human subjects, and training in techniques or the assistance in development of new techniques and technologies for the metabolic and neurobehavioral assessment of humans.
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Communication for Health Applications and Interventions Core
Core that uses technologies to facilitate the translation of traditional evidence-based behavioral interventions into effective web- and mobile-based interventions in fields such as obesity and cancer prevention.
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center
Center whose goals include providing resources and support to investigators conducting multidisciplinary and interdisciplinary research in nutritional sciences and obesity, strengthening clinical nutrition training programs for medical students, practicing physicians, and allied health personnel, and translating findings from obesity and nutrition research to the general public.
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Metabolic Molecular Phenotyping Core
Core whose goals are to encourage and facilitate the use of biomarkers for nutritional epidemiological and intervention studies. It provides access to techniques and equipment to bench scientists, as well as assays for investigators without lab facilities.
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Nutrigenetics Core
Core facility whose services include grant writing assistance and consultation, laboratory analyses, brokerage services, and analytical services.
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Animal Metabolism Phenotyping Core
Core that offers technical support and expertise for measuring traits related to metabolism in mouse models of obesity and nutritionally relevant disease. It provides access to methods, equipment, and populations to support high quality and high throughput phenotyping of energy balance components in mice.
University of Alabama at Birmingham Nutrition and Obesity Research Center Animal Models Core
Core that provides specialized expertise in the use of animal models and instrumentation to facilitate animal research related to nutrition and obesity.
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Biostatistics Program
Core whose services include data management, manuscript development, sample size and power calculations, statistical consultation, and statistical programming for nutrition and/or obesity researchers.
University of Michigan Nutrition and Obesity Research Center Administrative Core
Core that provides leadership, infrastructure and resources to promote the integration of basic research technologies into preclinical, clinical and translational research studies, oversee the Investigational Weight Management Clinic, and recruit, train and retain basic, clinical and population-based researchers in the area of nutrition interventions and obesity and related metabolic disorders.
University of Washington Nutrition and Obesity Research Center Energy Balance Core
Core that provides affiliated investigators with a resource for measuring energy balance and body composition in rodent models, and for applying neuroscience techniques to nutrition and obesity-related research.
University of Washington Nutrition and Obesity Research Center Analytic Core
Core that provides affiliated investigators with access to nutritional assays, new methods development, and consultation services. Services also include quantitative measures of nitrogen-containing compounds, carbohydrates and related compounds, lipids and related compounds, and more.
University of Washington Nutrition and Obesity Research Center Administrative and Enrichment Core
Core that is responsible for the overall administrative coordination of the NORC. It also administers the Biostatistics Subcore, Pilot and Feasibility Program, and Enrichment Seminar Series.
Washington University St. Louis Nutrition Obesity Research Center
Research center whose activities aim to enhance understanding of the basic and clinical aspects of nutrition in the prevention, etiology, pathophysiology and therapy of nutrition-related diseases.
Program that aims to enhance the effectiveness of research related to noncancerous urologic dysfunction by encouraging collaboration amongst investigators.
University of Alabama at Birmingham Nutrition and Obesity Research Center Physical Activity Core
Core that provides physical activity services and consultation for UAB investigators. Services include aerobic fitness tests, supervised resistance training, submaximal ease/economy locomotion tests, and strength and functional tests, with respective measurements taken.
University of Washington Nutrition and Obesity Research Center
Research center that facilitates the integration and coordination of the ongoing activities of the University of Washington system. Its overarching goals are to foster interdisciplinary research collaborations, stimulate new research activities, improve nutrition and obesity education, and facilitate optimal nutritional management of patients.
O'Brien Center for Benign Urologic Research at University of Wisconsin-Madision and University of Massachusetts-Boston
Research center that is dedicated to improving urologic health in aging men by promoting development of urologic research, disseminating urologic research knowledge, and performing other research-related tasks.
O'Brien Center for Benign Urologic Research at University of Wisconsin-Madision and University of Massachusetts-Boston Rodent Urinary Function Testing Core
Core that designs, validates, and disseminates protocols for rodent urinary function testing. It also provides urinary function testing services, expertise, laboratory space, vivarium, and equipment for complete mouse urinary function testing.
University of Michigan Nutrition and Obesity Research Center Integrative Biostatistics and Informatics Core
Core facility whose services include expertise in experimental design and modeling for preclinical, clinical and translational research studies that integrate clinical, molecular, neurobehavioral and other phenotype data. It also offers support for data acquisition and analysis by the MMOC phenotyping Cores and Investigational Weight Management Clinic, expertise in database construction, maintenance and security relevant to investigators studies, and development and use of database and software tools for information organization and visualization of tightly-linked multiscale data for T1 translation of research knowledge relevant to obesity.
Columbia University George M. O'Brien Urology Center
Research center that brings together research programs in human genetics and mouse models to address the causes of congenital urinary tract malformations.
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Research Facilitation Program
UNC Nutrition and Obesity Research Center
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 23,2019. Center that provides bioinformatics and metabolomics support to UNC members for nutrition and obesity-related clinical and translational research.
University of Washington Nutrition and Obesity Research Center Adipose Tissue and Obesity Core
Core that provides affiliated investigators with assistance for in vivo and in vitro studies in both subcutaneous and visceral human adipose tissue. Body and liver fat measurement by DXA and MRI are also provided, as is support for translational studies that assist investigators in the design conduct of clinical obesity research.
Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present.
Transcriptome architecture of adult mouse brain
Image collection of transcriptome architecture of adult mouse brain revealed by sparse coding of genome-wide in situ hybridization images.
Code that segments, detects and extracts the spines from three dimensional in vivo images of dendrites with spines.
Platform provides tools and web services for multicolor fluorescence experiment design, flow cytometry, and microscopy. Provides online spectra viewer and flow cytometry panel design tools and spectral analysis. By integrating experiment design tools featuring preloaded instrument configurations with comprehensive antibody database, panel builder speeds up flow cytometry experiment design.
Microscope system performs fluorescence, bright-field and phase-contrast imaging on various specimen holders. The system allows users to switch between four fluorescent channels, automatically adjusting the filter and exposure time while preserving the longevity of the specimen.
Statistical checking software for psychology manuscripts. Users can upload APA-formatted PDF or HTML files to find errors in statistical reporting.
Commercial organization which supplies products for bioseparation and cell line management.
Commercial provider of purpose-bred animals for biomedical research. They provide dogs, pigs, ferrets, mice, and guinea pigs in physically and psychologically healthy condition.
Weighted implementation of Maximal Information Component Analysis, a co-expression network analysis algorithm for analysis of large interconnected networks and the identification of modules of similarly-acting nodes within the larger network.
Searchable database of comprehensive annotations of eukaryotic long non-coding RNAs. Entries are manually curated from referenced literature.
Database of homeobox genes in humans, mice, chickens, frogs, zebrafishes, amphioxuses, fruitflies, beetles, honeybees, and nematodes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Compilation of mammalian mitochondrial tRNA genes. Sequences are classified into families according to the amino acid specificity of the different tRNAs as defined by the anticodon triplets. Each sequence is displayed linearly with color codes indicating secondary structural domains.
Web-based transporter resource that provides access to the TransCure interdisciplinary research network, the Genomic Transporter Database, and the Biomedical Transporter Conferences page.
Searchable, manually curated collection of Kruppel-type zinc finger genes (KZNFs) in primates with finished or high quality draft genomes.
Assessment and Accreditation of Laboratory Animal Care International
Assessment and Accreditation of Laboratory Animal Care
Assessment and Accreditation of Laboratory Animal Care (AAALAC)
Private, nonprofit organization that promotes the humane treatment of animals in science through voluntary accreditation and assessment programs.
Collection of standardized stimuli of dynamic, prototypical facial expressions of pain, the six basic emotions, and a neutral display. The set can be used in cognitive, social, clinical, and neuroscience studies on facial expressions and their social communicative functions.
Fully automated tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is available for use with publicly available eukaryotic transcriptomes.
Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria.
Multi-State Markov and Hidden Markov Models in Continuous Time
Multi-State Markov and Hidden Markov Models in Continuous Time (MSM)
Source code for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. It was originally designed for processes observed at arbitrary times in continuous time but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time.
Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution.
Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species.
Source code in Python for implementation of the warped linear mixed model. It automatically learns an optimal "warping function" (or transformation) for the phenotype as it models the data.
Software that analyzes and estimates heritability. LDAK adjusts for linkage disequilibrium (LD) by calculating SNP weightings which downweight the contribution of SNPs in highly tagged regions.
Lasso and Elastic-Net Regularized Generalized Linear Models
Procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. The algorithm uses cyclical coordinate descent in a path-wise fashion.
Factored Spectrally Transformed Linear Mixed Models
FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets.
Gene prediction method that identifies potential coding regions based on the mapping of reads from an RNA-Seq experiment.
Database for visualizing and making use of public ChIP-seq data. ChIP-Atlas covers almost all public ChIP-seq experiments and data submitted to the SRA (Sequence Read Archives) in NCBI, DDBJ, or ENA.
Consortium of clinical study data providers. Its aim is to help the data sharing community drive scientific progress and improve medical care by facilitating access to patient-level data from clinical studies.
Software tool for making a BLAST database from various data structures. It maps large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
Mixed Effect Model of Genetic-Set and Environment Interaction
Mixed Effect Model of Genetic Set and Environment Interaction
Mixed Effect Model of Genetic Set and Environment Interaction Toolbox
MATLAB Toolbox which provides a mixed effect model for gene-environment interaction (MixGE) on neuroimaging phenotypes, such as structural volumes and tensor-based morphometry (TBM). This model incorporates both fixed and random effects of genetic-set and environment interaction in order to investigate homogeneous and heterogeneous contributions of sets of genetic variants and their interactions with environmental risks to phenotypes.
Software tool used to generate a list of PubMed IDs to query and generate associations between publications. It utilizes a local SQLite cache in a configurable location to keep a local copy of relevant SRIDs, PMIDs, and the Abstract sections for the PMIDs.
Project to house templates used to build other projects. It is also known as the NeuroImaging and Analysis Group, which employs various physiological, functional and structural neuroimaging methodologies in both research and clinical domains.
Patient Repository for EEG Data and Computational Tools
Patient Repository for EEG Data and Computational Tools (PREDiCT)
Patient database that contains EEG data sets, executable tasks, and computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Real-time task-based and resting-state fMRI analysis software. This software is developed and distributed to researchers by NeurInsight LLC.
Software toolkit that provides several multi-modal tools to assess brain disconnections and remote effects of lesions. All modules are designed to process brain lesion data with a normalization algorithm, a module to estimate the probability and the severity of white matter disconnections, and a tool to build a map of the disconnected areas.
Neurocare | Neuroconn DC-Stimulator Plus
Device for administering transcranial electrical stimulation. It has applications in cranial electrotherapy that provides a weak direct current for non-invasive Interventional Neurophysiology.
Instrument and software tool used to visualize, trace, analyze, and process white matter fiber tracts of Diffusion Tensor Imaging (DTI) data in real-time. It supports pre-operative surgical planning, post-surgery evaluation, and general evaluation of fiber tracts around tumors and lesions in connection with functional areas.
NeuroImaging and Analysis Group Addiction Data
Data set of addiction studies compiled by the NeuroImaging and Analysis Group (NIAG).
Metric Optimization for Computational Anatomy
Metric Optimization for Computational Anatomy (MOCA)
Collection of software tools for the computational analysis of brain anatomy with MRI data. It includes automated software tools from surface reconstruction to their mapping via metric optimization in the Laplace-Beltrami embedding space. It is general and can be applied to a wide range of anatomical structures including cortical, sub-cortical, and fiber bundle surfaces.
UManitoba - JHU Functionally Defined Human White Matter Atlas
UManitoba JHU Functionally Defined Human White Matter Atlas
UManitoba-JHU Functionally-Defined Human White Matter Atlas
Probabilistic atlas of human white matter tracts/regions underlying several well-known resting state brain networks. The atlas includes group probability maps for each network, as well as each individual tract that are aligned to both the SPM and MRIStudio ICBM templates.
Computer vision and machine learning software library which provides a common infrastructure for computer vision applications. The algorithms within the library can be used to detect and recognize faces, identify objects, classify human actions in videos, track camera movements and moving objects, extract 3D models of objects, produce 3D point clouds from stereo cameras, stitch images together to produce a high resolution image of an entire scene, find similar images from an image database, and follow eye movements, recognize scenery and establish markers to overlay it with augmented reality. It has C++, C, Python, Java and MATLAB interfaces.
Software toolkit with various functions for the analysis of nucleosome and protein occupancy by sequencing.
Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host.
Commercial organization that provides services and products in global healthcare and diagnostics.
Graph-based alignment of next generation sequencing reads to a population of genomes.
Platanus - PLATform for Assembling NUcleotide Sequences
PLATform for Assembling NUcleotide Sequences
De novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Cloud-based executable research platform for discovering and running scientific code. Code Ocean is designed to give researchers and developers a way to share, discover and run code published in academic journals and conferences. Users can upload code and data in various programming languages and link working code in a computational environment with the associated article, with Code Ocean assigning a Digital Object Identifier (DOI) to the algorithm.
Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals.
Ocean general circulation model; more specifically, a data-assimilative hybrid isopycnal-sigma-pressure (generalized) coordinate ocean model.
Public repository of mass spectral data which allows users to search similar spectra on a peak-to-peak basis, on a neutral loss-to-neutral loss basis, or by the m/z value and molecular formula, search chemical compounds by substructures, and keyword search chemical compounds
Metadata-centric, auto-curating repository designed for storage and querying of mass spectral records. It contains metabolite mass spectra, metadata and associated compounds.
In vivo/ In silico Metabolite Database (IIMDB)
Database of known biochemical compounds collected from existing biochemical databases, as well as computationally generated human phase I and phase II metabolites of known compounds.
Cloud-based mass spectrometry data processing platform for metabolomics and lipidomics.
Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification.
Non-redundant collection of publicly annotated DNA, CDS, and protein sequences of protein coding intronless genes from human genome.
Atlas was created from MRI scans of squirrel monkey brains. The atlas is currently comprised of multiple anatomical templates, diffusion MRI templates, and ex vivo templates. In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels.
Cell repository that aims to share cell samples for the scientific advancement of Type 1 Diabetes research. Cell lines can be requested from their cell bank inventory.
Software package for structural determination and other functions in the field of structural biology. Its programs can perform strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, and other functions.
Software tool for designing short interfering error-free RNA oligos.
Toolkit of MATLAB functions for computing integrated information ('phi' or 'Φ') from neural data. The toolbox consists of downloadable codes that perform practical computation.
Simulation submission manager for computational neuroscience. It manages simulation processing, file transfers, and job submission for a heterogeneous mixture of standalone server, cluster, and cloud servers.
Web-based resource that reorganizes mass spectrometry-based proteomics data to explore expressed proteins in fetal tissues/adult tissues/hematopoietic cells obtained from human. All samples used to generate these data were obtained from histologically normal samples.
COMPARTMENTS Subcellular localization database
Web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. All evidence is mapped to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.
Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository.
Database that provides gene expression profiles of genes and gene signatures in healthy and malignant hematopoiesis and includes data from both humans and mice. In addition to the default plot, which displays an integrated expression plot, two additional levels of visualization are available: an interactive tree showing the hierarchical relationship between the samples, and a Kaplan-Meier survival plot. The database is sub-divided into several datasets that are accessible for browsing.
Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally.
Non-profit initiative of the Belgian Diabetes Registry (BDR), the Beta Cell Therapy consortium (BCT), the Flemish Center for Medical Innovation (CMI) and the Brussels Institute for Research and Innovation (Innoviris). It aims to support medical research into the epidemiology, prevention, diagnosis and treatment of diabetes.
Nikon Eclipse 80i Advanced Research Microscope
Digital-imaging microscope that uses Nikon's CFI60 optics and high signal-to-noise ratios to produce fluorescence images. It utilizes Nikon’s “fly-eye” technology, VC Plan Apo objectives and both intelligent and motorized digital imaging heads.
Nikon DS-Ri1 High Resolution Color Camera
High-resolution microscope camera designed for low magnifications and enlargements in brightfield imaging. Its features include fast focusing, a large native pixel size, and a supported cooling combine for clear fluorescent imaging and documentation.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 7, 2017. Software designed for objective quantification/counting of PLA signals in cells and tissue images generated from fluorescence microscopy. The nuclei are automatically detected and cytoplasm size estimated, enabling single cell statistical analysis of expression levels in tissue or cell populations.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 6, 2017. Detection instrument that gathers absorbance, fluorescence, and luminescence data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Statistical modeling program that provides a wide choice of models, estimators, and algorithms in a program that has graphical displays of data and analysis results. Mplus allows the analysis of both cross-sectional and longitudinal data, single-level and multilevel data, data that come from different populations with either observed or unobserved heterogeneity, and data that contain missing values. Analyses can be carried out for observed variables that are continuous, censored, binary, ordered categorical (ordinal), unordered categorical (nominal), counts, or combinations of these variable types. In addition, Mplus has extensive capabilities for Monte Carlo simulation studies, where data can be generated and analyzed according to any of the models included in the program. The Mplus modeling framework draws on the unifying theme of latent variables. The generality of the Mplus modeling framework comes from the unique use of both continuous and categorical latent variables. Continuous latent variables are used to represent factors corresponding to unobserved constructs, random effects corresponding to individual differences in development, random effects corresponding to variation in coefficients across groups in hierarchical data, frailties corresponding to unobserved heterogeneity in survival time, liabilities corresponding to genetic susceptibility to disease, and latent response variable values corresponding to missing data. Categorical latent variables are used to represent latent classes corresponding to homogeneous groups of individuals, latent trajectory classes corresponding to types of development in unobserved populations, mixture components corresponding to finite mixtures of unobserved populations, and latent response variable categories corresponding to missing data.
Geneticist Biorepository of Human Tissue Samples
Biorepository that stores human tissue, blood, and biofluid samples in frozen, ffpe, and tissue microarray form for research.
ImageJ plugin that performs semiautomated analysis of randomly selected sets of nervous system fibers.
Ontology of drug targets to be used as a reference for drug targets, with the longer-term goal of creating a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The project itself aims to develop a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families.
European project that aims to improve the care for patients with Traumatic Brain Injury. It provides general information and aims to be a communication platform for patients, scientific participants and investigators.
Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry.
Software tool for quantification of root system architectures in range of plant species, grown and imaged in variety of ways. Root phenotyping software driven by deep learning. Measurements can be exported directly in RSML format, where additional traits can be calculated later using simple plug-in system.
Software tool which allows the automatic and high throughput measure of root length, as well as extra associated measures such as curvature. The user must supply start points for each root, and exemplar patches of nearby background. The software will then trace the main root to the tip, in every image in a timeseries, and record the results.
Integrative Human Microbiome Project (iHMP)
Provides human microbiome datasets and minimum reporting standards established by DCC, from both initial HMP-1 phase and iHMP. Offers to query and retrieve metagenomic, metatranscriptomic, human genetic, microbial culture, and many other data types from each project. Provides integrated longitudinal datasets from both microbiome and host from different cohort studies of microbiome associated conditions.
Community of scientists focused on the study of epithelial cell function and mucosal biology including inflammation and host defense of the gastrointestinal tract. It focuses on the intestinal and inflammatory bowel diseases; gut microbiology; and stem cell and developmental biology of the intestine and liver in organ physiology, regenerative medicine, and metabolism.
Harvard Digestive Diseases Center Biomedical CORE C: Epithelial Cell and Mucosal Immunology
Core facility that provides the infrastructure, biologic resources, expertise, and training for cross-disciplinary research on epithelial biology and immune function in mucosal surfaces and solid organs of the GI tract.
Hopkins Conte Digestive Diseases Basic and Translational Research Core Center
Center that aims to advance basic science and translational digestive diseases research at the Johns Hopkins University School of Medicine. Its goal is to improve the health of patients with the broad spectrum of gastrointestinal and hepatic disorders.
Harvard Digestive Diseases Center Bio-Repository and Data Registry for Human Material
Core facility that supports basic, translational, and clinical research in the digestive diseases by providing access to human materials and resources in statistics and study design. It also aims to to forge connections and support collaboration between HDDC Clinical Associates and Members, support a well-organized infrastructure for acquisition and storage of clinical samples, and provide professional support in biostatistics and study design to HDDC members and Clinical Associates.
Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Integrated Physiology Core
Core facility that provides Center investigators and their laboratories the tools and advice needed to establish and study mouse (including transgenic and knockout) and human (i.e. GI organoids) physiology of GI disease.
Harvard Digestive Diseases Center Clinical Translational Research Program
Core facility that supports basic, translational, and clinical research in the digestive diseases by providing access to human materials and resources in statistics and study design. Its services promote translation of basic research advances into improved clinical care by offering fresh and archived human specimens, associated clinical metadata, biostatistics and aid in study design.
Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Image Core
Core facility that provides state-of-art light microscopy technology to the members of the Hopkins Basic Research Digestive Disease Development Center and to the whole Hopkins scientific community.
Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Translational Research Enhancement Core
Core facility whose services include establishing Best Practices (BP) and uniform Standard Operating Procedures (SOPs) for the collection, annotation, processing, storage, management, distribution, and ethical use of human specimens, and to provide access to specimens by investigators as well as patient identification, patient recruitment, facilitation of patient trials, translational research and basic research through creation of a patient registry and database.
Center whose goal is to integrate bench science with clinical investigation, in support of its vision to understand and cure human liver diseases.
Core that takes advantage of local expertise and resources to enable Center members to analyze cell populations in mouse or human livers. It performs complex analyses on small numbers of human cells, such as those obtained from liver biopsies.
Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Proteomics Core
Core facility that uses mass spectrometry coupled to one (1D) and two (2D) dimensional separations by column chromatography or gel electrophoresis to identify, quantify or characterize proteins and their post-translational modifications, that are expressed in well characterized protein fractions from the small intestine, colon, kidney, liver and pancreas. Techniques such as difference gel electrophoresis (DIGE), isobaric tag for relative and absolute quantitation (iTRAQ), tandem mass tags (TMT) and stable isotope labeling of amino acids in cell culture (SILAC) as well as non-labeling methods (MudPIT, multi-dimensional protein identification technology) are available for quantifying relative differences in protein expression and post-translational modifications, such as acetylation, glycosylation, phosphorylation, nitrosation, ubiquitination and novel cleavage sites.
UCSF Liver Center Clinical & Translational Core
Core that supports study design to sample procurement and storage, to data analysis and presentation, and also focuses on research involving human subjects.
UCSF Liver Center Pathology & Imaging Core
Core that provides services from routine liver histology to complex microscopy and image analysis.
Core whose purpose is providing primary and immortalized liver cells for experimental use as well as other material such as human liver cells, primary hepatocytes, and immortalized cell lines.
University of Chicago Digestive Diseases Research Core Center
Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis.
University of Chicago Digestive Diseases Research Core Center Administrative Core
Core that has oversight of the other four cores of University of Chicago's Digestive Disease Research Core Center and determines the center's overall direction.
University of Chicago Digestive Diseases Research Core Center Host-Microbe Core
Core that consists of two components: The Enteric Microbiology and The Gnotobiotic Mouse components. The Enteric Microbiology component offers novel screening and advanced technologies for compositional and functional profiling of the resident microbial communities in the gastrointestinal tract. The Gnotobiotic Mouse component enables investigators to study the effects and causal role of specific microorganisms or profiles in vivo.
University of Chicago Digestive Diseases Research Core Center Tissue Engineering and Cell Models Core
Core that provides services such as a repository for intestinal cell lines, Tissue Engineering Models, experimental materials, and supplies for digestive disease research.
University of Michigan Center for Gastrointestinal Research
Center whose goal is to investigate signal transduction mechanisms regulating homeostasis and GI disorders. Their approach includes studies on genetics and gene regulation, cellular signaling pathways, receptors and ion channels.
University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core
Core that serves as both a central repository for all the samples and data shared by the other cores and a catalyst for interdisciplinary research.
University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core
Core whose services include anatomic pathology review of human and experimental animal tissues as well as consultation in the best approaches for such analyses, cost-effective and high quality processing and staining of formalin-fixed paraffin-embedded tissues, and making collections of human tissue and imaging technologies available to researchers.
University of Michigan Center for Gastrointestinal Research In Vivo Animal and Human Studies Core
Core facility that consists of the following 4 distinct programs: In Vivo Small Animal Studies Program, Organoid/Enteroid Modeling Program, Biospecimens Banking Service, and Clinical Design and Statistics.
University of Michigan Center for Gastrointestinal Research Protein Localization, Identification and Folding Core
Core facility whose services include the following programs: Imaging Core Program, Proteomics Core Program, Protein Folding Core Program, and Consultation.
University of Michigan Center for Gastrointestinal Research Molecular Biology Core
Core whose services include the following programs: Transgenic Rodent Program, Genome Editing Program, Viral Vector Program, and Integrated Genomics Program.
University of Michigan Center for Gastrointestinal Research Microbiome and Metabolomics Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8,2025. Core whose services include consultation, Nucleic Acid Isolation, Microbiome (16S) Data Analysis, MiSeq-base 16S rRNA Gene Sequencing, Genomic/Metagenomic shotgun sequencing, Bacterial transcriptomics and metatranscriptomics, Multiplatform Metabolomic Profiling, Metabolomic sample preparation, and Germ-free & Gnotobiotic Mouse Facilities.
University of North Carolina Center for Gastrointestinal Biology and Disease
Center at UNC Chapel Hill and North Carolina State University for collaborative GI research. Its mission is to promote and enhance multidisciplinary digestive disease research.
University of North Carolina Center for Gastrointestinal Biology and Disease Advanced Analytics Core
Core facility provides solutions for studying proteins, peptides, and other molecules, including mRNA and cDNA. The Core's immunotechnologies (IT) component provides consultation, ordering, and immunoassay services, and supports a variety of analytes in both traditional ELISA/EIA and xMAP-based multiplex bead assay formats.
University of North Carolina Center for Gastrointestinal Biology and Disease Histology Core
Core facility that provides a full range of histology services, encompassing routine and specialized grossing, tissue processing, paraffin embedding, microtomy, H&E and special staining, and immunohistochemistry. It also offers image analysis and consultations to CGIBD members and non-members.
University of North Carolina Center for Gastrointestinal Biology and Disease Gnotobiotic Core
Core facility that supports animal model and basic research projects of CGIBD investigators. Investigators use this resource to examine physiologic and pathophysiologic differences in germ-free, gnotobiotic, and specific pathogen free colonized mice of various genetic backgrounds.
University of North Carolina Center for Gastrointestinal Biology and Disease Biostatistics and Data Management Core
Core facility that provides comprehensive statistical and data management services. Its statistical analysis services include study design, power and sample size analysis, randomization, statistical programming, consultation and the development of analysis plans, graphs, figures and reports.
University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases
Center that aims to unite investigators with interests in digestive, liver and pancreatic physiology and disease in the exploration of creative experimental approaches. The scientific focus of the Center revolves around the molecular controls of cellular growth and differentiation in the digestive tract, liver and pancreas with the goal of achieving a new level of integration in biology, pathobiology, and therapy.
University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Molecular Pathology and Imaging Core
Core facility that provides histological services, equipment usage, and technical expertise to digestive and liver research projects.
University of North Carolina Center for Gastrointestinal Biology and Disease Large Animal Models Core
Core facility that provides consultation and procedural expertise on development on novel models of relevant digestive diseases in large animals.
University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Host-Microbial Analytic and Repository Core
Core facility that provides services that will enhance the analysis of both host and microbial biological processes as well as facilitate translation into the clinical arena via human subject research.
University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Cell Culture Core
Core facility that maintains a centralized repository of cells and reagents pertinent to digestive, liver and pancreatic disease research. It also provides training for labs in new cell culture (2D and 3D) techniques.
University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Genetically-Modified Mouse Core
Core facility that provides a centralized service to efficiently produce genetically altered mice for basic research, resulting in reduction in effort and cost to participating investigators.
Software toolkit for filtering and manipulating annotated files. After annotation, the software's filter function can find relevant genomic variants in large data files.
Perl tool that generates linkage mapping input files using data from HAPMAP Phase III populations. It provides rudimentary error checks and is easily amended for personal linkage mapping preferences.
Software customized for copy number and cytogenetics research analysis and reporting. ChAS enables the user to view and summarize chromosomal aberrations, which may include copy number gain or loss, mosaicism, or loss/absence of heterozygosity (LOH/AOH).
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures.
Cerebrovascular Disease Knowledge Portal
Cerebrovascular Disease Knowledge Portal (CDKP)
Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data.
Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox.
Software that implements Infomax ICA, which is an algorithm to perform Independent Component Analysis, in CUDA (a parallel computing platform and programming model).
WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).
Browsable Atlas of Behavior-Anatomy Maps
Browsable Atlas of Behavior-Anatomy Maps (BABAM)
Graphical user interface for exploring hypotheses of correlations between neural activity in regions of the brain and behavior for Drosophila melanogaster. These correlation hypotheses are the result of our thermogenetic neural activation screen from the Janelia GAL4 collection.
Software toolkit for data-driven validation of neuron and ion channel models using SciUnit. NeuronUnit implements an interface to several simulators and model description languages, handles test calculations according to domain standards, and enables automated construction of tests based on data from several major public data repositories.
Software that creates graphs from brain scan data. ndmg is a 1-click structural connectome estimation pipeline and is the successor of the MRCAP, MIGRAINE, and m2g pipelines.
SpineCreator: Graphical Editor for SpineML
Graphical editor software which can be used to create and edit neural network models. Models can be read from, and saved in the SpineML format.
Search engine for querying novel microbiome samples against a comprehensive database of curated samples. Visibiome accepts rRNA data in the form of BIOM files.
Simulation software which can execute neural network models specified in the SpineML format (an extension of the INCF's NineML). It is used as the canonical simulator backend by SpineCreator and translates the SpineML specification of the model into object code and a SystemML specification of the network.
The Spiking Neural Mark-up Language (SpineML)
Declarative XML based model description language for large scale neural network models. Its syntax is designed primarily for the specification of large scale networks of point neurons but also has the flexibility to describe biologically constrained models consisting of non standard components (such as gap junctions).
Simulation software that runs network simulations where the network is specified in its own format called SystemML. The components of the network can be implemented in C, C++, Python or Matlab and are used in SpineML_2_BRAHMS to provide a simulation back-end for SpineML models.
Web application for combined transmembrane topology and signal peptide prediction. Used for whole genome annotation of signal peptides and transmembrane regions. Predictor is based on hidden Markov model (HMM) that models different sequence regions of signal peptide and different regions of transmembrane protein in series of interconnected states.
Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences.
Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
Software that translates nucleic acid sequences to their corresponding peptide sequences. It can translate to the three forward and three reverse frames, and output multiple frame translations at once.
Software toolkit for small-angle scattering data analysis from biological macromolecules.
Source code for a soma segmentation method suitable for datasets with touching soma distributions. The method contains three main parts: soma detection based on DT and local maximum searching and refining; an improved Rayburst sampling algorithm for isolated and touching soma surface detection; and ellipsoid fitting to generate the segmentation results.
Portal for platforms available to conduct and compete in challenges aiming to improve scientific progress. Challenges allow researchers to share their research and problems with other subject matter experts for collaborative progress.
Simulation software tool that performs comprehensive predictive science application for for small molecules.
Software for x-ray detection and processing single-crystal monochromatic diffraction data recorded by the rotation method. XDS can process data images from CCD-, imaging-plate-, multiwire-, and pixel-detectors in a variety of formats.
lme4: Linear Mixed-Effects Models using 'Eigen' and S4
Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue."
Software to fit and compare Gaussian linear and nonlinear mixed-effects models.
lmerTest: Tests in Linear Mixed Effects Models
Source code of statistical tests for linear mixed effects models as implemented in lme4. The package also provides the calculation of population means for fixed factors with confidence intervals and corresponding plots.
RVAideMemoire: Testing and Plotting Procedures for Biostatistics
Software package that contains miscellaneous functions useful in biostatistics, such as univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions shorten existing procedures and implement plotting functions that can be used with a variety of methods and packages.
LMERConvenienceFunctions: Model Selection and Post-hoc Analysis for (G)LMER Models
Software package that performs backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization.
Data Analysis GUI for R. The program is based on Java's Swing GUI library and includes an Excel-like spreadsheet for easy data viewing and editing.
psy: Various procedures used in psychometry
Software package implementing various statistical procedures used in psychometry.
GeneMarker: The Biologist Friendly Software
Genotype analysis software which enhances the speed, accuracy, and ease of analysis. The software is an alternative to Applied BioSystems Genotyper®, GeneScan®, and other genotype analysis software.
Data visualization software inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs as well as most nonstandard requirements.
Database of drug information created and maintained by the Division of Translational Informatics at University of New Mexico. It provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic action.
Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence.
Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence.
Disease Ontology Annotation Framework (DOAF)
Project portal for a collaborative database aiming to provide a comprehensive annotation to human genome.It uses the computable, controlled vocabulary of Disease Ontology (DO) and NCBI Gene Reference Into Function (GeneRIF).
Database of annotations of drug indications in FDA drug labels. LabeledIn contains an expert curated set of indications and a crowdsourced set of indications.
MEDI--an Ensemble MEDication Indication Resource
Medication indication software for primary and secondary uses of electronic medical record (EMR) data. MEDI was created based on multiple commonly used medication resources (RxNorm, MedlinePlus, SIDER 2, and Wikipedia ) and by leveraging both ontology and natural language processing (NLP) techniques.
Evolutionary Rate Covariation (ERC) Analysis
Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes.
Human Reference Protein Interactome Project
HuRI: The Human Reference Protein Interactome Mapping Project
Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies.
Cloud-based data repository for storing, publishing and accessing scientific data. Mendeley Data creates a permanent location and issues Force 11 compliant citations for uploaded data.
MATLAB Toolbox for presenting stimuli and recording responses with precise timing. It also provides additional utilities for the manipulation of sound, keyboard, mouse, joystick, serial port, parallel port, subject responses and physiological monitoring hardware.
Spindles Slow Oscillation and Power-spectral-density
Software for detection and reporting of spindle or slow oscillation events, simple automatic EMG artifacts, and their co-occurance or respective matching non-events. SpiSOP was designed to process large data quanta at once and multiple datasets in parallel.
Broad Institute Connectivity Map 02 Build
Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
DIAGRAM (DIAbetes Genetics Replication And Meta-analysis) consortium
Consortium of researchers aiming to characterize the genetic basis of type 2 diabetes with a principal focus on samples of European descent. DIAGRAM also features a database of DIAGRAM publications and diabetes-related research data.
Trans-Omics for Precision Medicine (TOPMed) Program
Funding program for Precision Medicine genome sequencing from the National Institutes of Health, NHBLI.
This engine presents case-control association results from the UK Biobank hospital in-patient health-related outcomes summary information data (Data-Field 41202); computational grouping of phenotypes with cancer (Category 100092) registry, death registry data (Category 100093), algorithmically-defined outcomes (Category 42), and verbal questionnaire data (Category 100071); and manually curated grouping of phenotypes.
A biobank is a repository that stores and manages biological samples known as biospecimens for use in research. The Precision Medicine Initiative (PMI) Cohort Program biobank has been awarded to Mayo Clinic in Rochester, Minnesota. The biobank will support the collection, analyses, storage and distribution of biospecimens for research use. Data from laboratory analyses of biospecimens will be combined with an array of other lifestyle and health information provided by volunteers to help researchers continue to unravel individual differences that contribute to disease and response to treatments.
CRowd Extracted Expression of Differential Signatures
CREEDS: CRowd Extracted Expression of Differential Signatures
Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures.
Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features.
GENE Expression and Enrichment Vector Analyzer
Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme.
ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA. The website enables downloading of the data in H5 format for programmatic access as well as a 3-dimensional view of the sample and gene spaces. Search features allow browsing of the data by meta data annotation, ability to submit your own up and down gene sets, and explore matching samples enriched for annotated gene sets. Selected sample sets can be downloaded into a tab separated text file through auto-generated R scripts for further analysis. Reads are aligned with Kallisto using a custom cloud computing platform. Human samples are aligned against the GRCh38 human reference genome, and mouse samples against the GRCm38 mouse reference genome.
A web interface for the scoring of biomedical digital objects by user evaluation according to the FAIR data principles: Findability, Accessibility, Interoperability, and Reusability. Prototype currently available at: http://amp.pharm.mssm.edu/fairshake
Software toolkit for analyzing and visualizing data of single cell qPCR/RNA-seq. It offers methods for identifying gene expression and mutation patterns at the single-cell level and is designed for use with Biomark and C1 systems.
Fluidigm Real-time PCR Analysis software
Sequence analysis software for rt-qPCR analysis. It establishes standard curves, calculates delta delta Ct and automatically determines the ideal threshold setting for each run.
Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
The main purpose of Cufflinks.cuffmerge is to merge together several Cufflinks assemblies, making it easier to produce an assembly GTF file suitable for use with Cufflinks.cuffdiff. Cufflinks.cuffmerge also runs Cuffcompare in the background and automatically filters out transcribed fragments (transfrags) that are likely to be artifacts. Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 2013;31:46-53.
Implements an algorithm to conduct advanced gene set enrichment analysis on the results of genomics experiments. Simillion C, Liechti R, Lischer HE, Ioannidis V, Bruggmann R. Avoiding the pitfalls of gene set enrichment analysis with SetRank. BMC bioinformatics. 2017;18(1):151. doi: 10.1186/s12859-017-1571-6.
Oncotopix Discovery is a comprehensive solution powered for whole slide image analysis of tissue sections, TMA slides across any image analysis application. Simple to program also for scientists without an IT background.
Disease portal for Hepatitis that provides information about causes, symptoms, treatments, and other characteristics of Hepatitis. This webpage is curated by Verywell, a health and wellness organization.
The Black Dog Institute is dedicated to understanding, preventing and treating mental illness. We are about creating a world where mental illness is treated with the same level of concern, immediacy and seriousness as physical illness; where scientists work to discover the causes of illness and new treatments, and where discoveries are immediately put into practice through health services, technology and community education.
A commercial software package that works with Carl Zeiss microscopy; AIM 4.2 software.
Tools for querying and analysis of genomic data. These libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined regions of interest (epigenetic enrichment, transcription factor binding sites, etc.). This library works with these tables and provides a set of common tools for working with them. Opening and saving common tab-delimited text formats Support for BED, GFF, VCF, narrowPeak files Scoring intervals with datasets from microarray and sequencing ChIPSeq, RNASeq, microarray expression Support for Bam, BigWig, BigBed, wig, and USeq data formats Intersection with other known annotation Works with any genomic annotation in GTF, GFF3, and UCSC formats The libraries provide a unified and integrated approach to analyses. In many cases, they provide an abstraction layer over a variety of different specialized BioPerl and related modules. Instead of writing numerous scripts specialized for each data format (wig, bigWig, Bam), one script can now work with any data format.
A script to convert Bam alignments into a wig representation file.
Kit for assessing motor function and endurance in mice and rats. IITC’s Rotarod Test is capable of having up to five mice or rats tested at a time standard.
Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code.
Software application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions.
Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
Data set of thalamo-centric mesoscopic projection maps to the cortex and striatum. The maps are established through two-color, viral (rAAV)-based tracing images and high throughout imaging.
Software for image analysis, processing and quantitation. This software analyzes standard JPEG, BMP, PNG, TIFF images; 16-bit TIFF images; and .GEL files produced by Phosphorimager, Typhoon and Storm instruments.
Metabolite Imaging and Data Analysis System
MIDAS: Metabolite Imaging and Data Analysis System
Software for processing, display, and analysis of magnetic resonance spectroscopic imaging data. MIDAS supports a "whole-brain" MRSI acquisition method that has been implemented on MRI systems from three major manufacturers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software package for pan-genome analysis. This software is suitable for bacterial genomes and the study of intra-specific eukaryotic pan-genomes.
Software scripts for the assembly of chloroplast genomes out of whole-genome sequencing reads.
Software for processing NGS sequence reads in FASTQ and FASTA formats. split_pairs.pl is suited particularly for the task of sorting pair end reads and for modifying their headers with Perl-style regular expressions.
Open source software to evaluate, quantify, compare, and predict the metabolic machinery of interest in large ‘omic’ datasets. This protocol finds informative protein families and uses them to score metagenomic sets.
Perl software script that can annotate barley sequences with Gene Ontology terms inferred by homology. It uses the IBSC2012 barley GO annotation and supports both nucleotide and peptide sequences.
Barleymap was designed to search the position of barley genetic markers on the Barley Physical Map and the POPSEQ map. Its three main functions are finding markers, aligning sequences, and locating by position.
Web application for predicting transcription factors which bind a specific DNA site or motif, as well as DNA motifs or sites likely to be recognized by a specific DNA-binding protein. footprintDB also lists several databases and repositories relevant to DNA transcription.
Web application for structural alignment of DNA motifs and protein domains from DNA binding protein complexes in Protein Data Bank.
Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats.
Web application for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages. It implements an extended CODEHOP strategy and evaluates thermodynamic properties of the oligonucleotide pairs.
Web application that scans a library of protein-DNA complexes and builds comparative models of proteins bound to DNA. Its results include complex coordinates, schematic interface diagrams, interface alignments and DNA motifs.
Source code for a machine learning method to detect somas on confocal microscopic images of the Drosophila brain. The method can be applied to the original raw images where the noises are not removed and the number of somas is unknown.
randomForest: Breiman and Cutler's Random Forests for Classification and Regression
Software package for classification and regression based on a forest of trees using random inputs.
Image analysis software package that allows non-destructive image marking, input for further image processing, and marking the results of automatic measurements. Object-Image integrates measurements, macros, graphical objects and image names in a closed unit called 'object file' so that it reduces file clutter.
Pediatric Centers of Excellence in Nephrology
Portal with detailed information about various research centers that focus on pediatric medicine and nephrology. These centers are funded by NIDDK.
NLREG: Nonlinear Regression and Curve Fitting
Statistical analysis program that performs linear and nonlinear regression analysis as well as surface and curve fitting. NLREG can handle linear, polynomial, exponential, logistic, periodic, and general nonlinear functions.
Web application for designing gRNAs for CRISPR/Cas9 experiments. It selects target sites for CRISPR/Cas9, CRISPR/Cpf1 or TALEN-directed mutagenesis.
Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression.
Software used in tandem with the Polygon 400 from Mightex systems to define areas of illumination, control light intensity and duration, and calibrate the device.
Repository of matlab code for reconstruction and analysis of effective connectivity in vitro.
Bisulfite Sequencing Virus integration Finder
BSVF: Bisulfite Sequencing Virus integration Finder
Software code for bisulfite sequencing virus integration. This finder is for directional libraries only and does not support PBAT and indirectional libraries.
Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
Database of RNA-seq gene expression in hippocampal principal neurons. Hipposeq can analyze and visualize RNA-seq data for all excitatory cell populations in the hippocampus at multiple levels of granularity.
Software toolbox which finds and displays temporal relations amongst components. This can help determine causal relations in the brain.
University of Pennsylvania Diabetes Research Center
NIDDK center that serves diabetes-oriented investigators from University of Pennsylvania as well as additional institutions from the mid-Atlantic region. The Penn DRC represents many basic science and clinical departments at Penn and the other institutions, and supports research in diabetes and obesity via Scientific Cores, a Pilot and Feasibility Grant Program, and a series of seminars, retreats, and other academic enrichment activities.
Joslin Diabetes Center Molecular Phenotyping and Genotyping Core
Molecular Phenotyping and Genotyping Core
Core facility that supports the study of molecular mechanisms of disease by providing equipment, expertise, and services in molecular phenotyping, including nucleic acid sequence analyses, gene expression, and other "omics" analyses, which would be too specialized or costly for individual laboratories to perform independently. Formerly known as the Advanced Genomics and Genetics Core, the Molecular Phenotyping Core is newly-named in recognition of the expansion of its analytical capacities to reflect not only genetic and genomic analyses but also metabolic phenotyping.
Database of cardiology information and ex-vivo human hearts. The atlas features information about specific regions of the heart as well as patient information from ex-vivo subjects.
3D editing software for manifold triangle meshes with advanced repairing features. It can post-process polygon meshes coming from digitization sessions and automatically filter out most of the typical flaws that models may have when coming from a 3D digitization session (degenerate triangles, isolated vertices, noise, topological artefacts, holes, ...).
3D visualization software for working with triangle meshes. This software also can clean up 3D scans, design objects for 3D printing, and perform other 3D design-related functions.
Operating software for a supercomputer in Spain. The software is maintained and updated by the Centro Nacional de Supercomputación (Barcelona Supercomputing Center) and is used for research projects on climate change, gravitational waves, a vaccination against AIDS, new radiation treatments to fight cancer, and other subjects.
Web application that identifies genomic instances for a given combination of gRNA(s), PAM, number of mismatches, and seed. This tool is limited to a single 1,000 nucleotides sequence or fewer than twenty CR-separated 20-mers.
Operating software for QIAGEN's PCR cycler the Rotor-Gene Q. This software works with the instrument to streamline qPCR workflows and perform complex data analysis functions.
Cellular and Hemodynamic Image Processing Suite
CHIPS: an open-source Cellular and Hemodynamic Image Processing Suite
Image processing software designed to analyse functional images of cells and blood vessels, primarily from two-photon microscopy. CHIPS is a set of classes and functions for MATLAB that integrates a number of algorithms, both novel and existing, into a complete image processing pipeline.
THIS RESOURCE HAS BEEN DISCONTINUED. Documented October 3, 2017. Operational software created by Agilent Technologies to operate with its ChemStation hardware. The software can manage all parameters for instrument control, data acquisition and evaluation, including integration, quantification and reporting.
Range-based people tracker classifiers Benchmark Dataset
Benchmark dataset for evaluation of range-based people tracker classifiers in mobile robots
Dataset for performance evaluation of different approaches for detecting and tracking people by using lidar sensors. Information contained at the dataset is specially suitable to be used as training data for neural network-based classifiers.
Software for the analysis of multi-site neuronal spike signals. SPICODYN processes electrophysiological signals, focusing on spiking and bursting dynamics and functional-effective connectivity analysis.
Software designed to clean-up biosensor data. It can zero and crop data, align injection times, correct for DMSO effects and fit binding curves and offrates.
Data processing software that performs X-ray diffraction data processing. It handles multi-pass, multi-wavelength data sets and supports remote access to synchrotron facilities.
Data processing software for x-ray diffraction data. AIMLESS scales together multiple observations of reflections, and merges multiple observations into an average intensity.
Data processing software for X-ray diffraction data. autoPROC is a set of tools and programs to automate steps involved in data processing, such as image analysis, integration, indexing, and determination.
Proteins Interfaces Structures and Assemblies
Web application for exploration of macromolecular interfaces. It calculates structural and chemical properties of macromolecular surfaces and interfaces, as well as quaternary structures (assemblies), their structural and chemical properties and dissociation patterns.
iNPS: An improved algorithm for accurate nucleosome positioning from sequencing data
Software for nucleosome detection that builds on the NPS software. Its application to T-cell activation data demonstrates a greater ability to facilitate detection of nucleosome repositioning, uncovering additional biological features underlying the activation process., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software for alignment, comparison of macromolecules, and performing least-squares superpositioning of biomacromolecules. The program offers a superset of the LSQ- functionality inside O and removes some of the limitations and irritations of the LSQ-commands.
Software for detecting the integrated copy number variation regions (CNVRs) using population sequencing data. The high-confidence CNVRs are discovered and refined by both individual and population criteria, and the result is a VCF format genotype file which can be used in GWAS/QLT research.
Software that supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiplehypothesis testing.
Analysis software for analysis of finite elements and simulations of 3D shape changes in a tissue that result from patterns of growth. It works with Matlab to model biological growth of leaves, petals, and similar organs.
MVGC Multivariate Granger Causality Matlab Toolbox
Matlab software toolkit designed to facilitate Granger-causal analysis with multivariate and possibly multi-trial time series data. Annotated demonstration scripts are available which may be used as templates to assist in this the toolbox's functions.
Real time localization system for autonomous robots Benchmark Dataset
Benchmark dataset for analysis of cyber-attacks to an indoor real time localization system for autonomous robots
Dataset that can be used to analyze cyber-attacks to an indoor real time localization system for autonomous robots. Data have been gathered in an indoor mock-up apartment using an autonomous robot with an on-board Real Time Location System (RTLS).
Machine learning models cyber-attack detection Benchmark Dataset
Benchmark dataset for training/testing of Machine Learning Models to detect cyber-attacks to an indoor real time localization system for autonomous robots
Dataset that can be used to train and test Machine Learning Models to detect cyber-attacks to an indoor real time localization system for autonomous robots. The data was gathered in an indoor mock-up apartment using an autonomous robot with an on-board Real Time Location System (RTLS).
doGlycans - Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins Glycolipids and Carbohydrate Polymers for GROMACS
Software toolkit for atomistic simulations to explore how carbohydrates function. Applications include the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins.
NAPR: Neuroanatomical Age Prediction using R
Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3.
Workflow software and methods language to improve the reproducibility of research results in the scientific community. The Aquarium Project aims to provide the means to specify, as precisely as possible, how to obtain a result using a combination of formal statements, informal descriptions, and photographs.
Software language for methods to simplify protocols into reusable components that can be exchanged or removed to produce simple, reproducible, and scalable workflows. It allows users to develop, execute, and analyse biological experiments faster, while also introducing standardization and modularity to bioengineering.
Robot with open source software that allows for configurable robotic science. The robot's primary function is automating pipette functions in biological research in order to save time for research labs.
METAFLUIDICS: Open Repository for Fluidic Systems
Protocol repository for microfluidics experiments and chips. METAFLUIDICS provides a home for digital design files and other information necessary to reproduce or remix a microfluidic device.
Language standard for automating English language protocols. Autoprotocol specifies experimental protocols for biological research as a way to define experiments that could be run over the internet on remote robotic automation.
Hominid: host-microbiome interaction identification
Software for identifying associations between host genetic variation and microbiome composition. HOMINID is a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host SNPs that are correlated with microbial taxa abundances.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 6,2026. Platform for mediation and integration of schizophrenia neuroimaging-related databases. It provides access to federated databases, novel mediation software, and large-scale data-sharing features.
The Adolescent Brain Cognitive Development Study
Long-term study of brain development and child health in the United States. The study tracks subjects' biological and behavioral development through adolescence into young adulthood to determine how childhood experiences (such as sports, videogames, social media, unhealthy sleep patterns, and smoking) interact with each other and with a child’s changing biology to affect brain development and social, behavioral, academic, health, and other outcomes.
Imaging software that works with G:BOX Chemi and PXi imaging systems to automatically or manually capture images. GeneSys also includes a database containing information about applications such as fluorescence, chemiluminescence and chemifluorescence.
Software for read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC). Sim3C's potential applications include addressing questions directed at the spatial organization of DNA in samples of eukaryotic tissue, single cells, and microbial communities.
Software for digital video camera recording that allows users to control and acquire dadta from multiple cameras simultaneously in a singleuser interface. StreamPix provides a complete management console for cameras, simplifying the setup, control and acquisition from any number and type of camera.
Perl software for transcription factor binding site detection and analysis. It implements classes for the representation of objects encountered in analysis of these protein-binding sites.
Genesis: Cluster analysis of microarray data
Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.
Software for metabarcoding of DNA. SOAPBarcode takes advantage of high throughput capacity of next-generation-sequencing (NGS) platforms and can characterize the biodiversity of large volumes of eukaryote samples.
kernel current source density method - python
Source code for the Python implementation of the kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes.
Dataset of functionally characterized rice genes and members of different gene families. The dataset was created by integrating data from available databases and reviewing publications of rice functional genomic studies.
Community portal for a distributed data sharing platform and open protocol for building apps. The Dat Project imagines a web of commons created by global communities on open and secure protocols.
BeatBox—HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology.
Simulation environment that combines flexible script language user interface with computational tools in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level. It aims to include cell excitation, tissue/anatomy models, and stimulation protocols in BeatBox scripts so that simulation run either sequentially or in parallel (MPI) without re-compilation.
Software for flow cytometry data analysis. Flowing Software has many common analysis tools, such as dot plots, histograms, quadrants, statistics, overlay histograms etc.
CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data
Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments.
Acquisition software for mass spectrometry data from TripleTOF instrument(s). Analyst provides functionality for instrument control, data analysis, reporting, and audit trail.
Software for spectral analysis and data interrogation to identify, superimpose, compare samples, and label peaks. PeakView Software supports mass spectrometer systems for qualitative review of LC-MS and MS/MS data as well as optional detectors such as UV and DAD.
Private company offering a wide range of mass spectrometry-based proteomics data analysis services, including large-scale peptide and protein identification and quantitative proteomics. Notably, the company offers robust analysis of isobaric tagging and label-free quantification experiments, along with guidance in design of experiments and quality control issues.
Software that can perform calculations on cells from fluorescence microscopy images. BlobFinder can perform two types of analysis: an average count analysis to count the number of fluorescent signals and nuclei in an image, and a single cell analysis to simulate a cytoplasm and assign each signal to a particular cell.
Bertec | Fully Instrumented Treadmill (FIT)
Research standard treadmill that reduces gait lab space requirements and eliminates the limitations inherent in a traditional gait walkway. Researchers and clinicians can perform numerous testing conditions in a compact 2 meter space with variable incline and speed settings.
Image analysis software for developing new cellular assay analysis routines. This software provides a selection of advanced segmentation, pre-processing and post-postprocessing tools.
Software for viewing and analyzing medical DICOM images. The software suite includes a viewer, a report generating feature, and a DICOM network connection.
Software that acquires, displays and analyzes physiological signals. It covers cardiovascular, respiratory and nervous system research areas and technologies from in vitro action potentials to live in vivo physiological signals monitoring with video and implantable telemetry.
Web application for mapping functional networks of long or circular forms of non-coding RNAs. It supports the uploading and processing of user-defined NGS-based gene expression matrix data.
Image analysis software that acquires, analyzes, and archives research data without altering raw findings. It integrates data and changes how pixels are mapped to the screen for clearer display, rather than altering the pixels of the image data itself.
Software for sound analysis, audio editing, and audio recording. It features multitrack, waveform, and spectral display for creating, mixing, editing, and restoring audio content for research or non-research purposes.
VaDiR: an integrated approach to Variant Detection in RNA
Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets.
Campden Instruments Inc. McIlwain Tissue Chopper
Equipment for preparing samples of tissue for metabolic experiments that can also prepare small and irregular samples for biopsy or from small organs. It can perform rapid chopping of tissue without causing excessive stress damage.
Equipment that provides physical support for cell cultures. These cell culture inserts feature attachment and suspension cells that can access media from both their apical and basolateral sides.
Equipment that is a chamber for generation of a hypoxic environment for tissue culture. It is a self-contained and sealed chamber that fits inside existing laboratory incubators and utilizes a surface-type seal in which all portions of the O-ring are uniformly compressed.
Equipment that is a microscope for routine inverted microscopic analysis. Its features include pre-centered phase contrast, relief contrast, and UIS2 DIC optics for visualization across all magnifications for both thin and thick specimens.
Software toolkit that analyzes changes in fluorescence by using videocameras, photomultipliers, and photometry. It also combines the advantages of both imaging and photometry.
Fluorospectrometer for broad spectrum fluorescence analysis. It uses as little as 1 μL of sample volume and lowers the mass detection limit more than an order of magnitude.
Thermo Fisher | StepOnePlus Real-Time PCR System
Equipment and software system that is a real-time thermal cycler for intuitive data analysis of polymerase chain reactions. It comes with analysis software, instrument control software, and a LED-based 4-color optical recording feature.
Sequence Detection System (SDS) Software
Software for high-throughput gene expression and genotyping analysis for use with the Applied Biosystems® 7900HT Fast Real Time PCR System. It features automation software tools to fully automate high-throughput applications for gene expression and SNP genotyping.
Equipment that is a re-sealable 3 well fluidic platform optimized for effective perfusion. It supports the dynamic testing of pancreatic islets for glucose-stimulated insulin secretion (GSIS) and concomitant live-cell imaging.
Equipment that is a magnetic micropore chip for rapid unbiased circulating tumor cell isolation and in situ RNA analysis. The chip detects tumor cells and can help doctors treat patients with these tumors.
High Content Screening Automation Leica HCS A
Software supporting Leica Microsystem microscopes by performing high content screening automation. The software combines the flexibility of a point-scanning confocal with the high speed of a camera-based widefield system to compensate for specimen drift, single object tracking and immersion fluid.
Software for the analysis of short reads obtained from end-sequence RNA-seq. ESAT is designed for expression analysis of Digital expression (DGE) libraries that target transcript "ends."
ProphTools: Heterogeneous network prioritization tools
Source code for tools that perform general prioritization for heterogeneous biological networks. It prioritizes from a query network to the target network by means of a hybrid approach.
Software that performs hybrid error correction for long, PacBio reads. LoRDEC can correct insertions, deletions, and substitutions in PacBio reads.
Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping.
Imaging software for high-frequency processing and analysis. Some of its features include modes for blood flow quantification, single line acquisition, 3D-Mode imaging & volume analysis, nonlinear contrast imaging, and other image processing functions.
Equipment that is a 10-20 configuration Lycra EEG cap. Quik-Caps are available in electrode configurations from 12 to 256 channels as well as in 5 different sizes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Neuroscan SynAmps RT 64-channel Amplifier
Equipment that is an EEG signal amplifier for 64-channel montages. It is suitable for recording data from high sampling rate (20,000 Hz) Auditory Brain Stem recordings and Spike Spindles to true DC recordings of CNV and P300.
Time in Motor Games (Tiempo en Juegos Motores)
Web application that records the time devoted to each of the actions that are performed while playing motor games or active games. This recording system has applications in physical activity research and physical education.
BRAIN Initiative Cell Census Network (BICCN)
Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains.
Query-based web application that helps users find bioinformatics and artificial intelligence (AI) software. G6GFINDR is powered by "semantic annotation" vs. keyword search, which take advantage of semantic web graph technology.
DiPDE (Integro-partial differential equation with displacement)
Simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. DiPDE can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity.
Statistics software that performs common frequentist analyses and Bayesian analyses. It conducts ANOVA, linear regression, and correlation, among other statistical tests.
Software plug-in for ImageJ that allows users to determine the size of worms. It can calculate volume, surface area, and other parameters of worm specimens.
Software toolkit for analyzing tool for microscopic images. It contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis.
FiberApp: An Open-Source Software for Tracking and Analyzing Polymers
Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects.
Web application and database for analyzing cancer transcriptome data. It also has applications is facilitating tumor subgroup gene expression and survival analyses.
Software that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks.
BECA - Brain Explorer for Connectome Analysis
Brain Explorer for Connectome Analysis (BECA)
Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.
Chemoproteomic identification and therapeutic validation of proteins of metabolic significance
Database portal for a project that aims to discover and characterize new molecular pathways that can be targeted pharmacologically to revert obesity-linked adipocyte defects that drive systemic insulin resistance and type 2 diabetes. It works to identify in tandem physiologically-relevant proteins and chemical tools in order to expedite their functional annotation and therapeutic validation.
p-[(123)I]iodo-L-phenylalanine (IPA)-SPECT template in MNI-coordinates
p-[(123)I]iodo-L-phenylalanine( IPA)-SPECT template
Template for p-[(123)I]iodo-L-phenylalanine( IPA)-SPECT in MNI-coordinates. This template was obtained from 12 human subjects in an NITRC study.
A Web Application for Indirect Calorimetry Analysis
A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates.
Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN).
Database of sequence data generated from high-throughput immunosequencing of the TCR beta chain (TRB) and B cell receptor (BCR) immunoglobulin heavy chain (IGH). This data comes from cells from NPOD donors.
ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences
Algorithm Based Automatic Contiguation of Assembled Sequences
Algorithm Based Automatic Contiguation of Assembled Sequences (ABACAS)
Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account.
Supercomputing service located in the UK for researchers who study problems with a global impact. It is part of the PRACE initiative giving leading scientific users access to a European pool of supercomputers.
Institute that provides resources and researches the concepts and mechanisms which underlie the complexities of biology. In particular, it incorporates concepts in physics and mathematics to resolve, unravel, and explain complex biological mechanisms and conditions.
University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Stanford University.
Matlab-based routines for the detection and clustering of putative single units from a multi-unit time series, along with quality metrics. This sofwtare was developed by the David Kleinfeld Laboratory at UC San Diego.
Software for a 2D elastic beam model that can be used to model quasistatic bending of the vibrissa to compute forces and bending moments at the base. Elastica2D is part of the Digital Rat software project that that aims to enable morphologically and mechanically accurate modelling of the rat head and vibrissal (whisker) array.
Clinical Trials in Organ Transplantation (CTOT)
Clinical Trials in Organ Transplantation
Project portal for a cooperative research program to improve short and long-term graft and patient survival. CTOT is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for transplant recipients.
Clinical Trials in Organ Transplantation in Children (CTOT-C)
Clinical Trials in Organ Transplantation in Children
NIAID Clinical Trials in Organ Transplantation in Children
Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients.
Growing Gene and Cell Therapy Cooperative
Project portal for a collaboration between Boston Children’s Hospital, Cincinnati Children’s Hospital Medical Center, and the University of California Los Angeles with funding from NIH NCATS. It aims to support investigators to rapidly translate complex gene and cell therapies to early phase, investigator-initiated clinical trials.
Preventing Early Renal Loss in Diabetes (PERL)
PERL is a clinical trial for people with type 1 diabetes who have early signs of kidney problems. Its goal is to test a new way to reduce loss of kidney function using a safe and inexpensive medicine.
GIN: Modern Research Data Management for Neuroscience
Data services that provides a platform for comprehensive and reproducible management and sharing of neuroscience data. Building on well established versioning technology, GIN offers the power of a web based repository management service combined with a distributed file storage.
Source code that allows users to simultaneously track the movement of individual paws during spontaneous grooming episodes and walking in multiple freely-behaving mice/rats. This toolbox provides a simple platform to perform trajectory analysis of paw movement.
Software for a de novo OTU-picking pipeline integrating single- and paired-end 16S sequence tags. It is designed to take Illumina paired-end sequencing reads as input and output the OTU BIOM table, together with their representative sequences and a phylogenetic tree of OTUs.
Biobank for reagents such as antibodies, mice, and cell lines. Ximbio aims to maximise scientists' commercial opportunities and encourage the sharing of tools and information among the research community.
Artificial intelligence image analysis platform that facilitates life science research. It offers data analysis, processing functions, and security features to accelerate research productivity.
Framework for spike sorting that includes tools for pre-processing, spike detection, spike sorting, and sorting quality evaluation. It is principally designed for sorting of single-wire microwire recordings in humans, but is being used for other types of recordings as well.
Short Read Sequence Typing for Bacterial Pathogens
SRST2: Short Read Sequence Typing for Bacterial Pathogens
Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
Software package to elucidate complex interactions between subsets of neuroanatomical features and subsets of cognitive features. briancog specializes in differential correlation analysis.
Software for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.
Python software package that offers quantitative PET image reconstruction and analysis with high accuracy and precision. It is written in CUDA C and embedded in Python C extensions.
Algorithm for MATLAB and the EEGLAB toolbox that enables the automatic detection of independent components from an ICA that represent event-related brain potentials. It performs automatic Independent Component (IC) selection with respect to the contributions of the ICs to a certain ERP.
Software toolkit designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files, and generate native makefiles and workspaces that can be used in the compiler environment of your choice.
Source code for processing continuous local field potentials (LFP). The interface implements different documented algorithms for HFO detection, and provides several tools for signal visualization and manipulation.
Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.
ASaiM (Auvergne Sequence analysis of intestinal Microbiota)
ASaiM: Auvergne Sequence analysis of intestinal Microbiota
Auvergne Sequence analysis of intestinal Microbiota
Software that analyzes intestinal microbiota data. This environment is composed of a framework to process and analyze microbiota data from raw sequences to taxonomic and functional assignations.
Software toolkit for analyzing nanopore sequence data.
Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
Project that aims to provide a collection of Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure.
MetaNetX: Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks
Web application to perform automated model construction and genome annotation for large-scale metabolic networks. Platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways.
Research project that aims to learn more about the number of people who have monogenic diabetes, why and how it happens, and how best to treat it. Any adult or child with a known genetic cause of diabetes may join the MODY Registry.
Algorithm for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry and works by decomposing a query and target neuron into short segments; matched segment pairs are scored using a log-likelihood ratio scoring matrix empirically defined by the statistics of real matches and non-matches.
National Glycohemoglobin Standardization Program
NGSP: National Glycohemoglobin Standardization Program
Project that aims to standardize Hemoglobin A1c test results to those of the Diabetes Control and Complications Trial (DCCT) and United Kingdom Prospective Diabetes Study (UKPDS) which established the direct relationships between HbA1c levels and outcome risks in patients with diabetes.
Chronic Prostatitis Collaborative Research Network Clinical Trial- Alfuzosin
Efficacy & Safety Study of Pregabalin to Treat Chronic Prostatitis/Chronic Pelvic Pain Syndrome (CP/CPPS) (CPCRN RCT#2)
Clinical trial by the Chronic Prostatitis Collaborative Research Network (CPCRN chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS)) that was established to conduct randomized clinical trials of promising therapies for this syndrome. In response to the findings of previous trials, the CPCRN conducted a multicenter, randomized, placebo-controlled trial of alfuzosin to determine whether the symptoms CP/CPPS could be reduced in men who had recently received a diagnosis of CP/CPPS and who had not previously been treated with this class of drug.
Image repository that allows researchers to interactively explore a collection of cellular-resolution colour histology images detailing mouse development. The original histological sections have been re-digitised at high resolution, in colour and in collaboration with Elsevier, the eHistology Atlas provides the annotations as presented in the original printed version.
Database for the UK Brain Expression Consortium (UKBEC) dataset that comprises of brains from individuals free of neurodegenerative disorders. The aim of Braineac is to release to the scientific community a valid instrument to investigate the genes and SNPs associated with neurological disorders.
Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders.
Software toolbox for SPM that is aimed at facilitating the interpretation of fMRI data in the context of intrinsic connectivity networks (ICNs) by describing fMRI maps in function-oriented, objective and quantitative way using a set of 15 metrics conceived to quantify the degree of ‘engagement’ of ICNs for any given statistical map of interest. Besides the functionally-derived atlasing capabilities (based on the BrainMap ICN data) the toolbox provides anatomy-based atlasing (based on the JHU and Brainnetome Atlas data), as well.
Pattern Component Modeling toolbox for multivariate analysis
Software for a Bayesian approach for evaluating representational models that specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. PCM evaluates the ability of models to predict novel brain activity patterns and integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model.
Web application that is a phylogenetic tree viewer based on d3.js. It was developed as an alternative to Archaeopteryx inspired by d3.phylogram.js.
BOINC - Berkeley Open Infrastructure for Network Computing
Berkeley Open Infrastructure for Network Computing
Berkeley Open Infrastructure for Network Computing (BOINC)
Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science.
Data processing basecaller for the Oxford Nanopore sequencer that identifies DNA sequences directly from raw data. It enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data.
Organization that provides instructions for and research on the Natural Stress Relief (NSR) meditation method.
Method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. RNAcompete identifies expected and previously unknown RNA binding preferences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Vanderbilt Digestive Disease Research Center Biostatistics Administrative Core
Core facility for the Vanderbilt Digestive Disease Research Center.
Emory Epithelial Pathobiology Research Development Center
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th, 2023. Center for pathobiology research development.
University of Michigan Kidney Translational Core Center
George M. O'Brien Michigan Kidney Translational Core Center
Center for kidney research at the University of Michigan to assist investigators and clinicians worldwide in kidney disease research. Core services are available to Center researchers to promote their basic, translational and clinical kidney disease research.
Emory Epithelial Pathobiology Research Development Center Cell Culture Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th, 2023. Core facility for the Emory Epithelial Pathobiology Research Development Center.
MMPC Vanderbilt University School of Medicine Body Weight Regulation Core
Core facility for MMPC Vanderbilt University School of Medicine for studying impact of genetic, surgical, dietary and pharmacologic manipulations on body weight regulation. Core provides measurement of food intake, energy expenditure, and behavioral factors. Energy balance studies are performed in mouse home cage to minimize stress. Mitochondrial function is assessed on permeabilized tissues, isolated cells, or isolated mitochondria. Mouse models of bariatric surgery have been developed and studied extensively.
Emory Epithelial Pathobiology Research Development Center Gene Expression Analysis Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Core facility for the Emory Epithelial Pathobiology Research Development Center.
Cystic Fibrosis Center - University of Pennsylvania Animal Models Core
Core facility for the Cystic Fibrosis Center - University of Pennsylvania.
Emory Epithelial Pathobiology Research Development Center Image Analysis Core
University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center Molecular and Cellular Analytical Core Facility
Core facility for University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center. Supports investigation of human and non-human metabolism from cellular/molecular perspective. Investigation areas include Lipidomics and mass spectrometry, Bioinformatic analysis of RNAseq data, Mitochondrial respiration.
MMPC-Vanderbilt University School of Medicine Microvascular Complications Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 6th,2023. Core facility for the MMPC-Vanderbilt University School of Medicine.
University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center Clinical Intervention and Translation Core Facility
Core facility for the University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center. Core provides NORC members assistance with clinical research studies involving modification of body weight.
University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center Enrichment Program Core Facility
Core facility for the University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center. Promotes research in obesity and nutrition on campus by coalescing team science ventures, fostering development of trainees that are well positioned for interdisciplinary collaboration, and leveraging resources from existing institutional programs to spawn interdisciplinary team science and translational outreach programs related to nutrition and obesity.
University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center Energy Balance Assessment Core Facility
Core facility for University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center. Provides support for measurement of components of energy balance and for assessing consequences of alterations in energy balance. Provides expertise and support for obesity and nutrition related basic, clinical, translational, and transdisciplinary research for NORC investigators and its affiliates. Provides services to assess body composition, bone density, physical fitness, and energy expenditure values in research participants.
Vanderbilt Digestive Disease Research Center Biostatistics Component Core
Vanderbilt Digestive Disease Research Center Biostatistics Component of the Administrative Core
Core facility for the Vanderbilt Digestive Disease Research Center. Provides professional expertise in biostatistics for all DDRC projects, investigators, and participants. Functions provided by this component include development of experimental designs, power analysis, and sample size computation; data acquisition and database development; statistical analysis and interpretation of findings; collaboration on presentation of results; education in biostatistical methods; and development of tools with application to clinical trials and laboratory research.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Center for pathobiology research development.
MMPC - Vanderbilt University School of Medicine Microvascular Complications Core
Marion Bessin Liver Research Center Administrative and Supporting Services
Core facility for the Marion Bessin Liver Research Center.
Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references.
Algorithm for alignment-free scaffolding graph construction from short or long reads. It allows the reuse of efficient algorithms designed for short read data and permits the definition of novel modular hybrid assembly pipelines.
Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track.
Analysis software for life science data. This software package is for presentation and evaluation of sensorgram data from real-time BIA analyses.
Software for a head-fixed behavioral environment that uses a lightweight physical maze floating on an air table that moves around the animal’s body under the direct control of the animal itself, solving many problems associated with using virtual reality for head-fixed animals. It works with recording equipment (e.g., 2-photon imaging, patch recordings, etc.) that frequently requires head fixation.
Repository of open source tools for behavioral neuroscience research. OpenBehavior features hardware (tools, devices, apparatuses), as well as software for data acquisition and analysis and for the investigation of animal behavior and cognition. Dedicated to accelerating research through promotion of collaboration and open source projects.
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them.
LiGeA - a comprehensive database of human gene fusion events
LiGeA: a comprehensive database of human gene fusion events
Portal provides an easy access to a comprehensive database designed for storing, displaying and annotating gene fusion events detected from NGS data. It can query a database of somatic fusion genes events predicted and annotated starting from paired-end RNA-seq data.
Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).
Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging.
Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller.
The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies.
Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Visualization software that links unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool for image processing and analysis.
Software basecaller for Oxford Nanopore Technologies' sequencers.
Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer.
Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.)
Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.
scater (single-cell analysis toolkit for gene expression data in R)
Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.
Laser equipment that contains two wavelengths on the same handset, Red Laser and Infrared Laser. Currently Lasertherapy has acted in the different dental specialties as an indispensable technological tool. The use of this Photonic Therapy, associated to the most different dental procedures, provides greater comfort to the patients and greater reliability in the work of the dental surgeon.
Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12.
NeuroImage Field-of-View Normalization Tool
FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets.
Freezing microtome. Microm Laborgerate GmbH. Equipment for obtaining thick slices from small organs.
Thermo Fisher Scientific. Catalog number. P36934. ProLong™ Gold Antifade Mountant. Cellular Imaging
Perimed. Monitor blood circulation in real-time. Range of probes for different flaps. Sensitive laser Doppler technique
Zeiss | LSM 800 with Airyscan Microscope
Compact confocal microscope with highly sensitive GaAsP detection and fast linear scanning. The airyscan system allows capture images with high sensitivity and superresolution compared with conventional confocal microscope., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Marmoset Monkey Cerebral Cortex Connectivity Atlas
Brain connectivity atlas to create systematic, digital repository for data on connections between different cortical areas, in primate species. Data repository for connections between different cortical areas in marmoset monkeys. Allows access to data set and enables other interpretations of data, in light of future evolution of knowledge about marmoset cortex.
AEGeAn: analysis and evaluation of genome annotations
Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.
Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).
Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer.
ALTER: ALignment Transformation EnviRonment
Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.
Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method.
Analysis software for dynamic contrast enhanced magnetic resonance images with implementation of a pixel-by-pixel deconvolution approach. It quantifies T1-weighted contrast-enhanced dynamic MR imaging (DCE-MRI) perfusion data as an OsiriX plug-in.
Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.
Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle.
Software that detects tRNA genes and tmRNA genes in nucleotide sequences. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
ARDEN: Artificial Reference Driven Estimation of false positives in NGS data
Artificial Reference Driven Estimation of false positives in NGS data
Software for specificity control of read alignments using an artificial reference. It estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation.
Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.
BCI P300 Speller Kaggle Dataset for Healthy subjects
Dataset replicating the experiment done on BNCI-HORIZON 008-2014 dataset. BCI P300 Speller Kaggle Dataset for Healthy subjects
Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB.
Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock.
Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples.
Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.
Software for molecular visualization and modeling. It provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features.
Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.
Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments.
Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.
TraDIS:Transposon Directed Insertion Sequencing
Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.
Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites.
Barrnap: Basic rapid ribosomal RNA predictor
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Management and Analysis System for Enormous Reads:loadBED2ge_db
One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadBED2ge_db software is for visualizing mapping data by Genome Explorer on the web.
Management and Analysis System for Enormous Reads: loadGffToGe_db for custom genome
One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGffToGe_db for custom genome software loads GFF files of custom genomes to a database for Genome Explorer. It allows the user to browse the results through the GE.
Management and Analysis System for Enormous Reads: loadGtfToGe_db
One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGtfToGe_db software loads GTF files to a database for Genome Explorer. It allows the user to browse the results through the GE.
Management and Analysis System for Enormous Reads: regist custom genome
One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide.. Regist custom genome software registers custom genomes to Genome Explorer (IN: FASTA).
ReproNim: A Center for Reproducible Neuroimaging Computation
Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible.
Commercial organization that builds and supplies research-related equipment such as amplifiers.
Software for birdsong analysis that performs automated recording and analysis of animal vocalization. It can record, analyze and manage sound data over prolonged periods.
Vocal Inventory Clustering Engine (VoICE)
VoICE (Vocal Inventory Clustering Engine)
VoICE: A semi-automated pipeline for standardizing vocal analysis across models
VoICE: Vocal Inventory Clustering Engine
Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations.
Algorithm for a reasoner for ontologies written using the Web Ontology Language (OWL). Given an OWL file, HermiT can determine whether or not the ontology is consistent, identify subsumption relationships between classes, and much more.
Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude.
Redcap: Research electronic data capture
Software for metadata-driven electronic data capture to export REDCap data dictionaries and data to the NIMH National Data Archive (NDA). Prepares data submissions as csv formatted spreadsheets for data dictionary spreadsheets and for data spreadsheets.
Software which provides a framework for the secure storage of Personal Identifyable Information (PII) for a multi-site longitudinal project centrally. Used in Adolescent Brain Cognitive Development (ABCD) Study.
Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive.
Visualization software that calculates derived scores for the electronic record system REDCap (Research Electronic Data Capture) to build and manage online surveys and databases. Used in the ABCD-STUDY (Adolescent Brain Cognitive Development - STUDY) report framework.
Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository.
Software to capture subject information about substance use using local copies of external files provided by the abcd-report framework of ABCD. No connection to REDCap is attempted to get events and participant names but local files are read in to supply this information.
Software tool to manage data and derived results. It is used for import of derived measures into REDCap (Research Electronic Data Capture).
Software to measure item level completion in a large REDCap project. It provides a web-interface to review data and it is used in the ABCD project to assess data collection sites for the reached level of completion.
Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests.
Software for sharing the ABCD (Adolescent Brain Cognitive Development) study data on the National Data Archive (NDA).
Software to measure the amount of ghosting artifacts in T1-weighted DICOM images. This program reads DICOM images and calculates a measure of the noise structure in one part of the image.
Software for research study observation that visualizes study related events per day. Any event generating function sends a 'tick' event to this application which will be visible on this applications web-interface.
Software for online quality control operations performed on Phantom MRI data. It checks the accuracy and reproducibility of data.
Software for a numerical computation library that performs numerical calculations. Used in ABCD study.
Software application to upload functional MR imaging runs produce auxilary data that can be collected centrally. Connects to a subject database research electronic data capture (REDCap).
Software that contains multiple sequential lines of MATLAB commands and function calls for numerical computing for ABCD study protocol compliance.
Software tool to organize and deploy custom hooks in a single project or across the entire instance. It features multi-language support for data entry and survey pages, a bar-code for text fields, and highlighting of rows on data entry and survey pages that have been filled out.
Data collection software for centrally and securely storing data from the NIH iPad application. It allows users to capture results from multiple iPads at a central location.
Software application as a simple system to review study progress. Used in ABCD study.
Software that performs a delay-discounting task measuring impulsivity. Used in ABCD study.
Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import.
Software that conducts the Stroop Color Task. Used in the ABCD Study.
Data collection software as an end-point for centrally storing data from the Pearsons Q-Interactive.
Software that conducts a jspsych test for response time evaluation. Used in the ABCD Study.
µV Amplifier filter with offset compensation and gain.
Amplifier that records with patch, sharp, metal or carbon fiber electrodes. It includes a variety of other neuroimaging functions.
Hardware resource. Connector Module for EPMS for up to 4 standard headstages.
Data acquisition interface from Cambridge Electronic Design Limited. Works with Spike2 to provide continuous acquisition tasks. Records waveform data, digital and marker information, and can generate waveform and digital outputs simultaneously for real-time, multi-tasking experiment control.
Software for coding video data for research purposes such as animal behavior. Solomon Coder can handle several video formats, represent behaviors and events with buttons, analyze various types of data, and perform other necessary video coding functions.
Research-tested Intervention Programs (RTIPs)
Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials.
Database that contains behavioral and social science measures organized by theoretical constructs. GEM is designed to enable researchers to use common measures with the goal of exchanging harmonized data.
Software that maps whole-genome and targeted bisulfite sequence reads to reference genomes. It is especially useful for reads obtained using post-bisulfite adaptor tagging (PBAT)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
G-Anchor: A novel approach for cross-species comparison
Software for comparing large genomes and exploiting highly conserved sequences as evolutionary-stable "anchors". The pipeline maps a newly sequenced genome (assembled in scaffolds) on a reference genome without the need of a supercomputer.
Software for acquiring images from a video source, such as vision cameras, frame grabbers and video converters. It can capture single images, sequences of single images, and live video streams from connected video sources.
m6ASNP: Annotation of genetic variants by m6A function
Web server implemented in JAVA and PHP for annotating genetic variants by m6A function. It predicts and annotates N6-methyladenosine (m6A) alterations from genetic variants data such as germline SNPs or cancer somatic mutations. It employs two accurate prediction models for human and mouse using Random Forest algorithm. It conducts a statistical analysis for all the predicted m6A alterations. Provides statistical diagrams and a genome browser to visualize the topology characteristics of predicted m6A alterations.
Gannet - Batch Analysis of Edited Magnetic Resonance Spectroscopy (MRS) Data
Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data.
Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy.
Software for merging massive VCF files into a single VCF file or TPED file. Source codes can be slightly modified to fit into other types of sorted merging of Omics data.
Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together.
Command line program to read, modify, annotate and generate genomic data. Can write files to .gff3 or to the NCBI's .tbl format.
Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics.
Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity.
Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records.
Software that automates assembly circularization and produces accurate linear representations of circular sequences. It is used for assembling of DNA sequence data of complete bacterial and small eukaryotic genomes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.
Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.
Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets.
Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands.
Computational Structural Biology Toolbox
Computational Structural Biology Toolbox (CSB)
Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses.
Software alignment tool to find all significant local alignments between long and noisy, up to 15% on average reads encoded in a Dazzler database. Used for DNA sequence assembly, specifically for next generation long-read sequencers such as the Pacbio RS II and Sequel sequencers.
Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts.
Software application to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. The application accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users.
Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data.
DeepNano: alternative basecaller for MinION reads
DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads
Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate.
Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.
Cysteines Disulfide Bonding State and Connectivity Predictor
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.
Software toolkit for a cross-platform JSON-framework for describing command-line tools and their parameters. It is accompanied by a Python tool which facilitates the creation, validation, simulation, execution, publishing, evaluation, and testing of tools described in this format.
Statsmodels: Econometric and Statistical Modeling with Python
Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html
Software for handling multimedia files. FFmpeg can record, convert and stream audio and video.
Comenius University; Bratislava; Slovakia
Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences.
Software for an efficient maximal exact match (MEM) computation program that does not use full text indexes, uses less space and is amenable to parallelization. It can be used as a stand alone application or a drop-in replacement for MUMmer3 system for rapidly aligning entire genomes.
Ecopcr: Electronic polymerase chain reaction
Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
EDTSurf: Quick and accurate construction of macromolecular surfaces
Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening.
Software for protein domain search. It is a part of Embassy software package.
Software commands for Extra EMBOSS and protein domain alignment. The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.
Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt.
Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers.
Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes.
Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths.
Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together.
Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences.
Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq.
Department of Computer Science; University of Western Ontario; London; Ontario; Canada
University of Western Ontario; Department of Computer Science; London; Ontario; Canada
Software toolkit for a charting library written in pure JavaScript. It offers a way to add interactive charts to a web site or web application.
Programming language framework for HTML, CSS, and JS. It is used for developing responsive, mobile projects on the web.
Database of barcoded food products. Food Repo provides data that is on the package of each product, and collects its data via food distributors and volunteer contributors.
Software plug-in for ImageJ that was developed for registering 3D volumes of images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Hardware for performing patch clamping for in vivo cell recordings of freely moving animals. The setup consists of a support column with an enlarged base for mounting the assembly, a clip which allows for flexibility in placement, and an actuated axis fitted with a capillary holder for the reference electrode.
Algorithm for spike detection and sorting that uses wavelets and super-paramagnetic clustering. It generates an unsupervised solution, but this can be modified according to the experimenters’ preference for semi-automatic sorting.
Hardware that is a miniature headstage (without casing) for in-vivo experiments in freely moving animals'.
Software that combines reference and assembled transcriptomes for RNA-Seq analysis. It replaces many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations.
Software toolkit of MATLAB functions that conduct data analysis of MEG and EEG data. It performs tasks such as EEG and MEG forward calculations, inverse calculations, power and coupling measures, decomposition, statistics, and visualization.
Organizational software that supports exposure of executables and metadata for discoverability. The software includes a known filesystem structure, a definition for a set of environment variables describing it, and functions for generation of the variables and interaction with the libraries, metadata, and executables located within.
Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software.
Software that generates container-based behavioral experiments for reproducible science. It offers a library of experiments, games, and surveys, support for multiple kinds of databases, and robust documentation for the provided tools.
Software toolkit of Matlab functions for analyzing and visualizing large numbers of t-tests performed on event-related potential data. The toolbox supports within-subject and between-subject t-tests with false discovery rate controls and control of the family-wise error rate via permutation tests.
iELVis (intracranial electrode visualization)
Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization.
Database and index for huge amounts of small files. Files are stored concatenated in one big data file, with second file contains plain text index, giving name, offset and length of small files.
Software package that sorts data into groups, shuffles the order of data, and computes descriptive statistics based on the data. These FILe and stream Operations can be used independently or together.
Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling.
Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).
Software for a statistical multiple sequence alignment algorithm which uses a "distance-based" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned.
Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data.
GAMGI: General Atomistic Modelling Graphic Interface
General Atomistic Modelling Graphic Interface
Software application which provides a graphical interface to build, view and analyze atomic structures. It provides a graphical interface to study atomic structures, to prepare images for presentations, and teach the atomic structure of matter.
Genetic Algorithm for Rapid Likelihood Inference
Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution.
Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences.
Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame.
Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization.
Maximal Information Coefficient (MIC) Tools
Software which combines the TICe and MICe measures into a two-step procedure that allows to identify relationships of various degrees of complexity in large datasets. TICe is used to perform an efficient high throughput screening of all the possible pairwise relationships and a permutation based approach is used to assess their significance.
Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data.
An instrument. Navigation system for transcranial magnetic stimulation (TMS).
Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.
Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis.
Glam2: Gapped local alignment of motifs 2
Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.
Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences
Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations.
Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Used for sequence-based protein function and structure prediction what depends on sequence-search sensitivity and accuracy of the resulting sequence alignments.
Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications.
Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution.
Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.
Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information.
Clinker - Fusion Super Transcript generator and Plotter
Software for a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, Pizzly, etc). They can be then be either viewed in genome viewers such as IGV or through the included plotting feature developed with GViz.
Software for a Python feature selection repository that contains a variety of feature selection algorithms, including traditional feature selection algorithms and some structural and streaming feature selection algorithms. It serves as a platform for facilitating feature selection application, research and comparative study.
Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience.
Hardware that is used to test and assess pain and inflammation of the hind limbs on mice and rats. Dynamic weight bearing enables the test to be implemented on both limbs, while inflicting less stress on the subject animal.
Biophysical Interactions of Orfeome-based comPLEXes (BioPLEX)
BioPlex (biophysical interactions of ORFeome-based complexes)
Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection.
GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues)
Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.
Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes.
Database for investigating and visualizing protein-protein interactions. It aims to maintain coverage, quality, convenience, and transparency in the field of PPI research.
Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium.
Software for an integrated network combining multiple biological network database sources into a single human protein interactome. The software package contains gene interaction pairs corresponding to the unified global network.
Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects.
Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.
Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes.
Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations.
Software repository holding a cloud-ready demonstration of the use of Kafka as a genomic database.
Knowledge repository established to describe molecular mechanisms of Parkinson's Disease. It compiles literature-based information on PD into an easy to explore and freely accessible molecular interaction map and offers research-facilitating functionalities such as the overlay of experimental data and the identification of drug targets on the map
Software package for signal-level analysis of Oxford Nanopore sequencing data.
DEAP - Data Exploration and Analysis Portal
DEAP: Data Exploration and Analysis Portal
Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.
Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.
The Alzheimer's Association created The Global Alzheimer's Association Interactive Network (GAAIN) to connect Alzheimer’s and dementia researchers and speed discovery by connecting potential collaborators to those sharing data (GAAIN Data Partners). GAAIN's powerful interactive tools allow users to explore data and create cohorts across multiple data sources and run immediate preliminary analysis while upholding the data control, security, and privacy policies of the data owners. These tools are freely accessible to all at www.gaaindata.org. A wide and vastly varying range of metadata from nearly 500,000 subjects can be explored using these tools. Attributes include demographics, assessments, health factors, biologicals, imaging and genetics.
Music composition and manipulation software.
HyPhy:Hypothesis Testing using Phylogenies
Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.
Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time.
iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations
Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations.
NGSimple (Next-Generation illumina SIMulation PipeLinE)
NGSimple (Next-Generation illumina SIMulation PipeLinE), mainly written in perl is designed to simulate NGS parameters (illumina sequencing type, read length, insert size and coverage) based on a given reference, and give a report to choose the best parameter combination that could contribute to a good assembly.
This pipeline and the included scripts are used to filter useful reads for SSPACE.
Virtual Slide Microscope Software by Olympus. This software will be read the data captured by VS120/cellSens. Images saved with VSI or Multi-Tiff file format can be read.
Berkeley Advanced Reconstruction Toolbox
Image reconstruction software for MRI. Its library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms.
CytoBackBone is an R package for merging of phenotype information from different cytometric profiles. Single-cell technologies are the most suitable techniques for the characterization of cells by the differential expression of the molecules that define their roles and functions in tissues. Among these techniques, mass cytometry represents a leap forward by increasing the number of available measurements to approximately 40 cell markers. Thanks to this technology, detailed immune responses were described in several diseases. However, the study of immune responses, such as that due to viral infections or auto-immune diseases, could be further improved by increasing the number of simultaneously measurable markers. To increase this number, we designed an algorithm, named CytoBackBone, which combines phenotypic information of different cytometric profiles obtained from different cytometry panels.
CATNAP - Compile Analyze and Tally Neutralizing Antibody Panels
Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application.
International Institute for the Advancement of Medicine
Biomaterial supplier that links organ and tissue donors with the scientific community. After securing the appropriate consent, IIAM provides non-transplantable organs and tissues to researchers for use in medical discovery and education.
Web application for a code and text writing environment. It uses javascript and can be used to produce executable papers.
Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools.
L1000FWD: Large-scale Visualization of Drug-Induced Transcriptomic Signatures
Web application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase.
Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources.
L1000 Characteristic Direction Signature Search Engine
LINCS L1000 characteristic direction signatures search engine. Software tool to find consensus signatures that match user’s input gene lists or input signatures. Underlying dataset is LINCS L1000 small molecule expression profiles generated at Broad Institute by Connectivity Map team. Differentially expressed genes of these profiles were calculated using multivariate method called Characteristic Direction.
The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. Unlike an encyclopedia, a lexicon provides the meaning of a term, and not all there is to know about it. InterLex is being constructed to help improve the way that biomedical scientists communicate about their data, so that information systems like NIF and dkNET can find data more easily and provide more powerful means of integrating that data across distributed resources. One of the big roadblocks to data integration in the biomedical sciences is the inconsistent use of terminology in databases and other resources such as the literature. When we use the same terms to mean different things, we cannot easily ask questions that span across multiple resources. For example, if three databases have information about what genes are expressed in cortex, but they all use different definitions of cerebral cortex, then it is hard to compare them. InterLex allows for the association of data values (i.e. the value of a field or text within a field) to terminologies enabling the crowdsourcing of data-terminology mappings. InterLex was built on the foundation of NeuroLex (see Larson and Martone 2013 Neurolex: An online framework for neuroscience knowledge. Frontiers in Neuroinformatics, 7:18) and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies. NIFSTD currently has about 60,000 concepts (includes both classes and synonyms) that span gross anatomy, cells, subcellular structures, diseases, functions and techniques. InterLex models terms using primitives of the Web Ontology Language (OWL) and can export directly to a variety of standard ontology formats. A primary goal of interlex is to provide a stable layer on top of the many other existing terminologies, lexicons, and ontologies (i.e. provide a way to federate ontologies for data applications) and to provide a set of inter-lexical and inter-data-lexical mappings. In the future, InterLex will support user specific namespaces so that users can customize the exact definitions or ontologies they source from, as well as the relationships on those terms. Importantly, however, InterLex enforces a simple rule which is that terms which represent the same concept under the same superclass will maintain the same identifier fragment (i.e. 'ilx_1234567'). However, each user will be able to 'fork' a term into their own namespace (e.g. http://uri.interlex.org/user/ilx_1234567). This enables the various perspectives on a term or concept to have equal space so that the full diversity of views on a term can be seen and expressed. Sign-up for updates to get notified about updates to InterLex and when new features are available.
System to record continuous measurements of left ventricular pressure with a conductance pressure-volume catheter.
Prucka CardioLab system delivers the EP data and visualization we need for electrophysiological study and catheter ablation.
LINCS Joint Project - Breast Cancer Network Browser
Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations.
EEG/EMG, biometric data, and synchronized video recording software.
Software for EEG and synchronized video playback and seizure detection based on RMS and line length.
Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations.
Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures.
Johns Hopkins University Integrated Imaging Center Core Facility
Imaging and flow cytometry core facility at Johns Hopkins University Homewood Campus.
Direct Infusion Metabolite Database (DIMEdb)
Database of metabolite structures and annotations. The sources are from multiple existing metabolic and chemical databases such as HMDB, PubChem, CHEBI, BioCyc, and KEGG.
Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes.
Software for the acquisition, visualization, measurement, and analysis of sounds. Raven supports annotations for research-related analysis.
Data acquisition software for TriKinetics activity monitors. TriKinetics systems quantify animal movement over time, and can be used to measure behaviors such as circadian rhythm, sleep, longevity, social interaction, geotaxis, phototaxis, learning, and drug response in various species.
Hardware that is a electrical pulse generator.
Software for acquisition and analysis for imaging applications. The acquisition section has a variety of triggering and averaging modes, while the analysis section has extensive provisions for displaying traces (intensity vs time) and movies of propagating activity.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th, 2023. Software that uses long reads to close gaps in the assemblies.
Software that defines a data model for annotated scientific datasets. It includes data together with metadata, and a corresponding file format based on HDF5 for storing and sharing such datasets.
Software application for real-time, interactive, multi-camera recording. It is compatible with all Pixelink PL-B and PL-D line of cameras.
HIRN Consortium on Beta Cell Death and Survival
Consortium on Beta Cell Death and Survival (HIRN-CBDS)
Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is using human tissues to discover highly specific biomarkers of beta cell injury in asymptomatic T1D and developing strategies to stop beta cell destruction early in the disease process.
HIRN Consortium on Human Islet Biomimetics
Consortium on Human Islet Biomimetics (HIRN-CHIB)
Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is combining advances in beta cell biology and cell biology with tissue engineering technologies to develop microdevices that support functional human islets.
HIRN Consortium on Modeling Autoimmune Interactions
Consortium on Modeling Autoimmune Interactions (HIRN-CMAI)
Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is developing innovative approaches to model basic aspects of human T1D immunobiology using novel in vivo and in vitro platforms.
HIRN Consortium on Targeting and Regeneration
Consortium on Targeting and Regeneration (HIRN-CTAR)
Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is investigating methods to increase or maintain functional beta cell mass in T1D through targeted manipulation of islet plasticity or engineered protection of beta cells from immune-mediated destruction.
Human Pancreas Analysis Program (HIRN-HPAP)
Program is performing deep phenotyping of human endocrine pancreas and its interaction with immune system to better understand cellular and molecular events that precede and lead to beta cell loss in Type-1 Diabetes (T1D) and islet dysfunction in Type-2 Diabetes (T2D).
The Bioinformatics Center is located within the Department of Diabetes and Cancer Discovery Science at City of Hope and was established in 2014 to support the Human Islet Research Network (HIRN). The overall objective of the Bioinformatics Center is to advance type 1 diabetes knowledge generated through HIRN by providing the bioinformatics capability and infrastructure needed to support the Network. To achieve this goal, the Bioinformatics Center provides investigators with tools, processes, and methods to facilitate long term sharing, maintenance, and management of HIRN developed resources, including datasets, technologies, documents, and bioreagents. Collaboration and communication are cultivated through consultation and outreach activities. In 2019, HIRN received funding to continue HIRN Coordinating Center (CC) and Bioinformatics Center (BC) as Human Islet Research Enhancement Center (HIREC).
Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines.
Source code for a bash pipeline that quantifies splice-leader (SL) trans-splicing events by genes in the nematode C. elegans. It is designed to work downstream of read mapping and takes the reads left unmapped as primary input.
Blog for summaries of neuroscience journal papers and articles. BrainPost sends its subscribers digestible and accessible versions of scientific findings in the field of neuroscience.
Software for syntax highlighting for computational biology.
Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images.
Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data.
Stanford Diabetes Research Center Diabetes Immune Monitoring Core
Core facility that provides immune monitoring assays at the RNA, protein, and cellular level, as well as archiving, reporting, and data mining support for clinical and translational studies related to Diabetes. The DIMC is a specialized subcore of the Human Immune Monitoring Center (HIMC) at Stanford.
Stanford Diabetes Research Center Stanford Islet Research Core
Core facility whose services include: Islet Isolation, Islet transplantation, Islet Culture, Islet Perifusion & Islet Hormone Assays. The SIRC is supported by the Stanford Diabetes Research Center (SDRC).
Stanford Diabetes Research Center Diabetes Clinical and Translational Core
Diabetes Clinical and Translational Core
SDRC Diabetes Clinical and Translational Core
With the following services from the Diabetes Clinical and Translational Core (DCTC), members will receive training in biospecimen preservation, study design, data analysis, data management, use of statistical software and clinical trial conduct.
Stanford Diabetes Research Center Diabetes Genomics Analysis Core
Core facility that offers library preparation and sequencing services on a variety of platforms - Illumina HiSeq 4000, MiSeq, HiSeq 2500 and PacBio Sequel - as well as bioinformatics analysis. It can sequence a variety of commercial sample preparation kits as well as custom workflows. DGAC provides access to high throughput sequencing and analysis to researchers at the Stanford Diabetes Research Center.
BraTS: Multimodal Brain Tumor Segmentation
Organization that provides a conference about the methods for the segmentation of brain tumors in magnetic resonance imaging (MRI) scans. Its conferences utilize multi-institutional pre-operative MRI scans and focus on the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas.
SegAN: Semantic Segmentation with Adversarial Learning
Semantic Segmentation with Adversarial Learning
Semantic Segmentation with Adversarial Learning (SegAN)
Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps.
Software tool as robust preprocessing pipeline for functional MRI.Used for preprocessing of diverse fMRI data.
Software that facilitates the handling of metadata collections stored in the odML format. Some supported operations include reduction, merging of odml structures, and the conversion from the hierarchical odML format to tabular formats.
Bravissima: Human Brain Artery NIfTI Atlas
Project that is a translation of the BraVa arterial vasculature database into the NIFTI MRI file format that can be applied to stroke studies, fMRI resting state imaging studies and other clinical neuroscience studies. Group artery region labels and arterial density maps are provided as well. Human Brain Major Artery Atlas 10.7490/f1000research.1114378.1
Software toolkit that is designed for configuration and control of TDT hardware. It can also display and analyze neurophysiology data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Organism supplier that provides guinea pigs exclusively for the research community.
Mapping Population-based Structural Connectomes
Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis.
Software for analysis and fitting routines of electrophysiological data. Analysis can be performed on the levels of Sweeps/Traces and Series.
Boruta: Wrapper Algorithm for All Relevant Feature Selection
Algorithm that performs feature selection. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
Software for analysis and simulation of gene sequences and structural variants. This software works with FASTA, FASTQ, BAM, VAR, META, and NEWICK file formats.
Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability.
International Initiative for Traumatic Brain Injury Research
International Initiative for Traumatic Brain Injury Research (InTBIR)
Project whose goal is to improve health care and lessen the global burden of TBI through the discovery of causal relationships between treatments and clinically meaningful outcomes. InTBIR seeks to encourage well-designed, hypothesis-driven studies that include the collection of high quality data followed by rigorous statistical analysis.
Service for monoclonal antibody protein sequencing. It derives the sequences directly from the protein using mass spectrometry and without the need to access the cell line.
WILD (W-ion Isoleucine Leucine Determination)
Service that distinguishes Isoleucine and Leucine using mass spectrometry experiments.
Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions.
Software plugin for 2D and 3D non-negative, iterative, deconvolution.
Database for singularity containers. It hosts container collections as well as articles about scientific advancements.
Web application and registry for institutional deployment of Singularity containers.
Software written in Python, and plugin to Hypothes.is, that creates automated annotations.
Text-mining software that reviews methods sections of scientific articles. It provides a numerical score to represent the "reproducibility" of the article's research.
Software used to analyze glomerular filtration rate (GFR) measurement from MediBeacon GFR monitor. It is used with the Transdermal Continuous Renal Function Monitor.
Software for the interpretation of sedimentation equilibrium and sedimentation velocity experiments. Sednterp is useful both for computing molecular structural estimates from experimental data and for interpolating physical parameters of common buffers used in sedimentation experiments.
Software for the global analysis of sedimentation velocity, sedimentation equilibrium, and/or dynamic light scattering experiments. It is a stand-alone sedimentation equilibrium analysis software that also processes isotherms of weight-average sedimentation coefficients, weight-average molar mass values, and other components., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software for the characterization of macromolecules and nanoparticles via multi-angle and dynamic light scattering. It simplifies MALS and DLS analysis for assessment of molar mass, size, conformation, conjugation, and other essential physical parameters.
Software for quantitative MR image analysis, simulation, and protocol optimization. It aims to provide the community with a tool for data fitting, plotting, simulation and protocol optimization for a variety of different quantitative models.
Algorithm for co-registration of pairs and groups of neuron morphologies based on maximization of spatial overlap. The algorithm is written in Python and work with SWC files.
Database of ligands and diseases. Its goal is to develop a knowledge-base for the Druggable Genome (DG) in order to illuminate the uncharacterized and/or poorly annotated portion of the genome. DG, focusing on four of the most commonly drug-targeted protein families: G-protein-coupled receptors (GPCRs); nuclear receptors (NRs); ion channels (ICs); and kinases.
Model of assessment with the baseline default characteristics of the HOMA2 computer model of fasting insulin glucose interaction. iHOMA2 enables the mathematical functions describing the organs and tissues involved in the glucose and hormonal compartments to be modified using simple visual analogue controls.
Software for calculating different measures of glycaemic variability (GV). It analyzes continuous glucose monitoring data using a simple interface.
Observed Variability and Lability (OVAL)
OVAL (Observed Variability and Lability)
Software that allows you to quantify glucose homeostasis in type 2 diabetes and control subjects. OVAL also has the capacity to quantify sequential deterioration and monitor effects of intervention.
DALAN: Disconnectivity Atlas for Lesion Analysis of Networks
Atlas of human white matter diffusion streamlines for predicting medium/long range brain connectivity. The atlas uses the popular Harvard-Oxford (H-O) cortical and subcortical atlas as endpoint targets so that WM connectivity deficits can be analyzed in conjunction with corresponding GM deficits.
Software for fluorescence lifetime imaging and correlation. SymPhoTime 64 is the data acquisition software for PicoQuant's time-resolved confocal microscope MicroTime 200 and LSM upgrade kits.
FV 1200 Super resolution software module
THIS RESOURCE HAS BEEN DISCONTINUED. Documented May 7, 2018. Software module for biological confocal laser scanning microscope FV 1200. Olympus's proprietary super resolution technology FV - OSR (Olympus Super Resolution) realizes XY resolution of about 120 nm exceeding the conventional 3D confocal microscope.
ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration.
Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence.
Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”.
Center for Expanded Data Annotation and Retrieval
Develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.Center to improve metadata and its use throughout biomedical sciences. Develops information technologies that make authoring complete metadata more manageable through better interfaces, terminology, metadata practices, and analytics. Optimizes metadata pathway from provider to end user. Provides way for funders to specify what metadata they want to collect as part of research life cycle.
Center for Expanded Data Annotation and Retrieval Workbench
Web application for creating, collecting, testing, and sharing metadata. It provides templates for metadata models or structures, and is capable of testing those models quickly using real data.
Web based software for analyzing genomic variants CNVs, SNVs, and Indels and phenotypes. It aims to represent the relationships between discovered variants and phenotypes.
Database that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. Part of Gemma, a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data.
Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy.
Software for dynamic clamping. It uses National Instruments Boards.
Software for error correction of optical mapping data.
integrated database of HLA supertype specific epitopes
Database of HLA supertype-specific epitopes. It describes major histocompatibility complex (MHC) molecules that bind short peptides derived from endogenous or exogenous antigens and present them onto the surface of antigen-presenting cells (APCs) for T-cell receptor (TCR) recognition.
Database for MHC antigenic peptide of Mycobacterium tuberculosis. It aims to make a comprehensive repository of synthetic antigenic peptides predicted from several MHC predication servers.
Database of naturally processed MHC-restricted peptide ligands and epitopes for customized computational vaccinology.
The HMP Unified Metabolic Analysis Network 2
Software for profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data Used for millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members.
Database of events about articles that is run by CrossRef. It allows users to view social media mentions, news publication references, annotations, and more.
Longitudinal neuroimaging hippocampal markers for diagnosing Alzheimer's disease
Software based on robust registration and simultaneous hippocampal segmentation and longitudinal marker classification of brain MRI of an arbitrary number of time points. The framework comprises two parts: a longitudinal segmentation and a longitudinal classification step.
Software that provides all the necessary functionality for full-model build up, from CAD data to ready-to-run solver input file. Its integrated Batch Meshing tool leads to results for both shell and volume meshing.
SIGEN: SImulation of Geometrical and Electrical properties of Neuron
SImulation of Geometrical and Electrical properties of Neuron
Software to extract and trace neuronal structure from confocal laser scanning microscope images. It performs the automatic reconstruction of neurons for image stacks and can generate compartmental models of neurons as swc file format data.
Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis.
Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes.
Software package for processing of high-resolution neuroimaging data. Nighres is a community-developed project that aims to make neuroscience data tools easier to install, use and extend.
BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway)
Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power.
Software for computating and calculating elementary flux modes. EFMtool computes elementary flux modes (EFMs) of metabolic networks. EFM computation is a special case of extreme ray enumeration of polyhedral cones.
Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software for combined elementary flux mode and network-embedded thermodynamic analysis.
Software package which allows to produce clustering trees and visualize clusterings at different resolutions. Used in the analysis of large data sets to group together samples with similar properties.
Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability.
Software for advanced primer design. Can be used for some advanced primer functions, such as adjusting mispriming parameters and creating a primer catalog. Suitable for determining the best primer pairs or probes for PCR, sequencing, and hybridization experiments.
Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software for commercial data analysis and statistical software package for Microsoft Excel.
Norwegian e-Infrastructure for Life Sciences
Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project.
Software for Covaris Focused-ultrasonicators.
Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes.
Web tool for exploring circular RNAs and their interacting proteins and microRNAs. Predicts the miRNAs which can potentially target the circRNA.
Software for molecular weight, quantification of bands, colony counting and distance calculation in Vilber Lourmat gel documentation imaging systems. Used in molecular biology laboratories.
Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.
Software for multi electrode array recording for Axion Biosystems. Used in enhancing cardiac and neural analysis through data processing and signal monitoring.
Software application for PhoxX® Diode Laser to support Omicron products. It is related to uManager open source microscopy software for control of microscopes.
Data Sharing for Demographics Research (DSDR)
DSDR disseminates, archives, and preserves data for population-based studies. By providing access to data on topics including mortality and health, fertility, family and household structure, and children and youth, DSDR aims to facilitate demographic research.
Data and sample repository for National Children's Study. Provides access to data and samples collected from over 5,600 U.S. birth families to study environmental influences on child health and development. Data and biological and environmental samples are freely available, with approved request, for scientific research.
Database for study of early phonological development using Phon program. Child phonology component of TalkBank system.
Database for study of development of fluency in both normal and disordered populations. Participants include normally-developing monolingual and bilingual children, children with disfluencies (CWD), adults with disfluencies (AWSD), and second language learners.
Repository to store and access de-identified data from NICHD funded research studies for purposes of secondary research use. It serves as mechanism for NICHD-funded extramural and intramural investigators to share research data from studies in accordance with NIH Data Sharing Policy and NIH Genomic Data Sharing Policy.
Archive of Data on Disability to Enable Policy (ADDEP)
Archive of Data on Disability to Enable Policy
Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies.
Repository for distribution of various types of molecular data from human, cell-based and animal model biosamples, analytical results and research tools generated through multiple NIA-supported programs. Currently Portal supports AMP-AD Target Discovery and Preclinical Validation and MOVE-AD Consortia and translational center, MODEL-AD.
Shared database of multimedia interactions for the study of communication in aphasia.Access to the data in AphasiaBank is password protected and restricted to members of the AphasiaBank consortium group.
The NINDS Human Cell and Data Repository (NHCDR)
NINDS Human Cell and Data Repository (NHCDR)
Cell sources currently include fibroblasts and/or induced pluripotent stem cells for Alzheimer's Disease, Amyotrophic Lateral Sclerosis (ALS), Ataxia-telangiectasia, Frontotemporal Lobar Degeneration (FTD), Huntington's Disease, Parkinson's Disease, and healthy controls. Cell sources, including isogenic cell lines for current and new diseases covered by the NINDS will be added over the next several years.
Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users.
Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .
Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.
Portal to provide a repository for beta-cell data, to connect researchers from different backgrounds interested in contributing data, models and/or ideas for new insights into beta-cell biology. Used to understand beta-cell biology and diabetes through a cross-disciplinary approach for the assembly of spatiotemporal multi-scale whole cell models of human pancreatic beta-cells.
Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data.
Software for multifunctional recording designed to provide Brain Products GmbH- Solutions for Neurophysiological Research amplifier with a platform for recording setup and execution.
Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.
Software as an EEGLAB tool used for LIBEEP recordings.
The Bergen fMRI Toolbox Plugin for EEGLab
Software package as a set of Matlab tools which allow the correction of fMRI-related gradient artifacts from EEG data. Designed to work within the EEGLAB environment, providing a GUI to remove fMRI gradient artifacts from the EEG. Can also be used from the Matlab command line, providing expert users with the ability to use them in custom scripts.
Python based software module for the simulation of peripheral nerves. Used in the field of computational neuroscience.
Molecular Identifier Guided Error Correction
Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires.
Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles.
Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations.
Model based Analysis of Single Cell Transcriptomics
Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Software as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.
R t-Distributed Stochastic Neighbor Embedding
Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.
JavaScript plug-in software application for web environments to analyze data. It is an interactive Venn diagram viewer.Used for comparing lists with Venn Diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized.
Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.
Software as an open source machine learning framework for everyone. Library for high performance numerical computation. Allows deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices.
Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text.
The Molecular Atlas of Lung Development Program
Portal for lung histochemistry data. For structural and molecular data regarding normal perinatal and postnatal lung development in the mouse and human. For public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology .Contains lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers. Used to serve as a research resource and public education tool.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 17, 2024. Software application as a high-accuracy quantification function that supports various biological specimens. Used in KEYENCE automated imaging system for images captured using BZ series fluorescence microscopes.
Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.
Database as an open science framework with a scientific data extracted from scientific literature about various altered states of consciousness assessed with questionnaires. Used to compare what experiences are elicited by different drugs and non-pharmacological methods that induce altered states to help to understand human consciousness functions. Is listed by Neuroimaging Informatics Tools.
Software library of extended edit similarity measurement for high dimensional discrete-time series signal. Python module that offers functions for measuring the similarity between two segmented multi-neuronal spiking activities with implemented extended edit similarity measurement.
ROIs selection with a non-graphical user interface
It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets.
A Matlab adapter class and user interface to control the Reglo ICC peristaltic pump provided by Ismatec.
Elephant: a convolutional network for spike detection from calcium traces
Program based on convolutional neural networks for spike detection from calcium traces. It is written in Python and Keras.
Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.
Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool.
Statistical Meta Analysis for Gene EXPression
Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.
Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction.
Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis.
Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories.
Software application to perform systematic and collaborative curation of neuroscientific literature. Graphical User Interface (GUI) for the Python package NeuroAnnotation Toolbox (NAT). Used for the systematic annotation of relevant statements and model parameters to be traceable, reusable across projects, structured with controlled vocabularies.
Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches.
Electric Cell-substrate Impedance Sensing
Electric Cell-substrate Impedance Sensing Model
Instrument that electronically monitors cells grown in tissue culture. It is a real-time, label-free, impedance-based method to study the activities of cells. Used for analysis in cell biological dynamics for cells that do not form tight monolayers such as cancer cell lines. The system supports communication to a PC, allowing data acquisition, analysis, and storage.
Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.
Database of death record information on file in state vital statistics offices. Working with these state offices, the National Center for Health Statistics (NCHS) established the NDI as a resource to aid epidemiologists and other health and medical investigators with their mortality ascertainment activities.
Harvard Medical School (HMS) LINCS Center
Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation.
A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images
Software plugin for Fiji/ImageJ that performs retrospective image correction for optical microscopy. It is based on low rank and sparse decomposition, which corrects both shading in space and background bleaching in time.
Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data.
Supplier of Frogs and Tadpoles for the scientific community.
Software that detects kinase-specific phosphorylation sites. GPS provides a platform able to perform its prediction based on a group-based phosphorylation scoring algorithm. It allows users to query multiple protein sequences through a batch prediction mode.
Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software for genomics and bioinformatics analysis. GenPipes includes several python pipelines that cover many genomics applications, such as RNASeq, ChIPSeq, DNASeq, WGBS, HiC, Metagenomics, PacBio assembly, etc.
Benchtop next-generation sequencer to sequence DNA and RNA.
MiniSeq System to perform range of targeted DNA and RNA applications for low numbers of samples.
MiSeq System offers wide range of sequencing applications. Capable of automated paired end reads and up to 15 Gb per run, delivering over 600 bases of sequence data per read. The library prep kits are optimized for variety of applications, including targeted gene, small genome, and amplicon sequencing, 16S metagenomics.
MiSeqDx System is FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD) testing. System offers both diagnostic and research modes.
The NextSeq 550 System brings the power of a high-throughput sequencing system to your benchtop. With tunable output and high data quality, it provides the flexible power you need for whole-genome, transcriptome, and targeted resequencing.
MiSeq FGx Forensic Genomics System is the first fully validated, next-generation sequencing (NGS) solution designed for forensic science. Dedicated library kits and analytical software take you from DNA-to-answer with streamlined efficiency.
High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world.HiSeq 2500 System has been discontinued. Illumina will support the instrument and intends to supply the reagents through February 28, 2023.
Sequencer that is CE-in vitro diagnostic (IVD) marked, enabling clinical laboratories to develop and perform a wide range of applications, from NGS IVD assays using targeted panels, to clinical research applications that include methods from targeted panels to whole genomes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. Sequencer for whole-genome sequencing. System consists of HiSeq X ultra-high-throughput instruments that deliver over 18,000 human genomes per year.
Illumina HiSeq 3000/HiSeq 4000 Sequencing System
Sequencer that uses patterned flow cell technology to provide high-performance sequencing. Perform production-scale, high-throughput exome or transcriptome sequencing projects quickly and economically.
Illumina | NovaSeq 6000 Sequencing System
High-throughput platform used for next-generation sequencing (NGS) applications, including whole-genome, whole-exome, and whole-transcriptome sequencing. It is designed to provide a scalable, high-volume, and reliable way to sequence DNA and RNA for a wide range of genomic studies, from research to clinical applications.
Can scan thousands of array samples per day, without sacrificing data quality or reproducibility. Supports expansive portfolio of genetic analysis assays, from high-throughput genotyping to DNA methylation analysis.
Software that performs automatic filtering, trimming, error removing, and quality control for fastq data.
Software that employs machine learning techniques and high-performance computing for analyzing task-based fMRI datasets. It applies Feature Analysis, Hyperalignment, Multi-voxel Pattern Analysis (MVPA), Representational Similarity Analysis (RSA), and more.
Software that performs quantitative analysis of angiogenesis. It specializes in quantitative assessment of various vessel morphometric and spatial parameters, including vessel length and density, branching index, lacunarity, etc.
Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models.
Human Islet Research Center Coordinating Center
Consortium that provides infrastructure to promote communication and collaboration among current and future HIRN participants, facilitating scientific advances and the sharing of data, tools, and reagents among HIRN members and the research community at large.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 14, 2018. An XML-RPC client of a web-service server which provides the service to recognize named entities in the biomedical articles. It is Gene Mention Tagger (GMT) for Biological Text Mining.
Algorithm for computational imaging of MRI data that detects and quantifies ischemic core–penumbra using only a single MRI modality (T2- or diffusion-weighted imaging, T2WI/DWI). It can be used with 3D data on lesions and normal-appearing brain matter (NABM) volumes.
Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.
Center for Animal Resources and Development
CARD:Center for Animal Resources and Development
Center for Animal Resources and Development is an international repository and distribution center for production, cryopreservation, and supply of genetically engineered mice.Provides a summary of institutions, organizations, and individuals contributing mouse resource information to the IMSR database.
University of North Carolina Systems Genetics Core Facility
Core focused on systems genetics approach to understanding diseases, development, aging, and fertility in mouse. Projects range from development of new community resources, such as Collaborative Cross, to development of tools and assays for measuring genetic diversity and discerning genomic structure. Collaborative Cross is reference population for mapping multigenic traits that would be free of population structure and it is new panel of recombinant inbred lines generated by randomizing genetic diversity of existing inbred mouse resources.
The Animal Resources Centre (ARC) is a self-funding Statutory Authority of the Government of Western Australia for biomedical research to produce and supply genetically-defined, specific pathogen free (SPF) research rats and mice. Provides contribution of mouse resource information to the IMSR database.
Centre for Molecular Medicine and Therapeutics MAPS
Centre for Molecular Medicine and Therapeutics Mouse Animal Production Service
Supplier of mice for research purposes. The service is run by Dr. Elizabeth M. Simpson, Ph.D. and is affiliated with her lab.
National Laboratory Resource Center Rodent Model Resource Center
National Resource Center for Mutant Mice
Model Animal Resource Imformation Platform
Model Animal Resource Information Platform
Nanjing University Model Animal Research Institute
National Resource Center for Mutant Mouse
Inc. SMOCShanghai Model Organisms Center
Supplier of mice for research purposes. Provides technical services, model organisms, gene editing and decoding.
The Oak Ridge National Laboratory (ORNL)
Software package for image analysis to determine the orientation of filamentous structures on digital images. Used as an image‐processing tool for analyzing cytoskeleton and cellulose fiber orientation in pant imagesk.
Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.
Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.
A peel and stick in-room ambulatory fetal monitoring solution by Monica Healthcare Ltd. Measures fetal heart rate (FHR), maternal heart rate (MHR) and uterine activity (UA).
Software tool to analyze the promoters of genes and look for motifs that are enriched in the target gene promoters relative to other promoters. Used for gene based analysis to provide a list of genes that should contain the same elements, such as genes that are co-regulated. It includes gene ontology analysis and can be used to look for RNA motifs in mRNAs.
Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters.
Fetal actocardiograph instrument provided by TOITU CO., LTD.
Software tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings.
Software tool to collect and analyse data on images of tissue slides or welled plates.Supports high-throughput immunofluorescence and immunohistochemistry, stereology, densitometry, and 3D modeling. Used in bioscience research in animal models and human biopsy, developmental neuroscience, traumatic brain/spinal cord injury, glaucoma, eye-movement disorders, cardiovascular disease and muscle disorders.
Software tool for analyzing recordings from multielectrodes. Source code for the Matlab implementation of the Kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes.
Web based database interface for orthology prediction for the inference of orthologs among complete genomes. Used to relate genes across many species., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data.
Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines.
Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.
Web application viewer for large microscopy data.
Software tool for flow and image cytometry data analysis by De Novo Software company.
CONP:Canadian Open Neuroscience Platform
Web interface that facilitates open science for neuroscience community by simplifying global access to and sharing of datasets and tools. Portal internalizes typical data cycle of research project, beginning with data acquisition, followed by data processing with published tools, and ultimately publication of results with link to original dataset. Platform to form interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing. Provides unified interface to Canadian neuroscience research community. Open neuroscience research with sharing of both data and methods, to create large-scale databases, development of standards for sharing, facilitation of advanced analytic strategies, open dissemination to global community of neuroscience data and methods, and establishment of training programs for next generation of computational neuroscience researchers.
Software package for processing two-photon recordings. Available together with a graphical user interface that allows manual curation of the results. Used in two-photon microscopy for the analysis of data from two-photon imaging. Registers raw movies, detects active cells, extracts their calcium traces and infers their spike times.
Open resource for nonhuman primate imaging.Used for aggregation independently acquired non-human primate magnetic resonance imaging (MRI) datasets and openly sharing them via the International Neuroimaging Data-sharing Initiative (INDI).Consortium and data collection for the neuroimaging community to map the non-human primate connectome. Anatomical, functional, and diffusion MRI datasets openly shared via the International Neuroimaging Data sharing Initiative (INDI).
Clinical Research in ALS and Related Disorders for Therapeutic Development
Biorepository of samples collected from patients with ALS, ALS-frontotemporal dementia (ALS-FTD), primary lateral sclerosis (PLS), progressive muscular atrophy (PMA), hereditary spastic paraplegia (HSP) and multisystem proteinopathy (MSP). Used by Consortium members and the scientific community to advance therapeutic development through study of the relationship between clinical phenotype and underlying genotype, and also through the discovery and development of biomarkers.
Open-source web application for managing digital repositories. Allows to create custom computing environments that can be shared and used by many remote users.Turns a GitHub repository containing a collection of Jupyter Notebooks into a collection of interactive notebooks. With Binder, open those notebooks in an executable environment, making your code immediately reproducible by anyone, anywhere.
This equipment is used for the purpose of monitoring fetal status.
Software tool for visual test battery in form of a free computer program.Can be run within your browser or download as a stand-alone program. Used by many vision labs, optometrists and ophthalmologists.
Software package to analyze, manage, and export recorded activity data from all Actiwatch models. Used to view long-term sleep/wake patterns, activity, illuminance, and event markers in an easy-to-read actogram format.
Collects and provides data on the human genome and epigenome to facilitate genetic studies of type 2 diabetes and its complications. A component of the AMP T2D consortium, which includes the National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK) and an international collaboration of researchers.
Software for filtering invalid Splice junctions from pre-aligned RNA-seq data. It takes as input a BAM file generated by an RNAseq mapper, then analyses and quantifies all splice junctions in the file before filtering (culling) those which are unlikely to be genuine.
MIES - Multichannel Igor Electrophysiology Suite
MIES: Multichannel Igor Electrophysiology Suite
Multichannel Igor Electrophysiology Suite
Multichannel Igor Electrophysiology Suite (MIES)
Software for Electrophysiology functions. It was developed by the Allen Institute.
ACQ4 Neurophysiology Acquisition and Analysis System
Neurophysiology acquisition and analysis for Python
Python-based software for experimental neurophysiology. It includes support for patch-clamp electrophysiology, multiphoton imaging, scanning laser photostimulation, and many other experimental techniques.
Software development environment that helps users build containerized software using Docker and Kubernetes softwares. It is executable on desktop and cloud, and allows access to a vast library of community containerized content in Docker Hub.
Mutant Mouse Resource and Research Center - Jackson Laboratory
Jackson Laboratory Mutant Mouse Resource and Research Center
JAX Mutant Mouse Resource and Research Center
Mutant Mouse Resource and Research Center - JAX
Center for mutant mouse research and distribution. The objectives of the JAX MMRRC are to: identify and evaluate biomedically-significant mice, import/acquire and archive mouse strains, distribute mouse strains, and operate a control program to ensure genetic stability.
Mutant Mouse Resource and Research Center - University of Missouri
Mutant Mouse Resource and Research Center - UM
UM Mutant Mouse Resource and Research Center
Center that supplies mice and conducts research projects focused on the role of mice as animal models. Some of these projects include refinement of models to ensure study reproducibility, as well as development and improvement of economical methods for cryopreservation of mouse strains.
University of California at Davis Mutant Mouse Resource and Research Center
Mutant Mouse Resource and Research Center - UCD
Mutant Mouse Resource and Research Center - University of California at Davis
Mutant Mouse Resource and Research Center UC Davis
UC Davis Mutant Mouse Resource and Research Center
UCD Mutant Mouse Resource and Research Center
Center that imports, archives, maintains, and distributes mutant mouse alleles as live mice, frozen germplasm, stem cells, and molecular vectors for use in biomedical research. The MMRRC Davis receives transgenics, knockouts, and other kinds of mutant mouse lines at no cost to the donor, and after re-derivation and cryopreservation, distributes breeding stock, germplasm, cells, or tissues of genetically-defined and pathogen-free mice for a small fee to requesting investigators.
Mutant Mouse Resource and Research Center - University of North Carolina
Mutant Mouse Resource and Research Center UNC
Mutant Mouse Resource and Research Center University of North Carolina
UNC Chapel Hill Mutant Mouse Resource and Research Center
University of North Carolina Mutant Mouse Resource and Research Center
Center that is a mouse cryoarchive and distribution center, which incorporates research goals that synergize with and extend the value of the resource. The goals of the UNC Chapel Hill center are to streamline and improve operating procedures, establish a comprehensive cryoarchive, develop and disseminate computational tools for mouse genotyping, and examine the effect of paternal age and epigenetics on mutation rate.
Gaussian-Copula Mutual Information (GCMI)
gcmi : Gaussian-Copula Mutual Information
Software package of functions for calculating mutual information and other information theoretic quantities using a parametric Gaussian copula.
Software for video analysis with modules to track insect antenna and proboscis movements. Its purpose is to assess the aggregate movement or activity levels of groups or swarms of animals.
University of Nebraska Medical Center Translational Mouse Model Core Facility
UNMC Translational Mouse Model Core Facility
Center that conducts and supports research with mouse models. It also supplies mouse models to researchers.
Referral Center for Animal Models of Human Genetic Diseases
PennVet Referral Center for Animal Models of Human Genetic Diseases
University of Pennsylvania School of Veterinary Medicine Referral Center for Animal Models of Human Genetic Diseases
UPenn Referral Center for Animal Models of Human Genetic Diseases
Center that aims to discover, characterize, maintain breeding colonies, and make available dog and cat models with hereditary diseases homologous to those found in human patients that can be used to translate preclinical trials from kennel to clinic. The animal models represent true orthologs of their respective human disease, involving defects in homologous genes resulting in similar molecular, biochemical, pathological, and clinical phenotype as in human patients.
Monitors the electrical signals on the patient’s abdomen by using the abdominal fECG and mECG wave shape to uniquely identify and separate the maternal and fetal heart rates.
Software as an open source informatics platform to facilitate the implementation and operation of distributed health data networks. Consists of a web-based portal for distributing requests and administering the network, and the DataMart Client. Designed by the Therapeutics Research and Infectious Disease Epidemiology (TIDE) group at the Department of Population Medicine (DPM) of the Harvard Pilgrim Health Care Institute (HPHCI) to enable creation, operation, and governance of distributed health data networks.
Software that uses ellipses to automatically draw accurate area-proportional Venn diagrams for 3-set data. It generates an exact diagram for most of the cases, and when it fails, the best diagram obtained through the hill climbing search is displayed, together with the inaccuracy values for each region.
Software application to take large sets of overlapping images in 2D and 3D and produce registered 3D volumes of any size and scale. Registered slices may be exported as a single large images or viewed/annoted with Viking viewer. Used on transmission electron microscopy, scanning electron microscopy images, and light microscopy images.
NCBI Biocollections:National Center for Biotechnology Information Biocollections
Registry of bio-collections linked to genomes. Collection of curated dataset of metadata for culture collections, museums, herbaria and other natural history collections, including Darwin Core institution and collection codes, and URL formulae for mapping specimen ids to web pages at the collection site.
Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.
Microbal Resource Research Infrastructure
Microbial stock center. Collaborative platform for the pan-European research infrastructure for microbial resources. Provides access to microorganisms, their derivatives, associated data and services for research, development and application.
Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.
Center to help translate life science research into products that improve human health. Available to internal and external users, through the Institute for Applied Life Sciences (IALS).
NRRL:Northern Regional Research Laboratory
Center that collects, deposits, maintains bacteria and fungi, and facilitates microbiological research to advance agricultural production, food safety, public health, and economic development. Housed within the Mycotoxin Prevention and Applied Microbiology Research Unit at the National Center for Agricultural Utilization Research in Peoria, Illinois.
UAMH Centre for Global Microfungal Biodiversity
Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi.
Centre for Agriculture and Biosciences International
CABI:Centre for Agriculture and Biosciences International
An international not-for-profit organization to solve problems in agriculture and the environment. Specialize in microbial identification and verification, and provide professional microbiology services in support of industry, academia and agriculture. Established by a United Nations.
Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.
Software tool as an open source knowledge mapping software that increases the visibility of research findings for science and society. Visual interface to the world's scientific knowledge.
Database of free scholary articles. Content from over 50,000 publishers and repositories easy to find, track, and use. A website featuring web-based tools created and maintained by Impactstory, Inc.
Pipeline for construction and graphical visualization of annotated pangenome networks from microbial genomes. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data provides pangenome analysis to uncultured microbial taxa., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins.
Sustainability Coalition for Open Science Services
Network to facilitate funding to ensure the long-term sustainability of the world’s open science infrastructure. A community-led effort to provide a framework for libraries, policymakers and other stakeholders to collectively fund and stabilize an infrastructure of freely available open science services.
Lenntech activity coefficient calculator
Software tool to calculate the activity coefficient of an ion in solution by Lenntech B.V. Determines the ionic strength of solution by using the concentration of ions present in drinking water.
Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data.
CERVO Canadian Optogenetics and Vectorology Foundry Core Facility
Canadian Molecular Tools Platform Core Facility
Canadian Neurophotonics Centre Molecular Tools Platform Core Facility
Canadian Neurophotonics Platform - Viral Vector Facility
Canadian Neurophotonics Platform Viral Vector Core
Neurophotonics Platform Viral Vector Core
Core facility responsible for custom adeno-associated virus (AAV) and lentivirus production available through Canadian Neurophotonics Platform. Services include design, cloning and production of molecular constructions in order to produce plasmid expression vectors or to generate transgenic animals and design, including advice and assistance for choice of suitable vectors required by investigators.
K.Kucharczyk Electrophoretic Techniques (Techniki Elektroforetyczne Spzoo, Poland)
Commercially available services for biomedical research. Includes the quantitative determination of the methylation level of selected epigenetic markers, designing and validation of primers and conditions for the multiplication of selected markers by PCR and determination of their methylation level by the pyrosequencing method. Service electro-optical laboratory equipment and offers specialized repair services: PCR thermal cyclers, Laboratory power supplies, ELISA plate readers.
Software package for statistics. Used to analyze and visualize data. Extensions can be used, Python and R programming language code, to integrate with open source software. Available for Windows and Mac operating systems.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago. Versions that were released after the acquisition would be given origin or publisher of IBM Corp. in Armonk, NY.
Software for cephalometric analysis. Customizable. Allows rendering, viewing and measuring of 3D data from CT scanners. Used in orthodontic departments for analysis of the dental and skeletal relationships of a human skull.
Software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment.
Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data.
Software tool for systematic review. A not-for-profit service working in partnership with Cochrane library to improve the production and use of systematic reviews.
Probabilistic Neural Networks MiceMachineVision
Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera "Cocaine-induced preference conditioning: a machine vision perspective".
Library of Integrated Network based Cellular Signatures
Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.
Software tool with approaching infers network structure by measuring the pairwise associations between the data observed in the individual network nodes. It follows the more general statistical perspective of GRN inference, where no explicit model of the data is built or assumed.
Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures.
Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use.
Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint.
Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions.
Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.
Software tool used in visual object recognition software research to analyze images for scenes, objects, faces, and other content. A convolutional neural network for large scale image recognition. Weights for the VGG-16 model architecture trained on an image database Imagenet.
Leica | Vibratome VT1000S Leica | Microsystems
Leica Vibratome VT1000S Leica Biosystems
Vibrating blade microtome for sectioning by Leica Biosystems. Used in neurophysiology, neuropathology, experimental pathology, botany (roots and plants) and industry (foams)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Tests for deviation from Hardy-Weinberg equilibrium
Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases.
Software platform to perform image processing, analysis, and data reporting for microscope-based research and quality inspection.
Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems.
Software tool for anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Used to describe the sample motion as a local deformation that varies smoothly throughout the exposure. A program running on Linux.
Software tool as a Graphics Processing Units (GPU) accelerated computer program for real-time contrast transfer function (CTF) determination and correction. Used for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery.
computational imaging system for Transmission Electron Microscopy
Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
Software package and a platform for the processing of electron micrographs in structural biology. Supports different image file formats used in electron microscopy (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions.
Drug target Interaction Network Inference Engine based on Supervised analysis
Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference.
Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.
Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases.
Software application as an open source Pyton library to search and predict miRNA targets.
Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets.
Software tool to search for the targets of annotated miRNAs based on microT-CDS algorithm.
Modular In vivo Multiphoton Microscopy System
Modular platform for performing two‐photon laser scanning microscopy (TPLSM) optimized for in vivo applications.
University of Dundee Behavioural Neuroscience Core Facility
University service for testing behaviour of rodents. Provides facilities and training for researchers to conduct experiments themselves within the core facility.
Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain.
EPSD Eukaryotic Phosphorylation Site Database
Eukaryotic Phosphorylation Site Database
Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies.
Thermo Fisher | Nanodrop 1000 Spectrophotometer
Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution.
Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations.
Thermo Fisher | GeneChip� Scanner 3000 7G
Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis.
AbundantOTU:Abundant Operational Taxonomic Unit
Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset.
Positioner for automated rotation of a head-fixed rodent specimen about the anterior-posterior and medio-lateral axes for imaging or other purposes. Provides automated Z translation and can be customized to accommodate various head bar designs.
Departamental portal of Applied Biochemistry, School of Engineering, Tokai University, Japan. Used for computed tomography (CT) and visualizing 3D structures of biological soft tissues represented with Cartesian coordinates.
Software tool as a catalog of comprehensive reference of human cells based on their stable properties, transient features, locations and abundances. Map to show the relationships among its elements. Open data international collaborative project involving diverse scientific communities to provide a framework for understanding cellular dysregulation in human disease.
Software tool as a program for tomographic reconstruction and image processing of micro/nano-CT data taken at SPring8 and APS Argonne.
Software tool as a program for building skeletonized models of 3D structures with a graphical user interface. GUI based neuronal network model building.
Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.
Software tool written in Java that reads DICOM-files from Dynamic Susceptibility Contrast (DSC) Magnetic Resonance Imaging (MRI) and calculates standardized Time-to-Peak (stdTTP) parameter. Maps from this calculation are provided as RGB- and Monochrom2-Dicom files and may be sent to a PACS automatically. Works on windows® platforms on PC’s (Intel® CPUs from Pentium I up to the I7-octo cores) together with the Philips 1.5T ACS-NT up to the Ingenia Systems (n> 20.000), with the Philips 3.0T Systems (n ~ 1.000), the Siemens 1.5T Avanto (SQ-machine) (n> 10.000) and the Siemens 3.0T TimTrio (n ~ 200) so far. Works with uncompressed DICOM-standard files.
Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data.
Dataset. We have a DataNote paper in Gigascience, in press which introduces a large videography dataset that is freely available for anyone to study the principles of tactile navigation.
Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions.
Facility for biomedical research and a teaching hospital of Harvard Medical School located in the West End neighborhood of Boston, Massachusetts. The third oldest general hospital in the United States and conducts the largest hospital-based research program in the world.
Library of a test driven framework for formally validating scientific models against experimental data used for validation testing of spiking neuron network simulations on the network activity level.
Software tool as an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations and large-scale annotation efforts.
Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph.
Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release.
Software environment for the quantification of biomedical images. Biomedical image processing, analysis, and modeling software. Consists of set of tools for kinetic modeling, parametric mapping, image registration, 3D rendering and pattern analysis. Used for quantification of PET data. Many quantification methods are generic and can be applied to other modalities such as SPECT, MR and CT.
Warsaw University of Technology; Warsaw; Poland
The oldest technical university in Poland, located in Warsaw, with faculties including architecture, machine design, electrical engineering, automotive and construction machinery engineering, electronics , information technology, mechatronics , geoinformatics, automatic control and robots, and biomedical engineering.
University Hospital Zurich; Department of Nuclear Medicine; PET Center; Zurich; Switzerland
Center for functional imaging examinations on patients using radioactive substances by using scintigraphy, SPECT and PET to visualize biochemical processes in the body (such as active cancer, inflammation, tissue perfusion, etc.) and combine these technologies with cross-sectional methods such as CT and MRI for precise anatomical localization.
User Friendly Functional Connectivity - UF²C
Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters.
Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease.
international Micro Injection Tracking System
This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products.
Software as a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
Microscope software platform which integrates Leica automated microscopes and digital cameras and provides one common user interface.
Software package for the analysis of image and time series data in Python. Provides data structures and algorithms for loading, processing, and analyzing these data. Runs locally or against a Spark cluster with an identical API.
Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework.
Software analysis tools for electrophysiological somatosensory cortex databank. Allows to estimate the information content of spiking in single neuron resolution. It accompanies the open source intracellular recording database by Lantyer and colleagues.
Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light.
Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.
Software tool for comparing lists with Venn's diagrams.
Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis.
Software tool for phonetics research to analyse, synthesize, and manipulate speech.
Python library for materials analysis codes. Defines core object representations for structures and molecules.
Software tool for reconstruction, visualization and analysis of neuronal processes .Fiji's framework for semi-automated tracing of neurons and other tube-like structures (blood vessels) through 3D image stacks.
Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software package available through Fiji to image large biological specimen at high resolution. Comes with 2 different plugins to reconstruct big images/stacks : Pairwise Stitching to stitch two 2d-5d images, and Grid/Collection Stitching to stitch an arbitrary amount of 2d-5d input images.
Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.
Commercial provider of antibodies, antigens and recombinant proteins from Braintree, Massachusetts . Biotechnology company which provides custom oligonucleotides synthesis service.
Software tool as a Common Workflow Language (CWL) based automated bioinformatics workflow to assemble haploid/diploid eukaryote genomes of non-model organisms using PacBio long-reads and Illumina short-reads.
Systems Approach to Biomarker Research in CardioVascular Disease
Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation.
Software tool for discovering relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.
Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity.
Apnea, Bariatric surgery, and CPAP study
Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore.
System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community.
Software tool to screen a nucleic acid sequence for vector contamination. Detects foreign DNAs such as vector, linker, adapter, and primer regions involved in nucleotide sequences by using blast search against vector sequence database. The main unit of this tool is vecscreen program obtainable from NCBI.
Finland United States Investigation of NIDDM genetics
Portal to map and identify genetic variants that predispose to type 2 diabetes mellitus (T2D) or are responsible for variability in diabetes-related quantitative traits. Used for analysis of affected-sibling-pair (ASP) families in Finland, and association fine mapping based on these family members and additional T2D cases and controls.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 12,2024. Software tool for DNA sequence submission. Used for submitting and updating entries to the GenBank or EMBL sequence databases.
Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads.
Best Apnea Interventions for Research (BestAIR) sleep study
Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume.
Cleveland Children's Sleep and Health Study
Portal for population based pediatric cohorts studied with objective sleep studies. Includes children with in-home sleep studies, acoustic reflectometry, anthropometry, spirometry, blood pressure (BP), and neuropsychology (NP) and behavioral assessments. Signals recorded include EEG, ECG, EOG, EMG, SpO2, airflow (thermocouple) nasal pressure, respiratory effort, position, plethysmography, light, HR.
Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore.
Honolulu-Asia Aging Study of Sleep Apnea
Honolulu Asia Aging Study of Sleep Apnea
Portal for sleep-disordered breathing (SDB) in an elderly cohort of Japanese-American men under surveillance for Alzheimer disease (AD) and other dementias. Data to assess relationships between SDB and cognitive performance in late life.
Software tool for estimating pairwise relatedness from next-generation sequencing data.
Software for multichannel dynamic fluorescence image acquisition and analysis by INDEC BioSystems.
Software program to implement transfer learning for a connectome convolutional neural network trained to classify functional connectomes using Tensorflow.
resting state functional MRI and functional connectivity calculation
resting state functional MRI pre processing and Functional Connectivity calculation
Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity.
Nuclear Magnetic Resonance PROcessing FLOW
Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.
Resource of chemokines and receptors with detailed information including taxonomy, nomenclature, structure, physiological function, tissue information, and phenotype, collected from IUPHAR/BPS, UniGene, and UniProt public databases.
Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data.
Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools.
Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Office of Cyber Infrastructure and Computational Biology
Office of Cyber Infrastructure and Computational Biology of NIAID.
National Institute of Allergy and Infectious Diseases is a leading research institution to understand, treat, and prevent infectious, immunologic, and allergic diseases.
Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information.
Database of Antimicrobial Activity and Structure of Peptides
Collection of manually curated data regarding structure and antimicrobial activity of natural and synthetic peptides. Provides the information and analytical resources to develop antimicrobial compounds with the high therapeutic index.
University of FLorida College of Medicine Molecular Pathology Core Facility
University of Florida Molecular Pathology Core
Histology and light microscopy facility for paraffin and frozen blocks and all aspects of sample preparation, fixation, embedding, sectioning, staining, and imaging. Consultations, technical assistance and training are also provided. Standard operating procedures compliant with good laboratory and clinical processes are followed for all procedures. Services include cryosectioning, whole slide imaging, hematoxylin and eosin staining, immunfluorescence, and tissue microarrays..
Comprehensive Analysis of RNAi-screen Data
Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data.
Simplified Presentation of Incredibly Complex Evaluations
Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.
Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics.
MTA open version of the material transfer agreement for biological samples from the BioBricks Foundation. Supports the transfer of material between researchers at all types of institutions, including academic, industry, government and community laboratories.
Software tool to identify the most reliable differences between any two groups . Used to identify differentially expressed genes between two groups.
Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples.
Throughput Ranking by Iterative Analysis of Genomic Enrichment
Platform to facilitate prediction, analysis, and hypothesis generation from genome wide perturbation studies like those designed with RNAi and CRISPR technologies.
N linked GLYCosylation PREDiction server
Web based server to discriminate between glycosylated and non-glycosylated N-X-(T/S) sequons by incorporating structural information and patterns.
Software platform for accelerating genetic discoveries for sleep disturbance and circadian traits.
Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Suite of software applications for capturing, enhancing and analyzing microscope images for SPOT camera by SPOT Imaging, a division of Diagnostic Instruments, Inc.
Collection of open chromatin regions from sequencing data. Metadata as entire curated DNase-I hypersensitive sites (DHS) on the whole genome datasets and data specific to each chromosome.
Web server to visualize phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of homology models. Database and structural visualization platform for comparative models of influenza A hemagglutinin proteins.
Software interactive tool for visualizing and analyzing network data in the spatial context of the chromosome. Used to discover the role of gene organization in functional regulatory networks. Plugin enables users of Cytoscape to overlay networks onto a circular chromosomal map.
ABC Bacterial Transporter Systems Database
Collection of classified bacterial ATP-binding cassette (ABC) transporter systems. The transporter systems identified fulfill the three roles characterized by the nucleotide-binding domain (NBD) , transmembrane domain (TMD), and solute-binding protein (SBP) domains.
Software package to define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator.
Software tool to analyze human immunoglobulin V(D)J recombination and performing Ig nucleotide and amino acid alignment, as well as extensive mutation and Complementarity Determining Region 3 (CDR3H) analysis.
Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies.
Open framework for evaluating correspondence between brain images and teaching neuroanatomy.
Web server as semi automated tool that identifies nucleotide sequences in scientific publications, determines whether they are correctly identified. Seeks for nucleotide sequences in pdf files and then call local version of blastn. Text mining and text analysis tool to allow peers to identify errors in published or forthcoming scientific literature. Used to search and extract gene identifiers and nucleotide sequences against human genomic and transcript database.
Parser for Schrodinger Maestro files. This format is used for computational modeling, and stores molecules with 2D or 3D coordinates and detailed atom and bond information.
Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers.
Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics.
Software tool as a command-line program that automates the creation of sequence records for submission to GenBank. Records need no additional manual editing before submission.
Project for assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. The nucleotide and protein data from all WGS projects go into the BLAST database.
Software tool for comparing EST profiles in order to identify genes with significantly different expression levels.
Interactive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse.
Web application for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.
Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.
Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database.
Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long.
Software tool that helps taxonomists find closest database neighbors of submitted query sequences by generating a phylogenetic tree from BLAST results.
Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus.
Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes.
Particle Metrix | ZetaView Nanoparticle Tracking Analyzer
Instrument for nanoparticle tracking analysis. A semi-automated method for the characterization of extracellular vesicles with associated analysis software by ParticleMetrix GmbH.
Software package for eye tracking studies by New Bio Technology Ltd. Used for designing eye movement studies and recording, analyzing, visualizing data of eye tracking results.
Core provides technology for functional proteomics studies and centralized, standardized and quality controlled services locally and globally.
Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data.
Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes.
Software tool to identify pockets on protein surface to predict ligand-binding sites.
Software tool for multi level analysis of applications optimized for ImageXpress instruments. High-content image analysis software featuring time lapse analysis. Used for 2D and 3D imaging.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software tool for general particle picking in the single-particle processing of unknown macromolecules. Reference free particle picker with ability to sort particles based on size or it can be used to bootstrap the creation of templates or training datasets for other particle pickers. Used to facilitate particle selection in single particle electron microscopy., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries.
Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS
Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.
Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses.
Platform as a web-based interactive environment to automatically identify, explore and visualize homology and functional annotations for assembled transcripts.
Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data.
Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
Genome Analysis Toolkit (GATK) Indel Genotyper
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer.
Platform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems.
Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers.
Python implementation of the Loom file format to store and organize very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations and sparse graph objects. Used to store single-cell gene expression data. Official Python library (API) used to create, read, and manipulate .loom files, supporting out-of-memory operations to handle datasets larger than RAM.
Software imaging platform to generate datasets of whole mouse brains imaged at submicron resolution that allow reconstructions of complete axonal arbors of individual neurons across the entire mouse brain.
Interactive web platform for anyone to explore, search, filter and visualize the single neuron reconstructions.
Software tool to model genotypes in their microenvironment and to predict single- and multi-cellular behaviour. A 3D virtual microenvironment for perturbation biology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Open Data Commons for Spinal Cord Injury
Portal for sharing spinal cord injury data from basic and clinical research to promote transparency, rigor and reproducibility. Community based repository for spinal cord injury research.
A-M SYSTEMS | Model 2100 Isolated Pulse Stimulator
Instrument used for a variety of physiological stimulation protocols, including behavioral feedback, LTP/LTD, lesion making, electrode marking, ultrafast timing applications, orthodromic/antidromic stimulation, and kindling. Used in a neurophysiological and physiological experiment protocols.
Neuronexus | Neural Probe A1x16-3mm-100-703
Instrument as a 16 channel linear electrode array from NeuroNexus Technologies, Ann Arbor, Michigan. Used to map brain function, detect neural activity, and stimulate or modulate neural circuits when brain function is impaired. Used for small and large animal models for neuroscience and clinical applications.
Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome.
Center for Computational Biology at JHU
Center for Computational Biology at Johns Hopkins University
Center for Computational Biology as a joint research center in the McKusick-Nathans Institute of Genetic Medicine, spanning the School of Medicine, the Whiting School of Engineering, the Bloomberg School of Public Health, and the Krieger School of Arts & Sciences. Multidisciplinary center dedicated to research on genomics, genetics, DNA sequencing technology, and computational methods for DNA and RNA sequence analysis.
Commerciall organization to develop study protocols collaboratively to run and manage animal research studies for academic, government, biotech and pharmaceutical labs. Provides services, including product installation and configuration, user training, customization services and ongoing support.
Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format.
Stanford Center for Reproducible Neuroscience
Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects.
Web based neuroscience application for analyzing task-related functional networks over time and frequency. Interactive visualization tool for exploring functional brain connectivity.
R package from CRAN to extract and visualize the results of multivariate data analysis.
Software R package from CRAN as a modular leaf ordering methods for dendrogram nodes. Used as sorting methods to improve readability and interpretability of tree structure. Used for comparison of different distance measures or linkage types, identification of tight clusters and outliers, and for coupled heatmap visualization.
Instrument for cutting specimens at room and low temperature. Used to produce both semi- and ultra-thin sections as well as smooth surfaces of biological samples.
BD Biosciences | FACSAria III Cell Sorter
Instrument for cell sorting by BD Biosciences where positive air pressure forces sample cell through an optically gel-coupled cuvette . Hydrodynamic focusing guides particles in a single-file stream through the cuvette, where laser light intercepts the stream at the sample interrogation point.Fluorescence activated cell sorting instrument. Flow cytometer as high speed fixed alignment benchtop cell sorter. Enables multicolor analysis of up to 13 fluorescent markers and two scatter parameters at time.
Software package which brings to R color scales. Created for the Python matplotlib library.
Software tool to provide color schemes for maps and other graphics. R package to create colorful graphs with pre-made color palettes that visualize data.
SoftwareR package from CRAN for statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.
Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment.
BioRevo microscope BZ II viewer software
THIS RESOURCE IS NO LONGER IN SERVICE. BioRevo microscope BZ II viewer software, discontinued product, software for the BZ 9000 Fluorescence Microscope, no download available.
Instrument provides acquisition of up to 12 parameters with optical design for enhanced sensitivity for multicolor assays. With customized forward scatter, to achieve accurate size measurement, and optimized electronics for high resolution and fast, accurate processing for researchers needs.
Zeiss | libra 120 transmission electron microscope
Electron microscope by Carl Zeiss AG which combines flexibility and ease of use of new control electronics, Windows® based user interface and a vacuum system.
Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions.
Modeling Alternative Junction Inclusion Quantification
Software package to detect and quantify local splicing variations (LSV) from RNA-Seq data. Used to automatically detect and downweight outliers in RNA-Seq datasets with replicates for differential splicing (SD) analysis.
Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing.
Software tool for working with data frame like objects, both in memory and out of memory. It is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges: mutate, select, filer, summerise, arrange.
Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing.
Intramolecular ligated Nanopore Consensus Sequencing
Software for accurate single molecule reads using nanopore sequencing. Used for 16S rRNA-based profiling to investigate complex bacterial communities.
Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps.
Science and Technology Facilities Council
One of nine Councils within United Kingdom Research and Innovation, an organisation that brings together the UK’s Research Councils, Innovate UK and Research England. Works in partnership with universities, research organisations, businesses, charities, and government to create the environment for research and innovation.
Florida State University Physical Biochemistry Core Facility
The Physical Biochemistry Facility (PBF)
Facility for biophysical studies of macromolecules with emphasis on providing resources, instrumentation, training, and guidance to graduate and undergraduate students.
Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging.
Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures.
Comprehensive Lab Animal Monitoring System
Instrumentation for monitoring behavior and physiology in lab animals by Columbus Instruments. Used for simultaneous multi parameter assessment of 1 to 32 test animals with automated operation for experiments lasting up to three days.
Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders.
identiﬁcation of Drug Target Interaction using Evolutionary and Structural features with Boosting
Software tool for identiﬁcation of Drug Target Interaction using Evolutionary and Structural features with Boosting. Used to predict drug-protein interactions.
Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems.
Software R package for comprehensive analysis of metabolomics data. Contains the R functions and libraries underlying MetaboAnalyst web server, including functions for metabolomic data analysis, visualization, and functional interpretation.
Web based tool to create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space (genes/proteins, microRNAs, transcription factors or metabolites).
Graphical user interface to visualize EEG data. The applications can vary from scoring High Frequency Oscillations, to observing Theta and Gamma Synchrony.
Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting.
Software tool for creation and distribution of surveys which can be taken on computers or smart phones to carry out complex research with advanced survey functionality and analytics. Qualtrics platform used to design, send and analyze surveys online.
National resource for systematics research on medically important arthropods and maintainance of the U.S. mosquito collection based in the Smithsonian Institution. Provides an online repository for vector collection data and clearinghouse where individuals and organizations can contribute vector occurrence records, search for vector information, and use tools for the visualization of various vector collections.
Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data.
System designed for automated collection of images from a transmission electron microscope.
Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4.
Software tool for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. Used to process electron microscope images of single molecules and complexes to obtain reconstructions at the highest possible resolution.
Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools.
Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type.
Python-based Hierarchical ENvironment for Integrated Xtallography.refine
Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB.
Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases.
Software framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions. Electron Microscopy (3DEM). waiting for pdf from Joe
Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype.
Columbia University Human Immune Monitoring Core Facility
Columbia University Human Immune Monitoring Core
Human Immune Monitoring Core at Columbia University
Research core facility for advanced immunology studies including multiplex tissue and spatial analysis, high-parametric cytometry, single-cell sequencing, experimental design, sample processing, data acquisition and processing, data analysis and management.
Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies.
Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems.
Software Project Management Univariate Plus
Software Project Management (SPM) tools which contain a collection of functions that can be used at different stage of a standard massive univariate fMRI data analysis. Used to improve mass univariate analysis.
Commercial comprehensive cheminformatics computing environment. Used in discovery of novel therapeutic agents.
Software program for pKa prediction and protonation state generation for drug like molecules.
Software tool to correct and optimize the ligands by generating different protonation states, stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures.
Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex.
Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data.
Software tool for correcting common structural problems and creating reliable, all atom protein models.
Software tool for shape-based superposition and similarity searching. Identifies new compounds with shapes (and, if desired, other properties) that are similar to the known binder.
Soft­ware envi­ron­ment for custom stim­u­lus and task design as well as presen­ta­tion. Compumedics Neuroscan’s design system which can be inte­grated in fMRI, MEG, and other func­tional neuro-imaging appli­ca­tions. Provides inter­face to design and present visual and audi­tory stim­u­la­tion paradigms.
Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.
Software application for Excel statistics.
System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies.
Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.
Software to generate phased, whole genome de novo assemblies from a Chromium prepared library. Used to create true diploid de novo assemblies and can separate homologous chromosomes over long distances.
Florida State University Protein Expression Core Facility
Core to facilitate the large scale expression of recombinant proteins in bacterial, insects, and mammalian cells. Serves primarily faculty and students from the laboratories in the Kasha Laboratory Building and laboratories in Biology, Biochemistry, Chemistry and Nutrition at Florida State University, Tallahassee, FL.
Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome.
Web site for resources (statistical calculators, p-value calculators, descriptive statistics) for students and researchers working with statistics in the social sciences. All the calculators and tools have been designed with ease of use.
Software used to draw chemical structure. ChemDraw, along with Chem3D and ChemFinder, is part of the ChemOffice suite of programs and is available for Macintosh and Microsoft Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software package for image acquisition, analysis, display, and archiving. Used to quantify the autoradiography data from Cyclone apparatus from Perkin Elmer.
microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies.
Commercial provider of automated laboratory instruments and solutions for clinical diagnostics, basic and translational research and drug discovery.
Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins.
ImageJ plug-in to quantify fibrillar structures in raw microscopy images. Used to evaluate the orientation of fiber orientation pattern and plots the results in the image.
Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows.
Network of European BioImage Analysts to advance life science imaging and to boost the productivity of bioimaging based research projects in Europe.
Privately held Michigan based software company. They provide taxonomic and analytical services, data, software and technology licensing for the academic publishing industry, life sciences research, commercial partners and federal laboratories.
Research coordination network for ex situ Microbial Germplasm Collections to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of humankind by providing opportunities for US culture collection workers to engage with each other and with the broader culture collection community.
Natural history collections. Offers a stable, straightforward and flexible framework for biodiversity data. Community-developed biodiversity data standard. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing identifiers, labels, and definitions. Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, samples, and related information.
Collection of wild yeast in the world. Academic and industrial resarchers utilize this collection for a variety of research and applications, including pigments, enzymes, food ingredients, and hosts for protein expression. Provides contract screening and strain selection services.
Culture Collection of Algae at the University of Texas
The UTEX Culture Collection of Algae includes different strains of living algae, representing most major taxa. Cultures in the Collection are used for research, teaching, biotechnology development, and various other projects throughout the world.
Collection of plant species for use by both academia and industry.The PCCL enables R&D exploitation of monocot, dicot and gymnosperm cultures.
Cooperative effort by U.S. state and federal government and private organizations to preserve the genetic diversity of plants. The NPGS aids scientists and the need for genetic diversity by acquiring, preserving, evaluating, documenting and distributing crop germplasm. The NPGS is managed by the Agricultural Research Service (ARS), the in-house research agency of the United States Department of Agriculture (USDA). Funding for the NPGS comes primarily through appropriations from the U.S. Congress.
High Content Analysis Studio Cell Analysis software
High Content Screening Studio Cell Analysis software
Software packages for quantitative cell analysis. Used in image cytometry, quantitative cell analysis or automated cell analysis in biological research and drug discovery.
Software for automatic neuron 3D reconstruction and analysis. Used by neuroscientists to reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses.
Computational Python library for the motion analysis of biological single-cell and collective motion for high content screens. Framework to quantify and discover cellular motion phenotypes.
FV1000 confocal laser scanning biological microscope features twin scan system which enables spectroscopy of living intercellular contents and analysis of objects down to a 2nm wavelength resolution. Image size is increased to 4096x4096 pixels.
HBio: Multichallel Systems | Electro Square Porator ECM 830, BTX
ECM 830 is a square wave pulse generator designed for in vitro and in vivo applications for gene, drug and protein delivery for mammalian cells, zebra fish tissue and embryos, nuclear transfer, embryo manipulation, plant protoplast and basic bacteria and yeast transformations. Used in ECM 830 SQUARE WAVE ELECTROPORATION SYSTEM.
P-97 Flaming / Brown Micropipette Puller is an instrument for fabricating micropipettes, patch pipettes and microinjection needles with improvements in mechanical, electronic and software design for better control of the pulling process and a higher degree of reproducibility.
Software designed for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples.
Instrument designed for cryosectioning in biomedical, neuro-anatomical and pharmaceutical research.
Software tool as a code to support figure generation for the manuscript by Roth, Muench et al. Used to perform analysis.
Software Python package as a semiparametric test for enrichment in ranked lists. Used for determining gene set enrichment.
Software genome-wide tool to predict transcript biomarkers of gene essentiality in cancer. This tool can be used to predict new potential target genes with their corresponding biomarkers (either transcript or gene expression).
Software tool as an European Data Format EDF/EDF+ viewer and manual sleep scoring program. Used in EEG and Sleep investigations, but can be used for almost any (also non-medical) sequential time series and event lists.
Software tool for the analysis of EEG and MEG event-related scalp field data using global randomization statistics.
Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms.
University of Muenster; Muenster; Germany
The University of Münster is a public university located in the city of Münster, North Rhine-Westphalia in Germany. It is Germany fifth largest university.
Section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.
Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome.
generalized linear mixed models using AD Model Builder
generalized linear mixed models using ADMB
Software R package for fitting generalized linear mixed models (GLMMs) using AD Model Builder. Fits mixed-effects models to count data using Poisson or negative binomial response distributions.
Discriminative Regular Expression Motif Elicitation
Software tool to discover short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in sequences compared with shuffled sequences or control sequences (sample output from sequences).
Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions.
Network Interchange for Neuroscience Modeling Language
Simulator independent language for unambiguous description of spiking neuronal network models that aims to facilitate model sharing, portability, and re-usability. Used as a model description language for neuroscience.
Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.
Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
The Plant GeneSet Enrichment Analysis Toolkit
Websever for gene set enrichment analysis of plants. Used for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets.
Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography.
Allele Specific Copy Number Analysis of Tumors
Allele-Specific Copy Number Analysis of Tumors
Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data.
The International Affective Picture System
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,20225. Collection of pictures designed to provide a standardized set of pictures for studying emotion and attention. Provides normative ratings of emotion (pleasure, arousal, dominance) for a set of color photographs that provide a set of normative emotional stimuli for experimental investigations of emotion and attention. Used in psychological research.
Software tool which is a PHP and SQL based server platform. Provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralized data management.
Model organism Aggregated Resources for Rare Variant ExpLoration
Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.
The Genotype 2 Mendelian Phenotype database
Collection of phenotypic profiles for affected individuals and, for unaffected individuals, the phenotypic profile of their affected. Collaborative, shared resource for the human genetics community.
Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing.
Chromeleon Chromatography Data System (CDS) Software
Chromeleon Chromatography Data System (CDS)
Software system to support chromatography operations, to ensure data quality and manage all the analytical processes from instrument control, to raw data storage and processing, through to generating the final results.
Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data.
Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time.
Software package as a metabolomic data processing pipeline in R codes.
Software package as a growth curve automatic processing pipeline in Matlab.
Open source software suite environment for nonlinear statistical modeling enabling model development, numerical stability, computation, and accuracy parameter estimates. Language built around the AUTODIF Library, a C++ language extension which transparently implements reverse mode automatic differentiation.
Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance.
Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.
Single Nucleotide Polymorphisms 2 Transcription Factor Binding Site
Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs.
Software interactive perl/tk application which can read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles. Extensible WYSIWYG protein sequence alignment editor for publication quality figures.
Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal.
Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables.
Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Web tool for CRISPR/Cas9 target prediction. Identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation.
Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions.
single molecule Molecular Inversion Probesfil
Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.
Software tool as a combined strategy to identify junction reads from back spliced exons and intron lariats. Computational pipeline to precisely identify junction reads from Circularized Exons. Used to identify circular RNAs (circRNAs and ciRNAs).
Neuroimaging Informatics Technology Initiative (NIfTI) and Analyze Image data
Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform.
co-localization single molecule spectroscopy
co-localization single-molecule spectroscopy
Co-localization Single-Molecule Spectroscopy Analysis
Software tools for analyzing co-localization single-molecule spectroscopy image data.
Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging.
Förster Resonance Energy Transfer Bursts
Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data.
Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise.
Xenonucleic Acid Computing Group Wiki Template
Molecular computing based on XNA-built alphabets.
National Resource for Translational and Developmental Proteomics
The National Resource for Translational and Developmental Proteomics
Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists.
Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.
Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data.
Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.
Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software as a cross platform gene expression visualization tool. Extensible viewer for microarray data in the PCL or CDT format. Interactive display of clustered gene expression data. Java application for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it into a figure.
ENteric Immunity SImulator (ENISI) Multi scale model
ENteric Immunity SImulator Multi Scale Model
Software tool for simulating the mucosal immune responses to Helicobacter pylori infection in stomach.
Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.
Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States.
ValIdated Systematic IntegratiON of epigenomic data
International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human.
Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.
Prevention of Lower Urinary Tract Symptoms
Research consortium from many different fields to plan, perform and analyze the studies that are needed to help researchers conduct future prevention and intervention for Lower Urinary Tract Symptoms (LUTS) in women.
Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC).
Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes.
Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches.
Med Associates | NIR Video Fear Conditioning Package for Mouse
Equipment with product number MED VFC SCT M supplied by Med Associates. Fear conditioning package eliminates the need for bright visible light, visible light can be used within a session as a cue without impacting the video recording, real time video recordings allows software to distinguish between subtle movements such as whisker twitch or tail flick, as well as freezing behavior.
Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest, Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes.
Digital Expression Explorer 2 Source Code
GitHub repository of the Digital Expression Explorer 2 resource. It contains information related to the pipeline, docker image, backend analysis, webserver, and R package getDEE2.
Digital Expression Explorer 2 Docker Image
Docker image that is used to process all of the data present in the Digital Expression Explorer 2 dataset. It can be freely used by anyone to process data on NCBI SRA or process their own RNA-seq fastq files. Used for bulk reprocessing of public RNA-seq data from SRA. The pipeline tallies the reads assigned to each gene or transcript.
Digital imaging and Communications in Medicine for Quantitative Imaging
The Digital imaging and Communications in Medicine for Quantitative Imaging
Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.
Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open
Data collected from subjects scanned 3 times (V1, V2, V3), with V1 and V2 on a scanner, V3 on another scanner in another site. Resting state blood oxygenation level dependent functional MRI (BOLD fMRI), pseudo continuous arterial spin labeling (pCASL), and high resolution 3D T1 imaging were performed under eyes open (EO) and eyes closed (EC) conditions.
Hangzhou Normal University; Hangzhou; China
Public university in Hangzhou, the capital of Zhejiang Province, China. It is a comprehensive university with an excellence in teacher training and professional development.
International Human Epigenome Consortium
Consortium to coordinate epigenome mapping and characterization worldwide to avoid redundant research effort, to implement high data quality standards, to coordinate data storage, management and analysis and to provide free access to the high resolution reference human epigenome maps for normal and disease cell types to the research community. Promotes data sharing. You may view, search and download the data already released by the different IHEC associated projects via the IHEC Data Portal.
Software tool to annotate structural variant calls with sequence depth information that can add or remove confidence to SV predicted to affect copy number. Indicates the presence of a rapid change in depth relative to the regions surrounding the breakpoints. Allows the run time to be nearly independent of the number of variants important for large, jointly called projects with many samples. Annotates structural variant predictions made from both short read and long read data.
Software tool for data analysis and exploration. Statistics software for Mac.
Clustered Regularly Interspaced Short Palindromic Repeats P
Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.
Software tool as an algorithm to infer gene regulatory networks from spatial and temporal datasets. Spatial dataset or any data that can provide information about coexpression is used by the first step of the algorithm to perform clustering and separate the genes in the network in smaller coexpressed groups. Temporal dataset is used by the second step of the algorithm to infer regulations among the genes, based on Bayesian networks.
Software package of python scripts made to simplify the processing of crystal diffraction images.
Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.
Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.
Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.
Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates.
Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Software tool to create spreadsheets that include tables and images. You can use Apple Pencil on your iPad to add diagrams and colorful illustrations.
Software tool for professional photo editing.
Software tool for vector illustrations. Professional graphic design software.
ImageJ plugins and macros for whisker tracking. Set of Fiji plugins and macros for tracking a single whisker.
Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.
Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.
Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products.
Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis.
Portal for Science Dynamics projects with open source framework to provide way to query datasets. Code framework, including tutorials for project, titled Over Optimization of Academic Publishing Metrics Observing Goodhart Law in Action, to interactively explore and understand how various properties of journals have changed over time. Datasets, software implementations, code tutorials and interactive web interface for investigating studied networks.
Software tool as a full probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.
Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.
Software tools to make developing R packages easier by providing R functions that simplify and expedite common tasks.
Software tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data.
Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them.
Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform.
Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.
Software tool for finding and removing adapters from Oxford Nanopore reads.
Software suite of bioinformatics tools for analysis of DNA and RNA sequence data. Used for file formats such as fastq, fasta, sam, scarf, fasta plus qual, compressed or raw, with autodetection of quality encoding and interleaving. Written in Java and works on any platform supporting Java, including Linux, MacOS, and Microsoft Windows.
Bestus Bioinformaticus Decontamination Using kmers
Software tool for trimming and filtering sequencing data. Used to combine data quality related trimming, filtering, and masking operations into a single tool adapter. BBDuk2 allows multiple kmer based operations in a single pass.
Software tool to merge two overlapping paired reads into a single read. Used in amplicon studies and in assembly, where longer reads allow the use of longer kmers or fewer comparisons.
Software tool for generic streaming read processing tasks that have low memory or computational demands, such as format conversion, sub sampling, and various filtering operations.
Commercial organization providing laboratory solutions in the fields of psychophysiology, neuroscience, social science, life science, child and behavioral development. Offers a wide array of products and services including signal acquisition hardware used to collect a variety of measures including Cardiac Impedance, HRV, GSR/GSC, ECG/EKG, HR, BP, and EMG supplemented with software suite of analysis applications.
American multinational corporation and technology company headquartered in Santa Clara, California, in the Silicon Valley. Semiconductor chip maker being overtaken by Samsung. Inventor of the x86 series of microprocessors, the processors found in most personal computers (PCs). Intel supplies processors for computer system manufacturers such as Apple, Lenovo, HP, and Dell. Intel also manufactures motherboard chipsets, network interface controllers and integrated circuits, flash memory, graphics chips, embedded processors and other devices related to communications and computing.
Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data.
Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications.
Affymetrix Data for Demonstration Purpose
Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.
Provides Prism softwares and services that integrate advanced imaging into the clinical workflow for brain mapping from acquisition through processing, visualization, and export to PACS. Prism integrates functional MRI, diffusion MRI, perfusion, MR spectroscopy, and PET/CT into a unified workflow for diagnosis and treatment planning in brain disorders. Processing is also available as a cloud deployed service, Prism Serve. Research support includes import/export for imaging and derived quantitative data in both DICOM and research formats such as AFNI and Trackviz.
Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis.
Fluorescence microscope of BZ-X series by KEYENCE CORPORATION of America. Captures high resolution images without the blurring caused by out of focus fluorescent signals. Optical sectioning allows the user to obtain images comparable to those captured on a laser confocal microscope, but in a fraction of the time and without the damaging effects of a laser., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
ZEISS Axio Zoom.V16 for Materials​ system
ZEISS Axio Zoom.V16 microscope system includes high resolution zoom microscope for large fields. Focuses on reflected light microscopy of materials. Uses optical components to manage reflected light from specimen surface. Designed for observing surface properties and structures of materials using reflected light. System focuses on providing high resolution image quality and contrast for reflected light microscopy of solid materials., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Model to cover data for macromolecular NMR spectroscopy from the initial experimental data to the final validation. Used for the large scale data deposition, data mining and program interoperability. Enables movement from one software package to another without difficulties with data conversion or loss of information. Works with CcpNmr Analysis software for analysis and interactive display, CcpNmr FormatConverter for allowing transfer of data from programs used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment. Used within the CCPN software suite for NMR spectroscopy and at the BioMagResBank for converting existing deposited restraint lists to a standard IUPAC nomenclature.
The Collaborative Computing Project for NMR
Project provides tools and knowledge to maximize the impact of the biological NMR studies. CCPN software facilitates data analysis and software integration. Project promotes the exchange of knowledge and provides training and best practices for the NMR community and has leading role in the development of NMR data sharing standard and coordination of NMR instrumentation proposals. Includes CCPN Data Model for macromolecular NMR and related areas, CcpNmr suite of programs like Analysis for spectrum visualization, resonance assignment and analysis, ChemBuild to create chemical structure templates in an NMR aware manner, FormatConverter for data exchange with common textual NMR formats and SpecView for swift, format independent peak and spectrum visualization.
Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix.
Software Python tool for scripting and presenting stimuli for visual neuroscience.
NONlinear Mixed Effects Modeling software
Nonlinear mixed effects modelling software
Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.
Genotype and phenotype database for maize images based on BioDIG. Supports multiple reference genomes and has been integrated with the MaizeGDB Genome Browser to make custom tracks showing mutant phenotypes within their genomic context. Allows for custom tagging of images to highlight regions related to the phenotypes. This is accomplished through an interface allowing users to create links from images to genomic coordinates and to curate and search images by gene model ID, gene symbol, and gene name.
Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.
Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9.
Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections.
Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.
Software tool as a framework for fitting and describing connectivity patterns between regions that is a simple extension from the current population receptive field models in the visual neuroscience literature. The connectivity from each voxel in a designated seed region to a mapping region is modeled as a 3-dimensional Gaussian, providing location parameters and spread parameters. This allows the direct description of the relative mapping from one region to another.
Collection of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. It results from high-quality measurements of natural and synthetic peptides conducted on a triple quadrupole mass spectrometer.
Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system.
Cellular Taxonomy of the Mouse Visual Cortex
Cellular Taxonomy of the Mouse Visual Cortex Allen Institue for Brain Science
Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing.
Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.
Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others.
Software tool for molecular characterization and quantification of lipid species from electrospray mass spectrometry data. Enables lipid profiling by searching parent and fragment ion masses against lipid fragment database and reports numerical and graphical output for various lipid molecular species, lipid classes, fatty acids, and long chain bases.
International Neuroinformatics Coordinating Facility Neurobot
Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis.
reproducible Cluster Analysis of Single Cells
Software package for reproducible classification analysis of single cell sequencing data.
Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers.
University in Turin in Piedmont region of north western Italy. One of the oldest universities in Europe, and continues to play an important role in research and training.
Bulked segregation analysis tools for outbreeding species
Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data.
Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version.
Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.
Software package for single cell RNA-seq data analysis using k-NN graph partitions. Used to analyze group of scRNA profiles that are highly similar and provides features for deriving them. Can be used with large datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach.
Olympus | FluoView FV3000 Confocal Laser Scanning Microscope
Microscope enables 2D-6D (x,y,z,t,λ,p) macro to micro imaging of cells, tissues, and small organisms. Supports complete workflows from image acquisition to processing and analysis. Used in cell biology, cancer research, stem cell research, neuroscience, electrophysiology, and developmental biology.
Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms.
Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows.
Web based ontology enrichment tool for lipidomic data analysis. Used for lipidomics to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations. Freely accessible in a platform independent way.
Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility.
Refinement and Reduction of Animals in Research
UK’s national organization for the 3Rs (Replacement, Reduction and Refinement) to advance the 3Rs framework for performing more humane animal research by focusing on scientific impacts and benefits to better reflect contemporary scientific practice and developments.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th, 2023. Software that uses long reads to close gaps in the assemblies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool to operate the EMX series of spectrometers by Bruker. Provides rapid data analysis of 1D and 2D data sets, provides environment for acquisition and processing of CW-EPR and CW-ENDOR spectra with the EMXplus and EMXmicro series of spectrometers.
Software tool for calculating optimal pretension conditions for microvascular or any small tubular tissue research. DMT Normalization Add-On, provided by ADInstruments, is included as part of LabChart Pro or can be purchased separately.
Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.
Software tool as fast, batch processing feature extraction software for differential analysis that supports data from Agilent GC/MSD, GC/Q-TOF, LC/TOF and LC/Q-TOF instruments. Speeds up differential and flux analysis workflows using intuitive user interface. Used to analyze raw mass spectrometry data, choose peaks.
Software R package to derive toxicogenomic fingerprints from microarray data.
Software tool to visualize and explore toxicogenomic fingerprints of three model substances.
Software tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools.
Miniature Inverted repeats Transposable Elements Tracker
Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.
Software package for automated functional annotation of LTR retrotransposons for comparative genomics studies. Used to perform de novo functional annotation of LTR retrotransposons from any genome assembly in fasta format.
Software tool as end to end software for data acquisition, processing, and result extraction of Arabidopsis thaliana growth. Framework uses photometric stereo based 3D imaging system with computer vision and deep learning for tracking and quantifying both plant growth and movement parameters.
Interactive web service for analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. Includes features like read count normalization, filtering read counts by gene annotation and visualization options.
Open source software tool for de novo transcriptome assembly reference free quality analysis. Used to examine assembly in detail and compare it to sequencing reads, reporting quality scores for contigs and assemblies to allow to choose between assemblers and parameters, filter out bad contigs from an assembly, and help decide when to stop trying to improve assembly.
DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation
Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences.
Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias.
Software tool for de novo transcriptome assembly from RNA-Seq data.
Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.
Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.
Software package for simple data retrieval and versioning.
Stimulating Peripheral Activity to Relieve Conditions
SPARC data repository as of 2023 is an open data repository developed as part of the NIH SPARC initiative and has been used by SPARC funded investigator groups to curate and publish high quality datasets related to the autonomic nervous system. We are thrilled that as of August 2022, SPARC is accepting datasets from investigators that are not funded through the NIH SPARC program. The NIH's Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of these nerve-organ interactions and ultimately advance neuromodulation field toward precise treatment of diseases and conditions for which conventional therapies fall short.
Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows.
Cross platform open source extension loading library. Provides efficient run time mechanisms for determining which OpenGL extensions are supported on target platform. OpenGL core and extension functionality is exposed in single header file. Operating systems Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris.
Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids.
Open source software package for handling Unique Molecular Identifiers in NGS data sets.
J oint A nalysis of NGS replicates via M ixture M odel clustering
Joint Analysis of NGS replicates via Mixture Model clustering
Software tool as peak finder for joint analysis of NGS replicates. Used for peak finding in next generation sequencing broad and narrow datasets like ChIP-Seq, ATAC-Seq, DNase-Seq. Can integrate information from biological replicates and assign peak boundaries accurately.
Software tool as executable program that measures sizes and other properties of colonies arrayed in grid format from jpeg images. Intended for 768, 384, or 96 colonies on agar plates.
Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.
Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies.
Closed- and Open-loop Sleep Stimulations with Auditory Stimuli
Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton.
Collection of publicly available data of curated receptors, ligands and their interactions. Integrates existing datasets that pertain to cellular communication and new manually reviewed information. Used to search for particular ligand or receptor or to interrogate single cell transcriptomics data.
Software tool for nucleotide sequence alignment. Graphical version of multiple sequence alignment program for DNA and proteins. Windows interface for ClustalW multiple sequence alignment program. Provides integrated environment for performing multiple sequence and profile alignments and analyzing results. Available on Linux, Mac and Windows.
Software R package for calculating, applying, evaluating and plotting results of polygenic risk scores analysis. Performs simulation study to estimate P value significance threshold for high resolution PRS studies and produces plots for inspection of results. Operating Unix/Linux.
Open source software designed in modular way, aimed at facilitating user interaction with Docker environments in three different computational layers like infrastructure, platform and application.
Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability.
Kinesiological Instrument for Normal and Altered Reaching Movements End-Point Lab
Robotics research tool designed to make quantitative neurological assessments of sensorimotor, proprioception, and cognitive brain function by BKIN Technologies. Robotic manipulandum with display for studying arm movements. Allows to assess coordination of limbs at multiple joints while measuring joint specific force.
Italian Institute for Genomic Medicine; Turin; Italy
Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience.
Data collection of CBP/p300 regulated acetylome, proteome, and transcriptome in murine embryonic fibroblasts. Composed of Symbol search for quantified acetylation sites, proteins and transcripts abundance in CBP/p300, Domain search for batch query of proteins by specific domain and Conserved sites for acetylation sites that are conserved between mouse and human, and their regulation in KATi treated cells.
C. elegans RNAi feeding library distributed by Source BioScience Ltd. Designed for genome wide study of gene function in C. elegans through loss of function studies.
Software tool as plugin for ImageJ. Used for 3D objects and image can be segmented directly within plugin via 3D segment button.
Software tool as plugin for ImageJ. Counts the number of 3D objects in stack, quantifies for each found object, generates results representations.
Generally Applicable Gene-set Enrichment
Generally Applicable Gene-set Enrichment for pathway analysis
Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.
Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers.
Non negative Matrix Factorization Toolbox
Non-negative Matrix Factorization toolbox
Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach.
List of diseases and conditions on Centers for Disease Control and Prevention website., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Open source scripts for medical image processing. Provides set of scripts in Python shell. These scripts use essentially tools from Anima to perform more complex series like image preprocessing, model estimation, atlas creation.
Source code for analysis of GC-MS data - Rice HxD Project
Source code used in the analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice exposed to combined drought and heat stress.
Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts.
Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes.
Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux.
Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit.
Machine learning repository for microbiome datasets.
Genotype Investigator for Genome Wide Analysis
Web tool to explore genotyping metdata by filtering it on basis of variant features, including functional annotations and matching genotype patterns. May be deployed on workstation or as data portal. Allows to feed MongoDB database with VCF, PLINK or HapMap files and provides interface to filter data in real time. Used to export filtered data into formats and features connectivity with online genomic tools and with standalone software such as FlapJack or IGV. Gigwa hosted datasets are interoperable via two standard REST APIs such GA4GH and BrAPI.
Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS.
Surface Modified Amperometry Complementary Metal Oxide Semiconductor IC
Integrated circuit device used as tool for amperometry measurement as replacement of conventional carbon fiber microelectrode. Surface modified structures with SU 8 microwells increases life span of each individual device and achieves single cell measurement efficiency by trapping cells inside microwells.
Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton.
Software tool as collection of Multiple Criteria Decision Analysis methods integrated into scientific Python stack.
Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis.
Software tool for writing scientific workflows of shell commands that depend on each other in Go programming language. Workflow library for agile development of complex and dynamic bioinformatics pipelines. Used in bioinformatics and cheminformatics, but works for any problem involving pipelines of commandline applications.
Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline.
Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows.
Software tool as single nucleotide variant expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired tumour and normal cancer samples. Algorithms for calling somatic mutations.
Software tool as cancer genome project insertion or deletion detection workflow for Pindel.
Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements.
Software tool as installation helper, perl wrapper and R program Battenberg which detects subclonality and copy number in matched NGS data.
Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets.
Software R package for analyzing and interactively exploring large single cell RNAseq datasets.
Software as database and query tool for homologous pseudogene and coding gene families. Collection of human pseudogenes and gene associations. Supports search, graphical visualization and functional analysis of pseudogenes and coding genes based on PGG families.
Software tool as open source programming language to build simple, reliable, and efficient software. Developed by team at Google and many contributors from open source community.
American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook.
Pathway And Gene set OverDispersion Analysis
Software tool for analyzing transcriptional heterogeneity to detect statistically significant ways in which measured cells can be classified. Used to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.
Software process modeling tool for conceptual design, optimization, and performance monitoring for chemical, polymer, specialty chemical, metals, minerals, and coal power industries.
Software R package for easily tidy data with spread and gather functions. Used for simplifying process of creating tidy data.
Web based interactive visual analytics tool for miRNA target predictions and integrative analyses of multiple prediction results. Used for sequence based miRNA target prediction by exploiting miRNA-mRNA expression profile data.
International research instruments company that develops, manufactures and markets NMR and CT-based whole body composition and tissue characterization equipment.
Manufacturer of optical sensors including, photomultiplier tubes, electric light sources, and other optical devices and their applied instruments for scientific, technical and medical use.
Commercial provider of innovative DNA extraction technologies and products for life science research. Reagents for preparation of DNA from mouse tails, ear pieces, yolk sac, and culture cells, DNA extracts, DNA markers.
Software tool for complete physiologic data acquisition and analysis used by physiologists, pharmacologists, and toxicologists to collect, analyze, and summarize preclinical study data. Allows to custom design configuration based on needs, budget and convenience without need for any programming.
Portal to provide integrated and federated system that interconnects diverse microbiome data sets, bioinformatics tools, and community resources. Built on guiding principles for FAIR data. Open source, community driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with broader community. Partners with CyVerse and XSEDE.
Comparative Metatranscriptomics Workflow
Software tool for standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads. Used for classification of these reads using assembled contigs to reference databases.
Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs.
Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.
Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.
Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG.
Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots.
Software tool as graph based unsupervised biclustering algorithm to identify alterations in tumors based on hypothesis that gene pairs relevant to clinical process share statistically significant number of samples with extreme expression.
Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.
Web service as calculator for statistics and analysis. Used on variety of browsers as well as mobile and tablet devices.They include Z-score, sample size, t value, One Way ANOVA Calculator, Percentile Calculator, Chi Square, p Value, and more.
Waxholm Space Atlas of the Sprague Dawley Rat Brain
Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format.
Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.
Software tool as interactive Shiny web application that provides user interface to mass cytometry data processing pipeline implemented in CATALYST R Bioconductor package.
Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation.
Software tool as supervised machine learning algorithm that classifies and sorts single cell mass cytometry data according to their cell cycle, which allows to correct for cell cycle state and cell volume heterogeneity. Reveals signaling relationships and cell heterogeneity that were otherwise masked. Computational method to quantify cell cycle and cell volume variability.
Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes.
Constant distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry
System to extend constant distance mode mass spectrometry imaging using nanospray desorption electrospray ionization by integrating shear force probe with nano DESI probe to improve imaging capabilities. Used for imaging biological samples of complex topography in their native states. Enables ambient imaging of biological samples with high sensitivity and minimal sample pretreatment.
Microfluidic device to attain high spatial and temporal control of oxygen
Device to control spatial and temporal variations in oxygen tensions to better replicate in vivo biology. Consists of three parallel connected tissue chambers and oxygen scavenger channel placed adjacent to these tissue chambers. Provides consistent control of spatial and temporal oxygen gradients in tissue microenvironment and can be used to investigate important oxygen dependent biological processes present in cancer, ischemic heart disease, and wound healing.
Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc.
Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps.
Clinical Proteomic Tumor Analysis Consortium
Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies.
Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents.
Open source resources to execute stop signal task and analyze resulting data. Simulation code is provided, and can be used in planning stage for investigation of response inhibition and impuls control.
Penn machine learning benchmark repository
Python wrapper for Penn Machine Learning Benchmark data repository. Large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms. Part of PyPI https://pypi.org/
Relief Based Algorithm Training Environment
Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity .
Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions
Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods.
Software suite as top view based behavior analysis system by CleverSys Inc. Uses animal body parts to provide behavior analysis results. Used in experiments with animal tracking task.
Bruker | Ultima In Vitro Multiphoton Microscope System
Bruker Ultima In Vitro Multiphoton Microscope
Fluorescence microscopy system by Bruker. Multiphoton imaging system for intravital imaging applications in neuroscience, oncology and immunology using Bruker Prairie View software to provide turnkey operation for imaging as well as synchronizing Ultima system with external stimulus and experimental control devices.
Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles.
University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility
University Medical Center Hamburg Eppendorf Core
Core provides bioinformatics services for researchers at University Medical Center Hamburg Eppendorf and related institutions. Focusing on high throughput sequencing data. Services include data analysis, consulting, software development, and bioinformatical training.
Centre for Genome Regulation Bioinformatics Core Facility
Provides services of consultation and data analysis, with focus on Next Generation Sequencing and other high throughput experiments, software and database development, and training in basic and advanced bioinformatics techniques. Services provided for fee to support collaborative grant funded investigations.
Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data.
University of Tübingen Quantitative Biology Center
Central unit for bioinformatics and omics technologies of University of Tübingen, Medical Faculty and Max Plank for Developmental Biology. Through partnering with on campus core facilities, offers services on full range of omics technologies. Data generation is complemented by integrated bioinformatics analyses, and all high throughput data is managed centrally.
Babraham Institute Babraham Bioinformatics Core Facility
Provides bioinformatics services to research groups in Babraham Institute, United Kingdom and external commercial consultancy service. Provides assistance in genomics, proteomics, statistics, microarrays, and custom software development.
Whitehead Institute Bioinformatics and Research Computing Core Facility
Core provides consultation, training, software and educational tools in bioinformatics and graphics.
University of Edinburgh Wellcome Trust Centre for Cell Biology Bioinformatics Core Facility
University of Edinburgh WTCCB Bioinformatics Core Facility
Facility provides regular training sessions, tools, advice and data analysis services to Centre members.
Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility
Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services.
Israel Weizmann Institute of Science Bioinformatics Unit Core Facility
Bioinformatics and Biological Computing Unit
Core promotes and supports adoption, use, and development of bioinformatics tools for advancing biological research. Organizes and teaches courses and workshops for all services needed by Weizmann researchers.
University of Cambridge Bioinformatics and Computational Biology Services Core Facility
Provides assistance in characterization and analysis of genomic variants, next generation sequencing data processing and analysis, computational systems biology, HPC and big data software development for genome scale data analysis, machine learning and data mining, cloud based solutions to process and manage large amounts of data, databases and genome scale data visualization.
University Medical Center Hamburg-Eppendorf
Teaching hospital of University of Hamburg located in Eppendorf, Hamburg, Germany.
National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University (BGU) of the Negev, Israel, Bioinformatics Core Facility
Provides customized data analysis services and consultation to scientists at BGU and all over Israel from academia and industry. Goal to help scientists advance their research using bioinformatics methodologies, to design and analysis of experiments that use genomic technologies like next generation sequencing, mass spectrometry proteomics and metabolomics profiling, microarrays as well as mining and reanalysis of publicly available datasets. Facility develops software tools for automation of data analysis workflows like NeatSeq-Flow, Microbe-Flow.
University of Cape Town Centre for Proteomic and Genomic Research (CPGR) Core Facility
Center for Proteomic and Genomic Research
Centre for Proteomic and Genomic Research
Services to life science and biotech communities in South Africa. Based in Cape Town, combine information about genomic and proteomic technologies with bio computational pipelines to create fit for purpose offerings for customers in academia and industry.
Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment.
Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility
Core provides assistance in primary analysis of sequencing data and other large scale biocomputing. For our internal users we host extensive web services, workflows and customized tools that help with data management, visualizations, standardized analyses and data sharing.
Mayo Clinic Rochehster Bioinformatics Core Facility
Division of Biomedical Statistics and Informatics
Core assists in genomics, proteomics and metabolomics data acquisition, management, analyses and interpretation to Mayo investigators. Participates in Basic science research, Clinical trials, Population health, and Translational science to execute analytical workflows and manage large omics data sets. Provides support to Mayo Clinic Center for Individualized Medicine and Mayo Clinic Cancer Center. Has its academic home in Department of Health Sciences Research within Division of Biomedical Statistics and Informatics.
Software for 3D reconstruction from serial slices. Used to create 3D model to analyse organs, tissues and cells, create photos and videos to help scientists in life science, biology and medicine, visualize, analyze and exploit information from serial slices and get accurate quantitative information from reconstructed 3D models.
University of Liege Interdisciplinary Cluster for Applied Genoproteomics Bioinformatics Core Facility
Interdisciplinary Cluster for Applied Genoproteomics
Core provided by interdisciplinary center of biomedical research of Liege University. Develops and applies computational methods to extract information from large sets of biological and biomedical data.
University of Cambridge Department of Plant Sciences Bioinformatics Core Facility
University of Cambridge Bioinformatics Core Facility
Core provides assistance in data analysis to support members of Plant Sciences.
Indiana University Center for Genomics and Bioinformatics Core Facility
Indiana University Bloomington Center for Genomics and Bioinformatics
CGB offers range of genomic services, including high-throughput DNA/RNA extraction, library preparation, next-generation sequencing, and bioinformatic analysis.
University of Oxford Computational Biology Research Group Core Facility
Core provides bioinformatics training and analysis tools. Supports bioinformatics analysis at University of Oxford.
University of Idaho IBEST Institute for Bioinformatics and Evolutionary Studies Core
institute for Bioinformatics and Evolutionary Studies
Genomics, Computational and Northwest Knowledge Network core facilities for researchers from University of Idaho and their collaborators.
University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility
Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice.
University of Malaga Andalusian Platform of Bioinformatics Core Facility
Provides assistance in computing, nanotechnology, and biological fields. Provides scientific support and resources to the UMA research groups, public institutions and private companies.
Max Planck Institiute of Immunobiology and Epigenetics; Freiburg; Germany
Interdisciplinary research institute that conducts basic research in modern immunobiology, developmental biology and epigenetics.
University of Manchester Bioinformatics Core Facility
Core provides assistance in integrative analysis of genomic datasets to support faculty.
Johns Hopkins Medicine Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core Facility
Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core
Core provides assistance with Single Cell RNA and DNA Sequencing, Spatial Transcriptomics, Next-Generation Sequencing libraries.
University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility
Computational Genomics Analysis and Training Core Facility
Computational Genomics: Analysis and Training Core Facility
Core provides genomics training, as well as assistance in next generation sequencing analyses.
Duke University Omics Data Analysis Core Facility
Genomic Analysis and Bioinformatics core for data analysis associated with performing complex and data intensive projects in life science research of Duke University and Duke Medical School. Provides expertise, training, data analysis in next generation sequencing, array and proteomic based technologies.
Vall dHebron Institut de Recerca Statistics and Bioinformatics Unit Core Facility
Support Unit in Methodology for Biomedical Research
Core at Vall dHebron Institut de Recerca, Barcelona, Spain to provide data analysis, softwares and training programs in statistics and bioinformatics for clinical research at VHIR.
Montreal Clinical Research Bioinformatics Core Facility
Institute of Clinical Research of Montreal
Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses.
University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility
University of Manitoba BIT Core Facility
BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management.
UCSF Gladstone Institutes Bioinformatics Core Facility
UCSF Gladstone Institutes Bioinformatics Core
Core provides consulting services, sequencing, data analysis, and programming assistance. Used for Experimental Design and Power Analysis Consultation, RNA-seq, ChIP-seq, ATAC-seq analysis, Statistics consulting, Variant calling, Data normalization across multiple projects, General programming, Custom Figures for publication, tutorials for learning common software tools.
University of Michigan School of Medicine Center of Computational Medicine and Bioinformatics Core Facility
Computational Medicine and Bioinformatics
Center of Computational Medicine and Bioinformatics
UM School of Medicine Computational Medicine and Bioinformatics
University interdisciplinary academic center for bioinformatics, biomedical data science, and translational precision health informatics. Core provides training programs.
University of Illinois Urbana-Champaign High Performance Biological Computing Core Facility
Core provides infrastructure for bioinformatics, combining hardware, software, databases, training, consulting and services for all campus researchers at University of Illinois requiring computational resources and expertise for biomedical research.
University of North Carolina Charlotte Bioinformatics Services Division
Core to assist with analyzing and interpreting data produced by genomic technologies.
Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems.
ReproIn: The ReproNim image input management system (featuring DataLad)
Software tool for automatic generation of shareable, version controlled BIDS datasets from MR scanners.
Sainsbury Laboratory Bioinformatics Core Facility
Core develops tools for high throughput sequence data to study non reference, non model organisms.
Cambridge Institute for Medical Research Bioinformatics Core Facility
Core provides biological data handling and analysis in differential expression analysis, next generation sequencing, networks, protein architecture, and motif searching for in house researchers.
Harvard School of Public Health Microbiome Analysis Core Facility
Core assists with consultation for microbiome project development, provides validated meta omic analysis of microbial community data, and supports fully collaborative grant funded investigations.
City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility
Integrative Genomics and Bioinformatics Core
Core provides genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators.
University of Gothenburg Bioinformatics Core Facility
Core assists with statistical and bioinformatics consultation and data analysis.
Gulbenkian Institute of Science Bioinformatics and Computational Unit Core Facility
IGC Core in Oeiras, Portugal, promotes use of computational methods in biological research, through training and development of resources and materials, supports biological data analysis using computational methods, conducts research and development in bioinformatics, in particular in data flows, data warehousing and data analyses.
Software tools for analysis of cellular cryo-ET data.
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility
Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training.
Genome Institute of Singapore Scientific and Research Computing Core Facility
Core provides research computing resources including bioinformatics, application development, data management and IT infrastructure to support next generation sequencing technologies, human genotyping, high throughput screening and computational biology researchers.
University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility
College of Medicine & Veterinary Medicine
College of Medicine and Veterinary Medicine
Institute of Genetics and Molecular Medicine
MRC Institute of Genetics and Molecular Medicine BAC
Core provides advice, training, provision of computational tools and collaborative expertise to all IGMM researchers.
Collection of biological samples linked to participant medical data from individuals living with type 1 diabetes. Unifies samples and data from eight different clinical studies related to type 1 diabetes.
Software Python package to extend Airflow functionality with Common Workflow Language support. Lightweight pipeline manager supporting Common Workflow Language. Can be used to run workflows on standalone MacOS/Linux servers, on clusters, or on cloud platforms.
Software tool to make artificial mate pairs from long sequences for scaffolding.
Software tool to separate contaminating reads from FASTQ files.
Software suite of functions for EMG data visualization and processing. Open source Matlab toolbox for electromyography combined with transcranial magnetic stimulation. MATLAB toolbox for the collection, analysis, and visualization of EMG and TMS.
Keyence | BZ X-710 fluorescent microscope
All in one fluorescence microscope BZ-X710 by Keyence, Japan.
Open source pulse train generator that allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Generates precisely timed pulse sequences for use in research involving electrophysiology or psychophysics.
Software tool as source code used in analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice collected during rewatering after exposure to combined drought and heat stress.
Software tool as analysis application BZ-H1A by Keyence, Japan for fluorescence microscope BZ-8100 series.
Microarray Scanner is part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays.
Software tool to display surface of macromolecule and its properties. Uses projections to map van der Waals or solvent accessible surface of macromolecule onto plane., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Purdue University; West Lafayette; Indiana
Public research university in West Lafayette, Indiana, and flagship campus of Purdue University system. University was founded in 1869 after Lafayette businessman John Purdue donated land and money to establish college of science, technology, and agriculture in his name.
Software tool as analyzer for kidney single cell datasets. Allows users to query gene expression from mouse or human kidney and human kidney organoid single cell datasets. For details about datasets visit ReBuilding a Kidney website.
Platform for Interactive analysis and Visualization Of Transcriptomics
Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows.
Software suite of proprietary databases that contain one of longest running and largest collection of privately and publicly insured, de identified patient data in USA. Family of data sets that fully integrate many types of data for healthcare research.
Marshall Scientific | PTC-150 MiniCycler
Mini Thermal Cycler PCR is compact thermal scanner, catalog number PTC-150 Cycler with Hot Bonnet heated lid for oil free cycling by MJ Research.
Accessible artificial intelligence from University of Pennsylvania
Open source software tool to leverage supervised machine learning techniques to analyze data. Can assist with tasks such as choosing appropriate models for data. Data science assistant for generating results from large and complex data problems.
Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program.
Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter.
Software event based framework for processing and controlling data streams. Visual language designed for making software systems that require rich and rapid interaction with external world.
Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles.
Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals.
Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.
Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases.
Cloud based web platform connecting researchers, research organisations, funders and publishers in automated workflow management tool. Platform provides infrastructure for researchers, funders and publishers participating in Open Access Publishing. Features searchable database of journals compliant with research funders Open Access policies, connects researchers directly to journals submission systems, coordinates open access fee payments for funder with publisher upon acceptance, and supports compliancy by overseeing deposition of papers to designated repositories.
Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.
Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps.
Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly.
Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.
Pairwise Sequentially Markovian Coalescent
Software package for implementation of Pairwise Sequentially Markovian Coalescent model. Infers population size history from diploid sequence.
Open source and stand alone software for assessing vascular reactivity. Used in pressure myograph system.
Computational Suite for Bioinformaticians and Biologists
Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments.
Catalog of Inferred Sequence Binding Preferences
Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.
Software R package to measure reproducibility of ﬁndings identiﬁed from replicate experiments and to provide highly stable thresholds based on reproducibility.
Case Western Reserve University Cystic Fibrosis Mouse Models Core
Core facility for cystic fibrosis mouse strains. Services include mouse production from current strains and creation of new strains, mouse strain maintenance, tissue acquisition, genotyping and treatment of mice with IACUC approved drugs to test potential therapies. Maintains centralized database that contains breeding history, phenotypes observed and experimental records of various CF mouse strains.
Contract research organization that provides genetically engineered mouse models (GEMMs) and services to global preclinical Research and Development communities. Specializes in developing animal models using cutting edge gene-editing technologies with large collection of cKO/KO (conditional knockout/knockout) mice, humanized mice, immunodeficient mice, and germ-free mice.Provides preclinical services, including mouse model customization, pharmacology services such as drug efficacy testing and mouse phenotyping, CRISPR/Cas9 gene-editing, cryopreservation, rapid expansion, and customized breeding.
University of British Columbia Centre for Molecular Medicine and Therapeutics
Centre for Molecular Medicine and Therapeutics
University of British Columbia (UBC) Centre for Molecular Medicine & Therapeutics
Center is part of University of British Columbia Faculty of Medicine, located at British Columbia Children Hospital Research Institute (BCCHR) in Vancouver, British Columbia, Canada. Research at CMMT is focused on discovering genetic susceptibility to illnesses such as Huntington Disease, Type 2 diabetes and bipolar disorder.
Algorithm for derivation of cell lineage trees based on RaceID2 results and predicts multipotent cell identites. StemID2 is algorithm for identification of lineage trees based on RaceID3 analysis. Used for better understanding of differentiation dynamics in variety of systems. Written in R computing language.
Software R package for inference of cell fate bias from single cell RNA-seq data. Iterative supervised learning algorithm for probabilistic quantification of cell fate bias in progenitor populations.
Secure Access to Research Data and E-Infrastructure
Secure Access to Research Data and E-Infrastructure (EUROPE)
Platform for Secure Access to Research Data and E-Infrastructure based on European Standards for Health Case information. Used for secure processing of sensitive personal data in research in health and care sector.
Software R package as single cell regulatory network inference and clustering. Used for simultaneous gene regulatory network reconstruction and cell state identification from single cell RNA-seq data.
Software R package for 3D visualisation and analysis of biological image data, especially tracings of single neurons.
Software tool as support for working with light and electron microscopy fly brain data. Part of suite of R packages based on NeuroAnatomy Toolbox. Provides tools to move between adult brain EM and light level data, emphasising interaction between CATMAID web application and R Neuroanatomy Toolbox package.
Software Python tool as viewer for MRI data and numpy arrays.
Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools.
Web server for RNA secondary structure prediction. Predicts RNA secondary structure from RNA sequence. Based on generalized centroid estimator.
Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference.
Brain Imaging Data Structure (BIDS) Validator
Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure.
Software tool for folding RNA secondary structures, including two limited classes of pseudoknots. Performs abstract shape analysis for structures holding pseudoknots up to complexity of kissing hairpin motifs. Successor of pknotsRG. Used for secondary structure prediction including kissing hairpin motifs.
Normalization and Differential expression
Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.
Software platform used for production of animations, rich Internet applications, desktop applications, mobile applications, mobile games and embedded web browser video players. Adobe will stop updating and distributing Flash Player in 2020. For existing Flash content, eventual, final version of Flash plug-in will still work after 2020, and Adobe will work with browser makers to ensure security vulnerabilities are patched.
Open source software tool to provide template for command line bioinformatics tools in various programming languages. Program reads one or more input FASTA files, computes variety of statistics on each file, and prints tabulated output. Used as basis for learning and as foundation for starting new projects.
brainGraph - Graph Theory Analysis of Brain MRI Data in R
Software R package for performing graph theory analyses of brain MRI data.
Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications.
Software tool that combines steps of image processing, non rigid image registration, and spot localisation. Performs registration of 3D imaging data and localization of spots, active synapses in light microscopy images, in semi automatic mode with graphical user interface.
Glomerular Disease Study & Trial Consortium
Consortium to bring together clinicians, pathologists, researchers, and biotech innovators to create scalable network of stakeholders interested in helping patients with glomerular kidney disease. Makes collective expertise of its members available for discussion of individual cases, provides infrastructure for biomarker studies, enables genomic research, and facilitates clinical trials.
Pangenome Iterative Refinement And Threshold Evaluation
Software pangenomics toolbox for clustering diverged orthologues in bacteria. Used to identify and classify orthologous gene families in bacterial pangenomes over wide range of sequence similarity thresholds.
BRAIN Initiative Cell Census Network Cell Registry
Searchable table of datasets. Data generated from projects through BRAIN Initiative Cell Census Network. Datasets can be filtered by species, research investigator, grant number or experimental technique. Includes links to data directories at data archives and links to protocols.
Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data.
Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.
Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets.
Public, NIH-funded repository and analysis ecosystem for brain microscopy data, designed to store, share, and process massive volumetric datasets. It enables researchers to access whole-brain images, neuron morphologies, and spatial data without needing to download, fostering collaborative discovery. Used to deposit, analyze, mine, share and interact with large brain image datasets.
Brain Observatory Storage Service and Database (BossDB)
Block and Object Storage Service Database
Brain Observatory Storage Service and Database
BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest.
AcceGen offers most complete human and animal cell products and cell/molecular biology services for life science researchers worldwide. Cell line collections include primary cells, tumor cell lines, transfected stable cell lines, stem cells and immortalized cell lines. miRNA agomir/antagomir, nucleic acid kits, enzymes and custom cell/molecular biology services.
Drosophila induction-based torque compensator
Compensator measure rotational force of tethered fly around its vertical body axis (yaw torque). Used as behavioral read-out after sensory stimulation or to control various environmental stimuli in different kinds of behavioral experiments. Measurement device uses measurement principle that is based on magnetic induction and compensates for any movement of fly.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan.
Automatic Molecular Replacement Pipeline
Software package for molecular replacement protein structure solution using X-ray data. Includes database and set of programs for structure solution. Automatic molecular replacement pipeline.
Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data.
Relaxed Electrophysiological Data Acquisition
Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings.
Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12.
Retina inspired event based camera for low latency, real time image processing by iniVation. Works with graphical interfaces such as jAER.
Open source microcontroller board based on Microchip ATmega328P microcontroller and developed by Arduino. Board is equipped with sets of digital and analog input, output pins that may be interfaced to various expansion boards and other circuits.
Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data.
Software tool for scalable clustering of RNAs based on sequence and secondary structures similarities. Implemented within Galaxy framework. Used for studying RNA function.
Software package that evaluates correspondence between stated sexes, relationships, and ancestries in pedigree file and those inferred from genotypes in VCF file resulting from human whole genome sequencing or whole exome sequencing studies. Facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems.
Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information.
Collection of data about variants, genes, phenotypes and diseases involved in mitochondrial functionality. Users can search for variant position, gene, phenotype or disease and retrieve all related information through integrated network of biological entities.
Software package for densitometry measurements of electrophoresis gels by Silk Scientific Inc. Gel analysis software. Turns scanner into gel densitometer. Works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source. Can quantify Western blots, Agarose gels, PCR gels, TLC.
Magnetic Resonance signal processing and analysis
Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab.
Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function.
Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu .
Software tool for fast tomographic reconstruction on multicore computers. Used for electron tomography studies with increasing resolution needs.
Software tool for electron tomography and 3D image processing. Software package used in electron tomography for marker free alignment and 3D reconstruction of tilt series. Tomography software package distributed for linux operating system and developed by Hanspeter Winkler.
Software tool used to conduct life table analysis focused on development of cohort or population for animal species with two sexes. Parent organization is National Chung Hsing University, Taichung, Taiwan.
Software R package for tree ensembles such as random forests, regularized random forests and gradient boosted trees. Provides functions for extracting, measuring and pruning rules, selecting compact rule set, summarizing rules into learner, calculating frequent variable interactions, formatting rules in latex code.
Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R.
Software R package to implement extensions to Freund and Schapire AdaBoost algorithm and Friedman gradient boosting machine. Includes regression methods for least squares, absolute loss, t distribution loss, quantile regression, logistic, multinomial logistic, Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and Learning to Rank measures.
Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.
BAyesian STructured coalescent Approximation
Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations.
Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019.
Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.
Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain.
Software application as image segmentation tool. Brain volumetry assessment software. Processes MRI scans and provides self explanatory patient report with total brain volume, hippocampal volume and volumetric data on key segments of brain measured against healthy database.
Software tool for data analysis and scientific visualization by IONDEV SRL.
Project to determine organization of neuronal connections between nervous system parts. Source for documented connections in rat brain.
Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks.
Atlas with global nervous system nomenclature ontology and flatmaps for structure of rat brain. Open access resource for neuroscience community.
IncuCyte™ Chemotaxis Cell Migration Software by Essen Bioscience. Add on software module for IncuCyte ZOOM® live cell analysis system. To analyze label free and fluorescently labeled chemotactic cell migration images acquired using ClearView Chemotaxis Plate.
Software tool for microplate reading. Software supports myriad applications, enabled using BioTek microplate readers.
Software as branch of FieldTrip with added functionality for sleep analyses, like calculating sleep tables, descriptives, ploting hypnograms, detecting slow waves, sleep spindles, REMS and their cooccurrence etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
BPC Instruments | Biomethane Potential Test
Automatic Methane Potential Test System (AMPTS) II
Automatic Methane Potential Test System (AMPTS) II is analytical tool for conducting various anaerobic batch fermentation tests. This includes performing, with up to 15 test vials, biochemical methane potential (BMP) tests, anaerobic biodegradability studies, specific methanogenic activity (SMA) assays, as well as conducting residual gas potential (RGP) analyses on digested slurry.
Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience.
Software for comprehensive annotation and delineation of tissue structures by MBF Bioscience. Creates 3D model from image data and annotates regions of interest from customizable ontology list. Map images acquired with brightfield, confocal, two-photon, widefield fluorescence, or light sheet microscopes.
Software tool to automatically align serial sections and visualize entire 3D organ. Generates full resolution 3D reconstructions from serial sections imaged with whole slide scanners and research microscopes. Used to assist with cell mapping, cytoarchitectonics, and other measures that require visualizing neuronal circuitry to create comprehensive anatomical reference.
Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.
Technical Report Archive and Image Library
Repository of technical reports from US government. Identifies, acquires, catalogs, digitizes and provides unrestricted access to U.S. government agency technical reports. Ensures preservation, discoverability, and persistent open access to government technical publications regardless of form or format. Search interface is hosted by University of Washington and searches all TRAIL content found at HathiTrust and UNT.
University of Johannesburg; Johannesburg; South Africa
Public university located in Johannesburg, South Africa. Came into existence on 1 January 2005 as result of merger between Rand Afrikaans University, Technikon Witwatersrand and Soweto and East Rand campuses of Vista University.
Software interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community.
A repository for geosciences software. Registry for software for geoscientists. Part of NSF EarthCube OntoSoft project.
Ten hour course describing sample size calculations, when they can and should be used. Online program for graduate students and research professionals. Participants learn to apply knowledge and skills gained to improve rigor, transparency and reproducibility in their own research.
Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.
Software tool for PacBio hybrid error correction through iterative short read consensus.
Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics.
Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats.
Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses.
Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data.
Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.
Software package for graphical visualization of organellar genomes. Converts annotations in GenBank format into graphical maps. Used to create visual representations of circular and linear annotated genome sequences provided as GenBank files or accession numbers.
Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments.
Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed.
Software tool as open source medical image viewer. Enables to browse and visualize medical imaging libraries.
Software as open source, multiplatform tool used to segment structures in 3D medical images.
Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.
Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R.
Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics.
Software as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography.
Software for automatic identification and delineation of brain regions within experimental mouse brain sections. NeuroInfo registers serial section images of any orientation to Allen Mouse Brain Atlas, corrects for distortion due to histological processing, delineates anatomies in experimental section, and detects and reports on cell number within selected anatomies.
Companion analytical software for Neurolucida and Neurolucida 360, designed to perform extensive morphometric analysis on neuron reconstructions, serial section reconstructions, and brain maps.
Data analysis and 3D visualization for connectomics and serial electron microscopy. This toolbox provides missing 3D visualization and analysis tools for cylinder-based annotations. Integration with contour, skeleton based annotations and common morphology file formats is also supported.
Software tool to correct for batch effects in single-cell expression data using fast version of mutual nearest neighbors (MNN) method.
Human miRNA tissue atlas. Database showing distribution of miRNA expression across human tissues.
Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.
Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Web based manually curated experimentally validated database of microRNA-Target interactions. Collection of MTIs data validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.
Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are.
Co-expression Meta-analysis of miRNA Target
Interactive database of miRNA targets and miRNA-regulated gene networks to integrate expression data from hundreds of cellular and tissue conditions. Website includes CoMeTa corank lists and additional targets for all of human miRNAs, their associated pathways resulting from COOL analysis, and miRNA communities with their corresponding enriched functional categories. Website is searchable by miRNA, target gene, or biological function of interest, and represents unique resource to gain insight into miRNA-controlled gene networks and functions.
National High Magnetic Field Lab DC Field Core Facility
Facility located at MagLab headquarters near Florida State University in Tallahassee. Contains 14 resistive magnet cells connected to 56 megawatt DC power supply and 15,000 square feet of cooling equipment to remove heat generated by magnets. Includes several superconducting magnets operating at millikelvin temperatures. Among these instruments is 45-tesla hybrid magnet, which offers scientists strongest continuous magnetic field in world. Research is supported by magnet plant and cryogenic system operators. Technicians design, build and repair instruments for user research.
National High Magnetic Field Laboratory Electron Magnetic Resonance Core Facility
EMR Facility offers home-built, high-frequency and high-field continuous-wave instruments providing frequency coverage from 9 GHz to 1 THz, with additional frequencies available up to 2.5 THz using molecular gas laser. EMR covers variety of magnetic resonance techniques associated with electron like Electron Paramagnetic/Spin Resonance (EPR/ESR). EPR/ESR can be performed on any sample that has unpaired electron spins and used in applications in physics, materials science, chemistry and biology, including studies of impurity states, molecular clusters, antiferromagnetic, ferromagnetic and thin film compounds, natural or induced radicals, optically excited paramagnetic states, electron spin-based quantum information devices, transition-metal based catalysts; and for structural and dynamical studies of metallo-proteins, spin-labeled proteins and other complex bio-molecules and their synthetic models.
National High Magnetic Field Laboratory High B/T Core Facility
High B/T (magnetic field / temperature) Facility
Facility to conduct experiments in high magnetic fields up to 15 tesla and at very low temperatures down to 0.4 mK simultaneously. Located at University of Florida in Gainesville, it is operated as part of Physics Department Microkelvin Laboratory.
National High Magnetic Field Laboratory Ion Cyclotron Resonance Core Facility
National High Magnetic Field Laboratory Ion Cyclotron Resonance Facility
NHMF Laboratory Cyclotron Resonance Facility
Facility provides service operations for sample analysis that requires ultrahigh resolution and high mass accuracy of Fourier Transform Ion Cyclotron Resonance. Used for research in biomolecular analysis, hydrogen-deuterium exchange and environmental and petrochemical analysis. Four FT-ICR mass spectrometers feature high magnetic fields including the world-record 21 tesla and are compatible with multiple ionization and fragmentation techniques.
National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility
Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Facility
National High Magnetic Field Laboratory (MagLab) site. It provides researchers with advanced NMR, MRI, and spectroscopy tools (human/animal imaging) for biomedical studies, specializing in high-field magnetic resonance technology. Hosts spectrometers and scanners, including high-field NMR (up to 1.5 GHz), MR microscopy, and human/animal MRI systems (e.g., 3T and 900 MHz). Offers expertise in high-resolution solution NMR, solid-state NMR, and specialized imaging for in vivo animal models and humans.Features an RF coil lab that designs, builds, and tests custom MRI/NMR coils to optimize data collection. Supports research into Alzheimer's, cancer, metabolism, and brain development.
Commercial organization located in New York, USA which provides amplifiers. designs and manufactures standard or custom RF/Microwave Power Amplifiers/Accessories for military (CPC is ITAR registered), industrial, scientific and medical applications.
Commercial organization located in Massachusetts, USA, for scientific instruments and analytical and diagnostic solutions. Bruker equipment can be used in life science molecular research, in applied and pharma applications,microscopy, nano-analysis and industrial applications. Provider of high-performance systems for cell biology, preclinical imaging, clinical phenomics and proteomics research, clinical microbiology, and for molecular pathology research.
Commercial organization located in Abingdon, United Kingdom for high technology products. Manufactures instruments for agriculture, astronomy, automotive, aerospace, bio-imaging, life science, chemical and catalysis, energy generation and storage, forensics, environmental industries, geology, metallurgy, pharmacy, photonics, polymers, quantum technology, data storage, and microelectronics. Products are divided into atom force microscopy, electron microscopy, deposition and etch tools, low temperature systems, optical imaging, nuclear magnetic resonance, MRI and CT servicing, Modular optical spectroscopy, and X-Ray.
Commercial organization located in Warminster, Pennsylvania, USA, part of SP Industries, Inc. Provides VirTis, FTS Systems, Hotpack, Hull, Genevac, and PennTech scientific equipment. Manufactures freeze drying/lyophilization, centrifugal evaporation and concentration, temperature control/thermal management, glassware washers, controlled environments, vial washing and tray loading machines., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Commercial organization located in Warminster, Pennsylvania, USA is manufacturer of specialty equipment, scientific glassware, laboratory and lab safety supplies, and home healthcare products serving pharmaceutical, biotechnology, educational, industrial, OEM, and commercial markets under market leading brand names. Products include pharmaceutical, scientific research, industrial, aeronautic, semiconductor and healthcare. Flagship brands are SP Scientific, SP Scienceware, and SP Ableware.
Commercial organization, located in Houstion, Texas, USA, for products for magnetic resonance spectroscopy. Manufactures NMR, NQR and amp, MRI instrumentation including nuclear magnetic resonance spectrometers and full consoles, system upgrades, and solid-state NMR / NQR probes. Tecmag was acquired by Avingtrans PLC and became subsidary of Scientific Magnetics Ltd. (UK).
Commercial organization, located in Houston, Texas, USA. Scientific Magnetics is trading name of Space Cryomagnetics Ltd. and specializes in cryogen free super conducting magnets. Products including cryogen free horizontal superconducting magnets, UHV compatible magnets, magnetic separation products, MRI site planning, and liquid helium filling.
Machine industry company located in Chatteris, Cambridgeshire, United Kingdom and engaged in provision of highly engineered components, systems and services to energy, medical and traffic. Has investment in Energy Divisions, Medical Division, and Aerospace Industries.
Manufacturer located in Palo Alto, California, USA, that has made developments in fields of radiotherapy, radiosurgery, X-ray tube technology, digital image detectors, cargo screening, and non-destructive testing. Varian technology and software for processing diagnostic X-ray images is being used in radiotherapy and analysis.
Manufacturer, located in Cary, North Carolina, USA, of amplifiers, RF/microwaves, and other electrical components which come in boards, modules, or systems.
Repository of mainly CellML models powered by collection of software tools and libraries with PMR2 software suite as core power. Third party integration suites are RICORDO, Virtuoso, BiVeS/BudHat, OpenCOR, CombineArchive Web, WebCAT, Morre/MaSyMoS.
Software tool as analysis application BZ-H3A by Keyence, Osaka, Japan for fluorescence microscope BZ-X series.
Software tool by Applied Biosystems to design primers and probes using TaqMan and SYBR Green I dye chemistries for gene quantitation and allelic discrimination (SNP) real-time PCR applications. Developed for use with StepOne, StepOnePlus, 7300, 7500, 7500 Fast, 7900HT, ViiA 7, and QuantStudio real-time PCR systems. Provides customized application specific documents for absolute⁄relative quantitation and allelic discrimination.
Laser scanning confocal microscope designed for high-quality imaging of biological and material samples. Member of the seventh generation of confocal microscopes from Carl Zeiss. Point scanning confocal microscope., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Florida State University Chemistry and Biochemistry Nuclear Magnetic Resonance Core Facility
Florida State University Chemistry and Biochemistry NMR Laboratory
Facility provides NMR spectroscopy services for FSU campus. Has spectrometers to perform experiments ranging from protein structure determination to solid state characterization of inter-metallic species and nearly all experiments in between.
Image analysis of V1 ocular dominance patterns
Software tool to quantify ocular dominance patterns of primary visual cortex in different animals.
University of Florida Department of Chemistry Nuclear Magnetic Resonance Core Facility
Facility serves students and faculty of University of Florida, and researchers from industry who use facility instruments to check outcome of reactions or characterize compounds. Instruments include Inova 500 MHz magnet with 2 RF Channels, Inova 500 MHz magnet with 3 RF Channels, Mercury 300 MHz (m4n and m8n), Mercury 300 MHz Broadband, Agilent 600 MHZ Magnet, and several NMR probes.
Biospecimen Repository Access and Data Sharing
Access to data from the Division of Intramural Population Health Research (DIPHR) of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) from completed studies, including biospecimens and ancillary data.
Medical Information Mart for Intensive Care-III
Medical Information Mart for Intensive Care
Collection of comprising deidentified health related data associated with patients who stayed in critical care units of Beth Israel Deaconess Medical Center between 2001 and 2012. Database includes information such as demographics, vital sign measurements made at bedside (~1 data point per hour), laboratory test results, procedures, medications, caregiver notes, imaging reports, and mortality (both in and out of hospital).
Science of Behavior Change Research Network
Science of Behavior Change (SOBC) Research Network
Repository for behavioral science measures that have been validated or are in process of being validated in accordance with SOBC Experimental Medicine Approach.
Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 1, 2023. System developed under guidance of experts in reproduction and andrology from Andrological Branch of Chinese Medical Association and Research Institute of National Health Planning Commission. Designed according to standard of 5th edition of World Health Organization laboratory manual for examination and processing of human semen.
Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data.
To create stitched enhancers, and to separate super enhancers from typical enhancers using sequencing data given file of previously identified constituent enhancers .
Software tool to create interactive heatmap matrix of pairwise linkage disequilibrium statistics.
Software tool to provide text and label geoms for ggplot2 that help to avoid overlapping text labels. Labels repel away from each other and away from data points.
Software tool as Galaxy based training resource for single cell RNA-seq quality control and analyses.
Data Access Quality and Curation for Observational Research Designs
Software tool for practical self assessment and reporting method for clinical research studies, to capture key information about data acquisition and quality control measures. Linked to dataset so that potential research collaborators can determine if data meets their needs and expectations.
Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler.
Software tool for description of connectivity in small and large scale neuronal network models. It provides operators to form more complex sets of connections from simpler ones and also provides parameterization of such sets. Can be used as component of neuronal network simulators or other tools.
Neuroimaging Meta Analysis Research Environment
Neuroimaging Meta-Analysis Research Environment
Software Python package for coordinate and image based meta analysis of neuroimaging data.
Research study of brain development in infants and children with autism. Consortium of researchers across North America that work together to discover early changes in brain development of young children with autism. Participants will travel to their closest study location to receive developmental and behavioral assessments, MRI scan of the brain. Participants will be reimbursed for travel and related expenses. Families of children at high risk for developing symptoms of autism will receive assistance with referrals for local services. check if data repository is in the papers
Software tool for analysing pathogen genetic diversity and relationships between and within hosts at once, in windows along genome. Inferring transmission from within and between host pathogen genetic diversity.
AntiBodies Chemically Defined Expert Protein Analysis System database
ExPASy ABCD (AntiBodies Chemically Defined) Database
The AntiBodies Chemically Defined Database
Repository of sequenced antibodies, integrating curated information about antibody and its antigen with cross links to standardized databases of chemical and protein entities. Manually curated repository of sequenced antibodies, developed by Geneva Antibody Facility at University of Geneva, in collaboration with CALIPHO and Swiss Prot groups at SIB Swiss Institute of Bioinformatics. Database provides list of sequenced antibodies with their known targets. Each antibody is assigned unique ID number that can be used in academic publications to increase reproducibility of experiments.
Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results.
An ontology for describing the complex phenotypes of neurons.
Behavior instrument, cage allows for assess to home cage behavior and cognitive performance of up to 16 individual mice or rats separately while they are living in social environment. This unique experimental setup fosters natural social behavior in biologically relevant, enriched but highly standardized home cage context. Minimizes need for handling and human intervention, thereby increasing task validity, data reproducibility and ensuring high level of animal welfare.
Software tool for assessment of predictive power, with support for neuroimaging features. Easy machine learning and standardized predictive analysis of biomarkers.
Software tool for subject wise networks from morphometric features and structural MRI. Single subject morphometric networks for neuroscience connectivity applications.
Miniature microscope for imaging calcium activity in neural circuits by Inscopix, Inc.
Mosaic software features apps designed to help you derive deeper insights from videos of large scale circuit dynamics by Inscopix Inc.
Software tool for analysis of mass spectrometry imaging data implemented in Galaxy framework. Provides options to analyze mass spectrometry imaging data in imzML file format, including quality control, visualization, preprocessing, statistical analysis, image co-registration and feature identification.Galaxy docker container for mass spectrometry imaging.
Software package for statistical analysis by SAS Institute Inc, Cary, NC.
Software tool as preprocessing pipeline for diffusion MRI. Pipeline used for preprocessing of diverse dMRI data. Workflow dispenses of manual intervention, thereby ensuring reproducibility of results.
Software tool as graphical user interface designed to assist with manual annotation of different parts of the inflorescence. Used in deep plant phenotyping. Works with DeepPod.
Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences.
Software package for metagenomics data. Discovers accurate predictive signatures and provides unprecedented interpretability. Package contains three methods for suppervised learning based on ternary coefficients. Used to discover classification models for quantitative metagenomics data.
Software based on deep learning model for auto detect corneal diseases. Sample may contain multiple categories. After learning thousands of corneal images, you can make automatic judgments on subtypes of cornea.
Software tool for identifying K mAjor cell population groups in single-cell RNA-seq analysis. Algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets improves identification of major cell types and facilitates cell ontology curation.
Medical image repository to store medical research data.
Public repository of reference image datasets from published scientific studies. Platform for publishing, mining and integrating bioimaging data, following FAIR principles and Euro-BioImaging/ELIXIR imaging strategy using OMERO and Bio-Formats open source software built by Open Microscopy Environment. Deployed on OpenStack cloud running on EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super resolution microscopy, and digital pathology.
Storage and search platform supported by Beilstein-Institut that incorporates STRENDA Guidelines. For authors who prepare manuscript containing functional enzymology data, STRENDA DB provides means to ensure that data sets are complete and valid before submitting them to journal.
Kinetic Models of Biological Systems (KiMoSys)
Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community.
Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data.
Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser.
Software tool to generate Dockerfiles and Singularity recipes for neuroimaging with simple command-line interface. Command line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers. Supports AFNI, ANTs, Convert3D, Dcm2niix, FreeSurfer, FSL, Matlab Compiler Runtime, MINC, Miniconda, MRtrix3, NeuroDebian, PETPVC, and SPM12.
HeuDiConv: a heuristic-centric DICOM converter
Software tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts.
Protein Circular Dichroism Data Bank (PCDDB)
Public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. For authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. Includes links for each entry to bioinformatics databases. Data are freely available to accessors either as single files or as complete data bank downloads.
Inorganic Crystal Structure Database (ICSD)
Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research.
Web service for automatic phonetic transcription of non-prompted speech. Ludwig Maximilian University of Munich, Munich, Germany is parent organization.
Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data.
Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain.
Software open source R package for executing, evaluating and visualizing different clusterings of experimental data, including data from single cell RNA-Seq studies. Software for running and comparing different clusterings of single cell sequencing data.
Software tool for interactive graphs of high dimensional data. Interactive cloud based software tool by DIBSVIS.
Mediation Analysis of Causality under Confounding
Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method.
Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing.
Model Implied Instrumental Variable Estimation of Structural Equation Models
Software R package for estimating structural equation models using instrumental variables.
Neurophysiological spike sorting software.
Software package for p value based multiple testing that also implements dependence test and p-value simulation.
Software package for extracting neural activity codes.
Software for computational neurophysiology. Simulation environment is used for building and using computational models of neurons and networks of neurons. NEURON Users Group can participate in collaborative development of documentation, tutorials, and software.
Software tools for converting data files into persistence diagrams and distance matrices.
Open source software neural simulation toolbox. C++ library for designing and deploying large scale neurally inspired computational models. Object oriented neural simulation toolbox optimized for high performance multi core, multi node computer architectures.
Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.
Python Rayleigh-Sommerfeld integral for acoustics with optional CUDA graphics processing unit (GPU) implementation.
Two photon microscope control software with multi area capabilities.
Analysis and modeling code for waves of seizure activity.
Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system.
Software tool to facilitate tractography based deep brain stimulation (DBS) electrode targeting within patient specific stereotactic coordinate system used in operating room.
Methods for reconstructing transcriptional regulatory networks.
Software tool to automate sequencing center operations. This pack provides re-usable units for automating tasks at sequencing core facility using StackStorm event-driven automation platform.
Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored.
Automatic Localization of Intra-Cranial Electrodes
Software tool for automatic localization of intra-cranial electrodes for clinical and high density grids. Software for coregistering high density ECoG grids to MRI anatomy.
Software tool for neuronal recording in intact brain.
Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory.
Software tool as processing code. Alternating direction method of multipliers (ADMM) algorithm for recovering 3D volumes from 2D raw data captured with DiffuserCam.
Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data.
Consortium to design and conduct pilot and feasibility studies of novel therapies to reduce morbidity and mortality for patients treated with maintenance hemodialysis. Data Coordinating Center (DCC) for consortium provides scientific expertise and operational support for pilot studies that will be conducted at HDPSC Participating Clinical Centers. Data Coordinating Center for Hemodialysis Pilot Studies Consortium.
Analysis, Visualization, and Informatics Lab-space (AnVIL)
Analysis Visualization and Informatics Lab-space
Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces.
Knowing what you know (kwyk) - Bayesian Brain Parcellation
Software tool as deep neural network for predicting FreeSurfer segmentations of structural MRI volumes. This tool is implemented as both Docker and Singularity containers. Used for brain parcellation and uncertainty estimation.
Software tool to uniformly process and normalize large amounts of data. Harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.
Open source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement.
Portal with information about twins in Italy.
Twin panel consists of three nationwide samples of Finnish twin pairs. Major studies include nicotine dependence, eating disorders and brain imaging and alcohol use.
Registry contains information about twin pairs for which zygosity is known, both mono- and dizygotic pairs. Registry covers older, middle, and younger cohorts. There are approximately 30 projects ongoing based on data from this registry.
Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain.
Cardiff Study of all Wales and North West of England Twins
Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people.
Independent academic and research institution to establish registration for twins in Sri Lanka , to facilitate study of twins. Center for twin, sibling, family and genetic studies for South Asian Region.
Twin registry to studying causes of cancer, gene inheritance and environment. Contains information on twins born in Denmark. Comprises twins born through more than 125 years.
Organization of twins and their families who are willing to consider taking part in twin-based, health-related research. For twins of any age, ethnicity, and zygosity (identical or fraternal), as well as higher order multiples such as triplets, quadruplets and quintuplets. Most of twins registered in MATR are from Virginia, North Carolina, and South Carolina, but twins from all over the country and all around the world are welcome to register. MATR repository containing DNA samples provided by twins and allows to study twin data collected by studies along with their DNA.
Portal for Twins Research Australia. Brings twins and researchers together for vital health research in twins.
MethBase: a reference methylome database
Central reference methylome database created from public BS-seq datasets. Provides methylation level at individual sites, regions of allele specific methylation, hypo- or hyper-methylated regions, partially methylated regions, and detailed meta data and summary statistics.
Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community.
Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis.
Canadian Epigenetics, Environment and Health Research Consortium Network
Network to connect Canadian epigenetics researchers and expand their reach to broader health research community in Canada and beyond. Curated epigenomics sequence focused on common human diseases.
Accessible Resource for Integrated Epigenomics Studies
Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time.
Collection of epigenetic data browsers and repositories. Repository of epigenetics tools and databases by EpiGenie team.
Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool for analysis of expression data for microRNA function.
Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data.
Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain.
Compilation of Genetics Resource Databases
Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse.
GO Gene Ontology Consortium and Knowledgebase
Consortium integrates resources from variety of research groups, from model organisms to protein databases to biological research communities actively involved in development and implementation of Gene Ontology. Mission to develop up to date, comprehensive, computational model of biological systems, from molecular level to larger pathways, cellular and organism level systems.
Collection of color illustrations that follow main events of embryogenesis and post embryonic development of Drosophila.
Atlas providing structure and development of Drosophila brain lineages. Used to learn about projection pattern of lineages as first step towards reconstructing and understanding all neurons.
Mouse lines expressing proteins that activate, inhibit or detect neuronal activity are available from The Jackson Laboratory Repository. Many of these strains have been generated by HHMI Janelia Farm GENIE Project or by Allen Institute for Brain Science.
Gene Expression Nervous System ATlas Cre-Mice
Project provides transgenic BAC-Cre recombinase driver lines that allow for cell-specific gene manipulations in central nervous system of mouse. Gene Expression Nervous System Atlas Project provides Cre driver lines that will target selected neuronal or glial populations in brain and spinal cord. Cells can be ordered from MMRRC.
Allen Brain Atlas expression map of Cre and other drivers
Allen Brain Atlas Data Portal Transgenic Characterization
Data detailing transgene expression in Cre and other driver lines for adult and developing brain. Experiments include colorimetric in situ hybridization, fluorescent in situ hybridization and other histological methods. Expression maps of transgenic Cre and other driver lines in mice.
Authoritative source of official names for mouse genes, alleles, and strains. Nomenclature follows rules and guidelines established by International Committee on Standardized Genetic Nomenclature for Mice.
Knockout Mouse Project Repository at JAX
Information from JAX about their contributions to KOMP project coordinated by International Mouse Phenotyping Consortium. National Institutes of Health has funded three KOMP2 centers in United States, including one at Jackson Laboratory, to work together on task of producing and phenotyping mice to establish resource of knockout mice and related database of gene function.
Database of different optogenetics resources like hardware, protocols, sequence information.
Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.
Software tool to access various mouse genome information in batch format. Batch data and analysis tools.
MGI contains homology information for mouse, human, rat, chimp, dog and other species. Complete set of human, chimpanzee, rhesus macaque, dog, cattle, rat, chicken, western clawed frog and zebrafish Homology Classes for mouse genes. Report includes Chromosome and EntrezGene and OMIM IDs. Report of Human and Mouse Homology Classes sorted by HomoloGene ID includes associated nucleotide and protein sequences, Chromosome and OMIM IDs. Report of Human and Mouse Homology with phenotype annotations. Several additional MGI reports are available, including those for Gene Ontology, Phenotypes and Nomenclature.
MGI integrates comparative data on inbred strain characteristics including SNPs, polymorphisms, and quantitative phenotypes.
MGI GO project provides functional annotations for mouse gene products using Gene Ontology. Functional annotation using Gene Ontology (GO).
Functional Mapping and Annotation of Genome Wide Association Studies
Functional Mapping and Annotation of Genome-Wide Association Studies
Platform that can be used to annotate, prioritize, visualize and interpret GWAS results. To submit your own GWAS, login is required for security reason. You can browse public results of FUMA from Browse Public Results without registration or login.
Collection of published and potential mouse models of human disease, discovery of candidate genes and investigation of phenotypic similarity between mouse models and human patients. Mouse mutation, and phenotype and disease model data from Mouse Genome Informatics database are integrated with human gene to disease relationships from the National Center for Biotechnology Information and Online Mendelian Inheritance in Man and human disease to phenotype relationships from the Human Phenotype Ontology.
Enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes.
Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models.
Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Knockout Mouse Phenotyping Project, JAX information about their contributions to KOMP2 project. Project to generate and phenotype single gene KO mouse strains from KOMP ES cell lines. Strains are phenotyped using protocols in pipeline designed by International Mouse Phenotyping Consortium. There are three NIH-funded phenotyping centers in United States: JAX, BaSH Consortium (Baylor College of Medicine, the Wellcome Trust Sanger Institute and MRC Harwell), and the DTCC Consortium (University of California at Davis, the Toronto Center for Phenogenomics, Children’s Hospital Oakland Research Institute (CHORI) and Charles River ).
Software Python package to automate building of ML pipelines by combining flexible expression tree representation of pipelines with stochastic search algorithms such as genetic programming.
Atlases enable alignment of individual scans to improve localization and statistical power of results, and allow comparison of results between studies and institutions. Set of multi subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque.
Nonhuman Primate Reference Transcriptome Resource
Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species.
Project to facilitate primate research by enabling neuroscience researchers to access collections either on-site or via the web for use in their own research programs. Collections of macaque brain tissue available to investigators worldwide to provide cost effective means for researchers to conduct de novo studies on non-human primate brain.
Pharmacogenetics of Nicotine Addiction Treatment
To identify role of pharmacokinetic and pharmacodynamic gene variation in nicotine dependence phenotypes, with focus on prospective smoking cessation and medication response.
Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility.
Delivering Agile Research Excellence on European e-Infrastructures
EU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously.
Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics.
Cryostat for routine histology and cryosectioning including critical applications such as Mohs surgery. Brain sectioning. Actively cooled quick freezing shelf with defrost function and refrigeration system are provided.
Epigenomics Workflow on Galaxy and Jupyter
Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter.
Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results.
Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes.
Bidirectional Encoder Representations from Transformers for Biomedical Text Mining
Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc.
Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge.
LabChart data analysis software creates a platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds. LabChart Reader is free version of software that allows to analyse with some limitations. LabChart Reader doesn’t allow saving of data - export image only. Has data pad for analysis.
Rotor-Gene real-time analysis software system for ROTOR GENE 6000 REAL-TIME PCR machine. Software has been refined to provide an intuitive, Wizard driven interface, enabling flexibility and automation. Build-in extensive analysis, graphing and statistical functions. Unlimited use software license for Windows XP, Pentium IV (2GHz) or higher PC.
Professional feed formulation software for Windows 10 and Macs by Agricultural Software Consultants Inc. Complete feed formulation solution for professional nutritionists and feed producers. Software offers ingredient databases for various domesticated and wild species.
variational Bayes single particle tracking
Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants.
Software tool to generate hints for Augustus in ab initio gene prediction using 2 step mapping by Gsnap.
Software tool as Autorun Evidence Modeler. Requires EVidenceModeler (aka EVM) software which combines ab into gene predictions and protein and transcript alignments into weighted consensus gene structures.
Software tool as pipeline to make anntotations using cDNA and CDS sequences.
Software tool as pipeline to map ATAC-seq data to large genome, for example, for wheat. It splits large genome files into parts and do mapping and then finally merge them.
Software tool as script used to design primers for homoeologs, to amplify either homoeolog specific or all homoeologs.
Open source software package as high performance computing imbalance aware machine learning tool for genome wide detection of pathogenic variants.
National research resource to provide interactive views of publicly available All of Us Research Program participant data including electronic health record data, biospecimens, surveys, and other measures taken at time of participant enrollment. Data platform will be open to researchers all over world and show data for groups of de-identified participants. Data is updated periodically.
Warning this group of python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain a bug. Please see PMID:31591889. Script A. Write a Gaussian input file for each structure (local minimum) obtained from operation I (write-g09-inputs.py and variants thereof that use different functional and basis set combinations). Script B. Check for redundant conformers or any that has an imaginary frequency (duplicate_conf_and_imag_freq-check.py). Script C. Extract the NMR shielding tensor for a DFT-computed reference compound of interest (get-ref-shifts.py). Script D. Perform the Boltzmann analysis to generate the weighted-averaged, referenced chemical shifts for each proton and carbon in the candidate structure (nmr-data_compilation.py).
Danish, privately owned company specializing in non-invasive stimulation systems for treatment of major depressive disorder and neuroscience research based on use of transcranial magnetic stimulation.
Japanese manufacturer of optics and reprography products specializing in microscopes and thermometers.
Repository to share analysis procedure, data and help readers or reviewers to know more detail of this work, reproduce or make use of results they are interested in.
Multichannel Illinois Institute of Technology and Rush University Aging atlas
Atlas for studies of older adult brain. Includes T1-weighted template of older adult brain and tissue probability maps. Exhibits high image sharpness, provides higher inter-subject spatial normalization accuracy compared to other standardized templates and similar normalization accuracy to well-constructed study-specific templates.
Software tool to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in web browser. To explore gene expression heatmap across cell types in datasets, search for genes of interest, explore tSNE visualization, colored by cell types or expression of genes of interest, visualize dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions, find cell type of interest in one visualization and see its characteristics in different visualization.Used for Allen Brain Map Cell Types Database to Browse Data: Human - Multiple Cortical Areas, and Mouse - Cortex and Hippocampus.
Federal University of Parana Center for Electron Microscopy core facility
Center for Electron Microscopy of the Federal University of Paraná
Laboratory to support scientific research in system of multi user operation of UFPR. Available equipment in electron microscopy.
Carl Zeiss Stemi SV6 Stereomicroscope. Manufacturer: ZEISS. Model: Stemi SV6 Stereomicroscope. This equipment is out of production. Available from the third party sellers.
Distributed Archives for Neurophysiology Data Integration
Free, cloud-based platform for publishing, sharing, and processing standardized neurophysiology data, primarily using the Neurodata Without Borders (NWB) format. Supported by the BRAIN Initiative, it enables researchers to collaborate, reuse datasets, and adhere to FAIR data principles.
Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data.
Software package provides interface from R to JAGS library for Bayesian data analysis. Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis.
Software tool for experimental design, sample size determination and analysis by Tempest Technologies.
Software tool to represent ontologies and data described using ontologies as Neo4j graph. Ontology serving middleware tool using Neo4J as base server, able to ingest ttl files, and serve them to quickly create services that can underpin autocomplete, term lookup and tree traversal.
Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits.
Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions.
Next Generation Genotype Imputation Service
Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping.
Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com.
Software tool to provide algorithms, functions, and apps for designing and testing computer vision, 3D vision, and video processing systems for MATLAB. You can perform object detection and tracking, as well as feature detection, extraction, and matching. For 3D vision, toolbox supports single, stereo, and fisheye camera calibration; stereo vision; 3D reconstruction; and lidar and 3D point cloud processing. Computer vision apps automate ground truth labeling and camera calibration workflows.
Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.
Consortium is investigating physical and functional organization of human islet tissue environment, cell-cell relationships within pancreatic tissue ecosystem, and contributions of non endocrine components (acinar, ductal, vascular, perivascular, neuronal, lymphatic, immune) to islet cell function and dysfunction. HPAC consists of research grants as well as the Human Pancreas Analysis Program (HPAP).
Software tool for screening papers for systematic reviews. Web and mobile app to help to expedite initial screening of abstracts and titles using process of semi automation while incorporating high level of usability.
Screen based eye tracker that combines high-speed capabilities at 500 Hz.
3DNA-Driven DNA Analysis and Rebuilding Tool
DNA structure modelling server. Web server for generating custom 3D structural models of DNA with control over local and global conformation.
Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure.
Yet Another Scientific Artificial Reality Application
Software tool to obtain structural guidance in biocatalytic investigations. Program for molecular visualising, modelling, and dynamics. Initial stage YASARA View is for free while higher stages YASARA Model, YASARA Dynamics, YASARA Structure require license fee. Program for Windows, Linux, MacOS and Android. YASARA View is available for free and contains all functions to explore macromolecular structure interactively.
Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers.
Software Python package bundling popular tasks in computational molecular biology, from sequence analysis to structural bioinformatics. Comprehensive library for computational molecular biology. Package features sequence and structure data analysis and editing functionality, support for common sequence and structure file formats, visualization capabilities, interfaces to external software (MSA software, BLAST, DSSP). Operating system(s): Windows, OS X, Linux.
Web based tool for annotating bioassay protocols using semantic web terms. Enables searching, sorting, clustering and analyzing of assays without needing to read through original text. Exploits Common Assay Template based on underlying vocabularies and semantic standards from BioAssay Ontology, Drug Target Ontology, Cell Line Ontology and others. Users can identify similar assays and examine similarity of assays between and within organizations.
Software Java tool for quantitative analysis of behavior. Used to address any theoretical problem that requires complex sequence of actions to be scored by human observer. Runs on microcomputer providing Java Virtual Machine[TM] and has been tested on Windows[TM] and Macintosh[TM] systems. Legacy version (version 0.9) works on older systems (Macintosh OS-9 and Windows-98), while Version 1.0 works well on Macintosh OS-X and Windows XP systems. JWatcher Video works best on Windows XP systems and has reduced functionality running in Macintosh OS-X. JWatcher-Palm can be used to acquire data on Palm OS[TM] equipped device and analyze it on your main computer.
Public research university based in Sydney, Australia, in suburb of Macquarie Park. Founded in 1964 by New South Wales Government, it was third university to be established in metropolitan area of Sydney.
Software toool as search engine for academic software. Used to get correct citation for diverse research products including, software, datasets, preprints, and traditional articles to help creators of such products get full credit for their work.
Network for Computational Modeling in Social and Ecological Sciences
Open community of researchers, educators, and professionals with goal of improving way we develop, share, use, and re-use agent based and computational models for study of social and ecological systems. Develops and maintains CoMSES Model Library, digital repository that supports discovery and good practices for software citation, digital preservation, reproducibility, and reuse.
Web based data management system that allows users to share, annotate, organize and analyze large collections of datasets. Software tool for creating some metadata about software tools automatically. Open source data management for long tail data. Provides support for extensible metadata annotation and distributed analytics for automatic curation of uploaded data. Open source software that can be customized and deployed on your own cloud.
Software repository for DOE funded software tools. DOE software services platform and search tool for DOE-funded code – DOE CODE. Provides functionality for collaboration, archiving, and discovery of scientific and business software. DOE CODE replaces OSTI old software center, Energy Science and Technology Software Center (ESTSC).US Department of Energy new open source software services and search platform for sharing research software between national institutes.
Code repository for all government funded software. Designed to support reuse and public access to custom developed Federal source code. It requires new custom developed source code developed specifically by or for Federal Government to be made available for sharing and re-use across all Federal agencies. Provides tools to help government and public collaborate on open source projects.
Data and software repository from CalTech.
California Institute of Technology; Pasadena; USA
Private doctorate granting research university in Pasadena, California. Known for its strength in natural science and engineering.
Registry for source codes of interest to astronomers and astrophysicists, including solar system astronomers, and lists codes that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. ASCL is indexed by SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net .
Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets.
Eastern Connecticut State University; Connecticut; United States
Public liberal arts university in Willimantic, Connecticut.
Repository of math software. Information service for mathematical software. Provides access to database of information on mathematical software and includes systematic linking of software packages with relevant mathematical publications. Database for references on mathematical software.
Software framework for performing benchmarks of machine learning classification algorithms. Containerized benchmarking tool for machine-learning classification of tabular data.
Software tool for chemical similarity enrichment analysis of metabolomics datasets. Used in studies to uncover biological mechanisms in organisms under genetic or environmental stress in system biology manner or finding risk factors for chronic diseases in exposome wise association studies using blood specimens. Allows users to realize pathway analysis.
Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields.
Molecular Transducers of Physical Activity Consortium Data Hub
National research consortium designed to discover and perform preliminary characterization of range of molecular transducers that underlie effects of physical activity in humans. Used to study molecular changes that occur during and after exercise and to advance understanding of how physical activity improves and preserves health. Six year program into mechanisms of how physical activity improves health and prevents disease led by NIH Office of Strategic Coordination, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute on Aging, and National Institute of Biomedical Imaging and Bioengineering.
New Enabling Infrastructure for Neuroscience Knowledge Graph
Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems.
Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together.
Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB.
Pipeline for reassigning primary contigs that should be labelled as haplotigs. Used for third generation sequencing based assemblies to automate reassignment of allelic contigs, and to assist in manual curation of genome assemblies.
Software tool for separation haplotigs from genome assembly. Method to separate haplotigs based on sequence similarity.
Software tool as modular command line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Used for interrogation of genome assemblies. Assists in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants.
Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates.
coNvex Gap-cost alignMent for Long Reads
Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection.
Software set of tools that facilitate overlapping, patching, correction and assembly of noisy long reads.
Software tool as de novo assembler for PacBio and Oxford Nanopore data. It produces assembly from all-vs-all raw read alignments without error correction stage. Allows to read overlapping, rescue missing overlaps, identify low-quality regions and chimaera and produce better consensus.
Software package for identification of long terminal repeat retrotransposons (LTR-RTs). Removes false positives from initial software predictions. Achieves very high specificity, accuracy, and precision without significantly sacrificing sensitivity, hence significantly outperforming existing methods. Can construct LTR libraries directly from self-corrected PacBio reads prior to genome assembly.
Software tool for computing genome assembly likelihoods.Computes likelihood of reads with respect to assembly and statistical model which can be used as metric for evaluating assemblies. Novel likelihood based approach to assembly assessment in absence of ground truth.
Recognition of Errors in Assemblies using Paired Reads
Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.
Open source web application that tracks progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. Allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted.
Miniaturized microscope that allows imaging from two brain regions. Integrates inertial measurement unit (IMU) and optogenetic LED driver. Used to perform dual miniscope recordings in multiple configurations and works with cross-platform software enabling operation on MSWindows, MacOS and Linux.
Laboratory of Analysis in Neurosciences Toolbox
Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB.
System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording.
Software for organizing and analyzing blot and gel images captured on iBright Imaging Systems. Available as desktop version PC and Mac OS compatible and cloud-based version accessible via web browser through Connect platform.
Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes.
24 channel mobile electroencephalographic recording system. Supports synchronization with other sensors and simultaneous multi amplifier streaming via labstreaming layer. Wearable device that features motion sensors so body and head movements can be detected.
Web based program for collating results generated by program STRUCTURE. Provides assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of number of genetic groups that best fit data. Reformats data for use in downstream programs, such as CLUMPP.It is complement for using software Structure in genetics population. Website and program for visualizing STRUCTURE output and implementing Evanno method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms.
Software tool to find restriction endonucleases. Helps restriction map nucleotide sequences. Tool with customizable interface, platform independent accessibility, interfaces to NCBI's GenBank, DNA sequence database, and NEB's REBase, and restriction enzyme database. In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including option of finding restriction sites that can be introduced into sequence by silent mutagenesis.
Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs).
Monkey Connectivity Based Parcellation; MonkeyCBP: A toolbox for connectivity-based parcellation of monkey brain
Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community.
Software tool as image and photo editor for PCs that run Windows. Features user interface with support for layers, unlimited undo, special effects, and variety of useful and powerful tools.
Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.
Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps.
Ligating Adjacent Chromatin Enables Scaffolding In Situ
Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies.
Pseudo Agent System for Transposable Elements Classification
Software tool for automatic transposable element classification. Used for searching for structural features and similarity to classify transposable elements.
Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species.
Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.
Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark.
Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format.
Dockerized environment for winning algorithm in 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3.
Software tool from 3DHISTECH Ltd. designed for work with whole slide images. Digital microscope application for supporting histopathological diagnostic workflow and microscope examination process. Advanced slide viewing software for Windows and Mac used in clinical pathology and research.
Portal for identifying genetic and pharmacologic dependencies and biomarkers that predicts them by providing access to datasets, visualizations, and analysis tools that are being used by Cancer Dependency Map Project at Broad Institute. Project to systematically identify genes and small molecule dependencies and to determine markers that predict sensitivity. All data generated by DepMap Project are available to public under CC BY 4.0 license on quarterly basis and pre-publication.
Web tool with systematic, objective means to critically evaluate journals, with quantifiable, statistical information based on citation data. Provides information about academic journals in natural sciences and social sciences, including impact factors in database integrated with Web of Science. Sourced from Web of Science Core Collection,citation index on Web of Science platform.
Data analytics company that operates a collection of services: Web of Science (EndNote, InCites, Journal Citation Reports, Publons, Kopernio), Cortellis, Derwent, Derwent World Patents Index, CompuMark, MarkMonitor, Techstreet, Publons, EndNote, Kopernio, and ScholarOne. Deliver critical data, information, workflow solutions and deep domain expertise to innovators everywhere.
Omics database for spaceflight experiments. Interactive, open access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Enables exploration of molecular network responses of terrestrial biology to space environment. Contains curated omics data, metadata and radiation dosimetry for model organisms. Supports standard guidelines for submission of datasets, MIAME for microarray, ENCODE Consortium Guidelines for RNA-seq and MIAPE Guidelines for proteomics.
Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications.
Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.
Language for representing scientific findings in life sciences in reusable, shareable, and computable form. Captures causal and correlative relationships in context, where context can include information about biological and experimental system in which relationships were observed, supporting publications cited and process of curation.
Software tool for reproducible bioinformatics that unifies workflow engines, package managers, and containers. Implemented as lightweight library on top of Nix deployment system. Bioinformatics workflows in functional Nix language.
Condor project maintains, distributes, and supports variety of computing systems that are deployed by commercial and academic interests world wide. Explores social and technical problems of cooperative computing on scales ranging from desktop to world wide computational Grid.
Software tool to automatically align sections to visualize brains in 3D. Assists with cell mapping, cytoarchitectonics and other areas requiring characterization of neuronal circuitry to create comprehensive anatomical reference. Automatically creates full resolution, 3D reconstructions of entire brain or any organ from serial sections of whole slide images. Allows to view cells, structures, and lesions, locate neurons expressing particular gene or visualize axonal projections of specific neurons with full anatomical context.
Stereo Investigator - Whole Slide Edition
Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses.
Stereo Investigator - Cleared Tissue Edition
Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses.
Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays.
Software tool as ultra fast, multi channel resonant scanning laser confocal microscope system for rapid 2D and 3D slide scanning, and cleared tissue imaging. System for imaging of slide mounted specimens and cleared tissue imaging. Utilizes strip mosaic scanning process to rapidly and accurately collect fluorescent image data while stage moves specimen continuously in y-axis.
Software tool for dendritic spine analysis that enables to visualize and quantify spine morphology over time. After loading image data acquired at different time points from in vivo and in vitro imaging sessions, automatically aligns images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics such as length, thickness, and overall number, for accurate quantitative comparison.
Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program.
Software tool to dig out more robust and reliable differentially expressed genes between two groups. Samples from different groups will be re-sampled randomly associated with total number of samples.
Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more.
Pipeline for Environmental DNA Metabarcoding Analysis
Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution.
Software tool for identifying hub objects and sub-networks from complex interactome. Predicts and explore nodes and subnetworks in given network by several topological algorithms. Provides interface to analyze topology of protein-protein interaction networks, such as human, yeast, rat, mouse, fly etc. Plugin works with Cytoscape 2.6 or above, which requires Java 1.5 or above.
Spreadsheet program included as part of free, web-based software office suite offered by Google within its Google Drive service. Service also includes Google Docs and Google Slides, word processor and presentation program respectively.
Genetic Algorithm for Demographic Model Analysis
Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data.
Institute for Systems Biology Cancer Genomics Cloud
Web tool as flexible cloud-based platform for cancer genomics research. Platform that serves as large-scale repository and provides computational infrastructure necessary to carry out cancer genomics research at unprecedented scales. ISB-CGC is providing access to TCGA data and computation on Google Cloud Platform.
Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.
Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.
Open source software package for R programming language that is used to acquire chemical information from online data sources. Package contains functions that allow programmer to interact with webpages and APIs to retrieve chemical information.
Rhode Island INBRE Molecular Informatics Core Facility
Rhode Island INBRE Molecular Informatics
RI-INBRE Bioinformatics Core; RI Genomics and Sequencing Center
Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research.
Vermont University Genetics Network Bioinformatics Core Facility
Vermont Genetics Network Bioinformatics Core
Core provides expertise in biostatistics, microarray data analysis, proteome informatics, next generation sequencing data analysis, functional analysis, database development and information technology, including data storage infrastructure and high performance computing. Working closely with VGN Proteomics Facility, offers investigators experimental design consultations, comprehensive data analysis, data management and publishing, and manuscript and grant support. Core personnel also engage in teaching and training activities for data analysis and compute resources necessary for VGN network investigators. Our goal is to provide network researchers with bioinformatics expertise.
New York State Advanced Genomic Technology Core Facility
Advanced Genomic Technologies Cluster provides next-generation sequencing and Sanger sequencing. Next-generation sequencing services are provided using Illumina MiSeq and NextSeq sequencers. Services are available for amplicon re-sequencing, viral or microbial whole genome sequencing and 16S microbiome sequencing. Sanger DNA Sequencing can be performed on DNA templates such as PCR products and plasmids using ABI 3730xl and ABI3130xl instruments.
Vermont University Center for X-Ray Crystallography Core Facility
Core for high resolution structural biology at the University of Vermont. X-ray crystallography allows biological and biomedical researchers to visualize proteins, RNA, DNA and their complexes at atomic resolution. The molecular details of specimens as small as DNA binding domains and as large as the ribosome have been elucidated via this powerful method. The CXX provides resources for all stages of macromolecular structure determination.
Yale University DNA Analysis on Science Hill Core Facility
Core supports DNA Sequencing of PCR, Plasmid, BAC and Fosmid templates, Fragment Analysis of Microsatellites, AFLP, t-RFLP, SHAPE Experiments and Human Cell Line Authentication.
Brown University Transgenic and Gene Targeting Core Facility
Mouse Transgenic and Gene Targeting Facility
MTGTF is to support the investigators in using genetically modified mouse models in Brown University, affiliated hospitals and academic institutions in Rhode Island and other states. Provides services of molecular design and generation of transgenic and knock-out mouse models as well as general advice on use and management of such models. Conventional ES cell gene-targeting system is employed to serve as alternative or to fill the limitations of CRISPR/Cas9 system. Routine services include genotype analysis, sperm or embryo cryopreservation and storage, rederivation, in vitro fertilization (IVF). Other services, such as mouse vasectomy, embryo transfer, colony scale-up, intracytoplasmic sperm injection (ICSI) are also available. New services requiring MTGTF resources can be created through request.
Memorial Sloan Kettering Cancer Center Antibody and Bioresource Core Facility
ABCF can provide MAbs from established hybridomas for RESEARCH PURPOSES ONLY, can assist in generating MAbs, offers a weekly mycoplasmal contamination screening service for tissue culture samples, distributes cell lines developed at Memorial Sloan Kettering Cancer Center and Rockefeller University.
NYU School of Medicine Rodent Genetic Engineering Laboratory Core Facility
New York University Langone Medical Center Rodent Genetic Engineering Laboratory
New York University School of Medicine Langone Health Rodent Genetic Engineering Laboratory Core Facility
NYU Langone Rodent Genetic Engineering Laboratory
Core to apply advanced molecular genetic techniques in rodent models of physiology and disease. Generates novel mutant mouse strains by using gene targeting in embryonic stem cells (ESCs) and by developing novel methods of modifying rodent genomes and assaying genetically modified cells in vivo.Offers sperm and embryo cryopreservation and storage technologies for strain preservation and recovery.
Weill Cornell Medical College Microscopy and Image Analysis Core Facility
Microscopy and Image Analysis Core Facility
Core sassist users with all their microscopic imaging needs, from the conception of idea, to final image analysis and presentation. Offers regular widefield microscopes for fluorescence and brightfield imaging, laser scanning microscopes (confocal and multiphoton), super-high resolution microscope (Zeiss Airyscan), automated high content optical microscopy, and electron microscopy.Provides access to several image analysis software packages, and image analysis workstations that are optimized for handling large amounts of imaging data. Available software include MetaMorph, MetaXpress and Imaris, Fiji/ImageJ.
Rockefeller University Flow Cytometry Resource Center Core Facility
Core offers researchers multi laser and multi color flow cytometry sorters and analyzers, including spectral and imaging flow cytometers.
Albany University RNA Epitranscriptomics and Proteomics Resource Core Facility
RNA Epitranscriptomics and Proteomics Resources
Resource offers range of mass spectrometry instrumentation, expertise in analysis of RNA, RNA modifications, and proteins involved in RNA metabolism/regulation, supports projects involving analysis of biomolecules, metabolites, and small synthetic molecules, provides consulting on experimental design, sample preparation and data interpretation, whole project development and grant writing contributions.
University of Delaware CBCB Bioinformatics Data Science Core Facility
Center for Bioinformatics and Computational Biology Bioinformatics Core
CBCB Bioinformatics Data Science Core builds upon infrastructure of the Center for Bioinformatics and Computational Biology. Delaware Biotechnology Institute , Delaware Data Science Institute, and Protein Information Resource. Core helps with planning your research or analyzing your current data. Services:Consultation and Collaboration, Proposal Assistance,Training, Bioinformatics Software, Computational Hardware, Database and Web Services, Next Gen Analysis, Custom Analysis.
McGill University Advanced BioImaging Facility (ABIF)
McGill University Advanced BioImaging Core Facility
Core offers light microscopy platforms providing guidance to researchers with their projects from sample preparation to data analysis, expertise in cellular imaging including live cell imaging, FRAP, Fluorescence Lifetime Imaging Microscopy (FLIM), FRET, FCS, image correlation spectroscopy, TIRF, spectral imaging, lattice lightsheet, stimulated emission depletion (STED), high content screening, cellular image analysis, and custom image analysis, consultations, image processing, image analysis and preparation of data for publication.
Connecticut University Health Center Flow Cytometry Core Facility
Facility provides flow cytometric analysis and cell sorting services. Located on 6th floor of E building in room E6014, consists of lab space, complete with fume hood, centrifuge, and sink space and has instruments available for cellular analysis and cell sorters.
Massachusetts University Medical School Xray Crystallography Core Facility
Core provides instrumentation for determination of crystal structures using X-ray diffraction techniques. System in Biotech II is comprised of RU300HR X-ray generator, Osmic optics, MAR Image Plate System and Oxford liquid nitrogen cryogenic crystal cooler. LRB includes MicroMax-007 HF Microfocus rotating anode X-ray generator, Osmic optics and Saturn HG CCD detector mounted on AFC11 4-axis goniometer. Sample crystals can be cooled to -180˚C with CSCOBRA Cryogenic system. This system permits very rapid and accurate diffraction data collection.
Albert Einstein College of Medicine Analytical Imaging Core Facility
Analytical Imaging Facility provides state of art methods in modern light and electron microscopy imaging to biomedical scientists with all levels of expertise. Available techniques include Electron microscopy: TEM, SEM, and sample preparation , Light microscopy: confocal, multiphoton, fluorescence, and bright-field imaging , Image analysis: Volocity, Imaris, Imod, Quant Center and ImageJ.
Massachusetts University Medical School Bioinformatics Core Facility
Core to evaluate, select, and implement computational solutions for analysis of biological data.
Massachusetts University Medical School Deep Sequencing Core Facility
Facility offers high throughput sequencing and library building services for UMass campuses and outside customers. Operates several types of Illumina next gen sequencers, and is closely integrated with PacBio Core Enterprise and Molecular Biology Core Labs.
Genome Quebec Center of Expertise and Services
Core for full DNA and RNA analysis services. Canada's largest integrated provider of sequencing, genotyping and biochips services. Offers scientific community around the world genomic services in support of research in human health, agrifood, forestry and sustainable development.
Massachusetts University Medical School Machine Shop Core Facility
Core includes three shops: Custom Machine, Harvard Medical School SEAS Scientific Instrument and WPI Manufacturing Labs. Service include consultation, design, manufacturing, modifications, and instrument repairs.
Massachusetts University Medical School Drosophila Resource Core Facility
Facility provides labs with media necessary for Drosophila research. Includes Low Yeast Brown Food, High Yeast Brown Food, and Yellow Food media available in narrow vials, wide vials, and bottles.
Massachusetts University Medical School Morphology Core Facility
Histology lab that provides histology services in support of investigators at UMass Medical School, including routine histological preparations,special stains,immunohistochemistry,frozen sections.
Massachusetts University Medical School RNAi Core Facility
Facility houses complete collections of human and mouse lentiviral short hairpin RNA (shRNA) libraries from Open Biosystems/GE Dharmacon, Mammalian Gene Collection (MGC) cDNA Library, and human and mouse CRISPR/Cas9 GeCKO v2 libraries from Addgene.
Massachusetts University Medical School Radio Labeling Small Animal Translational Imaging Core Facility
UMMS Radio Labeling Small Animal Imaging Core Facility
Core provides consultation services to assist researchers in designing imaging studies, limited labeling services and data acquisition and analysis.Core offers following services:Single Photon Computerized Tomography (SPECT),Positron Emission Computerized Tomography (PET), X-Ray Computerized Tomography (CT),NIR Optical Imaging of small animals.
Massachusetts University Medical School Transgenic Animal Modeling Core Facility
Core to produce genetically modified mice, rats, and stem cells for the UMMS Scientific Community.Composed of two facilities: Animal Modeling Facility and Gene Targeting and Stem Cell Facility.
Maine Medical Center Research Institute Proteomics and Lipidomics Analysis Core Facility
Core provides protein and small molecule structural and functional analysis, and quantitation using technologies and software applications. Services in Nano-liquid chromatography,Protein identification and quantitation using SWATH,Protein post translational modification identification,Lipid profiling and identification (MS/MSALL),Targeted multiple reaction monitoring (MRM) for lipids.
University of Texas MD Anderson Cancer Center Proteomics Core Facility
Facility provides mass spectrometry analysis of proteins. Provides access to mass spectrometry based proteomics technologies and services including Protein Identification, Molecular Weight Determination, Quantitative Protein Analysis, Post-translational Modification Analysis, LC or LC-MS Analysis, Equipment Usage, Additional Data Analysis:Bioinformatics, statistics, pathway analysis and Assistance preparing materials for manuscripts or grants.Consultations for custom assays for other MS Services are also available.
Rockefeller University Structural Biology Resource Center Core Facility
Core for protein expression and purification as well as all equipment needed for determination of three dimensional structures of biological macromolecules via X-ray crystallography. Houses Rigaku/MSC microMax 007HF generator for X-ray diffraction data collection, equipped with Varimax optics, X-stream 2000 cryosystems and two RaxisIV++ detectors.Also available is stereomicroscope, Nikon SMZ18, for crystal tray observations and crystal mounting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University of North Dakota School of Medicine and Health Sciences Imaging Core Facility
Provides advanced instrumentation for researchers interested in investigating biological processes at cellular, sub cellular and molecular level.Instrumentation include Confocal Microscope Systems :Zeiss LSM-510 Meta Confocal Microscope, Olympus FV1000 MPE Basic Multiphoton Microscope;Brightfield/Fluorescence: Nikon Eclipse TE300 (inverted) Fluorescent Microscope, Nikon Eclipse 80i (upright) Fluorescent Microscope, Leica Thunder Imager; TIRF Systems:Olympus TIRF Microscope; Transmission Electron Microscopy:Hitachi 7500 TEM, RCM MTX Ultramicrotomes;Scanning Electron Microscopy:Hitachi 4700 Field Emission SEM, Denton Desk II Sputter and Turbo-sputter Coaters.Light and electron microscopic facilities, complete with ancillary support equipment, are located in close proximity to each other within suite of rooms housed in medical school.
Idaho University IBEST Computational Resources Core Facility
Provides evolutionary and computational biology investigators with computing and large data storage capacity for use in analyzing and managing large volumes of research data. Core contains advanced mix of high performance computing clusters, servers and data storage components, knowledge and technical skills required to compress years of analysis into days.
Beth Israel Deaconess Medical Center Mass Spectrometry Core Facility
Provides servies in mass spectrometry, proteomics, metabolomics and lipidomics. Services include Thermo Orbitrap Elite and Thermo QExactive HF Orbitrap microcapillary LC-MS/MS:Protein identification, Post-translational modification site mapping,Relative quantification: Label-free, SILAC, TMT, etc.;AB/SCIEX 5500 QTRAP LC-MS/MS:Polar metabolomics profiling,13C/15N metabolic flux analysis;Thermo QExactive Plus/HF Orbitrap LC-MS/MS:Untargeted Lipidomics profiling, Untargeted Metabolomics Profiling.
Nebraska University Medical Center Flow Cytometry Research Core Facility
Provides central location for flow cytometry instrumentation and education. Services include Flow Cytometry,Cell sorting, data analysis, training. Software packages to analyze data include ModFit LT, BD FACSDiva v6, Cell Quest Pro, and FlowJo vX, from facility workstations.
MIT KIICR Biopolymers and Proteomics Core Facility
KI Swanson Biotechnology Center Biopolymers and Proteomics Core Facility
Facility provides integrated synthetic and analytical capabilities for biological materials, including proteins, peptides, and nanoparticles, range of technical expertise and instrumentation. Access is available to all members of MIT community. Priority access is given to KI members, NCI-funded research projects and other contributing user groups in recognition of funding support. In special circumstances, access may be available to non-MIT users.
West Virginia University Flow Cytometry and Single Cell Core Facility
WVU Flow Cytometry and Single Cell Core Facility
Facility provides instrumentation and scientific support for single cell analysis and sorting. Routinely performs analysis of both eukaryotic and prokaryotic cells for expression of intracellular and extracellular proteins, cell cycle, cell proliferation, cytokine production, and cell sorting based on expression of cell surface antigen(s) and/or expression of genetically engineered intercellular fluorescent proteins.
Maryland University Proteomics Core Facility
Facility is equipped withThermoFisher Orbitrap Fusion Lumos Tribrid mass spectrometer that is interfaced to Dionex Ultimate3000 RSLCnano HPLC system. Facility also maintains 2 separate data stations dedicated for proteomics data processing, database searching, and generation of reports.
University of California Davis DNA Technologies and Expression Analysis Core Facility
DNA Technologies and Expression Analysis Core at the UC Davis Genome Center
Genomics and transcriptomics core at the UCD Genome Center provides high throughput sequencing, genotyping, single-cell multi-omics and spatial transcriptomics services, training and consultation. Initial consultations are free. The lab uses liquid handling robots to minimize sample handling variation and to provide fast turnaround times.
Arkansas University College of Medicine Flow Cytometry Core Facility
Biopolymers and Proteomics Core Facility
Core provides flow cytometry instrumentation and analysis. Instruments include Fortessa, FacsAria and Image Stream.
Zurich University Functional Genomics Center Core Facility
Laboratory performs services in proteomics, genomics and metabolomics by FGCZ personnel without need for user to access labs. Services include Proteomics:Protein identification,quantification,characterization,Glycan/glycoprotein analyses, Analysis of Biomolecules, Fractionation; Genomics:DNA sequencing, RNA sequencing; Metabolomics/Biophysics services.
South Dakota University SD BRIN Proteomics Core Facility
Core provides proteomics services to researchers from South Dakota and the surrounding region to rapidly analyze and identify protein expression patterns in their experimental systems.Develops experimental design, protocols, data analysis and interpretation.Provides consulting and advice in grant proposal, as well as data preparation to be submitted to proteomics journal according to requirements.Offers training in use of common equipment such as scanner, spot cutter, imaging software, technique and protocol issues, and sample preparation.
West Virginia University Transgenic Animal Core Facility
Core serves as central molecular biology resource for conception and execution of new projects and provide resources to help offset high costs of developing genetically engineered mice. Ensures better quality control, turn-around time, and cost effectiveness than commercially available services. TACF staff is available for education, assistance and consultation during all stages of project development and production.Serves research staff at West Virginia University, Blanchette Rockefeller Neuroscience Institute and National Institute of Occupational Safety and Health.
Rensselaer Polytechnic Institute Center for Biotechnology and Interdisciplinary Studies BioImaging Core Facility
Core provides equipment with support of research technicians. Research animals are cared for in transient housing rooms. Multiple anesthesia systems and telemetry equipment are available. All procedures are reviewed by Rensselaer Institutional Animal Care and Use Committee (IACUC) and attending veterinarian. Fully outfitted sample and subject preparation workspaces also are available. Additional fees may be incurred for bioresearch animal technician assistance.
Delaware Biotechnology Institute Protein Characterization Core Facility
Facility consists of a Beckman Coulter ProteomeLab XL-I analytical ultracentrifuge is configured with a scanning UV/Vis detection system and Rayleigh Interference Optics. Used to characterize variety of biophysical properties of macromolecules such as molecular weight, sedimentation coefficient, diffusion coefficient, equilibrium constant and stoichiometry. Can assess sample heterogeneity (aggregation and purity), molecular conformation (folded or unfolded), composition (assembled or unassembled) and thermodynamic properties of interacting systems. Provides spectrum of data for protein characterization in solution.
Columbia University Quantitative Proteomics and Metabolomics Core Facility
Quantitative Proteomics and Metabolomics Center
Core provides identification of proteins and metabolites with differential quantitative expression in cells, tissues or in protein affinity purifications. Particular emphasis is on quantitative analysis of posttranslational modifications such as phosphorylation.
Duke University Sequencing and Genomic Technologies Core Facility
Duke Cancer Institute Sequencing and Genomic Technologies Shared Resource
Basic research oriented core provides genomic services.Services include Next Generation Sequencing Solutions,DNA and RNA sequencing, Illumina, PacBio, NGS Library preparation including single-cell RNA-seq, Nucleic Acid Extraction Services, total RNA extraction from blood samples in PAXgene tubes, total RNA extractions from cell pellets and miRNA extraction from serum/plasma.
Kansas University at Lawrence Protein Production Group Core Facility
Core focuses on cloning, expression and purification of prokaryotic and eukaryotic proteins for COBRE and other investigators in Kansas and region. Laboratory maintains equipment to support production of properly folded proteins in quantities suitable for structural studies (X-ray and NMR), functional studies (catalytic or biological), label-free binding studies (SPR) and/or high throughput (HTP) screening studies.
Kansas University at Lawrence Synthetic Chemical Biology Core Facility
Core provides synthetic chemistry expertise. Includes novel and commercially unavailable small molecules, fluorescent molecules and peptides. Assists in identifying hits for medicinal chemistry optimization in infectious disease targets and provides synthesis capabilities for structure activity studies. Core staff will work with investigators to design and synthesis novel molecular probes. Core provides access to model organism Danio rerio (zebrafish), and allows investigators to image embryonic and adult zebrafish treated with molecular probes for phenotypic drug discovery and other projects, encompasses Purification and Analysis Laboratory that provides purification, analysis and quality control of compounds via HPLC-MS, utilizes automated mass directed fractionation for purification in both reversed and normal phases (including chiral separations), provides relative purity analysis by UPLC coupled to high-resolution mass spectrometer for structure confirmation.
Kansas University at Lawrence Applied Bioinformatics Laboratory Core Facility
Molecular Graphics and Modeling Laboratory
Research oriented service laboratory providing informatics support to research community. Services include data analysis and mining in proteomics, genomics and chemistry, systems biology approaches such as pathway, network and interaction analyses, large scale statistical and machine learning studies, protein structure, function and stability prediction, sequence and domain analyses,d esign and implementation of relational databases and software programs, consultation on experimental design involving data acquisition, management and analysis, report, grant, and manuscript preparation.
Kansas University at Lawrence High Throughput Screening Laboratory Core Facility
High Throughput Screening Laboratory at KU
Core offers high throughput screening of large chemical libraries of compounds to identify novel chemical entities that target biological system of interest.Provides target identification and validation, assay development, high throughput screening, hit confirmation, data mining and medicinal chemistry to facilitate hit to lead development.
Hawaii University School of Medicine Mouse Phenotyping Core Facility
Core provides murine echocardiography, blood pressure determinations, surgical procedures and phlebotomy, as well as assistance with mouse husbandry and genotyping.
Darthmouth College Electron Microscope Core Facility
Provides electron microscopy services for faculty, staff and students of Dartmouth College community, including College, Thayer School of Engineering, Dartmouth Medical School, and Dartmouth-Hitchcock Medical Center. Provides training about how to use instruments and service assistance available for those unable to spend time on microscopes, and for processing of biopsy samples from DHMC.
Nebraska University Medical Center Mouse Genome Engineering Core Facility
UNMC Mouse Genome Engineering Core Facility
Core Facility provides expertise and advice for experimental design of transgenic or gene knockout experiments, including DNA construct production and genotyping assays, makes reagents available for generation of transgene or gene targeting constructs, and performs all experimental aspects, which include pronuclear injection of transgene constructs, generation of recombinant mouse ES cells, blastocyst injection, and embryo transfer surgeries, for generation or rederivation of genetically manipulated mouse strains. Transgenic founder mice or chimeric animals with targeted alleles are then transferred to individual investigator for analysis.
Darthmouth Geisel School of Medicine DartMouse Core Facility
Core dedicated to facilitation and development of congenic mice for pre clinical projects across United States. Provides genotyping, background checks to verify purity of mice DNA.
Wisconsin-Madison University Biotechnology Center Gene Expression Center Core Facility
Core provides RNA library preparation services for Illumina, PacBio and Oxford Nanopore sequencing platforms. Single Cell RNA and Spatial Transcriptomics services are available with 10X Genomics technology. Provides RNA extraction, RNA QC and SNP genotyping and methylation bead array services. Provides support from project design through downstream analysis.Service facility, from hypothesis to publication.Microarray: expression and genotyping Affymetrix, Agilent, Nimblegen. Sequencing: RNA, gDNA, ChIP, Capture, 16SNovaSeq, HiSeq 2500, 3000, MiSeq.
Wyoming University Jenkins Microscopy Core Facility
Core to assist researchers and students in their imaging needs of fluorescence and electron microscopy and to increase use of microscopes in science education. Consultation, training or touring facility is also available by appointment.
Wisconsin-Madison University Biotechnology Center DNA Sequencing Core Facility
Core provides sequencing resources. Service support for Illumina Next Generation and Sanger sequencing projects, from project design and sample preparation through downstream analysis. Provides DNA extraction, SNP genotyping, and fragment analysis services, and can facilitate custom projects upon request.
Chicago University Cytometry and Antibody Technology Core Facility
Cytometry and Antibody Technology Core Facility
Core offers services in cytometry and antibody technology, helps to design projects, data acquisition, analysis and/or interpretation beyond routine practices,critical drafting and/or revision of manuscript for intellectual content purposes.
University of Nevada at Reno Nevada Proteomics Center Core Facility
Core offers mass spectral proteomic analysis. Assists with qualitative and quantitative characterization of proteins in biological matrices such as plasma/serum, tissue, cell lines and other biological material to gain understanding of physiological pathways, molecular interactions and regulatory signaling.
Vermont University Vermont Advanced Computing Core Facility
Core provides access to computing infrastructure while offering technical support. Provide tools and instruction allowing for inclusion of high performance computing in classroom.
University of Illinois at Chicago Electron Microscopy Core Facility
Core provides electron microscopy imaging and analytical characterization, surface analysis by XPS or Raman, access to instrumentation, training, and service for using scanning (SEM), transmission (TEM) and scanning transmission (STEM) electron microscopy, surface analysis and vibrational spectroscopy, specimen preparation.
Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas.
Northwestern University Behavioral Phenotyping Core Facility
Facility dedicated to help to determine behavioral effects of genetic manipulations, potential pharmaceuticals, aging, and other manipulations upon normal behavior, and learning and memory capacities of rodents used as model systems. Provides mouse and rat stereotaxic surgery, helps design behavioral studies.
Northwestern University Cancer Center Flow Cytometry Core Facility
Robert H. Lurie Comprehensive Cancer Center Flow Cytometry Core Facility
Provides 6 cell sorters and 5 benchtop analyzers. Helps investigators to define their projects in the early stages of development to make optimal and efficient use of flow cytometry. Educates ALL users (faculty and staff) in the science and technology of flow cytometry.
Northwestern University Biological Imaging Core Facility
Northwestern University Biological Imaging Facility
Shared use and training facility. Servies include Confocal Laser Scanning Microscopy, DIC (Differential Interference Contrast Microscopy), FCS (Fluorescence Correlation Spectroscopy), FLIP (Fluorescence-Loss-In-Photobleaching), FRAP (Fluorescence Recovery After Photobleaching),FRET (Fluorescence/ Forster Resonance Energy Transfer),Live-cell Imaging,Phase Contrast Microscopy,Widefield Fluorescence Microscopy,Image Processing and Analysis. Services include poster printing, and specimen preparation. Provides training for most instruments. Instruments include Leica DM6B Fluorescent Microscope (Hogan 5-112), Leica TCS SP8 Confocal Microscope (Hogan 5-128),Leica SP5 II Confocal Microscope (Hogan 5-114),Leica Spinning Disk Confocal Microscope (Hogan 5-113),DeltaVision Deconvolution Microscope (Hogan 5-111),Olympus IX83 Inverted Fluorescent Microscope (Silverman Hall 1-567),Olympus IX53 Inverted Color Microscope (Silverman Hall 1-567), LionHeart Automated Microscope BioTeck (Hogan 5-110).
Northwestern University Mary Beth Donnelley Clinical Pharmacology Core Facility
Mary Beth Donnelley Clinical Pharmacology Core Facility
Core provides quantitative mass spectrometry based support for in vitro studies and both preclinical and clinical studies of variety of small molecules, including cancer chemotherapeutic agents, analgesics, and antidepressants. Expertise includes optimizing design, conduct, analysis, interpretation, and reportage of pharmacokinetic studies. Helps with biological sample preparation, quantitative mass spectrometric drug concentration measurement, and drug concentration versus time data modeling. Small molecule concentrations in plasma and other body fluids are measured using Sciex 6500 QTrap with UPLC and nano LC or an Agilent HPLC system linked to Applied Biosystems API 3000 triple quadrupole mass spectrometer after sample preparation by, for example, solid-phase extraction. Drug concentration versus time relationships are fitted to various compartmental pharmacokinetic models using commercially available and specialized software.
Northwestern University School of Medicine Lurie Cancer Center Pathology Core Facility
Centralized, comprehensive, core laboratory providing histology, immunohistochemistry, molecular analysis and extraction and microscopic evaluation services for human tissue-based studies. Serves integral marker studies that require biomarker-based treatment arm assignment. Performs procurement of fresh biospecimens for clinical trials and biobanking.
Northwestern University Center for Atom Probe Tomography Core Facility
Northwestern University Center for Atom-Probe Tomography
Facility specializes in high resolution chemical imaging by three dimensional atom probe tomography. APT produces three-dimensional (3D) atom-by-atom elementally and isotopically resolved image with sub-nanometer spatial resolution of sample volume typically 100 x 100 x 300 nm^3, by simultaneous high resolution direct-space imaging and atom-by-atom time of flight mass spectrometry. APT is particularly suited to study nano- or nanostructured materials.
Northwestern University School of Medicine Transgenic and Targeted Mutagenesis Laboratory Core Facility
Transgenic and Targeted Mutagenesis Facility
Shared resource designed to produce genetically engineered mice for investigators.
Northwestern University Quantitative Bulk-Elemental Information Core Facility
Provides imaging and quantification instrumentation for analyzing metal quotas at scales ranging from subcellular level to entire ecosystems shaping global biogeochemical cycles. Instruments are capable of quantitatively imaging biologically essential elements in individual cells. Used for research in co-evolution of microbial and eukaryotic life within broad range of challenging chemical environments. Services including instrument training, sample preparation and analysis, experiment design, and grant proposal assistance.
Hunter College Digital Bio-Imaging Core Facility
Core provides access to instruments, ranging from simple white light wide field microscopes to fluorescent multidimensional super resolution and confocal imaging systems. Provides expertise in areas of microscopy including laser scanning confocal microscopy, super resolution microscopy, two photon microscopy. Helps with image analysis software packages, including, Imaris, Volocity, Autoquant, MetaMorph, and NIS-Elements.
Texas University Health Science Center at San Antonio Biomolecular NMR Core Facility
Core offers high field NMR instrumentation for structural studies of biological macromolecules. Instrumentation includes four-channel Bruker Avance 500, 600, and 700 MHz NMR spectrometers, ultra high sensitivity 5mm 1H-13C-15N triple-resonance cold probe for 600 MHz spectrometers. Service include acquisition and analysis of required spectra for elucidation of small molecule structures (includes synthetic molecules, natural products, cofactors, lipids, and short peptides (30 amino acids or less)). Types of projects conducted collaboratively include determination of three-dimensional structures of biological macromolecules, including proteins and nucleic acids, both alone and as complexes with various ligands.
Stowers Institute for Medical Research Molecular Biology Core Facility
Core services include DNA sequencing, site directed mutagenesis, genome engineering (TALENs & CRISPRS), plasmid preparations and distributing clones/vectors from in house collections. Supports real time quantitative PCR through instrument training, troubleshooting and experimental design. Stowers researchers also have access to Illumina Next Generation Sequencing technology. Constructs libraries, performs sequencing and assists with high throughput genome sequencing, RNA-seq and ChIP-seq projects. Utilizes liquid handling and colony manipulation robots to automate many of services. Provides automation expertise and collaborate with researchers on custom automation projects.
Iowa State University Genomic Technologies Core Facility
Provides expertise and equipment to conduct high throughput research. Services and equipment include:Next Generation Sequencing Services,Ion Torrent Proton sequencing,High Throughput Nucleic Acid Manipulation,Qiagen BioSprint 96 high-throughput DNA/RNA extraction system,Eppendorf AF2200 Plate Reader (absorbance and fluorescence based quantification),Lyophilization and Tissue Grinding,PCR Instruments,Two MJ Research 384 well 4 block DNA engine tetrads,Two Applied Biosystems 384 well 2 block Gene Amp PCR,Roche Lightcyler 480 RealTime thermocycler,Miscellaneous Services and Instruments,Blue Pippin and E-gel size selection systems,Agilent Bioanalyzer,Eppendorf epMotion M5073 liquid handling system.
University of Missouri Genomics Technology Core Facility
University of Missouri Genomics Technology Core
Core research facility providing services in high-throughput DNA sequencing that includes staff experience in the construction of libraries for targeted amplicons, miRNA analysis, transcriptome profiling (RNA-Seq), whole exome sequencing (WES), epigenomic and genomic DNA analysis. Services in single cell library preparation are available using the 10x Genomics Chromium X system. In addition, spatial transcriptomics services using Visium HD arrays are provided. The GTC maintain and operate Illumina sequencing platforms; NovaSeq X Plus and MiSeq i100 instruments.
Northwestern University Micro/Nano Fabrication Core Facility
Northwestern University micro/nano fabrication facility
NUFAB Northwestern University micro/nano fabrication facility
Central micro/nano fabrication facility of Northwestern University. Provides range of nanofabrication equipment and technical expertise. Supports research in all areas of science, engineering, medicine, and interdisciplinary fields.
Iowa State University Office of Biotechnology Protein Core Facility
Protein Facility of the Iowa State University Office of Biotechnology
Core offers protein/peptide sequencing, large and small scale peptide synthesis (Fmoc), matrix assisted laser desorption/ionization (MALDI) mass spectrometry, SDS-PAGE/electroblotting, 2-D gel electrophoresis, isoelectric focusing (IEF), in-gel and solution digestion, tandem mass spectrometry (LC-MS/MS), ion mobility mass spectrometry (IM-MS), digital image acquisition and analysis using Typhoon imaging system and 2D gel documentation/analysis system, and semi-preparative, analytical and micro-analytical high performance liquid chromatography (HPLC). MALDI, HPLC, SDS-PAGE/blotting, IEF, 2D gel electrophoresis, 2D gel documentation/analysis and Typhoon imaging system are all available for user operation after appropriate training.
Brigham Young University College of Life Sciences DNA Sequencing Center
Brigham Young University DNA Sequencing Center
Core services include Custom DNA Sequencing (3730xl for dideoxy sequencing chemistry, or Illumina HiSeq 2500 for large scale sequencing projects),DNA Fragment Analysis,Sequencing and PCR troubleshooting and training,SNP analysis,Primer walking, Contig assembly and editing.
Boston University Microarray and Sequencing Resource Core Facility
Boston University Microarray & Sequencing Resource
Core provides analysis of gene expression using Affymetrix GeneChip platform. Offers next generation sequencing via Illumina NextSeq and Ion Torrent PGM and Proton instruments, analysis of RNA and DNA using Agilent Bioanalyzer.
Donald Danforth Plant Science Center Tissue Culture and Transformation Core Facility
Plant Tissue Culture and Transformation Facility
Facility operates as full service facility delivering transgenics and cell cultures to researchers and self service facility providing high quality space for researchers to use for their own specific project needs. Services available include transformations and cell/ tissue culture in many different plant species, project consultation, training workshops, self-service hood usage and offering high quality growth space. Facility staff has developed portfolio of transformation and tissue culture systems such as: Setaria, tobacco, petunia, tomato, Arabidopsis, soybean, Indian mustard, maize, rice and various different cell cultures. Within the facility, researchers have also produced cassava, sweet potato, and potato. Transformation systems will be added, developed, inherited, or modified as needed.
Buffalo University Genomics and Bioinformatics Core Facility
Core sequencing services include Illumina Sequencers, Single-Cell RNA-Seq,Single-Cell Immune Profiling,Single-Cell ATAC-Seq,Linked-Read Sequencing. Provides bioinformatic analysis including Single-Cell RNA Analysis,Linked-Read Genome Analysis,ChIP-Seq Analysis Package,RNA-Seq Analysis Package,miRNA Analysis Package,Custom Project Requests,A La Carte Bioinformatics. Provides services including QX100 Droplet Digital PCR Machine (Biorad),Nucleic acid extractions from bio-specimens, Sample QC,Realtime PCR.
Quebeck Sherbrooke University Genomic Core Facility
Laboratoire de genomique fonctionnelle de l'University de Sherbrooke
Provides system for Splicing isoform Annotation. This LISA platform allows high throughput annotation and functional analysis of Alternate Splicing in humans.
Massachusetts University Medical School Quantitative Methods Core
Provides University of Massachusetts Medical School investigators with clinical research support in biostatistics, experimental design, and data management.
Stanford University Cell Sciences Imaging Core Facility
Provides high resolution, light and electron microscopy technologies for imaging and analyzing molecular and structural organization of cells, tissue and bioengineered materials. Operates two sites at Stanford University: SOM Beckman Center CSIF and SOE Shriram Center CSIF.
Stanford University Shared FACS Core Facility
Provides flow cytometry instrumentation and expertise. Provides operator assisted analyzer and sorter use, as well as training and support for user instrument operation.
Nebraska-Lincoln University Metabolomics and Proteomics Core Facility
Metabolomics and Proteomics Core Facility
Provides tools of modern functional proteomics and metabolomics. Facility is equipped with chromatography and mass spectrometry based technologies for proteomics and metabolomics (Clinical and non clinical), personalized experimental design consultation and comprehensive, individualized bioinformatics support.Services include:Small molecule exact mass determination or quantitation using positive or negative ion mode;Protein identification using LC/MS/MS analysis and MASCOT and SEQUEST database search;Shot gun proteome analysis of biological samples;Biomarker discovery from biological fluid;Drug protein or drug nucleic acid protein interaction;Protein complex isolation and identifying interacting partners and its quantitation;Protein differential expression analysis and quantitation by 2D-LC MS/MS (MudPIT);Global PTM analysis and quantitation;Specialization in phosphorylation and oxidation analysis;Coomassie Blue and Silver Stained Gel analysis; de novo peptide sequencing by tandem mass spectrometry;Confirmation of mutations in protein ;Customized sequence search of in-house proteins that are not available in database; Post translational modifications (phosphorylation, sumoylation, ubiquitination, oxidation, etc.); Determination of oxidation state of cysteine (disulfide bonds);Intact proteins and peptides mass determination.
Iowa State University Genome Informatics Core Facility
Provides help with grant review, information on data management plans,suggestion best practices for bionformatics analyses, advise on experimental design for Next Gen Sequencing (NGS) projects.Services include:Genome assembly and annotation,Transcriptome assembly and annotation,SNP/InDel calling,RNA-Seq analysis,ChiP-seq,Introgression mapping,novel gene discovery,Personalized GBrowse instances for data visualization,Access to high performance computing, Custom big data projects.
Rockefeller University Bio-Imaging Resource Center Core Facility
Frits and Rita Markus Bio-Imaging Resource Center
Provide members of University and their visitors with wide spectrum of optical microscopy equipment and extensive training in its use.
Rockefeller University Electron Microscopy Resource Center Core Facility
Provides support to University researchers for transmission- and scanning-electron microscopy. Based on center capacity, support is also available to researchers from other not-for-profit institutions.
Nebraska-Lincoln University Center for Virology Bioinformatics Core Facility
Bioinformatics Core at Nebraska Center for Virology
Facility is equipped with high performance computers, bioinformatics related software, biological databases, and data storage. Provides bioinformatics and computational services in virology, molecular biology, genomics, proteomics, next generation high throughput sequencing, and other biological related fields. For special requirements, can design and develop new algorithms, and implement programs and customize data processing pipelines. Core promotes education in bioinformatics to students and researchers, develops and delivers training material, including workshops that facilitate practical application of bioinformatics knowledge by students, postdoctoral fellows, and faculties in NCV community.
Stanford University School of Medicine High Throughput Bioscience Center Core Facility
Core provides fully automated high throughput screening (HTS) of Compound Libraries (130,000+ compounds) for both enzyme/protein-based assays and cell-based assays, using Caliper Life Sciences Staccato system;Genomic siRNA screening with siARRAY whole human genome siRNA library from Dharmacon targeting 21,000 genes, using Agilent Bravo system;High-Content Screening using ImageXpress Micro automated fluorescent microscope with live cell, bright field, phase contrast and integrated plate handling with Thermo Catalyst CRS, and image analysis using MetaXpress software;High Throughput Molecular Biology reagents and services, including access to cDNA libraries (Human ORFeome collection, 15,000 genes) and 96 and 384-well bead clean-ups and PCR setup (Biomek FX and Agilent Bravo), and other automation steps in collaboration with SFGF;High-throughput assay development assistance with cell culture, experiment design, robotic programming and Standard Operating Procedure drafting;Screening data analysis assistance with protocols, hit determination and structure activity analyses using MDL chemical database ISIS/HOST, Plate Manager, Assay Explorer and Report Manager. Use of microplate reader detection systems, including Tecan Infinite M1000 and Infinite M1000 PRO and Molecular Devices Analyst GT for fluorescence; fluorescence polarization; time-resolved fluorescence; absorbance and luminescence (with injectors and AlphaScreen); and Flexstation II 384, for kinetic fluorescence reads to measure calcium mobilization and ion channels.Use of liquid-handling robots, including Sciclone ALH3000 (96- and 384-well pipetting), Agilent Bravo (96- and 384-well pipetting), Velocity11 VPrep (96-well pipetting), Bio-Tek plate washers/dispensers, Matrix Wellmate and Titertek/Labsystems Multidrop microplate dispensers, and Velocity11 PlateLoc plate heat sealer;Training for most of these services.
Oklahoma Medical Research Foundation Human Antibody Core Facility
Core produces fully human, full length, antigen specific antibodies for use in studying human immune responses. Produces high affinity protective antibodies to influenza, anthrax lethal toxin, and various S. pneumonia polysaccharides. Helps quantify antibody secreting cell responses after vaccination and by generating human monoclonal antibodies to be characterized. Pathogen specific human monoclonal antibodies are also available for licensing agreements and other forms of commercial development. Services include to define temporal human immune responses after vaccination and to generate human monoclonal antibodies to supplement research,development of novel methods to produce human monoclonal antibodies after acute infection and other immune events, investigation of new technologies for characterization of human monoclonal antibodies produced by core.
Delaware University Surface Analysis Core Facility
Core provides consulting and services in X-ray Photoelectron Spectroscopy (XPS or ESCA), Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS), X-ray Photoelectron Imaging, Auger Electron Spectroscopy (AES), Scanning Auger Microscopy or Imaging (SAM), Secondary-Electron Microscopy (SEM), Ion-Scattering Spectroscopy (ISS or LEIS), Scanning Probe Microscopy (STM and AFM).
The Rockefeller University Proteomics Resource Center Core Facility
Rockefeller University Proteomics Resource Center
Rockefeller University Proteomics Resource Center Core Facility
Core provides analysis of proteins, peptides, lipids, polar metabolites and small molecules by high resolution/high mass spectrometry. Targeted and hypothesis free analysis are offered combined with relative quantitation based on either label free, tandem mass tags or metabolic labelling. Acquisition tools include Data Dependent (DDA) and Data Independent (DIA).
Nebraska-Lincoln University Morrison Microscopy Core Facility
Morrison Microscopy Core Research Facility
Core provides imaging systems including light/fluorescence microscopes, confocal laser scanning microscopes and electron microscopes.Provides services, teaching, training and technical support for multi disciplinary research.
Wisconsin-Madison University Biotechnology Center Bioinformatics Resource Center Core Facility
Facility within UW Biotechnology Center (UWBC) for assisting researchers with their data analysis needs. Helps with variety of common sequencing related projects, DNA-seq, ChIP-Seq, RNA-Seq, 16S metagenomics, and small RNA analyses.
Nebraska University Medical Center Epigenomics Core Facility
Core assists with epigenetic analysis including DNA Methylation, Chromatin Immunoprecipitation and Real Time Quantitative PCR gene expression analysis. Services include DNA Methylation Analysis, Specific Genomic Location Analysis:Methylation Specific PCR,Bisulfite Sequencing,Bisulfite Pyrosequencing,Qiagen PyroMark Pyrosequencer Instrumentation;Genome Wide Analysis:High Throughput Sequencing Methylation Analysis, Methyl-Sensitive Cut Counting (MSCC),Methyl CpG Binding Domain - Isolated Genome Sequencing (MiGS);Chromatin Immunoprecipitation Analysis (ChIP):Analysis of Histone Modifications,DNA-Protein Interactions,Chromatin Positions analyzed using:Quantitative PCR Analysis (Real-Time QPCR),High Throughput Sequencing Analysis (ChIP-Seq);Gene Expression Analysis (QPCR):Real-Time Quantitative PCR Gene Expression.
Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility
Vincent Coates Foundation Mass Spectrometry Laboratory
Core mass spec and proteomic services include open access lab for trained users with GC/MS, LC/MS, high resolution LC/MS, and MALDI-TOF instruments, help with intact protein analysis, targeted quantitation, drug discovery support, pathway analysis, protein interactions, FFPE tissue analysis, both labeled and label-free proteomics, and more. Please contact SUMS to discuss these and other custom projects including new application development.
Nevada University at Reno Nevada Bioinformatics Center Core Facility
Provides bioinformatics research resources, services and training in support of existing research programs and in development of new programs and grant applications. Provides next-generation sequencing data analysis including RNA-Seq and QuantSeq analysis, de novo transcriptome assembly, whole-genome sequencing, genome resequencing, single-cell sequencing, metagenomics, microbiome, mass spectrometry proteomic analysis of label-free (DIA) and TMT data, analysis of metabolomics, microbiome, multi-omics data, data mining, modeling, and visualization. Provides customized bioinformatics and statistical services including data quality control, power studies, hypothesis tests, regression, clustering, network analysis, function annotation, pathway analysis including iPathwayGuide.
Maine University DNA Sequencing Core Facility
Provides services in sequencing using ABI model 3730 DNA Sequencer with the XL Upgrade,design and have synthesized primers for primer walking experiments, DNA fragment analysis such as microsatellites, AFLP, SNP analysis.
Concordia University Center for Microscopy and Cellular Imaging Core Facility
Centre for Microscopy and Cellular Imaging
Services include advise on microscope to use for research project, image acquisition, optimization image analysis and sample preparation, free of charge access to 500GB per laboratory on CMCI server in order to store data for project. Facility houses four wide-field, near-field (TIRF), three confocal (swept-field and laser-scanning) microscopes and laser capture microdissection system.
Arkansas University Biodosimetry Diagnostic Core Facility
Core using ultrahigh performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) offers high-throughput analytical services for determining diagnostic amino acids and their precursors or metabolic products. Available biomarkers include citruilline and tetrahydrobiopterin. Determination of other small molecules is possible.
Virginia Commonwealth University Chemical and Proteomic Mass Spectrometry Core Facility
Chemical and Proteomic Mass Spectrometry Core Facility
Core provides mass spectrometric services, from basic mass measurement to complex proteome analyses.Services include basic mass measurement, ESI-MS/MS,LC-MS,Exact mass measurement,Protein identification.
University of Texas Southwestern Medical Center Moody Foundation Flow Cytometry Core Facility
Moody Foundation Flow Cytometry Facility
Core provides flow cytometry services to scientists, offers analytical cytometry and high-speed sorting either in investigator operated format or facility staff assisted format, offers training for research personnel interested in learning how to design flow cytometry experiments, operate instrumentation and analyze data. Services include experimental design, protocol development, sample staining, instrument operation, data analysis, graphical production, sample processing as a Service (SpaaS). Facility is equipped with three cell sorters and four cell analyzers.
Stanford University School of Medicine Magnetic Resonance Laboratory Core Facility
Stanford Nuclear Magnetic Resonance Laboratory
Core provides instrumentation in area of solution phase, high resolution NMR spectroscopy and expertise. Primary solution state spectroscopy of bio molecules including, but not limited to, studies of polymers, minerals, soils, and extracts. Equipment includes: 800MHz Varian Inova Spectrometer, 600MHz Varian Inova Spectrometer, 500MHz Varian Inova Spectrometer, and staff assistance/consultation is available.
Johns Hopkins University School of Medicine Transgenic Mouse Core Facility
Core provides complete CRISPR services, design, production of gRNAs & Cas9 mRNA, and injection.
Charite - Universitatsmedizin Berlin 7T Experimental MRIs Core Facility
Core provides two experimental 7 Tesla magnetic resonance imaging machines which were purchased by Center for Stroke Research CSB (Device 1) and Cluster of Excellence NeuroCure (Device 2) with aim of creating experimental platform for small animal imaging. Services projects in areas of experimental neuroimaging and molecular imaging, but projects in other fields of research are explicitly encouraged.
Saint Louis University School of Medicine Protein Core Facility
Core facility that supports expression, purification, and analysis of reagent and preclinical proteins by providing instrumentation and consultation for protein production from small to large scale. Available equipment includes shaking incubators, 5 L fermentor, high pressure cell disruptor, hollow fiber concentrator, Maxwell16 magnetic bead purification system, AKTA Purifier chromatograph, analytical ultracentrifuge, analytical HPLC, and MALDI-QIT-TOF mass spectrometer.
Princeton University Confocal Microscopy Core Facility
Core provides researchers with ability to visualize samples, from monolayers and small organisms, such as developing fly and fish embryos, to very thick sections from brain and other organ tissues by using instruments including laser point (LSCM) and field scanning confocal (CSU), Total Internal Reflectance Fluorescence (TIRF), Multi Photon (MP), and Widefield (WF). Services in imaging in mammalian cells, yeast cells, Drosophila and Zebrafish embryos and ovaries, bacteria, sections of brain and other tissues, in both fixed and live specimens, Quantitative imaging methods such as FRAP, FLIP, and FRET, software packages for image processing, analysis, and 3D image reconstruction.
Core provides seven mass spectrometry platforms, for shotgun and targeted analyses, run by core staff. Services include protein and peptide identification from gels and solutions, identification and localization of post translational modifications, relative and absolute quantitation of peptides and proteins, intact mass analysis of proteins in solution.
University of Delaware BioImaging Center Core Facility
Delaware University BioImaging Center Core Facility
University of Delaware Bio-Imaging Center
Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies.
Albert Einstein College of Medicine Molecular Cytogenetics Core Facility
Molecular Cytogenetics Core Albert Einstein College of Medicine
Core provides tools for preparation of human and murine samples suitable for molecular genetic and cytogenetic analysis of entire genome. These tools include establishment of EBV transformed cell lines; isolation of DNA and mRNA from variety of tissue culture samples as well as primary biopsies; preparation of metaphase chromosomes suitable for fluorescence in situ hybridization (FISH) and Spectral Karyotyping (SKY) or whole chromosome paints for human and mouse genome. Core personnel is trained to hybridize commercial probes and to designed locus specific probes for regions of interest to investigators. All probes are custom designed and in house generated.
University of Miami Hussman Institute for Human Genomics Biorepository Core Facility
University of Miami Miller School of Medicine Biorepository Core Facility
University of Miami School of Medicine Biorepository Core
Core provides services and houses samples collected over the last 30 years. Biorepository processes, archives, and retrieves biological samples for genomic research. Offers variety of sample processing options including but not limited to automated DNA extraction using Autogen FLEXSTAR+ instrument, automated DNA/RNA extraction using Qiagen QIASymphony, peripheral blood mononuclear cell (PBMC) isolation, serum, plasma and buffy coat isolation, creation of blood cards, DNA/RNA quantitation and qualitation, whole genome amplification, cell-line lymphoblast immortalization and primary fibroblast tissue culture. Offers sample solutions tos uit customized needs.Services also include DNA/RNA Extraction,Sample archiving, retrieval and allocation,Unique and custom labels printing,DNA/RNA quantitation and qualitation,Tissue culture,Whole genome amplification.
Miami University SCCC Flow Cytometry Core Facility
Core provides analytical and preparative flow cytometers, to facilitate range of experiments in biology of both normal and cancer cells. Experimental analyses, including:Complex, 19 fluorescence parameter immuno-phenotyping;DNA content, ploidy and cell cycle analysis; 17 fluorescence parameter cell sorting and single-cell flow cloning; High speed (10,000 � 30,000+ cells per second) and efficiency (95%+ purity) cell sorting;Assessment of apoptosis;Molecular cytogenetics;Cell function studies;Micro-biological applications;Multiplexed and micro-particle-based analysis;Mass cytometry analysis and imaging;Fluidigm Helios plasma mass cytometer. Cells are labeled with antibodies conjugated to heavy metal markers, vaporized in plasma and detected with time-of-flight mass spectrometry;Fluidigm Hyperion solid tissue imager provides simultaneous imaging of labeled solid tissue sections, for mass cytometry analysis. FCSR has bank of metal reagent kits (for custom antibody conjugation), available for purchase at favorable rates compared to those available commercially. The bank has 35 unique labeling metals, for users to create custom reagents and panels. Please contact FCSR for further information and pricing. Robotic automated cell transfer A.L.S. CellCelector automated cell transfer robot. For automated transfer of single cells and colonies from culture plates, without pre-treatment. Integral bio-safety cabinet for BSL-2 cultures.
Kansas University Medical Center Mass Spectrometry/Proteomics Core Facility
KUMC Mass Spectrometry/Proteomics Core Laboratory
Core provides access to mass spectrometry based proteomics applications, customizes mass spectrometry designs that fit individual needs. Used for general proteomics evaluations and protein identification designs, quantitation techniques, hydrogen/deuterium exchange, and oxidative footprinting. Equipment includes Orbitrap Fusion Lumos.
Miami University Mass Spectroscopy Laboratory Core Facility
Core provides two mass spectrometers at UM Department of Chemistry, Bruker MicroQ-TOF ESI, and Agilent Technologies 5975C GC/MS with autosampler.
University of Miami Hussman Institute for Human Genomics Genotyping Core Facility
University of Miami Miller School of Medicine Genotyping Core Facility
Core provides services in analyzing genetic variation, performing genome-wide association studies, conducting non-human genotyping. Offers flexible platforms from low to high throughput, tailored to research needs. Specializes in Illumina Genotyping Arrays and TaqMan Allelic Discrimination Assays, with fully automated processing using Tecan EVOs and BioMek liquid handlers and Genologics LIMS for reliable data tracking.Applications include: GWAS – Identify genetic variants linked to traits and diseases; PRS Analysis – Assess genetic risk for complex diseases; Pharmacogenomics – Study genetic factors in drug response; Population Genetics – Explore ancestry and genetic diversity; CNV Analysis – Detect large-scale genomic variations; Methylation Analysis.
Neural Stem Cell Institute NeuraCell Core Facility
Core facility provides neural stem cells (NSC) and everything you need to grow them, custom lentiviral shRNA and over-expression vectors, consult based characterization service where we can assess how your products or reagents affect stem cell performance and behavior. Services include:Cell Supply,Adult SVZ Neural Stem Cells,Any Age Embryonic stem cells from any region of the brain,Human Retinal Pigmented Epithelial cells,RPE iPSCs,iPSCs,Neural Progenitor Cells (NPCs),Custom Orders,Media/ Dissociation Reagents,High-performance Media formulated according to optimal cell growth conditions,Complete Defined Media for Neural Stem Cell Culture,Complete Defined Media for Human Retinal Pigmented Epithelial Culture,Cell characterization. Performs assays to verify how stem cell populations behave in response to certain environments, plastics, reagents, etc., using trade secret assays via FACS and cell culture techniques. This can be used for neural stem cells as well as embryonic stem cells.Cell banking solutions shall ensure that their integrity is maintained, and that sufficient supply is readily available. We will also expand cells, harvest cells, generation the freezing medium and thaw cells to test performance. Provides Generation of custom lentiviral shRNA constructs,Generation of custom lentiviral over-expression constructs,Supply of NSC lines already expressing these shRNA or over-expression constructs.
Miami University Veterinary Clinical Pathology Laboratory Core Facility
Full service veterinary reference laboratory directed by members of faculty of University of Miami Miller School of Medicine. Offers clinical pathology and histopathology services to meet needs of avian, exotic, lab animal, and wildlife veterinarians. Services include Acute Phase Protein Laboratory. Provides recent diagnostic testing developments which may not yet be available in other veterinary diagnostic testing environments.
Howard Hughes Medical Institute at Janelia Research Campus Advanced Imaging Center Core Facility
Facility provides imaging methods and instruments, microscopes that reveal biological processes in three-dimensional detail and behavior of single molecules in high resolution. Welcomes proposals with high-risk/high-gain projects. AIC will cover lodging and basic experimental cost for scientists whose proposals have been accepted to come to Janelia to perform their experiments.
Miami University X-Ray Crystallography Resources Core Facility
Core provides upgraded Bruker SMART 1000 CCD single crystal diffractometer to SMART APEX II CCD Area Detector, and its low-temperature LT3 device to KRYO-FLEX low-temperature device. Instrument which is equipped with Mo radiation source is used for small molecule crystal structure determination.
University of Miami Miller School of Medicine Gene Expression Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 27,2025. CGT gene expression core utilizes Affymetrix GeneChip Arrays and Illumina BeadChips to identify gene expression variation in single genes, targeted set of genes, or entire genomes. Affymetrix GeneChip Arrays Human Gene ST,Human Transcriptome Array 2.0, Human Exon ST, Human miRNA, Illumina Expression, HumanHT-12 v4 BeadChip.
University of California Davis Flow Cytometry Shared Resource Laboratory Core Facility
UC Davis Flow Cytometry Shared Resource Laboratory
University of California Davis Health Flow Cytometry Shared Resource Laboratory Core Facility
Core provides access to expertise and instrumentation for analytical flow cytometry, cell sorting and laser scanning cytometry.Cell sorting and analytical cytometers are located at three sites in Davis and Sacramento for research use on recharge basis. Provides cell sorters for assisted sorting on appointment basis and provides training to investigators in acquiring data on analytic cytometers.Can advise on experiment design for flow cytometry, provides training to enable independent use of analytical cytometers, and familiarize investigators with popular data analysis software tools such as BD Diva and CellQuest, FlowJo, ModFit and iBrowser.
Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Genomics Core Facility
Genomics Core at Scripps Research Florida
Scripps Research Institute - Florida Genomics Core Facility
Core provides services in Next Generation Sequencing (NGS), library preparation, consultation on sample preparation and procedures.
University of Miami Hussman Institute for Human Genomics Sequencing Core Facility
University of Miami Miller School of Medicine Sequencing Core Facility
Core Facility offers services utilizing Illumina Novaseq X Plus, Pacific Biosciences Revio, ONT Promethion, and 10x Genomics platforms. The core has extensive knowledge of DNA/RNA library preparation for short-read, long-read and single cell sequencing. Sample preparation is fully automated on Perkin Elmer robotic workstations and tracked via the Clarity LIMS. Services include, but are not limited to, whole genome, exome and custom capture protocols, as well as, bulk RNAseq, small RNAseq, and single cell RNA sequencing.
University of Virginia School of Medicine Flow Cytometry Core Facility
Virginia University School of Medicine Flow Cytometry Core Facility
Services include unassisted and assisted sample acquisition, cell sorting, mass cytometry (CyTOF), Luminex cytokine assays, antibody conjugation and data analysis.
Scripps Research Institute - Florida Flow Cytometry Core Facility
Flow cytometry core to measure phenotypic, biochemical and molecular characteristics of individual cells or particles suspended in fluid stream.Flow Cytometry Core on Jupiter, Florida campus of Scripps Research provides services including Cell Sorting, Analytical Cytometry,Data Analysis,Microdissection and Imaging. Hematology services including:Cell Sorting on ARIA: violet, blue, green and red lasers and on FUSION: violet, blue, green and red lasers; Cell Analysis on LSR2: ultra-violet, violet, blue, green and red lasers, GALLIOS: violet, blue, green and red lasers,CANTO: violet, blue and red lasers;Laser Microdissection and Fluorescence Imaging using LEICA LMD 7000;Hematology using HEMAVET 950FS.
Penn State College of Medicine Mass Spectrometry and Proteomics Core Facility
Penn State College of Medicine's Mass Spectrometry & Proteomics Core
Core provides mass spectrometry analyses and identification of proteins, peptides, oligonucleotides, carbohydrates and small molecules.Other services include separations of complex protein and/or peptide mixtures; protein expression analysis (iTraq, SILAC, SWATH/DIA label-free); quantitation of protein, cytokine, amino acid and other small-molecule levels; bioinformatics; spot-cutting and robotics; and gel imaging and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Princeton University Macromolecular Crystallography Core Facility
Macromolecular Crystallography Core Facility
Facility helps with structure determination and analysis on service basis, but also encourages users with prior experience to use facilities independently. Offers services for setting up crystallization trials, x-ray data collection, structure determination and structure analysis. Assists in interpretation of existing structures available in Protein Data Bank and assists in homology modeling.
Scripps Research Institute - Florida Nuclear Magnetic Resonance Core Facility
Research Services Nuclear Magnetic Resonance Facility
Core provides NMR spectroscopy to researchers in Scripps Research, as well as spectral service to local biotech communities.Facility houses six NMR spectrometers:Bruker AVIII HD 600 NMR spectrometer equipped with 5 mm CPQCI (H-C-N-P) CryoProbe This spectrometer also has 1.7 mm CPTCI (H-C-N) CryoProbe which can be installed upon requested for experiments on micro-gram scale compounds;Bruker AVIII HD 600 NMR spectrometer equipped with 5 mm CPDCH (C-H) CryoProbe. This CryoProbe provides high sensitivity for C-13 NMR experiments;Bruker AV NEO 500 NMR spectrometer with 5 mm BBFO Smart Probe;Bruker AVIII 400 NMR spectrometer equipped with 5 MM BBFO probe ;Bruker AV NEO 399 spectrometer equipped with 5 mm BBFO Smart Probe. All BBFO probes have capabilities to perform NMR experiments on nuclei with resonance frequencies between Ag-109 and P-31, as well as H-1, and F-19.Bruker DPX-400 NMR spectrometer equipped withQ NP (H-F-P-C) probe and B-ACS 120 sample changer.
Scripps Research Institute - Florida X ray Crystallography Core Facility
Macromolecular X-ray Crystallography Core facility
Core provides equipment and resources for crystallographic analysis of target macromolecules and small inorganic or organic molecules. Performes crystallization, X-ray diffraction data collection (both in-house and synchrotron sources) processing, phasing, crystallographic refinement, model building, and visualization. Structural data provide information including biological functions, 3D-folding, ligand binding (small molecule or protein), or mutational effect of target macromolecules. Services include Crystallization Screening; Data Collection Service: Diffraction experiments will be performed at in-house X-ray facility as well as synchrotron beam lines; Structure Determination and Analysis: complete data set collected at home or synchrotron will be processed for inorganic, organic, protein or nucleic acid structure determination, model building and crystallographic refinement. Other Structural Biology Related Services: core facility offers thorough analysis of macromolecular structure for publication or grant applications, also provides computational experiments such as homology modeling and in silico ligand docking.
North Carolina University at Chapel Hill R.L. Juliano Structural Bioinformatics Core Facility
R. L. Juliano Structural Bioinformatics Core facility at UNC-Chapel Hill
Core provides consultations and collaborations on research studies requiring computational structural biology methods. Analyses available are to study of static structures, molecular dynamics studies for analyzing contribution of dynamic and collective motions to macromolecular functionality. Trains researchers in computational structural biology techniques, or works in collaborative manner with researchers.Provides access to software tools for protein and DNA sequence analysis, protein fold determination, homology modeling, active site identification, and analysis of effects of various mutations on structure and function of protein, along with additional computational analyses.
North Carolina University at Chapel Hill School of Medicine High Throughput Peptide Synthesis and Array Core Facility
UNC High-Throughput Peptide Synthesis and Array Facility
Core offers services for: High quality synthetic peptides, stable isotope labeled peptides, peptides with PTM and fluorescent and affinity tags, synthesis of peptide libraries. Analysis of synthetic peptides. Purification, lyophilization and aliquoting of synthetic peptides.
Wisconsin University Great Lakes Genomics Center Core Facility
Core provides services which include massively parallel sequencing on Illumina MiSeq, traditional Sanger sequencing, fragment analysis, quantitative PCR, nucleic acid extractions and QC, and digital PCR. Offers various level of service for Sanger sequencing and qPCR from full service to ready to load plates. Trains researchers in laboratory techniques and provide protocols. Each MiSeq sequencing project and qPCR project is unique and specifically designed so experimental design should be discussed before collecting samples.
North Carolina University at Chapel Hill School of Medicine Macromolecular X-Ray Crystallography Core Facility
Core provides support and infrastructure necessary to initiate and successfully complete structural biology or structural chemistry project. Offers services in Crystallization,X-Ray DiffractionData Collection,Structure Determination and Refinement.
Steve and Cindy Rasmussen Institute for Genomic Medicine Clinical Laboratory Core Facility at Nationwide Children�s Hospital
Institute for Genomic Medicine Clinical Laboratory
Core performs and analyzes integrated clinical genomic, molecular, microarray, FISH, and cytogenetic analyses to diagnose broad range of inherited diseases and cancer. Serves as centralized clinical testing laboratory for Children Oncology Group leukemia, Wilms tumor, medulloblastoma, and rhabdomyosarcoma studies. Emphasizes collaborative interactions between clinicians, physician-scientists, and basic science investigators to quickly transition cutting edge research results into cutting edge diagnostics, using technology platforms. Services include Whole Exome Sequencing (WES),cytogenetic chromosome analysis,Fluorescence in situ Hybridization,Chromosomal microarray analysis,Molecular Genetic Testing - Inherited Diseases,Molecular Genetic Testing - Cancer.
North Carolina University at Chapel Hill School of Medicine Biomolecular NMR Laboratory Core Facility
Core to support academic and industrial users. Spectrometer time is available to trained users for an hourly fee. Lab manager trains new users, consults to determine whether NMR will be useful in their research, and helps design experimental plan to obtain information they need. Manager also operates spectrometer for users whose experiments do not justify time and expense of individual training.
Max-Planck-Institute for Molecular Cell Biology and Genetics High Throughput Technology Development Studio Core Facility
High-Throughput Technology Development Studio
Provides expertise in assay development towards high-throughput applications and high content screening services, provides technologies for cell-based screening such as robotic liquid handling stations, plate readers and several automated microscopes. Services include developing complex automated image analysis pipelines and multi-parametric analysis of high content imaging applications.Equipment:Flexible liquid handling work stations Biomek FXp (Beckman), Freedom Evo 200 (TECAN);Multilabel microtiter plate readers Envision (Perkin Elmer), GENios Pro (TECAN);Acoustic dispensing (Labcyte Echo 550);CellVoyager CV7000 automated live cell confocal microscope (Yokogaw);Perkin Elmer OPERA;Operetta widefield microscope (Perkin Elmer);Automated confocal microscopy OPERA (Perkin Elmer);Washers, dispensers;96-well electroporation system (amaxa nucleofector).
North Carolina University at Chapel Hill School of Medicine Protein Expression and Purification Core Facility
Core specializes in production of pure, functional proteins for structural, biophysical, and biochemical studies. Facility offers three categories of service:Protein Expression,Protein Purification,Scientific Consultation, Mentoring, and Training; Offers Isotope labeled proteins for NMR;High production scales for immunizations, drug discovery, structural biology;Endotoxin-free protein production;Stable cell line generation;Expert baculovirus expression;Custom packages to efficiently suit your needs.
Centre for Cellular and Molecular Platforms High Throughput Screening and Imaging Core Facility
Core assists in developing and performing high-throughput assays involving NCEs, siRNA, shRNA and dsRNA.Core also houses High Content image-based platform for chemical and biology research using both live and fixed cells. Services include High Throughput Screening,Assay development and validation (Cell-based/ Biochemical),siRNA screens,Small molecules screens,Proof of concept with validation.
Indiana University - Bloomington Electron Microscopy Center Core Facility
Core provides access to electron microscopy equipment and services which includes AFS 2 Freeze Substitution robot,Denton DV502 Carbon Evaporator,JEOL JEM 1010,JEOL JEM 1400plus,JEOL JEM 3200FS,Polaron E5100 sputter coater,Vitrobot Mk3,Wohlwend High Pressure Freezer. Users have to be included on user e-mail lists and have iLab account in order to use core.
Albert Einstein College of Medicine shRNA Core Facility
Core Facility was closed in November 2016. Services of shRNA Core were redistibuted to other existing facilities at Einstein.Gene Modulation Services: CRISPR, RNAi and ORF. CRISPR-Cas9 services for cell lines will now be performed in Gene Modification Facility. Gene Modification Facility already offers CRISPR services for genetic modification of mice and will utilize this scientific expertise to provide CRISPR services for the gene modification of cell lines as well. You can access these services through core's site in iLab.The human and mouse whole genome shRNA library has been relocated to the Molecular Cytogenetic Core. The core staff will pull requested shRNA and ORF clones from our collection for investigators. You can access this service through the core's site in iLab.Access and operation of the Operetta instrument for high-content imaging will now be coordinated through the Macromolecular Therapeutics Development Facility (MTDF). You can access this service through the core's site in iLab. Lentivirus prep from shRNA and CRSPR constructs can be obtained from our Gene Therapy Core from clones obtained from the Molecular Cytogenetic Core. You can access this service through the core's site in iLab.
Rockefeller University Antibody and Bioresource Core Facility
Core used to develop custom monoclonal antibodies and obtain large scale quantities of existing ones for experiments. Core provides cell line distribution service and tests samples for mycoplasma contamination.
Scripps Research Institute - Florida Core Microscopy Core Facility
Core Microscopy Facility at Scripps Research
Core provides researchers with equipment and expertise required for multi-dimensional imaging of cells and tissues at high resolution and to perform quantitative image analysis. Resources include widefield, confocal, multi-photon, TIRF, super-resolution and electron microscopy, as well as equipment for live cell imaging and image analysis. Services include sample preparation, imaging, molecular localization, and image analysis. Provides training, technical support, sample preparation, imaging assistance, collaboration and consultation.
Garvan Institute of Medical Research Molecular Genetics Core Facility
Core facility for high throughput services covering the areas of Capillary Sequencing, Mouse Genotyping, SNP Genotyping, Clinical Diagnostic Sequencing, Cell Line Identification, Gene Expression Analysis and DNA/RNA extraction.
Memorial Sloan Kettering Cancer Center Molecular Cytogenetics Core Facility
Core supports cytogenetic analysis of cells from human and research animal sources. Range of chromosome analysis techniques are ranging from basic G-banded karyotyping, to 24-color Spectral Karyotyping (SKY), as well as Fluorescence in situ Hybridization (FISH) mapping of cloned DNAs.Services include:Karyotype characterization of new cell lines,Confirmation of cell line identity or stability,Karyotype screening of ES cells prior to transgenesis,Mapping of transgene integration sites,Chromosome or locus copy number enumeration,Publication-quality illustrations.Cytogenetic techniques available:Short-term cell culture,Metaphase chromosome preparation,G-banded karyotyping.FISH techniques available:DNA labeling for custom probe generation (for FISH projects),DNA amplification by DOP-PCR,Chromosome painting,FISH mapping (on chromosomes, interphase nuclei or DNA fibers),Tissue FISH (paraffin or frozen sections),Immuno-FISH (DNA FISH combined with fluorescent immunostaining) , Spectral karyotyping (SKY),Q-FISH (measurement of telomere lengths).
University of California-Davis Mouse Biology Program CRISPR Based Genome Editing Service Core Facility
Core located on campus of UC Davis, providing fully customized support for scientific research using genetically altered mice. Provides access to develop, plan, execute, and analyze research project involving genetically-altered mice. Provides description of project, including alternative approaches, accurate timelines, and cost estimates.Provides regular and informative communication throughout project, including email updates on completion of each milestone. Project progress can be followed at each stage by viewing detailed information anytime by accessing our online and secure project tracking system (PTS) available 24 hours a day.
University of California at Berkeley Cancer Research Laboratory Molecular Imaging Center Core Facility
Microscopy core specializing in laser based fluorescence techniques. Offers training and expertise in 20 different microscope systems, including live cell and in vivo imaging, laser scanning (LSM) and spinning disk (SDC) confocal, multi-photon (2p), fluorescent lifetime imaging (FLIM), light-sheet microscopy (SPIM), super resolution (Airyscan), slide scanning and patterned illumination for optogenetic manipulation and readout. Provides offline computer analysis workstations for image processing, visualization and analysis, including GPU workstations. MIC operates in 3 different buildings on campus, with primary locations in Life Sciences Addition (LSA), North-side core in Barker Hall, and small outpost in Li Ka Shing Center for Biomedical and Health Sciences (LKS).Provides equipment in categories:Confocal and multi photon laser scanning microscopes,Spinning disk confocal microscopes,Lightsheet (SPIM) microscopes,Epifluorescence/widefield scopes and Computer workstations.
Memorial Sloan Kettering Cancer Center Investigantional Products Support Core Facility
Core mission is to ensure quality and regulatory compliance of Memorial Sloan Kettering Cancer Center�s clinical trials investigational products and Investigational New Drug (IND) applications, and to promote efficiency in our drug development projects, through combination of advisory, project management, and quality assurance (QA) oversight services.
Nemours/A.I.duPont Hospital for Children Cell Science Core Facility
Core specializes in cell, protein, and small molecules analysis as well as cell culture techniques. Services include:2-D gel electrophoresis, 2-D DIGE, LC-MS/MS, HPLC, flow cytometry, fluorescence-activated cell sorting (FACS), cell and tissue culture, and immortalization of cell lines. Our staff works closely with investigators to help design, perform, and analyze experiments.Offers training and assistance in flow cytometry, tissue culture, and operation many of our walk-up instruments.Instruments:Cell Sorter: FACS Aria III, BD Biosciences;Flow Cytometers, analyzers:C6, Accuri/BD Biosciences;Novocyte 3000, ACEA Biosciences;software for analysis: FSC Express, DeNovo software;LC-MS/MS: 6460 Triple Quadrupole, Agilent;Typhoon Trio Scanner, GE Lifesciences;Blood Analyzer: Hemavet 950, Drew Scientific.Plate Readers:;Victor Nivo 5F, Perkin Elmer;Luminometer: Centro XS, Berthold.Services:Cell Sorting (FACS);2-D gel electrophoresis/2D-DIGE;LC-MS/MS analysis of compounds; Cell immortilization.
Washington University Histology and Imaging Core Facility
Core provides servises including:Immunohistochemistry,Image analysis,Quantitative microscopy,Histology,Luminex cell based multiplex assay,Comparative pathology consultation.Offers experience, expertise and instrumentation across all platforms. HIC utilizes automated immunohistochemistry stainers which provide efficiency and consistency as well as standardization of protocols across studies of all sizes.
Baylor College of Medicine RNA In Situ Hybridization Core Facility
Core performs non-radioactive, RNA in situ hybridization (ISH) on tissue sections. Provides services including: collecting animal tissue specimens, preparation of frozen and paraffin sections, preparation of RNA probes from customer templates, conducting high-throughput ISH, and documentation and quantification of expression patterns by microscopy. We also do X-gal and Cresyl Violet staining on sections. For human studies, customers must provide tissue sections.
Loyola University Genomics Core Facility
Core provides next-generation sequencing capabilities using Illumina MiSeq. Helps with experimental design, quality control analysis, library preparation, and data analysis. MiSeq desktop sequencer allows to access applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression, amplicon sequencing, and HLA typing.MiSeq is capable of delivering up to 15 Gb of output with 25 million sequencing reads and 2x300 basepair read lengths.
University of Massachusetts Boston Advancing Personalized Cancer Medicine Through Research Genomics Core Facility
Center for Personalized Cancer Therapy Genomics Core offers sequencing services on Illumina HiSeq 2500 (v4; 1TB enabled) and Illumina MiSeq platforms, library preparation from DNA and RNA and sample QC services.Please create an iLab account to be able to use services.
Washington University In Vivo Services (IVS) Core Facility
In Vivo Services Core in the Department of Comparative Medicine
Core provides rodent colony management. IVS staff oversee maintenance, breeding, weaning, identification, and record keeping of mouse and rat colonies. Core offers sample collection, sample administration, and testing of drug compounds in rodents. Services include Colony Management,Technical Procedures,Drug Testing.
Duke University Molecular Genomics Core Facility
Core offers variety of experimental platforms to facilitate genomics research. Accredited as Duke Shared Resource facility offers experience with genetic, genomic and epigenomic study design and technology, working closely with researchers to customize experiments to meet their needs. Applications include 10x Genomics NGS library generation for both single cell and gDNA experiments, DNA methylation microarrays, SNP genotyping and copy number microarrays, and Taqman targeted SNP genotyping.
Brown University Leduc Bioimaging Core Facility
Core provides equipment and training dedicated to high resolution imaging in life sciences. Facility includes Transmission Electron Microscope, a Scanning Electron Microscope, three Fluorescence Microscopes, Fluorescence Stereomicroscope, four Confocal Laser Scanning Microscopes,Multiphoton Microscope, and software for image analysis.Maintains equipment for sample preparation, including critical point dryer, sputter coater, and microtomes for ultrathin sectioning. Listed within CoresRI.org.
University of California at San Francisco, Nikon Imaging Center Core Facility
Core provides light microscopy instrumentation, microscopy training and education and can provide assistance with experiment design, data acquisition, and image analysis. Provides training for users.Services include:Fluorescence imaging (up to 5 colors) Brightfield, phase contrast, and DIC imaging;High speed imaging (over 100 frames per second);Automated imaging, including multiwell plates;Super-resolution imaging (SIM / STORM / PALM);Single molecule imaging;3D confocal imaging;Gigapixel image stitching;Live cell time lapse imaging;Photoactivation and photobleaching;Light sheet imaging of cleared tissues.
University of Washington Transgenic Resources Program Core Facility
University of Washington Transgenic Resources Program
Core facility that creates transgenic and gene-targeted mice using pronuclear microinjection, targeted ES cell microinjection, and CRISPR/Cas9 gene editing. Offers mouse rederivation services to create specific pathogen free mice or to rederive cryopreserved mouse lines. Additionally, embryo and sperm cryopreservation services are available to provide long-term storage of valuable mouse strains or stocks. Services include:Pronuclear Microinjection,ES Cell Microinjection,ES Cell Electroporation CRISPR/Cas9,In Vitro Fertilization,Sperm Cryopreservation,Embryo Cryo,Embryo Rederivation.
Nebraska University Medical Center Electron Microscopy Core Facility
University of Nebraska Medical Center Electron Microscopy Core Facility
Core provides instrumentation and technical assistance to research programs utilizing Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM). Available for consultation and service.
London Regional Genomics Centre Core Facility
Core provides Next Generation Sequencing and Bioinformatics services.Services include:RNA assessment using Agilent 2100 Bioanalyzer,Next Generation Sequencing:Single cell RNA-seq,DNA-seq,RNA-seq,miRNA-seq,ChIP-seq,Microbiome (16S rRNA),ATAC-seq,Data Analysis (Partek Flow, Transcription Analysis Console).
Northwestern University Jerome B. Cohen X-ray Diffraction Core Facility
Jerome B.Cohen X-Ray Diffraction Facility
Core provides general purpose x-ray equipment for diffraction and fluorescence studies. Examples of current measurements are: powder diffraction, single-crystal diffraction, thin-film reflectivity, thin-film diffraction, crystal truncation rod scattering, small angle scattering, Laue diffraction, residual stress, pole figures, EDX-ray fluorescence, x-ray standing waves, high-resolution x-ray diffraction, and grazing incidence small angle scattering.
Mayo Clinic Immunochemical Core Facility
Immunochemical Core Lab (ICL) - Mayo Clinic
Provides immunochemical, chemistry and immune testing to clinical and basic science researchers, develops and validates new assays, and improves current assay methodology. Services include Assay development, Automated chemistry analysis, Immunoassay analysis, Small molecule analysis,Mass Spectrometry, LC-MS/MS and HRAM LC-MS,Enzyme-linked immunosorbent (ELISA), Meso Scale Discovery (MSD), Luminex, and radioimmunoassay (RIA) procedures for various analytes.
Northwestern University Surface Science Core Facility
Core provides multiple technique characterization of variety of surfaces with regard to atomic structure, surface chemical composition, and chemical bonding characteristics. Equipment includes:AFM/Nanoindentor for high resolution imaging and nanoindentation studies;Laser writing for generating controlled surface roughness and patterns;Optical profilometers: Two optical interferometers (Zygo and Aliconia) are available for surface topographic imaging;Three-target magnetron sputter-deposition system. Provides Training Seminars/Workshops.Provisions have been made to accommodate routine short term measurements by user groups as well as more extended studies. User and research groups are encouraged to work with facility staff to tailor facility resources to research project.
Northwestern University Cryogenics Core Facility
Facility provides liquid helium and liquid nitrogen to researchers and laboratories at Northwestern University.
Northwestern University Mouse Histology and Phenotyping Laboratory Core Facility
Mouse Histology and Phenotyping Laboratory
Core provides assistance with standard and customized research specific histology services for variety of tissues (i.e., mouse, rat, sheep, pig, zebrafish, etc.) for routine histology, and immunohistochemistry. Provides Pathologist consultation to help develop strategies to elucidate phenotypes and gain mechanistic insight regarding biologic actions of targeted molecule(s) or toxicity of exogenously administered substances.Provides training opportunities for learning histology techniques and phenotyping analysis.Services include Immunohistochemistry (IHC) . Using tyramide signal amplification (TSA) and ABC methods (automated), with DAB chromogenic substrate; Immunofluorescence (IF)- Single and multiple staining;TUNEL assay; Freezing and embedding of tissues for histology;Frozen sections;Paraffin block processing and Paraffin sections;Hematoxylin and Eosin staining of sections;Specialized histochemical staining of sections (e.g. Trichrome, PAS, Luxol fast blue, Cresyl violet, and many other stains);Dissection and tissue collection;Histopathology (slide interpretation);Histopathology toxicity evaluation;Training in necropsy techniques including perfusion of mice and special tissue dissection;Assistance with development of animal pathology protocols.
Northwestern University Comprehensive Metabolic Core Facility
Core provides hormone analyses for both human and animal studies for scientific community at Northwestern, small rodent metabolic phenotyping resources for diabetes, obesity and other metabolic research.Maintains quality control and standardize internal references for hormone assays.Maintains reference database information on mouse metabolic phenotyping models from Northwestern University community.Services include:Immunoassays for endocrine hormones, assays using technology from Luminex,Lipid and glucose chemical analyeses,Roche Cobas e 411 analyzer employing sophisticated electrochemiluminescence (ECL) technology to deliver excellent low-end sensitivity and broad dynamic range of assays including metabolic and reproductive hormones, thyroid function test, cardiac markers, maternal care, tumor markers and bone turnover markers.,TSE LabMaster Automated Phenotyping system is a state-of-the-art system for studying energy metabolism at whole animal level.
Northwestern University Recombinant Protein Production Core Facility
Core provides quality controlled recombinant proteins. rPPC operates based on the two service models: Training model where Northwestern researchers use specialized bioreactor systems and participate in hands-on-training activities and Production model where staff carry out expression (mg to gm scale) and purification of recombinant or synthetic biologics, including potential therapeutic proteins and peptides, among others. Main focus of rPPC is to be user-facility;facility has parallel bioreactor systems for multiplexed lab-scale cultivation of microbial, insect, and mammalian cells. rPPC also serves as a production facility, providing low-cost recombinant biologics for researchers at Northwestern University.Services include: TRANSFECTION/TRANSFORMATION, ANALYTICAL (SMALL SCALE) EXPRESSION IN E.COLI AND MAMMALIAN CELLS,PROTEIN EXPRESSION IN E. COLI (LARGE SCALE),PROTEIN EXPRESSION IN MAMMALIAN CELL SYSTEM (LARGE SCALE),PROTEIN EXPRESSION IN INSECT CELL SYSTEM,GENERATION OF MOUSE HYBRIDOMA, PRODUCING MONOCLONAL ANTIBODIES, per one fusion,RESCUING AND CULTIVATING EUKARYOTIC CELLS,DOWNSTREAM PROCESSING OF GROWN CULTURE (BEFORE PROTEIN PURIFICATION),RECOMBINANT PROTEIN PURIFICATION,TAG CLEAVAGE WITH TEV. PROTEASE,LARGE SCALE mAb PRODUCTION ,DNA PLASMID PROPAGATION AND PURIFICATION,SDS-PAGE ANALYSIS,WESTERN BLOT ANALYSIS, INSTRUMENT TIME SHARING TECHNICAL/INSTRUMENT ASSISTANCE TIME,PROTEIN RECOVERING FROM INCLUSION BODIES.
Northwestern University Stem Cell Core Facility
Core provides iPSC technology services.Specialize in creating custom patient-derived iPSCs, providing training in stem cell culture, project consultation, CRISPR gene editing services, cell banking, and facility usage.
Northwestern University Integrated Molecular Structure Education and Research Center Core Facility
Integrated Molecular Structure Education and Research Center at Northwestern
Core provides access to NMR, mass spectrometry, X-Ray crystallography instruments and education on use of instrumentation needed for molecular structure characterization.
Northwestern University Central Laboratory for Materials Mechanical Properties Core Facility
Central Laboratory for Materials Mechanical Properties
Core provides mechanical testing machines and accessories for conducting educational, research, and outreach experiments on most solid materials.
Northwestern University Center for Translational Imaging Core Facility
Core is Northwestern Radiology research facility providing translational imaging capabilities that promote pre-clinical and clinical research efforts. CTI occupies space in basement of Olson building housing imaging equipment along with research staff. Services include Cardiovascular Imaging for development, analysis and application of MRI methods providing insights into structure and function of cardiovascular system,NeuroImaging for functional MRI using spectroscopy and diffusion-weighted imaging to studying human anatomy and physiology during development and disease,Small Animal Imaging for molecular and functional imaging of biological processes in living animal models to study diseases and responses to intervention.
Northwestern University High Throughput Analysis Laboratory Core Facility
Northwestern Highthroughput Analysis Laboratory
Core provides expertise and resources for large scale biology. Helps to set up, run, gather data and perform analysis in drug discovery research, biochemistry, cell and organismal biology, functional genomic screening, and synthetic genetic. Works with proteins, nucleic acids, small model organisms, and microbial strains. Provides tissue culture,produces and uses lentivirus particles, screens compound libraries, does experiments for investigators,generates preliminary data to figure out if idea is workable, discusses project development. Services include Macromolecular binding, biochemical, and cell-based assays,High content screening with widefield or confocal optics,Nanoliter liquid handling up to 1536-well density,Whole-plate kinetic assays (ion currents, GPCR signaling),Compound library screening,CRISPR/Cas9 screening (multiplexed libraries),Analysis of large data sets,Fluorescence Thermal Shift assay (measures protein melting),Complex liquid handling work flows.
Northwestern University and Northwestern Memorial Health Mathews Center for Cellular Therapy Core Facility
Core offers researchers, clinicians and biotech companies regulatory compliant labs and services to manufacture minimally manipulated and complex biotechnology products.
Maine Medical Center Research Institute Viral Vector Core Facility
Core provides viral vector services dedicated to development and production of viral vectors for angiogenesis, stem cell and regenerative medicine and clinical renal research. Viral vectors are produced in dedicated BL2 facility within MMCRI building. Vector systems currently being used include adenovirus, retrovirus and lentivirus. Services Available:Transfection and transduction of gene-specific viral DNA provided by principal investigators;Small, large and custom scale production of adenovirus;retrovirus and lentivirus (2nd and 3rd generation packaging);TCID50 titration of adenovirus;Titration of retrovirus and lentivirus (fluorescence marker or antibiotic resistance);Test for replication competent virus (RCV) in lentivirus preparations.
University of New England In Vivo Behavior Core Facility
Core provides technical expertise, training, instrumentation and related services for assessing behavior in animals to help to gain insight into function of nervous system and mechanisms of acute and chronic pain. Services include Behavioral Testing; General Behavioral Phenotyping: Observational Screens, Motor Function; Pain/Sensory Testing: Thermal, Mechanical, Chemical; Additional Neurobehavioral Tests: Psychiatric, Addiction, Learning and Memory;Miscellaneous Systems: GI Transit, Cardiovascular and Respiration. Other Services: Assistance choosing behavioral test and statistical tests for assessing results; Training in surgical techniques for small animal surgeries; Staff expertise includes surgical methods for producing pain models; dosing of drugs/anesthetics including central, systemic and localized administration; and tissue extractions.
University of New England COBRE Histology and Imaging Core Facility
Core provides access to expertise, training and specialized instrumentation related to tissue processing, sectioning, staining, immunohistochemistry and microscopy. Offers services and training related to image analysis and image analysis software to guide investigators in choosing best methods for presenting their data.Services include Trimming of wet tissues,Tissue processing into paraffin, OCT and paraffin embedding, Sectioning of paraffin-embedded/frozen tissues, Routine and special histochemical staining, Immunohistochemistry/Immunofluorescence, Antibody optimization, Brightfield/ widefield/ confocal microscopy, Image capture and image analysis.Core has cryostats, microtomes and microscopes available for reservation.
Brown University Flow Cytometry and Sorting Core Facility
Core provides technical assistance to Brown researchers by performing flow cytometry-based analysis and sorting. Facility has 4-laser, 19-parameter BD FACSAria IIIu for flow and sorting applications, as well as 3-laser, 15-parameter BD FACSCelesta equipped with high throughput system for analysis of samples from 96 well plates.
Washington University Gnotobiotic Animal Core Facility
Core at University of Washington (UW) is managed by Department of Comparative Medicine and open to investigators with research needs to maintain mice free of any microorganisms (germ-free), or with known population of microorganisms (gnotobiotic).Services provided include Rederivation, Germ-Free (GF) Mice, Isolator Maintenance of GF Mice, Experimental Study Support, Diet Sterility Testing, Technical Procedures.
Kansas University Medical Center Analytical Core Facility
Core provides access to advanced chromatographic and mass spectrometry instrumentation. Main analytical focus is quantitative analysis of small molecules (drugs, drug metabololites, endogenous metabolites, xenobiotics and toxicants) and intact large molecules (biologics, intact proteins, and biopolymers like hyaluronan). Provides analytical instruments including Liquid Chromatography and Mass Spectrometry, Microbalances, Quantitative PCR (qPCR or Real-Time PCR), Sample Preparation Aids, Pharmacology Department Shared Instruments.
Northwestern University Pulsed Laser Deposition Core Facility
Core provides means to grow thin films of metals and metal oxides. Facility contains two state of art deposition chambers PVD PLD/MBE 2300 and a PVD nanoPLD 1000. PLD provides convenient way to make thin films of materials heretofore studied in bulk by pressing and sintering target from bulk material; facilities are available at Northwestern for pressing and sintering of targets.
Kansas University at Lawrence Computational Chemical Biology Core Facility
Core provides computational resources and expertise to enhance productivity of researchers studying infectious diseases. Assists with virtual screening, protein-small molecule docking, binding site prediction, protein modeling and design, prediction of protein stability changes upon mutation, fragment based probe design, as well as preparation of presentation graphics.Specializes in initial hit identification of non-traditional drug targets such as protein-protein or protein-RNA interfaces by offering high-throughput virtual screening via pocket optimization with exemplar screening at protein-protein interfaces and hotspot pharmacophore mimicry of protein-RNA interactions.CCB works in collaboration with Molecular Graphics and Modeling Laboratory.
New England University Microscopy Core Facility
Core Facility provides access to Atomic Force Microscope and Leica SP5 Scanning Laser Confocal Microscope, located in Room 122 of Pickus Center for Biomedical Research on Biddeford Campus.
Massachusetts Institute of Technology Koch Institute Flow Cytometry Core Facility
Swanson Biotechnology Center Flow Cytometry Facility
Core provides technical expertise, training and access to instrumentation, enabling and supporting use of flow cytometry techniques. Allows simultaneous multiparametric analysis of many thousands of cells per second, enabling trained researchers to rapidly analyze complex cell populations using benchtop analysis flow cytometers. High-speed assisted cell sorting services provide researchers with fast, objective and quantitative recording of fluorescent signals from individual cells combined with physical separation of cells of particular interest.Services include High-end, staff assisted cell sorting, using four different high speed sorters;Unassisted bench-top analysis available 24/7;Assisted bench-top analysis available by appointment;Extensive training on bench-top analyzers;Extensive training on FACS Aria sorters;Consultation on experimental design and data interpretation.
North Carolina University School of Medicine Histology Research Core Facility
Facility offers histological services including Tissue Sectioning:Paraffin embedding and frozen embedding in OCT;Paraffin section serial, random, serial interrupted;Frozen section thaw mount cold/warm, serial, free floating,thick slice, random and serial interrupted, CryoJane tape transfer;Vibratome section;Routine staining, i.e., H+E, Nuclear Fast Red Special staining, Alcian Blue, Cresyl Violet, PAS, Oil Red , Toluidine Blue, Von Kossa, Combined Massons Elastin, Picrosirius Red, Sudan IV, Thionin, Prussian Blue, Movats Pentachrome, Masson Trichrome, Alcian Blue/Phloxine/Tartrazine, others available upon request. Immunohistochemistry/Enzyme:ABC method (direct/indirect);Fluorescence;Biocytin detection;HRP;Single and multiple-labeling;Edu/Brdu,in situ Hybridization,RNAScope,BaseScope.
Massachusetts Institute of Technology Koch Institute Bioinformatics and Computing Core Facility
Barbara K. Ostrom Bioinformatics Facility
The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility
Core provides support, assistance and training in wide range of bioinformatics topics. Maintains high-performance computing resource offering many bioinformatics applications, substantial processing power and secure storage. Provides support for desktop computing and poster printing. Services include Data Analysis, Software Support (access to proprietary bioinformatics resources Ingenuity Pathway Analysis and GeneGO MetaCore, Training sessions covering various bioinformatics topics, Linux compute cluster, data storage.
Nanowell Cytometry platform is shared resource housed in Flow Cytometry Core that provides Koch Institute and MIT researchers access to Microengraving and SeqWell technologies, developed in Love and Shalek Laboratories at Koch Institute. Microengraving platform enables measurement of multiple traits from individual cells derived from wide array of tissues or cell types, such as immune cells either in their native condition or upon stimulation. Platform allows simultaneous assessment from small or large numbers of cells. Additionally, it is possible to obtain genetic information from individual cells of interest. Platform has been employed in projects related to antibody discovery, tumor profiling from various cancer tissues, and immune cell functions in various allergic, infectious or auto-immune diseases.Core offers access to CellCelector, tool which enables users to isolate single cells using ultra-precise robotic micromanipulator. Offers access to nanowell microplates which enable automated isolation of monoclonal and viable clones. Seq-Well is portable, low-cost platform for massively-parallel single-cell RNA-Seq. Barcoded mRNA capture beads and single cells are sealed in array of subnanoliter wells using semi-permeable membrane, enabling efficient cell lysis and transcript capture.
Purdue University Bioinformatics Core Facility
Core to facilitate, amplify, and accelerate biological research and discovery through application of bioinformatics. Provides bioinformatic analysis services for Next Generation Sequencing (NGS) data.
Texas A&M University Integrated Metabolomics Analysis Core Facility
Open access core facility available to all TAMU users for Metabolomics service and research. Provides different levels of service from drop-off to collaborative projects.Training for TAMU postdoctoral fellows and students to use instrumentation in support of specific projects.Short courses and workshops on advances in metabolomics. Instrumentation for targeted and untargeted metabolomics analysis.Provides mass spectrometers that are coupled to liquid chromatography (LC) or gas chromatography (GC) separation systems.
Brown University Molecular Pathology Core Facility
Core provides equipment and technical expertise for evaluation of molecular and morphological changes in cells, tissues, and organs following exposure to complex environmental contaminants. Provides equipment, including automated tissue processor, paraffin embedding center, two automated microtomes, cryostat, vibratome for soft-tissue sectioning, multiheaded light microscope with projection capabilities, system for laser capture microdissection, and slide scanner with analysis software for identification and quantification of morphological structures.Offers expertise in histopathological and immunocytochemial methods, including fixation, dehydration, embedding, sectioning, histological staining, immunolabeling, high-resolution imaging, and quantitative image analysis. Services in sample preparation, offers assistance in imaging and image analysis and provides consultation for ongoing or future research projects, training program for students and investigators who use centrally available equipment.
Massachusetts Institute of Technology Koch Institute Preclinical Modeling Core Facility
Core provides service support to all MIT investigators who utilize specialized in vitro cells such as stem cells, organoids, or primary cell lines and/or novel mouse models to study human diseases such as cancer. Projects involve generation of new model system, such as CRISPR-mediated gene editing in mouse to introduce mutation that mimics one found in patients. Helps with projects required optimization of finicky cell cultures and other challenges.Provides customizable set of service options to match specific needs of each project, including consultative advice and troubleshooting, complete tissue culture and microinjection services within our facilities or hands-on training to enable investigators to perfom these experiments either at their own laboratory or within our facilities.Services Include:Gene Targeting genomic modification through traditional or CRISPR/Cas9 locus targeting, assistance with targeting strategies and vector designs;Embryonic Stem Cells generation of new ES lines from mouse strains, importation and testing of lines from outside sources, differentiation of ES lines into specific cell lineages or cell types and more;Microinjection injection of mouse ES cells into blastocysts to generate chimeras and injection of DNA, RNA or CRISPR RNPs into the pronucleus of fertilized mouse eggs to generate transgenic and edited mice;Specialized Tissue Culture establishemnt of new primary cell cultures from a tumor, tissue or organ; Isolation of fibroblasts (MEFs) from mice for culture and analysis;Tissue Culture for Xenograft and Syngenic Modeling optimization, validation and testing of cell lines for orthotopic placement into mice, coordinated with Preclinical Testing Facility;Repository of Reagent Mice Commonly used wild type mice such as C57BL/6j as well as KrasG12D-based models of cancers are maintained on campus for efficient distrubution;Training and Troubleshooting for all aspects of embryonic stem cells, primary cultures, animal breeding etc.;Serum, DMEM, LIF and other media components that have been tested and verified for use with ES cells.
Brown University Structural Biology Core Facility
Core provides equipment used for structural modeling in crystals and in solution, using X-ray diffraction and scattering, as well as magnetic resonance.
South Florida University College of Medicine Fred Wright Jr Flow Cytometry Core Facility
USF COM Fred Wright Jr Flow Cytometry Core
Core is equipped with two benchtop analyzers from BD Immunocytometry Systems (3 laser/8 color BD Canto II and 4 laser/17 color BD LSR II). These instruments support large variety of applications, including multicolor cell phenotyping, apoptosis, cell cycle and bead arrays. After orientation and training, equipment is available for use directly by investigators. Alternatively experiments can be run and analyzed by Core Facility staff.For sorting purposes facility is equipped with high speed BD FacsAria IIu sorter (4 laser/11 colors), as well as magnetic sorter (AutoMacs Pro) from Miltenyi Biotech. FacsAria IIu is enclosed in Baker Bioprotect III to support sort of biohazardous agents level 1 and 2.
University of California at San Francisco Embryonic Stem Cell Targeting Core Facility
Core provides ES cell services with high probability of germline transmission. Offers ES cell targeting, genomic DNA extraction from 96-well plates, expansion of targeted ES cells, chromosome counts, and preparation of ES cells for microinjection.Prior to initiation of project, consultation is available on entire procedures of generating knockout mice. Core works with Gladstone Transgenic Gene Targeting Core for your microinjections to deliver full-range gene targeting service;CRISPR gRNA cloning,Cell-based functional test to identify best-performing TALENs or sgRNAs for your gene-editing experiment via mismatch-based assays such as Surveyor or T7E1;In vitro RNA synthesis - can help to make RNAs for your zygote injection or RNA transfection. We have TALEN and Cas9 plasmids with either T7 or T3 promoter subcloned in for efficient in vitro synthesis.sgRNAs for CRISPR can be synthesized off T7-sgRNA PCR product. Quality of synthesized RNAs will be checked via bioanalyzer;Custom TALEN to make double-strand breaks in genome;ES cell targeting (feeder-independent).Investigators targeting construct will be electroporated by core personnel. We have two feeder-independent ES cell lines, E14 (129-derived) and JM8A3.N1 (C57BL/6-derived) you can choose from. After drug selection for about one week, up to 300 colonies will be picked. When they are about to be confluent, we will split them as duplicate, one master plate to freeze for future expansion of positive clones and one plate for genotyping to identify targeted ES cell clones. Your plates for genotyping will be ready for pick-up 2-3 weeks after electroporation date.Genomic DNA extraction from ES cells on 96-well plate;Expansion of targeted clones from core targeting (up to 5 clones),A maximum of 5 positive clones will be thawed from 96-well plates and expanded to 6-wells. We will freeze 5 vials (each about 1 million)/clone for future use and give you 1 vial-equivalent cells to validate your genotyping before injection. It takes about 10 days to expand and freeze down cells;Expansion of ES cells from outside resources (per clone) Investigators provide one vial of frozen ES cells with information about culture condition from original resource. We will revive, nurture, and refreeze ES cells (5 vials) when they are ready. In addition, we will give you 1~2 million cells for your genotyping verification;Preparation for microinjection;Chromosome counting;Custom services.
University of California at San Francisco Division of Experimental Medicine Flow Core Facility
Flow cytometry facility offering training and services including:Access to two, 17-color BD LSR II analytical instruments with High Throughput Sampler (HTS) module,Configurations:LSRII 1,LSRII 2;Help with Flow Cytometry Panel Design;Fluorofinder (access our cytometers under CFAR Immunology Core);BD Panel designer;SFGH LSRII Flow Core Protocols;LSRII Startup and Shutdown;How to run the CST calibration assay;Access to a 17-color BD FACSAria II for fluorescence-activated cell sorting (FACS);4-way tube sorting;96 well plate sorting;Index sorting;SFGH ARIA Flow Core Protocols and configuration;ARIA Startup;Determining Drop Delay;Side Stream Set Up;Clog Procedure;ARIA Shutdown Protocol;ARIA Configuration;DNA analysis with standard dyes;Analysis of CFP, GFP, YFP, mRFP, mTomato, and mCherry gene expression proteins;Calcium flux measurements using Indo-1;Training of users on the operation of instruments and experimental design through the CIL Flow Cytometry Course;Maintaining and Upgrading Instruments;Research Support Services (study design, assay selection, grant and paper writing support).
Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available.
Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature.
University of California at San Francisco Immunology Lab Core Facility
University of California at San Francisco Core Immunology Lab
Provides immunology assays, expert consultation, and education to UCSF and global research community. CIL specializes in developing immunology research tools, and initiating and stimulating innovative research projects to address emerging questions in immunologic diseases including HIV pathogenesis.Services include:Isolation of PBMC for staining, cell sorting, or viable cryopreservation;Isolation of mucosal mononuclear cells (MMC) from mucosal tissue biopsies;Immunomagnetic bead isolation of untouched cell populations for functional studies;Immunophenotyping of whole blood, PBMC, MMC and cerebrospinal fluid for: NK, B and T cells percentages, and their subsets, including maturation, trafficking, senescence, activation, in vivo proliferation and chemokine receptor expression;Flow cytometric functional assays, including NK cell function, antigen-specific CD4+ and CD8+ T cell cytokine expression, degranulation and proliferation;Evaluation of T cell signaling by phosflow using monoclonal antibodies specific for phosphorylated protein;Training and Support;Flow Cytometry Training Course;Three-hour lecture and lab course designed to cover basics of flow cytometry including:Fluorescence emission and detection,Fluidics,Operation,Panel design,Controls.
University of Massachusetts Amherst Genomics Resource Laboratory Core Facility
Core provides services and advanced instrumentation support for nucleic acid (DNA and RNA) analysis, high-throughput next-generation sequencing, including solutions for sample processing such as nucleic-acid isolation, nucleic-acid quantitative and qualitative analysis, NGS library preparation, quantitative-PCR analysis, etc. Provides sample processing and library preparation such as whole genome sequencing, shotgun metagenomics, metatranscriptomics, targeted amplicon sequencing, RNA-Seq, ChIP-Seq, Exome Sequencing, Methyl-seq, Single Cell Genomics, etc. Facility accepts samples and will perform requested analysis. Offers training to users to conduct experimentation.
Johns Hopkins University School of Medicine Synthesis and Sequencing Core Facility
Core provides services including Peptide Synthesis and Purification,Protein/Peptide Sequence Analysis,DNA Synthesis and Purification,Sanger DNA Sequencing,Next Generation Sequencing.
Oregon State University Nuclear Magnetic Resonance Core Facility
Nuclear Magnetic Resonance (NMR) Facility
Facility maintains instrumentation, provides hands-on training to new users, experimental design expertise, assistance with data analysis and support for incorporating NMR into grants and manuscripts. NMR spectrometers are available at 800 MHz, 700 MHz, 500 MHz and 400 MHz (2), corresponding to magnetic field strengths ranging from 18.8 T to 9.4 T. Data processing and analysis software is available on workstations in NMR Facility. The facility supports scientific inquiry in research areas such as structural biology, organic chemistry, natural products analysis and environmental studies.
Brown University Division of Biology and Medicine Proteomics Shared Resource Core Facility
NSF/EPSCoR Proteomics Shared Resource Facility
Core provides instrumentation and proteomics expertise to Brown University and Rhode Island-EPSCoR scientific communities and training in emerging proteomic techniques. Mass Spectrometry proteomics resources and services are provided by COBRE Center for Cancer Research Development (CCRD) at Rhode Island Hospital: Proteomics Core.
Iowa State University W.M. Keck Metabolomics Research Laboratory Core Facility
Iowa State University Metabolomics Research Laboratory
Iowa State University W.M. Keck Metabolomics Research Laboratory
W. M. Keck Metabolomics Research Laboratory
Core facility that conducts fee for service mass spectrometry-based non-targeted and targeted metabolomic studies. The facility serves and partners with both on- and off-campus clients.
University of Sheffield Genomic Core Facility
Core provides DNA sequencing services including DNA extraction, cell line identification, microsatellite analysis, and antibody sequencing,DNA Sequencing, Monoclonal Antibody Sequencing,Nucleic Acid Quantification,PCR Machine Hire,Real-Time PCR Robotic Liquid Handling,Taqman SNP Analysis.
University of North Carolina at Chapel Hill Microscopy Services Laboratory Core Facility
Core provides training, assistance and services in light microscopy, electron microscopy and image analysis. UNC core facility that is part of Department of Pathology and Laboratory Medicine, and are light microscopy core for Lineberger Comprehensive Cancer Center.
University of Chicago Cellular Screening Center Core Facility
University of Chicago Cellular Screening Center
Facility provides high throughput cell- and non-cell-based screening. Has number of validated cell lines and variety of small molecule or siRNA screening libraries available to investigators.
Chicago University Biophysics Core Facility
Core provides access to biophysics equipment, integral to research community at University of Chicago.Provides tools, training, and assistance for quantitative analysis of macromolecules and their interactions. Instruments include Seahorse XFe-96 Extracellular Flux Analyzer,Jasco J-1500 CD Spectrometer,Synergy Neo HST Plate Reader,Wyatt DAWN HELEOS II SLS,Wyatt DynaPro Plate Reader DLS,Wyatt DynaPro NanoStar DLS,HORIBA Fluorolog-3,Microcal iTC200,Molecular Imager,Bio-Rad ProteOn XPR to Biacore 8K,Agilent 8453 Spectrophotometer. Core provides staff assistance in conducting experiments.
University of Chicago Human Immunologic Monitoring Core Facility
Facility serves as specialized laboratory performing correlative assays for cancer-based clinical trials. Participates in project development to assist in assay selection and optimization prior to study initiation. Offers pick-up service for specimens from patients at U of C Hospital or outpatient clinics, and process samples as indicated for assays being performed. For some studies, isolation and freezing of peripheral blood lymphocytes for analysis at later date is performed, while for others immediate staining of whole blood for specific cell surface markers of interest is carried out. Prepares clinical grade products, such as peptide vaccines, for administration into patients.Assays performed include ELISA, ELISPOT, tetramer binding assays, detection of cell surface markers by flow cytometry, and biochemical assays such as Western Blots, RNA extraction from tumor biopsies and either real time RT-PCR for specific transcripts or preparation of samples for gene expression profiling. Facility is equipped with MACSQuant Flow Cytometer, ELISA microplate reader, ELISPOT reader, PCR thermocyclers, CO2 incubators, biosafety cabinets, centrifuges, and equipment for Western blot analysis. Performs assays on human samples but consideration will be given to expanding these services to mouse-model systems.
Case Western Reserve University Imaging Research Core Facility
Core provides preclinical and clinical imaging instrumentation and techniques.Preclinical services include Bioluminescence,Fluorescence,In situ cryoimaging,Magnetic Resonance Imaging (MRI),Positron Emission Tomography (PET),Radiochemistry Synthesis, Scintigraphy,Ultrasound,X-ray / Computed Tomography (CT) / micro CT,Image Processing / Quantification clinical research imaging systems. Clinical services include Comprehensive MR imaging research services, Dedicated Siemens Skyra 3T MRI scanner, Large animal preclinical studies, or clinical human research may be conducted,Structural and functional brain scanning can be performed with Avotec LCD Projection System, Coodination of access to PET and CT scanners for additional preclinical and human imaging studies. Core includes PET radiopharmaceutical core facility. Core staff provide radiochemistry synthesis.
Core provides training to use latest episomal techniques to reprogram, expand and characterize human and mice iPS cells from skin or blood tissues of healthy subjects and diseased patients. Develops capability to differentiate iPS cells into specific somatic cells, such as neutrons, cardiomyocytes, and hepatocytes.
University of California San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences NMR Core Facility
Core provides access to NMR technology. Users can collect their own data, facility staff can do it all for you, or collaborative projects can be developed. Provides training in instrument operation and can offer advice for data analysis or project feasibility. Facility houses two 600 MHz Bruker Avance III spectrometers with cryogenically cooled probes.
Kansas University Medical Center Hoglund Brain Imaging Center Core Facility
Core provides imaging capabilities, including magnetic resonance imaging, magnetoencephalolgraphy, electroencephalography, magnetocardiography, and ultrasound,expertise in cognitive neuroscience, neurobiology, biomedical physics, and computing, together with support team of technologists, nurses, research associates, and research assistants. Through strong collaborations, these individuals assist with study design, collection of data, analysis, and interpretation of results. HBIC supports investigators with new technique development, feasibility studies, pilot funding, preparing grant applications and manuscripts, and compliance. Carries out investigator-initiated research and research/clinical trials sponsored by public and private agencies. Offers education and training.
University of Texas Southwestern Medical Center Mouse Genome Engineering Core Facility
Core provides production of mouse models to support fundamental and translational research. Provides transgenic, gene targeting,DNA microinjection services, CRISPR/Cas9 microinjection, ES cell manipulation and other microinjection services to generate transgenic mice, knock-in/knock-out mice and chimeric mice harboring select genetic mutations. Other services include mouse sperm cryopreservation and recovery, in vitro fertilization (IVF), rederivation of pathogen free mouse lines and derivation of mouse embryonic stem cell lines. Provides general consultations on experimental designs and vectors for gene modification-related projects, DNA preparation, recombinant ES clones, mouse genotyping, colony breeding and husbandry, customize services as requested to support development of animal models for modeling human diseases.
Florida State University X-Ray Crystallography Core Facility
Shared macromolecular x-ray crystallography facility provides instruments and expertise for screening, optimizing, imaging, growing, and storing crystals of biological macromolecules. The X-Ray Facility coordinates single crystal x-ray diffraction data collection at third generation synchrotron x-ray source using FSU's membership at the National Synchrotron Light Source II at Brookhaven National Lab, Upton, NY. XRF also offers custom buffer preparation, optimization, and crystal set-up using multi-well format crystallization blocks and plates.XRF has ARI Crystal Gryphon robot, Formulatrix Rock Imager, Formulator 16, Rock Maker software, RUMED incubator, Cryo storage and shipping dewars, Leica S8 AP0 Zoom microscope and other amenities.
Chicago University Integrated Small Animal Imaging Research Resource Core Facility
Integrated Small Animal Imaging Research Resource
Core offers imaging modalities, techniques, and services for in vivo imaging of small animals and ex vivo imaging of tissue/organ specimens. iSAIRR sub-cores feature magnetic resonance imaging and spectroscopy (MRIS); optical imaging (bioluminescence and fluorescence); positron emission tomography, single photon emission computed tomography, and computed tomography (PET/SPECT/CT).Services include Assistance with experimental design,Assisted and/or independent image acquisition,Veterinary support for all imaging modalities,Assistance with data processing and interpretation.
University of California, Berkeley Biosciences Divisional Services Cell Culture Core Facility
Core provides cell cultures (mammalian and insect), media, supplies and expertise and consultation regarding cell culture needs, media, and experimental design.Provides tested media, serum, and cell lines at exceptionally low prices, large scale production of cells, expansion and harvesting of hybridoma lines,cryopreservation of cell lines, Cell Authentication by STR analysis provided in conjunction with DNA Sequencing Facility, Mycoplasma screeening,Use of 2 laminar flow hoods for mammalian or insect cell manipulation.
New York University School of Medicine Langone Health Proteomics Laboratory Core Facility
New York University School of Medicine Langone Health Proteomics Laboratory
Core offers specialized expertise for analysis of proteins and peptides using mass spectrometry. Develops new methods and customized approaches for proteomic analysis and suggests experimental strategies and sample preparation prior to mass spectrometry analysis. Services include:comprehensive protein identification ,analysis of affinity purified complexes,characterizing protein post-translational modifications,de novo sequencing,label and label-free quantitation ,multiplexed quantitation global phosphorylation and ubiquitin analysis,analysis of laser-capture microdissected formalin-fixed paraffin-embedded tissue,secretome analysis,crosslinking analysis,disulfide mapping.
Children's Hospital Oakland Research Institute Elemental Analysis Core Facility
Core provides sample preparation, metal extraction, dissolved solids measurement, analytic consultation, and technical writing assistance) in support of wide range of clinical and biomedical research projects.Instruments include Agilent 5100 SVDV Inductively-Coupled Plasma-Optical Emission Spectrometer, SPS3 Robotic Autosampler,MARS5 Microwave Sample Digestion Oven,ICPExpert Advanced Workstation.Analytic Capabilities:Simultaneous, multi-element quantitation over wide dynamic range;Broad elemental detection capability with high precision and sensitivity;Compatible with range of clinical, nutritional, basic research, and pharmaceutical samples;Tolerant of high total dissolved solids and complex matrix components;NIST-traceable calibrants, standards, and other QA/QC controls included in analyses.
New York University School of Medicine Langone Health Experimental Pathology Research Laboratory Core Facility
New York University School of Medicine Langone Health Experimental Pathology Research Laboratory
NYU Langon Experimental Pathology Research Laboratory
Core provides services, access to instruments, and training to facilitate production of animal tissue samples for morphological and molecular analyses. Supports multiplex immunofluorescence staining, RNA in situ hybridization (ISH), and imaging analysis. Services include tissue preparation, processing, and sectioning, as well as histochemistry and immunohistochemistry of fresh, frozen, and fixed animal tissues, can optimize and validate commercial or proprietary antibodies for chromogenic or fluorescence-based immunohistochemistry including seven-color multiplexing.Provides access to database listing antibodies that have been tested in lab to date and are currently in stock.Offers basic imaging resources and digital whole-slide scanning of stained tissue sections, which allows researchers to view their slides online at their convenience.Researchers can also rent our self-service instruments. These include embedding station, microtome, cryostat, and vibratome. Provides access to brightfield and fluorescence upright and dissecting microscopes,laser capture microdissection scope, and high-throughput multispectral imaging system.To reserve time on instrument, faculty, staff, and investigators must be registered in iLab.
New York University School of Medicine Langone Health Genome Technology Center Core Facility
New York University School of Medicine Genome Technology Center
New York University School of Medicine Langone Health Genome Technology Center
Core provides range of services related to genome, epigenome, and transcriptome analysis. Offers technologies including Illumina deep sequencing and sample preparation for variety of applications, including DNA and RNA sequencing (DNA- and RNA-seq), exome sequencing, targeted capture, chromatin immunoprecipitation sequencing (ChIP-seq), methylation sequencing (Methyl-seq), metagenomics, and many others;Automation of Illumina library and targeted capture preps, including 16S ribosomal RNA (rRNA) sequencing;Oxford Nanopore sequencing (long reads);Bio-Rad Droplet Digita polymerase chain reaction (PCR);Nanostring nCounter;Single-cell RNA- and DNA-seq using the C1 Auto Prep System from Fluidigm, and 10x Genomics Chromium System.Provides expertise on strategies to achieve research goals in any field related to genomics, and can tailor bioinformatics analysis to individual project. If you supply us with nucleic acids, we can perform every step required to help you achieve your desired results.
New York University School of Medicine Langone Health Center for Biospecimen Research and Development Core Facility
New York University School of Medicine Langone Health Center for Biospecimen Research and Development
NYU Langone Center for Biospecimen Research and Development
Core mission is to drive scientific discovery through use of human specimens.Helps facilitate translational research, match human specimen resources to scientific needs, foster multi-investigator collaborative projects, and catalyze scientific innovation,improving researcher access to existing biospecimen resources, and enhancing institution-wide tissue-banking efforts and capacity. Another priority is to implement campus-wide policy for human biospecimen collection and storage to ensure regulatory compliance.
University of Wisconsin-Madison Chemistry Instrumentation Center - Mass Spectrometry Core Facility
Core provides mass spectrometers including Thermo Q Exactive Plus,Bruker impact II ,Bruker microflex LRF,Bruker ULTRAFLEX III,Shimadzu GCMS-QP2010S,Waters Acquity LCMS.
New York University School of Medicine Langone Health Genotyping Core Laboratory Core Facility
New York University School of Medicine Langone Health Genotyping Core Laboratory
Core provides fast, accurate, convenient, and affordable genotyping technologies. We use conventional polymerase chain reaction (PCR) and gel electrophoresis methods. By pooling samples from group of users, we can better ensure accuracy, cost-effectiveness, and quality control.
Queensland University of Technology Central Analytical Research Facility (CARF) Proteomics and Small Molecule Mass Spectrometry Core Facility
Proteomics and small molecule mass spectrometry
Core provides liquid chromatography and gas chromatography mass spectrometry instrumentation for selective identification and reproducible quantification of trace-level biomolecules in complex samples. Services include qualitative, quantitative and structural analysis of proteins, lipids, metabolites, pesticides, pharmaceuticals and volatile organic compounds. Tests can be performed as long as molecules of interest are amenable to ionisation technique employed in source of mass spectrometer. Depending on instrument type, samples may be solid, liquid or gas. Mass spectrometry platforms include Liquid Chromatography Mass Spectrometry (LC-MS) and Gas Chromatography Mass Spectrometry (GC-MS). Analysis include volatile organic compounds (odour analysis),pharmacokinetics (bioavailability, bioefficacy),drug development (determining structures of drugs and metabolites),clinical testing (biomarkers discovery and endogenous compounds),genomics (oligonucleotide sequencing) epigenetics (global DNA methylation analysis),environmental research (testing water, soil, food and air quality).
New York University School of Medicine Langone Health Microscopy Laboratory Core Facility
Core offers comprehensive light and electron microscopy technologies. Our scientists use light microscopes and electron microscopes at resolutions ranging from centimeters to angstroms, providing clear and detailed images.We assist at every stage of your experiment, offering research-design consultation and instrument training, as well as guidance in study execution, analysis, and presentation for publication.
New York University School of Medicine Langone Health Metabolomics Laboratory Core Facility
New York University School of Medicine Langone Health Metabolomics Laboratory
Core offers custom metabolomics services,specializes in mass spectrometry based metabolomics, offering global (untargeted) and targeted methods for metabolite identification and quantification.Commonly assayed targets include glycolytic and tricarboxylic acid (TCA) cycle intermediates, amino acids, nucleotides, and lipids. Using custom-targeted method, we can perform absolute or relative quantification, flux analysis, and biotransformation analysis.
New York University School of Medicine Langone Health Precision Immunology Laboratory Core Facility
New York University School of Medicine Langone Health Precision Immunology Laboratory
NYU Langone Immune Monitoring Laboratory
NYU Langone Precision Immunology Laboratory
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 20,2025. Core to study immune cell phenotype and function, characterizes antitumor immune responses, determines mechanisms of immune escape and evasion, and develops biomarkers that predict patient outcomes or possible toxicities. Offers services for immune monitoring,provides expert knowledge that guides choice of technologies used for study, coordinates purchase, quality control, and use of reagents. Stand-alone services include high-quality cell processing and storage to support correlative studies. These services allow convenient batched analysis of trial samples.Staff purifies peripheral blood mononuclear cells daily from clinic visits and another staff member is available for on-demand and after-hours processing. Samples are cryopreserved on-site in temperature-monitored LN2 freezers for short-term storage. For long-term storage, samples are transferred to Novare Biologistics,off-site cGMP-compliant, New York State-licensed, and FDA-registered biorepository. Routinely assess quality of processing and cryopreservation. Core meets performance targets for cell viability and recovery necessary for certification by Integrated Biobank of Luxembourg. Offers service for isolating tumor-infiltrating lymphocytes using dissociation protocols optimized for various tumor tissues. Offers flow cytometry at Perlmutter Cancer Center, along with expert service and training. Sterile fluorescence-activated cell sorting (17 colors) is routinely performed with options for high-speed (50K cells per second), single-cell deposition (into polymerase chain reaction plates), and BSL-3 sorting for unscreened or infected human material. Data analysis workstations are also available.Offers single-cell analysis through our cutting-edge 30-parameter flow cytometry technology and Integrated Molecular Cytometry Platforms (IMCPs).
New York University School of Medicine Langone Health Preclinical Imaging Laboratory
NYU Langone Preclinical Imaging Laboratory
Core provides investigators with access to imaging technologies and strategies to image live animals on organ, tissue, cell, or molecular level.Core for studying and monitoring disease in small living subjects.Performs noninvasive and nonlethal three-dimensional imaging. Equipped with instruments for micromagnetic resonance imaging, micropositron emission tomography, X-ray microcomputed tomography, bioluminescence and fluorescence scanning, and high-frequency ultrasound.
University of Illinois at Urbana-Champaign Core Facilities at IGB
Core for biological microscopy and image analysis. Offers high-end equipment,user training,ongoing support, including experiment design and data interpretation,twenty-four hour access Services,3D Printing, Transfer Files, Image Analysis,Histology,Instrument Training.
Northern Arizona University Environmental Genetics and Genomics Laboratory
NAU Environmental Genetics and Genomics Laboratory
Core facility for genomics research offers range of DNA sequencing, assistance and advising in planning, data acquisition, and data analysis. Provides genetic and genomic support to environmental and biomedical research projects. Creates education and training opportunities for students and professionals.
Gladstone Institutes Histology and Light Microscopy Core Facility
Core provides technical assistance, training, consultation and assistance with all aspects of experimental design, sample preparation, image processing, and data analysis to scientists from Gladstone, UCSF, and Bay Area scientific community. Core is equipped with expertise in histological techniques including complex immunolabeling and histological image analysis, high-resolution imaging, confocal microscopy, light-sheet microscopy, spinning disk microscopy, and optical projection tomography and advanced image analysis.Histology Services includeTissue dissection and fixation, Paraffin processing and embedding,Frozen (cryo) processing and embedding,Tissue sectioning,Section staining.Microscopy Services include Epifluorescence, confocal and light sheet microscopy,Whole slide scanning,Microscopy consultation and training,Digital image analysis.
Northwestern University Materials Research Center Cleanroom Core Facility
Materials Processing and Microfabrication Facility
Cleanroom facility is devoted to materials processing, growth, device fabrication, characterization and electronic and photonic materials. Provides microfabrication and thin film processing capabilities. Facility includes class 100 and 1000 cleanrooms.Training of equipment and assisted use within facility is available to provide necessary expertise.Provides centralized resource for deposition of metal, semiconductor and dielectric thin films, photolithography, etching, bonding, dicing, characterization and materials processing.
New York University School of Medicine Langone Health Rodent Behavior Laboratory
Core offers equipment, facilities, and expertise to quantitatively assess broad range of behaviors in mice and rats, develop and validate novel paradigms to improve translation of preclinical behavioral results to clinically relevant outcome measures and create better tools for biobehavioral research.Core helped develop novel touch-screen tests to assess rodent attention, working memory, and reinforcement learning.
Northwestern University Biostatistics Collaborative Center
Core where division members engage in statistical methods development and application, research design and statistical computing for health science research. Faculty interests encompass Bayesian methods, bioinformatics, causal inference, computational biology, clinical trials, diagnostic testing, longitudinal modeling, missing data modeling, observational data methods, semi-parametric models, spatial modeling, statistical genetics and survival analysis.
Northwestern University Proteomics Core Facility
Northwestern University Proteomics Center of Excellence Core Facility
Core offers multiple types of experiments from simple protein identification to protein quantitation. Performs traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Services include proteins identification after in-gel or in-solution digestion, top-down mass spectrometry to preserve post-translationally modified forms of proteins present in vivo by measuring them intact, IP-MS Pulldown,BioID service to identify target of biotin ligase that has been tagged onto their protein via traditional cloning methods,Untargeted Quantitative Peptide Proteomics,Targeted Quantitative Peptide Proteomics,Epiproteomic Histone Modification Panel A,Epiproteomic Histone Modification Panel B,Untargeted Metabolomics,Phosphoproteomics,PTM Scan,ChIP-MS.
Oregon Health and Science University Bioinformatics and Biostatistics Core Facility
Oregon Health and Science University Bioinformatics and Biostatistics Core
Core provides statistical and big data analysis support. Performs data analysis and manuscript preparation services in Biostatistics, such as statistical genetics, longitudinal, survival, and high-throughput/high-dimensional omics data analysis; and Bioinformatics, such as DNA- and RNA-seq alignment, single cell DNA- and RNA-seq analysis, variant calling, differential expression and pathway analysis, data integration, online data submission, and custom script writing. Provides training to lab staff to enable them to perform future analyses.
Northwestern University Materials Characterization and Imaging Core Facility
Materials Characterization and Imaging Facility
Core offers characterization and sample preparation equipment. Characterization techniques include optical microscopy, thermal imaging, thermal analysis (DSC, TGA), hardness testing (Vicker, Knoop, Rockwell), electronic characterization (Hall Effect, Impedance Spectroscopy, Kelvin Probe, Charge Transport) and rheological characterization. Sample and surface preparation capabilities include mounting (castable mounts, hot pressure mounting, vacuum impregnation), cutting, sectioning and wafer dicing, polishing/grinding, electropolishing, ion beam milling and cross-sectional polishing. Tube and box furnaces are available with temperature range up to 1700C for thermal processing.
Northwestern University Developmental Therapeutics Core Facility
Core evaluates therapeutic agents and diagnostics, as well as existing therapeutics being considered for novel uses, through continued development and deployment of relevant animal models and in vitro cell lines and tissue models. Provides services to investigators to suit many needs, including those who may lack laboratory facilities and/or expertise for conducting experiments associated with preclinical therapeutic hypothesis testing.Services include Proliferation and Apoptosis Assays, Therapy-Response Experiments, Exploratory PK and Tox, Device Implantation and Monitoring,PDX Models,Immunization.
Texas University Southwestern Medical Center Whole Brain Microscopy Core Facility
Core suited to advance study of traumatic brain injury, as well as other neurological and psychiatric disorders.Utilizes microscopy strategies to evaluate neuropathology across micro-, meso-, and macro-scales of inquiry. Provides access to microscopes including TissueCyte 1000 multi-photon microscopes,Hamamatsu NanoZoomer 2.0-HT,Zeiss Axioscan.Z1. Offers access to fluorescence stereomicroscope and upright microscope, both with digital cameras, as well as sectioning equipment (cryostat, microtome, and vibrotome). Provide computer available for use running MicroBrightField Stereo Investigator and Neurolucida software packages for offline stereological analysis, neuron tracing, and 3D rendering of large, whole-brain datasets.
Beth Israel Deaconess Medical Center Translational MRI Research Core Facility
Core provides MRI capabilities for imaging human subjects and potentially large animals as part of research studies. Facility operates GE Discovery MR750 3T whole-body scanner and can provide access to 1.5T system. Scanner is FDA cleared for clinical use. It has proprietary software including pulse programming environments and reconstruction programs and customizable software and protocols for applications including functional and structural brain imaging, abdominal perfusion and diffusion, muscle functional imaging and spectroscopy are available to users.Support for fMRI acquisition and visual and auditory stimulus presentation, diffusion tensor imaging, spectroscopy, and high quality anatomic imaging is available. The system has specialized receiver coils for sensitive imaging of particular anatomy. Additional customized coils can be manufactured in our RF lab. The system also has full broadband capability for multinuclear MRI and MRS, including (F-19, C-13, P-31, and Na-23).Our facility can also provide Image Post-processing and computerized image transfer, assistance to ensure MRI equipment safety, and can facilitate Clinical Readings.
North Carolina University at Chapel Hill Nanomedicines Characterization Core Facility
Nanomedicines Characterization Core Facility
Core provides physicochemical characterization of nanoscale entities. Offers characterization of several classes of nanomaterials:Polymer conjugates,Polymeric micelles,Liposomes,Nanogels,Polyion complexes of small drugs and biomacromolecules (proteins, DNA, and RNA),Inorganic/metal nanoparticles,Bio-derived nanoparticles such as exosomes with protein and nucleic acid cargo.
Northwestern University School of Medicine Structural Biology Core Facility
Core provides equipment, training, technical support, and maintenance of equipment for studying structures of biological macromolecules and materials. Serves with expertise in structural and computational biology. Services offered include Macromolecular Structure Determination and Analysis,Macromolecular crystallography at LS-CAT,Robotics equipment for crystallization experiments,UV crystal imaging capabilities,Software for structure analysis,Graphics facilities for visualization/presentation of molecular structures,Computer servers specialized for structural biology calculationss,Support and Training ,X-ray crystallography, from designing crystallization experiments to structure determination and refinemen,Molecular graphics for analysis and presentation,CryoEM and EM training.Resources Available:Crystallography Art Robbins, Inc. Phoenix and Gryphon crystallization robots,TTP Labtech Dragonfly liquid handler for crystal tray setup,Jansi UVEX UV/Vis microscope/imaging system,Stereomicroscopes (camera equipped, at room temperature and 4 degrees C),Incubators for temperature-controlled crystallization,Coordination of access to LS-CAT for Northwestern University users,CryoEM,JEOL 3200FS TEM equipped with in-column energy filter (omega filter), field emission gun capable of operating at 200 or 300 kV and Gatan K2 Summit Direct Electron Detector,JEOL 1400 with Gatan 4k x 4k Ultrascan CCD camera,Solarus Plasma Cleaner and Pelco easyGlow Discharge Cleaning System,Cressington 308R carbon coater,Gatan Cryoplunge 3 and FEI Vitrobot Mark IV,Gatan 626 cryoholders with 655 Turbo pump stations.Resources available Computational:50+ node cluster running Linux including several single- and multi-GPU nodes,7 Quad-core Intel Xeon 3.4GHz workstations (3D stereo equipped for visualization and model building) 3 Dual Quad-core Intel Xeon 3.5GHz workstations with GPU computing capabilities (3D stereo equipped for visualization, model building, and GPU computing),LTO6 writers for quick data backup,45 tape LTO6 system for continuous data backup,Over 200 Tb of disk storage including RAID systems,10 Gigabit fiber Ethernet connection to APS.Software Crystallography,CCP4 suite,PHENIX,SHARP,SOLVE,HKL2000,XDS,CryoEM,CryoSparc,Relion3,Leginon,cisTEM,Appion,NMR,CNS,FELIX,Aria Modeling, graphics, and simulations,COOT,Pymol,Chimera,APBS,GROMACS,AMBER,VMD/NAMD.
South Carolina Medical University Bioenergetics Profiling Core Facility
Core provides several technologies that enable researchers to quantify fluxes of these metabolic reactions in cells, tissues, organoids and small animal models such as zebrafish embryos and nematodes.Technologies include high resolution respirometry using XF technology from Seahorse Biosciences/Agilent. Instrumentation utilizes 96-well microplates to provide sufficient sample numbers to provide flux profiles of glycolysis, mitochondrial respiration, fatty acid oxidation, glutamine utilization and other related metabolic processes. Rapid, high-throughput imaging optimized to XF plate architecture provides normalization of cell/tissue numbers, health, and other.Provides training, data analyses support and aid in experimental design.
South Carolina Medical University Cell and Molecular Imaging Core Facility
Core provides COBRE investigators access and assistance for high end laser scanning confocal/multiphoton/super-resolution microscopy and related imaging techniques. Houses confocal/multiphoton systems: Zeiss LSM 880 NLO Quasar confocal/multiphoton microscope with Fast Airyscan super-resolution detector; Olympus FV1200 silicone oil optics multiphoton microscope configured especially for intravital imaging; Olympus FV10i LIV confocal microscope with water immersion optics for live cell imaging; Zeiss LSM 510 META laser scanning confocal microscope for general purpose imaging of live and fixed specimens; BD CARV II disk-scanning confocal microscope for video rate real-time confocal imaging providing sophisticated imaging technologies, expertise and training.
South Carolina Medical University Analytical Redox Biology Core Facility
Core provides analytical redox biochemistry methods and mentoring support for COBRE junior faculty with goal to advance their research endeavors, publications and fundability. Specific aims are:Provide ROS /RNS identification and quantification, Perform quantitative analysis of ROS/RNS. Provides expertise and technology for in depth biochemical analysis of thiol-centered enzyme activities and define protein:protein interactions.
Virginia Tech Mass Spectrometry Incubator Core Facility
Virginia Tech Mass Spectrometry Incubator
Facility supports Virginia Tech's research infrastructure as mass spectrometry analysis and education center. Provides training in sample preparation, instrument operation and data analysis, with strong emphasis on metadata and analytical requirements for publication of metabolomic and proteomic results.
Northwestern University DevSci Neurodevelopmental Core Facility
Developmental Sciencies Neurodevelopmental Core
Core provides services in support of research, education, and assessment technology related to neurodevelopmental research methods. Services include Scientific Consultation, Workshops and Training,EEG/ERP,Eye-tracking,Clinical and Behavioral Measure Services.Services include Data Collection, Use of Equipment, Experimental Task Creation and Preparation.
Virginia Tech Biocomplexity Institute Genomics Sequencing Center Core Facility
Core for development and application of Next-Generation Sequencing technologies. Provides experimental design consultation, and genomic, transcriptomic, and functional-genomics services. Specializes in development and application of Next-Generation Sequencing technologies and bioinformatics analyses. Instruments include Illumina NovaSeq 6000, Illumina NextSeq 500,Illumina MiSeq,Thermo Ion S5. Services include mRNA-Seq: Stranded and non-stranded, high levels of multiplexing up to 96 or more samples on NovaSeq;Standard amounts, Stranded-Seq: 500 ng total RNA, RIN 8;Low Input amounts, Stranded-Seq: 5 ng to 100 ng total RNA;Ultra Low Input amounts, Non-Stranded-Seq: 1-1000 cells or 10 pg - 10 ng;Total RNA-Seq - Stranded: 5-250 ng;Small RNA-Seq: 1 ug, multiplexing up to 48 samples/NextSeq run;Partially degraded samples - Stranded and Non-Stranded: LCM, FFPE samples, both stranded and non-stranded, 50 -100 ng;Microbial rRNA depletion and RNA-Seq with amounts as low as 1-5 ug of total RNA;Whole Genome Sequencing;Human / Animal / Plant;Microbial;As low as 1 ng De novo Sequencing;Exome/Targeted capture re-sequencing: Enables high sequencing depths;Agilent and Illumina platforms;Human, Mouse, Canine and other species;Targeted re-sequencing: High levels of multiplexing up to 200 samples / MiSeq run;PCR Amplicon sequencing;Illumina and Agilent platforms;ChIP-Seq;Transcription factor analysis;Histone modifications;DNA Methylation;MeDIP- and MBD-Seq;MethylC-Seq;Agilent SureSelect MethylC-Seq;Nucleosome Mapping;FAIRE-Seq and DNAse I-Seq;16S / 18S / ITS amplicon sequencing;Whole Genome Metagenomic sequencing;Metatranscriptomic analysis;DNA/chromatin fragmentation by Covaris DNA / RNA quality analysis: BioAnalyzer / TapeStation assay, Qubit (Picogreen) assays;qPCR services.
South Carolina Medical University Mass Spectrometry Core Facility
Core provides expertise, services, education, and instrumentation to enhance biomedical research through LC-MS/MS-based proteomics. Services are offered for protein identification; characterization of post-translational modifications; and quantitative proteomics to identify differentially expressed/degraded proteins, regulated sites of post-translational modification, protein-protein interactions, and protein targets of drugs identified in phenotypic screens. Analyses include sample preparation, LC-MS/MS, database searching, generation of reports, and assistance with data interpretation. Faculty and staff assist with experimental design and development/optimization of customized methodology for analysis of post-translationally modified peptides (e.g. phosphorylation and O-GlcNAc modification, N- and O-linked glycosylation, Cys modifications including S-glutathionylation, and glycation of Lys and Arg). Quantitative approaches including metabolic labeling (SILAC), isobaric tagging (iTRAQ/TMT), and label free proteomics (LFQ) are performed on Orbitrap Elite or Orbitrap Fusion Lumos Mass Spectrometers. Developes methodology to identify alterations in post-translational modifications that impact signal transduction, transcription, translation, and response to therapeutics with goal of enabling investigators to discover molecular mechanisms underlying disease progression and therapeutic response.
Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions.
Software visualization tool for direct volume rendering with no segmentation required. Enables users to view, annotate and analyze 3D data in VR. Data visualization and annotation system that allows rendering of large, volumetric data in its true, three- or four-dimensional form.
Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets.
Database of intracellular recordings of non-human primates (NHP) cells sampled from the lateral prefrontal cortex. 249 patch clamp recordings for 2 protocols: 1 second current pulse and 3 millisecond pulse. Morphology obtained by biocytin injections and confocal imaging at 63x magnification.
Software R package baseline correction for accurate copy number calling from 450k methylation array. Baseline correction for copy number data from cancer samples. Implements maximum density peak estimation (MDPE) method together with interactive reviewing to efficiently correct baseline in cancer samples.
Optics and Imaging Company. Vieworks has developed imaging technologies for various areas and has offered solutions suitable for the digital X-ray detector, industrial camera, and in vivo imaging system.
Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit.
Software tool to merge multiple GenBank records using defined spacer sequence.Used to turn multiple GenBank records either in multiple files or single multi-record file into single record.
Calculator to estimate appropriate annealing temperature when using NEB PCR products.Tm calculator provided by New England Biolabs.
Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction.
Lesion Identification with Neighborhood Data Analysis
Software R package for automated segmentation of chronic stroke lesions. Automated segmentation algorithm capable of learning relationship between existing manual segmentations and single T1-weighted MRI.
Software for analyzing mouse behavior by Omnitech Electronics Inc.
Software tool as novel k-FLBPCM method for detecting morphologically similar crops and weeds based on combination of contour masks and Local Binary Pattern operators.
Software tool for visualisation and quantification of DNA methylation at candidate features.
Web tool as artificial neural network method that predicts phosphorylation sites in independent sequences. Web application based on determination of activity of protein kinases using in vitro assays with either naturally occurring peptides or synthetic peptides. NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. Generic predictions are identical to predictions performed by NetPhos 2.0. Kinase specific predictions are identical to predictions by NetPhosK 1.0. NetPhos 3.1 is available as stand-alone software package.
Pairwise mApping Format reference-based Scaffold
Software as Pairwise mApping Format reference based Scaffold anchoring and super scaffolding tool. Dsigned for mapping genome assembly scaffolds to closely related chromosome level reference genome assembly.
Software tool for applying user guided nonlinear refinements (inplane) to existing, affine 2D-to-3D registration. Used for precise quantitative analysis of residual anatomical variability among test subjects after registration.
Desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics sequencing technologies, it generates short reads at large scale. BGI/MGI Sequencer.
Sequencer developed by MGI Tech Co. Ltd. Next generation sequencing platform. Its sequencing principle relies on DNB and cPAS technologies also used in previous version of BGISEQ-500 device, but reagents for MGISEQ-2000 are refined and platform utilizes updated software. Built with new chip system that can flexibly support variety of different sequencing models.
Sequencer can generate 1-6Tb of high quality data per day, for wide range of applications including Whole Genome Sequencing, Deep Exome Sequencing, Epigenome Sequencing, Transcriptome Sequencing, and targeted panel projects. Powered by DNBSEQTM Technology, DNBSEQ-T7 makes sequencing more efficient and productive with advances in biochemical, fluidics, and optical systems. Detection and characterization of copy number variants based on whole-genome sequencing by MGI platforms.
Thermo Fisher Ion Torrent Sequencer. Ion Proton System for Next-Generation Sequencing. Used for accurate high-throughput sequencing.
Thermo Fisher | Ion Personal Genome Machine System
Ion Personal Genome Machine (PGM) System
Ion Personal Genome Machine™ (PGM™) System
Thermo Fisher Ion Torrent Sequencer. System combines semiconductor sequencing technology with natural biochemistry to directly translate chemical information into digital data. Coupled with Torrent Suite Software performs preliminary reference genome alignment and outputs data in BAM format for easy downstream analysis with optional third party analysis tools. It can also provide access to web portal for data review and sharing.
Thermo Fisher | HID Ion GeneStudio S5 Prime System
Thermo Fisher Ion Torrent Sequencer. Semiconductor based next generation sequencing system that enables simple targeted sequencing workflows. With cartridge based reagents, system is simple to use and offers scalability and flexibility. Uses Ion 5 Series chips to support broad range of forensic applications including mitochondria sequencing, STR analysis, and SNP genotyping.
Portable, real time device for DNA and RNA sequencing, putting you in control of your sequence data. Portable DNA/RNA sequencing by Oxford Nanopore Technologies.
Benchtop sequencing and analysis device designed to run and analyse up to five individually addressable MinION or Flongle Flow Cells by Oxford Nanopore Technologies. Good for labs with multiple projects that need advantages of nanopore sequencing: simple library preparation, real-time analysis and new biological insights from long reads.
Oxford |Nanopore Technologies | PromethION
System offers real-time, long-read, direct DNA and RNA sequencing by Oxford Nanopore Technologies. System suitable for large scale projects such as population-scale sequencing or plant genomics, or for large scale service offerings. PromethION 24 and PromethION 48 systems offer ability to run 24 and 48 flow cells respectively. System allows on demand sequencing, using any flow cell at any time. Users can start and stop running individual experiments as required, or deploy multiple flow cells onto single experiments for greater speed or throughput.
Sequencer by Pacific Biosciences. System allows scientists to generate finished genome assemblies, reveal and understand epigenomes, and characterize genomic variation. It achieves longest read lengths and highest consensus accuracy. Finishes microbial genomes and improves assembly of larger organisms with multi-kilobase reads and unbiased coverage regardless of GC content. No amplification is required.
Single Molecule, Real-Time sequencer by Pacific Biosciencies. System provides higher throughput, more scalability, reduced footprint and lower sequencing project costs compared to PacBi RS II System, while maintaining benefits of SMRT technology. Ideal for projects such as generating high quality, whole genome de novo assemblies for larger genomes, such as human, plants, and animals. Provides characterization of wide variety of genomic variation types, including those in complex regions not accessible with short-read or synthetic long-range sequencing technologies, while simultaneously revealing epigenetic information.
Sequencer by Pacific Biosciencies. System provides advantages of SMRT Sequencing and now makes it more affordable for all scientists to drive discovery with comprehensive views of genomes and transcriptomes. Generates 8 times more data than original Sequel System. Provides access to highly accurate long reads (HiFi reads). Reduces project time for faster results. Makes sequencing more affordable.Supports range of SMRT Sequencing applications.
Compact sequencer for DNA sequencing by GenapSys, Inc. Sequencing is carried out on microfluidic chips that have scalable number of detectors, allowing for applications ranging from targeted sequencing of specific amplicons to genome-scale data collection. System utilizes electrical sequencing chip., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Whole genome imaging instrument by Bionano Genomics for high speed, high throughput structural variant detection and analysis with exceptional sensitivity and specificity. Detects structural variations ranging from 500 bp to megabase pairs in length. For mosaic samples or heterogeneous cancer samples, detects all types of structural variants down to 5% Variant Allele Fraction. Calls repeats and complex rearrangements.
Alberta University Diabetes Institute IsletCore Core Facility
University of Alberta Diabetes Institute IsletCore
Core as campus based lab that offers pancreatic islet isolations accompanied by various assays of islet function and metabolism. Provides service for variety of procedures including: Human pancreatic islet isolation, Islet banking, Basal characterization of donor islets, Limited experimental work, Coordination of ethical approvals.
Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed.
System for scientific and industrial nanofocus computed tomography nanoCT and 3D metrology. Realizes unique spatial and contrast resolution on wide sample and application range. Used in material science, precision injection moulding, micromechanics, electronics geology and biology. Used in 3D CT applications. Allows many analysis, e.g. non-destructive visualization of slices, arbitrary sectional views, or automatic pore analysis.
Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data.
Software tool that controls microscope camera by Touptek Photomics. Provides functions to fully control camera and present video stream processed by Ultra FineTM color engine at high speed, which includes dedicated pipeline to process raw data into realistic scene. Compatible with ToupCam full series of digital cameras. With authorized license, ToupView software could be used with other cameras which support Twain or DirectShow interface. Used in field of medical microscopic imaging, industrial detection, machine vision, astronomical observation, etc.
Open source scientific visualisation software. Multi platform, volume exploration and presentation software. Used for visualising volumetric data, such as tomography data, electron microscopy data, etc.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 20,2024. Modular software for working with multi-channel 2D, 3D and 4D images from high speed confocal, Light Sheet/ SPIM and 2 Photon systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Digimeter | DS5 Isolated Bipolar Current Stimulator
Stimulator allows computer control of stimulus amplitude and timing parameters. Designed to speed up and enhance human peripheral nerve diagnostics by facilitating semi-automated nerve excitability tests. It also has roles in wider aspects of clinical neurophysiology research, including psychological, vestibular system and nociceptive testing. CE marked medical device under European Medical Device Regulation.
methylation quantitative trait loci database
Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES).
Illumina HumanMethylation data on sorted blood cell populations.
Epigenetic Dissection of Intra-Sample Heterogeneity
Software R package provides tools to infer proportions of priori known cell-types present in sample representing mixture of such cell-types. Comparison of reference based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies.
Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid.
High-throughput sequencing system. Support of instrument and supply reagents will be provided through February 28th, 2023. Other instruments that support same applications as HiSeq 1500 System are available. Use Sequencing Platform Comparison Tool to find the best instrument for your needs.
Integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Platform to streamline processing and downstream interpretation of microarray data in clinical context. Analysis tools include CNV analysis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases.
Bidirectional Encoder Representations from Transformers
Technique for Natural Language Processing pre-training developed by Google. Pre-training of Deep Bidirectional Transformers for Language Understanding. Language representation model designed to pre-train deep bidirectional representations from unlabeled text by jointly conditioning on both left and right context in all layers.
Colaboratory is product from Google Research. Allows anybody to write and execute arbitrary python code through browser, and is especially well suited to machine learning, data analysis and education. Colab is hosted Jupyter notebook service that requires no setup to use, while providing free access to computing resources including GPUs.
Web based interactive annotation and filtering platform that automatically annotates variants with allele frequencies, functional impact, pathogenicity predictions and pathway information. Allows filtering by all annotations, under dominant, recessive or de novo inheritance models. Flexible annotation and filtering portal for next generation sequencing data.
SonarCloud Vulnerable Code Prospector for C
Software tool to collect vulnerable source code from open-source repositories linked to SonarCloud. Dataset repository with tagged files with BufferOverflow features associated to source code repositories publicly available.
Camera raw data processing software. Cloud-based service to edit, organize, store, and share photos across any device.
Open source software application with data analysis tools and spreadsheet templates used to manage, process and visualize data. LibreOffice Calc is spreadsheet component of LibreOffice software package developed by Document Foundation.
Web server for modeling protein structure by using Multiple Mapping Method. Approach to sequence-to-structure alignment in comparative protein structure modeling.
Automatic T-maze setup to quantify various cognitive functions of animals. Single maze system by O'HARA and CO.,LTD.
Multiplexed biosignal amplifier used to record neural signal by Amplipex Ltd. Related to electrophysiology experiments with multichannel extracellular recordings in freely moving rodents.
Universal Scientific Equipment Discovery Tool
Project that attempts to identify instruments used in research by assigning universal unique identifiers and standardized set of information for each piece of equipment.
Microdrive for chronic implantation of neural probe by NeuroNexus.
Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.
Software tool for binding free energies from Amber-generated MD trajectories. Alternative to MM-PBSA software provided by AMBER distribution. Virtual alanine mutations are also possible. Solvated interaction energies are calculated using parameters that have been fitted to reproduce binding free energies of data set of 99 protein-ligand complexes.
Online Peri-Event Time Histogram for Open Ephys
Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them.
Single Read Paired Read Indel Substitution Minimizer
Software tool as single read paired read indel substitution minimizer.
Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases.
Luminex | 100 Flow Cytometry Analyzer System
Flow cytometry analyzer system for individual labs that performs up to 100 different tests in single reaction volume and can use either magnetic beads or plain polystyrene beads.
Suspension array system which offers protein and nucleic acid researchers multiplex assay solution permiting analysis of up to 100 biomolecules in single sample.
Compact benchtop platform that enables rapid and full walk-away automation of next generation sequencing applications. Paired with PrepX reagents, Apollo 324 line offers complete sample-toanswer solution for NGS library prep. Apollo 324 automated protocols and PrepX reagent kits combine liquid handling and proven chemistries to produce high quality libraries for all major NGS platforms. System provides complete, walkaway solution using validated protocols and chemistries that produce consistent libraries for DNA-seq, RNA-seq, and ChIP-seq applications.
Genetic sequencer that sequences clinically relevant exons and identifies genomic variations in solid tumors treated with antibody-based medicine. Scaled version of Genome Sequencer FLX System for use by individual labs. Features include simple sample preparation workflow, overnight sequencing and data processing, and suite of data analysis software.
Select Science | Carestream Gel Logic 212 PRO Imaging System
Carestream Gel Logic 212 PRO Imaging System
Automated gel imaging system for imaging fluorescence or colorimetric data in sample formats such as gels (DNA/Coomassie/Silver stain) membranes, and 96 well plates. Features include autofocusing and directed autoexposure.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10,2024. Automatic film processor for low-volume processing or back-up purposes. Its features include fast start up (7 minutes from cold start) and 125-second cycle time. Uses simple, accessible film transport system with fewer rollers than conventional heavy roller racks, infrared dryer instead of hot-air dryer, 400 watts of power when in operation and 100 watts in standby mode, and automatic temperature control and drying.
Molecular Devices | Molecular Dynamics Storm 840 Molecular Imager
Molecular Dynamics Storm 840 Phosphorimager Scanner
Molecular imager system for performing gel and blot analysis. This system provides both PhosphorImager capabilities along with non-radioactive fluorescent labeling techniques-direct fluorescence and chemifluorescence. It can be used for non-radioactive gel and blot analysis methods or radioisotope techniques. Storm 840 scans storage phosphor screens plus fluorescent gels and chemifluorescent blots in the 35 x 43 cm scanning area.
Molecular Devices | Molecular Dynamics Storm 860 Molecular Imager
Multifunction phosphoimager fluorimager laser scanner that collects fluorescent or storage phosphor images from gels, membranes and phosphor screens. It is equipped with blue (450 nm) and red (635 nm) lasers, can scan at resolutions down to 50 microns. It is able to quantify radioactive gels for commonly used isotopes such as 32P, 33P, 125I, 35S, and 14C. There are three detection modes: phosphor screen mode, red/blue fluorescence, chemifluorescence.
Paraffin embedding station that provides constant, reproducible paraffin flow at ten different flow rate settings. All instrument functions, including automatic starting time, are individually programmable at press of button. Compact dimensions, ease of operation, and high standards of convenience. Separately-heated paraffin dispensing system with integrated filter provides constant, reproducible paraffin flow at ten different flow rate settings.
Thermo Fisher: Affymetrix | GeneChip 450 Fluidics Station Microarray Processer
Microarray processor that washes and stains GeneChip arrays.110V and 220V compatible.
JEOL | 1230 Transmission Electron Microscope
JEM 1230 Transmission Electron Microscope
High performance, high contrast, 40-120kV transmission electron microscope that performs imaging for biological and materials science applications.
Agilent | 1200 High Performance Liquid Chromatography System
Liquid chromatography analyzer that achieves high levels of sample throughput by use of either binary or quaternary pumps and interchangeable autosamplers. High pressure operation and use of short columns with small diameter media result in fast, high resolution separations. Features includedu al-lamp design and temperature control of diode array detectors.
Perkin Elmer | EnVision 2105 Multimode Plate Reader
Multimode microplate reader that provides speed, ultra-high throughput, and maximum sensitivity across all detection technologies. Provides higher sensitivity for time-resolved fluorescence TRF applications, and Enhanced Security software option includes tools to facilitate 21 CFR Part 11 compliance for integration into regulated environments GxP.
Zeiss | LEO 1525 Field Emission Scanning Electron Microscope
Field emission scanning electron microscope that performs ultra high resolution imaging and analysis. Designed for requirements of nano-analysis, chamber of LEO 1525 is capable of accommodating both EDS and full-focusing Wavelength-dispersive X-ray spectroscopy WDS spectrometers as well as rage of other accessories. Coincident and short working distances allow signals from these detectors to be acquired simultaneously.
Manual rotary microtome that sections tissue samples. Features include precise feed mechanism, powerBase that ensures stable operation for vibration-free sectioning, advanced knife holder and specimen clamp securely align cutting edge to block, user-selectable coarse feed wheel turn direction and retraction functions, hand wheel, in-built safety guards and rounded shape with arm rests for fatigue-free sectioning,quick-exchange specimen clamp and orientation system for object head allow rapid set up for any block, and two trim steps.
Leica | Biosystems RM2265 Fully Automated Rotary Microtome
Automated rotary microtome that sections tissue samples. Specimen feed system with zero-backlash and maintenance-free cross roller guides and stepper motor operated coarse feed system are located in dust-proof plastic housing. Equipped with safety handwheel with handle that can be centered, as well as mechanical handwheel lock. In manual operation retraction can be adjusted. In motorized operation retraction value varies with selected sectioning speed.
Thermo Fisher | NanoDrop 2000 Spectrophotometer
Full-spectrum, UV-Vis spectrophotometer used to quantify and assess purity of DNA, RNA, Protein and more. The NanoDrop 2000 is microvolume spectrophotometer with patented sample retention technology that measure sample volumes as small as 0.5L.
Bioanalyzer system is automated electrophoresis tool that provides an analytical evaluation of various samples types in many workflows, including next generation sequencing NGS, gene expression, biopharmaceutical, and gene editing research. Digital data is provided in timely manner and delivers assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for accurate result, and data may be exported in many different formats.
GE | Biacore 3000 Real Time Biomolecular Interaction Analyzer
Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants.
Thermo Fisher: Applied Biosystems | 2720 Thermal Cycler
Personal sized 96-well thermal cycler that performs both basic PCR and cycle-sequencing applications using 0.2 mL reaction tubes or 96-well reaction plates. Its dimensions are 21 cm (8.3 in.) wide and 36 cm (14.2 in.) deep with cooling vents.
Thermo Fisher: Applied Biosystems | 3130 Genetic Analyzer
Applied Biosystems 3130 (4-capillary) Genetic Analyzer
Genetic analyzer can run sequencing and fragment analysis applications including microsatellite analysis, AFLP, LOH, SNP validation, and SNP screening. Maintenance time is reduced by eliminating manual syringe washing and filling with automated polymer delivery. Can increase data quality for sequencing and fragment analysis applications by longer read length, and higher resolution with shorter run times. Uses 96- or 384-well plates with four capillary array.
GE: Healthcare | 9410 Variable Mode Imager
Typhoon 9410 Multi-Image scanner (GE Healthcare)
Variable mode imager that operates in three different modes, including phosphorescence, fluorescence, and chemiluminescence. Can scan in visible range using reflected light. Scanning resolution ranges from 1000um down to 10um. Scanning software is linked to ImageQuant TL 7.0 analysis software. ImageQuant is capable of quantifying Typhoon images such as those from Northern or Western blots. Images can be saved in various formats and imported into Powerpoint slides. Instrument has three excitation lasers (532nm, 633nm, 488nm). Instrument utilizes 536SP, 670BP, 520BP emission filters for fluorescence. For DNA, RNA and protein samples you may choose from: storage phosphor auto-radiography, direct blue-excited fluorescence (457-488 nm), direct green-excited fluorescence (532 nm), direct red-excited fluorescence (633 nm), and chemiluminescence.
Thermo Fisher: Applied Biosystems | 3130xl Capillary Array
Applied Biosystems 3130xl capillary fluorescence sequencer
Genetic analyzer that performs fragment analysis and rapid sequencing applications. Usage per array is 100 runs with use of Applied Biosystems reagents.
Molecular Devices | GenePix 4000B Microarray Scanner
Microarray scanner that performs genetic and compound analysis. Coupled with GenePix ProMicroarray Image Analysis Software and Acuity Microarray Informatics Software for acquisition and analysis of data from all types of arrays, including nucleic acids, proteins, tissues, and cells. Scanner flexibility allows to configure scanning and analysis of one slide or many, whether they are all alike or each is different. Slide loader accommodates low- and high-density, opaque, mirrored, or translucent, plastic or glass, commercial or homebrew slides.
Refridgerated centrifuge with 18 place capacity rotor that accomdates low to medium capacity in 1.5 or 2.0 mL tubes and Microtainer. Speed allows for standard molecular biology applications. Compact size and quiet operation.
Thermo Fisher: Applied Biosystems | 7500 Real-Time PCR System
Real-time PCR system that performs high performance, multicolor real-time PCR. Has five color platform that is calibrated for broadest range of dyes available: FAM, SYBR Green I, VIC, JOE, NED, TAMRA, Cy3, ROX, Texas Red, and Cy5 dyes. Thermal cycling block is built to reduce environmental exposure and contamination risk.
Thermo Fisher: Applied Biosystems | 3730 Genetic Analyzer
Medium to high throughput genetic analyzer that performs DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Upgradeable to 96 capillaries.
SCIEX | TripleTOF 5600+ Mass Spectrometer System
Mass spectrometry system that combines SCIEX Triple Quad technology with Accelerator TOF Analyzer, to deliver nominal mass and accurate mass benefits in single platform. Integrates comprehensive, qualitative exploration, rapid profiling, and high-resolution quantitation workflows.
Bruker | 9.4T Biospec Biospec Magnetic Resonance Imaging
MRI system that performs preclinical and molecular MR imaging. MRI CryoProbe technology combined with ultra high field USR magnets deliver high spatial resolution in-vivo. Any small animal MR imaging application in life science, biomedical and preclinical research can be conducted.
BD Biosciences | FACSCanto Flow Cytometer
Flow cytometry system that performs reliable performance, accuracy, and ease-of-use for clinical diagnostic services. System has 10 color capability, optical enhancements, and 4-3-3 configuration deliver high sensitivity and resolution for accurate results.
BD Biosciences | Canto II Flow Cytometer
Benchtop flow cytometer features reliable performance and accurate results for experiments requiring up to 10 parameters. Fixed alignment flow cell minimizes startup time and improves reproducibility. Patented optical design maximizes signal detection and increases sensitivity and resolution for each color in multicolor assay.
Bio-Rad | CFX384 Real-Time Detection System
Real Time PCR instrument in 384-well format that performs high-throughput data acquisition. System utilizes temperature control and sensitive, 4-color detection optics to deliver qPCR results for singleplex or multiplex reactions. Quickly set up runs and monitor amplification traces in real time on integrated LCD touch screen, or use CFX Maestro Software to design experiment and analyze results from connected computer.
Femto Pulse System separates large molecular weight DNA fragments and detects nucleic acids into femtogram range.Fragment analyzer that provides pulsed field power supply which allows large molecular weight DNA fragments to be separated and nucleic acids detected into femtogram range. Ability to separate high molecular weight DNA up to 165 kb and detect nucleic acids down to 50 fg per uL input concentration makes system ideal for long-read NGS QC, gDNA, small RNA, or cfDNA analysis from low concentration samples.
Thermo Fisher: Applied Biosystems | 3730xl Capillary Genetic Sequencer
Applied Biosystems 3730xl Capillary Sequencer
96-capillary DNA analyzer that performs DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Has multiple automation features. Performs sequencing and fragment analysis applications including resequencing, microsatellite analysis, AFLP, LOH, SSCP, SNP screening and SNP validation.
Thermo Fisher: Applied Biosystems | 7900HT Fast Real-Time PCR System
Real Time quantitative PCR system that combines 96- and 384-well plate compatibility and the TaqMan Low Density Array with fully automated robotic loading and now also offers optional Fast real-time PCR capability. High-throughput Real-Time PCR system that detects and quantitates nucleic acid sequences. Uses fluorescent-based PCR chemistries to provide: Quantitative detection of nucleic acid sequences using real-time analysis and Qualitative detection of nucleic acid sequences using end-point and dissociation-curve analysis.
Highly adaptable cryostat platform that can be tailor-made for each laboratory. Cryostat with encapsulated microtome and separate specimen cooling features UV disinfection system, optional integrated extraction system for section waste and optional motor for motorized sectioning. Designed to produce frozen sections for biological, medical and industrial applications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Zeiss LSM-510 META NLO Laser Scanning Confocal Microscope with multiphoton capability
Versatile laser scanning confocal microscope system that is available in both upright or inverted format. Equipped with ICS-Optics. Selection of dry, water immersion and oil immersion objectives are available. ICS-Optics are infinity color corrected.
Zeiss | LSM 710 Confocal Inverted Microscope
Inverted microscope that enables confocal microscopy in cell and developmental biology.
Bio-Rad | CFX96 Real-Time PCR Detection System
Real Time PCR detection system that combines optical technology with temperature control. Six channel, five colors and one FRET channel, real-time PCR instrument for singlexplex or multiplex reactions. Quickly set up runs and monitor amplification traces in real time on integrated LCD touch screen, or use included CFX Maestro Software to design experiment and analyze results from connected computer.
Bio-Rad | iCycle iQ Real-Time Detection System
PCR detection system that features broad spectrum light source. Filter based optical design allows selection of optimal wavelengths of light for excitation and emission. Pixel array on CCD detector allows for simultaneous imaging of all 96 wells every second. Simultaneous image collection insures that well-to-well data may reliably be compared. Reports data on PCR in progress in Real Time, allowing immediate feedback on reaction success.
Benchtop cell sorter that sorts wide range of cell sizes for many applications using microfluidic sorting chips. Integrated with comprehensive fluidics controls and advanced automation for set-up, acquisition, sort and analysis. System software supports sorting into tubes and 96- and 384-well plates. Software generates FCS 3.0 and FCS 3.1 files that can be exported to third party analysis tools. For non-clinical research use only. For applications in which cross-contamination is concern, optional e-beam sterilized consumables can be used to replace sample line and sorting chip. Optional class A2 Level II biosafety cabinet provides protection for personnel and products. Biosafety cabinet meets international standards.Optical design offers up to four collinear excitation lasers (488 nm, 405nm, 561nm and 638nm) and six fluorescence detectors. The six free-form PMTs enable detection of fluorescence signals from any laser based on filter selection.
Sony Biotechnology Inc. SP6800 Spectral Cell Analyzer
Analyzer that uses spectral technology to collect photons from 420nm to 800nm. Global standardization mode automatically sets system to master specification with single click. Sony patented Flowpoint core stability and tracking system and automated QC ensure highest resolution possible of target populations.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. Data repository for scientific data. Open data library to explore neuroscience data for neurodegenerative diseases for which there are no disease modifying treatments.
Software tool to leverage power of Docker and Spark to run and scale your serial tools in MapReduce fashion.
Suite of open software command line tools to develop high-quality pictures from high-throughput sequencing samples. Source code is designed to be integrated into existing bioinformatics pipelines. SeqCode web is web interface implemented to show only selection of features of standalone distribution. Suite of command-line software for high-performance comprehensive analysis of ChIPseq data. Designed to develop high-quality images and perform genome-wide calculations from high-throughput sequencing experiments. Presented into two distinct modes: web tools and command line.
Software tool that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Corrects micrographs for global and local motion, estimates local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Software includes deep-learning-based models for accurate particle picking and image denoising.
Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS.
Select Science | Genomic Solutions OmniGrid 100 Microarrayer
GeneMachines OmniGrid 100 Microarray Printer
OmniGrid 100 microarrayer is high capacity multi axis microarrayer that prints biological samples onto solid substrates with speeds that give high throughput array production. Can be integrated with optional Server Arm 3 for fully automated handling of up to 72 input plates.
Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided.
Amylotrophic Lateral Sclerosis online Database
Collection of published Amyotrophic lateral sclerosis associated genes and variants. Database can be searched to look for specific type of mutation like compound, insertion, deletion, substitution or non-pathological variant in ALS gene of interest including SOD1, ALS2, VAPB or NEFH. For each mutation DNA position mutated, original DNA sequence, mutated DNA sequence, original amino acid, mutated amino acid, intron/exon location, zygosity, and link to hypothetical mutant structure, can be identified.
Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach.
Circadian gene expression profiles DataBase
Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans.
Large scale dose response curve fitting and curve classification software. Automated curve fitting and classificatoin software. Web deployed software. Algorithm recognizes bell shaped curves, implements standard hill equation, extensible for other models.
Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials.
Software R package as streamlined plot theme and plot annotations for ggplot2. Provides various features that help with creating publication quality figures with ggplot2, such as set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images.
Thermo Fisher: Applied Biosystems | 3130xl Genetic Analyzer
Applied Biosystems 3130xl Genetic Analyzer 16-Capillary Array System
3130xl Genetic Analyzer is latest generation of 16-capillary electrophoresis instruments by Applied Biosystems.
Software R package to import excel files into R. Has no external dependencies for easy installment and use on all operating systems. Designed to work with tabular data.
Software tool for statistics and data visualization by Red Rock Software, Inc. Provides unparalleled chart selection, data analysis and graph customization capabilities.
Epigenome-Wide Association Studies- Galaxy
Software suite for population epigenetics integrated into Galaxy. Galaxy Docker repository for population epigenetics data analysis.
Database of genes related to Repeat Expansion Diseases
Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest.
Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.
Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs
Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs.
Swinging bucket benchtop centrifuge. Eppendorf 5920 R refrigerated centrifuge.
Semi automated pipetting system by Mettler Toledo. Instrument for semi-automated 96/384-well plate pipetting. Semi-Automated 96/384-Well Pipetting System where pipetting options range from 0.5 uL to 1000 uL.
Beckman Coulter | Biomek i7 Hybrid Automated Workstation
Liquid handling instrument designed to optimize dependability and walk-away time. Biomek i7 Hybrid with enclosure has up to 45 deck positions and includes both Multichannel and Span-8 pipette heads in enclosed work space.
Benchtop fluorometer designed to accurately measure DNA, RNA, and protein quantity. Measures RNA integrity and quality. Touch screen to select and run assays with results displayed in few seconds.
Single Nucleus Accessibility Profile Tools
Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets.
Software tool to detect doublets in single-cell RNA-seq data. Software algorithm to remove doublets. Python code for identifying doublets in single-cell RNA-seq data. Framework for predicting impact of multiplets in given analysis and identifying problematic multiplets.
Iterative Clustering for Analysis of Transcriptomics
Software R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute.
Linked Inference of Genomic Experimental Relationships
Software R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets.
Open source software package for standard and precise positioning with global navigation satellite system. Consists of portable program library and several application programs utilizing library. Program Package for GNSS Positioning.
Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model.
Stand alone software that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales. Successor of PhotoScan and is advanced image-based 3D modeling solution aimed at creating professional quality 3D content from still images.
Software tool as advanced image-based 3D modeling solution aimed at creating professional quality 3D content from still images by Agisoft LLC.
Resource presents information about animal lectins involved in various sugar recognition processes.
Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists.
Software tool to draw CGO cylinder representing rotation axis for given transformation. Useful for drawing axes of rotational symmetry in oligomeric assembly.
Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures.
Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.
Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment.
Webserver to process, analyse and visualise CLIP-Seq data. Software tools to process and visualise RNA protein interactions. CLIP-Seq data analysis in Galaxy. Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to iCLIP workflows also FLASH, and uvCLAP.
Software package for analysis of trends using joinpoint models where several different lines are connected together at joinpoints. There are two versions available. Desktop version has graphical user interface and is for interactive use. Command-line version is for use in batch mode or called from other software, such as SAS or R.
Software Python tool as data visualization library based on matplotlib. Provides interface for drawing attractive and informative statistical graphics. Statistical data visualization using matplotlib.
Software tool to implement pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in field of metagenomics.
Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures.
Software tool as online calculator of molecular weight of proteins in dilute solution from experimental SAXS data measured on relative scale. Software package for easy processing of small angle X ray scattering data from mono disperse systems in diluted solution.
Software Python package for machine learning, statistics and data mining. Contains library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical data sets, and examples of analyzing and visualizing astronomical data sets. Repository of common tools and routines used for statistical data analysis in astronomy and astrophysics.
Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time.
Python Flow Cytometry Calibration Library
Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.
Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.
Droplet sequencing data analysis software tools
Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.
Software package as collection of modules implementing methods of analysis that form self-contained and empirically grounded toolbox for handling longitudinal data within person oriented paradigm.
Reference database for pathway mapping in KEGG Mapper. Collection of manually drawn pathway maps representing knowledge on molecular interaction, reaction and relation networks for metabolism, genetic information processing, environmental information processing, cellular processes, organisms systems, human diseases, drug development.
Galaxy cloud on demand workflow workbench
Software tool for automatic deployment of virtual Galaxy environments for life science. Can be deployed over common cloud architectures supported both by public and private e-infrastructures. User interacts with Laniakea based service through simple front end that allows general setup of Galaxy instance, then Laniakea takes care of automatic deployment of virtual hardware and software components. User gains access with full administrative privileges to private, production grade, fully customized, Galaxy virtual instance, and to underlying virtual machine.
Web application that enables users to build and publish own custom manikins. Used to build three dimensional model of human body using parts registered in BodyParts3D. Server returns image of assembled 3D model as still image, rotating animation, interactive image, etc. Each part can be downloaded as polygon mesh file that can be used with 3D printer.
Community software Pyton library for astronomy. Collection of software packages written in Python programming language for use in astronomy. Package contains key functionality and common tools needed for performing astronomy and astrophysics with Python. Core of Astropy Project, which aims to enable community to develop ecosystem of Affiliated Packages covering broad range of needs for astronomical research, data processing, and data analysis.
Software tool as Microsoft Excel spreadsheet calculator designed to estimate epidemiological cutoff values (ECVs, ECOFFs) for minimal inhibitory concentrations or minimal effective concentrations of wild-type bacterial or fungal populations.
List of Prokaryotic names with Standing in Nomenclature Database
Database lists names of prokaryotes that have been validly published in International Journal of Systematic and Evolutionary Microbiology directly or by inclusion in Validation List, under Rules of International Code of Nomenclature of Bacteria. Has classification of prokaryotes and information on prokaryotic nomenclature and culture collections.
Picospritzer III - Intracellular Microinjection Dispense Systems
Intracellular microinjection dispense system by Parker Hannifin. Supplies repeatable pressure pulses. Designed for rapid and reproducible ejections of picoliter and nanoliter volumes used in conjunction with intracellular or extracellular studies while avoiding inherent desensitization of nerve cells which accompanies Iontophoretic methodology. System comes complete with high speed valves and necessary tubing assemblies.
Processor for auditory research delivers processing power, data transfer and sample rate of 200 kHz by Tucker-Davis Technologies . Can be equipped with up to 4 high-performance DSPs to support complex stimulus control, high frequency applications, and real time normalization for speakers and microphones.
Dolomite Bio | Nadia High Throughput Cell Analyzer Platform
Automated, microfluidic droplet based platform for single cell research that encapsulates up to 8 samples. Instrument has sample temperature control from 4 degrees Celsius to 40 degrees Celsius. System detects single use cartridges for specific applications.
S2 Genomics | Singulator 100 Automated Single Cell Prep Automated System
Singulator to automate tissue preparation for single cell and single nucleus analyses. Bench top Singulator System and single use cartridge enable tissue dissociations into singulated cells or nuclei suspensions.
Mizar Imaging | Tilt High Resolution Light Sheet Imaging System
Modular light sheet illumination system designed to image living samples with minimal photobleaching or phototoxicity by Mizar Imaging. Enables high spatial and temporal resolution light sheet imaging to be added to existing or new microscope system.
Web medaka pattern match tool for short sequence and/or pattern. Used to search database of medaka genome on target and off target sites when editing genome with CRISRP-Cas9.
Python implementation of conditional expectation maximization algorithm that estimates epigenetic landscapes and state of individuals and may be used to study nonlinear epigenetic aging. Fast conditional expectation maximization algorithm used to model epigenetic states associated with phenotype of interest. Can model non linear epigenetic trait associations directly without transformation of phenotype of interest.
Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern.
Web tool to convert genome coordinates and genome annotation files between assemblies. Used to translate genomic coordinates from one assembly version into another and retrieves putative orthologous regions in other species using UCSC chained and netted alignments.
Web tool as multiple sequence and structure alignment server. Automatically identifies homologs with known 3D structures for input sequences, derives structural constraints through structure based alignments and combines them with sequence constraints to construct consistency based multiple sequence alignments. Aligns sequences of multiple input structures, with output representing multiple structure based alignment refined in combination with sequence constraints.
Web based analytics environment for genomic data arising from BRAIN Initiative Cell Census Network, based on AnnoJ browser. AnnoJ browser displays epigenomic data, including base resolution DNA methylation, RNA-Seq, ChIP-Seq, as well as annotations.
Software used to analyze images obtained from microscope. ZEN Black is software Zeiss uses to run their laser-based instruments.
Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.
Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.
Software plugin for bone image analysis in ImageJ. Used for standard bone measurements. Provides free, open source tools for trabecular geometry and whole bone shape analysis.
Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R.
single-cell RNA Velocity generalized to transient cell states
Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling.
Leica | SP8 LIGHTNING confocal microscope
Confocal microscope by Leica Microsystems to capture up to five true color channels simultaneously at high speed without need for trade-offs in multicolor experiments. Provides super resolution live cell imaging, simultaneous multicolor imaging, live specimen imaging thanks to fast acquisition rates, sample protection thanks to low phototoxicity.
Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data.
Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.
Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.
Software package to build, manipulate and display phylogenetic trees. Designed for building gene trees with known species tree and is highly efficient and accurate.
Web tool for display, annotation and management of phylogenetic trees. Accessible with any modern web browser.
Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis.
Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree.
Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data.
Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling.
Software tool as algorithm that represents nodes as vectors by integrating bioentity attribute such as RNA sequence and bioentity behavior that is relationship between bioentities.
Database provides access to genotype and phenotype data from experiments with Diversity Outbred mice. Data can be searched by publication, investigator, and data type and can be downloaded in zipped CSV or R/QTL2 formats. Users can download full studies or subset of samples, genotypes, clinical phenotypes and molecular phenotypes including transcript, proteomic, and metabolomic profiling data.
Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations.
Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).
Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas.
Web tool for calculating number of cells that must be sampled in order to see at least n cells of each type for single cell genomics experiments.
Web tool as probabilistic approach to visualizing protein or nucleic acid sequence motifs. Used for motif visualization in which residue heights are scaled relative to their statistical significance. Supports real time conditional probability calculations and visualizations.
Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast.
common Repository of Adventitious Proteins
List of proteins commonly found in proteomics experiments that are present either by accident or through unavoidable contamination of protein samples. List is based on analysis of current version of GPMDB, as well as suggestions by users. Current version of cRAP in FASTA format can be obtained from the GPM FTP site.
Software package for motion capture analysis by Innovision Systems Inc.
Culture chamber for cell culture by BioSpherix. Functionalized by gas controllers for all bioactive gases, e.g. O2, CO2, CO, NO, etc. Made of clear polycarbonate. Magnetic seal door. Temperature is controlled. Combines with ProOx 110, ProCO2, ProOx C21, OxyCycler Series.
Web server to predict ΔGapp for membrane insertion of potential TM helix. Given amino acid sequence of putative transmembrane helix, server gives prediction of corresponding apparent free energy difference for insertion of this sequence into Endoplasmic Reticulum membrane by means of Sec61 translocon.
Software tool as code to extract electrophysiological parameters of neurons. Code is continuously being updated to handle more kinds of voltage traces and extract different kinds of features.
Web tool as basic math calculator to do simple calculation. Can generate any one of values from other three in half life formula for substance undergoing decay to decrease by half.
Software Python tool for flow cytometry data. Data generated by flow cytometer can be read by FlowPy. Used for data extraction, data visualization, data clustering, histogram subtraction.
Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing.
Sustainability Monitoring and Assessment RouTine
Web and offline tool for holistic sustainability assessment of farms. Tool operationalizes Sustainability Assessment of Food and Agriculture Systems Guidelines of Food and Agriculture Organisation of United Nations. Tool consists of questionnaire software, centralized database, pool of indicators and scientifically based assessment methodology. Different stakeholders can use results of this assessment e.g. for comparing different farms, production systems or for strategic development, improvement, monitoring and communication to business partners.
Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome.
Sleep recording software by Kissei Comtech Co., Ltd. Can measure signals of up to 32 channels while monitoring wave forms in real time. Addition of video recording option enables simultaneous recording of biological signals and video.
Sleep analysis for animals by Kissei Comtec Co., Ltd. Enables to generate various types of reports which are required as standard in basic sleep research field like sleep quality and sleep quantity. Version 3.0 is much more faster than prior method of sleep scoring.
Software tool for analysis of qualitative data, operating on basis of lists of peptides and proteins identified in samples generated by Mascot database system. Responsible for preparing data for quantitative analysis of proteins both with use of stable isotope labeling and without isotope labeling.
Chemical inventory for occupational chemical information. Collects information from several government agencies and organizations. Includes information about identification and physical properties, exposure limits, sampling.
University of California San Francisco Parnassus Flow Cytometry Core Facility
University of California San Francisco Diabetes Research Center Cytometry and Cell Sorting Core
University of California San Francisco Diabetes Research Center Parnassus Flow Cytometry CoLab
Core assists investigators whose research requires molecular marker characterization of cells in suspension as well as isolation of cells based on those markers. Advanced cell sorting and cytometric analyses by Flow or Mass Cytometry are provided.
Computed tomography system designed to achieve precise inspection results for wide range of applications by YXLON. Available in single or dual tube configuration, it is perfect for very small to medium sized parts inspection in automotive, electronics, aviation, and material science industries.
Software tool that provides scalable way of keeping track of data and learned annotations. Initially built for Scanpy. Used as generic class for handling annotated data matrices. Stores data matrix with annotations of observations (samples, cells) and variables (features, genes), and unstructured annotations.
Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.
Software tool to select particular records in file and perform operations upon them. awk utility interprets special purpose programming language that makes it possible to handle simple data reformatting jobs with few lines of code. Source code for latest release of GNU awk is available from GNU project ftp server and its many mirrors.
Software tool to searches one or more input files for lines containing a match to a specified pattern. Prints lines that contain match for one or more patterns. Command-line utility for searching plain-text data sets for lines that match regular expression. When finds match, it copies line to standard output (by default), or produces whatever other sort of output you have requested with options.
Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).
Software Python package for data analysis providing labeled data structures similar to R data. Provides data structures designed to make working with relational or labeled data. Software as building block for doing practical, real world open source data analysis and manipulation tool.
Software tool as non interactive command line text editor. Command line that works with streams of characters for searching, filtering and text processing. Used for extracting part of file using pattern matching or substituting multiple occurrences of string within file.
Software tool to create tar archives, as well as various other kinds of manipulation. Used to extract files, to store additional files, or to update or list files which were already stored. Can direct its output to available devices, files, or other programs, can access remote devices or files.
Uniform Manifold Approximation and Projection
Software package as dimension reduction technique that can be used for visualization similar to t-SNE, but also for general non-linear dimension reduction. Used for dimensionality reduction for visualizing single-cell data.
Software R Package that provides parameter-free method for optimizing trade-off between resolution of clusters and their replicability across datasets. Dune method takes as input set of clustering results on dataset, and iteratively merges clusters within those clusterings in order to maximize their concordance. Iterative merging of clusters to improve mean ARI
Structure Analysis and Verification Server
Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server.
Web resource for immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system (RPI). Comprises LIGM expertized data on immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system.
Software environment that includes tools and integrations for professional Python and Web development. Integrated Development Environment by JetBrains. Used for development in Python and frameworks like DJango. Can be customized with themes and plugins.
Free online archive and distribution server for complete but unpublished manuscripts in the medical, clinical, and related health sciences. Preprints are preliminary reports of work that have not been certified by peer review. They should not be relied on to guide clinical practice or health related behavior and should not be reported in news media as established information. Research articles, systematic reviews and meta analyses, clinical research design protocols and data articles may be posted.
Discontinued software tool used to analyse images. Documented on March 30, 2020. Cheshire intended for clinical use for teleradiology, telecardiology, in hospital view stations and image review for referring physicians.
Software package as spatial graph based computing engine for ecological big data. Modular open source knowledge engine designed to import, organize, analyse and visualize big spatial ecological datasets using power of graph theory. Handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. Data are linked with relationships that are stored in graph database, while tabular and geospatial data are stored in relational database management system.
Beckman Coulter | Ultracentrifuge OPTIMA XPN - 90
Floor model preparative ultracentrifuge by Beckman Coulter Inc. with max. speed 90,000 rpm. Offers simplified use, optimized control and security, and increases productivity. Rotors, labware, and services are available.
Software package for data analysis by Shimadzu Oceania.
Comprehensive and manually annotated resource for mycobacterial genomes. Genomic and proteomic data repository for pathogenic mycobacteria. Provides manually curated annotations and tools to facilitate genomic and proteomic study of these organisms. Integrates genome details, protein information, drug and transcriptome data, mutant and operon annotation.
Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software.
Swiss Federal Institute of Technology Lausanne
Rsearch institute and university in Lausanne, Switzerland, that specializes in natural sciences and engineering. It is one of the two Swiss Federal Institutes of Technology, and it has three main missions: education, research and technology transfer at the highest international level.
Software R package for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization.
Haplotype-resolved Assembly for Synthetic long reads using a Trio-binning strategy
Software tool for partition stLFR reads based on trio binning using prenatally unique markers. Haplotype resolved assembly for synthetic long reads using Trio-Binning strategy.
Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results.
Software tool for automatic generation of multiple 2D ligand-protein interaction diagrams from 3D coordinates. Diagrams portray hydrogen-bond interaction patterns and hydrophobic contacts between ligand(s) and main-chain or side-chain elements of protein. Used for drug discovery for analyzing series of small molecules binding to same protein target, single ligand binding to homologous proteins, or where both protein and ligand change.
Software tool to calculate fraction of shared bound peptides between HLA proteins. Command-line tool to calculate fraction of shared bound peptides between HLA alleles from NetMHCpan binding predictions. Compares fraction shared between HLA allele and individual taking into account HLA and KIR genotypes.
Global Initiative on Sharing All Influenza Data
Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data.
COVID-19 Crowd Generated Gene and Drug Set Library
Software tool as interface to submit, serve, and analyze COVID19 related gene and drug sets. Collection of gene and drug sets related to COVID-19 research contributed by community.
National Center for Biotechnology Information Virus
Community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories. Integrative, value added resource designed to support retrieval, display and analysis of curated collection of virus sequences and large sequence datasets. Used to increase usability of data archived in GenBank and other NCBI repositories.
Microvascular health measurement system that measures endothelial glycocalyx layer of vessels by MicroVascular Health Solutions. Software automatically identifies measurable micro vessels, below 30 µm thickness, during acquisition by contrast between RBC and background. After acquisition, software undergoes series of quality checks to measure vascular segments that are of good quality. Video microscope is placed under tongue, showing live movement of red blood cells as they travel through micro vessels.
Software R package for simultaneous inference in general parametric models. Offers interface to perform multiple comparisons in general context. Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models.
Enables visualization, storage and sharing of large image data. Cloud based system by MBF Bioscience to help with data from 2D and 3D slide scanners, confocal Z-stacks, lightsheet whole brain images. System for data storage and management, data analysis and visualization. Data is stored in secure and permanent way. Available also is free application named Biolucida Viewer, for viewing public images or images shared by collaborators owning Biolucida.
Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.
Consortium to unite efforts and resources from experts across globe to advance effective, antibody based therapies against novel coronavirus, SARS-CoV-2. Represents multidisciplinary convergence of structural biology, virologists, immunologists, clinicians and bioinformaticians from academic and industry settings. Collects antibodies for testing as part of CoVICS. Contributed antibodies are blinded and will only be known as code name. Antibody contributors will be able to see performance of their own molecules and take part in analysis. Contributors retain ownership of their antibodies and may continue to publish on them using original antibody names. Goal is to determine relative in vitro potency and in vivo efficacy using centralized standardized assays to identify best individual mAbs and rational combinations of mAbs. Consortium will recommend ideal therapeutic molecules for human use to protect vulnerable populations from COVID-19 disease. CoVIC database (CoVIC-DB) will serve as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them.
Expression quantitative trait loci (eQTLs) and Epigenomics
Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.
Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates.
Group-based Prediction System -Small Ubiquitin-like MOdifiers
Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup.
University at Albany SUNY Center for Functional Genomics Microarray and Next Gen Sequencing Core Facility
UAlbany Center for Functional Genomics Microarray and Next Gen Sequencing Services
University at Albany SUNY Center for Functional Genomics
Provides services for DNA microarrays for large scale analysis of gene expression,gene regulation, exon splicing, epigenetics. Provides instrumentation for scanning of protein arrays.Offers services in RNA sequencing, ChIP-seq, ChIRP-seq, metagenomics and miRNA sequencing.Provides bioinformatics tools for analysis of results of microarray and sequencing experiments. Houses Illumina Nextseq500 and Ion PGM platforms for next generation sequencing. Provides instruments for Next gen sequencing including Illumina, MinIon, Wafergen-Takara, 10x genomics and for DNA microarrays including Affymetrix, Agilent.
University of Massachusetts Medical School Molecular Biology Core Facility
University of Massachusetts Medical School - Molecular Biology Core Lab (MBCL)
University of Massachusetts Medical School Molecular Biology Core Lab
Core services including UMass Oligo Discount Program which provides discounted oligos to researchers, Reagent Program offers discounted pricing on TAQMAN, qPCR reagents, enzymes, etc. from ThermoFisher (Life Technologies/Ambion), and Empirical Biosciences, Fragment Analyzer Service, Sequencing Library Preparation, Sanger Sequencing and GeneMapper/ARISA. Provides DNA fragment analysis, Genotyping, and SPR services on an ABI capillary sequencer, and DNA/RNA fragment analysis on the Advanced Analytical (Agilent) Fragment Analyzer.
Develops research projects in pediatric genetics and provides essential services in molecular biology and genetics to Nemours clinicians and research staff and to affiliates researchers of University of Delaware and Thomas Jefferson University. Resource for staff of Alfred I. duPont Hospital for Children, Nemours affiliates, COBRE / INBRE investigators and outside customers. Offers expertise in molecular genetics and genomics. Operates according to policies set forth by federal CLIA standards.Services provided include Ion Torrent PGM Next Generation Sequencing, QuantStudio (QS) 3D Digital PCR, Cell Line Authentication, Nucleic Acid Quality Number (AATI Fragment Analyzer),Genotyping including Allelic Discrimination Probes (SNP Real-Time PCR), Affymetrix Microarray (CNV CytoScan, SNP arrays), Fragment Analysis (Capillary Electrophoresis up to 1200 bp), DNA Sequencing (Sanger Sequencing), Expression Analysis including Affymetrix Microarray (global gene expression, transcriptome assays), Pathway-focused Real-Time qPCR (mRNA and miRNA). Shared Instrumentation including Beckman Biomek 3000 Liquid Handler, NanoDrop 2000c, ABI7900 384-well Real-Time Genetic Analyzer, PCR Tamer, Thermocyclers.
Stanford University Human Immune Monitoring Center Core Facility
Stanford University - Human Immune Monitoring Center
Core designed for immune monitoring services for clinical and translational studies. Goals include providing standardized, state-of-the art immune monitoring assays at RNA, protein, and cellular level, testing and developing new technologies for immune monitoring, archive, report, and mine data from immune monitoring studies. HIMC uses online database for integration of data from standard HIMC assays, along with de-identified clinical and demographic data.
Pasteur Institute Biophysics of Macromolecules and their Interactions Core Facility
Centre of Biophysics of Macromolecules and their Interactions
Paris - Biophysics of Macromolecules and their Interactions
Pasteur Institute Centre of Biophysics of Macromolecules and their Interactions
Provides services and instrumentation for characterization of biological macromolecules with technical and methodological expertise. Provides characterization of macromolecules including shape, folding, stability auto-association,and they interactions including stoichiometry,thermodynamic and kinetic parameters.
Harvard Medical School Center for Macromolecular Interactions Core Facility
Center for Macromolecular Interactions (CMI) in the department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School
Harvard Medical School Center for Macromolecular Interactions
Core provides scientific consultation, training and access to shared biophysical equipment for characterization and analysis of macromolecules and their complexes. Facility includes instruments measuring molecular interactions and assessing protein quality by Isothermal Titration Calorimetry (ITC), Surface Plasmon Resonance (SPR), Biolayer Interferometry (BLI), MicroScale Thermophoresis (MST), Differential Scanning Fluorimetry (DSF), Circular Dichroism (CD), Analytical Size Exclusion Chromatography with Multi-Angle Light Scattering (SEC-MALS), and Dynamic Light Scattering (DLS).
Contract Research Org. specializing in custom protein analysis. Services Provided include SDS PAGE analysis, Western Blotting, Mass Spectrometry, protein staining ( silver,coomassie) for academia, federal institutions and industry.
Nevada University Genomics Core Facility
Provides development and support of genomics-based research, serving investigators in Nevada and beyond. Staff can be contracted for select services including ABI 3130 DNA sequencing, BD FACSCalibur flow cytometry, Affymetrix microarray processing, Agilent 2100 Bioanalyzer analysis and Qubit analysis. Facility also provides equipment and training for real-time PCR, Western blot/gel/microarray scanning, and analysis of DNA, RNA and protein samples.
Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication.
Data and Computational Resources to Address COVID-19
NIH Open-Access Data and Computational Resources to Address COVID-19
Open Access Data and Computational Resources to Address COVID-19
COVID-19 open access data and computational resources provided by federal agencies, including NIH, public consortia, and private entities. Continuously updated as more information becomes available. These resources are being shared for scientific and public health interests, and content is responsibility of resource organizers.
Dataset of scholarly articles, including full text, on COVID-19, SARS-CoV-2, and related coronaviruses. Machine readable resource provided to enable application of natural language processing and other AI techniques. Open resource for global research community. Updated weekly as new research is published in peer-reviewed publications and archival services like bioRxiv, medRxiv, and others.
Dimensions COVID-19 publications, datasets and clinical trials
All Dimensions publications, datasets, and clinical trials related to COVID-19, updated daily.
Portal to discover COVID-19 open research data on Figshare. Figshare collection of COVID-19 related research data.
Broad Terra cloud commons for pathogen surveillance
Broad Terra cloud workspace for best practices with COVID-19 genomics data. Raw COVID-19 sequencing data from NCBI Sequence Read Archive. Workflows for genome assembly, quality control, metagenomic classification, and aggregate statistics.
NLM curated literature hub for COVID-19. Curated literature hub for tracking up-to-date scientific information about 2019 novel Coronavirus. Provides central access to relevant articles in PubMed. Articles are updated daily and are further categorized by different research topics and geographic locations for improved access.
Modeling Infectious Disease Agents Study online portal for COVID-19
Portal for COVID-19 modeling research. Public access data collections with documented metadata.Computational models to study transmission dynamics of broad range of infectious diseases.
Resource to aggregate all outbreak information into single location during outbreaks of emerging diseases, such as COVID-19.
Guidelines for data deposition in any common data hub or platform to facilitate data sharing in public health emergencies for scientific research.
Data warehouse using Observational Medical Outcomes Partnership standard to integrate patient data across University of California health systems. Data asset created by electronic health records from six health systems as well as claims data from UC self-funded health plans and external sources of data such as Vizient and California Office of Statewide Health Planning and Development. Shared data and analytic environment designed to improve research and patient treatments.
Network as federated AI-ready repository of COVID-19 data adherent to FAIR principles. SARS CoV-2 virus data FAIR, meaning that they are Findable, Accessible, Interoperable and thus Reusable by both humans and machines, during this epidemic of COVID-19.
Cloud resources for COVID-19 research provided by Rescale, Google Cloud, and Microsoft Azure. High performance computing resources immediately available for COVID-19 research.
COVID-19 High Performance Computing Consortium
COVID-19 High Performance Computing (HPC) Consortium
Consortium encompasses computing capabilities from powerful and advanced computers in the world. Used to empower researchers to accelerate understanding of COVID-19 virus and development of treatments and vaccines to help address infections. Teams who receive Consortium access will publish their results in open scientific literature. All supported projects will have name of principal investigator, project title and project abstract posted to COVID-19 HPC Consortium web site.
Group of volunteer data scientists, machines learning experts, bioinformaticians and professional software developers who have joined together to offer their expertise for any data analysis problems that arise in context of ongoing coronavirus pandemic.
NASEM Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats
and Medicine Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats
Committee provides expert consultation on data elements and systems design for modeling and decision making for COVID-19 pandemic. Assembled at request of White House Office of Science and Technology Policy and Office of Assistant Secretary for Preparedness and Response in response to COVID-19 outbreak. Provides expert consultations on several topics, such as surface stability and incubation, social distancing, and crisis standards of care.
Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses.
Portal includes vocabulary to assist global response to Coronavirus outbreak. Creates, maintains, and promotes schemas for structured data.
Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs.
Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis.
Gene Expression Profiling Interactive Analysis
Web server for cancer and normal gene expression profiling and interactive analyses. Interactive web server for analyzing RNA sequencing expression data of tumors and normal samples from TCGA and GTEx projects, using standard processing pipeline. Provides customizable functions such as tumor or normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis.
COVID-19 Portfolio Tool From the Office of Portfolio Analysis
NIH comprehensive, curated source for publications related to COVID-19. Includes articles from PubMed and pre-prints from arXiv, medRxiv, bioRxiv, and ChemRxiv. Updated daily. NIH Office of Portfolio Analysis has developed this resource to explore and analyze set of advances in COVID‑19 research as they accumulate in real time, and complements efforts by NLM to aggregate full text documents broadly related to COVID-19 and other outbreaks, and articles on COVID‑19 specific to PubMed database.
Software tool providing machine learning approach for identification and classification of CRISPR-Cas systems. Combines regression and classification approaches for improving quality of input protein cassettes and predicting their subtypes.
Eukaryotic Pathogen CRISPR guide RNA/DNA Design Tool
Web tool tailored to design CRISPR guide RNAs for Eukaryotic pathogens. Used to identify gRNAs in input sequence, and then calculate ranked list of those gRNAs based on on-target and off-target hits in selected or uploaded pathogen genome, to predict gRNA activity and to identified microhomology pairs flanking gRNA targeted cut site.
Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification.
Pittsburgh University HSCRF Genomics Research Core Facility
University of Pittsburgh Genomics Research Core
University of Pittsburgh HSCRF Genomics Research Core
Offers high throughput genomics services, technical expertise and support with experimental design and protocol development. Includes Nucleic Acid Services, genetic and genomic DNA analysis with sequencing available in standard, high-throughput and next-generation formats, Genome-wide MicroArray or RNA-seq and targeted RNA analysis, Next Generation Sequencing,Drop Seq.
Colorado University Boulder BioFrontiers Advanced Light Microscopy Core Facility
BioFrontiers Advanced Light Microscopy Core
University of Colorado Boulder BioFrontiers Advanced Light Microscopy Core
Facility designed to advance biological discovery through quantitative microscopy techniques. Houses multiple imaging technologies ranging from conventional widefield to state-of-the-art Super Resolution/localization microscopies.Offers N-STORM Super Resolution Microscopy,Laser Scanning Confocal Microscopy, Widefield Fluorescence Microscopy,Spinning Disc Confocal Microscopy,Total Internal Reflection Fluorescence (TIRF) Microscopy,Long-Term Imaging with Temperature, Oxygen, Carbon Dioxide, and Humidity Control,High-Content Screening,Analysis Workstation.
Miami University Miller School of Medicine Viral Vector Core Facility
University of Miami Viral Vector Core Facility
Viral Vector Core (VVC) Facility (Miami Project to Cure Paralysis)
Produces high titer lentiviral and AAV viral particles. Stock viruses including GFP-, mCherry-, and LacZ-expressing lentiviral and AAV particles can be purchased. For generating custom viral particles, investigator provides high quality maxiprep of transfer plasmid to be packaged into viral particle of choice. Turn around time is about 2 weeks for lentivirus and AAV viral particles.
New York University School of Medicine Center for Biospecimen Research and Development Histology Core Facility
NYU Grossman School of Medicine Center for Biospecimen Research and Development Histology
Assists researchers and clinicians with molecular and morphologic characterization of normal and disease tissues of interest in support of biomarker discovery and translational research. Offers both routine and advanced histology immunohistochemistry, in situ and whole slide scanning services.
Web tool to explore and visualize Antibiotic Resistance Genes found on Tara Oceans samples. Can be explored by individual ARG or grouped by antibiotic class.
Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data.
Software tool to find and visualize rearrangements in DNA sequences.
Measurement Control And Data Analysis Software
Software package for measurement control and analysis by Femtonics Ltd. Designed in MATLAB and used in field of cellular and network imaging. New version offers new scanning features and improved overall usability.
Software tool as instrument software for SPC- and DPC Modules by Becker and Hickl GmbH.
Fluorescent Imaging Analysis Software FIMAS
Software tool to perform basic and specific analysis procedures on fluorescent microscopy and fluorescent lifetime imaging microscopy data. Requires MATLAB with image processing and statistical toolboxes. Can import fluorescent data from Olympus, Biorad, Femtonics, TIFF, Excel, ASCII files.
Software tool as modeling system for mathematical optimization by GAMS Development Corporation. GAMS is designed for modeling and solving linear, nonlinear, and mixed-integer optimization problems. Used in genome scale modeling.
Software tool to accompany existing resources such as Python programming language resource and comprehensive Perl archive network (CPAN) resource. Perl is family of two high level, general purpose, interpreted, dynamic programming languages. Perl refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned sister language, Perl 6, before name was officially changed to Raku in October 2019.
Interactive web based tool for analyzing biomacromolecular channels, tunnels and pores. Enables two modes of calculation with one dedicated to analysis of channels and another for transmembrane pores. Can use PDB and mmCIF formats. Can analyze biomacromolecular structures stemming from NMR, X-ray and cryo-EM techniques. Interconnected with PDBe, CSA, ChannelsDB, OPM, UniProt to help setup and analysis of acquired results. Provides analytics for detection and structural characterization of channels and information about their physicochemical features.
Open source web application to create and share documents that contain live code, equations, visualizations and narrative text. Used for data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning.
Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install.
Software tool as cross platform, language agnostic binary package manager. Open source package management system and environment management system that runs on Windows, macOS and Linux. Can quickly install, run, and update packages and their dependencies. Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more. Created for Python programs, but it can package and distribute software for any language. Conda can be combined with continuous integration systems such as Travis CI and AppVeyor to provide frequent, automated testing of your code. Conda package and environment manager is included in all versions of Anaconda and Miniconda.
Severe Acute Respiratory Syndrome CoronaVirus 2 Sequences
Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released.
Reference library processing for JavaScript. Reference library processing for NodeJS.
Web application for data analysis and visualizing effect sizes. Data analysis with estimation graphics.
System for non-invasive vascular function assessment by Itamar Medical Ltd.
System for measuring pulse wave velocity, pulse wave analysis by ATCOR. System for noninvasive central blood pressure waveform assessment. Provides measures of central arterial pressure waveform and pulse wave velocity as well as assessment of arterial stiffness via waveform analysis e.g. augmentation index, augmented pressure, and reflected wave magnitude.
System for arterial assessment and diagnosis by Alam Medical. Device measuring pulse wave velocity and central pressure analysis in single acquisition.
Software tool for analysis of ultrasound data from vascular flow mediated dilation studies. Flow Mediated Dilation software endothelial function assessment by Quipu.
Jittered Boxplots for Toxicological Data
Web tool for creating box plots with dot plots. Boxplot for grouped and clustered data in toxicology. Jittered boxplots for visualizing grouped and clustered data from toxicological studies together with individual raw values and indications of statistical significance.
Interactive Repeated Experiments Dotplot
Web tool for creating interactive graphics. Enables authors to create interactive graphics from data obtained with repeated independent experiments. Designed for laboratory studies with repeated experiments.
Web-based tool to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of continuous variable across different study groups, visualization of subgroups or clusters of non-independent data. Web visualization tool for creating dot plots, box plots and violin plots for small sample size data sets.
Web based interactive visual analysis system for exploration of single cell data published in Allen Cell Types Database and for number of single cell data resources of Brain Initiative Single Cell Network. Allows interactive exploration of hierarchies of cell types, visualization of transcriptome wide gene expression in combination with metadata of individual cells, performing differential analyses and statistics between manual selections of cells, or between pre-defined clusters throughout cellular hierarchy and more.
Web application for plotting and annotating continuous data. Open source web app for plotting and annotating time series data. Used to inspect data and generate publication quality visualizations. Available options for plotting include lineplot, small multiples and heatmap, summary statistics and inferential statistics.
Collection of ontology of provisional cells determined by experimental methods.
Web app for visualizing data together with their summaries. Visualizes data and statistics to enable comparison of experimental conditions. Written in R and uses packages including shiny, ggplot2, dplyr, tidyr, readr, magrittr, ggbeeswarm, readxl, DT. Github page of PlotsOfData can be used to trace changes between different versions.
Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions.
Health Data Research UK COVID-19 Initiative
Initiative to mobilize talent and partnerships across United Kingdom to coordinate and connect national data science driven research efforts related to COVID-19 to address wider impact of COVID-19 pandemic.National Institute for Health Data Science for England, Wales, Scotland and Northern Ireland, is championing use of health data to respond to COVID-19.
COVID-19 Open Research Dataset Challenge
COVID-19 Open Research Dataset Challenge (CORD-19)
Collection of scholarly articles about COVID-19 and coronavirus family of viruses for use by global research community. Dataset is updated on weekly basis.
EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.
Web based platform on COVID-19 to maintain predicted diagnostic, drug and vaccine candidates and computational resources on novel coronavirus SARS-CoV-2 and its resulting disease COVID-19. Provides collected and organized information from literature and other resources from internet, links to appropriate literature . Integrated multi-omics repository dedicated to current genomic, proteomic, diagnostic and therapeutic knowledge about coronaviruses.
Coronavirus Immunotherapy Consortium Database
Serves as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. Most potent antibodies will guide development of vaccines to stop current outbreak and protect against future pandemics.
Initiative from scientific community to put all available resources including highly skilled scientists at service of fight against COVID-19.
Software tool as full text search engine for COVID-19 Open Research Dataset. Used to explore dataset and identify potential research efforts.
2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation
2019 Novel Coronavirus Resource (2019nCoVR)
Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data.
Data collection related to COVID-19 held at EMBL-EBI , including sequences of outbreak isolates and records related to coronavirus biology, protein expression, protein sequence, protein structure, proteome and translatome data and literature.
Curated list of open funding calls and other support for researchers, non profit organizations and commercial organizations, specifically for COVID-19 and coronavirus related research. Non profit and commercial funding opportunities relevant to COVID-19. Updated daily.
American Diabetes Association COVID-19 Resources and Webinar Series
Web page created by American Diabetes Association. Contains resources and information about COVID-19 for diabetes professionals and patients. ADA also provides online forum, webinar series and podcast. Online forum to exchange questions, answers, and best practices with leading clinicians from diabetes community. All ADA members can contribute, and any interested health professional can read forum and responses.
COVID-19 and Coronavirus plasmids and resources
Collections of Addgene plasmids, open access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists. Ordering or depositing plasmids related to COVID-19 research.
Software tool as method that takes cluster results from single cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. Utilizes random forest of decision trees machine learning approach. Used to determine minimum set of marker genes whose combined expression identified cells of given type with maximum classification accuracy.
Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology.
Software package to align brain slice images in atlas free manner.
Software tool as quality control and processing pipeline for High Throughput Sequencing data. Uses tab delimited fastq format that allows for streaming from application to application. Interoperable with other standard Linux tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software workflow management system for automated and distributed analysis of large scale experimental data. Implemented in Java and is thus platform independent.
Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2020. Software tool as automated Gene Ontology based multi species gene set generator for gene set enrichment analysis. Used to generate gene sets required for Gene Set Enrichment Analysis for almost any organism for which GO term association data exists. Gene set collections can be automatically created for wide variety of species.
Web tool implementing positional gene enrichment analysis of gene sets for high resolution identification of over represented chromosomal regions.
Web tool for graphical illustrations for biological systems by BioRender. Used for articles and presentations. Collection of pre made icons and templates from life science fields for scientific illustrations. Customized icons possible on request.
Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data.
Prediction system for GPI-anchored proteins. Used to predict presence of GPI-anchor and position of omega site. Prediction server based on support vector machine for discrimination of anchoring signal, and on Hidden Markov Model for prediction of most probable omega site. Method for screening whole proteomes.
Time-Dose INtegrated moDelling of toxicogenomics data
Software tool as framework for dose and time dependent gene expression analysis which aims to identify groups of genes that show dynamic dose response behaviour. Software R package to cluster gene expression by contour plots. Used to analyse toxicogenomics data with multiple dose levels and time points and to identify expression patterns with respect to both variables and to cluster molecular features.
Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.
Collaborative database for pregnancy and placental research studies worldwide by Global Pregnancy Collaboration CoLab . Database for collecting data for pregnancy studies in preeclampsia and other fields. Database has web based data entry platform with study specific user access. Data can also be entered offline using formatted spreadsheet template that can be uploaded to database in bulk or stored locally. Data is property of investigator but with permission can be combined into larger studies across centers and countries. Collaboration is enabled but not required.
Nencki Monash template of common Marmoset cortex
Nencki-Monash template of Common Marmoset cortex
Open access template of young adult marmoset brain, created from three dimensional reconstructions. Histology based average template of marmoset cortex with probabilistic localization of cytoarchitectural areas. Allows direct estimates of most likely coordinates of each cortical area, as well as quantification of margins of error involved in assigning voxels to areas, and preserves quantitative information about laminar structure of cortex.Enables integration with magnetic resonance imaging and tracer based connectivity data. Allows interoperability between NM template and other current digital atlases of marmoset cortex.
Fully automated analyzer for immunoassay analysis by Roche. Designed for in vitro assay determinations. Applications including anemia, bone, cardiac and tumor markers, critical care, fertility hormones, and infectious diseases. Available as rack or disk sample handling system.
Beckman Coulter | UniCel DxI 800 Access Immunoassay System
Beckman Coulter UniCel DxI 800 Access Immunoassay System
Immunoassay analyzer that can run up to 400 tests per hour and has standardized test menus, assay protocols, instrument processes and reference ranges. Sample types include serum, plasma, urine, amniotic fluid, and whole blood.
Immunoassay analyzer by Abbott for chemiluminescent microparticle immunoassay technology. Sample types include serum, plasma, whole blood, and urine.
Chicago University Human Imaging Research Office Core Facility
Assists University of Chicago investigators and research staff with medical imaging exams performed on human subjects for research purposes. Services include acquisition, analysis, collection, de-identification and distribution of image data for basic science research and clinical trials. Services ensure research-related imaging fulfills protocol requirements and allow investigators to obtain HIPAA- and IRB-compliant clinical research data. Provides services for all types of medical imaging, including x-ray, CT, MRI, ultrasound, nuclear medicine, PET, and most types of specialty imaging.
Oregon State University Center for Quantitative Life Sciences Core Facility
Center for Genome Research and Biocomputing
Formerly Center for Genome Research and Biocomputing Core Facility. Functions and facilities include services in genomics, functional genomics, genotyping and imaging.Biocomputing facilities with computing infrastructure, which includes managed cloud and shared resources, data analyses and training are customized to individual needs, including genome assembly and annotation, analysis of RNAseq, GBS, and metagenomics data, and GPU-enabled deep learning analyses.
Software tool for image analysis by Cytiva. Automated image analysis software for general purpose electrophoresis gel, blot, arrays and colony counting.
Software tool by eBioscience as part of eBioscience FlowCytomixTM Multiple Analyte Detection System, developed by Bender MedSystems. Used to analyze FlowCytomix assays.
Open access online video resource about dementia for researchers dedicated to bringing latest news and education in short form video format. Published by Oxford based Magdalen Medical Publishing.
Software toolkit for genome wide association studies optimized for GWAS like datasets by CSIRO. Machine learning framework that creates insights from high dimensional data, including genomics and clinical data.
Text mining algorithm to screen biomedical publications to find data sharing statements. Algorithm that parses set of publications and detects which publications disseminated Open Data or Open Code together with publication. Tailored towards biomedical literature.
R scripts for Fly Liquid Food Interaction Counter data analysis
Fly Liquid Food Interaction Counter Monitor
Software tool as user interface for running Fly Liquid Food Interaction Counter experiments.
Web tool to predict whether given protein sequence is intrinsically unfolded. Algorithm for predicting ordered and disordered regions in protein based on its primary structure amino acid sequence. Graphic web server to predict if given protein sequence is intrinsically unfolded implementing algorithm of Uversky and co-workers, which is based on average residue hydrophobicity and net charge of sequence.
SParx for HIgh Resolution Electron Microscopy
Software suite for access to cryo electron microscopy with goal of quality assessment and result reproducibility by statistical resampling. Cryo-EM processing software. Major programs within SPHIRE include Movie, Window, crYOLO, ISAC, VIPER, Meridien, Sort3D, LocalRes, Cinderella.
Software package for automatic particle picking for cryo-EM using neural networks. Particle picker for electron cryomicroscopy based on deep learning object detection system You Only Look Once YOLO. Distributed as part of image processing workflow in SPHIRE.
Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome.
Software for visualization of macromolecular structures, atomic coordinates, and 3D intensity maps, and for building macromolecular structures.
Software and algorithm for analyzing protein protein cross linking mass spectrometry data. Library of routines for peptide based mass spectrometry. Contains search engine for identification of crosslinked peptides.
Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra
Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria.
Software tool to perform label free quantification from shotgun proteomics experiments. Operates as node within Proteome Discoverer workflow environment. Makes use of multi core processors and can process data in parallel threads to speed up data analysis. Provides features such as retention time alignment and peptide identity propagation and more.
Web tool to visualise protein sequences as helices. Draws helical wheel diagram for protein sequence. EMBOSS pepwheel displays peptide sequences in helical representation.
Heka Elektronik | EPC 10 USB Patch Clamp Amplifier
Electrophysiology patch clamp amplifier for collecting electrical signals from tissues and cells. Can be controlled via USB. Designed and manufactured by HEKA Elektronik.
Software tool as free color blindness simulator for Windows, Mac and Linux. Design for Color Impaired. Takes guesswork out of designing for color blindness by showing you in real time what people with common color vision impairments will see.Color Oracle is open source, available on GitHub for Mac and Windows/Java.
Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops.
Software tool as objective method for quantifying qRT-PCR results using calculations based on kinetics of individual PCR reactions without need of standard curve, independent of any assumptions or subjective judgments which allow direct calculation of efficiency and CT. Algorithm provides objective and noise-resistant method for quantification of qRT-PCR results that is independent of specific equipment used to perform PCR reactions.
Software tool as 3D imaging software. Flexible and intuitive all-in-one dental software platform. Provides set of tools to meet imaging needs by any dental facility.
Intraoral scanner for taking digital impressions.
Electrophysiology system for dual or single patch clamp recording with movable microscope. Consists of SliceScope microscope, motorised XY translation stage, fixed stage platform, and two Patchstar motorised micromanipulators. Manufactured by Scientifica LTD.
Reproducible Untargeted Metabolomics Data Processing Workflow
Computational workflows for reproducible untargeted metabolomics data processing pipeline.
Vibrotome by Precisionary Instruments designed for cutting fixed tissue slices for histology studies. Offers two point stabilization of blade holder to eliminate unwanted chatter marks on surfaces of tissue slice. Fully automated to section fixed tissues with thickness range of 4 um to 2000 um with adjustable precision of 1 um.
VS120 Virtual Slide Microscope. Part of slide loader system for manually loading standard slides by Olympus.
Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available.
Jupyter protocol implementation and client libraries. Part of Project Jupyter which exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages. Jupyter-client contains reference implementation of Jupyter protocol and provides client and kernel management APIs for working with kernels.
Terminal based console frontend for Jupyter kernels. This code is based on single process IPython terminal.
Battery powered amplifier with high and low pass filtering for recording extracellular signals by World Precision Instruments.
Jupyter core package. Software package on which Jupyter projects rely.
Software Python library for symbolic mathematics. It aims to become full featured computer algebra system (CAS) while keeping code as simple as possible in order to be comprehensible and easily extensible.
Software tool to extend unittest to make testing easier. Python unit test framework. Note, Nose has been in maintenance mode for the past several years and will likely cease without a new person/team to take over maintainership. New projects should consider using Nose2, py.test, or just plain unittest/unittest2.
Software package to test and visualize gene overlaps. Given two gene lists, tests significance of their overlap in comparison with genomic background.
Python interface to graph visualization software Graphviz Dot.
Software brain connectivity toolbox for Python.
Software tool to check Python source files for errors. Passive checker of Python programs Used to analyze programs and detect various errors. Works by parsing source file, not importing it, so it is safe to use on modules with side effects.
Software tool as composable cycle creator in python.
Utilities to compute Wasserstein distance between persistence diagrams. Project has been renamed to Hera.
Collection of tools to provide algorithms, databases and software for interpreting and archiving data in systematic framework ranging from analysis of expression regulation from deep sequencing data, annotation of miRNA regulatory elements and targets to interpretation of role of ncRNAs in various diseases and pathways. Includes target prediction algorithms microT v4 and microT-CDS, databases of experimentally verified miRNA targets on coding and non-coding RNAs like TarBase v7.0 and LncBase, and software capable of identifying potentially altered molecular pathways by expression of single or multiple miRNAs , mirPath. Provides Web Server (v5.0) to support series of workflows enabling users to perform miRNA analyses.
A platinum/iridium electrode use for stimulating tissue samples. Manufactured by FHC Neural microTargeting Worldwide.
Extending Guilt by Association by Degree
Software package implements series of highly efficient tools to calculate functional properties of networks based on guilt by association methods. Ultra fast functional analysis of gene networks.
Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code.
Webserver for identifying targets for genetically modified crop breeding pipelines. Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard.
Thermo Fisher: Applied Biosystems | ABI 3100 Capillary Genetic Analyzer
Benchtop capillary genetic analyzer multicolor fluorescence based DNA analysis system with 16 capillaries. It can process 96 or 384 well plates.
Thermo Fisher: Applied Biosystems | ABI 3700 Genetic Analyzer
Automated capillary gel electrophoresis genetic analyzer that sequences up to 96 DNA templates per run and is used for PCR sequencing and short tandem repeat genotyping.
Thermo Fisher: Applied Biosystems | ABI Voyager DE Pro MALDI-Mass Spectrometer
Benchtop MALDI TOF mass spectrometer that has linear and reflector analyzer. It is used to analyze organic and inorganic compounds, protein identification, synthetic peptide validation, and polymer analysis.
Agilent 3100 OFFGEL Fractionator performs isoelectric focusing of proteins or peptides in immobilized pH gradient (IPG) gel strips.
American Optical | 860 Sliding Microtome
THIS REOURCE IS NO LONGER IN SERVICE. Documented on September 29,2023. Sliding microtome used for cutting hard objects such as bone, wood, frozen celloidin, and paraffin preparations. Cutting thickness is adjustable from 1 to 40 microns.
Agilent 4200 Tapestation Genetic Analyzer
Benchtop genetic analyzer. Electrophoresis system for DNA and RNA sample quality control. It can be used for next generation sequencing or Biobank workflow.
Thermo Fisher: Applied Biosystems | GeneAmp 9700 PCR Thermocycler System
Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C.
SCIEX | | API 5000 Triple Quadrupole Liquid Chromatography Mass Spectrometer System
Triple quadrupole liquid chromatography mass spectrometer for analysis of bioanalytical samples. It can be used for DMPK and ADME studies.API 5000 LC/MS/MS System delivers the lowest limits of detection for the most demanding DMPK and ADME studies.
Thermo Fisher: Applied Biosystems | 3500xl Genetic Analyzer
Applied Biosystems 3500xL 24-capillary Genetic Analyzer is used for the Human Identification application.Genetic analyzer that utilizes capillary electrophoresis for genetic analysis. It has capillary lengths of 50 cm or 36 cm and can use 384 well plates or 96 well plates.
Digital hand held pocket refractometer that measures urine specific gravity. It has measurement temperature of 10 to 35 C and sample volume of 0.3ml.
Thermo Fisher: Applied Biosystems | 433A Peptide Sequencer
Automated peptide synthesizer for chain assembly steps in solid phase peptide synthesis or FastMoc chemistry. Data is based on conductance or ultraviolet UV absorbance of reagent, solutions, and solvents in the synthesis cycle.
Vibrating microtome for cutting tissue slices, similar to cryostats and vibrating microtomes. Fully automated for sectioning fixed and live tissues, with down to 1 um precision. Can cut tissue slice thicknesses ranging from 3 um to 2000 um, at 1 um intervals.
Leica VT1200 S vibrating blade microtome
Fully automated Leica VT1200 S vibrating blade microtome designed for sectioning for cutting fresh and fixed tissue in neuroscience by Leica Biosystems.
GigE camera with Sony ICX445 CCD sensor, 30.3 fps by Allied Vision. 1.2 megapixel GigE machine vision camera that incorporates high quality Type 1/3 (6.0 diagonal) Sony ICX445 CCD sensor with EXview HAD technology. At full resolution, this camera runs frames per second. With smaller region of interest, higher frame rates are possible.
Molecular Devices | MultiClamp 700B Microelectrode Amplifier
Computer controlled amplifier for current clamp and voltage clamp applications from Molecular Devices, LLC. Amplifier used for electrophysiology and electrochemistry.
Sliding microtome from Leica Biosystems with low maintenance cross roller bearing slideways designed to easily section either paraffin embedded or fixed, frozen specimens. Features knife holder for both standard knives and disposable blades. Please note: this product is discontinued and no longer available for sale.
Automated slide scanner from Leica Biosystems. This product is discontinued.
Diode laser, 810 nm wavelength with manufacturer from CAO group, USA. Commodity code: 002-00102. Used for rehabilitation procedures to promote healing, reduce pain and inflammation.
Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest.
Campden Instruments | Vibroslice vibrating microtome
Vibrating microtome manufactured by Campden Instruments. 752 Vibroslice tissue cutter for manual tissue transport.
Software tool for growth curve fitting and visualization. Program allows to fit growth curve using simple GUI or advanced scripting environment. Used to fit growth curves generated for data collected in microtiter plates or elsewhere.
Software tool as open source spreadsheet program that is part of GNOME Free Software Desktop Project. Can do some statistical analysis such as Student t-tests. Spreadsheet application that replicates basic features of popular commercial programs like Microsoft Excel.
Kaleidoscope Pro analysis software automatically scan field recordings to discover species of interest. Kaleidoscope Viewer enalbes for examining ultrasonic and acoustic sound files visually.
Prime 95B Scientific CMOS camera brings light in from back of sensor. Photons land directly onto light receiving surface, maximizing light collecting capability. Back illuminated sCMOS camera.
Software tool for fast and accurate in silico Mycobacterium spoligotyping from sequence reads.
Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.
Software tool to simplify creation and management of computing environments in Neuroimaging.
Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy.
Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles.
Software tool as big image data compatible Fiji plugin for trainable image segmentation.
Cell Line Adenosine-to-Inosine RNA editing database
Cell Line Adenosine-to-Inosine RNA editing database. Searchable catalogue of RNA editing levels across cell lines. Used to facilitate rational choice of appropriate cell lines for future work on A-to-I RNA editing.
Comprehensive database of A-to-I RNA Editing Events. Atlas of A-to-I RNA editing events in human and other organisms. Collection of A-to-I events in body sites of healthy individuals from GTEx project. RNA Editing sites can be searched by genomic region, gene name and other relevant features as tissue of origin. Query results are shown in sortable and downloadable tables in which main characteristics of individual RNA editing events are reported. RNA-Seq and DNA-Seq coverage per site as well as RNA editing levels are provided.
Tool recommender system in Galaxy using deep learning
Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network.
Open knowledge base that can be read and edited by both humans and machines. Storage for structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. Provides support to many other sites and services beyond just Wikimedia projects.
Software text mining tool aiding curation at Rat Genome Database. Ontology driven, concept based literature search engine developed at RGD. Tags abstracts with gene names, gene mutations, organism names and terms from ontologies vocabularies used at RGD. Open and fully customizable.
METAdata of GEnomics studies on a web based NOTEbook
Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository.
Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
Web server for in silico prediction of allergens. Alignment free server for in silico prediction of allergens based on main physicochemical properties of proteins. Used to predict the route of allergen exposure: food, inhalant or toxin.
Software suite that works by themselves, and with Amber20 itself. Can be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.
Web tool that automatically screens bioRxiv preprints for rainbow colormaps, which are not colorblind safe. Emails authors information on replacing these colormaps with colorblind safe alternatives. Screens preprints to improve data representation and colour-blind accessibility.
Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems.
Software tool based on hashing algorithm and approach to genomic reference indices from Noblis. Used to indexing genomic references. Aligns reads on reference genomes at random positions where k-mer indexes are matched with reference genomes.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18, 2020. Software package to create, visualize and analyze biological networks. Can include coding relations to distinguish between genes and their products. BisoGenet client is designed to work as Cytoscape plugin for querying server along with graph topology analysis and visualization options for easing interpretation process.
Database provides cell markers for various cell types in tissues of human and mouse. Manually curated resource of cell markers in human and mouse. Provides user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Summarized marker prevalence in each cell type is graphically presented., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Database includes genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome. Facilitates genetic variation analyses and recombinant gene design. Derived from all available GenBank and RefSeq data.
ProTox-II - Prediction Of Toxicity Of Chemicals
Web server for prediction of toxicity of chemicals. Virtual lab for prediction of toxicities of small molecules. Used for prediction of multiple toxicological endpoints related with chemical structure.
Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps.
Software automated screening tool that detects bar graphs of continuous data in preprints submitted to bioRxiv. Used for detection of bar graphs for continuous data in BioRxiv preprints.
Advanced benchtop tandem quadrupole mass spectrometer which expands scope of ultimate sensitivity analysis. Fatures probe design which allows users much easier maintenance, optimization and improved reproducibility between operators. Method transfer onto Xevo TQ-XS is made simple by Xtended Dynamic Range detector which allows six orders of linear dynamic range. Wider compound coverage without changing ionization technique is delivered by the revolutionary UniSpray source option.
Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.
Interactive web application that depicts daily disease trends at level of US counties using time series plots and maps.
Web Application for distilling systemic implications of COVID-19 pandemic with Natural Language Processing.
Web server for prediction of protective antigens, tumor antigens and subunit vaccines. Alignment free approach for antigen prediction, which is based on auto cross covariance transformation of protein sequences into uniform vectors of principal amino acid properties.
Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis.
Win Bayesian inference Using Gibbs Sampling
Software package for Bayesian analysis of complex statistical models using Markov chain Monte Carlo methods.
Sample Parameter Reconstruction via Iterative TEchniques
Web app to generate possible distributions of data matching given mean, SD, sample size, and range. Used for recovering data from summary statistics. Implementation of SPRITE in R programming environment.
Broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation, calculation of various molecular properties needed in QSAR, molecular modelling and drug design, high quality molecule depiction, molecular database tools supporting substructure and similarity searches. Molinspiration tools are platform independent and may be run on any PC, Mac, UNIX or LINUX machine. Software is distributed in form of engines, which may be used as stand-alone computational engines, used to power web-based tools, or incorporated into larger in-house Java applications.
Software as open source virtual screening tool. Calculation is based on various druglikeness rules like Lipinski's rule, MDDR-like rule, Veber rule, Ghose filter, BBB rule, CMC-50 like rule and Quantitative Estimate of Drug-likeness (QED). Uses Chemistry Development Kit (CDK), Java library for descriptor calculation. Used for fast calculation of drug like properties of molecule.
Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information.
Data Analysis in Molecular Biology and Evolution
Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers.
Neural network and web server, which determines cysteine oxidation state and disulfide connectivity of protein, given only its amino acid sequence. Used to predict disulfide connectivity topology. Predicts which half-cystines are covalently bound to which other half-cystines. DiANNA 1.1 is extension of DiANNA web server for ternary cysteine classification.
Web server to predict discontinuous B cell epitopes from protein three dimensional structures.
Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation.
Software package as automated MATLAB based trainable image cell segmentation, fluorescence quantification and analysis suite. Used for high throughput time lapse fluorescence microscopy of in vivo bacterial cells. Robust image segmentation, analysis and lineage tracking of bacterial cells.
Software R package for dynamic report generation using Literate Programming techniques. Comprehensive software tool for reproducible research in R.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Software tool as direct-to-Excel-based software that gives flexibility in data retrieval, storage, and analysis. Software comes preloaded with protocols for Promega luminescent assays. It is also possible to create, store, and retrieve user-defined protocols.
Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research.
Open source machine learning library based on Torch library, used for applications such as computer vision and natural language processing. Software Python package that provides tensor computation with strong GPU acceleration and deep neural networks built on tape-based autograd system.
Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes.
Estimate Time Varying Reproduction Numbers from Epidemic Curves
Framework and software to estimate time varying reproduction numbers during epidemics. Tools to quantify transmissibility throughout epidemic from analysis of time series of incidence. Used to estimate time varying instantaneous reproduction numbers from incidence time series.
Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics.
Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling.
Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.
Software package for peptides designing and prediction. In silico approach for predicting toxicity of peptides and proteins. Used for predicting peptide toxicity or non toxicity, minimum mutations in peptides for increasing or decreasing their toxicity, toxic regions in proteins.
Software R package to impute missing values particularly in case of mixed type data. Non parametric, mixed type imputation method for any type of data for statistical software R. Predicts missing values.
Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST.
Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI.
Software Python package for Bayesian statistical modeling and probabilistic machine learning which focuses on advanced Markov chain Monte Carlo and variational fitting algorithms. Allows model specification directly in Python code.
Open source virtual screening software for computational drug discovery with intuitive user interface. Runs on operating systems Linux, Windows, and Mac OS. Used to screen libraries of compounds against potential drug targets.
Software R package to combine differential gene expression results. Differential expression meta analysis tool. Gene expression meta analysis visualization tool. Used to identify genes whose expression is consistently perturbed across several studies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences.
Software tool as Next Generation Sequencing assembler. Optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single cell assembly. Can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs in time and memory efficient manner on single server.
Web tool for maximizing usable data in alignment. Maximizes number of characters that are present in gap free columns alignment area by selecting optimal subset of sequences. Removes sequences with many gaps in post process of alignments in order to improve alignment area.
Software workflow and set of tools for scholarly publishing to enable collaborative authoring of scholarly manuscripts. Used to write manuscript in markdown, track it with git, automatically convert it to .html, .pdf, or .docx, and deploy it to destination of choice.
Software technical plotting, curve fitting and data analysis application. Provides graphical user interface for data exploration as well as various statistical analysis tools, peak fitting options, raster or vector formats of publishable plots. Graphing software for medical writers.
Desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Used to interrogate different views of 10x data to gain insights into underlying biology.
Software package for sequence alignment. Pairwise aligner for aligning DNA sequences. Designed to handle sequences size of human chromosomes and from different species. Useful for sequences produced by NGS sequencing technologies.
Software tool as model building program for cryo-electron microscopy. Processes cryoEM maps through secondary structure stage and Cα stageA. Template matching based automatic model building program for high resolution Cryo-Electron Microscopy maps.
Web server for protein structure prediction and refinement. Used to predict protein structure from sequence by template based modeling. Used for refinement after providing starting model structure and locations of loops or termini to be refined.
Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression.
Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.
Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations.
Significance Analysis of INTeractome Express
Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.
Web tool to predict linear antigenic epitopes. Predicts antigenic epitope with latest sequence input from IEDB database. Method to predict antigenic epitopes using support vector machine to integrate Tri-Peptide similarity and propensity.
Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes.
Large scale electron microscopy datasets. Large scale electron microscopy database for Human Type 1 Diabetes.
Alberta Diabetes Institute IsletCore database
Collection of data from all pancreatic islet isolations.
Collection of human pancreas data and images. Platform to share data from human pancreas samples. Houses reference datasets from human pancreas samples, achieved through generosity of organ donors and their families.
Web tool to classify citation statements from scientific articles using deep learning. Used for discovering and evaluating scientific articles via Smart Citations.
Software tool which allows to control Doric hardware and acquire all required data simultaneously. Incorporates different modules for each devices connected.
Portal dedicated to funding lung cancer research by LUNGevity Foundation. Supports patient focused research and convene multi stakeholder meetings to streamline research process and accelerate progress to patients. Seeks to empower patients to be active decision makers in their treatment process through educational resources, online peer-to-peer support, and in-person survivorship programs.
Probe uses semi permeable membrane with pore size of 30 kDa which enables small hydrophilic compounds from brain extracellular space to diffuse passively into perfusate. Used to measure extracellular ACh level and glucose metabolites directly without purification.
Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data.
Software tool to calculate ratio of intensity in nuclei and cytoplasm. It needs two images as input cytoplasm channel and nuclei channel.
Web server for inter residue interaction calculations in single site. Determines accessible surface area and residue depth, which is distance of residue from surface of protein. Recognizes specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near surface or deep inside. Recognizes interactions including disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation interactions within protein or between proteins in complex.
Thermo Fisher | Isotemp 280A Vacuum Oven
Fisher Scientific Isotemp 280A is a Vacuum Oven offers a temperature range from ambient up to 200C with internal dimensions of 11.125"D x 9.75"W x 9.75"H. Front-mounted power indicator and dial thermometer with top-mounted analog vacuum gauge. The 280A's hydraulic thermostat controls temperature. Large glass panel front door and stainless steel chamber.
Homogenizer with speeds from 8,000 to 30,000 RPM for volumes of up to 100ml. Homogenizer for production of dispersions and emulsions, plant tissues, human tissues, animal tissues, resins, and pigments.
Fluidigm | C1 Single-Cell Automated Preparation System
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14,2023.Automated preparation system that isolates and prepares single cell templates for analysis. It can analyze mRNA and DNA sequencing, epigenetics or miRNA expression. It can extract, reverse transcribe, amplify, and analyze gene expression.
HPLC liquid handler with midsize bed capacity and fraction collector. It has maximum flow rates up to 200 mL per min, injection loop volumes of 2 uL to 25 mL, and max sample mass of 15 grams per injection.
Genetic amplifier that uses amplification to create single molecule DNA templates and dispense reagents. It also controls reaction times, flow rates, and temperatures.
EImaging scanner that images fluorescent and radioisotopic samples. It can be used for protein electrophoresis, genomics array analysis, fluorescence, radioisotope detection, and chemiluminescence detection by direct detection method.
Hamilton | StarPlus Automated Liquid Handler
Liquid handling robot with 8 channel pipetting arm, dual HEPA filter top, and 96 channel pipeting head with 1ml capacity. It can have tube racks, microplate racks, and 50mL temperature controlled tube rack.
Illumina | NeoPrep Library Preparation System
Library preparation system that produces 16 sequencing ready libraries per run. There are steps in NeoPrep workflow run preparation, library card loading, and library collection.
Molecular Devices | Gemini EM Microplate Reader
Microplate reader with top and bottom read capability with dual monochromators for fluorescence intensity assays using multiple point well scanning. Temperature sensitive reactions are from ambient to 45 C. Measures fluorescence on variety of sample formats from 6 to 384 well microplates in endpoint, kinetic, spectral scan, and well-scan modes.
Kent Scientific | Coda Blood Pressure System
CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. Using the included software allows you to continuously view data in real-time.
JPK Instruments | 300 Force Robot Automated Force Spectroscope
Force spectroscope that automates routine procedures, data acquisition and evaluation. Force curves without events are filtered out before processing.
Labconco | CentriVap Refrigerated Centrifugal Concentrator
Refrigerated centrifugal concentrator that concentrates heat sensitive samples using centrifugal force, vacuum, and controlled temperature. Concentrator has heater and refrigeration systems have temperature range of negative 4 C to 100 C.
Labnet | C2400 Spectrafuge 24D Microcentrifuge
Microcentrifuge with brushless drive that accelerates rotor to maximum speed of 13,300 rpm and 16,000 x g. Features precise digital microprocessor control. Speed knob sets speed in either rpm or g-force. Timer knob sets time parameter.
Luminex | Amnis ImageStreamX Mk II System
Luminex Amnis ImageStream MkII Multispectral Imaging Flow Cytometer
Luminex ImageStream MkII Multispectral Imaging Flow Cytometer
Bench top multispectral imaging flow cytometer designed for the acquisition of up to 12 channels of cellular imagery. It combines per cell information with statistical significance of sample sizes of standard flow cytometry.
Malvern Panalytical | Microcal ITC 200 Isothermal Titration Calorimeter
Isothermal titration calorimeter for label free, in solution, study of biomolecular interactions. It delivers measurement of binding parameters with minimum of 10 ug sample.
Thermo Fisher: Life Technologies | Countess Automated Cell Counter
Invitrogen benchtop automated cell counter. Can perform cell counts, viability calculations, hemocytometry, fluorescent protein expression, and measure fluorescence capabilities. There are also reusable slides, fluorescence capabilities, and brightfield fluorescence channels.
Miligram balance that is used for weighing, tarring, percent weighing, and dynamic weighing for unstable samples. Has maximum capacity of 310 grams. Lab balance utilizes mono block weighing technology with permanent shock protection and built in overload protection as well as automatic calibration.
Illumina | LabChip GXII Touch protein characterization system
LabChip GXII Touch is a protein characterization system that provides reproducible quantitation, molecular weight sizing and percent purity analysis of protein samples. Leveraging microfluidic electrophoretic separation technology, the LabChip GXII Touch system enables rapid characterization with minimal sample preparation setup and sample input volume.
Malvern Panalytical | Microcal VPViewerTM Differential Scanning Calorimeter VP--DSC
Differential scanning calorimeter for study of samples in solution. It measures intramolecular stability of proteins, nucleic acids, oligomeric proteins, nucleic acid duplexes, lipid and detergent micellar system.
Electronic microtome cryostat upright standing with open top working area that can cut temperature to negative 35 degrees Celsius. Equipped with automatic 24 hour defroster with interrupt key and handwheel brake.Provides protection for knife and specimen as it retracts specimen at the end of the cut. Motorized coarse feed system allows sample to be moved forward and backward.Two knife carriers are available. Standard knife carrier is for knives to be easily clamped in place and adjusted, and the disposable blade holder EC for high- and low-profile blades.
Miltenyi | AutoMACS Magnetic Cell Sorter
Benchtop manager cell sorter for cell isolation in automated workflows. Sorts cells directly from whole blood or bone marrow without density gradient centrifugation or erythrocyte lysis.
Nuclear imager for quantitative 3D functional imaging of SPECT tracers down to 0.12 mm ex vivo and 0.25 mm in vivo. Used for quantitative sub mm imaging of higher energy and theranostic isotopes such as 131I, 188Re, 213Bi, 225Ac, and 223Ra.
Molecular Devices | Spectramax Plus384 Microplate Reader
Microplate reader that can read one sample or up to 384 in single plate read using any standard cuvette, 12 x 75 mm test tube, or 96 or 384 well microplate. It can run standard spectrophotometer and microplate reader applications.
MP Biochemicals | FastPrep24 Sample Preparation
Sample disruption instrument that can homogenize, grind, or lyse biological samples. Samples are added to individual lysing matrix tubes and shaken in tridimensional motion.
Thermo Fisher | NanoDrop 8000 Spectrophotometer
Microvolume UV Vis spectrophotometer for nucleic acid and protein quantification that can measure multiple samples using 1 to 2 uL of samples. Can analyze spectrum of 220nm to 750nm and measure 96 samples in less than six minutes. Can measure multiple samples in one measurement cycle, up to eight samples at one time. Has single sample mode. Can analyze the full spectrum from 220 to 750nm and calculates sample purity ratios 260/280.
Marshall Scientific | MJ Research PTC-100 PCR Thermocycler
Thermocycler that operates with 96 well and 60 well microplates. Has temperature configurations from 0 C to 105 C and pressure and height adjustment via thumbwheel. Comes with 14 pre-programmed protocols.
Nikon Instruments AZ100 C1si is macro confocal microscope system combining stereo and compound microscopes into single hybrid imaging system for dynamic imaging of single cells or whole specimens.System covers range of magnifications from 5x to 400x. Has triple nosepiece that can switch magnifications. AZ100 C1si boasts simultaneous 32 channel spectral image acquisition over spectral range of 320 nm in single scan. Simultaneous 32 channel acquisition at 10 nm, 5 nm or 2.5 nm bandwidths, all software controlled, is possible.
Olympus | IX70 Inverted Fluorescence Microscope
Olympus IX70 Inverted Fluorescence Tissue Culture Microscope
Inverted fluorescence tissue culture microscope capable of imaging specimens in brightfield, darkfield, phase contrast, Hoffman modulation contrast, fluorescence, and differential interference contrast modes.TIRFM-IX illuminator is this microscope accessory which attaches to the rear lamphouse port and contains FC connector for external laser source and port for mercury or xenon lamp housing.
Nikon 1500 Fluorescence Dissection Microscope
SMZ1500 stereoscopic zoom microscope is system with apochromatic objectives, zoom ratio of 15 to 1, range of magnifications from 0.75x to 11.25x for total magnifying capability of 3.75x up to 540x, and is best for in depth imaging.Zoom knob allows to zoom from 1x to 11x at 1x-intervals without interrupting observations. Other facets include high eyepoint eyepieces with built-in diopter adjustments, wide field of view, and built-in aperture diaphragm for achieving optimal depth of focus and improved photomicrography.Provides options of either low eye-level viewing tube or tilting eyepiece tube, with or without eye-level risers. Three different diascopic stands with built-in power supplies may also be utilized with instrument, or standard stand that features low profile for increased clearance.
Nikon | Eclipse E600 Fluorescence Microscope
Microscope equipped with CFI60 infinity optical system, providing images in all applications. Incorporates specifications adopted for CFI60 series objectives, including 60 millimeter parfocal distance, 25 millimeter thread size, and standard 22 millimeter field of view. Main components of CFI60 infinity optical system include objective, tube lens to converge light beam, and eyepiece lens to enlarge intermediate image. Fluorescence microscope that has detachable substage, 12 volt 100 watt tungsten halide lamp, filter magazine, and choice of sextuple nosepiece or sextuple DIC nosepiece.Has objectives for brightfield, darkfield, Nomarski DIC, epi fluorescence, or phase contrast techniques.
Olympus | IV-100 Intravital Laser Scanning Microscope
Intravital laser scanning microscope for small animal imaging with up to four lasers 488nm, 561nm, 633nm, and 748nm. Able to image multiple fluorescence probes simultaneously. Scan head has tilting capability to image objective orientation in three dimensions.Three magnifications of MicroProbe lenses enable to capture either large field of view or high resolution images on living animal. Certain conventional microscope objectives can also be used on IV100 as well.
SelectScience | PELCO BioWave 34700 laboratory microwave system
Laboratory microwave system that includes True Variable Wattage, water recirculation system, temperature restrictive temperature probe, RS232 Port, Cable and Software, Programmable times, Four intermittent power settings, Magnetron prewarming, Air Bubbler, and Vacuum Cycling. System has precision temperature control and monitoring for microwave assisted processing of tissue. Can be used for formalin fixation, decalcification, special stains, immunocytochemistry and complete processing of tissue into paraffin.
Gamma counter available in single, five, or ten detector configurations. Can count RIA tubes, 16x100mm and variety of smaller micro tubes using available adapter.This instrument has dot Matrix Printer, tube racks, and protocol ID tags.Single detector model is available in 2 inch or 3 inch crystal configurations for research grade capabilities.
Perkin Elmer | Packard Tri-Carb 2900TR Liquid Scintillation Analyzer
Packard 2900TR Liquid Scintillation Analyzer
Benchtop liquid scintillation analyzer that detects small amounts of alpha, beta, and gamma radioactivity. Time resolved liquid scintillation counting is used for low background counting of LS samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Perkin Elmer | Titan MPS 16 Position Microwave Sample Preparation Device
Microwave sample preparation device system designed to count and size particles individually. It can used for in service oil samples with only 4 mL of 10 times diluted samples.
Olympus | MVX10 Macroview Stereo Fluorescence Microscope
Microscope employs single zoom optical path with large diameter, which is optimized to collect light with efficiency and resolution at all magnifications. From fluorescent observation of whole organisms, such as zebrafish, at low magnification to detailed observation of gene expression at cellular level at high magnification, features pupil division mechanism in light path to mimic effect of stereo microscope.
Luminometer combines instrumentation and software for uses includinh bioluminescent assays, protocols and support. You can measure flash or glow-type luminescence, have two fluorescent modules available, and it accommodates 1.5ml microcentrifuge tubes and 35mm petri dishes, with optional 12mm × 50mm test tube adapter. Measure light output from liquid and solid samples; no minimum volume requirements. The GloMax 20/20 blends user-friendly operation and a small footprint.This Instrument Was Retired September 1, 2023. Accessories and service available until September 1, 2028.
Promega | GloMax 96 Microplate Luminometer
Microplate luminometer that features two optional injectors and reads both glow- and flash-luminescent reactions in 96-well plates. The sensitivity and range enable a wide range of luminescent assays, including Promega bioluminescent reporter, cell-based and biochemical assays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Dual channel fluorimeter for fluorescence measurements when calibrated with known concentration to measure compounds at low concentration with low assay volume.
Perkin Elmer | Zephy G3 NGS liquid handler
Benchtop liquid handler designed to automate construction of 48 to 96 next generation sequencing libraries per day.
Sequencing and quantification platform for epigenetics, mutation gene expression analysis, and microbial identification and resistance typing. With its 96-well format, automatic base-calling function, and dedicated software solutions for methylation analysis and assay design.
Purification system that performs fully automated purification of nucleic acids and proteins in molecular biology applications.
Sequencer that uses pyrosequencing technology for real time, sequence based detection, quantification of sequence variants, and epigenetic methylation. Used for analysis of CpG methylation, SNPs, insertion deletions, STRs, variable gene copy number, and for microbial identification and resistance typing.
Perkin Elmer | IVIS Spectrum In Vivo Imaging System
In vivo imaging system that combines two dimensional and three dimensional optical tomography in one platform.The system uses leading optical technology for preclinical imaging research and development best for non-invasive longitudinal monitoring of disease progression, cell trafficking and gene expression patterns in living animals.
PCR Setup Robot. Compact benchtop instrument for setup of PCR experiments with setup and automatic calculation of all mixes, eliminating the need to program pipetting steps.
Qiagen Tissue Lyser II RNA/DNA Purification
RNA and DNA purification analyzer that disrupts biological samples through high speed shaking in plastic tubes with stainless steel, tungsten carbide, or glass beads.Can analyze up to 48 or 192 samples at the same time.
Genetic analyzer that automates electrophoresis analysis of your DNA and RNA samples.
Liquid handling system for production of complex liquid formulations produced from individual stock solutions of various chemical and liquid properties. With a CV of less than 2%.
Roche | LightCycler 480 Real Time PCR System
Roche LightCycler 480 II Real Time PCR System
System includes: LightCycler 480 instrument which is real-time PCR device, allowing the use of additional thermal block cycler units (96-well and 384-well format) with the system; LightCycler 480 Software which provides intuitive, easy-to-navigate user interface for real-time PCR programming, data capture, and data analysis to study gene expression and genetic variation. LightCycler 480 II represents newer generation of the same real-time PCR system, with improved features like enhanced optics for more uniform plate analysis across all wells, potentially leading to increased accuracy and consistency in data collection compared to original LightCycler 480.
Hybrid quadrupole time of flight mass spectrometer with MS mass range 6,000 and 40,000 m z designed proteomics, drug discovery, metabolomics, and drug development. Instrument used with Analyst QS software.
Thermo Fisher | Shandon Cytospin 3 Centrifuge
Thermo Shandon Cytospin 3 is low speed centrifuge used to separate and deposit monolayer of cells on slides while maintaining cellular integrity.Centrifuge has speed range between 200 and 2000 RPM, and has holding capacity of up to 24 samples in 12 chambers.
Roche | Cobas Integra 400 Plus Chemistry Analyzer
COBAS INTEGRA 400 plus analyzer is a chemistry analyzer with a broad test menu comprises over 120 assays and applications that consolidate clinical chemistry with specific proteins, therapeutic drug monitoring and drug abuse testing.The Cobas 400 analyzer is best for laboratories running up to 400 samples per day. This compact tabletop analyzer offers maximum versatility to improve efficiency and reduce costs. It uses the convenient cobas c pack reagent format, which standardizes patient results across integrated laboratory networks.
Hybrid triple quadrupole linear ion trap mass spectrometer for drug discovery and development, metabolite identification, contaminant testing, proteomic applications, post translationally modified proteins discovery, protein identification, and biomarker validation.
UV crosslinker designed to crosslink DNA or RNA to nylon, nitrocellulose, or nylon reinforced nitrocellulose membranes in 25 to 50 seconds. It is equipped with internal photodetector to compensate for aging ultraviolet bulbs.
Thermo Fisher | Shandon 325 Manual Microtome
Thermo Scientific Shandon Finesse 325 Manual Microtome
Manual microtome with flywheel for routine paraffin sectioning. Can cut 1 to 30 um speciment thickness, and specimen tilt or orientation is plus or minus 5 degrees using X Y micro adjustment.Has quick release cassette clamp and x-y orientation head supplied as standard, disposable blades or standard microtome knives.
Rigaku | X-Stream 2000 Cryo-Freezing System
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 11,2024. Self contained cryo freezing system designed cooling crystals with range of negative 80C to 4C. It produces nitrogen, which is then cooled to negative 196C, and then rewarmed to desired temperature.
Siemens | Dade Behring BNII Nephelometer System
Siemens Dade Behring BN II Nephelometer is leading fully automated system for plasma protein determinations. BN II systems offer advanced nephelometric technology that provides performance in plasma protein analysis. This instrument's menu covers assays, which support various clinical tests including cardiac risk assessment, kidney diseases and nutritional assessment. markers such as Cystatin C and Carbohydrate-Deficient Transferrin (CDT) are also supported. Other features of the Dade Behring BN II Nephelometer include rapid processing, easy operation and random-access mode. The nephelometer also permits users to put up to 100 samples on board, making it best for mid to high-volume processing.
Automated cell sorter that has microfluidics sorting chip integrated with six fluorescence detectors and up to four collinear excitation lasers of 488 nm, 405 nm, 561 nm and 638 nm.
Pipette puller that fabricates pipettes for use in intracellular recording, patch clamping, transferring ICSI, ES Cells , microinjection, aspiration, and microperfusion. P-97 puller can indirectly sense viscosity of glass, giving the ability to pull pipettes from all glasses except quartz. Even difficult to pull formulations, such as aluminosilicate glasses, are handled with relative ease.
TA Instruments | Electroforce 3200 Mechanical Testing Apparatus
TA Instruments Electroforce 3200 Series Mechanical Testing Apparatus
Mechanical testing apparatus with 225 N or 450 N maximum force and range of static to 300 Hz frequency response. Tests include torsion testing, creep under dynamic loading, special environment hot cold chambers, biomedical research, and engineered materials test applications..
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22,2024. Bench top 96 or 384 channel liquid handler capable of automating pipetting tasks, including low volume and viscous sample transfers. It utilizes syringe based technology to dispense solutions.
TissueVision | TissueCyte 1000 Photon Imaging System
Whole organ serial two photon tomography imaging platform that allows imaging of whole fixed organs based on high speed two photon microscopy TPM and integrated tissue sectioning. TissueCyte 1000 is a specialized Serial Two-Photon (STP) tomography system manufactured by TissueVision, Inc.. It is not available off-the-shelf. To acquire the TissueCyte 1000 or inquire about their newer platforms, you must contact TissueVision directly to request a hardware consultation, quote, or system setup.
Sutter | P-2000 Laser Micropipette Puller
Microprocessor controlled, CO2 laser based micropipette puller.Default configuration allows fabrication of micropipettes for intracellular recording, patch clamping, microinjection and microperfusion.Can store up to 100 separate programs, each consisting of up to 8 command lines. The five parameters set in each command line allow exquisite control of the micropipette taper geometry. Allows the use of wide range of glass diameters from 0.125 to 1.2 mm.
Thermo Fisher | Arcturus Cellect Laser Capture Microdissection System
Laser capture microdissection system that includes infrared lasers. It can be used for laser capture microdissection LCM, ultraviolet UV laser cutting, sanger sequencing, next generation sequencing, and quantitative PCR.
Tousimis | Autosamdri 815B Critical Point Dryer
Critical point dryer with wafer holders that allow automatic anti stiction processing up to 5 pieces of either 100mm, 75mm, 50mm wafers or 10mm square die per process run. All internal surfaces are inert to CO2 and ultra pure alcohols.
Roche | Ventana Discovery XT Immunohistochemistry Processor
Immunohistochemistry processor that can be used for immunohistochemistry and in situ hybridization slide preparation and processing.
Cook Medical | WilliamA Cook Australia K-MINC-1000 Benchtop Incubator
Benchtop incubator microprocessor controlled, gassed, humidified, incubator intended for use in cell culture. It is designed to maintain temperature between 35 and 40 degrees celsius and gas flow within range of 15 to 25 ml min.
Zeiss | 922 Transmission Electron Microscope
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12, 2024. Transmission electron research microscope with accelerating voltages of 120 and 200kV and has magnification from 80X to 1,000,000X with resolution line of 0.12nm.
Thermo Fisher | Cytomat 6001 Automated Wide Range Incubator
Automated wide range incubator used to minimize plate movement, receive samples, store plates, and track plates.Temperature range is from 10 to 50 degrees Celsius with humidity level of up to 95 rH.
Optical tweezers system for contact free cell manipulation as well as to trap, move, and sort microscopic particles, sort live cells, organelles, and other large biomolecules.
Plate reader that automates dynamic light scattering measurements on macromolecular and nanoparticle samples in situ in 96, 384, or 1536 well microplates. It screens for particle size, thermal stability, aggregation temperature tonset, colloidal stability via diffusion interaction parameter kD or D1, and viscosity of protein solutions.
High performance liquid chromatographic system with quaternary, low pressure mixing pump and inline vacuum degassing. It has wavelengths of 190 to 800 nm and flow rates from 50 uL per min to 5 mL per min with 2.1 mm ID columns and larger. Autosampler has maximum capacity of 120 vials (12x32, 2 mL) with programmable temperature control from 4 to 40C. Heated column compartment provides temperatures from 5 degrees above ambient to 65C.
Thermo Fisher | TSQ Quantiva Triple-Stage Quadrupole Mass Spectrometer
Triple stage quadrupole mass spectrometer for low level quantitation and has mass range of mass per charge 10 to 1800 mass per charge. Laboratory room temperature must be maintained between 18 to 27 C and cannot change by more than 5 C.
Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition.
Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.
Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.
Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models.
BD Biosciences | LSRFortessa Cell Analyzer
BD LSRFortessa system can be configured with up to 7 lasers, blue, red, violet, UV and yellow-green. The instrument can accommodate the detection of up to 18 colors simultaneously with defined set of optical filters that meet or exceed the majority of today's assay requirements. BD FACSDiva software controls the efficient setup, acquisition, and analysis of flow cytometry data from the BD LSRFortessa workstation. The software is common across BD FACS instrument families, including the BD FACSCanto cell analyzer and BD FACSAria cell sorter systems.
McKinley | Cellometer Auto 2000 Cell Viability Counter
Cell viability counter. Touchscreen fluorescent automated cell counter for primary samples by Nexcelom Bioscience.
Web based application for visualization and presentation of HXMS data. Comprises tools helping in preparation of H/D experiments as well as tools for turning simple tables with data on H/D exchange into different ways of representation.
Non-Parametric Trend Tests and Change-Point Detection
Software package includes tests for trends and change points detection. Used in analysis of environmental data.
Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves.
Web service for querying or retrieving gene annotation data.
Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.
Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections.
Electronic Health Records temporal variability
Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users.
Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries.
Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R.
Protein sets from fully sequenced genomes. Proteomes portal offers protein sequence sets obtained from translation of completely sequenced genomes. Published genomes from NCBI Genome are brought into UniProt if genome is annotated and set of coding sequences is available. Number of predicted coding sequences falls within statistically significant range of published proteomes from neighbouring species.
Vermont University Proteomics Core Facility
University of Vermont Proteomics Facility
Provides central resource of mass spectrometry based proteomics technologies to identify, characterize and quantify target proteins in various biological and biomedical samples. Provides mass spectrometry expertise for analyzing proteins and peptides for proteomics studies, support for data analysis from proteomics measurements, training in proteomics methods, and experimental design.
Stanford University School of Medicine Protein and Nucleic Acid Core Facility
Stanford School of Medicine Protein and Nucleic Acid Facility
Stanford University Protein and Nucleic Acid Facility (PAN)
Offers instrumentation and technical capabilities and plays significant consultative role in application of these technologies to basic science projects.Genomic Services include Oligo Synthesis,Gene Expression,Real-Time PCR,PyroSequencing,Next-Generation Sequencing (NGS),DNA Sequencing (Sanger)/Fragment AnalysisSingle Cell Genomics,RNA-DNA QC - Bioanalyzer and Fragment Analyzer QC.Protein Services include Peptide Synthesis,Mass Spectrometry,Protein Analytics - Mass Mapping/Edman Sequencing,Surface Plasmon Resonance (Biacore).
Johns Hopkins University School of Medicine Genetic Resources Core Facility
Genetic Resources Core Facility (GRCF) BioRepository and Cell Center
Established to produce immortalized cell lines from human blood (EBV transformations). Offers genomics applications for single cells, including RNA-seq, gene expression profiling by qPCR and DNA amplification for whole-genome or targeted (exome or PCR-based analysis) through 10x Genomics Chromium platform (similar to Drop Seq). Offers custom genotyping to analyze short tandem repeats, variable number tandem repeats and single nucleotide polymorphisms.
Rochester University Human Immunology Center Core Facility
Rochester Human Immunology Center Core Laboratory
Designed to enhance multi-disciplinary research initiatives catalyzing key clinical and basic immunology research in vaccines, HIV/AIDS, autoimmunity, allergy/asthma, transplantation as well as cancer immunology.Provides expertise in multichromatic flow cytometry (immunophenotyping, antigen-specific intracellular cytokine staining and cell sorting), T and B cell Elispot, Fluorispot, T regulatory cell assays, magnetic bead selection of cell populations, and Luminex multiplexed bead array assays.Provides specialized clinical specimen analysis services for clinical studies or contracts.
Kansas University Lawrence Biomolecular NMR Laboratory Core Facility
Kansas University Lawrence Bio-NMR Laboratory
NMR Laboratory maintains two high field NMR spectrometers in support of structural and dynamics studies of biomolecules. Its capabilities include determining high resolution structures, biological macromolecules, elucidation and structural mapping of protein-protein, protein-nucleic acid, protein-peptide, protein-drug interactions, and studies of dynamics of proteins and their complexes in solution. Laboratory staff provide advice,consultation, training,assistance and complete structure elucidation services.Staff is responsible for maintenance, upgrades, implementation of new NMR pulse sequences, and assisting local and remote users with technical problems.Equipped with Bruker Avance 800 MHz NMR instrument fitted with TCI cryoprobe and Bruker Avance III 600 MHz with variety of probes.
University of Massachusetts Medical School Metabolic Disease Research Center Core Facility
Massachusetts University Medical School Mouse Phenotyping Center Core Facility
Massachusetts University Medical School National Mouse Metabolic Phenotyping Center
National Mouse Metabolic Phenotyping Center
UMass Medical School Metabolic Disease Research Center
University of Massachusetts Medical School Mouse Phenotyping Center Core Facility
UMass Metabolic Disease Research Center (MDRC), formerly the National Mouse Metabolic Phenotyping Center, is a core facility that performs standardized experiments using state-of-the-art equipment for the purpose of investigating transgenic mouse models of diabetes, obesity, and metabolic liver disease. Provides metabolic and functional characterization of mouse models of human diseases that are developed by academic and industry researchers in joint efforts to understand metabolic diseases and to identify new therapies.
Harvard Center for Biological Imaging Core Facility
Harvard Center for Biological Imaging (HCBI)
Microscopy facility. Contains microscopes including confocal, super-resolution, multi-photon, light sheet, live cell imaging, high-content screening, slide scanning, laser dissection and macroscopy stations. Features wet lab space, eukaryotic and prokaryotic incubation, and access to nearby animal care facilities for wide range of species.Services include Cell Imaging,Confocal Microscopy,Consultations,Data Analysis,Data Processing And Interpretation,High Content Screening,Laser Capture Microdissection,Microscopy,Multiphoton Microscopy,Optical Imaging,Slide Scanning,Whole Slide Imaging.
Massachusetts Institute of Technology Swanson Biotechnology Center Nanotechnology Materials Core Facility
Bio and CryoEM in the Nanotechnology Materials Core
Provides instruments for materials and nanomaterials research and full service TEM and cryoTEM sample preparation and imaging. Conducts CLEM and cryoCLEM workflows utilizing cryoFluorescence, cryoSEM and cryoFIB with focus on bio samples.Provides equipment and expertise to work with nanomaterials for characterization and imaging purpose. Core imaging capabilities include high performance field emission transmission electron microscope equipped with STEM, EELS, EDS and cryo-imaging, high performance field emission scanning electron microscope and focused ion beam equipped with STEM and cryo-imaging, cryo-fluorescent confocal microscope for CLEM workflows, and atomic force microscope equipped with liquid cell. Instrumentation for material characterization includes high throughputdynamic light scattering, nanoparticle sizing and counting, and rheometry.
Pennington Biomedical Research Center Genomics Core
Provides services which include Sanger and next-generation DNA sequencing,DNA fragment analysis,qualitative and quantitative analysis of DNA, protein, and RNA samples, quantitative PCR, microarray RNA labeling, hybridization, and scanning robotics,bioinformatics.Individual and small group training and consultation services are offered for sequence analysis, real-time PCR, next-generation sequencing and microarray analysis.
Rutgers Waksman Institute of Microbiology Cell and Cell Products Fermentation Core Facility
Cell and Cell Products Fermentation Facility
Waksman Institute of Microbiology (Busch Campus)
Provides fermentation services. Produces range of bulk biologics including antimicrobials, cosmetic substrates, flavors/fragrances, biopesticides/bioherbicides and plasmid derived proteins, enzymes, growth factors and diagnostics. Exceptions for pathogenic or opportunistic organisms and mammalian and insect cell lines. Includes Material Preparation Laboratory,Fermentation In-Process/Computer Control,Product Recovery and Analytical Services.
University of Tennessee JIAM Diffraction Core Facility
University of Tennessee JIAM X-Ray Diffraction Core
Provides users with access to Panalytical XPert3 MRD and Panalytical Empyrean XRD platforms to perform variety of X-ray diffraction experiments including phase identification, phase quantification, crystallite size and microstrain determination, pole figures, residual stress, high-temperature in situ measurements. These instruments are available for both assisted and unassisted use with prior approval.
Provides services for USED lab instrument repairs.Recertified laboratory equipment commercially available. Comes fully re-certified to manufacturers standards with 90 day warranty.
Software tool for protein identification and relative protein expression analysis. Used in protein research to identify proteins and search large numbers of post translational modifications. Compatible with all proteomics MS/MS systems.
Software R package for structural variant analysis. Contains helper functions for dealing with structural variants in VCF format. Contains functions for parsing VCFs from number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.
Database contains manually curated natural carbohydrate structures, taxonomy, bibliography, NMR data. Bacterial and Plant and Fungal databases were merged to improve quality of content-dependent services, such as taxon clustering or NMR simulation. These separate databases will be supported in parallel until 2020.
Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points.
Stanford Medicine Research Data Repository
Platform developed and operated by Stanford Medicine Research IT team for working with clinical data for research purposes. Permits collection and aggregation of all clinical data generated at Stanford for care purposes, and articulates formal approval process each research project must follow in order to obtain and work with this data for research purpose. Home of stride/web tools for Cohort Discovery and Chart Review.
Rapid Response Viral Data Collection Portal
Community portal to crowd source viral data collection and viral resources.
Population based collection of white matter atlases represented in both volumetric and surface coordinates in standard space. These atlases include white matter fascicles derived from different tractography techniques including Automated Fiber-tract Quantification, Automated Fiber-tract Quantification clipped, Recobundles, Tracula, TractSeg, and Xtract.
Ren lab web portal for chromatin accessibility data
Atlas of gene regulatory elements in adult mouse cerebrum. Atlas of CIS elements, providing information on accessible chromatin in individual cells from regions of adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei. Uses resulting data to define candidate cis-regulatory DNA elements in distinct cell groups. Many are linked to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Used for analysis of gene regulatory programs of mammalian brain and interpretation of non-coding risk variants associated with various neurological disease and traits in humans.
Web tool for exploring variants in islet expression quantitative trait loci. Data is result of collaboration between Michigan University Parker lab, Department of Biostatistics and Center for Statistical Genetics at University of Michigan, National Human Genome Research Institute, Jackson Laboratory for Genomic Medicine, Department of Genetics at University of North Carolina, European Bioinformatics Institute, Department of Preventive Medicine at University of Southern California, and Department of Physiology and Biophysics at University of Southern California.
Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.
Thermo Fisher | LTQ-Orbitrap Elite nano LC/MS system
LTQ-Orbitrap Elite mass spectrometer with Waters nanoAcquity system. Used for proteomic applications.
Agilent GC/MS is single quadrupole instrument with electron ionization. GC/MS runs under ChemStation open access software, and trained open access users select from menu of standard methods to analyze their samples.
Bruker | Microflex MALDI TOF mass spectrometer
Bruker Microflex MALDI-TOF mass spectrometer
Microflex LRF mass spectrometer is specialized for protein, peptide, and polymer analysis. This MALDI-TOF instrument can be operated in linear mode for high mass accuracy characterization, or in reflector mode to achieve enhanced resolution.
Bruker micrOTOF-Q II is benchtop Q-Tof mass spectrometer, applied to applications such as small molecule accurate mass determination, intact protein analysis including antibodies, peptide mapping, and other custom projects. This system is operated with Agilent 1260 UPLC and includes inline diode array detector and ESI source.
Bruker | Scion TQ GC/MS mass spectrometer
Scion GC triple quad is applied to targeted trace level analysis of metabolites and other small molecules. Electron ionization combines with MS/MS capability for outstanding selectivity. Samples are often derivatized for compatibility with GC/MS.
Stanford Shimadzu 8030 LC/MS mass spectrometer
Shimadzu 8030 triple quadrupole mass spectrometer used for targeted quantitation applications. Listed by Stanford University Mass Spectrometry Vincent Coates Foundation Instruments.
Thermo Fisher | Exactive Orbitrap LC/MS system
Thermo Exactive benchtop Orbitrap operates with Waters Acquity UPLC and generates high resolution, high mass accuracy full MS data. Available to advanced open access users for reversed phase and HILIC LC/MS applications.
LTQ XL ion trap mass spectrometer with Agilent 1100 HPLC system for metabolite identification, stability testing, degradation products, and high abundance quantitation.
Thermo Fisher | Orbitrap Fusion nanoLC/MS system
System includes Thermo Orbitrap Fusion Tribrid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments.
Thermo Fisher | QE-HFX mass spectrometer
Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer
HFX offers scanning rate to improve proteomic depth for discovery applications. Integrates well with targeted applications such as parallel reaction monitoring. Mass Spectrometer to identify and quantify proteins, peptides, lipids, glycans and small molecules accurately.
Thermo Fisher | Vantage LC/MS mass spectrometer
Triple quad mass spectrometer for quantitative work and selective assays of targeted analytes. Can analyze metabolites, peptides from matrices such as serum, tissue, cell culture, and other biological sources.
Micromass (now Waters) Quattro Premier triple quadrupole operates with Agilent 1100 HPLC and specializes in quantitative work and selective of targeted analytes including metabolites and other small molecules, and peptides from complex matrices such as serum, tissue, cell culture, and other biological sources.
Thermo Fisher | Cellinsight CX7 High-Content Screening Platform
Thermo Scientific CellInsight CX7 High-Content Screening Platform
Integrated software and instrument system for performance in cell-based screening and analysis.
Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites.
Quantitative Analysis of Spatial distributions in Images using Mosaic segmentation and Dual parameter Optimization in Histograms
Stimulating Peripheral Activity to Relieve Conditions Anatomy Working Group
Group of anatomical experts tasked with enhancing structured vocabularies around nerve to organ connections. Responsible for integrity of anatomical knowledge in SPARC. Provides relevant guidance and expertise about defining and naming anatomical terms, maintaining ontologies and anatomical knowledge, compliling and curating computable knowledge about multiscale route pathways. Provides access to data generated by SAWG which includes links to documentation about vocabulary services, term request and connectivity. Page will be continuously updated.
Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design.
Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search.
Thermo Fisher | QuantStudio 3 Real Time PCR System
Applied Biosystems QuantStudio 3 Real-Time PCR System
Life Technologies QuantStudio 3 Real Time PCR System
System designed for users who need easy-to-use real-time PCR system. QuantStudio 3 Real Time PCR System supports 96-well (0.2ml or 0.1ml) or 384-well (QS5 only) consumables. Can detect extremely small changes in gene expression, as little as 1.5-fold. Its dynamic range of up to 10 logs allows for tracking wide range of expression changes across various sample types and conditions. When connected to Thermo Fisher Cloud, QuantStudio 3 system provides access to your data wherever and whenever you want.
Leica DMI6000 B Fully Automated Inverted Research Microscope
Inverted microscope for biomedical research. Offers Differential Interference Contrast for relief imaging of specimens with varying indices of refraction. Used for fluorescence, live cell, time-lapse imaging, high-speed multi-fluorescence optical sectioning, and micromanipulation. Features automated contrast and illumination manager, motorized Z focus, parfocality function, automatic brightness and diaphragm adjustment, and many other automated functions that provide convenience and reproducible results. Archived Product. Replaced by DMi8 S.
Confocal microscope covers broad range of requirements in confocal and multiphoton imaging with array of scan speeds at highest resolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
System for processing Affymetrix microarrays. Microarray analysis system. Includes array strip and hybridization assembly, Fluidics station, Imaging station.
Software tool for RNA-seq analysis of non model species using cloud computing. Provides user friendly front end to operate Amazon hardware resources and to control workflows of bioinformatic analysis of de novo RNA-seq, reference-based RNA-seq and functional annotation specifically oriented to plant species.
Affymetrix Transcriptome Analysis Console Software
Software to generate differential expression analysis and visualization for easy interpretation. Takes normalized and summarized data from Affymetrix Expression Console software to next level, providing differential expression analysis and visualization for easy interpretation.
Animal Research: Reporting of In Vivo Experiments
Guidelines to improve reporting of research using animals by maximizing information published and minimizing unnecessary studies. Guidelines, originally published in PLOS Biology, were developed in consultation with scientific community as part of NC3Rs initiative to improve standard of reporting of research using animals. Can be applied to any area of bioscience research using laboratory animals.
Consolidated Standards of Reporting Trials
Standards for transparent trials reporting. Encompasses various initiatives developed by CONSORT Group to alleviate problems arising from inadequate reporting of randomized controlled trials. Main product of CONSORT is CONSORT Statement, which is evidence based, minimum set of recommendations for reporting randomized trials. CONSORT Statement is endorsed by medical journals and leading editorial organizations.
Preferred Reporting Items for Systematic Reviews and Meta-Analyses
Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.
Web server to indicate severity of anisotropy in data set. Degree of anisotropy is indicated by anisotropic delta B statistic.
Library with storage capacity of over million compounds possessing diversified structures. Coupled with this library will be advanced sample handling, information management and quality control systems. As important material and information resource, CNCL will work with both domestic and international stakeholders to promote sustained development of Chinese pharmaceutical industry.
Software tool as microscopy image file format converter by MBF Bioscience. Converts common microscopy image files to JPEG2000 and OME-TIFF. Used to view, analyze, and share big image data from many sources.
Software tool to processes big immunome data from raw sequences to quantitated clonotypes by MiLaboratory LLC. Universal software for analysis of T- and B-cell receptor repertoire high throughput sequencing data. Software for comprehensive adaptive immunity profiling.
Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology.
Web accessible database for visualizing and mining global yeast genetic interaction network. Allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize sub networks, using data driven network layouts in intuitive and interactive manner. Used for storing and visualizing genetic interactions in S. cerevisiae.
Web tool for conserved domains searching within protein or coding nucleotide sequence.
Software tool as deep learning framework based on variational autoencoder to impute missing values in transcriptome and methylome data analysis.
Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes.
Open source Python codebase that provides real-time interface between open-hardware devices for electrophysiological recordings like EEG, EMG, and ECG, and analog and digital devices like MIDI, OSC, and analog synthesizers. This allows one to use electrical brain/body activity to flexibly control devices in real-time.
Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell.
Software R package to obtain estimated marginal means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays.
Software molecular visualization application for Mac OS X operating system. Tool for chemists and molecular biologists used for handling small and large molecules, loading multiple molecules, moving and rotating them independently, or displaying molecular dynamics trajectory. Allows loading molecules using file formats: PDB, XYZ, MOL2, HIN, CAR, ALC, BIO.
Virginia University School of Medicine Advanced Microscopy Core Facility
University of Virginia UVA Advanced Microscopy Facility
Advanced Microscopy Facility is microscopy service and shared instrumentation facility in University of Virginia biomedical research community. Pprovides expertise and instrument access for electron and light microscopy imaging technologies as well as image analysis tools and services for basic scientists and clinical researchers within University of Virginia and across Commonwealth.
Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features.
Software tool for automated acquisition of high resolution images from large areas.
Software tool set to assess quality of per read phasing information and help to reduce errors during this process.
Database for meta analysis of prognostic value of genes from server at Kyushu Institute of Technology. Collection of publicly available cancer microarray datasets with clinical annotation, as well as tool for assessing biological relationship between gene expression and prognosis. Provides platform for evaluating potential tumor markers and therapeutic targets.
Cooled Focht Chamber System 2 designed for live cell imaging. Has same optical and specimen accommodations as standard FCS2 but is modified to include fluid ports in base to accommodate circulation of external refrigerant.
Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs.
Software tool to recognize self acknowledged limitation sentences in biomedical articles. Automatic recognition of self acknowledged limitations in clinical research literature to support efforts in improving research transparency.
Functional gene pipeline and repository. Functional gene repository provides collections of genes in interactive platform, while functional gene pipeline offers suite of tools for functional gene amplicon processing and analysis. Together they enable key steps in functional gene based microbial community analysis, from target selection and primer analysis to amplicon processing and ecological discovery.
Web tool for meta analysis based discovery and validation of survival biomarkers. Assesses effect of genes on survival using cancer samples including breast, ovarian, lung, and gastric cancer. Sources for databases include GEO, EGA, and TCGA.
Hierarchical Unsupervised Generative Embedding toolbox
Hierarchical Unsupervised Generative Embedding
Hierarchical Unsupervised Generative Embedding (HUGE) toolbox
Software toolbox to implement hierarchical extension to dynamic causal models for analyzing task based fMRI data.
Software R package and web app, which facilitates rapid production of publication quality risk of bias assessment figures. Used to produce high quality figures that summarize the risk-of-bias assessments performed as part of systematic review or research synthesis project.
Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence.
Portal for centralized national data to study COVID-19 and identify potential treatments.Centralized, secure analytics platform where patient privacy is protected. Enables collection and analysis of clinical, laboratory and diagnostic data from hospitals and health care plans. Data are provided after executing data transfer agreement with National Center for Advancing Translational Sciences. N3C is partnership among NCATS supported Clinical and Translational Science Awards Program hubs and National Center for Data to Health with overall stewardship by NCATS.
SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation
Portal for quantitative models using virus sequence variation to predict mutation effects for SARS-CoV-2 proteins, alignments to homologs in other viruses, 3D structures, evolutionarily coupled residues and structure predictions.
Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement.
Rosetta Online Server that Includes Everyone
Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.
Software Java based suite of tools for creation, annotation and display of RNA secondary structure diagrams.Provides editing tools for easy modification of publication quality secondary diagrams that can be either drawn manually, or through automatic generation. Other features include grouping, numbering and structure annotation. Secondary structures may be saved in native format, or exported as postscript for printing and further manipulation in programs such as Adobe Illustrator.
Minimum Norm current Estimates - Brain Imaging Data Structure
Software Python package to link Brain Imaging Data Structure and MNE-Python software for analyzing neurophysiology data with goal to make analyses faster to code, more robust to errors, and easily shareable with colleagues. Provides programmable interface for BIDS datasets in electrophysiology with MNE-Python. Used for organizing electrophysiological data into BIDS format and facilitating their analysis.
Web application to generate random DNA sequences.
Database, part of 3Rs Database Programme, provides overview of FCS free media for cell culture. Forum function for each record allows researchers to discuss applicability of each product. Database is offered by 3Rs-Centre ULS in collaboration with Animal Free Research UK.
object oriented Discrete Event-Simulation tool
Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models.
Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data.
prediction of protein sorting signals and localization sites in amino acid sequencies
Web tool for prediction of protein sorting signals and localization sites in amino acid sequencies. Recommended for animal/yeast sequences. Analyzes input sequence by applying stored rules for various sequence features of known protein sorting signals to report possiblity for input protein to be localized at each candidate site with additional information.
Provides data integrity using blockchain. Used for protecting integrity and provenance of research data.Open science chain utilizes distributed ledger technology (consortium blockchain) to securely store information about scientific data including its provenance to enable independent verification of its authenticity to establish trust in the research community.
Software experimental data table management system to make research data accessible and available for reuse with minimal effort on part of data provider. Allows any scientist or data researcher to be able to explore dataset and then extract some or all of data according to their needs. Designed to manage experimental data tables in quick and easy way for users.
Web prediction tool for molecular binding in simulation of immune system. Agent based simulator of immune response that represents pathogens, as well as lymphocytes receptors, by means of their amino acid sequences and makes use of bioinformatics methods for T and B cell epitope prediction.Calculates immune response to generic pathogenic secondary structure. Allows users to submit antigen protein sequence and specify schedule of its injection as well as host haplotype.
Software R package to run minimum hypergeometric test.
Computer algorithm for ab initio protein structure prediction and protein peptide folding, which aims to construct correct protein 3D model from amino acid sequence only. Server is suitable for proteins that do not have homologous templates in PDB library.
Web tool for secondary structure prediction. Used for network protein sequence analysis.
Web tool as sequence-based, alignment-free and pathogen-independent predictor of protein antigenicity.Predicts likelihood that protein is protective antigen. Integrated in SCRATCH suite of predictors.
Web tool for prediction of allergens based on similarity of known epitope with any region of protein. Used for prediction of allergenic proteins and mapping of IgE epitopes.
Web tool for prediction of surface accessibility, secondary structure, disorder, and phi/psi dihedral angles of amino acids in amino acid sequence. Used to predict solvent accessibility, secondary structure, structural disorder, and backbone dihedral angles for each residue of input sequences.
Trec | Thomas Motorized Electrode Manipulator
Thomas Motorized Electrode Manipulator (MEM)
Thomas recording - Motorized electrode manipulator
Driver system for electrode wires or linear electrode arrays. Microdrive system for extracellular recordings by Thomas RECORDING GmbH. Can be used with different conventional extracellular recording electrodes and preamplifier systems. MEM System is adapted to special requirements e.g. MEM holder is customized so that it fits to your stereotaxic instrument.
Plexon 16-channel digital headstage (Generation 2)
Headstage that attaches to 16-channel linear electrode arrays by Plexon Inc. Digitizes analog voltage signals and outputs them to data acquisition systems.
Linear electrode array used for intracranial electrophysiological recordings. V-Probe is multi-use, multi-site, linear electrode with recording sites positioned on side of sharpened, symmetric cone by Plexon Inc. Minimizes trauma to brain tissue upon insertion. Durable, highly customizable, and often used in acute research with medium to large animals.
Indiana University School of Medicine Chemical Genomics Core Facility
Indiana University at Purdue University Indianapolis IUSM-Chemical Genomics Core Facility
Core provides collection of diversity-oriented, drug-like, and natural small molecules in non-redundant libraries, variety of automated liquid handling and assay detection systems such as EnVision Multiplate reader and ArrayScan HCA System, modern equipment for medicinal and analytical chemistry including NMR, LC-QTOF MS, HPLC, Peptide Synthesizer, and sophisticated chemoinformatics tools. Besides traditional high-throughput screening and hit compound optimization services, newly adapted technologies include arrayed CRISPR screening, phage display, and SAR by NMR.
Software tool to predict lipophilicity and aqueous solubility of molecules. ALOGPS 2.1 can increase its prediction for molecules up to 5 times LIBRARY mode. You can create and use your own LIBRARY.
Planning Research and Experimental Procedures on Animals: Recommendations for Excellence
Guidelines to improve planning of animal experiments. Covers areas which determine quality of preparation for animal studies including formulation, dialogue between scientists and animal facility, and quality control of various components in study.Includes harm–benefit assessment, health risks, waste disposal and decontamination, quarantine and health monitoring,use of humane endpoints, fate of animals like humane killing, release, re-use or re-homing, and necropsy.
Strengthening the Reporting of Observational Studies in Epidemiology (STROBE)
Guidelines for strengthening reporting of observational studies in epidemiology. International, collaborative initiative of epidemiologists, methodologists, statisticians, researchers and journal editors involved in developing recommendations on what should be included in accurate and complete report of observational study. Recommendations to cover study designs in cohort, case-control, and cross-sectional studies.
Website for study pre-registration. Defines minimum required criteria for pre-registration and allows authors to pre-register their study. It is standardized pre-registration that requires only what is necessary to separate exploratory from confirmatory analyses.
Web interface for simulation of biological molecular networks. Web based environment for creation and simulation of reaction-diffusion models integrated with molecular repository. Allows to import, combine and simulate existing models expressed with BNGL and SBML languages. Application is integrated with number of solvers for reaction-diffusion systems of equations.
Viral Integrated Structural Evolution Dynamic Database
Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein.
Database by Medisapiens Ltd. as fully integrated and annotated human gene expression data source. All genes are comparable across all samples. Provides data analysis options using database of human transcriptome.
Collection of comprehensive miRNA expression profiles in extracellular vesicles from tissues. Includes miRNA expression profiles, miRNA regulated pathways, miRNA function, miRNA related drugs and publications to support miRNA biomarker discovery.
Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data.
Software tool as custom analysis code combining single-cell traces and spot detection from live imaging movies and using Imaris output.
Software tool as module for automated validation and comparison of models of auditory steady state response deficits in psychiatric disorders. Module that integrates databases of experimental studies on ASSR deficits in psychiatric with repository of computational models of these deficits using SciUnit framework.
Behavioral apparatus to study locomotion. Small animal treadmill used for forced exercise training and accurate testing of fatigue in rodents. Apparatus consists of rolling belt with adjustable speed and slope, and control Unit, enabling forced exercise training and accurate testing of fatigue in rodents.
Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments.
Web application for data storage and analysis to explore brain tumors datasets from Chinese cohorts. Data portal for storage and interactive exploration of multi-dimensional functional genomic data that includes primary and recurrent glioma samples from Chinese cohorts. Allows users to browse DNA mutation profile, mRNA/microRNA expression profile and methylation profile, and to do correlation and survival analysis in specific glioma subtype.
Web tool as high throughput protein structure prediction service. High throughput server for protein structure prediction.
Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure.
Collection of published mutations and sequence variations in genes that cause Neuronal Ceroid Lipofuscinoses together with unpublished data included with permission. There are two tables for each human NCL disease gene - Patient Datasheets list all published or reported patients and families, and Mutation Datasheets list all published or reported mutations, cross-referenced to patient table. Datasheets are available to view or download as excel files for off-site use to aid local needs or interests. Database follows mutation nomenclature recommendations of Human Genome Variation Society.
Web tool for computing metal ion concentrations in physiological solutions. Used for determining free metal concentration in presence of chelators or total metal given desired free concentration.
Bench-top microwell plate based image cytometer for adherent and suspension cells.
Harmony high content imaging and analysis software. Used to quantify complex cellular phenotypes. Designed for PerkinElmer high content screening systems.
High content image acquisition instrument. Automatic cell imaging system designed for quantitative cellular analysis of fixed or live cells. Contains sCMOS camera that provides large field of view and high resolution image capture.
Software suite as collection of programs intended to assist with analyzing diffraction X-ray images. MuscleX diffraction X-ray image analyzing toolkit. Data reduction software for X-ray fiber diffraction data.
Scalable Analytics for Brain Exploration Research
Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines.
Software tool as library of supporting code for numerical modelling (JSON config, HDF5 data, Modern OpenGL visualization). This code builds shared library called libmorphologica which contains simulation support facilities for our simulations of dynamical systems.
Global Mouse Models for COVID-19 Consortium
Portal for Global Mouse Models for COVID-19 consortium. Presents consortium, its statement and membership, and URLs for mouse COVID-19 resources worldwide.
Assisted Model Building with Energy Refinement parameter database
Assisted model building with energy refinement parameter database. Family of force fields for molecular dynamics of biomolecules. Collection of equations and associated constants designed to reproduce molecular geometry and selected properties of tested structures.
Software package to support parsing and extracting data from bibliometric datasets.
Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach.
Vermont University Larner College of Medicine Microscopy Imaging Center Core Facility
University of Vermont Larner College of Medicine Microscopy Imaging Center
Vermont University Larner College of Medicine Microscopy Imaging Center
Core provides imaging equipment including JEOL 1400 transmission electron microscope with AMT 11 megapixel digital camera,JEOL JSM 6060 scanning electron microscope with attached Oxford INCA energy dispersive spectroscopy detector for element analysis,Nikon Air HD confocal scanning laser microscope, Nikon C2 confocal scanning laser microscope, Andor Spinning Disk confocal microscope, Zeiss LSM 7 Multiphoton confocal microscope, Nikon STORM super-resolution light microscope, Olympus BX50 research microscope for transmitted light, phase contrast, and epi-fluorescence microscopy, Asylum Research MFP-3D BIO atomic force microscope, Asylum Research Cypher Environmental atomic force microscope,Arcturus XT-Ti Laser Capture Microdissector system, Olympus IX70 inverted microscope with associated Applied BioPhysics Electri Cell-Substrate Impedance Sensing (ECIS Ztheta) system, Leica VERSA 8 whole slide imager, Dell workstations containing Molecular Devices MetaMorph image analysis software for complex quantitative image analysis, Indica Labs HALO software, Improvision Volocity, MBR StereoInvestigator.
Harvard Medical School PCMM Microscopy Core Facility
Harvard Medical School PCMM Microscopy Core
Core with advanced instrumentation in Light and Electron Microscopy.Core provides confocal, multiphoton microscopy,electron microscopy,image analysis.
University of Michigan ULAM Pathology Core Facility
University of Michigan In Vivo Animal Core Facility
Our core is affiliated with the Unit for Laboratory Animal Medicine (ULAM) at the University of Michigan-Ann Arbor. We provide animal pathology services in support of non-GLP preclinical, translational, or basic science studies. Services include histology preparation, immunohistochemistry, animal hematology and serum chemistry assays, digital slide scanning/image analysis, and pathology interpretation by board-certified veterinary pathologists. Our core mission is to reduce bias and increase rigor within non-GLP animal research by providing high quality, documented, pathology support that may not be otherwise accessible within individual laboratories. Our laboratory maintains internal SOPs, documented quality control practices, and accountability/chain-of-custody records for all submissions. Additionally, we participate in an external quality control program through the Veterinary Laboratory Association.
University of Kentucky College of Medicine, Lexington, Pathology Research Core Facility
University of Kentucky College of Medicine
Core facilitates COCVD projects by providing equipment and technical expertise to paraffin-embed and section tissue specimens and perform chemical staining of tissue sections to be examined, photographed and analyzed chromogenically by light microscopy.Training in immunohistochemical staining is available.
Kentucky University, Lexington, Energy Balance and Body Composition Core Facility
Core primary focus is to identify mechanisms linking obesity to cardiovascular disease. Provides equipment and technical expertise for measurement of lean/fat mass and whole body metabolism in mice. Provides equipment for computerized quantitative measurement of oxygen consumption, food intake, water intake, and physical activity in mice.Echo MRI is utilized for non invasive quantitative assessment of lean and fat mass.
Vanderbilt University Genome Editing Resource Core Facility
Vanderbilt University Genome Editing Resource
Provides services, consultation, and collaborations to enable generation, storage and regeneration of genetically altered mice.Services include CRISPR-Cas9 Mouse Editing, Pronuclear Microinjection of DNAs,Sperm or Embryo Cryopreservation,In vitro Fertilization and Rederivation,Genome-Editing Design and Analysis Services.
New York University School of Medicine Langone Cytometry and Cell Sorting Core Facility
New York University Cytometry and Cell Sorting Laboratory
Facility provides cytometry and cell sorting services. Services include immunophenotyping, cell cycle analysis, and intracellular fluorophore detection. Services can be tailored to research needs, certified cytometrists are available to help plan experiments. Offers online and hands-on training in use of cell analyzers and analysis software.
University of Nebraska Medical Center Nanoimaging Core Facility
Provides service and expert advice to researches in their projects related to nanoimaging studies of molecular systems at single molecule and single cell levels utilizing Atomic Force Microscope, combination of Atomic Force Microscope with Fluorescence Optical Microscope, combination of Atomic Force Microscope with Raman Spectroscopy.
Iowa State University Hybridoma Core Facility
Iowa State University Hybridoma Facility
Core provides services for monoclonal or polyclonal antibodies production,animal immunization, cell fusion and hybridoma culture maintenance, cell culture and maintenance of other cell lines used in biotechnology and virology labs, large scale mammalian cell culture (bioreactor), blood sera collection, antibody purification and isotyping, cryopreservation and cryostorage of cell lines, and ELISA tests.
University of Nebraska Medical Center Animal Behavior Core Facility
University of Nebraska Medical Center UNMC Animal Behavior Core
Provides investigators with expertise, equipment, and space that is required to conduct innovative acoustic, behavioral, and cognitive research with focus on rigor, reproducibility, and maintaining the highest standards of animal welfare.
Software tool as hybrid pipeline for reconstruction and analysis of viral and host genomes at multi-organ level. Pipeline for identification, assembly, and analysis of viral genomes, that combine DNA sequence data from multiple organs. Cooperation between compression based prediction, sequence alignment, and de-novo assembly. Provides transmission and storage of data.
Virginia Commonwealth University School of Pharmacy Institute for Structural Biology, Drug Discovery and Development Core Facility
Biophysical Analysis and HT Screening and Imaging facility
Drug Discovery and Development Resources
VCU School of Pharmacy Institute for Structural Biology
Core provides services for Molecular Modeling, Biophysical Techniques, X-ray Crystallography, Protein Production,High Throughput Screening. Provided instruments to use after reservation include Clariostar Multimode Plate Reader, Echo 550 Acoustic Liquid Handler, X-Ray Diffractometer.
ADInstruments | PowerLab/4SP acquisition system
Integrated system of hardware and software designed to record, display, and analyse experimental data. Consists of PowerLab recording unit and possible ancillary devices, software that run on computer to which PowerLab is connected. PowerLab/4SP has four inputs for recording external signals.
Harvard Apparatus | Inspira Advanced Safety Ventilator, Volume Controlled
Volume Controlled Ventilator delivers desired tidal volume to animal by precisely controlling stroke of piston. Since actual stroke length may be modified for given stroke, sigh breaths are supported.
Maryland University School of Medicine Flow Cytometry and Mass Cytometry Core Facility
CVD Flow Cytometry and Mass Cytometry Core
Maryland University School of Medicine Flow Cytometry and Mass Cytometry Core
Core provides researchers with flow cytometry and mass cytometry services and equipment and help from highly trained and experienced staff.
Claflin University Molecular Science Research Center Core Facility
Core facility is equipped with instrumentation to support proteomic and metabolomic research, as well as equipment for materials characterization. Key instruments include a Bruker 700MHz NMR, two Bruker XRDs (Powder and Crystal), and Bruker Micro ToF mass spectrometer.
BX50 fluorescence microscope comes with 4 position mercury fluorescence lamphouse and power supply. Filters can be added as needed. Trinocular viewing head allows you to add camera to this system.
Millar | PCU-2000 Pressure Control Unit with Patient Isolation
PCU-2000 Dual Channel Pressure Control Unit
Pressure Control Unit is two channel, patient isolated, line powered bridge amplifier for connecting one or two single sensor Millar Mikro-Tip catheters to clinical patient monitor or standalone data acquisition system. Provides built in ridge excitation eliminating need for separate bridge amplifier. Analog output signal level of 1V/100 mmHg is compatible with most pressure monitors and data acquisition systems. In line power supply adapts automatically to line voltages from 100 to 240 volts AC.
Molecular Devices | Axoprobe 1A microelectrode amplifier
Multipurpose microelectrode amplifier contains two microelectrode amplifiers ME1 and ME2. These amplifiers may be independently used for intracellular and extracellular voltage recording with simultaneous current passing, or for recording with ion sensitive electrodes.
Cost effective Data Acquisition Unit (CED)
Unit records waveform data, digital event and marker information and can simultaneously generate waveform and digital outputs in real time for multi tasking experimental control.
Leica | SP8 DIVE multi photon microscope
Multiphoton confocal microscope with spectrally tunable detection. Equipped with 4Tune, tunable, non descanned detection unit.
High definition color microscope camera equipped with 5.9 megapixel CMOS image sensor which enables capture of high definition images of up to 2880 x 2048 pixels. Enables various observations such as brightfield, DIC, phase contrast and fluorescence.
Two photon microscope capable of imaging deep within living specimens when combined with Ti:Sapphire Laser. Provides 3D objective movement and rotation allowing specimen to remain stationary.
Software tool for real time analysis and data visualization. Software system for experimental control and quantitative data analysis in microscopy and spectroscopy.Integration of data processing and acquisition allows real time analysis and visualization of experimental results.
Molecular Devices | Axopatch 200B Patch Clamp Amplifier
Axopatch 200B Capacitor Feedback Patch Clamp Amplifier
Patch clamp amplifiers to minimize signal to noise ratio.
Software tool for creating solid 3D CAD objects. Used for creating 3D models focusing on CAD aspects of 3D modeling of machine parts. Reads in script file that describes object and renders 3D model from this script file.
Cell chamber with coverslip holder designed for viewing live cell specimens on upright or inverted microscopes. Surgical stainless steel chamber is autoclavable so cells can be grown directly on coverslips within unit. O-ring seal is designed to prevent samples from being contaminated by oil or leakage of media from coverslips. Chamber accepts 25 mm round coverslips and mounts in standard 35 mm diameter stage holder.
Axio Imager 2 resolves samples from tissue sections in pathology to brain specimens in neuroscience to multi dyed FISH specimens. Works with ZEN imaging software.
Software tool as DNA compressor that uses neural network to do mixing of experts.
Open source software tool to extract metadata from DICOM files for indexing and storage in SQL database.
Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes.
Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.
Software suite of tools for cataloguing and anonymising DICOM files, as used for Scottish Medical Imaging project. Software suite of microservices for loading, anonymising, linking and extracting large volumnes of dicom medical images to support medical research. Platform allows dicom tags extracted from clinical images to be loaded into MongoDB and relational database tables for purposes of generating anonymous linked research extracts including image anonymisation.
Collection of guidelines to encourage rigorous and reproducible research practices for cardiovascular physiology.
Virginia University School of Medicine Genome Analysis and Technology Core Facility
University of Virginia School of Medicine Genome Analysis and Technology Core Facility
University of Virginia UVA Genome Analysis and Technology Core
Core offers instrumentation and expertise in all areas of bulk and single cell NGS genomics and transcriptomics, as well as training to access core shared instrumentations. Services include RNA Seq, CHIP Seq, ATAC Seq, Amplicon DNA Seq, 16S ribosomal gene sequencing, shot gun sequencing for small genomes and whole exome sequencing.10X Genomics resources include single cell CNV, VDJ, and 3 or 5 RNA seq as well as linked reads.Core provides real time and droplet digital PCR services most suitable for targeted gene expression, SNP genotyping and CNV discovery.
Medical University of South Carolina College of Dental Medicine Gnotobiotic Animal Core Facility
Medical University of South Carolina MUSC Gnotobiotic Animal Core
Core offers investigators opportunity to address research questions that require use of gnotobiotic animals. Standard services provide germ free mice (e.g. BALB/c, C57BL/6), deriving new strains of mice into germ free state by caesarean section, tissue collection and/or fluid from mice that have not received treatment or manipulations, exporting germ free mice in sterile transporters to other institutions. Non-Standard Services include maintaining and breeding newly derived germ free mice, administration of specialized diets, administration of compounds as therapeutic or disease-inducing agents, tissue collection and/or fluid from mice that have received treatment or manipulations.
Marshall University School of Medicine Genomics Core Facility
Marshall University Genomics and Bioinformatics Core Facilities
Marshall University Genomics Core Facility
Core provides services including high throughput next generation sequencing (NGS) to support whole genome, whole exome, RNA-Seq, single cell RNA-Seq, microbiome and global chromatin and methylation studies, biostatistical and bioinformatic support for NGS projects, access to DNA/RNA sequence analysis software, automated Sanger DNA sequencing, genotyping and RNA/DNA quality assessment, access to shared instrumentation such as plate readers, real time thermal cyclers, Agilent Bioanalyzers, fluorimeters, and spectrophotometers.
Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation.
statistical analysis of taxonomic and functional profiles
Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups.
University of Melbourne Biological Optical Microscopy Platform (BOMP) Core Facility
Core provides access to fluorescence microscopy equipment including Deltavision OMX Blaze Super Resolution (3D-SIM/SMLM), Leica SP8 inverted confocal, La Vision Ultramicroscope II Lightsheet Microscope,Nikon Andor WD spinning disk, Nikon A1R inverted confocal x2, Olympus FV-MPERS Multi Photon,Olympus FV3000 inverted confocal (live cell) ISS Fast-FLIM, Perkin Elmer Operetta High Content Imaging, Zeiss LSM800 upright Airyscan, Zeiss LSM880 upright Airyscan fast, Zeiss Elyra/LSM880 inverted (live cell), super resolution (Airyscan/SMLM). Staff can help with image analysis, super resolution microscopy, fluorescence lifetime imaging microscopy, high content imaging and light sheet microscopy techniques.
Master-8 EIGHT CHANNEL PROGRAMMABLE PULSE GENERATOR
Pulse generator that can hold 8 different pre-programmed paradigms all of which can use up to all 8 channels.
Plexon | PlexStim Electrical Stimulator System
PLEXON PlexStim Electrical Stimulator System
Programmable constant current stimulator system with 16 channels.
A-M SYSTEMS | model 2200 analog stimulus isolator
A‐M SYSTEMS MODEL 2200 ANALOG STIMULUS ISOLATOR
Stimulus isolator which does opto-electrical isolation, signal scaling, and signal conversion.
Beckman Coulter | Life Sciences MoFlo Astrios EQ Cell Sorter
Millar | MPVS Ultra Pressure Volume Loop System
Pressure volume loop system with seven available volume segments, range of gain settings, integrated internal ECG circuit and dual pressure amplifiers. System can be used in either large or small animal subjects, depending on which size catheter is used.
Fluorescent microscope which supports fluorescence contrast techniques. This product is archived and has been replaced by the Leica DM4000 B LED.
Leica | DM5500 B Automated Upright Microscope System
Fluorescence microscope capable of contrast microscopy and has ability for fully automated Differential Interference Contrast techniques. This product has been archived and replaced with the Leica DM4 B and DM6 B microscopes.
Ripple Neuro | Grapevine Neural Interface Processor
Interface processor as 512 channel stimulation and recording electrophysiology tool. Designed to be safe for human subjects.
Software used for 3D printing, can integrate with CAD software and has variety of custom settings.
Perma Pure | Nafion Fuel Cell Humidifier
FC Series humidifier. Nafion tubing provides consistent, repeatable humidification of air and hydrogen across specified flow range, for portable, stationary, automotive and aerospace applications. Perma Pure Fuel Cell Humidifier features low pressure drop and do not require power to operate.
Open source 3D printing software which supports multi part printing and has slicers.
Software tool to construct 3D models of soft tissue using CT-like cross sectional imaging.
Spike sorting software for multi day recordings from high channel count probes during electrophysiology experiments.
Gene Set Enrichment for Mathematical Biology
Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function.
Relationship with Addiction Through Searches of PubMed
Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords.
Open source community driven guide to reproducible, ethical, inclusive and collaborative data science. Provides information that data scientists in academia, industry and government need at start of their projects to ensure that they are easy to reproduce and reuse at the end. Expanded to series of books covering reproducible research, project design, communication, collaboration, and ethical research.
CAMARADES Preclinical Systematic Review and Meta analysis Facility
Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies Preclinical Systematic Review
Software tool as fully integrated online platform for performing systematic reviews of preclinical studies.
Optimus is a pipeline developed by the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA) Project that supports processing of any 3' single-cell and single-nuclei expression data generated with the 10x Genomic v2 or v3 assay. It is an alignment and transcriptome quantification pipeline that corrects cell barcodes, aligns reads to the genome, corrects Unique Molecular Identifiers (UMIs), generates an expression matrix in a UMI-aware manner, calculates summary metrics for genes and cells, detects empty droplets, returns read outputs in BAM format, and returns gene counts in NumPy matrix and Loom matrix formats.
Software tool for detection threshold aware CNV calling in matched whole exome sequencing data.
Database of protein abundance averages across all three domains of life. Protein abundance database, which contains whole genome protein abundance information across organisms and tissues. Publicly available experimental data are imported and mapped onto common name space and, in case of tandem mass spectrometry data, re-processed using in-house standardized spectral counting pipeline. All datasets in are scored and ranked by importing protein network information. Orthology relations at various hierarchy levels are pre-computed for each protein.
Adolescent Brain Cognitive Development ReproNim Course
Course provides training for reproducible analyses of Adolescent Brain Cognitive Development Study data. Designed to provide comprehensive background to ABCD study while delivering hands on instruction on reproducible ReproNim workflows and outcomes.
Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.
Project to bridge gap between in vitro human islet studies and clinical studies in human subjects. Used to integrate cellular and medical research data, collected by partners, with computational modelling to identify pathophysiological mechanisms and markers of spectrum of biological and cellular processes involved in pancreatic beta cell failure leading to impaired glucose tolerance and T2D.
Group of academic institutions committed to studying diabetic foot conditions, such as foot ulcers and wound healing, to develop predictive biomarkers which can be later used to create better treatment plans and improve health and quality of life for people living with diabetes.
Spot: File-based localization of numerical perturbations in data analysis pipelines
Open source software tool for file based localization of numerical perturbations in data analysis pipelines. Identifies components in pipeline, at resolution level of system process, that produce different results in different execution conditions.
Leica | ASP300S Fully Enclosed Tissue Processor
Processor that automatically washes tissue sample which needs to be usable in downstream processes. Designed for routine and research histopathology of up to 300 cassettes.
Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.
Pipeline developed in collaboration with Bing Ren lab and supports processing of BICCN single-cell/nucleus ATAC-seq datasets. Pipeline uses python module SnapTools to align and process paired reads in form of FASTQ files. Produces hdf5-structured Snap file that includes cell-by-bin count matrix. Final outputs also include GA4GH compliant aligned BAM and QC metrics.
The Smart-seq2 Single Nucleus Multi-Sample (Multi-snSS2) pipeline was developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays.
Software drug discovery platform to integrate purchasable chemical space with molecular modeling tools. Chemical marketplace for drug discovery with services based around small molecule compound sourcing. Integrated molecular modeling tools, compound database, IT infrastructure and compound procurement service with web interface. Virtual screens can be run to identify new hits and modeling applications can be used to improve their affinity and other properties.
Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.
Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics.
Computational Analysis of gene Family Evolution
Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny.
Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics.
Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation.
Software fast and lightweight tool for processing sequences in FASTA or FASTQ format.
Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software.
Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.
Transcriptome Functional Annotation and Analysis
Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
Software R package to produce publication ready volcano plots with enhanced colouring and labeling. Used to visualise results of differential expression analyses.
Molecular Devices | SpectraMax 190 microplate reader
Microplate Reader from Molecular Devices is ideal for UV-Vis life science applications, especially DNA analysis. Multi channel design mimics dual beam spectrophotometer. Each sample has discrete sample beam and reference beam so that each well is measured directly, eliminating error due to variations in light output between optic fibers. System consists of eight sample beams and detectors and eight reference beams and detectors to deliver both precision and speed of reading across microplate through 4.0 OD. Detects 16 ng per well of DNA and quantitates 50 ng of DNA.
Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.
BD Biosciences | FACSAria II Cell Sorter
Cell sorter features hardware and software enhancements that improve overall ease of use, flexibility,and aseptic capability. Offers new options in lasers and nozzles to support more advanced multicolor applications. Built on fixed alignment technology. FACSAria II cell sorter is first generation of BD FACSAria system where flow cell is in true fixed alignment with laser, to reduce startup time and improve reproducibility.
Rapid Alignment of Proteins in terms of Domains
Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains.
Web server for macromolecular structure model optimisation and databank of optimised structure models. Focuses on automating final steps of crystallographic process: optimisation of structure model through refinement, rebuilding, and validation. Can automatically optimise most of crystallographic structure models based on input model and diffraction data. Web server works on user provided data, databank has updated versions of Protein Data Bank entries based on original experimental data that were deposited with atomic coordinates in PDB.
Web tool as HMM plus similar protein based gene prediction. Used for multiple gene prediction in genomic DNA with using information from similar protein. Used if you know protein sequence similar with protein which is encoded by gene in your sequence.
Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables.
Portal for islet research community. Data for eight scRNA-seq datasets are combined to give consensus overview of islet cell type defining genes. Tools are provided for interacting with and comparing novel genesets generated.
Software tool as image analysis and processing solution for quantitative microscopy which provides control of Leica microscopes and Leica digital cameras. Capability ranges from simple interactive image measurements to automatic, multi-parameter measurements. Available in editions including QWin Runner, QWin Lite, QWin Plus, QWin Standard and QWin Professional.
Software R package for creation of HTML report of differential expression analyses of count data. Integrates some of code mentioned in DESeq2 and edgeR vignettes, and reports ranked list of genes according to fold changes mean and variability for each selected gene.
Computational Psychiatry Research Map Database
Software tool for visualizing research papers from computational psychiatry as two dimensional map. Shows distribution of papers along neuroscientific, psychiatric, and computational dimensions to enable anyone to find niche research and deepen their understanding of the field. Database for visualizing research papers.
Automate Scientific | Brain Slice Keeper 4
Slice keeper holds four sets of brain slices and features container with lid and integrated air stone for bubbling carbogen into ACSF, needle valve for adjusting gas flow included, and curved bottom designed to keep bubbles away from slices while promoting fresh solution flow over slices.
FHC | Platinum-Iridium Cluster Bipolar Electrode CE2C55
Cluster microelectrode for recording or stimulation in chronic applications. Custom Microelectrode Code CE2C55 with Inner Pole Diameter 25 um and Length 50mm.
ISO-Flex- The Flexible Stimulus Isolator
Flexible stimulus isolator since it is optically isolated. Unit can be switched to constant current or constant voltage. You can get bipolar pulses by connecting two isolators.
A-M SYSTEMS | Model 1800 2-Channel Microelectrode AC Amplifier
Two channel, differential amplifier by A-M Systems, intended for extracellular recording and/or stimulating with high impedance metal microelectrodes. Used for single cell spike recordings, applications requiring extracellular neurophysiological recording from excitable tissue such as nerve, muscle EMG, EEG, EKG, and ERG recordings. Each channel contains high gain, low noise differential amplifier stage followed by low pass, high pass, and notch filters. Three operating modes are available to accomodate recording, stimulating, and verification of electrode impedance.
Digitizer offers analog I/O, digital I/O, and four 32‑bit counters/timers for PWM, encoder, frequency, event counting, and more. Delivers functionality leveraging high throughput PCI Express bus and multicore optimized driver and application software. Suited for broad range of applications, from basic data logging to control and test automation.
Microscope with differential interference contrast ,bright field, dark field components. TR30-2 Trinocular observation head with WH10X 22 eyepieces. 0.5X parfocal C mount camera adapter. Universal reflected and transmitted light stage. Capable of both transmitted and reflected light observations.
Olympus | Compact Stereo Microscope SZ61
Standard model SZ61 Zoom Stereomicroscope with magnification range from 6.7x to 45x (using 10x eyepieces), with wide zoom ratio of 6.7:1, enabling macro to micro zooming that speeds routine workflows. Inward angle allows combination of high level flatness and depth of focus for 3D viewing.
Donald Danforth Plant Science Center Advanced Bioimaging Laboratory Core Facility
Donald Danforth Plant Science Center Integrated Microscopy Facility
Core provides instruments for live cell imaging including Leica SP8-X confocal microscope and other fluorescence microscopes. Facility provides workstation for confocal image processing, ancillary equipment required for transmission electron microscopy. Services are provided as self services after user training by IMF staff or as full services done by core facility staff.
Software tool as spatial database extender for PostgreSQL object relational database. It adds support for geographic objects.
National Culture Collection of Pathogenic Fungi Core Facility
National Culture Collection of Pathogenic Fungi
National core facility for deposition, maintenance, identification and supply of all pathogenic fungi. Services include depositing cultures, retrieval of same and identification of isolates and more. Facility of international standard for preservation and to handle deposits of medically important fungi and to supply authentic strains to investigators in India. Scientists have access to database of preserved medically important fungi. Will initiate fungal taxonomy research and impart training on taxonomy.
Gilson | Minipuls Evolution peristaltic pump
Multi channel peristaltic pump for applications with different viscous or abrasive fluids. Allows for channel cartridges, from one to sixteen, to be changed while pump is running.
Harvard Apparatus | Single Animal Tabletop Isoflurane Anesthesia System with Small Induction Box
Tabletop anesthesia system suitable for mice, rats and other small animals under 10 lb. Passive scavenging systems. Funnel fill isoflurane vaporizers.
Web server for protein protein affinity prediction. Used for predicting binding affinity of protein protein complexes.
Community project portal by team consisting of members of eLife Early Career Advisory Group, Protocols.io, Addgene and Code Ocean, developing resources and teaching workshops to enable researchers to do reproducible research. Collaboration between volunteers in research, industry, and startups in area of reproducibility to make researchers aware of tools that they can use to improve reproducibility of their work.
Software R tool used to identify and retrieve CPRD clinical additional record information such as, smoking, weight/BMI, and medical tests.
Web server allows comparing different Ga protein sequences and structures by mapping them to Common Ga Numbering system. Used as superscript for individual positions of specific G protein.
Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments.
Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data.
Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences.
Software tool as pipeline for accurate and automated gene prediction in novel eukaryotic genomes. Automated gene prediction training and gene prediction pipeline.BRAKER1 is eukaryotic genome annotation pipeline. BRAKER2 is extension of BRAKER1 which allows for fully automated training of gene prediction tools GeneMark EX R14, R15, R17, F1 and AUGUSTUS from RNA Seq and/or protein homology information, and that integrates extrinsic evidence from RNA-Seq and protein homology information into prediction.
Open source software tool to manipulate files in GFF format. Used to convert, sort, filter, transform, or cluster genomic features.
Software tool to identify, orient and trim full length Nanopore cDNA reads. Able to rescue fused reads.
Dot plot large GENomes in an Interactive
Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.
Software tool for eﬃciently solving large scale sequence matching tasks.
Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons.
Software tool for de novo detection of full length LTR retrotransposons in large sequence sets. Delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs.
Database provides information on research status of gene related diseases, gene expression in different tissues, regulatory relationship among genes, information of diseases, mRNA, Transcription Fctor, miRNA and other information shared among genes.
Web tool for calculating DNA methylation based predictors of human traits and health.
Web translational and research tool for DNA methylation based health profiling.
Software tool for assembly of DNA sequence alignment files in BioEdit fasta format into NEXUS format ready for analysis in programs such as PAUP or MrBayes. Used to calibrate gap in sequence after alignment.
Database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference. Tool to rapidly disseminate organized caspase sequence data. Includes all animal species with currently available annotated genomes in NCBI genome database. Manually curated and not curated sequences are available to download.
Qiagen RT PCR cycler for performance in Real Time PCR. Enables streamlined analysis for wide range of applications.
Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.
Software package for display of light microscopy images together with atomic force microscopy images.
Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.
Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes.
Web tool for browsing genome wide fitness experiments for diverse bacteria from Deutschbauer lab, the Arkin lab, and collaborators. Collection of mutant phenotypes for bacterial genes of unknown function.
Laboratory portal about research including new approaches for precision gene editing, delivery of molecular and genetic cargo, discovery of novel programmable systems, and engineering of immune system to develop next generation of therapeutics. Provides collection of tools for guide design.CRISPR.MIT.EDU of Guide Design Tools is no longer available, documented on August 28,2020.
Software R package for flexibly restructuring and aggregating data.
Colorado University at Boulder JILA Keck Lab and Fabrication Core Facility
W. M. Keck Optical Measurement Lab JILA Micro and Nanofabrication Facility
Core provides number of specialized measuring tools for optical and surface characterization, as well as expertise in fiber optics.Fabrication facility is clean room for fabrication at micron and nanometer scale. Training and consultation is provided.
Colorado University at Boulder Shared Instrumentation in Nanofabrication and Characterization Core Facility
Colorado Shared Instrumentation in Nanofabrication and Characterization
Multidisciplinary core research facility and service center, within College of Engineering and Applied Science, that provides access to equipment in areas of micro and nanofabrication, nanomaterials characterization and metrology and offers expertise and advanced hands-on training. Offers common platform for convergence of multiple scientific and engineering disciplines and facilitates collaborative research with strategic partners and information exchange.
Colorado University at Boulder Biochemistry Shared Instruments Pool Core Facility
Provides access to multitude of instruments and techniques, including EPR, CD and fluorescence spectroscopy, DLS, Sec-MALS, ITC, MST, stopped-flow spectroscopy, chemical quench-flow, imaging systems, centrifuges, scintillation counters, sonicators and more.
Colorado University at Boulder Center for Infrastructure, Energy, and Space Testing Core Facility
Provides centrally managed experimental testing facility offering geotechnical centrifuge, structural dynamics and materials testing. Facility boasts unique large-scale, fast loading rate, gravitational and environmental control capabilities.
Colorado University at Boulder Biochemistry Cell Culture Core Facility
Provides investigators within the Department a user-friendly, shared environment where researchers can advance discovery in diverse areas such as cancer biology, drug discovery, nanomaterial analysis and basic life science. Provides Biosafety Cabinets, CO2 Incubators including viral and variable oxygen (tri-gas) Insect cell incubator and shaker, Large-scale mammalian incubator, Routine mycoplasma testing,FBS testing,Training, In-house media preparation.
Colorado University at Boulder Green Labs Core Facility
CU Green Labs Shared Ultra-Low Temperature (ULT) Freezers
University of Colorado – Boulder Green Labs
Core provides help to efficiently use of resources by involving individual laboratory members in identifying opportunities for efficiency in their laboratory and promoting efficient behaviors, upgrading inefficient laboratory equipment and techniques, compelling labs to use lab space, fume hoods, and lab equipment resources efficiently and in collaborative manner, developing means to reduce large flow of lab materials into waste stream, promoting green chemistry and chemical re-use where feasible.Core provides instruments including Shared Stirling Ultracold Ultra Low Temperature Freezer and Shared Thermo Scientific Ultracold Ultra Low Temperature Freezer.
Colorado University at Boulder Intermountain Neuroimaging Consortium Core Facility
Magnetic resonance imaging research facility. Provides Tesla Siemens MAGNETOM Prismafit MRI scanner, located at Center for Innovation and Creativity (CINC) on CU Boulder campus.
Colorado University at Boulder Central Analytical Mass Spectrometry Core Facility
Central Analytical Mass Spectrometry Laboratory
Offers analytical and instructional expertise in mass spectrometry with practical training and access to instrumentation.Located in room C1B90 of Jennie Smoly Caruthers Biotechnology Building houses six mass spectrometry systems.Instruments are interfaced with chromatographic system in order to separate complex mixture samples. Offers training for open access to some instruments including Thermo ISO LT GCMS, Synapt G2 HDMS, Agilent 6120 LCMS, and 4000 Q-trap QQQ instruments.
Colorado University at Boulder Light Microscopy Core Facility
Provides access to instruments and training. Instruments including Dell Precision 7910 Analysis PC,Leica DMRXA Upright Widefield Microscope, Nikon E600 Upright Widefield Microscope, Nikon N-SIM structured illumination super-resolution and A1 laser scanning confocal microscope, Nikon Inverted Spinning Disk Confocal Microscope, Zeiss 510 Laser Scanning Confocal Microscope.
Colorado University at Boulder Stem Cell Research and Technology Resource Center Core Facility
CU Boulder Stem Cell Research and Technology Resource Center
Stem Cell Research and Technology Resource Center
Shared facility provides space for culturing human induced plurupotent stem cells on second floor of Porter Biosciences. Provides biosafety cabinets,CO2 and variable oxygen control incubators, inverted phase contrast microscopes, and sterile dissection hood equipped with dissecting microscope and heated stage,inverted fluorescence microscopes with live-cell time-lapse capabilities, centrifuges, liquid nitrogen cryostorage space, refrigerators, freezers, water baths, dedicated bioengineering space, and viral expression core. Routine mycoplasma testing is performed in-house and karyotyping services are carried out via contract.
Unrestricted Leveraging of Targets for Research Advancement and Drug Discovery
Project aim is to identify and validate novel targets in auto immune and inflammatory diseases. Used to create and profile target directed chemical and antibody probes in patient cell derived assays, provide biomarker and phenotypic read outs in more disease relevant context.
Software for Organizing Data Automatically
Software application intended to simplify dataset curation and submission process for SPARC investigators by providing one stop tool to accomplish all required steps. Desktop software to facilitate data organization and submission process for Stimulating Peripheral Activity to Relieve Conditions (SPARC) investigators and thus promote FAIR Data Principles. Git repository tool for SODA data deposition for SPARC researchers.
open online Simulation platform for Stimulating Peripheral Activity to Relieve Conditions
Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response.
Software toolkit for visualizing multiscale anatomy schematics with phenotype related information. Used for visualisation of multiscale physiology circuitboards and to support clinical and scientific graphical user interfaces and dashboards for biomedical resource management and data analytics. Creates FAIR models of vascular and neural connectivity information for molecular, subcellular, cellular and tissue conduits across multiple scales. Provides interface between physiology knowledge and data relevant to physiology through intuitive graphical interface for managing semantic metadata and ontologies relevant to physiology. Brings together expertise in computer science, image processing, bioengineering and medicine to manage knowledge in physiology and pathology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Open platform that accepts data from peripheral nervous system data. It was previously the Blackfynn data platform. Pennsieve provides advanced functionality to organize files and complex metadata describing datasets and allows users to interact, search, and analyze these data through web application or programmatically using Python client. Provides end-to-end solution for publishing datasets through Pennsieve Discover, assigning DOIs and ensuring that published data becomes available to larger academic community in sustainable and FAIR manner.
Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives.
3D scaffold fitting software designed for making connection between 3D scaffold and data in dataset.
3D scaffold creation software designed for capturing anatomical features using image data.
Software tool to generate whole connected 3D brain ventricular shape model and encode ventricular surface deformation information that is inaccessible by ventricle volume measure. Contains automated segmentation approach and surface based multivariate morphometry statistics.
Real-Time Experimental Control with Graphical User Interface
Software tool as open source network based parallel processing solution for performing behavioral control, high precision stimulus presentation, and high density neurophysiological measurements. Framework uses network based parallel processing to implement experimental control and synchronize devices.
Distributed Archives for Neurophysiology Data Integration client
Command line client to facilitate common operations.
Software R package for performing Mendelian randomization using genome wide association study summary data.
Web based database of proteins, RNA, lipids and metabolites that are identified in extracellular vesicles. Compendium for extracellular vesicles with continuous community annotation and with manually curated data from published literature.
Global Natural Products Social Molecular Networking
Web based mass spectrometry ecosystem that aims to be open access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass spectrometry data. Database of mass spectrometry datasets.
Allen Institute Mouse Whole Cortex and Hippocampus SMART-seq
Mouse Whole Cortex and Hippocampus SMART-seq
Collection of data set including single cell transcriptomes from multiple cortical areas and hippocampal formation. Samples were collected from dissections of brain regions from 8 week old male and female mice, primarily from pan GABAergic, pan glutamatergic, and pan neuronal transgenic lines, with addition of more specific transgenic lines and some retrogradely labeled cells in VISp and ALM.
Hiroshima University Amphibian Research Center
Stock center that provides amphibian organisms, frogs and newts, primarily to Japanese investigators. The center runs the National BioResource Project (NBRP) Clawed frogs / Newts, which is financially supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, to distribute these resources. Contributes to maintenance of biologically important strains of frogs and study biological characteristics of amphibian focusing genetics, developmental regulation, speciation, phylogeny, phenotype expression, and environment-induced mutagenesis.
Software tool as Java based framework to store, share and publish research data. Free software infrastructure to FAIRly maintain and publish in-house stored research data. Used for version tracking, metadata management, information retrieval, journal and founding agency proven registration of persistent identifiers (DOI), embedded HTTP(S) server for public data access, access as network file system, and scalable storage backend.
Software Python package for analysis of trajectories in clinical datasets.
Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella.
Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets.
Case Western Reserve University Genomics Core Facility
Case Western Reserve University CWRU Genomics Core
Core provides centralized resource working to take difficulty out of Next Generation Sequencing projects for both novice and experienced users alike. Provides assistance in all facets of experimentation from design to data analysis including grant and manuscript preparations.Offers NGS, Sanger, Informatics and Genotyping services based off of Illumina platform.
Web server predicts presence of N-terminal presequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (luTP). Predicts potential cleavage site for sequences predicted to contain N-terminal presequence.
Web server for prediction of mitochondrial targeting sequences.
Web server for simple multiple sequence alignment. Can align protein, DNA and RNA sequences.
Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures.
Software tool used for setting up PyroScience FireStingO2 (FSO2-4) oxygen meter and calibrating sensors. Measured values are displayed numerically and graphically and can be logged in respective data files for further data processing.
Cole-Parmer | Masterflex L/S Variable Speed Digital Drive with Remote I/O peristaltic pump
Masterflex L/S Variable-Speed Digital Drive with Remote I/O
Peristaltic pump with flow rate 0.06 to 3400 mL/min, three digit LED display, reversible motor, LED indicators to confirm motor direction and speed range from 6 to 600 rpm.
Toolbox for Representational Similarity Analysis
Software Matlab toolbox to perform representational similarity analysis for neural data.
Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools.
University of Virginia School of Medicine Molecular Electron Microscopy Core Facility
University of Virginia Molecular Electron Microscopy Core
Facility dedicated to high resolution electron cryomicroscopy and electron cryotomography. It houses three electron microscopes,120kV Spirit, 200kV F20, and 300kV Titan Krios. These microscopes are available to researchers either for direct use, or aided by MEMC personnel, to collect data aimed at high resolution structural biology projects.
Sainte-Justine University Hospital Research Center Platform for Imaging by Microscopy Core Facility
Centre Hospitalier Universitaire Sainte-Justine CHUSJ - PIM Platform for Imaging by Microscopy
CHUSJ - PIM Platform for Imaging by Microscopy
Core offers light microscopy instruments, image analysis tools, consultations and training. Platform for imaging by microscopy.
Tecan | Infinite M200 Pro Multimode Microplate Reader
Tecan Infinite M200 Pro is multi-detection microplate reader used for biological applications including protein quantification, ELISA, binding studies, DNA quantification, gene expression, immunoassays, toxicity, cell viability, RNA quantification, cell-based and enzyme assays.This modular Tecan plate reader is monochromator based system, with no need for filters, giving range from 230-1000 nm Abs or 300-600nm FI in 1 nm steps. With spectrally enhanced, red-sensitive PMT, the FI range extends to 330-850nm for NIR readings. Modules featured can be Monochromator absorbance, fluorescence top, fluorescence bottom, Luminescence, Incubation, injection, and enhanced photomultiplier tube (PMT) for red sensitivity that brings the detection limit to 45 pM. Please see individual SKU numbers for a list of installed modules. Heating module that’s installed on the microplate reader, allows for the chamber to keep at 37°C for those temperature sensitive samples. Can read microplates from 6 up to 384 well plates, along with PCR plates. Tecan M200 Microplate Reader is driven by Magellan software, which allows you to easily navigate run from start to finish. The user can choose from predetermined assays or build their own from scratch.
Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer.
Bio-Rad | Trans-Blot SD Semi-Dry Transfer Cell
Transfer cell allows fast, efficient, economical blotting without a buffer tank or gel cassettes.
Instrument for imaging and analyzing gels and western blots by Bio Rad. Designed to address multiplex fluorescent western blotting, chemiluminescence detection, general gel documentation applications, and stain-free technology imaging needs.
Open source cloud based pipeline and analysis service for metagenomic pathogen detection and monitoring. Hypothesis free global software platform that helps scientists identify pathogens in metagenomic sequencing data. IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes assembly based alignment pipeline which results in assignment of reads and contigs to taxonomic categories.
Cellular process and Metabolism molecule in the bacterial proteins.
Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule.
R Analysis and Visualization of intracranial EEG
Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG).
Software tool as molecular graphics program designed to give straightforward and complex static and dynamic representations of macromolecular structures. Used to create publication quality images and movies and to superpose and analyse structures.
subCELlular LOcalization prediction with functional Gene Ontology annotation
Web server for protein subcellular localization prediction with functional gene ontology annotation. Web based system for screening various properties of targeted protein and its subcellular localization.
Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.
Web server is focused on protein ligand interactions. Provides support for initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Furthermore, advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported.
Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python.
Microprocessor based, programmable ultrasonic processor. Features include pulse mode and digital display of both wattage and joules.Used for standard cell disruption, DNA/RNA shearing, homogenization and many other applications.
Thermo Fisher | MicroCL 21R microcentrifuge
Refrigerated benchtop microcentrifuge with rotor designed to provide acceleration up to 21,100xg.
Oregon Health and Science University Medicinal Chemistry Core Facility
Oregon Health and Science University OHSU Medicinal Chemistry Core
Core helps researchers investigate interactions between small molecules and biological systems by providing medicinal chemistry and chemical biology expertise and organic synthesis support.
Donald Danforth Plant Science Center Phenotyping Core Facility
Donald Danforth Plant Science Center DDPSC-Bellwether Phenotyping Facility
Core provides instruments including Scanalyzer 3D platform which consists of multiple digital imaging chambers connected to controlled environment Conviron growth house by conveyor belt system, resulting in continuous imaging loop and enables repeatedly image plants at multiple points throughout time.RGB imaging allows visualization and quantification of plant color and structural morphology. Near-infrared (NIR) enables visualization and quantification of plant water-use efficiency.Watering and weighing stations are customizable to deliver water and nutrients on specified schedule by volume or weight. Standard phenotyping services include operation and maintenance of LemnaTec Scanalyzer system, as well as technical support and troubleshooting.
Web based gene expression database and analysis platform. Used for integrative data mining of genotype and phenotype data, with optimized workflows.
Software tool for macromolecular structure visualization. Molecular visualization framework to visualize crystallographic models of macromolecules. Used to visualize and create publication quality images of macromolecular structures with user friendly interfaces.
Software Python package part of nonnegative matrix factorization NMF. Features various classification, regression and clustering algorithms including support vector machines, random forests, gradient boosting, k-means and DBSCAN, and is designed to interoperate with Python numerical and scientific libraries NumPy and SciPy.
Software package serves as companion R package for online guide Doing Meta-Analysis in R - A Hands-on Guide written by Mathias Harrer, Pim Cuijpers, Toshi Furukawa and David Ebert. Guide shows how to perform meta-analyses in R from scratch with no prior R knowledge required.
Software general R package providing standard methods for meta analysis.
Software tool accepts image files (like PNG, JPEG and TIFF) containing graphs, and recovers the data points from those graphs. Used to convert graphs to data points. Imports image file and then digitizes it by placing points along axes and curves.
Colorado University at Boulder BioChemistry Krios Electron Microscopy Core Facility
BioChemistry Krios Electron Microscopy facility
Provides single particle cryo EM and cryo tomography of plunge frozen samples. Using Titan Krios G3i for high resolution data collection on Gatan K3 Direct Detection Camera facility is able to offer data collection at atomic level resolution.Facility uses Serial EM for SPA and cryo-ET data acquisition.
Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup.
Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies.
University of North Carolina at Chapel Hill School of Medicine Neuroscience Microscopy Core Facility
UNC School of Medicine Neuroscience Microscopy Core Facility
University of North Carolina at Chapel Hill UNC Neuroscience Microscopy Core
Microscopy Core for high resolution imaging and aims to make this technology accessible to neuroscientists and other scientific researchers.Provides advanced systems for cellular and molecular imaging of in vitro and in vivo samples, implements new imaging technologies, particularly related to real time and tissue clearing based imaging of neurodevelopment and neural functions, offers training, consultation, data analysis, image processing, and centralized technical expertise.
International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol.
Collegiate research university, located in the city of York, England. Established in 1963, the university has expanded to more than thirty departments and centres, covering a wide range of subjects.
UMass Amherst Mass Spectrometry Core Facility
Core offers instrumentation for characterizing elements and compounds across the entire mass range. Specialized mass spectrometers encompass variety of ionization techniques and separation devices to cover wide range of analytical capabilities.Facility accepts samples and will perform requested analysis.Offers training to conduct experimentation. Instruments include Bruker SolariX FT-ICR,Bruker MicroTOF II ESI,Bruker MicroFLEX MALDI,JEOL MStation sector with EI and FAB sources.
Open source data platform and multidisciplinary online repository where research groups and different organizations store and make public their datasets, managed by Scayle. Collection of public datasets are available through open.scayle.es and can be reused. NetFlow is network protocol developed by Cisco for collection and monitoring of network traffic flow data generated. Netflow datasets have been used to train machine learning models.
Spanish public university with campus in Leon and Ponferrada.
Software tool as tutorial for genome annotation using Augustus and PASA pipelines. Annotation of Hapalochlanea maculosa genome. Contains all scripts and code required to reproduce annotation of Blue Ringed Octopus genome.
Atlas includes co-registered templates constructed from MR images frequently used to characterize macroscopic brain structure T2/SPACE and T1/MP-RAGE, and diffusion tensor imaging template.
Expert curated resource that provides framework for integration of lipid and lipidomic data with biological knowledge and models. Provides curated knowledge of lipid structures and metabolism which is used to generate in silico library of feasible lipid structures. These are arranged in hierarchical classification that links mass spectrometry analytical outputs to all possible lipid structures, metabolic reactions and enzymes. Provides reference namespace for lipidomic data publication, data exploration and hypothesis generation.
Open access tool to convert, cross-match, and link various lipid annotations to tools supporting lipid ontology, pathway, and network analysis aiming systems wide integration and functional annotation of lipidome dynamics in health and disease.Data transfer hub to support integration of large scale lipidomics datasets.
Driving transcriptional programs using AutoEncoder based Relevance scores
Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data.
Clinical and Functional TRanslation of CFTR
International initiative led by team of researchers and clinicians and supported by the US Cystic Fibrosis Foundation that seeks to provide complete, advanced and expert reviewed functional and clinical information on CFTR mutations. Provides information for patients, researchers, and general public about specific variants. For each variant or variant combination included in database, website will provide information about whether variant or variant combination is CF-causing, and information about sweat chloride, lung function, pancreatic status, and Pseudomonas infection rate in patients in CFTR2 database with this variant or variant combination.
Integrated long non coding RNA knowledgebase to explore lncRNA biology in context of tissue of interest, disease of interest, or simply browse by names. Knowledgebase of tissue specific functional annotation and trait association of long noncoding RNA.
Software tool as bisulfite sequencing analysis platform. Offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation. Works with array of bisulfite sequencing data,including whole genome bisulfite sequencing, reduced representative bisulfite sequencing data, and targeted methylation sequencing data.
Mass spectrometry screening software for confirmation of target or suspect compounds, and for identification of unknown analytes. Advanced data mining and processing options let find all detectable compounds and confirm targets or identify unknowns. Results can be displayed using data reporting with either preconfigured reports that simplify basic analyses, or completely customized PDF reports.
Software package to quickly transform microscope images into quality figures. User friendly tool for creating and formatting scientific figures, can export files into popular softwares like Adobe Illustrator, Microsoft Powerpoint, and Inkscape.
Software tool to help humans interactively assess artifacts or situations against set of rules. Model consists of n-dimensional space and decision graph that guides users through that space using questions. Open source software tool for DataTags Decision Graph language, used to create questionnaires and tag spaces. Can be used to perform interactive interviews which yield concrete treatment that is both human readable and machine actionable. Models can also be visualized, and can be analyzed to find caveats or loopholes.
University of Hawaii at Manoa Cancer Center Genomics and Bioinformatics Shared Resource Core Facility
UHCC Genomics and Bioinformatics Shared Resource
University of Hawaii at Manoa UHCC Genomics and Bioinformatics Shared Resource
Core offers central service that uses genomic technologies combined with expert data analysis.Provides genomic analyses and bioinformatics as well as technical and scientific consultation,collaboration and initial data interpretation to all UH faculty with priority given to Cancer Center members with federal funding for cancer related projects. Offers expertise in molecular biology, genetics, genomics and bioinformatics, and can provide project planning, advice, and troubleshooting at all phases of the project.Genomic analysis services include DNA/RNA isolation, plating, and quality analysis, custom genotyping, Real-Time qPCR-based gene expression, copy number and methylation assays, pyrosequencing, Affymetrix and Illumina microarray based assays,Next Generation Sequencing on NextSeq500, iSeq100, NanoString nCounter analysis.
University of British Columbia NeuroImaging and NeuroComputation Centre Core Facility
UBC NeuroImaging-NeuroComputation Centre
University of British Columbia UBC NeuroImaging-NeuroComputation Centre
Core facility at Djavad Mowafaghian Centre for Brain Health located at University of British Columbia Hospital on Point Grey campus in Vancouver, BC. NINC offers access to advanced imaging systems and computational resources including confocal and two photon microscopes,live cell imaging, optical coherence tomography, training students and researchers in neuroscience research techniques.
Software tool to allow managing files with git, without checking file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space.
Web application to design gRNA sequences. Uses algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. Used for fast CRISPR target site identification. Enables designing of multiple libraries and creates genome scale libraries for several organisms in few hours.
DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data.
High Ambiguity Driven protein-protein DOCKing
Software tool as information driven flexible docking approach for modeling of biomolecular complexes.User friendly integrative modeling of biomolecular complexes.HADDOCK v 2.2 offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in user friendly interface.
Type 2 Diabetes Mellitus Associated Complex Disorders
Gene atlas of Type 2 Diabetes Mellitus associated complex disorders. Provides curated and integrated information about genes involved in development and progression of Type 2 Diabetes Mellitus, genes and pathways with evidence for role in diabetes under risk factors including obesity, diet, inflammation, stress and complex disorders that are associated with Type 2 Diabetes Mellitus including atherosclerosis, diabetic retinopathy, diabetic nephropathy, diabetic neuropathy, cardiovascular disease.
Manually curated database of single cell transcriptome for human diseases. scRNA-seq database derived from numerous human studies. Provides researchers with encyclopedia of biomarkers at level of genes, cells, and diseases.
Portal provides table of statistical hypothesis tests accessible to anyone wishing to do statistical calculations. All calculations available on this site are carried out using R statistics software.
Video capture software for Dino-Lite USB camera/microscopes. Works with Dino-Lite USB products.
COVID-19 Data Discovery from Clinical Records
Resource for questions and answers about COVID-19.Electronic health record data from leading medical centers to answer clinical questions related to COVID-19 while maintaining patient and institutional privacy. Data never leaves medical centers, only aggregate statistics are exchanged.
Sample size software for clinical trial, pharmaceutical, and other medical research where sample size calculation or evaluation is needed. Provides sample size tools for statistical test and confidence interval scenarios. Each tool has been validated with published articles and texts.
NEuroelectroMagnetic data Archive and tools Resource
Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource.
Copy Alterations Intuitive Rendering Navigator
Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions.
Web tool to choose representative subsets of data for use with replicates or groups of different sample sizes. Used to retain distribution information at single datum level and may be considered for standardized use in fair publishing practices.
Software R package to create and use Ensembl based annotation resources.
Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency.
Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings.
Inter-university Consortium for Political and Social Research
Web service of Inter-university Consortium for Political and Social Research. Self-publishing repository for social, behavioral, and health sciences research data. Used for deposit of replication data sets for researchers who need to publish their raw data associated with journal article so that other researchers can replicate their findings.
Provides data analysis software for spectroscopy and imaging. Includes FRETmatrix software, a|e software, DecayFit software and AniFit software.
Company provides analytics software tools for mass spectrometry. Proteomics and metabolomics software tools for mass spectrometry analysis.
Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource.
Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects.
Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications.
Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models.
University of Zurich Center for Microscopy and Image Analysis Core Facility
Center for Microscopy and Image Analysis
University of Zurich Center for Microscopy and Image Analysis
Advanced imaging facility providing various imaging techniques in microscopy. Focus is on techniques, instrumentation and know-how in electron and light microscopy including preparation.
Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies.
Warsaw International Institute of Molecular and Cell Biology Core Facility
International Institute of Molecular and Cell Biology in Warsaw
Core provides services in bioimaging and high throughput screening, structural biology, mass spectrometry, biomolecular analytics, cell biology and genomics.
University of Florida ICBR Cytometry Core Facility
Cytometry core offers project consulting, experimental design and optimization as well as data analysis services. Provides tools and staff expertise for both live and fixed cell analysis. Provides FACS ARIA and SONY SH800 sorters to help users sort cells of interest. Offers microscopes for self service users. Microscope brands include Leica SP5 Confocal, Nikon Multiphoton Confocal system, Nikon Live cell Imaging platform, Olympus spinning Disk Confocal instruments, Keyence BZX800.
University of Florida ICBR Bioinformatics Core Facility
University of Florida UF ICBR Bioinformatics
Core offers bioinformatics consulting and data analysis services to help researchers analyze and understand large data sets acquired from next generation sequencing and array based technologies.Bioinformatics staff members have extensive experience in bioinformatics, genomics, transcriptomics and translational informatics in plant, animal and microbial systems. Expertise includes big data analysis, statistical analysis, software development and high performance computing.
Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more.
Software tool for phylogenetic analysis under parsimony as well as extensive tree handling and diagnosis capabilities.
Visualization and Organization of Spectral Colour Data
Software R package for perceptual analysis, visualization and organization of spectral colour data. Software framework for parsing, analyzing and organizing colour from spectral data. Used for spectral and spatial analysis of color patterns.
Software R package contains functions to test for significant differences in coefficients of variation among multiple groups of observations.
Software R package to support functions and datasets for Venables and Ripley MASS. Used for statistical and graphical analysis of data.
Commercial organization provides software PRIMER and PERMANOVA for multivariate analysis. PRIMER v7 used for range of univariate, graphical and multivariate routines for analysing arrays of species by samples data from community ecology.​
National Cancer Institute Imaging Data Commons
Portal for finding and analyzing cancer imaging data. Part of Cancer Research Data Commons to support cancer imaging research. Provides cloud based access to medical imaging data and library of analytical tools and workflows to share, analyze, and visualize multi modal imaging data from both clinical and basic cancer research studies.
Cloud based data science infrastructure that provides secure access to cancer research data from NCI programs and key external cancer programs. Serves as coordinated resource for public data sharing of NCI funded programs. Users can explore and use analytical and visualization tools for data analysis. Enables to search and aggregate data across repositories including Cancer Data Service, Clinical Trial Data Commons, Genomic Data Commons, Imaging Data Commons, Integrated Canine Data Commons, Proteomic Data Commons.
Software package for education and data analysis. Used for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy.
Biosynthetic Gene clusters - Super Linear Clustering Engine
Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data.
System that consists of Application Programming Interface which controls access to information stored in database, and web interface that provides way of interacting with data stored in GenTaR database. Users can track production and phenotyping of different types of mutant allele. Allows consortia to follow progress made in characterising set of genes that they are interested in. To create new project or plan, or to view consortium gene list in GenTaR credentials to log into GenTaR are required. Project search box enables to look for projects working on specific gene by entering gene symbol or gene MGI accession identifier. Search results without logging in will only include public data. Otherwise application search results also include data for Protected and Restricted projects.
Software tool for genome annotation. Eukaryotic gene prediction tool focused on evidence supported by expressed sequences like transcripts and conserved proteins alignments. Can be used to reannotate genomes, to do comparative gene prediction and improve existing genome annotation. Can predict gene models with canonical and non-canonical splice sites.
Lightweight Analysis of Morphological Abnormalities
Open source pipeline to automatically identify embryo dysmorphology from 3D volumetric images. Automated image analysis for developmental phenotyping of mouse embryos.
Software statistical framework for reconstructing genomes from metagenome data. Open source software tool for accurately reconstructing single genomes from complex microbial communities.
Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.
Open source software tool for assigning objective taxonomic classifications to bacterial and archaeal genomes based on Genome Database Taxonomy. Designed to work with recent advances that allow metagenome assembled genomes to be obtained directly from environmental samples. Can also be applied to isolate and single cell genomes.
Web interface to Elastic Network Model that provides tool for computing, visualizing and analysing low frequency normal modes of macromolecule. Normal mode web server for protein movement analysis and generation of templates for molecular replacement with no upper limit to protein size that can be treated. Input of protein structure is in Protein Data Bank format.
RIKEN BDR Laboratory for Animal Resources and Genetic Engineering Core Facility
Laboratory for Animal Resources and Genetic Engineering
Riken Center for Biosystems Research Laboratory for Animal Resources and Genetic Engineering
Integrates advanced reproductive and developmental biology technologies. Environment for animal research experiments through innovative research in development of novel experimental animal models and related technical support activities. Manages SPF rodent facility at RIKEN Kobe Campus and accommodates variety of animal research needs, including animal material and resource support, technical training, and education for proper conduct of animal research. Provides established colonies of Soricomorpha species, suncus (Suncus murinus), metatherian species, gray short-tail opossum (Monodelphis domestica), and reptilian species, gecko (Paroedura picta) for prospective distribution services of these new resources to research community. Generates and distributes novel genetically engineered mice with domestic and international biomedical research community, as well as conducting original research projects in live imaging and analyses of early mouse development.
Silhouette images of animals, plants, and other life forms, available for reuse. Database stores reusable silhouette images and phylogenetic taxonomy of all organisms. Each image is associated with one or more taxonomic names and indicates roughly what ancestral member of each taxon looked like.
Neutron Scattering Length and Cross Sections
Web tool for thermal neutron cross sections. Data of scattering lengths and corresponding scattering and absorption cross sections of elements. Data go through element number 96Cm. Used for study of condensed matter structure and dynamics.
Cardiff University Central Biotechnology Services Core Facility
Core provides facilities including cell analysis and imaging, genomics and bioinformatics, proteins and diagnostics. Services include experimental design advice, sample preparation,data generation,data analysis.
Mobile genome analysis application, with capabilities to align reads, call variants, and visualize results entirely on iOS device. Optimized to run in mobile environment and has performance comparable to popular desktop genomics software.
Electronic database that tracks controlled substance prescriptions in state. PDMPs can provide health authorities timely information about prescribing and patient behaviors that contribute to epidemic and facilitate nimble and targeted response. This public tool is used for drug overdose monitoring from Centers for Disease Control and Prevention.
Portal about prospective investigations into risk factors for major chronic diseases in women. Nurses were selected as study population because of their knowledge about health and their ability to provide complete and accurate information regarding various diseases, due to their nursing education.The largest longitudinal study of women. Started in 1976, involving 275000 participants.
University of Florida ICBR Gene Expression and Genotyping Core Facility
University of Florida ICBR Gene Expression and Genotyping
Core provides services and consultation on Single Cell RNA-Seq, RNA-Seq, 16s metagenomics and Affymetrix gene expression arrays. High-throughput RNA-seq libraries, 16s libraries and sequencing capture libraries can be done by using Agilent Bravo robot. QuantiGene RNA Assays measure up to 80 gene targets directly with degraded and cross-linked RNA in FFPE tissues and blood, with no RNA purification required.BioRad QX200 AutoDG Droplet Digital PCR System provides absolute quantification of target DNA or RNA molecules with greater precision and sensitivity than qPCR, sensitivity off ddPCR System can facilitate expanded analysis of single cells. Genotyping services include fragment analysis using AB3730, 96 capillary technology, development of microsatellite libraries using Illumina sequence data, and genotyping using mouse tails or ear punches.
University of Florida ICBR Electron Microscopy Core Facility
University of Florida UF ICBR Electron Microscopy
ICBR Electron Microscopy supports researchers in visualizing microscopic structures through imaging projects and user training. Provided serives include room temperature and cryo transmission and scanning electron microscopy, confocal laser scanning microscopy, sample preparation and user training.
University of Florida ICBR Monoclonal Antibody Core Facility
University of Florida UF ICBR Monoclonal Antibody
Core develops new mouse monoclonal antibodies for investigators to use in basic and applied research.Provided services include immunization of mice, cell fusion, cell cloning, screening by ELISA and Western blot, monoclonal antibody production, purification and labeling, monoclonal antibody analyses such as antibody/antigen affinity measurements, epitope binning and identification of matched antibody pairs. Customer training on select self-service instruments is also offered.
Differential Methylation Analysis Package
Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity.
Software tool as snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.
National Collaborative on Childhood Obesity Research
Brings together Centers for Disease Control and Prevention, National Institutes of Health, Robert Wood Johnson Foundation, and U.S. Department of Agriculture to accelerate progress in reducing childhood obesity in America, to manage projects and reach common goals, to coordinate funding to make the most of available resources, to share insights and expertise to strengthen research. NCCOR focuses on efforts that have to benefit children, teens, and their families, and communities in which they live.
University of Florida ICBR Proteomics and Mass Spectrometry Core Facility
ICBR Proteomics and Mass Spectrometry Facility
UF ICBR Proteomics and Mass Spectrometry
Provides service and training in proteomics and mass spectrometry. Services in proteomics, differential proteomics, two dimensional difference gel electrophoresis, isobaric tags for relative and absolute quantitation, tandem mass tags, iodoTMT, stable isotope labeling with amino acids in cell culture, quantification of proteins by label-free LC-MS/MS, and analysis of protein post translational modifications and molecular weight determination. Core offers education, consultation, data processing and reporting, and support of grant application.
University of Florida ICBR NextGen DNA Sequencing Core Facility
University of Florida UF ICBR NextGen DNA Sequencing
Core provides platforms including Illumina NextSeq500 and MiSeq, HiSeq3000 and Pacific Biosciences SEQUEL system. Offers free consultation in sequencing technologies including read length, error rate, predominant type of error, data output/run, speed, cost. Services include de novo sequencing of whole genomes, targeted sequencing, transcriptome sequencing, chromatin immunoprecipitation sequencing, methylation analysis and metagenomics.
University of Heidelberg Interdisciplinary Neurobehavioral Core Facility
Interdisciplinary Neurobehavioral Core INBC
Multidisciplinary in vivo core facility equipped with equipment for detailed behavioral analyses and surgical procedures in context of mouse and rat models of neurological, cognitive and psychiatric disorders.Services include Behavioral analyses, Cognitive function,learning and memory, Sensory motor function, Emotional function and social interactions,Pain sensitivity tests, Disease models, Viral gene delivery, stereotactic and surgical manipulations, Optogenetics, In vivo electrophysiology.
Automated image analysis software package for accurately visualizing and quantifying biomarkers in tissue sections. Designed to meet workflow and throughput needs of research pathology, oncology, immunology. Used for tissue analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool as whole slide viewer for slides scanned with Vectra Polaris and Vectra 3 ., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software for acquisition, deconvolution, processing, analysis, and display of DeltaVision images. Used in DeltaVision OMX SR imaging system., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool for rapid high resolution structure determination from ideal protein fragments. Pipeline to determine crystal structures using molecular replacement with small fragments followed by density modification. It is available through CCP4.
Portal as central source of Australian open government data. Used to find, explore and reuse Australia public data. Anyone can access the anonymised public data published by federal, state and local government agencies, publicly funded research data and datasets from private institutions that are in public interest.
Repository for biodiversity data products managed by Department of Planning, Industry and Environment, New South Wales, Australia. It stores species sightings, systematic surveys, threatened biodiversity records and species names.
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 14, 2023. Repository of specimen in European Union associated with DISScO project.
Project Manager for Next Generation Sequencing
Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution.
Dartmouth Geisel School of Medicine Immunoassay and Flow Cytometry Core Facility
DartLab Immune Monitoring and Flow Cytometry Shared Resource
Dartmouth College Geisel School of Medicine DartLab
Geisel School of Medicine at Dartmouth DartLab Immune Monitoring and Flow Cytometry Shared Resource
Mount Desert Island Biological Laboratory Light Microscopy Core Facility
Core provides professional scientific expertise in light microscopy. Offers access to hardware and software as well as expert guidance at any step of imaging project, from experimental design to image analysis.Comprises eight microscope systems including two laser scanning confocal microscopes including one Olympus inverted confocal microscope system (FV1000) and one Zeiss inverted confocal microscope system (LSM-980) equipped with Airy scan 2 for super resolution and 2-photon technology for in-vivo deep imaging with temperature controlled chamber. One spinning disk confocal including Nikon inverted spinning disk microscope system with incubation chamber (Eclipse Ti with Yokogawa disk CSU-W1), two Zeiss widefield microscopes for brightfield and epifluorescence illumination (Zeiss Apotome and Zeiss Colibri), three macroscopes systems to observe large samples or complete model organisms in brightfield and epifluorescence including one Olympus stereomicroscope system (MVX10) and two Zeiss stereomicroscope systems (SteREO Discovery V12), fully automated and one AxioZoom V16 , fully automated with ApoTome attachment.
UMass Medical School Media Prep Core Facility
Provides custom made microbiological media for bacteria,yeast,C.elegans,Chlamydamonas research in liquid and agar forms. Common lab buffers and solutions are also available.
University of Michigan Medical School Bioinformatics Core
Core helps researchers identify and interpret patterns in RNA and DNA by placing sequencing data into biologically meaningful context. Services include experimental design, developing reproducible workflows, analyzing next-generation sequencing data, and supporting manuscript development/publication.
Rutgers New Jersey Medical School Molecular Resource Core Facility
Rutgers University at Newark Molecular Resource Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2022. Provides services in molecular biology with DNA sequencing, capillary and high throughput services, single cell sequencing services using 10X genomics and Drop-Seq platforms, Luminex, oligonucleotide synthesis (IDT), HPLC analysis and purification, real time PCR and others.
University of North Carolina at Chapel Hill Flow Cytometry Core Facility
UNC School of Medicine Flow Cytometry Core Facility
Core provides flow cytometry services to UNCCH research community as well as to others in Research Triangle Park area.Provides help with experimental design, sample acquisition, data analysis, and sorting, training to run analyzers independently at reduced cost, guidance about rigor and reproducibility in all aspects of experimental design, data acquisition, analysis and reporting.
University of Chicago Transgenic and ES Cell Technology Mouse Core Facility
Transgenic and ES Cell Technology Core (Mouse)
Transgenic Mouse and Embryonic Stem Cell Facility
Provides investigators with genetically manipulated mice through transgenic technology or embryonic stem cell manipulation. Provides fully operational construction and gene targeting service. Offers annual course in Mouse Handling and Breeding. Provides transgenic plasmid and BAC, CRISPR and TARGATT injections, ES Cell targeting, screening, culture and blastocyst injections, rederivation, breeding and mouse services and consultation on project development.
University of Kentucky College of Medicine Protein Core Facility
University of Kentucky Lexington UK Protein Core
Core provides nanobodies production for research as well as protein production, purification, and macromolecular characterization. Offers training on all instruments and equipment, as well as higher level of assistance when projects warrant.
University of Miami Center for Advanced Microscopy Core Facility
University of Miami Center for Advanced Microscopy (UMCAM)
Provides scanning electron microscopy services including biological tissues and cells,and particulate characterization.
Boise State University Biomolecular Research Center Core Facility
Designed to provide supportive environment for interdisciplinary research and education with opportunities for students and faculty members alike with focus on biomolecules study with emphasis on proteins and protein interactions. Provides instrumentation and facilities for characterization of biomolecules and their role in variety of biomedical and environmental processes. Partnerships between Center and Idaho-BRIN/INBRE, UI, ISU, Boise VA Medical Center, College of Idaho, and Northwest Nazarene University. BRC provides seminars, training workshops, and other networking opportunities.
University of Alberta Faculty of Medicine and Dentistry Transgenic Core Facility
Faculty of Medicine and Dentistry Transgenic Core
Core provides mouse transgenic and cryopreservation services including Sperm cryopreservation, Mouse in vitro fertilization, Mouse Rederivation, Transgenic Mouse Generation,DNA microinjection,CRISPR/Cas9-Mediated Genetically Engineered Mouse Production. Core equipment includes Hamilton Thorne Computer-Aided Sperm Analysis System,Sutter Xenoworks Micromanipulator,Sutter Xenoworks Digital Microinjector,Nikon TE2000 inverted microscope,MINC benchtop incubator,Leica M165 dissecting microscope.
University of Alberta Faculty of Medicine and Dentistry Lipidomics Core Facility
Faculty of Medicine and Dentistry Lipidomics Core
University of Alberta Lipidomics Core Facility
Core assists researchers in isolating and quantifying lipids and lipid related molecules in experimental samples.Core uses high performance liquid chromatography, gas chromatography, and fast protein liquid chromatography for both qualitative and quantitative analysis of lipids and lipoproteins, as well as other compounds by special request.Not-for-profit, pay-per-use facility, with graduated fee schedule based on client affiliation.
Massachusetts Institute of Technology Koch Institute Histology Core Facility
Koch Institute at MIT Histology Facility
Massachusetts Institute of Technology Koch Institute at MIT Histology Core Facility
MIT Koch Institute Histology Core Facility
Core assists in producing quality histological slides.Provides equipment and expertise to produce sections from frozen, paraffin-embedded, and resin-embedded tissues,routine hematoxylin and eosin stained slides, immunohistochemical and special stains.Registration to iLab required.
New York University Grossman School of Medicine Applied Bioinformatics Laboratories Facility
Core provides computational analysis for high throughput genomic data, including but not limited to, next generation sequencing data. Our mission is to accelerate scientific discoveries by guiding experimental design, performing robust data quality assessment, and carrying out comprehensive computational analyses. Registration to iLab required.
New York University Grossman School of Medicine Langone Health Cytometry and Cell Sorting Laboratory Core Facility
Provides access to flow cytometry and cell sorting technologies and instruments. If your research requires cytometric analysis, instruments acquire optical measurements using different lasers to detect fluorophores with high level of precision.
University of Alberta Faculty of Medicine and Dentistry Autoclave Repair Core Facility
Faculty of Medicine and Dentistry Autoclave Repair Core
Core provides on-site repair and maintenance services for autoclaves and laboratory washers.Core is also responsible, in collaboration with Environment, Health and Safety, for temperature probe calibrations of autoclaves located in FoMD enhanced biocontainment facilities.
University of Alberta Faculty of Medicine and Dentistry Workshop Core Facility
Faculty of Medicine and Dentistry Workshop
Core provides services, including repair of lab equipment and biosafety cabinets, metal and acrylic fabrication, woodworking, welding, machining, and calibration of pipets.
University of Alberta Faculty of Medicine and Dentistry High Content Analysis Core Facility
Faculty of Medicine and Dentistry High Content Analysis Core
Core houses equipment to manage and automate large-scale experiments in areas such as drug discovery and single cell analysis. From sample processing and liquid handling to quantitative analysis of sequencing, imaging, and fluorescent data, core offers high throughput methods for screening needs.
Collection and distribution of chimpanzee neuroimaging data and postmortem brain tissue. Portal to access chimpanzee brain atlas tools, data repository, bibliography of publications, educational information, and links to other chimpanzee brain resources and datasets on the Internet. Serves as repository for in vivo structural MRI scans of chimpanzee brains, in vivo and postmortem diffusion tensor images (DTI), as well as postmortem fixed and frozen brain specimens.
Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry.
Software R package to simplify creation of .xlsx files by providing high level interface to writing, styling and editing worksheets.
Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses.
Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data.
Server Program for Hydrogen Exchange Rate Estimation
Web service for Hydrogen exchange rate estimation. Predicts peptide amide hydrogen exchange rates using correction factors and empirical rates.
Poulsen IDP/IUP random coil chemical shifts
Web tool to calculate random coil chemical shifts for any protein sequence.
Software tool used for non destructive marking and linked results in ImageJ. Integrates image analysis across many images or stacks into single project file.
Research Diets | BioDAQ E3 food intake monitoring system
Research Diets BioDAQ (E3) food intake monitoring system
BioDAQ E3 by Research Diets Inc., features automated gate controller to program gate to open or close at specified time when specified amount of food or liquid is consumed.
Software tool for acquiring and analyzing assay data using MSD instruments. Version 4.0 includes features designed to increase efficiency and improve data quality. Tools for plate layout and experimental design simplify workflows. Enhanced functions for data analysis and visualization make generating reports and presentations easy.
Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data.
Software R tool that allows user to upload data and visualize it in user friendly interface.
University of Alberta Faculty of Medicine and Dentistry Flow Cytometry Core Facility
Faculty of Medicine and Dentistry Flow Cytometry Facility
Flow Cytometry Facility offers analytical flow cytometry, cell sorting and data analysis.Instruments include FACSArias, FACSCanto II, LSR-Fortessas, Attune NxT, and Amnis ImageStream mkII.
University of Chicago Functional Genomics Core Facility
Facility offers Next-Gen Illumina and Pacific Biosciences Sequencing and Library prep services, Micro-array Illumina genotyping and EPIC arrays services, Sanger DNA Sequencing, and Bioanalyzer/Fragment analyzer sample QC services. For Single Cell sequencing project Facility operates DROP-SEQ and 10X Genomics instrument., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University of Chicago Integrated Light Microscopy Core Facility
Offers microscopy imaging, including bright field color and DIC, fluorescence multi-dimension,TIRFM including bleaching, ablation, FLIM and high resolution, highspeed, high sensitivity, confocal, and physiologic techniques, STED, GSD3D, lightsheet selective plane illumination and lattice lightsheet structured illumination super resolution microscopy.
University of Chicago Advanced Electron Microscopy Core Facility
Offers instruments including Titan Krios with Gatan K3 detector, Aquilos Cryo-DualBeam system, Apreo Volume Scope Serial Blockface SEM, FEI Talos Cryo-EM.
University of Chicago Human Tissue Resource Center Core Facility
Coordinated, centralized, and dedicated program for procuring, processing, dispersing and assessing all types of biospecimens together with downstream histology services. CAP Accredited.
University of Alberta Faculty of Medicine and Dentistry Cell Imaging Centre Core Facility
Faculty of Medicine and Dentistry Cell Imaging Centre
Cell Imaging Centre provides services and training for imaging and analysis of live or fixed cells and tissues.Image acquisition equipment and expert consultation for experimental design related to light and electron microscopy are offered, with full technical assistance, from sample processing through image analysis.
University of Chicago Cellular and Tissue Based Processing cGMP Core Facility
Cellular & Tissue Based Processing cGMP Facility
Facility to manufacture cell based products and clinical grade reagents for treatment of patients on Phase I, II and III clinical trials. Cleanroom environment for manufacturing and preparing human cells, tissues and tissue based products. CAP Accredited.
New York University School of Medicine Langone Health Cryo-Electron Microscopy Laboratory Core Facility
New York University School of Medicine Langone Health Cryo-Electron Microscopy Laboratory
Shared resource hosting advanced cryo–electron microscopes fitted with direct detectors as well as equipment for sample preparation.
Comprehensive database of Short Tandem Repeat DNA profiles for all of ATCC human cell lines. ATCC data collection as part of continuing efforts to characterize and authenticate cell lines in Cell Biology collection.
Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays.
Online community for whole brain connectomics.Game like platform open to all to help crowdsource first complete wiring diagram of centralized brain. In fruit fly brain sliced and imaged by electron microscopy, we identified pieces of neurons by artificial intelligence. Players search for right pieces and put together 3D neurons that advance understanding of brain circuits. Enables circuit analysis by reconstructing and analysing connectome of mechanosensory neurons.
Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine.
Software tool for managing extraction of large volumes of data from primary sources among multiple users, and then reconciling differences between them. Designed for use in systematic review projects in academic context.
Platform of Biorelate to all auto curated data captured from millions of textual articles. Galactic lets you build intuitive queries and explore results through different views that best suit your research needs.Used by pharmaceutical and biotech companies to explore auto curated knowledge from millions of text sources, revealing hidden insights that might otherwise be lost.
Web service for all stages of manuscript writing and publication. Offers Translation services where manuscript will be converted to English by translators ,Publication Support services to assist with journal selection and journal submission, manuscript editing.
University of California at Los Angeles Lipidomics Lab Core Facility
Offers automated sample preparation and two distinct mass spectrometry platforms with services, ranging from shotgun lipidomics to isotope labeling and mathematical modeling of lipid flux parameters.Offers data analysis and consultation services to provide users with accurate analysis of lipid metabolic parameters.
Software tool as R script to provide function that takes two arguments: path to folder of plain text files named by their DOI, and output filename. For each file in folder, it searches for trial identifiers based on regex matching and writes CSV that contains all trial registration numbers and in case of ClinicalTrials.gov entries, whether they correspond to registry entry on ClinicalTrials.gov.
Genomic Annotation in Livestock for positional candidate LOci
Software R package developed for accurate annotation of genes and quantitative trait loci located in regions identified in common genomic analyses performed in livestock, such as Genome Wide Association Studies and transcriptomics using RNA-Sequencing. Allows graphical visualization of gene and QTL annotation results, data comparison among different grouping factors like methods, breeds, tissues, statistical models, studies and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens.
Software graphical gene set enrichment tool for animals and plants. Graphical web application to gain insights from gene sets. Features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for retrieval of pathway diagrams and protein-protein interaction networks.
Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis.
South Dakota State University; South Dakota; USA
Public land grant research university in Brookings, South Dakota. Founded in 1881, it is the largest and most comprehensive university and the oldest continually operating university in South Dakota.
Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein.
Coalition for Publishing Data in the Earth and Space Sciences
Project to connect Earth and space science publishers and data facilities to help translate aspirations of open, available, and useful data from policy into practice. Community driven project to implement common policies and standards to accelerate scientific discovery by promoting open and FAIR data.
Canadian data repositories project. Data submitted to FRDR is housed on Compute Canada managed infrastructure at University of Victoria, BC or at University of Waterloo, ON. Research data submitted to FRDR does not leave Canada.Most of metadata is shared with Globus, running on Amazon Web Services in the USA, to be indexed and made available for discovering datasets. Certain metadata fields, for example, submitter contact information, are not shared with Globus.Larger uploads are made using Globus, only public metadata is stored there.
Software tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.
Collection of mutation data in cancer, with focus on copy number abnormalities for all types of human malignancies.
Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported.
Software tool to convert data files from Mac program such as Igor and Pulse or John Dempster CDR, WinTida, to ABF formats and analyze them with Mini Analysis Program.
Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system.
Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus.
dkNET service that assists researchers in preparing authentication plans for cell lines or antibodies to comply with NIH Submission Policy when submitting proposal or publication. Automated tool to enable researchers to create customized report based on key biological resources they plan to use. These customized reports provide additional information such as known problems with particular cell line or antibody.
dkNET service that provides detailed overview of individual research resources along with citation metrics from biomedical literature, community feedback and alerts, information about who used resource, and information about what resources have been used together. The only integrated data set and analytics platform combining Research Resource Identifiers (RRIDs), text mining and data aggregation. Users can identify key resources while also tracking resource use and performance.
Software Python package to collect, organise and manage neuroscience data in Brain Imaging Data Structure format.Software package for Windows 10 to collect, organise and manage neuroscience data in BIDS format.
Software tool for mass downloading of historical clinical trial data from ClinicalTrials.gov.
Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set.
Phase Holographic Imaging | HoloMonitor live cell imaging and analysis system
HoloMonitor live cell imaging and analysis system
HoloMonitor live cell imaging and analysis system by Phase Holographic Imaging PHI AB. Contains small, digital live cell, quantitative phase imaging microscope HoloMonitor M4 designed to operate constantly inside incubator and HoloMonitor cell imaging software App Suite or Hstudio to continuously monitor and quantitatively analyze both individual cells and cell populations over time without any cellular labels or stains. Microscope can operate in cell incubator, hypoxia chamber or on lab bench.
Perkin Elmer | VICTOR3 multilabel plate reader
Versatile plate reader that can be used to measure fluorescence intensity from both top and bottom of plate, colorimetric absorbance and luminescence.
Remote Assessment of Disease And Relapses
Open source mobile health platform for collecting, monitoring, and analyzing data using sensors, wearables, and mobile devices. Enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access. Allows study participants to share their health data with clinicians and researchers in secure way.
Free curriculum, resources, and research for those considering incorporation of remote health monitoring.
UCSD based bioinformatics lab composed of several projects in different biomedical disciplines. Established in 2008 as Neuroscience Information Framework and has since expanded to include broader field of biomedical research. Leader in developing and providing novel informatics infrastructure and tools for making data FAIR: Findable, Accessible, Interoperable and Reusable. FAIR Data informatics laboratory develops SciCrunch.org platform.
Software suite to enable discoverability of datasets. Enables submission of metadata on datasets to DataMed. Has core set of elements, which are generic and applicable to any type of dataset, and extended set that can accommodate more specialized data types. Platform independent model developed by NIH BD2K bioCADDIE project for DataMed Data Discovery Index prototype being developed. Also available as annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex.
Electron Microscopy Public Image Archive
Public archive for raw electron microscopy image data. Resource for raw 2D electron microscopy images. Used to browse, upload and download raw images to build 3D structure. Provides access to raw data to facilitate methods development and validation. Complements Electron Microscopy Data Bank where 3D volumes are stored, and uses Aspera platform for data transfers.
TRAjectory-based Differential Expression analysis for SEQuencing data
Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data.
Cellular Indexing of Transcriptomes and Epitopes by Sequencing Count
Software python package that allows to count antibody TAGS from CITE-seq and/or cell hashing experiment. Software tool that allows to get UMI counts from single cell protein assay. Used to count (UMI counts) antibody-derived-tags (ADTs) or Cell Hashing tags (HTOs) in raw sequencing reads and build count matrix.
Software tool as scalable GWAS Association Testing pipeline for biobank scale datasets.
Software tool as scalable GWAS Quality Control pipeline for biobank scale datasets.
Software tool to distinguish virulent and temperate phage derived sequences in metavirome data with deep learning approach. Used to identify virome sequences as temperate phage derived or virulent phage derived fragments.
Open source software platform for studying fruit fly brain function, and for investigating fruit fly brain disease models that are highly relevant to mechanisms of human neurological and psychiatric disorders. Collaborative ecosystem for accelerating discovery of functional logic of fruit fly brain. Includes FlyBrainLab and BrainMapsViz. Stores and integrates fruit fly brain research data. Repository of tools and methods to build, emulate and compare fruit fly brain models in health and disease. Open framework for fruit fly brain data processing and model execution.
University of Queensland School of Biomedical Sciences Imaging and Analytics Core Facility
Provides microscopes for life science research, including number of confocals, widefield systems, slide scanners, and analysis packages. Provides analytic instruments such as flow cytometers, imaging systems, and PCR equipment among others. Our team consists of experienced biologists and are available to help you with experiment building, troubleshooting, and data analysis.
MRI Compatible and Customizable Microdrive Design for Neuroscience Research
Open source designs for customizable, MRI compatible microdrive capable of positioning probes including stimulating electrodes, recording electrodes, drug cannulae, or optogenetic fibers within brain. Design integrates cranial implant, penetration grid for guiding probes, and microdrive body assembly with actuators. Used by neuroscience community related to electrical microstimulation, neuronal recording, and local drug delivery.
An antibody manufacturer based in Aurora, Colorado.
Commercial antibody company that focuses on the development, production, purification, conjugation, and commercialization of antibodies.
Commercial antibody company that uses proprietary selection criteria and selects antibodies to be sold under their name.
A manufacturer of early discovery research products including antibodies, recombinant proteins, ELISA kits, second step reagents and other life sciences products.
Open software pipeline for analyzing RNA-seq to predict neoepitopes derived from small to large sized indels. Used for identifying indel derived neoantigens using RNA-Seq data.
Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software.
Project to provide data on genome and epigenome of human lung to facilitate research efforts of investigators studying diseases of lung including COVID-19.Collaboration among multiple groups at University of California including Center for Epigenomics, Gaulton lab and Sun lab at UCSD Department of Pediatrics. This work is conducted as part of LungMAP consortitum.
Software tool as deep collaborative learning with application to study of multimodal brain development. Uses deep network to represent original data and then seeks their correlations, while also linking data representation with phenotypical information.
Software tool as parallel processing framework for large scale generation of secondary RNA structures and folding statistics for transcriptome of any species.
Research infrastructure for the EU Human Brain Project. Provides digital tools and services which can be used to address challenges in brain research and brain inspired technology development. Digital research infrastructure, created by EU-funded Human Brain Project, that gathers extensive range of data and tools for brain-related research. EBRAINS will capitalize on the work performed by the Human Brain Project teams in digital neuroscience, brain medicine, and brain-inspired technology.You can share your neuroscience data, models and software.
Software reproducible, continuously updating platform which benchmarks performance of spike sorting codes across large curated database of electrophysiological recordings with ground truth. Website and open source computing framework for evaluating and comparing spike sorting algorithms for neurophysiology data analysis. Project of Center for Computational Mathematics at Flatiron Institute.
EIDORS:Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software
Free software algorithms for forward and inverse modelling for Electrical Impedance Tomography (EIT) and Diffusion based Optical Tomography, in medical and industrial settings, and to share data and promote collaboration between groups working these fields.
Software tool that integrates histology reconstruction, MRI co-registration, and manual segmentation tools in easy-to-use and intuitive interface. Permits real-time interaction with complex and large histology datasets during co-registration steps of histology reconstruction. Software tool for interactively mapping 2D and 3D molecular and anatomical histology into Common Coordinate Frameworks. Has simple, interactive registration workflows that connect user images with CCFs.
Open source and multi-platform pinning software tool to facilitate mapping samples into common 3D spaces. Desktop application based on 3D Slicer that displays Allen Institute for Brain Science CCF or MNI atlas, color segmented by structure of brain, and allows user to create planar polyline annotation to facilitate mapping samples into corresponding atlas.
Semi-Manual Alignment to Reference Templates
Software tool that extends WholeBrain framework in R for segmenting and registering experimental images to Allen Mouse Common Coordinate Framework (CCF). Streamlines processing of large volumetric LSFM datasets and solves issues with non-uniform morphing across anterior-posterior axis with interactive “choice game.” Accounts for duplicate cell counts in adjacent z images and presents new ways to easily parse apart and interactively visualize final mapped datasets.
Describes number, types, and positions of cells in all areas of mouse brain. Provides densities and positions of all excitatory, inhibitory and neuromodulatory neurons, as well as astrocytes, oligodendrocytes and microglia in each of brain regions defined in Allen Mouse Brain Atlas. Users can download cell numbers for statistical analysis, cell positions and types for modeling and visualizing brain areas. Underlying workflow uses imaging data from Allen Institute Common Coordinate Framework to generate cell positions and assign their type using API for data access.
Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas
Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform.
Cloud comparison for Transcript-Annotation data analysis pipeline
Cloud comparison for transcript annotation data analysis pipeline. Workflow for comparing transcriptome annotation pipelines.
Software tool for rapid and comprehensive quality assessment of raw sequence reads. It generates comprehensive list of QC statistics, including ancestry and contamination estimation.
Neural Module by Axion BioSystems Inc, provides simplified approach to set up, execution and analysis of neural experiments. Enables Maestro Pro and Edge to record and analyze key parameters of neural network function, including activity, synchrony, and network oscillations.
Standalone application for 3D visualisation and manipulation of mathematical field models. Cmgui is part of Continuum Mechanics, Imaging, Signal processing, System identification mathematical modelling environment. Generic open source modelling and visualisation package used to enable researchers to visualise biomedical images alongside dynamic geometry fields from computer models of cells, tissues and organs.
Software tool as molecular structure drawing application by ACD Labs. Allows user to Draw chemical structures, reactions, and schema, and access variety of graphical tools and templates, Generate names from molecular structure and vice versa, Calculate molecular properties from chemical structure, Create professional reports, presentations, and publication ready figures, Communicate scientific information with clarity and ease.
An R package that automatically identifies and extracts indicators of transparency (data availability, code availability, statements of conflicts of interest, statements of funding, statements of protocol registration) from TXT and PMC XML versions of published research articles in biomedicine.
Gene Expression Deconvolution Interactive Tool
Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices.
Electrophysiological recording software for use with RHD USB Interface Board by Intan Technologies.
Software tool as SPM extension for longitudinal and repeated measures data. Modelling of longitudinal and repeated measures neuroimaging data.Implemented as Matlab toolbox for SPM8 or SPM12.
Software tool to model population dynamics as discrete, sequential events that occur according to probabilities that are random variables following user-specified distributions.Simulation of deterministic forces as well as demographic, environmental and genetic stochastic events on wildlife populations.Can model many of extinction vortices that can threaten persistence of small populations.
Software tool to provide parameter estimates from marked animals when they are re-encountered at later time, to create population size estimates. Used for analysis of data from marked individuals.
Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Open source software application that enables services for online surveys. Provides advanced support for all steps of web survey process. Conduct research and analysis from beginning to end.
University of Nottingham NASC Nottingham Arabidopsis Stock Centre
NASC-Nottingham Arabidopsis Stock Centre
University of Nottingham NASC-Nottingham Arabidopsis Stock Centre
National and international arabidopsis germplasm resource.Stores over million genotypes in physical stocks servicing worldwide Arabidopsis community in more than 50 countries. Stocks are provided under identical cost recovery conditions to academic and commercial researchers. Non-transgenic stocks are sent gratis to K-17 institutions and in special cases. Provides seed and information resources to International Arabidopsis Genome Programme and research community. Maintains accessions of Arabidopsis thaliana (and small number of other related species), including Characterized lines, Mapping populations, and Insertion lines. You may browse or search catalog.
Auditory and visual stimulus delivery library for psychoacoustics in Python.
Open source acquisition program, based on Python programming language, for setting up BrainVision actiCHamp amplifier and storing data.
Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models.
Software tool as automated biomarker that outputs score linked to likelihood person sufferring from arteriolosclerosis based on brain MRI data and basic demographic information. MRI data processing pipeline and classifier are packaged into software container.Users do not need to perform any image processing, and are only required to install Singularity to run ARTS.
Microbiome Simulation via Generative Adversarial Network
Software tool as deep learning simulation framework for simulating realistic microbiome data. Can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from it.
Software R package as functions for inference of ploidy from Genotyping By Sequencing data, including function to infer allelic ratios and allelic proportions in Bayesian framework.
Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework.
Web app to help assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. Done by implementing one time-series model (ARIMA), one compartmental models (basic SIR), and six classical growth models, which all yield satisfactory prediction results in the past and current pandemics at early stage.
Software R package for extensive customization of violin plots. Violin plot is combination of box plot and kernel density plot.
Spatial Dependence: Weighting Schemes and Statistics
Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree.
Software R package as scale functions for visualization. Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.
Software R package to draw geographical maps.
Baylor College of Medicine Optical Imaging and Vital Microscopy Core Facility
Optical Imaging & Vital Microscopy (OiVM)
Core provides instrumentation, imaging and image analysis tools.Ddicated to vital and intravital imaging of cellular processes within cells, intact tissue explants, developing embryos and functioning organs within the live animal. Our users are focused on a variety of applications such as understanding cell migration, optimizing angiogenic therapies, how blood flow influences development and cancer, immune cell recruitment, stem cell-niche interactions and cancer metastasis.
University of Colorado Boulder Chemical and Bio. Engineering instrument and electronics Core Facility
Chemical and Bio. Engineering instrument and electronics
Colorado University at Boulder Chemical and Bio. Engineering instrument and electronics Core Facility
Provides mechanical and electrical design and fabrication services at CU Boulder.Provides solutions for instructional and research needs for any department or college. Collectively comprised of machine shop and electronics shop, both of which are located in basement level of Jennie Smoly Caruthers Biotechnology Building.
University of Colorado Boulder High Performance Computing PetaLibrary Core Facility
Colorado University at Boulder High Performance Computing PetaLibrary Core Facility
High Performance Computing - CU PetaLibrary
University of Colorado at Boulder High Performance Computing PetaLibrary Core Facility
Provides service to support storage, archival, and sharing of research data. Available at subsidized cost to any researcher affiliated with University of Colorado Boulder.
University of Colorado Boulder Earth Systems Stable Isotope Lab Core Facility
Colorado University at Boulder Earth Systems Stable Isotope Lab Core Facility
Earth Systems Stable Isotope Lab (CUBES-SIL)
University of Colorado at Boulder Earth Systems Stable Isotope Lab Core Facility
Designed to measure relative abundance of stable isotopes of light elements and molecules.
University of Colorado Boulder Organic Geochemistry Laboratory Core Facility
Colorado University at Boulder Organic Geochemistry Laboratory Core Facility
University of Colorado at Boulder Organic Geochemistry Laboratory Core Facility
Shared analytical facility for multidisciplinary and collaborative research in fields as diverse as biogeochemistry, geobiology, astrobiology, environmental microbiology, paleoceanography, paleoclimatology, and energy, among others.Focuses on extraction, purification, separation, and chemical and isotopic characterization of organic molecules extracted from environmental and culture samples.
University of Colorado Boulder BioCore Core Facility
Colorado University at Boulder BioCore Core Facility
University of Colorado at Boulder BioCore Core Facility
Purpose is to connect MCDB, EBIO, and IPHY researchers to campus research resources.
University of Colorado Boulder CU Thermochronology Research and Instrumentation Lab Core Facility
Colorado University at Boulder CU Thermochronology Research and Instrumentation Lab Core Facility
CU Thermochronology Research and Instrumentation Lab (CU-TRaIL)
University of Colorado at Boulder CU Thermochronology Research and Instrumentation Lab Core Facility
Fully equipped (U-Th)/He thermochronology facility.
Colorado University at Boulder Soft Materials Research Center X-Ray Diffraction Facility Core Facility
Soft Materials Research Center X-Ray Diffraction Facility
Provides cutting edge capabilities for probing large lengthscale structures such as polymers, biological macromolecules, meso- and nano-porous materials, and molecular self-assemblies.Techniques that can be applied to study materials include SAXS, GISAXS, WAXS, and GIWAXS. The 30W Xenocs Genix 3D x-ray source and state-of-the-art Dectris Eiger R 1M detector provide an excellent way to probe almost any material of interest. In-situ x-ray studies may be carried out using temperature controlled sample holders in both SAXS and GISAXS modes..
University of Colorado Boulder Raman Microspectroscopy Lab Core Facility
Colorado University at Boulder Raman Microspectroscopy Lab Core Facility
University of Colorado at Boulder Raman Microspectroscopy Lab Core Facility
Core research facility housed in Department of Geological Sciences for fast, non-destructive characterization and chemical imaging of diverse materials spanning minerals (thin sections and powders), biological samples, fluids, dissolved gases, and much more.
Colorado University at Boulder Facility for Electron Microscopy of Materials Core Facility
Facility for Electron Microscopy of Materials CU FEMM
Facility features electron microscopes housed in vibration, static-free, and temperature-controlled environment.
Colorado University at Boulder Materials Instrumentation and Multimodal Imaging Core Facility
Materials Instrumentation and Multimodal Imaging Core (MIMIC) Facility
Facility provides specialized services for assessment of material properties, chemistry and structure across multiple length scales with emphasis on assessment of biological tissues, biomaterials, and biologically inspired systems.
Colorado University at Boulder BioFrontiers Next-Gen Sequencing Facility Core Facility
BioFrontiers Next-Gen Sequencing Facility
Core instruments include Agilent Bioanalyzer 2100 system provides sizing, quantitation and quality control of DNA, RNA and proteins, Illumina MiSeq sequencer, able to sequence prepared Illumina DNA or RNA libraries at low- to mid- output (0.75 to 13 Gbp per run), Illumina NextSeq sequencer capable of sequencing Illumina DNA or RNA libraries, QuantStudio 6 Real-Time PCR uses fluorescence detection method for quantitative and qualitative analysis of nucleic acid sequences including gene expression, regulation and variation, Qubit Fluorimeter 3.0 capable of measuring DNA or RNA concentrations with high accuracy.
Colorado University at Boulder Flow Cytometry Shared Core Facility
Provides instruments including BD Accuri C6 Cytometer with Automated, multisampler/Flow Cytometer,BDFACSCelesta Flow Cytometer Analyzer,BD FACSAria Fusion Cell Sorter.
Colorado University at Boulder Macromolecular X-ray Crystallography Core Facility
Macromolecular X-ray Crystallography Core
Provides resources for crystallization and structure determination of biological macromolecules and complexes. Supports research in the Department of Biochemistry. We are happy to extend our help to researchers from the broader CU community and to researchers outside the university, if time and availability allow us too.
Colorado University at Boulder Nuclear Magnetic Resonance Spectroscopy Core Facility
Nuclear Magnetic Resonance Spectroscopy Facility
Core serves research needs of entire campus community as well as outside research entities. Facility maintains a variety of NMR spectrometers at variety of magnetic fields to support research needs.
Software R package implements functions for helping in process of disease patterns analysis by means of principal components. These include component visualization, interpretation and stability analysis.
Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.
Software R package provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. Used for isobaric tagged mass spectrometry data visualization, processing and quantitation.
Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations.
Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance.
alpha-helix coordinate frame simulation framework
Source code for alpha-helix simulation framework written in Matlab. Specifically tested on Talin-1 Rod Domain.
Cellular Indexing of Transcriptomes and Epitopes Fuse
Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data.
Software tool as MSS-MLE calculator for Luria–Delbrück fluctuation analysis.
Software tool to simplify and to speed calling and genotyping structural variants for short reads. Improves specificity by removing many spurious alignment signals that are indicative of low level noise and often contribute to spurious calls.
MSI applications for interactive analysis in MITK
Software tool enabling interactive signal processing and visualisation of mass spectrometry imaging datasets. Extends open source Medical Imaging and Interaction Toolkit. Designed to enable multi modal 2D registration and 3D MSI reconstruction.
10x Genomics | Chromium Controller Genetic Analyzer
Genetic analyzer, referred to as Chromium Controller for combining large partition numbers with a diverse barcode library to generate >100,000 barcode-containing partitions. Chromium Controller runs low- and standard-throughput assays. It does not run high-throughput assays.Chromium Controller uses advanced microfluidics to perform single cell partitioning and barcoding in a matter of minutes. Powered by Next GEM technology, the Chromium Controller enables integrated analysis of single cells at massive scale.
Modular stereomicroscope with 6.3:1 zoom with 7-position ratchet stop enables repetitive inspection and measurements at a specific zoom position.
Thermo Fisher | 384-well formats Thermo MultiDrop Combi with 50 plate feeders
Reagent dispenser that handles a wide selection of plates and volume range and provides fast dispensing and high-throughput operation. It dispenses over a 0.5 to 2500�L range, ensuring reproducible assay data and accommodates microplates from 6 to 1536 wells and plate heights of 5 to 50mm.
Thermo Fisher: Applied Biosystems | ABI 2700 GeneAmp PCR System
PCR bechtop thermal cycler measuring at only 36 x 21 x 22 cm and several machines can be stored and operated side-by-side.
Thermo Fisher: Applied Biosystems | ABI 5500xl 5500xl
Genetic Analyzer with two FlowChips, embedded quality controls, user workflows, and project scalability. It can be used for whole exome sequencing or targeted resequencing with up to 96 barcodes.
Thermo Fisher: Applied Biosystems | ABI 5800 Mass Spectrometer
AB Sciex 5800 MALDI TOF/TOF Mass Spectrometer
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8th, 2023. Mass spectrometer for biomarker discovery, MALDI mass spectrometry imaging, and protein identification.
Thermo Fisher: Applied Biosystems | ABI 5300 Genetic Analyzer
Genetic Analyzer used for human identification applications.
Thermo Fisher: Applied Biosystems | ABI 7500 Real Time PCR System 7500FAST
This Real-Time PCR System offers you high performance, multicolor real-time PCR.
Thermo Fisher: Applied Biosystems | 7300 Real-Time Instrument
Fast Real-Time PCR System uses fluorescent based PCR chemistries to provide quantitative detection of nucleic acid sequences using real-time analysis and qualitative detection of nucleic acid sequences using end-point and dissociation-curve analysis.
Hematology System is a bench-top analyzer designed for medium- to large-volume laboratories. This flow cytometry-based system uses light scatter, differential white blood cell (WBC) lysis, and myeloperoxidase and oxazine 750 staining to provide a complete blood cell count, a WBC differential, and a reticulocyte count. A cyanide-free method is used to measure hemoglobin colorimetrically.
Thermo Fisher: Affymetrix | 3000 7G Microarray Scanner
Microarray scanner that is an extension of the GeneChip Scanner 3000 (GCS 3000) series that allows you to scan next-generation higher-density arrays, including SNP arrays with up to 900,000 SNPs, tiling arrays for transcription and all-exon arrays for whole-genome analysis.
Thermo Fisher: Affymetrix | 428 Array Scanner
428 array scanner can analyze any microarray on a glass slide (25x75x1mm) that has been probed with DNA labeled with Cy3, or Cy5 as well as other common fluorescent dyes.
This mass spectrometer can be used for structural analysis of organic and inorganic compounds, protein identification studies, synthetic peptide validation experiments, small molecule and polymer analysis, and post source decay experiments.
Thermo Fisher | GeneChip 3000 7G Microarray Scanner
Thermo Fisher: Applied Biosystems | ABI 5500 Genetic Analyzer
Genetic Analyzer that provides a robust, next-generation sequencing platform and gives you the choice to optimize for turnaround time or throughput.
Thermo Fisher: Affymetrix | GeneAtlas Microarray Scanner
GeneAtlas System utilizes the array strip format to provide simplified hybridization, robustness that protects precious samples, and array processing with common microwell-based labware.
Thermo Fisher: Affymetrix | GeneTitan Microarray Scanner
GeneTitan Microarray Scanner integrates hybridization, washing, and imaging to provide automated array processing.
Model_Number_GeneChip Hybridization Oven 645
Thermo Fisher: Affymetrix | GeneChip Hybridization Oven 645 RNA Analyzer
Hybridization Oven with temperature and rotation control for hybridization of as many as 64 GeneChip cartridges at one time. The oven can be configured for 110 or 220V operation.
Model_Number_GeneChip Hybridization Oven 640
Thermo Fisher: Affymetrix | GeneChip Hybridization Oven 640 RNA Analyzer
GeneChip Hybridization Oven 640 automates your hybridization process for GeneChip brand probe arrays.
Agilent | 100 Automated Disintegration Apparatus
Automated Disintegration Apparatus provides compliant approach to disintegration testing. Used for drug dose disintegration testing. Reciprocating drive system, water bath, and heater/circulator are incorporated into single instrument. Apparatus is available in three basket model and comes complete with accessories required to perform standard United States Pharmacopeia disintegration test.
Agilent | 1100 High Performance Liquid Chromatography System
1100 HPLC system is an efficient mixing and pulse-free pump action liquid chromatography system and advanced diagnostics and data analysis software.
Model_Number_1220 Infinity II Analytical-Scale LC
Agilent | 1220 Infinity II Analytical-Scale LC Purification System
Analytical-Scale LC Purification System provides sample purification for applications from routine analysis to specialized workflow solutions.
Agilent | 1260 Infinity II Amino Acid Analysis System
Amino Acid Analysis System provides complete solution for automated HPLC amino acid analysis.
Model_Number_1260 Infinity II Analytical-Scale
Agilent | 1260 Infinity II Analytical-Scale LC Purification System
This system purifies multi milligram quantities of materials, handling flow rates between 0.1 and 10 mL min with 2.1 and 10.0 mm id columns.
This LC System performs routine HPLC analysis in analytical and QA QC labs.
Agilent | 1260 Infinity II Bio-Inert LC System
Bio-Inert LC System analyzes large biomolecules in biological samples.
This HPLC offers choice of modules for analytical HPLC and entry level UHPLC, delivering performance, reliability, and robustness.
Agilent | 1260 Infinity II GPC/SEC System
Bechtop thermal cycler. The small foot-print means that this device makes good use of available bench space, allowing this device to fit into any laboratory it will even fit easily on the researcher's personal work bench. The desktop footprint measures only 36 x 21 cm and it stands 22 cm above the desk. Because the air-flow for the cooling system is located at the back of the unit, several machines can be stored and operated side-by-side, with no space between, for efficient space usage.
Model_Number_1260 Infinity II Manual Preparative
Agilent | 1260 Infinity II Manual Preparative LC System
This binary gradient system delivers dynamic flow rates up to 50 mL min at 420 bar, equipped with manual injection valve.
Model_Number_1260 Infinity II Multi-Method
Agilent | 1260 Infinity II Multi-Method System
This Multi-Method System offers maximum system utilization with minimum manual interaction.
Model_Number_1260 Infinity II Multidetector Bio-SEC
Agilent | 1260 Infinity II Bio-SEC Multi-Detector System
Bio-SEC Multi-Detector System can be used to determine protein shape and size.
Model_Number_1260 Infinity II Method Development
Agilent | 1260 Infinity II Method Development System
Method Development System provides robust and technology for everyday automated HPLC method development challenges.
Agilent | 1260 Infinity II Prime LC System
Prime LC System provides sample purification for applications from routine analysis to specialized workflow solutions.
Model_Number_1260 Infinity II High-Temperature GPC
Agilent | 1260 Infinity II High-Temperature GPC System
High-Temperature GPC System provides information about engineering polymers.
Model_Number_1260 Infinity II Preparative LC/MSD
Agilent | 1260 Infinity II Preparative LC/MSD System
Preparative LC/MSD System increases daily sample throughput, maximizes purity and minimizes re analysis.
Model_Number_1260 Infinity II Preparative LC
Agilent | 1260 Infinity II Preparative LC System
Preparative LC System is used for automated sample injection.
Model_Number_1260 Infinity II SFC/UHPLC Hybrid
Agilent | 1260 Infinity II SFC/UHPLC Hybrid System
This hybrid system performs supercritical fluid chromatography SFC and ultrahigh performance liquid chromatography UHPLC.
2D-LC System separates co eluting compounds, achieves highest peak capacity and makes buffer separations compatible to MS detection.
Model_Number_1290 Infinity II Analytical-Scale LC
Agilent | 1290 Infinity II Analytical-Scale LC Purification System
This purification system detects UV or MS and clusters of multiple fraction collectors.
SFC System provides sample purification for applications from routine analysis to specialized workflow solutions.
Model_Number_1290 Infinity II Autoscale Preparative LC/MSD
Agilent 1290 Infinity II Autoscale Preparative LC/MSD System
Agilent Autoscale Preparative LC/MSD System enables automated transfer of purification methodologies from analytical to preparative scale purification.
Model_Number_1260 Infinity II Multi-Detector GPC/SEC
Agilent | 1260 Infinity II Multi-Detector GPC/SEC System
The Multi-Detector GPC/SEC System delivers accurate, absolute molecular weights and sizes, and can be used to analyze polymers.
Model_Number_1290 Infinity II Autoscale Preparative LC
Agilent | 1290 Infinity II Autoscale Preparative LC System
Agilent Autoscale Preparative LC System enables automated transfer of purification methodologies from analytical to preparative scale purification.
Model_Number_1290 Infinity II High-Throughput
Agilent | 1290 Infinity II High-Throughput System
This high-throughput system utilizes autosampler capacity of up to 16 cooled microplates to achieve highest analysis speeds.
Agilent | 1290 Infinity II GPC/SEC System
GPC SEC analysis solution that is capable of both analytical or microscale operation.
Model_Number_1290 Infinity II HDR-DAD Impurity Analyzer
Agilent | 1290 Infinity II HDR-DAD Impurity Analyzer System
HDR-DAD Impurity Analyzer System detects and quantifies every component in your sample.
This LC System provides sample purification for applications from routine analysis to specialized workflow solutions.
Model_Number_1290 Infinity II Method Development
Agilent | 1290 Infinity II Method Development System
UHPLC method development instrument provides maximum flexibility and performance to solve complex method development challenges.
Model_Number_1290 Infinity II Method Transfer
Agilent | 1290 Infinity II Method Transfer System
Method Transfer System delivers similar retention times and peak resolution for methods that were developed on legacy HPLCs or UHPLCs from other vendors.
Model_Number_1290 Infinity II Multi-Method
Agilent | 1290 Infinity II Multi-Method System
Multi-Method System is used for system utilization and automation with multiple method UHPLC capabilities for different users at same system.
Model_Number_1290 Infinity II Preparative LC
Agilent | 1290 Infinity II Preparative LC System
Preparataive LC System offers automated sample injection and fraction collection, smooth control of LC valves, and access to analytical and preparative columns.
Model_Number_1290 Infinity II Online SPE
Agilent | 1290 Infinity II Online SPE System
Online SPE System automates solid phase extraction to enrich analytes, remove matrix components or lower detection limits.
Agilent | 1290 Infinity II Preparative LC/MSD System
Preparative LC/MSD System enables high throughput purification and delivers high quality compounds.
This Bioanalyzer Laptop is used with Agilent Bioanalyzer to ensure processes are optimized.
Agilent | 240 AA Atomic Absorption System
Combines rugged and hardware with easy to use software, making it best for low throughput laboratories.
Agilent | 240Z AA Atomic Absorption System
Atomic Absorption System is used for detection limits and analyzes difficult matrices.
Agilent | 280-DS Mechanical Qualification System
Mechanical Qualification System measures physical parameters of dissolution apparatus and enables the physical qualification of any dissolution apparatus.
Agilent | 280FS AA Atomic Absorption System
Atomic Absorption System determines the concentration of all elements from a single aspiration.
Discontinued Superseded by 4210 MP AES System.
Agilent | 280Z AA Atomic Absorption System
Agilent | 400-DS Dissolution Apparatus 7
Dissolution apparatus 7 is used for small volume dissolution testing of combination drug products.
Agilent 4150 Tapestation Genetic Analyzer
System is automated electrophoresis platform for nucleic acid sample quality control. Allows analysis of DNA and RNA samples for up to 16 samples per run. Used for quality control of RNA and DNA samples in next-generation sequencing, biobank, or vaccine development workflows.
High sensitivity atomic emission spectrometer. MP-AES Instrument utilizes microwave plasma and as it runs on air instead of combustible gases, it can be installed in either centralized laboratory or remote location. Detection limits down to ppb levels and no sample pretreatment necessary.
Agilent | 240FS AA Atomic Absorption System
MP-AES provides detection limits and large linear dynamic range.
Handheld FTIR is used for mobile nondestructive testing and analysis of polymers, coatings, composites, bulk material, cleaning verification, and historical artifacts and artwork.
Agilent | 4500 Portable FTIR Spectrometer
Portable FTIR spectrometer supports efforts associated with on spot analysis of incoming materials and outgoing finished products in chemical, food and polymer industries.
Agilent | 4500a Forensics FTIR Analyzer Package
FTIR Analyzer Package identifies liquid or solid substances with little or no sample preparation.
Micro GC System is used for gas analysis and offers comprehensive system control, data acquisition and report generation..
Micro GC Biogas Analyzer is used to analyze biogas and related sample streams and provide results.
Agilent | 5100 Inductively-Coupled Plasma-Optical Emission Spectrometer
Agilent 5110 ICP-OES Instrument enables synchronous radial and axial measurements and runs samples up to 55% faster using 50% less argon.
490-Mobile Micro GC System allows analysis results to be viewed in full or reported in true/false.
This gas chromatograph delivers information with modular design and MEMS technology based components.
Fragment Analyzer System uses automated parallel capillary electrophoresis to redefine bounds of nucleic acid QC analysis
Capillary electrophoresis instrument that can separate up to 48 or 96 samples in parallel. Enables DNA quality control for NGS libraries, gDNA, cfDNA, and large DNA fragments. RNA quality can be checked by this system where small RNA, total RNA, and mRNA vaccines are applicable for RNA integrity, sizing, and quantification analysis.
Portable FTIR analyzer from Agilent 5500 Series with compact dimentions are small-sized, mid-infrared region spectrometers designed to provide capabilities of larger, traditional FTIR systems.
Agilent | 55B AA Atomic Absorption System
55B AA Atomic Absorption System is used for flame atomization
Agilent 5800 Inductively Coupled Plasma - Optical Emission Spectrometer
Spectrometer to identify spectral interferences that can affect accuracy, providing recommendations allowing to quickly select the best wavelength and preventing unnecessary remeasurement.Uses embedded sensors, algorithms and diagnostics to identify problems, maximize uptime and minimize the number of samples you need to remeasure.
Agilent | 5975C Gas Chromatography Mass Spectrometer
Agilent 5975C inert Mass Selective Detector delivers better MS resolution and the lowest mass deviation available and offers superior sensitivity and spectral integrity.The 5977 is the new Agilent GC/MSD platform and replaces the 5975C.
ICP-OES Instrument is used to run samples with Synchronous Vertical Dual View (SVDV) and captures both the axial and radial views of the plasma in one reading.
Fragment Analyzer System allows you to separate 12 samples in parallel in as little as 15 minutes.
Agilent | 6230B Time of Flight (TOF) LC/MS
Time of Flight LC/MS gives you full spectrum data for screening, profiling and identification of small molecules, large biologic compounds, and everything in between.
GC/MSD is used for environmental, chemical, petrochemical, food, forensic, pharmaceutical, and material testing.
Agilent | 6470 Triple Quadrupole Liquid Chromatography Mass Spectrometer System
Triple quadrupole LC/MS system for commercial, regulatory, life sciences, and research applications. It has Agilent Jet Stream ion source and curved geometry collision cell. It detects target compounds at low levels in diverse matrices, while achieving wide linear dynamic range.
Triple Quadrupole LC/MS detects target compounds at low levels in diverse matrices, while achieving wide linear dynamic range.
Q-TOF LC/MS is used for analysis for applications in the pharmaceutical industry as well as life sciences and governmental agencies.
6495C triple quadrupole LC/MS system is used for peptide quantitation and applications that require ppt sensitivity.
Agilent | 6530BA Quadrupole Time of Flight Liquid Chromatography Mass Spectrometer
Agilent 6530A Quadrupole Time of Flight LC/MS system analyzes low molecular weight compounds and delivers accurate mass quantitation.
Atomic force microscope with top-down scanning, environmental and temperature control, and modularity. The universal microscope base permits easy integration with an environmental chamber or an inverted optical microscope.
Agilent | 6538 Quadrupole Time of Flight Mass Spectrometer
Quadrupole time of flight mass spectrometer suitable for applications in the pharmaceutical industry as well as life sciences and governmental agencies.
THIS RESOURCE IS NO LONGER AVAILABLE. Documented on August 4th, 2023. Mid-range Quadrupole Time-of-Flight liquid chromatography mass spectrometer designed for untargeted sample analysis, it enables broad screening, comprehensive profiling, identification of unknowns, mass accuracy, and isotopic fidelity.
AdvanceBio LC/Q-TOF is used to access information at intact protein level, automatically confirm sequence through peptide mapping, and understand PTMs.
Agilent 6560 Ion Mobility Quadrupole Time-of-Flight Liquid Chromatography Mass Spectrometer
Ion Mobility LC/Q-TOF delivers unrivaled separation and selectivity by combining chromatography, ion mobility, and mass spectrometry.Quadrupole Time-of-Flight liquid chromatography mass spectrometer that combines chromatography, ion mobility, and mass spectrometry. The system has electrodynamic ion funnel technology and an attractive low field drift tube design.
LC/Q-TOF enables comprehensive workflows in metabolomics research, food safety, food authenticity, and environmental screening.
This iFunnel Q-TOF LC/MS used for proteomics research allows you to acquire fragment data faster and reduces duty cycle substantially.
7000D GC TQ is used to create and validate many now standard GC MS MS methods.
Agilent 7010B Triple Quadrupole GC MS can produce at least 20 times as many ions as previous generation.
Agilent | 7100 Capillary Electrophoresis System
Capillary Electrophoresis System offers fast separations with efficiency and resolution for analytical challenges.
Agilent | 7650A Automatic Liquid Sampler
Automataic Liquid Sampler provides fast and precise injections for Agilent GC and GC MS systems.
Agilent | 7693A Automatic Liquid Sampler
Headspace Sampler includes Automatic Leak Check, which ensures each vial is leak free prior to analysis.
GC/Q-TOF delivers full spectrum, resolution, and mass data with wide range for identifying and quantifying GC amenable compounds.
Discontinued. ICP-MS Instruments offer matrix tolerance and unmatched interference removal and deliver fast, accurate, and consistently reproducible results.
Discontinued. Has interference removal utilizing ORS3 cell that removes spectral interferences using He mode, reaction mode using hydrogen cell gas and 3rd cell gas line for other reaction gases, cool plasma capability also delivers ionized elements in high-purity materials in matrices, built-in tuning and method templates for common semiconductor applications, including collision and reaction mode and cool plasma, lower heat output and reduced exhaust vent flow with cooling air flow management system, uses ICP-MS MassHunter software platform, and compact benchtop design.
Modular system is used for manual or automated dissolution testing.
System provides capabilities for wide range of application areas, meeting regulatory and SOP needs for small to medium sized labs.
Sample Prep Workbench provides consistent precision and eliminates manual errors in procedures such as dilutions, internal standard additions, and derivatization.
Single quadrupole instrument is used for fragment spectra for volatile compounds. It uses ChemStation open access software.
7890 GC System features accurate temperature controls, precise injection systems, and high performance Electronic Pneumatic Control (EPC) modules for good retention time and area count repeatability.
Agilent | 78905975 Gas Chromatograph Mass Spectrometer
Single quadrupole mass spectrometer is used for fragment spectra for volatile compounds. It uses ChemStation open access software.
Quadrupole mass spectrometry system provides low detection limits, dynamic range, and helium collision mode.
Quadrupole ICP mass spectrometer simplifies routine ICP MS analysis and provides matrix tolerance, range, and control of polyatomic interferences.
Agilent | 8255 Nitrogen Chemiluminescence Detector
Nitrogen Chemiluminescence Detector produces linear and equimolar response to nitrogen compounds.
UV-visible spectrophotometer with diode-array technology, small footprint, prealigned deuterium and tungsten lamp light sources.
Agilent | 8700 LDIR Chemical Imaging System
Chemical Imaging System provides highly automated approach for obtaining high definition chemical images of constituents on surface.
Agilent | 8355 Sulfur Chemiluminescence Detector
Chemiluminescence Detector is used to simplify operation of centrifuge while maximizing productivity.
Triple Quadrupole ICP-MS enables MS MS operation, providing control of reaction processes in the ORS3 collision and reaction cell.
Agilent | 850-DS Dissolution Sampling Station System
Sampling Station System offers latest capabilities for centralizing laboratory workflow of sample transfer, filtration and collection.
Gas Chromatography System to deliver fast and accurate results with flexible configuration capabilities to address specific analysis demands.Gas chromatograph uses advanced electronic pneumatic control modules and high performance GC oven temperature control, which lead to extremely precise retention time reproducibility, the basis for all chromatographic measurement.
Triple Quadrupole ICP-MS offers range of configurations to cover applications from routine contract analysis to advanced research and high performance materials analysis.
Agilent | AA Duo Atomic Absorption System
AA Duo atomic absorption spectrometer is used for simultaneous operation of flame and graphite furnace.
Micro GC System is used to analyze gas samples.
ADM Flow Meter measures gas streams with composite gas composition.
GC System is used for routine GC analysis and addresses wide range of routine GC application areas.
Microplate Handler is a storage and handling system used for integration with variety of laboratory devices.
Dual channel blood alcohol analyzer delivers reproducible and court defendable data. Analyzer combines power of 8890 GC with either Agilent 8697 headspace sampler or Agilent 7697A headspace sampler, offering rapid cycle time to maximize sample throughput with no carryover.
Agilent | Artisan Link Pro Special Staining System
In vitro diagnostic device automates slide based special stains on formalin fixed, paraffin embedded tissue sections.
Automated Liquid Handling Platform facilitates processing of high numbers of microplates in small footprint.
Real-time PCR System is used for amplification, detection, and data analysis.
Gauge Controller automatically identifies active gauge connected and is compatible with FRG 7xx, PVG 5xx, PCG 75x and CDG 500 series of active gauges.
Discontinued. UV-Vis System is used in a range of applications and provides exceptional resolution and unmatched linearity.
Agilent | Array Scanner XTI Array Scanner
XTI Array Scanner provides automated cellular imaging and analysis and facilitates automated, quantitative cellular and subcellular imaging and analysis.
Workstation is built on Bravo automated liquid handling robot preconfigured for library prep and target enrichment using Next-Generation Sequencing protocols. Workstation modules add microplate handling. Intuitive Agilent VWorks software enables setup of preprogrammed protocols and allows users to create custom protocols., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Agilent | BIO-DIS Reciprocating Cylinder Dissolution Apparatus
Dissolution Apparatus is used for imitating pH changes that occur in body.
UV-Vis System offers photometric performance together with measurement capabilities and multizone multicell.
UV-Vis System is used for analyzing biotechnology samples with minimal sample preparation.
UV-Vis NIR System is used for materials science research and performs powerful analysis.
Agilent | Cary 60 Fiber Optic UV Dissolution System
Cary 60 UV Vis Spectrophotometer provides optical transmission and reproducibility capabilities and extended linear photometric range for fiber optic analysis.
Agilent | Cary 60 Multicell UV Dissolution System
Multicell UV Dissolution System takes samples simultaneously and reads each one sequentially.
Discontinued. UV-Vis System is used in a range of applications and provides exceptional resolution and unmatched linearity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Agilent | Cary 630 FTIR Spectrometer Benchtop System
FTIR Spectrometer Benchtop System provides quantitative and qualitative information for routine analysis of solids, liquids, and gases.
UV Visible NIR spectrophotometer is used for photometric performance and materials characterization spectroscopy.
Discontinued Agilent line of Cary 600 series infrared microscopy Cary 610 FTIR and chemical imaging systems Cary 620 FTIR.
Agilent | Cary 7000 Universal Measurement Spectrophotometer (UMS)
Cary 7000 UMS collects UV Vis NIR spectra, characterizes optical components and delivers solutions for research, development and QA QC in optics, thin films coatings, solar and glass.
Agilent | Cary 8454 UV-Vis Diode Array System
Agilent Cary 8454 UV-Visible spectroscopy system includes UV-Visible instrument based on leading LC photodiode array detector technology. System measures full spectrum, in as little as 0.1 seconds, has high throughput, low photometric noise, excellent wavelength accuracy and reproducibility, and excellent photometric stability. Spectrophotometer optical system is dual lamp set up consisting of deuterium-discharge lamp for ultraviolet wavelength range, and tungsten lamp for visible and short wave near-infrared wavelength range, from 190 to 1100nm.
Agilent | Cobalt Insight100 Series Aviation Security
Insight100M system screens all container types and provides detection with ultra low false alarm rate for non metallic containers.
UV-Vis Spectrometer is used to measure life-science samples without sample photodegradation.
Model_Number_Agilent_8890_Gas Chromatography
8890 Gas Chromatography based CO-CO2 analyzers for analysis of permanent gases. System can be selected from standard or custom analyzer configurations to addresses specific analytical requirements.
Agilent | Cobalt Insight200M Aviation Security - Bottle Screener for Liquid, Aerosols & Gels
Airport security liquid explosive detection system LEDS screens all common container types with low false alarm rate.
Agilent | Cary Eclipse Fluorescence Spectrophotometer
Fluorescence spectrophotometer gives you superior sensitivity, renowned reliability and enhanced sampling capabilities.
Agilent | Flame Photometric Detector Plus (FPD Plus)
Flame Photometric Detector Plus utilizes photomultipliers, proprietary deactivation treatments and other design enhancements to help its lower MDLs in sulfur or phosphorous modes.
Agilent | GC/MS SureTarget Water Pollutants Screener
SureTarget Water Pollutants Screener provides fast data review and reporting of water pollutants and screening for unknown compounds.
Agilent | Cary 8454 UV Dissolution System
UV Dissolution System analyzes single and select multicomponent products using diode array technology.
Agilent | Dako Omnis Solution for IHC & ISH
Omnis Solution for IHC & ISH enables you to run IHC, IF, FISH and CISH simultaneously, each with combination of reagents.
Agilent | Dako CoverStainer Automated H&E Staining
CoverStainer Automated H&E Staining automates H&E process from baking, dewaxing and staining through to dehydrated, coverslipped and dried slide.
Greenhouse Gas Analyzer helps industrial customers monitor GHG emissions.
Agilent | EPA 200.8 ICP-MS Water Analyzer
ICP-MS Water Analyzer streamlines steps taken to put ICP MS instrument in production and implements regulated water analysis.
Headspace Sampler is used for chemical performance over wide range of analyses without analyte degradation or loss.
Agilent | HLD BR15 Bench Helium Leak Detector
Bench Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems.
Agilent | HGC-536 Portable Gauge Controller
HGC-536 gauge controller displays vacuum readings in either numbers or easy-to-read graphs and helps baseline pumps by providing pump down graphics.
Agilent | HLD BD15 Bench Dry Helium Leak Detector
Bench Dry Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems.
Agilent | HLD MD15 Mobile Dry Helium Leak Detector
Mobile Dry Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems.
Agilent | HLD BR30 Bench Helium Leak Detector
Agilent | HLD MD30 Mobile Dry Helium Leak Detector
Agilent | HLD MR15 Mobile Helium Leak Detector
Mobile Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems.
Agilent | HLD BD30 Bench Dry Helium Leak Detector
Hybridizer is used for slide based fluorescence FISH and chromogenic CISH in situ hybridization.
Agilent | HLD MR30 Mobile Helium Leak Detector
Agilent | Infinity 1260 Liquid Chromatography System
A liquid chromatography system is an HPLC and UHPLC system that is compatible with legacy LC instrumentation and modular.
Notebook PC ensures that all Aria processes can be easily integrated into existing facilities and workflows without disrupting existing computing resources.
Agilent | HLD PR02 Portable Helium Leak Detector
Portable Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems.
Agilent | HLD PD03 Portable Dry Helium Leak Detector
Portable Dry Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems.
Gas Chromatography System eliminates column maintenance and changes columns and ensures reproducible chromatography and allows for higher throughput in laboratory.Gas chromatographer delivers reproducible and court defendable data.Provides fast, accurate and reproducible analysis of Class 1 and Class 2A B solvent content in pharmaceutical products.
Agilent | Micro-ECD GC Selective Detector
DC detector provides trace level analysis of halogenated organic compounds and aromatic pollutants.
Agilent | mRP-C18 High-Recovery Protein Column
High-Recovery Protein Column reduces or eliminates strong adsorption of proteins.
Agilent | MLC400 Laser Based Illumination System
Laser Based Illumination System is used for fluorescence and confocal microscopy research applications.
Agilent | ISO 17294 ICP-MS Water Analyzer
ICP-MS Water Analyzer streamlines steps taken to put ICP MS instrument in production and implement regulated water analysis.
Agilent | NovoCyte Advanteon Flow Cytometer
Advanteon Flow Cytometer accommodates multicolor flow cytometry assays and provides flexibility of 1, 2, or 3 laser options.
Agilent | Multiple Affinity Removal Spin Cartridge Mouse 3
Multiple Affinity Removal Spin Cartridge removes three interfering high abundance proteins from mouse plasma samples.
Auto Sampler Systems provide high sample capacity and greater automated sample preparation capability to optimize lab productivity.
PHD-4 Sniffer detects small leaks in objects that have slight helium air pressure inside.
Agilent Mx3005P is used for gene expression analysis, microarray data validation, SNP genotyping, pathogen detection, DNA methylation analysis, and chromatin immuno-precipitation studies.
Agilent | Positive Pressure Manifold 48 Processor (PPM-48)
Pressure Manifold 96 Processor is used to create consistent gas flow through every channel and ensures reproducibility from cartridge to cartridge.
Agilent | Positive Pressure Manifold 96 Processor (PPM-96)
Positive Pressure Manifold 96 Processor provides consistent gas flow for up to 96 cartridges in applications such as SPE and SLE.
Oligo Pro II System delivers accurate purity assessments of ssDNA and ssRNA oligonucleotides without use of dyes.
Agilent | RapidFire 365 High-Throughput Mass Spectrometry System
Mass Spectrometry System replaces HPLC with automated solid phase extraction SPE to increase throughput of LC MS analyses.
Agilent | PlateLoc Thermal Microplate Sealer
Pressure Manifold 48 Processor accommodates deep well, assay, PCR, and compound storage microplates with variety of seals for different applications.
Agilent | RapID Raw Material ID Verification System
Raw Material ID Verification System extends high throughput spectroscopic analysis through clear packaging to nontransparent and colored containers.
Agilent | Resolve Handheld Through-Barrier Identification System
Resolve handheld Raman spectrometer enables rapid identification of explosives, narcotics, toxic industrial chemicals, chemical warfare agents and other materials through sealed, opaque containers.
Agilent | Reciprocating Holder Dissolution Apparatus 7
Dissolution Apparatus 7 is used for automatic dissolution testing of dosage forms requiring a change of media, smaller volume or more vigorous agitation.
Agilent | RPS-1401/301 Roots Pumping System
Roots Pumping System is used for optimum system integration and enables continuous operation and monitoring of vacuum systems.
Agilent | RGC-100 and RGC-150 Rough Gauge Controllers
Rough Gauge Controllers are used for general vacuum measurement in rough vacuum range, monitoring forelines, chamber evacuation, and crossover to high vacuum pumps.
Agilent | RPS-751/301 Roots Pumping System
Seahorse XFe24 Analyzers measure OCR and ECAR of live cells in a 24-well plate format.
Seahorse XF HS Analyzer measures OCR and ECAR of live cells in 8 well miniplate format.
Agilent | RPS-1001/301 Roots Pumping System
Agilent | Seahorse XF Imaging and Normalization System
Seahorse XF Imaging and Normalization System acquires brightfield and fluorescence images, calculates cell number in each well and transfers images and cell counts into Wave 2.6 software.
Agilent | SureScan Dx Microarray Scanner
SureScan Dx microarray scanner system analyzes many genomics and cytogenetics microarrays.
Seahorse XFe96 Analyzer measures OCR and ECAR of live cells in 96 well plate format.
Agilent | TPS-compact Turbo Pumping System
TPS-compact Turbo Pumping System is used for pump operation, control, and recording of system parameters.
Standardize your data acquisition and analysis by using the Agilent validated TapeStation Laptop together with the TapeStation instrument. The laptop comes with the TapeStation Software and required drivers pre-installed and offers maximum convenience and security.
Agilent | Sulfur and Nitrosamine Analyzers
8890 Gas Chromatography system with Sulfur or Nitrosamine detectors for detection of trace level contaminants often found in refinery and petrochemical products. System can be selected from standard or custom analyzer configurations to addresses specific analytical requirements.
Agilent | TPS-mobile Turbo Pumping System
TPS-mobile Turbo Pumping System enables pump operation, control, and recording of system parameters.
Agilent | SureCycler 8800 PCR Thermal Cycler
PCR Thermal Cycler runs thermal cycling techniques including time and temperature increments, touchdown PCR, and temperature gradients.
Agilent | TPS-flexy Turbo Pumping System
TPS-flexy Turbo Pumping System is used for pump operation, control, and recording of system parameters.
Agilent | TwisTorr 304 FS AG Rack Controller
TwisTorr 304 FS Rack Controller drives the pump in real time and adapts speed and power as required by gas flow, gas type, pressures, and other factors such as cooling.
TPS-mini Tubro Pumping System is used for turbo pump operation, control, and recording of system parameters.
Agilent | TwisTorr 74 FS AG Rack Controller
TwisTorr 74 FS AG Rack Controller adapts speed and power as required by gas flow, gas type, pressures, and other factors such as cooling.
Agilent | TwisTorr 74 FS onboard controller
TwisTorr 74 FS onboard controller to read pressure via active gauges.
Agilent | TwisTorr 304 FS Onboard Controller
TwisTorr 304 FS Onboard Controller is used in analytical instruments such as mass spectrometry and microscopy systems and can reach low base pressures in experiments.
Agilent | TRS100 Quantitative Pharmaceutical Analysis System
Quantitative Pharmaceutical Analysis System enables whole tablet or capsule content uniformity and polymorph screening for pharmaceutical finished product testing and formulation development.
Agilent | TwisTorr 305 FS Remote Controller
Remote control unit drives pump in real time and adapts speed and power as required by gas flow, gas types, pressures, and other factors such as cooling.
Agilent | TwisTorr 84 FS onboard controller
TwisTorr 84 FS onboard controller is used to read pressure via active gauges.
Agilent | TwisTorr 84 FS-AG Rack Controller
TwisTorr 84 FS drives the pump in real time and adapts speed and power as required by gas flow, gas type, pressures, and other factors such as cooling.
Agilent | Vaya Raman Raw Material Identity Verification System
Handheld spectrometer increases raw material identity verification throughput and reduces need for sampling.
Vac Elut SPS 24 Manifold processes up to 24 SPE cartridges simultaneously.
This Gauge Controller accepts any of three different kinds of gauge cards which operate Agilent vacuum gauges.
Agilent | VS C15 Component Leak Detector
Modular leak testing package is used for applications in which leak detector components are more or less permanently mounted to system.
ISS | Alpha Science Corporation ChronosFD
ChronosFD offers all the benefits of a complete time-resolved fluorometer.
Beckman Coulter | analytical ultracentrifuges (Beckman XL-I and XL-A) XL-A
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 5th,2023. Centrifuge with in-solution characterization of proteins, oligomers, aggregates, particles, colloids, and small structures. It allows for In-solution testing in native conditions. It measures the relative change in the distribution of molecular weights, providing an efficient way to measure heterogeneity, stoichiometry and self-associating systems.
Automated DNA fragment analysis system for high-throughput workflows such as genotyping, PCR amplicons, restriction digests, and microsatellite analysis. Runs thousands of DNA fragment samples per 24 hours. Provides high resolution of separation and reliable sizing information for DNA fragment sizes between 35 and 20000 base pairs. Low sample volume and short run time abilities for rapid qualification analysis of DNA fragments.
Agilent | xCELLigence RTCA eSight Real-Time Cell Analyzer (RTCA)
Real-Time Cell Analyzer enables comprehensive insight into cell health, cell behavior, cell function and cell biology processes.
SCIEX | Triple Quad 5500 LC-MS/MS System
Triple Quad 5500 LC-MS/MS system delivers high levels of sensitivity and robustness for matrices.
Thermo Fisher: Applied Biosystems | 4700 Proteomics Analyzer
Applied Biosystems 4700 Mass Spectrometer
MALDI tandem time-of-flight mass spectrometer that provides a new level of productivity in high-resolution proteome analysis and complex systems biology. It can be used for carbohydrate, lipid, proteins, peptides, and other biological component analysis.
BridgePath | Arcturus PixCell II Laser Capture Microdissection Microscope
Arcturus (PXL-200) PixCell II LCM, built around an Olympus IX50 inverted microscope, uses a near-infrared diode laser and a CapSure Macro/HS LCM Cap to capture target cells. When the laser is fired, dimples are created in the cap. These dimples wet a matrix which attaches to a targeted cell, which can be lifted off the glass slide without taking other cells around it. Once the cells are captured they can be used for various experiments such as amplification of DNA or RNA from the isolated cell(s) for analyses. During microdissection, the laser never touches or damages any of the cells. Laser capture microdissection (LCM) is a technique that provides a method to obtain targeted cells from a multi-cell population.
Thermo Fisher: Applied Biosystems | 492 Protein Sequencer
Protein Sequencing System that cleaves N-terminal amino acids from protein/peptide chains and analyzes the resulting phenylthiohydantoin (PTH)-amino acid residues. It is composed of four integrated modules: the Procise Protein Sequencer, the Model 140C Microgradient Delivery System, the variable-wavelength UV detector, and a computer.
Art Robbins | Crystal Gryphon Liquid Crystal Polymer Setup System
Gryphon LCP is a setup system for Lipidic Cubic Phase sandwich plates and bicelle assays as well as traditional protein crystallography plates. A dedicated syringe based LCP head dispenses the protein, and a 96 head dispenses the buffer solutions. A 96 well sandwich plate can be sealed in less than 2 minutes. An optional non-contact dispenser can be added at any time to set up vapor diffusion sitting drop and hanging drop plates. The Crystal Gryphon is a small, fast and option for setting up all of your crystal plates. The Crystal Gryphon fits into tight lab spaces and tight lab budgets. The 96-channel positive displacement head quickly fills screen reservoirs and protein wells. The head has no disposable tips, so the cost of operation and environmental waste is minimized. The 1-channel non-contact dispenser quickly aspirates and dispenses your proteins allowing your plate to be sealed without evaporation being a problem. This dispense head is designed specifically to handle proteins, features flow-through washing and positive displacement aspiration, to handle all of your proteins.
Oxford | Asylum Research MFP 3D Atomic Force Microscopes
Asylum Research MFP-3D family of AFM's extend beyond basic topography measurements with diverse set of available accessories designed to enhance capabilities of the AFM. These include accessories for making nano-electric measurements, for example conductivity and piezoelectric response, measurements under magnetic fields, measuring nanomechanical properties, and controlling the temperature and humidity.
Thermo Fisher: Applied Biosystems | ViiA
ViiA 7 System provides enhanced fluorescence detection and enables more accurate and sensitive data analysis.
Thermo Fisher | B-Pure Water Purification System
Barnstead Pure Water Purification System
Water purification system that is used for pretreatment or deionization. A design provides the ability to add additional single, double or half size holders when need arises.
Ark Scientific | Hyb4 Microarray Hybridization System
Ark Scientific Hyb4 Microarray Hybridization System automates hybridization temperature cycles with efficient agitation and post-hybridization washes of DNA, oligo or protein microarrays.
Baker | EdgeGARD VF Laminar Flow Workbench
EdgeGARD VF provides protection for samples and work procedures where product protection and particulate control are required.
Baker's EdgeGARD HF provides HEPA-filtered air and product protection and precise control of airflow volumes and velocities.
Thermo Fisher | Barnstead LabTower RO Water Purification System
This water purification system converts tap water into reverse osmosis RO water with integrated 100L storage and allows user to read parameters with ultra modern controller.
Thermo Fisher | Attune Nxt Flow Cytometer
2020 Attune NxT Flow Cytometer makes multiparametric flow cytometry available to both new and experienced researchers.
BD Biosciences | Accuri C6 Plus Flow Cytometer
Compact 11 x 14.75 x 16.5-inch footprint, light weight of 30 lb, and operational simplicity, benchtop flow cytometer is equipped with blue and red laser, two light scatter detectors and four fluorescence detectors with optical filters optimized for detection of many popular fluorochromes, including FITC, PE, PerCP-Cy5.5 and APC. Data are digitally collected over wide dynamic range.
BD Biosciences | FACSAria IIu High Speed Cell Sorter
High Speed Cell Sorter's primary function is to examine complex populations of cells and yield pure populations of cells.
Flexible flow cytometry platform that has up to ten lasers and a modular architecture and a combination of detection capabilities, hands-on controls, and high performance. This resource is discontinued.
Thermo Fisher | Barnstead LabTower TII Water Purification System
This water purification system converts tap water into purity water with complete solution integrating purification and tank.
BD Biosciences | FACSAria Aria I Flow Cytometer
BD FACSAria cell sorter incorporates a fixed-alignment cuvette flow cell that can detect up to 13 colors, for a total of 15parameters.
FACScan system analyzes cells as they pass through a focused laser beam, can be used for routine research applications, immunophenotyping, and DNA cell-cycle analysis.
BD Biosciences | FACS Celesta Flow Cytometer
BD FACSCelesta flow cytometer makes multicolor flow cytometry more accessible and enables insights in cell analysis.
Cell sorter that uses principles of flow cytometry to collect only cells of interest from heterogenous suspension. Can be configured with up to three lasers and eight parameters.
Beckman Coulter | Biomek 3000 Liquid Handler
Biomek 3000 Laboratory Automation Workstation
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 28,2024. Biomek 3000 workstation is single head instrument with series of interchangeable tools. Different tools provide options for performing variety of functions, including liquid transfer and plate washing operations and moving labware around the deck. The modular design of the Biomek 3000 workstation allows expansion of the instrument capabilities to include additional operations such as filtration, plate shaking, photometric microplate measurement, and high-capacity operation.
Beckman Coulter | 680 Chemistry Analyzer
AU680 clinical chemistry analyzer delivers field-proven reliability and efficiency to laboratories around the world.
Beckman Coulter Microfuge 22R Refrigerated Centrifuge offers you flexible high speed and rapid cooling in an easy to use package. This quiet operating benchtop centrifuge has a sound rating of less than 58 dBa, meaning you can keep it nearby without being a distraction. This refrigerated microfuge is an best choice for pelleting of DNA, RNA and proteins, as well as cell virus isolation thanks to its high g-force of 21,920 x g, spinning at up to 14000 rpm. Parameters for this refrigerated benchtop centrifuge are easy to program from the user-friendly control panel set at the front of the unit. This micro centrifuge also features a timed function, where users can set time up to 30 minutes, or choose a continuous run or pulse. The Beckman Coulter Microfuge 22R Refrigerated Centrifuge keeps precious samples at 4C even at maximum speeds, and has stand by cooling to minimize downtime. The temperature can be set in 2C increments through a range of between -10 to 40C. Rotors for the refrigerated microcentrifuge are interchange able to meet your needs, and come with an aerosol tight lid to help minimize cross contamination in the event of a broken tube. All rotors for the Beckman Coulter Microfuge 22R Refrigerated Centrifuge are autoclavable at 121C.
Beckman Coulter | Access 2 Immunoassay System
Access 2 contains the robustness of a reference laboratory immunoassay analyzer and provides control over performance, reliability and speed.
COULTER LH 500 helps increase productivity, enhances linearity, improves diff flagging and reduces false positive flagging in white cell differential analysis.
Beckman Coulter | AcT 5diff CP (Cap Pierce) Hematology Analyzer
Hematology Analyzer reduces manual sample handling and enhances safety by eliminating operators exposure to biohazards.
Beckman Coulter | AcT diff Hematology Analyzer
AcT diff Hematology Analyzer is used for whole blood analysis from both venous and capillary collections.
Beckman Coulter | AU480 Chemistry Analyzer
Chemistry Analyzer delivers efficiency for laboratories around world.
Beckman Coulter | Allegra 6R Table top centrifuge
Beckman Allegra 6R is a Refrigerated Centrifuge features smart balance technology and has a high capacity with the GH-3.8 swing bucket rotor. This benchtop centrifuge and its rotor can accommodate a wide range of vessels, from 1.5 ml tubes to 750 ml bottles and generally including tubes, bottles, microplates, specialty bottles, and blood bags. The Allegra 6 reaches maximum speeds up to 6,100 RPM with maximum RCF of 5,710 x g. Refrigerated temperature range from -5C to 25C. Features automatic rotor imbalance detection, auto door interlock, rugged drive, and fine-tuned suspension for performance, reliability, and safety in the lab. This rotor reaches a maximum speed of 3,750 RPM.
Beckman Coulter | AUTION ELEVEN AE-4022 Semi-automated Urine Chemistry Analyzer
Semi-automated Urine Chemistry Analyzer provides clinically significant reporting ranges for urine chemistry
PA 800 Plus Pharmaceutical Analysis System runs multiple characterizations from a single system and produces qualitative and quantitative analyses.
MoFlo Astrios is the new standard for cell sorting with functionality, speed, and improved sensitivity. It is designed for researchers who desire high productivity with more analytical capability and with biosafety solutions. The ergonomic design of Astrios makes it faster and easier to operate. All components requiring operator control are within easy reach. Beyond the optic expansion, novel software components enhance the instruments capabilities. The Touch Screen Control Panel facilitates... Read more
Beckman Coulter | AU5800 Series Clinical Chemistry Analyzers
Clinical chemistry analyzers processes up to 2,000 tests per hour with full menu of assays, including Therapeutic Drug Monitoring and Drugs of Abuse.
Beckman Coulter | AUTION MAX AX-4030 Fully Automated Urine Chemistry Analyzer
AUTION MAX AX-4030 generates accurate and reliable urine chemistry results without interruption and offers high throughput and continuous loading.
Beckman Coulter | Biomek 4000 Automated Liquid Handler
Beckman Coulter Biomek 4000 Automated Liquid Handler helps standardize daily pipetting routines, maintain sample quality and generate repeatable results.
Beckman Coulter | Bruker MALDI Biotyper System
This microbiology system is used for microbial identification and can provide solution for ID and AST testing.
Beckman Coulter | CellaVision DM1200 and CellaVision DM9600 Solutions
CellaVision digital morphology solutions increase efficiency of hematology workflow systems for mid to large volume laboratories.
Beckman Coulter | ACT10 Cell differential counter
AcT 10 is an and hematology analyzer with whole blood and pre-dilute capabilities from Beckman/Coulter. Beckman/Coulter AcT 10 automated analyzer is intended for testing in any smaller lab facility and low-volume office labs. Ten parameters including WBC, RBC, Hgb, Hct, MCV, MCH, MCHC, Plt, Lymph # and Lymph % can be measured using this Beckman/Coulter AcT 10 analyzer. For abnormal samples, partial differential option is available. Sample volume required for the whole blood mode is 12 �L and 20 �L in pre-dilute mode.
Beckman Coulter | AutoMate 2500 Family Sample Processing System
Automated sample processing systems streamlines pre and post analytical processes and eliminates steps between sample receipt and analysis.
Beckman Coulter | Copan WASP DT: Walk-Away Specimen Processor
Copan WASP DT automated specimen processor is used for preanalytical specimen management to standardize and improve quality of specimen culturing activities.
Beckman Coulter | Coulter AcT 5diff AL Hematology Analyzer
Beckman Coulter Coulter AcT 5diff AL (Autoloader) Hematology Analyzer
AL Hematology Analyzer improves sample handling by eliminating manual sample loading.
Beckman Coulter | Biomek NXp Robotic Liquid Handler
Beckman Coulter Biomek NXp Robotic Liquid Handler is and automated liquid handler designed to handle every aspect of liquid handling, pipetting, dilution, dispensing and integration in to one compact unit that will let you add laboratory automation where you need it. This efficient robotic liquid handler is set with a Span-8 pipette model, 4 fixed tip heads and 4 disposables, with rotating gripper and 8 channel liquid level sensing for an efficient and hands-free workflow. This automated workstation has up to 12 deck positions, automated labware positioners, and labware stacking for on deck storage. The open-ended flexibility of this robotic handler helps keep your lab agile and adaptable to your needs.
Beckman Coulter | Coulter AcT diff2 Hematology Analyzer
Hematology Analyzer delivers performance in open and closed analysis modes, wide operating range and multiple output formats.
Beckman Coulter | CytoFLEX Flow Cytometer
Flow Cytometer provides performance needed for sensitivity and resolution throughout all configurations.
Beckman Coulter | Coulter LH 750 Hematology Analyzer
Hematology Analyzer is used for automated nucleated red blood cell NRBC enumeration.
Beckman Coulter | Coulter LH 780 Hematology Analyzer
Beckman Coulter | DiaSorin LIAISON XL Chemiluminescence Immunoassay Analyzer
Chemiluminescence Immunoassay Analyzer closes care gap and addresses challenges with blood viruses and infectious diseases.
Beckman Coulter | DU 530 Spectrophotometer
This spectrophotometer functions with single cell module and supports alternative cell holders, like 16 mm test tube, 1 cm standard, 10cm rectangular turbidity, and 50uL microcell.
Beckman Coulter | DxA 5000 Total Laboratory Automation System
This Automation System is used to provide consistent turnaround time for all samples and level of comprehensive pre analytical sample quality.
Beckman Coulter | DxC 700 AU Chemistry Analyzer
This chemistry analyzer achieves maximal uptime, high reliability, and precise performance .
Beckman Coulter | DxH 600 Hematology Analyzer
Hematology Analyzer uses multi dimensional, high definition technology to characterize individual cells.
Beckman Coulter | DxH 800 Hematology Analyzer
DxH 800 hematology analyzer utilizes data about individual cell size, shape and structure to provide high quality results.
Beckman Coulter | DxH Slidemaker Stainer II Cellular Analysis System
Cellular Analysis System prepares slides automatically based on customizable rules.
Beckman Coulter | DxM MicroScan WalkAway Microbiology System
MicroScan WalkAway Microbiology System detects emerging and critical antimicrobial resistance.
Beckman Coulter | DxH 520 Hematology Analyzer
Hematology analyzer helps low volume laboratory enhance patient care.
Beckman Coulter | Gallios Flow Cytometer
Flow Cytometer provides efficient acquisition of up to 12 parameters to achieve accurate size measurement and high resolution and processing.
Beckman Coulter | iChemVELOCITY Urinalysis Instrument
Urinalysis Instrument used for automated urine chemistry analysis to identify possible ascorbic acid interference with key chemistry assays.
Beckman Coulter | DxH 900 Hematology Analyzer
900 Hematology Analyzer delivers reliable, reportable WBC differential results.
Beckman Coulter | IMMAGE 800 Protein Chemistry Analyzer
Protein Chemistry Analyzer delivers Dual Detection Rate Nephelometric Technology and broad test menu including enhanced UDR capability.
Beckman Coulter | iQ200 Series Urinalysis Microscopy Instrument
iQ200 series automates sample microscopy and produces shortened TAT for low to high volume workloads.
Beckman Coulter | MicroScan autoSCAN-4 System
Beckman Coulter | iQ Series Urinalysis Workcell
iQ Workcell series of automated walk away workcells analyzes urine chemistry and deliver standardized and accurate results.
Beckman Coulter | iRICELL Series Urinalysis Workcell
Urinalysis Workcell combines urine chemistry and microscopy in fully automated, walk away workcell.
Cell sorter that combines high-speed sorting capability with an open flexible design to enable a wide variety of sorting applications.
Beckman Coulter | MicroScan WalkAway plus Microbiology System
Microbiology system used for mid to high volume identification and antibiotic susceptibility testing.
Beckman Coulter | PK7400 Automated Microplate System
Analyzer that uses agglutination technology and a comprehensive blood-typing menu to deliver the highest throughput of blood donor immunohematology testing.
Ultracentrifuge is used for centrifugation of subcellular particles, virus isolations, and high purity plasmid DNA.
Beckman Coulter | Optima L-90K Ultracentrifuge
Beckman Optima L-90K Ultracentrifuge has a performance capability of 694,000 x g at up to 90,000 rpm. This versatile floor model is compatible with a wide range of superior rotors including zonal and continuous flow for large-volume separations. The Optima L-90 K is for applications such as subcellular particles and virus isolations, and high-purity plasmid DNA. Featuring an imbalance-tolerant drive, the L-90 K provides unmatched reliability with its highly efficient vacuum-encased induction drive which allows smooth and quiet performance. Plus, this ultracentrifuge model is sized for efficient operation within laminar flow hoods. Equipped with easy-to-use, environment-friendly and microprocessor based control cooling systems, the Beckman L-90 K eliminated the use of CFCs and other dangerous liquid refrigerants. This Beckman centrifuge also has an overspeed system to ensure that rotors do not exceed maximum speed.
Beckman Coulter | PK7300 Automated Microplate System
Analyzer used for pre-transfusion, automated blood donor testing that features 300 sample per hour throughput, full online system status updates, data transfer capabilities, and aspiration and dispense monitoring intelligence.
Beckman Coulter | StatSpin CritSpin Digital Reader
Digital reader with a large display used for hematocrit determinations.
Beckman Coulter | ProteomeLab XL-I AUC XL-I
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 5th,2023. ProteomeLab XL-A/XL-I is a centrifuge with in-solution characterization of proteins, oligomers, aggregates, particles, colloids, and small structures delivers accurate results you can rely on time and again. In-solution characterization allows for testing in native conditions, meaning you determine the sample testing environment that best suits your needs. The column-free separating technique of the ProteomeLab XL-A/XL-I measures the relative change in the distribution of molecular weights, providing an efficient way to measure heterogeneity, stoichiometry and self-associating systems. And, because the measurements are based on the first principles of thermodynamics and hydrodynamics, no standards or calibrations are required. As a result, you spend less time on setup and more time on discovery. Our analytical ultracentrifuge platform offers a variety of customizable options, to meet your needs. Sensitive absorbance optics enable analysis of most samples, and interference optics can be used for low concentrations. Both systems can be implemented simultaneously, to maximize data acquisition in a single run. Additionally, we offer two different rotor configurations, and a variety of cell types, to enable multiple experimental designs. The wide range of rotational velocities also allow investigators to probe protein size, dimerization, and binding constants.
Beckman Coulter | StatSpin Cytofuge 2 Cytocentrifuge
Personal cytocentrifuge that provides high quality sample preparations with understandable controls and snap-seal filter concentrators.
Beckman Coulter | StatSpin Express 3 Centrifuge
Primary tube centrifuge that can spin eight tubes up to 10mL and provides high quality plasma or serum in two to five minutes.
Beckman Coulter | StatSpin Express 2 Centrifuge
Primary tube centrifuge that prepares high quality plasma or serum samples in two minutes.
Workcell that combines a chemistry and immunoassay testing to streamline laboratory operations and provide a rapid TAT.
Beckman Coulter | StatSpin MP Centrifuge
Centrifuge that is used for centrifuging microhematocrit tubes for packed cell volume determination, as well as rapid separation of whole blood and preparation of urine sediment for microscopic analysis.
Beckman Coulter | StatSpin Express 4 Centrifuge
High-speed horizontal centrifuge that can produce high-quality serum or plasma separation in 3-, 5- or 10-minute cycles.
Beckman Coulter | UniCel DxH Connected Workcell Solutions
Series of connected hematology workcells used for multidimensional high-definition cellular analysis.
Beckman Coulter | UniCel DxI 600 Access Immunoassay System
Immunoassay analyzer with a throughput of up to 200 tests per hour and up to 60 samples on board.
Beckman Coulter | Vi-CELL XR Cell Viability Analyzer
Cell counter that provides an automatic means to perform the Trypan Blue Dye Exclusion method, allowing users to load up to 9 samples at once for easy and automated cell analysis, and offers pre-programmed and customizable analysis options for consistent and accurate analysis.
Beckman Coulter | Moflo XDP Cell Sorter Flow Cytometer
Cell sorter that can perform 70,000 sorts per second and offers a wide variety of sorting applications.
Beckman Coulter | CyAn ADP High-Speed Analyzer
Flow cytometer engineered for precision analysis of cells, bacteria, and other similarly sized particles. CyAn ADP utilizes three excitation lines with independent, alignment-free focusing optics, simultaneous nine color and two scatter parameters, analysis rates of 70,000 events per second, a full 9 × 9 inter-laser compensation matrix, and high sensitivity. The instrument is optimized for cell cycle, kinetics, fluorescent protein work, and multi-color immunophenotyping. Rare-event analysis, such as MHC Dextramer studies, and no-lyse whole blood applications are easily performed on the CyAn ADP. The instrument also provides simplified compensation before, during, and after acquisition in all fluorescent parameters.
BD Biosciences | Aria IIu Flow Cytometer
Aria has four lasers, 405, 488, 561 and 633 nm, and can detect light in sixteen photomultiplier tubes. Its primary function is to examine complex populations of cells and yield pure populations of cells. The Aria can sort lymphocytes at a rate of approximately 15,000 events per second. For larger cells, the rate is much slower in order to optimize the passage of cells through the instrument. Cells from single populations can be sorted into 96-well plates. Alternatively, the Aria can sort into two 15-ml tubes or four 5-ml tubes. The Aria can purify samples that are simply positive and negative for a single fluorophore or as complex as nine-color samples with intricate gating schemes. The BD FACSAria IIu cell sorter is a high speed benchtop digital flow cytometer equipped with a sensitive, fixed-alignment cuvette flow cell. It has three spatially separated lasers - 405 nm, 488 nm and 633 nm. Its primary function is to analyze complex populations of cells and yield pure populations of cells meeting defined criteria. The sorter can purify samples that are simply positive and negative for a single fluorophore or as complex as multi-color samples with complex gating strategies. Sorting can be performed into two or four tubes with speeds up to 25,000 events/second. The system sorts by incorporating cells from the sample tube into a stream of sterile PBS. The stream is interrogated by the lasers at the flow cell and the system electronics keeps track of each cell as they pass through the laser and determines specific cells that meet the sort criteria. A transducer vibrates the stream and induces droplet formation, with cells in the stream being incorporated into the droplets. If a cell meets the sorting criteria and is in the last drop before the break off, the instrument will charge that drop. The charged droplet is then deflected into the proper collection tube by the charge plates. Different cell types can be sorted with the use of 70 �m, 85 �m and 100 �m nozzles. If you need a yellow-green (561 nm) laser, check the BD FACSAria III instead.
Beckman J2-21M is a high speed floor model centrifuge which features a brushless induction drive and maintenance-free system. Capable of performing at a speed of 21,000 rpm and forces up to 51,500 g, the J2-21M offers superior functionality, accuracy, and productivity. The system's microprocessor-controlled design provides quick and automatic operation. The J2-21M Centrifuge stores up to 10 programs and eliminates errors in repetitive runs. The system also offers a choice of ten dual-ramp acceleration and deceleration settings for gentle starts and quick running.
Beckman Coulter | StatSpin VT Centrifuge
Centrifuge that is designed for veterinarians and used for centrifuging microhematocrit tubes for packed cell volume determination, as well as rapid separation of whole blood and preparation of urine sediment for microscopic analysis.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Cell counter that offers rapid cell sample analyses for a single cell type or diverse cell population
Beckman Coulter | L8-70M Ultracentrifuge
Ultracentrifuge that provides 9 slow acceleration profiles for greater protection of the gradient and sample-to-gradient interfaces and 10 slow deceleration profiles for integrity of separations. It has 3 modes of operation: manual, automatic and programmed
Variable wavelength UV/Vis HPLC detector with low noise and drift over a wide wavelength range.
Estigen | Beecher ATA-27 Automated Tissue Arrayer
Automated Tissue Arrayer ATA-27 is designed for construction of high-density tissue microarray blocks fast, accurate and . Automated Tissue Arrayer ATA-27 is intended for laboratories requiring higher throughput in array production. It eliminates the tedious manual punching procedure from array construction workflow. After planning and designing the array layout using dedicated software, ATA-27 creates array blocks automatically using robotics to measure block heights, retrieve donor tissue cores, create holes in paraffin matrix and deposit tissue cores into holes.
Imager for proteomic studies that has the ability to image colorimetric and fluorescently-stained gels and blots to detect chemiluminescent and other low-light. It features red, green, blue and white epi-illumination and UV and white transillumination.
System for analysis of biomolecular interactions, based on GE Healthcare surface plasmon resonance (SPR) technology. Control Software supplied with system offers easy-to-use wizards for assay development and common applications together with flexible facilities for designing custom analysis methods using graphical interface called Method Builder.
MoFlo is a high speed cell sorter with three lasers, 9 colors, and two way sorting capability. It is equipped with a solid state 488nm laser, an I90 argon ion multiline UV laser, and an I70C spectrum tunable laser (providing wavelengths from 440nm to 568nm). A variety of collection devices may be used including: microscope slides, micro-tubes, 12 x 75ml test tubes, 15 or 50ml falcon tubes, as well as multi-well plates (6, 24, 96, or 384). This instrument is operated by staff on a fee for service basis.
Bio-Rad | Biologic Protein Purification System
Low-pressure chromatography system that is used for biomolecule purification with nucleic acid and protein detection. It has 254 and 280 nm filters, conductive cell, and a peristaltic pump with flow rate range of 0.05 to 40 ml per min.
Mixer that is designed for variety of mixing applications from gentle sample mixing to resuspending cell pellets.
Gel imaging system that enables visible light,RGB, far red, near infrared, FR, NIR, fluorescence and chemiluminescence detection. It visualizes proteins without gel staining.
PDS-1000/He is a Particle Delivery System that accelerates nucleic acid coated gold or tungsten microparticles (0.6 1.6 �m) to velocities necessary to transfect cells, tissues, or organelles. The system uses a burst of high-pressure helium gas to accelerate a plastic macrocarrier disk carrying microparticles toward target cells. The helium pressure used to propel the macrocarrier is determined by the choice of rupture disk, a plastic seal designed to burst at a specific pressure. A stopping screen retains the macrocarrier while allowing the microparticles to pass through and penetrate the target cells. To increase the efficiency of the process, the chamber may be evacuated to subatmospheric pressures, reducing the frictional drag on the microparticles as they travel toward the target cells
Bio-Rad | BioLogic DuoFlow Medium-Pressure Chromatography Systems
Series of chromatography systems that offer multiple system configurations, optional upgrades, and common software platform and are suitable for analytical and preparative chromatography.
Bio-Rad | DCode Universal Mutation Detection System
Universal mutation detection system that can scan for single-base changes by using a variety of electrophoretic techniques, including single-stranded conformation polymorphism, denaturing gradient gel electrophoresis, constant denaturing gel electrophoresis, and temporal temperature gradient gel electrophoresis.
Thermal cycler with a touchscreen interface and dual 48 well reaction module that allows multiple independent protocols to be run simultaneously.
Agilent: BioTek | ELx808 Microplate Reader
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 31,2023. Microplate reader that offers performance for many applications, from endpoint to fast kinetic protocols. Offers 4 Zone temperature control, which optimizes conditions for temperature sensitive assays.Can be used for Kinetic ELISA, Protein quantification, ELISA, Endotoxin analysis, and Microbial growth assays. It is used with Gen5 software.
Bio-Rad | Chemidoc XRS Gel Imaging System
Gel imaging system that is based on CCD detection technology and options for fluorescence, colorimetry, densitometry, chemiluminescence, and chemifluorescence.
Bio-Rad | Experion Automated Electrophoresis System
Electrophoresis system that automates nucleic acid and protein analysis and performs multiple electrophoresis steps in one platform.
Single-cell isolator that utilizes disposable microfluidic cartridges to coencapsulate single cells and barcodes into subnanoliter droplets, where cell lysis and barcoding occur.
Peristaltic pump that is used for low pressure chromatography or for pumping liquids in general laboratory procedures.
Benchtop microcentrifuge with an 18-place rotor that can accommodate 1.5 and 2.0 ml tubes.
Bio-Rad | NGC Discover 100 Pro Chromatography System
Chromatography system that includes 100 ml/min pumps, multi-wavelength (UV/Vis) and conductivity detection, expanded scouting options, large-sample injection, outlet valve and column switching of up to 5 columns, for method development. It also performs fraction collection in combination with large-volume collection using a 12-port outlet valve.
Bio-Rad | NGC Discover 100 Chromatography System
Chromatography system that includes 100 ml/min pumps, multi-wavelength (UV/Vis) and conductivity detection, expanded scouting options, large-sample injection, outlet valve and column switching of up to 5 columns, for method development.
Bio-Rad | NGC Quest 100 Chromatography System
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 31,2023. Chromatography system that is used for the all-purpose purification of biomolecules from samples in the mg to g range with accurate buffer gradients and high-resolution separations.
Bio-Rad | NGC Scout 10 Chromatography System
Chromatography system that includes 10 ml/min pumps, single-wavelength (UV) and conductivity detection, buffer blending options, for rapid pH scouting during sample purification.
Bio-Rad | NGC Quest 100 Plus Chromatography System
Chromatography system that is used for the all-purpose purification of biomolecules and simultaneous detection of proteins, peptides, nucleic acids, and chromogenic molecules at the mg to g scale with accurate buffer gradients and high-resolution separations.
Bio-Rad | NGC Scout 10 Plus Chromatography System
Chromatography system that includes 10 ml/min pumps, multi-wavelength (UV/Vis) and conductivity detection, buffer blending options, for rapid pH scouting during the purification of proteins, peptides, and nucleic acids.
Bio-Rad | NGC Scout 100 Chromatography System
Chromatography system that is used for the quick separation of proteins and peptides when rapidly scouting purification conditions with automated gradients and buffer preparation during purifications at the mg to g scale.
Bio-Rad | Pharos FX Molecular Imager System
Molecular imager system for fluorescence imaging that is used for analysis of DNA, RNA, or protein samples in gels, blots, or microplates.
Bio-Rad | NGC Scout 100 Plus Chromatography System
Chromatography system that is used for simultaneously detecting proteins, peptides, nucleic acids, and chromogenic molecules using expanded automated gradients, blending and scouting options during purifications at the mg to g scale.
Bio-Rad | Profinia Protein Purification Instrument
Discontinued.Protein Purification Instrument.
Bio-Rad | ProteOn XPR36 Protein Interaction Array System
Bio-Rad ProteOn XPR36 Protein Interaction Array System
ProteOn XPR36 Surface Plasmon Resonance System
ProteOn XPR36 protein interaction array system is surface plasmon resonance (SPR) biosensor platform that provides real-time label-free analysis of specificity, affinity and kinetics of biomolecular interactions.
Spot cutter instrument that is used for location, excision and loading into microtiter plates of protein spots after separation on 2D electrophoresis gels or PVDF membranes.
Bio-Rad | QX200 Droplet Digital PCR System
Droplet generator and reader that provides absolute quantification of target DNA or RNA molecules for EvaGreen or probe-based digital PCR applications.
Droplet generator and reader that is designed for high-throughput processing of samples in a 96-well format and provides precise and absolute quantification of target DNA and RNA molecules in a wide variety of research applications.
Bio-Rad | NGC Discover 10 Chromatography System
Chromatography system that includes 10 ml/min pumps, multi-wavelength (UV/Vis) and conductivity detection, expanded scouting options, large-sample injection, and column switching of up to 5 columns, for method development. This chromatography system may be used for method development, combining automated buffer blending with buffer inlets, a column switching valve, and a sample pump for expanded condition scouting options during the purification of proteins, peptides, and nucleic acids.
Cell sorter that allows performance of 1 to 4 color sorts and sorts large quantities of pure viable cells.
Fluorometer that provides fluorescent detection at high levels of sensitivity and selectivity for quantitating DNA, RNA, and proteins, detecting apoptosis, and performing reporter enzyme assays. This fluorometer has been discontinued.
Bio-Rad ZE5 Cell Analyzer Flow Cytometer
Bio-Rad ZE5/Yeti Cell Analyzer Flow Cytometer
BioRad ZE5 was formerly known as the Propel Labs YETI Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals.
Bio-Rad | QX200 AutoDG Droplet Digital PCR System
Droplet generator that provides absolute quantification of target DNA or RNA molecules for EvaGreen and probe-based Droplet Digital PCR (ddPCR) applications.
2100 Bioanalyzer system is an established automated electrophoresis tool for the sample quality control of biomolecules. The 2100 Bioanalyzer instrument, together with the 2100 Expert Software and Bioanalyzer assays, provide highly precise analytical evaluation of various samples types in many workflows, including next generation sequencing (NGS), gene expression, biopharmaceutical, and gene editing research. Digital data is provided in a timely manner and delivers objective assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for an accurate result, and the data may be exported in a many different formats for ease-of-use.
Bio-Rad | NGC Discover 10 Pro Chromatography System
Chromatography system that includes 10 ml/min pumps, multi-wavelength (UV/Vis) and conductivity detection, expanded scouting options, large-sample injection, outlet valve, and column switching of up to 5 columns, for method development. This chromatography system may be used for simultaneously detecting proteins, peptides, nucleic acids, and chromogenic molecules with expanded scouting options.
GE | Bioacore T200 Protein Analysis System
Biacore T200 software offers a range of tools for confident and kinetic analyses. These analyses can be performed using a multicycle approach (many samples against one ligand or when different ligands are immobilized), or alternatively, using singlecycle kinetics (fast runs without regeneration). Biacore T200 is a versatile system for high-quality characterization of molecular interactions, from ions to viruses. One platform for comprehensive characterization of molecular interactions in terms of kinetics, affinity, specificity, comparability, concentration, immunogenicity, and thermodynamics. ligand-binding assays, even for the most complex biologics Confident selection and characterization of the smallest organic compounds to large multidomain proteins Validated software meeting your regulatory expectations by supporting GxP procedures and 21 CFR Part 11 compliance
Synthesizer that is designed to synthesize DNA, RNA & LNA oligonucleotides in a column format using standard or modified chemistries and can synthesize 192 oligos in less than 3 hours.
Bio-Rad | IQ5 5-channel Real time qPCR instrument
Real Time PCR detection system that offers five-target analysis capabilities for multiplex PCR with a variety of detection chemistries.
Microplate washer that has simple user interface for creation and execution of wash, dispense, aspirate and maintenance protocols within extensive onboard software.
Handheld gene gun delivery system that provides direct transfection into range of targets in vivo. It uses adjustable low pressure helium pulse to sweep DNA, RNA, or biomaterial coated gold microcarriers from a plastic cartridge directly into target cells.
Bio-Techne | BioSpec TC-312 Thermal Cycler
Laboratory instrument used to amplify segments of DNA or RNA through a process called Polymerase Chain Reaction (PCR). By rapidly heating and cooling samples, it forces DNA to replicate exponentially, allowing scientists to analyze or identify genetic material.
Microplate washer that is designed to wash cell based assays, microsphere based assays and ELISA, for every application.
Agilent: BioTek | 800 TS Absorbance Reader
Microplate reader that measures absorbance in microplate-based assays. Applications extend from endpoint ELISA to temperature sensitive kinetic assays.
Microplate washer that automates aspirate, dispense, shake, and soak steps required for assays including cell based assays, biomagnetic and polystyrene bead based assays.
Agilent | BioTek BioSpa 8 Automated Incubator
Agilent BioTek BioSpa 8 Automated Incubator
Incubator that links readers and imagers together with washers and dispensers for full workflow automation of up to 8 microplates or other labware. Temperature and CO2/O2 control, plus humidity monitoring and lid handling ensure an ideal environment for cell cultures during all experiment stages, with minimal manual intervention.
BioTek Cytation 1 Cell Imaging Multi-Mode Reader
Multi-mode plate reader that combines fluorescence and high contrast brightfield imaging with conventional multi-mode detection.
Agilent: BioTek | Cytation Hybrid Multi-Mode Microplate Reader
Multi-mode plate reader offers UV-Vis absorbance, fluorescence and luminescence detection detection modes.
Agilent: BioTek | Cytation 5 Cell Imaging Multi-Mode Reader
Multi-mode plate reader that offers up to 60x magnification in fluorescence, brightfield, high contrast brightfield, color brightfield and phase contrast for maximum applications reach. The multi-mode detection modules include filter- and monochromator-based fluorescence detection, luminescence and UV-Vis absorbance detection.
Agilent: BioTek | Cytation 7 Cell Imaging Multi-Mode Reader
Multi-mode plate reader that combines automated digital upright and inverted widefield microscopy with conventional multi-mode microplate reading and provides sample visualization from 1.25x to 60x magnification in fluorescence, brightfield and color brightfield for a broad range of applications.
Agilent: BioTek | BioStack Microplate Stacker
Microplate stacker compatible with BioTek's washers, dispensers, detectors and imaging systems and accommodates assay workflows for 96- and 384-well plates.
Agilent: BioTek | EL406 Washer Dispenser
Microplate washer that is equipped for full plate washing along with three reagent dispensers in one and includes washing and dispensing for standard assays, biomagnetic separation and vacuum filtration protocols.
Biorad MyIQ single-channel QPCR instrument
MyiQ Single Color Real Time PCR Detection System builds on the strengths of the iCycler Thermal Cycler, which provides the optimum performance for PCR. The MyiQ system features a tungsten halogen lamp as the light source. The filter-based optical design allows the use of optimal wavelengths of light for excitation and emission, resulting in excellent sensitivity and discrimination between multiple fluorophores. The CCD detector captures a simultaneous image of all 96 wells. This results in a comprehensive data set illustrating the kinetic behavior of the data during each cycle. Simultaneous image collection insures that well-to-well data may reliably be compared. The MyiQ system reports data on the PCR in progress in real time, allowing immediate feedback on reaction success. All of these features demonstrate that the MyiQ system hardware was built to promote reliability and flexibility. The MyiQ software includes features that make software easy and useful. The software is designed for offering speedy setup and analytical results. Many functions are presented graphically for ease of use. Tips on usage are available as your mouse rolls over the buttons. In addition, the Online Help Manual is available at all times simply by pressing the F1 key. The MyiQ software automatically analyzes the collected data at the touch of a button, yet leaves room for additional optimization of results based on your analysis preferences.
Agilent: BioTek | ELx405 Select Deep Well Washer
Microplate washer that aspirates and dispenses into 96- and 384-well plates.
Agilent: BioTek | ELX405U Microplate Washer
Microplate washer that is designed to rapidly wash 96 or 384 well microplates. Keypad interface has independent control of plate position during dispense and aspiration cycles, as well as fully programmable fluid volumes and flow rates, shaking, and soaking.
Agilent: BioTek | Epoch 2 Microplate Spectrophotometer
Spectrophotometer that is used for UV-Vis measurements in 6- to 384-well microplates, cuvettes and in micro-volume samples with the available Take3 Micro-Volume Plate. Endpoint, kinetic, spectral scanning and well area scanning modes, plus incubation and shaking enable wide-ranging applications.
Agilent: BioTek | Epoch Microplate Spectrophotometer
Spectrophotometer that offers filter free, wide wavelength range for UV-Vis absorbance measurements in variety of microplate formats, and in 2 uL samples when available Take3 plate is used.
Bio-Rad | VersArray Chipwritter Pro System
Microarray that is used for printing DNA, proteins, or other biological samples. It has modular component design and software for microruns or unattended highthroughput prints.
Agilent: BioTek | FLX800 Multi-Detection Microplate Reader
Microplate reader that includes several models with options that meet specific needs of research and OEM users. Top and bottom reading are available to read anything from 6 well to 384 well microplates, and PCR plates. Optional external dispenser module allows running applications such as ion channel assays and flash luminescence assays.
Agilent: BioTek | Lionheart FX Automated Microscope
Microscope that offers up to 60x air; 60x and 100x oil immersion magnification, with fluorescence, brightfield, color brightfield, and phase contrast channels for maximum application reach.
Agilent: BioTek | Lionheart LX Automated Microscope
Microscope that enables augmented microscopy, which fully automates image capture, processing and analysis.
Agilent: BioTek | MultiFlo FX Multi-Mode Dispenser
Automated multi-mode reagent dispenser for 6- to 1536-well microplates.
Agilent | BioTek Synergy H1 Multimode Reader
BioTek Synergy H1 Hybrid Multi-Mode Microplate Reader
Modular multimode microplate reader, with monochromator-based optics and filter-based optics for fluorescence and luminescence detection, plus filter-free UV-Vis absorbance. Hybrid is the term that Agilent BioTek uses to describe the unique optical systems available for Synergy H1 multimode readers. Each of these readers is configurable to include filter-based or monochromator-based optics for fluorescence and luminescence detection, or they can include both filter- and monochromator-based optics for maximum assay flexibility, sensitivity, and specificity. The bandwidth can be set between 9 and 50 nm, in 1 nm increments, to fully optimize reader settings for best sensitivity and specificity compared to fixed bandwidth systems. Comes with Gen5 Data Analysis Software.
Agilent | BioTek Synergy HTX Multi-Mode Microplate Reader
Compact multimode reader for 6- to 384-well microplates and Take3 microvolume plates. The unique dual optics design provides superior performance for UV-Vis absorbance, fluorescence, luminescence, and AlphaScreen/AlphaLISA workflows. With incubation and shaking, plus a dual reagent injector module, the system will meet all your assay requirements now and in the future. Synergy HTX is controlled by the easy-to-use, yet powerful, Gen5 software for data collection, analysis, exporting, and reporting.
Agilent: BioTek | Synergy H4 Hybrid Plate Reader
Synergy H4 combines the sensitivity of a filter-based system with the of monochromator-based optics to provide the broadest range of applications available on the market today. Detection modes: Fluorescence Intensity, Time-Resolved Fluorescence, Fluorescence Polarization, AlphaScreen/AlphaLISA, Luminescence, UV-Visible absorbance, FRET, TR-FRET, BRET, well area scanning and spectral scanning.Synergy H4 optics incorporates two double-grating monochromators. This quadruple design provides the best in spectral scanning performance and flexibility. Synergy H4's filter/dichroic combination provides the best possible performance in fluorescence, time resolved fluorescence and fluorescence polarization applications.
BMG Labtech Spectrostar Nano Microplate Reader
BMG LABTECH's SPECTROstar NANO is the premiere absorbance microplate reader. The SPECTROstar NANO is a spectrometer-based absorbance reader that can capture a full UV-visible spectrum, 220nm to 1000nm, in less than 1 sec/well at 1nm resolution, offering you speed and precision that cannot be matched by older monochromator or filter absorbance reading technology. The SPECTROstar NANO has a built in cuvette port, 45C incubation, push button operation, is 1536 well capable, and has 2uL nano spot DNA quantitation capability allow the fastest measurements of DNA, RNA, ELISAs, and much more.
Select Science | BioTrove OpenArray NT Cycler System
Optical thermal cycler that is capable of cycling and imaging up to three OpenArray plates simultaneously. System includes: NT Cycler, computer, flat-panel monitor, OpenArray AutoLoader, and Case Sealing Station. Requires analysis software kit for operation.
Brookhaven Instruments | BI-200SM Research Goniometer
Brookhaven Instruments BI-200SM Goniometer
Goniometer that is used for macro molecular studies and submicron particle sizing with static and dynamic light scattering. It can be used with neutral density filters, polarizer, analyzer, and reference detector.
PCR assay kit that detects the five most prevalent carbapenemase gene families. Detection of carbapenemase genes from rectal swabs supports timely deployment of infection control procedures and appropriate patient management.
Bruker | Autoflex III MALDI TOF Mass Spectrometer
Bruker Autoflex III Smartbeam MALDI-TOF/TOF
Mass spectrometer that is used for analysis of large biomolecules (such as proteins, polymers, sugar, etc.) to identify and characterize the structures. The instrument has a capability of TOF/TOF technology (LIFT) for tandem MS (MS/MS). It is worked either linear or reflectron configuration with both positive and negative modes. System includes computer pre-loaded with software.
Bruker | Clinscan 7T Magnetic Resonance Imager
ClinScan is Bruker BioSpin's solution for an emerging market of research MRI systems that allows a direct and fast transfer of preclinical studies on animal models to clinical studies on humans. 7 T Bruker USR magnet (Ultra Shielded Refrigerated, bore size 20 cm or 30 cm) n Bruker gradient and shim coil (gradient strength of 290 mT/m or 630 mT/m, slew rate of 1160 T/m/s or 6300 T/m/s) n Bruker RF array coil technology in combination with numerous animal handling accessories n Siemens MAGNETOM Avanto technology with up to 32 receive channels n Clinical routine user interface syngo MR to enable efficient workflow and highly automated state-of-the-art MRI and MRS applications on small animals
Emerson | Branson 2510 Ultrasonic Cleaner
Ultrasonic bath that features heated cleaning with the ability to set temperatures from 20C/68F to 69C/156.2F and can also be used for cell separation, sample preparation and degassing of liquids.
D8 ADVANCE is a real quick-change artist that can be configured to take on a single analytical task with great focus and dedicated components, or a fully featured, multi-purpose solution that is capable of dealing with very diverse analytical needs with highest competence. Our famous DAVINCI design ensures for all those solutions easy (re)configuration and extensibility to exactly satisfy your analytical needs, now and in the future. XRD data are typically collected in one direction, 2Theta. Simultaneously collecting data along a second dimension, the Gamma direction, can speed up data collection and provide additional information about the properties of crystalline samples, such as texture, residual stress, grain size and epitaxial relations.
Bruker | BRAVO Handheld Raman Spectrometer
Mass spectrometer that features SSE and fluorescence mitigation, duo LASER excitation, intelliTip and automated measuring tip recognition, automated batch scan reporting, inbuilt wavenumber calibration, and wireless data exchange.
Agilent: BioTek | Synergy LX Multi-Mode Microplate Reader
Microplate reader with an optic design that provides accurate data in absorbance, fluorescence and luminescence detection modes, enabling many common assays including nucleic acid and protein quantification, ELISA, BCA, Bradford and cell viability.
Spectrometer that quantifies gases such as carbon dioxide and methane in the atmosphere by analyzing the radiation of the sun utilizing the CAMTracker system.
Agilent: BioTek | Synergy Neo2 Hybrid Multi-Mode Microplate Reader
Microplate reader that is designed for a screening laboratory and combines variable bandwidth quad monochromators, sensitive high transmission filter-based optics, laser TRF and up to 4 PMTs to provide fast measurements.
Spectrometer that is used for remote sensing of chemical substances in atmosphere.
Bruker | GLOBULYSER Homogenizer Efficiency Analyzer
Analyzer that is used for the determination of the mean fat globule size in milk and liquid milk products as well as in dissolved milk powders.
Bruker | InVi SPIM Light-Sheet Microscope
Microscope that has been optimized for long term 3D fluorescence imaging of living specimens.
Imaging remote sensing system that is based on combination of Michelson interferometer and focal plane array detector. Each pixel of array records interferogram from corresponding field of view. System allows identification, quantification and visualization of potentially hazardous gases from long distances.
Bruker | IRcube FTIR/FT-NIR Process Spectrometer
Spectrometer with splash proof housing and aligned optics that allows OEMs to create integrations and applications.IRcube can be used as UHV chamber coupling module, reflectance module, or gas analyzer.
Bruker MATRIX-MF FTIR/FT-NIR Process Spectrometer
Spectrometer that can be fiber optically coupled to measure chemical reactions in laboratory and/or process environments.
Bruker | LCS SPIM Light-Sheet Microscope
Microscope with a cuvette-based sample mounting approach that provides fast 3D imaging of large cleared samples.
Bruker | In-Vivo MS FX Pro In-Vivo Mass Spectrometer
MS FX PRO In-Vivo Mass Spectrometer brings the broadest range of imaging applications with multispectral fluorescence, luminescence, radioisotopic and high resolution X-ray imaging in one system. Functions range from protein blots to complex, longitudinal studies of disease states in vivo - to your lab. Whether you need to develop fluorescent probes; track NIR fluorescent nanoparticles, peptides or proteins; quantify changes in localization and tumor burden; screen radioisotopic probes in multiple animals; study changes in bone density or perform ex vivo validation, the MS FX PRO drives your research to new levels of excellence.
Gas analyzer that features a gas cell with 10 cm optical path length and is especially well suited for the quantification of gas compounds with very high concentration.
Bruker | maXis 4G Liquid Chromatography Time of Flight Mass Spectrometer
Mass spectrometer that measures and identifies small molecules, proteins and intact large molecules in both MS and MS/MS modes.
Gas analyzer that features a 2 m multi-reflection gas cell and is designed for the quantification of gas compounds in a very broad concentration range.
Gas analyzer that features a 5 m multi-reflection gas cell and is designed for the high-precision quantification of gas compounds from very low concentrations on the ppb level up to one hundred percent.
Bruker | M4 Tornado Micro X-Ray Fluorescence Device
M4 TORNADO is the tool of choice for sample characterization using small-spot Micro X-ray Fluorescence (Micro-XRF) for information on composition and element distribution. Optimized for analysis speed and without compromising accuracy it measures a wide range of samples. Whether small or large, even or irregularly shaped equipped with a large high-speed stage it supports 2D analysis of virtually any kind of inorganic, organic ,and even of liquid sample. Its large vacuum chamber enables light element detection.
Bruker | MicroFlex MALDI Microflex Mass Spectrometer
Mass spectrometer that is designed for automated protein identification and characterization, biomarker detection, oligonucleotide quality control, and SNP genotyping.
Bruker | micrOTOF-Q II Liquid Chromatography Mass Spectrometer
Benchtop Q-Tof, applied to a variety of applications such as small molecule accurate mass determination (HRMS), intact protein analysis including antibodies, peptide mapping, and other custom projects. This system is operated with an Agilent 1260 UPLC and includes an inline diode array detector and ESI source.
Dairy analyzer that can analyze parameters like fat, protein, total solids and lactose. High pressure homogenizer provides evenly homogenized samples for repeatability and accuracy. Can also determine freezing point.
Bruker | Multimode 8 Atomic Force Microscope
MultiMode 8-HR is an atomic force microscope which is well suited for imaging in both air and fluid. Heating to 250C, cooling to -35C with temperature control accessories. Nanothermal analysis for local polymer phase transition temperatures up to 350C.. Atomic resolution electrochemistry with AFM, STM, and SECPM. Invent your own mode by accessing and modifying any signal, high or low voltage. A large variety of standard operating modes and many capabilities enable the MultiMode 8-HR AFM system to characterize everything from mechanical to electrical properties
Spectrometer with OPUS software that controls data collection and manipulation functions for MultiRAM. Real time spectrum display permits software control of analysis conditions, including optimization of laser power and sample position.
Gas analyzer with a 19-inch rack mount box that is equipped with 5 m multi reflection gas cell, spectral resolution, TE cooled detector for sensitivity without need for liquid nitrogen, nickel plated gas cell and gold coated mirrors that enable measurement of corrosive gases, and accounts for variable pressure and temperature of gas by sensors included inside gas cell.
External spectrometer accessory that was developed for Polarization Modulation measurements. Both linear dichroitic measurement techniques, like PM IRRAS, and circular dichroitic experiments, like VCD spectroscopy, can be realized using this system.
Microscope that combines dual views with dual detection channels for large scale 3D imaging of life specimens and cleared samples. System enables transition between living and cleared tissue imaging.
Bruker | Opterra II 4D Fluorescence Confocal Microscopy
Confocal microscope that utilizes proprietary one dimensional pinhole array technology to combine resolution and speed. It has short acquisition times and cell protecting minimization of photobleaching and phototoxicity for advanced live cell imaging.
Energy-Dispersive X-ray Fluorescence spectrometer that features all requirements for S analysis from diesel to crude oils. This also includes continuous process control of higher sulfur levels in refineries as well as norm-compliant Ultra-Low Sulfur analysis of final products.
Bruker | MuVi SPIM Light-Sheet Microscope
Microscope with a 4-axis concept and two-sided illumination that allows for four combinations of illumination and detection.
WDXRF spectrometer that features compact WDXRF goniometer, closely coupled optics, and 400 W direct excitation power. It has linear range of more than two Million cps based on HighSense XE detector.
Spectrometer that is based on method of Fourier transform infrared spectroscopy. Infrared radiation is modulated by interferometer and transmitted to array of retroreflectors positioned at distance of typically several hundred meters using telescope. Reflected radiation is received by same telescope and focused onto detector.
Bruker | Scion TQ Gas Chromatograph Mass Spectrometer
Triple quadrupole gas chromatograph that provides targeted trace-level analysis of metabolites and other small molecules. Samples are often derivatized for compatibility with GC-MS.
Add-on module that can be coupled to a research spectrometer and allows automated switching between FT Raman and FT IR measurements.
Bruker | TruLive3D Imager Light-Sheet Microscope
Dual sided illumination light-sheet microscope that is optimized for 3D multi-sample imaging of live specimens in their 3D environment. It is especially suited for multi position imaging of small embryos, 3D spheroids, oocytes and more, enabling time lapse, high throughput imaging experiments.
Scanning imaging remote sensing system that allows identification, quantification, and visualization of potentially hazardous gas clouds from long distances. It is based on the combination of an infrared spectrometer with a single detector element and a scanner system.
Bruker Ultima 2Pplus Multiphoton Microscope
Multiphoton microscope that is designed for intravital imaging, with fully motorized control of objective X-Y-Z position, as well as two axes of rotation for precise imaging orientation. Second scan path enables simultaneous imaging and photoactivation.
Model_Number_Ultraflex III_MALDI-TOF/TOF
Bruker | Ultraflex III MALDI TOF/TOF Mass Spectrometer
MALDI (Matrix Assisted Laser Desorption/Ionization) tandem mass spectrometer specially designed for automated MS and MS/MS high throughput identification of proteins and peptides. Tandem Mass Spectrometry is a technique that utilizes more than one mass selective stage in a mass spectrometer.
Bruker | ultraXtreme X-Ray Imaging System
Smartbeam-II laser enables ultra-high data acquisition speed in both MS and MS/MS at full systems performance. The well-established proprietary smartbeam laser provides unprecedented analytical and matrix flexibility in workflows from protein tissue imaging, intact proteins analysis, Glycoproteomics, biologics or oligo QC, to LC-MALDI proteomics - all fully enabled at 1-2000 Hz repetition rates. Bruker's patented smartbeam technology is already widely accepted as the most viable MALDI imaging laser technology. The new ultrafleXtreme now enables low pixel sizes for high spatial resolution imaging. Importantly, outstanding spectral quality and signal intensity are maintained at even the smallest laser beam diameters.
Spectrometer that combines the quantitative capabilities of TG and the identification capabilities of FT-IR spectroscopy. Thermodynamic transitions, thermal stability, decomposition and chemical reactions can be detected and quantified with high accuracy over a broad temperature range.
95-C1700-160 SAMPLMET 2 Abrasive Cutter is a complete bench top unit with recirculating coolant system that includes totally enclosed cutter with 1 HP (735W) motor and 3400 RPM no load speed with a 1¼″ (32mm) diameter solid bar cutting capacity. The cutter has a 1½″ (38mm) vise capacity, light alloy base casting, molded glass-reinforced-plastichood, left-hand cam activated vise, operator controls, clean-out hose, recirculating system with 1â�„10 HP, 1 phase motor, baffled 7 gallon (27 liter) tank with flow control vavle, 1″ (25mm) coolant drain, interconnecting hoses and electrical cable. Includes samples of COOLMET and assorted 9″ (229mm) abrasice cut-off wheels.
Bruker | Vutara 352 Super Resolution Microscope
Fluorescence microscope that enables quantitative imaging at nanoscale using fluorescence microscopy based on single molecule localization. Includes techniques such as PALM, STORM, dSTORM, DNA PAINT.
Corbett | CAS 4200 Automated PCR Setup Robot
Pipetting robot for qPCR setup and compatible with any real-time instrument. All qPCR tube formats and plate types are supported, including capillaries. It easily interfaces with upstream sample-prep systems such Corbett X-tractor-Gene, Roche MagNA Pure, QIAGEN BioRobot M48 Workstation, and others. CAS-4200 is identical to the CAS-1200 quantitative PCR setup robot but with over twice the deck capacity.
Thermo Fisher | Bulb Replacement Kits for Environmental Chambers
Bulb replacement kit that contains 7 fluorescent bulbs for light module.
Bruker | Ultima Investigator Multiphoton Microscope
Multiphoton microscope that features a base system specifically optimized for in vivo studies and is designed for add-on flexibility with a host of specialized options.
Spectrometer extension that makes use of high precision semiconductor based photomixers, converting near infrared laser light into THz radiation. The extension provides access to the single digit wavenumber regime and highest resolution without the need of cryogenically cooled components.
Software package for streamlined import of omics metadata from European Nucleotide Archive into OMICS Data Paper manuscript. Omics Data Paper R Shiny app demonstrates workflow for automatic import of ENA genomic metadata into omics data paper manuscript. Streamlined conversion of metadata into manuscript facilitates authoring of omics data papers, which allow omics dataset creators to receive credit for their work and to improve description and visibility of their datasets.
Open source software suite for mass spectrometry based proteomics. Software repository and collection of free software for analysis of mass spectrometry data. Software and code snippets for visualization and analysis of mass spectrometry data with emphasis on automated methods for proteomics and protein analysis.
Open source machine learning and data visualization. Data Mining Toolbox in Python used to build data analysis workflows visually, with large, diverse toolbox.
Software tool to open and assess stereolithographic data. Software application tailored for additive manufacturing, rapid prototyping, and 3D printing.
McKinley | Cell Biosciences CB1000 Immunoassay
Immunoassay system that enables rapid, quantitative analysis of specific proteins in as few as 25 cells per assay. Detailed information is generated on the post-translational modification status of critical signaling proteins. The system is fully automated and speeds samples from a standard 384-well microplate to final results, ensuring sample-to-sample consistency., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Set of microfluidic plates with pre-primed, disposable plates for live cell analysis.
Thermo Fisher | Countess Cell Counting Chamber Slides
Countess Cell Counting Chamber Slides are designed for use with Countess Automated Cell Counter. This set includes 100 boxes of slides 50 slides per box and 2 × 100 mL bottles of trypan blue 0.4 percent. Provides total cell count, percent viable cells, and average cell size in 30 seconds. Each slide has two separate, enclosed chambers that can be used to count one sample in duplicate or to count two different samples.
Thermo Fisher | CO2 and LN2 Backup Systems Refrigerator and Freezer Accessories
CO2 and LN2 backup system that ensures security for critical samples by using ultra low temperature freezers. Systems inject liquid CO2 or LN2 into cabinet when cabinet temperature warms to preset level.
Covaris | E220evolution Focused ultrasonicator
Focused ultrasonicator that enables multi sample, batch preparation, capable of processing wide range of sample types and volumes.
Focused ultrasonicator with compact, easy to use system, formatted for 1 to 8 sample batch processing with integrated chiller and automated water management.
Focused ultrasonicator that was developed for superior precision and accuracy, new and advanced engineering designs enables easier maintenance and user friendly experience.
Spectrum Chemical | CL-1000 UV Crosslinker CL-1000
Preset and manual controls for UV or time exposure settings. Internal microprocessor measures and controls UV output, ensuring maximum energy efficiency. Consistent crosslinking takes seconds with 8W shortwave UV tubes. Select shortwave for sterilization and bonding DNA; midrange for gel electrophoresis; or long wave for UV curing. Crosslinker has maximum energy setting of 999,900 �J/cm2. Uses five 8W UV tubes. Digital LED displays settings. Viewing window blocks UV while allowing visibility of chamber interior. An internal interlocking safety system is designed for automatic shutoff when the door is opened. 115V, 60Hz; ETL-/ETLc-certified. External dimensions (D x W x H) in. (cm): 13.7 x 15.6 x 8.75 (34.8 x 39.6 x 22.2).
Focused ultrasonicator that can be fully integrated on many liquid handler platforms with high throughput sample processing with AFA energetics and AFA TUBE TPX plates.
Thermo Fisher | Cytomat 2 C4xx-LiN Series Automated Incubators
Series of automated incubators that ensure reproducible process, temperature uniformity and stability for incubation storage of cell culture applications. Cytomat incubators available in various temperature ranges and gate positions for hand off to lab automation robot. Can be integrated with mean access time of 12 sec.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 28,2024. RT PCR preparation liquid handler that features single channel dispense head capable of delivering volumes as low as 1 microliter. The single channel ensures precise dispensing for various tube types in addition to standard 96-well and 384-well microplates.
Cressington 208HR now offers real solutions to the problems encountered when coating difficult samples for FE-SEM. In order to minimize the effects of grain size the 208HR offers a full range of coating materials and gives unprecedented control over thickness and deposition conditions. To minimize charging effects the 208HR stage design and wide range of operating pressures allows precise control of the uniformity and conformity of the coating. The HIGH/LOW chamber configuration allows easy adjustment of working distance.
Nikon | Defonbrune SMZ-2B Microforage Stereo Microscope
Compact stereo microscope that is used for reflected light observation. Configurable with desk mount boom stand or base plate boom stands. Typical factory magnification comes 8 - 50X. It can accomodate a high intensity light source.
Analyzer with up to five lasers, three scattering channels, and 64 fluorescence channels, the Aurora suits every laboratory's needs, from to high complexity applications. A paradigm shifting optical design provides unprecedented flexibility, enabling the use of a wide array of new fluorochrome combinations without reconfiguring your system for each application. The state-of-the-art optics and low-noise electronics provide excellent sensitivity and resolution. Flat-top beam profiles, combined with a ly designed fluidics system, translate to outstanding performance at high sample flow rates.
Stylus profiler that can be configured with 4-inch Y auto stage to enable 3D imaging or be equipped with a 6-inch X-Y auto stage that, in addition to 3D mapping, provides automation and programmability of over 200 sample sites.
Blade server that features up to six-core processors. The blades are designed to combat data center sprawl and IT complexity.
Blade server that is designed for high-end databases and dense data center environments.
PowerEdge 6950 rack-dense 4U is a server that delivers performance with impressive low power consumption helping organisations address increasing datacentre complexity. Featuring quad-socket, dual-core AMD Opteron processing power, it provides high performance scalability. The design of the system provides for seamless upgrades from dual-core to quadcore within the same thermal envelope. The PowerEdge 6950 server is built to handle demanding enterprise applications without stressing datacentre resources making it for large databases, server consolidation, virtualisation and migrations from costly RISC-based systems.
Server delivers outstanding functionality in just 2U of rack space. With the combination of processors, large memory, fast storage options and GPU accelerator support, the R730 performs exceptionally well in a number of demanding environments.
Dell PowerEdge R815 is a 4-socket rack server offering the latest AMD Opteron processors with up to 48 processor cores and an excellent balance of advanced manageability, memory scalability, I/O, and redundancy in a space-saving 2U form factor.
Windows 7 Professional (32-Bit OS). Built for environments where space is at a premium, the Dell Precision T5500 delivers dual-socket workstation performance in a compact, quiet package. Incredibly fast and efficient despite its size, the Dell Precision T5500 features dual-socket Inte Xeon architecture with Intel QuickPath technology (in which each processor core features an integrated memory controller and high-speed interconnects), as well as support for up to 72GB* of DDR3 Registered ECC memory. For even more stunning levels of performance, the optional NVIDIA Tesla C2075 GPU card can be added, creating your own “personal supercomputerâ€� for CUDA-enabled applications.
Server with large memory capacity, multiple redundant fabrics and massive total throughput. The server delivers 24 DIMM slots, up to 192GB total RAM, and highly available redundant throughput capacity.
Thermal Evaporation system evaporates many of the metals and compounds involved in optical coatings, metallization, and electron microscope specimen preparation with no discernible contamination. This thin film deposition system also offers flexibility with a range of configurations available to meet your needs, including evaporation from a range of sources such as tungsten filaments, wire baskets, foil boats, baffle box heaters as well as carbon rod or yarn accessories., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Our most workstation delivers the multi-core processing punch you,ve been waiting for with levels of performance you,ve only dreamed about. Developed in close collaboration with hardware and software partners, the nextgeneration Dell Precision T7500 workstation helps you create, design, render and analyze without compromise. Designed to deliver groundbreaking performance, blistering speed and scalability for compute and graphics-intensive environments, the Dell Precision T7500 helps you power through the most complex tasks and complete projects even faster with up to 50% more system memory than its predecessor.
Custom Biogenic Systems | Dewer V1500-AB Isothermal Freezer
Custom BioGenic Systems V1500-AB Isothermal Liquid Nitrogen Freezers offer liquid nitrogen storage temperatures without liquid nitrogen contact. Liquid nitrogen is stored in our patented jacketed space in the wall of the freezer. This technology offers safe dry storage for your samples. With no liquid nitrogen in the storage area the risk of cross contamination and the safety risks associated with the handling of liquid nitrogen are greatly reduced. This also means that the entire storage space can be used for inventory. Our wide lid opening provides easy, unrestricted access to samples and won't affect the temperature inside the freezer. All Isothermal freezers use our time tested and 2301 controller with a dual temperature display, autofill and many additional features. Custom BioGenic Isothermal Liquid Nitrogen Freezers have an industry best temperature gradient that averages -193C inside the storage area.
Thermo Fisher | Dionex ICS-6000 Carbohydrate Removal Accessory Kit for ED Electrochemical Detection
Accessory for ion chromatography instruments that provides amino acid quantification by removing carbohydrates from amino acid samples in line.
Liquid Chromatography Mass Spectrometer system that has been designed to optimize low flow separations and facilitate easy coupling to mass spectrometry to provide the best resolution, sensitivity, and selectivity for nano LC and proteomics applications. Dionex has played a pioneering role in the field of nano HPLC, a technique that generally involves the application of columns with an internal diameter of 75,�m and low flow rates of around 300 nL/min. These configurations are best for analysis with limited sample starting amounts, due to the sensitivity enhancement of the smaller column i.d. Dionex offers several solutions to accommodate and robust nano LC as a front end to mass spectrometry and to fulfill three typical requirements:
Thermo Fisher | Dionex PC10 Postcolumn Pneumatic Delivery
PC10 Postcolumn Pneumatic Delivery System
Reaction system that ensures consistent, pulse free reagent delivery for applications with high background absorbances, such as trace level transition metal analysis using post column reaction with 4 2 pyridylazoresorcinol PAR. Provides reagent with less pressure pulsation by applying constant pressure, eliminating need for pump. Assures optimal flow by applying constant pressure, eliminating need for pump.
EpiSonic Multi-Functional Bioprocessor 1100 system
EpiSonic Multi-Functional Bioprocessor 1100 system is a multi-sample sonication instrument of the latest generation for use in a wide range of biological applications, in particular for DNA and chromatin shearing. This completely digital instrument allows for simultaneous optimized processing of 1 to 12 samples by tube, best for NGS applications, and can be easily integrated into existing lab workflows. Chiller is included at no additional charge. The EpiSonic 1100 sonicator was designed and built with the processing of biological samples specifically in mind, particularly NGS applications via Illumina or Ion Torrent workflows.
E-beam evaporator recommended for oxide and nitride materials. Designed to operate around the e-5 millibar vacuum range, EE-2 can also be used to deposit metals (non-toxic materials) if very low pressure is not a critical factor in your process. The water-cooled substrate holder can accommodate one wafer up to 3â€� diameter. EE-2 has a rotary-vane mechanical roughing pump and a turbo high-vacuum pump, and is a relatively low voltage (~3.8kV) electron beam evaporation deposition system with a 4-pocket, water-cooled rotating hearth.
Eppendorf | 5075 epMotion Automated Liquid Handling System
System provides precise, accurate alternative to time-consuming manual pipetting and liquid handling tasks. The combination of accelerated operational speed, new software & hardware features and an increased number of worktable positions make the systems best for and flexible laboratory use across a wide range of liquid handling applications. To ensure easy and consistent use, epMotion 5075 employs both Eppendorf's established epBlue software and an new software assistant concept. This supports the programming of applications and ensures that all users can use the system with only initial training. In addition, novel features such as a new CleanCap option, including UV light decontamination and a HEPA filter for purified air, offer new standards of decontamination and sample safety. This is supported even further by an optical sensor that checks labware, liquid levels and tip counts and type at the start of each cycle, hugely decreasing any risk of error during the run.
Benchtop centrifuge with maximum speed of 15,000 rpm. It features a 30-minute built-in timer, LED light that cycles at 1 second intervals, and a pushbutton switch for short momentary spins.
Eppendorf 5417R is a refrigerated centrifuge with a brushless motor that spins up to 16,400 RPM with maximum RCF up to 25,000 x g. The Eppendorf 5417R comes equipped with an integrated cooling fan that helps remove residual heat build-up. Compact design and quiet operation (<60dB) makes the Eppendorf 5417R on a crowded lab bench or in a cold room. Automatic rotor detection system senses the rotor type and prevents the centrifuge from exceeding the rotor speed limit. Time (selectable in minutes or seconds; up to 99 minutes or hold) and speed (variable in rpm or rcf) are easily set using the keypad and are displayed on the LED read-out. All functions are microprocessor controlled. The Eppendorf 5417R conforms to International Safety Standard IEC1010 and features a steel plated rotor housing and double locking lid for maximum end user protection. RS 232 interface provides data output for computer control or data recording.
Eppendorf centrifuge 5424 (Eppendorf microcentrifuge models 5424 and 5424R) are versatile 24-place centrifuges that set new standards for silence, speed, and simplicity in operation. The fixed-angle rotor is best for standard applications and centrifugation of biohazardous or radioactive samples. The miniprep spin column rotor features an extra-high rim to support open tube lids. The PCR tube rotor is best in "knockdown" spin applications for liquids after reaction setup. Certified aerosol-tight rotors have red screw-tops for easy identification. These are the direct replacements for the legendary models 5415D and 5415R.
Cross-over Centrifuge 5430 and 5430 R combine the best features of a microcentrifuge (small footprint) and multipurpose centrifuge (versatility) in one instrument. These centrifuges spin rotors for Eppendorf tubes and PCR strips as you would expect from any microcentrifuge. But that's not all. In a compact size, Centrifuge 5430 and 5430 R also accommodate rotors for microplates and 15/50 mL conical tubes. Now, the rotor program has been expanded with additional Eppendorf QuickLock rotors. This includes 48-place rotors (1.5/2.0 mL), a 16-place rotor for Eppendorf Tubes 5.0 mL and a swing-bucket rotor (24 × 1.5/2.0 mL). With their unmatched versatility, Centrifuge 5430 and Centrifuge 5430 R are the flagship products among the Eppendorf microcentrifuge portfolio. Available as keypad or knob variant
ibrVating blade microtome that is capable of preparing sections in the range of 10 to 1000 micrometres from a wide variety of both biological and materials specimens. The blade is clamped at a pre-set angle on a horizontally disposed ram which runs on precision engineered cross roller linear bearings.
Thermo Fisher | Dioxin Analyzer Mass Spectrometry System
Thermo Scientific Dioxin Analyzer to deliver quantitation of dioxins and dl-PCBs in food samples in compliance with EU regulations. Ensures quantitation of polychlorinated dibenzo p dioxins PCDDs, polychlorinated dibenzo furans PCDFs and dioxin like polychlorinated biphenyls dl PCBs in food and feed samples. Dioxin Analyzer includes Thermo Scientific TSQ 9000 Triple Quadrupole GC-MS/MS, consumables, system suitability check standard solutions, e-workflow with acquisition method, data processing software, isotope dilution calculation, and reporting methods in compliance with EU regulations.
Eppendorf | Biophotometer D30 Photometer
Spectrophotometer that processes data, records at fixed wavelengths and evaluates results. For specific methods, additional measurements are recorded and displayed as graph, making impurities quick to identify.
Centrifuge for medium to high-throughput laboratories with swing-bucket rotors and adapters accommodate tubes and bottles from 0.2 mL to 750 mL with a centrifugation speed of up to 14,000 rpm.
Eppendorf | CellTram 4r Air/Oil Injector
Pneumatic injector that is used for oil free micromanipulation and gentle holding of cells in suspension. It is also suitable for uptake and injection of cells, like sperm or ES cells.
Eppendorf | epMotion 5070 Automated Pipetting
Automated pipetting workstation that is used for serial dilutions, reagent distribution, sample transfer from tubes to plates, and sample normalization.
Eppendorf | epMotion 5070f Automated Pipetting
Automated pipetting workstation that allows for the automation of key processes such as seeding cells, media changes, or performing assays e.g. cytotoxicity. It enables you to handle 6, 24 or 48 well plate or even denser formats from 96 to 384 wells.
Eppendorf | epMotion 5073l Automated Pipetting
Automated pipetting workstation that with 6 deck positions, gripper option and automatic exchange of 2 tools for automatic PCR setup in the 96 or 384 plate formats.
Centrifuge for medium capacity needs that allows for molecular applications in tubes up to 250 mL and offers additional swing bucket and fixed angle rotors as well as deepwell plate capacity for versatility. It has a centrifugation speed of up to14,000 rpm.
Centrifuge that is used for medium to high throughput laboratories and combines versatility and capacity for both tubes and plates with compact footprint.
Eppendorf | epMotion 5073m Automated Pipetting system
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 3, 2023. Automated pipetting workstation that is tailored for nucleic acid purification, but can be used for other liquid handling tasks. Integrated magnetic finger and ThermoMixer module is used for magnetic bead based purifications.
Eppendorf | epMotion 5075l Automated Pipetting
Automated pipetting workstation with 15 worktable positions that is used for applications such as the purification of nucleic acids with magnetic beads or routine applications with several plates
Eppendorf | epMotion 5073m NGS Solution Automated Pipetting
Automated pipetting workstation that is used for low throughput Next Generation Sequencing library preparation of up to 24 samples.
Eppendorf | epMotion 5075m Automated Pipetting
Automated pipetting workstation that combines magnetic finger module and ThermoMixer to facilitate magnetic bead separation, mixing, and temperature control in one deck position.
Centrifuge 5804/5804 R is a high speed centrifuge for medium capacity needs. It allows for molecular applications in tubes up to 250 mL and offers additional swing,bucket and fixed,angle rotors as well as deepwell plate capacity for increased versatility. Eppendorf Centrifuge 5804/5804 R with its renowned quality and reliability offers you the most cost efficient solution for your medium throughput applications,now and in the future. It allows for molecular applications in tubes up to 250 mL and offers additional swing-bucket and fixed-angle rotors as well as deepwell plate capacity for increased versatility.
Eppendorf | epMotion 5075t NGS Solution Automated Pipetting
Automated pipetting workstation that combines automated liquid handling and software features with accessories and consumables for Next Generation Sequencing library preparation and NGS kit flexibility.
Eppendorf | epMotion 5075t Automated Pipetting
Automated pipetting workstation that includes a proprietary module to mix, heat or cool samples and reagents. The module can be loaded and unloaded with the gripper and pipetting to the mixer is possible before and after mixing steps.
Eppendorf | epMotion 5075v Automated Pipetting
Automated pipetting workstation that allows walk away automation of purification protocols that rely on vacuum filtration performing applications, such as nucleic acid purification or solid phase extraction away from workbench.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14,2023. Eppendorf's electronic microinjectors FemtoJet 4i and FemtoJet 4x with their operation menu and a range of functionalities are perfectly suited for injecting small to intermediate volumes. With a built-in compressor, the FemtoJet 4i is the tool of choice for injecting aqueous solutions into adherent cells and suspension cells. If your research demands injecting volumes greater than 100 pL and/or longer series at higher pressures, FemtoJet 4x with its external pressure supply (not included) delivers the precise and continuous pressure required. Featuring the same quality design and compatibility features as the FemtoJet 4i, the FemtoJet 4x is the "heavy duty" device for those more demanding applications. Both the FemtoJet 4i and FemtoJet 4x, form the system with Eppendorf micromanipulators, yet they integrate just as easily with non-Eppendorf micromanipulation systems. The electronic connection between FemtoJet 4i or 4x and TransferMan 4r or InjectMan 4 guarantees simple, rapid and reproducible microinjections into cells, simplifying your daily work and speeding up your workflow. The FemtoJet 4i/ 4x injectors are for research use only.
Microscope accessory that is suited for injecting small to intermediate volumes, up to 100 pL, featuring wide range of functionality, simple operation and built in compressor to independently deliver required pressure. Ideal for injecting aqueous solutions into adherent cells and suspension cells.
Eppendorf | epMotion 96 and 96xl Automated Pipetting
Automated pipetting workstation that automates multichannel pipetting, with reproducibility of results from cell based assays, ELISA, cell seeding, nucleic acid quantification, plate reformatting, or other applications.
IncuCyte ZOOM system is a live-cell imaging and analysis platform that enables automated quantification of cell behavior over time (from hours to weeks) by automatically gathering and analyzing images around the clock. The system provides insight into active biological processes in real-time which is not possible using single-point and end-point measurements. The system resides within the controlled environment of a standard cell incubator. All imaging is completely non-invasive and non-perturbing to cell health. The system can process multiple plates, flasks and dishes in parallel and does not depend on shuttling plates into and out of the incubator.
Benchtop concentrator that provides vacuum concentration of DNA and RNA, nucleotides, proteins and other liquid or wet samples. Coated lid provides chemical resistance against aggressive acids and organic solvents, like TFA and DMSO.
Biological shaker with heavy-duty drives that provide long life and quiet operation under moderate loads and at speeds up to 400 rpm.
MX-20 Cabinet X-ray System is utilized to produce highly detailed radiographs of seed and grain to inspect for viability, infestation, damage or contamination. The system is available with either our large 12 cm x 12 cm DC-12 camera or our smaller, less expensive 5 cm x 5 cm DC-5 camera. Both provide 10 lp/mm spatial resolution in contact mode. Magnification allows for spatial resolution of up to 50 lp/mm. The 20 �m nominal focal spot and up to 5X additional geometric magnification provide ultra high-contrast and high spatial resolution images. If a larger field of view is required, the MX-20 can be used with a CR plate and small, upright CR reader to obtain a field of view up to 10â€� x 12â€�.
FEI | Apreo SEM (Scanning Electron Microscope) for Life Sciences
Scanning electron microscope that provides a sub-nanometer or all-around nanometer resolution performance on materials spanning from catalysts, powders, nanoparticles, and bulk magnetic samples to nanodevices.
Thermo Fisher | FEI Aquilos 2 Cryo-FIB for Life Sciences
Sample preparation tool used for the preparation of thin, electron transparent lamellas for high resolution cryo electron tomography or MicroED of micro crystals.
FEI | flexProber System for Semiconductors
Nanoprobing platform that provides electrical characterization and fault isolation capabilities for process development, device design debug, and failure analysis.
Sample preparation workflow that is used for transmission electron microscopy (TEM) analysis.
FEI | Glacios Cryo-TEM (Transmission Electron Microscope) for Life Sciences
Microscope that features 200 kV XFEG optics and ensures a robust and contamination-free pathway throughout the entire workflow, from sample preparation and optimization to image acquisition and data processing.
LX-60 Specimen Radiography System is best for imaging larger animals and more dense specimens, due to its cabinet size and energy range of up to 60 kV. The system's large 12 cm x 12 cm camera offers 10 lp/mm spatial resolution. Magnification allows for spatial resolution of up to 60 lp/mm. The 10-12 �m typical focal spot and up to 6X additional geometric magnification provide ultra high-contrast and high spatial resolution images. If a larger field of view is required, the LX-60 can be used with a CR plate and small, upright CR reader to obtain a field of view up to 10â€� x 12â€� (25.4 cm x 30.5 cm).
Electrical failure analysis system for semiconductors that offers transistor probing for electrical characterization and fault localization in support of semiconductor technology development, yield engineering and device reliability improvement.
FEI | Helios NanoLab 1200AT DualBeam for Semiconductors
Wafer analysis system that can create site-specific transmission electron microscope (TEM) samples thin enough to capture a single transistor at the 10nm node, from wafers up to 300mm in diameter.
Transmission electron microscope that is used for automated applications such as single particle analysis, cryo-electron tomography, and micro electron diffraction.
FEI | Meridian 7 System for Semiconductors
Electrical failure analysis system for semiconductors that provides visible laser voltage imaging and probing and dynamic laser stimulation on sub-10nm devices.
FEI | Meridian V System for Semiconductors
Electrical failure analysis system for semiconductors with optimized dynamic LSM platform that supports automated test equipment docking and back side analysis with laser voltage probing, laser voltage imaging, and laser simulation for critical path analysis.
FEI | Meridian WS-DP System for Semiconductors
Electrical failure analysis system for semiconductors that enables faster defect localization by using production testers, load boards, and probe cards.
Semiconductor with enhanced lock in thermal emission that provides better signal to noise ratio, increased sensitivity and higher feature resolution than steady state thermography.
FEI | Meridian IV System for Semiconductors
Electrical failure analysis system for low-voltage, high-density semiconductor devices with the ability to diagnose wide ranging failure modes, including parametric failures and those resulting from design-process marginalities.
Transmission electron microscope that provides fast, precise measurements for semiconductor manufacturers to develop and control their wafer fabrication processes.
FEI | nProber III System for Semiconductors
Electrical failure analysis system for semiconductors with fault localization and transistor characterization that allows users to characterize individual transistor performance down to 7nm node.
Focused ion beam system that for semiconductors that enables a highly controlled beam profile and current, accurate navigation and ion beam placement, and reliable end-pointing.
Desktop scanning electron microscope that is used to scan sample and find suspect gunshot residue particles. If suspect particle is found, Energy Dispersive Spectroscopy technique is used to identify elements in that particle.
FEI | Meridian M System for Semiconductors
Electrical failure analysis system for semiconductors that uses high sensitivity broadband DBX photon emission and Static Laser Stimulation techniques to pinpoint the location of electrical faults.
Desktop scanning electron microscope that offers fast, high-resolution imaging in addition to an integrated energy-dispersive X-ray diffraction (EDS) detector for elemental analysis.
Desktop scanning electron microscope that provides high-quality images and features autofocus and automated source alignments.
Desktop scanning electron microscope with increased chamber size for large samples up to 100 mm x 100 mm.
Scanning electron microscope that combines a field emission gun (FEG) and three vacuum modes (high vacuum, low vacuum, and ESEM) to provide the flexibility to accommodate a wide range of samples, including those that are outgassing or otherwise not vacuum-compatible.
Desktop scanning electron microscope with CeB6 source that offers high brightness while requiring low maintenance. It allows sample structures to be physically examined and their elemental composition determined.
FEI | Talos F200C TEM and STEM (Scanning/Transmission Electron Microscope)
Microscope that is designed for performance and productivity across a wide range of samples and applications, such as 2D and 3D imaging of cells, organelles, asbestos, polymers, and soft materials, both at ambient and cryogenic temperatures.
Scanning electron microscope that is used for industrial research and development with environmental SEM capability.
Transmission electron microscope that is built for delivering high-resolution 3D characterization of biological samples and biomaterials in cell biology, structural biology, and nanotechnology research.
TEM and STEM microscope for dynamic microscopy.
Transmission electron microscope that combines high-resolution STEM and TEM imaging with energy dispersive X-ray spectroscopy signal detection.
Transmission electron microscope that is designed for performance and productivity across a wide range of samples and applications, such as 2D and 3D imaging of cells, cell organelles, asbestos, polymers, and soft materials, both at ambient and cryogenic temperatures.
Scanning/transmission electron microscope that is designed for high-speed imaging and analysis of semiconductor devices.
Next generation, ultra-high resolution, aberration corrected, scanning transmission electron microscope delivering the ultimate optical performance and flexibility with unprecedented reproducibility.
Thermo Fisher | Talos F200i Transmission Electron Microscope
Thermo Scientific Talos F200i is an integrated (S)TEM to perform both Transmission Electron Microscopy (TEM) and Scanning Transmission Electron Microscopy (STEM) in a single system. It acts as a 20-200 kV field emission instrument designed for high-resolution 2D/3D imaging, in situ observation, and EDX analysis.Designed for performance and productivity across a wide range of Materials Science samples and applications. Its standard X-Twin pole piece gap combined with a reproducibly performing electron column opens opportunities for high-resolution 2D and 3D characterization, in situ dynamic observations, and diffraction applications.
FEI | V400ACE Focused Ion Beam for Semiconductors
Focused ion beam system that can be configured for backside editing with an optional IR microscope and bulk silicon trenching package.
Microscope that is used for large volume samples with serial block face imaging and multi energy deconvolution.
Microscope that is used for characterization of nanomaterials with sub nanometer resolution and high material contrast SEM.
Eppendorf | FemtoJet 4x electronic microinjector
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14, 2023. Eppendorf electronic microinjectors FemtoJet 4i and FemtoJet 4x with their operation menu and a range of functionalities are perfectly suited for injecting small to intermediate volumes. With a built-in compressor, the FemtoJet 4i is the tool of choice for injecting aqueous solutions into adherent cells and suspension cells. If your research demands injecting volumes greater than 100 pL and/or longer series at higher pressures, FemtoJet 4x with its external pressure supply (not included) delivers the precise and continuous pressure required. Featuring the same quality design and compatibility features as the FemtoJet 4i, the FemtoJet 4x is the "heavy duty" device for those more demanding applications. Both the FemtoJet 4i and FemtoJet 4x, form the system with Eppendorf micromanipulators, yet they integrate just as easily with non-Eppendorf micromanipulation systems. The electronic connection between FemtoJet 4i or 4x and TransferMan 4r or InjectMan 4 guarantees simple, rapid and reproducible microinjections into cells, simplifying your daily work and speeding up your workflow. The FemtoJet 4i/ 4x injectors are for research use only.
Mass cytometer that enables deep profiling of translational and clinical research samples across range of cell surface and intracellular markers. Helios represents newer, more advanced iteration with improvements in throughput, detection range, and software capabilities.
Helios, a CyTOF system, comprises the most recent advances in mass cytometry and is designed to provide a new and improved tool for bioanalytical single-cell detection and analysis. This high-performance mass cytometer, from the CyTOF family of instruments, enables the analysis of more than 40 markers and ly allows their quantitative determination with negligible spectral overlap, a result of exquisite resolution between mass detection channels. Helios provides users with 135 detection channels that can simultaneously resolve multiple elemental probes at high acquisition rates, thereby maximizing the per-cell information obtained from a single sample. The expanded mass range of 75 209 amu and superior mass resolution provide researchers with the ability to differentiate adjacent peaks. The Helios system provides fast instrument startup, an easyto-use pneumatic sample loading system, an improved cell detection rate, and enhanced data storage capabilities. These attributes provide researchers with an unparalleled ability to generate high-resolution phenotypic and functional profiles of cells from normal and diseased states
FEI | Themis ETEM (Titan Environmental Transmission Electron Microscope)
Environmental transmission electron microscope that is used for in situ observation of structure dynamics at nanostructure-characteristic length scales.
Molecular Devices | Flexstation II Dual Monochromator Fluorescence Kinetics Flexstation
Molecular Devices FlexStation II is a benchtop scanning fluorometer and integrated fluid transfer workstation capable of conducting endpoint, kinetic, lambda scan and well scan experiments in a multi-well plate format (6, 12, 24, 48 and 96-well) and fluidics transfer experiments in 96-well format. The FlexStation II is best for measuring the activity of Gq-coupled receptors via the detection of intracellular calcium release. In addition, kits are available for the measurement of fatty acid uptake, cyclic GMP and AMP levels, potassium ion channel flux, and membrane potential. The dual monochromator optical bench design allows the user to choose multiple wavelengths and to optimize excitation and emission wavelengths for most fluorometric assays. Allow the user to obtain real-time kinetic data milliseconds before and after fluid transfer events. The dual monochromator optical bench design enables the user to choose multiple wavelengths and to optimize both excitation and emission wavelengths for most fluorometric assays.
Formulatrix | Formulator liquid handler for preparing crystallization reservoirs
Liquid handler specifically designed for Protein Crystallography that uses patented microfluidic technology to dispense up to 34 different ingredients. A 96-nozzle dispensing chip can dispense any volume of any ingredient of any viscosity into any well.
Thermo Fisher | Forma Steri-Cycle CO2 Incubators
Incubator that features an in-chamber HEPA air filtration system, which provides continuous protection against unwanted airborne contaminants, along with an on-demand, high-temperature sterilization cycle that simplifies routine cleaning.
Formulatrix | Mantis Automated Liquid Handler
Automated liquid handler with a diaphragm-based chip design that dispenses aqueous and organic solutions. It will dispense in any SBS template from 6 to 1536 well plates, and can be easily programmed to dispense to custom designs as needed.
Gatan | BioContinuum Imaging Filter Transmission Electron Microscope (TEM) Imaging and Spectroscopy
Microscope imaging filter that is optimized for cryo-EM and cryo-ET to gain further insight into system function and disease progression at the molecular level.
Gatan | ChromaCL2 iBSED Detector Scanning Electron Microscope (SEM) Imaging and Spectroscopy
Detector that is used for live color cathodoluminescence imaging in scanning electron microscopes.
Gatan | 930 Cryoplunge 3 Cryo Preparation System
Cryoplunge 3 system with GentleBlot technology is used for the preparation of frozen hydrated specimens for cryo-electron microscopy (cryo-EM). GentleBlot technology optimizes blotting force and pressure to provide gentle 1- and 2-sided blotting to minimize breakage of fragile specimen supports. Humidified plunging chamber safeguards the specimen from drying during the blotting process. Temperature controlled pot maintains the condensed ethane at its melting point. Specially designed quick disconnect mechanism on plunge rod allows fast and easy attachment of the plunge tweezers to facilitate specimen handling. Removable liquid nitrogen workstation provides a contamination free environment to protect the frozen hydrated specimen
Gatan | Dimple Grinder II Transmission Electron Microscope (TEM) Specimen Preparation
Instrument that prepares TEM specimens with mechanical method of pre-thinning to near electron transparency to greatly reduce ion milling times and uneven thinning.
Gatan | 3View System Scanning Electron Microscope (SEM) Imaging and Spectroscopy
Imaging system that automates sectioning and image capture of 3D ultrastructure using serial block face scanning electron microscopy.
Gatan | DigiScan II System Transmission Electron Microscope (TEM) Imaging and Spectroscopy
Detector and control system that uses digital beam control and image processing to enhance the photographic quality of digital images.
Single tilt liquid nitrogen cryo transfer holder that is designed for low temperature transfer and subsequent recording of electron beam sensitive, frozen hydrated specimens in TEM. Tilt ranges and compatibility of specimen holders vary according to TEM manufacturer, model, pole piece gap, and presence of in gap accessories.
Gatan | GIF Continuum and Continuum S Transmission Electron Microscope (TEM) Imaging and Spectroscopy
Microscopy system that is used for both EELS and EFTEM applications and has spectral acquisition rates as high as 8000 spectra per second.
Gatan | Ilion II System Scanning Electron Microscope (SEM) Specimen Preparation
Microscope accessory that is used for low energy surface preparation for SEM cross section viewing.
Gatan | K3 IS Camera Transmission Electron Microscope (TEM) Imaging and Spectroscopy
Large format camera for in-situ transmission electron microscopy.
Gatan | Murano In-Situ Stages Scanning Electron Microscope (SEM) Specimen Stages
SEM specimen heating stage that is specifically designed to enable in-situ research and designed to be compatible with geometrical requirements of different detectors including electron backscatter diffraction (EBSD) for dynamic observations.
Gatan | K3 Camera Transmission Electron Microscope (TEM) Imaging and Spectroscopy
Camera that is optimized for low-dose electron microscopy (EM) applications in both life science and materials science research and captures 1,500 full frames per second.
Gatan | OneView Camera Transmission Electron Microscope (TEM) Imaging and Spectroscopy
Camera that captures 16 MP images and video in all TEM applications.
Gatan | PECS II System Scanning Electron Microscope (SEM) Specimen Preparation
Argon ion polishing system that is designed to polish and coat samples for SEM imaging and analytical techniques.
Gatan | Monarc CL Detector Scanning Electron Microscope (SEM) Imaging and Spectroscopy
Cathodoluminescence detector that can determine the emission polarization properties of deep sub-wavelength structures like optical nanoantenna, nano-cavities, and photonic crystals.
Gatan | STEMPack Spectrum Imaging Transmission Electron Microscope (TEM) Imaging and Spectroscopy
Imaging system that supports the acquisition of data from a broad range of detectors, including: electron energy loss (EELS), characteristic x-ray emission (EDS), cathodoluminescence emission (CL), absorbed / induced current (EBAC/EBIC), and electron diffraction
Gatan | Solarus II Plasma Cleaner Transmission Electron Microscope (TEM) Specimen Preparation
Plasma cleaner that can remove hydrocarbon contamination from TEM and SEM samples and holders.
Gatan | Rio Camera Transmission Electron Microscope (TEM) Imaging and Spectroscopy
CMOS camera with scintillator and 1:1 fiber optic coupling to maximize light generation and collection.
Gatan | STEMx System Transmission Electron Microscope (TEM) Imaging and Spectroscopy
4D STEM diffraction system that enables a wide variety of 4D STEM experiments, including strain mapping, indexing, orientation mapping, virtual apertures, and differential phase contrast.
GE | AutoITC 200 Isothermal Titration Calorimeter
Isothermal titration calorimeter that can characterize molecular interactions of small molecules, proteins, antibodies, nucleic acids, lipids and other biomolecules. It can also be used to measure enzyme kinetics.
GE: Healthcare | Typhoon Trio Variable Mode Imager System
Variable mode imager that produces digital images of radioactive, fluorescent, or chemiluminescent samples and contains three internal lasers (blue, green, and red).
DPX Bravo provides you with tools for basic bone health assessment. Its footprint is smaller than most other DXA tables 186cm 74â€� long by 86cm 34â€� wide. feature, WHO FRAX fracture risk assessment tool allows you to accurately predict 10 year probability of patient suffering major fracture. It offers you you dual energy X ray absorptiometry DXA technology in small, space saving footprint. It also provides you with essential, bone densitometry applications, such as AP spine, dual femur and forearm.
Gatan | PIPS II System; Transmission Electron Microscope (TEM)
Transmission electron microscope that uses precision ion polishing system for precise centering, control, and reproducibility of the milling process.
GE: Healthcare | Discovery RF180; Radiography and Fluoroscopy System
Remote imaging system that can perform tomo, Auto Image Paste, DSA, and bariatric exams. It also includes variable SID to conduct chest exams and has a 705 lb (or 325 kg) weight capacity.
GE: Healthcare | GoldSeal Infinia Hawkeye 4; Imaging system
Dual detector SPECT/CT imaging system with extra large rectangular FOV detectors that incorporates hybrid imaging technology to help enable confident diagnosis, disease detection and precise localization.
GE: Healthcare | Precision 600FP; Imaging System
Flat panel radio-fluoroscopy system that provides ultra vivid imaging with frame rates ranging from 15 to 1 frames per second.
GE: Healthcare | OEC Elite CFD; Imaging system
System is bestly suited for range of surgical needs including vascular, cardiac, orthopedics, gastrointestinal, endoscopic, urologic, critical care, pain management and emergency procedures.It has efficient image capture with SmartView 180 180 pivot joint on Ergo C arm model. It consists of CFD CMOS Flat Detector. Enhanced imaging control and planning with Live Zoom, Digital Pen, measurements and annotations. Six dose control options that can be used alone or in various combinations Digital Spot, Digital Cine Pulse, High Level Fluoroscopy, Standard Fluoroscopy, Low Dose, Pulse
GE: Healthcare | Uroview 8K;Imaging system
Uroview 8K provides large field of view along with robust imaging platform to show you exact imaging detail. Designed to provide diagnostic image quality using dose saving strategies.Large field of view 17 inch x 17 inch dynamic digital flat panel detector.Superb resolution and grayscale with 2880 x 2880 resolution and 16 bit image processing. It has 32" inch high resolution LCD display monitor with picture in picture capability on articulating arms.Adjustable low table height 25.2 inches with near 360 degree SmartAccess.
GE: Healthcare | Biacore 3000 Real-time Biomolecular Interaction Analyzer
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8th,2024. Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants.
Compact imaging system that provides a stable platform for structured illumination microscopy (SIM) super resolution technology.
Typhoon FLA 9500 is a robust and versatile laser scanner that is bestly suited to multiuser environments. Biomolecular imaging applications include sensitive and quantitative measurements of Western blots, multiplex fluorescence, and radioisotopic labels by storage phosphor as well as digitization of colorimetric stains. The system is flexible and can be customized with lasers, filters and detectors for multiplex near infrared fluorescence with IRDye. Typhoon FLA 9500 provides 457/532/635 nm excitation and up to 10 �m resolution for gel, blot, tissue and array imaging. The system can be customized with 685/785 nm excitation, customized filters and detectors for multiplex and near infrared fluorescence applications.
GE | AKTA FPLC System, Protein Purification System
Purification system intended for microgram-scale protein purifications in Tricorn columns up to milligram-scale using HiTrap and HiScreen columns. For fast protein liquid chromatography of tens of grams of protein,can be used with flow rates up to 150 mL/min. This high flow rate is necessary when working with high-flow resins in large columns. Columns can even be packed at flow rates as high as 300 mL/min. System reduces hands-on time so that you can spend less time purifying proteins and more time focusing on your results. Easily switch between different users and applications. To get you up and running quickly, methods are easily created by dragging and dropping predefined templates in UNICORN 7. Purification of protein to sufficiently high yield and purity can be a time- and resource-consuming process. To address fast and efficient protein purification, Can be set up in different ways to handle multistep purification. With an additional column valve up to 10 columns can be connected enabling automation of several samples and steps.
QPixII offers high precision benchtop colony picking, gridding, and rearraying technology that has been specifically designed for high throughput genomics. It allows for automatic picking of 3500 colonies or plaques per hour. Constructed within a welded steel framework, the main bed is capable of holding 15 microtitre plates and 2 bioassay trays. The unit includes a sterilization bath and heated-air drier to ensure cleaning and drying of picking/gridding heads between the cycles. Colonies or plaques are visualized via CCD camera and picked from bioassay trays (QTrays) by a 96-pin picking head and inoculated into pre-filled 96 or 384 well QPlates. High accuracy picking, control and management at every step. Macroarrays are easily generated using the robots gridding software and accessories. Rearraying of clones can also be performed. The minimum computing requirements include WindowsTM software and an Intel Pentium III processor (600 MHz), 128 MB of RAM, and a 4 MB, 256 color video card. The unit is supplied with two picking/rearraying heads, one gridding head, and QSoft software including picking, gridding, and rearraying modules. Dimensions: 56.30"w x 28.74"d x 31.50"h.
Molecular Devices | Gemini XPS Microplate Reader
Reader with top-read capability measures fluorescence on variety of sample formats from 6- to 384-well microplates in endpoint, kinetic, spectral scan, and well-scan modes.
GE | 3.0T MR750 Magnetic Resonance Imager
Magnetic resonance imager that is built around a third-generation, short-bore, superconducting 3.0T magnet and can generate multiple image contrasts in a single MRI scan including T1, T2, STIR, T1 FLAIR, T2 FLAIR* and PD contrasts of the brain in a single acquisition.
Disruptor is available in analog or digital models, allows for Hands-Free disruption of up to twelve 1.5 or 2.0ml microtubes with timer from 0-15 minutes or continuous for analog models, and from 0-99 minutes or continuous for Digital models. Provides multi-directional action, which simultaneously agitates and vortexes at high speed, dramatically increasing cell disruption or sample resuspension efficiency. Suitable for use in cold rooms or incubators. best for difficult glass bead procedures - cell disruption/homogenization of yeast, bacteria, plant and animal tissue or anything that requires extremely violent high speed agitation. Digital model incorporates an adjustable speed alarm. Remove microtube holder and attach the supplied Pop-off Cup for high speed vortexing of single test tubes. The patented Disruptor Genie provides multi-directional action, which simultaneously agitates and vortexes at high speed, dramatically increasing cell disruption or sample resuspension effeciency.
Hamilton | RT STARlet Assay Ready Workstation
Assay ready workstation that combines qPCR setup and qPCR on one platform.
Cole-Parmer | GenoGrinder High Throughput Sample Homogenizer (SPEX)
Geno/Grinder is an automated high-throughput plant & animal tissue homogenizer and cell lyser. It is equipped with an adjustable clamp that accommodates a full range of sample vials from 2mL to 50mL centrifuge tubes or up to six deep-well titer plates. It is specifically designed for rapid cell disruption, cell lysis and tissue homogenization through bead beating. This enables fast and efficient extraction of nucleic acids, proteins and other molecules. The new model Geno/Grinder incorporates a password protected, touch screen control panel, enabling the user to program run time, rate, cycles and pause time. A full range of Kryotech accessories are available to preserve temperature sensitive samples such as proteins and RNA. The Geno/Grinder is also recognized as an excellent automatic axial extractor. It is the best tool for the QuEChERS method used for extracting pesticide residues and other organic compounds. The Geno/Grinder enables increased throughput, improved extraction efficiency and reproducibility over traditional sample preparation methods. A full range of pre-loaded sample vials for different sample types is also available for fast and set up.
Hamilton | [MPE]2 Solid Phase Extraction Device
Positive pressure module that automates positive pressure processes, such as solid-phase extraction (SPE) and other positive-pressure applications with high reproducibility.
Hamilton | Aliquot STARlet Assay Ready Workstation
Fully automates source-target sampling of blood and other homogeneous and heterogeneous biological samples for downstream applications. The walkaway process safely removes and replaces stoppers from a variety of commercial blood collection-type tubes, mixes the samples, and precisely aliquots daughter samples in under two minutes per tube. Up to 64 source tubes and 256 target tubes may be processed at once.
Hamilton | AutoLys STAR Assay Ready Workstation
Assay ready workstation that fully automates cell lysis and differential separation of DNA from biological evidentiary samples contained in specialized, barcoded spin-basket/filter type AutoLys Tubes.
Assay ready workstation that fully automates source target sampling of blood and other homogeneous and heterogeneous biological samples for downstream applications.
Hamilton | BiOS Automated Ultra Low Temperature Freezer system
BiOS is automated bio freezer storage system specifically designed to store sensitive biological samples. This ultra low temperature freezer is capable of reaching temperatures as low as minus 80°C, ensuring biological specimen integrity. BiOS can be scaled to fit your laboratory needs as a premier option for storing biological samples.Automated sample storage platforms run on INSTINCT S software.
Hamilton | easyBlood STARlet and STAR Assay Ready Workstation
Assay ready workstation that fully automates image based blood fraction detection and aliquoting steps.
Laboratory pH sensor that is commonly used for microtiter plate applications (especially solutions containing protein) with a slim tip that allows for immersion depth of only 7 mm.
Hamilton | ELISA NIMBUS Assay Ready Workstation
Assay ready workstation that automates ELISA processing of up to eight 96 well microplates in parallel.
Hamilton | Genomic STARlet Assay Ready Workstation
Assay ready workstation that was developed in collaboration with MACHEREY-NAGEL for their vacuum based chemistry to quickly isolate high quality nucleic acids.
Hamilton | LabElite DeCapper SL Benchtop Automated Sample Mangament Device
Hamilton | LabElite DeCapper Benchtop Automated Sample Management Device
Hamilton High Temperature GC Septa Laboratory Products
High temperature septa that is made of preconditioned PTFE/silicone rubber and is 3.175 mm (0.125 in) thick. The average life of these septa is up to 100 injections with a 26s gauge needle. The maximum operating temperature is 212C.
Hamilton | easyPunch STARlet Assay Ready Workstation
Assay ready workstation that simplifies pre-PCR workflows from evidentiary and DNA databasing biological samples collected via FTA cards.
Hamilton | LabElite DeFroster Benchtop Automated Sample Management Device
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8th,2024. Automated Rack Frost Remover.
Model_Number_LabElite_Integrated I.D._Capper
Hamilton | LabElite Integrated I.D. Capper
Hamilton LabElite Integrated I.D. Capper Benchtop Automated Sample Managment Device
Automated Screw Cap Decapping for Integration. Features all of utility of standalone version and allows users to seamlessly integrate these features with their Hamilton Microlab STAR. With the addition of extended linear rail, tube racks and cap holder racks can be presented directly onto the deck of the STAR allowing for easy automation of tube processing workflows. Easily swap decapping heads to decap tubes in 24-, 48-, and 96-format tube racks, all on a single device.
Hamilton | MagEX STARlet Assay Ready Workstation
Assay ready workstation used for magnetic bead based nucleic acid extraction and isolation of pathogen RNA from SARS CoV 2, which causes Coronavirus Disease 2019. It is designed to be used with variety of kit chemistries from leading partners, including those that are FDA approved, and can process up to 96 samples at time.
Hamilton | Low Bleed High Temperature GC Septa
Hamilton Low Bleed High Temperature GC Septa Laboratory Products
Low bleed high temperature septa that is designed for lowest bleed possible at temperatures up to 400 degrees C. They can be used in combination with Mass Spectrometers or in applications where septa bleed interferes with trace analysis.
Hamilton | foodInspect NIMBUS for 3M Molecule Detection System Assay Ready Workstation
Molecular detection system that uses air displacement technology for precision, accuracy and reproducibility to detect pathogens from food samples.
Hamilton | MassSTAR Assay Ready Workstation
Assay ready workstation used for fully automated CE-IVD certified mass spectrometry sample preparation.
Hamilton | LabElite I.D. Capper Benchtop Automated Sample Management Device
An automated I.D. capper that combines capping, decapping, and high-speed barcode reading in one device.
Hamilton Long Life GC Septa Laboratory Products
Autosampler septa that is designed for use with GC Autosamplers and uses a pre-pierced center depression to guide the syringe needle to the same injection point, which extends septa life. These septa are ideal for standard manual-injection GC and GC-MS.
Hamilton | Microlab 600 Stand Alone Syringe Pumps Laboratory Products
Syringe pump that is available as a standalone pump with single and dual syringe configurations. The standalone pump offers two communication capabilities Ethernet and RS-232.
Hamilton | Microlab Prep Automated Liquid Handling
Compact automated liquid handler made for convinience and efficiency.
Hamilton Microlab 600 Diluters Laboratory Products
Syringe pump that quickly performs analytical dilutions of standards and samples.
Hamilton | Microlab STAR Automated Liquid Handling
STAR Automated Liquid Handling uses pipetting technology to achieve high accuracy, precision, and repeatability from sub-microliter to large volumes.
Syringe dispenser that can perform aliquot, serial dispense, and titrate dispensing.
Hamilton | NGS STAR for Library Prep Asssay Ready Workstation
NGS STAR for Library Prep is used for Massive Parallel Sequencing.
Hamilton | Microlab VANTAGE Automated Liquid Handling
Automated Liquid Handling is used for precision engineering, performance, and craftsmanship.
Hamilton | NIMBUS Select Assay Ready Workstation
NIMBUS Select is used for high throughput, automated gel electrophoresis and nucleic acid size selection.
Hamilton | NIMBUS Presto and ID NIMBUS Presto Assay Ready Workstation
NIMBUS Presto and ID NIMBUS Presto optimize automated KingFisher magnetic bead based particle workflows.
pH electrode with 3 mm shaft that is used for general measurements in vials and test tube applications.
Hamilton | STARWorks for Water GlycoWorks Assay Ready Workstation
STARWorks for Waters GlycoWorks streamlines and automates your N glycan workflows.
Hamilton | Microlab NIMBUS Automated Liquid Handling
Compact, multi channel automated liquid handler with speed, flexibility, and easy usage.
Hamilton PCR Prep STARlet Assay Ready Workstation
PCR Prep STARlet assay ready workstation automates CDC authorized and FDA cleared testing kits for detection of SARS CoV 2.
Leica/Wild M3Z Stereo Microscope that has been serviced by a qualified microscope tech and meets factory specs. It has its Wild 10X, high eyepoint widefield eyepieces and a 1.0X bottom objective. In my opinion, the M-Series by Leica is the best stereomicroscope available. I like Zeiss as well, but have never had a Leica optical element delaminate. The M-Series is the microscope you want if you spend a lot of time looking through the eyepieces, want the brightest, flattest field and highest resolution. Built for demanding users, the Wild/Leica M-series is built to last.
Hamilton Three Layer GC Septa Labratory Products
Made of preconditioned silicone rubber and is 3.81 mm (0.150 in) thick. The average life of these septa is up to 100 injections with a 26s gauge needle. The maximum operating temperature is 200° C.
Hamilton | Verso Automated Freezer Sample Storage System
Hamilton Verso is modular compound management system for automated storage at temperatures from ambient to minus 20°C for high-throughput applications. This compound storage system can easily be configured to meet your needs.
Hatteras Instruments | MC4000 Blood Pressure and Heart Rate Analyzer
MC4000 Multi Channel Blood Pressure Analysis System helps researchers obtain accurate blood pressure measurements on mice and rats.
Thermo Fisher | Heraeus Biofuge Stratos Centrifuge Series
Centrifuge eliminates imbalances, provides reproducible results and delivers speed and flexibility.
Hamilton | STARWorks for Waters ProteinWorks
Hamilton STARWorks for Water ProteinWorks Assay Ready Workstation
STARWorks for Water ProteinWorks Assay Ready Workstation
STARWorks for Waters ProteinWorks simplifies protein bioanalysis workflow and quantifies proteins in serum or plasma.
Hitachi | 8100 Transmission Electron Microscope
Hitachi H-8100 TEM is a research grade scanning/transmission electron microscope (STEM) with analytical and high resolution imaging capabilities. Systematic theoretical instruction combined with practical hands-on training is the best way to thoroughly understand the utility and capabilities of this complex and delicate instrument. These instructions are meant only as a guide to the basic, daily alignments and operations of the H-8100, i.e. general imaging and diffraction. It is by no means a comprehensive guide to all operations of the microscope including ultra-high resolution imaging, SEM, EDX, cryo, and the various diffraction techniques. These advanced, specialized techniques will be dealt with on an as-need basis after mastery of the basic operations has been demonstrated.
Hitachi | 3400N Environmental Scanning Electron Microscope
Hitachi S-3400N SEM is a high performance, user-friendly scanning electron microscope. Features include: VP-mode that allows microscopy of wet, oily and non-conductive samples in their natural state without the need of conventional sample preparation.
Hitachi L-8800 Amino Acid Analyzer Hitachi L8800 professionally deinstalled and under service watch until such time used. Hitachi has manufactured over 1800 Amino Acid Analyzers for over 35 years. The L-8800 is capable of analyzing physiological fluids and protein hydrolysates. Hitachi offers the best solution to amino acid analysis.
Hamilton | VeriSeq NIPT Microlab STAR Assay Ready Workstation
Veriseq NIPT Microlab STAR automates PCR free whole genome sequencing during NGS MPS based non invasive prenatal testing.
Drew Scientific | HemaVet 950FS Blood Analyzer
HEMAVET 950FS can perform automated blood counts including; hemoglobin, hematocrit, white blood cells, platelets, differentials, and red blood cell indices for six animals.
Thermo Fisher | Heratherm Advanced Protocol Security Microbiological Incubators
Thermo Scientific� Heratherm� Advanced Protocol Security Microbiological Incubators, which include a unique 140�C decontamination routine, lockable incubator door with alarm for restricted access, and automatic over- and under-temperature alarms.
Hitachi | S-4800-II with Leica Cryo Stage
Hitachi S-4800-II Cold Field Emission SEM with Windows XP Pro OS. (Windows 7 optional). Fully refurbished with warranty and located in Northern California.
Hitachi | S4700 Field Emission Scanning Electron Microscope
Hitachi S-4700 is a field emission scanning electron microscope (FE-SEM). More than a standard SEM, the S-4700, under optimal conditions, can magnify images upwards of 500,000 times and resolve features to 2 nanometers. In addition, a cathodoluminescence detector, backscatter electron detector and energy dispersive x-ray spectrographic detector accompany the microscope., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Thermo Fisher | HM 430 Sliding Microtome
Ensures operation with automatic or manual fine sectioning abilities of Thermo Scientific HM 430 Sliding Microtome.
Horiba | 51 Series Explosion-proof Gas Analyzer
Explosion proof analyzers that provide safe, and accurate measurements when analyzing flammable gases or operating in explosive environments.
Hitachi | HT7700 Transmission Electron Microscope
HT7700 Transmission Electron Microscope with Dual-Mode objective lens features superior high-contrast and high-resolution performance together with analytical capabilities for biological and materials science. Digital design and sophisticated automation increase throughput for both novice and advanced users. Maximize contrast by lowering the high voltage through the 120-40 kV range and continue operation seamlessly. Configure the HT7700 to meet all of your advanced sample analysis needs, with customization options for BF-/DF-STEM, EDX, in-situ, cryo-microscopy, and electron tomography.
Thermo Fisher | HM 550 Cryostats Detach Block with Six Positions
Defrost and detach tissue from specimen stage outside cryo chamber with Thermo Scientific HM 550 Cryostats Detach Block, featuring six positions marked with letters A to F.
Horiba | APMC-370 Air Pollution Multigas Calibrator
Air pollution multigas calibrator that is designed to calibrate gas analyzers manually, remotely controlled or automatically. It is installed in air pollution monitoring stations for quality assurance in laboratory and also in production of gas analyzers.
Horiba | AP-370 Series Air Pollution Monitor
Highly sesitive ambient air pollutions monitors that give precise, realiable measurements, and are easy to maintain.
Horiba | 1000M Series Long Focal Length Spectrometer
Large focal length monochromators for spectroscopy applications such as Raman, Plasma Emission, and LIBS.
Hitachi | HD2300 Transmission Electron Microscope
Hitachi HD-2300 Dual EDS Cryo STEM (HD 2300) is a versatile Scanning Transmission Electron Microscope used for imaging and elemental analysis. The HD 2300 actually has three different electron detectors for different imaging modes (Transmitted Electron Detector, Annular Detector, and a Secondary Electron Detector) and features an electron Energy Loss Spectroscopy detector (EELS) and two EDS detectors (Energy Dispersive X-ray Spectroscopy) for elemental analysis and elemental mapping of a given sample. Overall, the HD 2300 is a multipurpose instrument for anyone who is looking to do research in material science, life science, chemistry and nanoscience.
Horiba | AQMS Air Quality Monitoring System
Air quality monitoring system that measures metrological parameters such as wind speed, wind direction, rainfall, radiation, temperature, barometric pressure and ambient parameters. It also integrates series of ambient analyzers to monitor concentration of air pollutants continously.
Hitachi | S3000N Scanning Electron Microscope
Hitachi S-3000N scanning electron microscope (SEM) is a PC controlled variable pressure SEM with the ability to switch between the high vacuum and variable pressure modes. It has a high density frame memory of 1280x960 pixels and an advanced image capture and archiving system. Four quadrant solid state backscatter allows imaging in the compositional, 3D and topographic modes by manipulating from each segment of the detector.
Horiba | Auto SE Spectroscopic Ellipsometer for Thin Film Measurement
Thin film measurement tool that allows full automatic analysis of thin film samples with push button operation. It includes automatic XYZ stage, real time imaging of measurement site and automatic selection of spot size.
Horiba | CM-200A/210A Hydrofluoric Acid Monitor
CM 200A 210A hydrofluoric acid monitors have been developed specifically to meet stringent demands of semiconductor manufacturing. CM 200A 210A provides real time read out of hydrofluoric acid concentration by measuring electric conductivity of sample solution. These superior units offer high repeatability even at low concentrations. CM 200A 210A can be used for variety of purposes ranging from monitoring etched wafer cleaning processes to any other industrial application of hydrofluoric acid.
Horiba | Aqualog Water Treatment Plant Analyzer
Water treatment plant analyzer that simultaneously measure both absorbance spectra and fluorescence Excitation Emission Matrices.
Horiba | Camsizer P4 Dynamic Image Analysis System Particle Size
Digital image processing particle size and shape analysis system that provides rapid and precise particle size and particle shape distributions for dry powders and bulk material in size range from 20 um to 30 millimeters. This technique provides wide variety of information about sample, from general size measurement, to shape parameters that can be closely correlated to specific performance characteristics. This also allows correlation to existing data from techniques as diverse as sieving, microscopy, and hand caliper measurement.
Horiba | CEMS Continuous Emission Monitoring System
Continuous Emission Monitoring System CEMS is integrated system to measure fuel flow, dust, and concentrations of air pollutants such as SO2, NOx, CO, CO2, THC and O2 in accordance with applicable regulations for emission source.
Horiba | Cryogenic Grinder 6870 Large Cryogenic Mill
Large cryogenic mill for cryogenic grinding and pulverizing tough and or temperature sensitive samples immersed in liquid nitrogen. It can be used for sample sizes ranging from 0.1 to 50 grams.
Horiba | CS-100 Series Stand-alone Type Chemical Concentration Monitor
Chemical concentration monitors that measure real time concentrations of various types of chemical solutions and control timing of automatic chemical spiking. Air is used for reference spectral measurements to be taken without abnormalities in solution flow.
CiCi Raman 785 is high performance spectrometer featuring aberration corrected concave holographic grating configured with Horiba Scientific's Syncerity TE cooled CCD camera with VIS NIR 2048 x 70 detector, in TE cooled Head at 50 degrees C.
Horiba | Benchtop LAQUA PH1200 Water Quality Meters
Benchtop model developed to provide simplicity with on site usability, from operation and maintenance to troubleshooting in water quality analysis.
CC 55 Imaging Multichannel Spectrometer Simultaneous acquisition 10 26 Fiber Inputs with diameters in range of 100 400 mic Interline CCD, may allow shutter free set up Call us Line imaging on tall Sony ICX285AL CCD.
Horiba | Camsizer X2 Dynamic Image Analysis System Particle Size
Dynamic image analysis system that provides particle size and shape distribution analysis needed for quality control of fine powders and suspensions, measuring 0.8 um to 8 mm.
Horiba | CS-100 F4 Multi-point Chemical Solution Monitor
Multi point chemical solution monitor with multipoint chemical measurement into single units used in etching and cleaning processes for semiconductor manufacturing.
Horiba | CS-600F Fiber Optic Type Chemical Concentration Monitor
Fiber optic type chemical concentration monitor for manufacturing, such as in line measurement of high temperature chemical solutions in various applications, such as semiconductor wet process.
Horiba | CVS-ONE Constant Volume Sampler
Designed for measurement of diluted emissions from vehicles and engines. Can be used to measure low emission levels such as SULEV.
Horiba | CS-700 Chemical Concentration Monitor
Chemical concentration monitor for measurement of individual chemical constituents of complex chemistries used in Semiconductor Manufacturing Processes.
Horiba | DeltaRAM X Random Access Monochromator
DeltaRAM X microscope fluorescence illuminator is used for quantitative intracellular ion research. It utilizes galvanometer based Random Access Monochromator that can switch between any wavelength in 2 milliseconds.
Horiba | DeltaDiode Pulsed Laser and LED Light Sources
DeltaDiodes utilizes laser diode and LED technology to generate short optical pulses over very wide range of repetition rates and wavelengths.
Horiba | DeltaFlex TCSPC Lifetime Fluorometer
Designed for measurement of luminescence lifetimes ranging over 11 orders of magnitude, without need to change cables or cards.
Horiba | DeltaPro TCSPC Lifetime Fluorometer
Enables seamless measurement of luminescence lifetimes from picoseconds to 1 second, using DeltaHub timing electronics. Takes advantage of interchangeable pulsed laser-diode and LED light-sources.
Horiba | Duetta Fluorescence and Absorbance Spectrometer
Spectrofluorometer that combines, simultaneously, functions of fluorescence and absorbance spectrometers. Can acquire full spectrum from 250 nm to 1,100 nm in less than one second.
DeltaTime integrates monochromators, polarizers, and other accessories with widest array of sources, like LEDs, laser diodes, supercontinuum lasers, and detectors, including NIR, providing lifetime coverage from 25ps to 1sec over wavelengths spanning UV to NIR.
DT type Hydraulic dynamometers are available with large variety of power ranges. Standard range extends from 700 kW up to 4,500 kW.
DYNAS3 dynamometers are designed for use in engine test stands. Combination of powerful DYNAS AC machine with variable frequency drive, fine tuned test stand controller and proven safety module produces reliable and accurate results.
Horiba | EasyRatioPro Ca++ Imaging System
Comprehensive system for measuring intracellular calcium, sodium, magnesium ion concentrations or pH and membrane potential. Includes tools required for image acquisition, analysis and calibration of intracellular dyes or intrinsic fluorophores.
Horiba | EC-5000 Series Exhaust Pressure Controller
Exhaust pressure controller can maintain consistent pressure within the chamber. High resolution stepper motor and butterfly valve ensures fast, sensitive response to any pressure changes.
Horiba | EasyLife X Lifetime Fluorescence Spectrometer
Time resolved fluorometer for lifetimes down to 150 ps with 10 percent binding efficiency, ANS binding to bovine serum albumin monitored with EasyLife X equipped with a 370 nm LED, and ratio of free ANS to BSA bound ANS, 9 to 1, can be determined from double exponential fit to fluorescence decay.
Horiba | Eco Web Data Management and Reporting Software
Data management and reporting software for use in Ambient Air Quality and Meteorological monitoring. Software package provides data collection, management, analysis and reporting.
Horiba | EasyLife L Phosphorescence Lifetime Spectrometer
Low cost phosphorescence spectrometer from few microseconds to 300 milliseconds.
Horiba | EMGA-930 Oxygen/Nitrogen/Hydrogen Analyzer
Oxygen, nitrogen, and hydrogen elemental analyzer with high accuracy and repeatability suiting to cutting edge technology's R and D, as well as quality control in market of steel, new materials, and catalyst. New generation model optimized to fit to user's requests.
Hydrogen elemental analyzer with high accuracy and repeatability suiting to cutting edge technology's R and D, as well as quality control in market of steel, new materials, and catalyst. New generation model optimized to fit to user's requests.
Horiba | EMIA-Pro Carbon/Sulfur Analyzer
Carbon and Sulfur Analyzer is based on expertise in Non Dispersive Infrared technology. It offers improved cleaning efficiency, enhanced software, durability, operability and maintenance to ensure efficient measurements and its shortened cycle time accelerates development and manufacturing speed.
Fluorolog-3 is a , modular system which allows the researcher to interchange a wide range of accessories to correspond precisely with the characteristics of a given sample. From analysis of steady-state or molecular dynamics to IR probes, the Fluorolog-3 comes equipped with a wide range and limitless configuration of accessories to enhance the accuracy and speed of it's performance. The Fluorolog-3 series enables you to customize your spectrofluorometer's performance to meet your research needs. It can also perform (TCSPC) Time Correlated Single Photon Counting lifetime measurements like the FluoroMax-4 and QM800.
Horiba | EMGA-920 Oxygen/Nitrogen Analyzer
Oxygen and nitrogen elemental analyzer with high accuracy and repeatability suiting to cutting edge technology's R and D, as well as quality control in market of steel, new materials, and catalyst. New generation model optimized to fit to user's requests.
Horiba | FTX-ONE FTIR Exhaust Gas Analyzer
Fast response and compact size FTIR analyzer for simultaneous measurement of multiple components of engine exhaust gases.
FluoroMax family, with its all reflective optics and photon counting was the first to bring the sensitivity of a modular fluorometer to a tabletop fluorescence instrument. It's a compact spectrofluorometer, yet offers the ultimate sensitivity in fluorescence investigations as well as features not found in most table-top fluorescence detection systems. The FluoroMax series consists of the FluoroMax-4, the latest generation of the original, high performance tabletop fluorometer, which offers extended performance with detection of emission spectra out to 1700 nm and (TCSPC) Time Correlated Single Photon Counting lifetime measurements as short as 25ps.
Horiba | Gemini 180 Double Monochromator
Fully automated, double additive grating scanning monochromator. Incorporation of toroidal optics provides for optimum throughput and spectral resolution.
Horiba | Geno Grinder 2020 Automated Tissue Homogenizer
Automated plant and tissue homogenizer that integrates with most robotic systems and platforms. Its vertical grinding motion prepares plant and animal tissue for extractions of DNA, RN or proteins in less than two minutes.
Provides constant, ultra high sensitivity and high precision monitoring of trace impurities, like CO, CO2 and CH4, for quality control at gas manufacturing facilities.
Horiba | EMIA-Expert Carbon/Sulfur Analyzer
Carbon and Sulfur Analyzer is based on expertise in Non Dispersive Infrared technology. It offers improved cleaning efficiency, enhanced software, durability, operability, and maintenance to ensure efficient measurements and its shortened cycle time accelerates development and manufacturing speed.
Horiba | GIANT 8000 Series Brake Test Systems
Has NVH test system providing with testing conditions for all types of vehicles. Test brake fixtures could be tested with complete wheel suspension system.
Horiba | GIANT 6000 Series Multi-Purpose Brake Dynamometers
Product line is multi purpose, full size inertia brake dynamometer for performance and NVH tests of brake systems from passenger vehicles to truck brakes, commercial vehicle assemblies and high speed railway applications.
Horiba | Geno Grinder 2010 High-throughput tissue homogenizer
High throughput plant and tissue homogenizer with adjustable clamp that accommodates variety of formats ranging from deep well titer plates to centrifuge tubes. Designed for rapid cell disruption, lysis and tissue homogenization while preserving temperature sensitive samples.
Horiba | H-CLUE Versatile Hyperspectral Cathodoluminescence
Direct coupled solution offers ultimate performance for Cathodoluminescence Imaging and Spectroscopy analysis.
Brake testing machine forms base of inertia brake dynamometers portfolio. All components are specifically tailored to needs of passenger car market segment.
Horiba | GI-700 Series Stack Gas Analyzer
Gas analyzer is designed to continuously measure concentrations of nitrogen oxides, sulfur dioxide, carbon monoxide, carbon dioxide, oxygen, and ammoni in stack flue gas streams.
Horiba | GR-300 Series Wafer Back Side Cooling System
Can control gases used to cool back side of wafers that are fixed in position by electrostatic chuck system.
H30 UVL allows working either in monochromator mode using exit slit or in flat field spectrograph mode using CCD detector.
Horiba | GIANT 9000 Series Brake Test Systems
Brakes can be exposed to either stop brakings or endurance brakings according to standardized NVH test matrix.
Horiba | HC-200F Fluoride Ion Concentration Meter
Industrial simplified fluoride ion concentration meter that is suitable for fluoride ion monitoring in effluent from factories and those of semiconductor FPD and glass manufacturers. 0 to 10,000 mg L wide measuring range, with 10 range switching.
Based on single holographic concave aberration corrected grating, H20 UVL is monochromator covering range 100 600 nm.
Horiba | H1034B OEM Imaging Scanning Spectrometer Monochromator
Ion Etched gratings combine advantages of holographic gratings with high efficiency. Aberration corrected concave gratings permit one piece opticsl design with imaging properties.
Horiba | HD-200FL Industrial Dissolved Oxygen Analyzer
Realizes both cartridge method membrane replacement and membrane internal liquid replacement regeneration system. Responds to wide range of measurements, like boiler, water, rivers, and aeration treatments.
Horiba | HD-200 Industrial Dissolved Oxygen Analyzer
Industrial dissolved oxgen analyzer that realizes both cartridge method membrane replacement and membrane internal liquid replacement regeneration system. Responds to wide range of measurements, like boiler, water, rivers, and aeration treatments.
Horiba | HC-300F Fluoride Ion Concentration Meter
Industrial simplified fluoride ion concentration meter that is suitable for fluoride ion monitoring in effluent from factories and those of semiconductor FPD and glass manufacturers.
Horiba | HC-200NH Ammonia Nitrogen Meter
HC 200NH is ammoni nitrogen meter using ion electrode method which is designed for aeration control in wastewater treatment.
Horiba | HD-300 Industrial Dissolved Oxygen Analyzer
Horiba | LAQUA EC1100 Benchtop Water Quality Meters
Developed to provide simplicity with on site usability, from operation and maintenance to troubleshooting.
Horiba | i-CLUE Fast Imaging Cathodoluminescence
Offers up to 10 times higher sensitivity compared to standard CL imaging solutions due to performance of high numerical aperture and low roughness collection mirror coupled to optimized acquisition chain and detection.
Horiba | LAQUA EC220 Handheld Water Quality Meters
Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places.
Horiba | LAQUA F-72 Benchtop Water Quality Meters
Horiba | LAQUA F-74 Benchtop Water Quality Meters
High end benchtop model developed to provide simplicity with on site usability, from operation and maintenance to troubleshooting in water quality analysis.
Horiba | LAQUA PC210 Handheld Water Quality Meters
Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places, making it ideal for field measurements in rivers and lakes.
Horiba | LAQUA F-73 Benchtop Water Quality Meters
Horiba | LAQUA EC210 Handheld Water Quality Meters
Horiba | HD-480 Industrial Dissolved Oxygen Analyzer
Industrial dissolved oxygen meter that takes sequential measurements of concentration of dissolved oxygen, which is indicator used in management of activated sludge tanks in waste water processing, and quality of water in boilers, or rivers and waterways.
Horiba | LAQUA PC1100 Benchtop Water Quality Meters
Horiba | LAQUA PH1100 Benchtop Water Quality Meters
High end benchtop model developed to provide simplicity, from operation and maintenance to troubleshooting in water quality analysis.
Horiba | LAQUA PH1300 Benchtop Water Quality Meters
Horiba | LAQUA PD210 Handheld Water Quality Meters
Horiba | LAQUA WQ-320-K Handheld Water Quality Meters
Dual channel handheld water quality meter that has large colour graphic LCD screen, measuring 70 x 52 mm, with backlight and built in foldable meter stand. It is IP67 waterproof and dustproof, battery and USB powered, eco friendly, shock proof, scratch resistant, and non slip.
Horiba | LAQUA PC220 Handheld Water Quality Meters
Horiba | LAQUA PD220 Handheld Water Quality Meters
Horiba | LAQUA WQ-310-K Handheld Water Quality Meters
Single channel handheld water quality meter that has large colour graphic LCD screen, measuring 70 x 52 mm, with backlight and built in foldable meter stand. It is IP67 waterproof and dustproof, battery and USB powered, eco friendly, shock proof, scratch resistant, and non slip.
Horiba | LAQUAact DO120 Handheld Water Quality Meters
Designed for use with one hand and with IP67 waterproof rating and shock resistant casing, Meter can be used for long periods, even in dark places.
Horiba | LAQUA PH210 Handheld Water Quality Meters
Horiba | LAQUA PH220 Handheld Water Quality Meters
Horiba | LAQUAact EC110 Handheld Water Quality Meters
Horiba | LAQUAact DO110 Handheld Water Quality Meters
Horiba | LAQUA WQ-330-K Handheld Water Quality Meters
Triple channel handheld water quality meter that has large colour graphic LCD screen, measuring 70 x 52 mm, with backlight and built in foldable meter stand. It is IP67 waterproof and dustproof, battery and USB powered, eco friendly, shock proof, scratch resistant, and non slip.
Horiba | LAQUAact PH110 Handheld Water Quality Meters
Horiba | LAQUAact PD110 Handheld Water Quality Meters
Horiba | LAQUAact EC120 Handheld Water Quality Meters
Horiba | LAQUAact PH120 Handheld Water Quality Meters
Designed for use with one hand and with IP67 waterproof rating and shock resistant casing, Meter can be used for long periods, even in dark places, making it ideal for field measurements in rivers and lakes.
Horiba | LAQUAact PC110 Handheld Water Quality Meters
Horiba | LAQUAtwin Ca-11 Pocket Water Quality Meters
Compact meter integrates electrode, display and sample container to enable on site testing by direct measurement from single drops.
Horiba | EMIA-Step Carbon/Sulfur Analyzer
Tubular electric resistance heating furnace type realizes accurate and sensitive analysis, and its variable heating temperature function enables quantitative analysis by separating it by temperature and condition and whole quantity analysis.
HP designjet 800ps printer (42-inch model) is a large-format 42 inch printer for architects, engineers and GIS professionals working in technical departments. Network ready printer, a "virtual-computer" inside processes files, quickly freeing up the computer.
Illumina Beadstation 500 is a high performance benchtop system designed for genetic analysis, particularly single nucleotide polymorphism (SNP) genotyping. High quality BeadArray technology provides the utmost in sensitivity thanks to a built in 30 fold redundancy and unparalleled quality control for every single feature on each array. Manual and automated processing is possible for both RNA- and DNA- based applications, and is made easy when the instrument is used in conjunction with liquid handlers and system software. For flexibility, the platform can be integrated with various other systems and robotics for meeting the requirements of many protocols. Reliability and reproducibility are ensured thanks to the scanner of the Beadstation. Additionally, sample throughput is adjustable. For gene expression (focused set), the unit can process 16 samples on one individual Sentrix BeadChip or 96 samples on a single Sentrix Array Matrix (SAM). For a 96 bundle matrix, processing times are as fast as 90 minutes or less. With a multiplex capability of as many as 1,536 plex, this system also provides great efficiency without sacrificing precision. Image resolution is less than one micron, and throughput can range from 16 to 192 (1536 SNP loci per array) per eight hour day for genotyping and 6 to 54 whole genome expression samples for gene expression. Minimal sample requirement (about 250 ng of DNA per assay for genotyping protocols and 50 ng to 100 ng total RNA for gene expression protocols) makes this system best for applications that use biopsies, fine needle aspirates, or preserved samples that are typically impossible to replace or are too low in quantity to meet the minimum input requirements of comparable instruments.
Horiba | LAQUAtwin EC-11 Pocket Water Quality Meters
ThorLabs | iCyte Automated Imaging Cytometer
iCyte Automated Imaging Cytometer combines digital microscopy with image processing and the real time population data analysis of analytical cytometry to produce high levels of information content with minimal investigation time.The iCyte combines the advantages of flow and image cytometry into a single system that provides unparalleled flexibility and power for rapid measurements of biochemical constituents or evaluating cell morphologies. It comes packaged with our iGen software for data acquisition and analysis. The system houses four lasers that are available in five different wavelengths (see Specs tab for more details) for laser-spot scanning illumination. The detection system, which combines PMTs for fluorescence detection and photodiodes for absorbance and scatter detection, offers excellent quantitative cytometric performance and imaging capabilities. iCyte provides fully automated operation for analysis of cellular and tissue samples that have been stained with fluorescent or chromatic dyes. Fluorescent excitation, laser light absorbance by chromatic dyes, and scatter signals may all be acquired simultaneously. This quantitative image analysis system enables both walk-away high-throughput applications (e.g., cell cycle screens on a 96-well plate in under ten minutes) and high-content analysis (where scanning and analysis can take longer depending on the level of multiplexing required, desired resolution and size of the scan area). It automatically segments and quantifies cellular and subcellular events. The automated analysis allows for the study of morphometric and fluorescent measurement correlations on thousands of cells per specimen. The iBrowser software automates the analysis of the measurement for quick and easy to understand analysis.
Horiba | LAQUAtwin EC-22 Pocket Water Quality Meters
Horiba | LAQUAact PH130 Handheld Water Quality Meters
Illumina | BeadArray Reader BeadArray Reader
BeadArray microarray technology is based on 3-micron silica beads that self assemble in microwells on either of two substrates: fiber optic bundles or planar silica slides. When randomly assembled on one of these two substrates, the beads have a uniform spacing of ~5.7 microns. Each bead is covered with hundreds of thousands of copies of a specific oligonucleotide that act as the capture sequences in a given Illumina assay.
HiScanSQ system (Figure 1) integrates the power and resolution of next-generation sequencing with the high-throughput capacity of genotyping, gene expression, and methylation arrays, delivering unprecedented flexibility for experimental design. The instrument features two distinct components, the HiScan Reader and the SQ Module. The HiScan Reader functions as a high-speed, precision imaging scanner for Illumina sequencing and microarray-based analyses. The SQ Module is a reagent handling fluidics device needed to perform Illumina next-generation sequencing.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15, 2023. HiSeq 2000 sequencing system for sequencing and fastest data generation rate.
Illumina | NextSeq 1000 Sequencing System
Benchtop sequencer that allows to explore new science across variety of current and emerging applications, with higher efficiency and fewer restraints.
Powered by Ion Torrent semiconductor chip technology, Ion Proton Sequencer is benchtop next generation sequencer to offer fast, affordable human genome and human exome sequencing. Powered by next generation of semiconductor sequencing technology, offers similar single day workflow to Ion PGM Sequencer.
Circular dichroism (CD) spectroscopy measures differences in the absorption of left-handed polarized light versus right-handed polarized light that arise due to structural asymmetry. The absence of regular structure results in zero CD intensity, while an ordered structure results in a spectrum which can contain both positive and negative signals.
JEOL | JEM-100CX II Transmission Electron Microscope
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 5,2023.JEOL JEM-100CX II transmission electron microscope is an electron microscope with imaging capabilities at low to high magnifications (90X to 800, 000X). A 10M-pixel HAMAMASTU C4742-95 digital camera is integrated to the system for high- image acquisition.
J-1500 allows for the maximum flexibility to upgrade your CD system with different measurement techniques. While the standard measurement modes are CD, LD, and absorbance, up to four simultaneous modes can be measured when combined with a wide range of sampling accessories. These accessories can measure a variety of samples, from liquids to films to solid-states. Temperature control systems can be coupled with multi-position cells to run thermal melts, providing researchers with CD and thermodynamic data sets for conformational and folding studies. Automated high-throughput CD can obtain measurements on up to 192 samples without user intervention, saving both time and money. Kinetic and protein dynamics studies can be performed with our dedicated stopped-flow systems that can measure both CD and fluorescence. The wavelength range has also been significantly extended, allowing measurements to be obtained in both the vacuum-UV and NIR spectral regions using the standard PMT detector (163 950 nm) and an optional InGaAs detector (up to 1600 nm). Additional features now allow researchers to optimize their parameter specifications in order to obtain data with the highest resolution and S/N performance for a specific application set.
Thermo Fisher | Ion Max Source Mass Spectrometer Accessories
Ion Max source's design imparts performance, allows interchangeability, and provides commonality between many different Thermo Scientific LC MS systems. Universal Thermo Scientific Ion Max source features rapidly interchangeable electrospray ionization ESI and atmospheric pressure chemical ionization APCI probes.
Thermo Fisher: Invitrogen | Countess Countess
Countess Automated Cell Counter from Invitrogen is a benchtop automated cell counter. It can perform cell counts as well as viability and cell calculations. The Countess has a touch screen display and allows data to be transferred via USB drive to a computer for data access and storage.
Mass spectrometer that offers both chromatographic separation and high resolution mass spectra. Offers variety of ion sources and features Instrument Detection Limit of 16 fg, statistically calculated from repeated injections of 100 fg octafluoronaphthalene.
Superconducting magnets including actively shielded magnets from 400 to 800 MHz, and ultra high field magnets from 900 to 930 MHz. Magnets feature low cryogen consumption cryostats, extremely small B0 drift characteristics and homogeneity.
JEOL | AccuTOF LC-plus 4G Time-of-Flight Mass Spectrometer
Mass spectrometer with analyzer design that employs elegant ion optics and ADC based digitizer to deliver dynamic range exceeding 4 orders of magnitude, without compromising resolution or mass accuracy.
JEOL | 2100F Transmission Electron Microscope
JEM-2100F is a multipurpose, 200 kV FE (Field Emission) analytical electron microscope. Variety of versions is provided to adapt user's purposes. The FE electron gun (FEG) produces highly stable and bright electron probe that is never achieved with conventional thermionic electron gun. This feature is essential for ultrahigh resolution in scanning transmission microscopy and in an analysis of a nano-scaled sample. Various analytical instruments and/or cameras such as EDS (Energy Dispersive X-ray Spectrometer) or EELS (electron energy loss spectrometer) or CCD cameras are ready for integration with a PC system of the microscope control.
JEOL | AccuTOF-DART 4G Mass Spectormeter
Mass spectrometer that provides solutions for wide variety of fields with interchangeable atmospheric and ambient ionization sources
JEOL | AccuTOF GCx-plus Mass Spectrometer
Mass spectrometer with high resolution and high mass accuracy that enables accurate elemental composition determination of unknown compounds and impurities
Plasma source that can be used as Ion Plating for thin films, especially optical thin films and with Film quality such as density, adhesion, flatness, index of refraction and absorption are improved by comparison with usual vacuum deposition method
Available from 300 to 500 MHz console is designed around modular, digital NMR electronics chassis controlled by intelligent acquisition computer. Both workstation and spectrometer may be connected to standard network, allowing seamless remote operation anywhere in world.
JEOL | EBG-300UA High Power Electron Beam Source
High power electron beam source that is designed to uniformly deposit metal oxides onto wide plastic films or steel plates in continuous feed such as in magnetic tape manufacture for high density recording or in wrapping film manufacture with oxide barrier function
JEOL | CRYO ARM 200 Transmission Electron Microscope
Transmission elecctron microscope that achieves unprecedented resolution and stability allowing for automatic and unattended acquisitoin of image data for Single Particle Analysis
JEOL | ElementEye JSX-1000S XRF Fluorescence Spectrometer
Fluoresence spectormeer that analyzes major to trace components on most sample types solids, powders, liquids with little or no sample preparation
JEOL | CRYO ARM 300 Transmission Electron Microscope
Transmission electron microscope field emission cryo electron microscope that allows for automated detection of holes on specimen grid for automated, unattended acquisition of high resolution images
JEOL | IB-29500VED/IB-29510VET Vacuum Evaporator Sample Preparation Tool
High vacuum specimen sample preparation tool. Preparation device that makes it easy to prepare samples for imaging and analysis with with electron microscopes.
Benchtop double focusing magnetic sector mass spectrometer operating in electron ionization mode with TSS 2000 software.
JEOL | JBX-3050MV Electron Beam Lithography System
Electron beam lithography system for mask reticle fabrication that meets design rule of 45 to 32 nm and pattern writing with high speed, high accuracy and high reliability, achieved by high end technology
JEOL | InfiTOF Multi-Turn Time-of-Flight Mass Spectrometer
Mass spectrometer that can determine elemental compositions for ions within range of m/z 1 to 1,000. Hydrogen ion H plus can be detected with multi turn and multi segment that obtains high resolution with small ion flight path design.
JEOL | JAMP-9510F Elecrostatic hemispherical analyzer (HSA)
Electrostatic hemispherical analyzer with multi channel detector optimally designed for Auger analysis that provides user selectable energy resolution for high throughput high resolution and high sensitivity.
JEOL | JEBG-1000UB High Power Electron Beam Source
JEOL | JBX-8100FS Electron Beam Lithography System
Electron beam lithography system that writes ultrafine patterns at faster rate of speed while minimizing idle time, especially during exposure process, thus increasing throughput.
JEOL | JBX-9500FS Electron Beam Lithography System
Electron beam lithography system that is versatile in its applications from basic research of elements to test production of optical elements to research and development for masks for high accelerating voltage exposure.
JEOL | JEBG-3000UB High Power Electron Beam Source
A high power electron beam source that is designed to uniformly deposit metal oxides onto wide plastic films or steel plates in continuous feed such as in magnetic tape manufacture for high density recording or in wrapping film manufacture with oxide barrier function
JEOL | JEM-2100Plus Transmission Electron Microscope
Multipurpose transmissoin electron microscope ombining optic system of original JEM 2100 with advanced control system for enhanced ease of operation.
JEOL | JEM-ARM300F Transmission Electron Microscope
Transmission electron microscope that is designed to meet most advanced materials development requirements for atom by atom characterization and chemical mapping
JEOL | JEM-F200 F2 Transmission Electron Microscope
Transmission scanning electron microscope that offers Cold Field Emission Gun and dual Silicon Drift Detectors
JEOL | JES-X310 Electron Spin Resonance (ESR) Spectrometer
Electron spin resonance spectrometer that is user friendly and provides high sensitivity, resolution, and stability.
JEOL | JES-X320 Electron Spin Resonance (ESR) Spectrometer
Focused ion bean that is milling and imaging system featuring high performance ion optical column
JEOL | JEOL | JEM-1400Flash Transmission Electron Microscope
Transmission electron microscope that can be used to first view samples at low magnification before studying fine structures of interest at high magnification.
JEOL | JCM-7000 NeoScope Benchtop Scanning Electron Microscope (SEM)
Scanning electron microscope that is equipped with large chamber, high and low vacuum modes, secondary and backscatter electron detectors, real time 3D imaging, highly advanced auto functions and option to add fully embedded EDS with real time, Live, analysis.
JEOL | JMS-TQ4000GC Triple-Quadrupole Mass Spectrometer
Mass spectrometer that accurately measures trace or residual pesticides in agricultural materials, trace levels of regulated chemicals in tap water, and simplifies quantitative analysis of persistent environmental pollutants such as dioxins and PCB's.
JEOL | JMS-Q1500GC Single-Quad Mass Spectrometer
Mass spectrometer that can be used for wide range of applications such as environmental analysis for agrichemicals and mold odor, material analysis, and aroma analysis.
JEOL | JNM-ECZR Nuclear Magnetic Resonance (NMR) Spectrometer
Nuclear magnetic resonance spectormeter that enables highly sophisticated measurements to be carried out while most routine measurement operations can be performed automatically.
JEOL | JNM-ECZS Nuclear Magnetic Resonance (NMR) Spectrometer
Nuclear magnetic resonance spectormeter that incorporates ultra high accuracy RF circuitry utilizing latest digital high frequency technology. Compact spectrometer equipped with functions normally only found on research models and supports most advanced NMR experiments.
JEOL | JES-X330 Electron Spin Resonance (ESR) Spectrometer
JEOL | JSM-IT200 InTouchScope Scanning Electron Microscope (SEM)
Scanning electron microscope that is compact and versatile and delivers high resolution imaging with unsurpassed low kV performance and high sensitivity solid state BSE detector included with LV models.
JEOL | JSM-F100 Field Emission Scanning Electron Microscope (SEM)
Scanning electron microscope that offers high spatial resolution imaging and analysis at nanoscale
Focused ion beam that can be used in morphological observations, elemental and crystallographic analyses of variety of specimens.
JEOL | JSM-IT500HR InTouchScope Scanning Electron Microscope (SEM)
Scanning Electron Microscope that provides high resolution imaging along with high sensitivity and high spatial resolution analysis
Model_Number_JSM-7610FPlus Field Emission
JEOL | JSM-7610FPlus Field Emission Scanning Electron Microscrope (SEM)
Scaning electron microscope with semi in lens detector with integrated electron energy filter r filter and in lens Schottky field emission gun to deliver ultrahigh spatial resolution with wide range of probe currents for all applications
JEOL | JSM-7900F Field Emission Scanning Electron Microscope (SEM)
Scanning electron microscope with flexible platform that combines high resolution imaging with nano scale microanalysis.
JEOL | JXA-iHP200F Field Emission Electron Probe Microanalyzer (EPMA)
Electron probe microanalyzer that provides both high imaging resolution and analytical resolution with very high and stable probe current for analytical performance.
Mass spectrometer with ion optics design that permits rapid and auto tuning with minimal operator intervention, even under high resolution conditions.
JEOL | Monochromated ARM 200F Transmission Electron Microscope
Transmission electron microscope that provides ultrahigh energy resolution EELS analysis of materials at atomic scale
JEOL | MALDI SpiralTOF Time-of-Flight (TOF) Mass Spectrometer
Mass spectormeter that has levels of mass resolution and sensitivity and system that has been acknowledged for its distinctive capabilities in various scientific studies.
Model_Number_Soft X-Ray Emission Spectormeter
JEOL | Soft X-Ray Emission Spectormeter Scanning Electron Microscope (SEM)
Scanning electron microscope that provides excellent light element detection and superb sensitivity that is best for chemial shift analysis of light elements
JEOL | NEOARM Transmission Electron Microscope
Transmission electron microscope that enables atomic resolution imaging
JEOL | JXA-iSP100 Electron Probe Microanalyzer (EPMA)
Electron probe microanalyzer that provides both high imaging resolution and analytical resolution with very high and stable probe current for analytical performance with new algorithms for auto functions of both SEM column and optical microscope.
JEOL | ROYAL HFX Nuclear Magnetic Resonance (NMR) Probe
NMR probe that has capability to switch between single tune and dual tune modes on high frequency coil.
JEOL | SpiralTOF-plus MALDI TOF/TOF Mass Spectrometer
Mass spectrometer with long flight path that results in ultrahigh resolving power greater than 75,000 and sub ppm mass accuracy.
M2Bio is the original hybrid stereo-compound fluorescence microscope available to customers worldwide from Kramer Scientific. It is the go-to microscope for genetic research, cell biology, neuroscience, and developmental biology. The continuous zoom capabilities in both stereo and compound make it for transgenic sorting and observation needs. While copied by others, the M2BIO still offers the best value and flexibility for those needing true stereo for picking with a compound light path for resolving more faint fluorescence markers.
Kent Scientific | 6 Blood Pressure System
CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. The included software allows you to continuously view data in real-time.CODA High Throughput System with 6 Activated Channels.
Primarily designed for the demanding needs of cryosectioning in biomedical, neuro-anatomical and pharmaceutical research. The Leica CM3050 S cryostat features superior user comfort with excellent safety standards for practically all types of cryosectioning applications. It is the instrument of choice for all research applications and for advanced clinical cryosectioning needs. Particularly when working with delicate specimens for example brain samples in neuroscience the precise specimen orientation and the specimen feed system guarantees reproducible, thin, serial sections of maximum quality.
Kratos | AXIS-165 XPS Surface Analylsis System
AXIS Nova combines XPS imaging and spectroscopic capabilities with a highly automated, large sample handling system and is the next generation of AXIS Nova spectrometer. The AXIS Nova is based on Kratos, AXIS technology comprising: magnetic and electrostatic transfer lenses; co-axial electron-only charge neutralisation; spherical mirror and hemispherical electron energy analysers. Kratos developed innovations such as the delay-line detector for spectroscopy and imaging modes and high energy X-ray excitation sources ensure the AXIS Nova is capable of performing in the most demanding research and development environments.
JEOL | ROYAL Nuclear Magnetic Resonance (NMR) Probe
Probe that combines performance of broadband probe for heteronuclear measurements and inverse probe for 1H and 19F measurements.
Greenough stereo microscope, Leica S8 APO with apochromatic 8:1 zoom and 75mm working distance allows easy access to specimen even at high magnification up to 80x which is best for quality control, cell sorting and microinjection applications. Ergonomic 38 viewing angle provides comfort, which helps increase productivity, reduce fatigue related inspection errors and acquire precise positioning while working with incident or transmitted light. Adjustable zoom stops allows fast, easy, repeatable measurements and inspections. The Integrated Documentation port allows to connect digital cameras.
Vitrified frozen structures are extremely sensitive to environmental influences and need to be protected from the formation of artefacts. Prepare your samples for detailed image evaluation under optimal conditions: Cold shield around the sample avoids water molecules freezing onto your sample, Accurate temperature control during the complete process, Clean Knife fresh blade for each cut avoids contamination, Instant, fast e-beam coating, which captures detailed surface information, and Protected vacuum transfer to other analysis systems.
Leica | Autostainer XL Automated Slide Stainer
Autostainer XL continues to provide reproducible, consistent, high-quality staining and increased workload throughput. Plus, combine it with the CV5030 Glass Coverslipper to create a workstation that eliminates the manual handling of slide racks between staining and coverslipping. Can be used stand-alone or integrated with the Leica CV5030 Glass Coverslipper to create a ‘walk-away, staining/coverslipping workstation. Upgrade at anytime to match your laboratory's specific needs.
Leica CM3050 S is a cryostat for routine as well as research applications in biology, medicine and industry. The instrument has been designed for rapid freezing and sectioning of tissue samples. The instrument has not been designed for unattended storage of tissue material.
Leica DFC495 is a digital camera with 8 Megapixel CCD that quickly captures high-resolution images microscopy in life science.. The scan preview in SXGA resolution provides up to 18 frames per second (fps) and allows the sample to be adjusted and focussed directly on the computer screen. The Peltier cooling reduces noise for imaging in low light conditions.
Leica CM1900 is a rapid sectioning cryostat for advanced routine diagnostics in histology and clinical histopathology. This Leica cryostat offers extremely rapid specimen freezing and frequent changes in specimen temperature, meeting even the highest demands for smooth operation and enhanced safety. With the CM1900's overall engineering and ergonomic concept, the system provides accurate results for any cryostat application. The CM1900 is equipped with an ergonomically positioned handwheel for extremely smooth movement and easy locking in the upper position. The model also provides a functional control panel, which includes self-explanatory single-function keys and easily readable LEDs to prevent operating errors. The motorized coarse advance is ergonomically positioned in the arm rest at the left and operated via push buttons.
Leica CM1800 is a cryostat for routine and research applications in biology, medicine and industry. It has been designed for rapid freezing and sectioning of tissue samples.
Leica | EM AFS2 Freeze Substitution and Low Temperature Embedding System
System for Light and Electron Microscopy. Performs freeze substitution and progressive lowering of temperature techniques and allows low temperature embedding and polymerization of resins. Leica EM FSP (freeze substitution processor), automatic reagent handling system combined with Leica EM AFS2, dispenses reagents for both freeze substitution and PLT applications. The LED illumination from within the chamber and the attached stereomicroscope for viewing and positioning of samples ensures ease of use.
Leica DM2000 microscopes are best for complex tasks in pathology and cytology. For special diagnostics requirements, the microscope is certified for in-vitro-diagnostics (IVD) like in-vitro-fertilization (IVF).
Leica DM2500 & DM2500 LED optical microscopes are two optical microscopes wih different illumination: DM2500 LED is equipped with LED illumination for transmitted light, DM2500 works with halogen. Both types of illumination render a realistic impression of the colors of the sample.
Leica DM1000 LED Histology Microscope features long-life LED illumination that provides near daylight, bright illumination with constant color temperature and emits less heat.. Users of the Leica DM1000 LED benefit from the system's ability to adapt to every user. the microscope is certified for in-vitro-diagnostics (IVD) like in-vitro-fertilization (IVF).
Leica Ultracut EM UC6 is an advanced ultramicrotome that features a Touch Screen Control Panel or a Keypad Control Panel. Both options enable fast and safer alignment of knife and specimen, and the programmable knife and cutting movements make trimming easy. With Leica's AutoTrim, you can automatically trim a specimen to a predetermined level in the block face, best for morphometric studies. Three dependent, built-in, brightness- controlled LED light sources provide outstanding illumination for top light, back light, and specimen transillumination.
Leica | EG1150H Heated Paraffin Embedding Module
Leica EG1150 H is a heated, paraffin dispensing module with 3-liter capacity and a heated work surface with storage areas for both cassettes and molds. All functions of the EG1150 H are controlled via an easy-to-read LED display, including the temperature settings for left and right hand warming trays, paraffin reservoir, and working surface.
Leica RM2255 rotary microtome is designed for fully motorized sectioning of both paraffin- and the Leica RM2255 in routine and in histology. Its two-in-one design concept, which allows motorized and manual sectioning, provides reproducible high-quality sections.
Leica | TCS SP2 Confocal Laser Scanning Microscope
Leica TCS SP2 is a spectral confocal laser scanning microscope with 405 UV laser 3CHDIC digital emission 400-800nm range designed to acquire high spatial resolution images of fluorescently labeled materials and for analysis of these images. The confocal principle utilizes a pinhole (confocal aperture) to eliminate out-of-focus light from fluorescently labeled specimens (i.e., provide “optical sectioningâ€�). Lasers provide intense, point illumination that is scanned over the preparation and the fluorescence at each point is quantified and used to construct a representation of the object brightness (an image). This method provides high resolution for the x and y planes as well as vertically (z plane). The SP2 is an advanced confocal system with nine laser excitation lines spanning the spectrum from UV to near IR. The following laser lines are available: 405nm, 458, 476, 488, 496, 514, 543, 594, and 633, all fiber coupled and controlled by AOTFs.
Leica | LMD7000 Laser Microdissection System
Specimen collection by gravity contact-free and contamination-free. Laser Microdissection (LMD) makes it possible to distinguish between relevant and non-relevant cells or tissues. It enables the researcher to obtain homogeneous, ultra-pure samples from heterogeneous starting material. Researcher can selectively and routinely analyze regions of interest down to single cells from all kinds of tissues, even living cells from cell culture, to obtain results that are relevant, reproducible, and specific.
Leica | TCS SP5 Broadband Confocal Laser Scanning Microscope
Leica TCS SP5 is a broadband confocal microscope that provides the full range of scan speeds at the a high resolution. With its SP detection (five channels simultaneously) and optional AOBS (Acousto Optical Bream Splitter), the Leica TCS SP5 delivers bright, noise-free images with minimal photo damage at high speed. The system is also the platform for the new Leica DM6000 CFS (Confocal Fixed Stage) for physiological and electrophysiological experiments and for the new super resolution Leica TCS STED confocal microscope.
Reichert/Leica UltraCut S ultramicrotome is designed for extremely precise cutting, and achieves consistent high quality ultra thin sections for electron microscopy, or semi-thin sections for light microscopy. It features a continuous feed range from 0 to 2.5 microns and has adjustable cutting speeds of 0.1 to 50 mm/sec. It has a 6V, 10W halogen illumination system.
4Pi microscopy uses a special phase- and wavefront-corrected double-objective imaging system linked to a confocal scanner to enable 4-7 fold increased axial resolution over confocal & two photon microscopy. Even in living specimens, axial sections of ~100 nm are obtained. The system maintains all advantages of fast scanning, Acousto-Optical Beam Splitting (AOBS) and Spectral Detection of the Leica TCS SP2 AOBS for routine operation. The first marked leap in resolution in commercial 3D fluorescence microscopy opens up new dimensions for research in cell and developmental biology. The Leica TCS 4PI system was developed in close cooperation with Prof. Stefan Hell, Head of the NanoBiophotonics Department at the Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany and was in part funded by the German Ministry of Education and Research (BMBF).
Leica | EM ACE600 High Vacuum Sputter Coater
EM ACE600 sputter coater is a versatile high vacuum film deposition instrument for your FE-SEM and TEM applications.
Thermo Fisher: Life Technologies | QuantStudio 3 Real Time PCR System
Applied Biosystems QuantStudio 3 Real Time PCR System
System designed for users who need easy-to-use real-time PCR system that doesn't compromise performance and quality. Using OptiFlex technology (featuring 4 coupled channels and white LED) and featuring three independent Veriflex temperature zones, the QuantStudio 3 system enables improved data accuracy and sensitivity for broad range of genomic applications.
Thermo Fisher | Life Technologies QuantStudio 6 Real Time PCR System
QuantStudio 6 Flex system accommodates the interchange of a 96-well, 96-well Fast, or 384-well block. The system is delivered with one block type (a 96-well block in this case); other block types may be purchased separately. For a system that also supports TaqMan array cards, as well as automation, please see our QuantStudio 7 Flex system. The QuantStudio 6 Flex system can also be upgraded to a QuantStudio 7 Flex system at a later date, as your needs change. For the ultimate in productivity, consider the QuantStudio 12K Flex system, which also accommodates TaqMan OpenArray plates.
Thermo Fisher: Life Technologies | QuantStudio 5 Real Time PCR System
Carry out rapid food protection testing with the Applied Biosystems QuantStudio 5 Food Safety Real-Time PCR System. The and easy-to-use system is best for users who need superior performance, maximum dye versatility, and security options in a real time PCR system. The QuantStudio5 Food Safety System is a high performance benchtop platform combining ease-of-use and system connectivity. Benefit from the flexibility of a 6-channel, 96-well, cloud-enabled open platform suitable for running our full range of PCR solutions for food safety, authenticity, and quality testing.
Leica | Reichert-Jung Ultracut E Microtome
Ultracut E microtome is designed for extremely precise cutting, and achieves consistent high quality ultra thin sections for electron microscopy, or semi-thin sections for light microscopy. It features a continuous feed range from 0 to 2.5,m and has adjustable cutting speeds of 0.1 to 50 mm/sec. Comes with a control box with power cord, a microtome sectioning unit, and a microscope assembly with AO Stereostar 570 zoom body (0.7X - 4.2X) with attached 10X eyepieces. It has a 6V, 10W halogen illumination system.
Thermo Fisher | Lindberg/Blue M Vacuum Oven Accessories
Configure Thermo Scientific Lindberg Blue M Vacuum Oven Accessories with vacuum oven for more effective lab tool.
Vibrating blade microtome for sectioning by Leica Biosystems used in neurophysiology, neuropathology, experimental pathology, botany. Fully automated Leica VT1200 S vibrating blade microtome for cutting fresh and fixed tissue in Neuroscience. To achieve sections of the highest quality that retain viable cells on the section surface, the vertical deflection of the blade can be measured by Leica's Vibrocheck measurement device and minimised with the blade holder. The instrument was designed in collaboration with Prof. Dr. Peter Jonas and his group at the Physiology Department, Freiburg Germany.
Thermo Fisher: Life Technologies | QuantStudio 7 Real Time PCR System
Applied Biosystems QuantStudio 7 Flex Real-Time PCR System advances your research further by enabling a broad range of real-time PCR-based applications through its multiplexing capabilities and interchangeable block formats. With a simplified workflow, software, automation capabilities, and touch-screen interface, the QuantStudio 7 Flex system offers reproducibility with minimal well-to-well and instrument-to-instrument variation.
Thermo Fisher | Lindberg/Blue M 1200C Split-Hinge Tube Furnaces
Configure Thermo Scientific Lindberg Blue M 1200 degrees C Split Hinge Tube Furnaces for horizontal or vertical use.
Bussey-Saksida Rat Touch Screen Chamber Package Model 80604
Bussey-Saksida Rodent TouchScreen Operant System
Bussey-Saksida Rodent Touchscreen System
Designed for efficient and high throughput cognitive evaluation of rodents. System contains multiple cognitive paradigms, prewritten to include the entire battery of tasks necessary to habituate, shape, and bring the animal to criteria on that particular application, as well as collect and analyze prepared Data Analysis Sets using the ABET II software.
Interactive digital platform helping scientists who study type 1 diabetes connect, collaborate, and gain funding for their best ideas. All volunteer team has received much positive support from the global population of scientists studying type 1 diabetes, as well as from Beyond Type 1, JDRF, and IPITA. Provides curated conversations, events and technology to scientific T1D focused audience. Non profit entity funded by donations and sponsorships with industry and academic partners to provide unique collaborative benefits and programs to researchers in the T1D academic research community.
Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools.
Analyzer packs 3-parameter analysis into compact benchtop device, making flow cytometry accessible to anyone, anytime. A user-friendly touchscreen interface, cell analysis software, and optimized assays work to simplify your research.
Single CCD chip based area detector and has a read-out time of three (3) seconds for a 2k x 2k image. Some other features of the marCCD 165 are: Very low noise, Fast read-out, Peltier cooled detector, Monolithic design with no gaps. and Computer controlled data collection.
Nucleic Acid and Protein Purification instrument that provides consistent, automated purification of high-quality DNA, RNA, viral total nucleic acid, or recombinant proteins using paramagnetic particles. There are no Clogs or Drips, Optimal Capture, Washing, and Elution of Target Material, Purifier Can Configure as an SEV or LEV Instrument, Preprogrammed Purification Protocols, For Purification of High-Quality DNA, RNA, and More. It works as a particle processor, not a liquid handler, so there are no clogs or drips, allowing optimal capture, washing, and elution of target material. Purification protocols are preprogrammed into the instrument and can be combined with purification kits containing prefilled reagent cartridges to maximize simplicity and convenience. The purifier can be configured as an SEV Instrument (Standard Elution Volume, 200 400 �L) for maximum yield or an LEV Instrument (Low Elution Volume, 30 100 �L) for maximum concentration. Accessories information: Kits are sold separately and contain enough materials to run 48 preps each.
Refractometer that utilizes advanced optical waveguiding techniques to rapidly and accurately measure both the thickness and the refractive index/birefringence of dielectric and polymer films as well as refractive index of bulk materials. The 2010/M offers advantages over conventional refractometers and instruments based on ellipsometry or spectrophotometry: Completely General no advanced knowledge of optical properties of film/substrate required, Routine index resolution of �.0005 (accuracy of up to �.0001 available for many applications see specifications), Routine index resolution of �.0003 (resolution of up to �.00005 available for many applications see specifications), High accuracy index measurement of bulk, substrate, or liquid materials including birefringence/anisotropy, Rapid (20-second) characterization of thin film or diffused optical waveguides or SPR sensor structures, measurement of index vs wavelength, Options to measure index vs temperature (dn/dT), and waveguide loss, and Wide index measurement range (1.0-3.35).
Zeiss-Microm DS-50 slide stainer is fully programmable and meets the requirements of histology, hematology, cytology, microbiology and pathology laboratories. The Zeiss-Microm DS-50 slide stainer offers the efficiency, safety features and ease of operation customers have come to expect from Carl Zeiss. Equally important, the system's flexibility allows you to define your own protocols and remain consistent with your laboratory's individual procedures and requirements.
Cut paraffin sections without a power supply with the robust Thermo Scientific HM 325 Rotary Microtome. The HM 325 features retraction at the return travel to protect the specimen and manual coarse advance for fast working.
Miltenyi | Bioscience MACSQuant Analyzer 16
Automated flow cytometer with expanded fluorescence capabilities, enabling measurement of up to 16 parameters.
Microfocus rotating anode X ray generator.Used for Protein crystallography, small molecule crystallography, SAXS, micro diffraction, phase contrast imaging. Home lab X-ray source for protein crystallography and a popular source for small molecule crystallographers who need the additional flux of a rotating anode generator. The original MicroMax 007 introduced the world to the concept of a sub-100 micron focal spot size along the increased brilliance that can be more effectively used to illuminate small crystals. The current HF version increases the power loading by 50% over the original model providing an X-ray source that rivals second generation synchrotron sources - but with better beam stability and, of course, easy access.
Miltenyi gentleMACS Dissociator Tissue Dissociator
Benchtop instrument for semi automated dissociation of tissues into single cell suspensions or thorough homogenates. Single sample or two samples in parallel can be processed.
Miltenyi | Bioscience MACSQuant Analyzer 10
MACSQuant Analyzer 10 brings to life the versatility and power required for modern flow cytometry applications. Whether mining for rare cells, analyzing the efficiency of your cell manufacturing process or investigating signaling pathways, you are equipped for the task at hand. With a range of automated features, this flow cytometer lays the foundation for true automation present in all instruments belonging to the MACSQuant Family of flow cytometers.
Used in combination with gentleMACS Dissociators for automated tissue homogenization, in order to isolate biomolecules like mRNA or total RNA, or to extract proteins.
Used in combination with gentleMACS Dissociators for automated dissociation of tissues to obtain single cell suspensions with high viability rate.
Miltenyi | gentleMACS Octo Dissociator with Heaters Tissue Dissociator
Benchtop instrument for fully automated and standardized tissue dissociation or homogenization of up to eight samples. Equipped with eight individual heating units and gentleMACS Programs.
Miltenyi | gentleMACS Octo Dissociator Tissue Dissociator
Benchtop instrument for semi automated and standardized tissue dissociation or homogenization of up to eight samples. Single cell suspensions or thorough homogenates from virtually any tissues are reproducibly obtained using uniquecanTubes or M Tubes.
Miltenyi | Prodigy Cell Manufacturing Platform
Offers advanced integrated solutions to streamline cell processing workflows from cell separation through cell culture to formulation of final product. Offers flexible platform for cell processing applications enabling magnetic separation of different cell types and customized cell processing protocols.
Molecular Devices | ImageXpress High Content Confocal Imaging System
ImageXpress Micro Confocal system is a high-content solution that can switch between widefield and confocal imaging of fixed and live cells. It can capture high quality images of whole organisms, thick tissues, 2D and 3D models, and cellular or intracellular events. The spinning disc confocal and sCMOS camera enable imaging of fast and rare events like cardiac cell beating and stem cell differentiation. With MetaXpress software and flexible options like water immersion objectives to choose from, the system enables many confocal imaging applications from 3D assay development to screening.
Molecular Devices | SpectraMax Gemini XS Microplate Spectrofluorometer
SPECTRAmax GEMINI XS Dual-Scanning Microplate Spectrofluorometer can perform a variety of fluorescent applications as well as some time-resolved fluorescent and luminescent assays. The extreme flexibility and high sensitivity of the SPECTRAmax GEMINI XS make it appropriate for applications within the fields of biochemistry, cell biology, immunology, molecular biology, and microbiology. The SPECTRAmax GEMINI XS uses two holographic diffraction grating monochromators which allow for individual optimization of wavelengths for both excitation and emission. The dual-scanning capability can also be used to determine excitation and emission settings for new fluorescent probes. Mirrored optics focus the light into the sample volume and cutoff filters are used to reduce stray light and minimize background interference. The light source is a highpowered Xenon flashlamp; additional flexibility is provided by allowing a variable number of lamp flashes per read. Microplates having 6, 12, 24, 48, 96, and 384 wells can be used in the SPECTRAmax GEMINI XS. Fluorescent detection is achieved from the top, through the entire depth of sample in the microplate well. Detection of species collected on membrane plates is also possible. Two plate carrier adapters are provided with the instrument. The blue adapter is required for optimum performance with standard 96- and 384-well format microplates. The red adapter has been optimized for use with Cliniplate 384 microplates.
Molecular Devices | Spectramax M2e Microplate Reader
Multidetection microplate readers with dualmonochromators, dual-mode cuvette ports, and top- and bottom-reading capability. Detection modalities include absorbance (UV-Vis Abs) and fluorescence intensity (FI). Endpoint, kinetic, spectrum and area-well scanning read types and the PathCheck Sensor allow homogeneous and heterogeneous microplate assays to be performed in one flexible system. SpectraMax M2 readers provide for easy conversion and optimization of very-low-throughput to medium-high-throughput assays, faster, more precise results and reagent savings. In addition, combined absorbance and fluorescence intensity assays can be run by issuing a single read command.
Molecular Devices | SpectraMax Gemini Microplate Reader
Microplate reader built on Gemini platform delivering high quality top and bottom reading for both solution and cell based assays. The Gemini EM can sample a variety of formats, from 6- to 384-well microplates, in different modes, such as endpoint, spectral scan, kinetic, and well scan. This reader's dual monochromators for excitation and emission cover the wavelength selection from 250 to 850 nm. Utilize both top and bottom fluorescence reading for the best optical sensitivity, and read up to four wavelength pairs in endpoint and kinetic measurements. The Gemini EM offers superb accuracy and reproducibility of results, possible with AutoPMT electronics, calibration for comparing RFUs between samples, consistent temperature regulation, programmable Automix, gentle movement, seamless automation, and comprehensive reader validation. Applications for the Gemini EM include enzyme assays, protein quantitation, microbial growth, ELISAs and immunoassays, transporter assays, nucleic acid quantitation, phosphotases/kinases, reporter gene assays, and cell viability, proliferation, and cytotoxicity.
Molecular Devices | Molecular Dynamics 8600 Imager
Typhoon 8600 Variable Mode Imager unites storage phosphor autoradiography technology with fourcolour fluorescent labelling techniques for maximum data quality in a single, high-throughput system.
Molecular Devices | SpectraMax M5 Multimode Plate Reader
Microplate Reader delivers single mode reader performance and can be equipped to read volumes as low as 2uL in one multimode reader package. The dual monochromator optics allow the widest range of applications to be utilized for bioresearch and drug discovery applications, all without the need to change filters. For fluorescence intensity, time resolved fluorescence, and fluorescence polarization assays, the SpectraMax M5 Microplate Reader optical design provides the highest level of flexibility. Users can select from top or bottom read modes for improved sensitivity for solution and cell-based assays. Assays can be better optimized by scanning across a range of wavelengths in increments as small as 1 nm. Up to 4 wavelength pairs can be read in one protocol for endpoint and kinetic measurements, allowing for fast setup of FRET and TR-FRET assays. For luminescence, the SpectraMax M5 Microplate Reader utilizes a dedicated luminescence photomultiplier tube (PMT), providing the user the maximum signal and lowest background possible for glow luminescence reporter gene assays. The SpectraMax M5 utilizes a single monochromator design for UV/VIS Absorbance, allowing the user to maximize sensitivity and tunability, and also uses patented PathCheck Pathlength Measurement Technology: the only temperature independent pathlength correction for microplates. The M5 can read volumes down to 2uL with the uMax Low Volume Plate.
General purpose imager that delivers the speed typical of laser scanners on both 1D and 2D barcodes, accommodating 2D barcodes without sacrificing performance. Users never need to take time to align the barcode with the scanner or pause between scans. Since the DS4208 can scan barcodes printed on paper labels or on mobile phone displays, users can drive revenue by attracting the millions of customers who are using their cell phones to better manage their lives. Retailers can accommodate customers who download mobile coupons, mobile loyalty cards and more. Quick service restaurants can accept mobile coupons at the register. Hotels can allow guests to use electronic loyalty cards stored on their cell phones, eliminating the need to carry physical cards. And since theaters, theme parks and stadiums can scan mobile tickets as easily as a paper ticket, they can offer customers an added convenience: paperless ticketing.
Molecular Devices | SpectraMax 340PC384 Microplate Reader
Microplate reader from Molecular Devices provides everything needed to measure absorbance in the visible range, including temperature control, a robotics-compatible interface and SoftMax Pro Data Acquisition and Analysis Software.
QuickPlex instrument is the newest multiplexing instrument from MSD, offering access to high-performance, electrochemiluminescence immunoassays. This compact system has been engineered for reliability, ease of use, and low cost of ownership. The combination of rapid read times and the ability to perform multiple, simultaneous tests on a single sample increases productivity, saves sample, and delivers results quickly. The QuickPlex has a wide menu of commercially available assay kits and a full line of components and reagents for developing your own assays.
Thermo Fisher | MSC-Advantage Class II Biological Safety Cabinets
Conserve energy with Thermo Scientific MSC Advantage Class II Biological Safety Cabinets, which combine design and value with energy efficiency. Units feature 60 percent less energy consumption and heat output and cabinets are certified to EN 12469 safety standard.
Princeton Cryo | MVE XC 47/11-6 Cryogenic Tank
Cryogenic tank for Specimen Sample Storage.This item includes the XC 47/11-6 dewar, cork/cover, and (6) 11" hanging round canisters. All other accessories sold separately. MVE XC Series tanks have capacities ranging from 700-5000 straws and 210 to over 1000 vials. .
Molecular Devices | SpectraMax M2 Microplate Reader
Multidetection microplate readers with dualmonochromators, dual-mode cuvette ports, and top reading capability. Detection modalities include absorbance (UV-Vis Abs) and fluorescence intensity (FI). Endpoint, kinetic, spectrum and area-well scanning read types and the PathCheck Sensor allow homogeneous and heterogeneous microplate assays to be performed in one flexible system. SpectraMax M2 readers provide for easy conversion and optimization of very-low-throughput to medium-high-throughput assays, faster, more precise results and reagent savings. In addition, combined absorbance and fluorescence intensity assays can be run by issuing a single read command.
SelectScience | Nano CT scanner: Xradia VersaXRM-500
VersaXRM-500 from Xradia VersaXRM family is the latest generation of 3D X-ray microscopy (XRM) solutions optimized for non-destructive micro tomography. The VersaXRM-500 advances industry and science with a versatile combination of world-leading resolution and contrast, sample flexibility and the large working distance required to address emerging research challenges. The system's source technology and high resolution detector provide unmatched sub-micron resolution, even for large samples.
Thermo Fisher | NanoDrop 2000c Spectrophotometer
Full-spectrum, UV-Vis spectrophotometer used to quantify and assess purity of DNA, RNA, Protein and more.NanoDrop 2000c combines micro-volume pedestal technology and cuvette capability in single instrument.Provides expanded measurement options for all types of samples.Provides broader concentration range for measuring very low concentrations and very high concentrations. Cuvette capability allows for kinetics (time or time/temperature studies) and cell culture (OD 600) measurements.
Malvern Panalytical | Nanosight NS500 Analyzer
Malvern Panalytical NanoSight NS500 instrument provides an easy-to-use, reproducible platform for nanoparticle characterization. The NS500 provides detailed and analysis of the size distribution and concentration of all types of nanoparticles from 10nm to 2000nm in diameter, depending on the instrument configuration and sample type being analyzed. Single particle zeta potential measurements on the NS500 provide inherent high resolution zeta distributions which can be measured simultaneously with other NTA measurements parameters like size, particle concentration and can even operate whilst in fluorescence mode.
Thermo Fisher | Nanodrop Qubit 3 Fluorometer
Benchtop fluorometer that can be used for the quantitation of DNA, RNA, microRNA, and protein using the highly sensitive and accurate fluorescence-based Qubit quantitation assays. Additionally, Ion Sphere Particle quality can be evaluated on the Qubit 3.0 Fluorometer using the Ion Sphere Quality Control Kit prior to performing a sequencing run on the Ion Personal Genome Machine (PGM) Sequencer. You can also use the Qubit 3.0 Fluorometer to directly measure the fluorescence of samples or to create new assay(s) using the MyQubit software pre-programmed into the instrument.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10, 2024. Professional 135/IX240 film scanner is a scanner that satisfies the need for quality and speed. 4,000-dpi true optical-resolution scanning,16-bit A/D converter featuring 16-/8-bit output for crisp, color-true images. Exclusive Scanner Nikkor ED high-performance lens elements for reduced color aberration and minimized image distortion. Proprietary LED illumination technology ensures consistently accurate color reproduction. Amazingly fast scanning (approx. 20 seconds including image transfer to display) at 4,000 dpi Newly-developed, high-quality 2-line CCD sensor Improved image processing algorithm for significant boost in scan quality of color negative film Multi-sample scanning capability of up to 16 passes for faithful reproduction and smoother gradation Quick AF & Quick Preview enhance operability and High-speed USB 2.0 interface for fast, easy image transfer Compatible with various film formats (35mm [135], IX240, etc.) Enhanced Color Management System for higher precision, in compliance with ICC (International Color Consortium) version 4 standards.
Marshall Scientific | New Brunswick Innova 4230 Incubator
Refrigerated Incubator Shaker has a heavy gauge stainless steel frame, both refrigeration and heating capabilities, and a internal shaking platform, this Refrigerated incubator is fully capable of handling just about any sample parameters. The internal Cabinet of the 4230 is composed of sturdy heavy gauge stainless steel and has a double paned glass window on the outside to allow internal sample viewing. The cabinet contains two adjustable stainless steel shelves and a fluorescent light for improved visibility. The 4230 also includes an internal AC receptacle for the sole purpose of the powering of internal devices. The built in shaker features an audible and visible alarm, control, display, timer and other onboard installations. The internal shaker drive is a triple eccentric counter balanced drive with 9 sealed for life ball bearings and has a motion of � circular standard. The rpm range is between 25 and 400 non stacked, and 25-300 stacked. The onboard timer has a time range of up to 99.9 hours setable in 0.1 hours. The temperature of the 4230 ranges from 20C below ambient with a minimum of 4C to maximum of 75C for 50 Hz units or 80C for 60 Hz units. Temperature alarms provide indication when temperature deviates > 1.0C
Marshall Scientific | New Brunswick C24KC Incubator Shaker
New Brunswick C24KC Incubator Shaker microprocessor controls allow for uniform heating, motion and accurate regulation of shaking speed. Audible and visual alarms come standard with built-in timer. Speed ranges from 50 to 400 RPM and temperature ranges from 5 to 60 C.
Nikon | A1R Confocal Laser Scanning Microscope
A1R model incorporates a hybrid scanner system utilizing a high speed resonant galvanometer capable of acquisitions up to 240 frames per second. Both scanners can be used simultaneously for experiments requiring acquisition and photoactivation by concurrently scanning the specimen. This supports advanced research methods using photoactivation fluorescence proteins and facilitates high-speed, live-cell work with a huge array of new imaging strategies. A spectral imaging detector further enables the A1 and A1R models to obtain up to 32 discreet spectral bandwidths of data in one acquisition, with spectral unmixing capabilities. The total system is controlled through NIS-Elements C applications software, which also enables full control of the Nikon Ti-E research inverted microscope equipped with Nikon's Focus System (PFS), widefield CCD cameras and an array of hardware devices.
Nikon | A1 Confocal Laser Scanning Microscope System
Basic confocal system consisting of a separate scan head, standard 5 PMT detectors, control module, and laser module. The A1 has a new multi-detector unit with 2 GaAsp PMT detectors to give brighter signals, enhanced signal-to-noise, and allow less phototoxicity.Fully automated A1 offers standard paired galvanometers with high resolution scanning at up to 4096 x 4096 pixels.
Nikon A1R MP is a multiphoton imaging system featuring a high resolution galvanometer scanner and a high speed resonant scanner that is capable of frame rates from 30 fps at 512 x 512 pixels to as fast as 420 fps in band scan mode. New 4 channel non-descanned detectors with higher sensitivity, reduced dark current and broad spectral range allow for real time unmixing of closely spaced probes for accurate and high-contrast spectral imaging. This is especially important in multiphoton microscopy because of the overlap of emission spectra of probes and autofluorescence, which is often unavoidable when using a single laser line.
E400 standard microscope is optimized for comfort in extended clinical applications.
Versatile Eclipse 55i clinical microscope offers optical capabilities, unsurpassed ergonomic features and is optimized for digital imaging. Its white LED illumination system provides a homogenous and bright distribution of illumination across the field for optimal viewing and digital imaging, resulting in spectacular, vivid, true-to-life colors. ergonomic features, like the stay-in-position stage handle and tilting/telescoping ergonomic eyepiece tube ensure best viewing posture, enabling long hours of observations to be carried out in comfort.
Nikon | Eclipse 800 Widefield Microscope
Eclipse 800 Microscope is a premier member of Nikon's advanced research microscope line. The E800 series incorporates Nikon's CFI60 optical system that (according to them) alleviates the limitations of conventional optics, allowing for very long working distances (for a tutorial on Nikon's CFI60 Optical System, click here). This system corrects chromatic aberrations over the entire field of view, generating a very sharp, clear image over the broadest magnification range. One can also put in a broad range of accessories without affecting optical quality. The microscope is designed so that the scientist can work with ease, especially in the dark, requiring little movement to operate the control knobs and handles. The CFI60 Optical System offers a 60mm objective parfocal distance, a 25mm objective thread size and a standard 25mm field of view all of which combine to provide a higher optical quality.
Nikon Eclipse TS100-F Inverted Microscope comes from a long line of microscopes. The Halogen bright-field lamp provides enough light for phase contrast and NAMC viewing. The Eclipse TS100-F Inverted Microscope Sidentopf eye piece from Nikon delivers constant brightness throughout the entire field of view. This microscope is best for applications such as tissue culture, plaque measurement and blood typing. Used in combination with Narishige manipulators, also available from Nikon, these microscopes can be used for a range of micromanipulation techniques necessary for cyto-engineering, developmental and genetic engineering, electrophysiology, pharmacology and neurochemistry. Eco-illumination provides a long lifetime of 60,000 hours and reduces the frequency of lamp replacement. Nikon Eclipse TS 100 highly acclaimed CFI60 optical system is used, providing flat, sharp and clear images, while achieving longer working distances and higher numerical apertures. The Eclipse TS100 is also outfitted for phase contrast applications with a phase ring slider and filter, and is camera mount ready. The compact high-performance inverted Nikon ECLIPSE TS100-F Microscope uses Eco-illumination, a newly developed LED illumination. Eco-illumination provides enough brightness for phase contrast and NAMC observations on the Nikon Eclipse TS100 F. With a fly-eye lens, uniform brightness is provided in the entire field of view. LEDs are an environmentally friendly low-power-consumption light source. Eco-illumination provides a long lifetime of 60,000 hours and reduces the frequency of lamp replacement. Nikon's highly acclaimed CFI60 optical system is used, providing flat, sharp and clear images, while achieving longer working distances and higher numerical apertures. The Nikon Eclipse TS100F is best for applications such as tissue culture, plaque measurement and blood typing. Used in combination with Narishige manipulators, also available from Nikon, these microscopes can be used for a range of micromanipulation techniques necessary for cyto-engineering, developmental and genetic engineering, electrophysiology, pharmacology and neurochemistry.
Building upon the success of the popular CFI60 optical system (60-millimeter parfocal distance and 25-millimeter objective thread size) first installed on the Eclipse E600, Nikon has moved a step further by introducing ultra-low magnification objectives and has increased the standard field of view to 25 millimeters. Introduced with the Eclipse E800 was a plan 0.5x magnification objective, which accommodates a 50-millimeter field of view at the unprecedented magnification of 0.5x. When coupled with a 2x projection lens, the 0.5x objective permits macrophotography at 1:1 magnification (in effect, actual size documentation). The new macro objective lens is particularly useful for investigating large specimens such as brain slices, developing embryos, and extensive tissue sections. This objective is easily accommodated into the microscope without major re-configuration, and is interchangeable with other objectives on a standard rotating nosepiece.
Nikon SMZ-1 and SMZ-1B zoom stereo microscopes offer legendary Nikon stereo performance. Developed to fit a variety of applications and OEM needs, these advanced-design stereo microscopes have the features and image quality you expect from Nikon. High-performance optics and a 6V/10W halogen illuminator deliver images with excellent contrast, resolution, and brightness. The SMZ-1 and SMZ-1B are human-engineered to allow long periods of operation without fatigue. Mechanical design is yet rugged for daily trouble-free operation in industrial, laboratory, and classroom environments. All controls are easy to use. Nikon's versatile modular approach allows the SMZ-1/1B to be easily adapted to various configurations such as stand, arm, or table mounting. Similarly, the illuminator can be fixed to the instrument stand, placed in a diascopic base, or attached externally for oblique lighting. The SMZ-1/1B use a Nikon-designed twin-lens objective system inclined at 12o. Only the center of the lenses is used to provide the sharpest three-dimensional image and enable the operator to work more accurately and efficiently for prolonged periods without eye strain.
Nikon | TE300 Inverted Fluorescence Microscope
Advent of the infinity-corrected CFI60 optical system spurred Nikon design engineers to upgrade their research-caliber inverted microscope from the Diaphot 300 to the Eclipse TE300 in 1997. The vastly improved instrument provides longer working distances that accommodate a wide variety of culture vessels and thick specimens, while maintaining high numerical apertures to ensure suitable levels of brightness, imaging contrast, resolution, and sharpness. The paired oculars of the instrument provide a standard 22-millimeter field of view, but like other microscopes in the Eclipse line, the Nikon TE300 is highly modular and provides several options for binocular and trinocular tubes, condensers, stages, and illumination systems. The standard condenser system fabricated for the Nikon TE300 microscope consists of a series of condenser top lenses and a five-position turret assembly with components for phase, differential interference, and Hoffman modulation contrast techniques. Also, Nikon designers patented a video enhancement contrast system for the microscope that features special polarizers and analyzers that enable the visualization of low contrast minutiae that would ordinarily go unnoticed by traditional video imaging methods.
Thermo Fisher | Nunc Cell Factory Shaker GEN 2
Automated system to perform horizontal, continuous accelerated and decelerated movement to Cell Factory System.Eliminates the need for manual methods of cell detachment, such as shaking and pounding.
Nikon | TMS Inverted Phase Contrast Microscope
Nikon TMS Inverted Phase Contrast Microscope produces high quality images for tissue culture labs, readily meeting biological and metallurgical research needs. This Nikon microscope offers operation with an easy-to-maintain inverted microscope frame. This inverted phase microscope is configured with 4x achromat, 10x Ph1, and 20x Ph2 objectives with critical halogen illumination. The TMS can accommodate a variety of Nikon CF objectives on its revolving triple nosepiece, along with multiple other accessories, such as stage adapters and extenders, sliders and rings, and extra long working condensers. The 4x achromat objective provides a lower magnification for a wider field of view, primarily best for when needing to view a large portion of a slide for study. The 10x Ph1 provides phase contrast low-power magnification, while the 20x Ph2 provides medium-power magnification with a larger aperture.
Offers higher magnification than conventional models, enabling high-resolution observation of minute structures. In combination with the new objective series, its improved chromatic aberration correction provides bright and sharp images through the entire viewfield. The parallel optics design allows ergonomic accessories and observation attachments to be used in a wide range of applications.
Thermo Fisher | Nunc Cell Factory Systems with Active Gassing Bioprocessing System
Flow system helps to ensure controlled, contamination free atmosphere in each culture tray by equally distributing user specified gas mixture. Available in 4,10 and 40 tray models.
Nikon Eclipse 90i is a fully motorized upright microscope configured to image in transmitted light, DIC and epi-fluorescence modes. Fluorescence cubes available for DAPI, GFP, RFP, and HYQ Cy5. Fluorescence illumination is provided by a Lumencor Sola Light Engine. You can do timelapse, XYZ position, Z stacks, multiple excitation or emission wavelengths, and tiling experiments. Equipped with a Hamamatsu Orca Flash 4.0 v2 CMOS monochrome camera and a Nikon D2-Fi2 color camera running on Nikon Elements software.
Olympus | AX70 Upright Fluorescence Microscope
Upright Fluorescence Microscope with automatic photomicrography system.Using the AX70 together with the U-PHOTO Universal Photo System provides a very advanced level of microscope performance and sophisticated photomicrography capabilities. Combining the mainframe and its corresponding auto focus function with the U-AFPHOTO and motorized units integrates technology with a system that fully supports automated photomicrography. This combination offers fast auto focus in brightfield, darkfield, fluorescence*, and Nomarski Differential Interference Contrast*, and provides automatic light intensity adjustment for the objective in use as well as automatic observation light path selection.
Next generation imaging system designed for high resolution, confocal observation of both fixed and living cells.FV1000 offers advances in confocal system performance while providing the speed and sensitivity required for live cell imaging with minimal risk of damage to living specimens.In addition, the FV1000 offers a revolutionary synchronized laser scanning system called the SIM Scanner. While one laser stimulates, the second laser simultaneously provides high-resolution imaging. This coordination of laser stimulation and imaging makes the FV1000 an ideal choice for FRAP, FLIP and photoactivation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Goal of the BH2 was superior optics and customizability, and it soon became very well known for both. Standard equipment on this microscope included 10x widefield high eyepoint eyepieces having a field number of 20, precentered halogen lamps, aspherical collector lenses, and fully enclosed light paths designed to exclude dirt and dust. Auxiliary components for the microscope included photoeyepieces, an automatic exposure photomicrography system, and a wide range of objectives covering the entire range of correction and magnification. In addition, both mechanical and circular stages were offered as were binocular and trinocular observation tubes. Contrast enhancing equipment included phase contrast, differential interference contrast, darkfield, fluorescence, and polarized light.
Olympus | FluoView 300 Confocal Microscope
Confocal microscopy can improve conventional fluorescence images by recording fluorescence generated from the focal plane within the sample, while rejecting all other light coming from above or below the focal plane. The efficient point-scan/pinhole-detection confocal optics of the FluoView systems virtually eliminate out of focus light to produce high-contrast images with superb resolution. The FluoView systems are fully integrated workstations that incorporate user-friendly image acquisition and image analysis software with high-resolution confocal optics that require no user alignment. An , Windows-based graphic user interface allows new users to quickly generate images in various scan modes, such as XY, XZ, XT, XYZ, XYT, and XYZT. Standard image formats, including TIFF and AVI, permit easy, direct export of FluoView images to off-line analysis packages. XY scanning is performed with a pair of galvanometric mirrors, yielding a wide scanning range to cover up to a field number of 20. The optical zoom (up to 10x magnification) can be performed by narrowing the scanning range while maintaining the maximum pixel resolution of up to 2048 x 2048 pixels.
Olympus | FV500 laser scanning microscope
Olympus launched FV500/300 laser scanning biological microscopes in 1998, shortly after releasing the AX, BX, and IX series of microscopes that featured infinity-corrected UIS optics. The FV500/300 produce 2048 x 2048-pixel images.
Olympus | IX 81 Inverted Fluorescence Automated Live cell Microscope
Olympus IX81 Inverted Fluorescense Phase Contrast Live cell Inverted microscope.
Olympus | BX61 Upright Wide Field Microscope
BX61 Upright Wide Field Microscope is specially designed to work with the Olympus laser based autofocus unit. With precise focus and active tracking, users can speed up routine inspections. Additional settings such as illumination level, lens selection and aperture setting can be set using push buttons on the microscope frame, a keypad or via the PC. A variety of motorized modules including nosepieces and illuminators are available to provide you with full flexibility in configuring your system.
Olympus | IX83 Automated Fluorescence Microscope
The Olympus IX83 inverted microscope has been integrated into our IXplore systems. IXplore Systems are designed to provide solutions-based packages that suit your research application needs.
Olympus IX73 inverted microscope has been integrated into our IXplore systems. IXplore Systems are designed to provide solutions-based packages that suit your research application needs.
Uses remote source specifically designed for atomic scale processing. Has low damage for sensitive substrates, fast cycle times and reliablity with uniform plasma exposure and film deposition, short plasma times, 250ms, short strike time, 80ms, for high throughput, and reproducible strike time and low reflected power for high yield.
Asylum Research Cypher ES builds on performance of Cypher S and adds full environmental control features. Same resolution, speed and stability are maintained while operating in controlled gas or liquid environments, at temperatures from 0 to 250 degrees C.
Oxford |FlexAL ALD System Plasma Technology
FlexAL systems provide newrange of flexibility and capability in engineering of nanoscale structures and devices by offering remote plasma atomic layer deposition processes and thermal ALD within single ALD systems.
Configuration of Cypher ES AFM designed for polymer science research, comes standard with blueDrive photothermal excitation, three techniques from NanoMechPro toolbox for nanomechanical characterization, and high temperature polymer heater.
Full featured video rate atomic force microscope. This high speed AFM allows researchers to measure nanoscale dynamic processes at video frame rates.
Oxford |Integra Superconducting Magnet System
Helium magnet system. Wide range of superconducting magnet systems up to 22 T, cooled by liquid helium. Ideal for highly vibration sensitive experiments.
IntegraAC range of recondensing helium systems has been developed to reduce consumption of liquid helium. By recondensing helium gas evaporated within system, this minimises running costs and conserves this limited resource. It is also compatible with wide range of superconducting magnets.
Oxford |Ionfab 300 IBE Plasma Technology
Ion beam etch offers flexibility coupled with uniformity and is suitable for wide range of applications. Systems have flexible hardware options including open load, single substrate load lock and cassette to cassette. System specifications are closely tuned to applications, enabling faster and repeatable process results.
Oxford |Ionfab Ion Beam Plasma Technology
Ion beam etch and deposition system is used for high quality material processing. Systems have flexible hardware options including open load, single substrate load lock, and cassette to cassette.
Oxford |PlasmaPro 100 Polaris Plasma Technology
PlasmaPro 100 Polaris single wafer etch system offers solutions to produce etch results needed to maintain competitive edge, with experience of etching materials such as GaN, SiC and Sapphire.
Large sample AFM that offers high speed imaging and extended range in single scanner. Jupiter provides complete 200 mm sample access and delivers resolution, results, and versatility for academic research and industrial R and D laboratories.
Magnet power supply system enables automated control of wide range of superconducting magnets, including NMR, high field, beamline and Vector Rotate magnet systems. MercuryiPS is bi polar and has high stability, four quadrant power supply with incorporated quench protection.
Oxford |Ionfab 300 IBD Plasma Technology
Ion beam deposition products produce deposited films with high quality, dense and smooth surfaces. Ion beam technology provides approach to etch and deposition by offering single tool and maximising system utilisation, which includes open load, single substrate load lock, and cassette to cassette.
Oxford |MercuryiTC Cryogenic Environment Controller
Cryogenic environment controller that includes single channel 24 bit high resolution temperature measurement circuit, which supports all standard cryogenic sensors, like ruthenium oxide, cernox, silicon diodes, platinum, thermocouple and RhFe. With constant voltage mode, it enables accurate temperature measurement using negative temperature sensors down to below 250 mK.
PlasmaPro 800 offers a flexible solution for Plasma Enhanced Chemical Vapour Deposition (PECVD) processes on large wafer batches and 300mm wafers, in a compact footprint, open-loading system. The large wafer platen allows for production scale batch processing and 300mm wafer handling.
Integrates AFM and optical microscopy for bioscience research. Bio AFM that uses AFM imaging resolution, force measurement performance, and application versatility while integrating optical techniques.
Features same core performance as MFP 3D Origin but includes support for complete range of innovative MFP 3D accessories.
Oxford |Nanonis Tramea Measurement System
Measurement system used for quantum transport measurements. In conjunction with cryogenic research tools, it offers multi channel measurements to for quantum technologies.
Features Asylum Research performance and quality and offers high resolution imaging, supports large samples, most imaging modes, and many accessories.
Oxford |OmniProbe 400 Electron Microscope
Ninth generation of nanomanipulator, OmniProbe 400 uses piezo actuation for nanoscale positioning. Nanomanipulator with high resolution and high throughput applications.
Oxford |PlasmaPro 100 Cobra Plasma Technolgy
PlasmaPro 100 Cobra ICP utilises high density plasma to achieve etching and deposition rates. Process modules offer uniformity, high throughput, high precision and low damage processes for wafer sizes up to 200mm.
Oxford |PlasmaPro 100 ALE Plasma Technology
PlasmaPro 100 ALE delivers precise process control to create and manipulate thinner layers through specialised hardware including precise control of gas dose, repeatability of low power RF delivery, and switching enabled by fast PLC.
Oxford |PlasmaPro 100 Estrelas Plasma Technology
Platform is designed to give total flexibility for Deep Silicon Etch applications. Serves diverse set of process requirements across Micro Electro Mechanical Systems and Advanced Packaging and Nanotechnology markets.
Oxford |PlasmaPro 100 PECVD Plasma Technology
PECVD process modules are designed to produce uniformity and high rate films, with control of film properties such as refractive index, stress, electrical characteristics and wet chemical etch rate.
Oxford |PlasmaPro 100 ICPCVD Plasma Technolgy
ICPCVD process module is designed to produce films at low growth temperatures, enabled through high density remote plasmas that achieves film quality with low substrate damage.
Oxford |PlasmaPro 100 RIE Plasma Technology
PlasmaPro 100 RIE modules deliver anisotropic dry etching. Being compatible with all wafer sizes up to 200mm, it has rapid change between wafer size, uniformity, high throughput and high precision processes, in situ chamber cleaning and end pointing, and wide temperature range electrode, from 150 degrees C to 400 degrees C.
Oxford |PlasmaPro 80 ICP Plasma Technology
PlasmaPro 80 ICP is compact, small footprint system offering ICP etch solutions with open loading. Open load design allows fast wafer loading and unloading, ideal for research, prototyping and low volume production. It enables high performance processes using optimised electrode cooling and substrate temperature control.
Oxford |PlasmaPro 80 ICPCVD Plasma Technology
PlasmaPro 80 is compact, small footprint system offering etch and deposition solutions with open loading. Open load design allows fast wafer loading and unloading, ideal for research, prototyping and low volume production. It enables high performance processes using optimised electrode cooling and substrate temperature control.
Oxford |PlasmaPro 800 PECVD Plasma Technology
PlasmaPro 800 offers solution for Plasma Enhanced Chemical Vapour Deposition processes on large wafer batches and 300mm wafers, in compact footprint, open loading system. Large wafer platen allows for production scale batch processing and 300mm wafer handling.
Oxford |PlasmaPro 80 PECVD Plasma Technology
Oxford |PlasmaPro 80 RIE Plasma Technology
PlasmaPro 80 reactive ion etch is compact, small footprint system offering etch and deposition solutions with open loading. Open load design allows fast wafer loading and unloading, ideal for research, prototyping and low volume production. It enables high performance processes using optimised electrode cooling and substrate temperature control.
Oxford |SpectromagPT Superconducting Magnet System
Split pair, horizontal field magneto optical Cryofree superconducting magnet system. It provides optical access to sample in variable magnetic field and low temperature environment.
Self supporting Secondary Insert that enhances adaptability, enabling rapid exchange of full experimental setups for multi user, multi experiment system. Upgradeable Secondary Inserts are cross compatible and transferrable between ProteoxTM family systems. Has large experimental volume and abundant line of sight access.
Oxford |PlasmaPro 100 Nano Plasma Technology
Chemical Vapour Deposition and PECVD tools for growth of 1D and 2D nanomaterials and heterostructures. PlasmaPro 100 Nano delivers performance growth of nanomaterials with in situ catalyst activation and process control, with flexible temperatures up to 1,200 degrees C.
Oxford |TeslatronPT Superconducting Magnet System
Integrated Cryofree® superconducting magnet system with variable temperature inserts. Has standard magnetic fields up to 14 T in compact geometry, integrated variable temperature insert providing sample temperatures between 1.5 K and 300 K, and range of high performance sample rods with height adjustment and rotation options.
TritonXL is used for research applications where sample temperatures below 5 mK is required, for integrating larger numbers of signal lines or very high magnetic fields. Has two integrated 1.5 W pulse tube coolers, decoupled with flexible braids and bellows to minimize vibrations.
Oxford |PlasmaPro 1000 Stratum Plasma Technology
Maximised large area etching and deposition production solutions available in load lock or cluster configurations with up to 3 chambers and vacuum load lock as standard with cluster capability options.
Oxford |Ultim Extreme Electron Microscopy
Ultra high resolution FEG SEM application and delivers solutions beyond micro and nano analysis. It uses radical geometry for both imaging and EDS performance in ultra high resolution FEG SEMs while working at low kV and short working distance, with EDS resolution that approaches that of SEM.
Symmetry uses customised CMOS sensor to unlock combination of speed, sensitivity and diffraction pattern detail.
Perkin Elmer | 7000 Automated Confocal Microscope
Optima 7000 DV brings advanced technology to laboratories requiring flexibility and excellent analytical performance for varied and moderate sample loads.Totally eliminating peak search algorithms, the UV sensitive, backside illuminated CCD array detector allows you to collect a complete analyte spectrum at speeds that far exceed competitive systems.Automatic dual viewing ensures the lowest detection limits and the widest working ranges.
Perkin Elmer | Chemagic 360 Genetic isolation Workstation
Nucleic Acid Extractor for Medium to High Throughput. Based on our patented chemagen magnetic bead technology the chemagic 360 instrument represents the best solution for nucleic acid isolation in a huge variety of research market segments including but not limited to Biobanking/Human Genetics, HLA Typing, Virus and Bacteria Detection. Experience the revolutionary compact benchtop design of our newly developed chemagic 360 Nucleic Acid Extractor. Based on the well-established chemagen Technology, the system offers a flexible solution for different sample processing and throughput needs. Configurable with three kinds of chemagic Rod Heads (see table below) the system can process sample volumes from 10 �l 10 ml.
Evolution Precision Pipetting System as flexible automated liquid handler for both low and high throughput microplate applications using 96 or 384 channel disposable tip dispense heads. EP3 can be configured for many common applications.
SelectScience | PELCO easiGlow Glow Discharge Cleaning System
System uses automated and quick cycle with fully selectable parameters.Microprocessor controlled system also offers full manual control for all parameters and an advanced protocol programming feature for custom designed glow discharge applications. Parameters and protocols can be stored to facilitate consistent glow discharge results. Open the shipping box, plug it in, and you can start. The PELCO easiGlow Glow Discharge Cleaning System is a compact, quick and easy to use standalone system. It is primarily designed for cleaning TEM grids and hydrophilization of TEM carbon support films, which have the tendency to be hydrophobic. A glow discharge treatment with air will make a carbon film surface negatively charged (hydrophilic) which allows aqueous solutions to spread easily.
Oxford |PlasmaPro 800 RIE Plasma Technology
PlasmaPro 800 offers solution for reactive ion etching processes on large wafer batches and 300mm wafers, in compact footprint, open loading system. Large wafer platen allows for production scale batch processing and 300mm wafer handling.
Perkin Elmer | Nexion 300Q Inductively-Coupled Plasma-Optical Emission Mass Spectrometer
NexION 300Q Inductively-Coupled Plasma-Optical Emission Mass Spectrometer the best solution for analyses requiring accepted interference-correction capabilities. This configuration does not include cell technology but it can be field upgraded to include a Universal Cell at any time. The NexION 300Q is best suited for markets such as geochemical analysis. The PerkinElmer NexION 300 offers three modes of operation (Standard, Collision and Reaction) and can be quickly switched from one mode to another. The PerkinElmer NexION is the only ICP-MS that lets you maximize productivity without compromising sensitivity or performance. For the first time ever, a single ICP-MS instrument offers both the simplicity and of a collision cell and the detection limits of a true reaction cell.
Perkin Elmer | Scanarray Microarray Scanner
Packard ScanArray Express Line of Microarray Scanners from PerkinElmer Life Sciences with easy to use software, breakthrough technology and uncompromising data quality. With the introduction of the first commercial microarray scanner, originally by GSI Lumonics, the ScanArray line offered the only upgradeable 2-wavelength scanner, the only scanning instrument to have patents that covered acquisition, barcoding and automation, and today is the brand most often found in microarray labs worldwide. Only the ScanArray family can visualize the spotting process on each array before hybridization. Without the use of special reagents or any change to your protocol, if salts are used in the spotting buffer, the user simply scans the array using the red laser and a PerkinElmer standard equipment filter. ScanArray Express and Express HT scanners equipped with PerkinElmer's blue laser readily display immobilized DNA on microarrays. Using ethidium bromide, which is easily washed off, there is no fluorophore cross-talk or interference with hybridization.
Perkin Elmer | MultiProbe II Robotic Liquid Handler
8 tip robotic liquid handling system designed for the efficient automation of sample preparation procedures utilized in Drug Discovery and Molecular Biology. The MultiPROBE II HT system is controlled by WinPREP applications software, a package which operates under Windows NT operating system. This easy-to-use graphical user interface allows programming of even complex liquid handling protocols.
Teledyne | Photon Machines Analyte Excite Laser Ablation Source Analyte
Laser ablation system that offers excimer technology at 193 nm with all the analytical capabilities you require, and a price you can afford. The Excite delivers finely controlled, homogenizer-flat ablations with high sensitivity and split second response. Fire-on-the-fly lasing that is synchronized to the stage motion, combined with fast washout ablation cells, make precision depth profiling of spots, lines and areas possible and enables high spatial resolution elemental mapping. The Excite is equipped with a high definition, color GigE camera on a high magnification, optical zoom, video-microscope capable of resolving 2 �m features. Transmitted, reflective and ring illumination, cross polarizers plus software selectable camera settings give the user enhanced viewing capabilities. The combination of ultra-short pulse length and 193 nm wavelength is unsurpassed in coupling efficiency. The Excite ablates all materials, from opaque to highly transparent, including delicate powders, hard quartz and resilient carbonates with depth penetration in the tens of nanometers per shot. The beam energy profile is homogenized to ensure uniform ablations across the entire range of spot sizes and on a wide range of materials.
Facilitates library construction system for NGS platforms, and is recommended by Illumina and Ion Torrent for certain workflows. The platform features the ability to collect narrow and even fragment distributions, as well as the flexibility to collect wide ranges of fragments with minimal effort. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples per gel cassette may be run, with no possibility of cross contamination.
Bio-Techne | Protein Milo Single Cell Western Milo
Milo is Single-Cell Western platform. Milo measures protein expression in thousands of single cells in a single run so you can profile heterogeneity in your samples. Just load your cell suspension and the scWest chip captures ~1,000 single-cells. Milo then does a fast, 1 minute SDS-PAGE separation on each single-cell lysate on-chip. Then just probe with your favorite conventional Western antibodies to measure ~12 proteins per cell using a variety of multiplexing strategies. Use Single-Cell Westerns to unlock the single-cell proteome and measure more of the proteome than is possible with any other single-cell technique.
PerkinElmer UltraVIEW system (PerkinElmer Life Sciences Inc., MA, USA) is a Yokogawa (Yokogawa Corp. Japan) Nipkow Spinning Disk Confocal System. It uses a spinning disk with multiple pinholes to achieve confocality (e.g. the rejection of out-of-focus light). Emission light from the sample passes through the pinholes to generate a confocal image of the sample that can be detected with an EMCCD (Electron Multiplification Charge-Coupled Device) camera. Spinning disk confocal systems have 2 main advantages over conventional Laser Scanning Confocal Microscopes (LSCM): Higher imaging speed: up to 360frames/sec compared to 0.5-1 frames per second in a LSC and Lower photo-toxicity: around 5 times less than a LSCM, probably due to the fact that the system splits the laser light into thousands of minibeams.
Bio-Techne | Protein PeggySue Protein Analyzer
Peggy Sue lets you separate and analyze proteins by size or charge from 2-440 kDa either by immunoassay or total protein.
Protein Technologies peptide synthesizers are designed to cover synthesis scales from 0.005 to 200 mmol.
For fully automated nucleic acid extraction with QIAGEN's spin column kits.Automates over 80 QIAGEN kits with over 140 standard protocols for most frequently used applications Optional protocol customization expands use to virtually any application.Allows automated DNA, RNA and protein sample processing.Eliminates manual processing steps.Generates standardized results .Enables quick response times and remote run monitoring through provided tablet.QIAcube Connect is redefining benefits of automating sample processing. With advanced digital capabilities and connectivity QIAcube Connect with its accessories and consumables allows research labs to fully automate and track their well known QIAGEN spin column extraction and purification protocols at push of button..QIAcube Connect offers augmented user interface that provides new dimension of utility. Researchers can stay connected to their instrument through built in screen and also remotely with tablet included, containing pre installed QIAcube Connect App, enabling quick response times and ability to monitor runs while away from QIAcube Connect.
Philips | CM12 Transmission Electron Microscope
General purpose analytical transmission/scanning transmission electron microscope (TEM/STEM). It was used to visualize the structure, chemical composition, and arrangement of atoms in thin, extraordinary small specimens.
Automated nucleic acid purification workstation with liquid handling capabilities that purifies the DNA via magnetic separation within the pipette tips. It's pipettor head contains 6 syringe pumps that dispense 25-1000 microliters at a time.
Pressure BioSciences | NEP2320 Barocycler
Barocycler uses the Pressure Cycling Technology (PCT) platform based on repeated cycles of hydrostatic pressure between ambient (14.7 psi) and ultra-high levels (up to 45,000 psi). These rapid changes in pressure are used to control biomolecular interactions for applications such as accelerated proteolytic digestion and improved extraction of cellular components, including proteins and lipids. The PCT platform allows for a high degree of safety, speed, reproducibility, and in modern sample preparation protocols. Advantages of the PCT technology include:
For automated purification of nucleic acids from up to 14 human, forensic, or molecular diagnostics samples High quality genomic DNA and RNA from range of sample materials Viral RNA DNA and bacterial DNA from biomedical samples Throughput of up to 14 samples per run Effortless data management with full traceability UV lamp to help minimize contamination risk The EZ1 Advanced XL performs automated nucleic acid purification for wide range of sample types relevant for molecular diagnostics, human identity testing, forensics, biomedical research, and gene expression analysis.
Instrument for automated mid to high throughput nucleic acid purification in 96 well format DNA, RNA and miRNA extraction from virtually any sample type.Mid to high throughput solution with dedicated purification kits saves costs and time.User friendly software allows for easy data management and documentationdesign features increase safety and minimize cross contamination.Convenient, flexible and easy to use instrument with small footprint.QIAcube HT enables automated mid to high throughput nucleic acid purification in 96 well format using silica membrane technology. variety of QIAcube HT Purification Kits lets users quickly and easily purify DNA, RNA and miRNA from almost any type of sample including cells, tissues and stool samples, as well as from bacteria and viruses in animal samples. Automated protocols and dedicated accessories and consumables increase reliability and and save valuable time. system provides same high quality results as other trusted QIAGEN purification technologies.
Rainin Classic manual single-channel pipette, 100-1000 uL, uses universal-fit tips. Finger hook, light springs, silicone shock absorber, accurate, precise, economical (PR-1000)
Model_Number_E4XLS Electronic Multipipette
Rainin | E4 Electronic Pipette, LTS E4-20XLS+
E4 XLS electronic single-channel pipette, 2-20 uL, uses LTS LiteTouch tips.
DNA Sequence Analyzer RDT 1000 incorporates RainStorm microdroplet based technology to amplify hundreds to thousands of genomic loci with high specificity and uniformity. It leverages the sensitivity and specificity of polymerase chain reaction (PCR) methodology.Allows to isolate specific regions of the genome for subsequent sequencing.
Thermo Fisher | Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer Q Exactive
Identifies and quantifies proteins, peptides, lipids, glycans and small molecules. Combines segmented quadrupole for high performance precursor ion selection with high resolution, accurate mass, ultra high field Orbitrap mass analyzer to deliver combination of scan speed, resolving power, mass accuracy, spectral quality and sensitivity.
Compact versatile bench top unit, which has been developed specially for dry, wet and cryogenic grinding of small amounts of sample.It can mix and homogenize powders and suspensions in only a few seconds. It is also perfectly suitable for the disruption of biological cells as well as for DNA/RNA and protein extraction. With its high performance and great flexibility
RNA/DNA purification small bead mill for disruption of up to 12 samples at the same time. Disruption and homogenization occurs through high-speed shaking of samples in 2 ml microcentrifuge tubes with stainless steel or glass beads. The TissueLyser LT must be used in combination with the coolable TissueLyser LT Adapter, which holds tubes during the disruption process.
Small angle x ray scattering SAXS krakty camera system. Small angle scattering of macromolecules.
Custom focusing CMF X ray optics for X ray diffraction.
Model_Number_Single Channel Pipette Lite PR-2
Manual single-channel pipette, 0.1-2 ?L, uses universal-fit tips. Finger hook, light springs, silicone shock absorber, accurate, precise, economical (PR-2)
Rigaku | DSC8231 Differential Scanning Calorimeter
Quantifies energy changes in reactions such as melting, transition, crystallization and glass transition temperature.
Micro area residual stress measurement system that helps detect residual stress and lifetime of products.
Differential scanning calorimeter. Used to characterize heat gain or loss associated with phase transitions.
High resolution photon counting x ray detector from Dectris. X ray detector for single crystal X ray diffraction.Small Molecule Crystallography Product.
Multilayer optics for extreme UV lithography patterning of semiconductor wafers. High efficiency multilayer optics for 13.5 nm, 6.x nm wavelengths.
Handheld LIBS metal alloy analyzer for metal grade identification.Used for for fast and accurate metal grade identification.
High intensity microfocus rotating anode X-ray generator.
Sequential wavelength dispersive XRF spectrometer for large samples film thickness and composition measurements on large and heavy samples, wafers, and media disks.
X-ray metrology tool to perform high throughput measurements on product and blanket wafers ranging from ultrathin single layer films to multilayer stacks.
Parallel beam graded multilayer monochromator for XRD. Maximizes intensity for parallel X ray beam and high resolution diffraction.
Computed radiography mobile imaging plate scanner.
Hybrid photon counting x ray detector large area. Hybrid Photon Counting detector for single crystal X ray diffraction.
Wavelenght Dispersive X-ray Fluorescence Sulfur analyzer. Measures ultra low sulfur ULS in petroleum fuels by ASTM D2622 10 and background intensity.
Rigaku | Max-Flux TXRF Optic monochromator
Focusing graded multilayer monochromator for TXRF. Maximizes intensity on sample within total external reflection angle for TXRF.
Microfocus high intensity sealed tube X ray source. X ray source component for X ray diffraction and crystallography.
Compact Photon Counting X-ray detector.Two dimensional semiconductor X-ray detector.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10,2024. Benchtop single element wavelength dispersive XRF analyzer with high precision and high sensitivity elemental analysis.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10,2024. Wavelength dispersive x ray fluorescence sulfur analyzer that measures ultra low sulfur in petroleum fuels ULSD.
Benchtop powder x ray diffraction instrument that gives qualitative and quantitative phase analysis of polycrystalline materials.
X ray microscope with microtomography of large samples at high resolution.
Benchtop small angle X-ray scattering instrument designed for nano structure analyses.Non-destructive measurement of particle size and size distribution.
Small angle and wide angle x ray scattering instrument Advanced SAXS WAXS for nanostructure analysis.
Hybrid XRF and optical metrology fab tool. Used for thickness, composition, defect identification and sizing of films and structures on blanket and patterned wafers.
Modernized 2D Kratky system that eliminates data corrections required of traditional systems.
Light element analyzer for laboratory XRF instruments.Enables light element analysis in laboratory XRF Instruments.
Multi-purpose rotating anode X-ray generator. X-ray source component for X-ray diffraction and crystallography.
Rigaku | Progeny ResQ FLX Raman analyzer
Advanced narcotics analyzer. Identifies narcotics, including opiods and fentanyl analysis, in seconds.
Photon counting X-ray detectors from Dectris.Hybrid pixel array detector HPAD for X ray crystallography.
R-AXIS HTC was designed with speed in mind. High throughput crystallography requires an area detector that can measure accurate data rapidly. The R-AXIS HTC combines the data quality that is achieved with an imaging plate area detector with data acquisition speed that approaches that of an electronic detector. It combines three large active area imaging plates with minimal dead-time and a wide dynamic range, making it best for collecting fast, accurate diffraction data from the widest ranges of samples in the home laboratory. High dynamic range is achieved through use of a dual photomultiplier configuration that allows high intensities to be measured by a second, attenuated photomultiplier.
Original 1064 NM handheld raman for chemical threat analysis. Used for rapid chemical identification of unknown substances.
Next generation benchtop total reflection X ray fluorescence TXRF spectrometer. Rapid trace elemental analysis and thin film characterization.
Small, light weight non destructive testing X ray generator. Performs inspections by X ray radiography in narrow or high places.
R- AXIS IV is a two- dimensional X- ray detector which collects diffracted X- ray data used for small or macromolecular crystal structure analysis. A complete X-ray detector system consists of the X- ray generator, optics, R-AXIS IV main body, R-AXIS IV controller, and control/data processing software (com-puter).
300 kV microcomputerized directional industrial X ray system
200 kV microcomputerized directional industrial X ray system.
Foreign object X ray inspection instrument.
New 1064 NM handheld raman analyzer for explosives and narcotics detection fast chemical detection
Foreign object X ray inspection instrument. Metals checks in shoes, bags, general merchandise and apparel products by X ray.
Rigaku | Progeny Handheld Raman spectrometer
Advanced 1064 NM handheld raman spectrometer for raw material identification, material verification and authentication.
Tube above simultaneous wavelength dispersive X-ray fluorescence spectrometer.Used for high-throughput elemental analysis of solids, powders and alloys.
Automated multipurpose X-Ray diffractometer with guidance software. Power diffraction, thin film metrology, SAXS, in plane scattering, and operando measurements.
Non destructive portable stress analyzer for field and indoor use.
Multipurpose X-ray diffraction system with built in intelligent guidance that includes powder diffraction, thin film diffraction, SAXS, pole figure, and residual stress and non ambient experiments.
Humidity Controlled TG-DTA.Compact humidity generator HUM 1 is connected to TG DTA for measurements under constant relative humidity water vapor atmosphere. Measures weight changes and endothermic or exothermic reactions.
Surface contamination metrology. Used to measure elemental contamination at discrete points or with full wafer maps.
Simultaneous Thermal Analyzer.Measures weight changes and endothermic or exothermic reaction.
Humidity controlled TMA.Measurement of mechanical property change with respect to temperature and humidity.
Wafer surface contamination metrology by TXRF with measurement of trace elemental surface contamination.
Automated multipurpose diffractometer. Powder diffraction, thin film diffraction, SAXS, pole figure, and residual stress and in plane experiments.
High power benchtop sequential WDXRF spectrometer.Used for elemental analysis of solids, liquids, powders, alloys and thin films.
Wafer surface contamination metrology by VPD TXRF with measurement of ultra trace elemental surface contamination.
18 kW rotating anode X-ray generator. A high powered X-ray source that can produce point or line focus X-ray beams.
Thermomechanical analyzer. Measurement of a mechanical property change with respect to temperature.
In line, simultaneous WDXRF spectrometer film thickness and composition measurements on blanket wafers.
Dual wavelength Confocal Max Flux CMF optics for single crystal X ray diffraction. Focuses and monochromatizes two different X ray wavelengths for single crystal X ray diffraction applications.
Simultaneous WDXRF spectrometer film thickness and composition measurements on wafers and media disks.
Surface contamination metrology that measures elemental contamination at discrete points or with full wafer maps.
Benchtop single crystal x ray diffractometer.
Compact 2D X ray camera for topography and imaging applications X ray and EUV detector.
Automated in situ x ray crystallography that screens protein crystals on single crystal X ray diffractometer.
Compact 2D X ray camera with micron and sub micron resolution for imaging.
Tube above sequential WDXRF spectrometer with elemental analysis of solids, liquids, powders, alloys and thin films,from Oxygen fhrough Uranium.
Sequential WDXRF spectrometer for large samples with elemental analysis of solids, liquids, powders, alloys and thin films.
Sequential WDXRF spectrometer with elemental analysis of solids, liquids, powders, alloys and thin films, from beryllium Be through uranium U
Thermo Fisher | CRS F3 Robot Arm and C500C Controller
Thermo Scientific CRS F3 Robot Arm and C500C Controller is designed for light payload applications and provides an articulated robot arm with six degrees of freedom, plus a powerful, multitasking controller. The system sets a new standard for "human-scale" robots, delivering a combination of high speed, reliability, ease of use, and value. It dramatically increases walk-away time and reduces human error by automating container handling for a wide variety of instruments and devices. The F3 can carry payloads up to 3kg, enabling it to carry multiple containers at once. The arm of the system communicates with its external controller, sensors and other devices along a dedicated communication network, eliminating the masses of wires required by traditional robots. The F3 arm can store position data for up to eight weeks, even if the robot and controller are disconnected.
Roche | Elecsys 2010 Immunoassay Analyzer
THIS RESOURCE IS NO LONGER IN SERVICE. April 10,2024. Roche Diagnostics Elecsys 2010 has the power and efficiency to meet the needs of medium and large volume testing facilities. Roche Elecsys 2010, which is available in the form of sample disk or a rack handling system, can be operated in both continuous and random access modes. The throughput rate of this analyzer is 86 tests per hour and on-board capacity is of 15 tests. Elecsys 2010 disk and Elecsys 2010 rack holds 30 and 100 positions for samples respectively. With Roche Elecsys 2010 system at your workstation, you can attain benefits such as easy and trouble free operation, workflow flexibility, faster turnaround times, broad measuring ranges, and more.
PIN diode based X-ray detector.Applications ranging from alignment and testing of laboratory devices to long term precision monitoring of X-ray intensity.
Confocal x ray optical assembly that focuses and monochromatizes X ray beam for single crystal X ray diffraction.
Tube above sequential WDXRF spectrometer with elemental analysis of solids, liquids, powders, alloys and thin films, from beryllium Be through uranium U
Used for DNA Size Selection for Next-Gen Sequencing, with Pulsed-Field (100bp � 50kb).BluePippin has the DNA capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA. For long-range genomic applications, high-pass filtering allows users to collect all fragments above a size threshold set by the user. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples/gel cassette may be run, with no possibility of cross contamination.
MagNA Lyser Instrument is a benchtop device that automatically disrupts cells or other biological materials. The instrument facilitates the production of a supernatant containing nucleic acids (NA) and proteins suitable for subsequent purifi cation, extraction or analysis. During a MagNA Lyser Instrument run, the rotor, which is fi lled with special tubes, rapidly oscillates.
Marshall Scientific | Sanyo MCO-19AIC UV CO2 Incubator
Incubator features humidity and temperature control technology, which provides both stability control for cultures. The direct heat and air jacket system eliminate the inconvenient use of water in the incubator and provides heat from the door, side, and bottom of the unit. The Sanyo MCO-19AIC utilizes a dual detector infrared CO2 sensor, which is not affected by changes in humidity or temperature, maintains constant conditions via the microprocessor control, and automatically calibrates using room air temperature as reference. Also features Safe Cell UV contamination control system.
Shimadzu 8030 triple quadrupole mass spectrometer is for targeted quantitation applications.
Shimadzu | 8040 Triple Quadrupole Liquid Chromatograph Mass Spectrometer
Spectrometer delivers scan speeds of up to 15,000 u/second with a 0.1 Dalton step width.
Scanco | VivaCT40 Microcomputed Tomography Scanner
vivaCT 40 is a fast and flexible in-vivo microCT (micro-computed tomography) scanner for preclinical studies. The low X-ray dose allows serial measurements of individuals. Whole-body scans or scans from selected regions of mice can be made, while head and hind limbs of larger rodents can be scanned using beds supplied with the system. A range of beds for in-vivo use as well as specimen scans are supplied. .
Immunoassay analyzer with a maximum throughput of 200 tests per hour. Immunoassay system is designed specifically for optimum efficiency and consolidation in medium- and high-volume laboratories. The IMMULITE 2000 software, and graphical user interface, offers streamlined information management, from remote test ordering to sophisticated analysis of results.
Shimadzu | LCMS-8060 Triple Quadrupole Liquid Chromatograph Mass Spectrometer
LCMS-8060 is a mass spectrometry helping to transform LC/MS/MS data quality.
Model_Number_Single Channel Pipette Lite PR-20
Rainin Classic manual single channel pipette, 2-20 uL, uses universal-fit tips. Finger hook, light springs, silicone shock absorber, accurate, precise, economical..
QTRAP 5500 system Performs multiple reaction monitoring (MRM) for quantitation using this high-sensitivity triple quadrupole system. Identify, characterize, and quantitate metabolites more quickly and easily.Discover and quantitate targeted biomarkers. Enable high-sensitivity full-scan MS, MS/MS, and MS3 with high-selectivity from true triple quadrupole precursor ion (PI) and neutral loss (NL) scans.
Yokogawa | Solarmere CSU10 Fluorescence Confocal Spinning Disk Microscope
Solarmere CSU10 Fluorescence Confocal Spinning Disk Microscope is a confocal microscopy that has enabled z-axis resolution of a thick specimen by employing pin-point illumination. Now, as fast as 360 frames/sec. scanning speed and high S/N design of Yokogawa Model CSU10 enables direct viewing of clear-cut confocal images of fluorescent specimens in real time at its eyepiece. Discontinued.
Sorvall Discovery 100SE floor ultra-centrifuge.
Legend RT is a general-purpose tabletop centrifuge for biotechnological and pharmaceutic research. .The user-friendly "QUIKset" control panel permits easy selection of speed, RCF value, run time and deceleration profile, as well as temperature of the Legend RT. You can switch from speed to RCF display and vice versa, with a touch of a button and even during a run
SY3200 cell sorter platform is expandable to a dual system layout, effectively enabling two systems in one.
Thermo Scientific Sorvall RC 6 Plus Centrifuge has been discontinued. Please consider our recommended replacement: Thermo Scientific Sorvall LYNX Superspeed Centrifuge Series.
SORVALL MT-6000 improves the accuracy and reproducibility of the time-tested SORVALL mechanical advance system. Other improvements include a new fiber optics approach lighting system, a diffuse lighting and viewing system, a highly effective built-in vibration dampening system, precise digital speed and thickness controls, and the Visutrac system. All combine to make the MT-6000 an excellent microtome for electron or light microscopy.
Multifunction phosphoimager/fluorimager laser scanner used to collect fluorescent or storage phosphor images from gels, membranes and phosphor screens.
Agilent | Stratagene Mx3000P Real Time PCR System
Agilent Mx3000P QPCR System has been replaced with the AriaMx system. Used for gene expression analysis, microarray data validation, SNP genotyping, pathogen detection, DNA methylation analysis, and chromatin immuno-precipitation studies. Agilent qPCR software, MxPro, provides users with an interface, quick experiment design, data analysis and easy report generation.
LectroPol-5 is designed for automated electrolytic polishing and etching of metallographic specimens. A scanning function for easy determination of parameters, built-in safety features, and a database with methods for various materials enables short polishing times and maximum reproducibility. LectroPol-5 consists of two units, the control unit and the polishing unit. The two units can be separated from each other. LectroPol-5 features a scanning function that helps to determine the correct voltage for both polishing and etching, thus saving time and avoiding human error. LectroPol-5 displays the scan curve, while the user selects and sets the voltage. The LectroPol-5 comes with ten polishing/etching methods for various materials, enabling immediate preparation of a wide range of materials without any lengthy and time-consuming trials.
Siemens 3T MAGNETOM Skyra scanner with new software that enables rapid imaging.
Spectradyne | Spectradyne nCS1 Particle Counter
nCS1 particle counter is a tool for obtaining detailed size and concentration information about particle distributions in liquids.
MA/BA6 mask aligner is designed for all standard lithography applications and wafer sizes of up to 150 mm. For thick-resist MEMS applications, the MA/BA6 offers high resolution and optimum edge quality. The bottom side alignment option allows for pattern printing on both sides of the substrate. The MA/BA6 additionally provides tailored features for fragile III-V compounds, thinned or warped wafers, transparent substrates and pieces or single dies.
Powered by either 1 x 1.34 GHz or 2 x 1.5 GHz UltraSPARC IIIi processors, the Sun Fire V240 server is an entry-level, data center-class server. It provides high availability and expandability in a compact, 2U package. Four autonegotiating Gigabit Ethernet ports provide multiple connectivity for high-speed, high-bandwidth networking, while hot-swappable, front-accessible disk drives and redundant, hot-swappable power supplies (with independent cords) further enhance the Sun Fire V240 server's uptime. With expandability features such as three PCI slots, up to four disk drives, and 16 GB of memory, the rack-optmized Sun Fire V240 server easily scales to meet the needs of Tier 1 and Tier 2 applications. With a low-cost, integrated SSL option on the motherboard, the Sun Fire V240 server provides fast, secure Web transactions without sacrificing CPU cycles or a PCI slot. The standard System Configuration Card and serviceability features help enable quick upgrades and repairs, while the unit's Sun Advanced Lights Out Manager (ALOM) provides remote management to a large number of servers from virtually anywhere on the network.
Computer controlled manual wafer load profilometer with Max wafer size of 8"/200mm that measures roughness, waviness, step height, and other surface characteristics. Capabilities of this instrument include: Measurement of vertical features ranging from under 100Ã… (0.4 min.) to approximately 300 �m (11 mils), with a vertical resolution of 0.5, 2, or 10Ã…, A virtually unlimited number of data points per profile guarantee that the horizontal resolution is limited by the stylus radius and not by the number of data points, Measurement of many roughness and waviness parameters, with user-selectable cutoff filters to isolate roughness and waviness, Ability to fit and level a scan, allowing accurate step height measurements on curved surfaces, and the Ability to detect the edge or apex of a profile feature, allowing automated data analysis relative to the feature. The KLA P-10 to repeat a scan up to ten times and automatically calculate the average, thereby minimizing the effects of environmental noise on measurements. KLA-Tencor P10 can profile a variety of materials including: Semiconductor wafers, Thin-film heads, Precision-machined and polished surfaces, Ceramics for micro-electronics, Glass for flat panel displays, and Optical surfaces
Agilent: BioTek | Synergy HT Plate Reader
Luminescent assays are sensitive and quantitative tools commonly used for a variety of purposes in biomedical and pharmaceutical research. Quantitation of ATP can be used to detect and measure cellular growth, as well as bacterial contamination. Luminescent genetic reporting assays are widely used to study gene expression and cellular responses to external stimuli in Prokaryotic and Eukaryotic organisms. Dual-reporter assays use two independent reporter systems simultaneously to improve experimental accuracy. One reporter is used to measure the response resulting from the experimental conditions and is often referred to as the “experimentalâ€� reporter. The second reporter is designed not to respond to the experimental conditions, acting as an internal control from which data generated by the experimental reporter can be normalized. Normalization of the data serves to compensate for variability caused by differences in transfection efficiency, cell viability, cell lysis, and pipetting. Promega's Dual-Luciferase System uses the activities of luminescent proteins (luciferases) from the firefly (Photinus pyralis) beetle and the sea pansy (Renilla renformis) to serve as an experimental and a control reporter respectively (See Figure 1). The Synergy HT Multi-Detection Reader (BioTek Instruments, Winooski, VT) is a robotic compatible microplate reader that can measure absorbance, fluorescence, and luminescence in all plate formats up to 384-well plates with performance in all three detection modes, that has recently been optimized for luminescence measurements (Figure 2). The Synergy HT utilizes a dual optics design that has both a monochromator/xenon flash system with a silicone diode detector for absorbance and a tungsten halogen lamp with blocking interference filters and a photomultiplier tube (PMT) detector for fluorescence. Reagent addition is accomplished by an optional external injector module, which controls two independent injector syringes. Each syringe is connected to a separate injector tip. Emitted luminescence is captured using either the top or bottom probes and measured using the Synergy HT's low noise PMT operated in photon integration mode. Here we describe the use of a Synergy HT Multi-Detection Microplate Reader (BioTek Instruments) to perform dual-luciferase measurements with purified recombinant enzymes.
COBE 2991 cell processor offers an alternative to labor-intensive methods for the separation of cell products, such as manually layering blood over a density gradient separation medium using conical tubes. These methods involve a large number of operator steps and manual pipetting techniques that require significant practice, introducing variability and the opportunity for operator error. Automated processing puts control at the user's fingertips. Protocols can be easily programmed for efficient, reproducible results while saving time and reducing the number of manual operating steps. For maximum flexibility, nearly all aspects of operation can be controlled manually. operation saves training time, requires little technical support and reduces the opportunity for operator errors.
Quickly seal in heat with the Thermo Scientific ALPS 3000 Automated Microplate Heat Sealer. This compact sealer is designed for optimal robotic integration in high throughput labs, yet still allows for manual benchtop control.
Thermo Fisher | Capit-All Screw Cap Tube Capper and Decapperr
Maintain sample integrity with a hands-free method of capping and decapping tubes quickly and easily with the Thermo Scientific Capit-All Screw Cap Tube Capper/Decapper. Designed for benchtop or integrated use, Capit-All instruments cap and decap 24-, 48-, and 96- format Thermo Scientific Matrix and Thermo Scientific Nunc ScrewTop tubes with precision and ease. All instruments cap tubes to optimal torque.
Tecan | Infinite 200 PRO Multimode Microplate Reader
Infinite 200 PRO is multimode plate reader family that offers affordable high performance detection solutions empowered by monochromator or filter based technologies. The six new tailored configurations provide excellence in ELISA assays, nucleic acid quantifications, reporter assay technologies, and drug discovery assays including HTRF and fluorescence polarization. This fully upgradeable reader family is designed to simplify your target applications.
Discovery Series Hybrid Rheometer (DHR) system combines a patented advanced drag cup motor, a second generation magnetic bearing, force rebalance transducer (FRT), and the new patent-pending True Position Sensor (TPS) in a single-head Hybrid rheometer. The DHR has unprecedented performance specification and delivers unsurpassed direct strain control, direct stress control, and normal force measurement accuracy. The DHR features all popular TA innovations including patented Smart Swap geometries and the widest range of Smart Swap temperature systems and accessories commercially available. The result is the most advanced, versatile rheometer platform imaginable. The HR-2 is an outstanding general-purpose rotational rheometer for a wide range of analytical, research, and production uses. With performance characteristics suitable for the most demanding measurements and a track-record of reliability, the HR-2 is at home anywhere a rheometer is needed, from around-the-clock production control to cutting-edge research.
Thermo Fisher | Q Exactive HF Orbitrap LC-MS/MS System
Thermo Exactive benchtop Orbitrap operates with a Waters Acquity UPLC and generates high resolution, high mass accuracy full Mass Spectrometry data.
Thermo Fisher | CellInsight CX7 High Content Screening Platform
Integrated system for performance in screening and analysis.Provides the user a choice of imaging modes to extract the information you need from your samples. Use the entire fluorescence spectrum to optimize your assay, and select either widefield or confocal optics for any channel. You also have 4-color brightfield options for colorimetric analysis of tissue sections.
Liquid handler for all microplate filling needs. With a volume range of 1 to 2000 �l, the Matrix WellMate accommodates a wide selection of labware and improves cost-efficiency with disposable, presterilized and pre-calibrated tubing cartridges.
Thermo Fisher | Orbitrap Elite Hybrid Ion Trap Orbitrap Mass Spectrometer
Mass spectrometer for analyzing demanding proteomics, metabolomics, lipidomics and metabolism samples. This instrument combines a high-field Thermo Scientific Orbitrap mass analyzer and Thermo Scientific Velos Pro ion trap technology.
Thermo Fisher | LTQ Orbitrap XL ETD Hybrid Ion Trap-Orbitrap Mass Spectrometer
Thermo Scientific LTQ Orbitrap XL ETD Hybrid Ion Trap-Orbitrap Mass Spectrometer can be used to identify, characterize and quantify proteins and peptides using. This instrument is a comprehensive solution for a range of proteomics applications including complex PTM analysis; intelligent sequencing of peptides; top-down and middle-down analysis; label-free quantitation; or quantitation using stable isotope labeling methods such as TMT and iTRAQ.
Thermo Fisher | Orbitrap Velos Mass Spectrometer
Hybrid mass spectrometer with dual-pressure ion trap with the high resolution and outstanding mass accuracy of Orbitrap technology.
Thermo Fisher | LTQ Orbitrap Discovery Mass Spectrometer
Hybrid mass spectrometer that incorporates LTQ XL linear trap and Orbitrap. Consists of linear ion trap for sample ionization, selection, fragmentation, and AGC, intermediate storage device that is required for short pulse injection, and Orbitrap analyzer for Fourier transformation based analysis.
Thermo Fisher | Exactive Plus Orbitrap Mass Spectrometer
Screen, identify and quantify compounds in complex samples rapidly and with confidence using the Thermo Scientific Exactive Plus Orbitrap Mass Spectrometer. This benchtop LC-MS system delivers high-resolution, accurate-mass (HR/AM) data and fast full-scan capabilities to increase your sample throughput and confidence in results. Easy-to-use and cost effective to operate, it is the best instrument for analytical laboratories performing food safety or environmental screening, clinical research, forensic toxicology, DMPK, metabolomics and biopharma (intact protein analysis) applications.
Thermo Fisher | Qubit 2.0 Fluorometer Qubit 2.0
Invitrogen Qubit Flex Fluorometer can selectively, accurately measure the concentration of up to 8 samples of DNA, RNA or protein simultaneously. Compared to single sample microvolume fluorometers, using the Qubit Flex Fluorometer for multiple samples reduces your time to data by up to 50%, with time savings beginning with batches of as few as 8 samples. Combining the one-of-a-kind Qubit Flex Fluorometer and optimized Invitrogen Qubit reagents and tube strips offers a complete solution for DNA, RNA and protein quantification.
Thermo Fisher | LTQ XL Linear Ion Trap Mass Spectrometer
Ion trap mass spectrometer with Agilent 1100 HPLC system is used for a variety of studies including metabolite identification, stability testing, degradation products, and high-abundance quantitation.
Thermo Fisher | Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass Spectrometer
HFX is our newest addition to the proteomics resource. It offers the fastest scanning rate of our Orbitraps, which improves proteomic depth for discovery applications, and integrates well with targeted applications such as parallel reaction monitoring.
Thermo Fisher | Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer
Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer has increased performance and new options that enhance applications from confident DMPK qual/quan screening studies to characterization of intact monoclonal antibodies.
Thermo Fisher | Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer
Identify and quantify more proteins, peptides, lipids, glycans and small molecules accurately and in less time with the Thermo Scientific Q Exactive HF hybrid quadrupole-Orbitrap mass spectrometer. The Q Exactive HF system combines a state-of-the-art segmented quadrupole for high-performance precursor ion selection with a high-resolution, accurate-mass (HR/AM) ultra-high-field Orbitrap mass analyzer to deliver a superior combination of scan speed, resolving power, mass accuracy, spectral quality and sensitivity. Identify, quantify and confirm in a single analysis with a single instrument with the Q Exactive HF mass spectrometer.
Thermo Fisher | Orbitrap Fusion Tribrid Mass Spectrometer
Thermo Orbitrap Fusion Tribrid mass spectrometer and Waters M-Class Acquity nanoUPLC is a versatile platform. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments.
Thermo Fisher | ISQ 7000 Single Quadrupole GC-MS System
Thermo Scientific ISQ 7000 is a Single Quadrupole GC-MS system offers extended uptime and robustness to maximize sample throughput, along with routine easy-to-use smart tools to simplify operation and speed up instrument familiarization. Featuring a range of configurations at different level of performances, the ISQ 7000 GC-MS is a flexible fit-for-purpose platform, fully upgradable from base to advanced highly sensitive configuration to boost performance when needed and ready-to-fit with continuous changing in regulations.
Thermo Fisher | Orbitrap Fusion Lumos Tribrid Mass Spectrometer
Spectrometer performs analysis including low level PTM analysis, multiplexed relative quantitation using isobaric tags, intact protein characterization, and MSn analysis of small molecules. System incorporates the brightest ion source, segmented quadrupole mass filter with improved selectivity and ion transmission, Advanced Vacuum Technology, and ETD HD.
Uses high capacity transfer tube for maximum ion loading, electrodynamic ion funnel that accomodates and transmits ions over broad mass range. These components enable identification and analysis of peptides, label free and TMT quantitation, top down proteomics analyses, sophisticated DDA and DIA, dynamic Retention Time PRM and BioPharma characterization.
Thermo Fisher | Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer
Identify, quantify and confirm more compounds rapidly and with confidence using the Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer. This benchtop LC-MS/MS system combines quadruple precursor ion selection with high-resolution, accurate-mass (HRAM) Orbitrap detection to deliver performance and versatility. The Q Exactive Mass Spectrometer is equally useful for untargeted or targeted screening and a broad range of qualitative and quantitative applications in drug discovery, proteomics, environmental and food safety, clinical research and forensic toxicology.
Thermo Fisher | Q Exactive GC Orbitrap GC-MS/MS
Orbitrap mass spectrometry System provides comprehensive characterization of samples in single analysis for highest confidence in compound discovery, identification, and quantitation. Offers quantitative power of GC triple quadrupole MS combined with high precision, full scan HRAM capabilities.
Thermo Fisher | Q Exactive Focus Hybrid Quadrupole-Orbitrap Mass Spectrometer
The sensitivity, selectivity, flexibility, and ease-of-use provided by hybrid quadrupole-Orbitrap mass spectrometers set the standard for screening, quantitation, identification, and confirmation of targeted and untargeted compounds. The Thermo Scientific Q Exactive Focus hybrid quadrupole-Orbitrap MS makes this power accessible to environmental, food safety, clinical research, forensic toxicology, and pharmaceutical labs challenged by growing sample volumes and constrained by strict budgets. The Q Exactive Focus system simplifies method development, saving time and decreasing costs while reliably delivering unsurpassed results.
Microplate washer designed for 96-well plate format in both landscape and portrait orientation. 96-well plates and strips designed to be washed in 1x8 or 1x12 format and prepare plates for mainly enzyme-linked immunosorbent assay tests. Allows shaking and is controlled through the built-in graphical user interface and keypad.
Thermo Fisher | Shandon Finess 325 Manual Microtome Finess
Manual microcotme that ontains quick release cassette clamp and x y orientation head, disposable blades or standard microtome knives, Accu Feed System that provides reproducible sections throughout the length of specimen travel, specimen tilt and orientationusing X Y micro adjustment, free running flywheel with ergonomic design, and removable deep debris tray.
Thermo Fisher | Q Exactive UHMR Hybrid Quadrupole-Orbitrap Mass Spectrometer
Perform the highest - quality native intact mass and top-down analysis in structural biology and biopharma research. The Thermo Scientific Q Exactive UHMR (Ultra-High Mass Range) Hybrid Quadrupole-Orbitrap Mass Spectrometer is the first UHMR MS to combine substantially increased sensitivity and mass resolution at high m/z, MS2, and psuedo-MS3 capabilities in a single platform.
Thermo Fisher | Shandon Finesse Microtome Series Finesse
Features models ranging from fully automated to precision manual that cuts wax or resin with ergonomic design and safe precision for cutting quality sections.
Combines quadrupole, ion trap, and Orbitrap mass analysis into Tribrid architecture to provide depth of analysis. Enables analyzing of low-abundance, high-complexity samples to identify compounds and to quantify accurately and elucidate structures thoroughly.
Thermo Fisher | TSQ Vantage Mass Spectrometer
Quantify small molecules, peptides, biosimilars, and biologics using the Thermo Scientific TSQ Vantage Triple Quadrupole Mass Spectrometer.
Model_Number_Merlin M150 LR 400/50 CP55 L/LF RS232
Thermo Fisher | Merlin M150 LR 400/50 CP55 L/LF RS232 Recirculating Chiller
Compact recirculating chiller that has a cooling capacity of up to 4,282 watts and delivers a continuous supply of it to your samples using a CP55 pump
Model_Number_Merlin M150 LR 230/60 CP55 L/LF RS232
Thermo Fisher | Merlin M150 LR 230/60 CP55 L/LF RS232 Recirculating Chiller
Compact recirculating chiller that has a cooling capacity of up to 4,832 watts and delivers a continuous supply of it to your samples using a CP55 pump
Model_Number_Merlin M75 LR 208/60 PD2 FLUORINERT
Thermo Fisher | Merlin M75 LR 208/60 PD2 FLUORINERT Recirculating Chiller
Compact recirculating chiller that has a cooling capacity of up to 1,800 watts and delivers a continuous supply of it to your samples using a PD2 pump
Thermo Fisher | Triple Quadrupole TSQ Vantage LC-MS system
Vantage triple quad and Accela UPLC/MS specializes in quantitative work and selective assays of targeted analytes, including metabolites and other small molecules, and peptides from complex matrices such as serum, tissue, cell culture, and other biological sources.
Thermo Fisher | Matrix Tubing Set for Peristaltic Pump Head
Additional tubing set to combine with Thermo Scientific Matrix PlateMate Peristaltic Pump Head.
Thermo Fisher | SAHARA Acrylic S6T Heated Bath Circulators
Heated bath circulator that provides efficient heating from ambient plus 13 degrees C to maximum of 80 degrees C, with maximum bath volume of 6 liters
Model_Number_Merlin M150 LR 230/60 T1 RS232
Thermo Fisher | Merlin M150 LR 230/60 T1 RS232 Recirculating Chiller
Compact recirculating chiller that has a cooling capacity of up to 4,832 watts and delivers a continuous supply of it to your samples using a T1 pump
Model_Number_Nucleic Acid Extraction WorkStation
Thermo Fisher | Automated Nucleic Acid Extraction WorkStation
Automate high speed purifications that enables faster, cleaner, more consistent nucleic acid extraction.Based on magnetic separation technology.Enables to process any sample from virtually any source with guaranteed sample integrity.
Thermo Fisher | SAHARA S49 PC200 Heated Bath Circulator
Stainless steel heated bath circulator with a temperature range of Ambient +13� to 200�C and a voltage of 100/115 V
Thermo Fisher | SAHARA S49 AC200 Heated Bath Circulator
Stainless steel heated bath circulator with a temperature range of Ambient +13� to 200�C and a voltage of 100 V
Thermo Fisher | SAHARA S49 AC150 Heated Bath Circulator
Stainless steel heated bath circulator with a temperature range of Ambient +13� to 150�C and a voltage of 100 V
Thermo Fisher | SAHARA S49 SC100 Heated Bath Circulator
Stainless steel heated bath circulator with a temperature range of Ambient +13� to 100�C and a voltage of 100 V
Thermo Fisher | Polar Series Accel 500 LC Recirculating Chiller
Chiller that offers 500 watts of cooling, with a working temperature range of 10� to 80�C
Thermo Fisher | SAHARA S49 SC150 Heated Bath Circulator
Stainless steel heated bath circulator with a temperature range of Ambient +13 to 150 C and a voltage of 100 V.
Thermo Fisher | SAHARA S49 SC150L Heated Bath Circulator
Thermo Fisher | SAHARA S49 PC201 Heated Bath Circulator
Stainless steel heated bath circulator with a temperature range of Ambient +13� to 200�C and a voltage of 200/230 V
Thermo Fisher | ThermoChill II LR, 115V/60Hz, PD-1 RS232 Recirculating Chiller
Recilculating chiller with a colling capacity of up to 1,000 watts and a flow rate of 1.2 gpm @ 60 psid
Thermo Fisher | Sample Preparation Automated Liquid Handler
Automated liquid handler designed to gain greater consistency through automation and allow lab staff to focus on results.
Thermo Fisher | ThermoChill II LR, 115V/60Hz, PD-2 RS232 Recirculating Chiller
Recirculating chiller with a colling capacity of up to 1,000 watts and a flow rate of 3.6 gpm @ 60 psid (13.6 lpm @ 4.1 bar)
Thermo Fisher | ThermoChill III LR, 230V/ 50Hz, PD-1 RS 232 Recirculating Chiller
Recirculating chiller with a cooling capacity of up to 1,900 watts and temperature setpoints between -10C to +30C.
Model_Number_ThermoChill II LR 115V/60HZ MDCI
Thermo Fisher | ThermoChill II LR 115V/60HZ MDCI Recirculating Chiller
Recirculating chiller with a colling capacity of up to 1,000 watts and a flow rate of 2.0 gpm @ 15 psid (7.6 lpm @ 1.0 bar
Thermo Fisher | ThermoChill III LR, 230V/50Hz, PD-1 Recirculating Chiller
Recirculating chiller with a cooling capacity of up to 1,900 watts and temperature set points between -10C to +30C.
Thermo Fisher | ThermoChill II LR, 230V/50Hz, PD-2 Recirculating Chiller
Recirculating chiller with a cooling capacity of up to 900 watts and a flow rate of 2.5 gpm @ 60 psid (9.4 lpm @ 4.1 bar)
Model_Number_ThermoChill II 115V/ 60Hz PD-2
Thermo Fisher | ThermoChill II 115V/ 60Hz PD-2 Recirculating Chiller
Thermo Fisher | ThermoChill III LR, 230V/50Hz, PD-2 Recirculating Chiller
Thermo Fisher | ThermoChill II LR, 230V/50Hz, PD-1 Recirculating Chiller
Recirculating chiller with a cooling capacity of up to 900 watts and a flow rate of 1.2 gpm @ 60 psid (4.5 lpm @ 4.1 bar)
Model_Number_SampleArray Base Weight Station
RESOURCE IS DISCONTINUED; A base weight station that can Array sample tubes in 48-, 96-, or 384-format racks �quickly and easily for optimal downstream sample processing
Thermo Fisher | ThermoChill III LR 208-230V/60HZ, MDCI, RS232 Recirculating Chiller
Recirculating chiller with a cooling capacity of up to 2,000 watts and temperature setpoints between -10C to +30C.
Thermo Fisher | ThermoChill II LR, 230V/ 50Hz, PD-1 RS 232 Recirculating Chiller
Thermo Fisher | ThermoChill III LR, 208-230V/ 60Hz, MDCI Recirculating Chiller
Thermo Fisher | ThermoChill II LR,115V/60HZ, MDCI RS232 Recirculating Chiller
Recirculating chiller with a cooling capacity of up to 1,000 watts and a flow rate of 2.0 gpm @ 15 psid (7.6 lpm @ 1.0 bar)
Thermo Fisher | ThermoChill II LR, 230V/50Hz, PD-2 RS 232 Recirculating Chiller
Thermo Fisher | ThermoChill II LR, 115V/60Hz, PD-1 RS232 Recirculating
Recirculating chiller with colling capacity of up to 1,000 watts and flow rate of 1.4 gpm @ 60 psid 5.3 lpm @ 4.1 bar
Model_Number_ThermoChill III LR 230V/50Hz
Thermo Fisher | ThermoChill III LR, 230V/50Hz, PD-2 RS 232 Recirculating Chiller
Recirculating chiller with a cooling capacity of up to 1,900 watts and temperature setpoints between -10�C to +30�C
Thermo Fisher | ThermoChill III LR, 208-230V/ 60Hz, PD-2, RS232 Recirculating Chiller
Thermo Fisher | ThermoChill III LR, 230V/50HZ, MDCI Recirculating Chiller
Thermo Fisher | ThermoChill III LR, 230V/50HZ,MDCI RS232 Recirculating Chiller
Recirculating chiller with a cooling capacity of up to 900 watts and a flow rate of 2.0 gpm @ 15 psid (7.6 lpm @ 1.0 bar)
Thermo Fisher | ThermoChill III LR, 208-230V/60Hz, PD-1 RS 232 Recirculating Chiller
Thermo Fisher | ThermoChill III LR, 208-230V/60Hz, PD-2 Recirculating Chiller
Thermo Fisher | ThermoChill III LR, 208-230V/60Hz, PD-1 Recirculating Chiller
Thermo Fisher | ThermoChill III, 208-230V/60Hz, PD2 Recirculating Chiller
Recirculating chiller with a cooling capacity of up to 2,000 watts and temperature setpoints between 5C to 30C.
Model_Number_Toxicity Testing Workstation
Thermo Fisher | Toxicity Testing Workstation Automated Liquid Handler
Automated liquid handler that is adaptable to both specific and common cytotoxity assays and can be used with any commom cells lines and primary cells
Thermo Fisher | Versette Automated Liquid Handler
Automated liquid handler that can support a wide range of applications, including high-throughput Mass Spectrometric Immunoassay (MSIA), plate stamping, plate reformatting, serial dilution and many other applications
Model_Number_AC 200 230V/50Hz (with bridge)
Thermo Fisher | AC 200 230V/50Hz with bridge Immersion Circulator
MantainsT between 13� to 200�C with greater pumping performance, ramp programming, and application alarms
Model_Number_AC 200 100V/50-60Hz (with bridge)
Thermo Fisher | AC 200 100V/50-60Hz with bridge Immersion Circulator
An immersion circulator that can maintain temperature between 13� to 200�C with greater pumping performance, ramp programming, and application alarms
Model_Number_AC150 100V/50-60Hz (without bridge)
Thermo Fisher | AC150 100V/50-60Hz (without bridge); Immersion Circulator
Immersion circulator that can maintain temperature between 13� to 200�C
Thermo Fisher | AC 200 115V/60Hz Immersion Circulator
Thermo Fisher | AC150 115V/60Hz; Immersion Circulator
Model_Number_AC150 230V/50Hz (with bridge)
Thermo Fisher | AC150 230V/50Hz (with bridge); Immersion Circulator
Thermo Fisher | AC 200 230V/50Hz Immersion Circulator
Immersion circulator that can maintain temperature between 13� to 200�C with greater pumping performance, ramp programming, and application alarms
Model_Number_AC 200 115V/60Hz (with bridge)
Thermo Fisher | AC 200 115V/60Hz with bridge Immersion Circulator
Thermo Fisher | AC150 230V/50Hz; Immersion Circulator
Model_Number_AC150 115V/60Hz (with bridge)
Thermo Fisher | AC150 115V/60Hz (with bridge); Immersion Circulator
Model_Number_AC150 100V/50-60Hz (with bridge)
Thermo Fisher | AC150 100V/50-60Hz with bridge Immersion Circulator
Thermo Fisher | ARCTIC A10 AC200 115V/60Hz; Refrigerated Circulator
Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters
Thermo Fisher | ARCTIC A10 AC150 230V/50Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A10 AC200 230V/50Hz; Refrigerated Circulator
Model_Number_AC 200 100V/50-60Hz (without bridge)
Thermo Fisher | AC 200 100V/50-60Hz without bridge Immersion Circulator
Model_Number_ARCTIC A10 AC200 100V/50-60Hz
Thermo Fisher | ARCTIC A10 AC200 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A10 AC150 100V/50-60Hz
Thermo Fisher | ARCTIC A10 AC150 100V/50-60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A10 AC150 115V/60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A10 SC150 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A10B AC150 100V/50-60Hz
Thermo Fisher | ARCTIC A10B AC150 100V/50-60Hz; Refrigerated Circulator
Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters
Model_Number_ARCTIC A10 SC100 100V/50-60Hz
Thermo Fisher | ARCTIC A10 SC100 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A10 SC150 100V/50-60Hz
Thermo Fisher | ARCTIC A10 SC150 100V/50-60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A10 SC150 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A10B AC200 100V/50-60Hz
Thermo Fisher | ARCTIC A10B AC200 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A10B AC150 230V/50Hz
Thermo Fisher | ARCTIC A10B AC150 230V/50Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A10 SC100 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A10B AC200 115V/60Hz
Thermo Fisher | ARCTIC A10B AC200 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A10B SC150 100V/50-60Hz
Thermo Fisher | ARCTIC A10B SC150 100V/50-60Hz Refrigerated Circulator
ThermoFisher ARCTIC A10B SC150 100V/50-60Hz Refrigerated Bath Circulator
Refrigerated water bath that features temperatures ranging from 10C to +100C and maximum bath volume of 30 liters.
Model_Number_ARCTIC A10B AC150 115V/60Hz
Thermo Fisher | ARCTIC A10B AC150 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A10B AC200 230V/50Hz
Thermo Fisher | ARCTIC A10B AC200 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A25 AC150 100V/50-60Hz
Thermo Fisher | ARCTIC A25 AC150 100V/50-60Hz; Refrigerated Circulator
Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters
Thermo Fisher | ARCTIC A25 AC150 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A25 AC200 100V/50-60Hz
Thermo Fisher | ARCTIC A25 AC200 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A10B SC100 230V/50Hz
Thermo Fisher | ARCTIC A10B SC100 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A10B SC150 115V/60Hz
Thermo Fisher | ARCTIC A10B SC150 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A10B SC100 115V/60Hz
Thermo Fisher | ARCTIC A10B SC100 115V/60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A25 AC200 115V/60Hz; Refrigerated Circulator
Rfrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters
Model_Number_ARCTIC A25 SC100 100V/50-60Hz
Thermo Fisher | ARCTIC A25 SC100 100V/50-60Hz; Refrigerated Circulator
Refrigerated circulator that features temperatures ranging from 25 to +200 C and maximum bath volume of 12 liters
Model_Number_ARCTIC A10B SC150 230V/50Hz
Thermo Fisher | ARCTIC A10B SC150 230V/50Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A25 PC200 115V/60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A25 AC150 115V/60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A25 SC100 115V/60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A25 PC200 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A25 PC200 100V/50-60Hz
Thermo Fisher | ARCTIC A25 PC200 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A10B SC100 100V/50-60Hz
Thermo Fisher | ARCTIC A10B SC100 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A25 SC150L 100V/50-60Hz
Thermo Fisher | ARCTIC A25 SC150L 100V/50-60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A25 AC200 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A25 SC150L 115V/60Hz
Thermo Fisher | ARCTIC A25 SC150L 115V/60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A25 SC150 115V/60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A25 SC150 230V/50Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A25 SC100 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B AC150 100V/50-60Hz
Thermo Fisher | ARCTIC A25B AC150 100V/50-60Hz; Refrigerated Circulator
Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters
Model_Number_ARCTIC A25 SC150 100V/50-60Hz
Thermo Fisher | ARCTIC A25 SC150 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B AC150 115V/60Hz
Thermo Fisher | ARCTIC A25B AC150 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B AC150 230V/50Hz
Thermo Fisher | ARCTIC A25B AC150 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B SC100 115V/60Hz
Thermo Fisher | ARCTIC A25B SC100 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A25 SC150L 230V/50Hz
Thermo Fisher | ARCTIC A25 SC150L 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B AC200 100V/50-60Hz
Thermo Fisher | ARCTIC A25B AC200 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B SC150 115V/60Hz
Thermo Fisher | ARCTIC A25B SC150 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A40 AC150 100V/50-60Hz
Thermo Fisher | ARCTIC A40 AC150 100V/50-60Hz; Refrigerated Circulator
Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters
Thermo Fisher | ARCTIC A40 AC150 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B SC100 100V/50-60Hz
Thermo Fisher | ARCTIC A25B SC100 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B SC100 230V/50Hz
Thermo Fisher | ARCTIC A25B SC100 230V/50Hz; Refrigerated Circulator
Refrigerated circulator that features temperatures ranging from 25 to +200 C and maximum bath volume of 21 liters.
Thermo Fisher | ARCTIC A40 AC150 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B AC200 230V/50Hz
Thermo Fisher | ARCTIC A25B AC200 230V/50Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A40 PC200 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A40 PC200 100V/50-60Hz
Thermo Fisher | ARCTIC A40 PC200 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B SC150 100V/50-60Hz
Thermo Fisher | ARCTIC A25B SC150 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B SC150 230V/50Hz
Thermo Fisher | ARCTIC A25B SC150 230V/50Hz; Refrigerated Circulator
Model_Number_ARCTIC A40 SC150 100V/50-60Hz
Thermo Fisher | ARCTIC A40 SC150 100V/50-60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A40 PC200 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A25B AC200 115V/60Hz
Thermo Fisher | ARCTIC A25B AC200 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A40 AC200 100V/50-60Hz
Thermo Fisher | ARCTIC A40 AC200 100V/50-60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A40 AC200 230V/50Hz; Refrigerated Circulator
Thermo Fisher | CW3 Cell Washer; Centrifuge
Centrifuge that is designed to provide thorough, reproducible blood cell washing, up to 12-24 tubes per run
Model_Number_ARCTIC A40 SC150L 100V/50-60Hz
Thermo Fisher | ARCTIC A40 SC150L 100V/50-60Hz; Refrigerated Circulator
Model_Number_ARCTIC A40 SC150L 115V/60Hz
Thermo Fisher | ARCTIC A40 SC150L 115V/60Hz; Refrigerated Circulator
Model_Number_ARCTIC A40 SC150L 230V/50Hz
Thermo Fisher | ARCTIC A40 SC150L 230V/50Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A40 SC150 115V/60Hz; Refrigerated Circulator
Thermo Fisher | ARCTIC A40 SC150 230V/50Hz; Refrigerated Circulator
Thermo Fisher | Decapper 550; Lab Automation
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Lab automated tool with an integrated barcode reader that provides automated decapping and capping of Thermo Scientific Matrix and Nunc tubes with screw top closures in ANSI racks.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27th,2024. Immersion cooler that is used for the direct cooling of small samples with a temperature range of -45�C to +40�C
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Immersion cooler that is used for the direct cooling of small samples with a temperature range of -90C to +40C.
Thermo Fisher | Heraeus Megafuge 16; Centrifuge
Centrifuge that is perfect for clinical protocols, cell culture applications and microplate processing, the refrigerated version is designed for handling temperature-sensitive sample processing
Thermo Fisher | Decapper 500; Lab Automation
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Lab automated tool that provides automated decapping and capping of Thermo Scientific Matrix and Nunc tubes with screw top closures in ANSI racks.
Thermo Fisher | Heraeus Multifuge X3F; Centrifuge
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Centrifuge that can process a range of general purpose applications including cell culture, microplate, bioproduction, blood separation and microbiology.
Thermo Fisher | EK45FP; Immersion Cooler
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Immersion cooler that is used for the direct cooling of small samples with a temperature range of -45C to +40C.
Thermo Fisher | Heraeus Freso 21; Centrifuge
Refrigerated microcentrifuge available with 7 different rotors and designed to provide acceleration up to 21,100xg
Thermo Fisher | Heraeus Multifuge X1; Centrifuge
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Centrifuge that can handle a range of general-purpose processing, including cell culture, microplate, bioproduction, blood separation and microbiology.
Thermo Fisher | Heraeus Multifuge X3FR; Centrifuge
Thermo Fisher | Heraeus Pico 17; Centrifuge
Ventilarted microcentrifuge that provides outstanding processing power, unique safety features and a broad array of microcentrifuge rotors and accessories for microcentrifuge tube processing
Thermo Fisher | Heraeus Megafuge 8; Centrifuge
Small benchtop centrifuge that can spin 50mL conical tubes at over 12,000 x g or a wide range of microtubes at speeds up to 30,279 x g
Thermo Fisher | F7 Industrial Robot; Lab Automation
Lab automation robot that has,� 0.02 mm repeatability at full, 5 kg payload and full speed within the entire robot work envelope ensures maximum accuracy and superior positions
Microcentrifuge that provide outstanding processing power, unique safety features and broad array of microcentrifuge rotors and accessories for microcentrifuge tube processing with refrigeration available.
Small benchtop centrifuge that can perform both routine clinical and life science separations
Thermo Fisher | Heraeus Multifuge X1R; Centrifuge
Ventilated centrifuge with lightweight microcentrifuge rotors designed to provide acceleration up to 21,100xg in as little as 12 seconds
Thermo Fisher | F5 Robot System; Lab Automation
Lab automated robot with,�0.02mm repeatability at full, 5kg payload and full speed within the entire robot work envelope that ensures maximum accuracy and superior positioning (NA, RIA Cert. and EU, CE Cert.)
Thermo Fisher | Heraeus Megafuge 8R; Centrifuge
Thermo Fisher | inSPIRE Platform Bundle; Lab Automation
Lab automation system that integrates SmartShelves (3-6 Available with each bundle) and allows you to configure the right solution for your automated workflow
Ventilated centrifuge that processes sample prep at up to 17,000 x g
Thermo Fisher | PC 200 100-115V/50-60Hz; Immersion Circulator
Immersion circulator that has an extreme temperature performance ranging from 13� to 300�C
Model_Number_Orbitor RS2 Microplate Robot
Thermo Fisher | Orbitor RS2 Microplate Robot; Lab Automation
Lab automation microplate robot with Its innovative bi-directional telescoping arm that provides exceptional reach and precision; available with 3-6 Stacks, 3-6 Hotels, or a Mix of both 3-6 total
Thermo Fisher | Multifuge X4R Pro-MD; Centrifuge
Centrifuge that has nine acceleration speeds and can easily access and track all runs, rotor life and centrifuge health
Model_Number_PC 200 100-115V/50-60Hz (with bridge)
Thermo Fisher | PC 200 100-115V/50-60Hz (with bridge); Immersion Circulator
Thermo Fisher | Heraeus Pico 21; Centrifuge
Ventilated microcentrifuge available with 7 different rotors and designed to provide acceleration up to 21,100xg
Thermo Fisher | PC 200 200-230V/50-60Hz; Immersion Circulator
Thermo Fisher | Multifuge X4 Pro; Centrifuge
Thermo Fisher | Multifuge X4 Pro-MD; Centrifuge
Thermo Fisher | PC 201 (with bridge); Immersion Circulator
Immersion circulator with an all stainless-steel pump that offers extreme temperature ranging from 13� to 300�C
Thermo Fisher | Precision SWB 15 Shaking Water Bath
Shaking water bath with capacity of 15L that supports a range of sensitive life science. Precision Shallow form shaking bath has removable tray that allows for use with smaller sample containers. Precision Dubnoff shaking water baths are designed specifically for applications that require your samples to be incubated in controlled atmosphere.
Thermo Fisher | SAHARA PPO S14P AC150; Heated Bath Circulator
Heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 14 liters and a voltage of 100 V
Model_Number_PC 200 200-230V/50-60Hz (with bridge)
Thermo Fisher | PC 200 200-230V/50-60Hz (with bridge); Immersion Circulator
Thermo Fisher | PC 300 (with bridge); Immersion Circulator
Immersion circulator with an all stainless-steel pump that offers extreme temperature ranging from 50� to 300�C
Thermo Fisher | PC 201; Immersion Circulator
Thermo Fisher | Precision TSCIR35; Circulating Water Bath
Circulating water bath that can Achieve enhanced temperature uniformity with perimeter-directed water flow and has a max capacity of 35 L
Thermo Fisher | SAHARA PPO S14P AC200; Heated Bath Circulator
Heated bath circulator that offers efficient heating from ambient 13 to 100 C with a max bath volume of 14 liters and a voltage of 100 V.
Thermo Fisher | SAHARA PPO S14P SC100; Heated Bath Circulator
Thermo Fisher | Precision SWB 27; Shaking Water Bath
Water bath with a capacity of 27L that supports a range of sensitive life science and is designed specifically for applications that require your samples to be incubated in a controlled atmosphere
Thermo Fisher | Precision DUB 15; Shaking Water Bath
Shaking water bath with a capacity of 15L that supports a range of sensitive life science and is designed specifically for applications that require your samples to be incubated in a controlled atmosphere
Thermo Fisher | SAHARA PPO S21P SC150; Heated Bath Circulator
Heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 21 liters and a voltage of 100 V
Thermo Fisher | SAHARA PPO S21P AC200; Heated Bath Circulator
Thermo Fisher | Precision TSCIR89; Circulating Water Bath
Circulating water bath that can Achieve enhanced temperature uniformity with perimeter-directed water flow and has a max capacity of 89 L
Thermo Fisher | PC 300; Immersion Circulator
Thermo Fisher | SAHARA S12T AC150; Heated Bath Circulators
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13, 2024. Acrylic heated bath circulator that provides efficient heating from ambient plus 13C to a maximum of 80C, with maximum bath volume of 12 liters and a voltage of 100 V.
Thermo Fisher | Precision TSCIR19; Circulating Water Bath
Water bath that can Achieve enhanced temperature uniformity with perimeter-directed water flow and has a max capacity of 19 L
Thermo Fisher | SAHARA PPO S21P AC150; Heated Bath Circulator
Thermo Fisher | SAHARA PPO S21P SC100; Heated Bath Circulator
Thermo Fisher | SAHARA S13 AC150; 100V; Heated Bath Circulator
Stainles-steel heated bath circulator that offers efficient heating from ambient 13 to 300C and a voltage of 100 V
Thermo Fisher | SAHARA S13 AC200; Heated Bath Circulator
Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C and a voltage of 100 V
Thermo Fisher | SAHARA S13 PC200; Heated Bath Circulator
Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C and a voltage of 100/115 V
Thermo Fisher | SAHARA PPO S14P SC150; Heated Bath Circulator
Thermo Fisher | SAHARA S12T SC100; Heated Bath Circulators
Acrylic heated bath circulator that provides efficient heating from ambient plus 13�C to a maximum of 80�C, with maximum bath volume of 12 liters and a voltage of 100 V
Thermo Fisher | SAHARA S13 PC300; Heated Bath Circulator
Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C and a voltage of 200/230 V
Thermo Fisher | SAHARA S12T AC200; Heated Bath Circulators
Thermo Fisher | SAHARA S13 SC100; Heated Bath Circulator
Thermo Fisher | SAHARA S21 SC150; 100V; Heated Bath Circulator
Stainless-steel heated bath circulator that has efficient heating from Ambient +13C to 150C, max bath volume of 19 liters, and a range voltage of 100 V.
Thermo Fisher | SAHARA S19T SC100; 100V; Heated Bath Circulator
Heated bath circulator that offers efficient heating from ambient 13C to 80CC with a max bath volume of 19 liters and a voltage of 100 V.
Thermo Fisher | SAHARA S13 PC201; Heated Bath Circulator
Thermo Fisher | SAHARA S13 SC150; Heated Bath Circulator
Thermo Fisher | SAHARA S13 SC150L; Heated Bath Circulator
Thermo Fisher | SAHARA S21 AC200; 100V; Heated Bath Circulator
Stainless-steel heated bath circulator that has efficient heating from Ambient +13C to 200C, max bath volume of 19 liters, and a range voltage of 100 V.
Thermo Fisher | SAHARA S19T AC200; 100V; Heated Bath Circulator
Heated bath circulator that offers efficient heating from ambient 13C to 80C with a max bath volume of 19 liters and a voltage of 100 V.
Thermo Fisher | SAHARA S45 AC150; 100 V; Heated Bath Circulators
Stainless-steel heated bath circulator with a temperature of ambient +13C to 150C, max bath volume of 41 liters, and range voltage of 100 V
Thermo Fisher | SAHARA S45 AC200; Heated Bath Circulators
Stainless-steel heated bath circulator with a temperature of ambient +13� to 200�C, max bath volume of 41 liters, and range voltage of 100 V
Thermo Fisher | SAHARA S19T SC150; Heated Bath Circulator
Heated bath circulator that offers efficient heating from ambient 13� to 80�C with a max bath volume of 19 liters and a voltage of 100 V
Thermo Fisher | SAHARA S5P SC100; Heated Bath Circulator
Heated bath circulator that can maintain temperatures from ambient +13� to 100�C, with maximum bath volume of 5 liters and voltage of 100 V
Thermo Fisher | SAHARA S19T AC150; Heated Bath Circulator
Thermo Fisher | SAHARA S45 SC 150L; Heated Bath Circulators
Stainless-steel heated bath circulator with a temperature of ambient +13� to 150�C, max bath volume of 41 liters, and range voltage of 115 V
Thermo Fisher | SAHARA S21 SC100; Heated Bath Circulator
Stainless-steel heated bath circulator that has efficient heating from Ambient +13� to 100�C, max bath volume of 19 liters, and a range voltage of 100 V
Thermo Fisher | SAHARA S5P SC150; Heated Bath Circulator
Thermo Fisher | SAHARA S15 PC300; Heated Bath Circulator
Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C with a max bath volume of 17 liters and a voltage of 200/230 V
Thermo Fisher | SAHARA S21 AC150; Heated Bath Circulator
Stainless-steel heated bath circulator that has efficient heating from Ambient +13� to 150�C, max bath volume of 19 liters, and a range voltage of 100 V
Thermo Fisher | SAHARA S45 SC 150; Heated Bath Circulators
Stainless-steel heated bath circulator with a temperature of ambient +13� to 150�C, max bath volume of 41 liters, and range voltage of 100 V
Thermo Fisher | SAHARA S45 SC100; Heated Bath Circulators
Stainless-steel heated bath circulator with a temperature of ambient +13� to 100�C, max bath volume of 41 liters, and range voltage of 100 V
Thermo Fisher | SAHARA S7 AC200; Heated Bath Circulator
Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 200�C with a max bath volume of 8 liters and a voltage of 100 V
Thermo Fisher | SAHARA S7 AC150; Heated Bath Circulator
Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 150�C with a max bath volume of 8 liters and a voltage of 100 V
Thermo Fisher | SAHARA S7 PC200; Heated Bath Circulator
Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 200�C with a max bath volume of 8 liters and a voltage of 100/115 V
Thermo Fisher | SAHARA S7 PC201; Heated Bath Circulator
Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 200�C with a max bath volume of 8 liters and a voltage of 200/230 V
Thermo Fisher | SAHARA S45 PC200; Heated Bath Circulators
Stainless-steel heated bath circulator with a temperature of ambient +13� to 200�C, max bath volume of 41 liters, and range voltage of 200/230 V
Thermo Fisher | SAHARA S7 SC100; Heated Bath Circulator
Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 8 liters and a voltage of 100 V
Thermo Fisher | SAHARA S6T SC100; Heated Bath Circulators
Acrylic heated bath circulator that provides efficient heating from ambient plus 13�C to a maximum of 80�C, with maximum bath volume of 6 liters and a voltage of 100 V
Thermo Fisher | SAHARA S6T SC150; Heated Bath Circulators
Thermo Fisher | SC100 115V/60Hz; Immersion Circulator
Immersion circulator that can maintain temperature between 13� to 100�C
Model_Number_SC_150L_230V/50Hz (with clamp)
Thermo Fisher | SC 150L 230V/50Hz (with clamp); Immersion Circulator
Immersoin circulator that can maintain temperature up to +150 C while increasing immersion depth to accomodate larger or deeper baths.
Thermo Fisher | SAHARA S7 SC150; Heated Bath Circulator
Thermo Fisher | SAHARA S7 PC300; Heated Bath Circulator
Model_Number_SC 150L 100V/50-60Hz (with clamp)
Thermo Fisher | SC 150L 100V/50-60Hz (with clamp); Immersion Circulator
Immersoin circulator that can maintain temperature up to +150�C while increasing immersion depth to accomodate larger or deeper baths
Thermo Fisher | SAHARA S7 SC150L; Heated Bath Circulator
Thermo Fisher | SC100 100V/50-60Hz; Immersion Circulator
Immersion circulator that can maintain temperature between 13 to 100 C.
Thermo Fisher | SC 150L 115V/60Hz; Immersion Circulator
Thermo Fisher | SC100 230V/50Hz; Immersion Circulator
Model_Number_SC100 230V/50Hz (with clamp)
Thermo Fisher | SC100 230V/50Hz (with clamp); Immersion Circulator
Thermo Fisher | SC 150L 230V/50Hz; Immersion Circulator
Model_Number_SC 150L 115V/60Hz (with clamp)
Thermo Fisher | SC 150L 115V/60Hz (with clamp); Immersion Circulator
Model_Number_SC150 115V/60Hz (with clamp)
Thermo Fisher | SC150 115V/60Hz (with clamp); Immersion Circulator
Immersion circulator that can maintain temperature between 13� to 150�C
Model_Number_SC100 115V/60Hz (with clamp)
Thermo Fisher | SC100 115V/60Hz (with clamp); Immersion Circulator
Model_Number_SC150 230V/50Hz (with clamp)
Thermo Fisher | SC150 230V/50Hz (with clamp); Immersion Circulator
Thermo Fisher | SC 150L 100V/50-60Hz; Immersion Circulator
Thermo Fisher | SC150 100V/50-60Hz; Immersion Circulator
Model_Number_SC100 100V/50-60Hz (with clamp)
Thermo Fisher | SC100 100V/50-60Hz (with clamp); Immersion Circulator
Thermo Fisher | SC150 115V/60Hz; Immersion Circulator
Thermo Fisher | Sorvall BP 16; Centrifuge
Centrifuge that is designed for blood banking and provides high-throughput sample processing
Centrifuge with simple push-button operation for routine applications
Thermo Fisher | SC150 230V/50Hz; Immersion Circulator
Thermo Fisher | Sorvall BP 8; Centrifuge
Model_Number_SC150_100V/50-60Hz (with clamp)
Thermo Fisher | SC150 100V/50-60Hz (with clamp); Immersion Circulator
Immersion circulator that can maintain temperature between 13 to 150 C.
Small benchtop centrifuge that features innovative technologies with a smart, simple interface and the flexibility to meet your clinical and research processes and protocols, available in ventilated and refrigerated models
Thermo Fisher | Sorvall Legend Micro 21; Centrifuge
Ventilated centirfuge that offers productivity, versatility, safety and convenience in a compact, easy-to-use lab instrument
Thermo Fisher | Sorvall Legend X1; Centrifuge
Centrifuge that can process a variety of diverse laboratory applications
Thermo Fisher | Sorvall MTX 150; Centrifuge
Micro-ultracentrifuge that offers powerful separation technology in a quiet, compact, easy-to-use benchtop design that combines advanced functionality, rotor management and controlled access.
Thermo Fisher | Sorvall MX 120 Plus; Centrifuge
Micro-ultra centrifuge that combines high-speed performance, versatile rotor capacities and a compact footprint with excellent processing capacity and sample separation performance up to 1,048,000 × g
Thermo Fisher | Sorvall MX 150 Plus; Centrifuge
Micro-ultra centrifuge that combines high-speed performance, versatile rotor capacities and a compact footprint with excellent processing capacity and sample separation performance up to 1,048,000 g
Low-speed floor model refrigerated centrifuge that can process the optimal capacity for small to medium size blood processing centers with the ability to spin 4 or 8 blood bags in a wide range of bag configurations
Thermo Fisher | Sorvall RC3BP Plus; Centrifuge
Low-speed centrifuge combines outstanding convenience with exceptional ease of use to expedite daily processing
Thermo Fisher | Sorvall Legend X1R; Centrifuge
Thermo Fisher | Sorvall ST 16R; Centrifuge
Centrifuge that can perform cell culture and blood processing applications
Thermo Fisher | Sorvall ST 8R; Centrifuge
Small benchtop centrifuge that provide exceptional capacity in a compact design with a smart, simple interface and the flexibility to support numerous applications
Thermo Fisher | Sorvall ST 8; Centrifuge
Thermo Fisher | Sorvall ST4 Plus-MD; Centrifuge
Centrifuge with 13 available motors that provides high-power spins for sample preaparation
Thermo Fisher | Sorvall ST 8FR; Centrifuge
Refrigerated floor-standing compact centrifuge that offers enhanced ergonomics and saves valuable bench space in your lab
Thermo Fisher | Sorvall ST4R Plus-MD; Centrifuge
Thermo Fisher | Sorvall ST 16; Centrifuge
Thermo Fisher | Sorvall ST4R Plus; Centrifuge
Thermo Fisher | Sorvall X4R Pro-MD; Centrifuge
Thermo Fisher | Sorvall X4 Pro-MD; Centrifuge
Thermo Fisher | Sorvall X4R Pro; Centrifuge
Thermo Fisher | Sorvall ST4 Plus; Centrifuge
Thermo Fisher | ThermoChill I LR, 115V/ 60Hz MDCI; Recirculating Chiller
Recirculating chiller that provides reliable temperature control with a temperature range from -10C to +30C.
Thermo Fisher | ThermoChill I LR, 115V/ 60Hz MDCI RS232; Recirculating Chiller
Thermo Fisher | ThermoChill I LR, 115V/ 60Hz, PD-1; Recirculating Chiller
Thermo Fisher | ThermoChill I LR, 230V/50Hz MDCI; Recirculating Chiller
Thermo Fisher | Sorvall X4 Pro; Centrifuge
Thermo Fisher | ThermoChill I LR, 230V/50Hz, PD-1 RS232; Recirculating Chiller
Thermo Fisher | ThermoFlex 10000; Recirculating Chiller
Recirculating chiller that provides reliable temperature control with a temperature range from -5�C to +90�C
Thermo Fisher | ThermoChill I LR, 230V/50Hz, PD-1; Recirculating Chiller
Thermo Fisher | Spinnaker Robot; Lab Automation
Lab automation robot that provides self-correcting precision as well as powerful sample tracking and inventory management
Model_Number_ThermoFlex 20000 (new T9 pump)
Thermo Fisher | ThermoFlex 20000 (new T9 pump); Recirculating Chiller
Recirculating chiller that provides reliable temperature control with a temperature range from 5�C to 40�C
Model_Number_ThermoFlex 15000 (new T9 pump)
Thermo Fisher | ThermoFlex 15000 (new T9 pump); Recirculating Chiller
Model_Number_ThermoFlex 24000 (new T9 pump)
Thermo Fisher | ThermoFlex 24000 (new T9 pump); Recirculating Chiller
Recirculating chiller that provides reliable temperature control with a temperature range from -5�C to +50�C
Thermo Fisher | ThermoFlex 3500; Recirculating Chiller
Recirculating chiller that provides reliable temperature control with a temperature range from 5�C to 90�C
Thermo Fisher | ThermoChill I LR, 230V/50Hz MDCI RS232; Recirculating Chiller
Thermo Fisher | ThermoFlex 1400; Recirculating Chiller
Thermo Fisher | ThermoFlex 7500; Recirculating Chiller
Thermo Fisher | ThermoFlex 2500; Recirculating Chiller
Thermo Fisher | ULT 179104241600; Bath Recirculator
Refrigerated bath recirculators that is designed for circulating to external applications and has a temperature range of -95�C to -30�C
Thermo Fisher | ThermoFlex 900 (Low Noise); Recirculating Chiller
Thermo Fisher | ThermoFlex 900; Recirculating Chiller
Thermo Fisher | ULT 179106241600; Bath Recirculator
Refrigerated bath recirculators that is designed for circulating to external applications and has a temperature range of -95 C to -30 C.
Thermo Fisher | ULT 180104201601; Bath Recirculator
Refrigerated bath recirculators that is designed for circulating to external applications and has a temperature range of -80�C to +80�C
Model_Number_Ultra-low Temp G50 AC200 230 VOLT
Thermo Fisher | Ultra-low Temp G50 AC200 230 VOLT; Refrigerated/Heated Bath Circulator
Refirgerated/heated bath circulator that delivers high heating and cooling capacities for rapid heat-up and cool-down times and has electrical requirements of 230 V
Thermo Fisher | ULT 180106201601; Bath Recirculator
Thermo Fisher | ThermoFlex 5000; Recirculating Chiller
Model_Number_Ultra-low Temp G50 AC150 208-230 VOLT 60HZ
Thermo Fisher | Ultra-low Temp G50 AC150 208-230 VOLT 60HZ; Refrigerated/Heated Bath Circulator
Refirgerated/heated bath circulator that delivers high heating and cooling capacities for rapid heat-up and cool-down times and has electrical requirements of 208/230 V 60 Hz
Thermo Fisher | ULT 180104201600; Bath Recirculator
Refrigerated bath recirculators that is designed for circulating to external applications and has a temperature range of --80�C to +10�C
Thermo Fisher | VersaCool; Refrigerated Circulating Bath
Refrigerated circulating bath that can circulate fluid from the bath to specific applications with a temperature range of -20�C to +150�C
Tissue Tek VIP E300 is a tissue processor that features a self-calculation delay mode which coordinates completion of processing to enhance workflow. The computer monitors all steps in the processing sequence safeguarding your specimens and protecting your system. Precisely located heater elements provide uniform reagent temperatures throughout the retort during processing. Gentle tidal agitation ensures optimal reagent mixing while reducing tissue cross-contamination. Paraffin cleansing automatically degasses the paraffin while in the oven, eliminating additional retort cleaning cycles. The Tissue Tek VIP E300 tissue processor features a full-screen display for complete information at a glance and an easy-access control panel for complete system management. The basket design allows for upright placement of cassette specimens and fits all standard embedding consoles.
Model_Number_Ultra-low Temp G50 PC200 208-230 VOLT 60HZ
Thermo Fisher | Ultra-low Temp G50 PC200 208-230 VOLT 60HZ; Refrigerated/Heated Bath Circulator
Refirgerated/heated bath circulator that delivers high heating and cooling capacities for rapid heat-up and cool-down times and has electrical requirements of 200/230 V 60 Hz 200 V 50 Hz
G8 HPLC Hematology Analyzer is the Tosoh's industry HPLC testing systems for fast and accurate HbA1c results. Tosoh designed the G8 HPLC Analyzer from the user's perspective, enhancing overall safety and of operation. The system utilizes Ion-exchange HPLC testing method, which is the gold standard for HbA1c diabetes measurement. The system is used for in vitro diagnostic measurement of HbA1c in blood specimens. The G8 uses a non-porous column and microcomputer technology to quickly and accurately measure the stable portion of HbA1c as a percentage of the total amount of hemoglobin present in the sample. The G8 provides accurate and precise separation of HbA1c from other hemoglobin fractions. Off-line pretreatment is not required, and there is no interference from the labile portion of HbA1c.
Thermo Fisher | TissueLoc Tissue Cassettes
Tissue Cassettes for specimen safety during processing and easy removal of cover while embedding with hinge design. Preassembled for added convenience.
Model_Number_Ultra-low Temp G50 AC200 208-230 VOLT 60 HZ
Thermo Fisher | Ultra-low Temp G50 AC200 208-230 VOLT 60 HZ; Refrigerated/Heated Bath Circulator
TBS-380 Mini-Fluorometer is a dual-channel fluorometer designed for quick, easy, and accurate fluorescence measurements. When properly calibrated with a standard of known concentration, the TBS380 displays the actual concentration of the measured compound. The new Minicell adaptor design enables the user to measure compounds at a low concentration with a low assay volume (e.g. dsDNA at 1ng/mL using PicoGreen, and RNA at 1 ng/mL using RiboGreen).
TTP Labtech | Mosquito HTS Automated Liquid Handler
Both TTP Labtech's mosquito HTS and mosquito HV make assay miniaturisation simple, leading to significant savings on precious reagents and time. Both liquid handlers are best for multi-user labs as you can just walk up to either one and use it. mosquito HTS offers an accurate and easy-to-use-solution to miniaturising any assay within an automated, high-throughput setting. Volume range is 25 nL 1.2 ΜL, which can be expanded to cover 25 nL 5 ΜL in conjunction with mosquito HV. By using mosquito's positive displacement pipetting technology, dead volumes are minimised to under 0.3 ΜL. Using mosquito HTS means you can prepare “assay readyâ€� plates containing test compounds direct from library stocks or dilution plates, as the disposable micropipettes guarantee zero carry-over between samples. mosquito HTS can aspirate from any source plate leaving dead volumes of less than 0.3 ΜL both critical cost areas to consider when capitalising on the savings of assay miniaturisation for high throughput screening assays. You can easily program mosquito HTS to perform traditional serial dilutions by aspirating, dispensing and mixing across a plate using miniaturised volumes ranging from 25 nL 1.2 ΜL. This allows you to effectively perform hit confirmation from high throughput screening assays using multiple compound concentrations.
Thermo Fisher | VaLet Robot; Lab Automation
Lab automated tool that automates applications from simple instrument loading to more complex, integrated workflows (with Plate Storage Only)
TTP Labtech | Mosquito HV Automated Liquid Handler
TTP Labtech introduced the mosquito HV liquid handler to bridge the gap between nanolitre and microlitre pipetting. It provides accurate liquid handling for low volume serial dilutions and assay plate preparation across the intermediate volume range of 500 nL 5 �L. TTP Labtech's mosquito HV can be employed for a wide range of chemical and biological-based applications; including compound and small molecule screening, cell- or bead-based assays, enzyme kinetic assays, ELISAs, and molecular biology applications including rtPCR/qPCR set-up, RNAi screening and SNP genotyping.
Immunoassay system analyzer by Beckman Coulter with standardized test menus, assay protocols, instrument processes and reference ranges. Sample types include serum, plasma, urine, amniotic fluid, and whole blood.
UMAX PowerLook 2100XL is a scanner for graphics professionals who require high resolution and fast color scanning of any image in a small package. You can scan illustrations, newspapers, magazines, transparencies, color photos, and even x-rays, textiles, and negatives. The scanning area measures a full 12" by 17", despite the small footprint of just over 18" by 24" to fit on any desktop. The scan area can accommodate up to thirty-two 35mm slides when used with the transparency adapter. High 3.4Dmax captures fine details of shadow areas -- especially important when scanning transparencies. In addition, batch scanning increases productivity by scanning more than one image in a single pass.
Varian | Prostar 210 Solvent Delivery System
High-Performance Liquid Chromatography (HPLC) solvent delivery module (pump). It is used in laboratories to precisely pump solvents at high pressures to separate, identify, and quantify the components of a chemical mixture.
Virtis | Virsonic 100 Ultrasonic Probe Homogenizer
VirTis Virsonic 100 is an ultrasonic probe homogenizer, designed for cell disruption and fluid processing. Uses a variety of probes to process fluid volumes from 0.2 to 60 mL.
Roche | Veeco Nanoscope IIIA Atomic Force Microscope
Veeco Multimode Nanoscope IIIa AFM has a resolution of ~ 0.3 nm with A scanner. The instrument is capable of imaging areas ~ 1 sq.,m (using the standard A scanner), ~12 sq.,m. (using vertical engagement EV scanner) and ~125 sq.,m (using vertical engagement JV scanner) in the XY direction. The scanning range in the Z direction for EV and JV scanner are ~ 2,m and ~ 5,m respectively. The AFM is capable of imaging in Contact mode and Tapping mode with Nanoindentation capabilities. Attachments include a Fluid Cell for imaging in liquids (Contact and Tapping mode) and an Anti-vibration suspension mount for atomic resolution imaging. A 15 mm sample disc is used to mount the samples with access to ~ 2-3 mm area at the center of the sample.
Bruker | |Veeco Multimode 8 Atomic Force Microscope
Itegrated, high-pressure, binary HPLC pump that feature on-board pulse dampening and efficient mixing. Their pulse-free solvent flow, from analytical to semi-preparative flow rates, makes them best for use with highly sensitive detectors. Designed for use with 2 to 4.6 mm I.D. columns in routine LC and LC/MS applications, these pumps have a programmable flow-rate range of 0.00 to 10.00 mL/min in 0.01 mL increments.
Waters 2996 PDA Detector can be used for in-vitro diagnostic testing to analyze many compounds, including diagnostic indicators and therapeutically monitored compounds. It also describes detector optics and the principles of Spectral Contrast used in the Millennium32 software for analyzing the data from the PDA detector.
Wallac | 1450 Liquid Scintillation Counter
Wallac 1450 MicroBeta is a liquid scintillation counter and luminescence detector that can accommodate either 1, 2, 3, 6, or 12 detectors, each of which can count in 96- and 24- or 96- and 384-well plate formats. Samples may be counted in microplates, tubes, or on filters for added flexibility. The counter features dual photomultiplier tubes (PMT), with the first PMT set over the sample and the second located below. This method of coincidence counting provides optimal productivity for any compatible assay, including proximity and filtration assays among others.
Synapt G2 Mass Spectrometry (MS) system is a hybrid, quadrapole/orthogonal acceleration, time-of-flight (oa-TOF) mass spectrometer controlled by MassLynx software. The Waters Synapt G2 is compatible with the Acquity UPLC and nanoAcquity UPLC systems. Hamilton STARplus liquid handling robot.
GE | VG Trio 2000 GE Healthcare Typhoon Trio Variable Mode Imager System
Typhoon instrument is a variable-mode imager that produces digital images of radioactive, fluorescent, or chemiluminescent samples. The Typhoon instrument is available in several models. The Typhoon Trio instrument contains three internal lasers (blue, green, and red).
ProteinLynx Global SERVER (PLGS) is a fully integrated Mass-Informatics platform for quantitative and qualitative proteomics research. It is the central analytical platform for Waters proteomics systems. PLGS leverages the selectivity of exact mass measured data and the specificity of MSE analysis. Combined with intelligent filtering and scoring routines, this minimizes the occurrence of false positive results. PLGS is based on open/pluggable system architecture, providing scalable, automated workflow for your high-throughput data processing and data interpretation. PLGS also includes project and database management tools with integrated results visualization and reporting. Import sample information and data into PLGS through XML (mzData supported), which provides integration of the PLGS toolset into a LIMS or Data Management System such as Waters NuGenesis SDMS. The PLGS custom report generation utility also allows you to produce publication-ready result reports.
Micromass (now Waters) Quattro Premier triple quadrupole mass spectrometer operates with an Agilent 1100 HPLC and specializes in quantitative work and selective of targeted analytes including metabolites and other small molecules, and peptides from complex matrices such as serum, tissue, cell culture, and other biological sources.
Plate Reader for dynamic light scattering (DLS) and static light scattering (SLS) measurements of the size, molecular weight and interactions of proteins, nanoparticles and other macromolecules in situ in industry-standard microwell plates. No liquid handling occurs after dispensing into the plates, to maximize throughput and minimize sample carryover.
Mass spectrometer with selectivity, in-spectrum dynamic range, speed of analysis, quantitative accuracy and exact mass performance simultaneously, for any UPLC/MS or UPLC/MSE experiment.
Wyatt | Calypso Composition-Gradient Multi-Angle Light Scattering (CG-MALS)
Composition-Gradient Multi-Angle Light Scattering machine that characterizes biomolecular interactions, label free and immobolization free. It is able to determine equilibrium dissociation constants self and hhetero association as well as more complex interactions.
Wyatt | Eclipse AF4 Field-Flow Fractionation system
Eclipse AF4 is optimal for all standard asymmetric flow field flow fractionation AF4 separations as well as frit inlet channels and semi preparative AF4. Combined with HPLC equipment and Wyatt's multi angle light scattering detectors, Eclipse AF4 excels at characterizing difficult samples.
Triple quadrapole mass spectrometer with both analytical and microflow UPLC separations. It can be used for MRM testing and has LC flow of up to 2 mL/min.
Refractive Index detector that offers high sensitivity and 50 times dynamic range of every other UHPLC RI detector. Like Optilab, it offers temperature control both above and below ambient, as well as measurement of absolute refractive index of solvents.
Wyatt | Eclipse DualTec Field-Flow Fractionation system
Field flow fractionation device supports both Hollow Fiber Flow FFF HF5 and Asymmetric Flow FFF AF4 in one instrument. Utilizing one HPLC stack and one set of Wyatt detectors, DualTec permits automated switching between any two of SEC, AF4 and HF5 separation followed by MALS and or DLS characterization.
Wyatt | microDAWN Multi-Angle Light Scattering Detector
Multi Angle Light Scattering Detector that can be coupled to any UHPLC SEC system to determine absolute molecular weights and sizes of proteins, peptides, polymers or nanoparticles below 50 nm in radius directly, without resorting to column calibration or reference standards.
Dynamic Light Scattering device DLS measures electrophoretic light scattering ELS and DLS simultaneously to determine zeta potential or molecular charge, automated by autosampler or manually, under wide range of solvents.
Wyatt | miniDAWN Multi-Angle Light Scattering Detector
Multi Angle Light Scattering Detector used to determine absolute molar mass and size to characterize proteins, peptides, small polymers and nanoparticles in solution.
Wyatt | DAWN Multi-Angle Light Scattering Detector
Multi Angle Light Scattering Detector most often used in conjunction with size exclusion chromatography SEC MALS or field flow fractionation FFF MALS to determine distributions of molecular weight, size and composition.
Refractometer based on semiconductor photodiode technology and proprietary computer algorithms. Can be used for standard chromatographic applications and measurements such as high concentrations, determination of sample refractive increments dn dc and solvent refractive index.
Wyatt | DynaPro NanoStar Dynamic Light Scattering Detector
Dynamic Light Scattering device that may be utilized to measure not just size, size distributions, particle concentration and weight average molar mass, but also solution properties relevant to sample stability.cuvette-based DLS instrument used for the analysis of proteins, promiscuous inhibitors, micelles, quantum dots, liposomes, metallic nanoparticles and more.
Differential viscometer used in conjunction with SEC MALS IV to determine size and conformation of all types of biopolymers, synthetic polymers and even proteins and peptides.
microViscoStar incorporates multiple novel technologies to provide highest sensitivity, stability and solvent compatibility of any available viscometer for UHPLC. Its ease of use and serviceability make it companion for Wyatt's microDAWN light scattering and microOptilab refractive index detectors for UHPLC.
Perkin Elmer | | Xenogen IVIS 100 Imaging System
In vivo imaging system that combines 2D optical and 3D optical tomography in one platform. The system can be used for preclinical imaging research and development best for non-invasive longitudinal monitoring of disease progression, cell trafficking and gene expression patterns in living animals.
X-ray inspection system for SMT, semiconductor, and laboratory assembly applications.
Computed tomography system for 3D inspection results at high resolution. In electronics and material science industries can use it for R&D, defect analysis, process monitoring, or CT metrology.
Wyatt | ultraDAWN Multi-Angle Light Scattering Detector
Multi Angle Light Scattering Detector that measures multi angle light scattering and reports results weight average molecular weight Mw and rms radius Rg in real time.
Thermal transfer barcode printer with label, receipt and tag-handling capabilities that connects via USB, serial, or parallel port.
X-ray machine for inspection of SMT, semiconductor, and laboratory assembly applications.
Yokogawa | CSU-22 Spinning Disk Confocal Microscope
Spinning disk confocal micrscope for observation of various life processes in living samples in real time, minimal photo bleaching and photo toxicity.
X ray inspection system has been developed to enable automated analysis for flaws in semi-conductors. Flaws can be found on wafer, on substrate, in strip in sub assembly or in final device.
Computed tomography system available in single or dual tube configuration. It can be used for small to medium sized parts inspection in automotive, electronics, aviation, and material science industries.
X ray inspection system for automatic analysis of smallest and most demanding features within 3D IC, MEMS and sensors.
Cryogenic Crystal Cooler is a self-contained apparatus designed for cooling crystals to a temperature within the range of -180C to 4C. The X-stream 2000 system takes room air, compresses it, and removes the impurities from it to produce clean, dry nitrogen. This gas is then cooled to nearly -196C, and then rewarmed to the desired temperature
Barcode label printer with 203 and 300 dpi print resolutions, multiple interface options (including serial, parallel, USB, Ethernet and 802.11b wireless connections). It has side-loading design and an 8" label roll capacity.
Electron microscope with pulsed laser beam that creates images in high resolution in the nanometre range. This miscroscope allows the user to investigate your samples with X-ray analysis, rework interesting sample positions, and analyze non-conducting material and complex geometries.
Zeiss | Axio Vert series Axiovert 200 inverted microscope
Inverted microscope that is used for the examination of cell and tissue culture of sediments in culture flasks, Petri dishes, microtiter plates, etc. in transmitted and reflected light. It hass attachment possibilities for various tools (micromanipulation), different light sources, temperature control devices., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Visible confocal microscope that acquires the X dimension simultaneously on a line CCD detector while scanning only in the Y dimension. This allows users to increase the speed of image acquisition compared to traditional confocal systems. This system is equipped with two fluorescence detectors and 4 lasers lines at 405nm, 488nm, 561nm and 633nm. It is capable of scanning over 120 FPS for a large field of view.
Computed tomography system with dual tube configuration for use with a wide variety of material types and parts size.
Upright microscopy imaging platform for complex research that is optimized for light transmission and extremely high contrast fluorescence imaging. This complete system comes fully configured for best performance, range and functionality.
Zeiss | Lightsheet Z.1 Fluorescence Microscope
Light sheet fluorescence microscope for the imaging of large cleared specimens. Lightsheet Z.1 with Clr Plan-Apochromat 20x/1.0 Corr nd=1.38 is used to perform experiments with tissue cleared by Scale medium (Hama et al, Nat Neurosci. 2011), which has a refractive index of n=1.38.
Monochromated field emitter that produces high resolution high contrast images due to the Zeiss proprietary electron gun monochromator (MC) and Kohler illumination system. The monochromator enables the operator to reduce the energy width of primary electrons to less than 0.2 eV and thereby allows for highest resolution in Electron Energy Loss Spectroscopy (EELS).
Industrial X ray and CT inspection system for broad applications in foundries, R&D, laboratories, universities, and educational institutions. system delivers image quality with digital flat panel detector and radioscopy.
Zeiss | LSM 780 Confocal Laser Scanning Microscope
Laser Scanning Microscopes (LSM) for high resolution imaging of biological or material samples. The compact scanning module can be fitted to an inverted (Axio Observer.Z1 RP or SP) or upright (Axio Imager.Z2, Axio Imager.M2 or Axio Examiner) microscope.
Confocal microscope that acquires the X dimension simultaneously on a line CCD detector while scanning only in the Y dimension. This system is equipped with two fluorescence detectors and 4 lasers lines at 405nm, 488nm, 561nm and 633nm. It is capable of scanning over 120 FPS for a large field of view.
Optical stereomicroscope with 7.7:1 zoom range (pancratic system 0.65x to 5.0x) zooms in continuously or with click stop. It has an object field size of 35mm, with an 0.3x attachment lens system permitting object fields of up to 118mm to be viewed.
Zeiss | LSM 880 with Airyscan Confocal Laser Scanning Microscope
Fully enclosed laser scanning confocal imaging microscopefor heating and environmental control with media perfusion capabilities and CO2 control. It can be used for Live Cell Imaging, FRET and Anisotropy, FRAP and FLIP, FCS, Photoactivation/ -conversion., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Zeiss | LSM 5 DUO Spectral Confocal Microscope
Laser scanning microscope for the high resolution imaging of biological or material samples.
Used to digitize specimens with the Axio Scan.Z1 slide scanner to create high-quality virtual slides. Axio Scan.Z1 tackles the most demanding virtual microscopy research tasks as easily as it handles your routine work. The software module ZEN slidescan is designed specifically for the workflow of capturing virtual slides, while ZEN image analysis tools prepare your data accurately. Organize your virtual slides with ZEN browser, the web-based database, then view your data from any location using any operating system , or share virtual microscopy images online with colleagues and organize your projects, even when you are on the go.
Zeiss | Sigma VP Scanning Electron Microscope
ZEISS SIGMA VP field emission scanning electron microscope (FE-SEM) for imaging of non-conducting samples. It images of bacteria, cells, plants and organisms. Uses ATLAS software and can be combined with 3View technology from Gatan Inc.
PALM MicroBeam scanning electron microscope for isolating uncontaminated source material simple.
Zeiss | Supra 25 Field Emission Scanning Electron Microscope
Field scanning electron microscope with analytical specimen chamber with choice of optional detectors and accessories. It has 5-axes motorised cartesian stage can handle multiple smaller specimens simultaneously. It can image bulky or irregular shaped specimens.
Software tool for detecting automatically generated academic papers. Discovers text that has been generated with SCIgen and other fake paper generators like Mathgen and Physgen. Provides on open source version of the scigen detector.
Hierarchical Analysis of Spatial and TEmporal data
Software toolkit for rapid development of cloud native intelligent data pipelines for scientific data streams. Hierarchical approach to acquisition, analysis, and interpretation of image data. Developed in the project Hierarchical Analysis of Spatial and Temporal Data.
Web tool for systematic reference data collection in land cover and use applications.Open source software tool for land monitoring. Systematic reference data collection tool for land cover and land use applications. Satellite image viewing and interpretation system developed by SERVIR joint efforts between NASA, FAO, US Forest Service and Google.
Software tool to calculate number of mapped exonic non duplicate reads in bam file containing RNA-Seq data.
Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers.
Portal for providing data and tools to promote understanding and treatment of type 1 diabetes and its complications.Enables browsing, searching, and analysis of human genetic information linked to type 1 diabetes and related traits, while protecting integrity and confidentiality of underlying data.Represents effort to coordinate collection and deposition of genomic and epigenomic data related to type 1 diabetes and its complications.
Common Metabolic Diseases Knowledge Portal
Portal enables browsing, searching, and analysis of human genetic information linked to common metabolic diseases and traits, while protecting integrity and confidentiality of underlying data. Aggregates and analyzes genetic association results, epigenomic annotations, and results of computational prediction methods to provide data, visualizations, and tools in open access portal.
Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.
iMagE Registration via autoMAtIc Differentiation
Registration toolbox written in pyTorch. Supports various image registration methods. Focuses on nonparametric registration approaches including stationary velocity fields and large discplacement diffeomorphic metric mapping models though simple affine registration is also possible. Allows for rapid prototyping of new image registration approaches and similarity measures.
Free cloud platform for secure neuroscience data analysis. Allows to manage data, processing and results, sharing projects privately with collaborators or publicly with brainlife.io community.Promotes engagement and education in reproducible neuroscience.You can share your neuroimaging data publicly or privately. Data on brainlife.io is organized as Datatypes to allow interoperability between Apps.
Software tool for flow cytometry data analysis by Miltenyi Biotec.
Software provides user interface for data acquisition on MACSQuant Analyzer Flow Cytometer Instrument and also works as stand alone application for flow cytometry data analysis.
Multi modal Image Registration And Connectivity anaLysis
Automated software resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling analysis of histological features across multiple fiber tracts and networks, and their correlation with in vivo biomarkers.Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Open source pipeline for automated registration of mice clarity data to Allen reference atlas, segmentation and feature extraction of mice clarity data in 3D, registration of mice multimodal imaging data to Allen reference atlas, tract or label specific connectivity analysis based on Allen connectivity atlas,comparison of diffusion tensort imaging/tractography, virus tracing using CLARITY and Allen connectivity atlas, statistical analysis of CLARITY and Imaging data, atlas generation and label manipulation.
Miniature Inverted repeat Transposable Elements Hunter
Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences.
Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals.
Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels.
Software tool as simulation framework for testing association of genomic intervals. Used for estimating significance of overlap between multiple sets of genomic intervals. Estimates statistical significance based on simulation and controls for multiple tests using false discovery rate.
Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.
Software tool to enable BLAST to identify homologous gene sequences. Graph based algorithm, which automatically filters High Scoring Pairs into well defined groups, each representing candidate gene in target genome.Used for identifying homologous sequences. Used for extracting relevant HSPs that represent candidate homologous genes from the entire HSP report.
Mapping the pancreas and its ecosystem at the cellular level in health and type 1 diabetes
Portal for scRNA-seq study. Includes dendrogram visualization and clustering of all cells in scRNA-seq study as well as interactive filtered views for cell type, gene and/or donor group.
Viewer for DNA Methylation Atlas of Mouse Brain at Single Cell Resolution. Browser to interactively explore single cell methylome dataset including exploration of methylation diversity of one gene at single-cell or cell-type level, exploration of cell type composition of adult mouse brain dissection regions and anatomical structures, explorartion of spatial distribution and methylation signature genes of one cell type.
Software package for quantitative analysis of PET/CT studies. Quantitative oncology molecular analysis suite. Allows for DICOM input of both PET and CT data. It includes several image processing steps such as rebinning/resampling, cropping and smoothing. After loading and processing PET/CT images, lesions can be delineated using a range of segmentation.
Tucsen camera image acquisition, managing and processing software by Tucsen Photonics Co., Ltd. Professional imaging software application developed by Tucsen for full control of Tucsen cameras.Tucsen continually upgrades TCapture.
Educational software that implements Analytic Hierarchy Process and Analytic Network Process. Provides tools to create and manage AHP and ANP models, enter your judgments, get results and perform sensitivity analysis on results. Provides support for complex, multilevel Benefits Opportunities Costs Risks models.
Portal to build, train and deploy state of the art models powered by reference open source in natural language processing.
Multi region exome sequencing analysis tool Kit
Software R package for dissecting cancer evolution from multi region derived tumor biopsies via somatic mutations. Used for characterizing cancer genomic ITH and inferring history of tumor evolution via implementation of well established computational and statistical methods.
ImageJ macro to detect, mark and count electron dense markers like goldgrains or quantum dots in electron micrographs.
Software suite of tools for reconstructing genomes using RNA-Seq data from multiparent population and for quantifying allele specific expression.
Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix.
Pulsed Interleaved Excitation analysis with MATLAB
Software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with focus on experiments using pulsed interleaved excitation. Open source software package written in MATLAB that offers workflow through its graphical user interface. Framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data.Supports most types of data collection modalities.
University of Leicester Advanced Imaging Facility
Open access light microscopy facility of College of Life Sciences. Offers wide range of confocal and conventional fluorescence microscopes and image analysis resources. AIF is part of Core Biotechnology Services CBS.
University of Freiburg Life Imaging Center Core Facility
University of Freiburg LIC - Life Imaging Center
Central core facility open to members of all faculties and the university clinic. Consists of 14 rooms in the Center for Integrative Signalling Analysis with 9 microscopy rooms with 20 microscope set-ups (3D-STED, confocal FLIM, two 2-photon confocal microscopes, 4 conventional confocal microscopes, lightsheet microscope, 4 high-end widefield ratio-imaging set-ups, 4 fluorescence stereo microscopes, 3 special set-ups for screening. LIC microscopes are hosted in Biosafety level S2 and S1 environments, connected to a large wet lab area and a cell culture room, both Biosafety level S2 classified. Additionally, the LIC offers a large computer lab with 12 high-end workstations for image processing and analysis. The LIC also covers two additional rooms, hosting 3 LSM systems in a neighboring building of the Signalling Campus Freiburg (SCF).
Olympus | LEXT OLS4100 laser confocal microscope
Laser scanning digital microscope for non-contact 3D observations and measurements of surface features at 10 nanometer resolutions with fast image acquisition and high-resolution images over wider area. Z-drive moves in steps less than 1nm, accuracy and repeatability guaranteed by Olympus. The system includes 5 objectives: 5x/0.15, 10x/0.30, 20x/0.60, 50x/0.95, and 100x/0.95.
Software R package to perform differential transcript usage analysis of bulk or single-cell RNA-seq data.
Clemson University Light Imaging Core Facility
Core light microscopy facility located on main campus of Clemson University. Offers access to multiple Leica Microsystems instruments, including SP8X LIGHTNING confocal with STED,SPE confocal, DMi8 widefield/TIRF/GSD system,THUNDER model organism imager, LMD6500, M125 stereoscope, and DM750P polarized light microscope.We also house Olympus LEXT OLS4100 optical profiler, GE InCell 2500HS high content screener, and Biorad S3e cell sorter. Offers assistance with equipment selection, image analysis, and sample preparation. Offers prepared slides for 4 color fluorescence imaging and can also prepare custom slides.
City of Hope Department of Pathology Core Facility
Department of Pathology at City of Hope combines state-of-the-art laboratories equipped with the latest diagnostic techniques and advanced instrumentation with superior investigative skills to accurately and rapidly identify even the rarest and most complex diseases. Our experts provide comprehensive services, from initial diagnosis to monitoring of prognostic indicators throughout the treatment process.
Beckman Research Institute of City of Hope
Not-for-profit medical research facility located at and partnering with the City of Hope National Medical Center in Duarte, CA, United States.Fields of research include Cancer, Diabetes, Metabolic disorder, HIV/AIDS.
Deep Transfer Graph Convolutional Network
Software tool as novel deep learning approach for multi-stage malaria parasites recognition in blood smear images using deep transfer graph convolutional network. DTGCN model is based on unsupervised learning by transferring knowledge learnt from source images that contain discriminative morphology characteristics of multi stage malaria parasites.
Software tool as feature selection method based on nearest neighbors for single-cell data.
Incorporated as non-profit member based organization promoting scientfic collaboration in computational neuroscience.Advances computational neuroscience by pushing limits of large scale simulations of biologically realistic neuronal networks.
Web tool for 3D data annotation for connectomics.Open source tool for annotating and exploring large 3D image datasets. Web based data sharing, annotation and visualization software for large scale 3D images. Provides flight mode, single view egocentric reconstruction method enabling to reconstruct for axons and for dendrites in 3D electron microscopic data from mammalian cortex. Supports skeleton and volumetric annotations as well as data management functionality.
Open platform for interoperable life science experimental metadata. Metadata framework as set of community specifications and software tools for enabling discovery, exchange and publication of metadata from experiments in life sciences. Python library for creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats.Provides programmatic metadata handling functionality to support automation, common interface and interoperable medium between two ISA formats, as well as with other life science data formats required for depositing data in public databases.
Single Nucleus Analysis Pipeline for ATAC-seq
Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset.
Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing.
Software toolbox, formerly called CPMjs, as framework to build interactive, explorable simulation models of cells and tissues in web browser. JavaScript library to build interactive Cellular Potts Models as command line applications or in web browser.
Non-Parametric Structural Variant Genotyper
Software Python tool for standalone genotyping of deletion and insertion structural variants in short read whole genome sequencing data. Implements machine learning based approach for SV genotyping that employs NGS simulation to model the combined effects of the genomic region, sequencer and alignment pipeline.
Rockefeller University Fisher Drug Discovery Core Facility
Fisher Drug Discovery Resource Center Core Facility
Rockefeller University Fisher Drug Discovery Resource Center Core Facility
Core guides researchers in drug discovery by improving efficiency of their bioassays, identifying compounds and targets of function, and in utilizing technologies for measurement of drug/receptor interactions.Center also has spectroscopic and calorimetric equipment for use in studies of interactions of drugs with their targets.
Rockefeller University Genomics Resource Center Core Facility
Core offers services and instruments to support genomics research. Houses Illumina NovaSeq, NextSeq, MiSeq sequencers, 10X Genomics Chromium Single Cell System, and Life Technologies QuantStudio 12K flex realtime PCR system. Provides several accessory instruments for sample quantity and quality validation: Agilent Bioanalyzer, Agilent TapeStation, NanoDrop spectrophotometer, and Qubit spectrophotometer.Offers full services for genomic DNA-Seq and RNA-Seq, specializing in preparation of libraries from very small amount of starting total RNA. Users can also prepare their own libraries and use the center�s sequencing-only services. Offers free consultations on experimental designs, library preparation options, sequencer choice, sequencing depth and coverage, and biological replicates.Performs initial sequencing data analysis for all users, and can assist with downstream analysis.
University of Manchester BioMS Core Facility
Core offers mass spectrometry services and associated technologies to the University of Manchester and beyond with focus on biological molecules such as proteins and metabolites in proteomics and metabolomics areas.Provides support from experimental design to advanced sample preparation and data processing and interpretation.
Rockefeller University Gruss Lipper Precision Instrumentation Technologies Resource Center Core Facility
Precision Instrumentation Technologies Resource Center
The Rockefeller University Gruss Lipper Precision Instrumentation Technologies Resource Center
The Gruss Lipper Precision Instrumentation Technologies (PIT) Resource Center provides access to various fabrication and rapid prototyping tools for qualified users. The PIT allows users to design and build their own research tools by providing access to wide array of prototyping and fabrication equipment, as well as design and fabrication consultation. The PIT also provides full prototyping service (design through fabrication and testing).
Software statistical analysis R package used for easy analysis and visualization of factorial experiments. Provides interface to common analysis techniques, including analysis of variance and mixed effects modeling. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling.
Cloud based research platform that allows researchers and students to quickly and easily create and deploy behavioural experiments online. Online behavioral experiment builder for running behavioural studies.
Software tool as Javascript encoder and decoder to use spectral power distributions in URL.
Software tool for pathology slide viewing. Used for access to color digital slide images to which you can adjust magnification, pan and zoom, compare different stains, annotate areas of interest, perform image analysis, and more. Allows to view slide images taken by Leica biosystems scanner.
Open access software platform to faciliate calculation of quantities related to light and lighting. Users can upload spectra and platform will calculate relevant quantites including luminance, chromaticity, and α-opic radiance and α-opic daylight luminances from spectra, generate visualisation of spectrum, and enable export of calculations in tabular form.
Software tool to allow characterization of parameters analyzed in fundamental and clinical studies in skeletal muscle field. Running on open source Fiji software platform, simultaneously analyzes parameters from immunofluorescent staining, imaged by different acquisition systems in completely automated manner.Used to analyze muscle cross-sectional area, fiber typing, localization of nuclei within muscle fiber, number of vessels, fiber associated stem cells parameters simultaneously.
Northwestern University Feinberg School of Medicine Center for Advanced Microscopy Nikon Imaging Center Core Facility
Center for Advanced Microscopy and Nikon Imaging Center
Northwestern University Center for Advanced Microscopy and Nikon Imaging Center
Core offers instrumentation and services for study of biological processes at whole animal, tissue, cellular and subcellular levels. Services include electron microscopy, super resolution microscopy, fluorescent laser scanning and spinning disk microscopy, fluorescent lifetime imaging, automated high throughput tissue cytometry, atomic force microscopy, laser capture microdissection, mutliphoton imaging, and whole animal bioluminescent and fluorescent imaging. Additionally we provide microinjection equipment, chambers for stable live cell observation, and anesthesia equipment. Provides training on numerous different instrument platforms, consultation on experiment design, as well as digital image processing and image analysis. We are a reference site for several companies including TissueGnostics. CAM is one of three Nikon Imaging Centers in the US, allowing us access and excellent support from Nikon to develop innovative solutions for the cutting edge imaging needs of users. This relationship has allowed our users to push super-resolution technologies to permit multi-color, 3D and live-cell applications. Additionally, we have been working together with Nikon to add confocal laser scanning to a low magnification upright dissection microscope, which is particularly useful to researchers interested in visualizing thick samples (such as epidermal raft cultures) at increased cellular resolution. We are also currently expanding our full service electron microscopy offerings. We currently support TEM and SEM sample preparation, immunogold labeling, platinum replicas, and CLEM.
University of Minnesota University Imaging Centers Core Facility
Center composes network of core imaging facility locations for advanced optical imaging and basic electron microscopy located within the AHC/Medical School (1-151 Jackson Hall, Minneapolis) and College of Biological Sciences (23 Snyder Hall, St. Paul) on the University of Minnesota Twin Cities Campus.UIC cores serve internal and external research clients in design of imaging experiments, choice of and training on suitable imaging systems, and subsequent image processing, visualization and analysis.Provides advanced imaging systems including macro spectral confocal microscopy,wide-field light and fluorescence microscopy, spinning disk confocal, laser-scanning confocal microscopes, multi photon/Second Harmonic Generation microscopes, total internal reflectance microscope, laser capture micro-dissection, live cell imaging systems, scanning and transmission electron microscopy, whole animal fluorescence, bioluminescence and chemiluminescence imagers, gel, print and film scanners,poster printers, full sample preparation capabilities.
McGill University Primary Airway Cell Biobank Core Facility
McGill University Primary Airway Cell Biobank
Nonprofit facility providing researchers worldwide with standardized, high-quality primary airway cells from normal and large variety of airway diseased donors with different genetic backgrounds, are essential for improving our understanding of CF and other respiratory diseases and for translational research to develop new therapeutic agents.The PACB is certified by the UBC Office of Biobank Education and Research Biobank Certification Program.
Allen Mouse Brain Common Coordinate Framework
The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas
3D reference atlas to use with online datasets or as standalone resources. Can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D. Intensity and shape population average template brain serves as basis of reference space and coordinate system. Average was constructed at 10 um voxel resolution by interpolating high resolution serial two photon tomography images from young adult C57BL/6J mice. Using multimodal reference data, entire brain was directly parcellated in 3D, labeling every voxel with brain structure from Allen Mouse Reference Atlas Ontology. In the 2017 release, the parcellation spanned 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures.
Developed for Allen Reference Atlas and follows terminology from Brain Maps: Structure for the Rat Brain (Swanson, 2004, 2018). The ontology has been subsequently extended and revised to also serve as structure ontology for Allen Mouse Common Coordinate Framework.Defines hierarchical partonomy of anatomical structures of adult mouse brain. At top level, brain is divided into gray matter, fiber tracts and ventricular systems. Gray matter is subdivided into cerebrum, brain stem, and cerebellum, which are themselves organized into subregions in hierarchical tree.
Software homology based protein function annotation tool that integrates multiple reference data sources. Custom reference data sources can also be added.Accepts as input aminoacids sequence fasta. Customizable and is available on Linux.
Software Perl toolkit for 10X single cell immunoglobulin repertoires analysis. Uses raw reads or output of Cellranger as input and performs reads quality control, immunoglobulin sequence assembly, sequence annotation, heavy- and light- chain pairing, computing statistics and visualizing.
Software tool as statistical calculator that conducts statistical analyses, interprets results, and makes suggestions for presenting results in reports, journal articles and dissertations.
Open source Python platform for machine learning based analysis and classification of adaptive immune receptors and repertoires. Supported by ELIXIR Norway.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 15, 2021. Software tool for analysis of cross-linked peptides.
Resource no longer available. Documented on March 15, 2021. Software tool to identify cross-linked peptides from complex samples and large protein sequence databases by combining isotopically tagged cross-linkers, chromatographic enrichment, targeted proteomics. Reduces search space by upstream candidate peptide search before recombination step.Search engine for cross-linked peptides from complex samples.
Scientific discovery game about neuroscience that helps to build models of brain cells.
Multilayer Connectome of Caenorhabditis elegans
Networks of extrasynaptic aminergic and peptidergic interactions in C. elegans
Crosslink Network Maps With Residue Resolution
Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains.
Web tool for creating digital profile of scientific discoveries in article and connecting them to related research. Authors describe molecular interactions supported by their results, letting researchers explore first hand account of article findings and connect to related articles and knowledge. Web based system for scientists to compose structured representation of networks of interactions between genes, their products, and chemical compounds, represented using power of formal ontology.
Software Python library for secure and private Deep Learning. Decouples private data from model training, using Federated Learning, Differential Privacy, and Encrypted Computation and Homomorphic Encryption within main deep learning frameworks. Used for computing on data you do not own and cannot see.
Translational Research in Neuroimaging and Data Science datasets
Neuroimaging datasets available from TReNDs including resting state MRI.
Software tool for management of animal facility data by Scionics Computer Innovation GmbH. Used by laboratory animal facilities. Used by researchers, animal house managers, animal keepers and others to access their data from same source. Available in English, French, German, Italian, Portuguese and Spanish.
Proprietary software package for data analysis by BMG Labtech.
Aperio VERSA Digital Pathology Scanner Software
Software tool designed to support Leica Biosystems Aperio VERSA scanner. Digital pathology scanning software. Used for diverse imaging needs for digital pathology.
Software tool as interface for reading and writing SAM files. Python module to read and manipulate mapped short read sequence data stored in SAM/BAM files. Lightweight wrapper of htslib C-API.
Software Python wrapper for bedtools. Wraps and extends BEDTools and offers feature level manipulations from within Python. Flexible Python library for manipulating genomic datasets and annotations.
Software tool to analyze morphological characteristics of complex roots.
Software tool as MRI brain segmentation system to obtain automatically volumetric brain information from RI data. Works in automatic manner and is able to provide brain structure volumes without any human interaction.
Software R package to analyze immune cell migration data. Supports pipeline for track analysis by providing methods for data management, quality control, extracting and visualizing migration statistics, clustering tracks, and simulating cell migration.Available measures include displacement, confinement ratio, autocorrelation, straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks, steps, or subtracks with varying length.
Software Python library to manipulate Neuroimaging Data Model.
University of Nebraska Medical Center Computational Chemistry Core Facility
University of Nebraska Medical Center Computational Chemistry Core
Core offers wide variety of services, including access to the Schrodinger platform and high-throughput computing. Services include examining molecular structures and mechanisms in atomic detail and provide graphically rich analysis suitable for inclusion in publications and grants.
University of Nebraska Medical Center Nebraska Biobank Core Facility
Nebraska Biobank is made up of residual blood samples from volunteer patients. Serum, Plasma, and DNA are recovered from the consented samples and stored for future research studies.Deidentified data from the Electronic Health Record (EHR) such as age range, diagnosis, and medications are linked to the stored samples. Any faculty member from the University of Nebraska system may request samples from the biobank for their research projects but all requests are subject to feasibility and scientific merit review.Offers sample management services to investigators for clinical trials and registries.
Laval University Proteomics Platform Core Facility
Universit� Laval ULaval_CHU_Proteomics Platform
Proteomics platform offers sample preparation, protein identification, post-translational modification (PTM) protein analysis, protein quantification (Label Free, Label based and tarteted proteomics by MRM or PRM) by mass spectrometry and statistical or functional bioinformatic analyses.
Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination.
Software tool used to manually segment and label 3D point cloud of corn and other crops.
Software tool as modular multi agent framework to detect concept drifts from batch or streaming data.
Software Python package enabling small teams to test parameter space in distributed and automated manner.Library to assist with running parameter sets across multiple systems. Provides tool set and pipeline that make organizing, running and analyzing large amount of parameters easier.
Innovadyne Technologies | Nanodrop 2 Pipetting System
Liquid handling system designed for high precision pipetting.
Provides laboratory chemicals, specialty chemicals, and clinical diagnostic reagents based on advanced technological development from academia, companies and medical fields.
Develops and distributes premium scientific equipment to enhance research of neurons, neuronal circuits and animal behaviour.
Specialized Ceramic blades for Campden Vibrating Microtomes. These blades are honed with single bevel for superior slicing, particularly in tissue from older animals. They also work with the VT100S, Leica Biosystems.
Major US manufacturer of specialized physiological research laboratory equipment with current headquarters in Holliston, Massachusetts.Now part of Harvard Bioscience family of companies.
Molecular Devices | DigiData 1440 digitizer
Digitizer for electrophysiology experiments, to send and receive signals from microelectrode amplifiers, and to interact with peripheral instruments such as solution changers and stimulators. High resolution, low noise digitizer intended for precision scientific applications. Digidata 1440A digitizer communicates with the host computer using USB 2.0. It is plug and play device, so it is automatically recognized by Windows.
MEA amplifier for upright microscopes.Raw data from up to 60 electrodes of microelectrode array is amplified by 60 channels of filter amplifiers that are built very small and compact using Surface Mounted Devices technology.
Molecular Devices | MultiClamp 700A Microelectrode Amplifier
Computer controlled microelectrode current and voltage clamp amplifier for electrophysiology and electrochemistry. It is a versatile instrument capable of single-channel and whole-cell voltage clamping, current clamping, ionselective electrode recording, voltammetry and amperommetry.
Molecular Devices | Digidata 1322A Digitizer
Digitizer intended for precision scientific applications.Digitizes at aggregate speed of 500 kHz. It provides sixteen multiplexed, 16-bit analog inputs and two nonmultiplexed, 16-bit analog outputs.
Sutter | P-1000 Next Generation Micropipette Puller
P-1000 include diagnostic testing of all puller components, built in error detection of air pressure loss or filament burnout, easy access to ramp test, measurement of jaw temperature, and access to previous pull results with heat on times for each cycle of program.Help topics are pre-loaded to assist with on-site troubleshooting and built-in glossary includes text, pictures, and diagrams explaining terms used in micropipette fabrication. Rotary dial is offered as alternative to keypad for numerical entry.
BLINK 2.0 Eyeblink conditioning analysis
Scientific setup used for both eyeblink conditioning and prepulse inhibition of startle reflex in animals. Used to measure kinetic and frequency domain properties of conditioned and unconditioned eyelid responses in freely moving mice. Allows determination of eyelid movements in time and space while using air puff as unconditioned stimulus.
ISCAN | ETL-200 Primate Eye Tracking Laboratory
Images and tracks one eye of human subject or lower animal at operator selected sampling rate at 120 Hz or 240 Hz. Contains all components to record eye movements as subject views imagery presented on computer screen or other visual display device. Configured to track one eye and allows for up to approximately one to two inches of side to side or up and down head movement.
Supplier of high purity metals, alloys and polymers including Aluminium, Indium, Platinum, Silver, Gold, Copper, Indium, Iridium, Rhodium and Tantalum in multiple forms, dimensions and purities.
Manufacturer of flexible shaft rotary power tools including specialized motors, handpieces, attachments, and accessories.
Manufactures range of high quality agonists, antagonists, inhibitors, activators, antibodies and fluorescent tools to support life science research.
Open source software tool as multiple choice microscopy pipeline for multiplexed whole slide imaging and tissue microarrays. Scalable, modular image processing pipeline for multiplexed tissue imaging. Used for performing sequential steps needed to transform large, multi channel whole slide images into single cell data.
dkNET service that assist researchers in generating research hypotheses. Brings together collection of online tools that will allow researchers to explore different dataset and utilize analytics and visualization tools. Hypothesis Center phenotype-genotype analytics module is currently performed utilizing data from Signaling Pathways Project , and Mouse Metabolic Phenotyping Centers, and it brings SPP and MMPC together to connect cellular signaling pathways and gene expression with physiological phenotypes. Used to find gene sets and signaling pathways relevant to mouse phenotypes for generating hypotheses.
UNet Model for Identifying Cells and Segmenting Tissue
Universal Models for Identifying Cells and Segmenting Tissue
Software tool as set of deep learning nuclei instance and semantic segmentation models that have been trained on 6 human tissue types: tonsil, small intestine, ovary, and cancers of brain, colon, prostate, and lung stained with Hoechst 33342 and combination of lamin B2 and nucleoporin98. Includes manually curated annotations as well as novel concept of introducing intentionally defocused and saturated images for robustness.
Software tool as testbed for text mining methods that assess Randomized Controlled Trial transparency, rigor, and reliability, and support methods for peer review and authoring assistance.
Exemplar Microscopy Images of Tissues ( and Tumors)
Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets.
Software R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams. ShinyApp for producing PRISMA 2020 compliant flow diagrams.
Software package contains data analysis and processing tools required for rapid and effective interrogation of imaging data. Allows for full integration of full spectrum molecular imaging experiments on SYNAPT family platforms, as well as DESI imaging on Xevo G2-XS QTof Mass Spectrometers, using single user interface.
Software for analyzing mass cytometry (CyTOF) data.
Software tool to subset samples in FlowJo software.Reduces number of events in data matrix by generating subpopulation containing cells distributed regularly or randomly throughout selected parent population.
Open source software for zebrafish eye tracking and visual stimulation. Used to evoke and track zebrafish eye movement in multiple larvae.Modular software able to control multiple aspects of oculomotor experiment, from stimulus presentation and data acquisition to eye tracking and data analysis, or to simply track eyes in existing video of larval zebrafish. In both cases, eyes of up to six fish can be tracked in parallel.Users can choose to control several alternative setups and optional hardware.
Software tool as interactive explorer for single cell transcriptomics datasets. Used to explore and visualize high dimensional single cell datasets in interactive way. Can visualize gene expression at level of entire dataset or particular subset of cells to help identify cell types, which can in turn help identify diseases. Enables plotting gene expression level against another gene to compare how these different genes are expressed across dataset. Open source cell visualization tool integrates with tools like SciPy and Jupyter.
Software tool as open simulation environment for cardiac electrophysiology. Cardiac electrophysiology simulator for in silico experiments. Offers single cell as well as multiscale simulations from ion channel to organ level. Includes functions for pre and post processing of data as well as visualization.
Software tool to produce graph using Graphviz from Ant build files forked from sourceforge vizant.
Software package provides R interface to NCBI EUtils API, to search databases like GenBank and PubMed, process of those searches. Provides functions that work with NCBI Eutils API to search, download data from, and otherwise interact with NCBI databases.
Software R package for hierarchical clustering with p-values. Used for assessing uncertainty in hierarchical cluster analysis.
Automating Biomedical Evidence Synthesis
Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials.
University of Michigan Center for Structural Biology Core Facility
University of Michigan Center for Structural Biology
University of Michigan�Ann Arbor Center for Structural Biology
Comprehensive structural biology resource.Provides high throughput protein laboratory for protein engineering, protein purification facilities for small- and large-scale protein production, macromolecular crystallization and crystallography laboratories for solving crystal structures of biological molecules, and X-ray facility with access to high energy synchrotron radiation. Provides expert guidance to researchers through every stage of project, collaborating and consulting with researchers who use the facilities. Service categories are Chemical, Material and Protein Characterization, Molecular Biology. Services include Cloning, Crystallization, Differential thermal analysis, Drug development, NMR (small molecule), PCR, Protein crystallography, Protein engineering, Protein production, Structure determination, Xray.
Open source administration and development platform for PostgreSQL.
Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems.
Inverted microscope delivers unparalleled 25mm field of view. With this FOV, the Ti2 maximizes sensor area of large format CMOS cameras without making compromises, and significantly improves data throughput. Stable, drift free platform designed to meet demands of super resolution imaging with high speed imaging applications. Status of each sensor is automatically recorded during acquisition, providing quality control for imaging experiments and enhancing data reproducibility.
Software tool as haplotype resolved de novo assembler for PacBio Hifi reads. Can assemble human genome in several hours.Introduces new graph binning algorithm and achieves haplotype resolved assembly given trio data. Takes advantage of long high fidelity sequence reads to represent haplotype information in phased assembly graph. Preserves contiguity of all haplotypes.
University of Wisconsin-Madison Advanced Genome Editing Laboratory
University of Wisconsin Madison Advanced Genome Editing Laboratory
University of Wisconsin Madison Genome Editing Core Facility
University of Wisconsin Madison UW-Genome Editing & Animal Models
UW Biotechnology Center Advanced Genome Editing Laboratory
Provides services and expertise to unlock genome editing tools to advance your research. Routinely generates new genome edited models, particularly mouse, rats, swine, and cell lines, as well as supports in vivo editing, novel preclinical therapeutic strategies, pooled lentiCRISPR screening, and other applications.
Pediatric Obesity Microbiome and Metabolism Study
Biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification.Biorepository is available as shared resource.
Software tool as computer aided design software that architects, engineers, and construction professionals rely on to create precise 2D and 3D drawings.
Compact and simple to use LED illuminator for microscopes. Provides broad spectrum of illumination, covering excitation bands of fluorophores such as DAPI, CFP, Aqua, FITC, TRITC, TxRed, Cy5 and many more. Operation is by manual control pod with instant on and off, irradiance control, with remote control available via USB or TTL trigger.
Software tool as data science notebook. Jupyter compatible with real time collaboration and running in the cloud.
Portfolio of software tools that addresses all aspects of product development process 3D design, simulation, manufacturing, data management and more. Combines speed and simplicity of direct modeling with flexibility and control of parametric design.
Software validation tool for Portable Encapsulated Projects or PEPs in python.
Software python package for reading Portable Encapsulated Projects or PEPs in R.
Software python package for reading Portable Encapsulated Projects or PEPs in python.
Software R package for analysis of short sequenced reads. Framework for small RNA analysis in R using Sequence Based Counts.Can be applied on any type of data generated by large scale nucleotide sequencing, where user wish to maintain sequence integrity during whole analysis.
Software application for Phantom cameras. Controls every camera function on every Phantom camera model. Fine-tune resolution, frame rate, exposure, memory segmentation, trigger modes and automatic functions prior to recording. PCC also makes it easy to work with synchronized cameras, manage Phantom Cine raw files and convert files to format for final project.Software is compatible with Windows 7 Pro and Windows 8.1 and Windows 10, for both 32 and 64-bit operating systems.
Small, sturdy camera with all standard Phantom features and image quality. Memory can be partitioned up to 63 times to deliver images from 1.3 Mpx sensor with 12-bit depth and tightly packed 5.6 micron pixel size. Miro C110 is capable of 1295 fps at 720p HD and up to 52445 fps at reduced resolutions.
Oxygen controlled hood for handling cells under physiologic or pathophysiologic conditions. Double door entry allows import/export of materials without perturbation of experimental conditions. Optional control of carbon dioxide as well. Receives C-Chamber Incubator Subchamber to transfer cells without exposure to room air.
BioSpherix | I Glove Incubator and Oxygen Glovebox chamber
Oxygen controlled Glovebox for both incubation and handling of cells in controlled physiologic or pathophysiologic conditions when used together with third party incubator. Carbon dioxide control is optional. Hosts C-Chamber Incubator Subchamber for transport of cells without exposure to room air.
Web application that uses annotated reference dataset to automate processing, analysis, and interpretation of new single cell RNA-seq experiment. Azimuth leverages reference based mapping, pipeline that inputs counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression. All results can be explored within the app, and easily downloaded for additional downstream analysis.
Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls.
Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples.
Software tool that scores components of pan genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes.Designed to take gene presence absence.csv file from Roary as well as traits file created by user and calculate associations between all genes in accessory genome and traits. It reports list of genes sorted by strength of association per trait.
Software package and script for calculation of genome scale average nucleotide identity. Python3 module that provides support for calculating average nucleotide identity and related measures for whole genome comparisons, and rendering relevant graphical summary output. Where available, it takes advantage of multicore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons.
Software tool for analyzing bacterial pan genome profile.Used to calculate pan genome profile of population with dozens of or hundreds of strains at extremely low time cost.
Software pipeline for pangenome investigation. Shares information between genomes to correct errors. Can call large structural variants.Fast and scalable to over 10k bacterial genomes.
Software tool for fast alignment free computation of whole genome Average Nucleotide Identity . Supports pairwise comparison of both complete and draft genome assemblies. to calcualte the average nucleotide identity (ANI) between your samples.
Software tool for Bayesian inference of ancestral dates on bacterial phylogenetic trees. Performs Bayesian dating of nodes of bacterial phylogenetic tree. This typically involves simultaneous Bayesian estimation of molecular clock rate and coalescent rate. Additional features include inference of root location, lost sampling dates and different evolutionary models.
Software tool for mass screening of contigs for antimicrobial and virulence genes. Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.
Software R package provides functions for facilitating survival analysis and visualization.
Software tool to quantify relative gene expression across large number of genes and samples. Allows to analyze gene expression data on any current Applied Biosystems real time PCR instrument.
Applied Biosystems QuantStudio 12K Flex RT PCR Software
QuantStudio 12K Flex Real Time PCR Software
Software supports QuantStudio12K Flex Real Time PCR System to open and analyze experiments. Enables to set up experiments, send experiments to instrument, control thermal cycling process in instrument, collect data and analyze collected data.
Thermo Fisher: Applied Biosystems | Veriti 96-Well Thermal Cycler
Thermocycles with added control of VeriFlex technology, with six independent temperature blocks that provide precise control over PCR optimization. Color touch screen simplifies setup and use. Optional setups for fast or standard PCR methods provide with flexibility to shorten your PCR cycling times. Equipped with astandard 0.2 mL block configuration.Will be discontinued on December 31, 2021.
Thermo Fisher: Applied Biosystems | QuantStudio 12K Flex RealTime PCR System
QuantStudio 12K Flex Real-Time PCR System
System can simultaneously run up to four 3072 reaction QuantStudio 12K Flex OpenArray plates in about four hours. When combined with the QuantStudio 12K Flex OpenArray AccuFill System, can produce up to 110000 data points or more in 8 hour day. Has touch screen interface and comprehensive software analysis tools for gene expression, genotyping, and digital PCR increase productivity. Has five interchangable block formats including: OpenArray plate, TaqMan Array card, 384-well, and 96-well (0.1 and 0.2 mL).
Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex.
Perkin Elmer | Opera Phenix Plus High Content Screening System
Opera Phenix Plus system for high throughput high content assays, phenotypic screening, assays using complex disease models, such as live cells, primary cells and microtissues, and fast response assays like calcium flux or cardiomyocyte beating.Optical design lets you generate information through confocal imaging and at higher throughput through simultaneous acquisition. Delivers speed without compromising sensitivity. Uses Harmony High Content Imaging and Analysis Software to quantify complex cellular phenotypes. Harmony software is designed for PerkinElmer high content screening systems.
University of New Hampshire University Instrumentation Center Core Facility
University of New Hampshire University Instrumentation Center
University wide core facility offers NMR,SEM including FIB, EBS, EBSD, Tensile Stage,Confocal,X-Ray Photoelectron Spectroscopy,X-Ray Microscope aka Micro CT, Expert analysis of research and industrial samples,Training in scientific instrument operation and data analysis, Maintenance, repair, and calibration of instruments,Specialty instrument engineering design and application services,Facilitation of access to scientific instruments throughout the university.
Software tool as cross platform package for population genetic analyses that runs within Microsoft Excel. Offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.Originally developed as teaching tool to facilitate teaching population genetic analysis at graduate level.
Software developed for forensic data analysis. When combined with the Applied Biosystems 3500 Data Collection Software v4.0 and Applied Biosystems STR kits, helps enhance productivity and confidence, as well as IT support and compliance, in HID laboratory data interpretation workflow.
New York State Department of Health Wadsworth Center Advanced Light Microscopy and Image Analysis Core Facility
Advanced Light Microscopy & Image Analysis Core
New York State Department of Health Wadsworth Center Advanced Light Microscopy and Image Analysis Core
Core facility is designed for Imaging living cells or tissues, Fluorescence imaging, Image analysis. Provides imaging of adherent cells or tissue fragments,drug delivery using perfusion chamber, gas exchange for the growth media, Rose chambers for imaging, image processing and analysis software to assist in data analysis and interpretation.
Memorial Sloan Kettering Cancer Center Flow Cytometry Core Facility
Memorial Sloan Kettering Cancer Center MSKCC-FCCF
Provides advanced instrumentation as well as high level technical and scientific expertise in multi dimensional Flow Cytometry and Cell Sorting, to facilitate science, improve the quality, and advance the scope of MSK research.
East Tennessee State University Quillen College of Medicine Molecular Biology Core Facility
Core provides Genomics, Transcriptomics and Proteomics Services to researchers.
University of Pennsylvania Penn Electronic Design Shop Core Facility
Provides electronic design services and medical device development including Embedded systems (Firmware, Hardware, and Software solutions), Electronic prototype design services,PLM (Product Life-cycle Management) for electronic design. Supports Product Management from concept to final customer deployment. Expertise to make electronic device complete consumer product that can be deployed for mass production,Sustaining and maintenance engineering for electronic products,Consulting services in the areas of CE/FCC compliance, EMI, and ESD for lab products and certain consumer electronics,Troubleshooting and repair of released electronic systems.
BioSpherix | I-Hood Protective Incubator Hood
Protective hood for removing fumes which may escape incubator.
OxyCycler C42 Dynamic O2 and CO2 Subchamber Controller
Incubator controls dynamic or static levels of O2 and CO2 and offers O2 and CO2 profiling. Dual channel and dual gas controller for incubators and C-Chambers. Oxygen and carbon dioxide control is managed via independently programmable channels for optimum control. Applications of OxyCycler C42 incubator controller include intermittent hypoxia, graded hypoxia, and timed hyperoxia.Comes with computer software for easy interface, real time trend charting, data logging, and remote operation.
O2 and CO2 controller that also features relative humidity limit control and monitoring of temperature conditions when used in combination with C-Chamber Incubator subchamber from BioSpherix.
BioSpherix | Oxycycler GT4181C Controller
and Carbon Monoxide Subchamber Controller System
Carbon Monoxide, O2, and CO2 controller that also features limit control of relative humidity and monitoring of temperature conditions when used in combination with C-Chamber Incubator Subchamber from BioSpherix. This system also features secondary monitor for Carbon Monoxide and may be used in combination with I-Hood Incubator Hood from BioSpherix for ventilating fumes.
BioSpherix | Oxycycler GT4181N Controller
and Nitric Oxide Subchamber Controller System
Nitric Oxide, O2, CO2 controller with limit control of relative humidity and monitoring of temperature conditions when used in combination with C-Chamber incubator subchamber from BioSpherix. Features secondary monitor of Nitric Oxide and may be used in combination with I-Hood Incubator Hood from BioSpherix in order to ventilate fumes.
BioSpherix | OxyCycler GT4181CN Controller
and Nitric Oxide Subchamber Cell Culture System
Carbon Monoxide, Nitric Oxide, O2, and CO2 controller with limit control of relative humidity and monitoring of temperature conditions when used in combination with C-Chamber incubator subchamber from BioSpherix. Features secondary monitors for both Carbon Monoxide and Nitric Oxide and may be used in combination with I-Hood Incubator Hood from BioSpherix to ventilate fumes.
University of California, Santa Cruz Chemical Screening Center Core Facility
Shared research facility dedicated to improving human health by finding next generation of therapeutic agents against wide variety of diseases. The CSC is driving innovation in drug discovery by bringing together experts in drug screening with cell and molecular biologists engaged in disease research. Has assembled diverse collection of compounds derived from marine organisms, setting our facility apart as a leader in the discovery of therapeutic natural products.
Phenotypic variation of transcriptomic cell types in mouse motor cortex.Repository contains analysis code and preprocessed data.Data includes exonic and intronic gene counts, extracted electrophysiological features, extracted morphological features and z-profiles. Datasets with recorded at room temperature and recorded at physiological temperature.
SYstems biology Computational Analysis and MOdeling Research Environment
Web browser based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Allows database supported modelling, basic model checking and estimation of unknown kinetic parameters based on protein structures. Integrates different online applications as well as locally installed software. Provides user guidance for sequence of steps associated with model building, model checking, simulation and analysis of results.
Software MATLAB toolbox for mathematical modeling of time dependent dynamical systems that can be expressed as chemical reaction networks or ordinary differential equations. Allows to automatically calibrate model parameters by fitting model to experimental measurements.Fits model to several data sets at once (multi-experiment fitting). Accessible via graphical user interfaces, from command line and scripts,determines parameter identifiability and confidence intervals,imports and exports SBML models and supports biochemical network modeling.
Initiative to develop community, and establish internationally sustained data and model management service to European Systems Biology community. Web accessible repository for storing and sharing data, models, protocols and publications relating to systems biology research projects.Repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) data, operating procedures and models.Contains data, SOPs models, publications and other research assets from large research programmes and independent projects, including SysMO consortium, ERASyAPP and Digital Salmon. Public service for users to upload and publish research assets.
Software tool for computing scaffold ordering that maximizes colinearity across collection of maps including genetic, physical or comparative maps into final chromosome build. Robust scaffold ordering based on multiple maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with input maps. Used in building high quality genome assemblies.
Forsyth Institute Advanced Microscopy Core Facility
The Forsyth Institute Forsyth-Advanced Microscopy Core
Offers microscopy imaging services to both internal and external users in the greater Boston area. The facility is equipped for live cell imaging, laser scanning confocal and super resolution microscopy. Common sample types imaged in the facility are live and fixed bacteria, biofilms, embedded soft tissue, cleared tissue, and mineralized tissue and samples can be labelled or label free. One area of expertise is imaging many fluorophores simultaneously using spectral imaging and linear unmixing. In addition to instrument training, we can also provide advice for sample preparation and image analysis. In some cases, we are able to provide full-service imaging for customers.
Stress controlled rheometer.THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 19,2026.
Penn State College of Medicine Genome Sciences Core Facility
Genome Sciences and Bioinformatics Facility
Pennsylvania State University Genome Sciences and Bioinformatics Facility
Provides consultation, instrumentation and services in genomic, epigenomic and transcriptomic studies, analysis of candidate SNPs and mRNAs to whole genome, exome, epigenome and transcriptome sequencing. Services are also available for variety of study designs extending from few laboratory samples to large clinical projects involving hundreds or thousands of samples.Bioinformatics service is available for data analysis.Facility receives either tissue, DNA/RNA or customer generated NGS libraries. Samples are processed based on agreement reached during consultations on design of experiment.
Allen Brain Map Cell Type Nomenclature CCN
Allen Cell Type Common Cell type Nomenclature
Framework for creating brain cell type nomenclature, and include examples using published datasets. System allows designation of cell types with or without hierarchical organization. Nomenclature convention initially applied to brain cells and types, is intended to encompass existing naming strategies used in publications across diverse research teams. Allows tracking of many different taxonomies, including those from different organ systems or across diverse areas of bioscience.
Portal devoted to suite of MORF reporter mice labels of Cre positive neurons and glia distributed stochastically throughout brain and can be imaged with endogenous fluorescence (mNeonGreen in MORF1 and EGFP in TIGRE-MORF) or stained for multivalent immunoreporter (Spaghetti Monster fluorescent protein V5, or smFP-V5, in MORF3). MORF technology used to label and reconstruct thousands genetically defined cells per brain for large scale, unbiased classification and quantitative analyses of CNS cell types brainwide.
Open source database used for analyzing and modeling compound interactions with human and animal organ models.Platform for experimental design, data management, and analysis, and to combine experimental data with reference data, to enable computational modeling. Resource for relating in vitro organ model data to multiple biochemical, preclinical, and clinical data sources on in vivo drug effects.
Controls CO2 levels for most physiologic concentrations and may be connected with either C-Chamber Incubator Subchambers or A-Chamber Animal Chambers from BioSpherix. May also be connected with chambers which are either home built or are available from other manufacturers. These include thermal incubators, flush boxes, culture chambers, glove boxes, and other semi sealed enclosures.
GE | IN Cell Analyzer 2000 cell imaging system
GE Healthcare IN Cell Analyzer 2000 cell imaging system
Cell imaging system for entire high content analysis (HCA) workflow. Delivers high performance hardware, software, and expert support for cell analysis.
BioSpherix ProOx 110 Compact O2 Controller
Compact, versatile O2 controller.Controls Oxygen and may be used with either C-Chamber Incubator Subchamber or A-Chamber Animal Chamber from BioSpherix. May be used with home-built or other manufacturers chambers.
ProOx 360 High Infusion Rate O2 Controller
Versatile high infusion rate O2 controller.Controls Oxygen and may be used with BioSpherix C-Chamber Incubator Subchamber, C-Shuttle Glove Box, I-Glove Incubator Glove Box, Xvivo System Model X3 Cytocentric Cell Incubation and Handling Platfrom, or A-Chamber Animal Chamber. Featuring capability to infuse gas over range 1-140 SCFH, may be used together with chambers which are either home built or are available from other manufacturers.
ProOx C21 Oxygen and Carbon Dioxide Subchamber Controller
Compact O2 and CO2 Subchamber Controller used together with C-Chamber Incubator Subchamber from BioSpherix or chambers from other manufacturers.
Barrow Neurological Institute Flow Cytometry and NanoString Core Facility
Barrow Neurological Institute Flow Cytometry and NanoString Facility
Flow Cytometry and NanoString Core Facility
Offers RNA integrity measurements and gene expression assays.Ask us how NanoStrings direct measurement of target molecules can help you avoid amplification bias in your studies.Facility offers flow cytometry and cell sorting services. Staff can help with panel design all the way through data analysis and one-on-one education about flow theory and applications.
Penn State Hershey College of Medicine Flow Cytometry and Cell Sorting Core Facility
Penn State Hershey College of Medicine PSU-College of Medicine Flow Cytometry Core
PSU-College of Medicine Flow Cytometry Core Hershey
Offers Flow Cytometry analysis, Cell sorting, Flow Imaging analysis.Available cytometers include 4-color BD FACSCalibur,10-color BD FACSCanto 10-color Amnis ImageStream X Mk II imaging cytometer,Special-order 16-color BD LSR II,16-color BD LSR Fortessa,17-color BD FACS Aria SORP high-performance cell sorter,23-color BD FACSSymphony.
University of California at Santa Cruz Life Sciences Microscopy Center Core Facility
Core facility affiliated with Institute for Biology of Stem Cells.Provides imaging instrumentation to biology research community including personalized assistance on various aspects of imaging.Offers assistance in experimental design,training on shared microscopes, image visualization and image analysis.
Large field of view, high resolution 5.5 megapixel sCMOS camera, ideal for research and OEM usage. Zyla 5.5 offers 100 fps frame rate and ultra low noise performance, in compact design.USB 3.0 version is available, offering up to 40 fps and industry fastest ROI speeds.
Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.
Software R package provides functions for creating and customizing ggplot2 based publication ready plots.Used for creation of ggplot2 based graphs.
Software R package to infer copy number variation from single-cell RNA-seq data.
Compact exposure masking system is UV-LED masking system equipped with LED based optical head, collimated and homogeneous.One level mask aligner. Its masking function enables to reach resolutions less than 1um. This system is compatible with any of photoresists such as AZ series, Shipley series, SU-8 and K-CL series.
Open source software tool as collection of image processing algorithms implemented in Python programming language.Image processing library that implements algorithms and utilities developed by active, international team of collaborators.
Provides connection of LineUp series modules to PC for software control to use Fluigent Software.
Flow sensor for use with any flow control system. Unit to monitor flow rates in any microfluidic system with precision and accuracy.
System for pressure based flow control. Enables to control or monitor flow rate as well as dispense volume. When combined with LINK module capabilities are extended by using Fluigent software to benefit from automation or live monitoring and recording of data. Flow EZ modules, are available in different pressure and vacuum ranges.
Rockefeller University Cryo Electron Microscopy Resource Center Core Facility
Rockefeller University Cryo Electron Microscopy Resource Center
The Evelyn Gruss Lipper Cryo-Electron Microscopy Resource Center
Offers new cryo-electron microscopy tools available to University researchers, allowing for visualization of three-dimensional structures of molecules and macromolecular complexes in solution.
University of Manchester Electron Microscopy Core Facility
University of Manchester UoM-FBMH_EM_Core_Facility
Offers expertise and equipment tailored for biological samples mostly. Houses four electron microscopes.Preparation laboratory includes range of specialised room temperature and cryo sample preparation equipment, ultramicrotomes and suite of computer workstations for image processing.Electron microscopy staff are available to train and assist.
University of Massachusetts Light Microscopy Core Facility
University of Massachusetts Amherst UMass-Amherst Light Microscopy Facility
Core provides resources for imaging model organisms, tissue, cells, biomaterials, and artificial structures and houses equipment including almost every light microscopy imaging modality presently available. Cell culture facilities are also available nearby as well as other routine items necessary for biological imaging and material imaging. This facility has been designated Nikon Centers of Excellence, thus providing unique opportunity for training, demonstration, instrument development, and research.We excel in use of telemicroscopy through use of remote imaging sessions, remote control of all instruments, and remote data analysis sessions available to all users.Provides training to all users that plan to conduct experimentation. Following an initial consultation in which experimental requirements, expected outcomes, and careful scrutiny of feasibility, training and/or access is arranged through the Director.
University of California, Santa Cruz IBSC Flow Cytometry Core Facility
Santa Cruz UCSC-Institute for the Biology of Stem Cells Flow Cytometry Facility
UCSC-Institute for the Biology of Stem Cells Flow Cytometry Facility
Facility offers multicolor cell analysis by BD LSRII cell analyzer and single cell sorting by BD Biosciences FACS Aria cell sorter. Provides user training for self-op use of BD FACS LSRII analyzer 3-laser and Self-op and Assisted sorting on BD FACS Aria IIU 5-lasers.
Software tool as unified framework for spike sorting. Python framework to unify preexisting spike sorting technologies into single codebase and to facilitate straightforward comparison and adoption of different approaches.Used to reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs.
Web application and standalone application to read, visualize and explore content of NWB:N 2 files.Used to share neurophysiological data in Neurodata Without Borders format.
Software Python toolbox for large scale calcium imaging data analysis and behavioral analysis.Used for motion correction, source extraction, spike deconvolution, and component registration across multiple days. It is suitable for both two-photon and one-photon fluorescence microscopy data, and can be run in both batch and online modes. Contains some routines for analysis of behavior from video cameras.
Software package for analyzing one and two photon calcium imaging datasets.Can be used to create GUI-less, command line ready analysis pipelines. Supports Neurodata Without Borders data standard for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, EXTRACT, etc.). Supports reading and writing NWB movie files with continued integration planned. Supports most major imaging movie file formats: HDF5, NWB, AVI, ISXD [Inscopix], and TIFF.
of widgets for visualization NWB data in Jupyter notebook. Widgets allow you to navigate through hierarchical structure of NWB file and visualize specific data elements. Designed to work with NWB 2.0 files and to be easy to extend.
Software timeseries visualizer and data processing tools for Electrocorticography (ECoG) signals stored in NWB files, for Python.
Software Matlab interface for reading and writing Neurodata Without Borders (NWB) 2.0 files.
Open source software tool as interactive image segmentation filter for multiplex microscopy that aids in identification and removal of cell segmentation instances corrupted by optical and image processing artifacts.
Software framework for analysis of single cell chromatin data. Used for analysis, interpretation, and exploration of single cell chromatin datasets including datasets that co-assay DNA accessibility with gene expression, protein abundance, and mitochondrial genotype. Analysis of single-cell chromatin data including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis, and interactive visualization.
Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.
Software tool as set of analysis pipelines that process Chromium Single Cell ATAC data. Cell Ranger ATAC includes four pipelines relevant to single cell chromatin accessibility experiments.Used to investigate number of chromatin-accessibility signatures.
Software package for estimating absolute rates of molecular evolution and divergence times on phylogenetic tree. Divergence time estimation on phylogenies.
Public knowledge base for information on evolutionary timescale of life. Data from thousands of published studies are assembled into searchable tree of life scaled to time.
Software tool for phylogenomic inference.
Curated component of UniProtKB (produced by the UniProt consortium). It contains hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants.
Software tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed eggNOG v5.0 clusters and phylogenies.
Software tool for assembly free construction of UTRs from short read RNA-Seq data on basis of coding sequence annotation.
Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences.
Open collection of Transposable Element DNA sequence alignments, hidden Markov Models, consensus sequences, and genome annotations.Dfam 3.2 provides early access to uncurated, de novo generated families.
Database of repetitive DNA elements.Database of prototypic sequences representing repetitive DNA from different eukaryotic species. Used in genome sequencing projects worldwide as reference collection for masking and annotation of repetitive DNA.
a package for automated de novo identification of repeat families from genomic sequences Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes.
Software tool for computing scaffold ordering that maximizes colinearity to collection of maps, including genetic, physical or comparative maps into final chromosome build.Robust scaffold ordering based on multiple maps.
Visualization and analysis software for Hi-C data.
Software tool to purge haplotigs and overlaps in assembly based on read depth.Used for haplotypic duplication identification. Designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.
Software tool to combine multiple subreads of same SMRTbell molecule using statistical model to produce one highly accurate consensus sequence, also called HiFi read, along with base quality values. This tool powers Circular Consensus Sequencing workflow in SMRT Link.
Xvivo System X3 Cytocentric Cell Incubation and Handling Platform
Hypoxia cell culture system includes hypoxia incubator and cell culture hood with glove sleeves.
OxyStreamer O2 and CO2 Controller for Live Cell Microscopy
Controller for live cell microscopy provides two identical streams of any mix of oxygen and carbon dioxide gas without use of premixed gas cylinders. Eliminates need for pre-mixed gas. Controller is used primarily to pre-condition perfusion media while simultaneously conditioning headspace above culture.
Animal Cage Enclosures for use in in vivo models that require control of experimental gases such as O2, CO2, NO, or CO. May be used together with gas controllers from BioSpherix. Chamber is outfitted with adjustable ventilation holes which permit ventilation of animal vapors and gases while simultaneously ensuring stable control of experimental conditions within. Available in three standard sizes.
Penn State Hershey College of Medicine cryo-EM Core Facility
Penn State College of Medicine cryo-EM facility
Cryo-electron microscopy (cryo-EM) facility providesTitan Krios cryo-transmission electron microscope that is fully equipped for high-throughput data collection of the utmost quality possible. It has the ability to determine the atomic structure of a single protein or view molecules interacting in their cellular context. Provides guidance, training or data collection for researchers at the College of Medicine.Equipment includes Zeiss LSM 980 Cryo-Confocal Microscope,300 kV Krios Cryo-TEM for SPA and tomography, Equipped with Volta phase plates, bioquantum energy filter and K3 direct electron detector,200 kV thermionic JEOL 2100 for cryo-imaging, cryo-tomography, and standard imaging of stained grids.
Software Python suite to convert electron diffraction images to SMV format. Used in three dimensional electron crystallography.Developed to accomplish tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination.
Forsyth Institute Micro Computed Tomography Core Facility
Core offers micro 3D X-ray imaging of small samples in high resolution and provides images and quantitative analyses of internal structures of ex vivo samples without any destructive procedures.Scanco CT40 system allows for visualization, measurement, and quantification of the structure of mineralized specimens. Contrast reagents permit visualization of soft tissue structures such as blood vessels.System creates 3D model from stack of 2D X-ray images taken around single axis of rotation. High-resolution scanner can capture detail at resolution of 6 to 32 microns. Non- destructive nature of this technology allows investigators to carry out complementary analyses of the same sample. There are two dedicated workstations for analyzing microCT data, the SCANCO analysis software or the Amira software package with XImagePAQ extension.
Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets.
A41OV OxyCycler A41OV Dynamic O2 Animal Chamber Controller
Provides either dynamic or static control of O2 condition for animal modeling when used in combination with A-Chamber Animal Chamber.
Provides either dynamic or static control of O2 and CO2 conditions for animal modeling when used in combination with one or two A-Chamber Animal Chamber(s).
OxyCycler A44C Dynamic CO2 Animal Chamber Controller
Provides either dynamic or static control of CO2 conditions for animal modeling when used in combination with one to four (1-4) A-Chamber Animal Chambers purposes.
BioSpherix | OxyCycler A84XOV Controller
OxyCycler A84XOV Dynamic O2 Animal Chamber Controller
Provides either dynamic or static control of O2 conditions for animal modeling when used in combination with the one to four (1-4) A-Chamber Animal Chambers.
BioSpherix | OxyCycler AT42CO Controller
OxyCycler AT42CO Carbon Monoxide Animal Chamber Controller
Provides either dynamic or static control of parts per million levels of carbon monoxide (CO) conditions in animal models modeling when used in combination with either one or two (1 or 2) A-Chamber Animal Chambers.
OxyCycler AT42N Nitric Oxide Animal Chamber Controller
Provides either dynamic or static control of parts per million levels of nitric oxide (NO) in animal models modeling when used in combination with either one or two (1 or 2) A-Chamber Animal Chambers.
BioSpherix | OxyCycler AT82NN Controller
OxyCycler AT82NN Nitric Oxide Animal Chamber Controller with NO2 Limit Control
Provides either dynamic or static control of parts per million levels of nitric oxide (NO) and limits the undesirable elevation NO2 in animal models when used in combination with either one or two (1 or 2) A-Chamber Animal Chambers.
Open source software for anonymizing sensitive personal data.Supports variety of privacy and risk models, methods for transforming data and methods for analyzing usefulness of output data.
Open source software for analysis of patch-clamp electrophysiological data. Integrated analysis environment including routines for curve fitting, post-synaptic event and action potential analyses, data resampling, filtering, detrending and more.
Northwestern University Center for Advanced Molecular Imaging Core Facility
Northwestern University Center for Advanced Molecular Imaging (CAMI)
Provides access to range of preclinical imaging modalities and support services. These include MRI, nuclear imaging (PET, SPECT, and CT), in vivo bioluminescence and fluorescence imaging, animal housing and prep spaces, and tissue culture. Image analysis services are available, as are software packages (JIM, Amira, Matlab) and a workstation for users to perform their own data analysis. Imaging services can be provided for investigators' own animal models, or animal models can be supplied by the Developmental Therapeutics Core.
Software Python package to merge cross species Illumina iScan genotype data with reference set of data from pre existing source.
Penn State Hershey College of Medicine Clinical Research Biospecimen Core Facility
Process, store and ship clinical trial samples from IRB approved studies. Collect remnant samples for outside company for instrument correlation, validation and specimen type verification with IRB approved protocol. CLIA Waver for urine pregnancy, urine dipstick results for participant study treatment.
University of Jordan School of Nursing; Amman; Jordan
Offers Baccalaureate Degree in Nursing and Ph.D. Nursing Program. Offers specialized and advanced graduate nursing education in Jordan.
ABRF CoreMarketplace project created for core facilities tracking. CoreMarketplace (CM) is searchable list of active core facilities that perform scientific research. The CM was initially created by Vermont IDeA Network of Biomedical Research Excellence (INBRE). CoreMarketplace is associated with Association of Biomolecular Research Facilities (ABRF) which is membership association to sponsor and help members to incorporate new biotechnology into their laboratories.
Portal allows researchers and clinicians to access and work across multiple Common Fund program data sets within digital cloud environment because biomedical research interaction with digital data is changing and no longer can large biomedical datasets be stored or analyzed using local computers and servers. Provides list of tutorials and resources to learn how to perform bioinformatic analyses and access data.
Penn State Hershey College of Medicine MRI Core Facility
PSU COM-Center for Nuclear Magnetic Resonance Research (CNMRR) /MRI Core Facility
MRI and NMR magnetic resonance imaging facility for animal and human research, providing MRI methodologies and expertise for in vivo studies Laboratory space includes biochemical, electronic and surgical suites, and fully equipped machine shop with (2) 3D printers. MRI Core facility has two MRI systems and EEG MRI-compatible system.3T Siemens PRISMA-Fit scanner equipped with True 2 Channel Tx and 64 Channel Rx. The latest RF coil set including a 64 Channel head coil and software packages with full clinical capability.7T Biospec 70/20 as small animal imaging system (Bruker Biospin, Ettlingen, Germany). Latest Hardware and Software. Avance NEO with Paravision 360. Full sensory fMRI stimulation systems:SenSaVue System for visual and auditory stimulation (Invivo Corp, FL, USA), which includes an LCD visual display, audio system, button response unit and software (E-Prime) for paradigm creation, patient management, protocol planning, precise delivery of brain stimulation, and behavioral analysis.ETT Olfactometer with full-programmable 6 independent channels for odor and trigeminal stimulation (ETT, LLC, Hershey, PA).Olfact Smell Test System (Osmic Enterprises, Inc., Cincinnati, OH) is a computerized instrument to test the smell functions of human subjects. The smell functions that can be tested are odor threshold, odor identification, and odor memory.ETT Gustatometer with full-programmable 7 independent channels for taste stimulation (ETT,LLC, Hershey, PA) Eye Link 1000 Plus system via SR Research: The EyeLink 1000 Plus Host PC performs real-time eye tracking at 250, 500,1000, or 2000 samples per second while computing true gaze position on the display viewed by the participant. The Host PC also performs on-line detection and analysis of eye-motion events such as saccades, blinks, and fixations. In addition to the sample data, these events are stored in a data file on the Host PC. They can be sent through the Ethernet link to the Display PC with a minimal delay or output as analog signals (if the optional analog/digital I/O card is installed). From the Host PC, the operator performs participant setup, monitors their performance, and can communicate with applications running on a Display PC.
Penn State Hershey College of Medicine Zebrafish Functional Genomics Core Facility
Penn State Zebrafish Functional Genomics Core
Provides Penn State research community with modern, centralized facility for housing, breeding and performing experiments with zebrafish.Provides physical and intellectual infrastructure for investigators whose research can benefit from use of zebrafish as model system.
Penn State Hershey College of Medicine Transmission Electron Microscopy Core Facility
TEM Facility at Penn State College of Medicine
Transmission Electron Microscopy Facility at Penn State College of Medicine
Provides consultation and training in TEM imaging of biological, chemical, and materials science samples.
University of Massachusetts Medical School Biomedical Imaging Group Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 11, 2025. Interdisciplinary team of engineers and scientists, representing fields of physics, mathematics, and computer science, that combine their expertise in areas such as microscopy, lasers, optoelectronics, applied mathematics, image and signal processing, computer graphics, computer vision, statistics, software engineering, and biophysics, to develop imaging approaches for cell biology. Pioneers in high-resolution 3D imaging using wide-field fluorescence microscopy together with digital image deconvolution, and image visualization and quantitative analysis techniques, especially as applied to statistical analysis of images to determine co-localization of fluorescence markers inside cells.Research includes development and application of light microscopy and imaging in cell biology and biophysics.Developed TESM microscope that combines Total internal reflection fluorescence (TIRF) with Epi-fluorescence Structured illumination to provide new views of trafficking in near plasma membrane domain of cells.Provides custom-built, ultra-high-speed microscope system for imaging dynamics of intracellular calcium channel events, called calcium sparks, that are being found to regulate expanding array of cellular processes. Provides two photon fluorescence microscope for looking deep inside tissue, completing range from molecule to organism. Areas of ongoing technology research include high-speed, high-resolution imaging of live cells and tissues, novel image processing approaches, high-performance computing, and computer graphics.
Software to create and edit sample sheet in order to perform next generation sequencing on Illumina paltforms. Used for MiniSeq, MiSeq, NextSeq 500/550, HiSeq, and NovaSeq 6000 Systems.
Isolator that provides physiologically relevant oxygen as well as low contamination risk cell incubation and handling. Subset of Cytocentric Platform designed for processing and producing cells in compliance with regulatory GMPs. Includes glovebox and tanked gases for atmosphere for controllable humidity and microbial risks. Modular and customizable.
Analyze Spheroid Cell Invasion In 3D Matrix
Software tool to measure area of invading spheroid in 3D cell invasion assay. Can also count and measure area of nuclei within spheroid.
ProCO2 120ppm Animal Chamber Off-Gas Limit Controller
Parts per million limit controller primarily used for assuring consistent and acceptable off gas levels in variety of animal enclosures.
Hood holds any animal lab chambers while continuously sweeping all experiment related off gases away.Used to capture and exhaust gases or vapors which escape from animal chamber and directs them to safe location.Helps to control animal odor in the lab. Available in standard and customized dimensions.
University of California at Santa Cruz CRISPR Core Facility
Facility that provides CRISPR services and expertise to facilitate study of gene function. Services include project consultation, sgRNA design and cloning, lentivirus production, custom CRISPR cell line generation and genome wide CRISPR screen.
Matchmaking platform for clinicians and scientists to facilitate collaborative research on rare and undiagnosed diseases. Used for collaborative projects that advance scientific knowledge and patient care. Currently supports Mouse, Rat, Frog, Zebrafish, Fruit Fly, Nematode Worm, Budding Yeast, Fission Yeast, and E. coli. Used to identify human ortholog of genes in these model organisms and vice versa. Scientists who register in ModelMatcher are asked to classify their genes of interest into Public or Restricted categories.The Match feature will allow Clinicians to obtain information on genes that Scientists classify as both Public and Restricted.
Islamabad Health Services Academy Core Facility
Provides short training courses to in service public health practitioners and professionals.Offers teaching, research, and policy advice in public health in Pakistan.
Software tool to create realistic networks of neurons, synapses placed using touch detection between axons and dendrites.Used to create detailed network of connected neurons, where connectivity is derived from reconstructed neuronal morphologies as well as from more qualitative experimental knowledge. Supports creation of network with connectivity based on touch detection.
Web based portal using web based tools for analyzing real-time qPCR or next-generation sequencing data. NGS modules support analysis of QIAGEN's QIAseq NGS library kits and target enrichment panels.
Software LabView package for two-photon calcium imaging acquisition. Used for controlling two-photon microscope and preprocessing of calcium imaging data.
Calliope calcium imaging processing package
Software package for image processing for MATLAB. Used for processing of calcium imaging data.
Friedrich Miescher Institute data repository
Data repository for Friedrich Miescher Institute for Biomedical Research in areas of epigenetics, quantitative biology, and neurobiology.
Portal for cross sectional study where population based sample of adult cancer patients were recruited for mailed survey (with telephone follow-up of non-responders) to evaluate equivalence of PROMIS measures across socio-demographic and clinical sub-groups.
Platform agnostic networked display architecture 3D
Two photon Calcium Imaging in Mice Navigating Virtual Reality Environment
Two-photon Calcium Imaging in Mice Navigating a Virtual Reality Environment
Behavioral two photon imaging system. Includes two photon scanning microscope, software and virtual reality set up. Used for chronic two photon imaging in mice exploring virtual environment. Tool in neuroscience to allow for chronic measurement of activity of genetically identified cells during behavior.
Software tool for modelling RNA binding protein binding preferences. Used to predict RPB binding sites. Computational RBP binding site prediction framework based on recurrent neural networks. Includes functionalities from dataset generation over model training to evaluation of binding preferences and binding site prediction.
Center for Epigenomics of the Mouse Brain Atlas MethylC Seq Pipeline
Software pipeline that supports processing of multiplexed single nuclei bisulfite sequencing data to detect methylated bases. Alignment and methylated base calling pipeline that trims adaptors, attaches cell barcodes, aligns reads to genome, filters reads based on quality and creates both VCF and ALLC file with Emethylation site coverage.
Software tool as reusable computational framework, enabling simplified access to modern scalable cloud based components. Implements FAIR data principles and extends them to provide fully FAIR Evidence, including machine interpretable provenance of datasets, software and computations, as metadata for all computed results.All objects are assigned persistent IDs, including software.
Software tool based on open source solutions to make deploying microservices easy. Used for deployment of modern IT environments. Allows to expose applications to network in dynamic environment.Traefik Stack by Traefik Labs Inc. as cloud native stack to help enterprises manage their entire network across data centers, on-premises servers and public clouds.Tools options include Traefik Proxy,Traefik Enterprise,Traefik Mesh,Traefik Pilot.
Open source identity and access management solution written in Java. Offers features such as Single-Sign-On, Identity Brokering and Social Login, User Federation, Client Adapters, Admin Console, and Account Management Console by WildFly, a division of Red Hat.
Stardog Enterprise Knowledge Graph platform
Software tool as knowledge graph platform to create flexible, reusable data layer for answering complex queries across data silos. Used for organizing data to highlight relationships between data points. Unifies data based on its meaning, creating connected network of knowledge.
General purpose, document based, distributed database built for modern application developers and for the cloud. Offers Community and Enterprise version of database.MongoDB Community is source available and free to use edition of MongoDB. MongoDB Enterprise is available as part of MongoDB Enterprise Advanced subscription and includes comprehensive support for your MongoDB deployment. MongoDB Enterprise also adds enterprise-focused features such as LDAP and Kerberos support, on-disk encryption, and auditing.MongoDB also offers Atlas,hosted MongoDB Enterprise service option in cloud which requires no installation overhead and offers free tier to get started.
Evidence Graph Ontology extends core concepts from W3C Provenance Ontology PROV-O to describe evidence for correctness of findings in biomedical publications. Semantic data model in EVI is expressed using OWL2 Web Ontology Language.
Open source software tool as 3D finite element grid generator with build in CAD engine and post processor. Provides meshing tool with parametric input and advanced visualization capabilities. Built around geometry, mesh, solver and post processing modules.Specification of any input to these modules is done either interactively using graphical user interface, in ASCII text files using Gmsh own scripting language (.geo files), or using C plus plus, C, Python or Julia Application Programming Interface.
Histo-Cytometric Multidimensional Analysis Pipeline
Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information.
Software tool designed by Data Coordination Platform of Human Cell Atlas to process single-cell RNAseq data generated by Smart-seq2 assays.Processes stranded or unstranded, paired- or single-end, scRNA-seq data from an individual cell.
Alzheimer Disease Preclinical Efficacy Database
Publicly available, searchable, data resource that aims to increase transparency, reproducibility and translatability of preclinical efficacy studies of candidate therapeutics for Alzheimer’s disease. Knowledge platform for dissemination of data and analysis to scientists, from academic centers, industry, disease focused foundations. Provides quick access and visibility to integrated preclinical efficacy data from published and unpublished studies.
Software package for diploid genome assembly analysis. Sequence analysis toolkit for number of different analyses related to diploid genome assembly.
Software tool for read-depth based genome size prediction. Wrapper for genome size estimate methods of Diploidocus.Uses long read depth of coverage and BUSCO single copy orthologue prediction to estimate genome size.
Software tool for BUSCO compilation and comparison. Used for assessing completeness in multiple genome assemblies.Used for assembly comparison designed to be robust to differences in assembly size and base calling quality.
Software tool to evaluate bone strength by considering entire bone as three dimensional structure and applying finite element analysis.
ENVironmental Research Infrastructures Knowledge Management System
Web tool as cluster-level knowledge base that allows different ENVironmental Research Infrastructures (ENVRI) users, such as Research Infrastructures (RI) developers and data managers, to effectively share their technical practices, identify common data and service requirements and design patterns, and facilitate search and analysis of existing RI solutions for environmental RI interoperability challenges.
Software tool as set of scripts for 3' RNA-seq quantification.
ZEISS Lattice Lightsheet 7 imaging system
System for long term volumetric imaging of living cells. Makes light sheet fluorescence microscopy available for live cell imaging at subcellular resolution. Automated system for volumetric imaging of subcellular structures and dynamics over hours and days with protection from photo damage.
Software R package of igraph network analysis library.
Software tool as extension of ggplot2 aimed at supporting relational data structures such as networks, graphs, and trees. While it builds upon foundation of ggplot2 and its API it comes with its own self-contained set of geoms, facets, etc., as well as adding concept of layouts to grammar.
Software R package for basic statistical tests including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. Output of each test is automatically transformed into data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate analysis of factorial experiments. Can compute several effect size metrics.Package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Nikon | ECLIPSE Ti inverted microscope system
ECLIPSE Ti Series of inverted microscopes combined with Nikon NIS-Elements imaging acquisition and analysis software, enables to generate data faster, more easily, and more accurately than ever before.Product Discontinued. Replaced by ECLIPSE Ti2 Series.
Educational microscope. Designed as simple system that reduces fatigue from use over long periods. With structure and anti mold design, offers high quality and accuracy that can be retained for years even in hot and humid environments.
Carl Zeiss Stemi DV4 Series Stereomicroscopes with LED Illumination
Carl Zeiss Stemi DV4 series stereomicroscope.
Collection of web-based software applications that enable users to execute bioinformatics workflows without coding. Turns Jupyter notebooks into fully functional standalone web-based bioinformatics applications. Each Appyter application introduces data entry form for uploading or fetching data, as well as for selecting options for various settings. Once user presses Submit, Appyter is executed in cloud and user is presented with Jupyter Notebook report that contain results. Report includes markdown text, interactive and static figures, and source code. Appyter users can share the link to the output report, as well as download the fully executable notebook for execution on other platforms.
Wikidata metadata curation service. Wikidata service to help create or link author items to published articles.
Software Python package and webapp for interaction with scholarly information in Wikidata. Wikidata profiling service.Wikidata service generating scholarly profiles, e.g. for authors, journals, topics, and organisations.
Web tool to draw chemical structure by PubChem.
Software package for detection and measurement of spontaneous synaptic events. Integrated software package for detection and management of spontaneous synaptic events. Used in neurophysiology to detect spontaneous postsynaptic currents, search and visualize them in custom way, and perform hypothesis testing of retrieved data.
TRAnsforming Nested Collections Efficiently
Software tool as framework for processing nested collection queries. Used to automate difficulties of designing distributed analyses with complex, biomedical data types. Uses query compilation and optimization techniques to ease difficulty of handling nested collections, and is designed for arbitrary, multi-modal analyses of complex data types.
Software tool as ggplot2 extension for alluvial plots. Used to visualize frequency distributions over time or frequency tables involving several categorical variables. Requires user to specify dimensions, either as separate aesthetics or as key-value pairs, relies on separate layers (stats and geoms) to produce strata, alluvia, and alluvial segments called lodes and flows.
VENTANA DISCOVERY ULTRA AUTOMATED SLIDE PREPARATION SYSTEM
Ventana DISCOVERY Ultra IHC/ISH research platform
Immunohistochemistry processor that can be used for immunohistochemistry and in situ hybridization slide preparation and processing. With 30 individual slide drawers, DISCOVERY ULTRA system enables to run both manual and fully automated experiments simultaneously with nosynchronization errors. Provides ability to fully automate broad range of IHC and ISH assays, including FISH, gene and protein IHC/ISH, mRNA ISH and multiplex assays with any combination of IHC and ISH.
Software Python package for spatially defined cellular phenotyping using image segmentation data from linearizable tissue.Software quantitative phenotyping tool intended for regionally defined analysis of Drosophila midguts based on objects detected from microscopy images.
Digital whole slide scanner.400 slide capacity brightfield scanner. High throughput with small footprint. 2x3 slide option available.Aperio AT2 runs on Microsoft Windows 10 operating system.
Automated tissue microarrayer, allowing precise selection and extraction of specific regions of interest on donor blocks and their insertion in recipient blocks.Controlled by TMA Control software.
Quantitative Insights Into Microbial Ecology 2
Software tool as next generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.Enables researchers to start analysis with raw DNA sequence data and finish with publication quality figures and statistical results. Used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities.
System which combines 3D printed open hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. Deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process.
Gait analysis system for quantitative assessment of footfalls and locomotion in rats and mice. System includes corridor that directs free movement in straight line, hardened glass walkway that enables CatWalk XT Illuminated Footprints technology,high speed color camera for spatial and temporal resolution, CatWalk XT software for recording and automated analysis of locomotor ability of rodents.
International data on all cause mortality. Country level data on all cause mortality in 2015–2021 collected from various sources for 94 countries and territories.
Software functional programming tools for R. Used for working with functions and vectors.
GNU Project shell. Sh-compatible shell that incorporates useful features from Korn shell (ksh) and the C shell (csh). Improvements offered by Bash include command-line editing, unlimited size command history,job control,shell functions and aliases,indexed arrays of unlimited size,integer arithmetic in any base from two to sixty four.
Software tool to provide color schemes for maps and other graphics designed by CARTO.Implementation of CARTOcolor palettes in R. It includes four types of palettes: aggregation, diverging, qualitative, and quantitative.
Open source software tool as file archiver with high compression ratio.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 23, 2022.
open source Speech and Music Interpretation by Large-space Extraction
Open source software toolkit for audio feature extraction and classification of speech and music signals. Used for audio analysis, processing and classification especially targeted at speech and music applications, e.g. automatic speech recognition, speaker identification, emotion recognition, or beat tracking and chord detection.Written in C plus plus and runs on desktop, mobile, and embedded platforms such as Linux, Windows, macOS, Android, iOS and Raspberry Pi.
Software tool for fitting kinetic and equilibrium data based on numerical integration of rate equation from any model input user. Simulation and data-fitting software for research and education designed specifically for the field of chemical kinetics.
Database for classifying allergenic proteins into protein families.You can browse lists of allergen families restricted by allergen source (plants, animals, fungi, bacteria) and route of exposure (inhalation, ingestion etc.) or search for specific allergens, sources or protein families. Every allergen family entry is linked to description of biochemical properties and allergological significance of family members as well as list of key references related to this family.
Device for automating tail immersion assay. Used for measuring acute thermal pain in rodents. Software recognizes several specific RFID keys as user interface commands, which allows TailTimer to be operated via RFID fobs.
Literature mining web service that searches all PubMed abstracts for user provided gene symbols in conjunction with set of custom keywords organized into customized ontology, as well as results from human genome wide association studies (GWAS). Searches gene symbols against list of keywords in PubMed to extract sentences that contain at least one gene and one keyword. Used to mine PubMed for gene relationships using custom ontology and deep learning.
Custom Dicer-Substrate siRNA (DsiRNA) generator
Integrated DNA Technology custom DsiRNAs generator
Web service to generate DsiRNAs for any sequence from any species by Integrated DNA Technologies.
University of California Santa Cruz Macromolecular Structure Function Core Facility
Macromolecular Structure Function Core Facility-UCSC
Provides instrumentation, supplies, and expertise to assist researchers in structural characterization of biological macromolecules. Resources are available for crystallization and structure determination as wells as biophysical characterization of macromolecular stability and interactions.
Dartmouth Geisel School of Medicine Mouse Modeling Core Facility
Dartmouth Mouse Modeling Shared Resource
Supports generation and utilization of genetically modified mice, design and production of genetic constructs with methods including yeast and E.coli recombineering, ES cell targeting (transfection, drug selection, and expansion). Produces transgenic mice: DNA injections into oocytes, ES cell injections into blastocysts.Provides humanized immune system mouse models.Offers start to finish experiment services to assist your many needs, please ask for more info.Other services include animal husbandry, IP and IV injections, blood drawing, necropsy and surgeries- embryo transfers, ovariectomy, vasectomy, tumor removal.
University of Kentucky College of Medicine Genetic Technologies Core Facility
Center for Molecular Medicine Genetic Technologies Core
Core provides services related to manipulation and delivery of nucleic acids to biological systems. Services include Production and titering of recombinant viral vectors,including Lentiviruses, Adenoviruses, and Adeno associated viruses;Subcloning;Tagging of open reading frames;Development of plasmids and/or RNAs for CRISPR/Cas manipulation;piggyBac transposon delivery systems;Real-time PCR analysis;Recombineering;In vitro transcription; Core maintains stock of plasmids that provide components for building constructs envisioned by investigator and provides consultative services.Provides training opportunities in the technologies described above, either as a for-credit, one semester class or on a project-related, fee-based basis.
Frederick National Laboratory Protein Expression Laboratory Core Facility
Comprises six service groups. Our services are available to all NIH intramural researchers, and by interagency agreements to FDA and US Army at Ft. Detrick. We are happy to consult and distribute materials to not-for-profit institutions.Clone Optimization service include DNA cloning for protein expression; Gateway-based; fluorescent, epitope, solubility, purification tags; mutagenesis; vectors for insect/ baculovirus, mammalian, E. coli, P. pastoris, K. lactis. Microbial Expression: E. coli, P. pastoris, K. lactis, 2 mL to 60 L, autoinduction and IPTG; fully instrumented fermenters.Eukaryotic Expression service include insect / baculovirus, mammalian transient and stable, monoclonal antibodies.Protein Purification service include parallel microscale for process development; affinity and native, tag and endotoxin removal; scale-up to low gram scale.Virus Technology service include custom and stock adenovirus and lentivirus production; titer determination; promoter and reporter panels in lentivirus ready to deliver.Molecular Detection: qPCR and ELISA assaysdeveloped and executed, focused on human viruses in human samples; qPCR assays for mycoplasma and human pathogenic viruses contaminating cell lines; cell line identity testing.
Cornell University BRC Epigenomics Core Facility
Cornell University Epigenomics Core Facility
Provides service that maps protein DNA interactions genome wide, tracks experimental metadata, and implements quality controlled data processing and research based analysis pipelines. Provides epigenomic and bioinformatic research resources and services that include sample preparation services and data generation. Open source platforms enable and reinforce FAIR data practices. Core is able to receive and process cell and tissue samples for various diagnostic epigenetic assays.
Northwestern University NUANCE BioCryo Core Facility
Provides source for characterization of biological, soft matter, and hybrid samples with TEM (Transmission Electron Microscopy), SEM (Scanning Electron Microscopy), and STEM (Scanning Transmission Electron Microscopy) at cryogenic or at ambient temperature.Provide expertise and access to equipment for cryofixation and processing of frozen hydrated samples by high pressure freezing, plunge freezing, freeze fracturing, cryo ultramicrotomy, freeze substitution, and turbo freeze-drying. Conventional samples can be processed at ambient temperature with chemical fixation, dehydration, and resin embedding, or critical point drying. Offers EDX (Energy Dispersive X-ray Spectroscopy) for elemental analysis.Offers training on instruments and sample preparation techniques.BioCryo staff mentors new users, advises on experimental design, and collaborates with researchers in experiments with challenging and unconventional samples.BioCryo Facility participates in numerous educational and outreach events, e.g. workshops, seminars, demos, and facility tours.
University of Vermont Larner College of Medicine Microscopy Imaging Center Live Imaging and PhysiologyCore Facility
The MIC Live Imaging and Physiology Core is a division of the Microscopy and Imaging Center of the UVM Larner College of Medicine. The Live Imaging and Physiology Core provides a wide range of imaging techniques mainly for live-cell, live-tissue and in-vivo preparations. We maintain a Noran/Prairie Technologies OZ LSCM (laser scanning confocal microscope), a DeltaVision RT restoration microscopy system, a Zeiss/BioRad 2100 dedicated multiphoton LSCM, a Zeiss LSM 7 MP dedicated multiphoton LSCM, a Nikon TIRF (total-internal reflection fluorescence) system, a Nikon/Yokogawa CSU-W1 spinning disk microscopy system, a PTI monochromator system, and a Nikon SMZ-1500 fluorescence stereoscope. Patch-clamp electronics are available for use on most microscope systems, and each system has an integrated perfusion setup.
University of North Carolina at Chapel Hill Biospecimen Processing Core Facility
Centralized, quality controlled facility and biorepository for processing, storage and disbursement of human specimens.Offers high throughput processing of human biospecimens, with specific emphasis on DNA and RNA isolation and purification.Provides laboratory support for investigator initiated large scale clinical, epidemiologic, and other studies.Functions as human specimen biorepository resource for clinicians who wish to store and study samples from unusual or potentially important patients.Biorepository is managed by custom LIMS, with sample accessioning, tracking and audits at each step.Provides scientific resource for investigators seeking advice or consultation on study design including specimen collection and storage methods, and human subject issues. Core staff act as liaison to other UNC core facilities and outside collaborators.
University of Alaska Fairbanks Genomics Core Facility
Facility provides nucleic acid analysis in evolutionary biology, molecular biology, and wildlife and fisheries management. UAF has been the beneficiary of NSF EPSCoR, NIH BRIN (INBRE), and an NIH COBRE grants, parts of which have been designated for genomic instrumentation. Provides ABI 373 slab gel sequencer, Illumina MiSeq and Oxford NanoPore MinION sequencers. Other Equipment listing is on our website for more information on instruments. Services include nucleic acid sample analysis, and maintenance and support for molecular instruments, training workshops and seminars for instrumentation and techniques to help students, faculty, and staff learn to use available equipment. Provides tours to middle and high school students/teachers, undergraduate students, graduate students, research staff, faculty candidates, and local or out of state visitors. The Core Lab has also been involved in several undergraduate/graduate classes offered by the Biology Department and the Chemistry Department.
Harvard Medical School DNA Resource Core Facility
DF/HCC DNA Resource Core at Harvard Medical School
Harvard Medical School Dana Farber/Harvard Cancer Center DNA Resource Core
Core offers high throughput Sanger sequencing for any number of samples with 24 hour turn around time,PCR cleanups and mini-preps as well as sample prep from colonies or pellets.Provides large plasmid repository with over 300,000 constructs.Provides ORFs from MGC, Yeast, Xenopus, Drosophila, mouse, as well as several many other organisms including bacterial species. Accept deposits.
Dartmouth Genomics and Molecular Biology Shared Resource (GMBSR)
Genomics Section provides services and instrumentation that enable DNA/RNA extraction and quality control, next-generation Illumina and Nanopore sequencing, epigenetic profiling, and microarray analysis on a whole-genome scale, from the level organisms to single cells. Molecular Biology Section provides DNA fragment analysis qPCR, Sanger sequencing and NanoString Technology.
Ohio State University Center for Electron Microscopy and Analysis Core Facility
Center for Electron Microscopy and Analysis
Centralized, coordinated imaging facility.Provides electron and ion beam analytical microscopy instruments.Full service facility from extensive sample preparation laboratories to image processing tools and support.
Software tool for importing clinical trials into Wikidata.
Software Python tool as Vanderbilt University curation tool.Used for exporting public profiles of university faculty from Vanderbilt University database into Wikidata.Used to create or update items in Wikidata using data from CSV spreadsheet data.
Web tool to edit property value of several items on one screen.Used to see and edit labels, descriptions, aliases, and properties for list of Wikidata items, in tabular form.
Web tool used to batch edit Wikidata items, based on simple set of text commands. Can add and remove statements, labels, descriptions, and aliases.Can add statements with optional qualifiers and sources.
Web tool as official query tool for Wikidata.
Software tool for importing data sets into Wikidata. Can list entries of some external databases, and allows users to match them against Wikidata items.
Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data.
University of British Columbia Vancouver Bioimaging Core Facility
University of British Columbia Bioimaging Facility
Provides optical and electron microscope infrastructure for live cell imaging, multi photon imaging, advanced sample preparation including cryo-preparation for electron microscopy, routine SEM and TEM, Cryo-TEM, TEM tomography, and Correlative Light and Electron Microscopy (CLEM). Equipped with 4 electron microscopes (1 SEM and 3 TEMs), 2 advanced fluorescence microscopes (confocal/multi-photon and spinning disk), cryo-fixation (High pressure freezer, Vitrobot) and EM processing equipment (Microwave, critical point dryer, coaters).Provides microscopy access, training and service.
Open source software Java tool for working with data. Used for loading data, cleaning up data, transforming data from one format into another and extending it with web services and external data.
Coevolution in OVerlapped sequences by Tree
Web server providing online analysis of coevolving amino acid pairs in overlapping genes, where residues might be located inside or outside overlapping region.
Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables.
Open Source software library for molecular simulation applications. Provides ready-to-use implementations of standard algorithms.Serves as code basis that can be easily extended and modified to deal with standard and non standard problems in molecular simulations.
Web app based tool as one of GLOBE Observer tools. Used to document what is on land. Once you have downloaded the app and created account, Land Cover tool will guide you through observation process. You will report on current surface conditions, then take photographs in all four cardinal directions, up and down. Optionally, you can classify land cover in your photographs, telling if it is grassland,forest or urban area, as well as compare your classification to satellite land cover observation and note any differences.
Portal within Wikipedia platform for presenting content, tools, and discussion related to clinical trials.Anyone can join to express their interest in developing content in Wikidata related to clinical trials.
Smart-seq2 Single Nucleus Multi Sample Pipeline
Smart-seq2 Single Nucleus Multi-Sample Pipeline
Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays.Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix.
Open source software tool as adapter and quality trimmer for Next-Generation Sequence data.
University of Nebraska Lincoln Nebraska Center for Biotechnology Proteomics and Metabolomics Core Facility
UNL Proteomics and Metabolomics Facility
Provides services using mass spectrometry, including identification and relative quantification of proteins and several advanced methods for profiling and quantitation of small molecules.Provides outreach and education program including workshops,seminars and courses.Proteomics services include Bottom-up Proteomics of whole organisms, organs, organelles, tissues, cell pellets, pulldowns, complex or single protein mixes from solutions or gels;Quantification by label-free or multiplexed labeling techniques with microscale subfractionation to increase coverage;Post Translational Modification Characterization especially phosphopeptide enrichment from whole organism digests, but also ubiquitylation, acetylation, etc.Metabolomics services include Untargeted Quantification of small molecules;Primary metabolism using GC-MS and NIST/Fiehn Libraries;Secondary metabolism using LC-MS and Progenesis QI, NIST Library, mzCloud;Targeted Quantification using HPLC or LCMS.
Software tool for video editing. Used for social sharing, TV, and film.
LED illumination system for transmitted light applications, including brightfield, darkfield, DIC, Dodt gradient contrast and phase contrast. Includes LED illuminator and controller.
Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.
University of California at Berkeley National Energy Research Scientific Computing Core Facility
National Energy Research Scientific Computing
Supercomputer user facility operated by Lawrence Berkeley National Laboratory for the United States Department of Energy Office of Science.Houses high performance computing and data systems used by scientists at national laboratories and universities around the country.
Software R package creating customizable presentation ready tables, summarizing data sets, regression models, and more. Used for publication ready data summary and analytic result tables.
Open source software tool for visually exploring ploidy with Next Generation Sequencing data.Used to visualize and explore ploidy levels in newly sequenced genome, exploiting short read data. Allows identification of ploidy level of newly sequenced genome in visual way. Implemented in Python and R.
University of Colorado Anschutz Medical Campus ImmunoMicro Flow Cytometry Core Facility
AMC ImmunoMicro Flow Cytometry Shared Resource
University of Colorado Anschutz Medical Campus ImmunoMicro Flow Cytometry Shared Resource
Provides access to high parameter cell analysis and sorting instrumentation along with scientific expertise.Services provided include Cell Sorting,FACS Cell Sorting,Flow Cytometric Analysis,Multi-color Flow Cytometry,Spectral Flow Cytometry.
Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.
ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline
Software tool as ChIP-seq pipeline for processing ChIP-seq reads, aligning to reference genome, peak calling, and IDR analysis of replicate data according to ENCODE standards.
Open source software R package for interacting with common Bioconductor classes Ranges and GenomicRanges. Grammar of genomic data transformation. Provides grammatical and consistent way of manipulating these classes to increase accessiblity for new Bioconductor users.
Software R package for interfacing with genome browsers.Supports integration of existing genome browsers with experimental data analyses performed in R. R interface to genome annotation files and UCSC genome browser.
Analyst module for statistical analysis and interactive visualization of complex data such as genotype, phenotype, and omics data. Provides data mining solution that can be integrated into existing research IT environments with rich set of APIs. Supports integration of R scripts.
Software R package to identify cells with active gene sets in single cell RNA-seq data. Used for analysis of gene set activity in single cell RNA-seq data.Used to calculate whether critical subset of input gene set is enriched within expressed genes for each cell.
Software R package that provides classes and methods for spatial data.
Prokaryotic Genomes Automatic Annotation Pipeline
Prokaryotic Genomes Automatic Annotation Pipeline (PGAP)
Software tool as NCBI prokaryotic genome annotation pipeline. Used to annotate both complete genomes and draft genomes comprising multiple contigs. Integrated into NCBI infrastructure and processes, and uses modular software framework, GPipe, developed at NCBI for execution of all annotation tasks, from fetching of raw and curated data from public repositories through sequence alignment and model based gene prediction, to submission of annotated genomic data to public NCBI databases.
Comprehensive collection of high quality microbial genomics reference data for bacteria, viruses, and fungi in holdings of American Type Culture Collection.
Antibody Characterization through Open Science
Canadian, public interest, open science company with mission of characterizing commercially available antibody reagents for every human protein. Antibody characterization methodology and dataset. Gold standard genetic characterization process uses both cell line expressing adequate endogenous levels of target protein and CRISPR knockout version of same cell line as negative control. Antibody characterization methodology follows seminal methodology formalized at Montreal Neurological Institute.
Software tool for porosity analysis of tree slice. Used for 3D image analysis, density analysis, 3D distances and angles, thickness and separation, automated batch analysis.
Community led catalog of extensions to Neurodata Without Borders data standard.
Software tool for generating documentation for data standard schema defined using HDMF specification language. Collection of CLIs, scripts and modules useful to generate NWB documentation.
Software tool to define collection of common, reusable data structures that build foundation for modeling of advanced data formats and is integrated with HDMF.Provided data structures include DynamicTable, VectorData, VectorIndex, ElementIdentifiers, DynamicTableRegion, AlignedDynamicTable and CSRMatrix.
University of Michigan Ann Arbor Life Sciences Institute Cryo Electron Microscopy Core Facility
University of Michigan Ann Arbor UM - Cryo-EM Facility
Facility uses MiCores/iLab to schedule time on microscopes.Allows scientists to study form and function of biological machines that are too large to study using X-ray crystallography. Provides instruments and faculty expertise specializing in cryo electron microscopy.
University of Hawaii at Manoa Molecular and Cellular Immunology Core Facility
Molecular & Cellular Immunology Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2022. Provides services for flow cytometry, cell sorting and immunological services through COBRE support. Helps in developing new or customized immunological methods for COBRE Investigators and other Core users, regularly schedules training sessions are held for COBRE Investigators and other faculty and students across university and broader research community.Services include Flow Cytometry, Analysis and Sorting,Cell Counting, Size, and Viability,Multiplex Bead Assays including Luminex and CBA Platforms for DNA, Protein, and Antibodies Assays, Immunospot Plate Reading including ELISpot and FRNT, Cell Irradiation. Flow Cytometry Assays including Cell Phenotyping, Cell Cycle with Live or Fixed Cells, Apoptosis, FRET, Calcium Flux, Phosphorylation, Intracellular Cytokine and Protein Detection, Fluorescent Protein Expression,Cell Population Isolation, Single Cell Sorting, Dye Dilution Assays, Proliferation,Training opportunities.Experienced staff will provide hands-on training to investigators in conducting IBC/IACUC/CHS approved MCI research protocols. Please refer to MCI training document to help you get started on the process for obtaining clearance to work in the JABSOM Molecular and Cellular Immunology Core Facility.
University of Oklahoma Health Sciences Center Laboratory for Molecular Biology and Cytometry Research Core Facility
Laboratory for Molecular Biology and Cytometry Research
University of Oklahoma Health Sciences Center Laboratory for Molecular Biology and Cytometry Research
Core facility offering services involving DNA, protein, and whole cell analysis. Services include sequencing (custom PCR, plasmid and DNA, RNA, 16s, miRNA, ChIP ) and microsatellite detection via Illumina MiSeq or SeqStudio capillary sequencer. Expression analysis using Nanostring nCounter SPRINT platform, Mass Spectrometry and Proteomics using Waters Synapt with 2D UPLC. Provides qualitative and quantitative analysis of protein samples (cell lysate, IP, in solution) as well as simple protein identification from solution or gel slice. Flow and Imaging division offers BSL2 cell sorting, flow cytometry, Luminex, and confocal imaging.
American Type Culture Collection Sequencing and Bioinformatics Center Core Facility
ATCC Sequencing and Bioinformatics Center Core Facility
Core genomics and bioinformatics group at American Type Culture Collection.Offers whole genome sequencing and advanced bioinformatics analysis for wide range of biological materials ranging from viruses and bacteria, to fungi and human or animal cell lines, genome assembly, verified annotation, functional genomics analysis, transcriptomics analysis, cell line contamination assessments, microbiome profiling, and advanced cell line authentication services.
Brown Alpert Medical School Women and Infants Hospital of Rhode Island Kilguss Research Institute Molecular Biology and Imaging Core Facility
Women and Infants Hospital of Rhode Island Kilguss Research Core
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2022. Core offers contemporary imaging, molecular biology, histology, flow cytometry, cell sorting, and real-time gene expression. Provides technologies and training including specialized microscope facility.
Population cage modeling code for Arp53D gene
Population cage modeling code for Schroeder et al, 2021 eLife publication on Arp53D gene.
Software package to take metadata for research articles and find published versions in CrossRef. Used to check if article has been published elsewhere.
Microscope with inverse platform for multimodal imaging of living and fixed specimens. Open and flexible inverted microscope platform with AI assisted experiment startup., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Portal enables browsing, searching, and analysis of human genetic information linked to lung diseases and related traits, while protecting integrity and confidentiality of underlying data.
University of California at Santa Cruz Institute for Biology of Stem Cells Cell Culture Core Facility
Institute for the Biology of Stem Cells (IBSC) Cell Culture Facility
Provides services for culture and analysis of stem cells. Provides space for embryonic stem cell growth and manipulation. Facility staff offers expertise in experimental design, protocol development, and data analysis.Equipment including biosafety hoods, centrifuges, microscopes.
Max Planck Institute for Biology of Ageing - FACS & Imaging Core Facility
Provides equipment including wide field and confocal microscopes, flow cytometry analyzers and sorters, shared histology equipment, and PC workstations for data analysis.Provides services such as software training, access to analysis software, and help with experimental planning and post acquisition analysis.
University of Vermont Innovate Model Fabricate Labs Core Facility
Core specializes in design and development of prototypes to advance research. Design engineers complete product development in Solidworks and testing in Labview. Machine shop exists to turn variety of materials into functional prototypes.
University of British Columbia Borgland Brain DNA and Tissue Bank Core Facility
Centralized resource for collection, storage, and distribution of pre and post mortem biospecimen and tissue at Djavad Mowafaghian Centre for Brain Health.Biobank facility also provides vast range of specimen processing and storage services to other research groups.
Software tool as JavaScript 3D Library.Used to create and display animated 3D computer graphics on Web browser. Three.js scripts may be used in conjunction with HTML5 canvas element, SVG or WebGL.
Software tool for tomographic reconstruction.
Open source software Python package for tomographic data processing and image reconstruction. Framework for analysis of synchrotron tomographic data.
University of California Santa Cruz Banana Slug Genomics Center Core Facility
University of California Santa Cruz Banana Slug Genomics Center
Provides next generation sequencing data analysis through automated platform. Banana Slug Analytics Platform is intuitive, point-and-click system that leverages proven algorithms for next generation sequencing data analysis and helps researchers manage large volume studies without having bioinformatics expertise. Center also performs custom bioinformatics analysis and consultation as requested.
Open source software tool as library for implementation of gradient boosting with various machine learning algorithms.Optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.Supports regression, classification, ranking and user defined objectives.
Software tool as unified framework for interpreting predictions of machine learning models. Used to explain output of any machine learning model. Connects optimal credit allocation with local explanations using classic Shapley values from game theory and their related extensions.
Software Python package providing multiple comparison statistical tests for various parametric and nonparametric analyses. Pairwise multiple comparison tests in Python.
Research Transmission Electron Microscope with accelerating voltage of 80kV used to image low contrast biological samples.
Research transmission electron microscope with accelerating voltage of 80-200kV. Transmission Electron Microscope from FEI (now Thermo Fisher Scientific) is equipped with LaB6 cathode. Enables both bright field EM and scanning transmission electron microscopy (STEM) at very high resolution (at 200kV: point resolution up to 0.27 nm).
High pressure freezing device for cryofixing of biological and industrial samples. Samples that are cooled to temperature of liquid nitrogen at high pressure are vitrified and sub cellular organisation is preserved to close to native state without formation of ice crystal.
High Pressure Freezing machine from Leica Microsystems to cryo fix biological samples for Electron Microscopy analysis.EM ICE machine allows light and electrical stimulation of samples prior to cryo fixation with millisecond time resolution.
University of Tennessee Knoxville Biological and Small Molecule Mass Spectrometry Core Facility
UTK Biological and Small Molecule Mass Spectrometry Core
Mass Spectrometry Core provides metabolomics, lipidomics, and small molecule analyses to researchers both on campus and in our affiliated local and other institutions.
Software tool as macro for SPSS, SAS, and R that conducts observed variable mediation, moderation, and conditional process analysis.Observed variable OLS and logistic regression path analysis modeling tool. Used for estimating direct and indirect effects in single and multiple mediator models parallel and serial, two and three way interactions in moderation models along with simple slopes and regions of significance for probing interactions, and conditional indirect effects in moderated mediation models with single or multiple mediators or moderators. Operates on Windows and Mac versions of SPSS and SAS.
Provides drug development software and services. Company offers drug development and clinical pharmacology strategy, regulatory strategy, writing and submission, as well as HEOR and market access solutions. Certara serves biopharmaceutical and medical technology customers worldwide.
Consulting company in field of research and development.Supervises joint projects - from EU Research Framework Program 2 to Horizon 2020 funding program.Belongs to PNO Group , one of the largest consulting firms for publicly funded research and innovation projects.
Biotechnology company providing biotechnology products and services including kits, reagents, instruments, and services to help researchers explore questions about gene discovery, regulation, and function. Subsidiaries including Takara Bio USA, Inc., Takara Bio Europe AB, and more.
Japanese multinational pharmaceutical and biopharmaceutical company. It is the largest pharmaceutical company in Asia and one of the top 20 largest pharmaceutical companies in the world by revenue.
Web tool to investigate genome wide association results in their local genomic context. Adds new features to LocusZoom such as Manhattan plots, annotation options, and calculations that put findings in context. Used for interactive and embeddable visualization of genetic association study results.Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.
American multinational pharmaceutical and biotechnology corporation. Develops and produces medicines and vaccines for immunology, oncology, cardiology, endocrinology, and neurology. Company has several blockbuster drugs or products that each generate more than US$1 billion in annual revenues.
Clinical stage company identifying and advancing transformative therapies for people with rare and specialty diseases. Former name was ArTara Therapeutics.
IQVIA, formerly Quintiles and IMS Health, Inc., is an American multinational company serving the combined industries of health information technology and clinical research.
Public Health Alliance for Genomic Epidemiology SARS-CoV-2 Contextual Data Specification
PHA4GE SARS-CoV-2 Contextual Data Specification
Software package as collection template and associated materials for SARS-CoV-2 metadata. Contains metadata collection template based on data standard designed to harmonize genomic surveillance contextual data (sample metadata, epidemiological/clinical/laboratory data, methods information) across datasets, laboratories and databases during pandemic, and beyond. Template contains standardized fields, terms and formats for structuring information, and is accompanied by field level reference guide which provides definitions, guidance and examples for populating fields. Fields have been prioritized using colour coding system as required (yellow), recommended (purple), and optional (white). Users can use as much or as little of specification as they wish, according to their needs, and need not share information unless permitted to do so. SOP and protocols for submitting to public repositories are also included.
Software R package to make surveys processing and analysis easier. Set of functions include interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.
Software R package for retrotransposed transcript detection from structural variants.
Software R package for Nuclear Mitochondrial integration events NUMT detection using structural variant calls.
Method for pose estimation that uses deep neural networks.Open source software tool as deep learning based framework for estimating positions of animal body parts.Supports multi animal pose estimation and tracking, and includes advanced labeling or training.SLEAP is next generation of LEAP and allows for tracking multiple animals.
Collection of tools to do video analysis in behavioral neuroscience applications.Offers open source software tools including SLEAP, LEAP and MotionMapper.
Software tool to work on videos (not poses).Uses image analysis and multivariate statistical methods to find stereotyped behaviors in flies, mice, and other species.
Behavioral Segmentation of Open-field in DeepLabCut
Software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.Unsupervised learning algorithm that discovers and classifies actions based on inherent statistics of data points provided.
Project related to processing video, extracting object position information, and streaming data.Provides set of programs for processing video for behavioral research. Includes OAT software tool as real time position tracker which was developed by Massachusetts Institute of Technology scientists.
Project related to behavior tracking and analysis. Provides deep learning toolbox that automates taking high speed quality video to track behavior in rodents and humans.
Portal provides tools for investigating visuomotor integration specific to high speed kinematic tracking in small model organisms in closed loop experiments. University of Toronto scientists developed suite of Bonsai modules for specifically tracking and analyzing zebrafish movements and integrating these data with closed-loop experiments. BonZeb modules can also be used in an open-loop fashion for collecting, analyzing, and integrating data from multiple sources in real time, or from offline sources for batch processing of pre-recorded data.
Project related to tracking animal behavior. Provided system includes two cameras and software package to track aquatic animals within captivity.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins.
Project related to study movement coordination in free walking mice. Provides noninvasive system consisting of cameras and machine learning algorithms that allow for three dimensional detection and tracking of mouse paws, tail, and nose.
Open source software package for markerless pose estimation. 2D keypoint detection in animals.
Open source, modular software tools for high resolution zebrafish tracking and analysis.Software suite of Bonsai modules for specifically tracking and analyzing zebrafish movements and integrating these data with closed loop experiments.Can be used in open loop fashion for collecting, analyzing, and integrating data from multiple sources in real time, or from offline sources for batch processing of pre-recorded data.
Project related to emotions and facial expressions. Includes open source guide to building affordable head mount for camera to maintain high temporal and spatial resolution of face throughout duration of experiment. Device is paired with FaceSync, Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.
Software package to track object in 3D based on 3D schematics of scene.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins.
Project related to pose estimation and tracking.Includes software toolkit for 2D pose estimation of user defined keypoints using deep learning.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior.
Open source software Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.Framework for recording facial expressions with head mounted cameras.
Software kinematics analysis tool used to study movement coordination and analyzing limb, head, and tail kinematics of freely walking mice.
Project for markerless pose estimation of user defined body parts with deep learning.
Project related to measurement of fast eye movement dynamics.Tracking eye position in head fixed applications system created by scientists from Boston University. Includes software tool as part of multithreaded eye tracker and Teledyne DALSA Camera with GigE-V framework APIs for Linux.
Project related to deep learning based pose estimator for studying how neural circuits control limbed behaviors in tethered Drosophila. Includes Deep Fly image annotation tool for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose.
Open source software tool used as part of multithreaded eye tracker.Video based eye tracker.
Software tool as PyTorch and PyQT5 implementation of 2D-3D tethered Drosophila pose estimation. Image annotation tool used for pose estimation and appendage tracking. Provides interface for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose.
NEUROscience Tool for Interactive Characterization
Project about synchronizing video and neural signals. Provides software Python toolbox for interactive characterization in neuroscience.Software tool used to review and annotate signal data synchronized with video, performs simple initial analyses including signal filtering and spike detection, supports variety of file formats.
Open Source Whisking Video Database portal
Portal provides shared database of videos featuring juvenile and adult male rats and adult male mice exploring stationary objects.This dataset includes wide variety of experimental conditions including genetic, pharmacological, and sensory deprivation interventions to explore how active sensing behavior is modulated by different factors. Database of high speed videos of whisking behavior in freely moving rodents.Open source high speed infrared videography database to study principles of active sensing in freely navigating rodents.
Software toolkit with high level API for 2D pose estimation of user defined keypoints using deep learning.Written in Python and built using Tensorflow and Keras.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior.
Software Python toolbox for interactive characterization in neuroscience.Users can read in variety of file formats for neural data and video, which they can then process, filter, analyze, annotate and plot.Used to review and annotate signal data synchronized with video, performs simple initial analyses including signal filtering and spike detection, supports variety of file formats.Facilitates collaborations by using portable specification for loading and processing data and retrieving data files from online sources.App for Windows, macOS, and Linux to review and annotate electrophysiology data and simultaneously captured video.
Shared database of videos featuring juvenile and adult male rats and adult male mice exploring stationary objects.This dataset includes wide variety of experimental conditions including genetic, pharmacological, and sensory deprivation interventions to explore how active sensing behavior is modulated by different factors. Database of high speed videos of whisking behavior in freely moving rodents.Open source high speed infrared videography database to study principles of active sensing in freely navigating rodents.
Project related to rodent tracking and task control.Provides closed loop system for machine vision rodent tracking and task control created by scientist from Washington University. System to track and report mouse activity while they are contained in simple arena. System uses OpenMV M7 microcontroller to acquire images of arena and process them in real-time to report mouse centroid data to text file. Wireless position tracker for automatically tracking mice in high contrast arenas.
Project for tracking interactions among freely moving monkeys.System includes integrated hardware and software for pose tracking in freely moving rhesus macaques.
Behavioral Segmentation of Open-field in DeepLabCut project
Project related to unsupervised behavior analysis.Carnegie Mellon University has shared B-SOiD, open source unsupervised algorithm for discovery of spontaneous behaviors. Includes software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.
University of Washington project SimBA for analysis of complex social behaviors.Used for automated behavioral scoring. Includes open source software toolkit for computer classification of complex social behaviors in experimental animals. Uses data from popular open source tracking tools in combination with small amount of behavioral annotations to create supervised machine learning classifiers that can then rapidly and accurately score behaviors across different background settings and lighting conditions.
Software tool as real time position tracker for behavioral research. Used for processing images, extracting object position information, and streaming data to disk and/or the network in real time.
Open source software toolkit for computer classification of complex social behaviors in experimental animals.
Software toolbox that automates taking high speed quality video to track behavior to analyze and track behavior in rodents and humans.
Low Cost Open Source Eye Tracking project
Project related to eye tracking system for human research.System includes open source software for accurate eye tracking. Can identify shapes such as circles, lines, and triangles.You can rotate and mirror images and also use variety of filters.Capable of processing video in real-time for optical flow. App for viewing multiple video streams from USB cameras.
Project related to involvement in larval zebrafish behavioral experiments.Provides integrated system for stimulation, tracking and closed loop behavioral experiments. Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations.
Project related to tracking individual animals in large collective groups.Provides algorithm and software for tracking individuals in large collectives of unmarked animals.Tracks animal identification and tracks when animals touch or cross paths in front of one another.
Project related to behavior analysis.Mt.Sinai scientist developed open source video analysis pipeline for investigation of animal behavior.Used to track location, motion, and freezing of animal.
Project related to calcium imaging.Provide open source tool for combined analysis of head mounted calcium imaging and behavior. Used to analyze imaging data from head mounted microscopes simultaneously with behavioral data.
Project related to sharing worm tracking data and analysis routines.Open access repository for storing, accessing, filtering data and analysis.
Project related to monitoring social interactions of mice. Provides real time behavioral analysis system for groups of mice.System includes random forest machine learning process, RFID sensors and infrared depth RGB-D camera.System includes software tool for Live Mouse Tracker analysis.
Project related to capturing detailed behavior in freely moving mice. System combines lightweight head mounted camera and head movement sensors to detect behaviors in mice. Used to monitor behaviors including eye position, whisking, and ear movements in unrestrained animals.Can be mounted in combination with neural implants for recording brain activity.Provides software Python package with functions for extracting and analyzing data recorded using camera.
Project related to tracking animals in large spaces. Picamera system allows for tracking of animals in large behavioral arenas.Open source scalable multi camera tracking system that can be used to track behavior in combination with wireless recording systems.Design is comprised of 8 overhead Raspberry Pi cameras, capable of recording at high frame rate in large field of view, recording video independently in individual Raspberry Pi microcomputers and processed using Picamera Python library.
Project related to high speed tracking of animals.Provides software tool for tracking organisms.Can handle one or several animals in one or several environments.Used for fish, insects, rodents, etc.
Project is related to Columbia University designed KineMouse Wheel, light weight running wheel for head fixed locomotion that allows for 3D positioning of mice with single camera. System uses single camera and DeepLabCut (or similar) software.
Project related to analysis of behavior in Drosophila.Provides system capable of real time video tracking. System includes raspberry pi and R package for data analysis. Enables high throughput analysis of behavior in Drosophila and other animals.
Head-Fixed Setup for Combined Behavior, Electrophysiology, and Optogenetics project
Project related to temporally controlled rodent behavior. Provides system which utilizes optimal open source setup of hardware and software through behavioral setup for temporally controlled rodent behavior. Used for combined behavior, electrophysiology and optogenetics experiments. System allows for training of head fixed animals with calibrated sound stimuli, precisely timed fluid and air puff presentations as reinforcers.Combines microcontroller based behavior control with sound delivery system for acoustic stimuli, fast solenoid valves for reinforcement delivery and custom built sound attenuated chamber.
Project related to videographic processing of head fixed rodent behaviors. Provides software toolbox for unsupervised video analysis of rodent behavior.
Project related to distraction free behavioral acquisition. Provides imaging setup for distraction free behavioral acquisition with automated tracking using open source ImageJ software and workflow for extraction of behavioral endpoints of zebrafish. Used for online tracking of larval zebrafish at high framerates.Provides user interface to run experiments as well as flexible design to allow definition of arbitrary open- and closed- loop experiments.
Portable behavioural set up that incorporates both gait analysis (using pedobarograph) and whisker movements (using high speed video camera and infrared light source).Automatically records both whisker and gait information and provides added statistical tools to analyse data. LocoWhisk system includes ARTv2 software for simultaneous measurement of locomotion behaviours and whisker movements.
Project related to motion tracking of specimen in open field. Provides software tool for motion tracking.Used to track path of object of interest in live feed from camera or recorded video. Used to track rodents in open field maze as well as retina of mice.New version of Pyper allows to customise image processing to track different kind of objects.
Project related to development of automated rodent tracking position and movement. Provides software tool to automatically track rodent.Used to track head movements, body movements and also aspects of body size.Identifies certain behaviours from video footage, such as rotations, moving forwards, interacting with objects and staying still.
Project related to tracking movement of labelled paws in grooming and freely behaving mice. Provides software toolbox for automated detection of forepaw trajectories in mice.
Behavioral Observation Research Interactive Software project
Behavioral Observation Research Interactive Software
Project related to computer based review of previously recorded videos or live observations. Related to study of animal and human behavior. Provides open source, multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.Developed by scientists from University of Turin.
Project related to video tracking, detailed ethography, and extraction of kinematic variables from digital video files of laboratory animals.Provides computational tool developed at Federal University of Santa Catarina.
Quantifying Animal Movement from Pre-recorded Videos project
Quantifying Animal Movement from Pre-recorded Videos
Project related to visualizing and quantifying movement from pre-recorded videos. Provides software toolbox for visualizing and quantifying movement.Used for summarizing animal movement data as single image ( spectral time lapse algorithm) as well as automate analysis of animal movement data.
Project related to training animal behavior. Provides system which includes full behavioral apparatus and software platform. System includes software tool for data logging and analysis.
Project related to animal behavior in complex mazes.Provides software MATLAB package for linearization of place fields in complex mazes.
Project related to measuring of muscular rigidity that can result from several factors including Parkinsons disease, or pharmacological exposure to antipsychotics or cannabis. Provides automated apparatus for measuring catalepsy that increases measurement accuracy and reduces observer bias.Catalepsy bar test automatically measures and records time it takes for rat to remove its forelimbs from bar. 3D printed test apparatus used to make catalepsy measurements in rats more standardized and accurate.
Project related to markerless computerized behavioral analysis for laboratory animals.Provides open source 3D video based behavioral analysis system for neuroscience. System includes open source software tool for 3D-video based markerless computerized behavioral analysis.
Project related to oral drug administration to group housed mice. Provides open source system for oral drug administration to group housed mice. System includes home cage attached device that weighs individual animals and administers daily dosage of drug solution based on each animal bodyweight through their drinking water. Group housed mice are identified through use of RFID tagging and receive both regular water and drug solution drops by licking at spout within PiDose module.
Project related to studying motor behavior and decision making in mice. Open source behavior training platform for studying motor control, decision making, and reaching reaction time. Enables behavioral work to study unexplored features of action selection, motivation, and value based decisions.
Project related to composing reactive and asynchronous data streams coming from video cameras, microphones, electrophysiology systems or data acquisition boards. Provides open source software tool as visual language for reactive programming.
Project related to streamlining behavioral neuroscience experiments.Provides open source software MATLAB toolbox for running behavioral neuroscience experiments and managing data.Used for probing neurons and behavior.
Automated Home Cage Rodent Two bottle Choice Test project
Automated Home Cage Rodent Two bottle Choice Test
Project related to studies of liquid ingestive behaviors used in neuroscience to investigate reward related behavior, metabolism, and circadian biology. Provides automated home cage sipper device for monitoring liquid ingestive behavior in rodents developed by Washington University, St. Louis scientists. Homecage fitted apparatus for automated, photobeam based detection of licks in two bottle choice task.
Project related to multifunctional neurobehavioral system developed by scientists at University of Zagreb School of Medicine, Zagreb, Croatia.System includes hardware and software tools.Provides software package for processing and visualising data from startle experiments in rodents or experiments measuring grip strength in rodents.
Project to detect spatial navigation behavior in animals.Provides open source software for analyzing spatial navigation search strategies developed by University of British Columbia scientists.
Project related to behavioral experiments.Provides software Python framework for running behavioral experiments designed by University of Oregon scientists.
Project related to analysis of behavior and of neural activity. Provides FPGA code for running main board of flyPAD.
Project related to rodent social communication through repertoire of ultrasonic vocalizations. Provides deep learning based system for quantification of Ultrasonic Vocalizations.Includes software MATLAB package for high throughput USV detection, classification, and analysis.
Project related to tracking and recording activity in rodent home cages.Provides device that utilizes passive infrared (PIR) sensor to detect movement in cages and logs data to microSD card. Device is wireless and battery powered, and can record data for about 3 weeks on charge.
Project related to measuring locomotor activity.System includes infrared motion detection and arduino to record activity in variety of chamber set ups. Provides actimeter and software tool to measure and record locomotor activity.
Project related to analysis of behavior and of neural activity. Provides system which allows for specific perturbation of specific groups of neurons. Used as method to induce appetitive and aversive effects on feeding through activating or inhibiting gustatory neurons in closed loop manner.
Project related to measuring licking behavior in mice.System includes device used for both real time measurement and manipulation of licking behavior in head fixed mice. System provides distribution package for Dual Port Lick Detector.Package includes files relevant to building lick detector.
Project related to saving precise times of behavioral events.Provides software tool to read MedPC data into Python and Matlab.
Project related to mouse tracking and analysis of mouse movements during computerized lab experiments. Provides open source software plugin to record and analyze mouse movements.
Automated mouse homecage two bottle choice test project
Automated mouse homecage two bottle choice test
Project related to assessing preferences by mice among fluids in their homecages.Provided system includes homecage fitted apparatus for automated, photobeam based detection of licks in two bottle choice task. Used for automated mouse homecage two bottle choice test.
Voluntary Access Static Incapacitance Chamber project
Voluntary Access Static Incapacitance Chamber
Project related to assessment of pain in animal models.Provided system includes weight bearing device for high throughput and unbiased behavioral pain assessment in rodents.Includes custom printed circuit board, infrared sensor, Arduino microcontroller, 3D printed parts, and open source software for analysis.
Portal as educational resource regarding construction and implementation of bioamplifiers as well as interpretation of biosignals.
Project related to detection and rewarding rodents in modified T-maze task. System designed to detect and reward rodents in modified T maze provided by Ruhr University Bochum, Germany scientists.
Portal related to biomedical signals.Provides wearable data acquisition device with special focus on biomedical signals such as heart activity (ECG), muscle activity (EMG) and brain activity (EEG).Open source high precision bluetooth data acquisition device.
Project related to self initiated conditioning and behavior tracking in mice. Provides automated system that can track large numbers (over 25) of socially housed mice through implanted RFID chips on mice. With RFID trackers and other analyses, behavior of mice can be tracked as they train and are subsequently tested on (or self-initiate testing in) odor discrimination task over months with thousands of trials performed every day.
Project related to individual mice positions analysis, specifically their nose positions. Includes software tool for analysis of mouse position data designed by Hebrew University scientists. Provides open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error.
Portal related to control and decision making, focusing on role of prefrontal cortex. American University scientists through their GitHub repository provide 3D print files for many of behavioral devices used in their lab, including Nosepoke and Lickometer designed from rats.
Project related to investigate mechanisms of oculomotor behavior.Included system is provided by New York University scientists to track eye movement.System includes camera module, lens, IR-Light source, mounting solution, data acquisition device, and general purpose PC. System consists of open source software and modular hardware solution to eye tracking for use in humans and non-human primates.
Project related to presenting visual and auditory stimuli, recording behavior in form of nose pokes or screen touches, and delivering liquid rewards. ProvidesOperant chamber built with iPod Touch and Arduino microcontroller as main components.
Project aims to establish computing platform for rodent behavior research using Raspberry Pi computer. They have built several devices for conducting operant conditioning and monitoring environmental data.
Open Source platform for Sensory Tasks project
Project related to report animal decision in response to stimulus.Includes software tool as Arduino and Python based platform for Go or No Go sensory task to report animal decision in response to stimulus provided by University of Melbourne, Melbourne, VIC, Australia scientists.
Project related to function of cerebral cortex. Included model system for studying cortical function is provided by UC Berkeley scientists. System includes lickometer which employs infrared beam and sensor to minimize electrical noise artifacts during neurophysiology experiments and can be easily mounted in micromanipulator for precise and repeatable positioning.Open source lickometer was designed in conjunction with open source water delivery system.Together, these provide basic hardware for DIY behavioral assay and reward system for mice.
Project related to real time acquisition and processing of electrophysiological data.Provides software tool for acquisition and processing of electrophysiological data.
Ultrasonic Vocalizations Detector project
Project related to ultrasonic vocalizations detection. Provides device designed for automatic detection of 50kHz ultrasonic vocalizations.
Project related to neural data analysis. Provides open-source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website.
Project related to preprocessing of images. Provieds software Python tool to processes raw macaque fMRI images using algorithms embedded in automatic pipeline.
Cerebro Wireless Optogenetic System project
Project related to wireless controlled optogenetic stimulation. Provides system for wireless optogenetic stimulation developed in Karpova Lab with ability to be customized.Features Cerebro,rechargeable, battery powered wireless receiver;head implant containing optical fibers and two independent laser diodes; base station for transmitting radio signals to Cerebro, controlled by Windows computer via USB or by TTL; charging dock; and Xavier, user friendly GUI for sending and logging base station commands.
Portal includes system for combined behavioral tracking, electrophysiology, and closed loop stimulation provided by University of Oslo scientists.Integrates Bonsai and Open Ephys with multiple modules.Provides guide for setting up this system.
Project related to neurophysiology data acquisition and analysis.Included open source software application for neurophysiology data acquisition and analysis is provided by Howard Hughes Medical Institute Janelia Research Campus scientists. Program is based in MatLab, and evolved from earlier open source software package called Ephus.
Project related to calcium imaging.Provides software library, CaImAn, for one and two-photon Calcium Imaging data Analysis.
Toolboxes for Spike and LFP Analysis project
Portal includes compared several toolboxes for spike and LFP analysis, connectivity analysis, dimensionality reduction, and generalized linear modeling. Discussion about major features of software available for Python and MATLAB including Brainstorm, Chronux, Elephant, FieldTrip, gramm, Spike Viewer, and SPIKY. They include succinct tables for assessing system and program requirements, quality of documentation and support, and data types accepted by each toolbox.
Project related to time series calcium imaging evaluation and pre-processing. Included open source graphical viewer for time series calcium imaging evaluation and pre-processing is provided by Swedish University scientists .
Project related to fluorescence imaging to record neural activity in awake, freely behaving mice.Provided system is developed by UCLA scientists. Miniscope system includes Miniscope with single, flexible coaxial cable to carry power, control signals, and imaging data to open source Data Acquisition hardware and software. Open source miniature fluorescence microscope uses wide-field fluorescence imaging to record neural activity in awake, freely behaving mice.
Project is related to working with atlas data from multiple species on common platform.Provides collection of Python tools for working with atlas data from multiple species on common platform and for morphological analyses in systems neuroscience.
An open source motorized swivel for in vivo neural and behavioral recordings project
An open source motorized swivel for in vivo neural and behavioral recordings
Project related to neural recordings such as electrophysiology, calcium imaging, and optogenetics. Provides 3D-printed, motorized commutator for neural recordings of small animals in vivo.Open source motorized swivel for in vivo neural and behavioral recordings.Device operates independently of data acquisition system, and it can be controlled through any popular platform such as Arduino or Raspberry Pi.
Project related to training mice on task that requires continued updating of action/outcome relationships. Behavioral project includes task protocol and corresponding build instructions.Open source behavioral box used to train mice on task that requires continued updating of action/outcome relationships. Permits investigation of motivated behavior that requires flexible relationships between sensory stimuli and motor action. Project provided by Harvard Medical School scientists.
Project related to fluorescent imaging. Provides single photon fluorescent imaging microscope systems. System includes modular in vivo all optical neurophysiology rigs with transparent hardware, and acquisition and analysis software.Provide designs for 3D printed, lightweight, wireless capable microscope and motorized commutator, designed for multi month monitoring neural activity of zebra finches while they sing their courtship songs. Adapted for rodents and birds such as canaries.
Project related to conducting research on effects of nicotine vapor. Provides open source chamber system for rodents to experience regulated nicotine vapor exposure from JUUL electronic cigarette.Vapor exposure apparatus comprised of Arduino Uno microcontroller that relays coded instructions to H-bridge motor controller.H-bridge then sends specific signals to motors that regulate produced vapor sent to exposure chambers.
Project related to accurately counting and monitoring the behavior of organisms.Provides open source capacitive touch sensing system.Capacitive sensors are positioned to readily detect direct physical touches from rodent under investigation. Device,designed around capacitive touch sensor MPR121,accurately counts and monitors behavior of organisms.
Project is related to transcranial Electrical Stimulation.Included system contains aluminum box stimulator with banana connectors for both anode and cathode on front panel,power supply on rear, power switch and serial port, LCD screen and three buttons on top panel that are used to input settings for stimulator. Device for delivering non-invasive neuromodulation techniques such as transcranial direct current stimulation. If device is used for certain types of tDCS (otDCS and tPCs) or external triggering, computer control must be used. Microcontroller is used to regulate operating speed and pulse width modulation switching frequency administrated by device.
Project related to study learning and memory in preclinical research.Included tracking system for object recognition tasks provides standardization across experiments and labs.Automates scoring process using capacitive sensors, while providing validated 3D-printed objects in order to standardize object recognition to study learning and memory in preclinical research.Used for accurate measurement of interaction time during object recognition tasks.
Project is related to measurement of complex phenotypes in homecage. Homecage automated open source behavioral testing sytem to enable high throughput 24h testing of many standard operant paradigms. Using Arduino platform and easily sourced inexpensive components system can display light cues and dispense liquid rewards and has nosepoke receptacles with infrared detectors for operant responses, within homecage.Method provided by Dartmouth College scientists.
Project related to study of orientation behavior and neural circuit functions, through creation and analysis of small, freely moving animals in virtual realities. Provides virtual reality tool system for behavioral and neural circuit studies of small animals.Closed loop platform to study unrestrained sensorimotor behavior.
Project related to creating and controlling visual environments.Provided open source software package for creating and controlling visual environments was developed by University College London scientists.
Home Cage Automated Skilled Reaching Apparatus project
Home Cage Automated Skilled Reaching Apparatus
Project includes system for individualized training of group housed mice in single pellet reaching task.System allows user to host up to 5 mice in their home environment and automatically administer single pellet reaching test to those animals.Platform for training and assessing skilled reaching in mice with minimal need for experimenter handling.
Precision Syringe Pump Controller project
Project related to dispensing precise volumes of fluid over precise timescales.System components include syringe holder and control board with syringe pump controller and programming library.Syringe pump controller was developed by American University scientists.
Project related to fear conditioning studies.Includes hardware and software tools. Provides Arduino based device for producing naturalistic stimuli which can be integrated with existing commercial operant chambers with few modifications.. Stores custom made .wav files on SD card, interfaces with Med System and plays the .wav files through ceiling mounted speakers.
Novel Gustometer for Human Taste Research project
Novel Gustometer for Human Taste Research
Project related to taste sensory system research in humans on behavioral, electrophysiological and hemodynamic activity levels.Provided system includes hardware and software tools.
Open source video analysis pipeline for investigation of animal behavior. Platform independent set of behavior analysis pipelines using interactive Python ( (iPython/Jupyter Notebook) that researchers with no prior programming experience can use.
Software tool as part of system designed to be easy to build and setup for real time eye tracking.Open source software provides accurate eye tracking. Can identify shapes such as circles, lines, and triangles.You can rotate and mirror images and also use variety of filters.Capable of processing video in real-time for optical flow. App for viewing multiple video streams from USB cameras.
Open source tool for combined analysis of head mounted calcium imaging and behavior. Used to analyze imaging data from head mounted microscopes simultaneously with behavioral data.
Software tool as Python Video Annotator software.Agorithm and tracking software that features two deep networks.Tracks animal identification and tracks when animals touch or cross paths in front of one another.
Open source software Python package to control stimulation and track behaviour.Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations.
Software tool as repository of documentation, software, and discussions to share worm tracking data and analysis routines.Open access repository for storing, accessing, and filtering data; interchange format for notating single or multi worm behavior; and file formats written in Python for feature extraction, review, and analysis.
Software Python package with functions for extracting and analyzing data recorded using camera system.Used to monitor behaviors including eye position, whisking, and ear movements in unrestrained animals.Can be mounted in combination with neural implants for recording brain activity.
Software tool for behavioral and video tracking analysis in laboratory animals. Used to support detailed ethography, video tracking, and extraction of kinematic variables from digital video files of laboratory animals.
Software package for Live Mouse Tracker analysis. lmt-analysis provides all analysis tools needed to extract information from tracking performed by live mouse tracker.
Open source software tool for 3D-video based markerless computerized behavioral analysis for laboratory animals.Used to reconstruct full 3D images of animals and fit skeletal models to 3D image to estimate 3D pose of animals.Open-source 3D video based behavioral analysis system for neuroscience.
Software R package for data analysis.Enables high throughput analysis of behavior in Drosophila and other animals.
Software toolbox for automated detection of forepaw trajectories in mice.Open source code to simultaneously track movement of individual paws during spontaneous grooming episodes and walking in multiple freely behaving mice/rats.
Open source event logging software for video/audio coding and live observations.Multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.
Software tool to automatically track rodent position and movement.Used to track head movements, body movements and also aspects of body size. It is able to identify certain behaviours from video footage too, such as rotations, moving forwards, interacting with objects and staying still.
Software tool for motion tracking.Provides real time or pre recorded motion tracking of specimen in open field. Used to track path of object of interest in live feed from camera or recorded video. Used to track rodents in open field maze as well as retina of mice.New version v2 of Pyper allows to customise image processing to track different kind of objects.
Software tool as event based framework for processing and controlling data streams. Open source software tool as visual language for reactive programming.Used for composing reactive and asynchronous data streams coming from video cameras, microphones, electrophysiology systems or data acquisition boards.
Software toolbox for unsupervised video analysis of rodent behavior.Used for videographic processing of head fixed rodent behavior.
Software tool for data logging and analysis.
Software toolbox for visualizing and quantifying movement from pre-recorded videos.Used for summarizing animal movement data as single image ( spectral time lapse algorithm) as well as automate analysis of animal movement data.
Software package for processing and visualising data from startle experiments in rodents or experiments measuring grip strength in rodents.
Open source software MATLAB toolbox for running behavioral neuroscience experiments and managing data.Used for probing neurons and behavior. Used for managing behavioral neuroscience experiments and acquiring experiment related data.
Software tool as open source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Toolkit of flexible modules to design experiments without rigid programming and API limitations.
Software MATLAB package for linearization of place fields in complex mazes.Graph theoretic approach for production of linear place fields in complex mazes. Used for producing linear place fields for hippocampal cells during behavior in complex mazes.Specifically designed to deal with mazes with one or more decision points (e.g., T-maze, W-maze, double T-maze, radial maze, plus maze, etc).
Open source software for analyzing spatial navigation search strategies.
Distribution package for Dual Port Lick Detector.Package includes files relevant to building lick detector.
FPGA code for running main board of flyPAD. Code written in VHDL using Quartus 2 web edition software.
Integrated, open source mouse tracking software package.Software plugin to record and analyze mouse movements in computerized lab experiments.Software plugin provides two items that implement mouse tracking in OpenSesame.
Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis.
Software tool for high speed eye tracking for Point Gray USB3.0 cameras.Oculomatic software tracks eye position within acquired image frame at frame rate dictated by image sensor.
Software Python tool to processes raw macaque fMRI images using algorithms embedded in automatic pipeline.
Software tool for analysis of mouse position data.Open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error.
Software tool to read MedPC data into Python and Matlab. MedPC code for saving precise times of behavioral events and MatLab and Python functions to convert MedPC data into time event codes.
Open source software application for neurophysiology data acquisition and analysis. Program is based in MatLab, and evolved from earlier open source software package called Ephus.
Software tool for real time processing of electrophysiological data.
Open source graphical viewer for time series calcium imaging evaluation and pre-processing.
Open source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website.
Open source software tool for scalable calcium imaging data analysis. Used for large scale calcium imaging analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
Open source software package for creating and controlling visual environments.Software package for Bonsai which allows for control of 2D and 3D environments.
Federal University of Santa Catarina; Santa Catarina; Brazil
Public university in Florianópolis, the capital city of Santa Catarina in southern Brazil.
Software package for generating structure based models. SMOG 2 is complete rewrite of original SMOG software. SMOG 2 is standalone software package for generating SMOG models. Useful if you want to modify force field (e.g. include new residues, design new variant, etc).
Software package for generating structure based models.
Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.
Software tool for panoramic stitching of single cell data. Algorithm identifies and merges shared cell types among all pairs of datasets and accurately integrates heterogeneous collections of scRNA-seq data.
Adaptively thresholded Low Rank Approximation
Software tool for genotype imputation for scRNA-seq based on low rank approximation. Used for imputation of missing values in single cell RNA-sequencing data.
Software R package for computational doublet annotation of single cell RNA sequencing data. Software tool for in silico identification of doublets in scRNA-seq data.
Software tool for accurate, fast and versatile mapping/quantification of single cell and single nucleus RNA-seq data. Used for mapping, demultiplexing and quantification for single cell RNA-seq. Comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR.
Portal to find and use small molecule reagents called chemical probes in biomedical research and drug discovery. Molecules are evaluated by recognized chemical probe experts (Scientific Expert Review Panel, SERP) and recommendations are provided how to best use these tools.Portal includes range of chemical tools, including small molecule inhibitors, agonists, PROTACs (proteolysis targeting chimeras) molecular glues, and molecular glue degraders.Portal also curates list of historical compounds, which have been used as inhibitors in the past but are no longer considered probes.
Mitochondrial Neuron Ubiquitin landscape
Shiny app for quick selection of ubiquitylation sites and proteins from diGly analysis of neurons stimulated with mitochondrial depolarisation.Used to visualise mitochondrial ubiquitin sites in neurons and search for ubiquitin components recruited to mitochondria upon mitochondrial depolarisation.
Visual stimulator with customizable light spectra
Project related to visual neuroscience.Provides spatial visual stimulator with arbitrary spectrum of light for visual neuroscientists.Open source, low cost visual stimulator which can be customized with up to 6 chromatic channels. Spectrum of light can be arbitrary and customizable to be adapted to different animal models based on their visual spectrum. Device details, including parts list and information for custom python library for generating visual stimuli (QDSpy), can be found in eLife publication.
Automated Center out Rodent Behavioral Trainer
Project related to studying motor behavior. University of Washington in Seattle scientists have developed and published their device for training rats to perform modified center out task.
Project related to animals learned perform action in order to achieve reward. Fully 3D printable chamber able to perform operant conditioning using off-the-shelf, low-cost optical and electronic components, that can be reproduced rigorously in any laboratory equipped with 3D printer.
Project related to auditory behavioral task data collection.Provided high throughput operant conditioning in mouse homecage system was developed by University of Maryland,College Park, scientists.Automated system for training up to hundreds of mice in auditory behavioral task features custom Matlab GUI running on desktop which connects to Raspberry Pi to administer auditory stimuli from USB soundcard and collects auditory data as well as licking data from water spout with commercially available capacitive sensors. Parts list and build instructions are readily available from paper and associated GitHub repository.
Project related to cognitive testing method for rodents.Provides touchscreen operant platform for testing learning and memory in rats and mice.Includes device chambers that can be used to measure rodent behavior.Not open source device.
Portal related to virtual reality for freely moving animals.Provides virtual reality system set up for unrestrained animals.System developed by University of Frieburg scientists. This Virtual Reality system can be used with number of different species including mice, zebrafish, and Drosophila.
Project related to studying reward and feeding behavior. Provides open source automatic feeding system that can be customized for food types from seeds to pellets.System integrates plexiglass tubes, Arduino Uno, motor driver, and piezo sensor to reliably deliver accurate amounts of food, and can also be built using 3D printed parts.
Portal related to signal generation. Provided system was developed by Columbia University scientists. System includes signal generator for scientific applications which generates digital or true analog signals (sine waves, step functions, and pulse trains) and can be controlled with intuitive serial monitor interface.
Project related to feeding behavior.Provides device for dispensing pre-measured quantities of food at regular intervals throughout day. Device uses 24 hour clock movement to rotate dispenser wheel one revolution per day.
Portal provides open source, cross platform Python library that adds 3D stimulus support to all OpenGL based 2D Python stimulus libraries. Ratcave comes with resources including basic 3D object primitives and wide range of 3D light effects. Intuitive object oriented interface allows for all objects, which include meshes, lights, and cameras, can be repositioned, rotated, and scaled.
Portal related to delivering stimuli and monitoring responses. Provided behavioral platform was developed by scientists from Huazhong University of Science and Technology, Wuhan, China. System uses Arduino UNO board and simple drive circuit along with stand-along GUI application. Experimental data is automatically recorded with built-in data acquisition function and entire behavioral schedule is stored within Arduino chip.
Modular Automated Platform for Large Scale Experiments project
Modular Automated Platform for Large -Scale Experiments
Portal related to measurement of fly social networks and behavior. Provides Drosophila handing robot that boasts modular design, allowing platform to both automate diverse phenotyping assays and aid with lab chores (e.g., collecting virgin female flies). MAPLE permits small part manipulator, USB digital camera, and fly manipulator to work simultaneously over platform of flies.
Portal related to Rodent Running Disk. Provided Rodent Running Disk was developed by University of California, Berkeley scientist. Acrylic disk mounted to optical encoder to achieve fast locomotion decoding.
Portal provides Moving Wall Box system used to testing strategy task where mouse is repeatedly forced to jump over small ice by slowly moving walls whereby presence of animal is automatically sensed via balances and analyzed by microcontroller board which in turn controls movements of walls. Device provided by Max Planck Institute of Psychiatry scientist. Used for repeated assessment of fear coping strategies.
Portal provides Teensy-Based Interface system. System includes Teensy 3.2 microcontroller based interface that is easily programmable, and offers high speed, precisely timed behavioral data acquisition and digital and analog outputs for controlling sCMOS cameras and other devices. Developed by Boston University scientists.
Portal provides head fixed behavioral environment that uses lightweight physical maze floating on air table that moves around animals body under direct control of animal itself.
Autonomous Training of a Forelimb Motor Task project
Autonomous Training of a Forelimb Motor Task
Portal related to individualized tracking of self directed motor learning in group housed mice performing skilled lever positioning task in home cage. Provides system for fully autonomous training of group housed mice on forelimb motor task. Task is run and controlled by Raspberry Pi microcomputer, which allows for cages to be monitored remotely through active internet connection. System was developed by University of Ottawa scientists.
Portal provides open source and affordable microscope experimental setup device based on Raspberry Pi, Arduino microcontroller and off-the-shelf electronic components. System design is based on 3D-printed mainframe, Raspberry Pi computer, and high definition camera system as well as Arduino based optical and thermal control circuits. All functions of FlyPi can be controlled through custom written graphical user interface.
Portal provides operant box designed to train small primates in auditory tasks.Device is based on computer and Arduino Mega 2560 board, named OBAT (Operant Box for Auditory Tasks), designed to present two different auditory stimuli to small primates.All schematics and software source code are available.
Portal for open source operant chamber, based on Arduino microcontroller platform, that can be used to train mice to respond for reward. Designed by NIDDK scientists.Apparatus contains two nose pokes, drinking well, and solenoid controlled sucrose delivery system. Chamber can run magazine training, fixed ratio and progressive ratio training schedules, and can be programmed to run more complicated behavioral paradigms.
Open source syringe pump apparatus developed by scientists from Michigan Technological University. Syringe pump is designed using freely available open source computer aided design (CAD) software and manufactured using open source RepRap 3-D printer and readily available parts.
Automated Home-Cage Functional Imaging project
Automated Home-Cage Functional Imaging system
Portal provides automated system for mesoscopic functional imaging that allows subjects to self initiate head fixation and imaging within home cage. Developed by University of British Columbia scientists. System for automated head fixation within mouse home cages.
Portal provides arduino based, 3D-printed nose poke device for rats. Includes set of instructions on how to build this device using arduino, some 3D printed parts and some off-the-shelf electronic components.
Portal provides Python based camera software GUI developed by Harvard University scientists. Open source software package that allows video to be recorded in sync with behavior. Python API to record video system timestamps from Imaging Source USB cameras.
Portal provides low cost, open source, wireless probe for optogenetic stimulation. This wireless system for optogenetic stimulation was developed by UCLA scientists. Device consists of two parts. Optical component is mounted on head permanently, whereas electronic component is removable and is applied for each experiment. Device is controlled via custom GUI (built with the TkInter Python 2.7 library) which sends pulses to device via Arduino Uno.
Portal provides open source control system for in vivo fluorescence measurements from deep brain structures developed by University of California, San Francisco scientists. Microcontroller based solution for controlling optical components in intracranial photometry system and processing resulting signal.
Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project
Portal provides brain implant developed by MIT scientists. Implant carries 16 movable tetrodes along with two optic fibers or two injection cannulas. Designed with help of 3D CAD software, allowing modifications for various experimental needs, such as targeting different brain regions and use in other animal species (e.g., rats and non-human primates). Implant can be designed to shape of skull of individual monkeys based on pre-implantation magnetic resonance imaging, thus optimizing fit with skull surface and making recording from deep brain regions more reliable.
Portal provides computer numerical controlled robot for cranial microsurgeries developed by University of Minnesota scientist. Included cranial microsurgery platform combines automated skull surface profiling with computer numerical controlled milling machine to perform variety of cranial microsurgical procedures on mice.
Portal provides system that combines open source hardware and software for control of behavioral experiments. Open source framework, combines Python scripts and Micropython microcontroller. Framework can be run through command line interface, or in user friendly graphical user interface that allows users to manage variety of devices such as nose pokes, LED drivers, stepper motor controllers and more. Data collected using this system can then be imported into Python for data analysis.
Portal provides open hardware used in labs for administering picoliters of liquid to biological samples. Pressure ejection system developed by University of Sussex scientist for reliably delivering picolitre volumes.
Portal provides open source, low cost, programmable pulse train generator for physiology and behavior. Device allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Arduino powered device that generates precise sequences of voltage pulses for neural stimulation and stimulus control. Controlled either through its APIs in MATLAB, Python and C plus plus, or as stand-alone instrument using its oLED screen and clickable thumb joystick.
Portal provides miniscope for fluorescence imaging and optogenetic stimulation. Used for monitoring of neural signals during unrestrained behavior.
Portal provides open source circuit for microwire tetrode gold plating. Circuit includes impedance meter and current generator for tetrode gold plating. Developed by University of Toyama scientist.
Portal provides system capable of frame differencing, color tracking, marker tracking, face detection, eye tracking, person detection (with TensorFlow Lite), and more. Supports very easy to use GUI, the OpenMV IDE.
Homecage Task Training and Mesoscale Imaging project
Homecage Task Training and Mesoscale Imaging
Project to build and use new generation of home cages with emphasis on training for simple headfixed tasks during simultaneous autonomous acquisition of mesoscale brain imaging data. Homecage platform for automated task training and mesoscale brain imaging for mice developed by University of British Columbia scientists.
Portal provides MouseMove software system used to analyze Open Field behavior of mice after experimental stroke to show reduced locomotor activity and to quantify laterality deficits. System is used in combination with open source program ImageJ and MTrack2 plugin to analyze pre recorded Open Field test video. System has two downloadable components, ImageJ macro and separate program with custom built MouseMove GUI. ImageJ is used to subtract background video from experiment and create image of animals total trajectory. MouseMove GUI then completes detailed analysis of movement patterns, measuring fractional time spent stationary, distance traveled, speed mean and various details of laterality.
Portal provides open source neural recording device for wireless transmission of local field potential data in freely behaving animals. Used for electrophysiological recording of local field potentials in freely behaving animals.
Robotic Flower System for Bee Behavior project
Portal provides system of robotic artificial flowers to study bumble bee behavior. System is designed to capture data when animal is feeding by placement of IR beams that are broken when engaged on flowers feeding mechanism and sends data to control unit.Developed by University of Oulu in Finland scientists. System includes control unit, separate artificial flowers, and personal computer. Control unit is to handle electronics of flowers, collect data from them, and to send data to computer. Flowers contain infrared sensor, their associated electronics, and electromechanical device that offers small, precise amount of sugar solution from reservoir. Computer runs software that controls refilling rate and data collection via the control unit. Circuit diagrams, parts list, and control software and source code are available in paper supplemental information.
Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior.
Portal provides open Source 3-D Printed Modular micro drive system for acute primate neurophysiology.
Portal provides open source Compact Head Mounted Endoscope for imaging in freely behaving mouse. Includes accessible and flexible set of calcium imaging tools for neuroscience research community.
Portal provides open source, RFID-based system for automated measurement and analysis of social preference and in-cohort sociability in mice. System was developed by Nencki Institute of Experimental Biology scientists.
An Opensource lickometer and microstructure analysis program
Portal provides open source lickometer that utilizes readily available or customizable components such as PC sound card and 3D printed drinking bottle holder. System consists of apparatus itself and open source software to collect and analyze data. Recording of raw data is handled by Audacity, open source audio program.
Microwave based Homecage Motion Detector project
Microwave based Homecage Motion Detector
Portal provides radar based motion detector for home cage activity monitoring in mice. System is used for motion detection without visual contact to animal and can be used with various cage types. Features custom printed circuit board and motion detector shield for Arduino, which saves raw activity and timestamped data in CSV files onto SD card.Developed by Max Planck Institute of Psychiatry scientists. Authors also provide Python script for data analysis and generation of actograms.
A Head Mounted Multi Camera System for Freely Moving Mice project
A Head Mounted Multi Camera System for Freely Moving Mice
Portal provides system of two multi camera head mounts for mice in order to record physiological changes in certain behaviors. System used for video tracking of rodents behavior.
Portal provides open source nose poke system utilizing Arduino microcontroller, several low cost electronic components, and PVC behavioral arena. System developed by University of Basel scientists for use in behavior experiments.
Portal provides touchscreen platform developed by Texas Christian University scientists. iPad apparatus set up consists of four wall operant chamber, remote desktop program, Visual Basic 6 software, and single wireless iPad. Wireless iPad allows for flexibility in setups during performing visual discrimination behavioral experiments.
Portal provides Arduino controlled stimulus isolator that allows for highly accurate, reproducible automated setting of stimulation currents. Automatic stimulation patterns are software controlled and parameters are set from Matlab coded simple, intuitive and user friendly graphical user interface.
Portal provides novel head cap and microdrive design for chronic multi electrode recordings in rats through use of 3D printing technology. Head cap and microdrive designs can be fabricated at little cost using consumer grade 3D printers.
Portal provides low profile in vivo imaging support and restraint system for mice. System is compact and provides sturdy head fixation, gas anesthesia mask, and warm water bed. Compact design allows to work with variety of microscope stages and use of 3D printed components makes this design customizable.
Automated Classification of Self-grooming in Mice project
Automated Classification of Self-grooming in Mice
Portal provides protocol that implements JAABA, open source machine learning based behavior detection system; motr, open-source mouse trajectory tracking software; and bonsai, open source system capable of streaming and recording video. Together they use these tools to process videos of mice performing grooming behaviors in variety of behavioral setups.
Software 3D graphics python package for cognitive psychology experiments. Open source, cross platform Python library that adds 3D stimulus support to all OpenGL-based 2D Python stimulus libraries. These libraries include VisionEgg, Psychopy, Pyglet, and PyGam.
Modular Automated Platform for Large Scale Experiments
Software tool to automate various fly handling tasks.Control software for Drosophila handling robot MAPLE.
Software tool as virtual reality engine built on ROS and OpenSceneGraph.Perspective correct Virtual Reality for freely moving animals engine. Used for multicomputer realtime tracking and display with goal of being useful for scientific studies of vision and behavior.Part of FreemoVR system.
Teensy microcontroller based interface for optical imaging camera control during behavioral experiments.
Software Python tool running on Raspberry Pi computer. Used for trial timing and data logging. Part of Autonomous Training of Forelimb Motor Task system.
Software tool as part of Operant Box for Auditory Tasks system.
Software tool as Arduino UNO/Mega based, visual programming and real-time behavioral platform for neuroscience. It can run Go/No-Go, 2AFPC and Optogenetic stimulation tasks. Stand alone and intuitive Gaphical User Interface application.Part of ArControl system.
Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology
Softwre tool as part of Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project for brain implant.
Software tool as part of Automated Home Cage Functional Imaging system.
Software tool as script to test if IR led, IR photodiode, arduino and 3D printed nose poke device work properly. Part of Nose Poke Device system.
Software tool as part of Craniobot system.Generates, sends, and receives commands to communicate with the Craniobot.
Software tool as part of Pulse Pal system which allows users to create and trigger software defined trains of voltage pulses with high temporal precision.
Open source software Python tool for behavioural experiment control. Part of pyControl system.
Code and model files for open source linear actuator. Part of Pearce Lab Syringe Pump system.
Open source software package that allows video to be recorded in sync with behavior. Python GUI and scripts allows investigators to record from multiple imaging source camera feeds with associated timestamps for each frame. Python API to record video system timestamps from Imaging Source USB cameras. Package requires Windows 10, Anaconda, and Git, and is compatible with Imaging Source USB3 cameras. Part of Camera Control project.
Software tool as part of CHEndoscope. Acquisition software that interfaces with CHEndoscope Ximea USB camera. This code is compatible with Linux and Windows systems.
Software Python code for automated control of behavioural apparatus and imaging for mice in home cage environment.Part of Homecage Task Training and Mesoscale Imaging system.
Open source program for semi automated analysis of movement and cognitive testing in rodents. Accurately quantifies numerous parameters of movement including travel distance, speed, turning, stationary fraction and laterality. Part of MouseMove system.
Boston University;Boston;Massachusetts;USA
Private research institution with two primary campuses in heart of Boston and programs around the world.
Michigan Technological University; Houghton; USA
Public research university founded in 1885.
Texas Christian University; Fort Worth; USA
Private Christian university in Fort Worth, Texas. It was established in 1873 by brothers Addison and Randolph Clark as the Add Ran Male and Female College.
Company to design and sell powerful neuroscience hardware that interfaces with open source software platform supported by large community of scientists and developers. Support efforts of open source community in commercially sustainable way.
Organization mission is to advance understanding of brain by promoting community ownership of neuroscience tools.Collaborative effort to develop, document, and distribute open source tools for systems neuroscience.Project aims to distribute reliable open source software as well as tools for extracellular recording and stimulation.
Human RNA-seq-based gene and transcript co-expression database.Functional genomics tool based on gene co-expression map that describes which genes tend to be activated and deactivated simultaneously in large number of RNAseq data samples.
Atlas is set of interactive tools built to promote retrieval, exploration, discovery, and analysis of Kidney Precision Medicine Project data by greater research community. Datasets available in repository are combination of raw and processed data from KPMP participant biopsies and reference tissue samples.
Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing.
Thermo Fisher | Sorvall X4R Pro 100V centrifuge
Tissue culture Pro series touch screen centrifuge enables programming for quicker results plus easily access and track all runs, rotor life and centrifuge health. With capacity up to 4L, including 196 blood tubes and 96 15mL conical tubes, AutoLock for fast rotor exchange.
Kent Scientific | SomnoFlow Low Flow Electronic Vaporizer
Kent Scientific SomnoFlow Electronic Vaporizer
Compact, standalone vaporizer that uses either ambient air with internal air pump or compressed gas. It delivers only anesthetic required by animal according to its weight with flows down to 0.05 LPM. Low flow isoflurane anesthesia machine.
International Institute of Molecular and Cell Biology in Warsaw, Biophysics and Bioanalytics Facility
IIMCB-Biophysics and Structural Biology Facility
International Institute of Molecular and Cell Biology IIMCB-Biophysics and Structural Biology Core Facility
Offers comprehensive selection of molecular biophysics techniques such as SPR, SEC-MALS, AUC, ITC, CD, FT-IR useful in characterization of macromolecule size and intermolecular interactions.
Rutgers New Jersey Medical School Genomic Center Core Facility
Rutgers New Jersey Medical School Genomic Center
The State University of New Jersey Genomic center
Provides NGS services for research and clinical samples in CLIP and CAP accredited laboratory.Services include consultation, sample processing, sequencing and data analysis , as well as interpretation and reporting.Service support for genomics based applications including experimental design, bioinformatics, development of novel assays, grant writing and manuscript preparation. We are experienced in broad range of biological disciplines including basic biology, infectious diseases, cancer, neurobiology, immunology and clinical research. Clinical Genomics lab has extensive experience in molecular diagnostics and clinical research, and specializes in clinical biomarker discovery, validation and diagnostic test development.
Web tool as prototype service to automatically generate Wikidata items using metadata from scholarly publications. Citation lookup tool in Wikipedia platform. Takes persistent identifier for scholarly article and processes it by importing bibliographic metadata into Wikidata items. In August 2018, it was merged with ORCIDator into single tool that allows for fully automated batch processing based on ISBN-13, DOI, ORCID iD, PubMed ID, PMCID identifiers.
Software tool as fast simulator of genetic data that samples from Discrete Time Wright Fisher process backwards in time. Used to simulate long chromosomes and large samples under DTWF, with computational time comparable to recent coalescent simulators.
Software tool for inferring patterns of population splits and mixtures in history of set of populations.
Texas A&M Health Science Center Integrated Microscopy and Imaging Laboratory Core Facility
TAMHSC-IMIL-Integrated Microscopy and Imaging Laboratory
Texas A&M Health Science Center TAMHSC-IMIL-Integrated Microscopy and Imaging Laboratory
Core supports research progress and grant development by encouraging researchers to explore advanced imaging modalities and to incorporate them into their existing research programs.Provides technical expertise and cutting edge microscope systems to support research of faculty and staff of Texas A&M University Health Science Center, Texas A&M University, and all other campuses.IMIL includes six microscopy rooms, supporting facilities, and image processing station.Technical staff is available to train and assist with design, implementation, and analysis of experiments as well as assist in troubleshooting.
neuronal reconstruction analysis project
Project for quantitative neuronal morphometry by supervised and unsupervised learning. Includes protocol to quantify and interpret morphological properties of individual neurons reconstructed from microscopic imaging.Includes information about installation of analysis tools and downloading datasets and custom codes.
Software tool to predict genes in anonymous genomic sequences designed with hierarchical structure. Predicts genes, exons, splice sites and other signals along DNA sequence. Has been trained on several species.
Software electronic health record system that provides clinical charting for health care professionals at midsized and community hospitals. Software solution for maintaining patient electronic health records and serving as laboratory information management system.
Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
Repository of gene phenotype associations for phenotypes derived from electronic health records, questionnaire data, and continuous traits computed on exomes released by UK Biobank. Repository was made available by AstraZeneca for public research.
Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.
Pegasus tool for massive single cell data processing
Software package for massive single cell data processing. Enables analysis of million scale single cell RNA-seq data and is functionally comparable to Seurat and SCANPY. Command line tool, Python package and base for Cloud based analysis workflows. Supports variety of analysis tasks, such as cell and gene level quality control, highly variable gene selection, dimension reduction, kNN graph building, data integration, clustering, differential expression analysis and putative cell type annotation.
Web interactive visualization tool for large scale single cell genomics data.Interactive web application for exploring million scale single cell datasets. Can be hosted on Google App Engine application for collaborative use or can be run in standalone mode on personal computer. Consists of client side component implemented in JavaScript and server component implemented in Python. Client uses React to manage state and WebGL to visualize variables on 2D/3D embeddings in performant manner. Server component consists of functions to manage datasets, slice variables from dataset stored in PARQUET, Zarr or H5AD formats.
Joint effort with Brain Architecture Portal and Single Cell Portal to visually combine anatomic and molecular brain data in. Users can search for neuroscience data using natural language and faceted search, and then this portal retrieves molecular data housed in the Single Cell Portal and anatomical data in the Brain Architecture Portal. Each study includes information on cell types, gene expression, related genes, and spatial transcriptomics. You can also download a study’s data to explore further and build on your science.
Open ecosystem of data repositories hosted by various partner organizations, who work together to ensure that their data can be federated across participating platforms. Open source platform for biomedical researchers to access data, run analysis tools, and collaborate. Terra powers important scientific projects including AnVIL, BioData Catalyst, Human Cell Atlas, BICCN, and many others. Easily access both open and access-controlled datasets hosted in cloud repositories. Explore, analyze, and visualize data using Jupyter Notebooks, RStudio, RShinyApps, and Galaxy.
Curates and compiles genome wide QTL summary statistics for many human molecular traits across tissues and cell types. Comprises tens of millions significant genotype molecular trait associations under different conditions. Users can visualize QTL results in phenome wide and tissue wide levels, and annotate their biological functions through comprehensive genomic features and functional evidence. QTLbase provides one stop shop of QTLs retrieval and comparison across multiple tissues and multiple layers of molecular complexity, and it will greatly help researchers interrogate biological mechanism of causal variants and guide direction of functional validation.
Interactive portal provides datasets, across variety of cell types, for LD biology, including transcriptional profiles of induced lipid storage, organellar proteomics, genome-wide screen phenotypes, and ties to human genetics. Provides comprehensive picture of genes and pathways affecting lipid droplet biology, including gene expression, proteomics, and LD morphology phenotypes, by integrating multiple relevant data types.
Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment.
Panorama: Repository Software for Targeted Mass Spectrometry Assays from Skyline
Open source data management system for mass spectrometry data processed with Skyline targeted mass spectrometry environment. System includes Repository Server application for targeted mass spectrometry assays that integrates into Skyline mass spec workflow and has been implemented as module within LabKey Server data management platform; Panorama Web application facilitates viewing, sharing, and disseminating results contained in Skyline documents via web browser; Panorama Public repository employs full data visualization capabilities of Panorama which facilitates sharing results with reviewers during manuscript review.
Software R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis.
Project provides miniature mirror stereoscope system for MRI-scanner. System takes advantage of commonly used display equipment, MRI head coil, and display screen. Miniature Wheatstone stereoscope is used for human neuroimaging.
Cellometer Auto T4 Bright Field Cell Counter
Nexcellom Bioscience Cellometer Auto T4 Bright Field Cell Counter
System includes automated cell counter for trypan blue viability for cell lines and bright field imaging and pattern recognition software to quickly and accurately identify and count individual cells. Cell count, concentration, diameter, and % viability are automatically calculated and reported.
Software tool for improved long read mapping and structural variant calling via dual mode alignment.
High speed, high resolution digital scanner with network features. User friendly full slide scanner designed to process up to 210 slides automatically.
Software tool as framework querying ontology terms within SciCrunch and SciCrunch SciGraph endpoints.
NanoString | GeoMx Digital Spatial Profiler
Integrated commercial system comprising hardware, software and nCounter chemistry that enables simultaneous, highly multiplex spatial profiling of proteins or RNA in FFPE tissues. DSP platform quantifies abundance of protein or RNA by counting unique indexing oligonucleotides assigned to each target of interest. Used to rapidly and quantitatively assess biological implications of heterogeneity within tissue samples.
Software Python package for accurate circRNA quantification and differential expression analysis. Comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data. Accurate quantification of circular RNAs identifies extensive circular isoform switching events.
Software tool for circRNA detection from RNAseq reads. Python code to detect head-to-tail spliced (back-spliced) sequencing reads, indicative of circular RNA in RNA-seq data.
Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq
Software tool as computational pipeline for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq. CIRCexplorer3-CLEAR is CLEAR pipeline for direct comparison of circular and linear RNA expression.
Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs.
High level, high performance, dynamic language for technical computing. It is a type system with parametric polymorphism in dynamc programming language.
Software pipeline for creating harmonized single cell RNA-seq dataset for retina with publicly available data. Platform for analysis of single cell eye in disk. Snakefile based process to turn 1.4 million ocular cells into unified meta-atlas. Meta-atlas that compiles 1.2 million single-cell back of the eye transcriptomes across studies, publications, and species.
Cornell University Weill Medical College Human Immune Monitoring Core Facility
WCM Human Immune Monitoring Core (HIMC) at Weill Cornell Medicine
Core provides technology platforms and services for single cell, in situ, and multiomic analysis for cutting edge immunology research and clinical studies to help make impactful discoveries and develop improved treatments for human diseases. Services include Spectral flow cytometry (Cytek Aurora), Imaging mass cytometry (Fluidigm Hyperion), CyTOF mass cytometry (Fluidigm Helios).
Software tool to make artificial RNAseq datasets with circRNA reads. Specific simulation tool for non-canonical transcripts. Takes FASTA-formatted reference file and GTF annotation file as input, and generates circular and linear RNA sequences.
Software tool for prediction of lysine acetyltransferase specific modification sites from protein sequences.
Software R package for analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on basis of single or multiple strata of count data presented in contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Software R package for design and analysis of disease surveillance activities. These functions were originally developed for animal health surveillance activities but can be equally applied to aquatic animal, wildlife, plant and human health surveillance activities. Utilities are included for sample size calculation and analysis of representative surveys for disease freedom, risk-based studies for disease freedom and for prevalence estimation.
Software R package to calculate probability of freedom from disease in population based on surveillance data.
Software tool as interface for designing and presenting visual stimuli.
Platform to manage and curate large scientific datasets. Used for scientific data management and analysis.Provides advanced functionality to organize files and complex metadata describing datasets and allows users to interact, search, and analyze these data through web application or programmatically using Python client. Provides end-to-end solution for publishing datasets through Blackfynn Discover, assigning DOIs and ensuring that published data becomes available to larger academic community in sustainable and FAIR manner.
Portal to release connectivity and functional imaging data collected by consortium of laboratories led by groups at Allen Institute for Brain Science, Princeton University, and Baylor College of Medicine, with support from broad array of teams, coordinated and funded by IARPA MICrONS program. Data include large scale electron microscopy based reconstructions of cortical circuitry from mouse visual cortex, with corresponding functional imaging data from those same neurons.
International, community based, nongovernmental, and nonprofit organization promoting sustainable and trustworthy data infrastructures governed by Standards and Certification Board. Offers to any data repository core level certification based on tDSA–WDS Core Trustworthy Data Repositories Requirements catalogue and procedures. CoreTrustSeal Data Repository certification replaces the DSA certification and WDS Regular Members certification.
Software tool as fast principal component analysis of large scale genome wide data. FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA2 used for principal component analysis of biobank scale genotype datasets.
Nonprofit organization with mission to work with companies and governments to build open, trustworthy data ecosystem. They work with range of organisations, governments, public bodies and civil society to create world where data works for everyone.
Software suite of interoperable software tools designed for global community of public health practitioners and researchers. Provides easy data entry form and database construction, customized data entry experience, and data analysis with epidemiologic statistics, maps, and graphs for public health professionals who may lack information technology background.Statistical software for epidemiology developed by Centers for Disease Control and Prevention in Atlanta, Georgia. Available for Microsoft Windows, Android and iOS, along with web and cloud version.
Portal created to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis and schwannomatosis.Public data repository that stores and shares data generated by multiple collaborative research programs focused on neurofibromatosis diseases.
Software tool for PRAGUI pipeline exploratory analysis.
Software pipeline to process and analyse RNAseq data. Contains files needed to process and analyse RNAseq data.
System used for detection of chemiluminescence, fluorescence, colorimetry,densitometry, gel documentation. It has been replaced by ChemiDoc Imager. BioRad continues to provide support for customers with ChemiDoc Touch Systems.
Software package for gradient boosting on decision trees library. Used for ranking, classification, regression and other ML tasks.
Open source, low code machine learning library in Python that allows you to go from preparing your data to deploying your model within minutes in your choice of notebook environment.
Software tool as wrapper feature selection method which combines both Boruta feature selection algorithm with shapley values.
Software tool as gradient boosting framework that uses tree based learning algorithms. Designed to be distributed and efficient with advantages:Faster training speed and higher efficiency;Lower memory usage;Better accuracy;Support of parallel, distributed, and GPU learning;Capable of handling large scale data.
Software Python package to tackle curse of imbalanced datasets in machine learning.Offers number of re-sampling techniques commonly used in datasets showing strong between class imbalance.
Software pacakge that uses Levenshtein Distance to calculate differences between sequences for string matching.
Catalog provides uniformly processed gene expression and splicing QTLs from all available public studies on human. Expression and splicing QTLs recomputed from public datasets.
Portal offers features to help discover associations between genes, variants, and traits including Browse and rank gene and variant associations identified by Locus-to-Gene (L2G) scoring pipeline, Uncover credible sets for variant and trait associations based on mapping analyses pipeline, Explore and compare studies from UK Biobank, FinnGen, and GWAS Catalog using multi-trait comparison tool eQTL Catalogue.
Platform for supporting systematic drug–target identification and prioritisation.Provides users with queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence.
Data portal as part of Human BioMolecular Atlas Program. Data available on HuBMAP Portal is open access data to be used for research of human biology. Certain data types with potential for re-identification are available in restricted access either directly through this portal by login-dependent permissions or through dbGAP. All data users are expected to respect privacy and confidentiality of donors who provided samples. Data are not to be used to re-identify donors or their family members without further approval from HuBMAP. Data for single-cell, three-dimensional maps of various human tissues. Data include discrete, complex organs (kidney, ureter, bladder, lung, breast, small intestine and colon); distributed organ systems (vasculature); systems comprising dynamic or motile cell types with distinct microenvironments (lymphatic organs: spleen, thymus, and lymph nodes).
Software annotation tool for audio and video recordings. Annotation can be sentence, word or gloss, comment, translation or description of any feature observed in media. Annotations can be created on multiple layers. Tiers can be hierarchically interconnected. Annotation can either be time-aligned to media or it can refer to other existing annotations. Content of annotations consists of Unicode text and annotation documents are stored in XML format (EAF).
Max Planck Institute for Psycholinguistics; Nijmegen; Netherlands
Institute is entirely devoted to psycholinguistics – the study of how we produce and understand language, and how we acquire these skills as first or second language learners. The only institution in the world entirely dedicated to psycholinguistics, and is also one of only three among total of 90 within the Max Planck Society to be located outside Germany.
Software tool for imputation of viral whole genome sequences from partially sequenced samples. Software tool for imputation of whole-genome SARS-CoV-2 sequences.
Open source application, built upon FluoRender, for visualization and analysis of 3D/4D datasets. Also supports advanced segmentation.
Software JavaScript framework for building UI on the web. Used for building user interfaces and single-page applications.
YAML is a human friendly data serialization language for all programming languages. Unicode based data serialization language designed around common native data types of agile programming languages. Useful for programming needs ranging from configuration files to Internet messaging to object persistence to data auditing.
Software tool for image analysis. Used in Quantitative Digital Pathology. Compatible with leading slide scanner manufacturers, data management software, and wide variety of microscopes and cameras.
System includes hardware and software. Options include nCounter SPRINT,nCounter MAX or nCounter FLEX. Platform used for multiplex analysis of up to 800 RNA, DNA, or protein targets. System can be combined with GeoMx Digital Spatial Profiler (DSP) to enable high-plex, spatially-resolved RNA, and protein quantification.
University of Texas at Austin Genomic Sequencing and Analysis Core Facility
Genomic Sequencing and Analysis Facility
The University of Texas at Austin Genomic Sequencing and Analysis Facility
Full service sequencing core that provides both Sanger and Next Generation Sequencing services, in addition to library prep and quality check services, open access to equipment and training. Works directly with the bioinformatics core who can provide assist in any of your analysis needs to data storage solutions.
Gladstone Institutes Gladstone Flow Cytometry Core Facility
Core offers operation, training and consultation on both cell sorters and analyzers.Our core comprises BDFACsAria II, two BDFACSAria Fusions, Fortessa X-20 and Attune, with analyzing and sorting up to 18 colors possible. Core also offers antibody staining, protocol optimization and data analysis services.
Software tool used to precisely segment cells from wide range of image types and does not require model retraining or parameter adjustments. Generalist algorithm for cellular segmentation. Anatomical segmentation algorithm written in Python 3.
Software tool as deep learning software for automated kymograph analysis. Uses artificial intelligence to trace lines in kymograph and extract information about particle movement. Speeds up analysis of kymographs by between 50 and 250 times, and comparisons show that it is as reliable as manual analysis.
Software tool for image processing to perform automated, semi-automated, and manual cell migration detection. Open source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. Written in MATLAB. Works with Windows, Macintosh and UNIX based systems.
Software tool as interactive image processing program for biologists written in Python. Used to write analyze images and movies of biological data.
Software tool calculates direction autocorrelation, plots and calculates other essential parameters to analyze cell migration in two dimensions: it displays cell trajectories individually and collectively, and it calculates average speed and mean square displacements (MSDs) to assess the area explored by cells over time.
Visually Aided Morpho-Phenotyping Image Recognition
Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity.
International Cancer Genome Consortium Data Portal
Portal provides tools for visualizing, querying, and downloading cancer data, which is released on quarterly schedule.
Web server predicts and visualizes mutation induced structure changes of single nucleotide polymorphism in RNA sequence. This covers changes in accessibility (single strandedness) of molecule, its intra molecular base pairing potential and its base pairing probabilities. One of Freiburg RNA tools.
Reference Free Sequence Classification Tool
Reference-Free Sequence Classification Tool
Software tool that using machine learning classifiers relies on ensemble of experts in order to provide efficient classification in metagenomic contexts. Used for DNA sequences in metagenomic samples.
Software package for ZEISS light microscopy systems. Universal user interface for every imaging system from ZEISS to assist to acquire images, process images, visualize big data by GPU powered 3D engine, analyze images via Machine Learning-based tools, correlate between light-light or light-electron microscopes, store raw data in secure format locally or in the cloud., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Mutational Signature Comprehensive Analysis Toolkit
Software R package to discover and predict, visualize and analyze mutational signatures. Used to count and combine multiple mutation types, including SBS, DBS, and indels. Calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type.
Cornell University BRC Genomics Core Facility
Cornell University BRC Genomics Facility
Full Service DNA Sequencing and Genotyping facility. Offers Sanger,Fragment Analysis, Illumina, RT and Digital PCR, Single Cell, large projects, sample/library prep and QC.Houses state of the art instruments for all your sequencing needs including, capillary DNA analysis, single cell applications, long read capabilities. We also provide many instruments that can be operated by you for sample preparation and quality control of all sample types.
University of Texas at Austin Biological Mass Spectrometry Proteomics Core Facility
The University of Texas at Austin UTA CBRS Biological Mass Spectrometry Facility
UTA CBRS Biological Mass Spectrometry Facility
Proteomics and Metabolomics services and collaborative efforts are provided at Biological Mass Spectrometry Facility. We use high resolution Orbitrap mass spectrometers with UPLC at high flow for metabolomics and nanoUPLC for proteomics work. We have Bruker Autoflex for self service MALDI. Our proteomics services are protein ID, quantitation, and modification analysis, with fractionation for deeper coverage and de novo sequencing of mAbs available. We collaborate for customized projects. We have untargeted metabolomics for quantitative or qualitative analysis of extracted metabolites using C18 column.
Stowers Institute for Medical Research Genome Engineering Core Facility
Stowers Institute for Medical Research SIMR Genome Engineering
Core supports genome engineering using CRISPR technology. Provide services to generate knockouts, insertions, deletions, and point mutations in various organisms. Services for genome engineering include guideRNA design, homology-directed repair template design, production of modified mammalian cell lines, preparation of reagents for delivery to embryos, and mutation detection by targeted deep sequencing. Pooled screening is also coordinated and supported by our team.We acquire, prepare, and validate pooled libraries as an Institute resource. In coordination of our pooled screen workflow, we work with other teams to track the progress of these projects. Once resulting cell populations from the screen are delivered, our team does genomic DNA purification, target amplification, and preparation for NGS. We now offer a TAIL-PCR service to identify the location of random integration events. We have successfully identified locations in killifish, fly, zebrafish, and sea anemone.Team is responsible for maintaining and distributing clone and vector collections for the Institute.
Collaborative environment hosting scientists from backgrounds ranging from neuroanatomy, to microscopy and computer science, facilitating production, collection, and analysis of brain wide connectivity data. Home of Mouse Connectome Project seeks to develop multimodal multiscale connectome and cell-type map of mammalian brain using advanced tracing, imaging, and computational methods.Crossdisciplinary group develops neuroanatomic and neuroinformatic approaches to understand connectivity patterns in health and disease. Portal includes iConnectome Viewer, iConnectome Maps and Atlas Viewer.
National research program to learn how genes, lifestyle, and military exposures affect health and illness.
Software tool as 3D adult zebrafish brain atlas for digital age. Built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains.
Software tool to profile enrichment of next generation sequencing reads at transposable elements. Method to estimate repetitive element enrichment using high throughput sequencing data. Used to study genome wide transcriptional regulation of repetitive elements.RepEnrich2 is updated method to estimate repetitive element enrichment using high-throughput sequencing data.
Software Python package.Python analysis module for AVATAR recording system. Uses three-dimentional coordinate data to produce motor coordination data from general information like velocity and total distance to behavior clustering based on python scripts.
Open Data Commons for Traumatic Brain Injury
Software as cloud based community driven repository to store, share, and publish traumatic brain injury research data. Aims to increase transparency with individual level data, enhance collaboration, facilitate advanced analytics, and conform to increasing mandates by funders and publishers to make data accessible. Members of ODC-TBI have access to private digital lab space managed by PI or multi-PIs for dataset storage and sharing. PIs can share their labs’ datasets with registered members of ODC-TBI community and make their datasets public and citable. ODC-TBI implements stewardship principles that scientific data be made FAIR (Findable, Accessible, Interoperable and Reusable).
University of Ottawa Louise Pelletier Histology Core Facility
Louise Pelletier Histology Core Facility
Core is full service histology laboratory available to faculty, researchers, clinicians and students.Provides histological services for both animal and human tissue. Services include paraffin processing and embedding, paraffin and frozen sectioning as well as routine and special histological staining.Equippemnt includes:Leica Bond III Immunostainer to provide automated immunohistochemistry, in-situ hybridization and immunofluorescence staining;Automated tissue processors for paraffin processing; Automated microtomes for paraffin sectioning; Automated stainer that can be programmed to provide wide variety of routine and special stains;Cryostats for sectioning frozen tissue; Tissue Microarray machine.LPHCF can also perform manual chromogenic or fluorescent staining (single or multi-color labelling) on frozen and paraffin sections. We also provide full service slide scanning using Axio Scan.Z1 for Brightfield or Fluorescent stained slides at either 20X or 40X magnification.Personnel in the LPHCF are available for consultation on project/protocol design, technical assistance and training on facility instruments.Infinity software system is used for all of our histological services and instrument training.
Yale University Chemical and Biophysical Instrumentation Center Core Facility
Yale Chemical and Biophysical Instrumentation Center
Core has range of instruments for characterization and structure elucidation of chemical and biophysical samples. Our staff maintains instruments and provides data collection services as well as training and support for self use of many of our instruments. We are most equipped in areas of NMR spectroscopy, Mass spectrometry and X-ray crystallography, but we also have optical and calorimetric instruments.
Software tool fo detecting genomic breakpoints of fusion transcripts in random hexamer RNA-seq data. Used for detection of exonic, intronic and intergenic fusion transcripts and their genomic breakpoints in poly(A)+ and rRNA-minus RNA sequencing data.
Cornell University BRC Flow Cytometry Core Facility
Facility provides training, consulting, assisted use and independent access for wide variety of cell sorting and analysis.
Cornell University BRC Imaging Core Facility
Facility provides instrumentation and training in following areas of High resolution X-ray CT,Small animal X-ray CT,Flow cytometry and sorting,Confocal microscopy,Multiphoton microscopy,Super resolution microscopy,Laser capture microdissection,Light microscopy,Spectrofluorometry,Bioluminescence imaging,High resolution ultrasound imaging,Image visualization and analysis.
University of Kansas Lawrence Protein Structure and X-ray Crystallography Laboratory Core Facility
Protein Structure and X-ray Crystallography Laboratory
Core laboratory with infrastructure and expertise to perform all aspects of protein and small molecule structure determination using X-ray crystallography. For protein structure determination, high-throughput methods are utilized to move projects rapidly from gene-to-structure.
Cornell University BRC Proteomics and Metabolomics Core Facility
BRC Proteomics and Metabolomics Facility
Facility provides diverse range of Mass Spectrometry based proteomics and metabolomics services.Services include sample preparation, sample analysis, and data interpretation.
Software R package for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis.Procedures for Psychological, Psychometric, and Personality Research. Used for personality, psychometric theory and experimental psychology.
Software R package for significance tests for canonical correlation analysis, including asymptotic tests and Monte Carlo method.
Yet Another Canonical Correlation Analysis
Software R package provides alternative canonical correlation,redundancy analysis function, with associated print, plot, and summary methods.
Platform for multilevel and longitudinal data.Provide researchers such as behavioral and social scientists with tools and education related to study design including Calculating power and sample size for any univariate or multivariate test for general linear multivariate model, assuming fixed predictors;Producing confidence intervals on power estimates for designs with fixed predictors;Producing power calculations for designs with single Gaussian covariate;Supporting designs with unequal group sizes, and complicated covariance structures;Creating basic power curves.
Integrated platform for designing clinical trials.
Project to align physical sample identifiers. Used to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications.
Ugo Basile | Dynamic Plantar Aesthesiometer
Dynamic Plantar Aesthesiometer for mechanical stimulation Model 37550
Ugo Basile Dynamic Plantar Aesthesiometer
Aesthesiometer for mechanical stimulation Model 37550. Instrument designed to automate assessment of touch sensitivity on plantar surface of rats or mice and comes ready with all necessary accessories. At each paw withdrawal, automatically detects and records latency time, and actual force at time of paw withdrawal reflex. Movable force actuator is positioned below plantar surface of animal and desired force and force speed is applied, as preset by operator. Von Frey type 0.5mm rigid filament exerts increasing force, until animal twitches its paw.
Set of automated workflows for common sequencing based (Illumina) protocols, such as RNA-seq, ChIP-seq, ATAC-seq, WGBS/RRBS methylation, whole genome/exome/targeted variant detection, and contaminant screening. Sequencing data analysis pipelines.
University of Hawaii at Manoa Microscopy, Imaging, and Flow Cytometry Core Facility
Core offers optical analysis instrumentation from specialized light microscopes to bioluminescence preclinical imagers to flow cytometers for multicolor cellular analysis. Services include high resolution optical sectioning of fixed cells and tissues, time lapse imaging of living cell cultures, non invasive monitoring of tumor formation in preclinical studies, and extracting specific cells of interest from tissue samples.
New York University School of Medicine IonLab Core Facility
Electrophysiology core facility that is part of Ion Channels and Transporters in Immunity Research Program.Research area includes ion channel and transporter function and ionic signaling in immune cells.Users who are studying other cell types or organ systems are welcome.Provides assistance with experimental design, training, implementation, and data analysis.
University of California at Santa Cruz Biomolecular Cryo Electron Microscopy Core Facility
Biomolecular Cryo Electron Microscopy Facility
Biomolecular facility equipped with JEOL 120kV and Glacios 200 kV with K2 Summit direct detector. Provides insights and high throughput data collection and analysis,single particle analysis, sample screening, and high resolution reconstruction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University of Texas at Austin Microscopy and Flow Cytometry Core Facility
Center for Biomedical Research Support Microscopy and Imaging Core Facility
Center for Biomedical Research Support Microscopy and Imaging Facility at UT Austin
Microscopy and Flow Cytometry Facility University of Texas at Austin
Provides light microscopy and flow cytometry equipment and services for ultra structural analysis of variety of sample types. Offers assisted use and training on its instrumentation and consultations on related research. Provides access to both standard and high-end imaging instrumentation to all levels of users.
Cornell University BRC Bioinformatics Core Facility
Facility provides access to high performance computing environment, BioHPC, which includes both hosted hardware and shared machines. Provides consulting and collaborations for Bioinformatics analysis and workflows.
Colorado State University Analytical Resources Core Facility
Core is comprised of Materials and Molecular Analysis (MMA), Imaging and Surface Science (ISS), and Bioanalysis and Omics (BIO) centers. MMA provides instrument capabilities and expertise in spectroscopic (optical, NMR, EPR), mass spectrometry, X-ray and materials (magnetic, thermal, physical) characterization of synthetic, environmental and biological materials, both at bulk and molecular scales; BIO provides analysis of complex biological samples using modern mass spectrometry based metabolomics and proteomics approaches, including supporting cheminformatics; ISS provides analysis of complex biological and inorganic samples using near and far field imaging methods, spectroscopy, and other surface analyses.
Center for research infrastructure combining genetic engineering capabilities, advanced phenotyping and imaging modalities, specific pathogen free animal housing and husbandry, cryopreservation and archiving at BIOCEV campus. Center aims to analyze effect of loss of function gene mutations in mice with goal to produce catalog of gene function, that will help identify causative factors of human diseases as well as novel targets for therapeutic intervention. Through adoption of standardized procedures and pipelines, and usage of quality control measures and cross validation, shared goal is to produce high quality data. Center has phenotyping capabilities to accommodate both mouse and rat disease models.
Collaboration between research institutes working to provide framework of regulatory genomic elements in individuals with neuropsychiatric disorders.Collaboration has resulted in comprehensive set of manuscripts published in Science providing new insights into biology of developing, adult, and diseased human brain.Manuscripts are organized around three flagship articles, first analyzing human development, second studying disease transcriptomes, and third integrating tissue and single cell data with deep learning approaches.
Knowledgebase of biomedical research resources. Repository for storing validation and problematic information about variety of entities within biomedical domain, such as antibodies, cell lines, etc. Enables researchers to submit their own claims about specific entity to make validation/problematic information F.A.I.R. (Findable, Accessable, Interoperable, Reuseable).
Web based interface designed for academic research data management and research data dissemination. Accepts all file types. Enables academics to upload, share, cite and discover all manner of research outputs with security of knowing our hosting options and platform support long term preservation of data.Used to share big datasets from 100GB up. Added features and expert guidance are also included for sharing your data FAIR-ly.During data deposit, personal email support is available and once submitted, Figshare data expert will conduct review of the metadata and spot check of your dataset files and offer guidance, with main aim of enhancing discoverability and reusability.
Open source relational database management system that is compatible drop in replacement for MySQL database technology. Includes selection of storage engines, including high performance storage engines, for working with other RDBMS data sources. Uses standard and popular querying language. Runs on number of operating systems and supports wide variety of programming languages.Modern Relational Database SQL on JSON support.
Software tool to perform rapid fluorescence and morphometric real time, synchronous data acquisition with IonOptix systems, as well as polynomial fitting and analysis for myocyte research. Features include data trace averaging and filtering,composite images, and transient analysis. Integrates presentation of fluorescence traces and images, analog voltages, and cell length data under intuitive interface. Analyzes raw data by performing ratio, ion, or linear calibration calculations.
BOC Sciences provides wide range of research chemicals and biochemicals including inhibitors, building blocks, GMP Products, impurities and metabolites, APIs for Veterinary, Natural Compounds, ADCs, Stem Cell Molecule and chiral compounds.
University of Alabama at Birmingham Biological Data Science Core
Core offers access to computational biology capabilities. Provide services, foster long term collaborations with UAB research community, and provide training for biomedical investigators on specific set of analysis tools and techniques.Places special emphasis in areas of genomics, transcriptomics, systems biology and translational medicine. Services include data analysis, biological interpretation, grant assistance, and training.
Custom service provider that has extensive experience in various antibody production and engineering fields.Services includes mouse and rat monoclonal antibody production using hybridoma technology, human, monkey, rabbit, chicken, dog, llama and camel monoclonal antibody production using various antibody library technologies (including phage display, bacterial display and yeast display).Conducting in depth antibody humanization and affinity maturation using phage display and DNA mutagenesis approaches.OEM services for bulk scale antibody manufacturing, including bacterial production of scFv, diabody, tandem scFv, miniantibody and Fab, and mammalian cell expression of minibody, chimeric IgG, and IgG, are also available at the most competitive price in industry.
Software tool for image acquisition using WiFi-enabled Zeiss microscopes. Compatible with Windows PCs and with Apple tablets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The Atherosclerosis Risk in Communities (ARIC) Study
Platform for prospective epidemiologic study conducted in four U.S. communities. One of most significant and longest running heart health studies and is the largest study of heart health in African Americans. ARIC investigates risk factors for heart disease and stroke, and connections between cardiovascular and cognitive health. ARIC includes two parts: Cohort Component and Community Surveillance Component. Cohort Component began in 1987, and each ARIC field center randomly selected and recruited cohort sample of individuals aged 45-64 from defined population in their community, to receive extensive examinations, including medical, social, and demographic data. In Community Surveillance Component, four communities are investigated to determine long term trends in hospitalized myocardial infarction and coronary heart disease deaths in men and women aged 35-84 years.
Software tool can be used to calculate kappa, chance adjusted measure of agreement, for any number of cases, categories, or raters.
Software implements germline and somatic variant calling pipelines based on best practices pipelines from Broad Institute using Spark framework. Produces VCF output file which contains single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) when supported by used tools. Program requires Spark on either local cluster with one or more nodes, Amazon EMR cluster or Docker image to run.
Core helps to carry out analysis and research on SARS-COV2 virus. Provides COVID-19/ SARS-COV2/ 2019-nCoV Research Tools and Services.Team has developed related proteins, antibodies, nucleic acid extraction kits and other products to help researchers quickly develop effective anti-COVID-19 drugs and vaccines.Provides preclinical research services, various in vivo and in vivo research models, and in vivo diagnostic immunoassay services.
Dual beam FIB/FESEM system, containing both focused Ga plus ion beam and ultra high resolution field emission scanning electron column and their combined use. Dual beam focused ion beam scanning electron microscope for nanofabrication.
Single photon avalanche diodes camera for time correlated single photon counting imaging. Time resolved photon counting camera with in pixel timing electronics what enables time tagging of incoming photons with accuracy of 55ps.
University of Vermont Integrative Genomics Resource Core Facility
Core provides services for Experimental Design, Metagenomics, Comparative Expression Analyses, Variant Analyses, and Systems Biology. Overarching umbrella encompassing four distinct shared resource facility arms: DNA Analysis,Microarray,Massively Parallel Sequencing Facilities,Bioinformatics Shared Resource.
Structural Variant Classifier Trained on Variants Rare and Exonic
Software tool as structural variant classifier for exonic deletions and duplications. Supervised learning method to predict pathogenicity of human genome structural variants.Used to distinguish pathogenic SVs from benign SVs that overlap exons.
Recursive Partitioning and Regression Trees
Software R package as recursive partitioning for classification, regression and survival trees. Implementation of most of functionality of 1984 book by Breiman, Friedman, Olshen and Stone.
Software to design gRNAs pools in non-model genomes and CRISPR-Cas systems. Used to design CRISPR-Cas guide RNA pools in non model genomes.
LFKRI New York Blood Center Flow Cytometry Core Facility
Core provides in house investigators and external clients with equipment for multiparameter flow cytometric analysis and cell sorting, training and expert assistance with various techniques in flow cytometry,cell sorting as well as consultation in experimental design, data analysis, presentation, and publication.
Unique Molecular Identifiers combines chromosome conformation capture
Software R package for analyzing UMI-4C chromatin contact data. Used to analyze chromatin contact profiles obtained by UMI-4C.
Web visualization tool that provides access to interactive exploration of pancreatic islet genomic data. Allows access and exploration of pancreatic islet epigenomic and transcriptomic data produced by different labs worldwide.
Forsyth Institute Multiplex Core Facility
Core provides researchers access to multiplex analysis of any sample type using commercially available or in house developed assays.Includes simultaneous measurement of multiple biomarkers in single small sample volume. Offers expertise in sample preparation and handling and knowledge that comes with extensive experience.
Idea Biomedical | WiScan Hermes High Content Imaging System
Microscopy imaging system. Easily generates publication quality images at high throughput speeds.
Software tool as open source controller for machine tools. Can drive milling machines, lathes, 3D printers, laser cutters, plasma cutters, robot arms, hexapods, and more.
NIDA center for genetic studies of drug abuse in outbred rats
Genes and Addiction NIDA center for GWAS in outbred rats
Portal includes information about genetic studies of drug abuse in outbred rats. Data center created in 2014 to perform genome wide association studies on numerous behavioral traits that have well established relevance to drug abuse using outbred rats.
Colorado University at Boulder High Throughput Screening Core Facility
Facility is equipped with instruments for both high throughput and high content biochemical and cell based assays, including live cell assays.
Open source software package for morphometric quantification of networks from 3D image stacks. Combines required tools for complete analytical workflow, from raw image to final measured values.
Kings College London Microscopy Innovation Centre Core Facility
Kings College London Microscopy Innovation Centre
Core works with academic and industrial partners to develop and house advanced microscopy instrumentation and analysis tools.Provides custom microscopes to support users in their advanced imaging needs.
Project combines immunology and computational biology laboratories in effort to establish complete road map of gene-expression and regulatory networks in all immune cells. Project will generate, with rigorously standardized conditions, complete compendium of genome-wide data sets showing expression of protein-coding genes for all defined cell populations of mouse immune system.
Software tool as source code for analyzing functional ultrasound data.
Software tool to detect epistasis between SNPs along edges of gene-gene interaction network.
Efficient Estimation of Bayesian SBMs and MLSBMs
Software R package to Fit Bayesian stochastic block models and multi level stochastic block models using efficient Gibbs sampling implemented in Rcpp. Models assume symmetric, non reflexive graphs with unweighted, binary edges. Data are input as symmetric binary adjacency matrix, or list of such matrices.
Repository of biological samples from genetically characterized outbred rats that exhibit compulsive like escalation of cocaine self administration. Biological tissue bank originating from outbred rats (Heterogenous Stock rats) that have been characterized as vulnerable or resistant to cocaine addiction. Samples are available under three different conditions to maximize compatibility with wide range of applications, including generation of iPSC lines (slow freezing/LN2), histology/neuroanatomy (perfused), and molecular biology (snap-frozen).
Interactive GUI Java software package for analysis of high throughput genomic sequencing data.
TriKinetics | Drosophila Activity Monitoring System
System from TriKinetics for monitoring Drosophila activity. Includes hardware and DAMSystem3 Software for data acquision and DAMFileScan Software for scanning data for errors. Applied to behavioral activity experiments, including sleep deprivation analyses and general studies of hypoactivity and hyperactivity.
Software tool for layout and page design software. Used for print and digital media to create graphic designs with typography from Adobe Stock. Publishing software, graph arrangement.
Website devoted to papers that contain machine learning datasets, code, methods and evaluation tables. Done together with community, supported by NLP and ML.All content on this website is openly licenced under CC-BY-SA and everyone can contribute.Also operates specialized portals for papers with code in astronomy, physics, computer sciences, mathematics and statistics.
University of Kansas Microscopy and Analytical Imaging Research Resource Core Facility
Microscopy and Analytical Imaging Research Resource Core Laboratory (MAI)
Microscopy and Analytical Imaging Shared Resource
Core laboratory in Room 1043 in Haworth Hall at the University of Kansas Lawrence campus.Provides life and physical sciences and engineering users with wide spectrum of sample preparation tools and techniques and imaging technologies.Provides training for undergraduate, graduate students, postdoctoral researchers, faculty, staff, and industry collaborators.
Open source software analysis and visualization platform for microbial omics including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in integrated fashion through extensive interactive visualization capabilities.
Software tool for sequence alignments evaluation. Multiple alignment evaluation of sequence neighbours using Bayesian inference system. Used to distinguish sections in multiple sequence alignments that are conserved across whole family or within subfamilies, and should be useful for automatic, high-throughput genome annotations, 2D/3D structure predictions, protein-protein interaction predictions etc.
Software tool as multiple sequence aligner. Algorithm for large scale multiple sequence alignments.Designed to produce rapid multiple sequence alignment of large protein families.
Software tool as multiple sequence alignement for global, local and semi global alignments.
University of Chicago Animal Resources Center Core Facility
University of Chicago UChicago Animal Resources Center
Core assists investigators in performing their animal research while ensuring appropriate and humane care of all laboratory animals.
Open source software platform for reproducible clinical neuroscience.Set of automatic pipelines for processing and analysis of multimodal neuroimaging data, as well as tools for statistics, machine learning, and deep learning.
Mouse Developmental Anatomy Ontology Browser
Browser for mouse developmental anatomy. Ontology of mouse developmental anatomy was originally developed by Jonathan Bard and his colleagues as part of Edinburgh Mouse Atlas Project (EMAP) in order to provide structured controlled vocabulary of stage specific anatomical structures for developing laboratory mouse.
Software tool for data collection to upload output from set of activity monitors and periodically saves it in disk files on Macintosh or Windows PC. Part of TriKinetics Drosophila Activity Monitoring System.
Software tool to collect outcomes and outputs of research from web, external data sources and researchers themselves.
SARS-CoV-2 Protein Interaction Network Analysis
Software tool to predict human proteins that interact with SARS-CoV-2 proteins and trace provenance of predictions.
Code for NHP-MRI e.g., Retinotopy, Curve-tracing, Figure-ground. Pipeline for processing of NHP MRI data.
Software tool as guide to process NHP anatomical MRI data with adapted version of Freesurfer to generate surfaces and flatmaps.
Software tool as adaptation for NHP brains and pipelines. Pycortex python based toolkit for surface visualization of fMRI data.
Software package for experimental control from Vision and Cognition Lab at Netherlands Institute for Neuroscience. Matlab based software for fMRI, Psychophysical experimentation and NHP training, with eye control using Measurement and Computing IO card. Interfaces with ISCAN eye tracker and communicates with the MRI console using trigger pulses. Uses Psychtoolbox3 graphics and control engine.
Software tool used in Drosophila Activity Monitor system to scann data for errors. Also allows user to extract data from monitor files and bin data in different lengths.
Software tool to calculate 2D tractions exerted by adherent cell on its substrate. Used in field of mechanobiology to study contractile responses of variety of cell types.
Software tool as fully automated pipeline for metagenomic analysis. Used for metagenomics covering all steps of analysis. Features several characteristics including co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of abundances of genes in each metagenome. Includes binning and bin checking for retrieving individual genomes.
Software tool to detect alternative polyadenylation and identify cell type specific APA in multi cluster setting.
Software R package to help explain which variables are most important in random forests. Various variable importance measures are calculated and visualized in different settings in order to get idea on how their importance changes classification or regression model accuracy.
Software R package used to karyoplots. Bioconductor package to plot customizable genomes displaying arbitrary data.
Software tool used to separate or demultiplex pooled barcodes.
Software tool to quantify comet parameters while studying DNA strand breaks. Automated tool for comet assay image analysis.
Cellecta CloneTracker 50M Lentiviral Barcode Library
CloneTracker 50M Lentiviral Barcode Library
Software library used to tag or barcode individual cell population with unique 18 nucleotide barcodes.
Software tool used to plot circular plots and visualize genomic data along genomic locations.
Bayesian Analysis of Single Cell Sequencing
Bayesian Analysis of Single-Cell Sequencing data
Software tool for Bayesian analysis of single cell sequencing data. Used to perform statistical analyses of single cell RNA sequencing datasets in context of supervised experiments.
Software tool for modeling species niches and distributions by applying machine learning technique called maximum entropy modeling. Used for maximum entropy modelling of species geographic distributions.
SCIEX | | AB SCIEX | QTRAP 6500 plus system
AB SCIEX QTRAP 6500 plus mass spectrometer
Used for performing applications requiring ultimate sensitivity for ultra low level quantitation of both small and large molecules.
University of Ottawa Preclinical Imaging Core Facility
Facility offers internal and external clients experimental solutions to carry out animal studies requiring in vivo imaging, including consultations, research plan design, protocol development, data collection, analysis, and reporting. PCIC offers modalities like MRI and ultrasound enabling translational research.
University of Edinburgh Clinical Research Mass Spectrometry Core Facility
Core is part of Edinburgh Clinical Research Facility, situated in the Centre for Cardiovascular Sciences in the Queen's Medical Research Institute. We train and host undergraduate students, PhD and post-doctoral students in practical skills and mass spectrometry operation. We have expertise in sample preparation, separation and mass spectrometry analysis for targeted small molecule analysis in clinical and pre-clinical studies. We operate under Good Clinical Practice for laboratories for clinical studies. Steroids, drugs and endogenous molecules and metabolic pathways in plasma, serum, tissue. We also have Imaging Mass spectrometry capabilities with a Waters Synapt G2Si, MALDI and DESI.
Web application to help biologists use 3D structures to gain insight into protein function. Used in revealing novel insights into molecular mechanisms underlying protein function in health and disease. System for incorporating 3D structures into variant analysis.
Web tool to visually summarise all available 3D structural information for all proteins comprising COVID-19 virus (SARS-CoV-2). Resource also gives access to structural models, generated by finding all sequence regions with detectable similarity to any currently published 3D structure. These structures are clustered into distinct states that provide insight into viral replication, mimicry, and hijacking.
Software tool as microbial community sample search method based on smart pair wise sample comparison without compromising accuracy. Used as microbial communities similarites calculation and comparison tool.
Software package to generate Lorenz plots and Coverage plots, directly from BAM file. It can also output tables as text documents so you can generate custom plots. There is also support to only analyse specific regions.
University of Edinburgh EdinOmics Core Facility
Research facility based in the School of Biological Sciences and the UK Centre for Mammalian Synthetic and Systems Biology that provides proteomics and metabolomics services for qualitative and quantitative analysis.
Childrens Mercy Variant Warehouse Database
Database of non identifiable, summary data on all variants identified in Childrens Mercy Genomic Medicine Center, including project data of Genomic Answers for Kids. Database can be searched and viewed with genomic annotations, population database cross references such as ClinVar, gnomAD and dbSNP, ACMG curations and local allele frequency. Variant data are available for bulk download as annotated VCF.
Flagship initiative of Childrens Mercy Research Institute and Genomic Medicine Center in Kansas City. This research program is building pediatric data repository to facilitate search for answers and novel treatments.Goal is to collect genomic data and health information for 30,000 children and their families to create a database of genomes.
NIH NCI list of FDA approved cancer drugs
Portal to find consumer friendly information about drugs for cancer and conditions related to cancer. The list is in alphabetical order by generic name and brand name.
Prediction of Activity Spectra for Substances Online
Web tool to estimate biological activity profiles for compounds under study based on their structural formula presented in MOLfile or SDfile format. General list of predictable biological activities consists of terms including pharmacotherapeutic effects, biochemical mechanisms, toxicity, metabolism, gene expression regulation, transporter related activities. Prediction is based on knowledge base about structure activity relationships for compounds with known biological activities.
Web tool for automated generation of interactive disease-disease network visualizations given input PheWAS summary data. Given genetic associations from Phenome-Wide Association Study, disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between phenotypes.
Cleveland Clinic Florida FRIC Flow Cytometry Core Facility
Cleveland Clinic Florida FRIC Flow Cytometry Core
Core offers cell sorting and high dimensional flow cytometric analysis as well as training, consultation and single cell partitioning for scRNA seq (10x).
University of Ottawa Cell Biology and Image Acquisition Core Facility
Cell Biology and Image Aquisition (CBIA) Core
University of Ottawa Cell Biology and Image Aquisition (CBIA) Core
Core provides advanced microscopes, image analysis tools, and technical support to facilitate your microscopy research. Offers consultations to determine appropriate microscope for your specific needs and proper design of your experimental set up.
Software Python tool to retrieve biodiversity data stored in NCBI databases and provide simple and explorable visualization. Used to elaborate and visualize molecular and taxonomic informations. Allows creation of interactive plots starting from NCBI search query or directly from offline taxonomic files.
Global Evaluation of SARS-CoV-2/hCoV-19 Sequences
Database of global evaluation of SARS-CoV-2/hCoV-19 sequences.Provides comprehensive analysis results based on tens of thousands of high-coverage and high-quality SARS-CoV-2 complete genomes.
Web server for predicting impact of mutations on protein conformation, flexibility and stability.
Sorting Intolerant From Tolerant For Genomes
Software tool to predict whether amino acid substitution affects protein function. Faster version of SIFT that enables to scale up and provide SIFT predictions for more organisms.
Cleveland Clinic Florida Research and Innovation Center Imaging Core Facility
Cleveland Clinic Florida JMH-Imaging Core
Imaging Core at CCF FRIC provides access to advanced imaging technologies, including: Wide-field and confocal fluorescent microscopes, FLIM capability, Live cell imaging microscopes, Pre-clinical imaging microscopes, BSL-3 imaging platforms for pre-clinical and basic research microscopy projects.Provides consultation on experimental design and optimization, post-acquisition image processing, and support for analysis, visualization, and interpretation of data.
Amersham Imager 600 is CCD camera system that produces digitial images of samples in gels or membranes in three different modes: chemiluminescence, colorimetric and fluorescent image capture. Provides imaging system to capture and analyze protein and DNA sample gels and membranes in high resolution.
Sustainable Grazing System Pasture Model
Software tool as biophysical simulation model for livestock systems. It has flexible interface for setting up and running simulations with extensive graphical and data output.
Software as automated pipeline method to close gaps in assemblies with long reads. Used to close assembly gaps using long reads at high accuracy.
University of Kansas Mass Spectrometry and Analytical Proteomics Core Facility
University of Kansas Mass Spec and Proteomics Core Laboratory
Provides range of mass spectrometry based services including small molecule analysis and quantitation, peptide and protein MW determination; MS based proteomics services and associated bioinformatics including: global proteome IDs and targeted proteomics, post-translational modification mapping, quantitative proteomics, consultation for designing proteomics experiments, thermal protein profiling and cellular thermal shift assay analysis.
Software tool implements Damerau-Levenshtein (DL) edit distance algorithm for Python in Cython for high performance.
Web tool for integrative visualization of multiple omic datasets onto KEGG pathways. Supports integrated visualization of multiple species of different biological kingdoms and offers user possibility to request any other organism present in KEGG database.
Portal to make all Human Pancreas Analysis Program data available to anyone in research community and to interact with and connect scientific community. Stores clinical, molecular, cellular, immunology, imaging, and pathology data from pancreatic tissue and cell samples from organ donors with and without type 1 or type 2 diabetes.
Platform for Epigenomic and Genomic Research
Web service platform logging metadata for genomic samples and high throughput sequencing, manages data processing workflows, and provides quality control reporting and visualization. PEGR links people, samples, protocols, sequencing and bioinformatics computation to comply with FAIR best practices for publications and data management plans.Tracks and quality controls experiments from conception to publication ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at wet bench, while continuing to fully support reproducibility and reliability for bioinformaticians through integration with Galaxy platform.
Data independent acquisition proteomics workbench
Software tools for analysis of data independent acqusition type proteomics data are implemented in Galaxy framework. Enables complete DIA data analysis including spectral library generation based on DDA type data, analysis of DIA data in raw or mzml format, and differntial statistical analysis. All tools are based on open-source software such as diypasef, OpenSwath, swath2stats and MSstats.
Allelic Dosage corrected Allele Specific human Transcription factor binding sites
Landscape of allele specific transcription factor binding in human genome. Creators conducted meta analysis of ChIP-Seq experiments and assembled database of allele specific binding events listing more than half million entries at nearly 270 thousand single nucleotide polymorphisms for several hundred human transcription factors and cell types.
Arthropoda Assembly Assessment Catalogue
Database of metadata and assembly quality metrics for all Arthropod assemblies on NCBI.
Analysis of Next Generation Sequencing Data
Software tool fo analysis of next generation sequencing data. Calculates various summary statistics, and performs association mapping and population genetic analyses utilizing full information in next generation sequencing data by working directly on raw sequencing data or by using genotype likelihoods.
Center for GWAS in Outbred Rats Database
Center maintains database containing all phenotypical data collected by Research Projects and Ancillary collaborators, as well as RNAseq and genotype data.Provides access to data generated by NIDA center for genetic studies of drug abuse in outbred rats and additional research projects that use N/NIH heterogeneous stock (HS) outbred rats and Center’s core services that support genotyping and analysis.Alignes data generated in HS rats with FAIR (Findable, Accessible, Interoperative, Reusable) data management principles.Provides structured access to data associated with research papers produced by research projects that use HS rats.
Physik Instrumente Motion Control Software
Software to control positioning systems without their own macro facility.
Consortium is creating new data driven approach to drug discovery based on cellular imaging, image analysis, and high dimensional data analytics. Creates public data set to validate and scale up this image based drug discovery strategy. By coordinating assay procedures across partners, future created data will be well matched. Aims to make cell images as computable as genomes and transcriptomes.
Software tool for deep learning based approach for fully self supervised protein localization profiling and clustering. Leverages self supervised training scheme that does not require pre existing knowledge, categories, or annotations. Used for encoding protein localization patterns from microscopy images.
Proteome scale collection of protein localization and interaction measurements in human cells. Proteome scale endogenous tagging enables cartography of human cellular organization.
Software package for basic visual stimulation, imaging analysis, plotting, and cell visual response properties analysis functionality for calcium imaging.
Python cloud pipeline for Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Remapping, and more. TaskQueue and CloudVolume based pipeline for producing and managing visualizable Neuroglancer Precomputed volumes.Uses CloudVolume for accessing data on AWS S3, Google Storage, or local filesystem.
Software package for working with neuronal meshes, skeletons, and annotations from electron microscopy data. Used to work with meshes, designed around use cases for analyzing neuronal morphology.
Platform for recognizing and promoting Open Research. Open online service that aims to offer fairer and more democratic platform for recognizing researcher contributions.Allows researchers to openly acknowledge colleagues for meaningful contributions to research process, such as Publication, Mentoring,Teaching,Data sharing,Reproducibility practices, Sharing negative results, Participation in discussion groups,Software development, Clinical trials management, Leadership, Community outreach, Public engagement. ORCID iDs, DOIs, grant IDs and other persistent identifiers are used where available as links to appropriate contributions.
Software tool for compressing genomes in FASTA or gzipped FASTA input format. Used for fast and efficient compression of bacteria species collections.
Software framework for human and nonhuman brain models.Combines open database with software for access, management, and vetting, allowing scientists to distribute their resources under FAIR principles. Supports multifaceted insight into brains across species, and enables multiverse analyses testing whether results generalize across standard references, scales.Community archive of imaging templates and atlases for improved consistency in neuroimaging R.
Digital Holographic Microscopy Utilities
Software package as collection of plugins for use in Digital Holographic Microscopy. Used for digital holographic microscopy processing in ImageJ. Main plugins include DHM Utilities Reconstruction, for reconstructing and propagating holograms; DHM Utilities Phase Unwrapping, for phase unwrapping; DHM Utilities Multi Image Landmark Correspondences, for aligning images.
Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise.
Interactive web service for recognition of errors in three dimensional structures of proteins.
Improved model quality assessments using Rosetta energy terms. Predictor combines training features from ProQRosCen, ProQRosFA and ProQ2.
Web tool for assessment of protein structure quality using interatomic contact areas. Method for estimation of single protein structure quality.
Local threading meta server, for quick and automated predictions of protein tertiary structures and spatial constraints. New generation of meta server approach to template based protein structure prediction and structure based function annotation, which integrates multiple deep learning based threading methods and profile based programs (FFAS3D, HHpred, HHsearch, MRFsearch, MUSTER, SparksX).
Interactive web server for efficient protein structure refinement with capability to perform web based statistical and visual analysis.
Web tool for prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.
Multilayered Fusion based Disorder predictor v. 2.00
Web tool for accurate prediction of disorder in proteins by fusion of disorder probabilities, content and profiles.
Web server to predict natively disordered regions of protein chain from its amino acid sequence. Returns disorder probability of each residue as prediction results.
Portal for connecting Artificial Intelligence researchers to Federal resources that can support their AI work from grant funding and datasets to computing and testbeds.
Software as scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation.
Software Python package for neurophysiological signal processing. Used to analyze physiological data.
Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences.
Community led project to develop open, sustainable, usable, and unique identifier for every research organization in the world. Implementation of ROR IDs in scholarly infrastructure and metadata will enable more efficient discovery and tracking of research outputs across institutions and funding bodies.
Audio visual stimulation system for functional MRI (fMRI) applications.
Software package for advanced time domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data.
Collection of curated modules for assembling workflows for major modalities of neurophysiology experiments, as well as related documentation, tools, and utilities.
Tecan | SPARK Multimode Microplate Reader
Multimode microplate reader as fully flexible detection platform with automation.Has four configurations to select from and then add or remove options.Optimised for genomics and proteomics, microbiology, cell based assays, and drug discovery areas. Performs measurements of fluorescent cell based assays. Has integrated, bright field cell imaging module. Enables label free cell counting, size distribution determination and trypan blue based cell viability analysis.
University of Texas at Austin Biomedical Imaging Center Core Facility
Multimodal imaging facility that supports human and preclinical imaging research. Hosts range of systems for MRI, PET, CT and optical imaging and accommodates both independent and assisted use for human MRI and PET/CT on its instruments. Provides in house training in scanner safety and operation and supports range of task for functional MRI studies.
Thermo Fisher: Applied Biosystems | PRISM 7000 Sequence Detection System
Real Time PCR system that detects and quantitates nucleic acid sequences. System components include 7000 Sequence Detector, Peltier based 96well block thermal cycling system,Tungsten halogen excitation source, Fluorescence detection via CCD camera, Sequence Detection software. Quantitative results are available immediately after PCR without additional purification or analysis.
Software tool as simulation program for insulin glucose feedback control. Based on nonlinear MiMe-NoCoDI model.
Thermo Fisher: Applied Biosystems | 3500/3500xL Genetic Analyzer System
Applied Biosystems 3500/3500xL Genetic Analyzer
Applied Biosystems 3500/3500xL Genetic Analyzer with 3500 Series Data Collection Software v 3.1
Applied Biosystems TM 3500/3500xL Genetic Analyzer
System includes fluorescence based DNA analysis instrument using capillary electrophoresis technology with 8 or 24 capillaries, computer workstation and monitor, and integrated 3500 Series Data Collection Software 3.1 for instrument control, data collection, quality control, base calling, and size calling of samples.
Motif Mutation Analysis for Regulatory Genomic Elements
Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.
Motif Alteration Genome wide to Globally Investigate Elements
Software Python package for identifying motifs mediating transcription factor binding and function. Links mutations of motif to changes of epigenomic feature without assuming linear relationship.
James Madison University Light Microscopy and Imaging Core Facility
James Madison University JMU-Light Microscopy and Imaging Facility
JMU-Light Microscopy and Imaging Facility
Core provides instrumentation, resources, training, and consultation. Facility offers access to diverse range of light microscope and imaging systems,image analysis software and solutions, practical and theoretical training for faculty, students and classes,consultation on data acquisition, analysis, and presentation.
High performance of GPU accelerated variant calling tool in genome data analysis.
Turing Way handbook for reproducible data science
Guide to reproducible data science to support students and academics as they develop their code, with aim of helping them produce work that will be regarded as gold standard examples of trustworthy and reusable research. Include training material on version control, analysis testing and open and transparent communication with future users.
Princeton Handbook for Reproducible Neuroimaging
The Princeton Handbook for Reproducible Neuroimaging
Handbook provides reference for best practices in reproducible fMRI research.Many elements of handbook are specific to Princeton Neuroscience Institute computing infrastructure, but principles are widely applicable.
Real Time PCR control and evaluation software, provides intuitive controls and automated evaluation. Part of Analytik Jena qTOWER3 system. Providies threshold calculation for determination of Ct values, standard curves, PCR efficiencies, and advanced evaluation methods.
Live cell imaging system. Includes CELLCYTE Studio software.
Company provides mitochondrial research products. Has team of scientists and is equipped with variety of high end instruments to create comprehensive mitochondrial research service platform. Provides customers with customized mitochondrial research services.
Web based, open source, operating system independent series of programs designed for use in public health and medicine for training or practice that provide number of epidemiologic and statistical tools for summary data. Developed in JavaScript and HTML, and can be run in modern web browsers. Program can be run from OpenEpi website or downloaded and run without web connection.
City University of New York Advanced Science Research Center Epigenetics Core Facility
CUNY Advanced Science Research Center-Epigenetics Core
Facility at Advanced Science Research Center of City University of New York provides research resources and services that include nucleic acid extraction and fragmentation, quantitative gene expression analysis, targeted DNA methylation analysis in specific genomic loci of interest, next generation sequencing RNA-seq and ChIP-seq, and single cell genomics.Provides advanced cell sorter with biosafety protection for flow cytometry service, services for RNAScope to allow for in situ hybridization detection of transcriptional targets with spatial resolution.
Weather data logging software used for all HOBO data loggers and wireless data nodes. Used to read out and plot data, and export to spreadsheets for further analysis.
Software R package to interpret fitted tree ensemble model.Used to extract and visualize how predictive variables contribute to tree ensemble model accuracy.
Software command line toolkit and Python library for detecting copy number variants and alterations genome wide from hight hroughput sequencing.
Software tool for statistical analyses on any device that has web browser and connection to internet.
Web tool as map based application for browsing, visualizing and analyzing diverse suite of curated global and regional geoscience data sets. These cover geophysics, geology, geochemistry, physical oceanography, climatology, and more. Runs with Java under Windows, Mac OS X, Linux and Unix/Solaris operating systems.
University of Puerto Rico Caribbean Primate Research Center Resource Distribution Core
Facilitates supply of conventional and specific pathogen free nonhuman primates and biological samples. Priority is given to NIH-funded investigators in universities, NIH Intramural Program, and contractors working on behalf of researchers conducting experiments under NIH-funded programs. Non-NIH-funded investigators may still be considered depending on resource availability.To request for CPRC animals, authorized representative of institution will need to submit Animal Allocation Request form.
Small compact 96well thermal cycler. PCR system features intuitive touch screen and thermal gradient technology to optimize reaction in single run.
Data acquisition software. Allows raw or filtered measurement data to be viewed in real time. Part of qNano system. Izon Control Suite Software V3.4 is maintenance software release that updates Izon current software.
Resource has been discontinued. Documented on January 13, 2022. Benchtop instrument for practical implementation of TRPS for fluid borne analysis of nano and micro scale particles by Izon Science Ltd. Single particle sizer. Directly measures particles using Tunable Resistive Pulse Sensing principle. Measures properties of individual nanoparticles in solution like particle diameter or volume, effective surface charge and zeta potential.
Population Analysis with Reticulate Trees
Software package that provides implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication ready figure production.Population genetics software. Used to understand evolutionary relationships among populations.
University of California at Santa Cruz Plasma Analytical Laboratory Core Facility
UC Santa Cruz Plasma Analytical Laboratory
Core facility provides Thermo Element XR high-resolution ICPMS,Thermo X-Series II quadrupole ICPMS,Thermo iCap 7400 ICP-OES, Photon Machines Analyte 193H excimer laser system, and Zygo NewView Element XR7200 Vertical Scanning Interferometer for depth profiling and analysis of laser pit morphology.
University of Freiburg Magnetic Resonance Development and Application Center Core Facility
MRDAC - Magnetic Resonance Development and Application Center
Core is registered in resources database of German Research Foundation under number RI_00444. Center origins in Medical Physics group, Dept. of Radiology, University Medical Center Freiburg, one of leading group in field of methodological developments in Magnetic Resonance Imaging and Spectroscopy and its application in clinics and research.Serves as platform for collaborations with partners in industry and research according to industrial quality and performance standards. Main branches of MRDAC include development of novel MR sequences and methods and design, implementation, and execution of pharmaceutical MR studies.Offers services such as teaching, training, and consulting.
University of Texas at Austin Mouse Genetic Engineering Core Facility
University of Texas at Austin Mouse Genetic Engineering Facility
Provides services to generate, cryopreserve, and recover transgenic mice for modeling human disease.MGEF is fully equipped to make genetically engineered mice and is staffed with skilled personnel with decades of transgenic experience.Generates transgenic mice for studying mammalian gene function and modeling human disease, cryopreserves and archives transgenic mouse lines.
Software pipeline for haplotype assembly of diploid genomes using paired end or PacBio reads.
Diverse mating phenotypes impact the spread of wtf meiotic drivers in S pombe
Diverse mating phenotypes impact the spread of wtf meiotic drivers in Schizosaccharomyces pombe
Software used for flow cytometry analysis.Holds functions used to analyze cytometry data and to simulate spread of wtf meiotic drivers given initial experimental parameters.
Source code for alpha helix structural optimisation written in MATLAB.
University of Luxembourg LCSB Genomics Platform Core Facility
University of Luxembourg LCSB Sequencing Platform Core Facility
Core offers next generation sequencing services.Provided sequencers include NextSeq2000 and MiSeq from Illumina, and MinION nanopore sequencer from Oxford Nanopore Technologies. Illumina sequencers allow sequencing tunable read lengths up to 300 bases of single as well as paired end runs while MinION sequencer complements by ultra long read lengths up to several hundreds of kilobases. Together this offers high flexibility for the different sequencing needs. Platform offers full service, starting with advice in experimental design up to sequencing data generation. Receiving RNA or DNA samples, sample quality check, sample shearing, library preparation, sequencing run, raw data generation and preliminary data quality control report is performed. General applications include RNA sequencing, metagenomics, small genome sequencing, targeted gene sequencing, amplicon sequencing, and HLA typing. Upon user request, sequencing platform works closely with bioinformatics platform to offer downstream data analysis. Besides wide range of standard services, platform also offers new method development.
Marion Technologies Genie 2000 Basic Spectroscopy Software
Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data.
RADIOMETER | ABL835 FLEX blood gas analyzer
Radiometer America ABL835 FLEX blood gas analyzer
Analyzer to measure full panel of up to 18 STAT parameters on same blood sample to support fast diagnosis of critically ill patients. Arterial blood gas analyzer with capacity to measure glucose concentrations.
Software memory efficient global scale contact network simulation toolkit. Collection of C plus plus implementations of graph generators for use in sampling contact networks in global scale pandemic simulations.
University of North Carolina at Chapel Hill Department of Chemistry Mass Spectrometry Core Facility
Department of Chemistry Mass Spectrometry Core Laboratory
University of North Carolina at Chapel Hill Department of Chemistry Mass Spectrometry Core Laboratory
Core specializes in small molecule analysis. Services include, but are not limited to, quantitative mass spectrometry, liquid chromatography separations, fragmentation and structural elucidation mass spectrometry, complex mixture analysis, molecular formula confirmation, high resolution and accurate mass analysis.Provides individualized user training for undergraduate, graduate, and post-doctoral scholars of Department of Chemistry.
Med Associates | Deluxe Behavioral Test Package with Rat Modular Chamber
Deluxe Behavioral Test Package w/Rat Modular Chamber
Operant behavior test package for rat built to meet needs of research studies requiring additional reward and stimulus flexibility. One of Med Associates, Inc. operant conditioning and general behavior product.
Vanderbilt University Mouse Metabolic Phenotyping Center Core Facility
NIDDK - Vanderbilt Mouse Metabolic Phenotyping Center
Vanderbilt Mouse Metabolic Phenotyping Center
Centralized resource for study of mouse models of diabetes, obesity, and related disease. Includes animal housing, energy balance, telemetry, and experiment rooms and surgical suites. Develops, standardizes, and provides surgical and experimental services for phenotyping mice. Surgical procedures include venous and arterial catheterizations, cannulation of brain regions, bariatric surgeries, and islet transplantations. VMMPC uses flexible platforms to study nutrient metabolism and energy balance that can be readily adapted for specific experimental requirements. Use of dual arterial and venous catheter implantation permit glucose clamps, treadmill exercise, metabolic flux analyses, and other procedures to be studied without the stress of handling mice. VMMPC offers courses annually to disseminate research laboratory practices for mouse.
Photopatterning software to control PRIMO system including UV illumination module, microscope, camera and stage, and to precisely define experimental conditions.Used to design your own micropatterning manipulations.
Photopatterning device for performing micropatterning, microfabrication and hydrogel polymerization.Part of PRIMO system.
Web service for statistical testing, data browsing and interactive visualization. Contains multiple statistical tests and new method to incorporate missing values. Robust statistical testing of proteomics data with missing values to improve detection of biologically relevant features., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University has campuses located in Southern Denmark and on Zealand with main campus in Odense and regional campuses in Slagelse, Kolding, Esbjerg and Sønderborg. University offers joint programes in co-operation with University of Flensburg and University of Kiel.
Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.
Human Atlas of Neonatal Development and Early Life Immunity
Human Atlas of Neonatal Development and Early-Life Immunity
HANDEL-1 program to better understand normal human immune development by acquiring stromal and mucosal tissues from infant and pediatric organ donors and to create novel and essential dataset informing immune system development in collaborative research project that leverages shared access to various tissues in conjunction with existing HANDEL-P program that seeks to understand development of pancreas and islet microenvironment in early life.
Polynomial Expansions of Protein Structures and Interactions SANS
Software tool as logical extension of Pepsi-SAXS method for small angle neutron scattering. Allows for explicit and implicit hydrogens, allows to specify deuteration level of sample and of buffer and exchange rate of labile hydrogens. Can also compute scattering intensity in absolute scale if sample concentration is provided. Can fit modelled profile on absolute scale within certain user specified margin. Instrumentation resolution is taken into account during processing of input data.
Software tool used for predictions of molecular packing and interactions. General purpose coarse grained force field for molecular dynamics simulations of biomolecular systems Martini 3 is refined model with improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability.
Open source, community developed library that provides range of different methods, which include enhanced sampling algorithms, free energy methods, tools to analyze vast amounts of data produced by molecular dynamics simulations. PLUMED 2 is complete rewrite of the code in object oriented programming language C plus plus. This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has simpler interface with the MD engines and provides single software library containing both tools and core facilities.
Nonlinear Rigid Block Normal-Mode Analysis Method
Software tool for non-linear normal mode analysis.
Independent biomedical research and science education organization in Grand Rapids, MI. Committed to improving health and changing lives of current and future generations through biomedical research and science education.
Software as collection of speech analysis, modification and resynthesis tools.
Heterogeneity through Discriminative Analysis
Software tool as novel non-linear learning algorithm for simultaneous binary classification and subtype identification. Can handle imaging and non-imaging data and can find applications in exploratory analyses other than clustering of brain images.Software performs clustering of heterogenous disease patterns within patient group.
Software tool for robust cell segmentation for fission yeast transillumination images.Used for robust segmentation of fission yeast micrographs, especially those with quality challenged images.
Manually curated database of exosomal proteins, RNA and lipids. Web based compendium of exosomal cargo. Database catalogs information from both published and unpublished exosomal studies. Mode of exosomal purification and characterization, biophysical and molecular properties are listed.
Manually curated database containing information on extracellular and circulating non-coding RNAs.You can search for RNAs typing in text area molecule of interest or you can browse database. Initially published in 2012, foreseeing relevance of ncRNAs as non-invasive biomarkers.miRandola 2017 is effort to update and collect accumulating information on extracellular ncRNAs that is spread across scientific publications and different databases with implemented new web interface.
DRSC/TRiP Functional Genomics Resources and DRSC-BTRR
Provides DRSC Drosophila cell-based screening, TRiP Drosophila fly stock production, Bioinformatics software tools and data access. Functional genomics platform for needs of Drosophila and broader community.Online tools include DIOPT for identification of orthologs (yeasts, worm, fly, frog, fish, mouse, rat, human),DIOPT-DIST for identification of human orthologs and links to disease, UP-TORR for RNAi reagent identification based on up-to-date gene annotations,DGET analysis of gene lists in the context of RNAseq data from modENCODE and others,Find CRISPRs and CRISPR efficiency evaluation online tools for CRISPR-Cas9 genome editing, FlyPrimerBank resource of pre-computed qPCR primers,RSVP RNAi fly stock validation database (data for TRiP, VDRC, NIG-Japan fly stocks), GeneLookup and Screen Summary views of DRSC cell screen data sets.
University of Southern California CHLA Cellular Imaging Core Facility
University of Southern California CHLA Cellular Imaging Core
Core provides equipment in microscopy and digital imaging. Primary focus is technology transfer and provision of facilities for acquisition and analysis of histological and cytological preparations. Provides training in the use of imaging instrumentation and in the application of image analysis procedures for generation of quantitative data.
Software tool used for improved phased assembly.IPA assembly for Hifi PacBio reads. Official PacBio software for HiFi genome assembly.
Software tool as PacBio assembly tool suite.
Van Andel Institute Optical Imaging Core Facility
Core helps investigators tackle wide range of research questions, from gene expression to cell motility, and is committed to providing training in microscopy best practices. Service requests are placed through CrossLab Solutions.
Hamamatsu | ORCA Flash4.0 LT plus digital sCMOS camera
ORCA-Flash4.0 LT plus Digital CMOS camera
Redesigned ORCA-Flash4.0 LT+ featuring 82 % peak quantum efficiency brings all advantages of sCMOS technology wide field of view, low light sensitivity, and large dynamic range increased flexibility and sensitivity of a scientific CMOS camera., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Highly controllable fluorescence microscopy Illumination System which offers broad spectrum LED illumination for imaging most common fluorophores. System offers precise control over wavelength irradiance and shuttering. Used for LED microscope lighting.
Wake Forest University Microscopic Imaging Core Facility
Wake Forest University WFU Microscopic Imaging Core
Light Microscopy and Scanning Electron Microscopy Facility managed by the Biology Department.
Database that aggregates, harmonizes and links records of various publication types from diverse sources, including Crossref and PubMed Central using automated routines and artificial intelligence technologies. Publications, ranging from articles published in scholarly journals, books and book chapters, to preprints and conference proceedings. All publications are contextualized with linked data sets, funding, publications, patents, clinical trials, and policy documents. You can also view associated categories, funders, institutions, and researcher profiles.
Software tool for learning fundamentals of RSLogix ladder logic programming.
University of Texas at Austin Biomedical Research Computing Core Facility
University of Texas at Austin UTA-Biomedical Research Computing Facility
UTA-Biomedical Research Computing Facility
Biomedical Research Computing Facility as core for Biomedical Research Support. Provides small, centrally managed compute clusters and storage, suitable for local, interactive computing, to biomedical research groups.
University of Colorado Anschutz Medical Campus Cancer Center Animal Imaging Shared Resource Core Facility
University of Colorado Anschutz Medical Campus Cancer Center Animal Imaging Shared Resource
Enables noninvasive imaging of animal models of human disease. Provides access and training on state-of-the-art animal scanners (MRI, CT, optical, PET/SPECT) for live imaging on rodents, perfoms all animal handling and assist with image analysis to establish imaging biomarkers.
University of Colorado Anschutz Medical Campus Cancer Center Biostatistics Core Facility
Bioinformatics - Biostatistics and Bioinformatics Shared Resource
Biostatistics provides quantitative support for planning, design, analysis, and presentation of basic science, clinical, and epidemiological investigations. We are dedicated to delivering high quality, methodically developed results to improve patient outcomes and clinical care.
University of Colorado Anschutz Medical Campus Cancer Center Cell Technologies Shared Resource Core Facility
Supports basic and translational research projects in biomedical research. CTSR produces hybridomas/monoclonal antibodies to enhance basic research and preclinal studies and makes recombinant proteins for mechanistic and structural studies on proteins.Provides multiple platforms and analytic modules for real time live-cell imaging of cultured cells and organoids to enhance analysis of cancer cell biology. In addition, we maintain a collection of authenticated human cell lines for use in biomedical research. Sign in to iLab using University of Colorado credentials.
University of Colorado Anschutz Medical Campus Cancer Center Bioinformatics Core Facility
Cancer focused bioinformatics group that assists in all needs related to omics and big data. We assist our collaborators with experimental design, data processing, interpretation, generating publication-quality figures, and preparing manuscripts and grants.
University of Colorado Anschutz Medical Campus Cancer Center Genomics Shared Resource Core Facility
GSR provides genome-wide analyses of DNA sequence, transcriptomes, epigenetics and cytogenomics using next generation sequencing (NGS) and gene microarrays; and single cell genomic and transcriptomic analyses including single cell immune profiling and spatial gene expression.
University of Colorado Anschutz Medical Campus Cancer Center Human Immune Monitoring Shared Resource Core Facility
Facilitates clinical and translational studies by dissecting immune based mechanisms with diagnostic and therapeutic applications. Offers assays including immunophenotyping and functional characterization, multicolor fluorescence tissue imaging, multiplex cytokine analysis, and cellular assays.Sign in to iLab using University of Colorado credentials.
University of Colorado Anschutz Medical Campus Cancer Center Drug Discovery and Development Shared Resource Core Facility
Drug Discovery and Development Shared Resource
Provides expertise and infrastructure to facilitate drug discovery at different stages of development pipeline, including assay development and validation, high throughput screening and image based high content screening discovery, validation and optimization, and in vitro and in vivo pharmacology including pharmacokinetics and pharmacodynamics as well as toxicology.Sign in to iLab using University of Colorado credentials.
University of Colorado Anschutz Medical Campus Cancer Center Functional Genomics Core Facility
Functional Genomics Shared Resource / Functional Genomics Facility
Core facilitates access to tools including shRNA, ORF, CRISPR to investigate gene function on genome wide scale. Provides protocols and expertise for use of these genomics tools. Serves as forum for scientific exchange and discussion in the field of functional genomics.Sign in to iLab using University of Colorado credentials.
University of Colorado Anschutz Medical Campus Cancer Center Mass Spectrometry Shared Resource Core Facility
Provides investigators with capabilities to identify, characterize, and quantify biomolecules present in tissues, cells, and biological fluids. Facility houses both Proteomics and Metabolomics Cores, and aims to assist members with solving difficult or previously intractable problems in biomedical research. Methods for biomolecule isolation, separation, quantification, identification and bioinformatics analysis, together with expert guidance in study design, are integrated into expertise offered by the Facility.
University of Colorado Anschutz Medical Campus Cancer Center Pathology Shared Resource Biorepository Core Facility
Pathology Shared Resource - Biorepository
Biorepository Section provides services to support biobanking, clinical trials, and research studies. Provides access to patient specimens collected from clinical and research procedures that are handled, processed, analyzed, and interpreted in uniform manner. Services include, collection, processing, storage, clinicopathological annotation, and distribution of biospecimens.
University of Colorado Anschutz Medical Campus Cancer Center PreClinical Human Immune System Mice Shared Resource Core Facility
PreClinical Human Immune System Mice Shared Resource
Core provides Human Immune System as preclinical in vivo model to study human immune system in experimental tractable animal model e.g. immune response to human tumors that readily grow in HIS-mice. Offers immune expertise, experimental procedures and data analysis of immune based assays, such as flow cytometry.
University of Colorado Anschutz Medical Campus Cancer Center Pathology Shared Resource Cytogenetics Core Facility
Pathology Shared Resource - Cytogenetics
Core, in collaboration with Colorado Genetics Lab, provides cytogenetic and cytogenomic research services. Services include tissue culture, chromosome analysis, fluorescence in situ hybridization (FISH), and chromosomal microarray. Offers design and development of customized FISH probes.Available for consultation on study design and data analysis.
University of Colorado Anschutz Medical Campus Cancer Center Population Health Shared Resource Core Facility
Core supports access to and expertise in data management, analyses, and mapping and data visualization of population based databases. These databases are ideal for studies requiring access to large samples of patients and/or providers; examination of trends in treatment, screening, or other healthcare services; impact of policy changes or recommendations on healthcare services; investigating dissemination of evidence based technologies and interventions; disparities of treatment or other health care services between groups; geographic distributions of cancer patients and relationships with other geospatial data.
University of Colorado Anschutz Medical Campus Cancer Center Organoid and Tissue Modeling Shared Resource Core Facility
Organoid and Tissue Modeling Shared Resource
Core facilitates access, generation, and usage of novel in vitro mouse and human organoid systems to promote innovative basic and translational research and disease modeling. Provides expertise in genome editing technologies for targeted knock outs, point mutations, and reporter generation in organoid systems. Provides many specialized medias and reagents to support most common organoid culture systems.
University of Colorado Anschutz Medical Campus Cancer Center Pathology Shared Resource Research Histology Core Facility
Pathology Shared Resource - Research Histology
Research Histology Section provides range of standardized paraffin histology procedures that can be tailored to specific research needs.Services include tissue grossing/cassetting, paraffin processing, sectioning, routine and special stains. We specialize in immunohistochemistry and antibody optimization procedures.
University of Colorado Anschutz Medical Campus Cancer Center Pathology Shared Resource Molecular Pathology Core Facility
Pathology Shared Resource - Molecular Pathology
Molecular Pathology Section offers clinical grade sample processing and molecular testing for research cases.All services are performed in CLIA certified environment and all molecular assays are accompanied by full data analysis including bioinformatics analysis for NGS data.
University of Colorado Anschutz Medical Campus Cancer Center Small Animal Image Guided Radiation Therapy Core Facility
Small Animal Image-Guided Radiation Therapy
Core specializes in targeted irradiation of small animals for use in preclinical trials of radiation therapy. Through use of XRAD-SmART Irradiator, core can use x-ray fluoroscopy and on board CBCT to accurately irradiate small lesion areas while protecting normal tissue. Provides experiment design, data analysis, and dosimetry calculations, as well as longitudinal acquisition of CBCT for temporal assessment of tumor growth kinetics.
University of Colorado Anschutz Medical Campus Cancer Center Structural Biology Shared Resource NMR Core Facility
NMR Structural Biology Shared Resource Facility
Structural Biology Shared Resource - NMR Facility
Core enables study of biomolecular structure, dynamics and interactions in solution at atomic level. Provides NMR spectrometers from 600 MHz to 900 MHz equipped for biomolecular NMR studies. Equipment include 900 MHz Bruker Avance Neo with Oxford 21 T magnet - TCI Cryoprobe 600 MHz Bruker Avance Neo with Bruker Sample Jet (2024) - TCI Cryoprobe 600 MHz Varian Inova with HCN cryoprobe.
University of Colorado Anschutz Medical Campus Cancer Center Structural Biology Shared Resource X Ray Crystallography Core Facility
Structural Biology and Biophysics Core Facilities X-ray Crystallography Core
Structural Biology X-ray Crystallography Core
Stuctural Biology Shared Resource - Xray Crystallography
Core performs all aspects of structure determination of large biomolecules such as proteins and nucleic acids including macromolecular crystallization, crystal screening, molecular structure and model building.
University of Colorado Anschutz Medical Campus Cancer Center Structural Biology Shared Resource CryoEM Core Facility
Structural Biology Shared Resource - CryoEM Facility
Provides equipment, expert technical assistance and image analysis expertise to enable all aspects of macromolecular structure determination by single particle cryo-electron microscopy.
Colorado State University Flow cytometry, cell sorting, and single cell analysis Core Facility
Provides access to flow cytometry and cell sorting instrumentation, services, and expertise for all researchers at Colorado State University. FCF includes spectral flow cytometers Cytek Aurora which enables users to perform more than 25 markers in a sample. FCF also has 10X Genomics chromium controller used to barcode single cells to perform single cell sequencing. Offers data analysis of these complex flow cytmetry and single cell sequencing samples using R programming or bash shell based pipelines.
Colorado State University Geospatial Centroid Core Facility
Core facility that provides technical guidance, project support, and diverse training opportunities in geospatial sciences. With expertise in geographic information systems, spatial analysis, web mapping, and cartography, Centroid supports researchers in spatial data development, analysis, visualization, and publication ready maps.
Colorado State University School of Advanced Materials Discovery Core Facility
School of Advanced Materials Discovery Core
Core facility that enables research and development programs by providing expertise and access to equipment for synthesis, processing and testing of materials. Support and enables materials research and education by offering range of materials synthesis, processing, and testing equipment, combined with individualized training and staff expertise.
Colorado State University Drone Center Core Facility
Offers consultation on drone systems, UAS project guidance, UAS piloting, assistance with UAS pilot training, liaison and navigation of FAA regulations, and as point of contact for UAS inquiries from outside the University. Assists in authorizing flight requests at CSU and managing Christman Airfield use for drone flights. Maintains fleet of sUAS aircraft and air borne sensors.
Colorado State University Institute for Research in the Social Sciences Core Facility
Institute for Research in the Social Sciences
Core facility that provides social science research expertise and resources for design, collection, management, analysis, and dissemination of original social science data, including interviews, focus groups, surveys, photo voice, social network analysis, program evaluation, team assessments, and mixed method studies.
Colorado State University Graybill Statistics and Data Science Laboratory Core Facility
Graybill Statistics & Data Science Laboratory
Core facility that provides statistical expertise for benefit of advancing quality of scientific research and education at CSU and beyond, while educating next generation of applied statisticians.
Software tool as multiworm tracker. Can be used as analysis toolkit for extracting morphological and behavioural data from videos of objects moving in 2D environment.
Software analysis toolkit for tracking blobs and extracting intensity values from imaging data, designed for use with ratiometric fluorescent sensors.
Software pipeline to analyse genome data from forward genetic screen. Identification of causal variants for specific phenotype.
THE COLLABORATIVE NEUROPATHOLOGY NETWORK CHARACTERIZING OUTCOMES OF TBI
Portal for traumatic brain injury data. Common Data Elements (CDEs) and Unique Data Elements (UDEs) for digital neuropathological data and clinical data that will be collected in all CONNECT-TBI center projects. Goal is to establish multi-center, digital neuropathological data and clinical data reporting network with case accrual from each center project. Collected neuropathological data and clinical data available by sharing with center site investigators approved by Administrative Core and by submitting into FITBIR. Central TBI data repository by collecting digital neuropathological data and clinical data from TBI cases and normal controls at each center and posting library of their holdings.
Software tool for estimating k-mer coverage histogram of genomics data. Streaming algorithm for estimating frequencies of k-mers in genomics datasets.
Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads.
Software tool as hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology. Used for correcting long reads by mapping short reads.
Software tool for scaffold long read assemblies with Hi-C data.
Software tool for scaffolding with RNA-seq read alignments. Used for improving genome assembly with RNA sequencing data.
Software tool as simple script to calculate N50/NG50 and auN/auNG.
Software interactive toolkit for assembly and analysis of restriction site associated genomic data sets including RAD, ddRAD, GBS, for population genetic and phylogenetic studies. Used for interactive assembly and analysis of RADseq data sets.
Software package provides comprehensive framework for evaluating, filtering, and analyzing gene models from range of input applications and preparing these annotations for formal publication or downstream analysis.
Software tool to identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
Software R package for fast Principal Component Analysis for outlier detection.Used to detect genetic markers involved in biological adaptation. Performs genome scans for selection based on principal component analysis.
Software R package for landscape and ecological associations studies.Dedicated to genomewide association tests in general, with emphasis on association with ecological gradients. Runs analyses of population structure and scans for genomic signatures of local adaptation.
Software R package for estimation and tests of hierarchical F statistics.Used to estimate hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in hierarchy.Intended for analysis of population structure using genetic markers.
Software R package for statistical analysis of mixed ploidy populations.Used for calculation of population structure and differentiation based on single nucleotide polymorphism genotype data from populations of any ploidy level, and/or mixed ploidy levels.
Wellcome Sanger Institute's High Performance Assembly Group's Paired REad TEXTure Mapper
Software tool to convert SAM formatted read pairs into genome contact maps. Prepares alignments for visualization with PretextView.
Wellcome Sanger Institute's High-Performance Assembly Group's Paired REad TEXTure Viewer
Software tool to enable visualization from PretextMap output. Desktop application for viewing pretext contact maps. OpenGL Powered Pretext Contact Map Viewer.
Software package as medical image viewer and image processing tool. Can open all QuickTime compatible image file formats as well as import most Digital Imaging and Communications in Medicine (DICOM) and ACR/NEMA file formats. DICOM is industry standard for medical images and is used for CT, MR and US images. Madena can open image files found within folder and all enclosed subfolders in single command. QuickTime images are grouped into subsets according to folder in which they were found.
Software tool as k-mer and metafeature approach to classify antimicrobial resistance from high throughput short read metagenomics data. Kmer- and matrix factorization based classifier for metagenomics data.
Software allows estimating growth and production at stand level of main forest species implanted in Argentine Mesopotamia such as Pino taeda, Eucalyptus grandis, Pino elliottii and Araucaria angustifolia. Areas for which models were adjusted correspond to province of Misiones, northeast of Corrientes and Concordia in province of Entre Ríos.
Software tool for custom calcium imaging analysis.
Software system for knowledge graph management and data driven science. Ecosystem allows to organize and better leverage data through use of Knowledge Graph.
Vector Generalized Linear and Additive Models
Software R package implementating multiple major classes of statistical regression models.
Shahid Sadoughi University of Medical Sciences; Yazd; Iran
Shahid Sadoughi University of Medical Sciences
Public university located in center of Iran in World Heritage city of Yazd.
Blue Brain Neocortical Microcircuit Portal
Neocortical microcircuit collaboration portal is resource for rat somatosensory cortex. NMC portal allows users to access experimental data used in reconstruction process, download cellular and synaptic models, and analyze predicted properties of microcircuit.
Polycystic Kidney Disease Research Resource Consortium
Consortium develops and shares investigative resources, reagents and expertise with broader research community to accelerate innovation and discovery in field of polycystic kidney disease.Provides assistance with protocols and trouble shooting. Provides funding opportunities.
System includes MicroTester G2 device and software. MicroTester G2 is mechanical test device that can be used to test properties of variety of tissues and materials. Main components of device are load application microbeam, actuators, imaging system, and fluid bath/test chamber. MicroTester G2 software is divided into two modules: data collection module and review and analysis module.
University of Colorado Anschutz Medical Campus Cancer Center Flow Cytometry Shared Resource Core Facility
Flow Cytometry Shared Resource at the CU Cancer Center
Provides cytometry based services including cell sorting, flow cytometry and mass cytometry. Provides training, education, and experimental design assistance.
Portal that provides multimedia educational content from courses, conference lectures, and laboratory exercises from some of leading neuroscience institutes and societies to be more accessible to global neuroscience community.
MBF Bioscience"s Neuromorphological file format
MDAR Framework establishes minimum set of requirements in transparent reporting applicable to studies in life sciences. MDAR checklist is tool for authors, editors and others seeking to adopt MDAR framework for transparent reporting in manuscripts and other outputs and designed to provide harmonizing principle for reporting requirements currently in use at various journals.
University of California at San Diego Electron Microscopy Core Facility
UCSD Cellular and Molecular Medicine Electron Microscopy core provides services in sample preparation and imaging by Transmission Electron Microscopy and Correlative Light and Electron Microscopy.
Software with graphical user interface for variance based structural equation modeling using partial least squares path modeling method. Users can estimate models with their data by using basic PLS-SEM, weighted PLS-SEM, consistent PLS-SEM, and sumscores regression algorithms.
Repository contains files for implementing the Sepsis-3 definition in the freely-accessible Amsterdam University Medical Centers Database.
Software package for dynamic modeling and parameter estimation in R.Provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc.
Platform that centralizes management of ophthalmic images. HEYEX interfaces with electronic medical record systems and third-party devices to allow exchange, storage, and dynamic review of diagnostic images. Heidelberg Engineering imaging products use Heidelberg Eye Explorer software platform and database to store patient information and images.
System includes stimulator units and data recording and analyzing software. Electrophysiological Test Unit is usable for Pattern VEP + Pattern ERG + Flash VEP, for scotopic and photopic ERG, EOG fast and slow, mf ERG Flash stimulation and mf VEP Pattern stimulation.
Colorado School of Mines Shared Instrumentation Facility Surface Characterization and Thin Film Deposition Core Facility
Colorado School of Mines Shared Instrumentation Facility Cleanroom and Thin Film Processing
Surface Characterization and Thin Film Processing
Facility houses cleanrooms with processing equipment for making and characterizing electronic devices, thin film deposition tools for creation of metallic and ceramic thin film devices, and characterization lab with tools for surface, morphological, and optical characterization of materials.
Colorado School of Mines Shared Instrumentation Facility Electron and Scanning Probe Microscopy Core Facility
Colorado School of Mines Shared Instrumentation Facility Electron and Scanning Probe Microscopy
Facility provides SEM, FIB, TEM, scanning probe, and optical techniques for analyzing materials.
Colorado School of Mines Shared Instrumentation Facility Time of Flight Secondary Ion Mass Spectrometry Core Facility
Colorado School of Mines Shared Instrumentation Facility Time of Flight Secondary Ion Mass Spectrometry
Time of Flight - Secondary Ion Mass Spectrometry
Core used to obtain elemental, isotopic, and molecular information from surface of solid materials and compacted powders.
Colorado School of Mines Shared Instrumentation Facility Rocky Mountain Environmental X-Ray Photoelectron Spectroscopy Core Facility
Colorado School of Mines Shared Instrumentation Facility Rocky Mountain Environmental X-Ray Photoelectron Spectroscopy
Rocky Mountain Environmental X-Ray Photoelectron Spectroscopy
Core to measure material surface compositions by measuring intensity of photoelectrons emitted as function of incident X-ray energy. Spectra features are used to identify surface species present and calculate fraction of surface occupied by each.Rocky Mountain E-XPS extends these traditional capabilities by enabling measurements in range of environmental conditions.
Colorado School of Mines Shared Instrumentation Facility Mechanical Testing Core Facility
Colorado School of Mines Shared Instrumentation Facility Mechanical Testing
Provides variety of monotonic, fatigue, temperature, and strain measurement capabilities. These capabilities cover wide range of load capacities and resolutions, displacement rates, loading configurations, and custom fixturing.
Colorado School of Mines Shared Instrumentation Facility Liquid Chromotography Mass Spectrometry Core Facility
Colorado School of Mines Shared Instrumentation Facility Liquid Chromotography Mass Spectrometry
Liquid Chromotography - Mass Spectrometry
Liquid Chromatography Mass Spectrometry is analytical technique for determining ion mass-to-charge ratio by partitioning particles within liquid and measuring time it takes for each particle to travel through selected mobile phase. Ultimately this helps in determining contents of liquid sample and can be used to analyze biochemical, organic and inorganic compounds.
Colorado School of Mines Shared Instrumentation Facility X-ray Diffraction and Computed Tomography Core Facility
Colorado School of Mines Shared Instrumentation Facility X-ray Diffraction and Computed Tomography
X-ray Diffraction and Computed Tomography
Facility encompasses X-ray diffraction, providing crystallographic, structural, and compositional information, and X-ray tomography, enabling nondestructive tomographic imaging and grain reconstruction used to distinguish between phases, identify defects, and provide 3D crystallographic grain reconstructions.
Colorado School of Mines; Golden; Colorado
Public research university in Golden, Colorado, founded in 1874. School offers both undergraduate and graduate degrees in engineering, science, and mathematics, with focus on energy and environment.
Powerful microscope mounted to produce microelectrodes for patch clamping.
Horizontal pipette puller to pull and polish microelectrodes from borosilicate capillaries.
Vertical pipette puller to create microelectrodes from borosilicate capillaries.
Web server of multi draft based scaffolder.Exploits information obtained from set of genomes from related organisms to determine correct order and orientation of contigs.
Web server for prokaryotic species circumscription based on pairwise genome comparison. Service for in silico calculating extent of identity between two genomes, parameter routinely used in process of polyphasic microbial species circumscription. Service measures average nucleotide identity.
Web tool for detecting and characterising biosynthetic gene clusters in bacteria and fungi. AntiSMASH 6 increases number of supported cluster types from 58 to 71, displays modular structure of multi modular BGCs, adds new BGC comparison algorithm, allows for integration of results from other prediction tools, and detects tailoring enzymes in RiPP clusters.
Software python package simplifies training fast and accurate neural nets using modern best practices.
Software package to filter out false discoveries in raw TE candidates and generate high quality non redundant TE library for whole genome TE annotations.Produces filtered non redundant TE library for annotation of structurally intact and fragmented elements.
Transposable Elements Pepresentation Learner
Software tool for classification of transposable elements by convolutional neural networks. Preprocesses and transforms one dimensional sequences into two dimensional space data, image like data of sequences, and apply it to deep convolutional neural networks.
Software tool to locate and display tandem repeats in DNA sequences. Used to analyze DNA sequences.
Randomized Axelerated Maximum Likelihood Next Generation
Software phylogenetic tree inference tool which uses maximum likelihood optimality criterion. Used for maximum likelihood phylogenetic inference. Offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML.
Multiple Collinearity Scan toolkit X version
Software toolkit for detection and evolutionary analysis of gene synteny and collinearity.
Software toolkit incorporating gamma series methods and sliding window strategies. Used for calculating nonsynonymous (Ka) and synonymous (Ks) substitution rates for evaluating sequence variations for protein orthologs across different species or taxonomical lineages with unknown evolutionary status.
Web portal related to Zika virus, including metadata collection for academic publications on the topic, structured data ontology of terms, and integrated resources in the Wikidata platform.
Creative Biogene Mitochondria Related Diseases
Creative Biogene provides comprehensive range of services and products to assist researchers in mitochondrial assays and studies. Service to validate and explore pathogenesis of mitochondria associated diseases and possible interventions.
Creative Biogene Mitochondria Associated Syndromes
Creative Biogene works with you to validate and explore pathogenesis of mitochondria associated syndromes and possible interventions, with professional services and products to support your research. Provides rapid mitochondrial function testing services, allowing clients to accurately analyze relationship between disease and mitochondria.
Creative Biogene Mitochondrial Gene Mutations
Creative Biogene provides comprehensive range of services and products to assist researchers in cancer related mitochondria studies. Offers tests and services with advantage of cell based and animal based models.
Creative Biogene Mitochondria and Cardiac Diseases
Creative Biogene provides range of services and products to assist researchers in cardiac disease related mitochondria studies. Offers comprehensive testing services for evaluation of variety of cardiac diseases. Mitochondria focused testings and services with advantage of animal based models.
University of Pittsburgh Microscopy and Imaging Suite Core Facility
University of Pittsburgh Microscopy and Imaging Suite
Facility equipped with instruments for optical and electron microscopy, and Flow Cytometry.Offers experimental design, equipment training, staff operated image acquisition, and image analysis. All users must be trained by Facility staff to access the equipment.
Software tool for searching metabolites in different databases including Kegg, HMDB, LipidMaps, Metlin, NP Atlas, KNApSAcK, MINE and in house library. Designed for searches through experimental masses obtained from mass spectrometry techniques. Metabolite annotation tool that uses expert system to score putative annotation based on analytical information acquired under different configurations.
Software pipeline to improve gene annotation for cross species analysis of single cell RNA-Seq. Cross-species transfer of high quality 3’UTR annotation for single cell RNA-Seq.
Web server for cancer miRNome interactive analysis and visualization based on human miRNome data of cancer types from The Cancer Genome Atlas, and public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus and ArrayExpress. Comprehensive database for interactive analysis and visualization of miRNA expression profiles.
Therapeutic Structural Antibody Database
Tracks all antibody and nanobody related therapeutics recognized by World Health Organisation, and identifies any corresponding structures in Structural Antibody Database with near exact or exact variable domain sequence matches. Synchronized with SAbDab to update weekly, reflecting new Protein Data Bank entries and availability of new sequence data published by WHO.
Web tool as structure based antibody prediction server. Collection of computational tools that make predictions about properties of antibodies, focusing on their structures. Single platform containing multiple applications which can: number and align sequences; automatically generate antibody variable fragment homology models; annotate such models with estimated accuracy alongside sequence and structural properties including potential developability issues; predict paratope residues; and predict epitope patches on protein antigens.
AAAAA aims to become the ultimate tool for antibody structural analysis, modelling and engineering.
Database containing all antibody structures available in the PDB, annotated and presented in consistent fashion.Each structure is annotated with number of properties including experimental details, antibody nomenclature (e.g. heavy-light pairings), curated affinity data and sequence annotations. You can use the database to inspect individual structures, create and download datasets for analysis, search the database for structures with similar sequences to your query, monitor the known structural repetoire of antibodies.
Creative Biogene Strain Anaerobic Culture Service Resource
Service for anaerobic bacteria cultivation and culture using variety of culture media and culture conditions. Includes collection, strain cultivation, isolation, identification and strain preservation.
Creative Biogene Isolation and Cultivation of Specific Bacteria Service Resource
Isolation & Cultivation of Specific Bacteria
Provides service for isolation and cultivation of specific bacteria connected with sequencing technology. Services include high throughput sequencing, determination of culture conditions, isolation, cultivation, purification and identification of target strain.
Creative Biogene Aerobic Cultivation Service Resource
Aerobic cultivation services to culture various microorganisms that can be isolated from readily available sources.
Creative Biogene Facultative Anaerobes Cultivation Service Resource
Service to culture various microorganisms that can be isolated from readily available sources. Assists with investigation of anaerobic processes such as glycolysis and lactic acid fermentation.
Creative Biogene Microbial Strains Preservation Service Resource
Provides service to culture and preserve various microorganisms that can be isolated from readily available sources. Microbiologists develop and optimize preservation methods to ensure long term viability of different microorganisms.
Service company that specializes in microbiological research related issues including sample collection, preservation methods, preliminary experiments and effect evaluation, experiments and data analysis. Simultaneously carries out Illumina MiSeq, Ion PGM, Roche 454 high-throughput sequencing analysis, PacBio third-generation high-throughput sequencing analysis, PCR-DGGE denature-gradient gel analysis, real-time quantitative PCR (Real-time qPCR), cloning library and other microbial analysis methods, to solve your problem from many aspects. Cooperates with many institutions and markets its products and services in various countries.
Howard Hughes Medical Institute at Janelia Research Campus Light Microscopy Core Facility
Howard Hughes Medical Institute at Janelia Research Campus Light Microscopy
Facility is open to Janelia scientists. Houses microscopes and multiple workstations dedicated to image processing.
Software tool for fibre photometry recordings analysis developed by Metofico LTD.
Creative Peptides Antibody Protein Bacteria Interactions Service Resource
Antibody (Protein)-Bacteria Interactions
Creative Peptides Antibody (Protein)-Bacteria Interactions
Provides Creative Peptides customers with experts and advanced surface plasmon resonance instruments. Provides high precision antibody bacterial interaction analysis services. Helps with projects, including methods development, validation, analysis of delivered samples and transfer to the client upon request. Provides ready to publish or ready to file data in any format required.
Creative Peptides Backbone Cyclized Peptides Service Resource
Service for chemical synthesis and biosynthesis. Scientists will tailor the most appropriate methods. Every step of peptide synthesis is subject to quality control. Typical delivery specifications include HPLC chromatogram, Mass spec analysis, Synthesis report, Certificate of Analyses.
Creative Peptides Cell Penetrating Peptide Design and Synthesis Service Resource
Cell Penetrating Peptide Design and Synthesis Services
Provides GMP grade cell penetrating peptide synthesis services such as HIV-TAT and Oligo-Arg, etc. Can also design new cell penetrating peptides with unsuitable or non-natural amino acids, peptide branches, and other modifications according to customer needs. Offers comprehensive series of cell penetrating peptides complying with specific purities, scales, and modifications for pharmaceutical and biochemical applications.
Creative Peptides Cosmetic Peptides Service Resource
Service to synthesize cosmetic peptides. Provides any level of cosmetic peptides, including GMP grades, using advanced peptide synthesis equipment. Used for development and production of cosmetic peptides.
Creative Peptides Design Platform Service Resource
Software Hi-C scaffolding tool, using Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal level scaffolds.
Software tool to analyse Hi-C and capture Hi-C data. Command line suite of tools to process, normalize and visualize Hi-C data.
Creative peptides is specialized in process development and manufacturing of bioactive peptides.Offers custom peptide synthesis, process development, manufacturing as well as catalog products for customers in industry and research area. Creative Peptides is staffed by scientific teams with experts in the fields of peptide technology, antibodies and synthetic chemistry.
Instrument aboard the James Webb Space Telescope. It has two major tasks, as imager from 0.6 to 5 micron wavelength, and as wavefront sensor to keep 18-section mirrors functioning as one. Imager covers infrared wavelength range 0.6 to 5 microns. NIRCam detects light from the earliest stars and galaxies in process of formation, population of stars in nearby galaxies, as well as young stars in Milky Way and Kuiper Belt objects. NIRCam is equipped with coronagraphs, instruments that allow astronomers to take pictures of very faint objects around central bright object, like stellar systems.
Software package for control of optical microscope setups with different hardware components optimized to perform multiplexed imaging experiments. Modular laboratory experiment management suite.
Least Bridges Graphs Mathematica package
Software tool as freely distributed computational method for analyzing distance relationships.
Software tool as somatic and germline variant caller for amplicon data. Calls low frequency variants, on linux or windows.Runs on tumor only samples, and search for SNVs, MNVs, and small indels. It takes in .bams and generates .vcf or .gvcf files. It is included with Illumina MiSeqReporter pipeline and various BaseSpace workflows. Can also be run as standalone program.
Creative Peptides Peptide Drug Discovery Service Resource
Creative Peptides Peptide Drug Discovery
Services include Structure Based Drug Discovery to design and optimize hits compounds using structural information obtained from X-ray crystallography, cryo-EM or NMR; Cell Based Drug Discovery by selecting correct cell models and culture to study pharmacological and biochemical properties; Ligand Based Drug Discovery.
Creative Peptides Target Validation in Peptide Drug Discovery Service Resource
Creative Peptides Target Validation in Peptide Drug Discovery
Target Validation in Peptide Drug Discovery
Services include Target analysis in silico, Protein sequence analysis and Homology modeling for targets; Target analysis in bioscience, Cell based models.
Creative Peptides Target Analysis In Silico Service Resource
Creative Peptides Target Analysis In Silico
Services include Binding site identification and druggability assessment, Protein sequence analysis, Protein multiple sequences alignments and selectivity analysis,Analysis of available structural data and protein structure,Homology modeling for targets lacking crystal structures,Design appropriate peptides against specific targets,Water assessment.
Creative Peptides Target Analysis in Bioscience Service Resource
Creative Peptides Target Analysis in Bioscience
Services include Value adding in vitro assays to measure biological activity of target, Characterize pharmacology and assess effects of modulating function, Synthesis of your peptide drug with reactive groups,Design experiments based on your objectives,Custom assay development,Protein expression, Cellular assays, Build cell based models,Peptide binding assays.
Creative Peptides Hit Identification in Peptide Drug Discovery Service Resource
Creative Peptides Hit Identification in Peptide Drug Discovery
Hit Identification in Peptide Drug Discovery
Provides Medium or high-throughput screening to perform rapid screening thousands of samples with biological activities at model organism, cell, pathway, or molecular levels, accelerating target analysis procedure; High content screening to analyze the way peptide compound interacts with target at subcellular level; Fragment screening to obtain higher affinity lead ligands by growing low molecular weight chemical fragments into larger drug like molecules;Virtual screening to automatically evaluate large databases with known 3D structures; Artificial Intelligence for difficult targets to support discovering and developing more drug candidates; Knowledge based design in hit identification;Hits identified by NMR screening.
BOC Sciences PROTAC Target Protein Services
Service provider in drug discovery and research. Provides one stop proteolysis targeting molecular drug discovery based on chimeric. Provides target protein services to customers to meet new drug discovery goals.
BOC Sciences Ligand Design for Target Protein Service Resource
BOC Sciences Ligand Design for Target Protein
BOC Sciences PROTAC Ligand Design for Target Protein
Service provider in drug discovery and development. Provides one stop development, which has become strategy in field of small molecular drug discovery. Provides ligand design for target protein to customers to meet new drug discovery goals.
BOC Sciences Peptide ligand for target protein Service Resource
Service provider in drug discovery and development. Provides one stop PROTA development, which has become strategy in field of small molecular drug discovery. Provides peptide ligand design for target protein to customers to meet new drug discovery goals.
BOC Sciences Small molecule target protein ligand Service Resource
BOC Sciences PROTAC Small molecule target protein ligand
BOC Sciences Small molecule target protein ligand
Provides small molecule target protein ligand service to customers to meet new drug discovery goals.
BOC Sciences Protein Ubiquitination Service Resource
BOC Sciences PROTAC Protein Ubiquitination Service
BOC Sciences Protein Ubiquitination Services
Service in field of drug discovery and research. BOC Sciences service in one stop Proteolysis Targeting Chimeric based molecular drug discovery which has become strategy in area of drug discovery.
Texas A and M University Microscopy and Imaging Center Core Facility
Texas A&M University TAMU-Microscopy and Imaging Center
Core with expertise in Transmission Electron Microscopy, Scanning Electron Microscopy, Light Microscopy, and supporting instruments. Staff members provide quality training and education through sessions, short courses, formal courses, open house seminars, and more.
Open source web application development framework. Model View Controller framework, providing default structures for database, web service, and web pages.
Creative Peptides PNA Synthesis Service Resource
Provides various types of PNA conjugates and tailor made PNA products.
Creative Peptides PNA Oligomer Synthesis Service Resource
Creative Peptides PNA Oligomer Synthesis
Provides two chemical synthesis methods to synthesize Peptide Nucleic Acid oligomers, including Boc chemistry and Fmoc chemistry.
Creative Peptides Chemical Synthesis of PNA Oligomers with Fmoc Service Resource
Chemical Synthesis of PNA Oligomers with Fmoc
Creative Peptides Chemical Synthesis of PNA Oligomers with Fmoc
Provides Fmoc based PNA synthesis. Route consists of repeated cycles of deprotection, activation, coupling and capping.Synthesis of small scale PNA oligomers, which can be performed on common DNA synthesis platforms.
Creative Peptides Synthesis by Mmt Chemistry Service Resource
Creative Peptides Synthesis by Mmt Chemistry
Provides service with chemical method to synthesized any new PNA/DNA chimera where only Mmt/acetyl protected monomers can not damage the DNA part, and can synthesize any desired sequence.
Creative Peptides PNA/DNA Chimera Synthesis Service Resource
Creative Peptides PNA/DNA Chimera Synthesis
Provides multiple types of PNA/DNA chimera related services. Uses HPLC analysis and mass spectrometry to ensure purity and confirm identity.
Software for advanced physics modeling capabilities and accuracy. Used to create advanced physics models and analyze variety of fluids phenomena. Fluent is software edited by Ansys in order to make computational fluid dynamics calculations.
Diagnostics for HierArchical Regession Models
Software R package to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Package also provides number of plot and test functions for typical model misspecification problems.
Software R package as functions to accompany J. Fox and S. Weisberg R companion to applied regression.
Software Perl tool for identification of leader TRS junctions and plotting graphs of results. Accepts fastq files derived from Illumina paired-end and Nanopore cDNA/direct RNA sequencing, and bam files produced by splicing alignment method with SARS-CoV-2 genome.
Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information.
App for searching human and mimivirus homologous proteins
Web interactive and searchable genome wide comparison tool for browsing human and mimivirus homologous proteins. User friendly Shinny app helps users browse protein sequence homology between humans and mimivirus at genome wide level for querying new homologs and generating new hypotheses.
Project aims to change anatomy atlas by building atlases through open data, community based collaborative development, and free distribution of medical knowledge. Provides access to several 2D and 3D browser based tools.
University of Southern California CHLA Extracellular Vesicle Core Facility
Saban Research Institute at Children"s Hospital Los Angeles Extracellular Vesicle Core
University of Southern California CHLA Extracellular Vesicle Core
Core provides isolation, characterization, and analysis of extracellular vesicles and other nano sized particles.
Bioneer Exicycler 96 RealTime Quantitative Thermal Block
Real Time quantitative thermal block. 96-well PCR system designed for real time qPCR application.
Portal to download and visualize rat gene expression and associations between genotypes and molecular phenotypes, uniformly processed across tissues.
Software R package for normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.
University of Vermont Larner College of Medicine Flow Cytometry and Cell Sorting Core Facility
Flow Cytometry and Cell Sorting Facility
University of Vermont Larner College of Medicine Flow Cytometry and Cell Sorting Facility
Harry Hood Bassett FCCS Facility is located in Given Medical Research Building Room C316-UVM. Facility provides flow cytometers and personnel provide scientific and technical consultation to faculty and staff in design of flow cytometric experiments, and assistance in data analysis and interpretation.
Image analysis software. Used for custom cell detection and colocalization analysis. Pipsqueak Pro takes moves Pipsqueak out of ImageJ/FIJI and into integrated interface.
Software image analysis tool as older ImageJ/Fiji plugin version.
Cloud based Electronic Data Capture system or clinical data management platform used to store quantitative data.
Software tool for designing and administering psychological tests and experiments on computers.
Vevo 3100 micro ultrasound imaging system
Vevo 3100 micro ultrasound imaging system reduces speckle noise and artifacts while preserving and enhancing critical information for small animal in vivo studies. System helps you visualize your data at high resolution.
Perkin Elmer | NexION 2000B ICP Mass Spectrometer
Allows to adjust signal transmission to measure elements with low and high concentrations in the same sample in the same run. This extends dynamic range up to 12 orders of magnitude and optimizes productivity while preserving lifetime of detector.
Software for recipe and menu management, food labels, diet and activity analysis, meal planning. Nutrition management software for healthcare, elite sport, food industry and education.
Harlow Healthcare Health For All Children
Portal for joint working party on child health surveillance.
Web tool for calculations for Mendelian Randomization. Power calculations for Mendelian Randomization. Used to calculate statistical power for Mendelian Randomization study, using Non Centrality Parameter based approach.
Colorado State University Laboratory Animal Resources Core Facility
Colorado State University Laboratory Animal Resources
LAR provides care for laboratory animals in support of Colorado State University research community. Oversees care and management of animals in animal holding space facility for small and large animals including animal biosafety level 3.
Software R package for cell type deconvolution of heterogeneous tissues based on bulk RNAseq data or single cell RNAseq expression profiles.Provides unified testing interface to rapidly run and benchmark multiple deconvolution methods.
Open source LC-MS data processing engine for simplifying metabolomics analysis. Mass spectrometry data processing engine that is optimal for isotopomer labeling and global metabolomic profiling experiments. Interactive software platform that accelerates analysis of LC-MS, GC-MS, and LC-MS/MS datasets.
Portal designed for Library and KM Professionals to locate internet resources related to their profession. Not for profit service to knowledge resources. Platform with links to e-resources on Knowledge Management, Librarianship, Philosophy, Health, Technology, ITES/BPO/ ITIL, Call Centers, Business Information etc.
Platform facilitates comprehensive discovery of and access to multidisciplinary microbiome data in order to unlock new possibilities with microbiome data science. Multi organizational effort to integrate microbiome data across diverse areas in medicine, agriculture, bioenergy, and environment. Founded to support long term advancement of microbiome science.
Department of Energy Systems Biology Knowledgebase
The Department of Energy Systems Biology Knowledgebase
Data science platform for predicting and designing biological function. Platform to model plant and microbial physiology and community dynamics. Knowledge creation and discovery environment for biologists and bioinformaticians. Integrates variety of data and analysis tools from US Department of Energy and other public services into platform that leverages scalable computing infrastructure and performs systems biology analyses. Enables scientists to analyze their own data within context of public data and share findings across system.
Validated Antibody Database and Reagents. Platform to search antibodies, siRNA/shRNA, ELISA, cDNA clones, proteins/peptides, assays, and biochemicals.
Cold Spring Harbor Laboratory Flow Cytometry Shared Resource Core Facility
Cold Spring Harbor Laboratory Flow Cytometry Shared Resource
Resource provides equipment, training, and operating assistance for cell sorting and analysis. Facility staff oversees equipment maintenance, trains new users, and assists with assay development and operation of equipment.
Forsyth Institute Histology Core Facility
The Forsyth Institute Forsyth Histology Core
Core offers consulting and support services for both soft tissue and precise hard tissue analysis. Services include: tissue processing, embedding, sectioning, staining, and guidance on protocols. Can embed samples in standard molds or custom molds in paraffin, resin, or as frozen tissue for routine histology. Provides special stains and immunohistological studies.
Forsyth Institute Oral Microbiome Core Facility
Offers Next Generation Sequencing (NGS) and comprehensive data analyses and interpretation for 16S rRNA gene amplicon sequences and other big data sequence applications. Offers analyses of previously obtained sequences. Many investigators are familiar with Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) as well as its predecessor the Human Oral Microbe Identification Microarray (HOMIM) for rapid 16S rDNA analyses of oral clinical samples. We continue in that tradition using bioinformatic methodology, which will provide the best possible taxa identification.
Interdisciplinary data platform provides access to research data and information from all fields of applied plasma physics and plasma medicine. Aims at distributing, publishing and archiving of data and information, supporting findability, accessibility, interoperability and re-use of data, for low temperature plasma physics community.Most of data are freely available and can be used under terms of license listed on dataset description page. Each dataset can be identified, cited and shared by using Digital Object Identifier.
North Carolina State University High Performance Computing Services Core Facility
North Carolina State University NCSU High Performance Computing
Core, available through NC State Office of Information Technology, provides entry and intermediate level computing resources and consulting support for research and instruction.
Texas A and M University College of Veterinary Medicine and Biomedical Sciences Flow Cytometry Core Facility
Texas A&M University TAMU Flow Cytometry Facility
Provides flow cytometry experimental design, data collection, data analysis and cell sorting services; training for flow cytometers, imaging flow cytometer, and data analysis using IDEAS and FlowJo software;staff assisted flow cytometry and imaging flow cytometry data acquisition, cell sorting, and data analysis, experimental design and consultation services. FCF currently has Beckman Coulter Moflo Astrios cell sorter, Luminex/Amnis Image Stream X Mark II, Luminex/Amnis Cell Stream, and Becton Dickinson Accuri C6 flow cytometer. Astrios cell sorter is housed in ClassII BSC and has 3 lasers (405nm, 488nm, 642nm) and 11 detectors and can sort up to 6 populations simultaneously. Image Stream X Mark II is equipped with 20x, 40x, 60x objectives, 4 lasers (405nm, 488nm, 561nm, 642nm), 10 detection channels, EV mode for small particle detection, and an autosampler.Cell Stream is equipped with 3 lasers (405nm, 488nm, 642nm), 13 detection channels, EV mode for small particle detection, and autosampler. Accuri C6 is equipped with 2 lasers (488nm, 642nm), and 4 detection channels.
University of California at Berkeley QB3 Genomics Core Facility
University of California at Berkeley UCB-QB3 Genomics
Partnership between Vincent J. Coates Genomics Sequencing Laboratory,Functional Genomics Laboratory, and Computational Genomics Resource Laboratory. Offers consultation on experimental design and data analysis, full suite of technical services related to high throughput sequencing and genomics experiments, and access to high performance computational infrastructure.
Agilent Spectrum Mill MS Proteomics Workbench
Software tool for high throughput processing of MS/MS and MS spectra to provide protein and peptide identifications and relative quantitation.
Software Matlab based MVPA toolbox for EEG analyses. Allows direct comparison of ERP/ERF results to MVPA results using any dataset in standard EEGLAB or Fieldtrip format. Performs and visualizes multiple comparison corrected group decoding and forward encoding results in variety of ways, such as classifier performance across time, temporal generalization (time-by-time) matrices of classifier performance, channel tuning functions (CTFs) and topographical maps of (forward-transformed) classifier weights.
Software Matlab based MVPA toolbox for EEG and MEG analyses. Classification and regression toolbox for multi dimensional data. Performs cross validation, hyperparameter tuning, and nested preprocessing. Computes various classification and regression metrics and establishes their statistical significance.
Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials.
System for Omics Data Access and Retrieval
Software package for managing data in omics research projects. Integrates with iRODS (integrated rules oriented data system) software for mass data management.
Software Python toolbox for brain parcellation evaluation.
Creative Biolabs Model Organism Antibodies Service Resource
Antibody group provides researchers with functional proteomics research platform. Antibody customization service provider. Custom antibody development team can work with you to create customized antibody solution to meet your specific research needs. Provides monoclonal antibody screening. Prepares monoclonal antibody library to screen monoclonal antibodies for appropriate peptide epitope of each protein.
Web portal for structure analysis of macromolecules.
Webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.Fixes PDB sequence numbering problem by replacing author numbering with numbering derived from corresponding UniProt sequences.
Web tool for analyzing RAS protein structures.Used to build updatable database of all available RAS structures in Protein Data Bank (PDB) with their catalytic switch 1 (SW1) and switch 2 (SW2) loopsconformationally classified and their molecular contents annotated. Database presenting updated and searchable dataset of human KRAS, NRAS, and HRAS structures in PDB, and which includes page for analyzing user uploaded RAS structures.
Software tool as protein sequence culling server. Used for culling sets of protein sequences from Protein Data Bank (PDB) by sequence identity and structural quality criteria. Can provide lists culled from entire PDB or from lists of PDB entries or chains provided by user.
Lexical database of English. Nouns, verbs, adjectives and adverbs are grouped into sets of cognitive synonyms (synsets), each expressing distinct concept. Synsets are interlinked by means of conceptual-semantic and lexical relations. Resulting network of meaningfully related words and concepts can be navigated with browser.
Open, community-driven ontology that integrates key medical and biomedical terminologies, supporting disease data integration to improve diagnosis, treatment, and translational research. Mondo records sources of all data and is continually updated, making it suitable for research and clinical applications that require up-to-date disease knowledge.
3DHISTECH | Pannoramic 250 Flash III slide scanner
Pannoramic 250 Flash III digital slide scanner
Scanner for digital pathology for scanning in brightfield and fluorescence. Offers fast scanning (35 sec/slide) and high throughput (60 slides/hour) (brightfield scanning, 41x optical magnification, 15mm x 15mm area, 15 FOVs Focus Distance, JPG compression, MRXS file format).Offers slide loading capacity 300 and continuous loading with vertical slide arrangement.
Research inverted system microscope. Olympus IX2 inverted microscope combined with UIS2 optical system. Used for live cell experiments.
Visualising Longitudinal and Cross-sectional Variant Effects
Software for visualising longitudinal and cross-sectional variant effects.
Software tool for GP2 data visualization.
Parkinson's Disease Genome-Wide Association Study Locus Browser
Web platform that aims to collect as much data as possible (including genetic, genomic and functional). to identify and characterize potential causal genes and underlying molecular mechanisms that contribute to PD risk and pathogenesis. Web tool provides users with method of identifying potential causal genes at all known PD risk loci from large‐scale PD genome‐wide association studies.
Software tool as coordinate free approach for comparing biological shapes using landmark data.
Thermo Fisher | EVOS XL Core Imaging System
Designed to eliminate complexities of microscopy, EVOS XL Core system captures high-quality brightfield cell images right at your benchtop within minute. Instrument for monitoring cell cultures, either within hood or in cell culture room.
Aperio slide scanner for fluorescent images. Used for whole slide scanning of slides stained with multiple fluorochromes. With quad multi-bandpass filter set, up to four color channels can be acquired; users can add other filters for greater flexibility. Advanced illumination, autoexposure, and autofocus capabilities eliminate need for trial-and-error scanning, reducing problem of photobleaching.
Software tool for sequence mapping.The next version of BWA-MEM. Used for aligning sequencing reads against large reference genome.
Software tool to locate and display tandem repeats in DNA sequences. Program to analyze DNA sequences.
Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences.
Software tool for chromosomal orthologous link analysis.
Software lightweight Python library for computational pipelines. Reproducible pipeline framework.
Software for segmenting individual cells in microscopy images using deep learning. Cell segmentation software.
Software R package which loads SomaLogic, Inc. proprietary data file, called an ADAT file ('*.adat'). Provides auxiliary functions for extracting and manipulating relevant information from ADAT, as well as exporting modified ADAT to file.
Statistical software tool. Predictive analytics software. Offers all tools in JMP plus advanced features for more sophisticated analyses.
Texas A and M Health Science Center IBT Protein Production, Characterization and Molecular Interaction Core Facility
Characterization and Molecular Interaction (PPCMI)
Texas A&M Health Science Center IBT-Protein Production
Core provides cloning, expression and purification services of functional proteins at scale that meets the quantity and purity benchmarks for structural, biophysical, biochemical, and therapeutics studies; characterizes macromolecular biophysics and interaction energetics using instrumentation and techniques that can analyze association and kinetic binding constants by surface plasmon resonance, enthalpies and entropies of binding by isothermal titration calorimetry, as well as determination of stoichiometry, stability, and homogeneity by both techniques.
Texas A and M University Veterinary Medicine and Biomedical Sciences Research Histology Unit Core Facility
Texas A and M University Veterinary Medicine and Biomedical Sciences Core Histology Laboratory Research Histology Unit Core Facility
Texas A&M University TAMU-CVMBS Core Histology Laboratory
Provides histology (including cryosectioning, IHC and IFC) digital pathology and veterinary pathology (board certified veterinary pathologist on staff) services.
Texas A and M University Materials Characterization Core Facility
TAMU-Materials Characterization Facility (MCF)
Texas A&M University TAMU-Materials Characterization Facility (MCF)
Core provides access to instrumentation essential for studies of surface and interfacial properties of materials, such as ion and electron based spectroscopies, electron, optical and scanning probe microscopies. Core provides training to students and faculty on instrumentation as well as consolation of measurements needs and data interpretation, supports educational activities involving lab tours, workshops, hands on demonstrations, outreach and broader impact related activities through our open house and lunchtime seminar series.Supports collaborative research projects with outside industrial users.
State University of Campinas Multidisciplinary Center for Biological Investigantion on Laboratory Animals Science Core Facility
Core produces mice and rats for biomedical research. Provides services for customers are researchers from Unicamp and other Institutions from Brazil.
National Autonomous University of Mexico Microscopy Core Facility
Core is specialized in stereology techniques, live cell imaging, CLSM (confocal microscopy), and STORM. Provided instruments include CONFOCAL microscopes Zeiss LSM 5 Pascal, Olympus BX51-WI,Olympus IX71 inverted microscope, Nikon Labophot-2 microscope,Nikon Optiphot 2 microscope.
State University of Campinas; São Paulo; Brazil
Universidade Estadual de Campinas (UNICAMP)
Public research university in Brazil commonly called Unicamp. Recognized as one of the best universities in Latin America.
Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data.
Software pipeline for processing and analysis of large scale spatial transcriptomics data. Enables reproducible data processing from raw sequencing data to automatically generated downstream analysis reports.
Software tool for simulating spatially inhomogenous biochemical reaction diffusion systems for modelling cell environment feedbacks. Simulation software for spatially organised biochemical systems.
Harvard Medical School Microscopy Resources On the North Quad Core Facility
Light microscopy core is open to HMS researchers, including Affiliated hospitals. Supports imaging modalities ranging from wide field, TIRF, spinning disk and single point scanning confocal, multiphoton, FLIM and supper resolution. Microscopes are embedded within Departments of Microbiology, Immunology, and Genetics, housed in five microscope rooms on five floors of NRB and HIM.
University of Toronto Advanced Instrumentation for Molecular Structure Mass Spectrometry Laboratory Core Facility
University of Toronto AIMS Mass Spectrometry Laboratory
Core mass spectrometry facility located in Department of Chemistry, University of Toronto, which houses several mass spectrometers. Services include:High resolution, accurate mass determinations of small molecules via EI, ESI and DART ionization;Mass determinations of intact peptides and proteins via ESI-QTOF-MS and MALDI-MS; HPLC-MS/MS analysis of protein digests via ESI-QTOF-MS; Quantitative analysis via HPLC-MS/MS using QqQ instrumentation.
University of South Carolina at Columbia College of Pharmacy Microarray Core Facility
South Carolina College of Pharmacy Microarray Core Facility
University of South Carolina at Columbia South Carolina College of Pharmacy Microarray Core Facility
Services include RNA quality control, amplification and labeling, array hybridization, scanning and data analysis, assisting customers in design and performance of microarray experiments, using Agilent (pre-made and custom) and Affymetrix arrays. Provides support for quantitation and quality assessment of DNA, RNA and protein on Agilent 2100 Bioanalyzer. Provides training and support for Agilent and Affymetrix Hybridization oven users. Provides support for microarray scanning and for data analysis with variety of software packages for both Agilent and Affymetrix platforms.Quantity and quality of your RNA, DNA, proteins and cells are determined with help of Agilent 2100 Bioanalyzer.
Thermo Fisher | Orbitrap Eclipse nanoLC/MS system
System includes Thermo Orbitrap Eclipse Tribid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments.
Texas A and M University Institute of Biosciences and Technology High Throughput Research and Screening Center Combinatorial Drug Discovery Core Facility
TAMU - Combinatorial Drug Discovery Program (CDDP)
TAMU IBT High Throughput Research and Screening Center CDDP
Texas A&M Health Science Center TAMU - Combinatorial Drug Discovery Program (CDDP)
Texas A&M University Houston IBT High Throughput Research and Screening Center CDDP
Core provides industry standard high throughput screening and automated microscopy capabilities to scientists performing drug discovery research. Provides access to automated infrastructure to support phenotypic and biochemical targets. Provides ready access to collections of current FDA approved drugs and clinical candidates exhibiting drug like qualities of acceptable solubility, desirable ADME/toxicology properties and adequate bioavailability. Has collections of mechanistically annotated informer sets that are pathway specific modulators for studying mechanism of action or target identification, collections of natural products and diverse sets of small molecules that can be interrogated for new target discovery. Each project is individually evaluated and team of scientists from CDDP is created to fit specific needs of project from assay design and development through primary, secondary and orthogonal screening.
Thermo Fisher | Exploris 480 nanoLC/MS system
Exploris 480 system is hybrid quadrupole Orbitrap mass spectrometer with Waters M-Class Acquity. Proteomics system for hands on use by highly trained users.
Thermo Fisher | Exploris 240 LC/MS system
Exploris 240 system is hybrid quadrupole Orbitrap mass spectrometer with Waters H-Class Acquity, ZipChip, and DART front ends. Flexible platform for wide range of small molecule and intact protein analyses.
System includes SQD2 as single quadrupole MS with Waters H-Class Acquity UPLC, operated as open access platform for trained users. SQ Detector2 is single quadrupole mass detector for chromatography compatible with range of chromatography platforms and ionization sources.
Pipetting Robot offers repeatable, traceable pipetting with connected single and multichannel electronic pipettes. Enables automation of many routine sample preparation workflows.
Creative Peptides Total Peptide Library Construction Service Resource
Total Peptide Library Construction Technology
Service uses bioinformatics methods to compress peptide information, which can integrate information of multiple peptide into one peptide. Provides collection of small peptide of specific length and different sequences, which includes permutation and combination of various amino acid sequences in short peptide of this length.Total peptide library for new drug research and development.
Creative Peptides Peptide Drug Bioconjugations Service Resource
Custom peptide synthesis, modification, and conjugation services involve chemical modification of peptide at highly specific sites. This allows for attachment of drugs or bioactive molecules though variety of coupling techniques.
Creative Peptides | Peptide Lead Optimization Service Resource
Provides optimized one stop solution for peptide lead drugs. Used to improve upon lead molecule that demonstrates activity at target of interest by optimizing its potency or selectivity at target and its absorption, distribution, metabolism and elimination properties.
Creative Peptides | Formulation Development Service Resource
Service to determine optimal dosage form, composition and manufacturing route for pharmaceutical products.
Software plugin to estimate chromosome sizes from karyotype images.
Sanford Burnham Prebys Medical Discovery Institute Proteomics Core Facility
Sanford Burnham Medical Research Institute Proteomics
Facility provides mass spectrometry based proteomics services with methods tailored to needs of scientific investigators for routine mass spectrometric analysis of peptides and proteins, identification of novel proteins, characterization of post translational modifications, and quantitative proteomics analysis of simple to complex biological samples. Core identifies, validates and develops new methods designed for characterization and identification of biologically important proteins. Supports users with software applications and development, data analysis and experimental design of proteomics studies. Expands its capabilities in large scale differential proteomics analysis and phosphoproteomics for unbiased discovery of potential biomarkers and mapping protein profiles.
Creative Peptides PNA Modification Service Resource
Peptide nucleic acid modification includes modification of backbone and base. Service provides Backbone modification, Nucleobase modification, Modification of connection between nucleobase and backbone.
Creative Peptides PNA Modification of Connection between Nucleobase and Backbone Service Resource
Modification of Connection between Nucleobase and Backbone
PNA Modification of Connection between Nucleobase and Backbone
Peptide nucleic acid modification service includes cooperation with customers at each stage of PNA development, providing complete test plan, selection of appropriate program and process, and monitoring entire test process.Provides modification strategies based on product diversity and inherent biological characteristics.Provides series of quality assurance studies, such as GC-MS, HPLC analysis, to achieve quality monitoring and understanding of effects of finished products.
Creative Peptides PNA Backbone Modification Service Resource
Peptide nucleic acid backbone modification service includes backbone modification of N-(2-aminoethyl) glycine unit structure of PNA to increase water solubility and enhancing hybridization performance.
Creative Peptides PNA N/C Terminal Modification Service Resource
Service to modify monomer backbone, including chemically active sites at both ends. Monomer N-terminal and C-terminal modification.
Creative Peptides PNA Modification by C Replacement Service Resource
PNA modification service provides replacement of backbone C.
Creative Peptides | Peptide Synthesis Service Resource
Provides peptide drug synthesis services, allowing researchers to synthesize peptide drug that is integral to drug discovery and development. Offers services in chemical synthesis of variety of peptide compounds.
Creative Peptides Active Peptide Ingredients from Natural Products Service Resource
Active Peptide Ingredients from Natural Products
Provides peptide drug extracting from natural products. Extracted peptides evaluated as possible therapeutic agents for various diseases.
Creative Peptides Peptide Drug Biosynthesis Service Resource
Services include Enzyme decomposition synthesis, Fermentation method, Genetic engineering method, Peptide design coupled with computational design, Peptide drug design and stabilization.
Creative Peptides Peptide Drug Chemical Synthesis Service Resource
Chemical synthesis service for peptide production by coupling carboxyl group of incoming amino acid to N-terminus of growing peptide chain.
Creative Peptides Custom Peptide Synthesis Service Resource
Custom peptide synthesis service. Provides solid phase peptide synthesis, liquid phase peptide synthesis, glycochemistry, small molecule synthesis and high throughput synthesis.
Creative Biogene Mitochondrial Genomics Service Resource
Office service platforms for mitochondrial genome monitoring and analysis.
Creative Biogene Mitoepigenetics Service Resource
Provides mitoepigenetics analysis platform to help carry out mitochondrial research. Services include mitochondrial DNA methylation and hydroxymethylation, physiological and pathological modification of mitochondrial epigenetics, interaction between mitochondria and nuclei, use of mitochondrial epigenetic products as biomarkers, and effects of environment and nutritious diet on mitochondrial epigenetics.
Creative Biogene Methylation and Hydroxymethylation Service Resource
Creative Biogene services for mitochondrial methylation and hydroxymethylation.
Creative Biogene Mitochondrial Physiological and Pathological Modifications Service Resource
Mitochondrial Physiological and Pathological Modifications
Provides multi species mitochondrial epigenetic analysis and customizes appropriate research route. Providies services on epigenetic characteristics of mitochondria under different physiological and pathological conditions.
Creative Biogene Mitochondrial Biomarkers and Therapeutic Targets Service Resource
Mitochondrial Biomarkers and Therapeutic Targets
Creative Biogene service for discovery of disease specific proteins associated with mitochondrial epigenetic products, which can be used as molecular targets for new drug design and provide molecular markers for early diagnosis of diseases.
Creative Biogene Autotrophic Bacteria Cultivation Service Resource
Provides service for autotrophic bacteria cultivation.
Creative Biogene Prosthecochloris Cultivation Service Resource
Service offers culture of Prosthecochloris bacteria with specific formulations of growth media for use in cloning, plasmid DNA preparation, and protein expression.
Creative Biogene Chlorobium Cultivation Service Resource
Creative Biogene Pelodictyon Cultivation Service Resource
Creative Biogene Clathrochloris Cultivation Service Resource
BOC Sciences PROTAC Design Services Service Resource
Provides service for one stop proteolysis targeting molecular drug discovery based on chimeric PROTAC.
BOC Sciences Linker Design and Optimization Services Service Resource
Provides Linker Design and Optimization services to meet new drug discovery goals.
BOC Sciences PROTAC Design based on Bioinformatics
Provides PROTAC design based on bioinformatics services to customers to meet new drug discovery goals. Used for analysis of large scale multi group data to discover potential drug targets based on biological network characteristics, multi gene chip, proteome, metabolome data.
BOC Sciences PROTAC diastereomer Design negative control Service Resource
PROTAC diastereomer Design negative control
Service to design PROTAC diastereomer to meet new drug discovery goals.
BOC Sciences PROTAC GMP Services Service Resource
Specializes in development and GMP manufacture of pharmaceutical grade products. Provides pharmaceutical discovery services to assist clients in reaching their R&D goals.
Automated workflow enabling benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. Results are presented in interactive HTML report where selected global and reference specific performance metrics can be explored.
PRE Clinical Interagency Research Resource TBI
PRE-Clinical Interagency Research Resource-TBI
Resource to accelerate development of therapies for traumatic brain injury by elevating rigor, reproducibility, and transparency in preclinical research.
Software provides analysis functions for sleep, circadian rhythm and physical activity alongside device and data management tools within one integrated solution. Accelerometer data from MotionWatch or PRO-Diary is interpreted by software algorithms to provide the end points. Intuitive graphical user interface provides valuable insights into subject behaviour while providing flexible data selection and reporting tools.
Public private partnership combining genotype data from Finnish biobanks and digital health record data from Finnish health registries. Provides opportunity to study genetic variation in relation to disease trajectories in isolated population.
OSTI ID:1812943; re3data DOI:10.17616/R31NJN56; FAIRsharing DOI:10.25504/FAIRsharing.45bf5b
Pacific Northwest National Laboratory DataHub: Scientific Data Repository
Provides tools and services to meet scientific data challenges at Pacific Northwest National Laboratory . DataHub helps researchers address the full data life cycle for their institutional projects and provides path to creating findable, accessible, interoperable, and reusable data products. Although open science data is crucial focus of DataHub’s core services, we are interested in working with evidence based data throughout PNNL research community.
Open source software tool for correlation and functional enrichment of proteome wide systems genetics. Analyzes genetic variants associated to protein networks and phenotypic traits. Uses proteomics data to perform correlation network analysis and annotates protein-protein interactions, subcellular localizations and drug associations.
Software library for reading data and formatting information from Excel files in .xls format.
Software Python library to read and write Excel 2010 xlsx/xlsm/xltx/xltm files.
Software package contains colormaps for commonly used oceanographic variables.
Software library for automatically adjustment of text position in matplotlib plots to remove or minimize overlaps with labels and data points.
Open source statistical package written in Python 3 and based mostly on Pandas and NumPy. Designed for users who want simple yet exhaustive stats functions.
System for efficient transfection of a variety of hard-to transfect cell lines and primary cells. Using certified aluminium electrode cuvettes this single cuvette system is capable of transfecting various substrates in a low throughput format.
Laser scanning confocal microscope for multiplex imaging and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software package for generation of pseudo long reads by using short reads of metagenomic sample and microbial reference genome sequences as input.
Software tool to find SNP sites from multi-FASTA alignment file. Can output results in multiple formats for downstream analysis.
Open browser to inform therapeutics development for tracking SARS-CoV-2 single nucleotide variations, lineages, and clades using virus genomes on GISAID database while filtering by location, date, gene, and mutation of interest. can Provides information on which virus mutations are present in area during specific period by processing data on mutations found in viral genetic material collected worldwide from hundreds of thousands of people with COVID-19, which are hosted in existing online database.
Software tool to calculate positional conservation for multiple sequence alignment. Used for calculation of positional conservation in protein sequence alignment.
Software tool for calculating and comparing synonymous codon usage and its impact on protein folding. Used to harmonize codon usage frequencies for heterologous gene expression. Codon usage calculator that evaluates relative usage frequencies of synonymous codons used to encode protein sequence of interest and compares these results to rigorous null mode.Evaluates synonymous codon usage patterns for any coding sequence from any fully sequenced genome.
Web tool for genomic HEXploring allows landscaping of novel potential splicing regulatory elements. Allows landscaping of splicing regulatory regions, provides quantitative measure of mutation effects on splice enhancing and silencing properties and permitts calculation of mutationally most effective nucleotide.
Software for comprehensive quantitative measure of splicing impact of complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts.
Coarse grained co-translational folding analysis
Coarse-grained co-translational folding analysis
Software for statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved, and also co-translational protein folding model.
Platform for global network of researchers to investigate role of human genetics in SARS-CoV-2 infection and COVID-19 severity. Provides results of three genome-wide association meta analyses that consist of patients with COVID-19 from studies across countries.
Web service for RNA/DNA folding predictions including pseudoknots and entangled helices.Used for prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.
Web server for analysis and design of nucleic acid systems. Enables thermodynamic analysis of dilute solutions of interacting nucleic acid strands. Analysis and design of nucleic acid secondary structure for systems involving one or more species of interacting strands.
SigCom Library of Integrated Network-based Cellular Signatures
Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures.
Software workflow for automatized spatio temporal plant positioning based on UAV images.
Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer.
Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference.
Software tool for precision HLA typing from next generation sequencing data.
Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X.
Software tool for genotyping of HLA region using next generation sequencing data. Performs alignment of reads to HLA sequences from international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database.
Software for HLA predictions from next generation shotgun sequence read data and supports direct read alignment and targeted de novo assembly of sequence reads. Used for identifying HLA alleles directly from shotgun sequence datasets.Supports predictions from variety of DNA sequencing technologies including those from Illumina, MGI, PacBio and Oxford Nanopore.
Software implements new graph alignment model for human leukocyte antigen, based on projection of linear alignments onto variation graph. Enables accurate HLA type inference from whole genome and whole exome Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data and from genome assemblies.
Software for accurate HLA typing at full resolution from whole genome sequencing data. Used to estimate the most likely HLA types from high throughput sequencing data.
Software HLA typing algorithm for next generation sequencing data.Can accurately determine HLA alleles with 6 digit precision from NGS data (fastq format). RNA-Seq data can also be applied.
Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq.
Texas A and M University Laboratory for Synthetic Biologic Interactions Core Facility
Laboratory for Synthetic-Biologic Interactions
Texas A&M University Laboratory for Synthetic-Biologic Interactions
Facility housed in Department of Chemistry.Designed to be multi user laboratory supporting major research initiatives. Instruments are currently available on fee for use basis, and others may be made available on case by case considerations.
University of Colorado Boulder Polymeric and Optical Materials Characterization Shared Core Facility
Polymeric and Optical Materials Characterization (POM-C) Shared Facility
University of Colorado Boulder Polymeric and Optical Materials Characterization
Facility specializes in material characterization of polymers, hydrogels, liquid crystals, and composites.
Harvard Medical School Research Computing Core Facility
Harvard Medical School HMS Research Computing Core
Promotes deeper collaboration across Harvard biomedical research ecosystem.This includes improved capabilities and performance by establishing more transparent and sustainable IT services for our research community.
Montpellier Imagining Resources MRI Core Facility
Cell imaging facility of Montpellier area, France.Offers access to cutting edge instruments for optical and electron microscopy, flow cytometry, and X-ray micro tomography. Instruments are housed in seven sites that mirror distribution of Life Science research campuses of the region. Mission is to support research by offering imaging instruments and image analysis solutions.
Software valifìdated for evaluation of body composition using Body Impedance Assessment.
Software MATLAB/Octave tools to interact with datasets conforming to Brain Imaging Data Structure format.
Portal to search, analyze and manage patent and scholarly data. Serves global patent and scholarly knowledge as public good to inform science and technology enabled problem solving.
Data discovery platform that facilitates curation, analysis and sharing of antibody/B-cell and T-cell receptor repertoires from multiple labs and institutions. Used to increase value of data through sharing with community. Platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories.
Software pipeline for sleep researchers to perform automatic sleep scoring for rodents. Artificial neural network for automated behavioral state classification in rats.
Software library for efficient text classification and representation learning.
Software tool to match bioRxiv preprints with their corresponding PubMed paper.
University of Montreal Structural Biology Platform Core Facility
Structural Biology Platform at the Universit� de Montr�a
Offers access to several scientific instruments intended to answer structural biological questions for scientific community.Consists of high field nuclear magnetic resonance spectrometers (500 MHz, 600 MHz with cryo-probe and 700 MHz) controlled with recent NEO consoles from Bruker, small angle X-rays scattering (SAXS) instrument, with high throughput robotics. SAXS can be coupled to liquid chromatography system for SEC-SAXS applications.Other instruments include size exclusion chromatography system coupled to multi angle light scattering detector (SEC-MALS), isothermal titration calorimetry (ITC) instrument as well as several liquid handling robots for rapid bio molecular crystal preparation and screening. Users have also access to bio-informatics room with several Linux computers for data analysis.Personnel is available and will teach and support users on instruments, research consultation and turn key services are also available upon request.
University of California at Berkeley QB3 High Throughput Screening CoreFacility
University of California at Berkeley QB3 High Throughput Screening Facility
Facility provides expert staff for training, services, and cell culturing space for HT automated cell seeding, liquid handling equipment, multi label plate reader and high content automated confocal imaging for any type of multi well, multi conditional mammalian cell experiments.
University of Cape Town Institute of Infectious Disease and Molecular Medicine Confocal and Light Microscope Imaging Core Facility
Confocal and Light Microscope Imaging Facility
Institute of Infectious Disease and Molecular Medicine Microscopy Unit
Light and fluorescence microscopy core facility with focus on applications in infectious disease, pathogen and human health research.
University of Pennsylvania School of Veterinary Medicine Center for Host Microbial Interactions Core Facility
Provides services in disciplines of genomics, microbiology and immunology. We engage in collaborative projects that benefit from close interactions with veterinarians and human clinicians alike.
University of Montreal BioImaging Platform Core Facility
University of Montreal Bio-Imaging Platform
Offers instruments and services to support research in microscopy.
McMaster University Centre for Advanced Light Microscopy Core Facility
Centre for Advanced Light Microscopy (CALM)
Provides access to light microscopy, photo-patterning, and light-assisted 3D printing techniques to help researchers in science, engineering and life sciences as well as our industrial partners achieve their scientific goals.
Roswell Park Cancer Institute Flow and Image Cytometry Shared Resource Core Facility
Flow and Image Cytometry Shared Resource
Roswell Park Cancer Institute Flow and Image Cytometry Shared Resource
Provides advanced flow cytometric and morphology services at cellular and subcellular levels of resolution.Services include investigator access to equipment, education and consultation, comprehensive sample processing, data acquisition and data analysis, luminex cytokine, chemokine and growth factor quantification, and core flow cytometry services for investigator and biotech sponsored clinical trials.
Single cell transcriptomic atlas of multiple organs from individual human donors. Multiple organ, single cell transcriptomic atlas of humans. Molecular reference atlas for cell types of human body. Provides molecular definition of these cell types and reveals many other aspects of human biology, including how same gene can be spliced differently in different cell types, how shared cell types in different tissues can have subtle differences in their identities, and how clones of immune system can be shared across tissues.
University of Aberdeen Iain Fraser Cytometry Centre Core Facility
Provides services and expertise in flow cytometry to government agencies, industry, educational and private individuals.
University of Aberdeen;Aberdeen;Scotland
Public research university in Aberdeen, Scotland.
Software tool for generating custom membranes for molecular simulations. Software Python script to setup Martini bilayer systems.
Software python script to generate Martini protein topology and structure files based on atomistic structure file. Used to convert (atomistic) protein structures to Martini coarse grain structures and topologies. Replaces old seq2itp, atom2cg and ElNeDyn scripts.
Software pipeline to estimate and predict genomic resolution of Hi-C libraries. Used for estimating and predicting HiC library resolution.
Software tool to manipulate reconstructions of geological and paleogeographic features through geological time. Interactively visualize vector, raster and volume data. Desktop software for interactive visualisation of plate tectonics.
Provides software tool to explore, download and apply statistical models on aggregated data collected for Fox Insight online clinical study. Study collects patient reported outcomes and genetic data from people with Parkinson's disease and their loved ones.
Aarhus University Fluorescence Activated Cell Sorting Core Facility
Facility is equipped with cell sorters, analyzers, ImageStream and full spectrum flow cytometer. Staff provides training and maintenance.
Emory University and Pediatric Winship Flow Cytometry Core Facility
Emory and Pediatric Winship Flow Cytometry Core
Core provides cytometry services for analysis and sorting of cells as well as expert consultation for experimental design and planning. Offers access to several analytical flow cytometers as well as high speed cell sorting. Training and technical expertise is available.
Pi-based Remote Acquisition Technology for Motion Capture project
Pi-based Remote Acquisition Technology for Motion Capture
Open source video recording system for acquiring video data that is scalable, flexible, and affordable.Utilizes Raspberry Pi (RPi) miniature computer and 8-megapixel Camera Board that allows for greater manipulation of recording parameters. System may be accessed on GitHub.
3D printed microdrive for electrophysiology and optophysiology. Consists of main body and head. Used for in vivo tetrode recording, optical imaging, and optogenetic manipulation in freely moving mice.Design files and build instructions for this device can be found on TetrODrive GitHub.Microdrive can be assembled in 15 min and price for all materials, including 3D printer, is lower than single commercial microdrive.
Software data management pipeline for camera synchronization and combined data directories.
Software Python package for visualizing and interacting with datasets registered to brain atlases. Used for visualization of neuroanatomical and morphological data.
Continuous Open Mouse Phenotyping of Activity and Sleep Status
Non invasive, infrared activity and sleep measurement system that uses passive infrared sensors and Arduino microprocessor. Publication provides protocol for assembling COMPASS as well as provides support protocols and python scripts for data analysis, best practices for optimum results, troubleshooting, and alternative protocols for different use scenarios.
Automated surgical instrument for brain tissue aspiration.Instrument for microendoscope implantation. Utilizes robotic control of needle connected to vacuum pump to aspirate brain tissue. System consists of robotic surgical instrument built around commercially available stereotaxic instrument and open source MATLAB-based GUI for control.
Open source Open access Reaction Time Test
Software Pyton scripts to run computerised task of Reaction Time. Scripts, together with their instructions and scoresheets.Used for assessment of RTs that is freely available, compatible with all operating systems, without license and activation costs, and based on open source software platform.
Software tool as generalist algorithm for cell and nucleus segmentation.
Open source software package to support rt-fMRI via data in formats generated by Siemens, Philips, and GE. Used to support real time functional magnetic resonance imaging.
Open source, MATLAB based software for forced swim test and tail suspension test video analysis.
Python based operant box system in 5-choice design
Open source operant box system optimized for use with tethered animals. System includes hardware and software. Control electronics are build on pyControl, controlling custom PCB integrating 5 infra-red break-beam sensors and 5 stimulus LEDs, single nose-poke for reward receptacle, stepper motor for control of custom peristaltic pump for reward delivery, audio board for tone generation through attached speaker, house light and fan, LED driver for optogenetic stimulation, and bidirectional communication with external devices via TTL pulses.
Interactive software for visualizing and uncovering function of circuits created from large scale fruit fly brain data. Interactive computing platform for studying function of executable circuits constructed from fruit fly brain data.
Software tool for data extraction and computation of spatial accuracy and precision of head mounted display based eye trackers. Allows for significant customization without altering source code but changes to the code allow for further alteration.
Software semi automated brain atlas based analysis pipeline for c-Fos immunohistochemical data. Used to analyze c-Fos in multiple brain regions simultaneously.
Data Analysis with Bootstrapped ESTimation
Software package for data analysis using bootstrap coupled estimation. Library combining Python, R, and MATLAB for estimation statistics.
Software R package for permutation test in linear model with nuisances variables.Used for permutation testing in regression, ANOVA, and comparison of signals.
Software MATLAB based toolbox for automated quantitative analysis of ultrasonic vocalizations. Utilizes image processing libraries to detect USVs and computational vision and machine learning algorithms to classify detected USVs. Used for analysis of ultrasonic vocalizations from mice using computer vision and machine learning.
Raspberry Pi based auditory stimulus generator
Raspberry Pi based auditory stimulus generator project
Stimulation system for auditory EEG experiments using Raspberry Pi3 B+ board, HiFiBerry audio card to enhance sound quality and trigger tone latency, and custom Python library to generate auditory stimuli.
Florida research open source synchronization tool
Open source system built around Arduino based microcontroller for analog and digital input and synchronization combined with custom printed circuit board. Hardware and Arduino-based firmware used to synchronize experimental and electrophysiological data.
Open source device consists of three LED matrices that can be independently controlled via open source Arduino Uno microcontroller. Matrices of LEDs are mounted above nose pokes to examine perceptual decision making in rats. Highly modifiable LED matrices for visual stimulus presentation in behavioral studies.Designs for printing these accessory devices are available in GitHub account for the project.
Software MARS based Python pipeline used for detection, pose estimation and behavior classification in experiments of any format. Repository contains all the code you'll need to train your own version of MARS.
Software Python pipeline for automated detection, pose estimation, and behavior classification in socially interacting mice.Used for pose estimation and behavior quantification in pairs of freely behaving mice.
Behavior Ensemble and Neural Trajectory Observatory
Software Matlab based tool to visualize and analyze multimodal datasets.
3D printed device for stereotaxic viral delivery into brains of neonatal mice.Used for stable and precise stereotaxic surgery in neonatal mice.
Statistical software platform for automated scoring of pain in mice.Software R package takes paw trajectory data in response to stimulus and provides automated scoring of pain.
Software tool as novel tracking algorithm that combines deep learning and background subtraction.
MRI compatible microdrive that can precisely position electrodes without causing significant imaging artifacts.
Software Python toolbox that makes fiber photometry data analysis intuitive and light on programming.Used to measure neural activity of freely behaving animals.
Software package for MATLAB that makes motion correction, segmentation, signal extraction and dimension reduction, analysis, and visualization of calcium imaging data easy to implement. Open source toolbox for analysis of calcium imaging data.
Software tool to extract relevant features from images and use time series of these features to classify whether given behavior is present in each frame of video recording.machine learning pipeline for supervised behavior classification from raw pixels. Performs action recognition ,automated behavior classification, over frames. Used for automated behavior classification to detect and track behavior over time.
Open source software for customized and reproducible microscope control. Software Python package that enables control of micro-manager as well as development of customized experiments integrated with real-time image processing.
University of Massachusetts Amherst Biophysical Characterization Core Facility
UMass Amherst Biophysical Characterization Core Facility
University of Massachusetts Amherst UMass Amherst Biophysical Characterization Core Facility
Provides expertise and access to instruments for study of structures and interactions of biological macromolecules such as proteins, nucleic acids, lipids, and complexes. Facility supports both discovery based research and assay development for translational applications. Offers to use equipment independently or with the help of faculty who have expertise in each method.
Open source framework for single cell characterization and visualization.Graphical user interface, standardized processing module and data structure for exploring and classifying single cells acquired using extracellular electrodes.
Software tool enables closed loop behavioral experiments using deep learning based markerless, real time posture detection.Closed loop behavioral experiment toolkit using pose estimation of body parts.
Software tool as single neural network model that learns how to segment spectrograms of birdsong into annotated syllables.
Open source animal tracking software tool. Used to visually track movement of multiple animals at once.
Software tool as multi subject keypoint detection library for real time pose estimation.Used to track behavior of monkeys in natural environments, without disrupting their typical pattern of behavior. Deep learning software system for body, face, hands, and foot estimation in monkeys.
Timed pressure control hardware and software for delivery of air mediated distensions in animal models
Timed pressure control hardware and software for delivery of air mediated distensions in animal models project
System uses Arduino microcontroller to control relay module that operates solenoid valve which all sit in 3D printed housing. Solenoid works in conjunction with flowmeter regulator to allow for controlled flow of pressurized air into target. Timing of distensions is controlled via either custom Python based UI, or by triggered TTL pulse.Timed pressure control hardware and software used for delivery of air mediated distensions in animal models.
Software pipeline for video analysis. Deep learning Swiss knife for behavioral data analysis.Performs segmentation, identification, pose-estimation and classification of complex behaviour. Used for analysis of behavior of multiple animals in complex environments.
Closed Loop Automated Reaching Apparatus
Closed Loop Automated Reaching Apparatus Project
Closed loop automated reaching apparatus for interrogating complex motor behaviors.Mechanical components include behavior box, series of cameras, and food pellet dispenser. Single workstation computer manages cameras, communicates with microcontroller, and analyzes mouse behavior in real time using modules extracted from DeepLabCut. Integrates fully automated, markerless kinematic tracking of multiple features to classify animal behavior and delivers neural stimulation based on behavioral outcomes. CLARA is compatible with advanced neurophysiological tools, enabling testing of neurostimulation devices and identification of novel neurological biomarkers.System fully automates trial initiation and pellet delivery and is capable of accurately delivering stimulation in response to trial outcome with short latency.
Vanderbilt University Creative Data Solutions Core Facility
Shared Resource that offers bioinformatics and informatics services for basic research and clinical projects.
Software R/Shiny application for interactive creation of Circos plot. Used for creation of Circos plot interactively.
PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors.
Knowledge based Identification of Pathway Enzymes
Software tool as automatic approach for identification of players in biosynthesis pathway. Used for automatic annotation of flavonoid biosynthesis steps in new transcriptome of genome sequence assembly. Various enzymes of entire metabolic networks can be identified if sufficient knowledge about functionally relevant amino acids is available.Combines comprehensive sequence similarity analyses with inspection of functionally relevant amino acid residues and domains in subjected peptide sequences.
Markov Affinity based Graph Imputation of Cells
Software tool for imputing missing values restoring structure of large biological datasets.Method that shares information across similar cells, via data diffusion, to denoise cell count matrix and fill in missing transcripts.
University of Pennsylvania Perelman School of Medicine Animal Biosafety Level 3 Core Facility
University of Pennsylvania Perelman School of Medicine Animal Biosafety Level 3 Core Facility (ABSL-3)
Facility offers procedural and animal housing to perform in vivo research with biosafety level 3 pathogens, such as SARS-CoV-2. Services include consultation, specialized training, and basic/advanced technical services. Provides equipment to longitudinally monitor mice over course of infection. Animal housing space includes three ABSL-3 separate housing cubicles with Allentown BCU-2 animal cages. Animals will be housed under pathogen free conditions at AAALAC accredited University Laboratory Animal Resources facilities within Vernon and Shirley Hill Pavilion using animal protocols approved by Institutional Animal Care and Use Committee.
University of Pennsylvania Perelman School of Medicine Cell and Developmental Biology Microscopy Core Facility
Cell & Developmental Biology Microscopy Core
University of Pennsylvania Perelman School of Medicine CDB Microscopy Core
Core provides personalized assistance on all aspects of imaging, from tips on sample preparation to training on one of our microscopes to assistance with image data analysis. Facility houses confocal microscopes, Bruker Vutara 352 super resolution system, Zeiss Z.1 Lightsheet system, three widefield light microscopes, and several computers dedicated to image processing and analysis. Offers scanning electron microscope sample preparation and imaging.
University of Pennsylvania Perelman School of Medicine Bioinformatics Core Facility
University of Pennsylvania Perelman School of Medicine Bioinformatics Core
Core provides bioinformatics services that include data analysis and consultation and building of efficient pipelines that handle various biomedical data including Next-Generation Sequencing (NGS) data.
University of Pennsylvania Perelman School of Medicine Electron Microscopy Resource Lab Core Facility
University of Pennsylvania Perelman School of Medicine Electron Microscopy Resource Lab
Training and service facility dedicated to providing both conventional transmission electron microscopy of cells and tissues and state of the art cryo-electron microscopy and cryo-electron tomography for structural investigation of macromolecules and cells.
University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory Core Facility
Cytomics and Cell Sorting Resource Laboratory
University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory
Flow cytometry shared resource laboratory at the University of Pennsylvania. Facility has instruments, which include analyzers, cell sorters, small particle detectors, dual fluorescence cell counter/viability instrument, tissue dissociator for cell preparation. Provides on-site and off-site support to instrument users, including analyzer and cell sorter training. Core's Research and Development team collaborates/consults with principal investigators in developing high-dimensional panels, as well as staining, acquisition, and analysis.
University of Pennsylvania Perelman School of Medicine Cell and Animal Radiation Core Facility
University of Pennsylvania Perelman School of Medicine Cell and Animal Radiation Core
Core provides services to users for performing precision, image guided radiotherapy with both Photons and Protons (including FLASH proton radiotherapy) on cells, rodents and larger animals. Physicists will provide expert dosimetry and treatment planning capabilities. Instrumentation consists of two image guided SARRP 200 Small Animal Radiation Research Platforms (Xstrahl) capable of irradiating rodent tissues from 1 mm-20 mm in diameter; research proton beamline (IBA, Roberts Proton Center); one X-RAD 320ix cabinet x-ray irradiator (Precision X-Ray); and two Cs gamma-ray irradiators (Shepherd Mark I), suitable for whole body radiation of rodents.
University of Pennsylvania Perelman School of Medicine CRISPR Cas9 Mouse Targeting Core Facility
University of Pennsylvania Perelman School of Medicine CRISPR Cas9 Mouse Targeting Core
Core facilitates use of CRISPR/Cas9 genome editing technology to generate novel mouse genetic tools.
University of Pennsylvania Perelman School of Medicine High Throughput Screening Core Facility
University of Pennsylvania Perelman School of Medicine High-Throughput Screening Core (HTSC)
Core provides distribution of lentivirus based shRNA and cDNA plasmid DNA clones; technical expertise in developing biological assays (i.e. biochemical-, cell-, and high-content) in miniaturized, multiwell microtiter plates that are laboratory automation compatible; high-throughput chemical and functional genomic screening, including data analysis and interpretation. Our goal is to use cutting biological models to discover genes and small molecules that enable scientists to further study functions of poorly understood proteins, signaling pathways, and cells in complex biological process relevant to human physiology and disease.
University of Pennsylvania Perelman School of Medicine Human Immunology Core Facility
University of Pennsylvania Perelman School of Medicine Human Immunology Core (HIC)
Core provides wet bench expertise and infrastructure support for early phase�clinical trials and other investigations. Offers purified cell subsets from healthy human apheresis donors. �HIC staff are qualified to�perform blood (PBMC)�and tissue processing for viable cryopreservation following validated�standard operating procedures. Offers�range of immunological assays including digital ELISA, ELISA, ELISPOT, Luminex, flow cytometry and immune repertoire profiling (NGS of BCR and TCR rearrangements in bulk and single cell formats).Offers investigators expertise and guidance in clinical trial sample processing, regulatory compliance, immunology assay design and validation, data analysis and grant writing support.
University of Pennsylvania Perelman School of Medicine Metabolomics Core Facility
University of Pennsylvania Perelman School of Medicine Metabolomics Core
Core is overseen by Cardiovascular Institute and is partnership with the Abramson Cancer Center and the Institute for Diabetes, Obesity and Metabolism at Penn. Provides expertise in targeted and untargeted metabolomics of biological samples using liquid chromatography/mass spectrometry. Performs assays and assists in interpretation of results.
University of Pennsylvania Perelman School of Medicine Next Generation Sequencing Core Facility
University of Pennsylvania Perelman School of Medicine Next Generation Sequencing Core (NGSC)
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 10,2025. Core provides services related to single cell and bulk whole genome, RNA-Seq, ATAC-Seq, BIS-Seq, Exome-Seq, ChIP-Seq, CLIP-Seq, etc.Provides Illumina NovaSeq 6000 in addition to NextSeq and MiSeq sequencers - which all feature self-service as well as full-service operation. Offers experience with difficult, low input samples as well as sequencing and analyzing novel library types. Small Oxford Nanopore sequencer allows for full-length RNA or cDNA sequencing as well as very long read (100KB) sequencing from genomes. Offers experimental design services prior to starting your experiment.
University of Pennsylvania Perelman School of Medicine Penn Genomic Analysis DNA Sequencing Core Facility
Penn Genomic Analysis Core: DNA Sequencing Facility
University of Pennsylvania Perelman School of Medicine Penn Genomic Analysis Core: DNA Sequencing Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 8th,2024. Facility offers sequencing services on three platforms, gold standard Sanger sequencing on ABI capillary sequencers, next generation sequencing (NGS) on Ion Torrent PGM and S5 and, Illumina MiSeq along with experimental design and data analysis.NGS service includes library preparation for multiple applications including targeted sequencing, RNA-Seq and Exome-Seq. Capillary sequencers also enable microsatellite genotyping and fragment analysis for VNTR, SNaPshot and Human Cell Line Authentication. Molecular biological services include PCR, cloning, subcloning, mutagenesis, construct preparation and, plasmid DNA preps at different scales.
University of Pennsylvania Perelman School of Medicine Penn Gnotobiotic Mouse Core Facility
University of Pennsylvania Perelman School of Medicine Penn Gnotobiotic Mouse Facility
Our core, which is part of the PennCHOP Microbiome Program, provides access for researchers to small experimental isolators for variety of in vivo studies using germ free mice. Core personnel provide technical support for germ-free experiments. New addition to core is state-of-the-art Isocage system.
University of Pennsylvania Perelman School of Medicine Small Animal Imaging Core Facility
University of Pennsylvania Perelman School of Medicine Small Animal Imaging Facility (SAIF)
Core provides comprehensive suite of imaging modalities including magnetic resonance imaging (MRI), spectroscopy (MRS), optical imaging (including bioluminescence, fluorescence, and near-infrared imaging), computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), and ultrasound (US). In addition, dedicated housing is available for mice and rats undergoing longitudinal imaging studies. Ancillary facilities and resources of SAIF are devoted to radiochemistry and image analysis.
University of Pennsylvania Perelman School of Medicine Neurobehavior Testing Core Facility
University of Pennsylvania Perelman School of Medicine Neurobehavior Testing Core (NTC)
Core provides equipment and services to investigate behavior phenotypes of models related to neurological and other disorders. Core is utilized by scientists across disciplines that are interested in behavioral consequences of unique physiological disruptions (e.g., metabolic, drugs etc.). Provides assessment of many domains of behavior including sensory, motor, social, communication, affect related behaviors and learning and memory. NTC was established in 2012 through generous startup funds from the Penn School of Medicine, the Institute for Translational Medicine and Therapeutics (ITMAT), Center for Sleep and Circadian Neurobiology (CSCN) and Penn Medicine Neuroscience Center (PMNC).
University of Pennsylvania Perelman School of Medicine Ovarian Cancer Research Center Tumor BioTrust Collection Core Facility
University of Pennsylvania Perelman School of Medicine OCRC Tumor BioTrust Collection
Provides specimens including gynecologic cancer specimens such as fresh and frozen tissues, plasma, serum, peripheral blood mononuclear cells, blood, formalin fixed paraffin embedded (FFPE) samples, and Tissue Microarrays (TMAs). All samples collected have clinical annotation including demographic patient profiles, pathological and clinical notations, treatment history, and detail disease information, etc. We are building and maintaining centralized research database according to HIPPA specifications and Penn IRB standards.
University of Pennsylvania Perelman School of Medicine Transgenic and Chimeric Mouse Core Facility
University of Pennsylvania Perelman School of Medicine Transgenic and Chimeric Mouse Facility
Facility provides centralized service to efficiently produce genetically altered mice for basic research.� They include transgenic, chimeric and genome edited mice carrying transgenes or gene knockout and Knockin of specific interest.�Core also provides embryo and sperm cryopreservation as well as in vitro fertilization and re-derivation of live and cryopreserved lines, along with long-term storage of cryopreserved samples.
University of Pennsylvania Perelman School of Medicine Penn Genomic Analysis Molecular Profiling Core Facility
Penn Genomic Analysis Core: Molecular Profiling Facility
University of Pennsylvania Perelman School of Medicine Penn Genomic Analysis Core: Molecular Profiling Core
Facility provides full service whole genome and targeted molecular profiling of DNA and RNA on multiple platforms. Core supports quantitative RNA profiling (gene expression) on Affymetrix GeneChips and high-throughput Gene Titan instruments, Fluidigm BioMark HD and, ABI QS 12K real-time PCR machine. DNA profiling (genotyping) is offered on Affymetrix SNP GeneChip and high-throughput Gene Titan instruments, Fluidigm BioMark HD and, ABI QS 12K. Agilent aCGH platform provides genome-wide chromosomal analysis.Users benefit from consultation and training available throughout their projects, including during experimental design and budget development, sample accrual, data management and analyses and, manuscript preparation.
University of Pennsylvania Perelman School of Medicine Chemical and Nanoparticle Synthesis Core Facility
Chemical and Nanoparticle Synthesis Core (CNSC)
University of Pennsylvania Perelman School of Medicine Chemical and Nanoparticle Synthesis Core (CNSC)
Provides expertise in medicinal chemistry, metal chelate chemistry, polymer synthesis, nanoparticle production and surface functionalization, and site-specific antibody labeling. Our chemists provide custom, problem specific support for researchers in medical, chemical, and materials science fields. Specific services include consultation and assistance with the design of chemical/medicinal compounds, in house synthesis of chemical/medicinal compounds, custom nanoparticle design and synthesis, custom nanoparticle surface functionalization, polymer and dendrimer synthesis, and site specific antibody labeling.
University of Pennsylvania Perelman School of Medicine Cell Center Services Core Facility
University of Pennsylvania Perelman School of Medicine Cell Center Services Facility
Facility provides basic cell culture training and services in various cell culture and related procedures e.g. Mycoplasma and Endotoxin testing. Services include cell culture at various scales, expansion of primary cells, seed cell cultures from on site cell bank, cell storage; large scale growth of hybridoma and other cell lines followed by antibody purification by protein G column or recombinant protein production; EBV induced transformation of lymphocytes.Offers hybridoma generation by cell fusion and screening and, transfection of mammalian cells. Facility prepares specialized cell culture media, Drosophila media and, various tissue culture and molecular biological reagents.
University of Pennsylvania Perelman School of Medicine Acute Care Biobanking Core Facility
University of Pennsylvania Perelman School of Medicine Acute Care Biobanking Core
Core encourages and facilitates microbiome focused research in pathogenesis, diagnosis and treatment of patients with critical illness. Core assists in research by providing de-identified samples with linked clinical metadata to support research in this area, collect specimens as needed in support of microbiome research, and offer support for development of such research in the critical care setting.
University of Pennsylvania Perelman School of Medicine Biostatistics Analysis Center Core Facility
University of Pennsylvania Perelman School of Medicine Biostatistics Analysis Center
Provides wide range of biostatistical and epidemiological consulting services.
University of Pennsylvania Perelman School of Medicine Brain Science Service Center Core Facility
University of Pennsylvania Perelman School of Medicine Brain Science Service Center
Provides infrastructure support for research on human cognition, perception, affect, disordered cognition, and extension to preclinical models. By consolidating methodological expertise in these domain areas as services, center seeks to facilitate cutting edge research using largely shared set of methods and tools for elucidating brain behavior relationships in health and disease.
University of Pennsylvania Perelman School of Medicine Center for Advanced Computer Tomography Imaging Services Core Facility
Center for Advanced Computer Tomography Imaging Services (CACTIS)
University of Pennsylvania Perelman School of Medicine Center for Advanced Computer Tomography Imaging Services (CACTIS)
CACTIS mission is to oversee proposed research protocols that involve human, animal, phantom or specimen studies in an effort to achieve two goals, to ensure that all research performed on CT scanners comply with CACTIS and University policy, and Federal Regulations, and to determine if CACTIS can maintain the resources required to carry out each research protocol, including personnel, software, hardware and scan time. Additionally, CACTIS oversees the day-to-day operations of all CT procedures associated with research protocols, provides information regarding the use of CT facilities to the research community at the University of Pennsylvania, provides CACTIS users with all of the policies of the institution governing research, and ensures that CACTIS is in compliance with these policies. The service center strives to support the Perelman School of Medicine�s research endeavors by providing CT research services for a fee designed only to cover actual costs.
University of Pennsylvania Perelman School of Medicine Center for Advanced Metabolic Imaging in Precision Medicine Core Facility
University of Pennsylvania Perelman School of Medicine Center for Advanced Metabolic Imaging in Precision Medicine (CAMIPM)
Core dedicated to development and application of innovative, novel magnetic resonance and optical imaging techniques. Provides research and computing resources for projects with focus on developing instrumentation, methodologies, and data analysis techniques for quantitative assessment of functional, structural, and metabolic parameters in humans with use of multinuclear magnetic resonance, novel spectral, perfusion, functional, and optical imaging techniques.
University of Pennsylvania Perelman School of Medicine Center for Biomedical Image Computing and Analytics Core Facility
Center for Biomedical Image Computing & Analytics (CBICA)
University of Pennsylvania Perelman School of Medicine Center for Biomedical Image Computing & Analytics (CBICA)
Offers development and application of advanced computational and analytical techniques that quantify morphology and function from biomedical images, as well as on relating imaging phenotypes to genetic and molecular characterizations, and on integrating this information into diagnostic and predictive tools in era of personalized medicine. Computational methods can contribute significantly to automated, reproducible and quantitative interpretations of biomedical images. Translates advanced computational and analytical imaging methods to clinic, by providing forum in which interactions between researchers and clinicians facilitate bidirectional flow of ideas, algorithms and data between laboratory and clinic.
University of Pennsylvania Center for Advanced Magnetic Resonance Imaging and Spectroscopy Core Facility
Center for Advanced Magnetic Resonance Imaging and Spectroscopy
Center for Advanced Magnetic Resonance Imaging and Spectroscopy Core Facility
Center for Advanced MRI and Spectroscopy (CAMRIS)
University of Pennsylvania Perelman School of Medicine Center for Advanced MRI and Spectrometry (CAMRIS)
Center for Advanced Magnetic Resonance Imaging and Spectroscopy (CAMRIS) is a Radiology research core at the University of Pennsylvania’s Perelman School of Medicine providing oversight in the responsible use and application of Magnetic Resonance (MR) in research at Penn. CAMRIS oversees eight state-of-the-art whole-body MR scanners and provides scanning services by experienced technologists to a diverse community of investigators conducting innovative human and animal research.
University of Pennsylvania Perelman School of Medicine Cell Center Stockroom Core Facility
Core is division of Genetics Core Facilities, University service center to provide consultation, training, and services in areas of cell culture and hybridomas. Stockroom serves University of Pennsylvania investigators and affiliate institutions by coordinating relations with various suppliers of molecular biological research materials. This involves not only bulk purchasing of these products, but negotiation of discounts and convenient delivery arrangements. Special ordering of non regularly stocked products is available from 28 bioreagent vendors with discounted pricing and overnight delivery.
University of Pennsylvania Perelman School of Medicine Center for Preventive Ophthalmology and Biostatistics Biostatistical Consulting Core Facility
Center for Preventive Ophthalmology and Biostatistics (CPOB) Biostatistical Consulting
University of Pennsylvania Perelman School of Medicine Center for Preventive Ophthalmology and Biostatistics (CPOB) Biostatistical Consulting
Service supports consultation and collaboration in areas of biostatistics and epidemiology to Penn vision scientists. Biostatisticians and data management experts provide advice on study design, and offer services in sample size determinations, data management, data analysis, data interpretation, and data presentation. They are active participants in the development and writing of grant applications and manuscripts.Consulting personnel are CPOB members. In addition to their methodological and technical expertise, consultants are knowledgeable about ocular conditions under study in Penn vision community, about commonly used measures that are unique to vision research (visual acuity, refractive error, visual field indices, etc) and specialized statistical analysis techniques required for many experimental designs used in vision research (correlated data techniques to handle appropriately data from two eyes of same subject). Majority of projects are patient oriented researchers,however, CPOB Consulting Service also works on data analysis with bench laboratory scientists.
University of Pennsylvania Perelman School of Medicine Center for BioMedical Informatics Core Facility
Center for BioMedical Informatics Core (BMIC)
University of Pennsylvania Perelman School of Medicine Center for BioMedical Informatics Core (BMIC)
Supports next generation infrastructure for clinical data storage and management, next generation analytics, next generation infrastructure for support of clinical research including new clinical trials management system and software, next generation infrastructure for centralizing and integrating external sources of data such as genomics data. Enables future clinical and translational research through biomedical informatics education and training targeted at graduate students, postdoctoral students, residents, fellows, as well as faculty across the biomedical research spectrum.
University of Pennsylvania Perelman School of Medicine Center for Human Phenomic Science (CHPS)
Center for Human Phenomic Science (CHPS)
CHPS is comprised of several Clinical Research Cores designed to facilitate research process. Provides resources, environment, operations, and training to support and promote high quality clinical and translational research by qualified investigators.
University of Pennsylvania Perelman School of Medicine Center for AIDS Research Virus and Reservoirs Core Facility
University of Pennsylvania Perelman School of Medicine CFAR Virus & Reservoirs Core
Facility provides comprehensive viral and molecular support in area of basic, translational and clinical HIV research, consultation, training, and mentoring.Is available to develop customized viral and molecular support services as needed. Offers deep sequencing support and single genome amplification services.
University of Pennsylvania Perelman School of Medicine Clinical Research Collaboration Unit Core Facility
Clinical Research Collaboration Unit (CRCU)
University of Pennsylvania Perelman School of Medicine Clinical Research Collaboration Unit (CRCU) Core Facility
Provides comprehensive services essential to the conduct of clinical research projects, including Phase I-IV, multi-center, randomized, clinical trials, registry, and cohort studies. Offers expert staff who maintain a strong focus on data integrity and quality and offers support in optimizing process tracking and management to enhance operational efficiency. Core specializes in the following: Study design and development; Site management and training; Data collection, processing, and quality control; Regulatory requirements and reporting; Database development, storage, and security; System integration (e.g., EPIC data); 21CFR Part 11 Compliance; Proposal development and administration; REDCap development; Honest Broker services.
University of Pennsylvania Perelman School of Medicine Radioimmunoassay and Biomarkers Core Facility
Radioimmunoassay and Biomarkers Core Facility
Core offers immunoassay, metabolite, and HPLC services to basic, translational, and clinical investigators performing diabetes and related metabolic disease research.RIA /Biomarkers Core is located on the 12th floor of Smilow Center for Translational Research.Approximately 100 different diabetes, obesity and metabolism-related biomarkers from multiple species including human can be assayed using radioimmunoassay (RIA), enzyme-linked immunosorbent assay (ELISA, both absorbance and fluorometric), multiplex ELISA on the Luminex platform, and enzymatic and HPLC methods for an expanding variety of diabetes and metabolism related metabolites, hormones, catecholamines and cytokines derived from blood, urine, and tissue samples.
University of Pennsylvania Perelman School of Medicine CUBIC (HPC Cluster)
Linux based High Performance Computing resource available to faculty conducting research related to medical imaging and informatics. There are over 150 compute nodes with more than 5000 Intel Xeon CPUs and 58TB of RAM, over 100 GPUs, and 600TB of storage in the cluster. Facility management structure is designed to encourage data sharing and use of common software on this powerful resource, particularly in development of new software and application of imaging to new domains.
University of Pennsylvania Perelman School of Medicine Cooperative Human Tissue Network Core Facility
University of Pennsylvania Perelman School of Medicine Cooperative Human Tissue Network (CHTN)
Human tissue procurement service within Department of Pathology at HUP, that assists investigators with collection, processing and preservation of research samples. Our staff will personalize sample acquisition and processing to meet project requirements. Samples (malignant, normal, diseased, etc.) and biofluids can be preserved in a range of methods (fresh, frozen, fixed, etc.).
University of Pennsylvania Perelman School of Medicine Community Engagement and Research Core Facility
University of Pennsylvania Perelman School of Medicine Community Engagement & Research (CEAR)
Core aims to facilitate and build capacity for community based research and community engagement, while enhancing translation of research and technological developments to key public health and community stakeholders. Offers consultation on community engagement, training in participatory research methods, and assistance with development, implementation, and evaluation of community translation activities. Core is part of the Penn Institute for Translational Medicine and Therapeutics (ITMAT).
University of Pennsylvania Perelman School of Medicine IBI Clinical Research Informatics Core Facility
University of Pennsylvania Perelman School of Medicine IBI Clinical Research Informatics Core
Core assists faculty, staff, and students with conducting research projects using electronic health record data.Facilitates access to clinical data and performs data analysis using artificial intelligence, ontologies, natural language processing, machine learning, and visual analytics. Provides innovative research services by applying data science to clinical data in order to learn actionable healthcare knowledge and develop impactful solutions for improving patient care. Services include facilitating access to Penn Medicine clinical data resources, performing data analysis using diverse computational methods, and providing tools for exploratory data analysis/visualize with priority access to the IBI Idea Factory for immersive display of data and research results. �
University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility
University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center
CyTOF�enables multi-parametric high-dimensional single�cell analysis�of more than 40 markers per cell, with�minimal background and compensation�issues.�Core�offers variety of�CyTOF-related services including�reagent distribution, consultation,�antibody conjugation, and data acquisition.�
University of Pennsylvania Perelman School of Medicine Pancreatic Islet Cell Biology Core Facility
University of Pennsylvania Perelman School of Medicine Pancreatic Islet Cell Biology Core
Provides support including experimental design, islet isolation, and performance of and/or training in range of assays for physiological, metabolic, and morphometric assessment of pancreatic islets as wells as many other tissues and cell types. Offers islet isolation and culture, free intracellular calcium ion measurements, quantitative oxygen consumption of pancreatic islets, electrode based closed cell respirometry, and access to Agilent�s� Seahorse Extracellular Flux Analyzer XFe96.
University of Pennsylvania Perelman School of Medicine Human Intervention Core Facility
University of Pennsylvania Perelman School of Medicine Human Intervention Core
Offers services to assist with design and implementation of microbiome studies.Assist with longitudinal studies as well as pilot studies.� Pilot studies can be rapidly implemented with human intervention core staff, project managers and research coordinators.
University of Pennsylvania Perelman School of Medicine ITMAT Study Design and Biostatistics Core Facility
ITMAT Study Design and Biostatistics Core (SDAB)
University of Pennsylvania Perelman School of Medicine ITMAT Study Design & Biostatistics Core (SDAB)
Core works with existing resources to provide targeted study design and biostatistics support to ITMAT/CTSA investigators.Services include protocol review, study design, proposal development, and performance of simple to potentially substantial complex analyses. SDAB integrates support available with HUP and CHOP Center for Human Phenomic Science (CHPSs), expertise and resources of faculty in Center for Clinical Epidemiology and Biostatistics / Department of Biostatistics and Epidemiology (CCEB/DBE), Biostatistics Analysis Center (BAC), and Biostatistics and Data Management Core (BDMC) at CHOP.
University of Pennsylvania Perelman School of Medicine Johnson Foundation Biophysical and Structural Biology Core Facility
Johnson Foundation Biophysical and Structural Biology Core (JFBSB)
University of Pennsylvania Perelman School of Medicine Johnson Foundation Biophysical and Structural Biology Core (JFBSB)
Provides unique equipment and expertise to facilitate modern biophysical characterization and structural analysis of proteins and other biomolecules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility
University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank
BioBank supports researchers by providing centralized access to large number of annotated blood and tissue samples.
University of Pennsylvania Perelman School of Medicine Host-Microbial Analytic and Repository Core Facility
Host Microbial Analytic and Repository Core (H-MARC)
University of Pennsylvania Perelman School of Medicine Host-Microbial Analytic and Repository Core (H-MARC)
Core within Division of Gastroenterology provides services which�represents intersection between host and their microbes in both�preclinical and clinical human subject research.Offers human biospecimen repository with associated clinical metadata, instrumentation/access to critical analytic services to characterize expression (i.e. genomics, transcriptomics, metabolomics, microbial culture, etc.) in both microbes and�their mammalian hosts, as well as expertise to extend pre-clinical in vitro and animal model research into human clinical domain. �
University of Pennsylvania Perelman School of Medicine Microbial Culture and Metabolomics Core Facility
University of Pennsylvania Perelman School of Medicine Microbial Culture & Metabolomics Core
Provides equipment for aerobic and anaerobic culture of microbial species in both batch and continuous systems, as well as targeted metabolomic services of amino, bile, and short chain fatty acids. Offers training and usage for culture equipment; consultation regarding experimental design, and; anaerobic culture services. Examples of culture studies include isolation of microbial taxa from mammalian samples; interrogation of the physiology of microbial strains under different conditions (e.g., anaerobic/microaerobic/aerobic, differing nutrient limitations) using isolated strains or strains obtained from culture collections (another service offered by the core); co-culturing of defined microbial consortia to investigate microbe-microbe interactions, and; preparation of microbial products (live bacteria, heat-killed bacteria, bacterial supernatants) from single or defined-mixed microbial cultures for use in mammalian cell culture and/or animal model systems.
University of Pennsylvania Perelman School of Medicine Mixed Methods Research Lab Core Facility
University of Pennsylvania Perelman School of Medicine Mixed Methods Research Lab (MMRL)
Fosters the use of qualitative and mixed methods research methodologies with focus on integrating key stakeholder perspectives and goals into research designs. Collaborates with investigators to address timely, pressing questions across diverse disciplines and works with investigators to provide conceptual as well as technical support for broad research programs, including clinical, community based, and implementation science research questions.
University of Pennsylvania Perelman School of Medicine Mouse Cardiovascular Phenotyping Core Facility
University of Pennsylvania Perelman School of Medicine Mouse Cardiovascular Phenotyping Core
Core provides services to assess cardiovascular function in mouse models and to provide validated surgical models of heart and vascular disease in mice to assess genetic or therapeutic interventions. Works with investigators to design and implement study along with any associated grant applications, animal protocol submissions and manuscript preparation. While central focus of facility is cardiovascular research, techniques employed are often useful to investigators in other fields. Helps to assess your needs and provide necessary technical training and scientific assistance in animal protocol preparation. Core runs on a fee for service model.�Accordingly, investigators will be responsible for costs incurred for their projects and prior animal protocol approval by Penn IACUC., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University of Pennsylvania Perelman School of Medicine Molecular Pathology and Imaging Core (MPIC)
Molecular Pathology and Imaging Core (MPIC)
Provides histological services, equipment, and technical expertise for processing and analyses of digestive, pancreatic, and liver tissues as well as three dimensional tissue culture models.�Part of the Center for Molecular Studies in Digestive and Liver Diseases
University of Pennsylvania Perelman School of Medicine Neurons R Us Core Facility
University of Pennsylvania Perelman School of Medicine Neurons R Us (NRU)
Core supplies suspensions of neuronal cells prepared from rodent brain for various downstream applications, including primary cell culture. Supplies rat or mouse cells isolated from cortex or hippocampus either in suspension or plates. Custom dissection services are available for other brain regions or for user supplied genetically modified mice.
University of Pennsylvania Perelman School of Medicine Muscle Physiology Assessment Core Facility
University of Pennsylvania Perelman School of Medicine Muscle Physiology Assessment Core
Core provides investigators with customizable tools and methodolgies to assess in vivo exercise performance, metabolism and respiratory function, as well as in vivo and ex vivo muscle contractility. Provides guidance and training to investigators who want to learn how to collect and process muscle samples for specific uses.
University of Pennsylvania Perelman School of Medicine Nuclear Medicine Physics and Instrumentation Group Core Facility
Nuclear Medicine Physics & Instrumentation Group
University of Pennsylvania Perelman School of Medicine Nuclear Medicine Physics & Instrumentation Group
Core focuses on imaging in nuclear medicine, and engages in collaboration with clinicians and research investigators to optimize new instruments for applications in both clinical and pre clinical (animal) imaging scenarios. Offers equipment to build, test and characterize detectors for PET imaging, operates cluster of high powered Linux computers, which reconstruct, process, and analyze imaging data. Focuses on technology, which increases signal to noise of reconstructed images for whole body studies. Conducts research on SPECT imaging with emphasis on applications to small animal and brain imaging, oversees operation of cyclotron and imaging probe synthesis facilities.
University of Pennsylvania Perelman School of Medicine Research Instrumentation Shop Core Facility
University of Pennsylvania Perelman School of Medicine Research Instrumentation Shop (RIS)
Shared resource machine shop serving various University of Pennsylvania Schools and Departments. Assists researchers to design and construct both laboratory and clinical instruments.
University of Pennsylvania Perelman School of Medicine MINS Machine Shop Core Facility
University of Pennsylvania Perelman School of Medicine MINS Machine Shop
Designes and buildes novel instruments and apparatus for research to user specifications. Works with users to develop initial project drawing, and will explore alternate designs to insure desired functionality. Fabricates user devices to high tolerance, using machine tools and materials, and can repair laboratory devices even if devices were constructed elsewhere.
University of Pennsylvania Perelman School of Medicine Induced Pluripotent Stem Cell Core Facility
University of Pennsylvania Perelman School of Medicine Induced Pluripotent Stem Cell Facility
Provides resources for disseminating human pluripotent stem cell technology within UPenn and surrounding research communities. �Our services include derivation of patient specific iPSCs, genome engineering of stem cell lines using CRISPR/Cas9 technology, and lineage specific differentiation of iPSCs/hESCs in 2D and 3D organoid culture.�Core has large collection of patient derived iPSC lines and cell lines of gastrointestinal tract (esophageal, pancreatic and intestinal) available to users.�Committed to training investigators in stem cell culture techniques and providing quality tested stem cell reagents to users.
University of Pennsylvania Perelman School of Medicine Rodent Metabolic Phenotyping Core Facility
Rodent Metabolic Phenotyping Core (RMPC)
University of Pennsylvania Perelman School of Medicine Rodent Metabolic Phenotyping Core (RMPC)
Core (RMPC, formerly MPPMC) is metabolic core. Offers technology and phenotyping services to allow investigators to study metabolism in pre-clinical rodent models. Services include measurements of body composition (fat and lean mass) using NMR and DEXA, energy balance (food intake, locomotor activity, energy expenditure) using indirect calorimetry in either Columbus Instruments CLAMS system or Sable Systems Promethion System (with optional gas analyzer), and other in vivo metabolic phenotyping services (glucose clamps, insulin and glucose tolerance tests, telemetric monitoring of blood glucose or blood pressure, bomb calorimetry).
University of Pennsylvania Perelman School of Medicine Translational Bio-Imaging Center Core Facility
University of Pennsylvania Perelman School of Medicine Translational Bio-Imaging Center (TBIC)
Mission is to act as portal for research community into Bio-medical imaging resources of University of Pennsylvania. Goals include creating and maintaining access for research community to Bio-medical imaging technologies, enabling research investigators to benefit from Bio-imaging expertise and experience, and educating researchers about Bio-medical imaging options through targeted seminars, research fellowships, and established training programs.
University of Pennsylvania Perelman School of Medicine Positron Emission Tomography Center Core Facility
University of Pennsylvania Perelman School of Medicine PET Center
Dedicated to continuing advancement of molecular imaging and seeks to build network of collaborators to conduct translational research using existing and new radiotracers to help better understand the diagnosis, physiology and treatment of multiple diseases. Educates referring clinicians and their patients about emerging benefits of PET/CT diagnostic procedures, other radiotracer imaging methods and radionuclide therapies as tools in their research and clinical practice.Provides opportunities and mentoring for individuals interested in pursuing work or collaborations within molecular imaging field. Provides scanners as well as cyclotron facility.
University of Pennsylvania Perelman School of Medicine Tumor Tissue Biospecimen Bank Core Facility
University of Pennsylvania Perelman School of Medicine Tumor Tissue/Biospecimen Bank (TTAB)
Centralized biorepository of human biosamples. TTAB is responsible for the collection, processing, and storage of human blood, fluid, and tissue at the University of Pennsylvania Health System. TTAB has a collection bench within Surgical Pathology Suite at Hospital of University of Pennsylvania (HUP).� Our collection bench sits adjacent to frozen section teams managing clinical sample collection and allowing for tight integration of tissue sample collection with clinical pathology teams.
University of Pennsylvania Perelman School of Medicine Ultrasound Research Laboratory Core Facility
University of Pennsylvania Perelman School of Medicine Ultrasound Research Laboratory
Develops new ultrasound technologies and clinical applications, to bridge gap between technology and clinical applications, and to provide ultrasound imaging resources to other research. Consists of core group of scientists, sonographers and technicians with expertise in ultrasound technology and computer programming. This group works with clinicians in multiple specialties; including radiologists, cardiologists and surgeons. Core provides ultrasound scanner, sonographer and part-time radiologist on staff to conduct clinical and pre-clinical imaging.Helps with studies involving measurement of angiogenesis, vascularity, tissue elasticity, contrast agents, and effects of various physical and pharmaceutical agents on blood flow and tissue vascularity. Studies include research on cancer, cardiovascular disease and musculoskeletal disease.
University of Pennsylvania Perelman School of Medicine Vector Core Facility
University of Pennsylvania Perelman School of Medicine Vector Core
Resource for investigators requiring viral vectors for preclinical studies and other basic research applications such as gene therapies for acquired and inherited diseases.Provides production of high quality vectors and distribution of improved vector technologies services.
University of Pennsylvania Perelman School of Medicine Viral Molecular High Density Sequencing Core Facility
Viral Molecular High Density Sequencing Core Facility
Offers Illumina sequencing and bioinformatic expertise to assist researchers�with gene therapy trial evaluations, viral integration profiling,�CRISPR off-target�analyses. Assists with bioinformatic analyses including RNAseq transcription profiling�and 16S taxonomic assignments.�
University of Pennsylvania Penn Vet Center for Host Microbial Interactions Core Facility
Penn Vet Center for Host Microbial Interactions
University of Pennsylvania Penn Vet Center for Host Microbial Interactions
Offers consultation and laboratory services for high-throughput sequencing (HTS) experiments, with particular expertise and interest in microbiome/metagenome and RNA-seq applications. Provides instrumentation, including Illumina NextSeq 2000 and single cell platforms from 10X genomics and 1CellBio. Offers full service options, as well as hands on instruction for trainees who want to learn best practices for wet lab aspects of genomics experiments. Offers consultation services for all phases of HTS studies, from study design to bioinformatics analysis.
University of Pennsylvania Animal Model Core Facility
University of Pennsylvania Perelman School of Medicine Animal Model Core
Supports discovery to invention to innovation in medical translation.Provides animal model development to enhance scientific rigor during in vivo studies in experimental or naturally occurring disease models. Studies can start on small scale leading towards pivotal non-clinical IND/IDE-enabling trials in support of FDA or OUS-FDA submissions. Core hosts PIs, trainees and sponsors during clinical procedures to support and enrich their experience in cross functional team setting.
University of Pennsylvania Penn Vet Imaging Core Facility
University of Pennsylvania Penn Vet Imaging Core
Provides access to optical imaging capabilities for researchers at the University of Pennsylvania, Perelman School of Medicine, Children's Hospital of Philadelphia, and Wistar Institute. Provides instruments and expertise to perform widefield, confocal, multiphoton/intravital imaging, fluorescence lifetime imaging, high content live cell screening, long term single cell imaging, second harmonic imaging, structured illumination super resolution, and total internal reflection fluorescence microscopy, as well as software tools for image analysis. Core has adjacent (in and out) ULAR approved facility to house animals for long term live animal studies.
University of Pennsylvania Leonard Davis Institute of Health Economics Data Analyst Pool Core Facility
LDI Health Economics Data Analyst Pool (HEDAP)
University of Pennsylvania Leonard Davis Institute of Health Economics LDI Health Economics Data Analyst Pool (HEDAP)
Provides LDI affiliated investigators access to high quality, skilled data analysts. HEDAP recruits, trains, and manages group of masters level and PhD level statistical analysts. These analysts work with multi disciplinary investigators across funded projects using statistical software packages such as SAS, Stata, and R to manipulate and analyze health care data under guidance of investigators and other collaborators.
University of Pennsylvania Penn Vet Comparative Pathology Core Facility
University of Pennsylvania Penn Vet Comparative Pathology Core
Provides support to investigators utilizing animal models to study disease. Comparative Pathology Core, Abramson Cancer Center shared resource, provides expert pathological characterization and validation of mouse and other animal models used in biomedical research by offering expertise of board certified veterinary pathologists and access to histology, immunohistochemistry, and digital pathology services.
University of Pennsylvania Leonard Davis Institute of Health Economics Health Services Research Data Center Core Facility
LDI Health Services Research Data Center (HSRDC)
University of Pennsylvania Leonard Davis Institute of Health Economics LDI Health Services Research Data Center (HSRDC)
Provides secure environment for investigators analyzing protected health information. �It coordinates acquisition, storage, and analysis of data from private and government sources (e.g., Medicare, Medicaid, and others) and facilitates their use by researchers who seek to answer important questions regarding health policy and health care.�
University of Pennsylvania Penn Vet Referral Center for Animal Models of Human Genetic Disease Core Facility
Penn Vet Referral Center for Animal Models of Human Genetic Disease
University of Pennsylvania Penn Vet Referral Center for Animal Models of Human Genetic Disease
Core mission is to discover, create, characterize, treat, and share naturally occurring hereditary disorders in dogs and cats that are orthologous to those found in human patients.�Provides expertise in discovering, characterizing, and developing therapies for genetic disease in dogs and cats, which serve as models of same diseases that occur in children.�Specializes in molecular discovery of mutations, clinical phenotyping, biochemical and histological characterization, development of therapies which are translatable to human patients and preclinical trials in animal models of human disease.�
University of Pennsylvania Penn Vet Transgenic Mouse Core Facility
University of Pennsylvania Penn Vet Transgenic Mouse Core
Offers embryological manipulation services, focused on, but not limited to, murine model systems. These services primarily enable generation of genetically modified murine models, as well as experimental research in germ cell function and early embryonic development.
University of Pennsylvania Penn Dental Medicine Live Cell Imaging Core Facility
Penn Dental Medicine Live Cell Imaging Core
University of Pennsylvania Penn Dental Medicine Live Cell Imaging Core
Offers wide array of live cell imaging applications.Provides Nikon A1R Laser Scanning Confocal Microscopy system equipped with 4 laser lines to provide 6 different excitation/emission configurations; multiple photomultiplier tubes (PMTs), 32-channel spectral detector, full complement of microscope objectives, high speed image scanner, fully motorized stage and completely controllable environmental chamber. Users have access to NIS Elements AR software and 2D/3D deconvolution module offering sophisticated image analysis and processing features.
University of Pennsylvania Penn Dental Medicine Flow Cytometry Core Facility
Penn Dental Medicine Flow Cytometry Core
University of Pennsylvania Penn Dental Medicine Flow Cytometry Core
Provides Becton Dickinson LSR II flow cytometer equipped with four lasers.Blue laser can be used to detect forward and side scatter and 4 colors (eg., FITC/Alexa 488, PE, PerCP-CY55, PE-CY7), red laser can be used to detect 2 colors (e.g., APC and APC-CY7), violet laser can be used to detect 2 colors (e.g., Pacific blue, Am cyan) and a UV laser which can also be used to detect 2 colors (e.g., INDO1 blue, Indo1-violet/DAPI). The instrument is located in Room 330 in the Levy Building (240 South 40th Street).
University of Pennsylvania Penn Vet Extracellular Vesicle Core Facility
Penn Vet Extracellular Vesicle (EV) Core Facility
University of Pennsylvania Penn Vet Extracellular Vesicle (EV) Core Facility
Provides comprehensive or selected services in necessary isolation, quantification and characterization of EVs. Isolation of EV is based on size exclusion using high-performance (SEC-HPLC) or gravity fed (e.g. iZon column) liquid chromatography, ultracentrifugation, and/or density gradient ultracentrifugation. Accurately characterizes EV particle size distribution and concentration using resistive pulse sensing techniques (nCS1, Spectradyne, LLC). Immunophenotype can be accomplished using nanoscale flow cytometry and/or chip array (ExoViewTM) techniques. Provides services in training and education for individuals and lab groups in all methods above and study design consultation.
Software Python GUI for graphing measures of liquid ingestion in rodents from Sippers. Python GUI for visualizing Sipper data.
Software tool for meta analysis. Facilitates integration and synthesis of effect sizes from different studies. Consists of set of workbooks designed for Microsoft Excel that automatically produces all required statistics, tables, figures, and more.
Software tool as amplicon sequence processing workflow using QIIME 2 and Snakemake management system.Enables rapid analysis of environmental and biomedical amplicon data, decreasing time from data generation to actionable results.
University of Ottawa Bioinformatics Core Facility
Core of University of Ottawa and Ottawa Hospital Research Institute. Provides advice on bioinformatics research design, conduct bioinformatics analysis, and provide support for grant proposals that involve bioinformatics (including conducting pilot studies, support/collaboration letters and methodological text). Areas of expertise include:Analysis of high throughput sequencing data; single cell (Chromium 10x), RNA-seq (including small RNA), ChIP-seq, ATAC-seq, Hi-C.Large scale analysis integrating multiple data types.Helps to arrange for analysis of your biological samples with local core facilities such as StemCore, Proteomics Resource Center, or OHRI Mass Spectrometry Core Facility. Provides yearly training courses in RNA-seq analysis and Bioinformatics analysis using R as well as individual training and analysis support on request.
University of Nebraska Medical Center Advanced Microscopy Core Facility
Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options.
University of Nebraska Medical Center Advanced Magnetic Resonance Imaging Core Facility
UNMC Core for Advanced Magnetic Resonance Imaging
Provides research MRI capabilities for investigators at UNMC and across greater Omaha area. Housed in Hixson-Lied Center, CAMRI operates Siemens 3T Prisma MRI instrument that can collect high quality data of any MR modality using advanced gradients and research grade pulse sequences. Variety of head coils (20-, 32-, and 64-channel) are available to optimize data collection for needs of specific studies. Studies incorporating functional MRI can take advantage of CAMRI�s suite of MRI-compatible response devices, mirrored 32-inch LCD screen, and integrated stimulus display computer.
Software tool for identification and classification of phage virion proteins using deep learning.
Fast Healthcare Interoperability Resources
Standard for health care data exchange, published by HL7. Platform provides healthcare information exchange standard that makes use of HL7-defined set of “resources” to support information sharing by variety of means, including documents, messages, services and RESTful interfaces. FHIR defines resources for clinical and administrative content (e.g. Observation, Patient, etc.) as well as resources for “infrastructure” purposes. Some of these infrastructure resources are used to define standard itself – i.e. what the characteristics of resources are, what codes can be used in them, etc.
Provides integration and analysis of publicly available resources as well as newly collected transcriptomic data following deubiquitinating enzyme (DUB) knockout or inhibition to facilitate exploration of DUB function in oncology.
VAME: Variational Embedding of Animal Motion
Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP.
University of Nebraska Medical Center Multiphoton Intravital and Tissue Imaging Core Facility
University of Nebraska Medical Center UNMC Multiphoton Intravital & Tissue Imaging (MITI) Core
UNMC Multiphoton Intravital & Tissue Imaging (MITI) Core
Core provides intravital imaging equipment to acquire advanced descriptive and quantitative data for imaging studies. Includes Olympus FVMPE-RS advanced multiphoton microscope, multichannel, multiphoton excitation system specifically tailored for intravital and deep tissue imaging.System is additionally equipped with 458 and 588 nm stimulation laser lines for photobleaching, light stimulation and/or photoactivation of various fluorescent or caged constructs. Uses Spectra-Physics InSight X3 dual-line, tunable multiphoton laser for ultrafast, multichannel imaging.Available Neurotar Mobile Home Cage allows researchers to integrate real-time imaging with behavioral/locomotion tracking. Offers training and access to imaging system, support in design of experimental procedures, acquisition of image data, and analysis of acquired images.
Texas A and M University Image Analysis Laboratory Core Facility
Texas A&M University TAMU - Image Analysis Laboratory
Provides advanced imaging technologies and image analysis tools including vital imaging of cellular processes within cells, tissue explants, and organoids.Supports services for transmission electron microscopy of biological samples.Imaging capabilities include fluorescence imaging of samples;Transmitted light imaging; Live cell imaging;FRAP, FLIP, Photoactivation/conversion;FRET, FLIM; Image processing, analysis, quantification; Transmission electron microscopy.Microscopes and Equipment include:Zeiss Axio Imager M2 Motorized Upright Microscope;Zeiss Cell Discoverer 7; Zeiss ELYRA S.1 Superresolution Microscope; Zeiss LSM 780 NLO Multiphoton Microscope;Zeiss TIRF3;Zeiss Stallion Digital Imaging Workstation;FEI Morgagni Transmission Electron Microscope;Leica UC6 Ultramicrotome;ImageXpress Pico & BioTek Cytation 7;Cryostar NX70 Cryostat.
University of California at Santa Cruz Marine Analytical Laboratory Core Facility
University of California at Santa Cruz Marine Analytical Laboratory
Operated by Institute of Marine Sciences with support from UCSC Division of Physical and Biological Sciences. Available to UCSC and University of California marine and coastal research community.Provides equipment including Shimadzu TOC-VCPH TC/TN analyzer,Dionex ICS-2000 Ion Chromatograph,UIC Carbon Coulometer Analyzer, Perkin-Elmer AAnalyst 100 Atomic Absorption Spectrophotometer, Thermo Genesys 10S UV-Visible Spectrophotometer, Turner Designs 10-AU Field Fluorometer, Turner Designs TD-700 Lab Fluorometer, Turner Designs TD-20/20 Luminometer,Lachat QuikChem 8000 Flow Injection Analyzer, Guildline 8410 PortaSal Salinometer, Labconco Freeze Dryer.
University of Nebraska Medical Center Bioimaging Core Facility
University of Nebraska Medical Center UNMC-Bioimaging Core Facility
Provides infrastructure for imaging based small animal research.Includes noninvasive anatomy, physiology, and biochemistry assessment for disease detection and therapeutic monitoring.
Texas A and M University Soft Matter Core Facility
Texas A&M University Soft Matter Facility
Facility is focused on characterization of multifunctional soft materials. Includes four instrumentation suites based on soft matter centered research areas which will be unified by general theme of characterization of hierarchically structured multicomponent, multifunctional soft materials: Molecular Characterization, Processing and Mechanics, Thin Films and Interfacial Analysis, and Nanostructure Characterization.
Software package for liquid chromatography mass spectrometry retention time alignment.
Flow cytometry analysis software for fast analysis, easy collaborative access to data, and tailored data visualization.
University of Pennsylvania Perelman School of Medicine Biomedical Data Science Core Facility
University of Pennsylvania Perelman School of Medicine Biomedical Data Science Core
Core provides consultations and fee for service support in big data analyses using methods of data science in biomedical and health research related to digestive disease and liver research.
University of Pennsylvania Perelman School of Medicine ITMAT Bioinformatics Laboratory Core Facility
University of Pennsylvania Perelman School of Medicine ITMAT Bioinformatics Laboratory
Provides project based bioinformatics support for ITMAT translational researchers. Provides computational infrastructure and programming support needed to conduct high-throughput proteomics experiments. We also support other genomics high-throughput technologies to a lesser extent. The projects range from building Web applications for data analysis pipelines, scripting, clinical and basic science research support, and database and algorithm development. Recent efforts have focused on explorations of new models of computation, specifically cloud computing and GPUs, for use in genomic scale research.
University of Pennsylvania Perelman School of Medicine Clinical Imaging Service Center Core Facility
RADCORE Clinical Research Core Facility (Clinical Imaging Core)
University of Pennsylvania Perelman School of Medicine Clinical Imaging Core Service Center
Clinical Imaging Core Service Center includes RADCORE, Tumor Response Assessment (TRAC) and Research imaging guided biopsies cores. Supports cancer clinical trials. RADCORE staff include clinical research professionals with range of expertise in imaging based clinical research protocols and offers services in consultation, management of research protocols and Radiology IND/IDE support office. Tumor Response Assessment Core (TRAC) team of Radiologist is skilled in evaluating tumor response imaging assessments for patients enrolled in cancer clinical trials being conducted at UPHS. Research imaging guided biopsies Interventional Radiology and technical staff provides consultation to define biopsy protocol and pathology tissue collection.
Python Meta Analysis and Regression Engine
Python Meta-Analysis and Regression Engine
Software Python library for mixed effects meta regression including meta analysis.
Transcriptional Regulatory Relationships Unraveled by Sentence based Text mining
Reference database of human transcriptional regulatory interactions. Manually curated database of human and mouse transcriptional regulatory networks.
Metabolomic Analysis and Visualization ENgine
Software program for interactive processing of LC-MS-based metabolomics data. Open source cross platform metabolomics data analyser. Used to reduce complexity of metabolomics analysis by developing highly intitute interface for exploring and validating metabolomics data. Program features multi-file chromatographic aligner, peak-feature detector, isotope and adduct calculator, formula predictor, pathway visualizer, and isotopic flux animator. Data from both triple quadropole and full spectrum instruments is supported.
Simon Fraser University Flow Cytometry Lab Core Facility
Simon Fraser University SFU-Flow Cyt Lab
Offers high speed cell sorting and bench top flow cytometric analysis services as well as training and support to research community.Instruments include BD FACSAria Fusion Cell Sorter,4-Laser | 16-Colour (2B/3R/5YG/6V) within Class II Type A2 BioSafety Cabinet and BD LSRFortessa X-20 Cell Analyzer 4-laser | 16-Colour (2B/3R/5YG/6V).
Software tool as adapter that abstracts SingleCellExperiment container in form of tibble and allows data manipulation, plotting and nesting.
Software R package for modeling beta distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of beta distributed response), bias corrected and bias reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided.
Software tool to calculate enrichment scores. Generates human and machine readable labels that quantify features enriched in sample. Used to identify multiple populations of cells and to compare each population to all of other remaining cells from original sample.
Software R package to create tidy data frames of marginal effects for ggplot from model outputs. Used to compute marginal effects and adjusted predictions from statistical models and returns result as tidy data frames.
Software R package for data analysis, graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables.
Software tools to register histological section images and cell count locations to mouse brain atlas. Semi automated workflow and GUI for automated brain slice histology alignment, registration, and cell quantification. Used to explore Allen Mouse Brain Atlas, register asymmetric slice images to atlas using manual input, and analyze region of interest data by registering locations of fluorescently labeled cells to standardized regions of Atlas.
University of Miami Sylvester Flow Cytometry Shared Resource Core Facility
UM Sylvester Flow Cytometry Shared Resource
University of Miami UM Sylvester Flow Cytometry Shared Resource
Provides researchers with sophisticated methods for analysis and preparative sorting of both normal and tumor cells. Helps researchers to measure parameters including apoptosis, gene expression, drug metabolism, immune responses and pathways of cellular activation, both normal and tumor related. Provides access to high parameter cytometry instrumentation including spectral cytometry, mass cytometry and imaging mass cytometry.
University of Miami Sylvester Onco Genomics Shared Resource Core Facility
UM Sylvester Onco-Genomics Shared Resource
University of Miami UM Sylvester Onco-Genomics Shared Resource
Provides access to technologies and services for study of genomics and epigenomics of cancer, in addition to providing technical expertise for project design, trouble shooting and pre and post award support. Services include next generation sequencing, single cell genomics, spatial genomics, gene expression assays and molecular quantitation, services for sample extraction and QC.
Software package for comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. Evaluates diverse collection of survival models for both clinical and omics datasets.
Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences.
Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting.
Software for data processing and analysis, automated reporting and data management, data normalisation, generation of dose response curves, generation of IC50. Captures data from all assays, regardless of therapeutic modality or area.
Software platform and infrastructure that aggregates, integrates, and analyzes human genetic and genomic data to spark insights into complex diseases. Data and software platform for storing, processing, and presenting genetic and genomic data.
Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates.
Software tool for linkage disequilibrium decay analysis based on variant call format files.
System includes Odyssey XF Imager and Empiria Studio Software for streamlined image acquisition, organization, and analysis of Western blots. Used for imaging near infrared and enhanced chemiluminescent Western blots, to detect multiple targets on same blot with two channel multiplex fluorescence, and document DNA gels.
Bonsai code for running GOFish platform for behavioural experiments in fish.
Software is post processing, data integrity software for quantitative protein expression analysis including In-Cell Western Assays, Western blots, membranes, slides, and gels.
Software to calculate p-distance matrix based Variant Call Format.
Software tool for integration of spatial information in spatial transcriptomics data clustering.
Software library to automatically reject bad trials and repair bad sensors in magneto/electroencephalography data.
Software framework for modeling sequence motifs based on maximum entropy principle.
Web tool to predict and analyze exonic splicing silencers.
Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers.
ridge regression Best Linear Unbiased Prediction
Software R package for mixed models with single variance component besides residual error, which allows for efficient prediction with unreplicated training data. Makes ridge regression and other kernel methods accessible to plant breeders interested in genomic selection.
Interface to H2O4GPU, collection of GPU solvers for machine learning algorithms.
Software R package as fast implementation of Random Forests for high dimentional data.
Software R package implements large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures.
Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy.
Software R package that contains functions for training and plotting classification and regression models. Includes methods for pre-processing training data, calculating variable importance, and model visualizations.
Analysis code relevant to scRNA sequencing analysis. Code for Fink and Sona et.al. (2022) publication.
Penn State Hershey College of Medicine Light Microscopy Imaging Core Facility
The Light Microscopy Imaging Core (Penn State COM)
Provides consultation and training in ultra high resolution imaging of cells and tissues in fixed or live states. Provides expertise in quantitative image analysis and consultations on microscopy related research projects.
Provider of measurement and analysis of Patient Reported Outcomes and their linkage to clinical data. By embedding resulting insights into individual treatments and care management, enables Value based Healthcare initiatives. Software company works from Berlin, Cologne and London on product development and supports centers, registries and research projects. Patient-Reported Outcomes are collected directly from patients in form of standardized questionnaires and provide insights into treatment effects and health related quality of life. Automatically linked with clinical observations, data based decision making basis is created for medical, therapeutic, and economic issues.
Food Processor Nutrition Analysis Software
Software tool for nutrition analysis, diet and exercise tracking, and menu planning. Combines researched food and ingredient database with interface for accurate and comprehensive nutrition analysis.
University of Texas Southwestern Medical Center Neuro Models Core Facility
University of Texas Southwestern Medical Center UTSW-Neuro-models Facility
Facilitates scientific research of nervous system function to enhance development and testing of novel therapeutic strategies for treatment of nervous system disorders. Provides resource capacity typically unavailable or impractical in individual laboratory. Major areas of specialization include surgical approaches to model production and assessment, behavior testing of sensorimotor functions, in vivo electrophysiological recording (EEG, EMG, ERP). Procedures are intended for mice and rats. Procedures can be developed based on client interests.
Web tool for text mining and semantic technologies for biomedical content discovery. Knowledge base of biomedical text mining results. Used to discover cause-effect relations between multiple entity types and deliver standardized representation of knowledge.
Open source software tool for automatic axon and myelin segmentation from microscopy data using convolutional neural networks.
Cornell University Biotechnology Resource Center Transcriptional Regulation and Expression Core Facility
BRC Transcriptional Regulation and Expression Facility
Transcriptional Regulation and Expression Facility
Facility offers genomics profiling services including RNAseq, small RNA sequencing, and ATACseq.
Texas A and M University AgriGenomics Laboratory Core Facility
Texas A&M University TAMU-AgriGenomics Laboratory
Assists graduate students, staff and faculty launch, economize and expedite their research, especially when it involves DNA extraction and quality checks, targeted genotyping and DNA content analysis. Facilitates usage of complementary cores and assists with research planning and data analysis.AGL members have free lab access and reduced costs for services as well as one-on-one training and advising with AGL staff.
Software tool provides annotation of non-synonymous single nucleotide variants in context of structural properties of resulting amino acid changes in corresponding proteins. Improved implementation of StructMAn, shipped in container form and extended to annotation of short in-frame indels and alterations arising as consequence of alternative splicing events. Produces range of structural features by combining information from experimentally resolved structures of many related proteins, which is unique feature of StructMAn family tools. Can also harness all protein structure models stored in AlphaFold Protein Structure Database.
Open source parametric 3D modeler to design real life objects of any size. Parametric modeling allows modify your design by going back into your model history and changing its parameters.
OHAUS CS lightweight, portable, compact balance for use in laboratory, industrial, education and home use applications. CS offers great value without sacrificing accuracy for weighing jobs of 200g to 5000g.
Hamamatsu | NanoZoomer S60 Digital slide scanner
Whole slide scanner that scan glass slides to convert them to digital data. NanoZoomer S60 supports both brightfield imaging, fluorescence imaging and double size slides.
BD Biosciences | FACSymphony A5 Cell Analyzer
Flow cytometer as novel cell analyzer that leverages inherent benefits of flow cytometry and enables simultaneous measurement of up to 50 different characteristics of single cell.
Open Source portable FPGA place and route tool.
Software package includes new cell reference for adult peripheral blood deconvolution arrayed using Illumina HumanMethylationEPIC.Optimized library for reference based deconvolution of whole blood biospecimens assayed using Illumina HumanMethylationEPIC BeadArray.
EMERALD METAGENOMICS ANNOTATIONS PIPELINE
Software metagenomics annotations pipeline that regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles in EuropePMC.
Miami Project To Cure Paralysis Drug Discovery Core
Core at Miami Project to Cure Paralysis leverages PerkinElmer Opera Phenix Plus high content screening system to provide assay development and phenotypic screening. Facility is also equipped with PerkinElmer Janus G3 liquid handler, featuring modular and variable dispense heads, to automate screening workflows and enhance throughput. Core supports phenotypic and target-based assays. Phenotypic assays range from 2D to 3D, widefield to confocal, and antibody to dye based. It collaborates with users to develop customized assays and analytical pipelines tailored to their specific needs. Current specializations include neurite tracing, lipid droplet quantification, cell viability, morphological and kinetic analyses, phagocytosis, cell marker detection, cell adhesion, among others.
Software tool for marking ant motion trajectories dataset from video. Provided marking software, three data quality analysis scripts, and tracking performance evaluation tool.
Software pipeline for assembly and analysis of highly heterozygous genomes. Used for diagnosis of hybrids, aneuploids, and other non standard architectures in genome assemblies.
Software tools for analyzing and quantifying effects of confounder variables on machine learning model predictions.
Software to control automated microscopes and microscope equipment in combination with multidimensional acquisition and analysis. Used for high speed image acquisition and processing.
Cornell University BRC Genomics Innovation Hub Core Facility
Cornell University BRC Genomics Innovation Hub
Core complements services provided by BRC Genomics Facility.Working on collaborative model, protocol and method development by early adopters pave the way for larger scale production services.
Software Python scripts to plot neuroimaging results especially functional connectivity results.
Software tool interprets Verilog descriptions of programmable hardware and transforms these into combinations of small look-up tables as provided on FPGAs from Xilinx or Lattice.
Software tool for analysis, visualization and animation of ribosome structures. Plugin for use with VMD that can automate download, structure alignment, analysis, visualization and animation of ribosome structures.
Software library that enables use of structure based SMOG models of biopolymers with OpenMM.
Software tool for complexity analysis viral sequences.
Transcriptional Regulatory Relationships Unrevealed by Sentence based Text mining database
TRUSST is reference database of human transcriptional regulatory interactions.TRRUST v2 is manually curated expanded reference database of human and mouse transcriptional regulatory interactions.
Software R package that helps format Seurat objects into objects that can be used for trajectory analysis in other packages such as Monocle
Cardiff University Bioimaging Hub Core Facility
Provides advanced light microscopy imaging modalities and histological services. Offers training and application support in experimental design, sample preparation, data generation and analysis through to scientific publication and grant assistance.
IP based prediction of RNA pseudoKNOTs plus plus
Web server is an improved version of IPknot web server, which provides services for predicting RNA secondary structures including wide class of pseudoknots. Can perform RNA secondary structure prediction including pseudoknots for very long sequences. Can predict consensus secondary structure when multiple alignment of RNA sequences is given.
Web server predicts RNA secondary structures using deep learning. RNA secondary structure prediction using deep learning with thermodynamic integration.
Abstract and indexing database with full text links that is produced by Elsevier Co. Combines expertly curated abstract and citation database with enriched data and linked scholarly literature across wide variety of disciplines.
Open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2 photon imaging. Device that rapidly time interleaves stimulation and detection epochs during two photon imaging.
Biosynthetic Gene Similarity Clustering and Prospecting Engine
Software tool that calculates distances between BGCs in order to map BGC diversity onto sequence similarity networks, which are then processed for automated reconstruction of Gene Cluster Families, groups of gene clusters that encode biosynthesis of highly similar or identical molecules.
Software tool for calculating average nucleotide identity.
Computerized morbidity registration network in Belgium based on general practice data.Contains demographic, clinical, biomedical, and prescription data, registered with computer generated keywords in electronic health record.
Web service to predict molecular interactions that may occur between target protein and small molecule. Protein small molecule docking web service based on EADock DSS.
Penn State College of Medicine Metabolic Phenotyping Core Facility
Penn State College of Medicine Rodent Metabolic Phenotyping Core
Supports research that requires comprehensive assessment of energy balance and body composition in experimental rodents by providing necessary equipment and expertise. Services include training in the use of equipment, consultation on experiment design, and help with data analysis. Instrumentation includes Bruker TD-NMR LF100 Minispec and TSE Phenomaster System with Integrated Stellar Telemetry.
Library of Integrated Network Based Cellular Signatures 2.0
Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.
Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format.
LED illuminator for BX53 is equivalent to or better than 100 W halogen lamp, delivering brightness appropriate for teaching or contrast methods. Can be customized for different observation methods, such as phase contrast and fluorescence, with modular components.
Platform to let you gather data from across NCBI databases. Allows to find and download gene, transcript, protein and genome sequences, annotation and metadata.
Open source software suite for analysis of fiber photometry data.
Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types.
Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded.
Software Python package to perform post-processing of cryo-EM maps. Deep learning model trained on pairs of experimental volumes and atomic model corrected volumes that is able to obtain post-processed maps using as input raw volumes, preferably half maps.
Software R package to format data, frame column names, provide quick counts of variable combinations and isolate duplicate records, format tabulation results.
Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0.
Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses.
Software platform to integrate transcription factor gene interactions and validate regulatory networks. Gene regulatory network validation.
COnditional SELection on the Excess of NonSynonymous Substitutions
Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups.
Software package to provide functions richGO, richKEGG,and enrich to do functional enrichment analysis. Used for function enrichment analysis and network construction.
Database for exploration of single cell RNA sequencing experiments from mouse and human. Collects and integrate data from multiple studies and present them through unified framework.
Web tool to predict effects of sequence variants on alternative splicing. Predicts changes in alternative 5' splice events as well as skipped exon events.
Nanofocus computed tomography system for applications in material science, precision injection moulding, micromechanics, electronics geology and biology. System includes nanofocus X-ray tube, precision mechanics and advanced software modules. Used for range of 3D CT applications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
MfN Berlin Micro-CT Laboratory Core Facility
Museum fuer Naturkunde Berlin Micro-CT Laboratory
Provides analysis of biological, palaeontological and geological objects using computer assisted methods. Center for research at museum and for digitisation of scientific collections. Open to external users. In addition to various devices for three dimensional scanning, laboratory has workstations for processing and analysing raw data using 3D volume processing software.
Open source, community curated registry, meta-registry, and compact identifier resolver. Used for unifying identification of biomedical entities through integrative, open,community driven metaregistry. The registry contains metadata about ontologies, controlled vocabularies, and resources including their preferred prefix, name, description, homepage, mappings to other registries, and more.
Wireless and fully standalone professional 3D scanner with new NVIDIA Jetson TX2 processor onboard. 3D scanning solution for data capture.
3D scanner based on blue light technology. Precision instrument for CAD users and engineers. Used for capturing small objects or intricate details of large industrial objects in high resolution, with accuracy and brilliant color.
3D scanner for making quick, textured, and accurate 3D models of medium sized objects such as human bust, alloy wheel, or motorcycle exhaust system. Used for capturing objects of almost any kind, including objects with black and shiny surfaces.
Encyclopedia of white and brown adipocyte secretome in mouse models and humans as key prerequisite to elucidating role of these mediators in normal physiology and disease.
Adaptive Immune Receptor Repertoire Data Commons API Specification
Provides programmatic access to query and download AIRR-seq data. ADC API uses JSON as its communication format, and standard HTTP methods like GET and POST. ADC API is read only and mechanism of inclusion of AIRR-seq studies into data repository is left up to repository. ADC API Specification explains how to construct and execute API requests and interpret API responses.
Adaptive Immune Receptor Repertoire Rearrangement Schema
Part of AIRR Data Model, defines annotations needed for rearrangements, which are sequences describing rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in tab delimited file and should be compatible with any TSV reader. Dataset is defined in this context as: TSV file, TSV with companion YAML file containing metadata, or directory containing multiple TSV files and YAML files.
Adaptive Immune Receptor Repertoire: Repertoire Schema
Part of AIRR Data Model, describes abstract organizational unit of analysis that is defined by researcher and consists of study metadata, subject metadata, sample metadata, cell processing metadata, nucleic acid processing metadata, sequencing run metadata, set of raw sequence files, data processing metadata, and set of Rearrangements. Repertoire gathers all of this information together into composite object, which can be easily accessed by computer programs for data entry, analysis and visualization. AIRR Repertoire Schema has been implemented in YAML/JSON, which provides mechanism to share AIRR Repertoire metadata between research projects.
Adaptive Immune Receptor Repertoire Data Model
Defines schema for MiAIRR data elements, structuring them within schema objects, defining relationship between those objects, and defining file format. Increased interest in immune system's involvement in pathophysiological phenomena coupled with decreased DNA sequencing costs have led to explosion of antibody and T cell receptor sequencing data collectively termed "adaptive immune receptor repertoire sequencing" (AIRR-seq or Rep-Seq). AIRR Community has been actively working to standardize protocols, metadata, formats, APIs, and other guidelines to promote open and reproducible studies of immune repertoire.
Adaptive Immune Receptor Repertoire Software Guidelines
AIRR Software Guidelines were created by AIRR Software Working Group to promote standards for AIRR software tools and resources in order to enable rigorous and reproducible immune repertoire research at largest scale possible.Established standards for software tools. Authors whose tools comply with this standard will, subject to ratification from AIRR Software WG, be permitted to advertise their tools as being AIRR compliant. Guidelines include compliance checklist, list of compliant tools, and recommended software evaluation data sets.
Minimal information about Adaptive Immune Receptor Repertoires
Checklist of minimally required information that we recommend journals adopt, and that could form requirements for submission to public data repository. AIRR sequencing studies apply high throughput sequencing technologies to profile B cell receptors (BCRs) and T cell receptors (TCRs). Standards were developed by AIRR Community Minimal Standards Working Group.
Network of distributed repositories that adhere to standards set out by AIRR Community. This collection contains standards and repositories either created by the AIRR community or approved for use within AIRR community.
Adaptive Immune Receptor Repertoire Community
Adaptive Immune Receptor Repertoire Community of The Antibody Society
Research driven group that is organizing and coordinating stakeholders in use of next generation sequencing technologies to study antibody/B-cell and T-cell receptor repertoires. Develops and promotes standards and recommendations for obtaining, analyzing, curating and comparing/sharing AIRR-seq datasets;using and validating tools for analyzing AIRR-seq data;relating AIRR-seq datasets to other “big data” sets, such as microarray, flow cytometric, and MiSeq and single-cell gene-expression data; legal and ethical issues involving use and sharing of AIRR-seq data sets derived from human sources.
Open source adaptive immune receptor genotype and haplotype database. Core collection is inferred from immune receptor repertoire sequences and genomically derived material. Provides customisable reports, which allow users to study gene and allele usage in various ways.
Single Cell Opioid Responses in the Context of HIV
Data coordination, analysis, and scientific outreach center to standardize and share single cell molecular HIV/SUD data by ensuring that data is FAIR. Program with mission of generating resources that would enable comprehensive tissue characterization at single cell level. This includes generating single nucleus transcriptomic data for identification of novel rare cell types, and enrichment of key cellular populations to inform pathophysiological understanding of CNS effects of SUD and HIV. Interdisciplinary effort, involving teams of investigators at ten institutions including Yale, Boston University, Mount Sinai, University of Nebraska Medical Center, Broad Institute, University of California San Diego, Weill Cornell Medicine, Allen Institute, Scripps Research as well as a Data Coordination Center hosted at Institute for Genome Sciences, University of Maryland Baltimore School of Medicine.
Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.
Portal provides genomic and transcriptomic data for researchers interested in Hydractinia genomics and molecular biology. Includes browsers for the H. symbiolongicarpus and H. echinata genome assemblies and interactive interface for interrogating H. symbiolongicarpus single cell gene expression atlas. Provides gene pages with functional annotation data for every gene model for both species, including protein domain composition and orthology predictions.
Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis.
Web server for potential drug target identification using pharmacophore mapping approach.Designed to identify potential target candidates for given probe small molecules including drugs, natural products, or other newly discovered compounds with binding targets unidentified using pharmacophore mapping approach. Used for potential drug target identification with comprehensive target pharmacophore database.
University of Texas Southwestern Medical Center Quantitative Light Microscopy Core Facility
Provides access to variety of microscope modalities including laser scanning and spinning disk confocal, multiphoton, wide field deconvolution, CFP/YFP FRET, TIRF, single molecule imaging, and more. Offers customized microscopy training, advise and help with sample preparation, image quantification, and offer basic microscope maintenance. Can streamline your data handling and image visualization as well as automate your image analysis workflow through customized Fiji macros.
Fred Hutchinson Cancer Center Genomics and Bioinformatics Core Facility
Fred Hutchinson Cancer Center Genomics and Bioinformatics Shared Resource Core
Provides set of services that encompass experimental design, data generation and data interpretation. Expert genomics and bioinformatics teams are available to consult and collaborate at every step of process and work closely together to develop optimized experimental strategies to ensure that appropriate technology and data analysis tools are used to address each unique scientific question.
Fred Hutchinson Cancer Center Shared Resources
Through Shared Resources, investigators in Fred Hutch/University of Washington Cancer Consortium and external academic and industry organizations can access services tailored to their specific research goals, including novel assay development or early access to new technologies.
Fred Hutchinson Cancer Center Antibody Technology Core Facility
Fred Hutchinson Cancer Center Antibody Technology
Fred Hutchinson Cancer Center Antibody Technology Shared Resource
Designs campaign strategies for generation and identification of novel monoclonal antibody compositions. Our projects encompass range of applications in oncology, viral therapeutics and diagnostics.
Fred Hutchinson Cancer Center Cellular Imaging Core Facility
Fred Hutchinson Cancer Center Cellular Imaging Shared Resource
Provides advanced light microscopy services for biomedical and translational research including workflow, training for independent work, assistance and technical support in microscopy techniques, quantitative image analysis. Offers training and support for imaging and analyzing gels and blots.
Fred Hutchinson Cancer Center Comparative Medicine Core Facility
Fred Hutchinson Cancer Center Comparative Medicine Shared Resource
Core teams of technicians, veterinarians, pathologists and operations specialists offer services in diagnostic and research pathology and support development and maintenance of preclinical mouse models, including mice bearing humanized immune system. Provides access to high quality technical services and immune deficient mice. Can perform individual technical services or complete entire in vivo experiments. Facilities are fully accredited by Association for Assessment and Accreditation of Laboratory Animal Care International and comply with all U.S. Department of Agriculture, Public Health Service, Washington state and local area regulations.
Fred Hutchinson Cancer Center Electron Microscopy Core Facility
Fred Hutchinson Cancer Center Electron Microscopy Shared Resource
Offers techniques to resolve structures from cellular ultrastructure to molecular interactions. Offers expertise in EM sample preparation and imaging, cryogenic electron microscopy, technologies and services, training through complexities of electron microscopy workflow, from sample preparation to image processing. All users must be trained by core staff.
Fred Hutchinson Cancer Center Experimental Histopathology Core Facility
Fred Hutchinson Cancer Center Experimental Histopathology Shared Resource
Provides expertise in anatomic pathology technologies. Offers routine and special staining, immunohistochemistry, in situ hybridization and digital pathology in support of internal and external investigators who rely on histological analysis.
Fred Hutchinson Cancer Center Flow Cytometry Core Facility
Fred Hutchinson Cancer Center Flow Cytometry Shared Resource
Includes services from sterile cell sorting for therapeutic applications to whole cell mass spectrometry, diagnostics and early stage clinical trials. Provides expertise from experimental design to data analysis and troubleshooting, therapeutic cell sorting. Supports isolation of cells for Phase 1 clinical trials of cellular immunotherapies.
Fred Hutchinson Cancer Center Hutch Data Core Facility
Fred Hutchinson Cancer Center Hutch Data Core Shared Resource
Helps investigators integrate, interpret and explore large and diverse datasets. Provides services that support analysis of large scale datasets for biomedical researchers, drawing on expertise in computational biology, software engineering and cloud architecture. Offers project based scientific analysis by bioinformaticians, automation of analytical pipelines using workflow management platforms, publication of complex datasets with web accelerated graphics, training and documentation to enable scientist driven computation.
Fred Hutchinson Cancer Center Immune Monitoring Core Facility
Fred Hutchinson Cancer Center Immune Monitoring Shared Resource
Supports investigators seeking evaluations of immunologic responses in basic and early stage clinical research settings. Provides resources and expertise to evaluate cellular immunologic processes and responses through reagents, molecular and cellular assays, assay development support and research consulting services.
Fred Hutchinson Cancer Center Preclinical Imaging Core Facility
Fred Hutchinson Cancer Center Preclinical Imaging Shared Resource
Provides in vivo imaging technology and infrastructure to support basic and preclinical research. Offers diverse array of imaging modalities, including ultrasound and optical imaging, MRI, micro-CT and multiphoton microscopy.
Fred Hutchinson Cancer Center Preclinical Modeling Core Facility
Fred Hutchinson Cancer Center Preclinical Modeling Shared Resource
Supports development and maintenance of preclinical mouse models, including patient derived xenografts, cell line xenografts and genetically engineered mouse models.
Fred Hutchinson Cancer Center Proteomics and Metabolomics Core Facility
Fred Hutchinson Cancer Center Proteomics and Metabolomics Shared Resource
Provides support for mass spectrometry based proteomics and metabolomics research. With advanced instrumentation and highly trained staff, core offers consultation and services in sample preparation, sample separation, data collection and data analysis.
Fred Hutchinson Cancer Center Specimen Processing and Research Cell Bank Core Facility
Fred Hutchinson Cancer Center Specimen Processing and Research Cell Bank Shared Resource
Provides biospecimen sample processing, extraction and biorepository services. Offers expertise to advance preclinical and clinical studies.
UNC School of Medicine Integrated Genomics Cores High Throughput Sequencing Core Facility
UNC School of Medicine HighThroughput Sequencing Facility
UNC School of Medicine Integrated Genomics Cores HighThroughput Sequencing Facility
University of North Carolina at Chapel Hill School of Medicine Integrated Genomics Cores High-Throughput Sequencing Facility
Full service sequencing facility to assist with genetic and genomic research. Part of Integrated Genomics Cores. Offers comprehensive library services, NextGen sequencing and alternative technologies including long reads. Offers library preparations and multiple sequencing platforms including MiSeq, HiSeq, NovaSeq, NextSeq, BioNano, Oxford Nanopore. Services also include using techniques and data analyses via sister core BARC.
Cincinnati Children's Hospital Animal Behavior Core Facility
Cincinnati Children's Hospital Animal Behavior Core
Offers behavioral phenotyping of rodent models as well as characterizing nervous system function in mouse and rat models through behavioral assays.
Cincinnati Children's Hospital Biomedical Informatics Core Facility
Cincinnati Children's Hospital Biomedical Informatics Core
Provides computational resources, services, and support to investigators including clinical research informatics, application and technology development, and bioinformatics analyses.
Cincinnati Children's Hospital Cell Processing Core Facility
Cincinnati Children's Hospital Cell Processing Core
Supplies mononuclear cells, stem cells or other enriched cell populations. Provides stem cells and other tissue samples from normal donor or patient populations such as disease specific repositories or specific research studies requiring sample processing. Samples are provided fresh or cryopreserved according to availability, unprocessed or with further lab processing.Common processing techniques include PBMC isolation,Serum and plasma isolation,Separation of marker specific populations,Flow cytometric characterization of samples,Interferon gamma EliSpot.Additional services may be available upon request
Cincinnati Children's Hospital Comprehensive Mouse and Cancer Core Facility
Cincinnati Children's Hospital Comprehensive Mouse and Cancer Core
Offers services for researchers exploring cancer systems through animal models. Provides animals from specific inbred mouse strains primarily used in cancer and hematopoietic research, offers cell transplant, harvest and irradiation services and can handle animal cancer model systems involving xenotransplant procedures.
Cincinnati Children's Hospital Data Management and Analysis Center Core Facility
Cincinnati Children's Hospital Data Management and Analysis Center
Centralized resource for clinical research data management, programming for clinical research databases, and statistical analysis.
Cincinnati Children's Hospital Cardiovascular Imaging Core Facility
Cardiovascular Imaging Core Research Laboratory
Cincinnati Children's Hospital Cardiovascular Imaging Core Research Laboratory
Offers imaging techniques using imaging and measurement tools. Offers consulting services ranging from educational seminars to assistance with grant and industry funding support.
Cincinnati Children's Hospital Cell Manipulation Laboratory Core Facility
Cincinnati Children's Hospital Cell Manipulation Laboratory
Supports development, scale -up and processing of innovative cell based therapies for clinical studies.
Cincinnati Children's Hospital Confocal Imaging Core Facility
Cincinnati Children's Hospital Confocal Imaging Core
Provides Cincinnati Children s Hospital Medical Center; Cincinnati; Ohio resources in confocal, wide-field, and spatial technique applications.
Cincinnati Children's Hospital Critical Care Media Lab Core Facility
Cincinnati Children's Hospital Critical Care Media Lab
Develops high quality video and animation to enhance medical education.
Cincinnati Children's Hospital DNA Sequencing and Genotyping Core Facility
Cincinnati Children's Hospital DNA Sequencing and Genotyping
Supports production and analysis of DNA and RNA related data. Provides DNA and RNA sequencing, Next Generation sequencing, DNA extraction and high and low throughput SNP genotyping.
Cincinnati Children's Hospital Imaging Research Center Core Facility
Cincinnati Children's Hospital Imaging Research Center
Provides access to advanced analytical imaging and image post-processing methods for collaborators involved in basic and clinical research.
Cincinnati Children's Hospital Discover Together Biobank Core Facility
Cincinnati Children's Hospital Discover Together Biobank Core
Provides access to services for standardized and centralized acquisition, processing, storage and distribution of biospecimens for research.
Cincinnati Children's Hospital Office for Clinical and Translational Research Core Facility
Cincinnati Children's Hospital Office for Clinical and Translational Resarch
Office for Clinical and Translational Reearch
Clinical research support center for investigators and industry sponsors.Provides support services, research tools, experienced research personnel, and facilities to conduct or facilitate pediatric and adult clinical research from identification and development of research opportunities to phase I through phase IV clinical research trials.
Cincinnati Children's Hospital Pluripotent Stem Cell Core Facility
Cincinnati Children's Hospital Pluripotent Stem Cell Facility
Supports all aspects of human pluripotent stem cell research, providing access to well characterized human embryonic stem cells and induced pluripotent stem cells for distribution to researchers. Consists of tissue culture facilities, access to microscopy and histology equipment, as well as equipment for cellular and molecular analysis of hESCs.
Cincinnati Children's Hospital Research Flow Cytometry Core Facility
Cincinnati Children's Hospital Research Flow Cytometry Core
Shared resource lab for flow cytometry instrumentation, training, education and analyte measurement (ELISA, Luminex, IsoLight). New users need to be trained for their instrument of choice.
Cincinnati Children's Hospital NMR based Metabolomics Core Facility
Provides all NMR related metabolomics services on human and animal cells, biopsies and body fluids.
Cincinnati Children's Hospital Pathology Research Core Facility
Cincinnati Children's Hospital Pathology Research Core
Provides technical support for routine morphology based techniques. Pathologists are on hand to help guide projects, interpret results and collaborate on publications. Core personnel provide technical support for routine morphology based techniques including tissue processing and embedding, routine and special histochemical staining, immunohistochemistry, in situ hybridization, and electron microscopy.
Cincinnati Children's Hospital Mass Spectrometry Core Facility
Cincinnati Children's Hospital Mass Spectrometry
Provides analytical resource focusing on application of mass spectrometry and allied chromatographies to analysis of small molecules, generally of less than 1,000 daltons molecular weight, in complex clinical and biological samples.
Cincinnati Children's Hospital Vector Production Core Facility
Cincinnati Children's Hospital Vector Production Facility
Facility manufactures lentiviral and retroviral vectors in support of early phase clinical trials.Services include large scale GMP lentiviral and retroviral vector and small to mid scale GMP like manufactured products. Supports certification and stability studies.
Cincinnati Children's Hospital Translational Trial Development and Support Laboratory Core Facility
Cincinnati Children's Hospital Translational Trial Development and Support Laboratory
Translational Trials and Development Lab
Provides facilities and expertise to support clinical assay development from technology developed in academic laboratories.Provides assay development and testing support for early phase clinical trials with focus on cell and gene therapy.
Cincinnati Children's Hospital Viral Vector Core Facility
Cincinnati Children's Hospital Viral Vector Core
Provides research grade retroviral, lentiviral and adeno associated virus vectors. Offers generation of stable producer lines, and non-GMP quality control testing including vector titer by functional assay FACS or PCR, endotoxin, mycoplasma, and USP sterility testing.Provides standard packaging plasmids, the investigator provides the viral vector to be used for the production run.
Cincinnati Children's Hospital Transgenic Animal and Genome Editing Core Facility
Cincinnati Children's Hospital Transgenic Animal and Genome Editing Core
Transgenic Animal and Genome Editing Core
Offers comprehensive CRISPR services to generate gene edited rodents and cells, and helps generate transgenic and chimeric mice via our microinjection service, cryopreserving unique mouse lines, and recovering them from liquid nitrogen storage via IVF and embryo transfer services.
Cincinnati Children's Hospital Medical Center; Cincinnati; Ohio
Nonprofit academic medical center established in 1883. One of the oldest and most distinguished pediatric hospitals in the United States. Affiliated with the University of Cincinnati Academic Health Center.
Software tool used to control Plexon pattern generator for optogenetic stimulation.
Sparse Inverse Covariance Estimation for Ecological Association Inference
Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets.
Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases.
Cincinnati Children's Hospital Magnetoencephalography Core Facility
Core facilitates study of normal and pathologic brain processes using magnetoencephalography.The purpose of the core is to make magnetoencephalography available to researchers across the institute.
Cincinnati Children's Hospital Microbial Metagenomics Analysis Center Microbial Genomics and Metagenomics Core Facility
Cincinnati Children's Hospital Microbial Metagenomics Analysis Center Microbial Genomics and Metagenomics Laboratory
Microbial Genomics and Metagenomics Laboratory
Provides solutions in areas of study design, bioinformatic processing of amplicon and shotgun metagenomic sequencing data, integration of metagenomic and clinical data structures, and statistical analyses of microbial community samples. MMAC works closely with Microbial Genomics and Metagenomics Laboratory to streamline workflows for metagenomic sequencing, bioinformatic processing, and statistical analysis of microbiome projects.
Cincinnati Children's Hospital Investigational Pharmacy Core Facility
Cincinnati Children's Hospital Investigational Pharmacy
Our Investigational Pharmacy team is responsible for dispensing both inpatient and outpatient investigational medication for industry-sponsored, grant-funded and investigator-initiated protocols. We provide pharmacy services customized to each research protocol conducted at Cincinnati Children�s.
Oregon Health and Science University Integrated Genomics Laboratory Core Facility
Oregon Health and Science University Integrated Genomics Laboratory
Lab houses three cores providing support and services from nucleic acid isolation through data generation on multiple genomic and molecular analysis platforms. Nucleic acid extraction, qPCR, and Nanostring profiling services are available through the Gene Profiling Shared Resource for gene expression profiling, microRNA profiling, DNA genotyping and copy number analysis, and DNA methylation analyses. Currently running QuantStudio real-time PCR system. Comprehensive RNA and DNA extraction and quality assessment services available. Massively parallel sequencing (NGS) services, including library preparation, are available through Massively Parallel Sequencing Shared Resource on Illumina NovaSeq 6000 and NextSeq platforms. 10x Genomics single-cell and single-nuclei analysis services available. Cell line authentication, DNA plating, and custom oligo services are available through DNA Services Core.
Cincinnati Children's Hospital Single Cell Genomics Core Facility
Cincinnati Children's Hospital Single Cell Genomics Core
Core to perform expression level analysis of thousands of genes in parallel.Uses RNA-Seq assays from Tecan Genomics, Takara and Illumina for samples with limited amounts of starting RNA. Microarray technology utilizing the Affymetrix GeneChip platform is also available.
Software tool for nutrition calculations and surveys.
The Bauer Core Facility at Harvard University
Helps to advance research efforts in life sciences that cannot readily be accomplished in the traditional academic laboratory because of need for expensive instrumentation or automation, scientific or organizational infrastructure, or multidisciplinary expertise. Provides expertise and hands-on training and use of instrumentation for nominal fee. Researchers can sign up to use instrumentation through on-line scheduling system and conduct their experiments independently.
Pressure Application Module (NPI Electronic)
Pneumatic drug ejection. Used to apply ionic and non-ionic substances in small amounts. Locally precise application with microJECT pipette holder with built-in valve. Also available as 19″ stand alone device.
Automated, high performance PCR/qPCR system that uses microfluidics technology to process samples at nanoliter scale volumes for gene expression, genotyping, sample identification, copy number variation analysis and digital PCR. With wide range of integrated fluidic circuit (IFC) formats available, scaling from mid to high throughput on single system.
University of Witwatersrand South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit
South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit
African led research unit in field of epidemiology of vaccine preventable diseases, and clinical development of life saving vaccines. Conducts translational research that informs local and global policy recommendations on infectious diseases and use of next generation and novel vaccines. Collaborates with core facilities on various trials and studies.
WPI | Constant Current Stimulus Isolator
Automated bipolar pulsing for zero net charge on biological preparations. Includes Constant current, Unipolar and bipolar stimulation modes, Built-in non-compliance alarm, Optically isolated input Standard TTL triggering, DC test mode. Powered by 9 V alkaline or rechargeable batteries.
Australia’s largest child health research centre.Research health conditions include diabetes, allergies, asthma, premature birth and mental health problems,cancer and genetic disorders. Located in Royal Children’s Hospital in Melbourne.
National Institute for Communicable Diseases; South Africa
NICD The National Institute for Communicable Diseases
National public health institute for South Africa, providing disease surveillance, specialised diagnostic services, outbreak response, public health research and capacity building to support the government’s response to communicable disease threats.
Web tool as oligonucleotide properties calculator. Computational engine for reporting DNA and RNA single stranded and double stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter molecular self complementarity estimation and intra molecular hairpin loop formation.
Python Fluorescence Decay After Photoconversion
Software tool as automated analysis of fluorescence decay after photoconversion (FDAP) experiments.
Python Fluorescence Recovery After Photobleaching
Software Python package for FRAP analysis. Simulation based analysis software that makes use of PDE simulations to analyze FRAP experiments in 3D geometries. Used to assess molecular diffusion.
System for total nucleic acid extraction from variety of sample types and volumes. System automates enhanced magnetic silica version of bioMérieux’s proprietary BOOM technology gold standard for universal extraction of RNA and DNA.Clinical use includes nucleic acid extraction in front of molecular infectious disease assays, molecular oncology assays, molecular genetics assays.
Portal to find all informations about epidemiology regarding public and suplementary health in Brazil.
University of Texas Health Science Center at San Antonio Mass Spectrometry Core Facility
University of Texas Health Science Center at San Antonio Mass Spectrometry Institutional Core Laboratory
University of Texas Health Science Center at San Antonio UTHSCSA Mass Spectrometry Laboratory
Mass Spectrometry for protein and small molecule analyses. Services cover full range from sample preparation through data processing and interpretation. Analyses include molecular mass determination, protein identification, protein relative quantification, localization of covalent protein modification and targeted quantitative metabolomics.Uses iLab.
Platform for helping science researchers by recommending gene symbol obtained by AI neural proprietary network able to scan millions of papers. Web tool to extract hidden patterns and correlations among genes and diseases from scientific papers.
Statistical software package from Stat-Ease Inc. to perform design of experiments. Offers comparative tests, screening, characterization, optimization, robust parameter design, mixture designs and combined designs.
Software pharmacokinetic tool. Used to calculate pharmacokinetic parameters, fit curves, calculate AV models, and conduct pharmaceutical statistics, including dissolution analysis, slice weight difference analysis, acceleration test.
System for small animal pulmonary function. Used for in vivo respiratory mechanics measurements. Goes beyond traditional resistance and compliance mechanics of pulmonary ventilation, and captures details about mechanical properties of conducting airways, terminal airways and parenchyma. Achieves sensitivity and reproducibility by precisely controlling experimental conditions.
BD Biosciences | FACSymphony A5 SE Cell Analyzer
Flow cytometer gains full visible spectrum coverage to collect all light emitted without need for filter changes, increasing dye flexibility and number of simultaneous colors. Uses unmix spectral data live in BD FACSDiva Software while retaining familiar compensation workflow. May improve resolution of difficult cells and populations using autofluorescence unmixing.
Software R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
Eagle Atlas Compilation for Vestibular Research
Collection of 1mm isotropic atlases for vestibular MRI research consisting of ROIs from Eickhoff et al. and Indovina et al., Brainnetome Atlas, Diedrichsen/SUIT Cerebellar Atlas, Najdenovska Thalamic Atlas, brainstem and diencephalon ROIs from Brainstem Navigator, and Neudorfer Anatomical Hypothalamus Atlas.
Software R package for taxonomic information from around web. Interacts with suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.
Software R package for exploratory data analysis and data visualization for biological sequence, DNA and protein, data.
Software R package to flexible rearrange, reshape and aggregate data. Reshape2 is reboot of reshape package.
Source code for paper "Disease classification for whole blood DNA methylation: meta-analysis, missing values imputation, and XAI" by A. Kalyakulina, I. Yusipov, M.G. Bacalini, C. Franceschi, M. Vedunova, M. Ivanchenko.
Northeastern University Institute for Chemical Imaging of Living Systems Core Facility
Northeastern University NU-Institute for Chemical Imaging of Living Systems Core Facility
NU-Institute for Chemical Imaging of Living Systems
Located in ISEC research center and includes advanced imaging instruments. CILS has three core facilities: Microscopy Core (confocal/multi-photon/lightsheet microscopes), Flow Cytometry Core (cell analyzer/sorter) and Preclinical Imaging Core (3T small animal MRI and ultrasound).
Wayne State University School of Medicine Lipidomics Core Facility
Wayne State University Lipidomics Core Facility
Conducts comprehensive analysis of cellular lipids that encompass fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, and prenol lipids.
University of Nebraska Medical Center Echocardiography Imaging Core Facility
University of Nebraska Medical Center Echo Facility
University of Nebraska Medical Center Echocardiography Imaging Facility
Preclinical ultrasound imaging. Provided instruments include Vevo 3100, Vevo 3100 LAZR-X, Perkin Elmer Vega.
Drexel University Materials Characterization Core Facility
Drexel University Materials Characterization Core
Facility provides technical expertise and instrumentation including nanoscience and engineering, polymer research, biomedical engineering, and chemistry and physics of solid materials.Houses electron microscopes, X-ray diffractometers, X-ray photoelectron spectrometer and suite of sample preparation tools. Staff members provide expert consultation, training and assistance to MCC users. Core is involved in teaching both undergraduate and graduate level courses in Materials Science and Engineering, Mechanical Engineering and Mechanics, Biomedical Engineering, and Biology. Trained and certified users are welcome to work independently on our instruments.
Van Andel Institute Flow Cytometry Core Facility
Van Andel Institute VAI Flow Cytometry Core Facility
Core provides cell analysis and sorting services. Instruments include Cytek Aurora, Beckman Coulter CytoFLEX S, Thermo Fisher Attune CytPix, SONY MA900, and BD FACSSymphony S6.
Structural equation modeling software helping support your research and theories by extending standard multivariate analysis methods, including regression, factor analysis, correlation and analysis of variance.
Purdue University Electron Microscopy Core Facility
Purdue University Life Science Microscopy Facility
Purdue University West Lafayette Purdue Electron Microscopy Facility
Provides Purdue researchers access to electron microscopy instrumentation including scanning electron microscopes, small dual beams and transmission electron microscopes. Expert staff scientists help with training and project support.
University of Texas at Austin Computational Biology and Bioinformatics Core Facility
Provides support for students, postdoctoral fellows, and faculty interested in the use of computational approaches to solving biological problems. Our goal is to lower as much as possible the threshold to enter the -omics area of the life sciences.
Drexel University Cell Imaging Center Core Facility
Facility housed in purpose built imaging suites in Papadakis Integrated Sciences Building and in Bossone Research Center. Serves light microscopy needs of Drexel researchers and supports teaching missions of Biology and Biomedical Engineering curricula and provides service to users from local biotech companies.Provides facility, expertise, and education in advanced quantitative light microscopy.
Howard Hughes Medical Institute at Janelia Research Campus Flow Cytometry Shared Resource Core Facility
Howard Hughes Medical Institute at Janelia Research Campus Flow Cytometry Shared Resource
Provides range of instrumentation and expertise for cell sorting and analysis that can support experimental needs related to single cells, cell line production, biosensor development, and dye analysis. Offers expertise in flow cytometry experimental design, operation of instruments, distribution of raw data and sort reports, interpretation of results, and preparation of graphics for presentation and publication.
Texas A and M University Center for Educational Technologies Core Facility
TAMU-The Center for Educational Technologies
Texas A&M University TAMU-The Center for Educational Technologies
Offers services to researchers looking for collaborators or contractors for their educational or training projects.Offers development tools and hosting services to educators creating their own online training resources.
Invitrogen™ Celleste™ 5.0 Image Analysis Software
Image analysis software for florescence microscopy.
Web tool for prediction of drug combination effects in cancer using different synergy metrics and ensemble learning. Allows user to input two drugs, in form of two distinct SMILE files and attain prediction of their synergistic effects on specific cancer cell lines.
Howard Hughes Medical Institute at Janelia Research Campus Quantitative Genomics Core Facility
Howard Hughes Medical Institute at Janelia Research Campus Quantitative Genomics
Provides services to anything related to genomic analysis, such as RNAseq, genome sequencing, ATACseq etc, from experiment design all the way down to data analysis.Provides expert services for cell isolation, transcriptome and epigenetic profiling, and de novo genome assembly using next generation sequencing platforms from Illumina.
Open source, docker based, and GPU enabled jupyterlab notebook infrastructure that runs on public compute infrastructure of Galaxy Europe for rapid prototyping and developing end-to-end AI projects. Jupyterlab notebook in GPU enabled docker container for machine learning and deep learning.
University of Vermont Larner College of Medicine Advanced Genome Technologies Massively Parallel Sequencing Core Facility
Advanced Genome Technologies Core Massively Parallel Sequencing Facility
University of Vermont Advanced Genome Technologies Core Massively Parallel Sequencing Facility
Provides support for design, execution, and analysis of experiments involving Next Generation Sequencing through access and use of Illumina HiSeq 1500. Sequencer performs wide range of analysis including target preparation for RNAseq, Exome Seq, ChIP seq, Methyl Seq, whole genome sequencing, and small RNA sequencing.Core is involved in all aspects of Nanopore sequencing.
Software tool as flexible, probablistic metrics for quality control of scRNA-seq data. Adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. Data driven QC metric that jointly models proportion of reads mapping to mtDNA and number of detected genes with mixture models in probabilistic framework to predict which cells are low quality in given dataset.
Cross platform software for advanced meta analysis.
University of Zagreb School of Medicine; Zagreb; Croatia
Public croatian university and the oldest continuously operating university in the area covering Central Europe south of Vienna and all of Southeastern Europe.
Software package for detection and handling of doublets/multiplets in single cell sequencing data.
University of Zagreb School of Medicine Laboratory for Regenerative Neuroscience Core Facility
UZSM - Laboratory for Regenerative Neuroscience / GlowLab
Multimodal preclinical in vivo imaging facility for small laboratory animals such as mice and rats. Expertise is in brain research, however it is possible to provide imaging services on any part of or on animal.Instruments include magnetic resonance imager (Bruker BioSpec 70/20 USR) and optical bioluminescence/fluorescence imager (Perkin Elmer IVIS Spectrum), fully equipped with anesthesia delivery and physiological monitoring/control system.Imaging unit is complemented by cell culture laboratory and small animal surgery room, allowing to set up and perform entire experimental protocols as needed. Provides longitudinal imaging services owing to animal housing unit within same space, equipped with individually ventilated cages for both rats and mice (Tecniplast Green line and Emmerald line). Home cage monitoring is also possible for mice as an additional service with our Tecniplast DVC cages.
University of North Carolina at Chapel Hill Functional Genomics Core Facility
University of North Carolina at Chapel Hill Functional Genomics Core
University of North Carolina at Chapel Hill UNC-Functional Genomics Core
Core performs expression profiling, SNP genotyping and copy number microarray (Thermo Fisher) services.
University of North Carolina at Chapel Hill Systems Genetics Core Facility
University of North Carolina at Chapel Hill UNC- Systems Genetics Core Facility
Provides access to multi parental genetic reference mouse population derived from eight founder inbred strains, encompassing genetic diversity. Strains have been sequenced and have much genomic data. All of CC strains are kept as live mouse strains. Provides breeding stock for internal use unless other permission is acquired, or experimental cohorts.
Provides customized display systems used in neuroscientific studies in insects and other small animals. System includes custom built modular LED panels and software. LED panels of various sizes can be arranged/grouped in different shapes for diverse setups. System provides millisecond refresh, precise synchronization, customizable color combinations, and varied display configurations and addresses most technical challenges of small animal vision experiments and is thoroughly documented for replicability.
EBSCO Dentistry and Oral Sciences Source
Full text research database for dental practitioners and researchers. Offers top dental and oral sciences journals commonly purchased by dental schools and related institutions.
Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database.
Database indexes top nursing and allied health literature available including nursing journals and publications from the National League for Nursing and the American Nurses Association.
Chemotaxis and Migration Tool version 2.0
Software tool for data analysis from time stack chemotaxis experiments. Based on NIH ImageJ image processing system.
Hierarchical Data Modeling Framework-Zarr
Software hdmf-zarr library implements Zarr backend for Hierarchical Data Modeling Framework as well as convenience classes for integration of Zarr with PyNWB to support writing of NWB files to Zarr. Library is intended to be used in conjunction with Hierarchical Data Modeling Framework.
Software tool to support RepeatMasker searches by adding necessary features to stock NCBI blastn program. RepeatMasker compatible version of standard NCBI blastn program.
Contextual Ontology based Repository Analysis Library
Software tool as framework for rigorous self validated data modeling and integrative, reproducible data analysis.
Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse.
Software R package for multivariate microbiome analysis. Statistical methods for analysing multivariate abundance data.
California Institute of Technology Water and Environment Laboratory Core Facility
California Institute of Technology Caltech Water and Environment Laboratory
Caltech Water and Environment Laboratory
Provides access to chromatography and mass spectrometry techniques including GC and GC-MS, IC and IC-MS, ICP-MS, LC and LC-MS, and other environmentally relevent techniques such as isotope ratio measurements of water, TIC/TOC, and laser diffraction particle size analysis.
University of Pennsylvania Electronic Phenotyping Resource Core Facility
University of Pennsylvania Electronic Phenotyping Resource
Shared resource dedicated to unlocking power of electronic health records for clinical and translational research in cancer care. Electronic phenotyping involves querying electronic health record systems and other clinical information systems and databases to identify patients who meet specific set of clinical characteristics. Can be used to support clinical and translational research pursuits, such as hypothesis generation, retrospective data gathering and hypothesis testing, research planning and grant preparation, subject recruitment for prospective clinical trials, and development of prospective research registries. Provides consultative and technical services.
University of North Carolina at Chapel Hill Mammalian Genotyping Core Facility
University of North Carolina at Chapel Hill Mammalian Genotyping Core
Core is component of Integrated Genomics Core/High Throughput Sequencing Facility. Supports population, basic, clinical and translational research by providing centralized cost efficient, high quality genotyping and methylation services using Illumina BeadArray and Infinium microarray assay technologies for Single Nucleotide Polymorphism Genotyping, Copy Number Variant, Loss of Heterozygosity, Insertions Deletion (indel), Structural Variant, and DNA Methylation Analysis. Can assist with selecting appropriate arrays to meet your needs.
GDSC Single Molecule Localisation Microscopy
Open source Java based software designed for single molecule localisation microscopy. Software can be used as stand alone library or as plugins for ImageJ image processing software.
University of Warsaw Center of New Technologies Genomics Core Facility
Core is dedicated to analysis of RNA and DNA sequence, structure and interactions in biological and biochemical processes.Specializes in Genomics, Metagenomics, Transcriptomics, Epigenomics, Interactomics, Oncogenomics, Structural Genomics and other fields. Equippment includes NovaSeq 6000, NextSeq 500 and MiSeq next generation sequencing systems and instruments for fractionation, quality and quantity assessment. Services include consultation and assistance, preparation of libraries from DNA (WGS, WES, Amp-seq, ATAC-Seq, ChIP-seq etc.) and RNA (different fractions: mRNA-seq, mRNA-seq, total RNA-seq, miRNA-seq, RIP-seq etc.), sequence custom libraries and conduct bioinformatic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data.
Fred Hutchinson Cancer Center Leica Center of Excellence Core Facility
Fred Hutch Leica Center of Excellence Core Facility
Leica Microsystems and Fred Hutch established Leica Center of Excellence in Pacific Northwest to provide researchers with advanced microscopy technologies, support generating scientific discoveries and developing new approaches to preventing and treating cancer and related diseases.
University of Massachusetts Medical School Sanderson Center for Optical Experimentation Core Facility
University of Massachusetts Medical School UMass Chan - SCOPE
Offers tools and expertise for quantitative microscopy techniques including super resolution imaging, multi photon intravital and live tissue imaging, confocal microscopy, and high speed time lapse imaging.Offers commercial and custom built microscopes, training and access to light microscopes, imaging services including whole slide scanning, MERFISH spatial transcriptomics, NanoString GeoMx DSP services, and image analysis support. Wet lab facilities, including cell culture, are also available at this BL2 facility. Imaging at BSL3 is available upon request.Offers remote imaging and data analysis sessions, including remote control of all instruments and workstations. All users are trained individually prior to use of the SCOPE equipment and workstations.
Open source platform for synchronizing multiple behavioral and physiological signals in neuroscience experiments.
Joint Acquisition, Recording and Voxel based Inference System
Software markerless 3D motion capture toolbox. Used for capturing precise 3D motion.
Mayo Clinic Immune Monitoring Core Facility
Provided services include Designing assays to identify and quantify immune cell subpopulations; Characterizing and measuring immune function; Monitoring immunological changes in response to both specific and nonspecific stimulation; Mass Cytometry (CyTOF, Helios); Imaging Mass Cytometry (IMC, Hyperion). Supports experimental systems to study human and mouse models by providing expertise and standardized assays to evaluate immune functions in broad range of diseases and therapies in models as well as in healthy human subjects with variable demographics.Provides services to all Mayo Clinic faculty and staff engaged in research. Selective services are available to investigators outside Mayo Clinic.
Fred Hutchinson Cancer Center Therapeutic Products Core Facility
Provides facilities and services in process development and manufacturing of Good Manufacturing Practice grade biologic and cellular therapeutic products for Phase 1/2 clinical trials. Supports the translation of ideas from academic laboratories to clinical trials.
University of Montreal CRCHUM Cell Imaging Core Facility
Optical and fluorescence microscopy facility. Provided instruments include range of microscopes from regular brightfield microscopes to high performence LSM900- Airyscan confocal microscope. Provides Image Analysis with Imaris Full Spectrum and ClearDeconvolution software.
Software toolkit for de novo discovery of microRNAs from sRNA-seq data. Used for miRNA discovery.
Purdue University West Lafayette Metabolite Profiling Core Facility
Purdue University Metabolite Profiling Facility
Purdue University West Lafayette Metabolite Profiling Facility
Provides technologies that enable both qualitative (defining all components of metabolome) and quantitative (determining differential concentrations of metabolites) metabolomics in complex biological systems.Provides sensitive mass spectrometry coupled with liquid chromatography and gas chromatography for precise sample analysis. Empowers researchers with new technologies, methods development, sample analysis, expert training, and consultation.
Enhancing Quality In Preclinical Data Quality System
Preclinical research quality system that can be applied in public and private sectors to ensure that early drug development research proceeds along structured lines. Used for ensuring generation of reliable preclinical data. Proposes guidance on expectations for quality related measures, defines criteria for adequate processes like performance standards, and provides examples of how such measures can be developed and implemented. EQIPD certification was established by EQIPD consortium and is now managed by its legacy organisation GoEQIPD.
Software package for predicting interferon stimulated human genes.
Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets.
Manual cryostat designed to accommodate needs of routine clinical laboratory by offering form fitting ergonomic design, with optional height adjustment, vacutome and cold D disinfection.
Web tool for identification of driver nodes between case control association networks.Methodology for understanding driver microbes from healthy and disease microbiome datasets.
Inferring correlations from 16S sequencing data. Capable of estimating correlation values from compositional data.
University of Pittsburgh Center for Research Computing Core Facility
Supports leading edge research with free access to advanced computing hardware and software.
AI powered image analysis software platform for digital pathology and related applications. Enables pathologists and scientist to easily create their own custom AI models to identify, quantify or measure different features and patterns in digitized tissue images.
University of California at San Diego Institute for Genomic Medicine Genomics Center Core Facilitiy
Provides services including sequencing library preparation and sequencing on Illumina MiSeq and NovaSeq 6000 platforms. Supports single cell sequencing on 10X Genomics Chromium Controller. Provides Illumina Infinium Beadchips, which includes variety of whole genome genotyping arrays as well as Infinium MethylationEPIC BeadChip.
Oregon Health and Science University Biostatistics and Design Program Core Facility
Core provides designing studies and developing statistical analysis plans in clinical trials, clinical and community based intervention studies, laboratory experiments, and observational studies.Provides expertise in traditional and modern statistical methods.Can help with trial design and analysis, epidemiologic analysis, sample size and power, high dimensional data analysis, risk prediction, complex survey analysis, time-to-event and longitudinal models, and statistical simulation,data management and wrangling, analytic variable coding and data set creation, research database design, data visualization, manuscript preparation, statistical programming, and much more.
Oregon Health and Science University Small Animal Research Imaging Core Facility
Provides in vivo imaging technology to evaluate anatomy, tissue function, cellular and molecular phenotype, blood/fluid flow, metabolism and to assess pharmacokinetics and stem cell function in small animal models.Offers spatial resolution, temporal resolution, tissue differentiation, sensitivity for contrast agent, and performance of contrast agents. Services include MicroPET/SPECT/CT imaging,Ultra-high frequency small animal ultrasound imaging,Biophotonics imaging.
University of Notre Dame Integrated Imaging Core Facility
NDIIF- Notre Dame Integrated Imaging Facility
Notre Dame Integrated Imaging Facility (NDIIF)
Provides microscopes and imaging stations. Expert staff offers guide to non-expert users. Facility offers imaging expertise in Electron Microscopy, Optical Microscopy, In Vivo Imaging, and Histology.
Oregon Health and Science University Biophysics Core Facility
Core services including ensurance that purified proteins and other biomolecules of interest are uncompromised in terms of their structure and stability. Facilitates analyses of catalytic activities and functional interactions.Examines thermodynamic and kinetic parameters for association between proteins and small molecules.Facilitates hypothesis generation through coalescence of experimental data and computational modeling.Assists in setting up protein crystallization assays.
Oregon Health and Science University Center for Radiochemistry Research Core Facility
Provides access to tools for imaging with short lived radionuclides, data analysis and is integrated with campus centers SARIC and nuclear medicine clinic for quantitative imaging of these tracers in vivo that provides spatial and temporal data in order to improve our basic understanding of biochemical pathways, disease processes and help select personalized treatments that enhance clinical care. Highlights of our center include On-campus capacity to develop and produce radiopharmaceuticals to address specific research questions using in-vivo, real-time imaging;PET/CT, SPECT/CT (and soon PET/MRI) imaging capability to quantify organ perfusion, assess metabolic pathways, receptor function and density, and measure pharmacodynamics.Applications are directed toward range of models, ranging from small animals to non-human primates, to humans.
Oregon Health and Science University Elemental Analysis Core Facility
Provides highly sensitive elemental quantification, including sample preparation, data analysis, and experimental guidance, through Inductively Coupled Plasma Mass Spectrometry (ICP-MS) technology.
Open source acoustic camera system for measuring ultrasound communication in rodents. System includes small phased microphone array combined with camera and comprises USV segmentation algorithms with modification for overlapping vocalizations that results in high accuracy. Enables simpler and faster USV localization and assignment.
Non-redundant RefSeq protein records are currently provided for archaeal and bacterial RefSeq genomes, with exception of selected reference genomes, by NCBI prokaryotic genome annotation pipeline. This scope definition may change in the future to include additional RefSeq sub-kingdoms or other organism groups and some GenBank conceptual translation protein records may provide cross-links to RefSeq non-redundant proteins.
Software package for scalable de novo isoform discovery from single molecule PacBio reads. Contains tools to identify transcripts in PacBio single molecule sequencing data.
Software pipeline for phasing and scaffolding polyploid genomes based on Hi-C data. Hi-C-based scaffolding algorithm that integrates pruning, partition, optimization and building functions to select contigs specific for polyploid genome assembly.
Japanese national university in Toyama Prefecture established in 1949. University of Toyama has three campuses, namely Gofuku, Sugitani, and Takaoka campuses.
Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries.
Software package to generate area proportional Euler diagrams using numerical optimization that display set relationships (intersections, unions, and disjoints) with circles or ellipses. Area Proportional Euler and Venn Diagrams with Ellipses.
Software R package with new, more intuitive visualization of concordant and discordant gene overlap where all regions in RRHO plots are meaningful. Used for identification of statistically significant overlap between gene expression signatures.
Software R package to add markdown helpfiles to shiny apps, using modal dialog boxes, with no need to observe each help button separately.
Software R package to create interactive Shiny based web applications to visualise single cell data via visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, visualising composition of different clusters / groups of cells using proportion plots and visualising expression of multiple genes using bubbleplots / heatmap.Shiny Interactive Web Apps for Single-Cell Data.
Software R package Themes for use with Shiny.
Open source program for ImageJ/Fiji. Automated and multithreaded Sholl for direct analysis of fluorescent images and/or traced morphologies. Features quantifications based on curve fitting. Analysis of profiles obtained by other software is also possible.
American healthcare analytics company established in 2008. Originally textbook marketing company, it came under scrutiny in May 2020 after it had provided large datasets of COVID-19 patients which were subsequently found to be extremely unreliable. The questionable data was used in studies published in The Lancet and The New England Journal of Medicine in May 2020. On 15 June 2020, company website was taken offline.
Network of healthcare organizations, together with data partners in Brazil, South Korea, and Japan, to bring clinical facts on more than 250 million patients around the world. Federated model so users of this data are ensured new patients, observations, and results every day, all harmonized to standard terminology like ICD-10 and LOINC without any data wrangling required at the point of care. The raw data is not available to authors of papers and papers in medicine are being retracted.
Yale University Open Data Access Project
Project to promote and facilitate sharing of clinical trial data. Provides set of policies to set standards to enhance data availability and transparency in support of strong scientific research which aims to advance scientific and medical knowledge with goal of improving public health and healthcare delivery. Project has the final decision making rights regarding these policies and granting or denial of data requests, as per contractual agreements between the YODA Project and its partners.
Software R script for identifying x controls within t distance of each case based on weighted PCA data.
Platform for individuals who want to make their own data available for research. Used by people to join network with others who wish to contribute to vital research in partnership with and alongside leading scientists. Personal tool for saving and displaying medical information.
Core provides access to light microscope systems to perform widefield, confocal, 2-photon/multiphoton, second harmonic generation, total internal reflection (TIRF), and high content imaging.
Multi dimensional image viewer for Python. Used for browsing, annotating, and analyzing large multi dimensional images. Can be coupled to machine learning and image analysis tools enabling more user friendly automated analysis.
Systems biology platform for integrating, mining and analyzing microbiome experiments.Data discovery and analysis web based resource that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. Used to mine complex microbiome and metagenome studies.
Software tool as framework for adaptive optics data analysis. Object oriented framework for organizing data, metadata and code related to adaptive optics experiment.
Software package to improve studying tumour microenvironment with single cell sequencing. Developers may use this package to obtain data for validation of new algorithms and researchers interested in tumour microenvironment may use it to study specific cancers more closely. Curated collection of scRNAseq datasets sequenced from tumours.
Software package to improve the ease of studying and integrating scATAC-seq datasets. Developers may use this package to obtain data for analysis of multiple tissues, diseases, cell types, or developmental stages. It can also be used to obtain data for validation of new algorithms.
Software tool for image quality. Used for labeling quality of images and labeling center point of 3D RI images. Used to mange 3D RI cell images taken from holotomography.
Software tool as metagenome assembler that exploits high accuracy of recent data. De novo metagenome assembler, based on haplotype resolved de novo assembler for PacBio Hifi reads. Workflow consists of optional read selection, sequencing error correction, read overlapping, string graph construction and graph cleaning.
Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies.
Software tool as naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus, with confidence estimates for each assignment.
Software viral contig verification tool. Classifies contigs as viral, non-viral or uncertain, based on gene content. Also for non-viral contigs it can optionally provide plasmid/non-plasmid classification.
Software tool for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing or metatranscriptomics experiments.
Histological E data Registration in rodent Brain Spaces
Open source, extendable, intuitive and interactive software platform for image visualisation and image registration. Python based GUI for histological E-data registration in brain space.
Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts.
Web tool for interactive visualization and analysis of diversity of genomic variants. Used for interactive exploration and analysis of very large SNP matrices based on VCF files.
MDC and BIH Technology Platform Genomics Core Facility
Facility comprises Next Generation Sequencing, Single Cell Technologies and Data Management teams. Offers professional project counseling, library preparation, and sequence production support for Max Delbruck Center for Molecular Medicine and Berlin Institute of Health at Charite institutes in Berlin.
A software to display, record and data processing of physiological signals. DataLyser is custom-built software developed at Walter Reed Army Institute of Research, Silver Spring, MD. It is not copyrighted.
Supervised ensemble machine learning classifier. Classification performance benchmark scripts.
Open index of scholarly works, authors, venues, institutions, and concepts. Catalog of scholarly papers, researchers, journals, and institutions along with all the ways they are connected to one another.
National Cancer Institute of Mexico Advanced Microscopy Applications Unit Core Facility
Advanced Microscopy Applications Unit (ADMiRA)
National Cancer Institute of Mexico Research Support Network Advanced Microscopy Applications Unit
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 26,2025. Imaging Core Facility located within National Cancer Institute of Mexico. Provides scientific and technical support in imaging and image analysis to any community. Imaging technologies in ADMiRA include: Confocal, Widefield, Super-Resolution, Lightsheet, FIB-SEM, Laser Microdisection, and Automated digital scanning.
University of California at Los Angeles California NanoSystems Institute Advanced Light Microscopy and Spectroscopy Core Facility
Advanced Light Microscopy & Spectroscopy Core
UCLA CNSI Advanced Light Microscopy & Spectroscopy Core
Offers microscopy services, consultation, and support for application of novel microscopic and spectroscopic methods and advanced image analysis techniques for study of macromolecules, cellular dynamics and nano-scale characterization of bio-materials. Provides collection of customized biological fluorescence microscopes and small-animal imaging devices to study biological processes with high spatial and temporal resolution in whole organisms and in living cells down to single molecule detection level with nanometer accuracy. Located in basement and second floor of CNSI building, two optical suites designed to house microscopes with the required environment control (low vibration, air-filtered, air-conditioned and light-tight) and services. Services include Wide-field Fluorescence Imaging Microscopy (on a limited basis), Confocal One-Photon and Two-Photon Laser Scanning Microscopy, (both point scanning and spinning disk), Fluorescence Correlation Spectroscopy (FCS), Fluorescence Resonance Energy Transfer (FRET), microscopic and macroscopic Fluorescence Lifetime Imaging (FLIM) with Time-Correlated-Single-Photon-Counting (TCSPC) and Near-Infrared (NIR) Detection, Stimulated Emission Depletion laser-scanning microscopy (STED) (a super-resolution technique), both microscopic and macroscopic (small animal) spectral unmixing and laser capture microdissection.
British Columbia Children's Hospital Research Institute Flow Cytometry Core Facility
Core provides equipment for flow cytometric analysis, full service cell sorting, training, and dissemination.
Software package provides cross modality image registration pipeline to support whole brain mapping projects. Contains three modules: (1) image preprocessing and global registration, (2) Coherent Landmark Mapping (CLM) based automatic registration, and (3) optional semi-automatic refinement.
Allen Brain Map Cell Type Knowledge Explorer
Software to examine multimodal data from thousands of cells across 3 mammalian species.
Provides molecular and anatomical foundational framework for study of brain function and disorders.Comprehensive Center on Human and Non-Human Primate Brain Cell Atlases with goal to build reference brain cell atlases that will be used throughout research community.
Software automated, terascale, cloud based image analysis pipeline for preprocessing and cross modal, nonlinear registration between volumetric datasets with artifacts. Automatic terabyte scale cross modal brain volume registration.
Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data.
Centralized, community driven platform for creation, exploration, and storage of cell annotations for single cell RNA sequencing datasets.
Software algorithm for integrating multiple high dimensional datasets. Port of harmony R package.
Pennsylvania State University Hershey College of Medicine Custom Antibody Core Facility
Penn State College of Medicine PSU-COM Antibody Core
Penn State Hershey College of Medicine Custom Antibody Core
Penn State Hershey College of Medicine Custom Antibody Core Facility
Provides service for production and purification of custom antibodies.Primary services include immunization of mice and rabbits to make mouse and rabbit monoclonal antibodies to select targets. Primary screening of hybridomas will be conducted using standard ELISA technology and positive lines will be preserved for cloning. Supernatants containing antibody selected as positive will be made available to investigators for secondary analyses in their labs (Westerns, immunofluorescence, functional assays). Investigator selected lines will be cloned, isotyped, and adapted to serum free culture for future production of high titer antibody if investigator requires large quantities of antibody. Standard purifications will be conducted as needed, and various modifications (fluorochrome, enzyme, biotin) are also provided as Antibody Core services.
Software package for prediction of protein backbone and sidechain torsion angles from NMR chemical shifts.
Command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
Software R package to work with sequence motifs in analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of obtained results are also provided.
single cell graph linked unified embedding
Software Python package implemented Graph Linked Unified Embedding framework for single-cell multi-omics data integration.
Software Python framework designed to work with multimodal omics data. Aims to provide convenience and speed to its users enabling standardised analysis while staying flexible and expandable. Muon stands on shoulders of and integrates with annotated data object specification and scanpy library for single cell analysis in Python.
Software R package for similarity and distance quantification between probability functions. Information Theory and Distance Quantification with R. Provides framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.
Software Python tool for approximate nearest neighbors. Provides Python implementation of Nearest Neighbor Descent for k-neighbor-graph construction and approximate nearest neighbor search.
Software to identify each cell’s top neighbours in each batch separately instead of entire cell pool with no accounting for batch. Nearest neighbours for each batch are then merged to create final list of neighbours for cell. Aligns batches in a quick and lightweight manner.
Project to help to end opioid addiction. Addiction Long-term Initiative or NIH HEAL Initiative, to speed scientific solutions to stem national opioid public health crisis. Initiative is funding hundreds of projects nationwide. Researchers are taking variety of approaches to tackle opioid epidemic through understanding, managing, and treating pain, and also through improving prevention and treatment for opioid misuse and addiction.
Software for Berthold ORION II (LB 965) microplate luminometers.
Software R package to correct systematic errors in nanopore sequencing reads of gene libraries. Retrieves true consensus sequences of variants identified by barcode, needing only few reads per variant.
Simple PC application for present audio/visual stimuli for fmri paradigms.
Software R package for bindings to liblwgeom library.
Software package to provide set of functions designed to make working with strings easy. Consistent wrappers for common string operations.
Allen Brain Map BRAIN Initiative Cell Census Network Data Catalog
BRAIN Initiative Cell Census Network Data Catalog
BRAIN Initiative Cell Census Network data catalog. Provides access to all major data sets of the BICCN with descriptions.
Highly segmented anatomical labels in the adult mouse brain common coordinate framework.
Labels provide resource to isolate and identify mouse brain anatomical structures. Cell type specific transgenic mice and an MRI atlas were used to adjust and further segment the labels. Highly segmented anatomical labels in the adult mouse brain common coordinate framework.
Software package to streamline workflow of imaging data management, visualization, reconstruction and collaboration, and data sharing.
EBRAINS service for image registration. Spatially register mouse and rat serial 2D brain images to 3D reference atlases.
Software cross platform mobile application that supports 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, and distributed collaboration.
Software Python package for reading and writing of image data in Neuroglancer precomputed format. Used to read and write Neuroglancer datasets programmatically.
Platform to search neurons of interest by neuron anatomy, morphology, and connectivity patterns. Used to Explore morphology and connectivity features of neurons of interest, Upload neuron (swc file or eswc file) and calculate morphology features, Search similar neurons, Explore 3D visualization of neurons, Explore cross species atlas. Open source pan-neuron table of morphology and connectivity.
Repository for co-ordinating work on ontologies for Brain Data Standards Project. Automate data driven cell type ontology development for Brain Data Standards initiative.
Joint computational research center with Carnegie Mellon University and University of Pittsburgh. Provides university, government and industrial researchers with access to several systems for high performance computing, communications and data storage available to scientists and engineers nationwide for unclassified research.
Carnegie Mellon University Molecular Biosensor and Imaging Center
Center for collaboration of biologists, chemists, and engineers to develop fluorescence technologies for biomedical applications used in drug discovery, neuroscience, biomedical imaging and cancer biology programs. Technologies launched from MBIC include the Cyanine Dyes (Cy3, Cy5, Cy7), High Content Screening (Cellomics, Inc), Difference In-Gel Electrophoresis (DIGE), Qdots for In-vivo imaging, Fluorogen Activating Proteins, and DNA Nanotags.
Web portal that explains technique of Diffeomorphic Mapping and Shape Analysis.
Software package for directed single cell fate mapping in diverse scenarios, including regeneration, reprogramming and disease. Automatically detects initial, intermediate and terminal populations, predicts fate potentials and visualizes continuous gene expression trends along individual lineages. Applied to lineage traced cellular reprogramming data, predicted fate probabilities correctly recover reprogramming outcomes.
Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression
Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data.
Gathers together imaging and omic datasets into molecular maps of normal and diseased tissue from human and animal models, with emphasis on cancer. Used to access datasets, educational curriculum and talks, and recommended methods and software.
Minimum Information about Tissue Imaging
Consortium provides guidelines for highly multiplexed tissue images. Standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology. Data and metadata standards consistent with Findable, Accessible, Interoperable, and Reusable (FAIR) standards that guide data deposition, curation and release.
Harvard Medical School Center for Cancer Systems Pharmacology
Center includes studies for responsiveness and resistance to anti cancer drugs. Committed to training students and postdocs, promoting junior faculty and ensuring that data and software are reproducible, reliable and publicly accessible. Member of National Cancer Institute’s Cancer Systems Biology Consortium.
Software tool as scalable, modular image processing pipeline for multiplexed tissue imaging. Transforms multi channel whole slide images into single cell data.
Qualitative Data Repository at Syracuse University
Archive for storing and sharing digital data (and accompanying documentation) generated or collected through qualitative and multi method research in social sciences. QDR provides data management consulting services and actively curates all data projects, maintaining value and usefulness of data over time, and ensuring their availability and findability for re-use.
Project related to video recording.Provides system for high throughput video capture. Pi USB Cam system includes low cost Raspberry Pi microcomputer, DIY electronics peripherals, freely available open-source firmware, and custom 3D-printed casings.
Web application for use by epidemiologists and researchers involved in estimating disease prevalence or demonstrating freedom from disease through structured surveys, or in other epidemiological applications.
Monte Carlo simulation software that makes quantitative risk analysis intuitive. Monte Carlo simulation Excel add-in that allows user to include uncertainty in their spreadsheet models.
Software is add-in tool for Microsoft Excel that computes and tracks many different possible scenarios in model using Monte Carlo simulation.Helps make better decisions through risk modeling and analysis.
Software tool as statistical framework for identifying distribution shapes in single-cell RNA-sequencing data.
Software Python tool to convert your source level neuroimaging data to BIDS. Application to convert source data to Brain Imaging Data Structure.
Software to allow construction, analysis, and simulation of complex models in spreadsheet format.
Software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post translational modifications and sequence variants (mutations), and peptide/protein de novo sequencing.
Software package includes combination of four cell references for umbilical cord blood deconvolution using IlluminaHumanMethylation arrays 450K and EPIC.
Software package as open source project benchmarks IBD detection tools with multiple measurements.
Special interest society focused on basic mechanisms involved in human urinary stone formation.
Stanford University School of Medicine O’Brien Urology Research Center Biospecimen/Bioimaging Core Facility
Core leverages infrastructure of Stanford Urology and Pathology Departments to provide services to benefit O’Brien Center investigators in CAIRIBU Network. Procures and provides biospecimens, including fresh, freshly-frozen, and formalin-fixed paraffin-embedded (FFPE) prostate issues.Provides tissue characterization services, including histology, tissue microarrays, laser microdissection, and multiplex immunohistochemistry (IHC) using MIBI-TOF (Multiplexed Ion Beam Imaging by Time of Flight). Stores and provides access to images including prostate MRIs, whole-mount histology and IHC, and MIBI-TOF data, as well as integrated multiscale data platform.
Software package for implementing algorithms proposed in Lanciano et al. "Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data".
Software for annotation of lipidomics spectra.
Pediatric KIDney Stone Care Improvement Network
Community of patients, caregivers, clinicians, and researchers who perform collaborative studies of kidney stones at pediatric healthcare systems in North America. Network to better understand treatment of kidney stones specifically comparative effectiveness of different surgical approaches to remove kidney stones, impact of these surgeries of patients’ lives, and insight into recovery period.
Software R package implementation of cumulative link models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit models.
Software R package with convenience functions for analyzing factorial experiments using ANOVA or mixed models.
Just the Docs Website Template LSP Edition
Just-the-Docs Website Template: LSP Edition
Platform containing documentation to create scientific websites using Just the Docs with Jekyll. This documentation includes overview of Markdown and instructions for configuring the site.
Website tutorial for creating Jekyll-based scientific website, including editing in GitHub, working locally with Jekyll and applying Jekyll and Markdown formatting basics, and using custom themes.
University of Nebraska Medical Center Center for Collaboration on Research Design and Analysis Core Facility
Center for Collaboration on Research Design and Analysis
University of Nebraska Medical Center Center for Collaboration on Research Design and Analysis
Provides advance clinical, translational and public health research at UNMC and in the community and region. Provides expertise in quantitative sciences, including biostatistics, epidemiology, and health services research, and coordinates collaborative design, planning, conduct, analysis and interpretation of laboratory, clinical, and public health research studies.Provides educational training opportunities for graduate students and educational opportunities for public health, clinical, and translational investigators.
University of Delaware Flow Cytometry Core Facility
Facility, located at the University of Delaware Main campus (UD) in Newark, Delaware, provides flow cytometry and hematology services. Facility is equipped with 15-color FACSAria Fusion high-speed cell sorters,BD Rhapsody Express Cell Processing Unit,VetScan HM5c veterinary hematology analyzer, Nexcelom Cellometer Vision cell counter, Zeiss Axiovert 200 inverted fluorescent microscope,Thermo Shandon Cytospin 4 & a Beckman Spinchron DLX centrifuge,General Laboratory facilities for Mammalian Cell Culture and Sample preparation,Laminar flow BSL-2 biosafety cabinets, microscopes and centrifuges.
University of California at Davis Veterinary Medicine Advanced Imaging Core Facility
Health Sciences District Advanced Imaging Facility
University of California at Davis Health Sciences District Advanced Imaging Facility
University of California at Davis Veterinary Medicine Advanced Imaging Facility
Fluorescence microscopy facility with two Leica confocal microscopes, one with superresolution capability,second with multi-photon imaging capability, and Zeiss Lightsheet microscope. Facility offers consultation, training, and support.
University of Pennsylvania School of Dental Medicine Tissue Processing Laboratory Core Facility
University of Pennsylvania School of Dental Medicine Tissue Processing Laboratory
Laboratory is located in Room 429 of the Levy Building.Services include tissue processing; H&E staining, trichrome, and other staining; creation of frozen sections; and deparaffinization. Provides cryostat for use by investigators within Penn Dental Medicine; cryostat training is available for a fee. Investigators requiring the services of the Tissue Processing Laboratory should contact the facility to arrange a meeting to set up the appropriate protocols. Special handling, specimen orientation, and any unique aspects of the tissue being processed will be discussed at that time; in some instances, it may be advantageous for the investigator to be present initially when the specimens are being oriented in the hot paraffin prior to the actual sectioning.
Java Graphical User Interface for suite of computational tools enabling comprehensive analysis of mass spectrometry based proteomics data.
Software tool for processing of data independent acquisition proteomics experiments. Universal automated software suite for DIA proteomics data analysis. Neural networks and interference correction enable deep proteome coverage in high throughput.
Penn State University Center for Applications of Artificial Intelligence and Machine Learning to Industry Core Facility
AIMI - Center for Applications of AI/ML to Industry
Penn State University Center for Applications of Artificial Intelligence and Machine Learning to Industry
Connects industry members with Penn State research community of artificial intelligence and machine learning researchers and their students to solve real world problems and seize market opportunities.
Reference atlas for mice. Contains both average and annotation templates.
Software R package contains Molecular Signatures Database (MSigDB) gene sets for multiple organisms in tidy data format. Gene sets in standard R data frame with key value pairs. Package includes human genes as well as corresponding symbols and IDs for frequently studied model organisms such as mouse, rat, pig, fly, and yeast.
Parallel multitool approach for phage prediction combined with annotation and classification downstream strategy. Used for identification and analysis of phage sequences. Phage identification via nextflow and docker or singularity.
Non-profit organization founded in 1983 by group of international urologists. Society sponsors annual meetings held at different sites of the world. Endourological Society has sub-societies through out the world including the British Society of Endourology, the Mexican Endourological Society, and the Korean Endourology and ESWL Society.
Laboratory of Systems Pharmacology program
Research and education program in Harvard Program in Therapeutic Science at Harvard Medical School to advance science and to develop technology needed to accelerate invention of new medicines and personalization of patient care. Used to study molecular causes of disease, ways drugs exert their therapeutic and adverse effects, design and interpretation of clinical trials.
Society of Urodynamics, Female Pelvic Medicine and Urogenital Reconstruction (SUFU)
Organization to optimize the care of women, men, and children with lower urinary tract dysfunction and/or pelvic floor disorders through education, research and involvement in health care policy. To improve the art and science of Urology through basic and applied clinical research in urodynamics and neurourology, voiding function and dysfunction, female urology and pelvic floor dysfunction, and to disseminate and teach these concepts.
Organization focused on disorder of men with benign prostate disease, and promote health and well-being of men by advancing the best care to every patient through integrated clinical practice, education and research. Provides collaborative platform to elevate knowledge base of members about pathophysiology, diagnosis, management, and treatment of prostate disease.
Collaborating for the Advancement of Interdisciplinary Research in Benign Urology
Community of researchers studying benign urology diseases at U54 O’Brien Cooperative Research Centers, P20 Exploratory Centers, and K12 Career Development Programs funded by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), one of the institutes within the National Institutes of Health (NIH). CAIRIBU Centers and Programs are united around the overall objectives of improving our understanding of the mechanisms of urogenital diseases and developing clinical therapies for treating them by building collaborative and interactive research platforms that span the gamut from basic to translational to population research.
Software to visualize and qualitatively analyze mass spectrometry data. Used to display chromatograms and spectra, detect and integrate chromatographic peaks, search mass spectral libraries, simulate mass spectra, subtract background spectra, apply scan filters, annotate plots with text and graphics, create and save layouts, view the status of various instrument parameters during data acquisition, and create a 2D or 3D representation of an analysis displaying the acquired mass/wavelength scans. Part of liquid chromatography mass spectrometry system.
University of Hawaii at Manoa ABSL3/BSL3 Biocontaminant Core Facility
University of Hawaii at Manoa ABSL_3/BSL_3 Biocontaminant Core
Research on microbial agents, which cause lethal diseases in humans and for which effective drugs or preventive vaccines are not available, must be conducted by well-trained investigators in specially built, well-maintained laboratories. Core provides the triad of service, research and development, and education and training.
Wayne State University Proteomics Core Facility
Wayne State University WSU Proteomics Core
Protein identification and proteome analysis using Orbitrao Eclipse,Fusion and Q Exactive LC-MS/MS platforms. Affinity selection for phosphopeptides with analysis using HCD, CID and ETD. Validation and quantitation of proteins using MRM with a TSQ Vantage triple quad.
University of Georgia Georgia Genomics and Bioinformatics Core Facility
University of Georgia Georgia Genomics and Bioinformatics Core
Core laboratory for nucleic acid sequencing and bioinformatics. Mission includes research support, education, and training.Services encompass range of genomic techniques and applications, sequencing technologies, and bioinformatics analyses. GGBC operates multiple platforms for short-, long-, and single-molecule sequencing reads (i.e., Illumina MiSeq and NextSeq, PacBio Sequel, and Oxford Nanopore MinIon). We also write letters of support (LOS) to offer our capabilities and expertise for grant applications submitted to funding agencies.
University of Ottawa Behaviour and Physiology Core Facility
University of Ottawa Behaviour and Physiology Core
Core provides access to state-of-the-art rodent behavioural testing equipment in facility optimized for behavioural testing. Provides expert assistance in project development, test design and execution, data analysis and interpretation, and novel test development.
University of Arizona Electron Paramagnetic Resonance Core Facility
Electron Paramagnetic Resonance (EPR) Facility
University of Arizona Electron Paramagnetic Resonance (EPR) Facility
Research facility for studying paramagnetic centers by continuous wave and pulsed EPR techniques to obtain information on electronic, chemical, and geometric molecular structures.
University of Arizona W.M. Keck Center for Nano Scale Imaging Core Facility
University of Arizona W.M. Keck Center for Nano-Scale Imaging
Interdisciplinary research facility in areas of imaging, nano-science and spectroscopy for measuring surface topography, surface properties, electrical measurements, fluorescence, sub-monolayer visible spectroscopy, and molecular structures.
University of Arizona Laboratory for Electron Spectroscopy and Surface Analysis Core Facility
Laboratory for Electron Spectroscopy and Surface Analysis (LESSA) Facility
University of Arizona Laboratory for Electron Spectroscopy and Surface Analysis (LESSA)
Core for surface science, thin films studies, and nano scale characterization. Provides analytical and educational services to department and university on preparation, modification, and study of solid surfaces.
University of Arizona Xray Diffraction Core Facility
University of Arizona X-Ray Diffraction (XRD) Facility
Facility for investigation of single crystal and powder/thin film samples by X-Ray diffraction techniques.
University of Arizona Electron Photoemission Spectroscopy and Imaging Laboratory for Observation at the Nanoscale Core Facility
Electron Photoemission Spectroscopy and Imaging Laboratory for Observation at the Nanoscale (EPSILON)
University of Arizona Electron Photoemission Spectroscopy and Imaging Laboratory for Observation at the Nanoscale (EPSILON)
Facility offers imaging spectroscopy. Equipped with Xray Photoemission Spectroscopy, Ultraviolet Photoemission Spectroscopy, Inverse Photoemission Spectroscopy, energy filtered Photoelectron Emission Microscopy, and spatially resolved Angle Resolved Photoemission Spectroscopy and spatially resolved Xray Photoemission Spectroscopy.
University of Arizona Molecular Structures Core Facility
University of Arizona Molecular Structures Core (MSC)
Core enables researchers to determine structures and dynamics, or motions, of large biomolecules such as proteins and DNA to understand how they interact with each other and with small molecules such as drugs.
University of Miami Sylvester Comprehensive Cancer Center Biospecimen Shared Resource Core Facility
University of Miami Sylvester Comprehensive Cancer Center Biospecimen Shared Resource
Provides biorepository resources, services and expertise in support of oncology research.Facilitates translational cancer research with standard operating procedures for patient consenting; protection of patient personal and clinical data; specimen procurement and processing; quality control of specimens; secured specimen storage, retrieval, and distribution; and provision of relevant de-identified clinical data. BSSR services include: biospecimen collection, annotation, processing, storage and distribution (including tissue, blood, and other fluids); plasma, serum, and peripheral blood mononuclear cell processing and cryopreservation; rapid acquisition of surgical tissue and fresh biopsies; participant screening and enrollment for biospecimen collection studies;formalin-fixed, paraffin embedded and frozen tissue retrieval, processing, sectioning, histological staining, and digital whole slide scanning; tissue microarrays production; support for non-therapeutic trials; consultation on project design, data analysis and interpretation. Offers access tobiobank of diverse tissue types, including clinically annotated neoplastic and non-neoplastic samples from diverse anatomical sites, and provides banked specimen as well as fresh specimen procurement at institution wide level.Through BSSR, investigators have access to specimens collected fromUniversity of Miami Hospital, Sylvester Comprehensive Cancer Center, Bascom Palmer Eye Institute, Jackson Memorial Hospital, as well as to specimens collected in more broadly based multi-site studies.
University of Miami Sylvester Comprehensive Cancer Center Biostatistics and Bioinformatics Shared Resource Core Facility
Sylvester Biostatistics and Bioinformatics Shared Resource
University of Miami Sylvester Comprehensive Cancer Center Biostatistics and Bioinformatics Shared Resource
Provides expertise and analysis support for basic and translational research, clinical trials, and both interventional and non-interventional population-based studies. Offers support for data and large scale data analysis projects. Services include support for data analysis and interpretation; software access; algorithm and database development; support of scientific review, monitoring, and oversight of clinical and population science research protocols; consultation, training, educational workshops, lectures and seminars.Biostatistics services include support for statistical design of clinical trials, population studies, and laboratory experiments; sample size determination and justification; statistical analysis plans; statistical support for data and safety monitoring of clinical trials; data analysis and interpretation; prediction model development using machine learning techniques; and database design and data management. Bioinformatics services include project design for high-throughput genomics studies; support for next generation sequencing data analysis (including whole transcriptome profiling; targeted region gene expression and single-cell RNA-seq; epigenomics profiling such as ChIP-seq and ATAC-seq; and exome or whole genome sequencing analysis); pathway analysis; microbiome data analysis; functional metagenomics analysis; drug sensitivity and genomic association analysis; genomic data integration using public databases; integration analysis of genomic data across multiple platforms; genomic data visualization; and bioinformatics methods, analysis pipeline, software and algorithm development. BBSR services can be utilized for QA/QC, including quality assessment of sequencing data, sample outlier detection, batch effect determination, evaluation of spike-in control methods, randomized block design, and other strategies for data normalization. T
University of Miami Sylvester Comprehensive Cancer Center Cancer Modeling Shared Resource Core Facility
Sylvester Cancer Modeling Shared Resource
University of Miami Sylvester Comprehensive Cancer Center Cancer Modeling Shared Resource
Provides small animal cancer modeling services to foster cancer research and to accelerate discovery of tailored anti-tumor therapies, including preclinical data for drug development, proof of principle for novel therapies, preclinical imaging, and disease biomarker studies. Services include facilitating in vivo modeling of human disease using mouse models; supporting preclinical in vivo efficacy and toxicity studies; devising treatment protocols; using noninvasive imaging for diagnosis and evaluation of responses to treatment; and performing histopathological analysis of targeted cancer therapies. Specific services include (1) support for the development of experimental murine models of cancer, including with cell line and patient-derived xenografts (PDXs), genetically engineered mouse models, and humanized models; (2) support for devising and implementing treatment protocols in a pre-clinical setting using murine models of human disease (e.g., drug toxicology and efficacy studies, drug formulation and delivery, and related assessments, like cell blood count, clinical chemistry, and flow cytometry analysis); and (3) diagnosis and evaluation of responses to treatment, using noninvasive small animal imaging for diagnosis and evaluation of responses to treatment, including in vivo bioluminescence and fluorescence optical imaging, high-frequency ultrasound imaging, structural and functional nuclear imaging, and magnetic resonance imaging (MRI); and (b) research histopathological analysis of targeted cancer therapies, including H&E and immunohistochemistry (IHC) sectioning, staining, scanning and analysis, and data storage of digital slide images. The CMSR also offers consultation, training, educational workshops and seminars. CMSR radiotherapy services support both small animal total body and image-guided radiation treatment delivery with sub-millimetric accuracy for development of radiation therapy regimens in a preclinical setting.
University of Miami Sylvester Comprehensive Cancer Center Molecular Therapeutics Shared Resource Core Facility
Sylvester Molecular Therapeutics Shared Resource
University of Miami Sylvester Comprehensive Cancer Center Molecular Therapeutics Shared Resource
Provides preclinical drug discovery and development services to facilitate discovery of small molecules that have potential to become cancer therapeutics.Offers expertise in drug discovery and facilitates process of uncovering novel treatments for cancer. Services include target evaluation and assay development; small molecule library preparation, screening, and curation; high throughput screening enablement; plate imaging and transfers; assay identification, development and implementation; standard and customized assays (including live cell metabolic assays, cell death assays, clonogenic assays, and alphascreen); support for hit-to-lead pharmacology (including pharmacokinetics and ADME/T); data analytics for hit-picking; investigational new drug (IND) enablement; and full pipeline project management.Offers consultation, training, educational workshops and seminars.
University of Miami Sylvester Comprehensive Cancer Center Behavioral and Community Based Research Shared Resource Core Facility
Sylvester Behavioral and Community-Based Research Shared Resource
University of Miami Sylvester Comprehensive Cancer Center Behavioral and Community Based Research Shared Resource
Provides services and expertise that facilitate behavioral, psychosocial, community, translational, and population based oncology research. Services include coordinating recruitment and retention of diverse study participants representative of Sylvester South Florida catchment area;supporting development of culturally and linguistically tailored study materials; facilitating data collection and management, including for biospecimens, in clinical and community setting; assisting with development and delivery of evidence based interventions across cancer continuum from prevention to survivorship; offering, seminars, workshops and training.Offers consultation on culturally appropriate approaches for study implementation and provides translation of study materials into Spanish and/or Haitian Creole. Engages diverse stakeholders throughout South Florida in dialogue about cancer prevention and collaborative research opportunities.
Software tool as Digital Imaging and Communications in Medicine (DICOM) viewer for medical images.
Bruker | 7 Tesla Bruker BioSpec 70/20 USR MRI system
Multipurpose research system for high resolution Magnetic Resonance Spectroscopy and Imaging. System is equipped with 7 Tesla superconducting magnet designed with Ultra Shielded Refrigerated magnet technology. USR technology significantly reduces stray field to close to magnet. Used for In Vivo Magnetic Resonance Imaging.
Interactive regional diabetes research community across four premiere research institutions in North Carolina, who currently garner over $70 million annually for support of their diabetes research: Duke University (Duke), The University of North Carolina at Chapel Hill (UNC), Wake Forest School of Medicine (WF), and North Carolina A&T State University (NC A&T State). NCDRC supports Research Cores that represent unique strengths at each institution.
University of Colorado Diabetes Research Center
Center to facilitate diabetes research at University of Colorado by integrating interdisciplinary basic, translational, and clinical diabetes research base; providing infrastructure and resources that are indispensable for continued discovery and progress towards diabetes research and developing improved prediction and disease prevention;providing P&F and enrichment programs to support DRC investigators and their trainees, and recruit new and young investigators into diabetes research.
Open online platform for single cell RNA-seq. Provides data management and analytics. Used to analyze public and private datasets and you can choose between several best practices workflows and browse existing analyses.
University of Pennsylvania Perelman School of Medicine Neuroimaging and Cognitive Core Facility
University of Pennsylvania Perelman School of Medicine Neuroimaging and Cognitive Core
Core aims to facilitate research in cognitive neuroscience through use of Computerized Neurocognitive Battery and neuroimaging.CNB is comprised of series of tests that have been applied in neuroimaging studies and can be used either in scanner as part of functional neuroimaging study or outside scanner for measuring individual differences in performance. Tests measure accuracy and speed of performance in major domains of cognition, including executive control functions (abstraction, attention, working memory), episodic memory (verbal, facial, spatial), complex cognitive processing (language reasoning, nonverbal reasoning, spatial processing), social cognition (emotion identification, emotion intensity differentiation, age differentiation) and sensorimotor and motor speed.
University of California at Los Angeles California NanoSystems Institute Electron Imaging Center for Nanomachines Core Facility
California NanoSystems Institute Electron Imaging Center for Nanomachines
Electron Imaging Center for Nanomachines
Provides advanced electron imaging tools covering scale range from tens of micrometers to angstroms, and delivering valuable structural information for cell biology, microbiology, biomolecular, molecular, and materials sciences.Offers all major electron microscopy modalities.
Project consists of suite of 3D-printed tools including superfusion chamber with independent brain presser and animal stand. Modular device that facilitates transfer of pharmacological agents and brain access for electrodes and/or lenses for imaging. Provides stable conditions for electrophysiological and neuroimaging recordings. Device can be print either in-house or through 3d-printing service.
Tissue Slicer with conventional vernier micrometer, resolution 10 micron. Designed to prepare thin slices of living brain, slicing other tissues, blocking fixed tissue for histology, and slicing electrophoretic gels. Sections as thin as 150 microns can be prepared.
University of Colorado Anschutz Medical Campus Diabetes Research Center Clinical Resource Core Facility
University of Colorado Diabetes Research Center Clinical Resource Core
Core leverages current clinical research facilities and equipment available at Barbara Davis Center for Childhood Diabetes, UC AMC Clinical Translational Research Center, University of Colorado Hospital, Denver Veteran Administration Medical Center and Children Hospital Colorado.Core integrates diabetes research across these institutions through communication and distribution of resources available, and creates shared sample and data biobanks and recruiting database of mothers, infants, children, adolescents and adults with diabetes, diabetes risk and controls.
University of Colorado Anschutz Medical Campus Diabetes Research Center Tissue Procurement and Processing Core Facility
University of Colorado Diabetes Research Center Tissue Procurement and Processing Core
Core facilitates access and usage of tissues and services to meet specialized needs of diabetes research community to expedite and catalyze innovative diabetes research at UC AMC. Provides resources to assist DRC investigators with acquisition and processing of rodent and human tissue, and specialized cell lines that are broadly required for diabetes research.
University of Colorado Anschutz Medical Campus Diabetes Research Center Disease Modeling Core Facility
University of Colorado Diabetes Research Center Disease Modeling Core
Provides diabetes researchers with access to novel human stem cell-derived in vitro cell models for investigating cellular and molecular features of both Type 1 and Type 2 diabetes. Recent progress in stem cell, organoid culture, gene editing and directed differentiation technologies has afforded opportunities to develop pre-clinical human models.Provides expertise, infrastructure and access to novel human model systems and technologies to DRC investigators. Provides expertise, resources and training in stem cell technologies together with quality control testing, validation standardization and authentication all model platforms and reagents.
University of Colorado Anschutz Medical Campus Diabetes Research Center Cell and Tissue Analysis Core Facility
University of Colorado Diabetes Research Center Cell and Tissue Analysis Core
Provides diabetes researchers at University of Colorado with access to microscopy and mass cytometry systems. Provides expertise and training to use equipment effectively for diabetes related tissues; expertise and validated diabetes related resources to prepare samples appropriately; guidance to design experiments; resources to analyze data; assistance with data interpretation.
North Carolina Diabetes Research Center Genomics and Proteomics Core Facility
North Carolina Diabetes Research Center Genomics and Proteomics Core
Provides resources and expertise in genomics and mass spectrometry at Wake Forest Center for Precision Medicine. Provides unique access to instrumentation and analytical expertise to NCDRC faculty in support of advancement of diabetes research.Overlooks the use of existing resources at NCDRC partner institutions (UNC, NC A&T, and Duke University) to coordinate work and data analysis with Metabolomics Core to provide omics analyses.Offers analytic services, expertise, and tools to integrate data to better understand interactive systems at play in disease processes.
North Carolina Diabetes Research Center Advanced Clinical Study Methods Core Facility
North Carolina Diabetes Research Center Advanced Clinical Study Methods Core
Core to leverage data, patient populations and investigators at each NCDRC institution, including accessing expertise and resources of regional Clinical and Translational Science Institute hubs (Duke, UNC, and Wake Forest). Research navigators in ACSMC provides input and navigation of clinical research resources available to diabetes investigators based on extensive experience in diabetes specific studies and methodology and deep knowledge of NCDRC resources available at each institution.
North Carolina Diabetes Research Center Metabolomics Core Facility
North Carolina Diabetes Research Center Metabolomics Core
Provides platform for quantitative targeted metabolic profiling by MS/MS and GC/MS, supported by library of stable isotope labeled standards as well as extensive scientific expertise to help researchers navigate core resources and use of services.
Software Python package presents interface to use isocortical streamlines of Allen Mouse Common Coordinate Framework. Used to support projection of Allen Common Coordinate Framework mouse brain volumetric data and coordinate data on to 2D representations.
Van Andel Institute Pathology and Biorepository Core Facility
Van Andel Institute VAI Pathology and Biorepository Core
Pathology and Biorepository Core (PBC) integrates anatomic pathology expertise with biorepository and biospecimen science. It provides emphasis on high-quality biospecimens and interpretable results to validate experimental models and extend them to clinical samples. The PBC offers a comprehensive range of biospecimen services, including histology, pathology, and biospecimen processing and storage.
Van Andel Institute Genomics Core Facility
Provides services including Next Generation Sequencing, single cell Genomics, and Spatial Transcriptomics facility. Provides experimental design support, library generation, and Illumina and Nanopore Sequencing.
Van Andel Institute Transgenic Core Facility
Provides genetically modified animal models for our collaborators. For preexisting models provides rederivation or reconstitution for purpose of importing animals into Vivarium barrier. In the absence of preexisting models core works closely with partnering labs to generate their ideal mutation de novo, often using CRISPR technology. Usually beginning with a brief consultation, this process involves discussing factors such as ideal background strain, molecular methods for optimizing the intended genetic change, mutation induction strategies, screening approaches and eventual QC of the new mutant line with the overall goal of giving our collaborators a fully informed, realistic picture of their projects timeframe, pitfalls and workflow. Core provides mouse sperm and embryo cryopreservation services for purpose of archiving and distributing valuable lines. Institute is an AAALAC-accredited facility. All procedures are conducted according to the NIH Guide for the Care and Use of Laboratory Animals.
University of Michigan Statistics Online Computational Resource Core Facility
Statistics Online Computational Resource (SOCR)
University of Michigan Ann Arbor Statistics Online Computational Resource (SOCR)
SOCR designs, validates and freely disseminates knowledge. The Resource develops AI/ML tools, mathematical models, and end-to-end data analytic protocols for biomedical and health studies. It provides portable online aids for probability, statistics and health science education, promotes technology enhanced instruction, supports efficient statistical computing, supports AI-services, and advances predictive big data analytics. The SOCR platform includes repository of interactive apps, datasets and case-studies, computational tools, visualization approaches, instructional resources, learning materials, and curricular components. SOCR faculty, staff, and students support data and information science collaborations and analytic partnerships involving biomedical, healthcare, and biostatistical investigations.
Software tool to reduce scoring time and simplify data analysis. Offers automated power analysis, semi-automated scoring methods, and advanced tabular and graphical analysis for investigating sleep data sets. Custom scoring and analysis are also available. Scoring sessions between two or more users can be compared. All EEG/EMG and video data sets recorded with Pinnacle software, as well as third party EDF files, can be imported.
Software platform to provide programmatic access to experimentally determined and theoretical protein structures. Provides unified programmatic access to experimentally determined and predicted structure models. Used for open collaboration between providers of macromolecular structure models to provide model coordinates and meta information from all contributing data resources in standardised data format, on unified platform.3D Beacons API retrieves and combines data from member data providers, and returns data in JSON format according to 3D-Beacons API specification.
Software qualitative analysis tool. Used by researchers and practitioners to uncover and systematically analyze complex phenomena hidden in unstructured data including text, multimedia, geospatial. Provides tools that let the user locate, code, and annotate findings in primary data material, to weigh and evaluate their importance, and to visualize relations between them. Consolidates documents and keeps track of all notes, annotations, codes and memos in all fields that require close study and analysis of primary material consisting of text, images, audio, video, and geo data. Provides analytical and visualization tools designed to open new interpretative views on material.
Fujifilm | VisualSonics Vevo 770 Imaging System
Vevo 770 High-Resolution In Vivo Micro-Imaging System
High resolution in vivo imaging system for small animal research. Provides visualization and measurement of anatomical and hemodynamic function in small animals down to 30 microns.
Software genome annotation pipeline using long sequencing reads alignments from animal genomes.
University of California at Los Angeles California NanoSystems Institute Nano and Pico Characterization Laboratory Core Facility
California NanoSystems Institute Nano and Pico Characterization Laboratory
NPC- Nano & Pico Characterization Laboratory
Offers curated collection of high end scientific instrumentation to enable physicochemical characterization of nanoscale materials, devices, and systems under wide range of experimental conditions.Technical capabilities and expertise include surface analysis by Scanning Probe Microscopy (SPM); hydrodynamic size and surface charge analysis by Dynamic Light Scattering (DLS) and Zeta Potential (ZP) measurements; elemental and chemical analysis by Inductively Coupled Plasma Mass Spectrometry (ICP-MS).
University of California at Los Angeles California NanoSystems Institute Integrated NanoMaterials Laboratory Core Facility
California NanoSystems Institute Integrated NanoMaterials Laboratory
INML- Integrated NanoMaterials Laboratory
Nanomaterials and nanostructures grown in INML are used in lasers, solar cells, detectors, transistors, modulators, and a wide range of other electronic and photonic devices.
Medical College of Wisconsin Mellowes Center for Genomic Sciences and Precision Medicine Core Facility
MC-Mellowes Center for Genomic Sciences and Precision Medicine
Medical College of Wisconsin Mellowes Center for Genomic Sciences and Precision Medicine
Core for advancing genomic sciences and precision medicine in fields of Omics, Data Science, and Systems Biology. Provides whole genome sequencing technologies to investigate how gene variants impact gene expression and to define genetic variants associated with rare and common disease, embryonic development, and effects of environmental factors and drugs upon gene expression and disease.
Microsoft software suite of business analytics tools to analyze data and share insights. Used for business and to get answers quickly with rich dashboards available on every device.
University of Chicago Proteomics Platform Core Facility
University of Chicago Proteomics Platform
Core to develop and utilize proteomics techniques to answer both basic and translational scientific questions.
University of Oklahoma Samuel Roberts Nobel Microscopy Laboratory Core Facility
Samuel Roberts Nobel Microscopy Laboratory
University of Oklahoma Samuel Roberts Nobel Microscopy Laboratory
Offers access to instrumentation, training, and service using advanced light microscopy, scanning electron microscopy, and transmission electron microscopy. Provides access to core imaging and analytical characterization technologies. In addition to instrument access, SRNML personnel offer advice, hands-on training, education, and research collaboration. Provides range of sample preparation equipment.
Simple Western instrument software to analyze assay data and processes results.
Software tool for single drug and drug combinations pharmacodynamics with automated simulations or dose efffect data analysis from enzymes, receptors, microorganisms, cells, animals and clinical trials.
University of Chicago Metabolomics Platform Core Facility
University of Chicago Metabolomics Platform
Equipped with Thermo Scientific Orbitrap IQ-X Tribrid mass spectrometer(+UVPD)- Vanquish Horizon UHPLC system. Provides experience in quantifying diverse groups of metabolites in cells, culture medium, bodily fluid, animal tissue, exhaled breath condensate, etc., and performes stable isotope tracing experiments using 13C, 15N, and 2H-labeled substrates. Support hypothesis generating untargeted and hypothesis driven targeted metabolomics studies from experimental design stage through data acquisition, data analysis, and interpretation.
University of Chicago Biomolecular Nuclear Magnetic Resonance Core Facility
Biomolecular Nuclear Magnetic Resonance Facility
University of Chicago Biomolecular Nuclear Magnetic Resonance Facility
Facility houses Bruker AVANCE IIIHD 600 and Bruker AVANCE III 500 NMR spectrometer. These are equipped with high sensitivity inverse and broadband probes, single axis gradients, pulse shaping capabilities, variable temperature control(-50C to 150C), and automatic tuning and matching.Bruker AVANCE IIIHD 600 is also equipped with robotic sample changer (Bruker SamplExpress) allowing automated acquisition of up to 60 samples. Sample preparation can also be automated with Gilson sample preparation robot.
University of Chicago Gnotobiotic Research Animal Core Facility
University of Chicago Gnotobiotic Research Animal Facility
One of the largest academic gnotobiotic mouse facilities internationally.Centrally managed gnotobiotic/germ free mouse facility located within centrally managed Knapp Center for Biomedical Discovery vivarium.GRAF currently maintains over 80 flexible film isolators with capacity for greater than 1045 mouse cages.
University of Chicago Organoid and Primary Culture Research Core Facility
Organoid and Primary Culture Research Core
University of Chicago Organoid and Primary Culture Research Core
The mission is to facilitate access, generation, banking, and usage of organoids and primary cells derived from patients and model organisms.
University of Chicago Human Disease and Immune Discovery Core Facility
University of Chicago Human Disease and Immune Discovery
Provides expertise, equipment and physical space for researchers to perform cutting edge, high resolution investigations of human immune system. Leverages innovative technologies from field of flow cytometry for data generation and analysis and through close collaboration with Genomics core facility to provide cellular component solutions to even higher resolution genomic investigations.
University of Chicago Center for Research Informatics Bioinformatics Core Facility
University of Chicago Center for Research Informatics Bioinformatics Core
Core offers services and expertise designed to allow BSD investigators to take full advantage of high throughput technologies.
Stanford Graduate School of Business Data, Analytics, and Research Computing Core Facility
Stanford Graduate School of Business Data
DARC facility engages directly with faculty members, preparing large scale datasets, assisting with data analysis, and consulting on research design. Provides expertise on machine learning, text processing, and cloud services. DARC team also supports Yen compute environment, linux cluster designed for data intensive workloads in business research.
Software tool as diagramming application that enables collaboration in real time.
Open source Python based hardware and software for fiber photometry data acquisition. System includes compact, low cost, data acquisition board built around Micropython microcontroller, and cross platform graphical user interface for controlling acquisition and visualising signals. Can acquire two analog and two digital signals, and control two external LEDs via built in LED drivers. Time division multiplexed illumination allows independent readout of fluorescence evoked by different excitation wavelengths from single photoreceiver signal.
Physi pharmacokinetics and pharmacodynamics
Open source PhysiCell based software package that allows users to include pharmacokinetics and pharmacodynamics in PhysiCell models. Used for module template for drug treatment in PhysiCell.
Software tool as quality assurance workflow for Brain Imaging Data Structure compliant anatomical and functional MRI datasets. Used to extract no-reference image quality metrics from structural and functional magnetic resonance imaging data.
Software package in Python for statistical analysis of Ecological Momentary Assessment data.
University of Chicago Engineering and Technical Support Group Core Facility
UChicago - Engineering and Technical Support Group
University of Chicago Engineering and Technical Support Group
ETSG serves University of Chicago faculty led research projects. ETSG staff is available to help plan, design, build, test, and install mechanical and electro mechanical apparatus.
City University of New York Advanced Science Research Center Live Imaging and Bioenergetics Core Facility
ASRC-Live Imaging and Bioenergetics Core
CUNY Advanced Science Research Center ASRC-Live Imaging and Bioenergetics Core
Provides Zeiss LSM880 upright two photon confocal microscope with Airyscan, FAST model and CLARITY lens; LSM880 inverted live cell imaging confocal microscope with Airyscan and FAST model; Agilent Seahorse XFe24 live cell metabolic analyzer.Supported applications include in vivo imaging of live animals, time lapse live cell imaging with high resolution optical sectioning, deep imaging of fixed CLARITY tissues, calcium imaging, photo switching and photo uncaging, Fluorescence Recovery After Photobleaching, Forster Resonance Energy Transfer, laser ablation, and measuring mitochondrial respiration and glycolysis in live cells in real time.Provides advanced imaging analysis software Imaris for data processing.
Data portal hosting access to behavioral data sets generated by International Brain Laboratory aiming to understand brain functions underlying decision making. Datasets are acquired in neuroscience laboratories performing experimental work. In each of these laboratories, mice are first trained in IBL decision making task following standardized training pipeline.
University of California at Santa Cruz Stable Isotope Laboratory Core Facility
Provides light stable isotope ratio analysis services to scientists from UCSC and from around the world.
Software package that enables signature classification of tumor samples by generating heatmaps using transcriptomic data.
Harvard Medical School Dana Farber Harvard Cancer Center Mouse Engineering Core Facility
Harvard Medical School DF/HCC Mouse Engineering Core
Core provides services for generation of transgenic and knockout mice.Provides Nikon Diaphot microscope equipped with Nomarski Optics and Narishige micromanipulators for microinjections, Nikon surgical microscopes for egg isolation and transfer, sutter needle puller and de Fonbrune microforge. Facility maintains mice necessary for egg donors, egg recipients, and vasectomized males.Core offers electroporation of targeting vectors into ES cells. Provides investigators with DNA to identify ES cells carrying desired recombination events and ES cell expansion for microinjection into blastocysts.Services also include CRISPR injections, sperm and embryo cryopreservation, and reanimation with fresh or frozen sperm via IVF or thawing and implanting embryos.
University of Texas at Austin Cryo Electron Microscopy Core Facility
University of Texas at Austin UTA CBRS Sauer Structural Biology Laboratory
UTA CBRS Sauer Structural Biology Laboratory
Offers training, assisted and unassisted use of microscopes and equipment, as well as consultations and collaborations. Support includes single particle cryo-EM, Cryo-ET, Micro-ED,simple characterization of samples in vitrified aqueous mixtures (e.g. nanoparticle size, etc.).
Source code for "Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation".
Penn State College of Medicine High Performance Computing Core Facility
Penn State College of Medicine High Performance Computing
Penn State College of Medicine PSCOM-HPC
Provides computational and storage tools needed to efficiently and effectively process data. High performance computing cluster housing compute cores, graphical processing unit cores, and directly attached high speed storage.
University of Ottawa Genome Editing and Molecular Biology Core Facility
University of Ottawa UO-Genome Editing and Molecular Biology facility
UO-Genome Editing and Molecular Biology facility
Facility assists researchers in mammalian genome editing and molecular biology, including CRISPR genetic libraries and screens as well as custom viral vector/particle production. Projects are customized to researchers needs, from full service cell line creation to design and cloning.Supported by Canadian Foundation for Innovation.
University of Chicago Pritzker Nanofabrication Core Facility
University of Chicago UC - Pritzker Nanofabrication Facility
Facility is ISO Class 5 cleanroom that specializes in advanced lithographic processing of hard and soft materials. Facility is focused on supporting basic science, applied research, research and development, and prototype production using micro and nanofabrication.
University of Califorania at Los Angeles California NanoSystems Institute Molecular Screening Shared Resource Core Facility
California NanoSystems Institute Molecular Screening Shared Resource Core Facility
California NanoSystems Institute MSSR- Molecular Screening Shared Resource
MSSR- Molecular Screening Shared Resource
Services include use of high throughput screening technology, compounds in various libraries, siRNA sets of druggable genome for mouse and human and database of results from screens. For compounds screens, data points are in singlets.For functional genomics screens we use duplicates. We typically utilize 384 well plates but are flexible in this regard. We can accomodate any plate type ranging from 96 to 1536 well plates. Specialty plates can be handled on needed base. We have special rates for consumables with many vendors based on volume we use. These reduced rates are passed on directly to our screeners.
Stanford University School of Medicine O’Brien Urology Research Center
Stanford University O’Brien Urology Research Center
Center for research to understand the network of cells that cause benign prostatic hyperplasia , the most common cause of urinary bother in men.
Software tool to estimate stochastic frontier models. Used to obtain maximum likelihood estimates of parameters of variety of stochastic production and cost frontiers, and estimates of mean and individual technical or cost efficiencies.
Brain Analysis Library of Spatial maps and Atlases
Database for hosting and sharing neuroimaging and neuroanatomical datasets for human and primate species. Includes 1) curated, user created Study datasets, extensively analyzed neuroimaging data associated with published figures/manuscripts, 2) Reference datasets mapped to brain atlas surfaces and volumes in human and nonhuman primates for use as general resources (e.g., published cortical parcellations), and 3) ConnectomeDB powered by BALSA for distributing HCP-Young Adult and related HCP-style processed imaging and phenotypic datasets. Datasets in BALSA may include PMID and/or DOI that links them directly to relevant publications.
Software pipeline for generating Circos based genome assembly consistency plot given set of contigs relative to reference genome. Intended to visualize large scale translocations or missassemblies in draft assemblies, but it can also be useful when trying to show synteny between whole genomes.Circos based tool to visualize genome assembly consistency
Software suite for ultra fast and sensitive sequence search and clustering. Used to search and cluster huge protein and nucleotide sequence sets. Designed to run on multiple cores and servers.
Software toolkit to assembly of organelle genome from genomic skimming data. Used for accurate de novo assembly of organelle genomes.
Software toolkit for reference free quality, completeness, and phasing assessment for genome assemblies. Genome assembly quality evaluation based on k-mers.
Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies.
Collaborative Brain Wave Analysis Pipeline
Software adaptable and reusable analysis pipeline for multi scale, multi methodology analysis of cortical wave activity. Pipeline ingests data from multiple measurements types of spatially organized neuronal activity, such as ECoG or calcium imaging recordings. Pipeline returns statistical measures to quantify dynamic wave like activity patterns found in data.
Harvard Medical School Biomolecular Nuclear Magnetic Resonance Core Facility
Harvard Medical School HMS-Biomolecular NMR Core
Offers services in fragment based screening and drug discovery, characterization and QC of biologics and biosimilar drugs, metabolomics, protein NMR, small molecule NMR, and NMR of natural products. Offers 400-700MHz systems, many with cryogenic probes.
Carleton University Tissue Engineering and Applied Materials Hub Core Facility
Carleton University Tissue Engineering and Applied Materials (TEAM) Hub
Tissue Engineering and Applied Materials (TEAM) Hub
Core research facilities include BioImaging Research Node which houses commercial and custom imaging systems and is focused on optical imaging; Tissue Engineering and Biomaterials Testing Research Node equipped with microfluidics 3D bioprinter and mechanical testers, which facilitate development of artificial 3D biological tissue models and biomechanical testing of different biomaterials and biomedical samples; Biochemistry and Molecular Biology Research Node which houses hypoxia chamber and systems for characterization and quantification of proteins, peptides, and nucleic acids; Cellular Biology Research Node to support development and use of 3D tissue models.It houses instruments including flow cytometer for phenotyping and performing functional testing of cells and bacteria, Seahorse Analyzer for evaluation of metabolic activity of cells, and Incucyte for live cell imaging of cells and tissues in culture.
National Institute on Drug Abuse Genetic Engineering and Viral Vector Core Facility
NIDA-Genetic Engineering and Viral Vector Core
Provides support to NIDA-IRP researchers by facilitating studies of brain function under physiological and pathological conditions through developing and producing genetic tools capable of modulating and monitoring molecules, cells and circuits in nervous system.Provided services include custom design and/or production of viral vectors/nanoparticles;in vitro molecular and cell biology services; consultation and training.
UTHealth Brain Collection for Research in Psychiatric Disorders
University of Virginia School of Medicine Biorepository and Tissue Research Core Facility
Biorepository & Tissue Research Facility
University of Virginia School of Medicine Biorepository & Tissue Research Facility
Core is involved in procurement and processing of human tissue and other biospecimens for basic, translational, and clinical research.Provides laboratory support services for clinical trials, tissue samples from remnant surgical resection and autopsy specimens linked to clinicopathologic data while maintaining patient confidentiality. Provides biorepository of human specimens.Offers advanced histology services including multi color immunohistochemistry, in situ hybridization, tissue microarrays, slide scanning, computerized image analysis, NanoString spatial profiling.
Platform for informing research participants and obtaining consent to share brain imaging data. Provides suggested wording/templates for MRI studies human participant consent forms (including GDPR version), reference of tools for data anonymization, etc to make prospective data sharing possible.
Software tool to acquire, analyze, view, and store physiological data generated during preclinical experiment. Has library of application specific analysis modules for real time signal processing.
Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.
Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression.
Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals.
Metagenomic TRajectory Analysis with Disease Endpoint and Risk factors
Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually.
Individual-Specific ceLl typE referencing Tool
Software R package to conduct signal deconvolution for general omics data. Can estimate individual specific and cell type specific reference panels, when there are multiple samples observed from each subject. Can solve for reference panel on individual basis. Can conduct test to identify cell type specific differential expression genes.
Bertin Technologies | Precellys 24 tissue homogenizer
The Precellys 24 homogenizer with automatic tube locking system with the ability to process up to 24 tubes simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Reichert Jung Ultracut E, article number 131-960, is used to cut ultrathin and semithin sections of resin embedded samples for electron microscopy.
Max Planck Institute of Molecular Cell Biology and Genetics Electron Microscopy Facillity FEI Tecnai T12 electron microscope
Tecnai T12 microscope combines all imaging, diffraction, and analytical techniques at good spatial resolution and detection efficiency. Transmission electron microscope with operating voltage range of 20 to 120 kV. FEI Tecnai T12 120kV TEM and 2k TVIPS camera.
Software R package for quality check of HTG EdgeSeq datasets.
Component of Accelerating Medicines Partnership Common Metabolic Diseases being developed at University of California San Diego as part of larger consortium of academic, industry and non-profit institutions worldwide. Resource is based on software developed by ENCODE DCC at Stanford University. Atlas provides epigenomics and other functional genomics data to promote understanding of genetic basis of common metabolic diseases.
Software is part of MouseOx Plus pulse oximeter system.
2Biol | BP-2000 Blood Pressure Analysis System for Mice and Rats
BP-2000 Blood Pressure Analysis System™ for Mice and Rats
Computerized, non invasive system for measuring mouse and rat blood pressure. Blood pressure analyzer is standard in transgenic and knockout mouse research.
Stanford University Community of Shared Advanced Research Platforms
Community of Shared Advanced Research Platforms
Center coordinates ideas and investments to advance and democratize access to Stanford cores, instrumentation, scientific and technical staff, allowing users to perform innovative, rigorous experiments.
Software tool as variant caller for SNVs and small indels. Implemented as software application written in C++ .
Software DNA and RNA sequence analysis pipeline.
Supplier for research frogs for biomedical research community worldwide. Supplies: Xenopus laevis and tropicalis frogs, frog ovary, oocytes, eggs, testes.
Software R toolbox for Archetypal Analysis and Pareto Task Inference for unsupervised characterisation of single cell data. Allows describing continuum of cell states by identifying representative cells with most distinctive expression. Detecting which genes and functional annotations make those cells distinctive gives marker genes and predicted functions for each state.
Software framework for unsupervised integration of multi-omics data sets. Used for discovering principal sources of variation in multi omics data sets.
quantification of the Tumor Immune contexture from human RNA-seq data
Software pipeline for quantification of Tumor Immune contexture from human RNA-seq data.
Software package for validating sample identity in next generation sequencing studies within and across data types. Used for identifying next generation sequencing data files from the same individual. Used for checking sample matching for NGS data.
Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering.
Repository of many types and sources of data including, but not limited to, assessments, imaging, wearable, and biological samples, collected from research projects at the Centre for Addiction and Mental Health. Data that individuals choose to share to advance mental health.
Software tool for rapid detection of structural variants and indels for germline and cancer sequencing applications. Used to call structural variants and indels from mapped paired end sequencing reads.
Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements.
Software tool as purity ploidy estimator for whole genome sequenced data. Used for copy number calling and determination of sample purity.
BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain
Project to develop and utilize imaging infrastructure to create human brain cell census and instantiate it in coordinate system that will enable immediate impact of all in vivo MRI studies of human brain. Consortium for creating cellular census of human cerebral cortex.
Software to detect regions of interests and distinguishes cells and sub-cellular objects within these target regions from immunohistochemistry specimen. Used for digital pathology image analysis.
Data Envelopment Analysis (Computer) Program
Software tool to construct Data Envelopment Analysis frontiers for calculation of technical and cost efficiencies and also for calculation of Malmquist TFP Indices.
Thermo Fisher: Applied Biosystems | QuantStudio 1 RealTime PCR System
qPCR instrument with basic features ideal for those new to qPCR or those who have limited budget. System offers quality, reliability, and advanced user experience of QuantStudio family of instruments.
Thermo Fisher: Applied Biosystems | SimpliAmp Thermal Cycler
Bentchtop Thermal Cycler for everyday PCR. Features innovative, safe heated lid and large LCD color touch screen.
Thermo Fisher | NanoDrop One/OneC Microvolume UV Vis Spectrophotometer
NanoDrop One OneC Microvolume UV Vis Spectrophotometer
NanoDrop™ One/OneC Microvolume UV-Vis Spectrophotometer
Benchtop spectrophotometer designed for DNA, RNA, and protein quantification, one sample at time using only 1–2 uL of sample without dilution, even for highly concentrated samples.
Sotware R package for differential discovery analyses in high dimensional cytometry data including flow cytometry, mass cytometry or CyTOF, and oligonucleotide tagged cytometry.
Software package for post acquisition data processing that allows users to visualize, review, and export Imaging Mass Cytometry data acquired with Hyperion Imaging System and CyTOF.
SyRI compares alignments between two chromosome level assemblies and identifies synteny and structural rearrangements.
Software pipeline to analyze read depth along long read contigs and to find outliers.
Eukaryotic Non-Model Transcriptome Annotation Pipeline
Software package as eukaryotic non model annotation pipeline.Used for bringing functional annotation to non-model eukaryotic transcriptomes to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. Addresses fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein-coding transcripts.
Web gene structure display server. GSDS 2.0 is upgraded gene feature visualization server with newly designed interface, supports for more types of annotation features and formats, as well as an integrated visual editor for editing generated figure.User specified phylogenetic tree can be added to facilitate further evolutionary analysis.
Web tool for secondary structural analysis. Used for secondary structure prediction.
Web application for integrating phylogeny and Gene Ontology terms into subcellular protein colalization prediction.Extensive high performance subcellular protein localization prediction system.
Web application for predicting subcellular localization of plant proteins including those with multiple sites.Top Down Strategy to Augment Power for Predicting Plant Protein Subcellular Localization.
Web protein hydrophilicity analysis tool.
Software integrative toolkit developed for interactive analyses of big biological data.
Database includes newly released genome sequences of Brassiceae species and published genomic data of most other Brassicaceae species.Data can be browsed in JBrowse or searched in BLAST. Offers service of searching for syntenic genes, which are generated based on their syntenic relationships to genes in Arabidopsis thaliana. Regularly updated with newly released reference genomes.
Web tool as Brassica napus genome browser.
Brassica napus Transcriptome Information Resource
Searchable database of Brassiceae genomic data hosted on the website.
New York University Langone Medical Center Research Software Engineering Core Facility
New York University Langone Medical Center Research Software Engineering Core
Core is resource launched by NYU Langone, based in Information Technology department in close collaboration with NYU Grossman School of Medicine.Used to design, develop, optimize, and customize software to accelerate research. Requires iLab log in.
Cold Spring Harbor Laboratory Microscopy Shared Resource Core Facility
Cold Spring Harbor Laboratory CSHL-Microscopy Shared Resource
Provides access to microscopes, technical advice and expertise in preparing cells or tissues for immunofluorescence/confocal microscopy, live cell imaging, super resolution imaging, transmission electron microscopy, and immunoelectron microscopy.
Meta Analysis for Diagnostic Test Studies
Software R package for bivariate meta analysis of diagnostic test studies using integrated nested Laplace approximation with INLA.
Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video.
Software R package to process raw data from ColonyRack system. In addition to generating pre processed data and quality control information, range of high level metrics are calculated together with convenient tools for analysis.
Web tool to identify generation and reuse of research outputs. Used to determine author compliance with Open Science policies in academic research texts.
Miniature microscope system that integrates in vivo cellular resolution calcium imaging with simultaneous or sequential optogenetic manipulation to causally link neural circuit activity with behavior.
Organization dedicated to improving patients’ quality of life by facilitating access to Patient-Centered Outcome information. Has access to any published COA article and subscribes to key journals in this field, such as Quality of Life Research and Value in Health. Library houses COAs, as well as their translations into some 130 languages. See PROQOLID on ePROVIDE for full range of availability.
Gait Analysis Instrumentation and Technology Optimized for Rodents
Software suite to analyse gait trials collected with Experimental Dynamic Gait Arena for Rodents. Used for rodent gait analysis.
Software tool as plug-in for ImageJ software. Used for tracing microscopic images.
University of Nebraska Medical Center UNMC MEG Core Facility
Equipped with magnetoencephalography (MEG) scanner to detect immediate changes in electrical brain activity. Provides 306 channel whole head MEG system (TRIUX, Neo, MEGin) and 128 channels EEG amplifier.MEG helmet does coverage for whole cortex, 1220 cm2. MEG system has three measurement positions:supine, lower and upper seated. MEG system is housed within magnetic shielded room equipped with active shielding and automated helium recycler.
University of Arizona CBC Machine Shop Core Facility
Provides full service precision machine shop specializing in design and construction of custom equipment for scientific research and teaching.
University of Arizona CBC Electronics Core Facility
University of Arizona CBC Electronics Facility
Supporting the research community through troubleshooting, repair and new designs for electronic instrumentation, equipment and experiments.
University of Arizona CBC Glassblowing Core Facility
University of Arizona CBC Glassblowing Facility
Provides full service facility for design and fabrication of specialized scientific glassware as well as repairs and modifications of existing glassware.
Software pipeline to identify poor quality joins and produce accurate, long range sequence scaffolds.
Software command line framework to process sequencing data from Hi-C experiment. Used to process pair end sequence alignments.
Software package for genome annotation. Built specifically for fungi, but will also work with higher eukaryotes. Used for genome prediction, annotation, and comparison.
Organization mission is to expand cooperative ventures in research with Oak Ridge National Laboratory and enhance science and engineering research programs at University of Tennessee. Organization is affiliated with Tennessee Center of Excellence. Funding resource.
Software package for 3D pose estimation. Uses DeepLabCut for 2D tracking and uses triangulation methods to project pose estimations into three dimensions.Toolkit for robust markerless 3D pose estimation.
Software pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas. Tools for handling and analysing data with ambiquities.
Initiative to enable cancer discovery and treatment based on complete elucidation of molecular networks underlying cancer. CCMI leverages advanced interaction mapping and computational facilities to generate and analyze cancer networks.
Software set of acquisition and data processing tools. LC/MS analytical software. Enables control of multi-channel LC, single quadrupole, triple quadrupole and high-resolution LC-MS systems, as well as IC and GC systems.
Software as isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. Natural abundance correction of mass spectrometer data.
Software package to indicate if two groups are significantly different. Used to add significance brackets to ggplots.
University of Florida UF Scripps Biomedical Research Bioinformatics and Statistics Core Facility
UF Scripps Biomedical Research-Bioinformatics and Statistics Core
University of Florida UF Scripps Biomedical Research Bioinformatics and Statistics Core
Core provides data management and analysis services for UF Scripps community as well as for external collaborators. Offers scientific support to assist in experimental design, analysis, integration and dissemination of biomedical data and knowledge. Supports data analysis for samples processed at Genomics, Proteomics, and Neurobehavior cores.
Software tool for transforming 2D poses to 3D coordinates on labaratory animals. Used for kinematic studies of laboratory animals. Tracking movements in three dimensions from behaving flies, mice, rats, and non-human primates.
Virginia Commonwealth University Genomics Core Facility
Virginia Commonwealth University VCU Genomics Core
Genomics Core facility in Richmond VA, maintains instrumentation to support advanced sample/library preparation, high-throughput sequencing, real-time PCR and analysis.
National Jewish Health Genomics Core Facility
National Jewish Health Genomics Facility
Facility housed within Center for Genes, Environment and Health, provides Next-Gen Sequencing services from expert planning through data analysis including RNA-Seq, Whole Exome Sequencing, Single-Cell sequencing and customized panels.Data is stored onsite and is ready for future data mining by our team or others when needed. Our team is trained to utilize both Illumina and Thermo Ion Sequencing Platforms, including many other technologies, to provide the best mix of capabilities for your genomics needs.
Ohio State University Wexner Medical Center Leukemia Tissue Bank Core Facility
Ohio State University Wexner Medical Center Leukemia Tissue Bank
Human tissue biorepository offering procurement and distribution services for samples obtained from patients with hematologic malignancies.
Reproducible Rehabilitation Research Education Course
Research education program to build sustainable national workforce of rehabilitation researchers equipped with basic data science skills in five years.
3-Dimensional Aligned Neural Network for Computational Ethology
Convolutional neural network that calculates 3D positions of user-defined anatomical landmarks on behaving animals from videos taken at multiple angles. Works on recorded video data from multiple cameras. Used for 3D markerless pose estimation and tracking.
Code is written to be run with Matlab version r2020b or higher. Model accepts wave assay pulse amplitude data, and simultaneously solves and fits protofilament deflection models to deduce fundamental biophysical properties of microtubule protofilaments.
Warner Instruments | Dual Channel Temperature Controller Model TC-344C
Temperature controller. Each channel supplies up to 22 watts into load of 10 ohms. Heat set point is controlled automatically in Auto mode via thermistor feedback. Loop speed selector provides three feedback response times to optimize tp thermal stability of device being heated. Heat set-point may also be manually controlled in Manual mode.
Olympus | BX51WI Fixed Stage Upright Microscope
BX51WI is for all physiological experiments such as patch clamping and intravital microscopy. Fixed stage and vibration free frame design ensures stability throughout experiment. Use of infrared light protects living cells and offers high penetration depths of thick tissue slices, while high NA optics allow magnification changes without moving objective.
Open source software Python application for high resolution analysis of metagenomes using distance trees. Tree based, taxonomy agnostic tool for identification of biologically relevant clades from shotgun metagenomic sequencing. Used for phylogenetic analysis of shotgun metagenomic data.
Web service for statistics with automated data analysis mode.
Software tool for resting state functional connectivity analyses. Allows to get optimal LPF-FD and GEV-DV volume censoring parameters for specified multiband resting state fMRI dataset.
Toolkit for MIRA LAB Striatal Segmentation
Software MATLAB pipeline that produces CNN-based segmentations of striatal regions of brain based on structural T1w image.
Open source software Python library for sensitivity analysis. Useful in systems modeling to calculate effects of model inputs or exogenous factors on outputs of interest.
Web based tool for multi-omics integration via intuitive visual analytics. Web based platform for visual analytics of multi-omics data to allow researchers to fuse statistical and visual streams of evidence together to make more informed judgements. Enables to dissect large and complex multi-omics datasets by facilitating pattern recognition and cognitive reasoning through intuitive visual analytics.
Software tool for data independent MS/MS deconvolution for comprehensive metabolome analysis. Universal program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters). Used for untargeted metabolomics and lipidomics supporting any type of chromatography/mass spectrometry methods.
Software tool to analyze data that are acquired with LECO time-of-flight instruments. Used for processing and analyzing large amounts of data that are acquired with LECO instruments. Offers control of instrument and its accessories, as well as intuitive interface with highly integrated data processing. Mass spectrometry data system to fully accommodate multidimensional chromatographic data.
Literature review software by DistillerSR Inc. Automates management of literature collection, screening, and assessment using AI and intelligent workflows. From systematic literature review to rapid review to living review, makes any project simpler to manage and configure to produce transparent, audit-ready, and compliant results.
Software tool to integrate somatic mutation types into comprehensive integrated somatic mutation matrix for downstream analyses.Somatic mutation integration platform that tames allelic heterogeneity, discovers causal mutations, integrates binary PAM and fusion with quantitative CNA data types, and overcomes known obstacles in cancer genetics. Used for systematic integration of protein affecting mutations, gene fusions, and copy number alterations into comprehensive somatic mutational profile.
Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts.
Software R package as visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.
Software R package for comprehensive visualization of genomic signal associations. Visualizes enrichment of genomic signals on specific target regions. Used to visualize e.g. how histone marks are enriched to specific sites.
Probabilistic Aggregate Consumer Exposure Model Web
Web tool for aggregate consumer exposure assessment. Model is based on realistic product usage information obtained from surveys. Information on usage, frequency and amount of personal care products and household cleaning products in various European countries is included.
Software tool contains set of models for simulating fate of chemicals in main environmental systems and in human body. Features include uncertainty and sensitivity analysis as well as consideration of pharmacokinetics.
Web tool for assessing exposure and human health risks at contaminated sites. Fate and distribution of chemical pollutants in soil are calculated according to steady-state conservation of mass principles.Risks are calculated by comparing exposures with toxicological reference values and concentrations with toxicological or legal reference concentrations.
Web search tool to gain overview of set of articles retrieved by PubMed query. Used to support user driven summarization, drill down and browsing of PubMed search results. Value-added PubMed search engine for analysis and text mining.
Web tool used to analyse PubMed search results. Text mining tool. Will query PubMed with your specified searchquery, get all abstracts and generate frequency tables. The first table will show journals in which your query is published the most.The second table will show the authors which are most active in the field of your query.The third table will show words that have been used most in the title and abstract of the articles.
Software tool to detect regions that are affected by tissue damage, labelling defects, artifacts or errors in image acquisition, regions that are poorly registered, or where registration cannot be verified. Makes it easier for the user to explore the atlas hierarchy and decide on customized hierarchy level for investigation. QCAlign was developed to support QUINT workflow which supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to reference atlas.
Software R package for exploration of single-cell and bulk T-cell/antibody immune repertoires. Framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires.
Differential Enrichment analysis of Proteomics data
Software R package provides integrated analysis workflow for analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment.
Offers genomic technologies to academic laboratories and biotechnology companies.Application portfolio includes Whole genome (re)sequencing, including the identification of variants (SNVs, mutations, indels, CNVs);Targeted sequencing, for instance exomes; Transcriptome analyses (RNA-Seq, small RNA-Seq, microarrays), including in single cells (single-cell 3 RNA-seq); Determination of chromatin structure and dynamics (ChIP-Seq, FAIRE-Seq, Hi-C); Epigenetic analyses (ChIP-Seq, RRBS, Bisulphite-Seq);Genotyping (RAD-Seq, GBS, microarrays).
Offers functional and structural analysis of protein complexes.Offers possibility to characterize all types of molecular interactions: ligand-target binding, protein-protein interactions, signal transduction, and signalling complexes. Staff members are skilled specialists in luminescence-based techniques and in receptor biology.Application portfolio includes Analysis of cell signalling, by measuring signal transduction;Ligand-target binding (pharmacological analysis, affinity, selectivity); Protein-protein interactions (oligomerization, effectors...); Activation of signalling pathways (G proteins, GRK, arrestins & internalization); Intracellular production of second messengers (cAMP, IP1, Ca2+); Phosphorylation of signalling proteins (ERK, AKT...); Measurement of global cell functions and of different cell parameters (proliferation, migration, invasion...).
Software tool that scores positions in human genome in terms of their regulatory probability. Regulatory Mendelian Mutation score was created for relevance prediction of non-coding variations (SNVs and small InDels) in human genome (hg19) in terms of Mendelian diseases.
Facility dedicated to expression of innovative recombinant proteins for all in vitro and in vivo studies. Innovative technology developed by the platform, called FlexiBac, uses baculovirus / insect cell expression system.
Rockefeller University CRISPR and Genome Editing Resource Center Core Facility
CRISPR and Genome Editing Resource Center
Rockefeller University CRISPR and Genome Editing Resource Center
Provides gene targeting and mouse embryonic stem cell technology for members of Rockefeller University, Memorial Sloan-Kettering Cancer Center and their collaborators.CRISPR and Genome Editing services include mouse genomic knock-out and knock-in, mouse conditional knock-out, establishing new ES lines for gene targeting services, establishing ES lines from mutant mouse embryos, preparing ES cells introduced from off campus resources for injection or other application, assisting in embryoid body culture and in vitro differentiation of ES cells, and purification and evaluation of DNA for pronuclear injection.
Rockefeller University Transgenic and Reproductive Technology Center Core Facility
Rockefeller University Transgenic and Reproductive Technology Center
Transgenic and Reproductive Technology Center
Provides services such as Pronuclear Injection, Blastocyst Injection, Embryo and Sperm Cryopreservation, Strain Recovery and Rederivation. Provides assisted reproductive techniques such as IVF and ICSI used for strain recovery. Core facility to the university for creation and maintenance of all transgenic animal models, refinement and development of new transgenic techniques, as well as training center for research personnel.
Children's Hospital of Philadelphia CHOP-Penn Proteomics Core Facility
Children's Hospital of Philadelphia Research Institute CHOP-PENN Proteomics Core
Children's Hospital of Philadelphia Research Institute Proteomics Core Facility
Core facility specializes in mass spectrometry-based proteomics with a commitment to quality, rigor, problem-solving, and innovation. Provides expert guidance.
Software pipeline to process ATAC-Seq data. Used for automated end-to-end quality control and processing of ATAC-seq and DNase-seq data.
Software multistage analysis pipeline which progressively discovers cell types or states while mitigating impact of technical artifacts.Used for single cell analysis.
Comprehensive resource of neuropeptides, which holds non-redundant neuropeptide entries. Data collected from resources including MEDLINE abstracts, full papers, UniProt,database at www.neuropeptides.nl and Neuropedia. Contains detailed annotations for each entry, including source organisms, tissue specificity, families, names, post-translational modifications, 3D structures and literature references. Amino acid compositions, isoelectric points, molecular weight and other physicochemical properties of peptides are also provided. Search database with keywords such as sequence, name, family, etc.,User friendly web tools like browsing, sequence alignment and mapping are also integrated.Users can submit new entries online. Each new entry is validated before incorporating it.
Assays for Transposase-Accessible Chromatin using sequencing Quality Control
Software R package for post alignment quality assessment of ATAC-seq data. Package also contains functions to preprocess aligned ATAC-seq data for subsequent peak calling.
University of Michigan Ann Arbor Center for Chemical Genomics Core Facility
University of Michigan�Ann Arbor Center for Chemical Genomics
Provides high throughput screening of extensive small molecule, natural product and siRNA libraries along with assay development and optimization for basic biology and drug discovery projects.
University of Michigan Ann Arbor Natural Products Discovery Core Facility
University of Michigan�Ann Arbor Natural Products Discovery Core
Core has developed library of natural product extracts derived from unique collection of diverse marine and terrestrial actinomycetes, fungi and cyanobacteria. Provides technology and expertise to develop candidates identified through high-throughput screening into unique, bioactive, patentable, small molecules.
University of Rochester Medical Center Mass Spectrometry Resource Laboratory Core Facilitiy
University of Rochester Medical Center Mass Spectrometry Resource Laboratory
URMC Mass Spectrometry Resource Laboratory
Provides instrumentation and technical expertise to local researchers seeking to conduct MS-based protein or small molecule assays.Staff provide assistance with project design, sample preparation, collection and interpretation of mass spectrometric data.Common analyses services include identification of unknown proteins, characterization of protein complexes, mapping of post-translational modifications and relative quantitation of peptides and small molecules from range of sample types, including complex clinical matrices, tissue extracts and cell lysates. Specialized MS instrumentation include Fusion Lumos Tribrid Orbitrap and Thermo Q Exactive Plus Hybrid Quadrupole-Orbitrap. In addition, the laboratory has access to a variety of automated database searching software as well as resources to facilitate discovery-based proteomics projects.
La Jolla Institute for Immunology Next Generation Sequencing Core Facility
La Jolla Institute for Immunology Next Generation Sequencing Facility
Core provides latest sequencing technology combined with Institute's expansive bioinformatics capabilities. Provides instrumentation including Illumina Miseq, Covaris Model E220, NovaSeq 6000, Agilent 2200 Tapestation, Beckman Coulter Biomek FXP, HiSeq 2500.
McLaughlin Research Institute for Biomedical Sciences Transgenic Core Facility
McLaughlin Research Institute Transgenic Facility
Provides services to create, rederive or cryopreserve mouse models.Specific services include:CRISPR/Cas9-mediated gene editing (experimental design service and/or consulting also provided); pronuclear Injection; ES Cell Injection; In Vitro Fertilization; rederivation of mouse lines to specific pathogen free status; embryo and sperm cryopreservation and recovery.
Web too that implements various methods for evaluating extent of agreement among two or more raters. For two raters, data can be organize either as contingency table (for categorical ratings only) or as two column table of raw categorical or quantitative ratings. For three raters or more, data can be in form of columns of raw scores (for categorical or quantitative ratings), or alternatively in form of distribution of raters by response category for categorical only. Data can be captured in two ways. You can key in ratings directly in data grid or import it from CSV text file or MS Excel. You can highlight portion of grid you want to analyze and click on red action button. Selected data will be described below associated red action button.
Seattle Alzheimer Disease Brain Cell Atlas
Open atlas based on single cell profiling technologies with quantitative neuropathology and deep clinical phenotyping from middle temporal gyrus from neurotypical reference brains and brains from SEA-AD aged cohort that span spectrum of Alzheimer’s disease. Produced via collaboration between Allen Institute for Brain Science, University of Washington Alzheimer Disease Research Center and Kaiser Permanente Washington Health Research Institute.
Commercial collaborative research platform for hosting and analyzing datasets.Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data.
Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments.
Software toolbox to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes.
Non coding RNA sequence database. Comprehensive ncRNA sequence collection representing all ncRNA types from broad range of organisms.
University of Pittsburgh Medical Center Children Hospital of Pittsburgh Health Sciences Sequencing Core Facility
Health Sciences Sequencing Core at UPMC Children Hospital of Pittsburgh
University of Pittsburgh Health Sciences Sequencing Core at UPMC Children Hospital of Pittsburgh
Sequencing Core offers Illumina next generation sequencing services to University of Pittsburgh research community. Offers expertise in next generation sequencing technologies. Encourages to contact Assistant Director to arrange for consultation.Staff is available to share their experience and expertise to assist with development of projects of all sizes, standard or custom assay design, and other specialized application needs.
Cornell University Biotechnology Resource Center Biomolecular Interactions and Properties Core Facility
BRC Biomolecular Interactions and Properties Facility
Cornell University BRC Biomolecular Interactions and Properties Facility
Provides investigators with access to advanced tools for measuring biomolecular interactions and properties through variety of techniques from high throughput screening via automation to single reaction cuvette based methods.Facility complements technologies and techniques available through our Imaging facility and Proteomics and Metabolomics facility.
Software R library to automate labor intensive actigraphy data preprocessing and analyses steps while improving transparency, reproducibility, and scalability over software suites traditionally used in actigraphy research practice. Provides streamlined preprocessing while validating circadian rhythm and sleep analysis.
Single-cell RNA-seq cell types Recognition
Software R package for unbiased cell type recognition of scRNA-seq data. Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer cell of origin of each single cell independently.
Software tool for de novo extraction of mutational signatures from data generated in matrix format. Identifies number of operative mutational signatures, their activities in each sample, and probability for each signature to cause specific mutation type in cancer sample.
Software tool to create mutational matrices for all types of somatic mutations. Used to generate mutational matrices for set of samples with associated mutational catalogues. Used for optimized exploration and visualization of mutational patterns for all types of small mutational events. In addition to extending classification of single base substitutions, provides support for classifying doublet base substitutions and small insertions and deletions.
Software R package is group of maximum likelihood dN/dS methods designed to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole-exome level.Used to detect cancer driver genes on datasets ranging from few samples to thousands of samples, in whole-exome/genome or targeted sequencing studies.
Algorithms and Framework for Nonnegative Matrix Factorization
Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms.
International data repository for science, engineering and design. Services include curation, sharing, long-term access and preservation of research datasets. These services are available to anyone around the world. In addition, 4TU.ResearchData also offers training and resources to researchers to support them in making research data findable, accessible, interoperable and reproducible (FAIR).
Antarctic Meteorological Research and Data Center Repository
AMRDC Repository provides archival, preservation, access, and metadata authoring services for Antarctic meteorological data, managing data from submission to end-user retrieval. The repository hosts data collected by the Antarctic Meteorological Research Center and Automatic Weather Station projects, as well as campaign meteorological datasets deposited by other Antarctic investigators.
Open access repository. Contains research outputs and supporting data from staff and students, including published articles, conference papers, reports, datasets and theses.
Aperta is the name of the Turkish Open Archive.You can upload your scientific studies within the scope of Aperta to this portal or you can easily access the uploaded studies.
Aston Publications Explorer is Aston University's repository for their open access publications. You may also be interested in Aston Data Explorer for Aston's research data and Aston Research Explorer for broader information about Aston's research work including research staff, awards and activities projects and research groups.
Arch is an open access repository for the research and scholarly output of Northwestern University. Log in with your NetID to deposit, describe, and organize your research for public access and long-term preservation. We'll use our expertise to help you curate, share, and preserve your work.
Repository of metadata and data that describes and provides access to diverse data sets generated by Arctic and Antarctic researchers. The metadata records follow ISO 19115 and Federal Geographic Data Committee (FGDC) standard formats to provide exchange with other data centres. The records cover a wide range of disciplines from natural sciences and policy, to health and social sciences. The PDC Geospatial Search tool is available to the public and researchers alike and allows searching data using a mapping interface and other parameters.
Aston University's repository for their research data. It is one of three services providing information about Aston University�s research. Aston Publications Explorer holds Aston's research publications and Aston Research Explorer has broader information about Aston's research work including research staff, awards and activities, projects and research groups.Metadata will be accessible to anyone free of charge. The metadata may be re-used in any medium without prior permission and re-sold commercially provided the repository is mentioned.Aston�s repository holds datasets and corresponding metadata that have been produced by Aston University staff and students. The datasets deposited in Aston Publications Explorer range from metadata records only through to full datasets. Content is the sole responsibility of the authors, and any questions over content should be directed to them.Aston Data Explorer, Aston Publications Explorer AND Aston Research Explorer allow users to re-use full-text and other full-data items under the terms of the Creative Commons Attribution Non-Commercial No Derivatives (CC BY NC ND) licence. This means that users must give appropriate credit to the authors and link to the licence. Users may not re-use the material for commercial purposes. Users cannot distribute material that has been remixed, transformed or built upon the original published output. Where a full-text or other full-data item has a licence that is more restrictive or permissive than the CC BY NC ND default licence, this licence should be adhered to.
Astrobiology Habitable Environments Database
Astrobiology Habitable Environments Database (AHED) is a new data system being developed as a long-term, open-access repository for astrobiology data. AHED is intended to store user-contributed results from NASA or externally-funded research in astrobiology, and to encourage sharing and synergy within the astrobiology community.
Interoperable online network of marine and climate data resources.AODN Portal provides access to all available Australian marine and climate science data and provides the primary access to IMOS data.
Used to store, publish and share research data in FAIR way. Facilitates research data storage, guarantees long-term persistence of data and allows data, results or ideas to be shared worldwide.Supports community domains with metadata extensions, access rules and publishing workflows.
International effort that seeks to increase our knowledge and understanding of Antarctic and Southern Ocean biodiversity.It is a community of researchers, data custodians and developers from around the world that supports the mobilisation publication, retrieval and analysis of Antarctic and Southern Ocean biodiversity data in a free and open manner in line with the Antarctic treaty and the FAIR data Principles (Finable, Accessible, Interoperable, Reusable). The SCAR Antarctic biodiversity Portal has a number of portals dedicated to specific types of data and information on Antarctic and Southern Ocean Biodiversity.We aim to create an information ecosystem of various data bases, data systems, web services tools etc that can be used by anyone with an interest in Antarctic and Southern Ocean biodiversity.Biodiversity.aq is an international initiative of the Scientific Committee on Antarctic Research (SCAR). It finds it roots in the Census of Antarctic Marine Life and started in 2005. The central facilities are hosted by the Royal Belgian Institute for Natural sciences (RBINS, www.naturalsciences.be) and the Belgian Biodiversity Platform (BBPf, www.biodiversity.be).The SCAR Antarctic Biodiversity Portal is the regional thematic node of the Ocean Biodiversity Information System (OBIS, www.obis.org), the Global Biodiversity Information Facility (GBIF, www.gbif.org) and works closely together with the Southern Ocean Observation System (SOOS, www.soos.aq).
Barbara A. Mikulski Archive for Space Telescopes
Astronomical data archive focused on optical, ultraviolet, and near infrared. Used for maximizing scientific accessibility and productivity of astronomical data. MAST hosts data from over dozen missions like Webb, Hubble, TESS, Kepler, and in the future Roman.
Portuguese distributed infrastructure for biological data and Portuguese node of ELIXIR.
Repository allows all researchers at Birkbeck to upload data, and get DOI.Data in the Birkbeck Data Repository is stored on Arkivum server.This is a very secure storage space, which will allow our data to remain unchanged and accessible for many years after it is deposited.
Scalable cloud-based platform for computational discovery designed for the brain health community.The BRAINCommons empowers the global research community by providing access to multi-model data, state-of-the-art tools and a secure interoperable system for data sharing.
BioHeritage National Science Challenge Data Repository
Data catalogue and repository for New Zealand's Biological Heritage National Science Challenge.
Provides open access to Climate and Earth System Data from scientists at the centre and their collaborators. Helps to make your data open, FAIR and visually appealing. Each dataset and source code in the Bolin Centre Database is assigned a unique DOI. This makes it easy to cite and find your data. If dataset has more than one version, each version will have its own DOI.
Repository of metadata and data that describes and provides access to diverse data sets generated by Arctic and Antarctic researchers.Metadata records follow ISO 19115 and Federal Geographic Data Committee standard formats to provide exchange with other data centres.Records cover wide range of disciplines from natural sciences and policy, to health and social sciences. The PDC Geospatial Search tool is available to the public and researchers alike and allows searching data using mapping interface and other parameters.
Collection contains open and publicly funded data sets created by Brown University faculty and student researchers. Increasingly, publishers, and funders are requiring that protocols, data sets, metadata, and code underlying published research be retained and preserved, their locations cited within publications, and shared with other researchers and the public. The deposits here endeavor to be in line with FAIR Principles (Findable, Accessible, Interoperable, Reusable). If you would like to deposit data set into this collection for the purposes of citation/linking within publication and public dissemination, then please log in, zip up and upload your file, and request digital object identifier (DOI) for your data citation.
Software repository for Python programming language.Used to find and install software developed and shared by Python community.
Integrated Quality Assurance System MDL-LDA Component Resources
Integrated Quality Assurance System Modeling document labels using Latent Dirichlet Allocation Component Resources
Modeling document labels using Latent Dirichlet Allocation is component tool under Integrated Quality Assurance System of Camarines Sur Polytechnic Colleges which categorizes text of particular document and use it for auto-tagging.
Thermo Fisher: Sartorius | IncuCyte S3 Live Cell Analysis System
Incucyte S3 Live-Cell Analysis Instrument
System that automatically captures and analyzes images of living cells around-the-clock for days, weeks, or months, while cells remain undisturbed inside standard tissue culture incubator. Kinetic, image-based measurements. Used for cell monitoring and surveillance, cell health and viability, migration and invasion, phenotypic cell based assays.
ERMA | Automatic blood cell counter PCE-210N
Automatic cell counting instrument. Used to count blood cells.
Software Python package to visualize outputs of AmpliconArchitect in style of Circos plots. General circular visualizations of genomic regions. Used to visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos style images.
Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers.
Software package to read, manipulate and visualize 'Pairwise mApping Format' data in R.
Software toolbox for synchronized dual camera acquisition. Library for acquisition of synchronized dual camera video. Videos are saved with alternate acquisition of frames what ensures equal number of frames.
Universal utility for programming FPGAs. Compatible with many boards, cables and FPGA from major manufacturers (Xilinx, Altera/Intel, Lattice, Gowin, Efinix, Anlogic, Cologne Chip). Works on Linux, Windows and macOS.
Software tool provides visualization techniques for clonal evolution. Available plots include shark plots as basic trees, showing phylogeny and optionally cancer cell fraction; dolphin plots as advanced visualization, showing phylogeny and development of CCFs over time; plaice plots as novel visualization, showing phylogeny, development of CCFs and development of remaining healthy alleles, influenced by bi-allelic events, over time. Provides algorithms for fully automatic interpolation of time points and estimation of therapy effect to approximate tumor's development in presence of few measured time points, as well as exploring alternative trees.
One of four functional modules of 4D-Nucleofector System. It supports Nucleofection of various cell numbers cells in different formats.
Rapid protein transfer apparatus that can transfer protein to membrane in 3 minutes.High performance western blotting transfer system designed to provide rapid transfers with high efficiency.
Software tool as R implementation of NicheNet method to predict active ligand-target links between interacting cells. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.
ChIP-X Enrichment Analysis Version 3 (ChEA3)
Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries.
Nikon | Eclipse TE2000 inverted microscope system
Nikon Eclipse TE2000 inverted microscope
TE2000 was developed as full system with 3 models, the S, the U and the E. TE2000E is high precision Z-focus automated model that features 5 output ports and 5-way motorized light path changer. Used for advanced research that requires image capture in 3D, including confocal microscopy and deconvolution processing.TE2000U is universal model that comes with 4 output ports as standard, plus optional fifth user defined position, thereby providing unprecedented 5-way light path.The U model also features integrated magnification changer module providing 1x or 1.5x magnification to all ports.
Princeton Instruments | Teledyne SpectraPro 2150 imaging spectrograph
150 mm focal length monochromator/spectrograph. It features astigmatism corrected optical system, dual indexable gratings and interchangeable grating turrets.
Second generation low noise 16 bit computer interface from Instrutech Corporation. 16-bit Multi-Channel Data Acquisition Interface with PCI or USB host adapter.
Luca-S camera of single photon sensitive imaging Andor family scientific cameras with Electron Multiplying Charge Coupled Device detector, designed for most challenging low-light imaging applications.
Scientific camera with EMCCD image sensor that is capable of detecting single photon events without image intensifier, achievable by way of unique electron multiplying structure built into the chip.
Children's Hospital Association Pediatric Health Information System
Comparative database with clinical and resource utilization data for inpatient, ambulatory surgery, emergency department and observation unit encounters for more than 49 children's hospitals.
Neurodegenerative Disease Knowledge Portal
Portal includes human genetic and functional genomic results generated via consortia based science focusing on neurodegenerative diseases such as ALS, Parkinson's disease, and Alzheimer's disease.
Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data.
Software tool to compute gene structure predictions.Gene structure predictions are calculated using similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments.
open Metadata Initiative for Neuroscience Data Structures
The openMINDS metadata framework comprises: schema specifications for multiple, interlocked metadata models for Linked Data, instance libraries for serviceable, well defined terms and constructs, as well as supportive tooling. openMINDS is developed as open source project by Open Metadata Initiative on GitHub. The framework is distributed over multiple, interlinked GitHub projects with one main GitHub repository for central access and maintenance.
Software for creating surveys and questionnaires.
Intraclass Correlations for Quantifying Inter Rater Reliability
Intraclass Correlations for Quantifying Inter-Rater Reliability
Software R package to calculate various intraclass correlation coefficients. Used to quantify inter-rater and intra-rater reliability.
Computing Chance Corrected Agreement Coefficients
Computing Chance-Corrected Agreement Coefficients
Software R package to calculate various chance-corrected agreement coefficients among 2 or more raters. Among CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses.
University of Rochester Light Microscopy Resource Core Facility
University of Rochester URMC Light Microscopy Resource
Core for conventional brightfield microscopy and confocal microscopy.
University of Rochester Medical Center Biosafety Level 3 Core Facility
Core facility is available for use by any researcher at university whose work requires manipulation of biological agents that may cause serious or potentially lethal disease as result of exposure by inhalation route.
Penn State Hershey College of Medicine Comparative Medicine Imaging Core Facility
Penn State Hershey College of Medicine Comparative Medicine Imaging
Core provides equipment and expertise for bioluminescence and fluorescence imaging, in-vivo, full-body, 3D anatomical, functional and molecular imaging and MRI.
Taiwan Bioresource Collection and Research Center
Bioresource Collection and Research Center
Systematic and service oriented BioResource Center in Asia. Member of World Federation for Culture Collections from 1984 until now. BCRC is the first BRC certified by international organization of ISO quality system. Approved by Taiwan Biodiversity Information Facility.
Collection as result of joint work of scientists, technicians and students from Federal University of Rio de Janeiro and Technical-Scientific Association Paul Ehrlich. Center of reference and excellence in cell culture in Brazil and in our continent. Collection of human and animal cells that operates as service provider in Brazil and is the largest in South America.
Collection of Cell Lines in Veterinary Medicine
Generates, characterises and collects cell lines which are of interest for veterinary research and diagnostics. Collection includes cell lines of farm animals such as cattle, pig, horse, sheep, goat and poultry and other mammals, birds, reptiles, fishes and insects (70 species).Authentication and quality-control tests (tests for contamination with mycoplasms, bacteria, BVDV) of the cultures are done routinely.Cell cultures are provided to scientists of the Friedrich-Loeffler-Institute and other non-commercial institutions worldwide after consultation of a scientific staff member of the CCLV.
Independent cell repository with rigorous monitoring, quality control and cell authentications to ensure that your cells are free of contaminations and with genuine genetic profile.
Was established in 1994 as core facility of National Institute of Cancer Research. Supplies human and animal cell lines; Short Tandem Repeat (STR) profiling of human cell lines; quality control service; mycoplasma detection and eradication service; safe deposit service and patent deposit service of cell lines and hybridomas. The catalogue of services is on-line, and the cell lines are distributed all over the world. Search allows to query catalogue on the basis of any word that may be included in the description of cell lines, including both encoded terms and free text information.
Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna Biobank
Provides maintaining and managing the largest veterinary biobank facility in Italy for the storage of biological resources. IZSLER Biobank of Veterinary Resources include mainly bacteria and viruses from different animal species isolated during the routine IZSLER diagnostic activity, carried out on biological samples from farm animals, pets and wildlife and from food and feed. Biobank includes more than 600 cell lines from human and animal origin. All the materials enrolled in our collection are submitted to different cultural and molecular biology control tests in order to evaluate their characteristics, purity and identity. IZSLER laboratories, that supply biological resources to IBVR, use testing methods performed according to UNI EN ISO/IEC 17025 quality system.
Integrated data set and analytics platform combining Research Resource Identifiers (RRIDs), text mining and data aggregation.
Japanese Collection of Research Bioresources Cell Bank
Japanese Collection of Research Bioresources (JCRB) Cell Bank
Collection of various human and animal culture cells including cancer and genetically modified cells. Cell resources are distributed to researchers across Japan and around the world. These cells are comprehensively qualified by testing microbial contamination, virus contamination and cross culture contamination. Some cells are characterized by karyotyping and/or cell surface markers. In collaboration with other major cell banks in the world, we are developing methods for cell culturing and quality control in order to support fundamental research on medical of pharmaceutical sciences.
Kunming Wild Animal Cell Bank of the Chinese Academy of Sciences
Cell Bank provides high quality resources and services including cell lines/tissues/DNA samples; cell culture training/trouble-shooting; cell culture/genetic research equipment; cell line karyotype analysis; STR/mycoplasma contamination detection; chromosome painting; cell line preservation.Cell Bank is branch of National Platform of Experimental Cell Resources for Science and Technology, Wildlife Resource Bank of the Chinese Academy of Sciences, the China Germplasm Bank of Wild Species, and also affiliated with Institute’s State Key Laboratory of Genetic Resources and Evolution.
Bank is located at the Cancer Research Institute of the Seoul National University College of Medicine. Collects cell lines from diverse laboratories but also continually develops new cell lines. We as well distribute our cell lines and provide researchers with detailed information about the cell lines.
National Cancer Institute Developmental Therapeutics Program
DTP supports number of Repositories for the acquisition, storage and distribution of chemical, and biological samples and standards to researchers worldwide. In many cases there is no, or only nominal fee for samples.
NIH HIV Reagent Program has been managed under contract by American Type Culture Collection (ATCC) since 2020. ATCC shall maintain the NIH HIV Reagent Program through identification, acquisition, production, receipt, storage, maintenance, distribution and disposal of biological and chemical research organisms and materials for HIV and other infectious diseases for use in basic and translational research.
Tohoku University Cell Resource Center for Biomedical Research Cell Bank
Cell Resource Center for Biomedical Research, Cell Bank is the collection, establishment, quality control, distribution of useful cell lines, and construction of database for researchers. The cell lines include transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells. Available cell line are listed in The Cell Line Catalog.
Web application that simplifies evaluation of confidence in findings from network meta analysis.
A measurement tool to assess systematic reviews
Guide tool to assess methodological quality of systematic reviews. Used to evaluate systematic reviews of randomised trials. AMSTAR 2 enables more detailed assessment of systematic reviews that include randomised or non-randomised studies of healthcare interventions, or both.
Imaging system enables comprehensive analysis of cellular phenotypes. Allows access to single cell insights. This includes deeper understanding of intricate spatial relationships of cells, pathways and phenotypes in tissue microenvironment.
Software toolkit that enables real-time basecalling and several post-processing features that works on Oxford Nanopore Technologies sequencing platforms. Data processing toolkit that contains Oxford Nanopore Technologies basecalling algorithms, and several bioinformatic post-processing features. Provided as binaries to run on Windows, OS X and Linux platforms, as well as being integrated with MinKNOW, Oxford Nanopore device control software.
University of Rochester Medical Center Cold Storage Core Facility
University of Rochester Medical Center Cold Storage Core
Provides controlled environment designed for long term storage of clinical/research materials in -20C or -80C freezers and in liquid nitrogen freezers.
Karolinska Institute Live Cell Imaging Core Facility
Light microscopy facility. Offers microscopes and training to image cell and tissues, live or fixed, BSL1/BSL2.
Open source software tool for closed loop neuroscientific experiments capable of sub-millisecond response latency over high-rate streaming data acquired from high-count multi-electrode arrays. Used for processing and controlling closed-loop neuroscience data.
Web service that works alongside the Galaxy SciWMS to enable dynamic training infrastructure.
Software tool to interpret and interact with taxonomic profiles produced by different taxonomic profiler methods beyond standard metrics used by scientific community. Interpretable analysis and visualization of metagenomics based taxon abundance profiles.
Software for standard implementation conforming to Global Alliance for Genomics and Health Workflow Execution Service API specification.
Web application for managing and executing Workflow Execution Service (WES) services.
Software CLI tool to support building and maintaining Yevis workflow registry.
Web application for browsing Yevis workflow registry.
Software CLI tool to verify workflow reproducibility.
Platform for archiving and sharing of primary data outputs from research on low dose radiation. Provides directory of bioresources and databases containing information and materials that investigators are willing to share. Supports creation of low dose radiation research commons.
Software package for including transposable elements in differential enrichment analysis of sequencing datasets. Used for including transposable elements in differential expression analysis of RNA-seq datasets. RNAseq TE quantification tool.
Cell sorter offers advanced automation technology with BD FACSChorus software and guides you through entire cell sorting process with its intuitive interface, on-screen instructions and tips and simple-to-read reports.
Van Andel Institute Cryo-Electron Microscopy Core Facility
Facility encompasses cryo-electron microscopes (Krios, Arctica), which are supported by expert staff and high performance computing cluster with extensive cloud capabilities.Provides wide range of cost effective and efficient biological EM services.
Van Andel Institute Vivarium Core Facility
Core provides and supports gold standard of high quality mouse, rat and zebrafish modeling services for VAI investigators, collaborators and greater research community.Facility includes high containment barrier. All procedures are conducted according to the National Institutes of Health Guide for the Care and Use of Laboratory Animals. The Institute is accredited at the highest standard of care through the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International.
Johns Hopkins Medical Institute Clinical and Translational Research Laboratory Core Facility
Johns Hopkins Medical Institution JHMI-ICTR Research Laboratory Core
Core performs high throughput assays for determination of proteins, peptides, hormones and other biochemical markers in support of preclinical and clinical research studies. Laboratory has equipment and capacity to perform standard immunoassays as well as multiplexed ELISAs. Provides standardized sample handling that upholds high quality control. Supports reduced investigator cost through batch analysis of samples and direct manufacturer pricing.
Software tool to predict protein coding genes in fungal genome assembly. Performs gene prediction on given genome assembly and RNA-seq reads. Runs multiple gene predictors, evaluates all predicted genes, and assembles gene models that are highly supported by homology to known sequences.
Stable models to generate tertiary structures that mimic natural features including backbone, local and distal characteristics, found in real proteins.
Software tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis.
Software tool to subset 10x Genomics BAM file based on tag, most commonly cell barcode tag.Takes 10x Genomics BAM file, CSV file defining subset of cells you want to isolate, and produces new BAM file with only alignments associated with those cells.Subsets BAM files output from CellRanger by tag which is usually cell barcode.
Asian Mouse Mutagenesis Resource Association
Mouse genetics and laboratory animal resources in the Asia Pacific. Collaborative group of development, archiving/distribution, coordination of phenotyping and informatics of mutant mice in Asia. Facilitates access to mouse resources in Asia for use of mouse models for understanding genome function and improvement of human health.
Mammalian cell colony, spheroid and organoid counter. PC software operated colony counter that automates detection, counting and analysis of mammalian cell colonies in multi-well plates, Petri dishes and T25 flasks.
Copy-number Haplotype Inference in Single-cell by Evolutionary Links
Software tool to infer allele and haplotype specific copy numbers in individual cells from low coverage single cell DNA sequencing data. Integrates weak allelic signals across individual cells, powering strength of single cell sequencing technologies to overcome weakness. Includes global clustering of RDRs and BAFs, and rigorous model selection procedure for inferring genome ploidy that improves both inference of allele specific and total copy numbers.
Software analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation, and compare heterogeneity among cells. Used in processing of single cell DNA sequencing performed on 10x Chromium platform.
Software pipeline for analysis of nfcore chromatine accessibility data including ChIP-Seq, DNAse-Seq or ATAC-Seq and nfcore RNA-seq count data. Performs DESeq2, TEPIC and DYNAMITE including all preprocessing and postprocessing steps necessary to transform data and provides plots for deep analysis of data.
Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally.
Web application as public data catalog, compute infrastructure, geospatial APIs and interactive app server. Geospatial processing service.
Software Python implementation of UpSet plots to visualize set overlaps.
Software spreadsheet based application for risk measurement and reporting, Monte Carlo simulation, time series forecasting, and optimization.Provides realistic and accessible way of modeling uncertainty, enabling you to measure and report on risk inherent in your key metrics.
System used to image and analyze Western blots. Odyssey Fc imager has been discontinued.
Stanford Graduate School of Business Library
Provides resources and services to support business related research and teaching at Stanford University. As part of GSB Research Hub, helps foster scholarship, teaching, and innovation by committing to access, dissemination, creation, and preservation of information and knowledge.
Stanford System Prototyping Core Facility
Electronics Shop where researchers can access and share expertise to build specialized electronics. Offers support to electronic sub-system design for researchers across campus in departments of Physics, Applied Physics, Electrical Engineering, Psychology, Psychiatry and Behavioral Sciences and Bioengineering.Provides expertise from independently using tools to requesting turnkey solution.
Group of service centers (Nanofabrication, Electron & Ion Microscopy, X-ray & Surface Analysis and Soft & Hybrid Materials) that include Stanford Nanocharacterization Laboratory, Nanopatterning Cleanroom, Ginzton Microfab, and Soft and Hybrid Materials Facility. Core provides shared scientific instrumentation, laboratory facilities, and expert staff support.
Stanford Graduate School of Business Behavioral Lab Core Facility
Stanford Graduate School of Business Behavioral Lab
Interdisciplinary laboratory designed for study of human subjects.Lab resources are available to all Stanford GSB faculty and PhD students to support research that uses human participants, whether your focus is organizational behavior, behavioral marketing, political economics, or behavioral economics.Assists with research by programming study, posting study to one or more of the available subject pools, paying participants, running participants through experiments in the lab, or creating study materials.Engages with faculty members and doctoral students in preparing and carrying out human subjects research, both in-person laboratory experiments and online survey research.Provides expert consultation on behavioral experiments, and implementations of technology in behavioral research, such as eye-tracking, psychophysiology, and other specialized technology used in research with human subjects.
Stanford Sarafan Medicinal Chemistry Knowledge Center Core Facility
ChEM-H Knowledge Centers Medicinal Chemistry
Medicinal Chemistry Knowledge Center (MCKC)
Core for drug discovery and prototyping. Provides chemical probes for biological pathways and supports small molecule custom synthesis.Provides expertise in medicinal chemistry to biologists and clinicians at Stanford. Expertise in each step of drug development process, including hit generation, drug design and optimization, and clinical selection. Provides instrumentation to support synthesis, purification and analysis of small molecules.
Stanford Sarafan Macromolecular Structure Knowledge Center Core Facility
Macromolecular Structure Knowledge Center
Service center and teaching lab focusing on molecular structural-functional studies. Jointly established by Sarafan ChEM-H, School of Engineering and SLAC National Accelerator Laboratory. Provides Stanford researchers with expertise, training and instruments for techniques in spectroscopy, bioimaging, crystallography, and scattering and diffraction.
One of four labs that are part of nano@stanford, under NSF National Nanotechnology Coordinated Infrastructure program. SNF includes cleanroom housing tools for device fabrication, satellite labs supporting Metal Organic Chemical Vapor Deposition,Experimental Fabrication methods and electronics shop for Systems Prototyping. SNF supports researchers in applications ranging from medicine and biology to fundamental physics and astronomy.
Stanford Sarafan Metabolomics Knowledge Center Core Facility
Provides scientific expertise and instrumentation for measurement of small molecules such as metabolites and lipids to ChEM-H and Stanford communities. Leverages expertise in mass spectrometry and allied techniques to understand biology of small molecules both metabolites and xenobiotics and to apply that understanding to advances in human health.
Stanford Sarafan Protein Engineering Knowledge Center Core Facility
MSKC is main gateway for Stanford faculty and students interested to study biological molecules using SLAC X-ray facilities and other major bioimaging facilities.
Stanford Sarafan Chemistry, Engineering and Medicine for Human Health Knowledge Centers Core Facility
Engineering & Medicine for Human Health (ChEM-H) Knowledge Centers
Shared resource to provide instrumentation and scientific expertise to Stanford researchers.Each Knowledge Center is organized around specific scientific area and offers services to the research community. Services, advice, training and instrument access, include area in High-Throughput Screening, Medicinal Chemistry, Crystallography, Cryo-EM, Metabolomics, Protein engineering, Protein expression.
Software metadata ingestion platform that helps to improve quality of metadata. Station allows users to record meta-data according to minimum information standards thereby ensuring FAIR scientific data management from the start.
Software tool as routine for given estimated SPM to find cluster extent threshold, such that only significant at defined corrected p-value clusters are displayed and listed.
SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.
Software R package as collection of functions that assist with streamline modeling. Works with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.
Washington University School of Medicine Genome Engineering and Stem Cell Center Core Facility
Genome Engineering & Stem Cell Center (GESC@MGI)
Washington University School of Medicine Genome Engineering & Stem Cell Center (GESC@MGI)
Provides support with technologies for cell and animal model needs. Services are ranging from CRISPR reagents with or without validation, to cancer/iPS cell line modification or animal model creation. Works closely with mouse cores from design, reagent validation to genotyping, process improvement and troubleshooting, when necessary. Provides next-generation sequencing (NGS) based human cell authentication and NGS-based genotyping services and general molecular biology assistance. Offers to culture, bank and store primary fibroblasts and renal epithelial cells from patient samples for investigators, and iPSC reprogramming service is provided from fibroblasts, RECs as well as peripheral blood mononuclear cells. Provides differentiation services on growing list of cell types.
Penn State College of Medicine Biomolecular NMR Core Facility
Penn State College of Medicine Penn State COM Biomolecular NMR
Provides services for multiple modern NMR applications, including structure elucidation of small molecules, triple resonance experiments of biomolecules, fragment-based drug discovery, metabolomic and tissue analyses.
University of Colorado Anschutz Medical Campus Gnotobiotic Core Facility
University of Colorado Anschutz Medical Campus CU Anschutz Gnotobiotic Core
Provides germ free and gnotobiotic mice, space in which investigators can complete their own studies or hire core to complete experimental manipulations.Facility includes 12 large soft sided vinyl isolators for breeding and 8 small soft sided vinyl isolators for experiments. There is option between using Allentown positive pressure racks and static cage for experimental use.
University of North Carolina at Chapel Hill Human Pluripotent Cell Core Facility
University of North Carolina at Chapel Hill Human Pluripotent Cell Core
Provides services to conduct basic as well as translational research using human induced pluripotent cells. Offers Reprogramming, Genome editing and directed cell differentiation.
Oslo University Norwegian Human Pluripotent Stem Cells Core Facility
Core Facility for Human Pluripotent Stem Cells
Norwegian Core Facility for Human Pluripotent Stem Cells
Core assists with production, characterization and differentiation of human pluripotent stem cells. Offers services related to research on human ES and iPS cells. Provides reprogramming of iPS cell lines from patients and healthy donors, for example for in vitro disease modeling. Offers already established human ES cell lines and large bank of human iPS cell lines established through ongoing REK-approved projects. Provides ES and iPS cell characterization services, and training in the culture and maintenance of human ES and iPS cells.
Stanford Vincent V.C. Woo Sandbox Laboratory Core Facility
Stanford Vincent V.C. Woo Sandbox Laboratory (SBCL)
Vincent V.C. Woo Sandbox Laboratory (SBCL)
Provides space and equipment for collaborative pilot projects between engineers and neuroscientists, workshops, training classes and product demonstrations as requested by members of Wu Tsai Neuro. Facility provides tissue culture suite with two biosafety cabinets, CO2 incubators, centrifuge and fluorescent microscope, in vivo procedure suite to allow animal surgeries, four curtained electrophysiological rig/microscope areas, two microscope rooms, -20C and -80C freezers and 4C cabinets for temporary sample storage.
Stanford Behavioral and Functional Neuroscience Laboratory Core Facility
Behavioral and Functional Neuroscience Laboratory (BFNL)
Stanford Behavioral and Functional Neuroscience Laboratory (BFNL)
Laboratory at Wu Tsai Neursciences Institute provides preclinical discovery platform for central nervous system target validation in preclinical in vivo and in vitro models. Neurobehavioral assessment tools in CNS disease models provide platform for screening and profiling of experimental therapeutics and genetic rodent models. Used to support understanding of human CNS disorders and development of therapeutic interventions.
Stanford Neuroscience Gene Vector and Virus Core Facility
Neuroscience Gene Vector and Virus Core (GVVC)
Stanford Neuroscience Gene Vector and Virus Core
Core centralizes process of producing and distributing viral vectors and cDNA plasmids.
Stanford Visualization Laboratory Core Facility
Used to explore new visualization technologies related to study of brain.Provides equipment and expertiese to help with project setup and planning. Hosts adaptive optics system that uses optical principles originally developed for visualizing distant stars to enable high resolution imaging of retina in human subjects.
Stanford Geochronology Cluster Core Facility
Core for comprehensive examination of evolution of Earth's crust using geochronologic approaches. Provides spectrum of analytical facilities that are all housed within School of Earth, Energy and Environmental Sciences.Provides data to many disciplines throughout geosciences, including tectonics, geodynamics, petrology, geochemistry, geomorphology, sedimentology, stratigraphy, paleontology, and paleoclimatology.
Stanford Stable Isotope Biogeochemistry Laboratory Core Facility
Stable Isotope Biogeochemistry Laboratory
Stanford Stable Isotope Biogeochemistry Laboratory
Stable Isotope Biogeochemistry Laboratory at Stanford University's School of Earth Sciences provides analytical facilities and technical expertise to members of Stanford community who need to determine stable isotope ratios of variety of organic and inorganic materials from both terrestrial and marine environments.
Stanford Neuroscience Preclinical Imaging Laboratory Core Facility
Neuroscience Preclinical Imaging Laboratory
Stanford Neuroscience Preclinical Imaging Laboratory
Provides preclinical Magnetic Resonance Imaging technology and expertise to Stanford community. Offers range of support from full project to independent user operation and training.
Stanford Environmental Measurements Core Facility
Stanford Environmental Measurements Facility
Provides instruments for solid, aquouse and gas sample analyses, quantitative analysis, technical expertise to members of Stanford community.
Stanford Microchemical Analysis Core Facility
Stanford Microchemical Analysis Facility
Facility is equipped with JEOL JXA-8230 SuperProbe electron microprobe. Electron microprobe measures elemental compositions of solid samples by detecting the X-rays emitted on excitation by focused electron beam, down to spatial resolution of about 1 micron. All elements heavier than beryllium can be detected, at concentrations as low as 10s of ppm. Highly quantitative analyses are made using 5 wavelength dispersive X-ray spectrometers (WDS) with calibrations based on known standard materials. Compositional images (maps) can readily be obtained with backscattered electrons (sensitive primarily to mean atomic number), or with WDS or EDS X-ray data. The instrument is adjacent to the Stanford Nanocharacterization Laboratory (SNL), at the west end of the first floor of the McCullough Building.
Stanford Neuroscience Microscopy Service Core Facility
Stanford Neuroscience Microscopy Service
Provides microscopy expertise and access to high resolution, state-of-the-art imaging technologies to Stanford University and surrounding academic and biotech researchers. Core provides training, design, implementation, and analysis assistance.
Stanford Doerr School of Sustainability Sample Preparation Laboratory Core Facility
Stanford Doerr School of Sustainability Sample Preparation Laboratory
Provides guidance, access, and hands-on training for rock preparation, equipment uses, and mineral separation techniques. The most common uses are Powdering samples for geochemical or isotopic analysis;Cutting/drilling/coring rocks for geophysical analysis or generating thin section billets;Separation of zircon and apatite from quartz and feldspar;Soil and/or sediment sieving.
Shared analytical facility specialized in areas of radiogenic isotope geochemistry, non-traditional stable isotope geochemistry, and low blank concentration determinations of natural and engineered materials. Provided equipment includes triple-quad ICP-MS (Agilent 8900) with laser ablation intake system (AS RESOlution laser system), multi-collector ICP-MS (Neptune XT), and specially designed Picotrace metal-free low particulate clean laboratory. Produces high quality isotopic and trace element data. Offers training.
Nationwide Children’s Hospital Abigail Wexner Research Institute Biopathology Center Core Facility
Provides services related to biospecimen procurement, banking, processing, and distribution. Housed biospecimen collections are from biorepositories of National Cancer Institute funded Children’s Oncology Group, NRG Oncology-Columbus (formerly the GOG Tissue Bank), SWOG, Pediatric Division of Cooperative Human Tissue Network, and Biospecimen Core Resource of Center for Cancer Genomics, as well as numerous biospecimen collections sponsored by funded NCH investigators. Cooperative Human Tissue Network is one of six institutions funded by National Cancer Institutes to access to remnant human tissues for biomedical researchers throughout the United States and Canada. Offers expertise in tissue preparation and preservation to meet the research needs of basic and applied scientists.
Shengqiang Technology |SQS-40P slide scanning imaging system
Slide scanning image analysis system independently developed and designed by Shengqiang Technology has flexible objective lens configuration, automatic slide loading, and super-large-size scanning. Can seamlessly stitch tens of thousands of pathological slice pictures into complete slice, and intelligently generate full-field digital slide can digitize, complete and permanently store slide information. Experts can browse from a macro image, and then place it at any position and any magnification to observe the details of the slice .
Roche COBAS 6000 analyzer automated system
Roche/Hitachi Cobas 6000 analyzer series
Roche/Hitachi Cobas 6000 analyzer series is fully automated, random-access, software- controlled system for immunoassay and photometric analyses intended for qualitative and quantitative in vitro determinations of wide variety of tests. Cobas 6000 modular analyzer is composed of core unit and combination of up to 3 analytical modules to best suit your needs.
Texas A and M University Rodent Preclinical Phenotyping Core Facility
Texas A&M University Rodent Preclinical Phenotyping Core
Core houses various instruments to measure and quantify mouse and rat physiology and behavior. Offers equipment to help expedite comprehensive research in many fields, including Behavior, Cardiovascular, Cancer, Pathological, Metabolic, Skeletomuscular, and Histology.
Emory University Emory Stem Cell Core Facility
Core is supported by Georgia Clinical and Translational Science Alliance and Emory University School of Medicine. One of Emory Integrated Core Facilities (EICF). Offers services for generating induced pluripotent stem cells from human somatic cells for research.
Software tool to perform analysis of microbiome studies and generates portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.
Eppendorf | Mastercycler nexus PCR Thermal Cycler
Thermal cycler conduct PCR runs with range of standard vessel types, from 0.2 mL tubes to 96 well plates using single 96-well aluminum block. Can accommodate 96-well PCR plates, 0.2 mL PCR tubes, 0.2 mL PCR tube strips, and 0.5 mL PCR tubes.Mastercycler nexus cycler can email you when PCR run is complete.
Thermo Fisher: Sartorius | Octet BLI systems
Octet BLI systems with Octet Analysis Studio
Octet BLI systems enable real-time, label-free analysis for determination of kinetics, affinity and antibody/protein quantitation. Includes Octet Analysis Studio for analysis of assays measuring kinetics and affinity values for drug-target binding and high-throughput kinetic screening for lead identification. Typical applications include kinetic analysis of protein-protein, protein-small molecules, antibody-antigen, antibody-VLP, antibody-Fc gamma receptors, including antibody-neonatal receptor (FcRn) interactions. Additional applications supported include lot release and stability analysis of drug molecules based on binding kinetics and affinity.
Web server for analyzing and visualizing helical, backbone and groove parameters of nucleic acid structures. Can also be used to analyse molecular dynamics trajectories., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Open source electrophysiology hardware and software package for simultaneous EEG and EMG acquisition from multiple subjects.
CellVoyager CV8000 High-Content Screening System
High content screening system with improved built-in incubator to analyze extended live cell responses. System includes proprietary Yokogawa High Speed Confocal Scanner, water immersion lens, up to four high field-of-vision cameras, microscopic stage with cell cultivation environment, integrated robotic pipetter and specialized analysis software, CellPathfinder.
Software tool provides automation and process control across wide variety of applications, creates planned data driven schedules in optimized and predictable scheduling environment.
Software package that gathers data and synthesizes runtime information from Biomek log files to capture each manipulation of sample during course of method.
Thermo Fisher | Cytomat 10 Hotel Ambient Storage
Storage used for high capacity random access storage (210 SBS microplates) at ambient conditions. The Cytomat 10 Hotel (PH) offers multiple transfer positions, dual access point (DAP) and as combined benchtop-under bench solution, it allows flexible placement within the laboratory.
Brightfield and fluorescent whole slide imager with Multispectral Imaging Technology.
Regions-Of-Interest for Mass Spectrometry Imaging
Source codes for manuscript "Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation".
Software application as machine learning model for image colorization.
Atlas presents cytoarchitectonic maps in several coordinate spaces, such as MNI colin27, MNI152, and freesurfer. These maps originate from peer-reviewed probability maps that define both cortical and subcortical brain regions and account for the brain's inter-individual variability by analyzing data from multiple post-mortem samples. For a whole-brain parcellation, the available probability maps are combined into a maximum probability map by considering for each voxel the probability of all cytoarchitectonic brain regions, and determining the most probable assignment. Atlas stands as reference atlas for the Human Brain Project and is embedded within the European research infrastructure platform, EBRAINS.
NuAire | NU-5700 Direct Heat CO2 Incubator
Direct heat, 160 liter capacity, closed loop HEPA filtration, IR sensor CO2 control incubator.Offers touch screen panel control and monitoring of temperature and CO2 levels.Can be stacked and still allow the user easy access to the top chamber.
University of Arizona Imaging Cores Electron Core Facility
University of Arizona Imaging Cores - Electron
Electron facility provides full Biological Transmission Electron Microscopy related research, consultation, and imaging services.Offers services using FEI Tecnai Spirit Transmission Electron Microscope.
University of North Carolina Neuroscience Center and the BRAIN Initiative Viral Vector Core Facility
BRAIN Initiative NeuroTools Vector Core Facility
BRAIN Initiative NeuroTools Vector Core UNC
Core provides affordable, custom viral vectors for neuroscience.
University of Virginia School of Medicine Spatial Biology Core Facility
Core offers spatial analysis which combines single-cell, spatial RNA sequencing, high-throughput microscopy, and quantitative image data analysis to enable large-scale spatial genomics and proteomics studies. Services include Spatial Transcriptome and Proteome analysis (GeoMx and CosMx), multiplex analysis (nCounter and Isoplexis), BSL2 laboratory, Confocal and Non-confocal image (Operetta), cell raft technology, sample preparation.
Pittsburgh Quantum Institute PQI Core Facility
Leading collaborative interdisciplinary organization that advances research, education, and training in quantum science and engineering. Helps to unify and promote research in quantum science and engineering in the Pittsburgh area. PQI members have faculty appointments from Carnegie Mellon University, Duquesne University, and the University of Pittsburgh in physics, chemistry, and engineering disciplines. Connects with team based science intitiatives and shared facilities.Resources and Facilities for Quantum Research include Carnegie Mellon Nanofabrication Facility,Center for Research Computing, Gertrude E. and John M. Petersen Institute of NanoScience and Engineering (PINSE), Materials Characterization Facility, Pittsburgh Supercomputing Center,QCFD (Quantum Computing/Computational Fluid Dynamics).
MRC Protein Phosphorylation and Ubiquitylation Unit MRC PPU Reagents and Services Core Facility
MRC Protein Phosphorylation and Ubiquitylation Unit MRC PPU Reagents and Services
Focused on cell signalling pathways, provides access to reagents and services involving kinase and ubiquitin targets and associated substrates and interacting proteins. Provides expertise and assistance in projects development. Offers services for protein generation and antibody development.
Albert Einstein College of Medicine Epigenomics Shared Core Facility
Albert Einstein College of Medicine Epigenomics Shared Facility (ESF)
Part of Einstein Center for Epigenomics and Illumina CSPro (certified service provider) laboratory, offers massively-parallel sequencing (MPS) including fully-automated library preparation, quality control and assurance, and number of assays to study the genome/epigenome. Data analytical services are provided by Computational Genomics Facility.
Open source web tool that identifies research outputs organizations have supported, analyzes their openness including OA policy compliance, and then streamlines taking action to make results more open. Covers almost any type of policy, e.g funder, university, and national. This includes policies that require submission dates, grant IDs, or other complex criteria to determine compliance.
Automated system used for generation of template positive Ion Sphere Particles for semiconductor sequencing. Performs template amplification as part of manual workflow for Ion PGM, Ion Proton, Ion S5, and Ion S5 XL systems. Provides scalable template preparation for all Ion semiconductor chips. Instrument has small footprint and fits easily on any bench top.
Part of Ion OneTouch System. Employs magnetic bead technology to isolate template positive Ion Sphere particles that can be loaded directly onto Ion semiconductor chip delivering automated, highly reproducible enrichment with every run.
Software package to analyze different behavioral tests in rodents semi-automatically. These tests include Open Field (OF), Elevated Plus Maze (EPM), Y-maze (YM) test and Morris Water Maze (MWM).
We aligned single-nucleus atlases of middle temporal gyrus (MTG) of 5 primates (human, chimp, gorilla, macaque and marmoset) and identified 57 consensus cell types common to all species. We provide this resource for users to: 1) explore conservation of gene expression across primates at single cell resolution; 2) compare with conservation of gene coexpression across metazoa, and 3) identify genes with changes in expression or connectivity that drive rapid evolution of human brain.
Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes.
Faith-based, not-for-profit healthcare organization and clinical care network in Miami-Dade, Broward, and Palm Beach counties. Baptist Health has 11 hospitals and in excess of 100 physician practices and outpatient facilities.
Central data repository containing clinical, research, and administrative data sourced from UNC Health Care System. Both Epic and legacy hospital systems are represented, with ability to query most data elements as far back as mid-2004. Used to mine UNC Health Care data to aid with trial recruitment, retrospective analyses, inter-institutional data sharing and much more.
Github repository for the paper "T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases" by Høye et al.
Akaike's Information Criterion and the second-order AIC model selection and multimodel inference based on (Q)AIC(c)
Software R package to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. Package implements classic model averaging for given parameter of interest or predicted values, as well as shrinkage version of model averaging parameter estimates or effect sizes. Package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities.
Clinical research platform and longitudinal observational study for Huntington’s Disease families intended to accelerate progress towards therapeutics. Collaboration between Huntington’s disease families, clinicians, and researchers to accelerate progress toward effective treatments.
Software tool can learn complex interconnections of epigenetic features and infer unmeasured data from any available input. Can learn cell type-specific properties, build biologically meaningful vector representations of cell types, and utilize these representations to generate cell type-specific predictions of effects of non-coding variations in human genome.
Software package to impute gene expression for all participants, whether they have partially or completely missing gene expression.
Multi-modal time series imputation model that can use additional modality (another cross-sectional or time-series data) to impute missing values in time series data. This multi-modal approach shows improved performance over uni-modal imputation models.
Physi Calibration and Optimization Of modeLing
Software Python library tailored to perform model calibration studies with PhysiCell. Generalized framework for model Calibration and Optimization Of modeLing projects.
University of Ottawa Flow Cytometry and Virometry Core Facility
Facility located at the Faculty of Medicine providing cutting edge instrumentation and expertise to researchers in Ottawa and around the world.
Max Planck Institute of Molecular Cell Biology and Genetics Light Microscopy Core Facility
Provieds acess to light microscopy techniques and instruments, consultation, training, and assists with project collaborations.Provides support with selecting imaging techniques, microscope systems, and setting up imaging experiments.Offers expertise in imaging techniques, such as Spinning disk confocal microscopy,Laser scanning confocal microscopy, 2-photon microscopy, Light sheet microscopy,Wide-field microscopy,Total internal reflection fluorescence (TIRF) microscopy ,Laser capture microdissection,Extended resolution microscopy,Quantitative phase imaging,Live cell and organoid imaging,Photomanipulation
Software package for use in complex networks and graph theory research. Mathematica interface for igraph. Provides Mathematica interface to popular igraph network analysis package, as well as many other functions for working with graphs in Mathematica. IGraph/M comes pre-packaged and ready to use on Windows, OS X and Linux (64-bit Intel), as well as the Raspberry Pi computer. The code is open source and can be compiled on other platforms as well (such as 32-bit Windows).
Survey software to design and host questionaires. Used as survey creator. Enables to choose from survey question types ranging from net promoter score questions for efficient customer satisfaction surveys to advanced multiple-choice and logic-based research questions.
Open-source tool for event organisation, archival and collaboration. Event management system made at CERN.
University of Nebraska at Omaha Movement Analysis Core Facility
University of Nebraska at Omaha UNO-Movement Analysis Core
Provides expertise and access to measurements of behavioral function and movement analysis for human movement variability research. Core services include access to human behavioral function measurements (3-D kinematics, kinetics, electromyography, and imaging), neuromuscular control of movements using virtual reality environments, EEG and fNIRS capabilities, dual-task measurements, blood flow and ultrasound technologies, portable pulmonary and energy expenditure assessments, movement modelling and simulation, and muscle strength measurements.
Software object oriented, lightweight and standalone Python toolbox for neural data analysis. Its core features five versatile timeseries objects from Pandas library, allowing it the versatility to be used with most raw neuroscience data types and produce some common analysis forms.
Software tool that analyses performance of several variant prediction methods at different levels. Used to benchmark variant effect predictors from VCF files.
Benchmark of human deep intronic variation
Repository of code, data, and documentation to reproduce computational evaluation performed to identify the best tools/models to predict genetic variation in deep intronic regions of human genome.
Software tool as set of scripts to prepare the input for several sequence-based RNA splicing methods from VCF files.
Web service that converts all 30 reconstruction formats (and 65 variations) described in scientific literature into SWC standard. Service is available open-source through user-friendly browser interface and Application Programming Interface.
Software R package for download, setup and access of Intensive Care Unit data sets. In addition to functions for running arbitrary queries against available data sets, a system for defining clinical concepts and encoding their representations in tabular ICU data is presented.
Software image analysis package for 3D object recognition in volumetric images developed for neuroscience research purposes. MATLAB application to recognize small structures in large volumetric image, plot their statistics and perform quantitative analysis such as nearest neighbor and colocalization analysis. Used to detect fluorescently labeled synapses in neuronal image stacks acquired using confocal or super resolution microscopes.
Web application as repository and launch platform for Psychopy experiments and other open-source tools.
Web application that allows users to view and explore brain cell data. Composed of three, interlinked tabs. GeneExp allows users to plot expression of one or two genes in Slide-seq atlas. SingleCell allows users to plot gene expression in snRNA-seq atlas. CellSpatial shows spatial localization of snRNA-seq cell types in Slide-seq dataset. Used to visualize, interact with, and download data.
Software toolkit of three dimensional models and software to study face perception. Collection of plugins used with MakeHuman to create face stimuli for experiments.
Software tool to create face stimuli for experiments. Used for making 3D characters.
University of Florida Scripps Florida Histology Core Facility
University of Florida Scripps Florida Histology Core
Provides histological services as well as technical support. Equipped with ventilated working areas and equipment to prepare, process and stain frozen or paraffin embedded specimens. Instrumentation include VIP Tissue Processor, BIOCARE NxGen Decloaking Chamber, Rotary Microtome, Staining Center, Leica Cryostat, Zeiss Axio Microscope/Camera Software, Leica Bond-Max Immunostainer, Leica Autostainer XL, General Data Laser Cassette Marker.
Stanford University Chemistry Department NMR Facility
Stanford University Chemistry Department NMR Laboratory
Core houses 5 Varian NMR Spectrometers including Inova 300, Varian 400, Neo 400, Inova 600, Inova 500.
Stanford University School of Medicine Beckman Center for Molecular and Genetic Medicine Core Facility
Stanford Medicine Beckman Center for Molecular and Genetic Medicine
Integrates laboratory research with clinical medicine.Creates and supports multidisciplinary programs that promote discovery and innovation in basic sciences and accelerates introduction and application of new technologies for use in basic research and clinical medicine.
Stanford School of Medicine Translational Applications Service Center Core Facility
Translational Applications Service Center
Offers analytical services, technical and scientific consulting and training, as well as pay-per-use research equipment.Provides scientific expertise and support for standard and customized assays, from initial study design to final interpretation and statistical analysis of experimental data. Services also include clinical sample acquisition, processing and archival for conducting inter-disciplinary translational research applications.
Software R package for developing heart rate variability analysis. Allows to import data files containing heartbeat positions in broadly used formats; eliminating outliers or spurious points present in time series with unacceptable physiological values; plotting HRV data and performing time domain, frequency domain and nonlinear HRV analysis.
Database reports all data from German 'Protection against Infection Act'. Robert Koch Institute maintains database of cases of notifiable diseases, and confirmation of pathogens, reported under the German ‘Act on the Prevention and Control of Infectious Diseases in Man’. SurvStat@RKI 2.0 is application that allows retrieval of aggregated data from limited version of German notification system database. Queries can be created individually or customized from pre-defined queries to generate tables, charts, and maps.
Software Python package to read, write, create, and plot ImageJ ROI format, an undocumented and ImageJ application specific format to store regions of interest, geometric shapes, paths, text, and whatnot for image overlays.
Software Python 2D Maxima finding algorithm. Re-implementation of Java plugin for ImageJ/Fiji.
Software tool as Python GUI and wrapper for control of visual stimuli designed using Psychopy libraries.
Open source project and Python package that introduces labels in form of dimensions, coordinates, and attributes on top of raw NumPy-like arrays, which allows for more intuitive, more concise, and less error-prone user experience. Includes large and growing library of domain agnostic functions for advanced analytics and visualization with these data structures.
Collection of foundational software libraries, upon which ImageJ2 and Fiji are built. It is a collaboration of projects providing software for scientific computing in effort to cooperate and reuse code.
Software provides set of wrapper functions for integration between ImageJ2 and Python. Supports original ImageJ API and data structures. Used to combine ImageJ and ImageJ2 with other tools available from Python software ecosystem, including NumPy, SciPy, scikit-image, CellProfiler, OpenCV, ITK and many more.
Software Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, efficient internal representation, and image processing capabilities. Core image library is designed for fast access to data stored in few basic pixel formats. It should provide solid foundation for general image processing tool.
Software Python library to store NumPy arrays in TIFF (Tagged Image File Format) files, and read image and metadata from TIFF-like files used in bioimaging. Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, DNG, STK, LSM, SGI, NIHImage, ImageJ, Micro-Manager NDTiff, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, BIF, ZIF (Zoomable Image File Format), QPTIFF (QPI, PKI), NDPI, and GeoTIFF files.
Software extensible environment for interactive and reproducible computing, based on Jupyter Notebook and Architecture. Next generation user interface for Project Jupyter offering all familiar building blocks of classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in flexible and powerful user interface. Can be extended using npm packages that use our public APIs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Stanford University School of Medicine Genetics Bioinformatics Service Center Core Facility
Stanford Genetics Bioinformatics Service Center
School of Medicine service center operated by Department of Genetics.Set up to facilitate massive scale genomics at Stanford and supports omics, microbiome, sensor, and phenotypic data types.
Stanford University School of Medicine Human Pathology Histology Services Laboratory Core Facility
Human Pathology Histology Services Laboratory
Provides broad range of tissue processing services to Stanford investigators in human disease research.Consolidates and centralizes tissue processing. Provides advice and expertise in tissue processing.
Stanford University School of Medicine In Vitro Biosafety Level3 Service Center Core Facility
In Vitro Biosafety Level-3 Service Center
Center consists of Virology BSL3 lab, separate BSL3 Bacteriology lab, and BSL2 lab. It is operated by School of Medicine as scientific service center and is open to all Stanford researchers after adequate training and subsequent use.
Stanford University School of Medicine PET/MRI Metabolic Service Center Core Facility
Houses whole-body PET/MRI scanner and carbon-13 hyperpolarizer device.Simultaneous PET/MRI scanner combines high spatial resolution and fine anatomical soft tissue detail of MRI with high molecular specificity of PET imaging.PMMSC is the World's first installation of a SpinLab hyperpolarizer along side a PET/MRI scanner.Individual researchers are required to undergo MR safety and radiation safety training.
Stanford University School of Medicine Richard M. Lucas Center for Imaging Core Facility
Stanford Lucas MRI Service Center Richard M. Lucas Center for Imaging
Houses four whole-body MRI systems (three 3.0T, one 7.0T). 3T2 and 3T3 are part of the Lucas Service Center. Individual researchers are trained in magnet safety and scanner operations by the magnet manager or MR research technologists.
Stanford University School of Medicine Center for Innovation in In vivo Imaging Core Facility
Stanford Center for Innovation in In vivo Imaging (SCi3)
Small animal imaginig service center.Instruments range from systems typically found in clinical setting, but scaled for rodent usage (such as MRI, PET, CT and ultrasound), optical systems for measuring bioluminescence, fluorescence, and Cherenkov light (IVIS, Ami, Lago and Maestro systems), new modalities (MPI and photoacoustic), as well as access to advanced image analysis software, computer workstations, and surgical preparation areas. Scientists are trained to use instruments independently and can schedule studies as needed.
Stanford University School of Medicine Biobank Core Facility
Provides infrastructure for self service sample management tools, centralized broad consent, standardized laboratory services, and long term sample storage solutions.Tracks biological samples collected in every study at Stanford and linking each with associated electronic health records (i.e., EPIC), REDCap, and molecular data.
Lightweight, modular web-based data management platform for biomedical research projects. Introduces multiple extension modules that support scientific data management. Used for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects.
Flow cytometry based multiplex bead array reader with ability to simultaneously acquire data for two reporter channels per analyte. Compact, flow based, multiplex platform that combines low- and high-plex capabilities, quick time to reliable results, and ability to simultaneously acquire data for two parameters per analyte.
Ottawa Hospital Research Institute Flow Cytometry and Cell Sorting Core Facility
OHRI-Flow Cytometry & Cell Sorting Facility
Facility, located at General Campus of Ottawa Hospital, was established in 1998 and now includes three flow cytometers, two of which have sorting capabilities. Offers sorting precision required for isolation of rare cell populations with high purity and yield, up to 20 000 events per second. Allows simultaneous analysis of variety of light scatter and fluorescence parameters on single cells.
Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier.
Software tool for aligning and filtering, library QC, generating contact map, and identifying chromatin structures from Omni-C data.
Wheel Running Activity acQuisition system
Open source microcontroller based system for wheel running activity in mice.Used to track circadian rhythms of rodents using microcontroller, powered by lithium polymer battery, and surveys exercise activity for up to 30 days. Data can be stored on microSD card or using online server using WiFi connection. Python software provides system interface with ActogramJ to analyze chronobiological aspects of data.Repository includes guide for installing integrated developmental environment and dependent libraries for building and setting up WRAQ systems - WRAQ and WRAQ-Wifi. WRAQ and WRAQ-WiFi are based on Adafruit Adalogger and DFRobot FireBeetle ESP32 connected to 4- and 8-bit binary counters receiving signal from reed switch attached to 5-inch flying saucer respectively.
Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas.
University of Arizona Imaging Cores Optical Core Facility
University of Arizona UArizona Imaging Cores - Optical
Facility with two locations:Marley and Life Sciences North. Dedicated to acquisition of images for research, industrial and clinical applications.Marley location features inverted point scanning confocal microscope, upright confocal/multiphoton microscope with superresolution capabilities, fluorescence stereo microscope and research quality microwave. Life Sciences North location features superresolution fluoresence microscope:structured illumination, SIM; inverted multifunction widefield microscope:color brightfield, polarized light, fluorescence; image analysis workstation.
Carnegie Mellon University Pitt Brain Imaging Data Generation and Education Center Core Facility
Carnegie Mellon University CMU-Pitt BRIDGE Center
Collaborative MRI facility that is jointly operated by the University of Pittsburgh and Carnegie Mellon University. Research neuroimaging facility, with focus on advanced data analytics and basic science research. Designed to support basic science research and next generation of brain scientists.
Preferred Reporting Items for Systematic reviews and Meta-Analyses literature Search extension
Extension to PRISMA Statement for Reporting Literature Searches in Systematic Reviews. Preferred reporting items for systematic reviews and meta analyses literature search extension. Complements PRISMA Statement and its extensions by providing checklist that could be used by interdisciplinary authors, editors, and peer reviewers to verify that each component of search is completely reported and therefore reproducible.
Thermo Fisher: Applied Biosystems | ViiA 7 Real-Time PCR System
Contains Viia7 RT-PCR system and QuantStudio software for running Viia7 RT-PCR system and processing data.
Software package as decision algorithms for solving binary classification problems. Faster and more frugal because every node allows making decision. Apart from being faster and requiring less information, FFTs tend to be robust against overfitting, and are easy to interpret, use, and communicate.
Productivity and collaboration PDF solution, combining Acrobat desktop software, mobile scan app, signature app and Acrobat Reader mobile app enhanced with premium mobile features and premium Document Cloud services.
Research assistant using language models like GPT-3 to automate parts of researchers’ workflows. Main workflow is Literature Review. If you ask question, Elicit will show relevant papers and summaries of key information about those papers in easy-to-use table.
Software critical appraisal tool for systematic reviews that include randomised or non-randomised studies of healthcare interventions, or both.Measurement tool to assess systematic reviews.
HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP.
Software suite of automation tools, purpose-built to speed up multiple steps in systematic review process. Assist with many steps of systematic review, including searching for citations, citation screening and write-up of review findings, among others. Existing tools are being continuously reviewed and refined, and additional tools are being developed. Systematic Review Accelerator project is based at the Bond University Institute for Evidence-Based Healthcare.
Automated Fiber Quantification in Python
Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry.
Open source software analysis tool to investigate space plasma turbulence and nonlinear DYNamics. Wraps comprehensive set of advanced data analysis methods meant to facilitate study of turbulence, nonlinear dynamics, and complexity in space plasmas.
Software tool as platform independent data interface and database for neuroscience physiology and imaging experiments. Platform independent standard that allows analyst to use and create software that functions independently from format of raw data or manner in which data are organized into files. Interface is rooted in simple vocabulary that describes common apparatus and storage devices used in neuroscience experiments. Results of analyses, and analyses of analyses, are stored as documents in scalable, queryable database that stores relationships and history among experiment elements and documents. Interface allows development of application ecosystem where applications can focus on calculation rather than data format or organization. This tool can be used by individual labs to exchange and analyze data, and it can serve to curate neuroscience data for searchable archives.
Van Hooser lab fluorescent time-series analysis software
Software VH Lab tools for analysis of calcium imaging data. Allows selection of ROIs and extraction of time series data from raster-scanned, line-scanned, or CCD images, written in Matlab.
University of Arizona Analytical and Biological Mass Spectrometry Core Facility
UArizona Analytical & Biological Mass Spectrometry Facility
University of Arizona UArizona Analytical & Biological Mass Spectrometry Facility
Provides equipment and expertise for analysis of variety of biological and small molecules.Services include protein analysis encompassing protein identification, protein and peptide sequence confirmation, intact protein molecular weight determination, complex protein sample analysis, and protein/antibody drug interactions.Developed metabolomics library to support metabolomic and lipidomics analysis. Can identify range of post-translational modifications, determining their presence or absence, as well as quantitating PTMs.Proteomics and small molecule services include workflows for label free,chemical labeling (iTRAQ/TMT) and metabolic labeling (SILAC).Service for molecular synthesis, with monitoring reaction steps,calculating percentage of product, testing for purity, and molecule characterization with high resolution and high mass accuracy.Provides molecular weight and chemical composition determinations, structure elucidations and compound identification analysis or confirmation and accurate mass measurements of synthetic products, measurement of polymers, nucleic acids (DNA/RNA), peptides, proteins, natural products, and assistance with determination of unknowns.
Centre for Genomic Regulation Advanced Light Microscopy Unit Core Facility
Core provides support with experimental design, sample preparation, acquisition, bioimage analysis and visualization.Consists of microscope systems specifically designed for fluorescence microscopy ranging from confocal, widefield to super resolution systems and helps reveal structures from macro to nanoscale.
Centre for Genomic Regulation Flow Cytometry Unit Core Facility
Centre for Genomic Regulation CRG/UPF Flow Cytometry Unit
Flow cytometry studies optical parameters emitted by particles (cells, cell fractions). Flow cytometers can study a series of parameters of individual particles simultaneously, quickly and on a large number of individualized particles in suspension. Flow cytometers use lasers as a source of light excitement; therefore, it must be possible to mark the particles with one or more fluorescent substances. Information is also collected regarding the size and structural complexity of each particle. This multiparameter study of each particle enables us to analyse subpopulations in complex samples through electronic sorting. Some cytometers are also equipped with sorting and collection modules for particles of interest. The most important applications of flow cytometry include those relating to the study of cell surface receptors, nuclear and cytoplasmic antigens, DNA content, enzyme activity, cell integrity and membrane permeability and calcium flows. The Unit currently hosts five analyzers and two sorters, and is therewith the largest Becton Dickinson site in Spain. The sorters are operated by the facility personnel, who also support the users in experimental design and data analysis. The analyzers are operated by the users themselves, after they have been trained. The facility personnel helps with the experimental design and supervises and monitors the experiments when necessary.
Centre for Genomic Regulation Bioinformatics Unit Core Facility
Centre for Genomic Regulation Bioinformatics Unit
Provides services of consultation, planning NGS and other genomic experiments, NGS data processing, analysis and management, software and database development, bioinformatics training, and access to high-performance computing resources at CRG. The Unit works in synergy with the Genomics Unit and the Biomolecular Screening and Protein Technologies Unit to support users using high throughput sequencing technologies from experiment planning to delivery of timely and reliable results.
Centre for Genomic Regulation Genomics Unit Core Facility
Centre for Genomic Regulation Genomics Unit
Supports next generation sequencing technologies and provides several next generation sequencing instruments. Several high-throughput technologies have been implemented to assess differential expression, inter-individual genetic variation, microRNA discovery, genome sequencing, targeted resequencing, epigenetic profiling and identification of binding sites of DNA or RNA-associated proteins.
Centre for Genomic Regulation Tissue Engineering Unit Core Facility
Centre for Genomic Regulation Tissue Engineering Unit
Provides latests technologies for stem cell biology, stem cell differentiation, organoid formation and induced pluripotent stem cells.Tissue Engineering platform works in collaboration with Biomolecular Screening and Protein Technologies Unit to provide CRISPR/Cas9 genome editing technology service.Unit also includes Histology In-house Service (only for PRBB residents) provides histopathological analysis required for analysing tissues from research performed in in vivo models. Histology In-house Service performs and optimizes histological processing and analysis of tissue, from experimental animal models and human origin.Provides mentoring and training in common histological techniques.
Centre for Genomic Regulation Protein Technologies Unit Core Facility
Centre for Genomic Regulation Protein Technologies Unit
Provides technology platform to perform protein production and automated processes in context of biomolecular and biochemical screening assays.Through staff assisted screening, users have access to equipment including liquid handlers, plate readers and small molecule libraries.Unit is aimed at supporting the researchers of the CRG institute by purchasing, seeking and maintaining valuable stocks of clones and strains.
Centre for Genomic Regulation Proteomics Unit Core Facilitiy
Centre for Genomic Regulation CRG/UPF Proteomics Unit
Proteomics Unit is joint effort of Universitat Pompeu Fabra and Center of Genomic Regulation. Provides proteomics services by offering state-of-the-art methods, advise and expertise to support basic and translational researchers; developing new methods and techniques that keep the unit up to date and at the forefront of the proteomics field; training community and actively disseminating proteomics science and methods.Part of Spanish National Infrastructure for Omics Technologies and European Proteomics Infrastructure Consortium, and it coordinates European innovative and interdisciplinary Research and Training network. The Proteomics Unit is also part of Spanish National Health System.
Catholic University of Louvain Institute of Experimental and Clinical Research Imaging Platform Core Facility
Institute of Experimental and Clinical Research Imaging platform
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5,2025. Core provided services include paraffin embedding, paraffin and cryo sectioning, histological stainings, immunostainings; Image acquisition includes brightfield, fluorescence and polarized light whole slide imaging,2D fluorescence microscopy, 3D fluorescence microscopy; Image analysis includes 2D images : ImageJ/Fiji support – ZEN Analysis (Zeiss),2D whole slide scans: Author (Visiopharm), Halo (Indicalab), QuPath, 3D images: Arivis (Zeiss), Imaris (Bitplane).
Software pipeline developed in collaboration with BRAIN Initiative Cell Census Network and BRAIN Initiative Cell Atlas Network. Supports processing of spatial transcriptomic data generated with Slide-seq commercialized as Curio Seeker assay.
Yale University West Campus Imaging Core Facility
Yale University West Campus Imaging Core
Provides access and training to instruments including optical microscopes with three confocal systems, two wide-field systems, light sheet system, laser-microdissection system, cell-culture microscope, stereomicroscope, optical tweezer system, and Atomic Force Microscope. Maintains cell culture equipment such as biosafety cabinet, incubators, refrigerator, and microfuges and lab support areas for cell culture and sample preparation.
Stanford Canary Center Preclinical Imaging Core Facility
Provides access to ultrasound, MRI, CT, and PET, instruments developed specifically for small animal work and photoacoustic imaging. All instruments are designed to image living subjects and allow for repeated imaging. The flexibility and rapid analyses of such animal models greatly accelerate the development of molecular imaging strategies.Facility houses surgical procedure room, histology slide scanner that converts glass slides into digital slides using both brightfield and fluorescence, and advanced image analysis workstations.Instruments include MicroPET Imaging Systems,Optical Imaging Systems,UltraSound Imaging System,Photoacoustic Imaging System,X-Ray Computed Tomography Imaging System,Magnetic Resonance Imaging.
Stanford University School of Medicine Transgenic, Knockout and Tumor model Center Core Facility
Services include genome editing of mice, rats and cell lines, mouse line cryopreservation and re-derivation, ES cell targeting, PDX models, drug screening.Crispr Mediated KO/KI and Conditional KO Mice,KI mouse by mouse ES cell genome editing,Integrase Mediated Transgenesis,Conventional Transgenic Mouse,Mouse Line Services,Cell Line Services. Tumor Model Services include In vivo tumor models,In vivo pharmacology,In vitro and biochemical assays,Translational imaging services.
Stanford University Computer Science Department Computer Core Facility
Stanford University Computer Science Department Computer Facilities
Academic service center specializing in planning, installation and maintenance of research computer systems.
Stanford University School of Medicine Animal Diagnostic Laboratory Core Facility
Stanford School of Medicine Animal Diagnostic Laboratory
Offers clinical laboratory services including hematology, cytology, serum chemistry, electrolyte analysis, coagulation profiles, fluid analysis, serology/immunology, parasitology, and microbiology; Specializes in diagnostic and research needs of laboratory animals. Committed to improving diagnostics, developing additional reference ranges for various clinical pathology parameters in laboratory animals, and supporting health surveillance and disease management.
Stanford University School of Medicine Institute for Stem Cell Biology and Regenerative Medicine FACS Core Facility
Core manager provides oversight and training on user-friendly instrumentation so that each investigator is able to perform sorts and analysis on their own.Manager also provides technical help with more complex sorts, ensures that instruments are maintained properly, and will perform troubleshooting as necessary. This novel design will allow for critical stem cell sorts to be done efficiently and economically.
Stanford University School of Medicine Clinical and Translational Research Unit Core Facility
Clinical and Translational Research Unit (CTRU)
Stanford University School of Medicine Clinical and Translational Research Unit (CTRU)
Collecting and banking freshly frozen tumor and normal tissue from surgical material and autopsy specimens.Provides fresh tumor tissue for viable cell studies,processes and banks blood from cancer patients,maintains tissue database with links to clinicopathological data,providing histological staining and pathological review,coordinating patient consent and assuring regulatory compliance.
Stanford University School of Medicine Cancer Institute Tissue Procurement Shared Resource Core Facility
Stanford Cancer Institute Tissue Procurement Shared Resource
Procures and provides needed tissue specimens to Stanford Cancer Institute investigators to support cancer related research. Services include collecting and banking freshly frozen tumor and normal tissue from surgical material and autopsy specimens;Providing fresh tumor tissue for viable cell studies;Processing and banking blood from cancer patients;Maintaining tissue database with links to clinicopathological data;Providing histological staining and pathological review;Coordinating patient consent and assuring regulatory compliance.Provides portal to virtual bank which links inventories of specialized satellite repositories, including collections of hematological and neurosurgical specimens.
Stanford University School of Medicine Veterinary Service Center Core Facility
Stanford School of Medicine Veterinary Service Center
Provides medical care, in vivo research support, and disease surveillance to laboratory animals at Stanford University . Our board certified and board eligible veterinarians offer consultation in appropriate animal modeling, animal care techniques, experimental methodology, anesthetic techniques, surgical techniques, pain management, humane euthanasia techniques, and animal use (APLAC) protocol consultation. AALAS certified veterinary technicians are available to provide technical support including dosing, biosampling, conducting anesthesia and post-operative care, for example.
Web-based design tool for CRISPR base editing. Guide RNA designer for CRISPR base editing. Provides all possible base editor target sequences in given input DNA sequence with useful information including potential off target sites.
Web application that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Enables searching for potential off-target sites in any sequenced genome rapidly without limiting PAM sequence or number of mismatched bases.
Software command line Python package for computation of chokepoint reactions in genome scale metabolic models. Used to compute chokepoints by taking into account both topology and dynamic information of network. Can compute and remove dead-end metabolites, find essential reactions and update flux bounds of reactions according to results of Flux Variability Analysis.
Colorado School of Mines Shared Instrumentation Facility Atom Probe Tomography Core Facility
light mass and heavy mass species identification
Core to capture mass spectral data obtained through time-of-flight measurements that can be used for 3D nanoscale compositional analysis to identify light mass and heavy mass species with equivalent sensitivity.
Software R package as set of standards that specify common storage and access model of geographic features made of mostly two dimensional geometries used by geographic information systems. Standardized way to encode spatial vector data. Formalized by Open Geospatial Consortium and International Organization for Standardization.
Software R package for mapping country data.Enables mapping of country level and gridded user datasets by facilitating joining to modern world maps and offering visualisation options. Country borders are derived from Natural Earth data v 1.4.0.
Software Python toolkit developed at Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images. Used for segmenting 3D intracellular structures in fluorescence microscopy images.
Classification and Tracking in depth (z)
Software tool for 3D tracking and automatic classification of rodent behavior. Used for acquisition, annotation, and automatic behavioral profile characterization of laboratory rodents' RGB-D videos. Utilizes video segmentation, tracking of body parts, and automated classification of behaviors through machine learning and computer vision methods. Setup uses low costing RGB-D cameras for tracking behaviors in various environments. Software includes GUI interfaces for video acquisition, annotation, and processing of behavioral data. Software is capable of automated behavior detection with only 30 minutes of annotated video.
Software tool as DNA sequence analyzer program.
Software R package provides quality control and semantic enrichment tools for preparation of health datasets. Enables semantic enrichment of dataset where metavariables are discovered from relationships between input variables determined from user provided ontologies.
Web tool identifies associations between genes and metabolites that are biosynthesized, metabolized, or transported by proteins coded by genes. Gene centric metabolomics information retrieval tool. Knowledge based, gene centric data aggregator that hierarchically retrieves information about genes, their related pathways, reactions,metabolites, and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. Information can be contextualized by filtering along species, anatomy tissue and disease or phenotype.
Stanford University School of Medicine Laboratory for Cell and Gene Medicine Core Facility
Laboratory for Cell and Gene Medicine (LCGM)
Stanford Laboratory for Cell and Gene Medicine
Stanford University School of Medicine Laboratory for Cell and Gene Medicine
Provides support and services to clinical investigators including consulting, technology transfer, process and analytical development, clinical manufacturing and regulatory affairs.
Stanford University School of Medicine Computational Services and Bioinformatics Core Facility
Computational Services and Bioinformatics Facility
Stanford Computational Services and Bioinformatics Facility
Provides variety of Macintosh, Windows, and Linux software for scientific research.Obtains concurrent network licenses that work under control of software license manager.This allows facility to purchase limited number of copies of expensive software and distribute software within Stanford network.CSBF has user community of over 200 research labs in 36 different departments at Stanford. Staff members have many years of experience in providing computer support to biomedical researchers.
Stanford University Chemistry Department Optics Core Facility
Stanford University Chemistry Department Optics Facility
Houses optical spectroscopy instruments including Fluorolog 3 Fluorimeter,Vertex 70 FTIR with RAM II Raman accessory, Cary 6000i UV/Vis/NIR Spectrometer.
Stanford University Biomaterials and Advanced Drug Delivery Laboratory Core Facility
Biomaterials and Advanced Drug Delivery (BioADD) Laboratory
Provides creation of biomaterials and drug delivery agents, expertise toward designing and analyzing biomaterials, development of drug delivery devices and formulations, pharmacokinetic and pharmacodynamic studies, and development of materials for biomedical applications.
Stanford University Cyclotron and Radiochemistry Core Facility
Provides clinical and pre-clinical radiotracers for understanding and detecting cancer, cardiac conditions, inflammatory disorders, and neurodegenerative diseases.
Stanford University Instrumentation Shop Core Facility
Stanford University instrumentation shop
Core for assisting with custom instrumentation and equipment needs at affordable price.Projects devices include microcontrollers, LCD displays, keypad interfaces, serial communication, signal conditioning electronics, analog and digital computer interfaces, photomultiplier tube amplifiers, DC motor, stepper motor and linear motor controllers, servomotors, rotary encoders, timed sequenced equipment, temperature controllers, peltier devices, solenoid valves, actuators, force transducers, profusion chambers, microscope adapters as well as mechanical design and limited machine shop services.
Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes.
Stanford Center for High Throughput Quantitative Biology Core Facility
Stanford Center for High Throughput Biology
Stanford Center for High Throughput Quantitative Biology
Provides access to technologies involving high-throughput microscopy, high-throughput biological assays, and microfluidics.
Stanford University High Performance Computing Center Core Facility
Stanford High Performance Computing Center
Stanford University High Performance Computing Center
Academic cost recovery center, operates number of HPC clusters to enable larger simulations, deeper analyses, and faster computation times than are possible using computers available to individual researchers. Provides mass data storage and archival systems to store data.
Stanford University Physics Machine Shop Core Facility
Provides services for all departments on campus, including library of materials and parts suppliers, arranging for off-campus services such as plating and specialized machining services,help with laboratory and research apparatus and repair of existing equipment, designs from sketches to final assembly by mechanical means (welding, brazing or soldering),computer numerically controlled mill and lathe, electro discharge machining.
Provides services with computing and data information for research proposals, data storage platforms,consultation,computational platforms and resources.Some services relate directly to physical hardware, including hosting and system administration. Hosting largely takes place at Stanford Research Computing Facility data center designed specifically to host high density, power consumptive computing equipment. SRCF is intended to meet research server hosting needs of campus for years to come.
Web tool as interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning. User can search papers over COVID-19 literature using keywords or or load specific paper through its DOI.
Jülich Research Institute; Jülich; Germany
One of the largest interdisciplinary research centers in Europe for inspiring science exchange from all over the world. It is member of the Helmholtz Association.
Software tool to provide data 3D visualization and processing. Used for reading and comparing CT, MR, 3D X-ray, PET, and PET/CT datasets.
Software application providing tools and features that may be used for general purpose radiological viewing and reading of image data from various imaging modalities, clinical review and performs functions of digital image processing, measurement, communications and storage.
Software tool used to calculate Homeostasis Model Assessment which takes account of variations in hepatic and peripheral glucose resistance, increases in insulin secretion curve for plasma glucose concentrations and contribution of circulating proinsulin. Provides access to HOMA2 model for researchers who wish to use model derived estimates of %B and %S, rather than linear approximations.
Drexel University Research Computing Core Facility
Drexel University Research Computing Facility
Provides high performance scientific computing and secure storage of protected health information to both Drexel community and other universities in Philadelphia area. Data center houses Picotte cluster, which consists of Standard CPU Nodes, Large Memory Nodes, GPU Nodes and secure scratch and persistent storage.
Fasteris Next Generation Sequencing Services
Fasteris, the brand of Genesupport SA for all Life Science Services, provides Next Generation Sequencing and Sanger sequencing services.Offers customized approaches and consulting services at each step of your projects.
University of Iowa Institute of Human Genetics Genomics Division Core Facility
Iowa Institute of Human Genetics (IIHG) Genomics Division
Provides broad spectrum of resources designed to make techniques of genomics, functional genomics, and recombinant DNA technology. Services include Next Generation sequencing, single cell analysis, spatial transcriptomics, Sanger Sequencing, qPCR, digital PCR, Nanostring, and microarray analysis.
Web tool to analyze survival data by single year of diagnosis and estimates changes in survival trends and year over year trend measures.
Software package contains tools for analyzing data from NanoString GeoMx Digital Spatial Profiler. Provides functions to read, quality control and normalize starting from Nanostring DCC and PKC files generated from NanoString GeoMx DSP. Contains definition of NanoStringGeoMxSet class which inherits from Biobase’s ExpressionSet class and NanoStringRCCSet class.
Software neuroscience laboratory environment for simultaneous neuronal imaging and behavioral monitoring. McGill-Mouse-Miniscope Touchscreen Behavior Platform. Standardized approach for high throughput imaging of neuronal dynamics during behavior.
Phython script for bootstraping Treemix snp trees to generate confidance intervals in the main tree.
Automated cell counter with software algorithm to provide accurate counting results for variety of cell types by automatically declustering clumped cells, performing size and roundness based sorting, and identifying live and dead cells. Can confirm cell counts prior to experimental data acquisition, quality check, passaging, or induction of differentiation.
Software tool to find shared repeats between mitochondrial genomes.
Software repository for mtDNA assembly project.
University of Virginia School of Medicine Molecular Imaging Core Facility
Provides imaging small animals and samples with variety of modalities depending on needs including MRI, X-Ray CT, PET, SPECT, luminescence, and fluorescence. Works closely with Radiochemistry Core Lab which can synthesize custom, targeted PET and SPECT imaging agents.Offers preclinical imaging tools designed for imaging rodents.
University of Arizona Flow Cytometry and Human Immune Monitoring Shared Resource Core Facility
UArizona Flow Cytometry and Human Immune Monitoring Shared Resource
University of Arizona UArizona Flow Cytometry and Human Immune Monitoring Shared Resource
Flow cytometry facility provides instrumentation for data acquisition, analysis, and cell sorting, technical expertise to interpret results and develop methods. Offers information about new techniques, and applications of flow cytometry through workshops and seminars, and provides training to interested facility users. Individual consultation services are available.Human Immune Monitoring Facility provides immune profiling, sample preparation,clinical trial support, technical expertise to clinical investigators and research scientists.Services include multispectral flow cytometry, metabolic analysis, blood services such as PBMC isolation and serum/plasma extraction, and full spectrum of immunological services.Offers custom assays and biobanking services upon request.Offers training, assisted, unassisted, and technician operated modalities for all instruments and will meet investigators at their desired level of engagement.
University of Arizona Functional Genomics Core Facility
University of Arizona UArizona Functional Genomics Core
Offers to run high-throughput compound, RNAi, and deletion library based screens for purpose of network analysis, drug and/or target discovery. Offers assistance to develop assay, carryout screen and/or analyze data. Equipment is also available for general (low-throughput) use. Helps with developing custom pipeline. Biomek FX liquid handling workstation with integrated Liconic shaker incubator (temperature, humidity, and CO2 controlled) can be used to setup and grow most cell types in 96 well plates. This robot is equipped to add RNAi constructs, drugs or other stimuli to each plate. Biomek FX can also be used to perform high-throughput biochemical assays. Cell based assays can be carried out using either Operetta CLS high-content analysis system or CLARIOstar plus. Both instruments have powerful, but easy to use software for data analysis.
Web application for multi-level multi-cluster selections in dendrogram. Provides interactive visualization of dendrogram in which users can divide dendrogram at any level and into any number of clusters.
Southern HIV and Alcohol Research Consortium
Southern HIV and Alcohol Research Consortium Biomedical Data Repository
The Southern HIV and Alcohol Research Consortium (SHARC)
Consortium to improve health outcomes and reduce HIV transmission among diverse range of populations affected by alcohol and HIV infection in Florida. Fosters interdisciplinary translational research, training and community engagement. One of five national Consortia for HIV/AIDS and Alcohol Research Translation (CHAART). Supports Researcher Hub for researchers interested in SHARC research, publication, presentations, and opportunity to access, and analyze datasets via SHARC Concepts System.
Medical wiki of interventions, regimens, and general information relevant to fields of hematology and oncology. Knowledge base for hematology and oncology providers, containing details about hematology/oncology drugs and treatment regimens. Any healthcare professional can sign up to contribute. Acuracy and completeness of content is overseen by Editorial Board.
ROBOKOP Graph Knowledgebase; Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways
ROBOKOP system consists of web based user interface, API server, and several worker servers. Biomedical knowledge graph that integrates and semantically harmonizes important knowledge sources. Contains nodes representing entities such as genes, chemicals, and diseases, and edges representing relationships between them. Abstraction layer and user interface for knowledge graphs to support question answering. Used for reasoning over structured biomedical knowledge databases as part of NCATS translator and reasoner programs. ROBOKOP Knowledge Graph Builder constructs KG and provides extensible framework to handle graph query over and integration of federated data sources.
Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression.
Web based collaborative text annotation tool. Used for managing multi-user, multi-label document annotation. Project managers can specify annotation schema for entities and relations and select annotators and distribute documents anonymously to prevent bias. Document input format can be plain text, PDF or BioC (uploaded locally or automatically retrieved from PubMed/PMC), and output format is BioC with inline annotations. Displays figures from full text.
Nonprofit organization with mission to advance molecular sciences by building open source software and sustainable communities for research software development. Focuses on working with hosted projects to support their software development and provide operational support, while also pursuing own community-service and community-building projects. Uses fiscal sponsorship as business model available to nonprofit organizations to assemble resources, provide support and advance open source projects in molecular sciences aligned with charitable purpose and general public interest.
Platform for connecting people, software, data, and equipment. Helps integrating software, instruments, and data across your lab’s existing ecosystem. Provides: workflows guide users through processes involving multiple systems;Centralized access to Thermo Fisher Scientific instrument service and expertise;Connectivity to monitor and maintain instruments and equipment;Granular data sharing controls to enhance collaboration;Secure environment.
University of California Davis Campus Mass Spectrometry Core Facility
University of California Davis Campus Mass Spectrometry Facilities
Mass spectrometry core is offering advanced mass spectrometry services including analysis of intact molecules including peptides, proteins, oligonucleotides, polymers and small organic molecules; MALDI, LCMS or direct loop injections; High resolution accurate mass measurements and tandem MS/MS;Routine quantitation.
University of California Davis Biological Electron Microscopy Core Facility
University of California Davis Biological Electron Microscopy Facility
Provides electron microscopy imaging services, expertise, training, training in sample preparation and equipment use.
University of California Davis Advanced Materials Characterization and Testing Laboratory Core Facility
Advanced Materials Characterization and Testing Laboratory
Davis Advanced Materials Characterization and Testing Laboratory
Provides electron microscopes, including aberration-corrected scanning transmission electron microscopes for characterization of hard and soft materials. Provides sample preparation equipment, high-resolution x-ray diffractometer, and different optical microscopes and image analysis software.
University of California Davis Nuclear Magnetic Resonance Core Facility
Davis UCD-Nuclear Magnetic Resonance Facility
Provides access to NMR instrumentation for spectroscopy and imaging. Spectrometers are multinuclear and variety of liquids, solids, surface, and imaging probes are available for use. Individual training, safety and operational training can be requested
University of California Davis Center for Molecular and Genomic Imaging Core Facility
Davis UCD - Center for Molecular and Genomic Imaging
UCD - Center for Molecular and Genomic Imaging
Provides in vivo animal imaging and biospecimen imaging. In Vivo Preclinical Imaging services.
University of California Davis West Coast Metabolomics Center Core Facility
Davis WCMC-West Coast Metabolomics Center
Provides services for analysis of small molecules in biological samples. Specializes in discovery, identification and quantitation of many metabolites and lipids. Provides metabolomics analysis services, professional courses in metabolomics analysis and data processing.
NuAire | LabGard ES NU-425-600E Biosafety Cabinet
NuAire LabGard ES (Energy Saver) NU-425 Class II
Designed for laboratory safety, proper ergonomics, and energy efficiency.Models available from GMI are 2-ft. NU-425-200, 3-ft. NU-425-300, 4-ft. NU-425-400, and 6-ft. NU-425-600. LabGard NU-425 biosafety cabinets feature control system to control blower, lights, and outlets, Minihelic gauge that measures plenum performance, and Attenumount vibration control system for attenuation of sound and vibration. Cabinets are equipped with highly efficient, energy-saving motor/blower to increase filter life and cut electricity costs.
GFL Water Baths models 1002 to 1013 are used for incubations and inactivations of cultures, heating media, carrying out chemical reactions or thawing samples.
Software Python package for inferring gene regulatory networks based on spatial gene expression data. Used for analyzing spatially resolved gene expression data. Software tool to infer TF-centred, spatial gene regulatory networks for spatially resolved transcriptomic data.
Software R package for analysis of populations with mixed modes of sexual and clonal reproduction. Used for genetic analysis of populations with mixed reproduction.
Software R package to read, write, manipulate and analyze variant call format data. Facilitates easy manipulation of variant call format (VCF) data.
Thermo Fisher: Applied Biosystems | StepOne Real Time PCR System
Applied Biosystems StepOne Real-Time PCR System
Applied Biosystems StepOne™ Real-Time PCR System
StepOne Real Time PCR System is 48-well plate, low throughput RT PCR instrument. Can be setup in variety of configurations and comes with intuitive data analysis and instrument control software.
Precise pH meter with documentation function to use in quality assurance, pharmaceutical industry and everywhere GLP supported documentation is required.
Advanced plate washer, designed for quick, parallel washing of entire 96- and 384-well plates. This avoids time differences between wells for uniform results. Provides full control of wash power for optimized washing of cells, beads and ELISAs. Equipped with 96 and 384 indexing wash head and optimized magnetic carriers.
Software R package for calculating and drawing variable trees. Variable trees display information about nested subsets of data frame.
Bench top size cell counter that is designed to count cells and verify viability accurately and precisely, using standard trypan blue technique and provides image analysis for cell counting.
GFL Gesellschaft Fuer Labortec GFL-3013 Shaker
GFL Gesellschaft Fuer Labortec™ GFL-3013 Shaker
Shaker with rocking movements, max. load capacity 15 kg. Angle platform shaker use slow and uniform rocking motion to create reproducible growth and processing conditions at low speeds.
Cytiva | AKTA pure 25 L chromatography system
Chromatography system for purification in research applications. Allows for customization due to its modular design with flow rate. Available with flow rate of up to 25 mL/min or flow rate of up to 150 mL/min. Offers more than 20 hardware options for custom system, including new UV monitor.Includes Air sensor L9;CELL 2 U KPL;Conductivity monitor C9n Cpl;Injection valve V9-Inj;Instrument control unit, I9, Äkta pure; Mixer M9;Pressure monitor R9-2 with pump restrictor; Pump P9 Cpl 2x; UV Monitor U9-L Cpl;Fraction collector F9-R, Cytiva, CAT# 29011362;Superdex 200 increase 10/300 GL, Cytiva, CAT# 28-9909-44.
Eppendorf | Research plus 30-300 uL 12 channel pipette
Eppendorf Research plus 30 to 300 uL 12 channel pipette
Eppendorf Research plus 300 uL 12 channel pipette
Eppendorf multichannel, manual, autoclavable, air-cushion pipette for accurate ergonomic pipetting of aqueous solutions.
Automated 2 Photon Imaging Compatible Platform for Assessing Working Memory
Automated 2-Photon Imaging-Compatible Platform for Assessing Working Memory
Open source automated platform for assessing working memory and prefrontal circuit function. Designed for automated, high-throughput assessments of working memory and simultaneous two-photon imaging in chronic stress studies. Physiology compatible behavioral platform designed specifically for studying circuit mechanisms underlying working memory and related cognitive functions in chronic stress states.
Eppendorf | Research plus 20 ��� 200 ��L yellow 1 channel pipette
Mechanical and autoclavable, manual, air cushion pipette for accurate, ergonomic pipetting of aqueous solutions.
Eppendorf | Research plus 2 ��� 20 ��L yellow 1 channel pipette
Eppendorf Research® plus 2 – 20 µL yellow 1-channel pipette
Eppendorf | Research plus 100-1000 uL 1 channel pipette
Eppendorf Research® plus 100-1000 uL 1-channel pipette
Eppendorf manual, autoclavable, air-cushion pipette for accurate ergonomic pipetting of aqueous solutions.
Software Python platform for recording, converting, and uploading videos to cloud and for performing scheduled video recordings. Repository also includes wiki section with comprehensive guide to setting up Raspberry Pis for this purpose. Raspberry Pis are often cheaper than camcorder and can produce HD video. They are also equipped with infrared camera, making them ideal for recordings of animals that are active in low light conditions.
CHRONO LOG | Model 700 Whole Blood Optical Lumi Aggregometer
CHRONO-LOG® Model 700 Whole Blood/Optical Lumi-Aggregometer
Aggregometer exclusively used in measuring platelet aggregation to observe phenotypes.
GloMax Discover System Software and Firmware
Promega GloMax Discover System Software and Firmware
System includes firmware and plate reader software for reading absorbance, fluorescence, or luminescence in 96-well plates.
Sonication system for optimal shearing of biological and chemical samples.
Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases.
Mexican National Laboratory for Advanced Microscopy Core Facility
Laboratorio Nacional de Microscop�a Avanzada-UNAM
Mexican National Laboratory for Advanced Microscopy
National Laboratory for Advanced Microscopy
Mexican national facility open to all sectors of scientific research and education.Offers light microscopy and image analysis services and consulting, has original research program with incorporated undergraduate and postgraduate students, and supports development of bioimaging community in Mexico through training and outreach activities.
Portal provides link to design and order pMTL plasmid backbones created at BBSRC/EPSRC Synthetic Biology Research Centre, Nottingham, UK, for general cloning, expression and gene engineering (random and directed) in variety of chassis, including Clostridium sp and other anaerobes,hermophilic bacilli (Geobacillus),Cupriavidus (Ralstonia), and methanotrophs, such as Methylococcus capsulatus.
Georgia State University Imaging Core Facility
Facility is located in Petit Science Center in Georgia State University downtown Atlanta campus.Provides advanced light and electron microscopy imaging based analytical capabilities through use of laser scanning confocal microscopy, biological light microscopy, and electron microscopy, etc. Services include investigations in neurosciences, biology, biomedical sciences, chemistry, geosciences, physics, and other disciplines.
University of Massachusetts Amherst Cell Culture Core Facility
Core provides space, equipment, plant and animal cell cultures, media, supplies and training on recharge basis for both academic labs and corporate partners. Labs are equipped with laminar flow hoods, incubators, centrifuges, refrigerators/freezers, basic microscopes and automated cell counters. Offers technical expertise and hands on support for custom research projects. Services include Cell Line expansion and cryopreservation;Stem cell culture;Liquid nitrogen storage;Assay Development/optimization; CRISPR based gene editing and stable clone selection; Mycoplasma testing; Lentiviral packaging, titer, transduction;Molecular biology.
Dartmouth College Microscopy Shared Resource Core Facility
Dartmouth College DCC - Microscopy Shared Resource
Light microscopy imaging facility within Dartmouth Cancer Center. Services offered include confocal microscopy with Airyscan, multispectral imaging slide scanner, high thoughput brightfield and multichannel fluorescence microscopy of live cells, multichannel TIRF microscopy, photopatterning and microfabrication.
Dartmouth Hitchcock Medical Center Geisel School of Medicine Pathology Shared Resource Core Facility
Geisel School of Medicine at Dartmouth DH Pathology Shared Resource
Facilitates project planning, clinical validation and implementation of novel translational technology and research in fields of molecular diagnostics, molecular therapeutics, pharmacogenomics, quantitative morphologic image analysis and immunohistochemistry in CLIA-certified, CAP-accredited laboratory ensuring optimal clinical quality assurance.
Project that aims to provide persistent, unique and resolvable identifiers for research projects based on global handle system, funded by Australian Research Data Commons.
Web application for displaying high resolution image series coupled with overlaid atlas delineations. Online pan and zoom type viewer with three operating modes including Display series with atlas overlay;Create or edit nonlinear alignments; Create markup which can be exported as MeshView point clouds or to Excel for further numerical analysis.
Project features single board real time input/output system including touch sensing joysticks to quantify mouse forelimb trajectories with micron millisecond spatiotemporal resolution, which resolves mouse forelimb kinematics and further allows extraction of primitives. Joystick increases spatial precision, and reduces displacement force. Joystick is then integrated into automated home cage system to train mice in center out reach task.
Software R package to retrieve, cluster and visualize protein data from UniProt knowledgebase. Used to process, parse and illustrate proteomics data to summarize all required protein information in readable data frame, Excel CSV file, and/or graphical output. Generates set of graphics including gene ontology, chromosomal location, protein scoring and status, protein networking, sequence phylogenetic tree, and physicochemical properties. Supports clustering of proteins based on primary gene name or chromosomal location, facilitating additional downstream analysis.
Mapping Alternative Splicing Events to pRoteins
Software package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events. Mapping alternative splicing events to proteins.
Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.
Software R package for adaptive shrinkage. Implements Empirical Bayes approach for large scale hypothesis testing and false discovery rate estimation.
Software tool to implement interface for querying SQLite-based annotation data packages. Used for manipulation of SQLite-based annotations in Bioconductor.
Software package for genome wide annotation for mouse, primarily based on mapping using Entrez Gene identifiers.
Software Python tool to disambiguate mixed species RNA-seq reads according to their species of origin.
Rhode Island Hospital Molecular Pathology Core Facility
Molecular Pathology Core of the COBRE Center for Cancer Res. Dev.
Core of COBRE Center at department of Pathology located on sixth floor of Aldrich building at Rhode Island Hospital.Provides services, instrumentation, training and support. Equipment includes ArcturusXT laser capture microdissector, Stratagene MX3005p realtime PCR instrument, BioRad iCycler, Agilent Bioanalyzer, Olympus fluorescence-capable microscope with image analysis software, Ventana Discovery immunohistochemistry processor, microtome, cryostat, Beecher tissue arrayer and Aperio ScanScope.Tissue bank has 40 cu ft of ultra-low freezer space and provides human tumor tissue samples to all interested investigators who have received IRB approval for academic testing and research.Services include Tissue Sample Processing,Histology,Immunohistochemistry,Digital slide scanning by Aperio ScanScope,Tissue Microarrays,DNA/RNA extraction, Microdissection,Macrodissection verification by pathologist,Digital image analysis,Visium Spatial Gene Expression Assay,RNAscope Assay,Enzyme Linked Immunosorbent Assays (ELISAs),Technical assistance,Pathologist consultation,Technical assistance, Equipment use and training.
Rensselaer Polytechnic Institute Nuclear Magnetic Resonance Core Facility
Rensselaer Polytechnic Institute NMR Core
Provides access to ultra high field NMR instrumentation including probes for solution and solid state NMR, and resonators and high power gradients for diffusion and magnetic resonance microimaging. Supports research programs including structure determination of small molecules, proteins, carbohydrates, nucleic acids, and macromolecular complexes at atomic resolution, quantitative analysis of complex mixtures, metabolomics applications, diffusion analysis, characterization of materials, and MR microimaging.Expert training and assistance is available in experiment design and/or pulse sequence customization, sample preparation, data acquisition, processing, analysis, and reporting of results e.g. manuscript and/or grant preparation, in addition to comprehensive support.
University of Miami School of Medicine Transmission Electron Microscopy Core Facility
Transmission Electron Microscopy (TEM) Core Facility
University of Miami Transmission Electron Microscopy Core Facility
Provides access to conventional transmission electron microscope and associated sample processing services.
University of Maryland School of Pharmacy Mass Spectrometry Center Core Facility
University of Maryland School of Pharmacy Mass Spectrometry Center
Provides access to cutting edge technologies in mass spectrometry, methodology, and instrumentation. Provided expertise include the fields of Chemical Biology,Pharmaceutical Biology,Cancer Biology,Microbial Biology,Infectious Disease,Metabolic Disease,Chronic Pain Research,Quantitative Biosciences, Drug Discovery and Drug Development,Translational and Regulatory Sciences,Nanotechnology,.Bioinformatics and Technology Development
Charite University and Berlin Institute for Health Research Central Biobank Core Facility
Charite - Central Biobank Charite/BIH (ZeBanC)
Integrated healthcare biobank that operates under certified conditions and strict SOPs. Enables biomedical and translational researchers to perform their analyses using high quality biospecimens and data to generate reliable and reproducible research data. Core offers modular biobanking portfolio that can cover workflow from blood collection to storage, including all pre-analytical steps and their documentation. Offers spectrum of additional services ranging from DNA/RNA extraction and virtual microscopy to entire management of sample and data flow for national and international research consortia. Provides secure conventional and automated storage of samples at various temperatures as well as secure data management.
University of Utah Cell Imaging Core Facility
University of Utah HSC Cell Imaging Core
Core offers services, training and provides access to optical microscopes and imaging.Offers collaboration for complex projects.
University of Massachusetts Medical School Viral Vector Core Facility
Viral Vector Core (VVC) of the Gene Therapy Center
Core uses technologies to create and produce variety of high quality viral vectors.Provides investigators with the most suitable and efficient gene transfer vectors.Vectors produced include AD, AAV, and Lenti/retro. VVC staff can assist investigators with selection of gene transfer vector, its design and potential applications. Services include AdV vector creation and production, AAV vector production, Lentiviral vector production,AAV neutralizing antibody screening and titration.
One of the metadata models of openMINDS metadata framework. Composed of modular metadata schemas for spatial anchoring of neuroscience data structures, including brain atlas definitions.
Ontology for describing key metadata elements of spatial reference atlases. Ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures. Identifies and defines relationships between four common atlases and characterizes their properties and organization. This model can serve as suggestion for minimum requiremens for atlases and will accelerate neuroscience data integration.
Commercial organization provides software tools for video and data analysis used in healthare and education.Provides performance analysis solutions for team sports and individual athletes at every level.
Decision Support for computationally Demanding Optimization
Software Python framework for interactive multiobjective optimization methods.
Software tool for prediction of RNA–RNA, RNA–DNA, and DNA–DNA interactions. Both RIsearch1 and RIsearch2 enable quick localisation of potential near complementary interactions between given query and target sequences. RIsearch1 performs computation with whole sequences. RIsearch2 focuses on perfect complementary seed regions and extends them on both ends. User defined seed and extension constraints makes RIsearch2 applicable to all kinds of interaction predictions (e.g., siRNA and Cas9–gRNA off-target predictions).
Open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. Core unit of Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form network of biological interactions and are grouped into pathways including classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. External domain expert provides expertise, curator formalizes it into database structure, and external domain expert reviews representation. System of evidence tracking ensures that all assertions are backed up by primary literature. Website is designed to give the user graphical map of known biological processes and pathways that is also an interface. Database and website enable to find, organize, and utilize biological information to support data visualization, integration and analysis.
Software R package for detection, characterization and visualization of localized hypermutated regions, often referred to as kataegis. Aims to identify putative kataegis loci from common data formats housing genomic variants.
Part of Department of Health program for collecting, analyzing, and publishing information on all cancer cases in Puerto Rico. Information collected is obtained through active search for cancer cases, in places where cancer patients are studied, diagnosed or treated.
Software JavaScript library for creating behavioral experiments in Web browser. Used to create behavioral experiments in browser using JavaScript.
Resource to enable providers and staff of primary care clinics to promote organizational change to reduce health and healthcare disparities for SGM patients.
Open source computer vision controlled treadmill system for small running animals such as insects and mice. Treadmill is controlled by Python software, allowing for flexible control of video tracking parameters, behavioral triggers, distance ran, and feedback. Used for studying locomotor behavior.
Software tool for computerized cephalometric tracing for research related to orthodontic or orthognathic surgery. Used to analyze cephalometric radiographs and create progress superimpositions.
Restoring Joint Health and Function to Reduce Pain
Multi institutional consortium working to map network of sensory nerves that connect to temporomandibular joint and knee. Aims to understand how these types and patterns of sensory neuron networks in joints change with disease and aging. Part of larger HEAL consortium, trans agency effort to speed scientific solutions to stem national opioid public health crisis. Joint pain is recognized as contributing factor in the use of opioids.
Chemiluminescent enzyme immunoassay (CLEIA) analyzers from Fujirebio.
Software tool for constructing and visualizing bibliometric networks. These networks may for instance include journals, researchers, or individual publications, and they can be constructed based on citation, bibliographic coupling, co-citation, or co-authorship relations. Offers text mining functionality that can be used to construct and visualize co-occurrence networks of important terms extracted from body of scientific literature.
Software tool as DICOM to NIfTI converter.
Source tracking for Contamination Removal in microBiomes
Source-tracking for Contamination Removal in microBiomes
Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program.
Open source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution.
Pooled Resource Open Access ALS Clinical Trials Database
Publicly available repository of merged ALS clinical trials data.
Emory University Biostatistics Collaboration Core Facility
The Emory Biostatistics Collaboration Core (BCC)
Core is housed in the Department of Biostatistics and Bioinformatics in the Rollins School of Public Health of Emory University. BCC personnel are available for discussion at all stages of research, including: preparation of grants and contracts, assistance in analyzing and presenting research data, and statistical review of manuscripts in publication process. Provides access to computer hardware and software and personnel with expertise in using major statistical, graphics, and data management packages. Offers services from database development, implementation, and maintenance to production of publication quality graphic and tabular material.BCC tasks are classified into short term tasks that can be completed within three to six months with clear deliverables.
Emory University Center for Systems Imaging Core Facility
Center for Systems Imaging Core (CSIC CORE)
Emory University Center for Systems Imaging Core
Provides cross disciplinary scientific, administrative, and educational home for in vivo imaging at Emory University. Provides services for human and animal imaging studies.Supports advancement of scientific research focused on development of imaging biomarkers, and serves to build interdisciplinary educational symposia and training programs.
Emory University Division of Animal Resources Core Facility
Emory University Division of Animal Resources
Provides integrated team of animal care specialists, administrative professionals, veterinarians, veterinary technicians, logistics deliverers and information technology experts dedicated to high quality and comprehensive care of research animals.
Emory University Emory Glycomics and Molecular Interactions Core Facility
Emory Glycomics and Molecular Interactions Core (EGMIC)
Emory University Emory Glycomics and Molecular Interactions Core (EGMIC)
Provides access to methods and technology in area of glycomics and molecular interactions.Provides individual consultation with investigators to address questions regarding glycosylation, the most common posttranslational modification, and protein glycan interactions.Provides access to mass spectrometry and glycan microarray technologies to help understand functions of glycans and glycan binding proteins.
Emory University Emory Integrated Computational Core Facility
Emory Integrated Computational Core (EICC)
Emory University Emory Integrated Computational Core (EICC)
Provides computational support to Emory investigators with large datasets.
Emory University Emory Gnobiotic Animal Core Facility
Offers services to experimentally manipulate microbiomes of mice in controlled environment to gain insight into important biological mechanisms.
Emory University Emory Integrated Metabolomics and Lipidomics Core Facility
Emory Integrated Metabolomics & Lipidomics Core
Emory University Emory Integrated Metabolomics and Lipidomics Core
Provides quantitative analysis of lipids and soluble metabolites using cutting-edge mass spectrometry methods as a service to both clinical and basic biomedical research efforts. We deliver quantitative lipidomics and metabolomics analyses on samples from a wide variety of biological matrices, e.g. blood, serum, plasma, solid tissues, fecal/urine samples, cell extracts, etc., to support both clinical and basic research efforts.
Emory University Emory Multiplexed Immunoassay Core Facility
Emory University Emory Multiplexed Immunoassay Core
Core provides services involved with the latest multiplexed immunoassays.
Emory University Emory Integrated Genomics Core Facility
Emory University Emory Integrated Genomics Core (EIGC)
Core helps investigators use the latest genomics technologies in their research.
Emory University Emory Integrated Proteomics Core Facility
Emory University Emory Integrated Proteomics Core (EIPC)
Core is full service proteomics facility offering Emory researchers ability to use the latest technologies in their research.
Emory University Emory HPLC Bioanalytical Core Facility
Emory University Emory HPLC Bioanalytical Core
Core offers services to identify and quantify monoamine neurotransmitters, amino acids, purine bases, and nucleotides from variety of biological samples. Provides expertise to develop and validate HPLC methods to measure other small molecule compounds, peptides, and proteins.
Emory University Emory Investigational Drug Service Core Facility
Emory Investigational Drug Service (IDS)
Emory University Emory Investigational Drug Service (IDS)
Provides research pharmacy services to Emory patients, investigators and sponsors, and ensures that research drugs are handled safely, accurately and effectively. IDS strives to provide quality and efficiency in research drug management, enhance patient care in research and ensure audit readiness at all times.
Emory University Emory Cellular and Immunotherapy Core Facility
Emory University Emory Cellular and Immunotherapy Core
Clinical cell manufacturing facility that prepares cell and immunotherapy products under current Good Manufacturing Practices for development of investigational new drugs and diagnostics methods.Provides GMP compliant cell manufacturing and/or consultation for translational of Emory based or external research collaborations into early phase clinical trials.
Emory University Emory Integrated Cellular Imaging Core Facility
Emory Integrated Cellular Imaging Core (ICI)
Emory University Emory Integrated Cellular Imaging Core (ICI)
Provides light microscopy. Offers expertise in imaging for experimental needs.
Emory University Mouse Transgenic and Gene Targeting Core Facility
Emory University Mouse Transgenic and Gene Targeting Core (TMF)
Mouse Transgenic and Gene Targeting Core (TMF)
Provides equipment and expertise for generating and characterizing genetically altered mouse models. Please contact us so that we can discuss your experimental needs.
Emory University School of Medicine Flow Cytometry Core Facility
Emory University Emory Flow Cytometry Core
Core provides sorting, sample analysis and analyzer training.Provides quantitative flow cytometric analyses on samples including blood, bone marrow, spleen, serum, plasma, solid tissues, cell extracts to support both clinical and basic research efforts. These analyses will provide insight on cell function and precursors whose abundance can be monitored as biomarkers to predict and follow progression of a wide range of diseases, such as H1N1, yellow fever, dengue, neurodegenerative diseases, stem cell studies.Provides consultations, expert training, and support for all systems and provides access to equipment.
Emory University Robert P. Apkarian Integrated Electron Microscopy Core Facility
Emory University Robert P. Apkarian Integrated Electron Microscopy Core (IEMC)
Robert P. Apkarian Integrated Electron Microscopy Core (IEMC)
Core helps investigators use the latest technologies on structural research in their projects. Provides expertise in experimental needs.
Vanderbilt University Medical Center Vanderbilt Diet, Body Composition, and Human Metabolism Core Facility
Core provides valid, reliable, appropriate and cost effective methods to investigators that facilitate all types of human research (T1, T2 and T3) and study designs. These methods include 24 hour diet recalls, diet histories, food records/diaries, food frequency questionnaires, observed intakes and weighed intakes of all forms of dietary and nutrient intake (foods, beverages, dietary supplements, liquid nutrition supplements, enteral tube feedings, parenteral support and medications).
University of Nebraska Medical Center UNMC Genomics Core Facility
Provides Next Generation DNA and Sanger sequencing services; single cell genomics assays by 10x Genomics, and Nanostring technology targeted gene expression assays.
University of California BioPACIFIC MIP Core Facility
and Integrated Chemistry Materials Innovation Platform Core Facility
BioPolymers, Automated Cellular Infrastructure, Flow, and Integrated Chemistry Materials Innovation Platform is platform dedicated to scalable production of bio-derived building blocks and polymers from yeast, fungi, and bacteria. Automated high-throughput synthesis and characterization of bio-derived polymers aims to accelerate discovery and speed development of new high-performance materials.
Harmony High-Content Imaging and Analysis Software
Software tool designed by PerkinElmer for high content screening systems. Used to quantify complex cellular phenotypes. High content analysis software.
Software Python tool for removing bias introduced from having overlapped samples between base GWAS data and target genotype data for Polygenic Risk Score analyses. Used for adjusting inflation in PRS prediction and association statistics in presence of sample overlap or close relatedness between GWAS and target samples.
University of Vermont Functional Brain Imaging Core Facility
University of Vermont Functional Brain Imaging Core
Core to perform functional brain imaging studies collaboratively with Department of Radiology utilizing Tesla Phillips Achieva scanner and CNRU experimental image capture and analysis system. Works collaboratively with other laboratories within Psychiatry Department to serve mutual research interests. Collaborates across Neuroscience Consortium with investigators in Departments of Neurology, Anatomy, Psychology, as well as GCRC investigators to further develop brain imaging expertise at UVM. Functional imaging experimental and analysis expertise reside in CNRU-Psychiatry. Technical personnel necessary to operate imaging program including MR physicist, fMRI radiologist, and technicians are employed by Department of Radiology in College of Medicine.
Presents basic realities about world in which we live in and is one of the U.S. Government’s most accessed publications. Provides basic intelligence on history, people, government, economy, energy, geography, environment, communications, transportation, military, terrorism, and transnational issues for 266 world entities.
Former name Google Data Studio, is online tool for converting data into customizable informative reports and dashboards introduced by Google on March 15, 2016 as part of enterprise Google Analytics 360 suite. Online service for graphic data visualization.
Software R package and jamovi module for simplifying agreement and reliability analyses. Functions within this package include simple tests of agreement, agreement analysis for nested and replicate data, and provide robust analyses of reliability.Used for calculating absolute agreement and estimating required sample sizes for studies of absolute agreement.
Bacterial Isolate Genome Sequence Database
Platform for gene-by-gene bacterial population annotation and analysis. Designed to store and analyse sequence data for bacterial isolates. Used for scalable analysis of bacterial genome variation at population level.
Software tool for multi view child motor development dataset for AI-driven assessment of child development project.
Software tool as collection of bioinfomatics analysis pipelines to process single cell sequencing data generated with Singleron products. Single cell analysis pipelines developed by Singleron Biotechnologies.
Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.
Software tool as algorithm for finding maximal independent set of nodes in arbitrary undirected graph along with efficient implementation in C++. Used to discover unlinked markers, and unrelated individuals in populations.
Collaborative research effort among physicians, researchers, and patients at the University of Michigan with goal of combining patient electronic health record data with corresponding genetic data to gain novel biomedical insights. Biobank linking genotypes and electronic clinical records in Michigan Medicine patients. MGI participants agree to provide study team with access to EHR data for clinical information and biospecimen including blood or saliva.
Software R package for computing Polygenic Risk Scores from dosages.
Open database of polygenic scores and relevant metadata required for accurate application and evaluation. Used for reproducibility and systematic evaluation.
Web tool for retrieving available lexicon. It comes in app format, which can be downloaded from the tool's website, and in web format, which can be completed online.
Northwestern University Immune Monitoring Core Facility
Northwestern University Immune Monitoring Core
Core of Comprehensive Transplant Center provides translational mechanistic studies in human solid organ and cellular transplantations. Provides assistance with human immune monitoring needs for translational and clinical transplantation research projects.Offers immune monitoring services for translational mechanistic studies.
Colorado State University Experimental Pathology Core Facility
Colorado State University Experimental Pathology Facility
Core provides pathologic services ranging from animal model troubleshooting, and tissue fixation to stain slide prep and immunohistochemistry. Offers expertise in slide interpretations and quantitative histopathology in anatomic and clinical pathology. Offers molecular pathology services via Nanostring nCounter equipment.
Software package as heterogenous compute solution for Oxford Nanopore Technologies adaptive sampling also known as selective sequencing and Read Until. Read Until allows genomic reads to be analyzed in real-time and abandoned halfway, if not belonging to genomic region of interest. HARU takes advantage of heterogenous edge compute platforms and provides hardware acceleration using reconfigurable hardware on Multiprocessor system on chip.
Republic of Korea e-Government platform for major domestic, international and North Korean statistics. Web service provides official statistics produced by statistical agencies covering more than 500 subject matters as well as the latest data on international finance and economy from international organizations i.e. IMF, World Bank, OECD.
Software R package containing several basic utility functions including moving, rolling, running,window statistic functions, read, write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder,decoder, round-off-error-free sum and cumsum.
Software tool written in Bash to ease different standard preprocessing steps of short high throughput sequencing reads. Runs on UNIX, Linux and most OS X operating systems.
Software R package for randomization of clinical trials. Provides sound scientific evidence for choice of randomization procedure, on the basis of well founded criteria. Includes functions for generating randomization sequences from various randomization procedures as well as various issues for assessment of randomization procedures.
Software tool that performs SET Operations including Set Intersections, Set Unions and Set Differences over lists of words, numbers etc with formatted results . Used for comparing differences between two lists.
Software R package for query NCBI Entrez and retrieve PubMed records in XML or text format. Used to process PubMed records by extracting and aggregating data from selected fields. Large number of records can be downloaded via this simple-to-use interface to NCBI PubMed API. Used to search and retrieve scientific publication records from PubMed.
10x Genomics | Visium Spatial Gene Expression
Visium Spatial Gene Expression is next-generation molecular profiling solution for classifying tissue based on total mRNA. Allows to map whole transcriptome with morphological context in FFPE or fresh frozen tissues. Used to perform spatial transcriptomics, which combines histological information with whole transcriptome gene expression profiles to provide spatially resolved gene expression. System for classifying tissue based on total mRNA. Includes two software to analyze data. Space Ranger analysis software that automatically overlays spatial gene expression information on tissue image and identifies clusters of spots with similar transcription profiles. Loupe Browser visualization software to interactively explore results.
Software tool for rapid haploid variant calling and core genome alignment.
Software R package to create, modify, analyze, and visualize network graph diagrams. Graph and network visualization using tabular data in R.
University of Montreal Health Centre Rodent Metabolic Phenotyping Core Facility
Centre Hospitalier de University de Montr�al CRCHUM-Rodent Metabolic Phenotyping Core
CRCHUM-Rodent Metabolic Phenotyping Core
Core facility offers services unique in Canada for study of carbohydrate and energy metabolism in rodents such as routine tolerance tests of glucose, lipids, pyruvate, insulin and metabolic cages.Provides expertise in performing hyperglycemic clamps as well as Hyperinsulinemic-euglycemic clamps. Offers services for research projects carried out at the cellular or tissue level and on animals,complete metabolic phenotyping of genetically modified rodents, evaluation of effect of pharmacological or molecular interventions on carbohydrate and/or energy metabolism in healthy rodent models or in obese or diabetic models.All surgical procedures, metabolic tests, dosing and data analyses are carried out by our staff.
System includes 3D Printed Syringe Pump Rack composed by 5 Syringe Pumps to have 2 continuous flow systems and one remaining pump. Syringe Pump is used to gradually administer small amounts of fluid to patient or for use in chemical and biomedical research. Main features include Open hardware/software, Extremely compact size ( 7cm movement range ), High precision lead screw and nut, Simple to use (command line interface), Simple to replicate, Minimal clean Design.
University of Florida Health Mass Spectrometry and Proteomics Core Facility
University of Florida Health Mass Spectrometry and Proteomics
Core provides range of mass spectrometry based proteomics services to assist with protein characterization, identification and quantification, and apply these technologies to solve relevant biological problems. Equipment including Thermo Scientific Orbitrap Fusion Tribrid mass spectrometer, Thermo Scientific Q Exactive hybrid quadrupole-Orbitrap benchtopmass spectrometer, Agilent Technologies 1100 HPLC. Services include Mini SDS-PAGE,Gel Coomassie staining,Protein/Peptide Assay,Protein Precipitation,Solution or in-gel sample digestion and high resolution LC-MS/MS using 1-4Hr gradients,High resolution LC-MS/MS using 1-4Hr gradients (self-digested samples),High resolution MS and MS/MS via direct infusion,Protein digest clean up,TMT quantification,SILAC quantification,Label free quantification,HPLC peptide separation.
ImageJ plugin for quantitative evaluation and automated scoring of immunohistochemistry images of human tissue samples. IHC profiler has been developed as standard automated scoring tool.
Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data.
Life Science company providing human cell culture and cell biology products.
Life science company that develops and manufacture imaging and analyzing systems for fluorescence, chemiluminescence and bioluminescence applications.
Cytiva is the new name of the former GE Healthcare Life Sciences biopharma business following its acquisition by Danaher Corporation, according to an April 1, 2020 announcement. Provider of life sciences brands such as ÄKTA, Amersham, HyClone, MabSelect and Whatman.
Princeton University Chemistry Core Facility
Princeton University Chemistry Core Facileties
Department of Chemistry houses comprehensive array of research facilities to support diversity of scientific work. Staff members expertly maintain each facility and are available to help users set up experiments or interpret results. Our resources facilitate scientific progress from giving chemists deeper understanding of their data to providing essential characterization of compounds for publication.
University of California Davis Health Biorepository Shared Resource Core Facility
University of California Davis Health Biorepository Shared Resource
Provides specimens with annotated data for clinical and basic science research purposes.Biorepository functions as centralized tissue bank to provide researchers access to cancer- and non-cancer-related specimens including fresh or frozen tissue, paraffin blocks,sections and fluids, procured and stored using international standards of best practices and protocols compliant with Office for Human Research Protection. Specimens can be obtained prospectively as part of clinical trials or accessed through UC Davis Health Clinical Laboratories, where over 5.5 million blood specimens are processed annually.
University of California Davis Health Combinatorial Chemistry and Chemical Biology Shared Resource Core Facility
Davis UC Davis Combinatorial Chemistry & Chemical Biology Shared Resource
UC Davis Combinatorial Chemistry & Chemical Biology Shared Resource
Provides high throughput screening platform to discover unique chemical probes against biological targets using various one bead one compound and one bead two compound combinatorial libraries.Interacts closely with resource users on optimization of the lead compounds via focused libraries and standard medicinal chemistry techniques. Provides custom synthesis of telodendrimer based micellar nanoparticle platform for efficient drug delivery.
University of California Davis Health Biostatistics Shared Resource Core Facility
Davis UC Davis Biostatistics Shared Resource
Provides expertise in design, analysis and reporting of cancer related studies, including basic, translational, clinical and population based research. BSR affiliated faculty and staff work with investigators from the earliest stages of study planning. The shared resource is especially committed to mentoring early career cancer researchers.
University of California Davis Health Genomics Shared Resource Core Facility
Provides expertise and comprehensive services to accomplish virtually every application of next generation sequencing based genomics research, including gene expression profiling, mutation/variant analyses, copy number analysis, epigenomics, metagenomics, single cell sequencing and spatial transcriptomics services. GSR also specializes in development of custom protocols and extensive data analysis and integrative bioinformatics support. The shared resource provides wide range of additional services for translational and clinical genomics research.
University of California Davis Health Immune Modeling, Analysis and Diagnostics Shared Resource Core Facility
Analysis and Diagnostics Shared Resource
Clinical Laboratory Improvement Amendments certified laboratory established to provide scientific support to investigators conducting clinical studies in humans, preclinical studies in animals and/or studies in veterinary medicine. Conducts immunology based assays needed to monitor patients in clinical immunotherapy trials. Offers molecular and cellular assays for investigators in different fields, including custom assays designes.
University of California Davis Health Molecular Pharmacology Shared Resource Core Facility
Davis UC Davis Molecular Pharmacology Shared Resource
UC Davis Molecular Pharmacology Shared Resource
Provides services to support the development and implementation of clinical trials at UC Davis Comprehensive Cancer Center. Oversees high quality collection, processing, and analysis of clinical specimens,typically but not exclusively blood specimens, for pharmacokinetic and pharmacodynamics studies. Conducts preclinical modeling of novel anti cancer agents to test hypotheses and develop scientific rationale required for translation of laboratory concepts into clinical trials, including assessment of DM/PK/PD properties.
University of California Davis Health In Vivo Translational Imaging Shared Resource Core Facility
Davis UC Davis In Vivo Translational Imaging Shared Resource
UC Davis In Vivo Translational Imaging Shared Resource
Provides access to in vivo imaging technologies including molecular imaging, optical imaging, quantitative physiologic and anatomic imaging, and whole body PET/CT scanning in humans and animals. Provides targeted imaging probes and tracers as well as expertise in planning, executing and analyzing in vivo imaging studies. Supports imaging studies in small animals, large animals and humans.This resource is located in three adjacent buildings in the Health Sciences district of the Davis campus:Center for Molecular and Genomic Imaging (CMGI), Genome and Biomedical Sciences Facility (small-animal imaging);Nuclear Magnetic Resonance (NMR) Facility, Tupper Hall (small-animal MRI);Center for Imaging Sciences (CIS), Veterinary School (large-animal imaging).
Web tool for predicting DNA methylation sites. Identifies methylation sites for three different types of DNA methylation, namely N6-adenine, N4-cytosine, and 5-hydroxymethylcytosine. MuLan-Methyl-Multiple transformer based language models for accurate DNA methylation prediction.
Software parallel Big Data toolkit to process FASTA and FASTQ files at scale. Used to manipulate FASTA/Q files at scale with speed and scalability at its core.
Software package as collection of WDL workflows to build linkage maps from sequencing reads. WDL workflows to build genetic maps from sequencing reads.
Software tool for speeding up estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies.
Software tool for redesign and expansion of prediction on kinase specific phosphorylation sites. Machine learning based kinase specific phosphorylation site prediction tool.
Stellenbosch University Microscopy Unit Core Facility
Stellenbosch University SU_CAF Microscopy Unit
Provides access to advanced light and electron microscopes as well as imaging expertise. Applications range from material science to biomedical research. Provides custom image analysis, comprehensive sample preparation for light and electron microscopy, and consultation.
Software Python library for hierarchical clustering. Fast Hierarchical, Agglomerative Clustering Routines for R and Python.
single cell RNA-seq Data Visualization and Analysis
Interactive web server to explore and analyze single cell RNA-seq data. R shiny based tool used for single cell RNA-seq data visualization and analysis.
Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs.
Medical devices company that develops and supplies clinical diagnostics to pathology market. It is also research, instrument, and medical device company as well as division of Danaher Corporation with headquarters Wetzlar, Germany.
Direct sales organization that develops and manufactures automation sensors, vision systems, barcode readers, laser markers, measuring instruments, and digital microscopes. Founder Takemitsu Takizaki. Headquarters Osaka, Osaka, Japan.
Pioneer in high definition spatial proteomics, tissue imaging and analysis to accelerate medical discovery and improve human health. With MIBI technology and expertise of pathology and data science teams, Ionpath provides actionable insights to translational and clinical researchers at leading pharmaceutical, biotechnology, and research organizations in immuno-oncology, immunology, neuroscience, and infectious disease research.
American company engaged in design, manufacture and sale of biological research equipment based on integrated fluidic circuit technology. Founders leveraged their semiconductor experience to create integrated circuits that carried fluids rather than electrons.
Manufacturer of light, electron, X-ray and ion microscope systems. Offers solutions for correlative microscopy. Provides products and services for life sciences, materials and industrial research, as well as education and clinical practice.
Bruker Daltonics is subsidary of Bruker Corporation American. Bruker is manufacturer of scientific instruments for molecular and materials research, as well as for industrial and applied analysis.
Provides development and manufacture of high performance scientific digital cameras, microscopy systems and spectrographs for academic, industrial and government applications.
Zyla 4.2 PLUS is the latest sCMOS technology advancement from Andor. At its heart, Zyla 4.2 PLUS benefits from latest generation sCMOS sensor technology, delivering a further 10 % boost in QE, resulting in an unprecedented 82% QEmax.
Provides fully digitized image of speciment that can be viewed and edited from virtually anywhere.
Directed Acyclic Graphs using deep-learning VAriable SElection
Software tool for identifying nonlinear causal relations and estimating their effect size help to understand complex disease pathobiology.
Imaging platform, enabling phenotypic profiling and spatial analysis of tissue microenvironment. Enables over 40 markers to be visualized simultaneously with single step staining and single step imaging.
Sequencing system supports range of methods such as exome sequencing, target enrichment, single-cell profiling.
Instrument for probing molecular content of sample with MALDI-2. The timsTOF fleX is fully functional high speed, high sensitivity ESI instrument for all X-Omics analyses, combined with high spatial resolution Matrix-Assisted Laser Desorption Ionization (MALDI) source and stage specifically designed for resolving molecular distributions and bringing spatial dimension to OMICS analyses.MALDI-2 uses laser post-ionization to enhance and enrich the MALDI experiment providing access to chemical classes typically opaque to MALDI with enhanced sensitivities.
Cell imaging system for fast, automated imaging in fixed and live cells. Instrument can rapidly image cells using laser autofocusing, LED light source and CMOS camera.
Keyence | BZ-X800 Fluorescent Microscope
Automated high-resolution microscope for Life Science research. Provided with BZ-X800 Analyzer software. You can purchase different applications for the BZ-X800 analysis software to perform specific analyses, such as the BZ-H4C Hybrid Cell Count Application, which is used to count stained areas.
Thermo Fisher | Orbitrap Eclipse Tribrid mass spectrometer
Orbitrap Eclipse Tribrid mass spectrometer
Mass spectrometer designed for most difficult analytical challenges. Incorporates inventions in ion transmission and control, extended m/z range, and real-time decision making. System suited for proteomics, structural biology, small-molecule, and biopharmaceutical characterization experiments.
Software R package with several tools for microbiome data analysis.
Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines.
Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types.
Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations.
Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks.
Single cell atlas of human and mouse white adipose tissue.
Translational Human Pancreatic Islet Genotype Tissue-Expression Resource
Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets.
Portal to search liver single cell RNA-sequencing datasets. Datasets for expression of genes or proteins (when CITE-seq was performed). To search for gene enter the official gene name. To search for protein please click to see specific names to use for different markers included.
Atlas aims to provide regular information on state of diabetes. Reports, produced annually, epidemiological and diabetes related impact data including the impact of type 2 diabetes in indigenous peoples, type 1 diabetes across all age groups, COVID-19 among people with diabetes, and diabetes foot-related complications.
Platform that facilitates data driven hypothesis generation for diabetes and related metabolic disorder research community. Curated transcriptomics datasets from various Type 2 Diabetes studies are made available for download, visualization, and enrichment analysis.
Heterogeneous network Connectivity Search
Web app that allows users to search for the most important paths connecting any two nodes in Hetionet.
Presentation software developed by Microsoft Corporation. Part of Microsoft Office suite. Used for creating slideshows and delivering presentations.
Software R package that allows for multiple confidence intervals per row, custom fonts for each text element, custom confidence intervals, text mixed with expressions, and more. Advanced Forest Plot using 'grid' graphics. Used to extend the use of forest plots beyond meta analyses.
Stanford University Quantitative Sciences Unit Core Facility
Stanford University Quantitative Sciences Unit
Collaborative unit of faculty and staff with diverse data science expertise in Biomedical Informatics Research Division in Department of Medicine. Members collaborate with investigators to address questions about disease and human health through leading in practice of data science. QSU members are data scientists with expertise including data inference, evidence synthesis, computational biology, missing data, prediction modeling, statistical computing, database creation, and software development. QSU leads and collaborates on large scale scientific projects that includes serving as data coordinating center for large multi center randomized clinical trials.
Software library to filter documents based on XPath expression, return specific nodes for XPath/XQuery expression, transform documents using XSLT stylesheet. By providing some basic wrappers to Saxon, spark-xml-utils library exposes some basic XPath, XQuery, and XSLT functionality that can readily be leveraged by any Spark application.
Software library for parsing and querying XML data with Apache Spark, for Spark SQL and DataFrames. XML data source for Spark SQL and DataFrames.
Web based notebook that enables data driven, interactive data analytics and collaborative documents with SQL, Scala, Python, R and more. Multi purposed web based notebook which brings data ingestion, data exploration, visualization, sharing and collaboration.
University of Montreal CR-HMR Flow Cytometry Core Facility
Offers sorting and flow cytometry services. Equipment includes Cytek Aurora, BD ARIA III, SONY cell sorters and Cytek Aurora, 2 BD LSRFortessa X-20, BD FACSCelesta,BD LSR II, CANTO A analyzers. Individual mandatory training is necessary to access this facility. ARIA III cell sorter as well as SONY SH800 are equipped with negative pressure hood allowing sorting of potentially infectious samples including human cells from healthy donors.
Texas A and M University AggieFab Nanofabrication Core Facility
Shared nano/microfabrication facility located on the 1st floor of the Frederick E. Giesecke Engineering Research Building at Texas A&M University. Provides equipment for range of microscale and nanoscale fabrication of diverse materials, nanopatterning and deposition equipment. Equipment include Zeiss Orion Helium Ion Microscope/Nanofab, FEI Helios DualBeam Focused Ion Beam (FIB), ASM Atomic Layer Deposition (ALD) tool, Clustex Multi-target deposition tool, Oxford Estrelas DRIE tool, Heidelberg MLA150 Maskless Lithography tool.
Creative Biolabs Non-IgG Antibody Isotypes Services
Provides high quality custom non-IgG antibody services.
Web tool for identifying CRISPR target sites and evaluating their specificity. CRISPR Target Finder uses TagScan and algorithms based on large scale analyses of CRISPR-Cas9 specificity in cell lines and animals published to date to identify potential off target cleavage sites for given CRISPR target.
Open source, printable, open faced running wheels for mice residing in home cage that is automated to collect locomotor information such as distance traveled, wheel direction, and velocity. Running wheel system available on GitHub contains code and information to create and run running wheels. System consists of 3D printed wheel, Raspberry Pi 0 W, and supporting components.
LabChart data analysis software creates platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds.Used for collection and analysis of signals. Recommended for researchers and educators who want the capabilities without modules and automation of specific measurements.
BD Biosciences | FACSymphony A3 Cell Analyzer
Fluorescence activated cell analyzing instrument by BD Biosciences. Allows for the simultaneous detection of up to 30 parameters and 28 colors.
Pennsylvania State University Huck Institutes of the Life Sciences Genomics Core Facility
Huck Institutes of the Life Sciencies Genomics Core Facility
PennState Huck Institutes of the Life Sciencies Genomics Core Facility
Genomics Core Facility provides services including Whole-genome and transcriptome sequencing of non-model organisms, Amplicon sequencing for metagenomic studies, Differential expression analysis of mRNA and miRNA, Degradome sequencing, ChIP and RIP sequencing.
Portal for large scale fMRI dataset conducted at ultra high field strength at Center of Magnetic Resonance Research at University of Minnesota. Dataset consists of whole brain, high resolution fMRI measurements of healthy adult subjects while they viewed thousands of color natural scenes over course of scan sessions. While viewing these images, subjects were engaged in continuous recognition task in which they reported whether they had seen each given image at any point in experiment. These data constitute massive benchmark dataset for computational models of visual representation and cognition, and can support wide range of scientific inquiry.
Thermo Fisher | EVOS M5000 Imaging System
Microsoft system includes integrated digital inverted benchtop microscope for four-color fluorescence, transmitted-light, and color imaging. Provides interchangeable optics with autofocus, single-click multi-channel image acquisition.3.2 Megapixels, monochrome, CMOS camera. Offers software for acquisition, analysis, and automated cell counting.
Manufacturer of mass spectrometry instrumentation used in biomedical and environmental applications. Originally started by scientists from the University of Toronto Institute for Aerospace Studies, it is now part of Danaher Corporation with the SCIEX R&D division still located in Toronto, Canada.
Software R package contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in creation of these plots. Functions to create publication quality plots.
Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.
Software tool that suppresses errors in next generation sequencing data by using unique molecular identifers to amalgamate reads derived from same DNA template into consensus sequence.
Software Python command line tool for post processing of structural variant calls. Framework for rapid generation of structural variant consensus, to visualize genetic impact and context as well as process both genome and transcriptome data.
Structural Variant detection in Circulating Tumor DNA
Software tool for detecting structural variations from cell free DNA containing low dilutions of circulating tumor DNA.
Software R package as CNV detection tool for targeted NGS panel data. Extension of cn.mops package. Used for detecting copy number variations in targeted next generation sequencing panel data. Suitable to use for clinical geneticists for routine clinical diagnostics.
Software tool as variant caller for both single and paired sample variant calling from BAM files. Implements amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads.Novel and versatile variant caller for next generation sequencing in cancer research.
Kinase Associated Neural Phospho Signaling
Database system that provides phosphorylated sites and information about which substrates are phosphorylated by specific kinase and which extracellular stimuli activate or inhibit protein phosphorylation via intracellular signaling cascades.
Minimum Information about Biosynthetic Gene cluster
MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters.
Curated catalog of worldwide biological databases to provide landscape of biological databases throughout the world and enable easy retrieval and access to specific collection of databases of interest. Catalog of worldwide biological databases as well as their curated meta information and derived statistics.
Database of protein structure predictions by AlphaFold that are freely and openly available to global scientific community. Included are nearly all catalogued proteins known to science. Provides programmatic access to and interactive visualization of predicted atomic coordinates, per residue and pairwise model confidence estimates and predicted aligned errors.
Resting State Hemodynamic Response Function Retrieval and Deconvolution
Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images.
Catholic University of Louvain Institute of Experimental and Clinical Research Flow Cytomerty Platform
University of Pennsylvania Institute for RNA Innovation Engineered mRNA and Targeted Nanomedicine Core Facility
Engineered mRNA and Targeted Nanomedicine Core
Core focuses on exploring mRNA technology and lipid nanoparticles for various applications including tissue and cell targeting. Offers Optimization and production of in vitro transcribed mRNA, Small scale production of sequence optimized in vitro transcribed mRNA, Incorporation of modified nucleosides to modulate activity, Off the shelf in vitro transcribed mRNA encoding reporter genes or cancer antigens,Labelled mRNA for nanoparticle tracking and microscopy, Encapsulation into commercially available proprietary and non proprietary lipid nanoparticles through LNP core.
Software tool for single cell RNA sequencing analysis. Command line tool for easy and scalable single cell RNA sequencing analysis.
Repository for highly controlled sound presentation in freely moving rats. Provides all necessary information for building, adjusting, and using Ratphones to reliably present auditory stimulation to freely moving rats. Used for 3D printing of headphones designed for auditory psychophysics in behaving rats.
Software tool for classification of virus sequences based on sequence pairwise identity. Virus classification tool based on pairwise sequence alignment and identity calculation. Used to enable general virologists to consistently classify newly determined virus full genome sequences according to ICTV endorsed pairwise genetic identity based genus, species and strain demarcation recommendations. Also usable as amino acid sequence classifier for characterisation of novel highly divergent viruses.
Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs.
PowerMAG View! 3D-Neuronavigation system
System visualizes electromagnetic hot spot of the coil at individual, anatomical data record. MR-based navigation system integrated into TMS flexible arm enables optimal alignment with camera. Used to carry out neuronavigation.
Software tool writen in LabVIEW is acquisition program for BioSemi ActiveTwo system. Designed to display all ActiveTwo channels on screen and save all data to network disk in .BDF format. Basic acquisition program can be expanded with modules on client specification. Used for acquisition of EEG/ECG/EMG signals, as well as for data coming from additional sensors such as AnalogInputBox (AIB), digital triggers from USB2 receiver and extra sensors connected to AD-box. Several reference selections, filtering and downsampling options are provided.
American biotechnology company that designs and manufactures gene sequencing technology used in scientific research.
University of British Columbia Gut4Health Microbiome Core Facility
University of British Columbia UBC-Gut4Health Microbiome Core
Facilitates microbiome studies for researchers at British Columbia Children Hospital Research Institute and University of British Columbia. Core offers processing and storing biological specimens, and sequencing and analysis of microbial communities for various research studies, including basic science, clinical, translational, and epidemiological projects.
Software pipeline for marine Genomic Observatories data analysis. Used to address challenges of analysis of European Marine Omics Biodiversity Observation Network data.
Web tool to predict probability of proteins to undergo liquid-liquid phase separation.Used to perform sequence based identification of both droplet promoting regions and of aggregation promoting regions within droplets. Used to predict droplet promoting regions and proteins, which can spontaneously phase separate.
Software aplication for NGS data analysis of genomes, transcriptomes, and metagenomes. Allows researchers to easily process large and complex data sets, and streamline their analysis process. Software is structured in different modules, each with specific set of tools and functions designed to perform different types of analysis, such as de-novo genome assemblies, genetic variation analysis, differential expression analysis, and taxonomic classifications of microbiome data, including the functional interpretation and rich visualizations of results.
Multiple Sequentially Markovian Coalescent
Software application to infer population size history and population separation history from whole genome sequencing data. Used for inferring demographic history and population structure through time from genome sequences. MSMC2 is successor of MSMC.
Knowledge Graph-based Machine Learning framework for explainably predicting Drugs Treating Diseases
Software repository contains all scripts and instructions for running KGML-xDTD model, which is Knowledge Graph-based Machine Learning framework for explainably predicting Drugs Treating Diseases.
Cleveland Open Source Modular Implant Innovators Community
Open source neurostimulation and recording hardware instrument platform. Part of the SPARC project. COSMIIC is based on the Networked Neuroprosthesis developed at Case Western Reserve University.
Promptable segmentation system with zero shot generalization to unfamiliar objects and images, without need for additional training. Github repository provides code for running inference with SegmentAnything Model, links for downloading trained model checkpoints, and example notebooks that show how to use the model.
HORNET CENTER FOR AUTONOMIC NERVE RECORDING AND STIMULATION SYSTEMS
Parylene MEA Fabrication is related to SPARC. Repository for standard fabrication procedure for Parylene C microelectrode arrays and similar devices.
Software Python toolkit for modelling locomotion and neuronal activity in continuous environments. Used to model realistic rodent locomotion and generate synthetic electrophysiological data from spatially modulated cell types.
Dartmouth Geisel School of Medicine Biostatistics and Bioinformatics Shared Resource Core Facility
Biostatistics and Bioinformatics Shared Resource
Dartmouth Geisel School of Medicine Biostatistics and Bioinformatics Shared Resource
Core offers comprehensive statistical and bioinformatic analysis, consultation, collaboration, and technical services.
Software to increase image resolution. Gigapixel AI’s neural networks are continuously trained on sample images to increase resolution of different subjects like portraits, wildlife, landscapes, architecture and image types like DSLR, web/compressed, CG.
Platform about software application that helps you capture device's screenshot. Snipping Tool is used to make changes or notes, then save, and share. Used to make changes afer taking snapshot to copy words or images from all or part of PC screen.
University of Arkansas MicroCT Imaging Consortium for Research and Outreach
MicroCT Imaging Consortium for Research and Outreach
MicroCT Imaging Consortium for Research and Outreach is home of University of Arkansas’s micro computed tomography system. MICRO is nested within and managed by the Center for Advanced Spatial Technologies which is dedicated to applying geospatial technologies in research, teaching, and service.
Nikon XTH 225 ST microfocus Computer Tomography system
Provides insight into the inside of components and specimens, allowing users to visualize, analyze and measure complex internal geometry as well as surfaces, all non-destructively. Versatile microfocus CT system for high resolution inspection in R&D and failure analysis of components ranging from tiny plastic connectors up to aluminum castings.
Biological high-tech enterprise integrating R&D, production, sales and customer service. Provides services from sample storage to nucleic acid extraction and detection. Reagent supplier.
Software package for determining HLA genotypes for individuals from Illumina exome sequencing data. Program applies assembly, allele identification and allelic pair inference to short read sequences, and applies it to data from Illumina platforms.
Loss Of Heterozygosity in Human Leukocyte Antigen
Software tool to evaluate HLA loss using next-generation sequencing data. Computational tool to determine HLA allele-specific copy number from sequencing data.
Web tool to predict order and disorder from amino acid sequence. Used to predict of natural disordered regions in proteins.
Inverted microscope Axio Observer 5 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging.
Inverted microscope Axio Observer 3 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging.
Inverted microscope Axio Observer 7 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging.
Stanford Spectrum Biostatistics Epidemiology and Research Design Core Facility
Stanford CTSA-sponsored Biostatistics Epidemiology and Research Design (BERD)
Core provides CTR investigators with support for study design development, data curation and management, and analytic strategies. Provides infrastructure through Data Studio; Clinical Office Hours; Data Science Navigation.
Stanford University School of Medicine Cancer Institute Biostatistics Shared Resource Core Facility
Stanford Cancer Institute Biostatistics Shared Resource
Core provides statistical support to SCI members by engages them on their data related needs. Specifically, BSR members assist researchers at each stage of study’s lifecycle, including project design, mid study evaluation and interpretation and reporting of results. In addition, BSR members mentor SCI investigators in research methods. BSR assists with development and review of proposed studies and planning of research related data management systems.
Mendelian Randomization Pleiotropy RESidual Sum and Outlier
Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing.
Global Alzheimers Association Interaction Network
Open access integrated research platform, which links scientists, shared data, and analysis tools to accelerate Alzheimer’s disease research, disease preventions, treatments and cure. Unites diverse and geographically distributed network of data partners to foster cohort discovery, collaboration and sharing. Researchers can discover clinical, genetic, imaging and other data collected across many independent studies.
Software R package for extracting results from mixed effect model objects fit with 'lme4' package. Allows construction of prediction intervals efficiently from large scale linear and generalized linear mixed effects models. Used for analyzing mixed effect regression models.
Software workflow for streamlined assembly and binning of metagenomes. Used for assembly and binning of metagenomes. Performs quality control, basic functional and taxonomic annotation of assembled contigs, using NCBI COG database.
Identification of Prokaryotic and Eukaryotic Virus
Software tool to identify of Prokaryotic and Eukaryotic virus derived sequences in virome using deep learning. Used to calculate set of scores that reflect probability that input sequence fragments are prokaryotic and eukaryotic viral sequences.
Platform for data discovery to enhance the reuse of clinical neuroscience and neuroimaging data. Provides NeuroBridge ontology, and combines machine learning with ontology based search of both neuroimaging repositories like XNAT databases and open access full text journals such as PubMed Central. Connects researchers with potential neuroimaging data, by searching text of papers describing neuroimaging studies that contain information on neuroimaging data.
Web tool to estimates spectrum and frequency of small insertions and deletions generated in pool of cells by genome editing tools such as CRISPR/Cas9, TALENs and ZFNs. Used for quantification of small indels in DNA of targeted cell pool. Provides rapid and reliable assessment of genome editing experiments of target locus.
University of Miami Miller School of Medicine Biomarkers and Immunoassay Laboratory Core Facility
U of Miami Biomarkers and Immunoassay Laboratory
University of Miami Miller School of Medicine Biomarkers and Immunoassay Laboratory
University of Miami Miller School of Medicine Diabetes Research Institue Biomarkers and Immunoassay Laboratory
University of Miami U of Miami Biomarkers and Immunoassay Laboratory
Provides biomarker testing for human clinilcal research studies across multiple disciplines.Provides expertise with chemistry, special chemistry, radioimmunoassay, nephelometric and ELISA and multiplexing assay methods utilizing automated and manual procedures. Laboratory has Clinical Laboratory Improvement Act certification and follows guidelines established by CLIA for quality control and proficiency testing to ensure results. Core coordinates proper pre-analytical sample collection and processing procedures with project leaders; performs biochemical assays on samples submitted to the laboratory by investigators in manner that assures strict quality control both within and between assay runs; reports results to project staff in timely fashion; makes available expertise and technical assistance for establishing and validating new methodologies to support University of Miami investigators.
Northwestern University Analytical BioNanoTechnology Equipment Core Facility
Analytical BioNanoTechnology Equipment Core (ANTEC)
Northwestern University Analytical BioNanoTechnology Equipment Core (ANTEC)
Facility houses research equipment for evaluating materials and biological preparations, and offers 3D printing and 3D scientific illustration services. Available instruments include Cytation3 Automated Microscope Plate Reader, BioTek Inc.; Zetasizer Nano ZSP, Malvern Inc.; Lyophilizers FreeZone 6 and 6 Plus, Labconco; Azure300, Chemiluminescent Gel Imager, Azure Biosystems; Real-Time PCR I-cycler CFX-Connect, Bio-Rad Laboratories; Centrifuge Sorvall X1R, ThermoFisher; MCR302 Rheometer, Anton Paar Inc.; Plasma Cleaner, Harrick Plasma; NanoSight300, Malvern Instruments (Evanston); IncuCyte Live Cell Analysis System, Sartorius; Piuma Nanoindenter, Optics 11; Freezer/Mill, SPEX Sample Prep; J-1500 Circular Dichroism Spectrometer, JASCO.
Catholic University of Louvain Genomics platform Core Facility
Catholic University of Louvain Genomics platform-PGEN
University Catholique de Louvain UCLouvain-PGEN
Core provides services including Sequencing (Sanger, NGS); Genotyping (micro array, fragment analysis); Molecular karyotyping (micro array); Bioinformatics (exomes [WES], genomes [WGS], gene panels [panels], transcriptome [RNAseq]). Equipment includes Illumina MiSeq sequencer;Ion Torrent Ion Proton sequencer and an Ion Chef for sample preparation;HPC cluster for bioinformatics processing of NGS data (WES, WGS, panels, RNASeq);Affymetrix microarray platform;Sanger sequencer and fragment analyser;Contracts for outsourcing WES, WGS and RNAseq, according to public procurement regulations;Highlander software, developed in-house, for variant analysis from NGS data.
Software Django based framework for building scientific data management web apps. Framework for Django web application development.
Software Python API for ISA-Tab files. It is an alternative implementation of ISA-tools data model and ISA-Tab file format.
Web application for quality control, filtering, prioritization, analysis, and user based annotation of DNA variant data with focus on rare disease genetics. Comprehensive DNA variant analysis for diagnostics and research.
Software for web application to control Docker containers that run webserver. Used to facilitate presenting analysis results interactively by running Docker images that are constricting any application that offers web interface. Any image can be loaded, and Kiosc manages access to web interface of application.
Open source software for parallel control over multiple behavioral systems.C++ optimized control layer software to give access to Raspberry Pi connected hardware. Suitable for time critical operations, and to be simple to expand. Used for general automation in experimental laboratories with its control PC located at some distance.
Open source software package for building data infrastructure including data management, data integration, data flows, etc. Includes various data standards and provides software to work with data.
Open source platform provides containers to support suite of neuroimaging software. Provides containerised data analysis environment to facilitate reproducible analysis of neuroimaging data. Analysis pipelines for neuroimaging data rely on specific versions of packages and software, and are dependent on their native operating system.
Software for automated identification and relative quantitation of lipids. Provides automated identification of lipids and integrates entire dataset into concise report showing statistical differences between sample groups.
Texas A and M University Health Institute of Biosciences and Technology Microphysiological Lead Optimization and Toxicity Screening Core Facility
TAMU-Microphysiological Lead Optimization and Toxicity Screening facility (MLOTS)
Texas A&M Health Science Center TAMU-Microphysiological Lead Optimization and Toxicity Screening facility (MLOTS)
Supports lead optimization programs and has established roster of medium throughput microphysiologic screening platforms including tissue- and tumor-on-a-chip platforms, organoid, and spheroid culture systems that will be used to evaluate efficacy and toxicity of new lead compounds and drug combinations.Provides resources to identify toxic liabilities in lead series molecules before entering pre-clinical or clinical testing. MLOTS can evaluate NME for cardiovascular, neuro, or liver toxicity relative to reference standards using in vitro screening platforms. Facility will potentially enhance the effectiveness of CPRITs drug discovery programs.
Software package as collection of image analysis functions used to extract information from 3D images of porous materials typically obtained from X-ray tomography. Software Python toolkit for quantitative analysis of porous media images.
University of Pittsburgh Dietrich School Glass Shop Core Facility
Core is responsible for fabricating and repairing intricate pieces of glassware and apparatus, as well as constructing complete high vacuum systems.
University of Pittsburgh Dietrich School Machine Shop Core Facility
Core specializes in mechanical design, fabrication, and repair of research equipment and instrumentation.
Video based phenotyping platform for laboratory mouse. Provides complete details of software and hardware, including 3D designs used for data collection. Data acquisition system consists of video collection hardware and software, behavior labeling and active learning app, and online database for sharing classifiers. Hardware and software solution collects high quality data for behavior analysis.
Software library to calculate Pathways Activation Levels. It takes file that contains gene symbols in HGNC format, their expression levels for one or more samples and calculates PAL values for each pathway in each sample.
Structured curated collection of protein based and of metabolic human molecular pathways. Human molecular pathways database with tools for activity calculating and visualization.All pathways are functionally classified according to GO terms enrichment patterns. All pathway participants, their interactions and reactions are uniformly processed and annotated, and are ready for numeric analysis of experimental expression data.For every comparison graph is generated summarizing top up and down regulated pathways.
Lumenera | Infinity 2-1R USB Microscopy Camera
INFINITY2-1R 1.4 Megapixel USB 2.0 Microscopy Camera CCD
Scientific microscope camera for documentation and image analysis. Has dynamic range of 64 dB allowing users to image unevenly lit samples. Allows for long exposure times of several minutes.
CKX41 inverted microscope suitable for regular cell observation including GFP and other fluorescence applications. High angle tilting head is for simple visual checks, while advanced Universal Infinity System 2 (UIS2) optics produce images. Olympus relief contrast increases visibility with non-glass cell culture vessels and improves productivity with its pre centered slider. Post acquisition analysis, documentation, and archiving can be achieved with digital cameras and software.
Preprocessing tools for oligonucleotide arrays
Software R package to analyze oligonucleotide arrays at probe level. Supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). Used for annotation of Affymetrix Gene Array data.
Montpellier Imaging Resources Core Facility
Imaging and cytometry facility of the Montpellier area.
Software tool for simulation, computation, and visualization of low compexity regions in biological data. Used for alignment free simulation, mapping, and visualization of low complexity regions in FASTA data. Provides ability of fast sequence characterization through low complexity regions, ideally for scenarios entangling presence of new or unknown sequences. Effective in whole genomes, specifically those reconstructed with support of long reads.
Automated MALDI matrix deposition system offering speed, reproducibility, and smallest available crystals for sub-micron resolution mass spectrometry imaging. Features rectangular vacuum chamber that achieve sublimation conditions extremely quickly to maximize efficiency for imaging MS sample preparation.
Allows liquid surface extraction of analytes on surfaces and further analysis in HPLC-MS detector. Surface sample to be analyzed is mounted in custom sample tray. Then optical image of mounted sample is acquired using flatbed scanner controlled with DropletProbe Premium software.
M3+ Sprayer TM MALDI Imaging Sample Preparation System
M3+ Sprayer™️ MALDI Imaging Sample Preparation System
Sample preparation platform offering automated advanced MALDI matrix sprayer.
adjust both gas flow rate and nozzle velocity
preventing large matrix crystals formation
TM-Spraye TM MALDI Sample Preparation System
TM-Sprayer™️ MALDI Sample Preparation System
Allows users to adjust both gas flow rate and nozzle velocity to control drying time, preventing analyte delocalization and formation of large matrix crystals, known to create hot spots on MALDI images. Allows to heat matrix solution as it is being applied to their sample. By increasing temperature of matrix solution, absorption of matrix into sample is increased, resulting in greater MALDI image resolution.
Sprayer builds on capabilities of HTX TM-Sprayer providing innovative M5 chassis, high velocity stage and heated sample holder drawer. Sample plate holder is mounted on drawer mechanism to allow easy loading of samples, better protection of user and better alignment of various plate types. New High-Velocity XY stage allows nozzle displacement speed of up to 5,600mm/min and expands process range. Super dry spray can be achieved at high flow rates of solvent further improving instrument performance. E/Z trough gutter design improves chemical containement and is easy to remove and clean. Bulkhead connectors are directly mounted on it to also allow easy access to in line filter.
Company offers sample preparation solutions for Mass Spectrometry Imaging. HTX delivers customized solutions for sample preparation and workflow automation of advanced analytical platforms.
Dartmouth Health Hitchcock Medical Center Biorepository Core Facility
The Dartmouth-Hitchcock Health Biorepository
The Dartmouth-Hitchcock Health Biorepository (DH-Biorep)
Institutional resource collaboratively run by Office of Research Operations and Department of Pathology and Laboratory Medicine that provides services in support of Dartmouth Research Communities and in alignment with Institutional Review Board approved protocols including Clinical Trials. Provides collection, processing, storage, and distribution of annotated human bio-specimens to clinicians and other investigators in support of clinical trials, industry sponsored projects, and scientific investigations.
Software application to Pan-cancer characterization of ncRNA synergistic competition. Used to predict ncRNA synergistic competition network from gene expression data and predicted ncRNA-related ceRNA networks.
Automated Lightweight Provenance Capture
Software Python package for the capture of provenance information during the execution of Python scripts that process data. Alpaca provides a simple API for recording the details of the functions being executed, the data flow, and a description of parameters used. Using simple Python decorators, this is accomplished with minimal code instrumentation and user intervention. Provenance information is structured and serialized according to a model based on the W3C PROV format. In addition, provenance information can be simplified and prepared for interactive visualization by the researcher.
University of Texas at Austin Advanced Protein Therapeutics Core Facility
The University of Texas at Austin UT Austin Advanced Protein Therapeutics Core
UT Austin Advanced Protein Therapeutics Core
Core catalyzes translation of scientific discoveries into novel protein cancer therapies. Offers therapeutic antibody and enzyme discovery, engineering, and optimization services.
University of California Berkeley QB3 Cell and Tissue Analysis Core Facility
University of California Berkeley QB3 Cell and Tissue Analysis Facility
Facility provides cell culture equipment and instrumentation needed to grow and assess mammalian cells including flow cytometry, automated epifluorescence, confocal, and multiphoton imaging, as well as histology suite with cryosectioning equipment.
Software R package to visualize relationship between allele frequency and effect size in genetic association studies.
Software R package used for searching for optimal clustering procedure for data set.
Software R package for comprehensive science mapping analysis. Used for quantitative research in scientometrics and bibliometrics that includes all main bibliometric methods of analysis.
Spatial prioritization software used to identify priority areas to support conservation planning, land use planning, ecological impact avoidance and other similar tasks.
Platform provides maps and spatial data for all countries and their sub-divisions. You can browse maps or download data to make your own maps.
Software tool for basic image acquisition and analysis. Zeiss ZEN microscopy software to control of axiocam microscope cameras, image transformation and measurements, image processing, image alignment for correlative microscopy, various visualization options.
University of Texas at San Antonio Stem Cell Core Facility
Provides service, advice and training across spectrum of induced pluripotent stem cell workflow, from adult tissue to gene edited differentiated progeny. Provided services include Isolation and cryopreservation of cells from adult tissues, Reprogramming of adult tissues to IPSCs, Full quality control panel ensuring high quality iPSCs, Gene editing of pluripotent stem cells, Custom research utilizing pluripotent stem cells and their 2D and 3D differentiated progeny, Consultation and project planning assistance.
Software tool to extract cardiovascular parameters from transmitted light videos of zebrafish embryos or larvae. Used to investigate live and in non-invasive way scope of zebrafish larvae physiological parameters. Measures heartbeat and blood flow.
Platform that systematizes interpretation of cancer genomes and makes it automatic. Web tool to annotate genomic alterations and interpret their possible role in tumorigenesis and in response to anti cancer therapies. Used to support identification of tumor alterations that drive disease and/or which may be therapeutically actionable. Analyses mutations including single nucleotide changes and small insertions/deletions, copy number alterations including gene amplifications and deletions and translocations.
Inserter for precise electrode positioning, reduced tissue damage and standardized insertions, enabling researchers to obtain single and multi unit recordings immediately following insertion. Used to simplify surgical procedures and data analysis pipelines. Inserter uses ultrasonic micro vibration to reduce forces and resultant dimpling during neural implant insertions. Reduced insertion force facilitates slow 0.1 mm/s, accurate implant insertions while minimizing displacement/dimpling of cortical surface, helping to preserve integrity of underlying neural tissue.
Web tool to relate proteins based on set wise chemical similarity among their ligands. Used to rapidly search large compound databases and to build cross target similarity maps.
Software tool for group wise comparison and statistical analysis of relative expression results in real-time PCR. Used to compute expression ratio, based on real-time PCR efficiency and crossing point deviation of unknown sample versus control. Compares two groups, with up to 16 data points in sample and 16 in control group, for reference and up to four target genes.
Web tool to estimate the most probable macromolecular targets of small molecule, assumed as bioactive. Prediction is founded on combination of 2D and 3D similarity with library of known actives on proteins from three different species.
Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform
Pharmacology platform of Chinese herbal medicines that captures relationships between drugs, targets and diseases. Database includes chemicals, targets and drug-target networks, and associated drug-target-disease networks, as well as pharmacokinetic properties for natural compounds involving oral bioavailability, drug-likeness, intestinal epithelial permeability, blood-brain-barrier, aqueous solubility.
Hamamatsu | FDSS/uCELL Kinetic Plate Imager
Laboratory screening system that compactly integrates technologies developed in drug discovery screening. Simultaneous measurement and analysis of kinetics of a sample’s fluorescence or luminescence intensity in all wells at the time of compound addition are made possible by the high sensitivity two-dimensional sensor camera and dispenser head (96 tip type / 384 tip type). Screening various compounds at high throughput is enabled by measurement under the same conditions with no time lag between wells.
Hamamatsu | FDSS-GX Kinetic Plate Imager
Kinetic plate imager optimized for 96-, 384-, and 1536-well for high throughput screening, enabling whole microplate imaging and simultaneous injections to all wells. System achieves high sensitivity imaging with qCMOS sensor, and highly accurate and repeatable micro-dispensing by adopting 1536 ch dispensing unit capable of dispensing variable volumes. By combining optional parts, robot free semi automation system can be built according to user's purpose.
Hamamatsu | NanoZoomer S210 Digital slide scanner
NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S210 provides high performance capable of handling large number of slides.
Hamamatsu | NanoZoomer S360 Digital slide scanner
NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S360 is ideal for use in hospitals and clinical laboratories.
NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S60 supports brightfield imaging, fluorescence imaging and double size slides., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Hamamatsu | NanoZoomer-SQ Digital slide scanner
NanoZoomer is a family of whole slide scanners that convert glass slides into high resolution digital data by high speed scanning. Desktop single slide compact scanner for creating whole slide images of single tissue slides.
Hamamatsu | NanoZoomer S20 Digital slide scanner
NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S20 is compact, high speed, and adaptable scanner.
Odyssey Classic Imaging System provides flexible, multifunctional platform to accommodate variety of applications. Western blot imager, plate reader, slide scanner, luminescence imager. Performs membrane-, plate-, gel-, and slide based assays.
Biacore™ 4000 surface plasmon resonance system
High throughput Surface Plasmon Resonance system with high quality interaction data for better informed decision making in antibody selection, drug discovery and more., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
University of Nebraska Medical Center Bioinformatics and Systems Biology Core Facility
University of Nebraska Medical Center Bioinformatics and Systems Biology Core
Core fosters research and teaching activities related to bioinformatics and systems biology at UNMC. Provides infrastructure, resources, and educational training in bioinformatics with ultimate goal of promoting synergistic research activities at the intersection of computational and experimental disciplines. Used to analyze biomolecular datasets including DNA, RNA, proteins, etc.
Children's Hospital of Philadelphia Research Institute CHOP Biorepository Resource Center Core Facility
Core with capacity for approximately 2 million to 3 million samples, serves CHOP’s biobanking needs, avoiding specimen duplication, preserving precious materials, and providing organized data and materials. The BioRC operates under the following principles: An Operational Committee, which coordinates central and investigator-specific biobanking resources and programs at CHOP, governs and approves requests to utilize the BioRC; BioRC facilitates integration and enhancement of access to information about biorepository specimens and resources; BioRC assists investigators in developing new projects that require the collection and processing of shareable samples not currently available, or helps investigators with existing projects who would like to migrate storage and management of their shareable banked specimens and data to the BioRC. BioRC institutes and follows best-practice standard procedures for collection, processing, and storage of samples to ensure high quality specimens and data for all CHOP investigators.
University of Nebraska Medical Center Biosafety Level 3 Core Facility
Facility provides safe and secure work area for qualified and authorized researchers to perform studies that involve work with biohazarad materials. Negative air pressure handling system, secure entrance and exit doors, five individual and secure Principal Investigator (PI)-assigned working suites, two pass-through autoclaves, annually certified biosafety cabinets, and personal protective equipment contribute to biosafety of each researcher using this facility.
Software tool supports profiling resource utilization including CPU, memory, disk, and network metrics of containerized tasks. Resource utilization metrics are obtained across three levels: virtual machine (VM)/host, container, and process. Implementation leverages facilities provided by Linux operating system that is integral with Docker containers.
Digital pathology imager for spatial phenotyping.Provides accurate quantitative assessment of multiple immune phenotypes while capturing their tissue context and spatial distribution within tumor microenvironment.
PhenoCycler-Fusion system is integrated platform combining automated, ultrahigh-plex cycling platform, Akoya PhenoCycler, and its high-speed imaging platform, PhenoImager (formerly Phenoptics), into end-to-end, integrated workflow.
Spatial biology company offering solutions for high parameter tissue analysis from discovery through clinical and translational research, enabling development of more precise therapies for immuno-oncology and other drug development applications.
Artificial Iinteligence chatbot that uses natural language processing to create humanlike conversational dialogue. Notable for enabling users to refine and steer conversation towards desired length, format, style, level of detail, and language used. Sibling model to InstructGPT, which is trained to follow instruction in prompt and provide detailed response.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 25,2025. Web tool to parse Sanger sequencing chromatograms with double peaks into wildtype and alternative allele sequences. Used to separate chromatogram data containing ambiguous base calls into wildtype and mutant allele sequences.Used for identification of unknown indels using sanger sequencing of polymerase chain reaction products.
Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR.
Software to correct spelling and grammar.
Azure Biosystems | 600 Western Blot Imaging System
System offers two channel, laser based IR and chemiluminescent detection, with speed and sensitivity of film, with ability to image visible fluorescent dyes, standard EtBr and protein gels, and infrared laser excitation for quantitative Western blot imaging in NIR.
Manually curated database of experimentally supported lncRNAs associated with various human cancers. Cancer long non coding RNA database. Lnc2Cancer 3.0 is updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data.
Wind Integration National Dataset Toolkit
United States national wind dataset. Provides high spatial and temporal resolution wind power, wind power forecast, and meteorological data for 7-year period at over 126,000 locations throughout continental United States. The largest publicly available wind power data set in the world. Used for wind energy integration studies. It is accessible through Web-based API.
Software video tracking tool for tracking and analysing animal movement in different environments.
University of Freiburg Medical Center Lighthouse Core Facility
University of Freiburg UF-Lighthouse Core Facility
Core specializes in areas of flow cytometry and cell sorting; light microscopy including confocal, widefield fluorescence, high content screening, lightsheet, slide scanning, highly multiplexed microscopy; and digital PCR / QPCR. It is located at University of Freiburg Medical Center and hosts institutions including Dept. of Medicine I, Center for Chronic Immunodeficiency (CCI), CCCF / DKTK, and Medical Faculty of University of Freiburg.
South Dakota State University Functional Genomics Core Facility
South Dakota State University SDSU-Functional Genomics Core Facility
Core provides access and training on range of instruments in areas of genomics, molecular biology, imaging, and chemical/metabolite analysis to support research on the SDSU campus.
Software for individual genes functions determination that are relevant in particular biological context and experimental condition. Quantifies similarity between vector representations of gene and annotated GO terms through representation learning with random walks on condition specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks.
Kyoto Encyclopedia of Genes and Genomes graph
Software R package interface between KEGG pathway and graph object as well as collection of tools to analyze, dissect and visualize these graphs.
Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins.
The code that runs the OpenSAFELY platform used for analysis of electronic health records data.
University of Lethbridge Canadian Center for Hydrodynamics Core Facility
University of Lethbridge Canadian Center for Hydrodynamics (CCH)
Provides comprehensive solution characterization of macromolecules or macromolecular interactions and assemblies. This includes description of stoichiometry, size composition, cargo loading.Core is equipped with analytical ultracentrifuges featuring multi-wavelength UV-visible detection, as well as Rayleigh interference optics and fluorescence emission detection for fluorescent tags with 488 nm excitation.
University of Lethbridge; Alberta; Canada
University of Lethbridge with campuses in Lethbridge and Calgary, is one of Canada"s leading research institutions.
Advanced widefield microscope enabling use of 3D specimens with camera based fluorescence microscopes. System ensures low phototoxicity and photobleaching, i.e., higher throughput with optimal conditions.
Malvern Panalytical MicroCal PEAQ-ITC analysis
Malvern Panalytical MicroCal PEAQ-ITC Analysis software
MicroCal PEAQ-ITC Analysis Software v1.41
Software application for isothermal titration calorimetry performed on MicroCal PEAQ instrument by Malvern.
Software tool for effectively prioritizing altered genes on cancer type level by considering mutation pair genes. Used to prioritize cancer genes on cancer-type level by utilizing somatic mutation data, protein‒protein interaction networks, and differential expression data.
Beckman Coulter | Navios EX flow cytometer
Designed specifically for clinical laboratory NAVIOS EX 10-color flow cytometer delivers performance with improved sample traceability and reporting functions. Navios EX has two optional ready-to-use IVD reagent systems, the Navios Tetra System for simultaneous identification and enumeration of T, B and NK lymphocytes and the ClearLLab 10C System – the first FDA cleared and CE marked integrated leukemia and lymphoma immunophenotyping system.
CO2 Incubator for cell and tissue cultures grow. Offers precise temperature and CO2 control, humidification system to reduce recovery time and internal solid copper construction for durable contamination control.
Bio-Rad | iMark Microplate Absorbance Reader
Absorbance reader offers reading speeds of 6 sec at single wavelength detection, onboard software capabilities including protocols for kinetic assays, preprogrammed validation protocol, built-in plate shaker, and built-in thermal printer. Instrument can read flat-, U-, or V-bottom microplates or 8- or 12-well strip plates. Includes 415, 450, 490, 595, 655, and 750 nm filters, onboard software, USB and power cables.
Web server for miRNA set enrichment analysis. TAM 2.0 is updated version of this web server. Allows to test functional and disease annotations of miRNAs by overrepresentation analysis and to compare input de-regulated miRNAs with those de-regulated in other disease conditions via correlation analysis.
miRNA Enrichment Analysis and Annotation Tool
miRNA Enrichment Analysis and Annotation Tool (MiEAA)
Web tool for functional analysis of sets of miRNAs. Tailored for miRNA precursors and mature miRNAs of multiple frequently investigated species. Used for miRNA set enrichment analysis. miEAA 2.0 is updated version for integrating multi-species microRNA enrichment analysis and workflow management systems.
Lick Instance Quantifier Home cage Device
LIQ HD: Lick Instance Quantifier Home cage Device
Arduino code, 3D print design files, and tutorial video on how to build LIQ HD system. Open source tool for recording undisturbed two-bottle drinking behavior in home cage environment. All designs and software are open source to allow other researchers to build on the system and adapt LIQ HD to their animal home cages.
Nikon | N-SIM S Super Resolution Microscope
Microscope enables super solution imaging of live cells at ten times the speed of conventional SIM. Powered by ECLIPSE Ti2-E Inverted Research Microscope, taking advantage of its advanced optics, stability and features.
Florida Atlantic University FAU Laboratory Schools Marcus Research and Innovation Center Core Facility
FAU Laboratory Schools Marcus Research and Innovation Center
Florida Atlantic University FAUHS Owls Imaging Lab
Provides access to equipment to work on research projects, including cancer treatment research, vaccine development, and prosthetic creation. Instruments including micro-computed tomography (CT) scanner; scanning electron microscope (SEM); histology equipment; inverted fluorescence compound microscope; and stereoscope is available to FAU students (high school, undergraduate, graduate), post doctoral researchers, and faculty.
Creighton University Integrated Biomedical Imaging Core Facility
Creighton University CU-Integrated Biomedical Imaging Facility
CU-Integrated Biomedical Imaging Facility
Provides instruments for performing widefield light microscopy, multiphoton microscopy, and confocal microscopy. Offers software for analyzing imaging data.
Florida Atlantic University; Florida; USA
Public research university with its main campus in Boca Raton, Florida and satellite campuses in Dania Beach, Davie, Fort Lauderdale, Jupiter, and Fort Pierce. The university is a member of the State University System of Florida.
Automatic Texture Extraction from the Hippocampal region using Soft Computing
Hippo-ATESC:Automatic Texture Extraction from the Hippocampal region using Soft Computing
Software pipeline aiming at detecting transcripts enriched in hippocampal neuropil of adult mice, by systematically exploring high resolution images contained in Mouse Brain Atlas. Data mining tool that can provide information to select target genes whose nature will be studies and confirmed using biological tests.
Software package to simplify process of producing graphics for expression data available in the Allen Institute's Brain Atlases. Related to Allen Mouse Brain Atlas.
Web based gene expression energy visualization tool.Created for visualizing expression energy data from the Allen Brain Atlas.ABADV generates simple-to-analyze visualizations of numerous mouse gene expression data across brain structures.
Software tool for spatial expression data visualization, spatial heterogeneity delineation and single cell registration based on Allen Brain Atlas. Software toolkit to collect and preprocess expression data from Allen Brain Atlas and allow query to visualize spatial distribution of genes of interest, characterize spatial heterogeneity of brain, and register cells from single-cell transcriptomics data to fine anatomical brain regions via machine learning methods with high accuracy.
Software R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas.Used to test for gene set expression enrichment in adult and developing human brain.
Custom Brain Heatmaps on top of the Allen Brain Atlas. Platform to generate brain heatmaps for the human or mouse brain ontop of the Allen Brain Atlas by editing google spreadsheet template with specific brain region and gene information.
Software R package to the infer spatial location of neural progenitor subpopulations within the developing mouse brain by integrating single-cell RNA-seq data with in situ RNA patterns from the Allen Developing Mouse Brain Atlas.
Software R package contains various functions for using the data from the Allen Mouse Brain Atlas that is registered to the Common Coordinate Framework. The functionality includes retrieving 3D, CCF aligned, gridded ISH data from the Allen Brain Atlas API, rendering 2D plots of slices of ISH data, retrieving the Mouse Brain Atlas structural ontology, and generating 3D plots of brain structures like those presented in the Allen Brain Explorer.
Software atlas based imaging data analysis tool for quantitative mouse brain histology. Can automatically detect cells in histological mouse brain and spinal cord sections of interest.
Software tool to simplify creation of procedural meshes. Used to generate separate mesh files for each label present in segmentation volume, simplifying creations of procedural meshes.
Software Python package utilizes spatial, anatomical, microarray expression data from the Allen Institute for Brain Science. This program maps genes of interest (Goi) by their levels of expression to brain regions (Roi). The identified regions that co-express the input Goi can, in turn, be studied further with many experimental modalities. This program can be customized to map gene expression data and identify significant Roi from similar reference expression data in other contexts outside of neuroscience.
Software toolbox provides multi-modality murine image templates, all of which are spatially registered to the Allen Common Coordinate Framework. The images have been optimized for in-vivo preclinical imaging in terms of resolution and region-of-interest size. The ROIs have been derived from the Allen Brain Atlas. This image analysis tool can be used to facilitate the analysis of mouse PET-CT brain images.
Multimodal Environment for Neuroimaging and Genomic Analysis
MENGA: Multimodal Environment for Neuroimaging and Genomic Analysis
Software platform for integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas in order to create comprehensive, integrated data platform.
Software R package which links genetics and human brain imaging by using genes associated with disease and calculating normalized mRNA expression average of those genes in each brain region. By uploading lists of genes and brain regions of interest, this package will return csv with the results.
Software provides visualization and slicing of 3D isotropic image data as well as various atlases. Through orthogonal views of three standard planes (coronal, sagittal, horizontal) and custom-angle slice cut through the volume, CutNII produces custom-angle atlas slices that match histological sections with non-standard cutting angles. Custom slicing then allows for the inspection of anatomical features from non-conventional angles.Custom-angle slicer for brain atlas volumes.
Spatiotemporal pattern Exploration of Brain
Web based visual analytics tool for the comprehensive exploration of genomic and phenotypic patterns, especially for the spatiotemporal patterns, in the developing mouse brain. The tool is designed in JavaScript and D3.js, the data is based on Allen Developing Mouse Brain Atlas (ADMBA) data.
Software package for analysis of mouse brain STP data with respect to the Allen Reference Atlas. Collection of MATLAB functions to analyze mouse whole brain imaging data and the associated "sparse" point data such as cell locations, traced neurite trees, or traced projections from a bulk injection. This package relates sparse data to the Allen Mouse Brain Reference Atlas.
Respository contains two small software tools which render annotation and images of the Allen Mouse Brain Atlas. Both tools generate 1304 images of the Mouse Brain (456 sagital, 528 coronal and 320 axial).
Software tool analyzes single-cell RNA-seq dataset from the Allen Mouse Brain Atlas to isolate the analysis of hierarchical structure and the discovery of important genes in the mouse neocortex.
Software package for assessing brain organoid patterning, developmental state, and cell composition through systematic comparisons of single cell transcriptomes to three-dimensional in situ hybridization data from the Allen Brain Atlas and number of other useful reference datasets.
Software tools to work with Allen Inst CCF data in Matlab. MATLAB code to work with the Allen Mouse Brain CCF data.
Software tool to pull gene expression from Allen Brain Institute API in same annotation space as structural connectome.
Software package provides Python interface for aquiring and analyzing Allen Human Brain Atlas microarray expression data.Includes reproducible workflow for processing microarray expression data for further analysis.Used for the Allen Brain Atlas genetics data.
Software toolbox for ensemble-based multimodal gene-category enrichment analysis of human neuroimaging data.Performs ensemble-based gene-category enrichment analysis on volumetric human neuroimaging data via brain-wide gene expression patterns derived from Allen Human Brain Atlas. Utilizes nonparametric method using spatial autocorrelation-corrected phenotype null maps for estimation of gene-category null ensembles.
Software to download expression data from Allen Mouse Brain data portal ABI. This script will query database, download available data, convert it from the raw/mhd format to NIfTI, and register it to standard space. Package-manager-friendly archive of gene expression maps registered in SMRI standard space from the Allen Mouse Brain Atlas.
Software toolbox for gene category enrichment analysis false positives available. Used for analysis of statistical biases in Gene Set Enrichment Analysis applied to transcriptomic atlas data.
Software R package provides matrix of predefined set of marker genes for many regions of the human brain, using data from the Allen Human Brain Atlas.
Software package to test hypotheses about relation of patterns found in statistical maps with gene expression measured in postmortem brains. Refines corregistration coordinates provided by the Allen Institute.Used to compare statistical map of brain with gene expression patterns from Allen Human Brain Atlas.
Software tool for integrating tissue transcriptome and cytoarchitectonic segregation. Combines data from Allen Human Brain Atlas and the EBRAINS Human Brain Atlas, specifically to discover how gene activities and microanatomical architectures contribute to brain function and dysfunction. Both tissue transcriptome and probabilistic brain segregation data allow for integrating genetic expression, brain structure, and function knowledge.
Software tools to compute densities in context of brain atlases. Used to create BBP Cell Atlas, using Allen Mouse Brain Atlas and collected literature density values.Provides list of volumetric files that provides cell type density estimates for each voxel of mouse brain volume.
Software electrophysiology tool for planning Neuropixels recordings. Neuropixels trajectory planner for designing multi-probe insertions,utilizing the Allen Mouse Brain Common Coordinate Framework.
Software tools to compute direction vectors in context of brain atlases.
Software tools to split brain atlas regions and refine annotations accordingly. Applicable to the Allen Mouse Brain Atlas
Software Python CLI and library to measure jaggyness of brain parcellation volume. Used to measure slice-to-slice jaggedness of volumetric dataset, only in form of NRRD file.
Platform provides web interfaces for research institutions to exchange, share, and publish curated data and other digital resources.
Software tool to map histological slice sequences to Allen Mouse Brain Atlas without 3D Reconstruction. Automatically maps histological slice to its corresponding plane in Allen Mouse Brain Atlas to build plane wise mapping and then perform 2D nonrigid registration to build pixel wise mapping.
Software visualization and analysis tool based on the Allen Brain Atlas connectivity database. Produces custom visualizations and figures for input output strength of specific brain area.
Software data pipeline which aligns histology images to the Allen CCF.
Software lightweight python module to interact with atlases for systems neuroscience. Provides consistent way to process brain atlas data from various sources.
Software high-throughput Mask R-CNN based toolbox to generate brain atlas through deep learning. Used for segmenting brain regions of interest.
Web interactive visualization tool of brain architecture based on tracer database.There are four modes of visualization: surfarce, flat, coronal, and saggital.
Software Python package for downloading neurons morphological reconstructions from publicly available datasets. With the provided APIs, the user can download data of selected neurons and functionality to create 3d meshes with the neuronal reconstruction for visualization.
Software toolbox is cell counting and distribution mapping platform which can be used to analyze serial two-photon tomography (STPT) data.
Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space.
Software Python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.
Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas.
Software workflow includes suite of various software to form analysis pipeline of atlas-based quantifuication of labbeled features in histological images from mouse or rat brain. This workflow also suggests and explains with instructional videos the way these software work together. Used for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases.
Software Fiji plugin for registering thin serial sections: coronal, sagittal, horizontal, to compatible atlases including Allen Mouse Common Coordinate Framework, Waxholm Rat Brain Atlas, and all BrainGlobe atlases.
Software Python based tool that registers the template brain (e.g. from the Allen Reference Atlas) to the sample image.Automated 3D brain registration with support for multiple species and atlases.
Software package implements Bayesian multilevel models in R using probabilistic programming language Stan.
Deputy cabinet level agency directly under the State Council of China. Responsible for collection, investigation, research and publication of statistics concerning the nation's economy, population and other aspects of the society.
Pennsylvania State University Huck Institutes of Life Sciences Metabolomics Core Facility
Penn State Huck Metabolomics Core Facility
Core for conducting metabolomics studies on variety of biofluids and tissue extracts from plant and animal sources. Provided instruments include Agilent 5975C series GC-MSD, Bruker NEO 600 NMR, Thermo Exactive Plus, Thermo Orbitrap Exploris 120, Thermo Orbitrap Exploris 240, Thermo TSQ Quantis Plus, Thermo Orbitrap Fusion Lumos Tribrid.
Agricultural Production Systems sIMulator
Software platform for modelling and simulation of agricultural systems. Contains suite of modules that enable simulation of systems for diverse range of plant, animal, soil, climate and management interactions. Used to simulate biophysical processes in agricultural systems, particularly as it relates to the economic and ecological outcomes of management practices in the face of climate risk.
Creighton University Auditory and Vestibular Technology Core Facility
Creighton University CU-AVT Core Imaging Facility
Core was established to provide infrastructure to support Research Project Leaders and principle investigators associated with the Dr. Richard J. Bellucci Translational Hearing Center to conduct auditory and vestibular research across the full range of experimental model systems, from single molecule analysis to whole organism models. We also offer access to our services and instruments to outside users.
University of Notre Dame ND Biophysics Instrumentation Core Facility
ND Biophysics Instrumentation Core Facility
Offers instrumentation dedicated to characterizing biomolecular conformations and interactions, as well as equipment for isolation and purification of macromolecules for subsequent detailed biophysical analysis.
Software R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.
Web tool for transcriptome wide microRNA target prediction including lncRNAs.Used for whole transcriptome human microRNA target predictions based on the comprehensive GENCODE gene annotation, including long non-coding RNA genes. Coding genes are also covered, including atypical regions such as 5'UTRs and CDS. MicroRNA family definitions and names are consistent with TargetScan. Site conservation is aluated based on 46 vertebrates species.Map of putative microRNA target sites in the long non-coding transcriptome.
Software connectivity mapping based drug repurposing tool that identifies drugs that can potentially reverse query disease phenotype or have similar functions with query drugs.
Software tool bridges in vitro drug screening with in vivo drug and biomarker discovery. Predicts in vivo or cancer patient drug response and biomarkers to enrich for response from cell line screening data. Builds model using ridge regression, and enables biomarker discovery by imputing drug response in large cancer molecular datasets. Enables drug specific biomarker identification by correcting for general level of drug sensitivity shared among the population.
Software R package for converting and retrieving information of miRNAs in different miRBase versions. Used for converting and retrieving miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. Can process huge number of miRNAs in short time without other depends.
Method extending ’guilt by association’ principle to literature information by using Bayesian framework to suggest diseases associated with overlooked metabolites.
Beatson Institute for Cancer Research United Kingdom Beatson Advanced Imaging Resource Core Facility
Beatson Advanced Imaging Resource (BAIR)
Cancer Research UK Beatson Institute Beatson Advanced Imaging Resource (BAIR)
Core to uncover and interrogate important molecular pathways in cancer. Offers training scientists in all stages of modern microscopical research from advice on experimental design and sample preparation, basic and advanced microscope operation and data acquisition through to quantitative image analysis and interpretation.
Aarhus University Bioimaging Core Facility
Aarhus University Bioimaging Core Facility at the Department of Biomedicine
Core Facility offers equipment for wide range of light microscopy applications as well as access to advanced bioimaging software. Specialized staff offers personal training and assistance.
Circulating Cell-free Genome Atlas project
Circulating Cell-free Genome Atlas (CCGA)
Prospective, observational, longitudinal, study designed to characterize landscape of genomic cancer signals in blood of people with and without cancer. Sudy includes people in the USA and Canada who had cancer at the time of enrollment, newly diagnosed, and not yet received treatment, and people who did not have known cancer diagnosis.
University of Arizona Phenotyping Core Facility
University of Arizona UA Phenotyping Core (UAPC)
Core provides resources to investigate phenotypes of genetically altered mice and small animal models of disease. Offers investigators full service support of in vivo cardiovascular and physiology studies in normal and diseased states through surgical models, imaging techniques, and functional physiological assessments.Core provides services to assist researchers with phenotyping of small laboratory animals including mice, rats, guinea pigs, rabbits with focus on cardiovascular neuromuscular and respiratory function, and exercise tolerance. Services include Experiments with cardiovascular ultrasound, plethysmography, exercise studies, small animal surgeries LAD-ligation, transaortic constriction, and data analysis; Training with equipment, small animal surgeries or data analysis; Equipment rent to measure cardiovascular, neuromuscular, respiratory function, and exercise tolerance;Consultation on experimental design, physiological data-collection, analysis, interpretation and IACUC protocols, grant- and manuscript writing.
Collection of transcription factors annotated according to experimental and other evidence on their function as true DbTFs. Provides reference for both small scale experiments and genome scale studies. Curated compendium of specific DNA-binding RNA polymerase II transcription factors.
Pasteur Institute Human Disease Models Core Facility
Paris Human disease models core facility
Core Facility produces mice harboring human immune system and provides expertise for possible applications of this model. HIS mice engrafted with human Hematopoietic stem cells are advantageous in vivo models for long term studies in field of human immune cells biology, immune oncology and infectious disease. They constitute small animal model in which to analyze potency and safety of small animal model modulating immune system.
Software tool as modified awk version for biodata. Extension to Brian Kernighan's awk, adding support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds few built-in functions and command line option to use TAB as the input/output delimiter.
Open source system for behavioral control based on Arduino Mega microcontroller and MATLAB based graphical interface and analysis code. Behavior controller optimized and customized for associative learning and memory tasks. Provided software should be able to control many different types of hardware for different task configurations.
HGAP: Hierarchical Genome Assembly Process
PacBio Hierarchical Genome Assembly-Process (HGAP)
Software for High-quality de novo microbial genome assemblies using only single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool for analyzing images of spheroids. Designed to streamline process of spheroid segmentation, area calculation, and downstream analysis of spheroid image data, and can help to standardize and accelerate analysis of spheroid assay results.
University of California at Davis Bioinformatics Core Facility
UC Davis Bioinformatics Core helps researchers with their projects, from experimental design, through all analyses and to publication.Provides expertise in analyzing data from omics technologies, and other projects. Regularly offers bioinformatics training.
Hitachi | 16-bit 3-CCD color camera HV-F203GV / HV-F203SCL
High resolution 1/1.8" 3 CCD Progressive Scan Color Camera with 1600 x 1200 pixel (UXGA) that is installed in the ZEISS Axioscan Z1 slide scanner. Integrated functions include electronic shutter from 1/30s to 1/100000s, Long term Integration up to 4s, AGC, external Trigger, Auto Shading, 6 Colour Masking, Frame-On-Demand Function, White Balance, AGC, Black Level Adjustment and Partial Scan Function.
Software automatic pipeline for exploration of Sequence Read Archive datasets with sequences as query.
Multi-function microcentrifuge available with choice of three rotors. The flat microhematocrit rotor spins shorter capillary tubes and eliminates angled separation lines, clay blow-outs, and broken tubes. The six place microtube rotor spins 1.5 to 2.0ml tubes for serum and urine separations and comes with adapters for smaller sized tubes (0.2ml-1.5ml). The optional 16-place PCR strip rotor spins two 8-place strips. The ZipCombo is well-suited to accomplish blood and urine separations, microfiltrations, and DNA preparations.
Rainin | Pipet-Lite LTS Pipette L-200XLS+
Pipet-Lite™ XLS+ manual single-channel pipette, 20-200 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-200XLS+)
Rainin | Pipet-Lite LTS Pipette L-100XLS+
Pipet-Lite™ XLS+ manual single-channel pipette, 10-100 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-100XLS+)
Rainin | Pipet-Lite LTS Pipette L-1000XLS+
Pipet-Lite™ XLS+ manual single-channel pipette, 100-1000 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-1000XLS+)
Rainin | Pipet-Lite LTS Pipette L-10XLS+
Pipet-Lite™ XLS+ manual single-channel pipette, 0.5-10 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-10XLS+).
Software R package for training and practicing epidemiologists including methods for two-way and multi-way contingency tables.
Software analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate variety of analyses pertaining to gene expression , chromatin accessibility, and their linkage. Used to perform analyses that link chromatin accessibility and GEX.
GEnomic RNA hOmology aNd evolutIonary MOdeling
Software pipeline to conduct high-throughput homology searches of structural genes using covariance models. Utilises covariance models to conduct homology searches of RNA sequences across wide range of gene families in broad evolutionary context.
8-channel pipette, 100-1200 μL, uses LTS™ LiteTouch™ tips. Consistent sample pickup, all channels. Simple operation, advanced modes. Password-protection (E8-1200XLS+).
Vortex mixer suitable for single, small containers up to 30 mm in diameter.
Leiden University Medical Center Flow Cytometry Core Facility
Provides flow cytometers for users from the LUMC, Leiden University and external companies.Instruments include conventional and spectral analyzers, cell sorters and mass cytometers. These instruments allow analysis and sorting up to biohazard level ML-II, while one analyzer is available for ML-III material. Provides support for all aspects of cytometry, including experimental design, instrument setup, data acquisition and data analysis.
SunChrom | SunTissuePrep Tissue Section Preparation System
System automates all tissue section preparation steps that were previously performed manually. Deparaffinization, rehydration, antigen-retrieval and pH-adjustment steps are performed efficiently, reliably and fully automated.
SunDigest incubation device provides fully software controlled and highly reproducible digestion process under standardized conditions. Feature includes Temperatures precisely adjustable between 4 °C and 50 °C; On-Tissue digestion process under optimal humidity; Preservation of spatial resolution; High performance digestion at 50 °C; Full digestion process control.Essential for reproducible results.
CF-Spotter for MALDI-TOF Microbial Identification
CF-Spotter for MALDI-TOF microbial identification. Enables fast, efficient and reproducible sample preparation for MALDI-TOF microbial identification system and relieves your laboratory staff from tedious and time-consuming pipetting. Due to the non-contact application of the solutions, there is no carryover of the samples and the costs for consumables such as pipette tips are eliminated.
For tissue preparation for Imaging MALDI. The sprayer can handle fresh-frozen or FFPE tissue sections. Enzymes such as trypsin can be applied to the tissue for in situ digestion. Sprayer offers the following key features: Automated delivery of matrix, enzyme or derivatization solutions; 6 port PEEK valve with low dead-volume to minimise liquid usage; Automatic self-cleaning function at end of matrix application; 100 % biocompatible; Compact unit 36 x 49 x 40 cm (w,d,h);Preprogrammed spray protocols;Up to 8 sample slides can be sprayed simultaneously;Easy to use software.
Develops and manufactures scientific instruments. Specialists for system solutions in liquid chromatography, development and optimization of front-end applications and sample preparation systems for MALDI and MALDI-MSI.
NanoString | CosMx Spatial Molecular Imager
NanoString CosMx Spatial Molecular Imager
Integrated system with mature cyclic fluorescent in situ hybridization chemistry, resolution imaging readout, interactive data analysis and visualization software. Analysis platform to provide spatial multiomics with formalin-fixed paraffin-embedded and fresh frozen tissue samples at cellular and subcellular resolution. CosMx SMI enables rapid quantification and visualization of up to 1,000 RNA and 64 validated protein analytes. Spatial single-cell imaging platform that drives deeper insights for cell atlasing, tissue phenotyping, cell-cell interactions, cellular processes, and biomarker discovery.
Xenium Analyzer offers subcellular profiling of 100s to 1,000s of RNA targets alongside multiplexed protein, in fresh, frozen or FFPE tissue.
Biotechnology research company for molecular cartography. Applys the power of Molecular Cartography to enable scientists to gain new insights based on the highest-resolution view of single-cell spatial biology.
Publicly held biotech company offering discovery and translational research solutions. NanoString's products include the nCounter® Gene Expression System, the GeoMx® Digital Spatial Profiler, the CosMx™ Spatial Molecular Imager, and the AtoMx™ Spatial Informatics Platform.
Software R package for calling hypermethylated variant epiallele frequencies at level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map files as input. Used for sensitive allele specific methylation analysis in next generation sequencing data. Used for sensitive detection, quantification and visualisation of mosaic epimutations in methylation sequencing data.
Scientific Instrument Services provides technical support functions including repair and maintenance of lab equipment; custom design and fabrication of new fixtures and devices using CAD, 3-D printing, and traditional machining; protocol development and performance optimization of wide variety of automated liquid handlers deployed in many of our institutions core services.Services are provided for JAX faculty.
Affordable commutator that is equipped with novel sensing system that improves online tracking of cable rotations without impairing the 1-photon calcium imaging via Miniscope. Commutator to allow freely moving behaviors while recording neural activity from platforms such as Miniscope V4 and OpenEphys. Used to perform calcium imaging.
Molecular Devices | SpectraMax iD3 multi-mode microplate reader
Molecular Devices SpectraMax iD3 multi-mode microplate reader
SpectraMax® iD3 multi-mode microplate reader
Microplate reader to measure absorbance, fluorescence and luminescence.
Software tool monitors metrics available in sequencer, state of the computer to which the sequencer is connected, and the contents of the fast5 and fastq files. Real-time monitoring of Oxford Nanopore Technology sequencing run. Used for monitoring nanopore sequencing process.
MJFF in partnership with Aligning Science Across Parkinson’s are in the process of establishing data platform, CRN Cloud, leveraging Verily Workbench to share data generated by researcher labs funded through ASAP Collaborative Research Network. The data types include mainly raw and processed single cell RNA-seq, single nucleus RNA-seq, and bulk RNA-seq from both PD and healthy control samples.
Curated data resource of protein carbonylation sites.Manually curated data resource of experimentally confirmed carbonylated proteins and sites.Provides information on other related resources such as list of other oxidative protein modification databases, list of protein oxidation and carbonylation prediction tools.
Polycystic Kidney Disease Genome Browser
Chemyx | Fusion 4000-X Dual Independent Channels syringe pump system
Chemyx Fusion 4000-X Dual Independent Channels syringe pump
Fusion 4000-X independent dual-channel infuse and withdraw syringe pump
Syringe pump is built with 2 separate pump drives capable of independent pulseless, reproducible rates and movement. Programmable multi-step and cycle mode allows users to input complex flow profiles or perform flow cycling from computer Labview or the pump itself. This multi-channel syringe infusion pump system also can be expanded with 2-syringe push and pull rack attachment to increase the total syringe capacity to four.
Advanced infusion device for drug delivery applications in mice, rats and larger animals. With versatile programmable functions and refillable reservoir, this implantable infusion pump enables full control over dosing studies and empowers researchers to execute even the most complex dosing protocols, including multiple bolus dosing, variable/constant delivery, escalating drug administration, and more.
Cancer research platform that aggregates clinical, genomic and functional data from various types of patient derived cancer models, xenographs, organoids and cell lines. Open catalog of harmonised patient-derived cancer models. Standardises, harmonises and integrates clinical metadata, molecular and treatment-based data from academic and commercial providers worldwide. Data is FAIR and underpins generation and testing of new hypotheses in cancer mechanisms and personalised medicine development. PDCM Finder have expanded to organoids and cell lines and is now called CancerModels.Org. PDCM Finder was launched in April 2022 as successor of PDX Finder portal, which focused solely on patient-derived xenograft models.
Chemical Computing Group ULC Molecular Operating Environment
A software tool useful for finding the name origin, ethnicity of a name. It can infer gender, translate Chinese names and Japanese names, format a phone number, and split a full name via user interface and an API.
Agilent 6495 Triple Quadrupole LC/MS system
Stanford Agilent 6495 Triple Quadrupole LC/MS system
Agilent 6495C triple quadrupole LC/MS system increases capacity and sensitivity for targeted quantitation applications. Used to investigate more diverse and biologically relevant groups of targeted peptides, small molecules and metabolites in single experiment without compromising sensitivity, quantitative accuracy, or linearity.
Waters Select Series Multi Reflecting Time-of-Flight
Multi Reflecting Time-of-Flight features routine ppb mass accuracy and ultra-high resolution by extending the flight path via gridless electrostatic mirrors in mass analyzer. It is equipped with DESI and MALDI sources for imaging mass spectrometry.
Stanford Waters Select Series Cyclic IMS
Cyclic IMS pairs unique cyclic ion mobility separation which enables separation based on shape, with time-of-flight separation based on mass to charge ratio (m/z). It is equipped with DESI and electrospray sources for surface and solution analyses.
Software set of tools used in production and exploration of bacterial artificial chromosome restriction maps.
Open source modular apparatus to produce guide cannulas exploiting 3D printing technology. Step by step procedure to realize hippocampal guide cannulas. 3D-printed guide cannula implant, as well as rotary tool based cutting station for fabrication of cannulae. Useful to conduct research in all the fields where access to brain areas is needed.
Bibliographic database for sports and sports medicine research. Includes records from leading sports medicine journals. Includes rigorous curation and indexing of open access journals. Once validated and certified for inclusion, these journals are treated with subject indexing and full text linking.
Health Information National Trends Survey
Health Information National Trends Survey (HINTS)
The Health Information National Trends Survey (HINTS)
Regularly collects nationally representative data about American public’s knowledge of, attitudes toward, and use of cancer and health related information. HINTS data are used to monitor changes in fields of health communication and health information technology and to create more effective health communication strategies across different populations. Weighted, nationally representative probability based survey of civilian, non-institutionalized adults administered by National Cancer Institute on knowledge of and attitudes toward cancer relevant information.
CDC HPV and Cancer HPV-Associated Cancer
Comprehensive DNA methylation database. Provides genome wide mapping of methylation sites to target genes through integrating a large number of DNA methylation and gene expression profiles in human diseases, and to annotate methylation sites to abundant regulatory elements and TFs.
Software Python cross platform framework for creating, managing, and sharing workflows. Workflow consists of number of connected workflow steps. Framework is plugin-based application where the plugins are workflow steps. Can be used for visualising and mapping anatomical structures.
Sliding microtome produces sections for human paraffin sectioning applications.Microtome has enclosed micrometer feeding system with ergonomically positioned object head close to the user. Running sledge can be locked in 11 positions by using sledge brake.
University of Missouri Bioinformatics and Analytics Core Facility
University of Missouri MU Bioinformatics and Analytics Core
Provides expert bioinformatics, analytical, and data science consulting and analysis solutions. Offers support for the management and analysis of large scale biological datasets.
University of Wisconsin-Madison Biochemistry Optical Core Facility
Core provides instrumentation for light and fluorescence based microscopy, including epifluorescence, confocal, and super-resolution imaging.Provides access to and training on basic and advanced light microscopy techniques. Expertise and advice is available for the design of experiments involving these techniques.
Database of human regulatory elements like enhancers and promoters, and their inferred target genes which is embedded in GeneCards, human gene compendium. Associations between regulatory elements and target genes were based on multiple sources of linking molecular data, along with distance.
simulation of Adaptive Immune Receptor Repertoire data
Leica ST5010 Autostainer XL provides reproducible, consistent high quality staining, and increased workload throughput compared to manual staining.
South Dakota State University Genomics Sequencing Core Facility
South Dakota State University SDState-Genomics Sequencing Facility
Facility offers custom sequencing services from DNA/RNA extractions to sequencing using Illumina and Oxford Nanopore platforms. Projects examples include bulk RNAseq, 3\'RNASeq, Single Cell transcriptomics (10X Genomics), Genome sequencing, and amplicon sequencing (ie 16SRNA, genotyping). Services include experimental design and bioinformatics data analysis.
Software application as medical image viewer.Able to load series of special images stored in DICOM format for review. Able to query and fetch DICOM images from archive nodes (also called PACS) over the network. Designed to run under Linux.
Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings.
Software tool for specific, sensitive, and speedy trimming of NGS reads.
Software to get assembly statistics from FASTA and FASTQ files.
Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines.
Sotware tool designed to run Process S simulations on Slow Wave Activity profiles from human EEG recordings.Produces set of sleep homeostat parameters which can be used to describe and differentiate individual sleepers, such as short vs long sleepers, early vs late, etc.Sleep research experiment manager, with facility for reading, displaying, and manual and semi-automatic scoring EEG recordings in edf format; conventional PSD and EEG Microcontinuity profiles; artifact detection; Independent Component Analysis; basic sleep analysis NREM-REM cycle detection.
Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data.
Web analytics tool for detection of variants from assembly. Used to detect and analyze structural variants from genome assembly by comparing it to reference genome.
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets.
Software tools for common BAM file manipulations.
Software package contains lightweight C implementation of name collating BAM file input and BAM file output.
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets.
Software library for building minimal perfect hash function. Designed to handle large scale datasets.
Software bibliography processing backend for LaTeX biblatex package. Supports unsurpassed feature set for automated conformance to complex bibliography style requirements such as labelling, sorting and name handling. BibTeX replacement for users of BibLaTeX.
Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records.
Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution.
Software application as simultaneous Bayesian inference of alignment and phylogeny. Used to estimate multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. to explore the joint space of alignment and phylogeny given molecular sequence data. BAli-Phy version 3 is model based co-estimation of alignment and phylogeny. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. Implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously.
Open source framework for bioinformatics written in Objective-C. Provides Cocoa and GNUstep programmers with full suite of APIs for handling and manipulating biological sequences.
Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts.
Software package for analyzing, processing and visualizing multi-dimensional microscopy images. Multipurpose postprocessing tool for bioimaging. Can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once.
Software package to use BioMAJ providing biomaj-cli.
Software multi-purpose reflection library developped by Technogerma Systems France and then by Tegesoft. Provides extra layer of flexibility to programs, and allows them to fully expose their data structures at runtime.
Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site.
Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository.
Computer Assisted Medical Intervention Tool Kit
Software Computer Assisted Medical Intervention Tool Kit helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.Open source, cross-platform generic tool, written in C++, which can handle medical images, surgical navigations and biomechanical simulations.
Open Source software modular Java libraries for cheminformatics.
Collection of software tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, and reconstructing germline sequences.
COVID-19 Hospital Impact Model for Epidemics
Software designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily and running totals of inpatient hospitalizations, ICU admissions, and patients requiring ventilation.
Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies.
Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage.
Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally.
Software to create and extract conda packages of various formats.
Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation.
CONditional TRAining for RNA Secondary Structure Prediction
Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.
Comprehensive Antibiotic Resistance Database
The Comprehensive Antibiotic Resistance Database
Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes.
Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files.
Software gives your command-line tools a CTD-compatible interface. Module for enabling tools with CTD reading/writing, argument parsing, validating and manipulating capabilities.
Software tool to generate BED coverage tracks from BAM files.
Software for minimal but powerful thread pool in ANSI C.
Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis.
Software tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Signal level demultiplexer for Oxford Nanopore reads.
Software to support biomedical image computing.
Software Java program for analyzing and visualizing rooted phylogenetic trees and networks.
Open Source Computed Tomography Simulator
Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions.
Dextractor and Compression Command Library
Software as Bax file decoder and data compressor.
Software extensible open source radiation therapy research platform based on the DICOM standard. It also functions as a cross-platform DICOM RT viewer.
Software Python scripts to convert CTD files into other formats such as Galaxy, CWL.
Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files.
Software de novo adapter prediction algorithm for small RNA sequencing data.
Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files.
Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).
Efficient Mixed-Model Association eXpedited
Software statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.
Web browser enabled tool with versatile command line interface to perform exploratory investigations of 3D visualizations of microbial community data, such as principal coordinates plots. EMPeror includes set of controllers to modify features as function of metadata. Web interactive next generation tool for analysis, visualization and understanding of high throughput microbial ecology datasets.
Web based graphical user interface to the EMBOSS suite of bioinformatics tools.
Software tool provides graphical interface for tethered shooting, aka taking photographs with digital camera completely controlled from the computer.
Epidemiological Geo-referenced Analysis and Simulation system
Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior.
Open source C++ library and application for contact network epidemiology. Application programming interface that models the spread of infectious disease in population and generates and manipulates networks of nodes and edges.
Softwaare alignment free comparison tool for phylogenetic analysis and text comparison. Can be applied to nucleotide sequences, complete genomes, proteomes and for text comparison.
Software package for Bayesian tree inference. Used for large-scale analyses on computer clusters.
Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter.
Open source, multiplatform, universal viewer, annotator and toolbox intended for time-series storage files like EEG, EMG, ECG, BioImpedance, etc.
Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.
Software C++ library for accessing Oxford Nanopore Technologies sequencing data.
The Genome Analysis Toolbox with de-Bruijn graph
Software genome analysis toolbox with de-Bruijn graph. Library dedicated to genome assembly and analysis.
Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.
Software toolkit for performing set operations - union, intersection and complement on k-mer lists.
GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly.
Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time.
Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists.
Software library for handling sequence graphs in Python.
Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files.
Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences.
Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s).
Software repository implements the custom CRAM codecs used for "EXTERNAL" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data.
Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices
Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.
Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed.
Software library to generate images for odontograms.Allows to choose between png or jpg images.
Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.
Intake: A general interface for loading data
Software package for finding, investigating, loading and disseminating data.
Prerequisite for sharing magnetic resonance imaging reconstruction algorithms and code is a common raw data format. This repository describes such common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format.
Iterative Virus Assembler - de novo virus assembler of Illumina paired reads.
Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.
Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.
Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies.
Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research.
Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported.
Software tools for detecting DNA modifications from single molecule, real-time sequencing data. This tool implements the P_ModificationDetection module in SMRT� Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol.
Open source software Java implementation of the Needleman�Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model.
Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive.
Lambda: the Local Aligner for Massive Biological DatA
Software tool as local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools.
C++ software designed to infer V(D)J recombination related processes from sequencing data.
Software mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.Used for aligning high quality reads against highly redundant databases, where unique matches often does not exist. Works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on users demands.
Software package implements two significance tests for comparing digital gene expression profiles. They provide two programs: Kemp for the frequentist test and Basu for the Bayesian test, and some auxiliary scripts.
Bio-ASN1-EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene
Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record.
Ace - Object-Oriented Access to ACEDB Databases
Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously.
Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available.
Bio-Chado-Schema - A standard DBIx-Class layer for the Chado database schema
Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module.
AI-FANN - Perl wrapper for the Fast Artificial Neural Network library
Software Perl wrapper for the Fast Artificial Neural Network library
Bio-Graphics - Generate GD images of Bio-Seq objects
Software package to generate GD images of Bio::Seq objects.
Software memory efficient bioinformatics library written in D programming language whose aim is to provide platform for developing high performance computational biology applications using the D programming language through automatic parallelization of tasks where possible and by avoiding unnecessary memory allocations.
Bio-Coordinate - Modules for working with biological coordinates
Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.
Bio-EUtilities - BioPerl low-level API for retrieving and storing data from NCBI eUtils
Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.
Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.
Software Perl interface to SamTools library for DNA sequencing.
Bio-Tools-Run-Alignment-Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program
Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.
Bio-SCF - Perl extension for reading and writting SCF sequence files
Software Perl extension for reading and writting SCF sequence files.This module provides Perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back.
Bio-Tools-Phylo-PAML - Parses output from the PAML programs codeml
Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.
Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program.
Software library for generic access to chipcard readers and cards
Software C library for entropy measurement of byte streams and other data.
Relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.
FAST - FAST Analysis of Sequences Toolbox
Software Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records.FAST workflows are designed for serial processing of flatfile biological sequence record databases per-sequence, rather than per-line, through UNIX pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FASTQ format is supported. FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm.
Software library for processing of biomedical signals. Provides generic storage for biosignals, such as EEG, ECG, MEG. C++ implementation of GDF - " general dataformat for biosignals" version V2.20.
Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN.
Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes.
Edib: A lightweight and super fast C/C++ library for sequence alignment using edit distance.
Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance.
libdivsufsort: A lightweight suffix-sorting library
Software library that implements lightweight suffix array construction algorithm. Provides C API to construct suffix array and Burrows-Wheeler transformed string from given string over constant size alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of the string.
Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored.
Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality.
Bio-PrimerDesigner - Design PCR Primers using primer3 and epcr
Software package provides low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio-PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported.
Software C library with bioinformatic focus optimised for speed and clean API.
Software repository contains java code for NeXML processing.
libics- Image Cytometry Standard file reading and writing
Software reference library for Image Cytometry Standard, an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.Image Cytometry Standard file reading and writing.
Software core library and API of the Medical Image NetCDF toolkit.
Software library that exports C++ mmCIF accessors to Python.
Software C++11 library for next-gen sequence quality control and assessment.
SIMD Smith-Waterman C/C++ library for use in genomic applications. SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages.
Software library used by other RDP tools.TaxonomyTree building and traversal utility classes.
Software C++ htslib/bwa-mem/fermi interface for interrogating sequence data
Sort-Key-Top - select and sort top n elements
Functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures.
Software library as set of classes for creating statistical genetic programs.
Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.
Libxdf � a C++ library for loading XDF files
Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications.
Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image.
Software graphical desktop tool for semi-automatic postprocessing of de novopredicted LTR retrotransposon annotations, such as the ones generated by LTRharvestand LTRdigest. Interface displays LTR retrotransposon candidates, their putative families and their internal structure in a hierarchical fashion allowing the user to "sift" through results of de novo prediction software. It also offers customizable filtering and classification functionality.
Lucy DNA sequence quality and vector trimming tool
Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses.
Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework.
Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.
Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.
Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.
Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic.
Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc.
Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
Software C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.Wrapper to tabix indexer
Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation.
Software tool as general purpose cluster algorithm for both weighted and unweighted networks. Unsupervised cluster algorithm for graphs based on simulation of stochastic flow in graphs. Cluster algorithm for graphs.
Software tool to predict gene ontology terms for protein sequences through homology.
Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing.
Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates.
Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data.
Software OLC-based de novo assembler for noisy long reads.
Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.
Command lines tool to annotate miRNAs with standard mirna/isomir naming.
Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words.
Software tool for the design of multiplex pyrosequencing assays.
Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.
Software Python implementation of MacroMolecular Transmission Format API, decoder and encoder. Repository holds the Python 2 and 3 compatible API, encoding and decoding libraries.
Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets.
Open source multi platform molecular visualization program.
Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller.
Software package to remove reads mapping to the lambda phage genome from a fastq file.
MUltiple (protein) STructural AligNment alGorithm
Software tool for structural alignment of multiple protein structures. Used to produce sequence alignment. Reports multiple sequence alignment and corresponding superposition of structures.
Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.
Software package as plotting tool for long read sequencing data and alignments.
Web-compatible database search or multiple alignment viewer, Software tool as command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats.
Software tool as partner script to the popular ncbi-genome-download script. Allows to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API.
Software library of sequence alignment algorithms implemented in Java.
Software language-theory based homology detection tool across multiple large genomes.
Software alignment program that can align pairs of sequences using logarithmic and affine gap penalties.
Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling.
Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more.
Entrez Direct: E-utilities on the Unix Command Line
Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.
Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm.
NOn-Regular Secondary Structure predictor
NORSp - predictor of NOn-Regular Secondary Structure
Online predictor of NOn-Regular Secondary Structure for disordered regions in protein. Used to predict long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil then return e-mail to user about the presence and position of disordered regions.
Software DICOM library which provides user-friendly C++11 and Python API for different parts of the DICOM standard.
Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.
Software to count cell colonies and other circular objects. Used to facilitate enumeration of colony forming unit.
Software tool for detecting natural selection and recombination in DNA or RNA sequences.
Open source software for electronic health records and medical practice management solution.
Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases.
Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data.
Open source software framework that includes the necessary building blocks for surgical simulations, such as native device support, haptic feedback, graphics, discrete collision detection and physics simulation. Developers can refactor the physics engine, swap models, ODE solvers, or linear system solvers.
Open Network Interface for Image-Guided Therapy Link
Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback.
Software miRSeq data alignment workflow. Used to integrate genetic information to assess the impact of variants on miRNA expression. Used for integrating genome wide genotype data into miRNA sequence alignment analysis.
Software wrapper to speed up downloading process by dividing the work into multiple threads.
Software Python program to search for pathogen nucleic acid sequences in NGS datasets.Used for pathogen identification in metagenomic and clinical next generation sequencing samples.
Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications.
Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
Software Java program for calculating patristic distances and graphically comparing the components of genetic change.
Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.
Profile Consistency Multiple Sequence Alignment
Software tool for multiple sequence alignment based on profile consistency. Used to construct multiple sequence alignment given set of protein sequences.
Software Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data.
Software suite of tools to build and search generalized profiles.
Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.
Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables.
Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality.
Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods.
Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.
Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects.
Software tool for similarity and expression correction for strain level identification and quantification in metaproteomics. Peptide intensity weighted proteome abundance similarity correction tool to correct identification and spectral counting based quantification results. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor.
Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences.
Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads.
Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images.
Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems.
Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods.
Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures.
Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment.
Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures.
Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions.
Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools.
Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis.
Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format.
Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures.
Software tools for creating the sequence-to-structure alignment database PSSH2.
Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses.
Picking Unique Relevant Peptides for viraL Experiments
Software tool for selecting target specific peptide candidates directly from given proteome sequence data.
Software tool implementing novel indexing data structure for compacted de Bruijn graph and colored compacted de Bruijn graph.
Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data.
Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments.
Software airr reference library provides basic functions and classes for interacting with AIRR Community Data Representation Standards, including tools for read, write and validation.
Open source Python-based optimization modeling language with diverse set of optimization capabilities.
Python Nearest Alignment Space Termination tool
Software tool for aligning sequences to template alignment.
Software application for perpendicular line scanning fluorescence correlation spectroscopy.
Software application for efficient comparison of genomic intervals in Python.
Software Python library for analysis of genomic sequence data. Framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics.
Software provides command line interface and Python API for working with Biological Observation Matrix files.
Software library for sparse, compressed, binary persistent storage format used to store genomic interaction data, such as Hi-C contact matrices.Scalable storage for Hi-C data and other genomically labeled arrays.
Software Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
Software toolbox to fit psychometric functions and to test hypotheses about psychometric data.
Software Python library for phylogenetic computing. Provides classes and functions for simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data.
Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL.
Software tool set for molecular Quantitative Trait Loci discovery and analysis. Allows to go from raw sequence data to collection of molecular Quantitative Trait Loci in few easy-to-perform steps.
Software graphical interface for preparing AutoDock virtual screenings.Automates some of the most common operations performed when preparing virtual screening.
Software Python library and associated set of scripts for rapid implementation of genome scale analyses.
Software for quality control, quality trimming, adapter removal and sequence content check of NGS data.
Software tool for mapping RNA-seq reads to transcriptomes. Used for rapid sensitive and accurate read mapping via quasi-mapping
Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments.
Reference-Assisted Genome Ordering UTility
Software tool for chromosome level scaffolding using multiple references. Given initial assembly fragments and one or multiple related references it produces chromosome scale assembly.
Standalone software for sampling genomic sequences.Supports two modes, random subsampling of sequencing data to desired depth and file splitting to desired size in bytes.
Software package for molecular graphics visualisation.Used for visualisation of molecules.
Open source learning platform to provide educators, administrators and learners with integrated system to create personalised learning environments. Designed to help educators create online courses based on pedagogical principles.
Software tool as flexible freeware statistical calculator that computes sample size, effect size, and power statistics for factorial ANOVA designs.
New method for measuring daytime sleepiness. Self administered questionnaire to provide measurement of subject's general level of daytime sleepiness. Subjects are to rate the chances that they would doze off or fall asleep when in eight different situations commonly encountered in daily life.Used to give valid measurements of sleep propensity in adults.
The scale measures subjective level of sleepiness at particular time during the day. On this scale subjects indicate which level best reflects the psycho-physical sate experienced in the last 10 min.KSS is measure of situational sleepiness.
Ambulatory Monitoring | Psychomotor Vigilance Task system
PVT-192 Psychomotor Vigilance Task Monitor
System includes PVT-192 monitor and REACT software. Used for reaction time testing for long-term, large-scale testing of vigilance, effects of sleep deprivation, and drug effects. Used for PVT test wherever measures of performance or sleepiness effects are needed.
Web and programmatically accessible data service comprising allelic data covering strains at segregating sites. Mouse genetic variation service enables multi-trait, multi-population data integration and analyses. Interoperation with phenotype databases, analytic tools and other resources enable wealth of applications including multi-trait, multi-population meta-analysis. Mouse genetic resource that includes typed, sequenced, and imputed allelic states of 657 inbred mouse strains and their derivatives at 106.8M sites.
Software suite of Docker images with customized R environments for particular tasks. Docker containers for R to create, distribute, deploy, and run software applications using containers.
Software R package allowing integration of Ensembl querying with R workflow. Used to seemlessly integrate querying of Ensembl databases into your R workflow.
Software open-source, cloud-optimized pipeline developed in collaboration with members of the BRAIN Initiative (BICCN and BICAN Sequencing Working Group) and SCORCH. It supports the processing of 10x 3' single-cell and single-nucleus gene expression (GEX) and chromatin accessibility (ATAC) data generated with the 10x Genomics Multiome assay.
Software tools for generating high quality raster images of proteins or other molecules. Photorealistic molecular graphics. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.
Software R package for using R enviroments for annotation.
Software tool for detecting conserved amino-acid sites by computing relative evolutionary rate for each site in multiple sequence alignment. Used for identification of functional regions in proteins.
Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats.
Software R package provides functions that are needed by many other packages or which replace R functions. Base functions for Bioconductor.
Software R package contains convenience data structures and functions to handle cdfenvs.
Software R package defines many S4 generic functions used in Bioconductor.
Software R package to provide a client for the Bioconductor AnnotationHub web resource. AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered.
Software R package for interfacing with BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, limited support for writing biom-object back to biom-format file.
Software R package to provide set of utilities, color schemes and conventions for genomic data. Used for various high-level packages for biological data visualization.
Software R package provides infrastructure shared by all the Biostrings-based genome data packages.
Software R pacakge provides functions and load identifier mapping databases in R. Uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.
Software R package for export and import classification trees and clusters to other programs.
Software R package provides large scale identification and advanced visualization of sets of conserved noncoding elements.
Software R package provides functions for plotting genomic data
Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order.
Software R package provides efficient containers for storing and manipulating short genomic alignments. This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
Software R package for analysis of GRO-seq data. Used for identifying unannotated and cell type-specific transcription units from global run-on sequencing data
Software R package provides some basic functions for filtering genes.
Software R package to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package.
Software R package that implements some simple capabilities for representing and manipulating hypergraphs.
Software R package provides set of annotation maps describing entire Gene Ontology assembled using data from GO.
Software R package implements filtering procedure for replicated transcriptome sequencing data based on global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.
Software R package for imputation for microarray data.
Software R pacakage for multidimensional data integration to identify pathogenic perturbations to biological systems. Used for integrating multidimensional omics disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. Includes Marker set enrichment analysis and Weighted Key Driver Analysis parts.
Software R package to harmonize data management of multiple experimental assays performed on overlapping set of specimens.Provides user experience by extending concepts from SummarizedExperiment, supporting open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.
Software R package to determine features that are differentially abundant between two or more groups of multiple samples. Used to address the effects of both normalization and under-sampling of microbial communities on disease association detection and testing of feature correlations.
Software R package provides set of flexible functions to evaluate and visualize multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells.
Software R package has two functions. One reads Affymetrix chip description file and creates hash table environment containing location/probe set membership mapping. The other creates package that automatically loads that environment.
Software toolkit of high level functions for DNA motif scanning and enrichment analysis built upon Biostrings. Used for PWM enrichment analysis of already known PWMs. Also implements high-level functions for PWM scanning and visualisation.
Software R package to assess quality of NanoString mRNA gene expression data, to identify outlier probes and outlier samples. Provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and easily sharable html quality control output.
Software R package as interface to the graph algorithms contained in the BOOST library.
Software R package providing PCA methods for incomplete data. Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and conventional SVD PCA. Cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation.
Software R package as molecular informatics toolkit with integration of bioinformatics and chemoinformatics tools for drug discovery.
Software library of core preprocessing routines.
Quantitative Set Analysis for Gene Expression
Software R package is implementation Quantitative Set Analysis for Gene Expression method. Used to provide faster, more accurate, and easier to understand test for gene expression studies.
Software R package to help disambiguate transcriptome samples by automating differential expression, then gene set enrichment, and finally N-dimensional projection to quantify in which ways each sample is like either treatment group.
Software R package provides interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating Sequence Alignment Map, FASTA, binary variant call and compressed indexed tab-delimited files.
Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots.
Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table.
Software R package for analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.
Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage.
Software R package implementing bee swarm plots. Bee swarm plot is one-dimensional scatter plot like "stripchart", but with closely packed, non overlapping points.
Software R package provides memory efficient S4 classes for storing sequences externally.
Simulation and Analysis of Boolean Networks
Software R package provides functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks.
cmprsk: Subdistribution Analysis of Competing Risks
Software R package for estimation, testing and regression modeling of subdistribution functions in competing risks.
Softwar R package for comparative analysis of protein structures. Used to process, organize and explore protein structure, sequence and dynamics data. Used to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. Enables statistical and graphical power of R environment to work with biological sequence and structural data.
Software R package provides multivariate tools to analyze comparative data. Analysis of comparative evolutionary data. Used for investigating phylogenetic signal in biological traits.
DoseFinding: Planning and Analyzing Dose Finding Experiments
Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology.
distory: Distance Between Phylogenetic Histories
Software R package for geodesic distance between phylogenetic trees and associated functions.
DT: A Wrapper of the JavaScript Library 'DataTables'
Software R package for data objects in R to render as HTML tables using JavaScript library DataTables. DataTables library has been included in this R package.
biwt: Compute the Biweight Mean Vector and Covariance & Correlation Matrice
Software R package for compute multivariate location, scale, and correlation estimates based on Tukey's biweight M-estimator.
Epi: Statistical Analysis in Epidemiology
Software R package provides functions for demographic and epidemiological analysis in Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and function for interval censored data and some useful functions for tabulation and plotting, as well as number of epidemiological data sets.
Software R package to scrape data from Fitbit to generate graphs.
Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data.
epibasix: Elementary Epidemiological Functions for Epidemiology and Biostatistics
Software R package for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement.
Software R package provides functions and classes to compute, handle and visualise incidence from dated events for defined time interval. Dates can be provided in various standard formats.
Software R package for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
Software R package as implementation of LexRank algorithm. Used for computing sentence importance based on concept of eigenvector centrality in graph representation of sentences.
Software R package for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium.
dynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering Dendrograms
Software R package contains methods for detection of clusters in hierarchical clustering dendrograms.
Software R package for clinical trial simulations based on Clinical Scenario Evaluation approach. The package supports broad class of data models, analysis strategies and commonly used evaluation criteria.
Software R package for creating iterators, many patterned after functions in the Python itertools module, and others patterned after functions in the 'snow' package.
Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures.
Software R package provides framework to perform Non-negative Matrix Factorization.Used for nonnegative matrix factorization.Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.
Parallel Mutual Information Estimation for Gene Network Reconstruction
Software R package for parallel estimation of mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for reconstruction of gene regulatory networks.
Software R tools for visualizing, smoothing and comparing receiver operating characteristic. Partial area under curve AUC can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Software R package provides functions for principal component analysis by projection pursuit.
Software R package for recursive partitioning based on psychometric models, employing general MOB algorithm to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models.
Software R package useful in analyzing data from psychophysical experiments.Includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice data to be used with binomial family in glm and self-Start functions for estimating gamma values for CRT screen calibrations.
Software R package provides interface to Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. Provides elements of file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'.
Software R package provides access to phyloinformatic data in 'NeXML' format.
Software R package provides base S4 class for comparative methods, incorporating one or more trees and trait data. Used for phylogenetic analysis.
Software R package to create Q-Q and manhattan plots for GWAS data from PLINK output files.
Software R package implements S3 class for storing and formatting time-of-day values, based on the 'difftime' class.
Software R package for measurement theory, meta-analysis, reliability, item analysis, inter-rater reliability, classical utility, and correlation
Software R package provides R-interface to the NIfTI reference implementation the niftilib C-library.
Software R package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3).
Web server for R with documented API to interface between R and the server. The documentation contains the Rook specification and details for building and running Rook applications.
Software R package for aggregating ranked lists, especially lists of genes. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.
Software R package for design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints.
Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis.
Software R package provides environment for Time-Frequency analysis of 1-D signals.
Software R package used to compute near optimal low-rank singular value decomposition of massive data sets with high accuracy. Provides several randomized matrix algorithms such as randomized singular value decomposition (rsvd), randomized principal component analysis (rpca), randomized robust principal component analysis (rrpca), randomized interpolative decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot functions are provided.
Software R package for modeling and monitoring of time series of counts, proportions and categorical data, as well as for modeling of continuous-time point processes of epidemic phenomena.
Softare R package as implementation of the t-SNE algorithm.
Software R package provides interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling comprehensive phylogenetic tree for all named species.
Software R package as collection of plotting and table output functions for data visualization. Results of various statistical analyses that are commonly used in social sciences can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms. This package supports labelled data.
Software R package for basic wavelet routines for time series 1D, image 2D and array 3D analysis.
Software R package usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.
Software R package infers V genotype of individual from immunoglobulin repertoire sequencing data like AIRR-Seq, Rep-Seq. Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among sample sequences.
Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.
Software R package to support gene set enrichment analysis, network topology analysis.Can be integrated into other pipeline or simultaneously analyze multiple gene lists. The user-friendly output report allows interactive and efficient exploration of enrichment results.
Software package as Java based common sequence file format reader and sequence file manipulation.
Software tool identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria. Used for identification of acquired antimicrobial resistance genes in whole-genome data.
Software package as Nanopore read de-multiplexer.
Software tool as versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index.
Software tool as genetic distance plotting for recombination events analysis.
Software C program that performs single SNP, case control association testing in samples with partially or completely unknown population and pedigree structure.
Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing.
Software tool for rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene.
Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.
Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.
Software tool for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.
Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads.
Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem.
Software tools for working with SAM/BAM data
Software toolbox provides set of basic functions allowing SBML models to be used in both MATLAB and Octave.
Software tool to filter SAM file for soft and hard clipped alignments
Software application to expose file format conversion in BioPython in convenient way. Imagemagick like frontend to Biopython SeqIO.
Software tool for alignment to variation graph inducer.
Software pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies.
Open Source platform to host multiple Shiny applications on single server.
Software tool for estimation of haplotypes aka phasing for SNP array and high coverage sequencing data. The version 4 is refactored and improved version of SHAPEIT algorithm with multiple key additional features.
Software comparative genomics tool to assist biologists in analysing genomic variations that correlate with pathogens, or genomic changes that help microorganisms adapt in different environments. Used for evolutionary and genome rearrangement studies for multiple strains of microorganisms.
Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step.
Software tool designed to align expressed DNA sequence with genomic sequence, allowing for introns.
Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments,
Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections.
Software de-novo sequence read assembler for microbial genomes.Designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.SKESA contigs could be connected into GFA graph using GFA connector.
SISTR command-line tool. Open web accessible tool for rapidly typing and subtyping draft salmonella genome assemblies.
Software workflow for SEQuential alignment of SEQuences to build PAN-genome data structure and whole-genome-alignment.
Software framework to provide ludic-therapeutic activities for people with disabilities.Offers new forms of interaction based on computer vision, voice and other peripherals to produce result in form of image and sound. Used for continuous and remote interaction, attainable to majority of people with cognitive, sensory and physical disabilities.
Software for alignment free sequence comparison. Uses pattern of care and don't care positions. Compares frequencies of spaced words according to pre-defined pattern.
Open source software framework targeting at real-time simulation, with emphasis on medical simulation.
Software library for MinHash sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets.
Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping,
Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms.
Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces.
Software tool as Intuitive Editor for annotated multiple Sequence and Structure Alignments.
Software tool aims to cluster sequences in a way that is fast and exact at the same time.
Software tool to correct sequencing errors in single pass reads for de novo assembly.
Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps.
Machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.
Software object oriented Perl library to handle Swiss-Prot entries
Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps.
Software tool as clustering method for amplicon-based studies.
Software package written and supported by ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database.
Software tool as local sequence aligner intended for use with large biological DNA sequences, with more than 1 Millions of base pairs.
Software tool as structural variant calling.
Software tool to filter and slice Nanopore reads which have been basecalled with Albacore.
Software tool as read simulator for nanopore DRS datasets.
Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage.
Software tool as fast and flexible long read alignment with optimal breakpoint detection.
Open source software toolkit for medical image conversion.
Portable software library for volume rendering.
Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes.
Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations.
Software tool for detection of E. coli virulence genes. Used to identify viruelnce genes in total or partial sequenced isolates of bacteria. E. coli, Enterococcus, S. aureus and Listeria are available.for detection of E. coli virulence genes.
Software tool for flexible annotation of genetic variants.Extracts and summarizes attributes from multiple annotation files and integrates annotations within INFO column of the original VCF file.
Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments.
Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA.
Software tool for variant matching problem.Used for robust matching of small variant datasets using flexible scoring schemes
Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile.
Software suite of tools for classifying and analyzing sequences homologous to set of reference models of viral genomes or gene families.
Software tool for identifying regions of common ancestry between genome maps. Used for identification and statistical evaluation of segmental homologies in comparative maps.
Software to generate highly accurate single molecule consensus reads.
Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline.
Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias.
Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set.
Software tool as post-processor for TopHat unmapped reads that restores read information in the proper format.Enables downstream software to process plethora of BAM files written by TopHat.
Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping.
Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins.
Software tool to process raw sequenceing chromatograph trace files from EST projects into quality checked sequences, ready for submission to dbEST.
Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions.
Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal.
Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions.
Software tool for protein structure alignment based on TM-score.Used to identify structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming. Used for sequence independent protein structure comparisons.
Software pipeline management system, written in Python. Enables reproducible, open source, big biomedical data analyses.
Software tool for tensiometry measurements and contact angle hysteresis.
Galileo computer assisted tissue microarray
Galileo Fully Automated Tissue Microarray
Galileo computer assisted Tissue Microarray instrument allows TMA preparation with different paraffin block sizes, producing digital excel format reporting and possibility of data transfer to several Digital TMA Slide Scanners for complete tracking of Tissue Microarray process.
Geant4 Application for Tomographic Emission
Software toolkit for PET and SPECT. Simulation platform for medical imaging and radiotherapy. Used for modelling of planar scintigraphy, single photon emission computed tomography (SPECT) and positron emission tomography (PET) acquisitions, this platform is widely used to assist PET and SPECT research. Extension of this platform, released by OpenGATE collaboration as GATE V6, enables modelling of x-ray computed tomography and radiation therapy experiments.
Software imputation model for scRNA-seq data. Used to accurately and efficiently identify dropout values and impute them precisely, which helps to improve downstream analyses of single-cell RNA sequencing data.
Brain Wide-spectrum Audio/Visual Exposure
BrainWAVE: Noninvasive Rhythm Stimulation
Code to program and run flicker stimulation on BrainWAVE stimulator device. This brain oscillation stimulating software can be adapted across subjects and integrated into variety of experimental designs like electrophysiology, neuroimaging, EEG, MRI. Flexible method for noninvasive stimulation of brain rhythms across species. Used to measure effects of rhythmic brain activity on behavior.
Software R package for comprehensive analysis chromatin accessibility data. Analyzing chromatin accessibility data in R. Used for data quality control, exploratory analyses including unsupervised methods for dimension reduction, clustering and quantifying transcription factor activities, and identification and characterization of differentially accessible regions. Used for analysis of large bulk datasets comprising hundreds of samples as well as for single cell datasets.
Indiana University Bloomington Flow Cytometry Core Facility
Core offers flow cytometry analysis and cell sorting services. It houses FACS Aria II 5-laser, 14-color sorter, SH800 2-laser, 6-color user-run cell sorter, COPAS Select, Drosophila embryo and large particle sorter, LSRII, 4-laser, 14-color analyzer, MACSQuant VYB 3-laser, 8-color analyzer with 96-well plate option, as well as Moxi Z cell counter technology used for determining cell concentration and size distribution and Miltenyi QuadroMACS separator. Services include technician assisted sorting, as well as training for analyzers, SH800 and Moxi instruments. Help with experimental design is available.Facility maintains workstation with flow cytometry data analysis software, and has copy of this software as well as site license for use outside of facility.
Efficient and Adaptive Gaussian Smoothing
Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell.
National Autonomous University of Mexico Materials Research Institute Electron Microscopy University Laboratory Core Facility
National Autonomous University of Mexico Materials Research Institute Electron Microscopy University Laboratory
Universidad Nacional Autonoma de Mexico LUME
Core covers main techniques of electron microscopy, from scanning electron microscopy to scanning transmission electron microscopy, for characterization of morphology and structure of materials at micrometer and nanometer scale.Provides equipment for preparing samples for analysis by different electron microscopy techniques.
Open source software Learning Record Store implementing the xAPI (Tin Can API) e-learning standard.Type of data repository designed to store learning activity statements generated by xAPI (Tin Can) compliant learning activities.
Open source software that automatically registers coronal slices and quantifies fluorescent markers. Python based, AI registration algorithm for slice matching to the Waxholm rat atlas. Slice quantification can be trained on any atlas, which allows use for other subjects such as mice, zebrafish, and humans. AI-based software for registration and analysis of fluorescent markers on coronal brain slices.
Software Python tool for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files.
University of British Columbia Advanced Research Computing Core Facility
University of British Columbia Advanced Research Computing
Core supports high performance computing and data management needs of UBC researchers by providing consultation, expertise, and access to digital research infrastructure such as high performance computing clusters and storage.
Jackson Laboratory JAX Scientific Research Services Microscopy Services Core Facility
The Jackson Laboratory JAX Microscopy Services
Jackson Laboratory Microscopy Services, located in Bar Harbor, Maine and Farmington, Connecticut, provides essential support to their faculty labs. Service includes standard widefield microscopy; advanced fluorescent microscopy, including confocal and spinning disk; 2-photon and fluorescence lifetime microscopy ; longitudinal observation or live cell imaging, including imaging of iPS and ES cells under various environmental conditions; laser capture microdissection, image analysis and 3D visualization; high throughput cell based screening; brightfield slide scanning; automated fluorescence slide scanning.
Integrated web server developed for Ribo-seq data analysis. Platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Web based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs.
UK Renal Registry collection of data from acute kidney injury patients in England.
Software R package for detection of low frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. Provides functions to visualize found aberrantly methylated regions, to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.
US-based non-profit engaging bioimaging scientists across Canada, Mexico, the US and its territories by creating inclusive and supportive community to support bioimaging scientists through on-line events, registration assistance for professional development opportunities and the chance to visit peer imaging facilities to learn new techniques, develop or expand management skills, and/or image data management and analysis skills., through Exchange of Experience program.
Family of healthcare databases and related software tools and products developed through Federal-State-Industry partnership. Databases bring together data collection of State data organizations, hospital associations, private data organizations, and Federal government to create national information resource of encounter-level healthcare data. HCUP includes largest collection of longitudinal hospital care data in the United States, with all-payer, encounter-level information beginning in 1988. These databases enable research on broad range of health policy issues, including cost and quality of health services, medical practice patterns, access to healthcare programs, and outcomes of treatments at the national, State, and local market levels.
Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale.
Software R package to facilitate detection and analysis of clinical trial registration numbers. Data package of regular expressions and provides some R functions for implementing the regexes. Data Package and R Functions for Clinical Trial Registries and other MEDLINE Databanks.
Medical image viewer that allows to load overlays and draw regions of interest. Runs on Windows, Linux and OSX. Allows to view 2D slices and renderings of your brain imaging data. It can display many image formats and includes graphical interface for dcm2nii to convert DICOM images to NIfTI format. Allows to draw regions of interest which can aid lesion mapping and fMRI analysis.
Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems.
survival Receiver Operating Characteristic
Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data.
Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,
Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation.
Software R package for visually combining expression data with functional analysis.
Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot.
Software Python package for wavelet analysis.
Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats.
Software PCA-based toolkit for compression and analysis of molecular simulation data. Used for compression and analysis of molecular dynamics (MD) simulation data.
Software R package provides risk regression models and prediction scores for survival analysis with competing risks.
Web tool for detecting PROSITE signature matches in protein sequences.
Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package.
Web server predict secondary structures of single stranded RNA or DNA sequences.
Low cost platform for multianimal chronic Local Field Potential video monitoring with Graphical User Interface for seizure detection and behavioral scoring. Enables chronic monitoring of several animals simultaneously, synchronizes bilateral local field potential and video streams in real time, and parses recorded data into manageable file sizes. Hardware solution leverages Intan and Open Ephys acquisition systems and software solution is implemented in Bonsai. Data are synchronized and parsed in Bonsai, allowing for flexibility and scalability of up to 128 channels per animal. The use of Intan adapter board for LFP video recordings allows compatibility with large variety of recording devices. Custom made electrodes and cables were components for the chronic LFP recordings. Used as acquisition system for long term video neurophysiology recordings.
NutritionQuest Questionnaires and Screeners
NutritionQuest provides questionnaires and screeners for assessment of diet and physical activity. Questionnaires are derived from and based on Dr. Block's landmark research into the development of valid, user-friendly assessment methods. Questionnaires and dietary analysis services are available to nutritional epidemiologists and public health researchers.
Ecocyte Bioscience Xenopus laevis oocytes delivery service
Ecocyte Bioscience Xenopus laevis defolliculated oocytes
Ecocyte Bioscience offers weekly delivery service of Xenopus laevis oocytes for expression studies. Products include defolliculated and ready to use Xenopus Laevis oocytes used for mRNA or cDNA injections or other electrophysiological experiments.
Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils.
Software for managing geochemical data created by individual geochronology laboratory. Designed for flexibility and extensibility, so that it can be tailored to the needs of individual analytical labs that manage wide variety of data. Database set up for metadata tracking.
Software for image processing. Reads data captured by FV1200/FV1000/FV500/FV300 microscopes. Images saved with FV file format (OIF, OIB, FV Multi-Tiff) can be read.
Software digital library and cyberinfrastructure facilitating discovery and utilization of data and knowledge in published documents.
American healthcare company that provides data, analytics, and research to the life sciences industry, with particular focus on oncology and rare diseases.
National Cancer Institute Cancer Statistics Cancer Stat Facts
Collection of statistical summaries for number of common cancer types. They were developed to provide quick overview of frequently requested cancer statistics. Available statistics may include incidence, mortality, survival, stage, prevalence, and lifetime risk. Links to additional resources from NCI including risk factors, treatment, and clinical trials are also provided. The statistics will be updated annually to coincide with the SEER data release.
Enhanced application on generating single cell gene expression profile for high resolution spatial transcriptomics. Registers spatial gene expression map and cell membrane/wall staining image with nuclei staining image as intermediary, thus cell membrane/wall outlines can be directly segmented from cell membrane/wall staining image without correcting nuclei boundaries.
Software toolkit for Machine Learning Driven Data Analysis. Simplifies machine learning for data exploration, visualization and analysis.
Provides platform for visualizing multimodal single cell data across mammalian brain and aims to empower researchers to explore and analyze multiple whole brain datasets simultaneously. Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas. Atlas as part of Brain Knowledge Platform will enable neuroscience community to identify more cell types in brain; Investigate spatial location of cell types; Investigate gene expression and co-expression patterns in cell types; Refine boundaries and knowledge of brain regions defined by gene expression.
SPARC Connectivity Knowledge Base of the Autonomic Nervous system Composer
Web application authoring interface that permits users to display, inspect, survey, and formulate knowledge statements to be added to SCKAN, as well as the ability to query and augment knowledge information within SCKAN, the SPARC Connectivity Knowledge Base of the Autonomic Nervous system.
Software R toolbox for thorough metabolomic data analysis, integration and interpretation. Metabox 2.0 is updated version of R package Metabox and includes several methods for data processing, statistical analysis, biomarker analysis, integrative analysis and data interpretation.
European Research Infrastructure for Modelling Human Diseases
Non-profit organisation dedicated to advancing disease, understanding and treatment through cutting-edge models. Provides mouse model resources for modelling human diseases. Provides research infrastructure for generation, phenotyping, archiving, and distribution of mouse models in Europe. Through collaboration with other infrastructures, it fosters global data sharing and contributes to tackling significant health challenges.
Portal provides information on Cancer Statistics in Japan. Official website operated by National Cancer Center for cancer information.
Correlative electron microscopy and cross-platform imaging automation software. Imaging and correlative workflow software suite compatible with full line of Thermo Scientific SEM, DualBeam (FIB SEM) and TEM platforms.
Software for semi-automatic bone histomorphometry. Used for manual tracing of bone surfaces.
System for imaging of living and cleared specimens. Used to image large optically cleared specimens in toto with subcellular resolution. Dedicated optics, sample chambers and holders allow adaption to the refractive index of your chosen clearing method.
Resolve Biosciences Molecular Cartography
Resolve Biosciences Molecular Cartography platform
Platform is multi-analyte, multiplex spatial analysis technology that enables scientists to resolve complex biological challenges in areas such as oncology, neuroscience, and infectious disease. Platform produces contextual data sets that illuminate molecular interactions at subcellular resolution, while preserving the sample tissue.
Software Matlab app for analysis of high density imaging data like that from Array Tomography.
Software tool for MOB typing for plasmid metagenomic fragments based on language model.
Open source, adaptable tracking system for multiple rodents. Scalable and customizable system for tracking and behavior assessment consists of Raspberry Pi based video and RFID acquisition. Maximum of six rodents of any coat color can be tracked simultaneously in any user defined arena with few restrictions. For pose estimation and travel trajectory analysis, PyMouseTracks supports interfacing with open source packages such as DeepLabCut and Traja.
Pennsylvania State University Huck Institutes Cryo-Electron Microscopy Core Facility
Huck Institutes' Cryo-Electron Microscopy Facility
Cryo-Electron Microscopy Facility houses FEI Titan Krios microscope that offers data collection for life sciences while incorporating materials science applications. Used for creating super high definition 3D images of atoms and molecules. Facility allows for fully automated atomic resolution single particle and high contrast tomography tilt-series data collection. Additional microscopy components permit a full range of materials science applications, including EELS, STEM, and DPC. Facility also houses ThermoFisher Arctica G2.
Pennsylvania State University Huck Institutes Microscopy Core Facility
Microscopy facility specializes in areas of optical microscopy, electron microscopy, and histology. Facility is equipped with confocal microscopes, research fluorescence microscopes, and transmission and scanning electron microscopes. Research staff engage in experimentation, training, project collaboration, and consultation.
Pennsylvania State University Huck Institutes Automated Biological Calorimetry Core Facility
Huck Institutes' Automated Biological Calorimetry Facility
Automated Biological Calorimetry Facility provides infrastructure and support for individual investigators to undertake studies of macromolecule binding and folding, as well as protein and lipid quantification. Our calorimetry instruments are fully automated and require the least amount of sample of any commercially available instruments.Provides instrumentation and collaborative assistance for Isothermal titration calorimetry for studying ligand-macromolecule binding; Differential scanning calorimetry for investigating stability and folding thermodynamics. Staff is available to assist with project development and research.
Pennsylvania State University Huck Institutes CSL Behring Fermentation Core Facility
Huck Institutes CSL Behring Fermentation Facility
Biotechnology pilot plant capable of research and pilot scale production of microbial cells, recombinant proteins, and other microbial products over wide range of controlled conditions. Facility provides equipment and expertise to university affiliated and independent government and industry researchers interested in fermentation and related technologies, including cell separation and disruption, biomolecule production and purification, and process monitoring.
Pennsylvania State University Huck Institutes Flow Cytometry Core Facility
Huck Institutes' Flow Cytometry Facility
Facility is equipped with flow cytometers and cell sorters to examine cell samples within range of micron. Staff engage in experimentation, training, project collaboration, and consultation.
Pennsylvania State University Huck Institutes High Field Magnetic Resonance Imaging Core Facility
Huck Institutes' High-Field Magnetic Resonance Imaging Facility
Facility for investigating samples at micrometer scale using in vivo imaging and magnetic resonance microscopy. Facility houses Bruker BioSpec 70/30 horizontal magnet and Agilent 14.1 Tesla vertical magnet.
Pennsylvania State University Huck Institutes Proteomics and Mass Spectrometry Core Facility
Huck Institutes' Proteomics and Mass Spectrometry Core Facility
Facility offers highly sensitive and accurate mass spectrometry analysis, including identification and quantitation of proteins by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS-MS) or by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-TOF-MS).
Pennsylvania State University Huck Institutes Sartorius Cell Culture Core Facility
Huck Institutes Sartorius Cell Culture Facility
Sartorius Cell Culture Facility delivers hands-on training in cell culture to students, faculty, staff, and external personnel, while providing researchers across numerous Penn State disciplines access to the lab environment.
Pennsylvania State University Huck Institutes X-Ray Crystallography Core Facility
Huck Institutes' X-Ray Crystallography Facility
Facility provides infrastructure and support for investigators to undertake single crystal X-ray structural studies. Provides instrumentation, training, and collaboration for Protein characterization, including dynamic light scattering, differential scanning calorimetry, bio-layer interferometry, and circular dichroism; Binding studies using isothermal titration calorimetry; Robotic crystallization, incubators, UV, and digital microscopes;Robotic imaging; Diffraction data collection and processing; Structure determination and analysis; Molecular modeling; Small angle X-ray scattering. Staff is available to train researchers to use equipment and to assist with project development and research.
Web tool for exploration and sharing of mass spectrometry based proteomics data. Used for analysis and sharing of proteomics data, data visualization, export of plots in SVG format, assessment of experimental quality by correlation matrix and profile plot. User can analyze domain structure, AlphaFold predicted structure, reported interactors, relative expression, disease and pharmaceutical links, and mutagenesis information on all selected hits.
Software Python package for analysis of dynamic fluorescence microscopy data.
Photometrics acquisition software to capture, save and publish images and movies. Allows users of color and monochrome cameras to capture high quality images and videos from their microscope or lens system.
Pattern Health Digital Research Platform
Platform for researchers to economically create and manage digital health programs. Platform built for research management and digital interventions. Helps researchers collect data and engage participants.
Portal that aggregates tools that assist users ascertain FAIR-ness. Offers guidance to discover standards and repositories in FAIRsharing, which should be used to make data FAIR, as well as signpost other resources that enable FAIRness.
Karolinska Institute Biomedicum Flow Cytometry Core Facility
Biomedicum Flow Cytometry (BFC) Core Facility
Biomedicum Flow Cytometry Core Facility Karolinska Institutet
Facility is shared resource laboratory providing comprehensive suite of services to support research needs in flow cytometry. Offers conventional and full spectral cytometry for multi-parametric analysis, as well as multiparameter fluorescence activated cell sorting.
Independent research evaluation firm, based in the U.S. and Canada. Provider of research analytics services and data. Provides science research evaluation and analytics to assess science and technology activities. Headquartered in Montréal, Canada, Science-Metrix is known for independent bibliometric analysis and research evaluation and bibliometric and informetrics expertise. Science-Metrix was an early adopter of Elsevier’s abstract database Scopus and has worked closely with Elsevier. Elsevier has acquired Science-Metrix Inc. in 2018.
Software Python package to compute Euler Characteristic Curves of point cloud or image data.
Tosoh | AIA-900 Automated Immunoassay Analyzer
AIA immunoassay analyzer offers automation for immunoassay testing with flexible expansion capabilities. AIA-900 features: 90 tests/hour throughput; Load 10 racks on board; Load up to 5 tests/patient; First result in 18 minutes; Random access; Continuous processing; Simple touch screen operation; Bar coded primary tube sampling; Clot detection; Unit Dose Test Cup; Automated pretreatment; Automated dilution from 2 to 1000.
Cellular Autophagy Regulation and GOlgiphagy
Web browser for analysis of proteomic data. ShinyApp interface generated in R and RStudio.
Designs and develops neurocognitive and behavioral assessment tools and technologies. Provides clinicians and researchers with leading-edge technologies for improved neurocognitive and behavioral evaluation and management capabilities. Provides CNS Vital Signs which is reimbursable assessment procedure that utilizes scientifically validated, objective, and reliable computerized neuropsychological tests to evaluate neurocognitive status of patients and covers a range of mental processes from simple motor performance, attention, memory, to executive functions. CNS Vital Signs is available as both web/cloud platform and local platform.
Web based platform that enables data discovery from curated historical and on going oceanographic sequencing efforts. Enables discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers. Used to centralize and standardize contextual data associated with major marine 'omic datasets. Used for marine microbiology to discover and analyze interconnected 'omics and environmental data.
University of Arizona Molecular Clinical Core Facility
University of Arizona UA-Arizona Molecular Clinical Core
Core is CLIA certified/CAP accredited laboratory specializing in high complexity genetic and serological clinical testing and research. Provides inpatient and outpatient diagnostic testing services as well as support for clinical trial and clinical research activities for physicians, researchers and industry clients. The AZClinCore has aided in development of novel genetic testing and clinical trial protocols as well as providing evaluations for new technology and testing platforms. Supports end-to-end clinical testing as well as reference lab services.
Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools.
Local Run Manager DNA Amplicon analysis module aligns amplicon reads against reference specified in the manifest file. Variants are called for the targeted regions.
Florida State University Innovation Hub Core Facility
Hosts makerspaces, labs, and promotes design based frameworks toward iteration and innovation. Acts as open intersection of university departmental collaboration and provides access to low barrier prototyping tools. Supports FSU student, staff, and faculty research initiatives.
Software tool for merging paired-end reads via novel empirically derived models of sequencing errors. Used for merging paired-end reads and removing adapters. Corrects errors and ambiguous bases and assigns quality scores for merged bases that accurately reflect the error rates.
Software package to facilitate large scale analysis, using both rooted and unrooted trees.Used for dating gene duplications and optimizing gene family trees.Used for inferring duplication dates from gene trees automatically and can also be used as exploratory analysis tool for evaluating alternative hypotheses.
Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL.
Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations.
Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously.
Open Bayesian inference Using Gibbs Sampling
Software for analysing complex statistical models using Markov chain Monte Carlo methods.
Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras.
Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system.
Instrument control and data acquisition software for Agilent Seahorse XFe96 and XFe24 analyzers with Windows 10 64-bit OS only. Experiment design, instrument control, data analysis, and file management software. Software provides intuitive interface with predefined assay templates and streamlined experimental design for simplified metabolic analysis.
Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding.
Software tool to process micrograph images for particle size.
Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data.
Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide.
Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters.
Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree.
Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data.
Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology.
Sequence-based Rna Adenosine Methylation site Predictor
Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features.
Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees.
Web server predicts functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. Functional impact is assessed based on evolutionary conservation of affected amino acid in protein homologs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.
Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool.
Software pipeline for estimating species trees from multi copy gene trees.
Web application as E-value calculator that compute E-values for variety of outcome measures, including risk ratios, odds ratios, rate ratios, risk differences, hazard ratios, and standardized mean differences.
Software R package to estimate generalized additive mixed models.
Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data.
Software R package provides access to all of the capabilities of DAGitty web application for drawing and analysing Directed Acyclic Graphs within the R platform for statistical computing. Used for graphical analysis of structural causal models.
Software R package implements generalized estimating equations for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can handle clustered categorical responses. Used for fitting marginal generalized linear models to clustered data.
Software R package enables creation of Ridgeline plots in 'ggplot2'
Copynumber Karyotyping of Aneuploid Tumors
Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data.
Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides.
Software drawing R package designed for Manhattan plot of genomic analysis.
Software R package for choosing univariate class intervals for mapping or other graphics purposes.
Software R package for multiple imputation of missing data in multilevel modeling.
Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins.
Web server for the global and local quality estimation of 3D protein models
Software R package offers multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files.
Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy.
Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma.
Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library.
Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences.
Web server for local superposition free score for comparing protein structures and models using distance difference tests. Superposition free score that evaluates local distance differences of all atoms in model, including validation of stereochemical plausibility.
Software high throughput data extraction package for LC-MS data.Targeted Liquid Chromatography-Mass Spectrometry data processing package for relative quantitation of glycopeptides.
Software R package for genomic interval processing.Genomic regions processing using open-source command line tools to perform genome arithmetic e.g indexing, formatting and merging.
Stanford University Microfluidics Foundry Core Facility
Stanford University Stanford Microfluidics Foundry
Core in part of Bioengineering Department at Stanford University and is the main service provider of integrated microfluidic devices on Stanford campus servicing universities and academic institutions.
Stanford University Koret Human Neurosciences Community Laboratory Core Facility
Koret Human Neurosciences Community Laboratory
Stanford University Koret Human Neurosciences Community Laboratory
Core for collaborative human neuroscience research provides access to technology and expertise to high density electroencephalography recording and transcranial magnetic stimulation studies in human subjects.
Stanford University Additive Manufacturing and Printing Core Facility
Additive Manufacturing and Printing Facility
Stanford University Additive Manufacturing and Printing Facility
Advanced 3D printing facility enables digital design, prototyping, and small scale production as integrated innovation hub and shared use facility for innovation and commercialization for investigators spanning the Stanford campus and Silicon Valley.
Pennsylvania State University Huck Institutes Genomics Research Incubator Core Facility
Pennsylvania State University Huck Institutes Genomics Research Incubator
Provides access to highly specialized and custom genomics and epigenomics assays that Genomics Core Facility does not currently support. Examples include ATAC sequencing; RUN sequencing;Tag sequencing;Chromatin immunoprecipitation;Custom assays. Offers hands-on experiences and training for researchers in genomic technologies, methodologies, and instrumentation.
Variability analysis of proteomics data used for deep learning.
Software package annotates genetic variants with their predicted effect on splicing. Used to identify splice variants.
Transdermal Glomerular Filtration Rate monitor used to assess renal function in mouse and rat models of acute kidney injury and chronic kidney disease.
Software suite provides plugins to enhance 3D capabilities of ImageJ.
Leica | TP1020 Automatic Benchtop Tissue Processor Semi Enclosed
Leica TP1020 tissue processor is available in four configurations: basic instrument, basic instrument with vacuum, basic instrument with fume control system and basic instrument with both vacuum and fume control. Used for gentle specimen processing and high level of specimen safety at all stages of processing run.
10x Genomics | Chromium iX Single Cell Analyzer
Chromium iX offers cost effective, lower throughput single cell analysis, and can be upgraded to the high throughput full-range Chromium X.Chromium iX does not run high-throughput (HT) assays.
10x Genomics | Chromium X Single Cell Analyzer
Analyzer used for high throughput full range single cell analysis. Chromium X runs high-throughput assays. It runs all single cell assays, including high-throughput assays for Single Cell Immune Profiling and Single Cell Gene Expression.
Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies.
FAIR API ecosystem for inter-connected biomedical knowledge. Provides three components in its API development ecosystem: family of high-performance APIs for accessing up-to-date annotations for genes, genetic variants, chemicals and drugs; provides BioThings API packages its API-development best practice into reusable Software Development Kit to help other bioinformaticians to build same high-quality API to distribute their own specific knowledge; BioThings API provides platform to foster findability and interoperability across community developed biomedical APIs. Provides tools for authoring API metadata following community supported OpenAPI standard and hosts standardized interactive API documentation. Defines set of OpenAPI extensions to provide biomedical specific semantic annotations.
Web based platform that facilitates knowledge resolution by enabling users to traverse growing network of input datasets, semantically annotated API endpoints, and data visualization tools contributed by the ecosystem. Via user friendly web based user interface, workflows can be constructed from these building blocks without technical expertise.
Software package for analysis of sleep signal data. Open source C/C++ software for manipulating and analyzing polysomnographic recordings, with focus on sleep EEG.
Web Luna based interactive viewer for EDF signal and annotations, specifically designed for polysomnographic data. Supports visualization, analyses and manipulation of sleep signals, range of summary statistics and hypnogram based analyses including automated staging.
AI based software for detecting integrity issues in figures of scientific articles. Used for detecting integrity issues in life science articles. Detects inappropriate manipulation and duplication in many figure types, including blots, microscopy images, and light photography.
University of California at Berkeley Electron Microscope Laboratory Core Facility
UC Berkeley Electron Microscope Laboratory
University of California at Berkeley Electron Microscope Laboratory
University of California Berkeley UC Berkeley Electron Microscope Laboratory
Imaging core and shared resource facility. Provides electron microscopy services, education, and training. Equipped with high resolution transmission electron microscopes, scanning electron microscopes, high pressure freezer and ancillary sample preparation equipment. The equipment can provide nanometer scale analysis for biological, chemical and materials science. Offers Project consultation, Education and training for new users, Equipment for trained users who anticipate having long term EM projects, Full service microscopy.
Molecular Property Diagnostic Suite Covid-19
Galaxy based disease specific web portal for drug discovery research of COVID-19. Open access disease specific drug discovery portal.
Software tool for evaluating batch effects in data integration. Tool to improve accuracy and reliability of experimental results. Used to evaluate batch effect of dataset integration and output comprehensive report.
Platform as clinical knowledge base to search information to answer genomic questions. Connects clinicians, genetic counselors, and healthcare organizations by sharing genetic insights, enabling platform users to make impactful discoveries providing better patient care.
Software bulk RNA-seq cellular deconvolution tool. Used for analysis of healthy tissue and tumor biopsies. Based on RNA-seq NGS data of biological sample, Kassandra predicts cellular composition including stromal and immune elements by analyzing gene expression.
Emerging Technology Observatory Open Source Software Research and Community Activity
Open Source Software Research and Community Activity
Platform for data on open source software (OSS) used in science and technology research. Drawing on Github Archive, ETO’s Merged Academic Corpus, and many other data sources, ORCA tracks OSS usage, health, development activity, and community engagement across software projects and research subjects. Use ORCA to compare OSS projects in particular research area, track trends over time, and sort and filter projects by different metrics.
16-channel customizable multielectrode array
CMEA: Customizable Multielectrode Arrays
Simple, lightweight, and low cost customizable multielectrode array for Local Field Potential recordings. Used to collect LFP data from different brain regions simultaneously in rats. Can be modified to record single unit and multiunit activity in addition to LFP activity using both wired and wireless neural data acquisition systems.
Acts as part of statewide earthquake monitoring system, the California Integrated Seismic Network. Conducts essential research on earthquakes and solid earth processes while collecting and delivering high quality geophysical data. Data from these geophysical networks are recorded digitally and are archived at the Northern California Earthquake Data Center, which is located at the Berkeley Seismological Lab.
Platform provides resources for genomic observations from collection to analysis and publication. Works with standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets. Biocode Commons is also collaborating on development of Biological Collections Ontology, working to better integrate ontologies, vocabularies, and relevant standards that are related to BCO.
Resource designed to publish information and data about California coast reflecting current scientific understanding and data for the purpose of informing public policy and advancing the understanding of coastal processes.
University of Florida Scripps Institute for Biomedical Innovation and Technology Structural Biology Cryo Electron Microscopy Core Facility
Structural Biology Cryo-Electron Microscopy Core
The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology Structural Biology Cryo Electron Microscopy Core
UF Scripps Institute for Biomedical Innovation and Technology Structural Biology Cryo Electron Microscopy Core
Provides scientists with cryo-electron microscopy utilization, skills and knowledge to aid in their research.
Yale University Wu Tsai Institute BrainWorks Core Facility
Service core arm of Center for Neurocognition and Behavior. Used for measuring healthy human brain and behavior in action. Facility houses equipment, including MRI, SQUID and triaxial OPM MEG, EEG, NIRS, TMS, VR, eye-tracking, and body motion tracking.
Comprehensive Everglades Restoration Plan
South Florida Water Management District Comprehensive Everglades Restoration Plan
Platform provides framework for restoring, protecting and preserving the greater Everglades ecosystem. The plan is partnership between State of Florida and federal government.
Compact incubator total volume is 15 litres and it operates at temperatures from 5 °C above ambient to 50 °C. Temperature is displayed in increments of 0.2 °C. Air circulation system ensures heat distribution and minimizes the drying out of samples. Incubator can be set up directly on any counter top or work bench and is made of plastic that can be sterilised with standard disinfectants. Small opening on the housing can be used to accommodate cables for electrical devices placed inside the incubator. Reservoir for collecting spilled liquids is provided for additional safety.
Autoanalyzer is standalone system that provides consolidated testing from range of clinical chemistry applications. Allows determination of sodium, potassium and chloride in serum, plasma and urine using ion selective electrodes. Measurement of HbA1c levels in whole blood can also be performed.
TECAN Infinite M200 is laboratory device and accessory for multiplex luminescence and fluorescence applications. Device features automated robotic arm for dispensing samples or reagents onto cuvettes or microplates, as well as range of high speed and throughput sample injection capabilities. Infinite M200 is integrated with TECAN's proven laser-based multi-channel detection technology, to measure multiple biological responses simultaneously. System features graphical user interface to configure instrument for single or multiple sample injection processes. Accommodates range of different cuvette and microplate vessels, suitable for both 1.5ml and 0.2ml tubes as well as plates up to 384 wells. Multichannel optical detector can detect up to four different signals in parallel, with wide range of detection wavelengths. Designed for high-throughput applications with sensitive fluorescence and luminescence. Features automated sample injection unit that enables hands-free operation of 96 or 1,536 up to eight-channel multipoint experiments, providing maximum flexibility. Comes with range of software, including intuitive data collection and analysis interface. Designed with automated calibration settings, providing reliable, accurate and reproducible results.
Device designed for simultaneous measurement of multiple low volume samples. Consists of 16 precision manufactured quartz optics in user friendly format, offering precise, straightforward absorbance and fluorescence based measurements from sample volumes as low as 2 µl. Combined with Tecan’s Infinite series readers – the Infinite 200 PRO, Infinite F500 and Infinite M1000 PRO – the NanoQuant Plate provides solution for DNA or RNA quantification, allowing detection of concentrations down to 1 ng/µl for wide variety of applications.
Microplate reader software as user friendly interface for control of Tecan's Infinite series of microplate readers designed for professional use.
Leica | TCS SP8 DLS LightSheet microscope
Digital LightSheet full confocal with gentle single plane illumination microscope for easy light sheet imaging. TwinFlect mirror deflects illuminating light sheet at 90° angle, which allows integration of illumination and detection beam path into vertical axis of every inverted, Leica TCS SP8 confocal.
Software R package to predict drug functional similarity to drug repurposing.
Griffith University Compounds Australia Core Facility
Compounds Australia - Griffith University
Core for compound management and logistics. Through specialist infrastructure and expertise, we enable health researchers worldwide to outsource their sample logistics. Securely stores and curates suite of compound libraries (>1.5 million compounds), which are provided to researchers in flexible, assay-ready formats.
Griffith University; Brisbane; Australia
Griffith University, Brisbane, Queensland, Australia is public research university in South East Queensland on the east coast of Australia. One of Australia's leading universities. The university offers undergraduate, postgraduate, and research programs across range of disciplines, including business, law, science, health, education, engineering, and arts.
Web based tool that offers statistical, visual and network based approaches to understand miRNAs functions and regulatory mechanisms. Used for dissecting miRNA-target interactions and functional associations through network-based visual analysis.miRNet 2.0 is network based visual analytics for miRNA functional analysis and systems biology.
NovaSeq X Plus Sequencing System has ability to sequence more than 128 genomes per run. Provides faster run times, and the ability to process data directly on the instrument. Uses dual flow cells. Production scale sequencing system can also perform broad range of data intensive applications, from single-cell analysis to exome and circulating tumor DNA sequencing.
Updated NovaSeq to NovaSeq X. NovaSeq X Sequencing System achieves lower cost per genome by packing more genomes per flowcell, and that is because each flowcell has more wells for more fragments. NovaSeq X uses single flow cell.
Compact, benchtop instrument that enables transfer of transcriptomic probes from standard glass slides to Visium slides, enabling spatial profiling insights to be gained from even more samples. Enables whole transcriptomic spatial profiling insights across entire tissue section, and expanded compatibility with FFPE and/or FF samples.
Software R package to work with date-times and time-spans. Used for fast and user friendly parsing of date-time data, extraction and updating of components of date-time, algebraic manipulation on date-time and time-span objects.
University of Pennsylvania Institute for RNA Innovation Targeting Core Facility
University of Pennsylvania Institute for RNA InnovationTargeting Core
University of Pennsylvania Targeting Core
Core to support advancement of RNA biotherapeutics via enabling swift and low failure solutions of targeting related aspects. Provides methodologies, equipment, reagents, expertise and support in identification of epitopes and ligands, molecular design and testing of targeting RNA to diverse multitudes of desirable addresses in the body.
University of Pennsylvania Institute for Immunology and Immune Health I3H Core Facility
Core provides infrastructure and technical support for scaling clinical immune profiling of large scale clinical cohorts. Provides biospecimen processing, sample storage, high dimensional immune assays, computational analysis, and project management. Services are only available to investigators and teams whose cohorts have been approved by the Immune Health leadership.
Open source, and interactive platform to resolve trans disciplinary problems related to coastal and marine ecosystem. Data sharing and science communication portal holds amounts of fishery, reef, and mangrove data pertaining to Gulf of California and Mexico specific oceans, and delivers this information in interactive and easily digestible manner. Consistently expands library of datasets while improving functionality and overall usability of the platform. Facilitate access to scientific knowledge and data to promote transparency, education, and deeper understanding of Mexico’s ecosystems and their biodiversity to bridge gap between science and design process of conservation and resource management programs.
Platform provides tools, data, services, apps and community resources for geoscience researchers. EarthCube community works together to influence how data will be collected accessed, analyzed, visualized, shared and archived; participate in interdisciplinary and collaborative research; and contribute to transformation of geoscience research through emerging practices of digital scholarship, data and software stewardship, and open science.
Platform for Earth reference data and models supported by San Diego Supercomputer Center and Scripps Institution of Oceanography. Provides webservices and database.
The Engineering Biology Research Consortium (EBRC)
Non-profit, public-private partnership dedicated to bringing together inclusive community committed to advancing engineering biology to address national and global needs. We showcase cutting-edge research in engineering biology, identify pressing challenges and opportunities in research and application, articulate compelling research roadmaps and programs to address them, and provide timely access to other key developments in engineering biology.
Geotechnical Extreme Events Reconnaissance
Leading global organization for investigation and collection of highly valuable and perishable geotechnical insights and data and timely distillation and provision of that information to public through reports.
Kavli Institute for Theoretical Physics Online Talks
Most seminars, conferences, colloquia, and lectures at KITP since late 1997 have been archived on this website, in the form of slides, audio, video, and podcasts. Portal to foster scientific communication, education, and outreach.
Web-based platform for mass spectrometry imaging. Used for visualization, analysis and management of mass spectrometry imaging data. Used for management and storage of MSI data, visualization of hyper-dimensional contents of data, and statistical analysis.
Population biobank hosts heterogeneous collection of samples from general population spread across Flanders and over time and covers different ages. Biobank in which bio-specimen including human peripheral blood, cord blood, serum, plasma, cells, RNA, DNA), urine, hair, nails, exhaled breath condensate, saliva DNA, and human breast milk collected from non-diseased populations are preserved. These biospecimen were collected since 2002 in different human biomonitoring studies comprising European (e.g., DEMOCOPHES, HBM4EU), national (e.g., WHO human breastmilk studies), Flemish (Flemish Environment and Health Study (FLEHS) campaigns), and local (e.g., hotspots, 3xG project) well-defined and ethically approved research projects.
Software tool as succinct matplotlib wrapper for making publication quality graphics.
Northern Illinois University; DeKalb; USA
Northern Illinois University is a public research university in DeKalb, Illinois. It was founded as Northern Illinois State Normal School in 1895 by Illinois Governor John P. Altgeld to provide the state with college-educated teachers.
Northern Illinois University Molecular Analysis Core Facility
Northern Illinois University MAC core facility
Northern Illinois University MAC facility
Molecular Analysis Core offers analytical and instructional expertise in mass spectrometry. Provides instruments for spectroscopy, chromatography, and thermal analysis. Located in La Tourette Hall 304 and managed and supported by the Division of Research and Innovation Partnerships
Software Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses. Cartographic library with matplotlib support.
Software R package providing extensive library of plotting functions for use after fitting Bayesian models.Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow.
Publicly traded analytical laboratory instrument and software company headquartered in Milford, Massachusetts. Leading provider of lab equipment, supplies and software. Has pioneered chromatography, mass spectrometry, and thermal analysis innovations.
Business Services and Biotechnology Research company in Odense, Denmark.
Weill Cornell Medical College Department of Pathology and Laboratory Medicine Multiparametric In Situ Imaging Laboratory Core Facility
Core focuses on providing immunohistochemistry, multiplex immunofluorescence and high-plex histological imaging.Provides in situ-based profiling of cellular microenvironments at single cell resolution, in tumor and non-tumor tissues.
Open source web application created to analyze Live Mouse Tracker data easily and intuitively. Used to check reliability and to make some analysis of data from Live Mouse Tracker experiments. LMT stores data in SQLite files that requires some computer skills, but LMT-toolkit makes it easy to compute and extract behavioral profiles for each animal tested following step-by-step process.
Innovative Australian company that develops, manufactures and distributes advanced proteomics tools. Produces high performance nanoflow chromatography solutions for global research community.
Software Python library to manage wind data, draw windroses also known as polar rose plots, and fit Weibull probability density functions.
Software tool as Intel(R) Extension for Scikit-learn to speed up Scikit-learn application. Used to accelerate existing scikit-learn code. Accelerates Scikit-learn applications and still have full conformance with all Scikit-Learn APIs and algorithms. Software AI accelerator brings over 10-100X acceleration across variety of applications.
Marine and Coastal Research Institute of Columbia; Santa Marta; Colombia
Nonprofit marine and coastal research institute of Colombia linked to Ministry of Environment and Sustainable Development. Provides basic and applied scientific research on marine and coastal issues related to biodiversity, geosciences, resource use assessment, environmental quality and management of marine and coastal information. Coordinates Environmental Information System in marine and coastal aspects. Infrastructure has specialized laboratories with cutting-edge technology and Museum of Marine Natural History of Colombia. INVEMAR is recognized nationally and internationally for quality and leadership in its basic and applied research activities and its commitment to sustainable use of marine and coastal resources.
National Center for Ecological Analysis and Synthesis
Synthesis science center to help to transform ecology and environmental science to generate bigger insights. Leader in environmental data science, has led development of technological solutions to improve data access and management and efficiency of analyses, and helped set scientific standards in data ethics.
Data and software repository for Arctic section of National Science Foundation’s Office of Polar Programs. Repository has CoreTrustSeal certification so that the data can be used, shared, and preserved over long timespan. Helps research community reproducibly preserve and discover all products of NSF funded science in Arctic, including data, metadata, software, documents, and provenance that link these in coherent knowledge model. Initiative is the partnership between National Center for Ecological Analysis and Synthesis at UC Santa Barbara, DataONE, and National Centers for Environmental Information.
Cabinet level state body that works jointly with state and federal agencies, NGOs, tribes and public to ensure that California maintains healthy, resilient, and productive ocean and coastal ecosystems. The mission is to protect California’s coast and ocean by advancing innovative, science based policy and management, making strategic investments, and catalyzing action through partnerships and collaboration. Provides global model for ecosystem based protection and conservation.
Web application that creates CodeMeta files.
Software Heritage provides service for archiving and referencing historical and contemporary software with focus on human readable source code. The site was unveiled in 2016 by Inria and is supported by UNESCO. The project itself is structured as non‑profit multi‑stakeholder initiative.
Project aims to construct comprehensive, dynamic and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data.
Publishes documentation and data to make them discoverable and searchable on the Web. Publishing service archives data by integrating analyses, maps, media, and journals together. Open Context editors clean data and organize content. Every item receives unique identifier that allows citation of individual items. Your data publication receives DOI. Creative Commons licenses facilitate reuse. All Open Context data publications are preserved with California Digital Library.
Software R package for Bayesian applied regression modeling via Stan.
Tulane University TNBRC Anatomic Pathology Core Facility
Tulane University TNBRC Anatomic Pathology Core
Anatomic Pathology Core is responsible for post-mortem examinations, tissue collection and distribution, fixation, processing, slide preparation, routine and special staining, and diagnostic gross and histologic pathology services. Processes and interprets biopsy specimens for both research and diagnostic purposes and provides tissue trimming, paraffin processing, sectioning, and routine and special staining for clinical and research staff and faculty. APC works closely with clinical veterinarians, and through diagnostic pathology on biopsies and necropsies, plays major role in monitoring and maintaining health of animals in breeding colonies.
Tulane University TNBRC Immunology Assay Core Facility
Tulane University TNBRC Immunology Assay Core
Immunology Assay Core provides several immunology services to core and affiliate investigators. Offers multicolor staining for flow cytometry, access to inventory of commonly used antibodies, reagent compounding, sample processing such as cell isolation, automated cell separation through RoboSep, and irradiation of biological samples.Offers multiplex assays using MESO QuickPlex SQ 120 Imager to investigators.
Tulane University TNBRC Infectious Disease Aerobiology Core Facility
TNPRC Infectious Disease Aerobiology Core
Tulane University TNBRC Infectious Disease Aerobiology Core
Core focuses on infectious disease aerobiology. Core facilitates biomedical research efforts that require unique demands of aerosol and aerobiology in their respective performance.
Tulane University TNBRC Clinical Pathology Core Facility
Tulane University TNBRC Clinical Pathology Core
Clinical Pathology Core performs clinical diagnostic testing for all research and colony animals. This includes complete blood counts, routine chemistry panels, and microbial culture workups. The lab is equipped with Sysmex XN1000v veterinary hematology analyzer, Beckman AU480 chemistry analyzer, and Matrix assisted laser desorption ionization time of flight MALDI-TOF instrument for microbe identification. CPC is staff with American Society of Clinical Pathologist certified licensed Medical Technologists.
Tulane University TNBRC Unit of Collaborative Research Core Facility
Tulane University TNBRC Unit of Collaborative Research
Core serves as regional and national resource and center of excellence for biomedical research using Nonhuman Primate Models. Unit is staffed by personnel with expertise in veterinary medicine, research study design, budgeting, database management, IACUC issues, sample acquisition, processing, performing laboratory base assays and shipping.
Tulane University TNBRC Flow Cytometry Core Facility
Core provides analytical flow cytometry services and live cell sorting under enhanced Biosafety Level 2 conditions. Instruments available include six analyzers ranging from 4-30 color acquisition and three sorters using 1-,2-,4-way, and plate sorting between 6-18 colors. Provides experimental and panel design consultation. Provides continued education in seminar format and one-on-one sessions with user.
Tulane University TNBRC High Containment Research Performance Core Facility
TNBRC High Containment Research Performance Core
Tulane University TNBRC High Containment Research Performance Core
Provides full or partial support for researchers seeking to perform BSL3 and BSL2/BSL3 Select Agent studies and provides services for bacterial/viral culture and propagation, sample preparation, and processing of blood, BAL, single cell isolation, flow cytometry, and more. Offers project management assistance in study design, budgeting, and IACUC and IBC preparation. Our standard operating procedures have been tested to ensure consistent practices and have undergone rigorous quality assurance processes to ensure reproducibility. Offers assay services for qPCR, O ink Q100, Biorad Bioplex 200, Meso QuickPlex SQ120 Imager and Microscope Axio Observer.
Tulane University TNBRC Confocal Microscopy and Molecular Pathology Core Facility
TNBRC Confocal Microscopy and Molecular Pathology Core
Tulane University TNBRC Confocal Microscopy and Molecular Pathology Core
Core provides research support and training with molecular pathology skills, confocal microscopy, image analysis, and multicolor immunohistochemistry and in-situ hybridization techniques for internal and affiliate scientists. Services include assistance with experimental design, antibody selection, molecular probe selection, fixation and staining protocols, operating fluorescent and confocal microscopes, acquiring and storing imaging data, interpretation of results, and generation of publication-quality images. Image analysis services include assistance with capturing images for evaluation and with use of various image analysis software.
Tulane University TNPRC Pathogen Detection and Quantification Core Facility
TNPRC Pathogen Detection and Quantification Core
Tulane University TNPRC Pathogen Detection and Quantification Core
THIS RESOURCE IS NO LONGER AVAILABLE. SAME SERVICES ARE AVAILABLE IN Molecular Virology and Sequencing Core. Documented on January 28,2025. Core provides services for maintaining Specific Pathogen Free status in macaque breeding colonies. Services include antibody detection in serum or plasma by Luminex-based assays and /or ELISA for SPF-agents like SIV, SRV, STLV, B virus, SFV. CMV, RRV, SVV, SV40, and LCV, and non-SPF infectious agents like measles, Burkholderia pseudomallei, Tripanosoma cruzi, Mycobacterium tuberculosis, and SARS-CoV-2. Offers services of cytokines quantification, and molecular assays for detection of SRV, CMV, SFV, and RRV.Performs nucleic acid purification from blood and tissue samples as well as qPRC for SIV viral load in plasma, cells, or tissue.
Tulane University TNBRC Genetics and Genome Banking Core Facility
Tulane University TNBRC Genetics and Genome Banking
Core assists in design of breeding groups and monitors genetic diversity among colony breeding animals. Core is responsible for maintaining genome bank including DNA and cryopreserved primary fibroblast cell lines, including cell lines and DNA samples representing nearly 9,000 animals. Genotype data using NPRC standardized SNP array is available and whole genome sequence is available for over 520 animals. Genomic data is available via mGAP and can be integrated with physical resource and records by contacting the core. Targeted genotyping for new model development and specialized breeding is also available.
PRECISE Traumatic Brain Injury Model Catalog
PRE Clinical Interagency reSearch resourcE Traumatic Brain Injury Model Catalog
Platform for preclinical Traumatic Brain Injury model literature metadata. Model catalog to enhance reproducibility of preclinical TBI research by increasing ability to find and access preclinical TBI model papers.
Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat.
Brain Injury Knowledge Ontology Traumatic Brain Injury
Application ontology to formalize concepts and methods used in translational traumatic brain injury research. Multi species translational traumatic brain injury ontology to assist in formalizing concepts and methods used in traumatic brain injury research.
Software Python library for working with Resource Description Framework. Used for working with RDF which is standard model for data interchange on the Web.
Software Python package for image to image transformation in bioimaging applications. Can be used for semantic segmentation, instance segmentation, image restoration, image generation, and more.
Public-private partnership of universities, charities, and pharmaceutical and technology companies with core funding from Medical Research Council. Based at Oxford University, in the Department of Psychiatry, and have project sites at Swansea University and Cambridge University, we bring together expertise to enable breakthroughs in dementia research.
Mayo Clinic Medical Genome Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2026. Medical Genome Facility includes Cytogenetics Core, Genome Analysis Core and Proteomics Core. Available services include Sanger DNA sequencing, genotyping, gene expression and cytogenetic analysis, biospecimens accessioning and processing, tissue and cell molecular analysis, RNA interference, and oligonucleotide synthesis. Provides Illumina HiSeq2000 platforms and Pacific Biosciences RS single molecule real-time sequencer.Offers applied research services for development of innovative, personalized tests and treatments, especially with regard to biomarkers.
State University of Campinas Institute of Chemistry Microscopy Core Facility
UNICAMP - Institute of Chemistry - Microscopy Core Facility
UNICAMP Institute of Chemistry Microscopy Core Facility
Core offers services in advancing scientific research in the field of chemistry. Provides Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Confocal Laser Scanning Microscopy (CLSM), and Optical Microscopy. Offers sample preparation techniques, including ultramicrotome, ultracryomicrotome, and sputter coating,training and technical support.
Partnership for Interdisciplinary Studies of Coastal Oceans
Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO)
Academic consortium that conducts research to advance understanding of the coastal ocean within the California Current Large Marine Ecosystem and inform management and policy.
SDSC Center for Applied Internet Data Analysis
Center aimes at promoting greater cooperation in engineering and maintenance of global Internet infrastructure, better manage ever increasing volume of digitally based information including security and network data analysis. Provides open access data and tools.
Network of world class researchers and innovators to improve lives of people living in poverty by generating insights and tools for decision makers backed by rigorous, inclusive, and transparent research. Hub for research, training and innovation headquartered at University of California, Berkeley.
Provides advanced computing resources and services to support needs of UC San Diego research community. In addition, researchers from other academic institutions and industries can also participate in this research computing program. TSCC operates on two different computing models – Condo (a system purchase model) and Hotel (a pay-as-you-go model) to support broad range of research computing workloads including traditional HPC, HTC, and emerging big data pipelines.
The Project Production Systems Laboratory
UC Berkeley Project Production Systems Laboratory
Research institute dedicated to developing and deploying knowledge and tools for project management. Projects are temporary production systems. Dedicated to developing and deploying knowledge and tools for management of project production systems and the management of organizations that produce and deliver goods and services through such systems.
Provides research data and computing technologies, consulting, and community for the UC Berkeley campus to advance research through IT innovation.
Provides scholarly publishing and repository services that enable departments, research units, publishing programs, and individual scholars associated with University of California to have direct control over creation and dissemination of the full range of their scholarship.
Portal provides information about social science data.
University of California Medical Humanities Consortium
Faculty directors from UC Berkeley, UC Davis, UC Irvine, and UCSF support collaborative student research projects, publications, and resources with the aim to have substantial record of achievement and innovation pursued through allocated research funding to support humanism in medicine and health science education.
Library of ecosystems throughout California. Most of the state’s major habitat types are represented, from coastal tidepools to inland deserts, and lush wetlands to redwood forests.
Publishing house associated with University of California that engages in academic publishing. UC Press Foundation raises funds to uphold vital role as independent, nonprofit publisher, and receives philanthropic support.
University of California Santa Cruz Library
Library shares with other academic libraries commitment to intellectual freedom and access to information. This commitment is reflected in open stacks, active interlibrary loan service, online catalog, and Web site linked efficiently to other sites and databases. Has partnerships with libraries at other University of California campuses, local California State Universities, community colleges, and public libraries. Has active participation in California Digital Library.
Network for monitoring waves and beaches and prediction of waves and shoreline change along coastlines of United States. Since 1975 program has produced database of publicly accessible environmental data for use by coastal engineers and planners, scientists, mariners, and marine enthusiasts. Forefront of coastal monitoring, developing numerous innovations in instrumentation, system control and management, computer hardware and software, field equipment, and installation techniques. Operated by Ocean Engineering Research Group, part of Integrative Oceanography Division at Scripps Institution of Oceanography. CDIP measures, analyzes, archives and disseminates coastal environment data for use by coastal engineers, planners and managers, as well as scientists and mariners.
Consortium of UC San Diego organizations and number of partnerships including university collaborators, industry partners, fire departments, utilities, State’s CalOES and CPUC. Develops science driven technologies with fire management community using collaborative workflows integrating science and AI. Provides real time ﬁre modeling and predictions for ﬁreﬁghters. Harnesses emerging AI techniques to offer novel way to approach spatial heterogeneity and upgrading of data.
Collections include print and ebooks, newspapers, maps, photographs, art, historical archives, and other materials in physical and digital formats. Provides campuswide subscriptions to wide range of licensed resources, from journals and library databases to streaming media, clinical apps, and lab experiment videos. Offers access to UC collection as part of University of California.
New York Institute of Technology NYIT Visualization Center Core Facility
New York Institute of Technology NYIT Visualization Center
Core provides instruments including micro-computed tomography scanner, non-contact 3D optical profiler , and high powered workstations.
Broad Institute Imaging Platform Core Facility
Broad Institute Broad Institute Imaging Platform
Core to help users turn images into answers by offering assistance and training with open source image analysis tools, creating custom image analysis workflows, and creating custom software for image analysis when needed.
Software Python tool for viewing and downloading files from authorized European Genome-phenome Archive datasets. Python based EGA download client.
University of Connecticut Health Center for Cell Analysis and Modeling Microscopy Core Facility
University of Connecticut Health Center CCAM-Microscopy
CCAM Microscopy Facility provides access to equipment for quantitative fluorescence imaging applications. Instruments include laser scanning confocal microscopes equipped with 34 channel highefficiency QUASAR detectors. One of these microscopes supports nonlinear optical excitation, fluorescence correlation spectroscopy, and fluorescence lifetime imaging microscopy. Additionally, there is a light sheet microscope available for micro/mesoscale 3D imaging. The Zeiss Elyra 7 microscope is capable of total internal reflection fluorescence microscopy and supports several super resolution techniques such as lattice structured illumination microscopy, stochastic optical reconstruction microscopy, 3D photoactivated localization microscopy, and DNA points accumulation for imaging in nanoscale topography.
Software open-source, cloud-optimized pipeline developed in collaboration with members of the BRAIN Initiative (BICCN and BICAN Sequencing Working Group) and SCORCH. It supports the processing of 10x single-nucleus data generated with 10x Multiome ATAC-seq (Assay for Transposase-Accessible Chromatin), a technique used in molecular biology to assess genome-wide chromatin accessibility.
Leica | LMD7 Laser Microdissection microscope
Laser Microdissection system enables users to isolate specific single cells or entire areas of tissue. Powered by unique laser design and dynamic software, Leica LMD systems allow users to easily isolate Regions of Interest from entire areas of tissue down to single cells or even subcellular structures such as chromosomes. LMD7 provides higher laser power. Suited to dissect any kind of tissue independent of its size or shape.
Leica | LMD6 Laser Microdissection microscope
Laser Microdissection system enables users to isolate specific single cells or entire areas of tissue. Powered by unique laser design and dynamic software, Leica LMD systems allow users to easily isolate Regions of Interest from entire areas of tissue down to single cells or even subcellular structures such as chromosomes. Leica LMD6 is for standard tissue dissection. Used for standard applications dissecting soft tissues such as brain, liver, or kidney.
Leica | STELLARIS 8 DIVE multiphoton microscope
Multiphoton microscope provides flexible multicolor imaging beyond 1 mm in depth with spectrally tunable non-descanned detector to define up to four detection bands simultaneously or unlimited number when imaged sequentially. Possible fluorophore combinations to study complex processes, such as neuronal connectivity, organ structure, dynamic interactions, or spatial relationships of cells and proteins in much more detail.
Microscope, functional imaging, investigate cellular physiology,dynamics in living cells, video rate lifetime imaging acquisition,
Leica | STELLARIS 8 FALCON FLIM microscope
STELLARIS 8 FAst Lifetime CONtrast Fluorescence Lifetime Imaging Microscope
Microscope for functional imaging. Used to investigate cellular physiology and to explore dynamics in living cells. Enables video rate lifetime imaging acquisition for rapid kinetic studies in live cells. Adds new dimension of contrast to imaging for biosensing and tracking of interactions between proteins.
Leica STELLARIS 8 CRS Coherent Raman Scattering microscope
STELLARIS 8 CRS Coherent Raman Scattering microscope
Microscope enables to implement label free chemical imaging. Used to study structures that cannot be visualized with traditional fluorescent microscopy methods.
Leica STELLARIS 8 Stimulated Emission Depletion microscope
Microscope for imaging beyond the diffraction limit to obtain 2D and 3D nanoscopy results in no time with astounding image quality and resolution, while protecting sample. STED super resolution allows you to study multiple dynamic events simultaneously.
STELLARIS 5 microscope has core system with integrated WLL, combined with proprietary Acousto-Optical Beam Splitter and Power HyD S detectors. Together with the TauSense technology, STELLARIS 5 sets a new standard for the quality of images and quantity of information generated. Imaging with user interface, ImageCompass.
STELLARIS 8 microscope with core system addition of spectrum WLL and specialized detector options of Power HyD family to expand range of confocal applications. Can be combined with all Leica Microsystems modalities, including FAst Lifetime CONtrast (FALCON), Deep In Vivo Explorer (DIVE), STED, Digital Light Sheet (DLS) and CARS. STELLARIS 8 new features maximize the potential of these modalities.
Software tool for analyzing kinesiological data obtained from Noraxon Ultium EMG system, as well as older Noraxon legacy electromyography systems. Enables detailed insight for performance enhancement, injury prevention, and neuromuscular biofeedback.
Software application used to collect, store, view, and analyse all necessary data from the Brite Family devices, PortaMon, PortaLite, OctaMon and OxyMon developed by Artinis Medical Systems and highly customisable to individual requirements.
Software to scientifically analyse Wattbike sessions on Windows PC or Laptop, while Power Cycling is perfect for group training in health clubs and gyms.
Shaker for cultivation of microorganisms and cell cultures provides homogeneous conditions for cultivation up to 63 liters or 23 000 batches in parallel in less than square meter of space.
Climate Engine App is no-code solution for on-demand cloud computing and visualization of climate and satellite Earth Observation data. Provides rainfall, maximum and minimum temperature daily data.
Connectivity hub across medical genetics domain. Network of genomic information. Supports all vendors and workflows and thus enables any genetic professional to deliver more accurate, more actionable data insights.
Leica | STELLARIS 5 Cryo Confocal Light Microscope
STELLARIS 5 Cryo Confocal Light Microscope
Confocal light microscope system to target area of interest for cryo-electron tomography.
MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells.
Software suite for interactive data visualization and analysis. Python based desktop application using PyQt6 library for data visualization and analysis.
Open and extensible platform to retrieve, visualize and analyse 3D morphology.Extension to import microCT data and conduct 3D morphometrics in Slicer. Used for data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans, all within the 3D Slicer application.
Software R package for custom visualizations and functions for streamlined analyses of single cell sequencing.
NovoExpress software enables sample acquisition and analysis. User hands-on time is minimized with the walk-away autosampler functionality as well as batch analysis, statistics, and reporting.
University of Massachusetts Lowell Microscopy Core Facility
University of Massachusetts Lowell UML - Microscopy Core Lab
Core offers micro-imaging and micro-analysis solutions by providing access to several photon-, scanned probe-, ion beam-, and electron beam-based imaging and analytical instruments, services, and technical expertise for characterization of materials including nano-engineered materials, microelectronics, photonics, biomaterials, and others with applications in life sciences, drug discovery, environmental and energy research. Consultative services are also available.
Seattle Children's Research Institute Micro Computed Tomography Imaging and Visualization Lab Core Facility
SCRI Micro Computed Tomography Imaging and Visualization Lab
Shared instrument facility that has a Bruker Skyscan 1272 ex-vivo microCT that is capable of X-ray imaging at sub-microb resolution. The instrument can optionally be equipped with a 16-sample sample changer to automate the scanning queue. Core provides visualization and image analysis support for researchers, using open-source 3D Slicer biomedical imaging suite.
Tulane University TNPRC Virus Characterization, Isolation, Production and Sequencing Core Facility
Tulane University TNPRC Virus Characterization
THIS RESOURCE IS NO LONGER AVAILABLE. SAME SERVICES ARE AVAILABLE IN Molecular Virology and Sequencing Core. Documented on January 28, 2025. Core is divided into virus characterization, isolation, and production part and next generation sequencing part. Virus Characterization, Isolation and Production component provides virus expansion and characterization, viral titer by plaque and TCID50 assays, live virus neutralization and inhibition assays at both BSL-2 and -3 level including SARS-CoV-2. Next Generation Sequencing component provides expertise in next generation sequencing and genomic services including whole genome, epigenetics, targeted amplicons, and 16S metagenomics.
Tulane University TNBRC Vector Borne Infectious Disease and Diagnostic Parasitology Core Facility
TNBRC Vector-Borne Infectious Disease and Diagnostic Parasitology Core
Tulane University TNPRC Vector Borne Infectious Disease and Diagnostic Parasitology Core
Tulane University TNPRC Vector-Borne Infectious Disease and Diagnostic Parasitology Core
Tulane University Tulane National Biomedical Research Center Vector Borne Infectious Disease and Diagnostic Parasitology Core
Vector-Borne Infectious Disease and Diagnostic Parasitology
Vector Borne Infectious Disease core produces tick vectors for research on Lyme disease and other tick borne diseases. Diagnostic Parasitology component provides diagnostic services to clinical veterinarians and core and affiliate investigators when parasitic diseases are suspected in resident nonhuman primates. Services for affiliate investigators include blood parasite detection via microscopic examination of prepared blood smears and quantitative buffy-coat analysis, and intestinal parasite detection via microscopic examination of direct wet mounts, zinc sulfate flotation prepared slides, or parasite specific assays.
Software Python based app for analyzing polarization resolved microscopy data to measure molecular orientation and order in biological samples.
Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering.
Software R package as visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.Used for graphical display of correlation matrix, confidence interval. Contains some algorithms to do matrix reordering. Good at details, including choosing color, text labels, color labels, layout, etc.
NIMP: Neuroanatomy-anchored Information Management Platform for Collaborative BICAN Data Generation
Web application that tracks the status of the BICAN consortium tissue samples and related data.NIMP is developed under NIH BRAIN Initiative's BICAN U24MH130988 award as a part of the coordinating unit for biostatistics, informatics, and engagement (CUBIE) for the BRAIN Initiative Cell Atlas Network (BICAN) program.NIMP consists of two portals for BICAN collaborative data generation: the Specimen Portal and the Sequence Library (SeqLib) Portal. The Specimen Portal focuses on tissue management from donors to brain slabs and annotated brain samples. The SeqLib Portal manages the workflow starting from tissue, all the way downstream to track data deposition to assay-dependent, data-modality-specific archives. Both portals work in tandem to generate multimodal genomic data that can be traced back to their anatomical origins using the Allen Brain Atlas. The portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting. All of the underlying functionalities are achieved through a robust agile development strategy using NHash resource identifiers, metadata standardization, active combinatorial dashboarding, resource provenance linkage and rendering (e.g. Sankey diagrams), and dedicated interfaces with NIH Neuro Biobank, sequencing centers, NeMO, and the larger BICAN data ecosystem.
and End Results Cancer Statistics Review
National Cancer Institute SEER Cancer Statistics Review
Platform to report outlining trends in cancer statistics and methods to derive various cancer statistics from the Surveillance, Epidemiology, and End Results (SEER) program. Authoritative source for cancer statistics in the United States.
NCI Lymphoid Neoplasm Recode 2020 Revision Definition
Lymphoid Neoplasm Recode 2020 Revision Definition
National Cancer Institute Lymphoid Neoplasm Recode 2020 Revision Definition
NIH NCI Lymphoid Neoplasm Recode 2020 Revision Definition
Website describing International Classification of Diseases codes that corresponds to lymphomas in the Surveillance, Epidemiology, and End Results (SEER) registry.
NCI Site Recode ICD-O-3/WHO 2008 Definition
National Cancer Institute Site Recode ICD-O-3/WHO 2008 Definition
Website describing International Classification of Diseases-Oncology codes that corresponds to different cancer sites in the Surveillance, Epidemiology, and End Results (SEER) registry.
Software Python package to predict metabolite mediated cell-cell communications by single-cell RNA-seq data. Used for inferring metabolite, such as lipid, mediated cell-cell communication events using single-cell RNA-seq data.
Portal provides everything needed to start using Planet services. Planet Application Program Interface to retrieve Planet Labs PBC's satellite images and products.
Software application for predicting protein functions from protein sequences using deep neural networks combined with sequence similarity based predictions.
Web application to find and extract open reading frames (ORFs). Used to find and output sequences of open reading frames in one or more nucleotide sequences.
Epithelial Mesenchymal Transition Gene database
Database to establish comprehnsive gene resource for epithelial-mesenchymal transition.
Simple Insight Segmentation and Registration Toolkit
Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms.
Software package for digital image analysis. Used to search for optimal methods for image classification and segmentation. Computes shape, color and texture descriptors of arbitrary regions of interest. Color analysis includes RGB, CMY, HSY, YIQ, YUV, CIELab and CIEXYZ models. Texture feature extraction algorithms include co-occurrence matrix, run-length matrix, autoregression model, brightness distribution statistics, local binary patterns, histogram of oriented gradients, Haar and Gabor transforms. Enables calculation of morphological features such as moments of inertia, Feret diameters, ratios of Danielson, Blair-Bliss or Malinowska, and many others. Implements algorithms of discriminant analysis and data classification such as linear discriminant analysis, mutual information, convex decision boundary and support vector machines.
System consists of hardware and software for assessment of motor performance and motor learning in mice. Hardware includes two goal boxes with horizontal ladder in between. Touch sensitive rungs of the ladder make it possible to measure step durations and step types. ErasmusLadder software controls experiments by sending protocol and start command to apparatus. Sessions are performed automatically, and afterwards, data is sent back to software for storage and analysis.
System designed to facilitate behavioral observations in home cage environment. Instrumented observation cage to measure and test behavior of laboratory rodents. Device comes with PhenoTyper top unit which included lighting and camera, both powered by EthoVision XT, and range of optional sensors and stimuli.
Open source software tool providing automated analysis of foci images including foci counting and colocalization of foci. Focinator v2-0 is able to perform multi channel analysis of four channels and evaluation of protein-protein colocalization by comparison of up to three foci channels. This enables for example the quantification of foci in cells of specific cell cycle phase.
Software Python package to arbitrarily combine and subset datasets, while ensuring dataset integrity and automatically updating their description and other provenance for neuroscience and neuroimaging applications where each sample needs to be uniquely identified . Container data structure to encapsulate machine learning dataset with all the key info necessary.
Software R package for use in microbiome analysis. Used to provide comprehensive collection of tools and tutorials, with particular focus on amplicon sequencing data.
Center for Sudden Unexpected Death in Epilepsy Research
NIH funded center to provide system for sharing multimodal epilepsy data for Sudden Unexpected Death in Epilepsy. Modality Epilepsy Data Capture and Integration System (MEDCIS) is cross cohort query interface for SUDEP (Sudden Unexpected Death in EPilepsy) research.
Software interface to use R from Python.
Software R package for high-throughput toxicokinetics. Pre-made models that can be rapidly tailored to various chemicals and species using chemical specific in vitro data and physiological information. Used for prediction toxicokinetics (chemical absorption, distribution, metabolism, and excretion by the body).
Web tool for translation of nucleotide sequence to protein sequence.
Upright microscope platform for Life Science Research. System platform tailored to materials analysis tasks. System features include Universal stand transmitted-light; Motorized: luminous field stop; Light manager;Contrast manager; Motorized z-drive with 25nm step size; Reflected-light beam path; ACR for objectives; Apotome 3; 2- und 3-plate scanning stages; 2 TV tube motorized; Automatic image acquisition and analysis; 3D Imaging; Medium sample throughput; Multi-user environment.
Electrically controlled pneumatic microinjector designed to deliver and aspirate extremely small, precise volumes of liquid or gas (picoliters to microliters). It is primarily used in biological and medical research labs for microinjection into cells, transgenic organism creation, and patchingMulti-functional, motor-driven injector for precise control of small volumes.
Leica | Angle Two Computer Assisted Stereotaxic System
Leica Angle Two™ Computer-Assisted Stereotaxic System
System used for stereotaxic surgery on small animals (mice and rats).
Philips | FEI CM120 BioTwin Transmission Electron Microscope
Philips/FEI CM120 Bio Twin Transmission Electron Microscope
Transmission electron microscope with maximum acceleration voltage of 120 kv.Microscope primarily used for sample screening.
Emerson | Branson Digital Sonifier SFX250
Branson Sonifier ultrasonic cell disruptor / homogenizers are versatile laboratory units suitable for broad range of liquid processing applications. Digital sonifier to disrupt cells, bacteria, spores, or tissue. Ideal for initiating and accelerating chemical, biochemical, and physical reactions, and for degassing liquids. Used to prepare emulsion to 0.01 micron, homogenize immiscible liquids, polymerize some materials, and depolymerize others.
University of Nebraska Lincoln Flow Cytometry Core Facility
Provides flow cytometry services. Instruments include Beckman Coulter CytoFLEX SRT sorter and CytoFLEX LX, as well as NanoAnalyzer from NanoFCM. Facility staff are able to assist with everything from experimental design, instrument training, sample collection, and data analysis.
Software application for scanning sample specific miRNA regulation from bulk and single cell RNA sequencing data.
Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.
This repository contain the source code for the denoising of SR-SIM images.
Machine Learning Cumulative Performance Score for Classification Problems
MLcps: Machine Learning Cumulative Performance Score for Classification Problems
Machine Learning Cumulative Performance Score (MLcps), a novel evaluation metric for classification problems. MLcps integrates several pre-computed evaluation metrics into a unified score, enabling a comprehensive assessment of the trained model's strengths and weaknesses. We tested MLcps on four publicly available datasets, and the results demonstrate that MLcps provides a holistic evaluation of the model's robustness, ensuring a thorough understanding of its overall performance.
ToxCodAn-Genome is a computational tool designed to annotate toxin genes in genomes of venomous lineages.
X-omics ACTION demonstrator multi-omics analysis workflow
Software application as multi-omics data analysis workflow. Comprises genome-wide DNA methylation, targeted metabolomics and behaviour data pre-processing, and integrative analysis methods. Individuals of a cohort are clustered using Similarity Network Fusion (SNF), latent feature dimensions are uncovered using different unsupervised methods including Multi-Omics Factor Analysis (MOFA) and Multiple Correspondence Analysis (MCA), and correlations between -omics and phenotype dimensions are determined in downstream analyses including results visualisation.
Software scalable cloud based pipeline that performs microbial calling for single cell RNA sequencing data, enabling meta analysis of the single cell host microbial studies from AWS Open Data and other public domain.
Web tool for CD4 TCR specificity prediction and biology applications. Used for accurate prediction of CD4 T cell receptor binding specificity through transfer learning and ensemble approach. Repository comprises codes of Pep2TCR, providing comprehensive guidance for researchers interested in Pep2TCR.
Portal for discussion of scientific matters relating to use of home cages to behavioural research in laboratory animals, including experimental procedures, use of equipment, problem solving, ethical considerations, job offers and advertisement of community events.
University of Chicago MRI Research Center Core Facility
University of Chicago MRI Research Center
MRI Research Center houses magnetic resonance scanners and highly qualified experienced staff for support of research projects with MR imaging component.
Software tool that analyzes, compares and validates analysis and reanalysis datasets with observed dataset using statistical tests such as Mann Whitney (U-test), t-test, F-test, Root Mean Square Error (RMSE), correlation coefficient, BIAS, normalized BIAS, trend, scatter index and maximum anomalies.
Early Postnatal Developmental Mouse Brain Atlas
Suite of open access resources including 3D atlases of early postnatally developing mouse brain and mapped cell type density growth charts, which can be used as standalone resources or to implement data integration. Web platform can be utilized to analyze and visualize the spatiotemporal growth of GABAergic, microglial, and cortical layer-specific cell type densities in 3D. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system with an isotropic resolution of 20 μm (XYZ in coronal plane). Average transformations were conducted at 20 μm voxel resolution by interpolating high resolution serial two photon tomography images from primarily Vip-IRES-Cre;Ai14 mice at postnatal (P) ages P4, P6, P8, P10, P12, and P14. For all ages, anatomical labels from the P56 Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) were iteratively down registered to each early postnatal time point in a non-linear manner, aided by manual parcellations of landmarks in 3D, consistent with the Allen Mouse Reference Atlas Ontology.
Special orbital shaker for shaking two or four microtiter plates.
American Community Survey is annual demographics survey program conducted by the U.S. Census Bureau. American Community Survey releases new data every year through variety of data tables. Provides information about other special datasets, such as the ACS Experimental Data, ACS Summary File, and ACS Public Use Microdata Sample files.
Hematological Malignancy Research Network
Network provides information about leukaemias, lymphomas, myelomas, and related blood disorders. The statistics are based on data from the UK, and use the World Health Organization’s Classification for Oncology (ICD-O-3) which currently recognises over 100 different haematological malignancy subtypes.
Open source Python toolbox that facilitates the implementation of multi analysis dynamic Functional Connectivity assessment using MRI data.
Public research university in Boise, Idaho. Founded in 1932 by the Episcopal Church, it became independent junior college in 1934 and has been awarding baccalaureate and masters degrees since 1965. It became public institution in 1969.
Software tool to enhance Genome Wide Association Studies for diverse cohorts by addressing challenges associated with analyzing admixed populations. Admixed populations are often excluded from genomic studies due to concerns about how to properly account for their complex ancestry.Tractor facilitates the inclusion of admixed individuals in association studies by leveraging local ancestry, allowing for finer resolution in controlling for ancestry in GWAS, and empowering identification of ancestry-specific loci.
Portal dedicated to characterizing, discovering and defining rare and atypical forms of diabetes. Network of universities, hospitals and clinics across the United States dedicated to better understanding atypical diabetes. Team of academic institutions and scientists collaborates with physicians and healthcare groups to identify those with atypical diabetes and learn more about their health.
Boise State University Fabrication, Characterization, and Testing Core Facility
Core contains instrumentation and expertise for fabrication, characterization, and testing of biomedical devices, sensors, and systems. Core administratively combines 4 existing engineering cores: the Idaho Microfabrication Laboratory (IML); Boise State Center for Materials Characterization (BSCMC); Research Machining and Engineering (RME) center; and Biomechanics and Mechanobiology (BMMB) facility.Offers variety of instruments including 3D printers, deposition and photolithography tools, profilometers, SEM, TEM, light microscopy, confocal microscopy, cell culture. Offers services including design, machining, imaging, etc.
University of Massachusetts Lowell Nanofabrication Lab Core Facility
University of Massachusetts Lowell UML - Nanofabrication Lab
Core features 4,200 ft2 Class 100 clean room equipped with over 40 pieces of process and analytical instrumentation for complex research projects that require micro and nano scale fabrication.
University of Pennsylvania Bollinger Digital Fabrication Laboratory Core Facility
University of Pennsylvania UPenn-Bollinger Digital Fabrication Laboratory
UPenn-Bollinger Digital Fabrication Laboratory
Provides fabrication services and consultations contributing to innovation in teaching, learning, research, and clinical care at the University of Pennsylvania.
Stanford Cryo-Electron Microscopy Center Core Facility
Stanford Cryo-Electron Microscopy Center
Stanford Cryo-Electron Microscopy Center (cEMc)
Core enables macromolecular structure determination, mechanistic investigations, and drug discovery through cryo-electron microscopy. Services include High-resolution data collection for single-particle analysis (SPA), soft-matter research, and tomography; High-throughput cryo sample screening and collection of diagnostic small data sets; Screening negatively stained samples; Training and various levels of assistance for diverse experimental designs, including sample preparation, negative stain screening, and equipment operation; Full-service option for screening and data collection.
Laminar Flow Hood offer ISO Class 5 clean air product protection for USP 797 sterile non-hazardous drug compounding applications in pharmacy, microbiology labs, and agricultural research. Hood can be used where clean airflow per ISO 14644-1 is required to prepare injectable drugs, IV solutions, tissue culture, optics, microelectronics, and more. All workstations use ultra high efficiency motor to provide robust 90 FPM (0,46 m/s) laminar flow of HEPA filtered air to work zone composed of stainless steel walls and work surface made of stainless steel on PVC core.
Software R package as object for simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers.
Software R package to provide orthology mappings between species, based on NCBI Gene IDs and NCBI orthology mappings.
Software application for linear support vector classification. Used in classification problems.
Software tool to classify single cell RNA-Seq data across platforms and across species.
Software tool as supervised cell type identifier that accurately predicts cell identity for newly sequenced single cells.
Software R package to create and manipulate functions commonly used during modeling e.g. fitting the model, making predictions, etc.
Web server for predicting and designing interferon gamma inducing epitopes. Users are allowed to paste or upload file with multiple peptide sequences and each sequence would be predicted according to model selected. Used to predict IFN-gamma inducing peptide/epitope in set of peptides or peptide library.
Web server to predict IL-10 inducing peptides, where users are allowed to paste or upload file with multiple peptide sequences and each sequence would be predicted according to model selected. Used to design, discover and mapping of peptides that may induce IL-10.
Software application provides simple MATLAB commands for creating and interconnecting layers of deep neural network.
University of Calgary Live Cell Imaging Laboratory Core Facility
Snyder Institute- Live Cell Imaging Laboratory
University of Calgary Snyder Institute- Live Cell Imaging Laboratory
Offers advanced imaging technology, as well as training and support personalized to their imaging goals and experience. Provides Technology access and training; Assisted imaging and coaching at every step of the imaging workflow, from sample preparation to data analysis; Pilot experiments and feasibility testing; Developing custom image analysis pipelines; Image analysis consultation and training; Developing and testing new instruments and devices; Full scientific and technological collaborations and partnerships; Offsite coaching, assistance and consulting ; Collaborative projects in academic, health and allied industrial sectors;
University of Maryland School of Medicine Translational Genomics Laboratory Core Facility
UMSOM-Translational Genomics Laboratory (TGL)
University of Maryland Medical Center Midtown Campus Translational Genomics Laboratory
University of Maryland Medical Center Midtown Campus Translational Genomics Laboratory Core Facility
University of Maryland Medical Center Midtown Campus UMSOM-Translational Genomics Laboratory (TGL)
University of Maryland Medical Center Translational Genomics Laboratory
Core provides range of genomics technologies to support basic, translational, and clinical research.Services support basic research. Clinical assays offered are similar to those offered to support basic research, except that these assays are validated under CLIA, enabling them to be used in clinical decision making process in research protocols and for routine patient care.
Software tools for interactive viewing and fast sharing of large image data. Comprises Minerva Author, a tool to create and annotate images, and Minerva Story, a narrative image viewer for web hosting. Used for interpreting and interacting with complex images, organized around guided analysis approach. Enables fast sharing of large image data that is stored on Amazon S3 and viewed using zoomable image viewer implemented using OpenSeadragon, making it ideal for integration into multi-omic browsers for data dissemination of tissue atlases.
Software toolkit for analyzing spatial molecular data. Underlying framework is generalizable to spatial datasets mapped to XY coordinates. Package uses anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. Python based implementation efficiently deals with large datasets of millions of cells.
Software C toolkit for alignment free and spatial temporal analysis of multi-FASTA data. Used for entangling presence of multiple sequences from epidemic and pandemic events.
Web application to transform Nutil outputs and plots it on mouse anatomical heatmap.
NCI Center for Cancer Research Genomics Core Facility
National Cancer Institute Center for Cancer Research Genomics Core
NCI Center for Cancer Research Genomics Core
Core provides access to genomic technologies and Next-Generation Sequencing. Provides DNA and RNA quality control services, user accessible instrumentation, training, consultation services, bioinformatics support, and secure data delivery management.
Japanese multi omics reference panel. Provides multidimensional approach to diversity of Japanese population. Public database for plasma metabolome and proteome analyses. Updated to metabolome, genome, transcriptome, metagenome, number of samples, analysis methods of each dataset, expanding links between each layer and links between hierarchies.
JOint Spherical registration and Atlas building
Software tool for joint surface based registration and atlas construction of brain geometry and function.Cortical registration framework that jointly models mismatch between geometry and function while simultaneously learning unbiased population specific atlas.
Software pipeline for annotating predicted Nucleotide binding and leucine rich repeat genes from non-masked genome fasta file input.
Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats.
Software application to integrate scRNA-seq and scTCR-seq data to allow for more comprehensive analysis that leverages the strengths of both data types.Repository contains code and information of data used in the paper “scNAT: A deep learning method for integrating paired single cell RNA and T cell receptor sequencing profiles”. Source code for scNAT are in the scNAT folder, the tutorial is in the tutorials folder.
American Museum of Natural History Microscopy and Imaging Core Facility
American Museum of Natural History Microscopy and Imaging Facility
Shared instrumentation facility at the American Museum of Natural History with tools for X-ray tomography, electron microscopy, confocal microscopy, light microscopy and image analysis. Provides expert assistance in the use of all lab equipment.
University of Manchester Mass Spectrometry and Separations Core Facility
Core is part of the University of Manchester Faculty of Science and Engineering. Facility offers support and services in chemistry, biology and materials. Mass spectrometers including Orbitraps, Ion Mobility, MALDI, DESI, hyphenated LC-MS and GC-MS apparatuses. Other instruments are HPLC systems, UHPLC systems and GC systems.
Van Andel Institute Bioinformatics and Biostatistics Core Facility
VAI Bioinformatics and Biostatistics Core
Van Andel Institute VAI Bioinformatics and Biostatistics Core
Core provides bioinformatics and statistics expertise. Core develops and maintains automated and customizable workflows for processing and analyzing many types of genomic data; supports design of rigorous, robust and reproducible experiments and proposals; assists in preparation of manuscripts, grants and presentations; and provides education and training in use of software and analysis methods.Core can contribute to many types of bioinformatics or statistical projects.
University of Chicago PaleoCT Core Facility
Core utilizes dual tube micro X-ray computed tomography scanner for imaging specimens in fields of paleontology, comparative anatomy, evolution and development, basic biomedical studies, and research in geology and material sciences.It is equipped with 180 kV nano-focus and high power 240 kV micro-focus CT tube. This setup allows to scan very small specimens with high resolution using nano tube or dense fossils using high power tube.
Open source platform to support management of educational audio and video content. Institutions can use Opencast to produce lecture recordings, manage existing video, serve designated distribution channels, and provide user interfaces to engage students with educational videos.
Software tool for microsatellite instability detection using high throughput sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region sequencing data as input. Introduces multinomial distribution model to quantify polymerase slippages for each tumor sample and discriminative sites selection method to enable MSI detection without matched normal samples.
Software application to estimate presence of MRD in plasma cfDNA WGS through evaluation of matched tumour-derived mutations (SNVs or CNVs).
Software tool for annotating fusion transcripts, incorporated into Trinity Cancer Transcriptome Analysis Toolkit utilities, and leveraging databases including CTAT Human Fusion Lib.
Software tool that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. Used to simultaneously segment genome, predict large scale copy number alterations, and estimate tumor fraction of ultra low pass whole genome sequencing sample.
University of Luxembourg LCSB Metabolomics, Lipidomics and Proteomics Platform Core Facility
LCSB Metabolomics and Lipidomics Platform
LCSB Metabolomics Lipidomics and Proteomics Platform Core Facility
The Metabolomics, Lipidomics, and Proteomics Platform facilitates metabolism-related and molecular research, serving researchers from academia and industry in Luxembourg and beyond. We specialize in the comprehensive analysis of small molecules and proteins within complex biological matrices. Our advanced analytical infrastructure and broad method portfolio accelerate scientific discoveries across biology, biomedicine, and systems biology.
Software finite element analysis package. Used to solve field problems.
Feature-specific Information Transfer scripts
Software application as MATLAB scripts to compute measures of Feature-specific Information Transfer (FIT) and conditional FIT (cFIT). FIT quantifies direction and magnitude of information flow about specific feature S (such as feature of sensory stimulus) between simultaneously recorded brain regions X and Y. cFIT quantifies amount of directed feature information transmitted between regions X and Y that cannot be potentially routed through region Z.
Software code package associated to the paper: Lemke et al. Information flow between motor cortex and striatum reverses during skill learning. 2023. Quantifies information theoretic quantities used in the associated study.
Web service for online data drawing and analysis, personalized data analysis, scientific research mapping, online page/database development and hosting. Used for high throughput sequencing data analysis including eccDNA-seq, MeRIP-seq, circRNA-seq, miRNA-seq, mRNA-seq, LncRNA-seq, piRNA-seq, ChIP-seq, etc.
Louisiana State University in Shreveport Research Core Facility
Core provides access to research services, educational and training opportunities, and technologies including cellular metabolism, flow cytometry, fluorescence, confocal, super resolution confocal microscopy, next generation sequencing, and real-time PCR. Provides assistance with all aspects of these technologies, including experimental design, protocol optimization, instrument operation, and data analysis.
Louisiana State University in Shreveport Animal Models and Histology Core Facility
Louisiana State University in Shreveport Animal Models and Histology Core
Core provides services for mouse genotyping and tissue histology, access to tools for analyzing cardiovascular function, data analysis, expertise and training. Services include genotyping using PCR or RT PCR, histology services with tissue processing, paraffin-embedding and sectioning, along with several cardiovascular relevant histological stains such as Picrosirius Red and Masson Trichrome.
Louisiana State University in Shreveport Small Animal Imaging Core Facility
Louisiana State University in Shreveport Small Animal Imaging Facility
Core provides imaging support to investigators who use small animal models in their research. Offers bioluminescence and fluorescence imaging, X-ray imaging, computed tomography, and positron emission tomography. Core provides imaging support services for investigators, including assistance in experimental design, conducting animal studies including anesthetization and imaging acquisition, and processing and interpreting imaging data.
Louisiana State University in Shreveport Redox Molecular Signaling Core Facility
Facility includes Analytic Redox Biology and Molecular Signaling Sub-Cores. Provided services include measurements of reactive oxygen species, reactive nitrogen species, reactive sulfide species, protein, peptides, metabolites, and lipids in cell culture and tissue samples. High-performance liquid chromatography systems, coupled with UV-vis and fluorescence detectors to quantify cellular and mitochondrial superoxide production, hydrogen sulfide pools (free sulfide, sulfide bound to transitional metals, and sulfane sulfur), and thiols (glutathione, GSH/GSSG, cysteine, cystine, homocysteine, persulfides, and glutathionylation).Instruments include Sievers NO Analyzer (NOA 280i, GE), Agilent 8890 GC and 8335 sulfur chemiluminescence detector ,Thermo Scientific Orbitrap Exploris 480 and SCIEX Triple Quad 7500 mass spectrometer. Molecular Signaling Sub-Core offers services for molecular cloning and site-directed mutagenesis, design and production of vectors for CRISPR/Cas9 modification of vascular cells, services for endothelial, smooth muscle, and cardiac myocyte cell isolation, for generation of vascular cell lines, and for lentivirus production for transient or stable modification of cardiovascular cells, access to equipment and expertise for studying cellular effects of hypoxia/reoxygenation injury (Coy Hypoxic Chamber, CLARIOstar Spectrofluorometer), for automated capillary Western blot analysis (ProteinSimple Jess Simple Western), and for high-resolution fluo-respirometry to study mitochondrial function (Oroboros O2k modular system).
Louisiana State University in Shreveport CAIPP Bioinformatics and Modeling Core Facility
Core supports data analysis, network modeling, and data science research. Provides training and education opportunities.
Cincinnati Children's Hospital Bionutrition Research Core Facility
Cincinnati Children's Hospital Bionutrition Research Facility
Facility works with investigators to obtain and analyze high-quality nutrition and body composition data from study participants. Staff and facilities are located in the Schubert Research Clinic at Cincinnati Childrens Hospital. Core provides diet assessment services.
Louisiana State University in Shreveport CAIPP Immunophenotyping Core Facility
Immunophenotyping core provides services for isolation of cellular populations from tissues, automated quantification of cell numbers, quantification of GFP, DAPI, RFP, Cy5 or Cy7 positive populations, automated quantification of cytokine concentration in supernatants and biological samples, and flow cytometric and microscopic assay development and execution.Provides training and education opportunities.
Company for development, manufacture, sale and provision of solutions for biological microscopes, industrial microscopes, industrial endoscopes, non-destructive inspection equipment, X-ray analyzers, etc.
Flexible system that supports various slide sizes, different objectives, SILA optical sectioning device, oil dispenser, cameras, loaders, and LED/laser light sources with multiple filter sets. VS200 supports brightfield, darkfield, polarization, phase contrast, and fluorescence, with possibility to scan sample using multiple techniques at the same time. VS200 software supports offline analysis, deep learning, 3D deconvolution, and batch conversion to standard file formats. It also supports the NIS-SQL database for data management and the DICOM format for easy integration into lab information management system.
University of Manchester Services and Equipment Core Facility
Core to build partnerships with government, National Facilities, industrial and academic stakeholders at Harwell and beyond, to jointly address challenges set by UK’s Industrial Strategy through research and to discover and develop innovative techniques and technologies to enhance facility science, data analytics and workplace safety.
University of Manchester X-ray Diffraction Platform Core Facility
University of Manchester X-ray Diffraction Platform
Core to bring together community of knowledge and best practise from three Faculty of Science and Engineering Departments: Chemistry, EES and Materials. Provided equipment is housed across numerous parts of campus with bulk being operated from Engineering Building A and Chemistry. Offers technical expertise in techniques such as residual stress analysis, texture analysis, phase identification in crystalline and semi crystalline powders and solid materials, single crystal and small angle scattering. Machines are available for examination of both small specimens and large components, and for wide range of materials.
University of Manchester Magnetic Resonance and Related Technology Platform Core Facility
University of Manchester Magnetic Resonance and Related Technology Platform
Core is equipped with instrumentation supporting areas of NMR, EPR and related techniques.
University of Manchester Corrosion and Materials for Demanding Environments Core Facility
Corrosion and Materials for Demanding Environments
Core includes facilities and techniques, supporting exploration of this unique research space. Provides expertise and services for advanced materials and interdisciplinary research activity.
University of Manchester Biochemical and Biophysical Sciences Technology Platform Core Facility
University of Manchester Biochemical and Biophysical Sciences Technology Platform
Core includes range of facilities that support all biological related activity in Faculty of Science and Engineering. We work at the interface of physical sciences, engineering and biology and provide major link to facilities in Faculty of Biology, Medicine and Health. Supports research activities in areas that include physical understanding of biological systems, engineering biomolecules and biological processes, biomaterials and environmental sciences.
University of Manchester Surface Characterisation Core Facility
Core includes range of surface analysis techniques and supportive instruments across three research institutes: Henry Royce Institute, Photon Science Institute, and National Graphene Institute.
University of Manchester Advanced Manufacturing Platform Core Facility
Core offers services, teaching and collaboration between Laser Processing Research Laboratory, Manufacturing Technology Research Laboratory and Bioenergy laboratory.
Software application for robust comparative analysis and contamination removal for metagenomics. Implements robust method for removal of negative control and crossover taxa from the rest of samples. Analyzes results from taxonomic classifiers using interactive charts with emphasis on confidence level of classifications. In addition to contamination subtracted samples, provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.
MC FMRIB's Linear Image Registration Tool
Motion Correction FMRIB's Linear Image Registration Tool
Software intra-modal motion correction tool designed for use on fMRI time series for linear (affine) inter- and inter-modal brain image registration.
University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility
University of Nevada High Spatial and Temporal Resolution Imaging Core
Core provides high spatial and temporal resolution imaging methodologies and instrumentation for studying cellular structure, signaling pathways, and function in health and disease. Offers education, training and expertise in advising investigators in the use of the new technologies.
University of New England; Biddeford; USA
Private research university in Maine with campuses in Portland and Biddeford, as well as study abroad campus in Tangier, Morocco.
Thermo Fisher | 112xx Series Advanced Ultrasonic Cleaner
Dual frequency sonicating water bath with temperature control.
Benchmark Scientific | Orbi-Shaker MP4 orbital shaker
Orbi-shaker MP microplate shaker with 4 position platform
Orbital shaker for up to 4 microplates with digital speed control.Designed with 3mm mixing orbit, optimized for thorough mixing of microplates and/or PCR plates. Up to four plates can be placed on the included platform.
University of Wisconsin Madison Biotechnology Center Animal Models Core Facility
University of Wisconsin Madison Biotechnology Center Animal Models Core
UW Biotechnology Center-Animal Models Core
Core provides support for generation of novel animals including mice, rats and swine models using CRISPR or transgenic technology, cryopreservation, rederivation, and IVF recovery of rodent animal models.
Software tool for scRNA and spatial transcriptomics.Used to generate RNA data close to real bulk RNA-seq with constraints of scRNA-seq data, based on keras and tensflow framework.
Web server for protein-protein and protein-DNA/RNA docking based on hybrid strategy. With input information for receptor and ligand molecules either amino acid sequences or Protein Data Bank structures, the server automatically predicts their interaction through hybrid algorithm of template-based and template-free docking.
University of Manchester National X-ray Computed Tomography Core Facility
University of Manchester UoM-FSE-Section of The National X-ray Computed Tomography Facility
UoM-FSE-Section of The National X-ray Computed Tomography Facility
Provides access and expert support to run cutting-edge 3D and 3D time-lapse imaging experiments.Provides access to X-ray instruments, technical support for new and existing users, expertise to design complex experiments, infrastructure and resources to analyse 3D and 4D data.Funded by the Engineering and Physical Sciences Research Council (EPSRC).
University of Manchester Design, Fabrication and Testing Core Facility
University of Manchester UoM-FSE-Platform of Design
Core supports areas of research from Heavy Structures and Concrete design, fabrication and testing to Non-Destructive Testing, development and construction of novel fibre, polymers and composite materials.
Software Python library (C++ backend) for degree preserving network randomization.
Software graph neural network based tool for spatial domain deciphering. Used for deciphering spatial domains from spatially resolved transcriptomics.
Spectral Autofluorescence Image Correction By Regression
Software application as platform independent protocol and FIJI plug-in to correct for autofluorescence using standard filter sets and illumination conditions. Spectral autofluorescence correction method based on simple 2- or 3-Channel images implemented in Python and Fiji. Used for performing spectral autofluorescence correction on biological images.
Software package provides implementation of the Enformer model and examples on running the model.
Software application as bias factorized, base-resolution deep learning models of chromatin accessibility.
Software application as Python extension for quick access to bigWig and bigBed files.
Web application to download database for motif enrichment, motif annotations,cluster-buster implementation, precomputed regions for creating gene-based databases and to download lists of transcription factors for human, mouse and fly, chip-seq tracks annotations.
Software motif comparison tool. Compares one or more motifs against database of known motifs, ranks motifs in database and produces alignment for each significant match.
Software application for detection of sequences that regulate gene transcription, such as enhancers and silencers, but other types of biological regulation may be mediated by motif clusters too.
TF MOtif Discovery from Importance SCOres
Transcription-Factor Motif Discovery from Importance Scores
Software application as algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data.
Software package provides interface to HDF5 library from Python. The low-level interface is intended to be complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts.
Software package provides IPython kernel for Jupyter.
Software vector based drawing application for desk top publishing with Apple's macOS operating system. Illustration or drawing software application that offers vector-based graphics editing and creation capabilities for creating simple not-photographic drawings, technical diagrams and illustrations such as logos, icons, buttons and stylized art.
Software that quantifies vascular morphometry parameters like area covered by vessels, vessel width, skeleton length and branching or crossing points of vascular networks in tissues and in vitro assays.
Creighton University Innovative Genomics and Bioinformatics Core Facility
Creighton University Innovative Genomics and Bioinformatics Core
Innovative Genomics and Bioinformatics Core
Provides services for genomics research that range from sequencing to data analysis. Instruments available include Illumina NextSeq 2000, 10x Genomics Chromium iX Controller, Agilent TapeStation 4200, and Qubit Flex Fluorometer.
Creighton University Drug Discovery and Delivery Core Facility
Creighton University CU-DDD Core - Drug Design
Core subcores include Drug Design, Synthesis and Validation Laboratory, ADMETox Laboratory,Zebrafish Laboratory. Offers experts and technologies to provide services tailored to drug development needs. Can assist with drug screening and design from small molecules to peptides, development and applying methodologies to synthesize drug candidate, and validate its chemical structure and purity. Offers services to detect and quantify drugs in biological samples. Follow-up studies can be conducted using services of ADMETox subcore to characterize drug candidate toxicity, efficacy, and pharmacokinetic and pharmacodynamic profiles, and assist in developing appropriate formulation and delivery approaches.
Beth Israel Deaconess Medical Center Glycomics Core Facility
Beth Israel Deaconess Medical Center Glycomics Core
Glycomics Core provides services, instrumentation and expertise in glycomics. Services include Glycan Microarrays,Glycan analysis by Mass Spectrometry, Distribution of specific reagents,Trainings.
Beth Israel Deaconess Medical Center Precision RNA Medicine Detection Unit Core Facility,
Beth Israel Deaconess Medical Center Detection Unit Precision RNA Medicine Core
BIDMC Detection Unit Precision RNA Medicine Core
Detection Unit Precision RNA Medicine Core
Detection Unit of ncRNA Core can perform highly sensitive microRNA detection platform for diverse biospecimens.Technology is based on qPCR and uses single plate panel for simultaneous detection of 384 miRNAs using MIRXES technology. Services offered by unit include Detection of miRNA, Analysis of dysregulated miRNA,Consultation and support for non-coding RNA biology and research.
Software R package provides central location where curated data from experiments, publications or training courses can be accessed.
Database with search engine for querying annotated sets of drugs and small molecules for performing drug set enrichment analysis.
Standalone Python software to quantify enrichment of user-defined set of genes in target of clinical indication categories and to capture potentially repositionable drugs targeting gene set.
Software package provides several scale functions to break down ‘gg’ plot into pieces and align them together with gap plot or without (wrap plot or cut plot) ignoring subplots. Package was first designed to set breakpoints for truncating plot to shrink outlier long branch of phylogenetic tree. Set Axis Break for ggplot2.
Software R package to Rasterize Layers for ggplot2.
Software R package to combine separate ggplots into same graphic. Composer of Plots.
ColoPola: Colorectal cancer polarimetric image
Software application to classify colorectal cancer using ColoPola dataset.
Software tool as unsupervised contrastive learning model that employs expression of all measured genes and spatial location of cells, to integrate multiple tissue sections. Enables joint downstream analysis of multiple datasets in low-dimensional embeddings and also in reconstructed full expression space. Used for integrative analysis of time-series brain sections, including spatial clustering, differential expression analysis, and particularly trajectory inference that requires corrected gene expression matrix.
Anton Paar | NHT3 Nanoindentation Tester
Used for testing hardness, elastic modulus, creep and other surface properties at nanometer to micrometer scale. Its range is from 0.1 mN to 500mN with no need to wait to reach thermal stable state, and instrument indentation test can be performed immediately after startup.NHT3 is a versatile, research-grade platform suited for highly customizable mechanical surface testing.
BD Biosciences | FACSymphony A1 Cell Analyzer
Analyzer applies BD FACSymphony instrument technology to reduce background noise and increase detection sensitivity. Features low-noise electronics, high-powered lasers and tight beam spot to support immunophenotyping up to 16 colors. Enables independent analysis of large and small particles on single instrument. Optional small particle detector enables detection of small particles such as extracellular vesicles, viral particle and more. Compatible with broad portfolio of catalog and custom BD Horizon Brilliant Reagents and BD FACSDiva Software. Permits easy placement on standard lab bench with its compact format.
Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins.
Gives ability to introduce flow to research and drug discovery experiments with in vivo conditions. Microfluidic well plate format opens up multitude of experiments. Customizable BioFlux solutionon for ultimate imaging flexibility. Additional Standard Features to those in BioFlux 200 include Custom automated microscope configuration, User defined camera and Fully integrated control and analysis software.
Transonic | TS420 Perivascular Flow Module
TS420 Perivascular Flow Module with Flowprobes to fit every vessel in research models from mice to sheep and even giraffes, provides high resolution blood flow wave forms and arterial/venous flow measurements in mL/min or L/min. Gold Standard for blood flow measurement in cardiovascular research with outputs analog signals compatible with most data acquisition systems. Features plug and play set up routines to calibrate/scale/test and measure. Fit into 400-Series Instrumentation Consoles and compatible to mix and match with other 400-Series Modules. Perivascular Flowprobes are available for small and large vessel sizes, and for acute use and chronic implantation.
Automatic digital slide scanner with 12 slide capacity in one run, fluorescence scanning, 9 physical filter cubes and 45 logical fluorescence channels. Powered by PANNORAMIC Scanner Software. Supports Carl Zeiss objectives, achieving up to 43x or 86x magnification and 0.087 µm/pixel resolution within the same instrument, along with advanced FISH scanning technique.
Manual model using halogen light source, manual focus, motorized nosepiece and motorized fluorescence cube turret. Standard model suitable for brightfield observation of pathological specimens and digital imaging.
University of Washington I-LABS MEG Brain Imaging Center Core Facility
Institute for Learning and Brain Sciences (I-LABS) MEG Brain Imaging Center
Magnetoencephalography facility focusing on children. Equipped with MEGIN TRIUX Neo system with helium recycler, MAGSTIM EEG data acquisition system, Tucker-Davis Technologies RZ6 for stimulus generation, Epson Home Cinema 3200 for video projection, custom video recording system with 4 cameras, Eyelink eyetracker, and Polhemus 3D digitizer.
Software visualization grammar and GPU-accelerated toolkit for genomic data. Visualization grammar and GPU-accelerated rendering engine for genomic data. Grammar based toolkit for authoring tailored, interactive visualizations for genomic data analysis.
Neighborhood-Aware Variant Impact Predictor
Neighborhood-Aware Variant Impact Predictor (NAVIP)
Software tool for functional impact prediction for sequence variants. Neighborhood-Aware Variant Impact Predictor (NAVIP) considers all variants within a given protein coding sequence when predicting the functional consequences.
National Primate Research Center Consortium
The National Primate Research Center (NPRC) Consortium
The National Primate Research Center Consortium
NPRC Consortium is collaboration across seven Centers to increase access and promote sharing of NonHuman Primate related resources among biomedical researchers. NPRCs advance missions of NIH Institutes, Centers, and Offices by providing animals, facilities, expertise, and resources required by investigators in disease specific areas. Each Center provides expertise on the use of various NHP species as models of human disease to address specific research projects in major research fields such as infectious diseases, aging, cardiovascular disease, diabetes and metabolic disorders, neuroscience, pediatrics, regenerative medicine, reproductive health, and women’s health. ORIP supports Specific Pathogen Free rhesus macaque colonies at the California,Oregon, Southwest, Yerkes, and Tulane NPRCs and the Caribbean Primate Research Center in Puerto Rico. Additionally, SPF pigtail macaque colonies are maintained at the Washington NPRC and at the Johns Hopkins University School of Medicine.
Software application for creating scalable muscle spindles dataset based on kinematic data and define action recognition task as benchmark. Training and analysis of hierarchical neural networks to solve recognition task from muscle spindle inputs.
World Health Organization Health Action International project on medicine prices and availability
WHO/Health Action International project on medicine prices and availability
Project on Medicine Prices and Availability collaborative partnership between WHO and international non-governmental organization Health Action International. Through project, standardized survey methodology for measuring medicine prices, availability, affordability and price components was developed.
Organization responsible for official statistics and for other government statistics. Used to develop, produce and disseminate statistics, coordinate system for official statistics in Sweden, conduct long term cooperation projects with statistical offices in developing countries, which are financed by Sida.
Finland's statistical database contains collection of statistical tables on Finnish society and population of Finland including economy, housing, transport, tourism, consumption, prices, wages and salaries, energy, enterprises and other topics.
National Prostate Cancer Register of Sweden
National Prostate Cancer Register (NPCR) of Sweden
National Prostate Cancer Register of Sweden database.
Interactive On Line Report from National Prostate Cancer Register (NPCR) of Sweden
Online report from NPCR that contains data on prostate cancer care from all healthcare providers in Sweden. Source of knowledge about Swedish prostate cancer healthcare for all stakeholders, patients, healthcare professionals, researchers, administrators and decision makers.
Instrument features include High Speed: 22 hrs to 24 hrs for PE150 sequencing; High Flexibility: 4 Flow Cells, PE150, and PE100 at the same time; Ultra-high Throughput: 7 Tb per day; high quality data around the clock.
Provider of precision medicine serving customers in more than 100 countries, involving over 2,300 medical institutions. Relying on sequencing and bioinformatics technology, provides clinical molecular diagnostic solutions and high-throughput sequencing research services.
Provides expertise in multi-omics (Genomics, Transcriptomics, Epigenomics, Proteomics and Metabolomics), offering end-to-end next-generation sequencing and mass spectrometry solutions to researchers and healthcare professionals.
Compact scanner for any digital slide application. Scanning system with FS-Live software suite, optimized for frozen section, cytology, ROSE, and FNA adequacy evaluation, places control into hands of remote pathologist to pilot the system and provide diagnosis without travel time.
MoticEasyScan Pro scanner system scans up to 6 slides in one click and uploads digital slides to your slide management server. Ideal for any application that requires glass slide digitization.
MoticEasyScan Infinity 102 Scanning System
Scanning solution for high volume scanning. Scanner system scans up to 60 slides in one click, providing scanning at 20X and40X magnifications. With Infinity Scanning design, slides can be added to the system without interrupting the scanning process.
MoticEasyScan Infinity 60 Scanning System
Scanning solution for high volume scanning. Scanner system scans up to 60 slides in just one click, providing scanning at 20X and40X magnifications with Infinity Scanning design, slides can be added to the system at any time, without interrupting the scanning process.
Scanner system scans up to 6 slides in just one click. It scans and uploads high-quality digital slides to your slide management server. Multipurpose scanner for any application that requires glass slide digitization.
Compact scanner for any digital slide application. This scanning system with FS-Live software suite, optimized for frozen section, cytology, ROSE, and FNA adequacy evaluation, for remote pathologist to pilot the system and provide diagnosis without travel time.
Company provides innovative microscope and microscopy solutions designed for education, medical, clinical, and industrial needs. Motic Microscopes specializes in designing and manufacturing conventional and digital microscopy solutions. Motic Digital Pathology drives adoption of digital medicine by making whole slide imaging, AI, and software technologies approachable for hospitals and labs everywhere.Motic Electric designs, develops and manufactures High Voltage insulation components for transmission and distribution systems in the electric power industry.Motic Energy strives to lead in smart energy technology through our next-gen management platform, using big data, AI, and cloud technology to create networked energy ecosystem for the world.
Leica DM6 B Automated Upright Microscope System
Leica DM6 B Upright Microscope includes the Leica DFC7000 T Camera and LAS X Software.
Leica DM4 B Automated Upright Microscope System
Leica DM4 B Upright Microscopes are designed specifically for use in clinical and life science research applications. These microscopes simplify your workflow with automated functions and easy-to-use software. The DM4 features 19-mm sCMOS camera imaging port to capture publication quality images and LAS X Navigator Software. Variety of optional accessories are available.
Software tool that can resolve fine grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. Used for comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics.
Software R package to identify transcription factor binding motifs over represented on gene list. RcisTarget selects DNA motifs that are significantly over represented in surroundings of transcription start site of genes in gene-set, then annotates to TFs and those that have high Normalized Enrichment Score are retained and than candidate target genes are predicted. Used to identify transcription factor binding motifs enriched on list of genes or genomic regions.
StrataQuest tissue flow cytometry quantitative analysis system
Tissue flow cytometry quantitative analysis platform integrates precise quantitative analysis solution at single cell level in tissue provided by HistoQuest/TissueQuest software. Software is compatible with multiple types of tissue and cell samples, enabling quantitative analysis in different biological research fields.
Beth Israel Deaconess Medical Center Precision RNA Medicine Delivery Unit Core Facility
Beth Israel Deaconess Medical Center Precision RNA Medicine Core - Delivery Unit
Precision RNA Medicine Core - Delivery Unit
Delivery Unit offers training and services on the NanoAssemblr Spark, NanoAssemblr Ignite+, and Malvern Zetasizer for the purpose of synthesis and characterisation of Lipid Nanoparticles (LNPs). The Zetasizer is able to read zeta potential and size of particles, including exosomes, liposomes, and LNPs.
Cellosaurus Short Tandem Repeat search tool
Web tool to seach for similarity between cell line Short Tandem Repeat markers and those stored in Cellosaurus knowledge resource.Cellosaurus STR similarity search tool for cell line authentication.
Software for detecting and identifying high frequency oscillations observed in EEG recordings. MATLAB based graphical user interface for High Frequency Oscillation marking.
Platform collates tools, databases, information, and other resources that can be useful to researchers and data producing facilities working in the area of data driven life science. Hub for data driven life science research in Sweden.
Portal provides information, guidelines, data, services, and other resources aimed at supporting Swedish research community to share data related to pathogens and pandemic preparedness.
Software for reconstructing neurons from fluorescence microscope images. Used to generate neuron structure from 3D image with user interaction, which mainly consists of mouse clicks. It can also load SWC files from any other source for visualization or further editing.
Electromagnetic instrument to mount on stereotaxic device, that delivers accurate reproducible contact with small laboratory animals for preclinical research.
RWD-68094 (Mice) & Model RWD-68095 (Rats)
Precise spinal impactor used for reproducible impact on laboratory animals to generate neurotrauma injury for preclinical research.
AmScien Instruments | Fluid Percussion Device
Fluid Percussion Device w/ a PC-Based Pressure Measurement Unit
Device creates controlled and measurable fluid percussion in small to medium sized animals for preclinical research.
FP device consisting of falling pendulum that generates reproducible, hydraulic pulses to replicate closed TBI for neurological research.
Conduct Science | Weight Drop TBI apparatus
Weight drop device that allows for angled impact to the head of free-roaming laboratory animal for preclinical research.
AmScien Instruments | Pneumatic Cortical Impact Device
Pneumatic impact device designed to reproduce controlled cortical impact to laboratory animals for preclinical research.
Precision Systems and Instrumentation | Head Impactor TBI-0310
Computer controlled device with accurate and reproducible detection of cortical surface prior to initiating injury sequence, designed for preclinical research.
Custom Design and Fabrication | Fluid Percussion Injury Device
Fluid percussion device to be used on laboratory animals for neurologic research.
Beth Israel Deaconess Medical Center Functional Genomics and Bioinformatics Core Facility
Functional Genomics and Bioinformatics Core
Core provides consultative, laboratory, and bioinformatic services for next generation sequencing based applications.Core services include Pre- and post-experimental consultation to determine proper experimental approach, design, and interpretation; Standalone RNA preparation, RNA and DNA Bioanalyzer analyses, chromatin shearing/shear checks; Sample quality assessment of DNA and RNA using the BioAnalyzer and Qubit assays; Library preparation, sequencing, and analysis of transcriptomes (RNA-seq), cistromes (ChIP-seq), chromatin accessibility (ATAC-seq); Standalone sequencing on NextSeq500; Multiplexed 10x Single Cell/Nucleus Library RNA-seq Droplet generation, Library Preparation; Basic data analysis: quality assessment and normalization, genomic alignment, differential expression/enrichment, functional enrichment analysis (overrepresentation and GSEA), sample clustering, and motif enrichment; Bespoke data analysis, including integration of complex ChIP-seq and RNA-seq data sets, single-cell sequencing analyses.Core is located on the 7th floor of the Center for Life Sciences building in the Longwood Medical area (3 Blackfan Circle, CLS-728).
Optimized processor for fiber photometry.RZ5P is intended for use with TDT’s Synapse software.
Allows monitoring of wireless wheel running activity without running wires.
Med Associates | Wireless Running Wheel Hub
Device connects wireless running wheels to data acquisition computer via a USB cable.All wheels must be set to the same address as the hub with which they communicate.Hub relays data to Wheel Manager Software.
Software library of easy testing ML models directly from pandas DataFrames, while keeping the flexibility of using scikit-learn’s models.
San Diego Instruments | Rotor Rod System
System to study motor coordination using natural fear of falling response with reliability and accuracy. System measures motor function, motor learning, coordination, and equilibrium in both rats and mice.
Cross-platform, complete Integrated Development Environment for application developers to create applications for multiple desktop, embedded, and mobile device platforms, such as Android and iOS. It is available for Linux, macOS and Windows operating systems. In addition, you can use the experimental WebAssembly plugin to build applications in web format and run them in web browsers.
Arduino Integrated Development Environment
Software tool for working with whole slide images. Digital microscope application for supporting histopathological diagnostic workflow and microscope examination process. Advanced slide viewing software used in clinical pathology and research.
Software digital painting and drawing application. Used to create figures. Built for the latest stylus and touch devices, now including iPhones. Collection of vector and raster brushes, live brushes, to deliver natural painting and drawing experience.Vector and raster graphics editor developed by Adobe primarily for digital painting. Originally designed for the Apple iPad with Pencil support.
Software tool as unified interface to visualize statistical results of popular R packages. Provides unified interface that enables users to use one line of code to visualize statistical results of many R packages using ggplot2 idioms. Allows ggplot2 to handle some popular R packages.
Software R package to integrate popular Bayesian modeling methods into tidy data plus ggplot workflow.
Software tool as mapping based variant caller that implements several calling models within unified haplotype aware framework. Variant caller that uses polymorphic Bayesian genotyping model capable of modeling sequencing data from range of experimental designs within unified haplotype aware framework. Bayesian haplotype based mutation calling.
Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification.
Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end.
Web application for automated cell type annotation for scRNA-seq datasets. Allows for cell prediction using either built-in or custom models, in order to assist in accurate classification of different cell types and subtypes.
Portal used to find and download any of data sets published on CELLxGENE. Allows to download and visually explore data to understand functionality of human tissues at cellular level. Optimized for finding, exploring, and reusing single cell data. Collections Page lists collections hosted on CELLxGENE Discover and metadata that define tissue, assay, disease, organism, and cell count for each collection. Once you find published dataset of interest on CELLxGENE Discover, you can click on the explore button below the dataset description to explore the cells of that dataset using the CELLxGENE Explorer.
Web application to link single-cell epigenomes and cell types.
United States Cancer Statistics Public Information Data
United States Cancer Statistics public information data provided by Centers for Disease Control and Prevention.
Software Snakemake workflow for scoring and comparing multiple bacterial genome assemblies from Illumina and Nanopore to reference genomes.
Software Snakemake workflow for bacterial genome assembly plus polishing for Oxford Nanopore sequencing using multiple tools.
Software survival analysis library written in Python.
Software R package to create HTML tables of descriptive statistics, as one would expect to see as the first table in medical epidemiological journal article. Used for generating tables of descriptive statistics in HTML.
Analysis of Compositions of Microbiomes with Bias Correction 2
Software R package for differential abundance of microbiome. Used for performing differential abundance analysis of microbiome count data. Microbiome differential abudance and correlation analyses with bias correction.
Donald Danforth Plant Science Center Plant Growth Core Facility
Donald Danforth Plant Science Center DDPSC Plant Growth Facility
Core offers scientists variety of advanced plant growth spaces and expert horticultural services.This includes Greenhouse Complex,Growth Chamber facility and Headhouse space. Greenhouses are designed for cultivation and containment of research crops, including regulated and protected plant materials.All greenhouses are environmentally controlled for temperature, humidity and light levels, and have automated irrigation and nutrient delivery capability using Argus Control Systems. Many houses have 14 to 20 ft sidewalls for growing taller crops, as well as in-floor heating, height-adjustable light canopies and automated irrigation capabilities. Over 95% of the greenhouse complex utilizes high intensity, energy-efficient horticultural LED lighting. Plant Growth Facility has multiple special-use work spaces including potting areas, seed processing, seed storage coolers, plant dry-down and soil handling rooms, autoclave, fertigation/utility rooms, as well as general storage space.Core is also responsible for managing Seed Storage coolers housing Danforth Center Institutional Seed Collection.
Van Andel Institute Mass Spectrometry Core Facility
Van Andel Institute Mass Spectrometry Core
Core is committed to developing scientific partnerships with research labs to develop and deploy LC/MS and GC/MS methods specifically tailored to meet the needs of every project. Provides suite of technologies, experimental design support and staff expertise to deliver metabolomics, lipidomics, and proteomics capabilities to VARI scientists and collaborators. Analytical capabilities are combined with custom informatics and statistics solutions.Specific capabilities include: Metabolomics and Lipidomics liquid chromatography mass spectrometry (LC/MS) systems (Thermo Orbitrap ID-X, Thermo Orbitrap Exploris 240, and Agilent 6470 QQQ) and gas chromatography (GC)/MS systems (Agilent 5977b (2), Thermo 7610 ISQ) dedicated to small molecule analysis;Proteomics nano LC/MS systems (Orbitrap Eclipse and Orbitrap Exploris 480) for protein analysis; Bioinformatics for developing and maintaining informatics pipelines for mass spectrometry data analysis and visualization.Major equipment in the facility includes Thermo Scientific Orbitrap ID-X LC/MS,Thermo Scientific Orbitrap Exploris 240 LC/MS,Thermo Scientific Orbitrap Eclipse nanoLC/MS,Thermo Scientific Orbitrap Exploris 4800 LC/MS,Agilent 6470 Triple Quadrupole LC/MS ,Agilent Infinity 1290II UPLC,Agilent 5977B GC/MS,Thermo Scientific ISQ7610 EI/CI enabled GC/M.
University of Victoria Genome BC Proteomics Centre Core Facility
University of Victoria Genome BC Proteomics Centre
University of Victoria Proteomics Centre
Core for proteomics technology development and service. Provides mass spectrometry analytical services to academic, industrial, and government laboratories.
Beth Israel Deaconess Medical Center Spatial Technologies Unit Core Facility
Core for spatial and single cell technologies provides expertise, training, education and equipment. Supports projects, starting from consultation with matching right technologies to project needs, budget, and timeline. Provided services include single cell and spatial assays, tissue preparations, staining, sequencing, bioinformatic analyses.Equipment include 10x Genomics Visium,10x Genomics Xenium,Akoya PhenoImager HT whole slide scanner, Akoya Phenocycler Fusion,Bruker Vutara VXL,Nanostring GeoMX DSP, Vizgen MERSCOPE, Epredia TMA Grandmaster and more.
Fully automated robot for compound injection into oocytes, eggs, and embryos. Uses industry standard 96, 384, as well as custom well plates.
Roboocyte provides automated cDNA/mRNA injection and subsequent TEVC recording on Xenopus oocytes in 96-well microtiter plates. Roboocyte2 was designed not only for Xenopus oocyte expression system, but to also for drug discovery. Provides sequential two electrode voltage clamp recording in oocytes and classical perfusion of compounds.
Brand within Dassault Systèmes that develops and markets solid modeling computer-aided design, computer-aided engineering, 3D CAD design and collaboration, analysis, and product data management software.
Software R package for pathway analysis in scRNA-seq data. It’s a different approach to pathway analysis that defines pathway activity as a change in multivariate distribution of a given pathway across conditions, rather than enrichment or over representation of genes.
Software tool as Python based synaptic vesicle classifier algorithm to identify neurotransmitter vesicles in electron microscopy images using Pytorch.
Tulane University TNBRC Animal Resources
Tulane University TNBRC Animal Resources Core Facility
Tulane University Tulane National Biomedical Research Center Animal Resources Core Facility
Unit is part of Tulane National Primate Research Center. Provides services including routine husbandry care for animal colonies, reporting of animals abnormal clinical signs or activities to veterinary medical staff and faculty. Animal Care Technicians provide support during diagnostic and therapeutic procedures and administration of preventive medicine program. Coordinates its activities with research personnel to provide assistance, equipment and support for their work. After hours care includes administration of treatments, collection of biologic samples for research activities and observation of animals. TNPRC facilities are accredited by Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC).
Software application as interactive program for performing power and sample size calculations. Can determine the sample size needed to detect specified alternative hypothesis with required power, the power with which specific alternative hypothesis can be detected with given sample size, or the specific alternative hypotheses that can be detected with given power and sample size.
Whole organism atlas utilizing 2D and 3D imaging. Atlas at cellular resolution serves as foundation for characterization of tissue and cellular change in Daphnia.
University of California Los Angeles Broad Stem Cell Research Center Microscopy Core Facility
Los Angeles UCLA-Broad Stem Cell Research Center Microscopy Core
UCLA-Broad Stem Cell Research Center Microscopy Core
Microscopy Core is collaboration of Broad Stem Cell Research Center and Department of Molecular, Cell and Developmental Biology at UCLA. Provides high resolution technologies for imaging and analyzing molecular and structural organization of cells and tissue as well as bioengineered materials. Services include confocal, wide field fluorescence and live cell imaging, as well as image analysis software.
Software tool for high quality model based FMRI data analysis. Used for preprocessing and statistical analysis of FMRI data.
Multivariate Exploratory Linear Optimized Decomposition into Independent Components
MELODIC:Multivariate Exploratory Linear Optimized Decomposition into Independent Components
Software tool to use at both the subject and group level to decompose FMRI data into time courses and spatial maps using Independent Component Analysis. Used to decompose single or multiple 4D data sets into different spatial and temporal components.
Software command-line tool for approximate Bayesian inference using generative signal models.
BASIL:Bayesian Inference for Arterial Spin Labeling MRI
Bayesian Inference for Arterial Spin Labeling MRI
Software toolbox for kinetic model inversion to the data using Bayesian algorithm. Performs kinetic model inversion on ASL label control difference data.
VERBENA:Vascular Model Based Perfusion Quantification for DSC-MRI
Software tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain.
FAST:FMRIB's Automated Segmentation Tool
Functional Magnetic Resonance Imaging of the Brain's Automated Segmentation Tool
Software tool to segment 3D image of brain into different tissue types like Grey Matter, White Matter, CSF, etc., whilst also correcting for spatial intensity variations also known as bias field or RF inhomogeneities. Used to perform tissue type segmentation and bias field correction.
FMRIB’s Integrated Registration and Segmentation Tool
Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool
Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences.
Sotware automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.
Software tool to perform linear registration, meaning that it will translate, rotate, zoom and shear one image to match it with another.
Software tool to analyse structural data. Voxel based morphometry style analysis carried out with FSL tools.
Software package for both single-time-point and two-time-point analysis of brain change. Used to estimate percentage brain volume change between two input images, taken of the same subject, at different points in time.
Software tool to estimate total brain tissue volume, from single image, normalized for skull size.
Software flexible tool for subcortical segmentation. It differs from FIRST in that it can use complementary information in different MRI modalities and is less reliant on manual segmentations.
Brain Intensity AbNormality Classification Algorithm
BIANKA:Brain Intensity AbNormality Classification Algorithm
Software tool for automated segmentation of white matter hyperintensities. Classifies image’s voxels based on their intensity and spatial features, and the output image represents the probability per voxel of being WMH. Flexible in terms of MRI modalities to use and offers different options for weighting spatial information, local spatial intensity averaging, and different options for choice of number and location of training points.
Software tool for registering cortical surfaces. Capable of driving alignment using wide variety of descriptors of brain architecture, function and connectivity.
Software tool provides general pipeline for processing anatomical images.
Functional Magnetic Resonance Imaging of the Brain Diffusion Toolbox
Software toolbox for analysis of diffusion weighted images.
Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.
Software tool for correcting eddy currents and movements in diffusion data. Used to predict undistorted data, to which actual observed images can be aligned, to estimate and to correct for volume-to-volume movement and off-resonance fields, to signal dropout caused by movement during diffusion encoding, within-volume movement and movement-induced changes of susceptibility-induced off-resonance field. In addition to correcting for these effects, the output from this framework offers description of off resonance and subject movement effects present in uncorrected data.
Software tool for estimating and correcting susceptibility induced distortions.
Software tool allows to assess dMRI data both at single subject and group levels.Calculates average SNR across all voxels within brain mask to give summary measure of overall quality of dataset. Used to generate single subject and study wise reports and databases.
Software tool for nonparametric permutation inference on neuroimaging data.
Software application used to form clusters, report information about clusters and/or perform cluster based inference.
Software program which takes in p-value image and uses False Discovery Rate theory to carry out multiple comparison correction.
Software application used as part of group level resting state analysis to identify subject specific contributions to group level Independent Component Analysis.
Web application as FSL image viewer for visualising neuroimaging data.
Software application set of useful command line utilities which allow conversion, processing etc. of Analyze and Nifti format data sets.
Software tool designed to allow command line interrogation of atlas images supplied with FSL. It takes as input the name of one of FSL atlases together with either coordinate of interest or mask.
Web app for post-GWAS/QTL analysis that performs slew of novel bioinformatics analyses to cross GWAS/QTL mapping results with host of publicly available rice databases.
Database of protein components of mammalian stress granules.
Smallest Univalue Segment Assimilating Nucleus
Software tool to cover image noise filtering, edge finding and corner finding.
Software tools for Echo Planar Imaging distortion correction used in diffusion imaging, functional MRI and perfusion imaging.
Software tool to combine background image (raw FMRI or high resolution MRI) with one or two statistics images. Statistics images must be in registration with the background image.
Physics-Oriented Simulated Scanner for Understanding MRI
Software tool that produces realistic simulated MRI and FMRI images or time series.
Bayesian Chemical Exchange Saturation Transfer
Software tool for Bayesian analysis for chemical exchange saturation transfer z-spectra.
Software de-noising pipeline combines noise regressors identified by tools such as PNM and ICA (and FIX) and effectively prepares them for entry into single FEAT model, thus allowing the user to clean data in single step.
Software spectroscopy analysis package includes tools for preprocessing of raw spectroscopy data, including coil combination, frequency and phase alignment, and filtering. Spectroscopy processing package that incorporates Bayesian fitting of spectra.
Virtual environment for drug discovery where simulations, AI and data are integrated to discover new opportunities. Online platform for drug discovery applications.
University of South Carolina Instrumentation Resource Core Facility
USC Instrumentation Resource Facility (IRF)
USC School of Medicine Columbia Instrumentation Resource Facility (IRF)
IRF houses biotechnological equipment that provide investigation ranging from single cell and molecular level analysis to whole animal imaging. Additionally, the IRF maintains a full range of ancillary equipment available for sample preparation, image enhancement, and data analysis.
State university in Oslo and Kjeller in Norway. It is the result of the merger of many former vocational colleges in the Greater Oslo Region.
Database that collects phase separation related RNAs manually curated from publication and public databases.
Created to collate literature evidence that support gene or protein association with the stress granules (SGs) and P-bodies (PBs), with the goal of consolidating high-confidence proteomes of SG and PB. Protein database for mammalian SGs and processing bodies (PBs), which are related condensates.
Comprehensive database of RNAs involved in liquid-liquid phase separation.
Web server to detect disordered regions from primary sequence.
Database of mutations found in proteins involved in membrane-less organelles and liquid-liquid phase separation in human diseases.
Manually curated database of relations between phase separation and diseases.
Provides a collection of manually curated phase separation (PS) proteins and Membraneless organelles (MLOs) related proteins. Annotated phase separation-related proteins with droplet states, co-phase separation partners and other experimental information.
Database of proteins driving liquid–liquid phase separation. Stores over one hundred proteins that are able to drive LLPS, all curated and supported by literature references.
Database of proteins undergoing liquid–liquid phase separation in vitro. Contains LLPS related proteins together with the corresponding phase separation conditions validated by experiments.
Integrative database for proteins involved in liquid-liquid phase separation. Data resource of liquid–liquid phase separation in eukaryotes.
Web server developed for detecting sequences critical for phase separation related proteins. Software to detect sequences critical for liquid-liquid phase separation. Deep learning based prediction tool for detecting sequences critical for phase separation related proteins.
Web server as meta-predictor for phase-separating proteins. Displays proteome-level quantiles of different features, thus profiling PS propensity and providing crucial information for identification of candidate proteins.
CrowDsourcing COndensate Database and Encyclopedia
Comprehensive, semi-manually curated crowdsourcing database of biomolecular condensates and their constituents as well as encyclopedia for scientific terms used to describe them.
Database of Disordered Protein Predictions
Database of disordered protein predictions. Community resource for pre-computed disorder predictions on a large library of proteins from completely-sequenced genomes.
Web meta-server for visualization and annotation of low complexity regions in proteins. Used for discovering LCRs and provides functional annotations such as domain detection, transmembrane segment prediction, and calculation of amino acid frequencies.
Web and command-line application to identify proteins with prion-like amino acid composition. Searches protein sequences to identify probable prion subsequences using hidden-Markov model algorithm.
Web server for prediction of prion-like domains recruitment to stress granules upon heat stress.
Algorithm for prediction of granules formation in yeast.
Cornell University College of Veterinary Medicine Cornell Veterinary Biobank
Biobank for collecting biological samples from both ill and healthy animals. Samples are processed and cataloged with the appropriate clinical information. Biobank has ISO 20387 accreditation.
Scripts to download genomes from the NCBI FTP servers.
Wistar Institute Molecular Screening and Protein Expression Core Facility
Molecular Screening and Protein Expression
The Wistar Institute Molecular Screening and Protein Expression
Facility enables to discover molecular, genetic, and small molecule compounds suitable to study functions of poorly understood proteins, signaling pathways, and cells in complex biological processes relevant to human physiology and disease; provides technical assistance with viral vector preparation and expression and purification of recombinant proteins; fosters collaborations. Staff will also develop and implement new technology as needed. Education and training is also available. Provides opportunities to develop new innovative basic and translational research, preliminary data for hypothesis driven research grant applications, and public-private partnerships.
University of Massachusetts Lowell Nuclear Magnetic Resonance Spectroscopy Lab Core Facility
Nuclear Magnetic Resonance Spectroscopy Lab
UML - Nuclear Magnetic Resonance & Spectroscopy
University of Massachusetts Lowell UML - Nuclear Magnetic Resonance & Spectroscopy
Core provides JEOL 400 MHz NMR equipped with auto sampling and automatic tuning and matching. Instrument can perform temperature and kinetic studies as well as x-nuclei and 2D experiments.
University of Massachusetts Lowell Thermal and Mechanical Properties Lab Core Facility
UML - Thermal & Mechanical Properties Lab
University of Massachusetts Lowell UML - Thermal & Mechanical Properties Lab
Core houses thermal analysis suite. Researchers are able to investigate behavior of material under stress and temperature change. Service level work and technical expertise are provided.
University of Massachusetts Lowell Next Generation Sequencing and Genomics Core Facility
UML - Next Generation Sequencing & Genomics
University of Massachusetts Lowell UML - Next Generation Sequencing & Genomics
Core provides Next-Generation DNA and RNA sequencing services and technical expertise including NGS library prep, DNA and RNA quality assessment, Fluorometric quantification of DNA/RNA/Protein, DNA and RNA isolation, PCR/qPCR, Qubit fluorometry, gene expression and drug development studies. Consultative services are available.
Development of Immunological Reagents for the Identification of New World Monkey Biomarkers
Project portal for generating recombinant NWM proteins, producing mouse monoclonal antibodies against New World Monkeys, validating immunological assays using these reagents, and distributing reagents and related scientific information to interested investigators.
Portal for Hybrid Rat Diversity Program with goal to extend the use of rat models for clinical translation through establishing animal resource and genomic dataset to facilitate the translation of laboratory research to clinical relevance. Specifically, the Hybrid Rat Diversity Panel resource provides the research community with foundation for systems genetics and tool for forward genetics.
Center for Neuroanatomy with Neurotropic Viruses
This national resource was created to provide neuroscience community with access to reagents, training and facilities that are necessary to use neurotropic viruses as transneuronal tracers.
Software tool as classifier that utilizes k-mer composition of assembled sequences to identify eukaryotic genome fragments prior to gene prediction. Used for eukaryotic sequence identification. Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets.
Compositional Omics Model-Based Integration
Software R package for simultaneous exploration of multiple datasets. Compositional omics model based visual integration.Used to integrate omics data for visualization, with special focus on compositionality.
Web application for metaproteome data analysis, with initial focus on tryptic-peptide-based biodiversity analysis of MS/MS samples.Designed for metaproteomics data analysis with focus on interactive data visualizations. Unipept 4.0 introduces complementary functional analysis based on GO terms and EC numbers.
Software library providing Python interfaces to proteomic data. Provides set of modules to facilitate the most common tasks in proteomics data analysis.
Dutch National supercomputer system facilitates scientific research carried out in many Universities, independent research institutes, governmental organizations, and private companies in the Netherlands. Cluster of heterogeneous nodes built by Lenovo, containing predominantly AMD technology, with capabilities for high performance computing (parallel, symmetric multiprocessing), data-processing, and machine learning. Has several system specific storage resources, that are geared towards supporting the various types of computing. System has peak performance of 14 petaflop/s, making it the most powerful high-performance computing system in the Netherlands.
Louisiana State University Health Sciences Shreveport INLET High Throughput Screening Core Facility
Innovative North Louisiana Experimental Therapeutics program (INLET)
Facility focused on discovery and development of drugs and genetic targets that affect human diseases including cancer, fungal, bacterial and viral infection, neurological disorders and cardiovascular disorders. Both live and fixed high throughput microscopy is performed using Incucyte S3, Incucyte SX5 and Cellomics ArrayScan VTI HCS Reader. Provides expertise and protocol design for variety of assays including: Cell proliferation, Cell viability, Phagocytosis, Chemotaxis, Cell migration/invasion, 3D spheroid growth. INLET Core provides cutting edge, multiplexed functional imaging platforms to perform multi-well high-throughput live-cell imaging and analysis assays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software modeling and simulation package for pharmacodynamics and pharmacokinetics.
Pipette Finding Convolutional Neural Network
Software application for convolutional neural network that assesses pipette positioning before patch clamp is begun to minimize patch clamping errors in electrophysiology experiments. Used for detecting pipette positioning and making patch clamping procedures.
Algorithm to organize cells into clusters, utilizing information from both gene expression matrices and spatial coordinates. Comprehensive solution for cell clustering problem in spatial transcriptomics.
ntsm: nucleotide sequence sample matcher
Software alignment free, ultra low coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection. Used to count number of specific k-mers within sequence data. The counts can then be compare to other counts to determine to compute the probability that sample are of the same origin to discover incongruent samples or sample swaps.
Huron Technologies | TissueScope LE Slide Scanner
Huron Digital Pathology TissueScope LE Slide Scanner
Scanner for versatility, throughput, and ease of use. Scan up to twelve 1” x 3” brightfield slides, up to six 2” x 3” slides, or any size slide up to 6”x 8”.
Manufacturer in St. Jacobs, Ontario, Canada. Provides whole slide scanners to clinical and research institutions. Offers slide scanning services. Each customer is given secured access to view and download their images. After scanning is complete, the glass specimens are returned if requested by the customer.
Software suite for finite element analysis and computer aided engineering.
University of Rochester Medical Center Metabolomics Resource Core Facility
University of Rochester Medical Center Metabolomics Resource
Core specializes in metabolomic analysis. Provides Orbitrap Exploris 240 mass spectrometer, as well as dedicated staff for consultation and the analysis of biological samples.
University of Pennsylvania Penn Genomics and Sequencing Core Facility
University of Pennsylvania Penn Genomics and Sequencing Core
Provided services include molecular profiling of DNA and RNA on different platforms, Sanger sequencing, full service Next Generation Sequencing with different applications and bioinformatics, fragment analysis including human cell line authentication., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Stanford Geomicrobiology Shared Laboratories Core Facility
Geomicrobiology analytical facilities consist of four different labs in the Green Earth Sciences Building. Main areas of study are: molecular, bio(geo)chemical, and ecological aspects of microbial cycling of nitrogen, carbon, and metals in environment diversity, distribution, and activity of microorganisms driving greenhouse gas cycling in ocean and beyond molecular biomarkers in modern organisms to refine our interpretations of microbial fossil record.
Software set of pipelines bundled to map sequenced reads to their spatial location on tissue section, quantify corresponding gene expression levels and visually present spatial gene expression distribution.
Software virome analysis pipeline for analysis of Illumina sequence data. Integrated software platform for viral metagenomics.
Portable ultrasound system that provides high rich image quality. User friendly for fast and critical clinical applications. Ultrasounds with Doppler.
GE: Healthcare | Lunar Prodigy Advance system
GE Healthcare Lunar Prodigy Advance version ENCORE 18
System offers dual energy X-ray absorptiometry assessment. Bone densitometry scan with enCORE v18 software platform. Meets International Society for Clinical Densitometry testing guidelines. Used to take measurements to work out the strength of bones in advanced bone and metabolic health clinical applications.
Open Data Ludwig-Maximillians University
Data publication platform for publication and hosting of research data. Data repository contains open access journals published at Ludwig-Maximillians University, Munich, Germany. Server provides direct access to research data sets produced by projects at LMU. Open Journals LMU. Open Data LMU.
Lightweight Alignment Based Resolution of Alternative Three prime ends
Software application to quantify usage of alternative polyadenylation and cleavage sites in RNAseq data and identify genes whose usage of these sites varies across experimental conditions.
SciLifeLab Research Data Management Guidelines
Research Data Management guidelines to serve as information resource to life science researchers in Sweden regarding research data management committed to principles of FAIR (Findable, Accessible, Interoperable and Reusable) research data.
CRAPome:Contaminant Repository for Affinity Purification
Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.
Software application for network analysis and visualization of proteomics data. Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains appearance and many of features of STRING, and integrates data from associated databases.
3D printed pacifier shaped mouthpiece for fMRI compatible gustometers to deliver up to eight liquids during fMRI task. Can be utilized to study flavor, taste reactivity, reward or punishment with food, conditioning, and neurodegenerative conditions such as Alzheimers and Parkinsons, since taste and smell senses diminish early into disease acquisition.
University of Nebraska Lincoln Bioinformatics Core Facility
University of Nebraska�Lincoln UNL-Bioinformatics Core Research Facility
UNL-Bioinformatics Core Research Facility
Core offers education, analysis, and computational services in the area of bioinformatics and computational biology. Offers initial consultations to help with experimental design and power analysis of 'omics data for grant submissions and bioinformatics needs for current projects.
University of Nebraska Lincoln CryoEM Core Facility
Core facility is dedicated to structural characterization of biological samples and microcrystals using cryo-electron microscopy. CryoEM workflows including, single-particle CryoEM, Cryo-electron tomography , and Micro crystal electron diffraction. Instrumentation includes TFS 200kV Glacios CryoTEM, equipped with zero-loss Selectris Energy Filter, Flacon 4i Direct Electron Detector, and Ceta-D camera, Pelco Easy Glow Discharger, TFS Vitrobot Mark IV, and Leica EM GP2. We also present all the capacities for storing and shipping samples. Facility has Data storage Server and Live processing workstation for our users� convenience, including data processing suites RELION and CryoSPARC available at our campus supercomputer Swan cluster at the Holland Computer Center.
Software tool as set of Python scripts to modify GROMACS topology files, by adding content from different topology files and other GROMACS input files. Useful, particularly when system components are assembled outside of GROMACS, or in different steps within GROMACS. This helps prevent users from having to copy and paste significantly large blocks of text within topology files.
Web server to check whether given list of genes can be associated with stemness. Used to identify sets of genes considered essential to define stem cells. Used to explore presence of stemness signatures in user-defined gene sets. Analysis tool, based on curation of published stemness signatures defined by gene expression, RNAi screens, Transcription Factor binding sites, literature reviews and computational approaches.
Louisiana State University Health Shreveport Library
Provides systematic review literature searching services, writing review services, and resources in print and electronic format to faculty, students, and researchers in the schools of the health sciences. The Library also manages the SPSS and EndNote licenses for the campus.
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Software tool to identify important genes from genome-scale CRISPR-Cas9 screens. Used for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens.
Software package for general purpose sequence search and counting program for FASTQ files. Python3 program that counts sequence occurrences in raw FASTQ files. Used for CRISPRi-Seq, and for extracting and counting any kind of information from Illumina reads, such as barcodes.
Database of digitized plant specimens. Used for finding plant name, type, specimens and their label data.The collection also includes partner contributed reference works and primary sources. Used for research and teaching in botany, ecology, and conservation studies.
Global repository for all plant names with citation of its place of origin. Provides nomenclatural data, including spelling, author, types and first place/date of publication, for scientific names of vascular plants from family to infraspecific ranks.
Queen Square Brain Bank Digital Pathology Resource
University College London Queen’s Square Brain Bank Digital Pathology Resource
Platform for archival digital glass slide collection containing digital whole slide images from Lewy body disorders: Parkinson’s Disease, Parkinson’s Disease with Dementia and Dementia with Lewy Bodies, and control cases.E stained post-mortem brain tissues from patients with neurodegenerative diseases and controls.
Leica | ST5020 Multistainer Slide Stainer
Histology multistainer produces results for both routine and special stains and can perform single or multiple protocols at the same time. Contains 12 slide racks and 34 reagent stations.
Digital library of Internet sites and other cultural artifacts in digital form. Web history is accessible through Wayback Machine and they work with 1,200+ library and other partners through Archive-It program to identify more important web pages.
Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data.
Multi-mode microplate reader with three detection modes.Utilises ultra-fast UV/vis spectrometer or filters for absorbance as well as highly sensitive filters for all other detection modes.
Inverted microscpe for visualization of live cell culture.
SDI is composite measure of area level deprivation based on seven demographic characteristics collected in the American Community Survey and used to quantify the socio-economic variation in health outcomes.
Acceptor Photobleaching Fluorescence Resonance Energy Transfer
Software tool for analysis of acceptor photobleaching FRET images. Allows fully corrected, pixel-wise calculation and detailed, region of interest based analysis of FRET efficiencies in microscopic images.
Ratiometric Fluorescence Resonance Energy Transfer
Software tool used to calculate FRET efficiency on pixel-by-pixel basis from ratiometric FRET images. Allows to correct for channel cross-talk and to calculate FRET from image stacks, i.e., from 3D data sets. ImageJ plugin for intensity-based three-filter set (ratiometric) FRET.
Software R package for Orthologue assignment and Integration of single cell data. Functions for Orthologue Assignment and Integration of Single Cell Data between species.
Software application as starting point to MoSeq2 package suite. Unsupervised machine learning method which takes inputs from depth cameras in 3D and transforms them into different behavioral motifs which called syllables. Used to extract mouse pose from depth video and model how pose evolves over time.
Software application as machine learning-based platform for identifying behavioral modules from keypoint data without human supervision. Package provides tools for fitting MoSeq model to keypoint tracking data. Used to infer pose dynamics with keypoint data in addition to behavioral syllables.
Software error correction and accurate assembly tool for noisy long reads. De novo assembler for long reads. String graph-based de novo assembler for long reads like CLR, HiFi and ONT.
University of Colorado Boulder Geomicrobiology Lab Core Facility
Geomicrobial Physiology and Evolution Lab
University of Colorado Boulder GeoMicrobial Co-Culturing Lab
Microbial culturing facility focused on growing microorganisms with diverse physiologies from photosynthesis to methanogenesis.
Sorting long Reads of Y or other sex-limited chromosome
Software application for sorting long-read of sex-limited (Y or W) chromosome. Used to identify male specific k-mers based on population data.
Web-based platform to interactively build complex systems and prepare their inputs with well established and reproducible simulation protocols for molecular simulations.
Web server for accurate local and global model quality estimates. Composite scoring function to derive entire structure and residue absolute quality estimates on basis of one single model.
Web application for prediction of topology of both alpha-helical and beta-barrel transmembrane proteins. Used to predict alpha and beta transmembrane proteins using deep neural networks.
Fixed stage microscope for patch-clamp experiments on nerve cells and brain slices. With its design optimized for low vibration and generous room for micromanipulation and patch clamp accessories, Axio Examiner enables undisturbed low-noise single-channel recordings.
Single Nucleus Methly-Seq and Chromatin Capture
Single Nucleus Methly-Seq and Chromatin Capture (snM3C)
single-nucleus Methylome and Chromatin Contact
Software open-source, cloud-optimized computational workflow for processing single-nucleus methylome and chromatin contact (snm3C) sequencing data. The workflow is designed to demultiplex and align raw sequencing reads, call chromatin contacts, and generate summary metrics.
Software open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). It supports the processing of 3' single-nucleus histone modification data (generated with the paired-tag protocol]) and 10x gene expression (GEX) data generated with the 10x Chromium Multiome assay.
Artificial Intelligence engineering consortium, built on philosophy of open collaboration to improve AI systems to measure and improve accuracy, safety, speed and efficiency of AI technologies helping companies and universities around the world. Community-driven and community-funded effort.
Web application for calculating liquid junction potential between two solutions according to the stationary Nernst-Planck equation.
Software R package for flexible time-to-event figures creation. Used to create figures ready for publication.
Software package for converting between SingleCellExperiment objects and alternative objects for storing single-cell RNA-sequencing data. Used for conversion between scRNA-seq objects.
Software data-driven tool to identify understudied genes and characterize their tractability. Users submit list of human genes and can filter these genes down based on list of factors. Code to generate Find My Understudied Genes app for Windows, iOS and macOS platforms.
Zeiss | LSM 980 with Airyscan 2 Microscope
Upright laser scanning confocal microscope with Airyscan 2 technology. Airyscan module is new detector concept featuring 32 channel GaAsP-PMT area detector. Airyscan detector brings simultaneous improvements in spatial resolution and signal-to-noise ratio in comparison with conventional confocal microscopy.
Software Mendelian randomization R package. Encodes several methods for performing Mendelian randomization analyses with summarized data.
Community of cyberinfrastructure specialists and domain scientists working together to bring science online. SGX3 Center for excellence provides opportunity to participate with SGX3 to define the future intersection of science and cyberinfrastreucture.
Public research university in Kraków, Poland. Founded in 1364 by King Casimir III the Great, it is the oldest university in Poland and the 13th oldest university in continuous operation in the world. It is regarded as Poland's most prestigious academic institution.
Learning and Development data repository
NIH funded collaboration between researchers and librarians to build behavioral project oriented data repository containing decades of knowledge from educational and developmental sciences on individuals across the full range of abilities.
Software R package provides intuitive interface for working with competing risk endpoints. Used for competing risks estimation.
Software Python library for analyzing uncertainties and sensitivities in computational models by setting up, running, and analyzing Monte Carlo simulation wrapped around that model.
Software R package for generating circular multi-track plots.
Open source JIT compiler that translates subset of Python and NumPy code into fast machine code. Can compile large subset of numerically-focused Python, including many NumPy functions. Has support for automatic parallelization of loops, generation of GPU-accelerated code, and creation of ufuncs and C callbacks.
Software tool for determination of dispersion risks due to leaching and for determination of soil quality evolution.
Web server for predicting protein toxicity. Protein toxicity classifier, which relies on protein primary sequence. Used for predicting toxicity of biologics.
Software for processing and analyzing Targets and Tagmentation data. The illustration data used in this tutorial is the profiling of histone modifications in the human lymphoma K562 cell line, but the tutorial is generally applicable to any chromatin protein, including transcription factors, RNA polymerase II, and epitope-tagged proteins.
Software tool for predicting reservoir hosts of RNA viruses through viral genomes. Takes complete RNA viral genomes as input and predicts natural reservoir host groups from kingdom level to order level.
Company offers research chemicals and biochemicals for scientific use. Provides customer oriented services including customized order volume ranging from milligrams to kilograms scale, structurally and synthetically diverse biologically active compounds.
Biotechnology company in Nuaillé, France. Provides animal serum and cell culture media.
Sigma | Labnet MultiGene Gradient PCR Thermal Cycler
Labnet MultiGene™ Gradient PCR Thermal Cycler
PCR thermal cycler with 96 well block (12 8 x 0.2 mL strip tubes, 96 x 0.2 mL), AC/DC input 230 V AC.
Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package.
Beckman Coulter | CytoFLEX LX Flow Cytometer
This model is equipped with four lasers (405, 488 561 and 638nm), and is capable of detecting FSC, SSC and 16 colors.
Beckman Coulter | CytoFLEX SRT Cell Sorter
Offers multiple configurations with the option to easily upgrade. Instrument can be configured to use up to four lasers and up to 15-color detection to identify subtle differences between cells. Core Facility’s CytoFLEX SRT is four-laser platform (405, 488, 561 and 638nm) instrument capable of detecting FSC, SSC and 15-colors and is able to sort up to four separate populations from the same sample, and deposit them in variety of tubes and plates. Operates under CytExpert SRT Software.
High sensitivity flow cytometry for nanoparticle analysis for life science, nanoscience and nanotechnology studies. Can be used for multiparameter characterization of natural and synthetic nanoparticles (7-1000 nm) at the single particle level.Combining light scattering and fluorescence detection, high-resolution distributions of particle size and biochemical properties can be acquired simultaneously in 1-2 minutes. UNL Flow Cytometry Core NanoAnalyzer is equipped with two lasers (488 and 640nm), and is capable of detecting SSC and two colors. Operates under NF Professional Software. System is designed to measure size and concentration of nanoparticle samples.
Thermo Fisher | EVOS M7000 Imaging System
Fully automated, inverted, multi-channel fluorescence and transmitted light imaging system. System with acquisition tools with enhanced autofocus algorithms and automated routines for microwell plate assays, time-lapse live cell imaging, area scanning in time lapse and Z-stacks in scan mode to generate publication quality images and data.
Software tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities.
Penn State Hershey College of Medicine Atomic Force Microscopy Core Facility
Hershey College of Medicine Atomic Force Microscopy Core Facility
Provides College of Medicine research community with access to atomic force microscopy equipment and expertise.
Geisel School of Medicine at Dartmouth DCC Microscopy Shared Resource Core Facility
Geisel School of Medicine at Dartmouth DCC-Microscopy Shared Resource
Facility provides imaging instrumentation and analysis software along with training and expertise.Instrumentation and technologies available to users include Zeiss LSM800 AIRYSCAN confocal microscope integrated with Zen software; PerkinElmer / Akoya Vectra 3.0 Automated Quantitative Pathology Imaging System;Agilent/BioTek Cytation 5 with BioSpa8 live-cell microscopy system for fluorescence and phase contrast microscopy; Olympus IX-83 ZDC2 microscope equipped with PRIMO UV light-based bioengineering device for micropatterning and microfabrication; Olympus IX73 Inverted Fluorescence Microscope.Image analysis software hosted on appropriately powered workstations with cloud connectivity for high capacity storage: HALO3, Inform, Volocity, AutoDeblur, Image-J / Fiji.Transmission and scanning electron microscopy including FEI Talos F200i (200kV TEM and STEM electron microscope (TEM), equipped for micro-analysis, and cryo-EM;FEI Helios CX5 dual beam FIB-SEM system with X-ray microanalysis detectors; instruments for specimen preparation for transmission and scanning electron microscopy including ultramicrotomes Leica Ultracut UC6 and UC7, critical point dryer Samdri-970, Leica ACE 600 coater and ThermoFisher Vitrobot.
Geisel School of Medicine at Dartmouth DCC Irradiation, Imaging, Microscopy and Animal Cancer Models Core Facility
Geisel School of Medicine at Dartmouth DCC Irradiation
Integrated core offers services in Irradiation, pre-clinical imaging of small and large animals, light and electron microscopy, large and small animal cancer models. Irradiation Section assists investigators in radiation treatment planning and delivery of ionizing irradiation to cells, rodents and large animals with engineered, transplanted or spontaneous tumors.Imaging Section provides technologies for non-invasive, whole-animal imaging of animals used in preclinical research studies. Microscopy Section provides access to point scanning confocal microscopy with Airyscan super resolution, conventional bright field and fluorescence light microscopy, high throughput live imaging, automated slide scanning and image analysis resources. Electron microscopy resource provides scanning transmission electron microscopy. Animal Cancer Models section supports generation and utilization of large and small animals for modeling cancer and other human diseases. Section has expertise in generating cancer models using wild type or genetically engineered animals in immunocompetent and immunocompromised backgrounds, as well as mice with humanized immune system.
Ohio State University Campus Microscopy and Imaging Core Facility
Ohio State University Campus Microscopy and Imaging Facility
OSU-Campus Microscopy & Imaging Facility
Offers services from sample preparation to image processing.Provides instrumentation for use such as electron microscopy, light microscopy, and access to other instrumentation for use in sample prep.
University of Colorado Boulder Intermountain Neuroimaging Consortium Core Facility
University of Colorado Boulder Intermountain Neuroimaging Consortium
Magnetic resonance imaging research facility located at University of Colorado Boulder.
Colorado School of Mines Shared Instrumentation Facility Water Quality Analysis Core Facility
Core facility houses the capability to test water using multiple instruments and techniques including : Ion Chromatography, which is an analytical technique for determining the concentration of anions in aqueous solutions such as fluoride, chloride, nitrate, phosphate and sulfate; Carbon and nitrogen analysis, which incorporates measurements of total carbon, total inorganic carbon and total organic carbon together with total nitrogen; and other parameters such as pH, alkalinity, turbidity, conductivity (and others) using instrumentation and kits.
Software image analysis tool for digital pathology and spatial biology researchers.
Stanford University Cosmogenic Isotope Lab Core Facility
Core for understanding Earth surface processes in bedrock, soil, water, and sediment. Interactions between cosmic rays and Earth’s upper atmosphere create unique isotopes both in the atmosphere and in materials on Earth’s surface. By assessing the ratios and/or concentrations of these isotopes, we can get a deeper insight into the exposure age, soil production rate, catchment-averaged erosion, and processes of Earth’s varied landscapes.
University of Florida Systems Physiology and Omics Core Facility
University of Florida Systems Physiology and Omics Core
Provides specialized resources and expertise to support scientists that want to incorporate systemic measures of mouse activity, metabolism and feeding. The systems are also embedded within light regulated environments to capture circadian, time of day, based outcomes.Supports scientists wanting to perform circadian type analyses with either pre-clinical or clinical time series data. Supports scientists wanting to incorporate -Omics measures into their studies with experience in genomics, proteomics and metabolomics assays/analyses. These services are available to support new investigators, early-stage investigators and current investigators in aging.
Platform for Research in Medical Imaging
Software tool to support translation of basic research in medical image analysis into early clinical studies.
University of Wisconsin-Madison Carbone Cancer Center Flow Laboratory Core Facility
Facility provides technical and educational support for fluorescence based single cell analysis and isolation to further the characterization and understanding of cellular function, biomarkers, pathology, and treatment in basic, translational, and clinical research projects.
California Institute of Technology Flow Cytometry and Cell Sorting Core Facility
California Institute of Technology Caltech Flow Cytometry and Cell Sorting Facility
Caltech Flow Cytometry and Cell Sorting Facility
Facility offers cell analyzers and cell sorters as well as expertise in large range of traditional immunophenotyping and small particle, geo-physical applications.
Smithsonian National Museum of Natural History
Natural history museum administered by Smithsonian Institution, located on the National Mall in Washington, D.C., United States. Houses specimens and artifacts, which are mostly animals preserved in formaldehyde. Digital records are available online.
Convergence Research the Non-Clinical Tomography Users Research Network
FAIROS Research Coordination Network. Mirroring NSF’s “10 Big Ideas” of Convergence Research the Non-Clinical Tomography Users Research Network (NoCTURN) will leverage input from broad community of tomography educators, researchers, and industry stakeholders to propose improvements to data handling that cut across scientific disciplines. Primary goal is to develop practical recommendations that link today’s tomography data with tomorrow’s tomography discoveries.
Smithsonian Institution National Museum of Natural History Scientific Imaging Core Facility
Smithsonian Institution National Museum of Natural History
Scientific Imaging is comprised of Microscopy Lab, µCT Imaging Center (mCTIC), and Scientific Visualization Center (SciVis). Facility is user driven research core in support of National Museum of Natural History life sciences research. Provides preparation and examination of natural history specimens for scanning electron microscopy, stereo light microscopy, compound fluorescence microscopy, X-ray micro-computed tomography and 3D laser scanning. Produces reconstructed volumes of scanned specimens. Provides reconstruction, segmentation, analysis and animation of 3D datasets.
High Performance Computing cluster consisting of Linux compute servers with processing power and memory for running large, long or GPU-enabled jobs.
Network for Advanced Nuclear Magnetic Resonance
Provides distributed services from Universities of Connecticut, Georgia, and Wisconsin to democratize application of high-field NMR spectroscopy for applications in biomedicine, materials science, and chemistry. Multi-institution collaboration creating distributed research infrastructure for NMR applications including resource discovery, access to NMR spectrometers, ranging from bench top to ultra-high field, knowledgebases on best practices, and data archiving and sharing.
Software pipeline to handle data from PacBio and Oxford Nanopore platforms. Pipeline does read alignment, corrects for mismatches, microindels and non-canonical splice junctions and then provides quantitations and QC-metrics.
Virtual Multidisciplinary Stroke Care Clinic platform
Platform containing informative videos on stroke care and rehabilitation which was created in collaboration with multidisciplinary team of healthcare professionals.
Bio-Techne | ProteinSimple Jess Automated Western Blot System
Simple Western blotting device that performs capillary based immunoassays and fully automated Western blot analysis. Automates protein separation and immunodetection of traditional Western blotting.Traditional Western blotting steps of sample separation, wash buffer incubations, and immunodetection of target proteins occur inside hands free capillary instrument.
Roche Diagnostics develops and produces medical tests and digital tools that provide information to help healthcare professionals find the right treatment for patients and deliver the best patient care to improve, prolong and save lives.
Automated slide preparation system to run manual and fully automated experiments simultaneously with no synchronization errors. Ability to fully automate broad range of IHC and ISH assays, including FISH, gene and protein IHC/ISH, mRNA ISH and multiplex assays with any combination of IHC and ISH. Automated baking, deparaffinization, cell conditioning and staining including immunohistochemistry (IHC) and in situ hybridization (ISH) Enhanced multiplexing and immunofluorescence, 30 slide reaction chambers allow for independent protocols for each individual slide. Ready-to-use optimized reagents.
Software R package for calculation of standard and bootstrap confidence intervals.
Software Python library for unsupervised topic modeling, document indexing, retrieval by similarity, and other natural language processing functionalities, using modern statistical machine learning.
Software application as fast, extensible progress bar for Python and CLI.
Software suite of open source Python modules, data sets, and tutorials supporting research and development in Natural Language Processing. Platform for building Python programs to work with human language data. Provides interfaces to corpora and lexical resources such as WordNet, along with suite of text processing libraries for classification, tokenization, stemming, tagging, parsing, and semantic reasoning, wrappers for industrial strength NLP libraries, and active discussion forum.
University of Pittsburgh Unified Flow Cytometry Core Facility
University of Pittsburgh Unified Flow Core
Core provides flow cytometry and cell sorting services. Staff offers help with instrument setup, data analysis, and consultation for experiment design. Training is available to run analytical cytometers.Houses FACSAria cell sorters, Cytek Aurora Cell Sorter, LSR Fortessas , LSR IIs, ImageStreamx Mark II and 4 full spectral cytometers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Global Natural Product Social Molecular Networking Platform Mass Spectrometry Search Tool
Web application that is embedded in GNPS, which is community service. Web enabled mass spectrometry search engine for searches of all small molecule Mass Spectrometry data. Used to search single MS/MS spectrum against public GNPS spectral libraries and all public MS/MS datasets.
Software tool to detect single nucleotide variants by comparing data from next-generation sequencing experiments. Variant caller to detect single nucleotide variant positions from comparing RNA-DNA and/or RNA-RNA sequencing samples. JACUSA2 is one-stop solution to detect single nucleotide variants and reverse transcriptase induced arrest events in Next-generation sequencing data.
Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE.
Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data.
Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles.
Database containing detailed information about small molecules produced by human microbiome. Provides metabolite data including structure, names, descriptions, chemical taxonomy, chemical ontology, physico-chemical data, spectra and contains detailed information about microbes that produce these chemicals, enzymatic reactions responsible for their production, bioactivity of chemicals and anatomical location of these chemicals and microbes. Many data fields in the database are hyperlinked to other databases including FooDB, HMDB, KEGG, PubChem, MetaCyc, ChEBI, UniProt, and GenBank. Database is FAIR compliant.The data in MiMeDB are released under the Creative Commons (CC) 4.0 License.
Loyola University School of Medicine Flow Cytometry Core Facility
Loyola University Chicago Loyola Flow Cytometry Core
Core Facility with conventional, full-spectrum, cell sorting and flow cytometry services. Training provided by core personnel.
University of Pittsburgh Single Cell Core Facility
University of Pittsburgh Single Cell Core
Core offers single cell sequencing. Provides analysis of transcriptomics, proteomics and epigenomics at single cell level. Provides comprehensive approach for cell characterization and gene expression profiling. Services include single cell gene expression, immune profiling, ATAC, and multiome analysis.
Image capture brightfield whole slide scanner for low throughput with five slide capacity and 20X and 40x magnification capabilities. 2x3 slide option available for large slides. Aperio CS2 runs on Microsoft Windows 10 operating system.
Delft University of Technology Robotics Institute
Unites all Delft University of Technology research in the field of robotics. Its main challenge is to get robots and humans to work together effectively in unstructured environments, and real settings. Institute takes a leading role in the creation of the next generation robots.
University of Pittsburgh Dietrich School Electronics Shop Core Facility
Core specializes in electrical design, fabrication, and repair of research equipment and instrumentation.
Leica MyNeuroLab Impact One Stereotaxic Impactor
System used for small animal brain surgery. Allows to create neurotrauma model with unprecedented degree of reproducibility of the direction of impact and position of the injury. Controlled impact injury device. Device used for traumatic brain injury induction.
Software R package models, plans, and schedules flexible, such as agile, extreme, and hybrid project plans. The package contains project planning, scheduling, and risk assessment functions.
Software library and tool for accessing remote BLOW5 files. Used for fetching reads from remote BLOW5 files.
Software suite of business analytics tools to connect to all sorts of data and create visuals and reports. Interactive data visualization and reporting platform developed by Microsoft. Part of Microsoft Power Platform.
Housekeeping and Reference Transcript Atlas
Web based database to search human and mouse housekeeping and candidate reference genes/transcripts. It also offers tissue and cell selective candidate reference transcripts and some primers for quantitative PCR normalization.
Software tool for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice. Detects variations, specifically low allele frequency variation, in next generation sequencing data.
Web Java application for visualizing and analyzing trends and patterns in scientific literature. Provides various functions to facilitate understanding and interpretation of network patterns and historical patterns,finding citation hotspots, decomposing network into clusters, automatic labeling clusters with terms from citing articles, geospatial patterns of collaboration, and unique areas of international collaboration. Supports structural and temporal analyses of networks derived from scientific publications, including collaboration networks, author co-citation networks, and document co-citation networks. Supports networks of hybrid node types such as terms, institutions, and countries, and hybrid link types such as co-citation, co-occurrence, and directed citing links.
Adult Zebrafish Brain Gene Expression Database
Collection of in situ hybridization data of gene expression in the brain of adult fish. Data can be viewed and downloaded.
University of Pittsburgh Dietrich School Mass Spectrometry Core Facility
University of Pittsburgh Dietrich School Mass Spectrometry Facility
Core provides mass spectrometry instruments including Bruker Daltonics UltrafleXtreme MALDI TOF-TOF, Shimadzu Instrument LCMS-2020,Shimadzu Instrument QP2010S GCMS,Thermo Fisher Oribtrap Exploris 240,Thermo Scientific Q-Exactive Oribtrap for determining masses of particles, and elemental composition of sample or molecule.
University of Pittsburgh Nanoscale Fabrication and Characterization Core Facility
Core supports fabrication and characterization of nanoscale materials and structures, and integration of devices at all length scales. Houses advanced equipment with core nano-level capability for fabrication and characterization, including electron-beam lithography system, dual-beam system, plasma etching, thin film deposition, TEM, multifunctional scanning probe station, modular XRD, and more.
University of Pittsburgh Dietrich School X-ray Crystallography Core Facility
University of Pittsburgh Dietrich School X-ray Crystallography Facility
X-Ray Diffraction Facility located in Chemistry Instrumentation Center is equipped with Bruker X8 Prospector Ultra with Copper ImuS micro-focus X-ray source and Bruker D8 Venture Dual source (Molybdenum and Copper micro-focus X-ray tubes) diffractometer with Photon III CPAD detector. Data can be collected at nitrogen-cooled temperatures as low as 90K. Core provides sample submission services for small molecule crystalography.
University of Pittsburgh Dietrich School NMR Core Facility
University of Pittsburgh Dietrich School NMR Facility
Facility specializes in training users in both solution phase and solid state NMR across all active nuclei and multiple NMR experients
University of Pittsburgh Dietrich School Materials Characterization Laboratory Core Facility
University of Pittsburgh Dietrich School Materials Characterization Laboratory
Facility maintains large array of instrumentation for production and analysis of complex materials, including nanoparticles, thin films, polymers, ceramics, and molecular electronics.Oversees operations of Department Biological Instrumentation Cluster which provides access to specialized equipment used in molecular biology and biological chemistry.
Web tool to detect under- or over-dispersion in a baseline table from baseline table.
Company designs, develops and commercializes molecular pathology systems for tumor diagnosis, prognosis, precision medicine and life science research.
Caliper provides products and services for life sciences research. The firm, founded in 1995, is based in Hopkinton, Massachusetts with direct sales, service and application support operations in countries around the globe.
Spatial biology company, building multiplex immunofluorescence and IHC solutions for discovery and immuno-oncology research.Laboratory equipment supplier in Tolochenaz, Switzerland.
University of Pittsburgh School of Medicine Cell Imaging Core Facility
University of Pittsburgh Cell Imaging Core
Core for image based analysis, laser capture microdissection, and live cell fluorescence imaging. Provides range of consultation and laboratory services performed by core staff. Users training is available.Cell and Tissue imaging on confocal microscopes including Zeiss LSM 710, Leical Sp8 and Leica Stellaris.
University of Manitoba Genomic Centre for Cancer Research and Diagnosis Core Facility
Advanced imaging core for multi channel fluorescence imaging,3D imaging, super resolution imaging, scanning, image analysis in cancer research. Technical services are forcused on fluorescent in situ hybridization, immunohistochemistry, and microdissection of biological material.
University of Pittsburgh Luminex Core Facility
University of Pittsburgh Luminex Core Laboratory
Facility utilizes LabMA system developed by Luminex Co., for protein analysis that permits simultaneous quantitative analysis of up to 100 different proteins, peptides, or RNA molecules in single microtiter well. Commercially available assays from Millipore, R&D Systems, Bio-Rad or Thermofisher are also used for analysis.
University of Florida Herbert Wertheim College of Engineering Research Service Centers Core Facility
Herbert Wertheim College of Engineering Research Service Centers
University of Florida Herbert Wertheim College of Engineering Research Service Centers
Core provides access to characterization and process instrumentation. Expert staff provides assistance and guidance. Services include electron microscopy and analysis (SEM, TEM, FIB, EBSD, WDS), microelectronic device fabrication (7000 sq ft cleanroom, Class 100-1000), X-ray computed tomography (CT), particle system characterization (size, zeta potential, surface area, porosity, rheology), X-ray diffraction, surface analysis (AFM, profilometry, XPS, Auger), spectroscopy (UV/Vis with integrating sphere, FTIR/NIR with micro capability and micro-Raman).
The Douglas Research Centre: Neuroinformatics Platform
Core provides technical support and expertise to enable measurement based care and compute focused research. Service consists of computing platform, composed of redundant high-capacity storage system, along with compute cluster and workstations, tied together with unified single-sign-on user and group management. Platform has facilities for capturing form-based, interactive testing-based and arbitrary binary (imaging etc.) data. Allows clinical researchers to track the trajectories of participating patients across Douglas clinics.
Software R package for calculating Net Reclassification Improvement for risk prediction models with time to event and binary data. NRI for risk prediction models with time to event and binary response data.
University of Pittsburgh Advanced Imaging Center Core Facility
University of Pittsburgh UPitt-Advanced Imaging Center
Core provides instrumentation and expertise for high-field Preclinical Magnetic Resonance Imaging and Magnetic Resonance Microscopy. Facility has instruments: Bruker 9.4 Tesla/30 cm AVANCE 3 HD scanner and Bruker 11.7 Tesla 89 mm AVANCE 3 HD micro imaging system.
University of Chicago Single Cell Immunophenotyping Core Facility
University of Chicago Single Cell Immunophenotyping Core
Core is self service facility that provides access to specialized instrumentation for phenotyping and genotyping of immune cells. Offers single cell next generation sequencing and quality control technologies. All instruments are located in the laboratories of four different CIIC investigators (KCBD 10220E and 10220C), and are available for use by the larger UChicago community.
EMBOSS Water uses Smith-Waterman algorithm to calculate the local alignment of two sequences. Pairwise sequence alignment. Used for determining protein-to-protein homology.
Database of predicted three dimensional structures of Human Leukocyte Antigens molecules constructed by using homology modeling. Developed to improve epitope analysis in context of organ transplantation by providing 3D structures of HLA molecules present in current solid-phase assays for serum antibodies screening. Gives crystalographic modeling structure of HLA protein.Provides means to visualize target epitopes recognized by anti-HLA antibodies.
Database of theoretical and confirmed HLA eplets recognizable by B-Cell receptors. Eplets are sorted according to their amino acid sequence positions. Used for identifying HLA epitopes.
University of Pittsburgh Dietrich School of Arts and Sciences Pitt Isotope Tracer Lab Core Facility
University of Pittsburgh Dietrich School Pitt Isotope Tracer Lab
One of several isotope labs in Department of Geology and Environmental Science formerly known as Regional Stable Isotope Lab for Earth and Environmental Science Research, has capacity for wide variety of isotopic measurements in multitude of sample media. Capabilities include: Nitrate (?15N, ?18O, D17O);Greenhouse and trace gases like carbon dioxide (?13C, ?18O), nitrous oxide (?15N, ?18O), methane (?13C); Nitrogen, carbon, and sulfur (?15N, ?13C, ?34S) in organic and other solid materials (e.g., biota, soils);Ammonium (?15N); Dry reactive nitrogen deposition (?15N-NH3, ?15-NO2, and ?15N-HNO3); and Carbonates (?13C, ?18O).
System that combines proprietary 10x microfluidics technology using Chromium Automated Controller with precise, automated liquid handling that allows users to run 10x Genomics end to end library construction workflow with minimal user interaction. Integrates components customized for 10x Genomics single cell workflows, automation specific reagents and consumables, and touchscreen computer. Used to generate consistent and reproducible single cell gene expression results across experiments, users, and multiple sites.
MCDiagnostics | Ultima CPX Metabolic Stress Testing System
Metabolic stress testing system provides breath by breath metabolic analysis during both rest and exercise for complete assessment of functional capacity and cardiorespiratory diagnostics.Testing capabilities including Exercise Capacity,Direct Fick Cardiac Output and Spirometry.
Web tool for prediction of sgRNAs. Helps to select optimal guide RNA for gene of interest. Support for designing guide libraries. CRISPick ranks and picks candidate CRISPRko sgRNA sequences for targets provided, while attempting to maximize on-target activity and minimizing off-target activity.
Hosted drug discovery informatics platform that securely manages both private and external biological and chemical data. Provides core functionality including chemical registration, structure activity relationship, chemical inventory, and electronic lab notebook capabilities.
Dragonfly is a brand of Comet Technologies Canada Inc. Company develops applications to better understand image data. Providews advanced 3D visualization and analysis software for 2D, 3D, and 4D imaging studies.
University of Pittsburgh Genome Editing, Transgenic and Virus Core Facility
Core provides technical expertise, advice, and training and is comprised of three functional sections: Molecular cloning (plasmid, virus, CRISPR/Cas9); Viral vectors (lentivirus, adenovirus, adeno-associated virus); Animal services (transgenic, knockout, cryopreservation, re-derivation, and more). Services offered include Assistance for generating recombinant plasmids; Design and implementation of CRISPR/Cas9 technology for in vivo and in vitro work; Mouse and rat transgenesis,including transgenic and knockout/knockdown techniques using pronuclear injection, ES cell injection/chimera, and CRISPR/Cas9-mediated genome editing; Production of lentivirus, adenovirus, and adeno-associated virus vectors; Additional animal testing and procedures: teratoma and chimera testing to validate putative pluripotent stem cell lines, cryopreserve or re-derive of valuable transgenic lines (sperm or embryos).
University of Pittsburgh Small Animal Ultrasonography Core Facility
University of Pittsburgh UPitt - Small Animal Ultrasonography Core
UPitt - Small Animal Ultrasonography Core
Core provides expertise and high frequency ultrasound instrumentation suitable for image acquisition and analysis applicable to your research studies. Provides Fuji/Visualsonics Vevo 3100 ultrasound imaging machine to perform ultrasounds on small animals. The scanner has high temporal and spatial resolution; current imaging probes utilize frequencies from 13-55 MHz.
Penn State Institute for Computational and Data Sciences Center for Artificial Intelligence Foundations and Scientific Applications
Penn State Center for Artificial Intelligence Foundations and Scientific Applications
Aims to foster collaborative, interdisciplinary research across Penn State and beyond aimed at addressing the AI grand challenge of accelerating scientific progress through synergistic advances across multiple areas of AI.
Penn State Institute for Computational and Data Sciences
Institute for Computational and Data Sciences
ICDS brings researchers together to develop and apply innovative, high performance computation methods. Helps to apply big data and big simulation methods across research landscape.
MELQUEST | Lick Analysis Formula Selection Preference Experiment System LKP2
Rick analytical choice preference experiment system LKP2
Apparatus used for measuring mice licking pattern for particular solutions. Device records licking behavior by measuring number of licks per second , which is drawn as bar graph on the PC software screen .
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 14,2026. Device used for measuring blood glucose levels.
Electrophysiology acquisition software, compatible with HEKA EPC amplifiers.
Certara D360 Scientific Informatics Discovery Platform
Platform provides self service data access, integrated data visualization and analysis and collaboration tools that allow compound prioritization, development of SAR and many other scientific data workflows in chemistry and biology domains to improve effectiveness of data driven research.
Inverted fluorescence phase contrast microscope. Objective lenses. BZ Series infinite optical system.
Stimulus Evoked Behavioral tracking in 3D for Rodents
Software tool to automate and standardize ethologically driven observation of freely moving mice. Identifies different postures of mice and associates them with emotions, offering detailed analysis of their movements frame by frame. Used for tracking mouse body language and studying emotional behaviors.
Centers for Disease Control and Prevention NHIS Data, Questionnaires and Related Documentation
Questionnaires and Related Documentation
Collection of National Health Interview Survey (NHIS) data, questionnaires and related documents to monitor health of the United States population through collection and analysis of data on broad range of health topics.
Creighton University Histology Core Facility
Facility provides equipment and services for studies utilizing animal and human tissues. Services include Sample, Processing, Embedding, Sectioning, Histochemistry, Immunohistochemistry, Imaging, Microscopy. Equipment includes microtomes for paraffin sections, cryostat for frozen sections, vibratome for plastic sections, and Nikon Eclipse Ci-L microscope for brightfield and fluorescence applications.
Software toolbox as plugin for ImageJ that supports colocalization analysis in light microscopy. Used for subcellular colocalization analysis under ImageJ that integrates current global statistic methods and novel object-based approach.
Software Rust FHE library specialized for private information retrieval. Includes bindings to JS and Python. Software Development Kit for private data access, built on homomorphic encryption.
CUda accelerated Fully Homomorphic Encryption
Open source software library for Fully Homomorphic Encryption on CUDA enabled GPUs. CUDA accelerated Fully Homomorphic Encryption library.
Software GPU-accelerated library for homomorphic encryption schemes and homomorphic algorithms defined over polynomial rings.
Software Rust library for lattice-based additive homomorphic encryption.
Software library as implementation of leveled fully homomorphic scheme YASHE on GPGPUs. Used to obtain significant performance improvements.
Fastest Homomorphic Encryption in the West
Open-source software library distributed under the terms of the GNU General Public License. Used to homomorphically compute simple bit operations, and refresh, bootstrap resulting output, which runs on personal computer in just about half a second.
Faster FHE instantiated with NTRU and LWE
Software C++ FHE library as fully homomorphic encryption scheme based on NTRU and LWE. MIT license.
Software library implementing Fan-Vercauteren homomorphic encryption scheme.
Software library that implements homomorphic encryption that supports fixed point arithmetics. This library supports approximate operations between rational numbers.
Open-source software library that implements homomorphic encryption. Supports BGV scheme with bootstrapping and Approximate Number CKKS scheme. HElib also includes optimizations for efficient homomorphic evaluation, focusing on effective use of ciphertext packing techniques and on the Gentry-Halevi-Smart optimizations.
Computational Help Evaluating RNA-RNA Interactions
Software tool to detect functional RNA-RNA interaction sites, by evaluating if interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by RRI prediction algorithm by removing false positive interactions.
Software contains all scripts and instructions for running Knowledge Graph-based Thought model, which is knowledge graph enhanced LLMs framework for pan-cancer question answering.
Image viewing software to observe digital images to the details like microscope. Supports images from all NanoZoomer series of whole slide scanners that scan glass slides at high speed.
Software C++ implementation of multivariate quadratic FHE.
Software Haskell library for ring-based lattice cryptography that supports FHE.
Software library for lattice-based multiparty homomorphic encryption in Go. Go library for lattice-based crypto that implements various schemes.
Software C library implementing FHE scheme using large integers. Implementation of the Fully Homomorphic Smart-Vercauteren Cryptosystem.
Software symmetric somewhat homomorphic encryption library based on DGHV.
Software homomorphic encryption library. C++ FHE library implementing BFV and CKKS schemes. Allows computations to be performed directly on encrypted data. This enables software engineers to build end-to-end encrypted data storage and computation services where the customer never needs to share their key with the service.
Software NTT-based Fast Lattice library specialized on power-of-two polynomials. Open source C++ library dedicated to ideal lattice cryptography. It is specialized in polynomial rings quotiented by cyclotomic polynomial whose degree is a power of two.
Software homomorphic encryption library for TypeScript or JavaScript.
Software Python GPU-accelerated HE library, faster than cuFHE, that implements the tfhe algorithms.
Open-source Fully Homomorphic Encryption
Open-source Fully Homomorphic Encryption library enables performing computations over encrypted data without having access to the secret key. OpenFHE is an open-source FHE library that includes efficient implementations of all common FHE schemes.
Open source Lattice Crypto software library. Software lattice encryption library superseded by OpenFHE.
Software Python library that implements number of Privacy Enhancing Technologies.
Python for Homomorphic Encryption Libraries
Software Python library for addition, subtraction, multiplication and scalar product over encrypted integers (BFV/BGV schemes) and approximated floating point values (CKKS scheme). This library acts as optimized Python API for C++ Homomorphic Encryption libraries. Python wrapper for SEAL, HElib, and PALISADE.
Software library for Partially Homomorphic Encryption in Python. Partially HE based on Paillier scheme.
Software customzable pipeline for biomedical information extraction. Deep learning and dictionary- based biomedical Named Entity Recognition pipeline to automatically extract domain specific information from medical text and in particular research articles. Pipeline contains NER models on cell lines, chemicals, disease, gene/protein and species.
Graph Adversarial Learning with Alignment
Software tool for protein function prediction. Extracts information from both protein sequences and structures, facilitating unified learning of protein structural representations. GALA incorporates domain discriminator conditioned on both representations and predicted probabilities, which undergoes adversarial training to ensure representation invariance across diverse environments.
Software Python library binding for Microsoft SEAL library.
Software application as forked of Apache Spark with support for fully homomorphic encryption. Apache Spark with add-on for FHE computations.
Software application for building privacy preserving applications using Fully Homomorphic Encryption and later on zero-knowledge proofs as well. Rust compiler for BFV fully homomorphic encryption scheme.
Software library for doing homomorphic encryption operations on tensors built on Microsoft SEAL, with Python API.
Fast Fully Homomorphic Encryption Library over Torus
Software library is original version of TFHE that implements base arithmetic and functionalities (bootstrapped and leveled). Bootstrapping in less than 0.1 seconds. Fast Fully Homomorphic Encryption Library over the Torus.
Software library as pure Rust implementation of TFHE Scheme for Boolean and Integer arithmetics over encrypted data. Rust implementation of TFHE scheme for boolean and integers FHE arithmetics.
Software toolkit to simplify process of designing homomorphic circuits for CKKS homomorphic encryption scheme. HIT repository uses Microsoft SEAL homomorphic encryption library as backend.
Software toolkit as compiler toolchain and RTE for running C++ programs over encrypted data by means of fully homomorphic encryption techniques.
Software toolkit as FHE Compiler that converts Python programs into FHE equivalent. Simplifies the use of fully homomorphic encryption which enables performing computations on encrypted data directly without the need to decrypt it first. Concrete framework contains TFHE Compiler based on LLVM, making writing FHE programs easy task for developers.
Software Python-based toolkit for data scientists without prior FHE knowledge. Privacy preserving ML framework built on top of Concrete, with bindings to traditional ML frameworks.
Software toolkit as open source homomorphic encryption framework. Provides C++ classes for supporting computation on private data. Allows programmers to incorporate privacy to their programs without expertise in cryptography. Software framework for compiling C++ programs with encrypted operands.
Software toolkit as compiler for SEAL homomorphic encryption library. Automates away parts that require cryptographic expertise. Allows to write programs that operate on encrypted data without having access to the secret key. Native library written in C++ with bindings for Python. Both Linux and Windows are supported.
Software toolkit to perform Fully Homomorphic Encryption operations on encrypted data set. FHE compiler for C++ that converts subset of C++ programs into FHE circuits implemented in various backend libraries.
Software toolkit as C++ framework that translates between nearly plain text style user programs and FHE computations. Marble FHE library that translates between user programs written close-to-plaintext-style and FHE computations based on underlying FHE crypto libraries.
Software Homomorphic Encryption Evaluation Platform
Software toolkit as Homomorphic Encryption evaluation platform with set of native benchmarks and library agnostic language. Used to evaluate fully homomorphic encryption across libraries implementing different HE schemes within some cases incomparable security.
Software toolkit as extensible cross compiler and standardized benchmark suite enabling comparisons between Fully Homomorphic Encryption libraries. Cross compiler and standardized benchmarks for FHE computation that targets lattigo, HElib, PALISADE, Microsoft SEAL, and tfhe.
HEIR: Homomorphic Encryption Intermediate Representation
Homomorphic Encryption Intermediate Representation
Software toolkint as compiler for homomorphic encryption. Google MLIR-based toolchain for FHE compilers.
University of Chicago FIB-SEM Core Facility
Focused Ion Beam - Scanning Electron Microscope Core Facility
Facility in the Department of the Geophysical Sciences features instruments including TESCAN LYRA3 field-emission scanning electron microscope (FESEM) with focused ion beam (FIB). It is equiped to do EDS, WDS, EBSD, etc.
Magee-Womens Research Institute Confocal Microscope Core Facility
Confocal Microscope Core at Magee-Women's Research Institute
Magee-Womens Research Institute Confocal Microscope Core
Core for imaging from single plane acquisition, to Z-stacks and 3D reconstruction, and to live imaging on slides or in tissue culture dishes. Microscopes are user operated after intensive training and demonstration of proficiency.
University of Pittsburgh Clinical and Translational Science Institute Biostatistics, Epidemiology and Research Design Core Facility
University of Pittsburgh Clinical and Translational Science Institute Biostatistics
University of Pittsburgh CTSI Biostatistics
Core provides consultation regarding study design, statistical analyses, power and sample size calculations and data collection for clinical and translational studies and grant applications. BERD offers consultation for collecting and managing data using the REDCap system. BERD also offers a series of workshops to provide essential elements involved in data collection, data management and creating reports for research studies.
University of Pittsburgh Magnetic Resonance Research Center Core Facility
University of Pittsburgh Magnetic Resonance Research Center
Core is dedicated to development and application of magnetic resonance imaging and magnetic resonance spectroscopy for medical and biological research. MRRC is whole-body imaging capable with specialty in anatomical MRI imaging of brain, spine, extremities, liver, bladder as well as functional MRI to study cognitive, sensory, and motor function in the brain.
University of Pittsburgh Cryo-electron Microscopy Core Facility
University of Pittsburgh Cryo-electron Microscopy Facility
Facility provides access to cutting edge instrumentation for high resolution structural analysis of proteins, protein complexes, viruses, macromolecular assemblies, cellular organelles, and bacterial cells., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
The Cell Imaging Core Laboratory at John G. Rangos Sr. Research Center
Cell Imaging Core Laboratory at John G. Rangos Sr. Research Center offers cell imaging by confocal microscopy, including live cell as well as laser capture microdissection and LCM.
University of Pittsburgh Small Molecule Biomarker Core Facility
Small Biomarker Core provides accurate and sensitive quantitative analysis in biological samples, with or without sample processing, using state-of-the-art ultra performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS). In addition to well qualified assays for common targets, experienced, knowledgeable personnel can provide assay development for novel targets
University of Pittsburgh Peptide and Peptoid Synthesis Core Facility
Core offers services for custom synthesis and characterization of peptides, peptoids and small molecule constructs. The facility has extensive capabilities for technologically advanced custom modifications such as bioconjugations and targeted therapeutic strategies. State of the art HPLC and mass spectrometry capabilities as well as services in support of protein, siRNA, antibody and small molecule quantification and characterization are available
University of Pittsburgh School of Medicine Gnotobiotic Animal Core Facility
Gnotobiotic Animal Core Laboratory is a BSL2-compliant mouse facility providing isolators for studies requiring a controlled microbiotic environment. All husbandry and upkeep services are provided. Additional specialized support is also available.
University of Pittsburgh Drosophila Core Facility
Drosophila Facility specializes in producing drosophila media in bulk and making it available to local investigators.
University of Pittsburgh Health Sciences Mass Spectrometry Core Facility
Health Sciences Mass Spectrometry Core provides liquid chromatography high resolution mass spectrometry (LC-HRMS) services for metabolomics, lipidomics and proteomics. Expert staff provide assistance throughout the full lifespan of all projects from experimental design and sample preparation through statistical analysis and interpretation of datasets.
University of Pittsburgh School of Medicine Flow Cytometry Core Facility
Flow Cytometry Core at John G. Rangos Sr. Research Center
Flow Cytometry Core at John G. Rangos Sr. Research Center is a BSL2+ compliant cytometry analysis and sorting facility located at the John G. Rangos Sr. Research Center in Lawrenceville serving investigators from across the University of Pittsburgh.
University of Pittsburgh School of Medicine Metabolic Core Facility
Metabolic Core Facility at the John G. Rangos Sr. Research Center
Core provides Instrument Services for analysis of 1) endogenous metabolic pathway intermediates or biomarkers from biological fluids, cell cultures, and tissues using Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS), 2) energy metabolism (cell bioenergetics) in living cells using a Seahorse Analyzer, and 3) biomarkers/metabolites to quantitate pathway intermediates using HPLC with 3 detector options (ECD, UV-VIS, FLR).
Small Animal Ultrasonogrphy Core provides high frequency ultrasound for non-invasive, in vivo, real-time, high-resolution imaging of tissue structure and function in small animals.
University of Pittsburgh Health Services Research Data Center Core Facility
Health Services Research Data Center (HSRDC)
Health Sciences Research Data Center is HIPAA compliant secure computing environment where study teams can store data and do analytics from anywhere with internet access. Teams work in Windows virtual desktop with memory, storage, and computing power dedicated to each user. Knowledgeable facility staff can provide data management, help with regulatory documents like DUAs, maintain systems compliance, and custom application development.
University of Pittsburgh Center for Research on Healthcare Data Center Core Facility
Univerity of Pittsburgh Center for Research on Healthcare Data Center Core Facility
Provides expertise and research infrastructure across four key Cores of Biostatistics, Data Management and Information Systems, Qualitative Analysis, and Data Coordination.
University of Pittsburgh School of Medicine Bioinformatics Core Facility
Bioinformatics Core Facility at the John G Rangos Sr. Research Center
Bioinformatics Core Facility at the John G. Rangos Sr. Research Center provides bioinformatics as well as biostatistics services across a wide range of disease domains. The next-generation sequencing data analysis includes, but is not limited to, whole genome-, whole exome-, bulk and single cell epigenome-, bulk and single cell transcriptome, spatial transcriptome, microbiome, metabolome, proteome and lipidome data analysis. The facility specializes in T-, and B- cell repertoire data analysis, multi-omics initiatives, and multimodal analysis. Shiny dashboard and other web application development is also supported.
University of Pittsburgh Pitt Biospecimen Core Facility
Pitt Biospecimen Core provides human sample procurement in multiple UPMC hospitals across Pittsburgh. Standard operating procedures for procurement and processing are developed for each project in partnership with each study's principal investigator. A rigorous quality assurance program ensures SOP compliance. In addition to specimen banking and pathology consultation, research histology services by expert histology specialists are also available.
Magee-Womens Research Institute Magee Obstetric Medical and Infant Database and Biobank Core Facility
Magee Obstetric Medical and Infant Database and Biobank
Core provides collection of obstetric biological materials from prenatal visits through delivery along with annotated clinical information. In addition to specimen access, MOMI staff can provide study design assistance as needed.
University of North Carolina at Chapel Hill Translational Genomics Lab Core Facility
UNC LCCC Translational Genomics Lab (TGL)
University of North Carolina at Chapel Hill UNC LCCC Translational Genomics Lab (TGL)
Core facility within Lineberger Comprehensive Cancer Center that performs sample processing for the molecular, pathologic, and genomic characterization of patient-derived specimens using high-end instrumentation and state-of-the-art methods. Service offerings include nucleic acid extraction, gene expression profiling, spatial genomics, next-generation sequencing library preparation, and high-throughput sequencing. Protocols leverage the reproducibility and reliability of automated instrumentation to minimize batch effects and processing errors (e.g. sample swaps). These workflows have been continuously optimized over the last decade, with a sample-to-answer historic success rate of ~90% for the >15,000 FFPE samples TGL has processed.
Software tool to fix base errors SNV/Indel in genome generated by noisy reads. Used to correct error bases in reference genome.
Software tool for long read based human genomic structural variation detection. Collects signatures of various types of SVs and employs clustering-and-refinement method to analyze signatures to implement sensitive SV detection.cuteSV2 is upgraded version of cuteSV.
Software Python tool for detection of m6A from direct RNA-Seq data. Leverages multiple instance learning framework to detect m6a modifications from Nanopore Direct RNA Sequencing data.
Collection of spatial transcriptomics data of mouse CT26 sample generated by stereo-seq technology.
Software Python package for analysis and visualization of spatial transcriptomics data. Framework to spatially and quantitatively profile the cellular neighborhood organized iTME.
LCSB Disease Modelling and Screening Platform Core Facility
Luxembourg Centre for Systems Biomedicine Disease Modelling and Screening Platform
Core provides infrastructure, disease modelling and compound screening expertise, to facilitate translation of basic scientific discoveries into tangible hit drug candidates. Platform acts as interface between fundamental biomedical research and high-standard drug discovery.
Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task
Perkin Elmer | IVIS Lumina III In Vivo Imaging System
Imaging system for both fluorescent and bioluminescent imaging in vivo. Lumina Series III platform offers full spectrum of wavelengths to perform almost any in vivo optical application with tunability of 20 nm. The system includes highly sensitive CCD camera, light-tight imaging chamber and complete automation and analysis capabilities. As optical imaging platform for in vivo analysis, IVIS systems include range of practical accessories developed through experience in research laboratories worldwide.
Software Geo-fencing demo application based on Paillier scheme. Used for testing out homomorphic encryption.
Web application for scheduling meetings using lattigo. Program for Lattigo homomorphic encryption library.
Software privacy-preserving framework based on TensorFlow. Integrates with mainstream privacy-preserving computation technologies, including cryptography, federated learning and trusted execution environment. Used to provide privacy-preserving solutions for artificial intelligence without requiring expertise in cryptography, federated learning and trusted execution environment. Rosetta reuses the APIs of TensorFlow and allows to transfer traditional TensorFlow codes into a privacy-preserving manner with minimal changes.
Software framework for Encrypted Machine Learning in TensorFlow. Bridge between TensorFlow and Microsoft SEAL library. TF Encrypted aims to make privacy-preserving machine learning readily available, without requiring expertise in cryptography, distributed systems, or high performance computing.
Database system that can process SQL queries over encrypted data. Protecting confidentiality with encrypted query processing.
Software wrapper on MongoDB Python driver that enables to query encrypted data. Enables to store and query encrypted data on database.
Software application as cryptographic security layer for relational database systems, that currently supports Microsoft SQL Server, MySQL, MariaDB, PostgreSQL and CockroachDB. Security layer for relational database systems.
Encrypted time-series database using homomorphic encryption-based access control. End-to-end encrypted time-series data store where storage server does not see any data in the clear. The time-series streams are encrypted on the client-side, and only authorized parties can decrypt and verify queries.Used to support both scalable computation over encrypted time series data and fine-grained cryptographic access control on queries.
Lickometer system based on open-source hardware platform with user-friendly interface software, capable of simultaneously receiving data from eight automated cages with two drinking bottles each. Device to acquire high-quality and detailed data. Adaptable to new types of sensors or other neuroscience tools capable of measuring brain activity simultaneously to the behavior.
Softwate R package to work with "grid" graphics, notably to arrange multiple grid-based plots on page, and draw tables. Miscellaneous functions for Grid graphics.
Software R package that produces forest plots using 'ggplot2' from models produced by functions such as stats::lm(), stats::glm() and survival::coxph().
Software tool for visualing centromeres with multiple omics data. Designed for centromere sequence calling.
Washington University School of Medicine Knight ADRC Request Center Resources Core Facility
Provides on request resources including Data: clinical and cognitive measures as well as MRI and amyloid imaging scans; Tissue: frozen brain tissue, paraffin brain sections, antemortem CSF, DNA, fibroblast, dermal fibroblasts, plasma (fasting and non-fasting) and iPSC; Participants: eligible participants may be invited to enroll in research of other investigators after appropriate review. Researchers can use the request portal to review Center guidelines and policies; view available data and tissue; access data tables and codebooks; and submit request for resources.
Cobas 6000 modular analyzer with c501 analytical module for clinical chemistry testing for in vitro diagnostic use. Mid volume analyzer for clinical chemistry assays, determinations of sodium, potassium, and chloride, and for measuring HbA1c levels in whole blood. Module will perform up to 1,000 tests per hour (600 photometrics tests per hour and 400 ISE tests per hour) and holds up to 60 reagent packs on-board. Designed to use serum/plasma, urine, CSF, supernatant and whole blood sample types. Performs photometric assays as well as ion-selective electrode (ISE) determinations.
Cobas 8000 modular analyzer series is scalable module based Serum Work Area solution for range of in vitro diagnostics testing of clinical chemistry and immunochemistry designed for high throughput laboratories. Cobas 8000 modular analyzer with c 702 analytical module performs photometric assay tests for wide range of analytes and is equipped with reagent manager to allow for automatic reagent cassette decapping and loading/unloading during operation with throughput of up to 2000 tests/hour.
Cobas 8000 modular analyzer with e 801 analytical unit for immunoassay tests. Cobas e 801 immunochemistry module performs range of heterogeneous immunoassay tests using ElectroChemiLuminescence technology.
Web toolkit for studies of large scale T2T genomes. Collection of tools designed for T2T genome assembly and characterization, including reference guided genome assembly, ultra long sequence based gap filling, telomere identification, and de novo centromere prediction. Includes four modules: AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner. Modules can be used alone or in combination with each other for T2T genome assembly and characterization.
University of Auckland Biomedical Imaging Research Unit Molecular Devices ImageXpress Micro XLS
XLS model of ImageXpress Micro System to leverage large field-of-view optics to map macro-structures with minimal tiling. Querying of large cell populations is accelerated three fold, speeding up the characterization of highly heterogeneous samples or identification of rare sub-populations. Combined with software, the custom designed ImageXpress Micro System provides platform to translate new discoveries into scientific breakthroughs.
Software tool to analyze scratch assays. It measures the area of wound in cellular tissue on stack of images representing time-series.
Web ecosystem for sharing metadata. Designed to annotate datasets by creating metadata file to attach to storage space. Allows users to add descriptive metadata to datasets produced within collective of research unit, platform, multi-partner project, etc. to fit to data management plan about data organization and documentation, data storage and frictionless metadata sharing.
Software pipeline system for ReproStat, written primarily in OCTAVE/MATLAB. It facilitates reproducible, inclusive, and efficient neuroimaging analyses.
Computerized matching of cases to controls using greedy matching algorithm with fixed number of controls per case. Controls may be matched to cases using one or more factors (X’s).
University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology Biomedical Imaging Core Facility
University of Illinois at Urbana-Champaign Biomedical Imaging Center
Core supports molecular and magnetic resonance imaging. Provides facilities, equipment, and training for researchers across range of disciplines. Each BIC tool is supported by research scientists available to assist with study design, data collection, and data post-processing.
University of California at Davis Biological and Agricultural Engineering Shop Core Facility
University of California at Davis Biological and Agricultural Engineering Shop
Provides support to UC research through engineering, design, fabrication, and repair of custom equipment. We can take your ideas, napkin sketches, drawings, and models and turn them into real parts, machines, tools, and systems. Services: prototyping, welding, fabrication, machining, electrical, repairs, misc. technical labor.
University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology Microscopy Suite Core Facility
Beckman Institute for Advanced Science and Technology Microscopy Suite
University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology Microscopy Suite
Core imaging facility operating out of the University of Illinois. Offers many imaging modalities, including confocal, micro- and nano-CT, electron microscopy, scanned probe microscopy, Raman, and fluorescence. Assists users in preparing and collecting data on various projects.
University of Luxembourg LCSB Rodent Platform Core Facility
Assist researchers in development and analysis of various in vivo neurodegenerative and cancer models including humanized and germ-free animals. Facility has capacity to house different transgenic and germ-free mouse strains in more than 2500 IVC cages within SOPF breeding barrier.
Tutorial to custom-design and -fit implants to continuous and discontinuous skull surfaces. Universal Guide for Skull Extraction and Custom-Fitting of Implants to Continuous and Discontinuous Skulls.
University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center Cytometry and Microscopy to Omics Core Facility
Cytometry and Microscopy to Omics Facility
Facility, couples cytometry with microscopy, genomics and proteomics using instrumentation, expertise and services. Utilizes advanced super resolution microscopy techniques to gain understanding of cell sorting, analysis and enable cutting-edge spatial and single cell and multi-omics services.
University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center Metabolomics Core Facility
Core identifies and quantifies small molecules from variety of origins such as biological tissue, blood, serum, plasma, cell, cell medium, urine, feces, among others. Provides support for untargeted and targeted metabolite profiling, detecting such compounds as sugars and sugar phosphates, alcohols, amine and polyamines, amino acids, fatty acids, complex lipids, nucleotides, organic acids, phenolics, bile acids, steroids/hormones, neurotransmitters and neuromodulators, phthalates, and many more emerging metabolites. Helps execute projects, including protocol development, sample preparation, instrument method development, instrument data acquisition, and data processing.Multiple complementary analytical methods are utilized with mass spectrometry. Our laboratory has mass spectrometers, including liquid chromatograph-mass spectrometers such as Agilent 6560 ion mobility Q-TOF and Agilent 6546 Q-TOF systems, in addition to our Thermo Fisher Q Exactive hybrid quadrupole-orbitrap, Thermo Fisher Altis triple quadrupole, Sciex 6500+ triple quadrupole, and Sciex 5500 hybrid triple quadrupole-ion trap (QTRAP), as well as gas chromatograph-mass spectrometers including Agilent 5977A, Agilent 5975C, and Agilent 5973.
University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center Functional Genomics Core Facility
UIUC-Roy J. Carver Biotechnology Center Functional Genomics
Facility offers amplicon sequencing libraries, 16S sequencing, PacBio Revio long read 16S sequencing, custom long read amplicon libraries Standard Biotools (formerly Fluidigm) multiprimer amplicons, high throughput Gene Expression and SNP genotyping using Standard Biotools microfluidic system, Illumina beadchip arrays for genotyping and methylation analysis.
University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center DNA Services Laboratory Core Facility
Provides service and instrumentation to support basic, environmental, agricultural, and translational medical research.
University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center Proteomics Core Facility
Core provides expertise in characterizing proteins from diverse systems. Provides proteomics services including customized sample preparation, protein identification, detection of post-translational modifications, isotopic label based and label-free quantitation, and intact protein characterization. Equipped with high resolution mass spectrometers with nanoflow liquid chromatography systems or chip-based robots. Core uses software systems such as Mascot, Proteome Discoverer, Byonic, and MaxQuant for analysis of raw mass spectrometry data. Provides assistance in protein quantitation and deeper downstream bioinformatics analysis including gene ontology, visualization of protein networks, and pathway analysis. Consultations are always welcome.
University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center High Performance Computing in Biology Core Facility
Core for genomics research in Carl R. Woese Institute for Genomic Biology. Coordinates with IGB and National Center for Supercomputing Applications to provide technical expertise in high-performance computational biology.
Software metadata and text extraction and text manipulation tool set for statistical programming language R. Facilitates text mining projects on scientific articles in 'NISO-JATS' format by enabling individual selection of metadata and text parts.
Software cloud based data analysis platform developed by Metrichor Ltd for Oxford Nanopore Technologies. Suite of data analysis workflows for wide range of applications.
Molecular Devices | FlexStation 3 Multi-Mode Microplate Reader
FlexStation 3 Benchtop Multi-Mode Microplate Reader
Molecular Devices FlexStation 3 Benchtop Multi-Mode Microplate Reader
Monochromator based microplate reader combines performance of Molecular Devices SpectraMax M5e MultiMode Microplate Reader with integrated 8-channel or 16-channel pipettor into one compact benchtop reader. System provides multi-detection platform capable of increasing liquid handling throughput and flexibility for biochemical-based and cellbased assays.
Thermo Scientific NanoDrop 1000 Software
Operating software for Thermo Scientific NanoDrop 1000 Spectrophotometer. Free NanoDrop operating software to update your instrument.
Software package for automatic extraction of optimal co-expressed gene clusters from gene expression data. Automatic and optimised consensus clustering of one or more heterogeneous datasets.
Software for calculation of radiomic features for medical images. Enables calculation of conventional, histogram based, textural, and shape features from PET, SPECT, MR, CT, and US images, or from any combination of imaging modalities. Dedicated to researchers, radiologists, nuclear medicine physicians and oncologists to give access to 306 histogram, textural and shape indices in addition to conventional indices and where users can change calculation options.
BD Biosciences | LSRFortessa X-20 Cell Analyzer
Cell analyzer system can be configured with up to 5 lasers to detect up to 20 parameters simultaneously. BD FACSDiva Software controls the setup, acquisition and analysis of flow cytometry data from the BD LSRFortessa Workstation.
Web application for flow cytometry analysis. Used to analyze FCS files for free in web-based app. Supports most FCS file types including FCS2.0, FCS3.0, and FCS3.1. Provides collection of flow cytometry tools which can also be used for analysis.
AID Diagnostica | iSpot EliSpot FluoroSpot Plate Reader
Plate reader for analyzing Enzymatic and fluorescent based EliSpot assays. Besides functionality of AID Classic, AID iSpot allows to analyze 1-, 2- or 3-color FluoroSpot assays. Provides one-click switch between enzymatic and fluorescent mode, without the need of hardware changes. The “FluoroAID” image overlay technology permits exact detection of cells secreting multiple cytokines. Count results and all other parameters can be exported in various formats.
Software tool that compares snippets of methods sections from PubMed Central, open access subset to other snippets of methods sections.
Software tool that helps users write experimental protocols.
ChemoMetec | NC-250 Automated Cell Analyzer
NucleoCounter NC-250 Automated Cell Analyzer
Automated cell analyzer, which can characterize cell properties using fluorescence imaging. Offers optimized protocols to meet needs of all mammalian cell types grown under different conditions. Cell count can be performed even on cells growing on microcarriers and in sphere cultures. Performs high-speed cell count and viability determination and offers unique 5-minute Cell Cycle Assay and 1-minute Apoptosis Assay for up to eight samples at the time. The intuitive software has unlimited licenses and produces on-screen data analysis and automated PDF reports., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software graphical image annotation tool written in Python. Image polygonal annotation with Python (polygon, rectangle, circle, line, point and image-level flag annotation).
Framework for Open and Reproducible Research Training Replication Database
Database is crowdsourced effort to include unpublished and published replication results to estimate and track replicability along various fields and provide researchers with way to assess replicability of crucial studies in quick and transparent way.
Software as comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes. Enables integration of taxonomic and functional analyses in microbiome multi-omics data.
Web application to search for academic articles and research papers from various sources such as arXiv, medRxiv, bioRxiv, PMC, and Google PDF search. Provides user friendly interface to discover articles and access them for free. Provides direct links to original sources, allowing users to access full articles.
Software for preclinical imaging integrated with Bruker MRI spectrometers. Used with Bruker MRI, PET/MR, and PET/CT instruments. Enables easy and high throughput imaging. All images, protocols, and subjects are in one location with inherent co-registration, image fusion, data processing, and analysis.
Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base
Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase.
Beckman Coulter | Avanti J-30I High-Speed Centrifuge
Refrigerated centrifuge that generates centrifugal forces required for wide variety of applications. Together with Beckman Coulter rotors are designed for use in this centrifuge. Centrifuge is microprocessor controlled, providing interactive operation.
Thermo Fisher: Invitrogen | ZP10001 ZOOM Dual Power Supply
Two-in-one programmable power supple capable of handling high voltage/low current and high current/low voltage applications concurrently and independently. The high voltage/low current section is ideal for sample fractionation, IPG strips, IEF, and DNA sequencing applications while the low voltage/high current section is for SDS-PAGE, native PAGE, second-dimension SDS-PAGE, DNA/RNA electrophoresis, and blotting applications.
Functional annotation database of human fusion genes.FusionGDB 2.0 has updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with human genomic features across cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of protein feature retention of individual fusion partner genes in protein level.
Software R package to draw venn diagram by ggplot2.
Supports users in application of numerous radiological methods such as ultrasound, optical imaging, µPET, µCT, µSPECT and MRT measurements to collect and quantify morphological and functional data in vivo.
Bruker BioSpec preclinical MRI equipment at translational field of 3 Tesla, extends the range of multi-purpose, preclinical MRI and MRS systems in compact, easy to site footprint.
Stoelting | Motorized Mouse Stereotaxic Instrument
Compact stereotaxic instrument designed for use with knock-out and transgenic mice. Instrument includes 100 micron, 3-axes left-hand manipulator arm, mouse snout clamp and tooth bar, dual-sided ear bars, and corner clamp probe holder. Stoelting’s Motorized Stereotaxic Manipulator Arms are designed for fast, accurate positioning during stereotaxic surgery. Motorized manipulator arms employ touchscreen display for easy-to-control movement of each axis. Manual movement is available anytime. Optional Drill feature available.
python_data-independentAutomated Isolation Design
Software Python package for DIA with automated isolation design. Used for Data-Independent Acquisition providing Automated Isolation Design. Optimally generates dia-PASEF and synchro-PASEF methods and places them optimally within the m/z – ion mobility (IM) plane.
Software Python library for Gene Ontology analysis. Performs gene ontology enrichment analyses to determine over- and under-represented terms.
Software Python library that aims to complement existing network analysis libraries such as networkx, igraph, and graph-tool with publication-quality visualisations within the Python ecosystem. Publication-quality Network Visualisations in Python.
Massachusetts General Hospital MGH CCIB DNA Core Facility
Massachusetts General Hospital MGH CCIB DNA Core
Research core laboratory within Center for Computational and Integrative Biology at Massachusetts General Hospital in Boston. Provides access to instrumentation, methodologies and expertise Services include Sanger DNA sequencing,Next Generation Sequencing, Long read Sequencing, genotyping, laboratory automation, molecular biology.
University of California at Santa Barbara Biological Nanostructures Laboratory Core Facility
University of California at Santa Barbara Biological Nanostructures Laboratory
Multi-purpose core research facility with sub-cores. Genetics, Analytical, Autoclave and Cell Culture Cores. Genetics Core provides Next Generation Sequencing, DNA/RNA and protein quantitation, nucleic acid QC, Real-Time PCR, and Droplet Digital PCR. Analytical Core houses analytical instruments such as UV-Vis, nanoparticle analyzers and plate readers. Some basic molecular biology equipment are also available. Cell Culture Core for researchers who need access to BSL1/BSL2 cell culture facility. Also includes autoclaves or labware sterilization and biohazardous waste disposal.
University of Illinois at Chicago Research Informatics Core Facility
University of Illinois at Chicago Research Informatics Core
Research Informatics Core at University of Illinois-Chicago provides bioinformatics services including genomics, transcriptomics, epigenomics, metagenomics, metabolomics, and proteomics analysis, as well as applications in statistical analysis, systems biology, and machine learning.
Texas A and M University Health Institute of Bioscience and Technology Flow Cytometry and Cell Sorting Core Facility
IBT Flow Cytometry and Cell Sorting Core Facility
Texas A and M University Health Institute of Bioscience and Technology Flow Cytometry and Cell Sorting Facility
IBT Flow Cytometry and Cell Sorting Facility provides flow cytometry and cell sorting services, along with scientific expertise. Provides academic and commercial users with access to High Throughput Flow Cytometry automated platform in Texas Medical Center.
Software graphical tool to allow easy editing of (XML) model, create initial positions of cells, run simulation, and visualize results. To contribute, fork and make PRs to the development branch. Used to create, execute, and visualize multicellular model using PhysiCell.
Standalone program and library to plot beautiful genome browser tracks. Software Python plotting tool that combines multiple tracks. Enables reproducible and standardized generation of highly customizable and publication ready images.
Algorithm for generating unique study identifiers in distributed and validatable fashion, in multicenter research. Light-weight, block chain style resource identifier generation for tracking resource linkage, provenance, utilization, and visualization. NHash has unique set of properties: (1) it is a pseudonym serving the purpose of linking research data about study participant for research purposes; (2) it can be generated automatically in completely distributed fashion with virtually no risk for identifier collision; (3) it incorporates set of cryptographic hash functions based on N-grams, with combination of additional encryption techniques such as shift cipher; (d) it is validatable (error tolerant) in the sense that inadvertent edit errors will mostly result in invalid identifiers.
University of Chicago DNA Sequencing Core Facility
University of Chicago DNA Sequencing Core
University of Chicago UChicago Sanger Sequencing Core
Core provides Sanger sequencing and fragment analysis via capillary electrophoresis. Expected turnaround time is within 2 business days of order receipt.
Web browser-based JavaScript application for visualizing hierarchical cellular populations as interactive radial tree. Allows users to explore, filter, and manipulate hierarchical data structures through intuitive interface while also enabling batch export of high-quality custom graphics.
Software tool for predicting TS and risk from glioblastoma whole slide images. Used to predict risk scores and transcriptional subtypes from whole slide images of glioblastomas.
Software package for Hi-C/HiChIP interaction calling and differential analysis using efficient implementation of HiC-DC statistical framework. Enables principled statistical analysis of Hi-C and HiChIP data sets. Enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP
Software variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). Enables accurate variant calling in diploid genomes from single-molecule long read sequencing. Takes as input aligned BAM/CRAM file and outputs phased VCF file with variants and haplotype information.
Software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. Used for long reads, but works also well with short reads.
Software tool as peak-caller for genomic enrichment assays. Analyzes alignment files generated following assay and produces file detailing peaks of significant enrichment.
Software analysis tool that enables data analysis of multiplex experiments and advanced applications and assay strategies for Droplet Digital PCR (ddPCR). For use with data files generated on QX100 or QX200 Droplet Reader using QuantSoft Standard Edition Software versions 1.4 or later.
Software tool for gene embedding augmented by Graph Neural Network and single-cell omics data. Performs prediction and module detection simultaneously, and enhances high-dimensional information of gene embedding. Helps identify gene modules in specific tissue contexts, providing new ideas for studying gene regulatory functions in tissues and helps elucidate influence of regulatory genes on biological processes in specific tissue environment and infer more disease-related genes to explain disease risk.
Web application for mutagenic primer design for QuikChange mutagenesis experiments. Used to calculate/design appropriate primer sequences with optimal melting temperature.
Continuous 3D reference atlas for postnatal mouse brain.
Software desktop application as general purpose diagramming program with multi-document interface. Cross-platform Java application to generate high-quality diagrams. Runs on Windows, Linux, Mac OS, and other platforms that support Java Virtual Machine.
NCI Colorectal Cancer Risk Assessment Tool
Colorectal Cancer Risk Assessment Tool: Online Calculator
NCI Colorectal Cancer Risk Assessment Tool: Online Calculator
web application as calculator designed for doctors and other health care providers to use with their patients. Estimates the risk of colorectal over the next five years and the lifetime risk for men and women who are Between the ages of 45 and 85, White,Black/African American, Asian American/Pacific Islander,Hispanic/Latino.
Software Python implementation of clustering tool named TooManyCells. Software package for spectral clustering.
Software suite of tools, algorithms, and visualizations focusing on relationships between cell clades. This includes new ways of clustering, plotting, choosing differential expression comparisons. Identifies and visualizes relationships of single-cell clades.
University of Alberta Biological Sciences Advanced Microscopy Core Facility
University of Alberta BioSci Advanced Microscopy Facility
Core services include paraffin embedding and histology, epifluorescence microscopy and confocal LSM, SEM and TEM sample prep and imaging.
Fluid Acquisition Recording in Socially Housed Animal Research
Open source device for fluid tracking in socially housed rats. Device uses RFID and custom hardware to individually measure and record each rat's fluid consumption and licking microstructure.
Beckman Coulter | Optima XE-90 ultracentrifuge
Optima XE generates centrifugal forces for separation of particles. Classified S, it can be used with all currently manufactured Beckman Coulter preparative rotors. Uses diffusion pump in series with mechanical vacuum pump to reduce chamber pressure to very low level. Uses solid state thermoelectric refrigeration and heating system without coolant or water. Cooling is provided by forced air from the fans.
Software for performing pixelwise calibration of sCMOS cameras. MATLAB code and instructions for routine camera calibration.
Software for processing single-molecule and diffraction limited polarisation camera image data using dipole PSF fitting. MATLAB scripts and utilities for analysis of simulated and experimental POLCAM single-molecule orientation-localisation microscopy (SMOLM) data using RoSE-O, providing accurate and precise measurements of location and orientation of single molecules.
Software napari plugin to process and render polarisation camera data. Used for polarisation camera image processing.
Software for live processing of polarisation camera images.
Software for processing single-molecule and diffraction limited polarisation camera images.
National Marrow Donor Program HaploStats
Web tool for determining HLA locus and allele disequilibria by population ethnicity.
Software tool for discovery of novel immune systems in prokaryotes. Automatic annotation and classification of immune systems in prokaryotes using Deep Learning.
Web analysis tool for validating predictive biomarkers of chemotherapy/hormonal therapy/anti-HER2 therapy using transcriptomic data of breast cancer patients. Designed to validate and rank new predictive biomarker candidates in real time. Platform provides resource for researchers to mine database and to validate and rank future biomarker candidates.
Software R package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree. Helps users choose parameters to reflect age information for prior age distributions, visualise time priors, and produce output files ready to be used in MCMCtree. Used to prepare MCMCtree analyses and visualize posterior ages on trees.
Software tool as long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap2 computes each read mapping through collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats.
Software error correction and de-novo assembly tool for Nanopore long noisy reads. Nanopore data assembler.
drug perturbation Gene Set Enrichment Analysis
Software tool to detect phenotypically relevant drug targets through unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets. Exploratory tool to screen for possible drug targeting molecules.
Thermo Fisher: Applied Biosystems | SeqStudio Genetic Analyzer
SeqStudio Genetic Analyzer is fluorescent dye labeled genetic analysis system using capillary electrophoresis technology. Enables both sequencing and fragment analysis applications without the need to switch polymer type or capillary array length. Allows to perform both sequencing and fragment analysis in single run.
Primary Template-directed Amplification analysis TOol kit
Software tool for single cell WGS analysis. Used to accurately detect single base substitutions, insertions-deletions (indels), and structural variants in PTA-based WGS data.
Newcastle University Bioimaging Unit Core Facility
Light microscopy core facility at Newcastle University based in the Faculty of Medical Sciences, providing services, access, training and support for light microscopy.
University of Pittsburgh Hillman Cancer Center Biostatistics Core Facility
UPMC Hillman Cancer Center Biostatistics Facility (BF)
Provides statistical and computational methods for design, execution, analysis, and reporting of cancer-related research studies and trials including biomarker analysis and grant development.
University of Pittsburgh Hillman Cancer Center Cancer Bioinformatic Services Core Facility
UPMC Hillman Cancer Center Cancer Bioinformatic Services (CBS)
Provides bioinformatics support for translational genomics using sequencing, arrays, single cell, and other technologies.
University of Pittsburgh Hillman Cancer Center Cancer Genomics Core Facility
UPMC Hillman Cancer Center Cancer Genome Facility (CGF)
Supports genomics and transcriptomics platforms including nucleic acid extraction, sample QC, next-generation library preparation and sequencing. Specializes in paraffin-embedded tissue samples.
University of Pittsburgh Hillman Cancer Center Cancer Pharmacokinetics Pharmacodynamics Core Facility
Cancer Pharmacokinetics Pharmacodynamics Facility (CPPF)
UPMC Hillman Cancer Center Cancer Pharmacokinetics Pharmacodynamics Facility (CPPF)
Provides bioanalytical, pharmacokinetic and pharmacology research services that support preclinical and clinical research programs focused on oncology. Resources include HPLC-UV/fluorescence, ICP-MS, LC-MS/MS, LSC, ELISA, and in vivo rodent procedures, as well as advanced PK software suites and expertise for preclinical and clinical projects.
University of Louisville Micro/Nano Technology Center Core Facility
Expertise resides in micro and nanotechnology, sensors, transducers, microelectromechanical systems (MEMS), advanced materials, biomedical devices, space and governmental applications.Offers SEM and TEM imaging services for biological samples.
University of Pittsburgh Hillman Cancer Center In Vivo Imaging Core Facility
In Vivo Imaging Facility (pre clinical and clinical) (IVIF)
UPMC Hillman Cancer Center In Vivo Imaging Facility (pre clinical and clinical) (IVIF)
Provides novel quantitative imaging techniques that trace biomarkers of molecular events associated with effective cancer therapy.
University of Pittsburgh Hillman Cancer Center Cytometry Core Facility
UPMC Hillman Cancer Center Cytometry Facility (CF)
Supports analytical cytometry and cell sorting. Offers NanoString Digital Spatial Analyzer and nCounter service and support.
University of Pittsburgh Hillman Cancer Center Immunologic Monitoring and Cellular Products Laboratory Core Facility
Immune Monitoring and Cellular Production Laboratory (IMCPL)
UPMC Hillman Cancer Center Immune Monitoring and Cellular Production Laboratory (IMCPL)
Core operates 12 clean rooms and focuses on IND manufacturing under cGMP/cGTP. Operations are monitored 24/7 by expert staff. Specializes in and collaborates on preclinical research development involving process conceptualization, technology transfer and testing implementation on human cell-based drugs for clinical trials. Immunological monitoring services are available to support clinical trials. The facility is a FACT-, CLIA-, CAP-, and FDA-accredited laboratory.
Software pipeline is set to to non-model plant GO/KO function annotations using R. It can collect data from Eggnog-mapper of custom BLAST, convert data, and make OrgDB packages.
Mayo Clinic Arizona Flow Cytometry Core Facility
Provides cytometry services featuring sorting and analyzing. For analysis, we currently have BD LSR Fortessa, BD FACSymphony A3, and Cytek Aurora. Our cell sorters include 14-parameter, 4-laser Sony MA900 and 16-parameter, 5-laser FACSAria dedicated to BSL3 cell sorting.
Provides catalogue of confirmed and predicted DNA replication origin sites. At present this is limited to budding yeast and fission yeast. Data have been collated as culmination of number of genome-wide studies to identify location of replication origins throughout budding yeast genome. In addition to genome-wide studies data from large number of other origin mapping and characterization studies have been included.
Web tool for identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
Incucyte Cell-By-Cell Analysis Software Module
Software for analysis to determine live versus dead cells – no fluorescent dyes needed.
Markerless Mouse Tracking for Social Experiments
Markerless video-based tool to simultaneously track two interacting mice of the same appearance in controlled settings for quantifying behaviors such as different types of sniffing, touching, and locomotion to improve tracking accuracy under these settings without increased human effort. It incorporates conventional handcrafted tracking and deep-learning-based techniques. The tool is trained on small number of manually annotated images from basic experimental setup and outputs body masks and coordinates of the snout and tail-base for each mouse.
Thermo Fisher | NanoDrop Lite Spectrophotometer
Compact, personal UV-Vis microvolume spectrophotometer that complements the full-featured NanoDrop 2000/2000c and NanoDrop 8000 instruments.
Thermo Fisher: Invitrogen | Countess II Automated Cell Counter
Fully automated cell counter and assay platform that uses optics and image analysis algorithms to analyze trypan blue-stained cells in suspension. Benchtop device that measures cell concentration and viability.
Software application as coverage-guided approach for scalable construction of read overlapping graph. Used to handle numbers of datasets from large genomes, especially with limited computational resources.
Harvard University Chan School of Public Health Bioinformatics Core Facility
Harvard University HSPH Harvard Chan Bioinformatics Core
Provides single point of contact for Harvard researchers interested in bioinformatics support, applying genomic approaches together with established and developing methodologies from epidemiology, environmental health, biostatistics and bioinformatics to improve human health.Services include analysis all types of next-generation sequencing data from RNA-seq and single cell RNA-seq to variant sequencing (exome or whole genome), to ChIP-seq or bisulfite sequencing. Offers bioinformatics training program for Harvard researchers interested in learning basic data skills and analysis of high-throughput sequencing data.
University of British Columbia MRI Research Core Facility
University of British Columbia UBC MRI Research
Facility consist of Philips 3.0 Tesla MRI scanner for studies on humans, Bruker small bore 9.4 Tesla MRI scanner, and computing facility for image archival and analysis. Scanners are entirely dedicated to research, and MR scanning is carried out on cost recovery basis. The scanners were selected to cater to a very broad range of in vivo applications and the Imaging Centre staff is trained to support any research projects that the scanners can accommodate.
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Proteomics Core Facility
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Proteomics
Network Biology Collaborative Centre Proteomics
Provides mass-spectrometry based identification and quantification of proteins. Facility specializes in functional proteomics with focus on protein proximity and protein interaction mapping. Services include access to reagents, plasmids, sample preparation, mass spectrometry, and data analysis.Applications include: proximity-dependent biotinylation mapping to identify neighboring proteins in cells ,protein-protein interaction mapping,post-translational modification identification (with a focus on phosphorylation),differential protein abundance,chemical proteomics (identifying on- and off-target binding to small molecules or biologics)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Software plugin will open new cell counter GUI in ImageJ to facilitate manual cell counting.
Compact benchtop flow cytometer based on capillary system with HTS high throughput screening. Uses microcapillary laser based technology to detect mammalian and microbial cells, particles, and beads. System can resolve the fluorescence from up to 12 fluorophores simultaneously.
Open-source software Python package for developing and comparing radiomics models. Used to build radiomics models and evaluate them using independent testing dataset. It also provides easy model comparison and result visualization.
Interactive webserver for exploratory analysis and visualisation of bacteriophage genomes.
Head-fixed Environment for Rodent BehaviorS
Open source hardware and software solution for flexible implementation of complex behaviors in head-fixed mice. Low cost and requires little to no programming experience. Allows neural activity to be seen during testing, which will show relations between neuronal activity and behavior during tasks such as alternative forced choice, GoNoGo, and sensory stimulus presentation.
Lightsheet Aligned Mouse Brain Annotated Developmental Atlas
Reference atlas of the developing post-natal mouse brain. Provides data and annotations on distribution of cells and gene expression in mouse brain.
Dartmouth Genomic Data Sciences Core Facility
Geisel School of Medicine at Dartmouth Genomic Data Sciences Core
Core offers statistical analysis of genomics data. Provides suite of standardized analysis pipelines for common data types like RNA-seq, ATAC-seq, and genome assembly. For more complex datasets, such as single-cell genomics, provides tailored analysis solutions. Core team assists with all project stages, from experimental design to publication support and data management. GDSC hosts several multi-day bioinformatics workshops designed to introduce fundamental concepts for analysis of genomics data.
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Flow Cytometry Core Facility
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Flow Cytometry
Network Biology Collaborative Centre Flow Cytometry
Core provides flow cytometry analyzers and cell sorters, with specialty in image-based flow cytometry and cell sorting.Services include unassisted and full-service cell sorting, training on theory and on instruments, consultation on experiment design, protocol development, data analysis, manuscript preparation and grant submission. Applications include image-based analysis powered by machine learning on the Amnis ImageStream; image-based cell sorting using the BD BACS Discover S8; cell sorting for a variety of applications including multi-color sort for bulk culture, indexed cell sort into 96-well plates, cell cycle phase sort and primary tissue sorting for RNA or DNA analysis.
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Next-Generation Sequencing Core Facility
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Next-Generation Sequencing
Network Biology Collaborative Centre Next-Generation Sequencing
Core provides both short and long read sequencing capabilities for analysis of gene function and expression.Facility specializes in functional genomics and single cell biology. Services include consultation, sample preparation (especially for spatial and single cell applications), quality control, sequencing analysis, bioinformatics support, and assistance with grant and publication writing related to the services. Applications include:gene function analysis - pooled CRISPR screening, multiplexed barcode screens; whole genome sequencing - both short- and long-read sequencing; bulk gene expression profiling; single cell biology (single cells and single nuclei); spatial profiling; pathogen detection and profiling.
Medical research institute in Toronto, Ontario and part of the Sinai Health System. It was originally established in 1985 as the Samuel Lunenfeld Research Institute, the research arm of Mount Sinai Hospital, by an endowment from the Lunenfeld and Kunin families.
CISNET Publication Support and Modeling Resources
Portal provides access to technical modeling information, raw data, and publication extensions stemming from the work of the CISNET consortium to improve understanding of cancer control interventions in prevention.
Modelling Of cancer-specific Variants And sequencing Reads Simulation
Software simulator that leverages data-driven information to set both variants and reads characteristics, producing realistic tumoral samples. Computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation.
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Advanced Imaging Core Facility
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Advanced Imaging
Network Biology Collaborative Centre Advanced Imaging
Advanced imaging facility for microscopy needs where users have access to technologies in advanced microscopy.Services include consultation on experimental design, advice on appropriate systems, training and support for assisted and unassisted use, as well as help with data analysis and image generation for publications. Applications include Fluorescence and brightfield image acquisition; Whole-slide scanning; Dynamic live-cell imaging; Super-resolution imaging.
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre High-Throughput Screening Core Facility
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre High-Throughput Screening
Network Biology Collaborative Centre High-Throughput Screening
Provides instrumentation and expertise for the automation of laboratory processes. Facility has automated screening platforms and accessory equipment to enable flexible and scalable in vitro and in vivo assays including organoids. Services include access to chemical and genome-wide siRNA libraries, assay development and implementation, and data analysis. Applications include drug discovery and lead validation; ELISA-based assays for immune surveillance; protein biomarker discovery using OLINK proteomics technology; multiplexed barcode screening assays.
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre High-Content Screening Core Facility
Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre High-Content Screening
Network Biology Collaborative Centre High-Content Screening
Provides optical imaging and analysis of fixed and live cells. Services include assistance with selecting imaging platform, developing customized imaging assays, training in imaging and data analysis and assistance with image/data preparation for presentations and publications. Applications include Multi-plate based imaging applications; High-resolution cell characterization and sub-cellular localization using IN cell Analyzers;3D Spheroid and Organoid imaging using a Nikon A1R BioPipeline;Live-cell analysis (confluency, growth tracking) using Incucyte - imaging within incubator.
SeekGene | Scitech Korea Multicenter Animal Spinal Cord Injury Studies MASCIS impactor
Multicenter Animal Spinal Cord Injury Studies (MASCIS) impactor
Impactor that allows for reproducible spinal cord and head contusions.
Virginia Tech Advanced Blast Simulator large
A blast device that capable of accommodating large samples and it is available for cadaver, animal, materials, and physical surrogate testing. It is driven by a gas detonation system.
Pittsburgh Precision Instruments | Cortical Controlled Impactor
Pneumatic-powered CCI device, with adjustable velocity and angle on impact used for neuroscience research.
Virginia Tech Advanced Blast Simulator small
Blast device that is appropriate for testing specimens, such as small animals and material samples. It operates with compressed air or helium in the driver, which is seperated from the test section by a diaphragm.
Miniaturized calcium imaging microscope with integrated dense electrode technology for synchronous acquisition of neural activity across distant regions of the brain. Device based off open-sourced UCLA Miniscope to synchronously measure single cell activity at or near spike-time resolution across distant brain regions in freely behaving mice. Used to perform calcium imaging, with dense electrode electrophysiological recording, allowing simultaneous recordings from two remote brain regions in freely behaving mouse.
Benchtop shaker combines mixing performance with temperature control. Provides easy-to-exchange SmartBlocks for all common lab tubes, new and improved program functions, and high level of stability for every mixing frequency.
University of Ottawa Transmission Electron Microscopy Core Facility
Transmission Electron Microscopy (TEM) Core
University of Ottawa Transmission Electron Microscopy Core
Provides unique imaging (JEOL JEM-1400plus) and tissue processing solutions for your research, in partnership with CHEO’s Electron Microscope Laboratory. Provides training for use of the instrument, and training for sample preparation/processing.
Software pipeline for analysis of next-generation sequencing data derived from intra-host and environmental viral populations. Designed for analysing NGS data of short viral genomes. Used for assessing viral genetic diversity from high-throughput data.
International Radiosurgery Research Foundation
Foundation consists of academic and clinical centers of excellence where brain stereotactic radiosurgery is performed. Aims to facilitate retrospective and prospective clinical trials and outcomes analysis that evaluate the role of SRS for wide spectrum of clinical indications. Mission is to perform research, provide education, and publish information related to stereotactic radiosurgery for the purpose of improving public health.
Cryostat for histopathology applications. Intended for cutting frozen sections of standard and non-standard materials. Designed to rapidly freeze material in temperature controlled environment. Has ability to quickly disinfect the cryo chamber at any time with ultra-violet light (UVC). The UV light is intended to reduce the user to significant dangers from bacteria, spores, and viruses.
DokuMate helps standardize and reuse documents, simplifies and speeds-up editing, and automates many tedious tasks. A docId” is one of the “magic” Content Control tag names. A docId is an alphanumerical ID (e.g., “R01-01-C00”, “R01-11-100”, “R01-11-410”, “R01-30-100”) that uniquely identifies and sorts documents (e.g., Schedule C, Exhibit 1, Attachment 4.1, Appendix 1) within a larger set of documents, e.g., all documents belonging to (a) a specific RFP or (b) the set of contracts between a first party and a second party.
Organization that works with knowledge professionals to create, support and deliver programs, services and technologies that allow for equitable access to world knowledge and cultural heritage. Hosts data-migration, content licensing, and community supported soft​ware programs for libraries, archives, museums and research organizations worldwide.​​​
A cluster of the Nigerian Research and Education Network (NgREN). Network to support network connectivity and collaborations between education and research organisations as part of wider efforts for sustainable National Research and Education Network (NREN).
Web next-gen digital research platform for Institutional Research Data Management. Fully integrated sample management and electronic lab notebook solution. Electronic lab notebook for physical sciences. Works with IGSN.
Open source software interface and framework for controlling behavioral experiments in neuroscience and psychology. Python-based framework for designing and controlling behavioral experiments in animals. Used to develop, perform, and control behavioral tasks.
Software R package with web based GUI for spectral analysis of light.
Software R package to process personal light exposure data from wearables.
Software R package to automate RNAseq clustering processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning based functions.
Web comprehensive multi-omics integration and analysis tool. Used to identify gene-metabolite pairs with biological association by fusing transcriptomic and metabolomic data.
Software tool to automatically process Incucyte images and to analyze neurite dynamics with or without labels in living cells in each well of 96- or 384-well plates. Analyses can be performed directly on phase contrast images obviating need for cell labels in monoculture experiments, or on fluorescent images using non-perturbing probes as may be required in reagents for co-culture systems models.
Software tools for generating single-cell gene expression data. Software pipeline for high-resolution and large field-of-view spatial transcriptomic data of Stereo-seq. Provides comprehensive and systematic platform for generating high-confidence single-cell spatial gene expression profiles, which specifically includes image stitching, image registration, tissue segmentation, nuclei segmentation and molecule labeling.
3D Printed Hindlimb Stabilization Apparatus
Custom SolidWorks parts used in implementing hindlimb stabilization apparatus. Open source 3D-Printed Hindlimb Stabilization apparatus for measurement of stimulation evoked ankle flexion in rat.Apparatus is made up of 3 key components: Foot Pedal, Knee-Locking component, and Acrylic Base Platform. The design is adjustable for variations in anatomy across sex and size of rodents, and is low in cost. Components are almost entirely 3D-printed, and any other supplies are published along with the build instructions.
Maximum Likelihood Estimation of Relatedness
C++ program to infer biological relatedness from low coverage 2nd generation sequencing data. It uses information from genotype likelihoods rather than observed genotypes in maximum likelihood framework in order to estimate the overall coefficient of relatedness as well as individual kinship components between two samples. Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data.
Web app for creating, exploring, labeling and sharing volcano plots . The plot can be annotated to show genes/proteins based on their top ranking or based on user input.
Lyser simultaneously disrupts multiple biological samples through high-speed shaking in tubes or 96-well plates with stainless steel, zirconium, ceramic or glass beads. Using the appropriate adapter set, up to 192 samples can be processed at the same time. Alternatively, grinding jar set can be used to process large samples. Touchscreen and rotary knob make it easier to run and customize disruption protocols. Has pre-programmed protocols and customizable protocols for maximum sample versatility. Allows to create custom program cycles to set disruption parameters.TissueLyser II accessories, including adapter sets, are compatible with the TissueLyser III.
Marshall Scientific | J Research PTC-200 Thermal Cycler
Peltier Thermal Cycler-200 MJ Research PTC-200 Thermal Cycler
Hot Bonnet heated lid fitted into PTC 200 Thermo Cycler controls pressure and height.Various plastic wares can be accommodated by system. Enables oil-free cycling.Equipped with interchangeable sample blocks and heat pump. Single control units of this model can also be supplied with different alpha modules and alpha blocks to increase functionality.
Software framework for analyzing ST data by incorporating graph attention autoencoder and multi-scale deep subspace clustering.Used for Unveiling Patterns in Spatial Transcriptomic Data.
Software R package for model selection and multimodel inference. Used for automated model selection and model-averaging. Provides wrapper for glm and other functions, automatically generating all possible models with specified response and explanatory variables.
Software R package to create plots of meta-analytic data. Used to create forest plots, funnel plots, and their variants, such as rainforest plots, thick forest plots, additional evidence contour funnel plots, and sunset funnel plots. In addition, functionalities for visual inference with funnel plot in context of meta-analysis are provided.
Software tool for detecting and quantifying punctate co-localization in multi-channel images.
Software application as model of magnetic field distribution of magnetic coil visualized using COMSOL Multiphysics.
Yale School of Medicine Flow Cytometry Core Facility
Core provides comprehensive flow cytometry analysis and cell sorting including instrumentation, technical support, training and consultation.
University of Luxembourg LCSB Aquatic Platform Core Facility
Aquatic Platform consists of semi-automated installation that provides zebrafish housing, husbandry, and experimental services to support biomedical research and teaching activities. Facility can house adult zebrafish, offering robotic feeding, maintenance of constant micro-environmental parameters, and semi-automated cleaning systems that ensure excellent conditions for research quality and animal welfare.
functional diagnostics of nervous regulation of blood circulation
Design of SAKR-M device includes computer, pneutronic unit, spirometric sensor, finger cuff, ECG electrodes and power supply adapter. Used for functional diagnostics of nervous regulation of blood circulation. Integrated method of studying cardiorespiratory system to analyze heart rate variability , arterial blood pressure variability and respiratory patterns.
Peter MacCallum Cancer Centre Advanced Histology and Microscopy Core Facility
Centre for Advanced Histology and Microscopy
Peter MacCallum Cancer Centre Advanced Histology and Microscopy
Provides tools and expertise in bio image analysis, histology, and microscopy. Facility allows for the preparation, visualization, and quantification of biological samples at the cellular and sub cellular levels. Researchers can choose to utilize our instruments independently or collaborate with our skilled staff through our fee-for-service options.
University of Edinburgh Genomics Core Facility
Core provides secure receipt, processing, archiving and analysis of biological samples. Offers support for clinical research from sample collection to genetic analysis, working to the principles of Good Clinical Practice for Laboratories. Facility provides access to genomic technologies and services including next-generation sequencing (Illumina), third-generation sequencing (PacBio and Oxford Nanopore), bespoke bioinformatics analysis, and genomics and bioinformatics training.
Web server predicts peptide binding to any MHC II molecule of known sequence using Artificial Neural Networks.
Software toolkit to identify and visualize cancer neoantigens. Cancer immunotherapy tools suite consisting of following tools: pVACseq as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from VCF file; pVACbind as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from FASTA file; pVACfuse as tool for detecting neoantigens resulting from gene fusions; pVACvector as tool designed to aid specifically in construction of DNA-based cancer vaccines; pVACview as application based on R Shiny that assists users in reviewing, exploring and prioritizing neoantigens from results of pVACtools processes for personalized cancer vaccine design.
Software application as helper to run command, capture stdout/stderr and details about running.
Software tool extension to ImageJ for spinal cord. Used for efficient preparation and imaging of whole spinal cord and the absence of 3D reference atlas.
Software platform to annotate cell types.
Preferred Reporting Items for Systematic reviews and Meta-Analyses for Protocols
Reporting guideline published in 2015 and aiming to facilitate the development and reporting of systematic review protocols.
Web tool facilitating the conduct and assuring for the documentation of systematic reviews, systematic maps and further literature reviews.
Laboratory scale ultrasonic processor for nanoparticle dispersion, emulsification, cell lysis, homogenization, particle size reduction, and wide range of other applications.
Develops and supports KeyMolnet integrated platform for bioinformation, and provides analysis services using KeyMolnet. KeyMolnet provides support for disease mechanism analysis, drug discovery target discovery, expression data analysis obtained by microarrays and high-speed sequencers, and data analysis such as proteomics and metabolomics, based on molecular network information, disease information, and drug information collected by our researchers from the latest papers.
Software R library for parentage assignment using Bi-Allelic Genetic Markers. Used for assignment of parentage with molecular markers. Improved paternity assignment among close relatives using simple exclusion method for bi-allelic markers.
Software R package to assign offspring to their parents without any prior information other than offspring and parental genotypes, and user-defined, acceptable error rate among assigned offspring. Auto-adaptive parentage inference software that tolerates missing parents.
Software package for parentage analysis in plant and animal populations. It combines robust likelihood-based method with simple graphical interface.
Software wrapper command for command neighbor of the PHYLIP package. Implements Neighbor-Joining method of Saitou and Nei and UPGMA method of clustering. Constructs tree by successive clustering of lineages, setting branch lengths as the lineages join.
Software tool to calculate p-distance matrix based Variant Call Format.
University of Technology Sydney Microbial Imaging Core Facility
University of Technology Sydney UTS-Microbial Imaging Core Facility
University of Technology Sydney UTS-Microbial Imaging Facility
Provides services including High-resolution imaging of bacteria and parasites, and their interactions with host eukaryotic cells; High-resolution imaging of biological processes of larger eukaryotic cells, spheroids, tissues and organs including the use of micro-fluidic devices. Provides equipment for biological specimen preparation for optical and electron microscopy. Provides training and support on the use of both basic and advanced microscopes including:transmitted light, wide-field fluorescence, confocal laser-scanning, super-resolution, high-content imaging, slide-scanning microscopy and range of image analysis and 3D-image visualisation software like FIJI, Huygens, Leica AIVIA, ZEISS ZEN Intellesis and Bitplane Imaris.
University of Alabama at Birmingham Cryo-Electron Microscopy Core Facility
Cryo-Electron Microscopy Facility (CEMF)
University of Alabama at Birmingham Cryo-Electron Microscopy Facility
Core supports the application of cryo-EM in making new scientific discoveries. Provides access and training in the use of cutting edge cryo-EM technology and techniques for the characterization of biological samples from the cellular to the atomic scale.
Interactive web-based platform presenting global cancer statistics to inform cancer control and cancer research. Focuses on the visualization of cancer indicators using data from IARC’s Cancer Surveillance Branch (CSU), including GLOBOCAN;Cancer Incidence in Five Continents (CI5); International Incidence of Childhood Cancer (IICC); and several cancer survival benchmarking projects (SurvCan and SURVMARK).
Global resource for cancer epidemiology. Presents national estimates of incidence, mortality and rate. Enables comprehensive assessment of cancer burden worldwide in 2022, based on GLOBOCAN estimates of incidence, mortality and prevalence for year 2022 in 185 countries or territories for 36 cancer types by sex and age group. Provides data visualization tools for exploring global cancer burden in 2022.
Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding.
Software package provides implementation of inference pipeline of AlphaFold v2. Incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into design of deep learning algorithm. Used for protein structure prediction.
PhysiCell Microenvironment Structure Simulation
PhysiCell add-on which allows users to simulate ECM components as agents. PhysiCell addon for extracellular matrix modelling.
Secure One-health online platform that enables near real-time sharing under controlled access of pathogen sequencing data and their associated clinical/epidemiological metadata. Data exchange platform for bacterial, viral and fungal genomics and associated metadata.
Project titled Program to Reveal and Evaluate Cells-to-gene Information that Specify Intricacies, Origins, and Nature of Human Pain (PRECISION) Network to develop meaningful resource for knowledge transfer, and to integrate and share Human Pain Associated Genes and Cell Datasets. Building knowledge platform to visualize, query, and interact with these data will support researchers and help accelerate dissemination of vital data to the larger scientific community. These goals align with NIH Helping to End Addiction Long-term (HEAL) Initiative, which seeks to accelerate the discovery and successful translation of non-addictive pain therapeutics. PRECISION Human Pain Network will leverage prior interdisciplinary collaboration to create workflows, tools, and infrastructure to define data and metadata types, to improve data management and sharing, and to integrate datasets and visualization tools.
Software R package for comprehensive identification of enriched pathways in omics data through active subnetworks. Uses protein interaction networks to find enriched pathways from transcriptomic data.
Whole body magnetic resonance imaging scanner designed to support high resolution, high signal-to-noise ratio and fast scan times. This MRI system features superconducting magnet that operates at 3. O Tesla.
Provides digital infrastructure, data analytics and decision support tools to help in diagnosis, treatment and monitoring of patients.
Automated cell counter accurately counts cells in one simple step using auto-focus technology and cell-counting algorithm. Enables accurate cell counting in less than 30 seconds.
Instrument that runs Biolog's microplate metabolic arrays. Incubates and monitors 50 microplates, or 1,920 phenotypic assays simultaneously to measure physiological responses in diverse microbial cells. OmniLog PM system includes software for analysis of Biolog Phenotype MicroArray panels.
BEADL:BEhavioral tAsk Description Language
Universal framework for describing behavioral tasks. Language to abstract and standardize behavioral task descriptions on two layers. Graphical layer specifies elements to describe behavioral tasks as state machine in formal flow diagram and how task controlling system interacts with subject. This graphical layer has been designed to be easy to understand while retaining all aspects of behavioral task. The second layer is corresponding, XML-based description of task. This layer forms rigid, yet extensible foundation of BEADL and hides hardware implementation related details form graphical representation.BEADL-specific extension for Neurodata Without Borders data standard defines how behavioral outcomes of task are stored in NWB including corresponding BEADL task description.
Software Python-based package designed to asses quality of Neurodata Without Borders files and based on compliance with Best Practice. Meant as companion to PyNWB validator, which checks for strict schema compliance. Attempts to apply some commonsense rules and heuristics to find data components of file that pass validation, but are probably incorrect, or suboptimal, or deviate from best practices. In other words, while PyNWB validator focuses on compliance of structure of file with the schema, the inspector focuses on compliance of actual data with best practices. Meant as data review aid. It does not catch all best practice violations, and any warnings it does produce should be checked by knowledgeable reviewer.
Browser-based tool designed for visualization of Neurodata Without Borders files, whether stored locally or hosted remotely, and enables interactive exploration of DANDI Archive.
NWB Graphical User Interface for Data Entry
Desktop app that provides no-code user interface for converting neurophysiology data to Neurodata Without Borders.
Software that can handle NMR and MS data and combines both technologies for even deeper insights and more comprehensive analysis.
University of Virginia School of Medicine Biomolecular Magnetic Resonance Core Facility
Biomolecular Magnetic Resonance Facility
UVA School of Medicine Biomolecular Magnetic Resonance Facility
Facility has NMR spectrometers used to execute experiments typically used for structure elucidation and dynamics characterization of both small and large (ie. protein) molecules in solution. All spectrometers are connected to the internet. Data can be readily transferred for remote processing and the campus has a site license for Mestrenova NMR data processing and visualization software. Assistance is available for all who wish to use NMR spectroscopy. Advice on all aspects of solution NMR spectroscopy is available from the facility manager.
University of Virginia School of Medicine Research Histology Core Facility
UVA School of Medicine Research Histology Core
Core provides standard and customized research specific histology services including routine formalin fixation and paraffin embedding, and sectioning, automated Hematoxylin and Eosin staining as well as selection of manually prepared special stains and preparation of frozen section.
University of Virginia School of Medicine Radiochemistry Core Facility
University of Virginia School of Medicine Radiochemistry Core
UVA School of Medicine Radiochemistry Core
Provides access to high-quality novel and existing radiopharmaceuticals (radiolabeled small molecules, peptides, proteins, and antibodies), that can be imaged by Positron Emission Tomography (PET) method, to meet their preclinical and clinical needs. Radiochemistry core is Good Manufacturing Practices (cGMP) certified facility as required by the U.S. Pharmacopeia Chapter 823 and 21CFR part 212 and is BSL-2 certified facility to conduct research.
UVA School of Medicine Molecular Imaging Core
Core specializes in imaging small animals and samples with variety of modalities depending on the investigator’s needs. These modalities include MRI, X-Ray CT, PET, SPECT, luminescence, and fluorescence. We work closely with the Radiochemistry Core Lab which can synthesize custom, targeted PET and SPECT imaging agents.
University of Virginia School of Medicine Genetically Engineered Murine Model Core Facility
UVA School of Medicine Genetically Engineered Murine Model (GEMM) Core
UVA School of Medicine Genetically Engineered Murine Model Core
Core provides services to produce and preserve genetically engineered mouse strains for animal model research.Supports animal model research endeavors, to advance genetic and reproductive technologies for model creation and preservation, and to serve as resource for design, development and derivation of customized mouse strains.
University of Virginia School of Medicine Exercise Physiology Core Facility
University of Virginia School of Medicine Exercise Physiology Core Laboratory
UVA School of Medicine Exercise Physiology Core Laboratory
Promotes the expansion and enhancement of clinical research that incorporates exercise physiology and body composition into research questions. Offers measures of resting and exercise oxygen consumption, lactate threshold assessment, endothelial function, regional distribution of body fat, body composition assessment, anthropometry, and the use of acute exercise and/or exercise training as an intervention.
University of Virginia School of Medicine Center for Human Therapeutics cGMP Core Facility
University of Virginia School of Medicine Center for Human Therapeutics cGMP Facility
UVA School of Medicine Center for Human Therapeutics cGMP Facility
Offers manufacturing of cellular and biologics for safety and initial efficacy testing in first–in– human, pilot, and Phase I clinical trials. Facilitates bench–to–bed translation into novel cellular therapies. Provides focused scientific, technical, and regulatory support for investigator-initiated investigational new drug applications (INDs) in cell and gene therapy. Current and completed trials include hematologic malignancies multiple myeloma, breast cancer, prostate cancer, glioblastoma, neuroblastoma, and pancreatic cancer. The potential applications of cellular therapy and biologics are not limited to cancer, a large number of disease indications such as cardiovascular, autoimmune diseases, diabetes, neurological diseases, etc.
University of Virginia School of Medicine Biomolecular Analysis Core Facility
University of Virginia School of Medicine Biomolecular Analysis Facility
UVA School of Medicine Biomolecular Analysis Facility
Core provides services and expertise in the areas of proteomics, metabolomics, small molecules, and molecular interactions. The staff can assist in data collection for experiments as well as provide help in experimental design and data analysis. Value added work such as grant writing and publication methods/figures is provided free of charge.
Software for scientific image capture and analysis.
Software R package for power calcualtions. Basic functions for power analysis.
Software package to identify transcripts in PacBio single-molecule sequencing data. Scalable De Novo isoform discovery from single-molecule PacBio reads.
Software Pacbio analysis tool. Deconcat PacBio reads.
Software for DNA sequence clustering. General purpose DNA sequence clustering tool with strong focus on error correction.
Concatemeric Consensus Caller with Partial Order alignments.
Software to detect DNA splint sequence raw reads. Computational pipeline for calling consensi on R2C2 nanopore data.
Software tool to assist with manually counting objects in images. Used for many conservation applications.
Software package built for in-depth analyses of tRNA-derived small RNAs (tDRs), mature tRNAs, and inference of RNA modifications from high-throughput small RNA sequencing data. Used for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications.
Software workflow begins by preprocessing short-read samples of raw data to create counting colored De Bruijn graph. Graph based method for population genotyping of small and structural variants. Population genotyping workflow.
American College of Surgeons National Cancer Database
Clinical oncology database sourced from hospital registry data collected in Commission on Cancer-accredited facilities. These data are used to analyze and track patients with malignant neoplastic diseases, their treatments, and outcomes.
Seattle Children's Research Institute Microscopy and Histopathology Collaborative Laboratory Core Facility
Seattle Children's Research Institute Microscopy and Histopathology Collaborative Laboratory
Provides technology and service capabilities in super resolution microscopy, image analysis, immunohistochemistry, and histopathology services. Provides consultations and technical support on histopathology services and experimental design.
Seattle Children's Research Institute Genomics and Spatial Biology Collaborative Laboratory Core Facility
Genomics and Spatial Biology Collaborative Laboratory (CoLab)
Seattle Children's Research Institute Genomics and Spatial Biology Collaborative Laboratory
Provides technology and service capabilities in long and short read sequencing, spatial transcriptomics, and single cell assays.
University of Colorado Anschutz Medical Campus Genetically Engineered Murine Models Core Facility
Genetically Engineered Murine Models (GEMM) Core
University of Colorado Anschutz Medical Campus Genetically Engineered Murine Models (GEMM) Core
Core provides full-service mouse genetic engineering support to researchers.Helps to select model for your research program, design and build any requisite constructs and reagents, and produce live mice. The most popular requests are for CRISPR-based gene edited mice and transgenic mice. Services include creation of engineered alleles for knockouts, conditional knockouts, SNP knockins, tag and marker insertions, deletions of up to 300kb, duplications, and transgenic alleles. These novel mouse models have been made on a wide spectrum of genetic background strains, including but not limited to C57BL/6J, C57BL/6N, NOD, BALB/cJ, FVB/Crl, NSGS, various 129 substrains, collaborative cross strains, and on mice that are already genetically modified. Breeding and genotyping program supports breeding to establish germline transmission and can also create cohorts for investigators. Provides strain cryopreservation, rederivation and rescue services, as well as cryostorage.
University of Miami The Miami Project Imaging Core Facility
Imaging Core provides equipment and services available to all UM researchers. Offers training and assistance in range of light microscope techniques including spinning disk confocal, super resolution imaging, lightsheet imaging of cleared organ and stereology systems. Offers image analysis software (Imaris neuroscience package) including 3D image rendering, surface creation, spot detection and filament tracing.
Neural networks for RoB assessment in preclinical publications. BERT-model based automated tool that assesses bias of preclinical research studies.
consensus Non-negative Matrix Factorization
Source code and example data for running consensus Non-negative Matrix Factorization on single-cell RNA-Seq data.
Browser based platform for selecting, exchanging, and visualizing metabolomics data with controlled data access. Used to facilitate collaborative metabolomics research and to enable researchers to make their experimental data findable, accessible, interoperable, and re-usable as defined by the FAIR principles.
Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery.
Software tools for single-cell data processing.
Philips | Alice 6 LDx Diagnostic sleep system
Diagnostic sleep system developed by Phillips Respironics. Base station can be paired with LDxS head box for 19 EEG inputs or LDxN for 32 EEG inputs.
Open source hardware-software platform for analyzing reaching movement kinematics in mice. Used for studying fine motor skills in mice performing reach-to-grasp task. Behavioral platform uses readily available and 3D-printed components and was designed to be affordable and universally reproducible. Provides schematics, 3D models, code, and assembly instructions.
Versiti Blood Research Institute Shared Resources Core Facility
Versiti Blood Research Institute Shared Resources
Core forms network of laboratories dedicated to advancing biomedical research by providing access to specialized services, advanced equipment, and expert staff. Services include Bioinformatics, Biorepository, Flow Cytometry, Grant Application Support, Histology, Hybridoma, Microscopy, Molecular and Single Cell Biology, Protein Shared Instrumentation,Thrombosis and Hemostasis, Viral Vector.
Versiti Blood Research Institute is national leader in innovative blood health solutions. Provides blood and blood products to hospitals and collects blood annually. Investigators study blood disorders like hemophilia, blood cancers like leukemia, and other blood diseases.
Software R package to process and analyse mass spectrometry-based single cell proteomics data.
Roche | Ventana BenchMark ULTRA IHC/ISH System
Automated, standardized IHC and ISH staining system. Immunohistochemistry and in situ hybridization slide staining system with individual slide drawers.
Auburn University Flow Cytometry and High-Speed Cell Sorting Laboratory Core Facility
Auburn University Flow Cytometry and High-Speed Cell Sorting Laboratory
Flow Cytometry Laboratory at Auburn University College of Veterinary Medicine provides operator-managed and assisted support for flow cytometry analyses and high-speed cell sorting.
Vectra Polaris | Automated Quantitative Pathology Imaging System
Advanced, high-throughput digital scanning platform used in cancer immunology and pathology research. It allows scientists to visualize, analyze, quantify, and phenotype immune cells in intact tissue samples. Uses patented multispectral imaging to identify and measure up to nine overlapping biomarkers on a single tissue section or tissue microarray.
Software platform and database to manage studies from our in-lab PSG, Alice 6, and portable sleep testing devices, Alice NightOne and Alice PDx.
Software R package to detect differential transcript usage from data generated by commonly used polyA-captured scRNA-seq technology.
Software tools for developing Ordinary Least Squares regression models.
generalized linear mixed models using Template Model Builder
Software R package for fitting generalized linear mixed models and extensions, built on Template Model Builder.
Matrix Expression Quantitative Trait Loci
Software tool for ultra fast eQTL analysis via large matrix operations.
Software mutable, self-balancing interval tree for Python 2 and 3. Queries may be by point, by range overlap, or by range containment.
Software C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs.
Software R package to analyse overdispersed counts or proportions.
generalized version of principal components analysis
Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data.
Software application for model-based dimensionality reduction of scRNA-seq data. Quantifies uncertainty in each cell's latent position and leverages these uncertainties to assess confidence associated with given cell clustering. On real and simulated single-cell data produces low-dimensional embeddings that better capture relevant biological information while removing unwanted variation. Used for model-based dimensionality reduction for single-cell RNA-seq with generalized bilinear models.
GPU-assisted Distance Estimation Software
Software package to compute distance matrices in sparse or dense mode with GPU or CPU.
Software tool to identify barcode and primer sequences in PacBio single-molecule sequencing data. It powers the Demultiplex Barcodes GUI-based analysis application,
University of Colorado School of Medicine Electron Microscopy Core Facility
University of Colorado Anschutz Medical Campus Electron Microscopy Core Facility
Service facility which provides instrumentation and image analysis on recharge basis. Offers full specimen preparation and imaging services. Specimen preparation for electron microscopy studies including negative staining, plastic embedding, ultramicrotome and immunogold.
Seattle Children's Research Institute Flow Cytometry Core Facility
Flow Cytometry Core at Seattle Children's Research Institute, offers cell analyzer and sorter capabilities to researchers across the institute.
Indiana University School of Medicine Biochemical Genetics Laboratory Core Facility
Indiana University School of Medicine Biochemical Genetics Laboratory
Clinical testing lab that performs targeted metabolomics analyses designed to diagnose and manage patients with inherited metabolic disease.Services include Quantitative Acylcarnitine panel,Quantitative Amino acid panel,Quantitative Methylmalonic acid,Quantitative Free and Total Carnitine Analysis,Semi-Quantitative Urine Organic Acid Profile,Blood Spot Analyte Quantification,Custom Development of Quantitative Metabolite Assays.
Indiana University School of Medicine Behavioral Phenotyping Core Facility
Indiana University School of Medicine Behavioral Phenotyping Core
Facility where IUSM and external investigators can request studies within broad spectrum of rodent behavioral paradigms. Housed on the fourth and fifth floors of Stark Neurosciences Research Institute in the Neurosciences Research Building, the core, available to all IU School of Medicine investigators. Core validates all assays; allows for testing of pharmacological or other manipulations to study disease models; incorporates necropsy endpoints to behavioral assays as needed; provides guidance on interpretation and analysis of data.
Indiana University School of Medicine Biospecimen Management Core Facility
Indiana University School of Medicine Biospecimen Management Core
Core consists of the Specimen Storage Facility (SSF) and the Clinical and Translational Support Laboratory (CTSL), which together offer cost efficient sample processing and storage services with focus on consistent quality and sample integrity.
Indiana University School of Medicine Bioinformatics Core Facility
Indiana University School of Medicine Bioinformatics Core
Bioinformatics Core provides advanced computation and informatics approaches to analyze large and complex biological datasets. Core offers services including Next Generation Sequence Data Analysis; Microarray Data Analysis; Proteomics Data Analysis;Multi-omics Data Integration;Statistical Genetics;Pharmacokinetics/Pharmacodynamics Data Analysis; Drug Absorption, Disposition, Metabolism, Elimination and Transportation Prediction, and Drug Exposure Prediction;Public Domain Database Access and Custom Data Annotation.
Purdue University Biological Evaluation Core Facility
Core performs highly customizable efficacy testing of novel drug or therapies for antitumor activity. We also acquire blood or tissues for pharmacokinetic or pharmacodynamic analyses.
Indiana University School of Medicine Biostatistics and Health Data Science Core Facility
Indiana University School of Medicine Biostatistics and Health Data Science Core
Core collaborates with investigators in the planning, statistical design, data management, and analysis of health related clinical, laboratory and epidemiological research projects. Grant development assistance is provided without charge.
Indiana University School of Medicine Biospecimen Collection and Banking Core Facility
Biospecimen Collection and Banking Core (BC2)
Indiana University School of Medicine Biospecimen Collection and Banking Core
Core offers services related to biospecimen and data collection in support of cancer research. Provides collection of well-annotated samples from patients with malignancy and normal controls to support studies exploring the biologic basis of cancer, move basic findings to clinic, and probe the biology underlying clinical and population phenomena.
Indiana University Bloomington Biostatistics Consulting Center Core Facility
Provides study design and data analysis for health-related research, including grant or protocol development, sample size and power calculations, data management, data analysis, and scientific writing. Support can range from hourly support on a short-term project to including a biostatistician on a long-term grant collaboration.
Indiana University School of Medicine Cell and Gene Therapy Manufacturing Core Facility
Indiana University School of Medicine Cell and Gene Therapy Manufacturing
Core collaborates with investigators through all phases of cell and gene therapy manufacturing, from pre-clinical design through treatment of patients. Facility comprises the Cell Immunotherapy and Transduction Facility (CIT), the Vector Production Facility (VPF), and the Bioprocess Development and Cell Manufacturing Lab (BDL).
Purdue University Birck Nanotechnology Center Core Facility
Nanofabrication cleanroom, bio-pharma clean room, nanometrology laboratories, nanomanufacturing laboratories, microelectronics and microfuidics fabrication and testing laboratories, 3D cell culture and tissue chip laboratories.
Indiana University School of Medicine Medical Genomics Core Facility
Indiana University School of Medicine Center for Medical Genomics
Provides high-throughput genomics services including: genomic DNA sequencing, transcriptome RNA sequencing, miRNA sequencing, methylome or targeted methylation sequencing, protein DNA/RNA interaction (ChIP-seq, ATAC-seq and CLIP-seq), 10x single cell or single nuclei sequencing, and SNP genotyping.
Indiana University School of Medicine Cellular Response Technologies Core Facility
Indiana University School of Medicine Cellular Response Technologies Core
Conduct validated and highly reproducible in vitro and in vivo angiogenesis, endothelial, hematopoietic and multi-parametric flow cytometry assays and their role in normal and patient-related hematologic and cardiovascular disorders. The ABC also manages an IncuCyte Zoom and Seahorse XFp.
Purdue University Center for Research Computing Core Facility
CRC houses two complementary resources: the High-Performance Computing section, providing over 35,000 cores of computational power with the associated support infrastructure for both hardware and installed software, and the Cyberinfrastructure section, empowering Faculty and industry partners to develop research software and environments that support advanced data and information processing services including acquisition, storage, management, integration, mining
Purdue University Chemical Genomics Core Facility
Purdue University Chemical Genomics Facility
Provides access to large chemical and CRISPR libraries and state-of-the-art instrumentation in high-throughput screening (HTS) and high content screening (HCS) campaigns to facilitate the identification of chemical or genomic tools to study biological pathways and the discovery of lead agents for the development of novel therapeutics and diagnostic approaches. The facility also provides assistance in assay development
Indiana University School of Medicine Proteome Analysis Core Facility
Provides numerous types of mass-spectrometry based proteomics services, including global proteome quantitation, affinity purification-mass spectrometry, targeted mass spectrometry analysis for precise quantitation, post-translational modification analysis, and a variety of consulting services.
Indiana University School of Medicine Clinical Pharmacology Analytical Core Facility
Core provides drug and metabolite concentrations from a variety of biological matrices such as (but not limited to): plasma, urine, CSF, and tissue using HPLC-MS/MS. Additional services include protein binding of drugs, formulation studies, drug stability, drug metabolism, and metabolite screening.
Indiana University Bloomington CISAB Mechanisms of Behavior Laboratory Core Facility
Mechanisms of Behavior Core offers the equipment, reagents, bench space, and expertise to answer questions related to the roles of genetics and hormones in relation to animal behavior.
Purdue University Center for Comparative Translational Research Core Facility
Purdue University Comparative Translational Research
﻿Core facilities pre-clinical studies of orthopedic devices intended for animal and human use, clinical studies of treatment and prevention of respiratory diseases in horses and animal clinical trials evaluating the treatment of bladder cancer in Scottish Terriers, an animal model of human bladder cancer.
Software R package as collection of functions to compute the Clopper-Pearson Confidence Interval and the required sample size. Density, distribution function, quantile function and random generation for the Generalized Binomial Distribution.Enhanced model for burn-in studies, where failures are tackled by countermeasures.
Software R package to compute various confidence intervals for the Kaplan-Meier estimator, namely: Peto's CI, Rothman CI, CI's based on Greenwood's variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by Nair and Hall and Wellner.
3D Developmental Mouse Brain Common Coordinate Framework
Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain.
Purdue University Cryo-Electron Microscopy Core Facility
Facility provides access to instrumentation enabling users to collect data for high-resolution single particle reconstructions and tomographic studies of cells and larger complexes.
Indiana University School of Medicine Electrophysiology Core Facility
Indiana University School of Medicine Electrophysiology Core
Electrophysiology Core performs rodent brain slice electrophysiological recordings to measure brain cell function.
Purdue University Flow Cytometry and Cell Sorting Core Facility
Flow Cytometry and Cell Separation Facility
Purdue University Flow Cytometry and Cell Sorting Facility
Core Facility provides instrumentation, data analysis software, training and technical expertise for flow cytometry analysis and cell sorting. Our capabilities also include the characterization of genome and transcriptomes using the Fluidigm C1 and 10X Genomics systems, in partnership with the Purdue Genomics Core Facility.
Fully automated research stainer that automates staining step which ensures that microscope slides are produced with consistent, reproducible, and efficient way. Utilizes biological assay called immunohistochemistry.BOND RX model expands on the capabilities of IHC by including other assays.
Software application as minimap2 frontend for PacBio native data formats. SMRT C++ wrapper for minimap2's C API.
Peter MacCallum Cancer Centre Research Flow Core Facility
Peter MacCallum Cancer Center Research Flow Core
Peter MacCallum Cancer Center Research Flow Core (RFC)
Internationally recognised shared resource laboratory which provides researchers with access to equipment, education and expertise that enables isolation, separation and analysis of cell populations.
University of Nebraska-Lincoln Methodology and Evaluation Research Core Facility
Methodology and Evaluation Research Core Facility
Provides range of evaluation and data services to support client needs.Through consulting, evaluation, methodology, and training, we work to fill gaps and improve and empower data driven decision making.At the proposal stage of grants, we can design evaluation plans to meet your project needs, with the associated narrative text, budget, and letter of collaboration, as needed. We can also fill gaps post-award, or provide support with internal funding. We can assist with logic models, Broader Impacts, methodologies, needs assessments, survey design and implementation, support with Institutional Review Board applications, and trainings in our areas of expertise.
Notre Dame Freimann Life Science Center Core Facility
Home to virtually all laboratory animals. Services include Procurement, Animal care, Breeding, Training,Limited procedures for research.
Indiana University School of Medicine Genome Editing Center Core Facility
Indiana University School of Medicine Genome Editing Center
Provides access to genome editing technologies by assisting with generation of genetically modified mouse models and cell lines.
Indiana University School of Medicine HANDS In Autism Interdisciplinary Training and Resource Center Core Facility
HANDS In Autism Interdisciplinary Training & Resource Center
Helping Answer Needs by Developing Specialists in Autism Interdisciplinary Training & Resource Center
Indiana University School of Medicine HANDS In Autism Interdisciplinary Training and Resource Center
Provides evidence-based services, training, coaching and consultation across range of local community and state stakeholder networks e.g., families, medical providers, school personnel, community organizations. This involvement and integration in addressing the behavioral, educational, and vocational needs of consumers across a range of ages i.e., early childhood through adulthood, functioning and disability types has assisted in: providing consultative expertise related to assessment and intervention with autism spectrum disorder and related developmental e.g., developmental and/or intellectual disabilities or neurodevelopmental disorders; reaching extensive audience for recruitment efforts; facilitating efforts related to community-based mixed methods, clinical trials and other research endeavors e.g., survey development and dissemination, behavioral assessment and intervention related to individuals with ASD/DD/ID across lifespan.
Notre Dame Genomics and Bioinformatics Core Facility
Genomics and Bioinformatics Core Facility (GBCF)
Offers comprehensive services and support for genomics experiments and bioinformatics analysis. This includes next generation Illumina sequencing, a variety of standard and specialty DNA and RNA library construction methods, consultation, and analysis support.
Indiana University School of Medicine Histology and Histomorphometry Core Facility
Indiana University School of Medicine Histology and Histomorphometry Core
Provides histological and histomorphometric services for basic science (non-clinical) research. Mineralized (plastic embedded), soft tissue (paraffin embedded), and cryopreserved specimens can be processed by the facility. Histology Core is core facility of the Indiana Center for Musculoskeletal Health and part of the Bone and Body Composition Core of the Indiana Clinical Translational Sciences Institute (CTSI). Histology Core provides histological services for basic science (non-clinical) research. Both mineralized (plastic embedded) and soft tissue (paraffin embedded) specimens can be prepared by the facility.
Purdue University Bindley Genomics Core Facility
Core provides both next generation Illumina NovaSeq and MiSeq and Sanger sequencing with additional method to provide entire plasmid sequences via service called WideSeq.
Indiana University School of Medicine Human Vascular Imaging Core Facility
Indiana University School of Medicine Human Vascular Imaging Core
Core provides following services: Brachial artery flow-mediated dilation; Brachial artery nitroglycerin-mediated dilation; Carotid artery intima media thickness.
Purdue University Histology Research Laboratory Core Facility
Purdue University Histology Research Laboratory
Full service histology laboratory that provides general histology, immunohistochemistry, frozen sectioning, decalcified and undecalcified bone histology, and slide digitization services. Board certified veterinary pathologists are also available for consultation.
Indiana University School of Medicine South Bend Imaging and Flow Cytometry Core Facility
IU South Bend Imaging and Flow Cytometry Core Facility
IUSM South Bend Imaging and Flow Cytometry Core Facility
Provides standard confocal or multiphoton resources for imaging live or fixed samples and a 5 color flow cytometric analyzer are available. Data analysis software for each resource is also available on site.
American Association for Cancer Research
Cancer research organization dedicated to accelerating the conquest of cancer. The mission is to prevent and cure cancer through research, education, communication, collaboration, science policy and advocacy, and funding for cancer research. Through its programs and services, the AACR fosters research in cancer and related biomedical science, accelerates dissemination of new research findings, promotes science education and training, and advances the understanding of cancer etiology, prevention, diagnosis, and treatment throughout the world.
Software R package intended to simplify both installation and loading of packages from mlr3 ecosystem. Meta-package for installing/updating mlr3* packages.
Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms.
Indiana University Bloomington Imaging Research Core Facility
Neuroimaging facility that enables cutting-edge neuroscience research and training using non-invasive imaging methodologies, including both MRI and EEG.
Indiana University School of Medicine Infectious Diseases Laboratory Core Facility
Indiana University Infectious Diseases Laboratory
Indiana University School of Medicine Infectious Diseases Laboratory
Performs clinical research studies including evaluation of new molecular technologies for diagnosis of wide array of sexually transmitted and newly emerging pathogens, developing novel assays to meet the needs of individual research collaborators, and tailoring services to successfully meet study objectives. The laboratory has the capability to identify and type human papillomavirus.
Indiana University School of Medicine Immunohistochemistry Research Lab Core Facility
Immunohistochemistry Research Lab (IHC Research Lab)
Immunohistochemistry Research Lab specializes in assisting researchers with histologic and immunohistochemical labeling of cells or tissue sections as well as collaborations with surgical pathologists.
Indiana University School of Medicine In-Vivo Imaging Core Facility
Indiana University School of Medicine In-Vivo Imaging Core
Core provides imaging services for clinical trials, observational, and preclinical studies. Provides radiochemistry support for molecular imaging. Currently, the Imaging Core is equipped with state-of-the-art imaging systems, including 3T MRI scanners, PET-CT scanners, Bruker 9.4 T preclinical PET-MRI scanner, a Siemens Eclipse Medical Cyclotron, and Radiochemistry Facilities.
Indiana University School of Medicine Center for Biological Microscopy Core Facility
Indiana Center for Biological Microscopy
Provides researchers with access to laser-scanning confocal, 2-photon and epi-fluorescence microscopes. Personnel train individual researchers to use all imaging systems and provide expert help in design, conduct and analysis of imaging studies. As necessary, center personnel can also be hired to conduct microscopy studies for laboratories lacking necessary expertise.
Indiana University School of Medicine In Vivo Therapeutics Core Facility
Core supports research and development of safe and more efficacious drug treatment. Provides cost-effective and comprehensive services including, but not limited to, on-site breeding facilities as well as in vivo pharmacology models to facilitate development and testing of novel pharmacological and cellular therapies.
Open-source apparatus to enable continuous individual monitoring, training, and testing of rats without removing them from their social environment. This system utilizes RFID technology to track individual animals, minimizing human intervention and providing precise behavioral data.
Software R package used for machine learning. Extra learners for use in mlr3.
Software assists with any operations you may need to manage your organization’s users and resources.Helps to create environment for many different versions of Python and package versions. Used to install, remove, and upgrade packages in project environments.
University of California Irvine Center for Neural Circuit Mapping Viral Core Facility
Center for Neural Circuit Mapping Viral Core
University of California Irvine Center for Neural Circuit Mapping Viral Core
Viral production facility aims at development and production of viral vectors for in-vivo and in-vitro experimentation purposes. Equipment coupled with our expertise allows use to ensure high quality products. Provides all related sequence data, vector maps, plasmids and ready-to-use viruses once your orders are completed.
Emory University Pediatric Biomarkers Core Facility
Emory University Emory Pediatric Biomarkers Core
Biomarkers Core offers high quality analysis of biological samples to support pediatric research. Provides equipment and technical expertise to assay samples using methods that combine the features of gas-liquid chromatography and mass spectrometry.
Global pharmaceutical company that develops, manufactures and distributes essential medicines for hospitals and retail pharmacies.
Niguarda Hospital Milan Department of Hematology, Oncology and Molecular Medicine Core Facility
Niguarda Hospital Milan Department of Hematology
Core performs histopathological, cytopathological, intraoperative diagnostic and autopsy activities. Offers service of laboratory diagnostic tests. Facility also deals with evaluation of cytoaspiration sampling of mediastinal lymph nodes, using videobronchoscopic technique in collaboration with Thoracic Surgery.
Software environment to ease task of building macromolecular models into low to medium resolution experimental maps. Physically realistic environment for model building into low-resolution electron-density maps. Can generate maps directly from crystallographic F/sigF data in MTZ format and automatically re-calculate them when model changes, and/or generate "static" maps from pre-calculated F/phi data.
Portal contains information about the geographic locations of dam removals and any associated scientific studies evaluating outcomes to physical, biological, and water quality parameters. Results can be downloaded based on customized search criteria specified by the user.
CannSeek Database of Cannabis sativa SNPs
Database of Cannabis sativa Single Nucleotide Polymorphisms discovered from NGS sequences and BioSamples available in NCBI. Sequence reads were called against cs10, Purple kush, and Finola reference assemblies using GATK and Parabricks pipelines.
NIH-funded resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relationships.
Software R package to provide ggplot2 implementation of biplot, simultaneous plot of scores for observations and vectors for variables for principal component-like analyses.
Peter MacCallum Cancer Centre Victorian Centre for Functional Genomics Core Facility
Peter MacCallum Cancer Centre Victorian Centre for Functional Genomics
Victorian Centre for Functional Genomics
Core to perform novel discovery-based high throughput compound, CRISPR and RNAi screens at any scale in both 2D and 3D formats, using liquid handling instruments, automated high content imaging microscopes, live imaging systems and large reagent libraries.
Generates linear gradients using process called tilted tube rotation. Process involves layering two end point solutions directly in centrifuge tube, capping it and placing it in magnetic tube holder that adheres to rotary steel plate on instrument. Gradient Master takes over and tilts tube to the proper angle, rotates it for designated time and returns it to its original vertical position, ready to use.
BioComp Instruments | Piston Gradient Fractionator
Piston fractionation leaves gradient undisturbed while piston descends from the top, displacing layers through centre of its patented trumpet shaped tip, keeping flow smooth and precise. Used to fractionate based on distance rather than drop or time.
Beckman Coulter ultracentrifuge Optima XPN-100 IVD
Optima XPN generates centrifugal forces for separation of particles.Centrifuge is intended to separate human samples, including blood, urine, and other bodily fluids to prepare samples for downstream in vitro diagnostic procedures, which may include molecular diagnostic, chemistry, immunoassay, and coagulation tests. This centrifuge should be operated by laboratory professionals only.Floor model preparative ultracentrifuge offers temperature from 0 to 40℃, meets environmental protection requirements, adopts microcomputer controlled variable reluctance drive system, vacuum friction reduction system.
Automated system for comprehensive, label-free analysis and characterization of biomolecular interactions in real-time. Can be used for applications, including structure function studies, pathway analysis, biomarker discovery and validation, drug target identification and validation, and assay development.
Indiana University School of Medicine Center for Electron Microscopy Core Facility
IU School of Medicine Center for Electron Microscopy (iCEM)
Offers cryo-electron microscopy, transmission electron microscopy, and scanning electron microscopy. Provides technical services to help design and then implement experiments needing each type of microscopy.
University of Notre Dame Keck Center for Transgene Research Core Facility
University of Notre Dame Keck Center for Transgene Research
W. M. Keck Center for Transgene Research
Core develops and uses gene-targeting technology to investigate pathophysiological roles of genes of blood coagulation, anticoagulation, and fibrinolytic pathways in hemostasis, with associated relevance to embryonic development, cancer, infection, and inflammation.
Indiana University Bloomington Laboratory Animal Resources Core Facility
Indiana University Bloomington Laboratory Animal Resources
LAR provides housing, food, water, bedding, enrichment and medical care for animals housed in LAR animal facilities to be used for research.
Indiana University School of Medicine Laboratory Animal Resource Center Core Facility
Indiana University School of Medicine Laboratory Animal Resource Center (LARC)
Core provides basic husbandry, training, supplies, and specialized service support for medical research at IU School of Medicine.
Indiana University Bloomington Laboratory for Biological Mass Spectrometry Core Facility
Indiana University Bloomington Laboratory for Biological Mass Spectrometry (LBMS)
Laboratory for Biological Mass Spectrometry (LBMS)
Core uses mass spectrometry to characterize proteins as well as other biologically-derived molecules. Specializes in characterization of protein post-translational modifications, including glycosylation, phosphorylation, acetylation and persulfidation.Provides identification of protein-interactions including determination of protein-protein crosslinks and quantitative comparisons of complex samples.
Software environment for subtomogram averaging of cryo-EM data. Development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.
Software R package to analyse large volumes of data. Extracts structure of data without the need to build any model to represent it. Provides functions for data exploration via PCA, and allows the user to generate publication ready figures.
Cloud-based high performance computing for specialised analyses on environmental omics.
Purdue University Life Science Microscopy Core Facility
Electron microscopy core with both service and individual use options.
Notre Dame University Mass Spectrometry and Proteomics Core Facility
Notre Dame University Mass Spectrometry and Proteomics Facility
Core provides analysis of large and small molecules using several ionization methods, low or high resolution, hyphenated techniques, proteomics, and metabolomics.
Indiana University Bloomington Light Microscopy Imaging Center Core Facility
Indiana University Bloomington Light Microscopy Imaging Center
Provides access and training for confocal and super-resolution light microscopy systems with support for experimental design and data visualization.
Indiana University Bloomington Macromolecular Crystallography Integrated with Crystallization Automation Core Facility
Macromolecular Crystallography Facility Integrated with the Crystallization Automation Facility (MCF/CAF)
Macromolecular X-ray Crystallography Facility provides all resources for Crystal Screening and Optimization, Data Collection and Structure Determination of macromolecules.
Notre Dame University Magnetic Resonance Research Center Core Facility
Notre Dame University Magnetic Resonance Research Center
Core supports research in chemistry, biochemistry, molecular biology, engineering and related fields. The MRRC operates six solution-state NMR spectrometers (400 to 800 MHz), a solid-state 300 MHz NMR instrument, and an X-band EPR spectrometer. Most instruments are equipped with sample changers for increased sample throughput.
Workflow for preprocessing cfDNA samples. Unified, standardized, and ready-to-use workflow for processing whole genome sequencing cfDNA samples from liquid biopsies. Includes steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Provides specialized methods for extracting coverage derived signals and visualizations comparing cases and controls.
Software tool for spatial domain identification from spatially resolved transcriptomics with multi-modal feature representation.
Advanced Technologies for the Preservation of Biological Systems
Aims to stop biological time and extend ability to bank and transport cells, aquatic embryos, tissue, skin, whole organs, microphysiological systems and whole organisms. Builds advanced biopreservation technologies to eliminate or mitigate ice formation, cryoprotective agent toxicity, and slow and/or non-uniform rewarming.
Web infrastructure for visualizing and remixing microbial ‘omics data. Software visualization platform to view next-generation sequencing data, such as RNA-seq counts.
Differential Gene Set Enrichment Analysis
Differential Gene Set Enrichment Analysis (DGSEA)
Software tool to determine whether two priori sets of genes show statistically significant differences between two biological states. Statistical approach to quantify relative enrichment of two gene sets.
Software R package to perform statistical analysis of differential protein expression for quantitative proteomics data.
Australian Drosophila Transgenic Core Facility
Australian Drosophila Transgenic Facility
Core offers specialised microinjection services for generating transgenic strains of fruit fly Drosophila melanogaster.
Automated Systematic Search Deduplicator
Automated Systematic Search Deduplicator:ASySD
Open source, interoperable software tool to remove duplicate citations in biomedical systematic reviews.
Software 16S rRNA analysis workflow with QIIME2 and Snakemake.
University of Nebraska Lincoln Single Cell Genomics Core Facility
University of Nebraska Lincoln Single Cell Genomics
Facility provides access to Chromium iX platform from 10X Genomics. This allows user to barcode single cells or nuclei and process them for single cell RNA-seq, single nucleus ATAC-seq or single nucleus Multiome ATC + Gene Expression protocols.
Software object oriented Python library to analyze trajectories from molecular dynamics simulations in many popular formats.
Australian oncology research institute, cancer treatment and professional oncologist training centre located in Melbourne, Victoria.
Multiomic data integration software. R code to perform factorization and dimension reduction of bidimensionally linked data matrices. Used to decompose variation into series of low-rank components that may be shared across any number of row sets e.g., omics platforms or column sets e.g., cancer types.
Software for multi-omic data integration. Used to jointly decompose multiple biologically related experimental data sets with biological and technological relationships that can be structured into the decomposition.
Algorithm for regulatory network inference using gradient boosting, based on GENIE3 architecture. Used for inference of gene regulatory networks.
Software pipeline for DNAseq analysis. Used to calculate required modification of quality scores assigned to individual read bases of sequence read data.
Proteomics software used to convert ThermoFinningan RAW mass spectrometry files to mzXML format.
Plant cO-expression Transcription Factor regULators
Software Python pipeline for integrating co-expression and transcription factor target protein networks to infer gene regulation.
Software R package to select matched samples of original treated and control groups with similar covariate distributions. Can be used to match exactly on covariates, to match on propensity scores, or perform variety of other matching procedures. Nonparametric preprocessing for parametric causal inference.
Software R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology. Used for comprehensively interpreting multi-omics data.
Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments.
Software R package to detect and visualize Kataegis events from single nucleotide variants.
Peter MacCallum Cancer Centre Genotyping Core Facility
Provides mouse genotyping service, from extraction of genomic DNA from tissue to reporting of genotypes. Offers Mycoplasma testing of any cell line and authentication of human cell lines.
Northwestern University Reactor Engineering and Catalyst Testing Core Facility
Northwestern University Reactor Engineering and Catalyst Testing (REACT) Core Facility
Reactor Engineering and Catalyst Testing Core Facility
Core is dedicated to aiding students and investigators in advancement of understanding chemical properties of solid interfaces used for environmental and energy processes. Facility provides range of instrumentation and services for students and industrial researchers interested in catalysis.
Penn State College of Medicine Pulmonary Immunology and Physiology Core Facility
Penn State College of Medicine Pulmonary Immunology and Physiology Core
Pulmonary Immunology and Physiology Core
Core provides development and testing of small animal models to be used for pre-clinical pulmonary research. BSL2 facility that allows the assessment of pulmonary function related to airway hyper-responsiveness, ventilation-induced lung injury, postnatal lung development, airway remodeling, chronic inflammation, allergy, environmental exposures and infection. Services offered include oxygen profiling, infection and treatment; ability to deliver, measure and test pre-clinical potential of therapeutic interventions via aerosol; and housing of small animals.
Comprehensive database for regulations of Human Transcription Factors and their targets. Provides tools for visualization, interpretation, and analysis of pathway knowledge.
System features multi-component IonDrive technology including IonDrive High Energy Detector+ to enable to see low mass to high mass compounds, in positive or negative polarity in single injection.
American company based in Cambridge, Massachusetts, which develops, manufactures, and sells genomic profiling assays based on next-generation sequencing technology for solid tumors, hematologic malignancies, and sarcomas. Specializes in precision medicine. FMI routinely analyzes cancer specimens using advanced sequencing technology of FoundationOne to profile tumor genomics.
Biotechnology company in Baltimore, Maryland, specializing in liquid biopsy. Offers comprehensive NGS testing services for clinical trials, enhancing oncology drug development and patient outcomes.
Software R package implementation of Milo for testing for differential abundance in k-nearest neighbor graphs. Milo can identify perturbations that are obscured by discretizing cells into clusters. Used for differential abundance analysis on KNN graph from single-cell datasets.
Transcription factor target database. Platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments and target genes or transcripts across multiple organisms.
Mixed effects association testing for single cells
Mixed-effects Association testing for Single Cells
Mixed-effects modeling of Associations of Single Cells
Software tool for testing whether specified covariate influences membership of single cells in any of multiple cellular subsets while accounting for technical confounds and biological variation.
Weill Cornell Medicine Genomics Resources Core Facility
Core offers services from experimental design and sample preparation to instrumentation, data analysis, interpretation, and validation. Provides sequencing technologies and team of well trained staff.
Azure Biosystems | Sapphire FL Biomolecular Imager
Sapphire FL is second generation Sapphire and ultimate biomolecular imager for FLEXIBILITY. With customizable and user-changeable laser and filter modules. Offers customizable and user changeable optical modules, 5–1000 μm resolution scans, Z-plane range from -1.0 to +6 mm, 5 anesthesia ports for imaging living animals, chemiluminescence detection through Chemiluminescence Module.
Software tool as modified R ks.test to obtain sign and force exact p-value.
Software Python package for computing corrected test statistics for comparing machine learning models on correlated samples. Software package version of correctR.
Bruker tims Trapped Ion Mobility-Time-of-Flight Ultra
Bruker timsTOF Ultra boasts increased sensitivity and resolution whilst allowing for exceptionally low sample input and resolution whilst allowing for exceptionally low sample input.
Software genetic expression and variation data visualization tool for neurological diseases biomarkers.
Portal provides information about available datasets, resources, tools, and services related to pandemic preparedness in Norway. Portal gives researchers, clinicians and policymakers access to collection of biomolecular data about pathogens.
Software algorithm for fully automatic image stitching of volume electron microscopy.Used to stitch input biological tiles while correcting local distortion.
Searchable catalog of enhancer-adeno-associated viruses (AAVs) that have been developed and tested at the Allen Institute for Brain Science. We present a suite of enhancer AAVs that can provide access to specific cell types when delivered to the whole brain. Multiple epigenomic and transcriptomic datasets were interrogated to reveal candidate enhancers that are selectively accessible in particular cell populations. Enhancer AAVs were constructed and screened for desirable expression and a sizeable subset of enhancer AAVs were subjected to further characterization by single cell transcriptomics and/or brain-wide expression imaging in mouse. In the GTA, we present a large toolkit for selective gene expression in cell types of interest. Genetic Tools Atlas is part of the growing Brain Knowledge Platform.
Single-sample Mutation-based Pathway Analysis
Single-sample Mutation-based Pathway Analysis (ssMutPA)
Software R tool designed for single-sample mutation-based pathway analysis by integrating somatic mutation data with protein-protein interaction (PPI) networks.
Bio-Rad | Bio-Plex MAGPIX Multiplex Reader
Compact reader for analysis of up to 50 analytes in single sample.Designed to read assays developed on magnetic xMap (MagPlex) beads and comes with Bio-Plex Manager analysis software. Bio-Plex MAGPIX Multiplex Reader is now discontinued. Bio-Rad will continue to provide premium Luminex instrumentation: the Bio-Plex® 200 System and Bio-Plex® 3D Suspension Array System and service, support, accessories, and software for customers with the Bio-Plex MAGPIX Multiplex Reader.
Semmes-Weinstein Von Frey Aesthesiometer for touch assessment. The Semmes-Weinstein monofilaments provide an approximate logarithmic scale of actual force, and a linear scale of perceived intensity. They have a long history of effective use in clinical settings, and can be used to diagnose pathologies of hyper- or hypo-aesthesia. Subsets within the set of 20 probes distinguish pathologies on different parts of the body (foot, hand, lip, cheek,etc.).
Ugo Basile Hot/Cold Plate - Screening of Thermal Hyperalgesia/Allodynia
Instrument screens thermal hyperalgesia and allodynia,conditions often observed in patients with neuropathic pain or inflammation. Also used for testing analgesic and anti-inflammatory drugs. Plate test includes all the latest technologies necessary to run constant temperature, linear ramping temperature (toward hot or toward cold) and complex temperature ramps thanks to the included X-Pad software.New model includes keypad (cabled or optional Bluetooth) to score pain endpoints or stereotyped behaviors. Temperature range goes from -5° to 65°C and animal holders of different heights are available.
Database and query tool designed for cancer research community to facilitate integration and study of molecular and pharmacological data for the NCI-60 cancerous cell lines. The NCI-60, panel of 60 diverse human cancer cell lines used by the Developmental Therapeutics Program of the U.S. National Cancer Institute to screen over 100,000 chemical compounds and natural products since 1990.
Web application integrating cancer cell line pharmacogenomics. Enables exploration and analysis of cancer cell line pharmacogenomic data across different sources. Focuses on cancer patient-derived human cell line molecular and pharmacological data. CellMinerCDB (v1.2) includes several improvements.
Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning.
Software R package of ExpressAnalyst for gene expression analysis. Underlying R package synchronized with ExpressAnalyst web server.
Software tool as protein-protein/nucleic acid interaction site prediction model built by enhanced graph neural networks and prioritized radial basis function neural networks. Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning.
Software package for control of MAGPIX, Luminex 200, and FLEXMAP 3D. Software’s graphical user interface follows typical assay workflow but can be customized to meet the needs of specific laboratory. Navigation wizards and automated routine operations such as startup, shutdown, calibration, and performance verification further enhance system usability and result in increased walk-away time. Allows to acquire samples, perform analysis, and run system maintenance routines and remote web monitoring. Basic package includes the ability to calculate allelic ratios to analyze and/or normalize genotyping data.
Publicly accessible 3D data repository where subject experts, educators, and general public can find, view, interact with, and download 3D and 2D media representing physical objects important to the world’s natural history, cultural heritage, and scientific collections. Media data are contributed by a community that includes museums, institutions, researchers, scholars, and other subject experts who use MorphoSource to archive data, share findings, and increase scholarly impact. Contributed media represent both biological objects such as fossils and representatives of living species, as well as artifacts and objects created by humans that are critical to our shared cultural heritage.
Software integrated research platform for multimodal medical data analysis and prediction employing AI techniques. Offers comprehensive functionalities to support various stages of medical research, including data preprocessing, feature extraction, model training, and prediction.
MAP Database Guide for Membrane Protein Solubilization
Membrane Active Polymers Database Guide for Membrane Protein Solubilization
Open access web app that allows users to search for optimal condition for extraction of membrane proteins into membrane active polymers which allows for retention of native membrane environment around target protein.
Database of downscaled paleoclimate outputs at 2.5 minute resolution (~5 km at equator) that includes surface temperature and precipitation estimates from snapshot-style climate model simulations using HadCM3, a version of the UK Met Office Hadley Centre General Circulation Model. Database contains climatic data for three key time periods spanning from 3.3 to 0.787 million years ago: the Marine Isotope Stage 19 (MIS19) in the Pleistocene (~787 ka), the mid-Pliocene Warm Period (~3.264–3.025 Ma), and MIS M2 in the Late Pliocene (~3.3 Ma). Set of historical climate layers (climate grids) with spatial resolution of about 2.5 min. These data can be used for mapping and spatial modelling in Geographic Information Systems (GIS) or other computer programs.
Chinese National Earth System Science Data Center
A raster layer of global vegetation types, in Chinese. Please note the website is not functional from the US.
Web app for global DEM data with spatial resolution of about 30m. This data can be used for mapping and spatial modelling in GIS or other computer programs.
Chinese CASEarth Data Sharing and Service Portal
Portal built for the release and sharing of data resources of "Big Earth Data Science Engineering Program (CASEarth)" launched by the Chinese Academy of Sciences. A global raster data of land cover and land use. This data can be used for mapping and spatial modeling in Geographic Information Systems (GIS) or other computer programs. This website is not accessible from the USA.
University of Idaho UI COBRE Nutrition Analytics Core Facility
University of Idaho COBRE Nutrition Analytics Core Facility
Core facility that provides expertise and instruments/equipment to promote research in nutrition and/or women’s health by leveraging resources from new and existing institutional programs and fostering collaborations across disciplines. Consists of hub laboratory suite with wet bench laboratory, body composition assessment and resting metabolic rate laboratories, computer laboratory, metabolic kitchen, and network of partnering laboratories distributed across the UI and the state of Idaho.
Software R analysis code for analyzing fluorescence microscopy images to determine complexity of cultured astrocytes. Sholl profile analysis based on mixed-effect models.
Rockefeller University Comparative Bioscience Center Core Facility
Core provides comprehensive program of animal care in support of the university's in vivo research. Offers maintaining variety of common and unique laboratory animals in addition to providing veterinary, diagnostic and research technical services. Fully accredited by Association for Assessment and Accreditation of Laboratory Animal Care International. Comprehensive animal care and use program.
National Cancer Institute Genomics and Pharmacology Core Facility
Provides pharmacogenomics resource for study of cancer. Multiple tools are available, currently including the CellMiner family with CellMiner, CellMinerCDB (cross data-base), CellMinerCDB: Small Cell Lung Cancer (SCLC), CellMinerCDB: National Center for Advancing Translational Sciences (NCATS) andCellMinerCDB: Sarcoma. These sites include multiple cancerous cell lines sets and data types. In addition there is CIMMiner for cluster image maps and MIMminer, with several scholarly molecular interaction maps.
Web app for high-throughput structural modeling for B-cell and T-cell receptors. Used for generating atomic-resolution, three-dimensional models of B cell receptors or T cell receptors from their amino acid sequences.
Web application for antibody-specific epitope prediction. Used for predicting antibody-antigen complex structures from sequence.
Web structural modeling tool for TCR-pMHC complexes from amino acid sequences. TCR-pMHC modeling from amino acid sequences.
Database of opsin genotype-phenotype data and machine-learning models trained to predict opsin phenotypes. Database of all heterologously expressed opsin genes with λmax phenotypes.
Open-source software project for content collaboration and sharing and syncing of files in distributed and federated enterprise scenarios. Used for file synchronization and sharing of data. Platform that allows users to securely store, access, and manage files from anywhere, on any device. Designed for privacy and control, it offers customizable storage solutions, collaboration tools, and integrations, making it ideal for businesses and individuals seeking secure, self-hosted alternative to traditional cloud services.
Commercial software tool for technical drawing.Comprehensive 3D CAD, CAM, and CAE tool that integrates industrial and mechanical design, simulation, collaboration, and machining into single, cloud-based platform.
Duran i Reynals Hospital Flow Cytometry Core Facility
Hospital Flow Cytometry Platform from IDIBELL
Facility provides equipment for flow cytometry analysis and high-speed cell sorting. Unit personnel support users for experimental design, data analysis and acquisition.
Parametric, open-source implant for multi-area electrophysiological recordings in behaving and sleeping rats. 3D-printable implant for rats, capable of symmetric, bilateral wire electrode recordings, currently in up to six distributed brain areas simultaneously.
Thermo Fisher | 3DHistech PANNORAMIC SCAN II
Medium capacity digital slide scanner by 3DHISTECH with 150-slide capacity and brightfield and fluorescence scanning.
Web server for fast simulation of protein structure fluctuations. Protein modeling software and simulation engine that allows for modeling of large-scale conformational transitions of protein systems. CABS-flex web server version 2.0 new features include extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and new, enhanced web server interface.
Web server that implements integrated computational approach for predicting effects of missense mutations in protein-protein affinity. Used to study effects of single point mutations on protein-protein interactions.
New York University School of Medicine Langone Health Multi-Omics Study Design and Data Integration Core Facility
NYU Langone’s Multi-Omics Study Design and Data Integration Resource
Core facility that specializes in multi-omics data analysis, particularly within the realm of downstream statistical modeling and analysis.
Waters | ACQUITY UPLC H-Class System with 2D LC
ACQUITY UPLC Systems with 2D LC Technology
Used in field of analytical chemistry in liquid chromatography systems for sorting through complex mixtures of substances with samples containing many closely related compounds. System provides Enhanced Separation Power because two-dimensional approach enables higher resolution separation, particularly useful for complex samples with compounds that elute closely together; Increased Sensitivity by minimizing interference from co-eluting compounds, 2D LC improves detection and quantification limits for target analytes; Comprehensive Analysis for both targeted analysis of specific compounds and exhaustive profiling of complex mixtures are possible through combination of heart-cutting and comprehensive sampling techniques; Improved Peak Capacity with better peak resolution and more accurate identification.
Software R package contains functions for statistical calculations and random number generation.
Software R package to perform test of independence of response and one or more covariables using maximally selected rank statistics.
Molecular Devices CellReporterXpress Automated Image Acquisition and Analysis Software
CellReporterXpress Automated Image Acquisition and Analysis Software
Automated image acquisition and analysis software that works with the ImageXpress Pico system. Performs quantitative analysis of images acquired from automated microscopy. Enables distributed analysis of images from slides or microplates.
Automated electrochemiluminescence detector for immunoassay analysis. Designed for quantitative and qualitative in vitro assay determinations for broad range of applications including anemia; bone, cardiac and tumor markers; critical care; fertility/hormones; maternal care; and infectious diseases.
Collection of digitized images.Maintained primarily to support research in image processing, image analysis, and machine vision.
Image database where images are in PBM or PGM format and compressed with GNU Zip and GNU TAR.
Open system to manage data without central server. Peer-to-peer content delivery network built around the content addressing: store, retrieve, and locate data based on fingerprint of its actual content rather than its name or location.
Openly licensed platform to work with RNA-RNA and protein-RNA interactions with software and pipelines to deeply mining thousands of high-throughput sequencing data of RNA-RNA interactome, CLIP-seq and degradome sequencing.
Software for multiomic nonnegative matrix factorization.
Collection of literature and in-house MSn spectra data for research on plant metabolomics.
Beth Israel Deaconess Medical Center Genomics Proteomics Core Facility
BIDMC Genomics Proteomics Core (Proteomics)
Core provides high throughput transcriptional profiling, genotyping, protein quantitation, protein profiling and identification, real-time PCR and robotics. Genomics core offers Affymetrix gene chip technologies, both cartridge based and 96 well high throughput, analysis of genomic information with as little as 50ng of RNA, RNA extracted from paraffin based samples, or partially degraded RNA. Proteomics services include design, performance and analysis of proteomic studies.
GROUPING OF LYMPHOCYTE INTERACTIONS BY PARATOPE HOTSPOTS
Web tool to explore cluster TCRs that are predicted to bind the same MHC-restricted peptide antigen. When multiple donors have contributed to the clusters, and HLA genotypes for those donors are available, GLIPH additionally can provide predictions of which HLA-allele is presenting the antigen.
Software R toolkit for analyzing single-cell immune repertoire profiling. Used for single-cell immune receptor analysis.
University of Virginia School of Medicine Research and Clinical Trials Analytics Core Facility
Core provides multi-disciplinary team of specialists in human subject research data who support School of Medicine’s research community across the globe. Can create and supply datasets, reports, extracts, data marts and databases. Provides secure web applications for building and maintaining databases and surveys including 21 CFR part 11 compliance and research data biorepository database management.
Stereotaxic Topographic Atlas of the Mouse Brain
The Stereotaxic Topographic Atlas of the Mouse Brain (STAM)
3D topographical atlas that depict anatomical structures of whole mouse brain, achieving precise single-cell resolution localization. Visualization platform, which includes services for exploring two-dimensional canonical anatomical sections, three-dimensional topography, and arbitrary-angle slices of brain atlas. Platform integrates different functionalities such as neuroanatomical knowledge base, virtual surgery, and automatic registration of user-uploaded slices.
Collaborative life sciences platform built for life science organizations to manage multiple programs, track key results and biomarkers, and share biological data securely. Used to store, search, analyze, and visualize complex biological data including large, raw data files and run bioinformatics pipelines.
Peter MacCallum Cancer Centre Molecular Genomics Core Facility
Core works with researchers, clinicians and other research technology platforms to establish the best possible approach for any genomics experiment. Offers expertise on variety of off-the-shelf sequencing products and implementation or customisation of new protocols to meet demands of cancer research.
Software analysis tool that enables data analysis of multiplex experiments and advanced applications and assay strategies for Droplet Digital PC.
Image analysis and management system that provides cytogenetics laboratories with integrated, scalable platform for brightfield and fluorescence samples. Combines expertise in image analysis, robotics and microscopy to offer complete cytogenetics solution. Used for FISH imaging system and digital analysis.
University of Pittsburgh Organoid Research Core Facility
University of Pittsburgh UPitt- Organoid Research Core
Core has large collection of unique patient-derived organoids (PDOs). Staff provides high-quality training in organoid development and culture, consultation services to assist with experimental design, execution, and data analysis.
Peter MacCallum Cancer Centre Research Laboratory Support Services Core Facility
Peter MacCallum Cancer Center Research Laboratory Support Services
Core provides media and buffer preparation, labware sterilising services, consumable provision, general wet laboratory support services.
Multiplatform standalone program that allows user-specific coding environment to be set for computer-based review of previously recorded videos or live observations. Allows project-based ethogram to be defined that can then be shared with collaborators, or can be imported or modified. Event logging software for video/audio coding and live observations. BORIS is a free and open-source software available for GNU/Linux, Windows and MacOS.
Super resolution microscope with Lattice SIM² to double the conventional SIM resolution and to discriminate sub-organelle structures, even those no more than 60 nm apart. Enables to combine super-resolution and high-dynamic imaging without the need for special sample preparation or expert knowledge of complex microscopy techniques. Enables resolving structures down to 60 nm, observing live cell dynamics at up to 255 fps, accelerating image acquisition in all three dimensions, getting the sharpest sectioning in wide-field microscopy, utilizing imaging techniques on one platform.
Laser scanner with exceptional data quality through extremely sensitive detection, high image resolution, and very broad linear dynamic range. Amersham Typhoon 5 model offers five-laser configuration option with advanced photomultiplier tubes. Has the same capabilities as Amersham Typhoon RGB model, with the addition of near-infrared (NIR) functionality.
Software R package for demultiplexing single-cell RNA sequencing data.
Beckman Coulter | Optima Max-XP Tabletop Ultracentrifuge
Benchtop ultracentrifuge with separations for volumes as low as 175 ul, touch screen navigation, speeds up to 150,000 RPM, and RCF capability of up to 1019000 x g.
Effective Corneocyte Topographical Index_Atopic_Dermatitis
Software repository presents objective, quantifiable method for assessing severity of atopic dermatitis.
Imager has multiple detection modes with up to 19 fluorescent and luminescent channel combinations to power wide range of assays including 3-Color Quantitative Western Blots, 3-Color In-Cell Western Assays, Cell Analysis Studies, ELISA, Tissue Section Imaging, Viral Titration Assays. Imager includes sCMOS image sensor and 5-micron resolution.
Web application for data visualization and analysis to explore brain tumors expression datasets. Contains public glioma RNA seq data and analysis. Data portal for visualization and analysis of brain tumor expression datasets.
Web bioinformatics platform that integrates interactive bioinformatics tools, original omics books, bioinformatics forums, and video tutorials. Used for RNA seq analysis, heat map illustration, etc.
Thermo Fisher | Orbitrap ID-X Tribrid Mass Spectrometer
Mass spectrometer combines mass analyzer technology dedicated to small molecule analysis with data acquisition strategy of Thermo Scientific AcquireX smart MSn, to collect more meaningful data. Captures more low-abundance analytes.
Thermo Fisher | Vanquish Horizon UHPLC System
System for applications requiring high-quality Ultra High Performance Liquid Chromatography. Uses high pressure to separate and identify components of mixture. Provides accurate separation, retention times, peak area, detector sensitivity and reduced baseline noise for high flow rates.
Perkin Elmer | VICTOR X Multilabel Plate Reader
Bench top reader covering all of main non-radioactive reading technologies.VICTOR X models provide standard features such as temperature control, shaking, scanning, adjustable measuring height, bottom fluorescence reading, dual label/ratio reading and kinetics. System enhancements includes Expanded temperature control (up to +50 °C) for b etter control of assay conditions; New excitation filter wheel and expanded absorbance wavelength (up to 1000 nm) enable versatile use of filters and broader spectrum analysis for greater assay flexibility; Improved chassis design to facilitate maintenance; Improved dispenser unit for enhanced functionality in kinetics assays.
BD Biosciences | FACSAria Fusion Cell Sorter
Cell sorter has UV, Violet, Blue, Yellow/Green and Red lasers and can detect up to 18 colors. Can sort up to 4 populations simultaneously. Samples can be sorted into 12 x 75 mm FACS tubes or 1.5 ml Eppendorf tubes. Uses BD FACSDiva software to control setup, acquisition, and analysis of flow cytometry data from operator workstation.
Inverted microscope with LED light and built-in Diascopic/Epi-fluorescence illumination with cameras.
State University in Norway and the northernmost university. Located in the city of Tromsø, Norway.The main focus of the university is on auroral light research, space science, fishery science, biotechnology, linguistics, multicultural societies, Saami culture, telemedicine, epidemiology and spectrum of Arctic research projects. The close vicinity of the Norwegian Polar Institute, the Norwegian Institute of Marine Research and the Polar Environmental Centre gives Tromsø added weight and importance as international centre for Arctic research.
Developmental Activation Timing-based Longitudinal Acquisition System
Whole brain developmental map of neuronal circuit maturation. Generated by whole brain spatiotemporal mapping of circuit maturation during early postnatal development. Standard reference for normative developmental trajectory of neuronal circuit maturation, as well as high throughput platform to pinpoint when and where circuit maturation is disrupted in mouse models of neurodevelopmental disorders, such as fragile X syndrome.
Data visualization portal for HumanIslets project. Integrated platform for human islet data access and analysis. Includes data on human islet donors, allows users to access linked datasets describing molecular profiles, islet function and donor phenotypes, and to perform various statistical and functional analyses at donor, islet and single-cell levels. Provides set of resources and tools to support metabolism and diabetes research community.
Harmonized cell atlases using sc/snRNA-seq data obtained from dorsal root ganglia and trigeminal ganglio mammalian datasets.
Web application for drug sensitivity predictions for Cancer Genome Atlas RNA-seq data and Drug Sensitivity Predictions for GTEx RNA-seq data. Used to predict drug sensitivity for both normal and tumor tissues. You can query, visualize, and download predicted IC50 values of drugs using ID, name, target or pathway.
Software application as deep generative neural network based approach to impute drug response. Includes imputed half maximal inhibitory concentration (IC50) value of anticancer drugs.
Software framework for creating REST APIs. Python Flask-RESTful API frameworks.
Software structural framework for dynamic web service.Discontinued free and open-source JavaScript-based web framework for developing single-page applications.
Open-source angularjs theme. Element for Angular.
PAL:Proactive Automatized Lifestyle intervention
Behavior change intervention software. Participants enter their data as part of online survey, and software generates individualized feedback letters.
Penn State Hershey College of Medicine Institutional Biorepository Core Facility
Penn State Hershey College of Medicine Institutional Biorepository
Biorepository collection is comprised of blood samples, tissues and other biological materials donated by patients, coupled with information about their health, environment, lifestyle, medical care and responses to medical treatment. Biorepository is accredited by College of American Pathologists.
Software R package for detecting rhythmic signals from large scale time-series data. Used to evaluate periodicity in large scale data.
Software single data reduction pipeline to provide merging statistics and merged intensities in correct pointgroup as quickly as possible after data collection is complete, to test assumptions made in planning experiment, to characterize quality of data in terms of downstream requirements and to detect radiation damage. Fast Data Processsing with XDS.
96-Channel luminometer for circadian biology. Performs high throughput luminometry on self-luminous tissues. System is equipped with 8 photomultiplier tubes, each selected for low dark counts and high sensitivity in green portion of spectrum at which luciferase emits light. Turntable and moving PMT mounting alternately brings each sample under its detector. In addition to its high-precision photon counting hardware, LumiCycle has software for collection and analysis of circadian rhythms in luminometry data.
Multifunctional monochromator based microplate reader. Offers luminescence scanning to complement its existing 3D and ultra fast absorbance and fluorescence scanning capabilities. Allows for very low volume absorbance measurements. Provides double orbital shaking for more efficient reagent mixing, Optimal Read function for reliable cell-based measurements, and injector module for precisely controlled pipetting for triggering fast kinetic reactions and bulk dispensing.
University of Miami Miller School of Medicine Analytical Imaging Core Facility
Core provides access to analytical and imaging techniques for cellular and tissue imaging as well as molecular analysis of pathology specimens. Training is provided for investigators, fellows, and technical staff in proper use of techniques and instruments.
Software modular pipeline for constructing pathway/genome databases from environmental sequence information. Used for predicting metabolic functions of given DNA sequences. Produces structured data products as pathway-genome databases with human-readable and machine-interpretable representations. MetaPathways v3.5 is updated algorithm for sequence feature prediction, annotation, metabolic inference, and coverage metrics including genome resolved metagenomes.
Tapestri single-cell DNA sequencing platform provides both genotype and phenotype data from the same cell. Platform consists of instrument, DNA cartridge, which represents microfluidics device, and reagents. Cartridge is equipped with reservoirs that are used to load reagents required for automated cell processing. Pressure supplied by instrument drives reagents from reservoirs through microfluidic device and out to PCR collection tubes that are mounted below cartridge. Cartridge and tubes can be loaded and unloaded from instrument and disposed of after completion of workflow. User interacts with instrument via touch screen interface, which can be used to select programs, monitor status of running programs, and more.
Thermo Fisher: Applied Biosystems | QuantStudio Absolute Q Digital PCR System
PCR System is plate based digital PCR platform powered by proprietary microfluidic array plate technology that enables all necessary steps for dPCR including compartmentalizing, thermal cycling and data acquisition to be conducted on single instrument. Uses nucleic acid quantification technique that allows absolute quantification without the need for standard curves. Bulk reaction mix is distributed or digitized into thousands of small independent reactions so that each micro-chamber contains either one or zero copies of the target. Statistical methods are then used to calculate the original concentrations based on the number of positive and negative micro-chambers.
QuantStudio Absolute Q Digital PCR System Software
AppliedBiosystem QuantStudio Absolute Q Digital PCR System Software
System software used for analyzing dPCR data. If you have purchased QuantStudio Absolute Q Digital PCR system, you may download the system software. Software is available in Thermo Fisher Connect folder.
Max Planck Institute of Biochemistry Imaging Facility
Facility for light microscopy and flow cytometry. Users are instructed by staff in operation of hardware and software and, if necessary, are supported in acquisition, processing and quantitative evaluation of images.
Max Planck Institute of Biochemistry Crystallization Core Facility
Max Planck Institute of Biochemistry Cristallization Facility
Facility for protein crystallisation and X-Ray crystallography. Provides structural biology infrastructure and performs crystallization experiments.
Max Planck Institute of Biochemistry Protein Production and Structural Validation Core Facility
Max Planck Institute of Biochemistry Protein Production and Structural Validation Facility
Max Planck Institute of Biochemistry Protein Production Facility
Protein Production and Structural Validation Facility
Facility for protein production. Provides services for protein expression and purification, assists with projects in designing strategies for high level expression of soluble proteins, provides vectors and strains. Offers clonning the gene of interest into expression vectors, rapid screening for optimal combinations of vectors, strains and expression conditions and producing protein of interest in E. coli, Pichia pastoris, mammalian and insect cells. Produces biomass at 1L to 10L scale using multiple bioreactor system for high cell density fermentation of bacteria and yeast cells and reusable bioreactor for cell culture. Proteins are then purified using standard techniques and chromatography systems. Quality control is routinely assessing protein identity, purity, stability and folding using set of different biochemical and biophysical methods.
Max Planck Institute of Biochemistry Bioinformatics Core Facility
Facility for bioinformatics. Offers to assist wet-lab researchers in our institute for their bioinformatics data analysis.
Max Planck Institute of Biochemistry Biochemistry Core Facility
Facility for bioorganic chemistry and biophysics. Offers services for studying protein structure and folding, protein-protein or protein-ligand interactions and protein complex formation, synthesis, purification and characterization of organic compounds, automated solid phase synthesis of peptides.
Max Planck Institute of Biochemistry Cryo-EM Core Facility
Max Planck Institute of Biochemistry Cryo-EM Facility
Facility for cryo-electron microscopy. Provides microscope access, training as well as scientific and technical support for MPIB-internal users wishing to perform cryo-EM experiments, from sample preparation to data processing.
Max Planck Institute of Biochemistry Mass Spectrometry Core Facility
Max Planck Institute of Biochemistry Mass Spectrometry Facility
Mass spectrometry core facility. Facility uses chromatography systems, mass spectrometers and workflows for in-depth analysis of biomolecules.
Max Planck Institute of Biochemistry NGS Core Facility
Facility for high-throughput sequencing. Provides Next-Generation Sequencing services, supports library preparation and quality control for various applications including RNA-Seq: rRNA depletion-total RNA, mRNAseq; DNA-Seq: ChIP-Seq, Cut andTag seq, Hi-Cseq, Micro-Cseq, WGS; Single Cell: scRNAseq, scATACseq, snRNAseq, seRNAseq.
Augusta University Georgia Cancer Center Flow and Mass Cytometry Core Facility
Georgia Cancer Center Flow and Mass Cytometry Core
Core provides access to flow and mass cytometers, support equipment, and associated software and services. Our instrumentation affords the ability to perform almost every published flow and mass cytometry protocol.
Comprehensive database about Gram-positive model bacterium Bacillus subtilis. Provides curated information about its genes and proteins, as well as intricate protein–protein interactions, regulatory elements, expression data and metabolic pathways.
Delft High Performance Computing Centre Core Facility
Delft High Performance Computing Centre (DHPC)
Delft University of Technology High Performance Computing Centre
Provides computational services including hardware, software and expertise for complex analysis and modelling .
Thread and SIMD-based Trapezoidal pairwise/multiple sequence Alignment
Software tool as sequence alignment algorithm that combines SIMD instruction sets and thread acceleration. Pairwise and multiple sequence alignment accelerated by simd and threads
Gamma counter with optional internal balance specifically designed for nuclear medicine applications. Dedicated to Nuclear Medicine and PET applications. Used to measure gamma radiation emitted by radionuclide in samples.
Software that predicts three phage replication cycles, including virulent, temperate, and chronic cycles in viral sequences. Replication cycle decipher for Phages.
Industrial x-ray facilities with microfocus and high energy 2D and CT systems. Provides instruments for biological CT scanning as service.
Single-Cell Unified Polarization Assessment
Software R package for immune cell polarization assessment of scRNA-seq data. Single-cell unified polarization assessment of immune cells using single-cell foundation model. Used for comprehensive immune cell polarization analysis.
Software tool for quality assessment of microbial genomes. Used to predict completeness and contamination of bacterial and archaeal genomes. Provides taxonomic classification of the input. Feature-based learning and prediction of genome quality indices.
Multipurpose Small Angle X-ray Scattering instrument offers high brilliance, monochromatic and tuneable X-rays, with performance in low beam divergence, high X-ray flux, and variable beam size in both directions in full range of sample-detector distances provided by beamline up to 16 m. Several techniques are available through modular operation: time-resolved SAXS, SAXS/WAXS, protein solution SAXS, microfocusing SAXS, anomalous X-ray scattering and XPCS.
Oxford |Nanopore Technologies | Prometheus
Instrument that uses nanoDSF to analyze protein folding and stability. Provides precise stability data across multiple parameters to characterize thermal unfolding, particle sizing, and aggregation of proteins. Used in variety of applications, including protein engineering, membrane protein research, formulation development, and quality control.
Applied Photophysics | Chirascan V100 Circular Dichroism spectrometer
Chirascan V100 Circular Dichroism spectrometer
Chirascan V100 circular dichroism spectrometer for circular dichroism analysis, generating data that contribute to biomolecular characteristics, mechanisms, and interactions. Used for studying chiral molecules.
Light scattering system. Instrument measures size of particles contained within sample. Used to measure particle size of dispersed systems from sub-nanometer to several micrometers in diameter.
Revivity | VICTOR Nivo Multimode Microplate Reader
Microplate reader for biochemical and cell-based assays, it measures at any wavelength, with top and bottom reading of all standard technologies. Used to measure Absorbance, Luminescence, Alpha, Fluorescence Intensity, TR Fluorescence.
Fraction collector with automate extracellular vesicle isolation using combination of qEV size-exclusion columns to increase uniformity of collected volumes, decrease experimental run-time, and eliminate many inaccuracies that are inherent in manual collection of Packed Cell Volume.
University of Michigan Rogel Cancer Center Immune Monitoring Core Facility
University of Michigan Rogel Cancer Center Immune Monitoring Core
University of Michigan Rogel Cancer Center Immune Monitoring Shared Resource
Provides immunologic and biological support for ongoing research projects and clinical trials. Services include measuring multiple cytokines in single assay, determining cytokine concentrations in various biological specimens and monitoring immune cell activation through investigative analytic procedures. Offers sample processing expertise for blood and tissue samples, including both plasma or serum and peripheral bloodmononuclear cells.
University of Michigan Rogel Cancer Center Experimental Irradiation Core Facility
University of Michigan Rogel Cancer Center Experimental Irradiation Shared Resource
Core provides irradiation services for investigators, including those whose primary interests are not in radiation biology, but who need this tool in support of other efforts, such immunosuppression of animals prior to stem cell transplantation through total body irradiation. Facility is equipped to perform moderate dose rate gamma irradiation (0.1-4 Gy/min) of cell cultures, tissue specimens or animals as well as low dose rate irradiation (0.05-0.3 Gy/hr) of cell cultures.
Web server for accurate protein secondary structure prediction and fold recognition from circular dichroism spectra.
This resource is no longer in service. Documented on September 19,2024. Web application to provide predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures.
Software tool as GUI based Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data.Small-angle scattering data reduction and analysis. Available on Windows, macOS (and OS X), and Linux.
R2 Genomics Analysis and Visualization Platform
Platform for genomic analysis. Open access online genomics datascience and discovery platform designed to assist the bio-medical researchers with limited to no Bioinformatics skills to perform data mining tasks in the omics field.
Leica CM1860 UV cryostat for high-quality cryosections with compact design, and user-friendly interface for optimal results.
Thermo Scientific Vitrobot Mark IV System
Vitrification Robot is fully PC-controlled device for rapid cooling of aqueous samples. System offers semi-automated vitrification to provide fast, easy, and reproducible sample preparation for cryo-EM. Performs cryo-fixation process at constant physical and mechanical conditions like temperature, relative humidity, blotting conditions, and freezing velocity.
System for image-guided radiation with software and advanced set of imaging modalities, including Cone-Beam CT, µCT and Bioluminescence (BLI). Focal irradiation system that mimics clinical radiotherapy and imaging.
Fully automated multi-channel peptide synthesizer equipped with a two arm pipetting robot for faster washing and dispensing of reagents. Parallel synthesizer for solid phase peptide synthesis. Standard system is configured with two reactor blocks with other reactor block options available including heating block kits and Tip reactor blocks.
Software Python package that plots data on cortical surface.
Software multi-modality post-processing suite for SPECT, CT, PET, MR, Optical and and Autoradiography imaging data.
Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data.
Software quality control tool for digital pathology slides. Used to identify and delineate slide artefacts and discover cohort-level outliers.
University of California at San Francisco Advanced Microscopy Core Facility
W.M Keck Foundation Advanced Microscopy Laboratory
Core includes instrumentation for structural biology with focus on cryo-electron microscopy. Used for imaging ranging from atomic resolution to whole cells, with emphasis on linking structural and dynamics information with biological functions.
Software for evaluating, comparing and presenting real-time interaction data. Used for quantification of kinetics and affinity through curve fitting, with large number of binding models to choose from. Can extract experimental information from measurement, requiring minimal user input.
Software R package to perform feature specific quantile normalization. Designed to quantile normalize each feature in data set according to its corresponding feature in target distribution. This eliminates distribution based differences resulting from the use of different gene expression profiling platforms.
University of Maine Microscopy and Image Analysis Core Facility
Microscopy and Image Analysis Core at University of Maine
University of Maine Microscopy and Image Analysis Core
Core offers imaging for diverse applications, including multi-color experiments, live sample imaging, protein colocalization, large sample tiling, and Z-stack 3D/4D imaging, as well as weak label detection. Provides expert guidance in microscopy and image analysis, training and support to advance research across various model organisms.
Funding organization for neurodegenerative disorders and use of AI in it. 501(c)(3) philanthropic initiative that seeks to accelerate the use of artificial intelligence (AI) in the fight against neurodegenerative diseases.
University of Maine; Orono; United States
Public land-grant research university in Orono, Maine. It was established in 1865 as the land-grant college of Maine and is the flagship university of the University of Maine System.
interpretable machine learning for single cell
Software label transfer tool for single-cell RNA sequencing analysis. Scalable, Interpretable Modeling for Single-cell RNA-seq data classification.
University of Michigan School of Medicine Advanced Genomics Core Facility
University of Michigan Advanced Genomics Core Research Facility
University of Michigan School of Medicine Advanced Genomics Core Research Facility
Provides next generation services. Provides centralized expertise in advanced methods that enables all researchers to effectively exploit them for making scientific discoveries.
University of Michigan Institutional Animal Care and Use Committee Core Facility
University of Michigan Committee for Use and Care of Animals
Core ensures that animal welfare standards are maintained along with conduct of accurate, valid scientific research through supervision, coordination, training, guidance, and review of every project proposed to include use of vertebrate animals or cephalopods at University of Michigan.
University of Michigan Unit for Laboratory Animal Medicine Core Facility
University of Michigan Unit for Laboratory Animal Medicine
Core partners with University of Michigan research community to achieve animal welfare standards in pursuit of impactful science. Provides training laboratory animal veterinarians and veterinary care to all animals used at the University of Michigan.
Software tool to predict phage replication cycle.
Novo Nordisk | Metabolomics Platform Bruker timsTOF Pro 2 mass spectrometer coupled with Agilent 1290 Bio UPLC- Timon
Bruker timsTOF Pro 2 mass spectrometer coupled with Agilent 1290 Bio UPLC- Timon
University of Copenhagen Novo Nordisk Foundation Center for Basic Metabolic Research Metabolomics Platform Core Facility is equipped with a high resolution mass spectrometer with two distinct separation technologies - a second generation dual Trapped Ion Mobility Spectrometry (TIMS) analyzer which provides collision cross section values and Parallel Accumulation Serial Fragmentation (PASEF) which allows downstream selection of precursor ions for fragmentation. The mass spectrometer is coupled with Agilent 1290 Bio UPLC, with binary solvent pump, multi-sampler and thermostatted column oven.
Software R package to estimate mutation rates and quantify somatic selection in cancer.
University of Copenhagen Novo Nordisk Foundation Center for Basic Metabolic Research Metabolomics Platform Core Facility
Novo Nordisk Foundation Center for Basic Metabolic Research Metabolomics Platform
Provides standardized mass spectrometry-based services for detection of metabolites in various biological samples. Offers development of novel techniques, access to advanced analytical instrumentation, guidance with experimental design, support with post-acquisition data analyses and assistance with publications and planning future studies.
University of Cincinnati Center for Advanced Structural Biology Core Facility
University of Cincinnati Center for Advanced Structural Biology
Integrates technology in single-particle cryogenic electron microscopy. Thermo Scientific Talos L120C Transmission Electron Microscope is available for visualizing nanoparticles, negatively stained proteins or conventional biological samples. It can be operated at 80kV or 120kV. Thermo Scientific Glacios 200 kV cryogenic TEM is equipped with both Ceta-16M camera and TFS Falcon 4 direct electron detector, in addition to Selectris Energy Filter. This system is able to generate images for atomic resolution structures for single particle analysis projects. Glacios also includes software for micro-Electron Diffraction data set collection. Available services include Training and access to the Mark IV Vitrobot plunge freezer,Training and access to the Talos L120C TEM system, Training and access to the Glacios 200 kV cryogenic TEM system, Assisted TEM analysis by CASB personnel.
University of Cincinnati Advanced Cell Analysis Service Center Core Facility
University of Cincinnati Advanced Cell Analysis Service Center
Offers access to microscopes and flow cytometry equipment for researchers. Available services include Upright and inverted widefield microscopy, Confocal Microscopy (Zeiss LSM 710), Super-Resolution Microscopy (Nikon SIMe), Live Cell Microscopy (Incucylte), Flow Cytometry (BD LSR Fortessa), Cell Sorting (BD Aria III).
Software Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.
Benchmark Scientific | D1000 homogenizer
Rotor stator handheld homogenizer works by drawing sample, in liquid, into generator probe with variable speed rotor, and then forcing it out through slots in stator to mechanically shearing sample. Most samples are completely homogenized in 30 seconds or less. 130W motor drives rotor at speeds from 8,500 to 30,000 rpm. Speed is adjustable in six steps to meet sample processing needs. A separate on/off switch allows homogenizer to be left at appropriate setting. Generator probes are available in four sizes. 5mm and 7mm diameter have 50mm length for use with samples in microbtubes. 10mm x 115mm is ideal for use with 15 and 50ml tubes and 14mm x 130 mm, for 50ml tubes and vessels up to 250ml. The unit is supplied with one each of the 5mm and 7mm generator probes. All generator probes are made of stainless steel and can be sterilized by autoclaving.
Stanford University MicroCT Core Facility
Core provides nondestructive, high-resolution images of internal structure of variety of natural and engineered materials using X-ray micro-computed tomography. microCT can resolve structures on micrometer scale.
Stanford University Mineralogy and Petrology Lab Core Facility
Stanford University Mineralogy and Petrology Lab
Core offers qualitative and quantitative characterization of Earth materials by providing optical microscopes for high-resolution imaging of loose materials and thin sections, computational resources for image processing, and bench space for light processing of samples before or after use of the Sample Preparation Lab.
Python Single-Cell rEgulatory Network Inference and Clustering
Software tool as Python implementation of the SCENIC pipeline which enables to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
Software Python package for performing gene set enrichment analysis. Used for characterizing gene expression changes by analysis of large single-cell datasets.
Software application to infer copy number variation from single-cell transcriptomics data. Scalable Python library to infer CNV events from single cell transcriptomics data.
SINSAGE | MiniChemi Imaging and Analysis System
MiniChemi compact and advanced imaging system designed for chemiluminescent and fluorescent imaging with super-cooled CCD sensor and big prime lens. Weak chemiluminescent or fluorescent signals can be detected. Western Blot imager.
Software developed by Bruker for analysis and processing of spectroscopic data. Used for measurement, processing and evaluation of IR, NIR and Raman spectra.
Software analysis toolboxes extending Orange suite. Used to build flexible spectral data processing workflows and explore various analysis ideas interactively.
Statistical software for analysis of SEER and other cancer-related databases.Used to view individual cancer records and to produce statistics for studying impact of cancer on population.
NCI SEER Cancer Stage Variable Documentation
Portal provides links to documentation for several stage variables that are available in the SEER data for analysis.
NCI Division of Cancer Control and Population Sciences SEER-Medicare Comorbidity SAS Macros
Portal provides SAS Macros to calculate comorbidity weights. Used to assist SEER-Medicare investigators with their analyses. NCI recommends use of the 2021 macro. The 2014 and 2000 versions are provided for those needing to reproduce prior results. These macros offer the option of including Medicare hospital (MedPAR) claims only, or also considering physician (NCH) and outpatient claims. The Rule-Out option is recommended in the latter situation. Note that diagnoses using ICD-10 codes, starting in October 2015, are not included in the 2000 and 2014 macros. NCI does not accept responsibility for the completeness or accuracy of the codes and weights used in the macros. Investigators may modify the macros if they wish to include different diagnosis codes or condition weights.
NCI Division of Cancer Control and Population Sciences SEER-Medicare Linked Data Resource
Portal to reflect the linkage of two large population based sources of data that provide detailed information about Medicare beneficiaries with cancer.
Alex's Lemonade Stand Foundation for Childhood Cancer Childhood Cancer Repository
Repository stores tissue samples and uses them to create cell lines. The cell lines and xenografts can be used as model to understand cancers and to test new treatments. Researchers all over the world can request cell lines and models to use in their research.
Company offers range of products and services for next generation sequencing, CRISPR genome editing, qPCR, gene expression, and other molecular biology applications.
Danish Reagents and Diagnostics company with headquarters in Copenhagen, Denmark that offers Dextramer products for detecting and characterizing antigen-specific T and B cells, non-conventional T cells, and antigen-presenting cells.
Biotechnology company focused on development and commercialization of proprietary technologies related to the human leukocyte antigen system, exclusively licensed from the University of Oklahoma. Pure Protein, in conjunction with its affiliates and subsidiaries, aims to bring novel therapies and diagnostic tools to patients across wide range of application areas spanning from therapeutic development in fields of oncology, autoimmunity, and infectious disease, to antibody mediated rejection in transplantation.
Peptide company, which provides custom peptide synthesis, catalogue peptides, PepSet peptide libraries, reagents, antibodies, and array of other immunology services for research market, offering range of options for customisation and modification.
Public biotechnology company based in South San Francisco that manufactures synthetic DNA and DNA products, makes gene synthesis, oligo pools, exome, NGS target enrichment, variant libraries and other synthetic DNA tools. Researchers can access quality tools for more accurate NGS, highly customizable Gene Synthesis at scales that fit any workflow, more accurate genomic screens that require fewer resources, and libraries with optimized discovery power as every variant is directly synthesized.
Perkin Elmer | MicroBeta2 LumiJET Microplate Counter
Microplate counter that measure radioactivity, as well as luminescence, available in 1-, 2-, 6-, and 12-detector configurations with 16-shelf loading capacity. Robotic loading option allows efficient integration into robotics systems. MicroBeta2 LumiJET model is available with choice of single or dual injectors per detector, and is also available with 1-, 2-, 6-, and 12-detector configurations. Both 96- and 384-well plates can be used. The injector configuration of the MicroBeta2 LumiJET enables flash luminescence studies.
Company specializes in immune monitoring services within biotechnology sector. Offers expert Elispot services, flow cytometry experiment design, and statistical analysis for immune response testing.
Software application as ETL implementation for EuCanImage, encouraging semantic interoperability of clinical data obtained in studies by transforming it into machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create dictionaries following FHIR compliant structure. Code Language is written in Python 3.11. Outputs are JSON files compliant with FHIR 4.3 schemas.This script is specifically created for the Extract, Transform and Load implementation for EuCanImage, and will follow the structures obtained from the REDCap databases within the study.
Provides open access to suite of resources, with the aim to translate big data into big discoveries. Offers range of resources for biological big data deposition, integration, and translation.
Public archive of raw sequence data in National Genomics Data Center as part of the China National Center for Bioinformation. GSA accepts worldwide data submissions, performs data curation and quality control for all submitted data. Provides data storage and sharing services.
Software application as dendrimeric DNA coordinate barcoding design for spatial RNA sequencing, which offers both high sensitivity and high resolution in mRNA detection.
Akoya Biosciences | Vectra 3 Automated Quantitative Pathology Imaging System
Vectra 3 Automated Quantitative Pathology Imaging System
Vectra 3 automated quantitative pathology imaging system, together with the inForm software, provides multispectral and automated multi-slide imaging of up to 6 slides to detect and measure weakly expressed and overlapping biomarkers in H and E, IHC or IF intact FFPE tissue sections or TMAs within familiar digital pathology workflow.
Website and database providing access to integrated, high-precision samples of American population drawn from sixteen federal censuses, from the American Community Surveys of 2000-present, and from the Puerto Rican Community Surveys of 2005-present. Preserves and harmonizes U.S. census microdata and provides easy access to this data with enhanced documentation.
Centers for Disease Control and Prevention WONDER
Wide-ranging ONline Data for Epidemiologic Research
Databases utilize rich ad-hoc query system for the analysis of public health data. Reports and other query systems are also available.
Agilent | NovoCyte Quanteon Flow Cytometer Systems 4 Lasers
NovoCyte Quanteon Flow Cytometer Systems 4 Lasers
Quanteon 4 laser flow cytometer that can be configured with up to 25 independent photomultipliers.
Biotechnology company that specializes in collection and analysis of molecular and clinical data to advance precision medicine.
Software R package to compute gene expression signature scores.
Emory University Pediatric Biostatistics Core Facility
Emory University and Children's Healthcare of Atlanta Pediatric Biostatistics Core
Emory University EU-Pediatric Biostatistics Core
Offers statistical expertise and services. Provides assistance and collaboration in study design, grant applications, protocol development, data analysis, publication preparation, and statistical education.
Emory University Animal Physiology Core Facility
Emory University and Children's Healthcare of Atlanta Animal Physiology Core
Centralized core specializing in survival surgery, technical procedures, and ultrasound imaging for rats and mice and assistance for surgical procedures in other species.
University of Washington Mouse CRISPR Core Facility
University of Washington UW Mouse CRISPR Core
Service facility offering generation of novel transgenic mouse models using CRISPR/Cas9 gene editing technology. Standard service includes consultation, design, testing, prep, mouse embryo microinjection, and genotyping.
Harvard Medical School Single Cell Core Facility
Core specializes in single cell and spatial transcriptomics, and multiomics. Provides custom services, education, training and expertise in multiple high-throughput single cell technologies.
MadicLab | PSA094 Desktop Small Animal PET
MadicLab Box series uses PSA series microscopic PET technology for small animals. Compact, benchtop body design. Provides advanced technical support for whole-body imaging and in vivo characterization of preclinical small animal models.
Perkin Elmer | Quantum GX2 micro-CT imaging system
Offers increased imaging fields of view to accommodate larger samples in vivo and enables high-resolution imaging of ex vivo samples. Manual x-ray filter assembly provides opportunities to optimize imaging protocols and coupled with the high-resolution, high-speed integrated platform.
Software R package as global weighted model for disease ontology enrichment analysis. Used for annotating and enrichment analysis with disease ontology.
Harvard Medical School Harvard Cryo-Electron Microscopy Center for Structural Biology Core Facility
Harvard Cryo-Electron Microscopy Center for Structural Biology
Harvard Medical School Harvard Cryo-Electron Microscopy Center for Structural Biology
Joint effort by Harvard Medical School, Dana-Farber Cancer Institute, Boston Childrens Hospital, and Massachusetts General Hospital to provide cryo-EM instrumentation and expertise for Harvard structural biology community. Facility offers consultation and training by staff in specimen preparation, microscope operation, image acquisition, and data analysis.
Harvard Medical School Mouse Behavior Core Facility
Harvard Medical School HMS Mouse Behavior Core
Core offers mouse behavioral equipment and assays to test motor, cognitive, and affective behaviors. Trained users have access to behavioral testing rooms and procedure room. MBC staff offers consultation, training, and guidance in execution and interpretation of assays.
Software Python library for working with metadata in EBRAINS Knowledge Graph. High-level Python API for EBRAINS Knowledge Graph.
Harvard Medical School Nascent Transcriptomics Core Facility
Harvard Medical School Nascent Transcriptomics Core
Core specializes in analysis of nascent transcriptome using PRO-seq and TT-seq NGS methods. Provides services allowing users to submit prepared cells and receive analyzed data. Offers free consultations to help with experimental design, answer questions, and discuss data analysis.
Software tool to assist in optimizing nucleotide pooling strategies for high-throughput genomic analyses. Used to evaluate nucleotide distribution uniformity across positions and allows users to set customizable red flag thresholds, ensuring optimal results while accommodating variability.
Perth Scientific | Hirschmann Neubauer Haemocytometer Counting Chamber
Neubauer Haemocytometer Counting Chamber
Cell counting chamber. Used to count cells or other particles in suspensions under microscope.
Desktop application for Windows and MacOS that allows to interactively visualize data generated by the Xenium Analyzer instrument.
Software analysis pipeline that process 10x Genomics Visium data with brightfield or fluorescence microscope images, allowing users to map whole transcriptome in variety of tissues.
Software R package as whole genome DNA methylation analysis pipeline. Used for testing differentially methylated cytosines or regions in whole-genome bisulfite sequencing or reduced representation bisulfite sequencing experiments. Several options exist for either site-specific or sliding window tests, and variance estimation.
Software tool to process coordinate sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires indexed fasta file containing reference genome as well.
Software tool for fast and accurate alignment of BS-Seq reads using bwa-mem and 3-letter genome.
University of California at Berkeley Vincent J. Coates Proteomics/Mass Spectrometry Laboratory Core Facility
UCB Proteomics/Mass Spectrometry Laboratory
Core provides multidimensional LC-MS/MS analysis including Protein ID, Proteomics Profiling, Targeted Proteomics and Post Translational Modification analysis. Quantitative proteomic services are provided using label free quantitative proteomic (LFQ) profiling, Tandem mass tagging (TMT) or SILAC approaches. Provides support for macromolecular complexes using Nano ESI.
Software tool to leverage chimeric and discordant read alignments identified by STAR aligner to predict fusions. Component of Trinity Cancer Transcriptome Analysis Toolkit. Used to identify candidate fusion transcripts supported by Illumina reads. Maps junction reads and spanning reads to reference annotation set.
Software tool for gene fusion detection from RNA-Seq data. Fusion detection algorithm specifically designed to meet demanding requirements of HTS-assisted precision oncology. Capable of detecting aberrant transcripts that are not called by most fusion detection methods but may be clinically relevant. This includes tumor suppressor genes that are occasionally inactivated by rearrangements within the gene or by translocations to introns or intergenic regions.
Thermo Fisher: Applied Biosystems | Step One Plus Real-Time PCR System
Real-time PCR system that enables precise quantitative real-time PCR results. High-quality qPCR results, 4-color, 96-well PCR instrument.
Thermo Fisher | Orion Star A211 Benchtop pH Meter
Benchtop pH Meter to record accurate and reliable pH, mV, ORP and temperature measurements.
Collaborative open project of Chan Zuckerberg Initiative and Chan Zuckerberg Biohub. The no-code, cloud-based bioinformatics tool for researchers. Used to analyzing genomic data for free. Hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.
Harvard Medical School Beth Israel Deaconess Medical Center Bioinformatics Core Facility
Beth Israel Deaconess Medical Center BIDMC Bioinformatics Core
Harvard Medical School Beth Israel Deaconess Medical Center Bioinformatics Core
Harvard Medical School BIDMC Bioinformatics Core
BIDMC Bioinformatics Core is Unit of the Precision RNA Medicine Core and provides support for management, integration and contextual analysis of biological high-throughput data, training on tools, databases and best practice.
University of Freiburg Cryo-Electron Microscopy Core Facility
Cryo-Electron Microscopy Facility (CEF) Freiburg
University of Freiburg Cryo-Electron Microscopy Facility (CEF) Freiburg
Core offers services related to cryo electron microscopy. Services include grid preparation, screening and data collection, as well as user training.
National Cancer Institute Division of Cancer Control and Population Sciences Social Determinants of Health by US Census Tract
Social Determinants of Health by US Census Tract
Portal provides access to data set including, for each U.S. census tract (defined using 2010 census tract boundaries), certain social determinants of health data elements, including race/ethnicity, education, poverty, urban/rural, socioeconomic status, and racial residential segregation indices defined using 2008-2012 American Community Survey data and 2010 definitions of rural urban commuting areas.
Johns Hopkins University School of Medicine Mass Spectrometry and Proteomics Core Facility
Johns Hopkins University School of Medicine Mass Spectrometry and Proteomics Facility
Core assists investigators to identify and quantify proteins and their modifications that are differentially expressed in cells, tissues or body fluids, to track interactions with binding partners during changes in signal transduction, and to identify proteolytic cleavage sites and map post-translational modifications by providing following proteomic services: Consultation, Sample preparation,Protein Identification,Protein Modifications, Protein Quantification, Targeted Quantification, High Resolution Mass Analysis,Training and Self-Service Equipment. Core offers workshops to use the Core’s MALDI-TOF mass spectrometer, Typhoon gel imaging scanner and 2D gel electrophoresis equipment and proteomic software.
Web tool for protein structure prediction, leveraging sequence alignment, template-based modeling, deep learning, and validation techniques. With input of either amino acid sequence or FASTA file, ProStruc generates protein structures. ProStruc automates process of blast searches, template selection, structural modeling, and validation, including RMSD, TM-score, and QMEAN.
Software R package for DNA copy number detection from off-target sequence data. Used to extract DNA copy number information from targeted sequencing by utiizing off-target reads.
Molecular Devices | SpectraMax Paradigm Multi-Mode Microplate Reader
SpectraMax Paradigm Multi-Mode Microplate Reader
Microplate Reader measures absorbance, fluorescence, time-resolved fluorescence including HTRF, fluorescence polarization, AlphaScreen, AlphaLISA, and luminescence assays for up to 1536-well plates. Detection cartridge modularity allows for easy addition of new read modes within minutes without requiring service visit, while providing flexibility for future applications.
Boston Children's Hospital Molecular Genetics Core Facility
Provides genomic technology services and expertise. Services offered include Nanopore PromethION sequencing, Electronic optical mapping on Nabsys, Optical Genome mapping on Bionano Saphyr, NGS (Illumina-based), Sanger Sequencing, Single cell analysis/RNAseq, Transcriptomic spatial profiling, Gene expression analysis , Droplet Digital PCR & qPCR, Microsatellite/fragment analysis, SNP genotyping , Chromosomal microarray analysis, Sample prep and QC, Project consultation, Bioinformatics support.
Maxwell Rapid Sample Concentrator Instrument
Instrument provides automated DNA or RNA purification. Sample lysis and binding to paramagnetic particles is primary separation principle. Up to 16 samples can be prepared in single run. Instrument is controlled through graphical user interface running on Tablet PC and has ability to record and report sample tracking and method run data. Reports can be printed and exported to storage location or USB drive.
Software graphical application written in Python, to analyze videos and create notes for events in the video. Used to identify animals’ behaviors based on information extracted from video.
Strex | Manual Cell Stretching System STB-10
System for evaluative purposes applies cell stretching and compression force and is operated manually. Has two versions available: 4 cm2 or 10 cm2 stretch chambers. Can mechanically stimulate monolayer and cultured cells and tissue to increase cell growth and shape.
United Imaging Intelligence uAI Research Portal
AI-powered integrated research platform for one-stop analysis of medical images. Provides advanced functionality such as automatic segmentation, registration, and classification for variety of application domains. Has major merits including Advanced built-in algorithms applicable to multiple imaging modalities (i.e., CT, MR, PET, DR), diseases (i.e., tumor, neurodegenerative disease, pneumonia), and applications (i.e., diagnosis, treatment planning, follow-up); Iterative deep learning-based training strategy for fast delineation of ROIs of large-scale datasets, thereby saving clinicians' time and obtaining novel and more robust models; Modular architecture with customization and extensibility, where plugins can be designed for specific purposes.
RADIOMETER | ABL800 FLEX blood gas analyser
Radiometer ABL800 FLEX blood gas analyser
Radiometer blood-gas analyser is intended for in vitro testing of samples of whole blood for the parameters pH, pO2, pCO2, potassium, sodium, calcium, chloride, glucose, lactate, total bilirubin, and co-oximetry parameters (total hemoglobin, oxygen saturation, and the hemoglobin fractions FO 2 Hb, FCOHb, FMetHb, FHHb, FHbF).
RADIOMETER | ABL90 FLEX PLUS blood gas analyser
Radiometer ABL90 FLEX PLUS blood gas analyzer
Cassette-based ABL90 FLEX analyzer can deliver 17 parameters from sample as small as 65 μL. ABL90 measures blood gas, electrolytes, metabolites and co-oximetry. The ABL90 analyzer can measure sample from syringe, capillary tube or test tube. Portable, automated analyzer that measures pH, blood gases, electrolytes, glucose, lactate, bilirubin, creatinine.
Africa Microscopy Initiative Imaging Centre Core Facility
Africa Microscopy Initiative Imaging Centre
AMI Imaging Center houses advanced, commercial light microscopes. These instruments are tailored for use in the life sciences and provide high spatial and temporal resolution to study variety of biology.
Software suite based on BlobTools to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. Used for genome assembly QC and contaminant cobiont detection and filtering. Can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. Can be used during assembly to filter non-target DNA. BlobToolKit is comprised of four distinct components: BlobTools2 (command line tools to create and filter datasets), Specification (a formal specification and validator for the JSON-based data format), Viewer (interactive dataset visualization), and INSDC-pipeline (a Snakemake pipeline to run the BlobToolKit workflow on publicly available datasets).
Software tool as Oxford Nanopore basecaller. Used to determine nucleotide sequence.
SMAll RuminanTs breeding for Efficiency and Resilience Database
SMARTER-database aims to collect data produced by SMAll RuminanTs breeding for Efficiency and Resilience project and to merge them with already available genotype data. Used to explore genomic diversity in small ruminants.
Web-service that can generate highly accurate biomolecular structure predictions containing proteins, DNA, RNA, ligands, ions, and also model chemical modifications for proteins and nucleic acids in one platform. Powered by AlphaFold 3 model.
Software classifier tool based on deep learning methods for classification and annotation of large-scale fungal ITS sequences. Used for fungal species classification.
Software Python package for external validation of machine learning models with adaptive sample splitting.
Rockefeller University High Performance Computing Core Facility
Provide Rockefeller University researchers and collaborators with infrastructure necessary for computationally intensive workloads, as well as training and support for using these resources.
Agilent NovoCyte 3000 Flow Cytometer with 3 lasers (488, 405, 640 nm) and up 13 colors. 6 colors from violet laser; 5 colors from blue laser; 2 colors from red laser. NovoExpress software used for acquisition.
Colorado State University Microscopes for Open Access Imaging Core Facility
Colorado State University Microscopes for Open Access Imaging
Colorado State University Microscopes for Open Access Imaging (MOAI)
Microscopes for Open Access Imaging (MOAI)
Light and fluorescence microscopy core facility with Zeiss, Nikon, 3I, Leica and Olympus Microscopes. Distributed light microscopy core facility consisting of inverted and upright confocal microscopes (laser scanning and spinning disk) some with superresolution, atomic force microscopy, total internal fluorescence reflection (TIRF), high throughput multicolor imaging of fixed tissue sections or cells on slides, and live cell imaging in most modalities.
Brandeis University Light Microscopy Core Facility
Brandeis University Brandeis Light Microscopy Core Facility
Facility houses 13 high-end light microscopes including point scanning and spinning disk confocals, Airyscan, 3D-STED super resolution, widefield and TIRF systems. Core offers training, consultation and access to powerful analysis computers with licensed softwares.
University of Kansas Medical Center Mass Spectrometry and Proteomics Core Facility
Mass Spectrmetry/Proteomics Core Laboratory
University of Kansas Medical Center Mass Spectrmetry/Proteomics Core Laboratory
Oklahoma Medical Research Foundation OMRF Clinical Genomics Center Core Facility
Oklahoma Medical Research Foundation OMRF Clinical Genomics Center
Offers high-throughput sequencing and genotyping services utilizing cutting edge Illumina and Xoford Nanopore systems. Sequencing facility in Oklahoma. Equipped with an Illumina NovaSeq 6000, Illumina NextSeq 2000, Illumina MiSeq, Illumina iSeq, Oxford Nanopore PromethION 2, and Oxford Nanopore MinION,Illumina iScan and Autoloader for extremely-high throughput genotyping projects. Core can perform all aspects of NGS, ranging from whole genome sequencing to single-cell transcriptomics.
University of Cincinnati Proteomics Laboratory Core Facility
University of Cincinnati Proteomics Laboratory
University of Cincinnati Proteomics Laboratory (UCPL)
Core is equipped with protein separation and mass spectrometry equipment as well as trained personnel to perform comparative analyses of complex protein mixtures and to identify differentially-expressed proteins. Offers guidance and consultation.
Registry for describing, sharing and publishing scientific computational workflows. Aims to facilitate discovery and re-use of workflows in accessible and interoperable way. This is achieved through extensive use of open standards and tools, including CWL, RO-Crate, Bioschemas and GA4GH's TRS API, in accordance with FAIR principles.WorkflowHub supports workflows of any type in its native repository.
BGI | DNBSeq PE150 BGISEQ-500 sequencing system
System composed of DNBseq PE150 sequencing platform for RNA sequencing transcriptome with BGISEQ-500 desktop sequencer which uses DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics sequencing technologies to generate short reads at large scale. DNBseq PE150 sequencing platform uses DNA nanoballs that are loaded onto flow cells and then read using fluorescent probes. The platform then uses lasers to excite the probes and take millions of images to identify bases.
Siemens | Biograph mMR 3.0 Tesla scanner
Siemens Biograph mMR 3.0 Tesla PET/MR Scanner
Siemens Biograph mMR represents major technological breakthrough in imaging field by combining positron emission tomography (PET) and magnetic resonance imaging (MRI) in one scanner. This system allows simultaneous acquisition of MR and PET images in human subjects.
Peter MacCallum Cancer Centre Bioinformatics Core Facility
Peter MacCallum Cancer Center Bioinformatics Core Facility
Provides services for data analysis, pipeline management, and artificial intelligence research and operations. Data types analysed by the core include whole-genome and whole-exome sequencing, targeted re-sequencing, radiological images, RNA-sequencing, single-cell RNA sequencing, ChIP-sequencing, NanoString and various types of microarray data. Core also develops and maintains software infrastructure required for bioinformatics processing, including pipelines and cloud provision systems.
2023 U.S. Census Quick Facts about Alabama, Maryland, Missouri and Connecticut
Data about Alabama, Maryland, Missouri and Connecticut people and economy.
Software tool for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data.
Web server that integrated data visualization and graphing functions together. Can be run easily with all Web browsers, with user-friendly graphical interface, users can paste your data directly into input box according to defined file format. Resulting graphs can be downloaded in bitmap (PNG or TIFF) or vector (PDF or SVG) format in publication quality. Used for data visualization and graphing.
Flow Cytometric Analysis Program Array V3 software
Software can use data files exported in FCS 2.0 or 3.0 formats, providing analysis capability for major BD instrument platforms that use BD FACSuite, BD FACSDiva, BD FACSArray, BD Accuri C6, or BD CellQuest Pro software.
Unique stand-alone platform and voice-controlled DNA/protein gel workstation for gel imaging.
VR device based mental stress test program
Software is developed based on Android Unity 3D platform, utilizing Java language. Used to simulate mental stress tasks using VR device (from Huaxing Virtual Reality Co., Ltd.). During test, subjects rest calmly under starry sky in resting state. Mental stress test consists of three tasks, each lasting about 3 minutes: modified Stroop task, public speaking, and mental arithmetic tests. Download link also includes companion Android mobile monitoring app for viewing participant's VR screen.
UTHealth Houston Center for Advanced Microscopy Core Facility
Center for Advanced Microscopy at UTHealth at Houston
McGovern Medical School Center for Advanced Microscopy
Microscopy facility serving Texas Medical Center. Facilitates utilization of advanced light microscopy techniques and quantitative image analysis to advance research programs of McGovern Medical School, UTHealth, and the greater Texas Medical Center. Fluorescence microscopy and image analysis core.
Software tool for multiple species sequence alignment. Used for editing and annotating multiple sequence alignments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Provides comprehensive curated information on bacteria in human mouth and aerodigestive tract, including pharynx, nasal passages, sinuses and esophagus. eHOMD taxonomy provides provisional naming scheme for currently unnamed taxa, based on 16S rRNA sequence phylogeny, so that strain, clone and probe data from any laboratory can be directly linked to a stably named reference scheme.
Software R package for analyzing and interpreting results of PICRUSt2 functional prediction. Offers range of features, including pathway name/description annotations, advanced differential abundance methods, and visualization of differential abundance results. Used for PICRUSt2 predicted functional profile analysis and visualization.
Linear models for differential abundance analysis of microbiome compositional data
Linear models for differential abundance analysis of microbiome compositional data (LinDA)
Software linear models for differential abundance analysis of microbiome compositional data. Used to tackle compositional effects in differential abundance analysis. It fits linear regression models on centered log2-ratio transformed data, identifies bias term due to transformation and compositional effect, and corrects bias using mode of regression coefficients. It could fit mixed-effect models.
Apache HTTP Server Project is collaborative software development effort aimed at creating freely-available source code implementation of HTTP (Web) server. Project is jointly managed by group of volunteers located around the world, using the Internet and the Web to communicate, plan, and develop the server and its related documentation.
Software package contains functions for statistical calculations and random number generation.
Software remote control interface that enables introspection and control of user agents. Provides platform- and language-neutral wire protocol as way for out-of-process programs to remotely instruct behavior of web browsers.
Software R package as collection of useful utility functions from Seminar for Statistics (SfS) at ETH Zurich.
Web client/server system that allows its users to control number of processes on UNIX-like operating systems.
Open source Relational Database Management System that enables users to store, manage, and retrieve structured data efficiently.
PHP web application framework for building modern, full-stack web applications. Provides features such as thorough dependency injection, expressive database abstraction layer, queues and scheduled jobs, unit and integration testing.
Popular general-purpose scripting language that is especially suited to web development.
ArCH: Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline
Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline
Software somatic variant calling pipeline designed to detect low variant allele fraction clonal hematopoiesjsonsis variants.
Software R package for performing cell typing in SMI and other single cell data.
Software R package as unsupervised, reference-free approach to infer latent cell-type proportions and transcriptional profiles within multi-cellular spatially-resolved pixels from spatial transcriptomics datasets.
Software graph convolutional network to integrate gene expression and histology to identify spatial domains and spatially variable genes. SpaGCN integrates information from gene.
Software R package for spatial analysis of spatial transcriptomics data. Used for visualization and analysis of spatially-resolved gene expression.
Web application, a user friendly, point-and-click implementation of spatialGE R package. Contains collection of methods for visualization and spatial statistics analysis of tissue microenvironment and heterogeneity using spatial transcriptomics experiments. Used for user-friendly analysis of spatial transcriptomics data.
Code generated for use in Python to create DNA probes for use in hybridisation chain reaction, which allows for spatial resolution of mRNA expression with fluorescently tagged hairpins that bind to DNA probes. Used to generate HCR-style Probe Pairs for mRNA visualization.
Company provides reagents for detecting membrane and intracellular proteins (Flow cytometry antibodies), secreted proteins (ELISA kits), cell glycolipid metabolic intermediates and inorganic salts (Metabolism Assays), and comprehensive assessments of cellular function and health (Cell Apoptosis Assay, Cell cycle Assay, Cell Proliferation /Cytotoxicity/Viability).
Software Python library (Linux or Ubuntu only) for predicting cluster level Gene Ontology terms of plasmid encoded proteins.
Analytics platform for large-scale single-cell datasets, equipped with AI-assisted features, and designed for scientists without coding experience.
Manually curated cell type markers for fast and accurate cell type annotation in scRNA-seq datasets. Used for cell identification based on marker genes. Provides extensive search capabilities, more data and regular updates compared to other cell type marker databases, in addition to Manual curation of all data and annotations; Multiple marker gene sets for every cell type with information about publication, disease, tissue and experimental conditions, and reliability scores; Marker gene sets from single-cell and bulk RNA-seq experiments; Canonical markers for cell types;Consensus signatures for every cell type in different tissues and disease conditions;Cell type specific protein-protein interaction networks.
Johns Hopkins Reference Histology Core Facility
Provides histology services for Autopsy, Cytology, Renal Pathology and Medical Archives Office within Department of Pathology. In conjunction with Pathology Send Out and Archives divisions, provides histology for clinical trial requests, scientific study or interest involving pathology materials. Services include: Complete routine paraffin histology services, including processing and sectioning; Special stains, including but not limited to carbohydrates, connective tissue, fats, lipids, microorganisms, nuclear elements, pigments, silver techniques; Immunopathology slide preparation techniques;DNA slide preparations; Frozen tissue sections; Oversized tissue processing and sectioning ;Histopathology teaching sets; Customized procedures.Services are provided for both human and animal tissue samples.
Syracuse University BioInspired Materials Research Core Facility
Syracuse University BioInspired Materials Research Core
Provides services involved in fundamental studies of biochemical and physical processes controlling cell functions to development of new technologies for biomedical applications.
Open-source holeboard for studying rodent behavior. Used in neuroscience for assessing exploration, anxiety, and spatial memory in rodents. The project provides a cost-effective solution, offering detailed instructions on sensor integration, circuit assembly, and Arduino programming for conducting experiments. Design files and other details are available on GitHub.
Laboratory based X-ray beamline instrument. It performs Small-Angle X-ray Scattering (SAXS) and Wide-Angle X-ray Scattering (WAXS) to analyze the nanostructure of materials without requiring synchrotron facilities. SAXS system resolves nanostructures up to 620 nm. Offers flexible analysis of almost any material under ambient and non-ambient conditions. Number of additional optional features equip SAXSpoint 5.0 for future applications up to the micrometer range (USAXS).
Software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing data. Deep generative model for noise removal in droplet-based single-cell RNA sequencing.
Douglas Mental Health University Institute Douglas Brain Bank Core Facility
Douglas Mental Health University Institute Douglas Brain Bank
Based at the Douglas Research Centre, the Douglas Brain Bank (DBB) houses a large collection of brains from people with diverse psychiatric disorders, including schizophrenia, major depression, bipolar disorder and substance use disorders, as well as brains from individuals with various neurological and developmental disorders such as amyotrophic lateral sclerosis (ALS), Alzheimers disease and autism spectrum disorder (ASD). In addition, the DBCBB manages a large relational database containing demographic, clinical and developmental histories from donors.
Biotechnology company focused on pioneering cancer basic research services. Provides early discovery and development of preclinical studies. Offers services range from genetic analysis, tumor biology research, and biomarker validation, to comprehensive cancer model customization services.
Versiti Blood Research Institute Bioinformatics Core Facility
Core offers bioinformatics consultation, training, and data analysis to help investigators analyze and understand large-scale biological datasets required from different platforms, including next generation sequencing, array-based technologies and mass spectrometry. Provides development and operation of standard and advanced data processing pipelines, covering tasks such as bulk next-generation sequencing analysis (e.g., RNA-Seq, DNA-Seq, methyl-Seq, and ChIP-Seq), single-cell analysis, transcriptome and genome annotation, variant detection and interpretation and metagenomics. Our team members have extensive experience in bioinformatics, biostatistics, genomics, genetics, transcriptomics and translational informatics in human, animal and microbial systems. Our expertise includes big data analysis, statistical analysis, machine learning, neuro network, software development and high-performance computing. Our approach prioritizes scientific collaboration, going beyond mere service provision to leverage our skills and knowledge for the success of your projects. Offers support for grant applications, including key personnel involvement, support letters, and analytical method write-ups.
First digital broadband MR system. MRI scanner samples the Magnetic Resonance signal directly in the coil on the patient, and sends it to the reconstructor via fiber-optic cable. Enables imaging with fewer coils and reduce patient set up time.
Zeiss | Cirrus 5000 Optical Coherence Tomography scanner
Zeiss Cirrus 5000 Optical Coherence Tomography (OCT)
ZEISS CIRRUS 5000 non-invasive OCT angiography (OCTA) technology, you can confidently visualize retinal microvasculature and monitor change over time.
Analyzer allows detection and assessment of changes in glaucoma progression using mixed SITA tests taken on any HFA instrument.
Inverted microscope designed for advanced microscopy applications. Allows for observing samples from below, making it ideal for examining living cells and tissue cultures.Includes fluorescence, phase contrast, and differential interference contrast imaging. Can be upgraded to use modern digital camera systems through the side port or one of the two eyepiece tubes.
Software provides direct mapping refence between expanded molecular alphabet and N-nary digits in the absence of high-performance transcoding algorithm at present. Transcoding scheme for DNA data storage based on expanded molecular alphabet.
Portal showcases, aggregates, and facilitates the visualisation of non-human eukaryotic genome assemblies and genome annotations for species studied by Swedish research community, aiming to foster collaboration, highlight researchers’ work, and promote open science and FAIR data sharing.
Software program for pharmacokinetic and pharmacodynamic data analysis in Microsoft Excel.
Database of quality assessed protein-protein interactions in nine species.
Compact ultrasonic processor. This model is effective for standard cell disruption and many other small volume applications. Probes are available in three different sizes.
Covaris cryoPREP Dry Pulverizer enables dry, non-contact cryopulverization of tissue samples in a closed system without the risk of carryover or cross-contamination. The cryoPREP system provides a simple and robust tissue processing method for low and high mass inputs. The specially engineered tissueTUBE is used to process samples and extract biomolecules from a diverse set of tissue samples ranging in mass from 15 mg up to 2 g. Both manual and automated versions of the cryoPREP Dry Pulverizers are available to suit your needs.
MS Excel application for assessing the radiation doses delivered to patients undergoing CT examinations, based on computational methods that were used to analyze the data collected in the German survey on CT practice in 1999. The program enables the calculation of all dose quantities of practical value, such as axial dose free-in-air, weighted CTDI, dose-length product, effective dose and uterine dose. In contrast to existing programs for CT dose assessment, CT-Expo offers a number of unique features, such as gender-specific dose calculation for all age groups (adults, children, newborns), applicability to all existing scanner models including correction of scanner-specific influences, and the possibility of comparison with the results from the German CT survey on CT practice. Three different application modules offer free and standardized dose calculations as well as a comprehensive benchmarking section including guidance on dose optimization. The program is available as shareware in both German and English version.
Software synteny-based tool for annotation of bacteriophage genes. Used to predict function of phage hypothetical proteins using LSTM model trained with Phage Synteny.
Software tool for phage genome annotation using protein structures. Sensitive annotation tool for bacteriophage genomes and metagenomes using protein structural homology.
Software fast scalable bacteriophage genome annotation tool. Used to annotate bacteriophage genomes easily, rapidly and consistently with standards compliant outputs.
Single-source multislice CT scanner featuring adaptive scanning technology that adapts to patient and clinical conditions to reduce radiation dose. Medical imaging device that uses X-rays to create 3D pictures of the inside of the body.
Software Python package for extraction of Radiomics features from 2D and 3D images and binary masks.
Louisiana State University Health Sciences Center Shreveport Feist Weiller Cancer Center Biorepository Core Facility
Feist Weiller Cancer Center Biorepository
Louisiana State University Health Sciences Center Shreveport Feist Weiller Cancer Center Biorepository
Provides IRB-approved research projects or clinical trials with human tissue samples or hematological samples. Supports translational research by functioning as primary fresh-frozen tissue acquisition and processing facility for human solid tissue and hematopoietic specimens.FWCC Biorepository works in collaboration with medical and surgical teams at Ochsner LSU Health Shreveport, the Department of Pathology to procure remnant tissue for research purposes, and investigators in need of biospecimens for their research. Provides customized services and equipment to assist investigators in the procurement, analyses, and clinicopathologic correlation of human tissue specimens.
pracma: Practical Numerical Math Functions
Software R package provides functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.
Software literature management and referencing tool. Used for managing citations and stored articles.
Software application for analysis of force microscopy recordings, including images and force curves. Allows for fast and reliable processing of single force curves and force maps, providing estimation of mechanical properties of sample.
Manually curated database of T cell receptor sequences associated with various pathologic conditions including pathogen infections, cancer and autoimmunity and their respective antigens in humans and in mice. Links TCR sequences to their target antigen and/or to the organ with which they are associated and subsequent pathologies. Database can be searched by source organism, disease, tissue, T cell type, antigen sequence, MHC class, etc.
M Dialysis | 70 Brain Microdialysis Catheter
Sterile single use 70 Microdialysis Catheter is flexible catheter designed for implantation in brain tissue. Intended to enable microdialysis of the extracellular fluid of brain tissue.
Intercellular Junction Organization Quantification
Software Python tool for fully automated analysis of cell-cell junction integrity. Used for fluorescence microscopy analysis.
Software Python tool for semi-automated analysis of cell-cell junction phenotype. Used to semi-automate quantification of junctional protein presentation.
C++ software program for alignment of ancient DNA to a pangenome reference graph. Used to recover more alignments from ancient DNA samples, which suffer from characteristic substitution patterns due to chemical damage.
SEQUIN:Synaptic Evaluation and QUantification by Imaging Nanostructure
Synaptic Evaluation and QUantification by Imaging Nanostructure
Analysis software for identification of synaptic loci from 3D image datasets.
Hispanic Community Health Study/Study of Latinos
Multi-center epidemiologic study in Hispanic/Latino populations to assess role of acculturation in prevalence and development of disease, and to identify factors playing protective or harmful role in health of Hispanics/Latinos.
Software tool as streamlined code editor with support for development operations like debugging, task running, and version control. Aims to provide just the tools developer needs for quick code-build-debug cycle.
Software tool to discover somatic and germline structural variation breakpoints in whole genome sequencing data. Can report accurate breakpoints of Deletions, Duplications, Inversions and Translocations. Designed for Illumina paired-end data. Local assembly for breakpoint detection in cancer genomes.
Software tool for multiparametric analysis of complex flow cytometry data. Compatible with FCS standard files .Offers features to enhance data integration, interpretation, and visualization. Users can create personalized analysis templates for different types of analyses, with no limit on the number of profiles or diagrams.
Leica | THUNDER Imager Tissue microscope
Microscope allows real-time fluorescence imaging of 3D tissue sections typically used in neuroscience and histology research. Acquire rich, detailed images of thick tissues, free from the haze of out-of-focus blur.
Brain bank that houses donated brains from people with neurodegenerative diseases and neurologically normal age-matched controls. VAI Brain Bank drives insight and discovery by providing scientists the samples needed to investigate the intricate underpinnings of Parkinson’s, dementias, and other neurodegenerative diseases.
Roche | Ventana iScan Coreo Slide Scanner
Slide scanner provides automation for small-to medium-volume labs looking to make the transition to digital pathology. Scanner offers walk-away scanning of up to 160 slides, and produces high-quality images and offers advanced slide handling.
Douglas Institute Molecular and Cellular Microscopy Platform Core Facility
Douglas Institute Molecular and Cellular Microscopy Platform
Molecular and Cellular Microscopy Platform
Provides access to various microscopes and services, support and training for fluorescence microscopy experiments and image analysis. Facility offers imaging tasks from basic neuron reconstruction to high-speed, deep-tissue optogenetic experiments in brain slices or live animals.
Function-based gut microbiome health index.
Thermo Fisher | EVOS FL Auto Imaging System
High-performance, fully-automated, inverted, multi-channel fluorescence and transmitted light imaging system controlled by the integrated EVOS FL Auto software.
Software tool for genome-wide association study analysis, designed to perform range of basic and advanced meta-analytic methods.
Software package to perform genetic colocalisation analysis of two potentially related phenotypes, to ask whether they share common genetic causal variant(s) in a given region.Colocalisation Tests of Two Genetic Traits.
Summary-data-based Mendelian Randomization
Software tool to test for pleiotropic association between expression level of gene and complex trait of interest using summary-level data from GWAS and expression quantitative trait loci eQTL studies. Used to prioritize genes underlying GWAS hits for follow up functional studies.
Company specializing in antibody customization and antibody-related services. Develops functional antibodies and antibodies for detection of pharmaceutical targets and monoclonal antibodies with development time from six months to weeks.
Software to process non-targeted analyses from Bruker's ESI and MALDI imaging instruments. Supports workflows ranging from basic ID to advanced statistics.
Columbia University Zuckerman Institute Molecular Tools - Virology, Antibodies and Genetic Access Core Facility
Antibodies and Genetic Access Core Facility
Zuckerman Institute Molecular Tools Virology
Core provides investigators access to state-of-the-art vector technology for preclinical studies and other basic research applications.
University of South Carolina Engagement Studio
Platform brings together patients and caregivers, community groups, health system innovators and clinicians, and academic researchers to produce meaningful research and innovation that advances health and research outcomes.
Provides comprehensive national registry that systematically records all live births in Taiwan. It captures essential data on maternal and infant health, including maternal demographics, prenatal care, gestational age, birth weight, delivery method, and congenital anomalies. Established to facilitate public health monitoring and research, the TBRS enables studies on birth trends and outcomes, such as preterm birth and low birth weight, and provides a valuable resource for investigating the impacts of maternal health, environmental factors, and healthcare access on neonatal outcomes.TBRS database is instrumental in informing maternal and child health policies in Taiwan.
Taiwan National Health Insurance Database
Provides comprehensive dataset based on National Health Insurance program, which has covered over 99% of Taiwan's population since its launch in 1995. Database includes anonymized data on outpatient and inpatient visits, prescriptions, surgeries, diagnostics, and other medical information, ensuring individual privacy protection. NHI database is extensively utilized in fields such as public health, epidemiology, drug safety, and chronic disease monitoring, providing critical insights for research on major health conditions like cancer and cardiovascular diseases. Researchers use the NHIRD for long-term follow-up studies, treatment outcome analyses, and identifying disease risk factors, making it a valuable resource for healthcare policy and medical decision-making.
Biomedical company specializing in cancer diagnosis. Research oriented company with competitive networking and marketing skills by forming mutually beneficial partnerships. Aims to lead the popularization of cancer screening by changing the paradigm of cancer diagnostics that allows cancer screening anywhere, anytime.
Vanderbilt Cryopreserved Mouse Repository
Contains unique collection of genetically-modified mice that available for rederivation. All lines have been either generated or modified by Vanderbilt investigators, and are not available in any other repository.
Independent family-owned business established in 1960 by Roger Janvier. Company has become international company that is among the world leaders in the production of laboratory rodents and associated services.
Center to develop genetically engineered mice, analyze mouse phenotypes, and establish nationwide infrastructure for mouse research. South Korean government designated KMPC as principal organization for preclinical trials using mice and hamsters.
Company to mass-produce Specific Pathogen Free mice and rats, and has been supplying them to many bioscience related companies and research institutes. Total system supplier of experimental animals, their diets and equipment, to support bioscience research and development with vision of health, welfare, and environment for human.
Offers preclinical models and solutions to bio-pharmaceutical and academic researchers. Experienced in designing genetically modified models, featuring genetically modified mice, rats, and cell lines, and understanding of biological physiology to provide unmatched preclinical solutions.
Company supplies critical research models, including rodents, rabbits, and nonhuman primates.
Global provider of genetically modified rodent models and innovative cell and gene therapy solutions for research and development, including: disease model development, AAV discovery, drug efficacy studies, and more.
University of Northampton Advanced Imaging Core Facility
Northampton Advanced Imaging Facility (NAIF)
University of Northampton Advanced Imaging Facility (NAIF)
Core provides services for advanced imaging and flow cytometry. Equipment, training and services are available for both internal users and external users from other academic institutions and industry.
Basement Membrane Extract (BME)-free Database
Database with products that can serve as alternative for basement membrane extracts (BMEs) for in vitro applications. BME-free database is publicly available and is part of 3Rs Research Tools Programme, which is managed and hosted by 3Rs Centre Utrecht.
Manual high-performance microtome with mechanical precision specimen feed, designed above all for the manual sectioning of biological specimens embedded in paraffin.Can also be used for cutting harder materials. This product has been discontinued and replaced by HistoCore BIOCUT.
Sysmex | XT-1800i Automated Hematology Analyzer
Automated benchtop hematology analyzer for high quality blood cell analysis. Provides testing for up to 80 samples per hour, enabling rapid turnaround time.
Thermo Fisher | Prelude SPLC Sample Preparation and Liquid Chromatography System
Prelude SPLC Sample Preparation and Liquid Chromatography System
System to automate most aspects of sample preparation prior to liquid chromatography analysis, particularly for use with mass spectrometry, by integrating sample introduction, cleanup, and chromatographic separation on single platform, significantly reducing manual steps and improving sample throughput.
Software tool to discover haplotypes in sequenced data. Colors each individual as hybrid of all other sequences. The "coancestry matrix" exposes ancestral associations among individuals. ChromoPainter algorithm uses Hidden Markov Model and outputs range of features, such as expected number of recombination events and sample haplotypes.
Software tool as germline small variant caller for long-reads. Symphonizing pileup and full-alignment for high-performance long-read variant calling.
American Community Survey (2022) - Asian Ethnicities Table
American Community Survey is annual demographics survey program conducted by the U.S. Census Bureau. American Community Survey releases new data every year through variety of data tables. This table (B02018) specificially provides data on estimated number of individuals who identified as Asian, including ethnicities.
All of Us Research Program Social Determinants of Health Survey
National research resource within All of Us Research Program which asks about social determinants of health, including a participant’s neighborhood, social life, stress, and feelings about everyday life.
All of Us Research Program Basics Survey
National research resource within All of Us Research Program which is the core survey and asks basic demographic questions, including questions about a participant’s work and home.
All of Us Research Program Lifestyle Survey
National research resource within All of Us Research Program which asks about participant’s use of tobacco, alcohol, and recreational drugs.
iXon Life Electron Multiplying CCD platform for fluorescence microscopy applications and is engineered to deliver single photon sensitivity.
Microfluidic trapping chip for culture and assay of cell clusters and objects
Microfluidic cartridge for automatically hydrodynamically loading objects (e.g., cell clusters) into traps in parallel trapping channels with one object per trap. This improves loading of cell clusters compared to well-based systems.
Device and system for producing mature adipocytes
Device and system for 3-dimensional adipocyte expansion to produce mature adipocytes and synthetic adipose tissue with cellular properties of mature adult organisms, including cell size and cytoarchitecture, in vitro drug screening and/or toxicity assays, disease modeling, and therapeutic applications.
Cartridge-based system for long term culture of cell clusters
Microfluidic systems including housing configured to receive cartridge, housing including channels for loading one or more biological cells within wells of the cartridge. Three-dimensional scaffolds, devices, and systems comprising such scaffolds that mimic the in vivo structure, physical properties, and protein composition of extracellular matrix surrounding pancreatic islet cells and adipocytes, with use for, e.g., in vitro drug screening and/or toxicity assays, disease modeling, and therapeutic applications. The cartridge including a plurality of wells for receiving one or more biological cells. The microfluidic systems include a structure with channels for introducing a medium into the housing and through channels the cartridge.
CRISPR-Cas9 conjugation platform for engineering designer beta cells
This technology relies on newly described chemical modifications that allow site-specific and multiple-site conjugation of a wide assortment of molecules on both the termini and internal sites of Cas9, creating a platform for endowing Cas9 with diverse functions. Using this platform, Cas9 can be modified to more precisely incorporate exogenously supplied single-stranded oligonucleotide donor (ssODN) at the DNA break site. We demonstrate that the multiple-site conjugation of ssODN to Cas9 significantly increases the efficiency of precision genome editing, and such a platform is compatible with ssODNs of diverse lengths.
Software package to facilitate microbiome exploration and ensuring nice plotting.
Software tool for detecting transposon insertions using short-read whole-genome sequencing data. Used to detect germline transposon insertions, estimate number of uninherited/somatic transposon insertions by removing artificial insertion introduced by chimeric reads.
All of Us Research Program Data and Statistics Dissemination Policy
Guidelines for accessing and sharing data collected by the All of Us Research Program. It aims to ensure responsible data use while promoting transparency and collaboration in research to advance precision medicine.
Dartmouth Geisel School of Medicine Biological Mass Spectrometry and Proteomics Shared Resource Core Facility
Biological Mass Spectrometry and Proteomics
Geisel School of Medicine at Dartmouth Biological Mass Spectrometry and Proteomics
Core offers quantitative and qualitative proteomics services using LC-MS/MS technologies. Servies include sample preparation from harvested cell pellets, elutions post-enrichment or purification, or gel bands through data acquisition, quantification, and statistical analysis.
Software toolkit for detection of allele-specific RNA N6-methyladenosine modifications.
Web application as JavaScript-based intuitive search interface to explore the SPARC Connectivity Knowledgebase of the Autonomic Nervous System.
Web-based open-source data visualization software made in JavaScript. Aims at providing missing link between spreadsheet applications (e.g. Microsoft Excel, Apple Numbers, OpenRefine) and vector graphics editors (e.g. Adobe Illustrator, Inkscape, Figma).
Software package of open-source graph visualization tools. Provides also libraries for software applications to use the tools. Provides a way of representing structural information as diagrams of abstract graphs and networks.
Graph database supporting Blueprints and RDF/SPARQL APIs. Supports up to 50 Billion edges on single machine. It is in production use for Fortune 500 customers such as EMC, Autodesk, and many others. It supports key Precision Medicine applications and has wide-spread usage for life science applications. Used to support Cyber analytics in commercial and government applications.
SPARC Connectivity Knowledgebase of the Autonomic Nervous System
SPARC Connectivity Knowledgebase of the Autonomic Nervous System (SCKAN)
Semantic store of detailed, formal knowledge about ANS connectivity between the central nervous system and end organs. As key component of NIH SPARC program, SCKAN enables integration, discovery, and querying of ANS connectivity across multiple scales.
Software application provides researchers with scores for tumor purity, level of stromal cells present, and infiltration level of immune cells in tumor tissues based on expression data.
Software Matlab based toolbox for heart rate analysis.
Software R package to automate comparison of sequence data against prototype strains, streamlining genotype assignment process.
Source and cluster submission code for transdiagnostic patient-control classification in 17 ICD-10 diagnostic groups in the UK BioBank dataset.
Shenzhen Huixin Biomedical Technology | EXODUS
Automatic, label-free exosome isolation system. Used to isolate high-quality, intact exosomes with excellent yield and purity from variety of bio-fluids and sample volumes.
ALLSHENG | Nano100 Micro-specrophotometer
Nano-100 microspectrophotometer to measure concentration of nucleic acid, protein and cell solution. 0.5 to 2μl of sample volume is required for each measurement. No cuvette is required. At the end of measurement, sample could be either wiped off directly or recovered with pipettor.
Shanghai Cloud Sequence Biotechnology Co Ltd
Company is leader in the field of epigenetic modification and transcriptomics in China. Provides innovative enterprise to carry out RNA modification, transcriptome and eccDNA research in China, providing various RNA modifications, various RNA molecules (mRNA and non-coding RNA), various sequencing technologies (IP, single base) and eccDNA systematic solutions.
Thermo Fisher | Heracell 150i CO2 Incubator
Thermo Scientific Heracell 150i CO2 Incubator provides in-vitro environment for cultivating cell and tissue cultures. Allows simulation of special physiological conditions for these cultures due to exact control of temperature, CO2 and humidity.
CAM-SU Genomic Resource Center of Soochow University
CAM-SU Genomic Resource Center of Soochow University is National Center for International Research, shared UK-Chinese mutant ES Cell Repository for Asian-Pacific research community, and platform for mouse model production and phenotyping and mammalian genome function deciphering. Constructs human-specific gene mutations in human embryonic stem cells via CRISPR system for disease modeling, functional annotation, drug discovery, and more. CAM-SU Genomic Research Center also conducts research in stem cells and organoids to accelerate bioresource development.
Software R code for analysis of social evolution in bees. Social complexity trait database and code. R scripts for analysis of bees evolution.
Software tool as somatic variant caller designed for paired samples and primarily ONT long-read. Method for long-read somatic small variant calling.
Software R package for working with inForm data. Contains functions that make it easier to read and analyze data tables and images created by Akoya Biosciences' inForm software.
System is 3-part compact automated hematology analyzer designed for in vitro diagnostic to use in low volume clinical laboratories. Provides measurable results for comprehensive panel of hematological parameters, electronic impedance, absorption spectrophotometry, electronic valves, cyanide-free lyse reagent, LCD color touch screen and USB ports.
Stand alone gel imager for gel documentation. Provides high-resolution images of DNA, RNA or protein gels. Images can either be printed out directly or saved in internal storage. Transfer of data to PC is possible.
Automated Germline Variant Pathogenicity
Software tool integrates ClinVar variant annotation with modified InterVar classification approach, based on American College of Medical Genetics-Association for Molecular Pathology guidelines, to output germline variant classification. Since AutoGVP input only requires VCF file, it can facilitate large-scale, clinically focused classification of germline sequence variants.
Software automatic classification tool for PVS1 interpretation of null variants.
Integrated proteome resources center in China to accelerate data sharing in proteomics. Composed of data submission system and proteome database. Submission system is established under the guidance of data-sharing policy made by ProteomeXchange consortium. Registered users can submit their proteomic datasets to iProX in public or private modes. Once associated manuscript has been published, dataset becomes automatically public.
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
Software tool for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps in high resolutions (10kbp all the way to 500bp and even more). Used to detect chromatin loops caused by interaction of DNA segments with variable size.
Software modular Hi-C mapping pipeline for reproducible data analysis. Nextflow-based modular Hi-C mapping pipeline.
Software R package for visualization of intersecting sets and their properties.
Precision-Recall and Receiver Operating Characteristic
Software package for computing and visualizing precision-recall and receiver operating characteristic curves in R for weighted and unweighted data.
Software R package that extends ggplot2 by adding several functions to reduce complexity of combining geoms with transformed data. Some of these functions include pairwise plot matrix, scatterplot plot matrix, parallel coordinates plot, survival plot, and several functions to plot networks.
Software R package providing additional functions to cut, label and colour dendrogram clusters.
Software package extending R core dendrogram functions.
Software R data.table package extends data.frame. Provides high-performance version of base R's data.frame with syntax and feature enhancements for ease of use, convenience and programming speed.
Software suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Provides suite of computational tools with paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation.
Software tool to detect mobile element insertion in human short read sequencing data.
Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins.
Platform for data and statistics. Website provides data-driven services, collection of statistics, reports, and insights on over 80,000 topics.
Software pipeline that uses profile hidden Markov models of neuropeptide families to search query datasets for neuropeptide homologues.
Open-source software for video capture and video processing for Microsoft Windows. Designed to process linear video streams, including filtering and recompression. It uses AVI container format to store captured video. Video capture/processing utility for 32-bit and 64-bit Windows platforms. Used for processing AVI files, although it can read (not write) MPEG-1 and also handle sets of BMP images.
Western Blot Quantification Toolkit in MATLAB
Software package to quantify intensity of bands on western blot.
Software package contains suite of functions that enables analysis of flow cytometry data.
McGill University Goodman Cancer Institute Histology Innovation Platform Core Facility
Goodman Cancer Institute-Histology Innovation Platform
McGill University Goodman Cancer Institute-Histology Innovation Platform
Core provides expertise, cutting edge technology, and efficient workflows in histological processing, analysis and interpretation.
Stand-alone web-application for interactive analysis and visualization of multi-drug (2 or more drugs) multi-dose combination response data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Biotechnology company specialized in innovative solutions for cancer research. Provides Cancer Modeling Services to accelerate cancer therapeutics discovery and development. Contract research organization that specializes in early discovery and preclinical studies and provides cancer diagnostic biomarker development services.
Ergonomically designed sliding microtome with electronic control systems and high-precision mechanics to achieve optimal section quality and reproducibility of even the most difficult-to-cut specimens. It can accommodate specimen sizes up to 80 x 60 mm, and can cut sections ranging from 1 to 100 microns. Employs automatic fine/trim-feed system to protect knife and specimen by enabling specimen retraction during return travel. Enables continuous upward and downward travel of specimen through motorized coarse feed system. This system employs three different speed settings and multi-purpose button control, allowing fast adjustment of specimen and knife edge distance.
Software desktop application that facilitates installation, management and deployment of containerized bioinformatics workflows. Provides interactive interface to launch containerized analytical workflows that can be used to process biomedical data.
SAMHSA 2023 NSDUH Annual National Report on Drug Use and Health
2023 NSDUH Annual National Report on Drug Use and Health
Substance Abuse and Mental Health Services portal provides information about 2023 National Survey on Drug Use and Health. This report highlights 2023 estimates of substance use, mental health, and treatment in the United States. These national indicators are measured among people aged 12 or older in the civilian, noninstitutionalized population. Estimates are presented by age group and by race/ethnicity for selected measures. Along with the full report, which includes both figures and text descriptions, set of slides is available which includes just the figures from the report.
Web server for protein-ligand blind docking, integrating cavity detection, docking and homologous template fitting. Given the three-dimensional structure of protein and ligand, can predict their binding sites and affinity for computer-aided drug discovery.
Database for spatially resolved transcriptomes. Provides curated spatially resolved transcriptomic data from published papers, aiming to provide comprehensive and accurate resource of spatial gene expression profiles in tissues. Allows users to browse spatial gene expression profile and compare spatial gene expression profile of any two datasets generated by same or different techniques side by side.
Software R package provides number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.
Agilent | Bravo Automated Liquid Handling Platform
Agilent Bravo Automated Liquid Handling Platform
Robotic liquid handling system that automates sample preparation for screening applications such as compound management, cell-based assays, and genomic assays. Compact liquid handler can be placed on small bench and fits in flow hood. With more than 60 accessories ranging from thermal cycler to shaker, the system can be tailored to automate most sample preparation protocols. VWorks control software allows users to create and run flexible liquid handling protocols.
Paris Brain Institute Data Analysis Core Facility
Institut du Cerveau - Paris Brain Institute - ICM
Sorbonne Université Paris Brain Institute Data Analysis Core Facility; Data Analysis Core Facility Paris Brain Institute; Data Analysis Core
Core provides structural support and expertise in processing, integrating, analyzing and managing neuroscience data.
Life sciences contract research organization. Provides integrated life science services for drug discovery with expertise in chemistry, biology and pharmacology, DMPK, and exploratory toxicology as well as biologics discovery.
Software executable version of CELLxGENE and CELLxGENE-gateway to allow single-cell transcriptomic data to be annotated using without using the command line or installing extra software.
Software R package that streamlines single-cell RNA-seq analysis by integrating essential tools and databases with the Seurat framework. Provides comprehensive functionality for functional enrichment, trajectory inference, gene regulatory network reconstruction, and enhanced visualization.
Sakura | Tissue-Tek VIP 6 AI Vacuum Infiltration Processor
Tissue-Tek VIP 6 AI Vacuum Infiltration Processor
Tissue processor with automated onboard preparation of mixed solutions, automatic in-process reagent exchange, and Tissue-Tek iSupport remote monitoring.
Thermo Fisher | Ultimate 3000 RSLCNano UPLC system
Thermo Scientific UltiMate 3000 RSLCnano
System provides ProFlow technology for nano-flow applications and is designed to provide high resolution, speed, and sensitivity for low-flow LC or LCMS applications, such as proteomics and metabolomics. It has wide flow-pressure footprint that supports nano, capillary, and micro applications.
Thermo Fisher | Epredia HM 355S Automatic Microtome
Heavy duty, motorized microtome that can section large specimens with high quality. It's designed to be ergonomic and comfortable to use. Used for precise sectioning of hard and paraffin specimens in research, clinical, and industrial labs.
Leading-edge science and technologies in analytical and measuring instruments including chromatographs and mass spectrometry. Manufactures precision instruments, measuring instruments and medical equipment.
Software suite is designed to be of help when working with Human Genome Variation Society sequence variant nomenclature descriptions.
Software package called illustrator of biological sequences. Can be used for representing organization of either protein or nucleotide sequences. Multiple options are provided, and biological sequences can be manipulated, recolored or rescaled in user-defined mode. Final representational artwork can be directly exported into publication-quality figure. Used as illustrator for presentation and visualization of biological sequences. Standalone package was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available
Biotechnology company to research and develop cell products for experimental use. Provides normal human and animal cells, cell culture media and reagents, gene analysis tools, cell-derived molecular biology products, cell-based assay kits, and stem cell products for research community. Focused on studying and developing cell therapeutic strategies to significantly improve quality of life for patients with degenerative diseases.
Software Galaxy tools dedicated to ecology data management and analysis, available through Galaxy Tool Shed.
Software used for quantitative Western blot imaging and analysis. Designed to look at multiple proteins simultaneously on single assay. This software is sensitive enough to distinguish co-migrating proteins, such as phosphorylated and unphosphorylated.
Software application used with Bruker's atomic force microscopes and scanning probe microscopes. Software package for analyzing SPM data including images, ramp data, HSDC data, collected using Bruker SPMs.
Gene Expression Profiling Interactive Analysis 2
Enhanced web server for large-scale expression profiling and interactive analysis. GEPIA2 is updated and enhanced version of GEPIA, offering more functionalities, higher resolution data analysis, and additional features like ability to analyze specific cancer subtypes, quantify gene signatures based on single-cell sequencing studies, and allow users to upload their own RNA-seq data for comparison with the TCGA and GTEx datasets; essentially providing more comprehensive and advanced platform for gene expression analysis compared to the original GEPIA version.
Database that aims to comprehensively explore distinct functional states of cancer cells at the single-cell level. Provides functional state-associated PCG/lncRNA repertoires across all cancers, in specific cancers, and in individual cancer single-cell datasets. Provides interface for comprehensively searching, browsing, visualizing and downloading functional state activity profiles of cancer single cells and corresponding PCGs/lncRNAs expression profiles.
Software framework for processing spatial omics data. Data framework that comprises FAIR storage format and collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets.
Software tool for analysis and visualization of spatial molecular data. Scalable framework for spatial omics analysis. Builds on top of scanpy and anndata, from which it inherits modularity and scalability. Provides analysis tools that leverages spatial coordinates of data, as well as tissue images.
Software pipeline that simultaneously collects and processes Xenium In Situ Gene Expression data. Used for analyzing and visualizing in situ gene expression data produced by the Xenium Analyzer.
Deep learning framework, with support for JAX, TensorFlow, and PyTorch. Used to build and train models for computer vision, natural language processing, audio processing, timeseries forecasting, recommender systems. Offers consistent and simple APIs, minimizes number of user actions required for common use cases, and provides clear and actionable error messages. Keras also gives the highest priority to crafting documentation and developer guides.
Deep learnining based variational inference method to integrate scRNA-seq with spatial transcriptomics data. ENVI learns to reconstruct spatial onto for dissociated scRNA-seq data and impute unimagd genes onto spatial data.
Shared high-performance computing cluster. All research teams on Sherlock have access to a base set of managed computing resources, GPU-based servers, and a multi-petabyte, high-performance parallel file system for short-term storage. Stanford Faculty can supplement these shared nodes by purchasing additional servers. By investing in the cluster, PI groups not only receive exclusive access to the nodes they purchase, but also get access to all the other owner compute nodes when they're not in use, thus giving them access to the whole breadth of Sherlock resources.
Software tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. Performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length.
Software R package for single cell and other data analysis using diffusion maps. Package for diffusion maps, with additional features for large-scale and single cell data.
Web service to search for variants, CNVs, genes, transcripts, publications, diseases. Annotation tool and search engine for human genomic variants, and platform enabling sharing of knowledge on specific variants. Enables users to look up variants in their genomic context, collects data from multiple databases in central location and most importantly, aims to enable community to freely and easily share knowledge on human variation.
Software package provides framework of functions and shiny-applications to work with spatial expression data. Used for spatial transcriptomics analysis.
Luxembourg Centre for Systems Biomedicine
Research institute in Esch-sur-Alzette, Luxembourg to study brain and its diseases. Collaboration between biologists, medical and computer scientists, physicists, engineers as well as mathematicians offers new insights into complex biological mechanisms and disease processes, with the aim of developing new tools for diagnostics, prevention, and therapy. LCSB has established strategic partnerships with scientific partners worldwide and with all major biomedical research units in Luxembourg. Carries out collaborative projects with hospitals and research-oriented companies, accelerating translation of fundamental research results into clinical applications.
University of Texas Medical Branch at Galveston Next Generation Sequencing Core Facility
The University of Texas Medical Branch at Galveston UTMB NGS core
Core offers Next Generation Sequencing services using Element Biosciences AVITI short read sequencer, PacBio Revio and Oxford Nanopore Promethion/GridIon long read sequencers along with 10X Genomics X, 10X Genomics Visium CytAssist, and 10X Xenium Analyzer single cell/spatial technologies.
National Cancer Institute Advanced Microscopy Applications Unit Core Facility
Instituto Nacional de Cancerolog�a Advanced Microscopy Applications Unit (ADMiRA)
Core answers research questions in any scientific, medical or industrial discipline through capture, processing, image analysis, training and sample preparation services for microscopy. Provides technical and scientific support in advanced microscopy and image processing and analysis.
Software tool to discern whether peptide will be recognized by HLA as epitope. Capable of directly identifying peptides as epitopes without the need for inputting HLA alleles. Hybrid transformer model for peptide-HLA epitope detection.
Thermo Fisher: Applied Biosystems | MiniAmp Thermal Cycler
Thermal Cycler is benchtop PCR machine which features 5-inch color touchscreen for easy control and is also accessible through Thermo Fisher Connect , giving you the freedom to design and securely upload your methods from any mobile device or desktop computer. Designed for amplification of nucleic acids using Polymerase Chain Reaction process. User interface includes touchscreen with graphical display that shows time, status, and temperature for each run. Touchscreen keypad allows to enter information into fields on display screen.
Updatable online database of mammal taxonomic and biodiversity information hosted by American Society of Mammalogists. Provides information on species-level and higher taxonomic changes, thereby promoting more rigorous study of mammalian biodiversity worldwide. The initial objective has been to aggregate, curate, and compile, new citations on species descriptions and taxonomic revisions into regular releases that are downloadable in comma-delimited format. Downstream goals include expanded hosting of ecological, trait, and taxonomic data.
Deep learning phenotyping of Arabidopsis fruit morphology. Deep learning model weights and inference code to detect Arabidopsis thaliana siliques in scans of stem material. Phenotyping code to extract length, diameter area and volume metrics of siliques from model outputs.
Software lightweight GIMP plug-in to alllow for computer vision-assisted image annotation using GIMP selection toolbox.
University of South Carolina X-Ray Photoelectron Spectroscopy Core Facility
Facility provides quantitative compositional information from top atomic layers of sample surface for the elements lithium to uranium. Core can also obtain information regarding chemical states of any elements present. This facility houses Kratos AXIS Supera+ Spectrometer Unit.
University of South Carolina Mouse Experimentation and Germ-Free Core Facility
Mouse Experimentation and Germ-Free Core Facility (MEF/GFC)
Mouse Experimentation and Gnotobiotic Core
University of South Carolina Mouse Experimentation and Germ-Free Facility
Provides support to experiments that use mouse models to elucidate mechanisms of normal physiology and disease processes, and to develop and test novel agents and therapies to treat diseases. Provides centralized facililty for breeding, genotyping, maintaining colonies, conducting animal experiments, collecting tissues, analyzing experimental results, and training personnel in proper procedures for conducting animal experiments. Core also hosts germ-free mouse facility that works with PI's to produce, distribute, and conduct experiments in germ-free and gnotobiotic mouse models. MEF/GCF offers expertise with genetic, induced, or orthotopic models of disease and coordinates with other USC Cores with respect tissue processing and preparation for various types of analyses.
University of South Carolina Functional Genomics Core Facility
University of South Carolina Functional Genomics Core
Core offers resources and solutions for conducting genomics, transcriptomics, epigenomics and functional genomics projects. We work with researchers to determine project goals and design custom solutions. We assist at all stages of the project, from support in grant development to generation of publication-quality data. Services include Consultations, Bioinformatics, Nucleic Acids purification, quantification and QC DNA Sequencing (SANGER and NGS), Library Constructions for NGS applications,Microarray Hybridization, Real Time PCR, Custom epigenomics applications, Lentiviral vectors and lentiviruses construction and production, CRIPR-CAS9sgRNAs and RNAi/shRNAs knockdown of individual genes and functional screening of sgRNA and shRNA libraries for target identification.
University of South Carolina Electron Microscopy Core Facility
University of South Carolina Electron Microscopy Center
Electron Microscopy Center at USC is core facility providing all levels of technical support and consultation in area of light microscopy, electron microscopy, and elemental analysis. Provides microscopy and specimen preparation services for biological and materials science research. Offers training and access to all microscopes and ancillary equipmen.
COmpositinal Data Analysis with Recursive Feature Elimination
Software tool for selecting predictors such as bacteria for any continuous environmental variable such as pH, illness measurements, diseases index, etc. Sparse compositional microbiome-predictors selection and prediction of continuous environmental factors. Used for unlocking prediction of continuous environmental variables based on microbiome.
Software suite of scripts to detect and analyse de novo variants from multi-sample vcf.
Software MATLAB package for analyzing and categorizing behaviors using pose estimation data. Integrates semi-automatic labeling with machine learning, specifically Long Short-Term Memory neural networks, to classify behavioral "syllables” (distinct, repeatable behaviors). Combinatory approach of semi-automatic labeling and long short-term memory to classify behavioral syllables.
University of Louisville School of Medicine Molecular Modeling Core Facility
Core offers services including molecular modeling of proteins and nucleic acids, virtual drug screening, computational biophysics.
Softawer framework for de novo chromosome-by-chromosome assembly with long reads. Long-reads gap-free chromosome-scale assembler.
Software package for optimal matching in R. Distance based bipartite matching using minimum cost flow, oriented to matching of treatment and control groups in observational studies. Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination.
Software Python library for navigation, visualisation, and analysis of whole-brain quantification data. Integrated suite for multi-marker automated segmentation, whole-brain statistical analysis, and data visualisation. Used for quantitative multi-marker image analysis of whole-brain registered datasets.
Software tool for batched microscopy image contrast adjustment and pseudocoloring in Matlab.
Software tool for quantification of positive channel area in Matlab.
Pharma Proteomics Project is precompetitive biopharmaceutical consortium characterizing plasma proteomic profiles of UK Biobank participants. Collaboration between UK Biobank and biopharmaceutical companies characterising plasma proteomic profiles of UKB participants. Project generates the largest open-access plasma proteomics dataset to date, offering insights into trans protein quantitative trait loci across multiple biological domains, and highlighting genetic influences on ligand–receptor interactions and pathway perturbations across diverse collection of cytokines and complement networks.
Stanford Ecosystems Shared Laboratory Core Facility
Ecosystems Laboratory provides bench space, laboratory supplies, chemicals, sample preparation equipment, and sample storage space to enhance and facilitate research within Stanford University community.
Behavioral platform designed to distinguish between different navigational elements. Flexible and user-friendly software and hardware allows for modifications to the researcher’s specific needs, allowing for capabilities of testing in nonspatial tasks as well. Can be used in conjunction with in vivo electrophysiology, as well as video tracking methods.
Yale Keck Mass Spectrometry and Proteomics Resource Core Facility
Yale University YU-Keck MS & Proteomics Resource
Core provides proteomics and small molecule mass spectrometry services to separate, characterize, profile, and quantify analytes from complex biological samples.
Software tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.
Software repository to share the raw data processing and visualization codes used in the spatial tri-omics project.
University of Liverpool Egg Facility (LIV-SRF)
University of Liverpool Egg Core Facility
Through the use of fertilised hen's eggs, the Egg Facility offers researchers methods for scientific research that can reduce or replace the use of mammalian models. It provides expertise in chorioallantoic membrane assays, specialising in cancer xenograft models, including patient-derived xenografts, to translate in vitro cancer studies and test therapeutic approaches.
Software tool for computational deconvolution of mouse and human reads in tumor xenograft sequence data.
Artificial Intelligence detection software developed to identify artificially generated text, such as those produced by large language models.
Distribution company focused on providing products and services to biomedical and life science research communities. Offers high-quality adsorbent resins, catalyst resins, chelating resins, and other ion exchange resins.
North American Association of Central Cancer Registries
North American Association of Central Cancer Registries (NAACCR)
Professional organization that develops and promotes uniform data standards for cancer registration. Provides education and training, certifies population-based registries, aggregates and publishes data from central cancer registries and promotes the use of cancer surveillance data and systems for cancer control and epidemiologic research, public health programs, and patient care to reduce the burden of cancer in North America. Data Standards and Data Dictionary is intended for hospital and central cancer registries, programmers, and analysts. It provides detailed specifications and codes for each data item in the NAACCR data exchange record layout.
Software platform independent error correction tool for single and mixed genomes. Used for correcting errors across platforms.
Columbia University Zuckerman Institute Molecular Tools Core Facility
The Zuckerman Institute Molecular Tools Core
Zuckerman Institute: Molecular Tools - Virology
Full service viral vector production core that provides investigators access to vector technology for preclinical studies and other basic research applications. Staff will provide expert consultation services for advanced study design, safe use of viral vector technologies and viral construction services for multiple viral vector types.
Online database provides collection of gene sets based on quantitative inhibition and/or drug-induced gene expression changes data of drugs and compounds. Allows users to search, view and download drugs/compounds and gene sets.
Olympus | BX63 Automated Fluorescence Microscope
Fully motorized system allows automation of complex multidimensional experiments. Uses motorized nosepiece to focus onto sample, enabling stage to be fixed for added stability.
Scanner for in-vivo, low radiation imaging. Offers new micro-CT spatial beam shaper, which reduces absorbed radiation dose by up to five times while maintaining high quality image output. High throughput, high speed, microCT for scanning small laboratory animals including mice and rats. Has highly sensitive flat-panel detector that is able to deliver images of mouse heart and lung activities without using contrast agent, reducing animal stress and cost of study. Full-body animal scan can take 8 seconds or less, thus reducing overall run times and increasing the speed of data collection. Results can be directly sent to mobile devices for volume rendering and manipulations using software supplied.
Thermo Fisher | Orbitrap Astral Mass Spectrometer
Mass spectrometer combines faster throughput, deeper coverage, and higher sensitivity while delivering accurate and precise quantitation over high dynamic range. Suited for accurate and precise quantitation at unprecedented depth of coverage and higher throughput from single cells to bulk samples.
Commercial company, operating within healthcare technology sector, specifically focused on oncology. Develops oncology cloud platform, integrating clinical data and providing insights to cancer care providers and life science companies. Provides real-world evidence solutions, enabling collection, analysis, and interpretation of data from oncology patients.
Company produces anaerobic workstations. Offers range of units to suit all sizes of laboratories and will consider manufacture of special cabinets to customers' own specification. Anaerobic workstations can also be used for microaerophylic and other types of work by using different gas supplies.
Software Python package for correcting sequencing errors within Short Tandem Repeat regions from Oxford Nanopore (ONT) sequencing data and genotyping monoallelic STR regions.
Bio-Techne | ProteinSimple Wes Automated Western Blot System
Protein characterization system that automated the Western blotting process from protein separation, immunoprobing, detection, and analysis of data.Gel-free, blot-free, and hands-free. It used glass rods and tubes to form a column that separated proteins by molecular weight. The Wes system was discontinued on July 30, 2021, but ProteinSimple will continue to support the platform through July 30, 2026. Users can upgrade to Jess or Abby to get the functionality of Wes with additional features.
Baylor College of Medicine Metabolomics Core Facility
Metabolomics Core at Baylor College of Medicine
The Metabolomics Core at Baylor College of Medicine
Core provides Untargeted Metabolomics, Untargeted Lipidomics, Targeted Metabolomics, Metabolomics Flux and analysis services.
Software tool to embed scRNA-seq data into species-agnostic latent space to overcome batch effect and identify cell states shared between species. Deep learning algorithm for cross-species integration of scRNA-seq data.
Mitochondrial and Nuclear tRNA fragment database
Web-based framework that serves the dual-purpose of being content repository for tRFs and tool for interactive exploration of these newly discovered molecules. Framework for interactive exploration of mitochondrial and nuclear tRNA fragments. Can report comparative information on how tRF is distributed across all anticodon/amino acid combinations, provides alignments between tRNA and multiple tRFs with which user can interact, provides details on published studies that reported tRF as expressed.
International data-sharing consortium focused on generating an evidence base for precision cancer medicine by integrating clinical-grade cancer genomic data with clinical outcome data of cancer patients treated at multiple institutions worldwide.
Community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research. Cancer classification system for precision oncology.
University of California San Francisco Clinical Cancer Genomics Laboratory Core Facility
UCSF Clinical Cancer Genomics Laboratory (CCGL)
University of California San Francisco Clinical Cancer Genomics Laboratory (CCGL)
Core performs standard-of-care and advanced molecular testing for patients with cancer, and to provides special expertise in solid tumors. Services include targeted gene sequencing, microsatellite instability testing, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS). CCGL is staffed with board-certified surgical pathologists and board-certified molecular pathologists who can properly evaluate the quality of samples submitted for testing as well as make correlations between the pathologic diagnosis of a tumor and the molecular findings in the tumor.
IPD2 is updated version of InfectiousPathogenDetector, in-silico GUI-based automated pathogen analysis pipeline for seamless analysis of data from heterogenous NGS platforms. IPD performs integrated variants analysis, along with systematic quantification of pathogen genomes. IPD additionally has an in-built SARS-CoV-2 analysis module, for assignment of viral clades of the samples analyzed and an automated report generation.
Software tool for calling and analyzing SNVs from spatial transcriptomics data.
Software collection consisting of Python-based framework for connectome-based analysis using Ray to parallelize CPM and set of scripts to perform common operations and analyses on the Human Connectome Project's neuroimaging data with focus on task-based fMRI.
Software extension of t-distributed stochastic neighbor embedding, the spatially resolved t-SNE (SpaSNE) designed to preserve both global gene expression and spatial structure for spatially resolved profiling data. Gives comprehensive low-dimensional visualization that could best reflect the molecular similarities of cells and the spatial interactions between cells.
Web-based application for automated structural classification of chemical entities. Automated chemical classification with a comprehensive, computable taxonomy. Provides hierarchical chemical classification of chemical entities as well as structure-based textual description, based on chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds.
National Institute of Standards and Technology Chemistry WebBook
Database that provides access to organic compounds data compiled and distributed by NIST under the Standard Reference Data Program.
Free file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, and secure copy protocol client for Microsoft Windows.
Open source software for chromatography, spectrometry and spectroscopy. Data from different systems can be imported and analyzed. Runs under Windows, macOS and Linux. Supports to handle GC/MS, GC/FID, HPLC-UV/VIS, FTIR, PCR and NMR data.
Interactive website for cancer statistics using California Cancer Registry data. Provides detailed statistics for cancer site by gender, race/ethnicity, age, county/region, and for select number of cancer sites, by histology.
Montana State University Research Cyberinfrastructure Core Facility
Montana State University - Research Cyberinfrastructure
Core provides centralized support, systems, and services for IT specific to research. Systems and services include areas of high-performance computing, virtual machine hosting, large scale storage, and high-performance networking and data transfer.Provides MSU researchers with consulting on technology budgets and implementation for grants and support for IT components of major research instrumentation, software, and specialized or unique research technology needs.
Agilent Seahorse XF Cell Mito Stress Test Report Generator
Microsoft Excel Macro that automatically calculates and reports assay parameters of the Seahorse XF Cell Mito Stress Test as absolute Oxygen Consumption Rate in pmol O2/min and supports assay result data from all Agilent Seahorse XF Analyzers.
Software signal processing and spectral analysis toolbox designed for local field potential recordings.
Software integrated pipeline for plant NGS analysis.
Pharmaceutical, biopharmaceutical, and medical device company founded in December 2000 in Shanghai. Contract research organization.
Oncology translational research organization focused on development and utilization of Patient-Derived Xenograft models. Preclinical contract research organization specializing in patient-derived xenografts.
University of Texas MD Anderson Cancer Genomics Library Core Facility
University of Texas MD Anderson Cancer Genomics Library
Facility for sequencing samples for the MD Anderson Cancer Center.
Website for predicting the subtype of triple negative breast cancer sample based on its gene expression profile.
Software system for performing bioinformatics analyses. System includes knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. Backwards-chaining rule-based expert system comprised of data model that can capture richness of biological data, and inference engine that reasons on knowledge base to produce workflows. Knowledge base is populated with rules to analyze microarray and next generation sequencing data.
Provides data on protected areas and other effective area-based conservation measures, updated monthly with submissions from governments, non-governmental organizations, landowners and communities.Through Protected Planet website, users can explore World Database on Protected Areas (WDPA), World Database on OECMs, Global Database on Protected Area Management Effectiveness (GD-PAME), and associated information.
Provides information about family of funds for the environment. With GEF support,countries address the root causes of challenges as they strive for international environmental goals. Fund data from the Global Environment Facility.
World Health Organization Global Health Expenditure Database
Global Health Expenditure Database provides comparable data on health expenditure for 194 countries and territories since 2000 with open access to the public. WHO works collaboratively with Member States to update the database (Explore the Data) annually, using available information such as health accounts data, government expenditure records and official statistics.
Registered charity and company limited by guarantee with mission to conserve birds, their habitats and global biodiversity, working with people toward sustainability in the use of natural resources. Registered in England. Provides bird species range map.
Software R package also called event history analysis in social science, or reliability analysis in engineering, deals with time until occurrence of event of interest. However, this failure time may not be observed within the relevant time period, producing so-called censored observations. Used for analysis of time to event data.
Software R client for the Aggregate Content of ClinicalTrials.gov (AACT) database API.
Software repository hosts one of metadata models of openMINDS metadata framework. It defines modular metadata schemas for describing general origin, location and content of neuroscience research products.
openMINDS controlledTerms metadata model
Software repository is part of open Metadata Initiative for Neuroscience Data Structures (openMINDS). It contains the schema-templates as well as corresponding terminologies (as JSON-LDs) for all terms that are defined and maintained centrally in this repository. Where applicable, the defined terms are connected to a matching ontological term. Schemas of openMINDS_core as well as openMINDS_SANDS reference to these controlled terms.
Software repository hosts one of the metadata models of the openMINDS metadata framework. It defines modular metadata schemas for describing chemical substances and mixtures.
Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS core, by providing schema-templates for adding metadata for simulation, data analysis and visualization.
Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for in-depth descriptions of electrophysiology experiments.
Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for representing publications in neuroscience, including interactive publications such as Live Papers. It includes schemas for articles, books, preprints, blog posts, live papers, etc., linked to other openMINDS entities such as Datasets. The schemas closely follow those in Schema.org but extend them for improved interoperability with openMINDS.
Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for in-depth descriptions of specimen preparations (surgery, tissue slicing, etc.).
Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for in-depth descriptions of stimuli and stimulation protocols in neuroscience.
Field Museum of Natural History XCT Laboratory Core Facility
Field Museum of Natural History XCT Laboratory
Facility for computed tomography (3D) imaging of objects in the Field Museum and part of the Museum’s Core Lab Group. Includes two North Star Imaging (NSI) XCT scanners. The larger of the two scanners is an X5000 with a dual tube setup: one 450kV mini-focus tube, and one 225kV micro-focus tube. This scanner can house samples up to 500lbs and 1.2m in longest dimension, and has excellent penetrating power for imaging dense samples like fossils and meteorites. The smaller scanner is an X25 with a 150kV Hamamatsu tube, which is excellent for imaging smaller and/or less dense samples in extremely high resolution, such as small animal skeletons. In addition to the scanners, the lab is equipped with two high-powered computers for post-scan data processing. Available software includes NSI’s suite of inspection and reconstruction software, VG Studio, ORS Dragonfly, 3DSlicer, Meshlab, and Blender.
Paris Brain Institute Research and Development Unit Core Facility
Core provides development services for innovative hardware and software scientific equipment.
Software platform-independent application written in Java and R that provides both Graphical User Inteface and command-line interface to facilitate quality control of alignment sequencing data and its derivatives like feature counts. Used for advanced multi-sample quality control for high-throughput sequencing data.
Web isotopologue analysis tool for metabolomics experiment. Used to compute tracer analysis. Transforms raw mass spec AUC values into the percent representation of each isotopologue measured.
Software workflow that converts unprocessed reads into annotated binding sites using improved statistical framework. Used for analysis of CLIP-seq data and to process CLIP data from fastq files.
University of Texas MD Anderson Advanced Technology Genomics Core Facility
Advanced Technology Genomics Core (ATGC)
MD Anderson Advanced Technology Genomics Core
MD Anderson Advanced Technology Genomics Core Facility
Genomics core facility with goal to use instrumentation and innovative technical expertise in order to provide investigators with genomic data from comprehensive range of genomic services in timely manner. Services include Next-Generation Sequencing, Sanger Sequencing Single Cell Sequencing, Microarray Services, Fluorescent Fragment Length Analysis, nanoString nCounter Analysis, Bionano Optical Genome Mapping, Spatial Transcriptomics, Nanopore Sequencing.
University of Texas MD Anderson Cytogenetics and Cell Authentication Core Facility
MD Anderson Cytogenetics and Cell Authentication Core
MD Anderson Cytogenetics and Cell Authentication Core Facility
Facility offers conventional as well as molecular cytogenetic services including karyotyping, analysis of genomic instability, fluorescence in situ hybridization, telomere analysis, Spectral Karyotyping, species identification, inter-species and intra-species cell line contamination, STR fingerprinting service for cell line authentication, mycoplasma contamination testing and distribution of cell lines.
Mutation calling using a Markov Substitution model for Evolution
Software tool for detecting somatic point mutations in high throughput DNA sequencing data of tumors. Used for modeling evolution of allelic composition of tumor and normal tissue at each reference base. Adopts sample-specific error model to depict inter-tumor heterogeneity, which greatly improves overall accuracy.
Software tool for estimating genome copy numbers from high throughput DNA sequencing data. Allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Used to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
Software Python toolkit for mutational signature analysis. Used to estimate mutational signatures from somatic mutations in genome.
Software tool to distinguish host and graft reads from next generation sequencing assays of xenograft samples. Performs classification of xenograft-derived sequence read data.
Born of the desire to systematize analyses from The Cancer Genome Atlas pilot and scale their execution to the dozens of remaining diseases to be studied, GDAC Firehose now sits atop terabytes of analysis-ready TCGA data and reliably executes thousands of pipelines per month.
Medical image analysis software to measure, segment and analyze multi-slice scanner data.
Software R package used for calling Copy Number Variations from single-cell ATAC data.
University of Nebraska Medical Center Bioassay Core Facility
University of Nebraska Medical Center Bioassay Core
Core provides equipment, personnel, and protocols for routine and advanced cellular and molecular assays for research.
University of Texas at Austin Shared Instrumentation Facility
The University of Texas at Austin Shared Instrumentation Facility
Facility provides access to and operational support for easy-to-operate equipment for sample preparation and analysis, including gel imagers, plate readers, and qPCRs. They provide training on instrument operation and grant access for independent use after completed training.
Brandeis University Louise Mashal Gabbay Cellular Visualization Center Electron Microscopy Core Facility
Brandeis Electron Microscopy Facility- The Louise Mashal Gabbay Cellular Visualization Center
Brandeis University Brandeis Electron Microscopy Facility
Brandeis University Louise Mashal Gabbay Cellular Visualization Center Electron Microscopy Facility
Facility offers preparation and visualization ranging from standard 2D EM methods to high resolution 3D cryo-EM. Instruments, training and assisted use are available for Brandeis faculty, staff, and lab members, as well as members of the broader scientific community, including other academic institutions and for-profit organizations.
System automates sample imaging, imaging analysis, and cell segmentation, delivering high-resolution, high-throughput imaging without compromising sensitivity. Powered by MERFISH technology, MERSCOPE Ultra includes high-performance analysis computer, along with the necessary reagents and software to accurately quantify and localize RNA and protein in tissue samples. High-resolution in situ spatial genomics platform that offers tissue-wide view of up to 1000 custom genes at single-cell resolution.
Biotechnology company in Cambridge, Massachusetts, developing the next generation of genomic profiling tools that enable researchers to gain new insight into the biological systems that underlie human health and disease with spatial context. The company's MERSCOPE platform enables massively multiplexed, genome-scale nucleic acid imaging with high accuracy and unrivaled detection efficiency at subcellular resolution.
Self-contained X-ray system for delivering precise radiation dosage to specimens in biological or small animal research laboratory. The shielded cabinet includes Adjustable Specimen Shelf, Sample Viewing Window and Beam Hardening Filter Holder.TouchRAD Control Panel is multi-user, password protected touch screen interface with transportable database that can track individual system usage.Passwords, programmed exposure settings, and database management are controlled by super-user.X-ray tube is used specifically for radiation therapy having highly homogenous beam. Options available include: Dose Measurement & Control, Motorized Specimen Shelf,Turntable, Fixed Beam Collimators, Adjustable Collimator, and Specimen Holding Fixtures.
University of Louisville Biophysical Core Facility
Biophysical Core Facility supports structural biology studies focused on characterization of biophysical properties of biomolecules and their interactions with binding partners or novel drug candidates. Offers range of biophysical techniques for initial screening of hit/lead compound binding as well as rigorous characterization of the thermodynamic and hydrodynamic properties of various biological macromolecules (most commonly proteins and nucleic acids), macromolecular association reactions, and ligand-macromolecule interactions. Biophysical techniques include differential scanning fluorimetry, microscale thermophoresis, isothermal titration calorimetry, differential scanning calorimetry, circular dichroism spectroscopy, fluorescence spectroscopy, absorbance spectroscopy and analytical ultracentrifugation.
Website to identify the effects of certain gene mutations on splice behaviour.
Compact, dual-channel fluorometer designed to provide highly sensitive fluorescent detection when quantifying nucleic acids. Fluorometer is optimized with preprogrammed settings for Promega QuantiFluor Dye Systems (QuantiFluor dsDNA, RNA and ssDNA Systems) to quantitate nucleic acids and offers flexibility to create customized methods and quantitation settings for other fluorescent dyes.
Software set of command-line and R tools for performing Random-walk with performing Random-walk on multiplex networks in any species.
Software package to analyze amino acid content and hydrophobicity profile of given set of protein sequences in fasta file. Used for analysis of amino acid composition and hydrophobicity of test sequences from fasta files.
Software tool as implicit or explicit water model based docking with Autodock vina engine, supporting pharmacophore /position constrained docking.Facilitates drug design with support for explicit or implicit waters, pharmacophore or position-constrained docking, and external torsion parameters (akin to amber/gaff/charmm force fields). Water Model supported protein-ligand docking with Autodock Vina engine.
Software tool as trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
Software fast, reference-independent, allele-aware scaffolding tool based on Hi-C data. Allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules.
Software application provides dataset of all student-system interactions collected over 2 years by Santa, multi-platform AI tutoring service with more than 780K users in Korea available through Android, iOS and web.
Software tool to determine contribution of known mutational processes to tumor sample. Delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.
Bertin Technologies | Precellys Minilys Personal Tissue Homogenizer
Small sample tissue homogenizer for 0.5mL or 2mL tubes at 3.000, 4.000 or 5.000 rpm.
International registry for wide range of conditions that may be associated with difference or disorder of sex or pubertal development. Registry platform and network that aims to improve clinical practice, research and understanding of wide range of rare conditions affecting sex development and maturation through sharing of knowledge and experience.
University of Pennsylvania School of Medicine Advanced Core for Microscope Engineering Core Facility
Advanced Core for Microscope Engineering (ACME)
University of Pennsylvania Advanced Core for Microscope Engineering (ACME)
University of Pennsylvania School of Medicine Advanced Core for Microscope Engineering (ACME)
Core provides custom built ad hoc optical microscopy solutions, advanced image analysis, and consultation services to researchers across the Penn campus and beyond.
Cancer Therapeutics Response Portal (CTRP)
Cancer Therapeutics Response Portal (CTRP) links genetic, lineage, and other cellular features of cancer cell lines to small-molecule sensitivity with the goal of accelerating discovery of patient-matched cancer therapeutics. CTRP can be mined to develop insights into small-molecule mechanisms of action and novel therapeutic hypotheses, and to support future discovery of drugs matched to patients based on predictive biomarkers.
University of Western Australia Genomics WA Core Facility
University of Western Australia Genomics WA
Core provides consultation, expert advice and streamlined library preparation, next generation sequencing and data analysis services.
TUD Dresden University of Technology DRESDEN-concept Genome Center
TUD Dresden University of Technology DRESDEN-concept Genome Center Core Facility
Technology platform offering infrastructure and expertise in omics technologies, sequencing and data analysis. Organized in Technology Units: Short-Read, Long-Read, Single-Cell, Spatial Omics, Bioinformatics, and OpenLab.
Free online tool for performing codon optimization to improve gene expression. GenScript’s patented algorithms are integrated into the tool to optimize the computing capability of high-performance sequence generation. Used to optimize design of wild type or recombinant gene sequences towards higher expression in prokaryotic and mammalian expression systems.
Agilent | NovoCyte Penteon Flow Cytometer
NovoCyte Penteon Flow Cytometer Systems 5 Lasers
Provides flexibility to choose from up to 30 fluorescence channels utilizing up to 5 lasers with up to 30 independent detectors.
Thermo Fisher: Sartorius | IncuCyte SX5 Live Cell Analysis System
Live-cell imaging and analysis system. It leverages up to five total fluorescence channels (up to three simultaneously) including long wavelength, low phototoxicity NIR channel that makes it ideal for long-term time-lapse experiments. Offers high-resolution imaging, real-time kinetic monitoring and automated analysis capabilities.
Flow-based reader, is multiplexing platform from Luminex with fast read time, compatibility with both 96- and 384-well plates, and ease of integration with front-end automation systems for high-throughput applications. Can analyze up to 500 analytes in single sample and is compatible with all R &D System Luminex assays and Quantist Analysis Software.
Sony biotechnology | MA900 Multi-Application Cell Sorter
MA900 system include patented micro fluidic chip-based design, comprehensive fluidic controls, and advanced automation that simplifies operation to make sorting less subjective and improve reliability. Provides up to 14 parameters from 4 lasers with possibility to choose from 4 excitation lasers—488 nm, 405 nm, 561 nm, and 638 nm—on two beam spots. Free-form PMTs enable detection of fluorescence signals from each beam spot, allowing detection of up to 12 fluorescence parameters and two scatter parameters.
Compact analyzer that fits inside the flow hood for sterile and safe sample handling. Used to measure the avidity between immune cells and their targets, enabling to identify the most potent immunotherapeutic effector cells.
Spectral Instruments | Imaging Ami HTX system
General purpose imaging system capable of fluorescence, luminescence, and photographic imaging. Includes x-ray imaging capability.
Biotech company dedicated to advancing the frontiers of CRISPR cell and gene therapies through CRISPR technology and expertise. Provides genome engineering solutions and access to CRISPR solutions.CRISPRevolution is a line of products from Synthego and features synthetic guide RNA products designed to accelerate CRISPR/Cas9 and Cpf1 genome engineering research.
Design for chronic electrophysiology implant. Light-weight, can be used in head-fixed or freely moving mice, and is capable of probe recovery for multiple reuses of probes. Includes 3D print designs and step by step instructions for surgery, experimental sessions, and explantation. System includes micro drive, 3D printable Faraday cage, and miniaturized head-fixation system.
Penn State Critical Illness and Sepsis Research Center Core Facility
Penn State Critical Illness and Sepsis Research Center
Offers centralized access to critical care clinicians and researchers from diverse disciplines, fostering multidisciplinary collaboration. Supports investigators seeking intramural or extramural partnerships to advance research on sepsis and critical illness. Expands institutional biobanks by incorporating datasets and research specimens from adult and pediatric patients with sepsis. Utilizes immunologic assays and machine learning techniques to investigate different subtypes of sepsis.Develops translational rodent models that are relevant to the study of critical illness.Provides resources to educate clinicians, trainees and patients about septic illness.
Software R package for clustering and enhancing resolution of spatial gene expression experiments. Clusters low-dimensional representation of gene expression matrix, incorporating spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.
Conditional AutoRegressive Deconvolution
CARD: Conditional AutoRegressive Deconvolution
Conditional autoregressive-based deconvolution
Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations.
Thermo Fisher | TSQ 9000 Triple Quadrupole GC-MS/MS system
Triple quadrupole mass spectrometry system to study liquid, gaseous or solid samples. Mass analyzer enables absolute quantification of low-concentration metabolites. Designed for complex sample matrices in high-throughput applications. ExtractaBrite or AEI configuration are used to maximize uptime between routine maintenance interventions. The wireless ExtractaBrite ion source is heated throughout and includes the first RF region, commonly the first place susceptible to ion burn. This design ensures high matrix tolerance for high throughput applications. The AEI source is also heated throughout, with RF lenses and benefits from an innate ultra-robustness due to a more tightly focused ion beam, limiting ion burn on the source lenses.
Thermo Fisher | TRACE 1300 Gas Chromatograph
Intuitive single-button gas chromatography system, that provides ease of use with minimal instrument interaction and full data system control. Offers user-exchangeable, instant connect injector and detector modules and fast oven performance with exceptional retention time stability. Used for detecting wide range of compounds and it is sensitive and user friendly.
University of Alberta Precision Human Health Laboratory Core Facility
PHHL - Precision Human Health Laboratory
University of Alberta PHHL - Precision Human Health Laboratory
Core to advance understanding of mechanism of vascular dysfunction in chronic disease, identify how vascular dysfunction contributes to exercise intolerance, evaluate how exercise training improves vascular dysfunction and exercise intolerance using innovative clinical trial designs.
Medical College of Wisconsin Oxford Instruments Center for Advanced Microscopy Electron Microscopy Core Facility
MCW-Oxford Instruments Center for Advanced Microscopy- Electron Microscopy Core
Medical College of Wisconsin MCW-Oxford Instruments Center for Advanced Microscopy- Electron Microscopy Core
Institutionally available research service unit managed on behalf of the Medical College by the Department of Cell Biology, Neurobiology and Anatomy. OCAM-EM encompasses both Light and Electron Microscopy services.
Feature Representation Enhancement End-to-end Protein Interaction Inference
Software application encompassing autonomous feature extraction and feature representation enhancement for PPIs and protein complexes inference. FREEPII establishes feature maps that are consistent with model training, and emphasizes learning the feature representation of proteins rather than the feature representation of PPI, reducing the computational complexity from N^2 to N (N: number of proteins). FREEPII uses protein sequences to expand the information available for calculating data similarity between proteins. Furthermore, it introduces network-level information into the final feature representation to rescale the strength of interactions present in CF-MS data.
Web tool for comparison of gene expression in normal, tumor and metastatic tissues.
Portal provides access to cancer genomic data from variety of analyses: clinical, copy number, miR, miRseq, mRNA, mRNAseq, mutation and pathway analyses. Provides comprehensive suite of interdependent analyses of those data, including: correlations, clustering, and GISTIC and MutSigCV. Companion portal to the Broad Institute GDAC Firehose analysis pipeline, and was developed to cull and analyze data generated by The Cancer Genome Atlas (TCGA), which characterizes and identifies genomic patterns in human cancer models.
Software tool as Nanopore basecalling using Squeezeformer network to improve basecalling accuracy over recurrent neural network (RNN)-based model and Transformer-based models.
Collaborative Cohort of Cohorts for COVID-19 Research
Portal provides information about nationwide study of more than 50,000 individuals to determine factors that predict disease severity and long-term health impacts of COVID-19.
GloMax 96 Microplate Luminometer Software
Promega glomax software for older but still functional luminometer models. GloMax 96 Software requires that Microsoft Excel is also installed on the PC. GloMax 96 Software is compatible with Excel 2003, 2010 and 2013 versions.
Montana State University Cryo-EM Core Facility
Montana State University - Cryo-EM Core Facility
Core provides single particle analysis and cryo-electron tomography. Instrumentation includes 200 kV Talos Arctica with Gatan K3 camera, 120 kV Tecnai Spirit, and Vitrobot Mark IV allowing imaging of biological structures at single nanometer to sub-nanometer resolutions, and thus enable 3D modeling of cells, viruses, proteins, nucleic acid, and other soft matter at the atomic level.
Montana State University Imaging and Chemical Analysis Laboratory Core Facility
Montana State University - Imaging and Chemical Analysis Laboratory
Facility supports basic and applied research and education in all science, engineering, and STEM disciplines. Specializes in complementary surface, interfacial, and bulk characterization of materials via high-resolution imaging and spectroscopy. The lab promotes interdisciplinary collaboration between research, educational, and industrial fields.
Montana State University Social Data Collection and Analysis Services Core Facility
Social Data Collection and Analysis Services
Core enables collection of high-quality data for researchers employing variety of social and behavioral methods. This facility provides tools necessary for researchers to study interactions between human systems and other complex phenomena like public health and ecosystems.
Benaroya Research Institute Cell and Tissue Analysis Group Core Facility
Benaroya Research Institute Cell and Tissue Analysis Group
Core offers flow cytometry, imaging, and histology resources.Provides expertise in the fields of imaging, histology, and flow cytometry, physical space and instruments, critical support through the whole process, from hands-on training to experiment design and data analysis.
Montana State University Cellular Analysis Core Facility
Montana State University Cellular Analysis Core
flow cytometric analysis and cell sorting
Core provides access to functional, up-to-date equipment for flow cytometric analysis and cell sorting, histological samples preparation, and single cell RNA sequencing which is essential for all researchers in immunology, infectious disease, and cell biology and is highly useful for scientists in other related fields.
Thermal Imaging camera. Pro-Series Infrared Camera with Ignite Cloud.
Multi-mode microplate reader that measures chemical, biological, and physical reactions in microplates. It comes equipped with our LVF Monochromators, filters, and spectrometer. The instrument is upgradable and can be equipped with non-isotopic detection technologies:UV/vis absorbance, Fluorescence intensity, including FRET,Luminescence (flash and glow), including BRET,Fluorescence polarization/anisotropy,Time-resolved fluorescence, including TR-FRET AlphaScreen / AlphaLISA / AlphaPlexTM. Atmospheric Control Unit, temperature incubation, multiple shaking, well scan and reagent injectors make the CLARIOstar Plus the ideal platform for any live cell-based assay.
Thermo Fisher: Invitrogen | iBright FL1500 Imaging System
System to capture images and analyze data from western blots and gels. Supports main imaging applications of fluorescent, chemiluminescent, and colorimetric western blots, in addition to fluorescent stained nucleic acid gels, fluorescent stained protein gels, colorimetric stained protein gels, and colorimetric membrane stains.
Montana State University Geospatial Core Facility
Montana State University - Geospatial Core Facility
Provides equipment and team support to the workflow of all things geo-spatial from primary data collection using suite of different sensors and platforms to analysis that includes:Advanced mapping and geo-spatial analysis that leverage Uncrewed Aerial Vehicle (UAV) or drone-based sensors that use LiDAR, hyperspectral, thermal, orthoimagery, and Structure from Motion; High precision mapping and analysis using GPS and GNSS; Acoustic Doppler Profiles of rivers, reservoirs, and lakes;Data visualization and cartography;Remote sensing using active and passive sensors;Geo-spatial analysis, data development, and management;High Performance Computing infrastructure that leverages all of the above using open source and proprietary software.
Montana State University Montana Microfabrication Core Facility
Montana State University - Montana Microfabrication Facility
Micro and nanofabrication facility that offers range of processing and packaging capabilities including lithography, wet and dry etching, thin film deposition, dicing, wire bonding, metrology, and inspection.
Montana State University Nuclear Magnetic Resonance Core Facility
Montana State University - Nuclear Magnetic Resonance Facility
Montana State University Nuclear Magnetic Resonance Facility
Core provides open access availability to NMR spectroscopy instrumentation, training and sample preparation. Facility can be accessed individually or as full service center. NMR Facility has a total space of ~2,500 sq ft. divided among 3 rooms fully constructed with considerations for cooling, in-place floor dampening infrastructure and space for wet lab/sample preparation. Facility specializes in small molecule structure determination, small molecule characterization, biomolecular/protein structure determination, qualitative and quantitative NMR analysis, and small molecule purification from wide variety of sample sources.
BenchMark XT automated slide preparation system
Automated slide preparation system to expand test menu, process more slides, and improve turnaround times. Fully automated, random-access platform allows simultaneously run IHC and ISH tests and process patient case all at once. Can be used for CINtec PLUS preparation.
BD Biosciences | PrepStain Slide Processor
Becton Dickinson PrepStain Slide Processor
Slide processor to produce BD SurePath Liquid-based Pap Test slides. Liquid based thin layer cell preparation process intended as replacements for conventional gynecologic Pap smears, for use in screening and detection of cervical cancer, pre-cancerous lesions, atypical cells and all other cytologic categories.
Karolinska Mammography Project for Risk Prediction of Breast Cancer
Karolinska Mammography Project for Risk Prediction of Breast Cancer. Research group at Karolinska Institutet created the world’s best characterised breast cancer cohort with the aim to reduce mortality and incidence in breast cancer through translational research focusing on breast cancer screening and prevention.
2015 PQStat Statistical Calculation Software
Software application for statistical calculation.
Software R code for multi-modal analysis to delineate cell types using electrophysiology. Interpretable in vivo neuronal cell type identification using multi-modal analysis of electrophysiological data.
Massachusetts Institute of Technology Koch Institute High Throughput Sciences Core Facility
Massachusetts Institute of Technology Koch Institute High Throughput Sciences
Core offers automation and screening capabilities. Equipped with environmentally-controlled high-content microscopes, automated liquid handlers, plate washers and readers, and robotic platforms, HTS aims to accelerate experiments from small-scale assays to large screening campaigns.
Fully automated slide preparation and staining. Processes BD SurePathTM Liquid-based Pap test and Non-Gynaecological samples. Integrates slide creation and staining from enriched cell pellet. Allows for random sample loading.
University of Manitoba Grex High Performance Computing Core Facility
Grex High-Performance Computing system at University of Manitoba
Core offers computing and storage resources, along with support and training. Currently, Grex system consists of over 10,000 CPU cores connected via low-latency InfiniBand interconnect, several GPU compute nodes, 2 Petabytes of high-performance Lustre storage, and tape backup system. System also provides for condominium model of hosting researcher-contributed hardware funded by Canada Foundation for Innovation (CFI) and other granting agencies.
Northwestern University GIANTFab Core Facility
The Glovebox Inert Atmosphere (N2) Thin-film Fabrication and Testing (GIANTFab)
Core provides equipment to manufacture and test thin-film devices without ever exposing them to air or water, allowing measurements of device performance unaffected by environmental degradation.
Standard BioTools | CyTOF XT mass cytometer
Fully automated and affordable cytometer to simplify and standardize deep single-cell profiling studies.
University College London Darwin Research Core Facility
University College London Darwin Research Facility
Facility provides diverse range of equipment, expertise and training in field of biochemistry, molecular, structural and cellular biology. Facility consists of several research laboratories and support areas.
Molecular Devices | SpectraMax i3x Multi-Mode Microplate Reader
SpectraMax i3x Multi-Mode Microplate Reader
Microplate reader can perform wide range of essential cell-based and biochemical assays using included absorbance, fluorescence, and luminescence detection modes.
Standard-sized automated analyzer with its single-channel design, it can run 1~96 samples. Supports various types of applications, including DNA, RNA and protein fragment analyses and high-voltage fast analysis.
Weizmann Institute of Science Curated Cancer Cell Atlas
Collected, annotated and analyzed cancer scRNA-seq datasets. Data from different studies to reveal patterns of transcriptional ITH across tumour samples.
Interactive web-based application to facilitate data integration, discovery, and hypothesis generation across diverse Common Fund programs' datasets, highly processed data can be converted into gene-, metabolite- and drug-set libraries.
Web platform for large-scale public data reuse to model immunotherapy response and resistance. Provides integrated large-scale omics data and biomarkers on published ICB trials, non-immunotherapy tumor profiles, and CRISPR screens.
Montana State University Animal Resources Center Core Facility
Montana State University - Animal Resources Center
AAALAC approved animal research facility to study diverse number of animal species. Core maintains animal housing rooms, observation rooms, and procedure rooms at BSL 1 and 2 containment levels. The ARC is supported by certified veterinarians and animal care technicians who provide technical support and veterinary care.
University of Luxembourg LCSB Bioimaging Platform Core Facility
University of Luxembourg LCSB Bioimaging Platform
Bioimaging Platform provides access to and support for wide variety of advanced microscopy and flow cytometry instruments, enabling researchers to perform studies from the tissue level and down to sub-cellular scales. Provides access to analytical imaging technologies. As such, the platform comprises of advanced microscopy systems for high resolution studies of fixed and live samples as well as for low-phototoxicity imaging of whole organs and organisms.Bioimaging platform includes seven advanced microscopy systems, two flow cytometers and several high-performance analysis workstations.
Columbia University Confocal and Specialized Microscopy Shared Resource Core Facility
Columbia University Confocal and Specialized Microscopy Shared Resource
Confocal and Specialized Microscopy Shared Resource
Advanced microscope systems for multidimensional optical imaging of living and fixed cells and tissues. Microscopy technologies include confocal, super-resolution (Airyscan and SMLM), TIRF, and wide-field microscopy as well as plate reading and laser capture microdissection. Analysis workstation and software are available, with custom pipeline development for processing, analysis, and visualization.
Field Museum of Natural History Pritzker Laboratory for Molecular Systematics and Evolution Core Facility
Field Museum of Natural History Pritzker Laboratory for Molecular Systematics and Evolution
Field Museum Pritzker Laboratory for Molecular Systematics and Evolution
Pritzker Laboratory for Molecular Systematics and Evolution
Interdepartmental, multiuser core facility dedicated to genetic analysis and preservation of the world's biodiversity. Provides equipment used in molecular biology enabling to pursue study of genetic diversity throughout tree of life and at all taxonomic levels, from populations to classes to phyla of organisms.
Benaroya Research Institute Human Immunophenotyping Core Facility
Benaroya Research Institute Human Immunophenotyping Core
Core provides access to technologies and services enabling study of human immune-mediated diseases. Offers expertise in human immunology along with innovative assays and technology. Core specializes in high-parameter single-cell assays utilizing conventional, spectral, and mass cytometry (CyTOF), which can be paired with genomic and bioninformatic analyses through our connections with other outstanding BRI cores. Other services include cell sorting, short-term in vitro assays, DNA/RNA extraction, qPCR, and ELISA or multiplex protein analysis (Luminex), guidance on study design and training on new technologies, execution, data analysis and interpretation.
Software Python toolbox for fitting Hierarchical Sequential Sampling Models using Bayesian methods.
Software R package to run genome-wide association study (GWAS) and genome-wide by environment interaction study (GWEIS) scans using genetic data stored in binary dosage file.
University of Kentucky Flow Cytometry and Immune Monitoring Core Facility
UK Flow Cytometry & Immune Monitoring core facility
University of Kentucky Flow Cytometry and Immune Monitoring Core (FCIM-UKY)
University of Kentucky Flowcytometry and Immune Monitoring Core
Core supports research requiring flow cytometry techniques in basic and translational research. Provides access to equipment, and technical and scientific expertise for comprehensive analysis of immune responses. Uses standardized and optimized SOPs and study protocols to obtain reproducible and quality results for our collaborating investigators in cost-effective manner.
University of Kentucky Research Mass Spectrometry and Proteomics Core Facility
Research Mass Spectrometry and Proteomics Core
University of Kentucky Research Mass Spectrometry and Proteomics Core
Mass spectrometry core lab performing proteomics, small molecule, and lipidomic analyses. Provides access to advanced analytical equipment for quantitation and structural analysis. Offers assistance in sample preparation, method development, acquisition, and data analysis.
Northwestern University Keck Interdisciplinary Surface Science Core Facility
Keck Interdisciplinary Surface Science Facility (Keck-II)
Northwestern University Keck Interdisciplinary Surface Science Facility (Keck-II)
Core facilitates research, collaboration, education and outreach in all science from soft biological matter to hard physical matter, specializing in surface analysis and nano-scale characterization. Instruments include Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), X-ray Photoelectron Spectroscopy (XPS), Fourier Transform Infrared Spectroscopy (FT-IR), Confocal Raman System, High Resolution Stylus Profilometer, 3D Optical Microscope, Spectroscopic Ellipsometer, and Zetasizer.Staff provides hand-on training, collaboration and assistance.
Northwestern University Electron Probe Instrumentation Center EPIC Core Facility
Electron Probe Instrumentation Center - EPIC - part of NUANCE
Northwestern University Electron Probe Instrumentation Center - EPIC - part of NUANCE
Offers wide range of electron microscopy (both transmission and scanning), accessory instrumentation, and expertise to the scientific and engineering community through education, collaboration, and service. Provides facilities for preparation and examination of many types of bulk and thin specimens (foils/films), fine particles, and replicas, including biological materials, by transmission and scanning electron microscopy.
Massachusetts General Hospital NGS Core Facility
Massachusetts General Hospital MGH NGS Core
Core offers sequencing, upstream library construction (bulk RNA/DNA, single-cell), and post-sequencing analysis. Core uses Illumina NextSeq 2000 sequencers (and a MiSeq). Single-cell (fresh, frozen, FFPE) libraries (3' & 5' RNA-Seq, CITE-Seq, ATAC-Seq, Multiome, FLEX) are made with 10X Chromium X.
mice: Multivariate Imputation by Chained Equations
Multivariate Imputation by Chained Equations
Software package implements method to deal with missing data. The package creates multiple imputations (replacement values) for multivariate missing data.Various diagnostic plots are available to inspect the quality of the imputations.
Field Museum of Natural History Biomolecular Clean Laboratory Core Facility
Facility dedicated to study of degraded and low DNA yield samples, such as environmental DNA, historical DNA, or ancient DNA. Offers positive pressure lab spaces that follow strict decontamination procedures to prevent human, bacterial, and fungal contamination. It is physically isolated from tissue samples or polymerase chain reaction (PCR) products to avoid contamination from samples with higher DNA concentration and quality. The space has dedicated equipment necessary for DNA extraction and PCR-free sample preparation.
Fully automated patch clamp system which records from either 4 or 8 cells simultaneously. Automated electrophysiology machine.
Software application as genomic k-mer counter and sequence utility.
Software Foreign Contamination Screening - GX source code. Part of NCBI’s Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes.
Standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences.
Software Python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads. Used to find, circularise and annotate mitogenome from PacBio assemblies.
Software genome completeness evaluation tool based on miniprot.
Seattle Childrens Research Institute Behavioral Phenotyping Core Facility
Seattle Childrens Research Institute Behavioral Phenotyping Core
Core dedicated to the protocol driven collection, analysis, and reporting of behavioral data using a blend of classic and innovative assays. Supports neuroscience, psychology, pharmacology, genetics, cancer, and development by providing advanced tools and expertise for the precise measurement and interpretation of behavior.
UCSF Helen Diller Family Comprehensive Cancer Center Flow and Cell Sorting Core Facility
Provides access and training on two FACS Calibur benchtop cytometers, one FACS Canto II multi-laser digital cytometer, one FACS Aria II cell sorter, one FACS Aria III cell sorter, and one Sony SH800 cell sorter. These systems are primarily used for the rapid analysis and sorting of single-cell suspensions. To analyze the light scatter and fluorescence characteristics of a cell population, one of the benchtop machines is appropriate. For more complex assays requiring more than four differentiating markers, then the high-end multi-laser Canto II system would work well. To rapidly retrieve or sort a particular sub-group of cells from a mixed sample, then a cell sorter would be required.
Company from India specializes in Innovative Organic Chemistry and Synthesis of Unique Complex Molecules, Stable Isotope Labelled compounds and Metabolites.
DNA synthesis company provides comprehensive services including gene synthesis, protein expression, gene editing, etc., supporting one-stop solutions for global users.
Dabur Research Foundation (DRF), established in 1979, is Indian Contract Research Organization offering comprehensive preclinical services in Drug Discovery and Development. Focused on identifying potential lead molecules and developing drugs to conducting IND enabling studies.
Software tool to filter short artificial deletion variations by Oxford Nanopore Technologies (ONT) R9 and R10 flow cells and chemistries.
Software tool to embed bedgraph data into Pretext contact maps.
Repository of software curation tools. Contains curation tools guide.
Institute was created to support and develop research on the brain and nervous system, serving collaborative, interdisciplinary model conducive to innovation and breakthrough discoveries.
Northwestern University NUANCE SPID Core Facility
SPID provides imaging instrumentation and support facilities for atomic to molecular imaging. Supports broad range of nanoscale science and technology characterization needs at nanoscale by providing resources coupled with expert staff. Research at SPID encompasses physical and chemical sciences, engineering and life sciences, and has a strong inter-disciplinary emphasis.
Software R package for joint analysis of multiple single-cell RNA-seq datasets. Used to wire together large collections of single-cell RNA-seq datasets, which allows for both identification of recurrent cell clusters and propagation of information between datasets in multi-sample or atlas-scale collections.
Northwestern University Program Evaluation Core Facility
Program Evaluation Core staff and faculty collaborate with investigators to design evaluations plans for grant proposals, collect, analyze and interpret data, write reports and co-develop strategies for program improvement.
University of Kentucky Magnetic Resonance Imaging and Spectroscopy Center Core Facility
Magnetic Resonance Imaging and Spectroscopy Center (MRISC)
Service and consultation core supporting basic and clinical research. Provides advanced 3T Siemens PRISMA scanner with high performance gradients, echo-planar whole body imaging and hydrogen spectroscopic capabilities for both human and animal studies. For dedicated animal studies Bruker/Siemens 7T MR scanner has been installed.
Software comprehensive genome annotation pipeline with precision control through semi-supervised random forest gene model filter.
Commercial company dedicated to development of new products and technologies, with steadfast commitment to continuous innovation. Provides assistance to researchers from pharmaceutical, biotechnology, government, and academic organizations worldwide in expediting the drug discovery and development process for infectious diseases.
Biotechnology company specialises in providing protein expression services. Services include all steps from gene expression and purification to protein expression and purification, including selection and optimization of multiple expression platforms including bacterial, yeast, insect cell, and mammalian cell platforms.
Ace Therapeutics offers biomarker services for anti-psychotic drug development. Provides psychiatric biomarker testing services. Can perform experiments from variety of biological samples: tissues, cell lines, and RNA.
High-Precision Optical Fiber-Based Lickometer
Low-cost open-source lickometer that combines restricted infrared beam defined by optical fibers, with poke design that allows easy access to the tongue while limiting access of other body parts and external light sources. This device also includes features for detecting nose pokes and presenting visual cues during behavioral tasks. Used to study lick microstructure in combination with other techniques, such as imaging of neural activity, in freely moving mice.
Paris Brain Institute Quantitative Cellular and Molecular Imaging Core Facility
Core provides expertise in optical microscopy, electron microscopy, and image analysis for neuroscience research. The platform is open to all researchers. Offers access to advanced technologies, including electron microscopy, confocal microscopy, two-photon imaging, and super-resolution microscopy.
Paris Brain Institute PRISME Core Facility
Core facility dedicated to the study of human cognition and normal and pathological human behavior either via computer tests or in simulations, including using virtual reality.
Ludwig Maximilian University Hospital Munich Flow Cytometry Core Facility
Core Facility Durchflusszytometrie des Klinikums
Core Facility Flow Cytometry of the LMU Clinic
Core Facility for flow cytometry at the Ludwig-Maximilian-University Hospital Munich. Provides access and services for flow cytometry and cell sorters.
Salk Institute Single-Cell and Spatial Omics Core Facility
Single-Cell and Spatial Omics Core Facility at the Salk Institute
Core offers single-cell and spatial omics services. Provides consultation, expert guidance in experimental design, and technologies tailored for innovative research in genomics. Facility is equipped with 10x Genomics Chromium X and Xenium systems, Vizgen MERSCOPE, Bruker/NanoString GeoMx Digital Spatial Profiler, and nCounter MAX.
University of Louisville Medicinal Chemistry Core Facility
Core Facility provides essential medicinal and organic chemistry support for drug discovery. The core specializes in the lead optimization of an initial lead compound to improve biological activity and drug-like properties, and to elucidate structure activity relationships. Other services include the design and synthesis of fluorescent and isotopic probes, compound scale up (1 – 5 grams), and custom synthesis.
Agilent | Stratagene Mx3000P qPCR cycler
Real-time polymerase chain reaction (PCR) system used for quantitative PCR (qPCR) to measure and analyze nucleic acids in biological samples. Applications include gene expression analysis, pathogen detection, and DNA methylation analysis.
Microscopes International | uScopeMXII-20 Digital Microscope
Small size uScopeMXII-20 digital microscope comes with 20x/0.4NA 160mm conjugate objective. This model is suited to applications where very high depth of field is required. The uScopeMXII-20 has wider depth of field than higher power models of the uScopeMXII. So, tissue samples and smears can be thicker with more of the image in focus. This unit is able to produce very high-quality digital microscope while browsing or scanning an area of interest.
Software tool for rapid and standardized annotation of bacterial genomes via alignment free sequence identification. Implemented in Python 3 and runs on MacOS and Linux systems.
AutoDockTools: the Graphical User Interface for AutoDock
Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure.
Children's Hospital of Philadelphia Research Institute CHOP Gastrointestinal Epithelium Modeling Core Facility
Children's Hospital of Philadelphia Research Institute CHOP Gastrointestinal Epithelium Modeling (GEM) Core
CHOP Gastrointestinal Epithelium Modeling (GEM) Core
Core is component of the GEM Program collaborative research effort focused on accelerating discovery and innovation using patient tissue-derived organoids. GEM Core staff generate and maintain living biobank of tissue-derived organoids with matched original tissue and blood specimens and provide access to specialized training, protocols, and reagents.
University of Texas Southwestern Medical Center Dallas Metabolic Phenotyping Core Facility
University of Texas Southwestern Medical Center Dallas Metabolic Phenotyping Core
Academic core facility provides analytical and phenotypical measures to the scientific community. Provides services related to metabolic disorders (diabetes and obesity), cancer, aging neurological disorders, etc. Provides letters of support for grant proposals and research applications.
University of Kentucky Light Microscopy Core Facility
Core facility offers fluorescence, confocal, super resolution, multi-photon, laser capture and atomic force microscopy. Provides central preparatory laboratory and high-end computer workstations for data analysis and image processing. Technical support ranges from investigator training on instrumentation, allowing independent use, to complete processing of samples and final imaging by facility staff. The facility is GRP accredited, undergoes annual compliance checks and provides extensive standard operating procedures for all instrumentation.
Weighted Graph Anomalous Node Detection (WGAND)
Software tool designed to identify anomalous nodes in weighted graphs. By estimating expected edge weights and analyzing deviations, WGAND scores nodes to detect anomalies.
Software fast and flexible QC and signal summarization tool for long read sequencing data.
Software minimal tool for segmentation of irradiated tumor spheroids using optimized U-Net.
Software tool as virus-focused assembler that does both assembly and polishing into unified workflow. Viral genome assembler enables detection of subtle genomic variations that can significantly impact viral function and pathogenicity.
Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference.
Paris Brain Institute Electrophysiology Core Facility
Core develops solutions to meet your needs in electrophysiology data. Provides electrophysiology services to the neuroscience scientific community. Core has standard recording equipment such as patch clamp techniques or electroencephalographic (EEG) recordings.
Massachusetts Institute of Technology MIT BioMicro Center Core Facility
Massachusetts Institute of Technology MIT BioMicro Center
Integrated genomics/bioinformatics facility located at MIT. Provides Illumina HiSeq2000, NextSeq500 and MiSeq sequencing instruments as well as PacBio Sequel and Oxford Minion. Provides services in preparing Illumina libraries for high-throughput sequencing samples using several different methods, supports technologies including Agilent BioAnalyzer, AATI Fragment Analyzer, AATI FemtoPulse, Roche LC480 qPCR machines, automated liquid handling through Tecan Evo150s, TTP Labtech Mosquito HV. Supports 10X Chromium and single cell work using NamoCell single cell dispenser and custom oligo synthesis using Dr.Oligo 192. Supports informatics and bioIT tools. Core administers ~2PB of data storage on several platforms, including 600TB Isilon server. Hosts 400 processor Dell cluster and Dell Quad Core 2950 application server for Illumina sequencing and bioinformatic applications. All application servers and storage servers are interconnected by 1gigabyte private networks or by fiber optic lines and are administered by IT staff that are part of the BioMicro Center. Servers are configurable to provide secure data storage for clinical data if required.
Northwestern University School of Medicine SBDRC Skin Tissue Engineering and Morphology Core Facility
Northwestern University SBDRC Skin Tissue Engineering & Morphology (STEM) Core�
SBDRC Skin Tissue Engineering & Morphology (STEM) Core
Core provides services in human skin tissue procurement, isolation, and culture of human and murine skin-derived primary cells, 3D organotypic skin cultures, tissue processing, and basic histologic stains. The Core trains researchers in the development and use of these various techniques.
Miami University Center for Bioinformatics and Functional Genomics Core Facility
Center for Bioinformatics and Functional Genomics
Miami University Center for Bioinformatics and Functional Genomics
Core provides training and equipment. Instruments include Pacific Biosciences VEGA benchtop long-read system, Oxford Nanopore Technologies minION and an Illumina MiSeq Next Generation Sequencing instrumentation, ABI Capillary Electrophoresis Genetic Analyzer (3130xl); an Eppendorf epMotion 5073m NGS liquid handling workstation; Promega MaxwellRSC Nucleic Acid extraction robot; real-time qPCR instruments (Rotor-Gene Q with HRM, Bio-Rad CFX Connect, QuantStudio 7 Flex [384/96 well interchangeable blocks]), and Bio-Rad ddPCR QX200 system, laser Attune NxT Flow Cytometer for analysis, laser BD FACS Melody Flow Cytometer for sorting, UV NanoDrop spectro photometers (ND1000, ND2200), and NanoDrop (ND3300) Fluorospectrophotometer; Promega Quantus, Agilent Bioanalyzer 2100; Covaris M220 Ultrasonic Nucleic Acid Shearer, a Sage BluePippin, seven 96 well gradient capable PCR thermal cyclers, two thermally controlled table top centrifuges capable of accepting 96-well plates used for DNA template preparation; two Eppendorf ThermoMixer C mixing units (384 well PCR to 50 mL tube format), two benchtop micro-centrifuges, Molecular Devices SpectraMax iD5 microplate reader, KTA-FPLC with UV detector and fractions collector, UV-1600PC UV-VIS Spectrophotometer with Sipper module, AlphaInnotechHP Gel Imaging System, Bio-Rad ChemiDoc MP Imaging System, Bio-Rad Dodeca-Cell Criterion PAGE system, several Bio-Rad Mini-Protean Gel Apparatus, Bio-Rad IEF Focusing Cells; numerous power-packs for gel electrophoresis, DNA gel boxes, pipettors, multi-channel pipettors. Provides computers (Linux & Win10), including four Ubuntu O/S based workstations for genome assembly and related bioinformatics analyses. CBFG maintains paid licenses for CLC Genomics Workbench, CLC Main Workbench, BioBam OmicsBox, SnapGene, FlowJo 10, SoftMax 7.1, Biogazelle qBasePLUS, and CANOCO.
University of Idaho IIDS Genomics and Bioinformatics Resource Core Facility
IIDS Genomics and Bioinformatics Resource Core
University of Idaho IIDS Genomics and Bioinformatics Resource Core
Core provides access to technology, experience, and expertise in molecular biology methods.Offers expertise in bioinformatics needed to acquire, analyze, and visualize data generated from high throughput technologies used in genomics research. Services include Illumina sequencing,Bioinformatics and statistical analysis,PacBio sequencing,Oxford Nanpore sequencing,High-throughput DNA and RNA library preparation,Double-barcoded amplicon sequencing. GBRC also participates in many of the bioinformatic analyses from the projects including De novo genome and transcriptome assembly, RNAseq differential expression analysis, SNP calling, RAD sequence analysis, Dual-barcoded amplicon community analysis, Phylogenetic analysis, CRISPR transformant profiling,Speed congenics, Novel agriculture virus detection and assembly.
Northwestern University School of Medicine SBDRC Gene Editing, Transduction and Nanotechnology Core Facility
Transduction and Nanotechnology (GET iN) Core
Core provides services and R&D in cell engineering and gene expression modifications by using retro- and lentivirus, adenovirus, adeno-associated virus, shRNA/MIR and CRISPR-Cas9 genome editing methods.
Emory University EPC Genomics Core Facility
Core offers assistance in experimental design, sample preparation, library prep, sequencing, data analysis and bioinformatics. Provides experience working with non-human primate genomes and other non-standard genomes in addition to the more commonly studied human and mouse genomes. Provides expertise in the use of transcriptomics and genomics to study immune responses and repertoires.Houses Illumina NovaSeq 6000 and Illumina MiSeq.
Northwestern University School of Medicine SBDRC Translating Experimental Skin Testing with Immune Tracing, Informatics, and Technology Core Facility
SBDRC Translating Experimental Skin Testing with Immune Tracing
Core provides service, equipment, protocols, and training to help investigators differentiate healthy skin from skin with abnormal immune responses at the cellular and molecular level, to enable biomarker identification as well as to increasing our knowledge of skin immune responses.
TAMU College of Medicine Flow Cytometry and Cell Sorting Core Facility
TAMU College of Medicine Flow Cytometry and Cell Sorting Facility
Texas A and M University College of Medicine Flow Cytometry and Cell Sorting Facility
College of Medicine Flow Cytometry and Cell Sorting Facility (formerly SMACC) at Texas A&M Health provides cell analysis and cell sorting services and is managed by Department of Microbial Pathogenesis and Immunology.
University of Oklahoma Health Sciences Center OK INBRE Data Science Core Facility
University of Oklahoma Health Sciences Center OK INBRE Data Science Core
Core provides data science analysis support, training and promotion of data science education for undergraduate and high school students in the state of Oklahoma. Services include 1) Global analysis of gene expression data using custom spotted microarrays and commercial Affymetrix and Combimatrix arrays to examine gene expression patterns in mice, adenovirus-infected cells, and a variety of bacterial systems. 2) Genome annotation and comparative genomics analysis, including studies on several bacterial and viral pathogens important for human and agricultural disease. Informatics support for genome sequencing projects, annotation support, and post-sequence studies. Bioinformatics educational include analysis of laboratory data for DNA barcoding, instructional materials for protein structure analyses and phylogenetic analyses, and microbial and viral genome sequence annotation and analysis, career counseling to undergraduate students, both individually and in large groups, supervision of undergraduate summer interns and high school interns to enhance interest in pursuing bioinformatics as a career path, providing instructional materials for high school teachers interested in incorporating bioinformatics into their lesson plans.
FEI | Tecnai G2 Spirit BioTwin transmission electron microscope
Transmission electron microscope designed for general-purpose, high-resolution imaging of both biological and non-biological samples, offering capabilities like bright-field, dark-field, and diffraction modes, typically utilizing LaB6 electron gun and operating within voltage range of 20-120kV; it's particularly well-suited for analyzing the ultrastructure of delicate specimens with high contrast due to its "BioTwin" features, allowing for low-dose imaging of beam-sensitive samples like cryo-preserved biological materials.
Penn State Institute of Computational and Data Sciences Roar Core Facility
Provides advanced cyberinfrastructure resources including large scale compute and data storage. to the Penn State University research community under the operation of the Institute of Computational and Data Sciences
Penn State University Center for Immersive Experiences Core Facility
Visualization Hub provides immersive technologies, knowledge, and skills to the Penn State community with the goal to create leadership in immersive experiences by advancing the underlying science and integrating it into the academic spectrum through research, education, and outreach. Provides research and development support for immersive technology projects. Projects can range from developing virtual reality (VR), augmented reality (AR), mixed reality (MR) applications or experiences, access to VR/AR/MR hardware, digital twins, creating 3D models, etc.
Pennsylvania State University RISE Core Facility
Pennsylvania State University Research Innovations with Scientists and Engineers Core Facility
Research Innovations with Scientists and Engineers
Core team of computational scientists and software engineers provide serivces to bring high-performance computing to research projects under the Institute of Computational and Data Sciences at the Pennsylvania State University.
S220 Focused-ultrasonicator is based on Covaris Adaptive Focused Acoustics technology. Instrument designed for tissue homogenization, cell lysis, DNA or chromatin shearing, and other sample preparation steps. The system is comprised of the Treatment System which delivers the acoustic energy to the sample, the Safety System which protects users from inadvertently contacting the high intensity acoustic energy, and the Computer and Application Software which provides users an interface to control the device.
Software MATLAB toolbox for interacting with the Allen Brain Observatory.
Virginia Commonwealth University VCU Bioimaging and Applied Research Core Facility
VCU Bioimaging and Applied Research Core (BARC)
Virginia Commonwealth University VCU Bioimaging and Applied Research Core (BARC)
Core offers comprehensive instrumentation and technical support for all aspects of in vitro and in vivo pre-clinical non-human anatomical and molecular imaging. Studies may be conducted on samples prepared to exhibit characteristic features for a particular imaging modality. Within the intact environment, physiological and pathophysiological activity may be observed through imaging or numerous biological pathways and interactions involved in injury and disease progression, such as traumatic brain injury, cardiac disease, tumorigenesis, and therapeutic interventions.
Software tool for phasing and assembly of bacterial strains from long-read sequencing data (either Oxford Nanopore or PacBio). Given reference (or collapsed de novo assembly) and set of aligned reads as input, tool produces multi-allelic phasing, individual strain haplotypes and strain-specific variant calls. Used for phasing and assembly of strain haplotypes from long-read metagenome sequencing.
Open-source DataFrame library for data manipulation known for being one of the fastest data processing solutions on single machine. Features well-structured, typed API that is both expressive and easy to use. DataFrame interface on top of OLAP Query Engine implemented in Rust using Apache Arrow Columnar Format as the memory model.
Eastern Cooperative Oncology Group Performance Status Scale
ECOG Performance Scale describes patient’s level of functioning in terms of their ability to care for themself, daily activity, and physical ability (walking, working, etc.). Standard criteria for measuring how the disease impacts patient’s daily living abilities. Used to assess the functional status of patient.
World Health Organization Drug Dictionary
International reference guide for medicinal products maintained by the Uppsala Monitoring Centre. With its unique drug code hierarchy and extensive coverage, it provides consistent drug dictionary with exact terminology when coding concomitant medications. Dictionary is used to identify drug names and evaluate medicinal product information, including active ingredients and products’ anatomical and therapeutic classifications, from nearly 150 countries. Data covers both conventional medicines and herbal remedies. Data is continuously updated, with new releases twice a year, on 1 March and 1 September.
Uppsala Monitoring Centre; Uppsala; Sweden
Uppsala Monitoring Centre, located in Uppsala, Sweden, is the field name for the World Health Organization Collaborating Centre for International Drug Monitoring. UMC works by collecting, assessing and communicating information from member countries' national pharmacovigilance centres in regard to benefits, harm, effectiveness and risks of drugs since 1978.
Response Evaluation Criteria in Solid Tumors
Provides methodology to evaluate activity and efficacy of new cancer therapeutics in solid tumors, using validated and consistent criteria to assess changes in tumor burden. RECIST Working Group comprises representatives of the European Organization for Research and Treatment of Cancer (EORTC), National Cancer Institute (NCI) of the United States and Canadian Cancer Trials Group (CCTG), as well as several pharmaceutical companies. Its mission is to ensures that RECIST undergoes continued testing, validation and updating.
Web-based tool that screens for experiment-specific reference genes. Tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies.
Device to generate repetitive transcranial magnetic stimulation and is used in numerous fundamental and clinical research studies worldwide. Combines stimulation frequencies from 1Hz to 100Hz with touch screen interface which controls every aspect of stimulator’s control and operation.
Howard Hughes Medical Institute at Janelia Research Campus Viral Tools Shared Resource Core Facility
Core specializes in custom production with high titer, high standards, and fast turnaround. Provides services from designing viral constructs to troubleshooting experiments. Offers routine adeno-associated virus (AAV), rabies, and lenti/retrovirus vector production. Other viral vectors can be produced on as-needed basis.
Software R package to plot regression nomogram of regression objects. Covariate distributions are superimposed on nomogram scales and the plot can be animated to allow on-the-fly changes to distribution representation and to enable outcome calculation.
Software R package for estimation of time-dependent ROC curve and area under time dependent ROC curve in the presence of censored data, with or without competing risks. Confidence intervals of AUCs and tests for comparing AUCs of two rival markers measured on the same subjects can be computed, using the iid-representation of the AUC estimator.
Code for testing and operating NC4gate modules of modular gate system for autonomous control of rodent behavior. Fully customizable gate system that can be used in behavioral experiments involving rodent mazes (T-maze, Y-maze, radial arm, etc.).
Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis.
Software R package as data model, library and file format for storing and managing large amounts of data.
Software R package for Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data assembled using data from public repositories.
Thermo Fisher | Ion Torrent Genexus Integrated Sequencer
Ion Torrent Genexus Integrated Sequencer is part of the Ion Torrent Genexus System. Instrument that can automate library construction, templating, and sequencing in single-instrument run.
Instrument engineered to amplify specific genes (DNA or RNA), enable real-time detection and estimate absolute quantities.
Beckman Coulter | Allegra X-12R Refrigerated Centrifuge
Benchtop refrigerated centrifuge designed for routine processing, cell isolation, binding studies and separation, and more applications.
Element AVITI24 system is the benchtop platform enabling high-quality, low-cost sequencing and single cell multiomics in one powerful system.
Biotechnology company in San Diego, California focused on developing disruptive DNA sequencing and other omics technology for research markets.
Liquid chromatography-mass spectrometry (LC-MS/MS) system manufactured by AB Sciex, commonly used in research and analytical labs for high-sensitivity detection and quantification of chemical compounds in a sample, often used in fields like pharmaceuticals, environmental testing, and clinical research. atmospheric pressure ionization method used in this system allows for analysis of wide range of molecules.
Virginia Commonwealth University VCU Structural Biology Core Facility
Provides access to equipment, offering researchers capability to determine 3D structure of macromolecules and macromolecular complexes. Provides services for structure-based drug design, protein-ligand or DNA binding studies, testing mutational effects on target macromolecules, and finding the absolute stereochemistry of chiral compounds. Offers training, technical support, and collaborative opportunities, which are crucial for structural biologists and other researchers studying structure of biological macromolecules and other materials.Core encompasses X-ray crystallography, Cryo-Electron Microscopy (Cryo-EM), and Nuclear Magnetic Resonance (NMR) facilities, and is also closely associated with the School of Pharmacy Molecular Modeling facility.
Collection of open-source software used to create platforms for researchers to manage, share and access scientific data.
Proton-Transfer-Reaction Time-of-Flight mass spectrometer Data Analyzer
Software tool for analyzing HR PTR-TOF-MS data. GUI leads the user through the data analysis process which involves data selection, definition of the data analysis parameters and options, and an interactive edition of the data output. A series of graphical outputs is generated to allow for immediate and visual quality assurance. Output data are generated both in HDF5 and Excel file format.
IONICON ultra-sensitive PTR-TOF-MS - Trace VOC Analyzer,the PTR-TOF 1000 ultra, is the new benchmark for robust and compact real-time volatile organic compounds analyzer. Based on PTR-TOF 1000 platform, the PTR-TOF 1000 ultra offers outstanding sensitivity.
Cleveland Clinic Research Flow Cytometry Core Facility
Core provides investigators with resource for quantitative studies of cells, extracellular vesicles, and single-cell gene transcriptome analyses. Offers sample acquisition and analysis, cell sorting, and consultation for experimental design, interpretation and troubleshooting.
Software tool for integrating single-cell multimodal mosaic data. This framework represents single-cell data as graph structures and utilizes graph structures to preserve both local and global features of cells, maintaining topological structure of the data during dimensionality reduction. Additionally, the framework employs neighborhood graphs and contrastive learning to effectively eliminate batch effects.
Software tool enables full-resolution Human Leukocyte Antigen typing from sequencing data. Reconstructs entire diploid sequences of HLA genes and infers LOH events. Supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.
Software package to detect chromothripsis in whole-genome sequencing data.
Software R package for copy number prediction with correction for GC and mappability bias for HTS data.
Linetogel | Vu-C Chemiluminescence Imaging System
High-sensitivity imaging device used to imaging device for detecting and analysis signals in biological samples, commonly for Western blotting and other luminescent assays.
Software tool for quality control of short- and long-read sequencing data. Fast sequencing data quality metrics. Features adapter search, overrepresented sequence analysis, and duplication analysis and supports FASTQ and uBAM inputs.
Software segmentation toolkit to segment the Nanopore RNA signal. Preprocessing ONT-Nanopore RNA sequencing reads.
High-throughput experiment- and reference-guided database of traditional Chinese medicine.
University of Texas Institute for Personalized Cancer Therapy Cancer Genomics Laboratory Core Facility
Provides services and instrumentation including Illumina Next-Generation Sequencing, Single Cell Analysis and Spatial Transcriptomics. These techniques are developed and optimized by our lab scientists to deliver the highest-possible quality sequencing data from a wide variety of sample types such as peripheral blood, bone marrow, fresh frozen tissue and FFPE-derived tumor samples.
Software R package that enhances text rendering in ggplot2 by allowing the use of Markdown, HTML, and rich text formatting for annotations, labels, and titles in plots.
Software R package that provides scientific-themed color palettes for ggplot2, offering visually appealing and publication-quality color schemes inspired by scientific journals and data visualization standards.
Software tool for analysis of biological rhythms, particularly circadian rhythms, using curve fitting methods to model time-series data and determine key parameters such as period, amplitude, and phase.
Heart Rate Variability Analysis Software
Software tool used to assess heart rate variability.
Privately held German medical technology company headquartered in Munich, Bavaria. Brainlab develops software and hardware for radiotherapy and radiosurgery, and the surgical fields of neurosurgery, ENT and craniomaxillofacial, spine surgery, and traumatic interventions. Brainlab software and hardware devices create and enhance data to improve critical surgeries, radiosurgery treatments and operating room efficiency.
Augusta University Therapeutics Core Facility
Core offers services including assay development, FDA-drug library screening, unbiased compound screening, high-content imaging and screening. Facility can empower researchers to repurpose existing FDA-approved drugs and discover new compounds for drug development. Provides affordable platform for discovering therapeutic targets and interventions, supporting drug development from target identification to screening and validation. Features HTS facilities, including Biomek i7 Liquid Handling system, Pherastar FSX plate reader, ImageXpress Micro Confocal, and Pala cell sorter.
Software Python framework for integratig spatially resolved multi-omcis data. Framework capable of coordinating different spatial resolutions and sampling organizations between different spatial modalities to create one spatial omics dataset.
Algorithm for registration of stained fresh frozen serial images. Used for registration of stained histology images.
Software tool for ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash. Species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. Offers precise, efficient profiling with accurate containment ANI estimation even for low-coverage genomes.
Software tool to convert bioinformatics file formats to Zarr.
Software tool for partial reimplementation of bcftools for VCF Zarr.
Augusta University Integrated Genomics Shared Resource Core Facility
Core offers services from sample processing from both fresh and frozen, as well as fixed cells or tissues to library preparation and next-generation sequencing (NGS) for bulk DNA/RNA sequencing and single-cell/nuclei sequencing. For single-cell studies, core is equipped with Chromium X system from 10X Genomics. Sequencing capabilities include Illumina Novaseq6000 and NextSeq 500. Offers single cell spatial transcriptomics with CosMx SMI platform. Other equipped includes CytAssit instrument from 10X genomics for VISIUM spatial transcriptomic and QIAConnect from Qiagen for nucleic acid and protein extraction.
Harvard University School of Medicine BIDMC HIV-1 Neutralizing Antibody Core Facility
Beth Israel Deaconess Medical Center Neutralizing Antibody Core
Core provides in vitro HIV-1 neutralizing antibody assay services. Serves as resource for assessing breadth and potency of HIV-1 neutralizing antibodies, and for characterizing neutralization phenotype of HIV-1 isolates. Investigators send monoclonal antibodies or serum samples from vaccinated or HIV-1-infected individuals to the core for in vitro testing using the validated TZM.bl neutralizing antibody assay. The core also has the capability to phenotype primary HIV-1 isolates for sensitivity to broadly neutralizing antibodies. GCLP-compliant, In vitro testing of monoclonal antibodies or seurm samples, Validated TZM.bl neutralizing antibody assay, Phenotoyping of primary HIV-1 isolates.
Boston Children's Hospital Cellular Imaging Core Facility
Boston Children's Hospital Cellular Imaging Core
Cellular Imaging Core facility is light microscopy core in Boston Children's Hospital's Neurobiology Program. The Core maintains systems for Widefield, confocal, multiphoton, and lightsheet light microscopy as well as sample preparation and image processes tools and technologies to assist the microscopy community of Boston Children's Hospital in addition to the surrounding greater Boston area. Core services and equipment are available to all upon request, contact core staff for access.
Software tool that combines the utility of NanoFilt and NanoLyse, for filtering sequencing reads based on quality, length, and contaminating sequences, delivers 7-fold speed up compared to the Python implementation, making use of the Rust-Bio library and Rust bindings to minimap2.
Website serves as digital resource for plastic surgery professionals. Educational and resource platform dedicated to plastic surgeons, trainees, and researchers. Provides access to curated content, including links to major plastic surgery societies, journal repositories, clinical resources, and upcoming events. Serves as comprehensive hub for continuous professional development and collaboration in the field of plastic surgery.
Ribosomal Investigation and Visualization to Evaluate Translation
Software tool to automate statistical analysis of RNA seq data acquired from polysome profile or ribosome footprinting experiments.
Software C library for asynchronous DNS requests. Provides set of library functions, datatypes, and enumerations which integrators will use for their implementations.
Software tools that provide framework to help other GNU packages produce multi-lingual messages.
X.Org project provides open source implementation of X Window System. The development work is being done in conjunction with the freedesktop.org community. The X.Org Foundation is the educational non-profit corporation whose Board serves this effort, and whose Members lead this work.
Database contains code and data that represent the history of local time for many representative locations around the globe. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight-saving rules.
Software package for modern re-imagining of data frame. Provides 'tbl_df' class with stricter checking and better formatting than traditional data frame.
Software framework for integrating gene expression and chromatin accessibility, enabling the inference of regulatory mechanisms and the prediction of gene expression from cross-modal data. Repository contains code and tutorials for the following tasks: multimodal pretraining, cross-modal prediction, inferring regulatory network and potential analysis.
Thermo Fisher | Vanquish Neo UHPLC System
Low flow, high-sensitivity Liquid Chromatography-Mass Spectrometry system delivers retention time precision from nano up to 100 μL/min at pressures up to 1500 bar for reproducible nano-, capillary-, and micro-flow LC-MS.
Web application for comparing cell type assignments and other cell-based annotations (e.g., donor demographics, anatomic locations, batch variables, and quality control metrics). Used for connecting brain cell types across studies of health and Alzheimer's Disease.
Software lightweight header only C++ library for loading and traversing trees. Used for for loading and traversing trees.
Software repository contains scripts and notebooks for defining the limits, challenges and estimations of plant chemical space using MS data.
Histology Topography Cytometry Analysis Toolbox
Software package to visualize and analyse multiplexed image cytometry data interactively.
Software tool as parameter-free deep learning framework for nucleus segmentation using image style transfer. Cell segmentation tool.
Web application for sequence analysis employing conserved peptide patterns for determination of similarities between proteins.
Web tool for predicting nuclear localization of proteins. Analyses eukaryotic protein sequence and predicts if protein spends at least some time in nucleus or spends no time in the nucleus.
Web server for prediction of protein subcellular localization and sorting signals. DeepLoc 2.1 additionally classifies input proteins into membrane protein types Transmembrane, Peripheral, Lipid-anchored and Soluble. Used to predict subcellular localization and associated membrane type of eukaryotic proteins
Web service for protein localization prediction and visualization at subcellular and suborganellar levels.
Web application for feature-based prediction of non-classical and leaderless protein secretion.Used for prediction of mammalian secretory proteins targeted to non-classical secretory pathway, i.e. proteins without N-terminal signal peptide.
Database resource for plant cell wall proteomics. Aims at collecting cell wall proteomic experimental data. For each experiment, a scheme summarizing the strategy used for protein isolation and identification is provided.
Provides automated library preparation, template preparation, and chip loading for users at any experience level. Simplifies the Ion Torrent next-generation sequencing (NGS) workflow by integrating several manual and instrument steps into single process.
Ion S5 XL next-generation sequencing system enables simple targeted sequencing workflow for your lab with reliable performance and industry-leading speed.Torrent Server direct connection to the Ion S5 XL Sequencer is supported.
Software R package as dissimilarity-based functions for ecological analysis. Used for analyzing ecological data.
Software R package for microbiome data visualization and statistics. Docker image available.
Software RNA-seq quality control package. Used for quality control of RNA-seq experiments.
Software R package contains functions for drawing survival curves using 'ggplot2'.
Renishaw windows-based Raman Environment, WiRE, software can control acquisition of Raman data and provide users with dedicated data processing and analysis options.
Louisiana State University Mass Spectrometry Core Facility
Louisiana State University Mass Spectrometry Facility
Core provides analytical support and services. Services include data analysis, sample preparation, proteomics, metabolomics, lipidomics, Maldi and Maldi imaging, Agilent GC-MS, SPE purification.
Howard Hughes Medical Institute at Janelia Research Campus Immortalized Cell Line Culture Shared Resource Core Facility
Core offers support for various tasks such as plating, passaging, cryopreserving, transfection, and preparing cells for imaging and other applications. Our facility fosters collaboration, allowing researchers to reserve cell culture hoods and engage with fellow lab and staff members.
University of Louisville Protein Expression and Purification Core Facility
Core offers recombinant protein expression and purification in E. coli systems to investigators for functional and structural studies. Services include vector construction, expression optimization, protein purification using FPLC, and isotopically labeled protein expression for NMR. Clients can choose from expression strain delivery, optimized protocols, and/or purified protein, with fast turnaround times and consultation throughout the process.
University of Louisville Nuclear Magnetic Resonance Spectroscopy Core Facility
Core Facility houses 600 MHz Bruker Avance Neo NMR spectrometer available for both collaborative and fee-for-service use. The facility is equipped with a 14.1 T Bruker system and a nitrogen-cooled Prodigy probe, enabling a range of 3D experiments on isotopically labeled biomolecules with enhanced sensitivity for challenging samples. Services include biomolecular structure determination, characterization of biomolecular motions, and stable isotope-resolved metabolomics for studying metabolic pathways.
Beth Israel Deaconess Medical Center Biomarker and Metabolism Research Core Facility
Core provides access to XFe 96 Extracellular Flux Analyzer, seahorse technology, as well as additional services that include technical advice in experimental design, data analysis and basic training. Provides access to electrochemiluminescence immunoassays using MESO QuickPlex SQ 120. You can perform multiplex biomarker and cytokine assays, test for immunogenicity or toxicity, or we can help you develop your own unique assays. Core also provides access to ImageXpress Pico, the next generation of digital microscopy and access to SPECTRAMAX I3X, multi-mode microplate reader.
Montana State University CBE Bioimaging and Analytical Core Facility
Montana State University - CBE Bioimaging and Analytical Core
Montana State University CBE Bioimaging and Analytical Core
Core offers imaging and analysis of intact biofilms to capture with ultimate precision the position, interactions, activity, and identification of microbes in real-time from intact samples. With our broad range of analytical capabilities, we can determine how microbes are interacting and altering their environmental conditions. We provide one-on-one training, method development, proposal writing, troubleshooting and data analysis services to help you meet your biofilm-related analytical and imaging needs.
Hamamatsu | NanoZoomer-XR Digital slide scanner
High-resolution digital slide scanner designed for wide-field imaging of tissue samples. It captures high-quality digital images of microscope slides at up to 40x optical magnification. NanoZoomer XR scanner is capable of capturing images with a maximum resolution of 0.23 microns per pixel.
Leica Bond III automated IHC – ISH stainer to processes up to 30 simultaneous slides in under 2.5 hours. Used for immunohistochemistry for in situ hybridization slides staining.
Tecan | Infinite M Plex microplate reader
Multimode microplate reader with monochromator optics. Offers free wavelength selection and scanning capabilities. Used for all standard absorbance, fluorescence and luminescence assays.
4-in-1 digital hybrid microscope, combining four microscopes into one. ECHO Revolve is a hybrid microscope that can be used for viewing glass slides and live samples in fluidic chambers. It can be used for upright or inverted observation methods.
Hybrid Q-TOF mass spectrometer with integrated ion mobility.
Bruker MALDI-TOF mass spectrometry system. Enables time critical applications and faster decision making processes.
Bruker | amaZon Speed ETD mass spectrometer
Ion trap mass spectrometer with electron transfer dissociation capabilities. Sets analytical standard for proteomics and small molecule applications.
Shimadzu | LCMS-8060NX Triple Quad LC-MS/MS mass spectrometer
Triple Quadrupole Mass Spectrometer is liquid chromatograph mass spectrometer (LCMS) for fast, accurate detection, to quantify components of sample or to analyze their structure with increased specificity and sensitivity.
Shimadzu | Nexera HPLC/UHPLC Pump - LC-40D XS
High-performance liquid chromatography HPLC pump that s used for separation, sensitivity, and resolution. It s part of the Nexera series of HPLC and UHPLC systems from Shimadzu.
Shimadzu | Nexera HPLC/UHPLC Column Oven - CTO-40S
Oven used to control the temperature of the column in a liquid chromatography LC system.CTO-40S Slim Line column oven is ideal for saving space while maintaining excellent thermal stability.
Cost-effective, compact foot-print, and open-source Raspberry Pi-based widefield imaging system. Used for close-proximity dual-brain cortical mesoscale functional-imaging to simultaneously observe activity in two head-fixed animals in staged social touch-like interaction. We provide all schematics, code, and protocols for a rail system where head-fixed mice are brought together to a distance where the macrovibrissae of each mouse make contact.
Repository of integrated data and knowledge about adaptive immune receptors, the complex genomic loci encoding AIRs, and the antigens and epitopes bound by AIR.
Software R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo. Streamlines routine steps in TCGA data processing, including filtering and mapping gene and sample identifiers between modalities and allows modality-specific data transformation, such as normalization and cleaning.
Software package for finding the location of m6A sites in MeRIP-seq data.
Natural Products Magnetic Resonance Database
Database and respository for NMR data associated with natural products and specialized metabolites.
Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations.
University of Liverpool GeneMill Core Facility
Automation, synthetic biology and protein production facility. As founder member of Global Biofoundry Alliance we are part of UK government initiative to strengthen engineering biology capabilities in the country and beyond. GeneMill offers high-throughout, automated gene cloning, sequence diversity generation and phenotyping. Our portfolio also includes a full protein production service.
University of Liverpool High Field Nuclear Magnetic Resonance Core Facility
University of Liverpool High-Field NMR Facility LIV-SRF
Facility offers NMR technologies to determine content and purity of sample as well as its molecular structure, interactions and chemometrics of biological mixtures.
Nikon | AXR NSPARC super resolution inverted microscope
Confocal microscope provides enables collection of more data over wide area and down to deep regions in tissues. Its high sensitivity and high-speed scanning reduce phototoxicity to specimen and minimize damage. Equipped with image acquisition/analysis functions utilizing Artificial Intelligence (AI), the AX/AX R can efficiently acquire highly reliable data. Nikon Spatial Array Confocal (NSPARC) detector utilizes detector array to collect two-dimensional image at each scanned point. It adds additional potential to imaging by providing new level of ultra-low noise sensitive spatial detection, enabling improved lateral resolution of 1 airy unit/~230 nm and improved signal-to-noise ratio.
Next Advance | Bullet Blender Homogenizer
Tissue homogenizer for 24 samples in microcentrifuge tubes with very powerful motor. Cooling with dry ice or liquid nitrogen to maintain 4°C sample temperature. Includes starter kit of beads, scoop and tubes. CE certified.
Bruker | timsTOF Ultra mass spectrometer
Mass spectrometer used for proteomics research. Offers the ultimate fusion of trapped ion mobility spectrometry (TIMS) with quadrupole time-of-flight (QTOF) technology.
Bruker | timsTOF Ultra 2 mass spectrometer
Spectrometer timsTOF Ultra 2 is paired with CaptiveSpray Ultra 2 ion source for high sensitivity to work with challenging samples and detect low-abundance peptides. Used to analyze even the smallest amounts and uncover previously unseen peptides.
The timsTOF SCP (single-cell proteomics) is mass spectrometer from Bruker. Ultra-high sensitivity instrument for quantitative single cell biology research with unbiased, deep single-cell 4D-Proteomics, immunopeptidomics, epiproteomics and PTM analysis. It features an additional separation in the tims cell where ions get separated according to their ion mobility, leading to collision cross-section values.Allows the analysis of hundreds of samples with minimal sample load (<200 ng) at sequencing speeds exceeding 100 Hz.
Mass spectrometer is equipped with the 4th generation high capacity TIMS-XR analyzer and advanced digitizer technology (ADT). Offers higher dynamic range for unmatched analytical depth and quantitation in high-throughput proteomics experiments.
Mass spectrometry (MS)-based proteomics instrument designed for shotgun proteomics and phosphoproteomics, leveraging Parallel Accumulation Serial Fragmentation (PASEF) technology to enhance speed, sensitivity, and resolution.
Bruker | timsTOF Pro 2 mass spectrometer
Mass spectrometer used for research, particularly in proteomics and metabolomics, leveraging Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation Serial Fragmentation (PASEF) technologies for enhanced 4D-omics capabilities.
Rockefeller University Data Science Platform Core Facility
Rockefeller University Data Science Platform
Data Science Platform focuses on Artificial Intelligence, Signal Processing, Computer Vision with the aim of advancing the research of Rockefeller Laboratories. DSP owns and operates fully dedicated computing infrastructure, equipped with state of the art GPUs and large storage capabilities.
Software tool as data-driven network modeling algorithm for drug response analysis in cancer.
Mayo Clinic Spatial Biology Core Facility
Core provides broad range of spatial transcriptomic and targeted proteomics services including: Conventional nCounter analysis to determine RNA abundance, GeoMx Digital Spatial Profiling platform to determine protein and RNA abundance, CosMx Spatial Molecular Imaging platform for single cell spatial analysis of RNA and protein.
Brain Recording Analysis and Visualization Online
Web interface to easily import, visualize, and analyze brain signals. Used for analysis of longitudinal neural recording data.
CyTOF instrument uses atomic mass spectrometry to allow simple, independent detection of up to 33 metal labeled antibodies (and two DNA intercalators) based on currently available reagents. Has capacity to measure 100 independent signals. CyTOF system is inorganic mass spectrometer specifically built for biologists and single cell applications. Inductively coupled plasma mass spectrometer used extensively by analytical chemists and is proven in the quantification of elements and stable isotopes in variety of complex matrices.
Time-of-Flight mass spectrometer for high-speed acquisition of highly multi-parametric single cell data. Simultaneously resolves multiple parameters with minimal signal overlap, providing insights into the functional and phenotypic complexity of biological systems at the single-cell level. Analyzes cells labeled with panel of reagents conjugated to stable metal isotopes using time-of-flight mass cytometry technology. Includes over 120 detection channels and 35 Maxpar metal probes.
Web application to automate germline genomic variant curation from clinical sequencing based on ACMG guidelines. Aggregates multiple tracks of genomic, protein and disease specific information from public sources.
Software suite to search and cluster huge protein and nucleotide sequence sets. Sensitive protein sequence searching for analysis of massive data sets. Used for ultra fast and sensitive search and clustering.
Software tool for utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.
Software tools to find circRNAs in RNA-seq data. Used to detect head-to-tail spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data.
Software tool for RNAi-target design and off-target prediction. Used for long double-stranded RNAi-target design and off-target prediction.
Emory University NIH Tetramer Core Facility
Core produces and distributes of MHC/peptide tetramers and related reagents. Production and distribution to the research community of major histocompatibility complex (MHC) tetramers and related reagents for detection of T cell responses to viruses, bacteria, parasites, tumors, auto-antigens, and other model antigens. Reagents are provided to qualified investigators at no cost, except for shipping and handling fees and in cases where investigator is asked to provide the TCF with peptide or other appropriate ligands.
Mayo Clinic Stem Cell and Organoid Core Facility
Stem Cell and Organoid Core - Mayo Clinic
Core provides researchers with access to high-quality human induced-pluripotent stem cell (iPSC) production, expansion, validation, and quality control services, while strictly adhering to approved protocols, ensuring high-quality standards and consistency throughout the process.
Mayo Clinic Florida Multi-Omics Mass Spectrometry Core Facility
Mayo Clinic Florida Multi-Omics Mass Spectrometry
Core is equipped with instrumentation in mass spectrometry, sample preparation, and automation technology. Bruker timsTOF Ultra 2 ultra-high speed and sensitivity mass spectrometer for single cell and other low input proteomics methods. It comes equipped with the Bruker nanoElute 2 UHPLC and the alternative EvosepOne HPLC for high throughput applications. Sample preparation can be automated using the Opentrons Flex liquid handling robot.
Software tool for automated projection pursuit clustering. Alternative clustering approach that alleviates the curse of dimensionality by sequentially projecting high-dimensional data into a low-dimensional representation.
Software tool for formatting PhenoImager TIFF/OME-TIFF metadata for compatibility with MCMICRO workflow.
Software R package for scRNA-seq normalization. Uses Simple Good-Turing estimator for the per cell relative gene expression estimation.
Cleveland Clinic Lerner Research Institute Proteomics and Metabolomics Core Facility
Cleveland Clinic Proteomics and Metabolomics Core Facility
Lerner Research Institute Proteomics and Metabolomics Core
Core provides advanced mass-spectrometric instrumentation and for both proteomics and metabolomic experiments. Performs qualitative and quantitative analysis of proteins and post-translationally modified peptides and both targeted and untargeted LC/GC-MS based metabolomics.
University College London Centre for Cell and Molecular Dynamics Core Facility
UCL-Zeiss Centre for Cell and Molecular Dynamics Core Facility
University College London Centre for Cell and Molecular Dynamics CCMD - UCL-Zeiss Multiscale Imaging Centre UZMIC
UCL light microscopy platform. Provides wide variety of microscopes available in the Confocal Imaging unit.
Thermo Fisher: Invitrogen | iBright CL1500 Imaging System
System supports the main imaging applications of chemiluminescent and colorimetric western blots, in addition to fluorescent stained nucleic acid gels, fluorescent stained protein gels, colorimetric stained protein gels, and colorimetric membrane stains.
Software R package to predict epigenetic age and calculate age acceleration from DNA methylation data.
Software pipelines for benchmarking workflow for evaluating graph-based pangenome construction tools. The repository contains scripts to compare the performance of Minigraph-Cactus, PGGB, Minigraph pipelines using both simulated and real-world datasets. It includes data processing steps, evaluation metrics, and reproducible scripts for analyzing structural variants in pangenomes.
Software tool as entropy-based metric for assessing purity of single cell populations. Used to accurately quantify purity of identified cell clusters.
Pathway Enrichment Score-based Survival Analysis
Web tool for pan-cancer survival analysis and visualization by using results from single sample gene set enrichment analysis. Used for pathway enrichment score-based survival analysis in cancer.Users can quickly explore impact of target pathway on survival outcomes in different tumors, assisting clinicians and researchers in further investigating mechanism of tumor development and improving clinical decision-making.
Software R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. Enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility. Used for analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data.
Collection of databases, domain theories, and data generators that are used by machine learning community for empirical analysis of machine learning algorithms. Datasets approved to be in the repository will be assigned Digital Object Identifier (DOI) if they do not already possess one. Datasets will be licensed under a Creative Commons Attribution 4.0 International license (CC BY 4.0) which allows for the sharing and adaptation of the datasets for any purpose, provided that the appropriate credit is given
Automated rodent behavioral scoring system, complete with 3D design files and code/software. System monitors behavioral engagement using open-source software. 3D design files and necessary software has been made available, as well as code that can be used for data analysis.
University of British Columbia BCCHR Imaging Core Facility
University of British Columbia BCCHR Imaging Core
Core is multi-user facility located on the 4th floor in the Translational Research Building (TRB) at A4-110. It houses microscopes and image data analysis computers to provide imaging for wide range of samples, including cell structures in tissue sections, and subcellular structures and 3D morphologies of single cells. A full-time technician provides training, consultation, and guidance to researchers, from sample preparation to data analysis.
Web application tool as interactive website for SEER cancer statistics.
Software package as set of tools, primarily shell scripts, for processing multi-modal, high-quality MRI images for the Human Connectome Project. Minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space.
Platform for health data sharing and analytics that emphasizes patient privacy and security, provides transparent and speedy access, and simplifies data discovery and analysis. Houses datasets for applied AI learning and research. Repository of freely-available medical research data, managed by the University of Toronto Temerty Centre for AI Research and Education in Medicine.
Software tool as framework for knowledge graph construction and the current 4 KGs. Used to extract and integrate diverse knowledge about microbes from variety of structured and unstructured sources.
Augusta University Georgia Cancer Center Immune Monitoring Shared Resource Core Facility
Augusta University Georgia Cancer Center Immune Monitoring Shared Resource
Core provides services in Assay Development, Assays Experimental Design, Immune Monitoring, Cytokine Assays, ELISA, multiplex Flow based and Luminex based Bead Arrays, Project Based Flow Cytometry and Data Analysis.
Database that uses knowledge graph to consolidate genomic datasets and annotations. Graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome. Genomic entities and relationships are represented as diverse nodes and edges with properties.
Resource that integrates biomedical terms and biomedical relationships. This collection is curated from PubMed abstracts and biomedical repositories, offering unparalleled wealth of knowledge for researchers and practitioners in the field. The database is coupled with RESTful APIs and user-friendly web interface.
Centralized knowledge base of the human pancreas for diabetes research. Integrates diverse type 1 diabetes (T1D) datasets with expert-curated knowledge in centralized, open-source data hub. Since users will ultimately be able to contribute their own data, this will be repository for reproducible, collaborative research within the pancreas and T1D realms.
Knowledge Graph developed for the study of the human pancreas. By leveraging large language models (LLMs) and diverse data types, PanKgraph enables users to uncover biological connections and insights into diabetes pathogenesis. Previously disjointed entities such as genes, single nucleotide polymorphisms (SNPs), and pancreatic expression quantitative trait loci (eQTLs) can now be explored and connected in innovative ways.
Integrated Cell Browser features integrated single-cell RNA sequencing (scRNA-seq) and single cell ATAC-seq data from human donor-specific pancreatic islet cells. The browser enables detailed interrogation of single cell RNA-seq and single cell ATAC-seq data through intuitive visualizations. Within the single-cell browser, users can first identify and filter single-cell datasets and dataset collections. Users can visualize interactive plots of cell type clusters, gene expression, cell type abundance, and marker gene expression. Donors and their data were provided by external programs described here.
Software interface for interacting with brain atlases. Python client to brain atlas framework that integrates brain parcellations and reference spaces at different spatial scales, and connects them with broad range of multimodal regional data features. It aims to facilitate programmatic and reproducible incorporation of brain parcellations and brain region features from different sources into neuroscience workflows.
Software reference-free intraspecies sample anomalies detetion tool based on k-mer counting.
Beth Israel Deaconess Medical Center Preclinical Murine Pharmacogenetics Core Facility
Beth Israel Deaconess Medical Center Preclinical Murine Pharmacogenetics Facility
Preclinical Murine Pharmacogenetics Facility
Core provides expertise in the design and implementation of preclinical trials to test new drugs, drug combinations and novel therapeutic modalities in mouse models of human diseases.
Beth Israel Deaconess Medical Center Small Animal Imaging Core Facility
Beth Israel Deaconess Medical Center BIDMC - Small Animal Imaging Facility
Longwood Small Animal Imaging Facility (SAIF)
Provides small animal imaging services. Facility provides multi-modality imaging, advanced data analysis, image fusion resources, custom chemistry, and satellite animal facility for longitudinal studies.
University of British Columbia BCCHR Flow Cytometry Core Facility
University of British Columbia BCCHR Flow Core
Facility provides equipment for flow cytometric analysis and full-service cell sorting, as well as flow cytometry training and education for new users.
Charles University Vinicna Microscopy Core Facility
Faculty of Science; Charles University Vinicna Microscopy Core Facility
Facility is equipped with range of advanced microscopes, from traditional light microscopes to cutting-edge super-resolution and live cell imaging systems.Provides imaging and analysis services.
University of British Columbia BCCHR Analytical Core for Metabolomics and Nutrition Core Facility
Analytical Core for Metabolomics and Nutrition (ACMaN)
BCCHR Analytical Core for Metabolomics and Nutrition (ACMaN) Core
University of British Columbia BCCHR Analytical Core for Metabolomics and Nutrition (ACMaN) Core
Analytical Core for Metabolomics and Nutrition (ACMaN) is located on the first floor of the Varity Building. ACMaN allows researchers to analyze and track biological compounds, such as nutrients to track how these small molecules change during course of disease or treatment to better understand the disease itself and to develop new diagnostic tools and therapies. ACMaN plays role in research on metabolic diseases, hormones, and the effects of nutrition on childhood development.
University of British Columbia BCCHR Histology Core Facility
University of British Columbia BCCHR Histology Core
Core is a multi-user facility located on the 4th floor in the Translational Research Building (TRB) at A4-132. Histology facility offers services for processing tissue samples, automated equipment for tissue processing, paraffin embedding, micro-sectioning, and staining. Our technicians offer consultation, experimental design, and troubleshooting and work closely with researchers to get the most optimal tissue sections tailored to each project. The facility also provides training on the microtome and paraffin embedder to allow flexibility in workflow.
University of Liverpool Centre for Preclinical Imaging Core Facility
Provides access to imaging systems. Offers researchers technologies for multi-modality, non-invasive approaches to imaging on small, live animals, or tissues and organs extracted from animals . Our equipment can be used for pre-clinical models and non-biological samples.
University of Liverpool Shared Research Histology Core Facility
University of Liverpool Shared Research Histology Facility
Facility offers preparation of samples from fresh or fixed tissue through to scanned images. Provides training to prepare and use equipment to embed, section and hand stain tissues as required. Offers three different types of wax for embedding and sectioning as required. Fully equipped for methyl methacrylate and glycol methacrylate embedding and sectioning (including larger samples), freeze microtomy and high throughput slide imaging using our Zeiss Axioscan Z1.
Web application as crowd-sourcing platform to improve consensus and use of drug-target interactions. Users can search, view and download bioactivity data using various compound, target and publications identifiers.
Stanford Sciex 7500+ Triple Quadrupole LC/MS system
Sciex 7500+ Triple Quadrupole LC/MS system
Sciex 7500+ Triple Quadrupole Liquid Chromatography/Mass Spectrometry System enables rapid, sensitive screening for large panels of analytes, including metabolites, lipids, and environmental contaminants. SCIEX 7500+ system minimizes downstream contamination of the ion optics, maintaining instrument robustness over greater periods than the benchmark triple quadrupole mass spectrometers.
Cleveland Clinic Lerner Research Institute Microbial Sequencing and Analytics Core Facility
Microbial Sequencing and Analytics Resource (MSAAR)
Core provides services, from DNA and RNA extraction from diverse sample types such as tissue, stool, and bacterial isolates to next-generation sequencing, including whole-genome sequencing, total RNA-seq, metatranscriptomics, and dual RNA-seq, along with expert bioinformatics support. Core expertise spans 16S rRNA amplicon sequencing, shotgun metagenomics, metatranscriptomics, meta-omics analysis of dual RNA-seq, and single-cell RNA-seq data. Core also assists with experimental design and power calculations to ensure statistically robust results, offering consultation at every stage, from experimental design to data interpretation and troubleshooting.
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
Software application as updated version of original ssGSEA R-implementation. Depending on the input dataset and chosen database (gene sets or PTM signatures), the software performs either ssGSEA or PTM-SEA, respectively.
University of Texas MD Anderson Cancer Center Advanced Microscopy Core Facility
MD Anderson Cancer Center Advanced Microscopy Core
University of Texas MD Anderson Cancer Center Advanced Microscopy Core
Core provides microscopy services to departments at MD Anderson in high resolution and multispectral fluorescence microscopy for users from divisions including Basic Research, Cancer Medicine, Diagnostic Imaging, Surgery, Internal Medicine Pediatrics and Radiation Oncology, among others. Offers microscopy resources and expertise in fluorescence imaging to spatially and dynamically assess cells, tissues and their requisite contents across scales.
Software R package implementing multivariate lasso and ridge regression using stacked generalization. Used for predicting correlated outcomes.
Program of University of Wisconsin Population Health Institute, highlights policies and practices that can help everyone be as healthy as possible. Aims to grow shared understanding of health, equity and power of communities to improve health for all.
University of California at Irvine Optical Biology Core Facility
University of California at Irvine Optical Biology Core
Shared resource facility to provide researchers access to resources, including state of the art instrumentation and technical support, to conduct biomedical research. Provides access to light microscopes (confocal, mesoscale lightsheet, and Super Resolution), as well as software for 3D and 4D analysis.
University of California at Irvine Genomics Research and Technology Hub Core Facility
UCI Genomics Research and Technology Hub
University of California at Irvine-Genomics Research and Technology Hub
Core provides services ranging from DNA/RNA QC analysis, library construction and sequencing on various platforms. Offers several sequencing platforms from Illumina’s MiSeq and NovaSeq to PacBio’s Sequel II System.
University of California at Irvine Flow Cytometry Core Facility
University of California at Irvine Flow Cytometry Core
Core is part of the UCI Sue and Bill Gross stem cell research center. Provides various fee based services to researchers at UCI towards flow cytometry and cell sorting.
Cis-Regulatory Element sequence training
Software Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.
Software Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.
Software application for biological sequence analysis for the modern age.
Software Python library to train, interpret, and apply deep learning models to DNA sequences. Comprehensive framework for DNA sequence modeling and design.
Software Python/Rust package for single-cell epigenomics analysis.
Software Python package to optionally compute statistical test and add statistical annotations on plots generated with seaborn. Used to add statistical significance or custom annotations on seaborn plots.
Pipeline for Universal Mapping of ATAC-seq
Software pipeline for universal mapping of ATAC-seq.
Backend application to process high-resolution histology images to DeepZoomImage format, made of smaller tiles, for use in the QUINT Workflow.
Software Python tool to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.
Software library and associated tools for reading and writing bigwig and bigbed files. High-performance BigWig and BigBed library in Rust.
Open source Python-based image-analysis software that rapidly detects and segments berries and extracts morphometric data on fruit quality traits such as berry color, size, shape, and uniformity. Used for quantifying visual phenotypes of cranberries and other berries.
Software Python package to perform genomic selection. Predicts phenotypes from comprehensive multi-omics functional annotations with interpretable deep learning framework. Novel interpretable DL-based genomic prediction model that integrates comprehensive species- and tissue-level transcriptional regulatory functional annotations to predict phenotypes.
Fred Hutchinson Cancer Center Prevention Center Shared Resource Core Facility
Fred Hutch Cancer Center Prevention Center Shared Resource
Provides services in the conduct of exercise interventions, nutrition interventions, or prevention-based clinical interventions. Facility offers well-trained, specialized staff and inviting space for study participants to participate in population-based research.
Texas A and M University System Genomics and Bioinformatics Service Core Facility
Texas A&M University System Genomics & Bioinformatics Service
Core provides services including Sequencing, Library preparation, Bioinformatics Analysis and Processing. Experienced staff provide expertise to users.
Software tool for selecting the best-fit model of evolution for DNA and protein alignments. Used for selection of DNA and Protein evolutionary models.
Computational platform, which enables data-driven, fully-automated and ultra-fast cell-type identification based on given scRNA-seq data, combined with comprehensive cell marker database as background information. Deployed as both interactive web-tool and open-source R-package.
Pennsylvania State University Honey and Pollen Diagnostic Laboratory Core Facility
Penn State Honey and Pollen Diagnostic Laboratory
Pennsylvania State University Honey and Pollen Diagnostic Laboratory
Core offers researchers and beekeepers, throughout the world, services to identify floral resources and evaluate characteristics of honey and pollen.
Web application as fully automated RNA structure modeling server. Used for RNA tertiary structure prediction.
Web FFT-based protein docking server. First Fourier transform (FFT)-based protein docking server to be powered by graphics processors.Interactive protein docking and molecular superposition program. Hex understands protein and DNA structures in PDB format, and it can also read small-molecule SDF files.Hex will run on most Windows-XP, Linux and Mac OS X PCs.
Abbott | ARCHITECT i2000SR immunoassay analyzer
Analyzer offers maximum throughput of up to 200 tests per hour. Featuring load-up capacity of 135 samples with 35 priority and 100 routine areas. Has 25 refrigerated reagent positions. Designed for efficient and accurate analysis of various biological samples, including serum, plasma, and other bodily fluids.
Fully automated immunology analyzer designed to analyze biological samples like serum, plasma, and other bodily fluids, providing insights into immunological parameters. Has throughput of up to 120 tests per hour, with 9-minute STAT applications for time-sensitive tests. Can be used for testing broad range of parameters, including cytokines, antibodies, antigens, and immune cell populations.
Immunochemistry analyzer as mid-volume throughput immunochemistry module that performs broad range of heterogeneous immunoassay tests using ElectroChemiLuminescence (ECL) technology. Offers Heterogeneous immunoassays, Throughput of up to 170 tests/hour, 25 reagent positions, Reagent cassette loading/unloading during standby, Carryover-free disposable tips, Clot and air bubble detection.
Seahorse XF96 Extracellular Flux Analyzer
Seahorse XF96 Extracellular Flux Analyzer measures the rate of change of analytes dissolved oxygen and pH in media immediately surrounding living cells cultured in a microplate.
Platform to help scientists organize all biological knowledge into singular, unified resource that is searchable, accessible and capable of answering the most difficult questions in science. Used for bioinformatics analysis.
Software tools for manipulating scATAC-seq fragment files.
Softwre framework for multi-scale footprinting analysis of single-cell ATAC-seq data. Designed to identify and visualize regulatory elements that drive cell-type-specific gene expression programs through footprinting. Uses deep learning model to predict activity of transcription factors from single-cell ATAC-seq data. Provides suite of visualization tools to explore calculated multi-scale footprints.
U.S. Department of Agriculture Agricultural Research Service initiative hosted at Cornell University in Ithaca, New York. Assists USDA-ARS breeders by creating new opportunities in assimilating data-driven tools, technologies, and methods to remove barriers and more easily allow for the use of genomic insights. We integrate phenomics (trait analysis), genomics (genotypic data), data management, and software tools to help breeders increase the rate of genetic gain and create more healthy and nutritious specialty crops and animals. These gains improve on-farm production for many of America’s favorite specialty crops and animals.
Interactive web application for drug screening data analysis. It includes comprehensive quality control statistics, dose-response curve fitting, and calculation of quantitative scoring parameters such as EC50, IC50, drug sensitivity score and AUC. Used to facilitate quality control, dose-response curve fitting, and data visualization.
Software code for age prediction in fetal brain and organoid single cell data. This repository contains cell type agnostic models to predict the developmental age of brain cell types from single cell RNAseq data. Code contains 4 jupyter notebooks, which apply pretrained models to predict neurodevelopmental age of cell types in new human fetal brain and organoid datasets.
Northwestern University Evanston Single Cell Genomics Core Facility
Northwestern University Single Cell Genomics Facility
Core dedicated to supporting single cell and spatial biology experiments on the Evanston campus. Home of flow cytometry. Offers single cell encapsulation and library preparation services using the 10X Genomics platform. Provides experiments consultations.Shared use, training, and service facility. Instrumentation includes FACSDiscover S8 flow sorter, LSRFortessa flow analyzer, MERSCOPE spatial transcriptomics platform, 10X Genomics Chromium iX, Epredia NX70 Cryostat, QuantStudio 3 real-time PCR, VeritiPro Thermocycler, Agilent Bioanalyzer, Axiovert inverted microscope (DIC, Brightfield, 4 fluorescent channels), Revvity Cellometer K2 automated cell counter, Qubit 4 fluorometer, Nanodrop spectrophotometer. Services include assisted flow cytometry, 10X Genomics library preparation, spatial transcriptomics via MERSCOPE, cell counting, bioanalyzer analysis, bulk library preparation, and low input library preparation.
Swedish national resource supporting precision medicine research in Sweden through access to data sources, customised dashboards and guidance on data management with focus on making data FAIR and reusable.
Axion Biosystems Maestro Pro™ microelectrode array (MEA)
System for non-invasive, real-time, and label-free evaluation of cellular function in vitro, particularly for monitoring electrical activity of excitable cells like neurons and cardiomyocytes, as well as tracking cell growth and death. Used in neuroscience to measure electrical activity of network of cultured neurons.
3D-Hub-O specializes in production, manipulation and analysis of organoids from normal and tumor tissues. Physiological platform for research on living pathological tissues. Platform participates in knowledge transfer through customized training of specific organoid culture carried out by platform staff.
RWD Life Science | Standard Stereotaxic Holder
North Carolina State University College of Veterinary Medicine Flow Cytometry and Cell Sorting Core Facility
NCSU-CVM Flow Cytometry and Cell Sorting Core Facility
North Carolina State University NCSU-CVM Flow Cytometry and Cell Sorting Core Facility
Core provides flow cytometry services. Staff members will help with experimental design, instrument training, sample acquisition, data analysis with software provided, and conventional/spectral cell sorting.
Benaroya Research Institute Genomics Core Facility
Benaroya Research Institute BRI Genomics Core
Core provides services for genomics analysis, from sample processing through data generation. Available technologies focus on Illumina RNA and DNA sequencing. RNA-seq can be performed from a variety of sample types, including purified total RNA, cell populations (including low input samples of 50-1000 cells), or single cells (either plate-sorted rare populations or high-throughput 10x single-cell analyses). DNA-seq pipelines can also be performed, including bulk CUT and Tag/CUT and RUN, and ATAC-seq and single cell ATACseq and multiome capture. Custom prepared libraries can also be submitted for sequencing. Core laboratory houses Illumina sequencers, NextSeq2000 instruments and Miseq, plus 10x Chromium X and 10x CytAssist. Additional equipment includes ThermoFisher Kingfisher Flex, for extracting nucleic acid from variety of sample types using magnetic bead technology with throughput of up to 96 samples. Qiagen QIAcube Connect instruments automate extraction of nucleic acid using spin column technology. Ancillary equipment for sample processing includes Formulatrix Mantis Liquid Handler, Agilent TapeStation 4200 and Tecan NanoQuant.
Web application as resource of known and predicted human ubiquitin ligase substrate interaction network. E3-substrate interactions are derived from six data sources: mannual cruration, protein ortholog, protein domain, protein motif and network topology.Designed to explore predicted and reported E3-substrate interactions for query E3 or substrate, and ubiquitination sites for substrate protein.
Cloud-based lab animal colony management application with realtime ambient sensing. Platform for managing vivaria. It features cage management, user management, lab management, and real-time environmental monitoring with IoT sensors.
Stand-alone Raspberry Pi-enabled IoT system to monitor near-realtime sensor data in MyVivarium web app. Used to track environmental conditions of vivaria.
Software Python package for modular causal inference analysis and model evaluations. Used for inferring causal effects from observational data.
Software tool as simple test framework for Nextflow pipelines. Enables pipeline developers to test individual process blocks, workflow patterns and entire pipelines in insolation.
Cleveland Clinic Lerner Research Institute Cell Culture Core Facility
Core provides specialized cell culture services , ensures high-quality and contamination-free cultures by employing aseptic techniques and maintaining Mycoplasma and Quarantine facilities. Offers cell banking, with capacity to freeze and store up to 10,000 vials. Facility provides walk-in warm room and cold room, spinner apparatus capable of handling over 20 liters of cells in suspension, and roller bottle machine that accommodates more than 200 roller bottles. Additional equipment includes automated cell counter and ELISA reader.
Cleveland Clinic Lerner Research Institute Glassware Core Facility
Core provides glassware washing and sterilization of all types of glassware and pipettes. Facility maintains stock glassware in common storage area. Glassware personnel collect glassware from laboratories daily and cabinets are replenished regularly. Autoclaving of materials is offered on daily basis. Core can accommodate any special requests. Glassware Core maintains stock of all types of sterile laboratory glassware and pipettes in common storage area.
Cleveland Clinic Lerner Research Institute Hybridoma Core Facility
Core provides monoclonal antibody production services. Provides consultation to assist investigator in all aspects of monoclonal antibody production. Services are performed under strict quality control guidelines appropriate for antibodies that may have commercial potential.
Cleveland Clinic Lerner Research Institute Media Preparation Core Facility
Core offers quality controlled media at economical prices. Media is prepared in large batches ranging from 50L-300L from commercially produced powders. All products go through strict quality control program. Custom plates and media are offered by request and are usually available within 2-4 business days. All other orders placed online can be picked up on the next business day.
Augusta University Chemical and Biomolecular Analysis Core Facility
Core focused on metabolomics, lipidomics, medicinal chemistry, and small molecule analysis. Offers services, expertise, and collaboration for the research community. Instrumentation includes high field nuclear magnetic resonance (NMR), liquid chromatography–mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), high-performance liquid chromatography (HPLC), circular dichroism spectrometer (CD), inductively coupled plasma optical emission spectrometry (ICP-OES), and fluorimeter. Consulting is available to assist with experimental design and data interpretation.
Software tool that performs alignment, XIC extraction, peak detection and quantification on data obtained from Liquid Chromatography-Mass Spectrometry (LC-MS) techniques. Performs LC-MS data alignment and peptide quantification by peak area integration on extracted ion chromatograms.
Web server for management and validation of mass spectrometry-based proteomic data.
Azure Biosystems | Chemiluminescent Western Blot Imager Azure 300
Multichannel, multimodal imager, with visible fluorescence, visible light, and UV excitation channels. The system is fully upgradeable to fluorescent Western Blot Imaging System.
Leica DMi8 microscope is an inverted light microscope, intended as a general microscope for routine examinations of biological specimens.
Software Python library for deep probabilistic analysis of single-cell and spatial omics data. Used for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.
Cell Sorter, equipped with 5 lasers (355, 405, 488, 561 and 640 nm excitation wavelengths) and 78 channels which can measure the entire emission spectra of the fluorescent dyes, is the first spectral flow cytometer sorter with sort-capable image analysis.
Web-based simulation tool that evaluates cancer control strategies. Microsimulation model calibrated to Canadian input data primarily used to inform health economic policy of cancer screening and prevention strategies.
Species-agnostic web-based application for processing genotypic data in no-code RShiny user-friendly interface. Allows users without coding experience to process genetic data in all genome ploidy ranges and for multiallelic data, starting from number of input formats (including VCF). Also allows to perform downstream QC analyses (e.g., PCA) and run genomic analysis (e.g., Linkage mapping, QTL analysis, genome-wide association studies (GWAS), and genomic selection (GS).
Software R package contains functions developed within Breeding Insight to analyze diploid and polyploid breeding and genetic data. Provides set of functions for analyzing genomic and pedigree data in diploid and polyploid breeding programs. Used to streamline analysis of breeding and genetic data.
Molecular Interaction NEtwoRk VisuAlization
Standalone web server for visualization, exploration and management of molecular networks encoded in SBGN-compliant format.
Software R package to reduce and visualize Gene Ontology terms. Used for interpreting lists of Gene Ontology terms.
Software application that automatically adapts to given dataset. It will analyze provided training cases and automatically configure matching U-Net-based segmentation pipeline.
Karolinska Institutet Adaptive Immune Receptor Gene Variant Atlas
Immunology database of B and T cell receptor gene variants, providing population frequency data, FASTA downloads and tools to study IG variation at individual and population levels.
Publicly-traded life science technology company, which specializes in advanced next-generation sequencing (NGS) and multiomic technologies.
Singular Genomics | G4X Spatial Sequencer
Ultra high-throughput, spatial sequencing platform, for integrated multiomic analysis of FFPE samples at subcellular resolution. Spatial sequencing platform capable of simultaneous direct RNA.
Pennsylvania State University Nanofabrication Lab Core Facility
Fully-staffed, open access nanofabrication lab provides services including Lithography, Etch (Dry/Wet), Deposition and Characterization.
UCSC Genome Browser source tree. Stable branch: "beta".
Web-based visual exploration and analysis of genome interaction maps.
Software Python library for parallel and distributed computing. Enables parallel and out-of-core computation.
Web server for multistep T cell epitope prediction. Also considers proteasome cleavage and TAP binding, therefore it is able to mimic the MHC binding machnism in real life. At present only HLA class I alleles are included in the prediction.
Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes.
Interactive database of protein protein interactions modeled by AlphaFold multimer. Classifier-curated database of AlphaFold-modeled protein-protein interactions.
Software tool to call somatic short mutations via local assembly of haplotypes. Somatic variant caller that uses local assembly and realignment to detect SNVs and indels.
Emory University AI Image Extraction Core Facility
Emory University EU - AI Image Extraction Core
Core is supported by the Emory University School of Medicine. Enables large-scale, secure image extraction and de-identification to empower clinical, translational, and AI research.
Agilent Seahorse XF Pro analyzer measures and reports the oxygen consumption rate (OCR), proton efflux rate (PER) or extracellular acidification rate (ECAR), as well as ATP production rates of live cells in a 96-well format. This analyzer features excellent OCR precision at low rates, verified performance, optimized temperature control, and is automation enabled. The XF Pro analyzer is also equipped with advanced software, standardized workflows, and advanced data analytics available in the Agilent Seahorse Analytics software. These features greatly simplify the entire XF assay experience, from assay design to data QC and interpretation.
nano@stanford is a group of shared labs at Stanford University focused on fabrication and characterization at the nanoscale and microscale. The labs provide access to shared scientific instrumentation, laboratory infrastructure, and expert staff support to enable multidisciplinary research and educate tomorrow’s scientists and engineers.
University of Michigan Medical School BRCF Vector Core Facility
Vector Core produces gene transfer vectors that facilitate transfer of specific genes into either normal or aberrant cells. Provides intellectual and technical advice to researchers regarding the optimal use of these systems.
University of Michigan Medical School BRCF Flow Cytometry Core Facility
University of Michigan BRCF Flow Cytometry
Flow Cytometry Core provides instrumentation, expertise and services. Samples are prepared by individual investigators, who then deliver to the Core for flow cytometric analysis or cell sorting. The Core also provides assistance in grant and publication preparation, publication-quality graphics, and the development of experimental designs.
Software application to prepare figures for publication in reproducible way. This means you receive a figure representing your data and alongside a generated code file that can exactly reproduce the figure as you put them in the publication, without the need to readjust things in external programs. Offers interactive interface to find the best way to present your data in a figure for publication. Added formatting an styling can be saved by automatically generated code. To compose multiple figures to panels, pylustrator can compose different subfigures to a single figure.
Massachusetts Institute of Technology Preclinical Imaging and Testing Core Facility
Massachusetts Institute of Technology MIT-Preclinical Imaging and Testing Facility
MIT-Preclinical Imaging and Testing Facility
Core assists in evaluating disease and its cure within complete biological system. Combines expertise and instrumentation to assist investigations on the mechanisms of disease development, to enable the evaluations of drug efficacy and resistance, and to provide the means for testing novel strategies and devices for disease detection and drug delivery.
Ecosystem for Multi-modal Brain-behavior Experimentation and Research
Ecosystem for Multi-modal Brain-behavior Experimentation and Research (EMBER)
BRAIN Initiative data archive for multi-modal neurophysiological and behavioral data, supporting the Brain Behavior Quantification and Synchronization (BBQS) Program. Accessible and versatile data archive for storage, processing, and curation of multimodal neurophysiological and behavioral datasets. EMBER extends established BRAIN Initiative data infrastructure, provides new data harmonization and synchronization capabilities, and supports scalable integrations for data coordination and AI driven batch processing to enable the goals of the BBQS program.
Ohio State University Pharmacoanalytical Shared Resource Core Facility
Ohio State University Pharmacoanalytical Shared Resource (PhASR)
Core provides access to expertise and instrumentation for bioanalytical assay development and quantitative sample analysis, experimental design, data analysis and modeling applied in pre-clinical and clinical research involving development of novel therapies for cancer treatment and prevention, chemopreventive or carcinogenic components in food/environmental sources, and biomarkers relevant to drug therapy, nutrients, food products, and dietary patterns.
Software Python package to build gene regulatory networks using combined or separate single-cell gene expression and single-cell chromatin accessibility (scATAC-seq) data. Used for inferring and analyzing enhancer-driven gene regulatory networks using single-cell multiomic data.
Software ensembl based annotation R package. Exposes annotation databases generated from Ensembl. This package loads SQL connection to database containing annotations from Ensembl.
Fast And Robust DEconvolution of Expression Profiles
Software R tool for enumerating immune cell subsets from whole tumor tissue samples. Utilizes adaptive least trimmed square to automatically detect and remove outliers before estimating cell compositions.
Software repository provides optimization algorithms applied to Jarvis3 genomic compressor used for compression of genomic sequences.
Michigan State University Bioinformatics Core Facility
Michigan State University MSU Bioinformatics Core
Core brings together expertise from across MSU to support research through advanced omics data analysis, grant proposal assistance, and tailored training for researchers at all career stages.
Software suite of population scale analysis tools for single-cell genomics data.
Software Java-based package for statistical natural language processing, document classification, clustering, topic modeling, information extraction, and other machine learning applications to text.
Software tool as lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments. Rewrite of the original TF-MoDISCo code.
Portal provides information, guidelines, data, services, and other resources aimed at supporting the research community in the Netherlands to share data related to pathogens and pandemic preparedness.
Software R package for tidying output of statistical models.
Software tools for working with scATAC-seq fragment files.
Software R package to access and explore existing scRNA-seq data from various public repositories. Supports downloading scRNA-seq data types, including raw data (SRA and ENA), count matrices (GEO, UCSC Cell Browser, and PanglaoDB), and processed objects (Zenodo, CELLxGENE, and HCA). Can access and explore existing scRNA-seq data, load output/downloaded count matrices and annotations to R (SeuratObject/DESeqDataSet), extract a subset of the SeuratObject based on cell metadata and genes, and merge multiple SeuratObjects if applicable. Provides format conversions between different scRNA-seq objects, including SeuratObject, AnnData, SingleCellExperiment, CellDataSet/cell_data_set, and loom.
University of Michigan School of Nursing Applied Biostatistics Laboratory and Data Core Facility
School of Nursing Applied Biostatistics Laboratory University of Michigan
University of Michigan Applied Biostatistics Lab and Data Core
University of Michigan Nursing Applied Biostatistics Laboratory
University of Michigan School of Nursing Applied Biostatistics Laboratory
Core provides training, education, statistics and data management services. Services include: experimental design of new studies, advising on outcomes selection, determining or justifying sample size, designing randomization schemes,designing and writing the statistical analysis/modeling section(s), advising on appropriate database design and implementation methods, advising on the use of national data registries, health system data, grant writing on relevant sections within our specialties, creating custom databases and data entry portals for prospective studies, creating custom datasets or extracts from existing data sources for analysis, merging complex or multi-sourced data in concert with research aims and objectives, implementing blind, double-blind and other randomization schemes and more.
University of Michigan College of Pharmacy Biochemical Nuclear Magnetic Resonance Lab Core Facility
University of Michigan Biochemical Nuclear Magnetic Resonance Lab
University of Michigan Biochemical Nuclear Magnetic Resonance Lab Core Facility
Provides full-service consultation, sample processing and results. After running your samples, we will process your data using Mestranova and give you access to the raw data via email or Dropbox.
University of Michigan Biointerfaces Institute Nanotechnicum Core Facility
Nanotechnicum is a Biointerfaces Institute core facility providing Nanoparticle Size analysis and Zeta Potential characterization, Chiral materials spectroscopy, Material Pore Size and Porosity characterization, Materials Thermal analysis, and Biomolecular Binding characterization instrumentation and services. The Biointerfaces Institute offers instrumentation to the University of Michigan’s research community, fellow academic institutions, and industry.
University of Michigan Biological Mass Spectrometry Core Facility
University of Michigan Biological Mass Spectrometry Core
Facility provides specialized MS services. The major areas of focus of the lab are Analysis of intact proteins, multi-protein complexes, and protein structure; Identification and purification of compounds from complex mixtures coupled with quantitative analysis.; Purification using mass directed autopurification liquid chromatography. Users can be trained on the instruments for walk-up use or samples can be submitted for analysis.
University of Michigan Biomolecular Nuclear Magnetic Resonance Core Facility
Biomolecular Nuclear Magnetic Resonance (BioNMR) Core
University of Michigan BioNMR Core Facility (U-M BioNMR)
Core facility primary mission is to provide access to advanced NMR spectroscopic methods and tools to students, postdoctoral fellows, and faculty of the University for the advancement of their research.
University of Michigan Medical School BRCF Epigenomics Core Facility
Core provides resources and services to prepare samples for analysis in epigenetic regulation in both genome-wide and locus-specific manners.
University of Michigan Medical School BRCF Metabolomics Core Facility
University of Michigan BRCF Metabolomics Core
University of Michigan BRCF Metabolomics Core Facility
Offers full-service sample analysis to measure concentrations of small molecules in biological samples. Services include targeted and untargeted metabolomic screening, method development to explore novel metabolic pathways and systems. Staff helps with interpretation and visualization of your data, and the preparation of grants, proposals, and manuscripts.
University of Michigan Medical School BRCF Microscopy Core Facility
University of Michigan BRCF Microscopy Core
University of Michigan Medical School BRCF Microscopy Core
Offers microscopy instrumentation and services. Offers support and training on variety of high-end instrumentation and advanced methodologies for both light and electron microscopy, sample preparation services for electron microscopy, training and assistance with image analysis. Provides support across variety of open-source and commercial image analysis software packages.
University of Michigan Medical School BRCF Proteomics Resource Core Facility
University of Michigan BRCF Proteomics Resource Facility
University of Michigan Medical School Pathology BRCF Proteomics Resource Core Facility
University of Michigan Medical School Pathology BRCF Proteomics Resource Facility
Core is dedicated to protein analysis and applying mass spectrometry-based proteomic approaches to varied biological questions.
Software R package for ploidy and aneuploidy estimation using genotyping platform data.
Biological and life science product supplier.
University of Michigan Bru-Seq Lab Core Facility
Core facility provides nascent RNA sequencing using four techniques: Bru-seq, BruChase-seq, BruUV-seq, and BruDRB-seq. This service is all-inclusive, starting with cells and ending with basic data analysis. In addition, users will have access to our exclusive pipeline to perform further data analysis. Our areas of expertise are RNA isolation, cDNA library preparation, and sequencing data analysis.
University of Michigan Cancer Data Science Shared Resource Core Facility
University of Michigan Cancer Data Science Shared Resource
Core is part of the University of Michigan Rogel Cancer Center. Provides Rogel Cancer Center investigators with assistance in all quantitative aspects of cancer research -- including biostatistics, bioinformatics, computational biology, analytics and other emerging data-driven and data-intense endeavors.
University of Michigan Cardiovascular Regeneration Core Facility
U-M Cardiovascular Regeneration Core Laboratory
University of Michigan Cardiovascular Regeneration Core Laboratory
Core routinely generates patient-specific human induced pluripotent stem cells (hiPSCs) for basic science research purposes. Focus is on cardiovascular cell differentiation of hiPSCs to generate unlimited supplies of patient specific cardiovascular cells for in vitro research. Basic services include:hiPSC derivation, hiPSC characterization, hiPSC expanstion;hiPSC differentiation to: Cardiomyocytes, Endothelial Cells, Vascular Smooth Muscle Cells, Pancreatic Cells;3D organoids: Cardiac, Pancreatic;Cardiotoxicity Screening-Drug Discovery Projects;Arrhythmia Testing;High Content Time Lapse Imaging.
University of Michigan Center for Molecular Imaging Core Facility
University of Michigan Center for Molecular Imaging
Facility provides imaging instruments and imaging services for research community. Offers imaging systems including IVIS Spectrum bioluminescent/fluorescent imaging system, Bruker 7 Tesla horizontal bore MRI system, 4DMedical Permetium lung CT system, and Bruker SkyScan CT system.
University of Michigan Central Ligand Assay Satellite Services Laboratory Core Facility
University of Michigan Central Ligand Assay Satellite Services Laboratory
Core is unit of Department of Epidemiology at the University of Michigan’s School of Public Health. Offers support for clinical research projects throughout process of gathering samples, storing them, and coordinating the assay of the desired analytes. Offers collection kit designs tailor-made to your research study, with tubes and components labeled clearly with barcoded labels and unique sample IDs. Once collected, samples can be processed and stored in one of our 51 on-site ultra-low freezers or in our liquid nitrogen freezer, where their temperatures will be monitored 24/7. When all of the samples are collected, we can complete any combination of 40 different routine assays on them. We currently offer testing using ELISA plates, open channel chemistry analyzer, and coagulation analyzer.
University of Michigan Chemistry NMR Core Facility
University of Michigan Chemistry NMR Facility
NMR Facility provides qualified students and researchers in the Chemistry Department access to state-of-the-art NMR instrumentation. Provides support for variety of NMR studies including structure, conformation, dynamics, kinetics and reaction mechanisms of small organic and inorganic molecules and pharmaceuticals.
Software tool to predict Hi-C matrices based on ChIP-Seq data from histones using cGAN approach.
Pennsylvania State University Environmental Contaminants Analytical Laboratory Core Facility
Laboratory is equipped with sample preparation and analysis equipment that support established analytical procedures including:Organic fluorine compounds-PFAS screening: EPA 1621; PFAS targeted and non-targeted analysis: EPA 537.1, EPA 1633; Pharmaceuticals and personal care products: EPA 1694; Agricultural chemicals: pesticides, herbicides-targeted and non-targeted analysis: various methods GC-MS/MS and LC-MS/MS; Volatile organic compounds: EPA 8260D (SW-846); Semivolatile organic compounds: EPA 8270E (SW-846); Dioxins and furans: EPA 23; Total petroleum hydrocarbons: EPA 8440; Microplastics and nanoplastics.
Pennsylvania State University Energy and Environmental Sustainability Laboratories Core Facility
Fully-staffed, open access, analytical research facilities at Penn State's Institute of Energy and the Environment. Provided services include radiocarbon measurements on carbon-bearing materials using an Accelerator Mass Spectrometer; high-resolution 3D micro/nano computed tomography of biological and synthetic materials; analysis of environmental and biological samples for emerging and legacy contaminants using high resolution mass spectrometry including (Triple Quad GC-MS/MS, Triple Quad LC-MS/MS, Pyrolysis GC-MS, QExactive LC-MS, Combustion Ion Chromatography, DART-MS with Ion Rocket) and a Laser Direct Infrared Chemical Imaging System. Sample Preparation and Analysis. Provides training for researchers and equipment users, method development, data analysis.
Data analysis platform, enables scientists without coding or bioinformatics expertise to access and run the end-to-end data analysis workflow. The platform includes the Pipeline module which processes FASTQ files and the Insights module for downstream analysis.
Software tool that enables the automatic evaluation of muscle tissue on elastography imaging using MATLAB.
Software R package for detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
Software R package to quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library.
Software repository for cell segmentation benchmark.
University of Michigan LSA Chemistry Mass Spectrometry Core Facility
Core offers mass spectrometry services. Provided instruments include
University of Michigan LSA Chemistry X-Ray and Microporous Materials Characterization Core Facility
University of Michigan LSA Chemistry X-Ray and Microporous Materials Characterization
Core provides services for X-Ray and microporous materials characterization.
University of Michigan Pathology Clinical Core Facility
University of Michigan Clinical Core Facility
University of Michigan Pathology Clinical Core Laboratory
Core provides services in Clinical Chemistry, Clinical Mass Spectrometry , Hematology, Body Fluids, Urinalysis, Quantitative Flow Cytometry, Coagulation, BioChemical Genetics.
University of Michigan Conlsulting for Statistics, Computing, and Analytics Research Core Facility
University of Michigan Conlsulting for Statistics
Areas of Expertise:CSCAR staff have expertise in the areas of Biostatistical analyses; Formulation of research aims and development of plans for data collection and analysis; expertise in R, Python, SAS, SPSS, Stata, and Fortran. In addition, can advise clients on the use of number of other statistical and technical software packages.
University of Michigan Medical School CyTOF Core Facility
CyTOF Core shares equipment and expertise with researchers. Provided instruments include: Helios CyTOF System (Suspension CyTOF), Hyperion CyTOF System (Imaging CyTOF), Attune Flow Cytometer, ÄKTA Pure FPLC, NanoDrop 2000c Spectrophotometer. Offered services include Human immune profiling panel for 29-color analysis of cells in suspension; Mouse immune profiling panel for 16-color analysis of cells in suspension; Custom CyTOF antibody conjugation; Data acquisition of cells in suspension using Helios CyTOF; Image acquisition of tissue sections using Hyperion CyTOF.
University of Michigan Dental School Histology Core Facility
Histology core facility at the University of Michigan School of Dentistry provides histological services using standard histological techniques. The core specializes in sectioning of hard (demineralized) tissues.
University of Michigan Dental School MicroCT Core Facility
University of Michigan Dental School MicroCT Core
Core offers services and instruments. Offers Scanco μCT 100 micro-computed tomography system which provides high resolution scans of radio opaque specimens such as bone, contrasted soft tissue, bio materials, etc.
University of Michigan Dental School Molecular Biology Core Facility
University of Michigan Dental School Molecular Biology Core
Molecular Biology Core (MBC) is School of Dentistry core and provides real-time quantitative PCR service (ABI ViiA7, ABI-7500 instruments), methodology, technique and experiment design consultation, analytical software training, data analysis, statistics and result interpretation assistance
University of Michigan Digital Pathology Core Facility
University of Michigan Digital Pathology Core
Performs scanning on per-request basis; maintains secure database of scanned images and associated metadata; instructs and provides technical support to faculty and staff for DP use; supports of live-view microscopy for frozen sections and testing and validation of new whole-slide imaging solutions.
University of Michigan Electron Microbeam Analysis Core Facility
University of Michigan Electron Microbeam Analysis Lab
EMAL is part of University of Michigan’s School of Earth and Environmental Sciences. Houses CAMECA SX100 electron microprobes, Rigaku X-ray diffractometers, and JEOL JSM-7800FLV field-emission scanning electron microscope. These instruments are used by researchers for chemical and structural characterization of solid materials.
University of Michigan Medical School Radiology Functional MRI Laboratory Core Facility
University of Michigan Functional MRI Laboratory
Interdisciplinary unit organized under University of Michigan's Medical School - Department of Radiology, dedicated to supporting research on structures and functions of brain that underlie cognitive and affective processes, and research on functional MRI and associated research tools. Provides equipped physical facility and intellectual support services for investigators.
University of Michigan High Temperature Corrosion Core Facility
University of Michigan High Temperature Corrosion Lab
Facility to conduct experimental research on corrosion, stress corrosion cracking, and hydrogen embrittlement experiments in high temperature aqueous and gas environments and, in particular, simulated light water reactor environments. Conducts both high and low temperature corrosion, stress corrosion cracking experiments, electrochemical tests and mechanical tests. Consists of refreshed autoclave systems (titanium, Inconel, or stainless steel construction), mounted in constant extension rate machines and constant load machine. Experiments can be done in range of environments, including supercritical water, simulated BWR and PWR water, high temperature steam, and gas environments. Each autoclave is isolated from the other systems with independent water and computer monitoring systems. The lab also contains two full-featured corrosion measurement systems and additional potentiostats.
University of Michigan HomeLab Core Facility
Simulation lab that is designed as home. Provides space to researchers who want to observe participant behavior in more realistic environment. Offers environment that feels authentic and natural to human condition.
University of Michigan Human Research 3 Tesla Magnetic Resonance Imaging Core Facility
University of Michigan Human Research 3 Tesla Magnetic Resonance Imaging
Human Research 3 Tesla Magnetic Resonance Imaging provides high quality anatomic and advanced MR imaging services for IRB-approved research studies and clinical trials with funds allocated for non-standard-of-care research MRI scans.
University of Michigan Human Stem Cell Gene Editing Core Facility
University of Michigan Human Stem Cell and Gene Editing (HSCGE) Core
University of Michigan Human Stem Cell Gene Editing Core
Core supports neuroscience research using stem cell and gene editing technologies. Full service facility. Provides neuroscience research community valuable new sources of human pluripotent stem cells (hPSCs) for basic research, drug discovery, or cell therapy. Offers services including derivation of induced pluripotent stem cells from fibroblasts or blood cells, CRISPR/Cas9-mediated gene editing hPSCs, monolayer differentiation of hPSCs, cerebral organoid differentiation of hPSCs, and training for hPSC maintenance.
University of Michigan Ion Beam Core Facility
Laboratory is part of the Department of Nuclear Engineering and Radiological Sciences in the College of Engineering. MIBL is part of the National Nanotechnology Infrastructure Network. Services involve advancing our understanding of ion-solid interactions. Provides instruments for conducting ion beam surface modification and ion beam surface analysis under range of conditions. Experiments can be conducted at high or low temperature, in ultra-high vacuums, in reactive gas and in short turnaround times.
University of Michigan Irradiation Materials Testing Core Facility
University of Michigan Irradiation Materials Testing Lab
Core provides facility to conduct experimental research on neutron irradiated materials in aqueous environments. The IMTL consists of five refreshed autoclaves that can be mounted in constant extension rate or crack growth rate configurations. Capable of conducting experiments on stress corrosion cracking of neutron irradiated material in supercritical water.
Web application for 2D image registration to 3D atlas. Used for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution histological images, to 3D reference atlas space. Can generate user defined cut planes through atlas templates that match orientation of cutting plane of 2D experimental images (atlas maps).
Web application for nonlinear refinement of image registration after WebAlign.
Bio-Rad | CFX Connect Real-Time PCR System
CFX Connect Real-Time PCR System provides excellent thermal performance for two-target multiplex PCR and routine detection of single fluorophore experiments.
Provides information about the National Health Interview Survey (NHIS) data collection, its participants, and its protocols. It also provides analytic notes and references. They will help you understand, analyze, and us.e NHIS data.
Integrated Public Use Microdata Series Health Surveys
Integrated Public Use Microdata Series Health Surveys provide free individual-level survey data for research purposes from two leading sources of self-reported health and health care access information: the National Health Interview Survey (NHIS) and the Medical Expenditure Panel Survey (MEPS).
University of Michigan Isopaleo Lab Core Facility
Core specializes in precise measurements of rare isotopologues such as “clumped” isotopes of carbonate and CO2 and triple oxygen isotope distributions in waters, carbonates, phosphates and recently organics. Houses Nu Perspective IRMS mass spectrometers, EuroVector EA3000 and HT-PyrOH, NuCarb device for traditional carbon and oxygen isotopes, Thermo Fisher ISQ 7000 GC-MS, fully automated clumped isotope preparation line, semi-automated triple oxygen isotope preparation line, manual water fluorination line, multi-purpose vacuum extraction line, and ovens, balances, glassware, fume hoods, and other equipment used in experiments and sample preparation.
University of Michigan Lurie Nanofabrication Core Facility
University of Michigan Lurie Nanofabrication Facility
Lurie Nanofabrication Facility serves technology educators and creators through broad access to advanced nanofabrication equipment and staff expertise in safe, collaborative environment. Equipment and processes are available for research on silicon integrated circuits, MEMS, III-V compound devices, organic devices and nanoimprint technology. We also encourage researchers from non-traditional disciplines to make use of our processes, such as metal and dielectric coatings, vacuum processes, fabrication of micro and nano components and metrology tools.
University of Michigan Marine Hydrodynamics Lab Core Facility
Aaron Friedman Marine Hydrodynamics Laboratory
University of Michigan Marine Hydrodynamics Lab
Research facility dedicated to the study and testing of various marine and hydrodynamic phenomena. It is part of the Department of Naval Architecture and Marine Engineering at the University of Michigan. Conducts research and experiments related to fluid dynamics, ship design, offshore engineering, and other areas relevant to marine and naval architecture.
University of Michigan Marine Renewable Energy Laboratory Core Facility
University of Michigan Marine Renewable Energy Laboratory
Core dedicated to developing technology to harness abundant, clean, and renewable marine energy in environmentally sustainable way and at competitive cost.
University of Michigan LSA MCDB Imaging Core Facility
University of Michigan MCDB Imaging Core
MCDB Imaging Facility in the Biological Sciences Building provides microscopes available to any University of Michigan researcher. Access to scope time granted after appropriate training. Provides microscope equipment, image capture systems, software to assist researchers with their sample imaging.
University of Michigan MDRC Chemistry Laboratory Core Facility
Michigan Diabetes Research Center Chemistry Laboratory
University of Michigan MDRC Chemistry Laboratory
Core supports investigators interested in assays related to diabetes, heart disease, and hypertension. Analytical methods include general blood chemistry, chemiluminescence, immunoassay, radioimmunoassay, multiplexing, and ELISA.
University of Michigan MDRC Islet Core Facility
Michigan Diabetes Research Center Islet Core
Islet Core provides consultative advice and equipment and services for isolation and study of pancreatic islet structure and function in support of diabetes-related research.
University of Michigan Center for Materials Characterization Core Facility
Michigan Center for Materials Characterization
University of Michigan Michigan Center for Materials Characterization
Facility dedicated to micron and nanoscale imaging and analysis of materials. The center, housed in Building 22 of the North Campus Research Complex, provides instruments and professional training.
University of Michigan Elemental Analysis Laboratory Core Facility
University of Michigan Elemental Analysis Laboratory
University of Michigan Michigan Elemental Analysis Laboratory
Core accommodates mass spectrometers (ICP-MS) – Quadrupole ICP-MS and High-Resolution ICP-MS. Provides solution-based elemental analysis on variety of materials from rock through to natural waters in concentration ranges from ppm to ppt in biological, environmental, geological and industrial materials.
University of Michigan Micro and Nano Computed Tomography Advanced Imaging Core Facility
Nano Computed Tomography Advanced Imaging Core
University of Michigan Micro and Nano Computed Tomography Advanced Imaging Core
Core provides services for acquiring three-dimensional imaging and quantitative analysis of biological and engineered structures/materials. The core is capable of imaging mineralized tissues (e.g., bone, teeth) and soft tissues (e.g., tendons, ligaments, cartilage, blood vessels, muscle) with the aid of radiographic contrast agents. This core is managed and operated by members of the Orthopaedic Research Laboratories.
University of Michigan MicroCT Scanning Laboratory Core Facility
University of Michigan MicroCT Scanning Laboratory
University of Michigan Museum of Zoology MicroCT Scanning Laboratory
Core allows researchers to generate high resolution tomographic data of bone, fossils, and contrast enhanced tissues. These data can include 3D surface visualizations of anatomy and morphology, that can facilitate morphometric studies, phylogenetics analysis, and biomechanics modelling.
University of Michigan Morphomic Analysis Core Facility
University of Michigan Morphomic Analysis Group
Core identifies bio-markers using medical imaging that provides insight into disease processes, treatment options, and outcome variability.
University of Michigan ORL Histology Core Facility
University of Michigan ORL Histology Core
University of Michigan Orthopaedic Research Laboratories Histology Core
Core offers instruments including Reichert-Jung Polycut microtome for decalcified or undecalcified samples, Reichert-Jung rotary microtomes for decalcified specimens, diamond band saws, cryostats for frozen sections with special features for bone section, slow speed diamond saws, high speed grinding cutoff wheel, precision grinding and polishing machines (Buehler Automet 300),complete embedding and preparation equipment and supplies for paraffin, methacrylate, epoxy, and other resins for embedding of biologic specimens, automated tissue processor for plastic and paraffin embedding preparation (Leica ASP 300S)
University of Michigan Pathology Flow Cytometry Core Facility
University of Michigan Pathology Flow Cytometry Core Lab
Core provides instruments including Becton-Dickinson FACSCelesta or ACEA NovoCyte flow cytometer for use after training . Pathology core staff member is assigned to support instruments, answer questions, and, offer on-demand hardware, software, fluidics and technical expertise. Instrument users must ultimately run their own samples and be responsible for technical and scientific legitimacy of their experiments.
University of Michigan Pharmocokinetic and Mass Spectometry Core Facility
University of Michigan Pharmocokinetic and Mass Spectometry Core
Core offers partnership options, including collaboration, fee-for-service and self-service. Helps to discover new medicines, obtain research funding, file patent applications and publish academic research findings. Offers to analyze drug/compound concentration in biological specimens and develop assays.
University of Michigan LSA Chemistry Raman Spectroscopy Core Facility
University of Michigan Raman Spectroscopy Core
University of Michigan Raman Spectroscopy Core Facility
Core offers services and instrumentation including Renishaw inVia microscopes, High sensitivity ultra low noise RenCam CCD detector,Multiple lasers on hand (532nm, 633nm, 785nm),< 1 cm-1 spectral resolution capability. Supports sampling accessories such as fiber optic probes and temperature control stages (liq. He – 300ºC). Offers Automated XYZ stage with 100nm positioning control and Compositional mapping.
Patient monitoring company, which offered wide range of patient monitors in the OR, emergency care, and critical care environments for over 50 years.
University of Wisconsin-Madison Intellectual and Developmental Disabilities Models Core Facility
Intellectual and Developmental Disabilities (IDD) Models Core
Intellectual and Developmental Disabilities Models Core Facility
Models Core in Waisman Center provides resources including mouse models of human conditions, along with behavioral testing capabilities to characterize these models and test new therapies; stem cell technologies to support creation of induced pluripotent stem cell lines for IDD conditions as well as specialized genome editing services; microscopy technology and expertise for characterization of both stem cell and mouse models of IDD conditions.
Wisconsin National Primate Research Center Pathology Services Core Facility
Wisconsin National Primate Research Center Pathology Services
Pathology Services Core is essential to nonhuman primate colony health and research at the WNPRC. PSU team consists of pathologists with ACVP and/or ACLAM board certification, research program manager, and research specialists. Unit works with clinical veterinary staff to provide rapid diagnosis and effective monitoring and interpretation of acute and chronic conditions affecting colony animals as well as subjects assigned to research studies. Core offers services including clinical pathology testing; cytology evaluation; surgical biopsy evaluation; gross post mortem examination, specialized sample collections; and histology with unbiased interpretation of lesions in reference to spontaneous disease, experimental questions, and research goals. PSU is responsible for collection, banking, and distribution of NHP samples through both Nonhuman Primate Biological Materials Distribution core and National Institute on Aging Nonhuman Primate Tissue Bank.
Data server to download subsets of scientific datasets in common file formats and make graphs and maps. This particular ERDDAP installation has oceanographic data (for example, data from satellites and buoys).
Nonprofit that optimizes access to remote scientific data through free open-source software. Discipline-neutral data access protocol (DAP) to access and to provide data over the internet. OPeNDAP was originally developed by and designed for oceanographers, but today the protocol is applied across many diverse domains in which large, complex, distributed datasets are used. Serves data in format that works well with most end users’ preferred data analysis applications. End user can inspect datasets remotely through web URL or number of data tools.
Thermo Fisher | Varioskan LUX Multi-Mode Microplate Reader
Varioskan LUX is modular, upgradable instrument that offers usability for range of applications. Reader for absorbance, fluorescence intensity, chemiluminescence, AlphaScreen, and time-resolved fluorescence.
Fast Unified Random Forests for Survival
Software R package for random forests regression, classification, survival analysis, competing risks, multivariate, unsupervised, quantile regression, and class imbalanced q-classification. Extreme random forests and randomized splitting. Suite of imputation methods for missing data.
Software R package defines S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.
DDRTree: Learning Principal Graphs with DDRTree
Software R package provides implementation of framework of reversed graph embedding which projects data into reduced dimensional space while constructs principal tree which passes through middle of data simultaneously.
Software R package for full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings objects.
Max Planck Institute for Biological Intelligence Imaging Core Facility
Max Planck Institute for Biological Intelligence Imaging Facility
Light microscopy facility. Users are supported with experiment design, image acquisition and operation of microscopes and quantitative processing and analysis of images.
Software UNIX-based, modular bioinformatics toolkit designed to streamline comparative genomics for analyzing microbial communities. It integrates genome annotation, gene spread calculation, plasmid-mediated horizontal gene transfer (HGT) detection and resistance-virulence ranking within the analysed microbial community to help researchers identify potential resistance-virulence hotspots in complex microbial datasets.
Augusta University Medical College of Georgia Cell Imaging Core Facility
Augusta University Medical College of Georgia Cell Imaging Core
Core provides imaging and expert technical assistance and instrumentation in support of investigators.
University of Michigan LSA Biophysics Single Molecule Analysis in Real-Time Center Core Facility
University of Michigan LSA Biophysics Single Molecule Analysis in Real-Time Center
University of Michigan Single Molecule Analysis in Real-Time Center
Microscopy core facility that provides university researchers with imaging and manipulation tools to detect, track, manipulate, and analyze biomolecules. Offers training and data acquisition support as well as experienced consultation on experimental design and analysis.
University of Michigan LSA Stable Isotope Core Facility
University of Michigan Stable Isotope Core Facility
University of Michigan Stable Isotope Facility
Facility performs stable isotope and elemental analyses that support research in climate change, geology, oceanography, and paleontology.
University of Michigan Thermocron Lab Core Facility
Provides facilities for (U-Th)/He thermochronology on variety of accessory minerals, including apatite, sphene, monazite and zircon. The low closure temperature of the (U-Th)/He system in these minerals makes it ideal for application to geological problems in geomorphology, surface processes, tectonics, structural geology, basin evolution, and thermal maturation.
University of Michigan Tissue and Molecular Pathology Shared Resource Core Facility
Rogel Cancer Center Tissue and Molecular Pathology (TMP) Shared Resource
University of Michigan Tissue and Molecular Pathology Shared Resource
Core consists of services relating to procurement and evaluation of tissue for research: Tissue Procurement, Histology, and Molecular Pathology. Provides pathology-sanctioned procurement of surgically resected neoplastic and non-neoplastic tissue (fresh and frozen), sample processing, embedding, sectioning, routine H and E, special staining, and immunohistochemistry. Molecular Pathology Research Laboratory performs immunohistochemistry, in-situ hybridization, multiplex immunofluorescence, FISH staining, and tissue microarray construction.
University of Michigan Battery Lab Core Facility
Full-service battery cell fabrication and testing facility open to any academic or industry user.The lab is an IP-protected safe zone to prototype, test, scale-up, and analyze batteries and the materials that go into them.
University of Michigan LSA Biological Station Core Facility
University of Michigan Biological Station
Core mission is to advance environmental field research, engage students in scientific discovery, and provide information needed to understand and sustain ecosystems from local to global scales. Seek solutions to critical environmental challenges.
University of Michigan College of Pharmacy Vahlteich Medicinal Chemistry Core Facility
University of Michigan Vahlteich Medicinal Chemistry Core
University of Michigan Vahlteich Medicinal Chemistry Core Facility
Design and synthesize drug-like molecules and diagnostic probes in your biomedical investigations to translate your research in all therapeutic areas and disease states.
University of Michigan ULAM Animal Surgery Operating Rooms Core Facility
University of Michigan ULAM Animal Surgery Operating Rooms
Core is part of Unit for Laboratory Animal Medicine. Provides services to perform sterile, minimally-invasive, and non-sterile surgical procedures on both small and large animals. Facility personnel are licensed veterinary technicians and AALAS Technologists.ULAM Veterinary Board-Certified Surgeon also oversees daily operations.Users must have an approved animal use protocol from the Institutional Animal Care & Use Committee (IACUC) prior to utilizing ASOR services and facilities.
University of Michigan ULAM ABSL3 Animal Housing Core Facility
University of Michigan ULAM ABSL3 Animal Housing
ABSL3 core is specialized in environments designed to facilitate safe research with Risk Group-3 microbial pathogens, which pose significant risk of airborne transmission and serious disease. Core safe for conducting high-level infectious disease research.
Software set of pipelines to analyze piRNA/transposon from different Next Generation Sequencing libraries (small RNA-seq, RNA-seq, Genome-seq, ChIP-seq, CAGE/Degradome-Seq).
Augusta University Medical College of Georgia Electron Microscopy and Histology Core Facility
Augusta University Electron Microscopy and Histology Core
Augusta University Medical College of Georgia Electron Microscopy and Histology Core
Core offers variety of specimen preparation services for transmission and scanning electron microscopy, vibratome, paraffin, cryostat and JB-4 sectioning.Offers routine staining and various histological special stains, PASH, Masson Trichrome, Van Gieson and many others, immunohistochemical services including immuno-EM studies. Core staff performs all aspects of the ultrastructural procedures from specimen processing to imaging (for Electron Microscopy, TEM and SEM) and processing, sectioning, and staining for light microscopy (paraffin, cryostat, and JB-4).
National Academy of Sciences of Armenia Institute of Molecular Biology Sequencing Core Facility
Sequencing core facility provides access to high-throughput DNA sequencing technologies and related services. Equipped with sequencing instruments, including long-read platforms, Illumina systems, and more. Provides comprehensive suite of tools to support sample preparation and ensure the quality of all sample types.
National Academy of Sciences of the Republic of Armenia is the Armenian national academy, functioning as the primary body that conducts research and coordinates activities in the fields of science and social sciences in Armenia.
Software R package provides interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. Allows users to integrate tools from various packages at different stages of analysis workflow.
Software tool as enhanced version of NRSA for analyzing nascent transcription profiles generated by PRO-seq, GRO-seq, (m)NET-seq, and Butt-seq data.
Cleveland Clinic Lerner Research Institute Engineering Core Facility
Core provides mechanical and biomedical engineering expertise and services. Specializes in early-stage development and proof-of-concept prototypes. Utilizes 3D modeling, 3D printing, nitinol shape setting, and laser cutting to design and fabricate custom medical devices, test fixtures, and CT/MRI-based anatomy models.
Database that attempts to consolidate information on known clinical and selected set of pre-clinical biomarkers into single resource. Database includes five major types of biomarkers (condition specific, protein, chemical, karyotypic and genetic) and six biomarker categories (diagnostic, risk, prognostic, safety, monitoring, and response). Provides information such as: biomarker names and synonyms, associated conditions or pathologies, detailed disease descriptions, detailed biomarker descriptions, biomarker specificity, sensitivity and ROC curves, standard reference values (for protein and chemical markers), variants (for SNP or genetic markers), sequence information (for genetic and protein markers), molecular 2D and 3D structures (for protein and chemical markers), tissue or biofluid sources (for protein and chemical markers), chromosomal location and structure (for genetic and karyotype markers), clinical approval status and relevant literature references. Users can browse the data by conditions, condition categories, biomarker types, biomarker categories or search by sequence similarity through the advanced search function.
Software R package for data cleaning, exploring, and simple reporting. At its core reside the following four functions: freq(), ctable(), descr(), and dfSummary(). Used to quickly and neatly summarize data.
Software R package for computing pseudo-observations for censored data regression. Computes pseudo-observations for modeling: competing risks based on the cumulative incidence function, survival function based on the restricted mean, survival function based on the Kaplan-Meier estimator.
University of Michigan Medical School Microbiome Core Facility
University of Michigan Medical School Microbiome Core
Core provides microbial sequencing, high-throughput nucleic acid extraction, microbial cultivation, and strain identification.
Web portal contains information on how to calculate DNA methylation (DNAm) age based on data measured using the Illumina Infinium platform.
Software tool as simple wrapper of tabula-java to extract table from PDF into pandas DataFrame. Python wrapper of tabula-java, which can read tables in PDF. Also enables you to convert PDF file into CSV, TSV or JSON file.
Cleveland Clinic Lerner Research Institute Mechanical Prototyping Core Facility
Mechanical Core provides variety of fabrication, customization and repair services for mechanical devices and equipment. Offers precision machining of metals and plastics, welding of structural and exotic metals, instrument refurbishing and mechanical repair.
Software R tool for generating brain-predicted age value, using Gaussian Processes regression. Used for generating brain-predicted age value from raw T1-weighted MRI scan.
Software Python commandline tool for rapid calculation and correction of fragment length specific GC biases in WGS cfDNA sequencing datasets for liquid biopsy applications. Used for evaluating and correcting GC biases in cell-free DNA at fragment level.
Database including classification and annotation of genome-wide transcription factors and transcription cofactors in animal genomes. Annotation and prediction of animal transcription factors.
Provides a range of assay kits, ELISA kits, high-quality antibodies, antigens, recombinant proteins, and DNA/RNA extraction kits all of which undergo stringent quality control measures at every stage of production to ensure they meet the highest standards of precision and reliability.
Revvity | LabChip GX Touch Nucleic Acid Analyzer
Automated microfluidic electrophoresis system that rapidly quantifies and sizes DNA and RNA with high sensitivity using minimal sample volume.
Molecular Devices | ImageXpress Pico Automated Cell Imaging System
ImageXpress Pico Automated Cell Imaging System
Digital microscope, combining high-resolution imaging with analysis. Whether running fluorescence imaging or brightfield assays, automated imager features comprehensive preconfigured protocols for cell-based assays to shorten learning curve.
Howard Hughes Medical Institute at Janelia Research Campus Molecular Genomics Shared Resource Core Facility
Core provides services and expert advice on routine and specialized molecular biology techniques including plasmid preps, genome editing, mutation detection, digital PCR and spatial transcriptomics.
Automated microbial detection system. Instrument for detecting bacteria in biologic and non-biologic samples.
Source code for pose recognition model for laboratory mice based on yolov8. Real-time spatiotemporal network model for robust mouse pose estimation.
Organ Level INternal Dose Assessment/EXponential Modeling
Software to evaluate mean absorbed doses to organs and tumors in radionuclide images, providing simple and fast solution for radionuclide imaging and treatment of new drugs in clinical trials. Calculates radiation doses to organs and the whole body based on established human body models.
Software R package for deconvolution of mixed cells from spatial and/or bulk gene expression data. Algorithm for quantifying cell populations defined by single cell sequencing within regions of spatial gene expression studies. Used for mapping cell types in spatial gene expression studies.
Software tool as text and source code editor for use with Microsoft Windows.
Software tool as second version of Kraken taxonomic sequence classification system.
University of Bergen Genomics Core Facility
Provides genomic services to study genome structure, dynamics and function using Illumina next generation sequencing. Offers expert advice on experimental design and bioinformatics analysis, training and assistance on data storage solutions.
NIH Center for Cancer Research Sequencing Core Facility
NIH Center for Cancer Research Sequencing Facility
Provides access to the latest technologies, with consultation and services available throughout the design and execution of sequencing projects.
University of Queensland Institute for Molecular Bioscience Advanced Microscopy Core Facility
University of Queensland Institute for Molecular Bioscience Advanced Microscopy Facility
Microscopy Facility supports cancer research, cell and developmental biology, and cross-disciplinary studies spanning molecular mechanisms to translational applications. Houses imaging platforms including widefield, confocal, multi-photon, super-resolution, spinning disk, and light sheet systems. Enables advanced modalities such as TIRF, FRET, STED, SHG/THG, and FLIM for detailed exploration of cell behaviour and microenvironments. Facility staff offer training, expert consultation, image analysis support, and troubleshooting.
University of Michigan Rogel Cancer Center Single Cell Spatial Analysis Shared Resource Core Facility
University of Michigan Health Single Cell Spatial Analysis Shared Resource
University of Michigan Rogel Cancer Center Single Cell Spatial Analysis Shared Resource
Provides expertise through experimental design consultations,cell isolation,single cell analytics (RNA, DNA, protein),biomarker validation,novel statistical and bioinformatics analyses. Services include Single cell targeted gene expression, Single cell RNA Seq, Single cell DNA Seq, Tissue sectioning, Tissue spatial analysis, Spatial transcriptomics and proteomics.
University of Michigan Bioinnovation in Brain Cancer High-Plex Immunocytochemistry Core Facility
University of Michigan High-Plex Immunocytochemistry Core
University of Michigan Immunocytochemistry Core Facility
Core utilizes Akoya PhenoCycler-Fusion to enable high-plex spatial phenotyping of whole tissue slides at single-cell resolution.
University of Michigan Bioinnovations in Brain Cancer Formulation and Translation Core Facility
University of Michigan Bioinnovations in Brain Cancer Formulation and Translation Core
University of Michigan Formulation and Translation Core
Core offers sample analysis and experiment design, market assessment and FDA regulation, facilitate interactions for intellectual property protection and support submission of translational grant applications within University of Michigan and government agencies.
University of Michigan Medical School Central Biorepository Core Facility
University of Michigan Central Biorepository
University of Michigan Medical School Central Biorepository
Core provides annotated biospecimens for basic, clinical, and translational research. Helps researchers access, collect, manage, and protect biospecimens using automated processes and quality control. Offers safe and monitored management of biospecimens including temperature-controlled storage, preparation of derivatives from these specimens, aliquoting, distribution, and production of specimen collection kits.
Software Python tool for detecting and counting nematode eggs from microscopy images.
Structure Parameter Inference Approach Carbohydrate Homeostasis
Software tool to deliver estimated structure parameters of endocrine feedback control systems in vivo from serum or plasma hormone levels. Used for the evaluation of insulin-glucose homeostasis. Allows for calculating the secretory capacity of pancreatic beta cells (SPINA-GBeta), insulin receptor gain (SPINA-GR) and a static disposition index (SPINA-DI) from fasting concentrations of insulin and glucose. Additionally, HOMA, QUICKI and other calculated parameters are delivered as well. Binaries are available for macOS and Windows. For other operating systems, including Linux, Solaris and BSD, SPINA Carb is available as source code. Building from source requires Lazarus/Free Pascal. A special version of the calculation engine is available for modern S implementations, e.g. R.
Cleveland Clinic Lerner Research Institute BioRobotics and Mechanical Testing Core Facility
Core provides biomechanical testing of biological structures and biomaterials. Allows investigators to conduct research of mechanical properties of existing biological structures and constructs, as well as to quantify potential for new technologies and clinical advancements. Robotic simulators are built around the simVITRO software platform and are designed for in vitro simulation of major joints including knee, spine, foot, ankle, hip, shoulder, elbow, wrist and more. Provides testing capabilities for range of biomechanical modalities and will offer expert advice and support for development of new test protocols, innovative techniques for instrumentation and data collection. Modalities include tissues, joints, and multi-articular units, such as foot or spine segments.
Cleveland Clinic is renowned for its advancements in cardiac care, including pioneering coronary artery bypass surgery, and its focus on research and education. It's also known for its strong performance in numerous other specialties, including neurosurgery, gastroenterology, and oncology
ZenCELL owl | live cell imaging and analysis system
innoME GmbH ZenCELL owl live cell imaging and analysis system
24 channels microscope for incubator with automated remote monitoring of cell cultures. 24 independent cameras are used to acquire brightfield or darkfield scans and perform image analysis of up to 24 wells of cell culture in parallel automatically. Culture quality and data can be checked from PC. It enables real-time, non-invasive, label-free monitoring of cell growth directly inside standard incubators. The system captures time-lapse images and performs automated quantitative analysis, generating dynamic growth curves and detailed cellular behavior profiles.
Manually curated database of ferroptosis regulators and ferroptosis-disease associations. There are two secondary categories of ferroptosis regulators: (1) genes and (2) substances. Gene regulators include driver, suppressor, marker, and unclassified regulator. Substances cover range of chemical entities, including pure substances (e.g., iron, erastin) and mixtures (e.g., herbal extracts). Substance regulators include inducers and inhibitors. FerrDb V2 is updated database.
Software R and Python package for comparison and visualization of biological identifiers lists using area-proportional Venn diagrams. Also offers option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Used to create area-proportional Venn diagram of 2 or 3 circles.
Software tool to project scRNA-seq data into reference single-cell atlases, enabling their direct comparison in stable, annotated system of coordinates. Predicts effects of cell perturbations and identifies gene programs that are altered in different conditions and tissues. Used for interpretation of cell states using reference single-cell maps.
Benchtop, high-resolution, spectral imaging instrument that integrates quantitative immunofluorescence and brightfield imaging.
Rush University Medical Center Genomics and Microbiome Core Facility
RUSH University Genomics and Microbiome Core Facility
Core provides full service genomics and Next Generation sequencing. Specializes in microbial sequencing.
Rush University Medical Center is academic medical center for basic and clinical research, with physicians and scientists involved in hundreds of research projects developing and testing the effectiveness and safety of new therapies and medical devices. Offers residency and fellowship programs in medical and surgical specialties and subspecialties.
Web application provides users with visualization interface to explore and analyze interaction networks between miRNAs and target genes.
Software tool for multi-level visualization of genomic statistical variables on rectangular chromosomes.
University of Nebraska Medical Center Single Cell and Spatial Transcriptomics Core Facility
University of Nebraska Medical Center UNMC- Spatial Profiling Hub Core Facility
UNMC- Spatial Profiling Hub Core Facility
Core offers spatial omics processing on many different tissue types. Facility provides instrumnets including Bruker's GeoMx DSP ready for launch with anticipated launch of 10x Visium. Offers expert collaboration from project design to data handoff. Core has established workflows with additional shared resources on UNMC campus to allow for expertise throughout entire project.
Cancer Research Institute IFOM EMSM Electron Microscopy Single Molecules Core Facility
IFOM EMSM - Electron Microscopy Single Molecules Core Facility
Facility uses transmission electron microscopy coupled to low angle rotary shadowing to visualize nucleic acids. This technique allows the inspection of the fine ultrastructure of in vivo chromosomal DNA intermediates on properly enriched genomic DNA samples.
Cancer Research Institute IFOM CERD Cancer Engineering R&D Core Facility
IFOM CERD - Cancer Engineering R&D Core Facility
Core focuses on development of innovative biomedical technologies and devices for cancer research as well as biomedical applications using microfabrication and 3D printing.
Cancer Research Institute IFOM EMCT Electron Microscopy Cells & Tissues Core Facility
IFOM EMCT - Electron Microscopy Cells & Tissues Core Facility
Core performs routine transmission and scanning Electron Microscopy and all kinds of immune Electron Microscopy, correlative light electron microscopy, three-dimensional EM (3DEM), quantitative stereological evaluation of data and more.
Cancer Research Institute IFOM CPM Cellular And Preclinical Models Core Facility
IFOM CPM - Cellular And Preclinical Models Core Facility
Specialized laboratory designed for growth, maintenance, and experimentation of living cells under controlled conditions. This facility is used in various fields such as biomedical research, drug development, and supports the culture of primary cells, immortalized cell lines, human-induced pluripotent stem cells (hiPSCs), and organoids, among others.
Cancer Research Institute IFOM FC Flow Cytometry Core Facility
Core Facility provides technology, instrumentation, and expert support for applications, including Immunophenotyping, Cell cycle and proliferation analysis, Metabolic studies, Apoptosis detection, Fluorescent protein expression analysis, Cytokine, chemokine, and intra/extracellular protein detection.
Cancer Research Institute IFOM ALM Advanced Light Microscopy Core Facility
IFOM ALM - Advanced Light Microscopy Core Facility
Core Facility provides technological platforms in the field of light microscopy. A team of highly qualified and experienced professionals supports IFOM's research activities, assisting in sample preparation and acquisition, data post-processing and image analysis.
Cancer Research Institute IFOM FGS Functional Genomic Screening Core Facility
IFOM FGS - Functional Genomic Screening Core Facility
Core specializes in high-throughput CRISPR screening using pooled or arrayed libraries in diverse cellular models. This technology assesses the effects of thousands of genetic perturbations at single-cell resolution with CRISPR knockout (CRISPR KO), CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa). It also utilizes base and prime editing to investigate specific mutations, such as those relevant to cancer development and progression.
IFOM ETS - The AIRC Institute of Molecular Oncology; Milan; Italy
FIRC Institute of Molecular Oncology - IFOM
Cancer research institute focused on the study of cancer formation and development.
Northwestern University SynBio Foundry Core Facility
Core facility for synthetic biology experimentation including pilot-scale fermentation, high throughput automation, biological sample analysis, and cell-free protein synthesis.
Cleveland Clinic Lerner Research Institute Electronics Core Facility
Electronics Core is electronics design, development and repair facility which specializes in proof-of-concept design and prototyping, and early stage development of medical devices and laboratory research instrumentation. Services include system design, schematic capture, printed circuit board layout, board fabrication, assembly and testing.
University College London LMCB Light Microscopy Core Facility
University College London LMCB Light Microscopy Facility
Core provides imaging systems for advanced microscopy including confocal, multi-photon and super-resolution modalities, enabling users to address research questions in living systems across temporal and spatial scales. Staff offers training to use equipment, expertise about experimental strategy, design, image processing and analysis.
Software package contains all original code used to process MxIF data.
Code to analyse data from "Conserved pan-cancer microenvironment subtypes predict response to immunotherapy" by Bagaev et al.
Software R package to convert statistical analysis objects from R into tidy format. Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once.
Software R package provides two methods of plotting categorical scatter plots such that arrangement of points within category reflects the density of data at that region, and avoids over-plotting. Categorical Scatter (Violin Point) Plots.
High-performance computing facility. Its resources have been designed to support labs engaged in genetics and bioinformatics research, but are open to anyone on campus. The Stanford SCG Bioinformatics Cluster is optimized to support large memory, single-node threaded applications as well as applications and workflows that require many small files.
Software R package with various confidence intervals for binomial proportions inside. Confidence intervals are for single, paired and independent proportions. Various confidence interval methods for proportions.
Database compiles various types of data and information from literature and generalist databases on human TP53 gene variations related to cancer.
Thermo Fisher: Invitrogen | Qubit 4 Fluorometer with WiFi
Qubit fluorometer designed to accurately measure DNA, RNA, and protein quantity, and now also RNA integrity and quality. Qubit 4 Fluorometer was re-engineered to enable data transfer via WiFi as well as to run Qubit RNA IQ assay. Qubit 4 Fluorometer and RNA IQ Assay Kit work together to accurately distinguish intact from degraded RNA in two steps.
Leica | BOND-MAX Fully Automated IHC and ISH Staining System
BOND-MAX Fully Automated IHC and ISH Staining System
Bench-standing IHC/ISH stainer with three-tray system, with 3.5hour run times. Each tray functions independently, allowing on-demand access and enabling you to load slides as they become available. System accommodates up to 29 antibodies (with detection loaded) and allows for easy swapping of antibodies without interrupting ongoing staining processes.
Immunohistochemistry stainer is united with software and connectivity options. Can process 48 slides in less than three hours.
AI-powered scanner for H&E- and IHC-stained whole slide images that enables automated quality control workflow by detecting the most common artifacts generated during process of slide preparation and scanning including air bubbles, dust/debris, folds, out-of-focus areas, and pen marks. It is integrated into the HALO AP diagnostic digital pathology platform.
IN Cell 2500HS widefield cell imaging system
Fully-automated, widefield cell imaging system. Building on capabilities of earlier IN Cell Analyzer systems, it provides platform to deliver advances in speed, image quality, and throughput. Allows to perform analysis.
Covaris | LE220-plus Focused-ultrasonicator
Ultrasonicator is scalable, automated high-performance sample preparation instrument with automated water works to optimize user-to-user reproducibility and remote set-up and scheduling. Designed for integration with high-throughput laboratory automation. Includes integrated AFA ultraCUBE water chiller and water conditioning module.
Software command tool for metagenomic binning with deep learning, handles both short and long reads. Used for metagenomic binning at contig level which uses deep contrastive learning.
Software tool to predict completeness and contamination of genomic bins. Used for predicting genome quality of metagenome-assembled genomes. Assessing microbial genome quality using machine learning.
Software tool to identify genomic structural variation in target regions/genes from reference-aligned high-throughput sequence data. Used to identify structural variation from sequencing data in target regions.
Software tool for assignment of known mutational signatures to individual samples and individual somatic mutations.
Beckman Coulter | Vi-CELL BLU Cell Viability Analyzer
Cell counter automates trypan blue dye exclusion method for cell viability that has been performed with light microscope, pipette, and hemacytometer.
Xstrahl | Small Animal Radiation Research Platform (SARRP) system
Small Animal Radiation Research Platform (SARRP) system
System used for in vivo radiation therapy and imaging of in vivo radiation therapy and imaging, like mice and rats, in order to study tumor and normal tissue responses to radiation. It combines micro-CT imaging with conformal radiation delivery, allowing researchers to image small tumors and organs, then precisely deliver radiation therapy with sub-millimeter accuracy.
Revvity | SciClone G3 liquid handling workstation
Advanced automated liquid handling platform originally developed by PerkinElmer. Designed and programmed for next generation sequencing (NGS) applications. They feature library of over 120 pre-developed and verified or vendor qualified automated NGS preparation kits.
Michigan State University Flow Cytometry Core Facility
Core provides access to analytical flow cytometry instrumentation and cell sorting services, as well as training and experimental consultation.
Cleveland Clinic Lerner Research Institute Polymer Core Facility
Engineers in the Polymer Core work closely with physicians, surgeons, and researchers throughout Cleveland Clinic to provide extensive services on medical device design, prototype and evaluation. We help our inventors to “prove the concept” of their novel inventions, which will ultimately benefit our patients. We also help research groups at Lerner Research Institute to fabricate or repair research instruments, which are not commercially available, such as cell culture fixture, test instruments, etc.
University of New England In Vitro Analytical Core Facility
University of New England In Vitro Analytical Core
Core provides expertise and instrumentation to study cell-cell interactions and to delineate intracellular pathways in targeted cell types. Provides training, instrumentation, and technical services for development, analysis, and storage of in vitro cell models (such as stably transfected cell lines using genetically encoded biosensors), sample preparation for downstream analyses such as mass spectrometry and RNA-seq.
Software tool for analysis of simulated and real-world biomedical datasets.
Medical Imaging and Data Resource Center (MIDRC) data repository
Data repository that is hosting medical images.
Software pan-and-zoom type online viewer for viewing collection of high-resolution images in web browser. Images are expected to be in tiled multi-scale representation.
Sanofi-Aventis was the former name of the French multinational pharmaceutical and healthcare company Sanofi, now headquartered in Paris, France. Sanofi S.A. is global healthcare company focused on discovering, developing, and delivering medicines and vaccines.
Primary national agency of the Government of Canada dedicated to science and technology research and development. It is the largest federal research and development organization in Canada. Works closely with Canadian firms, helping them bring new technologies to market.
Software tool as scoring functions for Hi-C matrix prediction optimization. Regression models for predicted Hi-C data. The input for the regression are human expert rankings and different Hi-C evaluation scores.
Software mouse brain histology tool for neuroscientists. Semiautomated registration and cell counting tool for mouse neurohistology analysis.
Advanced Multilanguage Interface to CVODES and IDAS
Software toolbox implemented in C++/Python/MATLAB that provides efficient simulation and sensitivity analysis routines tailored for scalable, gradient-based parameter estimation and uncertainty quantification. Used for high-performance sensitivity analysis for large ordinary differential equation models.
Software Python package for parameter inference. Used for parameter estimation for dynamic models.
Repository contains PEtab specifications and additional documentation. Data format for specifying parameter estimation problems in systems biology. SBML and TSV based data format for parameter estimation problems in systems biology. Human- and computer- readable format for representing parameter estimation problems in systems biology.
African Genome Variation Database (AGVD)
Database for exploring genomic variation data within African populations.
AGMP provides researchers with platform from which they can retrieve existing information regarding genetic associations to disease-related phenotypes in African populations.
AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in standardised and structured format. AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using language or ethnicity identifier or synonyms.
Catalogue provides searchable metadata for datasets generated and used by the DS-I Africa consortium and external organisations/projects across the African continent.
Web portal provides interconnected resources and services for African genomics research data lifecycle management and implementation. African genotype imputation service using diverse African population reference panel. African genomics data hub.
Human Heredity and Health in Africa catalogue
Catalogue enables users to search for H3Africa datasets or biospecimens of interest. Catalogue is updated periodically with metadata from studies submitted to H3Africa Archive and corresponding biospecimen metadata uploaded from following biorepositories: IBRH3AU: Makerere University, Uganda; IHVN: Institute of Human Virology, Nigeria; CLS: University of the Witswatersrand School of Pathology, South Africa.
United States Core Data Interoperability
United States Core Data for Interoperability (USCDI) is standardized set of health data classes and constituent data elements for nationwide, interoperable health information exchange. USCDI is US Government common data elements for patient data.
Software suite of data collection toolkits that cover range of biomedical research fields. These toolkits provide data collection forms that can be used to build research database and can facilitate phenotype standardisation and harmonisation efforts on African continent and larger user community.
The timsTOF fleX is fully functional high speed, high sensitivity ElectroSpray Ionization (ESI) instrument for all Omics analyses with integrated Matrix-Assisted Laser Desorption Ionization (MALDI) source for fast MALDI Imaging.
Software package provides several functions and parameters for simulating genetic variations. Benchmarking variation simulator mimicking human variation spectrum.
Software Monte Carlo tool for particle simulation. Used for simulation of medical applications of ionizing radiation with the Monte Carlo method. Allows to assemble and control library of simulation objects (geometry components, particle sources, scorers, etc.) with no need to write C++ code and without knowledge of underlying Geant4 Simulation Toolkit.
Software application as quantum chemical based program that enables users to calculate mass spectra using Born-Oppenheimer Molecular Dynamics. Quantum mechanic mass spectrometry calculation program.
Software semiempirical extended tight-binding program package. Provides userfriendly interface for performing geometry optimizations, vibrational frequency calculations, and Molecular Dynamics simulations.
Open-source web application created for easy access, collaboration, and sharing of datasets through rich metadata search, filter, sort, and direct viewing in common industry applications or in our web-based 3D Volume Viewer.
University of Texas MD Anderson Functional Genomics Core Facility
University of Texas MD Anderson Cancer Center Functional Genomics Core
University of Texas MD Anderson Cancer Center Functional Genomics Core Facility
Core provides researchers with genetic tools, including shRNA, ORF and CRISPR for studying and annotating gene functions in cell-based assays. FGC personnel provides research support for investigators who are interested in genetic screens.
University of Texas MD Anderson Research Histology Core Facility
University of Texas MD Anderson Research Histology Core Laboratory
Core supports basic and clinical research by providing histological and molecular expertise, technical support and consultation to research investigators. Provides histological, molecular and consultation services. Services are performed by American Society of Clinical Pathology certified histologists with expertise in routine histology, whole slide scanning, image and digital analysis, pathology services, immunohistochemistry, tissue microarray, bone histomorphometry, Visium preparations and RNAscope single and co-detection assays.
IFOM ETS Cogentech QPCR Quantitative PCR Core Facility
Cogentech QPCR - Quantitative PCR Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 8th,2025. ogentech's Quantitative PCR (QPCR) Core Facility provides services including project design, assay selection and development, data analysis for quantitative analysis of any specific target sequence for gene expression, copy number variation or variant analysis, in low and high-throughput mode. Provides analysis using both Real Time PCR and digital PCR. Special protocols for small amounts of starting material have been implemented. The laboratory is ISO9001 certified.
IFOM ETS Cogentech HP Histopathology Core Facility
Cogentech HP- Histopathology Core Facility
Cogentech's Histopathology (HP) Core Facility provides services including consultation, tissue trimming and embedding, cutting, staining, photographic documentation for the evaluation and characterization of normal and pathological tissues. Provides Optimization of protocols for new stains or biological specimen.The laboratory is ISO9001 certified.
IFOM ETS Cogentech GU Genomics Core Facility
Cogentech's Genomic Core Facility (GU) provides professional support for workflow of research projects, from counseling on experimental design to functional interpretation of results. Support includes identification of the most suitable methodology to achieve the experimental aim, quality control of nucleic acid, generation of indexed fragment library, sequencing according to experimental needs and bioinformatic support for selected applications. Customized protocols can be set-up as well. Sequencing data are delivered using a password protected user-friendly web interface. The laboratory is ISO9001 certified.
IFOM ETS Cogentech BRF Biological Research Core Facility
Cogentech BRF - Biological Research Facility
Cogentech's Biological Research Facility (BRF) provides animal facility in which laboratory mice are maintained and bred for different research programs. The laboratory is ISO9001 certified.
IFOM ETS Cogentech Proteomics and Metabolomics Core Facility
Cogentech P&M - Proteomics & Metabolomics Core Facility
Cogentech's Proteomics and Metabolomics Core Facility provides infrastructure for identification, characterization and quantification of proteins, metabolites and lipids.Offers several instrumental platforms for separation of those molecules. Proteomics, metabolomics and lipidomics analysis rely on mass spectrometry coupled with liquid chromatography.
IFOM ETS Cogentech IGU Integrative Genomics Core Facility
Cogentech IGU - Integrative Genomics Core Facility
Cogentech's Integrated Genomics Core Facility (IGU) consists of units: Molecular Biology and Sequencing, Histopathology and Bioinformatics. Molecular Biology group provides expertise in various fields of application: nucleic acid extraction from different matrices, ddPCR and various types of sequencing (customised gene panels, Lowpass WGS, WES, WGS, total RNA-Seq, mRNA Seq, TCR-Seq, 16S Metagenomic Seq, ATAC-Seq, genome-wide methylation profiling). Bioinformatics unit provides pipelines for analysis of data produced by all sequencing workflows. In addition, it provides its expertise for implementation and development of customised pipelines. Histopathology unit offers services for slide preparation and staining, image digitisation and laser-capture microdissection. The laboratory is ISO9001 certified.
IFOM ETS Cogentech DSS DNA Sanger Sequencing Core Facility
Cogentech DSS - DNA Sanger Sequencing Core Facility
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 8th,2025. Cogentech's DNA Sanger Sequencing (DSS) Core Facility offers standard DNA sequencing and assistance for projects using on Sanger sequencing. We also offer the possibility to use fragment analysis for various applications, providing assistance in the pre-and post-analytical phase. The laboratory is ISO9001 certified.
IFOM ETS Cogentech Cancer Genetic Test Laboratory Laboratory Core Facility
Cogentech Cancer Genetic Test Laboratory
Cogentech CGT lab (Cancer Genetic Test Laboratory)
Cogentech's CGT lab is offering its diagnostic services for Hereditary Tumors (Cancer Risk) and for Personalized Medicine (Therapy) to clinicians, laboratories and hospitals.
Ugo Basile | Electronic Von Frey - e-VF Handheld
Electronic von Frey system for rodents. Used for touch sensitivity in unrestrained animals. The scientist gradually increases the force applied to the animal paw, until the peak detector scores the animal paw withdrawal (or the user scores it manually with the included pedal).
Software application for accurate and rapid prediction of IAV subtypes and host source.
National Institute on Drug Abuse Confocal and Electron Microscopy Core Facility
National Institute on Drug Abuse Confocal and Electron Microscopy Core
NIDA IRP Confocal and Electron Microscopy Core
NIDA IRP Confocal and Electron Microscopy Core (CEMC)
NIDA IRP Confocal and Electron Microscopy Core serves NIDA-IRP researchers by providing access to confocal and electron microscopic technologies to characterize cellular and ultrastructural properties of organelles, tissue culture and brain tissue. Provides expertise, consultations and training in adaptation and execution of confocal and electron microscopic techniques and procedures.
North Carolina State University Genomic Sciences Laboratory Core Facility
North Carolina State University NCSU Genomic Sciences Laboratory
Core provides equipment and infrastructure required to conduct advanced genomics research. Provides access to DNA sequencing, traditional Sanger sequencing and genotyping, and additional equipment services for functional genomic assays and mapping. Provides robotics and instrumentation to facilitate the handling of large numbers of samples, as well as many advanced sequencing and sequencing support applications.
Boise State University Biomedical Research Institute Biomolecular Research Core Facility
Biomedical Research Institute Biomolecular Research Core Facility
Biomolecular Research Core Facility (BRCF)
Biomolecular Research Core Facility (BRCF) has collection of instrumentation for characterization of biomolecules and their role in variety of processes. Instrumentation is accessible to internal and external customers. Available instrumentation focuses on mass spec, histology, imaging, and protein biochemistry.
National Institute on Drug Abuse Histology and Imaging Core Facility
National Institute on Drug Abuse Histology and Imaging Core
NIDA-IRP Histology and Imaging Core (HIC)
NIDA-IRP Histology and Imaging Core serves NIDA-IRP researchers by providing access to existing and emerging neuroanatomical technologies to map and characterize neuronal circuits. Provides expertiese, consultations and training to NIDA-IRP researchers in the adaptation and execution of neuroanatomical techniques and procedures.
Windows Subsystem for Linux (WSL) is feature of Windows operating system that enables to run Linux file system, along with Linux command-line tools and GUI apps, directly on Windows, alongside traditional Windows desktop and apps. Tool for developers, especially web developers, those working on open source projects, or deploying to Linux server environments.
Ubuntu terminal environment on Windows with Windows Subsystem for Linux (WSL). Used to streamline web application development, leverage cutting-edge AI/ML tooling, develop cross-platform applications and manage IT infrastructure without leaving Windows.
Software package that provides client interface to Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Client-side REST access to KEGG.
Software R package to generate Venn diagram.'ggplot2' implement of Venn Diagram.
Approximate Posterior Estimation for generalized linear model
Approximate posterior estimation for GLM
Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients.
Software for Kinship coefficient estimation from low coverage ancient (or degraded forensic) genome data. Used to infer relatedness up to the 4th degree from low-coverage ancient human genomes.
Software sequence simulator for ancient DNA. For ancient hominin samples can also simulate various levels of present-day human contamination and microbial contamination.
Ancient DNA genetic relatedness estimation software relying on pedigree simulations. Used to compute estimate of relatedness from randomly sampled pseudo-haploidized variant calls, and leverages high-definition pedigree simulations to bypass the use of cohort of individuals.
Software tool to estimate pairwise relatedness from ancient DNA, taking in account contamination, ROH, ascertainment bias. Used to identify identity-by-descent fragments and to estimate degree of relatedness from ancient DNA data.
Software framework for analyzing low-depth next-generation sequencing data in heterogeneous/structured populations using principal component analysis.
Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances.
Relationship Estimation from Ancient DNA
Software tool to infer family relationships for degraded samples. Used to infer degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for pair of low-coverage individuals.
Relationship Estimation from Ancient DNA version 2
Software Python3 tool for advanced, user-friendly detection and nuanced analysis of biological relatedness from ancient DNA samples in archaeogenomics. Can classify up to third-degree relatedness and differentiate between two types of first-degree relatedness, full siblings and parent-offspring.
Software ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data.
Software suite of algorithms used for arranging and visualizing graph structures. They provide variety of layout styles, such as hierarchical, organic, tree, circular, and orthogonal, each optimizing for different criteria and visualization needs.
Design and analysis software enables user to set up runs, send plates to the specific instrument, open completed run files, and analyze and review data in integrated and streamlined fashion. Software can be run with security, audit, and e-signature (SAE) enabled. The software also provides suite of analysis modules for secondary analysis and comes with multi-language support.
Thermo Fisher: Invitrogen | Countess 3 Automated Cell Counter
Automated cell counter was developed using advanced machine-learning image analysis algorithm to deliver accurate cell counts and viability measurements using slide containing cell sample in fewer than 30 seconds. Has automated lighting, focus, capturing, counting, and saving.
Viral Intra-Patient Evolution Reporting and Analysis
Software package to automate analysis of evolutionary trajectories over time of series of sequences from same viral infection. Snakemake workflow for SARS-CoV-2 viral intra-patient evolution reporting and analysis.
Software package for robust identification of somatic mutations in acute myeloid leukemia using RNA-sequencing. Detects clinically important somatic mutations from RNA-seq data on relatively small gene panel (typically less than 100 genes).
Software R package and shiny app for processing, plotting, and interactive exploratory data analysis of full-length scRNA-seq as SingleCellExperiments.
Benaroya Research Institute BRI Biorepository Core Facility
Benaroya Research Institute BRI Biorepository
BRI is home to rigorously maintained biorepositories containing blood and tissue samples donated by people with immune-mediated diseases and healthy controls.Provides the collection of samples from research participants, sample processing, storage, and sharing.
Implant for Reliable Diaphragm EMG Recordings in Awake, Behaving Rats
Low-cost implant for reliable diaphragm EMG recordings in awake, behaving rats.Diaphragm EMG implant.
University of Miami Hussman Institute for Human Genomics Induced Pluripotent Stem Cell Core Facility
Induced Pluripotent Stem Cell (iPSC) Core
Core provides standardized services for derivation and characterization of human iPSC lines from peripheral blood and tissue samples. Offerings include PBMC isolation, reprogramming, Sendai virus reprogramming vector removal and analysis, karyotyping, mycoplasma testing, in vitro differentiation of neural and hemopoietic progenitor cells, and immunocytochemical staining of cell type markers and imaging. Core additionally offers hands-on training and consultation to support the use of iPSC technologies in disease modeling.
Web-based analysis platform offering end to end analytics for spatial omics datasets.
Web platform that integrates multiple programming language environments and enables data processing, data analysis, and machine learning through visual interface.
High-performance nanoflow liquid chromatography system with intuitive and flexible user interface, covering broad range of applications from single cell to high throughput routine proteomics.
Software RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. Can be used to analyse RNA sequencing data obtained from organisms with reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix QC report.
Software tool for proteome-wide prediction of peptide tandem mass spectra by deep learning.
ICGC Accelerate Research in Genomic Oncology Workflows
ICGC-Argo genomic pipeline. Home of the ICGC ARGO (Accelerate Research in Genomic Oncology) Data Platform Scientific Workflows.
Biobeam GM 8000 blood irradiation system
Fully protected Gamma irradiation device for blood irradiation in transfusion medicine and research.
Berthold | Centro LB 960 Microplate Luminometer
Instrument for luminescence applications.
System provides peak performance for nanoflow applications up to 1200 bar. Dual in-line flow sensors before solvent mixing give excellent gradient precision. Its intuitive software facilitates rapid method setup and immediate system control.
Software package for analysing and visualising data. Graphical environment to arrange gene expression profiles in optimal linear order.
Software for interactive segmentation, reconstruction, 3D-visualization, and analysis of biomedical image data sets with user-friendly interface. Used for interactive analysis of biomedical volume data. Used for analysis of passive drug delivery systems, active targeting, biodistribution analysis, probe development, cell labeling, ballistic soap experiments, blood perfusion, dental implants, functional ultrasound, atherosclerotic inflammation, atherosclerotic calcifications, carotid artery stenoses, tissue-engineering, and quantification of body fat.
3DHISTECH | PANNORAMIC 1000 Digital Scanner
Pannoramic 1000 Whole Slide Digital Scanner
Slide digitalization system for high-volume scanning tasks. Its up-to-1200-slide capacity, up-to-100-slides per hour throughput offers for high-volume whole-slide imaging.
Software R package for visualising simple graphs (networks), plotting flow diagrams.
Software R package for estimation of effect size indices and standardized parameters. Used to work with indices of effect size and standardized parameters, allowing computation and conversion of indices such as Cohen’s d, r, odds-ratios, etc.
Software R package for estimation of causal mediation effects. Allows researchers to conduct sensitivity analysis for certain parametric models.
Software R package for splitting, applying and combining data. Used to split up big data structure into homogeneous pieces, apply function to each piece and then combine all the results back together.
Software R package to fit psychometric functions for multiple groups.Quickly fits and plots psychometric functions (normal, logistic, Weibull or any or any function defined by the user) for multiple groups.
Software Python PiPy package. It is library that makes it easy to scrape information from web pages. It sits atop HTML or XML parser, providing Pythonic idioms for iterating, searching, and modifying parse tree.
Software Python package. Requests allows you to send HTTP/1.1 requests extremely easily. There’s no need to manually add query strings to your URLs. Simple, yet elegant, HTTP library.
National Center for Atmospheric Research repository
Provides data for atmospheric and ocean sciences research. Contains collection of meteorological, atmospheric composition, and oceanographic observations, and operational and reanalysis model outputs, integrated with NSF NCAR High Performance Compute services to support atmospheric and geosciences research. The RDA is managed by the Data Engineering and Curation Services group of the Computational and Information Systems Laboratory at the NSF National Center for Atmospheric Research.
Exchange for Observations and Local Knowledge of the Arctic
Project portal to collect, preserve, and exchange local observations and Indigenous Knowledge. Collaborates with Arctic communities and Indigenous organizations, schools, and researchers to create customized data management products. ELOKA provides open and tailored data access, data stewardship for Indigenous communities, and services ranging from advising on data sharing ethics and protocols to handling different data types. Interactive digital atlases showcasing community-based observations of social and environmental change and related geospatial data, such as trail locations, place names, land-use demarcations, or local climate information. Customized websites containing cultural, historical, and/or environmental information significant to partner communities, often in the form of written interview transcripts, audio or video files, photographs, artwork, illustrations, and maps. Data sets of environmental and wildlife observations collected by Indigenous experts. Access to local weather station data, including temperature, snow thickness, and wind data.
Microbial ecology dataset describing the composition of publicly available human microbiome samples deposited in INSDC databases (Sequence Read Archive, European Nucleotide Archive, Digital Data Bank of Japan). Genus-level read counts are available for more than 168,000 samples from around the world, with additional curated metadata for samples and projects.
Software tool for identifying novel sequences, SVs, and repetitive regions. Used to annotate duplicate genes and visualize complex genomic landscapes. Provides insights into genetic diversity.
Software R package for Gene Ontology enrichment analysis. Offers several methods based on information content and graph structure for measuring semantic similarity among Gene Ontology terms, gene products and gene clusters.
Software package implements several visualization methods for interpreting functional enrichment results obtained from Over-Representation Analysis and Gene Set Enrichment Analysis.
Biotechnology company in San Diego, California. Provides life scientists with innovative research reagents including immunity and cell culture products.
Software application for quantification of masked fluorescence intensity and nuclear count from .lif files in MATLAB.
Software application for quantification of fluorescence channel area in TIFF images using MATLAB.
Thermo Fisher | Orbitrap Exploris 480 Mass Spectrometer
Orbitrap LC-MS with EASY-IC (Internal Calibration) mass spectrometer for high-resolution, accurate mass analysis of complex samples, providing detailed information about compounds for identification, quantification, and characterization. Liquid Chromatography-Mass Spectrometry combines the separation power of liquid chromatography with the mass analysis capabilities of mass spectrometer. Orbitrap mass analyzer offers high resolution and accuracy, enabling the separation and identification of even closely related compounds. Internal Calibration uses internally generated ions to improve mass accuracy.
BMG Labtech | PHERAstar FSX microplate reader
Microplate reader for High-Throughput Screening (HTS) requirements. Performs all leading detection technologies including UV/vis absorbance, Fluorescence intensity, including FRET, Luminescence (flash and glow), including BRET, Fluorescence polarization/anisotropy,Time-resolved fluorescence (TRF), including TR-FRET, AlphaScreen, AlphaLISA and AlphaPlexTM.
United Imaging uPMR 790 enables simultaneous PET/MRI imaging with high temporal and spatial resolution. Represents major technological breakthrough in imaging field by combining time of flight (TOF) positron emission tomography (PET) and magnetic resonance imaging (MRI) in one scanner. This system allows simultaneous acquisition of MR and PET images in human subjects.
Analysis of Operant Self-administration Behaviors with Supervised Machine Learning
Software repository contains protocol for video acquisition and pose estimation analysis using DeepLabCut and Simple Behavioral Analysis.
Company based in Beverly, Massachusetts, provides advanced DNA and RNA amplification reagents. Offers complete library prep solutions for Illumina NGS platforms, reagents for PCR and RT PCR amplifications.
Company located in Vienna, Austria, specializes in Austrian quality heparin sodium. Specialized in the distribution of pharmaceuticals in hospitals with special focus on heparin products.
Biotechnology company that has developed and commercialized DNA sequencing platform for human genome sequencing and analysis. The company is a wholly-owned subsidiary of MGI.
Platform to store, analyze, and share large amounts of various types of data to facilitate research, and ultimately, unravel the complex connections between the brain and the heart.
University College London Genomics Core Facility
Core facility with expertise in genomic technologies, project design and data analysis. Offers services including nucleic acid extractions; microarray-based methylation, genotyping and pharmacogenomic analyses; short- and long-read sequencing; and single cell and spatial technologies.
Software tool to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage).
Software tool for detecting regulatory elements using GRO-seq and PRO-seq.
University of Louisville Sequencing Technology Center Genomics Services Core Facility
Provides genomic sequencing services including next-generation sequencing (NGS), single-cell analysis, and spatial transcriptomics. Offers advanced short-read and long-read sequencing technologie including our status as a PacBio Certified Service Provider.
University of California Davis Comparative Pathology Laboratory Core Facility
Core is veterinary diagnostic laboratory and research pathology core. Provides laboratory animal diagnostics, clinical and health surveillance screening necessary for the care and use of animals in research, and expert pathology support for basic and translational research.
Baylor College of Medicine BCM Mass Spectrometry Proteomics Core Facility
Core provides services including project evaluation and design, sample processing and biochemical purifications, mass spectrometry measurements, data processing, and bioinformatics analysis performed by the experienced core personnel.
Software phylogenetic inference package for B cell repertoires. It implements codon substitution models designed that incorporate unique features of somatic hypermutation and allow for parameter estimation across lineages to characterize entire repertoires.
Software package contains deep learning models and related scripts for RoseTTAFold.Used for accurate prediction of protein structures and interactions using 3-track network.
Software tool for fast and sensitive comparisons of large structure sets. Used for comparisons of large protein structure sets, supporting monomer and multimer searches, as well as clustering. It runs on CPU, supports GPU acceleration for faster searches, and optionally allows ultra-fast and sensitive comparisons directly from protein sequence inputs using a language model, bypassing the need for structures.
Software tool to discrete two molecules onto orthogonal grids and performs global scan of translational and rotational space.
Open-source, cross-platform FTP application, consisting of FileZilla Client and FileZilla Server. Clients are available for Windows, Linux, and macOS. Both server and client support FTP and FTPS (FTP over SSL/TLS), while the client can in addition connect to SFTP servers. Used to transfer files between local computer and remote server. It facilitates uploading and downloading files, making it popular for managing website files and web hosting.
Cerebral Autoregulation Research Network Transfer Function Analysis Function
Software function as Matlab implementation of the TFA as specified in the White Paper (2015). An example of use on the supplied data (tfa_sample_data.txt) is given in tfa_demo.m and results are reported at the end of this report.
Health tech company specializing in AI-based neuroimaging software used by physicians in clinical diagnosis and treatment. The company's platform uses AI to create advanced images from non-contrast CT, CT angiography, CT perfusion, and MRI diffusion and perfusion scans. They provide the RapidAI software platform, which uses AI to analyze medical images for conditions like stroke and aneurysm and it requires paid subscription.
Open source software tool developed in C# programming language on the .NET/Mono platform that allows the tool to run on Windows, Macintosh OS X, Linux Ubuntu operating systems. Allows to download or capture data from several medical device interfaces such as Datex AS3 S/5 Anesthesia, Philips Intellivue, GE Dash, Mindray, Spacelabs, Draeger Infinity, Draeger HL7 patient monitors, GE Engstrom, Draeger (Medibus), Maquet (Servo-i & Flow-i), Puritan Bennett ventilators, Covidien BIS Vista cerebral monitor, Fresenius Agilia, Alaris Carefusion, BBraun Spacecom syringe and volumetric pumps, Roche Cobas ASTM ABG analyzers. Requires Visual Studio 2022, .NET 8 or Visual Studio for Mac to compile. Android version requires Xamarin Studio, Android SDK to compile. Support for capture from other monitors is planned in future.
Software Python package for imputation, consistent segmentation, statistical analysis, and visualization of copy number profiles from heterogeneous datasets.
Web tool for interactive qPCR data analysis. Enables researchers to process, interpret, and visualize their qPCR data. Web-based Shiny application that requires no local installation.
St.Jude Research Center for Advanced Genome Engineering Core Facility
Genome-editing facility with the mission to provide low-cost, expeditious and collaborative genome-engineering services to St. Jude investigators. Core provides expertise and infrastructure to educate, assist, expedite and perform established and emerging technologies.
SPARC data structure is consistent file structure and naming convention, based on the Brain Imaging Data Structure (BIDS) to ensure that the diverse types of data in SPARC is organized in similar manner.
Dotmatics ELN and Data Discovery Platform
Dotmatics Electronic Lab Notebook and Data Discovery Platform
Software for scientific research and development. ELN captures and manages experimental data, while Data Discovery Platform enables users to explore, analyze, and visualize that data to gain insights.
Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference.
Artificial Intelligence Ready and Equitable Atlas for Diabetes Insights
Multidisciplinary data generation project which aims to create and share multimodal dataset optimized for artificial intelligence research in type 2 diabetes. At each release of the AI-READI dataset, two sets will be made available: public access and controlled access set. The public set will be stripped of Protected Health Information (PHI) as well as information related to the sex and race/ethnicity of the participants.
Portal stores health data from participants from across the United States. Provides interactive Data Browser where anyone can learn about the type and quantity of data that All of Us collects. Users can explore aggregate data including genomic variants, survey responses, physical measurements, electronic health record information, and wearables data.
FEI Helios NanoLab 600i DuaBeam Scanning Electron Microscope
Scanning Electron Microscope advanced DualBeam for ultra-high resolution imaging, analysis and fabrication at the nanoscale. Helios NanoLab 600i builds on the success of FEI’s winning DualBeam series offering advances in ion beam, electron beam, patterning and range of features to make milling, imaging, analysis and sample preparation down to nanoscale.
Software application as deep learning model leveraging large-scale proteomics, molecular graphs, and fingerprints to enhance prediction of synergistic effects in anti-cancer drug combinations.
Software multimodal AI-models to estimate Tyrosine Kinase Inhibitors and Immune Checkpoint Inhibitors therapy response across renal cell carcinoma.
University of Massachusetts Chan Medical School Metabolomics Core Facility
UMass Chan Medical School Metabolomics Core
Core offers the ability to perform both targeted (including stable isotope tracing studies) and untargeted metabolomics and lipidomics experiments using liquid- and gas-chromatography mass spectrometry (LCMS/MS and GCMS) on a fee-for-service basis. Offers expertise to assist with every stage of the metabolomics/ lipidomics experimental pipeline, including experimental design, method development, data acquisition and processing, data analysis and interpretation. Offers training on data analysis software including both open-source and vendor proprietary analysis software. Offers access to specialized equipment required for metabolomics/ lipidomics sample extraction and preparation, including a Cryomill and Bead Beater for homogenization of tumors, tissue, stool and whole organisms, and a liquid-handling robot for large scale plasma extractions.
Company specializing in antibodies for multiple applications, integrates research, production, and distribution. Provides antibodies for research and therapeutic applications.
Company provides technologies and products in neuroscience research field such as antibodies, proteins, cell lines.
Ultra high pressure liquid chromatography system. System is built with proven ACQUITY technology, which offers true UPLC performance, ultra-low dispersion, and high resolution. Designed with MaxPeak HPS Technology, the ACQUITY Premier System improves peak shape and reproducibility for the most challenging metal-sensitive compounds.
University of Nebraska-Lincoln Bureau of Sociological Research
Bureau of Sociological Research has conducted national, regional and local surveys using variety of survey research methods. Our professional staff has experience working with number of contemporary data collection methodologies and our involvement in conferences and organizations related to social research has enabled us to keep abreast of changes and trends in survey methodology.
Augusta University Small Animal Behavior Core Facility
Core provides services for researchers in need of behavioral analyses in small animals (specifically mice or rats). Core provides expertise in design and implementation of behavioral experiments as well as data analysis and interpretation. Core is equipped to accommodate behavioral tests relevant to learning and memory, attention, executive function, sensory gating, place/fear conditioning, motor function, nociception, and anxiety and depression-related behaviors etc. Testing facility is operated within centralized animal care program of Division of Laboratory Animal Services.
European company specializing in digital pathology. Based in Budapest, Hungary, they develop high-performance slide scanners and software tools that digitize and streamline pathology workflows for diagnostics, research, and education
Grayscale USB 3.0 microscope camera for routine fluorescence applications. You will receive crisp images due to its unique passive cooling architecture and its highly sensitive CCD sensor. Correlated pixel double sampling together with reduction of ambient temperature of the sensor offers exceptionally clear and noise-free signal. Its CCD sensor is particularly suitable for low light situations such as fluorescence and will capture even smallest amounts of light. Camera produces live images with up to 30 frames per second. The USB 3.0 interface provides for fast data transfer.
Leica | S6 D Greenough stereo microscope
Stereo microscope with 6.3:1 zoom and integrated video/photo port allows easy, fast documentation for assembly, quality control, OEM and research applications. Adjustable zoom stops allows fast, easy, repeatable measurements and inspections.
McLaughlin Research Institute Gene Editing and Mouse Models Assessment Core Facility
Gene Editing and Mouse Models Assessment (GEMMA) Core
GEMMA Core offers transgenic and genotyping services needed for experiments, phenotyping and behavioral services, and mouse colony management services to COBRE faculty. Consultation and training for lab staff is also available.
Independent, non-profit research organization in Great Falls, Montana near the Rocky Mountain Front.
Augusta University GCC Small Animal Imaging Core Facility
Augusta University GCC Small Animal Imaging Core
Core provides preclinical imaging and radiation treatment resources for animal research.
Institute of Molecular Biology of Plants Bioinformatics Core Facility
Institut de Biologie Moléculaire des Plantes
Institute of Molecular Biology of Plants IBMP Bioinformatics Core Facility
Core provides expertise in biological data analysis especially in high-throughput sequencing data analyses, by developing dedicated tools and workflows. Maintains computational and storage infrastructure in bioinformatics and organizes trainings for biologists and/or bioinformaticians.
Institute of Molecular Biology of Plants
Research institute focused on the study of plants at the molecular level.IBMP is a major CNRS center for plant sciences. Located at the Strasbourg site, it collaborates closely with the University of Strasbourg and our international partners in the Upper Rhine Valley region. Conducts research in areas of plant biology, including gene expression and RNA regulation, plant metabolism, organelles, and virology.
Thermocycler series with touch screen with precise fingertip control. MC X50 PCR thermocycler enables easy PCR optimization and standardization in routine PCR applications. It is also fitted for NGS.
Advanced and adaptable cell sorting system employs Full Spectrum Profiling technology to produce high-quality flow cytometric data along with Cytek portfolio of full spectrum instruments. Aurora CS system is the only commercially available spectral cell sorter that is paired with companion analyzer.
Columbia University Zuckerman Institute Cellular Imaging Core Facility
Provides access to imaging technology. Offers combination of both commercial platforms and not-yet commercialized technologies that enable innovative research centered around structural and functional imaging. Optical microscopy and image analysis platform.
Software tool to convert Virtual Contact File into Mutation Annotation Format, where each variant is annotated to only one of all possible gene isoforms.
Software repository provides open-source implementation of RGB imaging workflow for morphological and morphometric analysis of fruits and seeds.
Software application used for processing and editing 3D triangular meshes. Provides tools for editing, cleaning, repairing, inspecting, rendering, texturing, and converting meshes. This makes it suitable for variety of tasks related to 3D data, including preparing models for 3D printing.
Software package to quality control bulk cancer sequencing data. Used to visualise and manipulate i) somatic mutation data of both single-nucleotide variants and insertion-deletions, ii) allele-specific Copy Number Alterations (CNAs) and iii) tumour purity estimates. Used to validate copy number segmentations against variant allele frequencies of somatic mutations. Provides automatic copy number calling pipeline. Provides also algorithms to phase mutation multiplicities against CNAs and estimate Cancer Cell Fractions (CCFs) with their uncertainty.
Software retrieval-augmented knowledge mining method with deep thinking LLMs for biomedical research and clinical support. Cross-document question answering dataset addressing current QA limitations, and features Progressive Retrieval-Augmented Reasoning framework that combines advanced retrieval-generation techniques with self-reflection mechanisms and deep-thinking large language models to enhance answer accuracy and contextual relevance.Used to evaluate latent knowledge retrieval and multi-hop reasoning capabilities.
Software tool for predicting ncRNA-disease associations. Used for identifying association between ncRNAs and diseases.
Stanford University software shared computing cluster. All Stanford researchers have access to base set of managed computing resources, GPU-based servers, and multi-petabyte, high-performance parallel file system for short-term storage.
Leading manufacturer and supplier of flow cytometry products and services. Cytek’s compact, affordable instruments and wide ranging support offerings are used by researchers and clinicians all over the world.
CyTekBio | Northern Lights flow cytometer
Flow cytometer, with its easy-to-use workflow, is full spectrum flow cytometry solution. Instrument incorporates Cytek’s Full Spectrum Profiling technology allowing for wide array of new fluorochrome combinations without reconfiguring your system for each application. Uses SpectroFlo software.The 1-Laser, 2-Laser, and 3-Laser versions of this model are available.
Compact ultrasonicator for DNA shearing for MiSeq and PGM users. AFA technology in the M220 eliminates operator-induced variations, improves performance, increases efficiency, and provides standardized results.
Thermo Fisher: Applied Biosystems | ProFlex PCR System
Thermal cycler with flexible configuration and control features. System with Thermo Fisher Connect to design and upload methods and monitor runs from any smartphone or desktop computer. Has five different blocks that can be changed. Blocks allow up to three experiments to be run simultaneously, completely independently of each other and without interference. Dual 96-well and dual 384-well blocks are available for your high-throughput PCR sequencing needs, and dual flat block is available to support Applied Biosystems OpenArray plate technology for genotyping analysis on the Applied Biosystems QuantStudio 12K Flex Real-Time PCR System.
Thermo Fisher: Applied Biosystems | 7500 Fast Dx Real-Time PCR Instrument
Real-Time PCR Instrument, with Sequence Detection System (SDS) Software, is 96-well, 5-color real-time PCR instrument available for in vitro diagnostic use. Based on Peltier block technology, instrument is designed to deliver results, in 96-well format. SDS Software allows full control over thermal cycling protocols to further assist in developing or running custom assays.
Beckman Coulter | CytoFLEX S V4-B2-Y4-R3 Flow Cytometer
Flow Cytometer has 4 active lasers (405 nm, 488 nm, 561 nm, 638 nm) and 13 channels for fluorescence detection. This instrument can be upgraded with a maximum of 4 Violet, 2 Blue, 4 Yellow Green, and 3 Red channels. It includes 13 repositionable bandpass filters, 450/45, 525/40 (2), 585/42, 610/20 (2), 660/10 (2), 690/50 (2), 712/25, 780/60 (2). The complete system is supplied with computer work station with CytExpert Acquisition software, sheath and waste containers with harness.
Beckman Coulter | CytoFLEX LX N3-V5-B3-Y5-R3-I0 Flow Cytometer
CytoFLEX LX N3-V5-B3-Y5-R3-I0 Flow Cytometer
Flow Cytometer has 5 active lasers (375 nm, 405 nm, 488 nm, 561 nm, 638 nm) and 19 channels for fluorescence detection. This instrument can be upgraded with a maximum of 3 Near UV, 5 Violet, 3 Blue, 3 Red, and 2 Infrared channels. It includes 21 repositionable bandpass filters, 405/10, 450/45 (2), 525/40 (3), 585/42, 610/20 (3), 660/10 (2), 675/30 (2), 690/50, 710/50, 712/25, 763/43 (3), 840/20, 885/40. The complete system is supplied with computer work station with CytExpert Acquisition software, sheath and waste containers with harness.
McMaster University Single Cell and Spatial Profiling Core Facility
Core supports single cell and spatial biology research. Provides services and equipment for analyzing single cells in suspension or tissue sections from mice or humans for discovery and translational research projects. Services include flow cytometry, histology, human immune monitoring, and spatial proteomics and transcriptomics.
Software package and code for Pathogen Portal node (i.e. a local Pathogens Portal, such as the Swedish and Dutch Pathogens Portals). Allows users to create their own node quickly and easily.
Shanghai Hongshi Medical Technology | SLAN-96S Real-Time PCR System
High-throughput 96-well qPCR instrument with 4-6 fluorescence channels. Features ±0.1°C temperature precision, rapid thermal cycling (4°C/sec), and low-noise optical system. CE/SFDA certified for clinical diagnostics and research applications. Manufacturer: Shanghai Hongshi Medical Technology Co., Ltd.
Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis
Software application to preserving local relationships via graph regularization without requiring any prior correspondence information. Achieves global alignment through optimal transport while preserving local relationships via graph regularization.
Software text-mining tool that extracts and classifies authorship information from scientific articles.
ZEISS Axio Zoom.V16 microscope system includes fluorescence zoom microscope for large fields. Designed for brightfield and fluorescence microscopy of biological samples. Microscope design is optimized for fluorescence microscopy with specific optical components for light management involving specialized filters and dichroic mirrors.
Web application designed for calculating transition and transversion ratios in DNA sequences. It provides comprehensive matrix for comparative analysis and offers detailed insights into individual nucleotide changes.
Augusta University Centre for Biotechnology and Genomic Medicine Bioinformatics Core Facility
Augusta University Centre for Biotechnology and Genomic Medicine Bioinformatics Core
Core provides bioinformatics support for genomics, transcriptomics, epigenomics, and other high-throughput data. Offers data analysis, pipeline development, and consultation services to researchers across disciplines, with focus on reproducibility, scalability, and collaboration.
Cleveland Clinic Lerner Research Institute Genomics Core Facility
Core provides with easy access to state-of-the-art DNA and RNA services. Offers services, including Illumina microarray-based gene expression profiling, genotyping, and next-generation sequencing (NGS). Equipped with Illumina MiSeq and NovaSeq 6000 platforms, enabling efficient targeted and transcriptome-wide RNA analyses, as well as whole genome sequencing (WGS). Prepares and normalizes libraries for various applications, including RNA-seq, miRNA-seq, DNA-seq, whole-genome sequencing, and single-cell RNA-seq. Additional services include DNA/RNA quality control using Agilent Bioanalyzer and TapeStation systems, and DNA/chromatin shearing using Covaris S2 technology. In collaboration with Genomic Medicine Biorepository, provides DNA and RNA extraction services. Provides letters of support for federal and non-federal grant applications and are open to research collaborations.
Microscopes International (often branded as “uScope” by Microscopes International) is a Plano, Texas–based company (est. 2009) specializing in affordable, highly portable digital microscopes and whole‑slide scanning systems for scientific, clinical, and field applications.
Bruker solariX is magnetic resonance mass spectrometry (MRMS) platform, available with high-field magnets ranging from 7 T up to 15 T.
BD Biosciences | Rhapsody Single-Cell Analysis System
System allows high-throughput capture of multiomic information from single cells using cartridge workflow and multitier barcoding system. Used for high-throughput, multiomic profiling of single cells. Allows to analyze gene expression at both mRNA and protein levels, as well as other cellular characteristics, using microwell-based system with multitiered barcoding approach.This enables the generation of various next-generation sequencing (NGS) libraries for deeper analysis.
Flow Cytometer designed for clinical applications. Makes multicolor flow cytometry less complex by using avalanche photodiode (APD) detector technology. Streamlines high-complexity testing with 13-color capability and new detector technology for easier compensation. Avalanche photodiode detectors offer advanced sensitivity and improve diagnostic accuracy.
Open source active commutator for Open Ephys / Intan electrophysiology systems. Motorized device used in neuroscience research, particularly in studies involving freely moving animals, to manage wires or fibers connecting headstage or other device to external equipment. Addresses common issue of tether tangling during experiments with freely moving subjects. Relies on Hall-Effect sensor detecting rotation of cable, this information is continuously fed to Adafruit microcontroller that operates servo motor to counter-rotate cable as needed, preventing twisting and ensuring clear, uninterrupted data collection. System can also be paused, restarted, and its neutral position recalibrated with simple button presses, allowing for flexible operation.
Leica M80 is modular, ergonomic zoom stereomicroscope designed for range of routine applications in life sciences and industrial settings. It features 8:1 zoom range, providing continuous zoom from 7.5x to 60x, and is known for its high resolution, large field of view, and increased depth of focus. M80 is particularly well-suited for tasks like inspection, photography, and measurement of samples such as circuit boards, hairs, fibers, and biological tissues.
University of Massachusetts Flow Cytometry Core Facility
Core facility provides access to technologies in flow cytometry analysis including spectral analysis, high throughput imaging analysis (Amnis) and fluorescence assisted particle sorting (FACS). Instrument training, experiment and panel design, scientific consultation and sample processing are available. Offers training on facility equipment.
Microscopes International | uScopeHXII-20 microscope
Compact, high-resolution digital microscope and whole slide scanner designed for professionals in fields like pathology, histology, and research. It features 20x Infinity Plan Apochromatic objective with 0.65 numerical aperture, offering balance between magnification and depth of field—ideal for imaging thicker tissue sections and smears with enhanced clarity.
Beth Israel Deaconess Medical Center BIDMC Tissue Technologies Unit Core Facility
Beth Israel Deaconess Medical Center BIDMC Tissue Technologies Unit
Core provides research-focus histology, Immunohistochemistry, In-situ Hybridization (ACDBio RNAscope and Basescope) and Highplex Spatial-omics data generation (Akoya CODEX Fusion, 10X Genomics Visium HD, NanoString GeoMX and CosMX). Services also include BSL-2 NHP tissue processing and cryosectioning, tissue microarray (TMA) construction and multiplexing RNAScope and Protein marker staining (PANINI).
Software R package to efficiently compute robust markers across single-cell datasets. Robust marker signatures from single-cell data.
Video analysis software designed for the study of animal behavior.
University of Birmingham Protein Expression Core Facility
University of Birmingham Protein Expression Facility
Core, within College of Medicine and Health, offers expert support for all aspects of recombinant protein production. Using range of expression systems, produces proteins suitable for diverse downstream applications.
University of Birmingham Flow Cytometry Core Facility
University of Birmingham Flow Cytometry Facility
Facility supports flow cytometry, cell sorting, and mass cytometry across the University of Birmingham (UoB). Based in the College of Medicine and Health. Also supports instruments at Queen Elizabeth Hospital, Institute of Translational Medicine (ITM), and College of Life and Environmental Sciences. Services range from user training on self-service instruments to expert-supported cell sorting and GCP-compliant mass cytometry in dedicated ITM labs.
University of Birmingham Microscopy Core Facility
University of Birmingham Microscopy Facility
Facility, primarily based in Imaging Suite, offers range of imaging platforms, including widefield and confocal microscopes with fast detectors. Many systems support live imaging, including Selective Plane Illumination Microscopy (SPIM) system ideal for small animal models and spheroids.
Software package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects.
Shared on-premises computing cluster with security controls for high-risk data, managed by Stanford Research Computing. Carina contains base set of shared compute and storage resources available to Stanford researchers working with high-risk data (PHI, PII, etc.), with additional dedicated capacity available for purchase.
Google Cloud Platform projects with security controls for high-risk data, managed by Stanford Research Computing. Nero GCP offers managed GCP projects in several configurations available to and billed directly to Stanford researchers working with high-risk data (PHI, PII, etc.).
Clinical proteomic for patient care. Molecular diagnostics laboratory operated by OncoPlex Diagnostics, which is mProbe Inc company. The lab is CAP-accredited and CLIA-certified, meaning it meets high standards for clinical quality and regulatory compliance.
BioTanon | 5200 Series Automatic Image Analysis System
Tanon series chemiluminescence image analysis system equipped with advanced scientific research-grade cooling CCD and professional lens with fully automatic mechanical one-key switch various shooting modes, can be used for chemiluminescence, multi-color fluorescence, visible light, ultraviolet fluorescence detection to provide sample images.
Software application that simplifies mate allocation decisions for breeders. Allows to simplify mate allocation by filtering out possible crosses with negative EBVs and by using kinship threshold between parents set by the user.
Software R suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression.
Software R package to convert between human and non-human gene orthologs/homologs. Integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 , Eyre et al. 2007 , Seal et al. 2011 ).
McGill University Integrated Core for Animal Modeling MICAM Core Facility
McGill University Integrated Core for Animal Modeling
Core offers various services related to animal model generation and maintenance.
Potential of Heat-diffusion for Affinity-based Transition Embedding
Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances.
Software R package implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly), and characteristic pattern discovery along with interpretable time series classification.
Database of Statistics Netherlands (CBS). Contains lifestyle data of Dutch population living in private households. The numbers can be broken down by various personal characteristics.
Analytik Jena | Real-Time PCR System qTOWER 2.0
Standard RT PCR system allows quantitative PCR in established 96 well format, thus providing open platform for each kind of qPCR plastic ware from 0.2 mL single tubes to 96 well microplates.
University College London School of Pharmacy Nuclear Magnetic Resonance Core Facility
UCL School of Pharmacy Nuclear Magnetic Resonance (NMR) Facility
University College London School of Pharmacy NMR Core Facility
Core designed for range of solution-state pharmaceutical and biological chemistry applications. Facility is equipped with 600 MHz magnet equipped with high-throughput autosampler and QCI-F cryoprobe optimised for 1H and 19F sensitivity, and 400 MHz magnet dedicated to routine chemistry applications. Facility is also operating ligand-observed 19F-fragment library screening service for drug discovery.
Horizon Europe project aiming to collect concrete evidence of Open Science effects, study pathways of Open Science practices, from input to output, outcome and impact, including consideration of enabling factors and key barriers.
Korean National Health Insurance Service
Healthcare in South Korea is single-payer system organized through National Health Insurance Service (NHIS). Nearly all citizens receive universal medical care through this system. NHIS participates in health screening programmes to offer relevant and useful data for health researchers, especially in the field of non-communicable diseases and health risk factors, and policy-maker.
Software R package for storing the regulons. Gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. Confidence level was assigned to each TF-target interaction based on number of supporting evidence.
Software R package to infer biological activities from omics data using collection of methods.
Cleveland Clinic Lerner Research Institute Laboratory Diagnostic Core Facility
Core has maintained CAP (College of American Pathologists) and CLIA (Clinical Laboratory Improvement Act) accreditations since 2001 and has maintained the required standards for the past 20 years. Core offers automated clinical chemistry, immunology and hematology assays. Tests range from commercially available FDA approved methods to research grade ELISA’s.
PierceDirect | Duotronic III Embalming Machine
Fixation pump for anatomy laboratories. DUOTRONIC III features extra light 1/8 HP motor pump, ensuring considerable outflow without preliminary pressure. The pump is magnetic transmission, centrifugal device equipped with mixing system (based on the principle of the water fountain) allowing homogeneous mixing. Specifications: Stainless steel base with handles; 11 litre tank, graduation in litre; 15 Psi pressure; 220 mono 50 Hz/60 Hz.
Genomic Rearrangement IDentification Software Suite
Software suite containing tools for detection of genomic rearrangements. Multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using novel positional de Bruijn graph-based assembler. GRIDSS2 is structural variant caller to explicitly report single breakends-breakpoints in which only one side can be unambiguously determined.
Software tool to generate tumor BAF file for use in PURPLE from provided VCF of likely heterozygous SNP sites.
Software tool to determine read depth ratios of supplied tumor and reference genomes.
Software annotation, interpretation and visualisation tool for structural variants. Used to aid interpretation of structural variant and copy number data derived from short-read, whole-genome sequencing. Classifies raw structural variant calls into distinct events and predicts their effect on local structure of derivative chromosome and functional impact on affected genes.
Software tool to infer junction-balanced genome graphs with high fidelity. Builds genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments).
Software integrated library and plugins for mathematical morphology with ImageJ.Collection of generic tools based on Mathematical Morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins.
PRISM - Poisson RNA-profile Identification in Scaled Mixtures
Poisson RNA-profile Identification in Scaled Mixtures
Software statistical framework that allows simultaneous extraction of tumor sample composition and cell type and sample specific whole-transcriptome profiles from individual bulk RNA-seq samples.
Bayesian Analysis of Macroevolutionary Mixtures tools
Software R package for analysis and visualization of macroevolutionary dynamics on phylogenetic trees.
Software R package to quantify allelic imbalances associated with homologous recombination deficiency in ovarian cancer.
Software package for analysis of RNA expresison data. Used to make pythoneer bioinformatician workflow less colluded with R.
CPE: Concordance Probability Estimates in Survival Analysis
Software R package used in survival analysis that evaluates predictive accuracy of survival model. Measures how well model can distinguish between pairs of individuals with different survival times. Calculates proportion of all pairs of individuals whose predicted survival times are correctly ordered.
Software R package designed to streamline collection and use of cancer transcriptional signatures across bulk, single-cell, and spatial transcriptomics data. Used for collection and implementation of public transcriptional cancer signatures.
Software R package to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression.
Dartmouth College Life Sciences Light Microscopy Core Facility
Life Sciences Light Microscopy Core Facility at Dartmouth College
Light microscopy imaging core facility located in the Life Sciences Center at Dartmouth College (Hanover, NH). Facility personnel provide training and imaging guidance. Imaging instruments available to trained users include: laser scanning and spinning disk confocal systems (with super-resolution capability), a TIRF system, and a multiphoton microscope. Image analysis software (e.g. Nikon Elements, ZEN, Arivis Vision 4D, and Imaris Quant) is also available through the facility.
Tulane University TNBRC Molecular Virology and Sequencing Core Facility
Core offers advanced services to detect, quantify, and characterize pathogens, as well as assess host immune responses. Supports both standardized and custom assay developments. MVSC is composed of three integrated units: Virology Unit which provides viral stocks for variety of viruses at BSL2 and BSL3, as well as assay services including virus expansion and characterization, viral titer by plaque and TCID50 assays, live virus neutralization and inhibition assays at both BSL-2 and –3. Viruses currently in use by the core include SIV, HIV, Zika, Dengue, SARS-CoV-2, Mayaro, Eastern Equine Encephalitis Virus, Poliovirus, Enterovirus D68, and others. Luminex and Serology Unit Services include antibody detection in serum or plasma by Luminex-based assays and/or ELISA for SPF-agents such as SIV, SRV, STLV, B virus, SFV, CMV, RRV, SVV, SV40, and LCV, and non-SPF infectious agents like measles, Burkholderia pseudomallei, Trypanosoma cruzi, Mycobacterium tuberculosis, and SARS-CoV-2. This unit also offers services for cytokine quantification in body fluids including serum and CSF, as well as tissue culture supernatant. Sequencing Unit provides services related to quantitative PCR and RT PCR detection of viruses such as SIV, Zika, and SARS-CoV-2, as well as next generation sequencing services including whole genome (pathogen or host), epigenetics, targeted amplicons, and 16S and ITS metagenomics. Sequencing unit also performs single cell RNA-seq (10x and Parse) assays as well as NGS based genotyping of NHP, including for major histocompatibility complex (MHC) allelic genotyping.
Dresden University of Technology Mass Cytometry Core Facility
Facility provides customized solutions for complex single cell profiling with up to 45 markers simultaneously. Offers full service and established workflows from panel design, antibody labelling and sample processing to high-dimensional data analysis. Offers expertise in antibody conjugation, sample staining, and data analysis.
Nikon | ECLIPSE Ts2R inverted microscope
Compact inverted research microscope configurable with wide variety of observation methods such as epi-fluorescence, phase contrast, DIC, and more. The Ts2R features camera port for digital imaging while maintaining compact body.
Thermo Fisher | SpeedVac SPD1030 Integrated Vacuum Concentrator
Savant SpeedVac SPD1030 Integrated Vacuum Concentrator
Fully integrated system that combines concentrator, refrigerated cold trap, diaphragm pump and vacuum gauge in single, compact unit. Vacuum concentrator for drying DNA/RNA precipitates, PCR samples, proteins, enzyme, HPLC fractions in plates or tubes in water/ethanol or isopropanol and other organic solvents. SpeedVac SPD1030 System is designed for medium capacity (i.e.,120 x 1.5 mL tubes, other formats).
University of Texas at Dallas UTD Genome Center Core Facility
University of Texas at Dallas UTD Genome Center
Core provides library prep and NGS services using Illumina NextSeq 2000. Our services include sample QC, DNA, RNA bulk sequencing, single cell sequencing, and Sanger sequencing.
Software package provides flexible, queriable R interface to graphs and walks of reference genomic intervals. gGnome is written in R6 object oriented standard and built around GenomicRanges, data.table, and igraph backend, and thus supports agile interaction with graphs consisting of hundreds of thousands of nodes and edges.
Software package for batch correction of heterogeneous RNA-seq datasets through latent sample matching.
Software R package for finite mixtures of regression models using EM algorithm. General framework for finite mixture models and latent class regression in R.
Software R package implementing Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation.
Software toolkit for converting, compressing, viewing, indexing and manipulating data in SLOW5 format. Used for handling nanopore data in SLOW5 format.
File format for storing signal data from Oxford Nanopore Technologies sequencing devices. SLOW5 can be encoded in human-readable ASCII format, or more compact and efficient binary format (BLOW5) - this is analogous to the seminal SAM/BAM format for storing DNA sequence alignments.
Software library for reading and writing SLOW5 files. Designed to facilitate use of data in SLOW5 format by third-party software packages. Used for efficient parallelization and acceleration of nanopore data analysis.
Software library to read and write slow5/blow5 files. Python wrapper built on top of slow5lib (interfaced using Cython) to allow easy access to SLOW5 for Python programmers.
Software ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration).
Software tool for simulating nanopore raw signal data.Takes reference genome, transcriptome, or read sequences, and generates corresponding raw nanopore signal data.
Software tool to visualise and analyse nanopore raw signals.
Cleveland Clinic Lerner Research Institute Electron Microscopy Core Facility
Transmission (TEM), Scanning (SEM), 2D tile scanning SEM and 3DSEM electron microscopy are available in the Core for imaging and analyzing specimens at the ultrastructural level. Possible samples include fresh tissue specimens, cultured cells growing on a substrate, cells in suspension or subcellular fractions (for purity determinations). Sub-cellular localization of antigens within cells by immunogold labeling can be performed, as well as negative staining for visualizing samples such as microparticles and exosomes. Elemental analysis (EDAX) is also available together with SEM.
Ohio State University Campus Chemical Instrument Center NMR Core Facility
Ohio State University Campus Chemical Instrument Center NMR Facility
Advanced high-field NMR facility combines many capabilities spanning solution and solid state NMR, high sensitivity cryoprobes, ultrafast spinning MAS probes, as well as Dynamic Nuclear Polarization.
Cultivarium creates tools for life scientists to expand access to novel microorganisms, inspire new research avenues, and push the frontiers of biotechnology. Aggregates information, data, and publications for bacteria, fungi, archaea, and protists.
Focused Research Organization (FRO). Focused on identifying unintended gene product binding partners of pharmaceuticals and other bioactive compounds, to support better drug development and drug repurposing.Along with drug/protein interaction data, includes methods and tools to provide the scale, throughput, and economy that future pharmome mappers will require in order to continue mapping the vast and ever-expanding proteomic/chemical space that is the pharmome.
Nonprofit startup which focuses on impactful applications and scientific dissemination, ensuring maximum public benefit without commercial constraints. Forest's state-of-the-art tools, research, and discoveries will be shared with the broader scientific community, aligning with its commitment to open science. Company mission is to advance healthcare by making neurotechnology accessible, less invasive, and adaptable across range of neurological conditions.
E11 Bio was launched in 2022 as one of the first Focused Research Organizations (FROs), a novel form of non-profit startup for science. E11 Bio’s mission is to unlock connectomics at the scale of whole mammalian brains by radically cheaper and more accessible technologies.
Organization is part of a strategic global community effort to promote transparent and trustworthy research practices in the academic research systems. Part of the Association of African Universities.
Bayobab is a next-generation services company connecting Africa with digital solutions. We see Africa through the eyes of its’ population, a continent brimming with potential and possibility. Until May 2023, the company was known as MTN GlobalConnect. The transition to a new brand is a shift to an open-access business model structured to serve all industry participants and add value to stakeholders and partners.
RoRI was founded in 2019 with mission to accelerate transformative research on research systems, cultures and decision-making. Headquartered at University College London (UCL), RoRI partners and works closely with expanding international network of research funders, from across Europe, North America, Australia and Africa.
Code and supporting data for the article: "Exploring the role of normalization and feature selection in microbiome disease classification pipelines."
CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq
Coverage-based Limiting-cell Experiment Analysis for RNA-seq
Software workflow that identifies reliably quantifiable transcripts in limiting-cell RNA-seq (lcRNA-seq) data for differentially expressed genes (DEG) analysis. Coverage-based Limiting-cell Experiment Analysis for RNA-seq.
Enrichment of related pathways in genes.
System provides flexibility to record data in any environment. Used in implantable physiologic monitoring.Fully implantable Telemetry.Allows monitoring of many animals with just one receiver and facilitates group housing and social interaction.
Database platform that provides access to collection of peer-reviewed scientific literature, including journal articles and book chapters, from Elsevier and other publishers. Scientific Search Engine.
Software pipeline to identify high-confidence BSJs and full-length circRNA isoforms from isoCirc long-read data.
Software Bayesian statistical modeling R package for hierarchical statistical modeling (aka graphical modeling). It enables writing general models along with methods such as Markov chain Monte Carlo (MCMC), particle filtering (aka sequential Monte Carlo), Laplace approximation and other general methods.
Adam Mickiewicz University Cytometry Laboratory Core Facility
AMU CAT - Cytomics and Cell Analysis Core Facility
Core is utilized in medical biotechnology and in research focused on mammalian cells. Offers analyzing of impact of new drugs and pharmaceuticals on individual cells in vitro. Provides sorting of cell populations with desired characteristics, including fluorescent dye-stained cell sorting (FACS) analysis of cell populations for presence of specific factors, e.g. introduced fluorescent protein, surface markers, DNA content determining the size, granulation and shape of animal and other cells.
Virginia Commonwealth University Cryo-Electron Microscopy Core Facility
Facility offers sample preparation, visualization and analysis for high resolution 3D reconstruction of frozen-hydrated proteins and macromolecular complexes. Facility is endowed with Thermofisher Scientific Tundra cryo-electron microscope, Vitrobot Mark IV cryo-plunger, Pelco easyGlow glow discharge unit, Denton DV 502B evaporator, and linux server dedicated to image processing.
Software Napari plugin for quantifying membrane-associated periodicity and periodic co-localization in super-resolution microscopy images. It uses autocorrelation and cross-correlation analysis to provide unbiased metrics of periodicity and spatial shifts between channels.
Comprehensive multi-species platform for neuroscience teams to understand brain cells and anatomy. Brain Knowledge Platform includes catalog of relevant data and projects, as well as visualization tools for understanding brain cell types.
Software package for acquisition and device control for advanced research applications. Nikon’s flagship software package features fully automated image acquisition, advanced device control and powerful analysis and visualization tools.
Software package for recording and analysis developed by iWorx. LabScribe has intuitive, user-friendly interface for setting up acquisition screens, calibrating signals and analyzing data. Up to 128 channels of data can be displayed simultaneously at sampling rates as high as 100,000 samples/second.
Med Associates Small Animal Cystometry MED-CMG Software
Small Animal Cystometry MED-CMG Software
Med Associates Inc. data acquisition software for recording cystometrigrams from small laboratory animals, such as rats or mice.
Med Associates Cystometry Data Analysis Software
Med Associates software tool to automatically create graph of cystometrigram of exported data from MED-CMG. Analysis of data is made possible with readouts of bladder pressure, infusion pump, and scale traces to identify void and non-void contractions.
Washington University in St. Louis Human Cells, Tissues, and Organoids Core Facility
Core provides training and expertise on culturing human pluripotent cells and their downstream derivatives.
Software pipeline designed to streamline dataset generation for cryogenic electron microscopy (cryoEM)-based atomic model building. Supports large-scale AI training and benchmarking by providing standardized tools for data retrieval, preprocessing, labeling, and quality control. Enables flexible configurations for diverse biomolecular structures, improves modeling reproducibility, and facilitates retraining of AI models such as U-Net and CryoREAD. Python workflow used to curate cryoEM datasets for AI-driven structural biology.
YSI 2300 STAT PLUS Glucose and Lactate Analyzer
Laboratory instrument intended for use in clinical care and sports medicine applications. Provides measurements of glucose in whole blood, plasma or serum, and of L-lactate in whole blood, plasma, or cerebrospinal fluid (CSF). In whole blood or plasma, glucose and L-lactate can be measured simultaneously.
Flexible modeling language that allows you to author schemas in YAML that describe the structure of your data. Additionally, it is framework for working with and validating data in variety of formats (JSON, RDF, TSV), with generators for compiling LinkML schemas to other frameworks.Framework that simplifies the process of authoring, validating, and sharing data.
University of Birmingham Intravital Microscopy Core Facility
University of Birmingham UOB Intravital Microscopy
Imaging facility for intravital microscopy. Facility equipment includes widefield, confocal, and multiphoton microscopes. Additional tools, such as laser ablation systems, allow us to probe vascular events such as thrombosis in fine detail. We also have tools for measurement of vascular perfusion, such as full-field laser speckle and laser doppler.
Artificial Intelligence (AI)-powered website, which provides user-friendly open access analysis of extensive ChemPerturb-seq dataset.
Software tool as multimodal LLM-based AI agent that enables deep research about spatial transcriptomics data. Integrates multimodal large language models (LLMs) with specialized computational tools to transform weeks-long analysis tasks into minutes of automated processing. Enables autonomous deep research through integrated capabilities, including dynamic code generation for complex analytical workflows, visual reasoning for interpreting spatial patterns, real-time retrieval of relevant peer-reviewd scientific literature, and synthesis of comprehensive, actionable reports.
Software repository contains code for Inference of T2D metabolic subphenotypes (MuscleIR, Beta-cell Function, Incretin Effect, Hepatic IR), Identification of dominant metabolic subphenotype, Feature extraction from glucose tiemseries, Extraction of reduced representation of glucose tiemseries,Visualization of metabolic phenotypes based on various glucose-related metrics,Concordance between CGM and Venous glucose values from at home and at clinical setting, Classification of metabolic subphenotypes.
Data analysis resource and repository for biological data related to circadian rhythms, sharing public data from over 10,000 experiments (in 2025). The main features of BioDare2 are: fast analysis of rhythmic data (rhythm detection and period, phase, amplitude), timeseries processing, attractive visualizations, simple data description, data sharing with permalinks, easy data uploads and a modern UI.
Algorithm to align cells along differentiation trajectories. Models trajectories of differentiating cells by treating cell fate as probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Generates high-resolution pseudo-time ordering of cells and, for each cell state, assigns probability of differentiating into each terminal state.
Software toolkit for quantitative detection of DNA methylation from nanopore sequencing data without raw signals.
Software application is Shiny app for ancestry estimation using genotypic data. Designed to support any species and ploidy level, it enables users to estimate admixture proportions using reference populations and visualizes ancestry results interactively.
Fluidigm | Juno Targeted DNA Sequencing Library Preparation System
Juno Targeted DNA Sequencing Library Preparation System
Juno system used for preparing libraries for next-generation sequencing and IFS preparation for gene expression, genotyping and digital PCR application.
MBI Montreal Biotech | SensoQuest Labcycler Gradient
Thermocycler with gradient function used in PCR (Polymerase Chain Reaction) experiments. It allows for creation of temperature gradient across the sample block, enabling users to optimize annealing temperatures for different reactions simultaneously. Labcycler Gradient with 96 Wells (0.2 ml) Silver Block (± 20 °C).
Thermo Fisher: Sartorius | Secura Semi-Micro Balance
Semi-micro balance offers four different weighing ranges to fulfill the needs of most 5-digit weighing applications.
Telstar | Boreas Ultra-low temperature freezer
Ultra-low temperature (ULT) freezer known for Vacuum Insulation Panel insulation and ecological refrigerants. These freezers are designed for the safe and long-term storage of biological and chemical samples at extremely low temperatures, typically down to -86°C.
Leica RM 2035 BioCut Manual Microtome is perfect for manually sectioning paraffin or plastic-embedded specimens.
Vital River Laboratory Animal Technology Inc.
Company specializing in providing laboratory animal models and related services for biopharmaceutical research. It is a subsidiary of Charles River Laboratories, and is known for its expertise in refining breeding practices of specific pathogen-free (SPF) laboratory animals. VRL operates from state-of-the-art facilities and offers a wide range of rodent strains and related services to support research in China and internationally.
Guangzhou Geneseed Biotech. Co.,Ltd., founded in June 2010, is a pioneer in circRNA scientific research and application transformation.
Established in 2013, OBiO Technology（Shanghai）Corp.,Ltd. is Contract Research Organization and Contract Development and Manufacturing Organization in cell and gene therapy. Provides technical services for the field of Regenerative Medicine and Anti-aging, including cell preparation, production of recombinant proteins/exosomes, and cell storage.
Web-based software tool to explore current contents of SCKAN, semantic store housing comprehensive knowledge base of autonomic nervous system (ANS) and peripheral nervous system (PNS) nerve to end organ connectivity.
China National Center for Bioinformation Genome Sequence Archive for Human database
Genome Sequence Archive for Human (GSA-Human)
Genome Sequence Archive for Human database
Data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. Data repository specialized for human genetic related data derived from biomedical researches.
Deep feature extraction by UNet-based Neuroimaging-oriented autoEncoder
Software tool to extract low-dimensional deep features from multisequence brain MRI data using unsupervised autoencoders.
Teaching hospital located in Yeongeon-dong, Jongno-gu, Seoul, South Korea. It is general and teaching hospital of Seoul National University's College of Medicine.
Software tool to analyse coverage depths of structural variants or regions/genes of interest from long-read-sequencing datasets obtained by all available technologies as well as short-read sequencing datasets and optical genome mapping. Generates coverage statistics (min, max, Q1, Q3, mean, median) and/or coverage plots based on either the Binary Alignment Map (BAM) file(s) or OGM mapping files (CMAP, XMAP). Software optical mapping, high-throughput and long read coverage comparison and visualization tool.
Software tool as long read, high-throughput sequencing and optical mapping structural variant Comparator. Enables to compare structural variants (SVs) from long-read-sequencing (LRS) datasets obtained by all available technologies as well as short-read sequencing (SRS) datasets and optical genome mapping (OGM). Enables to analyse targeted or whole-genome sequencing datasets using reference genome of interest.
University of South Carolina Center for Elemental Mass Spectrometry Core Facility
Center for Elemental Mass Spectrometry (CEMS)
University of South Carolina Center for Elemental Mass Spectrometry (CEMS)
Core analytical facility with research focus on geochemistry and chemical oceanography. Provides plasma-source mass spectrometers for trace metal and isotope ratio measurements on wide variety of sample types.
University of South Carolina Mass Spectrometry Core Facility
Core provides services for EI and CI spectra including high and low resolution analyses available; for GC-MS including positive ion and negative chemical ionization, with high resolution and MS/MS available for high sensitivity work; Electrospray and APCI including low resolution or accurate mass analysis of purified compounds by direct infusion or loop injection analysis; MS/MS available for structural analysis;LC-MS including electrospray and APCI ionization available. Separation by narrowbore or capillary HPLC. MS/MS available for quantitation, peptide microsequencing and protein identification, etc.; MALDI-TOF/TOF including analysis of polymers and biomolecules; ICP-MS including trace elemental detection with high resolution. User training available for students and researchers who will be using the instrumentation for extended projects.
University of South Carolina Nuclear Magnetic Resonance Core Facility
University of South Carolina College of Pharmacy Microscopy and Flow Cytometry Core Facility
Core advise and assist investigators with advanced microscopy and flow cytometry procedures. Provides training and services in flow cytometry and biological imaging.
Bio-Techne | ProteinSimple FluorChem R System
System was high-performance gel imaging system for chemiluminescence, fluorescence, UV, and visible light applications, but it has been discontinued as of October 15, 2021. ProteinSimple (now part of Bio-Techne) will continue servicing these products through October 15, 2026.
Workflow Of Matrix BioLogy Informatics (TWOMBLI)
Software pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. FIJI macro for quantifying pattern in extracellular matrix.
Software Python package for handling mmCIF and BinaryCIF files compliant with the ModelCIF extension.
Software package for computing collection of clustering validation or quality criteria and partition comparison indices.
Software R package to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers. Can also be used to read data from .loom files.
SeuratObject:Data Structures for Single Cell Data
Software R package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users.
University of Nebraska Medical Center Institutional Biospecimen Biobank Core Facility
University of Nebraska Medical Center Institutional Biospecimen Biobank
UNMC Institutional Biospecimen Bank (IBB)
Core to procure and coordinate distribution of fresh frozen human tissue in optimal state of preservation for requesting investigators without impacting diagnostic quality, accuracy and safety in anatomic pathology. Additional services offered include biospecimen DNA or RNA extraction, sectioning of frozen tissues, short-term tissue culture, cytogenetic/molecular cytogenetic analysis, and tissue preparation via investigator-driven protocols.
Software toolkit containing lots of useful tools for genomics analyses. Used to check, fix, pad missing information (features/attributes) of any kind of GTF and GFF to create complete, sorted and standardised gff3 format.
Software repository provides the code for generalizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings.
Dragonfly spinning disk confocal microscopy system. Andor Dragonfly 600 series high-contrast multi-dimensional imaging platform for live cell imaging. Andor Dragonfly 620 is spinning disk confocal with many advanced modalities capable of widefield imaging, high-sensitivity or high-contrast spinning disk imaging, TIRF (critical angle, Hi-Lo), STORM (single molecule imaging), photostimulation of specific cellular regions and dual-camera recording.
Leica TCS SP8 with Acousto-Optical Beam Splitter
Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Leica TCS SP8 system is high precision confocal microscope with Acousto-Optical Beam Splitter that allows for flexible control of the excitation and emission light paths.
Software R package that supports different types of gene set enrichment workflows. Offers multiple enrichment, visualization, and sharing methods in addition to novel features such as hierarchical geneset analysis and built-in markdown reporting.
Software pipeline to build similarity maps of protein space. Identifies proteins related to query protein using sequence- and structure-based searches, compares all protein structures, and creates navigable map that can be used to look at protein relationships and make hypotheses about function.
Software phylogenomic pipeline designed to analyze proteomes from diverse organisms and inferring orthology, gene-family trees, and species tree. Highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionar history. Efficiently performs phylogenetic comparisons at any evolutionary scale.
Software pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT. Used to quickly screen for transferred genes.
Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Facility imaging system offers stable imaging conditions, especially crucial for high magnification and time-dependent studies. Z2m model is optimized for materials science applications. It is often used for tasks like 3D subsurface studies of transparent ceramics, metallography, corrosion studies, analysis of thin film uniformity, and inclusion analysis in metals. It is particularly well-suited for situations that require motorized stage to handle large samples.
Olympus FVMPE-RS multiphoton imaging system
Multiphoton imaging system for deep imaging in biological tissue. For advanced applications,dual-wavelength excitation extending to 1300 nm is available. Independent control of visible or multiphoton laser light stimulation and ability to synchronize with patch clamp data are also possible. Multiple configurations are available.
Software accurate read-based phasing tool that integrates multiple methodologies to enhance phasing accuracy. Used to efficiently phase genomic data by linking sequencing reads across heterozygous sites, extending haplotype blocks, and incorporating pre-phased data when available. Read-based phasing algorithm with integrated multi-method support for enhanced accuracy.
Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Facility
Facility provides access to imaging equipment and analysis tools. It houses widefield, laser scanning confocal, spinning disk confocal, multi-photon, light-sheet, and super-resolution microscopes, along with two transmission electron microscopes and high-content screener. Offers centralized workstation for image processing, high-performance computing capabilities, and data storage. Provides access to several commercial software programs for image analysis and data quantification. Services include consultations for sample preparation, training on the microscopes, full imaging support, and assistance with analysis strategies. Provides several services related to transmission electron microscopy: tissue/cell processing, image acquisition training or assistance, and image analysis support. CoRE scientists can collaborate with investigators to develop novel imaging methods and analysis approaches.
Light sheet fluorescence microscope designed for high-resolution, three-dimensional imaging of large, cleared, and fluorescently labeled biological samples. It excels at visualizing entire biological systems like organs, embryos, or even small animals with cellular resolution, making it suitable for studying complex biological structures and processes.
High-speed, high-resolution light sheet microscope designed for imaging large, cleared tissue samples. Utilizes patented axially-swept light sheet technology to achieve uniform axial resolution across the entire sample, enabling rapid volumetric imaging. System is particularly well-suited for imaging cleared tissues, including whole organs and even entire juvenile mice, with options for both aqueous and organic clearing methods. Light sheet imaging for rapid volumetric acquisition of intact samples.
State University of Campinas Institute of Chemistry Laboratory of Mass Spectrometry and Chromatography Core Facility
LIEM-IQ - Mass Spectrometry and Cromatography Laboratory
Universidade Estadual de Campinas (UNICAMP) LIEM-IQ - Mass Spectrometry and Cromatography Laboratory
Core features several high- and low-resolution mass spectrometers, coupled with liquid and gas chromatographs, as well as an ICP-MS. In addition, we have liquid chromatographs available that operate with other types of detectors. The laboratory collaborates with activities carried out at the Institute of Chemistry, in external academic sectors, and also within private enterprise.
Quanterix Micro Arrays System Model 2470
Arrayer produces high quality microarrays of DNA, proteins, cell lysates and variety of other samples using its proprietary soft touch deposition technology.
This instrument is precision liquid handling instrument that enables non-contact, nanoliter-to-microliter scale dispensing of small molecules, biologics, or other reagents directly into assay plates for high-throughput drug screening and dose-response studies.
Software R package for Affymetrix Human Genome U133 Plus 2.0 Array annotation data.
State University of Campinas Institute of Chemistry Nuclear Magnetic Resonance Laboratory LIRMN-IQ Core Facility
Universidade Estadual de Campinas (UNICAMP) LIRMN-IQ
Institutional laboratory of Nuclear Magnetic Resonance (NMR) of the Institute of Chemistry of UNICAMP.The Institutional Nuclear Magnetic Resonance Laboratory has 6 NMR spectrometers, two for solids and four for solution probes, with the possibility of analyzing different nuclei.
Arcadia organisms selection portal. Uses data to suggest model organisms based on relevance to human gene of interest or suggest monogenic diseases to model based on organism of interest.
Standalone software and web-based platform for predicting top lncRNA–disease associations using advanced biological feature processing and machine learning. Given input lncRNA or disease, along with associated sequences or target data, PrediLnc uses our custom model GARNet (Graph convolution Attention RNA Network) to return the most relevant predictions.Used for hypothesis generation in biomedical research. LncRNA diseases association predictor.
Software Python package for construction of Slepian wavelets in the spherical and manifold (via meshes) settings. Slepian scale-discretised wavelets in Python.
Weill Cornell Medicine Human Therapeutic Organoid Core Facility
Human Therapeutic Organoid Core Facility
Weill Cornell Medicine Human Therapeutic Organoid Core (HTOC)
Facility serves as central facility for human organoid technology to accelerate organoid-based scientific discovery. Provides human pluripotent stem cell (hPSC) derived as well as tissue derived cells and organoids.
Weill Cornell Medicine, originally Cornell University Medical College, is the medical school of Cornell University, located on the Upper East Side of Manhattan in New York City.
PanoScore is a commercial-grade pathology image analysis platform for quantitative tissue segmentation, AI-powered cell phenotyping, and spatial biology research. It supports whole-slide imaging (WSI), multiplex staining analysis (H&E/IHC/IF), and tissue microarray (TMA) processing, enabling reproducible quantification of tumor microenvironments, cell proximity metrics, and biomarker expression.
Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Mouse Behavior Core Facility
Mouse Behavior Core provides equipment and software for measuring mouse behavior. The MBC can support mouse phenotyping/drug discovery test batteries as well as more focused behavioral projects.
Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Genetic Perturbation Screening Core Facility
The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology - Genetic Perturbation Screening Core
Core provides guidance in planning and helps with executing gene expression modulation experiments. Currently uses technology based on shRNA for gene knock-down and cDNA libraries for overexpression studies. Core is equipped with genome-wide retroviral shRNA libraries for both human and mouse genomes, Mammalian Gene Collection (MGC) cDNA library, as well as smaller focused sets targeting selected gene families.
Software package for visualization of functional enrichment results as network graphs.
Web application for RNA-protein interactions prediction.
Web application for prediction of interactions between two RNA molecules. Used to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions. IntaRNAv2 enables enhanced parameterization as well as fully customizable control over prediction modes and output formats.
Standalone software tool to detect cells, to obtain calcium spikes, and to determine underlying network structure of neuronal cell cultures. CALIMA 2.0 is updated version of software tool that detects and analyzes fluorescent signals and correlates cellular activity to identify possible network formation in Brain-on-chip cultures. Used to process calcium fluorescence imaging data.
Software R package to calculate similarity metrics to facilitate copy number variant comparison among samples and/or methods.
Software repository contains the code for paper: Prediction of Drug-Target Interactions Based on Dual-Channel Heterogeneous Graph Neural Networks.
RAIDS (Robust Ancestry Inference using Data Synthesis)
Robust Ancestry Inference using Data Synthesis
Robust Ancestry Inference using Data Synthesis (RAIDS)
Software R package to enable genetic ancestry inference from various cancer sequence sources (RNA, Exome, and Whole-Genome sequences). This package also implements simulation algorithm that generates synthetic cancer-derived data. Used for accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms
Software R package creates 'D3' JavaScript network, tree, dendrogram, and Sankey graphs from R.
Software package to arrange genomic categories and to add self-defined graphics in plot. Genomic plot in trellis layout. Visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple-dimensional data, which are represented as tracks, describe different features from different aspects.
Software cloud-based proteomics ML workflow for biomarker discovery.
Augusta University Transgenic and Genome Editing Core Facility
Core provides services in gene editing using CRISPR/Cas9 approach, services on preserving lines by cryopreservation of sperms, and resurrecting mouse lines using in vitro fertilization (IVF) or embryo transfer. Additional services include rederivation to create pathogen-free mouse lines, developing molecular reagents for genetic engineering, and providing expert advice on mouse genetics and breeding schemes.
Augusta University Human Physiology Core Facility
Core provides services including body/bone composition, comprehensive assessments of cardiovascular health (conduit vessel, microvascular, and central arterial stiffness), comprehensive assessment of lung health (spirometry, diffusion, lung clearance index, exhaled NO), and metabolic/exercise testing. Expanded core services in humans include oral glucose tolerance testing and continuous glucose monitoring, 24h ambulatory blood pressure monitoring, and assessments of autonomic nervous system, cognitive function, mitochondrial function, intramuscular fat, and electrocardiograms.
Augusta University Georgia Cancer Center Biorepository Core Facility
Georgia Cancer Center Biorepository (GCCB)
Core provides collection, annotation, and storage solutions. This Biorepository is also home to a state-wide resource, the Biorepository Alliance of Georgia for Oncology (BRAG-Onc), which functions to collect samples from 6 participating sites across the State to represent the diversity of cancer patients within the State and to enhance cancer research in Georgia.Tissue specimens are fast-frozen in vapor phase liquid nitrogen to preserve their integrity and stored in large cryofreezers at -170 to -190°C. Blood is routinely separated into serum or plasma and buffy coats prior to freezing. Blood derivatives are stored at -70 to -80°C. The freezers are monitored constantly and are connected to an alarm system to ensure that the low temperatures are maintained.
Software Python pipeline for one-step retrieval and integrative analysis of public single-cell RNA sequencing data.
NDC-Systematic Online Living Evidence Summaries
Web application to systematically collect, synthesise, and display experimental evidence in genetically-modified animal models of neurodevelopmental conditions.
Software R package provides Consensus Molecular Subtype (CMS) classification of colorectal cancer pre-clinical models. Used for consensus molecular subtyping of colorectal cancer pre-clinical models.
Augusta University Visual Function Assessment Core Facility
Core provides equipment, expertise, and training for researchers to assess rodent vision in vivo. Offers technical expertise, training, and instrumentation for in vivo visual function assessment in animal models including rodents.
University of Florida Scripps Institute for Biomedical Innovation and Technology Flow Cytometry Core Facility
Core provides flow cytometry and cell sorting services.
University of Florida Scripps Institute for Biomedical Innovation and Technology Metabolic Core Facility
Core for In Vivo and In Vitro metabolic phenotyping. Provides validated in vitro and in vivo tests. Phenotyping applications span from mitochondrial and cellular metabolism to whole body animal physiology. Provides instrument training, experimental design, data analysis. Studies can be performed by staff, but IACUC-approved Animal Use Protocols are also available to help investigators use resources on their own.
Florida State University College of Medicine Magnetic Resonance Imaging Core Facility
Florida State University College of Medicine Magnetic Resonance Imaging Facility
MRI facility is research-dedicated space that includes 3T Siemens Prisma (whole-body) scanner, an MR-compatible Brain Products system for EEG and psycho-physiological measures, eye tracker, mock scanner, and a MagPro X100 equipped with Localite TMS Navigator for brain stimulation.
Eclipse 50i has optical capabilities, utilizing Nikon CFI60 optics, and stress-free design with solid platform for routine digital imaging applications.
7 Tesla Bruker BioSpec 70/30 USR MRI system
High-field, preclinical imaging system primarily used for research on small animals like mice and rats. It enables researchers to conduct detailed anatomical and functional studies, including morphological imaging, functional MRI (fMRI), diffusion tensor imaging (DTI), and MR spectroscopy (MRS). The system's high field strength allows for high-resolution imaging, enabling researchers to visualize intricate anatomical details and subtle changes in tissue and organ function.
Specialized laser ablation system designed for high-resolution, high-speed bioimaging using LA-ICP-MS (Laser Ablation Inductively Coupled Plasma Mass Spectrometry). Built to analyze elemental composition of biological samples, particularly tissues and cells, with focus on speed and precision.
Zeiss | Axioscan 7 Digital Slide Scanner
High-throughput system designed for automated digitization of microscopy slides, primarily for life science research, clinical diagnosis, and geological applications. It excels at creating high-quality virtual slides from brightfield, fluorescence, and polarization microscopy samples.
Software tool to uncover cellular alternative splicing (AS) heterogeneity and regulatory mechanisms by integrating splicing patterns with gene expression in single-cell RNA-seq (scRNA-seq) data.
Configurable And Modular Program Allowing RNA Expression Emulation
Software tool as robust and configurable RNA expression simulator. Configurable and modular program allowing RNA expression emulation.
Software for simulation of RNA-seq reads. Combines flexible and highly configurable design with detailed simulation of entire library preparation and sequencing pipeline and is designed to include effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification.
Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data.
NIH-funded project that aims to engage scientists and bioethicists in creating human pangenome reference and resource that represents global human genomic variation. In the process of creating the pangenome, the HPRC is developing improved technology for genome assembly and a next-generation tool ecosystem that leverages the pangenome for comprehensive analyses.
Human Genome Structural Variation Consortium
Consortium to characterise and improve understanding of full spectrum of human genomic variation. HGSVC utilises the latest sequencing technologies to create high-quality maps of human structural variation, developing new tools for SV discovery and analysis. Consortium involves many groups internationally.
Software methylation analysis pipeline for genome graph. Genome-graph-based DNA methylation analysis using whole genome bisulfite sequencing.
Mayo Clinic Florida Cytometry and Cell Imaging Core Facility
Core provides researchers with access to equipment in three main pipelines: Cell and tissue imaging resources, including microscopes and a slide scanner; Flow cytometry, including analytical flow cytometry and cell sorting; Mass cytometry (CyTOF). Provides consultation services including panel and experiment design, sample preparation tips and technical troubleshooting, training for independent use on select equipment, data acquisition and cell sorting.
Collection of software tools for scaffolding and improving modern genome assemblies. Reference-based scaffolder. Used for fast and flexible genome assembly scaffolding and improvement.
Software application as ensemble approach to rank putative causal transcription factors that regulate set of query genes by prediction confidence.
Software variant annotation toolkit for GBA gene variants detected from Illumina/Gauchian tool. Command-line tool designed to annotate tsv files generated by the Illumina/Gauchian tool.
Software application for BTE RAG implementation for DMDB QA datasets. Provides implementation of BTE-RAG framework, designed specifically for retrieval-augmented question answering (QA) in biomedical contexts. BTE-RAG leverages explicit mechanistic knowledge retrieval from BioThings Explorer (BTE) to significantly enhance the accuracy and reliability of large language models (LLMs) on biomedical benchmarks.
Software application for classification of heterogeneous brain MRI data. Used for white matter-related classification of heterogeneous brain FLAIR MRIs.
Biotech company founded in Shanghai Hi-Tech Park. Global supplier and service provider of RNAi products and services for RNAi, gRNA, mRNA therapeutics and RNA biomarkers. Provides siRNA chemical synthesis, which include RNA monomer synthesis technology, custom and chemically-modified siRNA oligo synthesis technology, nucleic acid fluorescent labeling technology, and many nucleotide chemical modification technologies.
Open-source, cross-platform software for ecological and evolutionary meta-analysis.
Howard Hughes Medical Institute at Janelia Research Campus Janelia Experimental Technology jET Core Facility
HHMI's Janelia Research Campus Janelia Experimental Technology
Core team designs, builds and tests instruments, tools, and software that enable novel scientific investigation. Offers expertise in Data acquisition and analysis; Machine vision and image processing; Precision machining; Embedded systems design and programming; Laser, microscopy, and optical imaging systems engineering; Custom circuit design; Novel sensor systems; Lab automation, robotics and motion control; Mechanical design, machined and/or fabricated components and assemblies; Process automation.
Software application as convolutional neural network for inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. Used for depicting pseudotime-lagged causality for accurate gene-regulatory inference.
Software Camiels scATAC-seq analysis pipeline.
Software application for supplementary files and notebooks to recreate figures.
Software application as computational workflow for detecting coordinates of microbial-like or human-like sequences in eukaryotic and procaryotic reference genomes.
Cancer Research UK Scotland Institute Histology Core Facility
Offers processing fixed tissue for paraffin-embedded histology, cryo-microtomy, cell pellet processing, H+E staining and special histology stains or cellular material supplied. Immunohistochemistry, immunofluorescence and in-situ hybridisation service is available along with the capability to provide digital scanning and analysis. Many other techniques such as provision of tissue microarrays and other staining techniques such as TUNEL can be provided or set-up as required.
University College London School of Pharmacy Mass Spectrometry Core Facility
Core offers services including high throughput, high mass accuracy tandem mass spectrometry coupled with liquid chromatography. Research within the facility ranges from basic biomolecular science and biochemical studies through to proteomics, metabolomics and drug-protein and drug-nucleic acid interactions.
Oregon State University Electron Microscopy Core Facility
Core offers negative staining of protein, tissue processing including dehydration, fixation, staining and utra-microtomy, image biological samples at 80 keV on Generation 2 Titan with Rio CMOS side mount camera for low magnification too high magnification shots of cellular structures. Can also rapidly screen grids with Helios STEM in SEM capability. Provides Helios with auto slicenview and fully licensed Avizo for rendering 3D images of cells.
Augusta University Medical College of Georgia Pathology Research Services Core Facility
Core offers pathology services to prepare and stain animal and human tissue for basic and clinical research.
Government of Mexico Science and Technology Center for Research in Optics (CIO) Optical Microscopy Laboratory Core Facility
Centro de Investigaciones en Optica CIO-Laboratorio de Microscopia Optica
Government of Mexico Science and Technology Center for Research in Optics (CIO) � Optical Microscopy Laboratory
Core offers services in Confocal/Multiphotonic Microscopy, Raman Microscopy, Fluorescence/Pseudo Dark Field Microscopy,AFM. Available to students and researchers working and interested in research areas including optics, biology, materials, chemistry, and health sciences.
Weill Cornell Medicine Center for Translational Pathology Core Facility
Core provides tissue-based and clinical laboratory assays, biospecimens, consultative pathology services, multiparametric imaging, mass spectrometry, molecular pathology, mouse models and advanced cellular therapeutics for basic, translational, and clinical research.
Mayo Clinic Cytometry and Cell Imaging Core Facility
Cytometry and Cell Imaging Core provides researchers with access to equipment in three main pipelines:Cell and tissue imaging resources, including microscopes and a slide scanner;Flow cytometry, including analytical flow cytometry and cell sorting.;Mass cytometry (CyTOF).Core provides instrument training, help with experimental design and technical support. Core specializes in antibody-based techniques.Provides expertise in cell sorting, imaging and high-parameter analysis of cells and tissues.
System designed for the recording and analysis of animal vocalizations. It supports full-spectrum audio capture from up to four arenas simultaneously using USB microphones, enabling precise, synchronized data collection. The software architecture incorporates advanced analysis capabilities that streamline the identification, quantification, and interpretation of vocal behaviors. UltraVox XT can also process imported audio files, expanding its applicability beyond live recordings. These features make it a versatile tool for animal behavior researchers, with flexibility to meet both current and evolving experimental needs.
Software tool as simulation program of hypothalamus-pituitary-adrenal axis (HPA axis, aka corticotropic feedback control) for education and research, based on nonlinear MiMe-NoCoDI model and implemented with CyberUnits Bricks library.
Software supporting framework for "Foundation Model of Electronic Medical Records for Adaptive Risk Estimation".
Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Advanced Light Microscopy Core Facility
Core offers consultation and training to investigators on range of microscopy techniques, including super-resolution, confocal, multi-photon, and advanced fluorescence imaging and image analysis.
EC-LMGraph: Enzyme function and Catalytic Site
Software tool, which combine graph deep learning and protein language model, for accurate enzyme function and catalytic site prediction.
Software R package to identify, annotate and visualize isoform switches with functional consequences from both short- and long-read RNA-seq data. Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.
Thermo Fisher | Orbitrap Ascend MultiOmics Tribrid Mass Spectrometer
High-resolution mass spectrometer designed for comprehensive multiomics research. It combines a high-performance Orbitrap mass analyzer with a tribrid architecture (quadrupole, linear ion trap, and Orbitrap) for enhanced ion separation, fragmentation, and detection capabilities. This instrument is particularly well-suited for analyzing proteins, lipids, and metabolites in a single experiment, enabling researchers to gain deeper insights into biological systems
Nikon | Crest X-LightV3/DIP SIM spinning disk confocal microscope
X-Light V3 in combination with DeepSIM X-Light super-resolution system. Super-resolution microscopy system used to visualize cellular structures and dynamics at nanoscale resolution, typically around 100 nm in XY and 300 nm in Z. It's designed for both live and fixed cell imaging, including complex 3D models like tissues and organoids, and can be seamlessly integrated with existing confocal microscopes like the X-Light V3.
Leica | Cell DIVE Multiplex Imaging Solution
Cell DIVE Multiplex Imaging Solution is Leica Microsystems’ open, highly customizable platform that combines precision-engineered hardware, iterative staining/dye‑inactivation protocols, and intuitive software to visualize 60+ biomarkers from a single tissue section—delivering crystal-clear, whole‑tissue imaging at the single‑cell level.
Yale Center for Genome Analysis Core Facility
Core performs next generation sequencing for RNA and DNA samples, as well as provides support for downstream analysis.
Turtle-Tech | BioDigital-QING Digital PCR System
BioDigital Qing is a digital PCR system with automated droplet preparation and reagent formulation, enabling all essential steps of digital PCR—including compartmentalization, thermal cycling, and data acquisition—to be completed on a single instrument. Utilizing nucleic acid quantification technology, it allows for absolute quantification without the need for a standard curve. A large volume of reaction mixture is partitioned or digitized into thousands of small, independent reactions, such that each microchamber contains either one or zero target copies. The original concentration is then calculated using statistical methods based on the number of positive and negative microchambers.
Software application for identifying transcriptomic and epigenomic changes.
Web portal that ranks journals and countries based on their scientific influence, using data from the Scopus database. Provides bibliometric indicators like the SCImago Journal Rank (SJR) indicator, which measures citation impact, and the h-index, which reflects both the productivity and citation impact of a journal or researcher. Portal allows users to analyze journals by subject area, category, and country, offering a valuable tool for assessing research impact and comparing scientific performance.
Employer-sourced medical and drugs claims database of the under-65 working population and their dependents, as well as 65+ with Medicare supplemental insurance paid by employers.
Software tool to assess gene relevance while enhancing dimensionality-reduction performance. Used to quantify gene relevance and improve dimensionality reduction.
This integrated digital PCR device combines four functions—chip loading, droplet generation, PCR amplification, and signal reading—into one, achieving full process automation and significantly reducing human error. It is compact in size, making it easy to transport and maintain. It is compatible with multiple PCR mixes, has high droplet stability (≥95%), and uses a glass substrate chip to ensure high-quality signal output. It supports single-sample testing, avoiding waste of consumables, and is suitable for flexible and efficient experimental requirements. Translated with DeepL.com (free version)
Turtle-Tech | SCI Digital PRO Digital PCR System
Fully automated digital PCR system integrating four functions: chip loading, droplet generation, PCR amplification, and signal reading, enabling ultra-multiplex quantitative detection. The device adopts innovative "solid oil-water separation" droplet generation technology, ensuring stable droplets with a high effective ratio. It supports multi-color fluorescence channels and independent temperature control for dual modules, equipped with AI intelligent denoising and recognition functions.
University of Michigan Human Organoid Core Facility
formerly the Translational Tissue Modeling Laboratory)
Human Organoid Multi-organ Biosample Repository
University of Michigan Human Organoid Core (UM-HOC
University of Michigan Translational Tissue Modeling Laboratory Core Facility
Core enables the use of primary human organoids as tissue models for discovery, translation and regenerative medicine by providing:access to high-quality, well-characterized neonatal through adult human organoid lines from multiple organs for investigators studying human development and disease; access to detailed protocols; access to specialized, quality controlled and batch-tested reagents; expertise, guidance and training; help obtaining data;help establishing organoid lines;letters of support for grant submissions.
University of Michigan Eisenberg Family Depression Center Mobile Technologies Core Facility
Core provides University of Michigan investigators with guidance and resources needed to utilize mobile technologies and digital mental health measures in their studies. Our experienced faculty and staff offer hands-on consultative services to U-M investigators, regardless of research focus.
University of Michigan Eisenberg Family Depression Center Data and Design Core Facility
Core staff provides personalized consultations, knowledge and resources focused on helping investigators leverage secondary data to advance their mental health research. Offers consultations and guide in areas:Identifying secondary data sources for mental health studies,Data preparation (e.g., merging/appending data, preparing variables for analysis), Developing analysis plan, including pre-registration, Statistical analysis.
University of Michigan AI and Digital Health Innovation Core Facility
Core with mission to harness data and expertise to power innovations that improve people’s health through unification and enhancement of interdisciplinary efforts at the intersection of artificial intelligence (AI) and health at the University of Michigan. Provides data services, secure computing resources, support to strategically integrate and study AI models in clinical workflows at Michigan Medicine.
University of Michigan Advanced Research Computing Core Facility
Core provides access to and support for advanced computing resources including high performance computing, active and archive storage, cloud computing, and secure computing environments for sensitive data.
Web-based platform providing integrated and standardized Mendelian Randomization analysis workflow. This includes GWAS data quality assessment, power/ sample size estimation, MR analysis, SNP-to-gene enrichment analysis, and data visualization. Interactive R Shiny application designed for Mendelian randomization analysis.
University College London LMCB Electron Microscopy Core Facility
Electron microscopy facility specialising in cell biological electron microscopy for basic and medical research applications.
Keyence VK-X1000 3D laser scanning microscope
Non-contact profile, roughness, and film thickness measurements, nanometer resolution, material and shape independent with fully automatic measurement and analysis 3D laser scanning microscope.
Multi-scale Single-cell Clustering (MSC)
Software R package for multi-scale clustering to perform single-cell transcriptome clustering.
University of Exeter Centre for Cytomics Core Facility
Core offers high-dimensional spectral cytometry, conventional flow cytometry, nano cytometry, imaging cytometry, spatial biology, and multi-omics (proteomics and transcriptomics). Provides Cytek Aurora spectral cytometers with up to 64-colour capability, CytoFLEX LX for multiparameter conventional cytometry, and CytoFLEX nano for ultra-sensitive detection of viruses, extracellular vesicles, and submicron particles,FlowCam 8400 imaging system for real-time visualisation and analysis of plankton, microbial communities, and other aquatic particulates.Other instruments include Amnis ImageStreamX MKII, MACSima Imaging Cytomics System.Provides services from immunotherapy development, precision oncology, and regenerative medicine to environmental monitoring, plant sciences, and nanoparticle characterisation. All services are underpinned by advanced AI-driven analytics, leveraging R, Python, TensorFlow, and PyTorch on high-performance computing platforms to integrate and interpret complex datasets.
Thermo Fisher | Biometra TRIO PCR system
PCR system with three different PCR protocols that can be run simultaneously in three different sample blocks.
Leica | DMI4000 B Automated Inverted Microscope
Microscope for scanning cell and tissue cultures. System features fluorescence axis for ultra brilliant fluorescence imaging.Internal filter wheel with motorized excitation manager and FIM (Fluorescence Intensity Manager) enables excitation of fluorochromes in less than 20 milliseconds.
FCBF : Fast Correlation Based Filter for Feature Selection
Software R package to select features with high correlation with the target and little correlation with other variables. It does not use the classical Pearson or Spearman correlations, but metric called Symmetrical Uncertainty.
Emory University EHCF High Containment Core Facility
Emory University High Containment Facility
Core to enhance research capacity for high containment pathogens and strengthen epidemic and pandemic emergency preparedness capabilities. Offers infrastructure, technical support, training, and regulatory compliant environment to investigators.
Virginia Tech Fralin Life Sciences Institute Advanced Imaging and Microscopy Core Facility
Facility for Advanced Imaging and Microscopy (FAIM)
Light microscopy research resource facility offers confocal, extended and super resolution, and lightsheet imaging options, as well as assistance and training for researchers. The FAIM also has educational resources available for light microscopy basics, and image processing and analysis.
State University of Campinas Institute of Chemistry Cell Culture Laboratory Core Facility
Universidade Estadual de Campinas (UNICAMP) LICel-IQ - Cell Culture Laboratory
Provides services involving cultivation of mammalian and insect cells, including genetically modified organisms (GMOs). This laboratory is accredited by CTNBio (Brazilian National Technical Council of Biosafety), and its research activities are monitored by CIBio - IQ (Internal Commission of Biosafety).
University of North Carolina at Chapel Hill Bioinformatics and Analytics Research Collaborative BARC Core Facility
Bioinformatics and Analytics Research Collaborative (BARC)
University of North Carolina at Chapel Hill Bioinformatics and Analytics Research Collaborative (BARC)
Provides bioinformatics expertise and analysis for high throughput data. Services include analysis, visualization, interpretation, and management of big data while also offering custom solutions. Offers collaborative environment by hosting workshops, working groups, and seminars, and improve existing tools and/or invent new tools and algorithms.
Mexican Social Security Institute National Laboratory of Advanced Microscopy IMSS Core Facility
Laboratorio Nacional de Microscopia Avanzada-IMSS (LNMA-IMSS)
Core provides optical microscopy and histology services.
Exeter Archival Diabetes Biobank (EADB), formerly the Alan Foulis collection. The collection is managed by the University of Exeter Medical School, with images from the biobank made accessible via Pancreatlas. Collection of pancreatic tissues, largely from children who died shortly after a type 1 diabetes (T1D) diagnosis. Provides high-quality digital images of historical, formalin-fixed, paraffin-embedded samples.
NIH Cardiovascular Repository for Type 1 Diabetes
Cardiovascular Biorepository for Type 1 Diabetes Program (CaRe-T1D) to fill a major void of knowledge that exists related to cardiovascular disease in type 1 diabetes.
A model algorithm that integrates omics data and network data to predict essential genes.
Olympus BX41 is clinical and research grade microscope. Can be customized. Offered as pre-configured with your choice of viewing head - binocular, ergo binocular, or trinocular. This has Plan N 4x, 10x, 40x, 100x oil objectives but others can be provided if needed. Comes with XY mechanical stage with slide holder and focusable condenser.
The Tissue Properties database provides comprehensive estimates for tissue material parameter values and also statistical information about the spread and standard deviation per tissue for the different thermal and fluidic parameters. This information is important for assessment of the contribution to the uncertainty in a quantity of interest due to the selection of the material parameters in simulations. For some material parameters, e.g., perfusion, the variation can be large, which in turn can have a severe effect on simulation results.
Software segmentation/resquiggling tool for ONT signals. Dynamic programming approach to segment ONT signals.
Software application to provide well defined metadata instances for selected schemas of the openMINDS metadata framework.
AIME:Approximate Inverse Model Explanations
Software tool to address challenges faced by existing methods in providing intuitive explanations for black-box models. Offers unified global and local feature importance by deriving approximate inverse operators for black-box models.
Software tool for interactive exploration and analysis of single-cell trajectories in 3D space.
Custom Design and Fabrication | Electronic Cortical Contusion Injury Device
(ELECTRIC) CORTICAL CONTUSION IMPACTOR (eCCI)
Electronic CCI device, with adjustable depth, velocity, dwell time, and angle of impact used for neuroscience research.e CCI is constructed with sturdy aluminum frame to maximize rigidity thereby ensuring impact accuracy. The support base, animal platform, and impactor head are anodized to prevent oxidation and to ensure equipment longevity. The assembly includes the base and support frame, adjustable animal positioner with an aluminum animal platform to be used in conjunction with a variety of stereotactic mounts.
Software tool as comprehensive analysis framework for T-cell and B-cell repertoire sequencing data.
The International Physical Activity Questionnaire (IPAQ)
International Physical Activity Questionnaire to obtain comparable estimates of physical activity between populations and countries. It was designed for physical activity surveillance so it is particularly useful for large population studies, but can be used with care in other contexts.
CRUK Scotland Institute Deep Phenotyping Advanced Technology Core Facility
Core offers comprehensive pathologist-led spatial biology service comprising spatial proteomic, transcriptomic, and multiomic experimental design, including platform and panel selection, assay development, image acquisition, and digital image processing. The facility houses 2x Ventana Discovery Ultra autostainers, 2x 10 x Genomics Xenium platforms, a Lunaphore COMET, an Akoya PhenoImager, an Akoya PhenoCycler, an Olympus VS200 slide scanner and a Visiopharm image analysis suite.
Software tool for cell type based analysis of multiplexed imaging data. Interactive knowledge-based classifier for multiplexed images and proteomic datasets that avoids hard-set thresholds and manual labeling. Recovers fine-grained cell types, matching the gold standard annotations by human experts, can target ambiguous populations and discover phenotypically distinct cell subtypes.
Cancer Research UK Scotland Institute Molecular Technology Service Core Facility
Scotland Institute Molecular Technology Service Core Facility
Core provides Next Generation Sequencing (NGS) services and Single Cell services predominantly focussing on single cell RNAseq. Processes samples for variety of cancer associated projects, in both mouse and human derived materials. Offers full end-to-end service, from initial study design and planning, through sample QC, full library preparation, sequencing and data return. Offers range of standard molecular tests covering, plasmid purifications, Sanger sequencing and mycoplasma screening.
Giotto Suite is a major upgrade to the Giotto package that provides tools to process, analyze and visualize spatial multi-omics data at all scales and multiple resolutions. The underlying framework is generalizable to virtually all current and emerging spatial technologies. Our Giotto Suite prototype pipeline is generally applicable on various different datasets, such as those created by state-of-the-art spatial technologies, including in situ hybridization, sequencing, and imaging-based multiplexing/proteomics. These technologies differ in terms of resolution (subcellular, single cell or multiple cells), spatial dimension (2D vs 3D), molecular modality (protein, RNA, DNA, …), and throughput (number of cells and analytes).
Thermo Fisher | Orbitrap Exploris 120 high-resolution mass spectrometer
Orbitrap Exploris 120 LC-MS spectrometry instruments
Designed with non-statisticians in mind and intuitively developed, MarkerView software does the heavy lifting so you can focus on high-value decisions like reviewing trends and differences in targeted or untargeted mass spec workflows. Distil complex datasets quickly, find statistically significant differences and reveal key insights faster. MarkerView software is now integrated into the SCIEX OS ecosystem.
Augusta University Bioinformatics Shared Resource Core Facility
Georgia Cancer Center's Bioinformatics Core provides expertise in integrative computational based analysis solutions to basic, clinical, and translational research applications. Services include study design, analysis, and interpretation that may involve interaction with industry, government, and regulatory agencies in the areas of Clinical trials, Epidemiology, laboratory studies, in addition to data mining using local and national databases for hypotheses generation and scientific investigation.
iDEP: Integrated Differential Expression and Pathway analysis
Integrated web application for differential expression and pathway analysis of RNA-Seq data.
Software pipeline that generates protein families from amino acid sequences and/or updates existing families with new sequences. It takes a protein fasta file as input, clusters the sequences and then generates protein family Hiden Markov Models (HMMs) along with their multiple sequence alignments (MSAs). Optionally, paths to existing family HMMs and MSAs can be given (must have matching base filenames one-to-one) in order to update with new sequences in case of matching hits.
Software toolbox for SPM5 which offers plotting effect sizes, fitted responses, and BOLD time courses averaged across subjects from within 2nd level (random effects) analyses. The toolbox offers a large variety of plot configuration both suitable for data exploration and producing high quality figures for publications.
Cleveland Clinic Bioinformatics and Protein Engineering Core Facility
Core provides expert support and consulting in advanced bioinformatics analyses and state-of-the-art protein engineering.
Purdue University College of Agriculture Research Services Core Facility
ARGE Research Services is dedicated to empowering Purdue Agriculture research by providing expert solutions in conducting team science, implementing best practices for data acquisition, stewardship, and analysis.
Bruker’s Avance NMR spectrometers are utilized in various scientific fields to elucidate the structure, dynamics, and interactions of molecules. Avance spectrometers are composed of three main hardware components: console, which is the central control unit of the NMR spectrometer, and houses sophisticated electronics for the generation of the pulse sequences and for data acquisition and processing; superconducting magnet to generate homogenous and stable magnetic field to polarize the nuclear spins in the sample; probe for transmitting radiofrequency pulses and detecting the resulting signals from the sample.
Software machine learning-based genotyping correction tool specifically designed to address chimerism-induced errors in next-generation sequencing (NGS) data from Callithrix marmosets. It leverages an XGBoost classifier trained on allele balance metrics to improve variant calling accuracy in chimeric, non-blood tissues such as hair follicles, tail, and ear.
Software tool for simulating synthetic genotype data specifically designed for discrete nature of genotype representation. Implements evaluation framework that integrates metrics from both quantitative genetics and deep learning.
Software framework for machine learning models in text, computer vision, audio, video, and multimodal model, for both inference and training.
Software Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in tifffile, liffile, czifile, zarr, and other scientific image input/output packages.
Software Python library to read and write wide range of image data, including animated images, volumetric data, and scientific formats. It is cross-platform, runs on Python 3.9+, and is easy to install.
CRUK Scotland Institute (formerly the CRUK Beatson Institute)* is core-funded by Cancer Research UK and provides environment for its basic and translational scientists to understand the mechanisms that regulate cancer cell proliferation, survival and dissemination; to identify critical components of these pathways as targets for novel cancer therapies; and to help translate this knowledge to patient benefit.
Software for interactive and in-depth analysis of Mass Spectrometry Imaging (MSI) data.
Cleveland Clinic Lerner Research Institute Center for Therapeutics Discovery Core Facility
Cleveland Clinic Center for Therapeutics Discovery
Cleveland Clinic Center for Therapeutics Discovery (C3TD)
Core to promote translation of basic science discoveries by Cleveland Clinic researchers into new therapeutics. Through collaboration with investigators we de-risk promising approaches and illuminate fundamental biology using small molecule chemical probes. We have established a pipeline of innovative research programs directed toward improving patient care with a true bench-to-bedside vision. To achieve these goals, we use state of the art technologies in small molecule library screening, fragment-based methods, X-ray crystallography, computational tools, and target validation towards generating starting points for nascent hit-to-lead and lead optimization campaigns.
Software tool to analyse and elaborate sources for generating machine code from your design. Open-source analyzer, compiler, simulator and (experimental) synthesizer for VHDL, a Hardware Description Language (HDL).
SEnsible Step-wise Analysis of DNA MEthylation
Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.
State University of Campinas LIAFQ-IQ Laboratory of Physicochemical Analysis Core Facility
LIAFQ-IQ - Laboratory of Physicochemical Analysis
Universidade Estadual de Campinas (UNICAMP) LIAFQ-IQ - Laboratory of Physicochemical Analysis
Laboratory for Physicochemical Analysis of IQ-UNICAMP houses equipment for a range of analytical techniques:Thermal Analysis comprises techniques that measure the physical or chemical properties of a substance, or its reaction products, under controlled temperature variation;Atomic Spectrometry enables multi-element determination in solution samples;Elemental Analysis is used to determine the Carbon, Hydrogen, and Nitrogen content in solid and viscous samples.Nitrogen Physisorption is a technique used to determine the surface area and pore size of solid materials.
State University of Campinas LIBio-IQ Biosefaty Laboratories Core Facility
Universidade Estadual de Campinas (UNICAMP) LIBio-IQ - Biosefaty Laboratories
Core belongs to the Institute of Chemistry of UNICAMP and are structured to accommodate works involving pathogenic bacteria and fungi or genetically modified organisms (GMO). Part of CTNBio (Brazilian National Technical Council of Biosafety) accredited areas and have research activities monitored by CIBio -IQ (Internal Commission of Biosafety).
State University of Campinas LISpec-IQ Spectroscopy Core Facility
Universidade Estadual de Campinas (UNICAMP) LISpec-IQ-Spectroscopy Core Facility
Institutional Spectroscopy Laboratory is equipped with a comprehensive suite of instruments for spectroscopic analysis. Our capabilities include absorption spectroscopy (UV-Vis, NIR, and IR), Raman scattering, and fluorescence emission spectroscopy.
State University of Campinas LIRX-IQ X-Ray Institutional Laboratory Core Facility
Universidade Estadual de Campinas (UNICAMP) LIRX-IQ-X-Ray Institutional Laboratory
Institutional Laboratory of X-ray facility is equipped with instruments that work with following analytical techniques: single crystal X-ray diffraction (SCXRD), X-ray fluorescence (XRF), and small-angle X-ray scattering (SAXS).
Washington University School of Medicine Mass Spectrometry Technology Access Center Core Facility
McDonnell Genome Institute Mass Spectrometry Technology Access Center
Washington University School of Medicine McDonnell Genome Institute Mass Spectrometry Technology Access Center
Core services range from simple protein identification to quantification of proteins (relative and absolute) through bottom-up proteomics analyses. Offers intact, native, and top-down proteomics analyses. Provides comprehensive global quantitative analysis of post-translational modifications (PTMs) such as phosphorylation, ubiquitination, acetylation, and methylation, as well as epiproteomics histone PTM assays.
University of Liverpool Centre for Genomic Research Core Facility
University of Liverpool Centre for Genomic Research (LIV-SRF)
Core facility that provides academic and industrial researchers from around the world with affordable multi-platform sequencing, library preparation, data analysis and related services.
University of Kentucky Animal Behavior and Energy Balance Core Facility
Core conducts animal behavior tests for investigators at the University of Kentucky. Ensures that qualified and trained investigators have access to instrumentation and expertise necessary to perform behavior tests. Provides assistance in the design, implementation and analysis of behavioral experiments in rodents and other animals. Provides equipment for measurement of lean/fat mass and whole body metabolism in mice. Echo MRI is utilized for non-invasive quantitative assessment of lean and fat mass. Sable Promethion Calorimeter indirectly measures oxygen consumption (RER), food and water intake, and physical activity in mice.
Brain Cell type Annotation and Integration using Distributed AI
Web service providing annotations for brain cell type–specific marker gene sets derived from single-cell RNA-seq data spanning the entire mouse brain. It uses a multi-agent AI framework that combines fine-tuned large language models with retrieval-augmented generation, producing biologically grounded annotations supported by peer-reviewed literature.
Serendipity Engine Assaying Heterogeneous Omics Related Sampling Experiments
Web-based database and search tool for exploratory data analysis in which we have pre-computed statistical associations between available data elements. Large-scale, open-access data sets such as the Genotype Tissue Expression Project (GTEx) and The Cancer Genome Atlas (TCGA) include multi-omic data on large numbers of samples along with extensive clinical and phenotypic information. Allows users to explore significant associations using tabulated summary statistics, data visualizations, and functional enrichment analyses (using RNA-seq data) for identified sets of genes.
Software Python toolbox for functional ROI analysis of fMRI data. Provides analytic methods for fMRI data analyses that accommodate inter-subject variability in precise locations of functional activations. Supports several types of analyses, such as parcel generation, fROI definition, effect estimation, spatial correlation estimation, and spatial overlap estimation. The toolbox is compliant with the Brain Imaging Data Structure (BIDS), standardized framework for organizing and sharing neuroimaging data.
Target-to-Clinic Contract Research Organization (CRO) headquartered in San Diego, CA USA. ChemDiv executes pre-clinical discovery chemistry and biology for drug development and clinical trials for international portfolio of companies across the entire range of targets with small molecule and biotech drugs. The company operates multiple research and development (R&D) subsidiaries in Russia, Ukraine and China as well as business operations around the world.
JEOL | JCM-6000 Benchtop Scanning Electron Microscope
Compact Benchtop Scanning Electron Microscope. Intuitive operation is achieved via touch panel and new operation screens. The high or low vacuum mode is included in the standard configuration, and EDS can be installed, offering truly multi-functional benchtop SEM.
Horiba | Xplora Plus Confocal Raman Microscope
Confocal microscope incorporates unique and powerful functions in reliable, high performance system, ideally suited to the research and analytical lab. SWIFT™ Fast Raman images are the fastest fully confocal Raman images available, typically 10x faster than conventional Raman imaging. Has enhanced range of options such as multiple laser wavelengths, EMCCD detection, Raman polarisation and AFM Raman TERS combination.
Software tool for visualization of geometric organization of clusters. Mapper-inspired tool to visualize global layout of clusters.
University of Michigan Medical School Hybridoma Core Facility
Core provides research services in custom monoclonal antibody development (mAb) and bulk production of monoclonal antibodies from established hybridomas (somatic cell hybrids). Core has developed monoclonal antibodies against a wide variety of lymphocyte surface antigens, tumor cell antigens, purified proteins, hormones, hormone receptors and recombinant proteins and peptides.
Software application to identify spanning hypervariable region(s) from amplicon sequencing variants or SRA public runs (SRR). Aligns query sequences to reference E. coli full-length 16S rRNA gene and identifies spanning region through alignment. Used for identifying hypervariable regions in 16S rRNA big datasets.
Disease Ontology Semantic and Enrichment
Disease Ontology Semantic and Enrichment (DOSE)
Software R package for disease ontology semantic and enrichment analysis.
Software Python package and addon that takes NEURON simulator model and exports its 3D structure and membrane activity to Blender. Used to integrate NEURON simulator with Blender, allowing 3D visualization, animation, and modeling of NEURON models in Blender.
Software interactive platform for analysis and visualization of drug combinations. Used for analyzing drug combination effects (e.g., synergy, additivity, or antagonism). Offers advanced data visualization, including 2D/3D heatmaps and dose-response curves, and processes high-throughput data from Excel/CSV files. Users can customize models or extend functionality via Python scripting.
Software Python package for manipulation and analysis of geometric objects in the Cartesian plane.
Software R package for aligned rank transform for nonparametric factorial ANOVAs.
Software general visualization tool for 3D volumetric data and proof-reading in segmentation or reconstruction.
Software application as data acquistion system for patch-clamp recordings, based in CED1401 hardware, and IgorPro.
Software application for denoising from single noisy images.
Software scalable pipeline for overlap detection based on large-scale sequencing data. It is based on three steps: feature extraction, dimenality reduction, and approximate k-nearest neighbor search. Used for effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.
Software plugin for 'EEGLAB' MATLAB toolbox, which allows to whole-night sleep EEG using Artifact Subspace Reconstruction (ASR). Used to implement Artifact Subspace Reconstruction cleaning with whole-night sleep EEG. Automatic cleaning of whole-night sleep electroencephalogram using Artifact Subspace Reconstruction.
Software application for Period Amplitude Analysis (PAA) for slow wave detection using eeglab.
Software R package to inference from interval data. Given collection of observed events and geometric association measure between events and explanatory intervals, CORE finds given number of explanatory cores that maximizes the explanation. Combinatorial optimization procedure with depth chosen from considerations of statistical significance.
Software blazing fast toolkit to work with .hic and .cool files.
University of Michigan ISR-VR Lab Core Facility
Core provides flexible systems with built-in support for biometric data collection, dyadic interactions, and reproducible protocols. Provides access to pipelines that support reproducibility, custom data annotation, and seamless handoff to analysis tools in R, Python, and more. Provides access to IRB-ready templates and documentation, along with tested participant safety protocols and secure data management systems.
University of Michigan Medical School Nucleic Acid Therapeutics Core Facility
Nucleic Acid Therapeutics Core accelerates the development of gene-targeted therapies by providing custom oligonucleotide synthesis, expert consultation, and platform for cross-disciplinary collaboration.
Software application to apply limited-duration prevalence statistics from SEER*Stat to different population. The population would typically differ in year or geographic area. Enables users to project cancer prevalence data from SEER registries onto larger U.S. or other populations.
Text mining antibody specificity from literature. Helps researchers identify potential problems with antibody specificity. By mining the scientific literature and linking findings to Research Resource Identifiers (RRIDs), it provides alerts on antibodies that may yield unreliable results, supporting reproducibility in biomedical research.
Revvity | IVIS Spectrum 2 In Vivo Imaging System
In vivo optical imaging system used in preclinical research to non-invasively monitor and quantify biological processes in living animals over time. Designed with innovative camera with patented coating that delivers high sensitivity 2D and 3D bioluminescence and fluorescence imaging capabilities.
Web tool for merging csv files intended to be submitted to the open data commons databases including: ODC-TBI, ODC-SCI.
Software Python 3 library with good support for both reading and writing VCF. Reads and writes VCF files in Python.
Semantic Annotation Platform with Provenance (SAPP)
SPARQL Protocol and RDF Query Language (SPARQL)
Software Microbial Genome Processing toolkit. Flexible linked data framework for phenotype-genotype prediction of microbial traits using machine learning.
Software application as lightweight reimplementation of some of the algorithms in the MEME suite in Python.
Janelia Automatic Animal Behavior Annotator
Janelia Automatic Animal Behavior Annotator (JAABA)
Web application to create variety of automatic behavior classifiers. These classifiers input the animals' trajectories computed by tracking system, and they output time series indicating whether each animal is performing a given behavior in each video frame. Interactive machine learning for automatic annotation of animal behavior. Used to automatically compute interpretable, quantitative statistics describing video of behaving animals.
Web application to track the pose (position, orientation, size, wing- and leg positions) of multiple flies and maintain their identities throughout video. Outputs features (such as velocity, facing angle to other fly, and wing angles) useful for behavior analysis.
Software application for media browsing, analysis and annotation. MATLAB GUI for browsing, analyzing and annotating time-synchronized media files.
Software napari plugin for flexible mapping of various features (cell bodies, axonal densities, injections sites, optical fibers, Neuropixels probes) to standardized reference spaces included in BrainGlobe. Used for anatomical mapping.
Software DMC-Behavior Platform for standardized auditory decision-making tasks in head-fixed mice.
Software Python project for whole slide image acquisition using a fluorescence microscope.
Software Python package for analyzing transcription factor binding patterns from deep learning model attribution scores. It identifies and clusters sequence motifs from contribution scores, maps them to DNA-binding domains, and provides comprehensive visualization tools for regulatory genomics analysis. Used for transcription factor motifs and instances discovery.
Ottawa Hospital Research Institute Human Pluripotent Stem Cell Core Facility
Ottawa Human Pluripotent Stem Cell Facility
Training and support to research with human embryonic and induced pluripotent stem cells (iPSC). Offers opportunity to dissect early human development, generate models of disease, and develop cellular or drug therapeutics.
Software application that provides search and clustering functionality, typically used with amplicon sequence data. Used to assign sequences to clusters.
Bioscience division of the Japanese conglomerate Nichirei Corporation, specializing in biomedical products for the health and life science industries. The company develops, manufactures, and distributes products for immunohistochemistry (IHC), such as diagnostic and research reagents as well as products for cell biology, rapid diagnostics, functional materials, and natural materials processing. Their products support applications in pathological diagnosis, food safety, and cosmetic ingredients.
Japanese company that began as a textile manufacturer in 1882 and has expanded to become a global provider of high-function products, including films, functional polymers, industrial materials, and biotechnology products such as enzymes and diagnostic reagents. The company's business is organized around its core technologies in polymerization, modification, processing, and biotechnology, allowing it to contribute to fields like healthcare, environment, and electronics.
Software HLA typing tool to determine HLA-I germline alleles by aligning sequencing reads to HLA-A, HLA-B and HLA-C regions present in the IMGT/HLA database, optimized for cancer genomics analysis with support for tumor-normal paired samples and designed to handle complex scenarios including HLA-Y pseudogene detection and loss of heterozygosity assessment. Open-source integrative framework that characterizes the HLA-I locus, including its tumor status from WGS data.
University of Luxembourg Model Biobank and Tissue Analytics Platform Core Facility
Core offers advanced single and combined services including genomics, imaging, metabolomics and lipidomics, in vivo disease modelling, cell-based alternative methods, drug screening, and bioinformatics, providing researchers with essential tools for scientific exploration. Expert staff members offer advice on experimental design, data processing, and troubleshooting, as well as training to facilitate the use of our technologies.
University of Luxembourg LCSB Bioinformatics Platform Core Facility
Offers advanced single and combined services including genomics, imaging, metabolomics and lipidomics, in vivo disease modelling, cell-based alternative methods, drug screening, and bioinformatics, providing researchers with essential tools for scientific exploration. Staff members offer advice on experimental design, data processing, and troubleshooting, as well as training to facilitate the use of our technologies.
National Cancer Institute National Childhood Cancer Registry
Platform provides public health surveillance data to better understand the causes, outcomes, effective treatments, and later effects of cancer among children, adolescents, and young adults in the U.S. Developed under the NCI Childhood Cancer Data Initiative (CCDI), the NCCR contributes to the CCDI data ecosystem by serving as a linked infrastructure of central cancer registry data that will integrate various other childhood cancer data—from hospitals, research centers, heath care administrations, and other sources—to enhance access to and utilization of childhood cancer and survivorship data. The NCCR uses the Virtual Pooled Registry Cancer Linkage System to link multiple cancer registries and generate an accurate count of childhood cancer cases by combining information that appears in more than one registry.
Software Rust-Based suite of utilities for ultra-fast genomic feature extraction. Used for ultra-fast and scalable genome annotation access. Can be used both as a command-line tool and as a Rust library.
Ion S5 next-generation sequencing system enables simple targeted sequencing workflow for your lab with reliable performance and industry-leading speed. Torrent Server direct connection to the Ion S5 Sequencer is supported.
Independent, not-for-profit research institute dedicated to plant science located in the Olivette community of Saint Louis County, Missouri, United States.
Microenvironment Cell Populations-counter
Software to perform convolution of human bulk transcriptomics and evaluate abundance scores for 10 cell populations. Allows quantification of absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data.
Software tool as network inference in reduced diemnsion. Used to perceive contribution of regulatory components by transforming datasets into networks, using dimensionality reduction and assessing the overlapping structure with AUC metrics.
Open data repository to facilitate research on the relationship between neighborhoods and health, especially within the context of large federally funded surveys and cohort studies. Used to explore topics of interest to neighborhoods and communities. NaNDA measures can be readily linked to survey data, cohort studies, electronic medical records, or other microdata, via geographic identifiers, or combined and explored on their own. NaNDA datasets are created by researchers in the Social Environment and Health program at the University of Michigan Institute for Social Research.
Management Applications for Rich Metadata ObjecTs Graph
Knowledge graph system developed for managing and organizing rich metadata objects, initially for the Human Brain Project (HBP) and now extended to be a more generic, domain-agnostic solution. It is associated with CSCS (Swiss National Supercomputing Centre) and aims to provide a comprehensive toolset and API for working with knowledge graphs.
Software Python tool providing statistical tests for large-scale heterogeneous data with enhanced support for missing data.
Software R package for descriptive statistics and exploratory data analysis. Collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data.
Software R package for conditional inference procedures in permutation test framework. Conditional inference procedures for general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems described in.
Software Python package for inferring transcription factor binding variability from scATAC-seq data by implmenting algorithm proposed in chromVAR. It is built on anndata and mudata therefore can work seamlessly with scanpy and muon pipeline.
400 slide scanner with Aperio ImageScope DX clinical viewing software, and high-performance viewing workstation including color-calibrated medical grade monitors. System can be used standalone, or in conjunction with Aperio Path DX case management software, for streamlined, clinical workflow. Developed from Leica Biosystems,enables to produce consistent, diagnostic quality images, enabling pathologists to diagnose with confidence.
Software tool to cluster cells using the genetic variants detected within the scRNAseq reads. Robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Used for clustering scRNAseq by genotypes.
Software tool for Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.
Software R package to analyse differences in cell type proportions in single cell RNA-seq data. Used for analysing single cell data.
Software minimum viable HPC pipeline. CGPipe is a replacement for the venerable "make" that aims to automate the process of running complex analysis pipelines on high-throughput clusters. Make is a standard build tool for compiling software.
Updated knowledgebase integrating more curated associations in plants and animals. manually curated resource of genome-wide genotype-to-phenotype associations for a wide range of species. Database of publicly available GWAS summary statistics. Each GWAS can be browsed with the manhattan plot, risk loci, MAGMA (i.e. gene-based) results, SNP heritability and genetic correlations with other GWAS in the database. Full summary statistics can be downloaded from the original source following the provided links.
3DHISTECH | Pannoramic 150 Digital Scanner
Digital pathology system designed for high-speed, high-resolution brightfield and fluorescence scanning. Equipped with continuously moving stage, advanced Plan-Apochromat optics including 10x objective, and a back-illuminated sCMOS camera. Capacity:150 slides (6 magazines, 25 slides each) with automatic loading and continuous scanning.Scanning:Dual-mode scanning (brightfield and fluorescence) with area scanning and autofocus.Motorized Camera ChangerIncluded, for seamless transitions between BF and FL imaging modes without manual intervention.Motorized Objective changer Included when two objectives are selected (supports two objectives).Brightfield Scanning Speed:1 minute 30 seconds for 15 mm x 15 mm area at 0.19 µm/pixel resolution. Fluorescence Scanning Speed:8 minutes 30 seconds for a 15 mm x 15 mm area with 3 fluorescent channels at 20 ms exposure time.Throughput Optimized for high-throughput workflows with fully automated slide handling. Objectives Plan-Apochromat 10x/0.3 NA, 20x/0.8 NA, and 40x Corr/0.95 NA objectives.Brightfield Magnification Up to 103x. Fluorescence Magnification Up to 98x (with 1.6x adapter). Image Output MRXS format with export options to JPG, JPEGXR, BMP, PNG, TIFF, Roche TIFF, SVS, and DICOM.Slide Compatibility: Slides measuring 75.0-76.2 mm (L) x 25.0-26.0 mm (W) x 0.9-1.2 mm (T) with No. 1 or 1.5 coverslips (0.13-0.19 mm).
Open-source software Python library that provides high-level interface for PyTorch deep learning framework.
Fred Hutchinson Cancer Center Biostatistics Shared Resource
Fred Hutchinson Cancer Center Biostatistics Shared Resource Core Facility
Biostatistics Shared Resource (BSR) provides free, short-term statistical support to Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium investigators, particularly those without dedicated funding. Services include consultations on study design, sample size, power, and analytic methods; assistance with data analysis, interpretation, and manuscripts; and development of statistical sections for grant proposals. While intended as short-term collaborations, BSR projects often lead to funded grants and longer-term partnerships with biostatisticians.
Software Nextflow pipeline for calling allele-specific variants (ASVs) from 5′ single-cell RNA sequencing data.
Software application as long-range genomic foundation model pretrained on context lengths of up to 1 million tokens at single nucleotide resolution.
Genomic language model trained on cross species data.
U.S. Department of Agriculture's Economic Research Service Rural-Urban Continuum Codes
Mission of U.S. Department of Agriculture's Economic Research Service is to anticipate trends and emerging issues in agriculture, food, environment, and rural America and to conduct high-quality, objective economic research to inform and enhance public and private decision making. Rural-Urban Continuum Codes distinguish U.S. metropolitan (metro) counties by the population size of their metro area, and nonmetropolitan (nonmetro) counties by their degree of urbanization and adjacency to a metro area. The codes allow researchers, policy makers, and others to view county-level data by finer residential groups—beyond metro and nonmetro—when analyzing trends related to population density and metro influence.
Appalachian Regional Commission Data Reports
Appalachian Regional Commission (ARC) Data Reports
Web data report tool uses publicly available data to generate reports for every Appalachian state and county across different topics. Provides detailed information on socioeconomic and demographic factors in Appalachian Region, serving to inform policymakers and regional partners for economic development and decision-making.
Bechman Coulter | Labcyte Echo 550 acoustic liquid handler
Non-contact liquid handler that uses Acoustic Droplet Ejection (ADE) technology to precisely transfer nanoliter-sized droplets of liquid for high-throughput applications in pharmaceutical research, drug discovery, and various areas of genomics and biology. Echo 555 / 550 Liquid Handler: 2.5 nL increment; Flow rate:0.25 – 1 µL/sec; Ideal for reactions of 0.05 – 1 µL; Supports 384 and 1536-well source plate formats; Used for transfer of small molecules for high throughput screening.
Cleveland Clinic Lerner Research Institute Light Microscopy Core Facility
Core services include: basic light microscopy (determine appropriate staining protocols and offer training and/or assistance in acquiring transmitted and fluorescent digital images with wide-field microscopes); optical sectioning (training and assistance in the use of confocal and multi-photon microscopes); whole slide scanning (brightfield or fluorescence mode). Laser MicroDissection instruments are available for isolating small areas of tissue or single cells. Total Interference Reflection Fluorescence (TIRF) microscopy is available for visualizing and quantifying cellular events localized at the basal plasma membrane. Live cell and tissue imaging can be done on both wide-field and confocal microscopes equipped with environmental chambers for heat/CO2 control.Investigators have access to Image Processing and Analysis workstations with variety of advanced software for extracting quantitative data from their images. They can also generate images and movies for presentations, grants and publications. Core is home to 2 LI-COR Odyssey, laser-based scanning systems for gels, Westerns, in-cell Westerns, ELISA/FLISA, EMSA/Gel Shift, Protein Detection, etc.
University of Michigan Robert B. Zajonc Experimental Lab Core Facility
Core provides researchers with facilities to conduct experimental research, particularly within the Research Center for Group Dynamics (RCGD) and across the U-M campus. The labs offer adaptable room configurations, specialized software like E-Prime and z-Tree, and shared access to cutting-edge technology, including a new Virtual Reality (VR) Lab, to support a range of interdisciplinary research projects focused on human social behavior and dynamics.
Houston Methodist HMRI Neurology Electron Microscopy Core Facility
HMRI Neurology Electron Microscopy Core Facility
Core is fee-for-service research laboratory providing internal and external users a wide spectrum of electron microscopy (EM) techniques. As part of the Houston Methodist Research Institute Department of Neurology, we routinely process samples related to the peripheral nervous system but can help with the ultrastructural study of many biological samples.
Duke University Shared Materials Instrumentation Facility (SMIF)
Pratt School of Engineering core facility that enables materials, devices, and integrated systems research at Duke University in a variety of fields that include materials, devices, and integrated systems. SMIF is housed in the Fitzpatrick Center for Interdisciplinary Engineering, Medicine and Applied Sciences (FCIEMAS). The facility consists of 7,000 square feet of clean room fabrication space, and nearly 3,000 square feet of specialized laboratory space for characterization and imaging equipment.
University of Pittsburgh Hillman Cancer Center Translational Oncologic Pathology Services Core Facility
Translational Oncologic Pathology Services (TOPS)
UPMC Hillman Cancer Center Translational Oncologic Pathology Services (TOPS)
TOPS is a UPMC Hillman Cancer Center managed and regulated resource that provides coordinated collection, processing, annotation, distribution, and storage of patient biospecimens to investigators and their respective collaborators.
Houston Methodist Hospital is the flagship quaternary care hospital of Houston Methodist academic medical center.Houston Methodist Hospital is ranked among the country's top hospitals
Software pipeline to quantify seed vigour in wheat and other cereal crops using deep learning powered dynamic phenotypic analysis.
Software application to perform Bayesian analysis on expression and gene dependency data across different cell lineages. Integrates expression as the dependent variable and gene dependency data as the independent variable. Used to identify cancer gene targets by jointly analyzing global transcriptomic and proteomic profiles with genetic dependency data of cancer cell lines across tissue lineages.
Software R package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R.
Transmission electron microscope developed for the fields of biology and materials science. Equipped with a highly sensitive CCD camera, the H-7650 delivers images with optimal contrast even under low-dose electron beam conditions. As the CCD camera is integrated into the microscope, it can be controlled either manually via the control panel or through a PC. Images displayed on the monitor can be stored in digital formats. With built-in autofocus, other automated functions, and database capabilities, the H-7650 provides users with a user-friendly operating environment during observation.
University of Ottawa Integrated Neurocognitive and Social Psychophysiology Interdisciplinary Research Environment (INSPIRE) Core Facility
Multidisciplinary facility designed to explore questions related to human behaviour from various perspectives, including human cognition, social interactions, and psychophysiology.
University of South Carolina Research Computing Core Facility
Reporting to the Division of Information Technology, and working in close partnership with the Office of Research, works with researchers to improve their project performance and secure computing resources not only at the university level but beyond, to National Labs and other high profile HPC resources.
Roland | Ganzfeld Q450SC Electrophysiological Test Unit
Electrophysiological Test Unit for animals. This is usable for Pattern VEP + Pattern ERG + Flash VEP, for scotopic and photopic ERG, EOG fast and slow, mf ERG Flash stimulation and mf VEP Pattern stimulation.
Mayo Clinic Structural Biology Core Facility
Core offers instrumentation and support for the structural characterization of biological macromolecules to investigators at Mayo Clinic and its partner institutions. Supports cryogenic sample electron microscopy (cryoEM), along with associated services such as training, data collection, processing, analysis, and data storage. Future services will include nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography.
Software application that predicts bacteriophage gene functions by leveraging gene synteny and genome-wide organizational patterns. Synteny-enhanced annotation of Bacteriophage genes.
University of Northampton; Northampton; United Kingdom
University of Northampton is public university based in Northampton, which offers students undergraduate and postgraduate courses. It was formed in 1975 as Nene College of Higher Education.
University of Vermont Bioinformatics Shared Resource Core Facility
University of Vermont Bioinformatics Shared Resource
Core offers bioinformatics and data modeling services. Focuses on support for reproducible, well documented, containerized, nextflow pipelines customized to address the specific research questions and biological systems of the investigators. Offers support from preprocessing -omics data, through data integration and manuscript support, based on grant support or a fee-for-service mechanism. Provides training for students and PIs in the form of individual help, seminars, and workshops.
Van Andel Institute Metabolism and Nutrition (MeNu) Program
Small foundation and think tank that seeks to equip brilliant scientists with leading technology, crucial collaborators and cutting-edge support to accelerate discoveries — transforming bold ideas into breakthroughs in metabolism.
University of Nevada at Reno Nevada Genomics Center Core Facility
Core to serve academic and industry researchers in their studies on the function and structure of genomes. Offers services for next-generation Illumina sequencing, 10X single-cell library preparation, Sanger sequencing, fragment analysis and nucleic acid quantification and sizing.
hd Weighted Gene Co-expression Network Analysis
Software R package for performing weighted gene co-expression network analysis in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics.
Louisiana State University in Shreveport Center for Cardiovascular Diseases and Sciences (CCDS) Surgical Models Core Facility
Center for Cardiovascular Diseases and Sciences (CCDS) Surgical Models Core
Core provides centralized service for performing technically challenging mouse models of cardiovascular disease, such as middle cerebral artery occlusion (MCAO) stroke model, coronary artery ligation model of myocardial ischemia, femoral artery ligation model of peripheral artery disease, and partial carotid artery ligation model of disturbed blood flow.
Louisiana State University in Shreveport Center for Cardiovascular Diseases and Sciences (CCDS) Virus Production Core Facility
Center for Cardiovascular Diseases and Sciences (CCDS) Virus Production Core
Core provides centralized service for generating AAV particles for cardiovascular studies. The CCDS Virus Production Core offers the production of either pre-made (ex. AAV8-GFP, AAV8 mPCSK9 D377Y) or custom AAVs.
Software R package for fully Bayesian inference of tumor microenvironment composition and gene expression deconvolution. Used to analyze bulk RNA-seq data and estimate cell type-specific expression profiles.
Instrument used to quantify biomolecular interactions and measure their binding affinity using MicroScale Thermophoresis. Can determine the strength of binding between all types of biomolecules, from single ions to large complexes, in various complex samples and buffer conditions.
Tampa General Hospital-University of South Florida Health Precision Medicine Biorepository
TGH-USF Health Precision Medicine Biorepository
Procures high-quality biologic specimens along with coded clinical and demographic data across broad ethnic, racial, and social demographic of patients. All specimens are systematically collected and processed so that their multi-functional potential for recovering high-quality bioanalytes (including RNA, genomic DNA, protein, enzymes and metabolites) is conserved. All specimens are stored and protected in a database hub to connect researchers conducting variety of scientific projects across multiple medical specialties. Muilti-disciplinary biorepository with capacity for generating specialized bioanalytes.
Visualization software tool for viewing large image files in a browser. Works with Brain Image Library, built for BICAN.
Icahn School of Medicine at Mount Sinai Stem Cell Engineering Core Facility
Icahn School of Medicine at Mount Sinai Stem Cell Engineering Core
Core provides services for generation and characterization of induced pluripotent stem cells (iPSCs) from somatic sources such as blood and fibroblasts, along with long-term cryobanking. Offers access to collection of well-characterized iPSC lines derived from both healthy donors and patients with various diseases, representing a range of ethnic backgrounds and sexes.Major focus of core is gene editing in pluripotent stem cells, with expertise in CRISPR-based applications from precise point mutation knock-in (correction or introduction) to the generation of reporter lines (e.g., GFP and other fluorescent reporters) and inducible systems such as Cre-lox, dTAG, and beyond.Core provides guidance and support for the differentiation of iPSCs into multiple cell types, using both monolayer and 3D organoid formats, enabling downstream disease modeling and functional studies.
Virginia Tech VT Surface Analysis Laboratory Core Facility
Virginia Tech VT Surface Analysis Laboratory
Core offers contemporary surface analysis techniques, featuring the latest PHI VersaProbe III Scanning XPS Microscope, and expertise.
Icahn School of Medicine at Mount Sinai Transgenic and Genome Editing Core Facility
Icahn School of Medicine at Mount Sinai MSSM-Transgenic and Genome Editing CoRE
Core offers services from consultation until delivery of germline-confirmed genetically engineered mouse models (GEMMs). Uses genome editing tools such as CRISPR/Cas9 to rapidly generate GEMMs with diverse genome modifications such as humanization, large insertion, conditional knockout, base substitution and deletion. Animals produced in the CoRE are thoroughly genotyped by our comprehensive genotyping services. Supports model creation via the traditional transgenesis and the gene targeting in the embryonic stem cells. Other services provided by the CoRE include sperm cryopreservation, in vitro fertilization, rederivation and custom embryology supports.
Software deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins.
Corning Incorporated is a global manufacturer of laboratory consumables and scientific equipment, widely known for its high-quality cell culture products, microplates, flasks, and filtration systems. Corning Life Sciences provides essential tools for cell biology, genomics, drug discovery, and bioprocessing applications.
German manufacturer specializing in advanced cell culture and imaging products, including µ-Slide chambers, microfluidic devices, and reagents for live-cell analysis. Ibidi’s technologies support high-resolution microscopy, cell migration assays, angiogenesis studies, and immunological research.
Microscope patented optics are setting new standards in modular common main objective stereomicroscopy. Thanks to higher resolution and significantly increased contrast, they provide 20% more image information – in addition to 3D images. The innovative operating concept SyCoP (Systems Control Panel) combines all essential functions of stereomicroscope in single handy operating unit. Used particularly for applications in materials research, quality control, biology and medical research.
Agilent | BioTek Cytation C10 Confocal Imaging Reader
Agilent BioTek Cytation C10 Confocal Imaging Reader
Imaging reader combines automated confocal and widefield microscopy with conventional multimode microplate reading. Automated water-immersion objectives capture more light, driving lower exposure times and reducing phototoxic impacts on live cells. Spinning-disk confocal module and accompanying disk pinhole options for looking deeper into thick sample biology with improved clarity and detail. High-quality components used in system, including Hamamatsu scientific CMOS (sCMOS) camera, Olympus objectives and laser-based illumination enable excellent image quality. Cytation C10 also includes widefield fluorescence, brightfield, and phase contrast optics. Onboard environmental controls enable live cell assays.
Concordia University Genome Foundry Core Facility
Core research facility dedicated to high-throughput DNA assembly, strain engineering, and automation-enabled synthetic biology. Equipped with state-of-the-art robotic platforms and expert technical staff, the Foundry supports academic and industry researchers in the design, construction, and testing of biological systems.
Concordia University is a public English-language research university located in Montreal, Quebec, Canada. Founded in 1974 following the merger of Loyola College and Sir George Williams University, Concordia is one of the three universities in Quebec where English is the primary language of instruction.
Van Andel Institute MiND Blood Biorepository
West Michigan Neurodegenerative Diseases (MiND) Program Biobank
Biorepository that collects and stores donated PBMCs, plasma, and WBC pellets from people with neurodegenerative diseases to support scientific research on Parkinson's disease, dementia, and other neurodegenerative disorders. It functions as a research-focused collection of biospecimens, providing scientists with samples to study the mechanisms and causes of these conditions. Informed consent is obtained through our clinical partners. All donors remain anonymous.
Project portal from the European Union that creates global geographical data about the evolution of human habitation on Earth. This information is in the form of population density maps, built-up maps, and settlement maps. This information is produced using new geographic data mining tools and knowledge and analytics based on empirical data.
Science and Technology Facilities Council Central Laser Facility OCTOPUS Microscopy Core Facility
CLF Optics Clustered to OutPut Unique Solutions Microscopy Facility
National imaging facility that offers access to single molecule imaging, confocal microscopy, superresolution imaging, light sheet microscopy, optical trapping and cryoscanning electron microscopy. Offers expert guidance and advice for light and electron microscopy experiments alongside advanced instruments for fluorescence and electron microscopy.
Supplier of drug reference standards for life science research, offering collection of small molecule inhibitors and modulators, targeting more than 850 biological pathways, including cell signaling, gene transcription, apoptosis, and CNS function. Provides expert contract research services, specializing in the custom synthesis of bioactive and drug-like molecules.
Software workflow for analysing Pore-c data for chromatin conformation capture.
Software application for discovery of communities in Pore-C concatemers.
University Health Network Biospecimen Services Core Facility
Core provide services for the enhancement and progression of novel and innovative research and discovery. Provides human biospecimen samples such as: fresh frozen and formalin fixed paraffin embedded (FFPE) tissue, compartmentalized blood components such as serum, plasma, and whole blood peripheral blood mononuclear cells (PBMCs) and other biofluids, including saliva and urine; Tissue microarray (TMA) construction and quantitative image analysis of TMA sections, Laser capture microdissection (LCM), digital slide scanning, quantitative image, and pathological/clinical analysis for various tumour sites and DNA/RNA extraction; support and guidance to researchers and biobanks on accessing, collecting, and using human biospecimens and associated data for health research.
University Health Network Joint Department of Medical Imaging Research Office JDMI RO Core Facility
Joint Department of Medical Imaging Research Office (JDMI RO)
Core services include Imaging Modalities:MRI,PET-MRI,CT,PET-CT,Ultrasound / X-Ray,Interventional / Biopsies;Consultation:Pre-grant submission consultations,Pre-trial launch consultations / site initiation visists,Feasibility assessments MRI physics consultation; Protocol Development / Site Feasibility:Industry site feasibility questionnaires, Protocol development of medical imaging studies and clinical trials; Post-Processing of Images:Tumour measurements, Volumetric measurements.
University Health Network McCain GU Biobank
Core supports biomarker discovery and enhancing future cancer research in the areas of genomics, proteomics and epidemiology. Provides serialized collections of biospeciments throughout patient prognosis. Clinical time point collections are based on input from our expert surgical, medical, and radiation oncologist teams.
University Health Network Princess Margaret Cancer Biobank Core Facility
Core offers biobanking services and diverse inventory of biospecimens in the field of Oncology. Offers prospective protocol specific banking tailored to your research needs, including patient eligibility, screening, consenting, biospecimen procurement, handling, and processing, clinical data annotation, short and long-term sample storage, and shipping.
University Health Network Princess Margaret Living PDX Core Facility
Core provides services for the use of Xenograft (PDX) models listed in open global catalogue of PDX models for comprehensive search and attribute filtering support for clinico-pathological and molecular data. Molecular data and visualization of profiled models could be accessed through the institute's portal.
University Health Network Princess Margaret Genomics Centre PMGC Core Facility
Core is dedicated to providing access to cost-effective and high quality genomics services including standard and custom-tailored DNA sequencing using Illumina technologies, epigenomics, panel-based profiling (Luminex and Nanostring) and functional genomics. Single cell genomics applications on variety of popular platforms.
University Health Network Advanced Molecular Diagnostics Laboratory Core Facility
Advanced Molecular Diagnostics Laboratory (AMDL)
AMDL is a clinical CAP/CLIA accredited molecular diagnostics laboratory at the Princess Margaret Cancer Centre. Supports clinical trials and translational research projects requiring clinical-grade (CAP/CLIA) molecular testing at Princess Margaret Cancer Centre. AMDL works closely with Molecular Diagnostics lab in Toronto General Hospital to transition protocols into clinical tests.
University Health Network PMCRT and PGCRL UHN-SickKids Joint Core Facility
Princess Margaret Cancer Research Tower (PMCRT) and Peter Gilgan Centre for Research and Learning (PGCRL) UHN-SickKids Joint Facility
Facility provides analytical flow cytometers and high-speed cell sorting, as well as training, education and consultation services.
University Health Network Quantitative Imaging for Personalized Cancer Medicine Advanced Imaging Core Facility
Quantitative Imaging for Personalized Cancer Medicine (QIPCM) Advanced Imaging Core Lab
Provides testing and analysis support for clinical trials to improve consistency and reliability in clinical trial data.Helps clinical investigators achieve systematic image collection and improved collaboration. Can help with handling large volume functional and dynamic imaging data.
University Health Network Biostatistics Core Facility
Core offers services including Study planning and design; Grant writing and protocol creation; Data collection form design; Data capture instrument construction; Complex data processing and linkage; Quality control involvement; Statistical analysis, figure, and table generation; Manuscript drafting and presentation preparation; Response to manuscript reviews from regulatory agencies and journals.
University Health Network Krembil Discovery Tower Flow Cytometry Core Facility
Krembil Discovery Tower (KDT) Flow Cytometry Core Facility
Core offers cell sorting and flow cytometry services. Provided instruments include BD FACS Canto II, Beckman Cytoflex LX, BD FACS ARIA III, AutoMacs Cell Separator.
University Health Network Princess Margaret Living Biobank PDO Core Facility
Core provides services for the use of patient-Derived tumor Organoid (PDO) model.Organoid models are derived from patient-derived xenograft tissues, primary tumors, and metastatic patient tissues. PMLB organoid repository includes models generated from colorectal, pancreatic, and lung cancer tissues.
University Health Network Spatio-Temporal Targeting and Amplification of Radiation Response Core Facility
Spatio-Temporal Targeting and Amplification of Radiation Response (STTARR)
Offers services to support studies in medical fields across oncology, cardiology, metabolic diseases, radiotheranostics and more.Helps with study design to final data analysis, including GLP-compliant histopathology services.
University Health Network Bioinformatics and High Performance Computing HPC Core Facility
Bioinformatics and High Performance Computing (HPC) Core
Core provides services including Basic High-Throughput Sequencing Analysis, Advanced Data Analysis, High Performance Computing.
public research and teaching hospital network in Toronto, Ontario, Canada. It is affiliated with the Temerty Faculty of Medicine at the University of Toronto, and is the largest health research organization in Canada, ranking first in the country for total research funding.
Artificial Social Agent Questionnaire (ASAQ)
Artificial Social Agent Questionnaire (ASAQ), an instrument for evaluating human interaction with an artificial social agent (ASA), resulted from multi-year efforts involving more than 100 Intelligent Virtual Agent (IVA) researchers worldwide within the OSF work-group of Artificial Social Agent Evaluation Instrument (https://osf.io/6duf7/). It has 19 measurement constructs constituted by 90 items, which capture more than 80% of the constructs identified in empirical studies published in the IVA conference 2013-2018. In addition, a representative item of each construct or dimension was selected to create a 24-item short version of the ASA questionnaire. Whereas the long version is suitable for a comprehensive evaluation of human-ASA interaction, the short version allows quick analysis and description of the interaction with the ASA.
University Health Network Advanced Optical Microscopy Core Facility
Advanced Optical Microscopy Facility (AOMF)
Core offers services in optical microscopy experiments including: confocal, multiphoton, super-resolution, FRAP, FRET, live-cell timelapse, whole-slide scanning, image analysis and more.
University Health Network Histology Biomarker Lab Core Facility
Core provides biospecimen processing and performs automated slide-based biomarker methods (protein/RNA/DNA), implementing good clinical laboratory practices.Offers specialized consultation and perform biomarker development and analyses within clinical study and research program protocols.Provides services to the clinical trials and pre-clinical research community and expertise in biomarker selection, method development, optimization and standardization, and provision of quality consultation on biomarkers for clinical research protocols.
University Health Network Princess Margaret Flow Cytometry Core Facility
Princess Margaret Flow Cytometry Facility
Core offers services in Analytical Flow Cytometry, Fluorescence Activated Cell Sorting, consultation and data analysis. Staff provides training, assisted acquisition, consultation, and data analysis upon request.
Software suite of tools designed to build information services for developing regions.
Software tool for extracting information from scholarly documents.
Icahn School of Medicine at Mount Sinai Metabolomics Core Facility
Core provides mass-spectrometry solutions for small-molecule research. Supports experimental design, ensuring proper handling, appropriate controls, and adequate statistical power, and then executes analyses on Thermo Orbitrap IQ-X and Agilent 6495D LC/MS systems and an Agilent 5977C GC/MS system. Using validated methods annotated against a library of 1,000+ compounds, we maximize metabolite and small-molecule coverage. We also offer untargeted profiling for biomarker and novel metabolite and lipid discovery, as well as stable-isotope tracing for measuring substrate utilization. Results are delivered with custom informatics and statistical interpretation for faster, more approachable insights.
Science and Technology Facilities Council Octopus Core Facility
Provides expert advice and guidance for collaborative research projects involving the use of fluorescence and electron microscopy. Access to advanced fluorescence and electron microscopes for external users after a peer-review process.
Gladstone Institutes Stem Cell Core Facility
Core offers a fully functional tissue culture facility with specialized instruments, media, reagents, cell lines, and expertise for new or established researchers to perform cutting-edge stem cell research. In addition, our core provides comprehensive human induced pluripotent stem (iPS) cells related training, consultations, and standard and customized scientific services, including derivation of iPS cells, differentiation of iPS cells and genome editing in iPS cells to stem cell researchers.
Mayo Clinic Antibody Hybridoma Core Facility
Core can generate custom monoclonal antibodies in mouse and hamster systems. Can also produce large amounts of antibodies (of all species) and recombinant proteins in-vitro. Purification is also available for various systems.
George Washington University Milken Institute School of Public Health Genomics Core Facility
Milken Institute School of Public Health Genomics Core
Genomics Core team has expertise in bacterial genomics, computational biology, infectious disease, HIV, population and conservation genetics. Offers NGS services. Capable of supporting projects at any stage, from planning to sample processing to sequencing. keith crandall
University of Connecticut Advanced Light Microscopy Core Facility
University of Connecticut Advanced Light Microscopy Facility
Facility provides training and access to advanced light microscopy systems at an hourly rate. In addition, we are available to consult with and support users at every stage of a project including: experimental design, sample preparation, image acquisition, analysis, and data preparation.
University Health Network Nuclear Magnetic Resonance Core Facility
NMR Core Facility is equipped with NMR spectrometers allowing researchers to Characterize bio-molecular structures at the atomic resolution with exquisite details;Identify protein interactions with binding partners in order to understand their architecture;Study protein dynamic;Study protein post-translational modifications acting as molecular switches;Study structure-function relationships of biological proteins to gain insight into biological processes in relation to human disease;Screening of High-throughput drug-like leads for novel therapeutic targets;Study Metabolites of interest.Core facility houses high-field NMR spectrometers equipped with cryogenically cooled probes (1H or 13C optimized) for enhanced sensitivity.
General-purpose polarizing microscope designed for all polarization inspection tasks in the petroleum, mining, and structural characterization industries. It is also an all-round instrument suitable for industrial analysis and quality control , such as analyzing glass, plastics, textiles, and fibers, as well as inspecting display panels in the semiconductor industry.
High-performance scientific CMOS (sCMOS) digital camera designed for low-light microscopy and advanced imaging applications. Its key features include an exceptionally low and uniform readout noise, high quantum efficiency (QE) of up to 95%, and a patented "Lightsheet Readout Mode" optimized for light-sheet microscopy. This combination makes it ideal for detecting faint signals with high signal-to-noise ratios in challenging experiments, such as time-lapse, fluorescence, and single-molecule tracking.
Agilent | 7000E Triple Quadrupole GC/MS system
Agilent 7000E triple quadrupole GC/MS instruments incorporate intelligent technology that reduces instrument downtime and improves run times for maximum productivity in analytical labs. Mass spectrometer is used for routine, high-sensitivity analysis of targeted compounds in complex samples, especially for trace-level detection in areas like food safety and environmental testing.
Cancer Incidence in Five Continents (CI5)
Cancer Incidence in Five Continents (CI5) is a collaboration between the International Agency for Research on Cancer (IARC) and the International Association of Cancer Registries (IACR) that produces a benchmark series of data on cancer incidence worldwide. This multi-volume publication, released approximately every five years, compiles standardized data on newly diagnosed cancer cases from population-based cancer registries across the globe. The data provide a unique source of comparable information on the global burden and distribution of cancer and help inform cancer control programs.
Web tool, developed by the U.S. National Cancer Institute (NCI), performs statistical modeling of cancer incidence or mortality data using age-period-cohort analysis. It allows users to examine and interpret temporal trends while disentangling the effects of age, calendar period, and birth cohort. The tool supports data import, graphical output, and model fit assessment via interactive web interface.
Tennessee Tech University Research Computing and Data Core Facility
Tennessee Technological University Research Computing and Data Core Facility
Core empowers students, faculty, and staff across all disciplines by providing the tools, training, and equipment for advanced computing for more robust, reproducible research with reduced time to results. Manages the campus cluster, and also facilitate access to larger federally-funded clusters at zero cost. Provided data transfer and network performance monitoring services enable researchers and collaborators to move data quickly.
Tennessee Technological University; Cookeville; United States
Public research university in Cookeville, Tennessee. It was formerly known as Tennessee Polytechnic Institute, and before that as University of Dixie, the name under which it was founded as a private institution.
University of Manchester Advanced Metal Development Core Facility
Core supports all processing of metal related activity and houses equipment in the areas of thermomechanical processing, additive manufacturing, mechanical testing (including testing under a variety of environments), thermomechanical simulation/testing and heat treatment.
Waters | DIL805 A/D/T Quenching Dilatometer
805 Series Quenching Dilatometers are the benchmark instruments for scientists and engineers interested in determining dimensional changes and phase transformations of steel alloys. Extremely flexible and configurable, designed to accommodate a wide range of add-on modules enabling it to be tailored to specific user requirements. Quenching, compression, tension, alpha and sub-zero alpha modes all provide highly accurate dimensional change measurements under different conditions and environments.Used for determination of critical parameters in steel manufacturing and heat treatment processes.
Software R package for visualizing genomics data. Provides a user-friendly, flexible and comprehensive suite of tools for visualizing complex genomic data in three categories (small variants, copy number alterations and data quality) for multiple species of interest.
SYSTRONICS | AU- 2704 X Flashing Xenon Lamp Spectrophotometer
Double-beam UV-Vis spectrophotometer used for precision measurements in various scientific and industrial applications, such as quality control, environmental monitoring, and biochemical analysis. Its flashing xenon lamp provides a high-intensity, broadband light source for fast, reliable measurements across a wide wavelength range, and its double-beam design ensures accuracy by measuring both the sample and a reference simultaneously.
CAMTHC:Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
Software R package for deconvolving tissue heterogeneity using convex analysis of mixture models.
Software successor to the Reconstruct annotation tool. PyReconstruct runs on all major operating systems, breaks through legacy RAM limitations, features intuitive and collaborative curation system, and employs flexible and dynamic approach to image registration. Used to analyze, display, and publish experimental or connectomics data. Suited for generating ground truth to implement in automated segmentation, outcomes of which can be returned to PyReconstruct for proofreading and quality control.
Software tool aimed at data modelers, curators, wrangers, and creators of standards and datamodels. It is aimed at people who prefer to develop these standards using spreadsheet tools over more developer-centric tooling. Human-friendly spreadsheets with machine-actionable models.
Brain Knowledge Base Interaction Toolkit
Software package contains tools to use the BICAN Knowledgebase Data Models.
Icahn School of Medicine at Mount Sinai Neuropathology Brain Bank and Research CoRE Facility
Icahn School of Medicine at Mount Sinai Neuropathology Brain Bank & Research CoRE
Neuropathology Brain Bank & Research CoRE
Provides access to collection of human postmortem brain tissues, including fresh, frozen, and formalin-fixed paraffin-embedded (FFPE) specimens, along with detailed clinical histories and neuropathological assessments. Available histology services include processing and embedding, slide sectioning for FFPE and cryosections, immunohistochemistry (IHC), immunofluorescence (IF), and advanced RNA assays such as RNAscope, BaseScope, and miRscope. High-resolution digital slide imaging is performed using the GT450 scanner. CoRE scientists also collaborate with investigators and trainees to support project development, method optimization and troubleshooting, data analysis.
University of Bern Translational Research Unit Platform TRU Core Facility
Core facility offers researchers access to histological services, tissue visualization, slide scanning, digital image analysis, and next-generation tissue microarrays. Our team processes more than 800 projects per year related to patient tissue, patient-related data, clinical studies, and animal models.
Software pipeline as open-source, cloud-optimized workflow for processing spatial transcriptomics data. It supports data derived from spatially barcoded sequencing technologies, including Slide-tags-based single-molecule profiling. The pipeline processes raw sequencing data into spatially resolved gene expression matrices, ensuring accurate alignment, spatial positioning, and quantification.
Software tool to convert FastA and Eggnog-mapper annotation files to GenBank files containing GO terms and EC number annotations, suitable for metabolic network reconstruction using Pathway Tools. Used for creation of genbank files from Eggnog-mapper annotation outputs.
Icahn School of Medicine at Mount Sinai RNA Nanocore Core Facility
Icahn School of Medicine at Mount Sinai RNA Nanocore
Core Facility at the Icahn Genomics Institute (IGI) offers custom-made lipid nanoparticles and RNA technology to develop new therapeutics and nanomedicines.
Icahn School of Medicine at Mount Sinai Human Immune Monitoring Center Core Facility
Icahn School of Medicine at Mount Sinai Mount Sinai Human Immune Monitoring Center
Mount Sinai Human Immune Monitoring Center
Core provides team of experts in the characterization of immune profiles and treatment responses across a diverse range of diseases, such as cancer, autoimmunity, allergy, and neuro-immune disorders. Offers equipment in the field for research at Genomic, cellular and proteomic analysis. Develops assays to balance innovation with protocols and operating procedures to ensure data quality and reproducibility.
Icahn School of Medicine at Mount Sinai Center for Advanced Genomics Technology Core Facility
Icahn School of Medicine at Mount Sinai Center for Advanced Genomics Technology
Core has built technology toolbox with access to and application of novel and existing methods in multitude of genomics technologies. These capabilities span bulk, single-cell, spatial, and in situ genomic sequencing methods, all of which are leveraged to generate complementary cross-platform, orthogonally validated datasets to foster novel discovery and advance clinical applicability using human cohorts and model systems
Donald Danforth Plant Science Center Data Science Core Facility
Core Facility provides infrastructure for high-performance computing and data storage (local and cloud). Services include access and training for use of high-performance computing resources, data analysis and visualization, data integration, statistical analysis, and image analysis.
Software tool that reverts normalised single-cell omics data to raw counts, preserving the integrity of the original measurements and ensuring consistent data processing during integration. Denormalization tool for single-cell transcriptomics data.
caper: Comparative Analyses of Phylogenetics and Evolution in R
Comparative Analyses of Phylogenetics and Evolution in R
Software R package used to conduct comparative analyses on phylogenetic data sets.
Automatic Magnetic Bead Cell Isolation System. Benchtop instrument for the purification and extraction of DNA, RNA, proteins, and cells in laboratory settings. It uses magnetic particle technology to handle medium to high throughput processing of 24 or 96 samples per run, providing a more efficient and consistent alternative to manual methods.
Software multi-user server for Jupyter notebooks.
University of Maryland Baltimore County High Performance Computing Facility
Facility maintains and administers the chip high performance computing cluster. The chip cluster is built from more than 150 machines featuring Intel CPUs and NVIDIA GPUs.
Beth Israel Deaconess Medical Center BIDMC Clinical Research Coordinator Core Facility
BIDMC Clinical Research Coordinator Core
Clinical Research Coordinator Core is available to support and collaborate with investigators and their research teams in all phases of clinical research, providing services that include assisting with the organization, implementation and completion of clinical research studies.
Software R package to facilitate proteogenomics studies. Houses functions to create customized protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. Used to generate protein variant sequences based on imported mutations from VCF, MAF and additional files to generate protein-variant database for use in proteogenomics studies.
Software pipeline for complete analysis of bacterial genomes.
University of Pittsburgh Western Pennsylvania Quantum Information Core Facility
Western Pennsylvania Quantum Infrastructure Core
Core is equipped with suite of cryostats and measurement systems for probing electrical, magnetic, and quantum properties at cryogenic temperatures. Sample preparation capabilities include tools for wafer processing, nanomaterial transfer, and inert atmosphere handling. Deposition systems support thin film growth and surface treatment using a variety of techniques. Wirebonding and related sample preparation tools enable precise device packaging and integration, supporting a broad range of experimental workflows in quantum and nanoscale science.
Oregon Health and Science University Primate Genetics Core Facility
Core provides services for comprehensive genetic and genomic analysis of NHPs, including DNA sequencing, nucleic acid extraction, macaque-specific genotyping assays, and NHP DNA Bank distribution services.
Augusta University Qualitative Research Lab Core Facility
Core provides services including consultation on research design, training on interviewing, grant development, conducting focus groups, data analysis.
Medical College of Wisconsin Cancer Center Geospatial, Epidemiology and Outcomes Shared Resource Core Facility
Epidemiology and Outcomes Shared Resource (GEOSR)
Core provides services including Geospatial Data Technology and Analysis, Epidemiological Information about the Catchment Area, Cancer Outcomes Data and Analysis.
Fred Hutchinson Cancer Center Collaborative Data Services Core Facility
Core provides data-related support to cancer researchers by offering services like study design consultation, data management, programming, and access to patient data. Its purpose is to help researchers develop and execute studies, manage data, analyze results, and ultimately accelerate cancer research by making large, complex datasets more accessible and usable. CDS team uses evidence-based standards and effective quality assurance procedures from project design to study end. All CDS study staff are HIPAA-compliant and certified in Human Subjects and Good Clinic Practice training.
Virginia Tech NMR Spectroscopy Core Facility
Facility features 7 state of the art high field NMR instruments ranging from 400 to 600 MHz. The facility provides a diverse selection of probes including room temperature, LN2 cooled probes, 10mm Polymer probes, Diffusion and Solid-State NMR probes. The entire suite of 1D, 2D, Diffusion and Solid-State NMR capabilities are available for a broad range of nuclei.
Open-access, browser-based visualization and summary tool for venom transcriptomic and proteomic data. R Shiny–based interactive application designed as visualization and reporting interface for venom transcriptomic and proteomic data. It enables users to explore annotation metrics, toxin gene families, and quality-control summaries generated by analysis pipelines. While it will eventually serve as part of the VenomsBase front end, VenomView currently operates as standalone prototype. Provides interactive dashboards showing assembly quality, annotation scores, toxin gene families, and functional domains generated by the VenomFlow analysis pipeline. Connected to VenomLanding, VenomView currently features Doryteuthis pealeii (Squid), linking metadata with detailed annotation summaries. The expanded version will include Sepia bandensis (Cuttlefish), Octopus bimaculoides, and arachnid species.
Software tool as comprehensive framework for integration of single-cell omics data with probabilistic contrastive learning.
Convenience wrapper function around the following three functions that are often run together when mapping query data to a reference: TransferData, IntegrateEmbeddings, ProjectUMAP.
University of Washington Translational BioImaging Core Facility
The Translational BioImaging Core (TBIC)
Core has resources available at Fred Hutch and UW in collaboration with multi-disciplinary imaging research groups specializing in respective imaging technologies. Provides services including: support for animal imaging; consultation for appropriate use of imaging; training and education; help with protocol development; infrastructural support; and strategic acquisition of new imaging equipment. Provides animal imaging equipment, including MRI, PET, US and optical to support scientific projects within the UW-FH Cancer Consortium.
Sysmex | UF-5000 automated urine particle analyzer
UF-5000 automated urine particle analyzer
New type of analyzer that is capable of analyzing the birefringence of particles and the amount of nucleic acid content and size information of the cell, coupled with the complexity of internal structure, using a blue semiconductor laser (488 nm).
Siemens | Healthineers Atellica UAS 800 Analyzer
Atellica UAS 800 Analyzer is automated urine sediment analyzer designed to minimize the need for manual microscopy.
Software R package to quantify relation between two measurement methods. Addresses regression problems with errors in both variables and without repeated measurements.
Software tool as deep learning framework for analyzing viral protein sequences at genomic scale using transformer-based models with sparse attention mechanisms. The tool processes complete viral genomes (up to 61,000 amino acids) to predict protein-protein interactions and identify functional relationships between viral proteins through attention-based contact analysis.
Traumatic brain injury (TBI) Common Data Elements (CDEs) created by the PRE Clinical Interagency reSearch resourcE-TBI (PRECISE-TBI) group to harmonize (or merge) language and variables across the preclinical TBI neuroscience landscape.
Olympus BX43 is a popular clinical and research grade microscope that can be configured for many different applications. Modular components enable you to customize the microscope for brightfield, polarization, phase contrast, and fluorescence. BX43 microscope utilizes a high color rendering white LED with a luminosity equivalent to a 30 W halogen lamp. The longlasting LED provides users a consistent color temperature at any brightness level.With an optional low magnification condenser, users can change the objective magnification from 2X to 100X (dry) without changing the condenser or moving the top lens.
University of Washington Northwest Metabolomics Research Center Core Facility
Northwest Metabolomics Research Center (NW-MRC)
Core provides targeted and untargeted measurements of small molecule metabolites utilizing LC-MS, high-field NMR and GC-MS analytical platforms. We also perform quantitative lipidomics and oxylipns metabolic flux analysis, statistical and pathway analysis, and biological interpretation.
State University of Campinas Gleb Wataghin Physics Institute LAMULT/IFGW Core Facility
Gleb Wataghin Institute of Physics (IFGW/UNICAMP) hosts a multi-user equipment facility, the LAMULT – an Open Facility-type Multi-user Laboratory that integrates various scientific instruments within single location.
Liverpool University Biobank Core Facility
University of Liverpool Liverpool University Biobank Core Facility
Core provides facilities including state of the art 2-D barcoded storage and LIMS, sample processing, histology, automated tissue microarray generation and spatial genomics profiling. Research Tissue Bank provides collection of both adult and paediatric biosamples, and is able to confer project-specific approval for their use.
Software Common Data Elements (CDEs) mapping tool to bridge the gap between local data elements and National Institutes of Health (NIH) CDEs. Elasticsearch and Large Language Model (LLM)-powered mapping tool designed for biomedical and clinical researchers to efficiently map study variables to the NIH Common Data Elements (CDEs). It integrates essential and advanced services into a user-centered mapping workflow, allowing users to choose different mapping strategies based on their project's needs.Used for enhancing National Institutes of Health common data element use with large language models.
Generative AI tool capable of creative and analytical tasks like writing, summarizing, coding, and visual analysis. Developed by AI company Anthropic. Claude is known for its ability to process large amounts of text quickly and for its focus on safety through its "constitutional AI" training method. Free basic version can be used for Chat on web, iOS, Android, and on your desktop; Generation code and data visualization; Writing, editing, and content creation; Text and images analysis; searching the web. You can Unlock more from Claude with desktop extensions.
Icahn School of Medicine at Mount Sinai Biorepository and Pathology Core Facility
Icahn School of Medicine at Mount Sinai Biorepository & Pathology Core
Core supports tissue and body fluid procurement, storage, and tracking from consented and de-identified collections. Pathologists responsible for procurement can be contacted for consultation to determine investigator requirements for human specimens in translational and basic research and then arrange procurement as feasible. Basic histology services include process, embed, and section fixed and frozen tissues (both animal and human), histochemistry, immunohistochemistry, immunofluorescence, in situ hybridization, laser capture microdissection, special stains for routine light microscopic evaluation. Offers full digital scanning capability with our quantitative and qualitative digital image analysis service (HALO), and support DNA/RNA/miRNA extraction from fluids and tissue specimens (both fixed and frozen) for downstream next generation sequencing and other applications.
Tulane University School of Medicine Flow Cytometry and Cell Sorting Core Facility
Tulane University School of Medicine Department of Microbiology/Immunology Flow Cytometry and Cell Sorting Facility
Tulane University School of Medicine Department of Microbiology/Immunology Flow cytometry and cell sorting shared resource facility. Provides education, training and services, Applications include analysis and sorting of immune subsets and fluorescent-reporter expressing cells, DNA content, multi-plex bead assays and functional assays. Expert assistance with experimental design and data analysis, as well as instrument training, are available at no charge.
Delaware, USA based leading chromatography product manufacturer and service provider specializing in biological separation areas. We offer unique ranges of HPLC columns for bioanalytical characterization and testing, as well as process media for downstream process and purification of MAb, BsMAb, ADC, Proteins, AAV, VLP, DNA, RNA, and various biologic samples.,
Fully automated urine microscopy system intended for the in vitro quantitative determination of erythrocytes and leukocytes, semi-quantitative determination of squamous and non-squamous epithelial cells, bacteria, and hyaline casts and qualitative determination of pathological casts, crystals, yeasts, mucus, and sperm in urine.
Software with approach that leverages machine learning and network biology to predict brain gene expression from blood-derived features.
Web discovery, analytics, and reporting tool powered by the links between works, people, and organizations in DataCite DOI metadata. DataCite Commons supports searches for works (with DOIs), people (with ORCID iDs), organizations (with ROR IDs), and repositories. By providing analytics dashboards, DataCite Commons empowers researchers and organizations to gain insights and make informed decisions based on comprehensive and interconnected metadata.
2-Plate ELISA processing system processes two 96-well microplates and up to 12 different assays simultaneously. Features user-friendly control system, chain of custody management and on-board instrument diagnostics.
Subsidiary of OraSure Technologies, Inc. focuses on providing biological sample collection products and services for human genomics, microbiome and infectious disease applications. Offers Research Use Only products to collect and preserve large amounts of DNA or RNA from multiple sample types.
University of Toronto Centre for Immune Analytics Core Facility
University of Toronto Centre for Immune Analytics
Core offers specialized services supported by research infrastructure, including flow cytometry, imaging mass cytometry (IMC), single-cell genomic sequencing, and dynamic live cell-culture imaging. Our facility is located in the Medical Sciences Building next to Queen’s Park, a central and convenient location for users across the Greater Toronto Area.
Software R package that supports the handling and processing of IMC multiplex imaging data. Used for handling and analysing imaging mass cytometry data.
Unified search engine for infectious and immune-mediated disease datasets. Enables users to find datasets from biomedical research repositories. It indexes metadata from multiple NIH-funded and generalist repositories. Provides filters, prebuilt queries, and dataset collections to simplify the discovery process for users. The Portal additionally provides documentation and an API for programmatic access to harmonized metadata.
Search engine for datasets hosted in web-based repositories and marked up according to schema.org. Helps users find datasets on the web. It aggregates information from publisher websites, digital libraries, and other sources, and uses metadata to allow users to filter results by criteria like last updated date, usage rights, download format, and topic. Users can find datasets across a wide variety of disciplines, including scientific, government, and commercial data.
Software R package as Tidy API for graph manipulation. Graph can be thought of as two tidy data frames describing node and edge data respectively. Used to manipulate these two virtual data frames using API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.
Web-based application for comprehensive and modular scRNA-seq data analysis. to easily retrieve datasets from repositories housing most publicly available single-cell data. Future expansions of scStudio will integrate additional databases, such as the Human Cell Atlas.
Georgia Institute of Technology Partnership for an Advanced Computing Environment Core Facility
Georgia Institute of Technology Partnership for an Advanced Computing Environment
Partnership for an Advanced Computing Environment (PACE)
Core provides high performance computing (HPC) resources with technical support services, infrastructure, software, and more. PACE maintains several computing clusters for Georgia Tech’s faculty, students, and staff.
Virginia Tech Crystallography Lab Core Facility
Core specializes in single-crystal structure determination of small molecules, inorganic materials, and minerals. The facility houses a Rigaku-Oxford Diffraction Synergy Single-Crystal X-ray Diffractometer equipped with both Cu and Mo sources, variable temperature capabilities (90 – 500 K) and the setup to perform high-pressure diamond-anvil studies.
Boise State University Biomedical Research Vivarium Core Facility
Core provides and supports gold standard of high quality mouse, rat and zebrafish care and services. All procedures are conducted according to the National Institutes of Health Guide for the Care and Use of Laboratory Animals. The BRV is accredited at the highest standard of care through the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International.
Virginia Tech Department of Chemistry Chromatography Core Facility
Facility enables complete qualitative and quantitative analysis of components within complex sample matrices. Provides services for separating mixtures, and supports critical research across numerous fields, including:Chemistry and Biochemistry, Biology and Medicine, Environmental Science and Toxicology, Food, Nutrition, and Pharmaceutical Development. Provides extraction, separation, detection, and quantification of organic and other complex mixtures from gas, solid, or liquid matrices.
Software tool for predicting long-term relapse of tumor spheroids from early post-treatment brightfield image data. We deploy a dataset consisting of time-series radiomics features for predicting the treatment response of tumor spheroids.
Lady Davis Institute Cell Imaging Core Facility
Core provides expertise in confocal, live cell, and fluorescent microscopy. Provides services in experimental design, instrumentation, training, technical assistance, and scientific guidance from sample preparation to data analysis and publication.
Jewish General Hospital Lady Davis Institute for Medical Research; Montreal; Canada
Medical hospital-based research institute in Montreal, Quebec, Canada.
Software R package for statistical analyses and comparison of two circadian rhythms. Used to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms.
Montana State University Biophotonics Core Facility
Montana State University - Biophotonics Facility
Core provides multiphoton characterization of Genetically-Encoded Probes for the BRAIN Initiative researchers and broader neuroscience community. Services include Measuring of 2-photon absorption spectra in absolute, cross section values; Measuring 3-photon absorption spectra and cross sections; Characterizing multiphoton photobleaching parameters, i.e. quantum yields, nonlinear absorption cross sections:Measuring one-photon absorption, emission, and excitation spectra;Measuring fluorescence quantum yields and lifetimes;Evolving brighter two-photon probes.
Harmonized Ontology of Mammalian Brain Anatomy (HOMBA)
Harmonized Ontology of Mammalian Brain Anatomy
Harmonized cross-species taxonomy of brain and spinal cord structures. Derived from the Allen Developing Human Brain Atlas (DHBA) ontology, the HOMBA is hierarchical, allowing users to aggregate structures from fine grain parcellations to broad regions. Terminology is harmonized across human, primate, and rodent structures with synonymous terms and includes transient developmental structures. HOMBA is designed for neuroanatomical applications including brain sampling and dissection, tissue block mapping, atlas building, cell-type and pathology localization, and linking cross-species and developmental datasets.
Software workflow is an open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN).
Software repository contains files needed to build the standard and its supplementary documentation. Changes are automatically pushed and built. Information about the SWC file specification.
Three-dimensional (3D) common coordinate framework (CCF) and reference atlas that defines the spatial organization of the basal ganglia of the adult human brain.
Automated sliding microtome with additional capability for cutting large and hard specimens. Offers Choice of manual or mechanized operation, Coaxial specimen orientation and memory function for rapid re-orientation of pre-cut blocks, User-friendly control panel for easy operation, Optional retraction to protect specimen.
Software tool for assigning single cells from scRNA-seq to spatial transcriptomics coordinates via optimization framework. Supports high-resolution cell/spot alignment, capacity-constrained/domain-aware placement, and outputs per-cell/per-spot assignments and probabilities for downstream visualization and analysis. Used for optimal mapping of scRNA-seq data to spatial transcriptomics data.
Software package for flexible spatial reconstruction of single-cell gene expression with optimal transport. Framework for de novo spatial reconstruction of single-cell gene expression. Assigns cells to tissue locations using probabilistic/optimal-transport models, with or without prior marker information, and returns spatial maps and assignment probabilities.
Software tool for reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly. Infers cellular spatial organization from scRNA-seq by modeling ligand–receptor-mediated self-assembly. It constructs 3D pseudo-space and quantifies cell–cell interactions for downstream visualization and hypothesis testing.
State University of Campinas Gleb Wataghin Physics Institute OFMEC/IFGW Core Facility
IFGW hosts a mechanical workshop that produces precision components for advanced research projects.
State University of Campinas Gleb Wataghin Physics Institute Criogenia/IFGW Core Facility
Core produces and supplies liquid helium and nitrogen to the entire IFGW academic community. Laboratory is equipped with helium liquefier from Linde and nitrogen liquefier from Stirling Cryogenics. In addition, it maintains complex support infrastructure essential for production and distribution of cryogenic liquids.
State University of Campinas Gleb Wataghin Physics Institute Vidraria/IFGW Core Facility
IFGW glass workshop, equipped with specialized staff, provides expertise in glass forming, welding, and cutting of Quartz and Borosilicate, as well as in design and technical drawing.
Three-dimensional brain reference atlas for macaque basal ganglia created based on annotation of BG structures on Mac25Rhesus template, an averaged MRI template from 25 M. Includes selected published subcortical parcellations to aid in comparing across parcellation schemes. Enables mapping of samples and integration of multimodal data within and across species.
HOMBA Adult Marmoset Basal Ganglia Atlas
Three-dimensional brain reference atlas based on the RIKEN25v1 MRI-derived template, based on an average of 25 C. jacchus brains resampled to 70 um3 voxel resolution. Includes selected published subcortical parcellations to aid in comparing across parcellation schemes.
University of Texas MD Anderson Cancer Center Small Animal Imaging Facility
Core provides access to imaging instrumentation and expertise that is necessary to integrate advanced imaging technologies into basic and translational biomedical research. Services include Assistance in experimental design; Developing specialty equipment and innovative procedures for imaging; Preparing animals for studies, inducing and maintaining appropriate anesthesia and immobilization of animals during imaging;Processing and interpreting data for publication or grant preparation.
Lady Davis Institute Flow Cytometry Core Facility
Core provides complete flow cytometry analysis and cell sorting services in terms of experimental design, instrumentation, training, technical assistance and scientific guidance from sample preparation to publication.
Software tool for comprehensive T‐Cell subsets abundance prediction and its application in cancer immunotherapy.
Web application for data visualization and data mining system that offers efficient analysis and discovery by integrating big data with intelligent and intuitive functionality.
Software R package for most bulk sequencing datasets. Creates shiny app for interactive data analysis and visualisation. Used for analysing and sharing bulk sequencing results.
Integrative database for human proteome structural and functional sites. Used for understanding role of specific residues in protein structures, complexes, and interaction networks. Integrates various structural and functional annotation layers for each residue, offering comprehensive understanding of protein functionality.
Icahn School of Medicine at Mount Sinai Mount Sinai Cryo-EM CoRE Core Facility
Cryo-Electron Microscopy Core facility at ISM offers EM services with state-of art instruments (Vitrobot for sample preparation, Glacios-2 TEM for imaging biological samples at atomic resolution). We offer single particle analysis (SPA) workflow, imaging drug delivery products (ex: liposomes, LNPs, AAVs..)
Software integrative pipeline for antimicrobial resistance genes, virulence factors, toxins, and biosynthetic gene clusters prediction in metagenomes. Used for predicting microbiome-based pathogenicity and resistance to better understand and address challenges posed by antimicrobial resistance and infectious diseases.
Beth Israel Deaconess Medical Center X-ray Crystallography Core Facility
Core offers comprehensive protein expression, purification, characterization, and structural biology services, including advanced methods such as Cryo-Electron Microscopy (Cryo-EM) and X-ray Crystallography.
Cancer Research UK Scotland Institute Mass Spectrometry Core Facility
Cancer Research UK Scotland Institute Mass Spectrometry Facility
CRUK Scotland Institute Metabolomics Facility
CRUK Scotland Institute Proteomics Facility
Core offers proteomics and metabolomics services. Provides support from experimental design to execution, sample processing, data interpretation, and assistance with presentations, manuscript preparation for publication and deposition of data in public repository and data storage on local server. Provides service analysis of post-translational modifications, such as phosphorylation, ubiquitination, acetylation, and others, with precise site localization on either single protein or for entire proteome.Uses Orbitrap Fusion Lumos coupled to Easy-nLC 1200 HPLC system. Facility instruments are operated with various acquisition methods, including classic Data Dependent Analysis (DDA) or more recent Data Independent Analysis (DIA). Acquired data from different methods are used to accurately identify and measure abundance of proteins and peptides employing different quantitation strategies: Label-free, TMT, pulsed-SILAC and Isotope-labelled Iodoacetamide (for Cysteine oxidation).Provides specialized data analysis software like MaxQuant and Mascot for DDA, Spectronaut for DIA of clinical samples and Perseus and Scaffold for data compilation, analysis, and dissemination.
Software algorithm for restitching overlapping image crops with intensity adjustment. Crops are intensity corrected and weight adjusted to produce uniform intensity composite image.
Benchtop plate reader with ResoVu software enables rapid, label-free detection in disposable 96-well plate format. Benchtop system with semi-automated fluidics with Disposable 96-well microarray plate format; User friendly, and easy to operate; Real-time data analysis features.
Software Python package for automated detection, morphology classification, tracking, and colocalization analysis of organelles in multichannel fluorescence microscopy data.
Advanced Cyberinfrastructure Coordination Ecosystem Services and Support Core Facility
Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support; Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support - ACCESS;
Provides advanced computing systems and services including supercomputer applications, AI and machine learning, big data analysis and storage. Offers suite of cyberinfrastructure coordination services targeted at supporting all areas of science and engineering research and education.
Software tool as frequency-aware prompt-guided network for nuclear segmentation and classification in immunohistochemistry images.
Free 3D/4D Microscopy Image Viewer. Used to visualize microscopy images (stacks) in 3D.
mirt:Multidimensional Item Response Theory
Software package for the R Environment. Used for estimating multidimensional item response theory parameters for exploratory and confirmatory models by using maximum-likelihood meth- ods.
Software R package for latent variable analysis. Used to estimate variety of multivariate statistical models. Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.
Software R package for analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach.
cmprskcoxmsm: Use IPW to Estimate Treatment Effect under Competing Risks
Software R package uses inverse probability weighting methods to estimate treatment effect under marginal structure model for the cause-specific hazard of competing risk events. Estimates also the cumulative incidence function (i.e. risk) of the potential outcomes, and provides inference on risk difference and risk ratio.
Software R package for Bounded Memory Linear and Generalized Linear Models. Regression for data too large to fit in memory.
Software tool for plotting Receiver Operating Characteristic (ROC) curves.
RCy3: Network biology using Cytoscape from within R
Software R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort.Network biology using Cytoscape from within R.
Software R package enables arbitrary ontologies to be read into R, supports representation of ontological objects by native R types, and provides a parsimonius set of performant functions for querying ontologies.
Software R package provides collection of reference expression datasets with curated cell type labels, for use in procedures like curated cell type labels or deconvolution of bulk RNA-seq.
Commercial vendor and service provider of laboratory reagents and antibodies located in Beijing, China. Supplier of scientific instrumentation, reagents and consumables, and software services.
Augusta University Human MRI Imaging Core Facility
Core dedicated to providing cutting-edge magnetic resonance imaging services for human participants. Provides Human 3 Tesla MRI system from Siemens for human research with proper IRB approval and approved MRI protocols.
Augusta University Proteomics and Mass Spectrometry Core Facility
Facility for characterization and expression level quantitation of proteins (isolated or in an extract) and small molecules/metabolites by mass spectrometry (MS) and/or chromatography. Services include protein identification, labeled and label-free comparative proteomics by Orbitrap mass spectometry, protein/small molecule quantification using targeted mass spectometry (PRM and SRM/MRM mass spectometry), high throughput protein immune-protein assays (384-well Luminex/ELISA assay), etc.
University of Montreal Institute for Research in Immunology and Cancer Genomics Platform Core Facility
Institute for Research in Immunology and Cancer of the Université de Montréal - Genomics Platform
Facility offers services, combining expert guidance and technologies including Sanger Sequencing, Next-Generation Sequencing, Single-Cell Sequencing, qPCR, Quantity and Quality of DNA and RNA measurement.
Van Andel Institute MiND iPSC and Screening Platform Core Facility
Core provides iPSC cell culture laboratory with access to curated and validated iPSC lines for neurodegeneration research. Provides robotic and fully automated high-content imaging system to perform high-throughput screening on living brain cells (iPSC derived through reprogramming) to understand the mechanisms behind neurodegeneration at the molecular level.
Institute of Ecology INECOL Advanced Microscopy Unit Core Facility
Advanced Microscopy Unit (UMA) at INECOL
Unidad de Microscopía Avanzada - INECOL (UMA-INECOL)
Core supports research in various scientific disciplines through advanced microscopy techniques (fluorescence, electron, and optical) and micro-CT. Provides technical services, consultation and training in advanced microscopy.
INECOL focuses on research on natural resources, conservation, and biodiversity, aiming to solve ecological problems and generate scientific knowledge.
Software tool to control Illumina HiSeq 2500 System. Open source Python code base and flow cell design that converts Illumina HiSeq 2500 instrument, comprising epifluorescence microscope with integrated fluidics, into open platform for programmable applications without need for specialized engineering or software development expertise.Enables non-specialists to develop and implement fluidics coupled imaging methods in benchtop system.
University of Missouri Kansas City UMKC Proteomics Core Facility
Federally funded facility committed to advancing scientific research by delivering high-quality proteomic data. Provides proteomics analysis, technology, services, and rigorous quality standards.
Augusta University High Performance Computing Core Facility
Augusta University High Performance Computing and Parallel Computing Services Core Facility
Core provides high memory parallel processing environments and software in support of the university research, academic, and cybersecurity missions. HPC clusters use multiple computers to process data in parallel, greatly reducing the time to solution for most computational science tasks. They also provide storage to manage very large data sets.
Software tool to read level DNA methylation analysis of bisulfite converted sequencing data.
Hub for clinical, genetic and functional datasets of preclinical cancer models.Provides details of cell model relationships, patient and clinical information, as well as access to associated genetic and functional datasets. Passports database contains curated details and standardized annotation for cell models, including cancer organoid cultures. Users can navigate database via tissue, cancer-type, genetic feature and data availability to select model. REST-API provides programmatic data access and exploration.
Web application for ligand binding site prediction. Used for prediction of ligand binding sites from protein structure.
Web application for protein-ligand binding site prediction. Starting from given structure of target proteins, COACH will generate complementray ligand binding site predictions using two comparative methods, TM-SITE and S-SITE, which recognize ligand-binding templates from the BioLiP protein function database by binding-specific substructure and sequence profile comparisons.
Semi-manually curated database for biologically relevant ligand-protein binding interactions. Structure data are collected primarily from Protein Data Bank (PDB), with biological insights mined from literature and other specific databases. Database used for serving needs of ligand-protein docking, virtual ligand screening and protein function annotation.BioLiP2 offers significantly greater coverage of nucleic acid-protein interactions, and interactions involving large complexes, integrates structural alignment algorithms with structure prediction techniques, which enables composite protein structure and sequence-based searching.
Web server for interactive and collaborative online docking to assist small compound molecular docking. In silico assessment of protein receptor interactions with small ligands.
Brigham and Women’s Hospital NeuroTechnology Studio Core Facility
Offers advanced instrumentation and expert support to advance understanding of brain function and brain disease by providing researchers with access to cutting-edge technologies. Provides access to advanced instrumentation for optical microscopy, genomics, metabolic imaging and other technologies, as well as image analysis software. Provides expert support and training, data quality and interpretation.
University of Wisconsin Madison Radiopharmaceutical Analytics and Specimen Research Lab Core Facility
Radiopharmaceutical Analytics and Specimen Research (RASR) Lab
Radiopharmaceutical Analytics and Specimen Research Lab
University of Wisconsin Madison Radiopharmaceutical Analytics and Specimen Research Lab
Core for radioactive sample analysis and storage. Provides next generation in-vivo metabolism and biological assessment of new radiopharmaceuticals in clinical and preclinical studies. Houses analytical instruments dedicated for use with radioactive biospecimens.
University of Coimbra ViralVector Core Facility
University of Coimbra ViralVector for Gene Transfer
Portuguese national research infrastructure which provides expert consultation for the safe and effective use of vector technologies, and offers custom design and production services for multiple viral types to the national research community and other stakeholders.
sandwich:Robust Covariance Matrix Estimators
Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods.
Software cancer genome and RNA sequencing data analysis pipeline that detects genomic variants and transcriptomic changes.
lightgbm:Light Gradient Boosting Machine
dcurves: Decision Curve Analysis for Model Evaluation
probably: Tools for Post-Processing Predicted Values
Software R package for conducting recalibration, conversion to hard probabilities, assessment of equivocal zones operations as well as calibration tools and conformal inference techniques for regression models.
Software application for C-CAT CALICO database. Used for Germline-focUsed analysis of tUmoUr-detected variants with Nomogram for C-CAT CALICO database.
Software R package for annotating cell clusters in scRNAseq data.
Custom software to control MERFISH imaging components. System consists of microscope body coupled with Nikon CFI Plan Apo 60X Lambda D oil immersion objective. Microscope control software.
Automated microscope that can convert between both Upright and Inverted configurations, ideal for imaging well plates and slides.Designed for developmental biology, cell biology, neuroscience, immunology, cancer research, and more, Revolution brings the capabilities of live-cell imaging, timelapse, tiling/mosaic imaging, and multi-well plate screening to the lab.
Company provides medical laboratory services, specializing in genetic and genomic testing.
Icahn School of Medicine at Mount Sinai Flow Cytometry CoRE Core Facility
Situated within the Icahn School of Medicine at Mount Sinai, our CoRE provides all members of the Mount Sinai Health System community with the instrumentation, expertise, and education required to incorporate flow cytometry and cell sorting into any research project.
Michigan State University Center for Advanced Microscopy Core Facility
Core provides instruction and access to scanning electron microscopes, transmission electron microscopes, laser capture microscopes, and confocal laser scanning microscopes. CAM staff members help with microscopes and microscopy analysis.
Software tool to detect problematic cell lines during text processing.Based on: SciSpacy NER model "en_ner_jnlpba_md" -- DNA, Cell Type, RNA, Protein, Cell Line Cellosaurus (Dump, FEV. 2021) and ICLAC (V10).
Bio-Rad | PTC Tempo Deepwell Thermal Cycler
Conventional PCR instrument built with fixed 96-deepwell reaction block that accommodates reaction volumes of 10 ul to up to 125 µl.
Web application to provide comparison of the risk predictions. Used to calculate the risk of lymph node metastasis in patients with T1 colorectal cancer.
University of Texas Southwestern Medical Center Dallas Histo Pathology Core Facility
University of Texas Southwestern Medical Center Dallas Histo Pathology Core
Core offers research histology and anatomic pathology services and customized pathology services. Facilitates morphologic and histologic assessment of murine transgenic and knockout phenotypes as well as experimental procedure-based models of disease for basic and clinical research. We utilize expertise in gross pathology, routine histology, immunohistochemistry, tissue microarray, spatial transcriptomics, spatial proteomics, laser-capture microdissection, materials science, photomicrography, and image analysis.
Software pipeline for multidimensional confocal analysis of mitochondrial morphology, function, and dynamics.
Core provides protein sequencing services including Next-Generation DNA Sequencing, Peptide Synthesis, Protein Sequencing, and Mass Spectrometry. Provides expert technical and analytical support.
Tufts University Laser Cytometry Core Facility
Tufts University Laser Cytometry Core Facility (TLC)
Core offers Flow and Laser Cytometry equipment and services including FACS Analysis and Cell Sorting, to the scientific community.
NIH Brain Development Cohorts (NBDC) Data Hub
Data platform providing centralized and secure access to rich, longitudinal brain, behavioral, and genomic data from both the Adolescent Brain Cognitive Development (ABCD) and the HEALthy Brain and Child Development (HBCD) Studies. By bringing together data from both studies, the NBDC Data Hub facilitates integrative research on early life and adolescent development, helping researchers explore developmental trajectories across the lifespan.
Texas A and M University Protein Chemistry Laboratory Core Facility
Texas A&M University Protein Chemistry Laboratory
Core provides instrumentation, systems, software, technical expertise and training for the application of novel protein and molecular biology technologies. Provides training and expertise. Offers protein and amino acid services.
A3D3a Molecular Vulnerability Picker (MVP)
Adaptive AI-Augmented Drug Discovery and Development Molecular Vulnerability Picker
Software tool as novel graph-based, cooperativity-led Markov chain model to exploit cooperativity of weak signals within cancer molecular network to enhance the signal of true molecular vulnerabilities. Used to identify molecular vulnerabilities from multimodal patient data.
BayGene Biotech | BG-gdsAUTO710 MINI Chemiluminescence Imaging Analysis System
Chemiluminescence Imaging Analysis System (BG-gdsAUTO710MINI)
Chemiluminescence imaging analysis system designed for Western-Blot membrane imaging. High-megapixel camera provides high resolution images and deep-cooled CCD with low background noise improves image quality even in case of long exposure time. For detection of the very weak bands, you can choose multiple binning options of software, from 1x1 to 4x4 binning modes, which collect more signals as you need.
Software R tool for detection of homologous recombination deficiency from shallow whole genome sequencing. Used to assess Homologous Recombination Deficiency of tumor based on the number of Large-scale Genomic Alterations (LGAs).
Software application for object detection with Star-convex Shapes. Used for phase-contrast cell images.
Software application for visual analysis and diagnostic to facilitate machine learning model selection. Visualizing the Scikit-Learn Model Selection Process. Used to evaluate stability and predictive value of machine learning models and improves the speed of the experimental workflow. Provides visual tools for monitoring model performance in real world applications. Provides visual interpretation of the behavior of model in high dimensional feature space.
Louisiana State University Health Sciences Center Shreveport Metabolomics and Machine Learning Core Facility
Metabolomics and Machine Learning Core provides metabolite profiling and stable-isotope tracing, molecular modeling, and machine learning to integrate datasets across transcriptomic, proteomic, and metabolomic analysis.
Web-based platform for interactive exploration of ribosome dynamics derived from 5′P mRNA degradome sequencing (5PSeq) data. Focused on changes in ribosome dynamics associated to mRNA decay that in some cases can be obscured in conventional ribosome profiling data.
Software for Quantifying Interspersed Repeat Expression
Software for Quantifying Interspersed Repeat Expression (SQuIRE)
Software RNA-seq analysis pipeline that provides quantitative and locus-specific picture of Transposable Elements expression.
Medical College of Wisconsin Echo Core Shared High-Frequency Ultrasound Imaging Core Facility
Echo Core-Shared High-Frequency Ultrasound Imaging Facility
Core provides VisualSonics Vevo 3100 high-frequency ultrasound imaging unit, small animal imaging station, micro-injection system, anesthesia unit; Linear array transducers (MX250, MX550D, MX700); VevoLab use.
Software R package for clustering and estimating cancer cell fractions (CCF) of somatic variants (SNVs/SVs) from bulk whole genome/exome data. Used for estimating cancer cell fractions .
Software application to group genetic structural variant rearrangements into rearrangement clusters and footprints. Used in the PCAWG-6 project.
Software R package containing methods for sub-clonal reconstruction through SNVs and/or CNAs from whole genome or whole exome sequencing data.
Software R package for analysis of mitochondrial DNA using sequencing data. Used for analyzing mtDNA single nucleotide variants and copy number variation. It has two components, mitoCaller and mitoCalc/fastMitoCalc.
Hotspot Missense mutation Areas in Protein Structures
Software tool to detect somatic mutation hotspot regions in 3D protein structures.
Software tool for detection and analysis of homologous recombination events.
Software tool for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients. Summarizes somatic mutations, genes and pathways involved in tumorigenesis.
Software tool for detecting microsatellite instability by next-generation sequencing.
Software tool designed to detect rare cancer driver genes from aggregated whole-exome sequencing data.
Software application to detect significant clustering signals across genomic regions. Sequence-based clustering method to identify cancer drivers.
Software tool that estimates accumulated functional impact bias of somatic mutations in any genomic region of interest based on local simulation of the mutational process affecting it.
Software application as PCAWG6 workflow to merge SVs from Sanger (BRASS), Broad Inst (DRanger and SnowMan ) and EMBL/DKFZ (DELLY).
Software tool to detect linear enrichment of somatic mutations in user-defined regions of interest.
Software tool to annotate high-impact five prime UTR variants either creating new upstream ORFs or disrupting existing upstream ORFs. Annotates variants in 5'untranslated regions (5'UTR) that create or disrupt upstream open reading frames.
Software tool to identify transposable element insertions from paired-end Illumina reads, barcode linked-reads, long reads (PacBio or Nanopore), or hybrid data from different sequencing platforms and takes whole-exome sequencing (WES) or whole-genome sequencing (WGS) data as input.
Software R package for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets.Method that first prioritises genes through multi-omics data fusion and then identifies enriched pathways with gene-level evidence from input datasets.
Software R package for discovery of cancer driver genes and non-coding elements in whole genome sequencing data. Cancer driver discovery tool for analysis of somatic mutations derived from whole genome sequencing.
Software R package containing the full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).
Software R package to time somatic mutations relative to clonal and subclonal copy number states and calculate relative timing of copy number gains.
Software R package for identifying peaks in data related to genomics, genetics, or epigenetics research.
Political Science Computational Laboratory
Software R package providing classes, methods and test data based on maximum likelihood and Bayesian inference.
T cell exome T cell Receptor Excision Circle
Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes.
Software R package to visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.
Software Python package used to compute mutational signatures.
Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots.
Software tool as Python script to remove bias from Isaac aligned data by clipping all reads for variant positions by 5 bases and producing a modified vcf file.
Software R package for estimating average telomere length (TL) for paired end, whole genome sequencing (WGS) sample.Telomere computational analysis tool.
Text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer.
High-definition likelihood inference of genetic colocalization (HDL-C)
High-Definition Likelihood Colocalization
Software tool for optimizing likelihood conditioning on high point estimate of local genetic correlation and assesses statistical evidence that the two traits not only exhibit correlated genetic effects but are likely influenced by shared causal variants.Enhances specificity and interpretability in detecting colocalized signals. This targeted framework improves causal inference in pleiotropic architectures, supporting more informed discovery of biomarkers and therapeutic targets.
Software R package for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, generalized k-nearest neighbour.
Software 3D Slicer plugin for Liver Anatomy Annotation by R-Vessel-X.
Software package provides different SHapley Additive exPlanations (SHAP) algorithms for calculating SHAP values, including Kernel SHAP. Used for explaining predictions made by complex machine learning models.
Bruker | ELEXSYS-E580 pulse X-/Q-band system
Bruker ELEXSYS-E580 pulse X-/Q-band instrument offers state-of-the-art capabilities for both standard and cutting-edge EPR spectroscopy across a broad range of sample types and experimental needs. High-performance Electron Paramagnetic Resonance (EPR) spectrometer used for advanced research in chemistry, materials science, biochemistry, and physics, enabling studies of paramagnetic molecules, protein structures, quantum states, and materials by combining X-band (9-10 GHz) and Q-band (34 GHz) frequencies for high-resolution, sensitive pulse techniques.
Augusta University Statistical Consulting Center Core Facility
Core offers services including statistical analyses, grant applications, prep for manuscript publications, etc.
Beth Israel Deaconess Medical Center BIDMC Zebrafish Research Core Facility
Core Facility is a 3,000+ fish tank facility, located in the Slosberg-Landay building, equipped with 48 racks which hold standard sized adult zebrafish tanks, three-rack nursery space for larval fish, and quarantine space containing two stand-alone housing systems. Wild-type lines are maintained inhouse for shared use. Wet lab space is available for breeding and line maintenance; core staff and facility-associated technicians perform daily feeding. The core includes a dedicated procedure room for embryo manipulation.
Bio-Techne | Simple Plex Ella Automated Immunoassay System
Benchtop automated Ella platform utilizes microfluidic Simple Plex assay cartridge designed to perform all reagent additions, wash steps, and incubations under precisely controlled conditions to run ELISA assays. Available for plexing up to 8 analytes.
Source code for training and inference of InstaNovo and InstaNovo+. InstaNovo is a transformer neural network with the ability to translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s).
Octopus bimaculoides Histotomography Blueprint
Resource serves as a 'Digital Specimen' for Digital Organismal Biology, providing interactive Neuroglancer-based visualization and 3D segmentation masks for major organ systems, including the digestive, respiratory, vascular, and nervous systems. It specifically annotates novel neural tracts including the Intermediate Longitudinal Tracts (iLT) and Arm-to-Arm U-Tracts (AAUT) as well as ~300 additional tissue and organ level segmentations. Provides high-resolution (0.7 µm isotropic), whole-organism microCT reconstruction of an intact hatchling Octopus bimaculoides.
University of Maryland School of Medicine Baltimore Electron Microscopy Core Imaging Facility
Electron Microscopy Core Imaging Facility (EMCIF)
UMB Electron Microscopy Core Imaging Facility
Core is part of the Center for Innovative Biomedical Resources (CIBR) and is located on the 6th floor of Howard Hall. All services, instrumentation, and training courses are available to anyone, academic or private users, with an interest in electron microscopy.EMCIF services are managed by iLab core facility management program. New users must register in iLab to access instrument and EMCIF services.
Beth Israel Deaconess Medical Center BILH/BIDMC REDCap Core Facility
REDCap (Research Electronic Data Capture) is a secure HIPAA compliant web-based data collection application hosted by Research and Academic Computing (ARC), a department of Beth Israel Deaconess Medical Center (BIDMC) which is itself part of Beth Israel Lahey Health (BILH). The function of the REDCap Core is to provide REDCap-related services and support to all BILH users.
Absorbance microplate reader offers all the functionality needed for photometric applications, including advanced 12-channel optics for fast, multichannel absorbance reading of ELISAs, temperature control function for enzyme kinetic assays, and tunable wavelength function for wavelength scanning.
Laval University IBIS Imaging and Microscopy Platform Core Facility
Laval University IBIS Imaging and Microscopy Platform
IBIS Microscopy platform offers sample preparation and acces to TEM, SEM, STED, confocals and other microscopes.
SYnthetic Lethal Vulnerabilities Exhibiting Reciprocation
Web application for identification of candidate synthetic lethal vulnerabilities in cancers.
Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer.
BIDMC Clinical Research Center Clinical Services Core Facility
Beth Israel Deaconess Medical Center Clinical Research Center Clinical Services Core Facility
Offers investigators clinical space, equipment, skilled nursing and nutrition services, project management and study coordinator support, resources for conducting community engagement research, as well as one-on-one consultation with Clinical/Translational Research Navigators.
BIDMC Division of Digital Psychiatry LAMP platform Core Facility
Beth Israel Deaconess Medical Center mindLAMP
Core collects data to capture and consider the real-time lived experiences of patients. Uses open-source digital platform and mobile app for neuropsychiatric research and clinical care, to monitor, support, and improve brain health by collecting real-time data (like location, activity, heart rate via sensors), conducting digital assessments (surveys, cognitive tests), and delivering interventions (meditation, journaling, psychoeducation) to patients and clinicians. It helps study behavioral patterns, track symptoms, and personalize mental health treatment through features organized around Learn, Assess, Manage, and Prevent.
Software R package to annotate cell types in scRNA-seq of tumour microenvironments.
Platform provides accurate, machine-executable computational models of how the brain gives rise to the mind. Enables researchers to quickly get a sense of the alignment of their model(s) to neural and behavioral measurements, and provides these models to experimentalists to prototype new experiments and make sense of biological data. All code is open-source and community members may choose to make their data or model weights fully public.
Data repository for Brain Imaging Data: MRI, PET, MEG, EEG, etc .. similar to OpenNeuro where each dataset is shared independently. Platform is GDPR compliant, allowing to share brain imaging data as FAIRly as possibly. The catalogue allows all metadata to be open and thus findable. As EU data have to be protected, we provide the necessary privacy protection by controlling user access.
Platform for sustainable research data management in cognitive neuroscience. Secure data storage and integrated tools to support maintenance, reuse, and FAIR-aligned management of neurocognitive research data. Data remains curated, documented, and accessible for the long term, supporting reproducibility and future discovery.
University of Oslo Services for sensitive data (TSD)
Platform to collect, store and analyze sensitive research data in secure environment. It comprises secure project area and integrated solution for collecting sensitive data (Nettskjema), accessible by anywhere in the world.
Software R package for analysis of condition-specific sex differences in omics data. Includes functions for differential expression, interaction testing, and gene regulatory network analysis. Used for analysis of sex differences in omics data for complex diseases.
University of Pittsburgh Mouse Embryo Services Core Facility
University of PMouse Embryo Services Core
Core provides services including generation of gene editing mice, transgenic mice, ES cell microinjection into blastocysts to create germline competent chimera, cryopreservation and long-term storage of mouse sperm/embryos, recovery of mouse lines from cryopreserved germplasm, in vitro fertilization for mouse line rescue and re-derivation of pathogen free mouse strains.
University of California at Irvine FIBRE Core Facility
UCI Facility for Imaging and Brain Research
Facility for Imaging and Brain Research houses 3T Siemens Prisma scanner, mock scanner, and data analysis facilities. Research dedicated MRI scanning facility designed to suit wide range of basic and translational research programs by researchers across the UCI campus and beyond.
Software R package contains functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.
American company in the life sciences and diagnostics business that is focused on selling to the pharmaceutical and biotechnology industries, especially in relation to approaches making use of new cell therapy or gene therapy developments.
Revvity | Opera Phenix Plus High-Content Screening System
Imaging system is confocal imaging platform designed for high-throughput biological assays. Supports phenotypic screening and imaging of complex biological models, including live cells, primary cells, and microtissues.
Software set of programs and utilities for working on SAM/BAM files.
Waters | SYNAPT G2-Si Mass Spectrometry System
High-resolution mass spectrometer with ion mobility, designed for deep, accurate analysis of complex samples across life science and analytical chemistry research. System adds Ion Mobility Separation to the original SYNAPT G2's high-resolution QuanTof technology, offering a third dimension of separation (size/shape) for superior selectivity, sensitivity, and structural insight in complex samples, beyond just mass and chromatography. The G2-Si integrates StepWave optics and enhanced data workflows for better performance in proteomics, metabolomics, and biomarker discovery.
Web based platform for exploring full brain connectomic datasets. Used for exploring and analyzing large connectomics datasets.
Augusta University GCC Biostatistics Core Facility
Augusta University GCC Biostatistics Core
Core provides biostatistical review of grant applications, offering clear, practical feedback on feasibility and statistical rigor to investigators and review panels. We support investigators across the research lifecycle, from grant proposal development and clinical protocol design to laboratory, animal, and epidemiologic study planning. Services also include short-term consultations, study monitoring, data analysis, manuscript preparation, and responses to peer review.
World-renowned institution dedicated to ending cancer through expert, compassionate patient care, pioneering research, and education for adults and children with all types of cancer, combining cutting-edge science with a holistic approach to treatment and support. Its mission focuses on innovative diagnosis and treatment (surgery, chemo, radiation, immunotherapy), supportive care (nursing, counseling, rehab), and training future cancer leaders.
Perkin Elmer | Victor X3 2030-0030 Multimode Microplate Reader
Multimode microplate reader for luminescence, fluorescence (top/bottom), and absorbance, featuring dual filter wheels, expanded temp control, and integrated software for real-time kinetics.
Software neuroscience library for Python, intended to complement the existing nibabel library. Can automatic download data and interpret them into Python data structures.
Software R package uses published biomarker algorithms to calculate three biological aging measures: Klemera-Doubal Method (KDM) biological age, phenotypic age, and homeostatic dysregulation. Used to quantify biological aging based on analysis of chronological age and mortality risk.
Software standalone package for protein-protein and protein-DNA/RNA docking based on hybrid algorithm of template-based modeling and ab initio free docking.
Web allosteric site prediction tool. Web server designed for prediction and visualization of protein allosteric sites, which are crucial locations on proteins for regulating their function and key targets for drug development. Helps researchers identify these regulatory sites on proteins, supporting efforts in allosteric drug discovery by analyzing protein structures from Protein Data Bank.
Web server for predicting interacting sites on protein surfaces. Analyzes solvent-accessible residues likely to participate in PPIs.Predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of protein complex.
Software C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. Used for Solvent-Accessible Surface Area analysis.
Web application for human-readable, searchable neuroimaging datasets using universally accessible JSON format and URL-based RESTful APIs. NeuroJSON.io is built upon highly scalable document-store NoSQL database technologies, specifically, open-source Apache CouchDB engine, that can handle millions of datasets without major performance penalties. Provides fine-grained data search capabilities to allow users to find, preview and re-combine complex data records from public datasets before download.
Memorial Sloan Kettering Cancer Center Bioinformatics Core Facility
Core provides bioinformatics support services including creating and maintaining repository of bioinformatics pipelines, providing customized data analysis support, assisting computational researchers in their research efforts, and training staff in computational and bioinformatics techniques. Provides bioinformatics software applications and pipelines for experimental assays ranging from standard genomics pipelines like RNAseq and variant detection to the growing demand for single-cell processing workflows and new spatial-based assays in transcriptomics and proteomics. Provides training and consulatation.
Memorial Sloan Kettering Cancer Center Antitumor Assessment Core Facility
Core provides support for early discovery and in vivo testing of antitumor detection and therapeutic agents. Provides resources, professional and technical expertise, and advisory services related to evaluation of agents with potential diagnostic or therapeutic activity. ATA Core works closely with investigators to establish preclinical models, including Patient-Derived Xenograft (PDX) and Patient-Derived Organoid (PDO) models, for the design and execution of pharmacokinetic (PK), toxicity, and in vivo efficacy studies. Assists investigators in determining the best formulation, administration route, and treatment schedule for each new compound, either alone or in combination with other agents.
Memorial Sloan Kettering Cancer Center Biobank and Pathology Core Facility
Biobank and Pathology Core provides resources for human biospecimen-based research to be used to study causes, detection, prevention, and treatment of cancer.Central facility for the collection, processing, storage, and distribution of fresh, frozen, and FFPE-processed human biospecimens (tissues, blood, bone marrow, urine, and other liquid samples) for research use. Core also serves as national resource, as evidenced by the several hundred samples from multiple tumor types that have been provided to the Cancer Genome Atlas (TCGA) and NCI’s CPTAC proteogenomic consortium. Histology Service within the Core facilitates selection of appropriate specimens for tissue analyses and provides the basic services of cutting, dissecting, and staining of fresh-frozen and formalin-fixed, paraffin-embedded tissues. It includes construction of tissue microarray blocks and laser capture microdissection for isolation of pure cell populations and tumor cell enrichment. The Core’s Immunohistochemistry Service provides immunostaining using optimized antibodies for clinico-pathologic research studies.
Memorial Sloan Kettering Cancer Center Biotherapeutics Core Facility
Core provides collaborative process development support to investigators across the Center engaged in new Biotherapeutics initiatives. Core staff are responsible for converting research-lab processes into GMP-compliant manufacturing processes. This includes establishing Standard Operating Procedures (SOPs) and batch records for cell processing, cell engineering, and vector production. Provides full support for cGMP manufacturing of cell products: handling patient cells in cGMP environment, from purification and transduction to expansion and formulation, for use in phase 1 and phase 2 clinical trials. Manufactures vector stocks, oversees biosafety and releases testing of generated projects for human use. This includes analysis of patient cells and vector stocks, assessing characteristics such as phenotype, potency, purity, and stability. Gene transfer and expression analyses are also performed. Core performs analytical post-infusion monitoring. For each trial, the Core develops a comprehensive set of analytical tests to ensure quality and safety of the manufactured drug products.
Memorial Sloan Kettering Cancer Center- Center of Comparative Medicine and Pathology Core Facility
Memorial Sloan Kettering Cancer Center- Center of Comparative Medicine and Pathology
Core supports animal model use in cancer research through teams including Research Animal Resource Center (RARC) and Laboratory of Comparative Pathology (LCP). Animals are employed in the development of new methods for diagnosis and treatment of cancer as well as the elucidation of the basic biological mechanisms resulting in neoplasia. CCMP’s professional and paraprofessional staff (152 FTE) serve as a consultative and technical resource for MSK investigators on all matters related to animal research.
Memorial Sloan Kettering Cancer Center Genome Editing and Screening Core Facility
Core Facility provides functional genomics, highthroughput screening (HTS), and high-content screening (HCS) services toward the discovery of novel cancer targets and elucidation of complex, aberrant cellular pathways. Offers assistance and training in range of cloning, customized library design, lentivirus production, assay development, screening, and image analysis considerations to assist researchers in harnessing these powerful target identification tools and drug screening methodologies. Offers CRISPR-mediated transcriptional activation/interference (CRISPRa/CRISPRi) technologies combined with lentivirus delivery systems, customized stable isogenic cell line generation (knockout, HDR-directed knock-in, knockdown, base editing, and prime editing) toward the generation of unique cancer cell line models.
Memorial Sloan Kettering Cancer Center Immune Monitoring Core Facility
Core provides laboratory services and translational research to support immune monitoring during cancer immunotherapy. Robust immune monitoring assays are essential for characterizing the immune status in patients receiving novel immune-modulating therapies, and the insights gained from studying the immune response in treated patients may help transition promising therapies from the clinical trial phase to standard of care.
Memorial Sloan Kettering Cancer Center Integrated Genomics Operation Core Facility
Core provides services and expertise to Center investigators interested in evaluating gene expression, chromosome structure, and nucleotide sequence on a broad scale. Enables basic, clinical, and translational research projects across the Center. Through its production group, the Core enables genomic and transcriptomic analyses and has the expertise to process challenging samples from all origins (tissue, dissociated single cells and cell pellets, paraffin curls, blood, serum, etc.). Bulk DNA/RNA assays operate in highly automated environment, from sample reception to sequencing library preparation.
Memorial Sloan Kettering Cancer Center Molecular Cytology Core Facility
Core delivers specialized histology, microscopy, and cytogenetics services for detection in situ (cells, tissue sections, organoids, and whole mounts) of biomarkers (proteins, glycoproteins, lipids, nucleic acids) and molecular processes in normal and pathological conditions. Performs comprehensive antibody validation on cells and tissues, trains investigators in basic staining principles and assists with experimental assay design and downstream analysis. Core maintains four whole-slide scanners and provides support for quantitative whole-slide analysis. Microscopy and dedicated image analysis staff provide support for simple or complex analysis pipelines.
Memorial Sloan Kettering Cancer Center Mouse Genetics Core Facility
Core facilitates the use of mouse molecular genetics at MSK for in vivo studies of gene functions germane to cancer. Provides expertise in generation and effective use of genetically engineered mouse (GEM) models—namely, molecular and cell biology, embryo micromanipulation, and reproductive biology. Molecular and cellular biology services cover design and assembly of genome engineering reagents, such as donor transgenes and CRISPR/Cas9; performing all aspects of gene targeting in mouse embryonic stem (ES) cells; identification and verification of alleles carried by a generated GEM model; and establishment of new ES cells from a variety of GEM lines. Provides consultation and training for the design and production of GEM models, ES cell culture and manipulation, and mouse reproduction and genetic crosses.
Memorial Sloan Kettering Cancer Center Nuclear Magnetic Resonance (Analytical) Core Facility
Core provides analytical services, access and education for analytical instrumentation and related shared scientific resources. Instrumentation includes high field nuclear magnetic resonance, mass spectrometry and optical spectroscopic instruments. Facility offers investigators the ability to monitor chemical reactions, analysis for determination of molecular structure, chemical mechanisms, purity, stability, biological uptake and other properties of chemical compounds.
Memorial Sloan Kettering Cancer Center Patient- Reported Outcomes, Community Engagement, and Language Core Core Facility
Core supports MSK investigators who wish to capture self-reported information from culturally diverse patients, caregivers, clinical staff, and community members. The faculty of the PRO-CEL Core are nationally recognized social and behavioral scientists and community engagement experts who provide technical assistance to all users throughout multiple stages of research, including grant and protocol development, research study assistant and support staff training, and result dissemination. Provides methodological support for clinical trial, behavioral, and population-based research that seeks to engage community or minority populations.
Memorial Sloan Kettering Cancer Center Radiochemistry and Molecular Imaging Probes Core Facility
Core functions include cancer biology, medicine, chemistry, physics, radiochemistry, pharmacology, and engineering.Provides investigators with radionuclides and to incorporate these radionuclides into radiolabeled diagnostic and/or therapeutic pharmaceuticals for both basic research investigations and patient formulations. Core provides services: Cyclotron Radionuclide Production Section, Radiolabeling Section, Development and Clinical Translation Section, and Hyperpolarized Magnetic Resonance Section.
Memorial Sloan Kettering Cancer Center Research Pharmacy Core Facility
Core is a full-service facility that prepares agents developed by MSK researchers to be used as investigational drugs in preclinical or clinical studies. The Core comprises three principal groups: the Pharmaceutical Product Facility (PPF) for drug formulation/stability and preparation; the Clinical Grade Production (CGP) Facility for bulk product manufacturing, purification, and vialing; and the Pharmacy Investigational Drug Service (PIDS), which develops, procures, prepares, and validates the preparation, packaging, and distribution of investigational drugs for clinical use. Core services include: formulation, analysis, and evaluation of drug release rates; prediction of interactions; and determinations of compatibility and physical stability of medications. Based on the expertise of the RP Core, MSK has been able to bring into early-phase clinical trials multiple types of pharmacologic agents, including traditional small molecules, radiopharmaceuticals, and vaccines.
Memorial Sloan Kettering Cancer Center Stem Cell Research Core Facility
Core stocks, characterizes, and distributes human pluripotent stem cell (hPSC) lines. Performs variety of hPSC-related applications for the stem cell community at SKI and beyond. We are a part of the Starr Foundation-funded Tri-Institutional Stem Cell Initiative that provides shared stem cell expertise and resources among Memorial Sloan Kettering, Weill-Cornell, and Rockefeller University.
Memorial Sloan Kettering Cancer Center Structural Biology Core Facility
Core provides expertise, advanced equipment, and leading software to support structural investigations. Core maintains equipment, including Krios cryogenic electron microscopes and computational resources for data collection, processing, and structure determination. These resources include graphical workstations and high-performance Linux cluster, supporting the analysis of large proteins, complexes, and macromolecular assemblies.Core has access to synchrotron beamlines and cryo-EM facilities.Provides training and assistance to users, collaborates with non-structural MSK groups on projects involving macromolecular crystallization and structure determination, offers modeling expertise and guidance, enabling labs to use available structural data in experiment design and interpretation.
Memorial Sloan Kettering Cancer Center Animal Imaging Core Facility
Core offers suite of animal imaging modalities, including MRI, PET, CT, SPECT, and ultrasound, all commonly used in clinical settings, enhancing the likelihood that findings in animal models will be translatable to human patients. Key instruments include 7.0T and 9.4T MRI systems, PET/MR, PET/CT, SPECT/CT, and advanced ultrasound systems, alongside specialized equipment including a small animal radiation therapy unit and variety of ancillary tools for advanced imaging analysis.
Memorial Sloan Kettering Cancer Center Proteomics and Metabolomics Core Facility
Core provides mass spectrometric sequencing and quantitation of peptides and proteins to support basic, translational, and clinical research programs at MSK. Utilizes modern high-resolution mass spectrometry and nanoscale liquid chromatography in conjuction with biochemical processing of samples with the end goal of determining the identity, relative abundance, and presence of post translational modifications from purified components, cell lysates, tissues, and select fluid such as cerebral spinal fluid. Advice is provided by the Core staff to facilitate the design, execution, and analysis of experiments.
Drosophila Aggression and Courtship Evaluator
Software pipeline to quantify aggression and courtship behaviors in Drosophila. Codes and classifiers for the DANCE manuscript.
Digital drug dispenser. Enables to eliminate serial dilution from dose-response workflow, miniaturize qPCR reaction volumes, and easily dispense any volume in any well for a broad array of low-volume dispensing applications. Accurately dispense volumes from picoliters to microliters for faster, more reliable dispensing of small molecules and biomolecules.
Aquatic Germplasm and Genetic Resources Center
Service resource affiliated with Louisiana State University with core mission to develop and commercialize genetic resources for aquatic species. Provides research, technology development, and services for commercial aquaculture and biomedical use, including large-scale cryopreservation.
Virginia Tech Flow Cytometry Core Facility
Virginia Tech�s Fralin Life Sciences Institute Flow Cytometry Facility
Facility offers traditional data acquisition, analysis, and cell sorting as well as imaging cytometry. Provided equipment includes: BD FACSAria Fusion: A cell sorter that can also be used as an analyzer, it is equipped with 488nm, 640nm, and 405nm excitation sources and is equipped to analyze up to fifteen parameters simultaneously. The Fusion is capable of processing up to 70,000 events per second and sorting up to four different cell populations at once. It is also equipped with an Automatic Cell Deposition Unit (ACDU) that allows sorting of cells into plates or onto slides; Amnis ImageStream MarkII: this imaging cytometer combines the speed and objectivity of flow cytometry with the detailed imagery of microscopy to allow you to objectively and quantitatively describe biological processes based on cell size, shape, and fluorescence location, texture, and signal intensity.This open platform enables new methods of research and improves traditional flow and imaging based applications. It is equipped with 405nm, 488nm, and 642nm excitation sources and is able to analyze up to twelve parameters simultaneously. It has 20X, 40X, and 60X objective lenses and Enhanced Depth of Field technology. It can process several thousand cells per second.
Perkin Elmer | Opera Phenix High Content Screening System
Fully automated, high-content imaging and analysis platform designed for high-throughput biological screening and detailed cellular phenotyping. It’s widely used in research settings for applications that require both high resolution and high throughput microscopy across a range of complex biological models.
Software tool to convert the .eeg/.qle data recorded by Quanlan devices into .edf format.
Software pipeline for filtering sequence errors found in formalin-fixed and paraffin-embedded (FFPE) samples.
Web platform for sharing machine learning models and data science applications. Users can interact with the deposited models and applications through a public URL or fetch the models and apps to run them locally on their own computer.
Memorial Sloan Kettering Cancer Center Biostatistics Core Facility
Core provides expertise on study design and statistical analysis. Devoted to developing and understanding ways to derive scientific inferences from quantitative data and to developing methods for achieving this aim. The staff are highly trained in this field and experienced in all of the specialized areas of statistical techniques including clinical trials methodology, survival analysis, epidemiologic methods, analysis of genomics data, statistical genetics, methods for diagnostic medicine, health services research, survivorship, evidence-based medicine and psychometric methods.
University of Cologne Center for Genomics (CCG) Core Facility
University of Cologne Center for Genomics (CCG)
Represents central facility and does not operate for profit, engaging in academic research collaborations and service provision on collaborative basis. Provides infrastructure for all kinds of sequencing, gene mapping and whole genome association studies in complex diseases as well as the validation of copy number variations.
Sakura | Accu-Cut SRM 500 Rotary Microtome
Compact, manual rotary microtome designed for preparation of thin sections of human and animal tissue samples of varying hardness, as far as they are suitable for manual cutting. Microtome for parafin sectioning. Can be used for all applications as diagnostic aid related to in vitro examination within the histopathological process.
Durable, modular, upright compound microscope known for clinical, educational, and research use, offering brightfield and phase contrast, UIS optics, and ergonomic features for comfortable, long-term observation, making it popular for routine pathology (like Mohs surgery) and teaching labs. As an earlier BX model, it's reliable, configurable with different heads (binocular, trinocular) and accessories, and often updated with modern LED lighting, providing excellent cost-performance for detailed specimen viewing.
Circular plot used to visualize flows, relationships, or connections between different groups or entities, showing the strength (weight) of these links with arc sizes and colors, ideal for network analysis, migration data, or interaction matrices.
Software lightweight Python framework and command-line tool for organizing, processing, and managing neuroimaging-clinical datasets, designed to make studies more reproducible and adhere to FAIR data principles (Findable, Accessible, Interoperable, Reusable). Provides standardized workflow to handle raw data (like DICOMs), apply containerized processing pipelines (e.g., fMRIPrep), extract analysis-ready features (IDPs), and track processing status, extending the Brain Imaging Data Structure (BIDS) standard for both imaging and clinical data. Includes three components: protocol for data wrangling to standardize generation of analysis-ready datasets; specification for dataset organization that extends the Brain Imaging Data Structure (BIDS) standard; command-line interface and Python package that provide user-friendly tools for applying the framework.
Lahore University of Management Sciences Syed Babar Ali School of Science and Engineering High Performance Computing Core Facility
LUMS High Performance Computing Centre (LUMSHPCC)
LUMS High-Performance Computing (HPC) facility
LUMS High-Performance Computing (HPC) facility is specialized computational research core providing high-density processing power and large-scale data storage. It serves as a central hub for faculty and students to execute data-intensive simulations, machine learning workflows, and complex modeling across various scientific disciplines.
Lahore University of Management Sciences; Lahore; Pakistan
Private research university in Lahore, Punjab, Pakistan. Founded in 1985, it is ranked as one of the most prestigious modern universities in Pakistan. In 1984, Syed Babar Ali recognized the shortage of qualified managers in the country.
Software package to facilitate inference of tree-shaped trajectories from single-cell data. These include linear, bifurcating, multifurcating, and other tree-shaped trajectories. Totem uses Slingshot to find linear curves through the lineages of the tree.
Software framework that adapts and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. All-in-one framework for cell-cell communication inference.
Software application for vendor-neutral, open-source acquisition and reconstruction protocols for fully harmonized multi-site functional MRI studies.
VPixx | TRACKPixx3 2 kHz binocular eye tracker
Device for 2 kHz eye/gaze-tracking solution supporting both monocular and binocular tracking with single mechanical configuration. Interchangeable lenses support tracker distances from 60 cm to over 160 cm for fMRI applications. TRACKPixx3 does not require a dedicated PC to process eye images and generate gaze information. All image processing is performed within TRACKPixx3 hardware. Gaze data can be logged within the TRACKPixx3 and retrieved by the testing PC with a simple low-latency USB interface. TRACKPixx3 video feed can be accessed directly through a console display for real-time visualization and adjustment of the tracker. These video feeds can also be accessed through the USB interface for remote control of the TRACKPixx3.
Software R package to identify mutually exclusive mutations. Used to identify mutually exclusive genomic events. Implements exact and approximate computations of the Poisson-Binomial.
Software graphical and containerized spatial proteomics workflow. End-to-end containerized spatial proteomics analysis workflow with QuPath integration. Consists of cell segmentation, batch correction, unsupervised clustering, validation of clusters on the image, and cell type clustering results visualization.
Open source resource of manually curated and expert reviewed infant brain segmentations hosted on OpenNeuro.org. and OSF.io. Anatomical MRI data was segmented from 71 infant imaging visits across 51 participants, using both T1w and T2w images per visit. Images showed dramatic differences in myelination and intensities across 1–9 months, emphasizing the need for densely sampled gold-standard segmentations across early life. This dataset provides a benchmark for evaluating and improving pipelines dependent upon segmentations in the youngest populations. As such, this dataset provides a vitally needed foundation for early-life large-scale studies such as HBCD.
Open data resource for mapping brain development and its associations with mental health. Integrates data from 5 large studies of brain development in youth from three continents (N = 6,346). Bifactor models were used to create harmonized psychiatric phenotypes, capturing major dimensions of psychopathology. Neuroimaging data were carefully curated and processed using consistent pipelines in a reproducible manner.
Software electrophysiological data analysis toolkit developed by Quanlan Technology for beginner neuroscience researchers and clinical electrophysiologists.
Melanoma Omics Dashboard for Multimodal Data Exploration
Platform provides suite of powerful tools to explore, visualize, and make sense of complex data that can help accelerate discoveries in melanoma research. By integrating data from multiple studies, including transcriptiomics, single-cell RNA-Seq, and proteomics (with more to come), MelOD allows for comprehensive examination of the molecular landscape of melanoma.
1.5 T Signa Explorer MRI scanner (GE Healthcare)
MRI scanner as medical imaging system used for detailed scans of the brain, spine, joints, heart, and other organs, focusing on high image quality, fast scans (using technologies like HyperSense), enhanced patient comfort (with Silent Suite for noise reduction and free-breathing options), and operational efficiency, making it suitable for diverse clinical needs like neuroimaging, orthopedics, and cardiovascular studies. It's designed to handle a broad range of applications and improve workflow, even for patients with MRI-conditional metal implants.
Medical College of Wisconsin Tissue Bank
College of American Pathologists-accredited biorepository that collects, processes, securely stores, and distributes human biospecimens (tissues and blood products) for medical research. Tissue Bank that is a CAP-accredited biorepository supporting four human consent programs. Provides fresh and frozen tissue and biological materials with known preanalytical variables to researchers as well as provides specialized processing and imaging services.
Software MATLAB-based application for spike sorting multi-electrode array (MEA) recordings. Used for efficient, reproducible spike sorting in high-throughput neuronal culture experiments. SAMS performs batched automated spike sorting processes and also allows the users to review and correct any clusters or spike assignments.
MPLAB X Integrated Development Environment (IDE)
Software program from Microchip, serving as a comprehensive, expandable platform for developing Microchip microcontroller applications, with many integrated tools like MPLAB Code Configurator (MCC) and MPLAB XC Compilers (free versions). Incorporates tools to discover, configure, develop, debug and qualify embedded designs for most of microcontrollers and digital signal controllers. MPLAB X IDE works seamlessly with the MPLAB development ecosystem of software and tools.
Software video analysis and modeling tool developed within the Open Source Physics (OSP) Java framework. Allows frame-by-frame tracking of anatomical landmarks and articulated structures from video recordings, enabling the extraction of time-dependent kinematic variables such as displacement, velocity, and acceleration. Tracker is well suited for biomechanical analyses of articulated systems, as it supports joint-based rotations, reference-frame definition, and the export of quantitative motion data for further post-processing.
Shipping Dewar Positional Cooling Device (SDPCD)
Shipping Dewar Positional Cooling Device (SDPCD) is 3-D printable vertical cooling device that can assist cryopreservation with various standard cooling rates by use with existing standard nitrogen vapor shipping dewars for on-site sperm cryopreservation for aquatic species.Device could hold 22 French straws (0.25-mL or 0.5-mL) and a quick-release ring design could eject straws directly into a canister inside a dewar by pressing a button after freezing. The final prototypes produced cooling rates of 1 to 68°C/min for 0.25-mL straws, and 3 to 37°C/min for 0.5-mL straws with a material cost of 3.5 USD for a single device
Open source software ecosystem designed to facilitate harmonization, search, and discovery of neuroimaging study cohorts across decentralized datasets. Allows researchers to find participants across different studies based on specific clinical, demographic, and imaging criteria without needing to merge all the original data into a single central database. Provides tools to connect a local neuroimaging dataset with others in decentralized framework using linked data principles.You can contribute to Neurobagel by enhancing its tools (annotation, querying), improving documentation, adding new features/models, fixing bugs, or sharing your own data/expertise to help researchers find and harmonize brain imaging cohorts through standardized metadata and knowledge graphs.
Software standardized framework for creating, sharing, and reusing cognitive and clinical assessments. Standardized form generation and data collection schema to harmonize results by design across projects. Used for enhancing research reproducibility through standardized survey data collection.
Software library for nested containment list data structure for interval overlap queries, like interval tree. It is a static interval-tree that is fast for both construction and lookups.
Software application for topic modeling with latent Dirichlet allocation.
Upright light microscope used in research, education, and routine lab work for detailed sample observation, documentation, and analysis in fields like pathology, histology, cytology, and materials science, supporting various techniques like brightfield, fluorescence, and polarization microscopy for capturing sharp digital images.
Particle analysis system that uses Nanoparticle Tracking Analysis (NTA) to measure the size distribution, concentration, and aggregation of nanoparticles (10-2000 nm) in liquid, crucial for research in exosomes, drug delivery, protein aggregation, and colloidal systems. It visualizes individual particles' Brownian motion with lasers and a camera, calculating hydrodynamic diameter and concentration, and includes fluorescence detection for specific labeled particles.
University of Massachusetts Amherst Electron Microscopy Core Facility
UMass Amherst Electron Microscopy Core Facility
EM Core Facility offers instrumentation and training for range of Electron Microscopy applications. Instrumentation includes Thermofisher Tundra cryo-TEM, Tecnai T12 TEM, Magellan 400 SEM, JEOL JEM-2200FS, Vitrobot Mark IV, (cryo)microtomes, and other auxiliary equipment.
Software Python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells. Facilitates visualization and comparison of single-cell 3D genomes.
Software tool that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). Genetic multiplexing of barcoded single cell RNA-seq.
Code to conduct combinatorial barcoding. scRNA-seq-compatible tracer for identifying clonal relationships.
University of Michigan MCity Core Facility
Core for building and testing mobility innovation is part of the University of Michigan Transportation Research Institute. Helps advance safe and efficient transportation and mobility solutions. Makerspace for mobility and transportation innovators. Offers open-source tools, remote or on-site testing.
University of Michigan M-Air Core Facility
Core for testing advanced air mobility (AAM), focusing on drones and electric aircraft, especially Beyond-Line-of-Sight (BVLOS) autonomous flight, to accelerate innovation and commercialization in the industry. It serves as a real-world "skyway" for researchers and companies to test new technologies like electric vertical takeoff and landing (eVTOL) aircraft, support Michigan Medicine's air transport, and foster aerospace startups, building on U-M's existing robotics and autonomous vehicle testing facilities.
University of Michigan Mixed Methods Program Core Facility
Provides mixed methods consulting services. Located in the Department of Family Medicine, team advises researchers at all levels in the health and social sciences who are developing proposals for funding, revising a manuscript, completing a research project or requiring Mixed Methods training.
Van Andel Institute Spatial Collaborative Services Core Facility
Van Andel Institute Spatial Collaborative Services
Spatial Collaborative Services combines expertise and technology from VAIs Genomics Core and Optical Imaging Core to offer investigators a seamless pipeline for spatial imaging. Services include consultation, histology preparation, sequencing and imaging based spatial platforms.
Software tools for fitting Generalized Linear Models (GLMs) with time dependence (a.k.a. filters).
Augusta University Medical Sculpture Core Facility
Department of Medical Illustration’s Medical Sculpture Core advances education and research capabilities in medical sculpture. The space serves as an AU Core Research Lab to provide expertise in medical sculpture, volumetric visualization, and 3D printing. This lab space will offer educational and research opportunities for students to develop medical models such as surgical simulation models and patient education models. The research will improve surgical and medical training and provide insight into materials and technology to improve patient care.
PIANO:Probabilistic Inference Autoencoder Networks for multi-Omics
Software novel variational autoencoder framework for inferring integrated latent space representations for single cell transcriptomics data that uses a negative binomial generalized linear model for stronger batch correction, and code compilation for ten times faster training than existing tools. Enables superior analyses of multiple atlases, solving challenging integration tasks across sequencing platforms, development, and species, while simultaneously preserving desired biological signals.
Massachusetts General Hospital Brigham Center of Excellence for Molecular Imaging Core Facility
Mass General Brigham Center of Excellence for Molecular Imaging
Massachusetts General Hospital Brigham Center of Excellence for Molecular Imaging
Core facility that provides microscopy training, imaging solutions, image processing and analysis services, and consultation. Offers imaging techniques and expertise, including spinning disc confocal microscopy, two-photon confocal microscopy, super resolution microscopy, total internal reflection microscopy, wide field microscopy, fluorescence spectroscopy, photo-manipulation techniques (e.g. FRAP, photoablation, optogenetics, and optical tweezers) and live cell imaging.
Software python library for working with Google Sheets allowing users to open spreadsheet by title, key or URL. It also allows to read, write, and format cell ranges and more.
Software R package to calculate the SHapley Additive exPlanations (SHAP) values in polynomial (instead of exponential) time. Supports models produced with xgboost, lightgbm, gbm, ranger, and randomForest packages.
Northwestern University Metabolomics Core Facility
Metabolomics Core Facility of Northwestern University
Metabolomics Core at Robert H. Lurie Comprehensive Cancer Center of Northwestern University provides LCMS based metabolomics services including identification, semi-quantification and quantification of metabolites and integrative genomics services related to metabolism.
Northwestern University Immunotherapy Assessment Core Facility
Northwestern University Immunotherapy Assessment Core
Core provides services for dissection of the immune response both phenotypically, functionally and transcriptionally at the single cell or population level. Technologies like single cell RNAseq (10x Genomics Chromium platform), multispectral fluorescent tissue imaging of FFPE tissues (Vectra 3 Imaging System, Akoya Biosciences), high-performance electrochemiluminescence plexing immunoassays (QuickPlex 120, MSD), and automated multiplexed single-cell and bulk protein analysis system (IsoLight, IsoPlexis) are available to investigators, providing immune cell (and beyond) characterization at the highest resolution. Other services also include project consultation, sample preparation, controlled rate freezing and cryopreservation/storage, as well as a comprehensive range of standardized and customizable immunological assays.
University of Canterbury Research Compute Hub
Platform is part of Research Computing and Services where researchers can perform compute-intensive tasks. It’s accessed through online user interface called Open OnDemand (via HPCNow!). The platform is run by Slurm, a job scheduler that manages and allocates resources, optimising resource use and power consumption. UC-RCH is housed in primary data centre on Dovedale, featuring 9 physical nodes and connecting to a virtual cluster with virtual machines and containers.
Software R tools for Blaser Lab Data Analysis. Package includes commonly used functions for R analysis in the Blaser Lab.
Michigan Technological University Materials Characterization and Fabrication Core Facility
Materials Characterization and Fabrication Facility(MCFF)
Michigan Technological University Materials Characterization and Fabrication Facility(MCFF)
Core facility provides tools for imaging, analysis, environmental testing, and micro/nanofabrication. Offers data, expertise, and hands-on training. From advanced materials to environmental systems, MCFF is the hub where discovery meets precision.
Washington State University WSU Spokane Research Histology Core Facility
Provides histology services from sample collection to data analysis.Training is available so that research staff understand the process. Contact us before you start your experiment so we can help you integrate histology with any other tissue-dependent assays you intend to perform.
Washington State University WSU Spokane Proteomics/Metabolomics Core Facility
Facility offers proteomics and metabolomics services.Provides training and instrumentation, such as the Orbitrap Q Exactive HF mass spectrometer from Thermo Fisher Scientific and advanced nano-LC systems.
Spectroscopic Imaging, VIsualization, and Computing (SIVIC)
Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.
Mid-volume, automated immunoassay system used in clinical labs to perform a wide range of tests for diagnosing and monitoring diseases, detecting infections, checking hormone levels, and assessing cardiac health, by analyzing biological samples like blood for specific proteins, hormones, and other markers with high reliability and efficiency, often integrated into the larger, flexible Atellica Solution for automated workflows.
Purdue University Research Repository (PURR)
Provides online, collaborative working space and data-sharing platform. Provides services with data management planning, boilerplate text for proposal, sample plans and individual consultation. Each dataset gets DOI. PURR publishes and archives digital datasets from researchers across campus and welcomes all kinds of open data from images and videos to spreadsheets and source code.
Software versatile all-purpose image and graphics editor for Windows, macOS, and Linux (via Wine) that combines raster (bitmap) and vector editing, making it a strong, affordable alternative to Adobe Photoshop, with features like layers, masks, color management (CMYK, Lab, 16-bit), batch processing, and web tools, presented in a comprehensive yet sometimes retro-looking interface . You can edit images or optimize them for the web, but you can also prepare print-ready PDF data.
Cloud-based data science platform for flow cytometry and single-cell analysis, streamlining complex workflows from raw data to insights, enabling collaboration, and ensuring reproducibility with automated tasks, machine learning, and integration for classical and high-dimensional cytometry data. Modern Cloud Software for classical and advanced Flow Cytometry analysis.
V-Dem Research Institute Academic Freedom Index
V-Dem Institute is an independent research institute that serves as the headquarters of the V-Dem Project a database that seeks to conceptualize and measure democracy. Provides interactive map for comprehensive overview of academic freedom in 179 countries and territories in 2024. Based on assessment of the de facto protection of academic freedom as of December 2024, users can compare countries and investigate developments within countries over time.
University of St Andrews Mass Spectrometry and Proteomics Core Facility
St Andrews University Mass Spectrometry and Proteomics Facility
Core provides services in mass spectrometry including protein identification and analysis, measuring the intact mass of proteins and quantitative proteomics.
Software R package to infer genome-wide copy-number variations (CNVs) from spatially resolved in situ mRNA profiles. SpatialInferCNV will generate CNV calls in each spatial region represented by barcoded spots.
Cell Neural Networks on Spatial Transcriptomics (CellNEST)
Software tool to decipher patterns of communication. Used to relay-network communication detection that identifies putative ligand–receptor–ligand–receptor communication. Detects T cell homing signals in human lymph nodes, identifies aggressive cancer communication in lung adenocarcinoma and colorectal cancer, and predicts new patterns of communication that may act as relay networks in pancreatic cancer.
Brain Initiative Cell Atlas Network Data Catalog
Database of complete listing of data sets generated by the Brain Initiative Cell Atlas Network (BICAN). Used to find, access, and use data from the BRAIN Initiative's efforts to map brain cell types, integrating molecular, anatomical, and functional data from mouse, primate, and human brains. Its purpose is to provide a comprehensive, open-access "parts list" of the brain, accelerate neuroscience discovery, and help understand brain disorders by offering links to raw data, visualizations, and tools for a vast array of cell types and circuits.
Collection of molecular genetic reagents to gain access to many different brain cell types. Provides scientists with advanced genetic tools, primarily AAV (Adeno-Associated Virus) vectors with cell-type specific "enhancers," to precisely target, map, monitor, and manipulate specific cell types and circuits in the brain and spinal cord.
Portal that allows users to explore taxonomy-guided genome selections, visualize epigenetic assays, and analyze chromatin data across basal ganglia cell populations identified by the BRAIN Initiative Cell Atlas Network (BICAN) with an interactive research platform. The portal allows for investigation of several key epigenetic assays including associated with active enhancers and promoters, repressed genes, and constitutive heterochromatin. Used to analyze complex genomic and epigenomic data from the brain, helping identify specific cell types, understand gene regulation, and map disease-related molecular events, ultimately aiding in understanding neurological disorders like Alzheimer's, autism, and depression by revealing what goes wrong at the cellular level, leading to better gene therapies.
Specialized monitor engineered for scientific rigor, replacing consumer displays with research-grade control and synchronization for visual experiments. Features high-performance industrial LCD glass, and a panel controller which has been custom designed to support vision research. Includes an array of peripherals which often need to be synchronized to video during an experiment, including stereo audio stimulator, button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and complete analog I/O subsystem.
Open Data Commons Data Quality APP (ODCdqa)
Web application for facilitating compliance with the minimal data standards (MDS) set by the open data commons for SCI and TBI.
Software application for fast phylogenetic maximum parsimony tree inference and bootstrap approximation.
Paris Brain Institute iPSC Core Facility
ICV-iPS platform at the Paris Brain Institute (ICM)
iPS cell culture facility of the Paris Brain Institute
As part of the cellular engineering and vectorology core facility (ICV), the iPSC core facility (ICV-iPS) proposes the generation and the genetic engineering of human induced pluripotent stem cells to internal research teams, external academic teams, and industrial partners. Services include generation of human iPSc with Sendai virus, full molecular and functional characterization of iPSc clones, genetic engineering of human iPSc with CRISPR/Cas9 system and theoretical and practical learning sessions on human iPSc culture. The core facility provides also access to L2 cell culture box dedicated to human iPSc culture.
Software package for quantifying transposable elements at a locus level for RNAseq datasets. TElocal base algortihm is derived from the published TEtranscripts tool.
Collection of Alternative Methods for Regulatory Application (CAMERA)
Collection of Alternative Methods for Regulatory Application
Interactive database and user interface providing online access to validated alternative methods for U.S. regulatory and other contexts of use. Central hub and unified resource of validated alternative methods that enhances accessibility to validation study reports, data, protocols / SOPs, and information on regulatory guidance.Users can filter searches by alternative method types, defined approaches, Test Method Endpoint, and regulatory guidance.
University of Victoria Biology Electron Microscopy Laboratory Core Facility
UVic-Biology Electron Microscopy Laboratory
Electron microscopy core provides microscopy and image analysis, applications development, and services.
Sweden Cancerome Analysis Network–Breast (SCAN-B) MutationExplorer
Web application to explore somatic mutations in large breast cancer RNA-sequencing datasets, particularly from the Sweden Cancerome Analysis Network–Breast (SCAN-B) project, helping to link genetic alterations to clinical features, patient outcomes (like survival), and potential drug targets, adding a dimension to gene expression analysis for guiding treatment.
Software command-line tool designed to simulate circular DNA and RNA sequences and generate corresponding sequencing reads. This tool can be helpful for researchers working with circular DNA (like eccDNA) or RNA, providing an easy way to simulate the coordinates of these molecules and generate sequencing files for further analysis.
Donald Danforth Plant Science Center Field Research Site Core Facility
Field Research Site is a core facility providing scientists with advanced field research infrastructure and crop management capabilities. Offers diverse agricultural practices including full tillage, no-till systems, irrigation, precision spraying, and plot planting for row crops and specialty crops. On-site resources include multiple drying rooms, walk-in freezers, and dedicated processing spaces for soil, tissue, and seed samples.
Human brain stimulated-echo diffusion MRI with the diffusion time of 1 second
This dataset includes human brain stimulated-echo (STE) diffusion MRI (dMRI) images acquired at the long diffusion time of 1 second from 10 healthy volunteers and an ex vivo brain hemisphere, as described by Aganj et al (MRM 2026). Also included are MPRAGE T1 images for all scans and standard dMRI images for the 10 in vivo scans. All images have been anonymized, and the T1 images have been de-faced.
University of Puerto Rico Center for Microbiome Sciences Core Facility
COBRE Puerto Rico Center for Microbiome Sciences
Puerto Rico Center for Microbiome Sciences
Core lab aids researchers in the design, compliance, methods, extractions, data analyses and training in microbiome research and innovation. Premier resource center, equipped with instrumentation, analytical capabilities, and training opportunities in microbiome.
BioGenex | EZ - Retriever� IR - Antigen Retrieval System
Automated, microwave-based instrument designed to perform rapid deparaffinization, rehydration, and antigen/nucleic acid retrieval on formalin-fixed, paraffin-embedded (FFPE) tissue sections. It handles up to 96 slides in 30 minutes, utilizing infrared (IR) technology for consistent, high-throughput staining.
Ultra-rapid, high-throughput, high insight system for multiplex immunofluorescence (IF) and biomarker discovery. System enables to perform highly-multiplexed imaging of entire cross sections with sub-cellular resolution. Fully automated workflows for tissue staining and imaging. A full-stack hyperplexing solution capable of visualizing up to 40 markers.
Cancer Research UK Cambridge Institute Flow Cytometry and Mass Cytometry Core Facility
CRUK Cambridge Institute Flow Cytometry and Mass Cytometry Core Facility
Core provides cell analysis, sorting instruments and expertise in regular fluorescence, spectral, and flow cytometry. Offers educational and cytometric services including stem cell analysis, immunophenotyping, cell cycle analysis, translocation and co-localisation of cell activation markers, chromatin density, and apoptotic and necrotic analyses. Performs cell sorting, expertise in experimental design and provides equipment training for all users.
University of Texas MD Anderson Cancer Center Mass Spectrometry Imaging Core Facility
University of Texas MD Anderson Cancer Center Mass Spectrometry Imaging Core
Core has personnel with expertise in all aspects of Mass Spectrometry Imaging. Provides spatial mapping of biomolecules from tissue sections using Matrix Assisted Laser Desorption/Ionization (MALDI) and Secondary Ion Mass Spectrometry (SIMS).
Bioinformatics software program for multi-omics data analysis and visualization. It is developed and maintained by Qlucore AB (Lund, Sweden). Delivers flexible and easy-to-use visualization of big data for fast analysis and results.
Web-based, and open-source platform designed to predict and optimize CRISPR-Cas13 guide RNAs (gRNAs) for targeting and knocking down specific RNA molecules. It is specifically used to select the most efficient guide RNAs for RfxCas13d to maximize RNA degradation (knockdown) efficacy, with applications in transcriptome engineering, functional genomics, and antiviral therapy.
Software R package for estimating dim-light melatonin onset (DLMO), implementing the hockey-stick method. Establishes a reproducible and sustainable foundation for melatonin-based circadian phase estimation and a modular platform for incorporating future quantitative approaches to DLMO detection.
Leica | MZ FLIII fluorescence stereomicroscope
Fluorescence stereomicroscope offers 3D image, larger panoramic field of view, more intense fluorescence, and longer working distances. Living objects can be observed spatially in large fields of view.
Medical College of Wisconsin Translational Metabolomics Shared Resource Mass Spectrometry Core Facility
Mass Spectrometry Core provides comprehensive LC-MS and MALDI imaging MS based analytical support for proteomics, lipidomics, metabolomics, glycomics, and spatial omics. Offers expertise in experimental design, optimized sample preparation, data acquisition, data analysis, and investigator training for NIH funded and translational research projects.
General, open-standard schema for cell annotations and related metadata. Provides programmatically accessible standard designed to record additional metadata about individual cell type annotations, including marker genes used as evidence and details of automated annotation transfer. Standard is represented as JSON schema as this allows all metadata to be gathered in a single, compact validatable file - which includes a link to a cell by gene matrix file of annotated data. However, the schema is designed so that it can be decomposed into individual tables suitable for use in dataframes/TSVs and flattened onto obs in AnnData format.
Software R package from the Allen Institute designed to build, standardize, and analyze single-cell RNA-seq-based cell type taxonomies. It utilizes a structured Allen Institute schema (AIT) to organize cell annotations and metadata, enabling hierarchical, data-driven cell type classification
UC Davis Health Comprehensive Cancer Center Molecular Pharmacology and Chemical Biology MPCBSR Core Facility
UC Davis Molecular Pharmacology and Chemical Biology Shared Resource
Molecular Pharmacology and Chemical Biology Shared Resource (MPCBSR) provides services for the assessment of new therapeutics, including clinical trial specimens and determination of clinical PK/PD and potential drug-drug interactions (DDI), pharmacological studies on novel therapeutics in preclinical models, including DM/PK/PD, on-target mechanisms, biomarkers, and combination effects, and chemical synthesis of new compounds and drug delivery nanomaterials for improved therapy.
UC Davis Health Comprehensive Cancer Center Mouse Biology Shared Resource MBSR Core Facility
Mouse Biology Shared Resource (MBSR) provides knockout, transgenic, and humanized murine cancer models and related services for advancing translational cancer research. Additionally, the MBSR offers services to enhance the use of existing mouse models or to facilitate the development of new mouse models for cancer research, including genetic alteration (e.g., CRISPR/Cas9-mediated gene targeting, transgenesis), surgical manipulation (e.g., patient-derived xenografts (PDX), cell-derived allografts (CDA) and xenografts (CDX)), and environmental challenges (e.g., diet, chemotherapeutic agents). can produce a wide range of allele-speci?c mouse models and offers innovative technologies to phenotype mouse models that mimic human conditions.
Knowledge base platform that provides scientists worldwide with tools for searching, exploring, and visualizing Neuroscience knowledge represented by knowledge graphs (KGs). Provides tools that enable scientists to contribute new information (or knowledge) to the platform and is expected to be a go-to destination for all neuroscience-related research needs. Allows making predictions and new inferences in addition to querying and viewing information.
MEtabolomes, TRaits, and INteractions-Knowledge Graph
Software pipeline for generating knowledge graph integrating emi, trydb, globi datasets. Code for constructing a knowledge graph that integrates enriched metabolite data from Experimental Natural Products Knowledge Graph (ENPKG), LOTUS (available through Wikidata), plant trait data from TRY, and biotic interaction data from Global Biotic Interactions (GloBI). It performs taxonomic alignment against Wikidata records and generates Resource Description Framework (RDF) triples representing taxonomic relationships, traits, and species interactions. The resulting knowledge graph is queryable via a SPARQL (SPARQL Protocol and RDF Query Language) endpoint.
Standardized, open-source framework of classes and properties designed to annotate and interlink data regarding metabolites, species taxonomy, ecological traits, and environmental interactions. It powers the METRIN-KG knowledge graph, mapping the chemical diversity of Earth's species to support biodiversity conservation. Knowledge representation schema designed to capture, contextualize, and structure chemical diversity data across all known species. It reuses and harmonizes several existing ontologies, while introducing over 100 new concepts and relations to enable interoperability and data reuse.
Software supervised learning framework for chromatin loop detection in genome-wide contact maps.
Software tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
Software tool for cell type specific enhancer-gene predictions using ABC model.
Software bioinformatic framework for reconstructing 4D spatial transcriptomics atlas and spatiotemporal analyses+.
Life Canvas Technologies | SmartClear II Pro
Instrument to increase the rate of tissue clearing. Provides optimal imaging and staining quality. Delipidates for best antibody diffusion and minimal light scatter, and ensures maximum preservation of fluorescent protein signals with optimized buffers that maintain pH. Nanoporous membranes prevent common issues including tissue damage, contamination, browning, black precipitates, and deformation.
University of Liverpool Micro-X-ray-CT Shared Research Core Facility
Micro X-ray Computed Tomography Shared Research Facility (XCT-SRF)
University of Liverpool Micro-X-ray-CT SRF
Micro X-ray Computed Tomography Shared Research Facility (XCT-SRF) provides access to an X-ray microscope and micro-CT instrument, and expertise in experiment planning, sample preparation, and data analysis and visualisation. The facility is capable of 3D imaging and analysing a wide range of material samples, with a focus on supporting research in healthcare, manufacturing, and energy applications.
Mississippi State University Institute for Imaging and Analytical Technologies I2AT Core Facility
Institute for Imaging and Analytical Technologies I2AT Core Facility
Core facility that provides instrumentation and related services including SEM, TEM, AFM, XRD, polishing and related sample prep equipment, Surface Imaging, Surface Roughness, Hardness and Electric Properties, Fluorescence Imaging, Surface Elemental Information, High Resolution Imaging of Ultrathin Sections or Nanoparticles, Phase Determination and Phase Orientation.
Fully automated high-content imaging platform that uses cyclic immunofluorescence to enable high-plex spatial profiling of hundreds of protein markers and dozens of RNAs on the same tissue section, accelerating spatial biology and multiomics research workflows.
Medical College of Wisconsin Cancer Center Structural Biology Shared Resource Core Facility
MCW- Structural Biology Shared Resources
SBSR core consists of the Protein Purification unit and the Structure Determination unit. Protein Purification unit produces homogeneous, high-quality proteins well suited for downstream biophysical studies and structure determination. Structure Determination unit employs X-ray crystallography, Cryo-EM, and advanced AI-assisted analytical tools for structure determination and imaging.
Software open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Enables to explore gene-metabolite co-regulation mechanisms through an intuitive web interface, revealing spatial heterogeneity in tissue development and disease progression.
Software set of tools useful in the analysis of benthic terrain. Includes tools for geomorphology and classification.
Windows-based software (PC use only) that provides a tool for the determination of coral cover using transect photographs. A specified number of spatially random points are distributed on a transect image and the features underlying the points are user-identified. Coverage statistics are then calculated and the results sent to Excel spreadsheets automatically. CPCe can be used for image calibration and area analysis of benthic features. Excel sheets are automatically generated to summarize the area calculations for each image.
Web interactive digital tool for tracking the health of vital reef ecosystems all around the world. Reef Life Survey program uses scientists and citizen scuba divers to survey fishes on coral and rock reefs throughout the world. Marine life monitoring programm.
Collaborative and Automated Tools for Analysis of Marine Imagery
CATAMI web site provides a location of the deposit and access of various underwater imagery, including data from Baited Remote Underwater Video (BRUV), Autonomous Underwater Vehicles (AUV), Diver Operated Video (DOV) and Towed Imagery (TI). CATAMI Classification Scheme provides standardised vocabulary for identifying benthic biota and substrata from underwater imagery.
Marine Life Information Network Biological Traits Information Catalogue
Database developed by the Marine Life Information Network (MarLIN) in collaboration with the Marine Biological Association (MBA) and Plymouth Marine Laboratory. It provides detailed, searchable, and downloadable functional trait information on marine benthic invertebrates and plants to support ecological research. The database emphasizes species found around the coasts and seas of the British Isles.
Database on biological traits of polychaetes (bristle worms, Polychaeta: Annelida). It covers information about morphological, behavioural, reproductive and larval characteristics of polychaete taxa which has been collected from the literature.
Provides morphological, life-history, and behavioral trait data for Arctic benthic invertebrate taxa. It facilitates trait-based ecological research in the Arctic by offering standardized, fuzzy-coded data (scores 0-3) on 19 traits (80 categories), with species names synchronized with the World Register of Marine Species (WoRMS).
Software R package to compute and illustrate the multiple facets of Functional Diversity. Provides graphical functions based on the ggplot library to illustrate FD values through customizable and high-resolution plots of species distribution among functional entities or in a multidimensional space. All functions include internal validation processes to check for errors in data formatting which return detailed error messages. Used to compute a global assessment of functional diversity by gathering computation of alpha and beta functional indices.
piecewiseSEM: Piecewise Structural Equation Modeling
Software R package for performing Piecewise Structural Equation Modeling, designed to fit complex causal networks by breaking them into smaller, manageable "pieces" (individual regressions) rather than using global covariance estimation. Used to analyze complex, direct/indirect ecological and evolutionary data.
Miniaturized, hand-held, real-time fluorescence confocal endomicroscope designed for preclinical research, allowing researchers to visualize live tissue at cellular and subcellular levels in vivo. It is primarily used to observe dynamic, 3D biological processes, such as tumor progression, drug interactions, and cell-to-cell interactions in animal models.
Software hepatocyte ploidy identification pipeline on the stereo-cell platform for accurate liver polyploidy classification via fluorescence staining and deep learning tools.
Developmental Human Brain Atlas Ontology (DHBA)
Machine-readable framework designed to standardize, organize, and annotate the anatomical structures, developmental stages, and spatial relationships of the human brain during development. It is primarily derived from the Allen Developing Human Brain Atlas (BrainSpan) to provide a structured, hierarchical taxonomy for researchers. Application ontology built by combining ontologised versions of the Allen Institute Developing Human Brain Atlas (DHBA) StructureGraph mapped to Uberon.
Software code for Monte Carlo diffusion simulation. Monte Carlo diffusion with reflecting or absorbing obstacles in 2 and 3D.
Software code for simulating diffusion in brain extracellular space images.
Software tool is revision of classic ilastik. Used for interactive (supervised) pixel-level image classification and segmentation.
Software Python library for spatial analysis of histological brain section images using a reference brain atlas. Implements the core quantification algorithms from the QUINT workflow, designed to replicate and extend the Quantifier feature of the Nutil software.
Software data-centric, backend-agnostic framework for zero-shot cell-type annotation. Data-centric marker distillation for zero-shot cell-type and spatial annotation with LLMs.
Louisiana State University Health Sciences Center Shreveport hiPSC and Cell Models Core Facility
Core enables generation of genetically defined human iPSC-derived hepatocytes, CRISPR/Cas9 mediated gene editing, and primary mouse hepatocyte isolation.
Software pipeline for identifying enhancers in bulk or single-nucleus ATAC-seq and multiomic data with a high degree of accuracy for prioritizing testing of promising candidate cell type enhancers for targeting homologous cell types across mammalian species.
GBM-TIME multi-dimensional transcriptomics workflow
Software pipeline for dissecting glioblastoma risk signatures in the tumor immune microenvironment based on single-cell, bulk, and spatial transcriptomic data.
Software tools for parsing measurement with threshold over time data (eg tumour treatment studies) and generating interactive and static plots.
Cancer Treatment Response gene signature DataBase
Data resource for clinical transcriptomes with cancer treatment response, and meanwhile supports various data analysis functions, providing insights into the molecular determinants of drug resistance. CTR-DB 2.0 is updated cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers.
Software tool for reconstruction of higher order chromatin from scRNA-seq and scATAC-seq. Chromatin compartment inference from single-cell RNA- and ATAC-seq.
Benchtop instrument designed for life science research, specifically for imaging, detecting, and quantifying protein and nucleic acids on gels and blots. It enables multi-channel analysis, including laser infrared (IR) fluorescence, RGB visible fluorescence, and chemiluminescence, allowing for multiplexed Western blots.
Penn State College of Medicine GPCR Assay Service Center Core Facility
Penn State College of Medicine GPCR Assay Service Center
Core to accelerate scientific discovery in G protein-coupled receptors (GPCRs) physiology and pharmacology. Provides services to identify signal transduction processes that are specific to their GPCR of interest (such as opioid, cannabinoid and muscarinic) that is either natively present or expressed heterologously in cell systems. Assists investigators with drug development studies. Support researchers with assay development and optimization, pilot data, and grant assistance. Houses instrumentation used.
Wallac | Victor2 1420 Multilabel Counter
PerkinElmer Victor2 1420 Multilabel Counter
PerkinElmer Wallac Victor2 1420 Multilabel Counter
Microplate reader designed for academic, clinical, and industrial laboratories to detect light-emitting or absorbing markers with Manufacturer/Brand: PerkinElmer (formerly Wallac Oy). It supports over 10 non-radioactive technologies, including fluorescence, luminescence, time-resolved fluorometry, and absorbance in various plate formats (1-864 wells). Accepts microtitration plates (up to 1536 wells), Petri dishes, slides, and filters.Equipped with shaking, scanning, and optional temperature control/liquid dispensers for kinetic studies. Operates as a stand-alone unit or integrates with robotic systems for high-throughput screening.
University of Pittsburgh McGowan Institute Histology Core Facility
Core offers full histology services including processing and embedding, cutting, staining, and immunohistochemistry. Our services can be customized to fit the needs of any research program.
University of Pittsburgh Rangos Histology Core Facility
Core provides histological services in order to facilitate productivity and success of investigators based in the Rangos Research Center and researchers in other units of the University of Pittsburgh and UPMC, as well as clients in other academic institutions in the Pittsburgh area.
University of Coimbra Department of Chemistry NMR Core facility
Core offers access to Nuclear Magnetic Resonance (NMR) spectroscopy studies. Facility houses three solution-state FT-NMR instruments operating at proton frequencies of 400, 500 and 600 MHz, a TD-NMR 20 MHz relaxometer and an EPR spectrometer. UC-NMR Core Facility provides researchers and institutions with expertise, services and tools to carry out research requiring solution Nuclear Magnetic Resonance spectroscopy.
Software open AI-Powered Platform for 2D Temporal Plant Phenotyping.
Charité Berlin University of Medicine Transgenic Technologies Core Facility
Transgenic Technologies Charité-Universitätsmedizin Berlin
Core provides services supporting generation, modification, cryopreservation, and rederivation of genetically modified rodent models for biomedical research, generates genetically modified mouse models via both targeted and random mutagenesis using tools such as CRISPR/Cas9 in zygotes or embryonic stem (ES) cells, provides cryopreservation and rederivation of existing animal models to preserve hygienic integrity. Services for rodent transgenic model development include: Pronuclear Injection and amp; Viral Transgenesis with introduction of genetic constructs into zygotes using microinjection or lentiviral systems; ES Cell-Based Techniques: use of embryonic stem cell manipulation for genetic targeting; Embryo Transfer: transferring manipulated embryos into recipient females; In Vitro Fertilization (IVF): assisted reproductive technology to generate embryos for manipulation or cryopreservation; Cryopreservation: freezing of embryos and sperm for archiving or rederivation of lines as required. Facility’s expertise includes quality control of cryopreserved material to ensure viability upon thawing.
Charité Berlin University of Medicine Cryo-Electron Microscopy Core Facility
Charité Universitätsmedizin Berlin cryo-Electron Microscopy (CFcryo-EM)
Cryo-Electron Microscopy of Charité - Universitätsmedizin Berlin
Facility for high resolution imaging of biological samples at cryogenic temperatures. Amongst other applications such as single particle data collection, our high-end instrumentation is suited to perform in situ structural biology by combining cryoCLEM, lamella FIB-milling, and cryo-electron tomography.
Charité Berlin University of Medicine Virchow Clinic Campus Experimental Hybrid Operating Room Core Facility
CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN - CAMPUS VIRCHOW KLINIKUM Experimenteller Hybrid-OP FEM CVK
Core offers large-animal experimental hybrid operating room equipped for cardiological and cardiothoracic interventions, including advanced angiography and multimodal intraprocedural imaging, to support patient-oriented preclinical research and education. Facility enables design, conduct, and veterinary-supervised aftercare of acute and chronic large-animal studies and hands-on training courses on implants, ventricular assist devices, artificial hearts, and percutaneous procedures for structural heart valve disease at phantom models and large-animal models. Core functions and services Performance of animal experimental studies and training courses in an experimental hybrid OR environment. Consultation on study design, model selection, and preparation of animal experiment applications for regulatory approval. Provision of anesthesia and surgical assistance, including perioperative and intensive care support. Specialist veterinary support for acute and chronic studies, ensuring animal welfare and scientific quality. Housing and husbandry for large laboratory animals such as sheep, pigs, and minipigs as part of the experimental program. Equipment and technology Hybrid operating room with Philips Allura Clarity FD20 angiography system tailored to cardiology and cardiac surgery interventions. Comprehensive software tools including Echo-, Heart-, and Vesselnavigator for image-guided procedures. EPIQ7 and CX50 ultrasound systems supporting TTE, TEE, ICE, and IVUS imaging modalities for structural and interventional procedures. Carto-3, OPTIS Integrated System, and XperCT platforms for 3D mapping and intravascular or intracardiac imaging. Heart–lung machine and ECMO systems for cardiopulmonary support during complex experimental interventions. Organizational context and availability Located at Campus Virchow-Klinikum as part of the Forschungseinrichtungen für Experimentelle Medizin and operated in cooperation with the Deutsches Herzzentrum Berlin. Provides core facility research infrastructure of the Charité faculty for translational cardiovascular research and advanced training in a large-animal setting. Certified according to ISO 9001:2015, indicating a documented quality management system for its services.
Waters | Xevo TQ Absolute Triple Quadrupole Mass Spectrometer
Xevo TQ Absolute Triple Quadrupole Mass Spectrometer
High-sensitivity, compact benchtop tandem quadrupole mass spectrometers designed for trace-level quantification in complex samples. Primarily used for PFAS testing, pharmaceutical bioanalysis, clinical diagnostics, and environmental contaminant analysis, offering enhanced performance for negative ion-mode compounds. Used for quantifying drug residues, metabolites in biological samples, and impurities, with specific IVD models available for clinical settings. Equipped with StepWave XR technology to handle high-throughput, complex matrix samples with minimal maintenance.
Software quality-assurance layer for pathway enrichment interpretation that converts enrichment term lists into context-conditioned, evidence-linked, schema-bounded claims and assigns PASS/ABSTAIN/FAIL via predefined, rule-based audit gates (stability, context validity stress tests, evidence-link integrity, and contradiction checks), producing decision-grade reports with audit logs. The LLM is confined to proposal-only steps; final decisions are mechanical and reproducible.
Charité Berlin University of Medicine Viral Core Facility
Viral Core Facility (VCF) of the Charité – Universitätsmedizin Berlin
Viral Core Facility of the Charité - Universitätsmedizin Berlin
Core provides comprehensive services for generation of viral particles from existing vectors or newly created vectors.
Web-based platform for flexible and reproducible neuroimaging meta-analysis. Enables to create customized, reproducible neuroimaging meta-analyses with no code/low code solutions. It integrates a regularly updated centralized literature database (NeuroStore) with tools for systematic study curation and annotation following PRISMA guidelines, allowing users to search across tens of thousands of indexed fMRI studies or import external study lists. Analyses can be executed locally or in the cloud using the NiMARE Python library, and results can be interactively reviewed, shared, and archived, facilitating transparent meta-analyses and collaborative knowledge building.
Mayo Clinic Precision Mouse Engineering Core Facility
Precision Mouse Engineering Core - Mayo Clinic
Core generates transgenic and gene-targeted mice for researchers at Mayo Clinic's campuses in Arizona, Florida and Minnesota to enable researchers to observe how genes, or mutant variations of genes, are expressed. Provides services to all Mayo Clinic faculty and staff engaged in research. Also, services are offered to non-Mayo investigators and research collaborators.
Mayo Clinic Biomedical Imaging Resource Core Facility
Biomedical Imaging Resource - Mayo Clinic
Mayo Clinic's Biomedical Imaging Resource Core in Rochester, Minnesota, focuses on supporting and advancing research in biomedical imaging and visualization sciences. Provides guidance on protocol design, routine image analysis, and custom software and hardware solutions. Also, media and model production resources are available to investigators for the creation of high-quality visualizations and physical models of research data.Core provides services to all Mayo Clinic faculty and staff engaged in research. Also, services may be available on a limited basis to investigators and research collaborators outside Mayo Clinic. Before scheduling, contact the core to design optimal settings for the specified imaging task.
University of Louisville Proteomics Technology Center PTC Core Facility
University of Louisville Proteomics Technology Center (PTC)
Core provides comprehensive proteomic analyses using LC-MS platforms, supporting post-translational modifications, protein-protein interactions, spatial proteomics, and single-cell workflows with bioinformatics.
Software tool for calling copy number variants (CNVs) from human DNA sequencing data. It can work either with germline data, or paired tumor/normal samples. Its primary input is aligned reads (in .bam format), and its primary output is a report (in a .vcf file) giving the copy number status of the genome.
Charité Berlin University of Medicine iPATH.Berlin Core Facility
Core provides immunopathological services from sample embedding and staining to microscopic evaluation. Full service for histopathology includes tissue embedding, staining of tissue sections and microscopic analysis: preparation of paraffin blocks,cutting of cryo and paraffin sections,histochemistry,immunohistochemistry/-fluorescence/multiplexing, in-situ hybridization,Scoring/quantification,storage.
FPGA-based data acquisition unit designed for real-time monitoring of neural activity in behaving animals. It synchronizes excitation light sources (LED drivers) with detection (photodetectors) to record fluorescence signals, typically using lock-in amplification to filter noise and separate multiple wavelengths (e.g., ).
Specialized, high-performance power supplies and controllers designed for neuroscience research, specifically to drive Connectorized LEDs and fiber-coupled light sources. They offer 1, 2, or 4 independent channels for controlling light intensity, modulation (CW, TTL, analog), and complex, software-defined, or automated pulse sequences required for optogenetics and photometry experiments.
Doric | 6 ports Fluorescence Mini Cube (iLFMC6)
Specialized, compact, all-in-one fiber photometry system designed to monitor neural activity or neurotransmitter levels in freely moving animals. By combining multiple built-in LEDs (405-440 nm, 460-490 nm, etc.) and photodetectors, it enables simultaneous, multi-wavelength measurement of calcium indicators (e.g., GCaMP) and red fluorophores alongside isosbestic controls to correct for movement artifacts.
Software open-source Python library providing graphical user interface for visualization and manual curation of large-scale electrophysiological data. It is optimized for high-density multielectrode arrays containing hundreds to thousands of recording sites.
Software R package for assessment of PCR artifacts in RNA-Seq data. Used for duplication rate quality control for RNA-Seq datasets.
Upright microscope designed for histology and pathology. With motorized z-focus, motorized and coded 7x nosepiece, fully automated transmitted light axis, and fully automated 5x or 8x fluorescence axis, the automated Leica DM6000 B research microscope provides all transmitted light contrast methods including the world’s first fully automated Differential Interference Contrast (DIC).
Imaging system used in laboratories for chemiluminescence and fluorescence imaging, specifically for detecting and analyzing protein bands (Western blot), DNA/RNA gels, and RGB fluorescence. It features a cooled CCD camera for detecting low-abundance samples.
Hitachi | HT7800 Transmission Electron Microscope
120 kV Transmission Electron Microscope (TEM) designed for high-contrast, high-resolution imaging in biological and materials science, often operated in, lighted rooms. It features a proprietary dual-mode objective lens for switching between wide-field and high-resolution views, along with automated, user-friendly software for navigation and image acquisition.
Software extended tools for correlation analysis and visualization.
Software tool to analyse interactions in microbial communities. Species metabolic interaction analysis (SMETANA) of microbial communities.
Software Python package to study microbial communities using metabolic modeling. Metagenome-scale modeling to infer metabolic interactions in the gut microbiota.
Web service provides functional annotation of cell types within the lung and combines functional and single cell data for a rigorous catalogue of cell lineages.
Medical College of Wisconsin Cancer Center Translational Metabolomics Shared Resource, Redox and Bioenergetics Core Facility
Redox and Bioenergetics core provides instrumentation, cutting-edge techniques, and expertise dedicated to investigating cancer cell metabolism and redox signaling, and to design custom probes for reactive oxygen species (ROS) for MCWCC members.
Charité Berlin University of Medicine Animal Behavior Phenotyping Core Facility
Charité Berlin University of Medicine Animal Behavior Phenotyping Facility (ABPF)
Core offers broad spectrum of behavioral tools to characterize novel animal models, including assays of cognition, exploratory behavior, social interaction, motivation, anxiety‑related behavior, and motor performance. In addition to classical tests such as the Barnes maze, elevated plus maze and open field, the facility develops and implements novel, high‑throughput and ethologically relevant approaches to monitor rodent behavior with particular emphasis on social interactions.
Charité Berlin University Medicine Research Institutes for Experimental Medicine Core Facility
Forschungseinrichtungen für Experimentelle Medizin (FEM)
Core research service unit at the Charité – Universitätsmedizin Berlin specializing in laboratory animal husbandry, breeding, and experimental usage for biomedical research. Provides infrastructure for animal-based studies, ensures compliance with animal welfare regulations (e.g., training, veterinary oversight), and supports the creation of genetically modified models.
Broad Institute Genomics Platform Core Facility
Facility that generates, analyzes, and interprets high-throughput genomic data to understand the genetic basis of disease. Genomics Platform has played leadership role in the design, data generation, and methods development in support of major genomic resource projects.Through the Broad Clinical Labs (BCL), formerly known as the Clinical Research Sequencing Platform (CRSP), it supports clinical trials, diagnostic testing, and major initiatives, including COVID-19 testing. Offers services including Nucleic Acid Extractions, Single Cell Sequencing (using 10x Genomics products), and GWAS Arrays.
Integra Biosciences | ASSIST PLUS Pipetting Robot
Pipetting Robot enables automated pipetting with mounted any of INTEGRA’s 25 multichannel electronic pipettes or D-ONE single channel pipetting modules onto the ASSIST PLUS pipette holder. Provides different pipetting programs.
Charité Berlin University of Medicine Advanced Medical Bioimaging Core Facility
Advanced Medical Bioimaging AMBIO Core Facility
Charité Berlin University of Medicine Advanced Medical Bioimaging AMBIO Core Facility
Core for advanced fluorescence bioimaging. Provides both the infrastructure and expertise necessary for researchers with diverse backgrounds to efficiently perform advanced fluorescence microscopy imaging projects on the molecular, cellular and tissue level. AMBIO services include individual user training and assistance, and if necessary supervised image acquisition and guidance for data analysis.
Software package to discover genes that coordinate their expression across spatially adjacent cells. Used for analysis of spatial transcriptomic data allowing in-depth analyses how genes coordinate their expression in space to perform tissue-level functions. Facilitates analysis and exploration of cross-expression patterns.
Hitachi | SU8100 scanning electron microscope
High-performance Field Emission Scanning Electron Microscope (FE-SEM) designed for ultra-high-resolution imaging and elemental analysis of nanostructures, semiconductor devices, and beam-sensitive materials. It features cold field emission technology for superior, low-voltage, high-resolution imaging (approx. 1.1 nm at 1kV).
Software package to provide interface for the most frequent tasks of survival analysis, with focus on the needs of clinical oncology. The syntax follows the tidyverse philosophy and is made to be used in a pipeline.
Software data analysis pipeline for spatial transcriptomics data tailored to polyploid organisms.
Software R package to create tables displaying results of univariate analyses, stratified or not by categorical variable groupings.
CDC Research Data Center United States Cancer Statistics
US Centers for Disease Control and Prevention Restricted access United States cancer statistics
Portal provides detailed, non-public data on cancer incidence, such as precise county-level data, specific site factors, and prognostic measures. The restricted access U.S. Cancer Statistics (USCS) dataset provides researchers access to cancer incidence and population data for all 50 states, the District of Columbia, and Puerto Rico. These statistics combine cancer registry data from CDC's National Program of Cancer Registries and the National Cancer Institute's Surveillance, Epidemiology, and End Results program.
CDC National Center for Health Statistics Research Data Center
Centers for Disease Control and Prevention NCHS Research Data Center
Secure facility that provides qualified researchers with access to restricted-use, non-public health data. It protects participant confidentiality while allowing analysis of detailed survey data, such as specific geographic locations or sensitive health info. Provides access to restricted data from the National Center for Health Statistics and from other federal government agency surveys and studies. Access is granted only to approved researchers under strict supervision, and all results undergo disclosure review before leaving the RDC.
CDC Federal Statistical Research Data Center
Federal Statistical Research Data Centers (FSRDCs)
Federal Statistical Research Data Centers (FSRDCs) are secure, specialized facilities operated by the U.S. Census Bureau in partnership with leading research institutions across the U.S.. They provide authorized researchers access to restricted-use, non-public microdata from federal agencies for statistical purposes while ensuring strict confidentiality and data protection. There are more than 30 FSRDC sites located throughout the United States. Researchers can access detailed, non-public data from the Census Bureau, Bureau of Labor Statistics, National Center for Health Statistics, and other agencies. Using FSRDC location to access NCHS restricted data involves additional requirements and costs. If you access National Center for Health Statistics (NCHS) data through FSRDC site, you will interact with both your assigned NCHS RDC analyst and the location's FSRDC administrator over the course of your project. Each of these people have their own roles and responsibilities.
Shanghai Xinruan | Sleep Deprivation Device
Device to systematically deprive mice/rats of sleep for a certain period each day. Uses feedback control by monitoring animal activity levels. It can activate the deprivation lever after the animal enters a specific sleep stage to deprive or break sleep. It has three working modes: feedback adjustment (software control mode), programmable adjustment (external control mode), and independent touch screen adjustment (standard mode). It can be used to create animal models of sleep deprivation or sleep breaking, and features precise adjustment and low physical exertion.
Tiangen Biotech | TGem Ultra Full Wavelength Spectrophotometer
TGem Ultra is an all-in-one full-wavelength ultraviolet-visible spectrophotometer with a wavelength range of 185-910 nm. The base can detect trace samples of 0.5–2 µl with very high accuracy and repeatability. The flagship version (OSE-260-06) also features a cuvette detection mode, suitable for measuring samples with low concentrations, high volatility, or low surface tension that do not easily form a liquid column. It can also be used for measuring bacterial concentrations and analyzing enzyme kinetics.
University of Louisville KY INBRE Data Science Core Facility
Predictive Analytics and Data Science (PADS) Hub
Specialized, collaborative unit providing bioinformatics, biostatistics, and data analysis services to researchers across Kentucky. It enhances biomedical research capacity through expert support in experimental design, grant application assistance, and high-throughput data analysis, primarily serving faculty and students at member institutions.
Compact, benchtop whole-slide scanner designed for high-speed, high-resolution digitization of glass slides, primarily used in research pathology, education, and tele-pathology. It converts slides into digital images (NDPI format) for viewing, analysis, and archiving, offering Z-stack imaging for thick tissues and optional fluorescence capabilities.
Arizona State University Knowledge Enterprise Eyring Materials Center Core Facility
Facility supporting analytical needs for materials. Provides advanced facilities and equipment for materials characterization, surface, optical and structural analysis, elemental composition, and high-resolution electron microscopy. The center supports materials analysis across a broad range of scientific disciplines, including physics, chemistry, life sciences, earth and space sciences, environmental sciences, and engineering. Offers electron microscopy, X-ray diffraction, ICP-MS, spectroscopy, and related techniques.
National Institute for Scientific Research Advanced Laser Light Source Core Facility
National Institute for Scientific Research Advanced Laser Light Source (ALLS)
Canadian national user facility located at INRS-EMT in Varennes, Quebec, designed to develop and apply high-power, ultrafast lasers for advanced scientific research. It produces intense, synchronized light pulses spanning from THz to hard X-rays for dynamic imaging, materials science, and medical applications. Home of the most powerful laser in Canada with 750 TW and high repetition rate laser systems to explore novel phenomena in matter with ultrafast tools.
National Institute of Scientific Research INRS
Institut National de la Recherche Scientifique
Specialized research and graduate training university in Quebec, Canada, founded in 1969. It is the only institution in Quebec dedicated exclusively to graduate studies (master's and doctoral level) and applied research in four key strategic sectors: water/environment, energy/materials/telecommunications, urbanization/culture, and health/biotechnology.
Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility.
Software application for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Used to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data. Analyzing sodium bisulfite conversion-based DNA methylation/modification data.
Software application for de novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.
Software R package for functional enrichment on genomic regions. Functional enrichment analysis directly performed on genomic regions.
Software R package for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Standardisation of cluster validation statistics by random clusterings and comparison between many clustering methods and numbers of clusters based on this. Cluster-wise cluster stability assessment
Web interactive set of tools for sampling and randomization of data sets and generation of random patterns. The tools include randomization and permutation of data (even stratified random sampling) and random assignments for studies, generation of random numbers following specific probability distributions, generation of random and quasi-random point distributions and sampling patterns, noise in one or two dimensions with adjustable spectral properties, random walks and Lévy flights. Own data tables can be provided for random sampling in a privacy-friendly way, as data processing takes place directly in the browser and no data is transferred to anywhere else. Random Number Lab also offers some educational material and worksheets and can be used for scientific and educational purposes.
Medical College of Wisconsin Cancer Center Cell Therapy Shared Resource Core Facility
MCW Cancer Center Cell Therapy Shared Resource
MCW Cancer Center Cell Therapy Shared Resource (CTSR)
Medical College of Wisconsin Cancer Center Cancer Center Cell Therapy Shared Resource
Core provides services including processing and production of cell therapy products for clinical use, expertise in translation of cellular therapies to the clinic, and instrumentation supporting the development of novel immunotherapy strategies and insights on mechanisms of action for effective therapies.
Web optimization tool for codon adaptation-based control of protein expression in C. elegans.
Open-source machine-learning software library and ecosystem written in Julia. Machine learning library for the Julia programming language providing tools for building neural networks including layers, optimizers, and automatic differentiation.
Software library within Julia ML ecosystem (JuliaML) designed for managing machine learning pipelines. Utilities for machine learning in Julia including data splitting, shuffling, batching, and preprocessing operations.
Software Julia package for data clustering. Clustering algorithms for the Julia programming language including k-means, hierarchical clustering, DBSCAN, and affinity propagation.
Software R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. Spatial cellular neighbourhood scanning in R.
University of Technology of Compiègne INGESYSBIO meta-platform Core Facility
Université de Technologie de Compiègne (UTC) INGESYSBIO meta-platform
Specialized research and technical core at the Université de Technologie de Compiègne (UTC), specifically within the BMBI (Bio-Mechanics and Bio-Engineering) CNRS lab, dedicated to the engineering of biological systems. Designed to support training, research, and development activities in the healthcare field, acting as a bridge between engineering and biology. Integrates complementary technological facilities dedicated to the engineering, production, culture, and characterization of biological systems, ranging from simple models to complex structures. It brings together expertise covering the entire experimental workflow, from the design and fabrication of technological devices and biological supports to their cultivation, monitoring, and functional analysis.
University of Technology of Compiegne; Compiegne; France
French public engineering school and research university founded in 1972, located in Compiègne. It combines the structure of a university with a Grande École, offering specialized, interdisciplinary programs in engineering, technology, and biotechnology, often blending French and North American educational styles.
Cancer Research UK Cambridge Institute Microscopy Core Facility
Core provides expertise, training and instrumentation for a range of advanced light microscopy techniques across scales and for a variety of samples. We offer wide-field, confocal, high-content, light sheet and multi-photon imaging systems for cell and tissue studies.
Berlin Center for Advanced Neuroimaging Core Facility
Berlin Center for Advanced Neuroimaging (BCAN)
Joint facility of the Charité - Universitätsmedizin Berlin and the Humboldt Universität zu Berlin. Research dedicated neuroimaging facility with two state of the art Siemens 128-channel 3 Tesla MRI systems equipped for cognitive, neurological and psychiatric experiments.
University of Montreal CRCHUM Metabolomics Core Facility
Core facility specializes in the analysis of key metabolites for metabolic diseases. Develops and performs targeted methods for quantifying water-soluble and lipid metabolites.
Software tool that predicts cancer metabolic fluxes from bulk RNA-seq and scRNA-seq data to address these analytic gaps. Used for characterizing metabolic circuits and output non-degenerative fluxes using cancer gene expression data.
Software essential for running the FLEXMAP 3D w/xPONENT 4.3 platform. Used to control instrument operations, manage data acquisition, and perform analysis for high-throughput multiplex assays. It enables automated maintenance, 96/384-well plate compatibility, and, in many cases, diagnostic, IVD, or research-use-only testing. Intended to measure and sort multiple signals generated in an in vitro diagnostic assay from a clinical sample.
Thermo Fisher | Luminex 200 Instrument System
Luminex 200 Instrument System is a high-throughput, flow cytometry-based, multiplexing analyzer designed for labs to simultaneously detect and quantify up to 100 different proteins or nucleic acids (analytes) from a single, small-volume biological sample. It is primarily used for research (RUO), including biomarker studies, drug discovery, and immunology.
Software package that allows users to use the Intel MKL library for Julia's underlying BLAS and LAPACK, instead of OpenBLAS, which Julia ships with by default. Julia interface to Intel Math Kernel Library for accelerated linear algebra.
SeekGene | SeekOne Digital Droplet System
SeekOne Digital Droplet (SeekOne DD) System
Automated instrument for single cell partitioning, capture, and labeling based on principle of microfluidics. In addition to general sample types, the DD system is particularly suitable for highly fragile cells, such as brain tissue, retinal tissue, and all tissues from aged individuals.
Chinese biotechnology company based in Beijing that designs and manufactures single cell sequencing technology used in scientific research. Company specializing in high-throughput single-cell multi-omics technology, providing tools, kits, and platforms for single-cell DNA methylation, RNA sequencing, and immune repertoire profiling. Founded in 2018, it offers the SeekOne™ Digital Droplet System.
SeekGene | SeekMate Tinitan Fluorescence Cell Counter
SeekMate Tinitan Fluorescence Cell Counter
Fluorescence cell analyzer designed for cell counting and viability detection. It can analyze up to 6 samples per run and supports both bright-field and fluorescence counting modes.
BiOptic Qsep400 is high-throughput, 4-channel automated capillary gel electrophoresis system designed for fast, accurate size and concentration analysis of DNA, RNA, and protein samples. It acts as a rapid quality control tool for NGS libraries, PCR fragments, and antibody purity in high-volume research and clinical labs.
Web application to plan and document cloning and genome engineering. Open source and open access tool, FAIR data principles compatible, designed to simulate and/or document genetic manipulation processes used in every day synthetic biology and molecular biology.
Mammalian Adipose Tissue Knowledge Portal
Open community portal for multi-species mammalian adipose biology. Aggregates data for adipose tissues and cell types, genes active within them, and their relationship to human phenotypes. Plans to offer reproducible analysis pipelines, wet lab and computational protocols, datasets, analyses, and visualizations for epigenomic, transcriptomic, proteomic, metabolomic, and imaging data. Designed to aggregate and harmonize multi-species (human and mouse) transcriptomic, genetic, and epigenomic data. Enables to explore adipose biology, cell-type-specific gene expression, and metabolic disease mechanisms through interactive tools like Single Cell Browsers.
Software simulation and documentation package for DNA assembly strategies using Python.
Software package provides implementation of the inference pipeline of AlphaFold 3.
Contract Research, Development, and Manufacturing Organization (CRDMO) supporting the life sciences industry. Founded in 2004, it provides comprehensive services for small molecules, biologics, and cell and gene therapies (CGT) from discovery to commercialization. Offers integrated R&D, laboratory services, and manufacturing.
Code to support closed-loop control of cutaneous optical stimulation in freely behaving mice, enabling controlled somatosensory input during movement in naturalistic settings.
Rush University Imaging Research Core Facility
Core that provides magnetic resonance imaging (MRI) services and image analysis. Facility contains 3 Tesla Siemens Prisma MRI scanner, variety of head and body receive coils (including 64-channel head coil), and extensive list of pulse sequences and packages providing advanced, accelerated whole-body imaging capabilities. Houses Nordic Neuro Lab hardware and software for functional MRI stimulus delivery, collecting subject feedback, and eye tracking.
Private university in Chicago, Illinois, United States. Founded in 1972, it is the academic arm of Rush University Medical Center.
University of Toronto Centre for Analysis of Genome Evolution and Function CAGEF Core Facility
University of Toronto UofT - Centre for the Analysis of Genome Evolution and Function
UofT - Centre for the Analysis of Genome Evolution and Function
Provides genomics, proteomics, and bioinformatic services, including next-generation-based genome, microbiome and metagenome sequencing, gene expression and transcriptome analysis, and proteome analysis. CAGEF has established internationally-recognized genomics expertise in the analysis of non-standard species, systems, and environments, with particular experience in microbial, plant, and environmental genomics and metagenomics.
Software package as nucleus caller for single-nucleus RNA sequencing data. Distinguishes between nuclei and empty droplets by combining summary metrics of cell barcodes—such as total UMI counts, fraction of intronic reads, and percentage of mitochondrial reads. It also incorporates gene expression to learn signatures characteristic of empty droplets.
Scripts used to process data for the first McCarroll lab BICAN manuscript
West Sacramento-based biotechnology company founded in 1985 that specializes in manufacturing cell culture and process liquid solutions for the biotech, cell therapy, and gene therapy industries. They operate cGMP-compliant facilities providing products like human serum, buffers, and media to support drug development from research to commercial production.
Seattle-based biotechnology company founded in 2006 that provides high-resolution, Next Generation Sequencing (NGS)-based genotyping services and kits for complex immune regions. They specialize in HLA, KIR, MIC A/B, and Fc receptor typing to support transplant programs, disease research, and clinical laboratories.
Global medical technology company specializing in high-quality plastic laboratory products for diagnostics, biotechnology, and pharmaceutical industries. With over 60 years of experience, they produce VACUETTE® blood collection systems, CELLSTAR® cell culture products, and specialized labware for sample storage.
University Health Network Princess Margaret Cancer Centre Leukemia Tissue Bank
Non-profit, specialized repository in Toronto that collects, stores, and distributes high-quality biospecimens—such as blood and bone marrow—from patients with hematologic malignancies. It supports worldwide research on leukemia and blood disorders to improve diagnosis and treatment.
University Health Network Princess Margaret Cancer Centre Integrative Immune Analysis Core Facility
Princess Margaret Cancer Centre Centre for Integrative Immune Analysis
Core provides specialized, high-dimensional immune profiling for clinical and translational studies. It enables researchers to analyze immune responses using advanced flow cytometry, CyTOF, genomics, and cytokine analysis, helping to improve cancer treatments and patient outcomes.
University of Michigan Medical School National Center of Rabbit Models for Translational Research Core Facility
National Center of Rabbit Models for Translational Research
Core dedicated to developing, characterizing, and distributing gene-edited rabbit models for biomedical studies. Team specializes in rabbit embryology, molecular biology, and animal reproduction, including developing Rabbit Gene Editing Technology (RbGET) workshops. Provides services including generating novel, customized gene-edited models (knockout/knock-in), and conducting preclinical, proof-of-concept studies to support drug development.
Paris Brain Institute Cellular Engineering and Vectorology ICV Core Facility
Cellular Engineering and Vectorology Platform - Cell Culture and Cytometry
Plateforme Ingénierie Cellulaire et Vectorologie - Culture Cellulaire et Cytométrie
Core facility provides infrastructure and services to academic researchers, biotech companies and industry partners that need vectors or cell culture models for their studies. Focuses on generating cell models, genetic modification, viral vector development, and advanced flow cytometry analysis.
Open-source, lightweight Java library providing comprehensive set of self-contained mathematics and statistics components. It fills gaps in the Java standard library, offering tools for numerical analysis, linear algebra, probability distributions, statistics, and optimization, following best practices for software development.
Software C++ API for acquiring neurophysiological data directly into the NWB (Neurodata Without Borders) format. Our goal is to provide a lightweight API to integrate with existing acquisition systems.
Software disease-agnostic Python framework for discovering molecular subtypes using pathway-level analysis and Gaussian mixture model clustering with built-in validation gates.
Michigan State University Mass Spectrometry and Metabolomics Core Facility
Michigan State University Mass Spectrometry and Metabolomics Core
MSU Mass Spectrometry and Metabolomics Core
Open-access research facility that provides advanced analytical services and hands-on training in high-resolution LC–MS/MS, GC–MS, MALDI imaging, and targeted quantitative metabolomics services supporting biomedical, agricultural, and environmental research.
Charité Berlin University of Medicine Central Radionuclide Laboratory Core Facility
Charité Central Radionuclide Laboratory Core Facility
Specialized, centralized facility that handles, manages, or researches radioactive isotopes for medical or scientific purposes. provides support for handling radionuclides, acquiring, disposing of radioactive substances, laboratory decontamination, activity measurements, and radiation safety advice.
Clinical Interpretation of Variants in Cancer
Open-access, community-driven knowledgebase designed to crowdsource and curate evidence on the clinical significance of cancer-related genomic variants. It helps researchers and clinicians interpret tumor DNA mutations to guide precision medicine.
Pan-cancer morphology atlas linking histological features to molecular and clinical outcomes. Structured way to explore cancer morphology at scale and connect tissue organization with patient outcomes and molecular signatures, enabling translational researchers to systematically discover and evaluate pathology-based biomarkers.
Software R package which implements simple single-sample gene signature scoring method that uses rank-based statistics to analyze sample's gene expression profile. Scores expression activities of gene sets at single-sample level. Single sample scoring of molecular phenotypes.
Georgia Institute of Technology AI Makerspace Core Facility
Georgia Tech AI Makerspace Core Facility
Advanced computing cluster for student learning and exploration in machine learning. Provides over 300 NVIDIA GPUs for students to learn machine learning skills and develop projects. Part of the Partnership for an Advanced Computing Environment facility. Student-focused supercomputing hub created in partnership with NVIDIA to provide hands-on experience with advanced AI tools. Empowers students to develop, train, and deploy AI models, fostering innovation in engineering, AR/VR, and other fields while preparing them for industry roles.
University of Manchester BioAutomation and Biofoundry Core Facility
Facility accelerates synthetic biology research by automating design-build-test-learn (DBTL) cycles. It enables high-throughput, reproducible strain engineering, metabolic engineering, and protein production, serving academic and industrial partners. Lab automation facility supporting Engineering biology/Synthetic biology pipelines i.e. Directed evolution of proteins and DNA pathway assembly.
University of Louisville Computing and Research Advanced Computing Core Facility
University of Louisville Advanced Computing Core
University of Louisville Computing and Research
Core to extend the scope of the resources and services provided by the Research Computing team to enable cutting-edge research at UofL and beyond. Provides high-performance computing (HPC) services, including the "Zurada" system, to accelerate research, AI development, data analysis, and complex simulations for researchers across the university. It supports data-intensive workflows with specialized NVIDIA GPUs and high-speed storage.
Software R package for conducting quantile regression analysis, which estimates relationship between variables across various points (quantiles) in distribution, rather than just average. Used to analyze non-normal data, handle outliers, and model extreme outcomes, such as 90th percentile. Used for conditional quantile functions: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included.
Cancer Research UK Cambridge Institute Research Instrumentation and Cell Services Core Facility
Core houses range of high-end equipment, specialised cell services and technical expertise required for day-to-day experiments. Provides access to equipment and specialised cell services. Offers technical and scientific support and training for equipment, cell and tissue culture. Provides access, tracking and storage of cell lines and routine cell culture quality control testing (mycoplasma/sterility testing and cell line authentication).
Public research university with two primary campuses in Fredericton and Saint John, New Brunswick. University founded in 1785, holding the title of Canada's oldest English-language university ranked as the top university in Atlantic Canada and a leader in engineering, computer science, and entrepreneurship.
University of New Brunswick Microscopy and Microanalysis Core Facility
UNB Microscopy and Microanalysis Facility
Provides high-resolution imaging and elemental analysis services. Supports diverse studies through electron microscopy, X-ray micro CT, and confocal microscopy, focusing on material science and biological research.
Human Brain Variation Project (McCarroll
Project provides data currently generated with support from the NIH Brain Initiative Cell Atlas Network (BICAN). Broad Institute collaboration supported by the NIH BRAIN Initiative, to create comprehensive atlas of cellular variation in the healthy human brain. It maps data from millions of cells across diverse individuals to understand how brain biology differs, helping researchers distinguish healthy variation from disease states.
Paris Brain Institute Vectorology Core Facility
Vectorology Core Facility (part of the Cellular Engineering and Vectorology platform) provides specialized, high-level expertise, tools, and services for designing, producing, and validating viral vectors used in neuroscience research and gene therapy development. It supports academic and industrial partners by generating modified, safe viral vectors (e.g., AAV, lentivirus) for gene transfer and cellular, including human iPS, engineering.
University of Oklahoma Protein Production and Characterization Core Facility
Offers access to instrumentation, training, and services for protein expression, purification, and biophysical characterization. In addition to instrument access, PPCC personnel offer advice, hands-on training, education, and collaboration. Provides a range of protein purification and characterization equipment.
University of Pittsburgh Rangos Animal Imaging Core Facility
Core provides multi-modal imaging services for academic investigators, national collaborators, and industrial partners.It facilitates longitudinal studies in animal models using MRI, PET, CT, and ultrasound, offering services such as image acquisition, analysis, and consultations for research, therapy assessment, and disease progression tracking.
Washington University in St. Louis Washington University Center for Cellular Imaging Core Facility
Washington University Center for Cellular Imaging (WUCCI)
Core offers access to advanced imaging technologies, expert consultation, training, and collaborative partnerships across the School of Medicine and Washington University research community. Provides access to light and electron microscopy platforms, guidance in experimental design, sample preparation, data acquisition, quantitative image analysis, expertise, and training to enable investigators to explore cellular and tissue architecture across scales.
Software R package for DNA copy number data evaluation using both their initial form (copy number as a noisy function of genomic position) and their approximation by a piecewise-constant function (segmentation), for the purpose of identifying genomic regions where the copy number differs from the norm. Pre-Process DNA Copy Number (CN) Data for Detection of CN Events.
San Diego biotechnology company that focuses on creating user-friendly, high-resolution imaging solutions for life science research, including confocal, fluorescence, and brightfield microscopy. Specializes in developing hybrid, digital microscopes that revolutionize life science research by replacing traditional eyepieces with high-resolution iPad displays. Their microscopes, such as the Revolve and Rebel, combine upright and inverted configurations, offering versatility for fluorescence, brightfield, and tissue culture imaging.
Pittsburgh Federal Statistical Research Data Center
Research facility jointly operated by the University of Pittsburgh and Carnegie Mellon University in partnership with the U.S. Census Bureau. It provides qualified researchers with access to restricted-use microdata from federal statistical agencies in a highly controlled environment, ensuring strict confidentiality through dedicated workstations without internet or external device access. By enabling analysis of detailed federal data, the center supports advanced research in fields such as economics, public health, business, social policy, political science, and demography, allowing investigators to address questions that cannot be answered with public datasets.
University of Pittsburgh Hillman Cancer Center Translational Pathology Imaging Laboratory Core Facility
UPMC Hillman Cancer Center Translational Pathology Imaging Laboratory (TPIL)
Facility permits interrogation of protein biomarkers in tissue through next-generation, quantitative histopathologic technologies. Utilizes Akoya Bioscience’s PhenoImager platform which includes multiplex IF reagent kits, multispectral imaging on the PhenoImager HT, and image analysis with inForm software.
University of Oklahoma Biomolecular Structure Core Facility
Offers access to instrumentation, training and services for structure determination of macromolecular molecules using single crystal X-ray diffraction and/or cryo-EM Single Particle Analysis (SPA). Instrumentation is available for initial crystallization trials, optimization of crystallization, single crystal X-ray diffraction and data collection at synchrotron radiation facilities, as well as electron microscopy grid preparation for cryo-EM (SPA), screening and data collection using a Thermo Scientific Tundra Cryo-TEM and assistance for data collection at national laboratories.
Allen Intrinsic Physiology Feature Extractor (IPFX)
Software Python package for computing intrinsic cell features from electrophysiology data. Used to compute intrinsic cell features from intracellular electrophysiology data.
OME-Zarr is the emerging community standard image file format for cloud (S3 object store) compatible image data storage. Thus it is important to know how to access S3 hosted OME-Zarr in various image analysis and visualisation platforms.
Developing Human Brain Atlas version 2 (DHBAv2)
Three-dimensional (3D) common coordinate framework (CCF) and reference atlas that defines the spatial organization of cortical and subcortical structures in the adult human brain. This atlas modifies and expands the Allen Human Reference atlas (2020). This atlas parcellates the MNI152 ICBM2009b symmetric template, an averaged template from 152 young adult brains (mean age: 25.02 years, range: 18-44 years, 86 male, 66 female). The template has been sampled to 500 um3 voxel resolution and symmetrized along the right-left axis. This atlas includes annotations for all subcortical and cortical structures using a unified ontology developed for cross-species comparisons, the Harmonized Ontology of the Mammalian Brain Anatomy (HOMBA).
Facility provides access to nuclear magnetic resonance spectroscopy for all. Houses spectrometers ranging in field strength from 400 to 600 MHz, including two 500 MHz Brukers equipped with nitrogen-cooled Prodigy CryoProbes. New users may operate a particular spectrometer independently once they complete the required training and demonstrate the knowledge required for operating each instrument.
Cornell University Chemistry MS Core Facility
Cornell University Chemistry MS Facility
Core specializes in the analysis of small organic and organometallic analytes. Provides access to mass spectrometers for all.
Software tool to find combinations of objects within categories. Can be utilized in bioinformatic analyses to transform two-mode target-pathway relationships to one-mode target-target relationships to generate combination of target genes within related pathways.
BRCA Exchange Knowledgebase for Clinical Cancer Genetics
Web application to search data on BRCA1/2 genetic variants and corresponding clinical data from around the world. Used to search for BRCA1 or BRCA2 variants.
Bioinformatics knowledge base and datacenter focusing on skeletal phenotypes. Provides searchable bone phenotyping data for knockout mouse lines, interactive histomorphometry plots, and raw data, supporting research into skeletal genetics, disease mechanisms, and personalized skeletal health treatments.
Osteoarthritis Initiative Knowledge base
Centralized, annotated repository for the Osteoarthritis Initiative (OAI) study, designed to accelerate research by organizing and linking extensive clinical, imaging (MRI/X-ray), and biomarker data. It aims to help researchers analyze knee osteoarthritis prevention, treatment, and progression.
NIEHS funded biomedical knowledgebase to provide a curated collection of geospatial datasets and associated information. It enables, data discoverability, data harmonization and data re-uses of GeoSpatial datasets in the USA. GeoSpace has three core modules.
Web-based resource for preserving and sharing pharmacokinetic data generated through preclinical and clinical HIV research.
Software aplication to predict scRNA-seq coverage and scATAC-seq insertion profiles along the genome at single-cell resolution. It leverages the pre-trained multi-omics profile predictor Borzoi as a foundation model, equips it with a cell-specific decoder, and fine-tunes its sequence embeddings.
George Washington University McCormick Bioinformatics Core Facility
Core provides advanced computational analysis and consultation for high-throughput genomics and multi-omics research. Supports investigators across GW and external collaborators with experimental design, data processing, statistical analysis, and biological interpretation of next-generation sequencing datasets. Offers expertise in bulk and single-cell transcriptomics, epigenomics, variant analysis, and integrative multi-omics approaches. Develops and maintains reproducible computational pipelines and collaborates closely with researchers to translate complex genomic data into actionable biological insights.
Nextflow pipeline to process whole genome long-read sequencing data generated in the context of ASAP project.
Yale University Wu Tsai Institute Microscopy Shared Core Facility
Wu Tsai Institute Microscopy Shared Facility
Provides optical microscopy tools to advance research in human cognition. Offers both commercial turnkey microscopes and in-house developments based on emerging techniques.
Software application as open source research basecaller for Oxford Nanopore reads.
University of Rwanda African Center of Excellence in Data Science Core Facility
African Center of Excellence in Data Science (ACE-DS)
African Centre of Excellence in Data Science (ACE-DS)
University of Rwanda African Center of Excellence in Data Science
Core mission is to train post-graduate students with combined expertise in statistics, economics, business, computer science, and engineering to use big data and data analytics to solve development challenges.ACE-DS has established a high-performance computing cluster comprising of one master node and four data nodes, all of which are equipped with NVIDIA GPUs for graphic acceleration.Data nodes are equipped with 32*2 cores of Intel(R) Xeon(R) Gold 6226R processors, which provide a total of 640GB of RAM per node, making 10GB/core. Additionally, each of the data nodes has 50TB of storage, all of which is GPU-enabled.For moderate workloads, there are workstations available that feature an i9 processor, 64GB of RAM, and 10TB of storage.Provides desktop computers that users can utilize for their data science and artificial intelligence work.
Sokoine University of Agriculture Southern African Centre for Infectious Disease Surveillance Core Facility
Southern African Center for Infectious Disease Surveillance (SACIDS)
Southern African Centre for Infectious Disease Surveillance (SACIDS)
One Health virtual research and training core to strengthen Africa's capacity to detect, identify, and monitor infectious diseases in humans and animals, serving the East and Southern African region.
Mzuzu University African Centre of Excellence in Neglected and Underutilised Biodiversity Core Facility
African Center of Excellence in Neglected and Underutilised Biodiversity
African Center of Excellence in Neglected and Underutilised Biodiversity (ACENUB)
African Centre of Excellence in Neglected and Underutilised Biodiversity
African Centre of Excellence in Neglected and Underutilised Biodiversity (ACENUB)
Research and training hub to enhance food security and nutrition in Africa.Offers postgraduate training, conducting research on nutrient-dense crops, promoting indigenous knowledge, and strengthening partnerships with agricultural industries. Focuses on exploiting neglected, indigenous, and underutilized biodiversity through sustainable, nutrient-dense cropse, value addition, and postgraduate training to improve livelihoods.
Haramaya University Africa Center of Excellence for Climate Smart Agriculture and Biodiversity Conservation Core Facility
Africa Center of Excellence for Climate Smart Agriculture and Biodiversity Conservation (Climate SABC)
Core to develop climate-smart agricultural practices, enhance biodiversity conservation, and build regional capacity to adapt to climate change.Serves as centralized facility offering specialized laboratory equipment, technologies, and modern teaching aids to support research activities.
Nelson Mandela African Institution of Science and Technology Africa Centre for Research, Agricultural Advancement, Teaching Excellence and Sustainability Core Facility
African Center for Research Agricultural Advancement
Teaching Excellence and Sustainability (CREATES)
Serves as a regional hub for developing sustainable agricultural solutions, bio-nanoscience, and climate resilience technologies in East and Southern Africa.Includes bio-repository for research and data repository to predict risks from climate variability. Works with partners such as the UNESCO National Commission in Tanzania and Ifakara Health Institute (IHI) to support malaria medicine discovery and regional nano-hubs.
Lilongwe University of Agriculture and Natural Resources Africa Center of Excellence in Aquaculture and Fisheries Science Core Facility
Africa Center of Excellence in Aquaculture and Fisheries Science (AQUAFISH)
World Bank-funded initiative established to strengthen the aquaculture and fisheries sector in Eastern and Southern Africa.Services are focusing on fish breeding, biotechnology, feeds (like black soldier fly), and integrated fish-animal-crop systems to boost production.
Eduardo Mondlane University Regional Center of Excellence in Engineering and Petroleum and Gas Technology Studies Core Facility
African Centers of Excellence Regional Center of Excellence in Engineering and Petroleum and Gas Technology Studies
Regional Center of Excellence in Engineering and Petroleum and Gas Technology Studies (CS-OGET)
Regional hub for research, specialized training, and consultancy in petroleum engineering, downstream hydrocarbons processing, and environmental management. As a key provider of technical expertise for the region, it drives innovation through MSc and PhD programs, professional training, and industrial research.
University of Rwanda African Center of Excellence in Energy for Sustainable Development Core Facility
African Center of Excellence in Energy for Sustainable Development
University of Rwanda African Center of Excellence in Energy for Sustainable Development (ACE-ESD)
World Bank-funded hub at the College of Science and Technology in Kigali.Provides interdisciplinary research and training in smart electrification, rural energy access, and sustainable energy management.Acts as a research hub for grid innovation and incubation, supported by international partnerships, including Italian research centers.Provides specialized training for experts in public, private, and academic institutions on topics like microgrid and smartgrid design.
Nelson Mandela African Institution of Science and Technology African Centre of Excellence Water Infrastructure and Sustainable Energy Futures Core Facility
Water Infrastructure and Sustainable Energy Futures
Water Infrastructure and Sustainable Energy Futures (WISE Futures)
Specialized research and training hub aimed at improving water resources, sanitation, and sustainable energy security across East and Southern Africa. Provides technical support, laboratory services (like Material Characterization), and consultancy to address regional development challenges.
Addis Ababa University Center for Innovative Drug Development and Therapeutic Trials for Africa Core Facility
Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa)
World Bank-supported regional center of excellence focused on building capacity for clinical trials, and developing novel vaccines, diagnostics, and therapeutics. Provides training in clinical trials and translational medicine, to foster homegrown health solutions.Training researchers, scientists, and clinical trial staff across Africa in trial management, data management, and scientific writing.
University of Rwanda African Center of Excellence in Internet of Things Core Facility
African Center of Excellence in Internet of Things
African Center of Excellence in Internet of Things (ACEIoT)
Specialized hub funded by the World Bank to train high-level African professionals and researchers in IoT, while fostering innovation in fields like health, agriculture, and energy. It provides advanced laboratory equipment for master's/PhD programs, research, and technical incubation to create sustainable, low-cost technological solutions for the region. Enables practical experiments, product design, and collaboration with local/international partners.
Uganda Martyrs University African Centre of Excellence in Agro-ecology and Livelihood Systems Core Facility
African Center of Excellence in Agro-ecology and Livelihood Systems (ACALISE)
African Centre of Excellence in Agro-ecology and Livelihood Systems (ACALISE)
Provides infrastructure for training, research, and innovation to enhance agricultural productivity in East/Southern Africa. Key facilities include soil lab, feed mill, agricultural mechanization units, radio station for knowledge dissemination, and specialized training/hosting spaces for students and farmers.
University of Rwanda African Centre of Excellence for Innovative Teaching and Learning Mathematics Science Core Facility
African Center of Excellence for Innovative Teaching and Learning Mathematics Science (ACEITLMS)
African Centre of Excellence for Innovative Teaching and Learning Mathematics Science (ACEITLMS)
Center runs three activities namely bringing innovation into teaching and learning, research and training, and community engagement.
Mbarara University of Science and Technology Africa Centre of Excellence Pharm-Bio Technology and Traditional Medicine Core Facility
Mbarara University of Science and Technology Africa Centre of Excellence Pharm-Bio Technology and Traditional Medicine Centre (PHARMBIOTRAC)
Mbarara University of Science and Technology African Center of Excellence Pharm-Bio Technology and Traditional Medicine Center (PHARMBIOTRAC)
Pharm-Bio Technology and Traditional Medicine Center (PHARMBIOTRAC)
Pharm-Bio Technology and Traditional Medicine Centre (PHARMBIOTRAC)
Core to advance, validate, and standardize traditional medicine and biopharmaceuticals in Africa. It serves as a regional platform for training, research, and innovation to improve health outcomes and reduce reliance on imported medicines.
University of Zambia Africa Centre of Excellence for Infectious Diseases of Humans and Animals Core Facility
Africa Centre of Excellence for Infectious Diseases of Humans and Animals (ACEIDHA)
African Center of Excellence for Infectious Diseases of Humans and Animals (ACEIDHA)
World Bank-funded Training and Research Centre for generating knowledge and skills for infectious disease prevention and control.
Copperbelt University African Centre of Excellence for Sustainable Mining Core Facility
African Center of Excellence for Sustainable Mining (CBU ACESM)
African Centre of Excellence for Sustainable Mining (CBU ACESM)
World Bank-funded hub focused on advancing sustainable mining practices in Zambia and Africa through research, education, and training in five core areas: occupational health, environmental restoration, energy/mining design, biodiversity, and community livelihoods. Provides training for postgraduate students and professionals in mining, metallurgy, environmental engineering, and biotechnology.
Addis Ababa University Africa Center of Excellence for Water Management Core Facility
Africa Center of Excellence for Water Management
Africa Center of Excellence for Water Management (ACEWM)
Provides technical, on-the-job training to build expertise in water management. Provides research, and training in water science, policy, and management to foster sustainable, community-driven water solutions across Eastern and Southern Africa.
Egerton University Africa Centre of Excellence in Sustainable Agriculture and Agribusiness Management Core Facility
Africa Centre of Excellence in Sustainable Agriculture and Agribusiness Management (CESAAM)
African Center of Excellence in Sustainable Agriculture and Agribusiness Management (CESAAM)
World Bank-funded hub aimed at improving food security in Africa through high-quality training, research, and technology transfer in sustainable agriculture and agribusiness. It enhances research capacity for postgraduate students and staff, offering specialized laboratories and supporting agribusiness innovations. Provides equipped specialized research laboratories and improved post-graduate study rooms.
Makerere University African Regional Centre of Excellence for Crop Improvement Core Facility
African Regional Center of Excellence for Crop Improvement (MaRCCI)
African Regional Centre of Excellence for Crop Improvement (MaRCCI)
Makerere University African Regional Center of Excellence for Crop Improvement
Makerere University African Regional Centre of Excellence for Crop Improvement
Specialized training and research hub designed to strengthen plant breeding and seed systems in Africa.Core facility includes laboratories for seed quality and plant diagnostics, molecular biology/microbial labs, and Bioinformatics Training Facility at the Makerere University Agricultural Research Institute Kabanyolo.
University of Malawi Center for Resilient Agri-Food Systems Core Facility
Center for Resilient Agri-Food Systems (CRAFS)
World Bank-funded center to strengthen agri-food systems through research, postgraduate training, and professional short courses. It fosters innovation in climate-resilient agriculture, food technology, and policy in Malawi and the SADC region.Offers scholarships for regional students, internships for graduates, and specialized training.
Lilongwe University of Agriculture and Natural Resources Centre of Excellence in Transformative Agriculture Commercialisation Core Facility
Center of Excellence in Transformative Agriculture Commercialisation (TACE)
Centre of Excellence in Transformative Agriculture Commercialisation (TACE)
World Bank-supported aimed at transforming farming into a commercial business through research, postgraduate training, agribusiness incubation, and technical agricultural technologies. Offers mentorship and incubation to help students and youth turn ideas into profitable enterprises.Provides sponsorship for MSc/PhD programs in Irrigation, Food Process Engineering, and Agribusiness Management. Promotes modern techniques, including drone-assisted fertilizer/herbicide spraying, climate-smart farming, and ,ropping to increase productivity.
Eduardo Mondlane University Regional Center of Excellence in Agri-food Systems and Nutrition Core Facility
African Centers of Excellence Regional Center of Excellence in Agri-food Systems and Nutrition
Regional Center of Excellence in Agri-food Systems and Nutrition (CE-AFSN)
Center transforms African agrifood systems through high-quality research, training, and education. It focuses on improving food security, nutrition, agricultural policy, and climate change resilience, acting as a core hub for Master�s/doctoral scholarships, short courses, and academic exchange visits.Offering training for students and professionals to enhance skills in agricultural policy analysis, risk management, and climate change.
Thermo Fisher: Applied Biosystems | QuantStudio 6 Pro Real Time PCR system
qPCR machine designed for rapid, reliable, and automated quantitative PCR (qPCR) in research laboratories. It enables gene expression analysis, SNP genotyping, and pathogen detection using a 96-well or 384-well format. The system features a smart workflow with facial authentication, voice commands, and cloud-based data management.
National University of Rwanda located in the city of Butare and was established in 1963 by the government in cooperation with the Congregation of the Dominicans from the Province of Quebec, Canada.
Sokoine University of Agriculture; Morogoro; Tanzania
Premier public university in Morogoro, Tanzania, founded in 1984, specializing in agriculture, forestry, veterinary sciences, and natural resources. Located at the foot of the Uluguru Mountains, it ranks among the top universities in Sub-Saharan Africa (27th in 2026), focusing on research-driven development.
University established in 1997 in Luwinga, Mzuzu City, is Malawi.Public university and the primary higher education institution in the Northern Region. It offers diverse bachelor, masters, and PhD programs, focusing on education, health sciences, environmental studies, and, notably, science, technology and innovation.
Haramaya University; Dire Dawa; Ethiopia
Public research university established in 1954, specializing originally in agriculture. It is one of Ethiopia oldest higher education institutions, offering diverse undergraduate and postgraduate programs across various fields, with a major focus on agricultural research, science, and technology.
Nelson Mandela African Institution of Science and Technology; Arusha; Tanzania
Research-intensive postgraduate institution focused on Science, Engineering, Technology, and Innovation (SETI). It trains next-generation scientists and engineers to foster sustainable development and economic growth in Sub-Saharan Africa.
Software for the acquisition, visualization, measurement, and analysis of sounds. Developed by the Cornell Lab of Ornithology, it is widely used for bioacoustics, allowing researchers to study animal vocalizations and other acoustic signals using spectrograms and waveforms.
Lilongwe University of Agriculture and Natural Resources; Lilongwe; Malawi
Public university in Malawi, established in 2011 (operational 2012) through a merger of Bunda College of Agriculture and the Natural Resources College. Based in Lilongwe, it focuses on agricultural sciences, natural resource management, and rural development, offering undergraduate, postgraduate, and online e-campus programs.
Eduardo Mondlane University; Maputo; Mozambique
Public university, founded in 1962. It is a comprehensive institution focused on higher education, scientific research, and community extension services to promote innovation and sustainable development. The university offers various faculties, including agriculture, engineering, arts, sciences, and medicine.
Addis Ababa University; Addis Ababa; Ethiopia
Ethiopia's oldest and largest public research university, founded in 1950 and located in the capital, Addis Ababa. It is the premier higher education institution in the country, featuring multiple campuses, extensive postgraduate programs, and ranking high among East African universities.
Uganda Martyrs University; Kampala; Uganda
Private Catholic chartered university in Uganda, established in 1993, with its main campus in Nkozi, near the Equator. It offers various degrees across faculties like business, health sciences, and engineering, focusing on ethical values, community engagement, and sustainable development.
Mbarara University of Science and Technology; Mbarara; Uganda
Public university in Uganda, established in 1989 in Mbarara to specialize in training health professionals. It is renowned for its focus on science, technology, and community-based education, offering programs in medicine, nursing, laboratory sciences, pharmacy, and computing.
Oldest and largest public university established in 1965 in Lusaka. Operating under the motto "Service and Excellence," it offers over 150 undergraduate and postgraduate programs across 13 schools, with major campuses at Great East Road and Ridgeway.
Public university in Kitwe, Zambia, established in 1987. It is a research-intensive institution focusing on technology, engineering, mining, and business. CBU operates several campuses, including the main Jambo Drive Campus in Riverside, and is known as a top Sub-Saharan African university.
Public institution of higher learning in Kenya, located in Njoro, 24 km from Nakuru city. Founded in 1939 as a farm school by Lord Maurice Egerton, it specializes in agriculture but offers diverse programs across 10 faculties, including Arts, Law, Commerce, Health Sciences, and Engineering.
University located in the historic city of Zomba, is the nation's oldest and largest public university, established in 1965. It serves as a major research hub offering diverse bachelor's, master's, and PhD programs, and is recognized for its commitment to high-quality education in southern Malawi.
Michigan State University Transgenic and Genome Editing Core Facility
Michigan State University Transgenic and Genome Editing Facility
Provides comprehensive CRISPR genome editing and transgenic services for animal models and stem cells, with both end-to-end and modular support for model generation. The core also offers full cryopreservation and cryorecovery services, plus rederivation, import/export assistance, genotyping support, and consultation in genome engineering and reproductive biology.
Indiana University School of Medicine Stark Neurosciences Research Institute Flow Cytometry and Microscopy Core Facility (SNRI-FCMCF)
Stark Neurosciences Research Institute Flow Cytometry and Microscopy Core Facility (SNRI-FCMCF)
Core provides access to cost effective instrumentation, software, and scientific consultation. First-come first-serve, fee-for-service core facility with fulltime staff to help users generate rigorous scientific data. Offers two point-scanning confocal microscopes, Nikon A1R and Zeiss LSM900, LSRFortessa X-20 and MACSQuant 10 analytic flow cytometers and 4 laser Sony MA900 cell sorter.
Cancer research institute located on the Cambridge Biomedical Campus, focused on understanding cancer biology to develop new diagnostics and treatments. It brings together multidisciplinary research groups to translate findings into improved patient outcomes. Part of the University of Cambridge, funded by Cancer Research UK.
Software R package, which is used for calculating sample size and power estimates for RNA-Seq studies.
Biopac Student Lab system is a flexible, integrated life science teaching solution that includes hardware, software, and curriculum materials. System to conduct basic physiology lab experiments including ECG, EEG, EMG, and EOG. BSL System uses dynamic lessons with students as subjects to increase interest and retention. Students can record data from their own bodies, guided by a detailed lab manual and full color onscreen guide, and analyze the results. Students can then compare data from different experimental conditions with others in their group and with all students in the lab.
Software tool for quick quality assessment of cram and bam files, intended for long read sequencing. Used for for BAM/CRAM quality evaluation, intended for long reads.
Software machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
Ultra-fast chromosome-scale phasing algorithm for small and large variants. Ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
Software tool for working with modified bases from Oxford Nanopore. Used for working with modified bases. Used for quickly converting modBAM to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics.
Software tools for parsing and plotting methylation patterns. Used for plotting methylation data in various ways.
Software semantic segmentation method that automatically adapts to given dataset. Self-configuring method for deep learning-based biomedical image segmentation. Used to analyze provided training cases and automatically configure matching U-Net-based segmentation pipeline.
File format for storing nanopore DNA data in an easily accessible way. High performance file format for nanopore reads.
Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches.
Software R package enables differential expression analysis on multi-sample single cell datasets using linear (mixed) models with precision weights.
Software tools for correcting single cell barcodes for various scATAC-seq techniques and creating fragment files and spltting BAM files per cluster.
Software end-to-end framework for perturbation analysisis. Ecosystem framework for analyzing large-scale single-cell perturbation experiments.
Software tool designed for mapping Quantitative Trait Loci (QTLs), particularly expression QTLs (eQTLs), by identifying statistical associations between genetic variants (genotypes) and molecular phenotypes (e.g., gene expression levels). Used in large-scale functional genomics projects, such as GTEx, to connect specific genetic variants to phenotypic variation. GPU-enabled QTL mapper, achieving ~200-300 fold faster cis- and trans-QTL mapping compared to CPU-based implementations.
University of Pittsburgh CRConnect Service Center Core Facility
University of Pittsburgh CRConnect Service Center
Provides flexible, cost-efficient clinical research coordinator support across disease areas and disciplines at the University of Pittsburgh. Offers full-service or targeted, as needed support. Services include study start up, regulatory assistance, budgeting and contracting, participant recruitment and enrollment, study visit conduct, data and query management, safety oversight, blood draws, and study closeout, as well as coordinating or participating center roles for multi-site trials. CRConnect can deploy highly experienced coordinators for only the services or amount of time required, reducing costs and providing coverage for investigators without full time staffing needs. The team supports a wide range of clinical research across Pitt and UPMC systems, including IND trials (Phase I–IV), multi center studies, IDE trials, interventional and observational studies, and collaborates closely with other Pitt and UPMC shared resources to ensure investigators are directed to the appropriate support.
Whitehead Institute; Cambridge; Massachusetts; United States
Whitehead Institute for Biomedical Research
Independent, non-profit research institution closely affiliated with MIT, with many of its members holding faculty positions in the MIT Biology Department. Dedicated to improving human health through basic biomedical research.
Whitehead Institute WM Keck Light Microscopy Innovation Center Core Facility
Offers guidance and support from the very beginning of project development to data analysis. Offers hands-on, personalized support throughout experimental process including experimental design, instruments training to develop microscopy skills.
VitroVivo Biotech - Histological Products and Services
Specialized biotechnology company that provides histology services, molecular pathology services, and specialized research reagents to accelerate biomedical research. They assist scientists in academia and industry with tissue preparation, immunostaining, 3D cell culture processing, and laser capture microdissection (LCM) for cancer, neuroscience, and drug development studies.
Uganda largest and oldest institution of higher learning, first established as a technical school in 1922, and the oldest currently active university in East Africa. It became an independent national university in 1970.
Ensembl Linkage Disequilibrium Calculator
Ensembl Linkage Disequilibrium Calculator (GRCh37)
Web tool for calculating Linkage Disequilibrium between variants using genotypes from selected population. We only support LD calculation for variants for which we have genotypes from at least 40 samples in the selected population. At the moment we only have sufficient amounts of genotype data from the 1000 Genomes project for human.
Trans-Omics for Precision Medicine Imputation Server
Free, secure cloud-based service used to impute missing genetic variants in human DNA data, primarily for genome-wide association studies (GWAS). It uses a massive, diverse reference panel of deeply sequenced human genomes to predict missing genotypes, significantly increasing genetic coverage and improving accuracy, particularly for rare variants. It leverages the Trans-Omics for Precision Medicine (TOPMed) panel, which includes over 400 million variants, allowing researchers to boost their genomic data from millions of SNPs to tens of millions.
Software used for live streaming and high-quality screen recording on Windows, Mac, and Linux. Allows to capture, mix, and arrange multiple audio/video sources—such as webcams, desktop screens, and games—in real-time to create, broadcast, or record customized video content. Cross-platform screencasting and live streaming software application.
Hierarchical Tumor Immune Microenvironment Epigenetic Deconvolution
Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens.
Hierarchical Tumor Artificial Intelligence Classifier
Web-based application to trace tumor tissue of origin in primary and metastasized cancers.
University of Edinburgh UK Zebrafish Imaging and Screening Core Facility
UK Zebrafish Imaging and Screening Facility
National facility providing advanced automated chemical and genetic in vivo screening for researchers, utilizing zebrafish embryos for studying disease mechanisms. Dedicated zebrafish-focused research imaging and screening facility adapting and developing cutting edge edge microscopy for automated multiscale imaging.
Cancer Research UK Cambridge Institute Histopathology and In Situ Hybridisation Core Facility
Core facilitates all aspects of histopathology including processing, embedding, sectioning, histochemical staining, tissue microarray building, immunohistochemistry, in situ hybridisation, whole slide scanning, and image analysis.
University of Pittsburgh Health Sciences High Throughput Genomics Core Facility
Core is CAP/CLIA-certified facility offering comprehensive next generation sequencing (NGS) and bioinformatics services. Supports flexible workflows from nucleic acid extraction and library preparation to sequencing and custom data analysis. Services include DNA/RNA extraction, quality checks, various types of RNA/DNA library prep, NGS, methylation, proteomics (Illumina IPP), metabolomics, lipidomics, pharmacogenomics, and microarray analysis, with options for end-to-end or modular support. Advanced instrumentation includes Illumina NovaSeq X Plus and 6000 platforms, MiSeqDX, Hamilton , Eppendorf, and Tecan liquid handlers, automated extraction systems, and more. HTGC also provides clinical-grade sequencing.
Rush University Research Bioinformatics Core Facility
Rush Research Bioinformatics Core (RRBC)
Core empowers researchers from genomic, clinical, and basic sciences disciplines at Rush and beyond with cutting-edge bioinformatics resources. Provides guided data analysis and hypothesis-driven research, large-scale data analysis, analytical plan development and results interpretation, algorithm and script development for custom data processing. Provides innovative infrastructure tools, including the Research Private Cloud and scalable cloud-based solutions. Services include customized analytical solutions, data storage and management workflows, training and support for bioinformatics tools.
Local desktop and cloud-based bibliometric and network analysis platform offered through a licensed access model.Supports literature-centered bibliometric and scientometric workflows, and it can also be applied to custom datasets with or without associated literature papers, including broader general network analysis use cases.
Software R package to visualize genetic maps and QTL analysis. Provides graphical user interface to integrate, visualize and explore results from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid species. The app is meant for interactive use and allows users to optionally upload different sources of information, including gene annotation and alignment files, enabling the exploitation and search for candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.
Software R package that provides comprehensive computational pipeline for predicting survival probabilities and risk groups in cancer patients. Includes dedicated modules to perform key steps such as data preprocessing, training/test splitting, and normalization.
Software Python package for bulk segregant analysis (BSA) and QTL mapping from pooled whole-genome sequencing data. Takes variant call format (VCF) input and produces ranked candidate genomic regions and genes through sliding window analysis with tricube kernel smoothing, Z-score and G-statistic significance testing, and optional snpEff functional annotation. Supports recessive and dominant inheritance modes, multi-sample bulk pooling, and integration with Nextflow and Snakemake workflow managers. Distributed via PyPI, Bioconda, and Docker.
Software suite for analyzing and visualizing in situ gene expression data produced by Xenium Analyzer. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data.
Texas State University 3-Zone Tube Furnace
Custom system intended for flexible annealing or chemical vapor deposition processing at temperatures < 1000oC. Process and/or purge gases (Ar, 4%H2 in Ar, N2) are introduced via a manifold into the quartz tube at either atmospheric or sub-atmospheric pressures. The maximum sample size is 60mm (~2").
Software deterministic reproducibility evaluation toolkit for biological machine learning pipelines. Implements 18-assertion compliance evaluation across 5 dimensions: explicitness, data provenance, reproducibility, stability, and bounded deployment envelope. Includes synthetic example dataset for reviewer verification without patient data.
Texas State University AJA Magnetron Sputter System
Texas State University Magnetron Sputtering System
Our AJA International, Inc. ATC Orion is a thin film deposition system based on physical ablation of target material by five (2RF/3DC) independently powered magnetron sputter sources. Substrates with maximum diameter of 100mm are load lock transferred to main chamber on Molybdenum substrate holder with variety of features including heating, rotation, Z motion, and RF biasing. Main chamber vacuum system consists of turbo-molecular pump, gate valve, mechanical pump, and 3 vacuum gauges. Quartz crystal monitor may be employed internally for rate calibration. Internal interlocks protect system/user from aberrant power, water, and vacuum states. Labview-based computer control allows for process development and automated sequencing. Physical vapor deposition system that deposits uniform thin films using magnetron sputtering in controlled vacuum environment.
Software bioinformatics tool for Helicobacter pylori genotyping.
Software pipeline to aid the curation of bird genome assemblies by identifying putative microchromosome scaffolds and moving them to start of the genome assembly FASTA file. Hi-C contact map can then be made using the MicroFinder-ordered assembly file for downstream manual curation. Conserved gene-set mapping and assembly ordering for manual curation of bird microchromosomes. Order FASTA file by microchromosome specific genes.
Company designs and manufactures specialized laboratory equipment for in vitro research on blood vessels and soft tissues. Based in Vermont, they provide tools for studying vessel pressure, flow, and diameter, primarily used by researchers to understand vascular physiology and disease. Instruments for in-vitro research studies of pressurized, perfused, cannulated blood vessels.
Paris Brain Institute PHENO Zfish Core Facility
Paris Brain Institute PHENO Zebrafish Core Facility
Facility provides infrastructure and technical expertise for maintenance, breeding, and experimental use of Danio rerio. The facility ensures standardized husbandry, health monitoring, and traceability of zebrafish lines in compliance with regulatory and ethical guidelines. Services include colony management, maintenance and distribution of wild-type, mutant, and transgenic lines, and support for experimental workflows. The platform offers technical services such as embryo microinjection (e.g., genome editing using CRISPR/Cas9), phenotypic screening, fin clipping for genotyping, and in vitro fertilization. Training and technical support are available for zebrafish handling, experimental design, and data reproducibility.
Texas State University Nanofabrication Research Service Center Core Facility
Texas State University Nanofabrication Research Service Center (NRSC)
Multi-user clean room facility where students and researchers can fabricate films, structures, and devices at micrometer and nanometer scale. Users must enter through the gowning area that contains garments required to protect the cleanroom from particles. The class 10,000 instruction area houses high temperature furnaces, physical vapor deposition systems, wet chemical benches, chemical storage, and electrical test equipment utilized by undergraduate courses. The class 1000 research area houses deposition, etching, thermal treatment, and metrology equipment to support sponsored research and graduate coursework. The class 100 research space hosts the most sensitive lithography process equipment. The utility chase houses support equipment such as water cooling, vacuum pumps, exhaust abatement, and compressed gas delivery systems.
Texas State University E-Beam Evaporator system
Facility Angstrom Engineering EvoVac is a thin film deposition system based on evaporation of source material that can deposit a wide range of materials including metals and inorganic compounds. Resistive evaporation results when electrical current heats a boat filled with source material whereas electron beam evaporation utilizes filament emission and magnetic focusing of a high energy electron beam which is swept within a crucible of deposition material. The deposition processes occur in a vacuum to permit long mean free paths from indexed multi-pocket sources at rates and terminal thicknesses controlled using a quartz rate sensor. The substrate can be heated, rotated, and plasma cleaned to control film morphology, uniformity, and adhesion. Vacuum-based deposition system that uses an electron beam to evaporate materials for high-purity thin film coatings with precise thickness control.
Facility plasma-enhanced atomic layer deposition (PEALD) system from Arradiance utilizes high-speed pulse valves to sequentially deliver reactants that combine to deposit thin films on the surface of a sample at temperatures up to 300C. Eight precursor positions (4 metalorganic + 4 oxidizer) and three plasma gases (N2, O2, H2) enable a wide range of films and process optimization. Plasma-enhanced atomic layer deposition system used for conformal, atomic-scale thin film growth with excellent uniformity and thickness control.
Plasma-Enhanced Chemical Vapor Deposition system
Facility plasma-enhanced chemical vapor deposition (PECVD) system from AGS utilizes plasma decomposition of silane (SiH4) in in presence of an oxygen or nitrogen source to deposit SiO2 and Si3N4 dielectric thin films. The capacitive coupled plasma reduces the required temperature for deposition to a minimum of ~150degC. A plasma-enhanced chemical vapor deposition system is used to deposit high-quality thin films at reduced temperatures for semiconductor and materials applications.
Texas State University Oxford ICP/RIE system
Facility Oxford ICP-RIE Plaslab 180 utilizes a 3kW RF power supply to generate a remote plasma of Cl2, BCl3, H2, Ar, NF3, O2, SF6, and/or C4F8 gas species that can be further accelerated (300W table bias) toward a substrate resulting in a combination of physical and chemical dry etching for material removal. The turbomolecular pumped system achieves a base pressure < 1E-7 Torr and is equipped with chuck temperature control from -110 to 350 degrees C. Advanced dry etching system combining inductively coupled plasma (ICP) and reactive ion etching (RIE) for highly anisotropic, high-precision material removal in semiconductor and nanofabrication processes.
Texas State University Rapid Thermal Annealer
Fcility AGA Heatpulse 610 is a benchtop rapid thermal annealer (RTA/RTP) that utilizes high power lamps to heat treat thin films and substrates for processes such as contact formation, silicide formation, and dopant diffusion/activation. Temperature control via PID loop has a maximum heating rate of ~50 C/s and maximum temperature of 1000 C. The chamber can also be atmospheric purged with N2, Ar, 4% H2balAr, or O2. A rapid thermal processing system that enables fast heating and cooling cycles for semiconductor wafers, used for dopant activation, oxidation, and material modification.
Texas State University Wafer Bonder system
Facility EVG 501 wafer bonder system applies pressure up to 10kN and temperature up to 450C to samples with prepared surfaces (specific chemical surface termination). When the system mechanically brings these surfaces into contact the temperature and pressure sequence activates chemical bonds at the interfaces that fuse the sample surfaces together. A precision wafer bonding system used to join semiconductor wafers using thermal, adhesive, or anodic bonding techniques for device integration.
Advanced, stylus-based surface profiler used for high-precision, 2D and 3D surface topography measurements, including step height, surface roughness, and waviness. System measures roughness in the nanometer range. It provides a step-height repeatability of 5Å. It uses a diamond-tip stylus to physically trace samples, offering sub-nanometer vertical resolution and high repeatability.
Filmetrics F20 Thin Film Measurement System
Filmetrics F20 is a versatile, benchtop thin-film measurement system designed to measure the thickness, refractive index, and extinction coefficient of thin films. Using spectral reflectance in less than a second, it measures single or multi-layer stacks.
Sunnybrook Research Institute Centre for Flow Cytometry and Scanning Microscopy Core Facility
Sunnybrook Research Institute Centre for Flow Cytometry and Scanning Microscopy
Core offers services including cell sorting,cell analysis, user training for the flow cytometer benchtop analyzers, user training for the widefield and confocal microscopes.
Sunnybrook Research Institute; Toronto; Canada
Premier Canadian academic medical research center located in Toronto, affiliated with the University of Toronto and Sunnybrook Health Sciences Centre focusing on translating scientific discoveries into clinical practice, with specialties in medical imaging, biology, and clinical trials.
University of Pittsburgh Hillman Cancer Center Population-based Cancer Data and Analytics Core Facility
Population-based Cancer Data and Analytics (PANDA)
University of Pittsburgh Hillman Cancer Center Population-based Cancer Data and Analytics (PANDA)
UPMC Hillman Cancer Center Population-based Cancer Data and Analytics (PANDA)
Core provides infrastructure and analytic support for population-based cancer research at UPMC Hillman Cancer Center. PANDA helps investigators access, manage, link, and analyze population-based cancer datasets to study cancer surveillance, treatment access, and survival in western Pennsylvania and across the United States using datasets such as SEER-Medicare, the Pennsylvania Cancer Registry (PACR), Pennsylvania Health Care Cost Containment Council (PHC4) hospital discharge data, the National Cancer Database (NCDB), and the UPMC Network Cancer Registry, along with area-level and geospatial data relevant to the Hillman catchment area.PANDA provides consultation on study design and data selection, assistance with data management and linkage, analytic dataset creation, population-level and geospatial analyses, and support for manuscripts and grant applications.
Mayo Clinic Genetic Screening and Engineering Core Facility
Genetic Screening and Engineering Core - Mayo Clinic
Core offers tools to precisely modify the genome of cells and organisms using CRISPR-Cas9-based editing, CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa) systems. Our platforms enable high-throughput genetic screening, gene knockouts, transcriptional modulation, and sequence editing with high efficiency and scalability.
Web tool to search life science articles with AI you can verify and control. Life science search engine designed to hit the sweet spot between classical search and AI-assisted research.
Neuroanatomy-Anchored Information Management Platform (NIMP)
Neuroanatomy-anchored Information Management Platform for collaborative BICAN data generation developed by UTHealth Houston. Serves as metadata tracking engine to support generation, management, and sharing of brain research data. Integrates data production pipelines across brain banks, laboratories, sequencing centers, and data archives. Platform enables integrative and collaborative, consortium-scale FAIR data generation within the BICAN project. Platform is designed to manage complex dataset, including tissue samples and sequencing data, through Specimen Portal and Sequence Library Portal. Portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting.
Vilber Lourmat Fusion FX7 imaging system
Image acquisition system to capture of chemiluminescence and fluorescence images. Using cooled CCD technology in combination with motorised optical lens, Fusion FX7 offers very high sensitivity and extended dynamic range. Data produced are directly compatible with image analysis software developed by VILBER and 1D image can be transformed into 3D results with Bio-1D and the Bio-Gene software.
Tokyo Chemical Industry Co., Ltd. (TCI) is a leading global manufacturer of specialty organic chemicals, founded in 1946. They produce over 30,000 research chemicals, including laboratory chemicals, reagents, and functional materials. TCI also acts as a supplier, offering custom synthesis and bulk production from milligrams to tons.
Gustave Roussy is Europe’s leading comprehensive cancer center, located in Villejuif near Paris, France. It is a premier institution dedicated entirely to cancer treatment, research, and teaching, often ranked among the top oncology hospitals worldwide. Founded in 1925, it specializes in personalized medicine, rare cancers, and complex tumors.
Gustave Roussy Microscopy and Cytometry Core Facility
Gustave Roussy Microscopy and Cytometry Core Facility (PFIC)
Core supports fundamental, translational, and clinical research by providing advanced services and expertise in cytometry, photonic microscopy, mass imaging, in vivo imaging, and bioinformatics. The cytometry and mass imaging unit offers flow, spectral and mass cytometry, cell sorting, multiplex panel development, and high‑dimensional data analysis. Photonic microscopy unit provides comprehensive support from sample preparation to image processing, with access to widefield, confocal, multiphoton and super‑resolution systems, and benefits from national recognition through IBISA and France BioImaging labels. The platform also hosts clinical transfer imaging activities (SP2I), developing optical tools for surgery and pathology in close collaboration with clinicians, with numerous funded projects and industrial partnerships.
Software tool to reverse-engineer transcriptional regulatory networks from co-expressed gene sets by identifying master transcription factors (TFs) and their direct target genes. It operates by scanning for enriched TF binding motifs in promoter regions, utilizing over 10,000 position weight matrices (PWMs) for human, mouse, and Drosophila. Used to enable gene regulatory network mapping directly based on motif enrichment in co-expressed gene set.
Software tool for processing Epi-Proteomics mass spectrometry data. Discriminates isobaric histone peptides using distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. EpiProfile 2.0 is extended version of v1.0 for enhanced quantification of histone peptides based on LC-MS/MS analysis.
Open-source foundation model for histology. Vision transformer model trained on haematoxylin and eosin stained tissue whole slide histology images. AI foundation model for pathology, developed by French startup Bioptimus. Launched as one of the largest open-source models for digital pathology, it is trained on histopathology slides for tasks like tissue classification, mutation prediction, and cancer subtyping.
NIH NCI Cancer Data Access System Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial Portal
Colorectal and Ovarian (PLCO) Cancer Screening Trial
National Cancer Institute (NCI)-sponsored randomized, controlled study (1993–2001) of ~155,000 adults aged 55-74 to evaluated whether organized, regular screenings could reduce cancer deaths compared to usual care. Portal provides randomized, controlled trial data used to determine whether certain screening exams reduce mortality from prostate, lung, colorectal and ovarian cancer.
Software nuclei instance segmentation and classification framework based on hybrid task cascade.
University of Iowa Roy J Carver Center for Imaging Core Facility
Roy J. Carver Center for Imaging (CCI) at the University of Iowa
Core offers light microscopy and imaging services. Provides access to and training on various confocal microscopes.
University of Iowa Roy J Carver Center for Genomics Core Facility
The Roy J. Carver Center for Genomics (CCG) is a research and service center within the Department of Biology on the campus of the University of Iowa (UI). The CCG maintains a centralized laboratory with equipment and instruments available for investigators to use in their molecular research.
Baylor College of Medicine Human Tissue Acquisition and Pathology Core Facility
Tissue bank and full service histology core. Provides support for tissue banks staining imaging and spatial applications.
Cincinnati Children's Hospital Medical Center Qualitative Methods and Analysis Collaborative Core Facility
Cincinnati Children's Hospital Medical Center Qualitative Methods and Analysis Collaborative (QMAC)
Qualitative Methods and Analysis Collaborative (QMAC)
Core promotes conduct of high-quality qualitative research with focus on integrating key stakeholder perspectives into research designs. It helps investigators with study design, funding proposals, data collection, and analysis to understand contextual, sociocultural, and experiential factors in health.
Stand-alone open-source software with graphical user interface for analysis of time-lapse microscopy images. Combines bio-image analysis and mathematical modeling for study of DNA repair dynamics.
Web-based tool for analysis of sets through Venn diagrams. Allows set unions in Venn diagrams to be explored thoroughly, by consequence extending the ability to analyze combinations of sets with additional observations, yielded by novel interactions between joined sets.
Source analysis and data processing code for article titled "Single-Cell Multi-Omics Insights into BMI-Mediated Immune-Related Disease Risk".
Gene Expression Profiling Interactive Analysis 3
Web based tool as advanced version of GEPIA that provides comprehensive analysis of gene/protein interactions across various cancer types. This version facilitates the investigation of treatment sensitivity utilizing both real-world patient data and cell line screens for over 1000 therapeutic agents, as well as the integration of RNA alterations derived from the pan-cancer analysis of whole genomes project. GEPIA3 represents a significant enhancement of the original platform, enabling in-depth exploration of gene regulation and cancer phenotypes, thereby supporting the identification of novel biomarkers and therapeutic targets.
University of Glasgow Cancer Sciences Flow Cytometry Core Facility
Cancer Sciences Flow Cytometry Facility is a joint facility between the School of Cancer Sciences at the University of Glasgow and the CRUK Scotland Institute. Provides access to flow cytometry instrumentation and support from technical experts in analysis and cell sorting.
Queen's University Translational Institute of Medicine TIME Core Facility
Core to maximize sharing of research platforms and expertise between research groups in the Department of Medicine and their collaborators. Provides research equipment and expertise to accelerate translation of laboratory discoveries into clinical applications to improve patient care. It supports translational research through advanced tools, expertise in biotechnology, biomolecular sciences, and the development of new treatments and biomarkers, aiming to advance first-in-person clinical trials.
University of Maine CORE Electron Microscopy Laboratory Core Facility
University of Maine Electron Microscopy Laboratory
University of Maine Electron Microscopy Laboratory Core Facility
Core offers tools and technical expertise for research and training in microscopy with both light and electron microscopes. Maintains and operates electron microscopes (SEM with EDS), confocal laser scanning microscope, and tancillary equipment needed for preparation of specimens for EM and other microscopy. Light microscopes encompass optics for bright-field, phase-contrast, Nomarski differential-interference, polarizing, and fluorescence imaging.
University of Maine CORE Small Animal Research Core Facility
UMaine Small Animal Research Facility (SARF)
University of Maine Small Animal Research Core Facility
University of Maine Small Animal Research Facility
Core provides animal care and assists investigators in fulfilling their obligation to plan and conduct animal research in accordance with scientific, humane and ethical principles. SARF has a multizone temperature and airflow control to allow for various environments necessary to research projects. SARF also features quarantine suite with separate entrance and personal protective equipment (PPE), and is outfitted with RAIR HD Super Mouse 750 ventilated rack holding 126 cages. Daily care and feeding is provided by trained staff, and surgery prep, surgical area, and recovery area are available for use.
University of Maine CORE Zebrafish Core Facility
University of Maine Zebrafish Core Facility
Facility is outfitted with the Aquatic Habitats for Accelerated Bioresearch (AHAB) fish rearing system (Aquatic Habitats, Apopka, FL). This system is composed of five-foot wide, five-level, stainless steel racks using any combination of tank sizes (3 and 10 liter). Water input lines deliver UV-sterilized water to each tank through an independent valve. The fish tanks have self-cleaning bottoms and the effluent system features an optically clear design. The filter system requires minimal maintenance, and maintains high water quality, dramatically reduced disease and mortality.
University of Maine CORE Environmental DNA Laboratory Core Facility
UMaine Coordinated Operating Research Entities eDNA Service Center Lab
Core offers processing and testing of environmental DNA samples, assay development, field surveys and training services. The equipment housed in the center allows users to receive fluorescence-based qPCR analyses, for quantifying DNA concentration and abundances, and plate preparation.
University of Maine CORE Microfabrication Cleanroom Core Facility
Facility supports micro- and nanoscale fabrication, microsensor development, and atomic-scale materials synthesis. Provides comprehensive technical capabilities, including microlithography (mask aligners, photoresist processing, laser lithography), thin film deposition (e-beam evaporation, sputtering, PECVD, atomic layer deposition), and advanced characterization tools (profilometry, spectroscopic ellipsometry). Fabrication processes are supported by both dry etching (DRIE, RIE) and wet chemical processing (RCA clean, KOH etch, solvent benches), as well as thermal processing systems such as diffusion furnaces and rapid thermal annealing.
University of Maine DNA Sequencing Facility
DNA Sequencing facility provides Sanger sequencing and other services to labs on campus and beyond. Users can choose the degree of in-house processing to accommodate individual needs, providing flexibility for clients of all levels.
Software R package to work with genomic regions. In addition to predefined randomization and evaluation strategies, regioneR is fully customizable. Implements function to evaluate local specificity of detected association. Used for association analysis of genomic regions based on permutation tests.
Software package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and creation of graphs. Incorporates strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. Builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.
Loom is an efficient HDF5-based file format for storing large, high-dimensional single-cell genomics datasets, including data, metadata, and clustering results. Loom file format is designed to efficiently hold large omics datasets. Typically, such data takes the form of a large matrix of numbers, along with metadata for the rows and columns. Loom files (.loom) are created in the HDF5 file format, which supports an internal collection of numerical multidimensional datasets. HDF5 is supported by many computer languages, including Python, R, MATLAB, Mathematica, C, C++, Java, and Ruby.
Structured schema used in single-cell biology to standardize how cell types are annotated, classified, and stored. It is frequently associated with the Allen Institute and Brain Initiative Cell Census Network (BICAN) to map cell taxonomy, linking cell sets to ontologies and providing evidence for annotations
On-line viewer for human striatum slide-tags spatial transcriptomics (10X Chromium 5' GEX) data set generated by the Macosko Lab comprising ~1.1 million cells from 19 human striatum donors.
Software tool for calculating sequence depth.
Software tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies.
Azure Ao Absorbance Microplate Reader AC3000
Filter-based 96-well plate absorbance microplate reader for ELISA, Bradford, Lowry assays and more.
Touchscreen-based gel documentation imaging system. It is designed for UV, color imaging, blue-excited DNA dyes, and Coomassie gel imaging.
Imaging system with the same sensitivity as chemiluminescent detection on film, but without need for darkroom and the expense of film developer.
Imaging system capable of three-channel visible fluorescence detection. Enables sensitive multiplex detection of Western blots, fluorescent biomolecules and Cy2/Cy3/Cy5 or similar fluorochromes. Allows you to simultaneously image and quantify up to three different targets.
Multichannel, multimodal fluorescent imager, with IR, visible light, and UV excitation channels. Able to image and quantify two different targets in the same position more efficiently using near-infrared (NIR). Normalize to fluorescent total protein stain or a housekeeping protein in the green channel without needing to strip and re-probe your Western blots.
Azure Cielo 3 is 96 well Real Time-PCR Machine available with 3 sample channels. Used for RT-PCR amplification and SYBR Green fluorescence detection. Engineered for variety of qPCR applications, with high sensitivity and wide dynamic range. Fast qPCR detection system for high-quality data with smart protocols, and robust durability.
Azure Cielo 6 is 96 well Real Time-PCR Machine available with 6 sample channels. Used for RT-PCR amplification and SYBR Green fluorescence detection. Engineered for variety of qPCR applications, with high sensitivity and wide dynamic range. Fast qPCR detection system for high-quality data with smart protocols, and robust durability.
Azure Sapphire FL+ Biomolecular Imager IS4100
Large format scanner for precise quantitation of molecular assays. Imaging System 4100 is high-performance laser-based scanner variant designed for fluorescence, phosphor, and chemiluminescence imaging.
Laboratory instrument used to erase residual signals from storage phosphor screens (imaging plates). It utilizes LED light source within drawer-based design to clear screens up to prepare them for reuse in radioactive sample imaging. Used for ensuring that high-sensitivity phosphor imaging assays are free from background noise from previous experiments.
Compact chemiluminescent imager for quantitative chemiluminescent and visible protein gels.
Research-based framework designed to guide planning, organization, and evaluation of transition services for students with disabilities. It serves as comprehensive tool to improve post-school outcomes in employment, education, and independent living. It encompasses several key dimensions, including student-focused planning, student development, interagency collaboration, family involvement, and program structure and attributes.
University of Wyoming Stable Isotope Core Facility
University of Wyoming Stable Isotope Facility
Facility performs stable isotope analysis and some sample preparation. Analyses include CNS(solid), OH(solid and liquid), DIC(liquids) and CO(solid carbonate, bone, enamel, etc...). Sample prep includes water extractions, soil acidification, grinding, encapsulation, and others.
University of Colorado Boulder Biochemistry Nuclear Magnetic Resonance Core Facility
CU Boulder Biochemistry Nuclear Magnetic Resonance (NMR) facility
University of Colorado Boulder CUB-BioNMR
Facility maintains 400MHz Bruker NMR capable of running NMR experiments, including solution NMR spectroscopy for small molecules, macromolecules, polymers, and proteins. The on-site analytical tools (Topspin, MestRenova) are here to facilitate your research success.
Publicly available repository of high throughput sequencing data. KRA stores qualified raw sequencing data and alignment information and facilitates reproducibility through cloud-based data analysis service. Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data has been migrated to KRA.
Software is the implementation of re-training and linear evaluation pipeline of BYOL. Bootstrap your own latent new approach to self-supervised learning.
University of Tennessee KnoxvilleAdvanced Microscopy and Imaging Center AMIC Core Facility
Advanced Microscopy and Imaging Center (AMIC)
Multi-user, multi-disciplinary facility that provides microscopy and imaging services. It houses instrumentation for optical microscopy including laser scanning confocal microscopy and total internal reflection microscopy (TIRF), scanning as well as transmission electron microscopy, MALDI mass spectrometry imaging, and an X-ray MicroCT. Offers complete technical support, individual training and courses that cover both the practical applications and physical principles of microscopy. Provides consultations for development of microscopy projects for inclusion in grant proposals.
NYU Langone Health Environmental Exposure and Analytical Chemistry Laboratory Core Facility
Environmental Exposure and Analytical Chemistry Laboratory
NYU Langone Health Environmental Exposure and Analytical Chemistry Laboratory
Facility for trace-level analysis of anthropogenic organic chemicals in environmental and biological specimens.Specializes in mass spectrometry based analysis, including targeted and nontargeted methods. Capable of quantifying nearly all the organic analytes monitored by the Centers for Disease Control and Prevention (CDC) in the National Health and Nutrition Examination Survey (NHANES) program. Commonly assayed targets include phthalates, bisphenols, per- and polyfluoroalkyl substances (PFAS), glyphosate, organophosphate flame retardants, organophosphate pesticides, and other compound classes at biologically and environmentally relevant concentrations. Our nontargeted analysis workflows are capable of detecting hundreds to thousands of chemical features in a single sample, enabling the identification of unknown organic compounds without a priori target selection.Laboratory operates as a shared resource within NYU Langone's Division of Advanced Research Technologies (DART), which is part of the Office of Science and Research (OSR). We provide precise chemical analysis to support studies on environmental exposures and their health impacts.
Paris Brain Institute Histomics Core Facility
Core offers workspaces and equipment for your histology techniques, as well as advice, training, and services.
Cancer Research UK Cambridge Institute Proteomic Facility
Core offers services for identification, quantification, and structural characterisation of proteins using next–generation mass spectrometry platforms. Uses mass spectrometry platforms that include Orbitrap Lumos, Ascend and Astral Zoom systems. Services include designing of experimental strategies, implementing and validating previously developed proteomic workflows to profile proteins from diverse biological samples, as well as developing methods and assays when required. Core focuses and specializes in using stable isotopic labelling strategies (Tandem Mass Tags) as well as label-free methods using different acquisition methods (DDA and DIA) for relative quantification of protein expression levels and enrichment within protein complexes. Develops and runs PRM (parallel reaction monitoring) assays for targeted quantification of defined panels of proteins.
Medical College of Wisconsin Children’s Research Institute CRI Imaging Core Facility
Imaging core houses microscopic imaging systems including several confocal microscopes, laser microdissection system and whole slide scanners. Core users will be trained and consulted on instrumentation, software, and analysis.
Medical College of Wisconsin Neuroscience Research Center NRC Microscopy Core Facility
Core offers confocal imaging systems for specialized imaging of neuronal tissue, including AxL Cleared Tissue Light Sheet Microscope along with appropriate software including Bitplane Imaris 10.0 F1 package and SVI Huygens Professional deconvolution software. The availability of a cleared tissue instrument enables unparalleled visualization of developmental processes, injury recovery, and disease-related pathology.
Northwestern University Center for Regenerative Nanomedicine Peptide Synthesis Core Facility
Peptide Synthesis Core Facility at the Center for Regenerative Nanomedicine (CRN)
Core offers custom peptide services. Facility provides expertise and instrumentation dedicated to chemical synthesis, purification, and characterization of peptides and peptide materials. Provides standard and catalog peptides, and synthesis of specialty custom peptides modified to fit specific research needs.
Flow cytometer that combines real-time imaging with spectral flow cytometry. Enables researchers to analyze cell morphology, protein location, and molecular characteristics simultaneously at high speeds, offering deeper single-cell insights than traditional flow cytometry.
High-performance, multicolor flow cytometer used to analyze and isolate (sort) specific cell populations with high precision, measuring up to 50–60 parameters. Offers 6-way sorting, indexing for single-cell sorting (e.g., RNA-seq), and BSL-2 biosafety containment.
Flow cytometer designed for comprehensive, high-parameter analysis of heterogeneous cell populations. It utilizes spectral technology supporting up to 7 lasers and 186 detectors to detect dim/rare populations and distinguish over 44 colors, making it ideal for advanced immunology and oncology research.
Medical College of Wisconsin Comprehensive Rodent Metabolic Phenotyping Core Facility
Comprehensive Rodent Metabolic Phenotyping Core (CRMPC) at the Medical College of Wisconsin
Core provides guided access to technologies for dissection of metabolic function in rodents and other small animals. Provides development, testing, and standardization of metabolic technologies and workflows to leverage both mouse and rat models of interest to the MCW research community. Offers 16-cage multiplexed metabolic phenotyping system (Promethion, Sable Systems International) that provides detailed mechanistic dissection of resting metabolic rate (RMR), physical activity, and ingestive behaviors of rodents in home style cage designs across the light cycle. Core combines RMR assessments with direct/combined calorimetry (total heat dissipation) to enable assessment of anaerobic forms of energy expenditure. Additional services include body composition analysis, metabolic caging, indirect calorimetry, bioimpedance spectroscopy, thermal imaging. Core experts provide guidance for experimental design, execution of studies, statistical analysis of resulting data, and regulatory assistance and compliance.
Software toolkit for inspection, validation, repair, and reproducible processing of neuronal morphology reconstructions stored in SWC format. It provides a desktop GUI, a command-line interface, and a Python API for issue-driven curation, automated neurite labeling, radii cleaning, simplification, geometry editing, batch processing, and structured reporting.
BOKU University Bioactive Molecules Screening and Analysis BMOSA Core Facility
BOKU Core Facility Bioactive Molecules Screening and Analysis (BMOSA)
Core provides high throughput microbiology screening services and high-end mass spectrometry for diverse range of molecules.
University of Toronto Research and Innovation Core Facility
University of Toronto Mississauga Research and Innovation Core
Core brings together UTM’s Growth Facilities, Imaging Facility, Life Sciences Facilities, and NMR Centre into a unified ecosystem that supports academic researchers with shared tools, expert support, and hands‑on training. Provided services include design of multi-scale experimental workflows,cross-platform training,coordinated sample preparation across scales,seamless facility operations,facilitation of data integration, and troubleshooting.
Roswell Park Comprehensive Cancer Center Gene Targeting and Transgenic Core Facility
Roswell Park Comprehensive Cancer Center Gene Targeting and Transgenic Facility
Core provides investigators in the Western New York area with genetically modified animals for their research through gene targeting and transgenic methodologies.
Medical College of Wisconsin Children's Research Institute Histology Core Facility
Children's Research Institute Histology Core
Medical College of Wisconsin Children's Research Institute Histology Core
Core offers histological and immunohistochemical services.Our staff includes ASCP certified Histologists and American Board of Pathology certified Pathologists who provide service, assistance, and quality control. Provided services include grossing specimens, frozen and fixed tissue sectioning, routine H&E and specialized histochemical staining, cytospin preparations, IHC/IF and antibody optimizations using investigator provided antibodies. Provides training for immunohistochemical and histochemical techniques.
Ohio State University Molecular Biology and Genomics Core Facility
Ohio State University Molecular Biology and Genomics Core (MBGC)
Core provides integrated, end-to-end support for molecular biology and genomics research. Services include DNA/RNA extraction, sample quality control, genotyping, qPCR/ddPCR, and next-generation sequencing using Illumina and Oxford Nanopore platforms. In addition to laboratory services, MBGC offers consultation, experimental design guidance, troubleshooting, and training to support high-quality and reproducible research outcomes.
Biacore S200 High Throughput Drug Screening Surface Plasmon Resonance System
Biacore S200 High Throughput Drug Screening SPR System
Surface Plasmon Resonance (SPR) biosensor system
Biosensor system designed for rapid, automated analysis of biomolecular interactions. It excels in characterizing and screening small molecule drug candidates and antibody interactions with high sensitivity, offering rapid fragment screening and affinity determination. Detects low molecular weight (LMW) compounds and weak binding interactions. Optimized for rapid screening of libraries with automated data evaluation for up to 384-well plates. Measures binding interactions in real-time without labeling.
Software tool for filtering and trimming next generation sequencing reads.
Software package for atomic model refinement and map calculation. Software for structure refinement and validation for crystallography and single particle analysis.
University of Wyoming Center for Advanced Scientific Instrumentation CASI Core Facility
Core provides instrumentation and service for the University of Wyoming scientific research community. Services include X-ray, Electron Microscopy, and Light microscopy analysis.
Microprocessor controlled UV-Vis spectrophotometer designed for quantitative and qualitative analysis of liquid samples. Used to scan, measure absorbance, and analyze samples within 190 to 1100 nm range, specializing in nucleic acid (DNA/RNA) quantification, protein assays (Bradford/Lowry), and enzyme kinetics. It is part of DU-600 series. DU-640 features micro-focused beam technology for samples as small as 5ul, full-screen scanning, and rapid data storage/analysis without external computer.
Manufacturer and distributor of high-resolution digital imaging systems specifically designed for Transmission Electron Microscopes (TEM). Based in Woburn, Massachusetts, and founded in 1990, the company specializes in developing CCD and sCMOS camera systems for life sciences and materials science applications.
ADInstruments PowerLab C data acquisition device
Digital data acquisition device used in life science research and education. It converts analog signals from sensors/transducers (e.g., blood pressure, ECG, EEG) into digital data, allowing real-time recording, visualization, and analysis of physiological signals on computer using LabChart software.
Compact, benchtop super-resolution fluorescence microscope designed for single-molecule localization microscopy (SMLM) and real-time tracking, allowing imaging of fixed and live cells with a resolution under 20 nm. It enables dSTORM, PALM, PAINT, smFRET, and TIRF imaging on standard lab bench. Used for quantitative studies of biological processes, including protein interactions in fixed/live cells, extracellular vesicle (EV) characterization, and lipid nanoparticle (LNP) analysis for drug delivery research.
Quantum Design DynaCool Physical Properties Measurement System
Automated, cryogen-free laboratory instrument used to measure electrical, magnetic, and thermal properties of materials. It controls temperatures from 1.8K to 400K and magnetic fields from 9T to 14T without liquid helium, using a pulse tube cooler.
An organization of core facilities in east Africa, spanning multiple countries whose goal is to support research, health, industry and education within Africa.
MTS Criterion Electromechanical Test System
High-precision, tabletop or floor-standing machine used for performing static (monotonic) materials testing, including tension, compression, flex/bend, and shear tests. Designed to measure mechanical properties of materials, such as plastics, metals, composites, and adhesives, ensuring they meet quality and durability standards. Offers a force capacity range typically between 1N to 600kN.
Emory University Translational Neuroscience Core Facility
Emory University Translational Neuroscience Core
Core provides services primarily on animal models to enable preclinical testing and translational research, accelerating the development of human neurological therapies. It specializes in neurosurgical procedures in rodents and large animals, specializing in gene/stem cell therapy and device testing.
University of Pittsburgh Pediatric Clinical Research Services PCRS Core Facility
University of Pittsburgh Pediatric Clinical Research Services (PCRS)
Core is responsible for overall clinical research management for studies engaging a pediatric population, both grant funded and industry sponsored clinical and translational research studies. For both Children Hospital of Pittsburgh and Magee-Women Hospital, the PCRS group provides comprehensive study engagement and helps investigators enroll research subjects. Services are available in two areas, allowing the group to best meet the needs of Pitt physicians and the patients they serve.
Medical College of Wisconsin MCW Engineering Core Facility
Medical College of Wisconsin MCW - Engineering Core
Core is a specialized team of biomedical engineers dedicated to supporting MCW medical research effort by expertly designing, fabricating, repairing, and calibrating research instrumentation tailored to lab-specific needs. By providing these services in-house at a fraction of the cost of commercial vendors, the Core enables cutting-edge research while maximizing budget efficiency.
University of Florida Nanoscale Research Facility NRF Core Facility
University of Florida Nanoscale Research Facility (NRF)
Core supports and enhance research and education by providing access to characterization and process instrumentation. Expert staff provides the assistance and guidance necessary so that students, faculty, and industry get the most effective and appropriate use of facility resources. NRF facilities encompass 100+ instruments, tools and techniques as well as a 7,000 sq. ft. Class 100-1000 Cleanroom facility. Facilities also include instrumentation that allows characterization of radioactive samples.
Fred Hutch Cancer Center Translational Pathology Core Facility
Fred Hutch Cancer Center Translational Pathology
Core provides high-plex immunohistochemistry (PhenoCycler/CODEX) on human and mouse FFPE tissues, image analysis (IHC, mIHC, high-plex), and support for collaborative and fee-for-service projects.
Northwestern University Magnet Low Temperature and Optics Facility MLTOF Core Facility
Low Temperature and Optics Facility (MLTOF)
Core offers instrumentation for electrical/magnetic/optical characterization of thin film and semi-conductor materials and devices. Temperature range depending on technique is -1.8K to 400K.
Software tools to measure the penetration depth of a fluorescently stained molecule into the skin.
Yale Center for Molecular Discovery YCMD Core Facility
Yale Center for Molecular Discovery (YCMD)
Full-service core facility specializing in high throughput assay development and screening of chemical and genomic probes.
Nepa Gene Super Electroporator NEPA21 Type II
Specialized gene transfection system designed to introduce molecules (DNA, RNA, siRNA, CRISPR/Cas9) into difficult-to-transfect cells, tissues, and embryos. It uses a unique 4-step, multi-pulse technology to maximize transfection efficiency while maintaining high cell viability.
Automated 3D cell culture bioreactor designed to grow large, functional organoids and spheroids by simulating microgravity via a clinostat. It provides a low-shear environment, enhancing nutrient/oxygen diffusion and cellular communication to produce more physiologically relevant tissue models compared to traditional methods.
Benchtop microfluidic cell sorter designed to gently analyze, sort, and plate live cells (stem cells, antibody-producing cells, immune cells) using low pressure and sterile, disposable fluidics. It enables high-viability sorting while preventing cross-contamination.
Software R packages with Shiny Interface. Modular R Shiny application that serves as a unified hub that lets users install and launch specialized breeding analysis tools - all from a single interface, with no command-line setup required.
Software user-friendly Shiny interface for measuring marker panel efficiency according to previous datasets and visualizing CNV profiles.
Medical College of Wisconsin Cancer Center Stem Cell and Organoid Core Facility
MCW-Stem Cell & Organoid Core (MCW-SCOC)
Medical College of Wisconsin Cancer Center MCW-Stem Cell & Organoid Core (MCW-SCOC)
Facility provides access to human stem cells, 3D organoids, and other human-relevant disease models to support more predictive drug discovery, improved safety and toxicity assessment, and deeper mechanistic insight. Leveraging organoid and microphysiological platforms, the core enables next-generation therapeutics and clinical trial-in-a-dish approaches that advance biomedical innovation and precision medicine.
DNA Technologies and Expression Analysis Core
Core offers high-throughput sequencing, genotyping, single-cell multi-omics, and spatial biology services as well as training and consultation. Next Generation Sequencing (NGS) technologies including Illumina and Element Biosciences short-read sequencing, PacBio and Nanopore long-read sequencing services provide sequencing and library preparation for these platforms. Genotyping is performed on the Fluidigm EP1 System for low to medium assay numbers, genotyping-by-sequencing assays, and with a range of genotyping-by-sequencing technologies (e.g. multiplexed amplicon, single-primer extension, reduced representation, and skim-seq protocols). Gene expression analysis is carried out by RNA-seq on short-read sequencers as well as full-length transcript sequencing on long-read systems. Single-cell transcriptome (high-throughput single-cell gene expression profiling) and multi-ome studies are enabled by our 10X Genomics Chromium X system and Parse Biosciences assays. Spatial transcriptome profiling is supported on the Xenium and Visium HD platforms with the help of our CytAssist instrument for fresh-frozen, fixed-frozen, and FFPE tissue sections. We offer annual Illumina and PacBio sequencing library preparation workshops, free consultations on project considerations and experimental design, and custom sequencing library prep solutions.
University of North Carolina at Chapel Hill Lineberger Office of Genomics Research Core Facility
Cancer genomics project management and data sharing support facility.
University of Cincinnati Genomics, Epigenomics and Sequencing Core Facility
Epigenomics and Sequencing Core Facility
University of Cincinnati College of Medicine Genomics
Facility focused on next-generation sequencing services. Offers advanced capabilities in next-generation sequencing, single-cell sequencing, and genomics and epigenomics services.
Nationwide Children's Hospital Flow Cytometry and Immune Monitoring Core Facility
Nationwide Children's Hospital Flow Cytometry and Immune Monitoring Core
Core provides instrumentation, training, and high-level scientific and technical expertise relating to conventional and spectral cytometry, cell sorting, small particle analysis, ELISA/ELISpot, PBMC processing and cryopreservation, and multiplex assays.
High-resolution 3D X-ray microscope (micro-CT) designed for non-destructive, submicron imaging of internal structures in materials science, electronics, and life sciences. It allows researchers to visualize 3D details at 500 nm resolution without cutting samples, using "Resolution at a Distance" (RaaD™) technology to image large or complex items.
Zeiss LSM5 PASCAL confocal laser scanning microscope system
University of Melbourne Zeiss LSM5 PASCAL confocal laser scanning microscope system
Specialized, compact confocal laser scanning microscope designed for high-resolution 3D fluorescence imaging. Key features include 2048 x 2048 pixel resolution, a point-scan mechanism, and compatibility with Zeiss Zen software for 3D reconstruction and image processing.
University College London Single Cell and Spatial Omics Platform Core Facility
Core offers services in the field of bulk, single cell, spatial omics, FACs sorting and sequencing.
Software tool for haplotype aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome. Haplotype aware analysis of somatic copy number variations from single-cell transcriptomes. It integrates signals from gene expression, allelic ratio, and population-derived haplotype information to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship.
Software R package to enable rapid reference mapping and annotation of new scRNA-seq data across the spectrum of normal and malignant hematopoietic contexts. Single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations.
Bruker CellScape spatial proteomics system
CellScape Precise Spatial Multiplexing platform
Automated microscopy system for high-plex, subcellular spatial proteomics. System integrates automated microscope, fluidics unit for automated staining, and analysis software. It utilizes cyclic immunofluorescence with EpicIF technology to image, remove signals, and restain tissues to map proteins at single-cell resolution. System is developed by Canopy Biosciences, a Bruker Company, and is often used alongside AI-powered data analysis tools to classify cell phenotypes and visualize tissue architecture.
ÉTS Montréal LaCIME Scientific Platform Core Facility
School of Higher Technology LaCIME scientific platform
Core provides equipment for the fabrication and advanced characterization of cyber-physical microdevices, particularly printed cyber-physical microdevices. Provide students and researchers with environment where engineers receive training with advanced skills in the analog, digital and mixed domains.
Mayo Clinic Genome Analysis Core Facility
Core provides genomics services including next-generation sequencing, gene expression, and genotyping. It enables studies on human disease mechanisms, cancer, and rare diseases.
École de Technologie Supérieure; Montreal; Canada
Public engineering school in Montreal, Canada, affiliated with the Université du Québec system. Founded in 1974, it specializes in applied engineering education and research, with a strong focus on cooperative education (mandatory internships), industry collaboration, and practical, hands-on training for bachelor, master, and doctorate students.
Longitudinal survival analysis and two-group comparison for predicting the progression of mild cognitive impairment to Alzheimer
Project to compare two approaches for the construction of longitudinal predictive models, which were used here to estimate the conversion of mild cognitive impairment (MCI) to AD.
MRI-based atlas package for the titi monkey brain that includes a single subject atlas (UC Davis Titi monkey Neuroimaging Atlas (UCD-TiNA)), alongside a population atlas (UCD-TiNA_group) and a manually segmented atlas compilation (UCD-TiNA_mac).
Automated instrument designed to extract, purify, and quantify nucleic acids (DNA/RNA) from diverse biological samples, preparing them for Next-Generation Sequencing (NGS). It accelerates laboratory workflows, allowing 20 minutes of hands-on time to yield NGS ready samples in ~2 hours.
Web application made for plotting genomic data. Used for genomic composite visualization for bioinformaticians and bench scientists to visualize and analyze signal occupancy across genomic regions.
Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival.
Web tool for analyzing, annotating and sharing multi-dimensional data. Visualisation platform used for spatial analysis.
Software tool as natural language interface integrated with MDV that allows users to generate high-quality interactive visualisations through natural language commands. ChatMDV employs a retrieval-augmented generation (RAG) pipeline combined with large language models (LLMs) to translate user queries into reproducible Python code and interactive output. Module to add chatbot functionality to query Multi-Dimensional Viewer projects.
Stand-alone software package for translation of individual tumor genomes for precision cancer medicine. PCGR interprets primarily somatic SNVs/InDels and copy number aberrations. The software extends basic gene and variant annotations from the Ensembl's Variant Effect Predictor (VEP) with oncology-relevant, up-to-date annotations, and produces interactive HTML reports intended for clinical interpretation.
Waters Xevo G3 TOF MS Mass Spectrometry System
Xevo G3 Quadrupole Time-of-Flight System
High-resolution, benchtop Quadrupole Time-of-Flight mass spectrometer designed for characterizing small molecules and biotherapeutics. Used for analyzing complex samples, offering quantitative/qualitative data, and seamless integration with ACQUITY Premier LC systems.
Software R package provides wrapper functions to compute parametric, nonparametric, and bootstrap confidence intervals (CIs) for comparing two samples, specifically designed for all-pairs or many-to-one comparisons. It enables, but does not enforce, adjustments for multiple testing.
New York Structural Biology Center (NYSBC)
Non-profit research consortium located in Harlem, NY, providing advanced structural biology technologies to academic and commercial researchers. Founded by nine institutions, it specializes in cryo-electron microscopy (Cryo-EM), NMR spectroscopy, and X-ray crystallography to analyze molecular structures for drug discovery.
Source code for work submitted to journal. Multimodal foundation model for pan-cancer prognosis prediction developed on 14,468 patients across 30 cancer types using a collaborative multi-expert architecture that retains unique signals from each modality while modeling their interactions.
Software code used in the multi-omics study of clear cell Renal Cell Carcinoma (ccRCC).
Combining a patch-based approach with a non-rigid registration-based label fusion method for the hippocampal segmentation
LF_Patches: Hippocampal Segmentation via Patch-based Label Fusion and Non-rigid Registration
Software MATLAB toolbox for the automatic segmentation of the hippocampus in brain MRI images. It implements a novel patch-based label fusion method that cooperates with a non-rigid registration-based label fusion approach. Used to automatically and accurately segment the hippocampus in MRI scans by combining two techniques.
University College London Molecular Biology Core Facility
University College London Molecular Biology Facility
Facility contains equipment for all basic molecular biology needs. Training and help are provided. Provides molecular biology services ranging from DNA preparations to cloning and mutagenesis projects.
Molecular Taxonomy of the Breast Cancer International Consortium (METABRIC)
Molecular Taxonomy of the Breast Cancer International Consortium (METABRIC) is a landmark study and dataset comprising primary breast tumour samples with detailed genomic, transcriptomic, and clinical data. It identified ten distinct "integrative clusters" (IntClust) based on copy number aberrations and gene expression, revealing new, clinically relevant subtypes with varying prognoses.
Thermo Scientific Orbitrap Astral Zoom Mass Spectrometer
Spectrometer includes: Fast Ion Filter, Bent Trap for Pre-Accumulation, High-speed Quadrupole, Faster Stepped Collision Energy, Enhanced Dynamic Range mode, TMT HR mode, low input mode, Enhanced Spectral Processing, support for Hybrid DIA experiments, and expanded BioPharma option including Thermo Scientific™ Astral™ analyzer support for top-down and middle-down measurements. Used to accelerate deep proteomics and single-cell analysis. Combines fast scan rates with high-resolution, accurate-mass (HRAM) measurements to detect more proteins, analyze thousands of cells daily, and improve precision oncology or clinical biomarker discovery.
JEOL JSM-7800F Field Emission Scanning Electron Microscope
JSM-7800F Field Emission Scanning Electron Microscope
Ultra-high-resolution, Schottky field-emission scanning electron microscope (FE-SEM) designed for advanced nano-characterization, combining in-lens technology with a super hybrid lens to achieve 0.8 nm resolution. It is utilized for high-resolution imaging, elemental analysis (EDS/WDS), and crystallographic analysis (EBSD) of materials, magnetic samples, and non-conductive specimens, even at very low voltages (down to 10 V).
CAMECA SX100 Electron Probe Microanalyzer
Fully automated instrument used for nondestructive, in-situ, micro-scale elemental characterization. It is generally equipped with five vertical crystal spectrometers (WDS) and an energy dispersive analyzer (EDS), operating via proprietary Windows-based Peak Sight software or updated with third-party software like Probe for EPMA.
Thermo Scientific Krios G3i Cryo-Transmission Electron Microscope
Krios G3i Cryo-Transmission Electron Microscope
Thermo Scientific™ Krios™ G3i Cryo-Transmission Electron Microscope (Cryo-TEM)
High-end 300kV instrument designed for automated, high-resolution 3D imaging of biological samples, such as proteins and viruses, at molecular or atomic levels. It enables researchers to study samples in their native, hydrated state, primarily for drug discovery and structural biology.
Attune CytPix Flow Cytometer combines acoustic focusing flow cytometry with a high-speed camera to simultaneously collect fluorescent data and high-resolution brightfield images for each cell. It is used for automated, AI-driven morphological analysis alongside traditional immunophenotyping, allowing users to validate cell populations, identify cell-to-cell interactions, and verify cell health (e.g., apoptosis, contamination) in real-time. Attune CytPix is a benchtop analysis cytometer with 4 lasers (488, 405, 561, and 633nm) and a brightfield camera.
University of Manchester Biomolecular NMR Core Facility
Core provides advanced NMR spectroscopy for researching the atomic-level structure, dynamics, and interactions of biological macromolecules. It supports structural biology, biocatalysis, and drug discovery by analyzing proteins, DNA, RNA, and carbohydrates. Includes 800MHz NMR spectrometer with H/F-C-N Cryoprobe.
New York Structural Biology Center SEMC Core Facility
New York Structural Biology Center Simons Electron Microscopy Center
Simons Electron Microscopy Center (SEMC)
Provides advanced resources in structural biology. Offers access to instruments, including multiple transmission electron microscopes (TEMs) and cryo-FIB/SEM systems. Trains scientists, from beginners to experienced users, on sample preparation (plunge/high-pressure freezers) and advanced EM techniques. Helps researchers solve the 3D structures of proteins and cellular components at atomic resolution.
Bruker Invenio S is an entry-level FT-IR spectrometer designed for routine productivity and basic research and development. Analytical instrument that identifies chemical compounds and molecular structures by measuring how samples absorb infrared light. Offers upgradable Invenio platform featuring the Transit channel and MultiTect technology.
Customizable polarimeter used to measure the optical rotation of chiral compounds. It identifies, analyzes, and determines the purity and concentration of liquids (specifically optically active samples) in pharmaceutical, chemical, and food manufacturing industries, featuring customizable light sources for UV-Vis to NIR regions.
High resolution UV-Visible spectrophotometer with double-beam, single monochromator, variable spectral bandwidth and a photomultiplier tube (PMT) detector. Used for measuring absorbance, transmittance, and reflectance of liquid or solid samples across the UV-visible range 190-900nm. Used for quantitative analysis (concentration measurement) and spectral characterization.
High-throughput, 32-spot Surface Plasmon Resonance (SPR) system. The "Pro" designation commonly used by Bruker highlights its capabilities, including 8 flow cells with 4 spots each, designed for rapid, label-free molecular interaction analysis. Used for the Real-Time, Label-Free characterization of molecular interactions.
University of California at Berkeley Cal-Cryo QB3-Berkeley Core Facility
Core provides researchers with access to Cryo Electron Microscopes and related tools for high resolution structural biology imaging experiments.
Nanolive 3D Cell Explorer 96focus Imaging System
Label-free live-cell imaging system designed for high-content screening. Label free live cell imaging microscope allows to instantly observe and analyze the inside of living cells in 3D without using toxic stains, leveraging AI-powered digital assays and holographic tomography to automate workflows and provide fast, high-resolution data.
Software tool for rules for DICOM tag based labelling. Regular expression used during the SCANDAN project to label MRI scans based on DICOM tag.
Software R package extension of ggplot2 designed to create information rich plots that include details from statistical tests directly within the visual output. Used to enhance {ggplot2} plots with statistical analysis.
Roswell Park Comprehensive Cancer Center Bioanalytics, Metabolomics and Pharmacokinetics Shared Resource BMPK Core Facility
Metabolomics & Pharmacokinetics Shared Resource (BMPK)
Core provides highly sensitive measurements for an extensive array of chemotherapeutic agents and metabolites to support basic research and preclinical/clinical drug development.
Roswell Park Comprehensive Cancer Center Genomics Shared Resource GSR Core Facility
Core offers services including expert technical staff performing all aspects of sample preparation, QC, assay design and analysis. Provides integrated set of tools and services for genomic analysis. Expertise and services include clone generation, high throughput mapping, array technology development. Offers genomics platforms including data analysis, training and education on instruments and methodologies, complete discovery/screening to validation services, and full Laboratory Information Management System (LIMS) request, workflow and sample management.
Medical University of South Carolina Hollings Cancer Center Cell and Molecular Imaging Core Facility
Core provides MUSC Hollings Cancer Center members with sophisticated equipment, technologies, training, and expertise required for successful, cell and tissue-based microscopic imaging and image analysis.Optical Microscopy Services include equipment and expertise to facilitate imaging of tissues and cells by Hollings members. Innovative Techniques service include development and application of new imaging techniques to meet the emerging scientific needs of Hollings members.Education and Training services include education, trainning, and consultation on imaging technologies that enable scientific discovery, including a biennial Charleston Workshop on Light Microscopy for the Biomedical Sciences, as well as a lecture series on cell and molecular imaging, especially as it relates to tumor biology.
Roswell Park Comprehensive Cancer Center Bioinformatics Shared Resource BIOINF Core Facility
Core provides bioinformatics assistance for design, analysis and interpretation of genomics, proteomics and other studies for better understanding of cancer biology, thereby facilitating translation of cancer omics discoveries to cancer treatment. Provides services in design of experiments, raw omics data processing, data analysis and interpretation, data mining and integration, informatics infrastructure for data sharing and management, review and prepare grants and manuscripts, software evaluation, new method and database development,bioinformatics education and training for investigators.
Roswell Park Comprehensive Cancer Center Biostatistics and Statistical Genomics Shared Resource BSGSR Core Facility
Biostatistics & Statistical Genomics Shared Resource (BSGSR)
Core offers services in design, oversight, implementation, analysis, publication, and reporting of scientific studies including articulating study objectives and hypotheses, grant writing, conceiving appropriate cost-effective designs and models for achievement of study objectives, monitoring interim and final analyses, and co-authoring abstracts and manuscripts.
Roswell Park Comprehensive Cancer Center Biomedical Research Informatics Shared Resource BRISR Core Facility
Biomedical Research Informatics Shared Resource (BRISR)
Core provides consultations and services for investigators and study teams in the areas of clinical research, informatics, and data science. BRISR helps researchers harness internal and external data resources and provide informatics-driven solutions for clinical and translational research. Offers the infrastructure and processes to establish and monitor data standards, quality integration and distribution, educational and training opportunities. Provide services in three main areas: (1) Clinical data management and delivery for research, (2) Custom software development for research, and (3) Artificial intelligence analysis for clinical and bioinformatics research.
Roswell Park Comprehensive Cancer Center GMP Engineering and Cell Manufacturing Core Facility
GMP Engineering & Cell Manufacturing Facility (GEM)
Core provides clean rooms, cell therapy equipment, manufacturing know-how, capabilities and comprehensive suite of quality assurance and control procedures.
University of Tennessee at Knoxville Genomics Core Facility
Genomics core is a self-supporting core facility specializing in Sanger sequencing, SNP/fragment analysis, and Next Generation DNA Sequencing using Illumina's MiSeq platform. Provides sequencing services.
University of Massachusetts Chan Medical School BioImage Data Management and Sharing Core Facility
BioImage Data Management and Sharing Core
Core helps research scientists and imaging core facilities produce, handle, safeguard, and share high-quality bioimage data. Ensures compliance with standards for image data management and sharing. Helps to plan experiments, track experimental conditions, and produce data.BioImage DMS eases the burden of data publication and sharing when the project is published.
Roswell Park Comprehensive Cancer Center Biorepository and Laboratory Services Shared Resource BLS Core Facility
Biorepository & Laboratory Services Shared Resource (BLS)
Core is comprehensive data and biospecimen bank (malignant and normal tissue and their derivatives, blood and bone marrow) for research along with a range of services that accompany biospecimens. Facilitates access to human tissue, blood and bone marrow for investigators with Institutional Review Board (IRB) approved protocols emphasizing translational research. Helps investigators to establish Biospecimen and Data Research (BDR) protocols and supports the submission of grants by providing feasibility analysis, cost estimates and letters of support.
Rensselaer Polytechnic Institute RPI-Proteomics Core Facility
Facility provides mass spectrometry-based analytical support.Houses multiple mass spectrometry platforms with complementary ionization capabilities, including EI, APCI, ESI, and MALDI, enabling qualitative and quantitative analysis of diverse sample types across a range of volatility, polarity, and molecular weight. Several systems are coupled with chromatographic separation platforms, allowing complex mixtures to be separated prior to mass spectrometric analysis. Supports research in areas including proteomics, small-molecule analysis, carbohydrate and glycosaminoglycan-related analysis, metabolomics-oriented method development, and drug-discovery-related projects.Particular strength of the Core is the analysis of complex biomolecules, including proteins, peptides, carbohydrates, and heparin/glycosaminoglycan-related samples. The Core works closely with investigators to evaluate feasibility, develop appropriate workflows, and interpret mass spectrometry data in the context of each project.
Roswell Park Comprehensive Cancer Center Advanced Tissue Imaging Shared Resource ATISR Core Facility
Advanced Tissue Imaging Shared Resource (ATISR)
Core offers streamlined, multiplexed tissue analysis services including tissue sectioning, staining, imaging, spatial RNA sequencing, analysis and interpretation of results.
University of Vermont Office of Animal Care Management Core Facility
Core oversees the operation of research animal facilities at the University of Vermont. Animal facilities houses mainly mice and rats. Animal models facilitate discovery in the areas of infectious disease, endocrinology and metabolic disease, cancer and chemotherapy, immunology and respiratory disease, among others. The University of Vermont's Animal Care program is fully accredited by the Association for the Assessment and Accreditation of Laboratory Animal Care (AAALAC, International).
Compact benchtop single quadrupole mass spectrometer designed for routine, high-performance liquid chromatography (LC-MS) applications. Used for molecular weight confirmation, impurity identification, and quantitative analysis. Compatible with a broad range of chromatography platforms and ionization sources, including APCI and UniSpray, the SQ Detector 2 is the ultimate single quadrupole mass detector for chromatography.
Waters Binary Gradient Modules Mixing Pumps
High pressure, precision solvent mixing pumps designed for HPLC and preparative scale purification. They mix two different solvents to create precise gradient compositions, allowing for, or improving, the separation and isolation of target compounds in chemical or biological samples.
Medical College of Wisconsin Cancer Center Biostatistics Shared Resource Core Facility
Core services include experimental design, sample size calculation, randomization, analysis plans, data analysis, grant and manuscript preparation, full clinical trial support, and innovative targeted methods development.
JEOL JEM-120i Transmission Electron Microscope
Modern 120 kV Transmission Electron Microscope (TEM) designed for high-throughput screening and ease of use in biological, materials science, and nanotechnology research. Resolution: Achieves 0.14 nm (High Resolution) to 0.2 nm (High Contrast) lattice resolution. Magnification: Range from x50 to x1,500,000 (HR) or x1,200,000 (HC). Imaging System: Includes a 4-megapixel, high-speed, high-sensitivity JEOL CMOS camera (NeoView) as standard, with options for a 19-megapixel (SightSKY) camera. Versatile Applications: It can be used for cryo-TEM screening, material sciences, and high-throughput asbestos analysis.
Johns Hopkins University School of Medicine Center for Proteomics Discovery CPD Core Facility
Core facility that helps biomedical researchers design and execute proteomics (and metabolomics/lipidomics) studies from sample preparation and LC-MS/MS data acquisition to protein/PTM identification and quantification and advanced bioinformatics/statistical analysis. CPD supports workflows, including label-free (DIA/DDA) and TMT multiplexed quantitative proteomics, phosphoproteomics/other PTMs, targeted PRM, single-cell proteomics, spatial proteomics, cell-type-specific proteomics, thermal proteome profiling, and more.
Amersham ImageQuant 800 Western Blot Imaging System
Compact imaging system designed for chemiluminescence, fluorescence (including IR) and colorimetric detection. Built with advanced charge-coupled device (CCD) technology, it delivers high-resolution, publication-quality images across a wide range of applications—including gels, membrane blots, multiwell plates and petri dishes.
ThermoFisher Scientific BB15 CO2 incubator
Laboratory instrument designed for cell and tissue culture, providing precise temperature (up to 55°C) and CO2 control for optimal, stable growth conditions. It features air-jacketed heating, a fast-recovering humidification system, and options for stainless steel or copper interiors to reduce contamination risk.
Cytek Amnis ImageStreamX Mk II Imaging Flow Cytometer
Benchtop, multispectral imaging flow cytometer that merges the high-throughput, quantitative capabilities of flow cytometry with the visual detail of microscopy. It captures up to 12 channels of images including brightfield, darkfield, and fluorescence for every cell in flow, allowing researchers to study protein localization, cell-cell interactions, and morphology at a rate of thousands of cells per second.
Roswell Park Comprehensive Cancer Center Translational Imaging Shared Resource TISR Core Facility
Translational Imaging Shared Resource (TISR)
Core provides specialized preclinical imaging services including image acquisition, quantitative image analysis, multidimensional renderings and data sets for research purposes.
Roswell Park Comprehensive Cancer Center Comparative Oncology Shared Resource COSR Core Facility
Comparative Oncology Shared Resource (COSR)
Core offers services for preclinical models including barrier facilities with fully automated environmental controls for the housing of research models. Specialized husbandry with trained staff who perform all manipulations inside Biosafety cabinets for maintenance of a pathogen-free environment for models held in micro isolation (MI) housing systems. In addition to housing pre-clinical models in state-of-the-art facilities, COSR provides Specialized Surgical Services and procedural training, consultation in experimental design, irradiation services, in-house hematological testing, genotyping services, design and conduct of pre-clinical toxicological studies.
Children's Hospital of Philadelphia CHOP Human Pluripotent Stem Cell Core Facility
Core generates induced pluripotent stem cell (iPSC) lines from somatic cells including peripheral blood mononuclear cells and fibroblasts. The Core has established standard operating procedures for Pluripotent stem cell growth and maintenance, Genome editing technologies including CRISPR-CAS9 and Differentiation to germ layer and derivative tissues of interest. Provides enrichment training courses for investigators interested in learning how to work with pluripotent stem cells and/or establish the pluripotent stem cell technology in their own labs.
Predicting Alzheimer’s conversion in mild cognitive impairment patients using longitudinal neuroimaging and clinical markers
Project to quantify the impact of longitudinal predictive models with single- or multisource data for predicting MCI-to-AD conversion and identifying a very small subset of features that are highly predictive of conversion.
Software Python package for interactive and static data visualization.Interactive visualization library for modern web browsers. Provides concise construction of graphics and affords high-performance interactivity across large or streaming datasets.
Environmental influences on Child Health Outcomes
Environmental influences on Child Health Outcomes (ECHO)
NIH Environmental influences on Child Health Outcomes
ECHO project to better understand the effects of physical, chemical, and biological exposures, social and behavioral factors, and the natural and built environments on child health and development, with focus in the following areas: Pre-, peri-, and post-natal outcomes; Upper and lower airway; Obesity; Neurodevelopment; and Positive health To achieve this goal, the ECHO program supports multiple, synergistic, longitudinal studies of existing and ongoing study cohorts.
Field Museum of Natural History Scanning Electron Microscopy Laboratory Core Facility
Interdepartmental core facility for scanning electron microscope imaging and elemental analysis of objects. Provides Hitachi SU7000 field emission scanning electron microscope, an Oxford Ultim Max 170 infinity EDS detector with BEX (backscatter electron and X-ray imaging detector), a Leica EM Ace600 sputter coater and a Hitachi IM4000II ion milling system.
Scientific and educational institution dedicated to exploring the diversity of life on Earth and human culture. It is renowned for its collection of over 40 million artifacts and specimens, including world-class dinosaur fossils, ancient cultural exhibits, and active scientific research labs.
Field Museum of Natural History Elemental Analysis Core Facility
Field Museum of Natural History Elemental Analysis Facility
Core consists of an Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) laboratory, an X-ray Fluorescence laboratory, a Raman laboratory, and an optical mineralogy laboratory. Museum curators and researchers are using this instrumentation extensively to further research programs on early state expansion in the Andes, evolving social networks on the north coast of Papua New Guinea, the social dynamics of early village societies and the emergence of early states, African pre-industrial civilizations and, trade and exchange around the Indian Ocean (Laure Dussubieux). In addition to research conducted by Field Museum staff, the EAF collaborates with scientists from other institutions, bringing researchers and students from all over the country to The Field Museum to learn about compositional analysis of ancient materials to enhance their research on a very wide range of anthropological topics.
Children's Hospital of Philadelphia CHOP Transgenic Core Facility
Transgenic Core at Childrens Hospital Research Institute, working in partnership with the University of Pennsylvania CRISPR Core Facility, build complex mouse and rat models,genetically manipulating the mouse and rat genome to meet specific research needs utilizing genetic engineering approaches. Core provides services for the generation and preservation of genetically altered mice or rats.
Children's Hospital of Philadelphia CHOP High Throughput Sequencing Core Facility
High Throughput Sequencing Core (HTS Core)
Core is service facility providing instrumentation, library preparation, and sequencing services to CHOP, UPenn, and external investigators in genomic, epigenomic and transcriptomic studies.
Children's Hospital of Philadelphia CHOP CAG Biorepository Core Facility
Pediatric biobank, hosting more than 600,000 biological samples that have been genotyped or sequenced in CAGs CLIA and CAP-accredited high-throughput centers. This core offers services in DNA and RNA extraction and QC.
Children's Hospital of Philadelphia CHOP CAG Genotyping Core Facility
Core is equipped with liquid handling technology and experienced staff members. Offers both standard and custom Illumina array project design. With the capacity to process >2300 samples/week and generate >480 million genotypes per day, the genotyping core fully integrates with our Biorepository and Bioinformatics group, offering the collaborator the opportunity for a seamless experience from DNA extraction to data release.
Children's Hospital of Philadelphia CHOP Single Cell Technology Core Facility
Core offers services and access to single-cell, spatial and in situ technologies. Provides instruments, experienced research assistants and bioinformaticians to experimental and computational support. Services include 10x Genomics single cell assays, 10x Genomics Visium CytAssist and Visium HD spatial transcriptomics, 10x Genomics Xenium in situ spatial transcriptomics, Vizgen MERSCOPE in situ spatial transcriptomics, NanoString GeoMx Digital Spatial Profiler RNA and protein assays.
Children's Hospital of Philadelphia CHOP Clinical Vector Characterization Core Facility
Core provides manufacturing of clinical and pre-clinical Adeno-Associated Virus (AAV) vectors of serotypes 1, 2, 5, 6, 8, 9, and Lentivirus (LV) vectors. Novel or modified serotypes will require development prior to scale-up. Products for clinical use are manufactured in compliance with Current Good Manufacturing Practices (cGMP) for Phase 1 and 2 clinical trials. To support pre-clinical work, including pharmacology and toxicology studies, core offers products manufactured using a GMP-comparable process. Research-grade products for proof-of- principle and bridging studies are also offered.Core Facility uses a patented vector production technology and a highly efficient purification process that uses combined column and gradient centrifugation-based process steps. This system has manufactured clinical-grade AAV vectors. Prior to the final release of the clinical vectors, the vector product is subjected to numerous tests to ensure quality. Core also provides federal regulatory documentation and necessary certifications.
Children's Hospital of Philadelphia CHOP Clinical In Vivo Gene Therapy Core Facility
Core experts offers complex gene therapy trials. Ensures licensed gene therapies are available in our clinics.
Children's Hospital of Philadelphia CHOP Large Animal Imaging Facility LAIF Core Facility
Children's Hospital of Philadelphia CHOP Large Animal Imaging Core (LAIF)
Core facilitates advanced MR image-guided interventional and noninvasive procedures to support research across a broad range of disease areas, including neurodegenerative, cardiothoracic, and reproductive disorders. Imaging capabilities span structural MRI, diffusion imaging, DCE and ASL perfusion, spectroscopy, angiography, cardiac imaging, tissue elastography, functional imaging, flow quantification, and quantitative T1, T2, and T2* mapping.In collaboration with the Division of Veterinary Resources (DVR), we encourage investigators to consult with our teams on all scientific, medical, technical, and compliance aspects of studies involving large animal models. Investigators are expected to obtain Institutional Animal Care and Use Committee (IACUC) approval before initiating study activities. Core provides comprehensive data processing, post-processing, and quantitative image analysis support to help investigators extract meaningful outcomes from complex imaging datasets. These services include image reconstruction workflows, multimodal image registration, segmentation, volumetric and regional quantification, diffusion and tract-based analysis, spectroscopy processing, and development of customized pipelines tailored to specific study needs.Provides support in generating high-quality preliminary data for grant applications, instrument proposals, and translational research initiatives by helping design imaging strategies, optimize acquisition protocols, and deliver rigorous quantitative analyses that strengthen scientific aims.For larger research programs, the LAIF Core can assist with processing and managing large-scale imaging datasets to support longitudinal studies, multisubject analyses, and publication-ready results.
Children's Hospital of Philadelphia CHOP Small Animal Imaging Facility SAIF Core Facility
Core serves CHOP researchers with translational imaging capabilities. Provided imaging platform integrates multiple modalities including MRI, PET, CT, Optical, and US for monitoring disease progression and therapeutic response in vivo in small animal models. Services include Selecting the optimal imaging modality, Design and optimization of acquisition protocols, Expert execution of in vivo imaging experiments, Training for new users on image acquisition, Advanced data analysis and project management.Provides technical expertise and translational capability.
Children's Hospital of Philadelphia CHOP Pathology Core Facility
Pathology Core Laboratory Children's Hospital of Philadelphia Research Institute
Core provides histopathology, Immunohistochemistry, tissue microarray, and imaging services. Staff offer experience in all aspects of tissue processing, histological techniques, antibody work-up, and morphologic analysis. Offers tools to facilitate high throughput analysis of tissue sections and imaging. The Pathology Core is located in the A Level of Colket Translational Research Building (CTRB) Room A410. Staff is available for consultation, troubleshooting, and assistance in planning and interpreting experiments histopathology and related techniques.
Children's Hospital of Philadelphia CHOP Comparative Medicine Services Core Facility
Core provides support for nonclinical research programs. Offers expertise to design, conduct, and oversee a wide range of animal studies. Services include Grant and funding application support, Budget development and financial planning, Experimental design and study planning, Study protocol drafting, implementation, and management, IACUC protocol guidance and consultation, Standard Operating Procedure (SOP) development, management, and archiving, Training delivery and documentation, Study execution and data generation, Secure archiving of study materials and data. Core offers expertise in Pharmacokinetic studies, Biodistribution studies, Toxicology and reproductive toxicology studies, Medical device testing, Surgical model development.
Children's Hospital of Philadelphia CHOP Microbiome Center Core Facility
Core is sequencing and analytical resource of the PennCHOP Microbiome Program, providing end-to-end solutions for microbiome research. Sequencing lab offers expertise in next-generation DNA sequencing for microbiome studies, working with customers to provide optimized workflows and protocols customized for each study. Provides expertise in bioinformatics and statistical analysis of microbiome data. Develops an analytical plan specific to your project and can integrate microbiome data with other data sources, such as metabolomics or dietary intake information.
Children's Hospital of Philadelphia CHOP Research Vector Core Facility
Core provides premium recombinant adeno-associated viral (AAV) and lentiviral vectors to support basic research and preclinical studies. Provides expertise in producing custom vector constructs at multiple scales, rigorous quality control standards, and technical support. Services enable gene transfer and accelerate translational research and therapeutic development.
Children's Hospital of Philadelphia CHOP Biostatistics and Data Management Core Facility
Core offers biostatistics and data management services, expertise in the design of experiments, planning of clinical protocols, analysis and interpretation of data, and presentation and dissemination of results. Services include designing case report forms, developing databases, creating data management plans, developing metrics to report on study progress, and delivering high quality datasets for analysis. Core offers free limited consulting for data management and statistical questions. Offers experience with the submission of a Biologics License Application (BLA). Core is available to investigators seeking guidance with clinical trial start-up, oversight, and regulatory submission.
Children's Hospital of Philadelphia CHOP Small Molecule and Metabolite Core Facility
Core focuses on quantitative bioanalytical assay development, validation and implementation for drugs, metabolites and biomarkers in blood, serum, plasma, urine, ultrafiltrate and microdialysate utilizing mass spectrometry techniques.
Children's Hospital of Philadelphia CHOP Qualitative Research Core Facility
Core supports all Children's Hospital of Philadelphia Research Institute personnel and faculty who are interested in utilizing qualitative methods. Provides research support across a broad range of settings, including in-hospital clinical research, primary care, public health, and community-based settings. Services include free introductory videos, yearly seminars, customized project workshops, and hands-on project support and grantmaking.
Children's Hospital of Philadelphia CHOP Aquatic Zebrafish Core Facility
Core offers zebrafish research services and provides fish husbandry. Services include experiments designing and performing, teaching zebrafish techniques.Provides special expertise in disease modeling by creation of mutant and transgenic lines, analysis of disease phenotypes, and drug testing.
Children's Hospital of Philadelphia CHOP Engineered Cell Therapy Core Facility
Core provides services and expertise to advance chimeric antigen receptor (CAR) T or other cell therapy research.Services include guidance in the design, construction, and selection of CARs and other cell therapies against a multitude of targets and diseases. Core offers small-scale lentivirus production and small-scale T cell transduction and expansion for experimental purposes.
Children's Hospital of Philadelphia CHOP CAG Sequencing Core Facility
Cores Sequencing operations are integrated with Biorepository and Bioinformatics teams to keep all stages of a collaborators studies connected. Core offers genomics services in NovaSeq, Single Cell 10xGenomics, various library preparations including bulk RNAseq, Whole Genome/Whole Exome, and Sanger Sequencing including fragment analysis.
Software R package for collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.
Software Python package for network analysis and Leiden community detection/clustering algorithm commonly used in single cell analysis for biology.
Charité Berlin University of Medicine Scientific Workshop Core Facility
Core Facility for the development and manufacturing of experimental medical devices. Offers advise on experimental design, draft technical proposals, and support in the realization of prototypes and patent ideas.
Waters Discovery TGA 5500 Thermal Analyzer
Thermogravimetric analyzer used to measure a material’s weight change (decomposition, oxidation, or dehydration) as it is heated, cooled, or held at a constant temperature. It is used in research and quality control to analyze polymers, pharmaceuticals, and composites for stability and composition.
Web open decentralized science platform for peptide sequence analysis and community annotation. Researchers submit amino acid sequences for AI-powered bioactivity scoring, structure prediction, and toxicity assessment. Results are publicly annotated by the community and secured on the Solana blockchain for verifiable, censorship-resistant research records.
Software tool as context-based long-read simulator that models sequence-context-dependent errors from empirical sequencing data, coupled with a Bayesian optimization framework for systematic parameter tuning.
Comprehensive Cis-NATs Identifier Via RNA-seq data
Software Python package tool that facilitates the identification of total cis-NATs (cis-natural antisense transcripts) from gene datasets.
Software Jupyter notebook based genomic data visualization toolkit.
Software open-source Python/Flask framework for building online behavioral experiments and surveys. You describe your study in plain-text files: a TOML config for settings and page flow, JSON files for questionnaires, and HTML files for custom pages. BOFS handles participant routing, condition assignment, consent forms, data storage, and provides an admin panel for monitoring and export.
Ohio State University Immune Monitoring and Discovery Platform IMDP Core Facility
Immune Monitoring and Discovery Platform (IMDP)
Core provides technologies and expertise to accelerate discoveries in cancer immunology and immunotherapy. Offers advanced tools for immune profiling, spatial biology, and translational studies, enabling innovation that drives new therapies for patients.
University College London Cancer Institute Pathology Translational Technology Platform TTP Core Facility
Pathology Translational Technology Platform (TTP)
Facility provides a range of histology and tissue-based molecular services to research scientists within the UCL Cancer Institute and across UCL.The facility also maintains a range of equipment available for use by UCL researchers to support a range of projects involving human and animal samples. We work in close collaboration with the UCL / UCLH Biobank for Studying Health and Disease and the UCL/UCLH Cancer Biomarker Centre (CBC) which provides a framework for the governance of research involving human samples and supports researchers in meeting regulatory standards.
Cancer Research UK Scotland Institute Research Integrity Service Core Facility
CRUK Scotland Institute Research Integrity Service
Core enables and promotes responsible research practices to generate trustworthy data, and to safeguard research data. The service is comprised of 4 pillars; governance, good research practice support, stewardship and knowledge exchange.
University of Maryland Baltimore Confocal Microscopy Core Facility
University of Maryland School of Medicine Confocal Microscopy Facility
Core provides researchers with confocal imaging equipment to enable acquisition of high resolution images (both in vivo and in vitro). Offers training and assistance in the use of confocal microscopes. Optimization of data acquisition and image processing are both part of the training, thus enabling researchers to efficiently design studies, acquire image data and extract relevant data features.
GE Healthcare PETtrace 800 cyclotron system
Compact, automated, dual-particle cyclotron system designed for fast, easy and efficient production of PET tracers. It offers the efficiency required to facilitate your clinical schedules, flexibility for research protocols and the performance necessary to meet regional distribution demands. The PETtrace 800 is built around a compact negative ion cyclotron with a vertical mid-plane of proven design, featuring both protons and deuterons allowing maximum flexibility and low-cost isotope production.
Specialized, automated, cyclotron-based system designed for the decentralized, high-volume production of medical radioisotopes, such as Gallium-68,Technetium-99m, and Zirconium-89. It allows hospitals and radiopharmacies to produce PET and SPECT imaging agents locally, bypassing supply chain disruptions and reducing dependence on traditional nuclreactors.
University of Washington Histology and Imaging Core Facility
Core provides histology, immunohistochemistry, imaging, quantitative image analysis, and pathology consultation services. Offers experience, expertise and instrumentation across all platforms. Through the partnership with the Comparative Pathology Program (CPP), we have board certifies veterinary pathologists on staff who are available for research consultation and collaboration.
Software code and pipelines for the study of pan-cancer myeloid immunosenescence. Analytical framework integrates bulk RNA-seq (GTEx/TCGA) and multi-cohort single-cell RNA sequencing (scRNA-seq) data to construct high-resolution myeloid atlases, cellular communication networks, and clinical prognostic signatures.
Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser.
Software tool for identifying single nucleotide polymorphisms (SNPs) and insertion/deletion (indels) variants, offering high accuracy via local de-novo assembly of reads. It works by identifying "active regions" with potential variation, reassembling those reads, and calculating genotype likelihoods, making it superior for complex variant detection.
Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible
Software program designed for refining atomic models of multidomain proteins or complexes using Small-Angle X-ray Scattering (SAXS) data. It is specifically used in structural biology to help determine the 3D structure of complex molecules in solution.
Database of glycans 3D structural data and information that can be downloaded or used with Re-Glyco to rebuild glycoproteins from the RCSB PDB or EMBL-EBI AlphaFold repositories. Glycan structure database and toolbox designed to restore glycoproteins to their native and functional form.
Software tool for rapidly determining the low-resolution three-dimensional shape of biological macromolecules in solution using Small-Angle X-ray Scattering (SAXS) data. Used for rapid ab-initio shape determination in small-angle scattering.
Software application as discrete event simulation model built in the R programming language which simulates individual women through different risk-stratified breast screening programmes. Used to evaluate the costs, outcomes, and cost-effectiveness of different breast cancer screening strategies, particularly risk-stratified approaches in the UK. It helps policymakers determine the best screening intervals for women based on risk rather than just age.
Specialized service at Charité – Universitätsmedizin Berlin that provides researchers with fresh, high-quality primary human biospecimens. By bypassing standard supply chains, it connects operating and clinical wards directly to research laboratories, supporting human-based methods to reduce reliance on animal experimentation. Operates as a central contact point, taking care of the logistics from project initiation to sample transfer. It coordinates with surgical clinics, pathology departments, and tissue repositories. Alongside the living biospecimens, the pipeline helps safely transfer relevant, pseudonymized patient data to research groups.
Research-grade upright compound microscope used to visualize fluorescently labeled cells, tissues, and biological markers. Equipped with interchangeable filter cubes (e.g., DAPI, FITC, TRITC), it excites specific fluorophores to study gene expression, protein localization, and cellular dynamics. Beyond fluorescence, it supports brightfield, phase contrast, and Differential Interference Contrast (DIC) for examining unlabeled or transparent specimens. Often fitted with trinocular head and high-resolution digital camera to capture publication quality micrographs and record time-lapse imagery.
Laboratory instrument designed to analyze and quantify ELISpot, FluoroSpot, and FociSpot assays in 96-well plates. Used by immunologists and vaccine researchers to study individual immune cells and detect secretions like antibodies and cytokines. Capable of analyzing up to four analytes simultaneously.
Specialty contract research laboratory and biotechnology company that provides stem cell testing and in vitro toxicity screening, particularly for the blood-forming (hematopoietic) system. Provides high-throughput hematotoxicity screening and testing with its proprietary HALO®-Tox HT Platform. Provides the expertise to help in predicting toxicity, risk and safety of a drug or other agent.
Contract research organization based in San Leandro, California, that specializes in molecular pathology, genomics, and tissue analysis. Services for drug discovery, biomarker development, and personalized medicine. Provides histopathology and genomic services to the pharmaceutical and biotechnology industries.
Software R package read flat files (csv, tsv, fwf) into R. Used to read rectangular data like 'csv', 'tsv', and 'fwf'. Designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.
University of Oklahoma Health Sciences Center Tissue Pathology and Biospecimen Core Facility
Core provides tissue processing, histology and staining services. Services include embedding, sectioning, histochemical staining of mounted slides, immunohistochemical (IHC) staining for paraffin embedded and frozen tissues, immunocytochemical (ICC) staining for cultured cells (as tissue sections or cytospin slides), evaluation of new antibodies for IHC staining, enzyme histochemistry and special staining.Provides defined analyses including RNA / DNA preparation, reverse transcription and cDNA synthesis from total RNA, construction, staining and analysis of tissue microarrays, and construction and analysis of reverse proteomics array from user-defined biospecimens.Core is flexible to accommodate the development of new techniques and expanding its services based on the research requirements of SCC members and other investigators.
University of Wisconsin Madison Newcomb Imaging Center NIC Core Facility
Core provides services in confocal microscopy (CLSM, including FRET, ion imaging, and colocalization), scanning electron microscopy (SEM, including ESEM for wet samples), SEM prep instrumentation (critical point dryer and sputter coater), epifluorescence microscopy and polarizing microscopy.
Memorial Sloan Kettering Cancer Center MSKCC Clinical Grade Production Core Facility
MSKCC-Clinical Grade Production Core Facility
cGMP facility responsible for the bulk product manufacture, purification, and characterization of clinical-grade materials. Offers vialing of sterile investigational products such as peptides, proteins, carbohydrates, and adjuvants. Service also conducts lot release tests which are required for products release for preclinical and investigational use either in-house or with validated contract vendors.
Loma Linda University School of Medicine Advanced Imaging and Microscopy Core Facility
Core offers microscopy services. Provides three offline analysis systems with Intel Xeon-based processors. Two of these are custom-built Origin computers and the third is a Dell Precision computer. All analysis workstations have the most recent versions of the Fiji build of Image J and RStudio.
Matrix:Sparse and Dense Matrix Classes and Methods
Software R package for rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.
uwot: The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction
Software R package implementing the UMAP dimensionality reduction method. It also provides means to transform new data and to carry out supervised dimensionality reduction.
Georgetown University NanoScience and Microtechnology Laboratory GNuLab Core Facility
GNuLab - Georgetown NanoScience and Microtechnology Laboratory
This 3,300 square foot clean room is located in the Department of Physics in Regents Hall and includes instrumentation for fabrication and characterization of materials and electronic devices. Users have access to a Scanning Electron Microscope with ebeam lithography and EDS; optical lithography; magnetron sputtering; thermal evaporation; reactive ion etching; atomic layer deposition; chemical vapor deposition; wirebonding; a profilometer and various optical microscopes.
Software integrative analysis pipeline for analyzing bulk/single-cell ATAC-seq and RNA-seq data. Integrative multi-omics data analysis framework. It can be used as a standalone pipeline to analyze ATAC-seq, RNA-seq, single cell ATAC-seq or Drop-seq data. Used to integrate diverse datasets and use these information to construct regulatory network and identify candidate driver genes.
Austrian company that develops and manufactures high-end laboratory, analytical, and process measurement instruments. Their equipment is widely used in scientific research, quality control, and manufacturing.
Open-access structural database dedicated to the exploration, analysis, and design of protein nanopores, which serve as essential molecular gateways in biological membranes and form the basis of many advanced biosensing and sequencing technologies. This platform integrates large-scale structure-guided mining and deep learning-based modeling using AlphaFold-Multimer and AlphaFold3 to provide high-confidence multimeric nanopore structures. Each entry includes detailed information on membrane embedding, pore geometry annotation, and constriction profiling to support functional and biophysical interpretation.
Michigan State University Proteomics Core Facility
Core provides mass spectrometry resources and expertise to assist researchers in the identification and characterization of proteins and peptides. Experiments from simple protein discovery to complex differential proteome profiling, post-translational modification mapping and protein/peptide quantification can be performed using our instrumentation and software.
Faxitron Bioptics | MultiFocus X-ray system
Faxitron MultiFocus (now part of the Hologic portfolio) is a benchtop digital X-ray system designed for high-resolution specimen imaging, life sciences, and industrial applications. It features advanced Automatic Exposure Control and high geometric magnification for precise analysis
Olympus | FluoView FV4000 Confocal Laser Scanning Microscope
FLUOVIEW FV4000 Confocal Laser Scanning Microscope
Confocal laser scanning microscope used to capture high-resolution, multi-color 3D images of biological samples. It is primarily used in neuroscience, cell biology, and developmental biology to image both fixed tissues and live cells. Detects from 400 nm to 900 nm. Supports up to 10 laser lines for advanced, simultaneous multiplexing.
Ultra-micro UV spectrophotometer used in life science and biology labs to measure the concentration and purity of DNA, RNA, and protein samples. Measures DNA and RNA concentrations at a fixed wavelength of 260 nm.Measures purified protein concentration at 280 nm. Requires only 1 to 2 ul of sample, eliminating the need for cuvettes or capillaries.
Stratagene | 2400 Stratalinker UV Crosslinker
Stratagene UV crosslinker is designed to crosslink DNA or RNA to nylon, nitrocellulose, or nylon-reinforced nitrocellulose membranes. The crosslinking process takes only 25–50 seconds, in contrast to the traditional method of baking filters at 80°C for 2 hours. Additionally, crosslinking has been shown to significantly increase hybridization signals when compared to oven-baking. For optimal crosslinking performance, each Stratalinker UV crosslinker is equipped with an internal photodetector designed to compensate for the natural shift in power output of aging ultraviolet bulbs.
Software R package to create scatterpie plots, especially useful for plotting pies on a map. Used to display proportional or compositional data across spatial coordinates (such as maps) or scatter plot axes.
Software tool for querying and parsing of Genome Taxonomy Database's data.Command-line tool for querying the Genome Taxonomy Database (GTDB) directly from your terminal or scripts. It covers the core GTDB REST API, genome cards, metadata, taxonomic history, taxon lineages, and search, and adds features designed for real research workflows: batch input from files or stdin, automatic pagination, retry logic, flexible output formats (JSON, CSV, TSV), and per-item file splitting for large datasets.
University of Technology of Compiègne CARMOD meta-platform Core Facility
University of Technology of Compiègne CARMOD meta-platform
Université de Technologie de Compiègne (UTC) CARMOD meta-platform
CARMOD (characterization and modelling) meta-platform is a core research and technology unit within the Biomechanics and Bioengineering (BMBI) laboratory at the University of Technology of Compiègne.Interdisciplinary core facility dedicated to the mechanical characterization of biological systems, tissues, and biomechanical signals. Provides technological platforms dedicated to the characterization and modeling of biomechanical systems and electrophysiological signals. Offers expertise spanning various scales from the nanoscale to the entire organ in vivo as well as various characterization modalities and physical and numerical modeling.
Software pipeline that improves T cell characterization by simultaneously quantifying predefined gene expression programs (scRNA-Seq) capturing activation states and cellular subsets. Used to score cells based on a fixed, multidataset catalog of Gene Expression Programs from any tissues or cell-type.
Medical University of South Carolina MUSC Mouse Behavior Phenotyping Core Facility
Medical University of South Carolina MUSC Mouse Behavior Phenotyping Core
Core provides equipment, expertise, service and training for testing a range of common mouse behaviors to study neurological disorders, such as Autism Spectrum Disorder, intellectual disability, anxiety/depression, and Alzheimer Disease. Performs behavioral testing, data analysis, and data interpretation.Offers personnel training for investigator to have access to the behavior equipment if they prefer to test the mice themselves
Sam Houston State University SHSU-Microscopy Core Facility
Core provides specialized imaging services for primarily biological research, with additional applications for materials chemistry, forensic science, and engineering technology. Available instrumentation includes various light microscopes, a laser-scanning confocal, scanning and transmission electron microscopes, and X-ray imaging.
University of Colorado Anschutz Medical Campus DMBC Microscopy Core Facility
CU-AMC Developmental Biology Microscopy Consortium
University of Colorado Anschutz Medical Campus CU-AMC Developmental Biology Microscopy Consortium
Core offers services from bench to publication to all consortium members. Provides access to the facilities's microscopes and analysis workstations. Provides training, education, support, and mentorship in all aspects of preparing, acquiring, processing, analyzing, and publishing microscopy data.
University of Louisville Micro/Nano Technology Center Bioimaging Core Facility
Micro/Nano Technology Center Bioimaging Core
University of Louisville Micro/Nano Technology Center Bioimaging Core
Core provides biological electron microscopy services including sample preparation, SEM and TEM imaging, array tomography, and cryo-EM plunge freezing.
Medical College of Wisconsin Children's Research Institute Flow Cytometry Core Facility
Children's Research Institute Flow Cytometry Core
Core provides access to analytical cytometers and cell sorters for trained users and operator-assisted cell sorting by appointment during business hours. Assists with protocol and assay development, including sample preparation, selection of antibodies and fluorochromes, proper staining and compensation controls, and selection of appropriate buffers. Offers assistance with data analysis using FlowJo, FCS Express, DIVA and SpectroFlo software is also available by appointment.
University of Louisville Micro/Nano Technology Center Imaging and Characterization Core Facility
Micro/Nano Technology Center Imaging and Characterization Core
University of Louisville Micro/Nano Technology Center Imaging and Characterization Core
Core provides advanced imaging and characterization capabilities including SEM, AFM, and infrared thermal microscopy supporting research in engineering, materials science, biology, and more. Offers imaging and characterization for semiconductors and/or other Micro/Nano scale devices.
Sam Houston State University; Texas; USA
Public research university in Huntsville, Texas. Founded in 1879, it is the third-oldest public college or university in Texas. It is one of the first normal schools west of the Mississippi River and the first in Texas.